A corpus of GA4GH phenopackets: case-level phenotyping for genomic diagnostics and discovery.

The Global Alliance for Genomics and Health (GA4GH) Phenopacket Schema was released in 2022 and approved by ISO as a standard for sharing clinical and genomic information about an individual, including phenotypic descriptions, numerical measurements, genetic information, diagnoses, and treatments. A phenopacket can be used as an input file for software that supports phenotype-driven genomic diagnostics and for algorithms that facilitate patient classification and stratification for identifying new diseases and treatments. There has been a great need for a collection of phenopackets to test software pipelines and algorithms. Here, we present Phenopacket Store. Version 0.1.19 of Phenopacket Store includes 6668 phenopackets representing 475 Mendelian and chromosomal diseases associated with 423 genes and 3834 unique pathogenic alleles curated from 959 different publications. This represents the first large-scale collection of case-level, standardized phenotypic information derived from case reports in the literature with detailed descriptions of the clinical data and will be useful for many purposes, including the development and testing of software for prioritizing genes and diseases in diagnostic genomics, machine learning analysis of clinical phenotype data, patient stratification, and genotype-phenotype correlations. This corpus also provides best-practice examples for curating literature-derived data using the GA4GH Phenopacket Schema.

Multiple Lactobacillus Infections Caused by Probiotics at Pediatric and Adult Academic Medical Centers.

BACKGROUND: Probiotics are synthetic oral supplements containing live bacterial and fungal species hypothesized to help with various gastrointestinal conditions. However, they can cause infection if the organism spreads outside of the gastrointestinal tract. The aim of this study was to identify and describe patients who experienced systemic infections caused by probiotic use. METHODS: This study was a retrospective chart review of pediatric and adult patients at academic medical centers who received probiotics and subsequently developed positive cultures from a sterile site for probiotic-related species. Two individuals completed the chart reviews to determine if the probiotic was the true cause of the infection. RESULTS: Lactobacillus, Bifidobacterium, and Saccharomyces cultures were reviewed, with a total of 71, 8, and 2 cultures isolated from sterile sites for each organism, respectively. Further review revealed 23 Lactobacillus cultures from 13 unique patients who were taking Lactobacillus-containing probiotics. Four patients without gastrointestinal tract compromise were included in the final analysis, including 1 patient whose culture was confirmed as identical to the probiotic. Types of infections included meningitis and bacteremia. Targeted antimicrobial therapy included ampicillin, ampicillin-sulbactam, and piperacillin-tazobactam, with total durations of therapy ranging from 10 to 22 days. No patients had mortality attributed to Lactobacillus infection. CONCLUSIONS: Probiotics are not harmless supplements as they come with risk of serious infection as demonstrated in this review. Before use, the risks of probiotics should be considered carefully for each individual patient. Clinicians should consider avoiding probiotics in hospitalized patients, especially those with vascular or extra-ventricular access devices.

Effect of Semaglutide on Physical Function, Body Composition, and Biomarkers of Aging in Older Adults With Overweight and Insulin Resistance: Protocol for an Open-Labeled Randomized Controlled Trial.

BACKGROUND: Older adults with type 2 diabetes mellitus (T2DM) or prediabetes are at increased risk of adverse changes in body composition, physical function, and aging-related biomarkers compared to those with normal glucose tolerance. Semaglutide is a glucagon-like peptide 1 receptor agonist that has been approved for T2DM and chronic weight management. Although semaglutide is effective for weight loss and T2DM management, its effects on lean body mass, physical function, and biomarkers of aging are understudied in older adults. OBJECTIVE: This study aims to compare the effects of lifestyle counseling with and that without semaglutide on body composition, physical function, and biomarkers of aging in older adults. METHODS: This is an open-label randomized controlled trial. A total of 20 adults (aged 65 years and older) with elevated BMI (27-40 kg/m2) and prediabetes or well-controlled T2DM (hemoglobin A1c 5.7%-7.5%) are recruited, stratified by sex, and randomized 1:1 to one of 2 groups (semaglutide plus lifestyle counseling vs lifestyle counseling alone) and followed up for 5 months. Those in the semaglutide group are titrated to 1 mg weekly, as tolerated, for 12 weeks. Lifestyle counseling is given by registered dietitians and based on the Diabetes Prevention Program Lifestyle Change Program. Our primary outcomes include changes in lean mass, physical function, and biomarkers of aging. Body composition is measured by dual-energy x-ray absorptiometry and includes total fat mass and lean mass. Physical function is measured by 6-minute walk distance, grip strength, and short physical performance battery. Biomarkers of aging are measured in blood, skeletal muscle, and abdominal adipose tissue to include C-reactive protein, interleukin-6, tumor necrosis factors α, and ß galactosidase staining. RESULTS: The study was funded in December 2021 with a projected data collection period from spring 2023 through summer 2024. CONCLUSIONS: Despite the elevated risk of adverse changes in body composition, physical function, and biomarkers of aging among older adults with glucose intolerance and elevated adiposity, the benefits and risks of commonly prescribed antihyperglycemic or weight loss medications such as semaglutide are understudied. This study aims to fill this knowledge gap to inform clinicians about the potential for additional clinically meaningful, nonglycemic effects of semaglutide. TRIAL REGISTRATION: ClinicalTrials.gov NCT05786521; https://clinicaltrials.gov/study/NCT05786521. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/62667.

The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics.

Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.

Methanolic Extract of Rhizophora mangle (Rhizophoraceae) Leaves: Phytochemical Characterization and Anthelmintic Evaluation against Schistosoma mansoni.

Rhizophora mangle is commonly used in traditional medicine to treat infections, reduce inflammation, and promote healing. This study aimed to analyze the phytochemical profile of the methanolic extract of R. mangle leaves (MELRm) and evaluate its in vitro schistosomicidal activity against Schistosoma mansoni as well as its cytotoxicity. Plant material was collected in Itamaracá City, Pernambuco, Brazil. The extract was analyzed using UV/Vis spectrophotometry and high-performance liquid chromatography (HPLC). The motility, mortality, and cell viability of adult worms were assessed in a schistosomicidal assay, while cytotoxicity was evaluated through a colorimetric assay with MTT on RAW 264.7 cells. The primary compounds identified in MELRm were phenolic compounds. In the schistosomicidal assay, all concentrations of MELRs induced changes in the motility of adult worms. At a concentration of 400 µg/mL, MELRs resulted in 56.25% mortality after 72 h of incubation. After 120 h, mortality rates of 75%, 62.5%, and 50% were observed at MELRm concentrations of 400, 200, and 100 µg/mL, respectively. No eggs were detected at any MELRm concentration. MELRs did not show cytotoxicity towards RAW 264.7 cells at the concentrations tested. These results indicate that MELRs demonstrate schistosomicidal activity in vitro, suggesting they are promising candidates for in vivo studies.

Emerging Evidence and Critical Issues with the Use of Single-Drop Capillary Blood for the Measurement of Hemoglobin Concentration in Population-Level Anemia Surveys.

Accurate and precise measurement of hemoglobin concentration is critical for reliable estimations of anemia prevalence at the population level. When systematic and/or random error are introduced in hemoglobin measurement, estimates of anemia prevalence might be significantly erroneous and, hence, limit their usefulness. For decades, single-drop capillary blood has been the most common blood source used for the measurement of hemoglobin concentration in surveys, especially in low-income and middle-income countries. In this study, we highlight historical and emerging evidence that single-drop capillary blood introduces a high degree of random error (variability) to hemoglobin estimates, leading to less reliable estimates of anemia prevalence at the population level. At present, the best practice is to collect and use venous blood for measurement of hemoglobin with an automated hematology analyzer, following standard operating procedures and quality assurance measures. Where use of an automated analyzer is not possible, the analysis of venous blood in a point-of-care hemoglobinometer by trained phlebotomists or specimen collectors should be considered. A forthcoming systematic review will provide additional evidence on the accuracy and precision of single-drop capillary blood for hemoglobin assessment. In the meantime, we raise caution when using single-drop capillary blood for hemoglobin measurement as it can result in inaccurate hemoglobin estimates and less reliable anemia prevalence estimates.

Correction: Leppäniemi et al. Nutrition Profile for Countries of the Eastern Mediterranean Region with Different Income Levels: An Analytical Review. Children 2023, 10, 236.

In the original publication [...].

Insights into the State of the Art of Urogenital Schistosomiasis with a Focus on Infertility.

Schistosomiasis is a neglected tropical disease that affects developing countries worldwide and is caused by several species of parasites from the Schistosoma genus. Chronic infection is characterized by the formation of granulomas around the parasite eggs, the leading cause of pathology. The hepatosplenic clinical form is one of the most common, but urogenital schistosomiasis is another relevant clinical presentation responsible for infertility in men and women. Inflammatory response, anatomical deformations, and endocrine/biochemical changes are involved in the development of infertility. Schistosome parasites can synthesize catechol estrogen-like molecules and affect the sexual hormone balance in their host. Here, we review many aspects of the pathology of urogenital schistosomiasis, specifically infertility, and point to the biochemical and endocrinal elements that must be investigated in the future.

Evidence Surrounding Dietary Behavior Interventions in Community-Dwelling Stroke Survivors: A Scoping Review.

Objective: To identify and summarize studies that have implemented dietary behavior interventions and reported dietary outcomes in community-dwelling adult stroke survivors. Design: Scoping Review; Setting: Not applicable. Participants: Studies eligible for review included peer-reviewed studies describing both a dietary intervention and a dietary outcome among community-dwelling stroke survivors published between January 2000 and June 2022. Results: We identified 14 articles that included both a dietary behavior intervention and a dietary outcome. All studies (5 pilot randomized controlled trials (RCTs), 6 non-pilot RCTs, 3 cohort studies) delivered multimodal health behavior interventions that included a dietary component. Interventions were delivered weekly to every other month and lasted for 1-24 months. Most studies did not use standardized assessments to assess dietary outcomes; however, 8 studies reported improvement in dietary outcomes. Conclusions: This review provides support for the efficacy of dietary behavior interventions in stroke survivors. Variability in intervention format and assessment measures across studies impedes the ability to conduct meta-analyses of outcomes to inform research knowledge and clinical practice. Additional research is needed to determine mechanisms-of-action for dietary behavior change in stroke survivors.

MYC Induces Oncogenic Stress through RNA Decay and Ribonucleotide Catabolism in Breast Cancer.

Upregulation of MYC is a hallmark of cancer, wherein MYC drives oncogenic gene expression and elevates total RNA synthesis across cancer cell transcriptomes. Although this transcriptional anabolism fuels cancer growth and survival, the consequences and metabolic stresses induced by excess cellular RNA are poorly understood. Herein, we discover that RNA degradation and downstream ribonucleotide catabolism is a novel mechanism of MYC-induced cancer cell death. Combining genetics and metabolomics, we find that MYC increases RNA decay through the cytoplasmic exosome, resulting in the accumulation of cytotoxic RNA catabolites and reactive oxygen species. Notably, tumor-derived exosome mutations abrogate MYC-induced cell death, suggesting excess RNA decay may be toxic to human cancers. In agreement, purine salvage acts as a compensatory pathway that mitigates MYC-induced ribonucleotide catabolism, and inhibitors of purine salvage impair MYC+ tumor progression. Together, these data suggest that MYC-induced RNA decay is an oncogenic stress that can be exploited therapeutically. Significance: MYC is the most common oncogenic driver of poor-prognosis cancers but has been recalcitrant to therapeutic inhibition. We discovered a new vulnerability in MYC+ cancer where MYC induces cell death through excess RNA decay. Therapeutics that exacerbate downstream ribonucleotide catabolism provide a therapeutically tractable approach to TNBC (Triple-negative Breast Cancer) and other MYC-driven cancers.

Long Non-Coding RNAs Differentially Expressed in Swine Fetuses.

Long non-coding RNAs (lncRNAs) are non-coding transcripts involved in various biological processes. The Y chromosome is known for determining the male sex in mammals. LncRNAs on the Y chromosome may play important regulatory roles. However, knowledge about their action mechanisms is still limited, especially during early fetal development. Therefore, we conducted this exploratory study aiming to identify, characterize, and investigate the differential expression of lncRNAs between male and female swine fetuses at 35 days of gestation. RNA-Seq libraries from 10 fetuses were prepared and sequenced using the Illumina platform. After sequencing, a data quality control was performed using Trimmomatic, alignment with HISAT2, and transcript assembly with StringTie. The differentially expressed lncRNAs were identified using the limma package of the R software (4.3.1). A total of 871 potentially novel lncRNAs were identified and characterized. Considering differential expression, eight lncRNAs were upregulated in male fetuses. One was mapped onto SSC12 and seven were located on the Y chromosome; among them, one lncRNA is potentially novel. These lncRNAs are involved in diverse functions, including the regulation of gene expression and the modulation of chromosomal structure. These discoveries enable future studies on lncRNAs in the fetal stage in pigs.

GIS-based methodology for tracking the grazing cattle site use.

Interest in tracking and monitoring animals in livestock farming using wearable sensors has been steadily increasing. The use of these devices is particularly crucial in extensive livestock systems where direct interaction between animals and farmers is infrequent, necessitating strenuous efforts in long-distance herd monitoring. Internet of Things (IoT) technologies offer a promising solution to address the challenges posed by vast distances, enabling real-time and remote animal monitoring. In this study, an experimental trial was conducted using a custom-designed device, located in a Polyvinyl Chloride (PVC) case, specifically tailored to fit onto a collar. This case incorporates an integrated SigFox communication system, i.e., a Low Power Global Positioning System (LP-GPS) omnidirectional system, and a power supply. The trial took place in two grazing areas located in different territorial zones, designated as Case Study I and II. A LP-GPS collar was provided for each selected animal, and the data were recorded at 20-min intervals for Case Study I and 10-min intervals for Case Study II. The acquired data were then imported and analysed using Geographical Information Systems (GIS) software. Information was collected through a purpose-built web application (AppWeb). The objective was to analyze those territorial areas mostly occupied by animals within the two considered grazing areas by developing a GIS-based methodology. Specifically, customized algorithms such as Heatmap and Kernel Density Estimation (KDE) plugins were employed to conduct spatial analyses. The maps obtained through Heatmap plugin, showed the temporal-spatial distribution of animals within their grazing areas. Additionally, the KDE tool was used to classify preferred territorial areas, generating tailored charts for each animal in the sample. The individual Core Areas, determined through KDE evaluation for each animal, were overlaid to provide a comprehensive analysis of the monitored animals.The results achieved applying the GIS-based methodology facilitated the identification of animal positions and could be adopted to provide insights into feeding behavior and soil erosion, thereby aiding in the prevention of environmental issues.

Oceanic seabirds chase tropical cyclones.

In late summer and autumn, the passage of intense tropical cyclones can profoundly perturb oceanic and coastal ecosystems. Direct negative effects on individuals and marine communities can be dramatic, especially in the coastal zone,1,2,3,4 but cyclones can also enhance pelagic primary and secondary production.5,6,7,8,9 However, cyclone impacts on open ocean marine life remain poorly understood. Here, we investigate their effects on the foraging movements of a wide-ranging higher predator, the Desertas petrel (Pterodroma deserta), in the mid-latitude North Atlantic during hurricane season. Contrary to previously studied pelagic seabirds in tropical and mid-latitude regions,10,11 Desertas petrels did not avoid cyclones by altering course, nor did they seek calmer conditions within the cyclone eye. Approximately one-third of petrels tracked from their breeding colony interacted with approaching cyclones. Upon encountering strong winds, the birds reduced ground speed, likely by spending less time in flight. A quarter of birds followed cyclone wakes for days and over thousands of kilometers, a behavior documented here for the first time. Within these wakes, tailwind support was higher than along alternative routes. Furthermore, at the mesoscale (hours-weeks and hundreds of kilometers), sea surface temperature dropped and surface chlorophyll sharply increased, suggesting direct effects on ocean stratification, primary production, and therefore presumably prey abundance and accessibility for surface-feeding petrels. We therefore hypothesize that cyclone wakes provide both predictably favorable wind conditions and foraging opportunities. As such, cyclones may have positive net effects on the demography of many mid-latitude pelagic seabirds and, likely, other marine top-predators.

Eosinophils as drivers of bacterial immunomodulation and persistence.

Traditionally, eosinophils have been linked to parasitic infections and pathological disease states. However, emerging literature has unveiled a more nuanced and intricate role for these cells, demonstrating their key functions in maintaining mucosal homeostasis. Eosinophils exhibit diverse phenotypes and exert multifaceted effects during infections, ranging from promoting pathogen persistence to triggering allergic reactions. Our investigations primarily focus on Bordetella spp., with particular emphasis on Bordetella bronchiseptica, a natural murine pathogen that induces diseases in mice akin to pertussis in humans. Recent findings from our published work have unveiled a striking interaction between B. bronchiseptica and eosinophils, facilitated by the btrS-mediated mechanism. This interaction serves to enhance pathogen persistence while concurrently delaying adaptive immune responses. Notably, this role of eosinophils is only noted in the absence of a functional btrS signaling pathway, indicating that wild-type B. bronchiseptica, and possibly other Bordetella spp., possess such adeptness in manipulating eosinophils that the true function of these cells remains obscured during infection. In this review, we present the mounting evidence pointing toward eosinophils as targets of bacterial exploitation, facilitating pathogen persistence and fostering chronic infections in diverse mucosal sites, including the lungs, gut, and skin. We underscore the pivotal role of the master regulator of Bordetella pathogenesis, the sigma factor BtrS, in orchestrating eosinophil-dependent immunomodulation within the context of pulmonary infection. These putative convergent strategies of targeting eosinophils offer promising avenues for the development of novel therapeutics targeting respiratory and other mucosal pathogens.

Genomic Comparative of Pseudomonas aeruginosa Small Colony Variant, Mucoid and Non-mucoid Phenotypes Obtained from a Patient with Cystic Fibrosis During Respiratory Exacerbations.

Pseudomonas aeruginosa, the most prevalent opportunistic pathogen in chronic obstructive pulmonary disease, associated with high morbidity and mortality in patients with cystic fibrosis (CF), is practically impossible to be eradicated from the airways in chronicity. Its extraordinary genomic plasticity is possibly associated with high antimicrobial resistance, virulence factors, and its phenotypic diversity. The occurrence of P. aeruginosa isolates promoting airway infection, showing mucoid, non-mucoid, and small colony variant (SCV) phenotypes, was observed simultaneously, in the present study, in sputum cultures obtained from a male CF young patient with chronic pulmonary infection for over a decade. The isolates belonged to a new ST (2744) were obtained in two moments of exacerbation of the respiratory disease, in which he was hospitalized. Genetic background and phenotypic analysis indicated that the isolates exhibited multi- and pan-antimicrobial resistant profiles, as well as non-susceptible to polymyxin and predominantly hypermutable (HPM) phenotypes. Whole genome sequencing showed variations in genome sizes, coding sequences and their determinants of resistance and virulence. The annotated genomes were compared for antimicrobial resistance, hypermutability, and SCV characteristics. We highlight the lack of reported genetic determinants of SCV emergence and HPM phenotypes, which can be explained in part due to the very short time between collections of isolates. To the best of our knowledge, this is the first report of genome sequencing of P. aeruginosa SCV from a CF patient in Brazil.

FAST SOLVER FOR DIFFUSIVE TRANSPORT TIMES ON DYNAMIC INTRACELLULAR NETWORKS.

The transport of particles in cells is influenced by the properties of intracellular networks they traverse while searching for localized target regions or reaction partners. Moreover, given the rapid turnover in many intracellular structures, it is crucial to understand how temporal changes in the network structure affect diffusive transport. In this work, we use network theory to characterize complex intracellular biological environments across scales. We develop an efficient computational method to compute the mean first passage times for simulating a particle diffusing along two-dimensional planar networks extracted from fluorescence microscopy imaging. We first benchmark this methodology in the context of synthetic networks, and subsequently apply it to live-cell data from endoplasmic reticulum tubular networks.

A corpus of GA4GH Phenopackets: case-level phenotyping for genomic diagnostics and discovery.

The Global Alliance for Genomics and Health (GA4GH) Phenopacket Schema was released in 2022 and approved by ISO as a standard for sharing clinical and genomic information about an individual, including phenotypic descriptions, numerical measurements, genetic information, diagnoses, and treatments. A phenopacket can be used as an input file for software that supports phenotype-driven genomic diagnostics and for algorithms that facilitate patient classification and stratification for identifying new diseases and treatments. There has been a great need for a collection of phenopackets to test software pipelines and algorithms. Here, we present phenopacket-store. Version 0.1.12 of phenopacket-store includes 4916 phenopackets representing 277 Mendelian and chromosomal diseases associated with 236 genes, and 2872 unique pathogenic alleles curated from 605 different publications. This represents the first large-scale collection of case-level, standardized phenotypic information derived from case reports in the literature with detailed descriptions of the clinical data and will be useful for many purposes, including the development and testing of software for prioritizing genes and diseases in diagnostic genomics, machine learning analysis of clinical phenotype data, patient stratification, and genotype-phenotype correlations. This corpus also provides best-practice examples for curating literature-derived data using the GA4GH Phenopacket Schema.

Perspectives on the future of host-microbe biology from the Council on Microbial Sciences of the American Society for Microbiology.

Host-microbe biology (HMB) stands on the cusp of redefinition, challenging conventional paradigms to instead embrace a more holistic understanding of the microbial sciences. The American Society for Microbiology (ASM) Council on Microbial Sciences hosted a virtual retreat in 2023 to identify the future of the HMB field and innovations needed to advance the microbial sciences. The retreat presentations and discussions collectively emphasized the interconnectedness of microbes and their profound influence on humans, animals, and environmental health, as well as the need to broaden perspectives to fully embrace the complexity of these interactions. To advance HMB research, microbial scientists would benefit from enhancing interdisciplinary and transdisciplinary research to utilize expertise in diverse fields, integrate different disciplines, and promote equity and accessibility within HMB. Data integration will be pivotal in shaping the future of HMB research by bringing together varied scientific perspectives, new and innovative techniques, and 'omics approaches. ASM can empower under-resourced groups with the goal of ensuring that the benefits of cutting-edge research reach every corner of the scientific community. Thus, ASM will be poised to steer HMB toward a future that champions inclusivity, innovation, and accessible scientific progress.

Development and Feasibility Pilot Study of Indigenous Recovery Planning: A Community-Engaged Approach to Addressing Substance Use in a Native Community.

Although Native (American Indian and Alaska Native [AI/AN]) populations have high rates of abstinence from alcohol, health problems associated with substance use remain a pressing concern in many AI/AN communities. As part of a longstanding community-based participatory research (CBPR) project involving five years of relationship building and three preliminary studies, our team of academic and community co-researchers developed a culturally grounded intervention to facilitate recovery from substance use disorders among tribal members from a rural AI reservation. Our Indigenous Recovery Planning (IRP) intervention consists of six weekly sessions and aims to provide inroads to existing resources in the community, affirm and enhance Native identity, address culturally relevant risk factors, and build upon strengths. Results from a feasibility pilot study (N = 15) suggest that IRP is feasible to implement and acceptable to the community. Although there was insufficient statistical power to conduct hypothesis testing, there were changes between pretest and posttest scores in the expected directions. Future directions and limitations of this research are discussed.

Dietary Strategies in Postmenopausal Women with Chronic and Metabolic Diseases.

As women age, their nutritional needs change, governed by changes in hormones, level of physical activity, and dietary intake [...].