bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serratia inhibens sp. nov., a new antifungal species isolated from potato (Solanum tuberosum)
Authors: Hennessy Rosanna C. , Dichmann Søs I. , Martens Helle Juel , Zervas Athanasios , Stougaard Peter 
Published: June 2020

A novel bacterial strain, S40T, with strong antifungal activity was isolated from the rhizosphere of green potato collected from Zealand, Denmark. Polyphasic analysis with a combined phenotypic, phylogenetic and genomic approach was used to characterize S40T. Phylogenetic analysis based on the 16S rRNA gene and MLSA (concatenated gyrB, rpoD, infB and atpD sequences) showed that strain S40T was affiliated with the genus

Serratia

and with

Serratia plymuthica

PRI-2C as the closest related strain [average nucleotide identity (ANI), 99.26 %; DNA–DNA hybridization (dDDH), 99.20%]. However, whole genome sequence analyses revealed that S40T and

S. plymuthica

PRI-2C genomes displayed lower similarities when compared to all other

S. plymuthica

strains (ANI ≤94.34 %; dDDH ≤57.6 % relatedness). The DNA G+C content of strain S40T was determined to be 55.9 mol%. Cells of the strain were Gram-negative, rod-shaped, facultative anaerobic and displayed growth at 10–37 °C (optimum, 25–30 °C) and at pH 6–9 (optimum, pH 6–7). Major fatty acids were C16 : 0 (27.9 %), summed feature (C16 : 1
ω6c/C16 : 1 ω7c; 18.0 %) and C17 : 0 cyclo (15.1 %). The respiratory quinone was determined to be Q8 (94 %) and MK8 (95 %) and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The results of phenotypic, phylogenetic and genomic analyses support the hypothesis that strain S40T represents a novel species of the genus

Serratia

, for which the name Serratia inhibens sp. nov. is proposed. The type strain is S40T (=LMG 31467T=NCIMB 15235T). In addition, we propose that

S. plymuthica

PRI-2C is reclassified and transferred to the species S. inhibens as S. inhibens PRI-2C.
Proteomics Uncovers Immunosuppression in COVID-19 Patients with Long Disease Course
Authors: Tang Shaohua , Sun Rui , Xiao Qi , Mao Tingting , Ge Weigang , Huang Chongquan , Luo Meng , Qian Liujia , Chen Hao , Zhang Qiushi , Li Sainan , Liu Wei , Li Shufei , Xu Xueqin , Li Huanzheng , Wu Lianpeng , Dai Jianyi , Gao Huanhuan , Li Lu , Lu Tian , Liang Xiao , Cai Xue , Ruan Guan , Liu Kexin , Xu Fei , Li Yan , Zhu Yi , Huang Jianping , Guo Tiannan 
Published: June 2020

AbstractLittle is known regarding why a subset of COVID-19 patients exhibited prolonged positivity of SARS-CoV-2 infection. Here, we studied the sera proteomic dynamics in 37 COVID-19 patients over nine weeks, quantifying 2700 proteins with high quality. Remarkably, we found that during the first three weeks since disease onset, while clinical symptoms and outcome were indistinguishable, patients with prolonged disease course displayed characteristic immunological responses including enhanced Natural Killer cell-mediated innate immunity and regulatory T cell-mediated immunosuppression. We further showed that it is possible to predict the length of disease course using machine learning based on blood protein levels during the first three weeks. Validation in an independent cohort achieved an accuracy of 82%. In summary, this study presents a rich serum proteomic resource to understand host responses in COVID-19 patients and identifies characteristic Treg-mediated immunosuppression in patients with prolonged disease course, nominating new therapeutic target and diagnosis strategy.
Density Dependent Resource Budget Model for Alternate Bearing
Authors: Esmaeili Shadisadat , Hastings Alan , Abbott Karen , Machta Jonathan , Nareddy Vahini Reddy 
Published: June 2020

ABSTRACTAlternate bearing, seen in many types of plants, is the variable yield with a strongly biennial pattern. In this paper, we introduce a new model for alternate bearing behavior. Similar to the well-known Resource Budget Model, our model is based on the balance between photosynthesis (carbon accumulation) and reproduction processes. We consider two novel features with our model, 1) the existence of a finite capacity in the tree’s resource reservoir and 2) the possibility of having low (but non-zero) yield when the tree’s energy level is low. We achieve the former using a density dependent resource accumulation function, and the latter by removing the concept of the well-defined threshold used in the Resource Budget Model. At the level of an individual tree, our model has a stable two-cycle solution, which is suitable to model plants in which the alternate bearing behavior is pronounced. We incorporate environmental stochasticity by adding two uncorrelated noise terms to the parameters of the model associated with the carbon accumulation and reproduction processes. Furthermore, we examine the model’s behavior on a system of two coupled trees with direct coupling. Unlike the coupled Resource Budget Model, for which the only stable solution is the out-of-phase solution, our model with diffusive coupling has stable in-phase period-2 solutions. This suggests that our model might serve to explain spatial synchrony on a larger scale.
Neuronal firing in the medial temporal lobe reflects human working memory workload, performance and capacity
Authors: Boran Ece , Hilfiker Peter , Stieglitz Lennart , Grunwald Thomas , Sarnthein Johannes , Klaver Peter 
Published: June 2020

2AbstractThe involvement of the medial temporal lobe (MTL) in working memory is controversially discussed. Critically, it is unclear whether and how the MTL supports performance of working memory. We recorded single neuron firing in 13 epilepsy patients while they performed a visual working memory task. The number of colored squares in the stimulus set determined the workload of the trial. We used the subjects’ memory capacity (Cowan’s K) to split them into a low and high capacity group. We found MTL neurons that showed persistent firing during the maintenance period. Firing was higher in the hippocampus for trials with correct compared to incorrect performance. Population firing predicted workload particularly during the maintenance period. Prediction accuracy of single trial activity was strongest for neurons in the entorhinal cortex of low capacity subjects. We provide evidence that low capacity subjects recruit their MTL to cope with an overload of working memory task demands.1SignificanceHumans are highly limited in processing multiple objects over a short period of time. The capacity to retain multiple objects in working memory is typically associated with frontal and parietal lobe functioning, even though medial temporal lobe (MTL) neural architecture seems capable to process such information. However, there are conflicting findings from patient, electrophysiological and neuroimaging studies. Here we show for the first time that correct performance, workload and individual performance differences are reflected in separate mechanisms of neural activity within the MTL during maintenance of visual information in working memory. The data suggest that low capacity subjects use the MTL to process the overload of information.
Comparative analysis of coronavirus genomic RNA structure reveals conservation in SARS-like coronaviruses
Authors: Sanders Wes , Fritch Ethan J. , Madden Emily A. , Graham Rachel L. , Vincent Heather A. , Heise Mark T. , Baric Ralph S. , Moorman Nathaniel J. 
Published: June 2020

AbstractCoronaviruses, including SARS-CoV-2 the etiological agent of COVID-19 disease, have caused multiple epidemic and pandemic outbreaks in the past 20 years1–3. With no vaccines, and only recently developed antiviral therapeutics, we are ill equipped to handle coronavirus outbreaks4. A better understanding of the molecular mechanisms that regulate coronavirus replication and pathogenesis is needed to guide the development of new antiviral therapeutics and vaccines. RNA secondary structures play critical roles in multiple aspects of coronavirus replication, but the extent and conservation of RNA secondary structure across coronavirus genomes is unknown5. Here, we define highly structured RNA regions throughout the MERS-CoV, SARS-CoV, and SARS-CoV-2 genomes. We find that highly stable RNA structures are pervasive throughout coronavirus genomes, and are conserved between the SARS-like CoV. Our data suggests that selective pressure helps preserve RNA secondary structure in coronavirus genomes, suggesting that these structures may play important roles in virus replication and pathogenesis. Thus, disruption of conserved RNA secondary structures could be a novel strategy for the generation of attenuated SARS-CoV-2 vaccines for use against the current COVID-19 pandemic.
Bio-JOIE: Joint Representation Learning of Biological Knowledge Bases
Authors: Hao Junheng , Ju Chelsea J.-T , Chen Muhao , Sun Yizhou , Zaniolo Carlo , Wang Wei 
Published: June 2020

AbstractThe widespread of Coronavirus has led to a worldwide pandemic with a high mortality rate. Currently, the knowledge accumulated from different studies about this virus is very limited. Leveraging a wide-range of biological knowledge, such as gene on-tology and protein-protein interaction (PPI) networks from other closely related species presents a vital approach to infer the molecular impact of a new species. In this paper, we propose the transferred multi-relational embedding modelBio-JOIEto capture the knowledge of gene ontology and PPI networks, which demonstrates superb capability in modeling the SARS-CoV-2-human protein interactions.Bio-JOIEjointly trains two model components. Theknowledge modelencodes the relational facts from the protein and GO domains into separated embedding spaces, using a hierarchy-aware encoding technique employed for the GO terms. On top of that, thetransfer modellearns a non-linear transformation to transfer the knowledge of PPIs and gene ontology annotations across their embedding spaces. By leveraging only structured knowledge,Bio-JOIEsignificantly outperforms existing state-of-the-art methods in PPI type prediction on multiple species. Furthermore, we also demonstrate the potential of leveraging the learned representations on clustering proteins with enzymatic function into enzyme commission families. Finally, we show thatBio-JOIEcan accurately identify PPIs between the SARS-CoV-2 proteins and human proteins, providing valuable insights for advancing research on this new disease.
Early impacts of the COVID-19 pandemic on mental health care and on people with mental health conditions: framework synthesis of international experiences and responses
Authors: Rains Luke Sheridan , Johnson Sonia , Barnett Phoebe , Steare Thomas , Needle Justin J , Carr Sarah , Taylor Billie Lever , Bentivegna Francesca , Edbrooke-Childs Julian , Scott Hannah Rachel , Rees Jessica , Shah Prisha , Lomani Jo , Chipp Beverley , Barber Nick , Dedat Zainab , Oram Sian , Morant Nicola , Simpson Alan ,   COVID-19 Mental Health Policy Research Unit Group
Published: June 2020

AbstractPurposeThe COVID-19 pandemic has many potential impacts on people with mental health conditions and on mental health care, including direct consequences of infection, effects of infection control measures and subsequent societal changes. We aimed to map early impacts of the pandemic on people with pre-existing mental health conditions and services they use, and to identify individual and service-level strategies adopted to manage these.MethodsWe searched for relevant material in the public domain published before 30 April 2020, including papers in scientific and professional journals, published first person accounts, media articles, and publications by governments, charities and professional associations. Search languages were English, French, German, Italian, Spanish, and Mandarin Chinese. Relevant content was retrieved and summarised via a rapid qualitative framework synthesis approach.ResultsWe found 872 eligible sources from 29 countries. Most documented observations and experiences rather than reporting research data. We found many reports of deteriorations in symptoms, and of impacts of loneliness and social isolation and of lack of access to services and resources, but sometimes also of resilience, effective self-management and peer support. Immediate service challenges related to controlling infection, especially in inpatient and residential settings, and establishing remote working, especially in the community. We summarise reports of swiftly implemented adaptations and innovations, but also of pressing ethical challenges and concerns for the future.ConclusionOur analysis captures the range of stakeholder perspectives and experiences publicly reported in the early stages of the COVID-19 pandemic in several countries. We identify potential foci for service planning and research.
Economic burden of smoking attributed illnesses in Pakistan
Authors: Saqib Muhammad Arif Nadeem , Malik Ashar , Rafique Ibrar , Raza Faiz Ahmed , Obaidullah  , Sajjad Shaimuna Fareeha , Abid Sumera , Majid Rukhsana , Kamal Tahira , Islam Ziauddin 
Published: June 2020

ABSTRACTBackgroundThe estimates of economic burden due to smoking attributed illnesses provide an opportunity to assess its overall impact on the economy and generate evidence for public health policy interventions for tobacco control. In this study, we estimated out of pocket expenditures on tobacco attributed illnesses and smoking attributable burden in Pakistan.MethodsWe used a prevalence-based disease-specific cost approach by including three major tobacco attributed illnesses i.e. lung cancer, chronic obstructive pulmonary disease, and cardiovascular diseases. Our analysis included out of pocket healthcare expenditures including direct and indirect costs which were estimated by interviewing the patients of selected illnesses. The smoking-attributable expenditure was calculated by the WHO tool kit.ResultsIn 2018, the economic burden attributed to smoking related illnesses was Rs 192 billion (USD 1.3 billion). Smoking-attributable expenditure on cardiovascular disease was Rs 123 billion (USD 0.9 billion) which was 69% of the total economic cost of tobacco attributed illnesses in Pakistan. The economic cost in males was nearly three times higher than females.ConclusionsOur study showed a significant economic burden due to tobacco attributed illnesses in Pakistan which can be prevented by implementing tobacco control policies effectively.
A compound Dirichlet-Multinomial model for provincial level Covid-19 predictions in South Africa
Authors: de Waal Alta , de Waal Daan 
Published: June 2020

AbstractAccurate prediction of COVID-19 related indicators such as confirmed cases, deaths and recoveries play an important in understanding the spread and impact of the virus, as well as resource planning and allocation. In this study, we approach the prediction problem from a statistical perspective and predict confirmed cases and deaths on a provincial level. We propose the compound Dirichlet Multinomial distribution to estimate the proportion parameter of each province as mutually exclusive outcomes. Furthermore, we make an assumption of exponential growth of the total cummulative counts in order to predict future total counts. The outcomes of this approach is not only prediction. The variation of the proportion parameter is characterised by the Dirichlet distribution, which provides insight in the movement of the pandemic across provinces over time.
Willingness and acceptability of anxiety and depression screening among women living with HIV in Ethiopia
Authors: Yousuf Abdilahi , Musa Ramli , Isa Muhammad Lokman Md. , Arifin Siti Roshaidai Mohd 
Published: June 2020

AbstractIntroductionIntegration of related health services, such as screening of depression in HIV care is crucial for improving the quality of care and enhancing the use of scarce resources in developing countries. However, commonly these interrelated health services are commonly provided separately and there are many missed opportunities. Little is known about the client-related non-implementation issues. This study aims at examining the acceptability of anxiety and depression screening among women living with HIV.Material and methodsThis was a facility based cross-sectional study which included women living with HIV attending two hospitals in Jijiga town, Ethiopia. The study participants were identified using systematic random sampling method. An exit interview was conducted with the use of a pretested questionnaire. The gathered data was analysed using SPSS version 23 and multivariate logistic regression model was used to determine factors associated with the factors associated with the acceptance of anxiety and depression screening.ResultsA total of 409 women participated in this study. Though, only 115 (28.1%) were aware about the existence of anxiety and depression screening, 357 (87.3%) accepted to receive the screening for anxiety and depression. Requisite of partner approval was the most common reason for not accepting the screening of anxiety and depression 21 (40.4%). When used multivariate logistic regression model; holding college level education, divorced and were living without partner, being self employed by occupation, aware of the existing screening service, source of information from health care providers and history of previous screening were significantly associated with acceptance of depression screening.ConclusionThis research has shown that women participant living with HIV were willing to undergo the screening for depression, hence future interventions should focus on the integration of mental health screening in HIV clinical setup.
Impact of Daily Weather on COVID-19 outbreak in India
Authors: Gupta Amitesh , Pradhan Biswajeet 
Published: June 2020

AbstractThe COVID-19 pandemic has outspread obstreperously in India. As of June 04, 2020, more than 2 lakh cases have been confirmed with a death rate of 2.81%. It has been noticed that, out of each 1000 tests, 53 result positively infected. In order to investigate the impact of weather conditions on daily transmission occurring in India, daily data of Maximum (TMax), Minimum (TMin), Mean (TMean) and Dew Point Temperature (TDew), Diurnal Temperature range (TRange), Average Relative Humidity, Range in Relative Humidity, and Wind Speed (WS) over 9 most affected cities are analysed in several time frames: weather of that day, 7, 10, 12, 14, 16 days before transmission. Spearman’s rank correlation (r) shows significant but low correlation with most of the weather parameters, however, comparatively better association exists on 14 days lag. Diurnal range in Temperature and Relative Humidity shows non-significant correlation. Analysis shows, COVID-19 cases likely to be increased with increasing air temperature, however role of humidity is not clear. Among weather parameters, Minimum Temperature was relatively better correlate than other. 80% of the total confirmed cases were registered when TMax, TMean, TMin, TRange, TDew, and WS on 12-16 days ago vary within a range of 33.6-41.3° C, 29.8-36.5° C, 24.8-30.4° C, 7.5-15.2° C, 18.7-23.6° C, and 4.2-5.75 m/s respectively, hence, it gives an idea of susceptible weather conditions for such transmission in India. Using Support Vector Machine based regression, the daily cases are profoundly estimated with more than 80% accuracy, which indicate that coronavirus transmission can’t be well linearly correlated with any single weather parameters, rather multivariate non-linear approach must be employed. Accounting lag of 12-16 days, the association found to be excellent, thus depict that there is an incubation period of 14 ± 02 days for coronavirus transmission in Indian scenario.
Risk of Depression in Family Caregivers: Unintended Consequence of COVID-19
Authors: Gallagher Stephen , Wetherell Mark A. 
Published: June 2020

BackgroundCOVID-19 is likely to exacerbate the symptoms of poor mental health family caregivers. To investigate whether rates of depression increased in caregivers during COVID-19 and whether the unintended consequences of health protective measures, i.e., social isolation, exacerbated this risk. Another aim was to see if caregivers accessed any online/phone psychological support during COVID.MethodData (1349 caregivers; 7527 non-caregivers) was extracted from Understanding Society, UK population level dataset. The General Health Questionnaire cut-off scores identifying those with and without depression were our primary outcome.ResultsAfter adjustment for confounding caregivers had a higher risk of having depression compared with non-caregivers, Odds ratio (OR) = 1.22 (95% confidence interval (95% CI), 1.05-1.40)), p=.008 evidenced by higher levels of depression pre-COVID-19 (16.7% vs 12.1%) and during COVID-19 (21.6% vs 17.9%), respectively. Further, higher levels of loneliness increased the risk of depression almost 4-fold risk in caregivers, OR = 3.85 (95% confidence interval (95% CI), 3.08-4.85)), p<.001), while access to therapy attenuated the risk (47%. While 60% of caregivers with depression reported not accessing any therapeutic support (e.g., online or face to face) during COVID-19.ConclusionCOVID-19 has had a negative impact on family caregivers’ mental health with loneliness a significant contributor to caregiver’s depression. However, despite these detriments in mental health, the majority of caregivers do not access any online or phone psychiatric support. Reducing feelings of isolation therefore provides an opportunity for psychiatric services and health care professionals to support at-risk caregivers.
Steep increases in fentanyl-related mortality west of the Mississippi River: synthesizing recent evidence from county and state surveillance
Authors: Shover Chelsea L. , Falasinnu Titilola O. , Dwyer Candice L. , Santos Nayelie Benitez , Cunningham Nicole J. , Vest Noel A. , Humphreys Keith 
Published: June 2020

ABSTRACTBackground and AimsOverdose deaths from synthetic opioids (e.g., fentanyl), increased 10-fold in the United States from 2013-2018, despite 88% of deaths occurring east of the Mississippi River. Public health professionals have long feared that further spread of fentanyl could greatly exacerbate the opioid epidemic. We aimed to measure and characterize recent fentanyl deaths in jurisdictions west of the Mississippi River.DesignSystematic search of states and counties in the Western U.S. for publicly available data on fentanyl-related deaths since the most recently published Centers for Disease Control and Prevention (CDC) statistics, which cover through December 2018. Longitudinal study using 2019 and 2020 mortality records to identify changes in fentanyl-involved mortality since most recent CDC statistics.SettingsU.S. states west of the Mississippi River.MeasurementsAnnual rate of fentanyl-involved deaths per 100,000 population. Proportion of fatal heroin-, stimulant, and prescription pill overdoses also involving fentanyl.FindingsWe identified nine jurisdictions with publicly available fentanyl death data through December 2019 or later - State of Arizona; Denver County, CO; Harris County, TX; Humboldt County, CA; King County, WA; Los Angeles County, CA; San Francisco County, CA; Siskiyou County, CA; Dallas-Fort Worth, TX metro area (Denton, Johnson, Parker, Tarrant counties. Fentanyl deaths increased in each jurisdiction. Their collective contribution to national synthetic narcotics mortality tripled from 2017 to 2019. First quarter 2020 data (available from all but San Francisco County) showed a 33% growth in fentanyl-mortality over 2019. Fentanyl-involvement in heroin, stimulant, and prescription pill deaths has grown substantially over time.ConclusionsFentanyl has spread westward, which could dramatically worsen the nation’s already severe opioid epidemic. Increasing standard-dose of naloxone, expanding Medicaid, improving coverage of addiction treatment, and public health educational campaigns should be prioritized.