bluuebunny/crossref_metadata_2025_split huggingface dataset:
In-hospital mortality and its predictors among stroke patients in sub-Saharan Africa: A systemic review and meta-analysis
Authors: Mohammed Ammas Siraj , Degu Amsalu , Woldekidan Nigist Alemayehu , Adem Fuad , Edessa Dumessa 
Published: July 2021

Objective: To assess the in-hospital mortality from acute stroke and its predictors in sub-Saharan Africa. Method: The literature search was conducted in the databases of PubMed/Medline, Embase, CINAHL, and Google Scholar. The retrieved studies were screened by titles and abstracts, and then full texts were assessed for eligibility. The methodological quality of the included studies was assessed using the Joanna Briggs Institute’s critical appraisal checklist. The publication bias was assessed using the funnel plot asymmetry and the Egger tests. Data were analyzed using Stata software version 15.0 in a random-effect model. Result: A total of 27 studies with a total sample size of 6331 were included in this systematic review and meta-analysis. The pooled estimated prevalence of in-hospital mortality due to stroke was 22% (95% confidence interval = 0.17–0.27). Stroke mortality in Western Africa (37%, 95% confidence interval = 0.24–0.50) was higher than in Eastern Africa (15%, 95% confidence interval = 0.12–0.19) and Southern Africa (18%, 95% confidence interval = 0.06–0.19). In three studies, mortality was higher in hemorrhagic stroke (25%) than ischemic stroke (14%). Risk factors associated with higher mortality were admission Glasgow Coma Scale, stroke severity, age, sex, presence of hypertension, and declined renal function. Conclusion: The in-patient mortality of stroke in sub-Saharan Africa was high. Therefore, there is an urgent need for further stroke epidemiology studies in stroke subtypes and the performance of patient-level meta-analysis to understand the risk factors associated with mortality and herald appropriate intervention to curb the high mortality rate in the region.
COPLA, a taxonomic classifier of plasmids
Authors: Redondo-Salvo Santiago , Bartomeus-Peñalver Roger , Vielva Luis , Tagg Kaitlin A. , Webb Hattie E. , Fernández-López Raúl , de la Cruz Fernando 
Published: July 2021

Abstract
Background
Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust method for plasmid classification is necessary to better understand the genetics and epidemiology of many pathogens. Until now, plasmid classification systems focused on specific traits, which limited their precision and universality. The definition of plasmid taxonomic units (PTUs), based on average nucleotide identity metrics, allows the generation of a universal plasmid classification scheme, applicable to all bacterial taxa. Here we present COPLA, a software able to assign plasmids to known and novel PTUs, based on their genomic sequence.

Results
We implemented an automated pipeline able to assign a given plasmid DNA sequence to its cognate PTU, and assessed its performance using a sample of 1000 unclassified plasmids. Overall, 41% of the samples could be assigned to a previously defined PTU, a number that reached 63% in well-known taxa such as the Enterobacterales order. The remaining plasmids represent novel PTUs, indicating that a large fraction of plasmid backbones is still uncharacterized.

Conclusions
COPLA is a bioinformatic tool for universal, species-independent, plasmid classification. Offered both as an automatable pipeline and an open web service, COPLA will help bacterial geneticists and clinical microbiologists to quickly classify plasmids.
InvertypeR: Bayesian inversion genotyping with Strand-seq data
Authors: Hanlon Vincent C. T. , Mattsson Carl-Adam , Spierings Diana C. J. , Guryev Victor , Lansdorp Peter M. 
Published: July 2021

Abstract
Background
Single cell Strand-seq is a unique tool for the discovery and phasing of genomic inversions. Conventional methods to discover inversions with Strand-seq data are blind to known inversion locations, limiting their statistical power for the detection of inversions smaller than 10 Kb. Moreover, the methods rely on manual inspection to separate false and true positives.

Results
Here we describe “InvertypeR”, a method based on a Bayesian binomial model that genotypes inversions using fixed genomic coordinates. We validated InvertypeR by re-genotyping inversions reported for three trios by the Human Genome Structural Variation Consortium. Although 6.3% of the family inversion genotypes in the original study showed Mendelian discordance, this was reduced to 0.5% using InvertypeR. By applying InvertypeR to published inversion coordinates and predicted inversion hotspots (n = 3701), as well as coordinates from conventional inversion discovery, we furthermore genotyped 66 inversions not previously reported for the three trios.

Conclusions
InvertypeR discovers, genotypes, and phases inversions without relying on manual inspection. For greater accessibility, results are presented as phased chromosome ideograms with inversions linked to Strand-seq data in the genome browser. InvertypeR increases the power of Strand-seq for studies on the role of inversions in phenotypic variation, genome instability, and human disease.
The Framingham risk score is associated with incident frailty, or is it?
Authors: Shi Hui , Ge Mei-Ling , Dong Birong , Xue Qian-Li 
Published: July 2021

AbstractBackgroundsCardiovascular disease (CVD) risk factors are individually associated with frailty. This study examined whether Framingham CVD risk score (FRS) as an aggregate measure of CVD risk is associated with incident frailty among Chinese older adults.MethodsThis study used data from the China Health and Retirement Longitudinal Study. A sample of 3,618 participants aged 60 to 95 years and without CVD at baseline were followed for four years. FRS was calculated at baseline. Frailty status was defined as not-frail (0–2 criteria) or frail (3–5 criteria) based on the physical frailty phenotype consisting of five binary criteria (weakness, slowness, exhaustion, low activity level, and weight loss). After excluding subjects who were frail (n = 248) at baseline, discrete-time Cox regression was used to evaluate the relationship between FRS and incident frailty.ResultsDuring a median follow-up of 4.0 years, 323 (8 %) participants developed CVD and 318 (11 %) subjects had frailty onset. Higher FRS was associated with greater risk of incident frailty (HR: 1.03, 95 % CI: 1.00 to 1.06) after adjusting for education, marital status, obesity, comorbidity burden, and cognitive function. This association however was no longer significant (HR: 1.00, 95 % CI: 0.97 to 1.03) after additionally adjusting for age. These findings remained essentially unchanged after excluding subjects with depression (n = 590) at baseline or incident CVD (n = 323) during the 4-year follow-up.ConclusionsThe FRS was not independently associated with incident frailty after adjusting for chronological age. More research is needed to assess the clinical utility of the FRS in predicting adverse health outcomes other than CVD in older adults.
Risk of mother-to-child transmission of hepatitis B virus after fetal blood sampling: a report of six cases
Authors: Han Zhenyan , Zhang Yuan , Zhou Jin , Wang Qingqing , Huang Yonghua , Hou Hongying 
Published: July 2021

Abstract
Background
Hepatitis B virus (HBV) remains a major global public health problem worldwide; in endemic areas, mother-to-child transmission (MTCT) of HBV is the most common transmission route. Previous studies have shown that amniocentesis for prenatal diagnosis increases the risk of MTCT of HBV among highly viraemic mothers. However, no data is available on MTCT related fetal blood sampling (FBS) because of the paucity of cases or lack of attention. We present a case series of HBV-infected women who underwent FBS with or without antiviral therapy during pregnancy and discuss the risk of MTCT after FBS.

Case presentation
Six hepatitis B surface antigen (HBsAg)-positive pregnant women who underwent FBS for prenatal diagnosis were retrospectively reviewed. Their infants were followed up with HBV serology parameters until at least 12 months of age. Among 6 cases, two hepatitis B e-antigen (HBeAg)-positive mothers had high viral loads > 7.0 log10 IU/mL, and one of them received antiviral therapy at 26+ 3 gestational weeks and achieved an anticipated level of 4.52 log10 IU/mL before FBS, while the other one did not receive any antiviral treatment. The other 4 cases were HBeAg-negative with low viral loads. Only a child born to the HBeAg-positive mother, who had no antiviral therapy with a viral load of 7.48 log10 IU/mL before FBS, was found to have MTCT with HBsAg persistently positive from birth to 12 months of age. The other 5 children were both HBsAg-negative and HBsAb-positive at the end of follow-up.

Conclusions
FBS may increase the risk of MTCT of HBV in women with HBeAg-positive and high viral loads; therefore, FBS should be avoided in this high-risk population. Maternal HBV serologic testing and awareness of the potential risk of MTCT should be recommended before FBS. Antiviral therapy may be effective to decrease the risk of MTCT after FBS in highly viraemic women.
Neurological deterioration in a patient with HIV-associated cryptococcal meningitis initially improving on antifungal treatment: a case report of coincidental racemose neurocysticercosis
Authors: Kalata Newton , Ellis Jayne , Benjamin Laura , Kampondeni Samuel , Chiodini Peter , Harrison Thomas , Lalloo David G. , Heyderman Robert S. 
Published: July 2021

Abstract
Background
Managing HIV-associated cryptococcal meningitis (CM) can become challenging in the presence of concurrent unusual central nervous system infections.

Case presentation
A 58-year old HIV infected woman new ART starter, who was being treated effectively for cryptococcal meningitis, represented with worsening of neurological symptoms. Brain MRI revealed a multicystic lesion in the left temporal lobe. Anti-fungal treatment was escalated for a suspected cryptococcoma, but post-mortem CSF serological test confirmed racemose neurocysticercosis.

Conclusion
Patients with HIV-associated CM are highly immunocompromised and may have multiple pathologies simultaneously. In endemic countries, neurocysticercosis should be considered in the differential diagnosis where there is central nervous system deterioration despite effective therapy for CM.
SARS-CoV-2/DENV co-infection: a series of cases from the Federal District, Midwestern Brazil
Authors: Schulte Heidi Luise , Brito-Sousa José Diego , Lacerda Marcus Vinicius Guimarães , Naves Luciana Ansaneli , de Gois Eliana Teles , Fernandes Mariana Sirimarco , Lima Valéria Paes , Rassi Carlos Henrique Reis Esselin , de Siracusa Clara Correia , Sasaki Lizandra Moura Paravidine , Cerqueira Selma Regina Penha Silva , de Albuquerque Cleandro Pires , Reis Ana Paula Monteiro Gomides , Gomes Ciro Martins , Kurizky Patricia Shu , da Mota Licia Maria Henrique , Espindola Laila Salmen 
Published: July 2021

Abstract
Background
Since the novel coronavirus disease outbreak, over 179.7 million people have been infected by SARS-CoV-2 worldwide, including the population living in dengue-endemic regions, particularly Latin America and Southeast Asia, raising concern about the impact of possible co-infections.

Methods
Thirteen SARS-CoV-2/DENV co-infection cases reported in Midwestern Brazil between April and September of 2020 are described. Information was gathered from hospital medical records regarding the most relevant clinical and laboratory findings, diagnostic process, therapeutic interventions, together with clinician-assessed outcomes and follow-up.

Results
Of the 13 cases, seven patients presented Acute Undifferentiated Febrile Syndrome and six had pre-existing co-morbidities, such as diabetes, hypertension and hypopituitarism. Two patients were pregnant. The most common symptoms and clinical signs reported at first evaluation were myalgia, fever and dyspnea. In six cases, the initial diagnosis was dengue fever, which delayed the diagnosis of concomitant infections. The most frequently applied therapeutic interventions were antibiotics and analgesics. In total, four patients were hospitalized. None of them were transferred to the intensive care unit or died. Clinical improvement was verified in all patients after a maximum of 21 days.

Conclusions
The cases reported here highlight the challenges in differential diagnosis and the importance of considering concomitant infections, especially to improve clinical management and possible prevention measures. Failure to consider a SARS-CoV-2/DENV co-infection may impact both individual and community levels, especially in endemic areas.
Characterisation of tuberculosis mortality in informal settlements in Nairobi, Kenya: analysis of data between 2002 and 2016
Authors: Gichuki Judy , Mategula Donnie 
Published: July 2021

Abstract
Background
Tuberculosis (TB) remains one of the key public health problems in Africa. Due to multifaceted challenges, its burden is poorly described in informal settlements. We describe tuberculosis mortality in two informal settlements in Nairobi, Kenya.

Methods
This is a secondary analysis of 2002–2016 verbal autopsy data from informal settlements in the Nairobi Urban Health Demographic Surveillance System (NUHDSS). A descriptive analysis of deaths assigned as caused by TB was done. Pearson chi-square tests were used to determine differences between socio-demographic factors. Logistic regression was carried out to examine the risk of death from TB within the characteristics.

Results
There were 6218 deaths in the NUHDSS within the period of analysis, of which 930 (14.96%) were deaths from TB. The average number of TB deaths per year was 62(SD 23.9). There was a reduction in TB deaths from 21.2% in 2005 to 1.7% in 2016. Males had 1.39 higher odds of dying from TB than females (AOR 1.39; 95% CI 1.18–1.64; p-value < 0.001). Compared to those aged 30–39 years, the ≥50-year-olds had a 42% lower chance of dying from TB (AOR 0.57; 95% CI 0.47–0.73; p-value < 0.001). Those dying at home had 1.39 odds of dying from TB as compared to those who died in a health facility(AOR 1.93; 95% CI 1.17–1.64; p value< 0.001).

Conclusion
There was a reduction in TB deaths over the study period. Males had the highest risk of death. There is a need to strengthen TB surveillance and access to TB diagnosis and treatment within informal settlements to enhance early diagnosis and treatment.
Prognostic significance of occult lymph node metastases in breast cancer: a meta-analysis
Authors: Wang Guixin , Zhang Shuhao , Wang Meiling , Liu Lin , Liu Yaqian , Tang Lianjun , Bai He , Zhao Haidong 
Published: July 2021

Abstract
Background
Occult metastases in axillary lymph nodes have been reported to be associated with poor prognosis in patients with breast cancer. However, studies on the prognostic value of occult metastases have shown controversial results. This meta-analysis aimed to evaluate the prognostic significance of occult lymph node metastases in breast cancer.

Methods
Studies published until May, 2020, which retrospectively examined negative lymph nodes by stepsectioning and/or immunohistochemistry, were retrieved from MEDLINE, EMBASE, CNKI, and Cochrane Library databases. The pooled Relative Risk (RR) with 95% confidence interval (95% CI) for overall survival (OS) and disease-free survival (DFS) were calculated to examine the associations between occult metastases and prognosis.

Results
Patients with occult metastases in axillary lymph nodes had poorer five-year DFS (RR = 0.930; 95% CI = 0.907–0.954) and OS (RR = 0.972; 95% CI = 0.954–0.990). Furthermore, the DFS (RR = 0.887; 95% CI = 0.810–0.972) and OS (RR = 0.896; 95% CI = 0.856–0.939) of patients with occult metastases were significantly lower after a ten-year follow-up.

Conclusions
Occult metastases in the axillary lymph nodes are associated with poorer DFS andOS of patients with breast cancer. Occult metastases might serve as a predictive factor of survival outcomes in patients with breast cancer.
Comparison of the optical quality after SMILE and FS-LASIK for high myopia by OQAS and iTrace analyzer: a one-year retrospective study
Authors: Yin Yewei , Lu Ying , Xiang Aiqun , Fu Yanyan , Zhao Yang , Li Yuanjun , Hu Tu , Du Kaixuan , Hu Shengfa , Fu Qiuman , Wu Xiaoying , Wen Dan 
Published: August 2021

Abstract
Background
To compare the correction effect and optical quality after small-incision lenticule extraction (SMILE) and femtosecond laser assisted laser in situ keratomileusis (FS-LASIK) for high myopia.

Methods
51 high myopia eyes after SMILE and 49 high myopia eyes after FS-LASIK were enrolled and divided into two groups retrospectively. The OQAS and iTrace analyzer were used for optical quality inspection. Between the two groups the spherical equivalent (SE), astigmatism, uncorrected distant visual acuity (UDVA), strehl ratio (SR), modulation transfer function cutoff frequency (MTF cutoff), objective scatter index (OSI) and wavefront aberrations were analyzed and compared before surgery and at 1, 6 and 12 months after surgery.

Results
After the operation: (1) SE and astigmatism declined and UDVA increased significantly in both groups, and UDVA was better after SMILE than FS-LASIK. (2) SR and MTF cutoff reduced and OSI increased significantly after SMILE and FS-LASIK. SR and MTF cutoff were significantly higher after SMILE than FS-LASIK. OSI was significantly lower after SMILE than FS-LASIK. (3) The total wavefront aberration, total low-order wavefront aberration, defocus and astigmatism aberration as well as trefoil aberration reduced significantly in both groups. The total high-order wavefront aberration increased significantly after FS-LASIK. The spherical and coma aberration increased significantly in both groups. The total high-order wavefront aberration and coma aberration at 1 month were higher after FS-LASIK than SMILE.

Conclusion
The optical quality descended after SMILE and FS-LASIK. SMILE was superior to FS-LASIK at the correction effect and optical quality for high myopia. The combination of OQAS and iTrace analyzer is a valuable complementary measurement in evaluating the optical quality after the refractive surgery.

Trial registration
This is a retrospective study. This research was approved by the ethics committee of Xiangya Hospital and the IRB approval number is 201612074.
Emodin inhibits viability, proliferation and promotes apoptosis of hypoxic human pulmonary artery smooth muscle cells via targeting miR-244-5p/DEGS1 axis
Authors: Yi Li , Liu JunFang , Deng Ming , Zuo Huihua , Li Mingyan 
Published: July 2021

Abstract
Objective
This study aimed to determine the effects of emodin on the viability, proliferation and apoptosis of human pulmonary artery smooth muscle cells (PASMCs) under hypoxia and to explore the underling molecular mechanisms.

Methods
PASMCs were cultured in a hypoxic environment (1% oxygen) and then treated with emodin. Cell viability, proliferation and apoptosis were evaluated using CCK-8 assay, EdU staining assay, western blot and Mito-tracker red CMXRos and Annexin V-FITC apoptosis detection assay. The microRNA (miRNA)/mRNA and protein expression levels were assessed by quantitative real-time PCR and western blotting, respectively. Based on transcriptomics and proteomics were used to identify potential signaling pathways. Luciferase reporter assay was utilized to examine the interaction between miR-244-5p and DEGS1.

Results
Emodin at 40 and 160 µM concentration-dependently suppressed cell viability, proliferation and migration, but enhanced cell apoptosis of PASMCs under hypoxia. Transcriptomic and proteomic analysis revealed that emodin could attenuate the activity of PI3K/Akt signaling in PASMCs under hypoxia. In addition, delta 4-desaturase, sphingolipid 1 (DEGS1) was found to be a direct target of miR-244-5p. Emodin could significantly up-regulated miR-244-5p expression and down-regulated DEGS1 expression in PASMCs under hypoxia. Furthermore, emodin-mediated effects on cell viability, migration, apoptosis and PI3K/Akt signaling activity of PASMCs under hypoxia were significantly attenuated by miR-244-5p knockdown.

Conclusions
Our results indicated that emodin suppressed cell viability, proliferation and migration, promoted cell apoptosis of PASMCs under hypoxia via modulating miR-244-5p-mediated DEGS1/PI3K/Akt signaling pathway. MiR-244-5p/DEGS1 axis was initially investigated in this current study, which is expected to further the understanding of the etiology of pulmonary arterial hypertension.
Time to first birth and its determinants among married female youths in Ethiopia, 2020: survival analysis based on EDHS 2016
Authors: Bitew Desalegn Anmut , Habitu Yohannes Ayanaw , Gelagay Abebaw Addis 
Published: August 2021

AbstractIntroductionThe first birth is the most significant events in a woman's life that indicates the beginning of undertaking the intensive responsibilities of motherhood and childcare. Age at first birth has health, economic and social consequences and implications. But little has been known on the time to first birth and its determinants in Ethiopia. Therefore, this research is planned to address this issue.Objectives of the studyTo assess the time to first birth and its determinants among married female youths in Ethiopia, 2020.MethodsThe data was accessed freely through (https://www.dhsprogram.com). Survival analysis of time to first birth was done based on EDHS 2016 data among 2597 weighted study subjects. The data was extracted using STATA version 14.0. Kaplan Meier’s survival and Log rank test were used to compare survival experiences of respondents using categorical variables. Proportional hazard assumption was checked and was not violated. Cox proportional hazard model was applied, hazard ratio with 95% CI was computed and variables withpvalue < 0.05 in the multivariable analysis were taken as significant determinants.ResultsOverall median survival time was 18 years (IQR = 17–20). The significant determinants of time to first birth are place of residence (being rural (AHR = 1.49, 95% CI 1.13, 1.97),Religion (being Muslim [AHR = 1.57, 95% CI 1.22, 2.02),being protestant (AHR = 1.73, 95% CI 1.34, 2.24)], age at first sex [first sex < 15 years (AHR = 1.68, 95% CI 1.23, 2.29)] and first sex between 15 and 17 years (AHR = 1.54, 95% CI 1.29, 1.85), age at first marriage (marriage < 15 years (AHR = 6.52, 95% CI 4.91, 8.64), marriage between 15 and 17 (AHR = 2.63, 95% CI 2.20, 3.14), unmet need for family planning (AHR = 1.23, 95% CI 1.00, 1.52)ConclusionIn this study, the median age at first birth was 18 years. This show, about 50% of study participants give birth for the first time before their 18th birth day. This age is the ideal age for schooling and to do other personal development activities. Therefore giving birth before 18 year will limit female youths from attending school and performing personal development activities in addition to health and demographic consequences of early child bearing.