bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota
Authors: Gupta Shashank , Hjelmsø Mathis H. , Lehtimäki Jenni , Li Xuanji , Mortensen Martin S. , Russel Jakob , Trivedi Urvish , Rasmussen Morten A. , Stokholm Jakob , Bisgaard Hans , Sørensen Søren J. 
Published: August 2020

AbstractBackgroundFrom early life, children are exposed to a multitude of environmental exposures, which may be of crucial importance for healthy development. Here, the environmental microbiota may be of particular interest as it represents the interface between environmental factors and the child. As infants in modern societies spend a considerable amount of time indoors, we hypothesize that the indoor bed dust microbiota might be an important factor for the child and for the early colonization of the airway microbiome. To explore this hypothesis, we analyzed the influence of environmental exposures on 577 dust samples from the beds of infants together with 542 airway samples from the Copenhagen Prospective Studies on Asthma in Childhood2010cohort.ResultsBoth bacterial and fungal community was profiled from the bed dust. Bacterial and fungal diversity in the bed dust was positively correlated with each other. Bacterial bed dust microbiota was influenced by multiple environmental factors, such as type of home (house or apartment), living environment (rural or urban), sex of siblings, and presence of pets (cat and/or dog), whereas fungal bed dust microbiota was majorly influenced by the type of home (house or apartment) and sampling season. We further observed minor correlation between bed dust and airway microbiota compositions among infants. We also analyzed the transfer of microbiota from bed dust to the airway, but we did not find evidence of transfer of individual taxa.ConclusionsCurrent study explores the influence of environmental factors on bed dust microbiota (both bacterial and fungal) and its correlation with airway microbiota (bacterial) in early life using high-throughput sequencing. Our findings demonstrate that bed dust microbiota is influenced by multiple environmental exposures and could represent an interface between environment and child.
Refraction wavefield migration
Authors: Shen Yang , Zhang Jie 
Published: August 2020

Refraction methods are often applied to model and image near-surface velocity structures. However, near-surface imaging is very challenging, and no single method can resolve all of the land seismic problems across the world. In addition, deep interfaces are difficult to image from land reflection data due to the associated low signal-to-noise ratio. Following previous research, we have developed a refraction wavefield migration method for imaging shallow and deep interfaces via interferometry. Our method includes two steps: converting refractions into virtual reflection gathers and then applying a prestack depth migration method to produce interface images from the virtual reflection gathers. With a regular recording offset of approximately 3 km, this approach produces an image of a shallow interface within the top 1 km. If the recording offset is very long, the refractions may follow a deep path, and the result may reveal a deep interface. We determine several factors that affect the imaging results using synthetics. We also apply the novel method to one data set with regular recording offsets and another with far offsets; both cases produce sharp images, which are further verified by conventional reflection imaging. This method can be applied as a promising imaging tool when handling practical cases involving data with excessively weak or missing reflections but available refractions.
Photoplasticization Behavior and Photoinduced Pressure-Sensitive Adhesion Properties of Various Polymers Containing an Azobenzene-Doped Liquid Crystal
Authors: Koike Mioka , Aizawa Miho , Akamatsu Norihisa , Shishido Atsushi , Matsuzawa Yoko , Yamamoto Takahiro 
Published: August 2020

Abstract
Photochemical control of the hardness and fluidity of polymeric materials is applicable to the development of photoreversible adhesives. Here, we report that common polymers show photoplasticization behavior, which is the photoinduced reduction of the glass transition temperature, just by adding an azobenzene-doped liquid crystal (azo-doped LC). We found that the photoplasticization effect that occurred in amorphous polymers with an azo-doped LC was due to a microscopic phase separation of the azo-doped LC from the polymers. In contrast, we did not observe any photoplasticization behavior in crystalline polymers because of the macroscopic segregation of the azo-doped LC from the polymers and high rigidity of the crystalline regions of the polymers. Based on the photoplasticization effect, we successfully achieved photochemical induction of tackiness, which is a pressure-sensitive adhesion property. Furthermore, the maximum tack strength was enhanced upon photoirradiation of the polymers. We inferred that this behavior originated from an increase in the interaction between the samples and the test probe based on the change in polarity of the samples by the photoisomerization of azobenzene. We conclude that “photoplastic” polymers composed of common materials can be used for photoresponsive pressure-sensitive adhesives.
Global Analysis of Cereal microProteins Suggests Diverse Roles in Crop Development and Environmental Adaptation
Authors: Bhati Kaushal Kumar , Kruusvee Valdeko , Straub Daniel , Chandran Anil Kumar Nalini , Jung Ki-Hong , Wenkel Stephan 
Published: August 2020

Abstract
MicroProteins are a class of small single-domain proteins that post-translationally regulate larger multidomain proteins from which they evolved or which they relate to. They disrupt the normal function of their targets by forming microProtein-target heterodimers through compatible protein-protein interaction (PPI) domains. Recent studies confirm the significance of microProteins in the fine-tuning of plant developmental processes such as shoot apical meristem maintenance and flowering time regulation. While there are a number of well-characterized microProteins in Arabidopsis thaliana, studies from more complex plant genomes are still missing. We have previously developed miPFinder, a software for identifying microProteins from annotated genomes. Here we present an improved version where we have updated the algorithm to increase its accuracy and speed, and used it to analyze five cereal crop genomes – wheat, rice, barley, maize and sorghum. We found 20,064 potential microProteins from a total of 258,029 proteins in these five organisms, of which approximately 2000 are high-confidence, i.e., likely to function as actual microProteins. Gene ontology analysis of these 2000 microProtein candidates revealed their roles in stress, light and growth responses, hormone signaling and transcriptional regulation. Using a recently developed rice gene co-expression database, we analyzed 347 potential rice microProteins that are also conserved in other cereal crops and found over 50 of these rice microProteins to be co-regulated with their identified interaction partners. Overall, our study reveals a rich source of biotechnologically interesting small proteins that regulate fundamental plant processes such a growth and stress response that could be utilized in crop bioengineering.
Integration of GWAS Summary Statistics and Gene Expression Reveals Target Cell Types Underlying Kidney Function Traits
Authors: Li Yong , Haug Stefan , Schlosser Pascal , Teumer Alexander , Tin Adrienne , Pattaro Cristian , Köttgen Anna , Wuttke Matthias 
Published: August 2020

Significance Statement
Genome-wide association studies (GWAS) are a powerful tool to identify genetic variants associated with CKD. However, knowledge of CKD-relevant target tissues and cell types important in the pathogenesis is incomplete. Integrating large-scale kidney function GWAS with gene expression datasets identified kidney and liver as the primary organs for kidney function traits. In the kidney, proximal tubule was the critical cell type for eGFR and urate, as well as for monogenic electrolyte or metabolic disease genes. Podocytes showed enrichment of genes implicated in glomerular disease. Compendia connecting traits, genes, and cell types allow further prioritization of genes in GWAS loci, enabling mechanistic studies.

Background
Genetic variants identified in genome-wide association studies (GWAS) are often not specific enough to reveal complex underlying physiology. By integrating RNA-seq data and GWAS summary statistics, novel computational methods allow unbiased identification of trait-relevant tissues and cell types.

Methods
The CKDGen consortium provided GWAS summary data for eGFR, urinary albumin-creatinine ratio (UACR), BUN, and serum urate. Genotype-Tissue Expression Project (GTEx) RNA-seq data were used to construct the top 10% specifically expressed genes for each of 53 tissues followed by linkage disequilibrium (LD) score–based enrichment testing for each trait. Similar procedures were performed for five kidney single-cell RNA-seq datasets from humans and mice and for a microdissected tubule RNA-seq dataset from rat. Gene set enrichment analyses were also conducted for genes implicated in Mendelian kidney diseases.

Results
Across 53 tissues, genes in kidney function–associated GWAS loci were enriched in kidney (P=9.1E-8 for eGFR; P=1.2E-5 for urate) and liver (P=6.8·10-5 for eGFR). In the kidney, proximal tubule was enriched in humans (P=8.5E-5 for eGFR; P=7.8E-6 for urate) and mice (P=0.0003 for eGFR; P=0.0002 for urate) and confirmed as the primary cell type in microdissected tubules and organoids. Gene set enrichment analysis supported this and showed enrichment of genes implicated in monogenic glomerular diseases in podocytes. A systematic approach generated a comprehensive list of GWAS genes prioritized by cell type–specific expression.

Conclusions
Integration of GWAS statistics of kidney function traits and gene expression data identified relevant tissues and cell types, as a basis for further mechanistic studies to understand GWAS loci.
Hnf4a Is Required for the Development of Cdh6-Expressing Progenitors into Proximal Tubules in the Mouse Kidney
Authors: Marable Sierra S. , Chung Eunah , Park Joo-Seop 
Published: August 2020

Significance StatementProximal tubule cells are the most abundant cell type in the mammalian kidney, and they perform the bulk of the renal reabsorption function. Despite the importance of these cells in kidney function, the molecular mechanisms of proximal tubule development and maturation are not well understood. Experiments reveal that, in the developing mouse kidney, Cadherin-6-expressing cells act as proximal tubule progenitors and they require Hnf4a to further develop into mature proximal tubules. Genomic analyses show that Hnf4a directly regulates the expression of genes required for reabsorption, such as transmembrane transporter genes and metabolism genes. This study advances understanding of how kidney proximal tubule cells form during development.BackgroundHepatocyte NF 4α (Hnf4a) is a major regulator of renal proximal tubule (PT) development. In humans, a mutation inHNF4Aimpairs PT functions and is associated with Fanconi renotubular syndrome (FRTS). In mice, mosaic deletion ofHnf4ain the developing kidney reduces the population of PT cells, leading to FRTS-like symptoms. The molecular mechanisms underlying the role of Hnf4a in PT development remain unclear.MethodsThe gene deletion toolOsr2CreremovedHnf4ain developing nephrons in mice, generating a novel model for FRTS. Immunofluorescence analysis characterized the mutant phenotype, and lineage analysis tested whether Cadherin-6 (Cdh6)–expressing cells are PT progenitors. Genome-wide mapping of Hnf4a binding sites and differential gene analysis ofHnf4amutant kidneys identified direct target genes of Hnf4a.ResultsDeletion ofHnf4awithOsr2Creled to the complete loss of mature PT cells, lethal to theHnf4amutant mice. Cdh6high, lotus tetragonolobus lectin-low (LTLlow) cells serve as PT progenitors and demonstrate higher proliferation than Cdh6low, LTLhighdifferentiated PT cells. Additionally, Hnf4a is required for PT progenitors to differentiate into mature PT cells. Genomic analyses revealed that Hnf4a directly regulates the expression of genes involved in transmembrane transport and metabolism.ConclusionsHnf4a promotes the differentiation of PT progenitors into mature PT cells by regulating the expression of genes associated with reabsorption, the major function of PT cells.
Dysplasia Epiphysealis Hemimelica (Trevor Disease) of the Patella
Authors: Vashisht Saurabh , Aggarwal Purnima , Bhagat Ranjeev , Garg Ankita , Gupta P. N. , Garg Sudhir Kumar 
Published: August 2020

Case:
We report a rare case of dysplasia epiphysealis hemimelica in an 11-year-old male child involving the patella. The patient noticed swelling in the right knee 6 months before presentation. On evaluation, there was a mass lesion originating from superior pole of the patella extending into the suprapatellar pouch. On opening the knee joint, it was found to be mainly cartilaginous in nature. Surgical excision of the mass was carried out.

Conclusion:
Trevor disease should be considered in the differential diagnosis of a mass originating from the patella in children. The recommended treatment is complete excision of the mass.
Prognosis of Pregnancy-associated Breast Cancer: A Meta-analysis
Authors: SHAO Chunchun , YU Zhi gang , XIAO Juan , LIU Li yuan , HONG Fan zhen , ZHANG Yuan , JIA Hong ying 
Published: August 2020

Abstract
Background Pregnancy-associated breast cancer (PABC) is defined as breast cancer that is diagnosed during pregnancy and/or the postpartum period. Deﬁnitions of the duration of the postpartum period have been controversial, and this variability may lead to diverse results regarding prognosis. Moreover, evidence on the dose-response association between the time from the last pregnancy to breast cancer diagnosis and overall mortality has not been synthesized. Methods We systematically searched PubMed, Embase, and the Cochrane Library for observational studies on the prognosis of PABC published up to June 1, 2019. We estimated summary-adjusted hazard ratios (HRs) and the corresponding 95% confidence intervals (CIs). Subgroup analyses based on diagnosis time, PABC definition, geographic region, year of publication and estimation procedure for HR were performed. Additionally, dose-response analysis was conducted by using the variance weighted least-squares regression (VWLS) trend estimation. Results A total of 54 articles (76 studies) were included in our study. PABC was associated with poor prognosis for overall survival (OS), disease-free survival (DFS) and cause-specific survival (CSS), and the pooled HRs with 95% CIs were 1.45 (1.30-1.63), 1.39 (1.25-1.54) and 1.40 (1.17-1.68), respectively. The corresponding reference category was non-PABC patients. According to subgroup analyses, the varied definition of PABC led to diverse results. The dose-response analysis indicated a nonlinear association between the time from the last delivery to breast cancer diagnosis and the HR of overall mortality (P<0.001). Compared to nulliparous women, the mortality was almost 60% higher in women with PABC diagnosed at 12 months after the last delivery (HR=1.59, 95% CI 1.30-1.82), and the mortality was not significantly different at 70 months after the last delivery (HR=1.14, 95% CI 0.99-1.25). This finding suggests that the definition of PABC should be extended to include patients diagnosed up to approximately six years postpartum (70 months after the last delivery) to capture the increased risk. Conclusion This meta-analysis suggests that PABC is associated with poor prognosis, and the definition of PABC should be extended to include patients diagnosed up to approximately six years postpartum.
HIV/AIDS research in Africa and the Middle East: participation and equity in North-South collaborations and relationships.
Authors: González-Alcaide Gregorio , Menchi-Elanzi Marouane , Nacarapa Edy , Ramos-Rincón José-Manuel 
Published: August 2020

Abstract
Background HIV/AIDS has attracted considerable research attention since the 1980s. In the current context of globalization and the predominance of cooperative work, it is crucial to analyze the participation of the countries and regions where the infection is most prevalent. This study assesses the participation of African countries in publications on the topic, as well as the degree of equity or influence existing in North-South relations.Methods We identified all articles and reviews of HIV/AIDS indexed in the Web of Science Core Collection. We analyzed the scientific production, collaboration, and contributions from African and Middle Eastern countries to scientific activity in the region. The concept of leadership, measured through the participation as the first author of documents in collaboration was used to determine the equity in research produced through international collaboration. Results A total of 68,808 documents published from 2010 to 2017 were analyzed. Researchers from North America and Europe participated in 82.14% of the global scientific production on HIV/AIDS, compared to just 21.61% from Africa and the Middle East. Furthermore, the publications that did come out of these regions was concentrated in a small number of countries, led by South Africa (41% of the documents). Other features associated with HIV/AIDS publications from Africa include the importance of international collaboration from the USA, the UK, and other European countries (75%-93% of the documents) and the limited participation as first authors that is evident (30% to 36% of the documents). Finally, the publications to which African countries contributed had a notably different disciplinary orientation, with a predominance of research on public health, epidemiology, and drug therapy.Conclusions It is essential to foster more balance in research output, avoid the concentration of resources that reproduces the global North-South model on the African continent, and focus the research agenda on local priorities. To accomplish this, the global North should strengthen the transfer of research skills and seek equity in cooperative ties, favoring the empowerment of African countries. These efforts should be concentrated in countries with low scientific activity and high incidence and prevalence of the disease. It is also essential to foster intraregional collaborations between African countries.
The impact of patient safety culture and the leader coaching behaviour of nurses on the intention to report errors: A cross-sectional survey
Authors: Chegini Zahra , Kakemam Edris , Jafarabadi Mohammad Asghari , Janati Ali 
Published: August 2020

Abstract
Background: There is growing interest in examining the factors affecting the reporting of errors by nurses. However, little research has been conducted into the effects of perceived patient safety culture and leader coaching of nurses on the intention to report errors.
Methods: This cross-sectional study was conducted amongst 256 nurses in the emergency departments of 18 public and private hospitals in Tabriz, northwest Iran. Participants completed the Hospital Survey on Patient Safety Culture (HSOPSC), Coaching Behavior Scale and Intention to Report Errors questionnaires and the data was analyzed using multiple linear regression analysis.
Results: Overall, 43% of nurses had an intention to report errors; 50% of respondents reported that their nursing managers demonstrated high levels of coaching. With regard to patient safety culture, areas of strength and weakness were “teamwork within units” (PRR = 66.80%) and “non-punitive response errors” (PRR = 19.66%). Regression analysis findings highlighted a significant association between an intention to report errors and patient safety culture (B=0.123, CI 95%: 0.005 to 0.328, P = 0.026), leader coaching behavior (B=0.172, CI 95%: 0.066 to 0.347, P = 0.004) and nurses’ educational status (B=0. 787, 95% CI: -.064 to 1.638, P = 0.048).
Conclusions: Further research is needed to assess how interventions addressing patient safety culture and leader coaching behaviours might increase the intention to report errors.
Combined and interaction effect of Chlamydia pneumoniae infection and smoking on lung cancer: a case-control study in southeast China
Authors: Xu Xin , Liu Zhiqiang , Xiong Weimin , Qiu Minglian , Kang Shuling , Xu Qiuping , Cai Lin , He Fei 
Published: August 2020

Abstract
Background: This case-control study investigated the role of Chlamydia pneumoniae (Cpn) infection in the pathogenesis of lung cancer and the combined and interaction effect of Cpn infection, smoking, and various environmental factors.Methods: The study comprised 449 lung cancer patients and 512 age- and gender-matched healthy controls. All participants provided a 5 ml fasting peripheral venous blood sample for testing Cpn-specific IgG and IgA by using micro-immunofluorescence. Besides analyzing the associations between Cpn and lung cancer, combined effect analysis, logistic regression, and the Excel table made by Andersson were used to analyze the combined and interaction effects of Cpn and environmental factors on lung cancer.Results: Compared to those with no evidence of serum Cpn IgA or Cpn IgG, those with both Cpn IgG+ and IgA+ had 2.00 times the risk (95% CI: 1.34–3.00) of developing lung cancer. Cpn IgG+ or IgA+ was associated with a significantly increased risk of lung cancer among smokers; the adjusted odds ratio (OR) was 1.79 (95% CI: 1.10–2.91) and 2.27 (95% CI: 1.38–3.72), respectively. Those exposed to passive smoking with Cpn IgG+ or IgA+ also showed an increased risk of lung cancer; the adjusted OR was 1.82 (95% CI: 1.20–2.77) or 1.87 (95% CI: 1.22–2.87), respectively. Similar results were also observed among alcohol drinkers. Multiplicative and additive interactions were not observed between Cpn infection and environmental factors. The combined effects of Cpn IgG+ or IgA+ with smoking, passive smoking, and family history of cancer on lung cancer were determined.Conclusion: Cpn infection is potentially associated with primary lung cancer in the Chinese Han population and has combined effects with smoking, passive smoking, and family history of cancer.