bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and validation of survival prognostic models for head and neck cancer patients using machine learning and dosiomics and CT radiomics features: a multicentric study
Authors: Mansouri Zahra , Salimi Yazdan , Amini Mehdi , Hajianfar Ghasem , Oveisi Mehrdad , Shiri Isaac , Zaidi Habib 
Published: January 2024

Abstract
Background
This study aimed to investigate the value of clinical, radiomic features extracted from gross tumor volumes (GTVs) delineated on CT images, dose distributions (Dosiomics), and fusion of CT and dose distributions to predict outcomes in head and neck cancer (HNC) patients.

Methods
A cohort of 240 HNC patients from five different centers was obtained from The Cancer Imaging Archive. Seven strategies, including four non-fusion (Clinical, CT, Dose, DualCT-Dose), and three fusion algorithms (latent low-rank representation referred (LLRR),Wavelet, weighted least square (WLS)) were applied. The fusion algorithms were used to fuse the pre-treatment CT images and 3-dimensional dose maps. Overall, 215 radiomics and Dosiomics features were extracted from the GTVs, alongside with seven clinical features incorporated. Five feature selection (FS) methods in combination with six machine learning (ML) models were implemented. The performance of the models was quantified using the concordance index (CI) in one-center-leave-out 5-fold cross-validation for overall survival (OS) prediction considering the time-to-event.

Results
The mean CI and Kaplan-Meier curves were used for further comparisons. The CoxBoost ML model using the Minimal Depth (MD) FS method and the glmnet model using the Variable hunting (VH) FS method showed the best performance with CI = 0.73 ± 0.15 for features extracted from LLRR fused images. In addition, both glmnet-Cindex and Coxph-Cindex classifiers achieved a CI of 0.72 ± 0.14 by employing the dose images (+ incorporated clinical features) only.

Conclusion
Our results demonstrated that clinical features, Dosiomics and fusion of dose and CT images by specific ML-FS models could predict the overall survival of HNC patients with acceptable accuracy. Besides, the performance of ML methods among the three different strategies was almost comparable.
Fulgor: a fast and compact k-mer index for large-scale matching and color queries
Authors: Fan Jason , Khan Jamshed , Singh Noor Pratap , Pibiri Giulio Ermanno , Patro Rob 
Published: January 2024

AbstractThe problem of sequence identification or matching—determining the subset of reference sequences from a given collection that are likely to contain a short, queried nucleotide sequence—is relevant for many important tasks in Computational Biology, such as metagenomics and pangenome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resource-efficient solution to this problem is of utmost importance. This poses the threefold challenge of representing the reference collection with a data structure that is efficient to query, has light memory usage, and scales well to large collections. To solve this problem, we describe an efficientcolored de Bruijngraph index, arising as the combination of ak-mer dictionary with a compressed inverted index. The proposed index takes full advantage of the fact that unitigs in the colored compacted de Bruijn graph aremonochromatic(i.e., allk-mers in a unitig have the same set of references of origin, orcolor). Specifically, the unitigs are kept in the dictionary in color order, thereby allowing for the encoding of the map fromk-mers to their colors in as little as 1 +o(1) bits per unitig. Hence, one color per unitig is stored in the index with almost no space/time overhead. By combining this property with simple but effective compression methods for integer lists, the index achieves very small space. We implement these methods in a tool called , and conduct an extensive experimental analysis to demonstrate the improvement of our tool over previous solutions. For example, compared to —the strongest competitor in terms of index space vs. query time trade-off— requires significantly less space (up to 43% less space for a collection of 150,000Salmonella entericagenomes), is at least twice as fast for color queries, and is 2–6$$\times$$×faster to construct.
Percutaneous kyphoplasty combined with pediculoplasty for the surgical treatment of osteoporotic thoracolumbar burst fractures
Authors: Xiao Changming , Wang Haozhong , Lei Yang , Xie Mingzhong , Li Sen 
Published: January 2024

Abstract
Objective
This study introduces a minimally invasive technique for efficient three-column reconstruction, augmentation, and stabilization of osteoporotic thoracolumbar burst fractures (OTLBFs).

Methods
Sixty-eight patients with OTLBFs and no neurological deficits were included from July 2019 to September 2020. The patients were divided into two groups: the simple percutaneous kyphoplasty (PKP) group (n = 32) and the percutaneous kyphoplasty combined with pediculoplasty (PKCPP) group (n = 36). The clinical and radiological outcomes were assessed during a minimum 1-year follow-up period. Clinical outcomes were assessed via the visual analog scale (VAS) and modified MacNab grading criteria. The radiological outcomes included the Cobb angle (CA), anterior wall height (AWH), and posterior wall height (PWH). The surgery duration, postoperative analgesic dosage, length of hospital stay, and complications were recorded.

Results
Surgery duration was not significantly different between the two groups (P > 0.05). The PKCPP group had a lower analgesic dosage and shorter hospital stay (P < 0.05). Postoperatively, the PKCPP group exhibited better VAS scores and modified MacNab scale scores (P < 0.05), but the differences at the last follow-up assessment were not significant (P > 0.05). Postoperative CA, AWH, and PWH correction were not significantly different on the first postoperative day (P > 0.05). However, the PKCPP group had significantly less CA and PWH loss of correction at the last follow-up visit (P < 0.05). The PKCPP group had significantly fewer complications (P < 0.05).

Conclusions
The PKCPP technique complements simple PKP for OTLBFs. It quickly relieves pain, maintains the vertebral body height and Cobb angle, ensures cement stabilization, and offers more stable three-column support.
Drivers of men’s use of intimate partner violence in conflict-affected settings: learnings from the Democratic Republic of Congo
Authors: Bourey Christine , Musci Rashelle J. , Bass Judith K. , Glass Nancy , Matabaro Amani , Kelly Jocelyn T. D. 
Published: January 2024

Abstract
Background
Intimate partner violence against women (IPVAW) is prevalent in conflict-affected settings. Yet, there is limited knowledge about the risk factors that influence men’s use of IPVAW in conflict-affected settings. This paper adopts a transdisciplinary perspective to understand how experiences hypothesized to increase men’s use of IPVAW relate to each other and to men’s use of IPVAW. The findings may help researchers and interventionists to better select and target interventions for IPVAW in conflict-affected settings.

Methods
We used baseline data from the Tushinde Ujeuri project in the Democratic Republic of Congo. Men with at least partial data for the variables of interest were included in the analysis (n = 2080). We estimated a structural equation model that explored how five constructs – interpersonal violence, mental health, socioeconomic adversity, gender inequitable attitudes, and conflict violence – influenced men’s self-reported past-year use of physical and/or sexual IPVAW.

Results
The model had acceptable fit (χ2 = 1576.574, p = 0.000; RMSEA = 0.041; CLI = 0.882; SRMR = 0.055). There was a statistically significant path from interpersonal violence to IPVAW (β = 0.875; OR = 2.40). Interpersonal violence also was linked to gender inequitable attitudes (β = 0.364), which were linked to increased use of IPVAW (β = 0.180; OR = 1.20). Moreover, interpersonal violence was linked to trauma symptoms (β = 0.331), which were linked to increased use of IPVAW (β = 0.238; OR = 1.27). Use of IPVAW decreased as conflict exposures increased (β=-0.036; OR = 0.96), and there was no path from socioeconomic adversity to IPVAW.

Conclusions
Our findings suggest interpersonal violence exposures, trauma symptoms, and gender inequitable attitudes are all risk factors for the use of IPVAW in a conflict-affected setting. While continuing to focus on gender inequitable attitudes and norms, interventionists should also consider addressing men’s experiences of victimization and mental wellbeing. Doing so can help to improve trauma symptoms and may hold promise to reduce IPVAW in conflict-affected settings.
The dopamine receptor D1 inhibitor, SKF83566, suppresses GBM stemness and invasion through the DRD1-c-Myc-UHRF1 interactions
Authors: Xue Zhiyi , Zhang Yan , Zhao Ruiqi , Liu Xiaofei , Grützmann Konrad , Klink Barbara , Zhang Xun , Wang Shuai , Zhao Wenbo , Sun Yanfei , Han Mingzhi , Wang Xu , Hu Yaotian , Liu Xuemeng , Yang Ning , Qiu Chen , Li Wenjie , Huang Bin , Li Xingang , Bjerkvig Rolf , Wang Jian , Zhou Wenjing 
Published: January 2024

Abstract
Background
Extensive local invasion of glioblastoma (GBM) cells within the central nervous system (CNS) is one factor that severely limits current treatments. The aim of this study was to uncover genes involved in the invasion process, which could also serve as therapeutic targets. For the isolation of invasive GBM cells from non-invasive cells, we used a three-dimensional organotypic co-culture system where glioma stem cell (GSC) spheres were confronted with brain organoids (BOs). Using ultra-low input RNA sequencing (ui-RNA Seq), an invasive gene signature was obtained that was exploited in a therapeutic context.

Methods
GFP-labeled tumor cells were sorted from invasive and non-invasive regions within co-cultures. Ui-RNA sequencing analysis was performed to find a gene cluster up-regulated in the invasive compartment. This gene cluster was further analyzed using the Connectivity MAP (CMap) database. This led to the identification of SKF83566, an antagonist of the D1 dopamine receptor (DRD1), as a candidate therapeutic molecule. Knockdown and overexpression experiments were performed to find molecular pathways responsible for the therapeutic effects of SKF83566. Finally, the effects of SKF83566 were validated in orthotopic xenograft models in vivo.

Results
Ui-RNA seq analysis of three GSC cell models (P3, BG5 and BG7) yielded a set of 27 differentially expressed genes between invasive and non-invasive cells. Using CMap analysis, SKF83566 was identified as a selective inhibitor targeting both DRD1 and DRD5. In vitro studies demonstrated that SKF83566 inhibited tumor cell proliferation, GSC sphere formation, and invasion. RNA sequencing analysis of SKF83566-treated P3, BG5, BG7, and control cell populations yielded a total of 32 differentially expressed genes, that were predicted to be regulated by c-Myc. Of these, the UHRF1 gene emerged as the most downregulated gene following treatment, and ChIP experiments revealed that c-Myc binds to its promoter region. Finally, SKF83566, or stable DRD1 knockdown, inhibited the growth of orthotopic GSC (BG5) derived xenografts in nude mice.

Conclusions
DRD1 contributes to GBM invasion and progression by regulating c-Myc entry into the nucleus that affects the transcription of the UHRF1 gene. SKF83566 inhibits the transmembrane protein DRD1, and as such represents a candidate small therapeutic molecule for GBMs.
Differential patterns of reproductive and lifestyle risk factors for breast cancer according to birth cohorts among women in China, Japan and Korea
Authors: Nabila Salma , Choi Ji-Yeob , Abe Sarah Krull , Islam Md Rashedul , Rahman Md Shafiur , Saito Eiko , Shin Aesun , Merritt Melissa A. , Katagiri Ryoko , Shu Xiao-Ou , Sawada Norie , Tamakoshi Akiko , Sakata Ritsu , Hozawa Atsushi , Kim Jeongseon , Nagata Chisato , Park Sue K. , Kweon Sun-Seog , Cai Hui , Tsugane Shoichiro , Kimura Takashi , Kanemura Seiki , Sugawara Yumi , Wada Keiko , Shin Min-Ho , Ahsan Habibul , Boffetta Paolo , Chia Kee Seng , Matsuo Keitaro , Qiao You-Lin , Rothman Nathaniel , Zheng Wei , Inoue Manami , Kang Daehee 
Published: January 2024

Abstract
Background
The birth cohort effect has been suggested to influence the rate of breast cancer incidence and the trends of associated reproductive and lifestyle factors. We conducted a cohort study to determine whether a differential pattern of associations exists between certain factors and breast cancer risk based on birth cohorts.

Methods
This was a cohort study using pooled data from 12 cohort studies. We analysed associations between reproductive (menarche age, menopause age, parity and age at first delivery) and lifestyle (smoking and alcohol consumption) factors and breast cancer risk. We obtained hazard ratios (HRs) with 95% confidence intervals (CIs) using the Cox proportional hazard regression analysis on the 1920s, 1930s, 1940s and 1950s birth cohorts.

Results
Parity was found to lower the risk of breast cancer in the older but not in the younger birth cohort, whereas lifestyle factors showed associations with breast cancer risk only among the participants born in the 1950s. In the younger birth cohort group, the effect size was lower for parous women compared to the other cohort groups (HR [95% CI] 0.86 [0.66–1.13] compared to 0.60 [0.49–0.73], 0.46 [0.38–0.56] and 0.62 [0.51–0.77]). Meanwhile, a higher effect size was found for smoking (1.45 [1.14–1.84] compared to 1.25 [0.99–1.58], 1.06 [0.85–1.32] and 0.86 [0.69–1.08]) and alcohol consumption (1.22 [1.01–1.48] compared to 1.10 [0.90–1.33], 1.15 [0.96–1.38], and 1.07 [0.91–1.26]).

Conclusion
We observed different associations of parity, smoking and alcohol consumption with breast cancer risk across various birth cohorts.
Bathing Adaptations in the Homes of Older Adults (BATH-OUT-2): study protocol for a randomised controlled trial, economic evaluation and process evaluation
Authors: Whitehead Phillip J. , Belshaw Stuart , Brady Samantha , Coleman Elizabeth , Dean Alexandra , Doherty Laura , Fairhurst Caroline , Francis-Farrell Sandra , Golding-Day Miriam , Gray Joanne , Martland Maisie , McAnuff Jennifer , McCarthy Andrew , McMeekin Peter , Mitchell Natasha , Narayanasamy Melanie , Newman Craig , Parker Adwoa , Rapley Tim , Rodgers Sara , Rooney Leigh , Russell Rachel , Sheard Laura , Torgerson David 
Published: January 2024

Abstract
Background
The onset of disability in bathing is particularly important for older adults as it can be rapidly followed by disability in other daily activities; this may represent a judicious time point for intervention in order to improve health, well-being and associated quality of life. An important environmental and preventative intervention is housing adaptation, but there are often lengthy waiting times for statutory provision. In this randomised controlled trial (RCT), we aim to evaluate the effectiveness and cost-effectiveness of bathing adaptations compared to no adaptations and to explore the factors associated with routine and expedited implementation of bathing adaptations.

Methods
BATH-OUT-2 is a multicentre, two-arm, parallel-group RCT. Adults aged 60 and over who are referred to their local authority for an accessible level access shower will be randomised, using pairwise randomisation, 1:1, to receive either an expedited provision of an accessible shower via the local authority or a usual care control waiting list. Participants will be followed up for a maximum of 12 months and will receive up to four follow-ups in this duration. The primary outcome will be the participant’s physical well-being, assessed by the Physical Component Summary score of the Short Form-36 (SF-36), 4 weeks after the intervention group receives the accessible shower. The secondary outcomes include the Mental Component Summary score of the SF-36, self-reported falls, health and social care resource use, health-related quality of life (EQ-5D-5L), social care-related quality of life (Adult Social Care Outcomes Toolkit (ASCOT)), fear of falling (Short Falls Efficacy Scale), independence in bathing (Barthel Index bathing question), independence in daily activities (Barthel Index) and perceived difficulty in bathing (0–100 scale). A mixed-methods process evaluation will comprise interviews with stakeholders and a survey of local authorities with social care responsibilities in England.

Discussion
The BATH-OUT-2 trial is designed so that the findings will inform future decisions regarding the provision of bathing adaptations for older adults. This trial has the potential to highlight, and then reduce, health inequalities associated with waiting times for bathing adaptations and to influence policies for older adults.

Trial registration
ISRCTN Registry ISRCTN48563324. Prospectively registered on 09/04/2021.
A physiotherapy group exercise and self-management approach to improve physical activity in people with mild-moderate Parkinson’s disease: a randomized controlled trial
Authors: Brauer Sandra G. , Lamont Robyn M. , O’Sullivan John D. 
Published: January 2024

Abstract
Background
Physical activity levels are low in people with Parkinson’s disease (PD) and have proved difficult to increase with exercise programs alone. Intervention approaches that address both the capacity to engage in physical activity and self-management strategies to change and maintain exercise behaviours are needed to address this intractable issue.

Methods
This will be an assessor-blinded, randomized controlled trial performed in Brisbane, Australia. Ninety-two people with mild-moderate PD will be randomly allocated to two groups: usual care, and a physiotherapy-led group exercise program combined with self-management strategies. In the intervention group, twelve, 80-min sessions will be conducted over 4 weeks in groups of up to 4 participants. The intervention will consist of circuit training including treadmill walking to target aerobic fitness, and activities targeting strength, balance, and gait performance. In addition, each session will also incorporate strategies focusing on self-management and behaviour change, augmented by the provision of a fitness activity tracker. Outcome measures will be collected at baseline (T1), immediately post intervention (T2) and at 6 months follow-up (T3). The primary outcome measure is free-living physical activity (average daily step count over 7 days) at pre (T1) and post (T2) intervention measured using an activPAL™ device. Secondary outcome measures captured at all time points include time spent walking, sedentary and in moderate intensity exercise over 7 days; spatiotemporal gait performance (step length, gait speed, endurance); health-related quality of life; and outcome expectations and self-efficacy for exercise.

Discussion
Sustainability of gains in physical activity following exercise interventions is a challenge for most populations. Our incorporation of a chronic disease self-management approach into the exercise program including fitness tracking extends previous trials and has potential to significantly improve free-living physical activity in people with PD.

Trial registration
This study has been prospectively registered in Australian and New Zealand Clinical Trial Registry (ACTRN12617001057370), registered on 19/07/2017. Available from www.anzctr.org.au/ACTRN12617001057370.aspx.
Efficacy and safety of azvudine in symptomatic adult COVID-19 participants who are at increased risk of progressing to critical illness: a study protocol for a multicentre randomized double-blind placebo-controlled phase III trial
Authors: Tian Xinlun , Xu Yan , Wang Luo , Dong Chongya , Yan Xiaoyan , Fan Junping , Xie Huaiya , Zhang Hong , Wang Jinglan , Liu Yongjian , Wang Yaqi , Pan Siqi , Wu Aohua , Liu Xueqi , Yao Chen , Wang Mengzhao 
Published: January 2024

Abstract
Background
Severe acute respiratory syndrome coronavirus 2 will coexist with humans for a long time, and it is therefore important to develop effective treatments for coronavirus disease 2019 (COVID-19). Recent studies have demonstrated that antiviral therapy is a key factor in preventing patients from progressing to severe disease, even death. Effective and affordable antiviral medications are essential for disease treatment and are urgently needed. Azvudine, a nucleoside analogue, is a potential low-cost candidate with few drug interactions. However, validation of high-quality clinical studies is still limited.

Methods
This is a multicentre, randomized, double-blind, placebo-controlled phase III clinical trial involving 1096 adult patients with mild-to-moderate symptoms of COVID-19 who are at high risk for progression to severe COVID-19. Patients will be randomized to (1) receive azvudine tablets 5 mg daily for a maximum of 7 days or (2) receive placebo five tablets daily. All participants will be permitted to use a standard treatment strategy except antiviral therapy beyond the investigational medications. The primary outcome will be the ratio of COVID-19-related critical illness and all-cause mortality among the two groups within 28 days.

Discussion
The purpose of this clinical trial is to determine whether azvudine can prevent patients at risk of severe disease from progressing to critical illness and death, and the results will identify whether azvudine is an effective and affordable antiviral treatment option for COVID-19.

Trial registration
ClinicalTrials.gov NCT05689034. Registered on 18 January 2023.
Developing, purchasing, implementing and monitoring AI tools in radiology: practical considerations. A multi-society statement from the ACR, CAR, ESR, RANZCR & RSNA
Authors: Brady Adrian P. , Allen Bibb , Chong Jaron , Kotter Elmar , Kottler Nina , Mongan John , Oakden-Rayner Lauren , dos Santos Daniel Pinto , Tang An , Wald Christoph , Slavotinek John 
Published: January 2024

AbstractArtificial Intelligence (AI) carries the potential for unprecedented disruption in radiology, with possible positive and negative consequences. The integration of AI in radiology holds the potential to revolutionize healthcare practices by advancing diagnosis, quantification, and management of multiple medical conditions. Nevertheless, the ever-growing availability of AI tools in radiology highlights an increasing need to critically evaluate claims for its utility and to differentiate safe product offerings from potentially harmful, or fundamentally unhelpful ones.This multi-society paper, presenting the views of Radiology Societies in the USA, Canada, Europe, Australia, and New Zealand, defines the potential practical problems and ethical issues surrounding the incorporation of AI into radiological practice. In addition to delineating the main points of concern that developers, regulators, and purchasers of AI tools should consider prior to their introduction into clinical practice, this statement also suggests methods to monitor their stability and safety in clinical use, and their suitability for possible autonomous function. This statement is intended to serve as a useful summary of the practical issues which should be considered by all parties involved in the development of radiology AI resources, and their implementation as clinical tools.Key points • The incorporation of artificial intelligence (AI) in radiological practice demands increased monitoring of its utility and safety.• Cooperation between developers, clinicians, and regulators will allow all involved to address ethical issues and monitor AI performance.• AI can fulfil its promise to advance patient well-being if all steps from development to integration in healthcare are rigorously evaluated.