bluuebunny/crossref_metadata_2025_split huggingface dataset:
Challenges and advances for transcriptome assembly in non-model species
Authors: Ungaro Arnaud , Pech Nicolas , Martin Jean-François , McCairns R.J. Scott , Mévy Jean-Philippe , Chappaz Rémi , Gilles André 
Published: October 2016

AbstractAnalyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence). Here we focus on gene identification and not on resolving the whole set of transcripts (i.e. the complete transcriptome). For simulated datasets, the transcriptome-guided assembly based on blastn recovers 94.8% of genes irrespective of read length at 0% divergence; however, assignment rate of reads is negatively correlated with both increasing divergence level and reducing read lengths. Nevertheless, we still observe 92.6% of recovered genes at 30% divergence irrespective of read length. This analysis also produces a categorization of genes relative to their assignment, and suggests guidelines for data processing prior to analyses of comparative transcriptomics and gene expression to minimize potential inferential bias associated with incorrect transcript assignment. We also compare the performances of de novo assembly alone vs in combination with a transcriptome-guided assembly based on blastn via simulation and empirically, using data from a cyprinid fish species and from an oak species. For any simulated scenario, the transcriptome-guided assembly using blastn outperforms the de novo approach alone, including when the divergence level is beyond the reach of mapping methods. Combining de novo assembly and a related reference transcriptome for read assignment also addresses the bias/error in contigs caused by the dependence on a related reference alone. Empirical data corroborate those findings when assembling transcriptomes from the two non-model organisms: Parachondrostoma toxostoma (fish) and Quercus pubescens (plant). For the fish species, out of the 31,944 genes known from D. rerio, the guided and de novo assemblies recover respectively 20,605 and 20,032 genes but the performance of the guided assembly approach is much higher for both the contiguity and completeness metrics. For the oak, out of the 29,971 genes known from Vitis vinifera, the transcriptome-guided and de novo assemblies display similar performance but the new guided approach detects 16,326 genes where the de novo assembly only detects 9,385 genes.
Distinctive BOLD Connectivity Patterns in the Schizophrenic Brain: Machine-learning based comparison between various connectivity measures
Authors: Han Hio-Been 
Published: October 2016

AbstractRecent functional magnetic resonance imaging (fMRI) studies have found distinctive functional connectivity in the schizophrenic brain. However, most of the studies focused on the correlation value to define the functional connectivity for BOLD fluctuations between brain regions, which resulted in the limited understanding to the network properties of altered wirings in the schizophrenic brain. Here I characterized the distinctiveness of BOLD connectivity pattern in the schizophrenic brain relative to healthy brain with various similarity measures in the time-frequency domain, while participants are performing the working memory task in the MRI scanner. To assess the distinctiveness of the connectivity pattern, discrimination performances of the pattern classifier machine trained with each similarity measure were compared. Interestingly, the classifier machine trained by time-lagging patterns of low frequency fluctuation (LFF) produced higher classifying sensitivity than the machines trained by other measures. Also, the classifier machine trained by coherence pattern in LFF band also made better performance than the machine trained by correlation-based connectivity pattern. These results indicate that there are unobserved but considerable features in the functional connectivity pattern of schizophrenic brain which traditional emphasis on correlation analysis does not capture.
The need to include phylogeny in trait-based analyses of community composition
Authors: Li Daijiang , Ives Anthony R 
Published: October 2016

SummaryA growing number of studies incorporate functional trait information to analyse patterns and processes of community assembly. These studies of trait-environment relationships generally ignore phylogenetic relationships among species. When functional traits and the residual variation in species distributions among communities have phylogenetic signal, however, analyses ignoring phylogenetic relationships can decrease estimation accuracy and power, inflate type I error rates, and lead to potentially false conclusions.Using simulations, we compared estimation accuracy, statistical power, and type I error rates of linear mixed models (LMM) and phylogenetic linear mixed models (PLMM) designed to test for trait-environment interactions in the distribution of species abundances among sites. We considered the consequences of both phylogenetic signal in traits and phylogenetic signal in the residual variation of species distributions generated by an unmeasured (latent) trait with phylogenetic signal.When there was phylogenetic signal in the residual variation of species among sites, PLMM provided better estimates (closer to the true value) and greater statistical power for testing whether the trait-environment interaction regression coefficient differed from zero. LMM had unacceptably high type I error rates when there was phylogenetic signal in both traits and the residual variation in species distributions. When there was no phylogenetic signal in the residual variation in species distributions, LMM and PLMM had similar performances.LMMs that ignore phylogenetic relationships can lead to poor statistical tests of trait-environment relationships when there is phylogenetic signal in the residual variation of species distributions among sites, such as caused by unmeasured traits. Therefore, phylogenies and PLMMs should be used when studying how functional traits affect species abundances among communities in response to environmental gradients.
Dual origins of measured phase-amplitude coupling reveal distinct neural mechanisms underlying episodic memory in the human cortex
Authors: Vaz Alex P. , Yaffe Robert B. , Wittig John H. , Inati Sara K. , Zaghloul Kareem A. 
Published: October 2016

AbstractPhase-amplitude coupling (PAC) is hypothesized to coordinate neural activity, but its role in successful memory formation in the human cortex is unknown. Measures of PAC are difficult to interpret, however. Both increases and decreases in PAC have been linked to memory encoding, and PAC may arise due to different neural mechanisms. Here, we use a waveform analysis to examine PAC in the human cortex as participants with intracranial electrodes performed a paired associates memory task. We found that successful memory formation exhibited significant decreases in left temporal lobe and prefrontal cortical PAC, and these two regions exhibited changes in PAC within different frequency bands. Two underlying neural mechanisms, nested oscillations and sharp waveforms, were responsible for the changes in these regions. Our data therefore suggest that decreases in measured cortical PAC during episodic memory reflect two distinct underlying mechanisms that are anatomically segregated in the human brain.
Leveraging uncertainty information from deep neural networks for disease detection
Authors: Leibig Christian , Allken Vaneeda , Ayhan Murat Seçkin , Berens Philipp , Wahl Siegfried 
Published: October 2016

AbstractDeep learning (DL) has revolutionized the field of computer vision and image processing. In medical imaging, algorithmic solutions based on DL have been shown to achieve high performance on tasks that previously required medical experts. However, DL-based solutions for disease detection have been proposed without methods to quantify and control their uncertainty in a decision. In contrast, a physician knows whether she is uncertain about a case and will consult more experienced colleagues if needed. Here we evaluate drop-out based Bayesian uncertainty measures for DL in diagnosing diabetic retinopathy (DR) from fundus images and show that it captures uncertainty better than straightforward alternatives. Furthermore, we show that uncertainty informed decision referral can improve diagnostic performance. Experiments across different networks, tasks and datasets show robust generalization. Depending on network capacity and task/dataset difficulty, we surpass 85% sensitivity and 80% specificity as recommended by the NHS when referring 0%–20% of the most uncertain decisions for further inspection. We analyse causes of uncertainty by relating intuitions from 2D visualizations to the high-dimensional image space. While uncertainty is sensitive to clinically relevant cases, sensitivity to unfamiliar data samples is task dependent, but can be rendered more robust.
Genome scale mutational analysis ofGeobacter sulfurreducensreveals distinct molecular mechanisms for respiration of poised electrodes vs. Fe(III) oxides
Authors: Ho Chan Chi , Levara Caleb E. , Jiménez-Oteroa Fernanda , Bond Daniel R. 
Published: October 2016

AbstractGeobacter sulfurreducensgenerates electricity by coupling intracellular oxidation of organic acids with electron transfer to the cell exterior, while maintaining a conductive connection to electrode surfaces. This unique ability has been attributed to the bacterium’s capacity to also respire extracellular terminal electron acceptors that require contact, such as insoluble metal oxides. To expand the molecular understanding of electricity generation mechanisms, we constructedGeobacter sulfurreducenstransposon mutant (Tn-Seq) libraries for growth with soluble fumarate or an electrode surface as the electron acceptor. Mutant libraries with over 33,000 unique transposon insertions and an average of 9 transposon insertions per kb allowed identification of 1,214 genomic features essential for growth with fumarate, including over 270 genes with one or more functional homologs that could not be resolved by previous annotation orin silicomodeling. Tn-Seq analysis of electrode-grown cells identified mutations in over 50 genes encoding cytochromes, processing systems for proline-rich proteins, sensory systems, extracellular structures, polysaccharides, metabolic enzymes and hypothetical proteins that caused at least a 50% reduction in apparent growth rate. Scarless deletion mutants of genes identified via Tn-Seq revealed a new putativec-type cytochrome conduit complex (extABCD) essential for growth with electrodes, which was not required for Fe(III)-oxide reduction. In addition, mutants lacking components of a putative methyl-accepting chemotaxis/cyclic dinucleotide sensing network (esnABCD) were defective in electrode growth, but grew normally with Fe(III)-oxides. These results suggest thatG. sulfurreducenspossesses distinct mechanisms for recognition, colonization, and reduction of electrodes compared to other environmental electron acceptors.
Genome-wide screen for haploinsufficient cell size genes in the opportunistic yeastCandida albicans
Authors: Chaillot Julien , Cook Michael A , Corbeil Jacques , Sellam Adnane 
Published: October 2016

ABSTRACTOne of the most critical but still poorly understood aspects of eukaryotic cell proliferation is the basis for commitment to cell division in late G1 phase called Start in yeast and the Restriction Point in metazoans. In all species, a critical cell size threshold coordinates cell growth with cell division and thereby establishes a homeostatic cell size. While a comprehensive survey of cell size genetic determinism has been performed in the saprophytic yeastsSaccharomyces cerevisiaeandSchizosaccharomyces pombe, very little is known in pathogenic fungi. As a number of critical Start regulators are haploinsufficient for cell size, we applied a quantitative analysis of the size phenome, using elutriation-barcode sequencing methodology, to 5,639 barcoded heterozygous deletion strains in the opportunistic yeastCandida albicans. Our screen identified conserved known regulators and biological processes required to maintain size homeostasis in addition to novelC. albicansspecific size genes, and provided a conceptual framework for future mechanistic studies. Interestingly, some of the size genes identified were required for fungal pathogenicity suggesting that cell size homeostasis may be elemental toC. albicansfitness or virulence inside the host.
CMPyMOL: An Interactive PyMOL extension for Protein Contact-Map Analysis
Authors: Krishnamani Venkatramanan 
Published: October 2016

AbstractContact–maps are reduced 2D representation of the 3D spatial configuration of a protein. Many valuable structural features like secondary structures, inter- and intra-protein interactions,interacting domains, etc., can be readily identified from these maps. However, it is not straightforward and intuitive to reckon the spatial organization of the contact regions from reduced representation. The CMPyMOL extention for molecular visualization software PyMOL attempts to bridge this gap as an interactive graphical tool for protein contact-maps that interfaces with PyMOL for 3D visualization. Specifically, CMPyMOL helps understand the functional importance of contacts by providing visual overlays of various structural and biochemical properties of a protein on top of its contact-map.
Na+/Ca2+exchangers and Orai channels jointly refill endoplasmic reticulum (ER) Ca2+via ER nanojunctions in vascular endothelial cells
Authors: Di Giuro Cristiana M. L. , Shrestha Niroj , Malli Roland , Groschner Klaus , van Breemen Cornelis , Fameli Nicola 
Published: October 2016

AbstractWe investigated the role of Na+/Ca2+exchange (NCX) in the refilling of endoplasmic reticulum (ER) Ca2+in vascular endothelial cells under various conditions of cell stimulation and plasma membrane (PM) polarization. Better understanding of the mechanisms behind basic ER Ca2+content regulation is important, since current hypotheses on the possible ultimate causes of ER stress point to deterioration of the Ca2+transport mechanism to/from ER itself. We measured [Ca2+]itemporal changes by Fura-2 fluorescence under experimental protocols that inhibit a host of transporters (NCX, Orai, non-selective transient receptor potential canonical (TRPC) channels, sarco/endoplasmic reticulum Ca2+ATPase (SERCA), Na+/K+ATPase (NKA)) involved in the Ca2+communication between the extracellular space and the ER. Following histamine-stimulated ER Ca2+release, blockade of NCX Ca2+-influx mode (by 10µM KB-R7943) diminished the ER refilling capacity by about 40%, while in Orai1 dominant negative-transfected cells NCX blockade attenuated ER refilling by about 60%. Conversely, inhibiting the high-ouabain-affinity NKA (10 nM ouabain), which may be localized in PM-ER junctions, increased the ER Ca2+releasable fraction by about 20%, thereby supporting the hypothesis that this process of privileged ER refilling is junction-mediated. Junctions were observed in the cell ultrastructure and their main parameters of membrane separation and linear extension were (9.6±3.8) nm and (128±63) nm, respectively. Our findings point to a process of privileged refilling of the ER, in which NCX and SOCE via the stromal interaction molecule (STIM)-Orai system are the sole protagonists. These results shed light on the molecular machinery involved in the function of a previously hypothesized subplasmalemmal Ca2+control unit during ER refilling with extracellular Ca2+.
Residential property prices’ modeling: evidence from selected European countries
Authors: Boitan Iustina Alina 
Published: November 2016

PurposeThe purpose of this study is to contribute to the relatively narrow existing residential real estate literature by developing and validating several univariate forecasting models, to reliably anticipate future house price dynamics across several European Union (EU) countries.Design/methodology/approachThe research approach relies on the time series analysis, by using the Box–Jenkins autoregressive integrated moving average (ARIMA) methodology to explore the trends of residential property prices in selected EU countries and to obtain a snapshot of the potential signs of change to be witnessed by domestic residential markets on a short time-period. The analysis has been performed distinctly for each country in the sample, to account for country-specific past and future trends as well as similarities in their house price growth rate evolutions. The models were estimated for a broad sample of quarterly observations during 1990-2015, while the forecast horizon ranged between the third quarter of 2015 and the fourth quarter of 2016.FindingsThe findings suggested that residential property prices’ real growth rate can be modeled through the Box–Jenkins method for France, The Netherlands, Sweden and UK. The pattern of Italy’s residential property prices’ real growth rate cannot be explained by means of univariate ARIMA models, being more suited for multivariate models.Originality/valueThe article subscribes to the need for timely, high-frequency and quality data about house price trends in Europe, to increase the accuracy of forecasts and prevent the appearance of bubbles on real estate market. It compares residential property prices’ dynamics across European countries to identify housing markets with similar patterns of their prices.
Real estate research in Europe
Authors: Hoesli Martin 
Published: November 2016

PurposeAgainst the background of initiatives, which have taken place to foster real estate research in Europe, this article seeks to analyse important dimensions of that research.Design/methodology/approachThe article investigates the evolution from 2000 to 2015 in the proportion of papers published by authors with a European affiliation in the three main international real estate journals (Real Estate Economics,Journal of Real Estate Finance and EconomicsandJournal of Real Estate Research). Then, focusing on papers with at least one European author and/or concentrating on Europe, the article analyses papers published from 2008 to 2015 in the two main European real estate journals (Journal of European Real Estate ResearchandJournal of Property Research) by authors’ country of affiliation, by country of study and by theme. Finally, we analyse links between author’s country of affiliation and country of study and theme, respectively.FindingsThe results show that the proportion of papers published by European authors in the three main international real estate journals has increased during the 2000-2015 period. The author's analyses of papers published in the two European real estate journals suggest that UK-based researchers are the most prolific. There is also a strong “home bias” in that authors largely focus on the country in which they are based. The interest in housing and valuation increased markedly during the period. Finally, the article reports linkages between country of affiliation and theme.Originality/valueThis paper should provide a much clearer understanding of several aspects of real estate research in Europe.
The articulation of neoliberalism: narratives of experience of chronic illness management in Bulgaria and the UK
Authors: Vassilev Ivaylo , Rogers Anne , Todorova Elka , Kennedy Anne , Roukova Poli 
Published: November 2016

AbstractThe shift from social democratic to a neoliberal consensus in modern welfare capitalist states is characterised by an emphasis on individual responsibility, consumer choice, market rationality and growing social inequalities. There has been little exploration of how neoliberalism has shaped the environment within which chronic illness is experienced and managed. This article explores the different articulations of neoliberalism manifest in the arena of personal illness management in Bulgaria and the UK. People with type 2 diabetes discussed their experiences in terms of struggling with diet, diabetes as a personal failure, integrating illness management and valued activities, and the trustworthiness of the healthcare system. The UK narratives were framed within an individual responsibility discourse while in Bulgaria lack of resources dominated discussions, which were framed as structurally generated and unrelated to individual capabilities and choices. Respondents faced personal management challenges related to consumer and healthcare market failures in both countries. Differences in market regulation and emerging stakeholder and interest coalitions influenced users' expectations and their navigation and adaption to market failures in managing their everyday illnesses. The UK and Bulgarian articulations of neoliberalism can be described differently: the first as a logic of managed choice and the second as a logic of unmanaged consumerism.
Probing the heat‐induced structural changes in bovine serum albumin by fluorescence spectroscopy and molecular modelling
Authors: Ursache Florentina‐Mihaela , Aprodu Iuliana , Nistor Oana‐Viorela , Bratu Mihaela , Botez Elisabeta , Stănciuc Nicoleta 
Published: November 2016

The fluorescence spectroscopy and in silico methods were used to evaluate the structural changes in bovine serum albumin (BSA) over a temperature range of 25–70 °C for 15 min. Experimental results indicated that the polypeptide chain rearrangements at temperatures higher than 40 °C lead to a lower exposure of hydrophobic residues causing the decrease in fluorescence intensity. The nonlinearity of the phase diagram indicated a sequential denaturation process involving several molecular species. The molecular dynamics simulations at the single‐molecule level showed the high stability of the BSA structure, compensating for the entropic costs associated with the prevalent helical folding.