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Comparing ARG Inference Methods Under Transmission of Reproductive Success: Tree Imbalance Matters.

Inferring coalescent trees from genomic data has become a major subject in population genetics, particularly with the recent advances in tree sequence reconstruction methods. However, it remains unclear how well these methods perform for imbalanced genealogies. Such imbalances can arise from processes such as cultural transmission of reproductive success (CTRS) or positive selection. Using simulated genomic data, we benchmarked three major software packages, SINGER, Relate, and tsinfer, by comparing the imbalance of reconstructed trees by these methods with that of the true simulated trees, for three indices that quantify this imbalance. The three methods performed well under scenarios yielding balanced trees. However, their accuracy declined as imbalance increased. Performances also varied with mutation rate, recombination rate, and sample size. This study opens possibilities for applying these methods to infer CTRS or positive selection in large-scale genomic datasets, using simulation-based inference such as approximate Bayesian computation.

Models, Genetic

A novel glutamine metabolism-based classification system for characterizing the heterogeneity of hepatocellular carcinoma.

BACKGROUND: Glutamine dependence is a hallmark of tumor cell metabolism, and further molecular classification based on glutamine metabolism in patients with hepatocellular carcinoma (HCC) may provide clinical value. This study thus comprehensively examined the patterns of HCC-specific alterations in glutamine metabolism. METHODS: Consensus clustering analysis was conducted on samples from The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) dataset based on glutamine metabolism-related genes, which was validated in the GSE76427, the Liver Cancer-France (LICA-FR) cohort, and the Liver Cancer-Japan (LIRI-JP) cohort from the ICGC. Somatic mutation features were evaluated with the Maftools package in R. The activity of oncogenic pathways was estimated via gene set enrichment analysis (GSEA) or single-sample GSEA (ssGSEA). The tumor microenvironment was analyzed using both the CIBERSORT algorithm (for immune cell infiltration estimation) and the ESTIMATE algorithm (for stromal and immune score calculation). Drug sensitivity and immune checkpoint blockade (ICB) response were also analyzed, for which a classifier was built via least absolute shrinkage and selection operator (LASSO). Immunohistochemistry (IHC) was performed to validate the protein expression levels of key differentially expressed genes (DEGs). Intracellular glutamine content under different glutamine concentrations was measured. The viability of HCC cell lines under varying glutamine concentrations was assessed via Cell Counting Kit-8 (CCK-8) assays. Cell migration and invasion were evaluated through Transwell assays, and protein expression was analyzed via Western blotting. RESULTS: HCC samples were classified into two glutamine metabolism-based clusters, with cluster 1 having a more advanced stage of disease and shorter survival than cluster 2. A higher frequency of genetic mutations and stronger activation of oncogenic pathways was found in cluster 1. There were substantial differences in immune cell infiltration and stromal scores between clusters 1 and 2. Cluster 1 exhibited significantly higher infiltration of immunosuppressive cells and lower stromal scores compared to cluster 2. Cluster 1 had a stronger response to ICB due as indicated by a higher tumor mutation burden (TMB) and T cell-inflamed gene expression profile score, immune checkpoints, and Tumor Immune Dysfunction and Exclusion (TIDE)-predicted data. Moreover, the LASSO classifier accurately differentiated the two clusters. The DEGs between the two clusters were validated in clinical samples. IHC confirmed the differential expression of glutamine metabolism-related genes in HCC samples. CCK-8 assays showed no significant effect of glutamine concentration on cell proliferation. However, Transwell assays revealed that glutamine deprivation (0.2 mM) reduced migration and invasion, while high-glutamine conditions (10 mM) promoted them. Western blotting showed increased expression of metabolism-related proteins under high-glutamine conditions and reduced expression under deprivation. CONCLUSIONS: Altogether, these findings indicate the involvement of glutamine metabolism in HCC and may help inform patient stratification and the formulation of precision therapeutics for this population.

Hepatocellular carcinoma (HCC)

Action of feedback regulator on adenylate cyclase.

A factor [the feedback regulator (FR)] formed by adipocytes after the stimulation of a cAMP raising hormone has been found to be a potent inhibitor of membrane-bound adenylate cyclase [EC 4.6.1.1.; ATP pyrophosphate-lyase (cyclizing)]. In a standard assay system using rat adipocyte plasma membrane as the source of adenylate cyclase, the FR inhibited adenylate cyclase by lowering the Vmax without affecting the apparent Km for ATP (0.3-0.6 mM). The apparent Ka for epinephrine (5-6 muM) was also not affected by FR. The inhibitory action of FR was partially countered by Mg2+ ions. An increase in phosphorylation of plasma membrane was observed when FR was present in the incubation system. The concentration required for a 50% inhibition was four times higher when adenosine 5-(beta,gamma-imino) triphosphate [AMP-P(NH)P] replaced ATP as the substrate for adenylate cyclase, implying that adenylate cyclase was inactivated by phosphorylation caused by FR. Increase in FR inhibition obtained by adding low concentrations of adenosine 5-(alpha,beta-methylene) triphosphate or ATP to AMP-(NH)P as the substrate supports this view. The inhibitory action was reversible. These results are consistent with the previously reported phenomena that (1) the undue to the formation of FR, and (2) the recovery of responsiveness of the stimulated cells by washing the cells with regular buffer medium is a result of the removal of FR. The hormone-initiated biphasic curve of cAMP levels in adipocytes is believed to be due to the negative feedback action of FR on adenylate cyclase. The mechanism of action of FR on inhibition of adenylate cyclase appears to be related to the phosphorylation of certain membrane components.

Adenosine Triphosphate

Empirical Meropenem Versus Piperacillin/Tazobactam for Critically Ill Adults With Sepsis: Feasibility of a Randomised Trial.

BACKGROUND: Meropenem and piperacillin/tazobactam are commonly used empirical antibiotics in critically ill adults with sepsis, but whether one is superior to the other is uncertain. METHODS: The Empirical Meropenem versus Piperacillin/Tazobactam for Adult Patients with Sepsis (EMPRESS) trial is an ongoing investigator-initiated, randomised, open-label, adaptive clinical trial with an integrated feasibility phase comparing empirical treatment with meropenem versus piperacillin/tazobactam in critically ill adults with sepsis. The integrated feasibility phase enrolled 200 participants across 10 intensive care units (ICUs) in Denmark between 28 June and 12 December 2025. Five pre-specified feasibility criteria were evaluated; if all feasibility criteria were met, the trial would proceed unaltered, whereas failure to meet one or more criteria would require intervention and re-evaluation. RESULTS: We randomised 200 of 284 screened patients (70.4%). The median age was 70&#x2009;years (interquartile range (IQR): 60-77), 65.5% were males. At randomisation, 80.0% received vasopressors or inotropes, and 43.5% were on invasive mechanical ventilation. Four of five pre-specified feasibility criteria were met: time to completion of the feasibility phase (5.5&#x2009;months vs. threshold <&#x2009;12.0&#x2009;months), recruitment proportion (70.4% vs. threshold &#x2265;&#x2009;50.0%), proportion of participants without consent to the continued collection of data (2.5% vs. threshold <&#x2009;5.0%) and protocol adherence (81.0% vs. threshold &#x2265;&#x2009;75.0%). The proportion of participants with timely primary outcome data availability (30-day mortality) within 45&#x2009;days was 85.5% and below the pre-specified threshold of &#x2265;&#x2009;95.0%. The proportions were low in the first 3&#x2009;months (33.3%, 22.2% and 30.8%, respectively), increasing to 95.8% in the last month of the feasibility phase. All-cause mortality at 30&#x2009;days was 30.5%, and specific serious adverse reactions occurred in 4.0% of participants. CONCLUSIONS: In this integrated feasibility evaluation of the EMPRESS trial comparing empirical meropenem versus piperacillin/tazobactam in critically ill adults with sepsis, four of five pre-specified feasibility criteria were met. The unmet criterion, timely primary outcome data availability, improved substantially during the feasibility phase. We consider the trial feasible and will proceed without modifications. EDITORIAL COMMENT: This feasibility study assessed recruitment, randomised allocation and data collection for the multicentre EMPRESS trial. For adaptive trials on trial platforms, careful interim checking of trial design functions is an important and necessary process. TRIAL REGISTRATION: Clinical Trials Information System EUCT number: 2023-509703-33-00; ClinicalTrials.gov identifier: NCT06184659; Universal Trial Number: U1111-1301-6379.

Humans

Some behavioral effects of morphine, naloxone and nalorphine in the squirrel monkey and the pigeon.

Morphine, naloxone and nalorphine were studied for their effects on the performance of squirrel monkeys and pigeons responding under multiple fixed-interval (FI), fixed-ratio (FR) schedules of food presentation. Morphine generally produced only dose-related decreases in responding in both monkeys and pigeons; monkeys were 10 times more sensitive to morphine than pigeons. The only effect of lower doses of naloxone (0.01-1 mg/kg, monkeys; 1-10 mg/kg, pigeons) was to increase FI responding in some pigeons. Higher doses of naloxone (10-56 mg/kg), produced gross disturbances such as tremors and vomiting and decreased FI and FR responding of both monkeys and pigeons. Nalorphine had strikingly different effects on the behavior of the two species. In the pigeons, nalorphine consistently increased both FI and FR response rates at doses from 0.3 to 10 mg/kg and decreased responding only at doses of 30 to 100 mg/kg. Nalorphine did not increase responding at any dose in the monkeys and the pigeons, nalorphine was only one-tenth as potent as naloxone in antagonizing the effects of morphine on FI and FR responding. Decreasing response rates caused by nalorphine appeared to limit further its usefulness as a morphine antagonist. Antagonism of the rate-decreasing effects of morphine on FI and FR responding occurred over a narrower range of doses with nalorphine than with naloxone, especially in monkeys.

Animals

Mutant of Dictyostelium discoideum defective in cell contact regulation of enzyme expression.

Previous work has shown that aggregation and disaggregation of cells during development of D. discoldeum significantly affects the expression of certain developmentally regulated enzymes. We have examined this cell contact regulation in a previously isolated mutant, Fr-17, and found that during the course of its developmental sequence it becomes specifically defective in this function.

Adenosine

Effects of acetone and toluene vapors on multiple schedule performance of rats.

Six rats were trained to press a lever for a liquid food reward on a multiple fixed ratio--fixed interval (FR--FI) schedule of reinforcement. When lever-pressing rates became relatively stable, the animals were exposed to 150 ppm of either acetone or toluene for duration times of 1/2, 1, 2 and 4 hr. Exposures were conducted at least three weeks apart. Acetone produced minimal changes on the FR--FI responding during the 1/2 hr exposure. During the 1 hr exposure period, both FR and FI rates increased while during the 2 hr exposure, both FR and FI responses decreased below control levels. During the 4 hr exposure FI responses approximated control levels for 2 rats and were above the control level for the third animal while FR rates were below controls for 2 of the 3 subjects. Rate changes under toluene were generally qualitatively similar to those produced by acetone. An initial enhancement of FR and FI rates occurred during the shorter exposure periods followed by a decrease in rates during the longer exposure periods.

Acetone

Capturing gene-cell duality in a cat's cradle.

SUMMARY: CatsCradle is an R package for single-cell analysis that exploits the duality between cells and the genes they express. Our package provides tools to cluster genes, visualize relationships between them, and to explore relationships between gene clusters (programmes) and cell clusters (cell types). AVAILABILITY AND IMPLEMENTATION: CatsCradle is available freely as an R Bioconductor package (https://bioconductor.org/packages/CatsCradle) and interfaces directly with Seurat (Hao et al. 2024) and SingleCellExperiment (Amezquita et al. 2020) data structures.

Software

Hormonal effects on the biosynthesis of sulfated glycoprotein in a microsomal fraction of the endometrium of rabbit uterus.

A crude microsomal fraction (M-Fr) was separated from the endometrial scrapings of uteri of ovariectomized rabbits with or without hormonal treatment. The effects of estrogen and progesterone on the incorporation into M-Fr of L-[U-14C]-fucose and N-acetyl-D-[6-3H]-glucosamine from their nucleotides were investigated. Estrogen increased the incorporation of these sugars, whereas progesterone suppressed this effect. The results of fractionation on a DEAE-Sephadex A-25 (Cl- form) column of the isotope-labelled complex saccharide mixtures, obtained by pronase digestion of the incubation mixtures, indicated that biosynthesis of sulfated glycoprotein was most sensitive to the hormones among the complex saccharides in M-Fr. Thus, a hormonal effects on the biosynthesis of sulfated glycoprotein in the endometrium of ovariectomized rabbit has been unambiguously confirmed at the microsomal level.

Acetylglucosamine

Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease.

We sought to identify new susceptibility loci for Alzheimer's disease through a staged association study (GERAD+) and by testing suggestive loci reported by the Alzheimer's Disease Genetic Consortium (ADGC) in a companion paper. We undertook a combined analysis of four genome-wide association datasets (stage 1) and identified ten newly associated variants with P &#x2264; 1 &#xd7; 10(-5). We tested these variants for association in an independent sample (stage 2). Three SNPs at two loci replicated and showed evidence for association in a further sample (stage 3). Meta-analyses of all data provided compelling evidence that ABCA7 (rs3764650, meta P = 4.5 &#xd7; 10(-17); including ADGC data, meta P = 5.0 &#xd7; 10(-21)) and the MS4A gene cluster (rs610932, meta P = 1.8 &#xd7; 10(-14); including ADGC data, meta P = 1.2 &#xd7; 10(-16)) are new Alzheimer's disease susceptibility loci. We also found independent evidence for association for three loci reported by the ADGC, which, when combined, showed genome-wide significance: CD2AP (GERAD+, P = 8.0 &#xd7; 10(-4); including ADGC data, meta P = 8.6 &#xd7; 10(-9)), CD33 (GERAD+, P = 2.2 &#xd7; 10(-4); including ADGC data, meta P = 1.6 &#xd7; 10(-9)) and EPHA1 (GERAD+, P = 3.4 &#xd7; 10(-4); including ADGC data, meta P = 6.0 &#xd7; 10(-10)).

ATP-Binding Cassette Transporters

Operant behavioural and neurochemical effects after neonatal 6-hydroxydopamine treatment.

Newborn rats were treated at 1 and 2 days after birth with 100 mg/kg 6-hydroxydopamine (60HDA), s.c. Testing on several operant behavioural tasks was begun at 6 months of age. On a fixed ratio 30 (FR 30) schedule of food reinforcement, the neonatal 60HDA treated rats responded at a significantly higher rate. Further analysis of the FR 30 response pattern indicated that the higher rate was due to a decrease in the amount of time spent pausing after the receipt of each reinforcer. The 60HDA treatment failed to alter the rat's behaviour during the extinction of the FR 30 response and on the progressive ratio or variable interval schedules of food reinforcement. Biochemical analysis of several brain areas at 9 months of age showed a decrease in noradrenaline (NA) levels in the cerebral cortex and hippocampus, while in the pons-medulla NA content was doubled. The tyrosine hydroxylase activity in these same brain areas was not significantly altered, but there appeared to be some decrease in the activity of this enzyme in the hippocampus. Comparison of the operant behavioural effects seen after various lesioning procedures in this and other studies, suggest the effects on FR performance are a result of destruction of NA neurons in the hippocampus and/or the apparent regeneration of neurons in the pons-medulla.

Animals

Measurement of postoperative cardiac output by thermodilution in pediatric and adult patients.

Serial cardiac output determinations were made by the thermodilution technique in 51 patients by means of a No. 2 Fr. thermistor catheter placed directly into the pulmonary artery at cardiac operation. Correlations were determined prospectively between thermodilution measurements of cardiac output and other commonly used indirect clinical parameters. Serial indicator dye-dilution curves were performed in 24 of these patients and compared with simultaneous thermodilution measurements. A high correlation (r = 0.97) was noted between dye curve measurements of cardiac output and thermal measurements. Statistically significant correlations were also seen between cardiac output and both the quality of the peripheral pulses and the duration of cardiopulmonary bypass, but no significant correlations were found between the measured cardiac outputs and other variables. This study confirms the necessity for direct measurement of cardiac output for its accurate assessment.

Adolescent

National gonorrhea therapy monitoring study: in vitro antibiotic susceptibility and its correlation with treatment results.

To monitor temporal trends and regional differences in antibiotic susceptibility, we measured the minimum inhibitory concentrations for penicillin G, ampicillin, tetracycline, and spectinomycin of 4405 pre-treatment gonococcal isolates from patients with uncomplicated gonorrhea. As compared to isolates studied in 1970-1971, recent United States isolates appeared equally sensitive to penicillin G and more sensitive to tetracycline. Relatively resistant strains were found throughout the country. We also studied 1974 patients, treated for uncomplicated gonorrhea according to the 1972 regimens recommended by the United States Public Health Service, to determine the relation between pretreatment minimum inhibitory concentrations and treatment results. For patients receiving the procaine penicillin-probenecid and ampicillin-probenecid regimens, minimum inhibitory concentrations to the treatment drugs were significantly higher in patients not cured than in those cured (P less than 0.01 fr penicillin and P less than 0.05 for ampicillin). In contrast, spectinomycin-treatment results appeared to be independent of the isolate's susceptibility to spectinomycin and other antibiotics.

Ampicillin

Voiding cystourethrography in infants and children: a new technique.

A technique for voiding cystourethrography utilizing a small caliber (3.5 Fr.) catheter that is left in place during the entire examination is described and illustrated. Urethral pathology is not obscured. The contrast is infused under pressure applied with a blood administration set. Visualization of voiding can be achieved in all cases.

Child

Abnormal ClC-3/TMEM9-mediated endosomal ion transport in CLCN3-associated neurodevelopmental disease.

Endolysosomal abnormalities are particularly detrimental to the nervous system and have been implicated in neuropsychiatric disorders. Key regulators of the lysosomal and endosomal luminal ion homeostasis are CLC chloride/proton exchangers. We report 15 individuals carrying variants in CLCN3, encoding a ubiquitous endosomal 2Cl-/H+ exchanger, and provide updated clinical information for 5 previously reported individuals. Subjects displayed a broad spectrum of neuropsychiatric symptoms, including developmental delay, intellectual disability, and epilepsy. To reveal the pathogenic mechanism, we investigated ClC-3 variants-mediated ion transport and its regulation by the recently discovered inhibitory beta subunit TMEM9. 12/20 missense variants exhibited altered properties and fell into two classes: those affecting the region binding inhibitory TMEM9 carboxy-termini, and those that broaden the voltage range over which ClC-3 conducts ions. Surprisingly, the latter variants also attenuated TMEM9-mediated inhibition. Both classes produced a toxic gain-of-function, as evident from endolysosomal vacuolization by mutant ClC-3/TMEM9 overexpression. Our results expand the genetic and clinical spectrum of CLCN3-related disease, provide a solid basis for genetic counseling, and uncover an unexpected link between gating-associated conformational changes and inhibition by TMEM9.

Chloride Channels

Artificial intelligence-based tumour infiltrating lymphocyte quantification in patients with triple-negative breast cancer: an independent validation study.

BACKGROUND: Tumour-infiltrating lymphocytes (TILs) are a robust prognostic marker in patients with triple-negative breast cancer. Artificial intelligence (AI)-derived computational tools assessing TILs could improve efficiency, but require independent validation against clinical outcomes. We aimed to compare the prognostic performance of AI-derived TIL scores with pathologist-scored TILs in a large, prospectively collected dataset pooled from randomised controlled trials. METHODS: CATALINA was an independent, external validation study using prospectively collected long-term clinical outcome data pooled from seven randomised clinical trials conducted at multiple sites. We independently evaluated two previously validated AI pipelines that generate five computationally assessed tumour-infiltrating lymphocyte (cTIL) scores by masked, independent deployment of locked models. cTIL scores were correlated with the mean of the pathologist-scored stromal TILs (sTILs) in 220 digitised haematoxylin and eosin whole slide images in a cohort of patients with early-stage triple-negative or HER-2 positive breast cancer, previously scored by trained pathologists in a TIL-reproducibility study. Prognostic performance was assessed in a separate cohort of patients with early triple-negative breast cancer pooled from seven prospective, randomised adjuvant trials. Multivariable Cox regression models adjusted for clinicopathological factors and study heterogeneity assessed associations of cTIL score and sTIL score with invasive disease-free survival, distant disease-free survival, and overall survival. 5-year discrimination was estimated using time-dependent area under the receiver operating characteristic curve (AUC). FINDINGS: Individual data were collated from 1759 patients, of whom 1356 had complete clinicopathological data, pathologist sTIL scores, and cTIL scores available. Modest correlation (r 0&#xb7;375-0&#xb7;473) was observed between cTIL scores and the mean pathologist sTIL score. Both sTIL and cTIL were independently associated with 5-year invasive disease-free survival, distant disease-free survival, and overall survival after adjustment for clinicopathological factors (hazard ratio for invasive disease-free survival was 0&#xb7;73 [95% CI 0&#xb7;66-0&#xb7;82]; q<0&#xb7;0001, distant disease-free survival was 0&#xb7;70 [0&#xb7;61-0&#xb7;79]; q<0&#xb7;0001, and overall survival was 0&#xb7;72 [0&#xb7;63-0&#xb7;82]; q<0&#xb7;0001 for sTIL scores and 0&#xb7;80 [0&#xb7;73-0&#xb7;89]; q<0&#xb7;0001, 0&#xb7;77 [0&#xb7;69-0&#xb7;86]; q<0&#xb7;0001, and 0&#xb7;79 [0&#xb7;70-0&#xb7;88]; q=0&#xb7;0002, respectively, for percentage_lymphocyte scores). In models adjusted for clinicopathological variables and sTIL score, cTIL score did not maintain a statistically significant prognostic association. Both sTIL and cTIL scores improved the 5-year AUC over clinicopathological variables alone, while cTIL score did not significantly further improve AUC when combined with clinicopathological variables and sTIL score. INTERPRETATION: Two cTIL models deployed entirely without retraining or modification provided statistically significant prognostic information and improved risk discrimination compared with clinicopathological variables alone in this large, platform-based, independent validation study. Although cTIL score did not incrementally improve prognostication compared with models combining clinicopathological variables with sTIL score, these findings support the application of cTILs as a reproducible prognostic biomarker, particularly in settings where routine or widespread pathologist assessment is unavailable. FUNDING: Breast Cancer Research Foundation (USA).

Humans