bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unexpected termite inquilines in nests of Constrictotermes cyphergaster (Silvestri, 1901) (Blattodea: Isoptera)
Authors: Costa Diogo , Marins Alessandra , DeSouza Og 
Published: April 2019

AbstractThe heterospecific termite-termite cohabitation in a single termitarium, so called in-quilinism, is a common event whose basal mechanisms remain hypothetical. While some termite hosts have plenty of inquilines, others house only a few. Among these, Constrictotermes cyphergaster are frequently found cohabiting with a single obligate inquiline species but have been unknown to house any facultative inquilines. Here we present the first record of facultative inquilines (Embiratermes festivellus, Nasutitermes kemneri, Obitusitermes bacchanalis and Subulitermes) to this host, evidencing that this was unlikely to have happened fortuitously. In an attempt to pose hypotheses on the mechanisms behind such invasions, we explored likely connections between the settlement of obligate and facultative inquilines and nest wall’s physical traits. We found that nests bearing atypical external walls (moist, eroded, and partially covered by mosses) held higher richness of facultative inquilines than nests presenting walls void of such traits (χ2 = 8.3965, 1 df, n = 17, P = 0.0038). The presence of healthy host colonies in all nests, including the atypical ones, reinforces the hypothesis that the settlement of these facultative inquilines depends less on host colonies biotic status and more on abiotic features associated to the nest. In addition, the presence of obligate inquilines was not affected by the nest wall status (χ2 = 8.3965, 1 df, n = 17, P = 0.0038), implying that invasion by facultative and obligate inquilines in these nests would obey distinct restrictions. While warning that these hypotheses require further testing, we suggest that their understanding could shed light on the determinants of cohabitation not only in C. cyphergaster but in termites in general. cohabitation interspecific interaction nest invasion barriers
Solart: A Structure-Based Method To Predict Protein Solubility And Aggregation
Authors: Hou Q. , Kwasigroch J. M. , Rooman M. , Pucci F. 
Published: April 2019

ABSTRACTMotivationThe solubility of a protein is often decisive for its proper functioning. Lack of solubility is a major bottleneck in high-throughput structural genomic studies and in high-concentration protein production, and the formation of protein aggregates causes a wide variety of diseases. Since solubility measurements are time-consuming and expensive, there is a strong need for solubility prediction tools.ResultsWe have recently introduced solubility-dependent distance potentials that are able to unravel the role of residue-residue interactions in promoting or decreasing protein solubility. Here, we extended their construction by defining solubility-dependent potentials based on backbone torsion angles and solvent accessibility, and integrated them, together with other structure- and sequence-based features, into a random forest model trained on a set of E. coli proteins with experimental structures and solubility values. We thus obtained the SOLart protein solubility predictor, whose most informative features turned out to be folding free energy differences computed from our solubility-dependent statistical potentials. SOLart performances are very good, with a Pearson correlation coefficient between experimental and predicted solubility values of 0.7 both in the training dataset and on an independent set of S. Cerevisiae proteins. On test sets of modeled structures, only a limited drop in performance is observed. SOLart can thus be used with both high-resolution and low-resolution structures, and clearly outperforms state-of-art solubility predictors. It is available through a user-friendly webserver, which is easy to use by non-expert scientists.AvailabilityThe SOLart webserver is freely available at babylone.ulb.ac.be/SOLART/
Systematics, biogeography and diversification ofScytalopustapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds
Authors: Cadena Carlos Daniel , Cuervo Andrés M. , Céspedes Laura N. , Bravo Gustavo A. , Krabbe Niels , Schulenberg Thomas S. , Derryberry Graham E. , Silveira Luis Fabio , Derryberry Elizabeth P. , Brumfield Robb T. , Fjeldså Jon 
Published: April 2019

AbstractWe studied the phylogeny, biogeography and diversification of suboscine birds in the genusScytalopus(Rhinocryptidae), a widespread, speciose, and taxonomically challenging group of Neotropical birds. We analyzed nuclear (exons, regions flanking ultraconserved elements) and mitochondrial (ND2) DNA sequence data for a taxonomically and geographically comprehensive sample of specimens collected from Costa Rica to Patagonia and eastern Brazil. We found thatScytalopusis a monophyletic group sister toEugralla, and consists of three main clades roughly distributed in (1) the Southern Andes, (2) eastern Brazil, and (3) the Tropical Andes and Central America. The clades from the Southern Andes and Eastern Brazil are sister to each other. Despite their confusing overall uniformity in plumage coloration, body shape and overall appearance, rates of species accumulation through time inScytalopussince the origin of the clade in the Late Miocene are unusually high compared to those of other birds, suggesting rapid non-adaptive diversification in the group which we attribute to their limited dispersal abilities making them speciation-prone and their occurrence in a complex landscape with numerous barriers promoting allopatric differentiation. Divergence times among species and downturns in species accumulation rates in recent times suggest that most speciation events inScytalopuspredate climatic oscillations of the Pleistocene. Our analyses identified various cases of strong genetic structure within species and lack of monophyly of taxa, flagging populations which likely merit additional study to establish their taxonomic status. In particular, detailed analyses of species limits are due inS. parvirostris, S. latrans, S. speluncae, theS. atratuscomplex, and the Southern Andes clade.
Consistent bacterial responses to land use change across the tropics
Authors: Petersen Ian AB , Meyer Kyle M , Bohannan Brendan JM 
Published: April 2019

AbstractBacterial communities are a major component of global diversity and are intimately involved in most terrestrial biogeochemical processes. Despite their importance, we know far less about the response of bacteria to human-induced environmental change than we do about other organisms. Understanding the response of organisms to land use change is especially pressing for tropical rainforests, which are being altered at a higher rate than any other ecosystem. Here, we conduct a meta-analysis of studies performed in each of the major tropical rainforest regions to ask whether there are consistent responses of belowground bacterial communities to the conversion of tropical rainforest to agriculture. Remarkably, we find common responses despite wide variation across studies in the types of agriculture practiced and the research methodology used to study land use change. These responses include changes in the relative abundance of phyla, most notably decreases in Acidobacteria and Proteobacteria and increases in Actinobacteria, Chloroflexi and Firmicutes. We also find that alpha diversity (at the scale of single soil cores), consistently increases with ecosystem conversion. These consistent responses suggest that, while there is great diversity in agricultural practices across the tropics, common features such as the use of slash-and-burn tactics have the potential to alter bacterial community composition and diversity belowground.
Targeting Age-Related Differences in Brain and Cognition with Multimodal Imaging and Connectome Topography Profiling
Authors: Lowe Alexander J. , Paquola Casey , Vos de Wael Reinder , Girn Manesh , Lariviere Sara , Tavakol Shahin , Caldairou Benoit , Royer Jessica , Schrader Dewi V. , Bernasconi Andrea , Bernasconi Neda , Spreng R. Nathan , Bernhardt Boris C. 
Published: April 2019

I.AbstractAging is characterised by accumulation of structural and metabolic changes in the brain. Recent studies suggest transmodal brain networks are especially sensitive to aging, which, we hypothesise, may be due to their apical position in the cortical hierarchy. Studying an open-access healthy cohort (n=102, age range = 30-89 years) with MRI and Aβ PET data, we estimated age-related cortical thinning, hippocampal atrophy and Aβ deposition. In addition to carrying out surface-based morphological and metabolic mapping, we stratified effects along neocortical and hippocampal resting-state functional connectome gradients derived from independent datasets. The cortical gradient depicts an axis of functional differentiation from sensory-motor regions to transmodal regions, whereas the hippocampal gradient recapitulates its long-axis. While age-related thinning and increased Aβ deposition occurred across the entire cortical topography, increased Aβ deposition was especially pronounced towards higher-order transmodal regions. Age-related atrophy was greater towards the posterior end of the hippocampal long-axis. No significant effect of age on Aβ deposition in the hippocampus was observed. Imaging markers correlated with behavioural measures of fluid intelligence and episodic memory in a topography-specific manner. Our results strengthen existing evidence of structural and metabolic change in the aging brain and support the use of connectivity gradients as a compact framework to analyse and conceptualize brain-based biomarkers of aging.
xml2jupyter: Mapping parameters between XML and Jupyter widgets
Authors: Heiland Randy , Mishler Daniel , Zhang Tyler , Bower Eric , Macklin Paul 
Published: April 2019

AbstractJupyter Notebooks [4, 6] provide executable documents (in a variety of programming languages) that can be run in a web browser. When a notebook contains graphical widgets, it becomes an easy-to-use graphical user interface (GUI). Many scientific simulation packages use text-based configuration files to provide parameter values and run at the command line without a graphical interface. Manually editing these files to explore how different values affect a simulation can be burdensome for technical users, and impossible to use for those with other scientific backgrounds. xml2jupyter is a Python package that addresses these scientific bottlenecks. It provides a mapping between configuration files, formatted in the Extensible Markup Language (XML), and Jupyter widgets. Widgets are automatically generated from the XML file and these can, optionally, be incorporated into a larger GUI for a simulation package, and optionally hosted on cloud resources. Users modify parameter values via the widgets, and the values are written to the XML configuration file which is input to the simulation’s command-line interface. xml2jupyter has been tested using PhysiCell [1], an open source, agent-based simulator for biology, and it is being used by students for classroom and research projects. In addition, we use xml2jupyter to help create Jupyter GUIs for PhysiCell-related applications running on nanoHUB [5].
An integrative analysis of GWAS and intermediate molecular trait data reveals common molecular mechanisms supporting genetic similarity between seemingly unrelated complex traits
Authors: Gu Jialiang , Fuller Chris , Zheng Jiashun , Li Hao 
Published: April 2019

AbstractThe rapid accumulation of Genome Wide Association Studies (GWAS) and association studies of intermediate molecular traits provides new opportunities for comparative analysis of the genetic basis of complex human phenotypes. Using a newly developed statistical framework called Sherlock-II that integrates GWAS with eQTL (expression Quantitative Trait Loci) and metabolite-QTL data, we systematically analyzed 445 GWAS datasets, and identified 1371 significant gene-phenotype associations and 308 metabolites-phenotype associations (passing a Q value cutoff of 1/3). This integrative analysis allows us to translate SNP-phenotype associations into functionally informative gene-phenotype association profiles. Genetic similarity analyses based on these profiles clustered phenotypes into sub-trees that reveal both expected and unexpected relationships. We employed a statistical approach to delineate sets of functionally related genes that contribute to the similarity between their association profiles. This approach suggested common molecular mechanisms that connect the phenotypes in a subtree. For example, we found that fasting insulin, fasting glucose, breast cancer, prostate cancer, and lung cancer clustered into a subtree, and identified cyclic AMP/GMP signaling that connects breast cancer and insulin, NAPDH oxidase/ROS generation that connects the three cancers, and apoptosis that connects all five phenotypes. Our approach can be used to assess genetic similarity and suggest mechanistic connections between phenotypes. It has the potential to improve the diagnosis and treatment of a disease by mapping mechanistic insights from one phenotype onto others based on common molecular underpinnings.
Synergistic interactions of quercetin with antibiotics against biofilm associated clinical isolates ofPseudomonas aeruginosa in vitro
Authors: Vipin C. , Mujeeburahiman M. , Saptami K. , Arun A.B. , Rekha P.D. 
Published: April 2019

AbstractDevelopment of extreme resistance to multiple antibiotics is the major concern in infections due to biofilm formingPseudomonas aeruginosa.The existing antibiotics have become ineffective against biofilm associated infections and hence, in this study, the combinatorial efficacy of antibiotics with a quorum sensing inhibitor (quercetin) was tested against biofilm formingP. aeruginosaisolates. The effect of drug combinations was studied by the checkerboard method. The fractional inhibitory concentration index (FICI) was calculated for determining the synergistic effect. Additionally, biofilm cell viability, time-kill and live-dead assays were performed to study the combinatorial effect. MIC of quercetin against all theP. aeruginosastrains was 500 μg/mL. However, quercetin at 125 μg/mL showed synergistic effect with ½ × MIC or ¼ × MIC of all the antibiotics against all the strains. Quercetin (125 μg/mL) with ½ MIC of levofloxacin and tobramycin combinations were highly effective with ≥80% killing of biofilm associated cells. Increasing the concentration to 250 μg/mL with ½ × MIC antibiotics could completely inhibit the biofilm cell viability in quercetin combination with amikacin and tobramycin. The findings show that quercetin combinations can enhance the treatment outcome againstP. aeruginosainfection and this approach may reduce antibiotic overuse and selection pressure.Graphical abstract
Genome-wide analyses indirectly implicate miRNA regulatory mechanisms in Obsessive-compulsive Disorder psychopathology
Authors: McGregor NW , O’Connell KS ,   TS/ OCD PGC Workgroup, Davis L , Mathews CA , Lochner C , Stein DJ 
Published: April 2019

ABSTRACTBackgroundMiRNAs are small, noncoding RNAs possessing the potential to modulate gene expression upon binding to their target messenger RNA (mRNA) constructs, and are known to play a role in the pathogenesis of a range of psychiatric disorders. To date, little work has focused on the role of miRNAs in obsessive-compulsive disorder (OCD). The aim of this study was to assess the potential involvement of miRNAs in OCD psychopathology.MethodsThe most significant variants (p ≤ 1×10−4) from the Psychiatric Genomics Consortium (PGC) TS/OCD Workgroup OCD meta-analysis were selected and investigated using miRBASE, TargetScan and SNPnexus to determine whether they influence miRNA- mediated regulation in the clinical manifestation of OCD.ResultsTwo-hundred and forty SNPs were identified from the PGC OCD summarystatistics, of which none were found to directly alter miRNA-related gene regulation usingin silicoanalyses. Enrichment analyses identified several potential indirect miRNA-mediated targets associated with both increased (ITPR3: mir-124A) and decreased risk (GPR109A: mir-520A, and mir-525;CGNL1: mir-98 and mir-219).ConclusionmiRNA-mediated regulation was indirectly implicated in the psychopathology of OCD. Enrichment analyses implicates intracellular calcium and immune dysregulation in the clinical manifestation of the disorder and warrants further investigation of the role the immune system may play in the manifestation of disease.
Demonstration of a fast and easy sample-to-answer protocol forMycobacterium tuberculosisdiagnosis in point-of-care settings
Authors: Ali Nasir , Bello Graziele Lima , Rossetti Maria Lúcia Rosa , Costa Alexandre Dias Tavares , Krieger Marco Aurelio 
Published: April 2019

AbstractBackgroundTuberculosis (TB) is currently the ninth leading cause of death worldwide and the leading cause from a single infectious agent, ranking above HIV/AIDS. Point of care diagnosis is one of the diagnostic aspects in the health care system that might have the potential to mitigate this worldwide epidemic. Although several qPCR tests are available, most cannot be taken to the field. Therefore, their use in POC settings is limited. Smooth sample preparation and streamlined DNA extraction constitute the biggest challenges for this limitation.MethodsSeventeenM. tuberculosissamples which were already previously analyzed by GeneXpert or culture technique were subjected to our in-house protocol. Of these samples, ten were positive and seven negatives when tested by GeneXpert, while seven were positive and ten negatives when analyzed by culturing.ResultsHere we present a “proof of concept” protocol for sputum liquefaction and disinfection, followed by FTA card DNA extraction. The resulting DNA is rapidly amplified andMycobacterium tuberculosis(MTB) DNA is detected with the use of a portable qPCR instrument. Our protocol is able to linearly identify down to 2 CFU/mL of MTB, showing great sensitivity on artificial samples. The protocol was challenged with patient samples, and showed excellent agreement with the gold-standard molecular protocol, allowing the detection of 9/10 positive samples (90%, or 10% of false negatives) and 7/7 of the negative (100%, no false positives). When compared to culture, 7/7 culture-positive samples were also found positive (100%, no false negatives), while 2/10 culture-negative were found positive by the present method (20% of false positives).ConclusionThe proposed sample preparation protocol provides a rapid and easy procedure with a small number of reagents and steps, as well as minimal use of equipments, resulting in an easy-to-use tool forM. tuberculosisdiagnosis in POC settings.
Additive genetic variance for lifetime fitness and the capacity for adaptation in an annual plant
Authors: Kulbaba Mason W. , Sheth Seema N. , Pain Rachel E. , Eckhart Vince M. , Shaw Ruth G. 
Published: April 2019

AbstractThe immediate capacity for adaptation under current environmental conditions is directly proportional to the additive genetic variance for fitness, VA(W). Mean absolute fitness,, is predicted to change at the rate, according to Fisher’s Fundamental Theorem of Natural Selection. Despite ample research evaluating degree of local adaptation, direct assessment of VA(W) and the capacity for ongoing adaptation is exceedingly rare. We estimated VA(W) andin three pedigreed populations of annualChamaecrista fasciculata,over three years in the wild. Contrasting with common expectations, we found significant VA(W) in all populations and years, predicting increased mean fitness in subsequent generations (0.83 to 6.12 seeds per individual). Further, we detected two cases predicting “evolutionary rescue”, where selection on standing VA(W) was expected to increase fitness of declining populations (< 1.0) to levels consistent with population sustainability and growth. Within populations, interannual differences in genetic expression of fitness were striking. Significant genotype-by-year interactions reflected modest correlations between breeding values across years (allr< 0.490), indicating temporally variable selection at the genotypic level; that could contribute to maintaining VA(W). By directly estimating VA(W) and total lifetime, our study presents an experimental approach for studies of adaptive capacity in the wild.
Grain Protein Content QTLs Identified in a Durum × Wild Emmer Wheat Mapping Population Tested in Five Environments
Authors: Fatiukha Andrii , Lupo Itamar , Lidzbarsky Gabriel , Klymiuk Valentina , Korol Abraham B. , Pozniak Curtis , Fahima Tzion , Krugman Tamar 
Published: April 2019

AbstractWild emmer wheat (Triticum turgidumssp.dicoccoides, WEW) was shown to exhibit high grain protein content (GPC) and therefore, possess a great potential for improvement of cultivated wheat nutritional value. A recombinant inbred line (RIL) population derived from a cross betweenT. durumvar. Svevo and WEW acc. Y12-3 was used for construction of a high-density genetic map and genetic dissection of GPC. Genotyping of 208 F6RILs with 15K wheat SNP array yielded 4,166 polymorphic SNP markers, of which 1,510 were designated as skeleton markers. A total map length of 2,169 cM was obtained with an average distance of 1.5 cM between SNPs. A total of 12 GPC QTLs with LOD score range of 2.7-35.9, and PEV of 2.6-26.6% were identified under five environments. Major QTLs with favorable alleles from WEW were identified on chromosomes 4BS, 5AS, 6BS and 7BL. The QTL region on 6BS coincided with the physical position of the previously cloned QTL,Gpc-B1. Comparisons of the physical intervals of the GPC QTLs described here with the results previously reported in other durum×WEW RIL population led to the identification of four common and two homoeologous QTLs. Exploration of the large genetic variation within WEW accessions is a precondition for discovery of exotic beneficial alleles, as we have demonstrated here, by the identification of seven novel GPC QTLs. Therefore, our research emphasizes the importance of GPC QTL dissection in diverse WEW accessions as a source of novel alleles for improvement of GPC in cultivated wheat.Key messageGenetic dissection of GPC in tetraploid durum × WEW RIL population, based on high-density SNP genetic map, revealed 12 QTLs, with favorable WEW allele for 11 QTLs.