bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian Confidence Intervals for Multiplexed Proteomics Integrate lon-Statistics with Peptide Quantification Concordance
Authors: Peshkin Leonid , Gupta Meera , Ryazanova Lillia , Wühr Martin 
Published: October 2017

SummaryMultiplexed proteomics has emerged as a powerful tool to measure relative protein expression levels across multiple conditions. The relative protein abundances are inferred by comparing the signal generated by isobaric tags, which encode the samples’ origins. Intuitively, the trust associated with a protein measurement depends on the similarity of ratios from the protein’s peptides and the signal level of these measurements. However, typically only the most likely results are reported without providing confidence for these measurements. Here we present a mathematically rigorous approach that integrates peptide MS-signal and peptide-measurement agreement into an estimation of the true protein ratio and the associated confidence (BACIQ). The main advantages of BACIQ are: 1) it removes the need to threshold reported peptide signal based on an arbitrary cut-off, thereby reporting more measurements from a given experiment; 2) confidence can be assigned without replicates; 3) for repeated experiments BACIQ provides confidence intervals for the union, not the intersection, of quantified proteins; 4) for repeated experiments, BACIQ confidence intervals are more predictive than confidence intervals based on protein measurement agreement. To demonstrate the power of BACIQ we reanalyzed previously published data on subcellular protein movement upon treatment with an Exportin 1 inhibiting drug. We detect ~2x more highly significant movers, down to subcellular localization changes of ~1%. Thus, our method drastically increases the value obtainable from quantitative proteomics experiments helping researchers to interpret their data and prioritize resources. To make our approach easily accessible we distribute it via a Python/Stan package.
Subsets of NLR genes drive adaptation of tomato to pathogens during colonisation of new habitats
Authors: Stam Remco , Silva-Arias Gustavo A. , Tellier Aurelien 
Published: October 2017

ABSTRACTNucleotide binding site, Leucine-rich repeat Receptors (NLRs), are canonical resistance (R) genes in plants, fungi and animals, functioning as central (helper) and peripheral (sensor) genes in a signalling network. We investigate NLR evolution during the colonisation of novel habitats in a model tomato species,Solanum chilense.We used R-gene enrichment sequencing (RENSeq) to obtain polymorphism data at NLRs of 140 plants sampled across 14 populations covering the whole species range. We inferred the past demographic history of habitat colonisation by resequencing whole genomes from threeS. chilenseplants from three key populations, and performing Approximate Bayesian Computation using data from the 14 populations.Using these parameters we simulated the genetic differentiation statistics distribution expected under neutral NLR evolution, and identified small subsets of outlier NLRs exhibiting signatures of selection across populations.NLRs under selection between habitats are more often helper genes, while those showing signatures of adaptation in single populations are more often sensor-NLRs. Thus, centrality in the NLR network does not constrain NLR evolvability, and new mutations in central genes in the network are key for R gene adaptation during colonisation of different habitats.
Machine-assisted cultivation and analysis of biofilms
Authors: Hansen Silla H. , Kabbeck Tobias , Radtke Carsten P. , Krause Susanne , Krolitzki Eva , Peschke Theo , Gasmi Jannis , Rabe Kersten S. , Wagner Michael , Horn Harald , Hubbuch Jürgen , Gescher Johannes , Niemeyer Christof M. 
Published: October 2017

AbstractBiofilms are the natural form of life of the majority of microorganisms. These multispecies consortia are intensively studied not only for their effects on health and environment but also because they have an enormous potential as tools for biotechnological processes. Further exploration and exploitation of these complex systems will benefit from technical solutions that enable integrated, machine-assisted cultivation and analysis. We here introduce a microfluidic platform, where readily available microfluidic chips are connected by automated liquid handling with analysis instrumentation, such as fluorescence detection, microscopy, chromatography and optical coherence tomography. The system is operable under oxic and anoxic conditions, allowing for different gases as feeding sources and offers high spatiotemporal resolution in the analysis of metabolites and biofilm composition. We demonstrate the platform’s performance by monitoring the self-organized separation of mixed cultures along autonomously created gradients, the productivity of biofilms along the microfluidic channel and the enrichment of microbial nanoorganisms.
A Double Error Dynamic Asymptote Model of Associative Learning
Authors: Kokkola Niklas H. , Mondragón Esther , Alonso Eduardo 
Published: October 2017

ABSTRACTIn this paper a formal model of associative learning is presented which incorporates representational and computational mechanisms that, as a coherent corpus, empower it to make accurate predictions of a wide variety of phenomena that so far have eluded a unified account in learning theory. In particular, the Double Error Dynamic Asymptote (DDA) model introduces: 1) a fully-connected network architecture in which stimuli are represented as temporally clustered elements that associate to each other, so that elements of one cluster engender activity on other clusters, which naturally implements neutral stimuli associations and mediated learning; 2) a predictor error term within the traditional error correction rule (the double error), which reduces the rate of learning for expected predictors; 3) a revaluation associability rate that operates on the assumption that the outcome predictiveness is tracked over time so that prolonged uncertainty is learned, reducing the levels of attention to initially surprising outcomes; and critically 4) a biologically plausible variable asymptote, which encapsulates the principle of Hebbian learning, leading to stronger associations for similar levels of cluster activity. The outputs of a set of simulations of the DDA model are presented along with empirical results from the literature. Finally, the predictive scope of the model is discussed.
MetaCompass: Reference-guided Assembly of Metagenomes
Authors: Cepeda Victoria , Liu Bo , Almeida Mathieu , Hill Christopher M. , Koren Sergey , Treangen Todd J. , Pop Mihai 
Published: November 2017

ABSTRACTMetagenomic studies have primarily relied on de novo approaches for reconstructing genes and genomes from microbial mixtures. While database driven approaches have been employed in certain analyses, they have not been used in the assembly of metagenomes. Here we describe the first effective approach for reference-guided metagenomic assembly of low-abundance bacterial genomes that can complement and improve upon de novo metagenomic assembly methods. When combined with de novo assembly approaches, we show that MetaCompass can generate more complete assemblies than can be obtained by de novo assembly alone, and improve on assemblies from the Human Microbiome Project (over 2,000 samples).
OMGene: Mutual improvement of gene models through optimisation of evolutionary conservation
Authors: Dunne Michael P. , Kelly Steven 
Published: November 2017

AbstractBackgroundThe accurate determination of the genomic coordinates for a given gene – itsgene model –is of vital importance to the utility of its annotation, and the accuracy of bioinformatic analyses derived from it. Currently-available methods of computational gene prediction, while on the whole successful, often disagree on the model for a given predicted gene, with some or all of the variant gene models failing to match the biologically observed structure. Many prediction methods can be bolstered by using experimental data such as RNA-seq and mass spectrometry. However, these resources are not always available, and rarely give a comprehensive portrait of an organism’s transcriptome due to temporal and tissue-specific expression profiles.ResultsOrthology between genes provides evolutionary evidence to guide the construction of gene models. OMGene (Optimise My Gene) aims to optimise gene models in the absence of experimental data by optimising the derived amino acid alignments for gene models within orthogroups. Using RNA-seq data sets from plants and fungi, considering intron/exon junction representation and exon coverage, and assessing the intra-orthogroup consistency of subcellular localisation predictions, we demonstrate the utility of OMGene for improving gene models in annotated genomes.ConclusionsWe show that significant improvements in the accuracy of gene model annotations can be made in both established andde novoannotated genomes by leveraging information from multiple species.
Equality between the sexes in plants for costs of reproduction; evidence from the dioecious Cape genusLeucadendron(Proteaceae)
Authors: Midgley Jeremy J. , West Adam G. , Cramer Michael D. 
Published: November 2017

AbstractIt has been argued that sexual allocation is greater for female function than male function in plants in general and specifically for the large dioecious Cape genusLeucadendron. Here, we use new interpretations of published information to support the hypothesis of equality between sexes in this genus. The explanations are based on the fire ecology of the Cape that results in reproductive synchrony, reproductive doubling and competitive symmetry. Firstly, strict post-fire seedling establishment of the reseeder life-history in the Cape results in single-aged populations. Consequently, the reproductive and vegetative schedules of males must synchronously track that of females. This implies equal allocation to sex. Secondly, after fires, dioecious females have double the seedling to adult ratio of co-occurring hermaphrodites. This indicates that being liberated from male function allows females access to resources that double their fitness compared to hermaphrodites. Therefore, male and female costs of reproduction are equal in hermaphrodites. Thirdly, competitive symmetry must occur because males and female plants will frequently encounter each other as close near neighbours. Competitive asymmetry would both reduce mating opportunities and skew local sex ratios. The evidence to date is for 1:1 sex ratios in small plots and this indicates competitive symmetry and a lack of dimorphic niches. Finally, vegetatively dimorphic species must also allocate equally to sex, or else sexual asynchrony, lack of reproductive doubling or competitive asymmetry will occur.
Subsoil arbuscular mycorrhizal fungal communities in arable soil differ from those in topsoil
Authors: Sosa-Hernández Moisés A. , Roy Julien , Hempel Stefan , Kautz Timo , Köpke Ulrich , Uksa Marie , Schloter Michael , Caruso Tancredi , Rillig Matthias C. 
Published: November 2017

AbstractArbuscular mycorrhizal fungi are recognized as important drivers of plant health and productivity in agriculture but very often existing knowledge is limited to the topsoil. With growing interest in the role of subsoil in sustainable agriculture, we used high-throughput Illumina sequencing on a set of samples encompassing drilosphere, rhizosphere and bulk soil, in both top- and subsoil. Our results show subsoil AMF communities harbor unique Operational Taxonomic Units (OTUs) and that both soil depths differ in community structure both at the OTU and family level. Our results emphasize the distinctness of subsoil AMF communities and the potential role of subsoil as a biodiversity reservoir.
The molecular basis for Pompe disease revealed by the structure of human acid α-glucosidase
Authors: Deming Derrick , Lee Karen , McSherry Tracey , Wei Ronnie R. , Edmunds Tim , Garman Scott C. 
Published: November 2017

AbstractPompe disease results from a defect in human acid α-glucosidase (GAA), a lysosomal enzyme that cleaves terminal α1-4 and α1-6 glucose from glycogen. In Pompe disease (also known as Glycogen Storage Disorder type II), the accumulation of undegraded glycogen in lysosomes leads to cellular dysfunction, primarily in muscle and heart tissues. Pompe disease is an active candidate of clinical research, with pharmacological chaperone therapy tested and enzyme replacement therapy approved. Despite production of large amounts of recombinant GAA annually, the structure of GAA has not been reported until now. Here, we describe the first structure of GAA, at 1.7Å resolution. Three structures of GAA complexes reveal the molecular basis for the hundreds of mutations that lead to Pompe disease and for pharmacological chaperoning in the protein. The GAA structure reveals a surprising second sugar-binding site 34Å from the active site, suggesting a possible mechanism for processing of large glycogen substrates. Overall, the structure will assist in the design of next-generation treatments for Pompe disease.
Head-Direction drift in rat pups is consistent with an angular path-integration process
Authors: Tocker Gilad , Borodach Eli , Bjerknes Tale L. , Moser May-Britt , Moser Edvard I. , Derdikman Dori 
Published: November 2017

SummaryThe sense of direction is a vital computation, whose neural basis is considered to be carried out by head-direction cells. One way to estimate head-direction is by integrating head angular-velocity over time. However, this process results in error accumulation resembling a random walk, proportional to , which constitutes a mark for a path integration process. In the present study we analyzed previously recorded data to quantify the drift in head-direction cells of rat pups before and after eye-opening. We found that in rat pups before eye-opening the drift propagated as a random walk, while in rats after eye-opening the drift was lower. This suggests that a path-integration process underlies the estimation of head-direction, such that before eye-opening the head-direction system runs in an open-loop manner and accumulates error. After eye-opening, visual-input, such as arena shape, helps to correct errors and thus compute the sense of direction accurately.
Distribution features and intellectual structures of digital humanities
Authors: Wang Qing 
Published: November 2017

PurposeThe purpose of this paper is to conduct a retrospective bibliometric analysis of documents about digital humanities, an emerging but interdisciplinary movement. It examines the distribution of research outputs and languages, identifies the active journals and institutions, dissects the network of categories and cited references, and interprets the hot research topics.Design/methodology/approachThe source data are derived from the Web of Science (WoS) core collection. To reveal the holistic landscape of this field, VOSviewer and CiteSpace as popular visualization tools are employed to process the bibliographic data including author, category, reference, and keyword. Furthermore, the parameter design of the visualization tools follows the general procedures and methods for bibliometric analysis.FindingsThere is an obviously rapid growth in digital humanities research. English is still the leading academic language in this field. The most influential authors all come from or have scientific relationships with Europe and North America, and two leading countries of which are the UK and USA. Digital humanities is the result of a dynamic dialogue between humanistic exploration and digital means. This research field is closely associated with history, literary and cultural heritage, and information and library science.Research limitations/implicationsThis analysis relies on the metadata information extracted from the WoS database; however, some valuable literatures in the field of digital humanities may not be retrieved from the database owing to the inherent challenge of topic search. This study is also restricted by the scope of publications, the limitation regarding the source of data is that WoS database may have underrepresented publications in this domain.Originality/valueThe output of this paper could be a valuable reference for researchers and practitioners interesting in the knowledge domain of digital humanities. Moreover, the conclusions of this retrospective analysis can be deemed as the comparable foundation for future study.
Prevalence and predictors of occupational stress among quarry workers in rural Rajasthan, India
Authors: Ahmad Absar 
Published: November 2017

PurposeDespite increasing recognition of the importance of mental health at the workplace, there is very little evidence and limited research information on the issue of the poor mental health of the workers, especially miners. The purpose of this paper is to assess the relationship between stress faced by quarry workers in consonance with their socio-demographic characteristics and their working conditions.Design/methodology/approachThis study was a cross-sectional study of quarry workers with comparison groups in the Karauli district of Rajasthan, a state located in north-western India. The study was conducted during the period May-September 2014, as part of a doctoral program. The study sample comprised a total of 218 quarry workers along with a comparison group of 203 non-miners. The level of occupational stress was assessed by using a General Health Questionnaire consisting of 12 questions.FindingsThis study found that the comparison group was at a low risk of psychological stress as compared to the mine workers. The independent risk factors for occupational stress among workers were illiteracy, gender (female), married, divorced/separated, and suffering from some occupational health problem.Social implicationsThis study concluded that mine workers are at a high level of stress, which underscores the need for urgent interventions from the government to address the issue. This is especially important as mine workers make significant contributions to the national income.Originality/valueThis paper fulfills an identified need to study the mental health status of quarry workers, thereby helping fill a persistent gap in Indian research on this issue.
Modes of soft skills learning: a case of university information professionals’ in Pakistan
Authors: Ahmad Sajjad , Ameen Kanwal , Ullah Midrar 
Published: November 2017

Purpose
The purpose of this paper is to investigate the university information professionals (UIPs) preferred modes of soft skills learning and differences in their opinions based on gender, designations and experience.

Design/methodology/approach
Quantitative research design using a questionnaire was used for data collection. Data were analyzed through SPSSS version 20.0, using descriptive and inferential statistics. The population of the study included all the UIPs working in the central libraries of the general public sector 33 universities in Pakistan, with nearly a population of 560.

Findings
The major findings showed that “mentoring sessions by experts” was the most preferred mode of soft skills learning followed by “learning from colleagues”. It showed that UIPs preferred to learn soft skills from experts and colleagues. Independent-samples t-test results found that “mentoring session by experts” was more preferred by females than males. A one-way ANOVA results found significant differences of opinion regarding the “mentoring session by experts” method between librarians and assistant librarians (p = 0.044). Results were statistically significant also between more experienced and less experienced regarding “real project/assignment-based method” and “mentoring session by experts”. In addition, for “formal online courses” and “self-training through reading books”, results were statistically significant between experienced groups of 1-5 years and 11-15 years. Overall results indicated that from UIPs’ perspective, soft skills should be taught to them using face-to-face methods.

Originality/value
This is the first study in Pakistan that dealt with the preferred modes of soft skills learning of UIPs by using a large group (N = 372) of respondents.
Nutritional functional trait diversity of crops in south‐eastern Senegal
Authors: Wood Stephen A. 
Published: November 2017

Abstract

Ecological trait diversity metrics have been used to highlight the impacts of agriculture. Such metrics can also be used to include human nutrition—an important dimension of human well‐being—into assessments of agroecosystem function and services. Although crop yield is a common agroecosystem metric, it does not capture the multiple ways in which agriculture impacts people and the environment.

Given that nutrient composition of crops is a set of functional traits, I apply a suite of functional diversity metrics—functional divergence, richness, evenness and dispersion—to crop production data from south‐eastern Senegal. I also propose a new nutritional diversity metric—potential nutrient adequacy—to assess nutritional outcomes of different agricultural systems.

I demonstrate high variability in nutritional diversity and potential adequacy among households and administrative departments in south‐eastern Senegal. I show that most households produce nutritionally similar crops, rather than crops with high nutritional diversity. As a result, most households currently do not produce enough nutrients to meet minimal nutritional requirements.

Using a scenario approach, I show that intensifying yields of staple crops and diversifying production to include non‐staples can increase nutritional production and the potential to meet nutritional needs. I further show that a combination of intensification and diversification is needed to meet the need for a diverse group of nutrients.

Policy implications. I develop a new metric that indicates the potential for a food system to meet the nutritional requirements of a population. This tool will allow practitioners to assess the nutritional adequacy of a food system and to design food systems that optimize nutritional outcomes. Application of this metric to different production scenarios showed that combining yield intensification with crop diversification is important to meeting full nutritional targets for smallholder agriculture. There is a broader need for incorporating other social and socio‐ecological traits into trait‐based assessments of agroecosystems.
Review article: Sepsis in the emergency department – Part 1: Definitions and outcomes
Authors: Macdonald Stephen PJ , Williams Julian M , Shetty Amith , Bellomo Rinaldo , Finfer Simon , Shapiro Nathan , Keijzers Gerben 
Published: November 2017

AbstractSepsis has recently been redefined as acute organ dysfunction due to infection. The ED plays a critical role in identifying patients with sepsis. This is challenging due to the heterogeneity of the syndrome, and the lack of an objective standard diagnostic test. While overall mortality rates from sepsis appear to be falling, there is an increasing burden of morbidity among survivors. This largely reflects the growing proportion of older patients with comorbid illnesses among those treated for sepsis.