text:
seizure focus as well as in distant structures. For this review we have compiled and compared findings from the various techniques to conclude that cognitive impairment in epilepsy results from a network disorder in which the (micro)structures as well as the functionality can be disturbed.},
	language = {eng},
	number = {10},
	journal = {Epilepsia},
	author = {Braakman, Hilde M. H. and van der Kruijs, Sylvie J. M. and Vaessen, Maarten J. and Jansen, Jacobus F. A. and Debeij-van Hall, Mariette H. J. A. and Vles, Johan S. H. and Aldenkamp, Albert P. and Backes, Walter H. and Hofman, Paul A. M.},
	month = oct,
	year = {2012},
	pmid = {22889330},
	keywords = {Humans, Brain, Epilepsy, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Oxygen, Cognition Disorders, PubMed},
	pages = {1690--1699}
}

@article{lu_extension_2012,
	title = {Extension of the intravoxel incoherent motion model to non-gaussian diffusion in head and neck cancer},
	volume = {36},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1522-2586},
	doi = {10.1002/jmri.23770},
	abstract = {PURPOSE: To extend the intravoxel incoherent motion (IVIM) magnetic resonance imaging (MRI) model to restricted diffusion and to simultaneously quantify the perfusion and restricted diffusion parameters in neck nodal metastases.
MATERIALS AND METHODS: The non-gaussian (NG)-IVIM model was developed and tested on diffusion-weighted MRI data collected on a 1.5-Tesla MRI scanner from eight patients with head and neck cancer. Voxel-wise parameter quantification was performed by using a noise-rectified least-square fitting method. The NG-IVIM, IVIM, Kurtosis, and ADC (apparent diffusion coefficient) models were used for comparison. For each voxel, within the metastatic node, the optimal model was determined using the Bayesian Information Criterion. The voxel percentage preferred by each model was calculated and the optimal model map was generated. Monte Carlo simulations were performed to evaluate the accuracy and precision dependency of the new model.
RESULTS: For the eight neck nodes, the range of voxel percentage preferred by the NG-IVIM model was 2.3-79.3\%. The optimal modal maps showed heterogeneities within the tumors. The Monte Carlo simulations demonstrated that the accuracy and precision of the NG-IVIM model improved by increasing signal-to-noise ratio and b value.
CONCLUSION: The NG-IVIM model characterizes perfusion and restricted diffusion simultaneously in neck nodal metastases.},
	language = {eng},
	number = {5},
	journal = {Journal of magnetic resonance imaging: JMRI},
	author = {Lu, Yonggang and Jansen, Jacobus F. A. and Mazaheri, Yousef and Stambuk, Hilda E. and Koutcher, Jason A. and Shukla-Dave, Amita},
	month = nov,
	year = {2012},
	pmid = {22826198},
	pmcid = {PMC3482143},
	keywords = {Female, Humans, Male, Middle Aged, Head and Neck Neoplasms, Algorithms, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Data Interpretation, Statistical, Lymphatic Metastasis, Computer Simulation, Imaging, Three-Dimensional, Least-Squares Analysis, Lymph Nodes, Models, Biological, Models, Statistical, Motion, Normal Distribution},
	pages = {1088--1096}
}

@article{vaessen_abnormal_2013,
	title = {Abnormal modular organization of functional networks in cognitively impaired children with frontal lobe epilepsy},
	volume = {23},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1460-2199},
	doi = {10.1093/cercor/bhs186},
	abstract = {Many children with frontal lobe epilepsy (FLE) have significant cognitive comorbidity, for which the underlying mechanism has not yet been unraveled, but is likely related to disturbed cerebral network integrity. Using resting-state fMRI, we investigated whether cerebral network characteristics are associated with epilepsy and cognitive comorbidity. We included 37 children with FLE and 41 healthy age-matched controls. Cognitive performance was determined by means of a computerized visual searching task. A connectivity matrix for 82 cortical and subcortical brain regions was generated for each subject by calculating the inter-regional correlation of the fMRI time signals. From the connectivity matrix, graph metrics were calculated and the anatomical configuration of aberrant connections and modular organization was investigated. Both patients and controls displayed efficiently organized networks. However, FLE patients displayed a higher modularity, implying that subnetworks are less interconnected. Impaired cognition was associated with higher modularity scores and abnormal modular organization of the brain, which was mainly expressed as a decrease in long-range and an increase in interhemispheric connectivity in patients. We showed that network modularity analysis provides a sensitive marker for cognitive impairment in FLE and suggest that abnormally interconnected functional subnetworks of the brain might underlie the cognitive problems in children with FLE.},
	language = {eng},
	number = {8},
	journal = {Cerebral Cortex (New York, N.Y.: 1991)},
	author = {Vaessen, M. J. and Braakman, H. M. H. and Heerink, J. S. and Jansen, J. F. A. and Debeij-van Hall, M. H. J. A. and Hofman, P. a. M. and Aldenkamp, A. P. and Backes, W. H.},
	month = aug,
	year = {2013},
	pmid = {22772649},
	keywords = {functional MRI, Humans, Adolescent, Brain, Magnetic Resonance Imaging, Child, Cognition Disorders, Nerve Net, epilepsy, Epilepsy, Frontal Lobe, neural networks, cognitive impairment, functional reorganization},
	pages = {1997--2006}
}

@article{besseling_tract_2012,
	title = {Tract specific reproducibility of tractography based morphology and diffusion metrics},
	volume = {7},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0034125},
	abstract = {INTRODUCTION: The reproducibility of tractography is important to determine its sensitivity to pathological abnormalities. The reproducibility of tract morphology has not yet been systematically studied and the recently developed tractography contrast Tract Density Imaging (TDI) has not yet been assessed at the tract specific level.
MATERIALS AND METHODS: Diffusion tensor imaging (DTI) and probabilistic constrained spherical deconvolution (CSD) tractography are performed twice in 9 healthy subjects. Tractography is based on common space seed and target regions and performed for several major white matter tracts. Tractograms are converted to tract segmentations and inter-session reproducibility of tract morphology is assessed using Dice similarity coefficient (DSC). The coefficient of variation (COV) and intraclass correlation coefficient (ICC) are calculated of the following tract metrics: fractional anisotropy (FA), apparent diffusion coefficient (ADC), volume, and TDI. Analyses are performed both for proximal (deep white matter) and extended (including subcortical white matter) tract segmentations.
RESULTS: Proximal DSC values were 0.70-0.92. DSC values were 5-10\% lower in extended compared to proximal segmentations. COV/ICC values of FA, ADC, volume and TDI were 1-4\%/0.65-0.94, 2-4\%/0.62-0.94, 3-22\%/0.53-0.96 and 8-31\%/0.48-0.70, respectively, with the lower COV and higher ICC values found in the proximal segmentations.
CONCLUSION: For all investigated metrics, reproducibility depended on the segmented tract. FA and ADC had relatively low COV and relatively high ICC, indicating clinical potential. Volume had higher COV but its moderate to high ICC values in most tracts still suggest subject-differentiating power. Tract TDI had high COV and relatively low ICC, which reflects unfavorable reproducibility.},
	language = {eng},
	number = {4},
	journal = {PloS One},
	author = {Besseling, René M. H. and Jansen, Jacobus F. A. and Overvliet, Geke M. and Vaessen, Maarten J. and Braakman, Hilde M. H. and Hofman, Paul A. M. and Aldenkamp, Albert P. and Backes, Walter H.},
	year = {2012},
	pmid = {22485157},
	pmcid = {PMC3317780},
	keywords = {Female, Humans, Male, Adult, Young Adult, Diffusion Tensor Imaging, Anisotropy, Reproducibility of Results, Neural Pathways, Brain Stem, Corpus Callosum, Gyrus Cinguli, Motor Cortex, Visual Pathways},
	pages = {e34125}
}

@article{jansen_correlation_2012,
	title = {Correlation of a priori {DCE}-{MRI} and (1){H}-{MRS} data with molecular markers in neck nodal metastases: {Initial} analysis},
	volume = {48},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1879-0593},
	doi = {10.1016/j.oraloncology.2012.02.001},
	abstract = {The aim of the present study is to correlate non-invasive, pretreatment biological imaging (dynamic contrast enhanced-MRI [DCE-MRI] and proton magnetic resonance spectroscopy [(1)H-MRS]) findings with specific molecular marker data in neck nodal metastases of head and neck squamous cell carcinoma (HNSCC) patients. Pretreatment DCE-MRI and (1)H-MRS were performed on neck nodal metastases of 12 patients who underwent surgery. Surgical specimens were analyzed with immunohistochemistry (IHC) assays for: Ki-67 (reflecting cellular proliferation), vascular endothelial growth factor (VEGF) (the "endogenous marker" of tumor vessel growth), carbonic anhydrase (CAIX), hypoxia inducible transcription factor (HIF-1α), and human papillomavirus (HPV). Additionally, necrosis was estimated based on H\&E staining. The Spearman correlation was used to compare DCE-MRI, (1)H-MRS, and molecular marker data. A significant correlation was observed between DCE-MRI parameter std(k(ep)) and VEGF IHC expression level (rho=0.81, p=0.0001). Furthermore, IHC expression levels of Ki-67 inversely correlated with std(K(trans)) and std(v(e)) (rho=-0.71; p=0.004, and rho=-0.73; p=0.003, respectively). Other DCE-MRI, (1)H-MRS and IHC values did not show significant correlation. The results of this preliminary study indicate that the level of heterogeneity of perfusion in metastatic HNSCC seems positively correlated with angiogenesis, and inversely correlated with proliferation. These results are preliminary in nature and are indicative, and not definitive, trends portrayed in HNSCC patients with nodal disease. Future studies with larger patient populations need to be carried out to validate and clarify our preliminary findings.},
	language = {eng},
	number = {8},
	journal = {Oral Oncology},
	author = {Jansen, Jacobus F. A. and Carlson, Diane L. and Lu, Yonggang and Stambuk, Hilda E. and Moreira, Andre L. and Singh, Bhuvanesh and Patel, Snehal G. and Kraus, Dennis H. and Wong, Richard J. and Shaha, Ashok R. and Shah, Jatin P. and Shukla-Dave, Amita},
	month = aug,
	year = {2012},
	pmid = {22366441},
	pmcid = {PMC3368067},
	keywords = {Aged, Female, Humans, Male, Middle Aged, Adult, Magnetic Resonance Imaging, Contrast Media, Magnetic Resonance Spectroscopy, Biomarkers, Tumor, Lymphatic Metastasis, Lymph Nodes, Carbonic Anhydrases, Carcinoma, Squamous Cell, Human papillomavirus 16, Hypoxia-Inducible Factor 1, alpha Subunit, Ki-67 Antigen, Mouth Neoplasms, Neck, Vascular Endothelial Growth Factor A},
	pages = {717--722}
}

@article{van_der_kruijs_functional_2012,
	title = {Functional connectivity of dissociation in patients with psychogenic non-epileptic seizures},
	volume = {83},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1468-330X},
	doi = {10.1136/jnnp-2011-300776},
	abstract = {INTRODUCTION: Psychogenic non-epileptic seizures (PNES) resemble epileptic seizures, but lack epileptiform brain activity. Instead, the cause is assumed to be psychogenic. An abnormal coping strategy may be exhibited by PNES patients, as indicated by their increased tendency to dissociate. Investigation of resting-state networks may reveal altered routes of information and emotion processing in PNES patients. The authors therefore investigated whether PNES patients differ from healthy controls in their resting-state functional connectivity characteristics and whether these connections are associated with the tendency to dissociate.
METHODS: 11 PNES patients without psychiatric comorbidity and 12 healthy controls underwent task-related paradigms (picture-encoding and Stroop paradigms) and resting-state functional MRI (rsfMRI). Global cognitive performance was tested using the Raven's Matrices test and participants completed questionnaires for evaluating dissociation. Functional connectivity analysis on rsfMRI was based on seed regions extracted from task-related fMRI activation maps.
RESULTS: The patients displayed a significantly lower cognitive performance and significantly higher dissociation scores. No significant differences were found between the picture-encoding and Stroop colour-naming activation maps between controls and patients with PNES. However, functional connectivity maps from the rsfMRI were statistically different. For PNES patients, stronger connectivity values between areas involved in emotion (insula), executive control (inferior frontal gyrus and parietal cortex) and movement (precentral sulcus) were observed, which were significantly associated with dissociation scores.
CONCLUSION: The abnormal, strong functional connectivity in PNES patients provides a neurophysiological correlate for the underlying psychoform and somatoform dissociation mechanism where emotion can influence executive control, resulting in altered motor function (eg, seizure-like episodes).},
	language = {eng},
	number = {3},
	journal = {Journal of Neurology, Neurosurgery, and Psychiatry},
	author = {van der Kruijs, Sylvie J. M. and Bodde, Nynke M. G. and Vaessen, Maarten J. and Lazeron, Richard H. C. and Vonck, Kristl and Boon, Paul and Hofman, Paul A. M. and Backes, Walter H. and Aldenkamp, Albert P. and Jansen, Jacobus F. A.},
	month = mar,
	year = {2012},
	pmid = {22056967},
	keywords = {Female, Humans, Male, Middle Aged, Adolescent, Adult, Brain, Electroencephalography, Magnetic Resonance Imaging, Young Adult, Case-Control Studies, Executive Function, Neuropsychological Tests, Seizures, Emotions, Psychophysiologic Disorders, Dissociative Disorders, Neural Pathways, Functional Neuroimaging, Stroop Test},
	pages = {239--247}
}

@article{vaessen_white_2012,
	title = {White matter network abnormalities are associated with cognitive decline in chronic epilepsy},
	volume = {22},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1460-2199},
	doi = {10.1093/cercor/bhr298},
	abstract = {Patients with chronic epilepsy frequently display cognitive comorbidity and might have widespread network abnormalities outside the epileptic zone, which might affect a variety of cognitive functions and global intelligence. We aimed to study the role of white matter connectivity in cognitive comorbidity. Thirty-nine patients with nonsymptomatic localization-related epilepsy and varying degrees of cognitive impairment and 23 age-matched healthy controls were included. Whole brain white matter networks were constructed from fiber tractography. Weighted graph theoretical analysis was performed to study white matter network abnormalities associated with epilepsy and cognition. Patients with severe cognitive impairment showed lower clustering (a measure of brain network segregation) and higher path length (a measure of brain network integration) compared with the healthy controls and patients with little or no cognitive impairment, whereas whole brain white matter volume did not differ. Correlation analyses revealed that IQ and cognitive impairment were strongly associated with clustering and path lengths. This study revealed impaired white matter connectivity, associated with cognitive comorbidity in patients with chronic epilepsy. As whole brain white matter volumes were preserved in the patient group, our results suggest an important role for the network topology rather than volumetric changes, in epilepsy with cognitive decline.},
	language = {eng},
	number = {9},
	journal = {Cerebral Cortex (New York, N.Y.: 1991)},
	author = {Vaessen, Maarten J. and Jansen, Jacobus F. A. and Vlooswijk, Marielle C. G. and Hofman, Paul A. M. and Majoie, H. J. Marian and Aldenkamp, Albert P. and Backes, Walter H.},
	month = sep,
	year = {2012},
	pmid = {22038907},
	keywords = {Female, Humans, Male, Adult, Brain, Epilepsy, Image Interpretation, Computer-Assisted, Cognition Disorders, Diffusion Tensor Imaging, Nerve Fibers, Myelinated, Neural Pathways, Chronic Disease},
	pages = {2139--2147}
}

@article{overvliet_correlation_2011,
	title = {Correlation between language impairment and problems in motor development in children with rolandic epilepsy},
	volume = {22},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1525-5069},
	doi = {10.1016/j.yebeh.2011.08.012},
	abstract = {OBJECTIVE: An association between impaired school performance and rolandic epilepsy is frequently reported. Language outcome, in particular, seems to be affected, although rolandic epilepsy originates from the motor-sensory cortex. In this study we tried to find a correlation between locomotion problems and language impairment.
METHODS: In this noncontrolled, open, clinical cohort study of 48 children with rolandic epilepsy, a 24-hour EEG and a neuropsychological assessment were obtained for all children.
RESULTS: Children with rolandic epilepsy had a significant delay in reading skills (reading words: mean=6 months, SD=11.9, P{\textless}0.002; reading sentences: mean=8.6 months, SD=12.7, P{\textless}0.001), compared with the healthy population. There was a significant correlation between problems in motor development and delays in reading skills (reading words: r=-0.426, P=0.006; reading sentences: r=-0.343, P=0.03).
CONCLUSION: Reading performance is impaired in children with rolandic epilepsy. Reading of sentences is more impaired than reading of words. There is a significant correlation between problems in motor development and language, suggesting their interaction at the level of the cortex.},
	language = {eng},
	number = {3},
	journal = {Epilepsy \& Behavior: E\&B},
	author = {Overvliet, Geke M. and Aldenkamp, Albert P. and Klinkenberg, Sylvia and Nicolai, Joost and Vles, Johan S. H. and Besseling, René M. H. and Backes, Walter and Jansen, Jacobus F. A. and Hofman, Paul A. and Hendriksen, Jos},
	month = nov,
	year = {2011},
	pmid = {21937281},
	keywords = {Female, Humans, Male, Electroencephalography, Retrospective Studies, Neuropsychological Tests, Child, Epilepsy, Rolandic, Statistics as Topic, Achievement, Gait Disorders, Neurologic, Language Development Disorders, Psychiatric Status Rating Scales, Reading, Statistics, Nonparametric},
	pages = {527--531}
}

@article{vlooswijk_loss_2011,
	title = {Loss of network efficiency associated with cognitive decline in chronic epilepsy},
	volume = {77},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1526-632X},
	doi = {10.1212/WNL.0b013e31822cfc2f},
	abstract = {OBJECTIVE: To study the relation between possibly altered whole brain topology and intellectual decline in chronic epilepsy, a combined study of neurocognitive assessment and graph theoretical network analysis of fMRI was performed.
METHODS: Forty-one adult patients with cryptogenic localization-related epilepsy and 23 healthy controls underwent an intelligence test and fMRI with a silent-word generation paradigm. A set of undirected graphs was constructed by cross-correlating the signal time series of 893 cortical and subcortical regions. Possible changes in cerebral network efficiency were assessed by performing graph theoretical network analysis.
RESULTS: Healthy subjects displayed efficient small world properties, characterized by high clustering and short path lengths. On the contrary, in patients with epilepsy a disruption of both local segregation and global integration was found. An association of more pronounced intellectual decline with more disturbed local segregation was observed in the patient group. The effect of antiepileptic drug use on cognitive decline was mediated by decreased clustering.
CONCLUSIONS: These findings support the hypothesis that chronic localization-related epilepsy causes cognitive deficits by inducing global cerebral network changes instead of a localized disruption only. Whether this is the result of epilepsy per se or the use of antiepileptic drugs remains to be elucidated. For application in clinical practice, future studies should address the relevance of altered cerebral network topology in prediction of cognitive deficits and monitoring of therapeutic interventions.},
	language = {eng},
	number = {10},
	journal = {Neurology},
	author = {Vlooswijk, M. C. G. and Vaessen, M. J. and Jansen, J. F. A. and de Krom, M. C. F. T. M. and Majoie, H. J. M. and Hofman, P. a. M. and Aldenkamp, A. P. and Backes, W. H.},
	month = sep,
	year = {2011},
	pmid = {21832213},
	keywords = {Female, Humans, Male, Middle Aged, Adolescent, Adult, Magnetic Resonance Imaging, Young Adult, Anticonvulsants, Cognition Disorders, Nerve Net, Chronic Disease, Epilepsies, Partial, Intelligence Tests},
	pages = {938--944}
}

@article{vlooswijk_memory_2011,
	title = {Memory processes and prefrontal network dysfunction in cryptogenic epilepsy},
	volume = {52},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1528-1167},
	doi = {10.1111/j.1528-1167.2011.03108.x},
	abstract = {PURPOSE: Impaired memory performance is the most frequently reported cognitive problem in patients with chronic epilepsy. To examine memory deficits many studies have focused on the role of the mesiotemporal lobe, mostly with hippocampal abnormalities. However, the role of the prefrontal brain remains unresolved. To investigate the neuronal correlates of working memory dysfunction in patients without structural lesions, a combined study of neurocognitive assessment, hippocampal and cerebral volumetry, and functional magnetic resonance imaging of temporal and frontal memory networks was performed.
METHODS: Thirty-six patients with cryptogenic localization-related epilepsy and 21 healthy controls underwent neuropsychological assessment of intelligence (IQ) and memory. On T(1) -weighted images obtained by 3-Tesla magnetic resonance imaging (MRI), volumetry of the hippocampi and the cerebrum was performed. Functional MRI (fMRI) was performed with a novel picture encoding and Sternberg paradigm that activated different memory-mediating brain regions. Functional connectivity analysis comprised cross-correlation of signal time-series of the most strongly activated regions involved in working memory function.
KEY FINDINGS: Patients with epilepsy displayed lower IQ values; impaired transient aspects of information processing, as indicated by lower scores on the digit-symbol substitution test (DSST); and decreased short-term memory performance relative to healthy controls, as measured with the Wechsler Adult Intelligence Scale subtests for working memory, and word and figure recognition. This could not be related to any hippocampal volume changes. No group differences were found regarding volumetry or fMRI-derived functional activation. In the Sternberg paradigm, a network involving the anterior cingulate and the middle and inferior frontal gyrus was activated. A reduced strength of four connections in this prefrontal network was associated with the DSST and word recognition performance in the patient group.
SIGNIFICANCE: Deficits in the processes involved in transient working memory, and to a lesser extent in short-term memory, in patients with localization-related epilepsy of both temporal and extratemporal origin cannot be attributed to hippocampal atrophy or function only, but are also related to reduced functional connectivity in the prefrontal brain. Because patients with symptomatic lesions or mesiotemporal sclerosis were excluded from this study, the results cannot be explained by structural lesions. Therefore, the current findings highlight the influence of epilepsy on the prefrontal network integrity as a possible underlying problem of memory impairment.},
	language = {eng},
	number = {8},
	journal = {Epilepsia},
	author = {Vlooswijk, Marielle C. G. and Jansen, Jacobus F. A. and Jeukens, Cécile R. L. P. N. and Majoie, H. J. Marian and Hofman, Paul A. M. and de Krom, Marc C. T. F. M. and Aldenkamp, Albert P. and Backes, Walter H.},
	month = aug,
	year = {2011},
	pmid = {21635235},
	keywords = {Female, Humans, Male, Adult, Brain, Epilepsy, Magnetic Resonance Imaging, Case-Control Studies, Memory, Cognition Disorders, Hippocampus, Nerve Net, Intelligence, Organ Size, Prefrontal Cortex},
	pages = {1467--1475}
}

@article{shukla-dave_dynamic_2012,
	title = {Dynamic contrast-enhanced magnetic resonance imaging as a predictor of outcome in head-and-neck squamous cell carcinoma patients with nodal metastases},
	volume = {82},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1879-355X},
	doi = {10.1016/j.ijrobp.2011.03.006},
	abstract = {PURPOSE: Dynamic contrast-enhanced MRI (DCE-MRI) can provide information regarding tumor perfusion and permeability and has shown prognostic value in certain tumors types. The goal of this study was to assess the prognostic value of pretreatment DCE-MRI in head and neck squamous cell carcinoma (HNSCC) patients with nodal disease undergoing chemoradiation therapy or surgery.
METHODS AND MATERIALS: Seventy-four patients with histologically proven squamous cell carcinoma and neck nodal metastases were eligible for the study. Pretreatment DCE-MRI was performed on a 1.5T MRI. Clinical follow-up was a minimum of 12 months. DCE-MRI data were analyzed using the Tofts model. DCE-MRI parameters were related to treatment outcome (progression-free survival [PFS] and overall survival [OS]). Patients were grouped as no evidence of disease (NED), alive with disease (AWD), dead with disease (DOD), or dead of other causes (DOC). Prognostic significance was assessed using the log-rank test for single variables and Cox proportional hazards regression for combinations of variables.
RESULTS: At last clinical follow-up, for Stage III, all 12 patients were NED. For Stage IV, 43 patients were NED, 4 were AWD, 11 were DOD, and 4 were DOC. K(trans) is volume transfer constant. In a stepwise Cox regression, skewness of K(trans) (volume transfer constant) was the strongest predictor for Stage IV patients (PFS and OS: p {\textless}0.001).
CONCLUSION: Our study shows that skewness of K(trans) was the strongest predictor of PFS and OS in Stage IV HNSCC patients with nodal disease. This study suggests an important role for pretreatment DCE-MRI parameter K(trans) as a predictor of outcome in these patients.},
	language = {eng},
	number = {5},
	journal = {International Journal of Radiation Oncology, Biology, Physics},
	author = {Shukla-Dave, Amita and Lee, Nancy Y. and Jansen, Jacobus F. A. and Thaler, Howard T. and Stambuk, Hilda E. and Fury, Matthew G. and Patel, Snehal G. and Moreira, Andre L. and Sherman, Eric and Karimi, Sasan and Wang, Ya and Kraus, Dennis and Shah, Jatin P. and Pfister, David G. and Koutcher, Jason A.},
	month = apr,
	year = {2012},
	pmid = {21601373},
	pmcid = {PMC3177034},
	keywords = {Aged, Aged, 80 and over, Female, Humans, Male, Middle Aged, Adult, Follow-Up Studies, Magnetic Resonance Imaging, Retrospective Studies, Contrast Media, Treatment Outcome, Analysis of Variance, Lymphatic Metastasis, Carcinoma, Squamous Cell, Mouth Neoplasms, Statistics, Nonparametric, Chemoradiotherapy, Disease-Free Survival, Gadolinium DTPA, Neoplasm Staging, Oropharyngeal Neoplasms, Proportional Hazards Models},
	pages = {1837--1844}
}

@article{jansen_tumor_2012,
	title = {Tumor metabolism and perfusion in head and neck squamous cell carcinoma: pretreatment multimodality imaging with 1H magnetic resonance spectroscopy, dynamic contrast-enhanced {MRI}, and [18F]{FDG}-{PET}},
	volume = {82},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1879-355X},
	doi = {10.1016/j.ijrobp.2010.11.022},
	abstract = {PURPOSE: To correlate proton magnetic resonance spectroscopy ((1)H-MRS), dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), and (18)F-labeled fluorodeoxyglucose positron emission tomography ([(18)F]FDG PET) of nodal metastases in patients with head and neck squamous cell carcinoma (HNSCC) for assessment of tumor biology. Additionally, pretreatment multimodality imaging was evaluated for its efficacy in predicting short-term response to treatment.
METHODS AND MATERIALS: Metastatic neck nodes were imaged with (1)H-MRS, DCE-MRI, and [(18)F]FDG PET in 16 patients with newly diagnosed HNSCC, before treatment. Short-term patient radiological response was evaluated at 3 to 4 months. Correlations among (1)H-MRS (choline concentration relative to water [Cho/W]), DCE-MRI (volume transfer constant [K(trans)]; volume fraction of the extravascular extracellular space [v(e)]; and redistribution rate constant [k(ep)]), and [(18)F]FDG PET (standard uptake value [SUV] and total lesion glycolysis [TLG]) were calculated using nonparametric Spearman rank correlation. To predict short-term responses, logistic regression analysis was performed.
RESULTS: A significant positive correlation was found between Cho/W and TLG (ρ = 0.599; p = 0.031). Cho/W correlated negatively with heterogeneity measures of standard deviation std(v(e)) (ρ = -0.691; p = 0.004) and std(k(ep)) (ρ = -0.704; p = 0.003). Maximum SUV (SUVmax) values correlated strongly with MRI tumor volume (ρ = 0.643; p = 0.007). Logistic regression indicated that std(K(trans)) and SUVmean were significant predictors of short-term response (p {\textless} 0.07).
CONCLUSION: Pretreatment multimodality imaging using (1)H-MRS, DCE-MRI, and [(18)F]FDG PET is feasible in HNSCC patients with nodal metastases. Additionally, combined DCE-MRI and [(18)F]FDG PET parameters were predictive of short-term response to treatment.},
	language = {eng},
	number = {1},
	journal = {International Journal of Radiation Oncology, Biology, Physics},
	author = {Jansen, Jacobus F. A. and Schöder, Heiko and Lee, Nancy Y. and Stambuk, Hilda E. and Wang, Ya and Fury, Matthew G. and Patel, Snehal G. and Pfister, David G. and Shah, Jatin P. and Koutcher, Jason A. and Shukla-Dave, Amita},
	month = jan,
	year = {2012},
	pmid = {21236594},
	pmcid = {PMC3137671},
	keywords = {Aged, Female, Humans, Male, Middle Aged, Adult, Magnetic Resonance Imaging, Contrast Media, Magnetic Resonance Spectroscopy, Head and Neck Neoplasms, Prospective Studies, Lymphatic Metastasis, Carcinoma, Squamous Cell, Statistics, Nonparametric, Chemoradiotherapy, Gadolinium DTPA, Antibodies, Monoclonal, Humanized, Antineoplastic Agents, Bevacizumab, Choline, Cisplatin, Diagnostic Imaging, Extracellular Space, Feasibility Studies, Fluorodeoxyglucose F18, Fluorouracil, Glucose, Glycolysis, Nasopharyngeal Neoplasms, Positron-Emission Tomography, Radiopharmaceuticals, Regression Analysis, Tongue Neoplasms, Tonsillar Neoplasms},
	pages = {299--307}
}

@article{vlooswijk_functional_2010,
	title = {Functional {MRI} in chronic epilepsy: associations with cognitive impairment},
	volume = {9},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1474-4465},
	doi = {10.1016/S1474-4422(10)70180-0},
	abstract = {Chronic epilepsy is frequently accompanied by serious cognitive side-effects. Clinical factors are important, but cannot account entirely for this cognitive comorbidity. Therefore, research is focusing on the underlying cerebral mechanisms to understand the development of cognitive dysfunction. In the past two decades, functional MRI techniques have been applied extensively to the study of cognitive impairment in chronic epilepsy. However, because of wide variation in study designs, analysis methods, and data presentation, interpretation of these studies has become increasingly difficult for clinicians. In patients with localisation-related epilepsy, whether findings of functional MRI represent the underlying neuronal substrate for cognitive decline remains a subject of debate.},
	language = {eng},
	number = {10},
	journal = {The Lancet. Neurology},
	author = {Vlooswijk, Marielle Cg and Jansen, Jacobus Fa and de Krom, Marc Cftm and Majoie, Hj Marian and Hofman, Paul Am and Backes, Walter H. and Aldenkamp, Albert P.},
	month = oct,
	year = {2010},
	pmid = {20708970},
	keywords = {Humans, Epilepsy, Magnetic Resonance Imaging, Cognition Disorders, Animals, Chronic Disease},
	pages = {1018--1027}
}

@article{vlooswijk_functional_2010-1,
	title = {Functional connectivity and language impairment in cryptogenic localization-related epilepsy},
	volume = {75},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1526-632X},
	doi = {10.1212/WNL.0b013e3181ebdd3e},
	abstract = {BACKGROUND: An often underestimated cognitive morbidity in patients with epilepsy is language dysfunction. To investigate the neuronal mechanisms underlying neuropsychological language impairment, activation maps and functional connectivity networks were studied by fMRI of language.
METHOD: Fifty-two patients with cryptogenic localization-related epilepsy and 27 healthy controls underwent neuropsychological assessment of IQ, word fluency, and text reading. fMRI was performed with a standard covert word-generation and text-reading paradigm. Functional connectivity analysis comprised cross-correlation of signal time series of the characteristic and most strongly activated regions involved in the language tasks.
RESULTS: After careful selection, 34 patients and 20 healthy controls were found eligible for analysis. Patients displayed lower IQ, lower fluency word count, and lower number of words correctly read compared to controls. fMRI activation maps did not differ significantly between patients and controls. For the word-generation paradigm, patients with epilepsy had significantly lower functional connectivity than controls in the prefrontal network. Patients performing worse on the word-fluency test demonstrated a significantly lower mean functional connectivity than controls. Text reading demonstrated lower functional connectivity in patients with epilepsy in the frontotemporal network. Similarly, lower mean functional connectivity was observed in patients with lowest reading performance compared to controls. A relation between reduced functional connectivity and performance on word-fluency and text-reading tests was demonstrated in epilepsy patients.
CONCLUSION: Impaired performance on language assessment in epilepsy patients is associated with loss of functional connectivity in the cognitive language networks.},
	language = {eng},
	number = {5},
	journal = {Neurology},
	author = {Vlooswijk, M. C. G. and Jansen, J. F. A. and Majoie, H. J. M. and Hofman, P. a. M. and de Krom, M. C. T. F. M. and Aldenkamp, A. P. and Backes, W. H.},
	month = aug,
	year = {2010},
	pmid = {20679633},
	keywords = {Female, Humans, Male, Middle Aged, Adolescent, Adult, Brain, Magnetic Resonance Imaging, Young Adult, Brain Mapping, Case-Control Studies, Language, Neuropsychological Tests, Language Tests, Language Disorders, Neural Pathways, Reading, Epilepsies, Partial, Intelligence Tests, Intelligence, Signal Processing, Computer-Assisted},
	pages = {395--402}
}

@article{jansen_non-invasive_2010,
	title = {Non-invasive imaging of angiogenesis in head and neck squamous cell carcinoma},
	volume = {13},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1573-7209},
	doi = {10.1007/s10456-010-9167-z},
	abstract = {Squamous cell carcinoma of the head and neck (HNSCC) is the seventh most common cancer in the United States. Angiogenesis, the process by which new blood vessels are formed, is an essential element at the basis of both tumor growth and metastases. This review discusses pertinent aspects of the role of imaging modalities in assessing angiogenesis and anti-angiogenic therapy in advanced HNSCC.},
	language = {eng},
	number = {2},
	journal = {Angiogenesis},
	author = {Jansen, Jacobus F. A. and Koutcher, Jason A. and Shukla-Dave, Amita},
	month = jun,
	year = {2010},
	pmid = {20383743},
	pmcid = {PMC2912423},
	keywords = {Humans, Head and Neck Neoplasms, Neovascularization, Pathologic, Animals, Carcinoma, Squamous Cell, Diagnostic Imaging},
	pages = {149--160}
}

@article{vaessen_effect_2010,
	title = {The effect and reproducibility of different clinical {DTI} gradient sets on small world brain connectivity measures},
	volume = {51},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1095-9572},
	doi = {10.1016/j.neuroimage.2010.03.011},
	abstract = {Advances in computational network analysis have enabled the characterization of topological properties in large scale networks including the human brain. Information on structural networks in the brain can be obtained in-vivo by performing tractography on diffusion tensor imaging (DTI) data. However, little is known about the reproducibility of network properties derived from whole brain tractography data, which has important consequences for minimally detectable abnormalities or changes over time. Moreover, acquisition parameters, such as the number of gradient directions and gradient strength, possibly influence network metrics and the corresponding reproducibility derived from tractography data. The aim of the present study is twofold: (i) to determine the effect of several clinically available DTI sampling schemes, differing in number of gradient directions and gradient amplitude, on small world metrics and (ii) to evaluate the interscan reproducibility of small world metrics. DTI experiments were conducted on six healthy volunteers scanned twice. Probabilistic tractography was performed to reconstruct structural connections between regions defined from an anatomical atlas. The observed reproducibility of the network measures was high, reflected by low values for the coefficient of variation ({\textless}3.8\%), advocating the use of graph theoretical measurements to study neurological diseases. Small world metrics were dependent on the choice of DTI gradient scheme and showed stronger connectivity with increasing directional resolution. The interscan reproducibility was not dependent on the gradient scheme. These findings should be considered when comparing results across studies using different gradient schemes or designing new studies.},
	language = {eng},
	number = {3},
	journal = {NeuroImage},
	author = {Vaessen, M. J. and Hofman, P. a. M. and Tijssen, H. N. and Aldenkamp, A. P. and Jansen, J. F. A. and Backes, W. H.},
	month = jul,
	year = {2010},
	pmid = {20226864},
	keywords = {Diffusion Magnetic Resonance Imaging, Female, Humans, Male, Adult, Brain, Image Interpretation, Computer-Assisted, Nerve Net, Algorithms, Image Enhancement, Reproducibility of Results, Sensitivity and Specificity, Neural Pathways},
	pages = {1106--1116}
}

@article{jansen_non-gaussian_2010,
	title = {Non-gaussian analysis of diffusion-weighted {MR} imaging in head and neck squamous cell carcinoma: {A} feasibility study},
	volume = {31},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1936-959X},
	doi = {10.3174/ajnr.A1919},
	abstract = {BACKGROUND AND PURPOSE: Water in biological structures often displays non-Gaussian diffusion behavior. The objective of this study was to test the feasibility of non-Gaussian fitting by using the kurtosis model of the signal intensity decay curves obtained from DWI by using an extended range of b-values in studies of phantoms and HNSCC.
MATERIALS AND METHODS: Seventeen patients with HNSCC underwent DWI by using 6 b-factors (0, 50-1500 s/mm(2)) at 1.5T. Monoexponential (yielding ADC(mono)) and non-Gaussian kurtosis (yielding apparent diffusion coefficient D(app) and apparent kurtosis coefficient K(app)) fits were performed on a voxel-by-voxel basis in selected regions of interest (primary tumors, metastatic lymph nodes, and spinal cord). DWI studies were also performed on phantoms containing either water or homogenized asparagus. To determine whether the kurtosis model provided a significantly better fit than did the monoexponential model, an F test was performed. Spearman correlation coefficients were calculated to assess correlations between K(app) and D(app).
RESULTS: The kurtosis model fit the experimental data points significantly better than did the monoexponential model (P {\textless} .05). D(app) was approximately twice the value of ADC(mono) (eg, in neck nodal metastases D(app) was 1.54 and ADC(mono) was 0.84). K(app) showed a weak Spearman correlation with D(app) in a homogenized asparagus phantom and for 44\% of tumor lesions.
CONCLUSIONS: The use of kurtosis modeling to fit DWI data acquired by using an extended b-value range in HNSCC is feasible and yields a significantly better fit of the data than does monoexponential modeling. It also provides an additional parameter, K(app), potentially with added value.},
	language = {eng},
	number = {4},
	journal = {AJNR. American journal of neuroradiology},
	author = {Jansen, J. F. A. and Stambuk, H. E. and Koutcher, J. A. and Shukla-Dave, A.},
	month = apr,
	year = {2010},
	pmid = {20037133},
	pmcid = {PMC2854270},
	keywords = {Aged, Aged, 80 and over, Diffusion Magnetic Resonance Imaging, Female, Humans, Male, Middle Aged, Adult, Image Processing, Computer-Assisted, Algorithms, Lymphatic Metastasis, Normal Distribution, Carcinoma, Squamous Cell, Feasibility Studies, Otorhinolaryngologic Neoplasms, Phantoms, Imaging, Software, Spinal Cord},
	pages = {741--748}
}

@article{colon_mrs-lateralisation_2010,
	title = {{MRS}-lateralisation index in patients with epilepsy and focal cortical dysplasia or a {MEG}-focus using bilateral single voxels},
	volume = {89},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1872-6844},
	doi = {10.1016/j.eplepsyres.2009.11.007},
	abstract = {PURPOSE: To evaluate if single voxel proton magnetic resonance spectroscopy (SV-MRS) can help in lateralising and sometimes in localizing an epileptogenic focus. The assumption is that in MRI negative patients the underlying pathology most often is focal cortical dysplasia (FCD). Several studies have shown that in the presence of FCD there are also (1)H-MRS abnormalities on the contralateral side. However, in most cases the studied group was not homogeneous and included different forms of dysplasias, including band heterotopias and polymicrogyria, and the studies used different spectroscopy protocols. In the present study, using bilateral SV-MRS we investigated the presence of a lateralisation index in two groups of patients with localisation related epilepsy: patients with focal cortical dysplasia on MRI and patients without MRI abnormalities with a focus identified by MEG. Aim of the study was to show that in both groups the expected epileptogenic side shows more pronounced metabolic alterations, making MRS a possible screening tool for clarifying lateralisation questions in patients with cryptogenic localisation related epilepsy.
METHODS: In ten patients a single voxel was placed over the FCD and in nine patients over the region of interest (ROI) as indicated by MEG. In all patients a voxel was also placed in the contralateral homologus location. We used metabolite concentrations as peak ratios relative to the creatine (Cr) peak to calculate a lateralisation index.
RESULTS: In both groups NAA/Cr was significantly lower on the affected side whereas the results for Cho/Cr were more diverse. There were no significant differences between the two groups. The limitations of the used methods and the implications of the findings are discussed.},
	language = {eng},
	number = {1},
	journal = {Epilepsy Research},
	author = {Colon, A. J. and Hofman, P. and Ossenblok, P. P. W. and Jansen, J. F. A. and Ter Beek, L. C. and Berting, R. and Stam, C. J. and Boon, P.},
	month = mar,
	year = {2010},
	pmid = {20022471},
	keywords = {Aged, Female, Humans, Male, Middle Aged, Adult, Brain, Epilepsy, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Brain Mapping, Malformations of Cortical Development, Magnetic Resonance Spectroscopy, Diagnosis, Differential, Functional Laterality, Magnetoencephalography},
	pages = {148--153}
}

@article{van_den_biggelaar_complementary_2010,
	title = {Complementary and alternative medicine in alopecia areata},
	volume = {11},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1175-0561},
	doi = {10.2165/11530040-000000000-00000},
	abstract = {Alopecia areata is an unpredictable hair-loss condition. As there is no cure for alopecia areata and no effective conventional therapy, a substantial number of alopecia areata patients resort to complementary and alternative medical remedies and therapies (CAM). This review on the application of CAM in alopecia areata addresses two pertinent aspects. First, it provides a current overview of the published medical literature on CAM used in alopecia areata, and alopecia areata-related studies. Second, it presents a thorough assessment of the considerations and limitations of the use of CAM for the treatment of alopecia areata. A systematic MEDLINE search yielded 13 studies of the clinical use of CAM in the management of alopecia areata, all belonging to one of the five main categories of CAM. Methodological quality was analyzed using objective assessment scores (Wilson and Lawrence scores). Unfortunately, no study was of sufficient internal validity to provide robust evidence of the benefit of CAM. This might be attributable to several specific disease characteristics of alopecia areata, which require an especially solid trial design to properly assess the therapeutic effects of CAM. The review concludes with some recommendations for improving the quality of trials incorporating CAM in the treatment of alopecia areata.},
	language = {eng},
	number = {1},
	journal = {American Journal of Clinical Dermatology},
	author = {van den Biggelaar, Frank J. H. M. and Smolders, Joost and Jansen, Jacobus F. A.},
	year = {2010},
	pmid = {20000871},
	keywords = {Humans, Treatment Outcome, Alopecia Areata, Complementary Therapies, Evidence-Based Medicine, Practice Guidelines as Topic},
	pages = {11--20}
}

@article{jansen_noninvasive_2010,
	title = {Noninvasive assessment of tumor microenvironment using dynamic contrast-enhanced magnetic resonance imaging and 18F-fluoromisonidazole positron emission tomography imaging in neck nodal metastases},
	volume = {77},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1879-355X},
	doi = {10.1016/j.ijrobp.2009.07.009},
	abstract = {PURPOSE: To assess noninvasively the tumor microenvironment of neck nodal metastases in patients with head-and-neck cancer by investigating the relationship between tumor perfusion measured using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and hypoxia measured by (18)F-fluoromisonidazole ((18)F-FMISO) positron emission tomography (PET).
METHODS AND MATERIALS: Thirteen newly diagnosed head-and-neck cancer patients with metastatic neck nodes underwent DCE-MRI and (18)F-FMISO PET imaging before chemotherapy and radiotherapy. The matched regions of interests from both modalities were analyzed. To examine the correlations between DCE-MRI parameters and standard uptake value (SUV) measurements from (18)F-FMISO PET, the nonparametric Spearman correlation coefficient was calculated. Furthermore, DCE-MRI parameters were compared between nodes with (18)F-FMISO uptake and nodes with no (18)F-FMISO uptake using Mann-Whitney U tests.
RESULTS: For the 13 patients, a total of 18 nodes were analyzed. The nodal size strongly correlated with the (18)F-FMISO SUV (rho = 0.74, p {\textless} 0.001). There was a strong negative correlation between the median k(ep) (redistribution rate constant) value (rho = -0.58, p = 0.042) and the (18)F-FMISO SUV. Hypoxic nodes (moderate to severe (18)F-FMISO uptake) had significantly lower median K(trans) (volume transfer constant) (p = 0.049) and median k(ep) (p = 0.027) values than did nonhypoxic nodes (no (18)F-FMISO uptake).
CONCLUSION: This initial evaluation of the preliminary results support the hypothesis that in metastatic neck lymph nodes, hypoxic nodes are poorly perfused (i.e., have significantly lower K(trans) and k(ep) values) compared with nonhypoxic nodes.},
	language = {eng},
	number = {5},
	journal = {International Journal of Radiation Oncology, Biology, Physics},
	author = {Jansen, Jacobus F. A. and Schöder, Heiko and Lee, Nancy Y. and Wang, Ya and Pfister, David G. and Fury, Matthew G. and Stambuk, Hilda E. and Humm, John L. and Koutcher, Jason A. and Shukla-Dave, Amita},
	month = aug,
	year = {2010},
	pmid = {19906496},
	pmcid = {PMC2888682},
	keywords = {Aged, Aged, 80 and over, Female, Humans, Male, Middle Aged, Magnetic Resonance Imaging, Retrospective Studies, Head and Neck Neoplasms, Lymphatic Metastasis, Lymph Nodes, Carcinoma, Squamous Cell, Statistics, Nonparametric, Positron-Emission Tomography, Radiopharmaceuticals, Cell Hypoxia, Misonidazole},
	pages = {1403--1410}
}

@article{jeukens_hippocampal_2009,
	title = {Hippocampal {MRI} volumetry at 3 {Tesla}: reliability and practical guidance},
	volume = {44},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1536-0210},
	doi = {10.1097/RLI.0b013e3181b4c180},
	abstract = {OBJECTIVES: Although volumetry of the hippocampus is considered to be an established technique, protocols reported in literature are not described in great detail. This article provides a complete and detailed protocol for hippocampal volumetry applicable to T1-weighted magnetic resonance (MR) images acquired at 3 Tesla, which has become the standard for structural brain research.
MATERIALS AND METHODS: The protocol encompasses T1-weighted image acquisition at 3 Tesla, anatomic guidelines for manual hippocampus delineation, requirements of delineation software, reliability measures, and criteria to assess and ensure sufficient reliability. Moreover, the validity of the correction for total intracranial volume size was critically assessed. The protocol was applied by 2 readers to the MR images of 36 patients with cryptogenic localization-related epilepsy, 4 patients with unilateral hippocampal sclerosis, and 20 healthy control subjects.
RESULTS: The uncorrected hippocampal volumes were 2923 +/- 500 mm3 (mean +/- SD) (left) and 3120 +/- 416 mm3 (right) for the patient group and 3185 +/- 411 mm3 (left) and 3302 +/- 411 mm3 (right) for the healthy control group. The volume of the 4 pathologic hippocampi of the patients with unilateral hippocampal sclerosis was 2980 +/- 422 mm3. The inter-reader reliability values were determined: intraclass-correlation-coefficient (ICC) = 0.87 (left) and 0.86 (right), percentage volume difference (VD) = 7.0 +/- 4.7\% (left) and 6.0 +/- 3.8\% (right), and overlap ratio (OR) = 0.82 +/- 0.04 (left) and 0.82 +/- 0.03 (right). The positive Pearson correlation between hippocampal volume and total intracranial volume was found to be low: r = 0.48 (P = 0.03, left) and r = 0.62 (P = 0.004, right) and did not significantly reduce the volumetric variances, showing the limited benefit of the brain size correction.
CONCLUSIONS: A protocol was described to determine hippocampal volumes based on 3 Tesla MR images with high inter-reader reliability. Although the reliability of hippocampal volumetry at 3 Tesla was similar to the literature values obtained at 1.5 Tesla, hippocampal border definition is argued to be more confident and easier because of the improved signal-to-noise characteristics.},
	language = {eng},
	number = {9},
	journal = {Investigative Radiology},
	author = {Jeukens, Cécile R. L. P. N. and Vlooswijk, Mariëlle C. G. and Majoie, H. J. Marian and de Krom, Marc C. T. F. M. and Aldenkamp, Albert P. and Hofman, Paul A. M. and Jansen, Jacobus F. A. and Backes, Walter H.},
	month = sep,
	year = {2009},
	pmid = {19692839},
	keywords = {Female, Humans, Middle Aged, Adult, Epilepsy, Magnetic Resonance Imaging, Image Interpretation, Computer-Assisted, Hippocampus, Algorithms, Image Enhancement, Reproducibility of Results, Sensitivity and Specificity, Imaging, Three-Dimensional},
	pages = {509--517}
}

@article{tijssen_assessing_2009,
	title = {Assessing and minimizing the effects of noise and motion in clinical {DTI} at 3 {T}},
	volume = {30},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1097-0193},
	doi = {10.1002/hbm.20695},
	abstract = {Compared with conventional MRI, diffusion tensor imaging (DTI) is more prone to thermal noise and motion. Optimized sampling schemes have been proposed that reduce the propagation of noise. At 3 T, however, motion may play a more dominant role than noise. Although the effects of noise at 3 T are less compared with 1.5 T because of the higher signal-to-noise ratio, motion is independent of field strength and will persist. To improve the reliability of clinical DTI at 3 T, it is important to know to what extent noise and motion contribute to the uncertainties of the DTI indices. In this study, the effects of noise- and motion-related signal uncertainties are disentangled using in vivo measurements and computer simulations. For six clinically standard available sampling schemes, the reproducibility was assessed in vivo, with and without motion correction applied. Additionally, motion and noise simulations were performed to determine the relative contributions of motion and noise to the uncertainties of the mean diffusivity (MD) and fractional anisotropy (FA). It is shown that the contributions of noise and motion are of the same order of magnitude at 3 T. Similar to the propagation of noise, the propagation of motion-related signal perturbations is also influenced by the choice of sampling scheme. Sampling schemes with only six diffusion directions demonstrated a lower reproducibility compared with schemes with 15 and 32 directions and feature a positive bias for the FA in relatively isotropic tissue. Motion correction helps improving the precision and accuracy of DTI indices.},
	language = {eng},
	number = {8},
	journal = {Human Brain Mapping},
	author = {Tijssen, Rob H. N. and Jansen, Jacobus F. A. and Backes, Walter H.},
	month = aug,
	year = {2009},
	pmid = {19086023},
	keywords = {Diffusion Magnetic Resonance Imaging, Female, Humans, Male, Adult, Brain, Young Adult, Algorithms, Anisotropy, Reproducibility of Results, Computer Simulation, Motion, Artifacts, Monte Carlo Method, Uncertainty},
	pages = {2641--2655}
}

@article{jansen_statin_2008,
	title = {Statin therapy and cognitive deficits associated with neurofibromatosis type 1},
	volume = {300},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1538-3598},
	doi = {10.1001/jama.2008.687},
	language = {eng},
	number = {20},
	journal = {JAMA},
	author = {Jansen, Jacobus F. A.},
	month = nov,
	year = {2008},
	pmid = {19033585},
	keywords = {Humans, Cognition, Child, Animals, Disease Models, Animal, Hydroxymethylglutaryl-CoA Reductase Inhibitors, Mice, Mice, Neurologic Mutants, Neurofibromatosis 1, Simvastatin},
	pages = {2369; author reply 2369--2370}
}

@article{jansen_short-_2008,
	title = {Short- and long-term limbic abnormalities after experimental febrile seizures},
	volume = {32},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1095-953X},
	doi = {10.1016/j.nbd.2008.07.010},
	abstract = {Experimental febrile seizures (FS) are known to promote hyperexcitability of the limbic system and increase the risk for eventual temporal lobe epilepsy (TLE). Early markers of accompanying microstructural and metabolic changes may be provided by in vivo serial MRI. FS were induced in 9-day old rats by hyperthermia. Quantitative multimodal MRI was applied 24 h and 8 weeks later, in rats with FS and age-matched controls, and comprised hippocampal volumetry and proton spectroscopy, and cerebral T2 relaxometry and diffusion tensor imaging (DTI). At 9 weeks histology was performed. Hippocampal T2 relaxation time elevations appeared to be transient. DTI abnormalities detected in the amygdala persisted up to 8 weeks. Hippocampal volumes were not affected. Histology showed increased fiber density and anisotropy in the hippocampus, and reduced neuronal surface area in the amygdala. Quantitative serial MRI is able to detect transient, and most importantly, long-term FS-induced changes that reflect microstructural alterations.},
	language = {eng},
	number = {2},
	journal = {Neurobiology of Disease},
	author = {Jansen, Jacobus F. A. and Lemmens, Evi M. P. and Strijkers, Gustav J. and Prompers, Jeanine J. and Schijns, Olaf E. M. G. and Kooi, M. Eline and Beuls, Emile A. M. and Nicolay, Klaas and Backes, Walter H. and Hoogland, Govert},
	month = nov,
	year = {2008},
	pmid = {18707002},
	keywords = {Diffusion Magnetic Resonance Imaging, Follow-Up Studies, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Magnetic Resonance Spectroscopy, Hippocampus, Animals, Neural Pathways, Disease Models, Animal, Hyperthermia, Induced, Protons, Rats, Rats, Sprague-Dawley, Seizures, Febrile, Time Factors},
	pages = {293--301}
}

@article{jansen_comment_2008,
	title = {Comment on "{Magnetic} resonance spectroscopy identifies neural progenitor cells in the live human brain"},
	volume = {321},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1095-9203},
	doi = {10.1126/science.1153997},
	abstract = {Manganas et al. (Reports, 9 November 2007, p. 980) reported the discovery of a biomarker specific for neural progenitor cells detectable using magnetic resonance spectroscopy. A new algorithm was developed to extract the biomarker from noisy in vivo data. We question how this algorithm was validated, because the biomarker overlaps with peaks from nonspecific lipid signals.},
	language = {eng},
	number = {5889},
	journal = {Science (New York, N.Y.)},
	author = {Jansen, Jacobus F. A. and Gearhart, John D. and Bulte, Jeff W. M.},
	month = aug,
	year = {2008},
	pmid = {18669846},
	keywords = {Humans, Brain, Magnetic Resonance Spectroscopy, Animals, Biomarkers, Algorithms, Mice, Embryonic Stem Cells, Lipids, Neurons, Stem Cells},
	pages = {640}
}

@article{jansen_white_2008,
	title = {White matter lesions in patients with localization-related epilepsy},
	volume = {43},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1536-0210},
	doi = {10.1097/RLI.0b013e31817e90d2},
	abstract = {OBJECTIVES: White matter lesions (WML) have been proven to be associated with cognitive impairment. As (1) the decline of cognitive function is the most frequent comorbid disorder in epilepsy, and (2) patients with epilepsy have a relatively high prevalence of WML, the question is raised whether WML in patients with epilepsy are also associated with cognitive decline.
MATERIALS AND METHODS: A high-resolution magnetic resonance imaging examination was performed at 3.0 T, comprising T1-weighted, T2 relaxometry, and fluid-attenuated inversion recovery (FLAIR) sequences. Patients with localization-related epilepsy with impaired and unimpaired cognitive functioning and a healthy control group were included. Furthermore, the performance of an automated WML detection algorithm, based on regional intensity evaluation, was assessed.
RESULTS: The prevalence of WML, detected on 3.0 T FLAIR images, is 63\% in healthy volunteers and 46\% in patients with localization-related, cryptogenic epilepsy. No relationship between WML volume and cognitive performance was observed. The WML volumes from the automated segmentation method were found to be significantly correlated to the volumes obtained by neuroradiologic assessment.
CONCLUSIONS: No relations could be found between WML and cognition in the well-defined population of patients with epilepsy. Other clinical characteristics of chronic epilepsy, such as seizures, age of onset, and medication are more likely to play an important role in cognitive decline. Furthermore, the automated WML detection algorithm using a regional Z-score analysis can successfully segment and quantify the WML on FLAIR images.},
	language = {eng},
	number = {8},
	journal = {Investigative Radiology},
	author = {Jansen, Jacobus F. A. and Vlooswijk, Marielle C. G. and Majoie, Hj Marian and de Krom, Marc C. T. F. M. and Aldenkamp, Albert P. and Hofman, Paul A. M. and Backes, Walter H.},
	month = aug,
	year = {2008},
	pmid = {18648254},
	keywords = {Female, Humans, Male, Middle Aged, Adult, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Neuropsychological Tests, Cognition Disorders, Algorithms, Epilepsies, Partial},
	pages = {552--558}
}

@article{jansen_cognitive_2008,
	title = {Cognitive {fMRI} and soluble telencephalin assessment in patients with localization-related epilepsy},
	volume = {118},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1600-0404},
	doi = {10.1111/j.1600-0404.2008.01005.x},
	abstract = {Objectives - The use of telencephalin as a possible marker for altered cortical function as demonstrated by functional MRI was investigated in a pilot study with 16 patients with localization-related epilepsy and secondarily generalized seizures. Materials and methods - Functional MRI of verbal working memory performance (Sternberg paradigm) and self-regulatory control processes (Stroop paradigm) was used to examine cortical activation in 16 patients with localization-related epilepsy and secondarily generalized seizures. Additionally, blood serum concentrations of soluble telencephalin (marker for neuronal damage) were determined. Results - In three patients (one temporal and two frontal focus), telencephalin was detected. All three patients had lower functional MRI activation in the frontotemporal region (P = 0.04), but not in other regions (P {\textgreater} 0.35) compared with patients without detectable telencephalin. Additionally, an association of levetiracetam and frontotemporal activation was observed. Conclusions - These preliminary data in a heterogeneous group suggest an association between decreased frontotemporal activation on fMRI and both detectable telencephalin serum levels and levetiracetam use. Future longitudinal studies with larger patient groups are required to confirm these observations. It is hypothesized that altered local function of the frontotemporal cortex in localization-related epilepsy might be better predicted by the biochemical marker telencephalin than epilepsy characteristics such as seizure focus.},
	language = {eng},
	number = {4},
	journal = {Acta Neurologica Scandinavica},
	author = {Jansen, J. F. A. and Vlooswijk, M. C. G. and de Baets, M. H. and de Krom, M. C. T. F. M. and Rieckmann, P. and Backes, W. H. and Aldenkamp, A. P. and {SEGAED Study Group}},
	month = oct,
	year = {2008},
	pmid = {18460045},
	keywords = {Female, Humans, Male, Middle Aged, Adult, Brain, Magnetic Resonance Imaging, Neuropsychological Tests, Pilot Projects, Anticonvulsants, Biomarkers, Epilepsies, Partial, Cell Adhesion Molecules, Nerve Tissue Proteins, Piracetam},
	pages = {232--239}
}

@article{vlooswijk_cognitive_2008,
	title = {Cognitive {fMRI} and neuropsychological assessment in patients with secondarily generalized seizures},
	volume = {110},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {0303-8467},
	doi = {10.1016/j.clineuro.2008.01.007},
	abstract = {OBJECTIVES: Cognitive dysfunction is a frequent comorbid disorder in epilepsy which has been associated with high seizure frequency. We examined the effect of secondarily generalized tonic-clonic seizures (SGTCS) on cognitive dysfunction using neuropsychological assessment and fMRI.
PATIENTS AND METHODS: Sixteen patients with localization-related epilepsy of varying etiologies and SGTCS underwent extensive neuropsychological assessment. Functional MRI was performed probing the frontal and temporal lobes with two paradigms aimed at investigating speed of mental processing and working memory.
RESULTS: A high number of total lifetime SGTCS was associated with lower intelligence scores. Moreover, a trend towards cognitive decline related to the number of SGTCS was observed. A relatively increased prefrontal activation related to the number of SGTCS was demonstrated, plus a trend towards a decreased activation in the frontotemporal areas.
CONCLUSION: High numbers of SGTCS are associated with a drop in intelligence scores and altered prefrontal brain activation. A shift from frontotemporal to prefrontal activation seems to have occurred, suggesting that a functional reorganization of working memory is induced by a high number of SGTCS. It remains uncertain if this reorganization reflects a compensation mechanism, or the underlying pathological processes of cognitive dysfunction.},
	language = {eng},
	number = {5},
	journal = {Clinical Neurology and Neurosurgery},
	author = {Vlooswijk, Marielle C. G. and Jansen, Jacobus F. A. and Reijs, Rianne P. and de Krom, Marc C. T. F. M. and Kooi, M. Eline and Majoie, H. J. Marian and Hofman, Paul A. M. and Backes, Walter H. and Aldenkamp, Albert P.},
	month = may,
	year = {2008},
	pmid = {18339478},
	keywords = {Female, Humans, Male, Middle Aged, Adult, Magnetic Resonance Imaging, Linear Models, Brain Mapping, Neuropsychological Tests, Seizures, Cognition Disorders, Frontal Lobe, Intelligence Tests, Prefrontal Cortex, Epilepsy, Tonic-Clonic, Memory, Short-Term, Problem Solving, Temporal Lobe},
	pages = {441--450}
}

@article{langers_enhanced_2007,
	title = {Enhanced signal detection in neuroimaging by means of regional control of the global false discovery rate},
	volume = {38},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1053-8119},
	doi = {10.1016/j.neuroimage.2007.07.031},
	abstract = {In the context of neuroimaging experiments, it is essential to account for the multiple comparisons problem when thresholding statistical mappings. Various methods are in use to deal with this issue, but they differ in their signal detection power for small- and large-scale effects. In this paper, we comprehensively describe a new method that is based on control of the false discovery rate (FDR). Our method increases sensitivity by exploiting the spatially clustered nature of neuroimaging effects. This is achieved by using a sliding window technique, in which FDR-control is first applied at a regional level. Thus, a new statistical map that is related to the regionally achieved FDR is derived from the available voxelwise P-values. On the basis of receiver operating characteristic (ROC) curves, thresholding based on this map is demonstrated to have better discriminatory power than conventional thresholding based on P-values. Secondly, it is shown that the resulting maps can be thresholded at a level that results in control of the global FDR. By means of statistical arguments and numerical simulations under widely varying conditions, our method is validated, characterized, and compared to some other common voxel-based methods (uncorrected thresholding, Bonferroni correction, and conventional FDR-control). It is found that our method shows considerably higher sensitivity as compared to conventional FDR-control, while still controlling the achieved FDR at the same level or better. Finally, our method is applied to two diverse neuroimaging experiments to assess its practical merits, resulting in substantial improvements as compared to the other methods.},
	language = {eng},
	number = {1},
	journal = {NeuroImage},
	author = {Langers, Dave R. M. and Jansen, Jacobus F. A. and Backes, Walter H.},
	month = oct,
	year = {2007},
	pmid = {17825583},
	keywords = {Female, Humans, Male, Adult, Brain, Magnetic Resonance Imaging, Image Interpretation, Computer-Assisted, Brain Mapping, Algorithms, Image Enhancement, Reproducibility of Results, Sensitivity and Specificity, Signal Processing, Computer-Assisted, Evoked Potentials, False Positive Reactions},
	pages = {43--56}
}

@article{jansen_reproducibility_2007,
	title = {Reproducibility of quantitative cerebral {T}2 relaxometry, diffusion tensor imaging, and 1H magnetic resonance spectroscopy at 3.0 {Tesla}},
	volume = {42},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {0020-9996},
	doi = {10.1097/01.rli.0000262757.10271.e5},
	abstract = {OBJECTIVES: The reproducibility of quantitative cerebral T2 relaxometry, diffusion tensor imaging, and H magnetic resonance (MR) spectroscopic imaging was assessed on a clinical 3.0 T MR system.
MATERIALS AND METHODS: Repeated measurements in 10 healthy volunteers were used to establish the reproducibility of quantitative measures derived from different quantitative MR techniques, namely the T2 relaxation time, the apparent diffusion coefficient (ADC), the fractional anisotropy (FA), and metabolite concentrations of N-acetyl-aspartate (NAA), creatine (Cr), choline (Cho), and myo-inositol (mI). Results were compared with previously reported reproducibility measures from 1.5 T.
RESULTS: The coefficient of variation (CV) was {\textless} or =1.6\% for T2, {\textless} or =1.6\% for ADC, and {\textless} or =5.3\%, for FA in the cerebrum. For metabolites the CV was {\textless} or =8.0\% in the frontal lobe and {\textless} or =20.4\% in the temporal lobe.
CONCLUSIONS: The reproducibility of quantitative brain MRI at 3.0 T is better than or at least comparable to the reproducibility at 1.5 T.},
	language = {eng},
	number = {6},
	journal = {Investigative Radiology},
	author = {Jansen, Jacobus F. A. and Kooi, M. Eline and Kessels, Alfons G. H. and Nicolay, Klaas and Backes, Walter H.},
	month = jun,
	year = {2007},
	pmid = {17507802},
	keywords = {Diffusion Magnetic Resonance Imaging, Female, Humans, Male, Adult, Image Processing, Computer-Assisted, Brain Mapping, Magnetic Resonance Spectroscopy, Anisotropy, Reproducibility of Results, Data Interpretation, Statistical, Choline, Aspartic Acid, Brain Chemistry, Creatine, Inositol, Reference Values},
	pages = {327--337}
}

@article{jansen_1h_2006,
	title = {1H {MR} spectroscopy of the brain: absolute quantification of metabolites},
	volume = {240},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {0033-8419},
	doi = {10.1148/radiol.2402050314},
	abstract = {Hydrogen 1 (1H) magnetic resonance (MR) spectroscopy enables noninvasive in vivo quantification of metabolite concentrations in the brain. Currently, metabolite concentrations are most often presented as ratios (eg, relative to creatine) rather than as absolute concentrations. Despite the success of this approach, it has recently been suggested that relative quantification may introduce substantial errors and can lead to misinterpretation of spectral data and to erroneous metabolite values. The present review discusses relevant methods to obtain absolute metabolite concentrations with a clinical MR system by using single-voxel spectroscopy or chemical shift imaging. Important methodological aspects in an absolute quantification strategy are addressed, including radiofrequency coil properties, calibration procedures, spectral fitting methods, cerebrospinal fluid content correction, macromolecule suppression, and spectral editing. Techniques to obtain absolute concentrations are now available and can be successfully applied in clinical practice. Although the present review is focused on 1H MR spectroscopy of the brain, a large part of the methodology described can be applied to other tissues as well.},
	language = {eng},
	number = {2},
	journal = {Radiology},
	author = {Jansen, Jacobus F. A. and Backes, Walter H. and Nicolay, Klaas and Kooi, M. Eline},
	month = aug,
	year = {2006},
	pmid = {16864664},
	keywords = {Humans, Brain, Magnetic Resonance Spectroscopy, Statistics as Topic, Signal Processing, Computer-Assisted, Brain Chemistry, Calibration},
	pages = {318--332},
	file = {06_jansen_radiology.pdf:/home/jaap/Zotero/storage/A8TTCEWE/06_jansen_radiology.pdf:application/pdf}
}

@article{jansen_stem_2006,
	title = {Stem cell profiling by nuclear magnetic resonance spectroscopy},
	volume = {56},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {0740-3194},
	doi = {10.1002/mrm.20968},
	abstract = {The classification of embryonic and adult stem cells, including their derivatives, is still limited, and often these cells are best defined by their functional properties. Recent gene array studies have yielded contradictory results. Also, very little is known about the metabolic properties of these exciting cells. In this study, proton (1H) NMR spectroscopy was used to identify the major low-molecular-weight metabolites in murine embryonic stem cells (ESC) and their neural stem cell (NSC) derivatives. ESC are characterized by an unusually low number of NMR-detectable metabolites, high phosphocholine (PC) content, and nondetectable glycerophosphocholine (GPC). The metabolic profiles of NSC resemble glial cells and oligodendrocyte progenitors, but with considerably higher PC, GPC, and myo-inositol content. The results suggest that NMR spectroscopy in vitro can provide markers to study the effects of differentiation on cell metabolism, and potentially to assess stem cell preparations for differentiation status.},
	language = {eng},
	number = {3},
	journal = {Magnetic Resonance in Medicine},
	author = {Jansen, Jacobus F. A. and Shamblott, Michael J. and van Zijl, Peter C. M. and Lehtimäki, Kimmo K. and Bulte, Jeff W. M. and Gearhart, John D. and Hakumäki, Juhana M.},
	month = sep,
	year = {2006},
	pmid = {16858672},
	keywords = {Magnetic Resonance Spectroscopy, Animals, Mice, Neurons, Stem Cells, Cell Line, Phosphorylcholine},
	pages = {666--670}
}

@article{jansen_functional_2006,
	title = {Functional {MRI} reveals declined prefrontal cortex activation in patients with epilepsy on topiramate therapy},
	volume = {9},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {1525-5050},
	doi = {10.1016/j.yebeh.2006.05.004},
	abstract = {Functional magnetic resonance imaging of covert word generation was used to examine brain activation abnormalities associated with topiramate-induced cognitive language impairment in patients with epilepsy. Compared with a control epilepsy group, in the topiramate-treated group, there was significantly less activation in the language-mediating regions of the prefrontal cortex; the topiramate group also had significantly lower neuropsychological language scores. These findings suggest that topiramate has a critical effect on the cerebral neural systems that mediate expressive language.},
	language = {eng},
	number = {1},
	journal = {Epilepsy \& Behavior: E\&B},
	author = {Jansen, Jacobus F. A. and Aldenkamp, Albert P. and Marian Majoie, H. J. and Reijs, Rianne P. and de Krom, Marc C. T. F. M. and Hofman, Paul A. M. and Eline Kooi, M. and Nicolay, Klaas and Backes, Walter H.},
	month = aug,
	year = {2006},
	pmid = {16793345},
	keywords = {Female, Humans, Male, Adult, Epilepsy, Magnetic Resonance Imaging, Neuropsychological Tests, Anticonvulsants, Cognition, Language Disorders, Prefrontal Cortex, Fructose},
	pages = {181--185}
}

@article{van_ingen_extension_2004,
	title = {Extension of the binding motif of the {Sin}3 interacting domain of the {Mad} family proteins},
	volume = {43},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {0006-2960},
	doi = {10.1021/bi0355645},
	abstract = {Sin3 forms the scaffold for a multiprotein corepressor complex that silences transcription via the action of histone deacetylases. Sin3 is recruited to the DNA by several DNA binding repressors, such as the helix-loop-helix proteins of the Mad family. Here, we elaborate on the Mad-Sin3 interaction based on a binding study, solution structure, and dynamics of the PAH2 domain of mSin3 in complex to an extended Sin3 interacting domain (SID) of 24 residues of Mad1. We show that SID residues Met7 and Glu23, outside the previously defined minimal binding motif, mediate additional hydrophobic and electrostatic interactions with PAH2. On the basis of these results we propose an extended consensus sequence describing the PAH2-SID interaction specifically for the Mad family, showing that residues outside the hydrophobic core of the SID interact with PAH2 and modulate binding affinity to appropriate levels.},
	language = {eng},
	number = {1},
	journal = {Biochemistry},
	author = {van Ingen, Hugo and Lasonder, Edwin and Jansen, Jacobus F. A. and Kaan, Anita M. and Spronk, Christian A. E. M. and Stunnenberg, Henk G. and Vuister, Geerten W.},
	month = jan,
	year = {2004},
	pmid = {14705930},
	keywords = {Humans, Animals, Amino Acid Motifs, Amino Acid Sequence, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Caenorhabditis elegans Proteins, Conserved Sequence, Crystallography, X-Ray, DNA-Binding Proteins, Fungal Proteins, Histone Deacetylases, Membrane Proteins, Molecular Sequence Data, Multigene Family, Nuclear Magnetic Resonance, Biomolecular, Protein Binding, Protein Structure, Tertiary, Repressor Proteins, Saccharomyces cerevisiae Proteins, Sequence Alignment, Sequence Homology, Amino Acid, Solutions, Surface Plasmon Resonance, Thermodynamics, Transcription Factors},
	pages = {46--54}
}

@article{spronk_sequence-specific_2001,
	title = {Sequence-specific assignment of the {PAH}2 domain of {Sin}3B free and bound to {Mad}1},
	volume = {19},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	issn = {0925-2738},
	language = {eng},
	number = {4},
	journal = {Journal of biomolecular NMR},
	author = {Spronk, C. A. and Jansen, J. F. and Tessari, M. and Kaan, A. M. and Aelen, J. and Lasonder, E. and Stunnenberg, H. G. and Vuister, G. W.},
	month = apr,
	year = {2001},
	pmid = {11370785},
	keywords = {Magnetic Resonance Spectroscopy, Animals, Mice, Amino Acid Sequence, Molecular Sequence Data, Protein Structure, Tertiary, Repressor Proteins, Sequence Homology, Amino Acid, Transcription Factors, Cell Cycle Proteins, Chromatin, Nuclear Proteins, Phosphoproteins, Protein Conformation},
	pages = {377--378}
}

@article{spronk_mad1-sin3b_2000,
	title = {The {Mad}1-{Sin}3B interaction involves a novel helical fold},
	volume = {7},
	copyright = {All rights reserved},
	issn = {1072-8368},
	doi = {10.1038/81944},
	abstract = {Sin3A or Sin3B are components of a corepressor complex that mediates repression by transcription factors such as the helix-loop-helix proteins Mad and Mxi. Members of the Mad/Mxi family of repressors play important roles in the transition between proliferation and differentiation by down-regulating the expression of genes that are activated by the proto-oncogene product Myc. Here, we report the solution structure of the second paired amphipathic helix (PAH) domain (PAH2) of Sin3B in complex with a peptide comprising the N-terminal region of Mad1. This complex exhibits a novel interaction fold for which we propose the name 'wedged helical bundle'. Four alpha-helices of PAH2 form a hydrophobic cleft that accommodates an amphipathic Mad1 alpha-helix. Our data further show that, upon binding Mad1, secondary structure elements of PAH2 are stabilized. The PAH2-Mad1 structure provides the basis for determining the principles of protein interaction and selectivity involving PAH domains.},
	language = {eng},
	number = {12},
	journal = {Nature Structural Biology},
	author = {Spronk, C. A. and Tessari, M. and Kaan, A. M. and Jansen, J. F. and Vermeulen, M. and Stunnenberg, H. G. and Vuister, G. W.},
	month = dec,
	year = {2000},
	pmid = {11101889},
	keywords = {Humans, Animals, Mice, Amino Acid Sequence, Conserved Sequence, Molecular Sequence Data, Nuclear Magnetic Resonance, Biomolecular, Protein Binding, Protein Structure, Tertiary, Repressor Proteins, Sequence Alignment, Solutions, Transcription Factors, Cell Cycle Proteins, Nuclear Proteins, Phosphoproteins, Binding Sites, Carrier Proteins, Models, Molecular, Protein Structure, Secondary, Substrate Specificity},
	pages = {1100--1104}
}

@article{kruijs_sjm_autonomic_2014,
	title = {Autonomic {Nervous} {System} {Functioning} {Associated} with {Epileptic} {Seizures}: {Analysis} of {Heart} {Rate} {Variability}},
	volume = {05},
	issn = {21559562},
	shorttitle = {Autonomic {Nervous} {System} {Functioning} {Associated} with {Epileptic} {Seizures}},
	url = {https://www.omicsonline.org/open-access/autonomic-nervous-system-functioning-associated-with-epileptic-seizures-analysis-of-heart-rate-variability-2155-9562-5-1000215.php?aid=30282},
	doi = {10.4172/2155-9562.1000215},
	number = {04},
	urldate = {2017-09-02},
	journal = {Journal of Neurology \& Neurophysiology},
	author = {Kruijs SJM, van der},
	year = {2014}
}

@article{jansen_multimodal_2015,
	title = {Multimodal {MRI} {Reveals} {Secondarily} {Generalized} {Seizure} {Related} {Abnormalities} at 1.5 {T}: {Preliminary} {Findings}},
	issn = {23332395},
	shorttitle = {Multimodal {MRI} {Reveals} {Secondarily} {Generalized} {Seizure} {Related} {Abnormalities} at 1.5 {T}},
	url = {http://www.ibimapublishing.com/journals/JMED/2015/397761/397761.html},
	doi = {10.5171/2015.397761},
	urldate = {2017-09-02},
	journal = {JMED Research},
	author = {Jansen, Jacobus and Vlooswijk, Mariëlle and {Department of Neurology, Maastricht University Medical Centre, Maastricht, the Netherlands} and Reijs, Rianne and {Department of Neurology, Maastricht University Medical Centre, Maastricht, the Netherlands} and Majoie, H.J. and {Department of Neurology, Maastricht University Medical Centre, Maastricht, the Netherlands} and Hofman, Paul and {Department of Radiology, Maastricht University Medical Centre, Maastricht, the Netherlands} and Aldenkamp, Albert and {Department of Neurology, Maastricht University Medical Centre, Maastricht, the Netherlands} and Backes, Walter and {Department of Radiology, Maastricht University Medical Centre, Maastricht, the Netherlands}},
	month = oct,
	year = {2015},
	pages = {1--16}
}

@article{backes_blood-brain_2017,
	title = {Blood-{Brain} {Barrier} {Leakage} in {Early} {Alzheimer} {Disease}},
	volume = {282},
	issn = {0033-8419, 1527-1315},
	url = {http://pubs.rsna.org/doi/10.1148/radiol.2017162578},
	doi = {10.1148/radiol.2017162578},
	language = {en},
	number = {3},
	urldate = {2017-09-02},
	journal = {Radiology},
	author = {Backes, Walter H. and van Osch, Matthias J. P. and van de Haar, Harm J. and Jansen, Jacobus F. A.},
	month = mar,
	year = {2017},
	pages = {923--925}
}

@article{barendse_working_2017,
	title = {Working memory network alterations in high-functioning adolescents with an autism spectrum disorder},
	issn = {1440-1819},
	doi = {10.1111/pcn.12602},
	abstract = {AIM: People with autism spectrum disorder (ASD) typically have deficits in the working memory (WM) system. Working memory is found to be an essential chain in successfully navigating in the social world. We hypothesize that brain networks for WM have an altered network integrity in ASD compared to controls.
METHODS: 13 adolescents (1 female) with autistic disorder (n = 1), Asperger's disorder (n = 7), and pervasive developmental disorder not otherwise specified (n = 5), and 13 typically developing control adolescents (1 female) participated in this study. Functional MRI was performed using an n-back task and in resting state.
RESULTS: The analysis of the behavioral data revealed deficits in working memory performance in ASD, but only when tested to the limit. Adolescents with ASD showed lower binary global efficiency in the working memory network than the control group with n-back and resting state data. This correlated with diagnostic scores for total problems, reciprocity, and language.
CONCLUSION: Adolescent with higher functioning autism have difficulty with the working memory system, which is typically compensated. Functional MRI markers of brain network organization in ASD are related to characteristics of autism as represented in diagnostic scores. Therefore, functional MRI provides neuronal correlates for memory difficulties in adolescents with ASD.},
	language = {eng},
	journal = {Psychiatry and Clinical Neurosciences},
	author = {Barendse, Evelien M. and Schreuder, Lisanne J. and Thoonen, Geert and Hendriks, Marc P. H. and Kessels, Roy P. C. and Backes, Walter H. and Aldenkamp, Albert P. and Jansen, Jacobus F. A.},
	month = sep,
	year = {2017},
	pmid = {28869354},
	keywords = {functional MRI, Autism spectrum disorder, higher functioning, network analysis, working memory}
}

@article{schnerr_pulsatility_2017,
	title = {Pulsatility of {Lenticulostriate} {Arteries} {Assessed} by 7 {Tesla} {Flow} {MRI}-{Measurement}, {Reproducibility}, and {Applicability} to {Aging} {Effect}},
	volume = {8},
	copyright = {All rights reserved},
	issn = {1664-042X},
	doi = {10.3389/fphys.2017.00961},
	abstract = {Characterization of flow properties in cerebral arteries with 1.5 and 3 Tesla MRI is usually limited to large cerebral arteries and difficult to evaluate in the small perforating arteries due to insufficient spatial resolution. In this study, we assessed the feasibility to measure blood flow waveforms in the small lenticulostriate arteries with 7 Tesla velocity-sensitive MRI. The middle cerebral artery was included as reference. Imaging was performed in five young and five old healthy volunteers. Flow was calculated by integrating time-varying velocity values over the vascular cross-section. MRI acquisitions were performed twice in each subject to determine reproducibility. From the flow waveforms, the pulsatility index and damping factor were deduced. Reproducibility values, in terms of the intraclass correlation coefficients, were found to be good to excellent. Measured pulsatility index of the lenticulostriate arteries significantly increased and damping factor significantly decreased with age. In conclusion, we demonstrate that blood flow through the lenticostriate arteries can be precisely measured using 7 Tesla MRI and reveal effects of arterial stiffness due to aging. These findings hold promise to provide relevant insights into the pathologies involving perforating cerebral arteries.},
	language = {eng},
	journal = {Frontiers in Physiology},
	author = {Schnerr, Roald S. and Jansen, Jacobus F. A. and Uludag, Kamil and Hofman, Paul A. M. and Wildberger, Joachim E. and van Oostenbrugge, Robert J. and Backes, Walter H.},
	year = {2017},
	pmid = {29225580},
	pmcid = {PMC5705621},
	keywords = {cerebral blood flow, cerebrovascular aging, damping factor, flow quantification, lenticostriate artery, middle cerebral artery, pulsatility, pulsatility index},
	pages = {961}
}

@article{wong_reproducibility_2017,
	title = {On the {Reproducibility} of {Inversion} {Recovery} {Intravoxel} {Incoherent} {Motion} {Imaging} in {Cerebrovascular} {Disease}},
	copyright = {All rights reserved},
	issn = {1936-959X},
	doi = {10.3174/ajnr.A5474},
	abstract = {BACKGROUND AND PURPOSE: Intravoxel incoherent motion imaging can measure both microvascular and parenchymal abnormalities simultaneously. The contamination of CSF signal can be suppressed using inversion recovery preparation. The clinical feasibility of inversion recovery-intravoxel incoherent motion imaging was investigated in patients with cerebrovascular disease by studying its reproducibility.
MATERIALS AND METHODS: Sixteen patients with cerebrovascular disease (66 ± 8 years of age) underwent inversion recovery-intravoxel incoherent motion imaging twice. The reproducibility of the perfusion volume fraction and parenchymal diffusivity was calculated with the coefficient of variation, intraclass correlation coefficient, and the repeatability coefficient. ROIs included the normal-appearing white matter, cortex, deep gray matter, white matter hyperintensities, and vascular lesions.
RESULTS: Values for the perfusion volume fraction ranged from 2.42 to 3.97 ×10-2 and for parenchymal diffusivity from 7.20 to 9.11 × 10-4 mm2/s, with higher values found in the white matter hyperintensities and vascular lesions. Coefficients of variation were {\textless}3.70\% in normal-appearing tissue and {\textless}9.15\% for lesions. Intraclass correlation coefficients were good to excellent, showing values ranging from 0.82 to 0.99 in all ROIs, except the deep gray matter and cortex, with intraclass correlation coefficients of 0.66 and 0.54, respectively. The repeatability coefficients ranged from 0.15 to 0.96 × 10-2 and 0.10 to 0.37 × 10-4 mm2/s for perfusion volume fraction and parenchymal diffusivity, respectively.
CONCLUSIONS: Good reproducibility of inversion recovery-intravoxel incoherent motion imaging was observed with low coefficients of variation and high intraclass correlation coefficients in normal-appearing tissue and lesion areas in cerebrovascular disease. Good reproducibility of inversion recovery-intravoxel incoherent motion imaging in cerebrovascular disease is feasible in monitoring disease progression or treatment responses in the clinic.},
	language = {eng},
	journal = {AJNR. American journal of neuroradiology},
	author = {Wong, S. M. and Backes, W. H. and Zhang, C. E. and Staals, J. and van Oostenbrugge, R. J. and Jeukens, C. R. L. P. N. and Jansen, J. F. A.},
	month = dec,
	year = {2017},
	pmid = {29217741}
}

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib


text:
@InProceedings{lic14,
  title = {Bayesian Max-margin Multi-Task Learning with Data Augmentation},
  author = {Chengtao Li and Jun Zhu and Jianfei Chen},
  pages = {415-423},
  abstract = {Both max-margin and Bayesian methods have been extensively studied in multi-task learning, but have rarely been considered together. We present Bayesian max-margin multi-task learning, which conjoins the two schools of methods, thus allowing the discriminative max-margin methods to enjoy the great flexibility of Bayesian methods on incorporating rich prior information as well as performing nonparametric Bayesian feature learning with the latent dimensionality resolved from data. We develop Gibbs sampling algorithms by exploring data augmentation to deal with the non-smooth hinge loss. For nonparametric models, our algorithms do not need to make mean-field assumptions or truncated approximation. Empirical results demonstrate superior performance than competitors in both multi-task classification and regression.},
  section = {cycle-2},
}

repository: mreid/papersite

repo_name: mreid/papersite

gha_license_id: MIT

gha_language: TeX


text:
fn max(&mut g: [Numeric] + Index) -> Numeric {
}

[T] - indexable
{T} - generically iterable...?
K->V - map- or function-like (input K, get V)
() - tuple-like

any - dynamic type
T? - nullable

Default: impl can decide whether values are copied or not, but values aren't mutable

mut -> like &mut
auto -> like RC or ARC<Mutex ...> (impl must detect whether it escapes the current thread)

fn add7(g: Numeric) -> Numeric {
}

fn add7(mut g: Numeric)

repository: BatmanAoD/belle-lang

repo_name: BatmanAoD/belle-lang

extension: be


text:
@incollection{vdl2017online,
  title={Online Targeted Maximum Likelihood Estimation of Causal Effects Based
    on Observing a Single Time Series},
  author={{van der Laan}, Mark J},
  booktitle={Targeted Learning in Data Science: Causal Inference for Complex
    Longitudinal Studies},
  pages={263--297},
  year={2017},
  publisher={Springer Science \& Business Media}
}


text:
@article{hutton_meijer_1998,
  title     = {Monadic parsing in {H}askell},
  volume    = {8},
  doi       = {10.1017/S0956796898003050},
  number    = {4},
  journal   = {Journal of Functional Programming},
  publisher = {Cambridge University Press},
  author    = {Hutton, Graham and Meijer, Erik},
  year      = {1998},
  pages     = {437–444}
}

@article{frost_1989,
    author = {Frost, R. and Launchbury, J.},
    title = {Constructing Natural Language Interpreters in a Lazy Functional Language},
    journal = {The Computer Journal},
    volume = {32},
    number = {2},
    pages = {108-121},
    year = {1989},
    month = {01},
    abstract = "{In this paper, we describe a method by which language parsers and interpreters may be implemented in a lazy functional programming language. The visual appearance of such interpreters mimics the BNP description of the grammar of the language being interpreted. The method is particularly well suited to the implementation of language interpreters that are based on the principle of ‘rule to rule’ correspondence (in which each production rule of the grammar has a translation rule associated with it). The main objective of the paper is to demonstrate that the method described provides a useful framework within which both grammars and semantic theories of languages many be investigated. We present the method by example: the simple natural language interpreter we construct is based loosely on principles proposed by Richard Montague.}",
    issn = {0010-4620},
    doi = {10.1093/comjnl/32.2.108},
    url = {https://doi.org/10.1093/comjnl/32.2.108},
    eprint = {https://academic.oup.com/comjnl/article-pdf/32/2/108/1445656/320108.pdf},
}

@article{hutton_1992,
  title={Higher-order functions for parsing},
  volume={2},
  DOI={10.1017/S0956796800000411},
  number={3},
  journal={Journal of Functional Programming},
  publisher={Cambridge University Press},
  author={Hutton, Graham}, year={1992}, pages={323–343}}

repository: parallelwindfarms/byteparsing

repo_name: parallelwindfarms/byteparsing

gha_language: Jupyter Notebook


text:
DESCRIPTION = "Tuxbox common files"
LICENSE = "GPL"
MAINTAINER = "PLi team"

PN = "tuxbox-common"
PR = "r2"

PV = "1.0+svn${SRCREV}"

# use cables.xml and terrestrial.xml from tuxbox.org
SRC_URI = "cvs://anoncvs@cvs.tuxbox.org/cvs/tuxbox/;module=cdk/root/share/tuxbox;method=ext;rsh=ssh;tag=dreambox;date=${SRCDATE} \
	"

SRCREV_FORMAT = "satsxml"

# everything else from openpli svn
SRC_URI += " ${PLISVNURL}/${PLISVNBRANCH}/cdk/cdk/root;module=share;proto=${PLISVNPROTO};name=satsxml \
	${PLISVNURL}/${PLISVNBRANCH}/cdk/cdk/root;module=etc;proto=${PLISVNPROTO}"

FILES_${PN} = "/"

S = "${WORKDIR}"

TRANSPONDER_LISTS = "satellites.xml terrestrial.xml"

#enigma1 need a cables.xml
TRANSPONDER_LISTS_append_dm7020 = " cables.xml"
TRANSPONDER_LISTS_append_dm500plus = " cables.xml"
TRANSPONDER_LISTS_append_dm600pvr = " cables.xml"

do_install() {
	install -d ${D}/etc/tuxbox/
	install -d ${D}/usr/share/tuxbox
	install -m 0644 ${S}/share/tuxbox/scart.conf ${D}/etc/tuxbox/scart.conf

	install -m 0644 ${S}/etc/timezone.xml ${D}/etc/tuxbox/timezone.xml
	ln -sf /etc/tuxbox/timezone.xml ${D}/etc/

	ln -sf /usr/share ${D}/share

	install -m 0644 ${S}/share/tuxbox/satellites.xml ${S}/tuxbox

	for i in ${TRANSPONDER_LISTS}; do
		install -m 0644 ${S}/tuxbox/$i ${D}/etc/tuxbox/$i
		ln -sf /etc/tuxbox/$i ${D}/etc/;
		ln -sf /etc/tuxbox/$i ${D}/usr/share/;
		ln -sf /etc/tuxbox/$i ${D}/usr/share/tuxbox/;
	done;
}

extension: bb


text:
% Encoding: UTF-8

@Electronic{cherkass,
  title     = {Управління ДСНС України у Черкаській області - РЕКОМЕНДАЦІЇ ЩОДО ДІЙ НАСЕЛЕННЯ У НАДЗВИЧАЙНИХ СИТУАЦІЯХ},
  url       = {https://ck.dsns.gov.ua/ua/REKOMENDACIYI-SCHODO-DIY-NASELENNYA-U-NADZVICHAYNIH-SITUACIYAH.html},
  timestamp = {2020-01-21},
}

@Electronic{iFrank,
  title     = {Памятка для УНС},
  url       = {http://www.if.gov.ua/files/%D0%9F%D0%B0%D0%BC%D1%8F%D1%82%D0%BA%D0%B0%20%D0%B4%D0%BB%D1%8F%20%D0%A3%D0%9D%D0%A1.pdf},
  timestamp = {2020-01-21},
}

@Comment{jabref-meta: databaseType:bibtex;}

repository: AChep/khpi-latex

repo_name: AChep/khpi-latex