bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maize GO Annotation - Methods, Evaluation, and Review (maize-GAMER)
Authors: Wimalanathan Kokulapalan , Friedberg Iddo , Andorf Carson M. , Lawrence-Dill Carolyn J. 
Published: December 2017

1SummaryWe created a new high-coverage, robust, and reproducible functional annotation of maize protein coding genes based on Gene Ontology (GO) term assignments. Whereas the existing Phytozome and Gramene maize GO annotation sets only cover 41% and 56% of maize protein coding genes, respectively, this study provides annotations for 100% of the genes. We also compared the quality of our newly-derived annotations with the existing Gramene and Phytozome functional annotation sets by comparing all three to a manually annotated gold standard set of 1,619 genes where annotations were primarily inferred from direct assay or mutant phenotype. Evaluations based on the gold standard indicate that our new annotation set is measurably more accurate than those from Phytozome and Gramene. To derive this new high-coverage, high-confidence annotation set we used sequence-similarity and protein-domain-presence methods as well as mixed-method pipelines that developed for the Critical Assessment of Function Annotation (CAFA) challenge. Our project to improve maize annotations is called maize-GAMER (GO Annotation Method, Evaluation, and Review) and the newly-derived annotations are accessible via MaizeGDB (http://download.maizegdb.org/maize-GAMER) and CyVerse (B73 RefGen_v3 5b+ at doi: doi.org/10.7946/P2S62P and B73 RefGen_v4 Zm00001d.2 at doi: doi.org/10.7946/P2M925).
Dynamic reorganization of nuclear architecture during human cardiogenesis
Authors: Fields Paul A. , Ramani Vijay , Bonora Giancarlo , Yardimci Gurkan , Bertero Alessandro , Reinecke Hans , Pabon Lil , Noble William S. , Shendure Jay , Murry Charles E. 
Published: December 2017

AbstractWhile chromosomal architecture varies among cell types, little is known about how this organization is established or its role in development. We integrated Hi-C, RNA-seq and ATAC-seq during cardiac differentiation from human pluripotent stem cells to generate a comprehensive profile of chromosomal architecture. We identified active and repressive domains that are dynamic during cardiogenesis and recapitulate in vivo cardiomyocytes. During differentiation, heterochromatic regions condense in cis. In contrast, many cardiac-specific genes, such as TTN (titin), decompact and transition to an active compartment coincident with upregulation. Moreover, we identify a network of genes, including TTN, that share the heart-specific splicing factor, RBM20, and become associated in trans during differentiation, suggesting the existence of a 3D nuclear splicing factory. Our results demonstrate both the dynamic nature in nuclear architecture and provide insights into how developmental genes are coordinately regulated.One Sentence SummaryThe three-dimensional structure of the human genome is dynamically regulated both globally and locally during cardiogenesis.
Cardiac metabolic effects of KNa1.2 channel deletion, and evidence for its mitochondrial localization
Authors: Smith Charles O. , Wang Yves T. , Nadtochiy Sergiy M , Miller James H. , Jonas Elizabeth A. , Dirksen Robert T. , Nehrke Keith , Brookes Paul S. 
Published: December 2017

AbstractControversy surrounds the molecular identity of mitochondrial K+ channels that are important for protection against cardiac ischemia-reperfusion injury. While KNa1.2 (Kcnt2 gene) is necessary for cardioprotection by volatile anesthetics, electrophysiologic evidence for a channel of this type in mitochondria is lacking. The endogenous physiologic role of a potential mito-KNa1.2 channel is also unclear. Herein, single channel patch-clamp of 27 independent cardiac mitochondrial inner membrane (mitoplast) preparations from wild type (WT) mice yielded 6 channels matching the known ion-sensitivity, ion-selectivity, pharmacology and conductance properties of KNa1.2 (slope conductance 138±1 pS). However, similar experiments on 40 preparations from Kcnt2-/- mice yielded zero such channels. The KNa opener bithionol uncoupled respiration in WT but not Kcnt2-/- cardiomyocytes. Furthermore, when oxidizing only fat as substrate, Kcnt2-/- cardiomyocytes and hearts were less responsive to increases in energetic demand. Kcnt2-/- mice also had elevated body fat, but no baseline differences in the cardiac metabolome. These data support the existence of a cardiac mitochondrial KNa1.2 channel, and a role for cardiac KNa1.2 in regulating metabolism under conditions of high energetic demand.
ZoonoticBabesia microtiin the northeastern U.S.: evidence for the expansion of a specific parasite lineage
Authors: Goethert Heidi K. , Molloy Philip , Berardi Victor , Weeks Karen , Telford Sam R. 
Published: December 2017

AbstractThe recent range expansion of human babesiosis in the northeastern United States, once found only in restricted coastal sites, is not well understood. This study sought to utilize a large number of samples to examine the population structure of the parasites on a fine scale to provide insights into the mode of emergence across the region. 228B. microtisamples collected in endemic northeastern U.S. sites were genotyped using published VNTR markers. The genetic diversity and population structure were analysed on a geographic scale using Phyloviz and TESS. Three distinct populations were detected in northeastern US, each dominated by a single ancestral type. In contrast to the limited range of the Nantucket and Cape Cod populations, the mainland population dominated from New Jersey eastward to Boston. Ancestral populations ofB. microtiwere sufficiently isolated to differentiate into distinct populations. Despite this, a single population was detected across a large geographic area of the northeast that historically had at least 3 distinct foci of transmission, central New Jersey, Long Island and southeastern Connecticut. We conclude that a singleB. microtigenotype has expanded across the northeastern U.S. The biological attributes associated with this parasite genotype that have contributed to such a selective sweep remain to be identified.Author summaryBabesiosis is a disease caused by a protozoan parasite,Babesia microti,related to malaria. The disease is acquired by the bite of the deer tick, the same tick that transmits Lyme disease. Although Lyme disease rapidly emerged over a wide range within the last 40 years, babesiosis remained rare with an extremely focal distribution. Within the last decade, the number of reports of babesiosis cases has increased from an expanded area of risk, particularly across the mainland of southern New England. We determined whether the expanded risk may be due to local intensification of transmission as opposed to introduction of the parasite. Historical fragmentation of the landscape suggests that sites ofB. microtitransmission should have been isolated and thus evidence of multiple genetically distinct populations should be found. By a genetic fingerprinting method, we found that samples from the new mainland sites were all genetically similar. We conclude that one parasite genetic lineage has recently expanded its distribution and now dominates, suggesting that it has some phenotypic attribute that may confer a selective advantage over others.
Elevated and sustained reactive oxygen species levels facilitate mesoderm formation during earlyXenopusdevelopment
Authors: Han Yue , Chen Yaoyao , Love Nick R. , Ishibashi Shoko , Amaya Enrique 
Published: December 2017

ABSTRACTFertilisation triggers embryonic development culminating with the activation of a number of highly co-ordinated and evolutionarily conserved signalling pathways, which induce and pattern the mesoderm of the developing embryo. Previous studies in invertebrates have shown that hydrogen peroxide (H2O2), a reactive oxygen species (ROS), can act as a signalling molecule for axis specification during early development. Using a HyPer transgenicXenopus laevisline that expresses a H2O2-sensitive fluorescent protein sensor maternally, we recently found that fertilisation triggers a rapid increase in ROS production. Here we show that this increase in ROS levels is sustained throughout early embryogenesis, lasting until the tailbud stages. In addition we show that lowering ROS levels from the blastula stage through the gastrula stages via antioxidant treatments disrupts mesoderm formation. Furthermore, we show that attenuating ROS levels during the blastula / gastrula stages affects some, but not all, growth factor signalling pathways involved in mesoderm induction and patterning, including the PI3K/Akt, TGF-β/Nodal, and Wnt/β-catenin signalling pathways. These data suggest that sustained elevated ROS levels during the blastula and gastrula stages are essential for early vertebrate embryonic development, at least partly, through their roles in promoting growth factor signalling.
Engineering a promiscuous pyrrolysyl-tRNA synthetase by a high throughput FACS screen
Authors: Hohl Adrian , Karan Ram , Akal Anstassja , Renn Dominik , Liu Xuechao , Dharamarajnadar Alaguraj , Ghoprade Seema , Groll Michael , Rueping Magnus , Eppinger Jörg 
Published: December 2017

AbstractThe Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNAPyl are used to facilitate the incorporation of non-canonical amino acids (ncAAs) into the genetic code of bacterial and eukaryotic cells by orthogonally reassigning the amber codon. Currently, the incorporation of new ncAAs requires a cumbersome engineering process composed of several positive and negative selection rounds to select the appropriate PylRS/tRNAPyl pair. Our fast and sensitive engineering approach required only a single FACS selection round to identify 110 orthogonal PylRS variants for the aminoacylation of 20 ncAAs. Pocket-substrate relationship from these variants led to the design of a highly promiscuous PylRS (HpRS), which catalyzed the aminoacylation of 31 structurally diverse lysine derivatives bearing clickable, fluorinated, fluorescent, and biotinylated entities. The high speed and sensitivity of our approach provides a competitive alternative to existing screening methodologies, and delivers insights into the complex PylRS-substrate interactions to facilitate the generation of additional promiscuous variants.
Three-way clustering of multi-tissue multi-individual gene expression data using constrained tensor decomposition
Authors: Wang Miaoyan , Fischer Jonathan , Song Yun S. 
Published: December 2017

AbstractThe advent of next generation sequencing methods has led to an increasing availability of large, multi-tissue datasets which contain gene expression measurements across different tissues and individuals. In this setting, variation in expression levels arises due to contributions specific to genes, tissues, individuals, and interactions thereof. Classical clustering methods are illsuited to explore these three-way interactions, and struggle to fully extract the insights into transcriptome complexity and regulation contained in the data. Thus, to exploit the multi-mode structure of the data, new methods are required. To this end, we propose a new method, called MultiCluster, based on constrained tensor decomposition which permits the investigation of transcriptome variation across individuals and tissues simultaneously. Through simulation and application to the GTEx RNA-seq data, we show that our tensor decomposition identifies three-way clusters with higher accuracy, while being 11x faster, than the competing Bayesian method. For several age-, race-, or gender-related genes, the tensor projection approach achieves increased significance over single-tissue analysis by two orders of magnitude. Our analysis finds gene modules consistent with existing knowledge while further detecting novel candidate genes exhibiting either tissue-, individual-, or tissue-by-individual specificity. These identified genes and gene modules offer bases for future study, and the uncovered multi-way specificities provide a finer, more nuanced snapshot of transcriptome variation than previously possible.
Spawning Biology and Induced Breeding of freshwater catfish Mystus dibrugarensis: An approach to conservation
Authors: Bailung Bhenila , Biswas S. P. 
Published: December 2017

AbstractSpawning biology of hormone induced bagridae catfish, Mystus dibrugarensis was observed in captive condition. Active involvement of male in courtship after 5-9 hr. of hormone administration was observed. Different doses of ovaprim 0.4, 0.6, 0.8, 1.0 ml/kg were used by maintaining 1:1, 2:1 and 3:1 ratio of M:F. All female successfully bred in all the condition in more or less amount. Overall 24.5-77.5% fertilization and 12-76% hatching rate was observed. However, considering the rate of fertilization, and hatching success in the present case, at 0.8 ml/kg body weight and sex ratio 2♂: 1 ♀ seems ideal for induced breeding of M. dibrugarensis. Apart from induced breeding certain reproductive aspects were also studied in the present experiment.
Deep learning with implicit handling of tissue-specific phenomena predicts tumor DNA accessibility and immune activity
Authors: Wnuk Kamil , Sudol Jeremi , Givechian Kevin B. , Soon-Shiong Patrick , Rabizadeh Shahrooz , Szeto Christopher , Vaske Charles 
Published: December 2017

AbstractDNA accessibility is a key dynamic feature of chromatin regulation that can potentiate transcriptional events and tumor progression. Recently, neural networks have begun to make it possible to explore the impact of mutations on DNA accessibility and transcriptional regulation by demonstrating state-of-the-art prediction of chromatin features from DNA sequence data in specific tissue types. We demonstrate enhancements to improve such tissue-specific prediction performance, and show that by extending models with RNA-seq expression input, they can be applied to novel tissue samples whose types were not present in training. We show that our expression-informed model achieved particularly consistent accuracy predicting DNA accessibility at promoter and promoter flank regions of the genome.Leveraging this new tool to analyze tumor genomes across tissues, we provide a first glimpse of the DNA accessibility landscape across The Cancer Genome Atlas (TCGA). Our analysis of the Lung Adenocarcinoma (LUAD) cohort reveals that viewing tumors from the perspective of accessibility at promoters uniquely highlights several immune pathways inversely correlated with an overall more open chromatin state. Further, through identification of accessibility sites linked with differential gene expression in immune-inflamed LUAD tumors and training of a classifier ensemble, we show that patterns of predicted chromatin state are discriminative of immune activity across many tumor types, with direct implications for patient prognosis. We see such models playing a significant future role in matching patients to appropriate immunotherapy treatment regimens, as well as in analysis of other conditions where epigenetic state may play a significant role.Significance StatementDNA accessibility determines whether proteins have access to DNA-binding sites and is a key dynamic feature that influences regulation of gene expression that differentiates cells. We improve and extend a neural network model in a way that expands its application domain beyond studying the impact of genetic sequence and mutations on DNA accessibility in specific cell types, to tissues for which training data is unavailable.Leveraging our tool to analyze tumor genomes, we demonstrate that in lung adenocarcinomas the accessibility perspective uniquely highlights immune pathways inversely correlated with a more accessible DNA state. Further, we show that accessibility patterns learned from even a single tumor type can discriminate immune inflammation across many cancers, often with direct relation to patient prognosis.
fluxweb: a R package to easily estimate energy fluxes in food webs
Authors: Gauzens Benoit , Barnes Andrew , Giling Darren , Hines Jes , Jochum Malte , Lefcheck Jonathan S. , Rosenbaum Benjamin , Wang Shaopeng , Brose Ulrich 
Published: December 2017

AbstractUnderstanding how changes in biodiversity will impact the stability and functioning of ecosystems is a central challenge in ecology. Food-web approaches have been advocated to link community composition with ecosystem functioning by describing the fluxes of energy among species or trophic groups. However, estimating such fluxes remains problematic because current methods become unmanageable as network complexity increases.We developed a generalisation of previous indirect estimation methods assuming a steady state system [1, 2, 3]: the model estimates energy fluxes in a top-down manner assuming system equilibrium; each node’s losses (consumption and physiological) balances its consumptive gains. Jointly, we provide theoretical and practical guidelines to use the fluxweb R package (available on CRAN at https://bit.ly/2OC0uKF).We also present how the framework can merge with the allometric theory of ecology [4] to calculate fluxes based on easily obtainable organism-level data (i.e. body masses and species groups -eg, plants animals), opening its use to food webs of all complexities. Physiological losses (metabolic losses or losses due to death other than from predation within the food web) may be directly measured or estimated using allometric relationships based on the metabolic theory of ecology, and losses and gains due to predation are a function of ecological efficiencies that describe the proportion of energy that is used for biomass production.The primary output is a matrix of fluxes among the nodes of the food web. These fluxes can be used to describe the role of a species, a function of interest (e.g. predation; total fluxes to predators), multiple functions, or total energy flux (system throughflow or multitrophic functioning). Additionally, the package includes functions to calculate network stability based on the Jacobian matrix, providing insight into how resilient the network is to small perturbations at steady state.Overall, fluxweb provides a flexible set of functions that greatly increase the feasibility of implementing food-web energetic approaches to more complex systems. As such, the package facilitates novel opportunities for mechanistically linking quantitative food webs and ecosystem functioning in real and dynamic natural landscapes.
Two consecutive microtubule-based epithelial seaming events mediate dorsal closure in the scuttle fly Megaselia abdita
Authors: Fraire-Zamora Juan J. , Jaeger Johannes , Solon Jérôme 
Published: December 2017

AbstractEvolution of morphogenesis is generally associated with changes in genetic regulation. Here we report evidence indicating that dorsal closure, a conserved morphogenetic process in dipterans, evolved as the consequence of rearrangements in epithelial organization rather than signaling regulation. In Drosophila melanogaster, dorsal closure consists of a two-tissue system where the contraction of extraembryonic amnioserosa and a JNK/Dpp-dependent epidermal actomyosin cable result in microtubule-dependent seaming of the epidermis. We find that dorsal closure in Megaselia abdita, a three-tissue system comprising serosa, amnion and epidermis, differs in morphogenetic rearrangements despite conservation of JNK/Dpp signaling. In addition to an actomyosin cable, M. abdita dorsal closure is driven by the rupture and contraction of the serosa and the consecutive microtubule-dependent seaming of amnion and epidermis. Our study indicates that the evolutionary transition to a reduced system of dorsal closure involves simplification of the seaming process without changing the signaling pathways of closure progression.Impact StatementEvolutionary reduction in tissue number involves the simplification of the seaming process but not signaling during epithelial fusion.
Responsibility, authority, and accountability in school-based and non-school-based management
Authors: Grinshtain Yael , Gibton Dan 
Published: December 2017

PurposeThe purpose of this paper is to understand how primary school principals in Israel cope with the gaps between authority and responsibility in their work, deriving from partially implemented decentralization processes, and how this relates to school-based management (SBM) and accountability principles.Design/methodology/approachUsing the qualitative method, 20 semi-structured interviews were conducted with school principals from one district in Israel. Thematic analysis was used in order to identify themes in the interviews that enable creating codes for the characteristics of authority and responsibility and for the principals’ strategies.FindingsGaps were found between authority and responsibility, with particularly low levels of authority alongside high levels of responsibility. Coupled with the demand for accountability, those gaps led principals to adopt three strategies – active, partly active, and passive – to help reduce the tension resulting from them. The SBM definition has links to the specific strategy that principals used.Originality/valueThe results indicate the importance of clear definitions of authority and responsibility in principals’ work. The current study deepens the understanding of the gaps between these concepts as key for understanding accountability at decentralized schools; tensions that principals cope with as a result of those gaps; and the strategies that enable principals to ease the tension for the benefit of all those involved in the principals’ work.
Aspiring to break away from the same old Spanish educational leadership model
Authors: Martínez Ruiz María A. , Hernández-Amorós María J. 
Published: December 2017

Purpose
The purpose of this paper is to seek insights into the demands and challenges faced by school principals in Spain, especially in their dealings with local education authorities.

Design/methodology/approach
In all, 100 principals from public infant, primary and secondary schools in Alicante (Spain) participated in the study, which was carried out from a qualitative research perspective using deductive content analysis.

Findings
Most participants noted the need to improve channels of communication with, and support from, the local education authority. They also stressed the desirability of increasing their autonomy, reducing bureaucratic tasks and improving working conditions, which is in line with the international framework. Their narratives make it clear that they remain tied to a management leadership model but actually aspire to an instructive leadership.

Research limitations/implications
An absence of triangulation and the use of a single data collection technique are the limitations of this paper.

Practical implications
These participants are practising professionals who are proposing ways to improve aspects of their working lives based on actual experience. Acknowledging their voices could inspire the design of policies aimed at improving the principal’s role in Spain.

Originality/value
Knowledge is contributed to the area of study into proposals for improving the role of the principal, but with new and contextualised insights.