bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic diversity of 39 samples ofPyropiaspecies grown in Japan
Authors: Nagano Yukio , Kimura Kei , Kobayashi Genta , Kawamura Yoshio 
Published: May 2020

AbstractSomePyropiaspecies, such as nori (P. yezoensis), are important marine crops. We conducted a phylogenetic analysis of 39 samples ofPyropiaspecies grown in Japan using organellar genome sequences. A comparison of the chloroplast DNA sequences with those from China showed a clear genetic separation between Japanese and ChineseP. yezoensis. Conversely, comparing the mitochondrial DNA sequences did not separate Japanese and ChineseP. yezoensis. Analysis of organellar genomes showed that the genetic diversity of JapaneseP. yezoensisused in this study is lower than that of Chinese wildP. yezoensis. To analyze the genetic relationships between samples of JapanesePyropia, we used whole-genome resequencing to analyze their nuclear genomes. In the offspring resulting from cross-breeding betweenP. yezoensisandP. tenera, nearly 90% of the genotypes analyzed by mapping were explained by the presence of different chromosomes originating from two different parental species. Although the genetic diversity of JapaneseP. yezoensisis low, analysis of nuclear genomes genetically separated each sample. Samples isolated from the sea were often genetically similar to those being farmed. Study of genetic heterogeneity of samples within a single aquaculture strain ofP. yezoensisshowed that samples were divided into two groups and the samples with frequent abnormal budding formed a single, genetically similar group. The results of this study will be useful for breeding and the conservation ofPyropiaspecies.
Mathematical Modeling and Simulation of SIR Model for COVID-2019 Epidemic Outbreak: A Case Study of India
Authors: Yadav Ramjeet Singh 
Published: May 2020

AbstractThe present study discusses the spread of COVID-2019 epidemic of India and its end by using SIR model. Here we have discussed about the spread of COVID-2019 epidemic in great detail using Euler's method. The Euler’s method is a method for solving the ordinary differential equations. The SIR model has the combination of three ordinary differential equations. In this study, we have used the data of COVID-2019 Outbreak of India on 8 May, 2020. In this data, we have used 135710 susceptible cases, 54340 infectious cases and 1830 reward/removed cases for the initial level of experimental purpose. Data about a wide variety of infectious diseases has been analyzed with the help of SIR model. Therefore, this model has been already well tested for infectious diseases by various scientists and researchers. Using the data to the number of COVID-2019 outbreak cases in India the results obtained from the analysis and simulation of this proposed SIR model showing that the COVID-2019 epidemic cases increase for some time and there after this outbreak decrease. The results obtained from the SIR model also suggest that the Euler’s method can be used to predict transmission and prevent the COVID-2019 epidemic in India. Finally, from this study, we have found that the outbreak of COVID-2019 epidemic in India will be at its peak on 25 May 2020 and after that it will work slowly and on the verge of ending in the first or second week of August 2020.
Red blood cell classification using image processing and CNN
Authors: Parab Mamata Anil , Mehendale Ninad Dileep 
Published: May 2020

AbstractIn the medical field, the analysis of the blood sample of the patient is a critical task. Abnormalities in blood cells are accountable for various health issues. Red blood cells (RBCs) are one of the major components of blood. Classifying the RBC can allow us to diagnose different diseases. The traditional time consuming technique of visualizing RBC manually under the microscope is a tedious task and may lead to wrong interpretation because of the human error. The various health conditions can change the shape, texture, and size of normal RBCs. The proposed method has involved the use of image processing to classify the RBCs with the help of Convolution Neural Networks (CNN). The algorithm can extract the feature of each segmented cell image and classify it in various types as Microcytes, Elliptocytes, Stomatocytes, Macrocytes, Teardrop RBCs, Codocytes, Spherocytes, Sickel cell RBCs and Howell jolly RBCs. Classification is done with respect to the size, shape, and appearance of RBCs. The experiment was conducted on the blood slide collected from the hospital and RBC images were extracted from those blood slide images. The obtained results compared with reports obtained by the pathology lab and realized 98.5% accuracy. The developed system provides accurate and fast results due to which it may save the life of patients.
Evidence for enhancer noncoding RNAs (enhancer-ncRNAs) with gene regulatory functions relevant to neurodevelopmental disorders
Authors: Asgari Yazdan , Heng Julian I.T. , Lovell Nigel , Forrest Alistair R. R. , Alinejad-Rokny Hamid 
Published: May 2020

AbstractNoncoding RNAs (ncRNAs) comprise a significant proportion of the mammalian genome, but their biological significance in neurodevelopment disorders is poorly understood. In this study, we identified 908 brain-enriched noncoding RNAs comprising at least one nervous system-related eQTL polymorphism that is associated with protein coding genes and also overlap with chromatin states characterised as enhancers. We referred to such noncoding RNAs with putative enhancer activity as brain ‘enhancer-ncRNAs’. By integrating GWAS SNPs and Copy Number Variation (CNV) data from neurodevelopment disorders, we found that 265 enhancer-ncRNAs were either mutated (CNV deletion or duplication) or contain at least one GWAS SNPs in the context of such conditions. Of these, the eQTL-associated gene for 82 enhancer-ncRNAs did not overlap with either GWAS SNPs or CNVs suggesting in such contexts that mutations to neurodevelopment gene enhancers disrupt ncRNA interaction. Taken together, we identified 49 novel NDD-associated ncRNAs that influence genomic enhancers during neurodevelopment, suggesting enhancer mutations may be relevant to the functions for such ncRNAs in neurodevelopmental disorders.
Human.miRFFL.DB-A curated resource for human miRNA coregulatory networks and associated regulatory-circuits
Authors: Khurana Pankaj , Varshney Rajeev , Sugadev R , Sharma YK 
Published: May 2020

AbstractGene regulation is viewed as a complex process where regulatory elements and their targets form highly complex network interactions thus affecting normal biological physiology and also disease-initiation and progress. Transcription factors (TF) and microRNA (miRNA) are fundamental transcriptional and post-transcriptional regulators of the gene expression controlling important biological processes. In recent years, many high throughput studies revealed that the complex regulatory interactions are mediated by the complex interplay between miRNA and TF regulating a Target Gene (TG) in conjunction. miRNAs and TFs are also known to regulate each other. This complex coregulatory mechanism may be represented in the form of miRNA:TF:TG coregulatory network. This network can be used to identify several small recurring subgraphs known as regulatory-circuits. One of these regulatory-circuits also called the Feed-Forward Loops (FFLs) is a three-node pattern which is composed of a miRNA and a TF, one of which regulates the other and both jointly regulate a TG. These regulatory-circuits have proven useful in elucidating the complex interplay of gene regulation during many physiological and pathological conditions.Human.miRFFL.DB is a comprehensive integrated resource for human miRNA:TF:TG coregulatory directed networks and their associated regulatory-circuits. In-house scripts based on the graph theory principle have been used to identify both types of FFL motifs i.e. miRNA-FFL and TF-FFL. The database additionally provides an interactive visualization of the coregulatory networks and associated FFLs. Human.miRFFL.DB can be used as a comprehensive ready reference for human miRNA:TF:TG coregulatory networks and associated FFLs for decrypting complex cellular interactions of these regulatory biomolecules. Human.miRFFL.DB is available online athttp://mirffldb.in/human/
Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies
Authors: Slater Luke T , Gkoutos Georgios V , Hoehndorf Robert 
Published: May 2020

AbstractBackgroundOntologies are widely used throughout the biomedical domain. These ontologies formally represent the classes and relations assumed to exist within a domain. As scientific domains are deeply interlinked, so too are their representations. While individual ontologies can be tested for consistency and coherency using automated reasoning methods, systematically combining ontologies of multiple domains together may reveal previously hidden contradictions.ResultsWe developed a method that tests for hidden unsatisfiabilities in an ontology that arise when combined with other ontologies. For this purpose, we combine sets of ontologies and use automated reasoning to determine whether unsatisfiable classes are present. We test the mutual consistency of the OBO Foundry and the OBO ontologies and find that the combined OBO Foundry gives rise to at least 636 unsatisfiable classes, while the OBO ontologies give rise to more than 300,000 unsatisfiable classes.We design and implement a novel algorithm that can determine justifications for contradictions across extremely large and complicated ontologies, and use these justifications to semi-automatically repair ontologies by identifying the minimal set of axioms that, when removed, result in a consistent and coherent set of ontologies. We applied our algorithm to each combination of OBO ontologies that resulted in unsatisfiable classes.ConclusionsWe identified a large set of hidden unsatisfiability across a broad range of biomedical ontologies, and we find that this large set of unsatisfiable classes is the result of a relatively small amount of axiomatic disagreements. Our results show that hidden unsatisfiability is a serious problem in ontology interoperability; however, our results also provide a way towards more consistent ontologies by addressing the issues we identified.
Cryopreservation of Ghagus chicken semen: effect of cryoprotectants diluents and thawing temperature
Authors: Murugesan Shanmugam , Mahapatra Ramkrishna 
Published: May 2020

AbstractThe present study evaluated the effects of cryoprotectants, semen diluents and thawing temperature during Ghagus chicken semen cryopreservation. Four different experiments were conducted; Experiment 1- semen was cryopreserved using 6% dimethylacetamide (DMA) and 2% dimethylsulfoxide (DMSO) in Sasaki diluent (SD) and Lake and Ravie diluent (LRD), Experiment 2 and 3- semen was cryopreserved using 8% Ethylene Glycol (EG) in SD, LRD and Red Fowl Extender (RFE), Experiment 4- semen was cryopreserved using 6% dimethylformamide (DMF) in SD, LRD and Beltsville Poultry Semen Extender (BPSE). Semen was cryopreserved in 0.5 ml French straws. Thawing was done at 5°C for 100 sec in ice water in Experiments 1, 2 and 4, whereas in Experiment 3 thawing was done at 37°C for 30 sec. The post-thaw sperm motility, live sperm and percent acrosome intact sperm were significantly (P<0.05) lower in cryopreserved samples in all the experiments. No fertile eggs were obtained from cryopreserved samples in Experiments 1 and 2, except for 8% EG RFE treatment where the fertility was 0.83%. In Experiments 3 and 4, highest fertility was obtained in LRD treatment 48.12 and 30.89% respectively. In conclusion, using cryoprotectant EG (8%) and thawing at 37°C for 30 sec, and DMF (6%) resulted in acceptable level of fertility in Ghagus chicken. Though the diluents influenced post-thaw in vitro semen parameters the fertility was not affected. In addition, results indicated that thawing temperature may be a critical stage in the cryopreservation protocol.
Dual Role of a Rubisco Activase in Metabolic Repair and Carboxysome Organization
Authors: Flecken Mirkko , Wang Huping , Popilka Leonhard , Hartl F. Ulrich , Bracher Andreas , Hayer-Hartl Manajit 
Published: May 2020

SUMMARYRubisco, the key enzyme of CO2fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone Rubisco activase (Rca) in a process that is not well understood. Here we performed a structural and mechanistic analysis of cyanobacterial Rca, a close homolog of plant Rca. In the Rca:Rubisco complex, Rca is positioned over the Rubisco catalytic site under repair and pulls the N-terminal tail of the large Rubisco subunit (RbcL) into the hexamer pore. Simultaneous displacement of the C-terminus of the adjacent RbcL opens the catalytic site for inhibitor release. An alternative interaction of Rca with Rubisco is mediated by C-terminal domains that resemble the small Rubisco subunit. These domains, together with the N-terminal AAA+ hexamer, ensure that Rca is packaged with Rubisco into carboxysomes. Cyanobacterial Rca is a dual-purpose protein with functions in Rubisco repair and carboxysome organization.
Acoustically driven cortical delta oscillations underpin perceptual chunking
Authors: Rimmele J.M. , Poeppel D. , Ghitza O. 
Published: May 2020

AbstractOscillation-based models of speech perception postulate a cortical computational principle by which decoding is performed within a window structure derived by a segmentation process. In the syllable level segmentation is realized by a theta oscillator. We provide evidence for an analogous role of a delta oscillator at the phrasal level. We recorded MEG while participants performed a target identification task. Random-digit strings, with phrasal chunks of two digits, were presented at chunk rates inside or outside of the delta range. Strong periodicities were elicited by acoustic-driven chunk rates inside of delta, in superior and middle temporal areas and speech-motor integration areas. Periodicities were diminished or absent for chunk rates outside of the delta range, closely in line with behavioral performance. No periodicities were observed for top-down driven chunking conditions. Our findings show that phrasal chunking is correlated with acoustic-driven delta oscillations, expressing anatomically specific patterns of neuronal periodicities.
Spatiotemporal variation in drivers of parasitism in a wild wood mouse population
Authors: Sweeny A.R. , Albery G.F. , Venkatesan S.V. , Fenton A. , Pedersen A.B. 
Published: May 2020

AbstractHost-parasite interactions in nature are driven by a range of factors across several ecological scales, so observed relationships are often context-dependent. Importantly, if these factors vary across space and time, practical sampling limitations can limit or bias inferences, and the relative importance of different drivers can be hard to discern.We collected a replicated, longitudinal dataset of >1000 individual wood mice (Apodemus sylvaticus) encompassing 6 years of sampling across 5 different woodland sites to investigate how environmental, host and within-host factors determine infection intensity of a highly prevalent gastrointestinal nematode,Heligmosomoides polygyrus.We used a Bayesian modelling approach to further quantify if and how each factor varied in space and time. Finally, we examined the extent to which a lack of spatially or temporally replication (i.e., within single years or single sites) and single (cross-sectional) versus repeated (longitudinal) sampling of individuals would affect which drivers were found to predictH. polygyrusinfection.Season, host body condition, and sex were the three most important determinants of infection intensity; however, the strength and even direction of these effects varied in time, but not in space. Additionally, longitudinal datasets, in which we can control for within-individual variation through repeat observations, provided more robust estimates of the drivers of parasite intensity compared to cross-sectional data.These results highlight the importance of accounting for spatiotemporal variation in drivers of disease dynamics and the need to incorporate spatiotemporal replication when designing sampling regimes. Furthermore, they suggest that embracing rather than simply controlling for spatiotemporal variation can reveal important insight into host-parasite relationships in the wild.
Reoxygenation after Evofosfamide Treatment in Pancreatic Ductal Adenocarcinoma Xenografts is due to Decreased Oxygen Consumption and not Increased Oxygen Supply
Authors: Kishimoto Shun , Brender Jeffrey R. , Saida Yu , Yamamoto Kazutoshi , Mitchell James B. , Krishna Murali C. 
Published: May 2020

AbstractEvofosfamide is designed to release a cytotoxic bromo-isophosphoramide (Br-IPM) moiety in a hypoxic microenvironment. This drug therefore preferentially attacks hypoxic regions in tumors where other standard anti-cancer treatments such as chemotherapy and radiation therapy are often ineffective. Various combination therapies with evofosfamide have been proposed and tested in preclinical and clinical settings. However, the treatment effect of evofosfamide monotherapy on tumor hypoxia has not been fully understood, partly due to the lack of quantitative methods to assess tumor pO2 in vivo. Here, we use quantitative pO2 imaging by EPR to evaluate the change in tumor hypoxia in response to evofosfamide treatment using two pancreatic ductal adenocarcinom a xenograft models; MIA Paca-2 tumors responding to evofosfamide and Su.86.86 tumors which do not respond. EPR imaging showed oxygenation improved globally after evofosfamide treatment in hypoxic MIA Paca-2 tumors, in agreement with the ex vivo results obtained from hypoxia staining by pimonidazole and in apparent contrast to the decrease in Ktransobserved in DCE MRI. This suggests reoxygenation after treatment is due to decreased oxygen demand rather than improved prefusion. Following the change in pO2 after treatment may therefore yield a way of monitoring treatment response. The observation that evofosfamide not only kills the hypoxic region of the tumor but also improves oxygenation in the residual tumor regions provides a rationale for combination therapies using radiation and anti-proliferatives post evofosfamide for improved outcomes.
NAIP–NLRC4-deficient mice are susceptible to shigellosis
Authors: Mitchell Patrick S. , Roncaioli Justin L. , Turcotte Elizabeth A. , Goers Lisa , Chavez Roberto A. , Lee Angus Y. , Lesser Cammie F. , Rauch Isabella , Vance Russell E. 
Published: May 2020

AbstractBacteria of the genusShigellacause shigellosis, a severe gastrointestinal disease that is a major cause of diarrhea-associated mortality in humans. Shigellosis develops upon oral ingestion of as few as 100 bacteria, but million-fold higher doses fail to cause disease in mice. The lack of a physiologically relevant mouse model of shigellosis has impeded our understanding of this important human disease, but why mice are resistant is unknown. Here we show that in human cells, but not in mice,Shigellaevades detection by the NAIP–NLRC4 inflammasome, an immune sensor present in intestinal epithelial cells (IECs). We find that NAIP–NLRC4-deficient mice are highly susceptible to oralShigellainfection and recapitulate the clinical features of human shigellosis, including bacterial replication in IECs and neutrophilic inflammation of the colon. Confirming a role for bacterial replication in IECs in our new model, aShigellamutant lacking IcsA, a factor required for cell-to-cell spread among IECs, is attenuated in otherwise susceptible NAIP–NLRC4-deficient mice. Although inflammasome-mediated cell death is widely held to promoteShigellainfection and pathogenesis, we instead demonstrate that IEC-specific NAIP–NLRC4-induced cell death is sufficient to protect the host from shigellosis. Thus, NAIP–NLRC4-deficient mice are a physiologically relevant and experimentally tractable model for shigellosis. More broadly, our results suggest that the lack of an inflammasome response in IECs may help explain the extreme susceptibility of humans to shigellosis.
A unique and evolutionarily conserved retinal interneuron relays rod and cone input to the inner plexiform layer
Authors: Young Brent K. , Ramakrishnan Charu , Ganjawala Tushar , Li Yumei , Kim Sangbae , Wang Ping , Chen Rui , Deisseroth Karl , Tian Ning 
Published: May 2020

AbstractNeurons in the CNS are distinguished from each other by their morphology, the types of the neurotransmitter they release, their synaptic connections, and their genetic profiles. While attempting to characterize the retinal bipolar cell (BC) input to retinal ganglion cells (RGCs), we discovered a previously undescribed type of interneuron in mice and primates. This interneuron shares some morphological, physiological, and molecular features with traditional BCs, such as having dendrites that ramify in the outer plexiform layer (OPL) and axons that ramify in the inner plexiform layer (IPL) to relay visual signals from photoreceptors to inner retinal neurons. It also shares some features with amacrine cells, particularly Aii amacrine cells, such as their axonal morphology and possibly the release of the inhibitory neurotransmitter glycine, along with the expression of some amacrine cell specific markers. Thus, we unveil an unrecognized type of interneuron, which may play unique roles in vision.Significance StatementCell types are the building blocks upon which neural circuitry is based. In the retina, it is widely believed that all neuronal types have been identified. We describe a cell type, which we call the Campana cell, that does not fit into the conventional neuronal retina categories but is evolutionarily conserved. Unlike retinal bipolar cells, the Campana cell receives synaptic input from both rods and cones, has broad axonal ramifications, and may release an inhibitory neurotransmitter. Unlike retinal amacrine cells, the Campana cell receives direct photoreceptor input has bipolar-like ribbon synapses. With this discovery, we open the possibility for new forms of visual processing in the retina.
The low complexity motif of cytoplasmic polyadenylation element binding protein 3 (CPEB3) is critical for the trafficking of its targets in neurons
Authors: Ford Lenzie , Asok Arun , Tripp Arielle D. , Parro Cameron , Fitzpatrick Michelle , de Solis Christopher A. , Shafiian Neeva , Fioriti Luana , Soni Rajesh Kumar , Kandel Eric R. 
Published: May 2020

SummaryBiomolecular condensates, membraneless organelles found throughout the cell, play critical roles in many aspects of cellular function. Ribonucleoprotein granules (RNPs), a type of biomolecular condensate found in neurons that are necessary for local protein synthesis and are involved in long-term potentiation (LTP). Several RNA-binding proteins present in RNPs are necessary for the synaptic plasticity involved in LTP and long-term memory. Most of these proteins possess low complexity motifs, allowing for increased promiscuity. We explore the role the low complexity motif plays for RNA binding protein cytoplasmic polyadenylation element binding protein 3 (CPEB3), a protein necessary for long-term memory persistence. We found that RNA binding and SUMOylation are necessary for CPEB3 localization to the P body, thereby having functional implications on translation. Here, we investigate the role of the low complexity motif of CPEB3 and find that it is necessary for P body localization and downstream targeting for local protein synthesis.