bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outbreak detection in Harar town and Kersa district, Ethiopia using phylogenetic analysis and source attribution
Authors: Thystrup Cecilie , Hald Tine , Belina Dinaol , Gobena Tesfaye 
Published: August 2024

Abstract
Background
Foodborne diseases (FBDs) represent a significant risk to public health, with nearly one in ten people falling ill every year globally. The large incidence of foodborne diseases in African low- and middle-income countries (LMIC) shows the immediate need for action, but there is still far to a robust and efficient outbreak detection system. The detection of outbreak heavily relies on clinical diagnosis, which are often delayed or ignored due to resource limitations and inadequate surveillance systems.

Methods
In total, 68 samples of non-typhoidal Salmonella isolates from human, animal and environmental sources collected between November 2021 and January 2023 were analyzed using sequencing methods to infer phylogenetic relationships between the samples. A source attribution model using a machine-learning logit-boost that predicted the likely source of infection for 20 cases of human salmonellosis was also run and compared with the results of the cluster detection.

Results
Three clusters of samples with close relation (SNP difference < 30) were identified as non-typhoidal Salmonella in Harar town and Kersa district, Ethiopia. These three clusters were comprised of isolates from different sources, including at least two human isolates. The isolates within each cluster showed identical serovar and sequence type (ST), with few exceptions in cluster 3. The close proximity of the samples suggested the occurrence of three potential outbreaks of non-typhoidal Salmonella in the region. The results of the source attribution model found that human cases of salmonellosis could primarily be attributed to bovine meat, which the results of the phylogenetic analysis corroborated.

Conclusions
The findings of this study suggested the occurrence of three possible outbreaks of non-typhoidal Salmonella in eastern Ethiopia, emphasizing the importance of targeted intervention of food safety protocols in LMICs. It also highlighted the potential of integrated surveillance for detecting outbreak and identifying the most probable source. Source attribution models in combination with other epidemiological methods is recommended as part of a more robust and integrated surveillance system for foodborne diseases.
Government funded suicide prevention in Australia – an environmental scan
Authors: Bassilios Bridget , Currier Dianne , Krysinska Karolina , Dunt David , Machlin Anna , Newton Danielle , Williamson Michelle , Pirkis Jane 
Published: August 2024

Abstract
Background
Suicide is a worldwide public health problem. In response to this problem, Australia was one of the first countries to develop national suicide prevention policy. Guided by the National Suicide Prevention Office (NSPO), which was established in 2021, suicide prevention in Australia is in a period of reform. The NSPO is driving a nationally consistent and integrated approach to suicide prevention including leading the development of a new National Suicide Prevention Strategy. This article summarises findings from an environmental scan of government-led suicide prevention in Australia, conducted as an input for the development of the new Strategy.

Methods
The scan was conducted from August 2022 to January 2023. We searched relevant government websites and Google to identify policy documents and programs and services. We undertook a desktop review of documents and programs/services using coding templates developed to address the objectives of the scan. Qualitative information was extracted in a systematic manner using these templates.

Results
Australia’s suicide prevention efforts are significant as demonstrated by activities ranging from policy documents intended to guide and plan activity, the National Mental Health and Suicide Prevention Agreement committing the Federal Government and jurisdictions to work together, and the availability of national, state, local area based, and digital services and programs. Suicide prevention approaches in Australia are mostly selective or indicated. There is less emphasis on universal approaches, wellbeing promotion, strengthening protective factors and mitigating the impact of known drivers of distress. In addition, there is limited evidence to demonstrate a whole-of-government or whole-of-system approach is operating in Australia. Findings should be interpreted in the context that suicide prevention in Australia is currently in a period of transition.

Conclusions
Current government emphasis on and investment in suicide prevention activity, together with strong commitment to lived experience and cross sectorial collaboration, are substantial and appropriate. There are also many opportunities to further progress cross-portfolio and cross-jurisdiction suicide prevention and response efforts. This requires urgently adopting a shared understanding of suicide, which includes the diverse drivers of suicidal distress, and improving protective factors and social wellbeing.
Learning effect of online versus onsite education in health and medical scholarship – protocol for a cluster randomized trial
Authors: Raffing Rie , Konge Lars , Tønnesen Hanne 
Published: August 2024

Abstract
Background
The disruption of health and medical education by the COVID-19 pandemic made educators question the effect of online setting on students’ learning, motivation, self-efficacy and preference. In light of the health care staff shortage online scalable education seemed relevant. Reviews on the effect of online medical education called for high quality RCTs, which are increasingly relevant with rapid technological development and widespread adaption of online learning in universities. The objective of this trial is to compare standardized and feasible outcomes of an online and an onsite setting of a research course regarding the efficacy for PhD students within health and medical sciences: Primarily on learning of research methodology and secondly on preference, motivation, self-efficacy on short term and academic achievements on long term. Based on the authors experience with conducting courses during the pandemic, the hypothesis is that student preferred onsite setting is different to online setting.

Methods
Cluster randomized trial with two parallel groups. Two PhD research training courses at the University of Copenhagen are randomized to online (Zoom) or onsite (The Parker Institute, Denmark) setting. Enrolled students are invited to participate in the study. Primary outcome is short term learning. Secondary outcomes are short term preference, motivation, self-efficacy, and long-term academic achievements. Standardized, reproducible and feasible outcomes will be measured by tailor made multiple choice questionnaires, evaluation survey, frequently used Intrinsic Motivation Inventory, Single Item Self-Efficacy Question, and Google Scholar publication data. Sample size is calculated to 20 clusters and courses are randomized by a computer random number generator. Statistical analyses will be performed blinded by an external statistical expert.

Discussion
Primary outcome and secondary significant outcomes will be compared and contrasted with relevant literature. Limitations include geographical setting; bias include lack of blinding and strengths are robust assessment methods in a well-established conceptual framework. Generalizability to PhD education in other disciplines is high. Results of this study will both have implications for students and educators involved in research training courses in health and medical education and for the patients who ultimately benefits from this training.

Trial registration
Retrospectively registered at ClinicalTrials.gov: NCT05736627. SPIRIT guidelines are followed.
Comparison of proton therapy and photon therapy for early-stage non-small cell lung cancer: a meta-analysis
Authors: He Junyi , Liu Yingxin , Zhang Xiaojing , Li Butuo , Yang Linlin , Wang Haohua , Wang Shijiang , Yu Jinming , Wang Linlin 
Published: August 2024

AbstractThe use of proton therapy (PT) in early-stage non-small cell lung cancer (ES-NSCLC) remains controversial, with insufficient evidence to determine its superiority over photon therapy (XRT). We conducted a systematic review of PT trials in ES-NSCLC, analyzing dosimetry, efficacy, and safety across to inform clinical decision-making. Our study showed that PT reduced lung and heart dosimetric parameters compared to XRT, with significant differences in lung V5, lung V10 and mean heart dose (MHD). In terms of efficacy, there were no significant differences in 1-year OS, 3-year OS and 3-year PFS between PT and XRT. For toxicity, no significant difference was observed in treatment-related adverse events (TRAEs) and radiation pneumonitis (RP). Single-arm analysis of PT found that V5, V10, V20 of lung and heart V5 were 13.4%, 11.3%, 7.9% and 0.7%, respectively. The mean lung dose and MHD were 4.15 Gy and 0.17 Gy, respectively. The single-arm pooled 1-, 2-, 3- and 5-year OS rates for PT were 95.3%, 82.5%, 81.3% and 69.3%, respectively. PFS rate and local control rate at 3 years were 68.1% and 91.2%, respectively. The rates of TRAEs of grade ≥ 3 and grade ≥ 2 were 2.8% and 19.8%, respectively. The grade ≥ 2 RP occurred at a rate of 8.7%. In conclusion, PT had acceptable efficacy and safety, and was better at protecting organs at risk than XRT in ES-NSCLC. However, the survival and safety benefit of PT was not significant compared to XRT.
Impact of Previous Surgery and/or Radiation Therapy on Endoscopic Reconstruction Outcomes
Authors: Snyder Rita , Rubino Franco , Seaman Scott , Banu Matei , Su Shirley Y. , Hanna Ehab Y. , DeMonte Franco , Raza Shaan M. 
Published: August 2024

BACKGROUND AND OBJECTIVES:
The impact of prior local therapies, including radiation and surgery, on reconstruction outcomes after endonasal surgery is currently not well known. Reconstruction nuances in the preoperative setting merit further evaluation to avoid potential postoperative complications that can hinder overall tumor management and negatively impact patient outcome. We sought to determine whether prior treatments increase risk of reconstruction-related postoperative morbidity and to evaluate the effectiveness of our current treatment paradigm for skull base reconstruction.

METHODS:
A retrospective review of all endonasal surgeries for tumor resection between March 2000 and March 2022 was performed. Patients were grouped based on treatment history. Patient demographics, operative, and postoperative reconstruction-related morbidity data were collected, including cerebrospinal fluid leak, sinonasal morbidity, and infectious complications. Variables significantly associated with postoperative complications in the univariate analysis were included in the multivariate Cox proportional hazards regression model. Complication-free survival curves were generated, and the log-rank test evaluated the relationship between complication-free survival and the different clinical, surgical, and treatment parameters. All statistical analyses were performed with SPSS 26 (IBM Corp) and Graph Pad 9.0 (GraphPad Software).

RESULTS:
A total of 418 patients were included. 291 patients had no prior treatments, 49 patients had previously received radiation, and 78 patients had prior surgeries. Of the 49 patients who had prior radiation, 27% underwent reconstruction with tunneled pericranial flaps vs 16% of treatment-naïve patients. On multivariate analysis, prior treatment was not significantly associated with reconstruction-related complications. Negative smoking history, no leak or small intraoperative leak, and use of vascularized flap in reconstruction were protective factors.

CONCLUSION:
In patients undergoing endonasal surgery, prior radiation and/or surgery does not appear to significantly increase the risk of immediate or delayed reconstruction complications using our current reconstructive management plan, which incorporates an upfront regional flap for high-risk cases.
Cerebro-spinal flow pattern in the cervical subarachnoid space of healthy volunteers: Influence of the spinal cord morphology
Authors: Leblond Lugdivine , Sudres Patrice , Evin Morgane 
Published: August 2024

Introduction
Toward further cerebro-spinal flow quantification in clinical practice, this study aims at assessing the variations in the cerebro spinal fluid flow pattern associated with change in the morphology of the subarachnoid space of the cervical canal of healthy humans by developing a computational fluid dynamics model.

Methods
3D T2-space MRI sequence images of the cervical spine were used to segment 11 cervical subarachnoid space. Model validation (time-step, mesh size, size and number of boundary layers, influences of parted inflow and inflow continuous velocity) was performed a 40-year-old patient-specific model. Simulations were performed using computational fluid dynamics approach simulating transient flow (Sparlart-Almaras turbulence model) with a mesh size of 0.6, 6 boundary layers of 0.05 mm, a time step of 20 ms simulated on 15 cycles. Distributions of components velocity and WSS were respectively analyzed within the subarachnoid space (intervertebral et intravertebral levels) and on dura and pia maters.

Results
Mean values cerebro spinal fluid velocity in specific local slices of the canal range between 0.07 and 0.17 m.s-1 and 0.1 and 0.3 m.s-1 for maximum values. Maximum wall shear stress values vary between 0.1 and 0.5 Pa with higher value at the middle of the cervical spine on pia mater and at the lower part of the cervical spine on dura mater. Intra and inter-individual variations of the wall shear stress were highlighted significant correlation gwith compression ratio (r = 0.76), occupation ratio and cross section area of the spinal cord.

Conclusion
The inter-individual variability in term of subarachnoid canal morphology and spinal cord position influence the cerebro-spinal flow pattern, highlighting the significance of canal morphology investigation before surgery.
Transition to Adulthood through Coaching and Empowerment in Rheumatology (TRACER): A feasibility study protocol
Authors: Reesor Emma , Borovsky Dorota , Herrington Julie , Jarvis Pamela , Clarke Megan , Berard Roberta , Beattie Karen , Batthish Michelle 
Published: August 2024

The transition from pediatric to adult care for patients with chronic disease is a vulnerable period, with risks of disengagement from care and subsequent complications of inadequately managed disease. This period comes at a time when there are many other transitions occurring in the young person’s life, including changes to vocation, social supports, and to their physiology. The aim of the TRACER study is to assess the feasibility of conducting a multi-center, randomized-controlled trial of a virtual Transition Coach Intervention in youth transferring from pediatric to adult rheumatology care. Patients are being recruited at their last pediatric rheumatology visit from McMaster Children’s Hospital and Children’s Hospital, London Health Sciences Centre in Ontario, Canada. Participants are then randomized to standard of care or to eight transition coaching sessions, covering topics around health management, future planning, and self-advocacy. The primary outcomes of the study are to demonstrate protocol feasibility, including optimal recruitment and consent rates, ≥ 90% coaching session completion, and complete data collection with ≤ 5% missing data. Baseline demographics, transition readiness, global functional assessment, disease activity, and self-efficacy will be collected to characterize the study population. Recruitment has begun and is estimated to last 19 months. This study will inform the design of a robust, multi-centered, randomized-controlled study to investigate the impact of a virtual transition coaching program in supporting the physical, mental, and social well-being of youth with rheumatic disease transitioning into adult care.
Clinical trial registration: ClinicalTrials.Gov protocol ID: 14499
Survival and predictors of mortality among colorectal cancer patients on follow-up in Hawassa University Comprehensive Specialized Hospital, Sidama region, Southern Ethiopia, 2022. A 5-year retrospective cohort study
Authors: Balta Bargude , Taylor Lesley , Bogale Netsanet , Hailu Dejene , Zerhouni Yasmin A. 
Published: August 2024

Background
The incidence and mortality of colorectal cancer were still rising rapidly in many low-income and middle-income countries, which was linked to ongoing societal and economic status. Colorectal cancer is the leading cancer in Ethiopia with relatively lower survival. However, colorectal cancer patients’ survival time and predictors have not been well studied in Southern Ethiopia.

Objective
This study aimed to assess five-year survival and predictors of mortality among colorectal cancer patients at Hawassa Comprehensive Specialized Hospital, Ethiopia.

Method
Facility-based retrospective cohort study was conducted among 323 patients who visited Hawassa Comprehensive Specialized Hospital from May 1st, 2017 to April 30th, 2022. The Kaplan-Meier survival curve with the Log-rank test was used to estimate the survival time. Bivariable and multivariable Cox proportional hazards regression models were used to determine the net effect of each independent variable on time to death after diagnosis.

Result
Over the 5-year observation period, the overall mortality rate was 38.5%, with an incidence density of 31 fatalities per 100 person-years observation. Survival at 1, 2, 3, 4, and 5 years was 78%, 53, 32.4%, 23.3%, and 18.7% respectively. The multivariable analysis showed that metastatic disease (AHR = 4.2, CI: 1.5–11.5), baseline carcinoembryonic antigen level ≥5ng/ml (AHR: 2.4, CI: 1.2–5.8), living in rural areas (AHR = 2.2, CI:1.03–4.8) and mucinous carcinoma (AHR = 0.33, CI: 0.13–0.87) were independent predictors of colorectal cancer mortality.

Conclusion
Overall survival of colorectal cancer patients in the study was low compared to similar studies in developing and developed worlds. A significantly low survival rate was observed for patients with advanced stage, elevated carcinoembryonic antigen levels, and rural residents indicating the key role of early detection and timely initiation of treatment to improve survival and quality of life of patients with colorectal cancer.
Situational assessment and epidemiology of HIV, HBV and HCV among people who use and inject drugs in Ghana
Authors: Guure Chris , Dery Samuel , Baptista da Silva Carlota , Asamoah-Adu Comfort , Ayisi-Addo Stephen , Diaba Kofi , Loglo Maria-Goretti , Mohammed Adamu , Sarpong Yaw Akrasi , Hanu Samuel , Torpey Kwasi 
Published: August 2024

Introduction
People who inject drugs (PWID) and people who use drugs (PWUD) are an important population group that remain under-served in Ghana. Though PWID and PWUD are among the key populations most-at-risk to acquire sexually transmitted or blood-borne diseases, they are among those with the least access to human immunodeficiency (HIV), hepatitis B (HBV) and hepatitis C (HCV) viruses’ prevention, care and treatment services in Ghana due to lack of data on them. We provide a rapid assessment of the PWUD and PWID situation in Ghana.

Methods
This rapid cross-sectional design undertook consultative meetings between the study team and relevant stakeholders, including Civil Society Organizations (CSO) working with PWUD/PWID. The assessment considered a representative sample of PWID and PWUD. It was conducted in four (4) selected regions of Ghana (Greater Accra, Ashanti, Western, and Northern). Overall, 323 participants were interviewed using respondent-driven sampling (RDS) approach. Information obtained from participants were demographics, HIV risk behaviors, human immunodeficiency (HIV) and sexually transmitted infections (STI)-related knowledge HIV/HCV/HBV screening, attitude, and practices among others. Analyses were conducted using Stata version 17 and RDSAT version 7.1.46 software.

Findings
Drug use was found to be more prevalent among the youth with a median age of 37 years. Majority of the respondents were males (86%). About 28% of the female respondents identified themselves as sex workers, while about 74% have been involved in transactional sex. The median age at which respondents started using and injecting drugs was 20 and 22 years respectively. Majority (68%) of the respondents consume drugs through smoking, with 20% through snorting, inhaling or swallowing and 12% through injection. The drug mostly used among the respondents was heroin (52%). The most commonly injected drug was cocaine (55%). About 64.7% of respondents reported mixing two or more drugs. HIV prevalence among respondents was 2.5%, 12.3% among women and 17.7% among women engaged in sex work, highlighting the overlap vulnerability. The prevalence of hepatitis C was 6.0%, and Hepatitis B was 4.5%. Access to care is limited, with 63% of the respondents never been tested for HIV.

Conclusion
These rapid assessment findings reveal the challenging conditions for people who use and inject drugs coupled with a relatively high prevalence of HIV and Hepatitis C compared to the general population. However, it also reveals that Ghana has a window of opportunity to prevent an exponential spread of HIV and Hepatitis in this population. Therefore, there is the need to implement prevention and treatment programs for HIV and hepatitis among people who use and inject drugs including essential strategies for an enabling environment in Ghana.
Drug-resistant tuberculosis care and treatment outcomes over the last 15 years in Ethiopia: Results from a mixed-method review of trends
Authors: Tesema E. , Biru M. , Leta T. , Kumsa A. , Liaulseged A. , Gizatie G. , Bogale T. , Million M. , Datiko D. G. , Gebreyohannes A. , Molla Y. , Hiruy N. , Mebnga M. , Suarez P. G. , Dememew Z. G. , Jerene D. 
Published: August 2024

Background and objectives
Drug resistant tuberculosis (DR-TB) remains a global challenge with about a third of the cases are not detected. With the recent advances in the diagnosis and treatment follow-up of DR-TB, there have been improvements with treatment success rates. However, there is limited evidence on the successful models of care that have consistently registered good outcomes. Our aim was to assess Ethiopia’s experience in scaling up an ambulatory, decentralized model of care while managing multiple regimen transition processes and external shocks.

Methods
This was a cross-sectional, mixed-method study. For the quantitative data, we reviewed routine surveillance data for the period 2009–2022 and collected additional data from publicly available reports. We then analyzed the data descriptively. Qualitative data were collected from program reports, quarterly presentations, minutes of technical working group meetings, and clinical review committee reports and analyzed thematically.

Results
The number of DR-TB treatment initiating centers increased from 1 to 67, and enrollment increased from 88 in 2010 to 741 in 2019, but declined to 518 in 2022. A treatment success rate (TSR) of over 70% was sustained. The decentralized and ambulatory service delivery remained the core service delivery model. The country successfully navigated multiple regimen transitions, including the recently introduced six-month short oral regimen. Several challenges remain, including the lack of strong and sustainable specimen transportation system, lack of established systems for timely tracing and linking of missed DR-TB cases, and data quality issues.

Conclusions
Ethiopia scaled up a decentralized ambulatory model of care, kept up to date with recent developments in treatment regimens, and maintained a high TSR, despite the influence of multiple external challenges. The recent decline in case notification requires a deeper look into the underlying reasons. The feasibility of fully integrating DR-TB treatment and follow up at community level should be explored further.