Expanding the Scope of Microvascular Inflammation: Unveiling Its Presence Beyond Antibody-Mediated Rejection Into T-Cell Mediated Contexts.

Microvascular inflammation (MVI) in kidney transplant biopsies is mainly associated with antibody-mediated rejection (AMR), sparking debate within the Banff Classification of Renal Allograft Pathology regarding its exclusivity. This study reviewed the literature on MVI in T cell-mediated rejection (TCMR) and analyzed MVI in our transplant population. We searched English publications in MEDLINE, Embase, Web of Science, Cochrane, and Google Scholar until June 2024, focusing on glomerulitis (g), peritubular capillaritis (ptc), or MVI in kidney transplant biopsies classified as TCMR.

BenchAMRking: a Galaxy-based platform for illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows.

Background: The Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) networks 'Seq4AMR' and 'B2B2B AMR Dx' were established to promote collaboration between microbial whole genome sequencing (WGS) and antimicrobial resistance (AMR) stakeholders. A key topic discussed was the frequent variability in results obtained between different microbial WGS-related AMR gene prediction workflows. Further, comparative benchmarking studies are difficult to perform due to differences in AMR gene prediction accuracy and a lack of agreement in the naming of AMR genes (semantic conformity) for the results obtained.

microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data.

Microbial research generates vast and complex data from diverse omics technologies, necessitating innovative analytical solutions. microGalaxy (Galaxy for Microbiology) addresses these needs with a user-friendly platform that integrates >220 tool suites and >65 curated workflows for microbial analyses, including taxonomic profiling, assembly, annotation, and functional analysis. Hosted on the main EU Galaxy server (microgalaxy.

Routine Capsular Closure Outperforms Incomplete Capsular Closure After Hip Arthroscopy: A Meta-analysis and Expected-Value Decision Analysis.

Purpose: To determine the optimal treatment decision for capsular management after primary hip arthroscopy for femoroacetabular impingement syndrome.

Methods: An expected-value decision analysis was performed (1) organizing the decision problem, (2) determining outcome probabilities, (3) determining outcome utilities, (4) performing fold-back analyses, and (5) performing sensitivity analyses. A decision tree was constructed (complete capsule closure vs incomplete closure) and a meta-analysis was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses framework, a systematic review was conducted to determine outcome probabilities.

A systematic benchmark of copy number variation detection tools for high density SNP genotyping arrays.

Copy Number Variations (CNVs) are crucial in various diseases, especially cancer, but detecting them accurately from SNP genotyping arrays remains challenging. Therefore, this study benchmarked five CNV detection tools-PennCNV, QuantiSNP, iPattern, EnsembleCNV, and R-GADA-using SNP array and WGS data from 2002 individuals of the DRAGEN re-analysis of the 1000 Genomes project. Results showed significant variability in tool performance.

Using Cognitive Task Analysis to Develop a Protocol for Teaching Ultrasound Pregnancy Diagnosis in the Bitch to Undergraduate Veterinary Students.

Pregnancy diagnosis in the bitch is routinely performed using ultrasound and is therefore an important skill for veterinarians to have been exposed to during undergraduate training. Proficiency of this skill is difficult to achieve, due to limited exposure to suitable live patients, and animal welfare considerations limiting repeated performance on the same bitch. Models have been beneficial in allowing undergraduates to perform a range of ultrasound techniques without the use of live animals.

Weathering and cementation of historic kimberlite residues from South Africa: Implications for residue stabilization and CO sequestration.

Enhanced weathering and carbon dioxide (CO) mineralization of ultramafic mine wastes, including kimberlite residues from diamond mining, provides secure storage of this greenhouse gas and may physically stabilize mine impoundments. Yet, the outcomes of these processes over extensive periods (i.e.

The tumor immune microenvironment in resected treatment-naive pancreatic cancer patients with long-term survival.

Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers worldwide. Presently, only a fraction of patients undergo successful surgical resection, the most effective treatment. Enhancing treatment strategies necessitates a deep comprehension of the factors underlying extended survival after surgical resection in patients.

Comparing Sequence-Based and Literature-Based Pathogenicity Scoring Methods for Human Variants.

Assessing the pathogenicity of genetic variants is a critical aspect of genomic medicine and precision healthcare. Over the last decades, the identification of genetic variants and their characterization has become simpler (advent of high-throughput sequencing technologies, analysis, and visualization support tools, etc.).

Prediction of molecular subclasses of uveal melanoma by deep learning using routine haematoxylin-eosin-stained tissue slides.

Aims: Uveal melanoma has a high propensity to metastasize. Prognosis is associated with specific driver mutations and copy number variations, and these can only be obtained after genetic testing. In this study we evaluated the efficacy of patient outcome prediction using deep learning on haematoxylin and eosin (HE)-stained primary uveal melanoma slides in comparison to molecular testing.

Nutrients and Nocioception: Diet in the management of pain.

Nutrition can play a pivotal role in the management of pain associated with chronic rheumatic diseases. There is a growing body of research linking certain nutrients from the diet to inflammation. Certain nutrients have been shown to improve pain associated with inflammation.

Cherry on Top or Real Need? A Review of Explainable Machine Learning in Kidney Transplantation.

Research on solid organ transplantation has taken advantage of the substantial acquisition of medical data and the use of artificial intelligence (AI) and machine learning (ML) to answer diagnostic, prognostic, and therapeutic questions for many years. Nevertheless, despite the question of whether AI models add value to traditional modeling approaches, such as regression models, their "black box" nature is one of the factors that have hindered the translation from research to clinical practice. Several techniques that make such models understandable to humans were developed with the promise of increasing transparency in the support of medical decision-making.

The heterogeneous sensitivity of pediatric brain tumors to different oncolytic viruses is predicted by unique gene expression profiles.

Despite decades of research, the prognosis of high-grade pediatric brain tumors (PBTs) remains dismal; however, recent cases of favorable clinical responses were documented in clinical trials using oncolytic viruses (OVs). In the current study, we employed four different species of OVs: adenovirus Delta24-RGD, herpes simplex virus rQNestin34.5v1, reovirus R124, and the non-virulent Newcastle disease virus rNDV-F0-GFP against three entities of PBTs (high-grade gliomas, atypical teratoid/rhabdoid tumors, and ependymomas) to determine their efficacy.

FAIR data retrieval for sensitive clinical research data in Galaxy.

Background: In clinical research, data have to be accessible and reproducible, but the generated data are becoming larger and analysis complex. Here we propose a platform for Findable, Accessible, Interoperable, and Reusable (FAIR) data access and creating reproducible findings. Standardized access to a major genomic repository, the European Genome-Phenome Archive (EGA), has been achieved with API services like PyEGA3.

Multiomic profiling of transplant glomerulopathy reveals a novel T-cell dominant subclass.

Kidney transplant (KTx) biopsies showing transplant glomerulopathy (TG) (glomerular basement membrane double contours (cg) > 0) and microvascular inflammation (MVI) in the absence of C4d staining and donor-specific antibodies (DSAs) do not fulfill the criteria for chronic active antibody-mediated rejection (CA-AMR) diagnosis and do not fit into any other Banff category. To investigate this, we initiated a multicenter intercontinental study encompassing 36 cases, comparing the immunomic and transcriptomic profiles of 14 KTx biopsies classified as cg+MVI DSA/C4d with 22 classified as CA-AMR DSA/C4d through novel transcriptomic analysis using the NanoString Banff-Human Organ Transplant (B-HOT) panel and subsequent orthogonal subset analysis using two innovative 5-marker multiplex immunofluorescent panels. Nineteen genes were differentially expressed between the two study groups.

A new species of terrestrially-nesting fanged frog (Anura: Dicroglossidae) from Sulawesi Island, Indonesia.

Herein, we describe a new species of terrestrially-nesting fanged frog from Sulawesi Island, Indonesia. Though male nest attendance and terrestrial egg deposition is known in one other Sulawesi fanged frog (Limnonectes arathooni), the new species exhibits a derived reproductive mode unique to the Sulawesi assemblage; male frogs guard one or more clutches of eggs festooned to leaves or mossy boulders one to two meters above small slow-moving streams, trickles, or seeps. This island endemic has thus far been collected at three sites on Sulawesi: one in the Central Core of the island, and two on the Southwest Peninsula-south of the Tempe Depression (a major biogeographical boundary).

Artificial intelligence-based recurrence prediction outperforms classical histopathological methods in pulmonary adenocarcinoma biopsies.

Introduction: Between 10 and 50% of early-stage lung adenocarcinoma patients experience local or distant recurrence. Histological parameters such as a solid or micropapillary growth pattern are well-described risk factors for recurrence. However, not every patient presenting with such a pattern will develop recurrence.

Artificial Intelligence in Digital Pathology for Bladder Cancer: Hype or Hope? A Systematic Review.

Bladder cancer (BC) diagnosis and prediction of prognosis are hindered by subjective pathological evaluation, which may cause misdiagnosis and under-/over-treatment. Computational pathology (CPATH) can identify clinical outcome predictors, offering an objective approach to improve prognosis. However, a systematic review of CPATH in BC literature is lacking.

Factors impacting resident outcomes from COVID-19 outbreaks in Residential Aged Care Facilities in Sydney Local Health District: testing an infection prevention and control scoring system.

Background: COVID-19 outbreaks have disproportionately affected Residential Aged Care Facilities (RACFs) around the world, with devastating impacts for residents and their families. Many factors such as community prevalence, facility layout, and infection control practices have been linked to resident outcomes. At present, there are no scoring systems designed to quantify these factors and assess their level of association with resident attack rates and mortality rates.

Elevational surveys of Sulawesi herpetofauna 1: Gunung Galang, Gunung Dako Nature Reserve.

The Indonesian island of Sulawesi has a unique geology and geography, which have produced an astoundingly diverse and endemic flora and fauna and a fascinating biogeographic history. Much biodiversity research has focused on the regional endemism in the island's Central Core and on its four peninsulas, but the biodiversity of the island's many upland regions is still poorly understood for most taxa, including amphibians and reptiles. Here, we report the first of several planned full-mountain checklists from a series of herpetological surveys of Sulawesi's mountains conducted by our team.

Ex vivo drug sensitivity screening predicts response to temozolomide in glioblastoma patients and identifies candidate biomarkers.

Background: Patient-derived glioma stem-like cells (GSCs) have become the gold-standard in neuro-oncological research; however, it remains to be established whether loss of in situ microenvironment affects the clinically-predictive value of this model. We implemented a GSC monolayer system to investigate in situ-in vitro molecular correspondence and the relationship between in vitro and patient response to temozolomide (TMZ).

Methods: DNA/RNA-sequencing was performed on 56 glioblastoma tissues and 19 derived GSC cultures.

Bewildering biogeography: Waves of dispersal and diversification across southern Wallacea by bent-toed geckos (genus: Cyrtodactylus).

Bent-toed Geckos, genus Cyrtodactylus, are one of the most diverse terrestrial vertebrate groups, and their range extends from South Asia into Australo-Papua and adjacent Pacific islands. Given the generally high faunal endemism on Wallacean islands, it is rather paradoxical that the diversity in these geckos appears to be so low (21 species in Wallacea, 15 in the Philippines) compared with continental shelf assemblages (>300 species on Sunda + Sahul Shelves + adjacent islands). To determine whether this shortfall was real or an artifact of historical undersampling, we analyzed mitochondrial DNA sequences of hundreds of southern Wallacean samples (Lesser Sundas + southern Maluku).

Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation.

The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands.

Editorial Commentary: Microfracture Remains a Foundational Tool for Cartilage Restoration During Hip-Preservation Procedures: Defying the Odds.

A comprehensive approach to arthroscopic hip preservation in patients whose pathology includes cartilage defects may include microfracture; microfracture has been shown to have long-lasting positive effects in most patients treated for femoroacetabular impingement plus full-thickness chondral pathology. Although modern cartilage treatment alternatives such as autologous chondrocyte implantation, autologous matrix-induced chondrogenesis scaffolds, allograft or autograft particulate cartilage graft, and others have been described for the treatment of high-degree cartilage acetabular lesions, microfracture remains a foundational tool in cartilage restoration procedures. That said, when determining outcome, comorbidity must be considered, and, moreover, it is difficult to determine whether outcomes are only attributable to the microfracture versus concomitant procedures or changes in postoperative activity of operated patients.