bluuebunny/crossref_metadata_2025_split huggingface dataset:
A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea
Authors: Aouad Monique , Flandrois Jean-Pierre , Jauffrit Frédéric , Gouy Manolo , Gribaldo Simonetta , Brochier-Armanet Céline 
Published: January 2022

Abstract
Background
The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea, projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental metabolisms as well as the origin of eukaryotes. Yet, resolving deep divergences remains a challenging task due to well-known tree-reconstruction artefacts and biases in extracting robust ancient phylogenetic signal, notably when analyzing data sets including the three Domains of Life. Among the various strategies aimed at mitigating these problems, divide-and-conquer approaches remain poorly explored, and have been primarily based on reconciliation among single gene trees which however notoriously lack ancient phylogenetic signal.

Results
We analyzed sub-sets of full supermatrices covering the whole Tree of Life with specific taxonomic sampling to robustly resolve different parts of the archaeal phylogeny in light of their current diversity. Our results strongly support the existence and early emergence of two main clades, Cluster I and Cluster II, which we name Ouranosarchaea and Gaiarchaea, and we clarify the placement of important novel archaeal lineages within these two clades. However, the monophyly and branching of the fast evolving nanosized DPANN members remains unclear and worth of further study.

Conclusions
We inferred a well resolved rooted phylogeny of the Archaea that includes all recently described phyla of high taxonomic rank. This phylogeny represents a valuable reference to study the evolutionary events associated to the early steps of the diversification of the archaeal domain. Beyond the specifics of archaeal phylogeny, our results demonstrate the power of divide-and-conquer approaches to resolve deep phylogenetic relationships, which should be applied to progressively resolve the entire Tree of Life.
Expression of immune response genes in human corneal epithelial cells interacting with Aspergillus flavus conidia
Authors: Arunachalam Divya , Ramanathan Shruthi Mahalakshmi , Menon Athul , Madhav Lekshmi , Ramaswamy Gopalakrishna , Namperumalsamy Venkatesh Prajna , Prajna Lalitha , Kuppamuthu Dharmalingam 
Published: January 2022

Abstract
Background
Aspergillus flavus, one of the causative agents of human fungal keratitis, can be phagocytosed by human corneal epithelial (HCE) cells and the conidia containing phagosomes mature into phagolysosomes. But the immunological responses of human corneal epithelial cells interacting with A. flavus are not clear. In this study, we report the expression of immune response related genes of HCE cells exposed to A. flavus spores using targeted transcriptomics.

Methods
Human corneal epithelial cell line and primary cultures were grown in a six-well plate and used for coculture experiments. Internalization of the conidia was confirmed by immunofluorescence microscopy of the colocalized endosomal markers CD71 and LAMP1. Total RNA was isolated, and the quantity and quality of the isolated RNA were assessed using Qubit and Bioanalyzer. NanoString nCounter platform was used for the analysis of mRNA abundance using the Human Immunology panel. R-package and nSolver software were used for data analysis. KEGG and FunRich 3.1.3 tools were used to analyze the differentially expressed genes.

Results
Different morphotypes of conidia were observed after 6 h of coculture with human corneal epithelial cells and found to be internalized by epithelial cells. NanoString profiling showed more than 20 differentially expressed genes in immortalized human corneal epithelial cell line and more than ten differentially expressed genes in primary corneal epithelial cells. Distinct set of genes were altered in their expression in cell line and primary corneal epithelial cells. KEGG pathway analysis revealed that genes associated with TNF signaling, NF-KB signaling, and Th17 signaling were up-regulated, and genes associated with chemokine signaling and B cell receptor signaling were down regulated. FunRich pathway analysis showed that pathways such as CDC42 signaling, PI3K signaling, and Arf6 trafficking events were activated by the clinical isolates CI1123 and CI1698 in both type of cells.

Conclusions
Combining the transcript analysis data from cell lines and primary cultures, we showed the up regulation of immune defense genes in A. flavus infected cells. At the same time, chemokine signaling and B cell signaling pathways are downregulated. The variability in the expression levels in the immortalized cell line and the primary cultures is likely due to the variable epigenetic reprogramming in the immortalized cells and primary cultures in the absence of any changes in the genome. It highlights the importance of using both cell types in host-pathogen interaction studies.
The elemental defense effect of cadmium on Alternaria brassicicola in Brassica juncea
Authors: Liu Zhe , Sun Zhenzhen , Zeng Chaozhen , Dong Xujie , Li Mei , Liu Zhixiang , Yan Mingli 
Published: January 2022

Abstract
Background
The elemental defense hypothesis states a new defensive strategy that hyperaccumulators defense against herbivores or pathogens attacks by accumulating heavy metals. Brassica juncea has an excellent ability of cadmium (Cd) accumulation. However, the elemental defense effect and its regulation mechanism in B. juncea remain unclear.

Results
In this study, we profiled the elemental defense effect and the molecular regulatory mechanism in Cd-accumulated B. juncea after Alternaria brassicicola infection. B. juncea treated with 180 mg Kg− 1 DW CdCl2 2.5H2O exhibited obvious elemental defense effect after 72 h of infection with A. brassicicola. The expression of some defense-related genes including BjNPR1, BjPR12, BjPR2, and stress-related miRNAs (miR156, miR397, miR398a, miR398b/c, miR408, miR395a, miR395b, miR396a, and miR396b) were remarkably elevated during elemental defense in B. juncea.

Conclusions
The results indicate that Cd-accumulated B. juncea may defend against pathogens by coordinating salicylic acid (SA) and jasmonic acid (JA) mediated systemic acquired resistance (SAR) and elemental defense in a synergistic joint effect. Furthermore, the expression of miRNAs related to heavy metal stress response and disease resistance may regulate the balance between pathogen defense and heavy metal stress-responsive in B. juncea. The findings provide experimental evidence for the elemental defense hypothesis in plants from the perspectives of phytohormones, defense-related genes, and miRNAs.
Stepwise implementation of a cardiovascular risk management care program in primary care
Authors: Smits Geert ,   on behalf of the PoZoB primary care group, Romeijnders A. , Rozema H. , Wijnands C. , Hollander Monika , van Doorn Sander , Bots Michiel 
Published: January 2022

Abstract
Background
Primary care plays a pivotal role in sustainable cardiovascular risk management (CVRM) but little is known about the organizational process of implementing the guidelines. The aim of the study was to describe the approach taken by a primary care group to implement the CVRM guideline.

Methods
Stepwise introduction and implementation of a programmatic CVRM care program was organized and facilitated by the care group between April 2010 and January 2013 in 137 affiliated general practices with 188 general practitioners (GPs), in the vicinity of Eindhoven, Netherlands. Care group support comprised sufficient staff, support with data extraction based on ICPC and ATC codes and with identification of eligible patients by scrutinizing patient health records and adequate coding of disease conditions.

Results
Patient selection based on availability of structured information on ICPC codes and risk factor levels from the electronic health records, led to 38,675 eligible patients in 2013. December 2019, the CVRM program was still running in 151 practices with 51,416 patients receiving programmatic CVRM care. Linking problems between 8 different electronic health record systems and the multidisciplinary information system for integrated care delayed adequate data collection until the beginning of 2013.

Conclusion
Commitment of affiliated GPs, a structured approach with adequate coding of diagnoses and risk factors, central data registration and additional funding for sufficient staff support are important conditions for the introduction and implementation of successful and sustainable programmatic CVRM care. This approach constitutes the basis for long-term follow up and annual evaluation.
Poliovirus immunity among adults in the Democratic Republic of the Congo: a cross-sectional serosurvey
Authors: Alfonso Vivian H. , Voorman Arie , Hoff Nicole A. , Weldon William C. , Gerber Sue , Gadoth Adva , Halbrook Megan , Goldsmith Amelia , Mukadi Patrick , Doshi Reena H. , Ngoie-Mwamba Guillaume , Fuller Trevon L. , Okitolonda-Wemakoy Emile , Muyembe-Tamfum Jean-Jacques , Rimoin Anne W. 
Published: January 2022

Abstract
Background
Vaccination efforts to eradicate polio currently focus on children under 5 years of age, among whom most cases of poliomyelitis still occur. However, in the Democratic Republic of the Congo (DRC), an outbreak of wild poliovirus type 1 occurred in 2010–2011 in which 16% of cases occurred among adults; in a related outbreak in the neighboring Republic of Congo, 75% of cases occurred among the same adult age-group. Given that infected adults may transmit poliovirus, this study was designed to assess adult immunity against polioviruses.

Methods
We assessed poliovirus seroprevalence using dried blood spots from 5,526 adults aged 15–59 years from the 2013–2014 Demographic and Health Survey in the DRC.

Results
Among adults in the DRC, 74%, 72%, and 57% were seropositive for neutralizing antibodies for poliovirus types 1, 2, and 3, respectively. For all three serotypes, seroprevalence tended to be higher among older age groups, those living in households with more children, and among women.

Conclusions
Protection against poliovirus is generally low among adults in the DRC, particularly for type 3 poliovirus. The lack of acquired immunity in adults suggests a potentially limited poliovirus circulation over the lifetime of those surveyed (spanning 1954 through 2014) and transmission of vaccine-derived poliovirus in this age group while underscoring the risk of these outbreaks among adults in the DRC.
The relationship between urinary albumin to creatinine ratio and all-cause mortality in the elderly population in the Chinese community: a 10-year follow-up study
Authors: Zhang Anhang , Li Man , Qiu Jiaojiao , Sun Jin , Su Yongkang , Cai Shuang , Bao Qiligeer , Cheng Bokai , Ma Shouyuan , Zhang Yan , Wang Shuxia , Zhu Ping 
Published: January 2022

Abstract
Background
In patients with diabetes and hypertension, proteinuria is independently associated with all-cause death. However, in the general population, urinary albumin to creatinine ratio (UACR) is less used to predict all-cause mortality. When the urinary albumin to creatinine ratio is within the normal range (UACR< 30 mg/g), the clinical relevance of an increased urinary albumin excretion rate is still debated. We studied the relationship between UACR and all-cause mortality in community populations, and compared UACR groups within the normal range.

Methods
The participants were the inhabitants from the Wanshoulu community in Beijing, China. The average age is 71.48 years, and the proportion of women is 60.1%. A total of 2148 people completed random urine samples to determine the urinary albumin to creatinine ratio (UACR). The subjects were divided into three groups according to UACR: Group 1 (UACR< 10 mg/g), Group 2 (10 mg/g < UACR< 30 mg/g), Group 3 (UACR> 30 mg/g). We used Kaplan-Meier survival analysis and Cox regression model to verify the relationship between UACR and all-cause mortality.

Results
At an average follow-up of 9.87 years (718,407.3 years), the total mortality rate were 183.4/1000. In the Cox proportional hazards model, after adjusting for possible confounders, those with normal high-value UACR (group 2) showed a higher all-cause mortality than those with normal low-value UACR (group 1) [hazard ratio (HR) 1.289, 95% confidence interval (CI) 1.002 ~ 1.659 for all-cause mortality]. Those with proteinuria (group 3) showed a higher all-cause mortality than those with normal low-value UACR (group 1) [hazard ratio (HR) 1.394, 95% confidence interval (CI) 1.020 ~ 1.905 for all-cause mortality].

Conclusion
Urinary albumin to creatinine ratio is an important risk factor for all-cause death in community population. Even if it is within the normal range (UACR< 30 mg/g), it occurs in people with high normal value (10 mg/g < UACR< 30 mg/g), the risk of all-cause death will also increase.
Prevalence and characteristics of hearing and vision loss in preschool children from low income South African communities: results of a screening program of 10,390 children
Authors: Eksteen Susan , Eikelboom Robert H. , Kuper Hannah , Launer Stefan , Swanepoel De Wet 
Published: January 2022

Abstract
Background
The majority of children with sensory impairments live in low- and middle-income countries. More studies of hearing and vision impairment prevalence are needed, in order to generate more accurate estimates of trends in sensory impairments. This study aimed to estimate the prevalence and describe the characteristics of hearing and vision loss among preschool children (4–7 years) in an underserved South African community following community-based mobile health (mHealth) supported hearing and vision services.

Methods
A screening program of sensory impairments was undertaken of children attending preschools in the communities of Khayelitsha and Mitchell’s Plain, Cape Town, from September 2017 until June 2019. Hearing and vision screening were done by trained community health workers using mHealth technology. Children who failed hearing and vision screening were seen for follow-up assessments at their preschools. Follow-up assessments were conducted using smartphones that host point-of-care validated and calibrated hearing and vision testing applications (hearTest app, hearX Group, South Africa and PeekAcuity app, Peek Vision, United Kingdom). Descriptive statistical analysis and logistic regression analysis were conducted after extracting data from a secure cloud-based server (mHealth Studio, hearX Group) to Microsoft Excel (2016).

Results
A total of 10,390 children were screened at 298 preschools over 22 months. Of the children screened, 5.6 and 4.4% of children failed hearing and vision screening respectively. Community-based follow-up hearing tests were done at the preschools on 88.5% (514) of children of whom 240 children (54.2% female) presented with hearing loss. A preschool-based follow-up vision test was done on 400 children (88.1%). A total of 232 children (46.1% female) had a vision impairment, and a further 32 children passed the test but had obvious signs of ocular morbidity. Logistic regression analysis found that age was a significant predictor of vision loss (p < 0.05), but not for hearing loss (p = 0.06). Gender was not a significant predictor of hearing (p = 0.22) or vision loss (p = 0.20).

Conclusions
Hearing loss is prevalent in at least 22 per 1000 and vision loss in at least 23 per 1000 preschool children in an underserved South African community. Timely identification of sensory losses can be facilitated through community-based hearing and vision services supported by mHealth technology.
Lung function and atherosclerosis: a cross-sectional study of multimorbidity in rural Uganda
Authors: Gilbert Rebecca F. , Cichowitz Cody , Bibangambah Prossy , Kim June-Ho , Hemphill Linda C. , Yang Isabelle T. , Sentongo Ruth N. , Kakuhikire Bernard , Christiani David C. , Tsai Alexander C. , Okello Samson , Siedner Mark J. , North Crystal M. 
Published: January 2022

Abstract
Background
Chronic obstructive pulmonary disease (COPD) is a leading cause of global mortality. In high-income settings, the presence of cardiovascular disease among people with COPD increases mortality and complicates longitudinal disease management. An estimated 26 million people are living with COPD in sub-Saharan Africa, where risk factors for co-occurring pulmonary and cardiovascular disease may differ from high-income settings but remain uncharacterized. As non-communicable diseases have become the leading cause of death in sub-Saharan Africa, defining multimorbidity in this setting is critical to inform the required scale-up of existing healthcare infrastructure.

Methods
We measured lung function and carotid intima media thickness (cIMT) among participants in the UGANDAC Study. Study participants were over 40 years old and equally divided into people living with HIV (PLWH) and an age- and sex-similar, HIV-uninfected control population. We fit multivariable linear regression models to characterize the relationship between lung function (forced expiratory volume in one second, FEV1) and pre-clinical atherosclerosis (cIMT), and evaluated for effect modification by age, sex, smoking history, HIV, and socioeconomic status.

Results
Of 265 participants, median age was 52 years, 125 (47%) were women, and 140 (53%) were PLWH. Most participants who met criteria for COPD were PLWH (13/17, 76%). Median cIMT was 0.67 mm (IQR: 0.60 to 0.74), which did not differ by HIV serostatus. In models adjusted for age, sex, socioeconomic status, smoking, and HIV, lower FEV1 was associated with increased cIMT (β = 0.006 per 200 mL FEV1 decrease; 95% CI 0.002 to 0.011, p = 0.01). There was no evidence that age, sex, HIV serostatus, smoking, or socioeconomic status modified the relationship between FEV1 and cIMT.

Conclusions
Impaired lung function was associated with increased cIMT, a measure of pre-clinical atherosclerosis, among adults with and without HIV in rural Uganda. Future work should explore how co-occurring lung and cardiovascular disease might share risk factors and contribute to health outcomes in sub-Saharan Africa.
Job requirements and physical demands (JRPD) questionnaire: cross-cultural adaptation and psychometric evaluation in Iranian Army personnel with chronic low back pain
Authors: Ramezani Mehdi , Pourghayoomi Ehsan , Taghizadeh Ghorban 
Published: January 2022

AbstractBackgroundBiomechanical risk factors have been identified as the main predisposing factor of chronic low back pain (CLBP), especially in Army personnel. The Job Requirements and Physical Demands (JRPD) questionnaire has been developed to assess the biomechanical exposures related to CLBP. Examining the biomechanical risk factors could prevent CLBP. This study aimed to translate and cross-culturally adapt the JRPD into Persian and assess its psychometric properties among Iranian male Army personnel with CLBP.MethodsIn this cross-sectional study, the content validation of the JRPD was assessed after translating to Persian. The Persian JRPD was administered to 198 male Army personnel with CLBP, with an interval of 7 days, to assess test-retest reliability, including Cronbach’s α, intraclass correlation coefficients (ICC), standard error of measurement (SEM), and minimal detectable change at 95% confidence interval (MDC95%). Scores of the Persian JRPD were correlated with the scores of visual analog scale (VAS), Borg’s category-ratio (CR10) scale, general health questionnaire-28 (GHQ-28), and physical functioning (PF1and PF2) subscale of the 12-item short-form health survey (SF-12) to assess convergent validity using Spearman correlation for a priori hypotheses.ResultsThe Persian JRPD had good content validity evidenced by the higher content validity index (> 0.70). The questionnaire had a significant positive negligible to weak correlation with the VAS (rho = 0.27;p < 0.001), Borg’s CR10 scale (rho = 0.19;p = 0.009), and the total score of GHQ-28 and its domains (rho ≤0.34;p < 0.05); and significant negative weak correlation with PF2(rho = − 0.27;p < 0.001) and significant negative moderate correlation with PF1(rho = − 0.35;p < 0.001), thus confirming the priori hypotheses (89%, 8/9). The internal consistency and ICC (α = 0.91; ICC = 0.80) were highly adequate, with SEM and MDC95%of 7.91 and 21.3 respectively.ConclusionsThe JRPD was successfully adapted into Persian and had adequate psychometric properties in terms of content and convergent validity, internal consistency, and test-retest reliability. The questionnaire is found useable to assess the CLBP-related biomechanical exposures in Iranian male Army personnel.
MicroRNA expression signature and target prediction in familial and sporadic primary macronodular adrenal hyperplasia (PMAH)
Authors: Tan Xiao-Gang , Zhu Jie , Cui Liang 
Published: January 2022

Abstract
Background
Primary macronodular adrenal hyperplasia (PMAH), previously termed ACTH-independent macronodular adrenal hyperplasia (AIMAH), is a rare cause of Cushing’s syndrome usually characterized by functioning adrenal macronodules and increased cortisol production.

Methods
To screen and analyse the microRNA (miRNA) profile of PMAH in order to elucidate its possible pathogenesis, a miRNA microarray was used to test tissue samples from patients with familial PMAH, patients with sporadic PMAH and normal control samples of other nontumour adrenocortical tissues and identify characteristic microRNA expression signatures. Randomly selected miRNAs were validated by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, the key signalling pathways and miRNAs involved in PMAH pathogenesis were determined by gene ontology and pathway analysis.

Results
Characteristic microRNA expression signatures were identified for patients with familial PMAH (16 differentially expressed microRNAs) and patients with sporadic PMAH (8 differentially expressed microRNAs). The expression of the selected miRNAs was confirmed by qRT-PCR, suggesting the high reliability of the miRNA array analysis results. Pathway analysis showed that the most enriched pathway was the renal cell carcinoma pathway. Overexpression of miR-17, miR-20a and miR-130b may inhibit glucocorticoid-induced apoptosis in PMAH pathogenesis.

Conclusion
We identified the miRNA signatures in patients with familial and sporadic PMAH. The differentially expressed miRNAs may be involved in the mechanisms of PMAH pathogenesis. Specific miRNAs, such as miR-17, miR-20a and miR-130b, may be new targets for further functional studies of PMAH.