gebhart/patrepeval huggingface dataset:
Robust metabolomic age prediction based on a wide selection of metabolites (2023)

Abstract Chronological age is a major risk factor for numerous diseases. However, chronological age does not capture the complex biological aging process. Biological aging can occur at a different pace in individuals of the same chronological age. Therefore, the difference between the chronological age and biologically driven aging could be more informative in reflecting health status. Metabolite levels are thought to reflect the integrated effects of both genetic and environmental factors on the rate of aging, and may thus provide a stronger signature for biological age than those previously developed using methylation and proteomics. Here, we set out to develop a metabolomic age prediction model by applying ridge regression and bootstrapping with 826 metabolites (of which 678 endogenous and 148 xenobiotics) measured by an untargeted high-performance liquid chromatography mass spectrometry platform (Metabolon) in 11,977 individuals (50.2% men) from the INTERVAL study (Cambridge, UK). Participants of the INTERVAL study are relatively healthy blood donors aged 18-75 years. After internal validation using bootstrapping, the models demonstrated high performance with an adjusted R 2 of 0.82 using the endogenous metabolites only and an adjusted R 2 of 0.83 when using the full set of 826 metabolites with age as outcome. The latter model performance could be indicative of xenobiotics predicting frailty. In summary, we developed robust models for predicting metabolomic age in a large relatively healthy population with a wide age range.
A phase 2 trial of combination low-dose thalidomide and prednisone for the treatment of myelofibrosis with myeloid metaplasia (2003)

Single-agent thalidomide (THAL) at "conventional" doses (> 100 mg/d) has been evaluated in myelofibrosis with myeloid metaplasia (MMM) based on its antiangiogenic properties and the prominent neoangiogenesis that occurs in MMM. THAL monotherapy at such doses produces approximately a 20% response rate in anemia but is poorly tolerated (an adverse dropout rate of > 50% in 3 months). To improve efficacy and tolerability, we prospectively treated 21 symptomatic patients (hemoglobin level < 10 g/dL or symptomatic splenomegaly) with MMM with low-dose THAL (50 mg/d) along with a 3-month oral prednisone (PRED) taper (beginning at 0.5 mg/kg/d). THAL-PRED was well tolerated in all enrolled patients, with 20 patients (95%) able to complete 3 months of treatment. An objective clinical response was demonstrated in 13 (62%) patients, all improvements in anemia. Among 10 patients who were dependent on erythrocyte transfusions, 7 (70%) improved and 4 (40%) became transfusion independent. Among 8 patients with thrombocytopenia (platelet count < 100 x 10(9)/L), 6 (75%) experienced a 50% or higher increase in their platelet count. In 4 of 21 patients (19%), spleen size decreased by more than 50%. Responses observed were mostly durable after discontinuation of the PRED. The dose of THAL in this study (50 mg/d) was better tolerated than the higher doses used in previous studies. Adverse events associated with corticosteroid therapy were mild and transient. Clinical responses did not correlate with improvements in either intramedullary fibrosis or angiogenesis. THAL-PRED is well tolerated and preliminarily appears to be a promising drug regimen for treating cytopenias in patients with MMM.
Characterization of CCW7 cell wall protein of film-forming Saccharomyces cerevisiae wine yeast strains at gene and protein level (2007)

Aging of Hungarian botrytized wine Tokaji szamorodni results aromatic compounds produced as by-products of the oxidative metabolism of yeasts taht are forming a biofilm at the surface of wines. Film-forming strains show a planktonic growth during the main fermentation phase but the cells rise to the surface afetrward and form a multylayerd biofilm on it. The cells metabolize mainly ethanol and glycerol during maturation and produce caracteristic aromatic compounds like acetaldehyde. However, the mechanism of attachment and the role of cell surface moleculs in film formationare not clarified at all. Our aim was to determine the possible role of certain cell wall proteins in film formation, therefore we looked for differences in the cell wall proteins of sedimenting and film-forming Saccharomyces cerevisiae strains. We found different protein patterns among alkali extractable cell wall proteins of laboratory and film-forming Saccharomyces cerevisiae strins. In the case of film-forming strains a smaller ccw7 protein was observed and isolated. For further investigation we designed a specific primer pair for the amplification of the Ccw7p encoding gene HSP150. PCR amplification of the gene confirmed the size difference between the ccw7 proteins of the laboreatory and film-forming strains. Almost all the film-forming isolates generated a single PCR product of the same size but two of them contained additional amplicons, a shorter or a longer one. Sequence analysis of the amplified common PCR products of film-forming yeasts revealed two deletions in the internal repetitive region of the gene. In the case of TDO4 strain that has an additional longer PCR amplicon we induced meiotic segregation aiming to check whether there is any correlation between the film forming ability and the CCW7 alleles. The alleles segregated during meiosis, however, both types of the segregants maintained the film forming ability. CCW7 amplicons of different lenghts. By the use of RFLP analysis of the CCW7 amplicons we found that majority of film forming yeasts formed a separate cluster of 100% similarity, while sedimenting wine yeast strains showed an extended length polymorphism.
UCSC cancer genomics browser. (2009)

Abstract Abstract #2022 As experimental techniques for a comprehensive survey of the cancer landscape mature, there is a great demand in the cancer research field to develop advanced analysis and visualization tools for the characterization and integrative analysis of the large, complex genomic datasets arising from different technology platforms.&amp;#x2028; The UCSC Cancer Genomics Browser is a suite of web-based tools designed to integrate, visualize and analyze genomic and clinical data. The secured-access browser, available at https://cancer.cse.ucsc.edu/, consists of three major components: hgHeatmap, hgFeatureSorter, and hgPathSorter. The main panel, hgHeatmap, displays a whole-genome-oriented view of genome-wide experimental measurements for individual and sets of samples/patients alongside their clinical information. hgFeatureSorter and hgPathSorter together enable investigators to order, filter, aggregate and display data interactively based on any given feature set ranging from clinical features to annotated biological pathways to user-edited collections of genes. Standard and advanced statistical tools are available to provide quantitative analysis of whole genomic data or any of its subsets. The UCSC Cancer Genomics Browser is an extension of the UCSC Genome Browser; thus it inherits and integrates the Genome Browser's existing rich set of human biology and genetics data to enhance the interpretability of cancer genomics data.&amp;#x2028; We demonstrate the UCSC Cancer Genomics Browser by integrating several independent studies on breast cancer including the I-SPY chemotherapy clinical trial and other studies focused on chemotherapeutic response or long-term survival. The types of data that are visualized and analyzed by the browser include microarray measurements of gene expression, copy number variation and phosphoprotein expression, MRI imaging measurements, and clinical parameters.&amp;#x2028; Collectively, these tools facilitate a synergistic interaction among clinicians, experimental biologists, and bioinformaticians. They enable cancer researchers to better explore the breadth and depth of the cancer genomics data resources, and to further characterize molecular pathways that influence cellular dynamics and stability in cancer. Ultimately, insights gained by applying these tools may advance our knowledge of human cancer biology and stimulate the discovery of new prognostic and diagnostic markers, as well as the development of therapeutic and prevention strategies.&amp;#x2028; Funding sources: CALGB CA31964 and CA33601, ACRIN U01 CA079778 and CA080098, NCI SPORE CA58207, California Institute for Quantitative Biosciences, NHGRI. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2022.
Ice-Affected Components of Locks and Dams (2002)

Abstract : Ice plagues the operation and maintenance of many U.S. Army Corps of Engineers locks and dams. Because these structures vary greatly in age, geographical setting, and design, their performance in ice also varies. This report describes the ice problems related to specific project components such as the lock approaches, miter gates, lock walls, and dam spillway gates. Post-construction solutions such as high-flow bubblers and heat deicing methods are also described. The report provides a one-source overview of the important ice problems faced by operators of Corps projects, available ice management solutions, and areas where improvements are most needed.
UV-induced photoproducts of para-aminobenzoid acid. (1985)

Cis- and trans- 4,4'-azodibenzoic acid (AZBA), two photoproducts of para-aminobenzoic acid (PABA), formed by the action of 313 nm light, have been characterized on the basis of UV and mass spectral data. The relative dose of UV light required for azodibenzoic acid formation is comparable to that obtained from a day of sunbathing. The same type of photochemical reaction could lead to the formation of PABA-protein conjugates. These photoproducts may be responsible for the known photosensitizing properties of PABA and perhaps its cytotoxic and mutagenic effects.
Removing rRNA from Deproteinized, Phenol-Extracted Total RNA by Enzymatic Digestion (2012)

Ribosomal RNAs (28S, 18S, 5.8S, and 5S rRNAs) comprise the vast majority of total cellular RNAs (>95%). When other RNAs are to be analyzed, it is very advantageous to remove the rRNA species. The best way to eliminate rRNA "contamination" is to pellet subunits before deproteinization. When this is not possible, certain RNAs can be separated from bulk rRNA after extraction. This protocol describes enzymatic digestion to remove rRNAs from deproteinized, phenol-extracted total RNA.
The Socioeconomic Impact Of AIDS On Health Care Systems (1987)

UpDate is a section that will report developments in health policy issues and scheduled conferences of relevance to the field. In this issue we offer a summary of a Project HOPE conference on acquired immunodeficiency syndrome (AIDS) and its socioeconomic impact on health systems worldwide. Also in this issue is a survey of funding for research on the Medicare prospective payment system by a group from Abt Associates, Inc.
The activities of ‘Pz-peptidase’ and ‘endopeptidase 24.15’ are due to a single enzyme (1989)

It was found that Pz-peptidase (assayed with 2,4-dinitrophenyl-Pro-Leu-Gly-Pro-Trp-D-Lys) and endopeptidase 24.15 (assayed with benzoyl-Gly-Ala-Ala-Phe-p-aminobenzoate) were co-purified from rat skeletal muscle, were co-eluted in high-resolution gel chromatography and co-existed in a homogeneous preparation of rat testis endopeptidase 24.15. The action of partially purified Pz-peptidase from rat testis on 4-phenylazobenzyloxycarbonyl-Pro-Leu-Gly-Pro-D-Arg was blocked by an inhibitor of endopeptidase 24.15, and also by a substrate of this enzyme. The partially purified enzyme hydrolysed two substrates of endopeptidase 24.15 with Km values similar to those published previously, and its action on 2,4-dinitrophenyl-Pro-Leu-Gly-Pro-Trp-D-Lys was inhibited by compounds that are considered specific for endopeptidase 24.15. We conclude that the activities previously attributed to two distinct enzymes are due to only one, and that the merging of the two literatures may lead to new lines of research.
Antagonizing and Measurement (1992)

Journal of Cardiovascular Pharmacology™ is a peer reviewed, multidisciplinary journal that publishes original articles and pertinent review articles on basic and clinical aspects of cardiovascular pharmacology. Appropriate subjects include new drug development and evaluation, physiological and pharmacological bases of drug action, metabolism, drug interactions and side effects, clinical results with new and established agents and novel methods. The focus is on pharmacology in its broadest applications, incorporating not only traditional approaches, but new approaches to the development of pharmacological agents and the prevention and treatment of cardiovascular diseases.
The Role of the Sympathetic Nervous System in Lipid Deposition. I. Increased Lipid Deposits in the Iris of the Sympathectomized Eye in Rabbits Fed an Atherogenic Diet (1971)

Rabbits on a high-cholesterol diet deposit more lipid in the iris of the sympathectomized eye. Histologically, the lipid deposits are composed of sudanophilic staining droplets localized both in smooth muscle cell cytoplasm of the iris dilator muscle and in larger oval cells. Possible metabolic and vascular mechanisms are noted which may underlie these findings. Potential clinical implications of these findings are cited.
Complex cells and Object Recognition (1997)

Nearest-neighbor correlation-based similarity computation in the space of outputs of complex-type receptive fields can support robust recognition of 3D objects. Our experiments with four collections of objects resulted in mean recognition rates between 84% (for subordinate-level discrimination among 15 quadruped animal shapes) and 94% (for basic-level recognition of 20 everyday objects), over a 40deg X 40deg range of viewpoints, centered on a stored canonical view and related to it by rotations in depth (comparable figures were obtained for image-plane translations). This result has interesting implications for the design of a front end to an artificial object recognition system, and for the understanding of the faculty of object recognition in primate vision.
Improving Microcirculation is More Effective Than Substitution of Red Blood Cells to Correct Metabolic Disorder in Experimental Hemorrhagic Shock (2004)

Microcirculatory perfusion deficits and impaired tissue oxygenation in nonvital organs frequently occur after hemorrhage and they contribute to potentially lethal complications. The aim of this study was to test the influence of colloid osmotic pressure, viscosity, and red blood cell (RBC) content of the resuscitative fluid on metabolic disorder, perfusion, and oxygenation in peripheral tissues. Awake hamsters were subjected to hemorrhage of 50% and were resuscitated with 25% of blood volume with solutions containing 6% pegylated bovine albumin only (PEG-BSA 0) and 6% PEG-BSA mixed with autologous RBCs to reach 4 g/dL (PEG-BSA 4) and 8 g/dL (PEG-BSA 8) of hemoglobin. PEG-BSA had a viscosity of 4.2 cP and a COP of 116 mmHg. Microhemodynamics and tissue pO2 were assessed in the hamster chamber window preparation with intravital microscopy. Arterial base excess tended to be lower than baseline for PEG-BSA 0 and PEG-BSA 4 (ns), whereas base deficit remained significantly decreased for PEG-BSA 8 (P<0.05 vs. baseline). Oxygen extraction was 91% +/- 2% of the oxygen delivery for PEG-BSA 0 compared with 85% +/- 2% for PEG-BSA 8 (P<0.05). Functional capillary density was 61%, 47%, and 45% for PEG-BSA 0 (P<0.05 vs. other groups), PEG-BSA 4 and PEG-BSA 8, respectively. We conclude that arterial base excess and oxygen extraction ratio in the tissue was better restored if a higher fraction of PEG-BSA and less RBCs were infused. This was attributed to a more homogeneous distribution of oxygen, as reflected by functional capillary density. Our results suggest that the transfusion trigger in hemorrhagic shock may be shifted toward lower hemoglobin concentrations if highly viscous and oncotic solutions are used.
Inelastic electron scattering by collective charge-density excitations at the surface of a semiconductor superlattice (1985)

We have studied the oscillator strength of the lowest 1s heavy excitons in GaAs-AlAs quantum wells as a function of well-layer thickness by means of optical absorption. The oscillator strength of the lowest 1s heavy excitons is largely enhanced with the decrease of well-layer thickness. The result is the first full experimental observation of two-dimensional shrinkage of the exciton wave function in quantum wells.
Analysis and Gate Driver Design Considerations of 10 kV SiC MOSFETs under Flashover Fault due to Insulation Failure (2020)

The behavior of 10 kV SiC MOSFETs during a flashover fault condition is investigated comprehensively. A larger turn-off gate resistance R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g,off</sub> is recommended for 10 kV SiC MOSFETs without Kelvin source to avoid very asymmetrical gate resistance, while a small R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g,off</sub> is recommended for 10 kV SiC MOSFETs with Kelvin source. Guidelines regarding gate loop inductance and selecting an external capacitor across gate and source terminal are also provided. 10 kV SiC MOSFETs have much higher energy loss under flashover fault compared to typical short circuit faults. The required response time for short circuit protection to safely clear flashover fault should be at least 350 ns shorter than the response time designed to clear conventional short circuit faults.
GREEN SYNTHESIS OF CALCIUM AND PHOSPHATE COMPOUNDS BY VARYING pH VALUE AND Ca/P ATOMIC RATIO USING AQUEOUS PRECIPITATIONS (2013)

Using an aqueous synthesis with varying pH values and changing ion source of calcium-to-phosphorus atomic ratios to clarify precipitations was the purpose of this study. The precipitation procedures were processed in two ways; firstly, a pH range of 3.0 to 12.0 was controlled while the ion source of relative Ca/P ratio was kept at 2.0. Secondly, the reaction was kept alkaline with a pH of 12.0 and the value range of Ca/P ratios in the precursor ion-solutions was 1.0 to 3.0. The physicochemical properties were measured to characterize the various precipitates. Results showed that when the pH was varied, the morphology of the precipitates gradually changed to micrometer column-like shape under acidic condition and nano-scale globular-like shape in alkaline environments. By controlling the pH and Ca/P ratio of ion-sources in aqueous reactions, precipitates in biphasics of calcium carbonate/apatite and calcium hydroxide/apatite were obtained with nanometer-scale morphologies. The precipitation procedures that are used in the synthesis of the biphasics provide a simpler, safer, less expensive and more environmentally friendly than the co-precipitation by sintering processes.
The surface acoustic wave propagation characteristics of 41° lithium niobate with thin-film SiO/sub 2/ (2002)

The surface acoustic wave (SAW) propagation properties of 41/spl deg/ Y-X lithium niobate (LiNbO/sub 3/) with SiO/sub 2/ film layers have been investigated using interdigital transducer structures. Different thicknesses of SiO/sub 2/ from 500 nm to 1500 nm were deposited on the 41/spl deg/ LiNbO/sub 3/ by RF diode sputtering from a glass target. An arrayed transducer pattern of aluminum interdigital transducer electrodes on the upper SiO/sub 2/ film surface facilitated the excitation of a wide frequency band of harmonic waves and permitted delineation of SAW velocity and propagation loss characteristics for several values of film-thickness to acoustic-wavelength (t//spl lambda/) ratio. With resonator patterns at the substrate/film interface, the capacitance ratio (C/sub m//C/sub 0/), related to coupling factor, and the temperature coefficient of frequency (TCF) were determined.
Gratuitous Catabolite Repression by Glucosamine of Maltose Utilization in Saccharomyces cerevisiae (1980)

Glucosamine acted as a gratuitous catabolite repressor of maltose utilization in Saccharomyces cerevisiae. This repression was relieved in a linear manner as the maltose concentration was increased. Three mutants were isolated in which maltose utilization was no longer repressed by glucosamine. One of these mutants may be generally deficient in catabolite repression since it was not defective in glucosamine transport but was insensitive to glucosamine repression on all catabolite repressible carbon sources tested. Each mutant possessed a maltose uptake system which was notably less sensitive to glucose repression than that of the wild-type strain. These results are discussed in terms of a proposed model for regulation of maltose utilization in S. cerevisiae.
Enhanced Luminescence of MoS2, WS2 and WSe2, Direct Band Gap Semiconductor Heterostructures (2018)

We introduce van der Waals heterostructures to amplify the otherwise negligible cathodoluminescence from monolayer transition metal dichalcogenides, which allowed to visualize the nanoscale variation of strain and photonic modes in the monolayer on engineered surfaces.
A respiratory self‐gating technique with 3D‐translation compensation for free‐breathing whole‐heart coronary MRA (2009)

Respiratory motion remains a major challenge for robust coronary MR angiography (MRA). Diaphragmatic navigator (NAV) suffers from indirect measurement of heart position. Respiratory self-gating (RSG) approaches improve motion detection only in the head-feet direction, leaving motion in the other two dimensions unaccounted for. The purpose of this study was to extend conventional RSG (1D RSG) to RSG capable of 3D motion detection (3D RSG) by acquiring additional RSG projections with transverse-motion-encoding gradients. Simulation and volunteer studies were conducted to validate the effectiveness of this new method. Preliminary comparison was performed between coronary artery images reconstructed from the same datasets using different motion correction methods. Our simulation illustrates that a proper motion-encoding gradient and derivation method enable accurate 3D motion detection. Results from whole-heart coronary MRA show that 3D RSG can further reduce motion artifacts as compared to NAV and 1D RSG and enables use of larger gating windows for faster coronary imaging.
Human and mouse homologs of Escherichia coli DinB (DNA polymerase IV), members of the UmuC/DinB superfamily (1999)

To understand the mechanisms underlying mutagenesis in eukaryotes better, we have cloned mouse and human homologs of the Escherichia coli dinB gene. E. coli dinB encodes DNA polymerase IV and greatly increases spontaneous mutations when overexpressed. The mouse and human DinB1 amino acid sequences share significant identity with E. coli DinB, including distinct motifs implicated in catalysis, suggesting conservation of the polymerase function. These proteins are members of a large superfamily of DNA damage-bypass replication proteins, including the E. coli proteins UmuC and DinB and the Saccharomyces cerevisiae proteins Rev1 and Rad30. In a phylogenetic tree, the mouse and human DinB1 proteins specifically group with E. coli DinB, suggesting a mitochondrial origin for these genes. The human DINB1 gene is localized to chromosome 5q13 and is widely expressed.