bluuebunny/crossref_metadata_2025_split huggingface dataset:
Safety of live attenuated herpes zoster vaccine in Australian adults 70–79 years of age: an observational study using active surveillance
Authors: Phillips Anastasia , Glover Catherine , Leeb Alan , Cashman Patrick , Fathima Parveen , Crawford Nigel , Snelling Thomas L , Durrheim David , Macartney Kristine 
Published: October 2022

ObjectivesTo assess the safety of live attenuated herpes zoster vaccine live (ZVL) through cumulative analysis of near real-time, participant-based active surveillance from Australia’s AusVaxSafety system.Design and settingZVL was funded in Australia for adults aged 70 years from November 2016, with a time-limited catch up programme for those up to 79 years. This cohort study monitored safety in the first two programme years through active surveillance at 246 sentinel surveillance immunisation sites.ParticipantsAdults aged 70–79 years vaccinated with ZVL who responded to an opt-out survey sent via automated short message service (SMS) 3 days following vaccination (n=17 458) or contributed supplementary data through a separate, opt-in online survey at 16 and 24 days following vaccination (n=346).Primary and secondary outcome measuresRates of overall and prespecified adverse events following immunisation (AEFI) by sex, concomitant vaccination and underlying medical condition. Signal detection methods (fast initial response cumulative summation and Bayesian updating analyses) were applied to reports of medical attendance.ResultsThe median age of participants was 72 years; 53% were female. The response rate following automated SMS was high (73% within 7 days of vaccination). Females were more likely than males to report any adverse event within 7 days of vaccination (RR 2.07, 95% CI 1.86 to 2.31); injection site reaction was the most commonly reported (2.3%, n=377). Concomitant vaccination was not associated with higher adverse event rates (RR 1.05, 95% CI 0.93 to 1.18). Rates of medical attendance were low (0.3%) with no safety signals identified. Supplementary opt-in survey data on later onset adverse events did not identify any difference in AEFI rates between those with and without underlying medical conditions.ConclusionsZVL has a very good safety profile in the first week after vaccination in older adults. Active, participant-based surveillance in this primary care cohort is an effective method to monitor vaccine safety among older adults and will be used as a key component of COVID-19 vaccine safety surveillance in Australia.
Perceptions of injury risk in the home and workplace in Nepal: a qualitative study
Authors: Joshi Elisha , Bhatta Santosh , Deave Toity , Mytton Julie , Adhikari Dhruba , Manandhar Sunil Raja , Joshi Sunil Kumar 
Published: October 2022

ObjectiveInjuries are a global health problem. To develop context-specific injury prevention interventions, one needs to understand population perceptions of home and workplace injuries. This study explored a range of views and perceptions about injuries in a variety of settings and identified barriers and facilitators to injury prevention.DesignQualitative study: interviews and focus groups.SettingThree administrative areas: Hetauda submetropolitan city, Thaha municipality and Bakaiya rural municipality in Makwanpur, Nepal.ParticipantsNine focus groups (74 participants) and nine one-to-one interviews were completed; workers from diverse occupations, residents (slum, traditional or modern homes) and local government decision-makers participated in the study between May and August 2019. The interviews and discussions were audio-recorded, transcribed verbatim, translated to English and analysed thematically.ResultsSix themes were developed: unsafe home and workplace environment; inadequate supervision and monitoring; perceptions that injuries are inevitable; safety takes low priority: financial and behavioural considerations; safety education and training; and government-led safety programmes and enforcement. Key barriers to injury prevention were perceived to be lack of knowledge about injury risk and preventive measures both at the community level and at the workplace. Facilitators were community-level educational programmes and health and safety training to employees and employers. Participants stressed the importance of the role of the government in planning future injury prevention programmes in different environments.ConclusionsThis study highlighted that both home and workplace injuries are complex and multifactorial. Lack of knowledge about injury risks and preventive measures, both at the community level and at the workplace, was found to be a common barrier to injury prevention, perceived to be mitigated by educational programmes. Together with previously published epidemiological evidence, the barriers and facilitators identified in this study offer useful basis to inform policy and practice.
Incidence of out-of-hospital cardiac arrests and survival rates after 1 month among the Japanese working population: a cohort study
Authors: Yamagishi Yasunobu , Oginosawa Yasushi , Fujino Yoshihisa , Yagyu Keishiro , Miyamoto Taro , Tsukahara Keita , Ohe Hisaharu , Kohno Ritsuko , Abe Haruhiko 
Published: October 2022

ObjectivesThe prevention and improvement of the prognosis of out-of-hospital cardiac arrests (OHCAs) are important issues especially with respect to their social and economic significance in working populations. The age distribution of the working population in Japan is expected to change continually due to its ageing society and extension of retirement; however, few reports have examined the long-term condition of OHCA in the working population, defined by age. The aim of this study was to determine the incidence of OHCAs and the survival rates after 1 month, among the Japanese working population, defined by age, considering the changing age distribution.Design and settingWe analysed the All-Japan Utstein registry, a prospective, nationwide, population-based, observational registry (2005–2016).ParticipantsFrom the registry, 212 961 patients with OHCA from the Japanese working population (defined aged 20–69 years), with only cardiogenic aetiology participated in this study. These patients were further divided into four groups according to the type of citizen bystander (family, friends, work-colleagues and passers-by).Primary and secondary outcome measuresThe main outcomes were 1-month survival with favourable neurological outcomes.ResultsThe incidence of OHCAs, in any age group, was almost constant during the 12-year period. The work-colleagues had the best prognosis despite having significantly longer times to initial defibrillations compared with the passers-by (13 vs 12 min, respectively, p<0.001) that was associated independently with 1-month survival with favourable neurological outcomes (adjusted OR: 0.94 (1 min increments), p<0.001).ConclusionsIn the 12-year period, the incidence of OHCAs in any age group remained almost constant, whereas the prognosis improved each year. Reducing the time to initial defibrillation may further improve the prognosis of OHCAs with a work-colleague bystander.
Impact of the COVID-19 pandemic on ongoing health research: an ad hoc survey among investigators in Germany
Authors: Bratan Tanja , Aichinger Heike , Brkic Nicole , Rueter Jana , Apfelbacher Christian , Boyer Lisa , Loss Julika 
Published: October 2022

ObjectivesTo gain insights into the impact of the COVID-19 pandemic on ongoing health research projects, using projects from a selected funding programme in Germany as an example.DesignOnline survey and validation workshop.SettingLockdowns and social distancing policies impact on clinical and public health research in various forms, especially if unrelated to COVID-19. Research institutions have reduced onsite activities, data are often collected remotely, and during the height of the crisis, clinical researchers were partially forced to abandon their projects in favour of front-line care.Participants survey120 investigators of health research projects across Germany, performed between 15 and 25 May 2020; workshop: 32 investigators, performed on 28 May 2020.ResultsThe response rate (78%) showed that the survey generated significant interest among investigators. 85 responses were included for analysis, and the majority of investigators (93%) reported that their projects were affected by the pandemic, with many (80%) stating that data collection was not possible as planned, and they could not carry out interventions as intended (67%). Other impacts were caused by staff being unavailable, for example, through child or elder care commitments or because of COVID-19 quarantine or illness. Investigators also reported that publications were delayed or not feasible at all (56%), and some experienced problems with PhD or Masters theses (18%). The majority of investigators had mitigation strategies in place such as adjustment of data collection methods using digital tools (46%) or of project implementation in general (46%), others made changes in research design or research questions (27%).ConclusionsThe COVID-19 pandemic has severely impacted on health research projects. The main challenge is now to mitigate negative effects and to improve long-term resilience in health research. The pandemic has also acted as a driver of innovation and change, for example, by accelerating the use of digital methods.
Are patients accurate forecasters of their emotional response to medical conditions? A scoping review on affective forecasting
Authors: Bosch G J van den , Roos R A N , Otten R , Bockting Claudi , Smulders Y M 
Published: October 2022

ObjectiveIn this paper, we challenge the premise that patients are capable of accurately predicting their emotional response or quality of life in anticipation of health changes. Our goal was to systematically review the published empirical evidence related to the reliability of affective forecasting in the context of medical conditions.DesignScoping review.SettingWe conducted a search string using both simple search terms as well as MeSH terms and searched the electronic databases of PubMed, Embase, CINAHL and Cochrane up to April 2021.ParticipantsWe initially selected 5726 articles. Empirical studies reporting on predicted and/or observed emotions or quality of life concerning deterioration, improvement in health or chronic illnesses were included. Furthermore, empirical studies of healthy individuals predicting emotional response or quality of life compared with patients reflecting on emotions or quality of life concerning deterioration or improvement in health or chronic illnesses were also included. Studies on healthy participants, psychiatric patients and non-English articles were excluded.Results7 articles were included in this review. We found that patients generally tend to systematically exaggerate both anticipated happiness and sorrow/grief after health improvement and deterioration, respectively.ConclusionPatients are less adept in predicting emotional response or quality of life regarding to health changes than we are inclined to assume. We discuss several biases which could explain this phenomenon. Our findings are relevant in the context of treatment decisions, advanced care planning and advanced care directives.
Measurement-based care educational programmes for clinical trainees in mental healthcare: a scoping review protocol
Authors: Freedman David Eli , Waddell Andrea Evelyn , Lam Henry , Bourdon Alexander , Wang Karen 
Published: October 2022

IntroductionMeasurement-based care (MBC) represents the approach of regularly using symptom rating scales to guide patient care decisions in mental healthcare. MBC is an effective, feasible and acceptable approach to enhance clinical outcomes in various disciplines, including medicine, psychology, social work and psychotherapy. Yet, it is infrequently used by clinicians, potentially due to limited education for care providers. The objective of this scoping review is to survey the characteristics of MBC educational programmes for undergraduate, graduate and postgraduate clinical trainees in mental healthcare.Methods and analysisUsing database-tailored search strategies, we plan on searching Medline, PsycINFO, Embase, CINAHL and Cochrane Central for relevant studies. Thereafter, we will analyse the selected studies to extract information on the delivery of educational programmes, the clinical and educational outcomes of these programmes, and the potential enablers and barriers to MBC education. In this paper, we articulate the protocol for this scoping review.Ethics and disseminationThis scoping review does not require research ethics approval. The findings from this scoping review will be incorporated into the creation of a novel MBC curriculum and handbook. Results will be disseminated at appropriate national or international conferences, as well as in a peer-reviewed journal publication.
Treatment of isolated and recurrent tracheoesophageal fistula in children: a case series and literature review
Authors: Sautin Aleh , Marakhouski Kiryl , Pataleta Aleh , Svirsky Aliaksandr , Averyn Vasili 
Published: October 2022

BackgroundDespite improvements in the treatment of esophageal atresia with tracheoesophageal fistula (TEF) in recent decades, complications still exist. The rate of fistula recanalization after surgical repair is ~5% in large cohorts. However, there is controversy regarding the gold standard of treatment. This research aimed to evaluate the efficacy of treatment of pediatric patients with isolated (H-type) and recurrent TEF in our clinic.MethodsWe retrospectively analyzed 12 patients (7 boys, 5 girls) aged 35 days–14.6 years. The median age of our patients was 632 days [95% CI (confident interval) 120.1 to 2118.7]; the mean birth weight was 2713 g (95% CI 2258 to 3169; median: 2763 g); and the mean gestational age was 37.1 weeks (95% CI 35.4 to 38.8; median: 37 weeks). All patients were managed for isolated or recurrent TEF between January 1, 2015 and December 31, 2020 using endoscopy (laser de-epithelialization).ResultsLaser de-epithelialization alone was effective in 8 of 12 patients (66.67%), with a mean number of de-epithelializations of 2.25 (range: 1–4). After one attempt at de-epithelialization, success was achieved in only two patients (n=16.67%). The mortality rate was 0%. The median follow-up for patients who received endoscopic treatment exclusively (n=8) was 3.7 years (95% CI 1.38 to 4.87) after the last stage of de-epithelialization.ConclusionFlexible endoscopy is an alternative treatment to open surgical repair of isolated and recurrent TEF in children. The effectiveness of endoscopic laser de-epithelialization alone with subsequent fistula obliteration was 66.7%, with a median follow-up of 3.7 years.
Engineering Nearly Linear-time Algorithms for Small Vertex Connectivity
Authors: Franck Max , Yingchareonthawornchai Sorrachai 
Published: October 2022

Vertex connectivity is a well-studied concept in graph theory with numerous applications. A graph is
k
-connected if it remains connected after removing any
k
−1 vertices. The vertex connectivity of a graph is the maximum
k
such that the graph is
k
-connected. There is a long history of algorithmic development for efficiently computing vertex connectivity. Recently, two near linear-time algorithms for small
k
were introduced by Forster et al. [SODA 2020]. Prior to that, the best-known algorithm was one by Henzinger et al. [FOCS 1996] with quadratic running time when
k
is small.

In this article, we study the practical performance of the algorithms by Forster et al. In addition, we introduce a new heuristic on a key subroutine called local cut detection, which we call degree counting. We prove that the new heuristic improves space-efficiency (which can be good for caching purposes) and allows the subroutine to terminate earlier. According to experimental results on random graphs with planted vertex cuts, random hyperbolic graphs, and real-world graphs with vertex connectivity between 4 and 8, the degree counting heuristic offers a factor of 2–4 speedup over the original non-degree counting version for small graphs and almost 20 times for some graphs with millions of edges. It also outperforms the previous state-of-the-art algorithm by Henzinger et al., even on relatively small graphs.
On the Relationship between Explanation and Recommendation: Learning to Rank Explanations for Improved Performance
Authors: Li Lei , Zhang Yongfeng , Chen Li 
Published: October 2022

Explaining to users why some items are recommended is critical, as it can help users to make better decisions, increase their satisfaction, and gain their trust in recommender systems (RS). However, existing explainable RS usually consider explanation as a side output of the recommendation model, which has two problems: (1) It is difficult to evaluate the produced explanations, because they are usually model-dependent, and (2) as a result, how the explanations impact the recommendation performance is less investigated.
In this article, explaining recommendations is formulated as a ranking task and learned from data, similarly to item ranking for recommendation. This makes it possible for standard evaluation of explanations via ranking metrics (e.g., Normalized Discounted Cumulative Gain). Furthermore, this article extends traditional item ranking to an item–explanation joint-ranking formalization to study if purposely selecting explanations could reach certain learning goals, e.g., improving recommendation performance. A great challenge, however, is that the sparsity issue in the user-item-explanation data would be inevitably severer than that in traditional user–item interaction data, since not every user–item pair can be associated with all explanations. To mitigate this issue, this article proposes to perform two sets of matrix factorization by considering the ternary relationship as two groups of binary relationships. Experiments on three large datasets verify the solution’s effectiveness on both explanation ranking and item recommendation.
Spatial Transcriptomic Analysis of a Diverse Patient Cohort Reveals a Conserved Architecture in Triple-Negative Breast Cancer
Authors: Bassiouni Rania , Idowu Michael O. , Gibbs Lee D. , Robila Valentina , Grizzard Pamela J. , Webb Michelle G. , Song Jiarong , Noriega Ashley , Craig David W. , Carpten John D. 
Published: October 2022

Abstract

Triple-negative breast cancer (TNBC) is an aggressive disease that disproportionately affects African American (AA) women. Limited targeted therapeutic options exist for patients with TNBC. Here, we employ spatial transcriptomics to interrogate tissue from a racially diverse TNBC cohort to comprehensively annotate the transcriptional states of spatially resolved cellular populations. A total of 38,706 spatial features from a cohort of 28 sections from 14 patients were analyzed. Intratumoral analysis of spatial features from individual sections revealed heterogeneous transcriptional substructures. However, integrated analysis of all samples resulted in nine transcriptionally distinct clusters that mapped across all individual sections. Furthermore, novel use of join count analysis demonstrated nonrandom directional spatial dependencies of the transcriptionally defined shared clusters, supporting a conserved spatio-transcriptional architecture in TNBC. These findings were substantiated in an independent validation cohort comprising 17,861 spatial features representing 15 samples from 8 patients. Stratification of samples by race revealed race-associated differences in hypoxic tumor content and regions of immune-rich infiltrate. Overall, this study combined spatial and functional molecular analyses to define the tumor architecture of TNBC, with potential implications in understanding TNBC disparities.

Significance:
Spatial transcriptomics profiling of a diverse cohort of triple-negative breast cancers and innovative informatics approaches reveal a conserved cellular architecture across cancers and identify proportional differences in tumor cell composition by race.
Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture
Authors: Yuan Jiapei , Houlahan Kathleen E. , Ramanand Susmita G. , Lee Sora , Baek GuemHee , Yang Yang , Chen Yong , Strand Douglas W. , Zhang Michael Q. , Boutros Paul C. , Mani Ram S. 
Published: October 2022

Abstract

Prostate cancer is one of the most heritable human cancers. Genome-wide association studies have identified at least 185 prostate cancer germline risk alleles, most noncoding. We used integrative three-dimensional (3D) spatial genomics to identify the chromatin interaction targets of 45 prostate cancer risk alleles, 31 of which were associated with the transcriptional regulation of target genes in 565 localized prostate tumors. To supplement these 31, we verified transcriptional targets for 56 additional risk alleles using linear proximity and linkage disequilibrium analysis in localized prostate tumors. Some individual risk alleles influenced multiple target genes; others specifically influenced only distal genes while leaving proximal ones unaffected. Several risk alleles exhibited widespread germline–somatic interactions in transcriptional regulation, having different effects in tumors with loss of PTEN or RB1 relative to those without. These data clarify functional prostate cancer risk alleles in large linkage blocks and outline a strategy to model multidimensional transcriptional regulation.

Significance:
Many prostate cancer germline risk alleles are enriched in the noncoding regions of the genome and are hypothesized to regulate transcription. We present a 3D genomics framework to unravel risk SNP function and describe the widespread germline–somatic interplay in transcription control.
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Clustering heterogeneous categorical data using enhanced mini batch K-means with entropy distance measure
Authors: Mahfuz Nurshazwani Muhamad , Yusoff Marina , Idrus Zainura 
Published: October 2022

<span lang="EN-US">Clustering methods in data mining aim to group a set of patterns based on their similarity. In a data survey, heterogeneous information is established with various types of data scales like nominal, ordinal, binary, and Likert scales. A lack of treatment of heterogeneous data and information leads to loss of information and scanty decision-making. Although many similarity measures have been established, solutions for heterogeneous data in clustering are still lacking. The recent entropy distance measure seems to provide good results for the heterogeneous categorical data. However, it requires many experiments and evaluations. This article presents a proposed framework for heterogeneous categorical data solution using a mini batch k-means with entropy measure (MBKEM) which is to investigate the effectiveness of similarity measure in clustering method using heterogeneous categorical data. Secondary data from a public survey was used. The findings demonstrate the proposed framework has improved the clustering’s quality. MBKEM outperformed other clustering algorithms with the accuracy at 0.88, v-measure (VM) at 0.82, adjusted rand index (ARI) at 0.87, and Fowlkes-Mallow’s index (FMI) at 0.94. It is observed that the average minimum elapsed time-varying for cluster generation, </span><em><span lang="EN-US">k</span></em><span lang="EN-US"> at 0.26 s. In the future, the proposed solution would be beneficial for improving the quality of clustering for heterogeneous categorical data problems in many domains.</span>