text:
},
   Accession Number = {19476300},
   year = {2009},
   type = {Ref–rence Type}
}

@article{
   author = {Sundstrom, B. and Wallberg-Jonsson, S. and Johansson, G.},
   title = {Diet, disease activity, and gastrointestinal symptoms in patients with ankylosing spondylitis},
   journal = {Clin Rheumatol},
   volume = {30},
   number = {1},
   pages = {71-6},
   note = {1434-9949
Sundstrom, Bjorn
Wallberg-Jonsson, Solveig
Johansson, Gunnar
Journal Article
Research Support, Non-U.S. Gov't
Germany
Clin Rheumatol. 2011 Jan;30(1):71-6. doi: 10.1007/s10067-010-1625-x. Epub 2010 Nov 27.},
   abstract = {The aims of this study were to investigate, firstly, the relationship between diet and disease activity and, secondly, the presence of gastrointestinal symptoms and their relationship to diet among patients with ankylosing spondylitis (AS) using a cross-sectional design. One hundred sixty-five individuals diagnosed with AS were invited to complete a self-administered postal questionnaire regarding demographic data, diet, medication, and gastrointestinal symptoms in addition to two established disease assessment questionnaires, i.e., the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) and Bath Ankylosing Spondylitis Functional Index (BASFI). No significant correlation between diet and disease activity was found. Overall, 27% of the patients reported aggravating gastrointestinal problems when consuming certain foodstuff(s). The 30% of patients who reported suffering from gastrointestinal pain had significantly greater disease activity and poorer functional status according to their BASDAI and BASFI scores (p < 0.01 and p = 0.01, respectively). Patients who reported gastrointestinal pain had a significantly higher consumption of vegetables (p < 0.01) and lower consumption of milk and soured milk (p = 0.04). No significant correlation was found between the use of non-steroidal anti-inflammatory drugs (NSAID) and gastrointestinal symptoms. In multiple regression models, BASDAI and the consumption of vegetables were independent and statistically significant predictors of gastrointestinal pain. To conclude, in a group of Swedish AS patients, no correlation between diet and disease activity could be detected. There were, however, correlations between diet and gastrointestinal pain. Gastrointestinal problems were also found to be prevalent in AS, independent of NSAID usage.},
   keywords = {Adolescent
Adult
Aged
Animals
Anti-Inflammatory Agents, Non-Steroidal/pharmacology
Cross-Sectional Studies
*Diet
Female
Food
Gastrointestinal Diseases/*complications/*diagnosis
Humans
Irritable Bowel Syndrome/complications/diagnosis
Male
Middle Aged
Milk
Regression Analysis
Severity of Illness Index
Spondylitis, Ankylosing/*complications/*diagnosis
Vegetables},
   ISSN = {0770-3198},
   Accession Number = {21110212},
   DOI = {10.1007/s10067-010-1625-x},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Sweetser, S. and Busciglio, I. A. and Camilleri, M. and Bharucha, A. E. and Szarka, L. A. and Papathanasopoulos, A. and Burton, D. D. and Eckert, D. J. and Zinsmeister, A. R.},
   title = {Effect of a chloride channel activator, lubiprostone, on colonic sensory and motor functions in healthy subjects},
   journal = {Am J Physiol Gastrointest Liver Physiol},
   volume = {296},
   number = {2},
   pages = {G295-301},
   note = {Sweetser, Seth
Busciglio, Irene A
Camilleri, Michael
Bharucha, Adil E
Szarka, Lawrence A
Papathanasopoulos, Athanasios
Burton, Duane D
Eckert, Deborah J
Zinsmeister, Alan R
K24-DK02638/DK/NIDDK NIH HHS/United States
R01-DK54681/DK/NIDDK NIH HHS/United States
RR0024150/RR/NCRR NIH HHS/United States
Journal Article
Randomized Controlled Trial
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
United States
Am J Physiol Gastrointest Liver Physiol. 2009 Feb;296(2):G295-301. doi: 10.1152/ajpgi.90558.2008. Epub 2008 Nov 25.},
   abstract = {Lubiprostone, a bicyclic fatty acid chloride channel activator, is efficacious in treatment of chronic constipation and constipation-predominant irritable bowel syndrome. The study aim was to compare effects of lubiprostone and placebo on colonic sensory and motor functions in humans. In double-blind, randomized fashion, 60 healthy adults received three oral doses of placebo or 24 microg lubiprostone per day in a parallel-group, placebo-controlled trial. A barostat-manometry tube was placed in the left colon by flexible sigmoidoscopy and fluoroscopy. We measured treatment effects on colonic sensation and motility with validated methods, with the following end points: colonic compliance, fasting and postprandial tone and motility indexes, pain thresholds, and sensory ratings to distensions. Among participants receiving lubiprostone or placebo, 26 of 30 and 28 of 30, respectively, completed the study. There were no overall effects of lubiprostone on compliance, fasting tone, motility indexes, or sensation. However, there was a treatment-by-sex interaction effect for compliance (P = 0.02), with lubiprostone inducing decreased fasting compliance in women (P = 0.06) and an overall decreased colonic tone contraction after a standard meal relative to fasting tone (P = 0.014), with greater effect in women (P < 0.01). Numerical differences of first sensation and pain thresholds (P = 0.11 in women) in the two groups were not significant. We concluded that oral lubiprostone 24 microg does not increase colonic motor function. The findings of decreased colonic compliance and decreased postprandial colonic tone in women suggest that motor effects are unlikely to cause accelerated colonic transit with lubiprostone, although they may facilitate laxation. Effects of lubiprostone on sensitivity deserve further study.},
   keywords = {Administration, Oral
Adult
Alprostadil/administration & dosage/*analogs & derivatives/pharmacology
*Chloride Channel Agonists
Colon/*drug effects/innervation/physiology
Compliance
Double-Blind Method
Fasting
Female
Gastrointestinal Agents/administration & dosage/*pharmacology
Gastrointestinal Motility/*drug effects
Humans
Lubiprostone
Male
Pain Threshold/drug effects
Postprandial Period
Pressure
Sensation/*drug effects
Sex Factors},
   ISSN = {0193-1857 (Print)
0193-1857},
   Accession Number = {19033530},
   DOI = {10.1152/ajpgi.90558.2008},
   year = {2009},
   type = {Ref–rence Type}
}

@article{
   author = {Thomas, D. W. and Greer, F. R.},
   title = {Probiotics and prebiotics in pediatrics},
   journal = {Pediatrics},
   volume = {126},
   number = {6},
   pages = {1217-31},
   note = {1098-4275
Thomas, Dan W
Greer, Frank R
American Academy of Pediatrics Committee on Nutrition
American Academy of Pediatrics Section on Gastroenterology, Hepatology, and Nutrition
Journal Article
Review
United States
Pediatrics. 2010 Dec;126(6):1217-31. doi: 10.1542/peds.2010-2548. Epub 2010 Nov 29.},
   abstract = {This clinical report reviews the currently known health benefits of probiotic and prebiotic products, including those added to commercially available infant formula and other food products for use in children. Probiotics are supplements or foods that contain viable microorganisms that cause alterations of the microflora of the host. Use of probiotics has been shown to be modestly effective in randomized clinical trials (RCTs) in (1) treating acute viral gastroenteritis in healthy children; and (2) preventing antibiotic-associated diarrhea in healthy children. There is some evidence that probiotics prevent necrotizing enterocolitis in very low birth weight infants (birth weight between 1000 and 1500 g), but more studies are needed. The results of RCTs in which probiotics were used to treat childhood Helicobacter pylori gastritis, irritable bowel syndrome, chronic ulcerative colitis, and infantile colic, as well as in preventing childhood atopy, although encouraging, are preliminary and require further confirmation. Probiotics have not been proven to be beneficial in treating or preventing human cancers or in treating children with Crohn disease. There are also safety concerns with the use of probiotics in infants and children who are immunocompromised, chronically debilitated, or seriously ill with indwelling medical devices. Prebiotics are supplements or foods that contain a nondigestible food ingredient that selectively stimulates the favorable growth and/or activity of indigenous probiotic bacteria. Human milk contains substantial quantities of prebiotics. There is a paucity of RCTs examining prebiotics in children, although there may be some long-term benefit of prebiotics for the prevention of atopic eczema and common infections in healthy infants. Confirmatory well-designed clinical research studies are necessary.},
   keywords = {Child
Dietetics/methods
*Food, Organic
Gastrointestinal Tract/microbiology
Humans
Nutritional Physiological Phenomena/*physiology
Nutritive Value
Prebiotics/*utilization
Probiotics/*therapeutic use},
   ISSN = {0031-4005},
   Accession Number = {21115585},
   DOI = {10.1542/peds.2010-2548},
   year = {2010},
   type = {Ref–rence Type}
}

@article{
   author = {Tompkins, T. A. and Xu, X. and Ahmarani, J.},
   title = {A comprehensive review of post-market clinical studies performed in adults with an Asian probiotic formulation},
   journal = {Benef Microbes},
   volume = {1},
   number = {1},
   pages = {93-106},
   note = {1876-2891
Tompkins, T A
Xu, X
Ahmarani, J
Journal Article
Review
Netherlands
Benef Microbes. 2010 Mar;1(1):93-106. doi: 10.3920/BM2008.1005.},
   abstract = {Probiotics as dietary supplements have been readily accepted by Asian populations. Use of certain probiotic preparations is widespread and the number of clinical trials undertaken with such products is unparalleled in western scientific literature. One such preparation, containing a combination of Enterococcus faecium R0026 and Bacillus subtilis R0179, has 23 publications on post-market clinical studies involving over 1,800 adults. The majority of these publications are printed in Chinese and Korean journals. This review examines the clinical findings with this probiotic combination. As mono-therapy, it has been used to overcome symptoms associated with chronic diarrhoea and irritable bowel syndrome. It has been used as co-adjuvant therapy with sulfasalazine and mesalazine to improve remission times in mild to moderate Ulcerative Colitis and to improve compliance with conventional triple therapy for Helicobacter pylori eradication. While the much of the data is preliminary and the study designs require refinement, the contribution of these trials should not be ignored. The information derived in this review will provide practitioners with practical information on appropriate applications for probiotic supplements, expected outcomes, dosing regimes, safety and reported adverse events. Furthermore, identification of problems in these trials should help researchers design better clinical trials when investigating probiotic products.},
   keywords = {Adult
Animals
Asia
Clinical Trials as Topic
Female
Gastrointestinal Diseases/*drug therapy/microbiology
Humans
Male
Probiotics/*therapeutic use
*Product Surveillance, Postmarketing},
   ISSN = {1876-2883},
   Accession Number = {21840798},
   DOI = {10.3920/bm2008.1005},
   year = {2010},
   type = {Ref–rence Type}
}

@article{
   author = {Trembach, G. A. and Korot'ko, G. F.},
   title = {[Using of adaptive biocontrolling feedbak in the treatment of irritable bowel syndrome]},
   journal = {Eksp Klin Gastroenterol},
   number = {1},
   pages = {67-71},
   note = {Trembach, G A
Korot'ko, G F
Clinical Trial
Comparative Study
English Abstract
Journal Article
Russia (Federation)
Eksp Klin Gastroenterol. 2009;(1):67-71.},
   abstract = {In original research are compared results of treatment of irritable bowel syndrome (IBS) by standard technique and treatment with to additional application of the control of a biofeedback. The analysis was carried out on dynamics of clinical symptoms in 1 and 6 months after course of treatment. Research showed improvement of results of treatment IBS in the group with additional treatment of a biofeedback.},
   keywords = {*Adaptation, Physiological
Adolescent
Adult
*Electric Stimulation Therapy
Feedback, Physiological/*physiology
Female
Humans
Irritable Bowel Syndrome/diet therapy/drug therapy/physiopathology/*therapy
Plethysmography, Impedance
Treatment Outcome
Young Adult},
   ISSN = {1682-8658 (Print)
1682-8658},
   Accession Number = {19548425},
   year = {2009},
   type = {Ref–rence Type}
}

@article{
   author = {Trinkley, K. E. and Nahata, M. C.},
   title = {Treatment of irritable bowel syndrome},
   journal = {J Clin Pharm Ther},
   volume = {36},
   number = {3},
   pages = {275-82},
   note = {1365-2710
Trinkley, K E
Nahata, M C
Journal Article
Review
England
J Clin Pharm Ther. 2011 Jun;36(3):275-82. doi: 10.1111/j.1365-2710.2010.01177.x. Epub 2010 Aug 24.},
   abstract = {WHAT IS KNOWN AND OBJECTIVE: The complexity and diversity of irritable bowel syndrome's (IBS) presentation make treatment difficult. Although there are reviews and guidelines for treating IBS, they focus on the efficacy of medications for IBS symptoms using high-priority endpoints, leaving those of lower priority largely unreported. Therefore, the aim of this review is to provide a comprehensive evidence-based review of the efficacy of medications to treat IBS symptoms, reported by IBS subtype, including secondary symptom endpoints that are often underreported. METHODS: A review of PubMed for articles published through December 2009 using the keywords: 'irritable bowel syndrome', 'therapeutics', 'antidiarrhoeals', 'laxatives', 'loperamide', 'dietary fibre', 'psyllium', 'calcium polycarbophil', 'bulking agents', 'lubiprostone', 'antidepressant agents, tricyclics' and its representative entities, 'serotonin reuptake inhibitors' and its representative entities, 'dicyclomine', hyoscyamine', 'peppermint oil', 'parasympatholytics' and its representative entities, 'rifaximin', 'pregabalin', 'gabapentin', 'clonidine', 'octreotide', 'atropine' and 'probiotics' is provided. Placebo-controlled trials were evaluated for the strength of evidence supporting the efficacy of each medication for explicit IBS symptoms. The efficacy of each medication for the symptoms of abdominal pain, bloating, stool form, mucus, urgency, feeling of incomplete evacuation, flatulence, frequency, or borborgymi and overall symptoms are reported by IBS subtype. RESULTS AND DISCUSSION: The literature search identified 58 placebo-controlled trials of the efficacy of medications for treating IBS symptoms, which were critically evaluated and reported. The available studies suggest improvement in various IBS symptoms with loperamide, fibre supplements, lubiprostone, tricyclic antidepressants (TCAs), selective serotonin receptor inhibitors (SSRIs), antispasmotics, rifaximin, pregabalin, gabapentin, clonidine, octreotide and probiotic treatments. WHAT IS NEW AND CONCLUSION: This review is the first to compile the available evidence on the efficacy of the various pharmacological treatments for IBS on the basis of IBS subtype and specific symptoms. This evidence is limited and more well-designed studies are required to better inform therapeutic decision-making in the management of this difficult syndrome.},
   keywords = {Abdominal Pain/etiology
Antidepressive Agents/therapeutic use
Antidiarrheals/therapeutic use
Constipation/etiology
Controlled Clinical Trials as Topic
Depression/etiology
Diarrhea/etiology
Dietary Fiber/therapeutic use
Dietary Supplements
Evidence-Based Medicine
Humans
Irritable Bowel Syndrome/*drug therapy/*physiopathology/therapy
Parasympatholytics/therapeutic use
Quality of Life},
   ISSN = {0269-4727},
   Accession Number = {21545610},
   DOI = {10.1111/j.1365-2710.2010.01177.x},
   year = {2011},
   type = {Ref–rence Type}
}

@article{
   author = {Valeur, J. and Berstad, A.},
   title = {["Five a day"--tough for the stomach?]},
   journal = {Tidsskr Nor Laegeforen},
   volume = {129},
   number = {22},
   pages = {2388-9},
   note = {0807-7096
Valeur, Jorgen
Berstad, Arnold
Historical Article
Letter
Norway
Tidsskr Nor Laegeforen. 2009 Nov 19;129(22):2388-9. doi: 10.4045/tidsskr.09.1246.},
   keywords = {Dietary Carbohydrates/administration & dosage/adverse effects
Dietary Fiber/administration & dosage/adverse effects
History, 20th Century
Humans
Irritable Bowel Syndrome/*etiology/history/physiopathology},
   ISSN = {0029-2001},
   Accession Number = {19935947},
   DOI = {10.4045/tidsskr.09.1246},
   year = {2009},
   type = {Ref–rence Type}
}

@article{
   author = {Verdu, E. F. and Armstrong, D. and Murray, J. A.},
   title = {Between celiac disease and irritable bowel syndrome: the "no man's land" of gluten sensitivity},
   journal = {Am J Gastroenterol},
   volume = {104},
   number = {6},
   pages = {1587-94},
   note = {1572-0241
Verdu, Elena F
Armstrong, David
Murray, Joseph A
R01 DK057892/DK/NIDDK NIH HHS/United States
R01 DK071003/DK/NIDDK NIH HHS/United States
Journal Article
Review
United States
Am J Gastroenterol. 2009 Jun;104(6):1587-94. doi: 10.1038/ajg.2009.188.},
   abstract = {The repertoire of gastrointestinal (GI) symptoms is finite; however, the etiologies and mechanisms underlying symptom generation and perception are diverse and, in many cases, unknown. This review examines the clinical and experimental evidence exploring the putative relationship between gluten sensitivity (GS) and the generation of GI symptoms. It explores the hypothesis that, in a proportion of patients, GS causes functional bowel disorder (FBD)-like symptoms. We propose a model for investigating and understanding the induction of GI symptoms and dysfunction by gluten in FBD and organic disease. We hypothesize that, even in the absence of fully developed celiac disease, gluten can induce symptoms similar to FBD. We discuss the hypothesis that GS and post-infectious irritable bowel syndrome (IBS) provide two triggers that can explain at least part of the spectrum that constitutes IBS, further advancing an understanding of the role of mucosal responses to luminal factors in FBDs. We propose that the animal model of GS in human leukocyte antigen (HLA)- DQ8 mice allows investigation of mucosal pathophysiological changes that occur before the onset of full-blown inflammation in a GS host. A better understanding of how gluten can cause symptoms in sensitive individuals will illuminate the interaction between host genotype, diet, and intestinal microbiota in generating one of the most common GI conditions.},
   keywords = {Animals
Celiac Disease/*etiology
Glutens/*adverse effects
Humans
Irritable Bowel Syndrome/*etiology
Prognosis
Risk Factors},
   ISSN = {0002-9270},
   Accession Number = {19455131},
   DOI = {10.1038/ajg.2009.188},
   year = {2009},
   type = {Ref–rence Type}
}

@article{
   author = {Wallace, B.},
   title = {Clinical use of probiotics in the pediatric population},
   journal = {Nutr Clin Pract},
   volume = {24},
   number = {1},
   pages = {50-9},
   note = {Wallace, Beth
Journal Article
Review
United States
Nutr Clin Pract. 2009 Feb-Mar;24(1):50-9. doi: 10.1177/0884533608329298.},
   abstract = {Probiotics are live microorganisms that produce a benefit to the host when provided in adequate amounts from food or supplements. There is an increased interest in the use of probiotics in the management and treatment of complex medical conditions. Recommendations for probiotic supplementation in the pediatric population are often conflicting due to limited research in many pediatric disease states. Research on single and multistrain probiotics has shown promise for some pediatric populations. This review discusses the research available for probiotic supplementation for children with irritable bowel syndrome, Crohn's disease, diarrhea, short bowel syndrome, human immunodeficiency virus, and food allergies. Probiotic safety also is discussed.},
   keywords = {Child
Crohn Disease/drug therapy
Diarrhea/drug therapy/prevention & control
Dietary Supplements
Food Hypersensitivity/drug therapy
HIV Infections/drug therapy/immunology
Humans
Intestinal Diseases/*drug therapy
Intestinal Mucosa/drug effects
Irritable Bowel Syndrome/drug therapy
Probiotics/adverse effects/*therapeutic use
Short Bowel Syndrome/drug therapy},
   ISSN = {0884-5336 (Print)
0884-5336},
   Accession Number = {19244149},
   DOI = {10.1177/0884533608329298},
   year = {2009},
   type = {Ref–rence Type}
}

@article{
   author = {Watier, A. and Rigaud, J. and Labat, J. J.},
   title = {[Irritable bowel syndrome, levator ani syndrome, proctalgia fugax and chronic pelvic and perineal pain]},
   journal = {Prog Urol},
   volume = {20},
   number = {12},
   pages = {995-1002},
   note = {Watier, Alain
Rigaud, Jerome
Labat, Jean-Jacques
English Abstract
Journal Article
Review
France
Prog Urol. 2010 Nov;20(12):995-1002. doi: 10.1016/j.purol.2010.08.060.},
   abstract = {OBJECTIVES: To define functional gastrointestinal pain, irritable bowel syndrome (IBS), levator ani syndrome, proctalgia fugax, the pathophysiology of these syndromes and the treatments that can be proposed. MATERIAL AND METHODS: Review of articles published on the theme based on a Medline (PubMed) search and consensus conferences selected according to their scientific relevance. RESULTS: IBS is very common. Patients report abdominal pain and/or discomfort, bloating, and abnormal bowel habit (diarrhoea, constipation or both), in the absence of any structural or biochemical abnormalities. IBS has a complex, multifactorial pathophysiology, involving biological and psychosocial interactions resulting in dysregulation of the brain-gut axis associated with disorders of intestinal motility, hyperalgesia, immune disorders and disorders of the intestinal bacterial microflora and autonomic and hormonal dysfunction. Many treatments have been proposed, ranging from diet to pharmacology and psychotherapy. DISCUSSION: Patients with various types of chronic pelvic and perineal pain, especially those seen in urology departments, very often report associated IBS. This syndrome is also part of a global and integrated concept of pelviperineal dysfunction, avoiding a rigorous distinction between the posterior segment and the midline and anterior segments of the perineum.},
   keywords = {Anus Diseases/complications
Chronic Disease
Humans
Irritable Bowel Syndrome/*complications/therapy
Pain/complications
Pelvic Pain/*etiology
*Perineum},
   ISSN = {1166-7087 (Print)
1166-7087},
   Accession Number = {21056377},
   DOI = {10.1016/j.purol.2010.08.060},
   year = {2010},
   type = {Ref–rence Type}
}

@article{
   author = {Wedlake, L. and A'Hern, R. and Russell, D. and Thomas, K. and Walters, J. R. and Andreyev, H. J.},
   title = {Systematic review: the prevalence of idiopathic bile acid malabsorption as diagnosed by SeHCAT scanning in patients with diarrhoea-predominant irritable bowel syndrome},
   journal = {Aliment Pharmacol Ther},
   volume = {30},
   number = {7},
   pages = {707-17},
   note = {1365-2036
Wedlake, L
A'Hern, R
Russell, D
Thomas, K
Walters, J R F
Andreyev, H J N
Journal Article
Research Support, Non-U.S. Gov't
Review
England
Aliment Pharmacol Ther. 2009 Oct;30(7):707-17. doi: 10.1111/j.1365-2036.2009.04081.x. Epub 2009 Jun 30.},
   abstract = {BACKGROUND: Recurrent, watery diarrhoea affects one-third of patients diagnosed with irritable bowel syndrome ('IBS-D'). Idiopathic bile acid malabsorption ('I-BAM') may be the cause. AIM: To determine the prevalence of I-BAM in patients suffering from IBS-D. METHODS: A systematic search was performed of publications reporting patients presenting with IBS-D type symptoms, who were subsequently confirmed as having I-BAM by SeHCAT scanning. RESULTS: Eighteen relevant studies, 15 prospective, comprising 1223 patients were identified. Five studies (429 patients) indicated that 10% (CI: 7-13) patients had severe bile acid malabsorption (SeHCAT 7 day retention <5% of baseline value). 17 studies (1073 patients) indicated that 32% (CI: 29-35) patients had moderate bile acid malabsorption (SeHCAT <10%). 7 studies (618 patients) indicated that 26% (CI: 23-30) patients had mild (SeHCAT <15%) bile acid malabsorption. Pooled data from 15 studies showed a dose-response relationship according to severity of malabsorption to treatment with a bile acid binder: response to colestyramine occurred in 96% of patients with <5% retention, 80% at <10% retention and 70% at <15% retention. CONCLUSIONS: Idiopathic adult-onset bile acid malabsorption is not rare. International guidelines for the management of irritable bowel syndrome need to be revised so that clinicians become more aware of this possibility.},
   keywords = {Adult
Anion Exchange Resins/*therapeutic use
Bile Acids and Salts/*metabolism
Cholestyramine Resin/*therapeutic use
Diarrhea/epidemiology/*etiology
Dose-Response Relationship, Drug
Humans
Irritable Bowel Syndrome/complications/epidemiology/*physiopathology
Malabsorption Syndromes/*complications/drug therapy/epidemiology
Prevalence
Prospective Studies
Retrospective Studies
Severity of Illness Index},
   ISSN = {0269-2813},
   Accession Number = {19570102},
   DOI = {10.1111/j.1365-2036.2009.04081.x},
   year = {2009},
   type = {Ref–rence Type}
}

@article{
   author = {Whitfield, K. L. and Shulman, R. J.},
   title = {Treatment options for functional gastrointestinal disorders: from empiric to complementary approaches},
   journal = {Pediatr Ann},
   volume = {38},
   number = {5},
   pages = {288-90, 292-4},
   note = {Whitfield, K Lynette
Shulman, Robert J
R01 05337/PHS HHS/United States
T32 DK007664-18/DK/NIDDK NIH HHS/United States
R01 NR005337/NR/NINR NIH HHS/United States
P30 DK056338-07/DK/NIDDK NIH HHS/United States
P30 DK056338/DK/NIDDK NIH HHS/United States
R01 NR005337-07/NR/NINR NIH HHS/United States
T32 DK007664-17/DK/NIDDK NIH HHS/United States
T32 DK007664/DK/NIDDK NIH HHS/United States
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Review
United States
Pediatr Ann. 2009 May;38(5):288-90, 292-4.},
   keywords = {Abdominal Pain/*therapy
Antidepressive Agents/therapeutic use
Child
Child, Preschool
Clinical Trials as Topic
Complementary Therapies
Dietary Fiber/therapeutic use
Dyspepsia/*therapy
Fructose/therapeutic use
Gastrointestinal Agents/therapeutic use
Humans
Irritable Bowel Syndrome/*therapy
Lactose/therapeutic use
Pediatrics/methods
Probiotics/therapeutic use
Psychotherapy
Treatment Outcome},
   ISSN = {0090-4481 (Print)
0090-4481},
   Accession Number = {19476303},
   year = {2009},
   type = {Ref–rence Type}
}

@article{
   author = {Whorwell, P. J.},
   title = {The problem of insoluble fibre in irritable bowel syndrome},
   journal = {Bmj},
   volume = {338},
   pages = {a3149},
   note = {1756-1833
Whorwell, Peter J
Comment
Letter
England
BMJ. 2009 Jan 6;338:a3149. doi: 10.1136/bmj.a3149.},
   keywords = {Dietary Fiber/*therapeutic use
Edible Grain/adverse effects
Humans
Irritable Bowel Syndrome/*therapy
Psyllium/*therapeutic use},
   ISSN = {0959-535x},
   Accession Number = {19126614},
   DOI = {10.1136/bmj.a3149},
   year = {2009},
   type = {Ref–rence Type}
}

@article{
   author = {Wiesner, M. and Naylor, S. J. and Copping, A. and Furlong, A. and Lynch, A. G. and Parkes, M. and Hunter, J. O.},
   title = {Symptom classification in irritable bowel syndrome as a guide to treatment},
   journal = {Scand J Gastroenterol},
   volume = {44},
   number = {7},
   pages = {796-803},
   note = {1502-7708
Wiesner, Maureen
Naylor, Sally J
Copping, Ann
Furlong, Anita
Lynch, Andrew G
Parkes, Miles
Hunter, John O
10825/Cancer Research UK/United Kingdom
Journal Article
England
Scand J Gastroenterol. 2009;44(7):796-803. doi: 10.1080/00365520902964705.},
   abstract = {OBJECTIVE: The treatment of irritable bowel syndrome (IBS) remains unsatisfactory. There are no objective markers for diagnosis, and classification (currently based on symptoms) provides little insight into potential causes or optimal therapy. The aim of this study was to determine whether a Swedish classification of IBS based on cluster analysis of patients' symptoms might provide a guide to successful treatment. MATERIAL AND METHODS: Patients in a research clinic for IBS were classified according to criteria published by Ragnarsson & Bodemar (R&B) and also assessed independently by a clinician. Patients fulfilling the R&B criteria for subgroups 1 and 2 received specific treatments, either bulk laxatives or dietary treatment to reduce colonic fermentation, respectively. Patients who did not fit into these categories were given "best treatment" targeted at their predominant symptoms, but not limited in any way. Results before and after follow-up were assessed using a validated symptom-scoring scale. RESULTS: Seventy-one successive patients were recruited, and the numbers falling into R&B subgroups 1 and 2 were 15 (21%), and 28 (39%), respectively, leaving 28 (39%) unclassified. Receiver operating characteristic plots showed that the criteria for separation into subgroups 1 and 2 correlated well with the clinician's assessment. After treatment, symptom scores for the whole group showed a significant improvement (p<0.0001), but results were significantly better in subgroups 1 and 2 than in those unclassified, even when allowance was made for a potential therapeutic placebo effect of 40%. CONCLUSION: The R&B classification provides a helpful guide to treatment in many cases of IBS.},
   keywords = {Adult
Cluster Analysis
Female
Humans
Irritable Bowel Syndrome/*classification/physiopathology/psychology/*therapy
Male
Middle Aged
ROC Curve
Statistics, Nonparametric
Surveys and Questionnaires
Treatment Outcome},
   ISSN = {0036-5521},
   Accession Number = {19452358},
   DOI = {10.1080/00365520902964705},
   year = {2009},
   type = {Ref–rence Type}
}

@article{
   author = {Williams, N. T.},
   title = {Probiotics},
   journal = {Am J Health Syst Pharm},
   volume = {67},
   number = {6},
   pages = {449-58},
   note = {1535-2900
Williams, Nancy Toedter
Journal Article
Review
United States
Am J Health Syst Pharm. 2010 Mar 15;67(6):449-58. doi: 10.2146/ajhp090168.},
   abstract = {PURPOSE: The pharmacology, uses, dosages, safety, drug interactions, and contraindications of probiotics are reviewed. SUMMARY: Probiotics are live nonpathogenic microorganisms administered to improve microbial balance, particularly in the gastrointestinal tract. They consist of Saccharomyces boulardii yeast or lactic acid bacteria, such as Lactobacillus and Bifidobacterium species, and are regulated as dietary supplements and foods. Probiotics exert their beneficial effects through various mechanisms, including lowering intestinal pH, decreasing colonization and invasion by pathogenic organisms, and modifying the host immune response. Probiotic benefits associated with one species or strain do not necessarily hold true for others. The strongest evidence for the clinical effectiveness of probiotics has been in the treatment of acute diarrhea, most commonly due to rotavirus, and pouchitis. More research is needed to clarify the role of probiotics for preventing antibiotic-associated diarrhea, Clostridium difficile infection, travelers' diarrhea, irritable bowel syndrome, ulcerative colitis, Crohn's disease, and vulvovaginal candidiasis. There is no consensus about the minimum number of microorganisms that must be ingested to obtain a beneficial effect; however, a probiotic should typically contain several billion microorganisms to increase the chance that adequate gut colonization will occur. Probiotics are generally considered safe and well tolerated, with bloating and flatulence occurring most frequently. They should be used cautiously in patients who are critically ill or severely immunocompromised or those with central venous catheters since systemic infections may rarely occur. Bacteria-derived probiotics should be separated from antibiotics by at least two hours. CONCLUSION: Probiotics have demonstrated efficacy in preventing and treating various medical conditions, particularly those involving the gastrointestinal tract. Data supporting their role in other conditions are often conflicting.},
   keywords = {Gastrointestinal Tract/physiopathology
Humans
*Probiotics/administration &
dosage/contraindications/pharmacology/poisoning/therapeutic use},
   ISSN = {1079-2082},
   Accession Number = {20208051},
   DOI = {10.2146/ajhp090168},
   year = {2010},
   type = {Ref–rence Type}
}

@article{
   author = {Wisniewska-Jarosinska, M. and Chojnacki, J. and Konturek, S. and Brzozowski, T. and Smigielski, J. and Chojnacki, C.},
   title = {Evaluation of urinary 6-hydroxymelatonin sulphate excretion in women at different age with irritable bowel syndrome},
   journal = {J Physiol Pharmacol},
   volume = {61},
   number = {3},
   pages = {295-300},
   note = {1899-1505
Wisniewska-Jarosinska, M
Chojnacki, J
Konturek, S
Brzozowski, T
Smigielski, J
Chojnacki, C
Journal Article
Poland
J Physiol Pharmacol. 2010 Jun;61(3):295-300.},
   abstract = {Melatonin (MT) exerts a beneficial action in the treatment of many diseases, among them also in irritable bowel syndrome (IBS). Its secretion decreases with age, particularly, in the postmenopausal period in women. It has not been determined whether these changes can have an impact on the clinical picture of IBS. The study aimed at evaluating the urinary excretion of the main MT metabolite - 6-hydroxymelatonin sulphate (6-HMS) in women at different age with IBS. The investigations were carried out in five groups of 30 women each. Group Ia (the controls) - premenopausal healthy women (20-39 years), group Ib (the controls) - postmenopausal healthy women (46-66 years), group II - women with constipation predominant IBS (IBS-C; 19-42 years), group III - women with diarrhoea predominant IBS (IBS-D; 20-39 years), group IV - women with IBS-C (49-68 years), group V - women with IBS-D (48-69 years). The diagnosis of IBS was based on the Rome III Criteria after excluding other diseases. On the day of the study the patients remained on the same liquid diet (Nutridrink - 3x400 ml) and 1500 ml of still mineral water. 6-HMS concentration in urine was measured by ELISA method applying IBL antibodies (RE-54031, Immunological Laboratories). The results showed that 24-hour urinary 6-HMS excretion in the studied premenopausal women were as follows: group Ia - 15.13+/-5.83 microg/24 h, group II - 28.85+/-12.59 microg/24 h (p<0,01), group III - 26.10+/-11.76 microg/24 h (p<0,01) and in the postmenopausal subjects they were: group Ib - 10.66+/-3.23 microg/24 h, group IV - 13.73+/-5.09 microg/24 h ((p=0,02), group V - 21.39+/-10.88 microg/24 h (p<0,01). In women with IBS-C the obtained results of 24-hour 6-HMS urinary excretion were independent on the intensity of clinical symptoms. On the other hand, in women with IBS-D, both in the group III and V, higher intensity of ailments was accompanied by significantly increased 6-HMS urinary excretion. The results of the study allowed drawing the following conclusions: (1). 24-hour 6-HMS urinary excretion in women with the constipation-predominant (IBS-C) as well as the diarrhoea-predominant IBS (IBS-D) is higher than in healthy persons both in the premenopausal and postmenopausal period. (2). Relatively high 6-HMS urinary excretion in postmenopausal women with IBS-D indicates an adaptive increase in MT secretion from EC in the gut.},
   keywords = {Adult
Aged
Female
Humans
Irritable Bowel Syndrome/metabolism/*urine
Melatonin/*analogs & derivatives/secretion/urine
Middle Aged
Serotonin/metabolism},
   ISSN = {0867-5910},
   Accession Number = {20610859},
   year = {2010},
   type = {Ref–rence Type}
}

@article{
   author = {Wu, J. and Xia, B. and von Blomberg, B. M. and Zhao, C. and Yang, X. W. and Crusius, J. B. and Pena, A. S.},
   title = {Coeliac disease in China, a field waiting for exploration},
   journal = {Rev Esp Enferm Dig},
   volume = {102},
   number = {8},
   pages = {472-7},
   note = {Wu, J
Xia, B
von Blomberg, B M E
Zhao, C
Yang, X W
Crusius, J B A
Pena, A S
Journal Article
Research Support, Non-U.S. Gov't
Spain
Rev Esp Enferm Dig. 2010 Jul;102(8):472-7.},
   abstract = {BACKGROUND: no systematic studies on the prevalence of coeliac disease (CD) have been reported from China. In western populations CD is more common in patients with insulin dependent diabetes mellitus (IDDM) and in diarrhoea-predominant irritable bowel syndrome (D-IBS). We have screened patients with these conditions presenting to the outpatient department of a large hospital of "Traditional Chinese Medicine" (TCM) in Nanjing, Jiangsu province, P.R. China. METHODS: we tested sera of 78 unrelated Han Chinese patients (5 IDDM and 73 D-IBS), using ELISA serological tests for IgG anti-gliadin antibodies (IgG-AGA) and IgA anti-tissue transglutaminase antibodies (IgA-tTG). RESULTS: six out of 78 patients (7.7%) were positive for IgG-AGA (two men and four women) and two (2.6%) were positive for IgA-tTGs. One of the latter patients was negative for IgG-AGA. Besides, one patient had a dubious IgA-tTG antibody and a positive IgG-AGA. None of the six patients agreed to undergo duodenal biopsy. Two out of these six patients followed a gluten-free diet for one year. In one patient the diarrhoea ceased and his body weight increased. Another stopped losing weight. CONCLUSIONS: this study previously published as a letter in GUT (Wu J, Xia B, von Blomberg BME, Zhao C, Yang XW, Crusius JBA, Pena AS. Coeliac disease: emerging in China? Gut 2010; 59(3): 418-9) demonstrated that CD may exist in the Jiangsu province of P.R. China. The present article draws attention to the difficulties of following a standard protocol in China such as established in western countries and highlights important factors less well known in the west in relation to the development of CD in China. Wheat production became significant in China between 1600 and 1300 B.C. After the Han dynasty (500-200 B.C.), wheat was one of the main cereals in China. One the major wheat fields in China is located in the Jiangsu province where the research for this article was performed. A review of Chinese literature shows that the predominant HLA-DQ CD risk alleles and haplotypes are present in the Jiangsu province. Genetic background, food consumption, and the results of our study suggest that CD should actively be investigated in P.R. China.},
   keywords = {Celiac Disease/*diagnosis/epidemiology
China
Female
Humans
Male
Middle Aged},
   ISSN = {1130-0108 (Print)
1130-0108},
   Accession Number = {20670067},
   year = {2010},
   type = {Ref–rence Type}
}

@article{
   author = {Wuthrich, B.},
   title = {[Food allergy, food intolerance or functional disorder?]},
   journal = {Praxis (Bern 1994)},
   volume = {98},
   number = {7},
   pages = {375-87},
   note = {Wuthrich, B
English Abstract
Journal Article
Switzerland
Praxis (Bern 1994). 2009 Apr 1;98(7):375-87. doi: 10.1024/1661-8157.98.7.375.},
   abstract = {The term "food allergy" is widely misused for all sorts of symptoms and diseases caused by food. Food allergy (FA) is an adverse reaction to food (food hypersensitivity) occurring in susceptible individuals, which is mediated by a classical immune mechanism specific for the food itself. The best established mechanism in FA is due to the presence of IgE antibodies against the offending food. Food intolerance (FI) are all non-immune-mediated adverse reactions to food. The subgroups of FI are enzymatic (e.g. lactose intolerance due to lactase deficiency), pharmacological (reactions against biogenic amines, histamine intolerance), and undefined food intolerance (e.g. against some food additives). The diagnosis of an IgE-mediated FA is made by a carefully taken case history, supported by the demonstration of an IgE sensitization either by skin prick tests or by in vitro tests, and confirmed by positive oral provocation. For scientific purposes the only accepted test for the confirmation of FA/FI is a properly performed double-blind, placebo-controlled food challenge (DBPCFC). A panel of recombinant allergens, produced as single allergenic molecules, may in future improve the diagnosis of IgE-mediated FA. Due to a lack of causal treatment possibilities, the elimination of the culprit "food allergen" from the diet is the only therapeutic option for patients with real food allergy.},
   keywords = {Adult
Child
Child, Preschool
Cross Reactions
Diagnosis, Differential
Food Hypersensitivity/classification/*diagnosis/diet therapy/etiology
Gastrointestinal Diseases/diagnosis
Histamine/toxicity
Humans
Infant
Irritable Bowel Syndrome/diagnosis
Patient Care Team
Psychophysiologic Disorders/*diagnosis
Referral and Consultation},
   ISSN = {1661-8157 (Print)
1661-8157},
   Accession Number = {19340768},
   DOI = {10.1024/1661-8157.98.7.375},
   year = {2009},
   type = {Ref–rence Type}
}

@article{
   author = {Yamada, K. and Yoshimura, S. and Kawasaki, M. and Enomoto, Y. and Asano, T. and Minatoguchi, S. and Iwama, T.},
   title = {Effects of atorvastatin on carotid atherosclerotic plaques: a randomized trial for quantitative tissue characterization of carotid atherosclerotic plaques with integrated backscatter ultrasound},
   journal = {Cerebrovasc Dis},
   volume = {28},
   number = {4},
   pages = {417-24},
   note = {1421-9786
Yamada, Kiyofumi
Yoshimura, Shinichi
Kawasaki, Masanori
Enomoto, Yukiko
Asano, Takahiko
Minatoguchi, Shinya
Iwama, Toru
Journal Article
Randomized Controlled Trial
Switzerland
Cerebrovasc Dis. 2009;28(4):417-24. doi: 10.1159/000235746. Epub 2009 Aug 26.},
   abstract = {BACKGROUND: Instability of carotid plaques has been reported to be associated with stroke and other cerebrovascular events. The purpose of this study was to examine whether cholesterol-lowering therapy with atorvastatin in nonhypercholesterolemic patients reduces carotid plaque instability as assessed by ultrasound integrated backscatter (IBS) analysis. METHODS: Consecutive non- or slightly hypercholesterolemic patients with moderate carotid artery stenosis were randomly assigned to a diet group (n = 20) or a statin group (atorvastatin; n = 20). Carotid plaques were monitored by measuring intima media thickness (IMT) and IBS values at baseline and after 6 months. RESULTS: Three-dimensional IBS imaging showed that relative lipid volume of carotid plaques significantly decreased from 58.4 +/- 25.6 to 47.8 +/- 23.5% in the statin group (p < 0.01), whereas there was no significant decrease in the diet group. Significant regression of IMT was not observed in either group. The changes of IBS values and relative lipid volume between baseline and 6 months were correlated with the change in low-density lipoprotein cholesterol (r = 0.31, p < 0.05, and r = 0.34, p < 0.05, respectively). CONCLUSIONS: Lipid-lowering therapy by atorvastatin decreased relative lipid volume without significant regression of plaque volume during short-term follow-up in patients with moderate carotid artery stenosis. Quantitative assessment of carotid plaques by IBS analysis was clinically useful for monitoring atherosclerotic lesions.},
   keywords = {Aged
Aged, 80 and over
Atorvastatin Calcium
Biomarkers/blood
Carotid Stenosis/blood/*diagnostic imaging/diet therapy/*drug therapy
Cholesterol/blood
Cholesterol, HDL
Cholesterol, LDL/blood
Diffusion Magnetic Resonance Imaging
Female
Heptanoic Acids/*therapeutic use
Humans
Hydroxymethylglutaryl-CoA Reductase Inhibitors/*therapeutic use
Image Interpretation, Computer-Assisted
Imaging, Three-Dimensional
Magnetic Resonance Angiography
Male
Middle Aged
Predictive Value of Tests
Prospective Studies
Pyrroles/*therapeutic use
Rupture
Severity of Illness Index
Time Factors
Treatment Outcome
Triglycerides/blood
Ultrasonography},
   ISSN = {1015-9770},
   Accession Number = {19707015},
   DOI = {10.1159/000235746},
   year = {2009},
   type = {Ref–rence Type}
}

@article{
   author = {Zwolinska-Wcislo, M. and Galicka-Latala, D. and Rozpondek, P. and Rudnicka-Sosin, L. and Mach, T.},
   title = {[Frequency of celiac disease and irritable bowel syndrome coexistance and its influence on the disease course]},
   journal = {Przegl Lek},
   volume = {66},
   number = {3},
   pages = {126-9},
   note = {Zwolinska-Wcislo, Malgorzata
Galicka-Latala, Danuta
Rozpondek, Piotr
Rudnicka-Sosin, Lucyna
Mach, Tomasz
English Abstract
Journal Article
Poland
Przegl Lek. 2009;66(3):126-9.},
   abstract = {Celiac disease is increasingly recognized autoimmune enteropathy caused by a permanent gluten intolerance. Gluten is the main storage protein of wheat, in genetically predisposed individuals. Celiac disease risk in first degree relatives is about 10%. Diarrhea and changes of bowel movement, observed as well in celiac disease as in IBS, may lead to misdiagnosis of IBS basing on the Rome criteria or may be associated with coexistence of both diseases. The aim of the study was to assess the celiac disease prevalence in patients with irritable bowel syndrome. The study group comprised 200 patients (120 women and 80 men) aged 18-78 years (mean: 46.7 years) with diarrhoeal form of irritable bowel syndrome (IBS), according to the Rome criteria II. At the beginning and after a three month period anti tissue transglutaminase antibodies (IgA tTG) were estimated. Gastroscopy with biopsy where performed in those with IgA tTG titre above 1/200. 40 patients were immunologically positive and 14 of them have histopathologically proven celiac disease. In the group of patients with detected celiac disease, gluten free diet was applied besides the treatment with trimebutin or mebewerin, recommended for IBS. After 6 months the decrease of IgA tTG titre in the serum was observed. In 5 of these patients IgA tTG level was negative. It was associated with the significant decrease of clinical symptoms, such as diarrhea and flatulence. The remaining symptoms, such as abdominal pain, feeling of incomplete defecation demanded continuation of IBS treatment. With regard to often atypical celiac disease symptoms--adult active searching should be performed to differentiate from irritable bowel syndrome.},
   keywords = {Adult
Aged
Biopsy
Celiac Disease/diagnosis/diet therapy/*epidemiology/pathology
Comorbidity
Disease Progression
Female
Gastroscopy
Humans
Irritable Bowel Syndrome/diagnosis/*epidemiology/pathology/therapy
Male
Middle Aged
Prevalence
Young Adult},
   ISSN = {0033-2240 (Print)
0033-2240},
   Accession Number = {19689036},
   year = {2009},
   type = {Ref–rence Type}
}

repository: KociOrges/pytag

repo_name: KociOrges/pytag


text: @misc{Cardoso02SWSandP,	address = {Irvine, CA, USA},	author = {Cardoso, Jorge and Bussler, Christoph and Sheth, Amit},	date = {October 28-29},	date-added = {2018-04-25 20:02:07 +0000},	date-modified = {2018-04-25 20:02:07 +0000},	keywords = {Tutorial},	owner = {Jorge Cardoso},	publisher = {On the Move to Meaningful Internet Computing and Ubiquitous Computer 2002, International Federated Conferences: DOA/ODBASE/CooPIS},	refid = {22},	timestamp = {2010.08.26},	title = {Semantic Web Services and Processes: Semantic Composition and Quality of Service},	webpdf = {/Tutorials/SWSP-Tutorial-27-Oct-02.pdf},	year = {2002}}

license: MIT

license_type: permissive

branch_name: refs/heads/master

gha_license_id: MIT

gha_language: TeX

extension: bib


text:
@article{gray_identification_1999,
  title = {Identification of an {{SCF}} Ubiquitin-Ligase Complex Required for Auxin Response in {{Arabidopsis}} Thaliana.},
  volume = {13},
  issn = {0890-9369},
  abstract = {The plant hormone auxin regulates diverse aspects of plant growth and development. We report that in Arabidopsis, auxin response is dependent on a ubiquitin-ligase (E3) complex called SCFTIR1. The complex consists of proteins related to yeast Skp1p and Cdc53p called ASK and AtCUL1, respectively, as well as the F-box protein TIR1. Mutations in either ASK1 or TIR1 result in decreased auxin response. Further, overexpression of TIR1 promotes auxin response suggesting that SCFTIR1 is limiting for the response. These results provide new support for a model in which auxin action depends on the regulated proteolysis of repressor proteins},
  number = {13},
  journal = {Genes Dev},
  author = {Gray, W. M. and {del Pozo}, J. C. and Walker, L. and Hobbie, L. and Risseeuw, E. and Banks, T. and Crosby, W. L. and Yang, M. and Ma, H. and Estelle, M.},
  year = {7 1999},
  keywords = {research support,Gene Expression Regulation,SKP Cullin F-Box Protein Ligases,Arabidopsis Proteins,Peptide Synthases,Plant Proteins,Sequence Alignment,u.s. gov't,p.h.s.,Arabidopsis,Indoleacetic Acids,Plant Roots,Plant,Amino Acid Sequence,Recombinant Fusion Proteins,Molecular Sequence Data,non-p.h.s.},
  pages = {1678--91},
  file = {files/15/Gray Estelle 1999 Identification of an SCF ubiquit.pdf}
}

@article{kepinski_auxininduced_2004,
  title = {Auxin-Induced {{SCFTIR1}}-{{Aux}}/{{IAA}} Interaction Involves Stable Modification of the {{SCFTIR1}} Complex.},
  volume = {101},
  issn = {0027-8424},
  doi = {10.1073/pnas.0402868101},
  abstract = {The plant hormone auxin can regulate gene expression by destabilizing members of the Aux/IAA family of transcriptional repressors. Auxin-induced Aux/IAA degradation requires the protein-ubiquitin ligase SCF(TIR1), with auxin acting to enhance the interaction between the Aux/IAAs and SCF(TIR1). SKP1, Cullin, and an F-box-containing protein (SCF)-mediated degradation is an important component of many eukaryotic signaling pathways. In all known cases to date, the interaction between the targets and their cognate SCFs is regulated by signal-induced modification of the target. The mechanism by which auxin promotes the interaction between SCF(TIR1) and Aux/IAAs is not understood, but current hypotheses propose auxin-induced phosphorylation, hydroxylation, or proline isomerization of the Aux/IAAs. We found no evidence to support these hypotheses or indeed that auxin induces any stable modification of Aux/IAAs to increase their affinity for SCF(TIR1). Instead, we present data suggesting that auxin promotes the SCF(TIR1)-Aux/IAA interaction by affecting the SCF component, TIR1, or proteins tightly associated with it},
  number = {33},
  journal = {Proc Natl Acad Sci U S A},
  author = {Kepinski, Stefan and Leyser, Ottoline},
  year = {8 2004},
  keywords = {research support,non-u.s. gov't,SKP Cullin F-Box Protein Ligases,Arabidopsis Proteins,Arabidopsis,Indoleacetic Acids,Plant,Amino Acid Sequence,Recombinant Fusion Proteins,Plants,Protein Structure,Tertiary,Genetically Modified,Benzamides,Base Sequence,Naphthols,DNA,Macromolecular Substances,Naphthoquinones},
  pages = {12381--6},
  file = {files/41/Kepinski Leyser 2004 Auxin-induced SCFTIR1-Aux_IAA.pdf}
}

@article{tan_mechanism_2007,
  title = {Mechanism of Auxin Perception by the {{TIR1}} Ubiquitin Ligase.},
  volume = {446},
  issn = {1476-4687},
  doi = {10.1038/nature05731},
  abstract = {Auxin is a pivotal plant hormone that controls many aspects of plant growth and development. Perceived by a small family of F-box proteins including transport inhibitor response 1 (TIR1), auxin regulates gene expression by promoting SCF ubiquitin-ligase-catalysed degradation of the Aux/IAA transcription repressors, but how the TIR1 F-box protein senses and becomes activated by auxin remains unclear. Here we present the crystal structures of the Arabidopsis TIR1-ASK1 complex, free and in complexes with three different auxin compounds and an Aux/IAA substrate peptide. These structures show that the leucine-rich repeat domain of TIR1 contains an unexpected inositol hexakisphosphate co-factor and recognizes auxin and the Aux/IAA polypeptide substrate through a single surface pocket. Anchored to the base of the TIR1 pocket, auxin binds to a partially promiscuous site, which can also accommodate various auxin analogues. Docked on top of auxin, the Aux/IAA substrate peptide occupies the rest of the TIR1 pocket and completely encloses the hormone-binding site. By filling in a hydrophobic cavity at the protein interface, auxin enhances the TIR1-substrate interactions by acting as a 'molecular glue'. Our results establish the first structural model of a plant hormone receptor},
  number = {7136},
  journal = {Nature},
  author = {Tan, Xu and Calderon-Villalobos, Luz Irina A. and Sharon, Michal and Zheng, Changxue and Robinson, Carol V. and Estelle, Mark and Zheng, Ning},
  year = {4 2007},
  keywords = {research support,n.i.h.,extramural,non-u.s. gov't,Molecular,Substrate Specificity,Arabidopsis Proteins,u.s. gov't,Arabidopsis,Indoleacetic Acids,non-p.h.s.,F-Box Proteins,Protein Structure,Tertiary,Models,Receptors,Cell Surface,Plant Growth Regulators,Binding Sites,Crystallography,X-Ray,Ubiquitin-Protein Ligases,Phytic Acid,Structure-Activity Relationship},
  pages = {640--5},
  file = {files/231/Tan et al. - 2007 - Mechanism of auxin perception by the TIR1 ubiquiti.pdf;files/47/Tan Zheng 2007 Mechanism of auxin perception by th.pdf}
}

@article{mitchell-olds_genetic_2006,
  title = {Genetic Mechanisms and Evolutionary Significance of Natural Variation in {{Arabidopsis}}},
  volume = {441},
  copyright = {\textcopyright{} 2006 Nature Publishing Group},
  issn = {0028-0836},
  doi = {10.1038/nature04878},
  abstract = {Genomic studies of natural variation in model organisms provide a bridge between molecular analyses of gene function and evolutionary investigations of adaptation and natural selection. In the model plant species Arabidopsis thaliana, recent studies of natural variation have led to the identification of genes underlying ecologically important complex traits, and provided new insights about the processes of genome evolution, geographic population structure, and the selective mechanisms shaping complex trait variation in natural populations. These advances illustrate the potential for a new synthesis to elucidate mechanisms for the adaptive evolution of complex traits from nucleotide sequences to real-world environments.},
  number = {7096},
  urldate = {2016-08-25},
  journal = {Nature},
  author = {Mitchell-Olds, Thomas and Schmitt, Johanna},
  month = jun,
  year = {2006},
  pages = {947--952},
  file = {/Users/clayw/Zotero/storage/9SF6GI98/Mitchell-Olds and Schmitt - 2006 - Genetic mechanisms and evolutionary significance o.pdf;/Users/clayw/Zotero/storage/CXUZVAQB/Mitchell-Olds and Schmitt - 2006 - Genetic mechanisms and evolutionary significance o.pdf;/Users/clayw/Zotero/storage/MBARU2HU/Mitchell-Olds and Schmitt - 2006 - Genetic mechanisms and evolutionary significance o.pdf;/Users/clayw/Zotero/storage/GUMUTTU7/nature04878.html;/Users/clayw/Zotero/storage/HQXJNVXG/nature04878.html;/Users/clayw/Zotero/storage/HUNZM7BE/nature04878.html}
}

@article{dezfulian_oligomerization_2016,
  title = {Oligomerization of {{SCF TIR1 Is Essential}} for {{Aux}}/{{IAA Degradation}} and {{Auxin Signaling}} in {{Arabidopsis}}},
  volume = {12},
  issn = {1553-7404},
  doi = {10.1371/journal.pgen.1006301},
  abstract = {Author Summary   The phytohormone auxin plays a diverse and critical role in plant growth and development. In Arabidopsis, the F-box protein TIR1 is a component of an E3 SCF ubiquitin-ligase complex that serves as the auxin receptor and directs the ubiquitin-dependent degradation of repressors of auxin signaling known as the Aux/IAA proteins. Little is known regarding the stoichiometry of the SKP1, CUL1, RBX1 and TIR1 subunits that comprise the SCF TIR1  complex. Here, we show that TIR1 is capable of oligomerization  in planta . We also show that mutant alleles that abolish TIR1 oligomerization impair the degradation of known SCF TIR1  substrates and fail to restore auxin signaling and response in  tir1  loss-of-function genetic backgrounds. The results suggest that TIR1 homo-oligomerization is an important aspect of the regulation of SCF TIR1  function and auxin signaling.},
  number = {9},
  urldate = {2016-09-14},
  journal = {PLOS Genet},
  author = {Dezfulian, Mohammad H. and Jalili, Espanta and Roberto, Don Karl A. and Moss, Britney L. and Khoo, Kerry and Nemhauser, Jennifer L. and Crosby, William L.},
  month = sep,
  year = {2016},
  keywords = {Ligases,Arabidopsis thaliana,Plant Biochemistry,Auxins,Protein extraction,Genetically modified plants,Protein interactions,Nicotiana},
  pages = {e1006301},
  file = {/Users/clayw/Zotero/storage/BFM2AT7I/Dezfulian et al. - 2016 - Oligomerization of SCF TIR1 Is Essential for AuxI.pdf;/Users/clayw/Zotero/storage/XSJNPTBH/Dezfulian et al. - 2016 - Oligomerization of SCF TIR1 Is Essential for AuxI.pdf;/Users/clayw/Zotero/storage/4F33KRN9/article.html;/Users/clayw/Zotero/storage/4V8UZQK6/article.html}
}

@article{alonso-blanco_135_2016,
  title = {1,135 {{Genomes Reveal}} the {{Global Pattern}} of {{Polymorphism}} in {{Arabidopsis}} Thaliana},
  volume = {166},
  issn = {0092-8674, 1097-4172},
  doi = {10.1016/j.cell.2016.05.063},
  language = {English},
  number = {2},
  urldate = {2016-09-15},
  journal = {Cell},
  author = {Alonso-Blanco, Carlos and Andrade, Jorge and Becker, Claude and Bemm, Felix and Bergelson, Joy and Borgwardt, Karsten M. and Cao, Jun and Chae, Eunyoung and Dezwaan, Todd M. and Ding, Wei and Ecker, Joseph R. and Exposito-Alonso, Moises and Farlow, Ashley and Fitz, Joffrey and Gan, Xiangchao and Grimm, Dominik G. and Hancock, Angela M. and Henz, Stefan R. and Holm, Svante and Horton, Matthew and Jarsulic, Mike and Kerstetter, Randall A. and Korte, Arthur and Korte, Pamela and Lanz, Christa and Lee, Cheng-Ruei and Meng, Dazhe and Michael, Todd P. and Mott, Richard and Muliyati, Ni Wayan and N{\"a}gele, Thomas and Nagler, Matthias and Nizhynska, Viktoria and Nordborg, Magnus and Novikova, Polina Yu and Pic{\'o}, F. Xavier and Platzer, Alexander and Rabanal, Fernando A. and Rodriguez, Alex and Rowan, Beth A. and Salom{\'e}, Patrice A. and Schmid, Karl J. and Schmitz, Robert J. and Seren, {\"U}mit and Sperone, Felice Gianluca and Sudkamp, Mitchell and Svardal, Hannes and Tanzer, Matt M. and Todd, Donald and Volchenboum, Samuel L. and Wang, Congmao and Wang, George and Wang, Xi and Weckwerth, Wolfram and Weigel, Detlef and Zhou, Xuefeng},
  month = jul,
  year = {2016},
  keywords = {Arabidopsis thaliana,GWAS,1001 Genomes,glacial refugia,population expansion},
  pages = {481--491},
  file = {/Users/clayw/Zotero/storage/DI4ZCE79/Alonso-Blanco et al. - 2016 - 1,135 Genomes Reveal the Global Pattern of Polymor.pdf;/Users/clayw/Zotero/storage/UVXHAJ29/Alonso-Blanco et al. - 2016 - 1,135 Genomes Reveal the Global Pattern of Polymor.pdf;/Users/clayw/Zotero/storage/5XP2BG57/S0092-8674(16)30667-5.html;/Users/clayw/Zotero/storage/RHR63G9A/showImagesData.html}
}


text:
@article{chinchilla-rodriguezGlobalComparisonScientific2018,
 abstract = {This study compares the flows of mobile researchers and the number of publications in international collaboration within the context of scientific and economic capacities. The goal is to identify the convergence or discrepancy of countries in mobility and collaboration and determine the positions and relative influence of countries in both processes. Using affiliation data from scientific publications, we analyze the distributions and networks of collaboration and mobility and their structural differences. The results show that there is a significant relationship between the flow of mobile researchers and the capacity for publishing with foreign partners in the more prolific countries, although mobility is always lower than collaboration. Size matters and scientific relationship are highly resource-dependent. The Advanced and Proficient countries accumulate the highest proportion of the mobile authors and international publications with an extremely low representation of mobility in Developing and Lagging countries. In addition, the placement of countries is not always consistent in both networks, revealing the distinct roles, with particular instability for lower income countries. The more resources available in a country (both scientific and economic) the greater the likelihood of attracting foreign partners and mobilizing human capital. The policy relevance of these structural differences are described and a brief description of the limitations and future research are provided.},
 author = {Chinchilla-Rodríguez, Zaida and Miao, Lili and Murray, Dakota and Robinson-Garc\á, Nicolás and Costas, Rodrigo and Sugimoto, Cassidy R.},
 doi = {10.3389/frma.2018.00017},
 file = {/Users/dakotamurray/Zotero/storage/FMXWX9SE/Chinchilla-Rodríguez et al. - 2018 - A Global Comparison of Scientific Mobility and Col.pdf;/Users/dakotamurray/Zotero/storage/WEZ2KJ5R/Chinchilla-Rodríguez et al. - 2018 - A Global Comparison of Scientific Mobility and Col.pdf;/Users/dakotamurray/Zotero/storage/XCL35QNQ/Chinchilla-Rodríguez et al. - 2018 - A Global Comparison of Scientific Mobility and Col.pdf},
 ids = {chinchilla-rodriguezGlobalComparisonScientific2018a,chinchilla-rodriguezGlobalComparisonScientific2018b},
 issn = {2504-0537},
 journal = {Frontiers in Research Metrics and Analytics},
 keywords = {international collaboration,mobility,scholarly communication,Science Policy,Scientific capacity},
 language = {English},
 title = {A Global Comparison of Scientific Mobility and Collaboration According to National Scientific Capacities},
 volume = {3},
 year = {2018}
}


text:
@article{macintyre2011ah,
 abstract = {The advantages of plant growth promoting rhizobacteria in an Advanced Life Support system on the Moon or Mars may be limited by a low partial pressure of oxygen (pO2). Raphanus sativus ‘Cherry Bomb II Hybrid’ was inoculated with Bradyrhizobium japonicum Tal 629 and grown hydroponically at ambient and low (7 kPa) pO2 for 18 days. Inoculation with B. japonicum was deleterious to radish productivity (22% reduction in dry weight overall) and this was slightly exacerbated by low pO2. The microbial load of the hydroponics system was not affected by inoculation, though it was reduced by low pO2. Microbial abundance declined after the first 5 days of chamber closure with no further changes after the next 10 days. Microbial community composition changed significantly with inoculation.},
 author = {MacIntyre, O.J.},
 copyright = {All rights reserved},
 journal = {Acta horticulturae},
 keywords = {community structure, Bradyrhizobium japonicum, hybrids, hydroponics, microbial communities, microbial load, oxygen, plant growth-promoting rhizobacteria, radishes, Raphanus sativus},
 number = {no. 893},
 pages = {pp. 1285--1292},
 title = {Application of plant growth promoting rhizobacteria in a hydroponics system for advanced life support in space},
 translator = {MacIntyre, O.J. and Trevors, J.T. and Dixon, M.A. and Cottenie, K.},
 url = {http://www.actahort.org/books/893/893_151.htm},
 year = {2011}
}

repository: karl-cottenie/academic-kickstart

repo_name: karl-cottenie/academic-kickstart


text:
@techreport{Fritzson86,
  title = {Systems and Tools for Exploratory Programming Overview and Examples},
  author = {Peter Fritzson},
  year = {1986},
  number = {R-86-36},
  institution = ida,
  note = {Also presented at the Workshop on Programming Environments - Programming Paradigms, Roskilde, Denmark, October 22-24, 1986}
}
@online{GHCi-commands,
  author = {The GHC Team},
  title = "{GHCi commands}",
  year = 2015,
  url = {https://downloads.haskell.org/~ghc/latest/docs/html/users_guide/ghci-commands.html},
  urldate = {2016-04-26}
}
@book{Graham93,
 author = {Paul Graham},
 title = {On Lisp},
 year = {1993},
 isbn = {0130305529},
 publisher = {Prentice Hall},
}
@inproceedings{Wurthinger13,
 author = {W\"{u}rthinger, Thomas and Wimmer, Christian and W\"{o}\ss, Andreas and Stadler, Lukas and Duboscq, Gilles and Humer, Christian and Richards, Gregor and Simon, Doug and Wolczko, Mario},
 title = {One VM to Rule Them All},
 booktitle = {Proceedings of the 2013 ACM International Symposium on New Ideas, New Paradigms, and Reflections on Programming \& Software},
 series = {Onward! 2013},
 year = {2013},
 isbn = {978-1-4503-2472-4},
 location = {Indianapolis, Indiana, USA},
 pages = {187--204},
 numpages = {18},
 url = {http://doi.acm.org/10.1145/2509578.2509581},
 doi = {10.1145/2509578.2509581},
 acmid = {2509581},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {dynamic languages, java, javascript, language implementation, optimization, virtual machine},
}
@article{Humer14,
 author = {Humer, Christian and Wimmer, Christian and Wirth, Christian and W\"{o}\ss, Andreas and W\"{u}rthinger, Thomas},
 title = {A Domain-specific Language for Building Self-optimizing AST Interpreters},
 journal = {SIGPLAN Not.},
 issue_date = {March 2015},
 volume = {50},
 number = {3},
 month = sep,
 year = {2014},
 issn = {0362-1340},
 pages = {123--132},
 numpages = {10},
 url = {http://doi.acm.org/10.1145/2775053.2658776},
 doi = {10.1145/2775053.2658776},
 acmid = {2658776},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {Java, domain-specific languages, dynamic languages, language implementation, self-optimizing programs},
}
@article{Grimmer15,
 author = {Grimmer, Matthias and Seaton, Chris and Schatz, Roland and W\"{u}rthinger, Thomas and M\"{o}ssenb\"{o}ck, Hanspeter},
 title = {High-performance Cross-language Interoperability in a Multi-language Runtime},
 journal = {SIGPLAN Not.},
 issue_date = {Feburary 2016},
 volume = {51},
 number = {2},
 month = oct,
 year = {2015},
 issn = {0362-1340},
 pages = {78--90},
 numpages = {13},
 url = {http://doi.acm.org/10.1145/2936313.2816714},
 doi = {10.1145/2936313.2816714},
 acmid = {2816714},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {cross-language, language implementation, language interoperability, optimization, virtual machine},
}
@book{Noyes92,
 author = {Noyes, James L.},
 title = {Artificial Intelligence with Common Lisp: Fundamentals of Symbolic and Numeric Processing},
 year = {1992},
 isbn = {0-669-19473-5},
 publisher = {D. C. Heath and Company},
 address = {Lexington, MA, USA},
}
@article{Brand00,
  title={Efficient annotated terms},
  author={van den Brand, Mark GJ and De Jong, HA and Klint, Paul and Olivier, Pieter A},
  journal={Software Practice and Experience},
  volume={30},
  number={3},
  pages={259--291},
  year={2000}
}
@inbook{Kahn87,
  author={Kahn, G.},
  editor={Brandenburg, Franz J. and Vidal-Naquet, Guy and Wirsing, Martin},
  title={Natural Semantics},
  bookTitle={STACS 87: 4th Annual Symposium on Theoretical Aspects of Computer Science Passau, Federal Republic of Germany, February 19--21, 1987 Proceedings},
  year={1987},
  publisher={Springer Berlin Heidelberg},
  address={Berlin, Heidelberg},
  pages={22--39},
  isbn={978-3-540-47419-7},
  doi={10.1007/BFb0039592},
  url={http://dx.doi.org/10.1007/BFb0039592}
}
@inproceedings{KonatKWV12,
  title = {Declarative Name Binding and Scope Rules},
  author = {Gabriël D. P. Konat and Lennart C. L. Kats and Guido Wachsmuth and Eelco Visser},
  year = {2012},
  doi = {http://dx.doi.org/10.1007/978-3-642-36089-3_18},
  researchr = {http://researchr.org/publication/KonatKWV12},
  cites = {0},
  citedby = {0},
  pages = {311-331},
  booktitle = {Software Language Engineering, 5th International Conference, SLE 2012, Dresden, Germany, September 26-28, 2012, Revised Selected Papers},
  editor = {Krzysztof Czarnecki and Görel Hedin},
  volume = {7745},
  series = {Lecture Notes in Computer Science},
  publisher = {Springer},
  isbn = {978-3-642-36089-3},
}
@inproceedings{Visser01,
  title = {Stratego: A Language for Program Transformation Based on Rewriting Strategies},
  author = {Eelco Visser},
  year = {2001},
  doi = {10.1007/3-540-45127-7_27},
  url = {http://link.springer.com/chapter/10.1007/3-540-45127-7_27},
  researchr = {http://researchr.org/publication/Visser01},
  cites = {0},
  citedby = {1},
  pages = {357-362},
  booktitle = {Rewriting Techniques and Applications, 12th International Conference, RTA 2001, Utrecht, The Netherlands, May 22-24, 2001, Proceedings},
  editor = {Aart Middeldorp},
  volume = {2051},
  series = {Lecture Notes in Computer Science},
  publisher = {Springer},
  isbn = {3-540-42117-3},
}
@phdthesis{Visser97,
  title = {Syntax Definition for Language Prototyping},
  author = {Eelco Visser},
  year = {1997},
  month = {September},
  tags = {syntax definition, SDF, syntax definition formalism, disambiguation, testing, language design, graph-rewriting, algebraic specification,  algebra, context-aware, rewriting, parsing, design, scannerless parsing, ASF+SDF, SGLR},
  researchr = {http://researchr.org/publication/Vis97.thesis},
  cites = {0},
  citedby = {6},
  school = {University of Amsterdam},
  advisor = {Paul  Klint},
}
@article{deJonge12,
 author = {de Jonge, Maartje and Kats, Lennart C. L. and Visser, Eelco and S\"{o}derberg, Emma},
 title = "{Natural and Flexible Error Recovery for Generated Modular Language Environments}",
 journal = {ACM Trans. Program. Lang. Syst.},
 issue_date = {December 2012},
 volume = {34},
 number = {4},
 month = dec,
 year = {2012},
 issn = {0164-0925},
 pages = {15:1--15:50},
 articleno = {15},
 numpages = {50},
 url = {http://doi.acm.org/10.1145/2400676.2400678},
 doi = {10.1145/2400676.2400678},
 acmid = {2400678},
 publisher = {ACM},
 address = {New York, NY, USA},
}
@inproceedings{Kats10c,
  title = "{Domain-Specific Languages for Composable Editor Plugins}",
  author = {Lennart C. L. Kats and Karl Trygve Kalleberg and Eelco Visser},
  year = {2010},
  doi = {http://dx.doi.org/10.1016/j.entcs.2010.08.038},
  tags = {C++, domain-specific language},
  researchr = {http://researchr.org/publication/KatsKV10},
  cites = {0},
  citedby = {0},
  journal = {Electronic Notes in Theoretical Computer Science},
  volume = {253},
  number = {7},
  pages = {149-163},
}
@inproceedings{Kats10b,
  title = "{Pure and declarative syntax definition: paradise lost and regained}",
  author = {Lennart C. L. Kats and Eelco Visser and Guido Wachsmuth},
  year = {2010},
  doi = {http://doi.acm.org/10.1145/1869459.1869535},
  researchr = {http://researchr.org/publication/KatsVW10},
  cites = {0},
  citedby = {1},
  pages = {918-932},
  booktitle = {Proceedings of the 25th Annual ACM SIGPLAN Conference on Object-Oriented Programming, Systems, Languages, and Applications, OOPSLA 2010},
  editor = {William R. Cook and Siobhán Clarke and Martin C. Rinard},
  address = {Reno/Tahoe, Nevada},
  publisher = {ACM},
  isbn = {978-1-4503-0203-6},
}
@inproceedings{Vollebregt12,
 author = {Vollebregt, Tobi and Kats, Lennart C. L. and Visser, Eelco},
 title = "{Declarative Specification of Template-based Textual Editors}",
 booktitle = {Proceedings of the Twelfth Workshop on Language Descriptions, Tools, and Applications},
 series = {LDTA '12},
 year = {2012},
 isbn = {978-1-4503-1536-4},
 location = {Tallinn, Estonia},
 pages = {8:1--8:7},
 articleno = {8},
 numpages = {7},
 url = {http://doi.acm.org/10.1145/2427048.2427056},
 doi = {10.1145/2427048.2427056},
 acmid = {2427056},
 publisher = {ACM},
 address = {New York, NY, USA},
}
@article{Heering89,
 author = {Heering, J. and Hendriks, P. R. H. and Klint, P. and Rekers, J.},
 title = "{The Syntax Definition Formalism SDF - Reference Manual}",
 journal = {SIGPLAN Notices},
 issue_date = {Nov. 1989},
 volume = {24},
 number = {11},
 month = nov,
 year = {1989},
 issn = {0362-1340},
 pages = {43--75},
 numpages = {33},
 url = {http://doi.acm.org/10.1145/71605.71607},
 doi = {10.1145/71605.71607},
 acmid = {71607},
 publisher = {ACM},
 address = {New York, NY, USA},
}
@inproceedings{Kats10a,
  title = "The {Spoofax} language workbench: rules for declarative specification of languages and {IDEs}",
  author = {Lennart C. L. Kats and Eelco Visser},
  year = {2010},
  doi = {http://doi.acm.org/10.1145/1869459.1869497},
  researchr = {http://researchr.org/publication/KatsV10},
  cites = {0},
  citedby = {1},
  pages = {444-463},
  booktitle = {Proceedings of the 25th Annual ACM SIGPLAN Conference on Object-Oriented Programming, Systems, Languages, and Applications, OOPSLA 2010},
  editor = {William R. Cook and Siobhán Clarke and Martin C. Rinard},
  address = {Reno/Tahoe, Nevada},
  publisher = {ACM},
  isbn = {978-1-4503-0203-6},
}
@book{Winskel93,
 author = {Glynn Winskel},
 title = {The Formal Semantics of Programming Languages: An Introduction},
 year = {1993},
 isbn = {0-262-23169-7},
 publisher = {MIT Press},
 address = {Cambridge, MA, USA},
}
@incollection{Milner97,
  title={Introduction},
  booktitle={The Definition of Standard ML: Revised},
  author={Robin Milner and Mads Tofte and Robert Harper and David MacQueen},
  isbn={9780262631815},
  lccn={gb97053933},
  chapter={1},
  year={1997},
  publisher={MIT Press}
}
@inproceedings{VerguNV15,
  title = "{DynSem: A DSL for Dynamic Semantics Specification}",
  author = {Vlad A. Vergu and Pierre Neron and Eelco Visser},
  year = {2015},
  doi = {10.4230/LIPIcs.RTA.2015.365},
  url = {http://dx.doi.org/10.4230/LIPIcs.RTA.2015.365},
  researchr = {http://researchr.org/publication/VerguNV15},
  cites = {0},
  citedby = {0},
  pages = {365-378},
  booktitle = {26th International Conference on Rewriting Techniques and Applications, RTA 2015, June 29 to July 1, 2015, Warsaw, Poland},
  editor = {Maribel Fernández},
  volume = {36},
  series = {LIPIcs},
  publisher = {Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik},
  isbn = {978-3-939897-85-9},
}
@article{knuth1984,
  title={Literate programming},
  author={Knuth, Donald Ervin},
  journal={The Computer Journal},
  volume={27},
  number={2},
  pages={97--111},
  year={1984},
  publisher={Br Computer Soc}
}
@article{ipython2007,
  title={IPython: a system for interactive scientific computing},
  author={P{\'e}rez, Fernando and Granger, Brian E},
  journal={Computing in Science \& Engineering},
  volume={9},
  number={3},
  pages={21--29},
  year={2007},
  publisher={AIP Publishing}
}
@article{lepton2012,
  title={Literate program execution for reproducible research and executable papers},
  author={Li-Thiao-T{\'e}, S{\'e}bastien},
  journal={Procedia Computer Science},
  volume={9},
  pages={439--448},
  year={2012},
  publisher={Elsevier}
}
@article{schulte2012,
  title={A multi-language computing environment for literate programming and reproducible research},
  author={Schulte, Eric and Davison, Dan and Dye, Thomas and Dominik, Carsten and others},
  journal={Journal of Statistical Software},
  volume={46},
  number={3},
  pages={1--24},
  year={2012},
  publisher={American Statistical Association}
}
@online{knuth-interview,
  author = {Donald E. Knuth and Andrew Binstock},
  title = {Interview with Donald Knuth},
  year = {2008},
  url = {http://www.informit.com/articles/article.aspx?p=1193856},
  urldate = {2016-04-27}
}
@online{swift-playgrounds,
  author = {Apple Inc.},
  title = {Swift Playgrounds},
  year = {2014},
  url = {http://devstreaming.apple.com/videos/wwdc/2014/408xxcm26svis12/408/408_swift_playgrounds.pdf},
  urldate = {2016-04-27}
}
@online{ipython-execution,
  author = {IPython},
  title = {Execution semantics in the IPython kernel},
  year = {2014},
  url = {http://ipython.readthedocs.io/en/stable/development/execution.html},
  urldate = {2016-05-03}
}
@online{jshell-repl,
  author = {OpenJDK},
  title = {jshell: The Java Shell (Read-Eval-Print Loop)},
  year = {2016},
  url = {http://openjdk.java.net/jeps/222},
  urldate = {2016-05-04}
}
@inproceedings{Gousios14,
  title={An exploratory study of the pull-based software development model},
  author={Gousios, Georgios and Pinzger, Martin and Deursen, Arie van},
  booktitle={Proceedings of the 36th International Conference on Software Engineering},
  pages={345--355},
  year={2014},
  organization={ACM}
}
@online{PythonExecutionModel,
  author = {Python Software Foundation},
  title = {Execution model},
  year = {2016},
  url = {https://docs.python.org/3/reference/executionmodel.html},
  urldate={2016-05-03}
}


text:
@article{liu_background_2015,
 author = {Liu, Xin and Zhao, Guoying and Yao, Jiawen and Qi, Chun},
 copyright = {All rights reserved},
 file = {Full Text:/Users/jiawenyao/Zotero/storage/PUGQQKFW/Liu et al. - 2015 - Background subtraction based on low-rank and struc.pdf:application/pdf;Snapshot:/Users/jiawenyao/Zotero/storage/LZU52CGK/7076585.html:text/html},
 journal = {IEEE Transactions on Image Processing},
 note = {Publisher: IEEE},
 number = {8},
 pages = {2502--2514},
 title = {Background subtraction based on low-rank and structured sparse decomposition},
 volume = {24},
 year = {2015}
}

repository: utayao/academic-kickstart

repo_name: utayao/academic-kickstart


text:
@article{KapurEtAlInreview,
  title = {Equilibrium Calculations for the next Generation of Spatial Assessment Models: Technical and Practical Considerations},
  shorttitle = {Equilibrium Calculations for the next Generation of Spatial Assessment Models},
  author = {Kapur, Maia and Siple, Margaret C. and Olmos, Maxime and {Privatera-Johnson}, Kristin and Adams, Grant D. and Best, John K. and {Castillo-Jord{\'a}n}, Claudio and {Cronin-Fine}, Lee and Havron, Andrea and Lee, Qi and Methot, Richard D.},
  year = {In review},
  abstract = {This paper reviews the challenges and research gaps in calculating reference points from spatially structured stock assessment models used within current fisheries management systems. We discuss methods for US and international fisheries that calculate equilibrium values and associated management quantities for fishery populations with spatial structure. Such fisheries inherently violate the assumption of a single well-mixed stock. Accounting for spatial structure accurately and easily is a major goal for the next generation of stock assessment software development. We propose a new method for calculating equilibrium quantities within a spatially  structured model and compare it to a widely used method (Stock Synthesis) for a set of scenarios. The proposed method aims to reconcile localized recruitment dynamics, which have previously hindered the calculation of equilibrium quantities for fishery populations structured as such. Our results show that the proposed method can respond more precisely to local population dynamics by unmasking localized depletion, a known problem in global-recruitment approaches. Finally, we address areas of research and development needed to integrate spatial models within existing management systems.},
  journal = {Fish. Res.}
}
% == BibTeX quality report for KapurEtAlInreview:
% ? Possibly abbreviated journal title Fish. Res.

gha_language: HTML


text:
# CMake generated Testfile for
# Source directory: G:/NNNNET/poco_1.7.9/poco/Data/samples
# Build directory: G:/NNNNET/poco_1.7.9/poco/buildwin32/Data/samples
#
# This file includes the relevant testing commands required for
# testing this directory and lists subdirectories to be tested as well.
subdirs("Binding")
subdirs("RecordSet")
subdirs("RowFormatter")
subdirs("Tuple")
subdirs("TypeHandler")

extension: cmake


text:
SUMMARY = "Glade - A User Interface Designer"
HOMEPAGE = "http://www.gnu.org/software/gnash"
LICENSE = "GPL-2.0-only & LGPL-2.0-only"
LIC_FILES_CHKSUM = "file://COPYING;md5=aabe87591cb8ae0f3c68be6977bb5522 \
                    file://COPYING.GPL;md5=9ac2e7cff1ddaf48b6eab6028f23ef88 \
                    file://COPYING.LGPL;md5=252890d9eee26aab7b432e8b8a616475"
DEPENDS = "gtk+3 glib-2.0 libxml2 intltool-native \
           gnome-common-native \
           autoconf-archive-native \
"

inherit features_check autotools pkgconfig gnomebase gobject-introspection mime-xdg

# xfce4 depends on libwnck3, gtk+3 and libepoxy need to be built with x11 PACKAGECONFIG.
# cairo would at least needed to be built with xlib.
ANY_OF_DISTRO_FEATURES = "${GTK3DISTROFEATURES}"

SRC_URI = "http://ftp.gnome.org/pub/GNOME/sources/glade/3.22/glade-${PV}.tar.xz \
           file://remove-yelp-help-rules-var.patch \
          "
SRC_URI[md5sum] = "c074fa378c8f1ad80d20133c4ae6f42d"
SRC_URI[sha256sum] = "edefa6eb24b4d15bd52589121dc109bc08c286157c41288deb74dd9cc3f26a21"

EXTRA_OECONF += "--disable-man-pages"

FILES:${PN} += "${datadir}/* ${libdir}/glade/modules/libgladegtk.so"
FILES:${PN}-dev += "${libdir}/glade/modules/libgladegtk.la"
FILES:${PN}-dbg += "${libdir}/glade/modules/.debug/libgladegtk.so"

repository: openembedded/meta-openembedded

repo_name: openembedded/meta-openembedded

gha_language: BitBake

extension: bb


text:
/* ==UserStyle==
@name           Read links green
@namespace      USO Archive
@author         Jack Simpson
@description    `Links to visited sites will be green.`
@version        2019326.19.7
@license        NO-REDISTRIBUTION
@preprocessor   uso
==/UserStyle== */
/*Green:visited -- Mark visited links Green (*DM)*/
/* ===================================================== */
/* David McRitchie,  2009-04-27 installed style 17357*/

@namespace url(http://www.w3.org/1999/xhtml);

a:visited,
.fl:visited
{
  color: #0B610B !important;
}
/* i really want this to be global */

branch_name: refs/heads/flomaster

gha_license_id: NOASSERTION

extension: css


text:
@article{stevens_theory_1946-1,
  title = {On the {{Theory}} of {{Scales}} of {{Measurement}}},
  volume = {103},
  issn = {00368075, 10959203},
  number = {2684},
  journal = {Science},
  author = {Stevens, Stanley S.},
  year = {1946},
  pages = {677-680}
}

@article{gower_general_1971,
  title = {A {{General Coefficient}} of {{Similarity}} and {{Some}} of {{Its Properties}}},
  volume = {27},
  issn = {0006341X},
  language = {en},
  number = {4},
  journal = {Biometrics},
  doi = {10.2307/2528823},
  author = {Gower, J. C.},
  month = dec,
  year = {1971},
  pages = {857},
  file = {/Users/JoseManuel/Documents/GITHUBs/BITSS_ToolsWorkshop/Readings/Gower - 1971 - A General Coefficient of Similarity and Some of It.pdf;/Users/JoseManuel/Documents/GITHUBs/ReproTaller/integrando/Gower - 1971 - A General Coefficient of Similarity and Some of It.pdf}
}

@article{reynolds_clustering_2006,
  title = {Clustering {{Rules}}: {{A Comparison}} of {{Partitioning}} and {{Hierarchical Clustering Algorithms}}},
  volume = {5},
  issn = {1570-1166, 1572-9214},
  shorttitle = {Clustering {{Rules}}},
  language = {en},
  number = {4},
  journal = {Journal of Mathematical Modelling and Algorithms},
  doi = {10.1007/s10852-005-9022-1},
  author = {Reynolds, A. P. and Richards, G. and {de la Iglesia}, B. and {Rayward-Smith}, V. J.},
  month = dec,
  year = {2006},
  pages = {475-504},
  file = {/Users/JoseManuel/Zotero/storage/GT9HDU5L/10.html}
}

@misc{maechler_cluster_2018,
  title = {Cluster: "{{Finding Groups}} in {{Data}}": {{Cluster Analysis Extended Rousseeuw}} et Al.},
  copyright = {GPL-2 | GPL-3 [expanded from: GPL ({$\geq$} 2)]},
  shorttitle = {Cluster},
  author = {Maechler, Martin and {original)}, Peter Rousseeuw (Fortran and {original)}, Anja Struyf (S and {original)}, Mia Hubert (S and {maintenance(1999-2000))}, Kurt Hornik (port to R; and Studer, Matthias and Roudier, Pierre and Gonzalez, Juan and Kozlowski, Kamil},
  month = apr,
  year = {2018},
  keywords = {Cluster,Environmetrics,Multivariate,Robust}
}

repository: escuela-alacip/dataViz

repo_name: escuela-alacip/dataViz


text:
@inproceedings{webservices:budapest,
 address = {Budapest, Hungary},
 author = {Puppin, Diego and Tonellotto, Nicola and Laforenza, Domenico},
 bibmarkers = {GRIN-2017 Classe -- Scopus Cit. 9 Google Cit. 15},
 booktitle = {Proceedings of the $11^th$ EuroPVM/MPI User's Group Meeting},
 doi = {10.1007/978-3-540-30218-6_32},
 isbn = {3-540-23163-3},
 issn = {0302-9743},
 month = {September},
 pages = {207--214},
 publisher = {Springer Verlag},
 series = {Lecture Notes in Computer Science},
 title = {Using Web Services to Run Distributed Numerical Applications},
 volume = {3241},
 year = {2004}
}

repository: khastagir/academic-kickstart

repo_name: khastagir/academic-kickstart


text:
@inproceedings{mulvihill2013lane,
 author = {Mulvihill, Christine and Salmon, Paul and Filtness, Ashleigh and Lenne, Michael and Walker, Guy and Cornelissen, Miranda and Young, Kristie},
 booktitle = {Proceedings of the 2013 Australasian Road Safety Research, Policing and Education Conference:},
 organization = {Australasian College of Road Safety (ACRS)},
 pages = {1--12},
 title = {Lane filtering and situation awareness in motorcyclists: An on-road proof of concept study},
 year = {2013}
}

license: Unlicense,MIT

detected_licenses: Unlicense MIT


text:
SUMMARY = "OpenType text shaping engine"
DESCRIPTION = "HarfBuzz is an implementation of the OpenType Layout engine (aka layout \
engine) and the script-specific logic (aka shaping engine)."
HOMEPAGE = "http://www.freedesktop.org/wiki/Software/HarfBuzz"

# Override value of DEBIAN_GIT_BRANCH variable in debian-package class
DEBIAN_GIT_BRANCH = "stretch-master"

inherit debian-package
PV = "1.4.2"

LICENSE = "MIT"
LIC_FILES_CHKSUM = " \
    file://COPYING;md5=e021dd6dda6ff1e6b1044002fc662b9b \
    file://src/hb-ucdn/COPYING;md5=994ba0f1295f15b4bda4999a5bbeddef \
"

inherit autotools pkgconfig

EXTRA_OECONF = "--with-gobject --enable-static"

PACKAGECONFIG ?= "cairo freetype glib graphite2 icu"
PACKAGECONFIG[cairo] = "--with-cairo=yes, --with-cairo=no, cairo"
PACKAGECONFIG[freetype] = "--with-glib=yes, --with-glib=no, glib-2.0"
PACKAGECONFIG[glib] = "--with-freetype=yes, --with-freetype=no, freetype"
PACKAGECONFIG[graphite2] = "--with-graphite2=yes, --with-graphite2=no, graphite2"
PACKAGECONFIG[icu] = "--with-icu, --without-icu, icu"
PACKAGECONFIG[gtk-doc] = "--enable-gtk-doc,--disable-gtk-doc,gtk-doc"

PACKAGES =+ "libharfbuzz-bin libharfbuzz-icu libharfbuzz-gobject"
FILES_libharfbuzz-bin = "${bindir}/*"
FILES_libharfbuzz-icu = "${libdir}/libharfbuzz-icu${SOLIBS}"
FILES_libharfbuzz-gobject = "${libdir}/libharfbuzz-gobject${SOLIBS}"

BBCLASSEXTEND = "native"

repository: meta-debian/meta-debian-extra

repo_name: meta-debian/meta-debian-extra

branch_name: refs/heads/morty


text:
@font-face {
    font-family: MDL2;
    src: url(../fonts/SegMDL2.ttf)
}

@font-face {
    font-family: Vag;
    src: url(../fonts/vag-world-bold.ttf);
}

* {
    margin: 0;
    padding: 0;
    border: 0;
    vertical-align: baseline
}

html {
    box-sizing: border-box
}

*, *:before, *:after {
    box-sizing: inherit;
    -webkit-touch-callout: none;
    -webkit-user-select: none;
    -khtml-user-select: none;
    -moz-user-select: none;
    -ms-user-select: none;
    user-select: none
}

*::-webkit-scrollbar {
    width: 3px;
    height: 3px
}

*::-webkit-scrollbar-button {
    background-color: #201f1f
}

*::-webkit-scrollbar-track {
    background-color: #999
}

*::-webkit-scrollbar-track-piece {
    background-color: #3d3a3a
}

*::-webkit-scrollbar-thumb {
    height: 50px;
    background-color: #0036ff;
    border-radius: 3px
}

*::-webkit-scrollbar-corner {
    background-color: #999
}

*::-webkit-resizer {
    background-color: #666
}

html, body {
    height: 100%;
    margin: 0
}

body {
    font-family: "Segoe UI", sans-serif;
    background-color: #1c1b1b;
    background-size: cover;
    color: #FFF;
    overflow: hidden;
}

header {
    display: block;
    position: fixed;
    height: 22px;
    width: 100%;
    background: #3d3a3a;
    -webkit-app-region: drag;
    z-index: 1;
}

#window-title {
    grid-column: 1;
    display: flex;
    align-items: center;
    font-size: 12px;
    margin-left: 10px;
    overflow-x: hidden
}

#window-title span {
    overflow: hidden;
    text-overflow: ellipsis;
    line-height: 1.5;
}

#window-controls .button {
    grid-row: 1 / span 1;
    display: flex;
    justify-content: center;
    align-items: center;
    width: 100%;
    height: 100%
}

#settings-button {
    grid-column: 1
}

#min-button {
    grid-column: 1;
}

#max-page-button {
    grid-column: 2
}

#change-button {
    grid-column: 2
}

#close-button {
    grid-column: 3
}

#window-controls {
    -webkit-app-region: no-drag
}

#window-controls .button {
    user-select: none;
    cursor: default;
    color: #BBB
}

#window-controls .button:hover {
    background: rgba(255, 255, 255, 0.2);
    color: #FFF
}

#window-controls #close-button:hover {
    background: #e81123;
    z-index: 1;
}

#window-controls {
    display: grid;
    grid-template-columns: repeat(3, 30px);
    position: absolute;
    top: 0;
    right: 0;
    height: 100%;
    font-family: "MDL2";
    font-size: 10px
}

#settingsBar {
    height: 100%;
    min-width: 230px;
    width: 20%;
    background: #71ffc46b;
    position: absolute;
    margin-top: 22px;
    font-family: Vag;
    z-index: 1;
    overflow: auto;
    padding-bottom: 20px;
}

#settingsBar>div>input, textarea, select {
    width: 80%;
    padding: 5px 15px;
    border-radius: 5px;
    border: 2px solid #0bf7d67d;
    background-color: #00ffff00;
    color: white;
}

#settingsBar>div>textarea {
    margin: 15px 0px 0px;
    min-height: 40px;
    resize: vertical;
    height: 40px;
}

option {
    color: black;
}

span {
    z-index: -1;
}

#categoryList {
    font-family: Vag;
    position: absolute;
    min-width: 180px;
    width: 18%;
    height: 15%;
    background-color: #00ff66b5;
    right: 0px;
    top: 22px;
    z-index: 1;
    overflow: hidden;
    overflow-y: auto;
    transition: opacity 1s;
}

#categoryList:empty {
    opacity: 0;
}

#categoryList>input {
    margin: 0px 10px;
}

#categoryList>span {
    white-space: nowrap;
}

.trueButton {
    background: #00ff2bbf;
    width: 80%;
    margin-top: 15px;
    border-radius: 3px;
}

.trueButton:hover {
    background: #00ff2b;
}

.falseButton {
    background: #ff5e00bf;
    width: 80%;
    margin-top: 15px;
    border-radius: 3px;
}

.falseButton:hover {
    background: #ff5e00;
}

::-webkit-input-placeholder {
    color: #41ff00;
}

#settingsBar>div {
    background-color: #ce00ff66;
    margin-top: 10px;
    padding: 10px 0px;
    text-align: -webkit-center;
}

#settingsBar>span {
    padding-left: 10px;
    font-size: 14px;
}

.element {
    width: 250px;
    height: 180px;
    box-shadow: 0px 0px 20px rgba(0, 255, 255, 0.5);
    border: 1px solid rgba(127, 255, 255, 0.25);
    cursor: default;
    overflow: hidden;
}

.element:hover {
    box-shadow: 0px 0px 20px rgba(0, 255, 255, 0.75);
    border: 1px solid rgba(127, 255, 255, 0.75);
}

.element .number {
    position: absolute;
    top: 20px;
    right: 20px;
    font-size: 20px;
    color: rgba(127, 255, 255, 0.75);
}

.element .symbol {
    position: static;
    top: 40px;
    width: 100%;
    font-size: 40px;
    text-align: center;
    color: rgba(255, 255, 255, 0.75);
    font-weight: bold;
    -webkit-filter: drop-shadow(0px 0px 20px rgba(0, 255, 255, 0.95));
    -moz-filter: drop-shadow(0px 0px 20px rgba(0, 255, 255, 0.95));
    -o-filter: drop-shadow(0px 0px 20px rgba(0, 255, 255, 0.95));
    -ms-filter: drop-shadow(0px 0px 20px rgba(0, 255, 255, 0.95));
    filter: drop-shadow(0px 0px 20px rgba(0, 255, 255, 0.95));
    word-break: break-all;
    max-height: 2.5em;
    overflow: hidden;
}

.element .date {
    color: #ffbd22;
    font-weight: bold;
    font-size: 24px;
    text-align: center;
}

.element .details {
    position: sticky;
    top: 125px;
    width: 100%;
    font-size: 18px;
    text-align: center;
    color: rgba(127, 255, 255, 0.75);
    word-wrap: break-word;
}

input[type=checkbox] {
    position: relative;
    cursor: pointer;
    color: black;
    margin: 5px
}

input[type=checkbox]:before {
    content: "";
    display: block;
    position: absolute;
    width: 16px;
    height: 16px;
    top: 0;
    left: 0;
    border: 1px solid #555555;
    border-radius: 3px;
    background-color: white;
}

input[type=checkbox]:checked:after {
    content: "";
    display: block;
    width: 5px;
    height: 10px;
    border: solid #1880e7;
    border-width: 0 2px 2px 0;
    -webkit-transform: rotate(45deg);
    -ms-transform: rotate(45deg);
    transform: rotate(45deg);
    position: absolute;
    top: 2px;
    left: 6px;
}


text:
@article{quintana2016efficient,
 author = {Quintana, Juan David and Sánchez-Oro, Jesús and Duarte, Abraham},
 journal = {International Journal of Computational Intelligence Systems},
 number = {6},
 pages = {1016--1027},
 publisher = {Taylor & Francis},
 title = {Efficient greedy randomized adaptive search procedure for the generalized regenerator location problem},
 volume = {9},
 year = {2016}
}

repository: jesussanchezoro/academic-kickstart

repo_name: jesussanchezoro/academic-kickstart