bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isoproterenol-induced Cardiac Dysfunction in Male and Female C57Bl/6 Mice
Authors: Grant Marianne K. O. , Abdelgawad Ibrahim Y. , Lewis Christine A. , Seelig Davis , Zordoky Beshay N. 
Published: April 2020

ABSTRACTSex-related differences in cardiovascular diseases are complex and context-dependent. The objective of this work was to comprehensively determine key sex differences in the response to acute and chronic adrenergic stimulation in C57Bl/6 mice. Cardiac function was assessed by trans-thoracic echocardiography before and after acute adrenergic stimulation (a single sub-cutaneous dose of isoproterenol 10 mg/kg) in male and female C57Bl/6 mice. Thereafter, chronic adrenergic stimulation was achieved by sub-cutaneous injections of isoproterenol 10 mg/kg/day for 14 days in male and female mice. Cardiac function and morphometry were assessed by trans-thoracic echocardiography on the 15thday. Thereafter, the mice were euthanized and the hearts were collected. Histopathological analysis of myocardial tissue was performed after staining with hematoxylin & eosin, trichrome, and MAC-2 antibody. Gene expression of remodeling and fibrotic markers was assessed by real-time PCR. Cardiac function and morphometry were also measured before and after isoproterenol 10 mg/kg/day for 14 days in groups of gonadectomized male and female mice and sham-operated controls. In the current work, there were no statistically significant differences in key echocardiographic parameters between male and female C57Bl/6 mice in response to acute adrenergic stimulation. After chronic adrenergic stimulation, there was similar degree of cardiac dysfunction, cardiac hypertrophy, and myocardial fibrosis in male and female mice. Similarly, chronic isoproterenol administration induced hypertrophic and fibrotic genes in hearts of male and female mice to the same extent. Intriguingly, gonadectomy of male and female mice did not have a significant impact on isoproterenol-induced cardiac dysfunction as compared to sham-operated animals. The current work demonstrated lack of significant sex-related differences in isoproterenol-induced cardiac hypertrophy, dysfunction, and fibrosis in C57Bl/6 mice. This study suggests that female sex may not be sufficient to protect the heart against a severe pathologic stimulus and underscores the notion that sexual dimorphism in cardiovascular diseases is highly model-dependent.
Higher vascularity at infiltrated peripheral edema differentiates proneural glioblastoma subtype
Authors: Chelebian Eduard , Fuster-Garcia Elies , del Mar Álvarez-Torres María , Juan-Albarracín Javier , García-Gómez Juan M. 
Published: April 2020

ABSTRACTBACKGROUND AND PURPOSEGenetic classifications are crucial for understanding the heterogeneity of glioblastoma. Recently, MR perfusion imaging techniques have demonstrated their ability to determine molecular alterations. In this work, we investigated whether perfusion markers within infiltrated peripheral edema were associated with proneural, mesenchymal, classical and neural subtypes.MATERIALS AND METHODSONCOhabitats open web service was used to obtain the cerebral blood volume at the infiltrated peripheral edema for MRI studies of 50 glioblastoma patients from The Cancer Imaging Archive: TCGA-GBM. ANOVA and Kruskal-Wallis tests were carried out in order to assess the association between vascular features and the subtypes. For assessing specific differences, Mann-Whitney U-test was conducted. Finally, the association of overall survival with molecular and vascular features was assessed using univariate and multivariate Cox models.RESULTSANOVA and Kruskal-Wallis tests for the maximum cerebral blood volume at the infiltrated peripheral edema between the four subclasses yielded false discovery rate corrected p-values of <0.001 and 0.02, respectively. This vascular feature was significantly higher (p=0.0043) in proneural patients compared to the rest of the subtypes while conducting Mann-Whitney U-test. The multivariate Cox model pointed to redundant information provided by vascular features at the peripheral edema and proneural subtype when analyzing overall survival.CONCLUSIONSHigher relative cerebral blood volume at infiltrated peripheral edema is associated with proneural glioblastoma subtype suggesting underlying vascular behavior related to molecular composition in that area.
Detecting turnover among complex communities using null models: A case study with sky-island haemosporidian parasites
Authors: Barrow Lisa N. , Bauernfeind Selina M. , Cruz Paxton A. , Williamson Jessie L. , Wiley Daniele L. , Ford John E. , Baumann Matthew J. , Brady Serina S. , Chavez Andrea N. , Gadek Chauncey R. , Galen Spencer C. , Johnson Andrew B. , Mapel Xena M. , Marroquin-Flores Rosario A. , Martinez Taylor E. , McCullough Jenna M. , McLaughlin Jade E. , Witt Christopher C. 
Published: April 2020

AbstractTurnover in species composition between sites, or beta diversity, is a critical component of species diversity that is typically influenced by geography, environment, and biotic interactions. Quantifying turnover is particularly challenging, however, in multi-host, multi-parasite assemblages where undersampling is unavoidable, resulting in inflated estimates of turnover and uncertainty about its spatial scale. We developed and implemented a framework using null models to test for community turnover in avian haemosporidian communities of three sky islands in the southwestern United States. We screened 776 birds for haemosporidian parasites from three genera (Parahaemoproteus, Plasmodium, andLeucocytozoon) by amplifying and sequencing a mitochondrial DNA barcode. We detected infections in 280 birds (36.1%), sequenced 357 infections, and found a total of 99 parasite haplotypes. When compared to communities simulated from a regional pool, we observed more unique, single-mountain haplotypes and fewer haplotypes shared among three mountain ranges than expected, indicating that haemosporidian communities differ to some degree among adjacent mountain ranges. These results were robust even after pruning datasets to include only identical sets of host species, and they were consistent for two of the three haemosporidian genera. The two more distant mountain ranges were more similar to each other than the one located centrally, suggesting that the differences we detected were due to stochastic colonization-extirpation dynamics. These results demonstrate that avian haemosporidian communities of temperate-zone forests differ on relatively fine spatial scales associated with adjacent sky-islands. Null models are essential tools for detecting turnover in complex, undersampled, and poorly known systems.
Exploiting Electrophysiological Measures of Semantic Processing for Auditory Attention Decoding
Authors: Dijkstra Karen , Desain Peter , Farquhar Jason 
Published: April 2020

ABSTRACTIn Auditory Attention Decoding, a user’s electrophysiological brain responses to certain features of speech are modelled and subsequently used to distinguish attended from unattended speech in multi-speaker contexts. Such approaches are frequently based on acoustic features of speech, such as the auditory envelope. A recent paper shows that the brain’s response to a semantic description (i.e., semantic dissimilarity) of narrative speech can also be modelled using such an approach. Here we use the (publicly available) data accompanying that study, in order to investigate whether combining this semantic dissimilarity feature with an auditory envelope approach improves decoding performance over using the envelope alone. We analyse data from their ‘Cocktail Party’ experiment in which 33 subjects attended to one of two simultaneously presented audiobook narrations, for 30 1-minute fragments. We find that the addition of the dissimilarity feature to an envelope-based approach significantly increases accuracy, though the increase is marginal (85.4% to 86.6%). However, we subsequently show that this dissimilarity feature, in which the degree of dissimilarity of the current word with regard to the previous context is tagged to the onsets of each content word, can be replaced with a binary content-word-onset feature, without significantly affecting the results (i.e., modelled responses or accuracy), putting in question the added value of the dissimilarity information for the approach introduced in this recent paper.
Genotypic characterization of the U.S. peanut core collection
Authors: Otyama Paul I. , Kulkarni Roshan , Chamberlin Kelly , Ozias-Akins Peggy , Chu Ye , Lincoln Lori M. , MacDonald Gregory E. , Anglin Noelle L. , Dash Sudhansu , Bertioli David J. , Fernández-Baca David , Graham Michelle A. , Cannon Steven B. , Cannon Ethalinda K.S. 
Published: April 2020

AbstractCultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a core collection on the basis of phenotype and country of origin. The present study reports genotyping results for the entire available core collection. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of 253 accessions was replicated, using between two and five seeds per accession, to assess heterogeneity within these accessions. the genotypic diversity of the core is mostly captured in five genotypic clusters, which have some correspondence with botanical variety and market type. There is little genetic clustering by country of origin, reflecting peanut’s rapid global dispersion in the 18th and 19th centuries. A genetic cluster associated with thehypogaea/aequatoriana/peruvianavarieties, with accessions coming primarily from Bolivia, Peru, and Ecuador, is consistent with these having been the earliest landraces. The genetics, phenotypic characteristics, and biogeography are all consistent with previous reports of tetraploid peanut originating in Southeast Bolivia. Analysis of the genotype data indicates an early genetic radiation, followed by regional distribution of major genetic classes through South America, and then a global dissemination that retains much of the early genetic diversity in peanut. Comparison of the genotypic data relative to alleles from the diploid progenitors also indicates that subgenome exchanges, both large and small, have been major contributors to the genetic diversity in peanut.All data is available at the National Ag Library:https://doi.org/10.15482/USDA.ADC/1518508and at PeanutBase:https://peanutbase.org/data/public/Arachis_hypogaea/mixed.esm.KNWV
Local climate and habitat continuity interact to alter contemporary dispersal potential
Authors: Sullivan Lauren L. , Portlas Zoe M. , Hamilton Jill A. 
Published: April 2020

AbstractUnderstanding the evolution of dispersal under changing global environments is essential to predicting a species ability to track shifting ecological niches. Two important, but anthropogenically altered, sources of selection on dispersal are climate and habitat continuity. Despite the likelihood these global drivers of selection act simultaneously on plant populations, their combined effects on dispersal are rarely examined. To understand the interactive effect of climate and habitat continuity on dispersal potential, we study Geum triflorum - a perennial grassland species that spans a wide range of environments, including both continuous prairie and isolated alvar habitats. We explore how the local climate of the growing season and habitat continuity (continuous vs isolated) interact to alter dispersal potential. We find a consistent interactive effect of local climate and habitat continuity on dispersal potential. Across continuous prairie populations, an increased number of growing degree days favors traits that increase dispersal potential. However, for isolated alvar populations, dispersal potential tends to decrease as the number of growing degree days increase. Our findings suggest that under continued warming, populations in continuous habitats will benefit from increased gene flow, while isolated populations will become increasingly segregated, with reduced potential to track shifting fitness optima.
Integration host factor bends and bridges DNA in a multiplicity of binding modes with varying specificity
Authors: Yoshua Samuel B. , Watson George D. , Howard Jamieson A. L. , Velasco-Berrelleza Victor , Leake Mark C. , Noy Agnes 
Published: April 2020

AbstractNucleoid-associated proteins (NAPs) are crucial in organizing prokaryotic DNA and regulating genes. Vital to these activities are complex nucleoprotein structures, however, how these form remains unclear. Integration host factor (IHF) is an Escherichia coli NAP that creates very sharp bends in DNA at sequences relevant to several functions including transcription and recombination, and is also responsible for general DNA compaction when bound non-specifically. We show that IHF–DNA structural multimodality is more elaborate than previously thought, and provide insights into how this drives mechanical switching towards strongly bent DNA. Using single-molecule atomic force microscopy and atomic molecular dynamics simulations we find three binding modes in roughly equal proportions: “associated” (73° of DNA bend), “half-wrapped” (107°) and “fully-wrapped” (147°), only the latter occurring with sequence specificity. We show IHF bridges two DNA double helices through non-specific recognition that gives IHF a stoichiometry greater than one and enables DNA mesh assembly. We observe that IHF-DNA structural multiplicity is driven through non-specific electrostatic interactions that we anticipate to be a general NAP feature for physical organization of chromosomes.
The beginning of the end: a chromosomal assembly of the New World malaria mosquito ends with a novel telomere
Authors: Compton Austin , Liang Jiangtao , Chen Chujia , Lukyanchikova Varvara , Qi Yumin , Potters Mark , Settlage Robert , Miller Dustin , Deschamps Stephane , Mao Chunhong , Llaca Victor , Sharakhov Igor V. , Tu Zhijian 
Published: April 2020

ABSTRACTChromosome level assemblies are accumulating in various taxonomic groups including mosquitoes. However, even in the few reference-quality mosquito assemblies, a significant portion of the heterochromatic regions including telomeres remain unresolved. Here we produce ade novoassembly of the New World malaria mosquito,Anopheles albimanusby integrating Oxford Nanopore sequencing, Illumina, Hi-C and optical mapping. This 172.6 Mbps female assembly, which we call AalbS3, is obtained by scaffolding polished large contigs (contig N50=13.7 Mbps) into three chromosomes. All chromosome arms end with telomeric repeats, which is the first in mosquito assemblies and represents a significant step towards the completion of a genome assembly. These telomeres consist of tandem repeats of a novel 30-32 bp telomericrepeatunit (TRU) and are confirmed by analysing the termini of long reads and through both chromosomalin situhybridization and a Bal31 sensitivity assay. The AalbS3 assembly included previously uncharacterized centromeric and rDNA clusters and more than doubled the content of transposable elements and other repetitive sequences. This telomere-to-telomere assembly, although still containing gaps, represents a significant step towards resolving biologically important but previously hidden genomic components. The comparison of different scaffolding methods will also inform future efforts to obtain reference-quality genomes for other mosquito species.100-word Article SummaryWe report AalbS3, a telomere-to-telomere assembly of theAnopheles albimanusgenome produced by integrating advancing technologies including Oxford Nanopore and Bionano optical mapping. AalbS3 features much of the difficult-to-assemble genomic ‘dark matters’ including previously missed transposons, centromeres and rDNA clusters. We describe novel telomeric repeats that are confirmed by analysis of long reads and by telomere hybridization assays. This reference-quality assembly represents a significant step towards completing the genomic puzzle pieces and informs efforts to improve the assembly of other mosquito species. Future research into the relationship between telomere and mosquito life span may have significant implications to disease control.
Structured sampling of olfactory input by the fly mushroom body
Authors: Zheng Zhihao , Li Feng , Fisher Corey , Ali Iqbal J. , Sharifi Nadiya , Calle-Schuler Steven , Hsu Joseph , Masoodpanah Najla , Kmecova Lucia , Kazimiers Tom , Perlman Eric , Nichols Matthew , Li Peter H. , Jain Viren , Bock Davi D. 
Published: April 2020

AbstractAssociative memory formation and recall in the adult fruit flyDrosophila melanogasteris subserved by the mushroom body (MB). Upon arrival in the MB, sensory information undergoes a profound transformation. Olfactory projection neurons (PNs), the main MB input, exhibit broadly tuned, sustained, and stereotyped responses to odorants; in contrast, their postsynaptic targets in the MB, the Kenyon cells (KCs), are nonstereotyped, narrowly tuned, and only briefly responsive to odorants. Theory and experiment have suggested that this transformation is implemented by random connectivity between KCs and PNs. However, this hypothesis has been challenging to test, given the difficulty of mapping synaptic connections between large numbers of neurons to achieve a unified view of neuronal network structure. Here we used a recent whole-brain electron microscopy (EM) volume of the adult fruit fly to map large numbers of PN- to-KC connections at synaptic resolution. Comparison of the observed connectome to precisely defined null models revealed unexpected network structure, in which a subset of food-responsive PN types converge on individual downstream KCs more frequently than expected. The connectivity bias is consistent with the neurogeometry: axons of the overconvergent PNs tend to arborize near one another in the MB main calyx, making local KC dendrites more likely to receive input from those types. Computational modeling of the observed PN-to-KC network showed that input from the overconvergent PN types is better discriminated than input from other types. These results suggest an ‘associative fovea’ for olfaction, in that the MB is wired to better discriminate more frequently occurring and ethologically relevant combinations of food-related odors.
Metabolism modulates network synchrony in the aging brain
Authors: Weistuch Corey , Mujica-Parodi Lilianne R , Amgalan Anar , Dill Ken A 
Published: April 2020

AbstractBrain aging is associated with hypometabolism and associated global changes in functional connectivity. Using fMRI, we show that network synchrony, a collective property of brain activity, decreases with age. Applying quantitative methods from statistical physics, we provide a generative (Ising) model for these changes as a function of the average communication strength between brain regions. In particular, we find healthy brains to be poised at a critical point of this communication strength, enabling a balance between segregated (to functional domains) and integrated (between domains) patterns of synchrony. However, one characteristic of criticality is a high sensitivity to small changes. Thus, minute weakening of pairwise communication between regions, as seen in the aging brain, gives rise to qualitatively abrupt changes in synchrony. Finally, by experimentally modulating metabolic activity in younger adults, we show how metabolism alone–independent of other changes associated with aging–can provide a mechanism for global changes in synchrony.
Genomic convergence of locus-based GWAS meta-analysis identifies DDX11 as a novel Systemic Lupus Erythematosus gene
Authors: Saeed Mohammad , Ibáñez-Costa Alejandro , Patiño-Trives Alejandra María , Estevez Eduardo Collantes , Aguirre María Ángeles , López-Pedrera Chary 
Published: April 2020

AbstractGenome-wide association studies (GWAS) of systemic lupus erythematosus (SLE) explain only ∼15% of genetic risk, indicating genes of modest effect remain to be discovered. Association clustering methods such as OASIS are more apt at identifying modest genetic effects. 410 genes were mapped to previously identified OASIS GWAS SLE loci and investigated for expression in SLE GEO datasets. GSE50395 dataset from Cordoba was used for validation. Blood eQTL for significant SNPs in SLE loci and STRING for functional pathways of differentially expressed genes was used. Confirmatory qPCR on monocytes of 12 SLE patients and controls was performed. We identified 55 genes that were differentially expressed in at least 2 SLE GEO datasets with all probes directionally aligned.DDX11was downregulated in both GEO (P=3.60E-02) and Cordoba (P=8.02E-03) datasets and confirmed by qPCR (P=0.001). The most significant SNP, rs3741869 (P=3.2E-05) in OASIS locus 12p11.21, containingDDX11, was a cis-eQTL regulatingDDX11expression (P=8.62E-05).DDX11interacted with multiple genes includingSTAT1/STAT4. Genomic convergence with OASIS and multiple expression datasets identifies novel genes.DDX11, RNA helicase involved in genome stability, is repressed in SLE.Summary StatementMore than 100 genes for SLE have been identified but they explain only ∼15% of heritability. GWAS are challenged by risk genes of modest effect. Using locus-based GWAS mapping and multiple gene expression replications,DDX11was identified as a novel SLE gene.DDX11, repressed in SLE, may be used as a clinical diagnostic tool.
Light effects on circadian and homeostatic regulation: alertness increases independent of time awake
Authors: Lok R. , Woelders T. , van Koningsveld M.J. , Oberman K. , Fuhler S.G. , Beersma D.G.M. , Hut R.A. 
Published: April 2020

AbstractLight induced improvements in alertness are more prominent during night-time than during the day, indicating circadian regulation or wake duration related dependence. Relative contributions of both factors can be quantified using a forced desynchrony (FD) designs. Here we investigate alerting effects of light in a novel 4×18 hours FD protocol (5h sleep, 13h wake) under dim (6 mlux) and bright light (1159 mlux) conditions. Hourly saliva samples (melatonin and cortisol assessment) and 2-hourly test-sessions were used to assess effects of bright light on subjective and objective alertness (electroencephalography and performance). Results reveal (1) stable free-running cortisol rhythms with uniform phase progression under both light conditions, indicating that FD designs can be conducted under high intensity lighting, (2) subjective alerting effects of light depend on elapsed time awake, while (3) light consistently improves objective alertness independent of time awake. Three dimensional graphs reflecting light induced alertness improvements depending on wake duration related variation and circadian clock phase suggest that performance is improved during daytime, while subjective alertness remains unchanged. This suggests that light during office hours might be beneficial for performance, even though this may not be perceived as such.