bluuebunny/crossref_metadata_2025_split huggingface dataset:
State-by-State prediction of likely COVID-19 scenarios in the United States and assessment of the role of testing and control measures
Authors: Zhai Zheng-Meng , Long Yong-Shang , Kang Jie , Li Yi-Lin , Zeng Lang , Han Li-Lei , Lin Zhao-Hua , Zeng Ying-Qi , Wu Da-Yu , Tang Ming , Xu Di , Liu Zonghua , Lai Ying-Cheng 
Published: April 2020

AbstractDue to the heterogeneity among the States in the US, predicting COVID-19 trends and quantitatively assessing the effects of government testing capability and control measures need to be done via a State-by-State approach. We develop a comprehensive model for COVID-19 incorporating time delays and population movements. With key parameter values determined by empirical data, the model enables the most likely epidemic scenarios to be predicted for each State, which are indicative of whether testing services and control measures are vigorous enough to contain the disease. We find that government control measures play a more important role than testing in suppressing the epidemic. The vast disparities in the epidemic trends among the States imply the need for long-term placement of control measures to fully contain COVID-19.
Demographic and Socio-Economic Factors, and Healthcare Resource Indicators Associated with the Rapid Spread of COVID-19 in Northern Italy: An Ecological Study
Authors: Buja Alessandra , Paganini Matteo , Cocchio Silvia , Scioni Manuela , Rebba Vincenzo , Baldo Vincenzo 
Published: April 2020

ABSTRACTBackgroundCOVID-19 rapidly escalated into a pandemic, threatening 213 countries, areas, and territories the world over. We aimed to identify potential province-level socioeconomic determinants of the virus’s dissemination, and explain between-province differences in the speed of its spread, based on data from 36 provinces of Northern Italy.MethodsThis is an ecological study. We included all confirmed cases of SARS-CoV-2 reported between February 24th and March 30th, 2020. For each province, we calculated the trend of contagion as the relative increase in the number of individuals infected between two time endpoints, assuming an exponential growth. Pearson’s test was used to correlate the trend of contagion with a set of healthcare-associated, economic, and demographic parameters by province. The virus’s spread was input as a dependent variable in a stepwise OLS regression model to test the association between rate of spread and province-level indicators.FindingsMultivariate analysis showed that the spread of COVID-19 was correlated negatively with aging index (p-value=0.003), and positively with public transportation per capita (p-value=0.012), the % of private long-term care hospital beds and, to a lesser extent (p-value=0.070), the % of private acute care hospital beds (p-value=0.006).InterpretationDemographic and socioeconomic factors, and healthcare organization variables were found associated with a significant difference in the rate of COVID-19 spread in 36 provinces of Northern Italy. An aging population seemed to naturally contain social contacts. The availability of healthcare resources and their coordination could play an important part in spreading infection.
Pooled RNA sample reverse transcriptase real time PCR assay for SARS CoV-2 infection: a reliable, faster and economical method
Authors: Gupta Ekta , Padhi Abhishek , Khodare Arvind , Aggarwal Reshu , Ramachnadran Krithiga , Mehta Vibha , Kilikdar Mousumi , Dubey Shantanu , Kumar Guresh , Sarin Shiv Kumar 
Published: April 2020

ABSTRACTBackgroundCorona virus disease 2019 (COVID-19) which initially started as a cluster of pneumonia cases in the Wuhan city of China has now become a full blown pandemic. Timely diagnosis of COVID-19 is the key in containing the pandemic and breaking the chain of transmission. In low and middle income countries availability of testing kits has become the major bottle neck in testing. Novel methods like pooling of samples are the need of the hour.MethodExtracted RNA samples were randomly placed in pools of 8 on a 96 well plate. Both individual RNA (ID) and pooled RNA RT-qPCR for the screening E gene were done in the same plate and the positivity for the E gene was seen.ResultsThe present study demonstrated that pool testing with 8 RNA samples can easily detect even up to a single positive sample with Ct value as high as 38. The present study also showed that the results of pool testing is not affected by number of positive samples in a pool.ConclusionPooling of 8 RNA samples can reduce the time and expense by one eighth, and can help expand diagnostic capabilities, especially during constrained supply of reagents and PCR kits for the diagnosis of SARS-CoV-2 infection.
Key predictors of attending hospital with COVID19: An association study from the COVID Symptom Tracker App in 2,618,948 individuals
Authors: Lochlainn Mary Ni , Lee Karla A. , Sudre Carole H. , Varsavsky Thomas , Cardoso M. Jorge , Menni Cristina , Bowyer Ruth C. E. , Nguyen Long H. , Drew David A. , Ganesh Sajaysurya , du Cadet Julien Lavigne , Visconti Alessia , Freidin Maxim B. , Modat Marc , Graham Mark S , Pujol Joan Capdevila , Murray Benjamin , Moustafa Julia S El-Sayed , Zhang Xinyuan , Davies Richard , Falchi Mario , Wolf Jonathan , Spector Tim D. , Chan Andrew T. , Ourselin Sebastien , Steves Claire J. 
Published: April 2020

AbstractObjectivesWe aimed to identify key demographic risk factors for hospital attendance with COVID-19 infection.DesignCommunity surveySettingThe COVID Symptom Tracker mobile application co-developed by physicians and scientists at King’s College London, Massachusetts General Hospital, Boston and Zoe Global Limited was launched in the UK and US on 24thand 29thMarch 2020 respectively. It captured self-reported information related to COVID-19 symptoms and testing.Participants2,618,948 users of the COVID Symptom Tracker App. UK (95.7%) and US (4.3%) population. Data cut-off for this analysis was 21stApril 2020.Main outcome measuresVisit to hospital and for those who attended hospital, the need for respiratory support in three subgroups (i) self-reported COVID-19 infection with classical symptoms (SR-COVID-19), (ii) selfreported positive COVID-19 test results (T-COVID-19), and (iii) imputed/predicted COVID-19 infection based on symptomatology (I-COVID-19). Multivariate logistic regressions for each outcome and each subgroup were adjusted for age and gender, with sensitivity analyses adjusted for comorbidities. Classical symptoms were defined as high fever and persistent cough for several days.ResultsOlder age and all comorbidities tested were found to be associated with increased odds of requiring hospital care for COVID-19. Obesity (BMI >30) predicted hospital care in all models, with odds ratios (OR) varying from 1.20 [1.11; 1.31] to 1.40 [1.23; 1.60] across population groups. Pre-existing lung disease and diabetes were consistently found to be associated with hospital visit with a maximum OR of 1.79 [1.64,1.95] and 1.72 [1.27; 2.31]) respectively. Findings were similar when assessing the need for respiratory support, for which age and male gender played an additional role.ConclusionsBeing older, obese, diabetic or suffering from pre-existing lung, heart or renal disease placed participants at increased risk of visiting hospital with COVID-19. It is of utmost importance for governments and the scientific and medical communities to work together to find evidence-based means of protecting those deemed most vulnerable from COVID-19.Trial registrationThe App Ethics have been approved by KCL ethics Committee REMAS ID 18210, review reference LRS-19/20-18210
Custommune: a web tool to design personalized and population-targeted vaccine epitopes
Authors: Tarek Mohammad , Elhefnawi Mahmoud , Maricato Juliana Terzi , Diaz Ricardo Sobhie , Shytaj Iart Luca , Savarino Andrea 
Published: April 2020

AbstractComputational prediction of immunogenic epitopes is a promising platform for therapeutic and preventive vaccine design. A potential target for this strategy is human immunodeficiency virus (HIV-1), for which, despite decades of efforts, no vaccine is available. In particular, a therapeutic vaccine devised to eliminate infected cells would represent a key component of cure strategies. HIV peptides designed based on individual viro-immunological data from people living with HIV/AIDS have recently shown able to induce post-therapy viral set point abatement. However, the reproducibility and scalability of this method is curtailed by the errors and arbitrariness associated with manual peptide design as well as by the time-consuming process.We herein introduce Custommune, a user-friendly web tool to design personalized and population-targeted vaccines. When applied to HIV-1, Custommune predicted personalized epitopes using patient specific Human Leukocyte Antigen (HLA) alleles and viral sequences, as well as the expected HLA-peptide binding strength and potential immune escape mutations. Of note, Custommune predictions compared favorably with manually designed peptides administered in a recent phase II clinical trial (NCT02961829).Furthermore, we utilized Custommune to design preventive vaccines targeted for populations highly affected by COVID-19. The results allowed the identification of peptides tailored for each population and predicted to elicit both CD8+T-cell immunity and neutralizing antibodies against structurally conserved epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).Overall, our data describe a new tool for rapid development of personalized or population-based immunotherapy against chronic and acute viral infections.
Interim Analysis of Pandemic Coronavirus Disease 2019 (COVID-19) and the SARS-CoV-2 virus in Latin America and the Caribbean: Morbidity, Mortality and Molecular Testing Trends in the Region
Authors: Simbaña-Rivera Katherine , Gómez-Barreno Lenin , Guerrero Jhon , Simbaña-Guaycha Fernanda , Fernández Raúl , López-Cortés Andrés , Lister Alex , Ortiz-Prado Esteban 
Published: April 2020

AbstractBackgroundThe relentless advance of the SARS-CoV-2 virus pandemic has resulted in a significant burden on countries, regardless of their socio-economic conditions. The virus has infected more than 2.5 million people worldwide, causing to date more than 150,000 deaths in over 210 countries.ObjectiveThe aim of this study was to describe the trends in cases, tests and deaths related to novel coronavirus disease (COVID-19) in Latin American and Caribbean (LAC) countries.MethodologyData were retrieved from the WHO-Coronavirus Disease (COVID-2019) situation reports and the Center for Systems Science and Engineering (CSSE) databases from Johns Hopkins University. Descriptive statistics including death rates, cumulative mortality and incidence rates, as well as testing rates per population at risk were performed. A comparison analysis among countries with ≥50 confirmed cases was performed from February 26th, 2020 to April 8th, 2020.ResultsBrazil had the greatest number of cases and deaths in the region. Panama experienced a rapid increase in the number of confirmed cases with Trinidad and Tobago, Bolivia and Honduras having the highest case fatality rates. Panama and Chile conducted more tests per million inhabitants and more tests per day per million inhabitants, followed by Uruguay and El Salvador. Dominican Republic, Bolivia, Ecuador and Brazil had the highest positive test rates.ConclusionsThe COVID-19 disease pandemic caused by the SARS-CoV-2 virus has progressed rapidly in LAC countries. Some countries have been affected more severely than others, with some adopting similar disease control methods to help slow down the spread of the virus. With limited testing and other resources, social distancing is needed to help alleviate the strain on already stretched health systems.
Radiological appearances of Anastomotic Leakage after Radical Gastrectomy
Authors: Sah Birendra Kumar , Yang Zhang , Huan Zhang , Jian Li , Wentao Liu , Chao Yan , Chen Li , Min Yan , Gang Zhu Zheng 
Published: April 2020

AbstractBackgroundAnastomotic leakage is a critical postoperative complication after gastric cancer surgery. Previous studies have not specified radiological findings of anastomotic leakage. We investigated the potential burden caused by postoperative anastomotic leakage and explored the objective appearances of anastomotic leakage on computed tomography (CT) examination.MethodsGastric cancer patients who underwent curative gastrectomy and had a CT examination after surgery were included in this study. Propensity score (PS) matching generated 70 cases (35 cases of anastomotic leakage and 35 cases of no anastomotic leak) among 210 eligible cases. Univariate and multivariate analyses were used to identify the predictive variables of CT findings.ResultsMore severe postoperative complications were observed in patients who had an anastomotic failure than those without anastomotic leakage(p<0.05). The median number of postoperative days (PODs) was 18 days for patients with no anastomotic leak, but the length of stay was almost three times longer (50 days) in patients with anastomotic leakage(p<0.05). In the univariate analysis, we observed a significant association between anastomotic leakage and five CT variables, including pneumoperitoneum, pneumoseroperitoneum (intra-abdominal accumulation of mixed gas and fluid), accumulation of extraluminal gas at the anastomosis site, seroperitoneum and extraluminal fluid collection at the anastomosis site (p<0.05). The multivariate analysis of the CT parameters revealed that the accumulation of extraluminal gas at the anastomosis site is the independent diagnostic parameters of a postoperative anastomotic leakage (p<0.05).ConclusionsThe occurrence of an anastomotic leakage significantly compromises the patients and increases the treatment burden. The CT variables of this study are beneficial to rule out anastomotic leakage after gastric cancer surgery. Extraluminal gas at the anastomosis site is highly suggestive of anastomotic leakage.
Altered sensory neuron development in CMT2D mice is site-specific and linked to increased GlyRS levels
Authors: Sleigh James N. , Mech Aleksandra M. , Aktar Tahmina , Zhang Yuxin , Schiavo Giampietro 
Published: April 2020

AbstractDominant, missense mutations in the widely and constitutively expressedGARS1gene cause a peripheral neuropathy that usually begins in adolescence and principally impacts the upper limbs. Caused by a toxic gain-of-function in the encoded glycyl-tRNA synthetase (GlyRS) enzyme, the neuropathology appears to be independent of the canonical role of GlyRS in aminoacylation. Patients display progressive, life-long weakness and wasting of muscles in hands followed by feet, with frequently associated deficits in sensation. When dysfunction is observed in motor and sensory nerves, there is a diagnosis of Charcot-Marie-Tooth disease type 2D (CMT2D), or distal hereditary motor neuropathy type V if the symptoms are purely motor. The cause of this varied sensory involvement remains unresolved, as are the pathomechanisms underlying the selective neurodegeneration characteristic of the disease. We have previously identified in CMT2D mice that neuropathy-causingGarsmutations perturb sensory neuron fate and permit mutant GlyRS to aberrantly interact with neurotrophin receptors (Trks). Here, we extend this work by interrogating further the anatomy and function of the CMT2D sensory nervous system in mutantGarsmice, obtaining several key results: 1) sensory pathology is restricted to neurons innervating the hindlimbs; 2) perturbation of sensory development is not common in mouse models of neuromuscular disease; 3)in vitroaxonal transport of signalling endosomes is not impaired in afferent neurons of all CMT2D mouse models; and 4)Garsexpression is selectively elevated in a subset of sensory neurons and linked to sensory developmental defects. These findings highlight the importance of comparative neurological assessment in mouse models of disease and shed light on key proposed neuropathogenic mechanisms inGARS1-linked neuropathy.
Fluorescent in situ sequencing of DNA barcoded antibodies
Authors: Kohman Richie E. , Church George M. 
Published: April 2020

AbstractBiological tissues contain thousands of different proteins yet conventional antibody staining can only assay a few at a time because of the limited number of spectrally distinct fluorescent labels. The capacity to map the location of hundreds or thousands of proteins within a single sample would allow for an unprecedented investigation of the spatial proteome, and give insight into the development and function of diseased and healthy tissues. In order to achieve this goal, we propose a new technology that leverages established methodologies for in situ imaging of nucleic acids to achieve near limitless multiplexing. The exponential scaling power of DNA technologies ties multiplexing to the number of DNA nucleotides sequenced rather than the number of spectrally distinct labels. Here we demonstrate that barcode sequencing can be applied to in situ proteomics by sequencing DNA conjugated antibodies bound to biological samples. In addition, we show a signal amplification method which is compatible with barcoded antibodies.
Sorting nexin-27 regulates AMPA receptor trafficking through the synaptic adhesion protein LRFN2
Authors: McMillan Kirsty J. , Banks Paul J. , Hellel Francesca L. N. , Carmichael Ruth E. , Clairfeuille Thomas , Evans Ashley J. , Heesom Kate J. , Lewis Phillip , Collins Brett M. , Bashir Zafar I. , Henley Jeremy M. , Wilkinson Kevin A. , Cullen Peter J. 
Published: April 2020

AbstractThe endosome-associated cargo adaptor sorting nexin-27 (SNX27) is linked to various neuropathologies through sorting of integral proteins to the synaptic surface, most notably AMPA receptors. To provide a broader view of SNX27-associated pathologies we have performed unbiased proteomics to identify new neuronal SNX27-dependent cargoes, and identified proteins linked to excitotoxicity (SLC1A3, SLC4A7, SLC6A11), epilepsy, intellectual disabilities and working memory deficits (KCNT2, ADAM22, KIDINS220, LRFN2). Focusing on the synaptic adhesion molecule leucine-rich repeat and fibronectin type-III domain-containing protein 2 (LRFN2), we establish that SNX27 binds to LRFN2 and is responsible for regulating its endosomal sorting. LRFN2 associates with AMPA receptors and knockdown of LRFN2 phenocopies SNX27 depletion in decreasing surface expression of AMPA receptors, reducing synaptic activity and attenuating hippocampal long-term potentiation. Our evidence suggests that, in contrast to previous reports, SNX27 does not directly bind to AMPA receptors, and instead controls AMPA receptor-mediated synaptic transmission and plasticity indirectly through the endosomal sorting of LRFN2. Overall, our study provides new molecular insight into the perturbed function of SNX27 and LRFN2 in a range of neurological conditions.
Entraining alpha activity using visual stimulation in patients with chronic musculoskeletal pain. A feasibility study
Authors: Arendsen Laura J. , Henshaw James , Brown Christopher A. , Sivan Manoj , Taylor Jason R. , Trujillo-Barreto Nelson J. , Casson Alexander J. , Jones Anthony K. P. 
Published: April 2020

AbstractEntraining alpha activity with rhythmic visual, auditory, and electrical stimulation can reduce experimentally induced pain. However, evidence for alpha entrainment and pain reduction in patients with chronic pain is limited. This feasibility study investigated whether visual alpha stimulation can increase alpha power in patients with chronic musculoskeletal pain and secondarily, if chronic pain was reduced following stimulation. In a within-subject design, 22 patients underwent 4-minute periods of stimulation at 10 Hz (alpha), 7 Hz (high-theta, control), and 1 Hz (control) in a pseudo-randomized order. Patients underwent stimulation both sitting and standing and verbally rated their pain before and after each stimulation block on a 0-10 numerical rating scale. Global alpha power was significantly higher during 10 Hz compared to 1 Hz stimulation when patients were standing (t = −6.08, p <.001). On a more regional level, a significant increase of alpha power was found in the right-middle and left-posterior region when patients were sitting. With respect to our secondary aim, no significant reduction of pain intensity and unpleasantness was found. However, only the alpha stimulation resulted in a minimal clinically important difference in at least 50% of participants for pain intensity (50%) and unpleasantness ratings (65%) in the sitting condition. This study provides initial evidence for the potential of visual stimulation as a means to enhance alpha activity in patients with chronic musculoskeletal pain. The brief period of stimulation was insufficient to reduce chronic pain. This study is the first to provide evidence that a brief period of visual stimulation at alpha frequency can significantly increase alpha power in patients with chronic musculoskeletal pain. Further study is warranted to investigate optimal dose and individual stimulation parameters to achieve pain relief in these patients.
Genome-Enabled Discovery of Anthraquinone Biosynthesis inSenna tora
Authors: Kang Sang-Ho , Pandey Ramesh Prasad , Lee Chang-Muk , Sim Joon-Soo , Jeong Jin-Tae , Choi Beom-Soon , Jung Myunghee , Won So Youn , Oh Tae-Jin , Yu Yeisoo , Kim Nam-Hoon , Lee Ok Ran , Lee Tae-Ho , Bashyal Puspalata , Kim Tae-Su , Kim Chang-Kug , Kim Jung Sun , Ahn Byoung Ohg , Rhee Seung Yon , Sohng Jae Kyung 
Published: April 2020

AbstractSenna torais a widely used medicinal plant. Its health benefits have been attributed to the large quantity of anthraquinones, but how they are made in plants remains a mystery. To identify the genes responsible for plant anthraquinone biosynthesis, we sequenced and annotated the genome ofS. toraat the chromosome level with contig N50 and super-scaffold N50 of 4.03 Mb and 41.7 Mb. Comparison among related plant species showed that a chalcone synthase-like (CHS-L) gene family has lineage-specifically and rapidly expanded inS. tora. Combining genomics, transcriptomics, metabolomics, and biochemistry, we identified a CHS-L responsible for biosynthesis of anthraquinones, the first example in plants. TheS. torareference genome will accelerate the discovery of biologically active anthraquinone biosynthesis pathways in medicinal plants.One Sentence SummaryThe chromosome-scale reference genome of a medicinal plantSenna tora, transcriptomics, metabolomics, and biochemical analysis provide new insights into anthraquinone biosynthesis in plants.
VoroCNN: Deep convolutional neural network built on 3D Voronoi tessellation of protein structures
Authors: Igashov Ilia , Olechnovic Kliment , Kadukova Maria , Venclovas Česlovas , Grudinin Sergei 
Published: April 2020

MotivationEffective use of evolutionary information has recently led to tremendous progress in computational prediction of three-dimensional (3D) structures of proteins and their complexes. Despite the progress, the accuracy of predicted structures tends to vary considerably from case to case. Since the utility of computational models depends on their accuracy, reliable estimates of deviation between predicted and native structures are of utmost importance.ResultsFor the first time we present a deep convolutional neural network (CNN) constructed on a Voronoi tessellation of 3D molecular structures. Despite the irregular data domain, our data representation allows to efficiently introduce both convolution and pooling operations of the network. We trained our model, called VoroCNN, to predict local qualities of 3D protein folds. The prediction results are competitive to the state of the art and superior to the previous 3D CNN architectures built for the same task. We also discuss practical applications of VoroCNN, for example, in the recognition of protein binding interfaces.AvailabilityThe model, data, and evaluation tests are available athttps://team.inria.fr/nano-d/software/vorocnn/.Contactceslovas.venclovas@bti.vu.lt,sergei.grudinin@inria.fr