bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synaptic polarity and sign-balance prediction using gene expression data in theCaenorhabditis eleganschemical synapse neuronal connectome network
Authors: Fenyves Bánk G. , Szilágyi Gábor S. , Vassy Zsolt , Sőti Csaba , Csermely Péter 
Published: May 2020

AbstractGraph theoretical analyses of nervous systems usually omit the aspect of connection polarity, due to data insufficiency. The chemical synapse network ofCaenorhabditis elegansis a well-reconstructed directed network, but the signs of its connections are yet to be elucidated. Here, we present the gene expression-based sign prediction of theC. elegansconnectome, incorporating presynaptic neurotransmitter and postsynaptic receptor gene expression data (3,638 connections and 20,589 synapses total). We made successful predictions for more than two-thirds of all chemical synapses and determined a ratio of excitatory-inhibitory (E:I) interneuronal ionotropic chemical connections close to 4:1 which was found similar to that observed in many real-world networks. Our open source tool (http://EleganSign.linkgroup.hu) is simple but efficient in predicting polarities by integrating neuronal connectome and gene expression data.Author SummaryThe fundamental way neurons communicate is by activating or inhibiting each other via synapses. The balance between the two is crucial for the optimal functioning of a nervous system. However, whole-brain synaptic polarity information is unavailable for any species and experimental validation is challenging. The roundworm Caenorhabditis elegans possesses a fully mapped connectome with a comprehensive gene expression profile of its 302 neurons. Based on the consideration that the polarity of a synapse must be determined by the neurotransmitter(s) expressed in the presynaptic neuron and the receptors expressed in the postsynaptic neuron, we conceptualized and created a tool that predicts synaptic polarities based on connectivity and gene expression information. We were able to show for the first time that the ratio of excitatory and inhibitory synapses inC. elegansis around 4 to 1 which is in line with the balance observed in many natural systems. Our method opens a way to include spatial and temporal dynamics of synaptic polarity that would add a new dimension of plasticity in the excitatory:inhibitory balance. Our tool is freely available to be used on any network accompanied by any expression atlas.
Modelling the response of the PIF plantain seedlings toTithonia diversifoliaand clam shells treatments in the nursery
Authors: Ewané Cécile Annie , Boudjeko Thaddée 
Published: May 2020

AbstractThe seeds availability is the main constraint for the agricultural explosion in sub-Saharan Africa countries. In the case of plantain, there is a lack of seedlings in quantity, but also in quality. The advent of the PIF method was an excellent opportunity to improve the availability of plantain seeds, although the quality is not fully guaranteed. Indeed, the PIF plants produced have posed many problems during the acclimation period indicating a need for solutions to improve their quality. Recent researches done with five treatments usingTithonia diversifoliaand clam shells have highlighted the improvement of the PIF seedlings quality in terms of growth promotion (biofertilizer action) and protection against black Sigatoka disease (biofungicide action). It seemed essential to determine the best model for robust PIF seedlings. The aim of this study was to analyse the different models that have enabled the production of improved PIF seedlings and to determine the best one. We have modelized the response of PIF seedlings to the different treatment’s protocols. It turns out that the best treatment to apply is T5 (T. diversifolialiquid extract), followed by T4 (T. diversifoliamulch). However, depending on the expected response in the PIF seedlings, all these treatments have proven to be impactful.Tithonia diversifolialiquid extract model is the best and in combination with clams, could be useful to boost the production at low cost and without chemical inputs of large amount of improved vigorous (clean and less susceptible) planting material, impacting thus the food security and poverty alleviation.
Effects of Old Age on Knee Extensor Fatigue and Recovery From High-Velocity Muscle Contractions
Authors: Fitzgerald Liam F. , Ryan Margaret M. , Bartlett Miles F. , Miehm Jules D. , Kent Jane A. 
Published: May 2020

ABSTRACTPurposeAlthough high-velocity contractions elicit greater muscle fatigue in older than young adults, the cause of this difference is unclear. We examined the potential roles of resting muscle architecture and baseline contractile properties, as well as changes in voluntary activation and low-frequency fatigue in response to high-velocity knee extensor work.MethodsVastus lateralis muscle architecture was determined in quiescent muscle by ultrasonography in 8 young (23.4±1.8 yrs) and 8 older women (69.6±1.1). Maximal voluntary dynamic (MVDC) and isometric (MVIC), and stimulated (80Hz and 10Hz, 500ms) isometric contractions were performed before and immediately after 120 MVDCs (240°·s−1, one every 2s).ResultsArchitecture variables did not differ between groups (p≥0.209), but the half-time of torque relaxation (T1/2) was longer in older than young women at baseline (151.9±6.0 vs. 118.8±4.4 ms, respectively, p=0.001). Older women fatigued more than young (to 33.6±4.7% vs. 55.2±4.2% initial torque, respectively; p=0.004), with no evidence of voluntary activation failure (ΔMVIC:80Hz torque) in either group (p≥0.317). Low-frequency fatigue (Δ10:80Hz torque) occurred in both groups (p<0.001), as did slowing of T1/2(p=0.001), with no differences between groups. Baseline T1/2was inversely associated with fatigue in older (r2=0.584, p=0.045), but not young women (r2=0.147, p=0.348).ConclusionsThese results indicate that differences in muscle architecture, voluntary activation, and low-frequency fatigue do not explain the greater fatigue of older compared with young women during high-velocity contractions. The inverse association between baseline T1/2and fatigue in older women suggests that factors related to slower muscle contractile properties may be protective against fatigue during fast, repetitive contractions in aging.
PD-L1 expression in equine malignant melanoma and functional effects of PD-L1 blockade
Authors: Ganbaatar Otgontuya , Konnai Satoru , Okagawa Tomohiro , Nojima Yutaro , Maekawa Naoya , Minato Erina , Kobayashi Atsushi , Ando Ryo , Sasaki Nobuya , Miyakosi Daisuke , Ichi Osamu , Kato Yukinari , Suzuki Yasuhiko , Murata Shiro , Ohashi Kazuhiko 
Published: May 2020

AbstractProgrammed death-1 (PD-1) is an immunoinhibitory receptor expressed on exhausted T cells during chronic illness. Interaction of PD-1 with its ligand PD-ligand 1 (PD-L1) delivers inhibitory signals and impairs proliferation, cytokine production, and cytotoxicity of T cells. We reported that the PD-1/PD-L1 pathway is closely associated with T-cell exhaustion and disease progression in bovine chronic infections and canine tumors. Moreover, we found that blocking antibodies targeting PD-1 and PD-L1 restore T-cell functions and may be used in immunotherapy in cattle and dogs. However, the immunological role of the PD-1/PD-L1 pathway remains unclear for chronic equine diseases, including tumors. In this study, we identified nucleotide sequences of equine PD-1 (EqPD-1) and PD-L1 (EqPD-L1) and investigated the role of anti-bovine PD-L1 monoclonal antibodies (mAbs) against EqPD-L1 usingin vitroassays. We also evaluated the expression of PD-L1 in tumor tissues of equine malignant melanoma (EMM).The amino acid sequences of EqPD-1 and EqPD-L1 share a high identity and similarity with homologs from other mammalian species. Two clones of the anti-bovine PD-L1 mAbs recognized EqPD-L1 in flow cytometry, and one of these cross-reactive mAbs blocked the binding of equine PD-1/PD-L1. Importantly, PD-L1 expression was confirmed in EMM tumor tissues by immunohistochemistry. A cultivation assay revealed that PD-L1 blockade enhanced the production of Th1 cytokines in equine immune cells.These results suggest that our anti-PD-L1 mAbs may be useful for investigating the expression and role of the equine PD-1/PD-L1 pathway. Further research is required to discover the immunological role of PD-1/PD-L1 in chronic equine diseases and elucidate a future application in immunotherapy for horse.
Methodological Issues with Search in MEDLINE: A Longitudinal Query Analysis
Authors: Burns C. Sean , Nix Tyler , Shapiro Robert M. , Huber Jeffrey T. 
Published: May 2020

AbstractThis study compares the results of data collected from a longitudinal query analysis of the MEDLINE database hosted on multiple platforms that include PubMed, EBSCOHost, Ovid, ProQuest, and Web of Science in order to identify variations among the search results on the platforms after controlling for search query syntax. We devised twenty-nine sets of search queries comprised of five queries per set to search against the five MEDLINE database platforms. We ran our queries monthly for a year and collected search result count data to observe changes. We found that search results vary considerably depending on MEDLINE platform, both within sets and across time. The variation is due to trends in scholarly publication that include publishing online first versus publishing in journal issues, which leads to metadata differences in the bibliographic record; to differences in the level of specificity among search fields provided by the platforms; to database integrity issues that lead to large fluctuations in monthly search results based on the same query; and to database currency issues that arise due to when each platform updates its MEDLINE file. Specific bibliographic databases, like PubMed and MEDLINE, are used to inform clinical decision-making, create systematic reviews, and construct knowledge bases for clinical decision support systems. Since they serve as essential information retrieval and discovery tools that help identify and collect research data and are used in a broad range of fields and as the basis of multiple research designs, this study should help clinicians, researcher, librarians, informationalists, and others understand how these platforms differ and inform future work in their standardization.
Genome and transcriptome analysis of the mealybugMaconellicoccus hirsutus: A model for genomic Imprinting
Authors: Kohli Surbhi , Gulati Parul , Maini Jayant , KV Shamsudheen , Pandey Rajesh , Scaria Vinod , Sivasubbu Sridhar , Narang Ankita , Brahmachari Vani 
Published: May 2020

AbstractIn mealybugs, transcriptional inactivation of the entire paternal genome in males, due to genomic imprinting, is closely correlated with sex determination. The sequencing,de-novoassembly and annotation of the mealybug,Maconellicoccus hirsutusgenome and its comparison withPlanococcus citrigenome strengthened our gene identification. The expanded gene classes, in both genomes relate to the high pesticide and radiation resistance; the phenotypes correlating with increased gene copy number rather than the acquisition of novel genes. The complete repertoire of genes for epigenetic regulation and multiple copies of genes for the core members of polycomb and trithorax complexes and the canonical chromatin remodelling complexes are present in both the genomes. Phylogenetic analysis withDrosophilashows high conservation of most genes, while a few have diverged outside the functional domain. The proteins involved in mammalian X-chromosome inactivation are identified in mealybugs, thus demonstrating the evolutionary conservation of factors for facultative heterochromatization. The transcriptome analysis of adult male and femaleM.hirsutusindicates the expression of the epigenetic regulators and the differential expression of metabolic pathway genes and the genes for sexual dimorphism. The depletion of endosymbionts in males during development is reflected in the significantly lower expression of endosymbiont genes in them.Author summaryThe mealybug system offers a unique model for genomic imprinting and differential regulation of homologous chromosomes that pre-dates the discovery of dosage compensation of X chromosomes in female mammals. In the absence of robust genetics for mealybugs, we generated and analysed the genome and transcriptome profile as primary resources for effective exploration. The expanded gene classes in the mealybugs relate to their unique biology; the expansion of pesticide genes, trehalose transporter, SETMAR and retrotransposons correlate with pesticide, desiccation and radiation resistance, respectively. The similarity in the genomic profile of two species of mealybugs strengthens our gene prediction. All the known epigenetic modifiers and proteins of the primary complexes like the PRC1,2 and the trithorax are conserved in mealybugs, so also the homologues of mammalian proteins involved in X chromosome inactivation. The high copy number of genes for many partners in these complexes could facilitate the inactivation of a large part of the genome and raise the possibility of formation of additional non-canonical complexes for sex specific chromosome inactivation. In adult males and females, the status of epigenetic regulation is likely to be in a maintenance state; therefore, it is of interest to analyze the expression of epigenetic regulators during development.
gEL DNA, a cloning- and PCR-free method for CRISPR-based multiplexed genome editing
Authors: Randazzo Paola , Daran Jean-Marc , Daran-Lapujade Pascale 
Published: May 2020

AbstractEven for the genetically accessible yeastSaccharomyces cerevisiae, the CRISPR/Cas DNA editing technology has strongly accelerated and facilitated strain construction. Several methods have been validated for fast and highly efficient single editing events and diverse approaches for multiplex genome editing have been described in literature by means of Cas9 or Cas12a endonucleases and their associated gRNAs. The gRNAs used to guide the Cas endonuclease to the editing site are typically expressed from plasmids using native PolII or PolIII RNA polymerases. These gRNA-expression plasmids require laborious, time-consuming cloning steps, which hampers their implementation for academic and applied purposes. In this study, we explore the potential of expressing gRNA from linear DNA fragments using the T7 RNA polymerase (T7RNAP) for single and multiplex genome editing inS. cerevisiae. Using Cas12a, this work demonstrates that transforming short, linear DNA fragments encoding gRNAs in yeast strains expressing T7RNAP promotes highly efficient single DNA editing. These DNA fragments can be custom-ordered, which makes this approach highly suitable for high-throughput strain construction. This work expands the CRISPR-toolbox for large-scale strain construction programs inS. cerevisiaeand promises to be relevant for other, less genetically accessible yeast species.
MealTime-MS: A Machine Learning-Guided Real-Time Mass Spectrometry Analysis for Protein Identification and Efficient Dynamic Exclusion
Authors: Pelletier Alexander R. , Chung Yun-En , Ning Zhibin , Wong Nora , Figeys Daniel , Lavallée-Adam Mathieu 
Published: May 2020

ABSTRACTMass spectrometry-based proteomics technologies are the prime methods for the high-throughput identification of proteins in complex biological samples. Nevertheless, there are still technical limitations that hinder the ability of mass spectrometry to identify low abundance proteins in complex samples. Characterizing such proteins is essential to provide a comprehensive understanding of the biological processes taking place in cells and tissues. Still today, most mass spectrometry-based proteomics approaches use a data-dependent acquisition strategy, which favors the collection of mass spectra from proteins of higher abundance. Since the computational identification of proteins from proteomics data is typically performed after mass spectrometry analysis, large numbers of mass spectra are typically redundantly acquired from the same abundant proteins, and little to no mass spectra are acquired for proteins of lower abundance. We therefore propose a novel supervised learning algorithm that identifies proteins in real-time as mass spectrometry data are acquired and prevents further data collection from confidently identified proteins to ultimately free mass spectrometry resources to improve the identification sensitivity of low abundance proteins. We use real-time simulations of a previously performed mass spectrometry analysis of a HEK293 cell lysate to show that our approach can identify 92.1% of the proteins detected in the experiment using 66.2% of the MS2 spectra. We also demonstrate that our approach outperforms a previously proposed method, is sufficiently fast for real-time mass spectrometry analysis, and is flexible. Finally, MealTime-MS’ efficient usage of mass spectrometry resources will provide a more comprehensive characterization of proteomes in complex samples.
An embryonic stem cell-specific heterochromatin state allows core histone exchange in the absence of DNA accessibility
Authors: Navarro Carmen , Elsässer Simon J 
Published: May 2020

ABSTRACTNucleosome turnover concomitant with incorporation of the replication-independent histone variant H3.3 is a hallmark of regulatory regions in the animal genome. In our current understanding, nucleosome turnover is universally linked to DNA accessibility and histone acetylation. In mouse embryonic stem cells, H3.3 is also highly enriched at interstitial heterochromatin, most prominently intracisternal-A particle endogenous retroviral elements. Interstitial heterochromatin is established over confined domains by the TRIM28/SETDB1 corepressor complex and has stereotypical features of repressive chromatin, such as H3K9me3 and recruitment of all HP1 isoforms. Here, we demonstrate that fast histone turnover and H3.3 incorporation is compatible with these hallmarks of heterochromatin. Further, we find that histone H3.3 is required to maintain minimal DNA accessibility in this surprisingly dynamic heterochromatin state. Loss of H3.3 in mouse embryonic stem cells elicits a highly specific opening of interstitial heterochromatin with minimal effects on other silent or active regions of the genome.
On Using Transfer Learning For Plant Disease Detection
Authors: Sagar Abhinav , Jacob Dheeba 
Published: May 2020

AbstractDeep neural networks has been highly successful in image classification problems. In this paper, we show how neural networks can be used for plant disease recognition in the context of image classification. We have used publicly available Plant Village dataset which has 38 classes of diseases. Hence, the problem that we have addressed is a multi class classification problem. We compared five different architectures including VGG16, ResNet50, InceptionV3, InceptionResNet and DenseNet169 as the backbones for our work. We found that ResNet50 achieves the best result on the test set. For evaluation, we used metrics: accuracy, precision, recall, F1 score and class wise confusion metric. Our model achieves the best of results using ResNet50 with accuracy of 0.982, precision of 0.94, recall of 0.94 and F1 score of 0.94.
Detection of a multi-disease biomarker in Saliva with Graphene Field Effect Transistors
Authors: Kumar Narendra , Gray Mason , Ortiz-Marquez Juan C. , Weber Andrew , Desmond Cameron R. , Argun Avni , van Opijnen Tim , Burch Kenneth S. 
Published: May 2020

AbstractHuman carbonic anhydrase 1 (CA1) has been suggested as a biomarker for identification of several diseases including cancers, pancreatitis, diabetes, and Sjogren’s syndrome. However, the lack of a rapid, cheap, accurate, and easy-to-use quantification technique has prevented widespread utilization of CA1 for practical clinical applications. To this end, we present a label-free electronic biosensor for detection of CA1 utilizing highly sensitive graphene field effect transistors (G-FETs) as a transducer and specific RNA aptamers as a probe. The binding of CA1 with aptamers resulted in a positive shift in Dirac voltageVDof the G-FETs, the magnitude of which depended on target concentration. These aptameric G-FET biosensors showed the binding affinity (KD) of ∼ 2.3 ng/ml (70 pM), which is four orders lower than that reported using a gel shift assay. This lower value ofKDenabled us to achieve a detection range (10 pg/ml - 100 ng/ml) which is well in line with the clinically relevant range. These highly sensitive devices allowed us to further prove their clinical relevance by successfully detecting the presence of CA1 in human saliva samples. Utilization of this label-free biosensor could facilitate the early stage identification of various diseases associated with changes in concentration of CAs.
Evidence for dosage compensation inCoccinia grandis, a plant with a highly heteromorphic XY system
Authors: Fruchard Cécile , Badouin Hélène , Latrasse David , Devani Ravi S. , Muyle Aline , Rhoné Bénédicte , Renner Susanne S. , Banerjee Anjan K. , Bendahmane Abdelhafid , Marais Gabriel A.B. 
Published: May 2020

AbstractSome ~15.000 angiosperms are dioecious, but mechanisms of sex determination in plants remain poorly understood. In particular, how Y chromosomes evolve and degenerate, and whether dosage compensation evolves as a response, are matters of debate. Here we focus onCoccinia grandis, a dioecious cucurbit with the highest level of X/Y heteromorphy recorded so far. We identified sex-linked genes using RNA sequences from a cross and a model-based method termed SEX-DETector. Parents and F1 individuals were genotyped and the transmission patterns of SNPs then analysed. In the >1300 sex-linked genes studied, X-Y divergence was 0.13 - 0.17, and substantial Y degeneration is implied by an average Y/X expression ratio of 0.63 and an inferred gene loss on the Y of ~40%. We also found reduced Y gene expression being compensated by elevated expression of corresponding genes on the X and an excess of sex-biased genes on the sex chromosomes. Molecular evolution of sex-linked genes inC. grandisis thus comparable to that inSilene latifolia, another dioecious plant with a strongly heteromorphic XY system, and cucurbits are the fourth plant family in which dosage compensation is described, suggesting it might be common in plants.
Innovating business processes in public administrations: towards a systemic approach
Authors: Forliano Canio , De Bernardi Paola , Bertello Alberto , Temperini Valerio 
Published: May 2020

PurposeThe purpose of this paper is to study the credit collection process in public administrations in order to develop a conceptual model which goes beyond the traditional logic of linearity, adopting system thinking approaches.Design/methodology/approachThis study analyses the case of an Italian local government-owned enterprise. Data collection through semi-structured interviews and document analysis has enabled the development of propositions, the identification of systemic variables, and the development of an explanatory modeling process based on the system dynamics approach.FindingsThis paper shows that public administrations can effectively involve external actors, especially citizens, as knowledge and public value co-creators only when considering systemic, unintended, and delayed implications of decision-making activities related to the provision of sensitive public services such as credit collection.Originality/valueBusiness process modelling should address some key fragilities of traditional modeling processes, especially in the public sector. This paper develops a novel systemic conceptual model which lays the groundwork for empirically testing business process innovation in public administrations.