bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ebola outbreak brings to light an unforeseen impact of tsetse control on sleeping sickness transmission in Guinea
Authors: Kagabadouno Moïse , Camara Oumou , Camara Mamadou , Ilboudo Hamidou , Camara Mariame , Rayaisse Jean-Baptiste , Diaby Abdoulaye , Traoré Balla , Leno Mamadou , Courtin Fabrice , Jamonneau Vincent , Solano Philippe , Bucheton Bruno 
Published: March 2018

AbstractIn addition to the thousands of deaths due the unprecedented ebola outbreak that stroke West Africa (2014-2016), national health systems in affected countries were deeply challenged impacting a number of diseases control programs. Here we describe the case of Human African Trypanosomiasis (HAT), a deadly neglected tropical disease due to a trypanosome transmitted by tsetse flies for which no vaccine nor chemoprophylaxis exists. Data are presented for the disease focus of Boffa in Guinea where a pilot elimination project combining medical screening and vector control was launched in 2012. During ebola, HAT active screening activities were postponed and passive surveillance also was progressively impaired. However, tsetse control using small insecticide impregnated targets could be maintained. The over two years disruption of screening activities led to a dramatic increase of HAT prevalence, from 0.7% in 2013 (21/2885) to 2% (69/3448) in 2016, reaching epidemic levels (>5%) in some villages. In deep contrast, control levels reached in 2013 (0.1%; 7/6564) were maintained in areas covered with impregnated targets as no cases were found in 2016 (0/799). In Boffa, ebola has thus incidentally provided a unique framework to assess the impact of current HAT control strategies. A first lesson is that the “screen and treat” strategy is fragile as rapid bursts of the disease may occur in case of disruption. A second lesson is that vector control reducing human-tsetse contacts, even implemented alone, is effective in providing a good level of protection against infection. This advocates for a greater attention being paid to the combination of tsetse control together with medical activities in aiming to reach the HAT elimination objective in Africa.
The Organizational Principles of Membranes Below 100 nm: Experimental Breakthroughs Occasion a “Modeling Manifesto”
Authors: Hsieh E. Lyman C.-L. , Eggeling C. 
Published: March 2018

AbstractNew experimental techniques reveal the plasma membrane to be heterogeneous and "scale-rich," from nanometers to microns, and from microseconds to seconds. This is critical information, as heterogeneous, scale-dependent transport governs the molecular encounters that underlie cellular signaling. The data are rich, and reaffirm the importance of the cortical cytoskeleton, protein aggregates, and lipidomic complexity to the statistics of molecular encounters. Moreover, the data demand simulation approaches with a particular set of features, hence the “manifesto”. Together with the experimental data, simulations which satisfy these requirements hold the promise of a deeper understanding of membrane spatiotemporal organization. Several experimental breakthroughs are reviewed, the constraints that they place on simulations are discussed, and the status of simulation approaches which aim to meet them are detailed.
Mechanical Properties of a Primary Cilium from the Stochastic Motions of the Cilium Tip
Authors: Flaherty J. , Feng Z. , Peng Z. , Young Y.-N. , Resnick A. 
Published: March 2018

ABSTRACTThe stochastic tip dynamics of a primary cilium held within an optical trap is quantified by combining experimental, analytical and computational tools. Primary cilia are cellular organelles, present on most vertebrate cells, hypothesized to function as a fluid flow sensor. The mechanical properties of a cilium remain incompletely characterized. We measured the fluctuating position of an optically trapped cilium tip under untreated, Taxol-treated, and HIF-stabilized conditions. We applied analytical modeling to derive the mean-squared displacement of the trapped tip of a cilium and compared the results with experimental measurements. We provide, for the first time, evidence that the effective flexural rigidity of a ciliary axoneme is length-dependent, and longer cilia are stiffer than shorter cilia. We then provide a rational explanation for both effects. We demonstrate that the apparent length-dependent flexural rigidity can be understood by a combination of modeling axonemal microtubules orthotropic elastic shells and including (actin-driven) active stochastic basal body motion. It is hoped that our improved characterization of cilia will result in deeper understanding of the biological function of cellular flow sensing by this organelle. Our model could be profitably applied to motile cilia and our results also demonstrate the possibility of using easily observable ciliary dynamics to probe interior cytoskeletal dynamics.
Stimulus predictability does not modulate bottom-up attentional capture
Authors: Meijs Erik L. , Klaassen Felix H. , Bokeria Levan , Gaal Simon van , Lange Floris P. de 
Published: March 2018

AbstractAttention can be involuntarily captured by physically salient stimuli, a phenomenon known as bottom-up attention. Typically, these salient stimuli occur unpredictably in time and space. Therefore, in a series of three behavioral experiments, we investigated the extent to which such bottom-up attentional capture is a function of one’s prior expectations. In the context of an exogenous cueing task, we systematically manipulated participants’ spatial (Experiment 1) or temporal (Experiment 2 and 3) expectations about an uninformative cue, and examined the extent of attentional capture by the cue. We anticipated larger attentional capture for unexpected compared to expected cues. However, while we observed robust attentional capture in all experiments, we did not find any evidence for a modulation of attentional capture by prior expectation. This underscores the automatic and reflexive nature of bottom-up attention.
Lag Penalized Weighted Correlation for Time Series Clustering
Authors: Chandereng Thevaa , Gitter Anthony 
Published: March 2018

ABSTRACTMotivationThe similarity or distance measure used for clustering can generate intuitive and interpretable clusters when it is tailored to the unique characteristics of the data. In time series datasets, measurements such as gene expression levels or protein phosphorylation intensities are collected sequentially over time, and the similarity score should capture this special temporal structure.ResultsWe propose a clustering similarity measure called Lag Penalized Weighted Correlation (LPWC) to group pairs of time series that exhibit closely-related behaviors over time, even if the timing is not perfectly synchronized. LPWC aligns pairs of time series profiles to identify common temporal patterns. It down-weights aligned profiles based on the length of the temporal lags that are introduced. We demonstrate the advantages of LPWC versus existing time series and general clustering algorithms. In a simulated dataset based on the biologically-motivated impulse model, LPWC is the only method to recover the true clusters for almost all simulated genes. LPWC also identifies distinct temporal patterns in our yeast osmotic stress response and axolotl limb regeneration case studies.AvailabilityThe LPWC R package is available at https://github.com/gitter-lab/LPWC and CRAN under a MIT license.Contactchandereng@wisc.edu or gitter@biostat.wisc.eduSupplementary informationSupplementary files are available online.
Functional genomics identifies AMPD2 as a new prognostic marker for undifferentiated pleomorphic sarcoma
Authors: Orth Martin F. , Gerke Julia S. , Knösel Thomas , Altendorf-Hofmann Annelore , Musa Julian , Alba Rubio Rebeca , Stein Stefanie , Dallmayer Marlene , Baldauf Michaela C. , Marchetto Aruna , Sannino Giuseppina , Ohmura Shunya , Li Jing , Hakozaki Michiyuki , Kirchner Thomas , Dandekar Thomas , Butt Elke , Grünewald Thomas G. P. 
Published: March 2018

ABSTRACTSoft-tissue sarcomas are rare, heterogeneous and often aggressive mesenchymal cancers. Many of them are associated with poor outcome, in part because biomarkers that can reliably identify high-risk patients are lacking. Studies on sarcomas often are limited by small sample sizes rendering the identification of novel biomarkers difficult when focusing only on individual cohorts. However, the increasing number of publicly available ‘omics’ data opens inroads to overcome this obstacle.Here, we combine high-throughput transcriptome analyses, immunohistochemistry, and functional assays to show that high adenosine monophosphate deaminase 2 (AMPD2) is a robust prognostic biomarker for worse patient outcome in undifferentiated pleomorphic sarcoma (UPS). Publicly available gene expression and survival data for UPS from two independent studies, The Cancer Genome Atlas (TCGA) and the CINSARC reference dataset, were subjected to survival association testing. Genes, whose high expression was significantly correlated with worse outcome in both cohorts (overall and metastasis-free survival), were considered as prognostic marker candidates. The best candidate, AMPD2, was validated on protein level in an independent tissue microarray. Analysis of DNA copy-number and matched gene expression data indicated that high AMPD2 expression is significantly correlated with copy-number gains at the AMPD2 locus. Gene-set enrichment analyses of AMPD2 co-expressed genes in both UPS gene expression datasets suggested that highly AMPD2 expressing tumors are enriched in gene signatures involved in tumorigenesis. Consistent with this prediction in primary tumors, knockdown of AMPD2 by RNA interference with pooled siRNAs or a doxycycline-inducible shRNA construct in the UPS cell line FPS-1 markedly inhibited proliferation in vitro and tumorigenicity in vivo.Collectively, these results provide evidence that AMPD2 may serve as a novel biomarker for outcome prediction in UPS. Our study exemplifies how the integration of available ‘omics’ data, immunohistochemical analyses, and functional experiments can identify novel biomarkers even in a rare sarcoma, which may serve as a blueprint for biomarker identification for other rare cancers.
Visual physiology of the Layer 4 cortical circuitin silico
Authors: Arkhipov Anton , Gouwens Nathan W. , Billeh Yazan N. , Gratiy Sergey , Iyer Ramakrishnan , Wei Ziqiang , Xu Zihao , Berg Jim , Buice Michael , Cain Nicholas , da Costa Nuno , de Vries Saskia , Denman Daniel , Durand Severine , Feng David , Jarsky Tim , Lecoq Jerome , Lee Brian , Li Lu , Mihalas Stefan , Ocker Gabriel K. , Olsen Shawn R. , Reid R. Clay , Soler-Llavina Gilberto , Sorensen Staci A. , Wang Quanxin , Waters Jack , Scanziani Massimo , Koch Christof 
Published: March 2018

ABSTRACTDespite advances in experimental techniques and accumulation of large datasets concerning the composition and properties of the cortex, quantitative modeling of cortical circuits under in-vivo-like conditions remains challenging. Here we report and publicly release a biophysically detailed circuit model of layer 4 in the mouse primary visual cortex, receiving thalamo-cortical visual inputs. The 45,000-neuron model was subjected to a battery of visual stimuli, and results were compared to published work and new in vivo experiments. Simulations reproduced a variety of observations, including effects of optogenetic perturbations. Critical to the agreement between responses in silico and in vivo were the rules of functional synaptic connectivity between neurons. Interestingly, after extreme simplification the model still performed satisfactorily on many measurements, although quantitative agreement with experiments suffered. These results emphasize the importance of functional rules of cortical wiring and enable a next generation of data-driven models of in vivo neural activity and computations.AUTHOR SUMMARYHow can we capture the incredible complexity of brain circuits in quantitative models, and what can such models teach us about mechanisms underlying brain activity? To answer these questions, we set out to build extensive, bio-realistic models of brain circuitry employing systematic datasets on brain structure and function. Here we report the first modeling results of this project, focusing on the layer 4 of the primary visual cortex (V1) of the mouse. Our simulations reproduced a variety of experimental observations in a large battery of visual stimuli. The results elucidated circuit mechanisms determining patters of neuronal activity in layer 4 – in particular, the roles of feedforward thalamic inputs and specific patterns of intracortical connectivity in producing tuning of neuronal responses to the orientation of motion. Simplification of neuronal models led to specific deficiencies in reproducing experimental data, giving insights into how biological details contribute to various aspects of brain activity. To enable future development of more sophisticated models, we make the software code, the model, and simulation results publicly available.
iTOP: Inferring the Topology of Omics Data
Authors: Aben Nanne , Westerhuis Johan A. , Song Yipeng , Kiers Henk A.L. , Michaut Magali , Smilde Age K. , Wessels Lodewyk F.A. 
Published: April 2018

AbstractMotivationIn biology, we are often faced with multiple datasets recorded on the same set of objects, such as multi-omics and phenotypic data of the same tumors. These datasets are typically not independent from each other. For example, methylation may influence gene expression, which may, in turn, influence drug response. Such relationships can strongly affect analyses performed on the data, as we have previously shown for the identification of biomarkers of drug response. Therefore, it is important to be able to chart the relationships between datasets.ResultsWe present iTOP, a methodology to infera topology of relationships between datasets. We base this methodology on the RV coefficient, a measure of matrix correlation, which can be used to determine how much information is shared between two datasets. We extended the RV coefficient for partial matrix correlations, which allows the use of graph reconstruction algorithms, such as the PC algorithm, to infer the topologies. In addition, since multi-omics data often contain binary data (e.g. mutations), we also extended the RV coefficient for binary data. Applying iTOP to pharmacogenomics data, we found that gene expression acts as a mediator between most other datasets and drug response: only proteomics clearly shares information with drug response that is not present in gene expression. Based on this result, we used TANDEM, a method for drug response prediction, to identify which variables predictive of drug response were distinct to either gene expression or proteomics.AvailabilityAn implementation of our methodology is available in the R package iTOP on CRAN. Additionally, an R Markdown document with code to reproduce all figures is provided as Supplementary Material.Contacta.k.smilde@uva.nl and l.wessels@nki.nlSupplementary informationSupplementary data are available at Bioinformatics online.
Benchmarking New CEASIOM with CPACS adoption for aerodynamic analysis and flight simulation
Authors: Jungo Aidan , Zhang Mengmeng , Vos Jan B. , Rizzi Arthur 
Published: April 2018

Purpose
The purpose of this paper is to present the status of the on-going development of the new computerized environment for aircraft synthesis and integrated optimization methods (CEASIOM) and to compare results of different aerodynamic tools. The concurrent design of aircraft is an extremely interdisciplinary activity incorporating simultaneous consideration of complex, tightly coupled systems, functions and requirements. The design task is to achieve an optimal integration of all components into an efficient, robust and reliable aircraft with high performance that can be manufactured with low technical and financial risks, and has an affordable life-cycle cost.

Design/methodology/approach
CEASIOM (www.ceasiom.com) is a framework that integrates discipline-specific tools like computer-aided design, mesh generation, computational fluid dynamics (CFD), stability and control analysis and structural analysis, all for the purpose of aircraft conceptual design.

Findings
A new CEASIOM version is under development within EU Project AGILE (www.agile-project.eu), by adopting the CPACS XML data-format for representation of all design data pertaining to the aircraft under development.

Research limitations/implications
Results obtained from different methods have been compared and analyzed. Some differences have been observed; however, they are mainly due to the different physical modelizations that are used by each of these methods.

Originality/value
This paper summarizes the current status of the development of the new CEASIOM software, in particular for the following modules: CPACS file visualizer and editor CPACSupdater (Matlab) Automatic unstructured (Euler) & hybrid (RANS) mesh generation by sumo Multi-fidelity CFD solvers: Digital Datcom (Empirical), Tornado (VLM), Edge-Euler & SU2-Euler, Edge-RANS & SU2-RANS Data fusion tool: aerodynamic coefficients fusion from variable fidelity CFD tools above to compile complete aero-table for flight analysis and simulation.
Team learning behaviours and innovative work behaviour in work teams
Authors: Widmann Andreas , Mulder Regina H. 
Published: April 2018

Purpose
The purpose of this paper is to get deeper insight into the complex nature of the relationship between team learning conditions, team learning behaviours (TLBs) and innovative work behaviour (IWB) by considering and combining different neglected aspects in research.

Design/methodology/approach
A questionnaire was filled out by 593 vocational educators of 117 interdisciplinary work teams in vocational colleges in Germany. Correlations were calculated and structural equation modelling at two levels was conducted.

Findings
The results indicate that TLBs, especially team reflexivity and boundary spanning, relate positively to IWB. Furthermore, team structure, task interdependence and group potency relate positively to TLBs. It means that TLBs can be fostered by establishing these team learning conditions and, thus, IWB can be fostered.

Research limitations/implications
The main limitation of the study is that the data collection was cross-sectional. Longitudinal studies are required to capture the dynamic character of team learning and to identify causal relationships.

Practical implications
It is important to make all employees in vocational education aware of the importance of TLBs especially of team reflexivity and boundary spanning.

Originality/value
This study provides practical implications for organisations to foster IWB and indications for a better understanding of the relationship between team learning conditions, TLBs and IWB considering and combining different neglected aspects such as examining TLBs separated in one study.
Integrated work-based placements – shifting the paradigm
Authors: Smith Sara 
Published: April 2018

Purpose
The role of higher education institutions in enhancing capability development of the healthcare professionals workforce has resulted in work-based learning becoming an essential component of awards linked to professional registration. The purpose of this paper is to explore how key stakeholders (academics, workplace tutors and students) on a programme leading to registration as a Biomedical Scientist (BMS) position themselves in their role and the subsequent impact of this upon delivery of pre-registration training and the development of professional capability.

Design/methodology/approach
Constructivist grounded theory methodology and a mixed-methods approach were drawn upon for the study.

Findings
Findings expose the challenges of a positivist focus and assumptions around workplace learning and professional development presenting a barrier to developing professional capability. In addressing this barrier, two strategies of “doing the portfolio” and “gaining BMS currency” are adopted. The registration portfolio has become an objective reductionist measure of learning, reflecting the positivist typology of practice in this profession.

Practical implications
To ensure that students are supported to develop not only technical skills but also professional capability there is a need for a paradigm shift from a positivist episteme to one that embraces both the positivist and socio-cultural paradigms, viewing them as complimentary and parallel.

Originality/value
The study provides a novel insight into how stakeholders interact with the pressures of internal and external influences and the impact this has upon behaviours and strategies adopted. The theoretical understanding proposed has a range of implications for practice and for the development of practitioner capability through pre-registration training and beyond.
Gendered patterning of relationships
Authors: Bhatia Bhanu , Salignac Fanny 
Published: April 2018

PurposeSocial capital has become a general tool for policy interventions in developing countries – often put forward as empowering and improving women’s socioeconomic position. Using the framework of gendered manifestations of networks in patriarchal setting of Bangladesh, the authors argue that while networks are crucial building blocks of social capital they are bound to manifest differently depending on the context in which they are embedded. The paper aims to discuss this issue.Design/methodology/approachBy combining methods of social networks and spatial analysis, this study provides insights into the embeddedness of networks in gender norms. The authors conduct the study in the context of reproductive health networks in rural Bangladesh.FindingsThe findings suggest that networks mirror the structure of the society in which they evolve, reproducing rather than challenging disadvantage.Research limitations/implicationsThe authors call for a more nuanced view of social capital leading to policy design that is sensitive to different manifestations of networks.Originality/valueThis study is the first to combine novel methods of social networks and spatial analysis to quantify the complex interplay between social networks and gender norms. This study further contributes to the diffusion literature by providing the first comparative view of women’s and men’s reproductive health networks that extend beyond actors’ direct tie.
Public attitudes towards the poor in the South Caucasus: a matter of solidarity and conditionality
Authors: Gugushvili Dimitri 
Published: April 2018

Purpose
The purpose of this paper is to explore public attitudes towards poor people in the South Caucasian countries.

Design/methodology/approach
The paper is based on an analysis of data from the tenth round of the Caucasus Barometer survey, one of the most reliable sources of public opinion data in the region.

Findings
The majority of the population in Azerbaijan and Georgia would consent to paying higher taxes or reducing public services if their governments used the extra resources to provide cash assistance to more poor people, but in Armenia the level of solidarity is considerably lower. However, the majority in each of the countries supports assistance being conditional on beneficiaries actively searching for work. In contrast to conventional wisdom, some better-off groups are more in favour of supporting the poor than those who face a higher risk of poverty. The author hypothesises that this may be driven by self-interest, as in relative terms the welfare sacrifices required for financing the extension of schemes might be higher for the vulnerable than for the better-off.

Originality/value
This paper is the first to provide a comparative analysis of public attitudes towards vulnerable groups in the South Caucasus. It also contributes to the scarce literature on perceived welfare deservingness of social assistance recipients and public preferences for imposing conditionality on them. In addition, it presents a strong case for using more comprehensive questions to construct measurements of people’s welfare attitudes than those commonly used.