bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity, activity and abundance of benthic microbes in the southeastern Mediterranean Sea: A baseline for monitoring
Authors: Rubin-Blum Maxim , Sisma-Ventura Guy , Yudkovski Yana , Belkin Natalia , Kanari Mor , Herut Barak , Rahav Eyal 
Published: January 2021

AbstractMicrobes are key players in marine sediments, yet they are not accessed routinely by monitoring programs. Here, we investigate the spatial and vertical trends in the abundance, activity and diversity of benthic archaea, bacteria and fungi of the southeastern Mediterranean Sea (SEMS), based on ∼150 samples collected by the National Monitoring Program in 2018-2020 in coastal, as well as deep-sea transects across the Israeli exclusive economic zone, using vertical profiles of short sediment cores (0-1, 1-2, 4-5, 9-10 and 19-20 cm below surface). Microbial abundance was usually low (0.01 ×108to 0.21×108cells gr-1sediment), while heterotrophic productivity was the highest in the nearshore stations (12±4 ng C gr-1sediment h-1), as opposed to 0.5±0.9 ng C gr-1sediment h-1at the offshore sites. Using amplicon sequencing of marker genes, we identified the changes in the diversity of microbes along environmental gradients, in the four dimensions (geographic location, seabed depth, distance from the sediment surface and time). We show high taxonomic diversity of bacteria and archaea (Shannon’sH’5.0-6.9) and lesser diversity of fungi (Shannon’sH’0.2-4.8). We use DESeq2 analyses to highlight the role of ammonia-oxidizing Nitrososphaeria in the aerated sediments of the continental slope and deep bathyal plain stations and organotrophic lineages in coastal, shelf, slope, and abyssal plain sediments. Based on taxonomic diversity, we infer the metabolic potential of these communities. Analyses of fungi diversity and guilds suggest the prevalence of the saprotrophic and pathotrophic microfungi Ascomycota (70±23%) and Basidiomycota (16±18%) in the SEMS sediments. We provide a comprehensive baseline of benthic microbial populations in the SEMS and pledge for the use of microbial indices in biomonitoring of the marine environment.
Modelling the Reserve Bank of Australia's Policy Decisions and the Case for a Negative Cash Rate
Authors: Anderson Timothy , Hawkins John 
Published: January 2021

AbstractTaylor's eponymous ‘rule’ models how central banks set policy rates in response to inflation and output. We estimate a Taylor rule for the Reserve Bank of Australia (RBA), modifying it to make it more realistic, while retaining its simplicity. The model implies that if the Bank responds to recent forecasts as it has on average since 1995, the cash rate could have briefly gone negative in 2020. But the RBA is wary of negative cash rates. There are grounds for caution; the economic outlook is particularly uncertain and the economy's response to negative rates is uncharted territory.
Modelling the Spread of the Coronavirus: A View from Economics
Authors: Lloyd Peter , Dixon Robert 
Published: January 2021

AbstractThis article reviews the modelling of the spread in Australia of COVID‐19 from the point of view of the discipline of Economics. After a brief overview of the epidemiological approach, we show that other modelling is needed for policy purposes and especially to provide a full understanding of the economic and social costs of disease control. We look at microeconomic aspects of infection, focusing on individual behaviour, the choices facing the individual and implications for policy. The use of a cost–benefit approach and macroeconomic aspects of the pandemic are examined together with the economic consequences of policy response.
SambaR: An R package for fast, easy and reproducible population‐genetic analyses of biallelic SNP data sets
Authors: de Jong Menno J. , de Jong Joost F. , Hoelzel A. Rus , Janke Axel 
Published: January 2021

AbstractSNP data sets can be used to infer a wealth of information about natural populations, including information about their structure, genetic diversity, and the presence of loci under selection. However, SNP data analysis can be a time‐consuming and challenging process, not in the least because at present many different software packages are needed to execute and depict the wide variety of mainstream population‐genetic analyses. Here, we present SambaR, an integrative and user‐friendly R package which automates and simplifies quality control and population‐genetic analyses of biallelic SNP data sets. SambaR allows users to perform mainstream population‐genetic analyses and to generate a wide variety of ready to publish graphs with a minimum number of commands (less than 10). These wrapper commands call functions of existing packages (including adegenet, ape, LEA, poppr, pcadapt and StAMPP) as well as new tools uniquely implemented in SambaR. We tested SambaR on online available SNP data sets and found that SambaR can process data sets of over 100,000 SNPs and hundreds of individuals within hours, given sufficient computing power. Newly developed tools implemented in SambaR facilitate optimization of filter settings, objective interpretation of ordination analyses, enhance comparability of diversity estimates from reduced representation library SNP data sets, and generate reduced SNP panels and structure‐like plots with Bayesian population assignment probabilities. SambaR facilitates rapid population genetic analyses on biallelic SNP data sets by removing three major time sinks: file handling, software learning, and data plotting. In addition, SambaR provides a convenient platform for SNP data storage and management, as well as several new utilities, including guidance in setting appropriate data filters. The SambaR source script, manual and example data set are distributed through GitHub: https://github.com/mennodejong1986/SambaR.
A rare case of primary solitary endobronchial plasmacytoma
Authors: Park Jong Il , Lee Yin Young , Lee Seok Soo , Ahn June Hong 
Published: January 2021

AbstractExtramedullary plasmacytoma (EMP) is a rare plasma cell tumor involving the organs but without bone marrow involvement or the characteristics of multiple myeloma. Primary solitary endobronchial plasmacytoma is extremely rare. Here we present the case of an 86‐year‐old male ex‐smoker who visited our outpatient clinic for an endobronchial mass in the left upper lobe of the lung. Fiberoptic bronchoscopy revealed a protruding mass in the left upper lobar bronchus; based on the bronchoscopic biopsy findings, a primary solitary endobronchial plasmacytoma was diagnosed. After radiation therapy the patient was well and 6 months after treatment showed no evidence of disease recurrence. Extramedullary plasmacytoma should be considered in the differential diagnosis of an endobronchial mass.
Precise resection of multiple pulmonary nodules using a three‐dimensional reconstruction model: A case report
Authors: Chu Xiang‐Peng , Chen Zi‐Hao , Lin Shao‐Min , Tang Wen‐Fang , Zhang Jia‐Tao , Lai Yao‐Ming , Fu Rui , Qiu Zhen‐Bin , Lin Jun‐Tao , Nie Qiang , Yang Xue‐Ning , Wu Yi‐Long , Zhong Wen‐Zhao 
Published: January 2021

AbstractA 48‐year‐old woman presented to our department and chest computed tomography (CT) revealed five pulmonary nodules, two of which were in the left upper lobe of the lung and three in the superior segment of the left lower lobe., All the lesions were resected for comprehensive histological assessment in order to distinguish synchronous multiple primary lung cancers (SMPLCs) from intrapulmonary metastases. The nodules were all successfully removed by minimally invasive surgery under the guidance of three dimensional (3D) reconstruction, in order to preserve as much lung function for the patient as possible. Postoperative histopathological examination demonstrated the presence of SMPLC. The patient was discharged from hospital on postoperative day 4 without any complications.
Characteristics, management and survival of ICU patients with coronavirus disease‐19 in Norway, March‐June 2020. A prospective observational study
Authors: Laake Jon H. , Buanes Eirik A. , Småstuen Milada C. , Kvåle Reidar , Olsen Brita F. , Rustøen Tone , Strand Kristian , Sørensen Vibecke , Hofsø Kristin 
Published: January 2021

BackgroundNorwegian hospitals have operated within capacity during the COVID‐19 pandemic. We present patient and management characteristics, and outcomes for the entire cohort of adult (>18 years) COVID‐19 patients admitted to Norwegian intensive care units (ICU) from 10 March to 19 June 2020.MethodsData were collected from The Norwegian intensive care and pandemic registry (NIPaR). Demographics, co‐morbidities, management characteristics and outcomes are described. ICU length of stay (LOS) was analysed with linear regression, and associations between risk factors and mortality were quantified using Cox regression.ResultsIn total, 217 patients were included. The male to female ratio was 3:1 and the median age was 63 years. A majority (70%) had one or more co‐morbidities, most frequently cardiovascular disease (39%), chronic lung disease (22%), diabetes mellitus (20%), and obesity (17%). Most patients were admitted for acute hypoxaemic respiratory failure (AHRF) (91%) and invasive mechanical ventilation (MV) was used in 86%, prone ventilation in 38% and 25% of patients received a tracheostomy. Vasoactive drugs were used in 79% and renal replacement therapy in 15%. Median ICU LOS and time of MV was 14.0 and 12.0 days. At end of follow‐up 45 patients (21%) were dead. Age, co‐morbidities and severity of illness at admission were predictive of death. Severity of AHRF and male gender were associated with LOS.ConclusionsIn this national cohort of COVID‐19 patients, mortality was low and attributable to known risk factors. Importantly, prolonged length‐of‐stay must be taken into account when planning for resource allocation for any next surge.
Triaging abnormal cervical cancer screening tests using p16INK4a detection by ELISA on fresh cervical samples
Authors: Leung Shuk On Annie , Feldman Sarah , Kalyanaraman Rajeshwari , Shanmugam Vignesh , Worley Michael J. , Berkowitz Ross S. , Horowitz Neil S. , Feltmate Colleen M. , Muto Michael G. , Lee Larissa J. , King Martin T. , Einarsson Jon I. , Ajao Mobolaji O. , Elias Kevin M. 
Published: January 2021

AbstractProblemCervical cancer screening strategies in the United States include cotesting (human papillomavirus (HPV) with cytology), primary HPV with genotyping and reflex cytology, and cytology alone. An ongoing challenge is the appropriate triage of patients to colposcopy to those at highest risk. We investigated whether incorporation of p16INK4a immunodetection by enzyme‐linked immunosorbent assay (ELISA) on fresh cervical samples obtained at the time of screening could improve appropriate referral to colposcopy.Method of StudyA derivation group comprised of cervical swabs collected from subjects with high‐grade dysplasia or cancer (positive control) and from subjects with negative screening history (negative control). Samples collected from colposcopy were used to evaluate the existing screening strategies individually and with incorporation of p16INK4a ELISA. Histology was used as the gold standard.ResultsAmong 163 subjects recruited, 138 were included. In the derivation group, mean p16INK4a level was 2.86 ng/mL (n = 31) and 0.58 ng/mL (n = 20) among positive and negative controls respectively (p = 0.002) with an area under the receiver operator characteristic curve of 0.79 (p < 0.001). Among colposcopy subjects, sensitivity/specificity for cotesting, primary HPV, and cytology were 94%/42%, 88%/45%, and 88%/49%, respectively. Incorporation of p16INK4a resulted in similar sensitivity and improved specificity (cotesting+p16 88%/58%, primary HPV+p16 88%/57%, cytology+p16 81%/62%; p = 0.23/p = 0.008) with decrease in colposcopy referrals by 15% to 22% (p = 0.01).ConclusionsThese results demonstrate the feasibility of quantifying p16INK4a by ELISA in fresh cervical samples, and its potential as an adjunct to existing screening strategies in the identification of high grade‐dysplasia while reducing the number of colposcopic referrals.
Catastrophic impact of Covid‐19 on the global stock markets and economic activities
Authors: Chowdhury Emon Kalyan , Khan Iffat Ishrat , Dhar Bablu Kumar 
Published: January 2021

AbstractThis paper intends to know the influence of COVID‐19 on the stock markets and economic activities across the world. To achieve the purpose, daily panel data of 12 selective countries covering four continents from January to April 2020 have been collected. The impact on stock markets has been measured by applying the event study method, while the panel vector autoregressive model has been applied to measure the impact on economic activities. The stock index of each country, purchasing managers’ index, COVID‐19 variables, namely the number of lockdown days, restriction in internal movement, restriction in international travel, fiscal measure, and confirmed cases have been used. The study observes the serious negative impact of the pandemic on stock market returns. European stock markets are the worst sufferer compared to others. All pandemic variables have a negative impact on stock markets; moreover, lockdown days and restriction on movement have a negative impact on economic activities. This study considers such countries which significantly represent the world economy and are a serious victim of COVID‐19 pandemic. The outcome‐based recommendations will help governments, regulatory authority, and policymakers to combat the crisis in different dimensions.
Gaussian graphical model‐based heterogeneity analysis via penalized fusion
Authors: Ren Mingyang , Zhang Sanguo , Zhang Qingzhao , Ma Shuangge 
Published: January 2021

AbstractHeterogeneity is a hallmark of cancer, diabetes, cardiovascular diseases, and many other complex diseases. This study has been partly motivated by the unsupervised heterogeneity analysis for complex diseases based on molecular and imaging data, for which, network‐based analysis, by accommodating the interconnections among variables, can be more informative than that limited to mean, variance, and other simple distributional properties. In the literature, there has been very limited research on network‐based heterogeneity analysis, and a common limitation shared by the existing techniques is that the number of subgroups needs to be specified a priori or in an ad hoc manner. In this article, we develop a penalized fusion approach for heterogeneity analysis based on the Gaussian graphical model. It applies penalization to the mean and precision matrix parameters to generate regularized and interpretable estimates. More importantly, a fusion penalty is imposed to “automatedly” determine the number of subgroups and generate more concise, reliable, and interpretable estimation. Consistency properties are rigorously established, and an effective computational algorithm is developed. The heterogeneity analysis of non‐small‐cell lung cancer based on single‐cell gene expression data of the Wnt pathway and that of lung adenocarcinoma based on histopathological imaging data not only demonstrate the practical applicability of the proposed approach but also lead to interesting new findings.
Random effects models of lymph node metastases in breast cancer: quantifying the roles of covariates and screening using a continuous growth model
Authors: Isheden Gabriel , Czene Kamila , Humphreys Keith 
Published: January 2021

AbstractWe recently described a joint model of breast cancer tumor size and number of affected lymph nodes, which conditions on screening history, mammographic density, and mode of detection, and can be used to infer growth rates, time to symptomatic detection, screening sensitivity, and rates of lymph node spread. The model of lymph node spread can be estimated in isolation from measurements of tumor volume and number of affected lymph nodes, giving inference identical to the joint model. Here, we extend our model to include covariate effects. We also derive theoretical results in order to study the role of screening on lymph node metastases at diagnosis. We analyze the association between hormone replacement therapy (HRT) and breast cancer lymph node spread, using data from a case‐control study designed specifically to study the effects of HRT on breast cancer. Using our method, we estimate that women using HRT at time of diagnosis have a 36% lower rate of lymph node spread than nonusers (95% confidence interval [CI] =(8%,58%)). This can be contrasted with the effect of HRT on the tumor growth rate, estimated here to be 15% slower in HRT users (95% CI = (−34%,+7%)). For screen‐detected cancers, we illustrate how lead time can relate to lymph node spread; and using symptomatic cancers, we illustrate the potential consequences of false negative screens in terms of lymph node spread.
The influence of context stability on physical activity and sedentary behaviour habit and behaviour: An ecological momentary assessment study
Authors: Maher Jaclyn P. , Rebar Amanda L. , Dunton Genevieve F. 
Published: January 2021

ObjectivesThis study used ecological momentary assessment (EMA) to empirically test the theoretical propositions that habit for and level of physical activity (PA) and sedentary behaviour (SB) should be associated with degree of context stability of those behaviours.DesignOlder adults (N = 104) completed a 10‐day EMA protocol and continuous accelerometer monitoring.MethodsAs part of the EMA protocol older adults answered 6 EMA prompts per day to assess current behaviour as well as social and physical contexts of behaviour. Temporal context was determined via time stamps of EMA questionnaires. Context stability was calculated as the reversed entropy scores of the contexts (physical, social, temporal, behavioural [i.e., type]) of PA and SB weighted for total frequency of context prompts. Habit for PA and SB (operationalized as self‐reported behavioural automaticity) was assessed via baseline questionnaire. An ActivPAL monitor was worn to assess average daily time spent in moderate‐vigorous PA (MVPA), light PA, and SB, and number of sit‐to‐stand transitions.ResultsMore stable physical contexts for physical activity predicted more MVPA (β = 10.22) and more stable social contexts for sitting predicted more SB (β = 1.36). More variety of time people tended to report engaging in SB, the more SB engaged in (β = −13.76). No context stability scores predicted light PA, sit‐to‐stand transitions, or habit.ConclusionsAlthough context stability was related to behaviour, this did not appear to be explained by habit, as habit did not differ by the degree of context stability surrounding bouts of PA or SB.
The inhibitory effect of human DEFA5 in growth of gastric cancer by targeting BMI1
Authors: Wu Zhongwei , Ding Zhaohui , Cheng Bo , Cui Zongchao 
Published: January 2021

AbstractDefensins, a class of small cysteine‐rich cationic polypeptides across cellular life, are identified as antimicrobial compounds that display direct antimicrobial and immune signaling activities that are involved in the host defense. In addition to their roles in the innate immune system, accumulating studies have reported that some members of defensins are expressed and involved in some cancer cells, such as colon cancer, colorectal cancer, lung cancer and renal cell carcinomas. However, the roles of α‐Defensin 5 (DEFA5) in tumorigenesis and development remain unknown. In the present study, bioinformatics analysis and quantitative PCR results showed that the expression level of DEFA5 was dramatically downregulated in human gastric cancer. Overexpression of human DEFA5 in gastric cancer cell lines SGC7901 and BGC823 effectively diminished cell proliferation and reduced the colony forming ability. Moreover, DEFA5 overexpression induced cell cycle arrest by significantly increasing the number of G1‐phase cells. Consistently, in vivo tumor formation experiments in nude mice showed the suppression of the tumor growth by DEFA5 overexpression, suggesting an inhibitory effect of DEFA5 in gastric cancer. Mechanistically, DEFA5 directly binds to BMI1, which subsequently decreased its binding at the CDKN2a locus and upregulated the expression of 2 cyclin‐dependent kinase inhibitors, p16 and p19. Taken together, we concluded that DEFA5 showed an inhibitory effect in gastric cancer cell growth and may serve as a potential tumor suppressor in gastric cancer.
Role of crosstalk between endothelial cells and smooth muscle cells in vascular calcification in chronic kidney disease
Authors: Zhang Yu‐Xia , Tang Ri‐Ning , Wang Li‐Ting , Liu Bi‐Cheng 
Published: January 2021

AbstractChronic kidney disease (CKD) is a severe health problem worldwide, and vascular calcification (VC) contributes substantially to the cardiovascular morbidity and high mortality of CKD. CKD is often accompanied by a variety of pathophysiological states, such as inflammation, oxidative stress, hyperglycaemia, hyperparathyroidism and haemodynamic derangement, that can cause injuries to smooth muscle cells (SMCs) and endothelial cells (ECs) to promote VC. Similar to SMCs, whose role has been widely explored in VC, ECs may contribute to VC via osteochondral transdifferentiation, apoptosis, etc. In addition, given their location in the innermost layer of the blood vessel lumen and preferential reception of various pro‐calcification stimuli, ECs can pass messages to vascular wall cells and communicate with them. Crosstalk between ECs and SMCs via cytokines through a paracrine mechanism, extracellular vesicles, miRNAs and myoendothelial gap junctions also plays a role in VC. In this review, we emphasize the role of intercellular crosstalk between ECs and SMCs in VC associated with CKD.
Characterization of CYP3A pharmacogenetic variation in American Indian and Alaska Native communities, targetingCYP3A4*1Gallele function
Authors: Fohner Alison E. , Dalton Rachel , Skagen Kasse , Jackson Konner , Claw Katrina G. , Hopkins Scarlett E. , Robinson Renee , Khan Burhan A. , Prasad Bhagwat , Schuetz Erin G. , Nickerson Deborah A. , Thornton Timothy A. , Dillard Denise A. , Boyer Bert B. , Thummel Kenneth E. , Woodahl Erica L. 
Published: January 2021

AbstractThe frequencies of genetic variants in theCYP3A4andCYP3A5genes differ greatly across global populations, leading to profound differences in the metabolic activity of these enzymes and resulting drug metabolism rates, with important consequences for therapeutic safety and efficacy. Yet, the impact of genetic variants on enzyme activity are incompletely described, particularly in American Indian and Alaska Native (AIAN) populations. To characterize genetic variation inCYP3A4andCYP3A5and its effect on enzyme activity, we partnered with AIAN people living in two regions of Alaska: Yup’ik Alaska Native people living in the Yukon‐Kuskokwim Delta region of rural southwest Alaska and AIAN people receiving care at the Southcentral Foundation in Anchorage, Alaska. We identified low frequencies of novel and known variation inCYP3A4andCYP3A5, including low frequencies of theCYP3A4*1GandCYP3A5*1variants, and linkage disequilibrium patterns that differed from those we previously identified in an American Indian population in western Montana. We also identified increased activity of theCYP3A4*1Gallele in vitro and in vivo. We demonstrated that theCYP3A4*1Gallele confers increased protein content in human lymphoblastoid cells and both increased protein content and increased activity in human liver microsomes. We confirmed enhanced CYP3A4‐mediated 4β‐vitamin D hydroxylation activity in Yup’ik people with theCYP3A4*1Gallele. AIAN people in Alaska and Montana who carry theCYP3A4*1Gallele—coupled with low frequency of the functionalCYP3A5*1variant—may metabolize CYP3A substrates more rapidly than people with the referenceCYP3A4allele.