bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viable Mycobacterium tuberculosis in sputum after pulmonary tuberculosis cure
Authors: Ambreen Atiqa , Jamil Muhammad , Rahman Muhammad Aqeelur , Mustafa Tehmina 
Published: July 2019

Abstract
Background

Pulmonary tuberculosis (TB) with detectable Mycobacterium tuberculosis in the sputum is a major source of transmission. In resource limited TB endemic settings, cure is declared by sputum smear examination for acid fast bacilli without performing culture. This may lead to erroneous treatment outcomes as viable bacteria may be missed by low sensitivity of direct smear method of acid fast staining. The aim of this study was to investigate if sterilizing cure is achieved among the new pulmonary TB cases declared cured by sputum smear conversion and the impact of addition of ethambutol in the continuation phase in achieving sterilizing cure.

Methods

New sputum smear positive pulmonary TB patients registered at a tertiary care hospital in Pakistan were followed under standard Directly Observed Treatment Short Course strategy for six months. Half of these patients received ethambutol in addition to isoniazid and rifampicin in continuation phase. Sputum specimens were examined on microscopy at 2 months and end of treatment. Sputa of patients with negative direct smear examination at the end of treatment were cultured on solid medium.

Results

Total of 533 newly diagnosed sputum smear positive pulmonary TB patients were registered from November 2013 to March 2014. Among these 504 converted sputum negative at 2 months and 348 converted at the end of six months of treatment and declared cured. Sputa of 204/348 patients were cultured, and 12/204 (6%) were culture positive. Culture positivity at 6 month was not associated with bacterial load, smoking, diabetes, presence of cavities, history of contact with TB, age, gender, socioeconomic status, or addition of ethambutol in the continuation phase of treatment.

Conclusion

Six month treatment does not provide sterilizing cure in all pulmonary TB leading to risk for relapse. Direct smear examination is not enough to declare cure in TB patients. Addition of ethambutol in the continuation phase did not result in better sterilizing cure. These findings emphasize the importance of performing culture and follow-up of patients to monitor relapse in routine TB care. More studies are needed to find the optimal duration of treatment for individual or carefully selected groups of patients.
Prevalence and Antifungal Susceptibility of Candida albicans Causing Vulvovaginitis Among Pregnant Women in Lebanon
Authors: Ghaddar Nahed , Anastasiadis Elie , Halimeh Rawad , Ghaddar Ali , Dhar Rita , AlFouzan Wadha , Yusef Hoda , Chaar Mira El 
Published: July 2019

Abstract
Background: Vaginal candidiasis is frequently prevalent in pregnant women and is associated with sepsis and adverse neonatal outcomes. This study determined the presence of Candida species in symptomatic pregnant women and evaluated the antifungal susceptibility profile of the isolated strains. It also aimed to explore whether Candida species predicts gestational complications and adverse neonatal outcomes.
Methods: A total of 258 pregnant women at 35 to 37 week of gestation participated in this study. Vaginal swabs from these patients were collected at various obstetrics and gynecology clinics in Lebanon for a period of 12 months. Candida isolates were identified at species level and antifungal susceptibility of Candida albicans to fluconazole (FCZ), amphotericin B (AMB), itraconazole (ICZ) and voriconazole (VCZ) was determined by the agar-based E-test method.
Results: Among 258 women tested, 100 (39%) were positive for Candida species. C. albicans, C. glabrata and C. krusei were isolated from 42%, 41% and 17% of the women, respectively. C. albicans had significant positive associations with gestational diabetes while C. kreusi or C. glabrata had significant positive associations with gestational complications and vaginal discharge. The antifungal susceptibility tests of C. albicans isolates revealed 97.5%, 90%, 87.5% and 97.5% susceptibility to AMB, FCZ, ICZ and VCZ, respectively. .
Conclusion: The current study revealed high incidence of both C. albicans and non-C. albicans strains causing vulvovaginitis among pregnant women in Beirut, Lebanon. Whereas the susceptibility rates of C. albicans against AMB and VCZ were high, FCZ and ICZ proved comparatively less efficacious. The resistance profile of circulating C. albicans among pregnant women can predict the best outcome of appropriate prophylaxis or treatment of neonatal candidiasis. Vaginal candida colonization might lead to adverse neonatal outcome or gestational complications thus Candida screening as antennal follow up is advised.
Finding new QTL for yield traits based on a high-density genetic map in the super hybrid rice Nei2You No.6
Authors: Zhang Miao , Zhou Zhengping , Chen Yuyu , Cao Yongrun , Deng Chenwei , Xue Pao , Anis Galal Bakr , Zhan Xiaodeng , Cao Liyong , Cheng Shihua , Zhang Yingxin 
Published: July 2019

Abstract
Background
Rice is one of the most important food crops in the world. To determine the genetic basis of yield components in super rice Nei2You No.6, 387 recombinant inbred sister lines (RISLs) were obtained for mapping quantitative trait loci (QTL) responsible for yield-associated traits, such as 1000-grain weight (TGW), grain number per plant (GNP), number of panicles per plant (NP), and grain yield per plant (GYP).
Results
Using whole genome re-sequencing, a high-density linkage map consisting of 3203 bin markers was constructed with total genetic coverage of 1951.1 cM and an average density of 0.61 cM. As a result of the multi-environment test, 43 yield-related QTL were mapped to all 12 chromosomes, among which 28 inherited from Nei2B showed a positive effect on yield traits. Nine QTL, qTGW-1a, qTGW-5, qTGW-7, qTGW-10b, qTGW-10c, qTGW-12, qNP-7, qGNP-6c, and qGYP-6b, showed stable effects across multiple environments. Five of the nine QTL were co-located with previously reported QTL, and four novel loci, qTGW-7, qTGW-12, qGNP-6c, and qNP-7, were identified in the present study. Subsequently, qNP-7, qTGW-12, and qTGW-7 were validated using corresponding paired lines which differed only in the target region.
Conclusions
the RISL population is an effective tool for mapping and validating QTL of complex traits, for instance, yield-associated traits, and newly detected QTL provide new genetic resources for research of yield components and molecular breeding in rice.
Functional categorization of de novo transcriptome assembly of Vanilla planifolia Jacks. potentially points to a translational regulation during early stages of infection by Fusarium oxysporum f. sp. vanillae
Authors: Cruz Marco Tulio Solano-De la , Adame-García Jacel , Gregorio-Jorge Josefat , Jiménez-Jacinto Verónica , Vega-Alvarado Leticia , Iglesias-Andreu Lourdes Georgina , Escobar-Hernández Esteban Elías , Luna-Rodríguez Mauricio 
Published: July 2019

Abstract
Background
Upon exposure to unfavorable environmental conditions, plants need to respond quickly to maintain their homeostasis. For instance, physiological, biochemical and transcriptional changes occur during plant-pathogen interaction. In the case of Vanilla planifolia Jacks., a worldwide economically important crop, it is susceptible to Fusarium oxysporum f. sp. vanillae (Fov). This pathogen causes root and stem rot (RSR) in vanilla plants that lead to plant death. To investigate how vanilla plants, respond at the transcriptional level upon infection with Fov, here we employed the RNA-Seq approach to analyze the dynamics of whole-transcriptome changes during two-time frames of the infection.

Results
Analysis of global gene expression profiles upon infection by Fov indicated that the major transcriptional change occurred at 2 days post-inoculation (dpi), in comparison to 10 dpi. Briefly, the RNA-Seq analysis carried out in roots found that 3420 and 839 differentially expressed genes (DEGs) were detected at 2 and 10 dpi, respectively, as compared to the control. In the case of DEGs at 2 dpi, 1563 genes were found to be up-regulated, whereas 1857 genes were down-regulated. Moreover, functional categorization of DEGs at 2 dpi indicated that up-regulated genes are mainly associated to translation, whereas down-regulated genes are involved in cell wall remodeling. Among the translational-related transcripts, ribosomal proteins (RPs) were found increased their expression exclusively at 2 dpi.

Conclusions
The screening of transcriptional changes of V. planifolia Jacks upon infection by Fov provides insights into the plant molecular response, particularly at early stages of infection. The accumulation of translational-related transcripts at early stages of infection potentially points to a transcriptional reprogramming coupled with a translational regulation in vanilla plants upon infection by Fov. Altogether, the results presented here highlight potential molecular players that might be further studied to improve Fov-induced resistance in vanilla plants.
Transcriptome Analysis Reveals Mechanism Underlying the Differential Intestinal Functionality of Laying Hens in the Late Phase and Peak Phase of Production
Authors: Wang Weiwei , Wang Jing , Zhang Haijun , Wu Shugeng , Qi Guanghai 
Published: July 2019

Abstract
Background
The compromised performance of laying hens in the late phase of production relative to the peak production was thought to be associated with the impairment of intestinal functionality, which plays essential roles in contributing to their overall health and production performance. In the present study, RNA sequencing was used to investigate differences in the expression profile of intestinal functionality-related genes and associated pathways between layers in the late phase and peak phase of production.

Results
A total of 104 upregulated genes with 190 downregulated genes were identified in the ileum of layers in the late phase of production compared to those at peak production. These upregulated genes were found to be enriched in little KEGG pathway, however, the downregulated genes were enriched in the pathways of PPAR signaling pathway, oxidative phosphorylation and glutathione metabolism. Besides, these downregulated genes were mapped to several GO clusters in relation to lipid metabolism, electron transport of respiratory chain, and oxidation resistance. Similarly, there were lower activities of total superoxide dismutase, glutathione S-transferase and Na+/K+-ATPase, and reductions of total antioxidant capacity and ATP level, along with an elevation in malondialdehyde content in the ileum of layers in the late phase of production as compared with those at peak production.

Conclusions
The intestine of layers in the late phase of production were predominantly characterized by a disorder of lipid metabolism, concurrent with impairments of energy production and antioxidant property. This study uncovers the mechanism underlying differences between the intestinal functionality of layers in the late phase and peak phase of production, thereby providing potential targets for the genetic control or dietary modulation of intestinal hypofunction of layers in the late phase of production.
A phenomics-based approach for the detection and interpretation of shared genetic influences on 29 biochemical indices in Chinese south men
Authors: hu yanling , tan aihua , yu lei , hou chenyang , kuang haofa , wu qunying , sun Jinghan , zhou Qingniao , zhu yuanyuan , Zhang Chenqi , wei wei , li Lianfeng , li weidong , huang yuanjie , huang hongli , xie xing , lu tingxi , zhang haiying , yang xiaobo , gao yong , li tianyu , Jiang yonghua , mo zengnan 
Published: July 2019

Abstract
Background: Phenomics provides a new technologies and platforms as a systematic phenome-genome approach. However, few studies have reported on the system mining of shared genetics among clinical biochemical indices based on phenomics methods, especially in China. This study aimed to apply phenomics to systematically explore shared genetics among 29 biochemical indices based on the Fangchenggang Area Male Health and Examination Survey cohort.
Result: A total of 1,999 subjects with 29 biochemical indices and 709,211 single nucleotide polymorphism were subjected to phenomics analysis. Three bioinformatics methods, namely, Pearson test, Jaccard index, and linkage disequilibrium score regression, were used. Results showed that 29 biochemical indices were from a network. IgA, IgG, IgE, IgM, HCY, AFP and B12 were in the central community of 29 biochemical indices. Key genes and loci associated with metabolism traits were further identified, shared-genetics analysis showed that 29 SNPs (P < 10-4) were associated with three or more traits. After integrating the SNPs related to two or more traits with the GWAS catalog, 31 SNPs were found to be associated with several diseases (P < 10-8). Taking ALDH2 as an example to preliminarily explore its biological function, we also confirmed that rs671 (ALDH2) polymorphism affected mutiple traits of osteogenesis and adipogenesis differentiation in 3T3-L1 preadipocytes.
Conculsion: All these findings indicated a network of shared genetics and 29 biochemical indices, which will helpfully understand the genetics participated in biochemical metabolism.
Effects of a vocational rehabilitation programme on return to work among sick-listed primary health care patients A population-based matched, case-control study
Authors: von Celsing Anna-Sophia , Kristiansson Per , Svärdsudd Kurt , Wallman Thorne 
Published: July 2019

Abstract
Background: To evaluate the efficacy of a multidisciplinary vocational programme in sick-listed, primary health care patients as compared to matched non-programme patients.
Methods: The design was a 3-year prospective population-based, matched case-control study. It was set in a large primary healthcare centre in the city of Eskilstuna, Sweden. The subjects were 943 sickness-certified patients (482 women and 461 men). Intervention: 170 high-risk patients and a matched control group (n = 340) with similar risk for not returning to work within expected time, based on propensity score was created. The intervention group passed a multidisciplinary medical assessment and a coordinated vocational programme, while the control group received usual care by their general practitioner. Main outcome measures: Sick leave conclusion and the day when it occurred.
Results: The follow-up time was subdivided into four periods. During the first two periods, days 1–14 and days 15–112 after baseline, the intervention group had a significantly lower sick leave conclusion rate than the control group (hazard ratios, (HR) 0.32, 95% CI 0.20–0.51, p < 0.0001 and 0.47, 95% CI 0.35–0.64). During the third period, days 113–365, the intervention group had an insignificantly lower conclusion rate (HR 0.70, 95% CI 0.46–1.08, p = 0.10), and during the fourth follow-up period, days 366–1096, the intervention group had an insignificantly higher conclusion rate than the control group (HR 1.16, 95% CI 0.69–1.96, p = 0.58). Across the total follow-up period, the intervention group had a lower conclusion rate than the control group (HR 0.55, 95% CI 0.45–0.66, p < 0.0001).
Conclusions: No positive significant effects of the rehabilitation programme on time to sick leave conclusion were found.
A LIFE-HISTORY PERSPECTIVE ON SEXUAL SELECTION IN A POLYGAMOUS SPECIES
Authors: Ke Gao , Wijk Michiel van , Clement Zoe , Egas Martijn , Groot Astrid 
Published: July 2019

Abstract
Background

Ever since Darwin, evolutionary biologists have studied sexual selection driving differences in appearance and behaviour between males and females. An unchallenged paradigm in such studies is that one sex (usually the male) signals its quality as a mate to the other sex (usually the female), who is choosy in accepting a partner. Here, we argue that in polygamous species these roles may change dynamically with the mating status of males and females, depending on direct reproductive costs and benefits of multiple matings, and on sperm competition. We test this hypothesis using a polygamous moth species, as in moths not males but females are the signalers and males are the responders.

Results

We found that multiple matings are beneficial as well as costly for both sexes. Specifically, the number of matings did not affect the longevity of males or females, but when paired with a new virgin mate every night for five nights, only 67% of the males and 14% of the females mated successfully in all five nights. The female’s reproductive output increased with multiple matings, although when paired with a new virgin male every night, additional matings beyond 3 decreased her reproductive output, so that the Bateman gradient for females fit a quadratic model better than a linear model. The male’s reproductive success was positively affected by the number of matings and a linear regression line best fit the data. Simulations of the effect of sperm competition showed that increasing last-male paternity increases the steepness of the male Bateman gradient and thus the male’s relative fitness gain from additional mating. Irrespective of last-male paternity value, the female Bateman gradient is steeper than the male one for up to three matings.

Conclusion

Our results suggest that choosiness in moths may well change throughout the mating season, with males being more choosy early in the season and females being more choosy after having mated at least three times. This life-history perspective on the costs and benefits of multiple matings for both sexes sheds new light on sexual selection forces acting on sexual signals and responses.
The Relationship between Dietary Patterns and Depression is mediated by Serum Level of Folate and Vitamin B12: A Case-Control Study
Authors: Khosravi Maryam , Sotoudeh Gity , Amini Maryam , Raisi Firoozeh , Mansoori Anahita , Hosseinzadeh Mahdieh 
Published: July 2019

Abstract
Introduction

Major depressive disorder is among main worldwide causes of disability. The low medication compliance rates in depressed patients as well as the high recurrence rate of the disease can bring up the nutrition-related factors as a potential preventive or treatment agent for depression. The aim of this study was to investigate the association between dietary patterns and depression via the intermediary role of the serum folate and vitamin B12, total homocysteine, tryptophan, and tryptophan/competing amino acids ratio.

Methods

This was an individually matched case-control study in which 110 patients with depression and 220 healthy individuals, who completed a semi-quantitative food frequency questionnaire were recruited. In addition, to measure the serum biomarkers 43 patients with depression and 43 healthy people were randomly selected from the study population. To diagnose depression the criteria of Diagnostic and Statistical Manual of Mental Disorders, fourth edition, were utilized.

Results

The findings suggest that the healthy dietary pattern was significantly associated with a reduced odds of depression (OR: 0.75; 95% CI: 0.61-0.93) whereas the unhealthy dietary pattern increased it (OR: 1.382, CI: 1.116–1.71). The mediation analysis showed that the healthy dietary pattern was associated with a reduced risk of depression via increased serum levels of the folate and vitamin B12; however, the unhealthy dietary pattern was associated with increased risk of depression via decreased serum levels of folate and vitamin B12, based on tree adjusted logistic regression models.

Conclusion

Dietary patterns may be associated with depression by changing the serum levels of folate and vitamin B12. Further studies are required to confirm the mechanism.
Diagnostic accuracy of QuickVue® Dipstick Strep A test and its effect on antibiotic prescribing in children in the United Arab Emirates
Authors: Shabestari Seyed Ali Safizadeh , Malik Zainab A. , Al-Najjar Fadil Y A 
Published: July 2019

Abstract
Background: Unnecessary antibiotic prescription to children with upper respiratory tract infections (URTIs) has led to the increase in antibiotics resistant bacteria rates. In this study, we evaluated the diagnostic accuracy of QuickVue® Dipstick Strep A test (QV-SAT) in children presenting with acute pharyngotonsillitis and its effect on antibiotic prescribing.

Methods: A single-gated diagnostic accuracy study of children with acute catarrh, fever, and inflamed tonsils presenting to a pediatric clinic between March 2016 and September 2018. Paired throat swabs for QV-SAT and culture were collected. None of the children received antibiotics prior to sample collection. Diagnostic accuracy of the QV-SAT was achieved by estimating the area under the ROC curve (AUC). Furthermore, the positive predictive value (PPV), negative predictive value (NPV), and likelihood ratios of the test were calculated.

Results: 204 children were included in this study. 111 (54.4%) were boys and 146 (71.6%) were under the age of five years. QV-SAT was positive in 44 (21.6%) and throat culture was positive for Group A β- haemolytic Streptococcus (GAS) in 42 (20.6%) of the children. The results of QV-SAT were highly consistent with culture results: only 2 (0.9%) children with negative results had a positive throat culture. The sensitivity of the QV-SAT in the identification of GAS infection was 100% (95% CI 91.6%, 100%) and the NPV was 100% (95% CI 70%, 95%). Only 42 children (21%) were given antibiotics, while 162 (79%) were not.

Conclusion: The QV-SAT is a quick and reliable test which can help dramatically reduce antibiotic prescriptions to children presenting with fever and acute pharyngotonsillitis.
Knowledge and perception of the role of water, sanitation and hygiene in containment of Ebola virus disease among secondary school students in Ibadan, Nigeria
Authors: Edoror Faith I. , Oloruntoba Elizabeth O. , Akinsete Shade J. 
Published: July 2019

Abstract
This study assessed the knowledge and perception of the role of water supply, sanitation and hygiene (WASH) in the containment of Ebola virus disease (EVD) among secondary school students in Ibadan, Nigeria. A cross-sectional study of 420 students from eight schools (public and private) in Ibadan was conducted. A semi-structured questionnaire and an observational checklist were used to collect data. Data were analysed using descriptive statistics, Chi-square test and logistic regression at 5% level of significance. Overall, 60% reported EVD was airborne. A majority (71%) of the respondents had good knowledge of EVD, while a majority (92%) had a good perception of the role of WASH in EVD containment. Class of respondents was significantly (p = 0.045) associated with knowledge of WASH. Although schools had satisfactory sanitary facilities, only a few (21%) sustained good hygiene practices at the end of the Ebola outbreak in Nigeria. Our findings revealed suboptimal knowledge on transmission of EVD, and unsustainable hygiene practices among secondary students post-Nigeria's EVD outbreak. High priority should be given to hygiene education among educators and students. Implementation of monitoring and evaluation of hygiene behaviour among secondary school students should also be a priority.