bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of common microRNA between COPD and non-small cell lung cancer through pathway enrichment analysis
Authors: Fathinavid Amirhossein , Ghobadi Mohadeseh Zarei , Najafi Ali , Masoudi-Nejad Ali 
Published: October 2021

Abstract
Background
Different factors have been introduced which influence the pathogenesis of chronic obstructive pulmonary disease (COPD) and non-small cell lung cancer (NSCLC). COPD as an independent factor is involved in the development of lung cancer. Moreover, there are certain resemblances between NSCLC and COPD, such as growth factors, activation of intracellular pathways, as well as epigenetic factors. One of the best approaches to understand the possible shared pathogenesis routes between COPD and NSCLC is to study the biological pathways that are activated. MicroRNAs (miRNAs) are critical biomolecules that implicate the regulation of several biological and cellular processes. As such, the main goal of this study was to use a systems biology approach to discover common dysregulated miRNAs between COPD and NSCLC, one that targets most genes within common enriched pathways.

Results
To reconstruct the miRNA-pathways for each disease, we used the microarray miRNA expression data. Then, we employed “miRNA set enrichment analysis” (MiRSEA) to identify the most significant joint miRNAs between COPD and NSCLC based on the enrichment scores. Overall, our study revealed the involvement of the targets of miRNAs (such as has-miR-15b, hsa-miR-106a, has-miR-17, has-miR-103, and has-miR-107) in the most important common biological pathways.

Conclusions
According to the promising results of the pathway analysis, the identified miRNAs can be utilized as the new potential signatures for therapy through understanding the molecular mechanisms of both diseases.
Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs
Authors: Wang Dan , Yang Liu , Ning Chao , Liu Jian-Feng , Zhao Xingbo 
Published: October 2021

Abstract
Background
Reference sequences play a vital role in next-generation sequencing (NGS), impacting mapping quality during genome analyses. However, reference genomes usually do not represent the full range of genetic diversity of a species as a result of geographical divergence and independent demographic events of different populations. For the mitochondrial genome (mitogenome), which occurs in high copy numbers in cells and is strictly maternally inherited, an optimal reference sequence has the potential to make mitogenome alignment both more accurate and more efficient. In this study, we used three different types of reference sequences for mitogenome mapping, i.e., the commonly used reference sequence (CU-ref), the breed-specific reference sequence (BS-ref) and the sample-specific reference sequence (SS-ref), respectively, and compared the accuracy of mitogenome alignment and SNP calling among them, for the purpose of proposing the optimal reference sequence for mitochondrial DNA (mtDNA) analyses of specific populations

Results
Four pigs, representing three different breeds, were high-throughput sequenced, subsequently mapping reads to the reference sequences mentioned above, resulting in a largest mapping ratio and a deepest coverage without increased running time when aligning reads to a BS-ref. Next, single nucleotide polymorphism (SNP) calling was carried out by 18 detection strategies with the three tools SAMtools, VarScan and GATK with different parameters, using the bam results mapping to BS-ref. The results showed that all eighteen strategies achieved the same high specificity and sensitivity, which suggested a high accuracy of mitogenome alignment by the BS-ref because of a low requirement for SNP calling tools and parameter choices.

Conclusions
This study showed that different reference sequences representing different genetic relationships to sample reads influenced mitogenome alignment, with the breed-specific reference sequences being optimal for mitogenome analyses, which provides a refined processing perspective for NGS data.
A low follicle-stimulating hormone level is a protective factor for non-alcoholic fatty liver disease in older men aged over 80
Authors: Zhu Yunxia , Xu Jun , Zhang Xiaoyan , Ke Yingying , Fu Guoxiang , Guo Qihao 
Published: October 2021

AbstractPurposeRecent studies have suggested the significant relationship between follicle-stimulating hormone (FSH) and non-alcoholic fatty liver disease (NAFLD) in postmenopausal women. However, it is unknown whether FSH impacts the risk of NAFLD in men. This study aimed to investigate the association between serum FSH levels and NAFLD in elderly Chinese men aged 80–98, a particular group with worse outcomes of NAFLD.Patients and methodsA cross-sectional analysis was performed in 444 subjects in a geriatric health center. The highest quartile of serum FSH was used as reference. Hepatic steatosis was defined according to the results of liver ultrasound. Fibrosis-4 (FIB-4) Index> 2.67 was defined as advanced fibrosis.ResultsBased on liver ultrasound, 108 (24.3%) subjects had NAFLD. FSH level were negatively correlated with total testosterone, estradiol, nutritional risk, and the prevalence of high education level (allP < 0.01), and positively correlated with age, luteinizing hormone, alanine aminotransferase and aspartate aminotransferase (allP < 0.05). The correlation between FSH and body mass index or antihypertensive drug usage was marginally significant (P = 0.057;P = 0.066, respectively). The percentage of subjects with NAFLD had a trend to increase following the quartiles of serum FSH (20.0% in quartile 1, 18.2% in quartile 2, 27.3% in quartile 3, and 31.6% in quartile 4). After adjustment for common pathogenic risk factors, nutritional risk, and other sex hormones, serum FSH were progressively associated with odds ratios for NAFLD. The adjusted odds ratios and 95% CIs for quartile 1, quartile 2, and quartile 3, compared with quartile 4 were 0.132 (0.034–0.516), 0.190 (0.052–0.702), and 0.404 (0.139–1.173), respectively. Obesity was not involved in the potential negative role of circulating FSH on the risk of NAFLD in our population. Furthermore, our results revealed no significant association between FSH and advance fibrosis, the OR (95% CI) for advanced fibrosis was 1.018 (0.983–1.054) (P = 0.316) after adjusting for the potential covariates, although a positive correlation of FSH and FIB-4 score was observed (r = 0.325,P = 0.001).ConclusionLow FSH level may decrease the risk of NAFLD in elderly Chinese men. These findings warrant replication in more extensive studies.
Mortality risk factors among hospitalized children with severe pertussis
Authors: Shi Tingting , Wang Ling , Du Shuling , Fan Huifeng , Yu Minghua , Ding Tao , Xu Xuehua , Zhang Dongwei , Huang Li , Lu Gen 
Published: October 2021

Abstract
Background
Some children hospitalized for severe pertussis need intensive care; moreover, some children die because of deterioration alone or in combination with other complications. The purpose of this study was to identify the mortality risk factors among hospitalized children with severe pertussis.

Methods
This study evaluated the medical records of 144 hospitalized children with severe pertussis at the Guangzhou Women and Children’s Medical Centre between January 2016 and December 2019.

Results
The median age of patients was 2 months (IQR 1–4 months), with 90.3% of the patients aged < 6 months and 56.9% of the patients aged < 3 months. A total of 38 patients were admitted to intensive care unit (ICU), 13 patients died, and the mortality of severe pertussis was 34.2%, with patients younger than 6 weeks accounting for 76.9% of the deaths. On the multivariate analysis, the independent risk factors for death were WBC > 70.0 × 109/L (odds ratio [OR], 230.66; 95% confidence interval [CI], 5.16–10,319.09 P = 0.005) and pulmonary hypertension (PH) (OR 323.29; 95% CI 16.01–6529.42; P < 0.001).

Conclusion
Severe pertussis mainly occurred in children aged < 3 months. The mortality of severe pertussis was 34.2%, with patients younger than 6 weeks accounting for the majority of the deaths. We recommend the first dose of diphtheria-tetanus-pertussis (DTP) should be advanced to the age of 2 months or even 6 weeks. The presence of a WBC > 70.0 × 109/L and PH were the prognostic independent variables associated with death.
Spatial analysis of tuberculosis cure in primary care in Rio de Janeiro, Brazil
Authors: Prado Junior José Carlos , Medronho Roberto de Andrade 
Published: October 2021

Abstract
Background
Tuberculosis (TB) presents a high burden of disease and is considered a global emergency by the World Health Organization (WHO), as the leading cause of death from infectious disease in adults. TB incidence is related directly to access to health services and socioeconomic determinants and inequality. Providing primary care settings can lead to improved access, shorter waiting times for patients, and enhanced TB case detection. The article aims to identify the spatial and temporal risk areas for TB and the relationship between TB cure and primary healthcare coverage from 2012 to 2014 in Rio de Janeiro, Brazil.

Methods
A cross-sectional study was conducted in Rio de Janeiro, Brazil. All cases of TB reported to the Information System on Diseases of Notification (SINAN) from 2012 to 2014 were included. Socioeconomic variables from the 2010 Brazilian national census were also added. Socioeconomic variables were selected from multivariate analysis using principal factors analysis. Spatial association was verified with generalized additive model (GAM). It was possible to identify areas at higher risk of failure to cure TB.

Results
TB rates showed strong positive spatial autocorrelation. TB cure rate varied according to schooling (individuals with complete secondary schooling had higher cure rates than illiterate individuals; OR 1.72, 95% CI 1.30–2.29), alcohol consumption (OR 0.47, 95% CI 0.35–0.64), contact investigation (OR 2.00, 95% CI 1.56–2.57), positive HIV serology (OR 0.31, 95% CI 0.23–0.42), and census tracts with higher elderly rates (OR 9.39, 95% CI 1.03–85.26). Individuals who had been covered by primary healthcare (PHC) for 35 to 41 months had 1.64 higher odds of cure, compared to those with no PHC coverage (95% CI 1.07–2.51).

Conclusion
A comprehensive risk map was developed, allowing public health interventions. Spatial analysis allowed identifying areas with lower odds of TB cure in the city of Rio de Janeiro. TB cure was associated statistically with time of coverage by primary healthcare. TB cure rate also varied according to sociodemographic factors like schooling, alcohol abuse, and population density.
This methodology can be generalized to other areas and/or other public health problems.

Highlights

We studied standardized municipal TB cure rates in an area of social inequality in Brazil.

TB rates showed strong positive spatial autocorrelation.

Higher rates were associated with population density and socioeconomic conditions. Illiterate individuals were less likely to achieve TB cure.

TB cure was less likely in individuals with HIV and alcohol abuse.

TB cure was greater in areas with high primary healthcare coverage.
Quality of dying in hospital general wards: a cross-sectional study about the end-of-life care
Authors: Binda Filippo , Clari Marco , Nicolò Gabriella , Gambazza Simone , Sappa Barbara , Bosco Paola , Laquintana Dario 
Published: October 2021

Abstract
Background
In the last decade, access to national palliative care programs have improved, however a large proportion of patients continued to die in hospital, particularly within internal medicine wards.

Objectives
To describe treatments, symptoms and clinical management of adult patients at the end of their life and explore whether these differ according to expectation of death.

Methods
Single-centre cross-sectional study performed in the medical and surgical wards of a large tertiary-level university teaching hospital in the north of Italy. Data on nursing interventions and diagnostic procedure in proximity of death were collected after interviewing the nurse and the physician responsible for the patient. Relationship between nursing treatments delivered and patients’ characteristics, quality of dying and nurses’ expectation about death was summarized by means of multiple correspondence analysis (MCA).

Results
Few treatments were found statistically associated with expectation of death in the 187 patients included. In the last 48 h, routine (70.6%) and biomarkers (41.7%) blood tests were performed, at higher extent on patients whose death was not expected. Many symptoms classified as severe were reported when death was highly expected, except for agitation and respiratory fatigue which were reported when death was moderately expected. A high Norton score and absence of anti-bedsore mattress were associated with unexpected death and poor quality of dying, as summarized by MCA. Quality of dying was perceived as good by nurses when death was moderately and highly expected. Physicians rated more frequently than nurses the quality of dying as good or very good, respectively 78.6 and 57.8%, denoting a fair agreement between the two professionals (k = 0.24, P <  0.001). The palliative care consultant was requested for only two patients.

Conclusion
Staff in medical and surgical wards still deal inadequately with the needs of dying people. Presence of hospital-based specialist palliative care could lead to improvements in the patients’ quality of life.
Determining the effect of tele-rehabilitation on patients with stutter using the goal attainment scaling (GAS)
Authors: Eslami Jahromi Maryam , Ahmadian Leila 
Published: October 2021

Abstract
Background
Lack of proper and timely patients' access to speech pathologists can affect the treatment and follow-up process; therefore, patients do not achieve the expected therapeutic goals. The aim of this study was to determine the effect of tele-rehabilitation on the stuttering patients using the goal attainment scaling (GAS).

Methods
This interventional study was carried out on patients who visited the rehabilitation centers affiliated to the Jahrom Welfare Office. They underwent remote speech therapy using Skype. To evaluate the treatment outcomes of the stuttering patients, GAS was used.

Results
The participants' speech and lingual skills improved using videoconferencing. The mean score of total GAS for patients was 53.08. Of 112 health goals, patients reached the expected or higher than expected levels in 78 goals.

Conclusions
Rehabilitation through video conferencing was effective for patients with stuttering, improved their speech, and decreased their stuttering. Since, application of remote rehabilitation services can provide regular access to healthcare services, it can lead to improving patient treatment provide more frequent and faster treatment follow-up.
The association between experience of hospital accreditation and nurses’ perception of patient safety culture in South Korean general hospitals: a cross-sectional study
Authors: Kwan M. R. , Seo H. J. , Lee S. J. 
Published: October 2021

Abstract
Background
Hospital accreditation programs can positively affect nurses’ perceptions of patient safety culture. However, no previous research has identified the association between experience of hospital accreditation and nurses’ perception of patient safety culture in general hospitals. This study aims to examine 1) the level of perception of each area of patient safety culture in nurses working in general hospitals and 2) the relationship between experience of hospital accreditation and nurses’ overall perceptions of safety in Korean general hospitals.

Methods
A cross-sectional survey design was used, with a convenience sample of 310 nurses from six general hospitals. Nurses were asked to complete the self-reported Korean version of the Hospital Survey on Patient Safety Culture and the experience of hospital accreditation. A hierarchical multiple regression analysis was used to examine the associations between hospital accreditation experience and perception of patient safety culture.

Results
The patient safety composites with the highest positive response were the frequency of events reported (90.6) and supervisor/manager expectations promoting patient safety (69.4%). The composites with the lowest scores were non-punitive responses to errors (22.9%) and organizational learning/continuous improvement (35.5%). Hierarchical multiple regression analysis showed that the experience of hospital accreditation had a very small increase on overall perceptions of safety (β = 0.097, p = 0.023).

Conclusions
This study found that general hospital nurses’ experience of hospital accreditation had very weak relationship with their overall perceptions of patient safety. Therefore, a longitudinal study is needed to confirm the influence of hospital accreditation on nurses’ patient safety culture in general hospitals.
A costing analysis of B-GAP: index-linked HIV testing for children and adolescents in Zimbabwe
Authors: Vasantharoopan Arthi , Maheswaran Hendramoorthy , Simms Victoria , Dziva Chikwari Chido , Chigwenah Tariro , Chikodzore Rudo , Nyathi Khulamuzi , Ncube Gertrude , Ferrand Rashida A. , Guinness Lorna 
Published: October 2021

AbstractBackgroundBy testing children and adolescents of HIV positive caretakers, index-linked HIV testing, a targeted HIV testing strategy, has the ability to identify high risk children and adolescents earlier and more efficiently, compared to blanket testing. We evaluated the incremental cost of integrating index-linked HIV testing via three modalities into HIV services in Zimbabwe.MethodsA mixture of bottom-up and top-down costing was employed to estimate the provider cost per test and per HIV diagnosis for 2–18 year olds, through standard of care testing, and the incremental cost of index-linked HIV testing via three modalities: facility-based testing, home-based testing by a healthcare worker, and testing at home by the caregiver using an oral mucosal transudate test. In addition to interviews, direct observation and study process data, facility registries were abstracted to extract outcome data and resource use. Costs were converted to 2019 constant US$.ResultsThe average cost per standard of care test in urban facilities was US$5.91 and US$7.15 at the rural facility. Incremental cost of an index-linked HIV test was driven by the uptake and number of participants tested. The lowest cost approach in the urban setting was home-based testing (US$6.69) and facility-based testing at the rural clinic (US$5.36). Testing by caregivers was almost always the most expensive option (rural US$62.49, urban US$17.49).ConclusionsThis is the first costing analysis of index-linked HIV testing strategies. Unit costs varied across sites and with uptake. When scaling up, alternative testing solutions that increase efficiency such as index-linked HIV testing of the entire household, as opposed to solely targeting children/adolescents, need to be explored.
Organizational factors associated with health worker protection during the COVID-19 pandemic in four provinces of South Africa
Authors: Zungu Muzimkhulu , Voyi Kuku , Mlangeni Nosimilo , Moodley Saiendhra Vasudevan , Ramodike Jonathan , Claassen Nico , Wilcox Elizabeth , Thunzi Nkululeko , Yassi Annalee , Spiegel Jerry , Malotle Molebogeng 
Published: October 2021

AbstractBackgroundHealth workers, in short supply in many low-and-middle-income countries, are at increased risk of SARS-CoV-2 infection. This study aimed to assess how South Africa, prepared to protect its health workers from SARS-CoV-2 infection.MethodsThis was a cross-sectional study design applying participatory action research in four provinces of South Africa. A semi-structured questionnaire and a qualitative observational HealthWISE walkthrough risk assessment was carried out to collect data on occupational safety and health (OSH) systems in 45 hospitals across four provinces to identify factors associated with health worker protection. Adapting the International Labour Organization (ILO) and World Health Organization (WHO) HealthWISE tool, we compiled compliance scores through walkthrough surveys. We used logistic regression to analyze the relationship between readiness indicators and the actual implementation of protective measures.ResultsWe found that health facilities in all four provinces had SARS-CoV-2 plans for the general population but no comprehensive OHS plan for health workers. Provincial Departments of Health (PDoH) varied in how they were organized to respond: Provinces A and D had an OSH SARS-CoV-2 provincial coordinating team and a dedicated budget for occupational health; Province A had an occupational health doctor and nurse; while Province B had an occupational health nurse; Province A and D PDoHs had functional OSH committees; and Province D had conducted some health risk assessments specific to SARS-CoV-2. However, none of the assessed health facilities had an acceptable HealthWISE compliance score (≥ 75%) due to poor ventilation and inadequate administrative control measures. While the supply of personal protective equipment was adequate, it was often not worn properly. Our study found that having an OSH SARS-CoV-2 policy was significantly associated with higher personal protective equipment and ventilation scores. In addition, our analysis showed that hospitals with higher compliancescores had significantly lower infection rates (IRR 0.98; 95% CI: 0.97, 0.98).ConclusionsDespite some initial preparedness, greater effort to protect health workers is still warranted. Low-and-middle-income countries may need to pay more attention to OSH systems and consider using tools, such as ILO/WHO HealthWISE tool, to protect health workers’ health.
Contextual and mental health service factors in mental disorder-based disability pensioning in Finland – a regional comparison
Authors: Karolaakso Tino , Autio Reija , Näppilä Turkka , Leppänen Helena , Rissanen Päivi , Tuomisto Martti T. , Karvonen Sakari , Pirkola Sami 
Published: October 2021

Abstract
Background
We investigated the regional differences in all mental disorder disability pensions (DP) between 2010 and 2015 in Finland, and separately in mood disorders and non-affective psychotic disorder DP. We also studied the contribution of several district-level contextual and mental health service factors to mental disorder DP.

Methods
Subjects were all those granted mental disorder DP for the first time between 2010 and 2015 in Finland (N = 36,879). Associations between the district-level contextual and mental health service factors and regional DP risks collected from the year 2015 were studied with negative binomial regression analysis in the Finnish hospital districts. The population number on the age (18 to 65 years), gender, occupational status and residential hospital district of the Finnish population from 2015 was used as exposure in the model.

Results
Significant differences in the regional mental disorder DP risks between and within hospital districts did not appear to follow the traditional Finnish health differences. A lower risk of DP was associated with contextual indicators of higher regional socioeconomic level. Furthermore, population density as a proxy for access to mental health services indicated a higher regional DP risk for lower density in all mental (IRR 1.10; 95% CI 1.06–1.14) and mood disorder (IRR 1.12; 95% CI 1.08–1.16) DP. Both the highest and the lowest regional numbers of all mental health outpatient visits were associated with a higher DP risk in all mental and mood disorder DP, whereas particularly low regional numbers of inpatient treatment periods and of patients were associated with a lower risk of DP.

Conclusions
In this comprehensive population-level study, we found evidence of significant regional variation in mental disorder DP and related district-level factors. This variation may at least partly relate to differences in regional mental health service systems and treatment practices. Adapting to the needs of the local population appears to be indicated for both regional mental health service systems and treatment practices to achieve optimal performance.