bluuebunny/crossref_metadata_2025_split huggingface dataset:
RemakingThe Making: E.P. Thompson’s Reception in Argentina and the Shaping of Labor Historiography
Authors: Poy Lucas 
Published: April 2016

AbstractThis article traces the reception of E.P. Thompson’s work in Argentina over the past three decades. It explores the context in which Thompson was read by labor historians as a means to analyse the way in which the country’s labor historiography was shaped over this period. It argues that, in the 1980s and the 1990s, against a context characterized by a crisis of the political left and a downturn in the labor movement, Thompson’s appropriation was focused on his critique of Marxist “determinism”. While this corresponded to similar developments in other countries, Argentinian labor historiography started to show a different path in the early 2000s, when a tremendous social, political, and economic crisis shook the country. The article concludes that recent developments in labor historiography in Argentina show a different pattern to those seen in the “Global North”.
E.P. Thompson in South Africa: The Practice and Politics of Social History in an Era of Revolt and Transition, 1976–2012
Authors: Hyslop Jonathan 
Published: April 2016

AbstractThe work of E.P. Thompson has had an enormous impact on the writing of history in South Africa since the 1970s. This article traces the rise of this historiographical trend, focusing especially on the History Workshop at Wits University (Johannesburg). It outlines how a South African version of Thompsonian historical practice was theorized, and sketches some of the ways in which Thompson’s ideas were utilized by South African historians. The article shows how the History Workshop attempted to popularize their research, and examines the political projects behind these activities. Finally, the article suggests that although the influence of Thompson-style South African social historians has declined, their work has had a lasting impact on the country’s literary culture, well beyond the academy.
A criterion for compactness in Lp(ℝ) of the resolvent of the maximal general form Sturm–Liouville operator
Authors: Chernyavskaya N. A. , Shuster L. A. 
Published: April 2016

We consider the equationwhere andWe assume that this equation is correctly solvable in Lp(ℝ). Under these assumptions, we study the problem of compactness of the resolvent of the maximal continuously invertible Sturm–Liouville operator . HereIn the case p = 2, for the compact operator , we obtain two-sided sharp-by-order estimates of the maximal eigenvalue.
Developing Navigation Competencies to Care for Older Rural Adults with Advanced Illness
Authors: Duggleby Wendy , Robinson Carole A. , Kaasalainen Sharon , Pesut Barbara , Nekolaichuk Cheryl , MacLeod Roderick , Keating Norah C. , Santos Salas Anna , Hallstrom Lars K. , Fraser Kimberly D. , Williams Allison , Struthers-Montford Kelly , Swindle Jennifer 
Published: April 2016

RÉSUMÉLes navigateurs aident les adultes ruraux âgés avec des maladies avancées, ainsi que leurs familles, de se connecter aux ressources, à l’information, et aux gens qui peuvent améliorer leur qualité de vie. Cet article décrit le processus utilisé pour engager des experts—en vieillissement en milieu rural, les soins palliatifs en milieu rural, et la navigation—ainsi que les intervenants dans les collectivités rurales, d’élaborer une définition conceptuelle d’une telle navigation et de délimiter les compétences pertinentes pour la prise en charge de cette population. Un document de discussion sur les considérations importantes pour la navigation dans cette population a été développé, suivi d’un processus Delphi en quatre étapes avec 30 membres invités experts. Les résultats de l’étude ont abouti à cinq compétences générales de navigation pour les fournisseurs de soins de santé qui prennent soin des personnes âgées rurales et de leurs familles à la fin de vie: la capacité de fournir le dépistage des patients / famille; à préconiser pour le patient / famille; de faciliter les relations avec la communauté; de coordonner l’accès aux services et aux ressources; et de promouvoir l’engagement actif. Les compétences particulières ont également été développées. Ces compétences constituent la base pour la recherche et le développement de programmes d’études en navigation.
Gene expression profiling of microbial activities and interactions in sediments under haloclines of E. Mediterranean deep hypersaline anoxic basins
Authors: Edgcomb Virginia P , Pachiadaki Maria G , Mara Paraskevi , Kormas Konstantinos A , Leadbetter Edward R , Bernhard Joan M 
Published: April 2016

Abstract
Deep-sea hypersaline anoxic basins (DHABs) in the Eastern Mediterranean Sea are considered some of the most polyextreme habitats on Earth. In comparison to microbial activities occurring within the haloclines and brines of these unusual water column habitats near the Mediterranean seafloor, relatively little is known about microbial metabolic activities in the underlying sediments. In addition, it is not known whether activities are shaped by the unique chemistries of the different DHAB brines and whether evidence exists for active microbial eukaryotes in those sediments. Metatranscriptome analysis was applied to sediment samples collected using ROV Jason from underneath the haloclines of Urania, Discovery and L’Atalante DHABs and a control site. We report on expression of genes associated with sulfur and nitrogen cycling, putative osmolyte biosynthetic pathways and ion transporters, trace metal detoxification, selected eukaryotic activities (particularly of fungi), microbe–microbe interactions, and motility in sediments underlying the haloclines of three DHABs. Relative to our control sediment sample collected outside of Urania Basin, microbial communities (including eukaryotes) in the Urania and Discovery DHAB sediments showed upregulation of expressed genes associated with nitrogen transformations, osmolyte biosynthesis, heavy metals resistance and metabolism, eukaryotic organelle functions, and cell–cell interactions. Sediments underlying DHAB haloclines that have cumulative physico-chemical stressors within the limits of tolerance for microoorganisms can therefore be hotspots of activity in the deep Mediterranean Sea.
High Resolution Dissection of Reactive Glial Nets in Alzheimer’s Disease
Authors: Bouvier David S. , Jones Emma V. , Quesseveur Gaël , Davoli Maria Antonietta , A. Ferreira Tiago , Quirion Rémi , Mechawar Naguib , Murai Keith K. 
Published: April 2016

AbstractFixed human brain samples in tissue repositories hold great potential for unlocking complexities of the brain and its alteration with disease. However, current methodology for simultaneously resolving complex three-dimensional (3D) cellular anatomy and organization, as well as, intricate details of human brain cells in tissue has been limited due to weak labeling characteristics of the tissue and high background levels. To expose the potential of these samples, we developed a method to overcome these major limitations. This approach offers an unprecedented view of cytoarchitecture and subcellular detail of human brain cells, from cellular networks to individual synapses. Applying the method to AD samples, we expose complex features of microglial cells and astrocytes in the disease. Through this methodology, we show that these cells form specialized 3D structures in AD that we refer to as reactive glial nets (RGNs). RGNs are areas of concentrated neuronal injury, inflammation and tauopathy and display unique features around β-amyloid plaque types. RGNs have conserved properties in an AD mouse model and display a developmental pattern coinciding with the progressive accumulation of neuropathology. The method provided here will help reveal novel features of the healthy and diseased human brain and aid experimental design in translational brain research.
Phase 2 Randomised Controlled Trial and Feasibility Study of Future Care Planning in Patients with Advanced Heart Disease
Authors: Denvir Martin A. , Cudmore Sarah , Highet Gill , Robertson Shirley , Donald Lisa , Stephen Jacqueline , Haga Kristin , Hogg Karen , Weir Christopher J. , Murray Scott A. , Boyd Kirsty 
Published: April 2016

AbstractFuture Care Planning (FCP) rarely occurs in patients with heart disease until close to death by which time the potential benefits are lost. We assessed the feasibility, acceptability and tested a design of a randomised trial evaluating the impact of FCP in patients and carers. 50 patients hospitalised with acute heart failure or acute coronary syndrome and with predicted 12 month mortality risk of >20% were randomly allocated to FCP or usual care for 12 weeks upon discharge and then crossed-over for the next 12 weeks. Quality of life, symptoms and anxiety/distress were assessed by questionnaire. Hospitalisation and mortality events were documented for 6 months post-discharge. FCP increased implementation and documentation of key decisions linked to end-of-life care. FCP did not increase anxiety/distress (Kessler score -E 16.7 (7.0) vs D 16.8 (7.3), p = 0.94). Quality of life was unchanged (EQ5D: E 0.54(0.29) vs D 0.56(0.24), p = 0.86) while unadjusted hospitalised nights was lower (E 8.6 (15.3) vs D 11.8 (17.1), p = 0.01). Qualitative interviews indicated that FCP was highly valued by patients, carers and family physicians. FCP is feasible in a randomised clinical trial in patients with acute high risk cardiac conditions. A Phase 3 trial is needed urgently.
Orthogonal NGS for High Throughput Clinical Diagnostics
Authors: Chennagiri Niru , White Eric J. , Frieden Alexander , Lopez Edgardo , Lieber Daniel S. , Nikiforov Anastasia , Ross Tristen , Batorsky Rebecca , Hansen Sherry , Lip Va , Luquette Lovelace J. , Mauceli Evan , Margulies David , Milos Patrice M. , Napolitano Nichole , Nizzari Marcia M. , Yu Timothy , Thompson John F. 
Published: April 2016

AbstractNext generation sequencing is a transformative technology for discovering and diagnosing genetic disorders. However, high-throughput sequencing remains error-prone, necessitating variant confirmation in order to meet the exacting demands of clinical diagnostic sequencing. To address this, we devised an orthogonal, dual platform approach employing complementary target capture and sequencing chemistries to improve speed and accuracy of variant calls at a genomic scale. We combined DNA selection by bait-based hybridization followed by Illumina NextSeq reversible terminator sequencing with DNA selection by amplification followed by Ion Proton semiconductor sequencing. This approach yields genomic scale orthogonal confirmation of ~95% of exome variants. Overall variant sensitivity improves as each method covers thousands of coding exons missed by the other. We conclude that orthogonal NGS offers improvements in variant calling sensitivity when two platforms are used, better specificity for variants identified on both platforms, and greatly reduces the time and expense of Sanger follow-up, thus enabling physicians to act on genomic results more quickly.
Nucleation processes of nanobubbles at a solid/water interface
Authors: Fang Chung-Kai , Ko Hsien-Chen , Yang Chih-Wen , Lu Yi-Hsien , Hwang Ing-Shouh 
Published: April 2016

AbstractExperimental investigations of hydrophobic/water interfaces often return controversial results, possibly due to the unknown role of gas accumulation at the interfaces. Here, during advanced atomic force microscopy of the initial evolution of gas-containing structures at a highly ordered pyrolytic graphite/water interface, a fluid phase first appeared as a circular wetting layer ~0.3 nm in thickness and was later transformed into a cap-shaped nanostructure (an interfacial nanobubble). Two-dimensional ordered domains were nucleated and grew over time outside or at the perimeter of the fluid regions, eventually confining growth of the fluid regions to the vertical direction. We determined that interfacial nanobubbles and fluid layers have very similar mechanical properties, suggesting low interfacial tension with water and a liquid-like nature, explaining their high stability and their roles in boundary slip and bubble nucleation. These ordered domains may be the interfacial hydrophilic gas hydrates and/or the long-sought chemical surface heterogeneities responsible for contact line pinning and contact angle hysteresis. The gradual nucleation and growth of hydrophilic ordered domains renders the original homogeneous hydrophobic/water interface more heterogeneous over time, which would have great consequence for interfacial properties that affect diverse phenomena, including interactions in water, chemical reactions, and the self-assembly and function of biological molecules.
Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors
Authors: Wang Jianwei , Zhang Yong 
Published: April 2016

AbstractWhen coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III–V and II–VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain–low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN and ZnO on the tensile strain side, Ge, Si and GaP on the compressive strain side.
Somatic embryogenesis and enhanced shoot organogenesis in Metabriggsia ovalifolia W. T. Wang
Authors: Ouyang Yao , Chen Yulu , Lü Jinfeng , Teixeira da Silva Jaime A. , Zhang Xinhua , Ma Guohua 
Published: April 2016

AbstractAn efficient protocol providing a dual regeneration pathway via direct shoot organogenesis and somatic embryogenesis for an endangered species, Metabriggsia ovalifolia W. T. Wang, was established from leaf explants. When applied at 2.5 μM, the cytokinins 6-benzyladenine (BA) or thidiazuron (TDZ) and the auxins indole-3-butyric acid (IBA), α-naphthaleneacetic acid (NAA) and indole-3-acetic acid (IAA) could induce shoots when on basal Murashige and Skoog (MS) medium. BA and TDZ could induce more adventitious shoots (19.1 and 31.2/explant, respectively) than NAA (4.6/explant), IBA (5.7/explant) or IAA (6.4/explant). BA and TDZ at 5–10 μM could induce both shoots and somatic embryos. A higher concentration of TDZ (25 μM) induced only somatic embryos (39.8/explant). The same concentration of BA induced both adventitious shoots (23.6/explant) and somatic embryos (9.7/explant). Thus, somatic embryogenesis in this plant needs a high cytokinin concentration (BA; TDZ), as evidenced by histology. Somatic embryos germinated easily when left on the same media, but formed adventitious roots in two weeks on MS supplemented with 0.5 μM NAA, 0.5 μM IBA and 0.1% activated charcoal. Over 93% of plantlets survived following acclimatization and transfer to a mixture of sand and vermiculite (1:1, v/v) in trays.
Leveraging family-specific signatures for AMP discovery and high-throughput annotation
Authors: Waghu Faiza Hanif , Barai Ram Shankar , Idicula-Thomas Susan 
Published: April 2016

AbstractAntimicrobial peptides (AMPs) are diverse, biologically active, essential components of the innate immune system. As compared to conventional antibiotics, AMPs exhibit broad spectrum antimicrobial activity, reduced toxicity and reduced microbial resistance. They are widely researched for their therapeutic potential, especially against multi-drug resistant pathogens. AMPs are known to have family-specific sequence composition, which can be mined for their discovery and rational design. Here, we present a detailed family-based study on AMP families. The study involved the use of sequence signatures represented by patterns and hidden Markov models (HMMs) present in experimentally studied AMPs to identify novel AMPs. Along with AMPs, peptides hitherto lacking antimicrobial annotation were also retrieved and wet-lab studies on randomly selected sequences proved their antimicrobial activity against Escherichia coli. CAMPSign, a webserver has been created for researchers to effortlessly exploit the use of AMP family signatures for identification of AMPs. The webserver is available online at www.campsign.bicnirrh.res.in. In this work, we demonstrate an optimised and experimentally validated protocol along with a freely available webserver that uses family-based sequence signatures for accelerated discovery of novel AMPs.
Mitigating methane emission from paddy soil with rice-straw biochar amendment under projected climate change
Authors: Han Xingguo , Sun Xue , Wang Cheng , Wu Mengxiong , Dong Da , Zhong Ting , Thies Janice E. , Wu Weixiang 
Published: April 2016

AbstractElevated global temperatures and increased concentrations of carbon dioxide (CO2) in the atmosphere associated with climate change will exert profound effects on rice cropping systems, particularly on their greenhouse gas emitting potential. Incorporating biochar into paddy soil has been shown previously to reduce methane (CH4) emission from paddy rice under ambient temperature and CO2. We examined the ability of rice straw-derived biochar to reduce CH4 emission from paddy soil under elevated temperature and CO2 concentrations expected in the future. Adding biochar to paddy soil reduced CH4 emission under ambient conditions and significantly reduced emissions by 39.5% (ranging from 185.4 mg kg−1 dry weight soil, dws season−1 to 112.2 mg kg−1 dws season−1) under simultaneously elevated temperature and CO2. Reduced CH4 release was mainly attributable to the decreased activity of methanogens along with the increased CH4 oxidation activity and pmoA gene abundance of methanotrophs. Our findings highlight the valuable services of biochar amendment for CH4 control from paddy soil in a future that will be shaped by climate change.
Prioritizing functional phosphorylation sites based on multiple feature integration
Authors: Xiao Qingyu , Miao Benpeng , Bi Jie , Wang Zhen , Li Yixue 
Published: April 2016

AbstractProtein phosphorylation is an important type of post-translational modification that is involved in a variety of biological activities. Most phosphorylation events occur on serine, threonine and tyrosine residues in eukaryotes. In recent years, many phosphorylation sites have been identified as a result of advances in mass-spectrometric techniques. However, a large percentage of phosphorylation sites may be non-functional. Systematically prioritizing functional sites from a large number of phosphorylation sites will be increasingly important for the study of their biological roles. This study focused on exploring the intrinsic features of functional phosphorylation sites to predict whether a phosphosite is likely to be functional. We found significant differences in the distribution of evolutionary conservation, kinase association, disorder score, and secondary structure between known functional and background phosphorylation datasets. We built four different types of classifiers based on the most representative features and found that their performances were similar. We also prioritized 213,837 human phosphorylation sites from a variety of phosphorylation databases, which will be helpful for subsequent functional studies. All predicted results are available for query and download on our website (Predict Functional Phosphosites, PFP,http://pfp.biosino.org/pfp).
Properties of Two Enterovirus Antibodies that are Utilized in Diabetes Research
Authors: Maccari Giuseppe , Genoni Angelo , Sansonno Silvia , Toniolo Antonio 
Published: April 2016

AbstractHuman enteroviruses (EVs) comprise >100 different types. Research suggests a non-chance association between EV infections and type 1 diabetes. Immunohistochemical studies with the anti-EV antibody 5D-8.1 have shown that the EV capsid antigen is present in pancreatic islet cells of diabetic subjects. When it was noticed that 5D-8.1 may cross-react with human proteins, doubt was casted on the significance of the above histopathologic findings. To address this issue, properties of EV antibodies 5D-8.1 and 9D5 have been investigated using peptide microarrays, peptide substitution scanning, immunofluorescence of EV-infected cells, EV neutralization assays, bioinformatics analysis. Evidence indicates that the two antibodies bind to distinct non-neutralizing linear epitopes in VP1 and are specific for a vast spectrum of EV types (not for other human viruses). However, their epitopes may align with a few human proteins at low expected values. When tested by immunofluorescence, high concentrations of 5D-8.1 yelded faint cytoplasmic staining in uninfected cells. At reduced concentrations, both antibodies produced dotted staining only in the cytoplasm of infected cells and recognized both acute and persistent EV infection. Thus, the two monoclonals represent distinct and independent probes for hunting EVs in tissues of patients with diabetes or other endocrine conditions.
Understanding of HLA-conferred susceptibility to chronic hepatitis B infection requires HLA genotyping-based association analysis
Authors: Nishida Nao , Ohashi Jun , Khor Seik-Soon , Sugiyama Masaya , Tsuchiura Takayo , Sawai Hiromi , Hino Keisuke , Honda Masao , Kaneko Shuichi , Yatsuhashi Hiroshi , Yokosuka Osamu , Koike Kazuhiko , Kurosaki Masayuki , Izumi Namiki , Korenaga Masaaki , Kang Jong-Hon , Tanaka Eiji , Taketomi Akinobu , Eguchi Yuichiro , Sakamoto Naoya , Yamamoto Kazuhide , Tamori Akihiro , Sakaida Isao , Hige Shuhei , Itoh Yoshito , Mochida Satoshi , Mita Eiji , Takikawa Yasuhiro , Ide Tatsuya , Hiasa Yoichi , Kojima Hiroto , Yamamoto Ken , Nakamura Minoru , Saji Hiroh , Sasazuki Takehiko , Kanto Tatsuya , Tokunaga Katsushi , Mizokami Masashi 
Published: April 2016

AbstractAssociations of variants located in the HLA class II region with chronic hepatitis B (CHB) infection have been identified in Asian populations. Here, HLA imputation method was applied to determine HLA alleles using genome-wide SNP typing data of 1,975 Japanese individuals (1,033 HBV patients and 942 healthy controls). Together with data of an additional 1,481 Japanese healthy controls, association tests of six HLA loci including HLA-A, C, B, DRB1, DQB1, and DPB1, were performed. Although the strongest association was detected at a SNP located in the HLA-DP locus in a SNP-based GWAS using data from the 1,975 Japanese individuals, HLA genotyping-based analysis identified DQB1*06:01 as having the strongest association, showing a greater association with CHB susceptibility (OR = 1.76, P = 6.57 × 10−18) than any one of five HLA-DPB1 alleles that were previously reported as CHB susceptibility alleles. Moreover, HLA haplotype analysis showed that, among the five previously reported HLA-DPB1 susceptibility and protective alleles, the association of two DPB1 alleles (DPB1*09:01, and *04:01) had come from linkage disequilibrium with HLA-DR-DQ haplotypes, DRB1*15:02-DQB1*06:01 and DRB1*13:02-DQB1*06:04, respectively. The present study showed an example that SNP-based GWAS does not necessarily detect the primary susceptibility locus in the HLA region.