gebhart/patrepeval huggingface dataset:
Resistance of Dynamin-related Protein 1 Oligomers to Disassembly Impairs Mitophagy, Resulting in Myocardial Inflammation and Heart Failure (2015)

We have reported previously that a missense mutation in the mitochondrial fission gene Dynamin-related protein 1 (Drp1) underlies the Python mouse model of monogenic dilated cardiomyopathy. The aim of this study was to investigate the consequences of the C452F mutation on Drp1 protein function and to define the cellular sequelae leading to heart failure in the Python monogenic dilated cardiomyopathy model. We found that the C452F mutation increased Drp1 GTPase activity. The mutation also conferred resistance to oligomer disassembly by guanine nucleotides and high ionic strength solutions. In a mouse embryonic fibroblast model, Drp1 C452F cells exhibited abnormal mitochondrial morphology and defective mitophagy. Mitochondria in C452F mouse embryonic fibroblasts were depolarized and had reduced calcium uptake with impaired ATP production by oxidative phosphorylation. In the Python heart, we found a corresponding progressive decline in oxidative phosphorylation with age and activation of sterile inflammation. As a corollary, enhancing autophagy by exposure to a prolonged low-protein diet improved cardiac function in Python mice. In conclusion, failure of Drp1 disassembly impairs mitophagy, leading to a downstream cascade of mitochondrial depolarization, aberrant calcium handling, impaired ATP synthesis, and activation of sterile myocardial inflammation, resulting in heart failure.
Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase (2016)

The Hsp90 molecular chaperone and its Cdc37 cochaperone help stabilize and activate more than half of the human kinome. However, both the mechanism by which these chaperones assist their "client" kinases and the reason why some kinases are addicted to Hsp90 while closely related family members are independent are unknown. Our structural understanding of these interactions is lacking, as no full-length structures of human Hsp90, Cdc37, or either of these proteins with a kinase have been elucidated. Here we report a 3.9 angstrom cryo-electron microscopy structure of the Hsp90-Cdc37-Cdk4 kinase complex. Surprisingly, the two lobes of Cdk4 are completely separated with the β4-β5 sheet unfolded. Cdc37 mimics part of the kinase N lobe, stabilizing an open kinase conformation by wedging itself between the two lobes. Finally, Hsp90 clamps around the unfolded kinase β5 strand and interacts with exposed N- and C-lobe interfaces, protecting the kinase in a trapped unfolded state. On the basis of this structure and an extensive amount of previously collected data, we propose unifying conceptual and mechanistic models of chaperone-kinase interactions.
The Test and Evaluation Uses of Heterogeneous Computing: GPGPUs and Other Approaches (2011)

Abstract : The test and evaluation community faces conflicting pressures: Provide more computing power and reduce electrical power requirements, both on the range and in the laboratory. The authors present some quantifiable benefits from the implementation of General Purpose Graphics Processing Units (GPGPUs) as heterogeneous processors. This produces power, space, cooling, and maintenance benefits that they have documented. Other efforts in the field of power reduction techniques will be outlined, e.g., the efficient low-power microprocessor approach of Prof. William Dally and IBM's well-publicized Blue Gene project. The utility of all of these techniques for the test and evaluation community is assessed. The authors will report on several aspects of their experience with GPGPUs: programmability, performance of codes implemented in several areas of computational science, and the compute power per unit of electrical consumption. An overview of code design and implementation approaches is discussed.
Discrimination between Single Protein Conformations Using Dynamic SERS (2016)

In biomedicine and biophysics, the discrimination of protein conformations is of critical importance for identifying the unfolding states in the diagnosis of neurodegenerative diseases. We develop a dynamic Raman spectroscopic approach based on a statistical analysis of the time series of spectral fingerprints of single protein. We show that the unfolded state of bovine serum albumin can be identified in the time series using the fluctuations of the Raman bands of some amino acids, tryptophan, tyrosine, leucine, and histidine, acting as biomarkers. The statistical analysis induces also the sorting between physisorption and chemisorption events. This is confirmed by the spectral analysis of the different characteristic spectra highlighted based on the amino acids fingerprints following, notably, the hydrophobicity
Exploiting a Bacterial Drug‐Resistance Mechanism: A Light‐Activated Construct for the Destruction of MRSA (2009)

Abstract Bakterien ein Strich durch die Rechnung : Ein enzymspezifisches Molekülkonstrukt macht sich die Überexpression von β‐Lactamase in wirkstoffresistenten Bakterien zu Nutze. Man beobachtet eine spezifische photodynamische Toxizität gegen β‐Lactam‐resistente methicillinresistente Staphylococcus aureus (MRSA), wobei der übliche Mechanismus der Antibiotikaresistenz – die Spaltung des β‐Lactam‐Rings – die phototoxische Komponente freisetzt (siehe Bild; Q: Fluoreszenzlöscher) magnified image
ChemInform Abstract: Synthesis of Substituted Quinazolines. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Indonesian Medicinal Plants. Part 17. Characterization of Quassinoids from the Stems of Quassia indica. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Creep properties of aluminium processed by ECAP (2016)

The creep behaviour of pure polycrystalline aluminium and single crystals processed by equal-channel angular pressing (ECAP) was investigated in order to understand the relationships between heterogeneity of microstructure and creep behaviour. Tensile creep tests were performed at 373 K on specimens processed by 1 and 4 ECAP passes. For comparison purposes, the creep tests were also carried out on coarse-grained specimens. Microstructure analyses showed that application of ECAP technique on polycrystalline aluminium and single crystals led to the formation of significantly different microstructures even after a relatively high number of ECAP passes. The different creep behaviour of ECAP-processed single crystals and polycrystalline aluminium is influenced by inhomogeneity of microstructure. Further, the creep behaviour of specimens processed by 4 ECAP passes is affected by grain-boundary mediated processes like enhanced recovery of dislocations at high-angle grain boundaries in grains finer than quasi-stationary subgrain size and grain boundary sliding. K e y w o r d s : equal channel angular pressing (ECAP),
Automated hyperspectral vegetation index derivation using a hyperparameter optimization framework for high-throughput plant phenotyping (2021)

Summary Hyperspectral vegetation indices (VIs) are widely deployed in agriculture remote sensing and plant phenotyping to estimate plant biophysical and biochemical traits. However, existing VIs consist mainly of simple 2-band indices which limits the net performance and often do not generalize well for other traits than they were originally designed for. We present an automated hyperspectral vegetation index (AutoVI) system for the rapid generation of novel 2- to 6-band trait-specific indices in a streamlined process covering model selection, optimization and evaluation driven by the tree parzen estimator algorithm. Its performance was tested in generating novel indices to estimate chlorophyll and sugar contents in wheat. Results show that AutoVI can rapidly generate complex novel VIs (≥4-band index) which correlated strongly (R 2 &gt; 0.8) with measured chlorophyll and sugar contents in wheat. AutoVI-derived indices were used as features in simple and stepwise multiple linear regression for chlorophyll and sugar content estimation, and outperformed results achieved with existing 47 VIs and those provided by partial least squares regression. The AutoVI system can deliver novel trait-specific VIs readily adoptable in high-throughput plant phenotyping platforms and should appeal to plant scientists and breeders. A graphical user interface of AutoVI is herein provided.
Next wave in Timing Innovation (2018)

Reducing development risks in communications applications with high-performance oscillators.
Supplementary Methods from Loss of <i>Phosphatase and Tensin Homologue Deleted on Chromosome 10</i> Engages ErbB3 and Insulin-Like Growth Factor-I Receptor Signaling to Promote Antiestrogen Resistance in Breast Cancer (2023)

Supplementary Methods from Loss of &lt;i&gt;Phosphatase and Tensin Homologue Deleted on Chromosome 10&lt;/i&gt; Engages ErbB3 and Insulin-Like Growth Factor-I Receptor Signaling to Promote Antiestrogen Resistance in Breast Cancer
A selective small-molecule nuclear factor-κB inhibitor from a high-throughput cell-based assay for “activator protein-1 hits” (2009)

NSC 676914 has been identified as a selective nuclear factor-kappaB (NF-kappaB) inhibitor that does not inhibit cell proliferation. This compound was originally identified in a high-throughput cell-based assay for activator protein-1 (AP-1) inhibitors using synthetic compound libraries and the National Cancer Institute natural product repository. NSC 676914 shows activity against NF-kappaB in luciferase reporter assays at concentrations much less than the IC50 for AP-1. A serum response element reporter used as a specificity control and indicator of cell proliferation was relatively insensitive to the compound. Pretreatment with NSC 676914 is here shown to repress 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced IkappaB-alpha phosphorylation and translocation of p65/50 to the nucleus but not the processing of p52 from p100, suggesting the inhibition of NF-kappaB regulator IKKbeta rather than IKKalpha. Inhibition of NF-kappaB activation occurred as a consequence of blocking phosphorylation of IKK. Induction of IkappaB-alpha phosphorylation by TPA was diminished by pretreatment of NSC 676914 even at 1.1 mumol/L. In contrast, kinases c-Jun-NH2-kinase and extracellular signal-regulated kinases 1 and 2, important for AP-1 activation, showed no significant repression by this compound. Furthermore, a Matrigel invasion assay with breast cancer cell lines and a transformation assay in mouse JB6 cells revealed that TPA-induced invasion and transformation responses were completely repressed by this compound. These results suggest that NSC 676914 could be a novel inhibitor having potential therapeutic activity to target NF-kappaB for cancer treatment or prevention.
Comparative assessment of structural and biological properties of biomimetically coated hydroxyapatite on alumina (α‐Al2O3) and titanium (Ti‐6Al‐4V) alloy substrates (2010)

Previous reports have shown the use of hydroxyapatite (HAp) and related calcium phosphate coatings on metal and nonmetal substrates for preparing tissue-engineering scaffolds, especially for osteogenic differentiation. These studies have revealed that the structural properties of coated substrates are dependent significantly on the method and conditions used for coating and also whether the substrates had been modified prior to the coating. In this article, we have done a comparative evaluation of the structural features of the HAp coatings, prepared by using simulated body fluid (SBF) at 25 degrees C for various time periods, on a nonporous metal substrate titanium-aluminium-vanadium (Ti-6Al-4V) alloy and a bioinert ceramic substrate alpha-alumina (alpha-Al(2)O(3)), with and without their prior treatment with the globular protein bovine serum albumin (BSA). Our analysis of these substrates by scanning electron microscopy (SEM), X-ray diffraction (XRD), and Fourier-transform infrared (FTIR) spectrometry showed significant and consistent differences in the quantitative and qualitative properties of the coatings. Interestingly, the bioactivity of these substrates in terms of supporting in vitro cell adhesion and spreading, and in vivo effects of implanted substrates, showed a predictable pattern, thus indicating that some coated substrates prepared under our conditions could be more suitable for biological/biomedical applications.
Immunologic analysis of the cloned platelet thrombin receptor activation mechanism: evidence supporting receptor cleavage, release of the N-terminal peptide, and insertion of the tethered ligand into a protected environment (1993)

The recently cloned functional thrombin receptor is thought to be activated by thrombin cleavage of the bond between R41 and S42, followed by the insertion of the new N-terminal region (“tethered ligand”) into an unknown site in the receptor. Antibodies to peptides at or near the cleavage site have been reported to inhibit thrombin- induced platelet activation to varying extents, but the precise mechanism(s) of their inhibition is unknown. We have produced: (1) a polyclonal antibody in rabbits to a peptide containing amino acids 34 to 52 (anti-TR34–52); enzyme-linked immunosorbent assays (ELISA) indicate that anti-TR34–52 contains antibodies to regions on both sides of the thrombin cleavage site; (2) two murine monoclonal antibodies (MoAbs) to a peptide containing amino acids 29 to 68; one antibody reacts primarily with residues N-terminal to the thrombin cleavage site, and the other reacts primarily with residues C-terminal to the cleavage site; and (3) a polyclonal rabbit antibody to a peptide containing amino acids 83 to 94 (anti-TR83–94). Anti-TR34–52 binds to platelets as judged by flow cytometry, and pretreating platelets with a thrombin receptor peptide ligand does not lead to loss of antibody reactivity, suggesting that platelet activation does not initiate redistribution or internalization of surface thrombin receptors. In contrast, pretreating platelets with thrombin leads to complete loss of anti-TR34–52 binding. Similarly, the binding of both MoAbs to platelets is dramatically reduced by pretreatment with thrombin. However, the binding of anti-TR83–94 is not decreased by thrombin activation, confirming that the receptor is not internalized. Anti-TR34–52 profoundly inhibits low dose thrombin-induced platelet shape change and aggregation, but the inhibition can be overcome with higher thrombin doses. However, anti-TR34–52 does not inhibit platelet aggregation induced by tethered ligand peptides. The TR34–52 peptide is a thrombin substrate, with cleavage occurring at the R41-S42 bond as judged by high performance liquid chromatography (HPLC) and platelet aggregation analysis. Anti-TR34–52 prevented cleavage of the TR34–52 peptide, suggesting that the antibody prevents platelet activation, at least in part, by preventing cleavage of the thrombin receptor. These data, although indirect, provide additional support for a thrombin activation mechanism involving thrombin cleavage of the receptor; in addition, they provide new evidence indicating that receptor cleavage is followed by loss of the N-terminal peptide, and insertion of the tethered ligand into a protected domain.
Large scale performance measurement of content-based automated image-orientation detection (2005)

With the proliferation of digital cameras and self-publishing of photos, automatic detection of image orientation will become an important part of photo management systems. In this paper, we perform a large scale empirical test to determine whether the common techniques to automatically determine a photo's orientation are robust enough to handle the breadth of real-world images. We use a wide variety of features and color-spaces to address this problem. We use test photos gathered from the Web and photo collections, including photos that are in color and black and white, realistic and abstract, and outdoor and indoor. Results show that current methods give satisfactory results on only a small subset of these images.
Blastogenesis of Autologous, Allogeneic, and Syngeneic (Identical Twins) Lymphocytes in Response to Lymphokines Generated in Dinitrochlorobenzene-Sensitive Human Leukocyte Cultures (1974)

Abstract Dinitrochlorobenzene (DNCB) coupled to peripheral blood erythrocytes or leukocytes forms a particulate complex (DNCB-antigen) capable of inducing lymphocyte transformation when added to peripheral blood leukocyte cultures prepared from human subjects specifically sensitized to DNCB. Biologically active soluble factor(s) are released into the cell-free supernatant of sensitive leukocyte cultures when stimulated by DNCB-antigen, but are not released in unstimulated control cultures. The active soluble supernatant factor(s) induced blastogenesis and DNA synthesis when added to secondary target leukocyte cultures prepared from subjects not sensitized to DNCB. Under the conditions employed in these experiments, maximal DNA synthesis was induced in secondary target leukocyte cultures when supernatants of primary sensitive cultures were collected 24 to 72 hr after stimulation and decreased rapidly thereafter. Increasing amounts of the active soluble factor(s) induced almost proportional increases in DNA synthesis in target leukocyte cultures, illustrating the quantitative nature of the blastogenic assay. Allogeneic and syngeneic leukocyte cultures from subjects not sensitized to DNCB showed levels of DNA synthesis comparable to autologous sensitive leukocyte cultures in response to the soluble factor(s). Thus, the soluble factor(s) which are specifically released after the induction of allergic contact dermatitis to DNCB appear to be lymphokine(s) which express blastogenic activity independent of the genetic origin or antigenic sensitivity of the target leukocyte population.
Selective Hydration of Rutile TiO2 as a Strategy for Site-Selective Atomic Layer Deposition (2022)

The feasibility of a site-selective hydration strategy that enables site-selective atomic layer deposition (ALD) is investigated among four rutile TiO<sub>2</sub> facets [(110), (100), (101) and (001)] and their most prevalent step edges. First-principles simulations of asymmetric slab models were utilized to create accurate representations of pristine terrace and step edge sites. The adsorption free energies for molecular and dissociative adsorption of H<sub>2</sub>O were calculated to evaluate this strategy as a viable route to step edge selectivity. We predict that selective hydroxylation is possible on the 110 and 001 step edges and further computationally evaluate three metalorganic ALD precursors for their compatibility with the selective hydration strategy. Experimental evidence for delayed nucleation of ALD on rutile (001), (110), and (100) TiO<sub>2</sub> single crystals corroborates predictions of the dehydration of the surface and suggests the possibility of site-selective ALD.
The Chiroptical Properties of the Carbon–Carbon Double Bond (2009)

Abstract Introduction The Spectroscopy of the Olefinic Chromophore The Planar C  C Chromophore Sector Rules for Chiral Olefins Isotope Effect Linear Dichroism Measurements
Alkyne Coordination to Organorhenium Oxides with Rhenium in High Oxidation States (1988)

Methylrhenium(VII) oxide 1 is an excellent starting substance for the synthesis of rhenium complexes with π-alkyne ligands. As depicted below, the oxygen-abstracting effect of polymer-bound triphenylphosphane ℗ can be exploited for the production of the new complexes. 2. According to theoretical studies the existence of such ReV compounds was highly improbable. Reduction of 2, R  R′  Me, led to the first ReIV-alkyne complex 3.
Predicting the Performance of the Acid-Stimulation Treatments in Carbonate Reservoirs With Nondestructive Tracer Tests (2015)

Summary Carbonate formations are very complex in their pore structure and exhibit a wide variety of pore classes, such as interparticle porosity, moldic porosity, vuggy porosity, and microporosity. Geologists have defined carbonate pore classes on the basis of sedimentology, thin sections, and porosity/permeability relationships, but the question remains concerning how these pore classes govern the acid flow through porous media. Core samples from six different carbonates, mainly limestone, were selected for the study. The samples were first investigated with thin-section analysis, high-pressure mercury-injection tests, and nuclear-magnetic-resonance measurements for pore-structure characterization, and X-ray diffraction for mineralogy examination. Next, tracer experiments were conducted, and the tracer-concentration profiles were analyzed to quantify the carbonate pore-scale heterogeneity. The heterogeneity is expressed with a parameter f—the available fraction of pore structure contributing to the flow. The data were used to study the flow of acid through carbonate rocks and correlate the pore classes to the acid response. More than 30 acid-coreflood experiments were conducted at 150°F and a hydrochloric acid concentration of 15 wt% on 1.5 × 6-in. core samples at different injection rates on each carbonate rock type. The objective of these sets of experiments is to determine the acid pore volume to breakthrough for each carbonate pore class. The findings of this study help us to connect the results from different characterization methods to the acid flow through the porous media of carbonate rocks. It was also found that the response of the acid depends on the carbonate pore classes. Application to the design of matrix acid treatments in carbonate rocks is discussed.
Multi-Garment Net: Learning to Dress 3D People From Images (2019)

We present Multi-Garment Network (MGN), a method to predict body shape and clothing, layered on top of the SMPL [40] model from a few frames (1-8) of a video. Several experiments demonstrate that this representation allows higher level of control when compared to single mesh or voxel representations of shape. Our model allows to predict garment geometry, relate it to the body shape, and transfer it to new body shapes and poses. To train MGN, we leverage a digital wardrobe containing 712 digital garments in correspondence, obtained with a novel method to register a set of clothing templates to a dataset of real 3D scans of people in different clothing and poses. Garments from the digital wardrobe, or predicted by MGN, can be used to dress any body shape in arbitrary poses. We will make publicly available the digital wardrobe, the MGN model, and code to dress SMPL with the garments at [1].
Near-field Imager Based on Nanophotodetector Array (2007)

A novel high-speed near-field imager is presented based on channelized nanoscale-pixel photodetector (NPD) array with metal-semiconductor-metal detector structure and graded In0.53Ga0.47As/In0.52Al0.48As superlattice as active medium. The NPD array can reach sub-wavelength spatial resolution of &lt;λ/8.
The effect of a heavy atom on the radiative pathways of an emitter with dual conformation, thermally-activated delayed fluorescence and room temperature phosphorescence (2019)

This study focuses on the photophysics of a donor–acceptor molecule with 2,4,6-triphenyl-1,3,5-triazine and phenoselenazine acceptor and donor units.