bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated analysis of directly captured microRNA targets reveals the impact of microRNAs on mammalian transcriptome
Authors: Bjerke Glen A. , Yi Rui 
Published: June 2019

AbstractMicroRNA (miRNA)-mediated regulation is widespread, relatively mild but functionally important. Despite extensive efforts to identify miRNA targets, it remains unclear how miRNAs bind to mRNA targets globally and how changes in miRNA levels affects the transcriptome. Here we apply an optimized method for simultaneously capturing miRNA and targeted RNA sites to wildtype, miRNA knockout and induced epithelial cells. We find that abundantly expressed miRNAs can bind to thousands of different transcripts and many different miRNAs can regulate the same gene. Although mRNA sites that are bound by miRNAs and also contain matches to seed sequences confer the strongest regulation, ∼50% of miRNAs bind to RNA regions without seed matches. In general, these bindings have little impact on mRNA levels and reflect a scanning activity of miRNAs. In addition, different miRNAs have different preferences to seed matches and 3’end base-pairing. For a single miRNA, the effectiveness of mRNA regulation is highly correlated with the number of captured miRNA:RNA fragments. Notably, elevated miRNA expression effectively represses existing targets with little impact on newly recognized targets. Global analysis of directly captured mRNA targets reveals pathways that are involved in cancer, cell adhesion and signaling pathways are highly regulated by many different miRNAs in epithelial cells. Comparison between experimentally captured and TargetScan predicted targets indicates that our approach is more effective to identify bona fide targets by reducing false positive and negative predictions. This study reveals the global binding landscape and impact of miRNAs on mammalian transcriptome.
A mechanical model reveals that non-axisymmetric buckling lowers the energy barrier associated with membrane neck constriction
Authors: Vasan R. , Rudraraju S. , Akamatsu M. , Garikipati K. , Rangamani P. 
Published: June 2019

AbstractMembrane neck formation is essential for scission, which, as recent experiments on tubules have demonstrated, can be location dependent. The diversity of biological machinery that can constrict a neck such as dynamin, actin, ESCRTs and BAR proteins, and the range of forces and deflection over which they operate, suggest that the constriction process is functionally mechanical and robust to changes in biological environment. In this study, we used a mechanical model of the lipid bilayer to systematically investigate the influence of location, symmetry constraints, and helical forces on membrane neck constriction. Simulations from our model demonstrated that the energy barriers associated with constriction of a membrane neck are location-dependent. Importantly, if symmetry restrictions are relaxed, then the energy barrier for constriction is dramatically lowered and the membrane buckles at lower values of forcing parameters. Our simulations also show that constriction due to helical proteins further reduces the energy barrier for neck formation compared to cylindrical proteins. These studies establish that despite different molecular mechanisms of neck formation in cells, the mechanics of constriction naturally leads to a loss of symmetry that can lower the energy barrier to constriction.Significance statementMembrane tubule constriction is a critical step of cellular membrane trafficking processes and is thought to be mechanically regulated. Mechanical modeling techniques employing the Helfrich Hamiltonian and axisymmetric continuum frameworks have previously described energy barriers to constriction as a function of location along a 26 membrane tubule. Recent advances in numerical modeling using spline basis functions (Isogeometric Analysis) enable us to conduct our analyses of membrane mechanics in a generalized 3D framework. Here, we implement a novel 3D Isogeometric Analysis framework and juxtapose it against an axisymmetric model to study the influence of location, symmetry constraints and helical collars on the constriction pathway. We show that an unsymmetric, “crushed soda can” neck consistently displays a lower energy barrier than a symmetric neck.
Virulence phenotypes result from an interaction between pathogen ploidy and genetic background
Authors: Feistel Dorian J. , Elmostafa Rema , Hickman Meleah A. 
Published: June 2019

AbstractStudying fungal virulence is often challenging and frequently depends on many contexts, including host immune status and pathogen genetic background. However, ploidy has often been overlooked when studying virulence in eukaryotic pathogens. Since fungal pathogens, including the human opportunistic pathogen Candida albicans, can display extensive ploidy variation, assessing how ploidy impacts virulence has important clinical relevance. Here, we assessed how C. albicans ploidy and genetic background impact virulence phenotypes in both healthy and immunocompromised nematode hosts. In addition to reducing overall host survival, Candida negatively impacted host reproduction, which allowed us to survey lethal and non-lethal virulence phenotypes. While we did not detect any global differences in virulence between diploid and tetraploid pathogens, there were significant interactions between ploidy and C. albicans genetic background, regardless of host immune function.
Binned Relative Environmental Change Indicator (BRECI): A tool to communicate the nature of differences between environmental niche model outputs
Authors: Wilson Peter D. 
Published: June 2019

AbstractNiche models are now widely used in many branches of the biological sciences and are often used to contrast the distribution of favourable environments between regions or under changes in environmental conditions such as climate change. Evaluating model performance and selecting optimal models is now accepted as best-practice, and a number of methods are available assist this process. One aspect of ENM application which has not received as much attention is developing methods to communicate the degree and nature of changes between model outputs (typically as raster maps). The method described in this paper, Binned Relative Environmental Change Index (BRECI), seeks to address this shortfall in communicating model results.
Transcriptome characterization analysis and molecular profiles of obligatory diapause induction of the Chinese citrus fruit fly,Bactrocera minax(Diptera: Tephritidae)
Authors: Zhou Zhixiong , Dong Xiaolin , Li Chuanren 
Published: June 2019

AbstractThe Chinese citrus fruit fly,Bactrocera minax, is a devastating citrus pest in China, Bhutan and India. It will enter obligatory pupal diapause in each generation at specific stage, while little is known about the course and the molecular mechanisms of diapause induction. To gain insight into possible mechanisms of obligatory pupal diapause induction, high-throughput RNA-seq data were generated from second-instar larvae (2L), third-instar larvae (3L) and pupal (P, one week after pupating). A total of 116,402 unigenes were assembled and researched against public databases, and 54,781 unigenes matched to proteins in the NCBI database using the BLAST search. Three pairwise comparisons were performed, and significantly differentially regulated transcripts were identified. Several differentially expressed genes (DEGs) expression patterns revealed that those highly or lowly expressed genes in pupal stage were predicted to be involved in diapause induction. Moreover, GO function and KEGG pathway analysis were performed on all DEGs and showed that 20-hydroxyecdysone (20E) biosynthesis, insulin signaling pathway, FoxO signaling pathway, cell cycle and metabolism pathway may be related to the obligatory diapause of the Chinese citrus fruit fly. This study provides valuable information about the Chinese citrus fruit fly transcriptome for future gene function research, and contributes to the in-depth elucidation of the molecular regulation mechanism of insect obligatory diapause induction.
The Effects of Quantitative Trait Architecture on Detection Power in Artificial Selection Experiments
Authors: Lou R. Nicolas , Therkildsen Nina O. , Messer Philipp W. 
Published: June 2019

ABSTRACTEvolve and resequence (E&R) experiments, in which artificial selection is imposed on organisms in a controlled environment, are becoming an increasingly accessible tool for studying the genetic basis of adaptation. Previous work has assessed how different experimental design parameters affect the power to detect the quantitative trait loci (QTLs) that underlie adaptive responses in such experiments, but so far there has been little exploration of how this power varies with the genetic architecture of the evolving traits. In this study, we use forward simulation to build a realistic model of an E&R experiment in which a quantitative polygenic trait experiences a short, but strong, episode of truncation selection. We study the expected power for QTL detection in such an experiment and how this power is influenced by different aspects of trait architecture, including the number of QTLs affecting the trait, their starting frequencies, effect sizes, clustering along a chromosome, dominance, and epistasis patterns. We show that all of the above parameters can affect allele frequency dynamics at the QTLs and linked loci in complex and often unintuitive ways, and thus influence our power to detect them. One consequence of this is that existing detection methods based on models of independent selective sweeps at individual QTLs often have lower detection power than a simple measurement of allele frequency differences before and after selection. Our findings highlight the importance of taking trait architecture into account in designing studies of molecular adaptation with temporal data. We provide a customizable modeling framework that will enable researchers to easily simulate E&R experiments with different trait architectures and parameters tuned to their specific study system, allowing for assessment of expected detection power and optimization of experimental design.
ModEx: A text mining system for extracting mode of regulation of Transcription Factor-gene regulatory interaction
Authors: Farahmand Saman , Riley Todd , Zarringhalam Kourosh 
Published: June 2019

ABSTRACTBackgroundTranscription factors (TFs) are proteins that are fundamental to transcription and regulation of gene expression. Each TF may regulate multiple genes and each gene may be regulated by multiple TFs. TFs can act as either activator or repressor of gene expression. This complex network of interactions between TFs and genes underlies many developmental and biological processes and is implicated in several human diseases such as cancer. Hence deciphering the network of TF-gene interactions with information on mode of regulation (activation vs. repression) is an important step toward understanding the regulatory pathways that underlie complex traits. There are many experimental, computational, and manually curated databases of TF-gene interactions. In particular, high-throughput ChIP-Seq datasets provide a large-scale map or transcriptional regulatory interactions. However, these interactions are not annotated with information on context and mode of regulation. Such information is crucial to gain a global picture of gene regulatory mechanisms and can aid in developing machine learning models for applications such as biomarker discovery, prediction of response to therapy, and precision medicine.MethodsIn this work, we introduce a text-mining system to annotate ChIP-Seq derived interaction with such meta data through mining PubMed articles. We evaluate the performance of our system using gold standard small scale manually curated databases.ResultsOur results show that the method is able to accurately extract mode of regulation with F-score 0.77 on TRRUST curated interaction and F-score 0.96 on intersection of TRUSST and ChIP-network. We provide a HTTP REST API for our code to facilitate usage.AvailibilitySource code and datasets are available for download on GitHub: https://github.com/samanfrm/modex HTTP REST API: https://watson.math.umb.edu/modex/[type query]
Appropriate Correction for Multiple Comparisons in Decoding of ERP Data: A Re-Analysis of Bae & Luck (2018)
Authors: Bae Gi-Yeul , Luck Steven J. 
Published: June 2019

AbstractBae & Luck (2018) reported a study of visual working memory in which the orientation being held in memory was decoded from the scalp distribution of sustained ERP activity and alpha-band EEG oscillations. Decoding accuracy was compared to chance at each point during the delay interval, and a correction for multiple comparisons was applied to find clusters of consecutive above-chance time points that were stronger than would be expected by chance. However, the correction used in that study did not account for the autocorrelation of the noise and may have been overly liberal. Here, we describe a more appropriate correction procedure and apply it to the data from Bae & Luck (2018). We find that the major clusters of time points that were significantly above chance with the original correction procedure remained above chance with the updated correction procedure. However, some minor clusters that were significant with the original procedure were no longer significant with the updated procedure. We recommend that future studies use the updated correction procedure.
Robust Optimization in Possibility Theory
Authors: Hose Dominik , Mäck Markus , Hanss Michael 
Published: June 2019

Abstract
In this contribution, the optimization of systems under uncertainty is considered. The possibilistic evaluation of the fuzzy-valued constraints and the adoption of a multicriteria decision making technique for the fuzzy-valued objective function enable a meaningful solution to general fuzzy-valued optimization problems. The presented approach is universally applicable, which is demonstrated by reformulating and solving the linear quadratic regulator problem for fuzzy-valued system matrices and initial conditions.
Prehospital delay and its associated psychosocial factors in patients presenting with acute appendicitis in a southwestern city in China: a single-centre prospective observational study
Authors: Li Jian , Xu Run , Hu Dengmin , Zhang Yao , Gong Tuping , Wu Xuelian 
Published: June 2019

ObjectivePrehospital delay is common among patients with acute appendicitis. The aim of this study was to measure the association of a wide range of psychosocial factors with the prehospital delay among adult patients with acute appendicitis in a southwestern city in China.MethodsSociodemographic, clinical, cognitive and psychosocial factors were collected from 421 adult patients with acute appendicitis from November 2016 to December 2017. In addition, factors associated with prehospital delay were determined by binary logistic regression, after adjusting for selected potentially confounding factors.ResultsOnly 179 (42.5%) of the 421 patients were transferred to the hospital within 24 hours; the mean prehospital delay was 27.68 hours with a median of 26 hours, while the mean in-hospital delay was 5.16 hours with a median of 5 hours. In the logistic regression analyses, eight variables or subvariables were found to be associated with prehospital delay >24 hours.ConclusionDelayed presentation for acute appendicitis was associated with older age, living alone, a lack of knowledge of the disease, low social support, an unstable introvert personality trait and negative coping style, intensity of the pain and the symptoms occurring on a workday. A better understanding of the association between psychosocial factors and prehospital delay can help identify patients with acute appendicitis at risk of prehospital delay and lead to the establishment of an effective campaign to promote hospital visits when the symptoms are noticed.
Lifestyle medicine and physical activity knowledge of final year UK medical students
Authors: Radenkovic Dina , Aswani Ram , Ahmad Imtiaz , Kreindler Jack , Robinson Rebecca 
Published: June 2019

ObjectivesIt has previously been reported in theBritish Journal of Sports Medicinethat final year UK medical students are lacking knowledge of the physical activity guidelines. This study assesses whether the knowledge and training of final year UK medical students has improved, whether knowledge correlates with lifestyle choices and whether there is a need for lifestyle medicine training, which includes physical activity guidance, to be offered to this cohort.MethodsA questionnaire consisting of nine key questions was sent to 1356 final year medical students from seven different UK medical schools.ResultsCompleted questionnaires (n=158) were analysed and revealed that 52% were unaware of the current exercise guidelines in the UK. 80% stated they had not received training in lifestyle medicine over the last 2 years while 48.1% were unacquainted with motivational interviewing. 76% wanted more lifestyle medicine teaching to be incorporated into the medical school curriculum.ConclusionsThese findings suggest that final year UK medical students still lack knowledge of the physical activity guidelines. In addition, there is a demand among this cohort for increased lifestyle medicine training which may in turn be an effective way of improving physical activity knowledge.
A multimodal MRI-based classification signature emerges just prior to symptom onset in frontotemporal dementia mutation carriers
Authors: Feis Rogier A , Bouts Mark J R J , de Vos Frank , Schouten Tijn M , Panman Jessica L , Jiskoot Lize C , Dopper Elise G P , van der Grond Jeroen , van Swieten John C , Rombouts Serge A R B 
Published: June 2019

Background
Multimodal MRI-based classification may aid early frontotemporal dementia (FTD) diagnosis. Recently, presymptomatic FTD mutation carriers, who have a high risk of developing FTD, were separated beyond chance level from controls using MRI-based classification. However, it is currently unknown how these scores from classification models progress as mutation carriers approach symptom onset. In this longitudinal study, we investigated multimodal MRI-based classification scores between presymptomatic FTD mutation carriers and controls. Furthermore, we contrasted carriers that converted during follow-up (‘converters’) and non-converting carriers (‘non-converters’).

Methods
We acquired anatomical MRI, diffusion tensor imaging and resting-state functional MRI in 55 presymptomatic FTD mutation carriers and 48 healthy controls at baseline, and at 2, 4, and 6 years of follow-up as available. At each time point, FTD classification scores were calculated using a behavioural variant FTD classification model. Classification scores were tested in a mixed-effects model for mean differences and differences over time.

Results
Presymptomatic mutation carriers did not have higher classification score increase over time than controls (p=0.15), although carriers had higher FTD classification scores than controls on average (p=0.032). However, converters (n=6) showed a stronger classification score increase over time than non-converters (p<0.001).

Conclusions
Our findings imply that presymptomatic FTD mutation carriers may remain similar to controls in terms of MRI-based classification scores until they are close to symptom onset. This proof-of-concept study shows the promise of longitudinal MRI data acquisition in combination with machine learning to contribute to early FTD diagnosis.
Replacement name for Alishania Bickel, 2004 (Diptera Dolichopodidae)
Authors: BICKEL DANIEL J. 
Published: June 2019

Alishania Bickel, 2004 was proposed for a single species, A. elmohardyi, from Taiwan. At the time, a search of the Nomenclator Zoologicus and the Zoological Record did not reveal this name to be preoccupied, and the Vilbaste paper appears to have been overlooked by both references. However, I was kindly informed that Alishania is preoccupied by Vilbaste, 1969 for a Homoptera genus, also from Taiwan. As these names are homonyms, Alishanimyia is proposed as a replacement name for Alishania Bickel 2004.
Severe hypersensitivity allergic reaction to filgrastim in a healthy stem cell donor
Authors: Doval Divya , Choudhary Dharma , Sharma Sanjeev K , Khandelwal Vipin 
Published: June 2019

Introduction Granulocyte–colony stimulating factor (G-CSF) has been approved for use for mobilization of hematopoietic progenitor cells from the marrow into the blood for peripheral blood stem cell collection. Commonly reported side effects of G-CSF include deep throbbing bone pain, severe myalgia and leucocytosis. Case report We describe a case of severe hypersensitivity anaphylactoid reaction after filgrastim administration in a healthy stem cell donor. This haploidentical donor was a 38-year old man with sickle cell trait, donating stem cells for his son, a case of sickle cell disease. On administration of G-CSF (10 µg/kg) he developed features of anaphylaxis. Management and outcome He was given supportive care with oxygen, IV fluid bolus, anti histaminics and steroids. The donor had complete recovery and underwent successful bone marrow harvest. Conclusion There have been various reports of hypersensitivity anaphylactoid reactions in patients undergoing chemotherapy but those associated with the first dose of G-CSF in healthy stem cell donors have rarely been reported.
Exploring correlations between anatomic characteristics of dialysis arteriovenous fistula stenosis and arteriovenous fistula blood flow rate (Qa)
Authors: Nassar George M , Beathard Gerald 
Published: June 2019

Background: Radiologic justification for endovascular treatment of a dialysis arteriovenous fistula circuit stenosis is currently based on ⩾50% severity. However, the clinical significance of any given stenosis is not always clear. The minimum luminal diameter of any stenotic lesion in the arteriovenous fistula circuit might exert a more predictive effect on the arteriovenous fistula blood flow rate (Qa). Methods: To investigate relationships between anatomic parameters of stenosis and Qa, this study was conducted in a cohort of patients with a variety of arteriovenous fistula stenotic lesions. The goals were to determine (1) the degree of correlation between arteriovenous fistula stenosis estimated during the procedure, and that which is measured, and (2) the correlations between two anatomic stenosis parameters (percent stenosis and stenosis minimum luminal diameter) and Qa. Results: The cohort comprised 113 patients. Only a moderate correlation between estimated and measured stenosis was seen. A correlation between measured stenosis and Qa for the whole cohort was not seen, but a weak correlation between estimated stenosis and Qa was seen. Correlations between stenosis minimum luminal diameter and Qa were superior. The superiority of stenosis minimum luminal diameter to percent stenosis in correlating with a Qa of <500 mL/h was also demonstrated by receiver operating characteristics curve analysis. Stenosis minimum luminal diameter cutoffs of ⩽2.5 mm or >4 mm seemed to have a good predictive value of Qa. Conclusions: Percent stenosis determination is fraught with uncertainty and exhibits a weak correlation with Qa. Compared with percent stenosis, the minimum luminal diameter of the stenosis demonstrates a superior correlation with Qa.