bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cannabis-Induced Acute Pancreatitis
Authors: Barkin Jodie A. , Nemeth Zsuzsanna , Saluja Ashok K. , Barkin Jamie S. 
Published: August 2017

Objectives
Cannabis is the most frequently consumed illicit drug in the world, with higher prevalence under the age of 35 years. Cannabis was first reported as a possible cause of acute pancreatitis (AP) in 2004. The aim of this systematic review is to examine cannabis use as an etiology of AP.

Methods
A search using PubMed/Medline, Embase, Scopus, and Cochrane was performed without language or year limitations to May 1, 2016. Search terms were “Cannabis” and “Acute Pancreatitis” with all permutations. The search yielded 239 results. Acute pancreatitis was defined by meeting 2 of 3 Revised Atlanta Classification criteria. Cannabis-induced AP was defined by preceding use of cannabis and exclusion of common causes of AP when reported. Sixteen papers met inclusion criteria dating from 2004 to 2016.

Results
There were 26 cases of cannabis-induced AP (23/26 men; 24/26 under the age of 35 y). Acute pancreatitis correlated with increased cannabis use in 18 patients. Recurrent AP related temporally to cannabis use was reported in 15 of 26. There are 13 reports of no further AP episodes after cannabis cessation.

Conclusions
Cannabis is a possible risk factor for AP and recurrent AP, occurring primarily in young patients under the age of 35 years. Toxicology screens should be considered in all patients with idiopathic AP.
Local and Systemic Expression of Immunomodulatory Factors in Chronic Pancreatitis
Authors: Komar Hannah M. , Hart Phil A. , Cruz-Monserrate Zobeida , Conwell Darwin L. , Lesinski Gregory B. 
Published: August 2017

Abstract
Inflammatory and fibrotic events that drive chronic pancreatitis (CP) are likely orchestrated via signaling of soluble cytokines and chemokines systemically and within the pancreas. However, a comprehensive summary of the expression of such factors during CP has not been reported to date. This information is important given continued interest in targeting cytokines that influence CP pathogenesis. Reported data on the expression change of soluble immunomodulatory factors in human CP patients were identified via a literature search using a single search term. Thirty-one articles meeting the prespecified inclusion criteria were identified to generate a compiled data summary. Compiled data demonstrated up-regulation of several factors in the blood or pancreas microenvironment of CP patients. Nine factors were elevated in both compartments, including fractalkine, IFN-γ, interleukin 1β, IL-6, IL-8, macrophage inhibitory cytokine 1, neutrophil gelatinase–associated lipocalin, transforming growth factor β, and tumor necrosis factor α. Most up-regulated factors could be classified into one of several functional groups, including inflammation, chemotaxis, angiogenesis, bone remodeling, extracellular matrix remodeling, and pain. After further validation, these factors may be used as biomarkers for disease diagnosis and identification of comorbidities, or as potential therapeutic targets.
Pathologic Prognostic Factors of Pineal Parenchymal Tumor of Intermediate Differentiation
Authors: Chatterjee Debajyoti , Lath Khushboo , Singla Navneet , Kumar Narendra , Radotra Bishan D. 
Published: August 2017

Introduction:
Pineal parenchymal tumor of intermediate differentiation (PPTID) is an uncommon tumor of the pineal gland. Although this behaves as a grade II/III tumor, the exact clinical behavior is not well known. There is no well-established pathologic factor that can predict the behavior of PPTID.

Aim and Objective:
The aim of this study was to determine the pathologic prognostic factors in PPTID.

Materials and Methods:
All PPTID cases diagnosed between 2006 and 2016 were analyzed retrospectively. Immunohistochemistry for synaptophysin, neurofilament protein (NFP), glial fibrillar acid protein, NeuN, and Ki-67 were performed in all cases. Cases were classified arbitrarily into low grade (mitosis <4/10 hpf and Ki-67 <5%) and high grade (mitosis ≥4/10 hpf and Ki-67 ≥5%). Clinical details including follow-up information were retrieved from the patients’ files.

Results:
A total of 16 patients (6 low grade and 10 high grade) were included in this study. The age ranged from 2 to 55 years (average, 28.2) with a mild male preponderance (male:female, 1.67:1). All cases showed strong and diffuse positivity for synaptophysin. Focal NFP positivity was seen in 2 low-grade and 3 high-grade tumors. Only 2 cases showed focal NeuN positivity. Average Ki-67 index was 1.7% and 12.6% in low-grade and high-grade tumors, respectively. All patients with low-grade tumor were alive without recurrence. Among the patients with high-grade tumors, 2 had local recurrence, 1 had spinal metastasis, and 3 patients died.

Conclusion:
Mitosis and Ki-67 proliferation index are the most important pathologic prognostic factors in PPTID. NFP expression does not carry any prognostic significance.
Subclinical Rhythmic EEG Discharge of Adult (SREDA) in a Child With Generalized Epilepsy and Literature Review of SREDA in Children
Authors: Goeden Marcie , Bansal Lalit R. 
Published: August 2017

Summary:
Subclinical rhythmic discharges of adult (SREDA) is a rare benign EEG variant in adults and is of unknown clinical significance. Its occurrence in children is extremely rare. In review of the literature, it has been described in only four children. We present a case of a 10-year-old female with generalized idiopathic childhood absence epilepsy who is noted to have SREDA in three subsequent EEGs performed across a 25-month span. She had no clinical change with these discharges and it was believed to be a benign variant. Including our patient, three of four children with SREDA presented with generalized epilepsy leading to the conclusion that, although rare, SREDA is more common in children presenting with generalized epilepsy.
Spatial protein analysis in developing tissues: a sampling-based image processing approach
Authors: Leonavicius Karolis , Royer Christophe , Miranda Antonio , Tyser Richard , Kip Anne-Marie , Srinivas Shankar 
Published: August 2017

ABSTRACTAdvances in fluorescence microscopy approaches have made it relatively easy to generate multi-dimensional image volumes and have highlighted the need for flexible image analysis tools for the extraction of quantitative information from such data. Here we demonstrate that by focusing on simplified feature-based nuclear segmentation and probabilistic cytoplasmic detection we can create a tool that is able to extract geometry based information from diverse mammalian tissue images. Our open-source image analysis platform, called ‘SilentMark’ can cope with noisy images and with crowded fields of cells to quantify signal intensity in different cellular compartments. Additionally, it provides tissue geometry related information, which allows one to quantify protein distribution with respect to marked regions of interest. The lightweight SilentMark algorithms have the advantage of not requiring multiple processors and graphics cards and can be run even with just several hundred MB of memory. This makes it possible to use the method as a web application, effectively eliminating setup hurdles and compatibility issues with operating systems. We test this platform on mouse pre-implantation embryos, embryonic stem cell derived embryoid bodies and mouse embryonic heart and relate protein localisation to tissue geometry.
Natural Language Processing for Classification of Acute, Communicable Findings on Unstructured Head CT Reports: Comparison of Neural Network and Non-Neural Machine Learning Techniques
Authors: Chokshi Falgun H. , Shin Bonggun , Lee Timothy , Lemmon Andrew , Necessary Sean , Choi Jinho D. 
Published: August 2017

AbstractBackground and PurposeTo evaluate the accuracy of non-neural and neural network models to classify five categories (classes) of acute and communicable findings on unstructured head computed tomography (CT) reports.Materials and MethodsThree radiologists annotated 1,400 head CT reports for language indicating the presence or absence of acute communicable findings (hemorrhage, stroke, hydrocephalus, and mass effect). This set was used to train, develop, and evaluate a non-neural classifier, support vector machine (SVM), in comparisons to two neural network models using convolutional neural networks (CNN) and neural attention model (NAM) Inter-rater agreement was computed using kappa statistics. Accuracy, receiver operated curves, and area under the curve were calculated and tabulated. P-values < 0.05 was significant and 95% confidence intervals were computed.ResultsRadiologist agreement was 86-94% and Cohen’s kappa was 0.667-0.762 (substantial agreement). Accuracies of the CNN and NAM (range 0.90-0.94) were higher than SVM (range 0.88-0.92). NAM showed relatively equal accuracy with CNN for three classes, severity, mass effect, and hydrocephalus, higher accuracy for the acute bleed class, and lower accuracy for the acute stroke class. AUCs of all methods for all classes were above 0.92.ConclusionsNeural network models (CNN & NAM) generally had higher accuracies compared to the non-neural models (SVM) and have a range of accuracies that comparable to the inter-annotator agreement of three neuroradiologists.The NAM method adds ability to hold the algorithm accountable for its classification via heat map generation, thereby adding an auditing feature to this neural network.AbbreviationsNLPNatural Language ProcessingCNNConvolutional Neural NetworkNAMNeural Attention ModelHERElectronic Health Record
TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information
Authors: Kulkarni Shubhada R. , Vaneechoutte Dries , Velde Jan Van de , Vandepoele Klaas 
Published: August 2017

ABSTRACTA gene regulatory network (GRN) is a collection of regulatory interactions between transcription factors (TFs) and their target genes. GRNs control different biological processes and have been instrumental to understand the organization and complexity of gene regulation. Although various experimental methods have been used to map GRNs inArabidopsis thaliana, their limited throughput combined with the large number of TFs makes that for many genes our knowledge about regulating TFs is incomplete. We introduce TF2Network, a tool that exploits the vast amount of TF binding site information and enables the delineation of GRNs by detecting potential regulators for a set of co-expressed or functionally related genes. Validation using two experimental benchmarks reveals that TF2Network predicts the correct regulator in 75-92% of the test sets. Furthermore, our tool is robust to noise in the input gene sets, has a low false discovery rate, and shows a better performance to recover correct regulators compared to other plant tools. TF2Network is accessible through a web interface where GRNs are interactively visualized and annotated with various types of experimental functional information. TF2Network was used to perform systematic functional and regulatory gene annotations, identifying new TFs involved in circadian rhythm and stress response.
The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space
Authors: Klughammer Johanna , Kiesel Barbara , Roetzer Thomas , Fortelny Nikolaus , Kuchler Amelie , Sheffield Nathan C. , Datlinger Paul , Peter Nadine , Nenning Karl-Heinz , Furtner Julia , Nowosielski Martha , Augustin Marco , Mischkulnig Mario , Ströbel Thomas , Moser Patrizia , Freyschlag Christian F. , Kerschbaumer Johannes , Thomé Claudius , Grams Astrid E. , Stockhammer Günther , Kitzwoegerer Melitta , Oberndorfer Stefan , Marhold Franz , Weis Serge , Trenkler Johannes , Buchroithner Johanna , Pichler Josef , Haybaeck Johannes , Krassnig Stefanie , Ali Kariem Madhy , Campe Gord von , Payer Franz , Sherif Camillo , Preiser Julius , Hauser Thomas , Winkler Peter A. , Kleindienst Waltraud , Würtz Franz , Brandner-Kokalj Tanisa , Stultschnig Martin , Schweiger Stefan , Dieckmann Karin , Preusser Matthias , Langs Georg , Baumann Bernhard , Knosp Engelbert , Widhalm Georg , Marosi Christine , Hainfellner Johannes A. , Woehrer Adelheid , Bock Christoph 
Published: August 2017

AbstractGlioblastoma is characterized by widespread genetic and transcriptional heterogeneity, yet little is known about the role of the epigenome in glioblastoma disease progression. Here, we present genome-scale maps of the DNA methylation dynamics in matched primary and recurring glioblastoma tumors, based on a national population registry and a comprehensively annotated clinical cohort. We demonstrate the feasibility of DNA methylation mapping in a large set of routinely collected formalin-fixed paraffin-embedded (FFPE) samples, and we validate bisulfite sequencing as a multi-purpose assay that allowed us to infer a range of different genetic, epigenetic, and transcriptional tumor characteristics. Based on these data, we identified characteristic differences between primary and recurring tumors, links between DNA methylation and the tumor microenvironment, and an association of epigenetic tumor heterogeneity with patient survival. In summary, this study provides a resource for dissecting DNA methylation heterogeneity in genetically diverse and heterogeneous tumors, and it demonstrates the feasibility of integrating epigenomics, radiology, and digital pathology in a representative national cohort, leveraging samples and data collected as part of routine clinical practice.
Context-Dependent Genetic Regulation
Authors: Kim Kyung Hyuk , Yerramilli Venkata Siddartha , Choi Kiri , Sauro Herbert M. 
Published: August 2017

AbstractCells process extra-cellular signals with multiple layers of complex biological networks. Due to the stochastic nature of the networks, the signals become significantly noisy within the cells and in addition, due to the nonlinear nature of the networks, the signals become distorted, shifted, and (de-)amplified. Such nonlinear signal processing can lead to non-trivial cellular phenotypes such as cell cycles, differentiation, cell-to-cell communication, and homeostasis. These nonlinear pheno-types, when observed at the cell population levels, can be quite different from the single-cell level observation. As one of the underlying mechanisms behind this difference, we report the interplay between nonlinearity and stochasticity in genetic regulation. Here we show that nonlinear genetic regulation, characterized at the cellular population level, can be affected by cell-to-cell variability in the regulatory factor concentrations. The observed genetic regulation at the cell population is shown to be significantly dependent on the upstream DNA sequences of the regulator, in particular, 5’ untranslated region. This indicates that genetic regulation observed at the cell population level can be significantly dependent on its genetic context, and that its characterization needs a careful attention on noise propagation.One Sentence SummaryGenetic regulation observed at the cell population level can be significantly affected by cell-to-cell variability in the regulatory factor copy numbers, indicating that the observed regulation is dependent on 5’ UTR of the regulator coding gene.
Demogenetic simulations reveal fragmenting effects of climate change on insular lizard populations
Authors: Rice Stephen E. , Clark Rulon W. 
Published: August 2017

ABSTRACTThe extinction risk of insular species with sessile life histories is expected to increase as they may be unable to track habitat in response to global climate change. Demogenetic simulations can couple population demography and niche modeling to produce spatially-explicit genetic and demographic information for all simulated individuals and provide insight into the effects of climate change at demographic and population genetic levels. We used CDMETAPOP to simulate a population of island night lizards (Xantusia riversiana) on Santa Barbara Island to evaluate its sensitivity to climate change to the year 2100 across 8 scenarios based on 2 climate models, 2 emissions pathways, and 2 connectivity models. We found that 1)X. riversianais sensitive to climate change with SDMs predicting a loss of suitable habitat of 93%-98% by 2038, 2) population genetic structure is expected to increase drastically to 0.209-0.673 from approximately 0.0346, and 3) estimated minimum abundance is expected to declined sharply over the 2007 to 2038 period and reached values of 0-1% of the 2007 population size in all scenarios by 2100. Climate change is expected to decrease census population size and result in extant habitat patches that are isolated from one another with very high levels of genetic divergence over short periods of time. These patterns may drive the Santa Barbara Island population to extinction under certain scenarios. Management plans should address methods to improve connectivity on the island and attempt to create refugial patches. Contingency plans, such as translocation, may be required to prevent population extirpation. This study highlights the utility of demogenetic simulations in evaluating population demographic and genetic patterns under climate change with suggestions on workflows for running simulations in a high-throughput manner.
A negative feedback mechanism in the insulin-regulated glucose homeostasis in Japanese flounderParalichthys olivaceusby two ways of glucose administration
Authors: Liu Dong , Han Dongdong , Guo Benyue , Deng Kangyu , Gu Zhixiang , Yang Mengxi , Xu Wei , Zhang Wenbing , Mai Kangsen 
Published: August 2017

AbstractThe present study comparatively analyzed the blood glucose and insulin concentration, the temporal and spatial expression of brain-gut peptides and the key enzymes of glycolysis and gluconeogenesis in Japanese flounder by intraperitoneal (IP) injection and oral (OR) administration of glucose. Samples were collected at 0, 1, 3, 5, 7, 9, 12, 24 and 48h after IP and OR, respectively. Results showed that the hyperglycemia lasted 5 hours and 21 hours in OR and IP group, respectively. The serum insulin concentration significantly decreased (1.58±0.21mIU/L) at 3h after IP glucose. However, it significantly increased at 3h (3.37±0.34mIU/L) after OR glucose. The gene expressions of prosomatostatin, neuropeptide Y, cholecystokinin precursor and orexin precursor in the brain showed different profiles between the OR and IP group. The OR not IP administration of glucose had significant effects on the gene expressions of preprovasoactive intestinal peptide, pituitary adenylate cyclase activating polypeptide and gastrin in the intestine. When the blood glucose concentration peaked in both IP and OR group, the glucokinase expression in liver was stimulated, but the expression of fructose-1,6-bisphosphatase was depressed. In conclusion, brain-gut peptides were confirmed in the present study. And the serum insulin and the brain-gut peptides have different responses between the IP and OR administration of glucose. A negative feedback mechanism in the insulin-regulated glucose homeostasis was suggested in Japanese flounder. Furthermore, this regulation could be conducted by activating PI3k-Akt, and then lead to the pathway downstream changes in glycolysis and gluconeogenesis.
Rapid responses of amygdala neurons discriminate facial expressions
Authors: Inagaki Mikio , Fujita Ichiro 
Published: August 2017

SummaryThe amygdala plays a critical role in detecting potential danger through sensory input [1, 2]. In the primate visual system, a subcortical pathway through the superior colliculus and the pulvinar is thought to provide the amygdala with rapid and coarse visual information about facial emotions [3–6]. A recent electrophysiological study in human patients supported this hypothesis by showing that intracranial event-related potentials discriminated fearful faces from other faces very quickly (within ∼74 ms) [7]. However, several aspects of the hypothesis remain debatable [8]. Critically, evidence for short-latency, emotion-selective responses from individual amygdala neurons is lacking [9–12], and even if this type of response existed, how it might contribute to stimulus detection is unclear. Here, we addressed these issues in the monkey amygdala and found that ensemble responses of single neurons carry robust information about emotional faces— especially threatening ones—within ∼50 ms after stimulus onset. Similar rapid response was not found in the temporal cortex from which the amygdala receives cortical inputs [13], suggesting a subcortical origin. Additionally, we found that the rapid amygdala response contained excitatory and suppressive components. The early excitatory component might be useful for quickly sending signals to downstream areas. In contrast, the rapid suppressive component sharpened the rising phase of later, sustained excitatory input (presumably from the temporal cortex) and might therefore improve processing of emotional faces over time. We thus propose that these two amygdala responses that originate from the subcortical pathway play dual roles in threat detection.
Inbred or Outbred? Genetic diversity in laboratory rodent colonies
Authors: Brekke Thomas D. , Steele Katherine A. , Mulley John F. 
Published: August 2017

ABSTRACTNon-model rodents are widely used as subjects for both basic and applied biological research, but the genetic diversity of the study individuals is rarely quantified. University-housed colonies tend to be small and subject to founder effects and genetic drift and so may be highly inbred or show substantial genetic divergence from other colonies, even those derived from the same source. Disregard for the levels of genetic diversity in an animal colony may result in a failure to replicate results if a different colony is used to repeat an experiment, as different colonies may have fixed alternative variants. Here we use high throughput sequencing to demonstrate genetic divergence in three isolated colonies of Mongolian gerbil (Meriones unguiculatus) even though they were all established recently from the same source. We also show that genetic diversity in allegedly ‘outbred’ colonies of non-model rodents (gerbils, hamsters, house mice, and deer mice) varies considerably from nearly no segregating diversity, to very high levels of polymorphism. We conclude that genetic divergence in isolated colonies may play an important role in the ‘replication crisis’. In a more positive light, divergent rodent colonies represent an opportunity to leverage genetically distinct individuals in genetic crossing experiments. In sum, awareness of the genetic diversity of an animal colony is paramount as it allows researchers to properly replicate experiments and also to capitalize on other, genetically distinct individuals to explore the genetic basis of a trait.
A population of adult satellite-like cells inDrosophilais maintained through a switch in RNA-isoforms
Authors: Boukhatmi Hadi , Bray Sarah 
Published: August 2017

SummaryAdult stem cells are important for tissue maintenance and repair. One key question is how such cells are specified and then protected from differentiation for a prolonged period. Investigating the maintenance ofDrosophilamuscle progenitors (MPs) we demonstrate that it involves a switch inzfh1/ZEB1RNA-isoforms. Differentiation into functional muscles is accompanied by expression ofmiR-8/miR-200, which targets the majorzfh1-longRNA isoform and decreases Zfh1 protein. Through activity of the Notch pathway, a subset of MPs produce an alternatezfh1-shortisoform, which lacks themiR-8seed site. Zfh1 protein is thus maintained in these cells, enabling them to escape differentiation and persist as MPs in the adult. There, like mammalian satellite cells, they contribute to muscle homeostasis. Such preferential regulation of a specific RNA isoform, with differential sensitivity to miRs, is a powerful mechanism for maintaining a population of poised progenitors and may be of widespread significance.