bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physically based morphostructural land surface segmentation: Case of the Alps and Western Carpathians
Authors: Bandura Peter , Minár Jozef , Bielik Miroslav 
Published: October 2021

AbstractThe presented morphostructural segmentation of the Alps and Western Carpathians uses physically based geomorphometric variables as input data and object‐based image analysis as a procedure to delineate objects of interest. A previous suitability evaluation of simple object‐based methodology showed its potential in recognition of morphostructural features. When segmenting the Western Carpathians, we moved towards a more specific object‐based approach—a fusion of segmentation and classification at several hierarchical levels. Such an approach was evaluated as not necessary in the less contrasting terrain in the Alps, where only a simple segmentation was used for evaluation of its efficiency. Use of physically based geomorphometric variables as input data brought enhancement of subsequent morphotectonic interpretations. After the segmentations, an index of steady state (ISS) for the entire object levels and their parts was computed. This ISS was used to evaluate and compare the two study areas in terms of their geodynamic development. Similarities and differences in development of these relatively alike mountain ranges are interpreted.
An atlas of the Norway spruce needle seasonal transcriptome
Authors: Bag Pushan , Lihavainen Jenna , Delhomme Nicolas , Riquelme Thomas , Robinson Kathryn M , Jansson Stefan 
Published: October 2021

SummaryBoreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce (Picea abies) needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 until June 30), cell walls, organelles, etc., were formed, and this developmental program heavily influenced the transcriptome, explained by over‐represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July–August), autumn (September–October), winter (November–February), and spring (March–April), where over‐represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.
Growth period QTL‐allele constitution of global soybeans and its differential evolution changes in geographic adaptation versus maturity group extension
Authors: Liu Xueqin , Li Chunyan , Cao Jiqiu , Zhang Xiaoyan , Wang Can , He Jianbo , Xing Guangnan , Wang Wubin , Zhao Jinming , Gai Junyi 
Published: October 2021

SummarySoybean (Glycine max(L.) Merr.) has been disseminated globally as a photoperiod/temperature‐sensitive crop with extremely diverse days to flowering (DTF) and days to maturity (DTM) values. A population with 371 global varieties covering 13 geographic regions and 13 maturity groups (MGs) was analyzed for its DTF and DTM QTL‐allele constitution using restricted two‐stage multi‐locus genome‐wide association study (RTM‐GWAS). Genotypes with 20 701 genome‐wide SNPLDBs (single‐nucleotide polymorphism linkage disequilibrium blocks) containing 55 404 haplotypes were observed, and 52 DTF QTLs and 59 DTM QTLs (including 29 and 21 new ones) with 241 and 246 alleles (two to 13 per locus) were detected, explaining 84.8% and 74.4% of the phenotypic variance, respectively. The QTL‐allele matrix characterized with all QTL‐allele information of each variety in the global population was established and subsequently separated into geographic and MG set submatrices. Direct comparisons among them revealed that the genetic adaptation from the origin to geographic subpopulations was characterized by new allele/new locus emergence (mutation) but little allele exclusion (selection), while that from the primary MG set to emerged early and late MG sets was characterized by allele exclusion without allele emergence. The evolutionary changes involved mainly 72 DTF and 71 DTM alleles on 28 respective loci, 10–12 loci each with three to six alleles being most active. Further recombination potential for faster maturation (12–21 days) or slower maturation (14–56 days) supported allele convergence (recombination) as a constant genetic factor in addition to migration (inheritance). From the QTLs, 44 DTF and 36 DTM candidate genes were annotated and grouped respectively into nine biological processes, indicating multi‐functional DTF/DTM genes are involved in a complex gene network. In summary, we identified QTL‐alleles relatively thoroughly using RTM‐GWAS for direct matrix comparisons and subsequent analysis.
Implication of the nuclear trafficking of rabies virus P3 protein in viral pathogenicity
Authors: Brice Aaron M. , Watts Ericka , Hirst Bevan , Jans David A. , Ito Naoto , Moseley Gregory W. 
Published: October 2021

AbstractAlthough the majority of viruses of the family Mononegvirales replicate exclusively in the host cell cytoplasm, many of these viruses encode proteins that traffic between the nucleus and cytoplasm, which is believed to enable accessory functions in modulating the biology of the infected host cell. Among these, the P3 protein of rabies virus localizes to the nucleus through the activity of several specific nuclear localization and nuclear export signals. The major defined functions of P3 are in evasion of interferon (IFN)‐mediated antiviral responses, including through inhibition of DNA‐binding by IFN‐activated STAT1. P3 also localizes to nucleoli and promyelocytic leukemia (PML) nuclear bodies, and interacts with nucleolin and PML protein, indicative of several intranuclear roles. The relationship of P3 nuclear localization with pathogenicity, however, is unresolved. We report that nucleocytoplasmic localization of P3 proteins from a pathogenic RABV strain, Nishigahara (Ni) and a non‐pathogenic Ni‐derived strain, Ni‐CE, differs significantly, with nuclear accumulation defective for Ni‐CE‐P3. Molecular mapping indicates that altered localization derives from a coordinated effect, including two residue substitutions that independently disable nuclear localization and augment nuclear export signals, collectively promoting nuclear exclusion. Intriguingly, this appears to relate to effects on protein conformation or regulatory mechanisms, rather than direct modification of defined trafficking signal sequences. These data provide new insights into the role of regulated nuclear trafficking of a viral protein in the pathogenicity of a virus that replicates in the cytoplasm.
Influence of unreported HIV prophylaxis on the kinetics of post‐blood donation HIV seroconversion
Authors: Nishiya Anna S. , Salles Nanci A. , de Almeida‐Neto Cesar , Witkin Steven S. , Ferreira Suzete C. , Nogueira Fátima A. H. , Facincani Tila , Rocha Vanderson , Mendrone‐Jr Alfredo 
Published: October 2021

AbstractBackgroundIn 2020, of 110,000 blood donors screened for HIV exposure two individuals were identified who were viral RNA‐positive but seronegative. One of the donors, borderline negative in a pooled screening test for HIV RNA, utilized antiretroviral drugs as post‐exposure, pre‐donation prophylaxis. The kinetics of subsequent HIV seropositivity in both donors are described.Study Design and MethodsBoth donors were recalled and interviewed, and blood was obtained at intervals for HIV antibodies and RNA testing.ResultsOne donor used antiretroviral prophylaxis for 30 days due to a relationship with an HIV‐positive partner. In follow‐up samples, seroconversion was noted at 70 days, and viral RNA was detected at 105 days, after blood donation. In contrast, the other donor seroconverted in <25 days and the appearance and titer of HIV RNA was in accordance with the typical pre‐seroconversion window.ConclusionThe use of anti‐viral prophylaxis by blood donors in the acute phase of HIV infection delays seroconversion. A 6‐month deferral in blood donation after HIV prophylaxis, as currently recommended in Brazil, would have been sufficient in this case to mitigate the risk of transfusion‐transmitted HIV. Ultimately, improvement in donor compliance with selection procedures for blood donation is needed to optimize blood safety.
Mixed Methods Process Evaluation of a National Peer-Led Training Program to Increase Brief Advice on Physical Activity Given By Health Care Professionals
Authors: Whelan Maxine E. , Carlin Liz , Musson Hayley , Adams Emma J. 
Published: October 2021

Introduction: Health care professionals are well-positioned to encourage physical activity. The Clinical Champions Physical Activity Training Program (CCTP) aimed to increase population-level physical activity across England. This study aimed to (1) evaluate CCTP uptake and utilization; (2) explore CCTP fidelity, barriers, facilitators, and satisfaction; and (3) provide recommendations for program improvement. Methods: Physical Activity Clinical Champions were recruited and trained to deliver training to other health care professionals about physical activity. The Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM) framework was used to conduct a process evaluation using data collected from CCTP training sessions delivered (often at hospitals and General Practitioner surgeries) between February and December 2018. Results: About 509 training sessions were delivered, with 89% of sessions delivered by doctor/physician and nurse Clinical Champions; 8917 health care professionals attended a training session. Sessions lasted on average 1 hour 28 minutes and core slide sets were used in 65% of sessions. Barriers related to arranging the sessions and time available to deliver sessions. Conclusion: The process evaluation demonstrated a national peer-led training program can reach all geographical regions of England; however, barriers need to be addressed. Recommendations include providing more administrative support to the Clinical Champions, improving communication and advertising to raise awareness of the CCTP, and standardizing training session duration and content.
Temporal Trends in Children’s School Day Moderate to Vigorous Physical Activity: A Systematic Review and Meta-Regression Analysis
Authors: Weaver Robert Glenn , Tassitano Rafael M. , Tenório Maria Cecília M. , Brazendale Keith , Beets Michael W. 
Published: October 2021

Background: Evidence from a limited sample of countries indicates that time for physical education and recess during school have declined. Schools are called to provide children with 30 minutes of moderate to vigorous physical activity (MVPA). This systematic review and meta-analysis estimated temporal trends in children’s school day MVPA. Methods: Three online databases were searched to identify studies with objectively measured MVPA, during school hours, in school aged children (5–18 y). Multilevel random-effects meta-analyses estimated MVPA by year, and meta-regression analyses estimated temporal trends in school day MVPA. Results: Studies (N = 65) providing 171 MVPA estimates, representing 60,779 unique children, from 32 countries, and spanning 2003–2019 were identified. Most studies were conducted in North America (n = 33) or Europe (n = 21). School day MVPA ranged from 18.1 (95% confidence interval, 15.1–21.1) to 47.1 (95% confidence interval, 39.4–54.8) minutes per day in any given year. Meta-regression analyses indicated that MVPA declined from 2003 to 2010 (approximately 15 min decline), plateaued from 2010 to 2015 (approximately 1 min decrease), and increased from 2015 to 2019 (approximately 5 min increase). Conclusions: School day MVPA decreased from 2003 to 2010 and has recently begun to increase. However, the majority of the evidence is from North America and Europe with some evidence from Oceania and very little evidence from Asia to South America.
Bacterial Domestication: Underlying Assumptions
Authors: Davis Bernard D. 
Published: October 2021

On the basis of well-established principles of evolutionary biology and microbiology, I conclude that (i) the deliberate introduction of a novel bacterial strain to the environment is not substantially more dangerous than the accidental release of a smaller number of cells; (ii) distant organisms are less (rather than more) likely to yield dangerous hybrids than more closely related ones; and (iii) the complex attribute of pathogenicity is not likely to emerge from genetic alterations in nonpathogens. If these conclusions are correct, most engineered bacteria need not be regulated more strictly than the bacterial strains that have been tested in the field in the past. The only exceptions would be strains derived from cells, or appropriate genes, of microbes pathogenic for plants or animals. Microbiologists not only recognize the need to handle pathogens with caution: they have long accepted regulations, such as those governing transportation, that reinforce that recognition.
It is remarkable that we can still be arguing, on the basis of analogies rather than firm scientific principles or evidence, about hypothetical disasters from kinds of organisms that are being produced in hundreds or thousands of laboratories without a trace of demonstrable harm. RAC required 6 years to adjust its initially conservative guidelines to the emerging understanding of the scientific realities, while maintaining public confidence. Since the level of public concern is not nearly as great today, EPA should be able to relax its excessive restrictions much more quickly. Even better would be a return to having RAC, or a single successor group, evaluate the problems of danger for all classes of engineered bacteria, since the applicable shared principles outweigh any specialized differences in the nature or use of the specific strains. But the regulations are unlikely to be unified in this way, or to be divested of unproductive restrictions, without broad encouragement from the scientific community—including, hopefully, many ecologists. The agenda has been set for too long by apocalyptic activists. To protect this promising field of research and technological application the scientific community must take initiative in helping the public and decision-makers to distinguish reasonable probabilities from remote fantasies.
Observational cohort study of the triggers, diagnoses and outcomes of the medical emergency team (MET) response in adult psychiatry inpatients colocated with acute medical services in Australia
Authors: Azraai Meor , Pham Jeanette H , Looi Wenye F , Wirth Daniel , Ng Ashley S L , Babu Umesh , Saluja Bharat , Lim Andy K H 
Published: October 2021

ObjectivesMedical emergencies in psychiatric inpatients are challenging due to the model of care and limited medical resources. The study aims were to determine the triggers and outcomes of a medical emergency team (MET) call in psychiatric wards, and the risk factors for MET activation and mortality.DesignRetrospective multisite cohort study.SettingPsychiatry units colocated with acute medical services at three major metropolitan hospitals in Melbourne, Australia.ParticipantsWe studied 487 adult inpatients who experienced a total of 721 MET calls between January 2015 and January 2020. Patients were relatively young (mean age, 45 years) and had few medical comorbidities, but a high prevalence of smoking, excessive alcohol intake and illicit drug use.Outcome measuresWe performed a descriptive analysis of the triggers and outcomes (transfer rates, investigations, final diagnosis) of MET calls. We used logistic regression to determine the factors associated with the primary outcome of inpatient mortality, and the secondary outcome of the need for specific medical treatment compared with simple observation.ResultsThe most common MET triggers were a reduced Glasgow Coma Scale, tachycardia and hypotension, and 49% of patients required transfer. The most frequent diagnosis was a drug adverse effect or toxidrome, followed by infection and dehydration. There was a strong association between a leave of absence and MET calls, tachycardia and the final diagnosis of drug adverse effects. Mortality occurred in 3% after MET calls. Several baseline and MET clinical variables were associated with mortality but a model with age (per 10 years, OR 1.61, 95% CI 1.29 to 2.01) and hypoxia (OR 3.59, 95% CI 1.43 to 9.04) independently predicted mortality.ConclusionVigilance is required in patients returning from day leave, and drug adverse effects remain a challenging problem in psychiatric units. Hypoxic older patients with cardiovascular comorbidity have a higher risk of death.
Cohort profile: Indian Network of Population-Based Surveillance Platforms for Influenza and Other Respiratory Viruses among the Elderly (INSPIRE)
Authors: Krishnan Anand , Dar Lalit , Amarchand Ritvik , Prabhakaran Aslesh Ottapura , Kumar Rakesh , Rajkumar Prabu , Kanungo Suman , Bhardwaj Sumit Dutt , Choudekar Avinash , Potdar Varsha , Chakrabarti Alok Kumar , Kumar CP Girish , Parameswaran Giridara Gopal , Dhakad Shivram , Manna Byomkesh , Choudhary Ashish , Lafond Kathryn E , Azziz-Baumgartner Eduardo , Saha Siddhartha 
Published: October 2021

PurposeWe describe here a multicentric community-dwelling cohort of older adults (>60 years of age) established to estimate incidence, study risk factors, healthcare utilisation and economic burden associated with influenza and respiratory syncytial virus (RSV) in India.ParticipantsThe four sites of this cohort are in northern (Ballabgarh), southern (Chennai), eastern (Kolkata) and western (Pune) parts of India. We enrolled 5336 participants across 4220 households and began surveillance in July 2018 for viral respiratory infections with additional participants enrolled annually. Trained field workers collected data about individual-level and household-level risk factors at enrolment and quarterly assessed frailty and grip strength. Trained nurses surveilled weekly to identify acute respiratory infections (ARI) and clinically assessed individuals to diagnose acute lower respiratory infection (ALRI) as per protocol. Nasal and oropharyngeal swabs are collected from all ALRI cases and one-fifth of the other ARI cases for laboratory testing. Cost data of the episode are collected using the WHO approach for estimating the economic burden of seasonal influenza. Handheld tablets with Open Data Kit platform were used for data collection.Findings to dateThe attrition of 352 participants due to migration and deaths was offset by enrolling 680 new entrants in the second year. All four sites reported negligible influenza vaccination uptake (0.1%–0.4%), low health insurance coverage (0.4%–22%) and high tobacco use (19%–52%). Ballabgarh had the highest proportion (54.4%) of households in the richest wealth quintile, but reported high solid fuel use (92%). Frailty levels were highest in Kolkata (11.3%) and lowest in Pune (6.8%). The Chennai cohort had highest self-reported morbidity (90.1%).Future plansThe findings of this cohort will be used to inform prioritisation of strategies for influenza and RSV control for older adults in India. We also plan to conduct epidemiological studies of SARS-CoV-2 using this platform.
Association between previous rheumatoid arthritis and COVID-19 and its severity: a nationwide cohort study in South Korea
Authors: Jung Younghee , Kwon Mihye , Choi Hyo Geun 
Published: October 2021

ObjectivesThe prevalence of rheumatoid arthritis (RA) among patients with COVID-19 and the association between RA and the outcome of COVID-19 remain unclear. We aimed to compare the prevalence of RA between participants with and without COVID-19; we then analysed the association between the presence of RA and the severity of COVID-19.DesignA cross-sectional study.SettingData from a nationwide COVID-19 cohort database by the Korea National Health Insurance Corporation were used.Participants and interventionsA total of 8070 patients with COVID-19 (1 January 2020 through 4 June 2020) were matched with 32 280 control participants with regard to age, sex and income. Patients with COVID-19 were confirmed by SARS-CoV-2 PCR and controls were collected from the database. RA was confirmed using the diagnostic code (International Classification of Disease, Tenth Revision) and medication claim codes. Conditional/unconditional logistic regression was applied to analyse the association between RA and COVID-19.Primary outcome and secondary outcomeLaboratory confirmation of SARS-CoV-2 infection was defined as the primary outcome. The secondary outcome was severe COVID-19 defined as a history of intensive care unit admission, invasive ventilation or death.ResultsThe prevalence of RA in the COVID-19 (0.4%, 35/8070) and control (0.4%, 121/32,280) groups did not differ (p=0.446). After adjusting for underlying diseases, no association between RA and COVID-19 was observed (adjusted OR=1.14, 95% CI: 0.78 to 1.67) and COVID-19 severity was not associated with RA (adjusted OR=0.62, 95% CI: 0.14 to 7.29). The overall mortality rate was 2.9% (237/8070) and RA was not significantly associated with mortality (adjusted OR=1.64, 95% CI: 0.33 to 8.15).ConclusionWe did not find an association between the presence of RA and COVID-19. In addition, RA was not associated with the severity of COVID-19.
Study on nanocrystalline grain size and quantitative change in Fe–Cu–Mo–Si–B soft magnetic alloy
Authors: Kim Jong Su , Yom Tong Son , Kim Myong Hak 
Published: October 2021

In this paper, we studied the grain size and volume fraction change of [Formula: see text]-Fe(Si) nanocrystalline phase as a function of Cu, Mo and Si content in Fe[Formula: see text]Cu[Formula: see text]Mo3Si[Formula: see text]B9, Fe[Formula: see text]Cu1Mo[Formula: see text]Si[Formula: see text]B9, Fe[Formula: see text]Cu1Mo3Si[Formula: see text]B[Formula: see text], and also the annealing temperature and time in Fe[Formula: see text]Cu1Mo3Si[Formula: see text]B9 alloy. Cu is an element promoting ultrafine structure and crystallization progresses, it causes the grain size of the [Formula: see text]-Fe(Si) phase to decrease suddenly, the volume fraction of [Formula: see text]-Fe(Si) phase to increase only by adding 0.5 at.% Cu. Also, Mo causes the grain size of [Formula: see text]-Fe(Si) phase to decrease like Cu, while suppressing the increase of the volume fraction of [Formula: see text]-Fe(Si) phase, Si has no little effect on the grain size of [Formula: see text]-Fe(Si) phase, diffuses into the inner part of [Formula: see text]-Fe(Si) phase upto Si 13.5 at.%, but suddenly increases grain size above Si 13.5 at.%. The microstructure of Fe[Formula: see text]Cu1Mo3Si[Formula: see text]B9 alloy is nearly completed at 520[Formula: see text]C for about 20 min, the grain size is approximately 13.8–14.1 nm, the volume fraction of [Formula: see text]-Fe(Si) phase is within 61–66%, initial permeability at 1 kHz is within 59,800–61,100.