bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lessons learned: establishing a CLIA-equivalent laboratory for targeted mass spectrometry assays – navigating the transition from research to clinical practice
Authors: Han Chia-Li , Lai Chi-Ting , Reyes Aaron James , Yang Hao-Chin , Lu Jin-Ying , Shih Shyang-Rong , Chen Kuen-Yuan , Hoofnagle Andrew N. , Yu Sung-Liang , Bocik William , Hiltke Tara , Chiu Huan-Chi , Wan Ching-Yi , Rodriguez Henry , Zhang Victoria , Chen Yu-Ju 
Published: February 2024

AbstractMass spectrometry (MS) assays offer exceptional capabilities in high multiplexity, specificity, and throughput. As proteomics technologies continue advancements to identify new disease biomarkers, transition of these innovations from research settings to clinical applications becomes imperative. To meet the rigorous regulatory standards of clinical laboratories, development of a clinical protein MS assay necessitates adherence to stringent criteria. To illustrate the process, this project focused on using thyroglobulin (Tg) as a biomarker and an immuno-multiple reaction monitoring (iMRM) MS-based assay as a model for establishing a Clinical Laboratory Improvement Amendments (CLIA) compliant laboratory within the Centers of Genomic and Precision Medicine, National Taiwan University. The chosen example also illustrates the clinical utility of MS assays to complement conventional immunoassay-based methods, particularly in cases where the presence of autoantibodies in 10–30% of patients hinders accuracy. The laboratory design entails a comprehensive coordination in spatial layout, workflow organization, equipment selection, ventilation systems, plumbing, electrical infrastructure, documentation procedures, and communication protocols. Practical aspects of the transformation process, including preparing laboratory facilities, testing environments, instrument validation, assay development and validation, quality management, sample testing, and personnel competency, are discussed. Finally, concordant results in proficiency testing demonstrate the harmonization with the University of Washington Medical Center and the quality assurance of the CLIA-equivalent Tg-iMRM MS assay established in Taiwan. The realization of this model protein MS assay in Taiwan highlights the feasibility of international joint development and provides a detailed reference map to expedite the implementation of more MS-based protein assays in clinical laboratories for patient care.
Global prevalence and burden of multidrug-resistant tuberculosis from 1990 to 2019
Authors: Lv Hengliang , Zhang Xin , Zhang Xueli , Bai Junzhu , You Shumeng , Li Xuan , Li Shenlong , Wang Yong , Zhang Wenyi , Xu Yuanyong 
Published: February 2024

Abstract
Background
Tuberculosis(TB) remains a pressing public health challenge, with multidrug-resistant tuberculosis (MDR-TB) emerging as a major threat. And healthcare authorities require reliable epidemiological evidence as a crucial reference to address this issue effectively. The aim was to offer a comprehensive epidemiological assessment of the global prevalence and burden of MDR-TB from 1990 to 2019.

Methods
Estimates and 95% uncertainty intervals (UIs) for the age-standardized prevalence rate (ASPR), age-standardized incidence rate (ASIR), age-standardized disability-adjusted life years rate (ASR of DALYs), and age-standardized death rate (ASDR) of MDR-TB were obtained from the Global Burden of Disease (GBD) 2019 database. The prevalence and burden of MDR-TB in 2019 were illustrated in the population and regional distribution. Temporal trends were analyzed by using Joinpoint regression analysis to calculate the annual percentage change (APC), average annual percentage change (AAPC) and its 95% confidence interval(CI).

Results
The estimates of the number of cases were 687,839(95% UIs: 365,512 to 1223,262), the ASPR were 8.26 per 100,000 (95%UIs: 4.61 to 15.20), the ASR of DALYs were 52.38 per 100,000 (95%UIs: 22.64 to 97.60) and the ASDR were 1.36 per 100,000 (95%UIs: 0.54 to 2.59) of MDR-TB at global in 2019. Substantial burden was observed in Africa and Southeast Asia. Males exhibited higher ASPR, ASR of DALYs, and ASDR than females across most age groups, with the burden of MDR-TB increasing with age. Additionally, significant increases were observed globally in the ASIR (AAPC = 5.8; 95%CI: 5.4 to 6.1; P < 0.001), ASPR (AAPC = 5.9; 95%CI: 5.4 to 6.4; P < 0.001), ASR of DALYs (AAPC = 4.6; 95%CI: 4.2 to 5.0; P < 0.001) and ASDR (AAPC = 4.4; 95%CI: 4.0 to 4.8; P < 0.001) of MDR-TB from 1990 to 2019.

Conclusions
This study underscored the persistent threat of drug-resistant tuberculosis to public health. It is imperative that countries and organizations worldwide take immediate and concerted action to implement measures aimed at significantly reducing the burden of TB.
Trends of Mycobacterium tuberculosis and Rifampicin resistance in Northwest Ethiopia: Xpert® MTB/RIF assay results from 2015 to 2021
Authors: Biset Sirak , Teferi Milto , Alamirew Haylemesikel , Birhanu Biniyam , Dessie Awoke , Aschale Abebe , Haymanot Anmaw , Dejenie Selamu , Gebremedhin Teshager , Abebe Wondwossen , Adane Gashaw 
Published: February 2024

Abstract
Background
Tuberculosis (TB) remains one of the leading causes of morbidity and mortality worldwide, particularly in countries with limited resources. The emergence of drug resistance in mycobacterium tuberculosis (MTB), particularly rifampicin (RIF) resistance, hindered TB control efforts. Continuous surveillance and regular monitoring of drug-resistant TB, including rifampicin resistance (RR), are required for effective TB intervention strategies and prevention and control measures.

Objective
Determine the trend of TB and RR-TB among presumptive TB patients in Northwest Ethiopia.

Method
A retrospective study was conducted at the University of Gondar Comprehensive Specialized Hospital (UoG-CSH). The study included TB registration logbook data from all patients who visited the hospital and were tested for MTB using the Xpert® MTB/RIF assay between 2015 and 2021. The SPSS version 26 software was used to enter, clean, and analyze the laboratory-based data.

Results
A total of 18,787 patient results were included, with 93.8% (17,615/18787) of them being successful, meaning they were not invalid, error, or aborted. About 10.5% (1846/17615) of the 17,615 results were MTB-positive, with 7.42% (137/1846) RIF resistant. Age, anti-TB treatment history, and diagnosis year were associated with the presence of MTB and RR-MTB. Tuberculosis (TB) prevalence was higher in productive age groups, whereas RR-TB prevalence was higher in the elderly. Regarding diagnosis year, the prevalence of TB and RR-TB showed a declining trend as the year progressed. While MTB was detected in 12.8% (471/3669) of new and 22.2% (151/679) of re-treatment presumptive TB patients, RR-MTB was detected in 8.5% (40/471) of new and 18.5% (28/151) of re-treatment TB cases.

Conclusion
The prevalence of TB and RR-TB in the study area showed a declining trend over the years. While TB was more prevalent in productive age groups (15 to 45 years), RR-TB was more prevalent in older populations (over 45 years), than others. Moreover, patients with a history of anti-TB drug exposure were more likely to be positive for DR-TB, highlighting the need to strengthen DOT programs for proper management of TB treatment.
Age-disparate and intergenerational sex partnerships and HIV: the role of gender norms among adolescent girls and young women in Malawi
Authors: Reed Domonique M. , Radin Elizabeth , Kim Evelyn , Wadonda-Kabondo Nellie , Payne Danielle , Gillot Myrline , Jahn Andreas , Bello George , Kalua Thokozani , Justman Jessica E. 
Published: February 2024

Abstract
Background
Age-mixing (age-disparate [5–9 years difference] and intergenerational [≥ 10 years difference]) partnerships are hypothesized drivers of HIV in adolescent girls and young women (AGYW; 15–24 years). These partnerships are often associated with increased gender inequities which undermine women’s agency and assertiveness. We assessed whether age-mixing partnerships were associated with HIV in Malawi and if endorsement of inequitable gender norms modifies this relationship.

Methods
We analyzed data from the Malawi Population-based HIV Impact Assessment, a nationally representative household survey conducted in 2015–2016. Participants underwent HIV testing and completed questionnaires related to actively endorsed gender norms and sexual risk behavior. We used multivariate logistic regression and multiplicative interaction to assess associations among AGYW who reported the age of their primary sex partner from the last year.

Results
The analysis included 1,958 AGYW (mean age = 19.9 years, SD = 0.1), 459 (23.4%) and 131 (6.7%) of whom reported age-disparate and intergenerational partnerships, respectively. AGYW in age-mixing partnerships accounted for 13% of all AGYW and were older, more likely to reside in urban areas, to be married or cohabitating with a partner, and to have engaged in riskier sexual behavior compared with AGYW in age-concordant partnerships (p < 0.05). HIV prevalence among AGYW in age-disparate and intergenerational partnerships was 6.1% and 11.9%, respectively, compared with 3.2% in age-concordant partnerships (p < 0.001). After adjusting for residence, age, education, employment, wealth quintile, and ever been married or cohabitated as married, AGYW in age-disparate and intergenerational partnerships had 1.9 (95% CI: 1.1–3.5) and 3.4 (95% CI: 1.6–7.2) greater odds of HIV, respectively, compared with AGYW in age-concordant partnerships. Among the 614 (31% of the study group) who endorsed inequitable gender norms, AGYW in age-disparate and intergenerational partnerships had 3.5 (95% CI: 1.1–11.8) and 6.4 (95% CI: 1.5–27.8) greater odds of HIV, respectively, compared with AGYW in age-concordant partnerships.

Conclusions
In this Malawi general population survey, age-mixing partnerships were associated with increased odds of HIV among AGYW. These findings highlight inequitable gender norms as a potential focus for HIV prevention and could inform interventions targeting structural, cultural, and social constraints of this key group.
Immune Dysregulation in SARS-CoV-2 patients coinfected with Mycobacterium tuberculosis (Mtb) or HIV in China
Authors: Li Lei , Zhang Jianxiang , Sun Ranran , Liu Hong , Cheng Genyang , Fan Feifei , Wang Chong , Li Ang , Liang Hongxia , Yu Zujiang , Wang Guiqiang , Ren Zhigang 
Published: February 2024

Abstract
Background
SARS-CoV-2 infections usually cause immune dysregulation in the human body. Studies of immunological changes resulting from coinfections with Mycobacterium tuberculosis (Mtb) or HIV are limited.

Methods
We conducted a retrospective study focusing on patients with COVID-19. A total of 550 patients infected with SARS-CoV-2 were enrolled in our study and categorized into four groups based on the presence of coinfections; 166 Delta-infected patients, among whom 103 patients had no coinfections, 52 who were coinfected with Mtb, 11 who were coinfected with HIV, and 384 Omicron-infected patients. By collecting data on epidemiologic information, laboratory findings, treatments, and clinical outcomes, we analyzed and compared clinical and immunological characteristics.

Results
Compared with those in the Delta group, the median white blood cell, CD4 + T-cell and B-cell counts were lower in the Mtb group and the HIV group. Except for those in the Omicron group, more than half of the patients in the three groups had abnormal chest CT findings. Among the three groups, there were no significant differences in any of the cytokines. Compared with those in the Delta group, the disease duration and LOS were longer in the Mtb group and the HIV group. For unvaccinated Delta-infected patients, in the Mtb and HIV groups, the number of B cells and CD4 + T cells was lower than that in the Delta group, with no significant difference in the LOS or disease duration. In the Mtb group, three (6%) patients presented with a disease duration greater than four months and had decreased lymphocyte and IL17A counts, possibly due to double infections in the lungs caused by SARS-CoV-2 and M. tuberculosis.

Conclusions
We found that SARS-CoV-2 patients coinfected with Mtb or HIV exhibited a longer disease duration and longer LOS, with a decrease in B cells and CD4 + T cells, suggesting that these cells are related to immune function. Changes in cytokine levels suggest that coinfection with Mtb or HIV does not result in dysregulation of the immune response. Importantly, we discovered a chronic course of coinfection involving more than four months of Mtb and SARS-CoV-2 infection.
Exploration of the factors influencing the quality of life among adolescents during the COVID-19 pandemic: the data from a cross-sectional study in Shandong
Authors: Li Hongjin , Yang Zhiping , You Libin , Liu Shaojie 
Published: February 2024

Abstract
Background
The COVID-19 pandemic has sparked unprecedented transformations in the lives of adolescents, with reshaping their routines, social dynamics, educational experiences, and overall well-being. Our study delves into the influence of various factors on adolescents’ quality of life (QOL) among the COVID-19 pandemic in Shandong Province, China.

Methods
Employing a cross-sectional research approach combined with multivariable analysis, we scrutinize the association of demographic factors (age, gender, education level, ethnic groups, urban area, and family economic status) and health-related behaviors (sleep duration, and self-reported health status) with QOL in 9953 students.

Results
During the pandemic, the average QOL for adolescents in Shandong Province was 133. Our analysis revealed that sleep duration and age had statistically significant associations with total QOL, with the OR values of 1.43 (95% confidence interval (CI): 1.03 to 1.83) and 0.44 (95% CI: 0.19 to 0.70), respectively. Notably, we observed that adolescents from economically disadvantaged families, or those with poorer self-reported health status, were more likely to report lower QOL scores.

Conclusions
Overall, our study highlights the potential association of sleep duration, age, family economic status, and self-reported health with the QOL of adolescents in Shandong Province during the pandemic. During similar public health crises, policymakers, educators, and healthcare providers can actively work through resource allocation and effective intervention measures towards alleviating financial burdens, improving health conditions, and ultimately enhancing the total QOL for adolescents.
Burden of colorectal cancer and its risk factors in the North Africa and Middle East (NAME) region, 1990–2019: a systematic analysis of the global burden of disease study
Authors: Haghighatdoost Fahimeh , Mehrabani-Zeinabad Kamran , Hajihashemi Parisa , Mohammadifard Noushin , Adibi Peyman 
Published: February 2024

Abstract
Objective
The geographical differences in incidence rates of colorectal cancer (CRC) and its burden due to modifiable risk factors warrant investigating the CRC burden and its risk factors in different regions. In the current study, we aimed to estimate the burden of CRC and the share of its risk factors in the North Africa and Middle East (NAME), from 1990 to 2019.

Study design
Systematic review.

Methods
The rates of incidence, prevalence, death, years of life lost (YLL), years lived with disability (YLD), and disability adjusted life years (DALYs) of CRC were estimated through the framework of the Global Burden of Diseases (GBD), Injuries and Risk Factors Study 2019 by age, sex, between 1990 and 2019. The CRC-related DALYs attributable to each lifestyle and metabolic risk factor was also estimated through a comparative risk assessment approach.

Results
In NAME region, the trends of incidence, prevalence, death, YLL, YLD, and DALYs of CRC were increasing, with higher rates in males than females over this period. High and high-middle socio-demographic index (SDI) countries had greater CRC DALYs rate compared with middle- and low-SDI countries in 2019, except for Palestine [434.66 (95% UI: 368.82, 503.88)]. In NAME region, like the global, dietary risk (33.18%), low whole grain intake (19.79%), and low intake of milk (15.77%) were the major contributing risk factors to DALYs due to CRC in 2019.

Conclusions
Due to increasing trend of CRC burden and the considerable role of lifestyle and metabolic factors in its burden in NAME region, implementing fundamental strategies to minimize CRC burden and its risk factors is imperative.
Loneliness among homeless-experienced older adults with cognitive or functional impairments: qualitative findings from the HOPE HOME study
Authors: Yuan Yeqing , Knight Kelly R. , Weeks John , King Stephen , Olsen Pamela , Kushel Margot 
Published: February 2024

Abstract
Background
Loneliness is more common in older adults and those who face structural vulnerabilities, including homelessness. The homeless population is aging in the United States; now, 48% of single homeless adults are 50 and older. We know little about loneliness among older adults who have experienced homelessness. We aimed to describe the loneliness experience among homeless-experienced older adults with cognitive and functional impairments and the individual, social, and structural conditions that shaped these loneliness experiences.

Methods
We purposively sampled 22 older adults from the HOPE HOME study, a longitudinal cohort study among adults aged 50 years or older experiencing homelessness in Oakland, California. We conducted in-depth interviews about participants perceived social support and social isolation. We conducted qualitative content analysis.

Results
Twenty participants discussed loneliness experience, who had a median age of 57 and were mostly Black (80%) and men (65%). We developed a typology of participants’ loneliness experience and explored the individual, social, and structural conditions under which each loneliness experience occurred. We categorized the loneliness experience into four groups: (1) “lonely– distressed”, characterized by physical impairment and severe isolation; (2) “lonely– rather be isolated”, reflecting deliberate social isolation as a result of trauma, marginalization and aging-related resignation; (3) “lonely– transient”, as a result of aging, acceptance and grieving; and (4) “not lonely”– characterized by stability and connection despite having experienced homelessness.

Conclusions
Loneliness is a complex and heterogenous social phenomenon, with homeless-experienced older adults with cognitive or functional impairments exhibiting diverse loneliness experiences based on their individual life circumstances and needs. While the most distressing loneliness experience occurred among those with physical impairment and mobility challenges, social and structural factors such as interpersonal and structural violence during homelessness shaped these experiences.
Perceptions of Pre-exposure Prophylaxis (PrEP) for HIV prevention among men living with HIV in the context of reproductive goals in South Africa: a qualitative study
Authors: Ntinga Xolani , Isehunwa Oluwaseyi O. , Msimango Lindani I. , Smith Patricia M. , Matthews Lynn T. , Van Heerden Alastair 
Published: February 2024

Abstract
Background
Pre-exposure Prophylaxis (PrEP) and Treatment as Prevention (TasP) are effective strategies to prevent HIV transmission within serodifferent couples. However, limited usage of PrEP, knowledge and interest has been amongst the barriers for men, alongside testing and treatment adherence. We explored the perceptions of PreP for HIV prevention with Men living with HIV (MWH) who have reproductive goals, to understand awareness and experiences related to PrEP use in the context of HIV prevention with their partners.

Methods
We undertook a qualitative study with 25 MWH aged 18 to 65 between April and September 2021 in South Africa. Potential participants were screened for eligibility and scheduled to participate in telephonic interviews. Interviews were audio recorded, transcribed, translated and thematically analysed.

Results
Themes were organized into opportunities and barriers that men with HIV articulate as important for using PrEP to meet individual, couple, and community reproductive goals. At the individual level, some men were willing to discuss PrEP with their partners to protect their partners and babies from acquiring HIV. Lack of knowledge about PrEP among men was a potential barrier to promoting PrEP among their female partners. At the couple level, PrEP use was seen as a way to strengthen relationships between partners, signifying care, trust, and protection and was seen as a tool to help serodifferent couples meet their reproductive goals safely. At the community level, PrEP was viewed as a tool to promote HIV testing and prevention efforts, especially among men, but participants emphasized the need for more education and awareness.

Conclusion
Despite PrEP implementation in South Africa, awareness of PrEP among men with HIV in rural areas remains low. Engaging MWH to support their partners in accessing PrEP could be an innovative strategy to promote HIV prevention. Additionally, providing men with comprehensive reproductive health information can empower them to make more informed decisions, adopt safer sexual practices, and challenge societal norms and stigmas around HIV.
Limited use of virtual reality in primary care physiotherapy for patients with chronic pain
Authors: Slatman Syl , Staal J. Bart , van Goor Harry , Ostelo Raymond , Soer Remko , Knoop Jesper 
Published: February 2024

Abstract
Background
Chronic pain is a disabling condition which is prevalent in about 20% of the adult population. Physiotherapy is the most common non-pharmacological treatment option for chronic pain, but often demonstrates unsatisfactory outcomes. Virtual Reality (VR) may offer the opportunity to complement physiotherapy treatment. As VR has only recently been introduced in physiotherapy care, it is unknown to what extent VR is used and how it is valued by physiotherapists. The aim of this study was to analyse physiotherapists’ current usage of, experiences with and physiotherapist characteristics associated with applying therapeutic VR for chronic pain rehabilitation in Dutch primary care physiotherapy.

Methods
This online survey applied two rounds of recruitment: a random sampling round (873 physiotherapists invited, of which 245 (28%) were included) and a purposive sampling round (20 physiotherapists using VR included). Survey results were reported descriptively and physiotherapist characteristics associated with VR use were examined using multivariable logistic regression analysis.

Results
In total, 265 physiotherapists participated in this survey study. Approximately 7% of physiotherapists reported using therapeutic VR for patients with chronic pain. On average, physiotherapists rated their overall experience with therapeutic VR at 7.0 and “whether they would recommend it” at 7.2, both on a 0–10 scale. Most physiotherapists (71%) who use therapeutic VR started using it less than two years ago and use it for a small proportion of their patients with chronic pain. Physiotherapists use therapeutic VR for a variety of conditions, including generalized (55%), neck (45%) and lumbar (37%) chronic pain. Physiotherapists use therapeutic VR mostly to reduce pain (68%), improve coordination (50%) and increase physical mobility (45%). Use of therapeutic VR was associated with a larger physiotherapy practice (OR = 2.38, 95% CI [1.14–4.98]). Unfamiliarity with VR seemed to be the primary reason for not using VR.

Discussion
Therapeutic VR for patients with chronic pain is in its infancy in Dutch primary care physiotherapy practice as only a small minority uses VR. Physiotherapists that use therapeutic VR are modestly positive about the technology, with large heterogeneity between treatment goals, methods of administering VR, proposed working mechanisms and chronic pain conditions to treat.