bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methylotenera oryzisoli sp. nov., a lanthanide-dependent methylotrophic bacteria isolated from rice field soil
Authors: Lv Haoxin , Sahin Nurettin , Tani Akio 
Published: March 2020

A new lanthanide (Ln3+)-dependent methanol-utilizing bacterial strain, La3113T, was isolated from rice field soil and its taxonomic position was investigated using polyphasic approaches. The strain was aerobic, Gram-stain-negative, strongly motile, catalase-positive and cytochrome oxidase-positive. It could neither catalyse the hydrolysis of urea nor reduce nitrate to nitrite. Growth was observed within a temperature range of 10–40 °C and a pH range of 6–8, with optimum growth at 28 °C and pH 7. Methylamine was utilized as the single source of energy, carbon and nitrogen, and it was oxidized by methylamine dehydrogenase. C16 : 1
ω7c, C16 : 1
ω6c and C16 : 0 were the dominant cellular fatty acids. Its draft genome (2.67 Mbp and 44.9 mol% G+C content) encodes genes including three Ln3+-dependent methanol dehydrogenase (XoxF-type MDH) genes, those for formaldehyde assimilation (ribulose monophosphate pathway), formate dehydrogenases and methylamine dehydrogenases, but not Ca2+-dependent MDH (MxaFI-MDH), which characterizes the species as a Ln3+-dependent methylotroph. The 16S rRNA gene sequence showed that strain La3113T belongs to the genus

Methylotenera

and is closely related to

Methylotenera mobilis

JLW8T (98.29 % identity). The digital DNA–DNA hybridization (dDDH) values (less than 30 %) and average nucleotide identity (ANI) values (less than 85 %) between genomes of strain La3113T and related type strains were lower than the thresholds for species delineation (70 % for dDDH and 95–96 % for ANI). On the basis of these polyphasic approaches, we propose a novel

Methylotenera

species, Methylotenera oryzisoli sp. nov. (type strain La3113T=NBRC 111954T=DSM 103219T).
Strongly heterogeneous transmission of COVID–19 in mainland China: local and regional variation
Authors: Wang Yuke , Teunis Peter 
Published: March 2020

SummaryBackgroundThe outbreak of novel coronavirus disease 2019 (COVID-19) started in the city of Wuhan, China, with a period of rapid initial spread. Transmission on a regional and then national scale was promoted by intense travel during the holiday period of the Chinese New Year. We studied the variation in transmission of COVID-19, locally in Wuhan, as well as on a larger spatial scale, among different cities and even among provinces in mainland China.MethodsIn addition to reported numbers of new cases, we have been able to assemble detailed contact data for some of the initial clusters of COVID-19. This enabled estimation of the serial interval for clinical cases, as well as reproduction numbers for small and large regions.FindingsWe estimated the average serial interval was 4·8 days. For early transmission in Wuhan, any infectious case produced as many as four new cases, transmission outside Wuhan was less intense, with reproduction numbers below two. During the rapid growth phase of the outbreak the region of Wuhan city acted as a hot spot, generating new cases upon contact, while locally, in other provinces, transmission was low.InterpretationCOVID-19 is capable of spreading very rapidly. The sizes of outbreak in provinces of mainland China mainly depended on the numbers of cases imported from Wuhan as the local reproduction numbers were low. The COVID-19 epidemic should be controllable with appropriate interventions.FundingNo specific funding.
Relationship between the ABO Blood Group and the COVID-19 Susceptibility
Authors: Zhao Jiao , Yang Yan , Huang Hanping , Li Dong , Gu Dongfeng , Lu Xiangfeng , Zhang Zheng , Liu Lei , Liu Ting , Liu Yukun , He Yunjiao , Sun Bin , Wei Meilan , Yang Guangyu , Wang Xinghuan , Zhang Li , Zhou Xiaoyang , Xing Mingzhao , Wang Peng George 
Published: March 2020

AbstractThe novel coronavirus disease-2019 (COVID-19) has been spreading around the world rapidly and declared as a pandemic by WHO. Here, we compared the ABO blood group distribution in 2,173 patients with COVID-19 confirmed by SARS-CoV-2 test from three hospitals in Wuhan and Shenzhen, China with that in normal people from the corresponding regions. The results showed that blood group A was associated with a higher risk for acquiring COVID-19 compared with non-A blood groups, whereas blood group O was associated with a lower risk for the infection compared with non-O blood groups. This is the first observation of an association between the ABO blood type and COVID-19. It should be emphasized, however, that this is an early study with limitations. It would be premature to use this study to guide clinical practice at this time, but it should encourage further investigation of the relationship between the ABO blood group and the COVID-19 susceptibility.
Reported symptoms differentiate diagnoses in children with exercise-induced respiratory problems: findings from the Swiss Paediatric Airway Cohort (SPAC)
Authors: Pedersen Eva SL , de Jong Carmen CM , Ardura-Garcia Cristina , Mallet Maria Christina , Barben Juerg , Casaulta Carmen , Hoyler Karin , Jochmann Anja , Moeller Alexander , Mueller-Suter Dominik , Regamey Nicolas , Singer Florian , Goutaki Myrofora , Kuehni Claudia E. 
Published: March 2020

AbstractBackgroundExercise-induced breathing problems with similar clinical presentations can have different aetiologies. This makes distinguishing common diagnoses such as asthma, extrathoracic and thoracic dysfunctional breathing (DB), insufficient fitness, and chronic cough difficult.ObjectiveWe studied which parent-reported, exercise-induced symptoms (EIS) can help distinguish diagnoses of EIS in children seen in respiratory outpatient clinics.MethodsThis study was nested in the Swiss Paediatric Airway Cohort (SPAC), an observational study of children aged 0-17 years referred to paediatric respiratory outpatient clinics in Switzerland. We studied children aged 6-17 years and compared information on EIS from parent-completed questionnaires between children with different diagnoses. We used multinomial regression to analyse whether parent-reported symptoms differed between diagnoses (asthma as base).ResultsAmong 1109 children, EIS were reported for 732 (66%) (mean age 11 years, 318 of 732 [43%] female). Among the symptoms, dyspnoea best distinguished thoracic DB (relative risk ratio [RRR] 5.4, 95%CI 1.3-22) from asthma. Among exercise triggers, swimming best distinguished thoracic DB (RRR 2.4, 95%CI 1.3-6.2) and asthma plus DB (RRR 1.8, 95%CI 0.9-3.4) from asthma only. Late onset of EIS was less common for extrathoracic DB (RRR 0.1, 95%CI 0.03-0.5) and thoracic DB (RRR 0.4, 95%CI 0.1-1.2) compared with asthma. Localisation of dyspnoea (throat vs. chest) differed between extrathoracic DB (RRR 2.3, 95%CI 0.9-5.8) and asthma. Reported respiration phase (inspiration or expiration) did not help distinguish diagnoses.ConclusionParent-reported symptoms help distinguish different diagnoses in children with EIS. This highlights the importance of physicians obtaining detailed patient histories.Highlights boxWhat is already known about this topic?Experts suggest that information about the symptoms and their onset and duration can assist accurate diagnosis of children with exercise-induced respiratory problems, but no original studies have tested this. (29/35 words)What does this article add to our knowledge?Exercise-induced symptoms reported by parents and further information about their onset, triggers, and effects of treatment help differentiate diagnoses in children with exercise-induced respiratory problems. (25/35 words)How does this study impact current management guidelines?Our results emphasize the importance of taking detailed symptom histories of children with exercise-induced problems, and suggest which questions are most helpful.
Impact assessment of non-pharmaceutical interventions against COVID-19 and influenza in Hong Kong: an observational study
Authors: Cowling Benjamin J. , Ali Sheikh Taslim , Ng Tiffany W. Y. , Tsang Tim K. , Li Julian C. M. , Fong Min Whui , Liao Qiuyan , Kwan Mike YW , Lee So Lun , Chiu Susan S. , Wu Joseph T. , Wu Peng , Leung Gabriel M. 
Published: March 2020

ABSTRACTBackgroundA range of public health measures have been implemented to delay and reduce local transmission of COVID-19 in Hong Kong, and there have been major changes in behaviours of the general public. We examined the effect of these interventions and behavioral changes on the incidence of COVID-19 as well as on influenza virus infections which may share some aspects of transmission dynamics with COVID-19.MethodsWe reviewed policy interventions and measured changes in population behaviours through two telephone surveys, on January 20-23 and February 11-14. We analysed data on laboratory-confirmed COVID-19 cases, influenza surveillance data in outpatients of all ages, and influenza hospitalisations in children. We estimated the daily effective reproduction number (Rt), for COVID-19 and influenza A(H1N1).FindingsCOVID-19 transmissibility has remained at or below 1, indicating successful containment to date. Influenza transmission declined substantially after the implementation of social distancing measures and changes in population behaviours in late January, with a 44% (95% confidence interval, CI: 34% to 53%) reduction in transmissibility in the community, and a 33% (95% CI: 24% to 43%) reduction in transmissibility based on paediatric hospitalization rates. In the two surveys we estimated that 74.5% and 97.5% of the general adult population wore masks when going out, and 61.3% and 90.2% avoided going to crowded places, respectively.ImplicationsContainment measures, social distancing measures and changes in population behaviour have successfully prevented spread of COVID-19. The social distancing measures and behavioural changes led to a substantial reduction in influenza transmission in early February 2020. However, it may be challenging to avoid fatigue and sustain these measures and population behaviours as COVID-19 continues to spread globally.FundingHealth and Medical Research Fund, Hong Kong
The first report of the prevalence of COVID-19 in Chronic myelogenous leukemia patients in the core epidemic area of China: multicentre, cross-sectional survey
Authors: Wang Dan-Yu , Guo Jing-Ming , Yang Zhuang-Zhi , Yuan Guo-Lin , Meng Li , Li Wei-Ming 
Published: March 2020

SummaryBackgroundSince late December 2019, the outbreak of the novel coronavirus disease, COVID-19, that began in Wuhan, has become endemic in China and more than 100 countries and regions in the world. So far, there is rare data on the prevalence of COVID-19 in patients with chronic myelogenous leukemia (CML). We aimed to describe the clinical course, outcomes of CML patients with COVID-19 and prevalence of COVID-19 in CML patients.MethodsIn this multicentre, cross-sectional survey, the clinical data of CML patients with COVID-19 in each center were collected. Simultaneously, an online survey was conducted for information about the CML patients under the management at each center by asking the CML patients to complete a questionnaire,from February 15, 2020 to February 21, 2020. The questionnaire includes demographic data, place of residence, smoking status, CML diagnosis and treatment, comorbidities, combined medications, epidemiological history, symptoms(fever, cough, shortness of breath, etc) during the epidemic. Additional clinical data was collected on respondents suspected or confirmed to have COVID-19. We described and analyzed the prevalence of COVID-19 in CML patients, and focus on the clinical characteristics and outcomes of COVID-19 patients. Data were compared between the CML patients with optimal response and those with non-optimal response. The primary outcome was prevalence of COVID-19 in CML patients, as of Feb 21, 2020. Secondary outcomes included the history of epidemiology of CML patients, the clinical characteristics and outcomes of CML patients with COVID-19.FindingsOf 392 respondents, 223(56.9%) were males, and 240(61.2%) were 50 years or younger. Only 10 patients took drugs irregularly due to the influence of the epidemic because of traffic control, pharmacies unable to operate normally, etc. In the history of epidemiology, there were 4 patients with definite contact with COVID-19, of which 3 were remote contact and 1 was close contact. 12 respondents had fever, cough or shortness of breath during the epidemic, 1 case (common type) was confirmed with COVID-19 and cured after treatment. 1 patient was clinically diagnosed and succumbed. 1 of 299 (0.3%) patients with an optimal response was diagnosed with COVID-19. Of the 50 patients who failed to respond to CML treatment or had a poor response, 1 patient (2%) had a clinical diagnosis of COVID-19.InterpretationWhile the 392 CML respondents required regular referrals to hospitals, they did not have much contact with COVID-19 patients during the outbreak. Patients who failed to achieved an optimal response to CML therapy appear more likely to have a symptomatic infection with SARS-CoV-2. Older patients with comorbidities are at increased risk of death.FundingThis work was supported by grants from the National Natural Science Foundation of China(NSFC)(81873440&81700142).
Safety and acceptability of clozapine and risperidone in progressive multiple sclerosis: a phase 1, randomized, blinded, placebo-controlled trial
Authors: La Flamme Anne Camille , Abernethy David , Sim Dalice , Goode Liz , Lockhart Michelle , Bourke David , Milner Imogen , Garrill Toni-Marie , Joshi Purwa , Watson Eloise , Smyth Duncan , Lance Sean , Connor Bronwen 
Published: March 2020

ABSTRACTObjectiveBecause clozapine and risperidone have been shown to reduce neuroinflammation in humans and mice, the CRISP trial was conducted to determine whether clozapine and risperidone are suitable for progressive multiple sclerosis (pMS).MethodsThe CRISP trial (ACTRN12616000178448) was a blinded, randomized, placebo-controlled trial with three parallel arms (n=12/arm). Participants with pMS were randomized to clozapine (100 to 150 mg/day), risperidone (2 to 3.5 mg/day), or placebo for six months. The primary outcome measures were safety (adverse events/serious adverse events) and acceptability (TSQM-9).ResultsAn interim analysis (n=9) revealed significant differences in the time-on-trial between treatment groups and placebo (p=0.030 and 0.025, clozapine and risperidone, respectively) with all participants receiving clozapine being withdrawn during the titration period (mean dose=35±15 mg/day). Participants receiving clozapine or risperidone reported a significantly higher rate of adverse events than placebo (p=0.00001) but not serious adverse events. Specifically, low doses of clozapine appeared to cause an acute and dose-related intoxicant effect in patients with pMS, who had fairly severe chronic spastic ataxic gait and worsening over all mobility, which resolved on drug cessation.InterpretationThe CRISP trial results suggest that pMS patients may experience increased sensitivity to clozapine and risperidone and indicate that the dose and/or titration schedule developed for schizophrenia may not be suitable for pMS. While these findings do not negate the potential of these drugs to reduce MS-associated neuroinflammation, they highlight the need for further research to understand the pharmacodynamic profile and effect of clozapine and risperidone in pMS patients.
Influence factors of death risk among COVID-19 patients in Wuhan, China: a hospital-based case-cohort study
Authors: Fu Lin , Fei Jun , Xiang Hui-Xian , Xiang Ying , Tan Zhu-Xia , Li Meng-Die , Liu Fang-Fang , Liu Hong-Yan , Zheng Ling , Li Ying , Zhao Hui , Xu De-Xiang 
Published: March 2020

AbstractBackgroundCoronavirus disease 2019 (COVID-19) triggered by infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been widely pandemic all over the world. The aim of this study was to analyze the influence factors of death risk among 200 COVID-19 patients.MethodsTwo hundred patients with confirmed SARS-CoV-2 infection were recruited. Demographic data and clinical characteristics were collected from electronic medical records. Biochemical indexes on admission were measured and patient’s prognosis was tracked. The association of demographic data, clinical characteristics and biochemical indexes with death risk was analyzed.ResultsOf 200 COVID-19 patients, 163 (81.5%) had at least one of comorbidities, including diabetes, hypertension, hepatic disease, cardiac disease, chronic pulmonary disease and others. Among all patients, critical cases, defined as oxygenation index lower than 200, accounted for 26.2%. Severe cases, oxygenation index from 200 to 300, were 29.7%. Besides, common cases, oxygenation index higher than 300, accounted for 44.1%. At the end of follow-up, 34 (17%) were died on mean 10.9 day after hospitalization. Stratified analysis revealed that older ages, lower oxygenation index and comorbidities elevated death risk of COVID-19 patients. On admission, 85.5% COVID-19 patients were with at least one of extrapulmonary organ injuries. Univariable logistic regression showed that ALT and TBIL, two indexes of hepatic injury, AST, myoglobin and LDH, AST/ALT ratio, several markers of myocardial injury, creatinine, urea nitrogen and uric acid, three indexes of renal injury, were positively associated with death risk of COVID-19 patients. Multivariable logistic regression revealed that AST/ALT ratio, urea nitrogen, TBIL and LDH on admission were positively correlated with death risk of COVID-19 patients.ConclusionOlder age, lower oxygenation index and comorbidities on admission elevate death risk of COVID-19 patients. AST/ALT ratio, urea nitrogen, TBIL and LDH on admission may be potential prognostic indicators. Early hospitalization is of great significance to prevent multiple organ damage and improve the survival of COVID-19 patients.SummaryIn this hospital-based case-cohort study, we found that serum urea nitrogen, TBIL, LDH and AST/ALT ratio, several markers of extrapulmonary organ injuries, were positively correlated with death risk of COVID-19 patients. We provide evidence for the first time that multiple organ damage on admission influences the prognosis of COVID-19 patients. Early hospitalization is beneficial for elevating the survival rate of COVID-19 patients especially critical ill patients.
Vibrio Cholerae O1 Transmission in Bangladesh: Insights from a Nationally-Representative Serosurvey
Authors: Azman Andrew S , Lauer Stephen , Rahman Bhuiyan M. Taufiqur , Luquero Francisco J , Leung Daniel T , Hegde Sonia , Harris Jason , Paul Kishor Kumar , Khaton Fatema , Ferdous Jannatul , Lessler Justin , Salje Henrik , Qadri Firdausi , Gurley Emily S 
Published: March 2020

AbstractBackgroundPandemic Vibrio cholerae from cholera-endemic countries around the Bay of Bengal regularly seed epidemics globally. Without reducing cholera in these countries, including Bangladesh, global cholera control may never be achieved. Little is known about the geographic distribution and magnitude of V. cholerae O1 transmission nationally. Here we use recent advances in cholera seroepidemiology to describe infection risk across Bangladesh overcoming many of the limitations of current clinic-based surveillance.MethodsWe tested serum from a nationally-representative serosurvey in Bangladesh of 2,778 participants with eight V. cholerae-specific assays. Using these data with a previously validated machine learning model we estimate the annual seroincidence rate and use Bayesian geostatistical models to create high-resolution national maps of infection risk.FindingsWe estimate a national seroincidence rate of 19.1% (95% CI 12.2-26.9%). Our high-resolution maps reveal large heterogeneity of infection risk, with community-level annual infection risk within the sampled population ranging from 2.4-69.0%. Across the country, we estimate that 31.0 million (95% CI 19.8-43.7 million) occurred in the year before the survey with most of these infections occurring in urban areas, including Dhaka, the capital.InterpretationSerosurveillance provides an avenue for identifying areas with high V. cholerae O1 transmission and exploring key risk factors for infection across geographic scales. This may serve as an important tool for countries to plan and monitor progress towards 2030 cholera elimination goals.
Laser capture microdissection-based single-cell RNA sequencing reveals optic nerve crush-related early mRNA alterations in retinal ganglion cells
Authors: Pan Dongyan , Xu Mengqiao , Chang Xin , Xia Mao , Fang Yibin , Fu Yinghua , Shen Wei , Wang Yue , Sun Xiaodong 
Published: March 2020

AbstractRetinal ganglion cells (RGC) are the primary cell type injured in a variety of diseases of the optic nerve, and the early changes of RGC’s RNA profiling may be important to understand the mechanism of optic nerve injury and axon regeneration. Here we employed the optic nerve crush (ONC) model to explore early mRNA alterations in RGCs using laser capture microdissection (LCM) and single-cell RNA sequencing. We successfully established an optimal LCM protocol using 30 μm-thick retinal tissue sections mounted on glass slides and laser pressure catapulting (LPC) to collect RGCs and obtain high-quality RNA for single-cell sequencing. Based on our protocol, we identified 8744 differentially expressed genes that were involved in ONC-related early mRNA alterations in RGCs. Candidate genes included Atf3, Lgals3, LOC102551701, Plaur, Tmem140 and Maml1. The LCM-based single-cell RNA sequencing allowed new insights into the early mRNA changes in RGCs, highlighting new molecules associated with ONC.
DeepDigest: prediction of protein proteolytic digestion with deep learning
Authors: Yang Jinghan , Gao Zhiqiang , Ren Xiuhan , Sheng Jie , Xu Ping , Chang Cheng , Fu Yan 
Published: March 2020

ABSTRACTIn shotgun proteomics, it is essential to accurately determine the proteolytic products of each protein in the sample for subsequent identification and quantification, because these proteolytic products are usually taken as the surrogates of their parent proteins in the further data analysis. However, systematical studies about the commonly used proteases in proteomics research are insufficient, and there is a lack of easy-to-use tools to predict the digestibilities of these proteolytic products. Here, we propose a novel sequence-based deep learning model – DeepDigest, which integrates convolutional neural networks and long-short term memory networks for digestibility prediction of peptides. DeepDigest can predict the proteolytic cleavage sites for eight popular proteases including trypsin, ArgC, chymotrypsin, GluC, LysC, AspN, LysN and LysargiNase. Compared with traditional machine learning algorithms, DeepDigest showed superior performance for all the eight proteases on a variety of datasets. Besides, some interesting characteristics of different proteases were revealed and discussed.
Human-derived NLS enhance the gene transfer efficiency of chitosan
Authors: Bitoque Diogo B. , Morais Joana , Oliveira Ana V. , Sequeira Raquel L. , Calado Sofia M. , Fortunato Tiago M. , Simão Sónia , da Costa Ana M. Rosa , Silva Gabriela A. 
Published: March 2020

AbstractNuclear import is considered one of the major limitations for non-viral gene delivery systems and the incorporation of nuclear localization signals (NLS) that mediate nuclear intake can be used as a strategy to enhance internalization of exogenous DNA. In this work, human-derived endogenous NLS peptides based on Insulin Growth Factor Binding Proteins (IGFBP), namely IGFBP-3 and IGFBP-5, were tested for their ability to improve nuclear translocation of genetic material by non-viral vectors. Several strategies were tested to determine their effect on chitosan mediated transfection efficiency: co-administration with polyplexes, co-complexation at the time of polyplex formation, and covalent ligation to chitosan. Our results show that co-complexation and covalent ligation of human-derived NLS peptides to chitosan polyplexes yields a 2-fold increase in transfection efficiency.These results indicate that the integration of IGFBP-NLS peptides into polyplexes has potential as a strategy to enhance the efficiency of non-viral vectors.