bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combinations of genes at the 16p11.2 and 22q11.2 CNVs contribute to neurobehavioral traits
Authors: Vysotskiy Mikhail ,   Autism Working Group of the Psychiatric Genomics Consortium,   Bipolar Disorder Working Group of the Psychiatric Genomics Consortium,   Schizophrenia Working Group of the Psychiatric Genomics Consortium, Weiss Lauren A 
Published: October 2022

AbstractThe 16p11.2 and 22q11.2 copy number variants (CNVs) are associated with neurobehavioral traits including autism spectrum disorder (ASD), schizophrenia, bipolar disorder, obesity, and intellectual disability. Identifying specific genes contributing to each disorder and dissecting the architecture of CNV-trait association has been difficult, inspiring hypotheses of more complex models, such as the effects of pairs of genes. We generated pairwise expression imputation models for CNV genes and then applied these models to GWAS for: ASD, bipolar disorder, schizophrenia, BMI (obesity), and IQ (intellectual disability). We compared the trait variance explained by pairs with the variance explained with single genes and with traditional interaction models. We also modeled polygene region-wide effects using summed ranks across all genes in the region. In all CNV-trait pairs except for bipolar disorder at 22q11.2, pairwise effects explain more variance than single genes, which was specific to the CNV region for all 16p11.2 traits and ASD at 22q11.2. We identified individual genes over-represented in top pairs that did not show single-gene signal. We also found that BMI and IQ have a significant association with a regionwide score. Genetic architecture differs by trait and region, but 9/10 CNV-trait combinations showed evidence for multigene contribution, and for most of these, the importance of combinatorial models appeared unique to CNV regions. Our findings suggest that mechanistic insights for CNV pathology may require combinational models.
Universal Amplicon Sequencing of North Imperial Valley Wetlands Microbiomes
Authors: Becker Scott , Graham Elaina , Sager Lindsay , Spreafico Roberto , McCarren Jay 
Published: October 2022

ABSTRACTDNA sequencing of complex microbial communities allows for the classification and quantification of thousands of distinct organisms in diverse environmental niches. We present a three domain “Universal Amplicon” (UA) method to simultaneously amplify DNA from the ribosomal small subunit locus from bacteria, archaea, and eukaryotes (and their organelles) using a single pair of amplification primers. We demonstrate the amenability of the UA to multiplexed Illumina library preparation and MiSeq-based sequencing. We validate the UA by sequencing a commercially available microbial community of known quantitative composition and through direct comparison to a shotgun metagenomics dataset. Following validation, we apply the UA to a time-course study of the wetlands of the Northern Imperial Valley in California and show substantial and variable microbial life in the Salton Sea and nearby waters. We demonstrate that the microbial ecology of the Salton Sea varies on at least a monthly basis and is distinct from the surrounding area. Finally, we contribute an open-source Shiny app for real-time analysis of complex metagenomic communities, with application to this study and far beyond.
Accurate measurement of inhibition and excitation in human motor pools during sensory stimulation
Authors: Soteropoulos Demetris S. , Del Vecchio Alessandro 
Published: October 2022

AbstractSurface electromyography (sEMG) is a pivotal approach in clinical and basic neurophysiology, allowing us to extract the summed activity of motor units in a given muscle. Due to the bipolar nature of the motor unit action potential, the sEMG is a non-linear representation of their underlying motor unit activity and therefore affected by signal cancellation. It is not clear how this cancellation influences evoked responses in sEMG. The aim of our study was to characterise how representative an evoked sEMG response was to the firing behaviour of the underlying motor pool. To do this, we first simulated a population of motor units (and their action potentials) that responded to a stimulus with a change in firing probability. Their activity was summed then rectified to generate a simulated sEMG signal or was rectified and then summed, to generate a sEMG signal with no cancellation. By comparing the two responses to that of the underlying pool we would then compare for discrepancies. We repeated this process but by using the responses of tibialis anterior motor units to weak tibial nerve stimulation. We find that both for the simulated and experimental data the response measured through the sEMG is almost always an underestimate of the evoked response in the underlying motor pool. This is the case for both inhibitory and excitatory evoked responses. The magnitude of the inaccuracy depends on the size of the evoked response, but it cannot be accounted solely by signal cancellation, suggesting other factors may also contribute.
Large-scale assessment of habitat quality and quantity change on declining European butterflies
Authors: Chazot Nicolas , Faurby Søren , van Swaay Chris , Ekroos Johan , Wahlberg Niklas , Bacon Christine D. , Antonelli Alexandre 
Published: October 2022

AbstractThe rapid decline of biodiversity as a consequence of increased environmental impact by human activities requires urgent action against the ongoing crisis. At the heart of conservation policy is the debate on quality versus quantity: should the post-2020 Global Biodiversity Framework focus on maximising total protected area, or pursue instead qualitative targets? To improve conservation practices, we need to both understand the current trend of biodiversity and the factors driving the decline. We address this by: (1) projecting current European butterfly population trends for the next 50 and 100 years, (2) comparing the decline in species richness, phylogenetic diversity and habitat specialization among different habitats, and (3) estimating the relationship between recent trends in habitat quality or quantity and the decline of multiple metrics of European butterfly diversity. We do not find any significant relationship between diversity loss and habitat area loss and conclude that neither long-term nor short-term changes in habitat area are primary predictors of large-scale butterfly decline in Europe. Habitat quality emerges as the most crucial factor in our analyses – both the area affected and the severity of habitat quality reduction. Habitat degradation causes vegetation changes in structure and diversity, which affect butterfly survival. We also estimate a higher decline of habitat specialists than generalist species. We conclude that habitat protection cannot focus solely on the maximization of habitat area but urgently needs to restore high quality ecosystems to provide the full range of ecological requirements for biodiversity.
Subchronic oral toxicity study of Aldicarb sulfoxide in Sprague-Dawley rats
Authors: Ji Yongchao , Liu Yi , Duan Juanjuan , Wang Yiting , Wang Yu , Wang Fan , Chen Chao , Zhang Wensheng 
Published: October 2022

AbstractAldicarb sulfoxide is the metabolite of the exceedingly deadly carbamate insecticide Aldicarb. Aldicarb sulfoxide is easily soluble in water and has been identified in groundwater. Moreover, Aldicarb sulfoxide is highly hazardous to mammals. However, the toxicity data of Aldicarb sulfoxide is scarce. Here, the effects of relatively low dosages of exposure to Aldicarb sulfoxide on the blood biochemical, hematological, and histopathological parameters were examined in SD rats. The rats were treated with Aldicarb sulfoxide orally at dosages of 0, 6.3, 18.9, and 56.7 μg per kg b.w. daily for 12 weeks. The results revealed that Aldicarb sulfoxide induced significant alterations in liver-related biochemical parameters, glucose level, cholesterol level, and uric acid level. Histopathological testing demonstrated cellular alterations in the liver of 18.9 and 56.7 μg/kg BW. Together, our data demonstrated that Aldicarb sulfoxide exposure causes liver injury. Furthermore, the no observed adverse effect level (NOAEL) was less than 6.3 μg/kg BW, and the lowest benchmark dose (BMD) value was 0.03 μg/kg BW. Accordingly, Aldicarb sulfoxide’s derived no-effect level (DNEL) was calculated as 0.00035 μg/kg BW. Thus, this work is an important reference for supervising Aldicarb sulfoxide in the environment and determining safe exposure limits for Aldicarb sulfoxide.
Diagnosis of type 2 Diabetes Mellitus (T2DM) using Paired microRNAs
Authors: Takada Yukichi , Ono Yasuhiro , Shibuta Tatsuki , Ishibashi Ayaka , Takamori Ayako , Fujimoto Kazuma , Hirooka Yoshitaka , Umemura Tsukuru 
Published: October 2022

AbstractType 2 Diabetes mellitus (T2DM) is one of the most common diseases in the world and its prevalence ratio is still increasing. Patients with T2DM have diverse pathophysiological changes like as macrovascular, microvascular diseases, cancers as well as abnormal glucose metabolism. Thus, there are urgent needs to develop relevant biomarkers for the broad range of pathophysiology in patients with T2DM. We analyzed the signatures of serum miRNAs with the miRNA array analysis and reverse-transcription based quantitative polymerase chain reaction (RT-qPCR) in 50 patients with type 2 DM (T2DM) and 15 normal subjects. Array analysis showed that 19 miRNAs were up-regulated more than 2-fold and 71 miRNAs were down-regulated less than 0.5 in T2DM in comparison with normal subjects. Top 5 of up-regulated miRNAs were miR-3619-3p, miR-557, miR-6850-5p, miR-3648, miR-4730, and 5 of most down-regulated miRNAs were miR-5100, miR-4454, miR-1260b, miR-7975, miR-6131. We selected 4 miRNAs for validation analysis with RT-qPCR based on the abundance enough for reliable analyses and disease-specificities reported in previous reports. Serum miR-126-3p was down-regulated (3.21-fold, p<0.05) in T2DM, and miR-10a up-regulated (1.94-fold, p<0.05). However, none of single miRNA had significant correlation with clinical data and state. Data of the paired miRNAs: miR-10a and miR-200c, or miR-126 and miR-10a, clearly differentiated T2DM patients from normal subjects (p<0.05). Our study showed the paired-miRNA analyses as the more effective diagnostics for T2DM than the single miRNA analysis.
Effects of antennal segments defects on blood-sucking behavior in Aedes albopictus
Authors: Zhou Yiyuan , Deng Dongyang , Chen Rong , Chen Qian 
Published: October 2022

AbstractAfter mating, female mosquitoes need a blood meal to promote the reproductive process. The blood-feeding transmits extremely harmful infections including malaria, yellow fever, dengue fever, and other arboviruses, making mosquitoes one of the most harmful creatures to human health. The selection and localization of the host by mosquitoes mainly depends on the trace chemical cues emitted by the host into the environment, and the sense of smell is the main way to perceive these trace chemical cues. However, the knowledge of the olfactory mechanism is not enough to meet the needs of mosquito control. Unlike previous studies that focused on the olfactory receptor recognition spectrum to reveal the olfactory mechanism of mosquito host localization. In this paper, we proposed that artificial defects in mosquito antennal flagellomeres may affect their blood-feeding behavior, and through rationally designed behavioral experiments, we found that the 6th and 7th flagellomeres on Aedes albopictus antenna are important in the olfactory detection of host searching. Meanwhile, the morphology and distribution of sensilla on each antenna flagellomere were also analyzed and discussed in this paper.
Active Fixation as an Efficient Coding Strategy for Neuromorphic Vision
Authors: Testa Simone , Sabatini Silvio P. , Canessa Andrea 
Published: October 2022

ABSTRACTContrary to a photographer, who puts a great effort in keeping the lens still, eyes insistently move even during fixation. This benefits signal decorrelation, which underlies an efficient encoding of visual information. Yet, camera motion is not sufficient alone; it must be coupled with a sensor specifically selective to temporal changes. Indeed, motion induced on standard imagers only results in burring effects. Neuromorphic sensors represent a valuable solution. Here we characterize the response of an event-based camera equipped with Fixational Eye Movements (FEMs) on both synthetic and natural images. Our analyses prove that the system starts an early stage of redundancy suppression, as a precursor of subsequent whitening processes on the amplitude spectrum. This does not come at the price of corrupting structural information contained in local spatial phase across oriented axes. Isotropy of FEMs ensures proper representations of image features without introducing biases towards specific contrast orientations.
Plant attributes interact with fungal pathogens and nitrogen addition to drive soil enzymatic activities and their temporal variation
Authors: Nwe Thu Zar , Maaroufi Nadia I. , Allan Eric , Soliveres Santiago , Kempel Anne 
Published: October 2022

AbstractNitrogen enrichment can alter soil communities and their functioning directly, via changes in nutrient availability and stoichiometry, or indirectly, by changing plant communities or higher trophic levels. In addition, soil biota and their associated functions may show strong temporal changes in their response to environmental changes, yet most current studies have only focused on one of these potential drivers or have measured soil functioning only once during the peak growing season. Therefore, we know little about the relative importance of the different mechanisms by which nitrogen enrichment affects soil communities, functioning and temporal stability.In a large grassland experiment manipulating nitrogen enrichment, plant species richness, functional composition and foliar pathogen presence, we measured activities of two enzymes, β-glucosidase and acid phosphatase, as indicators of soil functioning. We did so across different seasons and years to assess their temporal dynamics and how consistently they responded to multiple drivers.Nitrogen addition was the most important driver of β-glucosidase activity, and it increased β-glucosidase activity over time. However, interactions between plant attributes and fungicide application were the main drivers of acid phosphatase activity. The temporal stability of soil enzyme activity was differently affected by two facets of plant diversity (species richness [+] and functional diversity [-]), with nitrogen and fungicide addition dampening these effects.Synthesis: Fungicide effects, and their interactions with plant diversity, show the importance of foliar pathogens not only for above-but also for belowground processes, and highlight the possibility that these plant enemies are major modulators in the relationships between plant diversity and ecosystem functioning. We also show the need to consider temporal dynamics in belowground processes to better understand the responses of ecosystem functioning to environmental changes such as nutrient enrichment.
More than half of the variance inin-vivo1H-MRS metabolite estimates is common to all metabolites
Authors: Prisciandaro James J. , Zöllner Helge J. , Murali-Manohar Saipavitra , Oeltzschner Georg , Edden Richard A. E. 
Published: October 2022

AbstractThe present study characterized associations among brain metabolite levels, applying bivariate and multivariate (i.e., factor analysis) statistical methods to tCr-referenced estimates of the major PRESS1H-MRS metabolites (i.e., tNAA/tCr, tCho/tCr, mI/tCr, Glx/tCr), acquired from medial parietal lobe in a large (n=299), well-characterized international cohort of healthy volunteers (Povazan et al., 2020). Results supported the hypothesis that1H-MRS-measured metabolite estimates are moderately intercorrelated (Mr= 0.42,SDr= 0.11,ps < 0.001), with more than half (i.e., 57%) of the total variability in metabolite estimates common to (i.e., shared by) all metabolites. Older age was significantly associated with lower levels of common metabolite variance (CMV;β= -0.09,p= 0.048), despitenotbeing associated with levels of any individual metabolite. Holding CMV levels constant, females had significantly lower levels of total choline (i.e., unique metabolite variance or UMV;β= -0.19,p< 0.001), mirroring significant bivariate correlations between sex and total choline reported previously. If replicated, these results would suggest that applied1H-MRS researchers should shift their analytical framework from examining bivariate associations between individual metabolites and specialty-dependent (e.g., clinical, research) variables of interest (e.g., using t-tests) to examining multi-variable (i.e., covariate) associations between multiple metabolites and specialty-dependent variables of interest (e.g., using multiple regression). Without this shift, clear interpretation of associations of1H-MRS metabolites with specialty-dependent variables of interest may not be possible.
Changes in lung sialidases in male and female mice after bleomycin aspiration
Authors: Pilling Darrell , Sahlberg Kyle , Chen Wensheng , Gomer Richard H. 
Published: October 2022

AbstractAim of the studySialidases, also called neuraminidases, are enzymes that cleave terminal sialic acids from glycoconjugates. In humans and mice, lung fibrosis is associated with desialylation of glycoconjugates and upregulation of sialidases. There are four mammalian sialidases, and it is unclear when the four mammalian sialidases are elevated over the course of inflammatory and fibrotic responses, whether tissue resident and inflammatory cells express different sialidases, and if sialidases are differentially expressed in male and females.Materials and MethodsTo determine the time course of sialidase expression and the identity of sialidase expressing cells, we used the bleomycin model of pulmonary fibrosis in mice to examine levels of sialidases during inflammation (days 3 - 10) and fibrosis (days 10 - 21).ResultsBleomycin aspiration increased sialidase NEU1 at days 14 and 21 in male mice and day 10 in female mice. NEU2 levels increased at day 7 in male and day 10 in female mice. NEU3 appears to have a biphasic response in male mice with increased levels at day 7 and then at days 14 and 21, whereas in female mice NEU3 levels increased over 21 days. In control mice, the sialidases were mainly expressed by EpCAM positive epithelial cells, but after bleomycin, epithelial cells, CD45 positive immune cells, and alveolar cells expressed NEU1, NEU2, and NEU3. Sialidase expression was higher in male compared to female mice. There was little expression of NEU4 in murine lung tissue.ConclusionsThese results suggest that sialidases are dynamically expressed following bleomycin, that sialidases are differentially expressed in male and females, and that of the four sialidases only NEU3 upregulation is associated with fibrosis in both male and female mice.
Trends in Subcutaneous Tumour Height and Impact on Measurement Accuracy
Authors: Brough Daniel , Amos Hope , Turley Karl , Murkin Jake 
Published: October 2022

AbstractTumour volume is typically calculated using only length and width measurements, using width as a proxy for height in a 1:1 ratio. When tracking tumour growth over time, important morphological information and measurement accuracy is lost by ignoring height, which we show is a unique variable. Lengths, widths, and heights of 9,522 subcutaneous tumours in mice were measured using 3D and thermal imaging. The average width:height ratio was found to be 1:3 proving that using width as a proxy for height overestimates tumour volume. Comparing volumes calculated with and without tumour height to the true volumes of excised tumours indeed showed that using the volume formula including height produced volumes 36X more accurate. Monitoring the width:height relationship (prominence) across tumour growth curves indicated that prominence varied, and that height could change independent of width. Twelve cell lines were investigated individually; the scale of tumour prominence was cell line-dependent with relatively less prominent tumours (MC38, BL2, LL/2) and more prominent tumours (RENCA, HCT116) detected. Prominence trends across the growth cycle were also dependent on cell line; prominence was correlated with tumour growth in some cell lines (4T1, CT26, LNCaP), but not others (MC38, TC-1, LL/2). When pooled, invasive cell lines produced tumours that were significantly less prominent at volumes >1200mm3 compared to non-invasive cell lines (P<0.001). Modelling was used to show the impact of the increased accuracy gained by including height in volume calculations on several efficacy study outcomes. Variations in accuracy contribute to experimental variation and irreproducibility of data, therefore we strongly advise researchers to measure height to improve accuracy in tumour studies.
ATM-Mediated Double-Strand Break Repair Is Required for Meiotic Genome Stability at High Temperature
Authors: Zhao Jiayi , Gui Xin , Ren Ziming , Fu Huiqi , Yang Chao , Liu Qingpei , Zhang Min , Wang Wenyi , Wang Chong , Schnittger Arp , Liu Bing 
Published: October 2022

AbstractIn eukaryotes, the conserved kinase Ataxia Telangiectasia Mutated (ATM) negatively regulates DNA double-strand break (DSB) formation and plays a central role in DSB repair. Here, by using cytogenetic approaches, we demonstrate that ATM also plays an essential role in protecting meiotic chromosome integrity in Arabidopsis thaliana at extreme high temperature. We determined the chromosome localization patterns of DSB formation proteins SPO11-1 and DFO during prophase I, both of which were disturbed by heat stress. Evaluation of the number of RAD51, DMC1, SPO11-1 and DFO protein foci in meiocytes of Arabidopsis atm mutant clarifies that ATM does not mediate the heat-induced reduction in DSB formation. Interestingly, meiotic spread analysis showed that chromosome fragmentation level was significantly increased in atm but was lowered in the mre11 and mre11 atm mutants under high temperature, indicating that ATM-dependent meiotic chromosome integrity at high temperature relies on the functional MRE1-RAD50-NBS1 (MRN) complex. Moreover, contrary to the rad51 and mnd1 mutants, which exhibited enhanced meiotic chromosome integrity under heat stress, the rad51 atm and mnd1 atm mutants retained high levels of chromosome fragmentation at extreme high temperature. Furthermore, heat stress reduced chromosome fragmentation level in the syn1 and syn1 atm mutants. Collectively, these data suggest that ATM-mediated DSB repair is required for meiotic genome stability in plants at extreme high temperature, which possibly acts in a RAD51-independent manner and relies on functional chromosome axis.