bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Efficacy of Regenerative Therapies for Diabetic Foot Ulcers
Authors: Yang Hsi-An , Hsu Ren-Jun , Jheng Wun-Long , Weng Feng-Ju , Lee Jian-Jr 
Published: February 2025

Background
Diabetic foot ulcer (DFU) is one of the most dreaded complications of diabetes mellitus and is associated with a high risk of lower limb amputation and mortality. Because the efficacy of conventional treatments for DFUs is often limited, regenerative medicine therapy, such as growth factors and stem cells, may provide a solution to chronic wound healing. In this study, we compared several kinds of regenerative therapy for treating DFUs in terms of efficacy.

Methods
We systemically searched relevant studies on PubMed, Cochrane Library, and EMBASE. Randomized clinical trials on conventional treatment combined with platelet-rich plasma (PRP), epidermal growth factor (EGF), or stem cell therapy, compared with conventional treatment alone in patients with DFUs, were included in this study.

Results
A total of 1454 patients from 23 randomized controlled trials (RCTs) were included in the network meta-analysis. In terms of the number of completely healed ulcers, no significant difference was noted between PRP, stem cell therapy, and EGF group. We also performed surface under the cumulative ranking curve analyses to predict the rank of each intervention by the number of completely healed ulcers. The predicted ranking was as follows: stem cell, PRP, EGF, and the control group (conventional treatment alone). Furthermore, when we compared the mean of the wound healing time of DFUs among these four interventions, we found that the PRP group achieved significantly earlier ulcer healing than the stem cell, EGF, and control groups. No significant difference was observed in the time needed for wound healing between the stem cell and EGF groups. Funnel plot analysis demonstrated no publication bias.

Conclusions
PRP combined with conventional treatment significantly accelerates wound healing for DFUs. The mean wound healing time was similar between the stem cell and EGF groups. However, additional reviews of rigorous, large, well-designed RCTs are warranted for further validation of our findings.
Successful Perianal Wound Treatment Using the Fecal Management System
Authors: Yu Yi-Shang , Weng Yu-Tse , Wu Chien-Wei , Tzeng Yuan-Sheng 
Published: February 2025

Background
Fecal diversion is important for healing of perianal wounds. However, traditional fecal diversion with colostomy is associated with risks of general anesthesia and requires healthy abdominal skin for stoma creation. Alternative methods of fecal diversion are needed.

Aim and Objectives
We aimed to illustrate an effective alternate method of fecal diversion in patients with perianal wounds by reporting 2 patients with perianal wounds who were successfully treated using the fecal management system.

Materials and Methods
The first patient was a 79-year-old female with a grade IV sacral pressure injury who underwent operative debridements and vacuum-assisted wound closure. The second patient was a 21-year-old female with extensive perianal burn wounds who underwent a series of debridements, wound dressing changes, and split-thickness skin grafts. The fecal management system was utilized for fecal diversion in both patients.

Results
Satisfactory wound healing was achieved in each patient using the fecal management system for fecal diversion.

Conclusions
Based on our 2 patients and previous studies that have reported successful treatment of perianal wounds using the fecal management system, this system is feasible to use and effective. We suggest its use in patients with perianal wounds, particularly those in whom colostomy is not preferable or contraindicated.
Patient-Reported Outcomes and Aesthetic Evaluations in Autologous Breast Reconstruction at Taipei Veterans General Hospital
Authors: Cheng Qi-Rui , Feng Chin-Jung , Hsiao Fu-Yin , Tseng Ling-Ming , Huang Chi-Cheng , Tsai Yi-Fang , Lin Yen-Shu , Wang Shyh-Jen , Yu Wen-Chan , Perng Cherng-Kang 
Published: February 2025

Background
Improving the quality of life increases patients' expectations of postmastectomy breast reconstruction. Increased incidence of breast implant-associated anaplastic large cell lymphoma encourages patients to choose autologous breast reconstruction over implantation. This study aimed to analyze the aesthetic outcomes of autologous breast reconstruction and define factors associated with the results.

Methods
We recruited patients for immediate or delayed autologous tissue reconstruction after mastectomy from October 2015 to June 2021 at a single institute in Taiwan. Patient demographic data, operative complications, and secondary cosmetic revisions were identified through a medical chart review. Patient-reported outcomes (PROs) and perioperative imaging records were analyzed using the BREAST-Q questionnaire and Breast Cancer Conservation Treatment (BCCT).core, respectively, for aesthetic outcome evaluations.

Results
Eighty-three women were enrolled, with a 73% BREAST-Q questionnaire response rate, and followed-up for a mean 36 (6–78) months. The mean BREAST-Q score for satisfaction with breasts was 60.46 (standard deviation = 19.09). The postoperative BCCT.core evaluation did not differ significantly from the preoperative evaluation (P = 0.245), and most patients (70.59%) reported similar (50%) or better results (20.59%) after reconstruction. Postmastectomy radiotherapy impacted negatively on psychosocial well-being (P = 0.012), sexual well-being (P = 0.002), and satisfaction with breast (P = 0.026). Three-dimensional breast molds might improve psychosocial well-being BREAST-Q scores, sexual well-being, and breast satisfaction but was not statistically significant.

Conclusions
Breast reconstruction with autologous tissue had an acceptable complication rate and favorable aesthetic outcomes in PROs and BCCT.core. Postmastectomy radiotherapy resulted in worse PROs and a 3-dimensional breast mold may facilitate better outcomes.
The Seven-Day Method
Authors: Tanaka Eiko , Chuang Andy Deng-Chi , Chiu Wen-Kuan , Tsai Chia-Hsuan 
Published: February 2025

Introduction
Aesthetic reduction of the labia minora has increased in popularity over the recent decades. Numerous surgical techniques have surfaced, each with their advantages and shortcomings. Regardless of resection technique, recovery period of up to 6 weeks after labia minora reduction surgery has been recommended.

Method
A modification of the edge resection technique described herein eliminates the need for suture removal and allows for expedited recovery within a week. Patients receiving the eponymously named seven-day method at a single aesthetic center were evaluated for aesthetic outcome, complications, reoperation rate, and overall patient satisfaction.

Results
Of the 80 patients surveyed, aesthetic outcome and patient satisfaction were either “satisfied” or “very satisfied” in 96.9% and 87.5% of the patients, with a mean score of 4.6 and 4.2 out of 5, respectively. Complications included bleeding, uneven contour, dehiscence, swelling, stitch exposure, pain, and itching. Overall reoperation rate was 3.8% and were all for elective and aesthetic purposes.

Conclusions
The seven-day method is a relatively simple and undemanding technique that allows quick postoperative recovery without the need for follow-up, promising good patient satisfaction and outcome.
MolGene-E: Inverse Molecular Design to Modulate Single Cell Transcriptomics
Authors: Ohlan Rahul , Murugan Raswanth , Xie Li , Mottaqi Mohammedsadeq , Zhang Shuo , Xie Lei 
Published: February 2025

AbstractDesigning drugs that can restore a diseased cell to its healthy state is an emerging approach in systems pharmacology to address medical needs that conventional target-based drug discovery paradigms have failed to meet. Single-cell transcriptomics can comprehensively map the differences between diseased and healthy cellular states, making it a valuable technique for systems pharmacology. However, single-cell omics data is noisy, heterogeneous, scarce, and high-dimensional. As a result, no machine learning methods currently exist to use single-cell omics data to design new drug molecules. We have developed a new deep generative framework named MolGene-E to tackle this challenge. MolGene-E combines two novel models: 1) a cross-modal model that can harmonize and denoise chemical-perturbed bulk and single-cell transcriptomics data, and 2) a contrastive learning-based generative model that can generate new molecules based on the transcriptomics data. MolGene-E consistently outperforms baseline methods in generating high-quality, hit-like molecules from gene expression profiles obtained from single-cell datasets as validated by target knock-out experiments using CRISPR. This superior performance is demonstrated across diversede novomolecule generation metrics. Extensive evaluations demonstrate that MolGene-E achieves state-of-the-art performance for zero-shot molecular generations. This makes MolGene-E a potentially powerful new tool for drug discovery.
Unique Adaptations of a Photosynthetic MicrobeRhodopseudomonas palustristo the Toxicological Effects of Perfluorooctanoic Acid
Authors: Kathol Mark , Azme Anika , Saifur Sumaiya , Aich Nirupam , Saha Rajib 
Published: February 2025

ABSTRACTIn this study, we investigate the PFOA removal capabilities ofRhodopseudomonas palustris(R. palustris), a fluoroacetate dehalogenase containing microbe as a potential candidate for achieving bioremediation. In the 50-day PFOA uptake experiment, R. palustris removed 44 ± 6.34 % PFOA after 20 days of incubation, which was then reduced to a final removal of 6.23 ± 12.75 %. Results indicate PFOA was temporarily incorporated into the cell membrane before being released partially into the media after cell lysis. This incorporation might be attributed to the combined effect of hydrophobic interaction between PFOA and the cell membrane and the reduced electrostatic repulsion from the high ion presence in the growth medium. The growth ofR. palustrisduring the PFOA uptake experiment was 9-fold slower than their growth without PFOA. This study also completely defines the toxicity range of PFOA forR. palustristhrough a toxicity assay. Increasing PFOA concentration reduced the microbe growth, with complete inhibition around 200 ppm. For various concentrations of PFOA, R. palustris exhibits interesting diauxic growth behavior. An accelerated growth phase was followed by a temporary death phase in the first 24 hours in the presence of 12.5-100 ppm PFOA, implying a unique adaptation mechanism to PFOA.
Circularization of Single-Stranded DNA Donor Template Unleashes the Power of Non-Viral Gene Delivery for Long-Term HSCs editing
Authors: Letort Gil , Duclert Aymeric , Clerre Diane Le , Chion-Sotinel Isabelle , Salvatori Roger , Dessez Emilie , Sevin Margaux , Rotondi Marco , Ducani Cosimo , Duchateau Philippe , Valton Julien 
Published: February 2025

AbstractOver the past decade, non-viral DNA template delivery has been used with engineered nucleases to target single-stranded DNA sequences in hematopoietic stem and progenitor cells. While effective for gene therapy, this method has been limited to short DNA donor templates, restricting its applications to gene corrections. To expand its scope, we developed an editing process using kilobase-long circular single-stranded DNA donor templates and TALEN technology. Our results show that the CssDNA editing process achieves high gene insertion frequency in viable HSPCs. Compared to a conventional AAV-editing process, CssDNA-edited HSPCs show a higher propensity to engraft and maintain gene edits in a murine model. This positive outcome is partly due to higher levels of primitive edited HSPCs, a more quiescent metabolic state, and elevated expression of bone marrow niche adhesion markers. Our findings highlight the strong potential of CssDNA as a universal and efficient non-viral DNA template for gene therapy applications.
RBM15-MKL1 fusion protein promotes leukemia via m6A methylation and WNT pathway activation
Authors: Mayday Madeline Y. , Biancon Giulia , Wei Manyi , Ramirez Christian , Moratti Irene , Pintado-Urbanc Andreas P. , Wang Lin , Espinosa Jether Amos , Simon Matthew D. , Ofir-Rosenfeld Yaara , Rausch Oliver , Tebaldi Toma , Halene Stephanie , Krause Diane S. 
Published: February 2025

AbstractAcute megakaryoblastic leukemia driven by the RBM15-MKL1 fusion protein (RM-AMKL) is the only known recurrent mutation involving the N6-methyladenosine (m6A) writer complex. Dysregulation of m6A modification affects RNA fate and is linked to oncogenesis. Inhibition of m6A deposition via inhibition of the METTL3 writer protein has anti-tumour activity, but the mechanism underlying its efficacy and cancer specificity remains unclear. We treated murine RM-AMKL cells with a novel METTL3 inhibitor, STM3675, and showed apoptosisin vitroand prolonged survival of mice transplanted with RM-AMKL, implicating m6A as an essential component of AMKL and identifying Wnt signalling as a key driver of leukemogenesis. To elucidate the mechanism by which m6A contributes to leukemogenesis we employed a multi-omic approach, combining transcriptome-wide assessment of RNA binding, methylation and turnover. We show for the first time that RM retains the RNA-binding and m6A-modifiying functions of its RBM15 component, while also selectively regulating distinct mRNA targets, particularly genes involved in Wnt signalling including Frizzled. Frizzled genes are upregulated by RM and downregulated in RM-AMKL cells in response to METTL3 inhibition, providing an m6A-dependent explanation for their upregulation. Direct Frizzled knockdown reduced RM-AMKL growth, which was partially rescued by treatment with a β-catenin agonist, underscoring a functional role of Wnt signalling in RM-AMKL. Human AMKLs show elevated Wnt pathway and Frizzled gene expression, highlighting the relevance of our work. Together, our findings reveal that RM-specific m6A modifications and activation of Wnt signalling are critical drivers of RM-AMKL, highlighting these pathways as potential therapeutic targets.Key PointsRM retains functional abilities of RBM15 and additionally interacts with Wnt-related transcripts to increase expression of Fzd proteins.The METTL3 writer complex and WNT signalling pathways are essential for RM-driven leukemia.
Managing the genetic diversity of animal populations using cryobanks: optimizing the constitution ofex situcollection?
Authors: Jacques Alicia , Tixier-Boichard Michèle , Restoux Gwendal 
Published: February 2025

AbstractThe genetic diversity of populations is important for their long-term conservation and adaptive potential. Nevertheless, there is an erosion of genetic variability in all populations, whether a small population under conservation or a large breed under selection. Many countries have conserved animal genetic resourcesex situ, with the creation of cryopreserved collections. These cryopreserved genetic resources could open up new prospects for managing the genetic diversity of animal populations. Currently, there are as many strategies for conserving cryopreserved genetic resources as there are cryobanks. The aim of our study is to examine some parameters for optimizing the constitution of a gene bank.ResultsWe performed simulations of animal populations (i.e. selection or conservation) using different types of breeding strategy and changing (i) the size and age of the cryopreserved collection or (ii) the management of cryopreserved collections (entry and exit of frozen semen).We found that the age of genetic resources was the predominant factor for populations under selection, as this factor also quantifies the lag in breeding values. A more massive stocking of recent individuals seems to be the most relevant strategy for mobilizingex situgenetic resources in a breeding scheme. For populations in conservation, older reproductive material becomes highly relevant. A cryobank with a large number of old individuals enables better management of matings and avoids too rapid an increase in inbreeding over the long term, while the use of a more moderate number of old individuals enables some genetic progress to be maintained, but offers fewer possibilities for managing genetic diversity. Continuous collection supply is a relevant option for population management. Whatever the breeding strategy, the use of OCS can help mobilizeex situgenetic resources in animal breeding programs.ConclusionsCryopreserved genetic resources are an invaluable help in the management of domestic populations. It is important to continue research in order to optimize the use of cryopreserved genetic resources, and to set up collection management recommendations that are relevant and adapted to breeding programs.
Resource economics of tree communities control soil food web multifunctionality in European forests
Authors: Henneron Ludovic , Wardle David A. , Berg Matty P. , Hättenschwiler Stephan , Bauhus Jürgen , Buscot François , Coq Sylvain , Decaëns Thibaud , Fromin Nathalie , Ganault Pierre , Gillespie Lauren M. , Goldmann Kezia , Matula Radim , Milcu Alexandru , Muys Bart , Nahmani Johanne , Prada-Salcedo Luis Daniel , Scherer-Lorenzen Michael , Verheyen Kris , Wambsganss Janna , Kardol Paul 
Published: February 2025

AbstractPlants affect terrestrial ecosystem functioning by performing the primary production that energetically sustains heterotrophic organisms1, and by shaping the microenvironment2. However, the influence of plant diversity and community composition on ecosystem functioning through their effects on energy flow into food webs has been little studied3,4, especially for soil food webs that channel most of the plant-derived energy1,5. Applying a food web energetics approach6,7, we show that the resource economics of dominant tree species control soil food web multifunctionality across European forests. Specifically, tree communities dominated by resource acquisitive species promoted faster rates of multiple soil trophic functions simultaneously than did those dominated by resource conservative species. This was primarily driven by their production of plant litter with higher nutritional quality and their warmer forest microclimate, leading to a higher metabolic activity of soil organisms8. Tree species mixing had rather weak and negative effects on soil food web multifunctionality, mostly due to a shift in the resource-based energy channeling from living plant fine roots to litter and a cooling effect on the forest microclimate. Tree diversity effects were largely outweighed by community compositional effects, which were of similar magnitude to the effects of biogeographic differences among locations. Our findings emphasize the importance of plant functional traits related to resource economics as drivers of plant community effects on soil food web functioning5,9and highlight the consequences that climate-driven shifts in tree community composition could have for forest soil functioning.
Predicting High-Resolution Spatial and Spectral Features in Mass Spectrometry Imaging with Machine Learning and Multimodal Data Fusion
Authors: Haque Md Inzamam Ul , Kannan Ramakrishnan , Hinkle Jacob D. , Stopka Sylwia A. , Agar Nathalie Y. R. , Ovchinnikova Olga S. , Mukherjee Debangshu 
Published: February 2025

AbstractRecent advancements in molecular Mass Spectrometry Imaging (MSI) have sparked interest in integrating high spatial resolution methods with molecular mass-spectrometry-based chemical imaging. Fusion-based algorithms have proven effective in generating high spatial-resolution molecular mass spectra. However, a significant challenge stems from the differing physical mechanisms underlying image generation and data upsampling techniques, potentially leading to discrepancies in integrated information channels. Integrating physical constraints into data processing workflows is essential to tackle this issue. In this study, we propose an innovative approach that merges data from Fourier transform ion cyclotron resonance (FTICR), time- of-flight matrix-assisted laser desorption/ionization (MALDI-ToF), and time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging techniques. By leveraging FT-ICR’s unparalleled spectral resolution and ToF-SIMS’s exceptional spatial resolution, we achieve submicron spatial resolution, enabling the observation of intact molecular species with remarkable spectral precision. Canonical correlation analysis is employed to incorporate physical constraints. Through sophisticated image processing and machine learning techniques, the results of this fusion hold significant promise for advancing our comprehension of complex systems and unveiling concealed molecular intricacies.
Deciphering the dynamics of Cyanobacteria-Phage in a natural lake: Insights from a decade-long investigation
Authors: Stern Kiri , Vincent Jin , Taranu Zofia E , Fortin Nathalie , Martel Alexis , Robbe Andrea , Thaize Romane , Castelli Mathieu , Beckett Stephen J. , Poisot Timothee , Buckling Angus , Shapiro B. Jesse , Tromas Nicolas 
Published: February 2025

ABSTRACTPhages – viruses that infect bacteria – are often seen as key players in bacterial community dynamics and the ecosystem services those communities support. However, much of our understanding of phage-bacteria interactions comes from in vitro studies, which provide limited insights into how these interactions occur in natural environments. In this study, we used cyanobacterial blooms as a model microbial community to evaluate the potential role of phages in driving cyanobacterial populations. These blooms are characterized by massive and usually rapid accumulation of cyanobacterial biomass and occur worldwide, threatening aquatic systems. The frequency and intensity of cyanobacterial blooms are increasing over time, likely due to human activities, and, until now, the role of predators like phages has remained unclear. We used a deep amplicon sequencing approach targeting the g20 capsid gene to profile the cyanophage community in eutrophic Lake Champlain over time, comparing their dynamics and diversity with bacterial communities and examining their associations. We evaluated whether phages simply followed bacterial dynamics, with limited impact on bacterial composition, or instead whether they played an active role in drving bacterial community structure. We found that phages exhibited similar dynamics to their potential bacterial hosts and shared environmental niches. However, we also observed strong differences specific to the phage community, such as inter-annual variation and an increase in Shannon diversity over time. Phage-bacteria and phage-cyanobacteria co-variance uncovered potential interactions that resulted in strongly modular networks. However, while the network structure remained modular, the composition of the modules differed significantly between environmental and temporal conditions. Lastly, viral phylogeny partially explained phage-bacteria co-variance, but only for a small proportion of bacterial ASVs. Our results indicate that phage-bacterial interactions are partly genetically structured and vary within modules across environmental conditions.