bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population structure of drug-resistant Mycobacterium tuberculosis in Central Asia
Authors: Engström Anna , Antonenka Uladzimir , Kadyrov Abdylat , Kalmambetova Gulmira , Kranzer Katharina , Merker Matthias , Kabirov Olim , Parpieva Nargiza , Rajabov Asliddin , Sahalchyk Evgeni , Sayfudtinov Zayniddin , Niemann Stefan , Hoffmann Harald 
Published: October 2019

Abstract

Background
Drug-resistant tuberculosis (TB) is a major public health concern threathing the success of TB control efforts, and this is particularily problematic in Central Asia. Here, we present the first analysis of the population structure of Mycobacterium tuberculosis complex isolates in the Central Asian republics Uzbekistan, Tajikistan, and Kyrgyzstan.

Methods
The study set consisted of 607 isolates with 235 from Uzbekistan, 206 from Tajikistan, and 166 from Kyrgyzstan. 24-loci MIRU-VNTR (Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeats) typing and spoligotyping were combined for genotyping. In addition, phenotypic drug suceptibility was performed.

Results
The population structure mainly comprises strains of the Beijing lineage (411/607). 349 of the 411 Beijing isolates formed clusters, compared to only 33 of the 196 isolates from other clades. Beijing 94–32 (n = 145) and 100–32 (n = 70) formed the largest clusters. Beijing isolates were more frequently multidrug-resistant, pre-extensively resistant (pre-XDR)- or XDR-TB than other genotypes.

Conclusions
Beijing clusters 94–32 and 100–32 are the dominant MTB genotypes in Central Asia. The relative size of 100–32 compared to previous studies in Kazakhstan and its unequal geographic distribution support the hypothesis of its more recent emergence in Central Asia. The data also demonstrate that clonal spread of resistant TB strains, particularly of the Beijing lineage, is a root of the so far uncontroled MDR-TB epidemic in Central Asia.
An updated systematic review and meta-analysis of the prevalence of hepatitis B virus in Ethiopia
Authors: Yazie Teshiwal Deress , Tebeje Mekonnen Girma 
Published: October 2019

Abstract

Background
Hepatitis B virus is one of the major public health concerns globally. It is highly infectious and can be transmitted from person to person through vertically or horizontally via contaminated body fluids. Despite the provision of an effective vaccine, it remains a major problem worldwide, particularly among the developing countries.

Methods
Online electronic databases including PubMed, Google Scholar, Science Direct, African Index Medicus, African Journals Online, and WHO Afro Library were searched and published articles from 2010 to June 8, 2019, were considered. Both authors independently screened articles and extracted the data. Funnel-Plots and Egger’s test statistics were used to determine the presence of small-study effects and publication bias. The pooled prevalence of HBV was analyzed using the random-effects model. The possible sources of heterogeneity was analyzed through subgroup analysis, sensitivity analysis, and meta-regression.

Results
The overall pooled prevalence of HBV was 6% and among subgroups, pregnant women, healthcare workers, and HIV positive patients accounted for 5% for each group. Relatively low prevalence (4%) was obtained among blood donors. The Egger’s test statistics (p = 0.747) indicated the absence of publication bias. In addition, from the sensitivity analysis, there was no influence on the overall effect estimate while removing a single study at a time. The level of heterogeneity was reduced among pregnant women, HIV positive and studies with unknown sampling techniques. After conducting meta-regression, province, study group, screening method, and quality of papers were identified as sources of heterogeneity.

Conclusions
The overall pooled prevalence of HBV in Ethiopia was high. Strengthening and scaling up of the scope of the existing vaccination program and implementing novel approaches including screen-and-treat could be implemented to reduce the burden of the disease. Generally, the study can provide current prevalence estimate of HBV that could vital for intervention to tackle the disease.
Early and late mortality after malaria in young children in Papua, Indonesia
Authors: Patriani Dewi , Arguni Eggi , Kenangalem Enny , Dini Saber , Sugiarto Paulus , Hasanuddin Afdhal , Lampah Daniel Adrian , Douglas Nicholas M. , Anstey Nicholas M. , Simpson Julie Anne , Price Ric N. , Poespoprodjo Jeanne Rini 
Published: October 2019

Abstract

Background
In southern Papua, Indonesia, malaria is highly prevalent in young children and is a significant cause of morbidity and early mortality. The association between malaria and delayed mortality is unknown.

Methods
Routinely-collected hospital surveillance data from southern Papua, Indonesia, were used to assess the risk of recurrent malaria and mortality within 12 months of an initial presentation with malaria in all children younger than 5 years old attending the local hospital. Analysis was primarily by Kaplan Meier and Cox regression methods.

Results
In total 15,716 children presenting with malaria between April 2004 and December 2013 were included in the analysis; 6184 (39.3%) with Plasmodium falciparum, 7499 (47.7%) with P. vivax, 203 (1.3%) with P. malariae, 3 with P. ovale and 1827 (11.6%) with mixed infections. Within 1 year, 48.4% (7620/15,716) of children represented a total of 16,957 times with malaria (range 1 to 11 episodes), with the incidence of malaria being greater in patients initially presenting with P. vivax infection (1334 [95%CI 1307–1361] per 1000 patient years) compared to those with P. falciparum infection (920 [896–944]). In total 266 (1.7%) children died within 1 year of their initial presentation, 129 (48.5%) within 30 days and 137 (51.5%) between 31 and 365 days. There was no significant difference in the mortality risk in patients infected with P. vivax versus P. falciparum either before 30 days (Hazard Ratio (HR) 1.02 [0.69,1.49]) or between 31 and 365 days (HR = 1.30 [0.90,1.88]). Children who died had a greater incidence of malaria, 2280 [95%CI 1946–2671] per 1000 patient years preceding their death, compared to 1141 [95%CI 1124–1158] per 1000 patient years in those surviving.

Conclusions
Children under-5 years old with P. vivax malaria, are at significant risk of multiple representations with malaria and of dying within 1 year of their initial presentation. Preventing recurrent malaria must be a public health priority in this vulnerable population.
Interpreting HIV diagnostic histories into infection time estimates: analytical framework and online tool
Authors:   on behalf of the Consortium for the Evaluation and Performance of HIV Incidence Assays (CEPHIA), Grebe Eduard , Facente Shelley N. , Bingham Jeremy , Pilcher Christopher D. , Powrie Andrew , Gerber Jarryd , Priede Gareth , Chibawara Trust , Busch Michael P. , Murphy Gary , Kassanjee Reshma , Welte Alex 
Published: October 2019

Abstract

Background
It is frequently of epidemiological and/or clinical interest to estimate the date of HIV infection or time-since-infection of individuals. Yet, for over 15 years, the only widely-referenced infection dating algorithm that utilises diagnostic testing data to estimate time-since-infection has been the ‘Fiebig staging’ system. This defines a number of stages of early HIV infection through various standard combinations of contemporaneous discordant diagnostic results using tests of different sensitivity. To develop a new, more nuanced infection dating algorithm, we generalised the Fiebig approach to accommodate positive and negative diagnostic results generated on the same or different dates, and arbitrary current or future tests – as long as the test sensitivity is known. For this purpose, test sensitivity is the probability of a positive result as a function of time since infection.

Methods
The present work outlines the analytical framework for infection date estimation using subject-level diagnostic testing histories, and data on test sensitivity. We introduce a publicly-available online HIV infection dating tool that implements this estimation method, bringing together 1) curatorship of HIV test performance data, and 2) infection date estimation functionality, to calculate plausible intervals within which infection likely became detectable for each individual. The midpoints of these intervals are interpreted as infection time ‘point estimates’ and referred to as Estimated Dates of Detectable Infection (EDDIs). The tool is designed for easy bulk processing of information (as may be appropriate for research studies) but can also be used for individual patients (such as in clinical practice).

Results
In many settings, including most research studies, detailed diagnostic testing data are routinely recorded, and can provide reasonably precise estimates of the timing of HIV infection. We present a simple logic to the interpretation of diagnostic testing histories into infection time estimates, either as a point estimate (EDDI) or an interval (earliest plausible to latest plausible dates of detectable infection), along with a publicly-accessible online tool that supports wide application of this logic.

Conclusions
This tool, available at https://tools.incidence-estimation.org/idt/, is readily updatable as test technology evolves, given the simple architecture of the system and its nature as an open source project.
A foodborne outbreak of gastroenteritis caused by Norovirus and Bacillus cereus at a university in the Shunyi District of Beijing, China 2018: a retrospective cohort study
Authors: Chen Dongwan , Li Yongjin , Lv Jinchang , Liu Xiufeng , Gao Peng , Zhen Guoxin , Zhang Wenzeng , Wu Dan , Jing Hongbo , Li Ying , Zhao Yao , Ma Xiaochen , Ma Huilai , Zhang Lijie 
Published: October 2019

Abstract

Background
On September 4, 2018, a boarding school in the Shunyi District of Beijing, China reported an outbreak of acute gastroenteritis. At least 209 suspected students caused of diarrhea and vomiting. The case was investigated, and control measures were taken to prevent further spread.

Methods
A retrospective cohort study was conducted among the school students and staff in order to test hypothesis that high risk of food served at the school canteen. We collected information on demographics, refectory records, person to person transmission by uniform epidemiological questionnaire. Risk ratios (RR) and 95% confidence intervals (CI) were calculated. Stool specimens of cases and canteen employees, retained food, water, and environmental swabs were investigated by laboratory analysis.

Results
We identified 209 cases (including 28 laboratory-confirmed cases) which occurred from August 29 to September 10. All cases were students, and the average age was 20, 52% were male. The outbreak lasted for 13 days, and peaked on September 5. Consumption of Drinks stall and Rice flour stall on September 1 (RR:3.4, 95%CI:1.5–7.8, and RR:7.6, 95%CI:2.8–20.2), Rice flour stall and Fish meal stall on September 2 (RR:4.0, 95%CI:1.2–13.6, and RR:4.6, 95%CI:1.7–12.5), muslim meal stall on September 4 (RR:2.7, 95%CI:1.3–5.4), Barbeque stall on September 5 (RR:3.0, 95%CI:1.2–7.0) were independently associated with increased risk of disease within the following 2 days. Among 35 specimens of rectal swabs or feces from students, 28 specimens were positive. Norovirus GI.6 alone was detected in 23 specimens, Bacillus cereus alone in 3 specimens and both norovirus GI.6 and Bacillus cereus in 2 specimens. Ten specimens of rectal swabs from canteen employees were positive for norovirus GI, and 2 specimens were positive for Bacillus cereus. Four retained food specimens were positive for Bacillus cereus, and environmental samples were negative for any viruses or bacteria.

Conclusion
Our investigation indicated that canteen employees were infected by two pathogens (norovirus and Bacillus cereus) and transmission may have been possible due to unhygienic practices. Student consumption of food or drink at high-risk stalls was determined as the probable cause of the outbreak.
Prenatal maternal stress and birth outcomes in rural Ghana: sex-specific associations
Authors: Ae-Ngibise Kenneth Ayuurebobi , Wylie Blair J. , Boamah-Kaali Ellen , Jack Darby W. , Oppong Felix Boakye , Chillrud Steven N. , Gyaase Stephaney , Kaali Seyram , Agyei Oscar , Kinney Patrick L. , Mujtaba Mohammed , Wright Rosalind J. , Asante Kwaku Poku , Lee Alison G. 
Published: October 2019

Abstract

Background
In developed countries, prenatal maternal stress has been associated with poor fetal growth, however this has not been evaluated in rural sub-Saharan Africa. We evaluated the effect of prenatal maternal stress on fetal growth and birth outcomes in rural Ghana.

Methods
Leveraging a prospective, rural Ghanaian birth cohort, we ascertained prenatal maternal negative life events, categorized scores as 0-2 (low stress; referent), 3-5 (moderate), and > 5 (high) among 353 pregnant women in the Kintampo North Municipality and Kintampo South District located within the middle belt of Ghana. We employed linear regression to determine associations between prenatal maternal stress and infant birth weight, head circumference, and length. We additionally examined associations between prenatal maternal stress and adverse birth outcome, including low birth weight, small for gestational age, or stillbirth. Effect modification by infant sex was examined.

Results
In all children, high prenatal maternal stress was associated with reduced birth length (β = − 0.91, p = 0.04; p-value for trend = 0.04). Among girls, moderate and high prenatal maternal stress was associated with reduced birth weight (β = − 0.16, p = 0.02; β = − 0.18, p = 0.04 respectively; p-value for trend = 0.04) and head circumference (β = − 0.66, p = 0.05; β = − 1.02, p = 0.01 respectively; p-value for trend = 0.01). In girls, high prenatal stress increased odds of any adverse birth outcome (OR 2.41, 95% CI 1.01-5.75; p for interaction = 0.04). Sex-specific analyses did not demonstrate significant effects in boys.

Conclusions
All infants, but especially girls, were vulnerable to effects of prenatal maternal stress on birth outcomes. Understanding risk factors for impaired fetal growth may help develop preventative public health strategies.

Trial registration
NCT01335490 (prospective registration).
Date of Registration: April 14, 2011.
Status of Registration: Completed.
Serum gamma-glutamyltransferase and the overall survival of metastatic pancreatic cancer
Authors: Xiao Yuanyuan , Yang Haijun , Lu Jian , Li Dehui , Xu Chuanzhi , Risch Harvey A. 
Published: October 2019

Abstract

Background
Accumulating evidence suggests that Gamma-glutamyltransferase (GGT) may be involved in cancer occurrence and progression. However, the prognostic role of serum GGT in pancreatic cancer (PC) survival lacks adequate evaluation. In this study, we aimed to analyze the association between serum GGT measured at diagnosis and overall survival (OS) in patients with metastatic PC.

Methods
We identified 320 patients with histopathologically confirmed metastatic pancreatic ductal adenocarcinoma (PDAC) diagnosed during 2015 and 2016 at a specialized cancer hospital in southwestern China. Univariate and multivariate Cox proportional-hazards models were used to determine associations between serum GGT and OS in metastatic PDAC.

Results
Controlled for possible confounding factors, serum GGT was significantly associated with OS: serum GGT > 48 U/L yielded a hazard ratio of 1.53 (95% CI: 1.19–1.97) for mortality risk. A significant dose-response association between serum GGT and OS was also observed. Subgroup analysis showed a possible interaction between GGT and blood glucose level.

Conclusion
Serum GGT could be a potential indicator of survival in metastatic PDAC patients. Underlying mechanisms for this association should be investigated.
Exploring new potential role of DDB2 by host cell reactivation assay in human tumorigenic cells
Authors: Bassi Elisabetta , Perucca Paola , Guardamagna Isabella , Prosperi Ennio , Stivala Lucia A. , Cazzalini Ornella 
Published: October 2019

AbstractBackgroundThe Host Cell Reactivation assay (HCR) allows studying the DNA repair capability in different types of human cells. This assay was carried out to assess the ability in removing UV-lesions from DNA, thus verifying NER efficiency. Previously we have shown that DDB2, a protein involved in the Global Genome Repair, interacts directly with PCNA and, in human cells, the loss of this interaction affects DNA repair machinery. In addition, a mutant form unable to interact with PCNA (DDB2PCNA-), has shown a reduced ability to interact with a UV-damaged DNA plasmid in vitro.MethodsIn this work, we have investigated whether DDB2 protein may influence the repair of a UV-damaged DNA plasmid into the cellular environment by applying the HCR method. To this end, human kidney 293 stable clones, expressing DDB2Wtor DDB2PCNA-, were co-transfected with pmRFP-N2 and UV-irradiated pEGFP-reported plasmids. Moreover, the co-localization between DDB2 proteins and different NER factors recruited at DNA damaged sites was analysed by immunofluorescence and confocal microscopy.ResultsThe results have shown that DDB2Wtrecognize and repair the UV-induced lesions in plasmidic DNA transfected in the cells, whereas a delay in these processes were observed in the presence of DDB2PCNA-, as also confirmed by the different extent of co-localization of DDB2Wtand some NER proteins (such as XPG), vs the DDB2 mutant form.ConclusionThe HCR confirms itself as a very helpful approach to assess in the cellular context the effect of expressing mutant vs Wt NER proteins on the DNA damage response. Loss of interaction of DDB2 and PCNA affects negatively DNA repair efficiency.
Expression and clinical significance of PD-L1 and BRAF expression in nasopharyngeal carcinoma
Authors: Cao Yabing , Chan Kin Iong , Xiao Gungli , Chen Yanqun , Qiu Xibin , Hao Hu , Mak Sao Chi , Lin Tongyu 
Published: October 2019

Abstract

Background
The prognostic value of programmed death-ligand 1 (PD-L1) and BRAF expression in nasopharyngeal carcinoma (NPC) is not well-defined. In this study we investigated alterations in PD-L1, BRAF and EGFR by using immunohistochemistry analysis in a cohort of consecutively enrolled NPC patients.

Methods
A retrospective review of 154 NPC patients form our previous study (BMC Cancer. 2013; 13:226) were conducted. Survival and prognostic impacts were analyzed based on PD-L1, BRAF and EGFR expression levels.

Results
One hundred fifty four patients were included in this study. PD-L1 expression was detected in 87.7% of patients; 14.3% had 1–5% PD-L1 expression, 47.4% had 5–49% expression while 26% had ≥50% expression Higher PD-L1 expression was significantly associated with shorter PFS and OS. The median PFS was 25 months (95% CI 15.7–34.3 months) and OS was 35 months (95% CI 22.60–47.4 months) for patients with PD-L1 expression ≥50%; both median PFS and OS were not yet reached for patients with PD-L1 expression < 50%. PFS was significantly higher in BRAF mutation positive patients (5-year PFS: 55.1% vs. 30.8%, P = 0.044).

Conclusion
Tumor PD-L1 expression and BRAF mutation are associated with poor outcomes in patients with NPC. This study was retrospectively registered in ClinicalTrials.gov (NCT03989297) on 2019-6-18.
A descriptive study to explore working conditions and childcare practices among informal women workers in KwaZulu-Natal, South Africa: identifying opportunities to support childcare for mothers in informal work
Authors: Horwood Christiane , Haskins Lyn , Alfers Laura , Masango-Muzindutsi Zandile , Dobson Richard , Rollins Nigel 
Published: October 2019

Abstract

Background
Although women working in the informal economy are a large and vulnerable group, little is known about infant feeding and childcare practices among these women. The aim of this study was to explore childcare practices among mothers in informal work.

Methods
A cross-sectional survey among mothers with children aged < 2 years working in the informal economy in an urban and a rural site in KwaZulu-Natal, South Africa. Participants were selected using purposive and snowball sampling.

Results
A total of 247 interviews were conducted with 170 informal traders and 77 domestic workers. Most mothers lived with their child (225/247, 91.1%), had initiated breastfeeding (208/247; 84.2%) and many were still breastfeeding (112/247; 45.3%). Among 96 mothers who had stopped breastfeeding, the most common reason was returning to work (34/96; 35.4%). Many mothers relied on family members, particularly grandmothers, to care for their child while they were working (103/247, 41.7%) but some mothers took their child with them to work (70/247; 28.1%). Few fathers participated in the care of their child: 54 mothers (21.9%) reported that the father had ever looked after the child while she was away from home. Domestic workers were less likely than informal traders to take their child to work (p = 0.038).
Women reported receiving a salary from an informal employer (119), or being own-account workers (120) or being unpaid/paid in kind (8). Most participants were in stable work (> 4 years) with regular working hours, but received very low pay. Domestic workers were more likely than informal traders to have regular working hours (p = 0.004), and to be earning >$240 per month (p = 0.003). Mothers reported high levels of food insecurity for themselves and their child: 153 mothers (61.9%) reported having missed a meal in the past month due to lack of resources to buy food, and 88 (35.6%) mothers reported that their child had missed a meal for this reason.

Conclusion
This study provides a preliminary description of informal women workers who, despite having stable work, are vulnerable, low paid and food insecure. These women may require support to provide optimal childcare and nutrition for their children.