bluuebunny/crossref_metadata_2025_split huggingface dataset:
MuTATE—an R package for comprehensive multi-objective molecular modeling
Authors: Ayton Sarah G , Treviño Víctor 
Published: September 2023

Abstract

Motivation
Comprehensive multi-omics studies have driven advances in disease modeling for effective precision medicine but pose a challenge for existing machine-learning approaches, which have limited interpretability across clinical endpoints. Automated, comprehensive disease modeling requires a machine-learning approach that can simultaneously identify disease subgroups and their defining molecular biomarkers by explaining multiple clinical endpoints. Current tools are restricted to individual endpoints or limited variable types, necessitate advanced computation skills, and require resource-intensive manual expert interpretation.

Results
We developed Multi-Target Automated Tree Engine (MuTATE) for automated and comprehensive molecular modeling, which enables user-friendly multi-objective decision tree construction and visualization of relationships between molecular biomarkers and patient subgroups characterized by multiple clinical endpoints. MuTATE incorporates multiple targets throughout model construction and allows for target weights, enabling construction of interpretable decision trees that provide insights into disease heterogeneity and molecular signatures. MuTATE eliminates the need for manual synthesis of multiple non-explainable models, making it highly efficient and accessible for bioinformaticians and clinicians. The flexibility and versatility of MuTATE make it applicable to a wide range of complex diseases, including cancer, where it can improve therapeutic decisions by providing comprehensive molecular insights for precision medicine. MuTATE has the potential to transform biomarker discovery and subtype identification, leading to more effective and personalized treatment strategies in precision medicine, and advancing our understanding of disease mechanisms at the molecular level.

Availability and implementation
MuTATE is freely available at GitHub (https://github.com/SarahAyton/MuTATE) under the GPLv3 license.
A general framework for powerful confounder adjustment in omics association studies
Authors: Roy Asmita , Chen Jun , Zhang Xianyang 
Published: September 2023

AbstractMotivationGenomic data are subject to various sources of confounding, such as demographic variables, biological heterogeneity, and batch effects. To identify genomic features associated with a variable of interest in the presence of confounders, the traditional approach involves fitting a confounder-adjusted regression model to each genomic feature, followed by multiplicity correction.ResultsThis study shows that the traditional approach is suboptimal and proposes a new two-dimensional false discovery rate control framework (2DFDR+) that provides significant power improvement over the conventional method and applies to a wide range of settings. 2DFDR+ uses marginal independence test statistics as auxiliary information to filter out less promising features, and FDR control is performed based on conditional independence test statistics in the remaining features. 2DFDR+ provides (asymptotically) valid inference from samples in settings where the conditional distribution of the genomic variables given the covariate of interest and the confounders is arbitrary and completely unknown. Promising finite sample performance is demonstrated via extensive simulations and real data applications.Availability and implementationR codes and vignettes are available at https://github.com/asmita112358/tdfdr.np.
The Perceived Contribution of Older People to Climate Change Impact, Mitigation, and Adaptation: Measurement Development and Validation
Authors: Ayalon Liat , Roy Senjooti 
Published: September 2023

AbstractBackground and ObjectivesTo improve the understanding of ageism toward older people in the context of climate change, the present study developed and validated a new measure that examines the perceived negative and positive contributions of older people to climate change impact, mitigation, and adaptation efforts.Research Design and MethodsFour studies (N = 774) were conducted to develop a new measure and evaluate its reliability and validity, relying on exploratory factor analysis, reliability analysis, confirmatory factor analysis, multiple-group analysis (Australia and India), discriminative validity, and convergent and divergent validity.ResultsA 2-subscale measure covering older people’s perceived negative contribution to climate change effects (5 items) and perceived positive contribution to adaptation and mitigation measures (3 items; eg, negative, and positive ageism in the context of climate change) was supported by the data. The measure has demonstrated adequate validity and reliability.Discussion and ImplicationsThe measure highlights a relatively neglected area in current climate change discourse and may assist in identifying ways to improve intergenerational solidarity as part of climate change adaptation and mitigation efforts toward building a world for all ages under a healthy climate, which allows for healthy aging and healthy longevity. These objectives are in line with the current mission posed by the UN Decade of Healthy Ageing.
Acceptability and Feasibility of a Pain and Depressive Symptoms Management Intervention in Middle-Aged and Older African American Women
Authors: Taylor Janiece L , Clair Catherine A , Gitlin Laura N , Atkins Shelbie , Bandeen-Roche Karen , Abshire Saylor Martha , Hladek Melissa deCardi , Riser Tiffany J , Thorpe Roland J , Szanton Sarah L 
Published: September 2023

Abstract

Background and Objectives
The intersection of race, gender, and age puts older African American women at high risk of experiencing comorbid pain and depressive symptoms. The purpose of this study was to assess the feasibility and acceptability of a 12-week behavioral activation intervention to target self-selected goals related to pain and depressive symptoms in middle-aged and older African American women.

Research Design and Methods
This randomized waitlist control study included 34 self-identified African American women, 50 years of age or older, with moderate-to-severe chronic pain and depressive symptoms. The intervention consisted of 8 in-person or virtual 1-hour visits with a nurse. Follow-up acceptability assessments were conducted with 10 participants.

Results
The average age of the participants was 64.8 (standard deviation [SD] 10.5). They reported an average pain intensity score of 7.0 (SD 1.9) out of 10 and an average Patient Health Questionnaire-9 depressive symptoms score of 11.9 (SD 4.0) at baseline. Of the 34 participants who consented, 28 (82.4%) women started the intervention and 23 (82.1%) completed the intervention. Participants described the study as useful and beneficial. Participants recommended including a group component in future iterations. Effect sizes at 12 weeks were −0.95 for depressive symptoms indicating a substantial decrease in experienced depressive symptoms, but pain intensity was virtually unchanged (+0.09).

Discussion and Implications
The findings of this study demonstrate that the intervention is acceptable among middle-aged and older African American women and their personal goals were met. Including a group component and identifying effective ways to decrease attrition rates will be key in the next steps of development for this intervention. It is crucial to provide tailored, nonpharmacological approaches to pain, and depression symptom management in older adult populations who experience inequities in pain and mental health outcomes. This study emphasizes the importance of participant-driven goal-setting interventions.
Improving care safety by characterizing task interruptions during interactions between healthcare professionals: an observational study
Authors: Teigné Delphine , Cazet Lucie , Birgand Gabriel , Moret Leila , Maupetit Jean-Claude , Mabileau Guillaume , Terrien Noémie 
Published: September 2023

Abstract
Few studies have investigated interruptions to the work of professionals practicing in inpatient hospitals, and even fewer take account of the functions that make up the system. Safety of care can be improved by considering avoidable interruptions during interactions between managerial and care delivery functions. The present study describes the characteristics of interruptions to the work of professionals working in the inpatient hospital sector, with respect to their typology, frequency, duration, and avoidability in the context of interactions between functions. This direct observational study of interruptions in hospital care was performed in the Pays de la Loire (west coast) area of France. A total of 23 teams (17 institutions) working in medical or surgical specialties (excluding intensive care) were included. Observations were performed between May and September 2019, and lasted seven consecutive hours per team. A pair of observers simultaneously observed the same professional for ∼30 min. Each occupational category was examined. Reported characteristics were: (i) the method and duration of the request, (ii) the location of interrupted and interrupting persons, (iii) the reaction of the interrupted person, (iv) the characteristics of the interrupting person, and (v) the classification of interrupted and interrupting tasks according to their function. An avoidable interruption was defined. Interruptions during interactions between professionals were categorised in terms of their function and avoidability. Descriptive statistical analyses (mean, standard deviation, and distribution) were run. In particular, cross-comparisons were run to highlight avoidability interruptions and interactions between managerial and care delivery functions during the working day, for different professional categories, and for the location of the request. Overall, 286 interrupted professionals were observed and 1929 interruptions were characterised. The majority of interruptions were due to a face-to-face request (58.7%), lasting ≤30 s (72.5%). Professionals engaged in the response in 49.3% of cases. A total of 57.4% of interruptions were avoidable. The average number of interruptions was 10.5 (SD = 3.2) per hour per professional. An analysis of avoidability and interactions between managerial and care delivery functions found that the period between 12:00 and 13:00 was the riskiest in terms of care safety. This study highlighted the characteristics of interruptions to the activity of professionals working in inpatient hospitals. Care teams could focus on making medical and nursing professionals much more aware of the importance of interruptions, and each team could decide how to best-manage interruptions, in the context of their specific working environment.
Massive Violence Against Civilians in War
Authors: Mégret Frédéric 
Published: September 2023

Abstract
Armed conflicts have increasingly been characterized by a phenomenon of massive violence against civilians. Beyond a certain point, the question becomes whether such violence is properly characterized as incidental to the pursuit of hostilities or should be seen as conceptually detached from it. This article looks at the competing cases for dealing with this phenomenon of massive violence against civilians from the perspective of war crimes or crimes against humanity. The focus of war crimes particularly when committed as part of a policy at the International Criminal Court has further diminished the difference with crimes against humanity. This article finds that, given the dense overlap of both categories when it comes to massive violence against civilians in times of war, the expressivist finalities of international criminal justice are better served by emphasizing the fundamental nature of such violence as a crime against humanity. This better makes sense of the genealogy of international criminal law as emerging from a tradition of human rights and recuses any notion that systematic attacks against civilians have, in fact and in principle, anything to do with the pursuit of war.
Report on the exact methods for finding minimum-sized DFA
Authors: Wieczorek Wojciech , Strąk Łukasz , Nowakowski Arkadiusz 
Published: September 2023

Abstract
This paper presents four state-of-art methods for the finite-state automaton inference based on a sample of labeled strings. The first algorithm is Exbar, and the next three are mathematical models based on ASP, SAT and SMT theories. The potentiality of using multiprocessor computers in the context of automata inference was our research’s primary goal. In a series of experiments, we showed that our parallelization of the exbar algorithm is the best choice when a multiprocessor system is available. Furthermore, we obtained a superlinear speedup for some of the prepared datasets, achieving almost a 5-fold speedup on the median, using 12 and 24 processes.
Hyaline-vascular type unicentric Castleman disease with dysplastic follicular dendritic cell proliferative lesions: a case report
Authors: Horikawa Daisuke , Shimazaki Ryotaro , Manabe Kazuya , Ichimura Kentaro , Ishibashi Kei , Fukasaku Yasutomo , Ishikawa Takahisa , Koshizuka Yasuyuki , Shibaki Taiichiro , Yanagida Naoyuki , Akabane Hiromitsu , Yokoo Hideki , Sumi Yasuo 
Published: September 2023

Abstract
Castleman disease (CD) is a rare lymphoproliferative disease. Hyaline-vascular type unicentric CD has a good prognosis if completely resected during surgery. However, follicular dendritic cell proliferative lesions have the potential for recurrence and metastasis. A 22-year-old man was referred to our hospital with the chief complaint of nausea and vomiting. These symptoms were caused by a right mesocolonic tumor pushing the duodenum. The patient underwent laparoscopic tumorectomy and complete surgical excision. The postoperative course was uneventful, with no complications. Pathological examination confirmed that the tumor was an enlarged lymph node, typical of hyaline vascular-type CD; however, follicular dendritic cell proliferative lesions were noted. We report a rare case of hyaline-vascular-type CD with follicular dendritic cell proliferative lesions associated with malignancy, as limited case reports exist on this particular disease.
C-TERMINALLY ENCODED PEPTIDE (CEP) and cytokinin hormone signaling intersect to promote shallow lateral root angles
Authors: Chapman Kelly , Taleski Michael , Frank Manuel , Djordjevic Michael A 
Published: September 2023

Abstract
Root system architecture (RSA) influences the acquisition of heterogeneously dispersed soil nutrients. Cytokinin and C-TERMINALLY ENCODED PEPTIDE (CEP) hormones affect RSA, in part by controlling the angle of lateral root (LR) growth. Both hormone pathways converge on CEP DOWNSTREAM 1 (CEPD1) and CEPD2 to control primary root growth; however, a role for CEPDs in controlling the growth angle of LRs is unknown. Using phenotyping combined with genetic and grafting approaches, we show that CEP hormone-mediated shallower LR growth requires cytokinin biosynthesis and perception in roots via ARABIDOPSIS HISTIDINE KINASE 2 (AHK2) and AHK3. Consistently, cytokinin biosynthesis and ahk2,3 mutants phenocopied the steeper root phenotype of cep receptor 1 (cepr1) mutants on agar plates, and CEPR1 was required for trans-Zeatin (tZ)-type cytokinin-mediated shallower LR growth. In addition, the cepd1,2 mutant was less sensitive to CEP and tZ, and showed basally steeper LRs on agar plates. Cytokinin and CEP pathway mutants were grown in rhizoboxes to define the role of these pathways in controlling RSA. Only cytokinin receptor mutants and cepd1,2 partially phenocopied the steeper-rooted phenotype of cepr1 mutants. These results show that CEP and cytokinin signaling intersect to promote shallower LR growth, but additional components contribute to the cepr1 phenotype in soil.
Incidence of Shoulder Labral Pathology in United States Military Members
Authors: Allen Dexter , Somerson Jeremy S , Janney Cory F 
Published: September 2023

ABSTRACT

Introduction
Shoulder injuries account for approximately 8% to 24% of all musculoskeletal injuries in the military. Recently, a change was made to service-specific physical fitness tests. Knowledge of relative shoulder labral injury rates before and after this change would help guide future directions and preventive strategies. However, we found no previous literature evaluating the rates of labral injury among United States Military branch personnel by enlistment status (enlisted versus officer), gender, age, or race.

Materials and Methods
In this retrospective epidemiological study, we queried the Defense Medical Epidemiology Database for International Classification of Disease, Tenth Revision (ICD-10) code S43.43 (superior glenoid labrum lesion) to determine the total number of patients with a shoulder labral injury from 2016 to 2019. Results were assessed for demographic associations of shoulder labral injury with branch, service occupation, rank, gender, race, and age. Queries were limited to first-time occurrences and ambulatory data only.

Results
Overall, our study found the incidence of shoulder labral injuries to be largely conserved each year from 2016 to 2019 (3.22–3.35/1000/year). Incidence of labral injury was highest in males, White service members, the junior enlisted, the Army service branch, ages 20 to 29, and enlisted non-combat personnel.

Conclusions
With knowledge of injury patterns in specific military populations, initiatives may be taken to identify at-risk service members with the goal of informing future preventive strategies.
Reconceptualizing Music Therapy in Acute Mental Health Settings Part II: Clinical Applications of Single-Session Therapy
Authors: Silverman Michael J 
Published: September 2023

Abstract
By championing the strengths, resources, and resilience of service users and increasing treatment access while limiting costs, single-session therapy (SST) represents a collaborative, direct, and transparent approach to providing treatment. In SST, service users have active and empowered roles in determining the focus, solutions, and extent of the therapy. SST practitioners note that all circumstances, settings, and contexts are unique and thus provide service users with autonomy to help them address the concerns that brought them to seek treatment. In Part II, I describe various ways to implement SST for music therapy clinicians in acute mental health settings. As Carr et al. (2013) noted a need for a music therapy model in acute mental health settings, I highlight Soo-Hoo’s (2018) Strength-Based Multicultural Integrative Therapy model as a potential therapeutic framework. To help music therapists apply aspects of SST to their clinical practice, I also provide questions for therapists to use in SST, describe how to conclude SST, provide suggestions for single-session group music therapy and other applications of single-session therapy in music therapy, and conclude with a critical reflection of SST.
Transitional Support for Former Members of Parliament: Benchmarks for ‘Professional Parliaments’
Authors: Ferguson Peter , Nethery Amy , Nwokora Zim 
Published: September 2023

Abstract
Leaving parliament is often a time of significant financial, employment and emotional difficulty for MPs. However, few studies have examined the support provided by parliaments to departing and former members. Consequently, parliaments lack access to best-practice case studies to improve the transitional experience for MPs. This article develops five benchmarks for supporting former MPs, covering transitional financial assistance; retirement income; career, financial, life transitions and redundancy counselling; mental health and medical services; and social and networking opportunities. These benchmarks are used to assess the support provided to former members by 22 selected ‘professional parliaments’. Although most of these parliaments offer adequate retirement income, none currently provide sufficient transitional financial assistance for MPs who depart before pensionable age. In all cases, improvements are also required to mental health and other counselling services. Most parliaments provide adequate social and networking opportunities. Implementing and extending these measures will improve the transitional experience of former MPs and enhance democratic rotation by reducing impediments to high-quality candidates from diverse socioeconomic and cultural backgrounds from seeking political office, while easing the exit of MPs who are ready to leave.
Retrospective analysis of equity-based optimization for COVID-19 vaccine allocation
Authors: Stafford Erin , Dimitrov Dobromir , Ceballos Rachel , Campelia Georgina , Matrajt Laura 
Published: September 2023

Abstract
Marginalized racial and ethnic groups in the United States were disproportionally affected by the COVID-19 pandemic. To study these disparities, we construct an age-and-race-stratified mathematical model of SARS-CoV-2 transmission fitted to age-and-race-stratified data from 2020 in Oregon and analyze counterfactual vaccination strategies in early 2021. We consider two racial groups: non-Hispanic White persons and persons belonging to BIPOC groups (including non-Hispanic Black persons, non-Hispanic Asian persons, non-Hispanic American-Indian or Alaska-Native persons, and Hispanic or Latino persons). We allocate a limited amount of vaccine to minimize overall disease burden (deaths or years of life lost), inequity in disease outcomes between racial groups (measured with five different metrics), or both. We find that, when allocating small amounts of vaccine (10% coverage), there is a trade-off between minimizing disease burden and minimizing inequity. Older age groups, who are at a greater risk of severe disease and death, are prioritized when minimizing measures of disease burden, and younger BIPOC groups, who face the most inequities, are prioritized when minimizing measures of inequity. The allocation strategies that minimize combinations of measures can produce middle-ground solutions that similarly improve both disease burden and inequity, but the trade-off can only be mitigated by increasing the vaccine supply. With enough resources to vaccinate 20% of the population the trade-off lessens, and with 30% coverage, we can optimize both equity and mortality. Our goal is to provide a race-conscious framework to quantify and minimize inequity that can be used for future pandemics and other public health interventions.
Spreading expertise: think tanks as digital advocators in the social media era
Authors: Zhao Jing , Zhu Xufeng 
Published: September 2023

Abstract
Think tanks and their roles in rendering expertise in policy advice have been the subject of historical and ongoing research in policy sciences. However, the widening trend of digital behaviors of think tanks in the social media era is yet to be investigated. While social media is reshaping the political ecology and challenging conventional sources of knowledge, it also serves as a potential channel for think tanks to publicly share their expertise and policy advice with the public and decision-makers, thus evolving into “digital advocators.” Based on social media big data methods, this paper has constructed two sets of new think tank indicators with “network centrality” of social media accounts and “ripple effect” of social media citations from Facebook and Twitter to capture and observe the digital activities of 207 prominent think tanks in 62 countries or regions. We have concluded that think tanks have displayed their opinion and values and increased visibility as digital advocators by spreading expertise on social media platforms with online marketing skills. With various values and ideas, social media not only is hosting massive policy advocacy activities and being an expertise spreading arena for think tanks but has also been changing the ecology of the think tank industry and expertise markets.