bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dysphagia Rates after Anterior Cervical Diskectomy and Fusion: A Systematic Review and Meta-Analysis
Authors: Shriver Michael F. , Lewis Daniel J. , Kshettry Varun R. , Rosenbaum Benjamin P. , Benzel Edward C. , Mroz Thomas E. 
Published: May 2016

Study Design  Systematic review and meta-analysis. Objective Anterior cervical diskectomy and fusion (ACDF) is an effective surgical option for patients with cervical radiculopathy, myelopathy, or deformity. Although ACDF is generally safe, dysphagia is a common complication. Despite its high incidence, prolonged postoperative dysphagia is poorly understood; its etiology remains relatively unknown, and its risk factors are widely debated. Methods We searched MEDLINE, Scopus, Web of Science, and Embase for studies reporting complications for cervical diskectomy with plating. We recorded dysphagia events from all included studies and calculated effect summary values, 95% confidence intervals (CIs), Q values, and I2 values. Results Of the 7,780 retrieved articles, 14 met inclusion criteria. The overall dysphagia rate was 8.5% (95% CI 5.7 to 11.3%). The rate of moderate or severe dysphagia was 4.4% (0.4 to 8.4%). Follow-up times of <12, 12 to 24, and >24 months reported rates of 19.9% (6.0 to 33.7%), 7.0% (5.2 to 8.7%), and 7.6% (1.4 to 13.8%), respectively. Studies utilizing the Bazaz Dysphagia Score resulted in an increase in dysphagia diagnosis relative to studies with no outlined criteria (19.8%, 5.9 to 33.7% and 6.9%, 3.7 to 10.0%, respectively), indicating that the criteria used for dysphagia identification are critical. There was no difference in dysphagia rate with the use of autograft versus allograft. Conclusions This review represents a comprehensive estimation of the actual incidence of dysphagia across a heterogeneous group of surgeons, patients, and criteria. The classification scheme for dysphagia varied significantly within the literature. To ensure its diagnosis and identification, we recommend the use of a standardized, well-outlined method for dysphagia diagnosis.
Relativistic BEC-BCS Crossover in a magnetized Nambu-Jona-Lasinio Model
Authors: Duarte Dyana C. , Farias R.L.S. , Manso Patricía H.A. , Ramos Rudnei O. 
Published: May 2016

Abstract
The BEC-BCS crossover in the NJL model is studied in the presence of an external magnetic field. Particular attention is given to two different regularization schemes used in the literature and we show how they compare to each other. The comparison is made for the case of a cold and magnetized two color NJL model. We also make a brief discussion about the Nc
= 3 case without magnetic fields, as an extension of this work in the future.
Spectral identification of topological domains
Authors: Chen Jie , Hero Alfred O. , Rajapakse Indika 
Published: May 2016

Abstract
Motivation: Topological domains have been proposed as the backbone of interphase chromosome structure. They are regions of high local contact frequency separated by sharp boundaries. Genes within a domain often have correlated transcription. In this paper, we present a computational efficient spectral algorithm to identify topological domains from chromosome conformation data (Hi-C data). We consider the genome as a weighted graph with vertices defined by loci on a chromosome and the edge weights given by interaction frequency between two loci. Laplacian-based graph segmentation is then applied iteratively to obtain the domains at the given compactness level. Comparison with algorithms in the literature shows the advantage of the proposed strategy.
Results: An efficient algorithm is presented to identify topological domains from the Hi-C matrix.
Availability and Implementation: The Matlab source code and illustrative examples are available at http://bionetworks.ccmb.med.umich.edu/
Contact: indikar@med.umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm
Authors: Luo Huimin , Wang Jianxin , Li Min , Luo Junwei , Peng Xiaoqing , Wu Fang-Xiang , Pan Yi 
Published: May 2016

Abstract
Motivation: Drug repositioning, which aims to identify new indications for existing drugs, offers a promising alternative to reduce the total time and cost of traditional drug development. Many computational strategies for drug repositioning have been proposed, which are based on similarities among drugs and diseases. Current studies typically use either only drug-related properties (e.g. chemical structures) or only disease-related properties (e.g. phenotypes) to calculate drug or disease similarity, respectively, while not taking into account the influence of known drug–disease association information on the similarity measures.
Results: In this article, based on the assumption that similar drugs are normally associated with similar diseases and vice versa, we propose a novel computational method named MBiRW, which utilizes some comprehensive similarity measures and Bi-Random walk (BiRW) algorithm to identify potential novel indications for a given drug. By integrating drug or disease features information with known drug–disease associations, the comprehensive similarity measures are firstly developed to calculate similarity for drugs and diseases. Then drug similarity network and disease similarity network are constructed, and they are incorporated into a heterogeneous network with known drug–disease interactions. Based on the drug–disease heterogeneous network, BiRW algorithm is adopted to predict novel potential drug–disease associations. Computational experiment results from various datasets demonstrate that the proposed approach has reliable prediction performance and outperforms several recent computational drug repositioning approaches. Moreover, case studies of five selected drugs further confirm the superior performance of our method to discover potential indications for drugs practically.
Availability and Implementation: http://github.com//bioinfomaticsCSU/MBiRW .
Contact: jxwang@mail.csu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
MEANS: python package for Moment Expansion Approximation, iNference and Simulation
Authors: Fan Sisi , Geissmann Quentin , Lakatos Eszter , Lukauskas Saulius , Ale Angelique , Babtie Ann C. , Kirk Paul D. W. , Stumpf Michael P. H. 
Published: May 2016

Abstract
Motivation: Many biochemical systems require stochastic descriptions. Unfortunately these can only be solved for the simplest cases and their direct simulation can become prohibitively expensive, precluding thorough analysis. As an alternative, moment closure approximation methods generate equations for the time-evolution of the system’s moments and apply a closure ansatz to obtain a closed set of differential equations; that can become the basis for the deterministic analysis of the moments of the outputs of stochastic systems.
Results: We present a free, user-friendly tool implementing an efficient moment expansion approximation with parametric closures that integrates well with the IPython interactive environment. Our package enables the analysis of complex stochastic systems without any constraints on the number of species and moments studied and the type of rate laws in the system. In addition to the approximation method our package provides numerous tools to help non-expert users in stochastic analysis.
Availability and implementation: https://github.com/theosysbio/means
Contacts: m.stumpf@imperial.ac.uk or e.lakatos13@imperial.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Ensemble squid habitat model using three-dimensional ocean data
Authors: Alabia Irene D. , Saitoh Sei-Ichi , Igarashi Hiromichi , Ishikawa Yoichi , Usui Norihisa , Kamachi Masafumi , Awaji Toshiyuki , Seito Masaki 
Published: May 2016

Abstract
Neon flying squid (Ommastrephes bartramii) is a large pelagic squid internationally harvested in the North Pacific. Here, we examined its potential habitat in the central North Pacific using an ensemble modelling approach. Initially, ten statistical models were constructed by combining the squid fishing points, selected vertical layers of the sea temperature and salinity, sea surface height (SSH), and SSH gradient from the multi-variate ocean variational estimation system for the western North Pacific from June to July 1999–2011. The variable selection analyses have captured the importance of vertical temperature and salinity layers at the upper 300 and 440 m, respectively, coinciding with the reported vertical ranges of diel migration for the squid's primary prey species in the North Pacific. The evaluation of the habitat predictions using the independent sets of the presence data from 2012 to 2014 showed significant variability in the predictive accuracy, which is likely reflective of the interannual differences in environmental conditions across the validation periods. Our findings from ensemble habitat model approach using three-dimensional oceanographic data were able to characterize the near- and subsurface habitats of the neon flying squid. Moreover, our results underpinned the possible link between interannual environmental variability and spatio-temporal patterns of potential squid habitats. As such, these further suggest that an ensemble model approach could present a promising tool for operational fishery application and squid resource management.
Membrane state diagrams make electrophysiological models simple
Authors: Law Robert , Jones Stephanie R. 
Published: May 2016

AbstractIon channels are ubiquitous in living systems. Through interactions with membrane potential, ion channels both control metabolic events and mediate cell communication. Consequentially, membrane bioelectricity bears on fields ranging from cancer etiology to computational neuro-science. Conductance models have proven successful in quantitatively capturing these dynamics but are often considered difficult, with interpretation relegated to specialists. To facilitate research in membrane dynamics, especially in fields where roles for ion channels are just beginning to be quantified, we must make these models easy to understand.Here, we show that the membrane differential equation central to conductance models can be understood using simple circular geometry. The membrane state diagrams we construct are compact, faithful representations of conductance model state, designed to look like circular “cells” with currents flowing in and out. Every feature of a membrane state diagram corresponds to a physiological variable, so that insight taken from a diagram can be translated back to the underlying model. The construction is elementary: we convert conductances to angles subtended on the circle and potentials to radii; currents are then areas of the enclosed annular sectors.Our method clarifies a powerful but prohibitive modeling approach and has the potential for widespread use in both electrophysiological research and pedagogy. We illustrate how membrane state diagrams can augment traditional methods in the stability analysis of voltage equilibria and in depicting the Hodgkin-Huxley action potential, and we use the diagrams to infer the possibility of nontrivial fixed-voltage channel population dynamics by visual inspection rather than linear algebra.
Allowance for uncollectible accounts as a tool for earnings management
Authors: Lee Hyun-Ah , Choi Won-Wook 
Published: May 2016

Purpose
This study aims to verify the circumstances under which managing the allowance for uncollectible accounts is used as a tool of earnings management.

Design/methodology/approach
The authors investigate whether bad debt expense, which is an income statement counterpart of allowance for uncollectible accounts, is adjusted downward when pre-managed earnings is slightly above zero earnings, prior year’s earnings or analysts’ forecasts.

Findings
The findings of this study show that firms manage bad debt expense downward to avoid losses, sustain the prior year’s earnings and meet or beat analysts’ forecasts. The authors also find that the understatement of bad debt expense to meet earnings benchmarks is pronounced for firms with high tax costs.

Social implications
Standard setters and auditors can gain a better understanding in detail of the practices and methods of managing earnings via the allowance for uncollectible accounts.

Originality/value
This study is the first to examine earnings management via the allowance for uncollectible accounts in non-financial Korean firms. In addition, the findings provide the evidence that firms prefer to use the allowance for uncollectible accounts as a strategic tool to meet benchmarks, especially when their tax costs are high.
Nexus between financial inclusion and economic growth
Authors: Sharma Dipasha 
Published: May 2016

Purpose
The purpose of this study is to assess the nexus between the vast dimensions of financial inclusion and economic development of the emerging Indian economy.

Design/methodology/approach
In this study, vector auto-regression (VAR) models and Granger causality test were followed to test the main research question in Indian context. The data were collected on various dimensions of financial inclusion and economic development for the period 2004-2013.

Findings
Empirical results and discussion suggest that there is a positive association between economic growth and various dimensions of financial inclusion, specifically banking penetration, availability of banking services and usage of banking services in terms of deposits. Granger causality analysis reveals a bi-directional causality between geographic outreach and economic development and a unidirectional causality between the number of deposits/loan accounts and gross domestic product. The results obtained favor social banking experiments in India with a deepening of banking institutions.

Research limitations/implications
This study is limited to the banking institutions and specifically to the emerging and developing economies.

Practical implications
This study analyzes the quantitative value of social banking experiments and governments’ efforts to enhance financial inclusion in terms of economic growth.

Social implications
Financial inclusion plays a key role in developing a strong and an efficient financial infrastructure, which facilitates the growth of an economy. The findings of the study reveal that there is a strong association between banking penetration and growth. The discussion leads in the favor of deepening of the banking institutions, and therefore, policymakers can look forward to these findings to maintain a sustainable-inclusive-developed economic system in an emerging economy like India.

Originality/value
This study is original in nature and includes recent evidence and efforts to promote financial inclusion in the Indian economy. The findings of this study will be of value to banks and policymakers.
Tuning the Functional Properties of Polysaccharide–Protein Bio‐Based Edible Films by Chemical, Enzymatic, and Physical Cross‐Linking
Authors: Benbettaïeb Nasreddine , Gay Jean‐Pierre , Karbowiak Thomas , Debeaufort Frédéric 
Published: May 2016

AbstractAmong natural biopolymers, polysaccharides and proteins are very promising for biodegradable and edible wraps with different characteristics, so that their formulations can be tailor‐made to suit the needs of a specific commodity. Films prepared from polysaccharides have good gas barrier properties but exhibit lower resistance to moisture compared to protein films (edible) or polylactide films (biodegradable). Protein‐based films show better mechanical and oxygen barrier properties compared to polysaccharide films. For that reason, film performances may be enhanced by producing blend systems, where hydrocolloids (mixtures of proteins and/or polysaccharides) form a continuous and more cohesive network. However, the lower water barrier properties of hydrocolloid films and their lower mechanical strength in comparison with synthetic polymers limit their applications in food packaging. Therefore, the enhancement of biopolymer film properties has been studied to attain appropriate applications. This review provides an extensive synthesis of the improvement of the properties of edible polysaccharide–protein films by way of various chemical, enzymatic, and physical methods. These methods primarily aim at improving the mechanical resistance. They also permit to ameliorate the water and gas barrier properties and related functional properties.
Blood Pressure and Mortality in Hemodialysis Patients: A Systematic Review of an Ongoing Debate
Authors: Khan Yusra Habib , Sarriff Azmi , Adnan Azreen Syazril , Khan Amer Hayat , Mallhi Tauqeer Hussain 
Published: May 2016

AbstractHypertension is prevalent in 75–80% of hemodialysis patients and remains the most controversial prognostic marker in end stage kidney disease patients. In contrast to the general population where systolic blood pressure of ≤120 mm Hg is considered normal, a debate remains regarding the ideal target blood pressure in hemodialysis patients. Using the PUBMED and EMBASE databases, the research studies that evaluated the relationship between blood pressure measurements and mortality in hemodialysis patients were searched. Thirteen studies were identified from different regions of the world. Five studies reported low predialysis systolic blood pressure as a prognostic marker of mortality. Other studies showed varying results and reported postdialysis systolic blood pressure as well as ambulatory blood pressure as better predictors of mortality and emphasized their optimized control. One study in this review concluded that there is no direct relationship between mortality and blood pressure if the patients are on anti‐hypertensive medications. The observed all‐cause mortality varied from 12% to 36%, whereas the cardiovascular mortality varied from 16% to 60%. On the basis of studies included in the current review, a low predialysis systolic blood pressure (<120 mm Hg) is shown to be a widely accepted prognostic marker of mortality while ambulatory blood pressure best predicts CV mortality. Therefore, we recommend that apart from routine BP (pre, post and intradialysis) monitoring in centers, assessment of ambulatory BP must be mandatory for all patients to reduce CV mortality in hemodialysis patients.
Comparison and Characterization of Compounds with Antioxidant Activity in Lycium barbarum Using High‐Performance Thin Layer Chromatography Coupled with DPPH Bioautography and Tandem Mass Spectrometry
Authors: Lam Shing‐Chung , Luo Zhen , Wu Ding‐Tao , Cheong Kit‐Leong , Hu De‐Jun , Xia Zu‐Meng , Zhao Jing , Li Shao‐Ping 
Published: May 2016

AbstractMethanol extracts from 50 batches of Lycium barbarum (L. barbarum, wolfberry) in China were compared and characterized using high‐performance thin‐layer chromatography coupled with 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) bioautography (HPTLC‐DPPH) and electrospray ionization quadrupole time‐of‐flight tandem mass spectrometry (ESI‐Q‐TOF‐MS/MS), respectively. Results showed that similar components occupying the major antioxidant activity existed in L. barbarum collected from different origins. However, the average antioxidant capacities of methanol extracts of L. barbarum collected in Ningxia were significantly higher than those of Qinghai, Xinjiang, Inner Mongolia, and Gansu, which may contribute to rational use of L. barbarum in China. Furthermore, the chemical structure of compound with the highest antioxidant capacity was tentatively identified as 2‐O‐β‐d‐glucopyranosyl‐l‐ascorbic acid using ESI‐Q‐TOF‐MS/MS analysis, which possessed high potentials to be used as an antioxidant biomarker for the quality control of L. barbarum. Results are helpful for the bioactivity‐based quality control of L. barbarum, and beneficial for the improvement of their performance in functional/health foods area, suggesting that HPTLC‐DPPH bioautography with ESI‐Q‐TOF‐MS/MS could be used as a routine approach for quality control of antioxidant components in L. barbarum.
Is there an increased risk of falls and fractures in people with early diagnosed hip and knee osteoarthritis? Data from the Osteoarthritis Initiative
Authors: Smith Toby O. , Higson Emma , Pearson Matthew , Mansfield Michael 
Published: May 2016

AbstractAimsTo assess the probability of individuals with early‐diagnosed hip or knee osteoarthritis experiencing a fall and/or fracture compared to a cohort without osteoarthritis.MethodsData were analyzed from the Osteoarthritis Initiative dataset. We identified all people who were diagnosed with hip or knee osteoarthritis within a 12 month period, compared to those without osteoarthritis. We determined whether there was a difference in the occurrence of falls, with or without consequential fractures, between people newly diagnosed with hip or knee osteoarthritis compared to those who had not, using odd ratios (OR) and 95% confidence intervals (95% CI).ResultsFive hundred and fifty‐two individuals with hip osteoarthritis were compared to 4244 individuals without hip osteoarthritis; 1350 individuals with knee osteoarthritis were compared to 3445 individuals without knee osteoarthritis. People with knee osteoarthritis had a 54% greater chance of experiencing a fall compared to those without (OR: 1.54; 95% CI: 1.35–1.77). People with hip osteoarthritis had a 52% greater chance of experiencing a fall compared to those without hip osteoarthritis (OR: 1.52; 95% CI: 1.26–1.84). People with knee and hip osteoarthritis demonstrated over an 80% greater chance of experiencing a fracture in the first 12 months of their diagnosis compared to those without hip or knee osteoarthritis (total knee arthroplasty: OR 1.81; total hip arthroplasty: OR 1.84).ConclusionsThere is an increased risk of falls and fractures in early‐diagnosed knee and hip osteoarthritis compared to those without osteoarthritis. International guidelines on the management of hip and knee osteoarthritis should consider the management of falls risk.
Fluorinated alkyl substances and technical mixtures used in food paper‐packaging exhibit endocrine‐related activity in vitro
Authors: Rosenmai A. K. , Taxvig C. , Svingen T. , Trier X. , van Vugt‐Lussenburg B. M. A. , Pedersen M. , Lesné L. , Jégou B. , Vinggaard A. M. 
Published: May 2016

SummaryMigration of chemicals from packaging materials to foods may lead to human exposure. Polyfluoroalkyl substances (PFAS) can be used in technical mixtures (TMs) for use in food packaging of paper and board, and PFAS have been detected in human serum and umbilical cord blood. The specific structures of the PFAS in TMs are often unknown, but polyfluorinated alkyl phosphate esters (PAPs) have been characterized in TMs, food packaging, and in food. PAPs can be metabolized into fluorotelomer alcohols (FTOHs) and perfluoroalkyl carboxylic acids (PFCAs). Some PFAS have endocrine activities, highlighting the need to investigate these effects. Herein, we studied the endocrine activity of less characterized PFAS, including short‐chain PFCAs and FTOHs, PAPs, and TMs of unknown chemical composition. Long‐chain PFCAs were also included. We applied seven assays covering effects on estrogen, glucocorticoid, androgen, and peroxisome proliferator‐activated receptor (PPAR) activity, as well as steroidogenesis in vitro and ex vivo. In general, PAPs, FTOHs, TMs, and long‐chain PFCAs showed estrogenic activity through receptor activation and/or increasing 17β‐estradiol levels. Furthermore, short‐ and long‐chain PFCAs activated PPARα and PPARγ. Collectively, this means that (i) PAPs, FTOHs, and PFCAs exhibit endocrine activity through distinct and sometimes different mechanisms, (ii) two out of three tested TMs exhibited estrogenic activity, and (iii) short‐chain FTOHs showed estrogenic activity and short‐chain PFCAs generally activate both PPARα and PPARγ with similar potency and efficacy as long‐chain PFCAs. In conclusion, several new and divergent toxicological targets were identified for different groups of PFAS.