bluuebunny/crossref_metadata_2025_split huggingface dataset:
MAP kinase phosphatase 2 deficient mice develop attenuated experimental autoimmune encephalomyelitis through regulating dendritic cells and T cells
Authors: Barbour Mark , Plevin Robin , Jiang Hui-Rong 
Published: December 2016

AbstractMitogen-activated protein kinase phosphatases (MKPs) play key roles in inflammation and immune mediated diseases. Here we investigated the mechanisms by which MKP-2 modulates central nervous system (CNS) inflammation in experimental autoimmune encephalomyelitis (EAE). Our results show that MKP-2 mRNA levels in the spinal cord and lymphoid organs of EAE mice were increased compared with naive controls, indicating an important role for MKP-2 in EAE development. Indeed, MKP-2−/− mice developed reduced EAE severity, associated with diminished CNS immune cell infiltration, decreased proinflammatory cytokine production and reduced frequency of CD4+ and CD8+ T cells in spleens and lymph nodes. In addition, MKP-2−/− CD11c+ dendritic cells (DCs) had reduced expression of MHC-II and CD40 compared with MKP-2+/+ mice. Subsequent experiments revealed that CD4+ T cells from naïve MKP-2−/− mice had decreased cell proliferation and IL-2 and IL-17 production relative to wild type controls. Furthermore, co-culture experiments showed that bone marrow derived DCs of MKP-2−/− mice had impaired capability in antigen presentation and T cell activation. While MKP-2 also modulates macrophage activation, our study suggests that MKP-2 is essential to the pathogenic response of EAE, and it acts mainly via regulating the important antigen presenting DC function and T cell activation.
Unusual Five Copies and Dual Forms of nrdB in “Candidatus Liberibacter asiaticus”: Biological Implications and PCR Detection Application
Authors: Zheng Zheng , Xu Meirong , Bao Minli , Wu Fengnian , Chen Jianchi , Deng Xiaoling 
Published: December 2016

Abstract“Candidatus Liberibacter asiaticus” (CLas), a non-culturable α-proteobacterium, is associated with citrus Huanglongbing (HLB, yellow shoot disease) currently threatening citrus production worldwide. Here, the whole genome sequence of CLas strain A4 from Guangdong of China was analyzed. Five copies of nrdB, encoding β-subunit of ribonucleotide reductase (RNR), a critical enzyme involving bacterial proliferation, were found. Three nrdB copies were in long form (nrdBL, 1,059 bp) and two were in short form (nrdBS, 378 bp). nrdBS shared >99% identity to 3′ end of nrdBL and had no active site. Sequences of CLas nrdB genes formed a distinct monophyletic lineage among eubacteria. To make use of the high copy number feature, a nrdB-based primer set RNRf/RNRr was designed and evaluated using real-time PCR with 262 HLB samples collected from China and USA. Compared to the current standard primer set HLBas/HLBr derived from the 16S rRNA gene, RNRf/RNRr had Ct value reductions of 1.68 (SYBR Green PCR) and 1.77 (TaqMan PCR), thus increasing the detection sensitivity three-fold. Meanwhile, RNRf/RNRr was more than twice the stability of primer set LJ900f/LJ900r derived from multi-copy prophage. The nrdB-based PCR thereby provides a sensitive and reliable CLas detection with broad application, especially for the early diagnosis of HLB.
Chimera states in uncoupled neurons induced by a multilayer structure
Authors: Majhi Soumen , Perc Matjaž , Ghosh Dibakar 
Published: December 2016

AbstractSpatial coexistence of coherent and incoherent dynamics in network of coupled oscillators is called a chimera state. We study such chimera states in a network of neurons without any direct interactions but connected through another medium of neurons, forming a multilayer structure. The upper layer is thus made up of uncoupled neurons and the lower layer plays the role of a medium through which the neurons in the upper layer share information among each other. Hindmarsh-Rose neurons with square wave bursting dynamics are considered as nodes in both layers. In addition, we also discuss the existence of chimera states in presence of inter layer heterogeneity. The neurons in the bottom layer are globally connected through electrical synapses, while across the two layers chemical synapses are formed. According to our research, the competing effects of these two types of synapses can lead to chimera states in the upper layer of uncoupled neurons. Remarkably, we find a density-dependent threshold for the emergence of chimera states in uncoupled neurons, similar to the quorum sensing transition to a synchronized state. Finally, we examine the impact of both homogeneous and heterogeneous inter-layer information transmission delays on the observed chimera states over a wide parameter space.
Orthography and Modality Influence Speech Production in Adults and Children
Authors: Saletta Meredith , Goffman Lisa , Hogan Tiffany P. 
Published: December 2016

PurposeThe acquisition of literacy skills influences the perception and production of spoken language. We examined if orthography influences implicit processing in speech production in child readers and in adult readers with low and high reading proficiency.MethodChildren (n= 17), adults with typical reading skills (n= 17), and adults demonstrating low reading proficiency (n= 18) repeated or read aloud nonwords varying in orthographic transparency. Analyses of implicit linguistic processing (segmental accuracy and speech movement stability) were conducted. The accuracy and articulatory stability of productions of the nonwords were assessed before and after repetition or reading.ResultsSegmental accuracy results indicate that all 3 groups demonstrated greater learning when they were able to read, rather than just hear, the nonwords. Speech movement results indicate that, for adults with poor reading skills, exposure to the nonwords in a transparent spelling reduces the articulatory variability of speech production. Reading skill was correlated with speech movement stability in the groups of adults.ConclusionsIn children and adults, orthography interacts with speech production; all participants integrate orthography into their lexical representations. Adults with poor reading skills do not use the same reading or speaking strategies as children with typical reading skills.
What’s really new about New Atheism?
Authors: Kettell Steven 
Published: December 2016

AbstractThe rise of new atheism has attracted significant attention but its novelty is often assumed rather than explained. By exploring the origins of new atheism and drawing comparisons to earlier atheist forms, this article argues that new atheism contains aspects that are genuinely new. The most notable of these features are its expansive political activities and its hybrid combination of Enlightenment-based rationality with postmodern themes and concerns.
Experimental and theoretical evidence for bilayer-by-bilayer surface melting of crystalline ice
Authors: Sánchez M. Alejandra , Kling Tanja , Ishiyama Tatsuya , van Zadel Marc-Jan , Bisson Patrick J. , Mezger Markus , Jochum Mara N. , Cyran Jenée D. , Smit Wilbert J. , Bakker Huib J. , Shultz Mary Jane , Morita Akihiro , Donadio Davide , Nagata Yuki , Bonn Mischa , Backus Ellen H. G. 
Published: December 2016

Significance
Over 150 years ago, Faraday discovered the presence of a water layer on ice below the bulk melting temperature. This layer is important for surface chemistry and glacier sliding close to subfreezing conditions. The nature and thickness of this quasi-liquid layer has remained controversial. By combining experimental and simulated surface-specific vibrational spectroscopy, the thickness of this quasi-liquid layer is shown to change in a noncontinuous, stepwise fashion around 257 K. Below this temperature, the first bilayer is already molten; the second bilayer melts at this transition temperature. The blue shift in the vibrational response of the outermost water molecules accompanying the transition reveals a weakening of the hydrogen bond network upon an increase of the water layer thickness.
Stratospheric solar geoengineering without ozone loss
Authors: Keith David W. , Weisenstein Debra K. , Dykema John A. , Keutsch Frank N. 
Published: December 2016

Significance
The combination of emissions cuts and solar geoengineering could reduce climate risks in ways that cannot be achieved by emissions cuts alone: It could keep Earth under the 1.5-degree mark agreed at Paris, and it might stop sea level rise this century. However, this promise comes with many risks. Injection of sulfuric acid into the stratosphere, for example, would damage the ozone layer. Injection of calcite (or limestone) particles rather than sulfuric acid could counter ozone loss by neutralizing acids resulting from anthropogenic emissions, acids that contribute to the chemical cycles that destroy stratospheric ozone. Calcite aerosol geoengineering may cool the planet while simultaneously repairing the ozone layer.
GppFst: genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data
Authors: Adams Richard H , Schield Drew R , Card Daren C , Blackmon Heath , Castoe Todd A 
Published: December 2016

Abstract

Summary
We introduce GppFst, an open source R package that generates posterior predictive distributions of FST and dx under a neutral coalescent model to identify putative targets of selection from genomic data.

Availability and Implementation
GppFst is available at (https://github.com/radamsRHA/GppFst).

Supplementary information
Supplementary data are available at Bioinformatics online.
Wright–Fisher exact solver (WFES): scalable analysis of population genetic models without simulation or diffusion theory
Authors: Krukov Ivan , de Sanctis Bianca , de Koning A P Jason 
Published: December 2016

Abstract

Motivation
The simplifying assumptions that are used widely in theoretical population genetics may not always be appropriate for empirical population genetics. General computational approaches that do not require the assumptions of classical theory are therefore quite desirable. One such general approach is provided by the theory of absorbing Markov chains, which can be used to obtain exact results by directly analyzing population genetic Markov models, such as the classic bi-allelic Wright–Fisher model. Although these approaches are sometimes used, they are usually forgone in favor of simulation methods, due to the perception that they are too computationally burdensome. Here we show that, surprisingly, direct analysis of virtually any Markov chain model in population genetics can be made quite efficient by exploiting transition matrix sparsity and by solving restricted systems of linear equations, allowing a wide variety of exact calculations (within machine precision) to be easily and rapidly made on modern workstation computers.

Results
We introduce Wright–Fisher Exact Solver (WFES), a fast and scalable method for direct analysis of Markov chain models in population genetics. WFES can rapidly solve for both long-term and transient behaviours including fixation and extinction probabilities, expected times to fixation or extinction, sojourn times, expected allele age and variance, and others. Our implementation requires only seconds to minutes of runtime on modern workstations and scales to biological population sizes ranging from humans to model organisms.

Availability and Implementation
The code is available at https://github.com/dekoning-lab/wfes

Supplementary information
Supplementary data are available at Bioinformatics online.
The contribution of autoantibodies to post-translationally modified proteins to inflammatory arthritis
Authors: van der Woude Diane , Toes René E.M. 
Published: December 2016

Purpose of review
This article provides an overview of the recent findings present in the field of antimodified protein antibodies and their relevance for rheumatic disease, with a focus on rheumatoid arthritis.

Recent findings
Next to anticitrullinated protein antibodies, also other antimodified protein antibodies such as anticarbamylated protein antibodies or antiacetylated protein antibodies are emerging. Likewise, their possible pathological contributions are getting detailed attention. Their possible relation to disease, both from a clinical as well as biological perspective will be summarized.

Summary
Current evidence is pointing to the notion that especially a combination of antimodified protein antibodies associates best with clinical phenotype and outcome.
The Interface of Clinical Decision-Making With Study Protocols for Knowledge Translation From a Walking Recovery Trial
Authors: Hershberg Julie A. , Rose Dorian K. , Tilson Julie K. , Brutsch Bettina , Correa Anita , Gallichio Joann , McLeod Molly , Moore Craig , Wu Sam , Duncan Pamela W. , Behrman Andrea L. 
Published: December 2016

Background and Purpose:
Despite efforts to translate knowledge into clinical practice, barriers often arise in adapting the strict protocols of a randomized, controlled trial (RCT) to the individual patient. The Locomotor Experience Applied Post-Stroke (LEAPS) RCT demonstrated equal effectiveness of 2 intervention protocols for walking recovery poststroke; both protocols were more effective than usual care physical therapy. The purpose of this article was to provide knowledge-translation tools to facilitate implementation of the LEAPS RCT protocols into clinical practice.

Methods:
Participants from 2 of the trial's intervention arms: (1) early Locomotor Training Program (LTP) and (2) Home Exercise Program (HEP) were chosen for case presentation. The two cases illustrate how the protocols are used in synergy with individual patient presentations and clinical expertise. Decision algorithms and guidelines for progression represent the interface between implementation of an RCT standardized intervention protocol and clinical decision-making.

Outcomes:
In each case, the participant presents with a distinct clinical challenge that the therapist addresses by integrating the participant's unique presentation with the therapist's expertise while maintaining fidelity to the LEAPS protocol. Both participants progressed through an increasingly challenging intervention despite their own unique presentation.

Summary:
Decision algorithms and exercise progression for the LTP and HEP protocols facilitate translation of the RCT protocol to the real world of clinical practice. The two case examples to facilitate translation of the LEAPS RCT into clinical practice by enhancing understanding of the protocols, their progression, and their application to individual participants.

Video Abstract available for more insights from the authors (see Supplemental Digital Content 1, available at: http://links.lww.com/JNPT/A147).
BioMake: a GNU Make-compatible utility for declarative workflow management
Authors: Holmes Ian H. , Mungall Christopher J. 
Published: December 2016

AbstractThe Unix “make” program is widely used in bioinformatics pipelines, but suffers from problems that limit its application to large analysis datasets. These include reliance on file modification times to determine whether a target is stale, lack of support for parallel execution on clusters, and restricted flexibility to extend the underlying logic program. We present BioMake, a make-like utility that is compatible with most features of GNU Make and adds support for popular cluster-based job-queue engines, MD5 signatures as an alternative to timestamps, and logic programming extensions in Prolog. BioMake is available fromhttps://github.com/evoldoers/biomakeunder the Creative Commons Attribution 3.0 US license. The only dependency is SWI-Prolog, available fromhttp://www.swi-prolog.org/. Contact: Ian Holmesihholmes+biomake@gmail.comor Chris Mungallcmungall+biomake@gmail.com.
VHL inactivation without hypoxia is sufficient to achieve genome hypermethylation
Authors: Artemov Artem V. , Zhigalova Nadezhda , Zhenilo Svetlana , Mazur Alexander M. , Prokhortchouk Egor B. 
Published: December 2016

AbstractVHL inactivation is a key oncogenic event for renal carcinomas. In normoxia, VHL suppresses HIF1a-mediated response to hypoxia. It has previously been shown that hypoxic conditions inhibit TET-dependent hydroxymethylation of cytosines and cause DNA hypermethylation at gene promoters. In this work, we performed VHL inactivation by CRISPR/Cas9 and studied its effects on gene expression and DNA methylation. We showed that even without hypoxia, VHL inactivation leads to hypermethylation of the genome which mainly occurred in AP-1 and TRIM28 binding sites. We also observed promoter hypermethylation of several transcription regulators associated with decreased gene expression.
From food defence to food supply chain integrity
Authors: Davidson Rebecca K. , Antunes Wilson , Madslien Elisabeth H. , Belenguer José , Gerevini Marco , Torroba Perez Tomas , Prugger Raffaello 
Published: December 2016

Purpose
Consumer confidence in the European food industry has been shaken by a number of recent scandals due to food fraud and accidental contamination, reminding the authors that deliberate incidents can occur. Food defence methods aim to prevent or mitigate deliberate attacks on the food supply chain but are not a legal requirement. The purpose of this paper is to discuss how proactive and reactive food defence practices can help prevent or mitigate malicious attacks on the food chain and also food fraud, food crime and food safety. The authors look at how food defence differs from food safety and how it contributes to food supply chain integrity.

Design/methodology/approach
Food defence has been the focus of two different EU FP7 security projects, EDEN and SNIFFER. Food industry stakeholders participated in workshops and demonstrations on food defence and relevant technology was tested in different food production scenarios.

Findings
Food industry end-users reported a lack of knowledge regarding food defence practices. They wished for further guidelines and training on risk assessment as well as access to validated test methods. Novel detection tools and methods showed promise with authentication, identification, measurement, assessment and control at multiple levels of the food supply chain prior to distribution and retail.

Practical implications
The prevention of a contamination incident, prior to retail, costs less than dealing with a large foodborne disease outbreak. Food defence should therefore be integral to food supply chain integrity and not just an afterthought in the wake of an incident.

Originality/value
It is argued that food defence practices have a vital role to play across the board in unintentional and intentional food contamination incidents. The application of these methods can help ensure food supply chain integrity.
Documenting entrepreneurial opportunism in action
Authors: Smith Robert 
Published: December 2016

Purpose
The contemporary rustler is a shrewd businessman, or rogue farmer exploiting food supply chain anomalies. Indeed, the first conviction in the UK for 20 years was a farmer stealing from neighbouring farmers. The theft of sheep in the UK is an expanding criminal enterprise which remains under researched. The purpose of this paper is to examine what is known of the illegal trade and its links to food fraud from a supply chain perspective with an emphasis on food integrity issues.

Design/methodology/approach
There is a dearth of current viable literature on livestock theft in a western context making it necessary to turn to socio-historical research and to official documents such as those published by the NFU and other insurance companies to build up a picture of this illegal practice. This is supplemented by documentary research of articles published in the UK press.

Findings
From this raw data a typology of rustlers is developed. The findings point to insider “supply chain” knowledge being a key facet in the theft of livestock. Other examples in the typology relate to urban thieves wrestling live sheep into a car and to industry insiders associated with the abattoir sector.

Research limitations/implications
The obvious limitations is that as yet there are few detected cases of rustling in the UK so the developing typology of rustlers is sketchy. Another limitation is that much of the evidence upon which the typology is developed is anecdotal.

Originality/value
The typology should prove helpful to academics, insurance companies, investigators, industry insiders and farmers to help them understand this contemporary crime and how to prevent its spread. It also sheds light on food integrity in relation to the purchase and consumption of the end product in that customers expect to be purchasing legally and ethically reared animal products.
A supply chain integrity framework for halal food
Authors: Ali Mohd Helmi , Tan Kim Hua , Ismail Md Daud 
Published: December 2016

PurposeThe purpose of this paper is to propose a food supply chain (SC) integrity framework in the context of halal food.Design/methodology/approachThis paper provides a discussion on the development of food SC integrity framework using triangulation of interviews’ insights with literature.FindingsCurrent industry practices such as standards have not been sufficient in embracing the concept of food SC integrity. As the food SC is complex, food SC integrity framework is proposed as a solution. This paper proposes food SC integrity framework for halal food. It consists of four dimensions, namely: raw material, production, service, and information integrity. In addition, key elements for each dimension are derived from the interviews’ insights.Research limitations/implicationsThe framework provides the evidence that the safeguarding of halal food integrity does not rely solely on certification; but it requires an extensive effort beyond certification.Practical implicationsSafeguarding of food integrity should involve all stages and actors of the SC. Religious standards should incorporate SC integrity profiling through a controlling mechanism to promote higher food product integrity.Originality/valueFood SC integrity framework is important to religious food as it plays a significant role to the population. This study contributes to a newly developed SC integrity framework in the context of halal food.
Open accelerators for start-ups success: a case study
Authors: Battistella Cinzia , De Toni Alberto F. , Pessot Elena 
Published: December 2016

PurposeThe purpose of this paper is to investigate how the context of open innovation offered by accelerators can affect the successful growth of start-ups. The authors explore accelerators practices and tools in sustaining start-ups and increasing survival probability in their innovation process, with the aim of addressing the following research question: how can start-ups benefit from participation in an accelerator programme from an open innovation perspective?Design/methodology/approachA review of the literature on start-up successes and failures and on major practices in the open innovation paradigm was carried out, delineating them in the context of accelerators. Given the absence of literature on accelerator practices for supporting start-ups, and aiming at a comprehensive understanding of how the open environment within the accelerator influences a start-up’s survival (or even success) by mitigating the probability of failure, the authors conducted an exploratory case study in an English accelerator.FindingsThe open innovation practices mediated by an accelerator and the ones that are not covered, but that can benefit a start-up’s survival, are shown. On the one hand, main effective practices, such as dyadic co-creation with accelerator network partners and crowdsourcing, are revealed to address mostly the lack of, or wrong direction in, product, marketing and relative managerial abilities, which are not usually owned by a start-up due to its “newness”. On the other hand, some causes of failures, such as the intrinsic characteristics of founder teams, do not seem to be addressed by an open approach and neither does participation in an accelerator programme.Originality/valueThis paper is the first to study and link the literature on accelerators, start-ups and open innovation.