bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chitinophaga fulva sp. nov., isolated from forest soil
Authors: Dahal Ram Hari , Chaudhary Dhiraj Kumar , Kim Dong-Uk , Kim Jaisoo 
Published: January 2021

An aerobic, Gram-stain-negative, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped and yellow-coloured bacterium designated strain G-6-1-13T was isolated from Gwanggyo mountain forest soil. Strain G-6-1-13T could grow at 15–40 °C (optimum, 20–32 °C), pH 4.5–10.5 (optimum, pH 6.0–9.0), at 2 % (w/v) NaCl concentration, and produced flexirubin-type pigments. Phylogenetic analysis based on its 16S rRNA gene sequence showed that strain G-6-1-13T formed a lineage within the genus

Chitinophaga

that was distinct from other species of the genus. Closest member was

Chitinophaga varians

10–7 W-9003T (98.6 % sequence similarity) followed by

C. eiseniae

DSM 22224T (98.4 %),

C. qingshengii

JN246T (97.6 %) and

C. terrae

KP01T (97.4%). The major cellular fatty acids were iso-C15 : 0, C16 : 1
ω5c, and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1
ω6c). MK-7 was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine and an unidentified phospholipid. The DNA G+C content of strain G-6-1-13T was 48.7 mol%. Average nucleotide identity and in silico DNA–DNA hybridization were below the species threshold. On the basis of phenotypic, genotypic, phylogenetic and chemotaxonomic characterization, G-6-1-13T represents a novel species in the genus

Chitinophaga

, for which the name Chitinophaga fulva sp. nov. is proposed. The type strain is G-6-1-13T (=KACC 21624T=NBRC 114361T).
Widespread aberrant alternative splicing despite molecular remission in chronic myeloid leukemia patients
Authors: Schmitz Ulf , Shah Jaynish S. , Dhungel Bijay P. , Monteuuis Geoffray , Luu Phuc-Loi , Petrova Veronika , Metierre Cynthia , Nair Shalima S. , Bailey Charles G. , Saunders Verity A. , Turhan Ali G. , White Deborah L. , Branford Susan , Clark Susan , Hughes Timothy P. , Wong Justin J-L. , Rasko John E.J. 
Published: January 2021

AbstractBackgroundVast transcriptomics and epigenomics changes are characteristic of human cancers including leukemia. At remission, we assume that these changes normalise so that omics-profiles resemble those of healthy individuals. However, an in-depth transcriptomic and epigenomic analysis of cancer remission has not been undertaken. A striking exemplar of targeted remission induction occurs in chronic myeloid leukemia (CML) following tyrosine kinase inhibitor (TKI) therapy.MethodsUsing RNA sequencing and whole-genome bisulfite sequencing, we profiled samples from chronic-phase CML patients at diagnosis and remission, and compared these to healthy donors.ResultsRemarkably, our analyses revealed that abnormal splicing distinguishes remission samples from normal controls. This phenomenon is independent of the TKI drug used and in striking contrast to the normalisation of gene expression and DNA methylation patterns. Most remarkable are the high intron retention (IR) levels that even exceed those observed in the diagnosis samples. Increased IR affects cell cycle regulators at diagnosis and splicing regulators at remission. We show that aberrant splicing in CML is associated with reduced expression of specific splicing factors, histone modifications and reduced DNA methylation.ConclusionsOur results provide novel insights into the changing transcriptomic and epigenomic landscapes of CML patients during remission. The conceptually unanticipated observation of widespread aberrant alternative splicing after remission induction warrants further exploration. These results have broad implications for studying CML relapse and treating minimal residual disease.
Physician Perceptions of Catching COVID-19
Authors: Doraiswamy P. Murali , Chilukuri Mohan , Ariely Dan , Linares Alexandra R. 
Published: January 2021

AbstractBackgroundRisk perception, influenced and biased by multiple factors, can affect behavior.ObjectiveTo assess the variability of physician perceptions of catching COVID-19.DesignCross sectional, random stratified sample of physicians registered with Sermo, a global networking platform open to verified and licensed physicians.Main outcome measuresThe survey asked: “What is your likelihood of catching COVID-19 in the next three months?” The physicians were asked to give their best estimate as an exact percentage.ResultsThe survey was completed by 1004 physicians (40 countries, 67 specialties, 49% frontline [e.g. ER, infectious disease, internal medicine]) with a mean (SD) age of 49.14 (12) years. Mean (SD) self-risk estimate was 32.3% ± 26% with a range from 0% to 100% (Figure 1a). Risk estimates were higher in younger (<50 years) doctors and in non-US doctors versus their older and US counterparts (p<0.05 for all) (Figure 1b). Risk estimates were higher among front line versus non-frontline doctors (p<0.05). Risk estimates were higher for women than men (p<0.05) among respondents (60%) reporting gender.ConclusionsTo our knowledge, this is the first global study to document physician risk perceptions for catching COVID-19 and how it is impacted by age, gender, practice specialty and geography. Accurate calibration of risk perception is vital since both over- and underestimation of risk could impact physician behavior and have implications for public health.
Regression Tree Modelling to Predict Total Average Extra Costs in Household Spending During COVID-19 Pandemic
Authors: Lotfy Nesma 
Published: January 2021

AbstractBackgroundPrevention of coronavirus (COVID-19) regarding households has many aspects, such as buying masks, hand sanitizer, face shield, and many others. As a result of buying the previous items, the household spending per month will be increase during the COVID-19 pandemic period.AimsTo calculate the average costs of each extra item involved in households spending during COVID-19 pandemic and to predict the total average extra costs spending by households.MethodsA cross-sectional study was conducted at High Institute of Public Health (HIPH), University Alexandria. Exponential snowball sampling was used to recruit students at HIPH and their friends. Trimming costs was done to remove extreme low and high values. A regression tree modelling was implemented to predict the total extra costs spending during COVID-19 pandemic.ResultsMost of the respondents were female (81%) and aged between 30 and 40 (56.3%). About 63.1% of families had the same monthly income while 35.4% had a decrease in monthly income. A significant reduction in days of leaving home before and after COVID-19 pandemic was observed (before; mean= 5.86, after; mean = 4.66, P=0.000). The extra spending in grocery was the dominated item compared to other items (mean = 707.2, SD = 530.7). Regarding regression tree, the maximum average extra costs due to COVID-19 pandemic was 1386 L.E/month (around 88.23$/month) while the minimum average extra costs was 217 L.E/month (around 13.81$/month).ConclusionsThe effect of COVID-19 pandemic in households spending varies largely between households, it depends on what they do to prevent COVID-19.*Hint: Convert form L.E to dollar performed according to price of dollar at 18-12-2020
Race and ethnicity-related differences in neuroimaging markers of neurodegeneration and cerebrovascular disease in middle and older age
Authors: Turney Indira C. , Lao Patrick J. , Arce Rentería Miguel , Igwe Kay , Berroa Joncarlos , Rivera Andres , Benavides Andrea , Morales Clarissa , Schupf Nicole , Mayeux Richard , Gutierrez Jose , Manly Jennifer J. , Brickman Adam M. 
Published: January 2021

ABSTRACTINTRODUCTIONNumerous neuroimaging studies demonstrated racial and ethnic disparities in brain health at older ages. It remains unclear whether racial and ethnic disparities increase with aging and whether they are already apparent in midlife.METHODSWe investigated differences in MRI markers of aging and cerebrovascular disease in 969 participants from the Washington Heights-Inwood Columbia Aging Project (WHICAP; mean age: 75 years) and 496 participants from the Offspring study (mean age: 55 years) across race and ethnicity (white, Black, Latinx).RESULTSOlder whites had greater cortical thickness compared with Latinxs, who also had greater thickness than Blacks. Cortical thickness was similar across race in the middle-aged cohort. Regarding white matter hyperintensity (WMH) volume, Blacks had disproportionately greater WMH volume compared to both whites and Latinxs at older ages. Racial disparities are already apparent in midlife, where Blacks have disproportionately greater WMH than whites.DiscussionThese findings suggest that racial disparities in WMH volume are already apparent in midlife.
Simple Laboratory and Clinical Parameters as Predictor for Electrocardiographic Abnormalities Among Hospitalized Patients with Chronic Kidney Disease: A Cross-Sectional Study
Authors: Julario Rerdin , Nugraha Ricardo Adrian , Khrisna Bagus Putra Dharma , Putra Tony Santoso , Mulia Eka Prasetya Budi , Intan Ryan Enast , Alkaff Firas Farisi 
Published: January 2021

AbstractBackgroundIn developing countries, even electrocardiography (ECG) hasn’t been used widely in most health-care centers. The ability of physicians to refer to chronic kidney disease (CKD) patients for ECG, often collide with several barriers and costs. Therefore, we need to formulate the simplest and most efficient model to predict when CKD patients need to be referred due to potential ECG abnormalities.ObjectiveThe aim of this study was to develop several clinical and laboratory parameters as a predictor of any ECG abnormalities.Materials and MethodsA retrospective cross-sectional study design held at Dr. Soetomo General Academic Hospital, Surabaya, Indonesia. Subjects were hospitalized patients with CKD between 1 January to 31 December 2019. 198 CKD patients (101 males) were enrolled for the study. All patients had demographic information, detailed clinical profile, resting 12-lead ECG recording, complete blood count, serum electrolyte and renal function test profile during admission and results were interpreted blindly by two cardiologists. Statistical analysis was done by SPSS 17.0.ResultsA total of 198 patients were included in this study. Mean ages were 52.2±11.8 years old and fifty-one percent were males. Eighty-eight percent of patients from 198 patients had ECG abnormality. AUC of hemoglobin level to discriminate poor R wave progression, pathological Q wave, non-spesific ST-T changes, and frontal axis deviation were 0.532, 0.641, 0.556 and 0.693, respectively. In multivariate logistic regression analysis, only higher systolic blood pressure was determined as an independent predictor of abnormal ECG finding in CKD patients, as systolic blood pressure increase by one unit, the odds of having abnormal ECG is increased 1.02 times (95% CI: 1.00 – 1.02, p=0.042).ConclusionThe ECG abnormalities can be found in hospitalized CKD patients. Fragmented QRS and long QTc were the highest prevalent ECG abnormalities in our study. Serum creatinine and hemoglobin could predict peaked T wave and prolonged QTc among hospitalized CKD patients. Systolic blood pressure could predict prolonged QTc and fragmented QRS in CKD patients.
Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules
Authors: Jankowski Jakub , Lee Hye Kyung , Wilflingseder Julia , Hennighausen Lothar 
Published: January 2021

SummaryRecently, a short, interferon-inducible isoform of Angiotensin-Converting Enzyme 2 (ACE2), dACE2 was identified. ACE2 is a SARS-Cov-2 receptor and changes in its renal expression have been linked to several human nephropathies. These changes were never analyzed in context ofdACE2, as its expression was not investigated in the kidney. We used Human Primary Proximal Tubule (HPPT) cells to show genome-wide gene expression patterns after cytokine stimulation, with emphasis on theACE2/dACE2locus. Putative regulatory elements controllingdACE2expression were identified using ChIP-seq and RNA-seq. qRT-PCR differentiating betweenACE2anddACE2revealed 300- and 600-fold upregulation ofdACE2by IFNα and IFNβ, respectively, while full lengthACE2expression was almost unchanged. JAK inhibitor ruxolitinib ablatedSTAT1anddACE2expression after interferon treatment. Finally, with RNA-seq, we identified a set of genes, largely immune-related, induced by cytokine treatment. These gene expression profiles provide new insights into cytokine response of proximal tubule cells.
Greek High Phenolic Early Harvest Extra Virgin Olive Oil Reduces the Over-Excitation of Information Flow based on Dominant Coupling Model in patients with Mild Cognitive Impairment: An EEG Resting-State Validation Approach
Authors: Dimitriadis Stavros I. , Lyssoudis Christos , Tsolaki Anthoula C. , Lazarou Eftychia , Kozori Mahi , Tsolaki Magda 
Published: January 2021

AbstractObjectiveThe balance of cross-frequency coupling (CFC) over within-frequency coupling (WFC) can build a nonlinearity index (NI) that encapsulates the over-excitation of information flow between brain areas and across experimental time. The present study investigated for the very first time how the Greek High Phenolic Early Harvest Extra Virgin Olive Oil (HP-EH-EVOO) versus Moderate Phenolic (MP-EVOO) and Mediterranean Diet (MeDi) intervention in people with Mild Cognitive Impairment (MCI) could affect their spontaneous EEG dynamic connectivity.MethodsFourty three subjects (14 in MeDi, 16 in MP-EVOO and 13 in HP-EH-EVOO) followed an EEG resting-state recording session (eyes-open and closed) before and after the treatment. Following our dominant coupling mode model (DoCM), we built a dynamic integrated dynamic functional connectivity graph (iDFCG) that tabulates both the functional strength and the DoCM of every pair of brain areas.ResultsSignal spectrum within 1-13 Hz and theta/beta ratio have been decreased in the HP-EH-EVOO group in both conditions.FIDoCMhas been improved after the intervention across groups and conditions but was more prominent in HP-EH-EVOO group (p < 0.001). Finally,we revealed a significant higher post-intervention reduction of NI (ΔNITotal and α) for the HP-EH-EVOO compared to the MP-EVOO and MeDi groups (p < 0.0001).ConclusionsLong-term intervention with HP-EH-EVOO reduced the over-excitation of information flow in spontaneous brain activity.SignificanceOur study confirms the alteration of signal spectrum of EEG rhythms and dominant coupling mode due to the intervention with HP-EH-EVOO nutrition protocol.HighlightsNon-pharmaceutical intervention based on HP-EH-EVOO in MCI reduces the over-excitation of information flowNon-pharmaceutical intervention based on HP-EH-EVOO in MCI increases the human brain flexibilityReconfiguration of dominant coupling modes in EEG resting-state due to the intervention is modulated by alpha frequency
Gaps in maternal, newborn, and child health research: a scoping review of 72 years in Ethiopia
Authors: Chan Grace J , Daniel Jenna , Getnet Misrak , Kennedy Matthew , Olowojesiku Ronke , Hunegnaw Bezawit M , Unninayar Sarah , Taddesse Lisanu , Bekele Delayehu 
Published: January 2021

ABSTRACTObjectivesDespite significant reductions in maternal and child mortality over the past few decades, a disproportionate number of global deaths occur in low and middle-income country settings, such as Ethiopia. To prioritize research questions that would generate policy recommendations for better outcomes, we conducted a scoping review that gathers the current knowledge of maternal, newborn, and child health (MNCH) and illustrates remaining gaps in Ethiopia.DesignScoping review.MethodsWe conducted a search strategy from 1946-2018 in PubMed/MEDLINE, EMBASE, and the WHO African Index Medicus. The study team of reviewers independently screened titles, abstracts, and full-texts; abstracted data; and reconciled differences in pairs. Descriptive analyses were conducted.ResultsWe identified 7,829 unique articles of which 2,170 were included. Most MNCH publications in Ethiopia (70.0%) were published in the last decade, 2010-2018. Most studies included children aged one to less than 10 years old (30.5%), women of reproductive age (22.0%), and pregnant women (21.9%); fewer studies included newborns (7.0%), infants (6.6%), and postpartum women (2.9%). Research topics included demographics and social determinants of health (43.4%), nutrition (15.3%), and infectious diseases (13.0%). There were limited studies on violence (1.4%), preterm birth (0.8%), antenatal/postpartum depression (0.7%), stillbirths (0.1%), and accidents (0.1%). Most study designs were cross-sectional (53.6%). A few study designs included prospective cohort studies (5.5%) and randomized control trials (2.3%).ConclusionsThis is the first scoping review to describe the landscape of MNCH research in Ethiopia. Understanding the depth of existing knowledge will support the prioritization and development of future research questions. Additional studies are needed to focus on the neonatal, infant, and postpartum populations as well as preterm and stillbirth outcomes.STRENGTHS AND LIMITATIONS OF THIS STUDYTo our knowledge, this is the first published review to have comprehensively described or summarized this body of literature in Ethiopia, allowing for a deeper understanding of the expanse of existing knowledge.A quality assessment of each study was not feasible due to the broad range of included topics; however, one may be conducted in the future to further refine results.Although conclusions may not be widely generalizable beyond Ethiopia, this review may inform the need to conduct similar reviews for all sub-Saharan countries to support effective prioritization of future research questions.
Atrans-complementation system for SARS-CoV-2
Authors: Zhang Xianwen , Liu Yang , Liu Jianying , Bailey Adam L. , Plante Kenneth S. , Plante Jessica A. , Zou Jing , Xia Hongjie , Bopp Nathen , Aguilar Patricia , Ren Ping , Menachery Vineet D. , Diamond Michael S. , Weaver Scott C. , Xie Xuping , Shi Pei-Yong 
Published: January 2021

ABSTRACTThe biosafety level-3 (BSL-3) requirement to culture severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a bottleneck for research and countermeasure development. Here we report atrans-complementation system that produces single-round infectious SARS-CoV-2 that recapitulates authentic viral replication. We demonstrate that the single-round infectious SARS-CoV-2 can be used at BSL-2 laboratories for high-throughput neutralization and antiviral testing. Thetrans-complementation system consists of two components: a genomic viral RNA containing a deletion of ORF3 and envelope gene, and a producer cell line expressing the two deleted genes.Trans-complementation of the two components generates virions that can infect naive cells for only one round, but does not produce wild-type SARS-CoV-2. Hamsters and K18-hACE2 transgenic mice inoculated with the complementation-derived virions exhibited no detectable disease, even after intracranial inoculation with the highest possible dose. The results suggest that thetrans-complementation platform can be safely used at BSL-2 laboratories for research and countermeasure development.
Using Adversarial Images to Assess the Stability of Deep Learning Models Trained on Diagnostic Images in Oncology
Authors: Joel Marina Z. , Umrao Sachin , Chang Enoch , Choi Rachel , Yang Daniel X. , Duncan James S. , Omuro Antonio , Herbst Roy , Krumholz Harlan M. , Sanjay Aneja SM 
Published: January 2021

AbstractPurposeDeep learning (DL) models have rapidly become a popular and cost-effective tool for image classification within oncology. A major limitation of DL models is output instability, as small perturbations in input data can dramatically alter model output. The purpose of the study is to investigate the robustness of DL models in the oncologic image domain through the application of adversarial images: manipulated images with small pixel-level perturbations designed to assess the stability of DL models.Experimental DesignWe examined the impact of adversarial images on the classification accuracies of DL models trained to classify cancerous lesions across three common oncologic imaging modalities (CT, mammogram, and MRI). The CT model was trained to classify malignant lung nodules using the LIDC dataset. The mammogram model was trained to classify malignant breast lesions using the DDSM dataset. The MRI model was trained to classify brain metastases using an institutional dataset. We also explored the utility of an iterative adversarial training approach to improve the stability of DL models to small pixel-level changes.ResultsOncologic images showed instability with small pixel-level changes. A pixel-level of perturbation of .004 resulted in a majority of oncologic images to be misclassified by their respective DL models (CT 25.64%, mammogram 23.93%, MRI 6.36%). Adversarial training mitigated improved the stability and robustness of DL models trained on oncologic images compared to naive models [(CT 67.72% vs 26.92%), mammogram (63.39% vs 27.68%), MRI (87.20% vs 24.32%)].ConclusionsDL models naively trained on oncologic images exhibited dramatic instability to small pixel-level changes resulting in substantial decreases in accuracy. Adversarial training techniques improved the stability and robustness of DL models to such pixel-level changes. Prior to clinical implementation, adversarial training should be considered to proposed DL models to improve overall performance and safety.
NEWS2 and laboratory predictors correlated with clinical deterioration in hospitalised patients with COVID-19
Authors: Tuncer Gulsah , Surme Serkan , Bayramlar Osman Faruk , Karanalbant Hatice Kubra , Copur Betul , Yazla Meltem , Zerdali Esra , Nakir Inci Yilmaz , Cinar Ayse Kurt , Buyukyazgan Ahmet , Balli Hatice , Kurekci Yesim , Yavuz Serap Simsek , Sonmez Mehmet Mesut , Sengoz Gonul , Pehlivanoglu Filiz 
Published: January 2021

ABSTRACTBackgroundWe aimed to determine prognostic values of NEWS2 and laboratory parameters during the first week of COVID-19.MethodsAll adult patients who were hospitalized for a confirmed COVID-19 between the 11th of March and the 11th of May 2020 were retrospectively included. To evaluate the factors in prognosis which are admission to intensive care unit (ICU) and in-hospital death, univariate logistic regression analysis was performed at admission (D0), at day-3 (D3), day-5 (D5), and day-7 (D7). Additionally, receiver operating characteristic (ROC) analyses were performed.ResultsOverall, 611 patients were included. Clinical deterioration was observed in 79 (12.9%) patients during hospitalisation, 36 (5.9%) during the first three days, 54 (8.8%) during the first five days, and 62 (10.1%) during the first week of hospitalisation. Our results showed that NEWS2, procalcitonin, neutrophil/lymphocyte ratio (NLR), and albumin were the best predictors for clinical deterioration at D0, D3, D5, and D7. Procalcitonin had the highest odds ratio for clinical deterioration on all days in univariate analysis. ROC analyses showed that NEWS2 at D7, procalcitonin at D5, albumin at D7, and NLR at D5 had highest AUC values. Additionally, we detected a strong correlation between NEWS2 and laboratory parameters including neutrophil, lymphocyte, NLR, platelet/lymphocyte ratio, CRP, procalcitonin, ferritin, and urea on all days.ConclusionThis study provides a list of several laboratory parameters correlated with NEWS2 and potential predictors for ICU admission or in-hospital death during the clinical course of COVID-19. Dynamic monitoring of NEWS2 and laboratory parameters is vital for improving clinical outcomes.