bluuebunny/crossref_metadata_2025_split huggingface dataset:
Baseline Understanding of Urinary Incontinence and Prolapse in New Urogynecology Patients
Authors: Davidson Emily R.W. , Myers Erinn M. , De La Cruz Jacquia F. , Connolly AnnaMarie 
Published: October 2017

Objectives
Investigators sought to assess whether age was related to patient understanding of pelvic floor disorders; given studies show that increased age is associated with lower health literacy.

Methods
This was a cross-sectional survey of new urogynecology patients. Enrolled participants completed a survey including demographics, history of urinary incontinence (UI) and pelvic organ prolapse symptoms and treatment, the Prolapse and Incontinence Knowledge Questionnaire (PIKQ), self-assessment of UI and prolapse knowledge, and a pelvic anatomy diagram to label. To achieve 80% power to detect a 2-point difference in PIKQ score, 33 subjects were required per age group (<65 and ≥65 years old).

Results
One hundred thirty-five of 160 new urogynecologic patients completed the survey (84% response rate). Thirty-seven participants were older than 65 years, and 98 were younger than 65 years. Total PIKQ scores (maximum, 24), the primary outcome, for the older and younger groups were 15.3 and 15.0, respectively (P = 0.7). The 2 groups self-rated UI and prolapse knowledge similarly, rating knowledge as excellent, very good, or good in 60% (P = 0.3) and 40% (P = 0.2) of subjects, respectively.

Conclusions
Baseline patient understanding of UI and pelvic organ prolapse was low as assessed by PIKQ score and was not influenced by age.
Treatment options for posttraumatic epilepsy
Authors: Zimmermann Lara L. , Martin Ryan M. , Girgis Fady 
Published: October 2017

Purpose of review
Posttraumatic seizures (PTS) and posttraumatic epilepsy (PTE) are common and debilitating consequences of traumatic brain injury (TBI). Early PTS result in secondary brain injury by raising intracranial pressure and worsening cerebral edema and metabolic crisis. PTE is a localization-related epilepsy strongly associated with TBI severity, but risk factors for PTE and epileptogenesis are incompletely understood and are active areas of research. Medical management of PTS in adults and children is reviewed. Surgical options for posttraumatic drug-resistant epilepsy are also discussed.

Recent findings
Continuous electroencephalography is indicated for children and adults with TBI and coma because of the high incidence of nonconvulsive seizures, periodic discharges, and associated secondary brain injury in this population. Neuroinflammation is a central component of secondary brain injury and appears to play a key role in epileptogenesis. Levetiracetam is increasingly used for seizure prophylaxis in adults and children, but variability remains.

Summary
PTS occur commonly after TBI and are associated with secondary brain injury and worse outcomes in adults and children. Current medical and surgical management options for PTS and PTE are reviewed.
A test of four evolutionary hypotheses of pregnancy food cravings: evidence for the social bargaining model
Authors: Placek Caitlyn 
Published: October 2017

The onset of cravings for items not typically desired is often considered a hallmark of pregnancy. Given the ubiquity of cravings, this phenomenon remains surprisingly understudied. The current study tested four hypotheses of pregnancy food cravings: behavioural immune system, nutrient seeking, resource scarcity and social bargaining. The research took place in Tamil Nadu, South India, with pregnant women residing in rural villages (
N
= 94). Methods included structured interviews and anthropometric measures. Findings revealed that unripe mango and unripe tamarind were the two most frequently mentioned food cravings among this population, but were not sufficiently supported by the
a priori
models. Results confirmed that the social bargaining model was the best explanation for the etic category of toxic/pathogenic food items, suggesting that pregnant women crave dangerous foods when experiencing heightened social pressures. Finally, toxicity/pathogenicity was a confounding factor for the nutrient seeking and resource scarcity models, calling into question the validity of these models in adverse environments. Overall, these findings present important implications for research on pregnancy food cravings, such that in resource-scarce and pathogen-dense environments, cravings might target teratogenic items that signal a need for increased social support.
Utility of Shrimp andDer p 10specific IgE for Shrimp Allergy Diagnosis in Non-House Dust Mite Sensitized Patients
Authors: Tuano Karen Thursday S. , Anvari Sara , Hanson Imelda Celine , Hajjar Joud , Seeborg Filiz , Noroski Lenora M. , Guffey Danielle , Kang Grace , Orange Jordan Scott , Davis Carla M. 
Published: October 2017

ABSTRACTBackgroundThere are no set specific IgE (sIgE) to predict shrimp allergy as cross-reactivity with other arthropods play a role in shrimp sensitization.ObjectiveThis study identifies the allergens associated with shrimp allergy in house dust mite (HDM) and non-HDM sensitized patients.MethodsPatients with shrimp sensitization (positive skin prick test [SPT] and/or sIgE) with/without history of clinical reaction were recruited. Allergy was confirmed by oral food challenge (OFC) except for patients with history of anaphylaxis. Shrimp allergic (SA) and shrimp tolerant (ST) patients were further classified based on HDM sensitivity. The sIgE to shrimp, shrimp and HDM components were performed. Fisher’s exact test, Wilcoxon sum rank test and receiver operating characteristics analyses were done.ResultsOf 79 patients recruited, 12 SA (7 positive OFC and 5 with history of anaphylaxis), 18 ST and 10 non-shrimp sensitized controls (NC) were enrolled. In non-HDM sensitized patients, sIgE to shrimp (10.5 kUA/L, p=0.012) andDer p 10(4.09 kUA/L, p=0.035) were higher in SA patients. Shrimp sIgE ≥3.55 kUA/L had 100% sensitivity and 85.71% specificity (ROC=0.94[0.81, 1.0]).Der p 10sIgE ≥3.98 kUA/L had sensitivity of 80% and specificity of 100% (ROC=0.86[0.57, 1.0]).rPen a1 ≥1.1 kUA/L had sensitivity of 80% and specificity of 85.7% (ROC=0.80[0.47,1.0]).ConclusionsIn non-HDM sensitized patients, shrimp sIgE ≥3.55 kUA/L and Der p 10 sIgE≥3.98 kUA/L give 100% sensitivity and specificity, respectively, to diagnose shrimp allergy. HDM sensitivity can influence sIgE levels to shrimp and shrimp/HDM components due to cross-reactivity.
Sub-Confluent Culture of Mouse Embryonic Stem Cell-derived Ventricular Cardiomyocytes On & In Gels - Enhancement of Maturation Phenotype Relative to Tissue Culture Polystyrene via Enabling of Auxotonic Contraction
Authors: Mittal Nikhil , Atmanli Ayhan , Hu Dongjian , Groeneweg Daniel , Kausel Eduardo , Domian Ibrahim J 
Published: October 2017

AbstractCardiac myocytes (CMs) obtained by differentiating embryonic stem cells (ES-CMs) have an immature phenotype and promoting the maturation of such PSC-derived cardiomyocytes remains a major limitation in the development of stem cell models of human cardiovascular disease. We cultured murine ES-CMs in a collagen gel (3D) at a low density, or on collagen-coated polystyrene (2D) and found that 3D culture results in dramatic improvement of the maturation rate and end-state gene expression of ES-CMs. There are two main differences between CMs cultured in 3D versus 2D; in 3D the mechanical stiffness of the environment is lower, enabling auxotonic instead of isometric contraction; and, in 3D the amount of cell-cell interaction is higher. To isolate the contributions, we first cultured ES-CMsongels (2D substrates) that are softer than tissue culture plastic, enabling auxotonic contraction, while controlling for dimensionality and cell interaction. This indeed promoted a mature gene expression profile, while also enabling the maintenance of sarcomeres. Next, we determined that increased cell-cell interaction inhibits the mature gene expression of ES-CMs. Thus, auxotonic contraction is the likely mechanism for improved gene expression in sub-confluent 3D culture. However, 2D auxotonic contraction may offer a suitable compromise between obtaining enhanced gene expression and morphology. After 6 weeks of culture on gels, via Di-8-ANEPPs and WGA staining we also detected CMs forming a t-tubule network. Collectively these results demonstrate that 3D and 2D cultures that enable auxotonic contraction enhance aspects of the maturation of ES-CMs.
Behavioral and biochemical effects of ethanol withdrawal in zebrafish
Authors: da Silva Chaves Suianny Nayara , Rocha Gabriel Felício , Costa Bruna Patrícia Dutra , de Oliveira Witallo Etevaldo Araújo , Lima Monica Gomes , de Siqueira Silva Diógenes Henrique , Maximino Caio 
Published: October 2017

AbstractChronic alcohol use induces adaptations and toxicity that can induce symptoms of anxiety, autonomic hyperarousal, and epileptic seizures when alcohol is removed (withdrawal syndrome). Zebrafish has recently gained wide attention as a behavioral model to study the neurobehavioral effects of acute and chronic alcohol use, including withdrawal. The literature, however, is very contradictory on findings regarding withdrawal effects, with some studies reporting increased anxiety, while others report no effect. A meta-analytic approach was taken to find the sources of this heterogeneity, and ethanol concentration during exposure and exposure duration were found to be the main sources of variation. A conceptual replication was also made using continuous exposure for 16 days in waterborne ethanol (0.5%) and assessing anxiety-like behavior in the light/dark test after 60 min withdrawal. Withdrawal was shown to reduce preference for darkness, consistent with decreased anxiety, but to increase risk assessment, consistent with increased anxiety. Animals were also subjected to the withdrawal protocol and injected with pilocarpine in a sub-convulsive dose to assess susceptibility to epileptic seizure-like behavior. The protocol was sufficient to increase susceptibility to epileptic seizure-like behavior in animals exposed to ethanol. Finally, withdrawal also decreased catalase activity in the brain, but not in the head kidney, suggesting mechanisms associated with the behavioral effects of ethanol withdrawal.
A machine learning approach to predicting short-term mortality risk in patients starting chemotherapy
Authors: Elfiky Aymen A. , Pany Maximilian J. , Parikh Ravi B. , Obermeyer Ziad 
Published: October 2017

ABSTRACTBackgroundCancer patients who die soon after starting chemotherapy incur costs of treatment without benefits. Accurately predicting mortality risk from chemotherapy is important, but few patient data-driven tools exist. We sought to create and validate a machine learning model predicting mortality for patients starting new chemotherapy.MethodsWe obtained electronic health records for patients treated at a large cancer center (26,946 patients; 51,774 new regimens) over 2004-14, linked to Social Security data for date of death. The model was derived using 2004-11 data, and performance measured on non-overlapping 2012-14 data.Findings30-day mortality from chemotherapy start was 2.1%. Common cancers included breast (21.1%), colorectal (19.3%), and lung (18.0%). Model predictions were accurate for all patients (AUC 0.94). Predictions for patients starting palliative chemotherapy (46.6% of regimens), for whom prognosis is particularly important, remained highly accurate (AUC 0.92). To illustrate model discrimination, we ranked patients initiating palliative chemotherapy by model-predicted mortality risk, and calculated observed mortality by risk decile. 30-day mortality in the highest-risk decile was 22.6%; in the lowest-risk decile, no patients died. Predictions remained accurate across all primary cancers, stages, and chemotherapies—even for clinical trial regimens that first appeared in years after the model was trained (AUC 0.94). The model also performed well for prediction of 180-day mortality (AUC 0.87; mortality 74.8% in the highest risk decile vs. 0.2% in the lowest). Predictions were more accurate than data from randomized trials of individual chemotherapies, or SEER estimates.InterpretationA machine learning algorithm accurately predicted short-term mortality in patients starting chemotherapy using EHR data. Further research is necessary to determine generalizability and the feasibility of applying this algorithm in clinical settings.
Sexual dimorphism of complement-dependent microglial synaptic pruning and other immune pathways in the developing brain
Authors: Prilutsky Daria , Kho Alvin T. , Feiglin Ariel , Hammond Timothy , Stevens Beth , Kohane Isaac S. 
Published: October 2017

AbstractSexual dimorphism has been reported in the prevalence, onset and progression of neurodevelopmental and neurodegenerative disorders. We hypothesize that immunological signaling in the developing brain, notably the complement cascade underlying microglial synaptic pruning, could be one mechanism for this dimorphism. Here we show that genes differentially expressed between male and female normal cortical development are enriched for pathways associated with the activation of the innate immune system, complement cascade and phagocytic processes. Specifically, the male brain is enriched for the expression of genes associated with phagocytic function of microglia through complement-dependent synaptic pruning especially at the developmental stages before birth. Our results suggest the existence of a common regulatory module involved in both prenatal immune activation in males and postnatal immune activation in females. The activation of immune pruning pathways at different stages of normal male and female development could provide valuable insights about critical periods of plasticity and refinement in the human cortex that could explain the different vulnerabilities of males and females to neurological disorders.
An evidence-based approach to globally assess the covariate-dependent effect of MTHFR SNP rs1801133 on plasma homocysteine: a systematic review and meta-analysis
Authors: Jin Huifeng , Cheng Haojie , Chen Wei , Sheng Xiaoming , Brown Mark , Tian Junqiang 
Published: October 2017

BackgroundThe single nucleotide polymorphism (SNP) of the gene Methylenetetrahydrofolate Reductase (MTHFR) C677T (or rs1801133) is the most established genetic factor that increases plasma total homocysteine (tHcy) and consequently results in hyperhomocysteinemia. Yet given the limited penetrance of this genetic variant, it is necessary to individually predict the risk of hyperhomocysteinemia for a rs1801133 carrier.ObjectiveWe hypothesized that variability of this genetic risk is largely due to the presence of factors (covariates) that serve as effect modifiers and/or confounders, such as folic acid (FA) intake, and aimed to assess this risk in the complex context of these covariates.DesignWe systematically extracted from published studies the data of tHcy, rs1801133, and any previously reported rs1801133 covariates. The resulting meta-dataset was first used to analyze the covariates’ modifying effect by meta regression and other statistical means. Subsequently, we stratified tHcy data by the rs1801133 genotypes and analyzed under each genotype the variability of the risk resulted from the covariates’ confounding.ResultsThe dataset contains data of 36 rs1801133 covariates that were collected from 114,448 subjects and 249 qualified studies, among which 6 covariates (sex, age, race, FA intake, smoking, and alcohol consumption) are the most frequently informed and therefore included for statistical analysis. The effect of rs1801133 on tHcy exhibits significant variability that can be attributed to effect modification and, to a larger degree, confounding by these covariates. Via statistical modeling, we predicted the covariate-dependent risk of tHcy elevation and hyperhomocysteinemia in a systematic manner.Conclusionswe demonstrated an evidence-based approach that globally assesses the covariate-dependent effect of rs1801133 on tHcy. The results should assist clinicians in interpreting the rs1801133 data from genetic testing for their patients. Such information is also important for the public that increasingly receives genetic data from commercial services without interpretation of its clinical relevance.
Deep Learning for Multi-task Plant Phenotyping
Authors: Pound Michael P. , Atkinson Jonathan A. , Wells Darren M. , Pridmore Tony P. , French Andrew P. 
Published: October 2017

AbstractPlant phenotyping has continued to pose a challenge to computer vision for many years. There is a particular demand to accurately quantify images of crops, and the natural variability and structure of these plants presents unique difficulties. Recently, machine learning approaches have shown impressive results in many areas of computer vision, but these rely on large datasets that are at present not available for crops. We present a new dataset, called ACID, that provides hundreds of accurately annotated images of wheat spikes and spikelets, along with image level class annotation. We then present a deep learning approach capable of accurately localising wheat spikes and spikelets, despite the varied nature of this dataset. As well as locating features, our network offers near perfect counting accuracy for spikes (95.91%) and spikelets (99.66%). We also extend the network to perform simultaneous classification of images, demonstrating the power of multi-task deep architectures for plant phenotyping. We hope that our dataset will be useful to researchers in continued improvement of plant and crop phenotyping. With this in mind, alongside the dataset we will make all code and trained models available online.
Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen
Authors: Felten Judith , Vahala Jorma , Love Jonathan , Gorzsás András , Rüggeberg Markus , Delhomme Nicolas , Leśniewska Joanna , Kangasjärvi Jaakko , Hvidsten Torgeir R. , Mellerowicz Ewa J. , Sundberg Björn 
Published: October 2017

SummaryResearch conductedThe phytohormone ethylene impacts secondary stem growth in plants by stimulating cambial activity, xylem development and fiber over vessel formation. Here we report the effect of ethylene on secondary cell wall formation and the molecular connection between ethylene signaling and wood formation.MethodsWe applied exogenous ethylene or its precursor 1-aminocyclopropane-1-carboxylic acid (ACC) to wild type and ethylene insensitive hybrid aspen trees(Populus tremula x tremuloides)and studied secondary cell wall anatomy, chemistry and ultrastructure. We furthermore analyzed the transcriptome (RNA Seq) after ACC application to wild type and ethylene insensitive trees.Key resultsWe demonstrate that ACC and ethylene induce gelatinous-layers (G-layers) and alter the fiber cell wall cellulose microfibril angle. G-layers are tertiary wall layers rich in cellulose, typically found in tension wood of aspen trees. A vast majority of transcripts affected by ACC are downstream of ethylene perception and include a large number of transcription factors (TFs). Motif-analyses reveal potential connections between ethylene TFs (ERFs, EIN3/EIL1) and wood formation.ConclusionG-layer formation upon ethylene application suggests that the increase in ethylene biosynthesis observed during tension wood formation is important for its formation. Ethylene-regulated TFs of the ERF and EIN3/EIL1 type could transmit the ethylene signal.
Micro-encapsulation extends mycelial viability of Streptomyces lividans 66 and increases enzyme production
Authors: Zacchetti Boris , Andrianos Agathoklis , van Dissel Dino , de Ruiter Evelien , van Wezel Gilles P. , Claessen Dennis 
Published: October 2017

AbstractBackgroundFilamentous bacteria of the genus Streptomyces produce a large arsenal of industrially relevant antibiotics and enzymes. The industrial production of these molecules occurs in large fermenters, where many streptomycetes form dense mycelial networks called pellets. Pellets are characterized by slow growth and inefficient nutrient transfer and therefore regarded as undesirable from the perspective of productivity. Although non-pelleting strains have increased growth rates, their morphology also leads to a dramatic increase in the viscosity of the culture broth, which negatively impacts the process dynamics.ResultsHere, we applied immobilization of Streptomyces lividans 66 using alginate as semi-solid matrix. This alginate-mediated micro-encapsulation increased the production of the extracellular enzyme tyrosinase more than three-fold. The increased production was accompanied by extended viability of the mycelium and a dramatic reduction in the release of intracellular proteins into the culture broth.ConclusionsOur data demonstrate the utility of microencapsulation as a powerful technique to achieve higher yields and lower downstream-processing costs of streptomycetes.
Conservation of differentiation but transformation of initiation in hippocampal neurogenesis
Authors: Hochgerner Hannah , Zeisel Amit , Lönnerberg Peter , Linnarsson Sten 
Published: October 2017

ABSTRACTThe dentate gyrus in the hippocampal formation is one of few regions in the brain where neurogenesis persists in the adult, and is therefore studied in the context of neurodevelopment and regenerative medicine. However, the relationship between developmental and adult neurogenesis has not been studied in detail. Here, we used extensive and unbiased single-cell RNA-seq to reveal the molecular dynamics and diversity of cell types in perinatal, juvenile and adult mice. We found clearly distinct quiescent and proliferating progenitor cell types, linked by transient intermediate states to neuroblast stages and fully mature granule cells. The molecular identity of quiescent and proliferating radial glia shifted after postnatal day 5, and was then maintained through postnatal and adult stages. A similar shift was observed for granule cells at P20. In contrast, intermediate progenitor cells, neuroblasts and immature granule cells were nearly indistinguishable at all ages. These findings demonstrate the fundamental continunity of postnatal and adult neurogenesis in the hippocampus, and pinpoint the early postnatal transformation of radial glia from embryonic progenitors to adult quiescent stem cells.
KaryoScan: abnormal karyotype detection from whole-exome sequence
Authors: Maxwell Evan K. , Gonzaga-Jauregui Claudia , McCarthy Shane E. , O’Dushlaine Colm , Staples Jeffrey , Lopez Alexander E. , Bai Xiaodong , Penn John , Ulloa Rick , Gottesman Omri , Baras Aris , Dewey Frederick E. , Staples Jeffrey , Overton John D. , Puffenberger Erik , Habegger Lukas , Reid Jeffrey G. 
Published: October 2017

AbstractMotivationDetection of abnormal karyotypes from whole-exome sequencing has significant clinical potential, enabling a primary screen for chromosomal anomalies among samples undergoing short-read sequencing for nucleotide resolution genomic characterization.ResultsWe present KaryoScan, a high-throughput method for detecting chromosomal anomalies within large cohort exome sequencing studies. We detect and validate autosomal and sex chromosomal aneuploidies in a large exome sequencing cohort, and demonstrate detection of smaller and complex events (partial chromosome, mosaic, copy neutral, and complex rearrangements), representing the range of anomalies that can be uncovered from the exome.Availabilityhttps://github.com/rgcgithub/karyoscan