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PubMed1979

An investigation into the distribution of radial immunodiffusion quality control data.

Quality control data from routine radial immunodiffusion assays for IgG, IgA, IgM, C3, C4 and alpha1-antitrypsin were tested by the Kolmogorov--Smirnov procedure for gaussian distribution. All but alpha1-antitrypsin were nongaussian in type. Further analysis of these date by plotting on log-normal probability paper showed them to have a log-normal distribution. Treatment of the date by either gaussian or nonparametric statistical methods produced little difference in confidence limits. It does not appear necessary to use nonparametric methods to calculate confidence limits from quality control data for the procedures studied.

Complement C3↗

PubMed1977

Binding of synthetic double-stranded DNA by serum from patients with systemic lupus erythematosus: correlation with renal histology.

Detection of antibody to double-stranded DNA by direct binding assays has proved useful in clinical management of patients with systemic lupus erythematosus (SLE). Recent confusion regarding specificity of these antibodies for SLE appears to be due, at least in part, to contamination of natural DNA preparations with nondouble-stranded DNA antigens. Measurement of binding of a synthetic, self-complementary DNA copolymer (dAT) rather than of natural DNA (KB) has been shown to obviate some of these difficulties, apparently because of freedom of dAT from nondouble-stranded DNA antigens. Among the advantages found in this way was a higher degree of specificity of antibodies to double-stranded DNA for clinically-judged active lupus nephritis than had been suspected. Since activity of nephritis is difficult to assess clinically, histologic data were sought to confirm these observations. Thirty-two kidney specimens were examined by light and/or electron microscopy. The degree of histologic activity and the amount and location of glomerular electron-dense deposits were semiquantitated blindly. The binding of both dAT and KB DNA was measured by the ammonium sulfate method. Correlation with the amount of electron-defense deposits was highly significant for dAT binding and somewhat less so for KB DNA binding as determined by both parametric and nonparametric statistical methods. Significant correlation with histologic activity was found for dAT but not KB DNA binding. These results are consistent with previous data and suggest that dAT binding may provide a useful, noninvasive means of clinically assessing both nephritis activity and the intensity of glomerular immune-complex deposition as reflected by the amount of electron-dense deposits. If it can be confirmed that the latter provides long-term prognostic information, then dAT binding (and perhaps its reponse to therapy) may also prove of value in this regard.

Adenosine Monophosphate↗

PubMed1979

National Cooperative Crohn's Disease Study: study design and conduct of the study.

The design and execution of the National Cooperative Crohn's Disease Study are described in this paper. The Study incorporated several noteworthy features developed to meet specific demands of the disease and its therapy. A standard clinical grading system, the Crohn's Disease Activity Index (CDAI) was developed to allow uniform decentralized clinical evaluation and decision-making throughout the 5 yr of the study. All three drugs in widespread clinical use in Crohn's disease were studied both for suppressive and prophylactic efficacy and for toxicity. The study employed a scheme for double-blind evaluation of patient progress which allowed adjustment of prednisone dose according to the degree of illness and ensured continuous monitoring for serious toxicity of any study drug. Results were analyzed primarily by ranking the clinical outcome of every patient according to a uniform and detailed scheme and applying Wilcoxon nonparametric statistics. Outcome was also analyzed by life-table methods. Eleven hundred nineteen patients were entered and 604 patients were randomized at 14 study centers during the 5-yr duration of the study. Twenty patients were eliminated from analysis as not meeting diagnostic criteria for Crohn's disease, and another 15 patients were eliminated as not meeting other preestablished criteria for analysis. Nine percent of randomized patients, equally distributed in the four treatment groups, withdrew as noncompliant. Ninety percent of patients completed all or all but one protocol-specified visits, and 95% completed the final radiologic and sigmoidoscopic evaluation.

Azathioprine↗

PubMed2001

Linkage analysis of a complex pedigree with severe bipolar disorder, using a Markov chain Monte Carlo method.

Recently developed algorithms permit nonparametric linkage analysis of large, complex pedigrees with multiple inbreeding loops. We have used one such algorithm, implemented in the package SimWalk2, to reanalyze previously published genome-screen data from a Costa Rican kindred segregating for severe bipolar disorder. Our results are consistent with previous linkage findings on chromosome 18 and suggest a new locus on chromosome 5 that was not identified using traditional linkage analysis.

Algorithms↗

PubMed2001

Seven regions of the genome show evidence of linkage to type 1 diabetes in a consensus analysis of 767 multiplex families.

Type 1 diabetes (T1D) is a genetically complex disorder of glucose homeostasis that results from the autoimmune destruction of the insulin-secreting cells of the pancreas. Two previous whole-genome scans for linkage to T1D in 187 and 356 families containing affected sib pairs (ASPs) yielded apparently conflicting results, despite partial overlap in the families analyzed. However, each of these studies individually lacked power to detect loci with locus-specific disease prevalence/sib-risk ratios (lambda(s)) <1.4. In the present study, a third genome scan was performed using a new collection of 225 multiplex families with T1D, and the data from all three of these genome scans were merged and analyzed jointly. The combined sample of 831 ASPs, all with both parents genotyped, provided 90% power to detect linkage for loci with lambda(s) = 1.3 at P=7.4x10(-4). Three chromosome regions were identified that showed significant evidence of linkage (P<2.2x10(-5); LOD scores >4), 6p21 (IDDM1), 11p15 (IDDM2), 16q22-q24, and four more that showed suggestive evidence (P<7.4x10(-4), LOD scores > or =2.2), 10p11 (IDDM10), 2q31 (IDDM7, IDDM12, and IDDM13), 6q21 (IDDM15), and 1q42. Exploratory analyses, taking into account the presence of specific high-risk HLA genotypes or affected sibs' ages at disease onset, provided evidence of linkage at several additional sites, including the putative IDDM8 locus on chromosome 6q27. Our results indicate that much of the difficulty in mapping T1D susceptibility genes results from inadequate sample sizes, and the results point to the value of future international collaborations to assemble and analyze much larger data sets for linkage in complex diseases.

Adolescent↗

PubMed1979

Individualizing gentamicin dosage regimens in burn patients with gram-negative septicemia: a cost--benefit analysis.

Services provided by a clinical pharmacokinetics laboratory were evaluated in terms of an accepted cost--benefit model, and a model to evaluate clinical services provided by the pharmacist is presented. A retrospective study was conducted to evaluate the impact, in terms of patient outcomes, of individualizing gentamicin dosage regimens in severely burned patients. Analysis was conducted using multivariate statistical techniques and appropriate nonparametric and parametric tests to determine significant differences. This analysis provided the necessary data to quantify the impact of the pharmacokinetic service. The findings suggest that significant differences do exist in comparing individually dosed patients against those who were not, based upon discriminant and multiple regression analyses and/or nonparametric tests. Furthermore, the results will be useful for insurance companies, third-party payers, and government agencies in deciding which innovative clinical services should be reimbursed.

Burns↗

PubMed2025

Unveiling metabolic pathways in the hyperglycemic bone: bioenergetic and proteomic analysis of the bone tissue exposed to acute and chronic high glucose.

BACKGROUND: Bone fragility due to poor glycemic control is a recognized complication of diabetes, but the mechanisms underlying diabetic bone disease remain poorly understood. Despite the importance of bioenergetics in tissue functionality, the impact of hyperglycemia on bone bioenergetics has not been previously investigated. OBJECTIVE: To determine the effects of high glucose exposure on energy metabolism and structural integrity in bone tissue using an ex vivo organotypic culture model of embryonic chick femur. METHODS: Femora from eleven-day-old Gallus gallus embryos were cultured for eleven days under physiological glucose conditions (5.5 mM, NG), chronic high glucose exposure (25 mM, HG-C), or acute high glucose exposure (25 mM, HG-A). Bioenergetic assessments (Seahorse assays), proteomic analysis (liquid chromatography-mass spectrometry), histomorphometric and microtomographic evaluations, and oxidative stress measurements (carbonyl content assay) were performed. Statistical analyses were conducted using IBM® SPSS® Statistics (v26.0). The Mann-Whitney nonparametric test was used for group comparisons in microtomographic analysis, ALP activity, and carbonyl content assays. For Seahorse assay results, ANOVA with Tukey's post-hoc test was applied after confirming data homoscedasticity with Levene's test. RESULTS: Chronic high glucose exposure reduced bone mineral deposition, altered histomorphometric indices, and suppressed key osteochondral development regulators. Acute high glucose exposure enhanced glycolysis and oxidative phosphorylation, while chronic exposure caused oxygen consumption uncoupling, increased ROS generation, and downregulated mitochondrial proteins critical for bioenergetics. Elevated oxidative stress was confirmed in the chronic high glucose group. CONCLUSION: Chronic high glucose exposure disrupted bone bioenergetics, induced mitochondrial dysfunction, and compromised bone structural integrity, emphasizing the metabolic impact of hyperglycemia in diabetic bone disease.

Animals↗

PubMed2026

An end-to-end computational framework for "Record-seq" transcriptional recording data.

MOTIVATION: Record-seq captures cumulative transcriptional activity over time in engineered Escherichia coli by integrating cellular RNA-derived spacer sequences into clustered regularly interspaced short palindromic repeats (CRISPR) arrays, which are read out by sequencing. Unlike the approximately uniform transcript sampling of RNA-seq, Record-seq records biological signal as spacers sampled by the CRISPR spacer acquisition machinery. Consequently, standard RNA-seq analysis strategies are not directly applicable, limiting sensitivity and interpretability. Our previous pipeline addressed these challenges only partially, retained inherited RNA-seq assumptions, and had limited algorithmic efficiency. RESULTS: Here, we present an end-to-end computational framework for Record-seq data. To address the primary computational bottleneck of spacer sequence extraction, we implemented a wavefront alignment approach for efficient quasi-local pattern matching, achieving an approximately 30-fold speedup. We introduce transcription unit-based feature counting as an alternative to gene-body quantification to better represent prokaryotic transcription and increase statistical power by capturing signal from untranslated regions, which are spacer acquisition hotspots. For downstream analyses, we incorporate multiple normalization strategies and a nonparametric differential expression testing framework designed for sparse datasets. Further, we analyze spacer acquisition patterns and train sequence-based neural models that predict acquisition propensity from genomic sequence and annotations, providing a framework for assessing whether acquisition rules generalize as Record-seq is extended to new microbial hosts. AVAILABILITY AND IMPLEMENTATION: The primary analysis workflow, the recoRdseq package, acquisition modeling repository, and relevant data are all linked at https://github.com/plattlab/Record-seq-Framework. Acquisition models and training data are on Zenodo at https://doi.org/10.5281/zenodo.18891434.

Escherichia coli↗

PubMed2026

From Peaks to Power: Systematic Evaluation of Chromatographic Sampling Reveals Determinants of Quantification and Biological Discovery in DIA Proteomics.

Modern DIA proteomics increasingly emphasizes throughput and depth for large-cohort studies, but methods are often optimized using proxy metrics that can mask losses in quantifiable signal and statistical power. Here, we evaluate how data points per peak and other chromatographic features jointly contribute to quantification and downstream biological discovery. Using a matrix-matched calibration curve dataset, we checked how the number of data points per peak (DPPP) affects the limits of detection and quantification (LOD/LOQ). Reduced DPPP minimally affected LOD but substantially degraded LOQ. Feature modeling and nonparametric association analyses identified precursor peak area as the strongest feature-level predictor of LOQ, whereas DPPP showed weaker and context-dependent effects. Simulations of chromatographic peak integration recapitulated these trends, showing that increased sampling primarily improves integration precision, while quantitative accuracy is strongly governed by peak height and peak shape. Finally, when comparing 20 cancer vs 20 control plasma samples processed with Seer Proteograph, the decrease in DPPP led to a loss of statistical significance for proteins with low-abundance precursors. These findings argue that DIA optimization should prioritize LOQ and statistical power metrics─not identifications alone─by balancing sampling density with chromatographic peak height and quality to maximize useful biological signal.

Proteomics↗

PubMed2026

The Role of Genetic Variation in Phenotypic Variability in Loeys-Dietz Syndrome.

BACKGROUND: Loeys-Dietz syndrome (LDS) is a heritable connective tissue disorder caused by pathogenic variants in genes of the transforming growth factor-β (TGF-β) signaling pathway. Although genotype-phenotype correlations have been suggested, comprehensive comparative data across LDS subtypes remain limited. Improved understanding of these correlations is essential to guide individualized surveillance and management strategies. METHODS: We conducted a retrospective cohort study of adults with genetically confirmed LDS evaluated between 2018 and 2024 across Mayo Clinic sites. Patients with pathogenic, likely pathogenic, or suspicious variants in TGFBR1, TGFBR2, or SMAD3 were included. Clinical characteristics, physical examination findings, cardiovascular and noncardiovascular manifestations, surgical interventions, and mortality were compared across genotypes. Categorical variables were analyzed using chi-square tests and continuous variables using parametric or nonparametric methods as appropriate. RESULTS: A total of 93 patients were included (29 TGFBR1, 33 TGFBR2, 31 SMAD3). Demographics and mortality did not differ significantly between groups. Patients with TGFBR1 and TGFBR2 demonstrated trends toward higher rates of ascending aortic aneurysm and aortic dissection compared with SMAD3 patients, though these differences were not statistically significant. Renal artery aneurysms were significantly more common in TGFBR1 patients (13.8%, p = 0.010). SMAD3 patients had significantly higher rates of mitral regurgitation (54.8%, p = 0.04), peripheral neuropathy (29.0%, p = 0.018), and trends toward increased atrial fibrillation and osteoarthritis. A novel association was identified between TGFBR1 variants and migraine, which was significantly more prevalent in this group (62.1%, p = 0.017). The rates of major cardiovascular surgical interventions were high and comparable across all genotypes. CONCLUSION: Distinct genotype-phenotype associations exist among LDS subtypes. TGFBR1 and TGFBR2 variants are associated with a greater burden of aggressive vascular disease, whereas SMAD3 variants are linked to mitral valve disease, peripheral neuropathy, and osteoarthritis. We also identified a novel association between TGFBR1 genotype and migraine. These findings reinforce the importance of comprehensive genetic testing to inform personalized surveillance and management strategies in LDS.

Humans↗

PubMed2026

Mealtime satisfaction in public nursing homes: Associations with sensory, foodservice, and dining-room environment factors.

Satisfaction with meals is commonly used to assess how meals are experienced in nursing homes (NH), although limited evidence compares breakfast, lunch, and dinner within a unified analytical framework. This study examined the sensory and contextual factors associated with satisfaction across meals in public NH. A cross-sectional observational study was conducted using structured interviews with 290 residents aged ≥60 years (median 85 years; Q1-Q3: 81-88; 63.1% women) from 19 facilities in Galicia, Spain. Overall satisfaction and 12 factors related to sensory attributes of the food, foodservice characteristics, and dining-room environment were assessed using a 5-point Likert scale. Descriptive analyses used medians and quartiles, and group comparisons were performed using nonparametric tests. Three multivariable linear regression models, one per meal, were estimated including all factors simultaneously. In adjusted models, the largest standardized coefficients were observed for taste (lunch: β = 0.366; P < 0.001), food temperature at serving (dinner: β = 0.319; P < 0.001), and menu variety (breakfast: β = 0.301; P < 0.001). Taste, food temperature at serving, menu variety, and meal schedule showed statistically significant coefficients in all models. Overall satisfaction was lower at dinner (29.0% ≥ 4) than at breakfast (34.8%) and lunch (34.5%) (P = 0.003). Selected dining-room environment factors showed significant coefficients in meal-specific models. Mealtime satisfaction was mainly associated with sensory and contextual factors related to how meals are perceived. Lower satisfaction at dinner suggests this mealtime as a relevant context for understanding variations in meal perception in NH residents.

Humans↗