bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technical and Analytical Approach for Breast Reconstruction With IMAP Propeller Flap
Authors: Spaggiari Antonio , Morrison Wayne A. , Marra Caterina , Lusetti Irene Laura , Fiocchi Federica , Pinelli Massimo , De Santis Giorgio 
Published: December 2024

Background:
The breast-sharing technique uses the lower quadrants discarded from a contralateral symmetrizing reduction mammoplasty to reconstruct the breast after mastectomy. The aim of our study was to revisit this old technique and to improve its vascular predictability by preoperative computed tomography angiography (angio-CT) and intraoperative indocyanine green (ICG) imaging.

Methods:
Twenty-six patients were enrolled and assessed by a preoperative angio-CT to localize and evaluate the internal mammary artery perforator (IMAP). In the selected patients, a Wise skin-pattern reduction was designed to allow elevation of a transversely oriented flap including both inferior poles. The flap was based medially on the IMAP. After elevation, evaluation of its arterial and venous perfusion was assessed with ICG.

Results:
Eight patients were excluded after pre- and intraoperative studies. Sixteen breast-sharing flaps were performed. A distal flap venous compromise appeared in 2 cases, requiring debridement and flap repositioning, and an infection occurred in 1 case. Four patients had detectable firm lumps that resolved. There were no issues with donor site healing, and a repositioning of the areola was necessary in 2 patients.

Conclusions:
Breast-sharing techniques have not gained popularity for many reasons. By combining current understanding of breast cancer behavior, experience with perforator anatomy, and angio-CT and ICG, we believe this study gives a second life to this flap, identifying its weaknesses and improving them. The IMAP propeller flap, simpler and safer in the presence of comorbidities than a free flap, can be a good choice for well-selected candidates.
The Value of Whole-Volume Radiomics Machine Learning Model Based on Multiparametric MRI in Predicting Triple-Negative Breast Cancer
Authors: Xu Tingting , Zhang Xueli , Tang Huan , Hua Ting , Xiao Fuxia , Cui Zhijun , Tang Guangyu , Zhang Lin 
Published: December 2024

Objective
This study aimed to investigate the value of radiomics analysis in the precise diagnosis of triple-negative breast cancer (TNBC) based on breast dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and apparent diffusion coefficient (ADC) maps.

Methods
This retrospective study included 326 patients with pathologically proven breast cancer (TNBC: 129, non-TNBC: 197). The lesions were segmented using the ITK-SNAP software, and whole-volume radiomics features were extracted using a radiomics platform. Radiomics features were obtained from DCE-MRI and ADC maps. The least absolute shrinkage and selection operator regression method was employed for feature selection. Three prediction models were constructed using a support vector machine classifier: Model A (based on the selected features of the ADC maps), Model B (based on the selected features of DCE-MRI), and Model C (based on the selected features of both combined). Receiver operating characteristic curves were used to evaluate the diagnostic performance of the conventional MR image model and the 3 radiomics models in predicting TNBC.

Results
In the training dataset, the AUCs for the conventional MR image model and the 3 radiomics models were 0.749, 0.801, 0.847, and 0.896. The AUCs for the conventional MR image model and 3 radiomics models in the validation dataset were 0.693, 0.742, 0.793, and 0.876, respectively.

Conclusions
Radiomics based on the combination of whole volume DCE-MRI and ADC maps is a promising tool for distinguishing between TNBC and non-TNBC.
Candida tropicalis Liver Abscess in an Immunocompromised Patient With Pancreatic Head Cancer on 68Ga-FAPI PET/CT
Authors: Kim Jahae , Kim Seong Eun , Cho Eunae , Choi Kang-Ho 
Published: December 2024

Abstract

Candida infections have become a growing concern to the immunocompromised patients with cancer. We report a case of liver abscess causing Candida tropicalis candidemia in an immunocompromised patient with pancreatic head cancer on 68Ga-FAPI PET/CT. A 77-year-old man had a history of 10-year duration of uncontrolled diabetes, the presence of neutropenia, immunocompromised condition, and the progression of pancreatic cancer despite the 14 cycles of chemotherapy and palliative radiotherapy. After 3 weeks of radiotherapy, he presented with fever and elevated CRP level. 68Ga-FAPI PET/CT scan showed new intense uptake in the liver, and 2 pairs of blood culture revealed C. tropicalis.
Systematic Review of Integration Strategies Across the US Healthcare System: Assessment of Price, Cost, and Quality of Care
Authors: Satiani Bhagwan , Way David P , Hoyt David B , Ellison E Christopher 
Published: December 2024

Background.
In the last 30 years, consolidation of healthcare systems in the United States has accelerated through mergers and acquisitions. We completed a systematic literature review on integration to determine if its reputation for enhancing the value of healthcare by reducing price and cost/spending and improving overall quality of care is justified.

Methods.
A systematic review of the literature was completed for articles published in the United States from 1990-2024. Primary inclusion criteria were horizontal integration (joining two or more hospitals) (HI) and vertical integration (merging of physicians and hospitals) (VI) and reporting on at least one measure of value (price, cost/spending, or quality)

Results.
Neither HI nor VI has resulted in consistent and significant improvements in price, cost/spending, or quality associated with healthcare delivery. We screened 1297 articles and identified 37 that met inclusion criteria. Results from any form of integration were mixed. Thirteen of 14 studies (93%) about price reported price increases. Thirteen of 16 studies (81%) about cost/spending showed cost increases or no change. Twenty of 26 studies (77%) about quality showed reductions or no change from integration (HI, VI or both).

Conclusions.
Our review suggests that evidence is lacking to support the theory that integration is an effective strategy for improving the value of healthcare delivery. This finding represents an opportunity for healthcare leaders, including surgeons, to better define value in their efforts to improve quality while balancing the financial stability of the healthcare industry with a focus on benefiting the patient.
Dynamic modulation of IRE1α-XBP1 signaling by adenovirus
Authors: Jang Yumi , Bunz Fred 
Published: December 2024

AbstractThe abundant production of foreign proteins and nucleic acids during viral infection elicits a variety of stress responses in host cells. Viral proteins that accumulate in the endoplasmic reticulum (ER) can trigger the unfolded protein response (UPR), a coordinated signaling program that culminates in the expression of downstream genes that collectively restore protein homeostasis. The model pathogen adenovirus serotype 5 (HAdV5) activates the UPR via the signaling axis formed by inositol-requiring enzyme type 1 (IRE1α) and the X-box binding protein 1 (XBP1), a transcription factor required for immune function. Recent studies have suggested that IRE1α-XBP1 activity supports adenovirus replication. Here, we show that HAdV5 exerted opposing effects on IRE1α and XBP1. IRE1α was activated in response to HAdV5 but the production of the XBP1 isoform, XBP1s, was post-transcriptionally blocked. The tumor suppressor p53, which is eliminated by HAdV5 after infection, inhibited IRE1α activation. The de-repression of IRE1α following the degradation of p53 conceivably reflects a novel antiviral mechanism, which HAdV5 ultimately evades by suppressing XBP1s. Our findings highlight the defective antiviral defenses in cancer cells and further illustrate the opposing mechanisms used by adenoviruses and their host cells to exert control over the UPR, a critical determinant of cell fate.
Harmonising digitised herbarium data to enhance biodiversity knowledge: creating an updated checklist for the flora of Greenland
Authors: Whitley Brandon Samuel , Abermann Jakob , Alsos Inger Greve , Biersma Elisabeth M. , Gårdman Viktor , Høye Toke Thomas , Jones Laura , Khelidj Nora Meriem , Li Zhao , Losapio Gianalberto , Pape Thomas , Raundrup Katrine , Schmitz Paula , Silva Tiago , Wirta Helena , Roslin Tomas , Ahlstrand Natalie Iwanycki , de Vere Natasha 
Published: December 2024

SummaryInternational efforts to digitise herbarium specimens provide the building blocks for a global digital herbarium. However, taxonomic changes and errors can result in inconsistencies when amalgamating specimen metadata, that compromise the assignment of occurrence records to correct taxa, and the subsequent interpretation of patterns in biodiversity. We present a novel workflow to mass-curate digital specimens. By employing existing digital taxonomic backbones, we aggregate specimen names by their accepted name and flag remaining cases for manual review. We then validate names using site-specific floras, balancing automation with taxonomic expert-based curation. Applying our workflow to the vascular plants of Greenland, we harmonised 175,266 digitised herbarium specimens and observations from 92 data providers from the Global Biodiversity Information Facility (GBIF). The harmonised metacollection for the Greenland flora contains 780 plant species. Our workflow increases the number of species known from Greenland compared to other currently available species checklists and increases the mean number of occurrences per species by 42.6. Our workflow illustrates the integration required in order to create a global, universally accessible digital herbarium, and shows how previous obstacles to database curation can be overcome through a combination of automation and expert curation. From the specific perspective of the Greenland flora, our approach arrives at a new checklist of taxa, a new curated metacollection of occurrence data, and revised estimates of plant richness. The list of taxa and their prevalence allow a new basis for biodiversity assessment and conservation planning.Societal Impact StatementDigitising plant collections has allowed for data to be aggregated across multiple collections, forming a single harmonised resource of unprecedented scale. This resource is only accurate once the database names are assigned to one accepted name per species. We established a semi-automated workflow for processing plant name data, leveraging taxonomic backbones and employing taxonomic expertise at key stages. Applying our workflow to the flora of Greenland, we developed a curated checklist of 780 species, capturing greater species richness than previously published, while also curating 175,266 plant records. Our findings redefine our knowledge of Greenlandic plant diversity, while harmonising a vast digital collection for further research.
Patient-derived HCC cells recapitulating the transcriptomic landscape of primary HCV-related liver cancer
Authors: Kah Janine , Staffeldt Lisa , Volz Tassilo , Schulze Kornelius , Heumann Asmus , Rövenstrunk Götz , Goebel Meike , Peine Sven , Dandri Maura , Lüth Stefan 
Published: December 2024

AbstractBackgroundThe hepatocellular carcinoma is one of the leading causes of cancer-related mortality and is characterized by high heterogeneity and subsequently adaptation by developing resistance to current treatments. In this scenario the application of individualized models is crucial to understand the potential of approved therapies. Recently, we established a series of individual cell lines derived from patients who developed HCC on different entities, serving as a platform for individual approaches. In this study, we classified the LC4 cells derived from the center region of a HCC with underlying HIV-HCV co-infection, by using deep analysis on the pathway regulation level.MethodsWe employed DEG analysis, followed by pathway analysis to characterize the preservation level of the LC4 cells and the level of adoption. Next, we classify the model, by employing healthy donor samples, commonly used HCC cell lines and global RNAseq data sets.ResultsWe showed that the LC4 cells reflect significant characteristics of the parental region, including the replication of the immuno-suppressive and the proliferative milieu. The LC4 cells exhibit a metabolic reprogramming characterized by the downregulation of drug-metabolizing CYP enzymes compared to healthy individuals, indicating a transition to alternate metabolic pathways. Moreover, we identified common Biomarkers in the parental tissue, global datasets and the LC4 cells.ConclusionWe showed that the LC4 cell line is applicable as an individual model for pre-clinical testing of treatment regimens in HCC driven research.
A single-cell atlas of transcriptome changes in the intestinal epithelium at the suckling-to-weaning transition
Authors: Malonga Tania , Knudsen Christelle , Lhuillier Emeline , Aymard Patrick , Jones Elisabeth , Lencina Corinne , Despeyroux Manon , Riant Elodie , Cabau Cédric , Ivy Alyssa , Loving Crystal L. , Vialaneix Nathalie , Beaumont Martin 
Published: December 2024

AbstractThe suckling-to-weaning dietary transition is a key step in mammalian intestinal development. However, the relative contributions of genetically wired and nutritional factors in this maturation process remain to be elucidated. Moreover, the cellular diversity of the intestinal epithelium has been overlooked in this context. The aim of our study was to identify the transcriptome changes induced in each cell type of the intestinal epithelium at the onset of solid food ingestion. We compared the single-cell transcriptome of epithelial cells isolated from the caecum of age-matched littermate suckling rabbits ingesting or not solid food. Our dataset provides the first single-cell atlas of the rabbit intestinal epithelium and highlights the interest of the rabbit as a model for studying BEST4+epithelial cells, which are absent in mice. Solid food ingestion induced extensive transcriptome changes in each epithelial cell type, with the most pronounced changes noted in absorptive and BEST4+cells. Some of the effects of solid food introduction were common to most epithelial cell types, such as the upregulation ofALDH1A1, which encodes for a vitamin A processing enzyme. Solid food ingestion remodeled epithelial defenses systems, as observed by the increased expression of interferon-stimulated genes in mature absorptive and BEST4+cells. Solid food also upregulated the gene expression of the immunoglobulin transporterPIGR, specifically in cells located at the base of epithelial crypts and in goblet cells. In addition, solid food triggered epithelial differentiation, which was associated with modification of the expression of genes involved in handling of amino acids, lipids and bile acids, as well as changes in hormone expression by enteroendocrine cells. These cell type-specific transcriptome modifications induced by solid food ingestion coincided with changes in microbiota composition and metabolic activity, which may contribute to epithelial maturation. Overall, our work provides a single-cell atlas of the transcriptome changes induced in the intestinal epithelium at the suckling-to-weaning transition.
Anti-biofilm activity of new low molecular weight compounds produced byLactiplantibacillus plantarumSJ33 againstKlebsiella pneumoniae
Authors: Mohapatra Amrita Ray , Lakshmanan Divya , Jeevaratnam Kadirvelu 
Published: December 2024

ABSTRACTCommunity-acquired infections are partly attributed to biofilms formed by drug resistant bacteria signifying major health problems. Hence, there is a critical need for the development of new antibiotics with antibacterial activities. In this study, we investigated the biofilm inhibiting characteristics of antibacterial compounds C1 and C2 confirmed as (3-amino-5-hydroxy-6-(hydroxymethyl)-4-(1-hydroxyprop-2-yn-1-yl)-3,3a,4,5,6,7a-hexahydro-7H-indazol-7-one) and (1-(dimethylamino)-3-hydroxy-3-((2-hydroxypropan-2-yl)oxy)-1 (methylamino)butan-2-one) which were previously characterized and identified by our group. This compound exhibits antibacterial activity against Gram-negative bacteria including activity against clinical isolates ofKlebsiella pnemoniaeandEscherichia coli. Bactericidal activity againstK. pnemoniaewas revealed by scanning electron microscopic (SEM) images that showed cellular leakage by C1 and C2 which is probably the major cause of its antibacterial activity. These findings were supported by antibacterial assays of susceptible as well as resistant pathogens. Biofilm assays also proved anti-biofilm activity of C1 and C2 on biofilm inhibition as well as dispersion of mature biofilms using crystal violet assay and the results were confirmed by fluorescence and SEM observation. In conclusion, our results showed that C1 and C2 exert bactericidal action on target cells by membrane disruption. Biofilm inhibition and dispersion of preformed biofilms was also revealed by microscopic images, making it an interesting alternative for commercial antibiotics for the development of new antibacterial therapies. The bioactive compounds C1 and C2 not only inhibitK. pnemoniaegrowth but also eradicate the biofilm formation thus reducing the virulence ofK. pnemoniaepathogen.
Time is encoded by methylation changes at clustered CpG sites
Authors: Ochana Bracha-Lea , Nudelman Daniel , Cohen Daniel , Peretz Ayelet , Piyanzin Sheina , Gal Ofer , Horn Amit , Loyfer Netanel , Varshavsky Miri , Raisch Ron , Shapiro Ilona , Friedlander Yechiel , Hochner Hagit , Glaser Benjamin , Dor Yuval , Kaplan Tommy , Shemer Ruth 
Published: December 2024

AbstractAge-dependent changes in DNA methylation allow chronological and biological age inference, but the underlying mechanisms remain unclear. Using ultra-deep sequencing of >300 blood samples from healthy individuals, we show that age-dependent DNA methylation changes are regional and occur at multiple adjacent CpG sites, either stochastically or in a coordinated block-like manner. Deep learning analysis of single-molecule patterns in two genomic loci achieved accurate age prediction with a median error of 1.46-1.7 years on held-out human blood samples, dramatically improving current epigenetic clocks. Factors such as gender, BMI, smoking and other measures of biological aging do not affect chronological age inference. Longitudinal 10-year samples revealed that early deviations from epigenetic age are maintained throughout life and subsequent changes faithfully record time. Lastly, the model inferred chronological age from as few as 50 DNA molecules, suggesting that age is encoded by individual cells. Overall, DNA methylation changes in clustered CpG sites illuminate the principles of time measurement by cells and tissues, and facilitate medical and forensic applications.Abstract Figure
Pulmonary granuloma formation during latentCryptococcus neoformansinfection in C3HeB/FeJ mice involves progression through three immunological phases
Authors: Betancourt Jovany J. , Ding Minna , Yoder J. Marina , Mutyaba Issa , Atkins Hannah M. , de la Cruz Gabriella , Meya David B. , Nielsen Kirsten 
Published: December 2024

ABSTRACTCryptococcus neoformansis a fungal pathogen that can cause lethal disease in immunocompromised patients. Immunocompetent host immune responses, such as formation of pulmonary granulomas, control the infection and prevent disseminated disease. Little is known about the immunological conditions establishing the latent infection granuloma in the lungs. To investigate this, we performed an analysis of pulmonary immune cell populations, cytokine changes, and granuloma formation during infection with a latent disease-causing clinical isolate in C3HeB/FeJ mice over 360 days. We found that latently infected mice progress through three phases of granuloma formation where different immune profiles dominate: an early phase characterized by eosinophilia, high IL-4/IL-13, andC. neoformansproliferation in the lungs; an intermediate phase characterized by multinucleated giant cell formation, high IL-1α/IFNγ, granuloma expansion, and increased blood antigen levels; and a late phase characterized by a significant expansion of T cells, granuloma condensation, and decreases in lung fungal burden and blood antigen levels. These findings highlight a complex series of immune changes that occur during the establishment of granulomas that controlC. neoformansin the lungs and lay the foundation for studies to identify critical beneficial immune responses to Cryptococcus infections.IMPORTANCECryptococcus neoformansis a fungal pathogen that disseminates from the lungs to the brain to cause fatal disease. Latent C. neoformansinfection in the lungs is controlled by organized collections of immune cells called granulomas. The formation and structure of Cryptococcus granulomas are poorly understood due to inconsistent human pathology results and disagreement between necrotic granuloma-forming rat models and non-necrotic granuloma-forming mouse models. To overcome this, we investigated granuloma formation during latentC. neoformansinfection in the C3HeB/FeJ mouse strain which forms necrotic lung granulomas in response to other pathogens. We found that latentC. neoformansgranuloma formation progresses through phases that we described as early, intermediate, and late with different immune response profiles and granulomatous characteristics. Ultimately, we show that C3HeB/FeJ mice latently infected withC. neoformansform non-necrotic granulomas and could provide a novel mouse model to investigate host immune response profiles.
Prevalence of antimicrobial resistance phenotypes and genes in stable fly- and manure-derived bacterial isolates from clinically relevant taxa in dairy settings
Authors: Sommer Andrew J. , Kettner Julia E. , Worley Travis K. , Petrick Jordan , Haynie Caroline , Coon Kerri L. 
Published: December 2024

AbstractAimsThis study aimed to characterize and compare the antimicrobial resistance (AMR) profiles of clinically relevant bacterial taxa isolated from biting stable flies (Stomoxysspp.) and bovine manure samples collected at a dairy research facility over the course of an entire fly breeding season. The presence of extended-spectrum beta-lactamase (ESBL) and other antimicrobial resistance genes (ARGs) was also examined.Methods and resultsA total of 606 fly- and 180 manure-derived strains were tested via disk diffusion for susceptibility to commonly administered antibiotics used in veterinary and human medicine. A small percentage of Enterobacterales exhibited resistance to the tested antimicrobials, including ceftiofur and other beta-lactam antibiotics. Extended spectrum beta-lactamase genes (TEM, CTX, OXA, CMY) were detected by PCR amplification in ceftiofur-resistantEscherichia coli,KlebsiellaandEnterobacterspp. isolates. We additionally identified pirlimycin-resistantStaphylococcusandMammaliicoccusspp. isolates encodinglnuA, a lincosamide resistance gene found primarily on small mobilizable plasmids.ConclusionsThese findings highlight the significance of stable flies in the carriage of antimicrobial-resistant bacterial strains and plasmid-associated ARGs on dairy farms.