bluuebunny/crossref_metadata_2025_split huggingface dataset:
False-Positive Radioiodine Uptake Related to Posttraumatic Scab Demonstrated by SPECT/CT in a Patient With Differentiated Thyroid Cancer
Authors: Mostowski Romane , de Pontville Michel , Bardet Stéphane , Ciappuccini Renaud 
Published: November 2024

Abstract
A 20-year-old man with papillary thyroid cancer received a fourth radioiodine regimen to treat 131I-avid lung metastases. Posttherapeutic whole-body scan revealed focal radioiodine uptake on the anterior region of the left lower limb that was not visible on previous whole-body scan and which suggested skin contamination. Visual examination of the left leg evidenced a posttraumatic scab caused by a fall 2 weeks before. Skin metastasis was ruled out. 131I SPECT/CT acquisition ruled out bony uptake and confirmed that the skin uptake was related to the superficial scab.
Red Breast Syndrome—Where Has It Gone?
Authors: Navarro Yelissa , Makarewicz Nathan , Hinson Chandler , Thawanyarat Kometh , Coleman-Belin Janet , Loan Phillip , Modi Suraj , Nazerali Rahim S. 
Published: November 2024

Background
Red breast syndrome (RBS) has been noted in past literature as a possible complication of implant-based breast reconstruction (IBBR) with the use of acellular dermal matrices (ADMs). Since its first appearance in 2009, RBS has drawn growing medical attention with reported incidence ranging from 7%–9%. There has been a noted decrease in the emergence of RBS despite its inclusion among the analyzed complications in a number of studies. This systematic review aims to evaluate the trend in reported RBS incidence over time and appropriately determine an accurate incidence of RBS from reported literature since the emergence of the phenomena.

Methods
A systematic literature review was performed in July 2023 that analyzed the incidence of RBS among retrospective cohort studies on complication rates of IBBR with ADM. Patient demographics, RBS incidence rates, and all-cause complications were captured. The review was performed according to Preferred Reporting Items for Systematic Reviews and Meta-analysis guidelines and Methodological Index for Nonrandomized Studies criteria was used to assess study quality.

Results
From 2009 to 2023, a total of 48 studies (n = 6251) met inclusion criteria of which 35 studies from 2017 to 2023 were not already included in a prior systematic review (n = 5246). The mean incidence of RBS in the unreported studies was 2.88% with a weighted mean of 3.22%. Analysis of the trend in RBS over time shows an increasing reported incidence rate from 2009 with a peak in incidence between 2016 and 2017, followed by a steady decline through 2022. Twenty-six of the studies were published from 2016 to 2019.

Conclusions
The incidence of RBS among prior studies and systematic reviews has fluctuated significantly since its initial emergence in 2009. Reported incidence rates have been on the decline since 2018 with a true weighted incidence of 3.22% from analysis of recent reported studies. Potential causes for the decline in incidence include practice changes in ADM preparation, changes in the ADM brand used for IBBR, and improved categorization of RBS compared to cellulitis/infection. Despite more robust criteria for diagnosis, no consensus for management has yet been established.
Reduction Mammaplasty
Authors: Kalmar Christopher L. , White-Dzuro Colin G. , Mok Jean W. , Perdikis Galen 
Published: November 2024

Background
While there is mounting evidence that closed suction drains are not necessary, there is a paucity of literature to demonstrate that drains are harmful after breast reduction. The purpose of this study was to investigate the effect of drains on postoperative seroma, hematoma, and infection, as well as elucidate any risk factors that may be implicated in the development of these complications.

Methods
A retrospective cohort study was conducted of all reduction mammaplasty procedures at our university medical center between 2010–2020. Pedicle type, skin incision, drain utilization, breast excision mass, sternal notch to nipple distance, and inframammary fold to nipple distance were analyzed with postoperative outcomes including hematoma, seroma, infection, dehiscence, nipple necrosis, and fat necrosis.

Results
This study included 944 female patients undergoing reduction mammaplasty. Median age was 39.0 years, median body mass index was 31.9 kg/m2, and median breast mass resected was 742 grams per side. Drain utilization did not significantly reduce postoperative hematoma (P = 0.196), seroma (P = 0.185), nipple necrosis (P = 0.511), or fat necrosis (P = 0.113), but drain utilization significantly increased postoperative surgical site infection (P = 0.011). Patients with breast mass removed over 1500 g had significantly higher risk of hematoma (P = 0.002), fat necrosis (P < 0.001), and nipple necrosis (P < 0.001) compared to patients with less than 1500 g removed. In patients with greater than 1500 g resected, drain utilization did not significantly decrease risk of hematoma (P = 0.086) or seroma (P = 0.497).

Conclusions
Breast reduction greater than 1500 g per side significantly increased risk of hematoma, nipple necrosis, and fat necrosis. Drain utilization did not demonstrate any advantageous effects, rather it increased risk of infection. Future multicenter study will be needed to confirm these findings across different patient referral networks and practice patterns.
Rectal Eversion as an Anus-sparing Technique in Laparoscopic Low Anterior Resection With Double Stapling Anastomosis: Long-term Functional Results
Authors: Karagul Servet , Senol Serdar , Karakose Oktay , Eken Huseyin , Kayaalp Cuneyt 
Published: November 2024

Background:
Rectal eversion (RE) is a natural orifice specimen extraction (NOSE) method that allows anus-sparing resection in very low rectal tumors. This study aims to share the long-term results of RE in laparoscopic rectal resection performed with double stapling anastomosis.

Materials and Methods:
A single-center retrospective cohort study was conducted for patients who underwent laparoscopic low anterior resection with RE. Age, sex, body mass index, American Society of Anesthesiologists (ASA) classification, type of surgery, distance of the tumor to the dentate line, specimen extraction site, cancer stage, preoperative chemoradiotherapy, postoperative complications, and postoperative clinical follow-up findings were recorded. Incontinence was assessed using the Wexner score (WS). Low anterior resection syndrome (LARS) is determined by the LARS score. A 7-point Likert scale was used to evaluate the satisfaction of the patients.

Results:
A total of 17 patients underwent resection by RE for rectal tumors. Of the 11 patients included in the study, 4 were female and 7 were male. The mean age was 66.09±15.04 years. The mean follow-up was 64.18±16.83 months. The mean tumor diameter was 3.1 cm (range: 0.9 to 7.2 cm). The mean distance of the tumor from the dentate line was 2.7 cm (range: 1.2 to 5.6 cm). No anastomotic leak was observed in any patient. One patient had an anastomotic stenosis and was treated with balloon dilatation. The median LARS score was 16 (range 0 to 32) and 64% of the patients had no LARS. Two patients had minor LARS and 2 patients had major LARS. The median Wexner score was 3.5 (range 0 to 14). The median Likert scale was 7 (range 5 to 7). It was found that 55% of the patients were extremely satisfied, 18% were satisfied, and 27% were slightly satisfied with their surgery. There were no dissatisfied patients.

Conclusion:
RE is a safe NOSE technique in laparoscopic double stapling anastomosis for rectal resection. There is a high level of long-term patient satisfaction with anus-sparing procedures via RE, even in the presence of various symptoms.
Complete intraureteral stent placement reduces stent-related pain in normotensive subjects and in diabetes: Subgroup analysis of a prospective randomized clinical trial
Authors: Lu Yu-Cheng , Hsu Hung-Jen , Hu Su-Wei , Tzou Kai-Yi , Chen Kuan-Chou , Wu Chia-Chang , Ho Chen-Hsun 
Published: November 2024

Purpose:
Pain is a common symptom that is associated with ureteral stent placement, but its degree of perception might vary among individuals. Compared with conventional stent placement (C-SP), complete intraureteral stent placement (CIU-SP) has shown promise in reducing stent-associated pain. This study aimed to investigate the effect of patient characteristics and comorbidities on pain reduction after CIU-SP.

Materials and methods:
Patients who underwent ureteroscopic lithotripsy and stent placement were randomized into the CIU-SP and C-SP groups. Stent-associated symptoms were evaluated using the Ureteral Stent Symptom Questionnaire on day 7, immediately before stent removal. Stent-associated pain was determined by the answer to question P1 (yes or no). Subgroup analysis was conducted based on various patient characteristics and comorbidities.

Results:
Of the 103 randomized patients, 91 (45 in CIU-SP and 46 in C-SP) were included in the final analysis. Body pain was reported by 31 (68.9%) after CIU-SP and 41 (89.1%) after C-SP (P = 0.021). Compared with C-SP, CIU-SP significantly reduced pain in the normotensive population (66.7% versus 93.7%, P = 0.006) but not in hypertensive individuals (77.8% versus 76.9%, P = 1.000). Conversely, compared with C-SP, CIU-SP was associated with less pain in patients with diabetes (37.5% versus 88.9%, P = 0.05) but not in patients without diabetes (75.7% versus 89.2%, P = 0.221). Age, sex, stone laterality, body mass index, and smoking status did not influence the reduction of pain after CIU-SP.

Conclusion:
Compared with C-SP, CIU-SP was effective in reducing stent-associated pain, especially in normotensive and diabetic populations. These findings align with existing literature, which emphasized the potential impact of hypertension on decreased pain perception and highlighted the known association between diabetes and bladder hypersensitivity.
Effectiveness of Traditional Herbal Extracts Against Multidrug-Resistant Bacteria: A Review
Authors: Pane Yunita Sari 
Published: November 2024

AbstractThe rise of multidrug-resistant (MDR) bacteria has highlighted an urgent need for alternative antibacterial therapies. Traditional herbal extracts offer potential as natural antimicrobial agents with fewer side effects compared to conventional antibiotics. This review examines the effectiveness of specific herbal extracts—Curcuma longa (turmeric), Opuntia ficus-indica (cactus), and Linum usitatissimum (flaxseed)—against MDR bacterial strains. Data from various studies indicate that these extracts, particularly in methanolic and aqueous forms, exhibit inhibitory effects on pathogens such as Staphylococcus aureus, Escherichia coli, and Klebsiella pneumoniae. Notably, C. longa methanolic extracts showed the strongest antibacterial activity across strains, while O. ficus-indica extracts were effective in autoclaved forms against resistant strains. Comparatively, L. usitatissimum displayed minimal direct antibacterial action but may hold promise in combined therapies. This review also highlights synergistic effects observed when these herbal extracts are paired with conventional antibiotics, suggesting potential for reduced antibiotic dosages. Given the increasing antibiotic resistance, these findings support the integration of traditional herbal treatments as complementary options in antibacterial strategies. Future research should focus on optimizing extraction methods and evaluating the clinical applicability of these herbal alternatives in combating MDR pathogens.
Prediction of context-specific regulatory programs and pathways using interpretable deep learning
Authors: Doncevic Daria , Ramirez Alvarez Carlos , Li Albert , Zhang Youcheng , von Bachmann Anna , Noack Kasimir , Herrmann Carl 
Published: November 2024

AbstractVariational autoencoders (VAEs) are being widely adopted for the analysis of single-cell RNA sequencing (scRNA-seq) data. As with any non-linear models, however, they lack interpretability, which is a crucial aspect in the biomedical field where researchers want to be able to trust their model predictions. Our previously developed OntoVAE model addressed this issue by integrating biological ontologies in the decoder, which made the neuronal activations correspond to pathway activities. However, when multiple covariates are present, disentangling their relative contributions is challenging. To address this limitation, we developed COBRA, a VAE tool that combines the interpretable decoder part of OntoVAE with an adversarial approach that separates covariate effects in the latent space. In this work, we demonstrate the use of COBRA on two different scRNA-seq datasets in different contexts. We applied the tool to an interferon stimulated mouse dataset to separate the effects of celltype and treatment on transcription factors and biological pathways. We furthermore showed how COBRA can be used to predict the state of unseen celltypes.
Mapping the Molecular Landscape of Thyroid Neoplasms: A Comprehensive Proteomic and Phosphoproteomic Analysis Across Tumors of Follicular Origin
Authors: Bossart Jonas , Tajbakhsh Kiarash , Stanowska Olga , Weber Achim , Zboray Robert , Perren Aurel , Buljan Marija 
Published: November 2024

AbstractThyroid nodules are a widespread phenomenon, with follicular cell-derived thyroid tumors being the most prevalent type of endocrine tumor, spanning from benign through low grade malignant to aggressive neoplasms with dismal prognosis. In clinical practice, histopathological criteria are primarily used to determine malignancy and aggressiveness. Therefore, accurate classification may result in surgical procedures for diagnostic reasons, associated with an imbalanced risk/benefit ratio. In recent years, the use of integrated proteomic approaches has proven valuable in expanding the molecular understanding of thyroid neoplasms, with implications in classification, yet remains understudied in divergent thyroid nodules. Here we show the delineation of subtype-specific and malignancy-dependent molecular characteristics through integrative proteomic and phosphoproteomic analysis of 53 human thyroid tissues, encompassing five frequent benign and malignant tumors. We found that the (phospho)-proteomic profiles enable a clear stratification of malignant and benign thyroid tissues. The method also performs well in delineating follicular adenoma (FA) and follicular thyroid carcinoma (FTC) samples. Beside the dysregulation of cell cycle control, apoptosis, and metabolic reprogramming associated with tumor development and malignancy, we further report increased alterations within the well-established oncogenic RAS/BRAF/MAPK and AKT/MTOR signaling pathways, which, contrary to the prevailing paradigm, did not clearly differentiate between FTC and papillary thyroid carcinoma (PTC). In addition, activities of ATM, PLK2-3, and GRK5-6 kinases were predicted to be strongly upregulated in malignant subtypes. Together, this study provides an in-depth insight into molecular changes in different thyroid tumor subtypes. These findings highlight the potential of integrated proteomic approaches to refine our understanding of complex diseases like cancer. As such, they offer a pathway to more precise diagnostic and personalized treatment strategies.
Epigenetic signatures of regional tau pathology and cognition in the aging and pathological brain
Authors: Goldberg David C. , Wadhwani Anil R. , Dehghani Nadia , Sreepada Lasya P. , Fu Hongxiang , De Jager Philip L. , Bennett David A. , Wolk David A. , Lee Edward B. ,   PART Working Group, Farrell Kurt , Crary John F. , Zhou Wanding , McMillan Corey T. 
Published: November 2024

ABSTRACTPrimary age-related tauopathy (PART) and Alzheimer’s disease (AD) share hippocampal phospho-tau (p-tau) pathology but differ in p-tau extent and ß-amyloid presence. As a result, PART uniquely enables investigation of amyloid-independent p-tau mechanisms during brain aging. We conducted an epigenome-wide association (EWAS) study of PART, nominating 13 new and robust p-tau/methylation associations. We then jointly analyzed PART and AD epigenomes to develop novel epigenetic clocks, “TauAge”, that predict p-tau severity in region-specific, age-, and ß-amyloid-independent manners. Integrative transcriptomic analyses revealed that genes involved in synaptic transmission are related to hippocampal p-tau severity in both PART and AD, while neuroinflammatory genes are related to frontal cortex p-tau severity in AD only. Further, a machine learning classifier trained on PART-vs-AD epigenetic differences stratifies an independent cohort of neuropathologically indeterminate cases into pathological subgroups with disparity in cognitive impairment. Together, these findings demonstrate the brain epigenome’s substantial role in linking tau pathology to cognitive outcomes in aging and AD.
Integrating knowledge, omics and AI to develop patient-specific virtual avatars
Authors: Bekkar Amel , Santuari Luca , Xenarios Ioannis , Arpat Bulak 
Published: November 2024

AbstractWe propose a method for creating personalized regulatory networks, enabling the development of virtual avatars for cancer patients, with patient-derived xenograft (PDX) models as a test case. Starting from a Prior Knowledge Network (PKN) based on the hallmarks of cancer, we constructed gene networks that are contextualized to each sample by integrating sample-specific gene expression data. These networks were optimized using a genetic algorithm to align with individual molecular profiles, focusing on key cancer-related processes. Following network optimization, we employed Graph Convolutional Networks (GCNs) to classify samples based the structures and interactions of their individualized network models and molecular profiles. This personalized approach provides insights into drug responses and helps predict treatment outcomes, offering a path toward more targeted cancer therapies.Author summaryCancer treatment can be more effective when therapies are personalized to each patients unique molecular profile. In this study, we introduce a method to create virtual avatars of cancer patients by personalizing regulatory networks using patient-derived xenograft (PDX) models as a proof of concept. Starting from known cancer hallmarks, we developed individualized gene networks for each sample by leveraging their specific gene expression data. These networks were refined with an optimization process to match the distinct molecular characteristics of each sample. By applying advanced machine learning, specifically Graph Convolutional Networks (GCNs), we classified these personalized models to better understand likely drug responses and predict treatment outcomes. This approach brings us closer to tailoring cancer therapies to individual patients, potentially improving treatment success by targeting key cancer pathways unique to each person.
A National Active Case-Finding Program for Tuberculosis in Prisons, Peru, 2024
Authors: Jung Esther , Alarcón Valentina A. , Solís Tupes Wilfredo Santos , Avalos-Cruz Tatiana , Tovar Marco , Abregu Erika , Yang Max Z. , Andrews Jason R. , Huaman Moises A. 
Published: November 2024

AbstractFrom January to September 2024, a national active case-finding program in Peru’s prisons screened more than 38,000 incarcerated persons for tuberculosis using chest radiography with automated interpretation and rapid molecular diagnostics, yielding a tuberculosis prevalence of 2,800 per 100,000 persons, with 11.4% of cases rifampicin-resistant; 42.5% of cases were subclinical.Article Summary LineA recent, nationwide mass screening program in Peru’s prisons using digital radiography with automated interpretation and molecular testing identified high tuberculosis prevalence and rates of rifampicin resistance, highlighting the need for active case-finding as an efficient strategy to identify undiagnosed TB burden in high-risk populations.
CircAge: A Comprehensive Resource for Aging-Associated Circular RNAs Across Species and Tissues
Authors: Dong Xin , Zhou Zhen , Wang Yanan , Nisar Ayesha , Pu Shaoyan , Lv Longbao , Li Yijiang , Lu Xuemei , He Yonghan 
Published: November 2024

AbstractCircular RNAs (circRNAs) represent a novel class of RNA molecules characterized by a circular structure and enhanced stability. Emerging evidence indicates that circRNAs play pivotal regulatory roles in the aging process. Despite this, there is a lack of a systematic resource that integrates aging-associated circRNA data. Therefore, we developed a comprehensive database named circAge, which encompasses 689 aging-related samples from 7 species and 21 tissue types. We also generated 47 new tissue samples from mice and rhesus monkeys through high-throughput sequencing. Integrating predictions from multiple bioinformatics tools, we identified over 413,378 unique circRNAs. Our data analysis revealed a general increase in circRNA expression levels with age, with approximately 22% of circRNAs demonstrating sequence conservation across species. The circAge database systematically predicts potential interactions between circRNAs and miRNAs, RNA-binding proteins, and assesses the coding potential of circRNAs. This resource lays a foundation for elucidating the regulatory mechanisms of circRNAs in aging. As a comprehensive repository of aging-associated circRNAs, circAge will significantly accelerate research in this field, facilitating the discovery of novel biomarkers and therapeutic targets for aging biology and developing diagnostic and therapeutic strategies for aging and age-related diseases. CircAge is publicly available athttps://circage.kiz.ac.cn.
A simple method for computationally unstructuring proteins: some findings
Authors: Powell Alexander 
Published: November 2024

AbstractA methodology for computationally ‘unstructuring’ proteins is described and the results of its application to a variety of proteins analyzed and discussed. Some proteins prove more susceptible than others, and fold topology plays a part in this. Alpha helical structure is found to be generally somewhat robust, and, perhaps unsurprisingly, unstructuring often begins at exposed chain termini. Phosphofructokinase-1 and phosphofructokinase-2, which have similar sizes but different fold topologies, are found to differ markedly in their unstructuring behaviour.Subjects:biophysics, chemical biology, computational biology, protein science, structural biology
Towards a Social Media-based Disease Surveillance System for Early Detection of Influenza-like Illnesses: A Twitter Case Study inWales
Authors: Drakesmith Mark , Antypas Dimosthenis , Brown Clare , Camacho-Collados Jose , Song Jiao 
Published: November 2024

AbstractSocial media offers the potential to provide detection of outbreaks or public health incidents faster than traditional reporting mechanisms. In this paper, we developed and tested a pipeline to produce alerts of influenza-like illness (ILI) using Twitter data. Data was collected from the Twitter API, querying keywords referring to ILI symptoms and geolocated to Wales. Tweets that described first-hand descriptions of symptoms (as opposed to non-personal descriptions) were classified using transformer-based language models specialised on social media (BERTweet and TimeLMs), which were trained on a manually labelled dataset matching the above criteria. After gathering this data, weekly tweet counts were applied to the regression-based Noufaily algorithm to identify exceedances throughout 2022. The algorithm was also applied to counts of ILI-related GP consultations for comparison. Exceedance detection applied to the classified tweet counts produced alerts starting four weeks earlier than by using GP consultation data. These results demonstrate the potential to facilitate advanced preparedness for unexpected increases in healthcare burdens.