bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiology and transmission dynamics of COVID-19 in two Indian states
Authors: Laxminarayan Ramanan , Wahl Brian , Dudala Shankar Reddy , Gopal K. , Mohan Chandra , Neelima S. , Jawahar Reddy K. S. , Radhakrishnan J. , Lewnard Joseph A. 
Published: July 2020

AbstractAlthough most COVID-19 cases have occurred in low-resource countries, there is scarce information on the epidemiology of the disease in such settings. Comprehensive SARS-CoV-2 testing and contact-tracing data from the Indian states of Tamil Nadu and Andhra Pradesh reveal stark contrasts from epidemics affecting high-income countries, with 92.1% of cases and 59.7% of deaths occurring among individuals <65 years old. The per-contact risk of infection is 9.0% (95% confidence interval: 7.5-10.5%) in the household and 2.6% (1.6-3.9%) in the community. Superspreading plays a prominent role in transmission, with 5.4% of cases accounting for 80% of infected contacts. The case-fatality ratio is 1.3% (1.0-1.6%), and median time-to-death is 5 days from testing. Primary data are urgently needed from low- and middle-income countries to guide locally-appropriate control measures.
uBin – a manual refining tool for metagenomic bins designed for educational purposes
Authors: Bornemann Till L.V. , Esser Sarah P. , Stach Tom L. , Burg Tim , Probst Alexander J. 
Published: July 2020

AbstractResolving bacterial and archaeal genomes from metagenomes has revolutionized our understanding of Earth’s biomes, yet producing high quality genomes from assembled fragments has been an ever-standing problem. While automated binning software and their combination produce prokaryotic bins in high-throughput, their manual refinement has been slow and sometimes difficult. Here, we present uBin, a GUI-based, standalone bin refiner that runs on all major operating platforms and was specifically designed for educational purposes. When applied to the public CAMI dataset, refinement of bins was able to improve 78.9% of bins by decreasing their contamination. We also applied the bin refiner as a standalone binner to public metagenomes from the International Space Station and demonstrate the recovery of near-complete genomes, whose replication indices indicate active proliferation of microbes in Earth’s lower orbit. uBin is an easy to install software for bin refinement, binning of simple metagenomes and communication of metagenomic results to other scientists and in classrooms. The software is open source and available underhttps://github.com/ProbstLab/uBin.
Next generation cytogenetics: genome-imaging enables comprehensive structural variant detection for 100 constitutional chromosomal aberrations in 85 samples
Authors: Mantere Tuomo , Neveling Kornelia , Pebrel-Richard Céline , Benoist Marion , van der Zande Guillaume , Kater-Baats Ellen , Baatout Imane , van Beek Ronald , Yammine Tony , Oorsprong Michiel , Olde-Weghuis Daniel , Majdali Wed , Vermeulen Susan , Pauper Marc , Lebbar Aziza , Stevens-Kroef Marian , Sanlaville Damien , Smeets Dominique , Dupont Jean Michel , Hoischen Alexander , Schluth-Bolard Caroline , El Khattabi Laïla 
Published: July 2020

AbstractChromosomal aberrations and structural variations are a major cause of human genetic diseases. Their detection in clinical routine still relies on standard cytogenetics, karyotyping and CNV-microarrays, in spite of the low resolution of the first one and the inability to detect neither balanced SVs nor to provide the genomic localization or the orientation of duplicated segments, of the latter. We here investigated the clinical utility of high resolution optical mapping by genome imaging for patients carrying known chromosomal aberrations in a context of constitutional conditions.For 85 samples, ultra-high molecular weight gDNA was isolated either from blood or cultured cells. After labeling, DNA was processed and imaged on the Saphyr instrument (Bionano Genomics). Ade novogenome assembly was performed followed by SV and CNV calling and annotation. Results were compared to known aberrations from standard-of-care tests (karyotype, FISH and/or CNV-microarray).In total, we analyzed 100 chromosomal aberrations including 7 aneuploidies, 35 translocations, 6 inversions, 2 insertions, 39 copy number variations (20 deletions and 19 duplications), 6 isochromosomes, 1 ring chromosome and 4 complex rearrangements. High resolution optical mapping reached 100% concordance compared to standard assays for all aberrations with non-centromeric breakpoints.Our study demonstrates the ability of high resolution optical mapping to detect almost all types of chromosomal aberrations within the spectrum of karyotype, FISH and CNV-microarray. These results highlight its potential to replace these techniques, and provide a cost-effective and easy-to-use technique that would allow for comprehensive detection of chromosomal aberrations.
COVID-19 Detection on Chest X-Ray and CT Scan Images Using Multi-image Augmented Deep Learning Model
Authors: Purohit Kiran , Kesarwani Abhishek , Kisku Dakshina Ranjan , Dalui Mamata 
Published: July 2020

AbstractCOVID-19 is posed as very infectious and deadly pneumonia type disease until recent time. Despite having lengthy testing time, RT-PCR is a proven testing methodology to detect coronavirus infection. Sometimes, it might give more false positive and false negative results than the desired rates. Therefore, to assist the traditional RT-PCR methodology for accurate clinical diagnosis, COVID-19 screening can be adopted with X-Ray and CT scan images of lung of an individual. This image based diagnosis will bring radical change in detecting coronavirus infection in human body with ease and having zero or near to zero false positives and false negatives rates. This paper reports a convolutional neural network (CNN) based multi-image augmentation technique for detecting COVID-19 in chest X-Ray and chest CT scan images of coronavirus suspected individuals. Multi-image augmentation makes use of discontinuity information obtained in the filtered images for increasing the number of effective examples for training the CNN model. With this approach, the proposed model exhibits higher classification accuracy around 95.38% and 98.97% for CT scan and X-Ray images respectively. CT scan images with multi-image augmentation achieves sensitivity of 94.78% and specificity of 95.98%, whereas X-Ray images with multi-image augmentation achieves sensitivity of 99.07% and specificity of 98.88%. Evaluation has been done on publicly available databases containing both chest X-Ray and CT scan images and the experimental results are also compared with ResNet-50 and VGG-16 models.
The malaria parasite sheddase SUB2 governs host red blood cell membrane sealing at invasion
Authors: Collins Christine R , Hackett Fiona , Howell Steven A , Snijders Ambrosius P , Russell Matthew RG , Collinson Lucy M , Blackman Michael J 
Published: July 2020

AbstractRed blood cell (RBC) invasion by malaria merozoites involves formation of a parasitophorous vacuole into which the parasite moves. The vacuole membrane seals and pinches off behind the parasite through an unknown mechanism, enclosing the parasite within the RBC. During invasion, several parasite surface proteins are shed by a membrane-bound protease called SUB2. Here we show that genetic depletion of SUB2 abolishes shedding of a range of parasite proteins, identifying previously unrecognized SUB2 substrates. Interaction of SUB2-null merozoites with RBCs leads to either abortive invasion with rapid RBC lysis, or successful entry but developmental arrest. Selective failure to shed the most abundant SUB2 substrate, MSP1, reduces intracellular replication, whilst conditional ablation of the substrate AMA1 produces host RBC lysis. We conclude that SUB2 activity is critical for host RBC membrane sealing following parasite internalisation and for correct functioning of merozoite surface proteins.Key highlightsMany malaria parasite surface proteins are shed by SUB2 during RBC invasionSUB2-null merozoites either induce rapid host RBC lysis, or invade then dieMerozoite surface protein shedding is crucial for host RBC membrane sealing
Immunohistochemical Detection of early and late Human Papillomaviruses (HPV) proteins in Retinoblastoma tumors
Authors: Diniz Nara , Melo Thatiana C , Araldi Rodrigo P , Carvalho Rodrigo F. , Beçak Willy , de Medeiros Jonathan W , Albuquerque Giwellington S , Gurgel Ana Pavla , Hassan Rocio , Muniz Maria TC , de Cassia Stocco Rita 
Published: July 2020

AbstractIn this study, we evaluated the presence of early and late Human Papillomavirus (HPV) proteins in retinoblastoma Brazilian patients. For this, 8 formalin-fixed paraffin-embedded retinoblastoma tissue blocks were used. HPV DNA presence was determined by in situ hybridization (ISH). Immunohistochemistry were performed to verify HPV16/18 E6, E1^E4, and L1 proteins. HPV was detected in all retinoblastoma tumors and viral DNA was labeled in tumor cells, retinal layers and optical nerve structures. In addition, E1^E4, E6 and L1 proteins were detected in all samples in the same areas where HPV DNA was detected. Our data showed the presence and expression of early and late HPV proteins in retinoblastoma tumors from Brazilian children. However, further studies should be performed to clarify the role of HPV infection in retinoblastoma tumor.
Tele- Yoga therapy for Patients with Chronic Pain during Covid-19 Lockdown: A Prospective Nonrandomized Single Arm Clinical Trial
Authors: Sharma Neha , Modi Dipa , Nathwani Asha , Pandya Bhavna , Joshi Jaydeep 
Published: July 2020

AbstractBackgroundPain management services and support programs have been closed during pandemic. Self-management options, particularly for chronic pain, is required which can be undertaken at one’s own convenience and without leaving home.ObjectivesTo evaluate the impact of tele-yoga therapy on patients suffering with chronic pain reducing pain intensity, disability, anxiety and depression.Material and methodsIn total 18 patients with different chronic pain diagnosis were recruited to individual yoga Therapy sessions twice a week at home (tele-yoga) using a videoconference app. Each participant followed set of practices every day at home. Main outcome measures included pain intensity, pain disability, anxiety and depression scores. Data were collected at baseline and after 6-weeks of intervention.ResultsThere were significant improvement in pain intensity from Baseline to 6-weeks (P<0.001); also pain disability (P<0,001). Both scores of anxiety and depression reduced at the end of intervention period (P<0,001; P<0,001).ConclusionsPilot results suggest that tele-yoga therapy may be an effective tool to self-manage chronic pain and related functional and psychological impacts. Further larger studies, randomized, controlled trials are needed to confirm the preliminary outcome.Trial RegistrationClinicalTrials.govNCT04457388; https://clinicaltrials.gov/ct2/show/NCT04457388
Blood transcriptional module repertoire analysis and visualization using R
Authors: Rinchai Darawan , Roelands Jessica , Hendrickx Wouter , Altman Matthew C. , Bedognetti Davide , Chaussabel Damien 
Published: July 2020

AbstractTranscriptional modules have been widely used for the analysis, visualization and interpretation of transcriptome data. We have previously described the construction and characterization of generic and reusable blood transcriptional module repertoires. The third and latest version that we have recently made available comprises 382 functionally annotated gene sets (modules) and encompasses 14,168 transcripts. We developed R scripts for performing module repertoire analyses and custom fingerprint visualization. These are made available here along with detailed descriptions. An illustrative public transcriptome dataset and corresponding intermediate output files are also included as supplementary material. Briefly, the steps involved in module repertoire analysis and visualization include: First, the annotation of the gene expression data matrix with module membership information. Second, running of statistical tests to determine for each module the proportion of its constitutive genes which are differentially expressed. Third, the results are expressed “at the module level” as percent of genes increased or decreased and plotted in a fingerprint grid format. A parallel workflow has been developed for computing module repertoire changes for individual samples rather than groups of samples. Such results are plotted in a heatmap format. The use case that is presented illustrates the steps involved in the generation of blood transcriptome repertoire fingerprints of septic patients at both group and individual levels.
Temporally integrated single cell RNA sequencing analysis of controlled and natural primary human DENV-1 infections
Authors: Waickman Adam T. , Friberg Heather , Gromowski Gregory D. , Rutvisuttinunt Wiriya , Li Tao , Siegfried Hayden , Victor Kaitlin , McCracken Michael K. , Fernandez Stefan , Srikiatkhachorn Anon , Ellison Damon , Jarman Richard G. , Thomas Stephen J. , Rothman Alan L. , Endy Timothy , Currier Jeffrey R. 
Published: July 2020

AbstractControlled dengue human infection studies present an opportunity to address many longstanding questions in the field of flavivirus biology. However, limited data are available on how the immunological and transcriptional response elicited by an attenuated challenge virus compares to that associated with a wild-type DENV infection. To bridge this knowledge gap, we utilized scRNAseq to analyze PBMC from individuals enrolled in a DENV-1 controlled human challenge study and from individuals experiencing a natural primary DENV-1 infection. While both controlled and natural DENV infection resulted in overlapping patterns of inflammatory gene upregulation, natural DENV infection was accompanied with a more pronounced suppression in gene products associated with protein translation and mitochondrial function, principally in monocytes. This suggests that the immune response elicited by controlled and natural primary DENV infection are similar, but that natural DENV infection has a more pronounced impact on basic cellular processes to induce a multi-layered anti-viral state
Longitudinal analysis of the humoral response to SARS-CoV-2 spike RBD in convalescent plasma donors
Authors: Perreault Josée , Tremblay Tony , Fournier Marie-Josée , Drouin Mathieu , Beaudoin-Bussières Guillaume , Prévost Jérémie , Lewin Antoine , Bégin Philippe , Finzi Andrés , Bazin Renée 
Published: July 2020

ABSTRACTHéma-Québec, the blood supplier in the Province of Quebec, Canada, collects and tests convalescent plasma used in a clinical trial to determine the clinical efficacy of this product for the treatment of hospitalized COVID-19 patients. So far, we have collected 1159 plasma units from 282 COVID-19 convalescent donors. The presence of antibodies to the receptor binding domain (RBD) of SARS-CoV-2 spike protein in convalescent donors was established at the first donation. Seropositive donors were asked to donate additional plasma units every six days. Until now, 15 donors have donated at least four times and, in some cases, up to nine times. This allowed us to perform a longitudinal analysis of the persistence of SARS-CoV-2 RBD-specific antibodies in these repeat donors, with the first donation occurring 33-77 days after symptoms onset and donations up to 71-114 days after symptoms onset thereafter. In all donors, the level of antibodies remained relatively stable up to about 76 days after symptoms onset but then started to decrease more rapidly to reach, in some convalescent donors, a seronegative status within 100-110 days after symptoms onset. The decline in anti-RBD antibodies was not related to the number of donations but strongly correlated with the numbers of days after symptoms onset (r = 0.821). This suggests that de novo secretion of SARS-CoV-2 RBD antibodies by short-lived plasma cells stopped about 2-3 months after disease onset, an observation that has important implications for convalescent plasma collection and seroprevalence studies undertaken several months after the peak of infection.
Vector dynamics influence spatially imperfect genetic interventions against disease
Authors: Yuksel Mete K , Remien Christopher H , Karki Bandita , Bull James J , Krone Stephen M 
Published: July 2020

AbstractBackground and objectivesGenetic engineering and similar technologies offer promising new approaches to controlling human diseases by blocking transmission from vectors. However, in spatially structured populations, imperfect coverage of the vector will leave pockets in which the parasite can persist. Yet movement by humans may disrupt this local persistence and facilitate eradication when these pockets are small, essentially distributing parasite reproduction out of unprotected areas and into areas that block its reproduction.MethodologyWe develop formal mathematical models of this process similar to standard Ross-Macdonald models, but (i) specifying spatial structure of two patches, with transmission blocked in one patch but not in the other, (ii) allowing temporary human movement (travel instead of migration), and (iii) considering two different modes of mosquito biting.ResultsWe find that there is no invariant effect of disrupting spatial structure with travel. For both biting models, travel out of the unprotected patch has different consequences than travel by visitors into the patch, but the effects are reversed between the two biting models.Conclusions and implicationsOverall, the effect of human travel on the maintenance of vector-borne diseases in structured habitats must be considered in light of the actual biology of mosquito abundances and biting dynamics.Lay summaryGenetic interventions against pathogens transmitted by insect vectors are promising methods of controlling infectious diseases. These interventions may be imperfect, leaving pockets where the parasite persists. How will human movement between protected and unprotected areas affect persistence? Mathematical models developed here show that the answer is ecology-dependent, depending on vector biting behavior.
Towards More Reliable Unsupervised Tissue Segmentation Via Integrating Mass Spectrometry Imaging and Hematoxylin-Erosin Stained Histopathological Image
Authors: Guo Ang , Chen Zhiyu , Li Fang , Li Wenbo , Luo Qian 
Published: July 2020

AbstractMass Spectrometry Imaging (MSI) provides a useful tool to divide a tissue section into sub-regions with similar molecular profiles, namely tissue segmentation. However, owing to the lack of ground truth, there is no reliable evaluation approach to assess the validity of unsupervised segmentation outcomes of MSI. We propose a novel solution grounded on a presumption that a segmentation is reliable if it can be reproduced using distinct bio-information extracted from independent sources. Specifically, besides molecular information from MSI data, we also obtain morphological information over a tissue section from its Hematoxylin-Erosin (H&E) stained histopathological image. MSI has high molecular specificity but low spatial resolving power, the H&E image has no molecular specificity but it can capture microscopic details of the tissue with a spatial resolution two magnitudes higher than MSI. The whole H&E image is split into an array of small patches, which correspond to the spatial pixels of MSI. A spectrum of informative morphological features is computed iteratively for each patch and spatial segmentation can be generated by clustering the patches based on their morphological similarities. Adjusted Mutual Information (AMI) score measures the degree of agreement between MSI-based and H&E image-based segmentation outcomes, which is defined by us as an objective and quantitative evaluation metric of segmentation validity. We investigated various candidate morphological features: a combination of Deep Convolution Neural Network (DCNN) features and handcrafted Threshold Adjacency Statistics (TAS) features finally stood out. The most appropriate number of tissue segments was also determined according to AMI score. Moreover, we introduced Co-Clustering algorithm to MSI data to simultaneously group m/z variables and spatial pixels, so potential biomarkers associated to each sub-region were discovered without the need of further analysis. Eventually, by integrating the segmentation outcomes based on MSI and H&E image data, the confidence level of the segment assignment was displayed for each pixel, which offered a much more informative and compelling way to present the segmentation results.
Corporate communication and media coverage of abnormal returns – evidence from the Portuguese capital market
Authors: Alves Carlos Francisco , Silva Ana Luísa 
Published: July 2020

PurposeInvestor relations literature reports that after an era that “the higher the stock price, the better”, currently investor relations entered into a new era where “overvaluation is perhaps as bad as undervaluation” (Laskin, 2018a, p. 19). This paper searches for evidence on whether news coverage around abnormal returns indicates that corporate communication effectively seek fair value prices.Design/methodology/approachUsing data of the Portuguese market, it investigates if the news coverage and the investor relations' influence on such coverage (namely as a source of the news) are symmetrical before and after extreme abnormal positive or negative returns. This paper uses event study methodology, performs content analysis and applies statistical and econometric analyses.FindingsThe findings are consistent with the idea that companies communicate differently in face of positive and negative abnormal returns. Particularly, before the event, companies are more frequently cited as a source of the news for positive events. This indicates that companies seek to capitalize the positive impact of the favourable subsequent disclosures. After the occurrence of abnormal returns, companies are more often a source of the news for negative cases, seeking to mitigate their impact. Additionally, after negative events companies are more frequently mentioned in the news with a positive content than they are mentioned before.Social implicationsThe new approach of this study allows the companies' information stakeholders (namely investors and regulators) to become more informed and critical in the analysis of news coverage and its sources.Originality/valueAs far as the authors of the paper know, this is the first study that addresses the question of eventual asymmetric behaviour of companies’ communication in face of positive and negative abnormal returns.