bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of machine learning in the clinic: challenges and lessons in prospective deployment from the System for High Intensity EvaLuation During Radiation Therapy (SHIELD-RT) randomized controlled study
Authors: Hong Julian C. , Eclov Neville C. W. , Stephens Sarah J. , Mowery Yvonne M. , Palta Manisha 
Published: September 2022

Abstract
Background
Artificial intelligence (AI) and machine learning (ML) have resulted in significant enthusiasm for their promise in healthcare. Despite this, prospective randomized controlled trials and successful clinical implementation remain limited. One clinical application of ML is mitigation of the increased risk for acute care during outpatient cancer therapy. We previously reported the results of the System for High Intensity EvaLuation During Radiation Therapy (SHIELD-RT) study (NCT04277650), which was a prospective, randomized quality improvement study demonstrating that ML based on electronic health record (EHR) data can direct supplemental clinical evaluations and reduce the rate of acute care during cancer radiotherapy with and without chemotherapy. The objective of this study is to report the workflow and operational challenges encountered during ML implementation on the SHIELD-RT study.

Results
Data extraction and manual review steps in the workflow represented significant time commitments for implementation of clinical ML on a prospective, randomized study. Barriers include limited data availability through the standard clinical workflow and commercial products, the need to aggregate data from multiple sources, and logistical challenges from altering the standard clinical workflow to deliver adaptive care.

Conclusions
The SHIELD-RT study was an early randomized controlled study which enabled assessment of barriers to clinical ML implementation, specifically those which leverage the EHR. These challenges build on a growing body of literature and may provide lessons for future healthcare ML adoption.
Trial registration: NCT04277650. Registered 20 February 2020. Retrospectively registered quality improvement study.
Visualizing the knowledge structure and evolution of bioinformatics
Authors: Wang Jiaqi , Li Zeyu , Zhang Jiawan 
Published: September 2022

Abstract
Background
Bioinformatics has gained much attention as a fast growing interdisciplinary field. Several attempts have been conducted to explore the field of bioinformatics by bibliometric analysis, however, such works did not elucidate the role of visualization in analysis, nor focus on the relationship between sub-topics of bioinformatics.

Results
First, the hotspot of bioinformatics has moderately shifted from traditional molecular biology to omics research, and the computational method has also shifted from mathematical model to data mining and machine learning. Second, DNA-related topics are bridge topics in bioinformatics research. These topics gradually connect various sub-topics that are relatively independent at first. Third, only a small part of topics we have obtained involves a number of computational methods, and the other topics focus more on biological aspects. Fourth, the proportion of computing-related topics hit a trough in the 1980s. During this period, the use of traditional calculation methods such as mathematical model declined in a large proportion while the new calculation methods such as machine learning have not been applied in a large scale. This proportion began to increase gradually after the 1990s. Fifth, although the proportion of computing-related topics is only slightly higher than the original, the connection between other topics and computing-related topics has become closer, which means the support of computational methods is becoming increasingly important for the research of bioinformatics.

Conclusions
The results of our analysis imply that research on bioinformatics is becoming more diversified and the ranking of computational methods in bioinformatics research is also gradually improving.
Oxidative stress genes in patients with esophageal squamous cell carcinoma: construction of a novel prognostic signature and characterization of tumor microenvironment infiltration
Authors: Liu Wei , Yang Hao-Shuai , Zheng Shao-Yi , Luo Hong-He , Feng Yan-Fen , Lei Yi-Yan 
Published: September 2022

AbstractBackgroundOxidative stress plays an important role in the progression of various types of tumors. However, its role in esophageal squamous cell carcinoma (ESCC) has seldom been explored. This study aimed to discover prognostic markers associated with oxidative stress in ESCC to improve the prediction of prognosis and help in the selection of effective immunotherapy for patients.ResultsA consensus cluster was constructed using 14 prognostic differentially expressed oxidative stress-related genes (DEOSGs) that were remarkably related to the prognosis of patients with ESCC. The infiltration levels of neutrophils, plasma cells, and activated mast cells, along with immune score, stromal score, and estimated score, were higher in cluster 1 than in cluster 2. A prognostic signature based on 10 prognostic DEOSGs was devised that could evaluate the prognosis of patients with ESCC. Calculated risk score proved to be an independent clinical prognostic factor in the training, testing, and entire sets. P53 signaling pathway was highly enriched in the high-risk group. The calculated risk score was positively related to the infiltration levels of resting mast cells, memory B cells, and activated natural killer (NK) cells and negatively associated with the infiltration levels of M1 and M2 macrophages. The relationship between clinical characteristics and risk score has not been certified. The half-maximal inhibitory concentration (IC50) values for sorafenib and gefitinib were lower for patients in the low-risk group.ConclusionOur prognostic signature based on 10 prognostic DEOSGs could predict the disease outcomes of patients with ESCC and had strong clinical value. Our study improves the understanding of oxidative stress in tumor immune microenvironment (TIME) and provides insights for developing improved and efficient immunotherapy strategies.
The changing spectrum of microbial aetiology of respiratory tract infections in hospitalized patients before and during the COVID-19 pandemic
Authors: Serigstad Sondre , Markussen Dagfinn L. , Ritz Christian , Ebbesen Marit H. , Knoop Siri T. , Kommedal Øyvind , Heggelund Lars , Ulvestad Elling , Bjørneklett Rune O. , Grewal Harleen M. S. ,   the CAPNOR study group, Clark Tristan W. , Faurholt-Jepsen Daniel , Ravn Pernille , van Werkhoven Cornelis H. 
Published: September 2022

Abstract
Background
The COVID-19 pandemic was met with strict containment measures. We hypothesized that societal infection control measures would impact the number of hospital admissions for respiratory tract infections, as well as, the spectrum of pathogens detected in patients with suspected community acquired pneumonia (CAP).

Methods
This study is based on aggregated surveillance data from electronic health records of patients admitted to the hospitals in Bergen Hospital Trust from January 2017 through June 2021, as well as, two prospective studies of patients with suspected CAP conducted prior to and during the COVID-19 pandemic (pre-COVID cohort versus COVID cohort, respectively). In the prospective cohorts, microbiological detections were ascertained by comprehensive PCR-testing in lower respiratory tract specimens. Mann–Whitney’s U test was used to analyse continuous variables. Fisher’s exact test was used for analysing categorical data. The number of admissions before and during the outbreak of SARS-CoV-2 was compared using two-sample t-tests on logarithmic transformed values.

Results
Admissions for respiratory tract infections declined after the outbreak of SARS-CoV-2 (p < 0.001). The pre-COVID and the COVID cohorts comprised 96 and 80 patients, respectively. The proportion of viruses detected in the COVID cohort was significantly lower compared with the pre-COVID cohort [21% vs 36%, difference of 14%, 95% CI 4% to 26%; p = 0.012], and the proportion of bacterial- and viral co-detections was less than half in the COVID cohort compared with the pre-COVID cohort (19% vs 45%, difference of 26%, 95% CI 13% to 41%; p < 0.001). The proportion of bacteria detected was similar (p = 0.162), however, a difference in the bacterial spectrum was observed in the two cohorts. Haemophilus influenzae was the most frequent bacterial detection in both cohorts, followed by Streptococcus pneumoniae in the pre-COVID and Staphylococcus aureus in the COVID cohort.

Conclusion
During the first year of the COVID-19 pandemic, the number of admissions with pneumonia and the microbiological detections in patients with suspected CAP, differed from the preceding year. This suggests that infection control measures related to COVID-19 restrictions have an overall and specific impact on respiratory tract infections, beyond reducing the spread of SARS-CoV-2.
How socioeconomic status, social capital and functional independence are associated with subjective wellbeing among older Indian adults? A structural equation modeling analysis
Authors: Muhammad T. , Kumar Pradeep , Srivastava Shobhit 
Published: September 2022

Abstract
Background
Subjective well-being (SWB) is of particular interest among gerontologists and health researchers with important implications for interventions especially in poor-resource settings. This study aimed to explore the possible pathways from socioeconomic status (SES), functional independence and social capital towards SWB among older adults in India.

Methods
Cross-sectional data from the “Building a Knowledge Base on Population Aging in India” (BKPAI) survey with a total sample of 9231 older adults aged 60 years and above were used. The outcome variable was low SWB (LSWB). The study used univariate and bivariate analysis for reporting the initial results. Further, the study employed the structural equation modeling (SEM) technique using maximum likelihood estimation (MLE) procedure to estimate the covariance matrix.

Results
Overall, about 27% of older adults reported LSWB. Reporting LSWB was more prevalent among older adults who had no income (30.8%) and those who had income but not sufficient to fulfil their basic needs (39.4%, p < 0.001). The prevalence of reporting LSWB was significantly higher among older adults who had no asset ownership (36.5%, p < 0.001) than those who had asset ownership. The path from the SEM shows that LSWB and SES are negatively related to each other. Moreover, LSWB had significant negative relationship with independence (β = -0.032, p < 0.001) and social capital (β = -0.020; p < 0.001). In addition, results found a positive relationship between SES and independence (β = 0.019; p < 0.001), SES and social capital (β = 0.016; p < 0.001), and independence and social capital (β = 0.033; p < 0.001).

Conclusions
The findings highlight that higher SES, good physical functioning as well as favorable social capital are interdependent factors of late-life wellbeing and a multidimensional approach in policymaking can ensure a successful and active ageing among older Indian adults.
Intercalary frozen autografts for reconstruction of bone defects following meta-/diaphyseal tumor resection at the extremities
Authors: Yang Jingyan , Li Wenze , Feng Rongjie , Li Dong 
Published: September 2022

Abstract
Background
For patients with malignant limb tumors, salvage surgery can be achieved using endoprosthesis or biological reconstructions like allograft or autograft. In carefully selected patients, resected bone can be recycled after sterilization using methods like autoclaving, irradiation, pasteurization or freezing with liquid nitrogen. We evaluated the clinical outcome and complications of malignant limb tumors treated with intercalary resection and frozen autograft reconstruction.

Methods
We reviewed 33 patients whose malignant bone tumors were treated by wide resection and reconstruction with recycling liquid nitrogen-treated autografts between 2006 and 2017. Limb function, bone union at the osteotomy site and complications were evaluated. Functional outcome was assessed using the Musculoskeletal Tumor Society (MSTS) scoring system.

Results
The cohort comprised 16 males and 17 females, with a mean age of 35.4 years (14–76 years). The most common tumor was osteosarcoma (7 cases). Tumors were located in the humerus (5), ulna (1), femur (10) and tibia (17). The mean follow-up was 49.9 months (range 12–127 months). Of the 33 patients, 16 remained disease-free, and 3 were alive with disease. The mean size of the defect after tumor resection was 11.6 cm (range 6–25 cm). Bone union was achieved in 32 patients, with a mean union time of 8.8 months (range 4–18 months). Complications included 1 graft nonunion, 2 infections (1 superficial, 1 deep infection), 1 leg length discrepancy, 2 graft fractures and 3 local recurrences. The mean MSTS score was 87.2% (range 70–100%).

Conclusion
Liquid nitrogen-treated tumor-bearing autograft is an effective option for biological reconstruction after meta-/diaphyseal tumor resection of long bones. This method has excellent clinical outcomes and is especially recommended for patients with no severe osteolytic bone tumors.
Predicting IVF outcome in poor ovarian responders
Authors: Lebovitz Oshrit , Haas Jigal , Mor Nitzan , Zilberberg Eran , Aizer Adva , Kirshenbaum Michal , Orvieto Raoul , Nahum Ravit 
Published: September 2022

Abstract
Background
Poor responders to ovarian stimulation are one of the most challenging populations to treat. As a failed cycle can cause a considerable emotional and economical loss, adequate fertility counseling addressing patients’ expectations are highly important when facing patients with poor ovarian response. The study aimed to evaluate reproductive outcomes and to identify factors associated with live birth (LB) after fresh autologous IVF/intracytoplasmic sperm injection (ICSI) cycles of patients fulfilling the Bologna criteria for poor ovarian response (POR).

Methods
A retrospective study included 751 IVF/ICSI treatment cycles which yielded up to three retrieved oocytes, at a tertiary referral hospital between January 2016 and February 2020. A logistic regression analysis was used to adjust for confounders.

Results
Clinical pregnancy and LB rate per cycle were significantly higher among women younger versus older than 40 years (9.8% and 6.8% vs 4.5% and 2.1%, p < 0.01, respectively). Patients who achieved LB were significantly younger, had higher number of oocytes retrieved, fertilization rate and top-quality embryos (p < 0.05). Multivariable regression analysis identified patient’s age (OR 0.90; 95% CI 0.845–0.97; p = 0.005) and mean number retrieved oocytes (OR 1.95; 95% CI 1.20–3.16; p = 0.007) as factors significantly associated with the probability of a LB.

Conclusions
The woman’s age and the number of retrieved oocytes are both independent predicting factors of live birth in poor ovarian responders. Considering the risks, the high financial investment and poor reproductive outcomes involved in IVF treatments, raises questions regarding the adequacy of providing treatments in these patients' population. POR younger than 40 years may represent a possible exception due to acceptable probability for a LB.
A social ecological approach to promote learning health disparities in the clinical years: impact of a home-visiting educational program for medical students
Authors: Sagi Doron , Rudolf Mary Catharine Joy , Spitzer Sivan 
Published: September 2022

AbstractBackgroundThere is consensus that medical schools have a duty to educate students about social determinants of health (SDOH) and equip them with skills required to ameliorate health disparities. Although the National Academy of Medicine (NAM) urged the development of experiential long term programs, teaching is usually conducted in the pre-clinical years or as voluntary courses. ETGAR a required health disparities course, based on the social ecological model, was initiated to answer the NAM call. This study aimed to ascertain the course impact on students learning of SDOH and health disparities.MethodsStudents during their first clinical year cared for four patients in their transition from hospital back home, one patient in each internal medicine, surgery, pediatrics and obstetrics/gynecology rotation. The students home-visited their patients after meeting them in hospital and preparing a plain language discharge letter. Training session prior to the course, a tutorial in each rotation, and structured feedback gave the educational envelope. Mixed methodology was employed to evaluate the course impact. Quantitative data collected by students during the home-visit: patients’ characteristics and quality and safety of the transition back home using the Medication Discrepancy Tool and Care Transition Measure questionnaire. Stakeholders’ views were collected via interviews and focus groups with students representing all affiliated hospitals, and interviews with heads of departments most involved in the course.ResultsThree hundred six students in three academic years, between October 2016–July 2019, completed home visits for 485 disadvantaged patients with improvement in patients’ knowledge of their treatment (3.2 (0.96) vs 3.8 (0.57), Z = -7.12,p < .0001) and identification of medication discrepancies in 42% of visits. Four themes emerged from the qualitative analysis: contribution to learning, experience-based learning, professional identity formation, and course implementation.ConclusionsETGAR was perceived to complement hospital-based learning, making students witness the interaction between patients’ circumstances and health and exposing them to four patients’ environment levels. It provided a didactic framework for promoting awareness to SDOH and tools and behaviors required to ameliorate their impact on health and health disparities.The course combined communication and community learning into traditionally bio-medical clinical years and serves as a model for how social-ecology approaches can be integrated into the curriculum.
Men’s perception of information and psychological distress in the diagnostic phase of prostate cancer: a comparative mixed methods study
Authors: Søndergaard Maja Elisabeth Juul , Lode Kirsten , Husebø Sissel Eikeland , Dalen Ingvild , Kjosavik Svein Reidar 
Published: September 2022

Abstract
Background
Previous studies indicate that men experience frustration and uncertainty when confronted with an elevated prostate specific antigen (PSA) test and during further diagnostics for prostate cancer. The novel Stockholm3 test is an algorithm-based test that combines plasma protein biomarkers, genetic markers and clinical variables in predicting the risk of PCa. The test was introduced in a western part of Norway as a new tool for detecting prostate cancer. This study aimed to explore and compare men’s perception of information and possible experience of distress between a PSA group and a Stockholm3 group during the diagnostic phase of prostate cancer.

Methods
This study is a part of the trailing research evaluating the impact of the change from PSA to Stockholm3. It is a multicenter study using a comparative mixed method design. Data were collected in a PSA group (n = 130) and a Stockholm3 group (n = 120) between 2017 and 2019. Quantitative data were collected using questionnaires and qualitative data were collected using semi-structured interviews (n = 20). The quantitative and qualitative data were analysed and compared separately and then merged in a side-by-side discussion. The study adheres to the GRAMMS guidelines for reporting mixed-methods research.

Results
Compared with the PSA group, men in the Stockholm3 group reported that the information from the general practitioners was better. Similarly, men in the Stockholm3 group were more likely to indicate that they had received sufficient information regarding how examinations would be conducted. No differences were found between the groups regarding waiting time and distress. Three themes emerged from the qualitative analysis of the two groups: “Information affects the experience of comprehension”, “Stepping into the world of the healthcare system”, and “Periodically feelings of distress”.

Conclusion
The Stockholm3 test may facilitate the provision of information to patients. However, some patients in both groups experienced distress and would benefit from more information and additional support from healthcare professionals. Routines that ensure sufficient information from the interdisciplinary healthcare team should be of priority during the diagnostic phase of prostate cancer in order to provide patients with predictability and to avoid unnecessary distress.
Exploring patient experiences with a telehealth approach for the PRO-ACTIVE trial intervention in head and neck cancer patients
Authors: Khan M. M. , Manduchi B. , Rodriguez V. , Fitch M. I. , Barbon C. E. A. , McMillan H. , Hutcheson K. A. , Martino R. 
Published: September 2022

Abstract
Introduction
Following the COVID-19 directive to cease non-essential services, a rapid shift was made in the delivery of Speech Language Pathology (SLP) dysphagia management in the 3-arm, randomized PRO-ACTIVE trial. To inform future programs, this study explored patients’ experiences with telehealth when the planned in-person SLP intervention was moved to a telehealth modality.

Methods
A theory-guided qualitative descriptive approach was used. Willing participants who had received at least one telehealth swallowing therapy session participated in a one-time semi-structured interview. Interview transcripts were subjected to a standard qualitative content/theme analysis. Researchers reviewed all transcripts and used a multi-step analysis process to build a coding framework through consensus discussion. Summaries and key messages were generated for each code.

Results
Eleven participants recounted their telehealth experiences and reported feeling satisfied, comfortable and confident with the session(s). They identified that previous experience with teleconferencing, access to optimal technical equipment, clinician skill, and caregiver assistance facilitated their telehealth participation. Participants highlighted that telehealth was beneficial as it reduced commuting time, COVID-19 exposure and fatigue from travel; and also allowed caregiver participation particularly during COVID. In comparing their in-person SLP sessions to telehealth sessions, limitations were also identified, including: lack of previous experience with and/or poor access to technology, and less opportunity for personalization. Participants indicated that use of phone alone was less preferred than an audio/video platform.

Discussion
Patients reported that overall, telehealth sessions did not compromise their learning experience when compared to in-person sessions. Patients benefited from use of telehealth in several ways despite some limitations of the use of technology. Patient feedback about telehealth provides an important perspective that may be critical to inform best practices for care delivery.