The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.

Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI's ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.

The Human Phenotype Ontology in 2024: phenotypes around the world.

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.

Understanding potential opportunities and risks associated with feeding supplemental rumen available fats to mitigate enteric methane emissions in lactating dairy cows.

Supplemental dietary rumen available fats show promise as enteric methane (eCH4) mitigators for lactating dairy cows. However, concerns include variability in eCH4 response and possible negative effects on dairy cow performance. Successful implementation of this mitigation option requires better prediction of responses specifically to rumen available FA as well as understanding the modulating effects of other dietary and animal characteristics. Using meta-analytic and meta-regression techniques, 35 published studies with diet definition were used to assess changes in eCH4 emissions and lactation performance associated with supplemental fat, specific supplemental rumen available FA types, and other dietary characteristics. Enteric CH4 (g/d) was reduced by 3.77% per percentage unit of supplemental rumen available EE (RAEE). Supplemental rumen available PUFA (C18:2 and C18:3) and UFA (C18:1, C18:2, C18:3) mitigated eCH4 (g/d) emissions in dairy cows by 6.88 and 4.65% per percentage unit increase, respectively. The anti-methanogenic effects of PUFA, MUFA and MCFA increased with correspondingly greater basal dietary levels of each FA type. Higher rumen-degradable starch (RDS; > 18% DM) in the basal diet promoted greater reductions in eCH4 yield (eCH4/DMI, g/kg) with supplemental rumen available PUFA and UFA. Both milk fat percentage and yield (kg/d) were reduced with rumen available fat supplementation with a reduction of 7.8% and 6.0%, respectively, relative to control diets. Our results highlight the importance of determining basal levels of the rumen available FA before providing supplemental rumen available FA as an option for enteric eCH4 mitigation. Dairy nutritionists can use estimates generated from this analysis to predict changes in eCH4 emissions and dairy cow performance associated with dietary supplementation of rumen available EE and specific rumen available FA types for the purpose of eCH4 mitigation.

The Ontology of Biological Attributes (OBA)-computational traits for the life sciences.

Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for the annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings or any population-focussed measurable trait data. The integration of trait and biological attribute information with an ever increasing body of chemical, environmental and biological data greatly facilitates computational analyses and it is also highly relevant to biomedical and clinical applications. The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. OBA has a modular design which provides several benefits for users and data integrators, including an automated and meaningful classification of trait terms computed on the basis of logical inferences drawn from domain-specific ontologies for cells, anatomical and other relevant entities. The logical axioms in OBA also provide a previously missing bridge that can computationally link Mendelian phenotypes with GWAS and quantitative traits. The term components in OBA provide semantic links and enable knowledge and data integration across specialised research community boundaries, thereby breaking silos.

Effectiveness of Intrarectal Povidone-iodine Cleansing Plus Formalin Disinfection of the Needle Tip in Decreasing Infectious Complications After Transrectal Prostate Biopsy: A Randomized Controlled Trial.

PURPOSE: Prostate biopsy is mostly performed through the transrectal route worldwide and infectious complications may occur in up to 7% of cases. Therefore, alternative strategies to decrease infectious complications are needed. Our aim was to evaluate the effectiveness of intrarectal povidone-iodine cleansing plus formalin disinfection of the needle tip in decreasing infectious complications after transrectal ultrasound guided prostate biopsy. MATERIALS AND METHODS: We conducted a prospective, single-center, phase III trial in patients undergoing transrectal ultrasound guided prostate biopsy randomized 1:1 to rectal mucosa cleansing with gauze soaked in 10% povidone-iodine solution wrapped around the gloved index finger and needle tip disinfection by immersion in a 10% formalin solution before each puncture vs control group. The primary end point was the rate of infectious complications defined as 1 or more of the following events: fever, urinary tract infection, or sepsis. RESULTS: Overall, 633 patients were randomized to the intervention group and 623 to the control group. The infectious complication rate was 3.9% in the intervention group and 6.4% in the control group (RR 0.61; 95% CI 0.36-0.99; P = .049). The rates of sepsis, urinary tract infection, and fever were 0.3% vs 0.5% (P = .646), 2.3% vs 4.1% (P = .071), and 1.3% vs 1.9% (P = .443), respectively. The positive urine culture rate was 5.2% in the intervention group and 9% in the control group (RR 0.57; P = .015). There was no statistically significant difference between the groups regarding the occurrence of noninfectious adverse events. CONCLUSIONS: Intrarectal povidone-iodine cleansing plus formalin disinfection of the biopsy needle tip was associated with a reduction in infectious complications after transrectal prostate biopsy.

Cardamonin Presents in Vivo Activity against Schistosoma mansoni and Inhibits Potato Apyrase.

Schistosomiasis, a neglected tropical disease caused by Schistosoma species, harms over 250 million people in several countries. The treatment is achieved with only one drug, praziquantel. Cardamonin, a natural chalcone with in vitro schistosomicidal activity, has not been in vivo evaluated against Schistosoma. In this work, we evaluated the in vivo schistosomicidal activities of cardamonin against Schistosoma mansoni worms and conducted enzymatic apyrase inhibition assay, as well as molecular docking analysis of cardamonin against potato apyrase, S. mansoni NTPDase 1 and S. mansoni NTPDase 2. In a mouse model of schistosomiasis, the oral treatment with cardamonin (400 mg/kg) showed efficacy against S. mansoni, decreasing the total worm load in 46.8 % and reducing in 54.5 % the number of eggs in mice. Cardamonin achieved a significant inhibition of the apyrase activity and the three-dimensional structure of the potato apyrase, obtained by homology modeling, showed that cardamonin may interact mainly through hydrogen bonds. Molecular docking studies corroborate with the action of cardamonin in binding and inhibiting both potato apyrase and S. mansoni NTPDases.

Synthetic Aurones: New Features for Schistosoma mansoni Therapy.

In this work, two synthetic aurones revealed moderate schistosomicidal potential in in vitro and in vivo assays. Aurones (1) and (2) promoted changes in tegument integrity and motor activity, leading to death of adult Schistosoma mansoni worms in in vitro assays. When administered orally (two doses of 50 mg/kg) in experimentally infected animals, synthetic aurones (1) and (2) promoted reductions of 56.20 % and 57.61 % of the parasite load and stimulated the displacement towards the liver of the remaining adult worms. The oogram analysis revealed that the treatment with both aurones interferes with the egg development kinetics in the intestinal tissue. Seeking an action target for compounds (1) and (2), the connection with NTPDases enzymes, recognized as important therapeutic targets for S. mansoni, was evaluated. Molecular docking studies have shown promising results. The dataset reveals the anthelmintic character of these compounds, which can be used in the development of new therapies for schistosomiasis.

Rumen bacterial diversity in relation to nitrogen retention in beef cattle.

This study aimed to characterize the rumen bacterial diversity of beef steers differing in the efficiency of nitrogen retention (ENR). Eight castrated steers and fitted with ruminal silicone - and duodenal T-type cannulas were used in a cross-over design with three consecutive periods and three diets. During each experimental period, nitrogen balance was measured, and based on the efficiency of N utilization data, steers were split into three ENR groups: high (HNR, 56.6% ± 3.3%, n = 10), medium (MNR, 45.8% ± 2.2%, n = 6), and low (LNR, 37.7% ± 1.9%, n = 8) using the NbClust package version 2.0.4 in R. Prevotellaceae, Lactobacillaceae, Leuconostocaceae, Clostridiales_Incertae_Sedis_XIII, Lachnospiraceae, and Peptostreptococcaceae were more abundant in LNR (P < 0.05) compared to HNR or MNR. Negative correlations were found between N retention and Mogibacterium, Anaerofustis, Butyrivibrio, Coprococcus, Hespellia, Lactonifactor and Lachnospiraceae (r ≤ -0.61; P ≤ 0.05). Prevotella, Hespellia, Lactonifactor, Lachnospiraceae_other, and Anaerobiospirillum were positively correlated between urinary N excretion (r > 0.55; P < 0.01), and negative correlations were found with Elusimicrobia, Victivallis and Treponema (r < -0.41; P < 0.05). The adjustment of the rumen bacterial community differed significantly between the N use retention groups. The high N retention in beef cattle was associated with less abundant bacteria in the rumen; however, N fixation capacity and uncharacterized rumen microorganisms need to be elucidated in future studies. In contrast, lower N utilization was associated with high abundance of bacteria that promote greater urinary N excretion through ruminal protein degradation.

Impact of mining activities on areas of environmental protection in the southwest of the Amazon: A GIS- and remote sensing-based assessment.

The southwest Brazilian Amazon state of Rondônia has a relatively recent non-indigenous occupation, which subsequently develops a variety of human pressures and conflicts of interest presently identified in the region. Given such framework, it is worthwhile to note that there are 57 Conservation Units that must guarantee the biodiversity protection of Amazonia biome. However, due to the need for electricity and the international high demand for minerals, the highlighted scenario has dramatically changed in recent years. Official data from mining processes in the studied area demonstrated the existence of high interest for minerals, especially cassiterite and gold. Mining is indeed an essential activity for the nation mainly due to the generation of jobs and income. On the other hand, it produces several environmental and social impacts that vary accordingly to the peculiarities of the mining and with respect to the type of ore. Therefore, this research work investigated the concentration of mining projects in the state of Rondônia and complementarily evaluated the impact of such activities on areas of environmental protection. Landsat 8 OLI imageries were employed to map the diversity of land covers across the study area and also to evaluate the corresponding impact of mining activities. More than 500 processes have been identified within the Conservation Units. A significant part of the mining areas, covering about 26 km2, was observed inside one of the three types of evaluated areas (Integral Protection Sustainable Use Conservation Units and Damping Zone), clearly showing the development of the illegal activity, as defined in terms of the National System of Conservation Units. If deforestation is considered in this analysis, the area increases to about 6110 km2, representing more than 5.2% of the Conservation Units. In addition, we proposed the creation of the Mining Pressure Index (MPI), which allows classifying a Conservation Unit by the degree of pressure from mining activities. The proposed index revealed to be very efficient since it predicted high values over Conservation Units where it was expected a greater vulnerability. The index is a promising tool for public policy formulation and management of protected areas, as well as for enforcement action. The results provide a new horizon in terms of the perspective of importance and applicability of geotechnologies in the evaluation of environmental impacts, not restricted to mining activity.

Effects of partial replacement of maize in the diet with crude glycerin and/or soyabean oil on ruminal fermentation and microbial population in Nellore steers.

The objective of this study was to determine whether a combination of crude glycerin (CG) and soyabean oil (SO) could be used to partially replace maize in the diet of Nellore steers while maintaining optimum feed utilisation. Eight castrated Nellore steers fitted with ruminal and duodenal cannulas were used in a double 4×4 Latin square design balanced for residual effects, in a factorial arrangement (A×B), when factor A corresponded to the provision of SO, and factor B to the provision of CG. Steers feed SO and CG showed similar DM intake, DM, organic matter and neutral-detergent fibre digestibility to that of steers fed diets without oil and without glycerine (P>0·05). Both diets with CG additions reduced the acetate:propionate ratio and increased the proportion of iso-butyrate, butyrate, iso-valerate and valerate (P<0·05). Steers fed diets containing SO had less total N excretion (P<0·001) and showed greater retained N expressed as % N intake (P=0·022). SO and CG diet generated a greater ruminal abundance of Prevotella, Succinivibrio, Ruminococcus, Syntrophococcus and Succiniclasticum. Archaea abundance (P=0·002) and total ciliate protozoa were less in steers fed diets containing SO (P=0·011). CG associated with lipids could be an energy source, which is a useful strategy for the partial replacement of maize in cattle diets, could result in reduced total N excretion and ruminal methanogens without affecting intake and digestibility.

Computed Tomography Findings of Bronchiectasis in Different Respiratory Phases Correlate with Pulmonary Function Test Data in Adults.

OBJECTIVE: To investigate bronchiectasis variations in different computed tomography (CT) respiratory phases, and their correlation with pulmonary function test (PFT) data, in adults. METHODS: Retrospective data analysis from 63 patients with bronchiectasis according to CT criteria selected from the institution database and for whom PFT data were also available. Bronchiectasis diameter was measured on inspiratory and expiratory phases. Its area and matched airway-vessel ratios in both phases were also calculated. Finally, PFT results were compared with radiological measurements. RESULTS: Bronchiectatic airways were larger on inspiration than on expiration (mean cross-sectional area, 69.44 vs. 40.84 mm2; p < 0.05) as were airway-vessel ratios (2.1 vs. 1.4; p < 0.05). Cystic bronchiectasis cases showed the least variation in cross-sectional area (48%). Mean predicted values of forced expiratory volume in 1 s (FEV1) and forced vital capacity (FVC) were 81.5 and 77.2%, respectively, in the group in which bronchiectasis could not be identified on expiratory images, and 58.3 and 56.0%, respectively, in the other group (p < 0.05). Variation in bronchiectasis area was associated with poorer lung function (r = 0.32). CONCLUSION: Bronchiectasis detection, diameter, and area varied significantly according to CT respiratory phase, with non-reducible bronchiectasis showing greater lung function impairment.

Integration of C1 and C2 Metabolism in Trees.

C1 metabolism in plants is known to be involved in photorespiration, nitrogen and amino acid metabolism, as well as methylation and biosynthesis of metabolites and biopolymers. Although the flux of carbon through the C1 pathway is thought to be large, its intermediates are difficult to measure and relatively little is known about this potentially ubiquitous pathway. In this study, we evaluated the C1 pathway and its integration with the central metabolism using aqueous solutions of 13C-labeled C1 and C2 intermediates delivered to branches of the tropical species Inga edulis via the transpiration stream. Delivery of [13C]methanol and [13C]formaldehyde rapidly stimulated leaf emissions of [13C]methanol, [13C]formaldehyde, [13C]formic acid, and 13CO2, confirming the existence of the C1 pathway and rapid interconversion between methanol and formaldehyde. However, while [13C]formate solutions stimulated emissions of 13CO2, emissions of [13C]methanol or [13C]formaldehyde were not detected, suggesting that once oxidation to formate occurs it is rapidly oxidized to CO2 within chloroplasts. 13C-labeling of isoprene, a known photosynthetic product, was linearly related to 13CO2 across C1 and C2 ([13C2]acetate and [2-13C]glycine) substrates, consistent with reassimilation of C1, respiratory, and photorespiratory CO2. Moreover, [13C]methanol and [13C]formaldehyde induced a quantitative labeling of both carbon atoms of acetic acid emissions, possibly through the rapid turnover of the chloroplastic acetyl-CoA pool via glycolate oxidation. The results support a role of the C1 pathway to provide an alternative carbon source for glycine methylation in photorespiration, enhance CO2 concentrations within chloroplasts, and produce key C2 intermediates (e.g., acetyl-CoA) central to anabolic and catabolic metabolism.

Reduction of phosphorus concentration in mineral supplement on fertility rate, maternal ability and costs of beef cows reared in pastures of Urochloa decumbens.

Manufacturing and marketing of mineral mixtures with less than 40 g kg(-1) phosphorus (P) is prohibited under Brazilian regulations, although scientific evidence rejects this recommendation. Considering the hypothesis that P levels in commercial mineral supplements can be reduced without affecting animal performance and health, the objective of this experiment was to evaluate the effects of reducing the concentration of P in the mineral supplement (from 40 to 18 g kg(-1)) of a herd of beef cows grazing tropical pastures of signal grass (Urochloa decumbens). The experiment was carried out in the savanna region of Mato Grosso do Sul, Brazil, during the years 2011 to 2013. Variables analyzed included pregnancy rate, calving interval, weight of calves at weaning, and cost of mineral supplementation. There were no changes in the reproductive parameters of the herd and the weight at weaning of the calves. However, the cost of mineral supplementation was significantly lower when the herd was supplemented with the mineral mix containing only 18 g kg(-1) P. Phosphorus concentration of the forage was analyzed monthly during 1 year and averaged 1.9 ± 0.45 g kg(-1) DM. Thus, it appears possible to reduce P content and cost of mineral supplementation without any adverse effects on the health and productivity of beef cattle herds in the State of Mato Grosso do Sul. However, the final decision should be made based on the clinical-nutritional examination and by constant technical assistance to the farm.

Mediastinal lymph nodes and pulmonary nodules in children: MDCT findings in a cohort of healthy subjects.

OBJECTIVE: Existing data are very limited on incidentally detected pulmonary nodules or mediastinal lymph nodes in healthy children who undergo chest MDCT. We aimed to evaluate the prevalence, distribution, and average dimensions of these occasional findings in a cohort of otherwise healthy patients. MATERIALS AND METHODS: Two radiologists reviewed in consensus the scans of patients referred for chest MDCT during the preoperative workup for pectus carinatum or pectus excavatum treatments. Exclusion criteria included the presence of any documented malignancy (by date of MDCT or during the 2 years after the examination), history of recent infections, or trauma. Patients' records were assessed after 2 years for the development of any malignancy. RESULTS: A total of 99 individuals (63 boys, 36 girls; mean age, 13.5 years; range, 4-18 years) who fulfilled the study criteria were evaluated. The presence of at least one pulmonary nodule was observed in 75% of the patients, with a mean diameter of 2.8 mm. Of a total number of 225 pulmonary nodules, only 24 (10.7%) were calcified. Mediastinal lymph nodes were also identified in 81% of the cases, with a maximum diameter of 7 mm (smallest axis). CONCLUSION: The presence of pulmonary nodules or mediastinal lymph nodes on the basis of preoperative chest MDCT scans in healthy children is frequent. Given that 95% of the nodules and 100% of the lymph nodes measured less than 6 mm and 7 mm, respectively, we conclude that incidental findings under these limits are very unlikely to be pathologic.

Classification of pro-inflammatory status for interleukin-6 affects relative muscle strength in obese elderly women.

BACKGROUND: Obesity, defined by an excess amount of body fat or a percent body fat higher than 30 % for women is a complex chronic disorder with multifactorial etiology and is accompanied by chronic low-grade inflammation, which results in elevated pro-inflammatory cytokines. AIMS: The aim of this study was to compare muscle strength between high and low pro-inflammatory status in obese elderly women and to verify the relationship of IL-6 with muscle strength and fat-free mass. METHODS: Eighty-nine elderly women (age 69.47 ± 6.07 years; body mass 64.70 ± 12.04 kg; height 1.52 ± 0.06 m; body mass index 27.78 ± 4.75 kg/m(2)) were divided into two groups: high and low inflammatory status for IL-6. Lower limb muscle strength was tested using bilateral leg extension with the ten repetitions maximum test, IL-6 was measured by ELISA and body composition by dual-energy X-ray absorptiometry. RESULTS: Women classified from the high pro-inflammatory status presented lower relative muscle strength (P = 0.056) when compared with the low inflammatory status group, with no differences for absolute muscle strength (P = 0.18). There was a significant negative correlation of IL-6 with relative muscle strength (P = 0.03, R = -0.22) and a considerable trend toward significance (P = 0.06, R = -0.19) and negative association with fat-free mass (P = 0.84, R = -0.02). CONCLUSIONS: This study provides insights that a high pro-inflammatory status in sedentary obese elderly women might impair muscle strength and negatively affect fat-free mass. Thus, elderly women classified with high pro-inflammatory status for IL-6 should receive further health care attention to prevent this deleterious condition.

Impact of the COVID-19 Pandemic on Pharmacist Interventions: A Retrospective Study with Inpatients in a University Hospital.

Background: Despite growing interest in understanding the challenges faced by multidisciplinary health teams during the COVID-19 pandemic, there is a lack of studies specifically focusing on changes in pharmacist interventions and drug-related problems. Objectives: To analyze and compare the interventions performed by pharmacists during comprehensive medication management in the adult intensive care unit and general internal medicine ward of the University Hospital of the University of São Paulo, Brazil, for defined periods before the onset of the COVID-19 pandemic and during the pandemic itself. Methods: All pharmacist interventions performed in relation to inpatient prescriptions from March to December 2019 (before the pandemic) and from March to December 2021 (during the pandemic) were collected and tabulated. These interventions were then classified according to the Pharmaceutical Care Network Europe (PCNE) system, version 9.1, and categorized based on first-level codes of the Anatomical Therapeutic Chemical classification system. Results: The analysis revealed substantial changes in the patterns of pharmacist interventions and the therapeutic classes of drugs for COVID-19-positive and COVID-19-negative patients during the pandemic relative to patients in the pre-pandemic period. Among COVID-19-positive patients, interventions were predominantly related to enhancing patient safety (PCNE code P2), drug selection (C1), dose selection (C3), prescribing and dispensing processes (C5), the drug-use process (C6), and patient transfers between different levels of care (C8). The drug-related problems addressed by pharmacist interventions primarily involved COVID-19-positive patients in the pandemic period and were related to systemic hormonal preparations (excluding sex hormones and insulins), anti-infective agents for systemic use, nervous system and drugs for the blood and blood-forming organs. Conclusion: The results of this study highlight the adaptability and competence of pharmacists in responding to critical scenarios such as the COVID-19 pandemic. These scenarios are characterized by new work dynamics, the hiring of additional professionals, an increase in the number of beds, the rapid evolution of evidence-based information, and drug shortages that necessitate the use of alternative medications. Pharmacists play a crucial role in ensuring patient safety during these difficult times.

Contexte: Malgré un intérêt croissant pour la compréhension des défis auxquels les équipes de santé multidisciplinaires ont été confrontées pendant la pandémie de COVID-19, peu d'études portent sur les changements chez les interventions des pharmaciens et les problèmes liés aux médicaments en particulier. Objectifs: Analyser et comparer les interventions réalisées par les pharmaciens lors de la gestion globale des médicaments dans l'unité de soins intensifs pour adultes et le service de médecine interne générale de l'hôpital universitaire de l'Université de São Paulo, Brésil, pendant des périodes définies avant le début de la pandémie de COVID-19 et pendant la pandémie elle-même. Méthodologie: Toutes les interventions des pharmaciens réalisées en lien avec les prescriptions hospitalières de mars à décembre 2019 (avant la pandémie) et de mars à décembre 2021 (pendant la pandémie) ont été collectées et compilées. Ces interventions ont ensuite été classées selon le système du Pharmaceutical Care Network Europe (PCNE), version 9.1, et catégorisées sur la base des codes de premier niveau du système de classification anatomique, thérapeutique et chimique. Résultats: L'analyse a révélé des changements substantiels dans les types d'intervention des pharmaciens et dans les classes thérapeutiques de médicaments pour les patients positifs pour la COVID-19 et négatifs pour la COVID-19 pendant la pandémie par rapport aux patients d'avant la pandémie. Parmi les patients positifs pour la COVID-19, les interventions étaient principalement liées à l'amélioration de la sécurité des patients (code PCNE P2), au choix des médicaments (C1), à la sélection des doses (C3), au processus de prescription et de délivrance (C5), au processus d'utilisation des médicaments (C6), et aux transferts de patients entre différents niveaux de soins (C8). Les problèmes liés aux médicaments traités par les interventions des pharmaciens concernaient principalement les patients positifs pour la COVID-19 pendant la période de la pandémie et se rapportaient aux préparations hormonales systémiques (à l'exclusion des hormones sexuelles et des insulines), aux agents anti-infectieux à usage systémique, au système nerveux ainsi qu'au sang et aux organes hématopoïétiques. Conclusion: Les résultats de cette étude mettent en évidence l'adaptabilité et la compétence des pharmaciens pour répondre à des scénarios critiques tels que la pandémie de COVID-19. Ces scénarios se caractérisent par une nouvelle dynamique de travail, l'embauche de professionnels supplémentaires, une augmentation du nombre de lits, l'évolution rapide des informations fondées sur des données probantes et des pénuries de médicaments nécessitant le recours à des médicaments alternatifs. Les pharmaciens jouent un rôle crucial pour assurer la sécurité des patients pendant ces périodes difficiles.

Clinical Characteristics of Children with THRA Mutations: Variable Phenotype and Good Response to Recombinant Human Growth Hormone Therapy.

INTRODUCTION: Mutations in the thyroid hormone receptor alpha (THRA) gene are a rare cause of thyroid hormone resistance, which leads to a pleomorphic phenotypic spectrum. Hormonal profiles are variable and subtle, making laboratory diagnoses challenging. Genetic evaluation can be a helpful tool in diagnosing these cases. CASE PRESENTATION: Three patients (P1, P2, and P3) from unrelated families presented to their endocrinologists with short stature and abnormalities in thyroid function results. P1 showed hypoactivity and mild thyroid-stimulating hormone (TSH) elevation. P2 presented with a mild developmental delay and a hormonal profile initially interpreted as central hypothyroidism. Patient P3 had severe symptoms, including hypotonia, developmental delay, normal TSH, hypercholesterolemia, severe hypertriglyceridemia, high amylase levels, and mild pericardial effusion. All the patients had low free thyroxine (FT4) levels, mild constipation, and short stature. The patients underwent exome sequencing analysis that identified three different heterozygous variants in the THRA gene (P1 and P2 had missense variants, and P3 had a stop codon variant). All patients were treated with levothyroxine replacement, improving their clinical symptoms, such as constipation, and neurological symptoms. P1 and P2 were also treated with the recombinant human growth hormone (rhGH). The improvements in growth velocity and height standard deviation scores (SDS) were remarkable. Notably, P1 had a total height gain of 2.5 SDS, reaching an adult height within the normal range. CONCLUSION: THRA gene defects can lead to growth disorders with different phenotypes. Children with THRA mutations can benefit from adequate treatment with levothyroxine and may respond well to rhGH treatment.

Towards a standard benchmark for variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework.

Background: Computational approaches to support rare disease diagnosis are challenging to build, requiring the integration of complex data types such as ontologies, gene-to-phenotype associations, and cross-species data into variant and gene prioritisation algorithms (VGPAs). However, the performance of VGPAs has been difficult to measure and is impacted by many factors, for example, ontology structure, annotation completeness or changes to the underlying algorithm. Assertions of the capabilities of VGPAs are often not reproducible, in part because there is no standardised, empirical framework and openly available patient data to assess the efficacy of VGPAs - ultimately hindering the development of effective prioritisation tools. Results: In this paper, we present our benchmarking tool, PhEval, which aims to provide a standardised and empirical framework to evaluate phenotype-driven VGPAs. The inclusion of standardised test corpora and test corpus generation tools in the PhEval suite of tools allows open benchmarking and comparison of methods on standardised data sets. Conclusions: PhEval and the standardised test corpora solve the issues of patient data availability and experimental tooling configuration when benchmarking and comparing rare disease VGPAs. By providing standardised data on patient cohorts from real-world case-reports and controlling the configuration of evaluated VGPAs, PhEval enables transparent, portable, comparable and reproducible benchmarking of VGPAs. As these tools are often a key component of many rare disease diagnostic pipelines, a thorough and standardised method of assessment is essential for improving patient diagnosis and care.

Assessment of infection of Stomoxys calcitrans larvae by entomopathogenic nematodes Heterorhabditis amazonensis NEPT11.

This study aimed to evaluate the virulence of Heterorhabditis amazonenses NEPT11 against larvae of Stomoxys calcitrans. Groups of 10 third-instar fly larvae were deposited in Petri dishes, to which were added 50, 100 and 200 EPNs/larva in 4ml of distilled water. The volume of the control group was the same as the treated group, but without EPNs. Larval mortality was observed daily, until larvae died or adults emerged. The Petri dishes were kept on laboratory shelves at 27 ± 1 °C and 70 ± 10% RH. The experiment was replicated six times. A regression analysis revealed quadratic behavior with increasing concentrations, indicating that the concentration of 200 EPNs/larva (48%) was the most efficient among the tested concentrations, while concentrations of 50 and 100 EPNs/larva killed 26.6 and 40% of larvae, respectively. In general, none of the treatments resulted in a mortality rate of more than 50%, but all the treated groups exhibited a higher mortality than that of the control group. It is concluded that the EPN H. amazonensis NEPT11 shows a promising potential to control third-instar larvae of S. calcitrans. However, further studies are needed in different situations to better understand the activity of this organism against the immature stages of the stable fly.

Este estudo teve como objetivo avaliar a ação do NEP Heterorhabditis amazonenses NEPT11 frente larvas de S. calcitrans. Grupos de 10 larvas de terceiro instar da mosca foram depositados em placas de Petri, em seguida, adicionou-se 50, 100, 200, 300 e 400 NEPs/larva em 4ml de água destilada. O volume do grupo controle foi o mesmo dos tratados, porém sem NEPs. A mortalidade das larvas foi observada diariamente, até a morte das larvas ou emergência de adultos. As placas foram mantidas em estantes de laboratório a 27 ± 1 °C e 70 ± 10% UR. O experimento teve seis repetições. Por meio da análise de regressão, foi observado comportamento quadrático com o aumento das concentrações, sendo a concentração de 200 NEPs/larva (48%) a de maior eficiência entre as concentrações testadas, já as concentrações de 50 e 100 NEPs/larva mataram 26,6 e 40% das larvas, respectivamente. De modo geral, nenhum tratamento proporcionou mortalidade superior a 50%, todavia, todos os grupos tratados apresentaram mortalidade superior à observada no controle. Conclui-se que H. amazonenses NEPT11 mostrou-se promissor no controle de larvas de terceiro instar de S. calcitrans, porém mais estudos devem ser feitos para o melhor entendimento da ação deste organismo frente aos estágios imaturos da mosca-dos-estábulos.

Immunohistochemistry assessment of tissue neutrophil-to-lymphocyte ratio predicts outcomes in melanoma patients treated with anti-programmed cell death 1 therapy.

Elevated neutrophil-to-lymphocyte ratio (NLR) is associated with diminished immunotherapy response in metastatic melanoma. Although NLR assessment in peripheral blood is established, tissue dynamics remain insufficiently explored. This study aimed to evaluate tissue NLR (tNLR)'s predictive potential through immunohistochemistry in immunotherapy-treated melanoma. Fifty melanoma patients who underwent anti-programmed cell death 1 (PD-1) therapy were assessed. Hematological, clinical and tumor features were collected from medical records. Responses were categorized using the Response Evaluation Criteria in Solid Tumors for immunotherapy (iRECIST) guidelines. Immunohistochemistry for tumor-infiltrating T cells (cluster differentiation 3) and neutrophils (myeloperoxidase) was performed on formalin-fixed paraffin-embedded tumor samples. NLR, derived NLR (dNLR) and tNLR were calculated. Overall survival (OS) and survival following immunotherapy (SFI) were calculated from diagnosis or immunotherapy start to loss of follow-up or death. Patients with high tNLR presented improved OS ( P =  0.038) and SFI with anti-PD-1 therapy ( P =  0.006). Both NLR and dNLR were associated with OS ( P =  0.038 and P =  0.046, respectively) and SFI ( P =  0.001 and P =  0.019, respectively). NLR was also associated with immunotherapy response ( P =  0.007). In conclusion, tNLR emerged as a novel potential biomarker of enhanced survival post anti-PD-1 therapy, in contrast to classical NLR and dNLR markers.