bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sex-specific and age-related seasonal variations regarding incidence and in-hospital mortality of pulmonary embolism in Germany
Authors: Keller Karsten , Hobohm Lukas , Münzel Thomas , Konstantinides Stavros V. , Lankeit Mareike 
Published: June 2020

BackgroundStudies have reported seasonal variations regarding the incidence and the short-term mortality of pulmonary embolism (PE). The aim of this study was to identify sex-specific and age-related differences in seasonal patterns regarding hospitalisations and mortality of PE patients.MethodsWe analysed the impact of seasons on incidence and in-hospital mortality of male and female hospitalised PE patients in Germany (2005–2015) based on the German nationwide inpatient sample.ResultsThe German nationwide inpatient sample comprised 885 806 hospitalisations due to PE (2005–2015). Seasonal variations of both incidence (p=0.021) and in-hospital mortality (p<0.001) were of significant magnitude. Quarterly annual incidence (25.5versus23.7 of 100 000 citizens per year, p=0.021) and in-hospital mortality (17.0%versus16.7%, p=0.008) were higher in winter than in summer. Risk of in-hospital mortality in winter was slightly higher (OR 1.03 (95% CI 1.01–1.06), p=0.015) compared to summer, independently of sex, age and comorbidities. Additionally, we observed sex-specific differences during seasons: the highest number of hospitalisations of PE patients of both sexes was during winter, whereas the nadir of male patients was in spring and that of female patients was in summer. Both sexes showed a maximum of in-hospital mortality in spring. Seasonal variation regarding incidence and mortality was pronounced in older patients.ConclusionIncidence and the in-hospital mortality of PE patients showed a significant seasonal variation with sex-specific differences. Although it has to be hypothesised that the seasonal variation of PE is multifactorially dependent, variation in each season was not explained by seasonal differences regarding age, sex and the prevalence of important comorbidities.
In Situ-Formed and Low-Temperature-Deposited Nb:TiO2 Compact-Mesoporous Layer for Hysteresis-Less Perovskite Solar Cells with High Performance
Authors: Yu Miao , Sun Haoxuan , Huang Xiaona , Yan Yichao , Zhang Wanli 
Published: June 2020

AbstractRecently, reported perovskite solar cells (PSCs) with high power conversion efficiency (PCE) are mostly based on mesoporous structures containing mesoporous titanium oxide (TiO2) which is the main factor to reduce the overall hysteresis. However, existing fabrication approaches for mesoporous TiO2generally require a high-temperature annealing process. Moreover, there is still a long way to go for improvement in terms of increasing the electron conductivity and reducing the carrier recombination. Herein, a facile one-step, in situ, and low-temperature method was developed to prepare an Nb:TiO2compact-mesoporous layer which served as both scaffold and electron transport layer (ETL) for PSCs. The Nb:TiO2compact-mesoporous ETL-based PSCs exhibit suppressed hysteresis, which is attributed to the synergistic effect of the increased interface surface area caused by nano-pin morphology and the improved carrier transportation caused by Nb doping. Such a high-quality compact-mesoporous layer allows the PSCs assembled using optimized 2% Nb-doped TiO2to achieve a remarkable PCE of 19.74%. This work promises an effective approach for creating hysteresis-less and high-efficiency PSCs based on compact-mesoporous structures with lower energy consumption and cost.
Effects of forest bathing on pre-hypertensive and hypertensive adults: a review of the literature
Authors: Yau Katherine Ka-Yin , Loke Alice Yuen 
Published: June 2020

AbstractThe aim in this literature review was (1) to explore the physiologically and psychologically therapeutic benefits of forest bathing on adults suffering from pre-hypertension or hypertension, and (2) to identify the type, duration, and frequency of an effective forest bathing intervention in the management of pre-hypertension and hypertension, so as to provide directions for future interventions or research. The electronic databases PubMed, Cochrane Library, CINAHL, PsyINFO, and the China Academic Journals (CAJ) offered through the Full-text Database (CNKI) were searched for relevant studies published from the inception of the databases to April 2019. Of the 364 articles that were identified, 14 met the criteria for inclusion in this review. The synthesis of the findings in the included studies revealed that forest bathing interventions were effective at reducing blood pressure, lowering pulse rate, increasing the power of heart rate variability (HRV), improving cardiac-pulmonary parameters, and metabolic function, inducing a positive mood, reducing anxiety levels, and improving the quality of life of pre-hypertensive or hypertensive participants. Forest walking and forest therapy programs were the two most effective forest bathing interventions. Studies reported that practicing a single forest walking or forest therapy program can produce short-term physiological and psychological benefits. It is concluded that forest bathing, particularly forest walking and therapy, has physiologically and psychologically relaxing effects on middle-aged and elderly people with pre-hypertension and hypertension.
Proteome-Wide Analyses Reveal the Diverse Functions of Lysine 2-Hydroxyisobutyrylation in Oryza sativa
Authors: Xue Chao , Qiao Zhongying , Chen Xu , Cao Penghui , Liu Kai , Liu Shuai , Ye Lu , Gong Zhiyun 
Published: June 2020

Abstract
Background
Lysine 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, is known to regulate transcriptional activity in animals. However, extensive studies of the lysine 2-hydroxyisobutyrylome in plants and animals have yet to be performed.

Results
In this study, using LC-MS/MS qualitative proteomics strategies, we identified 4163 Khib sites on 1596 modified proteins in rice (Oryza sativa) seedlings. Motif analysis revealed 10 conserved motifs flanking the Khib sites, and subcellular localization analysis revealed that 44% of the Khib proteins are localized in the chloroplast. Gene ontology function, KEGG pathway, and protein domain enrichment analyses revealed that Khib occurs on proteins involved in diverse biological processes and is especially enriched in carbon metabolism and photosynthesis. Among the modified proteins, 20 Khib sites were identified in histone H2A and H2B, while only one site was identified in histone H4. Protein-protein interaction (PPI) network analysis further demonstrated that Khib participates in diverse biological processes including ribosomal activity, biosynthesis of secondary metabolites, and metabolic pathways. In addition, a comparison of lysine 2-hydroxyisobutyrylation, acetylation, and crotonylation in the rice proteome showed that 45 proteins with only 26 common lysine sites are commonly modified by three PTMs. The crosstalk of modified sites and PPI among these PTMs may form a complex network with both similar and different regulatory mechanisms.

Conclusions
In summary, our study comprehensively profiles the lysine 2-hydroxyisobutyrylome in rice and provides a better understanding of its biological functions in plants.
Transcriptome Sequencing and iTRAQ of Different Rice Cultivars Provide Insight into Molecular Mechanisms of Cold-Tolerance Response in Japonica Rice
Authors: Jia Yan , Liu Hualong , Qu Zhaojun , Wang Jin , Wang Xinpeng , Wang Zhuoqian , Yang Liang , Zhang Dong , Zou Detang , Zhao Hongwei 
Published: June 2020

AbstractBackgroundRice (Oryza sativaL.) is one of the most important crops cultivated in both tropical and temperate regions. However, it has a high sensitivity to cold stress and chilling stress limits its nitrogen uptake and metabolism. To identify the genes and pathways involved in cold tolerance, specifically within nitrogen metabolism pathways, we compared gene and protein expression differences between a cold-tolerant cultivar, Dongnong428 (DN), and a cold-sensitive cultivar, Songjing10 (SJ).ResultsUsing isobaric tags for relative or absolute quantification (iTRAQ) with high-throughput mRNA sequencing (RNA-seq) techniques, we identified 5549 genes and 450 proteins in DN and 6145 genes and 790 proteins in SJ, which were differentially expressed during low water temperature (Tw) treatments. There were 354 transcription factor (TF) genes (212 downregulated, 142 upregulated) and 366 TF genes (220 downregulated, 146 upregulated), including 47 gene families, differentially expressed in DN under control (CKDN) vs. DN under low-Tw(D15DN) and SJ under control (CKSJ) vs. SJ under low-TwD15SJ, respectively. Genes associated with rice cold-related biosynthesis pathways, particularly the mitogen-activated protein kinase (MAPK) signaling, zeatin biosynthesis, and plant hormone signal transduction pathways, were significantly differentially expressed in both rice cultivars. Differentially expressed proteins (DEPs) associated with rice cold-related biosynthesis pathways, and particularly glutathione metabolism, were significantly differentially expressed in both rice cultivars. Transcriptome and proteome analysis of the nitrogen metabolism pathways showed that major genes and proteins that participated in γ-aminobutyric acid (GABA) and glutamine synthesis were downregulated under cold stress.ConclusionCold stress conditions during reproductive growth, resulted in genes and proteins related to cold stress biosynthesis pathways being significantly differentially expressed in DN and SJ. The present study confirmed the known cold stress-associated genes and identified new putative cold-responsive genes. We also found that translational regulation under cold stress plays an important role in cold-tolerant DN. Low-Twtreatments affected N uptake and N metabolism in rice, as well as promoted Glu metabolism and the synthesis of ornithine and proline in cold-sensitive SJ.
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
Authors: Kieser Silas , Brown Joseph , Zdobnov Evgeny M. , Trajkovski Mirko , McCue Lee Ann 
Published: June 2020

Abstract
Background
Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers.

Results
Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license.

Conclusions
ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.
Gene expression predictions and networks in natural populations supports the omnigenic theory
Authors: Chateigner Aurélien , Lesage-Descauses Marie-Claude , Rogier Odile , Jorge Véronique , Leplé Jean-Charles , Brunaud Véronique , Roux Christine Paysant-Le , Soubigou-Taconnat Ludivine , Martin-Magniette Marie-Laure , Sanchez Leopoldo , Segura Vincent 
Published: June 2020

Abstract
Background
Recent literature on the differential role of genes within networks distinguishes core from peripheral genes. If previous works have shown contrasting features between them, whether such categorization matters for phenotype prediction remains to be studied.

Results
We measured 17 phenotypic traits for 241 cloned genotypes from a Populus nigra collection, covering growth, phenology, chemical and physical properties. We also sequenced RNA for each genotype and built co-expression networks to define core and peripheral genes. We found that cores were more differentiated between populations than peripherals while being less variable, suggesting that they have been constrained through potentially divergent selection. We also showed that while cores were overrepresented in a subset of genes statistically selected for their capacity to predict the phenotypes (by Boruta algorithm), they did not systematically predict better than peripherals or even random genes.

Conclusion
Our work is the first attempt to assess the importance of co-expression network connectivity in phenotype prediction. While highly connected core genes appear to be important, they do not bear enough information to systematically predict better quantitative traits than other gene sets.
Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications
Authors: Kim Goon-Bo , Lim Chae Eun , Kim Jin-Seok , Kim Kyeonghee , Lee Jeong Hoon , Yu Hee-Ju , Mun Jeong-Hwan 
Published: June 2020

AbstractBackgroundArtemisiain East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by insufficient diagnostic morphological characteristics and frequent natural hybridization. Development of novel DNA markers or barcodes with sufficient resolution to resolve taxonomic issues ofArtemisiain East Asia is significant challenge.ResultsTo establish a molecular basis for taxonomic identification and comparative phylogenomic analysis ofArtemisia, we newly determined 19 chloroplast genome (plastome) sequences of 18Artemisiataxa in East Asia, de novo-assembled and annotated the plastomes of two taxa using publicly available Illumina reads, and compared them with 11Artemisiaplastomes reported previously. The plastomes ofArtemisiawere 150,858–151,318 base pairs (bp) in length and harbored 87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNA genes in conserved order and orientation. Evolutionary analyses of whole plastomes and 80 non-redundant protein-coding genes revealed that the noncodingtrnH-psbAspacer was highly variable in size and nucleotide sequence both between and within taxa, whereas the coding sequences ofaccDandycf1were under weak positive selection and relaxed selective constraints, respectively. Phylogenetic analysis of the whole plastomes based on maximum likelihood and Bayesian inference analyses yielded five groups ofArtemisiaplastomes clustered in the monophyletic subgenusDracunculusand paraphyletic subgenusArtemisia, suggesting that the whole plastomes can be used as molecular markers to infer the chloroplast haplotypes ofArtemisiataxa. Additionally, analysis ofaccDandycf1hotspots enabled the development of novel markers potentially applicable across the family Asteraceae with high discriminatory power.ConclusionsThe complete sequences of theArtemisiaplastomes are sufficiently polymorphic to be used as super-barcodes for this genus. It will facilitate the development of new molecular markers and study of the phylogenomic relationships ofArtemisiaspecies in the family Asteraceae.
Response of grafting tobacco to low potassium stress
Authors: Hu Wei , Di Qing , Zhang Jie , Liu Jia , Shi Xiaojun 
Published: June 2020

Abstract
Background
In the previous study, we investigated the alleviation effect of grafting on potassium uptake in roots and tobacco growth inhibition under low potassium stress. However, the effect of grafting on the low potassium stress perception and coping mechanism of tobacco at the whole plant level is not clear now. In order to clearly understand the impact of grafting on potassium deficit responding mechanism in tobacco, a mutual grafting experiment has been conducted in two varieties of tobacco (‘Wufeng No.2’ and ‘Yunyan 87’) in different K supply level (5 mmol L− 1 and 0.5 mmol L− 1 K).

Results
The results show that compared with the self-rooted seedlings, grafting significantly increased the potassium content of the whole plant of Yunyan 87 (97.57 and 189.74% under normal potassium and low potassium conditions, respectively), and the increase in shoots was greater. The data of whole plant K content distribution and tobacco hypocotyls net K+ flux demonstrates that potassium stress makes plants more inclined to maintain K+ in the shoot rather than root. In addition, when K deficiency occurs, grafting could reduce the time required for downward net K+ flux in tobacco hypocotyl to decrease to stable levels. The results of net K+ flux in the roots indicated that K channel proteins and transporters play different roles in two rootstocks in terms of potassium tolerance. Transcription level analysis suggested that the increased circulating efficiency of K+ between the shoots and roots in tobacco constitutes one means to low potassium stress adaptation.

Conclusions
Grafting can activate more K+ channels in tobacco ‘Yunyan 87’, this means a more active K+ cycle, higher potassium content in shoot and faster response to low potassium stress signals in grafting tobacco. In addition, grafting can also change the K+ absorption mode of tobacco root from being dominated by HATS to being jointly responsible by HATS and LATS, greatly improving the ability of K+ transmembrane transportation on root surface under low potassium stress. These are undoubtedly the reasons why grafting tobacco performs better in coping with low potassium stress.
Dezocine prevents sufentanil-induced cough during general anesthesia induction: a meta-analysis of randomised controlled trials
Authors: Xiong Zhencheng , Yi Ping , Song Jipeng , Tan Mingsheng 
Published: June 2020

Abstract
Background
Sufentanil is one of the opioids currently used to induce general anesthesia, and cough is one of the most common complications. Many drugs have been used to prevent sufentanil-induced cough (SIC), and dezocine is one of them. Dezocine is an analgesic, acting as partial antagonist of κ-receptors and agonist of μ-receptors. The purpose of our meta-analysis is to evaluate the efficacy of dezocine on SIC.

Methods
We searched multiple databases including PubMed, Embase, ScienceDirect, the Cochrane Library, and China National Knowledge Infrastructure databases (CNKI) to identify studies that met the inclusion criteria. This meta-analysis focused on the incidence and severity of SIC after dezocine intervention, as well as adverse effects. This meta-analysis was registered on PROSPERO with reference number ID: CRD 42020144943.

Results
Five randomised controlled trials (RCTs) were identified, including 890 patients. Each study was a comparison of dezocine with an equal volume of 0.9% saline. When the injection dose of dezocine was 0.1 mg/kg, the incidence (pooled risk ratio (RR) = 0.03, [95% CI: 0.02 to 0.07], P < 0.00001, I2 = 0%) and severity (mild: RR = 0.07, [95% CI: 0.03 to 0.18], P < 0.00001, I2 = 0%; moderate: RR = 0.05, [95% CI: 0.02 to 0.16], P < 0.00001, I2 = 0%; severe: RR = 0.04, [95% CI: 0.01 to 0.16], P < 0.00001, I2 = 0%) of SIC were significantly decreased. There were no statistically significant differences in vital signs between the two groups based on the results of the pooled analysis.

Conclusion
This meta-analysis showed that dezocine significantly reduced the incidence and severity of SIC in the induction of general anesthesia, but had no significant effect on vital signs. More high-quality RCTs are needed to complement existing conclusions.
Depressive symptomatology and personality traits in patients with symptomatic and asymptomatic peripheral arterial disease
Authors: Tóth-Vajna Gergely , Tóth-Vajna Zsombor , Balog Piroska , Konkolÿ Thege Barna 
Published: June 2020

Abstract
Background
The aim of this study was to examine the relationship of depressive symptomatology and personality traits with peripheral arterial disease (PAD).

Methods
The sample of this cross-sectional study comprised of 300 individuals (Mage = 65.3 ± 8.7 years, 61.0% female) recruited from the offices of 33 general practitioners. Based on at-rest ankle-brachial index (ABI) values and claudication symptoms, four subsamples were formed: clear PAD-positive, clear PAD-negative, ABI-negative but symptomatic, and a non-compressible-artery group. The concurrent role of depression (assessed by a shortened version of the Beck Depression Inventory) and personality traits (measured by the Big Five Inventory) in predicting PAD status was examined using multinomial logistic regression – controlled for sex, age, hypertonia, diabetes, smoking, hazardous drinking, and body mass index.

Results
Depressive symptomatology was significant in predicting peripheral arterial disease status even after controlling for both traditional risk factors and personality traits. Among the Big Five personality traits, neuroticism showed a significant, positive relationship with PAD – independently of depression.

Conclusions
Patients with PAD – even those with asymptomatic forms of the disease – are at higher risk for suffering from depression compared to individuals without PAD, independently of neuroticism, other Big Five personality dimensions or traditional risk factors for cardiovascular diseases.
What is the level of uptake of partner notification services in HIV testing in selected health facilities in Gatanga Sub County, Muranga County – Kenya; a retrospective study
Authors: Kariuki Rewel Mwangi , Rithaa Gilbert Koome , Oyugi Elvis Omondi , Gachathi Daniel Muya 
Published: June 2020

Abstract
Background
Identification of people living with HIV is key in HIV prevention and control. Partner Notification service is a World Health Organization backed strategy of reaching out to sexual partners of people diagnosed with HIV for HIV testing. However, its adoption and success rate in Kenya remains unknown.

Methods
A cross sectional facility based study was undertaken in five purposely selected health facilities in Gatanga Sub county, Muranga County, Kenya. A retrospective review of patient medical records data for HIV positive index clients and their Sexual Partners conducted. Census approach was applied to extract data for study subjects from Partner Notification Services registers for the period covering January 2017 to August 2018. Epi Info software was used for data analysis.

Results
A total of 183 index clients were offered Partner notification services. The mean age of the indexed clients studied was 39(SD ±13.1). Females comprised 64% of clients studied. Of the 183 indexed clients, 89% accepted the services and elicited 216 sexual partners for tracing. The ratio of elicited sexual partners to index client was 1.3:1. Out of the 216 sexual partners, 77% were reached and tested. A total of 46 [32%] of the sexual partners elicited and traced, tested HIV positive. The most preferred approaches were provider referral (51%) and contract referral (45%). Dual referral (4%) was the least preferred approach.

Conclusions
Assisted Partner notification services is acceptable and an effective strategy of increasing HIV case identification and raising awareness to exposed sexual partners in low resource countries.