bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Reliability of Disease Activity Score in 28 Joints–C-Reactive Protein Might Be Overestimated in a Subgroup of Rheumatoid Arthritis Patients, When the Score Is Solely Based on Subjective Parameters
Authors: Jensen Hansen Inger Marie , Asmussen Andreasen Rikke , van Bui Hansen Mark Nam , Emamifar Amir 
Published: November 2016

Background
Disease Activity Score in 28 Joints (DAS28) is a scoring system to evaluate disease activity and treatment response in rheumatoid arthritis (RA). A DAS28 score of greater than 3.2 is a well-described limit for treatment intensification; however, the reliability of DAS28 might be overestimated.

Objective
The aim of this study was to evaluate the reliability of DAS28 in RA, especially focusing on a subgroup of patients with a DAS28 score of greater than 3.2.

Methods
Data from RA patients registered in the local part of Danish DANBIO Registry were collected in May 2015. Patients were categorized into 2 groups: First, those with DAS28 >3.2 with at least one swollen joint (SJ) or elevated C-reactive protein (CRP) (“objective group”), and second, patients with a DAS28 >3.2 who had no SJ, and CRP values were within the reference range (“subjective group”). Disease Activity Score in 28 Joints, Clinical Disease Activity Index, and Health Assessment Questionnaire scores were calculated for each group. We defined new score, DAS28 subjective, to focus on subjective parameters.

Results
Two hundred thirty patients were included; 198 (86.1%) and 32 (13.9%) patients were in the objective and subjective groups, respectively. Patients in the subjective group had lower mean values of DAS28 (P < 0.001) and Evaluator Global Assessment (P < 0.001) with less common immunoglobulin M rheumatoid factor (P < 0.001) and anti–cyclic citrullinated peptide positivity (P = 0.02) and contrarily higher mean values of tender joints (P = 0.04) and DAS28 based on subjective parameters (P = 0.003) compared with the objective group.

Conclusions
Rheumatoid arthritis scoring systems should be used cautiously in patients who are considered for treatment intensification. Patients with central sensitization and psychological problems and those with false-positive diagnosis of RA are at high risk of overtreatment.
Scalable variational inference for super resolution microscopy
Authors: Sun Ruoxi , Archer Evan , Paninski Liam 
Published: November 2016

AbstractSuper-resolution microscopy methods (e.g. STORM or PALM imaging) have become essential tools in biology, opening up a variety of new questions that were previously inaccessible with standard light microscopy methods. In this paper we develop new Bayesian image processing methods that extend the reach of super-resolution microscopy even further. Our method couples variational inference techniques with a data summarization based on Laplace approximation to ensure computational scalability. Our formulation makes it straightforward to incorporate prior information about the underlying sample to further improve accuracy. The proposed method obtains dramatic resolution improvements over previous methods while retaining computational tractability.
Resting-state fMRI correlations: from link-wise unreliability to whole brain stability
Authors: Pannunzi Mario , Hindriks Rikkert , Bettinardi Ruggero G. , Wenger Elisabeth , Lisofsky Nina , Martensson Johan , Butler Oisin , Filevich Elisa , Becker Maxi , Lochstet Martyna , Lindenberger Ulman , Kühn Simone , Deco Gustavo 
Published: November 2016

AbstractThe functional architecture of spontaneous BOLD fluctuations has been characterized in detail by numerous studies, demonstrating its potential relevance as a biomarker. However, the systematic investigation of its consistency is still in its infancy. Here, we analyze both the within- and between-subject variability as well as the test-retest reliability of resting-state functional connectivity (FC) estimates in a unique data set comprising multiple fMRI scans (42) from 5 subjects, and 50 single scans from 50 subjects. To this aim we adopted a statistical framework enabling us to disentangle the contribution of different sources of variability and their dependence on scan duration, and showed that the low reliability of single links can be largely improved using multiple scans per subject. Moreover, we show that practically all observed inter-region variability (at the link-level) is not significant and due to the statistical uncertainty of the estimator itself rather than to genuine variability among areas. Finally, we use the proposed statistical framework to demonstrate that, despite the poor consistency of single links, the information carried by the whole-brain spontaneous correlation structure is indeed robust, and can in fact be used as a functional fingerprint.
Anterior cingulate is a source of valence-specific information about value and uncertainty
Authors: Monosov Ilya E. 
Published: November 2016

SummaryExpectations of rewards and punishments can promote similar behavioral states, such as vigilance, as well as distinct behavioral states, such as approach or avoidance. However, the cortical circuits that underlie this behavioral diversity are poorly understood. In a Pavlovian procedure in which monkeys displayed a diverse repertoire of reward, punishment, and uncertainty related behaviors not mandated by the task, I show that many anterior-cingulate (ACC) neurons represent expected value and uncertainty in a valence-specific manner, for example about either rewards or punishments. This flexibility may facilitate the top-down control of many reward- and punishment-related actions and behavioral states.
Chromosome assembly of large and complex genomes using multiple references
Authors: Kolmogorov Mikhail , Armstrong Joel , Raney Brian J. , Streeter Ian , Dunn Matthew , Yang Fengtang , Odom Duncan , Flicek Paul , Keane Thomas , Thybert David , Paten Benedict , Pham Son 
Published: November 2016

AbstractDespite the rapid development of sequencing technologies, assembly of mammalian-scale genomes into complete chromosomes remains one of the most challenging problems in bioinformatics. To help address this difficulty, we developed Ragout, a reference-assisted assembly tool that now works for large and complex genomes. Taking one or more target assemblies (generated from an NGS assembler) and one or multiple related reference genomes, Ragout infers the evolutionary relationships between the genomes and builds the final assemblies using a genome rearrangement approach. Using Ragout, we transformed NGS assemblies of 15 differentMus musculusand oneMus spretusgenomes into sets of complete chromosomes, leaving less than 5% of sequence unlocalized per set. Various benchmarks, including PCR testing and realigning of long PacBio reads, suggest only a small number of structural errors in the final assemblies, comparable with direct assembly approaches. Additionally, we applied Ragout toMus caroliandMus paharigenomes, which exhibit karyotype-scale variations compared to other genomes from theMuridaefamily. Chromosome color maps confirmed most large-scale rearrangements that Ragout detected.
A lumenal interrupted helix in human sperm tail microtubules
Authors: Zabeo Davide , Heumann John M. , Schwartz Cindi L. , Suzuki-Shinjo Azusa , Morgan Garry , Widlund Per O. , Höög Johanna L. 
Published: November 2016

AbstractEukaryotic flagella are complex cellular extensions involved in many human diseases gathered under the term ciliopathies. Currently, detailed insights on flagellar structure come from studies on protozoa. Here, cryo-electron tomography (cryo-ET) of intact human spermatozoon tails showed a variable number of microtubules in the singlet region. Inside their lumen, a novel left-handed interrupted helix which extends several micrometers at their plus ends was discovered. This structure was named Tail Axoneme Intra-Lumenal Spiral (TAILS) and binds directly to 11 protofilaments on the internal microtubule wall, coaxial with the surrounding microtubule lattice. It leaves a gap over the microtubule seam, which was directly visualized in both singlet and doublet microtubules. We suggest that TAILS may stabilize microtubules, enable rapid swimming or play a role in controlling the swimming direction of spermatozoa.
Conformational landscape of the p28-bound human proteasome regulatory particle
Authors: Lu Ying , Wu Jiayi , Chen Shuobing , Sun Shuangwu , Ma Yong-Bei , Ouyang Qi , Finley Daniel , Kirschner Marc W. , Mao Youdong 
Published: November 2016

SUMMARYThe proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of AAA-ATPases, which is guided by at least four RP assembly chaperones in mammals: PAAF1, p28/gankyrin, p27/PSMD9 and S5b. We determined a cryo-EM structure of the human RP in complex with its assembly chaperone p28 at 4.5-Å resolution. The Rpn1-p28-AAA subcomplex in the p28-bound RP is highly dynamic and was resolved to subnanometer resolution in seven states, which recapitulate the conformational landscape of the complex. Surprisingly, the p28-bound AAA ring does not form a channel in the free RP. Instead, it spontaneously samples multiple ‘open’ and ‘closed’ topologies. Our analysis suggests that p28 guides the proteolytic core particle to select certain conformation of the ATPase ring for RP engagement in the last step of the chaperone-mediated proteasome assembly.
Host Vesicle Fusion Proteins VAPB, Rab11b and Rab18 Contribute to HSV-1 Infectivity by Facilitating Egress through the Nuclear Membrane
Authors: Saiz-Ros Natalia , Czapiewski Rafal , Stevenson Andrew , Epifano Ilaria , Swanson Selene K. , McElwee Marion , Vijayakrishnan Swetha , Richardson Christine A. , Dixon Charles , Pytowski Lior , Goldberg Martin W. , Florens Laurence , Graham Sheila V. , Schirmer Eric C. 
Published: November 2016

AbstractThe herpesvirus process of primary envelopment and de-envelopment as viral particles exit the nucleus has been for many years one of the least understood steps in the virus life cycle. Though viral proteins such as pUL31, pUL34, pUS3 and others are clearly important, these are likely insufficient for efficient fusion with the nuclear membrane. We postulated that host nuclear membrane proteins involved in virus nuclear egress would move from the inner to outer nuclear membranes due to membrane fusion events in primary envelopment and de-envelopment and then diffuse into the endoplasmic reticulum. Membrane fractions were prepared enriched in the nuclear envelope or the endoplasmic reticulum with and without HSV-1 infection and analyzed by mass spectrometry, revealing several vesicle fusion proteins as candidates in the viral nuclear egress pathway. Knockdown of three of these, VAPB, Rab11b, and Rab18, significantly reduced titers of released virus while yielding nuclear accumulation of encapsidated particles. Antibody staining revealed that VAPB visually accumulates in the inner nuclear membrane during HSV-1 infection. VAPB also co-localizes at early time points with the viral pUL34 protein known to be involved in nuclear egress. Most strikingly, VAPB was also observed on HSV-1 virus particles by immunogold labelling electron microscopy. Thus, these data reveal several new host cell vesicle fusion proteins involved in viral nuclear egress.Author SummaryHuman herpesviruses are associated with common human diseases such as chicken pox, shingles and mononucleosis and infect a wide range of animals making them economically important pathogens for livestock. Herpes simplex virus 1 (HSV-1) is most commonly associated with cold sores, but is also the leading cause of blindness by infection in the Western world. All herpesviruses share many aspects of infection. As large nuclear replicating dsDNA viruses with capsid sizes too large to use the nuclear pores to exit the nucleus, they have evolved a complex mechanism for envelopment and de-envelopment of primary herpesvirus particles, but this critical step in the virus lifecycle remains poorly understood. We have identified several host cell vesicle fusion proteins, VAPB, Rab11b and Rab18 that appear to contribute to this step in the HSV-1 life cycle. VAPB accumulates at the nuclear envelope with the HSV-1 pUL34 protein important for viral nuclear egress. Knockdown of any of these vesicle fusion proteins reduces viral titers, further arguing that they are important for nuclear egress. As there appears to be a specific subset of vesicle fusion proteins involved in viral egress, they could possibly represent novel targets for therapeutic interventions.
UNCROSS: Filtering of high-frequency cross-talk in 16S amplicon reads
Authors: Edgar Robert C. 
Published: November 2016

AbstractNext-generation amplicon sequencing is widely used for surveying biological diversity in applications such as microbial metagenomics, immune system repertoire analysis and targeted tumor sequencing of cancer-associated genes. In such studies, assignment of reads to incorrect samples (cross-talk) is a well-documented problem that is rarely considered in practice. By considering unexpected OTUs in artificial (mock) samples, I estimate that cross-talk occurred for ~2% of the reads in one Illumina GAIIx run and eleven Illumina MiSeq runs targeting 16S ribosomal RNA. I also describe UNCROSS, an algorithm for detecting and filtering cross-talk in OTU tables.
DIV-1/PolA2 Promotes GLP-1/Notch-Mediated Cellular Events inCaenorhabditis elegans
Authors: Yoon Dong Suk , Cha Dong Seok , Lee Myon-Hee 
Published: November 2016

ABSTRACTNotch signaling is a highly conserved cell signaling system in most multicellular organisms and plays a critical role in animal development. In various tumor cells, Notch signaling is elevated and has been considered as an important target in cancer treatments. InC. elegans, GLP-1 (one of twoC. elegansNotch receptors) activity is required for cell fate specification in germline and somatic tissues. In this study, we have identifieddiv-1gene as a positive regulator for GLP-1/Notch-mediated cellular events.C. elegans div-1encodes the B subunit of the DNA polymerase alpha-primase complex and is highly expressed in proliferative germ cells. Functional analyses demonstrated thati) DIV-1 is required for the robust proliferation typical of the germline,ii) loss of DIV-1 enhances and suppresses specific phenotypes that are associated with reduced and elevated GLP-1/Notch activity in germline and somatic tissues, andiii) DIV-1 works together with FBF/PUF proteins, downstream regulators of GLP-1/Notch signaling, to promote germline stem cell (GSC) maintenance and germline proliferation. To maintain GSCs and proliferative cell fate, GLP-1/Notch activity must remain above a threshold for proliferation/differentiation decision. Our results propose that DIV-1 may control the level of threshold for GLP-1/Notch-mediated germline proliferation. PolA2, a mammalian homolog of theC. elegansDIV-1, has been emerged as a therapeutic target for non-small cell lung cancer (NSCLC). Notably, Notch signaling is altered in approximately one third of NSCLCs. Therefore, the discovery of the DIV-1 effect on GLP-1/Notch-mediated cellular events has implications for our understanding of vertebrate PolA2 protein and its influence on stem cell maintenance and tumorigenesis.
Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men
Authors: Poznik G. David 
Published: November 2016

AbstractWe have developed an algorithm to rapidly and accurately identify the Y-chromosome haplogroup of each male in a sample of one to millions. The algorithm, implemented in the yHaplo*software package (yHaplo), does not rely on any particular genotyping modality or platform. Full sequences yield the most granular haplogroup classifications, but genotyping arrays can yield reliable calls, provided a reasonable number of phylogenetically informative variants has been assayed. The algorithm is robust to missing data, genotype errors, mutation recurrence, and other complications. We have tested the software on full sequences from phase 3 of the 1000 Genomes Project and on subsets thereof constructed by downsampling to SNPs present on each of four genotyping arrays. We have also run the software on array data from more than 600,000 males.
Chromatin accessibility dynamics reveal novel functional enhancers inC. elegans
Authors: Daugherty Aaron C. , Yeo Robin , Buenrostro Jason D. , Greenleaf William J. , Kundaje Anshul , Brunet Anne 
Published: November 2016

AbstractChromatin accessibility, a crucial component of genome regulation, has primarily been studied in homogeneous and simple systems, such as isolated cell populations or early-development models. Whether chromatin accessibility can be assessed in complex, dynamic systemsin vivowith high sensitivity remains largely unexplored. In this study, we use ATAC-seq to identify chromatin accessibility changes in a whole animal, the model organismC. elegans, from embryogenesis to adulthood. Chromatin accessibility changes between developmental stages are highly reproducible, recapitulate histone modification changes, and reveal key regulatory aspects of the epigenomic landscape throughout organismal development. We find that over 5,000 distal non-coding regions exhibit dynamic changes in chromatin accessibility between developmental stages, and could thereby represent putative enhancers. When testedin vivo, several of these putative enhancers indeed drive novel cell-type-and temporal-specific patterns of expression. Finally, by integrating transcription factor binding motifs in a machine learning framework, we identify EOR-1 as a unique transcription factor that may regulate chromatin dynamics during development. Our study provides a unique resource forC. elegans, a system in which the prevalence and importance of enhancers remains poorly characterized, and demonstrates the power of using whole organism chromatin accessibility to identify novel regulatory regions in complex systems.
Immunotropic aspect of theBacillus coagulansprobiotic action
Authors: Bomko T.V. , Nosalskaya T. N. , Kabluchko T. V. , Lisnyak Yu. V. , Martynov A. V. 
Published: November 2016

AbstractImmunotropic aspect of theBacillus coagulansprobiotic actionObjectiveCurrently, probiotics are increasingly used as the alternative to antibiotics as well as the preventive measures in humans. In particular, probiotics occupy a key position in the treatment of antibiotics-associated intestinal dysbiosis. A spore-forming microorganism lactobacillusBacillus coagulansis one of the most promising probiotics. However, some of its pharmacological effects remain poorly understood.Aim.This study is aimed at investigation of the effect ofBacillus coagulans(Laktovit Forte) on the intestinal dysbiosis syndrome in mice caused by streptomycin against the background of cyclophosphamide-induced cellular immunodeficiency.Methods.Pharmacological method: mouse model in vivo with immunodeficiency caused by cyclophosphamide.Key findings.In mice with colitis caused by streptomycin treatment, the administration ofBacillus coagulans(Laktovit Forte medicinal product) resulted in an antidiarrheal effect, normalization of gastrointestinal motility, and prevention of the animals’ weight loss. Given the cyclophosphamide-induced immunosuppression and streptomycin-associated diarrhoea, the immunity was completely restored only under the action ofBacillus coagulans.Conclusions.According to all parameters,Bacillus coagulanshas been proved to be more effective as compared to the Linex Forte reference product containing lacto‐ and bifidobacteria.
Information for decision-making in in-house and outsourced real estate management organisations
Authors: Palm Peter 
Published: November 2016

PurposeThe purpose of this paper is to examine how the real estate owner (decision maker) insures being able to make informed decisions and how they differ according to organisational form.Design/methodology/approachThis research is based on an interview study of nineteen firm representatives, six decision makers and thirteen management representatives, all from Swedish commercial real estate sector.FindingsThe study concludes that, regardless of organisational setting, the industry has a plan regarding handling information. The decision makers have all secured themselves access to the required/desired information. How this is done and what kind of information it is however differ, if the real estate management is in-house or outsourced. Furthermore, a clear focus on financial and contractual information is evident in both organisational settings.Research limitations/implicationsThe research in this paper is limited to Swedish commercial real estate sector.Practical implicationsThe insight the paper provides regarding required information can shed light on how information systems are built and how to improve your information sharing.Originality/valueIt provides an insight regarding how the industry, depending on organisation setting, prioritises different information and how the decision maker secures access to it.
Application of unstructured grid finite-volume coastal ocean model (FVCOM) to the Yangtze River hypoxic zone
Authors: Wan Zhanhong , Ren Zongfu , Wang Xiaochun , Zheng Honghao 
Published: November 2016

Purpose
To observe the relations between three important factors resulting in estuarial Hypoxia phenomena of Yangtze River – wind, river flow, and stratification. The purpose of the paper is to analyze the possible reasons why hypoxia occurs in late spring and disappears in October.

Design/methodology/approach
To overcome the difficulty in examining the role of physical and biological factors affecting hypoxia based on measurement alone, finite-volume community ocean model (FVCOM) was introduced into the investigation. Observed freshwater flux data from Yangtze River, monthly averaged wind speed data, and other observed data were input into the model; the accuracy of which was validated with various kinds of data. The authors used the trajectories of Lagrangian particles from Yangtze River to study the regions of strong riverine influence under different wind forcing conditions and compared the simulation results with former observations.

Findings
Trade wind is a significant factor to influence the forming and receding of hypoxia across the Yangtze River.

Originality/value
Using FVCOM to investigate estuary hypoxia is more economical and effective.
Bank risk-taking in the MENA region
Authors: Selma Mokni Rim Ben , Rajhi Mohamed Tahar , Rachdi Houssem 
Published: November 2016

PurposeThe purpose of this paper is to investigate determinants of risk-taking in Islamic banks and conventional banks located in the MENA region.Design/methodology/approachThe empirical study covers a sample of 15 conventional and 15 Islamic banks for the period 2002-2009. The authors estimate models using both generalized least square random effect and generalized method of moments system approaches.FindingsThe results of the empirical analysis show that the determinants’ risk-taking significance varies between Islamic and conventional banks.Originality/valueThe main aim is to develop a comprehensive model that integrates macroeconomic determinants, industry-specific determinants, and bank-specific determinants. This paper performs a comparison of the risk-taking between two different banking systems in the MENA region.