PDCM Finder: an open global research platform for patient-derived cancer models.

PDCM Finder (www.cancermodels.org) is a cancer research platform that aggregates clinical, genomic and functional data from patient-derived xenografts, organoids and cell lines. It was launched in April 2022 as a successor of the PDX Finder portal, which focused solely on patient-derived xenograft models. Currently the portal has over 6200 models across 13 cancer types, including rare paediatric models (17%) and models from minority ethnic backgrounds (33%), making it the largest free to consumer and open access resource of this kind. The PDCM Finder standardises, harmonises and integrates the complex and diverse data associated with PDCMs for the cancer community and displays over 90 million data points across a variety of data types (clinical metadata, molecular and treatment-based). PDCM data is FAIR and underpins the generation and testing of new hypotheses in cancer mechanisms and personalised medicine development.

The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease.

The International Mouse Phenotyping Consortium (IMPC; https://www.mousephenotype.org/) web portal makes available curated, integrated and analysed knockout mouse phenotyping data generated by the IMPC project consisting of 85M data points and over 95,000 statistically significant phenotype hits mapped to human diseases. The IMPC portal delivers a substantial reference dataset that supports the enrichment of various domain-specific projects and databases, as well as the wider research and clinical community, where the IMPC genotype-phenotype knowledge contributes to the molecular diagnosis of patients affected by rare disorders. Data from 9,000 mouse lines and 750 000 images provides vital resources enabling the interpretation of the ignorome, and advancing our knowledge on mammalian gene function and the mechanisms underlying phenotypes associated with human diseases. The resource is widely integrated and the lines have been used in over 4,600 publications indicating the value of the data and the materials.

Heat-induced hormesis in longevity is linked to heat-stress sensitivity across laboratory populations from diverse altitude of origin in Drosophila buzzatii.

Heat-induced hormesis in longevity is the increase in life span resulting from the previous exposure to a mild heat stress early in life. Here we examined heat-induced hormesis of Drosophila buzzatii in five mass-mating populations, which were derived from five wild populations along an elevation gradient from 202 to 1855 m above sea level in North-Western Argentina. Five day old flies were exposed to 37.5 °C for 90 min to induce hormesis and its possible variation across altitudinal populations. This heat treatment strongly extended longevity in lowland-derived flies from the most heat-resistant population only. Both heat-induced effects on longevity and heat-knockdown time (heat-stress sensitivity) were negatively correlated to altitude of population of origin. Hormesis was positively correlated to heat-knockdown time across populations. These results indicate that variation in heat-induced hormesis can not be considered as independent of heat-stress sensitivity (or heat-knockdown time) in populations of insects.

Structural analysis of receptors and actin polarity in platelet protrusions.

During activation the platelet cytoskeleton is reorganized, inducing adhesion to the extracellular matrix and cell spreading. These processes are critical for wound healing and clot formation. Initially, this task relies on the formation of strong cellular-extracellular matrix interactions, exposed in subendothelial lesions. Despite the medical relevance of these processes, there is a lack of high-resolution structural information on the platelet cytoskeleton controlling cell spreading and adhesion. Here, we present in situ structural analysis of membrane receptors and the underlying cytoskeleton in platelet protrusions by applying cryoelectron tomography to intact platelets. We utilized three-dimensional averaging procedures to study receptors at the plasma membrane. Analysis of substrate interaction-free receptors yielded one main structural class resolved to 26 Å, resembling the αIIbß3 integrin folded conformation. Furthermore, structural analysis of the actin network in pseudopodia indicates a nonuniform polarity of filaments. This organization would allow generation of the contractile forces required for integrin-mediated cell adhesion.

Real-world experience of vedolizumab use in Colombian patients with inflammatory bowel disease-EXVEDOCOL.

BACKGROUND: Real-world studies about the effectiveness and safety of vedolizumab (VDZ) in the treatment of inflammatory bowel disease (IBD) in Latin America are scarce. Our study describes the effectiveness and safety of VDZ in Colombian patients with IBD. METHODS: EXVEDOCOL (EXperience of VEDOlizumab in COLombia) was a retrospective, multicenter, observational study. Adults with IBD receiving a first dose of VDZ between July 2016 and October 2018 were included. The co-primary outcomes clinical response, and remission, were determined at week 14 and last visit during the maintenance phase (LVMP). The secondary outcomes, deep remission and loss of response were recorded at LVMP. RESULTS: Thirty-one patients (25 ulcerative colitis (UC), 6 Crohn's disease (CD)) were included. At week 14, clinical response was achieved by 87.1% (27/31) of the patients treated with VDZ, while loss of response was reported in 6.7% (2/30). The remission rate at week 14 was 65.5% (19/29) and 75.9% (22/29) at LVMP. Prior anti-TNF exposure was reported in 61.3% (19 patients) of whom 84.2% (16/19) achieved clinical response at week 14 and 89.5% (17/19) at LVMP. For anti-TNF naïve patients, clinical response was recorded in 91.7% (11/12) at week 14 and 100% (12/12) at LVMP. CONCLUSIONS: High clinical remission rates and safety profile highlight VDZ as a valuable treatment option for IBD patients. Anti-TNF naïve patients may derive greater benefit from therapy. Studies with larger cohorts could confirm these findings.

Comprehensive ECG reference intervals in C57BL/6N substrains provide a generalizable guide for cardiac electrophysiology studies in mice.

Reference ranges provide a powerful tool for diagnostic decision-making in clinical medicine and are enormously valuable for understanding normality in pre-clinical scientific research that uses in vivo models. As yet, there are no published reference ranges for electrocardiography (ECG) in the laboratory mouse. The first mouse-specific reference ranges for the assessment of electrical conduction are reported herein generated from an ECG dataset of unprecedented scale. International Mouse Phenotyping Consortium data from over 26,000 conscious or anesthetized C57BL/6N wildtype control mice were stratified by sex and age to develop robust ECG reference ranges. Interesting findings include that heart rate and key elements from the ECG waveform (RR-, PR-, ST-, QT-interval, QT corrected, and QRS complex) demonstrate minimal sexual dimorphism. As expected, anesthesia induces a decrease in heart rate and was shown for both inhalation (isoflurane) and injectable (tribromoethanol) anesthesia. In the absence of pharmacological, environmental, or genetic challenges, we did not observe major age-related ECG changes in C57BL/6N-inbred mice as the differences in the reference ranges of 12-week-old compared to 62-week-old mice were negligible. The generalizability of the C57BL/6N substrain reference ranges was demonstrated by comparison with ECG data from a wide range of non-IMPC studies. The close overlap in data from a wide range of mouse strains suggests that the C57BL/6N-based reference ranges can be used as a robust and comprehensive indicator of normality. We report a unique ECG reference resource of fundamental importance for any experimental study of cardiac function in mice.

Melatonin production by rhizobacteria native strains: Towards sustainable plant growth promotion strategies.

In the current context of climate change and water deficit, the selection of native beneficial microorganisms, such as plant growth-promoting rhizobacteria (PGPR), has become a trend for sustainable agriculture due to their ability to improve plant-bacteria interaction with a minimal adverse effect on the soil microbiota compared to commercial PGPR. Until now, the production of phytohormones like melatonin (MT) by native PGPR and their effect on endogenous MT levels in plants have been poorly studied. MT is a ubiquitous phytohormone that protects plants against biotic and abiotic stress by improving the tolerance of stressed plants. In this work, the production of MT by two native PGPR, Enterobacter 64S1 and Pseudomonas 42P4, was evaluated and both PGPR were applied in Arabidopsis thaliana plants grown under drought conditions to assess the inoculation effects. Parameters such as plant growth, leaf cellular membrane damage, leaf protective compounds, and endogenous MT levels under drought and irrigation conditions were evaluated. The results demonstrated that the native strains Pseudomonas 42P4 and Enterobacter 64S1 produce MT and increase the content of endogenous MT in A. thaliana plants under drought. These native strains improved the tolerance of arabidopsis plants to drought by preventing oxidative and membrane damages and improving plant growth. To the best of our knowledge, this is the first report on MT production by native PGPR and their effects on endogenous MT levels in arabidopsis plants, setting the bases to elucidate the role of native PGPR on water deficit conditions.

Graph-based clinical recommender: Predicting specialists procedure orders using graph representation learning.

OBJECTIVE: To determine whether graph neural network based models of electronic health records can predict specialty consultation care needs for endocrinology and hematology more accurately than the standard of care checklists and other conventional medical recommendation algorithms in the literature. METHODS: Demand for medical expertise far outstrips supply, with tens of millions in the US alone with deficient access to specialty care. Rather than potentially months long delays to initiate diagnostic workup and medical treatment with a specialist, referring primary care supported by an automated recommender algorithm could anticipate and directly initiate patient evaluation that would otherwise be needed at subsequent a specialist appointment. We propose a novel graph representation learning approach with a heterogeneous graph neural network to model structured electronic health records and formulate recommendation/prediction of subsequent specialist orders as a link prediction problem. RESULTS: Models are trained and assessed in two specialty care sites: endocrinology and hematology. Our experimental results show that our model achieves an 8% improvement in ROC-AUC for endocrinology (ROC-AUC = 0.88) and 5% improvement for hematology (ROC-AUC = 0.84) personalized procedure recommendations over prior medical recommender systems. These recommender algorithm approaches provide medical procedure recommendations for endocrinology referrals more effectively than manual clinical checklists (recommender: precision = 0.60, recall = 0.27, F1-score = 0.37) vs. (checklist: precision = 0.16, recall = 0.28, F1-score = 0.20), and similarly for hematology referrals (recommender: precision = 0.44, recall = 0.38, F1-score = 0.41) vs. (checklist: precision = 0.27, recall = 0.71, F1-score = 0.39). CONCLUSION: Embedding graph neural network models into clinical care can improve digital specialty consultation systems and expand the access to medical experience of prior similar cases.

Soft windowing application to improve analysis of high-throughput phenotyping data.

MOTIVATION: High-throughput phenomic projects generate complex data from small treatment and large control groups that increase the power of the analyses but introduce variation over time. A method is needed to utlize a set of temporally local controls that maximizes analytic power while minimizing noise from unspecified environmental factors. RESULTS: Here we introduce 'soft windowing', a methodological approach that selects a window of time that includes the most appropriate controls for analysis. Using phenotype data from the International Mouse Phenotyping Consortium (IMPC), adaptive windows were applied such that control data collected proximally to mutants were assigned the maximal weight, while data collected earlier or later had less weight. We applied this method to IMPC data and compared the results with those obtained from a standard non-windowed approach. Validation was performed using a resampling approach in which we demonstrate a 10% reduction of false positives from 2.5 million analyses. We applied the method to our production analysis pipeline that establishes genotype-phenotype associations by comparing mutant versus control data. We report an increase of 30% in significant P-values, as well as linkage to 106 versus 99 disease models via phenotype overlap with the soft-windowed and non-windowed approaches, respectively, from a set of 2082 mutant mouse lines. Our method is generalizable and can benefit large-scale human phenomic projects such as the UK Biobank and the All of Us resources. AVAILABILITY AND IMPLEMENTATION: The method is freely available in the R package SmoothWin, available on CRAN http://CRAN.R-project.org/package=SmoothWin. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Micro to macro scale simulation coupling for stray light analysis.

Stray light in an optical system is unwanted parasitic light that may degrade performance. It can originate from different sources and may lead to different problems in the optical system such as fogging, ghost images for imagers, or inaccurate measurements for time of flight applications. One of the root causes is the reflectivity of the sensor itself. In this paper we present a new optical simulation methodology to analyze the stray light contribution due to the sensor reflectivity by coupling electromagnetic simulation (to calculate the pixels' bidirectional reflectance distribution function, also named BRDF) and ray-tracing simulation (for stray light analysis of the camera module). With this simulation flow we have been able to reproduce qualitatively red ghost images observed on different sensors in our laboratory.

Genetic variation in the heat-stress survival of embryos is largely decoupled from adult thermotolerance in an intercontinental set of recombinant lines of Drosophila melanogaster.

In insects, thermal adaptation works on the genetic variation for thermotolerance of not only larvae and adults but also of the immobile stages of the life cycle including eggs. In contrast to adults and larvae, the genetic basis for thermal adaptation in embryos (eggs) remains to be tested in the model insect Drosophila melanogaster. Quantitative-trait loci (QTL) for heat-stress resistance in embryos could largely differ from previously identified QTL for larvae and adults. Here we used an intercontinental set of recombinant inbred lines (RIL), which were previously used to identify thermotolerance-QTLs in adults and larvae because of their high variation segregating for adult thermotolerance. Eggs appeared to be more heat resistant than larvae and adults from previous studies on these RIL, though different heat-shock assays were used in previous studies. We found that variation in thermotolerance in embryos can be, at least partially, genetically decoupled from thermotolerance in the adult insect. Some RIL that are heat resistant in the adult and larvae can be heat susceptible in embryos. Only one small-effect QTL out of five autosomal QTL co-localized between embryo and other ontogenetic stages. These results suggest that selection for thermal adaptation in adult flies and larvae is predicted to have only a small impact on embryo thermotolerance. In addition, heat-stress tolerance of insects can be measured across ontogenetic stages including embryos in order to better predict thermal adaptive limits of populations and species.

Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion.

Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package.

Negative genetic correlation between longevity and its hormetic extension by dietary restriction in Drosophila melanogaster.

Longevity is a highly malleable trait which is influenced by many genetic and environmental factors including nutrition. Mild stress of dietary restriction (DR) is often beneficial by extending longevity in many organisms. Here, DR-induced effects on longevity were tested for genetic variation in a set of recombinant inbred lines (RIL) in D. melanogaster. Genetic variability was significant in the longevity response following a DR-treatment across RIL, with detrimental effects in several RIL but beneficial effects in other RIL. One quantitative trait locus (QTL) was consistently significant in the middle of chromosome 2 for DR-induced changes in longevity, including hormesis (an increase in longevity by DR). Another QTL co-localized with a previously found QTL for starvation resistance in females. Several other QTL were also significant on most chromosomal arms. Longevity in controls was negatively correlated to DR effects across RIL for longevity in females, the sex showing higher DR-induced hormesis. This negative genetic correlation highlights the importance to further investigate the effects of genetic variation in the strength of DR-induced hormesis in longevity and its sex-specificity.

Determination of ellagic acid by capillary electrophoresis in Argentinian wines.

Rising interest in ellagic acid (EA) present in functional foods is supported by its antimutagenic, anticarcinogenic, antiviral, antibacterial and antioxidative effects. The present approach presents for the first time the determination of ellagic acid and other phenolics in wines by miniaturized solid phase extraction prior to capillary zone electrophoresis (CZE) with UV. The extraction was performed using a home-made miniaturized pipette tip column. The procedure allowed a significant reduction in conditioning/sample/washing/elution volumes. The effects of important factors affecting the extraction efficiency as well as electrophoretic performance were investigated to acquire optimum conditions. The analytes were separated within 10 min with a BGE containing 30 mmol/L sodium tetraborate 10% v/v MeOH pH 9.10. The optimized method was applied to the determination of ellagic acid in commercial and pilot-scale wines. Indeed, the content of EA was correlated with viticultural parameters such as grape varietal, production area, and aging conditions (oak wood guard and glass bottle ward). In order to validate the results, a comparison between the CZE and HPLC data was made.

Pencil graphite electrodes for improved electrochemical detection of oleuropein by the combination of Natural Deep Eutectic Solvents and graphene oxide.

A novel methodology is presented for the enhanced electrochemical detection of oleuropein in complex plant matrices by Graphene Oxide Pencil Grahite Electrode (GOPGE) in combination with a buffer modified with a Natural Deep Eutectic Solvent, containing 10% (v/v) of Lactic acid, Glucose and H2 O (LGH). The electrochemical behavior of oleuropein in the modified-working buffer was examined using differential pulse voltammetry. The combination of both modifications, NADES modified buffer and nanomaterial modified electrode, LGH-GOPGE, resulted on a signal enhancement of 5.3 times higher than the bare electrode with unmodified buffer. A calibration curve of oleuropein was performed between 0.10 to 37 µM and a good linearity was obtained with a correlation coefficient of 0.989. Detection and quantification limits of the method were obtained as 30 and 102 nM, respectively. In addition, precision studies indicated that the voltammetric method was sufficiently repeatable, %RSD 0.01 and 3.16 (n = 5) for potential and intensity, respectively. Finally, the proposed electrochemical sensor was successfully applied to the determination of oleuropein in an olive leaf extract prepared by ultrasound-assisted extraction. The results obtained with the proposed electrochemical sensor were compared with Capillary Zone Electrophoresis analysis with satisfactory results.

Histopathology of murine toxoplasmosis under treatment with dialyzable leukocyte extract.

BACKGROUND: Dialyzable leukocyte extracts (DLEs) contain molecules smaller than 10 kDa with biological activity in receptor organisms. Primarily, they participate in the regulation of the Th1 immune response, which is essential for the control of several intracellular infections, such as toxoplasmosis. This disease is associated with congenital infection, encephalitis or systemic infections in immunocompromised individuals. The clinical course of this infection fundamentally depends on a well-regulated immune response and timely treatment with the appropriate drugs. OBJECTIVE: The aim of this study was to evaluate the effect of treatment with a leukocyte extract, derived from crocodile lymphoid tissue, on the histopathology and brain parasite load in NIH mice that had been infected with cysts of Toxoplasma gondii (ME-49 strain). METHODS: The treatment was applied during the acute and chronic stages of the infection. Histopathological changes were evaluated in the ileum, liver and spleen at one, four and eight weeks after infection and in the brain at week 8. The parasite load was evaluated by counting the cysts of T. gondii found in the brain. FINDINGS: Compared to the control mouse group, the mice infected with T. gondii and under treatment with DLE showed less tissue damage, mainly at the intestinal, splenic and hepatic levels. In addition, a greater percentage of survival was observed, and there was a considerable reduction in the parasite load in the brain. CONCLUSIONS: The results suggest that DLE derived from crocodile is a potential adjunctive therapy in the conventional treatment of toxoplasmosis.

Quantitative Trait Loci and Antagonistic Associations for Two Developmentally Related Traits in the Drosophila Head.

In insects, some developmentally related traits are negatively correlated. Here, we mapped Quantitative Trait Loci (QTL) for traits of eye size and head capsule, in an intercontinental set of recombinant inbred lines (RILs) of Drosophila melanogaster Composite interval mapping identified QTL on all major chromosomes. Two negatively correlated traits (size of eyes and between-eyes distance) were influenced by one QTL that appeared to be antagonistic between the traits (QTL cytological range is 25F5-30A6), consistent with a negative genetic correlation between these traits of the head capsule. Comparisons of QTL across traits indicated a nonrandom distribution over the genome, with a considerable overlap between some QTL across traits. Developmentally-related traits were influenced by QTL in a pattern that is consistent both with 1) the sign of the genetic correlation between the traits and 2) a constraint in the micro-evolutionary differentiation in the traits.

Elevated extension of longevity by cyclically heat stressing a set of recombinant inbred lines of Drosophila melanogaster throughout their adult life.

An extremely high (about 100 %) increase in longevity is reported for a subset of recombinant inbred lines (RILs) of Drosophila melanogaster subjected to a cyclic heat stress throughout the adult life. Previous work showed that both longevity and heat sensitivity highly differed among RILs. The novel heat stress treatment used in this study consisted of 5 min at 38 °C applicated approximately every 125 min throughout the adult life starting at the age of 2 days. In spite of the exceptionally high increase in longevity in a set of RILs, the same heat stress treatment reduced rather than increased longevity in other RILs, suggesting that heat-induced hormesis is dependent on the genotype and/or the genetic background. Further, one quantitative trait locus (QTL) was identified for heat-induced hormesis on chromosome 2 (bands 28A1-34D2) in one RIL panel (RIL-D48) but it was not significant in its reciprocal panel (RIL-SH2). The level of heat-induced hormesis showed a sexual dimorphism, with a higher number of lines exhibiting higher hormesis effects in males than in females. The new heat stress treatment in this study suggests that longevity can be further extended than previously suggested by applying a cyclic and mild stress throughout the life, depending on the genotype.

Microchip electrophoresis for wine analysis.

The present critical review provides a summary of representative articles describing the analysis of wine by microchip electrophoresis. Special emphasis has been given to those compounds able to provide background information to achieve the differentiation of wines according to botanical origin, provenance, vintage and quality or assure wine authentication. This review focuses on capillary electrophoresis (CE) microchips dedicated to the analysis of wine covering all the contributions concerning this area. The most relevant compounds in wine analysis such as phenols, organic acids, inorganic species, aldehydes, sugars, alcohols, and neuroactive amines were considered. Moreover, a special section is dedicated to the potential of CE microchip for wine classification. Indeed, potential directions for the future are discussed.