bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulatory B10 cell development and function
Authors: Lykken Jacquelyn M. , Candando Kathleen M. , Tedder Thomas F. 
Published: August 2015

Abstract
B cells are known to instigate and promulgate immune responses by producing antibodies and presenting antigens to T cells. However, a rare but potent B-cell subset in both humans and mice is capable of inhibiting immune responses through the production of the anti-inflammatory cytokine IL-10. Regulatory B cells do not express any unique combination of surface markers but instead represent a small population of B cells that have acquired the unique ability to produce IL-10. This numerically rare B-cell subset is therefore functionally referred to as ‘B10 cells’ to reflect both their molecular program and the fact that their anti-inflammatory effects in models of autoimmunity, infection and cancer are solely attributable to IL-10 production. As with most B cells, B10 cell development and function appear to be predominantly, if not exclusively, driven by antigen-receptor signals. Once generated, B10 cells respond to both innate and adaptive immune signals, with a requirement for antigen-specific local interactions with T cells to induce IL-10 production and to provide optimal immune suppression in mouse models of autoimmune disease. B10 cells therefore provide an antigen-specific mechanism for delivering IL-10 locally to sites of immune activation and inflammation. The ability of B10 cells to regulate innate and adaptive immune responses makes them an ideal therapeutic target for the treatment of many immune-related disorders.
Active learning: a step towards automating medical concept extraction
Authors: Kholghi Mahnoosh , Sitbon Laurianne , Zuccon Guido , Nguyen Anthony 
Published: August 2015

AbstractObjective This paper presents an automatic, active learning-based system for the extraction of medical concepts from clinical free-text reports. Specifically, (1) the contribution of active learning in reducing the annotation effort and (2) the robustness of incremental active learning framework across different selection criteria and data sets are determined.Materials and methods The comparative performance of an active learning framework and a fully supervised approach were investigated to study how active learning reduces the annotation effort while achieving the same effectiveness as a supervised approach. Conditional random fields as the supervised method, and least confidence and information density as 2 selection criteria for active learning framework were used. The effect of incremental learning vs standard learning on the robustness of the models within the active learning framework with different selection criteria was also investigated. The following 2 clinical data sets were used for evaluation: the Informatics for Integrating Biology and the Bedside/Veteran Affairs (i2b2/VA) 2010 natural language processing challenge and the Shared Annotated Resources/Conference and Labs of the Evaluation Forum (ShARe/CLEF) 2013 eHealth Evaluation Lab.Results The annotation effort saved by active learning to achieve the same effectiveness as supervised learning is up to 77%, 57%, and 46% of the total number of sequences, tokens, and concepts, respectively. Compared with the random sampling baseline, the saving is at least doubled.Conclusion Incremental active learning is a promising approach for building effective and robust medical concept extraction models while significantly reducing the burden of manual annotation.
K2 and MAXI observations of Sco X-1 – evidence for disc precession?
Authors: Hakala Pasi , Ramsay Gavin , Barclay Thomas , Charles Phil 
Published: August 2015

Abstract
Sco X-1 is the archetypal low-mass X-ray binary and the brightest persistent extrasolar X-ray source in the sky. It was included in the K2 Campaign 2 field and was observed continuously for 71 d with 1 min time resolution. In this Letter, we report these results and underline the potential of K2 for similar observations of other accreting compact binaries. We reconfirm that Sco X-1 shows a bimodal distribution of optical ‘high’ and ‘low’ states and rapid transitions between them on time-scales less than 3 h (or 0.15 orbits). We also find evidence that this behaviour has a typical systemic time-scale of 4.8 d, which we interpret as a possible disc precession period in the system. Finally, we confirm the complex optical versus X-ray correlation/anticorrelation behaviour for ‘high’ and ‘low’ optical states, respectively.
High speed BLASTN: an accelerated MegaBLAST search
tool
Authors: Chen Ying , Ye Weicai , Zhang Yongdong , Xu Yuesheng 
Published: August 2015

Abstract
Sequence alignment is a long standing problem in bioinformatics. The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools. The explosive growth of biological sequences calls for speedup of sequence alignment tools such as BLAST. To this end, we develop high speed BLASTN (HS-BLASTN), a parallel and fast nucleotide database search tool that accelerates MegaBLAST—the default module of NCBI-BLASTN. HS-BLASTN builds a new lookup table using the FMD-index of the database and employs an accurate and effective seeding method to find short stretches of identities (called seeds) between the query and the database. HS-BLASTN produces the same alignment results as MegaBLAST and its computational speed is much faster than MegaBLAST. Specifically, our experiments conducted on a 12-core server show that HS-BLASTN can be 22 times faster than MegaBLAST and exhibits better parallel performance than MegaBLAST. HS-BLASTN is written in C++ and the related source code is available at https://github.com/chenying2016/queries under the GPLv3 license.
Diagnostic Accuracy of Respiratory Distress Observation Scales as Surrogates of Dyspnea Self-report in Intensive Care Unit Patients
Authors: Persichini Romain , Gay Frédérick , Schmidt Matthieu , Mayaux Julien , Demoule Alexandre , Morélot-Panzini Capucine , Similowski Thomas 
Published: August 2015

AbstractAbstract
In 220 intensive care unit patients able to communicate, an observational scale containing five nonverbal signs was derived and validated respective to dyspnea self-report. This should help better understand and manage mechanically ventilated patients in the future.
Supplemental Digital Content is available in the text.

Background:
Dyspnea, like pain, can cause major suffering in intensive care unit (ICU) patients. Its evaluation relies on self-report; hence, the risk of being overlooked when verbal communication is impaired. Observation scales incorporating respiratory and behavioral signs (respiratory distress observation scales [RDOS]) can provide surrogates of dyspnea self-report in similar clinical contexts (palliative care).

Methods:
The authors prospectively studied (single center, 16-bed ICU, large university hospital) 220 communicating ICU patients (derivation cohort, 120 patients; separate validation cohort, 100 patients). Dyspnea was assessed by dyspnea visual analog scale (D-VAS) and RDOS calculated from its eight components (heart rate, respiratory rate, nonpurposeful movements, neck muscle use during inspiration, abdominal paradox, end-expiratory grunting, nasal flaring, and facial expression of fear). An iterative principal component analysis and partial least square regression process aimed at identifying an optimized D-VAS correlate (intensive care RDOS [IC-RDOS]).

Results:
In the derivation cohort, RDOS significantly correlated with D-VAS (r = 0.43; 95% CI, 0.29 to 0.58). A five-item IC-RDOS (heart rate, neck muscle use during inspiration, abdominal paradox, facial expression of fear, and supplemental oxygen) significantly better correlated with D-VAS (r = 0.61; 95% CI, 0.50 to 0.72). The median area under the receiver operating curve of IC-RDOS to predict D-VAS was 0.83 (interquartile range, 0.81 to 0.84). An IC-RDOS of 2.4 predicted D-VAS of 4 or greater with equal sensitivity and specificity (72%); an IC-RDOS of 6.3 predicted D-VAS of 4 or greater with 100% specificity. Similar results were found in the validation cohort.

Conclusions:
Combinations of observable signs correlate with dyspnea in communicating ICU patients. Future studies in noncommunicating patients will be needed to determine the responsiveness to therapeutic interventions and clinical usefulness.
Two sides of the safety coin?
Authors: Schiffinger Michael , Latzke Markus , Steyrer Johannes 
Published: August 2015

Background:
Safety climate (SC) and more recently patient engagement (PE) have been identified as potential determinants of patient safety, but conceptual and empirical studies combining both are lacking.

Purposes:
On the basis of extant theories and concepts in safety research, this study investigates the effect of PE in conjunction with SC on perceived error occurrence (pEO) in hospitals, controlling for various staff-, patient-, and hospital-related variables as well as the amount of stress and (lack of) organizational support experienced by staff. Besides the main effects of PE and SC on error occurrence, their interaction is examined, too.

Methodology/Approach:
In 66 hospital units, 4,345 patients assessed the degree of PE, and 811 staff assessed SC and pEO. PE was measured with a new instrument, capturing its core elements according to a recent literature review: Information Provision (both active and passive) and Activation and Collaboration. SC and pEO were measured with validated German-language questionnaires. Besides standard regression and correlational analyses, partial least squares analysis was employed to model the main and interaction effects of PE and SC on pEO, also controlling for stress and (lack of) support perceived by staff, various staff and patient attributes, and potential single-source bias.

Findings:
Both PE and SC are associated with lower pEO, to a similar extent. The joint effect of these predictors suggests a substitution rather than mutually reinforcing interaction. Accounting for control variables and/or potential single-source bias slightly attenuates some effects without altering the results.

Practice Implications:
Ignoring PE potentially amounts to forgoing a potential source of additional safety. On the other hand, despite the abovementioned substitution effect and conjectures of SC being inert, PE should not be considered as a replacement for SC.
Mammalian development does not recapitulate suspected key transformations in the evolution of the mammalian middle ear
Authors: Ramírez-Chaves Héctor E. , Wroe Stephen W. , Selwood Lynne , Hinds Lyn A. , Leigh Chris , Koyabu Daisuke , Kardjilov Nikolay , Weisbecker Vera 
Published: August 2015

AbstractThe tympanic ring, malleus and incus of the mammalian middle ear derive from the ancestral primary jaw joint of land vertebrates. In Mesozoic mammals, evolutionary detachment of the mammalian middle ear from the lower jaw occurred when Meckel’s cartilage - the last connection between the middle ear bones and the dentary – disappeared. This disappearance is famously recapitulated in early mammalian development. By extension, it was suggested that other developmental processes also recapitulate specific evolutionary processes that led to mammalian middle ear detachment in Mesozoic mammals. Specifically, developmental posterior/medial displacement and negative allometry of the growing ear ossicles relative to the lower jaw are thought to reflect evolutionary triggers of mammalian middle ear detachment. However, these hypotheses rest on scant developmental data, and have not been tested in a quantitative framework. Here we show, based on μCT scans of developmental series of several marsupials and monotremes, that negative allometry of mammalian middle ear bones relative to the skull occurs only after mammalian middle ear detachment, ruling it out as a developmental detachment trigger. There is also no positional change of ectotympanic or malleus relative to the dentary. The mammalian middle ear bones are differently positioned in two monotreme species, a recent change which is not developmentally recapitulated. Together, our results challenge the developmental prerequisites of previously proposed evolutionary detachment processes, arguing specifically against causal links between mammalian middle ear detachment and brain expansion. Our data are more consistent with a biomechanical detachment trigger relating to the onset of dentary function, but more biomechanical work and palaeontological data are required to test this notion.
How to develop objective-driven comprehensive science outreach initiatives aiming at multiple audiences
Authors: Patel Sanjai , Prokop Andreas 
Published: August 2015

AbstractScience outreach has become increasingly important for researchers and needs to be of ever improving quality, although the time available aside our science, teaching and administration activities is steadily decreasing. To square this circle, effective strategies are required. Here we argue that this can be achieved by setting simple but ambitious overarching objectives for comprehensive outreach initiatives which target multiple audiences, supported by cumulative build-up of shared high-quality resources, as well as the exchange and collaboration amongst scientists with a common outreach aim. To exemplify this strategy, we explain the low-budget, yet high-quality outreach initiative of the Manchester Fly Facility which aims to promote public awareness of the importance of the model organismDrosophilafor biomedical research. (1) This initiative targets the general public at science fairs, through public videos, or through extracurricular activities in schools as well as the development of curriculum-relevant sample lessons for teachers - all supported by a dedicated website. (2) The initiative targets university students: by adapting the public outreach resources for their teaching, and through newly developed advanced training strategies that amalgamate the outreach objectives. (3) It targets fellow scientists through blogs, conference presentations and a second website that provides a one-stop-shop for resources, arguments and strategies. As will be explained, this multi-pronged approach is time-saving in the long run and it is powerful because it reaches a wide range of audiences, helps to gain momentum, to build resource, and to gradually improve quality through cross-fertilisation between different activities, and through exchange within the science community. This helps to build communities, and high-quality outreach will have further important added value: arguments that impress the public, tend to be most effective also with reviewers and grant panel members, and often help to readjust aspects of your own scientific work.
A digital approach to protein identification and quantity estimation using tandem nanopores, peptidases, and database search
Authors: Sampath G. 
Published: August 2015

AbstractA digital approach to protein identification and quantity estimation using electrical measurements and database search is proposed. It is based on an electrolytic cell with two (three) nanopores and one (two) peptidase(s) covalently attached to thetransside of a pore. An unknown protein is digested by a reagent or peptidase into peptides ending in a known amino acid; the peptides enter the cell, pass through the first pore, and are fragmented by a high-specificity endopeptidase. The second enzyme, if present, is an exopeptidase that cleaves the fragments into single residues after the second pore. Level transitions in an ionic blockade or transverse current pulse due to residues in a fragment or individual pulses due to single residues are counted. This yields the positions of the endopeptidase’s target in the peptide, and, together with the peptide’s terminal residue, a partial sequence. Search through the Uniprot database for such sequences identifies over 90% of the proteins in the human proteome. The percentage can be increased by repeating the procedure with other reagents and cells specific to other residues, close to 100% may be possible. Sample purification to homogeneity is not required as the method applies to an arbitrary mixture of proteins; the quantity of a protein in the sample is estimated from the number of identifying peptides sensed over a long run. A Fokker-Planck model gives minimum enzyme turnover intervals required for ordered sensing of peptide fragments. With thick (80-100 nm) pores, required pulse resolution times are within the capability of CMOS detectors. The method can be implemented with existing technology; several related issues are discussed.
Genome variation and meiotic recombination inPlasmodium falciparum: insights from deep sequencing of genetic crosses
Authors: Miles Alistair , Iqbal Zamin , Vauterin Paul , Pearson Richard , Campino Susana , Theron Michel , Gould Kelda , Mead Daniel , Drury Eleanor , O’Brien John , Ruano Rubio Valentin , MacInnis Bronwyn , Mwangi Jonathan , Samarakoon Upeka , Ranford-Cartwright Lisa , Ferdig Michael , Hayton Karen , Su Xinzhuan , Wellems Thomas , Rayner Julian , McVean Gil , Kwiatkowski Dominic 
Published: August 2015

AbstractThe malaria parasitePlasmodium falciparumhas a great capacity for evolutionary adaptation to evade host immunity and develop drug resistance. Current understanding of parasite evolution is impeded by the fact that a large fraction of the genome is either highly repetitive or highly variable, and thus difficult to analyse using short read technologies. Here we describe a resource of deep sequencing data on parents and progeny from genetic crosses, which has enabled us to perform the first genome-wide, integrated analysis of SNP, INDEL and complex polymorphisms, using Mendelian error rates as an indicator of genotypic accuracy. These data reveal that INDELs are exceptionally abundant, being more common than SNPs and thus the dominant mode of polymorphism within the core genome. We use the high density of SNP and INDEL markers to analyse patterns of meiotic recombination, confirming a high rate of crossover events, and providing the first estimates for the rate of non-crossover events and the length of conversion tracts. We observe several instances of recombination that modify copy number variants associated with drug resistance, demonstrating a mechanism whereby fitness costs associated with resistance mutations could be compensated and greater phenotypic plasticity could be acquired. We describe a novel web application that allows these data to be explored in detail.
The neglected part in historic districts: case studies on the non-heritage buildings in two historic blocks in Wuxi City, China
Authors: Wang Fang , Xue Xiaoning , Wang Yingying 
Published: August 2015

Purpose
– Maintaining a city’s identity and locality is an urgent problem in urban construction. Historical districts are very important parts of a city. However, non-heritage buildings, which make a significant contribution to the character and appearance of historical areas, are facing arbitrary demolition. They are more often ignored compared with buildings on the protection list. The paper aims to discuss these issues.

Design/methodology/approach
– This paper chooses two historic blocks in Wuxi, in which 256 non-heritage buildings were examined, the SPSS method and the AHP method are used to find renewal modes for the buildings that had not finished updates, and the two blocks are then used as practical cases to validate the matching results.

Findings
– In conclusion, on the one hand, according to different building categories, different renewal modes are found. On the other hand, this study finds differences in the renewal modes of different historic districts.

Originality/value
– The study shows a renewal method for non-heritage buildings, which require attention due to their dangerous situation, as these buildings in historical districts also contribute to a city’s uniqueness and locality. These results should be helpful in the planning and practices for urban historical districts.
Corporate environmental sustainability disclosures and environmental risk
Authors: Dobler Michael , Lajili Kaouthar , Zéghal Daniel 
Published: August 2015

Purpose– This paper aims to propose and apply a novel risk-based approach to explore whether socio-political theories explain the level of corporate environmental disclosures given inconclusive evidence on the relation between environmental disclosure and environmental performance.Design/methodology/approach– Based on content analysis of corporate risk reporting, the paper develops measures of environmental risk to proxy for a firm’s exposure to public pressure in regard to environmental concerns that should be positively associated with the level of corporate environmental disclosures according to socio-political theories. Multiple regressions are used to test the predictions of socio-political theories for US Standards and Poor’s 500 constituents from polluting sectors.Findings– The level of environmental disclosures is found to be positively associated with a firm’s environmental risk while unrelated to its environmental performance. The findings suggest that firms tend to provide higher levels of environmental disclosures in response to greater exposure to public pressure as depicted by broad environmental indicators. The results are robust to alternative measures of environmental disclosures, environmental risk and environmental performance, alternative specifications of the economic model and additional sensitivity checks.Research limitations/implications– This study is limited to US firms in polluting sectors. The risk-based approach proposed may not be appropriate to cover sectors where corporate risk reporting is less likely to address environmental risk, but it could potentially be adopted in other countries with advanced risk reporting regulation or practice.Practical implications– Findings are important to understand a firm’s incentives to disclose environmental information. Cross-sectional differences found in environmental disclosures, risk and performance, highlight the importance of considering industry affiliation when analyzing environmental data.Originality/value– This paper is the first to use firm-level environmental risk variables to explain the level of corporate environmental disclosures. The risk-based approach taken suggests opportunities for research at the multi-country level and in countries where corporate environmental performance data are not publicly available.