bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Malaise trap spacing on species richness and composition of terrestrial arthropod bulk samples
Authors: Steinke D , Braukmann TWA , Manerus L , Woodhouse A , Elbrecht V 
Published: October 2020

AbstractThe Malaise trap has gained popularity for assessing diverse terrestrial arthropod communities because it collects large samples with modest effort. A number of factors that influence collection efficiency, placement being one of them. For instance, when designing larger biotic surveys using arrays of Malaise traps we need to know the optimal distance between individual traps that maximises observable species richness and community composition. We examined the influence of spacing between Malaise traps by metabarcoding samples from two field experiments at a site in Waterloo, Ontario, Canada. For one experiment, we used two trap pairs deployed at weekly increasing distance (3m increments from 3 to 27 m). The second experiment involved a total of 10 traps set up in a row at 3m distance intervals for three consecutive weeks.Results show that community similarity of samples decreases over distance between traps. The amount of species shared between trap pairs shows drops considerably at about 15m trap-to-trap distance. This change can be observed across all major taxonomic groups and for two different habitat types (grassland and forest). Large numbers of OTUs found only once within samples cause rather large dissimilarity between distance pairs even at close proximity. This could be caused by a large number of transient species from adjacent habitat which arrive at the trap through passive transport, as well as capture of rare taxa, which end up in different traps by chance.
REC protein family expansion by the emergence of a new signaling pathway
Authors: Garber Megan E. , Frank Vered , Kazakov Alexey E. , Incha Matthew R. , Nava Alberto A. , Zhang Hanqiao , Keasling Jay D. , Rajeev Lara , Mukhopadhyay Aindrila 
Published: October 2020

AbstractThis report presents multi-genomes and experimental evidence that REC protein family expansion occurs when the emergence of new pathways give rise to functional discordance. Specificity between REC-domain containing response regulators with paired histidine kinases are under negative purifying selection, constrained by the presence of other bacterial two-component systems signaling cascades that share sequence and structural identity. Presuming that the two-component systems can evolve by neutral drift when these constraints are relaxed, how might the REC protein family expand when constraints remain intact? Using an unsupervised machine learning approach to observe the sequence landscape of REC domains across long phylogenetic distances, we find that within-gene-recombination, a subcategory of gene conversion, switched the effector domain, and consequently the regulatory context of a duplicated response regulator from transcriptional regulation by σ54 to σ70. We determined that the recombined response regulator diverged from its parent by positive episodic diversifying selection, giving rise to two new residues. Functional experiments of the parent of recombined response regulators in our model system,Pseudomonas putidaKT2440, revealed that the parent and recombined response regulators sense and respond to carboxylic acids and that the two new residues in the recombined regulator form a new interaction interface and prevent crosstalk. Overall, our study finds genetic perturbations can create conditions of functional discordance, whereby the REC protein family can evolve by positive diversifying selection.
Early changes in synaptic and intrinsic properties of dentate gyrus granule cells in a mouse model of Alzheimer’s disease neuropathology and atypical effects of the cholinergic antagonist atropine
Authors: Alcantara-Gonzalez David , Chartampila Elissavet , Scharfman Helen E 
Published: October 2020

ABSTRACTIt has been reported that hyperexcitability occurs in a subset of patients with Alzheimer’s disease (AD) and hyperexcitability could contribute to the disease. Several studies have suggested that the hippocampal dentate gyrus (DG) may be an important area where hyperexcitability occurs. Therefore, we tested the hypothesis that the principal DG cell type, granule cells (GCs), would exhibit changes at the single-cell level which would be consistent with hyperexcitability and might help explain it. We used the Tg2576 mouse, where it has been shown that hyperexcitability is robust at 2-3 months of age. GCs from 2-3-month-old Tg2576 mice were compared to age-matched wild type (WT) mice. Effects of muscarinic cholinergic antagonism were tested because previously we found that Tg2576 mice exhibited hyperexcitabilityin vivothat was reduced by the muscarinic cholinergic antagonist atropine, counter to the dogma that in AD one needs to boost cholinergic function. The results showed that GCs from Tg2576 mice exhibited increased frequency of spontaneous excitatory postsynaptic potentials/currents (sEPSP/Cs) and reduced frequency of spontaneous inhibitory synaptic events (sIPSCs) relative to WT, increasing the excitation:inhibition (E:I) ratio. There was an inward glutamatergic current that we defined here as a novel synaptic current (nsC) in Tg2576 mice because it was very weak in WT mice. Although not usually measured, intrinsic properties were distinct in Tg2576 GCs relative to WT. In summary, GCs of the Tg2576 mouse exhibit early electrophysiological alterations that are consistent with increased synaptic excitation, reduced inhibition, and muscarinic cholinergic dysregulation. The data support previous suggestions that the DG and cholinergic system contribute to hyperexcitability early in life in AD mouse models.HIGHLIGHTSGranule cells (GCs) in young Tg2576 mice had abnormal synaptic activity.Young Tg2576 GCs had increased excitatory and reduced inhibitory synaptic activity.GC intrinsic properties were altered in young Tg2576 mice.Muscarinic cholinergic regulation of GCs was altered in young Tg2576 mice.Atropine led to a novel spontaneous inward current that was very strong in Tg2576 GCs.
Improved protein model quality assessment by integrating sequential and pairwise features using deep learning
Authors: Jing Xiaoyang , Xu Jinbo 
Published: October 2020

AbstractMotivationAccurately estimating protein model quality in the absence of experimental structure is not only important for model evaluation and selection, but also useful for model refinement. Progress has been steadily made by introducing new features and algorithms (especially deep neural networks), but accuracy of quality assessment (QA) is still not very satisfactory, especially local QA on hard protein targets.ResultsWe propose a new single-model-based QA method ResNetQA for both local and global quality assessment. Our method predicts model quality by integrating sequential and pairwise features using a deep neural network composed of both 1D and 2D convolutional residual neural networks (ResNet). The 2D ResNet module extracts useful information from pairwise features such as model-derived distance maps, co-evolution information and predicted distance potential. The 1D ResNet is used to predict local (global) model quality from sequential features and pooled pairwise information generated by 2D ResNet. Tested on the CASP12 and CASP13 datasets, our experimental results show that our method greatly outperforms existing state-of-the-art methods. Our ablation studies indicate that the 2D ResNet module and pairwise features play an important role in improving model quality assessment.Availability and Implementationhttps://github.com/AndersJing/ResNetQAContactjinboxu@gmail.com
Nonlinear Reconfiguration of Network Edges, Topology and Information Content During an Artifical Learning Task
Authors: Shine James M. , Li Mike , Koyejo Oluwasanmi , Fulcher Ben , Lizier Joseph T. 
Published: October 2020

AbstractNetwork neuroscience has yielded crucial insights into the systems-level organisation of the brain, however the indirect nature of neuroimaging recordings has rendered the discovery of generative mechanisms for a given function inherently challenging. In parallel, neural network machine-learning models have exhibited breakthrough performance in tackling a range of complex problems, however the principles that govern learning-induced modifications to network structure remain poorly understood, in part due to a lack of analytic tools to quantify the dynamics of network structure. While the question of how network reconfiguration supports learning is mirrored in machine learning and network neuroscience, the different contexts of these fields provides a timely opportunity to bring them together synergistically to investigate the problem. Here we combine these two approaches to reveal connections between the brain’s network structure and the emerging network structure of an artificial neural network. Specifically, we train a shallow, feedforward neural network to classify handwritten digits and then used a combination of systems neuroscience and information theoretic tools to perform ‘virtual brain analytics’ on the resultant edge weights and activity patterns of each node. We identify three distinct phases of network reconfiguration across learning, each of which are characterised by unique topological and information-theoretic signatures. Each phase involves aligning the connections of the neural network with patterns of information contained in the input dataset or preceding layers (as relevant). We also observe a process of low-dimensional category separation in the network as a function of learning. Our results offer a systems-level perspective of how artificial neural networks function – in terms of multi-stage reorganization of edge weights and activity patterns to effectively exploit the information content of input data during edge-weight training – while simultaneously enriching our understanding of the methods used by systems neuroscience.
Interactions between seasonal human coronaviruses and implications for the SARS-CoV-2 pandemic: A retrospective study in Stockholm, Sweden, 2009-2020
Authors: Dyrdak Robert , Hodcroft Emma B. , Wahlund Martina , Neher Richard A. , Albert Jan 
Published: October 2020

AbstractObjectivesThe four seasonal coronaviruses 229E, NL63, OC43, and HKU1 are frequent causes of respiratory infections and show annual and seasonal variation. Increased understanding about these patterns could be informative about the epidemiology of SARS-CoV-2.MethodsResults from PCR diagnostics for the seasonal coronaviruses, and other respiratory viruses, were obtained for 55,190 clinical samples analysed at the Karolinska University Hospital, Stockholm, Sweden, between 14 September 2009 and 2 April 2020.ResultsSeasonal coronaviruses were detected in 2,130 samples (3.9%) and constituted 8.1% of all virus detections. OC43 was most commonly detected (28.4% of detections), followed by NL63 (24.0%), HKU1 (17.6%), and 229E (15.3%). The overall fraction of positive samples was similar between seasons, but at species level there were distinct biennial alternating peak seasons for the Alphacoronaviruses, 229E and NL63, and the Betacoronaviruses, OC43 and HKU1, respectively. The Betacoronaviruses peaked earlier in the winter season (Dec-Jan) than the Alphacoronaviruses (Feb-Mar). Coronaviruses were detected across all ages, but diagnostics were more frequently requested for paediatric patients than adults and the elderly. OC43 and 229E incidence was relatively constant across age strata, while that of NL63 and HKU1 decreased with age.ConclusionsBoth the Alphacoronaviruses and Betacoronaviruses showed alternating biennial winter incidence peaks, which suggests some type of immune mediated interaction. Symptomatic reinfections in adults and the elderly appear relatively common. Both findings may be of relevance for the epidemiology of SARS-CoV-2.
COVID-19 Pandemic in University Hospital: Is There an Effect on The Medical Interns?
Authors: Lim WeiHonn , Teoh Li Ying , Seevalingam Kanesh Kumaran A/L , Kuppusamy Shanggar 
Published: October 2020

AbstractIntroductionCoronavirus Disease 2019 (COVID-19) pandemic has disrupted the current healthcare system and carries a major impact to the healthcare workers (HCW). University Malaya Medical Centre (UMMC) has been selected as one of the centres in managing COVID-19 cases in Malaysia. Many HCW including the medical interns, are directly or indirectly involved in the management.MethodsThis is a cross-sectional, pilot study to determine the impact of the pandemic on UMMC medical interns. A survey which comprises 37-items was used. Data are analysed by Ordinal Logistic Regression Analysis.ResultsOur study shows that medical interns are tired (p = 0.014), starving (p = 0.004), have inadequate exercises (p = 0.004) and burdened with heavy workload (p=0.023) during pandemic period. Many are depressed (p = 0.043), scared to work (p = 0.03), and worried of getting infected (p < 0.05). Some quarrel with their colleagues (p < 0.05), losing contact with friends (p = 0.022) and feel that it will be beneficial to have a peer support group (p = 0.027).ConclusionIn summary, the impact of COVID-19 amongst medical interns is significant and their overall well-being should be protected without jeopardising their training.
Studying bone marrow-derived macrophages needs to consider the influence of cells apart from macrophage, especially the selection of markers
Authors: Chu Chenyu , Rung Shengan , Wang Yufei , Qu Yili , Man Yi 
Published: October 2020

AbstractCulturing macrophage in vitro is an important means to understand its reaction towards co-culture substances. However, the source of macrophages can be either purchased from specific cell line or extracted from bone marrow as differentiated macrophages. In order to assure the precision, when adopting extracted primary cell, screening in advance will be prominent before any processes to avoid results reserving that of non-macrophages. Here, we perform single-cell sequencing on open wound of skin in mice and focusing on the secreted proteins and surface markers related to traditional macrophage phenotypes (M1/M2) to ensure the importance of screening. The expression of CAMP when macrophages fight against candida albicans is another target to see its relationship with current classification. And results showed that identifying its phenotype without screening macrophages will far from the exact situation, and the expression of CAMP cannot be carried out by the traditional M1 and M2 macrophage. Thus, determining phenotype of macrophages based on function would be a promising way.
A test of altitude-related variation in aerobic metabolism of Andean birds
Authors: Gutierrez-Pinto Natalia , Londoño Gustavo A. , Chappell Mark A. , Storz Jay F. 
Published: October 2020

AbstractEndotherms at high altitude face the combined challenges of cold and hypoxia. Cold increases thermoregulatory costs, and hypoxia may limit both thermogenesis and aerobic exercise capacity. Consequently, in comparisons between closely related highland and lowland taxa, we might expect to observe consistent differences in basal metabolism (BMR), maximal metabolism (MMR), and aerobic scope. Broad-scale comparative studies of birds reveal no association between BMR and native elevation, and altitude effects on MMR have not been investigated. We tested for altitude-related variation in aerobic metabolism in 10 Andean passerines representing five pairs of closely related species with contrasting elevational ranges. Mass-corrected BMR and MMR were significantly higher in most highland species relative to their lowland counterparts, but there was no uniform elevational trend across all pairs of species.Summary statementWe tested for altitude-related variation in aerobic metabolism in species pairs with contrasting elevational ranges. Metabolic rates were significantly higher in most highland species but there was no uniform elevational trend.
Production of the infant formula ingredient 1,3-olein-2-palmitin in Arabidopsis seeds
Authors: van Erp Harrie , Bryant Fiona M , Martin-Moreno Jose , Eastmond Peter J 
Published: October 2020

ABSTRACTIn human milk fat, palmitic acid (16:0) is esterified to the middle (sn-2 or β) position on the glycerol backbone and oleic acid (18:1) predominantly to the outer positions, giving the triacylglycerol (TG) a distinctive stereoisomeric structure that is believed to assist nutrient absorption in the infant gut. However, the fat used in most infant formulas is derived from plants, which preferentially esterify 16:0 to the outer positions. We have previously showed that the metabolism of the model oilseedArabidopsis thalianacan be engineered to incorporate 16:0 into the middle position of TG. However, the fatty acyl composition of Arabidopsis seed TG does not mimic human milk, which is rich in both 16:0 and 18:1 and is defined by the high abundance of the TG molecular species 1,3-olein-2-palmitin (OPO). Here we have constructed an Arabidopsisfatty acid biosynthesis 1-1 fatty acid desaturase 2 fatty acid elongase 1mutant with around 20% 16:0 and ~70% 18:1 in its seeds and we have engineered it to esterify more than 80% of the 16:0 to the middle position of TG, using heterologous expression of the human lysophosphatidic acid acyltransferase isoform AGPAT1, combined with suppression of LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE 2 and PHOSPHATIDYLCHOLINE:DIACYLGLYCEROL CHOLINEPHOSPHOTRANSFERASE. Our data suggest that oilseeds can be engineered to produce TG that is rich in OPO, which is an important structured fat ingredient used in infant formulas.
Molecular Parallelisms and Divergences Between Human and Canine Cancers Would a dog be an appropriate experimental model for human cancers?
Authors: Ambreen Sadaf , Guanhan Li , Zhao Binbin , Bao Gang , Song Yiwen , Lin Degui , Wu Dafei , Hou Yali , Lu Xuemei 
Published: October 2020

AbstractCanine mammary cancer is poorly characterized at the genomic level. Dog really can be an appropriate experimental model for human cancers from the genomic and evolutionary perspective or not? Here, we perform a cross-species cancer genomics analysis, independent evolution of cancer from normal tissues, which provide us an excellent opportunity to address an evolutionary perspective of cancer. As, evolutionary theories are critical for understanding tumorigenesis at the level of species as well as at the level of cells and tissues, for the development of effective therapies. Analysis of canine mammary cancer reveals a diversity of histological types as compare to human breast cancer. Our systematic analysis of 24 canine mammary tumors with whole-genome sequences, reveals 185 protein-coding cancer genes carried exonic mutations. Cross-species comparative analysis of 1080 human breast cancers identifies higher median mutation frequency in human breast cancer and canine mammary cancer shows lower across exonic regions (2.67 and 0.187 average no. of mutations per tumor per megabase (Mb), respectively). A comparison of somatic mutations in thePIK3CAgene, reveals common recurrence of the conserved mutations, in both species. However, the Ka/Ks ratio in the humanPIK3CAgene 2.37 is higher and 1.43 in dogs is lower. To address the mutation accumulation and antagonistic pleiotropy theory, we investigated Ka/Ks value 237 aging-related genes from human and canine, the aging-related genes do not show selection in canine mammary cancer. It demonstrates new aspects of cancer genes that are evolving in different species instantaneously. These findings may suggest, the same organs in different mammals impose different selective pressures on the same set of genes in cancer. In both species, some genes may experience strong selective pressures, but do not converge genetically or the conserved genes do not show the same selection pressure in both species. However, human breast cancer shows transcriptomic similarity with canine mammary carcinoma but the other subtypes are quite different. We found canine mammary tumor can be used as a model for inter and intra-tumor heterogeneity. These findings provided insight into mammary cancer across species and possessed potential clinical significance. Collectively, these studies suggest a convergence of some genetic changes in mammary cancer between species but also distinctly different paths to tumorigenesis.
High Throughput RNA Sequencing of Germ-Free Mouse Retina Reveals Metabolic Pathways Involved in the Gut-Retina Axis
Authors: Nadeem Urooba , Xie Bingqing , Movahedan Asadolah , D’Souza Mark , Barba Hugo , Deng Nini , Leone Vanessa A. , Chang Eugene , Sulakhe Dinanath , Skondra Dimitra 
Published: October 2020

AbstractBackground and aimsConnections between the gut microbiome and retinal diseases such as age-related macular degeneration (AMD), diabetic retinopathy (DR), retinopathy of prematurity (ROP), and primary open-angle glaucoma (POAG) are recently being established. Communication between the gut microbiome and retina, referred to as the gut-retina axis, has been proposed; however, the biologic pathways and mediators involved in the interactions have not yet been elucidated. Using high-throughput RNA sequencing (RNA-seq) of whole retinas, we compare the retinal transcriptome from germ-free (GF) and specific pathogen-free (SPF) mice to investigate the effects of the gut-microbiome on both retinal gene expression and biologic pathways.MethodsRNA was extracted from whole retinas of GF and SPF mice (four animals per group) and cDNA libraries were created. RNA-seq was performed on NovaSEQ6000 using the paired-end method. After preprocessing the RNA-seq data, gene expression value was calculated by count per million (CPM). The differentially expressed genes (DEGs) were identified with the limma package from Bioconductor on the expression data. Functional enrichment and protein-protein interaction STRING protein-protein association network analyses were created for the differentially expressed genes (DEGs).ResultsRNA-sequencing reveals a cohort of 396 DEGs, of which, 173 are upregulated and 223 are downregulated in GF mouse retina. Enrichment analysis reveals that the DEGs are involved in glucocorticoid effects, transcription factor binding, cytoskeletal stability, lipid metabolism, and mitogen-activated protein kinase (MAPK). Multiple biologic pathways, including obesity/metabolic syndrome, longevity, insulin-like growth factor (IGF) signaling pathway, vascular endothelial growth factor (VEGF), hypoxia-inducible factor(HIF)-1 transcription pathway, and 5’ AMP-activated protein kinase(AMPK) signaling pathway are affected in the GF retinas. PPARG1a (PGC1a) gene is involved in 13 of the 35 significantly modulated pathways. Proteins with the greatest number of interactions in the PPI are E1A binding protein P300(EP300), forkhead box O3(FOXO3), and PGC1a.ConclusionsTo our knowledge, this is the first study demonstrating the involvement of the gut microbiome in driving the retinal transcriptome, providing evidence for the presence of a gut-retina axis. Future studies are needed to define the precise role of the gut-retina axis in the pathogenesis of retinal diseases.