bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-step preoperative sequential planning for pulmonary valve replacement in repaired tetralogy of Fallot using computed tomography
Authors: Ferraz Cavalcanti Paulo Ernando , Sá Michel Pompeu Barros Oliveira , Lins Ricardo Felipe de Albuquerque , Cavalcanti Catarina Vasconcelos , Lima Ricardo de Carvalho , Cvitkovic Tomislav , Bobylev Dmitry , Boethig Dietmar , Beerbaum Philipp , Sarikouch Samir , Haverich Axel , Horke Alexander 
Published: August 2020

Abstract

OBJECTIVES
Our goal was to compare results between a standard computed tomography (CT)-based strategy, the ‘three-step preoperative sequential planning’ (3-step PSP), for pulmonary valve replacement in repaired tetralogy of Fallot versus a conventional planning approach.

METHODS
We carried out a retrospective study with unmatched and matched groups. The 3-step PSP comprised the planning of mediastinal re-entry, cannulation for cardiopulmonary bypass (CPB) and the main procedure, using standard 3-dimensional videos. Operative times (skin incision to CPB, CPB time, end of CPB to skin closure and cross-clamp time) as well as postoperative length of stay and in-hospital mortality were compared.

RESULTS
Eighty-two patients (49% classical tetralogy of Fallot) underwent an operation (85% with pulmonary homograft) with 1.22% in-hospital mortality. The 3-step PSP (n = 14) and the conventional planning (n = 68) groups were compared. There were no statistically significant differences in the preoperative characteristics. Differences were observed in the total operative time (P = 0.009), skin incision to CPB (P = 0.034) and cross-clamp times (74 ± 33 vs 108 ± 47 min; P = 0.006), favouring the 3-step PSP group. Eight matched pairs were compared showing differences in the total operative time (263 ± 44 vs 360 ± 66 min; P = 0.008), CPB time (123 ± 34 vs 190 ± 43 min; P = 0.008) and postoperative length of stay (P = 0.031), favouring the 3-step PSP group.

CONCLUSIONS
In patients with repaired tetralogy of Fallot undergoing pulmonary valve replacement, preoperative planning using a standard CT-based strategy, the 3-step PSP, is associated with shorter operative times and shorter postoperative length of stay.
Edward Thomas and Hedges: England’s going out of Stile
Authors: Brooks Martin 
Published: August 2020

Abstract
Edward Thomas’s life and writing are marked by his attentiveness to rural England. With an overview of Thomas’ prose writings and then a set of close readings of his poetry, this essay describes how he presented hedges as an especially important part of the English countryside. Examining Thomas’s prose, the essay sets out how he saw hedges bringing natural life together into concentrated versions of landscapes, and how he argued that these concentrations could represent the English national identity. As the essay demonstrates, these ideas came into his poetry. His speakers see English field life as intricately interwoven. Some respond to the ongoing First World War by building on this intricacy. Their sense of being at home in England and belonging there is fuelled by treating hedges as portals to an eternal and a pre-industrial England. By considering the roles that hedges have in his poems, this essay shows how Thomas shaped them into a focal point for portraying speakers who have a connection to the national identity.
Primary care and all-cause mortality in urban China: a mixed-level analysis
Authors: Zhang Quan 
Published: August 2020

Abstract

Background
There is still a lack of evidence focusing on primary care supply in developing countries where the educational achievement of primary care practitioners is relatively low.

Objectives
By using a nationally representative longitudinal and prospective cohort study, this study examined whether primary care supply, measured by the availability and the number of community health centres (CHCs), was associated with 4-year mortality risk among community-dwelling participants aged 45 and above in urban China.

Methods
Using the 2011 and 2015 waves of the China Health and Retirement Longitudinal Survey (CHARLS), we conducted a longitudinal mixed-level logistic analysis to study the impact of the availability and the number of CHC on 4-year follow-up mortality risk, after adjusting community- and individual-level covariates.

Results
Individuals living in communities with CHC were 31% less likely to die during the 4-year follow-up (P &lt; 0.05) conditional on community-level characteristics, including the basic facilities availability, population size and physical area, and individuals’ socio-demographic and health characteristics and health behaviours. Also, an increased number of community-level CHC was shown to decrease residents’ 4-year mortality risk significantly (odds ratio = 0.82, P &lt; 0.05). Furthermore, the association was more pronounced among adults aged 65 and above.

Conclusion
This study provides additional evidence of the health-promoting effect of primary care supply among urban residents in China. Improving primary care coverage in China should be necessary to improve health care access, thus promoting population health.
Abundance, diversity and mobility potential of antibiotic resistance genes in pristine Tibetan Plateau soil as revealed by soil metagenomics
Authors: Li Bo , Chen Zeng , Zhang Fan , Liu Yongqin , Yan Tao 
Published: August 2020

ABSTRACTWidespread occurrence of antibiotic resistance genes (ARGs) has become an important clinical issue. Studying ARGs in pristine soil environments can help to better understand the intrinsic soil resistome. In this study, 10 soil samples were collected from a high elevation and relatively pristine Tibetan area, and metagenomic sequencing and bioinformatic analyses were conducted to investigate the microbial diversity, the abundance and diversity of ARGs and the mobility potential of ARGs as indicated by different mobile genetic elements (MGEs). A total of 48 ARG types with a relative abundance of 0.05–0.28 copies of ARG/copy of 16S rRNA genes were detected in Tibetan soil samples. The observed ARGs were mainly associated with antibiotics that included glycopeptide and rifamycin; the most abundant ARGs were vanRO and vanSO. Low abundance of MGEs and potentially plasmid-related ARGs indicated a low horizontal gene transfer risk of ARGs in the pristine soil. Pearson correlation and redundancy analyses showed that temperature and total organic carbon were the major environmental factors controlling both microbial diversity and ARG abundance and diversity.
Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment
Authors: Imchen Madangchanok , Kumavath Ranjith 
Published: August 2020

ABSTRACTSaline tolerant mangrove forests partake in vital biogeochemical cycles. However, they are endangered due to deforestation as a result of urbanization. In this study, we have carried out a metagenomic snapshot of the mangrove ecosystem from five countries to assess its taxonomic, functional and antibiotic resistome structure. Chao1 alpha diversity varied significantly (P &lt; 0.001) between the countries (Brazil, Saudi Arabia, China, India and Malaysia). All datasets were composed of 33 phyla dominated by eight major phyla covering &gt;90% relative abundance. Comparative analysis of mangrove with terrestrial and marine ecosystems revealed the strongest heterogeneity in the mangrove microbial community. We also observed that the mangrove community shared similarities to both the terrestrial and marine microbiome, forming a link between the two contrasting ecosystems. The antibiotic resistant genes (ARG) resistome was comprised of nineteen level 3 classifications dominated by multidrug resistance efflux pumps (46.7 ± 4.3%) and BlaR1 family regulatory sensor-transducer disambiguation (25.2 ± 4.8%). ARG relative abundance was significantly higher in Asian countries and in human intervention datasets at a global scale. Our study shows that the mangrove microbial community and its antibiotic resistance are affected by geography as well as human intervention and are unique to the mangrove ecosystem. Understanding changes in the mangrove microbiome and its ARG is significant for sustainable development and public health.
The type of microorganism and substrate determines the odor fingerprint of dried bacteria targeting microbial protein production
Authors: Sakarika Myrsini , Tzompa-Sosa Daylan A , Depoortere Mathilde , Rottiers Hayley , Ganigué Ramon , Dewettinck Koen , Rabaey Korneel 
Published: August 2020

ABSTRACT
The rapidly increasing demand for protein has led to the pursuit of new protein sources, among which microbial protein (MP) is one of the most promising. Although the nutritional properties of MP are important and often well-studied, the sensory properties of the microbial cells will in part determine the commercial success of the product and are much less investigated. Here we assessed the odor fingerprint of dried bacteria originating from pure cultures and enriched mixed microbial communities using an electronic nose (e-nose). The e-nose discriminated between the different MP sources, while the choice of culture and substrate substantially affected their volatile organic compound (VOC) profile. The most dominant odor descriptors (&gt;20% of VOC peak area) were sweet, fruity and fishy, while the mixed cultures presented higher peak areas indicating potentially more intense aromas than the pure cultures. The e-nose can detect the suitability of new MP sources and determine their best end-use.
Analysis of 5′-NAD capping of mRNAs in dormant spores of Bacillus subtilis
Authors: Craft D Levi , Korza George , Zhang Yaqing , Frindert Jens , Jäschke Andres , Caimano Melissa J , Setlow Peter 
Published: August 2020

ABSTRACT
Spores of Gram-positive bacteria contain 10s–1000s of different mRNAs. However, Bacillus subtilis spores contain only ∼ 50 mRNAs at &gt; 1 molecule/spore, almost all transcribed only in the developing spore and encoding spore proteins. However, some spore mRNAs could be stabilized to ensure they are intact in dormant spores, perhaps to direct synthesis of proteins essential for spores’ conversion to a growing cell in germinated spore outgrowth. Recent work shows that some growing B. subtilis cell mRNAs contain a 5′-NAD cap. Since this cap may stabilize mRNA in vivo, its presence on spore mRNAs would suggest that maintaining some intact spore mRNAs is important, perhaps because they have a translational role in outgrowth. However, significant levels of only a few abundant spore mRNAs had a 5′-NAD cap, and these were not the most stable spore mRNAs and had likely been fragmented. Even higher levels of 5′-NAD-capping were found on a few low abundance spore mRNAs, but these mRNAs were present in only small percentages of spores, and had again been fragmented. The new data are thus consistent with spore mRNAs serving only as a reservoir of ribonucleotides in outgrowth.
Function-Focused Person–Environment Fit for Long-Term Care Residents With Dementia: Impact on Apathy
Authors: Jao Ying-Ling , Liu Wen , Chaudhury Habib , Parajuli Jyotsana , Holmes Sarah , Galik Elizabeth 
Published: August 2020

AbstractBackground and ObjectivesApathy is a common symptom in dementia and is associated with rapid cognitive decline, poor quality of life, and higher mortality. Lawton’s Competence and Environmental Press model suggests that an individual’s behavior and affect are influenced by the fit of their functional abilities with the environmental demands. Yet, empirical evidence on the association between person–environment (P–E) fit and apathy is lacking. Thus, this study examined the relationship between P–E fit and apathy in dementia. Specifically, this study focused on the extent the physical environment fits individual functional limitations.Research Design and MethodsThis is a cross-sectional study using the baseline data from long-term care residents with dementia. The sample included 199 residents with moderate-to-severe cognitive impairment from 4 assisted living and 4 nursing homes. Function-focused P–E fit was measured using the Housing Enabler scale. Apathy was measured using the Apathy Evaluation Scale. Multilevel linear models were used to analyze the relationship between P–E fit and apathy.ResultsFindings revealed that greater P–E fit, specifically indoor environment, was significantly associated with lower apathy after controlling for age, gender, and years living in the facility. Yet, the association became not significant after controlling for individual physical function.Discussion and ImplicationsFindings support the association between function-focused P–E fit and apathy, but the association is no longer significant after physical function is adjusted. Future research may explore other aspects of P–E fit and the impact of social and organizational environment on apathy in dementia.
The chromosome-level draft genome of Dalbergia odorifera
Authors: Hong Zhou , Li Jiang , Liu Xiaojin , Lian Jinmin , Zhang Ningnan , Yang Zengjiang , Niu Yongchao , Cui Zhiyi , Xu Daping 
Published: August 2020

Abstract

Background
Dalbergia odorifera T. Chen (Fabaceae) is an International Union for Conservation of Nature red-listed tree. This tree is of high medicinal and commercial value owing to its officinal, insect-proof, durable heartwood. However, there is a lack of genome reference, which has hindered development of studies on the heartwood formation.

Findings
We presented the first chromosome-scale genome assembly of D. odorifera obtained on the basis of Illumina paired-end sequencing, Pacific Biosciences single-molecule real-time sequencing, 10x Genomics linked reads, and Hi-C technology. We assembled 97.68% of the 653.45 Mb D. odorifera genome with scaffold N50 and contig sizes of 56.16 and 5.92 Mb, respectively. Ten super-scaffolds corresponding to the 10 chromosomes were assembled, with the longest scaffold reaching 79.61 Mb. Repetitive elements account for 54.17% of the genome, and 30,310 protein-coding genes were predicted from the genome, of which ~92.6% were functionally annotated. The phylogenetic tree showed that D. odorifera diverged from the ancestor of Arabidopsis thaliana and Populus trichocarpa and then separated from Glycine max and Cajanus cajan.

Conclusions
We sequence and reveal the first chromosome-level de novo genome of D. odorifera. These studies provide valuable genomic resources for the research of heartwood formation in D. odorifera and other timber trees. The high-quality assembled genome can also be used as reference for comparative genomics analysis and future population genetic studies of D. odorifera.
Lava dome morphology inferred from numerical modelling
Authors: Tsepelev Igor , Ismail-Zadeh Alik , Melnik Oleg 
Published: August 2020

SUMMARY
Lava domes form when highly viscous magmas erupt on the surface. Several types of lava dome morphology can be distinguished depending on the flow rate and the rheology of magma. Here, we develop a 2-D axisymmetric model of magma extrusion on the surface and lava dome evolution and analyse the dome morphology using a finite-volume method implemented in Ansys Fluent software. The magma/lava viscosity depends on the volume fraction of crystals and temperature. We show that the morphology of domes is influenced by two parameters: the characteristic time of crystal content growth (CCGT) and the discharge rate (DR). At smaller values of the CCGTs, that is, at rapid lava crystallization, obelisk-shaped structures develop at low DRs and pancake-shaped structures at high DRs; at longer CCGTs, lava domes feature lobe- to pancake-shaped structures. A thick carapace of about 70 per cent crystal content evolves at smaller CCGTs. We demonstrate that cooling does not play the essential role during a lava dome emplacement, because the thermal thickness of the evolving carapace remains small in comparison with the dome's height. A transition from the endogenic to exogenic regime of the lava dome growth occurs after a rapid increase in the DR. A strain-rate-dependent lava viscosity leads to a more confined dome, but the influence of this viscosity on the dome morphology is not well pronounced. The model results can be used in assessments of the rates of magma extrusion, the lava viscosity and the morphology of active lava domes..
Epidemiological characteristics of patients with severe COVID-19 infection in Wuhan, China: evidence from a retrospective observational study
Authors: Wang Fang , Cao Jinhong , Yu Yong , Ding Jianbo , Eshak Ehab S , Liu Keyang , Mubarik Sumaira , Shi Fang , Wen Haoyu , Zeng Zixin , Bai Jianjun , Yu Chuanhua 
Published: August 2020

Abstract

Background
The new coronavirus (COVID-19) rapidly resulted in a pandemic. We report the characteristics of patients with severe or critical severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Wuhan city, China, and the risk factors related to infection severity and death.

Methods
We extracted the demographic and clinical data of 7283 patients with severe COVID-19 infection from designated Wuhan hospitals as of 25 February 2020. Factors associated with COVID-19 critical illness and mortality were analysed using logistic- and Cox-regression analyses.

Results
We studied 6269 patients with severe COVID-19 illness and 1014 critically ill patients. The median (IQR) age was 64 (53–71) years; 51.2% were male, 38.9% were retirees and 7.4% had self-reported histories of chronic disease. Up to the end of the study, 1180 patients (16.2%) recovered and were discharged, 649 (8.9%) died and the remainder were still receiving treatment. The number of daily confirmed critical cases peaked between 23 January and 1 February 2020. Patients with advanced age [odds ratio (OR), 1.03; 95% confidence intervals (CIs), 1.03–1.04], male sex (OR, 1.57; 95% CI, 1.33–1.86) and pre-existing diabetes (OR, 2.11), hypertension (OR, 2.72), cardiovascular disease (OR, 2.15) or respiratory disease (OR, 3.50) were more likely to be critically ill. Compared with those who recovered and were discharged, patients who died were older [hazard ratio (HR), 1.04; 95% CI, 1.03–1.05], more likely to be male (HR, 1.74; 95% CI, 1.44–2.11) and more likely to have hypertension (HR, 5.58), cardiovascular disease (HR, 1.83) or diabetes (HR, 1.67).

Conclusion
Advanced age, male sex and a history of chronic disease were associated with COVID-19 critical illness and death. Identifying these risk factors could help in the clinical monitoring of susceptible populations.
Vaginal and Penile Microbiome Associations With Herpes Simplex Virus Type 2 in Women and Their Male Sex Partners
Authors: Mehta Supriya D , Nandi Debarghya , Agingu Walter , Green Stefan J , Bhaumik Dulal K , Bailey Robert C , Otieno Fredrick 
Published: August 2020

AbstractBackgroundWe determined how the vaginal and penile microbiomes contribute to herpes simplex virus type 2 (HSV-2) serostatus within sexual partnerships.MethodsMicrobiomes were characterized in cervicovaginal lavage and penile meatal swab specimens through high-throughput 16s ribosomal RNA gene amplicon sequencing. HSV-2 antibody was detected in serum specimens. We modeled vaginal and penile taxa and covariates contributing to HSV-2 status in women and men using bivariate probit analysis.ResultsAmong 231 couples, HSV-2 was detected in both partners in 78 couples (33.8%), in the woman only in 52 (22.5%),in the man only in 27 (11.7%), and in neither in 74 (32.0%). Among the women (median age, 22 years) 10.9% had human immunodeficiency virus (HIV), and 21.4% had Bacterial vaginosis. Among men (median age, 26 years), 11.8% had HIV, and 55.0% circumcised. In an analysis with adjustment for sociodemographics and Bacterial vaginosis, enrichment of vaginal Gardnerella vaginalis and Lactobacillus iners was associated with increased likelihood of HSV-2 in both partners. Penile taxa (including Ureaplasma and Aerococcus) were associated with HSV-2 in women.ConclusionsWe demonstrate that penile taxa are associated with HSV-2 in female partners, and vaginal taxa are associated with HSV-2 in male partners. Our findings suggest that couples-level joint consideration of genital microbiome and sexually transmitted infection or related outcomes could lead to new avenues for prevention.
Organized immune cell interactions within tumors sustain a productive T-cell response
Authors: Cardenas Maria A , Prokhnevska Nataliya , Kissick Haydn T 
Published: August 2020

Abstract
Tumor-infiltrating CD8 T cells are associated with improved patient survival and response to immunotherapy in various cancers. Persistent antigen leads to CD8 T-cell exhaustion, where proliferation/self-renewal and killing are divided within distinct subsets of CD8 T cells in the tumor. CD8 T-cell responses in chronic antigen settings must be maintained for long periods of time, suggesting that mechanisms that regulate chronic CD8 T-cell responses may differ from those in acute settings. Currently, factors that regulate the maintenance of stem-like CD8 T cells in the tumor or their differentiation into terminally differentiated cells are unknown. In this review, we discuss the role of dendritic cells in the activation and differentiation of CD8 T-cell subsets within secondary lymphoid tissue and tumors. In addition, we examine changes in CD4 T-cell differentiation in response to chronic antigens and consider how subset-specific mechanisms could assist the stem-like and terminally differentiated CD8 T-cell subsets. Finally, we highlight how tumor-infiltrating CD4 T cells and dendritic cells interact with CD8 T cells within organized lymphoid-like areas in the tumor and propose a CD8 T-cell differentiation model that requires the collaboration of CD4 T cells and dendritic cells. These organized interactions coordinate the anti-tumor response and control disease progression by mechanisms that regulate CD8 T-cell differentiation, which permit the maintenance of an effective balance of stem-like and terminally differentiated CD8 T cells.
Generative transfer learning for measuring plausibility of EHR diagnosis records
Authors: Estiri Hossein , Vasey Sebastien , Murphy Shawn N 
Published: August 2020

Abstract

Objective
Due to a complex set of processes involved with the recording of health information in the Electronic Health Records (EHRs), the truthfulness of EHR diagnosis records is questionable. We present a computational approach to estimate the probability that a single diagnosis record in the EHR reflects the true disease.

Materials and Methods
Using EHR data on 18 diseases from the Mass General Brigham (MGB) Biobank, we develop generative classifiers on a small set of disease-agnostic features from EHRs that aim to represent Patients, pRoviders, and their Interactions within the healthcare SysteM (PRISM features).

Results
We demonstrate that PRISM features and the generative PRISM classifiers are potent for estimating disease probabilities and exhibit generalizable and transferable distributional characteristics across diseases and patient populations. The joint probabilities we learn about diseases through the PRISM features via PRISM generative models are transferable and generalizable to multiple diseases.

Discussion
The Generative Transfer Learning (GTL) approach with PRISM classifiers enables the scalable validation of computable phenotypes in EHRs without the need for domain-specific knowledge about specific disease processes.

Conclusion
Probabilities computed from the generative PRISM classifier can enhance and accelerate applied Machine Learning research and discoveries with EHR data.