bluuebunny/crossref_metadata_2025_split huggingface dataset:
CT-based AI model for predicting therapeutic outcomes in ureteral stones after single extracorporeal shock wave lithotripsy through a cohort study
Authors: Yang Huancheng , Wu Xiang , Liu Weihao , Yang Zhong , Wang Tianyu , You Weifan , Ye Baiwei , Wu Bingni , Wu Kai , Zeng Haoyang , Liu Hanlin 
Published: June 2024

Objectives:
Exploring the efficacy of an artificial intelligence (AI) model derived from the analysis of computed tomography (CT) images to precisely forecast the therapeutic outcomes of singular-session extracorporeal shock wave lithotripsy (ESWL) in the management of ureteral stones.

Methods:
A total of 317 patients diagnosed clinically with ureteral stones were included in this investigation. Unenhanced CT was administered to the participants within the initial fortnight preceding the inaugural ESWL. The internal cohort consisted of 250 individuals from a local healthcare facility, whereas the external cohort comprised 67 participants from another local medical institution. The proposed framework comprises three main components: an automated semantic segmentation model developed using 3D U-Net, a feature extractor that integrates radiomics and autoencoder techniques, and an ESWL efficacy prediction model trained with various machine learning algorithms. All participants underwent thorough postoperative follow-up examinations 4 weeks hence. The efficacy of ESWL was defined by the absence of stones or residual fragments measuring ≤2 mm in KUB X-ray assessments. Model stability and generalizability were judiciously validated through a fivefold cross-validation approach and a multicenter external test strategy. Moreover, Shapley Additive Explanations (SHAP) values for individual features were computed to elucidate the nuanced contributions of each feature to the model’s decision-making process.

Results:
The semantic segmentation model the authors constructed exhibited an average Dice coefficient of 0.88±0.08 on the external testing set. ESWL classifiers built using Support Vector Machine (SVM), Random Forest (RF), XGBoost (XB), and CatBoost (CB) achieved AUROC values of 0.78, 0.84, 0.85, and 0.90, respectively, on the internal validation set. For the external testing set, SVM, RF, XB, and CB predicted ESWL with AUROC values of 0.68, 0.79, 0.80, and 0.83, respectively, with the last one being the optimal algorithm. The radiomics features and auto-encoder features made significant contributions to the decision-making process of the classification model.

Conclusions:
This investigation unmistakably underscores the remarkable predictive prowess exhibited by a scrupulously crafted AI model using CT images to precisely anticipate the therapeutic results of a singular session of ESWL for ureteral stones.
Opportunities for Improving Detection of Cancer Predisposition Syndromes in Pediatric Solid Tumor Patients
Authors: Hu Benjamin , Kirkey Danielle , Wakeling Adrienne , McGuinness Molly , Kreimer Sara , Crane Jacquelyn , Spunt Sheri L. 
Published: June 2024

Background:
Detection of cancer predisposition syndromes (CPS) depends on identifying risk factors, including tumor type, family history, and physical findings, to prompt referral for genetic counseling/testing. Whether pediatric oncology providers (POPs) collect adequate family history information is unknown.

Methods:
A single-institution retrospective chart review of solid tumor patients <18 years of age referred for a CPS evaluation between January 1, 2017 and January 31, 2019 was performed. POP adherence to American Society of Clinical Oncology (ASCO) family history collection recommendations was measured and compared with genetic counselor performance. Whether sufficient family history was documented to satisfy the criteria of three genetic counseling referral guidelines [American College of Medical Genetics (ACMG), updated Jongmans (UJ), and McGill Interactive Pediatric OncoGenetic Guidelines (MIPOGG)] was evaluated.

Results:
POPs and genetic counselors achieved all 6 ASCO family history metrics in 3% and 99% of 129 eligible cases, respectively. POPs failed to document sufficient family history to satisfy genetic counseling referral criteria in most cases (74% ACMG, 73% UJ, 79% MIPOGG).

Conclusions:
POPs perform poorly in family history collection, raising concern that some patients at risk for a CPS based on their family history may not be referred for genetic counseling/testing. Interventions to improve family history collection are needed to enhance CPS detection.
Opalski syndrome: a rare variant of Wallenberg syndrome: a case report and literature review
Authors: Mansour Marah , Alwaw Ricarda , Almaalouli Bsher , Qasem Yasmine , Hassan Khalil , Charaf Obada , Chama Mohd Beshr , Mansour Nawar Akramah , allabwani Abd alqader , Hammad Yousha 
Published: June 2024

Background:
Opalski syndrome is a rare variant of Wallenberg syndrome (lateral medullary syndrome) that demonstrates concomitant ipsilateral hemiplegia due to infarctions within the lateral medulla and the cervical spinal cord, which also extend to the post-pyramidal decussation to affect the corticospinal tract.

Case presentation:
A 56-year-old man initially presented with a unilateral headache with right cervical pain. Consequently, he developed symptoms that indicate Wallenberg syndrome: vertigo, dysphonia, dysarthria, right limb ataxia with a tendency to fall, and ptosis, in addition to ipsilateral hemiparesis. The diffusion-weighted imaging MRI (DWI MRI) performed initially demonstrated an acute infarct in the dorsolateral medulla. Accordingly, an axial T2-weighted MRI showed a hyperintense focal region in the same area, even as magnetic resonance angiography (MRA) revealed complete stenosis of the corresponding vertebral artery.

Discussion:
Opalski syndrome can result from different etiologies such as vascular occlusion or dissection. Although symptoms may vary, patients commonly present with sudden weakness, vertigo, and gait instability. Diagnosis often relies on MRI or DW-MRI. Treatment is tailored depending on individual factors and may involve medications and monitoring. Complications like respiratory failure can occur but are not directly linked to Opalski syndrome. Proper management includes addressing ischemic risk factors and ensuring appropriate nutrition.

Conclusion:
This case highlights the importance of including Opalski syndrome early in the differential diagnosis of patients with clinically suspected ipsilateral lateral medullary infarction and hyperacute ipsilateral hemiparesis.
A comparison of textured vs smooth surfaced implants in sub fascial breast augmentation.
Authors: Brown Tim 
Published: June 2024

Background:
Subfascial placement of breast implants has the advantages of subglandular and submuscular placement without the adverse outcomes. This study examined the differences in outcomes between textured and smooth implants.

Methods:
A total of 385 patients underwent subfascial breast augmentation in two cohorts. The initial series (n=209) employed textured implants and the second (n=176) employed smooth implants. In all other respects, patient management was identical. Adverse outcomes, changes in breast morphometry, and patient satisfaction were compared between the two groups.

Results:
The follow-up period ranged from to 74-272 weeks for smooth implants (mean 164 weeks, STD 50.6) and 78-279 weeks for textured implants (mean= 186 weeks, STD=54). The incidence of capsular contracture was the same for smooth and textured implants (4.7% and 6.2%, P=.64). Changes in breast shape at the lower pole, patient satisfaction, and the incidence of other adverse outcomes were the same in both groups.

Conclusions:
Subfascial placement of smooth and textured breast implants yielded similar outcomes.
Peer-Delivered HIV Self-Testing, Sexually Transmitted Infection Self-Sampling, and Pre-exposure Prophylaxis for Transgender Women in Uganda: A Randomized Trial
Authors: Mujugira Andrew , Karungi Beyonce , Nakyanzi Agnes , Bagaya Monica , Nsubuga Rogers , Sebuliba Timothy , Nampewo Olivia , Naddunga Faith , Birungi Juliet E. , Sapiri Oliver , Nyanzi Kikulwe R. , Bambia Felix , Muwonge Timothy , Gandhi Monica , Haberer Jessica E. 
Published: June 2024

Background:
Peer-delivered HIV self-testing (HIVST) and sexually transmitted infection self-sampling (STISS) may promote adherence to oral pre-exposure prophylaxis (PrEP), but no studies have analyzed this approach among transgender women (TGW) in sub-Saharan Africa.

Setting:
The Peer study was a cluster randomized trial in Uganda (October 2020–July 2022; NCT04328025).

Methods:
Ten TGW peer groups, each with 1 TGW peer and 8 TGW, were randomized 1:1 to receive quarterly in-clinic HIV testing with PrEP refills as standard-of-care (SOC) or SOC plus monthly peer delivery of oral-fluid HIVST, STISS, and PrEP refills (intervention). Participants were followed for 12 months. The primary outcome was PrEP adherence.

Results:
We screened 85 TGW and enrolled 82 (41 per arm). The median age was 22 years (interquartile range [IQR] 20–24). Twelve-month retention was 88% (72/82). At the 3, 6, 9, and 12-month clinic visits, 10%, 5%, 5%, and 0% of TGW in the intervention arm had TFV-DP levels ≥700 fmol/punch, versus 7%, 15%, 7%, and 2% in the SOC arm, respectively (P = 0.18). At all visits, any detectable TFV-DP levels were significantly higher in SOC than the peer delivery group (P < 0.04). PrEP adherence was associated with sex work (incidence rate ratio 6.93; 95% CI: 2.33 to 20.60) and >10 years of schooling (incidence rate ratio 2.35; 95% CI: 1.14 to 4.84). There was a strong correlation between tenofovir detection in dried blood spots and urine (P < 0.001). No HIV seroconversions occurred.

Conclusions:
Peer-delivered HIVST and STISS did not increase low levels of oral PrEP adherence among TGW in Uganda. Long-acting PrEP formulations should be considered for this population.
Mental Health Trends in Patients With Symptomatic Macromastia After Reduction Mammoplasty
Authors: Park Rachel H. , Odega Ugochukwu K. , Kilmer Lee H. , Hollenbeck Scott T. , DeGeorge Brent R. 
Published: June 2024

Background
Symptomatic macromastia can significantly affect both physical and mental health. Although previous studies suggested that breast reduction (BR) improves quality of life and mental health conditions, they were limited to smaller sample sizes and largely based on survey feedback. This study aims to further assess the impact of BR on mental health outcomes, specifically looking at prescribing patterns for common antidepressants.

Methods
A national insurance–based database was utilized for data collection. Patients with a diagnosis of macromastia (ICD-10 N62) between the years 2010 and 2021 that either underwent bilateral BR (CPT 19318) or did not undergo BR were included in the study. Demographics and medical comorbidities were compared. Among those who underwent BR, preoperative and postoperative rates of mental health diagnoses and antidepressant use were compared. Logistic regression analysis was performed to determine variables associated with surgery.

Results
Patients with a history of macromastia with a history of BR were compared with those with a history of macromastia without BR. A significantly higher percentage of patients in the BR group reported a history of depression (48.5%), obesity (55.7%), and selective serotonin reuptake inhibitor (SSRI)/serotonin-norepinephrine reuptake inhibitor (SNRI) use (55.3%) when compared with that of the no-reduction group (46.3%, 50.8%, and 52.6%). Patients with history of depression and obesity were more likely to undergo BR (odds ratio of 1.11 and 1.31). Patients who underwent BR had significantly reduced rates of mental health outcomes including depression (38.6% to 27.4%), anxiety (4.3% to 3.1%), and SSRI or SNRI prescriptions (46.3% to 29.5%) postoperatively.

Conclusions
Patients who underwent BR for symptomatic macromastia showed significantly reduced rates of depression, anxiety, and most importantly, rates of SSRI/SNRI prescriptions postoperatively when compared to those who did not undergo BR for symptomatic macromastia.
Entrustable Professional Activities in Postgraduate General Surgery Training
Authors: Nel Daniel , Jonas Eduard , Burch Vanessa , Cairncross Lydia , Nel Amy , Alseidi Adnan , George Brian , ten Cate Olle 
Published: June 2024

Objective:
To provide an overview of the current use of Entrustable Professional Activities (EPAs) in postgraduate general surgery training internationally.

Background:
Entrustable Professional Activities (EPAs) were introduced to connect clinical competencies and the professional activities to be entrusted to trainees on graduation. The popularity of EPAs as a framework for assessment is growing globally, including in general surgery. Anecdotally, there appears to be substantial variation in how they are implemented, yet a formal comparison of their use in postgraduate general surgery training is lacking.

Methods:
A scoping review was performed, based on the original five-stage approach described by Arksey and O’Malley with the addition of protocol-specific items from the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocols extension for scoping reviews (PRISMA-ScR).

Results:
Twenty-nine published and grey literature sources were included in the review. Entrustable Professional Activity use in postgraduate general surgery training was identified in 11 unique contexts, including from North America, South America, Europe, Asia, Africa, and Australia. There were substantial differences in the scope and number of EPAs, tools used for EPA assessment, and how EPAs were sequenced through training. Despite wide variation, eight distinct EPAs were common to the majority (>80%) of countries. Several articles described findings of EPA use in postgraduate general surgery training, allowing identification of multiple barriers and facilitators to integration.

Conclusions:
This review provides guidance for certification and regulatory bodies, program directors, and institutions with ambitions to implement EPAs for assessment and curricular design. In settings where EPAs are already used, the data may facilitate refinement of programs and strategies.
Performance evaluation of TaqMan™Arbovirus Triplex Kit (ZIKV/DENV/CHIKV) for detection and differentiation of Dengue and Chikungunya viral RNA in serum samples of symptomatic patients
Authors: Panmei Kakhangchung , Hakeem Syed Abdul , Okafor Obiageli , Mammen Shoba , Abraham Asha Mary 
Published: June 2024

AbstractIntroductionGlobal outbreaks of mosquito-transmitted arbovirus infections, such as dengue (DENV) and chikungunya (CHIKV), are increasing. Differentiating these infections is challenging due to non-specific symptoms and serology limitations. PCR-based approaches offer higher sensitivity and specificity. This study evaluated the performance of TaqMan™ Arbovirus Triplex Kit (ZIKV/DENV/CHIKV) (TaqMan™ Kit) to detect DENV and CHIKV in clinical samples from patients in south India.MethodsIn total, 280 serum samples with 90 DENV-positive, 90 CHIKV-positive, and 100 negative samples were tested with TaqMan™ Kit and CDC Trioplex Real-Time RT-PCR assay. No Zika virus was detected. The sensitivity and specificity of viral RNA detection were determined, and discordant results were resolved using comparator PCRs, dengue NS1 antigen detection, virus-specific antibody results, or previously de-identified in-house PCR results.ResultsThe TaqMan™ Kit showed 100% agreement with the comparator for DENV detection in 92 positive samples. Among 188 samples negative for DENV by the comparator, 30 showed positive results with the TaqMan™ kit, and 23 of those were confirmed as true positives. The resulting sensitivity and specificity for DENV detection were 100% and 95.1%, respectively. For CHIKV, 77 positive and 195 negative results were concordant. Eight samples showed discordant results, but upon resolution testing, sensitivity and specificity for CHIKV were 93.9% and 100.0%, respectively.ConclusionThe TaqMan™ Arbovirus Triplex Kit demonstrated high sensitivity and specificity (>93%) for detecting circulating DENV and CHIKV strains. Multiplex PCR testing can improve case detection, surveillance, and public health responses while optimizing laboratory resources for outbreak control.
Factors involved in vulvar pain during sexual activity and persistence in sexual activity amidst pain
Authors: Oesterling Carlotta , Harder Amelie , Borg Charmaine , de Jong Peter 
Published: June 2024

AbstractEvidence suggests that women often endure pain during sexual activity, continue engaging in such activity despite experiencing pain, and tend to avoid communicating these painful experiences to their partners. The present study aims to shed light on psychosocial factors that may contribute to vulvar pain and the engagement in sexual activity despite pain, with a specific focus on the relevance of sexual self-esteem, the definition of sex (limited to penile-vaginal intercourse or inclusive of other intimate behaviours), sexual agency, and sexual motivation. A sample of N = 277 female students of a Dutch University was included. Participants were between 18 and 33 years old. The primary outcome measures were female sexual distress, sexual function, and vulvar pain. Engagement in sexual activity despite pain, pain communication, sexual agency, and relationship satisfaction were included as mediators. The majority of participants (80%) reported to experience pain at least sometimes, and 15% reported to experience pain more than half of the time. Engaging in penile-vaginal intercourse despite experiencing pain was common, with 42% of participants indicating to do so always or most of the time and 65% at least sometimes when experiencing pain. Of the affected women, 41% did not communicate pain to their partners. Low sexual self-esteem, a restrictive definition of sex, limited sexual agency, and low autonomous sexual motivation were all significantly related to at least one of the primary outcome variables. These associations were partly mediated by engagement in PVI despite pain, (no) pain communication, and (low) relationship satisfaction.
Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling
Authors: Regner Matthew J. , Garcia-Recio Susana , Thennavan Aatish , Wisniewska Kamila , Mendez-Giraldez Raul , Felsheim Brooke , Spanheimer Philip M. , Parker Joel S. , Perou Charles M. , Franco Hector L. 
Published: June 2024

SUMMARYAnnotation of thecis-regulatory elements that drive transcriptional dysregulation in cancer cells is critical to improving our understanding of tumor biology. Herein, we present a compendium of matched chromatin accessibility (scATAC-seq) and transcriptome (scRNA-seq) profiles at single-cell resolution from human breast tumors and healthy mammary tissues processed immediately following surgical resection. We identify the most likely cell-of-origin for luminal breast tumors and basal breast tumors and then introduce a novel methodology that implements linear mixed-effects models to systematically quantify associations between regions of chromatin accessibility (i.e. regulatory elements) and gene expression in malignant cells versus normal mammary epithelial cells. These data unveil regulatory elements with that switch from silencers of gene expression in normal cells to enhancers of gene expression in cancer cells, leading to the upregulation of clinically relevant oncogenes. To translate the utility of this dataset into tractable models, we generated matched scATAC-seq and scRNA-seq profiles for breast cancer cell lines, revealing, for each subtype, a conserved oncogenic gene expression program betweenin vitroandin vivocells. Together, this work highlights the importance of non-coding regulatory mechanisms that underlie oncogenic processes and the ability of single-cell multi-omics to define the regulatory logic of BC cells at single-cell resolution.
DecipheringArabidopsis thalianaAcclimation to Sublethal Combined Abiotic Stresses
Authors: Jiang Zhang , Verhoeven Ava , Li Yihong , Geertsma Romy , Sasidharan Rashmi , van Zanten Martijn 
Published: June 2024

AbstractPlants are frequently exposed to environmental challenges. Responses to sub-lethal abiotic stress combinations are complex and often distinct from responses to individual stresses and remain poorly understood. Investigating traits and molecular factors mediating acclimation to stress combinations is essential for the development of climate change-resilient field crops. Here, we studied the morphological, physiological, and molecular responses ofArabidopsis thalianato i) co-occurring high temperature and drought and ii) flooding sequentially followed by drought, both of which have increased in frequency due to climate change. A set of 15 physiological and morphological traits were assessed during single and combined stresses. By combining these comprehensive trait analyses with transcriptome characterization, we established the generally additive effects of simultaneous or sequential stresses on plant morphology and physiology compared to the corresponding individual stresses. Although drought had a mild effect in both stress combinations, a unique transcriptome signature emerged upon combination with high temperature simultaneously or flooding sequentially. Molecular processes identified as important for multi-stress resilience included plastid-nucleus communication, ABA signaling and photo-acclimation. Based on the RNA-seq data, a set of 39 genes was identified as potential multi-stress response regulators. Mutants were tested to validate their contribution to plant survival and phenotypic acclimation under combined stress. We confirmed the involvement of several genes in regulating phenotypic acclimation traits. Among the novel identified factors are EARLY FLOWERING 6 (ELF6) and ARABIDOPSIS TÓXICOS EN LEVADURA (ATL80), with significant effects on plant growth, leaf development and plant survival (wilting) during high-temperature drought and post-submergence drought respectively.
ESPRESSO: Spatiotemporal omics based on organelle phenotyping
Authors: Scipioni Lorenzo , Tedeschi Giulia , Navarro Mariana , Jia Yunlong , Atwood Scott , Prescher Jennifer A. , Digman Michelle 
Published: June 2024

AbstractOmics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have been instrumental to improving our understanding of complex biological systems. Despite fast-pace advancements, a crucial dimension is still left to explore: time. To capture this key parameter, we introduce ESPRESSO (Environmental Sensor Phenotyping RElayed by Subcellular Structures and Organelles), a pioneering technique that provides high-dimensional phenotyping resolved in space and time. Through a novel paradigm, ESPRESSO combines fluorescent labeling, advanced microscopy and bioimage and data analysis to extract morphological and functional information of the organelle network unveiling phenotypic changes over time at the single-cell level. In this work, we present ESPRESSO’s methodology and its application across numerous cellular systems, showcasing its ability to discern cell types, stress response, differentiation and immune cells polarization. We then correlate ESPRESSO phenotypic changes with gene expression and demonstrate its applicability to 3D cultures, offering a path to revolutionizing biological exploration, providing invaluable insights into cellular states in both space and time.