bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic characteristics of two most widely used BCG vaccine strains: Danish 1331 and Pasteur 1173P2
Authors: Asadian Mahla , Hassanzadeh Seyed Mehdi , Safarchi Azadeh , Douraghi Masoumeh 
Published: August 2022

Abstract
Background
Bacillus Calmette–Guérin (BCG) refers to a group of vaccine strains with unique genetic characteristics. BCG is the only available vaccine for preventing tuberculosis (TB). Genetic and biochemical variations among the BCG vaccine strains have been considered as one of the significant parameters affecting the variable protective efficacy of the vaccine against pulmonary tuberculosis. To track genetic variations, here two vaccine strains (Danish 1331 and Pasteur 1173P2) popularly used according to the BCG World Atlas were subjected to a comparative analysis against the Mycobacterium tuberculosis H37Rv, Mycobacterium bovis AF2122/97, and Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 reference genomes. Besides, the presence or absence of the experimentally verified human T cell epitopes was examined.

Results
Only two variants were identified in BCG Danish 1331 that have not been reported previously in any BCG strains with the complete submitted genome yet. Furthermore, we identified a DU1-like 14,577 bp region in BCG Danish 1331; The duplication which was previously seemed to be exclusive to the BCG Pasteur. We also found that 35% of the T cell epitopes are absent from both strains, and epitope sequences are more conserved than the rest of the genome.

Conclusions
We provided a comprehensive catalog of single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels) in BCG Danish 1331 and BCG Pasteur 1173P2. These findings may help determine the effect of genetic variations on the variable protective efficacy of BCG vaccine strains.
Results and lessons from dual extraction of DNA and RNA from formalin-fixed paraffin-embedded breast tumor tissues for a large Cancer epidemiologic study
Authors: Ondracek Rochelle Payne , Chen Jianhong , Marosy Beth , Szewczyk Sirinapa , Medico Leonard , Mohan Amrutha Sherly , Nair Priya , Pratt Rachel , Roh Janise M. , Khoury Thaer , Carpten John , Kushi Lawrence H. , Palmer Julie R. , Doheny Kim , Davis Warren , Higgins Michael J. , Yao Song , Ambrosone Christine B. 
Published: August 2022

Abstract
Background
The use of archived formalin-fixed paraffin-embedded (FFPE) tumor tissues has become a common practice in clinical and epidemiologic genetic research. Simultaneous extraction of DNA and RNA from FFPE tissues is appealing but can be practically challenging. Here we report our results and lessons learned from processing FFPE breast tumor tissues for a large epidemiologic study.

Methods
Qiagen AllPrep DNA/RNA FFPE kit was adapted for dual extraction using tissue punches or sections from breast tumor tissues. The yield was quantified using Qubit and fragmentation analysis by Agilent Bioanalyzer. A subset of the DNA samples were used for genome-wide DNA methylation assays and RNA samples for sequencing. The QC metrices and performance of the assays were analyzed with pre-analytical variables.

Results
A total of 1859 FFPE breast tumor tissues were processed. We found it critical to adjust proteinase K digestion time based on tissue volume to achieve balanced yields of DNA and RNA. Tissue punches taken from tumor-enriched regions provided the most reliable output. A median of 1475 ng DNA and 1786 ng RNA per sample was generated. The median DNA integrity number (DIN) was 3.8 and median DV200 for RNA was 33.2. Of 1294 DNA samples used in DNA methylation assays, 97% passed quality check by qPCR and 92% generated data deemed high quality. Of the 130 RNA samples with DV200 ≥ 20% used in RNA-sequencing, all but 5 generated usable transcriptomic data with a mapping rate ≥ 60%.

Conclusions
Dual DNA/RNA purification using Qiagen AllPrep FFPE extraction protocol is feasible for clinical and epidemiologic studies. We recommend tissue punches as a reliable source material and fine tuning of proteinase K digestion time based on tissue volume.

Impact
Our protocol and recommendations may be adapted by future studies for successful extraction of archived tumor tissues.
Characteristics and clinical outcomes of patients presenting with advanced HIV disease in the “treat all” era: a retrospective cohort study from rural Rwanda
Authors: Musengimana Gentille , Umugisha Jean Paul , Habinshuti Placide , Anderson Todd , Mukesharurema Geraldine , Remera Eric , Ndahimana Jean D’Amour , Barnhart Dale A. 
Published: August 2022

Abstract
Background
In 2016 Rwanda adopted “treat all” where all patients with HIV are immediately eligible for ART regardless of disease progression. Despite widespread availability of treatment, it is unknown whether presentation with advanced HIV persists.

Methods
We conducted a retrospective cohort among patients aged ≥ 15 who enrolled in care between July 2016 and July 2018 in three rural Rwandan districts. We estimated the prevalence of advanced HIV, defined as presenting with CD4 count < 200 cells/mm3 or WHO stage 3 or 4, and compared baseline characteristics of patients with and without advanced HIV. We compared cumulative incidences and time to events using Chi squared tests and Cox proportional hazards models, respectively, for (a) viral load tests; (b) viral suppression; (c) death; and (d) treatment failure (a composite of death, lost to follow up, or virologic failure).

Results
Among 957 patients, 105 (11.0%) presented with advanced HIV. These patients were significantly more likely to have low body mass index, come from Burera district, be older, and be identified through inpatient settings rather than through voluntary or prenatal testing. Patients with advanced HIV had significantly higher risks of death at 12-months (9.5% vs 1.5%, p < 0.001) and 18-months (10.5% vs 1.9%, p < 0.001) and significantly higher risk of treatment failure at 12-months (21.9% vs. 14.2%, p = 0.037). After adjusting for confounders, patients with advanced HIV had still higher rates of death (adjusted Hazard ratio [aHR] = 4.4, 95% CI: 1.9, 10.2, p < 0.001) and treatment failure (aHR = 1.7, 95% CI: 1.1, 2.5, p = 0.017), but no difference in viral load testing (aHR = 1.1, 95% CI: 0.8, 1.5, p = 0.442) or viral suppression (aHR = 1.0, 95% CI: 0.8, 1.4, p = 0.949). When allowing for the hazard ratio to vary over time, patients with advanced HIV experienced elevated rates of treatment failure in the first six of enrollment, but not after nine months.

Conclusion
Presenting with advanced HIV remains common and is still associated with poor patient outcomes. Sensitization of the community to the benefits of early ART initiation, identification of patients with advanced HIV, and holistic support programs for the first 6 months of treatment may be needed to improve outcomes.
Changes in working status after cancer diagnosis and socio-demographic, clinical, work-related, and psychological factors associated with it
Authors: Kang Danbee , Bae Ka Ryeong , Kim Ho Young , Ahn Yeojin , Kim Nayeon , Shim Youngmog , Sohn Tae Sung , Lee Woo Yong , Baek Ji Hyun , Kweon Sun-Seog , Cho Juhee 
Published: August 2022

Abstract
Background
While many studies investigated changes in working status in cancer survivors, most studies have been performed in survivors of breast cancer and few studies evaluated factors associated with changes in the working status of cancer survivors comprehensively. We aimed to evaluate the changes in the working status of cancer survivors after diagnosis and socio-demographic, clinical, work-related and psychological factors associated with it.

Methods
We conducted a cross-sectional survey of adult patients with cancer who were working at the time of diagnosis. A trained interviewer inquired about participants’ current working status, including leave of absence, discontinuing, continuing, and changing work. Sociodemographic, clinical, work-related and psychological factors were measured. Multinomial logistic regression was used to identify factors associated with changes in the working status.

Results
Among the 730 patients, 29%, 18% and 6% were currently on a discontinued working, leave of absence and had changed jobs, respectively. Patients who discontinued working after cancer diagnosis were more likely to be female, have ≥ $3,000 of monthly family income, not be the principal wage earners for their families and be blue-collar workers. In clinical characteristics, advanced-stage cancer and experienced cancer recurrence was associated with leave of absence and discontinued working. In work-related and psychological factors, stress due to insufficient job control (relative risk ratio [RRR] = 2.26), interpersonal conflict (RRR = 1.86), job insecurity (RRR = 2.63), organizational system (RRR = 3.49), and lack of reward (RRR = 11.76), and less meaning to work were more likely to discontinue working after a cancer diagnosis.

Conclusion
Occupational health care professionals and other stakeholders need to openly communicate with patients with cancer about potential barriers during the return-to-work trajectory.
Assessing whether genetic scores explain extra variation in birthweight, when added to clinical and anthropometric measures
Authors: Haulder Maneka , Hughes Alice E. , Beaumont Robin N. , Knight Bridget A. , Hattersley Andrew T. , Shields Beverley M. , Freathy Rachel M. 
Published: August 2022

Abstract
Background
Human birthweight is a complex, multifactorial trait. Maternal characteristics contribute to birthweight variation by influencing the intrauterine environment. Variation explained by genetic effects is also important, but their contributions have not been assessed alongside other key determinants. We aimed to investigate variance in birthweight explained by genetic scores in addition to easily-measurable clinical and anthropometric variables.

Methods
We analysed 549 European-ancestry parent-offspring trios from a UK community-based birth cohort.
We investigated variance explained in birthweight (adjusted for sex and gestational age) in multivariable linear regression models including genetic scores, routinely-measured maternal characteristics, and parental anthropometric variables. We used R-Squared (R2) to estimate variance explained, adjusted R-squared (Adj-R2) to assess improvement in model fit from added predictors, and F-tests to compare nested models.

Results
Maternal and fetal genetic scores together explained 6.0% variance in birthweight. A model containing maternal age, weight, smoking, parity and 28-week fasting glucose explained 21.7% variance. Maternal genetic score explained additional variance when added to maternal characteristics (Adj-R2 = 0.233 vs Adj-R2 = 0.210, p < 0.001). Fetal genetic score improved variance explained (Adj-R2 = 0.264 vs 0.248, p < 0.001) when added to maternal characteristics and parental heights.

Conclusions
Genetic scores account for variance explained in birthweight in addition to easily measurable clinical variables. Parental heights partially capture fetal genotype and its contribution to birthweight, but genetic scores explain additional variance. While the genetic contribution is modest, it is comparable to that of individual clinical characteristics such as parity, which suggests that genetics could be included in tools aiming to predict risk of high or low birthweights.
Financial impacts and community resources utilization of children with feeding difficulties
Authors: Okada June , Wilson Erin , Wong John , Luo Man , Fiechtner Lauren , Simione Meg 
Published: August 2022

Abstract
Background
To examine the extent to which financial impacts and community resources utilization are associated with pediatric feeding difficulties. We hypothesize that children with feeding difficulties will have more financial impacts and community resources utilization than children without feeding difficulties.

Methods
We conducted a secondary analysis of cross-sectional data from the 2017–2018 National Survey of Children’s Health (NSCH) regarding 14,960 children 0–5 years. NSCH utilized random sampling of families across the United States to collect nationally representative data. Outcomes included out-of-pocket costs, caregivers leaving a job due to the child’s health, food insufficiency, receival of food or cash assistance, and receival of special education and/or developmental services. We used a multivariable logistic regression controlling for sociodemographic factors to examine the associations of feeding difficulties with financial impacts and community resources utilization outcomes.

Results
Out of 14,690 respondents, children were a mean (SD) age of 2.53(0.03) years and 1.7% reported feeding difficulties. These children had higher odds of having out-of-pocket costs of ≥$1000 (OR: 3.01; 95% CI: 1.61, 5.62), having a caregiver that left a job due to their child’s health (OR: 3.16; 95% CI: 2.01, 4.98), experiencing food insufficiency (OR: 1.67; 95% CI: 1.03, 2.71), and receiving special education and/or developmental services (OR 3.98; 95% CI: 2.46, 6.45) than children without feeding difficulties.

Conclusions
Children with feeding difficulties are more likely to have financial impacts and community resources utilization than children without feeding difficulties. This information can be used to tailor interventions to improve family-centered care and outcomes for children.
Effect of the age of visual impairment onset on employment outcomes in South Korea: analysis of the national survey on persons with disabilities data
Authors: Jeon Boyoung , Koo Heejo , Lee Hye-Jae , Han Euna 
Published: August 2022

Abstract
Background
Opportunities for paid employment provide meaningful ways for those with disabilities to participate in society and achieve financial independence. Although the onset age of disabilities can alter individuals’ attitudes toward accepting their disabilities and their desire for work, the lack of data limits relevant empirical research. The purpose of this study is to examine the effect of the onset age on employment, job security (permanent vs. temporary), and wage level among visually impaired adults in South Korea.

Methods
We used three years of the National Survey on Persons with Disabilities data, 2011, 2014, and 2017, and included 583 participants in this study. We used a logistic regression model for the employment status and a multinomial logistic regression model for job security. We analyzed log monthly wage by a multivariate linear regression model, which subdivided the age groups, with 20–49 years old denoting prime-aged (n = 245) and 50–64 years old denoting late-middle-aged (n = 338). For each age group, we conducted a sub-analysis by sex.

Results
For prime-aged adults, the employment probability decreased as the age of visual impartment onset increased, and women in particular experienced a lower employment rate for both permanent and temporary jobs when their disability onset age was above 25. However, among permanent employees, monthly wages were higher if the onset age was 25 + compared to when the onset age was 0–5 years old. In late middle-aged adults, adult onset disabilities were associated with higher odds of employment and higher wages for temporary jobs, implying these individuals worked unskilled or manual jobs.

Conclusions
In prime-aged adults, higher monthly wages among permanent employees showed that they were more likely to continue their original work, whereas in late-middle-aged adults, adult-onset disabilities were associated with a higher employment rate and higher wages for temporary jobs, suggesting the need for further investigation into job quality. These findings indicate a need for differentiated policy approaches considering the onset age of visual impairment to improve labor market outcomes throughout individuals’ lifespans.
Health care utilization among individuals who die by suicide as compared to the general population: a population-based register study in Sweden
Authors: Bondesson Elisabeth , Alpar Tori , Petersson Ingemar F. , Schelin Maria E. C. , Jöud Anna 
Published: August 2022

Abstract
Background
Globally, 700 000 people die every year by suicide. Health care consultation patterns the period before suicide could be one potential way to identify people at risk for suicide. Therefore, this study examines health care patterns up to one year prior to the suicide by age, sex and prior diagnoses and specifically investigates if and how this differs from the general population of Skåne, Sweden.

Methods
This cohort study includes all individuals, aged 15 and older, that died by suicide in Region Skåne, Sweden from 2004 to 2015 (n = 1653). The individuals were identified through the Cause of death register and then linked to the Skåne healthcare register. Health care data was analyzed as proportions consulting different types of health care the month and year preceding the suicide, we also investigated the impact of age, sex and the occurrence of prior psychiatric and pain diagnoses. Additionally, we compared the proportion of consulting care among the suicide victims and the general population of Skåne.

Results
In the month before their death, 53% of the suicide victims had any health care consultation, compared with 20% in the general population of Skåne, a given month (p < 0.0001). The corresponding figures for the year prior to suicide was 86% among those who died by suicide, compared to 69% in the general population of Skåne, a given year (p < 0.0001). Women, and those having a documented history of psychiatric diagnosis were more likely to have health care consultations in the month and year preceding suicide (p < 0.001), compared to men and suicide victims without a history of psychiatric disease. Older adults that died by suicide, were less likely to consult psychiatric care compared to the younger suicide victims (p < 0.001).

Conclusion
A majority of the suicide victims consulted health care in the near time before death and the proportion of seeking health care was significantly higher than in the general population of Skåne and higher among female suicide victims as compared to males. Alternative preventive screening measures should be considered for individuals consulting health care, especially for older people and individuals outside the psychiatric care.
In vitro attrition wear resistance of four types of paste-like bulk-fill composite resins
Authors: Asadian Faeze , Hoseini Amirahmad Pahlavan , Ahmadian Leila , Rafeie Niyousha , Rezaei Samaneh , Moradi Zohreh 
Published: August 2022

Abstract
Background
Recently, the application of bulk-fill composite resins has increased significantly. Attrition wear and the consequently increased surface roughness of composite resins are among the causes of restoration failure in the posterior teeth. This study aimed to compare the attrition wear and surface roughness of four types of bulk-fill composite resins compared to a conventional composite resin.

Methods
EverX-Posterior, X-tra fil, SonicFill 2, and Filtek Bulk-Fill composites (bulk-fill) and Z250 composite (conventional resin composite) were evaluated. Thirty cylindrical specimens (n = 6) were weighed and monitored for 24 h until their weight was stabilized. The primary surface roughness of the specimens was measured by a profilometer. The specimens were then subjected to attrition wear in a chewing simulator. Next, the specimens were weighed, and the surface roughness was measured again. Data were analyzed by one-way ANOVA and Tukey’s post-hoc test at P < 0.05 significance level.

Results
According to one-way ANOVA, the difference in weight loss was significant among the groups (P = 0.004) but the difference in surface roughness of the groups was not significant after the attrition wear (P > 0.05). Tukey’s post-hoc test showed that the weight loss of bulk-fill composites was not significantly different from that of Z250 conventional composite after the attrition wear (P > 0.05).

Conclusion
Within the limitations of this study, it appears that the tested bulk-fill composite resins are comparable to the conventional composite regarding their attrition wear, increased surface roughness, and weight loss.
A quantitative study of nurses perception to advance directive in selected private and public secondary healthcare facilities in Ibadan, Nigeria
Authors: Ojedoyin Oluwaseyi Emiola , Jegede Ayodele Samuel 
Published: August 2022

Abstract
Objectives
The study evaluated nurses’ perceptions on the benefits, drawbacks, and their roles in initiating and implementing advance directives (AD) at private and public secondary healthcare units.

Methods
The study adopted a cross-sectional, comparative-descriptive research design and was anchored on the structural functional theory. A total of 401 nurses (131 private and 270 public) were chosen on purpose. The data was collected between January and March 2018 among nurses at the selected hospitals. Analysis was done via SPSSv28.0.1.0.

Results
Compared to nurses working in private healthcare facilities (72.5%), the majority of nurses at the public healthcare facilities (75.2%) indicated a more favorable opinion of AD’s benefits and (61.9%) felt they had a substantial involvement in the development and execution of AD than their private counterpart (56.5%). Similarly, 60.7% of nurses employed by the government agreed that AD has some disadvantages compared to those employed by the private sector (58.8%). Significantly, Christian nurses are 0.53 times less likely than Muslims to contest AD’s benefits; 0.78 times less likely than Muslim to disagree that AD has flaws; and 1.30 times more likely than Muslim nurses to deny they contributed to the development and execution of AD, though not significant.

Conclusion
Making decisions at the end-of-life can be challenging, thus AD should be supported across the board in the healthcare industry. Nurses should be trained on their role in developing and implementing AD, as well as on its advantages and how to deal with its challenges.
Exosome-based strategies for diagnosis and therapy of glioma cancer
Authors: Karami Fath Mohsen , Azami Jalil , Masoudi Alireza , Mosaddeghi Heris Reza , Rahmani Elnaz , Alavi Fatemeh , Alagheband Bahrami Armina , Payandeh Zahra , Khalesi Bahman , Dadkhah Masoomeh , Pourzardosht Navid , Tarhriz Vahideh 
Published: August 2022

AbstractGlioblastoma belongs to the most aggressive type of cancer with a low survival rate that is characterized by the ability in forming a highly immunosuppressive tumor microenvironment. Intercellular communication are created via exosomes in the tumor microenvironment through the transport of various biomolecules. They are primarily involved in tumor growth, differentiation, metastasis, and chemotherapy or radiation resistance. Recently several studies have highlighted the critical role of tumor-derived exosomes against immune cells. According to the structural and functional properties, exosomes could be essential instruments to gain a better molecular mechanism for tumor understanding. Additionally, they are qualified as diagnostic/prognostic markers and therapeutic tools for specific targeting of invasive tumor cells such as glioblastomas. Due to the strong dependency of exosome features on the original cells and their developmental status, it is essential to review their critical modulating molecules, clinical relevance to glioma, and associated signaling pathways. This review is a non-clinical study, as the possible role of exosomes and exosomal microRNAs in glioma cancer are reported. In addition, their content to overcome cancer resistance and their potential as diagnostic biomarkers are analyzed.