bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation between SiO v = 3 J = 1 → 0 maser excitation and the light curve of a long-period variable star
Authors: Oyadomari Miyako , Imai Hiroshi , Nagayama Takumi , Oyama Tomoaki , Matsumoto Naoko , Nakashima Jun-ichi , Cho Se-Hyung
Published: February 2018

In order to understand the excitation mechanisms of silicon monoxide (SiO) masers around long-period variables (LPVs), we have investigated distributions of the SiO v = 2 and v = 3 J = 1 → 0 masers around 12 LPVs by very long baseline interferometry (VLBI) observations with the VLBI Exploration of Radio Astrometry (VERA) and the Nobeyama 45 m telescopes. VLBI fringes of the v = 3 maser emission were detected for five LPVs. The composite maps of the v = 2 and v = 3 masers were made for T Cep, W Hya, WX Psc, and R Leo using the spectral line phase-referencing technique. The v = 2 maser spots were distributed in a ring-like form around the central stars, while it is difficult to recognize any specific morphology in the v = 3 maser distributions due to the small number of v = 3 spots detected. However in T Cep, we find that the distribution of the v = 3 maser spots correlates well with the v = 2 masers within a few milliarcseconds (0.2–0.3 au) in position and 1 km s−1 in line-of-sight velocity at the light curve phase of ϕ = 0.28 (ϕ = 0.0 and 1.0 correspond to the visible light maxima). This correlation implies that the mechanism of line-overlapping between the mid-infrared lines of H2O and SiO molecules works in T Cep at ϕ = 0.28. We discuss the possibility that the line-overlapping may work at the limited duration from the maximum to the minimum of the stellar light curve.
Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers
Authors: Borghi John A. , Van Gulick Ana E.
Published: February 2018

Neuroimaging methods such as magnetic resonance imaging (MRI) involve complex data collection and analysis protocols, which necessitate the establishment of good research data management (RDM). Despite efforts within the field to address issues related to rigor and reproducibility, information about the RDM-related practices and perceptions of neuroimaging researchers remains largely anecdotal. To inform such efforts, we conducted an online survey of active MRI researchers that covered a range of RDM-related topics. Survey questions addressed the type(s) of data collected, tools used for data storage, organization, and analysis, and the degree to which practices are defined and standardized within a research group. Our results demonstrate that neuroimaging data is acquired in multifarious forms, transformed and analyzed using a wide variety of software tools, and that RDM practices and perceptions vary considerably both within and between research groups, with trainees reporting less consistency than faculty. Ratings of the maturity of RDM practices from ad-hoc to refined were relatively high during the data collection and analysis phases of a project and significantly lower during the data sharing phase. Perceptions of emerging practices including open access publishing and preregistration were largely positive, but demonstrated little adoption into current practice.
The dynamic basis of cognition: an integrative core under the control of the ascending neuromodulatory system
Authors: Shine J.M. , Breakspear M. , Bell P.T. , Ehgoetz Martens K. , Shine R. , Koyejo O. , Sporns O. , Poldrack R.A.
Published: February 2018

The human brain integrates diverse cognitive processes into a coherent whole, shifting fluidly as a function of changing environmental demands. Despite recent progress, the neurobiological mechanisms responsible for this dynamic system-level integration remain poorly understood. Here, we used multi-task fMRI data from the Human Connectome Project to examine the spatiotemporal architecture of cognition in the human brain. By investigating the spatial, dynamic and molecular signatures of system-wide neural activity across a range of cognitive tasks, we show that large-scale neuronal activity converges onto a low dimensional manifold that facilitates the dynamic execution of diverse task states. Flow within this attractor space is associated with dissociable cognitive functions, and with unique patterns of network-level topology and information processing complexity. The axes of the low-dimensional neurocognitive architecture align with regional differences in the density of neuromodulatory receptors, which in turn relate to distinct signatures of network controllability estimated from the structural connectome. These results advance our understanding of functional brain organization by emphasizing the interface between low dimensional neural activity, network topology, neuromodulatory systems and cognitive function.

One Sentence Summary

A diverse set of neuromodulators facilitates the formation of a dynamic, low-dimensional integrative core in the brain that is recruited by diverse cognitive demands
Soil detrital inputs increase stimulate bacterial saprotrophs with different timing and intensity compared to fungal saprotrophs
Authors: Sukdeo Nicole , Teen Ewing , Michael Rutherford P. , Massicotte Hugues B. , Egger Keith N.
Published: February 2018

Soils contain microbial inhabitants that differ in sensitivity to anthropogenic modification. Soil reclamation relies on monitoring these communities to evaluate ecosystem functions recovery post-disturbance. DNA metabarcoding and soil enzyme assays provide information about microbial functional guilds and organic matter decomposition activities respectively. However bacterial communities, fungal communities, and enzyme activities may not be equally informative for monitoring reclaimed soils. We compared effects of disturbance regimes applied to forest soils on fungal community composition, bacterial community composition, and potential hydrolase activities (N-acetyl-β-D-glucosaminidase, acid phosphatase, and cellobiohydrolase) at two times (14 days and 5 months post-disturbance) and depths (LFH versus mineral soil). Using disturbance versus control comparisons allowed us to identify genus-level disturbance-indicators and shifts in hydrolase activity levels. We observed declines in disturbed LFH fungal biomass (ergosterol) and declines in ectomycorrhizal fungi abundance across all disturbed samples, which prompted us to consider necromass-induced (fungal, root) saprotroph increases as disturbance indicators. Fungal community composition strongly shifted away from ecotmycorrhizal dominance to saprotroph dominance (i.e. increasedMortierella, andUmbelopsis) in disturbed plots at 5 months, while bacterial community composition did not shift to distinguish control plots from disturbed ones at either sampling time. Soil potential hydrolase data mainly indicated that mixing LFH material into mineral soil increases the measured activity levels compared to control and replaced mineral soil. Bacterial saprotrophs previously associated with mycelial necromass were detected across multiple regimes as disturbance indicators at 14 days post-disturbance. Our results confirm that ectomycorrhizal fungal genera are sensitive and persistently impacted by soil physical disturbances. Increases in saprotrophic bacterial genera are detectable 14 days pot-disturbance but only a few persist as disturbance indicators after several months. Potential hydrolase activities appear to be most useful for detecting the transfer of decomposition hotspots into mineral soils.
Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome
Authors: Aliaga Goltsman Daniela S. , Sun Christine L. , Proctor Diana M. , DiGiulio Daniel B. , Robaczewska Anna , Thomas Brian C. , Shaw Gary M. , Stevenson David K. , Holmes Susan P. , Banfield Jillian F. , Relman David A.
Published: February 2018

Recent studies suggest that the microbiome has an impact on gestational health and outcome. However, characterization of the pregnancy-associated microbiome has largely relied on 16S rRNA gene amplicon-based surveys. Here, we describe an assembly-driven, metagenomics-based, longitudinal study of the vaginal, gut, and oral microbiomes in 292 samples from ten subjects sampled every three weeks throughout pregnancy. 1.53 Gb of non-human sequence was assembled into scaffolds, and functional genes were predicted for gene-and pathway-based analyses. Vaginal assemblies were binned into 97 draft quality genomes. Redundancy analysis (RDA) of microbial community composition at all three body sites revealed gestational age to be a significant source of variation in patterns of gene abundance. In addition, health complications were associated with variation in community functional gene composition in the mouth and gut. The diversity of Lactobacillus iners-dominated communities in the vagina, unlike most other vaginal community types, significantly increased with gestational age. The genomes of co-occurring Gardnerella vaginalis strains with predicted distinct functions were recovered in samples from two subjects. In seven subjects, gut samples contained strains of the same Lactobacillus species that dominated the vaginal community of that same subject, and not other Lactobacillus species; however, these within-host strains were divergent. CRISPR spacer analysis suggested shared phage and plasmid populations across body sites and individuals. This work underscores the dynamic behavior of the microbiome during pregnancy and suggests the potential importance of understanding the sources of this behavior for fetal development and gestational outcome.
Family-Companion: analyse, visualise, browse, query and share your homology clusters
Authors: Cottret Ludovic , Briand Martial , Rancurel Corinne , Carrere Sébastien
Published: February 2018

Identifying homology groups in predicted proteomes from different biological sources allows biologists to address questions as diverse as inferring species-specific proteins or retracing the phylogeny of gene families. Nowadays, command-line software exists to infer homology clusters. However, computing and interpreting homology groups with this software remains challenging for biologists and requires computational skills.

We propose Family-Companion, a web server dedicated to the computation, the analysis and the exploration of homology clusters. Family-Companion aims to fill the gap between analytic software and databases presenting orthologous groups based on a set of public data. It offers a user-friendly interface to launch or upload precomputed homology cluster analysis, to explore and share the results with other users. The exploration of the results is highly facilitated by interactive solutions to visualize proteome intersections via Venn diagrams, phylogenetic trees, multiple alignments, and also by querying the results by blast or by keywords.

Family-Companion is available at http://family-companion.toulouse.inra.fr with a demo dataset and a set of video tutorials. Source code and installation protocol can be found at https://framagit.org/BBRIC/family-companion/. A container-based package simplifies the installation of the web-suite.
Dynamic embedding of salience coding in hippocampal spatial maps
Authors: Sato Masaaki , Mizuta Kotaro , Islam Tanvir , Kawano Masako , Takekawa Takashi , Gomez-Dominguez Daniel , Kim Karam , Yamakawa Hiroshi , Ohkura Masamichi , Fukai Tomoki , Nakai Junichi , Hayashi Yasunori
Published: February 2018

Hippocampal CA1 neurons participate in dynamic ensemble codes for space and memory. Prominent features of the environment are represented by an increased density of place cells, but cellular principles governing the formation and plasticity of such disproportionate maps are unknown. We thus imaged experience-dependent long-term changes in spatial representations at the cellular level in the CA1 deep sublayer in mice learning to navigate in a virtual-reality environment. The maps were highly dynamic but gradually stabilized as over-representations for motivational (reward) and environmental (landmark) salience emerged in different time courses by selective consolidation of relevant spatial representations. Relocation of the reward extensively reorganized pre-formed maps by a mechanism involving rapid recruitment of cells from the previous location followed by their re-stabilization, indicating that a subset of neurons encode reward-related information. The distinct properties of these CA1 cells may provide a substrate by which salient experience forms lasting and adaptable memory traces.
Evolutionary insights into Bean common mosaic necrosis virus and Cowpea aphid borne mosaic virus using global isolates and thirteen new near complete genomes from Kenya
Authors: Wainaina James M , Kubatko Laura , Harvey Jagger , Ateka Elijah , Makori Timothy , Karanja David , Boykin Laura M. , Kehoe Monica A.
Published: February 2018

Plant viral diseases are one of the major limitations in legume production within sub Saharan Africa (SSA), as they account for up to 100 % in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out. The main aim was to gain insights into the selection pressure and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV), within symptomatic common beans and cowpeas. Eleven near complete genomes of BCMNV and two for CABMV sequences were obtained from SSA. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes was carried out. Three distinct well-supported clades were identified across the whole genome tree, and were in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. These results will contribute greatly to the knowledge gap surrounding the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and support the current breeding efforts towards resistance for BCMNV and CABMV.
Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-affected Corneas
Authors: Khaled Mariam Lofty , Bykhovskaya Yelena , Yablonski Sarah E.R. , Li Hanzhou , Drewry Michelle D. , Aboobakar Inas F. , Estes Amy , Gao Xiaoyi , Stamer W. Daniel , Xu Hongyan , Allingham R. Rand , Hauser Michael A. , Rabinowitz Yaron S. , Liu Yutao
Published: February 2018

PURPOSE

Keratoconus (KC) is the most common corneal ectasia. We aimed to determine the differential expression of coding and long noncoding RNAs (lncRNAs) in human corneas affected with KC.

METHODS

200ng total RNA from the corneas of 10 KC patients and 8 non-KC normal controls was used to prepare sequencing libraries with the SMARTer Stranded RNA-Seq kit after ribosomal RNA depletion. Paired-end 50bp sequences were generated using Illumina HiSeq 2500 Sequencer. Differential analysis was done using TopHat and Cufflinks with a gene file from Ensembl and a lncRNA file from NONCODE. Pathway analysis was performed using WebGestalt. Using the expression level of differentially expressed coding and noncoding RNAs in each sample, we correlated their expression levels in KC and controls separately and identified significantly different correlations in KC against controls followed by visualization using Cytoscape.

RESULTS

Using |fold change| ≥ 2 and a false discovery rate ≤ 0.05, we identified 436 coding RNAs and 584 lncRNAs with differential expression in the KC-affected corneas. Pathway analysis indicated the enrichment of genes involved in extracellular matrix, protein binding, glycosaminoglycan binding, and cell migration. Our correlation analysis identified 296 pairs of significant KC-specific correlations containing 117 coding genes enriched in functions related with cell migration/motility, extracellular space, cytokine response, and cell adhesion, suggesting the potential functions of these correlated lncRNAs, especially those with multiple pairs of correlations.

CONCLUSIONS

Our RNA-Seq based differential expression and correlation analyses have identified many potential KC contributing coding and noncoding RNAs.
FALCON-meta: a method to infer metagenomic composition of ancient DNA
Authors: Pratas Diogo , Pinho Armando J. , Silva Raquel M. , Rodrigues João M. O. S. , Hosseini Morteza , Caetano Tânia , Ferreira Paulo J. S. G.
Published: February 2018

The general approaches to detect and quantify metagenomic sample composition are based on the alignment of the reads, according to an existing database containing reference microbial sequences. However, without proper parameterization, these methods are not suitable for ancient DNA. Quantifying somewhat dissimilar sequences by alignment methods is problematic, due to the need of fine-tuned thresholds, considering relaxed edit distances and the consequent increase of computational cost. Additionally, the choice of the thresholds poses the problem of how to quantify similarity without producing overestimated measures. We propose FALCON-meta, a compression-based method to infer metagenomic composition of next-generation sequencing samples. This unsupervised alignment-free method runs efficiently on FASTQ samples. FALCON-meta quickly learns how to give importance to the models that cooperate to predict similarity, incorporating parallelism and flexibility for multiple hardware characteristics. It shows substantial identification capabilities in ancient DNA without overestimation. In one of the examples, we found and authenticated an ancient Pseudomonas bacteria in a Mammoth mitogenome.

FALCON-meta can be accessed at https://github.com/pratas/falcon.
A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks
Authors: Chan Jeffrey , Perrone Valerio , Spence Jeffrey P. , Jenkins Paul A. , Mathieson Sara , Song Yun S.
Published: February 2018

An explosion of high-throughput DNA sequencing in the past decade has led to a surge of interest in population-scale inference with whole-genome data. Recent work in population genetics has centered on designing inference methods for relatively simple model classes, and few scalable general-purpose inference techniques exist for more realistic, complex models. To achieve this, two inferential challenges need to be addressed: (1) population data are exchangeable, calling for methods that efficiently exploit the symmetries of the data, and (2) computing likelihoods is intractable as it requires integrating over a set of correlated, extremely high-dimensional latent variables. These challenges are traditionally tackled by likelihood-free methods that use scientific simulators to generate datasets and reduce them to hand-designed, permutation-invariant summary statistics, often leading to inaccurate inference. In this work, we develop an exchangeable neural network that performs summary statistic-free, likelihood-free inference. Our frame-work can be applied in a black-box fashion across a variety of simulation-based tasks, both within and outside biology. We demonstrate the power of our approach on the recombination hotspot testing problem, outperforming the state-of-the-art.
Gene expression is stronger associated with behaviour than with age and fertility in ant workers
Authors: Kohlmeier Philip , Alleman Austin R , Libbrecht Romain , Foitzik Susanne , Feldmeyer Barbara
Published: February 2018

The ecological success of social insects is based on division of labour, not only between queens and workers, but also among workers. Whether a worker tends the brood or forages is strongly influenced by age, fertility and nutritional status, with brood carers being younger, more fecund and corpulent. Here, we experimentally disentangle behaviour from age and fertility inTemnothorax longispinosusant workers and analyse how these parameters are linked to whole-body gene expression. Our transcriptome analysis reveals four times more genes associated with behaviour than with age and only few fertility-associated genes. Brood carers exhibited an upregulation of genes involved in lipid biosynthesis, whereas foragers invested in metabolism. Additional simulations revealed that the experimental disassociation of co-varying factors reduces transcriptomic noise, potentially explaining discrepancies between transcriptomic studies on worker behaviour in other social insects. Our study highlights the influence of nutritional status on task choice in ant workers.
Divergent genetic mechanism leads to spiny hair in rodents
Authors: Gonçalves Gislene L. , Maestri Renan , Moreira Gilson R. P. , Jacobi Marly A. M. , Freitas Thales R. O. , Hoekstra Hopi E.
Published: February 2018

Spines, or modified hairs, have evolved multiple times in mammals, particularly in rodents. In this study, we investigated the evolution of spines in six rodent families. We first measured and compared the morphology and physical properties of hairs between paired spiny and non-spiny sister lineages. We found two distinct hair morphologies had repeatedly evolved in spiny rodents: hairs with a grooved cross-section and a second near cylindrical form. Compared to the ancestral elliptical-shaped hairs, spiny hairs had higher tension and stiffness, and overall, hairs with similar morphology had similar functional properties. To examine the genetic basis of this convergent evolution, we tested whether a single amino acid change (V370A) in theEcdysoplasin A receptor (Edar)gene is associated with spiny hair, as this substitution causes thicker and straighter hair in East Asian human populations. We found that most mammals have the common amino acid valine at position 370, but two species, the kangaroo rat (non-spiny) and spiny pocket mouse (spiny), have an isoleucine. Importantly, none of the variants we identified are associated with differences in rodent hair morphology. Thus, the specificEdarmutation associated with variation in human hair does not seem to play a role in modifying hairs in wild rodents, suggesting that different mutations inEdarand/or other genes are responsible for variation in the spiny hair phenotypes we observed within rodents.
GENOME REPORT: High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing
Authors: Miller Danny E. , Staber Cynthia , Zeitlinger Julia , Hawley R. Scott
Published: February 2018

The Drosophila genus is a unique group containing a wide range of species that occupy diverse ecosystems. In addition to the most widely studied species, Drosophila melanogaster, many other members in this genus also possess a well-developed set of genetic tools. Indeed, high-quality genomes exist for several species within the genus, facilitating studies of the function and evolution of cis-regulatory regions and proteins by allowing comparisons across at least 50 million years of evolution. Yet, the available genomes still fail to capture much of the substantial genetic diversity within the Drosophila genus. We have therefore tested protocols to rapidly and inexpensively sequence and assemble the genome from any Drosophila species using single-molecule sequencing technology from Oxford Nanopore. Here, we use this technology to present high-quality genome assemblies of 15 Drosophila species: 10 of the 12 originally sequenced Drosophila species (ananassae, erecta, mojavensis, persimilis, pseudoobscura, sechellia, simulans, virilis, willistoni, and yakuba), four additional species that had previously reported assemblies (biarmipes, bipectinata, eugracilis, and mauritiana), and one novel assembly (triauraria). Genomes were generated from an average of 29x depth-of-coverage data that after assembly resulted in an average contig N50 of 4.4 Mb. Subsequent alignment of contigs from the published reference genomes demonstrates that our assemblies could be used to close over 60% of the gaps present in the currently published reference genomes. Importantly, the materials and reagents cost for each genome was approximately $1,000 (USD). This study demonstrates the power and cost-effectiveness of long-read sequencing for genome assembly in Drosophila and provides a framework for the affordable sequencing and assembly of additional Drosophila genomes.
Maps of variability in cell lineage trees
Authors: Hicks Damien G. , Speed Terence P. , Yassin Mohammed , Russell Sarah M.
Published: February 2018

New approaches to lineage tracking allow the study of cell differentiation over many generations of cells during development in multicellular organisms. Understanding the variability observed in these lineage trees requires new statistical methods. Whereas invariant cell lineages, such as that for the nematodeCaenorhabditis elegans, can be described using a lineage map, defined as the fixed pattern of phenotypes overlaid onto the binary tree structure, the variability of cell lineages from higher organisms makes it impossible to draw a single lineage map. Here, we introduce lineage variability maps which describe the pattern of second-order variation throughout the lineage tree. These maps can be undirected graphs of the partial correlations between every lineal position or directed graphs showing the dynamics of bifurcated patterns in each subtree. By using the symmetry invariance of a binary tree to develop a generalized spectral analysis for cell lineages, we show how to infer these graphical models for lineages of any depth from sample sizes of only a few pedigrees. When tested on pedigrees fromC. elegansexpressing a marker for pharyngeal differentiation potential, the maps recover essential features of the known lineage map. When applied to highly-variable pedigrees monitoring cell size in T lymphocytes, the maps show how most of the phenotype is set by the founder naive T cell. Lineage variability maps thus elevate the concept of the lineage map to the population level, addressing questions about the potency and dynamics of cell lineages and providing a way to quantify the progressive restriction of cell fate with increasing depth in the tree.

Author summary

Multicellular organisms develop from a single fertilized egg by sequential cell divisions. The progeny from these divisions adopt different traits that are transmitted and modified through many generations. By tracking how cell traits change with each successive cell division throughout the family, or lineage, tree, it has been possible to understand where and how these modifications are controlled at the single-cell level, thereby addressing questions about, for example, the developmental origin of tissues, the sources of differentiation in immune cells, or the relationship between primary tumors and metastases. Such lineages often show large variability, with apparently identical founder cells giving rise to different patterns of descendants. Fundamental scientific questions, such as about the range of possible cell types a cell can give rise to, are often about this variability. To characterize this variation, and thus understand the lineage at the population level, we introduce lineage variability maps. Using data from worm and mammalian cell lineages we show how these maps provide quantifiable answers to questions about any developing lineage, such as the potency of founder cells and the progressive restriction of cell fate at each stage in the tree.
Effects of chronic thermal stress on the reproductive performance of male Octopus maya
Authors: López-Galindo Laura , Galindo-Sánchez Clara , Olivares Alberto , Avila-Poveda Omar Hernando , Díaz Fernando , Juárez Oscar E. , Lafarga Fabiola , Pantoja-Pérez Jordi , Caamal-Monsreal Claudia , Rosas Carlos
Published: February 2018

In female Octopus maya the reproductive success has well-defined thermal limits; beyond which, spawning, number of eggs, fecundity, and the viability of the embryos are reduced. Observations of wild male O. maya suggest that temperatures below 27°C favour their reproductive performance. From these observations we hypothesize that, as in females, the temperature modulates the reproductive performance of adult O. maya males. The study was directed to evaluate the physiological condition, reproductive success, and histological damage in testis of male O. maya exposed to thermal stress, to determine the implications of ocean warming over their reproductive performance. High temperatures (28-30°C) negatively affect the growth and health of male O. maya. In octopuses maintained at 30°C, as a consequence of the thermal stress we observed an increment in the haemocytes number, a reduction in the oxygen consumption rate, and an inflammatory process in the testis. The number of spermatozoa per spermatophore was not affected by temperature, but higher spermatophores production was observed at 30°C. The paternity analysis showed that the offspring had multiple paternity with an average of 10 males contributing in a single spawn. The paternal contribution was affected by temperature with high, medium, or no paternal contribution in animals maintained at 24°C (control group), 28°C, and 30°C, respectively. The temperatures from 28°C to 30°C deeply affected the reproductive performance of Octopus maya males.
Integrated single-nucleotide and structural variation signatures of DNA-repair deficient human cancers
Authors: Funnell Tyler , Zhang Allen , Shiah Yu-Jia , Grewal Diljot , Lesurf Robert , McKinney Steven , Bashashati Ali , Wang Yi Kan , Boutros Paul C. , Shah Sohrab P.
Published: February 2018

Mutation signatures in cancer genomes reflect endogenous and exogenous mutational processes, offering insights into tumour etiology, features for prognostic and biologic stratification and vulnerabilities to be exploited therapeutically. We present a novel machine learning formalism for improved signature inference, based on multi-modal correlated topic models (MMCTM) which can at once infer signatures from both single nucleotide and structural variation counts derived from cancer genome sequencing data. We exemplify the utility of our approach on two hormone driven, DNA repair deficient cancers: breast and ovary (n=755 cases total). Our results illuminate a new age-associated structural variation signature in breast cancer, and an independently identified substructure within homologous recombination deficient (HRD) tumours in breast and ovarian cancer. Together, our study emphasizes the importance of integrating multiple mutation modes for signature discovery and patient stratification, with biological and clinical implications for DNA repair deficient cancers.
LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation
Authors: Machado Sarah , Mercier Vincent , Chiaruttini Nicolas
Published: February 2018

Bioimage analysis is an important preliminary step required for data representation and quantitative studies. To carry out these tasks, we developed LimeSeg, an easy-to-use, efficient and modular 3D image segmentation method. Based on the idea of SURFace ELements, LimeSeg resembles a highly coarse-grained simulation of a lipid membrane in which a set of particles, analogous to lipid molecules, are attracted to local image maxima. The particles are self-generating and self-destructing thus providing the ability for the membrane to evolve towards the contour of the object of interest. We characterize the emergent mechanical properties of this system and show how it can be used to segment many 3D objects from numerous types of image of biological samples (brain MRI, cell epithelium, cellular organelles). LimeSeg is available as a Fiji plugin that includes simple commands, a 3D visualizer, and customization options via ImageJ scripting.
The pharmacological perturbation of brain zinc impairs BDNF-related signalling and the cognitive performances of young mice
Authors: Frazzini Valerio , Granzotto Alberto , Bomba Manuela , Massetti Noemi , Castelli Vanessa , d’Aurora Marco , Punzi Miriam , Iorio Mariangela , Mosca Alessandra , Delli Pizzi Stefano , Gatta Valentina , Cimini Annamaria , Sensi Stefano L.
Published: February 2018

Zinc (Zn2+) is a pleiotropic modulator of the neuronal and brain activity. The disruption of intraneuronal Zn2+levels triggers neurotoxic processes and affects neuronal functioning. In this study, we investigated how the pharmacological modulation of brain Zn2+affects synaptic plasticity and cognition in wild-type mice. To manipulate brain Zn2+levels, we employed the Zn2+(and copper) chelator 5-chloro-7-iodo-8-hydroxyquinoline (clioquinol, CQ). CQ was administered for two weeks to 2.5-month-old (m.o.) mice, and effects studied on BDNF-related signalling, metalloproteinase activity as well as learning and memory performances. CQ treatment was found to negatively affect short- and long-term memory performances. The CQ-driven perturbation of brain Zn2+was found to reduce levels of BDNF, synaptic plasticity-related proteins and dendritic spine densityin vivo.

Our study highlights the importance of choosing “when”, “where”, and “how much” in the modulation of brain Zn2+levels. Our findings confirm the importance of targeting Zn2+as a therapeutic approach against neurodegenerative conditions but, at the same time, underscore the potential drawbacks of reducing brain Zn2+availability upon the early stages of development.
Role of the novel endoribonuclease SLFN14 and its disease causing mutations in ribosomal degradation
Authors: Fletcher Sarah J. , Pisareva Vera P. , Khan Abdullah , Tcherepanov Andrew , Morgan Neil V. , Pisarev Andrey V.
Published: February 2018

Platelets are anucleate and mostly ribosome-free cells within the bloodstream, derived from megakaryocytes within bone marrow and crucial for cessation of bleeding at sites of injury. Inherited thrombocytopenias are a group of disorders characterized by alow platelet count and are frequently associated with excessive bleeding. SLFN14 is one of the most recently discovered genes linked to inherited thrombocytopenia where several heterozygous missense mutations in SLFN14 were identified to cause defective megakaryocyte maturation and platelet dysfunction. Yet, SLFN14 was recently described as a ribosome-associated protein resulting in rRNA and ribosome-bound mRNA degradation in rabbit reticulocytes. To unveil the cellular function of SLFN14 and the link between SLFN14 and thrombocytopenia, we examined SLFN14 (WT/mutants) in in vitro models. Here, we show that all SLFN14 variants co-localize with ribosomes and mediate rRNA endonucleolytic degradation and ribosome clearance. Compare dto SLFN14 WT, expression of mutants is dramatically reduced as a result of post-translational degradation due to partial misfolding of the protein. Moreover, all SLFN14 variants tend to form oligomers. These findings could explain the dominant negative effect of heterozygous mutation on SLFN14 expression in patients’ platelets. Overall we suggest that SLFN14 could be involved in ribosome degradation during platelet formation and maturation.
Spatial moment description of birth-death-movement processes incorporating the effects of crowding and obstacles
Authors: Surendran Anudeep , Plank Michael J. , Simpson Matthew J.
Published: February 2018

Birth-death-movement processes, modulated by interactions between individuals, are fundamental to many cell biology processes. A key feature of the movement of cells within in vivo environments are the interactions between motile cells and stationary obstacles. Here we propose a multi-species model of individual-level motility, proliferation and death. This model is a spatial birth-death-movement stochastic process, a class of individual-based model (IBM) that is amenable to mathematical analysis. We present the IBM in a general multi-species framework, and then focus on the case of a population of motile, proliferative agents in an environment populated by stationary, non-proliferative obstacles. To analyse the IBM, we derive a system of spatial moment equations governing the evolution of the density of agents and the density of pairs of agents. This approach avoids making the usual mean-field assumption so that our models can be used to study the formation of spatial structure, such as clustering and aggregation, and to understand how spatial structure influences population-level outcomes. Overall the spatial moment model provides a reasonably accurate prediction of the system dynamics, including important effects such as how varying the properties of the obstacles leads to different spatial patterns in the population of agents.
Finite lifetime broadening of calculated X-ray absorption spectra: possible artefacts close to the edge
Authors: Šipr Ondřej , Vackář Jiří , Minár Ján
Published: February 2018

X-ray absorption spectra calculated within an effective one-electron approach have to be broadened to account for the finite lifetime of the core hole. For methods based on Green's function this can be achieved either by adding a small imaginary part to the energy or by convoluting the spectra on the real axis with a Lorentzian. By analyzing the FeK- andL2,3-edge spectra it is demonstrated that these procedures lead to identical results only for energies higher than a few core-level widths above the absorption edge. For energies close to the edge, spurious spectral features may appear if too much weight is put on broadeningviathe imaginary energy component. Special care should be taken for dichroic spectra at edges which comprise several exchange-split core levels, such as theL3-edge of 3dtransition metals.
Multifarious injection chamber for molecular structure study (MICOSS) system: development and application for serial femtosecond crystallography at Pohang Accelerator Laboratory X-ray Free-Electron Laser
Authors: Park Jaehyun , Kim Seonghan , Kim Sangsoo , Nam Ki Hyun
Published: February 2018

The multifarious injection chamber for molecular structure study (MICOSS) experimental system has been developed at the Pohang Accelerator Laboratory X-ray Free-Electron Laser for conducting serial femtosecond crystallography. This system comprises several instruments such as a dedicated sample chamber, sample injectors, sample environment diagnostic system and detector stage for convenient distance manipulation. Serial femtosecond crystallography experiments of lysozyme crystals have been conducted successfully. The diffraction peaks have reached to ∼1.8 Å resolution at the photon energy of 9.785 keV.
Modelling the drivers for sustainable agri-food waste management
Authors: Chauhan Ankur , Debnath Roma Mitra , Singh Surya Prakash
Published: February 2018

Purpose

The waste of invaluable agri-food produce is the concern of United Nations Organisation and all countries across the world. The purpose of this paper is to identify and model the drivers of agri-food waste management in India.

Design/methodology/approach

The interpretive structural modelling method is used to model the drivers in this study. This method helps in understanding the driver-dependent relationships among various drivers/criteria which are selected for studying.

Findings

The findings of the study vividly shows that the drivers such as disaster management planning, information dissemination, and training and awareness programs for farmers are most vital for tackling the issue.

Research limitations/implications

This work would help the policy makers in developing the effective policies regarding the management of agri-food waste in a sustainable manner.

Practical implications

This work would be very helpful for deeply understanding the causes of occurring waste and carefully handling it scientifically with a managerial perspective. Hence, it has the potential to reduce the generation of waste and saving the food for society.

Social implications

With the help of this study, the people, society, and underprivileged will be benefited directly. The savings in agri-food waste will not only help in controlling the prices of it but also its more availability would be beneficial for all in beating the hunger.

Originality/value

The identification of drivers for the sustainable management of agri-food is the novelty of this research.
The effects of employee behaviours on customer participation in the service encounter
Authors: Zhao Yufei , Yan Li , Keh Hean Tat
Published: February 2018

Purpose

There is considerable research examining the consequences and contingency factors of customer participation in the service encounter. In comparison, there is disproportionately less research examining the antecedents of customer participation. This paper aims to propose and test an appraisal-emotive framework of the effects of front-line employees’ in-role and extra-role behaviours on customer participation.

Design/methodology/approach

A survey on 583 customers of retail banks in China has been conducted to test the framework. Structural equation modelling and dominance analysis have been used for hypotheses testing.

Findings

Employees’ extra-role behaviour (i.e. organisational citizenship behaviour or OCB) has a stronger effect than their in-role behaviour (i.e. role-prescribed behaviour) in inducing customer participation. These effects are mediated by customer emotions. Specifically, the effect of employees’ in-role behaviour on customer participation was mediated by customers’ positive and negative emotions, whereas the effect of employees’ OCB was mediated by customers’ positive emotions but not by their negative emotions.

Practical implications

The findings reveal that strategic management of employee behaviours can influence customer participation. While organisations often provide training to enhance employees’ in-role behaviour to deliver service performance, they should also recognise and encourage employees’ OCB as a means of increasing customer participation. In particular, employees who display positive emotions tend to evoke positive emotions in customers, which increase customer participation in the service encounter.

Originality/value

To the authors’ knowledge, this is one of the few studies in marketing to examine the differential effects of employees’ in-role and extra-role behaviours on customer participation. Importantly, the findings show that employees’ OCB is not only more effective than employees’ in-role behaviour in influencing customer participation but also these two behaviours have varying effects on customer emotions. These findings are new and contribute to the literatures on customer participation, value co-creation and human resource management.
Performance management in public universities: overcoming bureaucracy
Authors: Angiola Nunzio , Bianchi Piervito , Damato Letizia
Published: February 2018

Purpose

Considering a micro performance perspective, the purpose of this paper is to analyze whether and to what extent the adoption of better performance management systems could improve the performance levels of a public university.

Design/methodology/approach

With reference to a period of four years (2011-2014), the quality of performance management systems of 29 Italian universities (response rate: 48 percent) was examined and the possible effects on performance levels of these institutions were analyzed by means of statistical methodologies (multiple regression analysis). Outcome indicators were considered.

Findings

The findings indicate the need to go further “measurement,” and to take care of performance “management,” especially in complex organizations as universities, where academicians identify themselves more with their professions than with the organization and where technicians and administrative employees might look at the performance-based reform with “bureaucratic eyes.” A fruitful cooperation between the professional soul and the bureaucratic one is paramount.

Originality/value

Studies which analyze organizational factors that could affect the adoption and implementation of performance management systems are rare, and use in prevalence qualitative methods or refer to machine bureaucracies, not many to professional ones as public universities. Moreover, the performance management literature in a public university context deepens the topic of the selection of KPIs and the focus is mainly on macro performance or on management tools for gathering and analyzing performance measures.
Survey of management practices enhancing labor productivity in multi-storey building construction projects
Authors: Gurmu Argaw Tarekegn , Aibinu Ajibade Ayodeji
Published: February 2018

Purpose

The purpose of this paper is to identify and prioritize management practices that have the potential to improve labor productivity in multi-storey building construction projects.

Design/methodology/approach

The study adopted two-phase mixed-methods research design and 58 project managers, contract administrators and project coordinators were involved in the survey. During Phase I, qualitative data were collected from 19 experts using interviews and the management practices that could enhance labor productivity in multi-storey building construction projects were identified. In Phase II, quantitative data were collected from 39 contractors involved in the delivery of multi-storey building projects by using questionnaires. The data were analyzed to prioritize the practices identified in Phase I.

Findings

Well-defined scope of work, safety and health policy, safety and health plan, hazard analysis, long-lead materials identification, safe work method statement, and toolbox safety meetings are the top seven practices that have the potential to improve labor productivity in multi-storey building projects.

Originality/value

The research identifies the management practices that can be implemented to enhance labor productivity in multi-storey building construction projects in the context of Australia. Being the first study in the Australian context, the findings can be used as benchmark for international comparison.
Why does performance management not perform?
Authors: Cunha Miguel Pina e , Vieira Daniel Veiga , Rego Arménio , Clegg Stewart
Published: February 2018

Purpose

The purpose of this paper is to ask why poor performance management practices persist in Portugal, in the middle of claims to increase productivity.

Design/methodology/approach

An inductive micro-practice analysis is used to understand barriers to management practice that do not require massive institutional changes.

Findings

The practice of performance management in Portugal typically displays three weaknesses: (1) insufficient planning (2) process and integrity issues, and (3) a non-meritocratic logic.

Research limitations/implications

The paper discusses the important topic of persistence of bad practices, showing how institutionalized patterns might be difficult to eradicate even they are suboptimal.

Practical implications

The authors identity key issues in the functioning of performance management, therefore helping managers in developing remedies to improve the quality of their practice.

Originality/value

The paper explains the persistence of bad management practice whose continuity hinders not only organizations’ effectiveness but also that of their members.