bluuebunny/crossref_metadata_2025_split huggingface dataset:
NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential
Authors: Guo Jing , Lin Feng , Zhang Xiaomeng , Tanavde Vivek , Zheng Jie 
Published: January 2017

Abstract

Summary
Waddington’s epigenetic landscape is a powerful metaphor for cellular dynamics driven by gene regulatory networks (GRNs). Its quantitative modeling and visualization, however, remains a challenge, especially when there are more than two genes in the network. A software tool for Waddington’s landscape has not been available in the literature. We present NetLand, an open-source software tool for modeling and simulating the kinetic dynamics of GRNs, and visualizing the corresponding Waddington’s epigenetic landscape in three dimensions without restriction on the number of genes in a GRN. With an interactive and graphical user interface, NetLand can facilitate the knowledge discovery and experimental design in the study of cell fate regulation (e.g. stem cell differentiation and reprogramming).

Availability and Implementation
NetLand can run under operating systems including Windows, Linux and OS X. The executive files and source code of NetLand as well as a user manual, example models etc. can be downloaded from http://netland-ntu.github.io/NetLand/.

Supplementary information
Supplementary data are available at Bioinformatics online.
chainCleaner improves genome alignment specificity and sensitivity
Authors: Suarez Hernando G , Langer Bjoern E , Ladde Pradnya , Hiller Michael 
Published: January 2017

Abstract

Motivation
Accurate alignments between entire genomes are crucial for comparative genomics. However, computing sensitive and accurate genome alignments is a challenging problem, complicated by genomic rearrangements.

Results
Here we present a fast approach, called chainCleaner, that improves the specificity in genome alignments by accurately detecting and removing local alignments that obscure the evolutionary history of genomic rearrangements. Systematic tests on alignments between the human and other vertebrate genomes show that chainCleaner (i) improves the alignment of numerous orthologous genes, (ii) exposes alignments between exons of orthologous genes that were masked before by alignments to pseudogenes, and (iii) recovers hundreds of kilobases in local alignments that otherwise would fall below a minimum score threshold. Our approach has broad applicability to improve the sensitivity and specificity of genome alignments.

Availability and Implementation
http://bds.mpi-cbg.de/hillerlab/chainCleaner/ or https://github.com/ucscGenomeBrowser/kent

Supplementary information
Supplementary data are available at Bioinformatics online.
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo
Authors: Kapli P , Lutteropp S , Zhang J , Kobert K , Pavlidis P , Stamatakis A , Flouri T 
Published: January 2017

Abstract

Motivation
In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced “Poisson Tree Processes” (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences.

Results
We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size.

Availability and Implementation
mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Generative adversarial networks recover features in astrophysical images of galaxies beyond the deconvolution limit
Authors: Schawinski Kevin , Zhang Ce , Zhang Hantian , Fowler Lucas , Santhanam Gokula Krishnan 
Published: January 2017

Abstract
Observations of astrophysical objects such as galaxies are limited by various sources of random and systematic noise from the sky background, the optical system of the telescope and the detector used to record the data. Conventional deconvolution techniques are limited in their ability to recover features in imaging data by the Shannon–Nyquist sampling theorem. Here, we train a generative adversarial network (GAN) on a sample of 4550 images of nearby galaxies at 0.01 &lt; z &lt; 0.02 from the Sloan Digital Sky Survey and conduct 10× cross-validation to evaluate the results. We present a method using a GAN trained on galaxy images that can recover features from artificially degraded images with worse seeing and higher noise than the original with a performance that far exceeds simple deconvolution. The ability to better recover detailed features such as galaxy morphology from low signal to noise and low angular resolution imaging data significantly increases our ability to study existing data sets of astrophysical objects as well as future observations with observatories such as the Large Synoptic Sky Telescope (LSST) and the Hubble and James Webb space telescopes.
Provoked Vestibulodynia
Authors: Dargie Emma , Gilron Ian , Pukall Caroline F. 
Published: January 2017

Objectives:
Provoked vestibulodynia (PVD) is an idiopathic vulvar pain condition characterized by burning pain at the vaginal opening in response to contact or pressure. Previous research has established some of the psychosocial difficulties experienced by these patients, but direct comparisons with other pain conditions are needed. The purpose of this study was to compare women with PVD to those with postherpetic neuralgia and pain-free control participants.

Materials and Methods:
Participants were invited to complete an anonymous online survey consisting of sociodemographic questions and a range of validated measures.

Results:
Women with PVD and postherpetic neuralgia (PHN) did not differ in terms of pain catastrophizing or pain anxiety, but women with PHN reported greater pain disability than those with PVD. Participants in both pain groups reported significantly more symptoms of stress, depression, anxiety, and sleep disturbances than pain-free controls; women with PHN reported more symptoms of depression than those with PVD, with no other differences between pain groups. Groups did not differ on relationship adjustment, but participants with PVD reported poorer sexual functioning than the other groups.

Discussion:
These results indicate that women with PVD and PHN experience similar mental health difficulties, but women with PHN experience more severe impact on their day-to-day functioning and mood. These results support the classification of PVD as a chronic pain condition, as both the pain groups differed from pain-free control participants on a range of measures. Finally, the presence of mental health difficulties and poorer sexual functioning highlights the importance of conducting biopsychosocial pain assessments.
A Holistic Approach to Antiaging as an Adjunct to Antiaging Procedures: A Review of the Literature
Authors: Saluja Sandeep S. , Fabi Sabrina G. 
Published: January 2017

BACKGROUNDAging is a multifactorial process and depends on both intrinsic and extrinsic factors. Procedural options for diminishing signs of intrinsic aging and cosmetic rejuvenation have expanded dramatically. However, less attention is paid to counseling patients on options for mitigating extrinsic factors related to aging.OBJECTIVEThe objective of this study was to review changes that occur with intrinsic and extrinsic aging, and provide evidence-based holistic counseling recommendations that can be used synergistically with aesthetic procedures to maximize antiaging interventions.MATERIALS AND METHODSA PubMed search was conducted for articles on intrinsic and extrinsic aging as it relates to skin, fat, muscle, and bone. Key clinical trials and studies on the effect of diet, hormones, exercise, sleep, stress, dental hygiene, smoking, pollution, and oxidative stress on the aging process are reviewed, and treatment recommendations are summarized based on available evidence.RESULTSConventional cosmetic procedures and cosmeceuticals work together with nutritious diet, exercise, dental hygiene, hormonal balance, stress reduction, smoking and pollution avoidance, and healthy sleep patterns for a better effect on antiaging.CONCLUSIONA combination approach of multiple nonsurgical modalities along with healthy lifestyle recommendations to minimize intrinsic and extrinsic aging factors allows cosmetic practitioners to target multiple facets of aging concurrently and maximize the aesthetic interventions cosmetic dermatologists/practitioners provide.
General Guidelines for Quality Assurance of Immunohistochemistry in a Mohs Lab
Authors: Kinas Carrie G. , Carroll Bryan T. 
Published: January 2017

BACKGROUND
The adoption of recently created protocols introduces Mohs laboratories to the principles of immunohistochemistry (IHC) performance validation and clinical laboratory regulations that are unique to these evolving technologies.

OBJECTIVE
To review Food and Drug Administration (FDA) IHC reagent classifications, IHC validation protocols, and quality assurance (QA) procedures and documentation needed in conjunction with IHC test guidelines.

METHODS
A focused review of IHC reagent classifications and guidelines in clinical testing laboratories was conducted using PubMed and FDA source documents.

RESULTS
The IHC regulation requirements are determined by the 3 FDA classifications of reagents: in vitro diagnostic reagents, analyte-specific reagents, and research use only reagents. To account for performance variability, IHC reagents benefit from routine validation and QA programs. We present our IHC adoption procedures for QA and documentation of IHC tests in a Mohs laboratory.

CONCLUSION
Incorporating a well-organized IHC validation and QA program into Mohs laboratories can increase regulatory compliance and reagent performance.
Association between anxiety and severe quality-of-life impairment in postmenopausal women: analysis of a multicenter Latin American cross-sectional study
Authors: Núñez-Pizarro Jorge L. , González-Luna Alejandro , Mezones-Holguín Edward , Blümel Juan E. , Barón Germán , Bencosme Ascanio , Benítez Zully , Bravo Luz M. , Calle Andrés , Flores Daniel , Espinoza María T. , Gómez Gustavo , Hernández-Bueno José A. , Martino Mabel , Lima Selva , Monterrosa Alvaro , Mostajo Desiree , Ojeda Eliana , Onatra William , Sánchez Hugo , Tserotas Konstantinos , Vallejo María S. , Witis Silvina , Zúñiga María C. , Chedraui Peter 
Published: January 2017

Abstract

Objective:
To evaluate associations between anxiety and severe impairment of quality of life (QoL) in Latin American postmenopausal women.

Methods:
This was a secondary analysis of a multicenter cross-sectional study among postmenopausal women aged 40 to 59 from 11 Latin American countries. We evaluated anxiety (The Goldberg Depression and Anxiety Scale), and QoL (Menopause Rating Scale [MRS]), and included sociodemographic, clinical, lifestyle, and anthropometric variables in the analysis. Poisson family generalized linear models with robust standard errors were used to estimate prevalence ratios (PRs) and 95% CIs. There were two adjusted models: a statistical model that included variables associated with the outcomes in bivariate analyses, and an epidemiologic model that included potentially confounding variables from literature review.

Results:
Data from 3,503 women were included; 61.9% had anxiety (Goldberg). Severe QoL impairment (total MRS score ≥17) was present in 13.7% of women, as well as severe symptoms (MRS subscales): urogenital (25.5%), psychological (18.5%), and somatic (4.5%). Anxiety was independently associated with severe QoL impairment and severe symptoms in the epidemiological (MRS total score: PR 3.6, 95% CI, 2.6-5.0; somatic: 5.1, 95% CI, 2.6-10.1; psychological: 2.8, 95% CI, 2.2-3.6; and urogenital: 1.4, 95% CI, 1.2-1.6) and the statistical model (MRS total score: PR 3.5, 95% CI, 2.6-4.9; somatic: 5.0, 95% CI, 2.5-9.9; psychological: 2.9, 95% CI, 2.2-3.7; and urogenital: 1.4; 95% CI, 1.2-1.6).

Conclusions:
In this postmenopausal Latin American sample, anxiety was independently associated with severe QoL impairment. Hence, screening for anxiety in this population is important.
Factors Determining the Uptake of Influenza Vaccination Among Children With Chronic Conditions
Authors: Chau Janita Pak Chun , Lo Suzanne Hoi Shan , Choi Kai Chow , Chau Matthew Hoi Kin , Tong Danny Wah Kun , Kwong Tany Kam Yuk , Thompson David R. 
Published: January 2017

Background:
Studies report that the influenza vaccination uptake rate among children with chronic conditions is alarmingly low. In Hong Kong, there has been no study examining parental decision making about influenza vaccination for children with chronic conditions, thereby limiting the knowledge base to inform the development of specific strategies to improve influenza vaccination rates. The aim of this study was to identify factors determining the uptake of influenza vaccination among children with chronic conditions.

Methods:
We conducted a cross-sectional survey of 623 parents with children having a chronic condition recruited from pediatric wards and specialty outpatient departments of 2 acute hospitals. A questionnaire developed by Daley et al based on the Health Belief Model was used to examine parents’ beliefs and attitudes toward influenza and vaccination.

Results:
The parents’ and their children’s mean age were 40.1 ± 8.1 and 8.0 ± 4.5 years, respectively. Among the children, the most prevalent chronic conditions were asthma, chronic respiratory disease and cardiomyopathy. One-third (33%) of the children had influenza vaccination in the past 12 months. More than one-third (39%) of parents intended to vaccinate their children against influenza in the coming influenza season. A multivariable logistic regression analysis revealed that all subscale scores except perceived severity and knowledge about influenza were independently significantly associated with uptake.

Conclusions:
The findings indicate that parents of children with chronic conditions lack awareness of the risks of influenza and have insufficient understanding about the benefits of vaccination. These findings could inform the development of interventions to promote vaccination uptake among children with chronic conditions.
Economic evaluation of an implementation strategy for the management of low back pain in general practice
Authors: Jensen Cathrine Elgaard , Riis Allan , Petersen Karin Dam , Jensen Martin Bach , Pedersen Kjeld Møller 
Published: January 2017

Abstract
In connection with the publication of a clinical practice guideline on the management of low back pain (LBP) in general practice in Denmark, a cluster randomised controlled trial was conducted. In this trial, a multifaceted guideline implementation strategy to improve general practitioners' treatment of patients with LBP was compared with a usual implementation strategy. The aim was to determine whether the multifaceted strategy was cost effective, as compared with the usual implementation strategy. The economic evaluation was conducted as a cost–utility analysis where cost collected from a societal perspective and quality-adjusted life years were used as outcome measures. The analysis was conducted as a within-trial analysis with a 12-month time horizon consistent with the follow-up period of the clinical trial. To adjust for a priori selected covariates, generalised linear models with a gamma family were used to estimate incremental costs and quality-adjusted life years. Furthermore, both deterministic and probabilistic sensitivity analyses were conducted. Results showed that costs associated with primary health care were higher, whereas secondary health care costs were lower for the intervention group when compared with the control group. When adjusting for covariates, the intervention was less costly, and there was no significant difference in effect between the 2 groups. Sensitivity analyses showed that results were sensitive to uncertainty. In conclusion, the multifaceted implementation strategy was cost saving when compared with the usual strategy for implementing LBP clinical practice guidelines in general practice. Furthermore, there was no significant difference in effect, and the estimate was sensitive to uncertainty.
Multimorbidity and the Risk of All-Cause 30-Day Readmission in the Setting of Multidisciplinary Management of Chronic Heart Failure
Authors: Wiley Joshua F. , Chan Yih-Kai , Ahamed Yasmin , Ball Jocasta , Carrington Melinda J. , Riegel Barbara , Stewart Simon 
Published: January 2017

Background:
Multimorbidity has an adverse effect on health outcomes in hospitalized individuals with chronic heart failure (CHF), but the modulating effect of multidisciplinary management is unknown.

Objective:
The aim of this study was to test the hypothesis that increasing morbidity would independently predict an increasing risk of 30-day readmission despite multidisciplinary management of CHF.

Methods:
We studied patients hospitalized for any reason with heart failure receiving nurse-led, postdischarge multidisciplinary management. We profiled a matrix of expected comorbidities involving the most common coexisting conditions associated with CHF and examined the relationship between multimorbidity and 30-day all-cause readmission.

Results:
A total of 830 patients (mean age 73 ± 13 years and 65% men) were assessed. Multimorbidity was common, with an average of 6.6 ± 2.4 comorbid conditions with sex-based differences in prevalence of 4 of 10 conditions. Within 30 days of initial hospitalization, 216 of 830 (26%) patients were readmitted for any reason. Greater multimorbidity was associated with increasing readmission (4%–44% for those with 0–1 to 8–9 morbid conditions; adjusted odds ratio, 1.25; 95% confidence interval, 1.13–1.38) for each additional condition. Three distinct classes of patient emerged: class 1—diabetes, metabolic, and mood disorders; class 2—renal impairment; and class 3—low with relatively fewer comorbid conditions. Classes 1 and 2 had higher 30-day readmission than class 3 did (adjusted P < .01 for both comparisons).

Conclusions:
These data affirm that multimorbidity is common in adult CHF inpatients and in potentially distinct patterns linked to outcome. Overall, greater multimorbidity is associated with a higher risk of 30-day all-cause readmission despite high-quality multidisciplinary management. More innovative approaches to target-specific clusters of multimorbidity are required to improve health outcomes in affected individuals.
Is Serial Electroneuronography Indicated Following Temporal Bone Trauma?
Authors: Remenschneider Aaron Kyle , Michalak Suzanne , Kozin Elliott D. , Barber Samuel , De Venecia Ronald K. , Hadlock Tessa A. , Jung David H. 
Published: January 2017

Objective:
Contemporary guidelines advise facial nerve (FN) decompression within 2 weeks of temporal bone trauma if a single electroneuronography (ENoG) demonstrates more than 90% degeneration of the FN. We report a case series demonstrating the potential of serial ENoG to guide FN management more than 2 weeks following injury.

Patients:
Adults with traumatic temporal bone fractures and resultant ipsilateral FN paresis.

Intervention:
Serial ENoG followed by observation or decompression of the FN.

Main Outcome Measure:
House–Brackmann (HB) graded FN function.

Results:
Nine cases of blunt temporal bone trauma resulting in ispilateral FN paralysis were identified and reviewed. Two patients were women, and average age at the time of trauma was 30 years (range, 17–52). Immediate paralysis occurred in four cases, while five were delayed. A single ENoG was performed in seven patients and was predictive of final function in six, while one patient had an initially reassuring ENoG but did not obtain full recovery of FN function (HB 4). Two patients underwent serial ENoG on a weekly basis which, while initially reassuring, demonstrated declining FN function on subsequent testing. Decompression was performed in both patients with excellent recovery of FN function (HB1 and HB2).

Conclusions:
The majority of ENoGs performed within 2 weeks of temporal bone trauma provide sufficient prognostic data for treatment decisions; however, in selected cases, a single ENoG may not adequately predict long-term FN outcomes. For patients failing to improve with observation alone, serial ENoG may capture declining FN function, identifying patients that may benefit from late decompression.
Maintenance and regulation of asymmetric phospholipid distribution in human erythrocyte membranes: implications for erythrocyte functions
Authors: Arashiki Nobuto , Takakuwa Yuichi 
Published: January 2017

Purpose of review
The article summarizes new insights into the molecular mechanisms for the maintenance and regulation of the asymmetric distribution of phospholipids in human erythrocyte membranes. We focus on phosphatidylserine, which is primarily found in the inner leaflet of the membrane lipid bilayer under low Ca2+ conditions (<1 μmol/l) and is exposed to the outer leaflet under elevated Ca2+ concentrations (>1 μmol/l), when cells become senescent. Clarification of the molecular basis of phosphatidylserine flipping and scrambling is important for addressing long-standing questions regarding phosphatidylserine functions.

Recent findings
ATP11C, a P-IV ATPase, has been identified as a major flippase in analyses of patient erythrocytes with a 90% reduction in flippase activity. Phospholipid scramblase 1 (PLSCR1) has been defined as a Ca2+-activated scramblase that is completely suppressed by membrane cholesterol under low Ca2+ concentrations.

Summary
For survival, phosphatidylserine surface exposure is prevented by cholesterol-mediated suppression of PLSCR1 under low Ca2+ concentrations, irrespective of flipping by ATP11C. In senescent erythrocytes, PLSCR1 is activated by elevated Ca2+, resulting in phosphatidylserine exposure, allowing macrophage phagocytosis. These recent molecular findings establish the importance of the maintenance and regulation of phosphatidylserine distribution for both the survival and death of human erythrocytes.