bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exposure to hypoxia causes stress erythropoiesis and downregulates immune response genes in spleen of mice
Authors: Wang Haijing , Liu Daoxin , Song Pengfei , Jiang Feng , Chi Xiangwen , Zhang Tongzuo 
Published: June 2021

Abstract
Background
The spleen is the largest secondary lymphoid organ and the main site where stress erythropoiesis occurs. It is known that hypoxia triggers the expansion of erythroid progenitors; however, its effects on splenic gene expression are still unclear. Here, we examined splenic global gene expression patterns by time-series RNA-seq after exposing mice to hypoxia for 0, 1, 3, 5, 7 and 13 days.

Results
Morphological analysis showed that on the 3rd day there was a significant increase in the spleen index and in the proliferation of erythroid progenitors. RNA-sequencing analysis revealed that the overall expression of genes decreased with increased hypoxic exposure. Compared with the control group, 1380, 3430, 4396, 3026, and 1636 genes were differentially expressed on days 1, 3, 5, 7 and 13, respectively. Clustering analysis of the intersection of differentially expressed genes pointed to 739 genes, 628 of which were upregulated, and GO analysis revealed a significant enrichment for cell proliferation. Enriched GO terms of downregulated genes were associated with immune cell activation. Expression of Gata1, Tal1 and Klf1 was significantly altered during stress erythropoiesis. Furthermore, expression of genes involved in the immune response was inhibited, and NK cells decreased.

Conclusions
The spleen of mice conquer hypoxia exposure in two ways. Stress erythropoiesis regulated by three transcription factors and genes in immune response were downregulated. These findings expand our knowledge of splenic transcriptional changes during hypoxia.
Reproducible and accessible analysis of transposon insertion sequencing in Galaxy for qualitative essentiality analyses
Authors: Larivière Delphine , Wickham Laura , Keiler Kenneth , Nekrutenko Anton ,   The Galaxy Team
Published: June 2021

Abstract
Background
Significant progress has been made in advancing and standardizing tools for human genomic and biomedical research. Yet, the field of next-generation sequencing (NGS) analysis for microorganisms (including multiple pathogens) remains fragmented, lacks accessible and reusable tools, is hindered by local computational resource limitations, and does not offer widely accepted standards. One such “problem areas” is the analysis of Transposon Insertion Sequencing (TIS) data. TIS allows probing of almost the entire genome of a microorganism by introducing random insertions of transposon-derived constructs. The impact of the insertions on the survival and growth under specific conditions provides precise information about genes affecting specific phenotypic characteristics. A wide array of tools has been developed to analyze TIS data. Among the variety of options available, it is often difficult to identify which one can provide a reliable and reproducible analysis.

Results
Here we sought to understand the challenges and propose reliable practices for the analysis of TIS experiments. Using data from two recent TIS studies, we have developed a series of workflows that include multiple tools for data de-multiplexing, promoter sequence identification, transposon flank alignment, and read count repartition across the genome. Particular attention was paid to quality control procedures, such as determining the optimal tool parameters for the analysis and removal of contamination.

Conclusions
Our work provides an assessment of the currently available tools for TIS data analysis. It offers ready to use workflows that can be invoked by anyone in the world using our public Galaxy platform (https://usegalaxy.org). To lower the entry barriers, we have also developed interactive tutorials explaining details of TIS data analysis procedures at https://bit.ly/gxy-tis.
Lactic acid bacteria that activate immune gene expression in Caenorhabditis elegans can antagonise Campylobacter jejuni infection in nematodes, chickens and mice
Authors: Jin Xing , He Yufeng , Zhou Yonghua , Chen Xiaohua , Lee Yuan-kun , Zhao Jianxin , Zhang Hao , Chen Wei , Wang Gang 
Published: June 2021

Abstract
Background
Campylobacter jejuni is the major micro-bacillary pathogen responsible for human coloenteritis. Lactic acid bacteria (LAB) have been shown to protect against Campylobacter infection. However, LAB with a good ability to inhibit the growth of C. jejuni in vitro are less effective in animals and animal models, and have the disadvantages of high cost, a long cycle, cumbersome operation and insignificant immune response indicators. Caenorhabditis elegans is increasingly used to screen probiotics for their anti-pathogenic properties. However, no research on the use of C. elegans to screen for probiotic candidates antagonistic to C. jejuni has been conducted to date.

Results
This study established a lifespan model of C. elegans, enabling the preselection of LAB to counter C. jejuni infection. A potential protective mechanism of LAB was identified. Some distinct LAB species offered a high level of protection to C. elegans against C. jejuni. The LAB strains with a high protection rate reduced the load of C. jejuni in C. elegans. The transcription of antibacterial peptide genes, MAPK and Daf-16 signalling pathway-related genes was elevated using the LAB isolates with a high protection rate. The reliability of the lifespan model of C. elegans was verified using mice and chickens infected with C. jejuni.

Conclusions
The results showed that different LAB had different abilities to protect C. elegans against C. jejuni. C. elegans provides a reliable model for researchers to screen for LAB that are antagonistic to C. jejuni on a large scale.
Intimal thickening and disruption of the media occur in the arterial walls of coronary arteries not associated with coronary arterial aneurysms in patients with Kawasaki disease
Authors: Tsuchihashi Tomoya , Kakimoto Nobuyuki , Takeuchi Takashi , Suenaga Tomohiro , Suzuki Takayuki , Shibuta Shoichi , Ino Yasushi , Kubo Takashi , Akasaka Takashi , Suzuki Hiroyuki 
Published: June 2021

Abstract
Background
Coronary artery aneurysm (CAA) is an important complication of Kawasaki disease (KD) that is associated with arterial structure damage. However, few studies have examined structural changes in coronary arteries that are not associated with CAA.

Methods
We examined coronary arteries in KD patients with CAAs who underwent follow-up coronary angiography (CAG) and optical coherence tomography (OCT). Coronary arterial branches with no abnormal findings during the most recent CAG were classified into two groups. Arteries with an acute-phase CAA that later regressed were classified as group R; arteries with no abnormal findings on either acute or convalescent phase CAG were classified as group N. Coronary arterial wall structural changes were compared between groups using OCT.

Results
Fifty-seven coronary arterial branches in 23 patients were evaluated by OCT. Thirty-six branches showed no abnormality during the most recent CAG. Both groups R and N comprised 18 branches. Maximum intimal thicknesses in groups R and N were 475 and 355 µm, respectively (p = 0.007). The incidences of media disruption were 100% and 67%, respectively (p = 0.02). Calcification, macrophage accumulation, and thrombus were not found in either group.

Conclusions
Intimal thickening and disruption of the media occur in coronary arteries with acute phase CAAs that later regress in the convalescent phase, as well as in arteries with normal CAG findings in the acute and convalescent phases.
Discovering the underlying typology of emergency departments
Authors: Demarquet Marine , Fraticelli Laurie , Freyssenge Julie , Claustre Clément , Martinez Mikaël , Duchenne Jonathan , El Khoury Carlos , Redjaline Abdesslam , Tazarourte Karim 
Published: June 2021

Abstract
Background
We hypothesized that monitoring the volume of activity and overall performance indicators is not sufficient to understand the underlying differences between emergency departments. We aimed to understand the underlying common characteristics of emergency departments and map their typology in order to propose adaptive solutions, that would take into account territorial specificities and manage existing resources.

Methods
We applied a multifactorial analysis based on input data at three levels; 1) the health care available in the area surrounding the emergency departments, 2) the level of medical technicality of the hospitals and 3) the profile of emergency department visits.

Results
We included 73 emergency departments in this study, representing 93.6% of the emergency departments in our region and seven groups were retained. The smallest group (n = 5) included both public and private structures with low volumes of activity. These medical structures were associated with the shortest length of stay and one of the lowest hospitalisation rates. The largest group (n = 21) included only public structures in peri-urban areas, which were associated with the highest rate of hospitalization in the region. The surrounding population was representative of the regional population, but the patients were older.

Conclusions
This approach represents a systemic response to target the organisational needs and constraints, propose appropriate solutions and adjust the financial resources allocated to hospitals. Future policies to improve care delivery may benefit from stratifying solutions and performance objectives depending on these groups.
A novel Longshi Scale measured activity of daily living disability in elderly patients affected by neurological diseases: a multi-center cross-sectional study in China
Authors: Zhao Jingpu , Liu Xiangxiang , Wan Li , Gao Yan , Huang Meiling , Zha Fubing , Long Jianjun , Li Dongxia , Nie Guohui , Wang Yulong 
Published: June 2021

Abstract
Background
Ability in the activities of daily life is often impaired in the older adults with a neurological disease. The Barthel Index is an instrument used worldwide to assess such ability. The Longshi Scale is a picture-based alternative, but its effectiveness has not been evaluated with older adult subjects. This study was to determine whether the Longshi Scale can effectively quantify the ability of older adults in the activities of daily living by comparing its ratings with those using the Barthel Index.

Methods
A multi-center cross-sectional study was conducted among patients over 65 years. A total of 2438 patients were divided into three groups, including bedridden, domestic, or community group based on their ability to go out of bed, move outdoors, and return indoors. Their ability in the activities of daily living among three groups was evaluated using both the Longshi Scale and the Barthel Index, and the results were compared.

Results
There was a significant difference in the average Barthel Index scores of three groups classified using the Longshi Scale. The average Longshi Scale scores also showed significant differences between the four groups classified using the Barthel Index. Spearman correlation coefficients showed strong correlation(>0.83) between the Longshi Scale and Barthel Index scores.

Conclusions
The Longshi Scale can efficiently distinguish the ability in the activities of daily living of people with a neurological disease. Its rating correlate well with those using the Barthel Index.
Comparison of renin–angiotensin–aldosterone system inhibitors with other antihypertensives in association with coronavirus disease-19 clinical outcomes
Authors: Bezabih Yihienew M. , Bezabih Alemayehu , Alamneh Endalkachew , Peterson Gregory M. , Bezabhe Woldesellassie 
Published: June 2021

AbstractBackgroundReports on the effects of renin–angiotensin–aldosterone system (RAAS) inhibitors on the clinical outcomes of coronavirus disease-19 (COVID-19) have been conflicting. We performed this meta-analysis to find conclusive evidence.MethodsWe searched published articles through PubMed, EMBASE and medRxiv from 5 January 2020 to 3 August 2020. Studies that reported clinical outcomes of patients with COVID-19, stratified by the class of antihypertensives, were included. Random and fixed-effects models were used to estimate pooled odds ratio (OR).ResultsA total 36 studies involving 30,795 patients with COVID-19 were included. The overall risk of poor patient outcomes (severe COVID-19 or death) was lower in patients taking RAAS inhibitors (OR = 0.79, 95% CI: [0.67, 0.95]) compared with those receiving non-RAAS inhibitor antihypertensives. However, further sub-meta-analysis showed that specific RAAS inhibitors did not show a reduction of poor COVID-19 outcomes when compared with any class of antihypertensive except beta-blockers (BBs). For example, compared to calcium channel blockers (CCBs), neither angiotensin-I-converting enzyme inhibitors (ACEIs) (OR = 0.91, 95% CI: [0.67, 1.23]) nor angiotensin-II receptor blockers (ARBs) (OR = 0.90, 95% CI: [0.62, 1.33]) showed a reduction of poor COVID-19 outcomes. When compared with BBs, however, both ACEIs (OR = 0.85, 95% CI: [0.73, 0.99) and ARBs (OR = 0.72, 95% CI: [0.55, 0.94]) showed an apparent decrease in poor COVID-19 outcomes.ConclusionsRAAS inhibitors did not increase the risk of mortality or severity of COVID-19. Differences in COVID-19 clinical outcomes between different class of antihypertensive drugs were likely due to the underlying comorbidities for which the antihypertensive drugs were prescribed, although adverse effects of drugs such as BBs could not be excluded.
Unusual erythematous plaque with white scales, a case of acquired syphilis in a child and literature review
Authors: Yang Wen-Jia , Hu Hong-Hao , Yang Yang , Li Jiu-Hong , Guo Hao 
Published: June 2021

Abstract
Background
Syphilis in children is uncommon with the mode of infection for this rare condition likely being congenital or acquired. While most acquired cases of syphilis in children result from sexual abuse, children can also be infected with syphilis through kissing, breastfeeding, sharing of daily necessities or pre-chewed food. Here, we report a case of acquired secondary syphilis in a child due to consumption of pre-chewed-food and provide a review of the literature on the characteristics of acquired syphilis in preschool children.

Case presentation
A 3-year-old girl presented with erythematous plaques and scales on her head, neck, and thighs as well as flat red papules with a moist, well circumscribed surface covered with a grayish-white film. The grandmother who cared for the girl was in the habit of pre-chewing food before giving it to the girl. The child and grandmother tested positive for RPR. The girl, who was not sexually abused, was diagnosed with acquired secondary syphilis, resulting from the transmission of pre-chewed food from her grandmother.

Conclusions
Our case report and literature review reveal that close contact among family members can result in the transmission of syphilis. We recommend that pre-chewing food should be discouraged by caregivers when caring for their children to avoid disease transmission.
Geographical distribution of risk factors for invasive non-typhoidal Salmonella at the subnational boundary level in sub-Saharan Africa
Authors: Lee Jung-Seok , Mogasale Vittal , Marks Florian , Kim Jerome 
Published: June 2021

Abstract
Background
Invasive non-typhoidal Salmonella (iNTS) is a growing health-concern in many parts of sub-Saharan Africa. iNTS is associated with fatal diseases such as HIV and malaria. Despite high case fatality rates, the disease has not been given much attention. The limited number of population-based surveillance studies hampers accurate estimation of global disease burden. Given the lack of available evidence on the disease, it is critical to identify high risk areas for future surveillance and to improve our understanding of iNTS endemicity.

Methods
Considering that population-based surveillance data were sparse, a composite index called the iNTS risk factor (iNRF) index was constructed based on risk factors that commonly exist across countries. Four risk factors associated with the prevalence of iNTS were considered: malaria, HIV, malnutrition, and safe water. The iNRF index was first generated based on the four risk factors which were collected within a 50 km radius of existing surveillance sites. Pearson product-moment correlation was used to test statistical associations between the iNRF index and the prevalence of iNTS observed in the surveillance sites. The index was then further estimated at the subnational boundary level across selected countries and used to identify high risk areas for iNTS.

Results
While the iNRF index in some countries was generally low (i.e. Rwanda) or high (i.e. Cote d’Ivoire), the risk-level of iNTS was variable not only by country but also within a country. At the provincial-level, the highest risk area was identified in Maniema, the Democratic Republic of Congo, whereas Dakar in Senegal was at the lowest risk.

Conclusions
The iNRF index can be a useful tool to understand the geographically varying risk-level of iNTS. Given that conducting a population-based surveillance study requires extensive human and financial resources, identifying high risk areas for iNTS prior to a study implementation can facilitate an appropriate site-selection process in the future.
IL-10 -1082 A/G polymorphism is related with the risk and clinical characteristics of acute kidney injury: a case-control study
Authors: Mu Haiyan , Zheng Qingqing , Hao Lihai 
Published: June 2021

Abstract
Background
Interleukin-10 (IL-10), a kind of anti-inflammation cytokine, has a key role in the development of acute kidney injury (AKI). Recently, several studies addressed the link between the risk of AKI and the IL-10 -1082 A/G polymorphism with conflicting findings.

Methods
To identify the effects of the IL-10 -1082 A/G polymorphism on the risk of AKI, we designed this case-control study. This study recruited 320 AKI patients and 408 ICU patients without AKI. The association between the AKI risk and this polymorphism was analyzed using the logistic regression analysis adjusted for confounding factors.

Results
The IL-10 -1082 A/G polymorphism enhanced the risk of AKI. After stratified analysis, this polymorphism increased the risk of AKI among the males, smokers, those aged exceeding 60 years old, and overweight individuals (BMI ≥ 25). Moreover, -1082 A/G polymorphism was remarkably related with APACHE II score and eGFR.

Conclusions
Collectively, the IL-10 -1082 A/G polymorphism is linked with an elevated risk of AKI. Further studies in China need be performed to verify these results.
Characteristics of ischemic stroke and intracranial hemorrhage in patients with nephrotic syndrome
Authors: Huang Wen-Yi , Chang Chun-Wei , Chen Chiung-Mei , Chen Kuan-Hsing , Chang Chien-Hung , Wu Hsiu-Chuan , Chang Kuo-Hsuan 
Published: June 2021

Abstract
Background
The incidence of cerebral stroke, including ischemic infarction and intracranial hemorrhage (ICH), increases in patients with nephrotic syndrome (NS). However, the clinical characteristics of patients with NS and stroke remain elusive. We aimed to investigate the clinical presentation and prognosis among patients with NS and ischemic stroke (IS) or ICH.

Methods
We conducted a population-based retrospective cohort study of patients with NS and acute stroke using the Chang Gung Research Database of Taiwan from January 1, 2001, to December 31, 2017. The participants were recruited from the 7 branches of Chang Gung Memorial Hospital.

Results
A total of 233 patients with IS and 57 patients with ICH were enrolled. The median age was 60 (52–70) years. The prevalence rates of hyperlipidemia, hyperuricemia, and smoking were higher in IS than in ICH. IS demonstrated lower white blood cell count (7.80 vs. 8.92 × 109/L) and high-sensitivity C-reactive protein level (33.42 vs. 144.10 nmol/L) and higher cholesterol (5.74 vs. 4.84 mmol/L), triglyceride (1.60 vs. 1.28 mmol/L), and albumin (24 vs. 18 g/L) levels compared with ICH. The dependent functional status and 30-day mortality were higher in ICH than in IS. The risk factors for 30-day mortality for patients with NS and stroke were coronary artery disease (CAD), ICH, and total anterior circulation syndrome. The multivariate Cox regression analysis revealed that CAD was positively associated with 30-day mortality in patients with IS (hazard ratio 24.58, 95 % CI 1.48 to 408.90). In patients with ICH, CAD and subarachnoid hemorrhage were positively associated with 30-day mortality (hazard ratio 5.49, 95 % CI 1.54 to 19.56; hazard ratio 6.32, 95 % CI 1.57 to 25.53, respectively).

Conclusions
ICH demonstrated a higher risk of dependence and 30-day mortality compared with IS in patients with NS. Intensive monitoring and treatment should be applied particularly in patients with NS and ICH.
Individual and community-level predictors of maternal alcohol consumption during pregnancy in Gondar town, Northwest Ethiopia: a multilevel logistic regression analysis
Authors: Addila Alemu Earsido , Azale Telake , Gete Yigzaw Kebede , Yitayal Mezgebu 
Published: June 2021

AbstractBackgroundPrenatal alcohol consumption is a serious public health concern that is considered as one of the preventable risk factors for neonatal and childhood morbidity and several adverse pregnancy outcomes. This study aimed to determine the individual- and community-level predictors of maternal alcohol consumption during pregnancy in Gondar town, Northwest Ethiopia.MethodsA community-based cross-sectional study was conducted among pregnant women in Gondar town from 13 June to 24 August 2019. A cluster random sampling technique was used to select 1237 pregnant women. Data collection was carried out using the AUDIT-C pretested standard questionnaire. Bivariable and multivariable multilevel logistic regression analyses were computed to identify predictors of alcohol consumption using the odds ratio, 95% CI, andp-value < 0.05.ResultsThe prevalence of alcohol consumption during pregnancy was found to be 30.26% (95% CI: 27.74%, 32.91%). The study revealed that pregnant women who have a low knowledge level on harmful effect of alcohol consumption (AOR = 3.2; 95% CI: 1.9, 5.4), positive attitude towards alcohol consumption (AOR = 7.5; 95% 5, 11), history of pre-pregnancy alcohol consumption (AOR = 4.8; 95% CI: 3.4, 6.9), whose partner consume alcohol (AOR = 3.9; 95% CI: 2.5, 6), a perception that alcohol consumption is culturally or socially acceptable (AOR = 3.6; 95% CI: 2.4, 5.3), who were encouraged by their partners to consume alcohol (AOR = 4; 95% CI: 1.9, 8) were significantly associated with pregnancy alcohol consumption. Concerning the community-level characteristics, who had not ever heard/media exposure about the risk of alcohol drinking during pregnancy (AOR = 3; 95% CI: 1.7, 5.5), and who were from low community women’s education attainment (AOR = 4; 95% CI: 2.2, 7.7) were statistically significant predictors of alcohol consumption during pregnancy.ConclusionsThe study revealed that alcohol consumption during pregnancy is prevalent in Gondar town. Both individual- and community-level predictors were found to be associated with alcohol consumption during pregnancy. Policymakers may take into account these predictors for individual and community-based interventions to which our results appear to point.