bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dimethyl fumarate blocks pro-inflammatory cytokine production via inhibition of TLR induced M1 and K63 ubiquitin chain formation
Authors: McGuire Victoria A. , Ruiz-Zorrilla Diez Tamara , Emmerich Christoph H. , Strickson Sam , Ritorto Maria Stella , Sutavani Ruhcha V. , Weiβ Anne , Houslay Kirsty F. , Knebel Axel , Meakin Paul J. , Phair Iain R. , Ashford Michael L. J. , Trost Matthias , Arthur J. Simon C. 
Published: August 2016

AbstractDimethyl fumarate (DMF) possesses anti-inflammatory properties and is approved for the treatment of psoriasis and multiple sclerosis. While clinically effective, its molecular target has remained elusive - although it is known to activate anti-oxidant pathways. We find that DMF inhibits pro-inflammatory cytokine production in response to TLR agonists independently of the Nrf2-Keap1 anti-oxidant pathway. Instead we show that DMF can inhibit the E2 conjugating enzymes involved in K63 and M1 polyubiquitin chain formation both in vitro and in cells. The formation of K63 and M1 chains is required to link TLR activation to downstream signaling and consistent with the block in K63 and/or M1 chain formation, DMF inhibits NFκB and ERK1/2 activation, resulting in a loss of pro-inflammatory cytokine production. Together these results reveal a new molecular target for DMF and show that a clinically approved drug inhibits M1 and K63 chain formation in TLR induced signaling complexes. Selective targeting of E2s may therefore be a viable strategy for autoimmunity.
Genetic markers of pigmentation are novel risk loci for uveal melanoma
Authors: Ferguson Robert , Vogelsang Matjaz , Ucisik-Akkaya Esma , Rai Karan , Pilarski Robert , Martinez Carlos N. , Rendleman Justin , Kazlow Esther , Nagdimov Khagay , Osman Iman , Klein Robert J. , Davidorf Frederick H. , Cebulla Colleen M. , Abdel-Rahman Mohamed H. , Kirchhoff Tomas 
Published: August 2016

AbstractWhile the role of genetic risk factors in the etiology of uveal melanoma (UM) has been strongly suggested, the genetic susceptibility to UM is currently vastly unexplored. Due to shared epidemiological risk factors between cutaneous melanoma (CM) and UM, in this study we have selected 28 SNPs identified as risk variants in previous genome-wide association studies on CM or CM-related host phenotypes (such as pigmentation and eye color) and tested them for association with UM risk. By logistic regression analysis of 272 UM cases and 1782 controls using an additive model, we identified five variants significantly associated with UM risk, all passing adjustment for multiple testing. The three most significantly associated variants rs12913832 (OR = 0.529, 95% CI 0.415–0.673; p = 8.47E-08), rs1129038 (OR = 0.533, 95% CI 0.419–0.678; p = 1.19E-07) and rs916977 (OR = 0.465, 95% CI 0.339–0.637; p = 3.04E-07) are correlated (r2 > 0.5) and map at 15q12 in the region of HERC2/OCA2, which determines eye-color in the human population. Our data provides first evidence that the genetic factors associated with pigmentation traits are risk loci of UM susceptibility.
Femtosecond laser inscribed Bragg grating arrays in long lengths of polymer optical fibres; a route to practical sensing with POF
Authors: Lacraz A. , Theodosiou A. , Kalli K. 
Published: August 2016

The first practical demonstration of readily useable fibre Bragg gratings in long lengths (>20 m) of polymer optical fibres (POFs) is reported; this is an increase in fibre length that exceeds two orders of magnitude for use in the C‐band. A low loss perfluorinated fibre and a femtosecond‐laser, direct‐write method to inscribe gratings at two different wavelengths are used. Gratings are fabricated to operate at ∼800 nm, where the optical loss is minimal, and in the C‐band, commonly used with traditional optical fibres for the majority of telecommunication applications. The development of POF Bragg gratings inscribed in long fibre lengths is the first important step for the integration of practical sensing devices and could promote the use of multiplexed POF sensors. The sensors were tested and characterised and demonstrate their compatibility with a commercial Bragg grating demodulator.
Application of fractional Fourier transform for classification of power quality disturbances
Authors: Singh Utkarsh , Singh Shyam Narain 
Published: August 2016

Proper mitigation of power quality disturbances (PQDs) requires a fast, accurate and highly noise immune classification technique. This study, therefore, presents fractional Fourier transform (FRFT) based feature extraction as a new technique for classification of PQDs. FRFT is a generalised version of Fourier transform (FT) with an additional order control and can give time, frequency and intermediate time‐frequency representations for a signal. The order control offers multi‐domain feature extraction, such that most robust feature matrix is utilised for classification under any condition. An expression is derived for the optimal classification order corresponding to maximum overall accuracy. Based on IEEE‐1159 standards, 15 PQDs are simulated and a database of pure and noisy signals is prepared. Features extracted from FRFT processed signals are tested with decision trees (DTs) and bagging predictors (BPs). The proposed technique shows better performance in most of the cases, when compared with Stockwell transform based classification under similar conditions. The classification accuracies of FRFT‐DT and FRFT‐BP are impressive even with significant reduction in training and features. Further, a validation using real PQDs obtained from an experimental setup is shown. The corresponding results closely resemble the simulation outcomes.
Minimally Invasive Direct Lateral Transpsoas Approach for the Resection of a Lumbar Plexus Schwannoma: Technique Report
Authors: Benjamin Carolina , Oermann Eric , Thomas J. , Distaso Casey , Sandhu Faheem 
Published: August 2016

Objective Traditional techniques for resection of lumbar plexus tumors have been associated with approach-related morbidity. We describe a case utilizing a minimally invasive transpsoas lateral access approach to resect a retroperitoneal tumor of the lumbar plexus.
Methods We report a case with an extradural retroperitoneal schwannoma of the L4 nerve root that was treated with a minimally invasive direct lateral transpsoas approach using atraumatic tissue dilators and an expandable tubular retractor. The use of directional and continuous electromyographic monitoring was critical in locating the plexus and positioning the retractor immediately anterior to the tumor.
Results The patient tolerated the procedure well without postoperative complications. The operative approach was direct and intraoperative blood loss was negligible. The patient demonstrated improved left leg strength and ambulation and resolution of paresthesias.
Conclusions A minimally invasive direct lateral transpsoas access approach is an effective technique to safely and adequately resect extradural retroperitoneal lumbar plexus tumors.
Quantum spin dynamics with pairwise-tunable, long-range interactions
Authors: Hung C.-L. , González-Tudela Alejandro , Cirac J. Ignacio , Kimble H. J. 
Published: August 2016

Significance
Cold atoms trapped along a photonic crystal waveguide can be used to simulate long-range quantum magnetism with pairwise-tunable spin–spin interactions mediated by guided virtual photons in a photonic band gap. Using a two-photon Raman addressing scheme, the proposed atom-nanophotonic system can achieve arbitrary and dynamic control on the strength, phase, and length scale of spin interactions. This promises new avenues for engineering a large class of spin Hamiltonians, including those exhibiting topological order or frustrated long-range magnetism.
Pre-strike Ballots, Picketing and Protest: Banning Industrial Action by the Back Door?
Authors: Dukes Ruth , Kountouris Nicola 
Published: August 2016

Abstract
Our aim in this article is to analyse the provisions of the Trade Union Act 2016 that deal with pre-strike ballots and picketing. We also consider Government proposals to legislate in respect of protests associated with industrial action (‘leverage action’), which were abandoned in favour of plans to amend the Code of Practice on Picketing. We note the suggestion made by several commentators and Opposition politicians that the Government might have intended with these changes to make it significantly more difficult for trade unions and workers to exercise their rights to take industrial action, and to engage in forms of protest associated with industrial action. Examining the stated policy aims of Government, and available evidence which speaks to those policy aims and to the likely impact of the new rules, we argue that the freedom of workers and trade unions to participate in and organise industrial action has indeed been narrowed very considerably by this Act; further, that the case for amending the existing legal framework was not at all well made.
Removing bias against short sequences enables northern blotting to better complement RNA-seq for the study of small RNAs
Authors: Choi Yun S. , Edwards Lanelle O. , DiBello Aubrey , Jose Antony M. 
Published: August 2016

ABSTRACTChanges in small non-coding RNAs such as micro RNAs (miRNAs) can serve as indicators of disease and can be measured using next-generation sequencing of RNA (RNA-seq). Here, we highlight the need for approaches that complement RNA-seq, discover that northern blotting of small RNAs is biased against short sequences, and develop a protocol that removes this bias. We found that multiple small RNA-seq datasets from the wormC. eleganshad shorter forms of miRNAs that appear to be degradation products that arose during the preparatory steps required for RNA-seq. When using northern blotting during these studies, we discovered that miRNA-length probes can have a ~360-fold bias against detecting even synthetic sequences that are 8 nt shorter. By using shorter probes and by performing hybridization and washes at low temperatures, we greatly reduced this bias to enable equivalent detection of 24 nt to 14 nt RNAs. Our protocol can better discriminate RNAs that differ by a single nucleotide and can detect specific miRNAs present in total RNA fromC. elegans. This improved northern blotting is particularly useful to obtain a measure of small RNA integrity, analyze products of RNA processing or turnover, and analyze functional RNAs that are shorter than typical miRNAs.
PBrowse: A web-based platform for real-time collaborative exploration of genomic data
Authors: Szot Peter S. , Yang Andrian , Wang Xin , Röhm Uwe , Ho Wong Koon , Ho Joshua W. K. 
Published: August 2016

ABSTRACTSummaryThe central task of a genome browser is to enable easy visual exploration of large genomic data to gain biological insight. Most existing genome browsers were designed for data exploration by individual users, while a few allow some limited forms of collaboration among multiple users, such as file sharing and wiki-style collaborative editing of gene annotations. Our work’s premise is that allowing sharing of genome browser views instantaneously in real-time enables the exchange of ideas and insight in a collaborative project, thus harnessing the wisdom of the crowd. PBrowse is a parallel-access real-time collaborative web-based genome browser that provides both an integrated, real-time collaborative platform and a comprehensive file sharing system. PBrowse also allows real-time track comment and has integrated group chat to facilitate interactive discussion among multiple users. Through the Distributed Annotation Server protocol, PBrowse can easily access a wide range of publicly available genomic data, such as the ENCODE data sets. We argue that PBrowse, with the re-designed user management, data management and novel collaborative layer based on Biodalliance, represents a paradigm shift from seeing genome browser merely as a tool of data visualisation to a tool that enables real-time human-human interaction and knowledge exchange in a collaborative setting.AvailabilityPBrowse is available athttp://pbrowse.victorchang.edu.au, and its source code is available via the open source BSD 3 license athttp://github.com/VCCRI/PBrowse.Contactj.ho@victorchang.edu.auSupplementary InformationSupplementary video demonstrating collaborative feature of pbrowse is available inhttps://www.youtube.com/watch?v=ROvKXZoXiIc.
Population genomics ofC. melanopterususing target gene capture data: demographic inferences and conservation perspectives
Authors: Delser Pierpaolo Maisano , Corrigan Shannon , Hale Matthew , Li Chenhong , Veuille Michel , Planes Serge , Naylor Gavin , Mona Stefano 
Published: August 2016

AbstractPopulation genetics studies on non-model organisms typically involve sampling few markers from multiple individuals. Next-generation sequencing approaches open up the possibility of sampling many more markers from fewer individuals to address the same questions. Here, we applied a target gene capture method to deep sequence ∼1000 independent autosomal regions of a non-model organism, the blacktip reef shark (Carcharhinus melanopterus). We devised a sampling scheme based on the predictions of theoretical studies of metapopulations to show that sampling few individuals, but many loci, can be extremely informative to reconstruct the evolutionary history of species. We collected data from a single deme (SID) from Northern Australia and from a scattered sampling representing various locations throughout the Indian Ocean (SCD). We explored the genealogical signature of population dynamics detected from both sampling schemes using an ABC algorithm. We then contrasted these results with those obtained by fitting the data to a non-equilibrium finite island model. Both approaches supported anNmvalue ∼40, consistent with philopatry in this species. Finally, we demonstrate through simulation that metapopulations exhibit greater resilience to recent changes in effective size compared to unstructured populations. We propose an empirical approach to detect recent bottlenecks based on our sampling scheme.
Synthetic Photosynthetic Consortia Define Interactions Leading to Robustness and Photoproduction
Authors: Hays Stephanie G. , Yan Leo L.W. , Silver Pamela A. , Ducat Daniel C. 
Published: August 2016

ABSTRACTBackgroundMicrobial consortia composed of autotrophic and heterotrophic species abound in nature, yet examples of synthetic communities with mixed metabolism are limited in the laboratory. We previously engineered a model cyanobacterium,Synechococcus elongatusPCC 7942, to secrete the bulk of the carbon it fixes as sucrose, a carbohydrate that can be utilized by many other microbes. Here, we tested the capability of sucrose-secreting cyanobacteria to act as a flexible platform for the construction of synthetic, light-driven consortia by pairing them with three disparate heterotrophs:Bacillus subtilis, Escherichia coli, orSaccharomyces cerevisiae. The comparison of these different co-culture dyads reveals general design principles for the construction of robust autotroph/heterotroph consortia.Main findingsWe observed heterotrophic growth dependent upon cyanobacterial photosynthate in each co-culture pair. Furthermore, these synthetic consortia could be stabilized over the long-term (weeks to months) and both species could persist when challenged with specific perturbations. Stability and productivity of autotroph/heterotroph co-cultures was dependent on heterotroph sucrose utilization, as well as other species-independent interactions that we observed across all dyads. One interaction we observed to destabilize consortia was that non-sucrose byproducts of photosynthesis negatively impacted heterotroph growth. Conversely, inoculation of each heterotrophic species enhanced cyanobacterial growth in comparison to axenic cultures Finally, these consortia can be flexibly programmed for photoproduction of target compounds and proteins; by changing the heterotroph in co–culture to specialized strains ofB. subtilisorE. coliwe demonstrate production of alpha-amylase and polyhydroxybutyrate, respectively.ConclusionsEnabled by the unprecedented flexibility of this consortia design, we uncover species-independent design principles that influence cyanobacteria/heterotroph consortia robustness. The modular nature of these communities and their unusual robustness exhibits promise as a platform for highly-versatile photoproduction strategies that capitalize on multi-species interactions and could be utilized as a tool for the study of nascent symbioses. Further consortia improvements via engineered interventions beyond those we show here (i.e. increased efficiency growing on sucrose) could improve these communities as production platforms.
Ancient European dog genomes reveal continuity since the Early Neolithic
Authors: Botigué Laura R. , Song Shiya , Scheu Amelie , Gopalan Shyamalika , Pendleton Amanda L. , Oetjens Matthew , Taravella Angela M. , Seregély Timo , Zeeb-Lanz Andrea , Arbogast Rose-Marie , Bobo Dean , Daly Kevin , Unterländer Martina , Burger Joachim , Kidd Jeffrey M. , Veeramah Krishna R. 
Published: August 2016

AbstractEurope has played a major role in dog evolution, harbouring the oldest uncontested Paleolithic remains and having been the centre of modern dog breed creation. We sequenced the whole genomes of an Early and End Neolithic dog from Germany, including a sample associated with one of Europe’s earliest farming communities. Both dogs demonstrate continuity with each other and predominantly share ancestry with modern European dogs, contradicting a previously suggested Late Neolithic population replacement. Furthermore, we find no genetic evidence to support the recent hypothesis proposing dual origins of dog domestication. By calibrating the mutation rate using our oldest dog, we narrow the timing of dog domestication to 20,000-40,000 years ago. Interestingly, we do not observe the extreme copy number expansion of theAMY2Bgene that is characteristic of modern dogs and has previously been proposed as an adaptation to a starch-rich diet driven by the widespread adoption of agriculture in the Neolithic.
Work environment and employee motivation to lead
Authors: Porter Tracy H , Riesenmy Kelly Diane , Fields Dail 
Published: August 2016

Purpose
– A key challenge for organizations is identification of candidates for development as organizational leaders. While selection criteria may vary, one important consideration is the extent to which an employee is motivated to lead. Previous studies have restricted investigation of the antecedents of these motivations to individual differences such as personality, self-efficacy, and previous leadership experiences, suggesting that leadership capacity may depend largely on employee selection. However, employee assessments of numerous aspects of the work environment may also have a substantial role in determining an employee’s motivation to lead (MTL), suggesting that an organization’s leadership capacity may depend on many other human resource practices. The paper aims to discuss these issues.

Design/methodology/approach
– In this study, the authors explored the role of employee assessments of work experiences as determinants of three types of MTL. This paper investigates the impact of a value-oriented organizational culture and the employee’s assessment of the work environment (pay satisfaction, promotion possibilities, recognition, job design, internal communication, and employee’s relationship with his/her current leader). Hierarchical multiple regression analysis was used to test the hypotheses.

Findings
– Based upon the results of 210 respondents the strength of relationship varies among the three alternative types of leadership motivation. The results suggest that besides individual differences, the perceived work environment may be a significant determinant of motivation to become an organizational leader. Employee assessments of pay, promotion opportunities, recognition, job design, quality of organizational communications, and workplace spirituality all play a role in determining employee MTL.

Originality/value
– This paper offers a number of implications for human resource management practices, hiring, and leadership development.
Nematode parasite diversity in birds: the role of host ecology, life history and migration
Authors: Leung Tommy L. F. , Koprivnikar Janet 
Published: August 2016

Summary

Previous studies have found that migratory birds generally have a more diverse array of pathogens such as parasites, as well as higher intensities of infection. However, it is not clear whether this is driven by the metabolic and physiological demands of migration, differential selection on host life‐history traits or basic ecological differences between migratory and non‐migratory species.

Parasitic helminths can cause significant pathology in their hosts, and many are trophically transmitted such that host diet and habitat use play key roles in the acquisition of infections. Given the concurrent changes in avian habitats and migratory behaviour, it is critical to understand the degree to which host ecology influences their parasite communities.

We examined nematode parasite diversity in 153 species of Anseriformes (water birds) and Accipitriformes (predatory birds) in relation to their migratory behaviour, diet, habitat use, geographic distribution and life history using previously published data.

Overall, migrators, host species with wide geographic distributions and those utilizing multiple aquatic habitats had greater nematode richness (number of species), and birds with large clutches harboured more diverse nematode fauna with respect to number of superfamilies. Separate analyses for each host order found similar results related to distribution, habitat use and migration; however, herbivorous water birds played host to a less diverse nematode community compared to those that consume some animals.

Birds using multiple aquatic habitats have a more diverse nematode fauna relative to primarily terrestrial species, likely because there is greater opportunity for contact with parasite infectious stages and/or consumption of infected hosts. As such, omnivorous and carnivorous birds using aquatic habitats may be more affected by environmental changes that alter their diet and range. Even though there were no overall differences in their ecology and life history compared with non‐migrators, migratory bird species still harboured a more diverse array of nematodes, suggesting that this behaviour places unique demands on these hosts and warrants further study.