bluuebunny/crossref_metadata_2025_split huggingface dataset:
Penis Reconstruction With Latissimus Dorsi Flap and Challenges for Penis Prosthesis in Phalloplasty
Authors: Nasır Serdar 
Published: February 2025

Background
Several methods of penile reconstruction have been described. Free flaps are considered the most functional and aesthetically appropriate treatment method. The main purpose of this reconstruction is to create the urinary tract and provide the most aesthetically similar structure to the biological penile tissue while also providing penile tissue of a size that will ensure adequate sexual intercourse.
This method was investigated through a retrospective analysis of patients who underwent penile reconstruction with a latissimus dorsi free flap, which we believe provides all these features. Thirty patients who underwent surgery between 2020 and 2023 were included in the study group.

Methodology
Latissimus dorsi flap is an important option for patients who need penile reconstruction, including those who want the donor site morbidity to be in a hidden area and those who have concerns about penis size.

Result
Tissue of a size that provides sexual function and a structure in which a penile prosthesis can be easily inserted is obtained in patients who have undergone penile reconstruction with the latissimus dorsi. In addition, there was no problem in creating a glans penis or corona using this method. Pendular urethral reconstruction was not performed in this case series.

Conclusions
We think that penile reconstruction with Latissimus dorsi, together with some of the modifications described, is one of the most functional and aesthetically appropriate methods.
The Modified Fragility Index and Perioperative Albumin as Predictors of Complications in Complex Abdominal Wall Reconstruction
Authors: Ash Makenna , Marxen Troy , Su Shannon , Losken Albert 
Published: February 2025

Background and Significance
Complex abdominal wall reconstruction (CAWR) is performed to restore the structure and function of the abdominal wall. These procedures carry the risk of complications such as delayed wound healing, skin necrosis, infection, recurrence, or even death. The 5-factor modified fragility index (5-mFI) has gained popularity as a concise method of evaluating preoperative risk across various surgical specialties. Additionally, perioperative hypoalbuminemia has been previously associated with delayed wound healing after surgery. The purpose of this study was to assess the utility of the 5-mFI in combination with perioperative albumin levels for assessing risk in complex abdominal wall reconstruction.

Methods
This was a retrospective, single-institution chart review study of all patients who underwent CAWR by the senior author (A.L.) from 2002 to 2023. Demographics, comorbidities, details of surgery, perioperative albumin levels, ASA scores, and complications were collected for each patient. Five-factor modified fragility indices were calculated for each patient. Statistical analysis consisted of χ2 and Fisher exact tests for categorical variables, t tests for continuous variables, and multivariate analysis.

Results
Our analysis included 437 patients. The average age of our patients was 54.3 years, the average BMI was 32.1 kg/m2, and the average length of follow-up with the plastic surgery service was 264 days. A total of 118 (27.0%) developed complications, with the most common complications being delayed wound healing (89 patients, 20.4%) and infection (78 patients, 17.8%). Other complications included skin necrosis, fistula formation, hematoma, seroma, infection, and death. Sixty patients (13.7%) experienced recurrence of their hernias within the follow-up period. An mFI of 2 or greater was significantly associated with delayed wound healing (LR, 11.42; P = 0.0436) as well as skin necrosis (LR, 4.826; P = 0.028). The presence of an mFI of 2 or greater and perioperative hypoalbuminemia was significantly associated with development of major complications (LR, 3.221; P = 0.0457), delayed wound healing (LR, 5.999; P = 0.0143), skin necrosis (LR, 9.19; P = 0.0024), and mortality (LR, 5.287; P = 0.0215). On multivariate analysis, the presence of an mFI of 2 or greater when combined with perioperative hypoalbuminemia was found to be independently associated with mortality (LR, 1524.5; P < 0.0001).

Conclusions
We found the 5-factor mFI to be significantly associated with delayed wound healing and skin necrosis in our patient population. When an mFI of 2 or greater was present along with perioperative hypoalbuminemia, patients were significantly more likely to experience complications, issues with wound healing, and mortality. Surgeons should take these findings into account when counseling patients preoperatively.
Comparison of dual-agent alpha-blocker treatment with single agent in management of refractory lower urinary tract symptoms
Authors: Ranjan Kumar Rajiv , Singh Dineshwar Pratap , Sarkar Debansu 
Published: February 2025

Introduction:
In patients with enlarged prostate whose lower urinary tract symptoms (LUTS) are refractory to an initial alpha-blocker, there are several options, including surgery, alternative alpha-blockers, or dose escalation. Alpha-blockers used clinically do not differ in efficacy, but only in their side effects profile. The possibility of synergy between different classes of alpha-blockers has not yet been explored. In this study, we compared the efficacy of single (silodosin) and dual (silodosin + alfuzosin) alpha-blocker therapy for treating patients with refractory LUTS due to an enlarged prostate. Additionally, we studied the incidence of adverse effects of single and dual alpha-blocker therapy.

Materials and methods:
It was a prospective comparative observational study with 250 participants, conducted at the department of urology, a tertiary care hospital in eastern India. Male patients with moderate to severe LUTS (international prostate symptoms score [IPSS] >7) of all age groups with enlarged prostate were included in this study.

Results:
The demographic profiles of the patients including age, baseline maximum flow rate, baseline IPSS, and adverse effects were comparable for both the groups. Mean improvement in IPSS and maximal uroflow rate were significantly higher in the dual alpha-blocker therapy group without significant difference in adverse effects between the 2 groups.

Conclusion:
Results of dual alpha-blocker therapy in refractory LUTS due to enlarged prostate are encouraging with acceptable adverse effects.
HGCPep: A Hypergraph-based Deep Learning Model for Enhancing Representation of Peptide Features in Cancer-associated ncPEPs Identification
Authors: Long Wentao , Li Zhongshen , Jin Junru , Qiao Jianbo , Wang Yu , Wei Leyi 
Published: February 2025

AbstractThe emergence of non-coding RNA-encoded small peptides (ncPEPs) has sparked significant interest within the realm of cancer immunotherapy, owing to their potential as valuable therapeutic targets and biomarkers. The identification and characterization of cancer-associated ncPEPs assume a crucial role in propelling cancer research forward and augmenting our comprehension of immune-related processes. However, prevailing methods for cancer-associated ncPEPs identification primarily rely on sequence order, neglecting the latent relationships between peptides. As widely acknowledged in the central dogma, peptides are translated from RNA via a many-to-many mapping. In this study, we capitalize on the translation relationship and introduce a hypergraph-based model called HGCPep to enhance the representation of peptide features. Specifically, RNA is regarded as a hyperedge connecting the peptides that are translated from it. Our experimental results validate that the HGCPep approach, leveraging the strengths of hypergraph and convolutional neural networks, outperforms alternative methodologies in the recognition of ncPEPs. Additionally, employing a reduction tool, we visualize the results of multi-label classification within a 2D latent space, shedding light on how multi-label classification task influence the representation of peptides. The dataset and source code of our proposed method can be found viahttps://github.com/Longwt123/HGCPep_Github.
Efficacy of Cerebrolysin Treatment as an Add-On Therapy to Mechanical Thrombectomy in Patients With Acute Ischemic Stroke Due to Large Vessel Occlusion in Anterior Circulation: Results of a three-month follow-up of a Prospective, Open Label, Single-Center Study
Authors: Staszewski Jacek , Dębiec Aleksander , Strilciuc Stefan , Gniadek-Olejniczak Katarzyna , Piusinska-Macoch Renata , Balo David , Harston George , Stępień Adam , Brzozowski Krzysztof , Zięcina Piotr , Narloch Jerzy , Wierzbicki Marek , Piasecki Piotr 
Published: February 2025

AbstractBackground and AimsThis study hypothesized that Cerebrolysin, a multimodal neuroprotective agent, enhances the efficacy and safety of mechanical thrombectomy (MT) in both acute ischemic stroke (AIS) and recovery stroke phases in selected patients with good collateral status (CTA-CS 2-3) and effective recanalization (mTICI 2b-3).MethodsA single-center, prospective, open-label, single-arm study with blinded outcome assessment of 50 consecutive patients with moderate-to-severe AIS treated with MT ≤6 hours of stroke onset followed by Cerebrolysin (30 ml iv within 8 hours of onset and continued to day 21, first cycle) and in a recovery phase (between 69-90 days, second cycle) compared to 50 historical controls matched by propensity scores. Key outcomes included functional independence (mRS 0–2 at 90 days), safety endpoints, and neurological recovery (NIHSS at 24h and 7 day post MT).ResultsPatients receiving Cerebrolysin achieved higher rates of mRS 0–2 at 90 days (68% vs. 44%, p=0.016, OR 2.7, 95%CI 1.2 - 6.1; NNT: 4.2), had reduced risk of secondary ICH (14% vs. 40%, p=0.02; RR 0.37, 95%CI 0.14-0.95), and had lower NIHSS on Day 7 (median [IQR]: 3 [4] vs. 6 [9], p=0.01). There was a significant difference in Barthel Index scores between the Cerebrolysin group and the control group at 30 days (median [IQR]: 77 [32] vs. 63 [50], p=0.03) and at 3 months (86 [22] vs. 75 [29], p=0.01) primarily driven by the increase in the mobility and transfer components. Multivariate analysis identified Cerebrolysin as an independent predictor of favorable outcomes at 3 months (OR 7.5, 95% CI 1.8–30.9), particularly in patients with diabetes (interaction OR 9.6, 95% CI 1.01–92). The overall mortality rates at 30- and 90-days were similar in both groups (2% vs 6% and 8% vs 12%, p>0.1).ConclusionCerebrolysin improved functional outcomes at 90 days, accelerated neurological recovery, and reduced complications post-MT in patients with small ischemic core, good collateral circulation and effective recanalization at baseline. These findings warrant further randomized trials to validate its efficacy and explore its long-term benefits.Registration: URL:https://www.clinicaltrials.gov; unique identifier:NCT04904341
A Mitochondrially Derived Plastidial Transporter Regulates Photosynthesis in the DiatomPhaeodactylum tricornutum
Authors: Giustini Cécile , Dal Bo Davide , Storti Mattia , Van Vlierberghe Mick , Baurain Denis , Cardol Pierre , Zhang Youjun , Fernie Alisdair R. , Fitzpatrick Duncan , Aro Eva-Mari , Allorent Guillaume , Albanese Pascal , Tolleter Dimitri , Curien Gilles , Finazzi Giovanni 
Published: February 2025

AbstractEukaryotic phototrophs depend on the activity of two engines (the plastid and the mitochondrion) to generate the energy required for cellular metabolism. Because of their overlapping functions, both activities must be closely coordinated. At the plastid level, optimization occurs through alternative electron transport, the diversion of excess electrons from the linear transport chain, and metabolic exchanges. A similar process takes place in the mitochondria, with documented evidence of energy and redox equivalents being exchanged between the two organelles. Organelle-organelle energy interactions at the physiological level are well established in diatoms, an ecologically significant member of phytoplankton. Yet the molecular components involved in this process remain largely unknown. Here, we identify a Mitochondrial Carrier Family (MCF) transporter, MCFc, located at the plastid envelope ofPhaeodactylum tricornutum, which seems to be widely distributed in complex algae. We then compare the performance of a wild-type and a mutant lacking MCFc. An analysis of spectroscopic and oxygen exchange data unveiled altered energetic interactions in the mutant, suggesting that MCFc, plays a role in plastid-mitochondrion communication. In silico analysis of MCFc implies a similar substrate-specific model to that of ADP/ATP carriers, although distinct motif differences in MCFc indicate potential variations in its function, with possible substrates including arginine, aspartate/glutamate, or citrate. These findings illuminate how mitochondrial energy contributes to fueling diatom photosynthesis.
Deep Learning-based Framework for Mycobacterium Tuberculosis Bacterial Growth Detection for Antimicrobial Susceptibility Testing
Authors: Vo Hoang-Anh T , Nguyen Sang , Tran Ai-Quynh T , Nguyen Han , Bich Hai Ho , Fowler Philip W , Walker Timothy M , Nguyen Thuy Thi 
Published: February 2025

AbstractTuberculosis (TB) kills more people annually than any other pathogen. Resistance is an ever-increasing global problem, not least because diagnostics remain challenging and access limited. 96-well broth microdilution plates offer one approach to high-throughput phenotypic testing, but they can be challenging to read. Automated Mycobacterial Growth Detection Algorithm (AMyGDA) is a software package that uses image processing techniques to read plates, but struggles with plates that exhibit low growth or images of low quality. We developed a new framework, TMAS (TB Microbial Analysis System), which leverages state-of-the-art deep learning models to detectM. tuberculosisgrowth in images of 96-well microtiter plates. TMAS is designed to measure Minimum Inhibitory Concentrations (MICs) rapidly and accurately while differentiating between true bacterial growth and artefacts. Using 4,018 plate images from the CRyPTIC (Comprehensive Resistance Prediction for Tuberculosis: An International Consortium) dataset to train models and refine the framework, TMAS achieved an essential agreement of 98.8%. TMAS offers a reliable, automated and complementary evaluation to support expert interpretation, potentially improving accuracy and efficiency in tuberculosis drug susceptibility testing (DST).Author summaryTuberculosis (TB) is one of the world’s leading causes of death from infectious diseases, with drug resistance making treatment increasingly difficult. Accurate and timely drug susceptibility testing (DST) is essential to determine which antibiotics remain effective against a given TB strain. A widely used DST method involves 96-well broth microdilution plates, where bacteria are exposed to different antibiotic concentrations to determine the minimum inhibitory concentration (MIC), the lowest concentration that fully prevents bacterial growth. However, manually interpreting these plates is time-consuming and prone to human error, while existing automated methods often struggle with imaging artifacts such as condensation, shadows, and contamination.In this study, we developed the Tuberculosis Microbial Analysis System (TMAS), a machine learning-based tool designed to automate MIC determination from plate images. Training on advanced deep learning models, TMAS can learn to detect bacterial growth with high precision, distinguishing true growth from artefacts such as shadows, bubbles, sediment, condensation and contamination. When tested on a large dataset, TMAS outperformed existing automated methods in accuracy, reliability and efficiency. By reducing the reliance on manual interpretation, TMAS has the potential to streamline TB diagnostics, improve efficiency in laboratories, and improve access to high-quality DST, particularly in resource-limited settings.
Making plant tissue accessible for cryo-electron tomography
Authors: Pöge Matthias , Dickmanns Marcel , Xu Peng , Li Meijing , Schiøtz Oda H. , Kaiser Christoph O. J. , Ma Jianfei , Bieber Anna , Capitanio Cristina , Brenner Johann , Riggi Margot , Klumpe Sven , Miras Manuel , Kazemein Jasemi Neda S. , Schulze Waltraud X. , Simon Rüdiger , Frommer Wolf B. , Plitzko Jürgen M. , Baumeister Wolfgang 
Published: February 2025

AbstractCryo-Electron Tomography (cryo-ET) allows to visualize the molecular architecture of pristinely preserved cells and tissues. The workflow of sample preparation for cryo-ET is rather complex; it involves vitrification by rapid freezing followed by cryo-Focused Ion Beam (FIB) milling rendering the volumes of interest thin enough for cryo-ET data acquisition. The established protocols for single cells grown on or deposited on EM-grids are not suitable for multicellular plant tissues. Plunge-freezing does not yield vitrified samples in most cases and must be replaced by high-pressure freezing. This, in turn, necessitates extensive modifications of the subsequent FIB milling procedures. In this communication we describe procedures for sample screening, targeted FIB milling guided by cryo-fluorescence microscopy and a novel lamella trimming step that allows to obtain homogenously thin lamellae suitable for cryo-ET. We have tested all the steps along the workflow with a variety of plant tissues including the mossPhyscomitrium patensand tissues ofArabidopsis thalianaandLimonium bicolor. We could demonstrate that the workflow optimized for plant tissues allows to attain subnanometer resolution in cases where subtomogram averaging is applicable.
Endothelial decorin is increased by ageing and, induces inflammation and diastolic dysfunction in the heart
Authors: Luxán Guillermo , Winkelmeier Timm , Bodemer Colin , Toğru Büşra Nur , Shumliakivska Mariana , Muhly-Reinholz Marion , Fischer Ariane , Ruz-Jurado Mariano , John David , Abplanalp Wesley T. , Dimmeler Stefanie 
Published: February 2025

AbstractAimsCardiovascular disease is the leading cause of death in the European Union and aging is one of its major risk factors resulting in the progressive deterioration of the cardiac structures and function. Here, we have combined single-nucleus-RNA-sequencing, imaging, and molecular and cell biology approaches to explore the maladaptive signals that drive cardiac ageing.Methods and resultsSingle-nucleus-RNA-sequencing analysis of young (3 months) and old (18 months) murine hearts revealed that the expression of decorin, a secreted proteoglycan expressed in the extracellular matrix of endothelial cells, is induced by ageing. Decorin treatment via osmotic mini-pump induced diastolic dysfunction and a pro-inflammatory environment in the myocardium characterized by increased infiltration of immune cells, increased expression of IL- 1β in endothelial cells and microvascular leakage in 3 months old mice. In vitro, decorin treatment induces cardiomyocyte hypertrophy, the expression of different pro-inflammatory cytokines likeIL1Bin endothelial cells, and compromises the endothelial barrier function.ConclusionsTogether, our results identify decorin as a novel player contributing to cardiac aging and disease. Decorin contributes to the age-related structural and functional dysfunction of the heart by inducing a pro-inflammatory environment in the myocardial microvasculature, a hallmark of cardiac ageing.Translational perspectiveAgeing is a major risk factor of cardiovascular disease and the molecular and cellular mechanisms that drive this process have not been completely described. The data presented here identifies decorin as a novel player contributing to systemic inflammation and microvascular dysfunction, two hallmarks of ageing. Although, because of its role regulating TGF-β signalling, decorin has been proposed for anti-fibrotic therapies, the pro-inflammatory effects observed on the cardiac microvasculature should be taken into account for the employment of decorin as an antifibrotic agent to treat disease associated cardiac fibrosis.
Extrafollicular activation of B cells contributes to the long-term survival of CD28KO mice infected with Sylvio X10/4Trypanosoma cruziparasites
Authors: Nascimento Rogério Silva do , Marinho Claudio R. F. , de Salles Érika Machado , D’Império Lima Maria Regina , Alvarez José M. 
Published: February 2025

ABSTRACTIn the initial phase of infections, prior to the development of the follicular antibody response, an extrafollicular B cell response develops in lymphoid organs, with activation of cells displaying B cell receptors with low affinity to the different epitopes of the invading pathogen. To evaluate if this response allows early protection in the murine host, we investigated its role during infection with Sylvio X10/4 (a low virulenceTrypanosoma cruziparasite) of CD28KO mice, a mouse strain that does not develop a follicular antibody response, in parallel with infected C57BL/6 mice (used as control). We observed thatT. cruziinfection allowed CD28KO mice to survive for a long period of time, ranging from a few weeks to almost a year. However, the CD28KO mice showed higher levels of subpatent parasitemia than C57BL/6 mice, as well as more intense and long-lasting inflammatory infiltrates in the heart. Following the CD28KO mice throughout the infection, we found a significant reduction in the number of CD8+T cells in the spleen, but not CD4+T cells, as well as a strong fluctuation in the number of B cells. Meanwhile, although the production of IFN-γ in the spleen was not affected by CD28 deficiency, a reduction in IL-2 production was observed in anti-CD3 stimulated CD4+T cells from infected CD28KO mice. Regarding the humoral response, after confirming that the T follicular helper (TFH) cells and germinal center B cells (GC-B) were absent in the infected CD28KO mice, we demonstrated that the extrafollicular antibodies, present in CD28KO infected mice, allowed an early protection in the murine host, since the transfer of serum from chronic CD28KO mice to naïve CD28KO mice, which were infected withT. cruzi24 hours later, promoted a significant reduction in parasitemia. These results demonstrate that low-affinity anti-T cruziextrafollicular antibodies contribute to the control of circulating parasites, allowing Sylvio X10/4-infected CD28KO mice to survive for a long time.AUTHOR SUMMARYLow-affinity anti-T cruziextrafollicular antibodies contribute to the control of circulating parasites, allowing Sylvio X10/4-infected CD28KO mice to survive for a long time.