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Direct estimation and inference of higher-level correlations from lower-level measurements with applications in gene-pathway and proteomics studies.

This paper tackles the challenge of estimating correlations between higher-level biological variables (e.g. proteins and gene pathways) when only lower-level measurements are directly observed (e.g. peptides and individual genes). Existing methods typically aggregate lower-level data into higher-level variables and then estimate correlations based on the aggregated data. However, different data aggregation methods can yield varying correlation estimates as they target different higher-level quantities. Our solution is a latent factor model that directly estimates these higher-level correlations from lower-level data without the need for data aggregation. We further introduce a shrinkage estimator to ensure the positive definiteness and improve the accuracy of the estimated correlation matrix. Furthermore, we establish the asymptotic normality of our estimator, enabling efficient computation of P-values for the identification of significant correlations. The effectiveness of our approach is demonstrated through comprehensive simulations and the analysis of proteomics and gene expression datasets. We develop the R package highcor for implementing our method.

Proteomics

[Some new aspects in the study of human cremations (author's transl)].

Thermally induced reactions of bone mineral are outlined. The shrinkage of cremated bones is due to sintering of bone mineral. In an electron microscopic study changes of bone structure caused by thermal treatment and sintered mineral units are described. The problems of estimating the shrinkage factor and the use of cremation weight for identification and discussed. There is a significant difference between mean weights of cremations of senile males and females. The absolute difference indicates, that cremation weight is not a useful criterion for identification. Even in cremated bones, cuts and saw marks can be detected.

Age Factors

Semicircular duct and ampulla dimensions in cat, guinea pig and man.

Predictions from the classic theory of semicircular canal operation, the torsion pendulum model, depend upon labyrinthine dimensions and the physical properties of the endolymph. The dimensions of the semicircular canal, duct and ampulla in cat, guinea pig and man were determined from measurements of magnified sections of decalcified temporal bones. Estimates of the effect of shrinkage were obtained from measures in fresh material and it appears shrinkage is probably only a fairly small factor. The dimensions so obtained were used to provide new estimates of the short time constant and other mechanical parameters of the torsion pendulum model in the three species.

Animals

The molecular compression of dextran.

The suggestion is made that, in solution, the flexible-chain molecules of dextran can undergo an osmotic compression as concentration is increased. Approaches are developed described the molecular shrinkage (i) as arising from intra- and inter-molecular forces, (ii) based on the molecular characteristics of the dextran, and (iii) as estimated by viscosity measurements. Comparison with the macroscopic shrinkage of cross-linked dextran (Sephadex) beads [Edmond, Farquhar, Dunstone & Ogston (1968) Biochem. J. 108, 755-763] is made. In all systems studied, the experimental estimates of compression, both from gel-shrinkage and viscosity measurements were in reasonable agreement with theoretical predictions. The interpretation of the viscosity concentration-dependence was applied to compact structures (albumin and Percoll). Their behaviour was in marked contrast with that of dextran. It is noted that molecular compression may be important in considering transport processes in and thermodynamic properties of concentrated systems.

Biopolymers

Intracellular motility of mitochondria: role of the inner compartment in migration and shape changes of mitochondria in XTH-cells.

Mitochondrial movements have been followed by phase-contrast microscopy in living XTH-cells (Xenopus laevis tadpole-heart cells) in tissue culture. The same organelles have been viewed subsequently in electron micrographs. Locomotion of mitochondria proceeds at velocities up to 100 micrometer/min. Formation of branches of mitochondria and other shape changes may occur with the same speed. Mitochondrial motility can be classified into 4 types: (I) Alternating extension and contraction at the two ends of rod-shaped mitochondria. (2) Lateral branching. (3) Alternate stretching and contraction of arbitrary parts of a mitochondrion amounting to a kind of peristaltic action. (4) Transverse wave propagation along the organelle. Types I to 3 can be reduced to the same underlying principle; they cause locomotion. Formation of mitochondrial extensions is due to elongation of cristae. The observations are discussed in terms of 4 specific proposals. (I) Intracellular locomotion of mitochondria is caused by local enlargements and contractions of the organelles. (2) The shape changes are correlated with alterations in the arrangement of the cristae. (3) Such arrangements are not associated with overall swelling or shrinkage of the mitochondrion; they are local features. (4) Estimates of the time required for rearrangement of the inner compartment amount to less than 0.3 s for single crista arrangements during the fastest shape changes, and less than 1-3 s during slower alterations. This high velocity is in good accord with the hypothesis of energy conservation by conformational events during oxidative phosphorylation.

Animals

The ratio of smooth muscle cell volume to cell surface area measured by electron microscopy with corrections for shrinkage.

The ratio of cell volume to cell surface area (V/A) has been measured by electron microscopy, for smooth muscle cells of the guinea-pig taenia coli. The extent of shrinkage which occurs during processing for electron microscopy has been estimated using Archimedes' principle. The corrected ratio of V/A is 0.8 mum which is lower than previously published estimates for this tissue. The contribution of the surface vesicles to V/A was not included in the present estimate, but the extra surface area contributed by these organelles would lower V/A even more.

Animals

HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data.

High-dimensional mixed-effects models are an increasingly important form of regression in which the number of covariates rivals or exceeds the number of samples, which are collected in groups or clusters. The penalized likelihood approach to fitting these models relies on a coordinate descent algorithm that lacks guarantees of convergence to a global optimum. Here, we empirically study the behavior of this algorithm on simulated and real examples of three types of data that are common in modern biology: transcriptome, genome-wide association, and microbiome data. Our simulations provide new insights into the algorithm's behavior in these settings, and, comparing the performance of two popular penalties, we demonstrate that the smoothly clipped absolute deviation (SCAD) penalty consistently outperforms the least absolute shrinkage and selection operator (LASSO) penalty in terms of both variable selection and estimation accuracy across omics data. To empower researchers in biology and other fields to fit models with the SCAD penalty, we implement the algorithm in a Julia package, HighDimMixedModels.jl.

Algorithms

Contraction stresses of composite resin filling materials.

The polymerization shrinkage of composite resin filling materials and the tensile stresses developed when the shrinkage is restrained were measured in an in vitro experiment. This allows an estimation to be made of the forces exerted upon the enamel walls of cavities filled with the resin in the acid etch technique. The results indicate that the stresses acting on the enamel are low compared to the tensile strength of the enamel.

Composite Resins

Swelling of skinned muscle fibers of the frog. Experimental observations.

Frog skeletal muscle fibers, mechanically skinned under water-saturated silicone oil, swell upon transfer to aqueous relaxing medium (60 mM KCl; 3 mM MgCl(2); 3 mM ATP; 4 mM EGTA; 20 mM Tris maleate; pH = 7.0; ionic strength 0.15 M). Their cross-sectional areas, estimated with an elliptical approximation, increase 2.32-fold (+/-0.54 SD). Sarcomere spacing is unaffected by this swelling. Addition of 200 mM sucrose to relaxing medium had no effect on fiber dimensions, whereas decreasing pH to 5.0 caused fibers to shrink nearly to their original (oil) size. Decreasing MgCl(2) to 0.3 mM caused fibers to swell 10%, and increasing MgCl(2) to 9 mM led to an 8% shrinkage. Increasing ionic strength to 0.29 M with KCl caused a 26% increase in cross-sectional area; decreasing ionic strength to 0.09 M had no effect. Swelling pressure was estimated with long-chain polymers, which are probably excluded from the myofilament lattice. Shrinkage in dextran T10 (number average mol wt 6,200) was transient, indicating that this polymer may penetrate into the fibers. Shrinkage in dextran T40 (number average mol wt 28,000), polyvinylpyrrolidone (PVP) K30 (number average mol wt 40,000) and dextran T70 (number average mol wt 40,300) was not transient, indicating exclusion. Maximal calcium-activated tension is decreased by 21% in PVP solutions and by 31% in dextran T40 solutions. Fibers were shrunk to their original size with 8 x 10(-2) g/cm(3) PVP K30, a concentration which, from osmometric data, corresponds to an osmotic pressure (II/RT) of 10.5 mM. As discussed in the text, we consider this our best estimate of the swelling pressure. We find that increasing ionic strength to 0.39 M with KCl decreases swelling pressure slightly, whereas decreasing ionic strength to 0.09 M has no effect. We feel these data are consistent with the idea that swelling arises from the negatively charged nature of the myofilaments, from either mutual filamentary repulsion or a Donnan-osmotic mechanism.

Animals

Memory disorder in Korsakoff's psychosis: a neuropathological and neuropsychological investigation of two cases.

Neuropathological findings in the brains of two alcoholic patients with Korsakoff's psychosis are reported. Their memory defects had been studied in detail quantitatively over a period of nine years in one case and three years in the other, relevant details of which are presented. Both patients had had a relatively pure long-term memory impairment in the absence of other cognitive deficits and in the absence of a short-term memory impairment. Their retrograde amnesia for public events and famous faces had been measured and found to have extended backwards over at least twenty-five years. There was severe impairment in anterograde recognition memory for both verbal and non-verbal material. On a newly prepared memory quotient battery both patients had scored well below the bottom of the normal scale (less than 60, where 100 is the mean with a standard deviation of +/- 15). Both patients had also shown the characteristic differential improvement in retention when tested by cued recall and also the characteristic 'prior learning effect', i.e. normal retention of one list of words when tested by cued recall but impaired retention of a second list sharing the same cues as the first list. There had been a slight but significant deterioration in intelligence in one of the patients in the two years prior to his death, although his IQ still fell within the normal range. The other patient remained undeteriorated until his death, and his IQ also was close to an estimated measure of his premorbid IQ. In the brains of both patients there was marked gliosis, shrinkage and discolouration bilaterally in the medial nuclei of the mammillary bodies. In addition there was a thin band of gliosis bilaterally between the wall of the third ventricle and the medial dorsal nucleus, the rostral limit lying anterior to the medial dorsal nucleus. In the patient with no intellectual deterioration these were the only pathological changes that were seen. In neither patient was there evident local loss of nerve cells, gliosis or any other qualitative evidence of abnormality in the hippocampi, the white matter of the temporal lobes or the greater part of the medial dorsal nuclei, although it is difficult to be certain whether there was any overlap between the band of gliosis and the most medial region of the medial dorsal nueleus and other adjacent thalamic nuclei. In the other patient there was also a small zone of softening in the cerebellum and an increase in astrocytes in other regions of the cerebral hemispheres, including the basal ganglia, amygdala, and brain-stem, but without noticeable loss of cells. The question of the minimal lesion for the alcoholic Korsakoff amnesic state, and some aspects of the related anatomy, is discussed in the context of other reports in the literature which are, however, difficult to assess in the absence of details of the specificity, severity and character of the memory disorders.

Aged

Postnatal head shrinkage in small infants.

The front-occipital circumference, frontooccipital and biparietal diameters, degree of suture overriding and weight were measured daily during the first week of life in 50 infants of birth weight under 2,000 gm. In a second similar group of 21 infants, fronto-occipital circumference, weight, and sodium balance were measured daily during the first week of life. Head volumes were estimated from the circumference and diameters of the head. The parameters of head size and derived volumes changed maximally and significantly in the direction of intracranial shrinkage around 3 days of age. The degree of shrinkage was significantly correlated (P less than .005) with the degree of weight and cumulative sodium losses, and decreasing gestational age. We postulate that postnatal head shrinkage results from shift of sodium and water outward from the intracranial cavity as a transient phenomenon during the first week of life. The significance of head shrinkage is discussed.

Cephalometry

Diabetic ketoacidosis with retinal tear.

A 59-year-old women with no previous history of diabetes mellitus was admitted in diabetic ketoacidosis. Ultrasonic biometry was used to measure axial vitreous length during therapy. Vitreous length increased from 14.09 mm shortly after admission to 14.26 mm (p less than 0.05) when the episode of diabetic ketoacidosis cleared. An interesting finding was the presence of a horseshoe-shaped retinal tear after the patient was discharged. Severe dehydration with resultant shrinkage of the vitreous compartment may provide sufficient vitreoretinal traction to cause a retinal tear. In addition, an estimate of volume change showed a comparable decrease in vitreous volume seen with therapy using osmotic agents measured in rabbits.

Diabetic Ketoacidosis

Genetic targets related to aging for the treatment of coronary artery disease.

BACKGROUND: Coronary Artery Disease (CAD) is the most common cardiovascular disease worldwide, threatening human health, quality of life and longevity. Aging is a dominant risk factor for CAD. This study aims to investigate the potential mechanisms of aging-related genes and CAD, and to make molecular drug predictions that will contribute to the diagnosis and treatment. METHODS: We downloaded the gene expression profile of circulating leukocytes in CAD patients (GSE12288) from Gene Expression Omnibus database, obtained differentially expressed aging genes through "limma" package and GenaCards database, and tested their biological functions. Further screening of aging related characteristic genes (ARCGs) using least absolute shrinkage and selection operator and random forest, generating nomogram charts and ROC curves for evaluating diagnostic efficacy. Immune cells were estimated by ssGSEA, and then combine ARCGs with immune cells and clinical indicators based on Pearson correlation analysis. Unsupervised cluster analysis was used to construct molecular clusters based on ARCGs and to assess functional characteristics between clusters. The DSigDB database was employed to explore the potential targeted drugs of ARCGs, and the molecular docking was carried out through Autodock Vina. Finally, single-cell data (GSE159677) of arterial intima was used to further explore the expression of aging signature genes in different cell subpopulations. RESULTS: We identified 8 ARCGs associated with CAD, in which HIF1A and FGFR3 were up while NOX4, TCF7L2, HK3, CDK18, TFAP4, and ITPK1 were down in CAD patients. Based on this, CAD patients can be divided into two molecular clusters, among which cluster A mainly involves functional pathways such as ECM receptor interaction and focal adhesion; cluster B mainly involves functional pathways such as amimo sugar and nucleotide sugar metabolism and pyrimidine metabolism. In addition, the molecular docking results showed that retinoic acid and resveratrol had good binding affinity with targets genes. Further single-cell analysis results showed that NOX4, TCF7L2, ITPK1, and HIF1A were specifically expressed in different types of cells in atherosclerotic tissues. CONCLUSION: Our study identified several ARCGs that may be involved in the pathogenesis and progression of CAD. Further, retinoic acid and resveratrol were potential candidate molecule drugs for inhibiting these targets.

Humans

The use of lanthanum to estimate the numbers of extracellular cation-exchanging sites in the guinea-pig's taenia coli, and its effects on transmembrane monovalent ion movements.

1. Tissues were allowed to equilibrate in a Tris-buffered Krebs solution and were then exposed to similar solutions containing up to 5 mM-La. La caused shrinkage and significant losses of tissue K, Na, Mg and Ca. The shrinkage was exactly accountable for by a reduction in the extracellular space (e.c.s.) as measured by [14C]sucrose. No significant change was seen in tissue Cl content. Exposure for 1 hr to 5 mM-La led to a total cation loss of 24-3 +/- 1-6 m-equiv/kg or, correcting for the small change in Cl content, a loss of positive charge of 23-8 +/- 2-2 m-equiv/kg fresh wt. 2. Using the radioisotope 140La it was shown that this loss of cation was balanced by an uptake of La3+. 3. Subtraction of the ions in the measured [14C]sucrose space from the total tissue ion contents led to estimates of the "cellular" ion contents. The effects of 1 hr exposure to 5 mM-La on these were a loss of 12-9 +/- 2-4 m-equiv/kg of cation and a gain of 10-0 +/- 2-6 m-equiv/kg of Cl. 4. Similar changes in ion content were produced by La on "Na-loaded" and "K-loaded" tissues, these being tissues which by exposure to K-free or Na-free (high K) solutions had replaced all their K with Na or vice versa. 5. The uptakes of 24Na and 36Cl by Na-loaded tissues were both describable as the sum of two exponentail processes: a fast component (t 1/2 congruent to 1/2 min), which was presumed to be extracellular and a slower, presumed transmembrane, component. La reduced the rapid component of uptake of 24Na by an amount greater than that predicted by the reduction in the e.c.s., the extra amount lost being some 10--15 m-equiv/kg. La also reduced the amount of rapidly exchanging 36Cl, bwt this reduction was entirely accounted for by the change in the e.c.s. La reduced the rate constant of the slow component of 24Na uptake. 6. La reduced the rapidly exchanging component of 42K uptake by normal tissues by an amount equivalent to about 0-5 m-mole/kg fresh wt. of K in excess of the change in the extracellular space. 7. La had little effect on the effluxes of 36Cl and 42K from normal tissues. However, it reduced the size of the fastest component of exchange of 42K efflux from K-loaded tissues by an amount equal to some 10-15 m-equiv/kg in excess of the reduction in the e.c.s. A similar reduction in the rapidly exchanging component of 24Na efflux from normal tissues was also seen. La slowed the efflux of 24Na from Na-loaded tissues at times when the tracer lost could safely be regarded as intracellular. 8. The taenia coli when exposed to K-free solutions gains Na and loses K. In the presence of La the gain in Na was completely blocked. K was still lost, however, being accompanied by Cl and increased shrinkage. La also prevented the uptake of Na from high Na media by ion-depleted tissues (produced by exposure to sucrose media), while having little effect on the uptake of K from high K media by such tissues. 9 Tedia by such tissues. 9. The cation displaced by La in excess of that lost due to the reduction of the e.c.s...

Animals

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)

Exploring Endoplasmic Reticulum Stress-Related Genes in Cartilage Defects: Implications for Diagnosis and Therapy.

INTRODUCTION: Cartilage defects (CDs) are orthopedic conditions with limited regenerative potential. This study aimed to identify endoplasmic reticulum (ER) stress-related biomarkers and construct a diagnostic model to enhance the early detection of CD. METHODS: This study analyzed the transcriptomic dataset GSE129147 to identify ER stressrelated differentially expressed genes (ERSRDEGs) between CD and control tissues using the limma package (version 3.58.1). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were employed for functional enrichment. Immune infiltration was assessed using cell-type identification, which involved estimating the relative subsets of RNA transcripts and single-sample gene set enrichment analysis. Diagnostic models were constructed using logistic regression, support vector machine, and least absolute shrinkage and selection operator regression. RESULTS: Twenty ERSRDEGs were identified, with CYBB, ATP6V1A, and TNFRSF12A significantly upregulated in CD samples. GO and KEGG analyses highlighted oxidative stress response and extracellular matrix remodeling as key mechanisms in CD pathogenesis. Immune analysis revealed an increase in regulatory T cells and a reduction in CD8. T cells. TNFRSF12A showed strong immune associations and, together with TWIST1 and ATP6V1A, formed the final preliminary diagnostic model. The preliminary LASSO model achieved satisfactory predictive accuracy (AUC: 0.7-0.9). DISCUSSION: These findings suggest that ER stress and immune imbalance jointly contribute to cartilage degeneration. The identified genes, particularly TNFRSF12A, TWIST1, and ATP6V1A, not only serve as potential biomarkers but also provide preliminary evidence for new mechanistic insights into stress-immune crosstalk in CD. CONCLUSION: This study reveals the key roles of ER stress and immune dysregulation in CDs. Moreover, the ERSRDEG-based diagnostic model provides preliminary bioinformatics evidence and potential molecular indicators for targeted diagnostics and therapies.

Humans

Estimation of parenchymal cell content of human parathyroid glands using the image analyzing computer technique.

By means of the image analyzing computer technique, a complete determination of the parenchymal tissue distribution in serially sectioned parathyroid glands were accomplished. The technique had good reproducibility. Taking into account the shrinkage of the different tissue components during histotechnical procedures and the tissue densities, it was possible to calculate the parenchymal cell mass of unfixed glands. The cell distribution varied considerably, and in most glands as many as 10 sections at different levels had to be examined to get a reliable ratio between the parenchymal and fat cell tissue. The results seriously question the validity of histopathologic examination of one or a few sections of parathyroid glands in evaluation of the parenchymal cell mass, as well as diagnoses based on examination of partial glandular biopsy specimens.

Adult

A prediction model for metachronous colorectal cancer: development and validation.

BACKGROUND: Being able to estimate the risk of metachronous disease in a patient with colorectal cancer (CRC) could enable risk-appropriate surveillance. The aim of this study was to develop a risk-prediction model to estimate individual 10-year risk of metachronous disease following a CRC diagnosis. METHODS: A population-based cohort of patients with CRC was recruited soon after diagnosis between 1997 and 2012 from the United States, Canada, and Australia. Cox regression with the least absolute shrinkage and selection operator penalization was used to identify factors that predicted the risk of a new primary CRC diagnosed at least 1 year after the initial CRC diagnosis. Potential predictors included demography, anthropometry, lifestyle factors, comorbidities, personal and family cancer history, medication use, age at diagnosis, and pathological features of the first CRC. Internal validation through bootstrapping was used to evaluate the discrimination and calibration. RESULTS: We included 6085 CRC cases; 138 (2.3%) of these cases were diagnosed with metachronous disease over a median of 12 years (IQR = 5-17 years). Metachronous CRC risk was predicted by body mass index; smoking status; level of physical activity; family history of cancer and synchronous CRC; stage, grade, histological type, and DNA mismatch repair status; and age at diagnosis of the first CRC. The model was valid with a C statistic of 0.65 (95% CI = 0.63 to 0.68) and a calibration slope of 0.873 (SD = 0.087). CONCLUSIONS: Metachronous CRC can be predicted with reasonable accuracy using a prediction model that consists of clinical variables collected as part of routine practice.

Humans