text:
ISSN = {1462-8910},
   Accession Number = {21689322},
   DOI = {10.1111/j.1463-1318.2011.02634.x},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Rufo, P. A. and Denson, L. A. and Sylvester, F. A. and Szigethy, E. and Sathya, P. and Lu, Y. and Wahbeh, G. T. and Sena, L. M. and Faubion, W. A.},
   title = {Health supervision in the management of children and adolescents with IBD: NASPGHAN recommendations},
   journal = {J Pediatr Gastroenterol Nutr},
   volume = {55},
   number = {1},
   pages = {93-108},
   note = {1536-4801
Rufo, Paul A
Denson, Lee A
Sylvester, Francisco A
Szigethy, Eva
Sathya, Pushpa
Lu, Ying
Wahbeh, Ghassan T
Sena, Laureen M
Faubion, William A
UL1 TR000423/TR/NCATS NIH HHS/United States
Journal Article
United States
J Pediatr Gastroenterol Nutr. 2012 Jul;55(1):93-108. doi: 10.1097/MPG.0b013e31825959b8.},
   abstract = {Ulcerative colitis (UC) and Crohn disease (CD), collectively referred to as inflammatory bowel disease (IBD), are chronic inflammatory disorders that can affect the gastrointestinal tract of children and adults. Like other autoimmune processes, the cause(s) of these disorders remain unknown but likely involves some interplay between genetic vulnerability and environmental factors. Children, in particular with UC or CD, can present to their primary care providers with similar symptoms, including abdominal pain, diarrhea, weight loss, and bloody stool. Although UC and CD are more predominant in adults, epidemiologic studies have demonstrated that a significant percentage of these patients were diagnosed during childhood. The chronic nature of the inflammatory process observed in these children and the waxing and waning nature of their clinical symptoms can be especially disruptive to their physical, social, and academic development. As such, physicians caring for children must consider these diseases when evaluating patients with compatible symptoms. Recent research efforts have made available a variety of more specific and effective pharmacologic agents and improved endoscopic and radiologic assessment tools to assist clinicians in the diagnosis and interval assessment of their patients with IBD; however, as the level of complexity of these interventions has increased, so too has the need for practitioners to become familiar with a wider array of treatments and the risks and benefits of particular diagnostic testing. Nonetheless, in most cases, and especially when frequent visits to subspecialty referral centers are not geographically feasible, primary care providers can be active participants in the management of their pediatric patients with IBD. The goal of this article is to educate and assist pediatricians and adult gastroenterology physicians caring for children with IBD, and in doing so, help to develop more collaborative care plans between primary care and subspecialty providers.},
   keywords = {Adolescent
Calcium, Dietary
Child
Child, Preschool
Colitis, Ulcerative/*diagnosis/*drug therapy/psychology
Crohn Disease/*diagnosis/*drug therapy/psychology
Diet
Dietary Supplements
Early Detection of Cancer
Female
Humans
Immunization
Immunosuppressive Agents/therapeutic use
Infant
Infant, Newborn
Male
Medical History Taking
Nutrition Assessment
Physical Examination
Tumor Necrosis Factor-alpha/*antagonists & inhibitors
Vitamin D/blood/therapeutic use},
   ISSN = {0277-2116},
   Accession Number = {22516861},
   DOI = {10.1097/MPG.0b013e31825959b8},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Sanapareddy, N. and Legge, R. M. and Jovov, B. and McCoy, A. and Burcal, L. and Araujo-Perez, F. and Randall, T. A. and Galanko, J. and Benson, A. and Sandler, R. S. and Rawls, J. F. and Abdo, Z. and Fodor, A. A. and Keku, T. O.},
   title = {Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans},
   journal = {Isme j},
   volume = {6},
   number = {10},
   pages = {1858-68},
   note = {1751-7370
Sanapareddy, Nina
Legge, Ryan M
Jovov, Biljana
McCoy, Amber
Burcal, Lauren
Araujo-Perez, Felix
Randall, Thomas A
Galanko, Joseph
Benson, Andrew
Sandler, Robert S
Rawls, John F
Abdo, Zaid
Fodor, Anthony A
Keku, Temitope O
P30 ES010126/ES/NIEHS NIH HHS/United States
P30DK034987/DK/NIDDK NIH HHS/United States
R01 CA044684/CA/NCI NIH HHS/United States
P30 DK034987/DK/NIDDK NIH HHS/United States
R01 DK081426/DK/NIDDK NIH HHS/United States
K01 DK 073695/DK/NIDDK NIH HHS/United States
R01 CA136887/CA/NCI NIH HHS/United States
K01 DK073695/DK/NIDDK NIH HHS/United States
P50 CA106991/CA/NCI NIH HHS/United States
R01 CA44684/CA/NCI NIH HHS/United States
Journal Article
Research Support, N.I.H., Extramural
England
ISME J. 2012 Oct;6(10):1858-68. doi: 10.1038/ismej.2012.43. Epub 2012 May 24.},
   abstract = {Differences in the composition of the gut microbial community have been associated with diseases such as obesity, Crohn's disease, ulcerative colitis and colorectal cancer (CRC). We used 454 titanium pyrosequencing of the V1-V2 region of the 16S rRNA gene to characterize adherent bacterial communities in mucosal biopsy samples from 33 subjects with adenomas and 38 subjects without adenomas (controls). Biopsy samples from subjects with adenomas had greater numbers of bacteria from 87 taxa than controls; only 5 taxa were more abundant in control samples. The magnitude of the differences in the distal gut microbiota between patients with adenomas and controls was more pronounced than that of any other clinical parameters including obesity, diet or family history of CRC. This suggests that sequence analysis of the microbiota could be used to identify patients at risk for developing adenomas.},
   keywords = {Adenoma/*microbiology/pathology
Bacteria/classification/genetics
Biopsy
Case-Control Studies
Colorectal Neoplasms/*microbiology/pathology
DNA, Bacterial/genetics
Female
Humans
Male
*Metagenome
Middle Aged
RNA, Ribosomal, 16S/genetics
Rectum/*microbiology/pathology
Sequence Analysis, DNA},
   ISSN = {1751-7362},
   Accession Number = {22622349},
   DOI = {10.1038/ismej.2012.43},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Sanchez-Fidalgo, S. and Cardeno, A. and Sanchez-Hidalgo, M. and Aparicio-Soto, M. and Villegas, I. and Rosillo, M. A. and de la Lastra, C. A.},
   title = {Dietary unsaponifiable fraction from extra virgin olive oil supplementation attenuates acute ulcerative colitis in mice},
   journal = {Eur J Pharm Sci},
   volume = {48},
   number = {3},
   pages = {572-81},
   note = {1879-0720
Sanchez-Fidalgo, S
Cardeno, A
Sanchez-Hidalgo, M
Aparicio-Soto, M
Villegas, I
Rosillo, M A
de la Lastra, C Alarcon
Journal Article
Research Support, Non-U.S. Gov't
Netherlands
Eur J Pharm Sci. 2013 Feb 14;48(3):572-81. doi: 10.1016/j.ejps.2012.12.004. Epub 2012 Dec 11.},
   abstract = {Extra virgin olive oil (EVOO) has demonstrated immunomodulatory and antiinflammatory properties in murine experimental ulcerative colitis (UC). In addition to its high monounsaturated fatty acid content, evidences have accumulated on the favorable properties of minor, although highly bioactive, components present in the unsaponifiable fraction (UF). The present study was designed to evaluate the effects of dietary EVOO's UF supplementation on acute UC. C57BL/6 mice were fed from weaning with sunflower oil (SD), EVOO diet and UF-enriched SD at 5% oil (SD+UF). After 30 days, mice were exposed to 3% dextran sulfate sodium (DSS) for 5 days developing acute colitis. After 4 days of DSS removal, animals were sacrificed and colons were histological and biochemically processed. Disease activity index and microscopic damage score were significantly improved in EVOO and SD+UF dietary groups versus SD group. In addition, both dietary treatments significantly induced decreases in MCP-1 and TNF-alpha levels, iNOS and COX-2 overexpression and p38 MAPKs activation in colon mucosa. Moreover, an upregulation of IkappaB expression was also observed after feeding the animals with both diets. However, no statistically differences between data from mice fed with EVOO or UF+SD diets were observed. Dietary enrichment with EVOO's UF reduces the damage in acute colitis model, alleviating the oxidative events and returning proinflammatory proteins expression to basal levels probably through p38 MAPK and NFkappaB signalling pathways. EVOO's UF diet might provide a basis for developing a new strategy in dietary supplementation for the prevention of UC.},
   keywords = {Animals
Anti-Inflammatory Agents, Non-Steroidal/*therapeutic use
Chemokine CCL2/antagonists & inhibitors/genetics/metabolism
Colitis, Ulcerative/immunology/metabolism/pathology/*prevention & control
Colon/*immunology/metabolism/pathology
Cyclooxygenase 2/chemistry/genetics/metabolism
*Dietary Supplements
Enzyme Activation
Female
Gene Expression Regulation
Hydrolysis
Intestinal Mucosa/*immunology/metabolism/pathology
Mice, Inbred C57BL
Nitric Oxide Synthase Type II/antagonists & inhibitors/genetics/metabolism
Olive Oil
Plant Extracts/*therapeutic use
Plant Oils/*chemistry/standards
Random Allocation
Tumor Necrosis Factor-alpha/antagonists & inhibitors/genetics/metabolism
Weaning
p38 Mitogen-Activated Protein Kinases/antagonists & inhibitors/metabolism},
   ISSN = {0928-0987},
   Accession Number = {23238173},
   DOI = {10.1016/j.ejps.2012.12.004},
   year = {2013},
   type = {Ref–rence Type}
}

@article{
   author = {Sanchez-Fidalgo, S. and Sanchez de Ibarguen, L. and Cardeno, A. and Alarcon de la Lastra, C.},
   title = {Influence of extra virgin olive oil diet enriched with hydroxytyrosol in a chronic DSS colitis model},
   journal = {Eur J Nutr},
   volume = {51},
   number = {4},
   pages = {497-506},
   note = {1436-6215
Sanchez-Fidalgo, Susana
Sanchez de Ibarguen, L
Cardeno, A
Alarcon de la Lastra, C
Journal Article
Research Support, Non-U.S. Gov't
Germany
Eur J Nutr. 2012 Jun;51(4):497-506. doi: 10.1007/s00394-011-0235-y. Epub 2011 Aug 27.},
   abstract = {PURPOSE: Recent epidemiological studies have shown that habitual consumption of extra virgin olive oil (EVOO), the characteristic culinary fat of the Mediterranean area, is effective in the prevention of diverse types of digestive disorders such as inflammatory bowel disease. Many of these benefits are, in addition to its high proportion of oleic acid, due to the high content of phenolic compounds. METHODS: Six-week-old mice were randomized into three dietary groups: standard, EVOO and hydroxytyrosol-enriched EVOO. After 30 days, mice that were exposed to 3% DSS for 5 days developed acute colitis that progressed to severe chronic inflammation during a regime of 21 days of water. RESULTS: Diets enriched with EVOO significantly attenuated the clinical and histological signs of damage, improving results from disease activity index and reducing about 50% the mortality caused by DSS. Moreover, hydroxytyrosol supplement showed better results. Cytokines study showed that TNF-alpha was maintained near to sham control and IL-10 levels were significantly improved in EVOO and EVOO plus hydroxytyrosol diet-DSS groups. In the same way, COX-2 and iNOS were downregulated, and the activation of p38 MAPK was reduced. We also observed a higher significant reduction in iNOS in hydroxytyrosol-enriched EVOO compared with EVOO alone. CONCLUSIONS: EVOO diets exerted a noteworthy beneficial effect in chronic DSS-induced colitis by cytokine modulation and COX-2 and iNOS reduction via downregulation of p38 MAPK. In addition to the beneficial effect by EVOO, supplementation of the diet with hydroxytyrosol may improve chronic colitis through iNOS downregulation plus its antioxidant capacity.},
   keywords = {Animals
Anti-Inflammatory Agents, Non-Steroidal/analysis/chemistry/therapeutic use
Antioxidants/analysis/*therapeutic use
Colitis, Ulcerative/blood/immunology/pathology/*prevention & control
Colon/immunology/metabolism/pathology
Cyclooxygenase 2/metabolism
Cytokines/metabolism
Dextran Sulfate
*Disease Models, Animal
Down-Regulation
Female
*Food, Fortified/analysis
Intestinal Mucosa/immunology/metabolism/*pathology
MAP Kinase Signaling System
Mice
Mice, Inbred C57BL
Nitric Oxide Synthase Type II/metabolism
Olive Oil
Phenylethyl Alcohol/*analogs & derivatives/analysis/therapeutic use
Plant Oils/chemistry/*therapeutic use
Random Allocation},
   ISSN = {1436-6207},
   Accession Number = {21874330},
   DOI = {10.1007/s00394-011-0235-y},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Santos Rocha, C. and Lakhdari, O. and Blottiere, H. M. and Blugeon, S. and Sokol, H. and Bermudez-Humaran, L. G. and Azevedo, V. and Miyoshi, A. and Dore, J. and Langella, P. and Maguin, E. and van de Guchte, M.},
   title = {Anti-inflammatory properties of dairy lactobacilli},
   journal = {Inflamm Bowel Dis},
   volume = {18},
   number = {4},
   pages = {657-66},
   note = {1536-4844
Santos Rocha, Clarissa
Lakhdari, Omar
Blottiere, Herve M
Blugeon, Sebastien
Sokol, Harry
Bermudez-Humaran, Luis G
Azevedo, Vasco
Miyoshi, Anderson
Dore, Joel
Langella, Philippe
Maguin, Emmanuelle
van de Guchte, Maarten
Journal Article
United States
Inflamm Bowel Dis. 2012 Apr;18(4):657-66. doi: 10.1002/ibd.21834. Epub 2011 Aug 11.},
   abstract = {BACKGROUND: The intestinal microbiota plays an important role in human health through the modulation of innate immune responses. While selected commensal bacteria are marketed in specific probiotic products to control these responses, relatively little is known about the immune modulation potential of dairy bacteria that have principally been selected for their fermentation properties. The modulation of innate immune responses may reduce chronic inflammation in inflammatory bowel diseases like ulcerative colitis. METHODS: A collection of dairy Lactobacillus delbrueckii strains was screened for immune modulation effects in vitro through the quantification of nuclear factor kappa B (NF-kappaB) activation in a human intestinal epithelial cell line. Selected bacterial strains were then tested in vivo in a mouse dextran sodium sulfate (DSS) colitis model. RESULTS: All L. delbrueckii strains tested showed anti-inflammatory effects in vitro, to an extent that varied between strains. These effects rely on bacterial surface exposed proteins and affect the central part of the NF-kappaB activation pathway. One of the selected strains significantly reduced the macroscopic and microscopic symptoms of DSS-induced colitis in the mouse intestinal tract, diminished body weight loss, and improved survival. CONCLUSIONS: The results of this study show that dairy lactobacilli that often are part of a regular diet can modulate innate immune responses, and may thus affect health more than generally thought. One of the strains tested alleviated the symptoms of DSS-induced colitis in mice, a model of human ulcerative colitis.},
   keywords = {Animals
Anti-Inflammatory Agents/immunology/*pharmacology
Colitis/chemically induced/immunology/*microbiology/therapy
Dextran Sulfate/toxicity
HT29 Cells
Humans
Intestines/immunology/*microbiology
*Lactobacillus delbrueckii
Male
Mice
Mice, Inbred BALB C
NF-kappa B/immunology},
   ISSN = {1078-0998},
   Accession Number = {21837773},
   DOI = {10.1002/ibd.21834},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Sasaki, M. and Fujiyama, Y.},
   title = {[Dietary therapy and nutritional therapy for inflammatory bowel disease]},
   journal = {Nihon Rinsho},
   volume = {70 Suppl 1},
   pages = {354-7},
   note = {Sasaki, Masaya
Fujiyama, Yoshihide
Journal Article
Japan
Nihon Rinsho. 2012 Feb;70 Suppl 1:354-7.},
   keywords = {Colitis, Ulcerative/*therapy
Crohn Disease/*diet therapy
Humans},
   ISSN = {0047-1852 (Print)
0047-1852},
   Accession Number = {23126117},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Scholz, D.},
   title = {The role of nutrition in the etiology of inflammatory bowel disease},
   journal = {Curr Probl Pediatr Adolesc Health Care},
   volume = {41},
   number = {9},
   pages = {248-53},
   note = {1538-3199
Scholz, Dietmar
Journal Article
Review
United States
Curr Probl Pediatr Adolesc Health Care. 2011 Oct;41(9):248-53. doi: 10.1016/j.cppeds.2011.04.005.},
   abstract = {Many foods have been implicated in theories about the etiology of inflammatory bowel disease. While evidence has accumulated that nutritional factors as part of overall lifestyle changes may play a role in the growing incidence, no specific dietary recommendations except the promotion of breastfeeding can currently be given to decrease the risk of developing Crohn's disease or ulcerative colitis. For the treatment of Crohn's disease in children and adolescents, however, enteral feeding with a semi-elemental diet seems to be as effective as corticosteroids in inducing and maintaining remission. In the meta-analyses, advantages of one formula over the other are evened out, and more research is warranted into the anti-inflammatory properties of different nutrients, such as polyunsaturated fatty acids, butyrate, glutamine, and cytokines, such as transforming growth factors-beta. Unfortunately, for practical reasons, nutritional therapy remains underutilized, even though pediatric patients are most vulnerable to the harmful effects of nutrient deficiencies on growth, pubertal development, and bone health. There is hope that in the future the new field of nutrigenomics may enable physicians to more accurately tailor a specific diet to the patient genotype.},
   keywords = {Adolescent
Adrenal Cortex Hormones/therapeutic use
Child
Child Nutritional Physiological Phenomena
Child, Preschool
Enteral Nutrition/*methods
Fatty Acids, Omega-3/therapeutic use
Humans
Inflammatory Bowel Diseases/diet therapy/*etiology/*therapy
Meta-Analysis as Topic
Nutrition Therapy/methods
Recurrence},
   ISSN = {1538-3199},
   Accession Number = {21939909},
   DOI = {10.1016/j.cppeds.2011.04.005},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Serban, D. E.},
   title = {Nutrition in pediatric inflammatory bowel disease: is it useful for prevention and therapy?},
   journal = {Rev Med Chir Soc Med Nat Iasi},
   volume = {116},
   number = {4},
   pages = {983-90},
   note = {Serban, Daniela Elena
Journal Article
Romania
Rev Med Chir Soc Med Nat Iasi. 2012 Oct-Dec;116(4):983-90.},
   abstract = {Countless studies aiming to discover the cause and cure of inflammatory bowel disease (IBD) have been conducted over the years world-wide. Food nutrients were believed to play a certain role in the causation of the disease, in conjunction with genetic, immunologic, environmental and other factors (especially intestinal microbiota). Various nutrients were found to be involved, sometimes with controversial results, possibly pertaining to geographic regions. Nutrition has to be especially considered in children as disease itself and/or the medication can severely impair normal growth and development, sometimes with permanent long-term sequels. We reviewed the data on the possible roles of diet in preventing the disease and relapses. We emphasize the crucial importance of enteral nutrition in inducing and maintaining the remission of Crohn's disease, according to the existing consensuses (benefits, indications, routes of administration, types of formula, duration, results). We also present data on parenteral nutrition in pediatric IBD, with current updates from literature.},
   keywords = {Body Mass Index
Child
Colitis, Ulcerative/therapy
Crohn Disease/therapy
*Enteral Nutrition/methods
Evidence-Based Medicine
Humans
Inflammatory Bowel Diseases/etiology/*therapy
Nutrition Therapy/methods
Obesity/complications
Overweight/complications
*Parenteral Nutrition/methods
Risk Factors
Treatment Outcome},
   ISSN = {0048-7848 (Print)
0048-7848},
   Accession Number = {23700876},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Shanahan, F.},
   title = {The microbiota in inflammatory bowel disease: friend, bystander, and sometime-villain},
   journal = {Nutr Rev},
   volume = {70 Suppl 1},
   pages = {S31-7},
   note = {1753-4887
Shanahan, Fergus
Journal Article
Research Support, Non-U.S. Gov't
Review
United States
Nutr Rev. 2012 Aug;70 Suppl 1:S31-7. doi: 10.1111/j.1753-4887.2012.00502.x.},
   abstract = {Ulcerative colitis and Crohn's disease, collectively known as inflammatory bowel disease, represent the heterogeneous outcome of three colliding influences: genetic risk factors, environmental modifiers, and immune effector mechanisms of tissue injury. The nature of these inputs is complex, with each having distinct and overlapping contributions to ulcerative colitis and Crohn's disease. Identification of specific genetic risk factors has improved the understanding of specific pathways to disease, but the primacy of environmental or lifestyle factors linked to changes in the gut microbiota, particularly in early life, is increasingly evident. Clarification of the molecular basis of host-microbe interactions in health and in susceptible individuals promises novel therapeutic strategies.},
   keywords = {Diet
Disease Susceptibility
Genetic Predisposition to Disease
*Host-Pathogen Interactions
Humans
Inflammatory Bowel Diseases/genetics/*immunology/*microbiology
*Metagenome
Risk Factors},
   ISSN = {0029-6643},
   Accession Number = {22861805},
   DOI = {10.1111/j.1753-4887.2012.00502.x},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Shirazi, K. M. and Somi, M. H. and Rezaeifar, P. and Fattahi, I. and Khoshbaten, M. and Ahmadzadeh, M.},
   title = {Bone density and bone metabolism in patients with inflammatory bowel disease},
   journal = {Saudi J Gastroenterol},
   volume = {18},
   number = {4},
   pages = {241-7},
   note = {1998-4049
Shirazi, Kourosh M
Somi, Mohammad H
Rezaeifar, Parisa
Fattahi, Ibrahim
Khoshbaten, Manuchehr
Ahmadzadeh, Masoumeh
Journal Article
Research Support, Non-U.S. Gov't
India
Saudi J Gastroenterol. 2012 Jul-Aug;18(4):241-7. doi: 10.4103/1319-3767.98428.},
   abstract = {BACKGROUND/AIMS: Patients with inflammatory bowel disease (IBD) are at high risk for low bone mineral density (BMD). This study aimed to evaluate BMD in IBD patients and its relationship with bone metabolism in a group of Iranian patients. PATIENTS AND METHODS: A cross-sectional study was conducted on patients with IBD to assess BMD status and serum biochemical factors. After getting the demographic data from 200 patients, they were screened using dual-energy X-ray absorptiometry of the lumbar spine (L2-L4) and femoral neck for BMD status. Serum levels of calcium, phosphate, alkaline phosphatase (ALP), and 25-hydroxyvitamin D (25-OH vitamin D) were measured to assess the bone metabolism status. RESULTS: Two hundred patients with IBD were enrolled in the study. One hundred and eighty three (91.5%) patients were identified as having ulcerative colitis (UC) and 17 (8.5%) as having Crohn's disease (CD). Based on the lumbar and femoral neck bone mass densitometry, 148 (74.4%) patients had low BMD at either lumbar spine or femoral neck. Of these, 100 patients (50.3%) were osteopenic and 48 patients (24.1%) were osteoporotic. A 58.6% and 61% of patients with UC had low BMD in the lumbar and femoral neck, respectively. These results for those with CD were 76.5% and 70.6%, respectively. The mean of femoral neck and lumbar T-scores in patients with UC were -1.14 and -1.38, and in patients with CD were -1.24 and -1.47, respectively (P > 0.05). The mean (+/-SD) levels for calcium (Ca) in UC and CD were in the normal range. The mean (+/-SD) levels of ALP and 25-OH vitamin D in both the groups were in the normal range, and in comparison between groups (UC and CD), no significant differences were observed (P = 0.20 for ALP and P = 0.44 for 25-OH vitamin D). In the assessment of correlation between biochemical markers and BMD, an inverse correlation between lumbar T-score and ALP or 25-OH vitamin D only in patients with UC was observed. CONCLUSIONS: The high prevalence of low BMD in the Iranian population with IBD needs attention. The subclinical vitamin D deficiency may contribute to bone loss in IBD patients, which is more pronounced in patients with UC in this study because of the small population of patients with CD.},
   keywords = {Absorptiometry, Photon
Adolescent
Adult
Age Factors
Aged
Bone Density
Bone Diseases, Metabolic/diagnosis/*epidemiology/metabolism
Cohort Studies
Colitis, Ulcerative/*complications/*metabolism/pathology
Crohn Disease/*complications/*metabolism/pathology
Cross-Sectional Studies
Diet
Female
Humans
Iran
Male
Middle Aged
Risk Factors
Sex Factors
Young Adult},
   ISSN = {1319-3767},
   Accession Number = {22824766},
   DOI = {10.4103/1319-3767.98428},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Sokol, H. and Beaugerie, L. and Maynadie, M. and Laharie, D. and Dupas, J. L. and Flourie, B. and Lerebours, E. and Peyrin-Biroulet, L. and Allez, M. and Simon, T. and Carrat, F. and Brousse, N.},
   title = {Excess primary intestinal lymphoproliferative disorders in patients with inflammatory bowel disease},
   journal = {Inflamm Bowel Dis},
   volume = {18},
   number = {11},
   pages = {2063-71},
   note = {1536-4844
Sokol, Harry
Beaugerie, Laurent
Maynadie, Marc
Laharie, David
Dupas, Jean-Louis
Flourie, Bernard
Lerebours, Eric
Peyrin-Biroulet, Laurent
Allez, Matthieu
Simon, Tabassome
Carrat, Fabrice
Brousse, Nicole
CESAME Study Group
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
United States
Inflamm Bowel Dis. 2012 Nov;18(11):2063-71. doi: 10.1002/ibd.22889. Epub 2012 Jan 23.},
   abstract = {BACKGROUND: It remains to be shown whether inflammatory bowel disease (IBD) is associated with an increased risk of primary intestinal lymphoproliferative disorders (PILD). We assessed this risk in the CESAME French nationwide prospective observational cohort. METHODS: In all, 680 gastroenterologists enrolled 19,486 patients with IBD (Crohn's disease in 60.3%) from May 2004 to June 2005. Follow-up ended on 31 December 2007. Available biopsy samples and surgical specimens from patients with PILD (n = 14) were centralized for review. The reference incidence of PILD in the general population was obtained from the Cote d'Or registry and was used as a comparator to assess the standardized incidence ratio (SIR). The influence of thiopurine exposure was explored in a nested case-control study. RESULTS: In the CESAME population the crude incidence of PILD was 0.12/1000 patient-years, with a corresponding SIR of 17.51 (95% confidence interval [CI], 6.43-38.11; P < 0.0001). The risk was highest in patients exposed to thiopurines (SIR 49.52, 95% CI 13.49-126.8; P < 0.0001), while it did not reach statistical significance in patients naive to thiopurines (SIR 4.83, 95% CI, 0.12-26.91; P = 0.37). The odds ratio associated with ongoing thiopurine exposure (vs. naive) was 2.97 (95% CI, 0.30-infinity; P = 0.38). All 14 cases of PILD were non-Hodgkin's B-cell LD, 78.6% occurred in males, 85.7% arose in IBD lesions, and 45.5% were Epstein-Barr virus-positive. Eleven cases occurred in patients with Crohn's disease. Mean (SD) age at PILD diagnosis was 55.1 (5.6) years and the median time since IBD onset was 8.0 years (interquartile range, 3.0-15.8). CONCLUSIONS: Patients with IBD have an increased risk of developing PILD.},
   keywords = {6-Mercaptopurine/*therapeutic use
Adult
Aged
Aged, 80 and over
Azathioprine/*therapeutic use
Case-Control Studies
Child
Colitis, Ulcerative/*complications
Crohn Disease/*complications
Female
Follow-Up Studies
France/epidemiology
Humans
Immunosuppressive Agents/*therapeutic use
Incidence
Lymphoproliferative Disorders/drug therapy/*epidemiology/etiology
Male
Middle Aged
Prospective Studies
Treatment Outcome
Young Adult},
   ISSN = {1078-0998},
   Accession Number = {22271569},
   DOI = {10.1002/ibd.22889},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Spehlmann, M. E. and Begun, A. Z. and Saroglou, E. and Hinrichs, F. and Tiemann, U. and Raedler, A. and Schreiber, S.},
   title = {Risk factors in German twins with inflammatory bowel disease: results of a questionnaire-based survey},
   journal = {J Crohns Colitis},
   volume = {6},
   number = {1},
   pages = {29-42},
   note = {1876-4479
Spehlmann, Martina E
Begun, Alexander Z
Saroglou, Ekaterini
Hinrichs, Frank
Tiemann, Ute
Raedler, Andreas
Schreiber, Stefan
Journal Article
Research Support, Non-U.S. Gov't
Twin Study
England
J Crohns Colitis. 2012 Feb;6(1):29-42. doi: 10.1016/j.crohns.2011.06.007.},
   abstract = {INTRODUCTION: Environmental factors may play an important role in the pathogenesis of IBD. The history of patients of the German IBD twin study was analyzed by questionnaires and interviews. METHODS: Randomly selected German monozygotic (MZ) and dizygotic (DZ) twins with at least one sibling suffering from IBD (n=512) were characterized in detail including demography, medical history and concomitant medications. Controls comprised of non-twin IBD patients (n=392) and healthy subjects (n=207). RESULTS: The most significant variables that were associated with Crohn's disease (CD) or ulcerative colitis (UC) included living abroad before time of diagnosis (OR, 4.32; 95% CI, 1.57-13.69), high frequency of antibiotic use (MZ CD OR, 5.03; 95% CI 1.61-17.74, DZ CD OR, 7.66; 95% CI, 3.63-16.82, MZ UC OR, 3.82; 95% CI, 1.45-10.56, DZ UC OR, 3.08; CI, 1.63-5.92), high consumption of processed meat including sausage (MZ CD OR, 7.9; 95% CI, 2.15-38.12, DZ CD OR, 10.75; 95% CI, 4.82-25.55, MZ UC OR, 5.69; 95% CI, 1.89-19.48, DZ UC OR, 18.11; 95% CI, 7.34-50.85), and recall of bacterial gastrointestinal infections (MZ CD OR, 15.9; 95% CI, 4.33-77.14, DZ CD OR, 17.21; 95% CI, 4.47-112.5, MZ UC OR, 5.87; 95% CI, 1.61-28.0, DZ UC OR, 11.34; 95% CI, 4.81-29.67). CONCLUSIONS: This study reinforced the association of life style events, in particular a specific dietary and infections history, with IBD. Alteration of gut flora or alterations of the mucosal immune system in reactivity to the flora could be an important factor to explain the relationship between life-style and disease.},
   keywords = {Adolescent
Adult
Aged
Child
Colitis, Ulcerative/*etiology
Communicable Diseases/complications
Comorbidity
Crohn Disease/*etiology
Diet
Diseases in Twins/*etiology
Female
Germany
Humans
Life Style
Male
Middle Aged
Risk Factors
Surveys and Questionnaires
Twins, Dizygotic
Twins, Monozygotic
Young Adult},
   ISSN = {1873-9946},
   Accession Number = {22261525},
   DOI = {10.1016/j.crohns.2011.06.007},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Steck, N. and Hoffmann, M. and Sava, I. G. and Kim, S. C. and Hahne, H. and Tonkonogy, S. L. and Mair, K. and Krueger, D. and Pruteanu, M. and Shanahan, F. and Vogelmann, R. and Schemann, M. and Kuster, B. and Sartor, R. B. and Haller, D.},
   title = {Enterococcus faecalis metalloprotease compromises epithelial barrier and contributes to intestinal inflammation},
   journal = {Gastroenterology},
   volume = {141},
   number = {3},
   pages = {959-71},
   note = {1528-0012
Steck, Natalie
Hoffmann, Micha
Sava, Irina G
Kim, Sandra C
Hahne, Hannes
Tonkonogy, Susan L
Mair, Katrin
Krueger, Dagmar
Pruteanu, Mihaela
Shanahan, Fergus
Vogelmann, Roger
Schemann, Michael
Kuster, Bernhard
Sartor, R Balfor
Haller, Dirk
P40 RR018603/RR/NCRR NIH HHS/United States
R01 DK053347/DK/NIDDK NIH HHS/United States
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
United States
Gastroenterology. 2011 Sep;141(3):959-71. doi: 10.1053/j.gastro.2011.05.035. Epub 2011 May 26.},
   abstract = {BACKGROUND & AIMS: Matrix metalloproteases (MMPs) mediate pathogenesis of chronic intestinal inflammation. We characterized the role of the gelatinase (GelE), a metalloprotease from Enterococcus faecalis, in the development of colitis in mice. METHODS: Germ-free, interleukin-10-deficient (IL-10(-/-)) mice were monoassociated with the colitogenic E faecalis strain OG1RF and isogenic, GelE-mutant strains. Barrier function was determined by measuring E-cadherin expression, transepithelial electrical resistance (TER), and translocation of permeability markers in colonic epithelial cells and colon segments from IL-10(-/-) and TNF(DeltaARE/Wt) mice. GelE specificity was shown with the MMP inhibitor marimastat. RESULTS: Histologic analysis (score 0-4) of E faecalis monoassociated IL-10(-/-) mice revealed a significant reduction in colonic tissue inflammation in the absence of bacteria-derived GelE. We identified cleavage sites for GelE in the sequence of recombinant mouse E-cadherin, indicating that it might be degraded by GelE. Experiments with Ussing chambers and purified GelE revealed the loss of barrier function and extracellular E-cadherin in mice susceptible to intestinal inflammation (IL-10(-/-) and TNF(DeltaARE/Wt) mice) before inflammation developed. Colonic epithelial cells had reduced TER and increased translocation of permeability markers after stimulation with GelE from OG1RF or strains of E faecalis isolated from patients with Crohn's disease and ulcerative colitis. CONCLUSIONS: The metalloprotease GelE, produced by commensal strains of E faecalis, contributes to development of chronic intestinal inflammation in mice that are susceptible to intestinal inflammation (IL-10(-/-) and TNF(DeltaARE/Wt) mice) by impairing epithelial barrier integrity.},
   keywords = {Animals
CD4-Positive T-Lymphocytes/physiology
Cadherins/metabolism
Cell Membrane Permeability/*physiology
Colitis/etiology/metabolism/*physiopathology
Disease Models, Animal
Enterococcus faecalis/*metabolism
Gelatinases/*metabolism
Gram-Positive Bacterial Infections/complications/metabolism/*physiopathology
Interleukin-10/genetics/metabolism
Intestinal Mucosa/cytology/*metabolism
Metalloproteases/*metabolism
Mice
Mice, Knockout
Mice, Mutant Strains
Tumor Necrosis Factor-alpha/genetics/metabolism},
   ISSN = {0016-5085},
   Accession Number = {21699778},
   DOI = {10.1053/j.gastro.2011.05.035},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Suwendi, E. and Iwaya, H. and Lee, J. S. and Hara, H. and Ishizuka, S.},
   title = {Zinc deficiency induces dysregulation of cytokine productions in an experimental colitis of rats},
   journal = {Biomed Res},
   volume = {33},
   number = {6},
   pages = {329-36},
   note = {1880-313x
Suwendi, Erwin
Iwaya, Hitoshi
Lee, Jae-Sung
Hara, Hiroshi
Ishizuka, Satoshi
Journal Article
Research Support, Non-U.S. Gov't
Japan
Biomed Res. 2012 Dec;33(6):329-36.},
   abstract = {Dextran sulfate sodium (DSS)-induced colitis is an experimental model of ulcerative colitis, although the precise mechanism has not yet been elucidated. We investigate whether Zn deficiency affects the pathogenesis of colitis induced by DSS with a focus on immune responses. Male WKAH/Hkm Slc rats were fed either a Zn-adequate (ZA, 30 mg Zn/kg diet) as a control or Zndeficient (ZD, 5 mg Zn/kg diet) diet for 21 days and then treated with 2% DSS via deionized drinking water for 7 days. The disease activity index (DAI) was recorded daily throughout DSS treatment. Serum Zn concentrations were significantly lowered in rats fed the ZD diet than those fed the ZA diet at day 7 and 14. Surprisingly, DSS treatment considerably reduced the serum Zn in both groups. The rats fed the ZD diet showed exacerbated colitis based on clinical outcomes, including weight loss, increased DAI, and shortened colon length. An in vitro study corroborated these results, showing that a large amount of TNFalpha was induced by rat mesenteric leukocytes in response to lipopolysaccharide in ZD medium, but not in ZA medium. These results indicate that a modulation of TNFalpha production due to Zn deficiency influences disease activity in DSS-induced colitis. In addition, more attention should be given to Zn for prevention of colitis.},
   keywords = {Animals
Body Weight
Colitis, Ulcerative/chemically induced/*metabolism/pathology
Colon/metabolism/pathology
Cytokines/*biosynthesis
Dextran Sulfate
Diet
Disease Models, Animal
Femur/metabolism
Liver/metabolism
Male
Organ Size
Peroxidase/metabolism
Rats
Severity of Illness Index
Zinc/*deficiency/metabolism},
   ISSN = {0388-6107},
   Accession Number = {23268956},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Tang, T. and Targan, S. R. and Li, Z. S. and Xu, C. and Byers, V. S. and Sandborn, W. J.},
   title = {Randomised clinical trial: herbal extract HMPL-004 in active ulcerative colitis - a double-blind comparison with sustained release mesalazine},
   journal = {Aliment Pharmacol Ther},
   volume = {33},
   number = {2},
   pages = {194-202},
   note = {1365-2036
Tang, T
Targan, S R
Li, Z-S
Xu, C
Byers, V S
Sandborn, W J
Journal Article
Multicenter Study
Randomized Controlled Trial
Research Support, Non-U.S. Gov't
England
Aliment Pharmacol Ther. 2011 Jan;33(2):194-202. doi: 10.1111/j.1365-2036.2010.04515.x. Epub 2010 Nov 30.},
   abstract = {BACKGROUND: Andrographis paniculata is an herbal mixture used to treat inflammatory diseases. An extract of the herb, HMPL-004, inhibits TNF-alpha and IL-1beta, and prevents colitis in animal models. AIM: To determine the efficacy and safety of HMPL-004 in patients with mild-to-moderate ulcerative colitis. METHODS: A randomised, double-blind, multicentre, 8-week parallel group study was conducted using HMPL-004 1200 mg/day compared with 4500 mg/day of slow release mesalazine (mesalamine) granules in patients with mild-to-moderately active ulcerative colitis. Disease activity was assessed at baseline and every 2 weeks for clinical response, and at baseline and 8 weeks by colonoscopy. RESULTS: One hundred and twenty patients at five centres in China were randomised and dosed. Clinical remission and response were seen in 21% and 76% of HMPL-004-treated patients, and 16% and 82% of mesalazine-treated patients. By colonoscopy, remission and response were seen in 28% and 74% of HMPL-004-treated patients and 24% and 71% of mesalazine-treated patients, respectively. There was no significant difference between the two treatment groups. CONCLUSION: HMPL-004 may be an efficacious alternative to mesalazine in ulcerative colitis.},
   keywords = {Acanthaceae/chemistry
Adolescent
Adult
Aged
Anti-Inflammatory Agents, Non-Steroidal/*therapeutic use
China
Colitis, Ulcerative/*drug therapy/physiopathology
Dietary Supplements
Double-Blind Method
Female
Humans
Male
Mesalamine/*therapeutic use
Middle Aged
Plant Preparations/*therapeutic use
Severity of Illness Index
Treatment Outcome
Young Adult},
   ISSN = {0269-2813},
   Accession Number = {21114791},
   DOI = {10.1111/j.1365-2036.2010.04515.x},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Teixeira, L. G. and Leonel, A. J. and Aguilar, E. C. and Batista, N. V. and Alves, A. C. and Coimbra, C. C. and Ferreira, A. V. and de Faria, A. M. and Cara, D. C. and Alvarez Leite, J. I.},
   title = {The combination of high-fat diet-induced obesity and chronic ulcerative colitis reciprocally exacerbates adipose tissue and colon inflammation},
   journal = {Lipids Health Dis},
   volume = {10},
   pages = {204},
   note = {1476-511x
Teixeira, Lilian G
Leonel, Alda J
Aguilar, Edenil C
Batista, Nathalia V
Alves, Andrea C
Coimbra, Candido C
Ferreira, Adaliene V M
de Faria, Ana Maria C
Cara, Denise C
Alvarez Leite, Jacqueline I
Journal Article
Research Support, Non-U.S. Gov't
England
Lipids Health Dis. 2011 Nov 10;10:204. doi: 10.1186/1476-511X-10-204.},
   abstract = {BACKGROUND: This study evaluated the relationship between ulcerative colitis and obesity, which are both chronic diseases characterized by inflammation and increases in immune cells and pro-inflammatory cytokines. METHODS: Mice with chronic ulcerative colitis induced by 2 cycles of dextran sodium sulfate (DSS) in the first and fourth week of the experiment were fed a high-fat diet (HFD) to induce obesity by 8 weeks. The animals were divided into 4 \ groups (control, colitis, HFD and colitis + HFD). RESULTS: Obesity alone did not raise histopathology scores, but the combination of obesity and colitis worsened the scores in the colon compared to colitis group. Despite the reduction in weight gain, there was increased inflammatory infiltrate in both the colon and visceral adipose tissue of colitis + HFD mice due to increased infiltration of macrophages, neutrophils and lymphocytes. Intravital microscopy of VAT microvasculature showed an increase in leukocyte adhesion and rolling and overexpression of adhesion molecules compared to other groups. Moreover, circulating lymphocytes, monocytes and neutrophils in the spleen and cecal lymph nodes were increased in the colitis + HFD group. CONCLUSION: Our results demonstrated the relationship between ulcerative colitis and obesity as aggravating factors for each disease, with increased inflammation in the colon and adipose tissue and systemic alterations observed in the spleen, lymph nodes and bloodstream.},
   keywords = {Adipokines/blood
Adipose Tissue/blood supply/*pathology
Adiposity
Animals
Antigens, CD/metabolism
Chemokines/metabolism
Colitis, Ulcerative/*chemically induced/*complications/pathology
Colon/pathology
Cytokines/metabolism
Dextran Sulfate
Diet, High-Fat
Epididymis/pathology
Gene Expression
Inflammation
Male
Mice
Mice, Inbred C57BL
Microvessels/pathology
Obesity/*complications/pathology
Receptors, Leptin/genetics/metabolism
T-Lymphocytes/metabolism/pathology
Toll-Like Receptor 4/genetics/metabolism},
   ISSN = {1476-511x},
   Accession Number = {22073943},
   DOI = {10.1186/1476-511x-10-204},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Todorovic, V.},
   title = {Providing holistic support for patients with inflammatory bowel disease},
   journal = {Br J Community Nurs},
   volume = {17},
   number = {10},
   pages = {466, 468-72},
   note = {Todorovic, Vera
Journal Article
England
Br J Community Nurs. 2012 Oct;17(10):466, 468-72.},
   abstract = {Inflammatory bowel diseases such as ulcerative colitis and Crohn's disease are life-long, complex conditions. They are characterised by periods of exacerbation and remission and surgical intervention may be required in severe cases. Drugs employed in the management of IBD are used to induce remission and maintain remission. IBD has a physical, psychological and sociological impact on individuals and IBD quality standards have been developed to provide a framework for addressing the services and care that should be available for them. Complementary and alternative medicine (CAM) therapies play an important role in the holistic approach to management of IBD as they are being increasingly used alongside conventional medical treatments. Community nurses have an important role to play in the management and care of individuals with IBD and in supporting them in making informed and appropriate choices that support their wellbeing and quality of life.},
   keywords = {*Complementary Therapies
*Holistic Nursing
Humans
Inflammatory Bowel Diseases/diet therapy/drug therapy/*nursing/*therapy
Malnutrition/prevention & control
Patient Education as Topic
Referral and Consultation
United Kingdom},
   ISSN = {1462-4753 (Print)
1462-4753},
   Accession Number = {23124372},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Vagianos, K. and Bernstein, C. N.},
   title = {Homocysteinemia and B vitamin status among adult patients with inflammatory bowel disease: a one-year prospective follow-up study},
   journal = {Inflamm Bowel Dis},
   volume = {18},
   number = {4},
   pages = {718-24},
   note = {1536-4844
Vagianos, Kathy
Bernstein, Charles N
Journal Article
Research Support, Non-U.S. Gov't
United States
Inflamm Bowel Dis. 2012 Apr;18(4):718-24. doi: 10.1002/ibd.21785. Epub 2011 May 20.},
   abstract = {BACKGROUND: The aim of this study was to longitudinally study serum homocysteine levels in patients with Crohn's disease (CD) and ulcerative colitis (UC) in relation to disease activity and B vitamin status. METHODS: In all, 98 consecutive adult patients (age 25-55 years) with CD (n = 70) and UC (n = 28) were enrolled and assessed at three timepoints over 1 year. RESULTS: There were no significant differences in levels of homocysteine, B vitamins, or dietary intake by disease type, disease activity, or across visits. 13% of all inflammatory bowel disease (IBD) patients had elevated homocysteine at least once during the study. Nine patients with CD had fluctuating homocysteine levels during the study but these were inconsistent, ranging from within normal range to elevated levels in any individual. Six of these nine patients were persistently in remission. 30% of all IBD patients had vitamin B6 deficiency, 11% had vitamin B12 deficiency, and one patient (CD) had folate deficiency. All vitamins showed a significant correlation between intake and serum levels (B6; r = 0.46, P < 0.001, B12; r = 0.42, P < 0.001, and folate; r = 0.26, P = 0.008). There was an inverse relationship between serum homocysteine in the blood and serum vitamin B12 (r = -0.241, P = 0.017). CONCLUSIONS: Serum homocysteine was mostly normal in patients with IBD and changed minimally over time. There was no association between disease activity and elevation of serum homocysteine. 30% of patients have vitamin B6 deficiency but vitamin B6 is not associated with elevated homocysteine. The routine measurement of homocysteine is not warranted.},
   keywords = {Adult
Dietary Supplements
Female
Folic Acid/blood
Folic Acid Deficiency/blood
Homocysteine/*blood
Humans
Inflammatory Bowel Diseases/*blood
Male
Middle Aged
Nutritional Status
Prospective Studies
Severity of Illness Index
Vitamin B 12 Deficiency/blood
Vitamin B 6 Deficiency/blood
Vitamin B Complex/*blood},
   ISSN = {1078-0998},
   Accession Number = {21604334},
   DOI = {10.1002/ibd.21785},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Valentini, L. and Schulzke, J. D.},
   title = {Mundane, yet challenging: the assessment of malnutrition in inflammatory bowel disease},
   journal = {Eur J Intern Med},
   volume = {22},
   number = {1},
   pages = {13-5},
   note = {1879-0828
Valentini, Luzia
Schulzke, Jorg-Dieter
Comment
Journal Article
Review
Netherlands
Eur J Intern Med. 2011 Feb;22(1):13-5. doi: 10.1016/j.ejim.2010.07.021.},
   abstract = {Protein-energy malnutrition (PEM) is defined as a "state of nutrition in which a deficiency or excess (or imbalance) of energy, protein, and other nutrients causes measurable adverse effects on tissue/body form (body shape, size and composition) and function, and clinical outcome". Although this definition resulted from a long discussion among experts, it lacks concise assessment criteria. Essential to an effective practice of nutrition support, however, is the ability to identify who actually needs medical nutrition therapy. Patients with active inflammatory bowel disease (IBD) are a high risk group for protein-energy malnutrition, with a prevalence ranging up to 75%.},
   keywords = {Body Mass Index
Colitis, Ulcerative/complications
Crohn Disease/complications
Germany/epidemiology
Humans
Inflammatory Bowel Diseases/*complications/diagnosis/diet therapy/epidemiology
Malnutrition/diagnosis/diet therapy/epidemiology/*etiology
*Nutrition Assessment
Nutritional Support/methods
Prevalence
Protein-Energy Malnutrition/etiology
Risk Factors
Severity of Illness Index},
   ISSN = {0953-6205},
   Accession Number = {21238886},
   DOI = {10.1016/j.ejim.2010.07.021},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Varnalidis, I. and Ioannidis, O. and Karamanavi, E. and Ampas, Z. and Poutahidis, T. and Taitzoglou, I. and Paraskevas, G. and Botsios, D.},
   title = {Omega 3 fatty acids supplementation has an ameliorative effect in experimental ulcerative colitis despite increased colonic neutrophil infiltration},
   journal = {Rev Esp Enferm Dig},
   volume = {103},
   number = {10},
   pages = {511-8},
   note = {Varnalidis, Ioannis
Ioannidis, Orestis
Karamanavi, Elisavet
Ampas, Zafeiris
Poutahidis, Theofilos
Taitzoglou, Ioannis
Paraskevas, George
Botsios, Dimitrios
Journal Article
Spain
Rev Esp Enferm Dig. 2011 Oct;103(10):511-8.},
   abstract = {PURPOSE: omega 3 polyunsaturated fatty acids have anti-inflammatory properties and can be beneficial in the treatment of inflammatory diseases, such as ulcerative colitis. Dextran sodium sulphate (DSS) colitis in rats appears to mimic nearly all of the morphological characteristics and lesion distributions of ulcerative colitis. The purpose of the current study was to investigate the efficacy of omega 3 fatty acids in the treatment of experimental ulcerative colitis. METHODS: thirty-six Wistar rats were randomly assigned to group A or group B receiving 5% dextran sulfate sodium (DSS) in their drinking water for eight days. For the next eight days post-DSS, group A animals received tap-water, and group B animals were fed a nutritional solution containing high levels of omega 3 polyunsaturated fatty acids (ProSure(R), Abbott Laboratories, Zwolle, Netherlands) once per day, administrated with a orogastric feeding tube. RESULTS: animals fed an omega 3 rich diet exhibited a statistically significant increase in hematocrit and hemoglobin levels, compared to animals drinking tap water, and a trend towards histopathological and clinical improvement, with the administration of omega 3 fatty acids ameliorating epithelial erosion by day 8 post-DSS, but no statistically significant difference was observed between group A and group B animals at 4 or 8 days post-DSS. Also, a statistically significant increase in neutrophil infiltration was observed, as depicted by myelohyperoxidase activity. CONCLUSION: our findings support a positive role of omega 3 polyunsaturated fatty acids supplementation in an experimental model of ulcerative colitis despite the increased colonic neutrophil infiltration. Further studies are needed in order to investigate the role of increased neutrophils in colonic mucosa.},
   keywords = {Animals
Blood Cell Count
Body Weight/drug effects
Colitis, Ulcerative/chemically induced/*drug therapy/pathology
Colon/pathology
Dextran Sulfate
Fatty Acids, Omega-3/*therapeutic use
Immunohistochemistry
Intestinal Mucosa/pathology
Male
Neutrophil Infiltration/*drug effects
Peroxidase/metabolism
Rats
Rats, Wistar
Tissue Fixation},
   ISSN = {1130-0108 (Print)
1130-0108},
   Accession Number = {22054266},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Vieira de Barros, K. and Gomes de Abreu, G. and Xavier, R. A. and Real Martinez, C. A. and Ribeiro, M. L. and Gambero, A. and de Oliveira Carvalho, P. and Silveira, V. L.},
   title = {Effects of a high fat or a balanced omega 3/omega 6 diet on cytokines levels and DNA damage in experimental colitis},
   journal = {Nutrition},
   volume = {27},
   number = {2},
   pages = {221-6},
   note = {1873-1244
Vieira de Barros, Karina
Gomes de Abreu, Gilclay
Xavier, Roberta Araujo Navarro
Real Martinez, Carlos Augusto
Ribeiro, Marcelo Lima
Gambero, Alessandra
de Oliveira Carvalho, Patricia
Silveira, Vera Lucia Flor
Journal Article
Research Support, Non-U.S. Gov't
United States
Nutrition. 2011 Feb;27(2):221-6. doi: 10.1016/j.nut.2009.11.014. Epub 2010 Apr 3.},
   abstract = {OBJECTIVE: High-fat diets have been shown to be a risk factor for ulcerative colitis (UC). Omega-6 polyunsaturated fatty acids are considered to increase lipid peroxidation, while the omega-3 polyunsaturated fatty acid exerts a chemopreventative effect. We evaluated the effect of high-fat diets (20%) enriched with fish or soybean oil on colonic inflammation and DNA damage in dextran sulfate sodium-induced colitis. METHODS: Male Wistar rats (28-30 days) were fed an American Institute of Nutrition (AIN)-93 diet for 47 days and divided into five groups: control normal fat non-colitic (C) or control colitis (CC), high soybean fat group (HS) colitis, high fish fat group colitis, or high-fat soybean plus fish oil colitis. UC was induced from day 35 until day 41 by 3% dextran sulfate sodium. On day 47, the rats were anesthetized; blood samples collected for corticosterone determination, and the distal colon was excised to quantify interleukin-4 (IL-4), IL-10, and interferon-gamma levels, myeloperoxidase activity, histological analyses, and DNA damage. The disease activity index was recorded daily. RESULTS: The disease activity index, histological analysis, myeloperoxidase activity, IL-4, interferon-gamma, and corticosterone levels did not differ among the colitic groups. IL-10 was significantly increased by the high fish fat group diet in relation to HS, but only the high soybean-fish fat diet increased the IL-10/IL-4 ratio (anti-inflammatory/pro-inflammatory) to levels closer to the C group and reduced DNA damage compared to the HS group (P<0.05). CONCLUSION: The data show that high-fat diets did not exacerbate UC and suggest that the soybean and fish oil mixture, more than the fish oil alone, could be a complementary therapy to achieve a cytokine balance in UC.},
   keywords = {Animals
Colitis, Ulcerative/*chemically induced
Colon/pathology
*DNA Damage
Dextran Sulfate/toxicity
Diet
Dietary Fats/*administration & dosage
Disease Models, Animal
Fatty Acids, Omega-3/*administration & dosage
Fatty Acids, Omega-6/*administration & dosage
Fish Oils/pharmacology
Interferon-gamma/blood
Interleukin-10/blood
Interleukin-4/blood
Male
Rats
Rats, Wistar
Risk Factors
Soybean Oil/pharmacology},
   ISSN = {0899-9007},
   Accession Number = {20363597},
   DOI = {10.1016/j.nut.2009.11.014},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Wedrychowicz, A. and Kowalska-Duplaga, K. and Jedynak-Wasowicz, U. and Pieczarkowski, S. and Sladek, M. and Tomasik, P. and Fyderek, K.},
   title = {Serum concentrations of VEGF and TGF-beta1 during exclusive enteral nutrition in IBD},
   journal = {J Pediatr Gastroenterol Nutr},
   volume = {53},
   number = {2},
   pages = {150-5},
   note = {1536-4801
Wedrychowicz, Andrzej
Kowalska-Duplaga, Kinga
Jedynak-Wasowicz, Urszula
Pieczarkowski, Stanislaw
Sladek, Malgorzata
Tomasik, Przemyslaw
Fyderek, Krzysztof
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
United States
J Pediatr Gastroenterol Nutr. 2011 Aug;53(2):150-5. doi: 10.1097/MPG.0b013e3182144c74.},
   abstract = {BACKGROUND AND AIM: Exclusive enteral nutrition (EEN) is an effective method of treatment in achieving remission in inflammatory bowel disease (IBD); however, its mechanism of action is still poorly understood. The objective of our study was to assess the influence of EEN on serum vascular endothelial growth factor (VEGF) and transforming growth factor-beta 1 (TGF-beta1) in children and adolescents with IBD. PATIENTS AND METHODS: Thirty-nine children and adolescents with IBD (24 with Crohn disease [CD] and 15 with ulcerative colitis [UC]) and 25 healthy controls were enrolled in the study. VEGF and TGF-beta1 were assessed at the baseline and after 2 and 4 weeks of EEN in CD and UC groups and once in controls using enzyme-linked immunosorbent assay immunoassays. RESULTS: At the baseline, we found increased serum VEGF in the CD versus UC group and controls (P < 0.05) and serum TGF-beta1 in the UC versus CD group and controls (P < 0.05). During EEN, VEGF decreased in the UC and CD groups, whereas TGF-beta1 increased in the CD group and decreased in the UC group. The CD group achieved disease remission faster than the UC group, and the weight gain of patients with CD during EEN was higher compared with patients with UC. Additionally, TGF-beta1 concentration correlated with protein and energies daily intake in the CD group (R = 0.95; P < 0.05). CONCLUSIONS: Different effectiveness of EEN in achieving remission in CD and UC may result from a modification of growth factor production. EEN stimulated TGF-beta1 production in CD but not in UC, which possibly resulted in higher effectiveness of EEN in this group of patients.},
   keywords = {Adolescent
Child
Colitis, Ulcerative/blood/therapy
Crohn Disease/blood/therapy
Dietary Proteins/administration & dosage
Energy Intake
*Enteral Nutrition
Female
Humans
Inflammatory Bowel Diseases/*blood/*therapy
Male
Remission Induction
Severity of Illness Index
Time Factors
Transforming Growth Factor beta1/*blood
Vascular Endothelial Growth Factors/*blood
Weight Gain},
   ISSN = {0277-2116},
   Accession Number = {21788755},
   DOI = {10.1097/MPG.0b013e3182144c74},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Weerasekara, D. and Fernando, N. and Meedin, F. and Holton, J. and Fernando, D.},
   title = {Clinical presentation and risk factors of inflammatory bowel disease in Sri Lanka},
   journal = {Trop Gastroenterol},
   volume = {32},
   number = {1},
   pages = {31-5},
   note = {Weerasekara, Deepaka
Fernando, Neluka
Meedin, F
Holton, John
Fernando, D
Journal Article
India
Trop Gastroenterol. 2011 Jan-Mar;32(1):31-5.},
   abstract = {BACKGROUND AND AIMS: There have been very few studies on inflammatory bowel disease (IBD) in Sri Lanka. This study was undertaken to determine the clinical presentation and whether a western style diet or infection with geo-helminths were associated with the condition. METHODS: Three questionnaires were given to the patients: one relating to diet, one relating to clinical presentation and one relating to quality of life. The disease was confirmed endoscopically and histologically. Faeces were examined for parasites. RESULTS: Forty four patients were enrolled (43-ulcerative colitis; 1-Crohn's Disease). All but one had ulcerative colitis. Most had no family history of disease. The peak age of onset was 21-40 y and 63% gave a history of more than 6 months symptoms prior to diagnosis. Clinical presentation was similar to cases in western countries although milder with less severe life-events. None of them had undergone surgery. All patients ate a rice-based diet and none ate bread made of refined flour. Only 2 patient was infected with a geo-helminth. CONCLUSIONS: Eating bread made of refined flour is not related to development of IBD in these patients. The prevalence of geo-helminths in the study population corresponded to the general population average. Delay in diagnosis occurs because of an initial assumption that the cause of symptoms is infective. A National Register of non-infectious gastrointestinal disease would aid the epidemiology and allocation of funding to this inflammatory condition.},
   keywords = {Adult
Aged
Biopsy
Diet
Female
Humans
Inflammatory Bowel Diseases/diagnosis/epidemiology/*etiology/parasitology
Male
Middle Aged
Prevalence
Quality of Life
Risk Factors
Sri Lanka/epidemiology
Surveys and Questionnaires},
   ISSN = {0250-636X (Print)
0250-636x},
   Accession Number = {21922853},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Werkstetter, K. J. and Ullrich, J. and Schatz, S. B. and Prell, C. and Koletzko, B. and Koletzko, S.},
   title = {Lean body mass, physical activity and quality of life in paediatric patients with inflammatory bowel disease and in healthy controls},
   journal = {J Crohns Colitis},
   volume = {6},
   number = {6},
   pages = {665-73},
   note = {1876-4479
Werkstetter, Katharina J
Ullrich, Jennifer
Schatz, Stephanie B
Prell, Christine
Koletzko, Berthold
Koletzko, Sibylle
Journal Article
Research Support, Non-U.S. Gov't
England
J Crohns Colitis. 2012 Jul;6(6):665-73. doi: 10.1016/j.crohns.2011.11.017. Epub 2012 Jan 9.},
   abstract = {BACKGROUND AND AIMS: Physical activity is important for muscle and bone strength in the growing child and may be impaired in paediatric patients with inflammatory bowel disease (IBD) even during quiescent disease. The SenseWearPro(2) armband allows to measure physical activity under everyday life conditions. METHODS: Thirty-nine IBD patients (27 Crohn's disease, 12 ulcerative colitis, 24 boys) in remission (n=26) or with only mild disease activity (n=13) were compared to 39 healthy age and sex-matched controls. Body weight, height, body mass index (BMI), lean body mass as phase angle alpha (determined by bioelectrical impedance analysis), and dynamometric grip force were expressed as age- and sex-related Z-scores. SenseWearPro(2) armbands were applied for three consecutive days to record number of steps, duration of physical activity and sleeping time. Quality of life was assessed with the German KINDL and IMPACT III questionnaires, energy intake with prospective food protocols. Differences between patients and pair-matched controls were analysed by paired t-test. RESULTS: Patients showed lower Z-scores for phase angle alpha (difference -0.72; 95% CI [-1.10; -0.34]) and lower grip strength (-1.02 [-1.58; -0.47]) than controls. They tended towards lesser number of steps per day (-1339 [-2760; 83]) and shorter duration of physical activity (-0.44 h [-0.94; 0.06]), particularly in females and patients with mild disease. Quality of life and energy intake did not differ between patients and controls. CONCLUSION: In spite of quiescent disease lean body mass and physical activity were reduced. Interventions to encourage physical activity may be beneficial in this lifelong disease.},
   keywords = {Adolescent
*Body Composition
Body Mass Index
Body Size
Case-Control Studies
Child
*Colitis, Ulcerative/pathology/physiopathology/psychology
*Crohn Disease/pathology/physiopathology/psychology
Disease Progression
Energy Intake
Energy Metabolism
*Exercise
Female
Humans
Male
Muscle Strength
*Quality of Life
Surveys and Questionnaires
Young Adult},
   ISSN = {1873-9946},
   Accession Number = {22398103},
   DOI = {10.1016/j.crohns.2011.11.017},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Windey, K. and De Preter, V. and Verbeke, K.},
   title = {Relevance of protein fermentation to gut health},
   journal = {Mol Nutr Food Res},
   volume = {56},
   number = {1},
   pages = {184-96},
   note = {1613-4133
Windey, Karen
De Preter, Vicky
Verbeke, Kristin
Journal Article
Review
Germany
Mol Nutr Food Res. 2012 Jan;56(1):184-96. doi: 10.1002/mnfr.201100542. Epub 2011 Nov 25.},
   abstract = {It is generally accepted that carbohydrate fermentation results in beneficial effects for the host because of the generation of short chain fatty acids, whereas protein fermentation is considered detrimental for the host's health. Protein fermentation mainly occurs in the distal colon, when carbohydrates get depleted and results in the production of potentially toxic metabolites such as ammonia, amines, phenols and sulfides. However, the effectivity of these metabolites has been established mainly in in vitro studies. In addition, some important bowel diseases such as colorectal cancer (CRC) and ulcerative colitis appear most often in the distal colon, which is the primary site of protein fermentation. Finally, epidemiological studies revealed that diets rich in meat are associated with the prevalence of CRC, as is the case in Western society. Importantly, meat intake not only increases fermentation of proteins but also induces increased intake of fat, heme and heterocyclic amines, which may also play a role in the development of CRC. Despite these indications, the relationship between gut health and protein fermentation has not been thoroughly investigated. In this review, the existing evidence about the potential toxicity of protein fermentation from in vitro animal and human studies will be summarized.},
   keywords = {Ammonia/metabolism
Animals
Colon/*metabolism
Colorectal Neoplasms/epidemiology/*metabolism
Cresols/metabolism
*Diet
Fermentation
Gastrointestinal Tract/*metabolism
Humans
Hydrogen Sulfide/metabolism
Meat
Phenols/metabolism
Proteins/*metabolism/pharmacology},
   ISSN = {1613-4125},
   Accession Number = {22121108},
   DOI = {10.1002/mnfr.201100542},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Wiskin, A. E. and Fleming, B. J. and Wootton, S. A. and Beattie, R. M.},
   title = {Anaemia and iron deficiency in children with inflammatory bowel disease},
   journal = {J Crohns Colitis},
   volume = {6},
   number = {6},
   pages = {687-91},
   note = {1876-4479
Wiskin, Anthony E
Fleming, Ben J
Wootton, Stephen A
Beattie, R Mark
Journal Article
Research Support, Non-U.S. Gov't
England
J Crohns Colitis. 2012 Jul;6(6):687-91. doi: 10.1016/j.crohns.2011.12.001. Epub 2012 Jan 17.},
   abstract = {BACKGROUND AND AIMS: Anaemia and iron deficiency are common in children with Inflammatory Bowel Disease (IBD) however it is not known if the prevalence of anaemia and iron deficiency alters following diagnosis. METHODS: Laboratory results from diagnosis, and at follow up one and two years later were recorded retrospectively in children with IBD recruited from a tertiary centre. Anaemia was defined using WHO standards and iron deficiency defined using published guidelines. RESULTS: 46 children (16 girls) with Crohn's disease and 34 children (18 girls) with UC were studied. 75% of children with IBD were anaemic at diagnosis, 30% were anaemic at follow up two years later. 90% of children with Crohn's and 95% of children with Ulcerative Colitis (UC) were iron deficient at diagnosis. At follow up two years later 70% of children with Crohn's and 65% of children with UC were iron deficient. CONCLUSIONS: Persistent anaemia and iron deficiency are common in childhood IBD, prevalence alters with duration of time from diagnosis.},
   keywords = {Adolescent
Anemia/blood/diagnosis/epidemiology/*etiology
Biomarkers/blood
Child
Child, Preschool
Cohort Studies
Colitis, Ulcerative/blood/*complications
Crohn Disease/blood/*complications
Female
Ferritins/blood
Follow-Up Studies
Humans
Iron/*deficiency
Male
Prevalence
Retrospective Studies
Transferrin/metabolism},
   ISSN = {1873-9946},
   Accession Number = {22398100},
   DOI = {10.1016/j.crohns.2011.12.001},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Wiskin, A. E. and Owens, D. R. and Cornelius, V. R. and Wootton, S. A. and Beattie, R. M.},
   title = {Paediatric nutrition risk scores in clinical practice: children with inflammatory bowel disease},
   journal = {J Hum Nutr Diet},
   volume = {25},
   number = {4},
   pages = {319-22},
   note = {1365-277x
Wiskin, A E
Owens, D R
Cornelius, V R
Wootton, S A
Beattie, R M
Journal Article
Research Support, Non-U.S. Gov't
England
J Hum Nutr Diet. 2012 Aug;25(4):319-22. doi: 10.1111/j.1365-277X.2012.01254.x. Epub 2012 May 16.},
   abstract = {BACKGROUND: There has been increasing interest in the use of nutrition risk assessment tools in paediatrics to identify those who need nutrition support. Four non-disease specific screening tools have been developed, although there is a paucity of data on their application in clinical practice and the degree of inter-tool agreement. METHODS: The concurrent validity of four nutrition screening tools [Screening Tool for the Assessment of Malnutrition in Paediatrics (STAMP), Screening Tool for Risk On Nutritional status and Growth (STRONGkids), Paediatric Yorkhill Malnutrition Score (PYMS) and Simple Paediatric Nutrition Risk Score (PNRS)] was examined in 46 children with inflammatory bowel disease. Degree of malnutrition was determined by anthropometry alone using World Health Organization International Classification of Diseases (ICD-10) criteria. RESULTS: There was good agreement between STAMP, STRONGkids and PNRS (kappa > 0.6) but there was only modest agreement between PYMS and the other scores (kappa = 0.3). No children scored low risk with STAMP, STRONGkids or PNRS; however, 23 children scored low risk with PYMS. There was no agreement between the risk tools and the degree of malnutrition based on anthropometric data (kappa < 0.1). Three children had anthropometry consistent with malnutrition and these were all scored high risk. Four children had body mass index SD scores < -2, one of which was scored at low nutrition risk. CONCLUSIONS: The relevance of nutrition screening tools for children with chronic disease is unclear. In addition, there is the potential to under recognise nutritional impairment (and therefore nutritional risk) in children with inflammatory bowel disease.},
   keywords = {Adolescent
Anthropometry
Body Mass Index
Child
Child, Preschool
Colitis, Ulcerative/complications
Crohn Disease/complications
Female
Humans
Inflammatory Bowel Diseases/*complications
Male
Malnutrition/*diagnosis/etiology
Mass Screening/methods
Nutrition Assessment
Pediatrics/*methods
Prospective Studies
Risk Factors},
   ISSN = {0952-3871},
   Accession Number = {22591201},
   DOI = {10.1111/j.1365-277X.2012.01254.x},
   year = {2012},
   type = {Ref–rence Type}
}

@article{
   author = {Wiskin, A. E. and Wootton, S. A. and Hunt, T. M. and Cornelius, V. R. and Afzal, N. A. and Jackson, A. A. and Beattie, R. M.},
   title = {Body composition in childhood inflammatory bowel disease},
   journal = {Clin Nutr},
   volume = {30},
   number = {1},
   pages = {112-5},
   note = {1532-1983
Wiskin, Anthony E
Wootton, Stephen A
Hunt, Toby M
Cornelius, Victoria R
Afzal, Nadeem A
Jackson, Alan A
Beattie, R Mark
Journal Article
Research Support, Non-U.S. Gov't
England
Clin Nutr. 2011 Feb;30(1):112-5. doi: 10.1016/j.clnu.2010.07.014. Epub 2010 Aug 21.},
   abstract = {BACKGROUND & AIMS: Little is known about the impact of disease and treatment on the pattern of growth in children with Inflammatory Bowel Disease (IBD). Significant deficits in height and weight in children with Crohn's disease have been reported but changes in fat and fat free mass are less well defined. This study aims to describe the height, weight and body composition of a cohort of children with IBD. METHODS: Height, weight, skinfold thicknesses and bioelectrical impedance analysis was performed. Disease activity was assessed with clinical scoring systems. RESULTS: 55 children, median age 13.7 years (range 6.5-17.7) were studied. Median (25th, 75th percentile) Standard Deviation Score for BMI, Height and Weight were - 0.3 (- 0.97, 0.65), - 0.56 (- 1.42, 0.06), - 0.62 (- 1.43, 0.19). In Crohn's disease, using multiple regression analysis disease activity measured by PCDAI was significantly inversely related to fat free mass (beta - 0.2, 95% CI -0.17, -0.03, p 0.005). CONCLUSIONS: Children with IBD were both under and overweight. Nutritional deficits were more common in Crohn's disease. Fat free mass was related to disease activity in children with Crohn's disease regardless of changes in weight. Weight or BMI may mask deficits in lean tissue in the presence of normal or increased proportions of body fat.},
   keywords = {Adolescent
*Body Composition
Body Height
Body Mass Index
Body Weight
Child
Colitis, Ulcerative/*complications
Crohn Disease/*complications
Female
Humans
Linear Models
Male
Nutrition Disorders/*complications},
   ISSN = {0261-5614},
   Accession Number = {20728967},
   DOI = {10.1016/j.clnu.2010.07.014},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Yamamoto, T.},
   title = {Elemental diet therapy for pouchitis following restorative proctocolectomy for ulcerative colitis},
   journal = {J Crohns Colitis},
   volume = {7},
   number = {4},
   pages = {e155},
   note = {1876-4479
Yamamoto, Takayuki
Comment
Letter
England
J Crohns Colitis. 2013 May;7(4):e155. doi: 10.1016/j.crohns.2012.09.004. Epub 2012 Sep 13.},
   keywords = {Feces/*microbiology
Female
*Food, Formulated
Humans
Male
Pouchitis/*diet therapy},
   ISSN = {1873-9946},
   Accession Number = {22981615},
   DOI = {10.1016/j.crohns.2012.09.004},
   year = {2013},
   type = {Ref–rence Type}
}

@article{
   author = {Yang, H. and Ge, Z. and Dai, J. and Li, X. and Gao, Y.},
   title = {Effectiveness of the immunofecal occult blood test for colorectal cancer screening in a large population},
   journal = {Dig Dis Sci},
   volume = {56},
   number = {1},
   pages = {203-7},
   note = {1573-2568
Yang, Haiyun
Ge, Zhizheng
Dai, Jun
Li, Xiaobo
Gao, Yunjie
Evaluation Studies
Journal Article
Research Support, Non-U.S. Gov't
United States
Dig Dis Sci. 2011 Jan;56(1):203-7. doi: 10.1007/s10620-010-1264-8. Epub 2010 May 11.},
   abstract = {BACKGROUND: Guaiac tests are the most widely used tests to detect colorectal cancer (CRC). However, their sensitivity is relatively low and results may be affected by various factors. Immunofecal occult blood test (IFOBT) is specific for human hemoglobin and does not require dietary restrictions. AIMS: The aim of this study was to evaluate the effectiveness of IFOBT for the screening of precancerous lesions and CRC. METHODS: From July 2006 to June 2007, IFOBT was performed on 5,919 adults who received periodic health examinations in our hospital. The positive cases were examined by colonoscopy and a double-contrast barium enema. Diagnosis was confirmed by histopathological analysis. RESULTS: Positive IFOBT was detected in 314 of 5,919 cases (5.30%). Further examinations were made in 264 IFOBT-positive cases. Of these, 116 cases with colorectal cancer (16 cases) or precancerous lesions (94 cases with colorectal adenomatous polyps and 6 cases with active ulcerative colitis) were detected. The total detection rate of CRC and precancerous lesions was 43.94% (116/264). TNM classification of 16 CRC cases was as follows: TNM I in eight cases (50.00%), TNM II in seven cases (43.75%) and TNM III in one case (6.25%), indicating IFOBT can detect CRC in the early stages. CONCLUSION: Regular IFOBT can detect precancerous lesions and CRC in early stages and can thus reduce mortality from CRC.},
   keywords = {Adenomatous Polyps/diagnosis/epidemiology
Adult
Aged
China/epidemiology
Colorectal Neoplasms/*diagnosis/epidemiology
Early Detection of Cancer/*methods
*Feces
Female
Humans
Male
Mass Screening/*methods
Middle Aged
*Occult Blood
Precancerous Conditions/diagnosis/epidemiology
Retrospective Studies
Sensitivity and Specificity},
   ISSN = {0163-2116},
   Accession Number = {20458621},
   DOI = {10.1007/s10620-010-1264-8},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Zhu, H. and Dougherty, U. and Robinson, V. and Mustafi, R. and Pekow, J. and Kupfer, S. and Li, Y. C. and Hart, J. and Goss, K. and Fichera, A. and Joseph, L. and Bissonnette, M.},
   title = {EGFR signals downregulate tumor suppressors miR-143 and miR-145 in Western diet-promoted murine colon cancer: role of G1 regulators},
   journal = {Mol Cancer Res},
   volume = {9},
   number = {7},
   pages = {960-75},
   note = {1557-3125
Zhu, Hongyan
Dougherty, Urszula
Robinson, Victoria
Mustafi, Reba
Pekow, Joel
Kupfer, Sonia
Li, Yan-Chun
Hart, John
Goss, Kathleen
Fichera, Alessandro
Joseph, Loren
Bissonnette, Marc
P30DK42086/DK/NIDDK NIH HHS/United States
P30 DK042086/DK/NIDDK NIH HHS/United States
R01 CA164124/CA/NCI NIH HHS/United States
R01 CA036745/CA/NCI NIH HHS/United States
CA036745/CA/NCI NIH HHS/United States
K08 CA142892/CA/NCI NIH HHS/United States
R37 CA036745/CA/NCI NIH HHS/United States
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
United States
Mol Cancer Res. 2011 Jul;9(7):960-75. doi: 10.1158/1541-7786.MCR-10-0531. Epub 2011 Jun 8.},
   abstract = {Epidermal growth factor receptors (EGFR) contribute to colonic tumorigenesis in experimental models of colon cancer. We previously showed that EGFR was also required for colonic tumor promotion by Western diet. The goal of this study was to identify EGFR-regulated microRNAs that contribute to diet-promoted colonic tumorigenesis. Murine colonic tumors from Egfr(wt) and hypomorphic Egfr(wa2) mice were screened using micro RNA (miRNA) arrays and miR-143 and miR-145 changes confirmed by Northern, real-time PCR, and in situ analysis. Rodent and human sporadic and ulcerative colitis (UC)-associated colon cancers were examined for miR-143 and miR-145. Effects of EGFR on miR-143 and miR-145 expression were assessed in murine and human colonic cells and their putative targets examined in vitro and in vivo. miR-143 and miR-145 were readily detected in normal colonocytes and comparable in Egfr(wt) and Egfr(wa2) mice. These miRNAs were downregulated in azoxymethane and inflammation-associated colonic tumors from Egfr(wt) mice but upregulated in Egfr(wa2) tumors. They were also reduced in human sporadic and UC colon cancers. EGFR signals suppressed miR-143 and miR-145 in human and murine colonic cells. Transfected miR-143 and miR-145 inhibited HCT116 cell growth in vitro and in vivo and downregulated G(1) regulators, K-Ras, MYC, CCND2, cdk6, and E2F3, putative or established targets of these miRNAs. miRNA targets Ras and MYC were increased in colonic tumors from Egfr(wt) but not Egfr(wa2) mice fed a Western diet. EGFR suppresses miR-143 and miR-145 in murine models of colon cancer. Furthermore, Western diet unmasks the tumor suppressor roles of these EGFR-regulated miRNAs.},
   keywords = {Animals
Antibodies, Monoclonal/pharmacology
Antibodies, Monoclonal, Humanized
Azoxymethane/pharmacology
Cetuximab
Colitis, Ulcerative/complications/metabolism
Colonic Neoplasms/etiology/genetics/*metabolism
Dextran Sulfate/pharmacology
Diet/*adverse effects
Down-Regulation
G1 Phase/genetics
Gene Expression Regulation, Neoplastic
*Genes, Tumor Suppressor
HCT116 Cells
Humans
Mice
MicroRNAs/*genetics
Neoplasms, Experimental/etiology/genetics/metabolism
Rats
Receptor, Epidermal Growth Factor/antagonists & inhibitors/genetics/*metabolism
Signal Transduction},
   ISSN = {1541-7786},
   Accession Number = {21653642},
   DOI = {10.1158/1541-7786.mcr-10-0531},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Zhu, Y. and Michelle Luo, T. and Jobin, C. and Young, H. A.},
   title = {Gut microbiota and probiotics in colon tumorigenesis},
   journal = {Cancer Lett},
   volume = {309},
   number = {2},
   pages = {119-27},
   note = {1872-7980
Zhu, Yuanmin
Michelle Luo, T
Jobin, Christian
Young, Howard A
HHSN261200800001C/RC/CCR NIH HHS/United States
HHSN261200800001E/CA/NCI NIH HHS/United States
ZIA BC010867-03/Intramural NIH HHS/United States
Journal Article
Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Review
Ireland
Cancer Lett. 2011 Oct 28;309(2):119-27. doi: 10.1016/j.canlet.2011.06.004. Epub 2011 Jun 24.},
   abstract = {The human gastrointestinal tract harbors a complex and abundant microbial community reaching as high as 10(13)-10(14) microorganisms in the colon. This endogenous microbiota forms a symbiotic relationship with their eukaryotic host and this close partnership helps maintain homeostasis by performing essential and non-redundant tasks (e.g. nutrition/energy and, immune system balance, pathogen exclusion). Although this relationship is essential and beneficial to the host, various events (e.g. infection, diet, stress, inflammation) may impact microbial composition, leading to the formation of a dysbiotic microbiota, further impacting on health and disease states. For example, Crohn's disease and ulcerative colitis, collectively termed inflammatory bowel diseases (IBD), have been associated with the establishment of a dysbiotic microbiota. In addition, extra-intestinal disorders such as obesity and metabolic syndrome are also associated with the development of a dysbiotic microbiota. Consequently, there is an increasing interest in harnessing the power of the microbiome and modulating its composition as a means to alleviate intestinal pathologies/disorders and maintain health status. In this review, we will discuss the emerging relationship between the microbiota and development of colorectal cancer as well as present evidence that microbial manipulation (probiotic, prebiotic) impacts disease development.},
   keywords = {Animals
Cell Transformation, Neoplastic
Colon/*microbiology/*pathology
Colorectal Neoplasms/*microbiology/pathology
Humans
Inflammatory Bowel Diseases/microbiology
Metabolic Syndrome X/microbiology
*Metagenome
Obesity/microbiology
*Probiotics
Symbiosis},
   ISSN = {0304-3835},
   Accession Number = {21741763},
   DOI = {10.1016/j.canlet.2011.06.004},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Zimmerman, M. A. and Singh, N. and Martin, P. M. and Thangaraju, M. and Ganapathy, V. and Waller, J. L. and Shi, H. and Robertson, K. D. and Munn, D. H. and Liu, K.},
   title = {Butyrate suppresses colonic inflammation through HDAC1-dependent Fas upregulation and Fas-mediated apoptosis of T cells},
   journal = {Am J Physiol Gastrointest Liver Physiol},
   volume = {302},
   number = {12},
   pages = {G1405-15},
   note = {1522-1547
Zimmerman, Mary A
Singh, Nagendra
Martin, Pamela M
Thangaraju, Muthusamy
Ganapathy, Vadivel
Waller, Jennifer L
Shi, Huidong
Robertson, Keith D
Munn, David H
Liu, Kebin
CA133085/CA/NCI NIH HHS/United States
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
United States
Am J Physiol Gastrointest Liver Physiol. 2012 Jun 15;302(12):G1405-15. doi: 10.1152/ajpgi.00543.2011. Epub 2012 Apr 19.},
   abstract = {Butyrate, an intestinal microbiota metabolite of dietary fiber, has been shown to exhibit protective effects toward inflammatory diseases such as ulcerative colitis (UC) and inflammation-mediated colorectal cancer. Recent studies have shown that chronic IFN-gamma signaling plays an essential role in inflammation-mediated colorectal cancer development in vivo, whereas genome-wide association studies have linked human UC risk loci to IFNG, the gene that encodes IFN-gamma. However, the molecular mechanisms underlying the butyrate-IFN-gamma-colonic inflammation axis are not well defined. Here we showed that colonic mucosa from patients with UC exhibit increased signal transducer and activator of transcription 1 (STAT1) activation, and this STAT1 hyperactivation is correlated with increased T cell infiltration. Butyrate treatment-induced apoptosis of wild-type T cells but not Fas-deficient (Fas(lpr)) or FasL-deficient (Fas(gld)) T cells, revealing a potential role of Fas-mediated apoptosis of T cells as a mechanism of butyrate function. Histone deacetylase 1 (HDAC1) was found to bind to the Fas promoter in T cells, and butyrate inhibits HDAC1 activity to induce Fas promoter hyperacetylation and Fas upregulation in T cells. Knocking down gpr109a or slc5a8, the genes that encode for receptor and transporter of butyrate, respectively, resulted in altered expression of genes related to multiple inflammatory signaling pathways, including inducible nitric oxide synthase (iNOS), in mouse colonic epithelial cells in vivo. Butyrate effectively inhibited IFN-gamma-induced STAT1 activation, resulting in inhibition of iNOS upregulation in human colon epithelial and carcinoma cells in vitro. Our data thus suggest that butyrate delivers a double-hit: induction of T cell apoptosis to eliminate the source of inflammation and suppression of IFN-gamma-mediated inflammation in colonic epithelial cells, to suppress colonic inflammation.},
   keywords = {Acetylation
Animals
Antigens, CD95/*metabolism
Apoptosis/*drug effects
Butyrates/*pharmacology
Cell Line
Cell Proliferation/drug effects
Cells, Cultured
Colon/*drug effects/metabolism/pathology
Histone Deacetylase 1/*metabolism
Humans
Inflammation/metabolism/pathology
Interferon-gamma/metabolism
Intestinal Mucosa/drug effects/metabolism/pathology
Mice
Promoter Regions, Genetic
Signal Transduction/drug effects
T-Lymphocytes/*drug effects/metabolism/pathology
Up-Regulation/*drug effects},
   ISSN = {0193-1857},
   Accession Number = {22517765},
   DOI = {10.1152/ajpgi.00543.2011},
   year = {2012},
   type = {Ref–rence Type}
}

repository: KociOrges/pytag

repo_name: KociOrges/pytag


text:
require gst-plugins.inc

SRC_URI += " \
	    file://0001-gstfbdevsink-Fix-depth-value-for-GST_VIDEO_CAPS_RGB_.patch \
"

SRC_URI[archive.md5sum] = "7c84766f6d24f41ba90c3f6141012ab8"
SRC_URI[archive.sha256sum] = "1031dff866df976a957f34039addbab4c0753406299a275f4cf1780e1dbe2a90"

DEPENDS += "orc-native orc libcdaudio gst-plugins-base openssl directfb libmodplug librsvg"

PR = "${INC_PR}.2"

# We don't have vdpau headers in OE and it creates crosscompile badness
EXTRA_OECONF_append = " --disable-vdpau --enable-sdl"

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bb


text:
@article{gao2019extracting,
 abstract = {Spatial patterns of tourist mobility are important for tourism management and planning. A large number of traveler-generated content accumulated on the internet provide a unique opportunity for revealing comprehensive spatial patterns of tourist movements. Instead of concentrating on a single city or attraction in previous research, this work investigates the intercity travel flows extracted from the online travel blogs in China from 2012 to 2016. The descriptive statistics of travel flows are first analyzed. The distribution of travel volume is found to satisfy the power-law distribution. Based on the intercity travel flows, a network structure is then constructed to investigate tourism interactions between cities. After four communities and 14 sub-communities being detected from the network, a tourism spatial layout with regional agglomeration effects are recognized. This research concludes that distance is essential in determining tourist movements based on a spatial interaction model. Intercity travel flows decline with distance under a power-law function. These results reveal the spatial patterns of tourist movements at an intercity scale. It will be helpful for arranging tourism resources, predicting tourist flows, and maintaining sustainable tourism.},
 annotation = {00000},
 author = {Gao, Yong and Ye, Chao and Zhong, Xiang and Wu, Lun and Liu, Yu},
 copyright = {http://creativecommons.org/licenses/by/3.0/},
 doi = {10.3390/su11133526},
 file = {/Users/baoyi/Zotero/storage/TM6MM9BB/Gao 等。 - 2019 - Extracting Spatial Patterns of Intercity Tourist M.pdf},
 journal = {Sustainability},
 keywords = {complex network,spatial interaction,spatial pattern,tourist movement},
 language = {en},
 month = {January},
 number = {13},
 pages = {3526},
 publisher = {Multidisciplinary Digital Publishing Institute},
 title = {Extracting Spatial Patterns of Intercity Tourist Movements from Online Travel Blogs},
 volume = {11},
 year = {2019}
}

branch_name: refs/heads/main

extension: bib


repository: embmike/RobotND-Home-Service-Robot

repo_name: embmike/RobotND-Home-Service-Robot

extension: cmake


text:
DESCRIPTION = "TI gdb-server to be used with c6xgdb."
LICENSE = "BSD-3-Clause"
LIC_FILES_CHKSUM = "file://../debian/copyright;md5=82c616b6c8f9c11c46feaaf8f9a11495"

DEPENDS = "ti-xdais ti-framework-components ti-cgt6x-native ti-sysbios ti-xdctools-native"

PR = "${INC_PR}.0"

S = "${WORKDIR}/git/gdbserver-c6x/src"

PLATFORM = ""
PLATFORM:dra7xx = "DRA7xx_PLATFORM"

EXTRA_OEMAKE = "PLATFORM=${PLATFORM}"

export XDAIS_DIR = "${XDAIS_INSTALL_DIR}"
export FC_DIR = "${FC_INSTALL_DIR}"
export TI_CGT_INSTALL = "${STAGING_DIR_NATIVE}/usr/share/ti/cgt-c6x"
export BIOS_DIR = "${SYSBIOS_INSTALL_DIR}"
export XDC_DIR = "${XDC_INSTALL_DIR}"

# The following is to prevent an unused configure.ac from erroneously
# triggering the QA check for gettext.
EXTRA_OECONF = "--disable-nls"
do_configure() {
    :
}

do_install() {
    install -d ${D}${datadir}/ti/gdbc6x/include
    install -d ${D}${datadir}/ti/gdbc6x/lib
    cp -f ../include/* ${D}${datadir}/ti/gdbc6x/include
    cp -f ../lib/* ${D}${datadir}/ti/gdbc6x/lib
}

COMPATIBLE_MACHINE = "dra7xx"
PACKAGE_ARCH = "${MACHINE_ARCH}"

FILES:${PN}-dev += "\
    ${datadir}/ti/gdbc6x \
"

include gdbc6x.inc

require recipes-ti/includes/ti-paths.inc

ALLOW_EMPTY:${PN} = "1"

PARALLEL_MAKE = ""

repository: YoeDistro/meta-ti

repo_name: YoeDistro/meta-ti

gha_license_id: MIT

gha_language: BitBake


text:
DESCRIPTION = "Meta package for Mamona"
LICENSE = "MIT"
PR = "r2"

inherit meta
EXCLUDE_FROM_WORLD = "1"

RDEPENDS_${PN} = " \
task-mamona \
"

include mamona-buildall.inc

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty

branch_name: HEAD


text:
@inproceedings{oliveira2015modular,
  title={Modular reifiable matching: a list-of-functors approach to two-level types},
  author={Oliveira, Bruno C d S and Mu, Shin-Cheng and You, Shu-Hung},
  booktitle={Proceedings of the 8th ACM SIGPLAN Symposium on Haskell},
  pages={82--93},
  year={2015},
  organization={ACM}
}

@book{pierce2002types,
  title={Types and programming languages},
  author={Pierce, Benjamin C},
  year={2002},
  publisher={MIT press}
}

@article{ragan2013halide,
  title={Halide: a language and compiler for optimizing parallelism, locality, and recomputation in image processing pipelines},
  author={Ragan-Kelley, Jonathan and Barnes, Connelly and Adams, Andrew and Paris, Sylvain and Durand, Fr{\'e}do and Amarasinghe, Saman},
  journal={ACM SIGPLAN Notices},
  volume={48},
  number={6},
  pages={519--530},
  year={2013},
  publisher={ACM}
}

@article{ragan2012decoupling,
  title={Decoupling algorithms from schedules for easy optimization of image processing pipelines.},
  author={Ragan-Kelley, Jonathan and Adams, Andrew and Paris, Sylvain and Levoy, Marc and Amarasinghe, Saman P and Durand, Fr{\'e}do},
  journal={ACM Trans. Graph.},
  volume={31},
  number={4},
  pages={32},
  year={2012},
  publisher={Citeseer}
}

@article{moczo2007finite,
  title={The finite-difference time-domain method for modeling of seismic wave propagation},
  author={Moczo, Peter and Robertsson, Johan OA and Eisner, Leo},
  journal={Advances in Geophysics},
  volume={48},
  pages={421--516},
  year={2007},
  publisher={Elsevier}
}

@article{johnson2008notes,
  title={Notes on perfectly matched layers (PMLs)},
  author={Johnson, Steven G},
  journal={Lecture notes, Massachusetts Institute of Technology, Massachusetts},
  year={2008}
}

@article{Muranushi2012Paraiso,
  title={Paraiso: an automated tuning framework for explicit solvers of partial differential equations},
  author={Muranushi, Takayuki},
  journal={Computational Science \& Discovery},
  volume={5},
  number={1},
  pages={015003},
  year={2012},
  publisher={IOP Publishing}
}

@techreport{kim2011closing,
  title={Closing the Ninja Performance Gap through Traditional Programming and Compiler Technology},
  author={Kim, Changkyu and Satish, Nadathur and Chhugani, Jatin and Saito, Hideki and Krishnaiyer, Rakesh and Smelyanskiy, Mikhail and Girkar, Milind and Dubey, Pradeep},
  year={2011},
  institution={Technical report, Intel Labs}
}

@inproceedings{satish2012can,
  title={Can traditional programming bridge the ninja performance gap for parallel computing applications?},
  author={Satish, Nadathur and Kim, Changkyu and Chhugani, Jatin and Saito, Hideki and Krishnaiyer, Rakesh and Smelyanskiy, Mikhail and Girkar, Milind and Dubey, Pradeep},
  booktitle={ACM SIGARCH Computer Architecture News},
  volume={40},
  number={3},
  pages={440--451},
  year={2012},
  organization={IEEE Computer Society}
}

@inproceedings{maruyama2011physis,
  title={Physis: an implicitly parallel programming model for stencil computations on large-scale GPU-accelerated supercomputers},
  author={Maruyama, Naoya and Nomura, Tatsuo and Sato, Kento and Matsuoka, Satoshi},
  booktitle={High Performance Computing, Networking, Storage and Analysis (SC), 2011 International Conference for},
  pages={1--12},
  year={2011},
  organization={IEEE}
}

@inproceedings{Schafer:2008:LGL:1431669.1431721,
  author = {Sch\"{a}fer, Andreas and Fey, Dietmar},
  title = {LibGeoDecomp: A Grid-Enabled Library for Geometric Decomposition Codes},
  booktitle = {Proceedings of the 15th European PVM/MPI Users' Group Meeting on
    Recent Advances in Parallel Virtual Machine and Message Passing Interface},
  year = {2008},
  isbn = {978-3-540-87474-4},
  location = {Dublin, Ireland},
  pages = {285--294},
  numpages = {10},
  url = {http://dx.doi.org/10.1007/978-3-540-87475-1_39},
  doi = {http://dx.doi.org/10.1007/978-3-540-87475-1_39},
  acmid = {1431721},
  publisher = {Springer-Verlag},
  address = {Berlin, Heidelberg},
  keywords = {Grid computing, hierarchical parallelization, self-adaptation},
}

@book{lipovaca2012Sugoi,
  title={すごい Haskell たのしく学ぼう!},
  author={Lipovača, Miran and Tanaka, Hideyuki and Muranushi, Takayuki},
  year={2012},
  publisher={株式会社 オーム社}
}

@incollection{claessen1999observable,
  title={Observable sharing for functional circuit description},
  author={Claessen, Koen and Sands, David},
  booktitle={Advances in Computing Science—ASIAN’99},
  pages={62--73},
  year={1999},
  publisher={Springer}
}

@article{conway1970game,
  title={The game of life},
  author={Conway, John},
  journal={Scientific American},
  volume={223},
  number={4},
  pages={4},
  year={1970},
  publisher={ACM Press}
}

@inproceedings{bedorf201424,
  title={24.77 Pflops on a gravitational tree-code to simulate the Milky Way Galaxy with 18600 GPUs},
  author={B{\'e}dorf, Jeroen and Gaburov, Evghenii and Fujii, Michiko S and Nitadori, Keigo and Ishiyama, Tomoaki and Zwart, Simon Portegies},
  booktitle={Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
  pages={54--65},
  year={2014},
  organization={IEEE Press}
}

@inproceedings{ishiyama20124,
  title={4.45 Pflops astrophysical N-body simulation on K computer--The gravitational trillion-body problem},
  author={Ishiyama, Tomoaki and Nitadori, Keigo and Makino, Junichiro},
  booktitle={High Performance Computing, Networking, Storage and Analysis (SC), 2012 International Conference for},
  pages={1--10},
  year={2012},
  organization={IEEE}
}

@inproceedings{tang2011pochoir,
  title={The pochoir stencil compiler},
  author={Tang, Yuan and Chowdhury, Rezaul Alam and Kuszmaul, Bradley C and Luk, Chi-Keung and Leiserson, Charles E},
  booktitle={Proceedings of the twenty-third annual ACM symposium on Parallelism in algorithms and architectures},
  pages={117--128},
  year={2011},
  organization={ACM}
}

@InProceedings{ansel:pact:2014,
  author    = "Jason Ansel and Shoaib Kamil and Kalyan Veeramachaneni and Jonathan Ragan-Kelley and Jeffrey Bosboom and Una-May O'Reilly and Saman Amarasinghe",
  title     = "OpenTuner: An Extensible Framework for Program Autotuning",
  url       = "http://groups.csail.mit.edu/commit/papers/2014/ansel-pact14-opentuner.pdf",
  slides    = "http://groups.csail.mit.edu/commit/papers/2014/ansel-pact14-opentuner-slides.pdf",
  keywords  = "OpenTuner",
  month     = "August",
  year      = "2014",
  address   = "Edmonton, Canada",
  booktitle = "International Conference on Parallel Architectures and Compilation Techniques",
}

@article{johnson2008notes,
  title={Notes on perfectly matched layers (PMLs)},
  author={Johnson, Steven G},
  journal={Lecture notes, Massachusetts Institute of Technology, Massachusetts},
  year={2008}
}

@inproceedings{rafkind2012honu,
  title={Honu: syntactic extension for algebraic notation through enforestation},
  author={Rafkind, Jon and Flatt, Matthew},
  booktitle={ACM SIGPLAN Notices},
  volume={48},
  number={3},
  pages={122--131},
  year={2012},
  organization={ACM}
}

@article{nishizawa2015scale,
  title={The detail formulation of {SCALE-LES}},
  author={Nishizawa, Seiya and Tomita, Hirofumi and {Team SCALE}},
  year={2015}
}

@article{latticesubwg2015formura,
  title={The Formura Specification},
  author={{Lattice Sub Working Group}},
  year={2015}
}

@phdthesis{rafkind2013syntactic,
  title={Syntactic extension for languages with implicitly delimited and infix syntax},
  author={Rafkind, Jon},
  year={2013},
  school={THE UNIVERSITY OF UTAH}
}

@article{pearson1993complex,
  title={Complex patterns in a simple system},
  author={Pearson, John E},
  journal={Science},
  volume={261},
  number={5118},
  pages={189--192},
  year={1993},
  publisher={American Association for the Advancement of Science}
}

repository: formura/formura

repo_name: formura/formura

gha_license_id: NOASSERTION

gha_language: C


text:
LICENSE="GPLv2"
LIC_FILES_CHKSUM="file://COPYING;md5=e197d5641bb35b29d46ca8c4bf7f2660"

inherit native

BPN="VirtualBox"

DEPENDS=" \
    libxml2-native glib-2.0-native libidl-native acpica-native cdrtools-native \
    libpng-native zlib-native openssl-native curl-native libcap-native \
    makeself-native libpam-native libxslt-native \
"

SRC_URI=" \
    http://download.virtualbox.org/virtualbox/${PV}/VirtualBox-${PV}.tar.bz2 \
    file://configure.patch \
    file://xpidl-build-fixes.patch \
    file://include-dir.patch \
    file://remove-x11.patch \
    file://fix-linker-flags.patch \
    file://disable-guest-additions.patch \
"

SRC_URI[md5sum] = "2701f423f2828cab4405098982f4f446"
SRC_URI[sha256sum] = "9134b04ca21ca23534e2300aab5ab7ff60d21b56bfd2e21504316bfee73afa87"

# export path to native libdir, as this is needed during build
# (see xpidl build fix patch)
export VIRTUALBOX_YOCTO_LIBDIR="${STAGING_LIBDIR_NATIVE}"

# The build files seem to override LDFLAGS, so re-export it with different name and patch files to use it
export VIRTUALBOX_YOCTO_LDFLAGS="${LDFLAGS}"

# Disable everything we do not need (which turns out to be almost everything)
VBOX_CONF = " \
    --disable-hardening \
    --disable-python \
    --disable-java \
    --disable-vmmraw \
    --disable-sdl-ttf \
    --disable-alsa \
    --disable-pulse \
    --disable-dbus \
    --disable-kmods \
    --disable-opengl \
    --disable-extpack \
    --disable-docs \
    --disable-libvpx \
    --disable-udptunnel \
    --disable-devmapper \
    --disable-vmmraw \
    --build-headless \
    --with-makeself='${STAGING_BINDIR_NATIVE}/makeself.sh' \
    "

# As we do not use either autotools or cmake, we have to call configure manually
do_configure() {
    ./configure ${VBOX_CONF}
}

do_compile() {
    . ./env.sh
    kmk
}

do_install() {
    # minimal set of files for VBoxManage
    ARCH_DIR=`ls ${B}/out`

    install -d ${D}${libdir}/vboxmanage
    install -m 0755 ${B}/out/${ARCH_DIR}/release/bin/VBoxManage ${D}${libdir}/vboxmanage
    install -m 0644 ${B}/out/${ARCH_DIR}/release/bin/VBoxDDU.so ${D}${libdir}/vboxmanage
    install -m 0644 ${B}/out/${ARCH_DIR}/release/bin/VBoxRT.so ${D}${libdir}/vboxmanage
    install -m 0644 ${B}/out/${ARCH_DIR}/release/bin/VBoxXPCOM.so ${D}${libdir}/vboxmanage
    install -m 0755 ${B}/out/${ARCH_DIR}/release/bin/VBoxSVC ${D}${libdir}/vboxmanage
    install -m 0755 ${B}/out/${ARCH_DIR}/release/bin/VBoxXPCOMIPCD ${D}${libdir}/vboxmanage

    install -d ${D}${libdir}/vboxmanage/components
    install -m 0644 ${B}/out/${ARCH_DIR}/release/bin/components/VBoxC.so ${D}${libdir}/vboxmanage/components
    install -m 0644 ${B}/out/${ARCH_DIR}/release/bin/components/VBoxSVCM.so ${D}${libdir}/vboxmanage/components
    install -m 0644 ${B}/out/${ARCH_DIR}/release/bin/components/VBoxXPCOMBase.xpt ${D}${libdir}/vboxmanage/components
    install -m 0644 ${B}/out/${ARCH_DIR}/release/bin/components/VBoxXPCOMIPCC.so ${D}${libdir}/vboxmanage/components
    install -m 0644 ${B}/out/${ARCH_DIR}/release/bin/components/VirtualBox_XPCOM.xpt ${D}${libdir}/vboxmanage/components

    install -d ${D}${bindir}
    ln -sf ../lib/vboxmanage/VBoxManage ${D}${bindir}/VBoxManage
}

repository: ostroproject/meta-ostro

repo_name: ostroproject/meta-ostro

gha_language: Python