bluuebunny/crossref_metadata_2025_split huggingface dataset:
The prevalence and impact of transient species in ecological communities
Authors: Snell Sara , Evans Brian S. , White Ethan P. , Hurlbert Allen H. 
Published: July 2017

AbstractTransient species occur infrequently in a community over time and do not maintain viable local populations. Because transient species interact differently than non-transients with their biotic and abiotic environment, it is important to characterize the prevalence of these species and how they impact our understanding of ecological systems. We quantified the prevalence and impact of transient species in communities using data on over 17,000 community time series spanning an array of ecosystems, taxonomic groups, and spatial scales. We found that transient species are a general feature of communities regardless of taxa or ecosystem. The proportion of these species decreases with spatial scale leading to a need to control for scale in comparative work. Removing transient species from analyses influences the form of a suite of commonly studied ecological patterns including species-abundance distributions, species-energy relationships, species-area relationships, and temporal turnover. Careful consideration should be given to whether transient species are included in analyses depending on the theoretical and practical relevance of these species for the question being studied.
Histopathological Effects of Therapeutic Doses of Combined XO-Inhibitors and ACE-Inhibitors on the Expression of VEGF-A in the Myocardium and Renal Cortex in Chronic Hypertensive Albino Rats
Authors: Rezk Hassan M. , Ibraheim Afaf 
Published: July 2017

AbstractBackgroundHypertension is risk factor for development of congestive heart failure. The pathogenesis of myocardial and renal cortex changes in hypertension includes structural remodeling and fibrosis.Aim of studyis to evaluate the effects of therapeutic doses of combined XO-Inhibitors and ACE-Inhibitors on expression of VEGF-A in the myocardium and renal cortex in chronic hypertensive albino rats.Material & MethodsThirty male albino rats were divided into: Group I: (control group), Group II (Non-treated Hypertensive rats), Group III (Allopurinol-treated Hypertensive rats), Group IV (Captopril-treated Hypertensive rats) and Group V (Allopurinol-Captopril-treated Hypertensive rats). At 4 and 8 weeks, the rats were anesthetized followed by obtaining of heart and left kidney to be stained with Masson trichrome and Anti-Vascular endothelial growth factor-A antibody.ResultsGroup II, one month hypertensive rats showed, myocardium showed disarray with significant increase in interstitial fibrosis. The renal cortex showed evidences indicating glomerulosclerosis. Immunohistochemistry, there was high significant decrease in the number of cells of renal cortex with +ve expression of VEGF-A. Later, they showed marked significant increase in interstitial fibrosis. In Group III, myocardium and renal cortex showed high significant increase in interstitial fibrosis. After two month, there were high significant decrease in the surface area of interstitial fibrosis in myocardium and renal cortex with high significant decrease number of the myocardium with +ve expression of VEGaF-A. In Group IV, myocardium showed disarray with marked significant reduction in interstitial fibrosis. The renal cortex showed marked significant reduction in the interstitial fibrosis with significant decrease in the number of cells with +ve expression of VEGF-A. Later, myocardium showed the most high marked significant reduction in interstitial fibrosis with highly significant increase in number of cells with positive expression of VEGF-A. In Group V after two month, both myocardium and renal cortex showed nearly normal architecture with marked significant reduction in interstitial fibrosis.ConclusionsLong term therapy with the combination between allopurinol and captopril decreases the fibrotic changes associated with hypertension and enhances the process of angiogenesis.
A Resource for the Allele-Specific Analysis of DNA Methylation at Multiple Genomically Imprinted Loci in Mice
Authors: Wasson Jadiel A. , Birol Onur , Katz David J. 
Published: July 2017

AbstractGenomically imprinted loci are expressed mono-allelically dependent upon the parent of origin. Their regulation not only illuminates how chromatin regulates gene expression but also how chromatin can be reprogrammed every generation. Because of their distinct parent of origin regulation, analysis of imprinted loci can be difficult. Single nucleotide polymorphisms (SNPs) are required to accurately assess these elements allele-specifically. However, publicly available SNP databases lack robust verification, making analysis of imprinting difficult. In addition, the allele-specific imprinting assays that have been developed employ different mouse strains, making it difficult to systemically analyze these loci. Here, we have generated a resource that will allow the allele-specific analysis of many significant imprinted loci in a single hybrid strain ofMus musculus. This resource includes verification of SNPs present within ten of the most widely used imprinting control regions and allele-specific DNA methylation assays for each gene in a C57BL/6J and CAST/EiJ hybrid strain background.
Three-dimensional single cell patterning for mid- to high-throughput studies of tumor cell and extracellular matrix heterogeneity
Authors: Gong Xiangyu , Mills Kristen L. 
Published: July 2017

AbstractCancer heterogeneity includes cancer cell genetic heterogeneity and heterogeneity in the tumor microenvironment (TME)—both stromal cells and extracellular matrix (ECM). Determining which combinations of the vast array of possibly interacting heterogeneities drive tumor progression presents a major multi-disciplinary challenge in cancer research. To make effective treatment decisions this challenge must be addressed. The practical challenge is assessing cellular heterogeneity in a statistically powerful way with respect to targeted TME characteristics. Here we present a simple, but extensible, and low-cost method for conducting mid- to high-throughput and long-term studies of heterogeneous cell responses to various biomechanical stimuli in 3D models mimicking the biomechanical properties of the ECM. Using a platform we term “the drop-patterning chip” thousands of cells are simultaneously transferred from microwells and fully embedded, only using the force of gravity, in precise patterns in 3D. This method allows for throughputs approaching flow-through methods, which lack phenotypic information on cell-matrix interactions, and does not rely on expensive or harsh patterning forces, which often times also result in a proximal stiff surface.
Disequilibrium of fire-prone forests sets the stage for a rapid decline in conifer dominance during the 21stcentury
Authors: Serra-Diaz Josep M. , Maxwell Charles , Lucash Melissa S. , Scheller Robert M. , Laflower Danelle M. , Miller Adam D. , Tepley Alan J. , Epstein Howard E. , Anderson-Teixeira Kristina J. , Thompson Jonathan R 
Published: July 2017

AbstractAs trees are long-lived organisms, the impacts of climate change on forest communities may not be apparent on the time scale of years to decades. While lagged responses to environmental change are common in forested systems, potential for abrupt transitions under climate change may occur in environments where alternative vegetation states are influenced by disturbances, such as fire. The Klamath mountains (northern California and southwest Oregon, USA) are currently dominated by carbon rich and hyper-diverse temperate conifer forests, but climate change could disrupt the mechanisms promoting forest stability– regeneration and fire tolerance— via shifts in the fire regime in conjunction with lower fitness of conifers under a hotter climate. Understanding how this landscape will respond to near-term climate change (before 2100) is critical for predicting potential climate change feedbacks and to developing sound forest conservation and management plans. Using a landscape simulation model, we estimate that 1/3 of the Klamath could transition from conifer forest to shrub/hardwood chaparral, triggered by an enhanced fire activity coupled with lower post-fire conifer establishment. Such shifts were more prevalent under higher climate change forcing (RCP 8.5) but were also simulated under the climate of 1950-2000, reflecting the joint influences of early warming trends and historical forest legacies. Our results demonstrate that there is a large potential for loss of conifer forest dominance—and associated carbon stocks and biodiversity- in the Klamath before the end of the century, and that some losses would likely occur even without the influence of climate change. Thus, in the Klamath and other forested landscapes subject to similar feedback dynamics, major ecosystem shifts should be expected when climate change disrupts key stabilizing feedbacks that maintain the dominance of long-lived, slowly regenerating trees.
Long-term community change through multiple rapid transitions in a desert rodent community
Authors: Christensen Erica M. , Harris David J. , Ernest S. K. Morgan 
Published: July 2017

AbstractWhile studies increasingly document long-term change in community composition, whether long-term change occurs gradually or via rapid reorganization events remains unclear. We used Latent Dirichlet Allocation (LDA) and a change-point model to examine the long-term dynamics of a desert rodent community undergoing compositional change over a 38-year span. Our approach detected three rapid reorganization events, where changes in the relative abundances of dominant and rare species occurred, and a separate period of increased variance in the structure of the community. These events coincided with time periods—possibly related to climate events—where the total abundance of rodents was extremely low. There are a variety of processes that could link low abundance events with a higher probability of rapid ecological transitions, including higher importance of stochastic processes (i.e., competitive interactions or priority effects) and the removal of structuring effects of competitive dominants or incumbent species. Continued study of the dynamics of community change will provide important information not only on the processes structuring communities, but will also provide guidance for forecasting how communities will undergo change in the future.
Dark period transcriptomic and metabolic profiling of two diverseEutrema salsugineumaccessions
Authors: Yin Jie , Gosney Michael J. , Dilkes Brian P. , Mickelbart Michael V. 
Published: July 2017

AbstractEutrema salsugineumis a model species for the study of plant adaptation to abiotic stresses. Two accessions ofE. salsugineum, Shandong (SH) and Yukon (YK), exhibit contrasting morphology, biotic, and abiotic stress tolerance. Transcriptome and metabolic profiling from tissue samples collected during the dark period were used to investigate the molecular and metabolic bases of these contrasting phenotypes. RNA sequencing identified 17,888 expressed genes, of which 157 were not in the published reference genome and 65 were detected for the first time. Differential expression was detected for only 31 genes. The RNA sequencing data contained 14,808 single nucleotide polymorphisms (SNPs) in transcripts, 3,925 of which are newly identified. Among the differentially expressed genes, there were no obvious candidates for the physiological or morphological differences between SH and YK. Metabolic profiling indicated that YK accumulates free fatty acids and long-chain fatty acid derivatives as compared to SH; whereas sugars are more abundant in SH. Metabolite levels suggest that carbohydrate and respiratory metabolism, including starch degradation, is more active during the first half of the dark period in SH. These metabolic differences may explain the greater biomass accumulation in YK over SH. The accumulation of 56% of the identified metabolites was lower in F1hybrids than the mid-parent averages and the accumulation of 17% of the metabolites in F1plants transgressed the level in both parents. Concentrations of several metabolites in F1hybrids agree with previous studies and suggest a role for primary metabolism in heterosis. The improved annotation of theE. salsugineumgenome and newly-identified high-quality SNPs will permit accelerated studies using the standing variation in this species to elucidate the mechanisms of its diverse adaptations to the environment.
Interferon Regulatory Factor 5 (IRF5) Interacts with the Translation Initiation Complex and Promotes mRNA Translation During the Integrated Stress Response to Amino Acid Deprivation
Authors: Warner James D. , Wiley Mandi , Wu Ying-Y , Wen Feng , Kinter Michael , Yanagiya Akiko , Tessneer Kandice L. , Gaffney Patrick M. 
Published: July 2017

ABSTRACTInterferon Regulatory Factor 5 (IRF5) plays an important role in limiting pathogenic infection and tumor development. Host protection by IRF5 can occur through a variety of mechanisms including production of type I interferon and cytokines as well as the regulation of cell survival, growth, proliferation, and differentiation. While modulation of these cellular processes is attributed to IRF5 transcription factor function in the nucleus, emerging evidence suggests that IRF5 may also retain non-transcriptional regulatory properties within the cytoplasmic compartment. Consistent with this notion, we report the ability of IRF5 to control gene expression at the level of mRNA translation. Our findings demonstrate that IRF5 interacts with the translation initiation complex in the absence of the m7GTP cap-binding protein, eIF4E. We observed that under nutrient deprivation-induced cell stress, IRF5 promoted mRNA translation of the master integrated stress response (ISR) regulator, Activating Transcription Factor 4 (ATF4). Enhanced ATF4 protein expression correlated with increased levels of downstream target genes including CHOP and GADD34 and was associated with amplification of eIF2α de-phosphorylation and translational de-repression under stress. The novel mechanism we describe broadens our understanding of how IRF5 regulates gene expression and may govern diverse cellular processes in the absence of stimuli that trigger IRF5 nuclear translocation.
Evidence of signaling and adhesion roles for β-catenin in the sponge Ephydatia muelleri
Authors: Schippers Klaske J. , Nichols Scott A. 
Published: July 2017

ABSTRACTβ-catenin acts as a transcriptional co-activator in the Wnt/β-catenin signaling pathway and a cytoplasmic effector in cadherin-based cell adhesion. These functions are ancient within animals, but the earliest steps in β-catenin evolution remain unresolved due to limited data from key lineages – sponges, ctenophores and placozoans. Previous studies in sponges have characterized β-catenin expression dynamics and used GSK3B antagonists to ectopically activate the Wnt/β-catenin pathway; both approaches rely upon untested assumptions about the conservation of β-catenin function and regulation in sponges. Here, we test these assumptions using an antibody raised against β-catenin from the spongeEphydatia muelleri. We find that cadherin-complex genes co-precipitate with endogenousEmβ-catenin from cell lysates, but that Wnt pathway components do not. However, through immunostaining we detect both cell boundary and nuclear populations, and we find evidence thatEmβ-catenin is a conserved substrate of GSK3B. Collectively, these data support conserved roles forEmβ-catenin in both cell adhesion and Wnt signaling. Additionally, we find evidence for anEmβ-catenin population associated with the distal ends of F-actin stress fibers in apparent cell-substrate adhesion structures that resemble focal adhesions. This finding suggests a fundamental difference in the adhesion properties of sponge tissues relative to other animals, in which the adhesion functions of β-catenin are typically restricted to cell-cell adhesions.
Tissue Folding by Mechanical Compaction of the Mesenchyme
Authors: Hughes Alex J. , Miyazaki Hikaru , Coyle Maxwell C. , Zhang Jesse , Laurie Matthew T. , Chu Daniel , Vavrušová Zuzana , Schneider Richard A. , Klein Ophir D. , Gartner Zev J. 
Published: July 2017

SUMMARYMany tissues fold during development into complex shapes. Engineering this process in vitro would represent an important advance for tissue engineering. We use embryonic tissue explants, finite element modeling, and 3D cell patterning techniques to show that a mechanical compaction of the ECM during mesenchymal condensation can drive tissue folding along programmed trajectories. The process requires cell contractility, generates strains at nearby tissue interfaces, and causes specific patterns of collagen alignment around and between condensates. Aligned collagen fibers support elevated tensions that promote the folding of interfaces along paths that can be predicted by finite element modeling. We demonstrate the robustness and versatility of this strategy for sculpting tissue interfaces by directing the morphogenesis of a variety of folded tissue forms from engineered patterns of mesenchymal condensates. These studies provide insight into the active mechanical properties of the embryonic mesenchyme and establish entirely new strategies for more robustly directing tissue morphogenesisex vivo,without genetic engineering.
Resurrecting ancestral genes in bacteria to interpret ancient biosignatures
Authors: Kacar Betul , Guy Lionel , Smith Eric , Baross John 
Published: July 2017

SummaryTwo datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physicochemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its ∼3.8 billion years of history on Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions. The geologic record provides an array of biologically independent indicators of macroscale atmospheric and oceanic composition, but provides little in the way of the exact behavior of the molecular components that influenced the compositions of these reservoirs. By reconstructing sequences of proteins that might have been present in ancient organisms, we can identify a subset of possible sequences that may have been optimized to these ancient environmental conditions. How can extant life be used to reconstruct ancestral phenotypes? Configurations of ancient sequences can be inferred from the diversity of extant sequences, and then resurrected in the lab to ascertain their biochemical attributes. One way to augment sequence-based, single-gene methods to obtain a richer and more reliable picture of the deep past, is to resurrect inferred ancestral protein sequences in living organisms, where their phenotypes can be exposed in a complex molecular-systems context, and to then link consequences of those phenotypes to biosignatures that were preserved in the independent historical repository of the geological record. As a first-step beyond single molecule reconstruction to the study of functional molecular systems, we present here the ancestral sequence reconstruction of the beta-carbonic anhydrase protein. We assess how carbonic anhydrase proteins meet our selection criteria for reconstructing ancient biosignatures in the lab, which we term paleophenotype reconstruction.
Resting-state connectivity and its association with cognitive performance, educational attainment, and household income in UK Biobank (N = 3,950)
Authors: Shen Xueyi , Cox Simon R , Adams Mark J , Howard David M , Lawrie Stephen M , Ritchie Stuart J , Bastin Mark E , Deary Ian J , McIntosh Andrew M , Whalley Heather C 
Published: July 2017

AbstractCognitive ability is an important predictor of lifelong physical and mental well-being and its impairments are associated with many psychiatric disorders. Higher cognitive ability is also associated with greater educational attainment and increased household income. Understanding neural mechanisms underlying cognitive ability is therefore of crucial importance for determining the nature of these associations. In the current study, we examined the spontaneous activity of the brain at rest to investigate its relationships with not only cognitive ability, but also educational attainment and household income. We used a large sample of resting-state neuroimaging data from UK Biobank (N=3,950). Firstly, analysis at the whole-brain level showed that connections involving the default mode network (DMN), fronto-parietal network (FPN) and cingulo-opercular network (CON) were significantly positively associated with levels of cognitive performance assessed by a verbal-numerical reasoning test (standardised β ranged from 0.054 to 0.097). Connections associated with higher levels of cognitive performance were also significantly positively associated with educational attainment (r=0.48, N=4,160) and household income (r=0.38, N=3,793). Further, analysis on the coupling of functional networks showed that better cognitive performance was associated with more positive DMN-CON connections, decreased cross-hemisphere connections between homotopic network in CON and FPN, and stronger CON-FPN connections (absolute β ranged from 0.034 to 0.063). The present study finds that variation in brain resting state functional connectivity associated with individual differences in cognitive ability, largely involving DMN and lateral prefrontal networks. Additionally, we provide further evidence of shared neural associations of cognitive ability, educational attainment, and household income.
Exploration of Western Himalayan region for identification of gold nanoparticles synthesizing bacteria
Authors: Thakur Rajni Kant , Shirkot Poonam 
Published: July 2017

AbstractThe development of eco-friendly methods for the synthesis of nanomaterial shape and size is an important area of research in the field of nanotechnology. In present study an indigenous bacterial strain GPI-1 has been isolated from a local gold mine Khaltunala. It was characterized morphological, biochemically and also by using 16S rrna gene technology and was identified asBacillus flexusGPI-1, the phylogeny of this bacterial strain was determined using various bioinformatics tools viz BLASTn and MEGA 5.0. To achieve maximuminvitrogold nanoparticles synthesis various parameters such as pH, incubation temperature, incubation time period and wavelength were optimized as 6.8, 37°C, 36 hrs, 560 nm respectively. Stable and cubical gold nanoparticles (GNPs) formation with 40-45 nm dimensions were synthesized successfully underinvitroconditions upon exposure of gold chloride trihydrates (HAuCl4) solution to the supernatant ofBacillus flexusstrain GPI-1. These gold nanoparticles have been characterized by Transmission electron microscope, Fourier transform infrared spectroscopy (FTIR). Thus in the present study successful biosynthesis method of stable and cubical gold nanoparticles in the size range of 12-30 nm using this efficientBacillus flexusGPI-1 strain. Thus in the present study leading to development of an easy bioprocess for synthesis of GNPs of desired size and shape, has been reported and this green route of biosynthesis of GNPs is a simple, economically viable and an eco-friendly process. The use of gold nanoparticles in biomedical research like X-ray computed tomography and magnetic resonance imaging, cancer research, drug delivery applications.