bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defective synapse maturation and enhanced synaptic plasticity in Shank2-/-mice
Authors: Wegener Stephanie , Buschler Arne , Vanessa Stempel A. , Shoichet Sarah A. , Manahan-Vaughan Denise , Schmitz Dietmar 
Published: September 2017

SummaryAutism spectrum disorders (ASDs) are neurodevelopmental disorders with a strong genetic aetiology. Since mutations in human SHANK genes have been found in patients with autism, genetic mouse models are employed for a mechanistic understanding of ASDs and the development of therapeutic strategies. In sharp contrast to all studies so far on the function of SHANK proteins, we observe enhanced synaptic plasticity in Shank2-/-mice, under various conditionsin vitroandin vivo. Reproducing and extending previous results, we here present a plausible mechanistic explanation for the mutants' increased capacity for long-term potentiation (LTP) by describing a synaptic maturation deficit in Shank2-/-mice.
Experimental warming reduces the diversity and functional potential of theSphagnummicrobiome
Authors: Carrell Alyssa A. , Kolton Max , Warren Melissa J. , Pelletier Dale A. , Glass Jennifer B. , Kostka Joel E. , Hanson Paul J. , Weston David J. 
Published: September 2017

AbstractClimate change may reduce biodiversity leading to a reduction in ecosystem productivity. Despite numerous reports of a strong correlation of microbial diversity and ecosystem productivity, little is known about the warming effects on plant associated microbes. Here we explore the impact of experimental warming on the microbial and nitrogen-fixing (diazotroph) community associated with the widespread and ecologically relevantSphagnumgenus in a field warming experiment. To quantify changes in the abundance, diversity, and community composition ofSphagnummicrobiomes with warming we utilized qPCR and Illumina sequencing of the 16S SSU rRNA andnifHgene. Microbial and diazotroph community richness and Shannon diversity decreased with warming (p<0.05). The diazotroph communities shifted from diverse communities to domination by primarilyNostocaceae(25% in control samples to 99% in elevated temperature samples). In addition, the nitrogen fixation activity measured with the acetylene reduction assay (ARA) decreased with warming treatment. This suggests the negative correlation of temperature and microbial diversity corresponds to a reduction in functional potential within the diazotroph community. The results indicate that climate warming may alter the community structure and function in peat moss microbiomes, with implications for impacts to host fitness and ecosystem productivity, and carbon uptake potential of peatlands.
SAMSA2: A standalone metatranscriptome analysis pipeline
Authors: Westreich Samuel T , Treiber Michelle L , Mills David A , Korf Ian , Lemay Danielle G 
Published: September 2017

AbstractBackgroundComplex microbial communities are an area of rapid growth in biology. Metatranscriptomics allows one to investigate the gene activity in an environmental sample via high-throughput sequencing. Metatranscriptomic experiments are computationally intensive because the experiments generate a large volume of sequence data and the sequences must be compared with many references.ResultsHere we present SAMSA2, an upgrade to the original Simple Annotation of Metatranscriptomes by Sequence Analysis (SAMSA) pipeline that has been redesigned for use on a supercomputing cluster. SAMSA2 is faster due to the use of the DIAMOND aligner, and more flexible and reproducible because it uses local databases. SAMSA2 is available with detailed documentation, and example input and output files along with examples of master scripts for full pipeline execution.ConclusionsUsing publicly available example data, we demonstrate that SAMSA2 is a rapid and efficient metatranscriptome pipeline for analyzing large paired-end RNA-seq datasets in a supercomputing cluster environment. SAMSA2 provides simplified output that can be examined directly or used for further analyses, and its reference databases may be upgraded, altered or customized to fit the specifics of any experiment.
Complexity of the Relationship between Life Expectancy and Overlap of Lifespans
Authors: Barthold Julia A. , Lenart Adam , Baudisch Annette 
Published: September 2017

AbstractLongevity has long been recognised as a key facilitator of reciprocal altruism because repeated cooperation of partners hinges on mutual survival. Although demographic tools can be used to quantify mutual survival and expected overlapping lifespans, studies on the evolutionary theory of cooperation take only limited advantage of demography. Overlap of lifespans depends on variation in survival across ages and can be high or low independently of high or low life expectancies. Here we develop formal demographic measures to study the complex relationships between shared life expectancy of two birth cohort peers, the proportion of their lives that they can expect to overlap, and longevity. We simulate age-specific mortality schedules using a Siler model to reveal how infant and senescent mortality, along with age-independent mortality, affect the relationship between the proportion of life shared and life expectancy. We find that while the proportion of life shared can vary vastly for similar life expectancies, almost all changes to mortality schedules that result in higher life expectancies also result in higher proportions of life shared. A distinct exception occurs if life expectancy increases due to lowering the rate of senescence. In this case the proportion of life shared decreases. Our work shows that almost all selective pressures that result in higher life expectancies also result in a larger proportion of life shared. Therefore, selective forces that extend life also improve the chances that a cooperative system would be stable in terms of reciprocal interactions. Since reciprocal interactions may also reduce mortality and result in a feedback loop with the evolution of longevity, our measures and findings can be used for future cross-species comparisons that aim to disentangle predecessor and successor in the evolution of longevity and cooperation.
Activation of theAndrogen Receptorgene by BORIS/CTCFL in prostate cancer cells
Authors: Hari-Gupta Yukti , Kita Georgia-Xanthi , Farrar Dawn , Klenova Elena 
Published: September 2017

AbstractBORIS/CTCFL, a paralogue of the chromatin architectural protein CTCF, is a member of the cancer-testis antigen family, normally present in the testes. BORIS is expressed in various tumours, including prostate cancers, however the function of BORIS in cancer cells is not well defined. The androgen receptor (AR) plays a critical role in the normal development of a human prostate gland and pathogenesis of prostate cancer. In our previous study we described a positive correlation between elevated levels of BORIS and AR in prostate cancers, and activation of theARgene by BORIS in prostate cancer cells. Elucidation of the mechanisms involved in the modulation of AR activity is important to understand prostate tumourigenesis and investigation of transcriptional regulation of theARgene by BORIS may provide new insights into this issue. Here we report the ability of BORIS to not only positively regulateARin androgen-dependent prostate cancer (ADPC) cells, but re-activate epigenetically silencedARin androgen-independent prostate cancer (AIPC) cells leading to the production of biologically active AR protein. CTCF, on the other hand, had repressive effects on theAR. In both, ADPC and AIPC cells, introduction of ectopic BORIS was associated with the reduction in theARpromoter methylation, increase in active and decrease in repressive chromatin marks, and decrease in CTCF occupancies at the two main upstream BORIS/CTCF binding sites. We propose a model of epigenetic regulation ofARby BORIS in prostate cells whereby BORIS remodels the chromatin at theARpromoter leading to transcriptional activation.
Estimating sampling completeness of interactions in quantitative bipartite ecological networks: incorporating variation in species’ specialisation
Authors: Macgregor Callum J. , Evans Darren M. , Pocock Michael J.O. 
Published: September 2017

AbstractBackgroundThe analysis of ecological networks can be affected by sampling effort, potentially leading to bias. Ecological network structure is often summarised by descriptive metrics but these metrics can vary according to the proportion of the total interactions that have been observed. Therefore, to know the likely degree of bias, it is valuable to estimate the total number of interactions in a network, and so calculate the proportion of interactions that have been observed (sampling completeness of interactions). Existing approaches to estimate sampling completeness of interactions use the Chao family of asymptotic species richness estimators to predict the total number of interactions, but do not fully utilise information about the relative specialisation of species within the network.ResultsHere, we propose a modification of previously-used methods, that places equal weight on each interaction (whether or not it has been observed), rather than on each species. Our approach is therefore equivalent to weighting the interaction sampling completeness of each species in the network according to its relative specialisation. We demonstrate that, for the subset of species that are observed and when assuming that species richness estimators accurately project the number of unobserved interactions per observed species, our approach is mathematically more accurate. Our approach can be universally applied to any quantitative, bipartite network.We propose two methods to estimation using our approach, using abundance-based and incidence-based species richness estimators respectively, and give recommendations when each should be applied. We discuss the effect of unobserved species and the potential use of a threshold of minimum abundance for species inclusion. Finally, we consider these advances in the context of some of the main issues surrounding estimation of interaction sampling completeness in network ecology.ConclusionsWe recommend that future studies of bipartite networks utilise our approach and methods to estimate the sampling completeness of interactions, to assist with the quantitative and comparative analysis and interpretation of network properties.
Genome-wide association analysis of 350,000 Caucasians from the UK Biobank identifies novel loci for asthma, hay fever and eczema
Authors: Johansson Åsa , Rask-Andersen Mathias , Karlsson Torgny , Ek Weronica E. 
Published: September 2017

AbstractEven though heritability estimates suggest that the risk of asthma, hay fever and eczema is largely due to genetic factors, previous studies have not explained a large part of the genetics behind these diseases. In this GWA study, we include 346,545 Caucasians from the UK Biobank to identify novel loci for asthma, hay fever and eczema. We further investigate if associated lead SNPs have a significantly larger effect for one disease compared to the other diseases, to highlight possible disease specific effects.We identified 141 loci, of which 41 are novel, to be associated (P≤3×10−8) with asthma, hay fever or eczema, analysed separately or as disease phenotypes that includes the presence of different combinations of these diseases. The largest number of loci were associated with the combined phenotype (asthma/hay fever/eczema). However, as many as 20 loci had a significantly larger effect on hay fever/eczema-only compared to their effects on asthma, while 26 loci exhibited larger effects on asthma compared with their effects on hay fever/eczema. At four of the novel loci,TNFRSF8, MYRF, TSPAN8, andBHMG1, the lead SNPs were in LD (> 0.8) with potentially casual missense variants.Our study shows that a large amount of the genetic contribution is shared between the diseases. Nonetheless, a number of SNPs have a significantly larger effect on one of the phenotypes suggesting that part of the genetic contribution is more phenotype specific. Identified loci and probable causal genes may in the future be used as targets for treatments of asthma, hay fever and eczema.
Parallel progress in perceived age and life expectancy
Authors: Steiner Ulrich K. , Larsen Lisbeth Aagaard , Christensen Kaare 
Published: September 2017

SummaryHuman life expectancy continues to rise in most populations. This rise not only leads to longer lives but is also accompanied by improved health at a given age, i.e. we see a reduction of biological age for a given chronological age in recent cohorts. Despite or even because of the diversity of biomarkers of aging, an accurate quantification of a general shift in biological age across time has been challenging. By comparing age perception of images taken in 2001 over a decade, we show that age perception changes substantially across time and parallels the progress in life expectancy. In 2012, people aged 70+ needed to look 2.3 years younger to be rated the same age as in 2002. Our results further suggest that age perception reflects the past life events better than predicts future length of life, i.e. it is written in your face how much you have aged so far, but does not predict well how fast you will age in the future. We draw this conclusion since age perception among elderly paralleled changes in life expectancy at birth but not changes in remaining life expectancies. We illustrate advantages of perceived age as a biomarker of aging and suggest that changes in age perception should be explored for younger age classes to inform on aging processes, including whether aging is delayed or slowed with increasing life expectancy.
Prediction of the intestinal resistome by a novel 3D-based method
Authors: Ruppé Etienne , Ghozlane Amine , Tap Julien , Pons Nicolas , Alvarez Anne-Sophie , Maziers Nicolas , Cuesta Trinidad , Hernando-Amado Sara , Martínez Jose Luís , Coque Teresa M. , Baquero Fernando , Lanza Val F. , Maiz Luis , Goulenok Tiphaine , Lastours Victoire de , Amor Nawal , Fantin Bruno , Wieder Ingrid , Andremont Antoine , Schaik Willem van , Rogers Malbert , Zhang Xinglin , Willems Rob J.L. , De Brevern Alexandre G. , Batto Jean-Michel , Blottière Hervé , Léonard Pierre , Léjard Véronique , Letur Aline , Levenez Florence , Weiszer Kevin , Haimet Florence , Doré Joël , Kennedy Sean P. , Dusko Ehrlich S. 
Published: September 2017

SummaryThe intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens. Yet, this question remains hypothetical because of the difficulty to identify ARDs from intestinal bacteria. Here, we developed and validated a new annotation method (called pairwise comparative modelling, PCM) based on homology modelling in order to characterize the Human resistome. We were able to predict 6,095 ARDs in a 3.9 million protein catalogue from the Human intestinal microbiota. We found that predicted ARDs (pdARDs) were distantly related to known ARDs (mean amino-acid identity 29.8%). Among 3,651 pdARDs that were identified in metagenomic species, 3,489 (95.6%) were assumed to be located on the bacterial chromosome. Furthermore, genes associated with mobility were found in the neighbourhood of only 7.9% (482/6,095) of pdARDs. According to the composition of their resistome, we were able to cluster subjects from the MetaHIT cohort (n=663) into 6 “resistotypes”. Eventually, we found that the relative abundance of pdARDs was positively associated with gene richness, but not when subjects were exposed to antibiotics. Altogether, our results support that most ARDs in the intestinal microbiota should be considered as intrinsic genes of commensal microbiota with a low risk of transfer to bacterial pathogens.
Cognitive deficits and increases in creatine precursors in a brain-specific knockout of the creatine transporter geneSlc6a8
Authors: Udobi Kenea C. , Kokenge Amanda N. , Hautman Emily R. , Ullo Gabriela , Coene Julie , Williams Michael T. , Vorhees Charles V. , Mabondzo Aloïse , Skelton Matthew R 
Published: September 2017

AbstractCreatine transporter (CrT; SLC6A8) deficiency (CTD) is an X-linked disorder characterized by severe cognitive deficits, impairments in language, and an absence of brain creatine (Cr). In a previous study, we generated floxedSlc6a8 (Slc6a8flox)mice to create ubiquitousSlc6a8knockout(Slc6a8-/y)mice.Slc6a8-/ymice lacked whole body Cr and exhibited cognitive deficits. WhileSlc6a8-/ymice have a similar biochemical phenotype to CTD patients, they also showed a reduction in size and reductions in swim speed that may have contributed to the observed deficits. To address this, we created brain-specificSlc6a8knockout (bKO) mice by crossingSlc6a8Floxmice withNestin-cremice. bKO mice had reduced cerebral Cr levels while maintaining normal Cr levels in peripheral tissue. Interestingly, brain concentrations of the Cr synthesis precursor guanidinoacetic acid were increased in bKO mice. bKO mice had longer latencies and path lengths in the Morris water maze, without reductions in swim speed. In accordance with data fromSlc6a8-/ymice, bKO mice showed deficits in novel object recognition as well as contextual and cued fear conditioning. bKO mice were also hyperactive, in contrast with data from theSlc6a8-/ymice. The results demonstrate that the loss of cerebral Cr is responsible for the learning and memory deficits seen in ubiquitousSlc6a8-/ymice.
Transplanted Adult Neural Stem Cells Express Sonic HedgehogIn Vivoand Suppress White Matter Neuroinflammation After Experimental Traumatic Brain Injury
Authors: Sullivan Genevieve M. , Armstrong Regina C. 
Published: September 2017

ABSTRACTNeural stem cells (NSCs) delivered intraventricularly may be therapeutic for diffuse white matter pathology after traumatic brain injury (TBI). To test this concept, NSCs isolated from adult mouse subventricular zone (SVZ) were transplanted into the lateral ventricle of adult mice at two weeks post-TBI followed by analysis at four weeks post-TBI. We examined Sonic hedgehog (Shh) signaling as a candidate mechanism by which transplanted NSCs may regulate neuroregeneration and/or neuroinflammation responses of endogenous cells. Mouse fluorescent reporter lines were generated to enablein vivogenetic labeling of cells actively transcribingShhorGli1after transplantation and/or TBI.Gli1transcription is an effective readout for canonical Shh signaling. InShhCreERT2;R26tdTomatomice,Shhwas primarily expressed in neurons and was not upregulated in reactive astrocytes or microglia after TBI. Corroborating results inGli1CreERT2;R26tdTomatohost mice demonstrated Shh signaling was not upregulated in the corpus callosum, even after TBI or NSC transplantation. Transplanted NSC expressedShh in vivobut did not increaseGli1labeling of host SVZ cells. Importantly, NSC transplantation significantly reduced reactive astrogliosis and microglial/macrophage activation in the corpus callosum after TBI. Therefore, intraventricular NSC transplantation after TBI significantly attenuated neuroinflammation, but did not activate host Shh signaling viaGli1transcription.
A Connectome Wide Functional Signature of Transdiagnostic Risk for Mental Illness
Authors: Elliott Maxwell L. , Romer Adrienne , Knodt Annchen R. , Hariri Ahmad R. 
Published: September 2017

AbstractBackgroundHigh rates of comorbidity, shared risk, and overlapping therapeutic mechanisms have led psychopathology research towards transdiagnostic dimensional investigations of clustered symptoms. One influential framework accounts for these transdiagnostic phenomena through a single general factor, sometimes referred to as the ‘p’ factor, associated with risk for all common forms of mental illness.MethodsHere we build on past research identifying unique structural neural correlates of the p factor by conducting a data-driven analysis of connectome wide intrinsic functional connectivity (n = 605).ResultsWe demonstrate that higher p factor scores and associated risk for common mental illness maps onto hyper-connectivity between visual association cortex and both frontoparietal and default mode networks.ConclusionsThese results provide initial evidence that the transdiagnostic risk for common forms of mental illness is associated with patterns of inefficient connectome wide intrinsic connectivity between visual association cortex and networks supporting executive control and self-referential processes, networks which are often impaired across categorical disorders.
Relationship between sustainable operations practices and performance: a meta-analysis
Authors: D’Agostini Marina , Tondolo Vilmar Antonio Gonçalves , Camargo Maria Emília , Dullius Angela Isabel dos Santos , Tondolo Rosana da Rosa Portella , Russo Suzana Leitão 
Published: October 2017

PurposeThe purpose of this paper is to examine the relationship between sustainable operations practices (SOP) and performance.Design/methodology/approachThis study was conducted through a systematic literature review followed by a meta-analysis of correlations.FindingsIn the results, 14 of the relationships examined showed a positive relationship and 12 the presence of moderators. The study findings indicate that contingency affects the relationship between SOPs and performance.Research limitations/implicationsThe research presented in this paper is mainly limited to databases that were searched. Among the quantitative articles selected from the databases, many did not have the data needed to conduct the meta-analysis, which may have limited the results of this study.Practical implicationsUsing the results of this study, practitioners can become aware of to the occurrence of moderating factors in the relationships, which can range from interference from other practices and variables to characteristics of the organization itself or the market in which organizations operate.Originality/valueThis study uses a multidimensional approach for both SOP and performance. This approach allowed a more complete and comprehensive result, showing how these SOPs influence the different categories of performance, expanding the understanding of the relationship between practices and performance.
Cash flow disaggregation and prediction of cash flow
Authors: Khansalar Ehsan , Namazi Mohammad 
Published: October 2017

Purpose
The purpose of this paper is to investigate the incremental information content of estimates of cash flow components in predicting future cash flows.

Design/methodology/approach
The authors examine whether the models incorporating components of operating cash flow from income statements and balance sheets using the direct method are associated with smaller prediction errors than the models incorporating core and non-core cash flow.

Findings
Using data from US and UK firms and multiple regression analysis, the authors find that around 60 per cent of a current year’s cash flow will persist into the next period’s cash flows, and that income statement and balance sheet variables persist similarly. The explanatory power and predictive ability of disaggregated cash flow models are superior to that of an aggregated model, and further disaggregating previously applied core and non-core cash flows provides incremental information about income statement and balance sheet items that enhances prediction of future cash flows. Disaggregated models and their components produce lower out-of-sample prediction errors than an aggregated model.

Research limitations/implications
This study improves our appreciation of the behaviour of cash flow components and confirms the need for detailed cash flow information in accordance with the articulation of financial statements.

Practical implications
The findings are relevant to investors and analysts in predicting future cash flows and to regulators with respect to disclosure requirements and recommendations.

Social implications
The findings are also relevant to financial statement users interested in better predicting a firm’s future cash flows and thereby, its firm’s value.

Originality/value
This paper contributes to the existing literature by further disaggregating cash flow items into their underlying items from income statements and balance sheets.