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Maturitas Jun 2024Cross-sectional evidence has shown that frailty is highly prevalent in patients with chronic kidney disease (CKD). However, there is limited evidence of the longitudinal...
OBJECTIVES
Cross-sectional evidence has shown that frailty is highly prevalent in patients with chronic kidney disease (CKD). However, there is limited evidence of the longitudinal associations between frailty, genetic predisposition to CKD, and the risk of CKD in the general population. Therefore, this study aimed to examine such associations among participants in the UK Biobank.
STUDY DESIGN
This is a prospective cohort study included 370,965 middle-aged and older adults from the UK Biobank. Physical frailty was assessed using a modified version of the Fried phenotype classification. A weighted genetic risk score was built using 263 variants associated with estimated glomerular filtration rate.
MAIN OUTCOME MEASURES
Incident CKD was identified from hospital inpatient records.
RESULTS
Over a median follow-up of 12.3 years, we documented a total of 11,121 incident CKD cases. Time-dependent Cox proportional hazards regression models indicated that individuals with frailty (hazard ratio [HR]: 1.94, 95 % confidence interval [CI]: 1.81-2.08) and pre-frailty (HR: 1.27, 95 % CI: 1.22-1.33) had an increased risk of developing CKD, compared with non-frail individuals. No significant interaction between frailty and genetic risk score was observed (P for interaction = 0.41). The highest risk was observed among the individuals with high genetic risk and frailty (HR: 2.31, 95 % CI: 2.00-2.68).
CONCLUSION
Our results demonstrated that frailty and pre-frailty were associated with increased risk of incident CKD in middle-age and older adults, regardless of genetic risk of CKD. Our study underscores the importance of frailty screening and intervention as a potential strategy to prevent CKD. Future clinical trials are needed to validate our findings.
PubMed: 38941958
DOI: 10.1016/j.maturitas.2024.108059 -
Annual Review of Food Science and... Jun 2024Many physical, social, and psychological changes occur during aging that raise the risk of developing chronic diseases, frailty, and dependency. These changes adversely... (Review)
Review
Many physical, social, and psychological changes occur during aging that raise the risk of developing chronic diseases, frailty, and dependency. These changes adversely affect the gut microbiota, a phenomenon known as microbe-aging. Those microbiota alterations are, in turn, associated with the development of age-related diseases. The gut microbiota is highly responsive to lifestyle and dietary changes, displaying a flexibility that also provides anactionable tool by which healthy aging can be promoted. This review covers, firstly, the main lifestyle and socioeconomic factors that modify the gut microbiota composition and function during healthy or unhealthy aging and, secondly, the advances being made in defining and promoting healthy aging, including microbiome-informed artificial intelligence tools, personalized dietary patterns, and food probiotic systems.
Topics: Humans; Gastrointestinal Microbiome; Life Style; Diet; Healthy Aging; Probiotics; Aging
PubMed: 38941492
DOI: 10.1146/annurev-food-072023-034458 -
Methods in Molecular Biology (Clifton,... 2024The development of high throughput methods has enabled the study of hundreds of samples and metaproteomics is not the exception. However, the study of thousands of...
The development of high throughput methods has enabled the study of hundreds of samples and metaproteomics is not the exception. However, the study of thousands of proteins of different organisms represents different challenges from the protein extraction to the bioinformatic analysis. Here, the sample preparation, protein extraction and protein purification for livestock microbiome research throughout metaproteomics are described. These methods are essential because the quality of the final protein pool depends on them. For that reason, the following workflow is a combination of different chemical and physical methods that intend an initial separation of the microbial organisms from the host cells and other organic materials, as well as the extraction of high concentrate pure samples.
Topics: Animals; Livestock; Proteomics; Microbiota; Proteins
PubMed: 38941014
DOI: 10.1007/978-1-0716-3910-8_6 -
Microbial Ecology Jun 2024Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and...
Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15-20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change.
Topics: Soil Microbiology; Fagus; Quercus; Forests; Microbiota; Soil; Seasons; Bacteria; Biodiversity; Forestry; Trees; Ecosystem
PubMed: 38940921
DOI: 10.1007/s00248-024-02402-2 -
Physical Chemistry Chemical Physics :... Jun 2024In this work, the ferroelectric and semiconducting properties of the organic semiconducting ferroelectric benzotrithiophene tricarboxamide (BTTTA), and especially their...
In this work, the ferroelectric and semiconducting properties of the organic semiconducting ferroelectric benzotrithiophene tricarboxamide (BTTTA), and especially their nonlinear coupling, are theoretically investigated. BTTTA is an exponent of a small class of semiconducting organic ferroelectrics for which experiments have established a surprising polarization direction dependence of the bulk conductivity at finite fields. First, molecular dynamics (MD) simulations are used to investigate the occurrence and, under the influence of an external electric field, the inversion of the macroscopic electric dipole that forms along the axis of supramolecular columns of BTTTA. The MD results are consistent with the experimentally observed ferroelectric behavior of the material. Building on the MD results, a QM/MM scheme is used to investigate the charge carrier mobility in the quasi-1D BTTTA stacks in the linear and non-linear regimes. Indeed, at finite electric fields, a clear resistance switching effect was observed in the form of a hole mobility that is a factor ∼2 larger for antiparallel orientations of the polarization and field than for a parallel orientation. This phenomenon can be understood as a microscopic ratchet that is based on the non-equilibrium interaction between the (oriented) dipoles and the (direction of the) charge transport.
PubMed: 38940915
DOI: 10.1039/d4cp01632g -
Developmental Dynamics : An Official... Jun 2024Previous studies have claimed that pharyngeal teeth in medaka (Oryzias latipes) are induced independent of retinoic acid (RA) signaling, unlike in zebrafish (Danio...
Differential retinoic acid sensitivity of oral and pharyngeal teeth in medaka (Oryzias latipes) supports the importance of pouch-cleft contacts in pharyngeal tooth initiation.
BACKGROUND
Previous studies have claimed that pharyngeal teeth in medaka (Oryzias latipes) are induced independent of retinoic acid (RA) signaling, unlike in zebrafish (Danio rerio). In zebrafish, pharyngeal tooth formation depends on a proper physical contact between the embryonic endodermal pouch anterior to the site of tooth formation, and the adjacent ectodermal cleft, an RA-dependent process. Here, we test the hypothesis that a proper pouch-cleft contact is required for pharyngeal tooth formation in embryonic medaka, as it is in zebrafish. We used 4-[diethylamino]benzaldehyde (DEAB) to pharmacologically inhibit RA production, and thus pouch-cleft contacts, in experiments strictly controlled in time, and analyzed these using high-resolution imaging.
RESULTS
Pharyngeal teeth in medaka were present only when the corresponding anterior pouch had reached the ectoderm (i.e., a physical pouch-cleft contact established), similar to the situation in zebrafish. Oral teeth were present even when the treatment started approximately 4 days before normal oral tooth appearance.
CONCLUSIONS
RA dependency for pharyngeal tooth formation is not different between zebrafish and medaka. We propose that the differential response to DEAB of oral versus pharyngeal teeth in medaka could be ascribed to the distinct germ layer origin of the epithelia involved in tooth formation in these two regions.
PubMed: 38940489
DOI: 10.1002/dvdy.723 -
Bioinformatics (Oxford, England) Jun 2024Cell-cell interactions (CCIs) consist of cells exchanging signals with themselves and neighboring cells by expressing ligand and receptor molecules and play a key role...
MOTIVATION
Cell-cell interactions (CCIs) consist of cells exchanging signals with themselves and neighboring cells by expressing ligand and receptor molecules and play a key role in cellular development, tissue homeostasis, and other critical biological functions. Since direct measurement of CCIs is challenging, multiple methods have been developed to infer CCIs by quantifying correlations between the gene expression of the ligands and receptors that mediate CCIs, originally from bulk RNA-sequencing data and more recently from single-cell or spatially resolved transcriptomics (SRT) data. SRT has a particular advantage over single-cell approaches, since ligand-receptor correlations can be computed between cells or spots that are physically close in the tissue. However, the transcript counts of individual ligands and receptors in SRT data are generally low, complicating the inference of CCIs from expression correlations.
RESULTS
We introduce Copulacci, a count-based model for inferring CCIs from SRT data. Copulacci uses a Gaussian copula to model dependencies between the expression of ligands and receptors from nearby spatial locations even when the transcript counts are low. On simulated data, Copulacci outperforms existing CCI inference methods based on the standard Spearman and Pearson correlation coefficients. Using several real SRT datasets, we show that Copulacci discovers biologically meaningful ligand-receptor interactions that are lowly expressed and undiscoverable by existing CCI inference methods.
AVAILABILITY AND IMPLEMENTATION
Copulacci is implemented in Python and available at https://github.com/raphael-group/copulacci.
Topics: Transcriptome; Cell Communication; Humans; Gene Expression Profiling; Single-Cell Analysis; Algorithms; Computational Biology; Ligands
PubMed: 38940134
DOI: 10.1093/bioinformatics/btae219 -
Journal of Child & Adolescent Trauma Jun 2024PTSD treatment that focused on a sensory symptoms is increasing. The study aimed to explore symptoms and abnormalities in the five senses exhibited by persons with PTSD...
PTSD treatment that focused on a sensory symptoms is increasing. The study aimed to explore symptoms and abnormalities in the five senses exhibited by persons with PTSD and to examine whether there are any differences depending on type of traumatic experience. Questionnaire was followed by interviews to clinical psychologists involved in the treatment of PTSD. 249 PTSD symptoms exhibited in the sensory organs were collected. Sensory symptoms were classified into three categories according to the type of symptoms and the type of traumatic events. Cluster 1 is a group formed by child abuse and violence together with audition, tactile, and hyperarousal. Cluster 2 is made up of natural disaster, accident, and sexual assault together with vision, olfaction and intrusion. Cluster 3 is made up of multiple traumas together with gustation and dissociation. It is speculated that the survivors of Child abuse and violence are hypersensitive to sounds, the presence of others, and physical contact because they try to quickly sense when a perpetrator is approaching. Natural disasters, accidents, and sexual assault are events with strong smell and severe visual impact, it is possible that they may easily cause reliving of the event in the form of shocking visual images and smells in flashbacks. Dissociation symptoms were related with complex trauma and taste. The mouth is the site of first contact between mother and child, and it is possible that gustatory dissociation may occur mainly in cases of severe and repeated trauma since early childhood.
PubMed: 38938954
DOI: 10.1007/s40653-023-00602-5 -
Journal of Child & Adolescent Trauma Jun 2024Unhoused children and adolescents have high rates of adverse childhood experiences (ACEs). The objective of this study was to characterize a large cohort of unhoused...
Unhoused children and adolescents have high rates of adverse childhood experiences (ACEs). The objective of this study was to characterize a large cohort of unhoused children and investigate rates of psychiatric diagnoses, medical diagnoses, and utilization of emergency department (ED) resources depending on the presence of additional documented ACEs. A retrospective cohort of all unhoused children who presented to the ED of a large Midwestern health system from January 2014 to July 2019 were included. Unhoused status was determined by address field or ICD-10 code for homelessness (Z59.0). Demographics and ED visits were extracted from the electronic health record. Past medical history, ACEs, chief complaint (CC), length of stay (LOS), imaging, and labs were extracted by chart review. T-tests, chi square tests, and Fisher's exact tests were completed for each sub-analysis. Unhoused children with at least one additional ACE had higher odds of the following psychiatric disorders: depression (OR = 5.2, 95% CI = 3.4- 7.9), anxiety (OR = 3.4, 95% CI = 32.1-5.5), behavioral disorder (OR = 7.2, 95% CI = 35.1- 10.4), psychoses (OR = 6.0, 1.9-18.4), bipolar disorder (OR = 19.8, 95% CI = 34.6-84.9), suicidal ideation (OR = 8.0, 95% CI = 34.8-13.4), post-traumatic stress disorder (OR = 10.1, 95% CI = 35.4-18.6), and attention deficit hyperactive disorder (OR = 4.1, 3.0-5.7). Patients with additional documented ACEs were also more likely to have a prior psychiatric admission (p < 0.001). Unhoused children and adolescents with exposure to additional documented ACEs are more likely to have some serious psychiatric and medical diagnoses compared to other unhoused children.
PubMed: 38938936
DOI: 10.1007/s40653-023-00608-z -
Essays in Biochemistry Jun 2024The role of malate dehydrogenase (MDH) in the metabolism of various medically significant protozoan parasites is reviewed. MDH is an NADH-dependent oxidoreductase that...
The role of malate dehydrogenase (MDH) in the metabolism of various medically significant protozoan parasites is reviewed. MDH is an NADH-dependent oxidoreductase that catalyzes interconversion between oxaloacetate and malate, provides metabolic intermediates for both catabolic and anabolic pathways, and can contribute to NAD+/NADH balance in multiple cellular compartments. MDH is present in nearly all organisms; isoforms of MDH from apicomplexans (Plasmodium falciparum, Toxoplasma gondii, Cryptosporidium spp.), trypanosomatids (Trypanosoma brucei, T. cruzi) and anaerobic protozoans (Trichomonas vaginalis, Giardia duodenalis) are presented here. Many parasitic species have complex life cycles and depend on the environment of their hosts for carbon sources and other nutrients. Metabolic plasticity is crucial to parasite transition between host environments; thus, the regulation of metabolic processes is an important area to explore for therapeutic intervention. Common themes in protozoan parasite metabolism include emphasis on glycolytic catabolism, substrate-level phosphorylation, non-traditional uses of common pathways like tricarboxylic acid cycle and adapted or reduced mitochondria-like organelles. We describe the roles of MDH isoforms in these pathways, discuss unusual structural or functional features of these isoforms relevant to activity or drug targeting, and review current studies exploring the therapeutic potential of MDH and related genes. These studies show that MDH activity has important roles in many metabolic pathways, and thus in the metabolic transitions of protozoan parasites needed for success as pathogens.
PubMed: 38938216
DOI: 10.1042/EBC20230075