bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced representation optical methylation mapping (R2OM2)
Authors: Grunwald Assaf , Sharim Hila , Gabrieli Tslil , Michaeli Yael , Torchinsky Dmitry , Juhasz Matyas , Wagner Kathryn R , Pevsner Jonathan , Reifenberger Jeff , Hastie Alex R , Cao Han , Weinhold Elmar , Ebenstein Yuval 
Published: March 2017

ABSTRACTReduced representation methylation profiling is a method of analysis in which a subset of CpGs is used to report the overall methylation status of the probed genomic regions. This approach has been widely adopted for genome-scale bisulfite sequencing since it requires fewer sequencing reads and uses significantly less starting material than whole-genome analysis. Consequently, this method is suitable for profiling medical samples and single cells at high throughput and reduced costs. Here, we use this concept in order to create a pattern of fluorescent optical methylation profiles along individual DNA molecules. Reduced representation optical methylation mapping (R2OM2) in combination with Bionano Genomics next generation genome mapping (NGM) technology provides a hybrid genetic/epigenetic genome map of individual chromosome segments spanning hundreds of kilobase pairs (kbp). These long reads, along with the single-molecule resolution, allow for epigenetic variation calling and methylation analysis of large structural aberrations such as pathogenic macrosatellite arrays not accessible to single-cell next generation sequencing (NGS). We apply this method to facioscapulohumeral dystrophy (FSHD) showing both structural variation and hypomethylation status of a disease-associated, highly repetitive locus on chromosome 4q.
Visually driven neuropil activity and information encoding in mouse area V1
Authors: Lee Sangkyun , Meyer Jochen F. , Smirnakis Stelios M. 
Published: March 2017

AbstractSpontaneous calcium fluorescence recorded from large cortical neuropil patches strongly correlates with the electro-corticogram, and is thought to arguably reflect primarily pre-synaptic inputs. Here we used in vivo 2-photon imaging with Oregon Green Bapta (OGB) to study neuropil visual responses to moving gratings in layer 2/3 of mouse area V1. We found neuropil responses to be more reliable and more strongly modulated than neighboring somatic activity. Furthermore, stimulus independent modulations in neuropil activity, i.e. noise correlations, were highly coherent across the cortical surface, up to distances of at least 200 μm. Pairwise neuropil-to-neuropil-patch noise correlation strength was much higher than cell-to-cell noise correlation strength and depended strongly on brain state, decreasing in quiet wakefulness relative to light anesthesia. The profile of neuropil noise correlation strength decreased gently with distance, dropping by ~12% at a distance of 200 μm. This was comparatively slower than the profile of cell-to-cell noise correlations, which dropped by ~30% at 200 μm. Interestingly, in spite of the “salt & pepper” organization of orientation and direction encoding across mouse V1 neurons, populations of neuropil patches, even of moderately large size (radius ~100μm), showed high accuracy for discriminating perpendicularly moving gratings commensurate to the accuracy of corresponding cell populations. These observations underscore the dynamic nature of the functional organization of neuropil activity.Conflict of InterestThe authors declare that no competing interests exist.
Effect of vaccinating health care workers to control Ebola virus disease: a modelling analysis of outbreak data
Authors: Robert Alexis , Camacho Anton , Edmunds W. John , Baguelin Marc , Tamfum Jean-Jacques Muyembe , Rosello Alicia , Kéïta Sakoba , Eggo Rosalind M. 
Published: March 2017

AbstractBackgroundHealth care workers (HCW) are at risk of infection during Ebola virus disease outbreaks and therefore may be targeted for vaccination before or during outbreaks. The effect of these strategies depends on the role of HCW in transmission which is understudied.MethodsTo evaluate the effect of HCW-targeted or community vaccination strategies, we used a transmission model to explore the relative contribution of HCW and the community to transmission. We calibrated the model to data from multiple Ebola outbreaks. We quantified the impact of ahead-of-time HCW-targeted strategies, and reactive HCW and community vaccination.ResultsWe found that for some outbreaks (we call “type 1”) HCW amplified transmission both to other HCW and the community, and in these outbreaks prophylactic vaccination of HCW decreased outbreak size. Reactive vaccination strategies had little effect because type 1 outbreaks ended quickly. However, in outbreaks with longer time courses (“type 2 outbreaks”), reactive community vaccination decreased the number of cases, with or without prophylactic HCW-targeted vaccination. For both outbreak types, we found that ahead-of-time HCW-targeted strategies had an impact at coverage of 30%.ConclusionsThe optimal vaccine strategy depends on the dynamics of the outbreak and the impact of other interventions on transmission. Although we will not know the characteristics of a new outbreak, ahead-of-time HCW-targeted vaccination can decrease the total outbreak size, even at low vaccine coverage.summaryTargeting health care workers for Ebola virus disease vaccination can decrease the size of outbreaks, and the number of health care workers infected. The impact of these strategies decrease depends on timing, coverage, and the dynamics of the outbreak.
Association between Mitochondrial DNA Copy Number and Sudden Cardiac Death: Findings from the Atherosclerosis Risk in Communities Study (ARIC)
Authors: Zhang Yiyi , Guallar Eliseo , Ashar Foram N. , Longchamps Ryan J. , Castellani Christina A. , Lane John , Grove Megan L. , Coresh Josef , Sotoodehnia Nona , Ilkhanoff Leonard , Boerwinkle Eric , Pankratz Nathan , Arking Dan E. 
Published: March 2017

ABSTRACTAimsSudden cardiac death (SCD) is a major public health burden. Mitochondrial dysfunction has been implicated in a wide range of cardiovascular diseases including cardiomyopathy, heart failure, and arrhythmias, but it is unknown if it also contributes to SCD risk. We sought to examine the prospective association between mtDNA copy number (mtDNA-CN), a surrogate marker of mitochondrial function, and SCD risk.Methods and ResultsWe measured baseline mtDNA-CN in 11,093 participants from the Atherosclerosis Risk in Communities (ARIC) study. mtDNA-CN was calculated from probe intensities of mitochondrial single nucleotide polymorphisms (SNP) on the Affymetrix Genome-Wide Human SNP Array 6.0. SCD was defined as a sudden pulseless condition presumed due to a ventricular tachyarrhythmia in a previously stable individual without evidence of a non-cardiac cause of cardiac arrest. SCD cases were reviewed and adjudicated by an expert committee. During a median follow-up of 20.4 years, we observed 361 SCD cases. After adjusting for age, race, sex, and center, the hazard ratio (HR) for SCD comparing the 1stto the 5thquintiles of mtDNA-CN was 2.24 (95% CI 1.58 to 3.19; p-trend <0.001). When further adjusting for traditional CVD risk factors, prevalent CHD, heart rate, and QT interval duration, the association remained statistically significant. Spline regression models showed that the association was approximately linear over the range of mtDNA-CN values. No apparent interaction by race or by sex was detected.ConclusionIn this community-based prospective study, mtDNA-CN in peripheral blood was inversely associated with the risk of SCD.
Sensory tuning does not match behavioral relevance of communication signals in free-living weakly electric fish
Authors: Henninger Jörg , Krahe Rüdiger , Kirschbaum Frank , Grewe Jan , Benda Jan 
Published: March 2017

AbstractSensory systems evolve in the ecological niches each species is occupying. Accordingly, the tuning of sensory neurons is expected to be adapted to the statistics of natural stimuli. For an unbiased quantification of sensory scenes we tracked natural communication behavior of the weakly electric fishApteronotus rostratusin their Neotropical rainforest habitat with high spatio-temporal resolution over several days. In the context of courtship and aggression we observed large quantities of electrocommunication signals. Echo responses and acknowledgment signals clearly demonstrated the behavioral relevance of these signals. The known tuning properties of peripheral electrosensory neurons suggest, however, that they are barely activated by these obviously relevant signals. Frequencies of courtship signals are clearly mismatched with the frequency tuning of neuronal population activity. Our results emphasize the importance of quantifying sensory scenes derived from freely behaving animals in their natural habitats for understanding the evolution and function of neural systems.
Sublethal effects of the neonicotinoid insecticide thiamethoxam on the transcriptome of the honeybee (Apis mellifera)
Authors: Shi Teng-Fei , Wang Yu-Fei , Qi Lei , Liu Fang , Yu Lin-Sheng 
Published: March 2017

AbstractNeonicotinoid insecticides are now the most widely used insecticides in the world. Previous studies have indicated that sublethal doses of neonicotinoids impair learning, memory capacity, foraging and immunocompetence in honeybees (Apis mellifera). Despite this, few studies have been carried out on the molecular effects of neonicotinoids. In this study, we focus on the second-generation neonicotinoid thiamethoxam, which is currently widely used in agriculture to protect crops. Using high-throughput RNA-Seq, we investigated the transcriptome profile of honeybees after subchronic exposure to thiamethoxam (10 ppb) over 10 days. In total, 609 differentially-expressed genes (DEGs) were identified, of which 225 were up-regulated and 384 were down-regulated. The functions of some DEGs were identified, and GO enrichment analysis showed that the enriched DEGs were mainly linked to metabolism, biosynthesis and translation. KEGG pathway analysis showed that thiamethoxam affected biological processes including ribosomes, the oxidative phosphorylation pathway, tyrosine metabolism pathway, pentose and glucuronate interconversions and drug metabolism. Overall, our results provide a basis for understanding the molecular mechanisms of the complex interactions between neonicotinoid insecticides and honeybees.Summary statementNR1, Cyp6as5, nAChRa9andnAChRβ2were up-regulated in honeybees exposed to thiamethoxam, whileCSP3, Obp21, defensin-1, Mrjp1, Mrjp3andMrjp4were down-regulated.
Natural Colonization of Laboratory Mice withStaphylococcus aureusPrimes a Systemic Immune Response
Authors: Schulz Daniel , Grumann Dorothee , Trübe Patricia , Pritchett-Corning Kathleen , Johnson Sarah , Reppschläger Kevin , Gumz Janine , Sundaramoorthy Nandakumar , Michalik Stephan , Berg Sabine , van den Brandt Jens , Fister Richard , Monecke Stefan , Uy Benedict , Schmidt Frank , Bröker Barbara M. , Wiles Siouxsie , Holtfreter Silva 
Published: March 2017

AbstractBackgroundWhether mice are an appropriate model forS.aureusinfection and vaccination studies is a matter of debate, because they are not considered as natural hosts ofS. aureus.Sparked by an outbreak of S.aureusinfections in laboratory mice, we investigated whether laboratory mice are commonly colonized with S.aureusand whether this might impact on infection experiments.MethodsWe characterized 99S. aureusisolates from laboratory mice (spatyping, virulence gene PCR), and quantified murine antibodies using FlexMap technology.ResultsSpecific-pathogen-free mice from various vendors were frequently colonized withS. aureus(0-21%).S. aureuswas readily transmitted from murine parents to offspring, which became persistently colonized. Most murine isolates belonged to the lineage CC88 (54%). Murine strains showed features of host adaptation, such as absence ofhlb-converting phages and superantigen genes, as well as enhanced coagulation of murine plasma. Importantly,S. aureuscolonization induced a systemic IgG response specific for numerousS. aureusproteins, including several vaccine candidates.ConclusionLaboratory mice are natural hosts ofS. aureusand, therefore, provide better infection models than previously assumed. Pre-exposure to S.aureusis a possible confounder inS. aureusinfection and vaccination studies.
Connexin43 controls N-cadherin transcription during collective cell migration
Authors: Kotini Maria , Barriga Elias H. , Leslie Jonathan , Gentzel Marc , Schambony Alexandra , Mayor Roberto 
Published: March 2017

AbstractConnexins are the primary components of gap junctions, providing direct links between cells in many physiological processes, including cell migration and cancer metastasis. Exactly how cell migration is controlled by gap junctions remains a mystery. To shed light on this, we investigated the role of Connexin43 in collective cell migration during embryo development using the neural crest, an embryonic cell population whose migratory behavior has been likened to cancer invasion. We discovered that Connexin43 is required for contact inhibition of locomotion by directly regulating the transcription of N-cadherin. For this function, the Connexin43 carboxy tail interacts with Basic Transcription Factor 3, which mediates its translocation to the nucleus. Together, they bind to the n-cad promotor regulating n-cad transcription. Thus, we uncover an unexpected, gap junction-independent role for Connexin43 in collective migration that illustrates the possibility that connexins, in general, may be important for a wide variety of cellular processes that we are only beginning to understand.HighlightsCx43 regulates collective directional migration of neural crest cellsCx43 carboxy tail controls cell polarity via n-cad regulationCx43 carboxy tail localises at the nucleus and that depends on BTF3BTF3 and Cx43 carboxy tail directly interact to bind and regulate n-cad promoter activity
Nanotube-mediated cross-feeding couples the metabolism of interacting bacterial cells
Authors: Shitut Shraddha , Ahsendorf Tobias , Pande Samay , Egbert Matthew , Kost Christian 
Published: March 2017

ABSTRACTBacteria frequently engage in cross-feeding interactions that involve an exchange of metabolites with other micro- or macroorganisms. The often obligate nature of these associations, however, hampers manipulative experiments, thus limiting our mechanistic understanding of the ecophysiological consequences that result for the organisms involved. Here we address this issue by taking advantage of a well-characterised experimental model system, in which auxotrophic genotypes ofE. coliderive essential amino acid from prototrophic donor cells using intercellular nanotubes. Surprisingly, donor-recipient cocultures revealed that the mere presence of auxotrophic genotypes in coculture was sufficient to increase amino acid production levels in donor cells. Subsequent experiments unravelled that this effect was due to the depletion of amino acid concentrations in the cytoplasm of donor cells, which delayed feedback inhibition of the corresponding amino acid biosynthetic pathway. This finding indicates that in newly established mutualistic associations, an intercellular regulation of exchanged metabolites can simply emerge from the architecture of the underlying biosynthetic pathways, rather than through the evolution of new regulatory mechanisms. Taken together, our results show that a single loss-of-function mutation can physiologically couple the metabolism of two cross-feeding cells in a source-sink-like relationship.
A quartet of poems
Authors: Maddock Lelys 
Published: March 2017

Purpose
These texts form part of a quartet, the purpose of this paper is to draw attention to the destruction of our planet by presenting the elements as deities of nature: in Agitation the god is earth, in Burning the boy-god is fire, and in Mater Lachrymosa the mother-goddess is air (the first poem’s persona is the goddess of water/rain. Titled Heat, it is published in Volume 29 Issue 5 of AAAJ). The inspiration for these poems was Mervyn King’s statement that “Effective integrated reporting requires careful collection and co-ordination of different types of data for analysis by multi-disciplinary teams”. (King III, 2009) and his thought-provoking advocacy of the idea that “the board should provide effective leadership based on an ethical foundation” (King III, 2009).

Design/methodology/approach
These poems are written in free verse (which mimics the nuances and cadences of spoken English).

Findings
Frequent media coverage of global warming, corporate social responsibility policies, integrated reporting and dwindling resources have become fashionable clichés. We need to empower the message. CSR and the integrated report have no value if they become tick-the-box exercises.

Originality/value
Poetry is not generally associated with accountancy, finance, environmental law or geography so these texts are unusual in their genre and approach. The underlying concept is the interconnectedness of the themes and looking at issues with new eyes.
Performance optimization of aircraft in frontline squadrons
Authors: Subash K. , Vijayaraja K. 
Published: March 2017

Purpose
The purpose of this paper is to indicate the increase in operational efficiency of the aircraft in frontline squadrons by implementation of effective condition-based predictive maintenance (CBPM) philosophy using data link data transfer in real-time operational environment.

Design/methodology/approach
Real-time data transfer from the aircraft to the maintenance hub using data link is used as the key feature behind achieving an increase in the operational efficiency.

Findings
Considerable amount of increase in the operational efficiency and decrease in down time could be achieved on utilization of real-time aircraft parameters in the decision-making process of CBPM.

Practical implications
Incorporation of this methodology in frontline operating environment would result in achieving maintenance optimization, thereby reducing the downtime of the aircraft.

Social implications
Helps in achieving performance optimization with comparatively reduced downtime.

Originality/value
Up to 20 per cent of reduction in downtime could be achieved if real-time data transfer using data link is used parameters in the decision-making process of CBPM.
Improvement of aircraft crashworthy performance using inversion failure strut system
Authors: Ren Yiru , Xiang Jinwu 
Published: March 2017

Purpose
The purpose of this paper is to improve the crashworthiness of aircraft by using the strut system as an energy absorption device without redesigning other components.

Design/methodology/approach
The novel strut system consists of metal stepped thin-walled tubes and articulated connecting hinges. The strut is suffering axial load during impact process for rotating of hinges, and the metal stepped tube has an inversion failure behaviour.

Findings
The metal stepped tube has lower initial impact load and more stable failure behaviour. The geometrical factors have a great influence on the impact load and energy absorption efficiency. The best length ratio between upper and lower sections is about 2:1 and 1:1 for the metal stepped circular and square tubes, respectively.

Practical implications
The metal stepped tube with inversion mechanism is suitable for aircraft strut system to improve crashworthiness performance.

Originality/value
A new strut system is provided using metal inversion failure stepped tubes and articulated connecting hinges to improve crash worthiness of aircraft.
Religious differentials in morbidity prevalence and health care seeking behaviours among older persons in India
Authors: Agrawal Gopal , Patel Sangram Kishor 
Published: March 2017

Purpose
A plethora of studies have documented evidence on morbidity patterns and treatment-seeking behaviour among older persons in India. However, so far no attempt has been made to understand differences in the morbidity prevalence rates and utilization of health care services among older adults between religion groups in India. The purpose of this paper is to make an effort in this direction.

Design/methodology/approach
Multivariate logistic regression models were fitted to examine the association between socio-demographic conditions and morbidity prevalence and health care-seeking behaviours among the two religion groups: Hindu and Muslim. Data from the 60th round of the National Sample Survey in 2004 were used.

Findings
This study provided interesting evidence that, overall, the morbidity prevalence rate was higher among Muslim older persons than their Hindu counterparts by seven percentage points and Hindu scheduled caste (SC) and scheduled tribe (ST) counterpart population (compared to SCs eight percentage points, and STs 20 percentage points); income had no association with the burden of disease among Muslim older population – an older person belonging to the first income quintile was equally likely to report ill-health as an older person of the fifth income quintile. However, despite the low socio-economic status, Muslim older persons were more likely to seek treatment for ill-health compared to Hindu older persons but spent less money for treatment. Also, loss of household income due to sickness was greater among Muslim compared to Hindu older adults.

Originality/value
The findings of this study are important to support the policy makers and health care providers in identifying individuals “at risk” and could be integrated into the current programs of social, economic and health security for the older persons.
Informality: does financial development matter?
Authors: Sirisankanan Aeggarchat 
Published: March 2017

PurposeFinancial development may be an alternative policy for controlling informal employment. However, there is still an ambiguous relationship between financial development and informal employment. The purpose of this paper is to examine the impact of financial development on informal employment.Design/methodology/approachThe paper is based on both the occupational choice model and on the concept of financial development and economic growth which can produce either a positive or negative relationship between financial development and informal employment. Consequently, the author formulated empirical specifications and applied an econometric technique to examine the actual relationship.FindingsThe empirical results indicated that financial development can reduce informal employment. The author also found that the relationship between financial development and informal employment varies, depending on the level of economic growth and development.Research limitations/implicationsEven though there are many types of informal employment, this paper uses only informal self-employment as a proxy of informal employment. To implement it properly, all types of informal employment should also be examined.Practical implicationsBecoming informal employment depends on several factors; policy makers for each country should carefully examine the specific relationship between financial development and informal employment for their own country.Social implicationsThe paper presents alternative choices for policy makers to control informal employment by increasing financial development, especially in developing countries. This policy also includes promoting microfinance which will contribute to both formality and increasing the strength of the community.Originality/valueFrom the two possible impacts of financial development on informal employment, this paper affirms that financial development can reduce informal employment.