bluuebunny/crossref_metadata_2025_split huggingface dataset:
A method for weld surface inspection and measurement based on AM U-Net
Authors: Shang Fei , Chen Huilin , Sun Bo , Han Yongquan , Cai Dandan , Wang Shaofeng , Gao Ting , Ji Chunsheng , Zhang Honghui 
Published: February 2025

Abstract
The quality of weld seams is critical to the performance and safety of industrial products. Traditional manual inspection methods are inefficient and prone to inaccuracies, particularly in complex environments. To address these challenges, this study introduces an automated weld seam inspection and dimensional measurement approach based on an enhanced U-Net architecture, termed AM U-Net. By integrating wavelet depth separable convolution, attention mechanisms, and multi-scale feature fusion, AM U-Net effectively captures intricate weld features while reducing computational complexity. Experimental results demonstrate that AM U-Net achieves a Dice coefficient of 0.94, outperforming the standard U-Net by 9.3%, and enhances inference speed by 33% with a 22.6% reduction in model parameters. Additionally, the proposed method for measuring weld seam dimensions combines sub-pixel edge detection with camera calibration, achieving millimeter-level accuracy with average relative errors of 0.16% for width and 0.25% for length measurements. This automated system offers a robust and efficient solution for weld seam inspection, meeting the precision requirements of industrial applications.
LTAU-FF: Loss Trajectory Analysis for Uncertainty in atomistic Force Fields
Authors: Vita Joshua A , Samanta Amit , Zhou Fei , Lordi Vincenzo 
Published: February 2025

Abstract
Model ensembles are effective tools for estimating prediction uncertainty in deep learning atomistic force fields. However, their widespread adoption is hindered by high computational costs and overconfident error estimates. In this work, we address these challenges by leveraging distributions of per-sample errors obtained during training and employing a distance-based similarity search in the model latent space. Our method, which we call LTAU (Loss Trajectory Analysis for Uncertainty), efficiently estimates the full probability distribution function of errors for any test point using the logged training errors, achieving speeds that are 2–3 orders of magnitudes faster than typical ensemble methods and allowing it to be used for tasks where training or evaluating multiple models would be infeasible. We apply LTAU towards estimating parametric uncertainty in atomistic force fields (LTAU-FF), demonstrating that it produces well-calibrated confidence intervals and predicts errors that correlate strongly with the true errors for data near the training domain. Furthermore, we show that the errors predicted by LTAU-FF can be used in practical applications for detecting out-of-domain data, tuning model performance, and predicting failure during simulations. We believe that LTAU will be a valuable tool for uncertainty quantification in atomistic force fields and is a promising method that should be further explored in other domains of machine learning.
Nanogel, a versatile nanoscopic platform for the simultaneous delivery of acyclovir and lignocaine for the treatment of Herpes simplex virus infection: formulation and characterizations
Authors: Aslam Adnan , Khan Barkat A , Khan M Khalid , Niazi Muhammad Bilal K 
Published: February 2025

Abstract
This study was designed to develop a nanogel formulation incorporating acyclovir and lignocaine (ALN). Various formulations were developed in which ALN-V (formulation-V) was optimized. ALN-V had an average spreadability of 32.3 ± 2.1, a pH of 5.8 ± 0.6 and was physically stable. The droplet size was 221.5 ± 0.5 nm while the surface charge was −7.59 ± 1.8 mV and the polydispersity was 0.145. ATR-FTIR analysis confirmed no interactions. The thermal analysis showed that the melting peak of lignocaine appeared at 65 °C, while that of acyclovir appeared at 256.54 °C. ALN-V showed approximately 72% release for acyclovir and 80% for lignocaine. The Higuchi model confirmed that the release mechanism follows controlled diffusion via a semipermeable membrane. ALN-V nanogels with pure acyclovir and blank nanogel formulations were tested for cytotoxicity and antiviral activity. ALN-V was capable of reducing the cytopathic effect of Herpes simplex virus (HSV) for up to 72 h. Moreover, the ALN-V nanogel inhibited (>95%) the virus titre even after 48 h, which confirmed that the ALN-V nanogel is nontoxic to cells and can effectively inhibit HSV. It was concluded that optimized nanogels can be loaded with combination drugs (lignocaine and acyclovir) and suitable candidates for transdermal delivery of both.
ImmunoTar—integrative prioritization of cell surface targets for cancer immunotherapy
Authors: Shraim Rawan , Mooney Brian , Conkrite Karina L , Hamilton Amber K , Morin Gregg B , Sorensen Poul H , Maris John M , Diskin Sharon J , Sacan Ahmet 
Published: February 2025

Abstract

Motivation
Cancer remains a leading cause of mortality globally. Recent improvements in survival have been facilitated by the development of targeted and less toxic immunotherapies, such as chimeric antigen receptor (CAR)-T cells and antibody-drug conjugates (ADCs). These therapies, effective in treating both pediatric and adult patients with solid and hematological malignancies, rely on the identification of cancer-specific surface protein targets. While technologies like RNA sequencing and proteomics exist to survey these targets, identifying optimal targets for immunotherapies remains a challenge in the field.

Results
To address this challenge, we developed ImmunoTar, a novel computational tool designed to systematically prioritize candidate immunotherapeutic targets. ImmunoTar integrates user-provided RNA-sequencing or proteomics data with quantitative features from multiple public databases, selected based on predefined criteria, to generate a score representing the gene's suitability as an immunotherapeutic target. We validated ImmunoTar using three distinct cancer datasets, demonstrating its effectiveness in identifying both known and novel targets across various cancer phenotypes. By compiling diverse data into a unified platform, ImmunoTar enables comprehensive evaluation of surface proteins, streamlining target identification and empowering researchers to efficiently allocate resources, thereby accelerating the development of effective cancer immunotherapies.

Availability
Code and data to run and test ImmunoTar are available at https://github.com/sacanlab/immunotar.

Supplementary information
Supplementary data are available at Bioinformatics online.
Engineered Extracellular Vesicles Derived from Pluripotent Stem Cells: A Cell-Free Approach to Regenerative Medicine
Authors: Wang Aline Yen Ling , Kao Huang-Kai , Liu Yen-Yu , Loh Charles Yuen Yung 
Published: February 2025

Abstract
The engineered extracellular vesicles (EVs) derived from pluripotent stem cells are a new concept in regenerative medicine. These vesicles are secreted from the embryonic stem cells as well as the induced pluripotent stem cells (iPSCs) and are involved in the transfer of bioactive molecules required for cell signaling. This review describes the possibilities for their use in the modification of therapeutic approaches in regenerative medicine and targeted therapies. Pluripotent stem cells can differentiate into various cell types which can be useful for tissue engineering or to generate models of diseases in a dish. Compared to cell therapies, engineered EVs are characterized by lower immunogenicity, higher targetability, and improved stability. Some of the applications are angiogenic, tissue restorative, immunomodulatory, and gene therapies for the treatment of certain diseases. iPSC-derived engineered EVs find application in regenerative medicine, drug delivery systems, diagnostics of diseases, and hydrogel systems. In regenerative medicine, they can promote the restoration of cardiac, bone, cartilage, and corneal tissues. Engineered EVs are also employed in drug targeting to particular sites as well as in the diagnosis of diseases based on biomarkers and improving image contrast. Hydrogels that contain EVs provide a depot-based delivery system to slowly release drugs in a controlled manner which enhances tissue repair. Thus, the results described above demonstrate the potential of engineered PSC-EVs for various biomedical applications. Future work will be directed toward expanding the knowledge of engineered PSC-EVs and their possibilities to create new therapeutic approaches based on the functions of these vesicles.
Improved Survival in Vascular Pythiosis with Surgery and Azithromycin, Doxycycline, and Itraconazole Therapy: A Phase II Multicenter, Open-Label, Single-Arm Trial
Authors: Torvorapanit Pattama , Worasilchai Navaporn , Manothummetha Kasama , Srisurapanont Karan , Thongkam Achitpol , Langsiri Nattapong , Leksuwankun Surachai , Meejun Tanaporn , Thanakitcharu Jaedvara , Lerttiendamrong Bhoowit , Susaengrat Nuttapon , Chuleerarux Nipat , Siriyakorn Nirada , Watcharasuwanseree Sureerat , Suparatanachatpun Pinyo , Chayangsu Sunee , Khemla Supphachoke , Kajeekul Rattagan , Wattanasoontornsakul Watchara , Bansong Ratiporn , Sakulkonkij Parichart , Wongkamha Thanyarak , Diewsurin Jaruwan , Laohasakprasit Kanokwan , Kongsakpaisal Prasopchai , Chayapum Poom , Chindamporn Ariya , Plongla Rongpong , Permpalung Nitipong 
Published: February 2025

Abstract

Background
Vascular pythiosis, caused by Pythium insidiosum, is a life-threatening disease with high mortality rate in patients with residual disease post-surgery. This study evaluated the effectiveness of a combination therapy of surgery, azithromycin, doxycycline, and itraconazole.

Methods
In this open-label, Phase II multicenter trial, 51 patients were enrolled. Patients were categorized based on residual disease post-surgery (unresectable lesions, incomplete resection, or persistent symptoms). Patients with residual disease received azithromycin (500 mg daily), doxycycline (100 mg twice daily), and itraconazole (200 mg thrice daily) until beta-d-glucan (BDG) levels were negative (&lt; 80 pg/ml) for three months. Those without residual disease received the same regimen for six months. Outcomes included all-cause mortality at six months, adverse events, changes in BDG levels over time, and factors associated with residual disease and mortality.

Results
At six months, the all-cause mortality rate was 15.7%. Mortality in patients with residual disease was 31.5% compared to 6.25% for those without (p=0.04). Lesions above the popliteal artery were a significant predictor of residual disease (incidence rate ratio [IRR] 3.20, 95% confidence interval [CI] 1.08-11.70). BDG levels decreased over time (odds ratio [OR] 0.82, 95%CI 0.77-0.88 per week, p&lt;0.001), but remained higher in the residual disease group (OR 4.29, 95% CI 1.55-11.92)

Conclusions
The combination therapy of surgery, azithromycin, doxycycline, and itraconazole improves survival in patients with vascular pythiosis, including those with residual disease. This regimen is well-tolerated and should be considered a standard of care, with further research needed for long-term outcomes.
PotatoBSLnc: a curated repository of potato long noncoding RNAs in response to biotic stress
Authors: Huang Pingping , Cao Weilin , Li Zhaojun , Chen Qingshuai , Wang Guangchao , Zhou Bailing , Wang Jihua 
Published: February 2025

Abstract
The biotic stress significantly influences the production of potato (Solanum tuberosum L.) all over the world. Long noncoding RNAs (lncRNAs) play key roles in the plant response to environmental stressors. However, their roles in potato resistance to pathogens, insects, and other biotic stress are still unclear. The PotatoBSLnc is a database for the study of potato lncRNAs in response to major biotic stress. Here, we collected 364 RNA sequencing (RNA-seq) data derived from 12 kinds of biotic stresses in 26 cultivars and wild potatoes. PotatoBSLnc currently contains 18 636 lncRNAs and 44 263 mRNAs. In addition, to select the functional lncRNAs and mRNAs under different stresses, the differential expression analyses and the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses related to the cis/trans-targets of differentially expressed lncRNAs (DElncRNAs) and to the differentially expressed mRNAs (DEmRNAs) were also conducted. The database contains five modules: Home, Browse, Expression, Biotic stress, and Download. Among these, the “Browse” module can be used to search detailed information about RNA-seq data (disease, cultivator, organ types, treatment of samples, and others), the exon numbers, length, location, and sequence of each lncRNA/mRNA. The “Expression” module can be used to search the transcripts per million/raw count value of lncRNAs/mRNAs at different RNA-seq data. The “Biotic stress” module shows the results of differential expression analyses under each of the 12 biotic stresses, the cis/trans-targets of DElncRNAs, the GO and KEGG analysis results of DEmRNAs, and the targets of DElncRNAs. The PotatoBSLnc platform provides researchers with detailed information on potato lncRNAs and mRNAs under biotic stress, which can speed up the breeding of resistant varieties based on the molecular methods.
Database URL: https://www.sdklab-biophysics-dzu.net/PotatoBSLnc
Comparison of bioprosthetic valves in primary isolated aortic valve replacement: a nationwide study
Authors: Kim Ji Seong , Kim Jinhee , Kang Yoonjin , Sohn Suk Ho , Hwang Ho Young , Kim Kyung Hwan , Kim Mi-Sook , Choi Jae Woong 
Published: February 2025

Abstract

OBJECTIVES
This study aimed to comprehensively compare the early and long-term clinical outcomes of bovine pericardial valve (BOV) and porcine valve (POV), specifically during the primary isolated aortic valve replacement (AVR), using data from the Korean National Health Insurance Service (NHIS) database.

METHODS
Using the Korean NHIS claimed data, all adult patients (age ≥19) who underwent primary isolated AVR using bioprosthetic valve from 2003 to 2019 were identified and propensity score matching (PSM) analysis was performed.

RESULTS
Overall, 5,470 patients with BOV (n = 3,947, Group B) or POV (n = 1,523, Group P) were enrolled, of whom 814 pairs were matched in a 1:1 ratio using PSM analysis. Early postoperative mortality and morbidities were comparable between the groups before and after PSM, considering inter-hospital clustering. The cumulative incidence of all-cause mortality was higher in Group P than in Group B in the total cohort (Group B 5.3%/patient-years vs Group P 6.4%/patient-years, adjusted hazard ratio: 1.20, P = 0.002), whereas those differences in call-cause mortality disappeared in PSM analysis (P = 0.24). The cumulative incidences of late stroke, reoperation, and infective endocarditis were not significantly different between the groups in PSM populations.

CONCLUSIONS
In Korean national database cohort patients with primary isolated AVR there was no significant difference in the early- and long-term clinical outcomes between BOV and POV.
Effects of perfluorooctane sulfonate (PFOS) on a novel reptilian toxicity test species, the brown anole (anolis sagrei)
Authors: Salice Christopher J , East Andrew , Weible Caitlin , Furst C Daniel , Rewerts Justin , Heron Christopher , Field Jennifer 
Published: February 2025

Abstract
Per- and polyfluoroalkyl substances (PFAS) are a broad class of chemicals with high environmental persistence and growing ecological and human health concern. Perfluorooctane sulfonate (PFOS) is among the most detected PFAS in environmental sampling and is often at high concentrations and has been measured in a variety of ecological receptors from around the globe. Despite the prevalence of PFOS, there are still important data gaps with regard to toxicity. For example, while studies have confirmed PFOS accumulation in tissues of wild reptiles, reptilian laboratory toxicity data are lacking. The purpose of this study was to first develop toxicity testing protocols using the brown anole, Anolis sagrei and, second, to conduct PFOS dosing studies to generate toxicity data to support ecological risk assessment of reptiles. We conducted two studies in which subadult males and then mature males were dosed with PFOS via pseudo-gavage with maximum doses in the range of 2 mg/kg/d. Subadults were exposed for 35 days while adult males were exposed for 90 days. While no significant mortality was observed, subadult male size and growth rate were significantly affected by PFOS at 2.98 mg/kg/d with a corresponding no effect level of 0.20 mg/kg/d and corresponding 10 and 20% effect levels for growth rate of 0.22 and 0.44 mg/kg/d, respectively. There were no significant effects on size metrics of mature male anoles from the 90-day study although several metrics showed dose-dependent decreases. These data may serve as the basis for toxicity reference values (TRVs) for use in ecological risk assessments of PFAS-contaminated sites in which reptiles may be exposed.
May Measurement Month 2022: an analysis of blood pressure screening results from Colombia
Authors: Lopez-Lopez Jose P , Otero Johanna , Urbina Zulma , Sanchez-Vallejo Gregorio , Narvaez Claudia , Camacho Paul A , Urina-Triana Miguel , Quintero Adalberto , Aroca Gustavo , Campos Alfonso , Arcos Edgar , Perez-Mayorga Maritza , Mosquera Walter , Garcia Luis , Beaney Thomas , Kerr Gabriele , Poulter Neil R , Lopez-Jaramillo Patricio 
Published: February 2025

Abstract
The May Measurement Month (MMM) campaign was carried out in Colombia in 2022 with the aim of raising awareness of raised blood pressure (BP). Here, we report on the findings of the campaign. Adults aged ≥ 18 years were recruited opportunistically at healthcare and public facilities in eleven departments. Three seated BP readings were taken for each participant, along with completion of a questionnaire on demographics, lifestyle factors, and comorbidities. Hypertension was defined as a systolic BP ≥ 140 mmHg and/or diastolic BP ≥ 90 mmHg or being on antihypertensive medication. Controlled BP was defined as being on antihypertensive medication with a BP &lt;140/90 mmHg. Multiple imputation was used to estimate any missing BP readings. In total, 38 924 were screened, with a mean age of 46.3 years and 52.9% of whom were female. Of all participants, 10 738 (27.6%) had hypertension, of whom 7058 (65.7%) were aware, and 6925 (64.5%) were on antihypertensive medication. Of those on antihypertensive medication, 4600 (66.4%) had controlled BP, and of all participants with hypertension, 42.8% had controlled BP. However, those under 50 years had lower hypertension control (&lt;30%). Women had a higher BP control than men (49.5 vs 36.3%). High education was associated with lower systolic BP (-2.37 mmHg). The MMM campaign in Colombia identified significant numbers of participants with either untreated or inadequately treated hypertension. MMM22 results point to the need to continue improving awareness and seek a broader implementation of strategies with proven efficacy in controlling hypertension.
Symposia Report of The Annual Biological Sciences Section Meeting of the Gerontological Society of America 2023, Tampa, Florida
Authors: Rogina Blanka , Anderson Rozalyn , Lebrasseur Nathan , Curan Sean , Yousefzadeh Matthew J , Ghosh Bhaswati , Duque Gustavo , Howlett Susan , Austad Steven , Demuth Ilja , Gerstorf Denis , Korfhage Justin , Lombard David B , Abadir Peter , Christensen Kaare , Carey James R , Alberts Susan C , Campos Fernando , Palavicini Juan Pablo , Palmer Allyson , Bell Justice , Basisty Nathan , de Cabo Rafael , Gomes Ana , Dixit Vishwa Deep , Sen Payel , Baur Joseph A , Imai Shin-ichiro , Li Xiaoling , Valdez Gregorio , Orr Miranda E , Pletcher Scott , Andersen Julie , Jones Leanne , Castillo-Azofeida David , Bonaguidi Michael , Suh Yousin , Duncan Francesca E , Murray Anna , Wang Meng C, , Burkewitz Kristopher  , Henne Mike , Zhou Kai , Bouhrara Mustapha , Benjamini Dan , Kolind Shannon , Walker Keenan A , Reiter David A , Dean III Doug , Gorbunova Vera , Gladyshev Vadim N , Palovics Robert , Niedernhofer Laura J , Fan Rong , Bueckle Andreas D , Hurley Jennifer , Esser Karyn A , Kapahi Pankaj , Sato Shogo , Jiang Nisi , Ashiqueali Sarah A , Diaz Jose , Mishra Sidharth Prasad , Ralmundo Nuno , Banarjee Reema , Allsopp Richard , Reynolds Lindsay M , Zhang Bohan , Sebastiani Paola , Monti Stefano , Schork Nicholas , Rappaport Noa 
Published: February 2025

Abstract
The aging process is universal, and it is characterized by a progressive deterioration and decrease in physiological function leading to decline on the organismal level. Nevertheless, a number of genetic and non-genetic interventions have been described, which successfully extend healthspan and lifespan in different species. Furthermore, a number of clinical trials have been evaluating the feasibility of different interventions to promote human health. The goal of the annual Biological Sciences Section of the Gerontological Society of America meeting was to share current knowledge of different topics in aging research and provide a vision of the future of aging research. The meeting gathered international experts in diverse areas of aging research including basic biology, demography, and clinical and translational studies. Specific topics included metabolism, inflammaging, epigenetic clocks, frailty, senescence, neuroscience, stem cells, reproductive aging, inter-organelle crosstalk, comparative transcriptomics of longevity, circadian clock, metabolomics, and biodemography.
Azithromycin as Host-Directed Therapy for Pulmonary Tuberculosis: A Randomized Pilot Trial
Authors: Dekkers Bart G J , Kerstjens Huib A M , Breisnes Helene W , Leeming Diana J , Anthony Richard M , Frijlink Henderik W , van der Werf Tjip S , Kosterink Jos G W , Alffenaar Jan-Willem C , Akkerman Onno W 
Published: February 2025

Abstract

Background
Adjunctive host-directed therapies that modulate host immune responses to reduce excessive inflammation and prevent tissue damage in tuberculosis are being investigated. Macrolides, including azithromycin, were shown to possess anti-inflammatory and immune-modulatory effects in addition to their antibacterial effects. In the current trial, we investigated whether azithromycin enhances resolution of systemic and pulmonary inflammation and decreases extracellular matrix-related tissue turnover in tuberculosis patients.

Methods
An open-label, randomized, controlled trial was performed. Adult patients with drug-susceptible, pulmonary tuberculosis aged above 18 years were randomly assigned to receive standard antituberculosis care or azithromycin 250 mg orally once daily in addition to standard care (SOC) for 28 days.

Results
Twenty-eight patients were included within 4 weeks after initiating antituberculosis treatment. Twelve patients in both arms completed the trial. Participants were mostly young, male, had a history of smoking, and had no comorbidities. No differences in baseline characteristics were observed between the study arms. In blood, azithromycin treatment significantly enhanced the reduction of the tuberculosis marker interferon-γ-induced protein-10 (SOC plus azithromycin, −38% vs SOC alone, −24% vs SOC, P &lt; .05) and the collagen type IV degradation product C4M (−26% vs −11%, P &lt; .05). In sputum, treatment with azithromycin significantly reduced neutrophils (−24% vs 0%, P &lt; .001), neutrophil elastase (−88% vs 75%, P &lt; .01), and transforming growth factor-β (−86% vs −68%, P &lt; .05). No significant effects were observed on other parameters. Treatment with azithromycin appeared to be safe.

Conclusions
The addition of azithromycin to standard antituberculosis treatment appears to diminish excess neutrophilic inflammation in patients with pulmonary tuberculosis.
Clinical Trials Registration. NCT03160638.