gebhart/patrepeval huggingface dataset:
Accurate Solution Structures of Proteins from X-ray Data and a Minimal Set of NMR Data: Calmodulin−Peptide Complexes As Examples (2009)

A strategy for the accurate determination of protein solution structures starting from X-ray data and a minimal set of NMR data is proposed and successfully applied to two complexes of calmodulin (CaM) with target peptides not previously described. Its implementation in the present case is based on the use of lanthanide ions as substitutes for calcium in one of the four calcium binding sites of CaM and the collection of pseudocontact shift (pcs) and residual dipolar coupling (rdc) restraints induced by the paramagnetic metals. Starting from the crystal structures, new structural models are calculated that are in excellent agreement with the paramagnetic restraints and differ significantly from the starting crystal structures. In particular, in both complexes, a change in orientation of the first helix of the N-terminal CaM domain and of the whole C-terminal domain is observed. The simultaneous use of paramagnetic pcs and rdc restraints has the following crucial advantages: (i) it allows one to assess the possible presence of interdomain conformational freedom, which cannot be detected if the rdc values are derived from external orienting media; (ii) in the absence of significant conformational freedom, the global orientation tensor can be independently and precisely determined from pcs values, which are less sensitive than rdc values to the presence of local structural inaccuracies, and therefore (iii) the relative rearrangement of a domain or a secondary structure element with respect to the metal-bearing domain can be detected.
Closure to “Discussions of ‘Radial-Flow Compressors and Turbines for the Simple Small Gas Turbine’” (1952, Trans. ASME, 74, pp. 1345–1346) (1952)

in brief, a number of its component design problems, their solutions and their limitations in the light of our experience and what is considered good practice in the available literature.
Microbial Carbonate Precipitation: Correlation of S-Wave Velocity with Calcite Precipitation (2011)

The use of microbial induced precipitation as a soil improvement technique has been growing in geotechnical domains where ureolytic bacteria that raise the pH of the system and induce calcium carbonate (CaCO3) precipitation are used. For many applications, it is useful to assess the degree of CaCO3 precipitation by non-destructive testing. This study investigates the feasibility of S-wave velocity measurements to evaluate the amount of calcite precipitation by laboratory testing. Two sets of cemented specimen were tested. The first were samples terminated at different stages of cementation. The second were samples that went through different chemical treatments. These variations were made to find out if these factors would affect the S-wave velocity- cementation relationship. If chemical reaction efficiency was assumed to be constant throughout each test, the relationship between S-wave velocity (Vs) and the amount of CaCO3 precipitation was found to be approximately linear. This correlation between S-wave velocity and calcium carbonate precipitation validates its use as an indicator of the amount of calcite precipitation
Convolutional Neural Networks using Logarithmic Data Representation (2016)

Recent advances in convolutional neural networks have considered model complexity and hardware efficiency to enable deployment onto embedded systems and mobile devices. For example, it is now well-known that the arithmetic operations of deep networks can be encoded down to 8-bit fixed-point without significant deterioration in performance. However, further reduction in precision down to as low as 3-bit fixed-point results in significant losses in performance. In this paper we propose a new data representation that enables state-of-the-art networks to be encoded to 3 bits with negligible loss in classification performance. To perform this, we take advantage of the fact that the weights and activations in a trained network naturally have non-uniform distributions. Using non-uniform, base-2 logarithmic representation to encode weights, communicate activations, and perform dot-products enables networks to 1) achieve higher classification accuracies than fixed-point at the same resolution and 2) eliminate bulky digital multipliers. Finally, we propose an end-to-end training procedure that uses log representation at 5-bits, which achieves higher final test accuracy than linear at 5-bits.
Impact of viral genotypes and naturally occurring mutations on biological properties of hepatitis B virus (2007)

Hepatitis B patients worldwide are infected with different viral genotypes. Within the same individual the dominant viral species evolves over the course of chronic infection to generate viral variants or mutants. The mutations, often selected by the host immune response or antiviral therapy, are sometimes restricted by viral genotypes. We are interested in characterizing mutations that affect the expression of hepatitis B e-antigen (HBeAg), a protein with a large effect on duration of infection and severity of liver diseases. HBeAg is encoded by the precore region in addition to the core gene. Core promoter mutations reduce HBeAg expression at the transcriptional level. We found that the hot spot mutations (A1762T/G1764A) only mildly reduced HBeAg expression and enhanced genome replication, while incorporation of additional core promoter mutations intensified both phenotypes. At the step of translation, a G1896A nonsense mutation in the precore region abolishes HBeAg expression. We first reportedthat the G1896A mutation rarely occurred in genotype A. Subsequent studies by others established the role of polymorphism at nucleotide 1858, rather than genotype, as the determinant for the G1896A mutation. Conversion of the precore/core protein to HBeAg requires proteolytic removal of both the amino and carboxy termini, and a (151)RRGR(154) motif has been implicated as the carboxy terminal cleavage site. In this regard, genotype A is unique in possessing a dipeptide insertion that expands the motif into (151)RRDRGR(156). We found that genotype A is cleaved primarily at R156, generating a mature HBeAg that is two amino acids longer than HBeAg from other genotypes. There are different avenues whereby HBeAg expression or its antigenicity can be modulated by viral genotype and naturally occurring mutations.
Effects of the methylxanthine derivative pentoxifylline on benzodiazepine and muscarinic binding sites in rat cerebral cortex. (1985)

The subcutaneous injection of the methylxanthine derivative pentoxifylline (3,7, dimethyl-1-(5-oxo-hexyl)-xanthine) was able to induce, 3 h later, a significant reduction of benzodiazepine binding sites in rat cerebral cortex. When tested in vitro, pentoxifylline displaced 3H-flunitrazepam from specific binding sites in a competitive manner. For this effect pentoxifylline was about 10 times more potent than caffeine. When given in two daily injections for 5 days, pentoxifylline brought about a significant elevation in the number of cortical benzodiazepine binding sites. Neither acute nor chronic pentoxifylline treatment modified cortical muscarinic cholinergic binding sites. Pentoxifylline has negligible affinity for cortical muscarinic receptors in vitro. These results suggest that pentoxifylline is able to affect the cortical benzodiazepine receptors differentially, depending on time of drug administration.
Preoperative Simulation of Outcomes Using Adaptive Optics (2000)

Measurements of the wavefront of light reflected from the retina of the human eye can be used to determine optical aberrations of the human eye for large pupils. An instrument based on the Hartmann-Shack principle was developed. The wavefront is refracted by a microlens array and detected by a CCD camera. In first clinical studies human volunteer eyes and preoperative and postoperative refractive surgical patient eyes have been examined. An adaptive optical closed loop system has been devised for preoperative simulation of refractive outcomes of aberration free refractive surgical procedures.
FABRICATE AND TEST AN ADVANCED NON-POLLUTING TURBINE DRIVE GAS GENERATOR (2003)

In September 2000 the Department of Energy's National Energy Technology Laboratory (DOE/NETL) contracted with Clean Energy Systems, Inc. (CES) of Sacramento, California to design, fabricate, and test a 20 MW{sub t} (10 MW{sub e}) gas generator. Program goals were to demonstrate a non-polluting gas generator at temperatures up to 3000 F at 1500 psi, and to demonstrate resulting drive gas composition, comprising steam and carbon dioxide substantially free of pollutants. Following hardware design and fabrication, testing, originally planned to begin in the summer of 2001, was delayed by unavailability of the contracted test facility. CES designed, fabricated, and tested the proposed gas generator as originally agreed. The CES process for producing near-zero-emissions power from fossil fuels is based on the near-stoichiometric combustion of a clean gaseous fuel with oxygen in the presence of recycled water, to produce a high-temperature, high-pressure turbine drive fluid comprising steam and carbon dioxide. Tests demonstrated igniter operation over the prescribed ranges of pressure and mixture ratios. Ignition was repeatable and reliable through more than 100 ignitions. Injector design ''A'' was operated successfully at both low power ({approx}20% of rated power) and at rated power ({approx}20 MW{sub t}) in more than 95 tests. The uncooled gas generator configuration (no diluent injectors or cooldown chambers installed) produced drive gases at temperatures approaching 3000 F and at pressures greater than 1550 psia. The fully cooled gas generator configuration, with cooldown chambers and injector ''A'', operated consistently at pressures from 1100 to 1540 psia and produced high pressure, steam-rich turbine drive gases at temperatures ranging from {approx}3000 to as low as 600 F. This report includes description of the intended next steps in the gas generator technology demonstration and traces the anticipated pathway to commercialization for the gas generator technology developed in this program.
Characterization of the Hematopoietic Transcription Factor NF-E2 in Primary Murine Megakaryocytes (1998)

Biochemical analysis of megakaryocytes, the precursors of blood platelets, is limited by their rarity in vivo, and studies on lineage-specific gene expression have been conducted exclusively in cell lines with limited megakaryocytic potential. Mice lacking the transcription factor NF-E2 display arrested megakaryocyte differentiation and profound thrombocytopenia. To study the heterodimeric NF-E2 protein in primary cells, we cultured mouse fetal livers with the c-Mpl ligand, obtained highly enriched megakaryocyte populations, and readily detected NF-E2 activity in nuclear extracts. As in erythroid cells, p45 NF-E2 is the only large subunit in primary megakaryocytes that dimerizes with distinct small Maf proteins to constitute a heterogeneous NF-E2 complex. Whereas p18/MafK is the predominant small Maf protein in erythroid cells, the related polypeptides MafG and/or MafF predominate in megakaryocytes. Although this represents the first example of differential small Maf protein expression among closely related blood lineages, the DNA-binding specificity of NF-E2 is similar in both cell types. Although the megakaryocyte protein preferentially binds an asymmetric AP-1-related motif, it also recognizes cAMP-responsive element-related sequences, albeit with lower affinity, and nucleotides outside the core sequence influence the DNA-protein interaction. These results demonstrate the feasibility of biochemical studies on primary murine megakaryocytes and provide a basis to dissect the critical functions of NF-E2 in megakaryocyte differentiation.
Epigenetic-aging-signature to determine age in different tissues (2011)

All tissues of the organism are affected by aging. This process is associated with epigenetic modifications such as methylation changes at specific cytosine residues in the DNA (CpG sites). Here, we have identified an Epigenetic-Aging-Signature which is applicable for many tissues to predict donor age. DNA-methylation profiles of various cell types were retrieved from public data depositories - all using the HumanMethylation27 BeadChip platform which represents 27,578 CpG sites. Five datasets from dermis, epidermis, cervical smear, T-cells and monocytes were used for Pavlidis Template Matching to identify 19 CpG sites that are continuously hypermethylated upon aging (R>0.6; p-value<10-13). Four of these CpG sites (associated with the genes NPTX2, TRIM58, GRIA2 and KCNQ1DN) and an additional hypomethylated CpG site (BIRC4BP) were implemented in a model to predict donor age. This Epigenetic-Aging-Signature was tested on a validation group of eight independent datasets corresponding to several cell types from different tissues. Overall, the five CpG sites revealed age-associated DNA-methylation changes in all tissues. The average absolute difference between predicted and real chronological age was about 11 years. This method can be used to predict donor age in various cell preparations - for example in forensic analysis.
Fuzzy concept graph and application in Web document clustering (2002)

This paper introduces the fuzzy concept graph method firstly. Based on the related definitions, it discusses its main characteristics and application in an intelligent customized search system.
More than Meets the Eye: The Aryl Hydrocarbon Receptor is an Environmental Sensor, Physiological Regulator and a Therapeutic Target in Ocular Disease (2022)

The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor originally identified as an environmental sensor of xenobiotic chemicals. However, studies have revealed that the AHR regulates crucial aspects of cell growth and metabolism, development and the immune system. The importance of the AHR and AHR signaling in eye development, toxicology and disease is now being uncovered. The AHR is expressed in many ocular tissues including the retina, choroid, cornea and the orbit. A significant role for the AHR in age-related macular degeneration (AMD), autoimmune uveitis, and other ocular diseases has been identified. Ligands for the AHR are structurally diverse organic molecules from exogenous and endogenous sources. Natural AHR ligands include metabolites of tryptophan and byproducts of the microbiome. Xenobiotic AHR ligands include persistent environmental pollutants such as dioxins, benzo (a) pyrene [B (a) P] and polychlorinated biphenyls (PCBs). Pharmaceutical agents including the proton pump inhibitors, esomeprazole and lansoprazole, and the immunosuppressive drug, leflunomide, activate the AHR. In this review, we highlight the role of the AHR in the eye and discuss how AHR signaling is involved in responding to endogenous and environmental stimuli. We also present the emerging concept that the AHR is a promising therapeutic target for eye disease.
Demonstration of strong saturation of traps in multiple, narrow, slightly asymmetric coupled quantum wells (1993)

Continuous-wave photoluminescence excitation spectra of multiple, narrow, slightly asymmetric coupled quantum wells at room temperature have been measured. As the laser intensity increases, the photoluminescence intensity initially increases at a rate that is higher than square-law dependence and finally approaches square-law dependence. This phenomenon can be attributed to the process in which a dominant nonradiative recombination at the traps undergoes strong saturation with weak radiative recombination of free carriers. The intensity-dependent trapping efficiency and ratio between electron and hole nonradiative decay times, and the ratio between trapping and nonradiative recombination rates have been determined from the experiment.
3D Segmentation Learning from Sparse Annotations and Hierarchical Descriptors (2021)

One of the main obstacles to 3D semantic segmentation is the significant amount of endeavor required to generate expensive point-wise annotations for fully supervised training. To alleviate manual efforts, we propose GIDSeg, a novel approach that can simultaneously learn segmentation from sparse annotations via reasoning global-regional structures and individual-vicinal properties. GIDSeg depicts global- and individual- relation via a dynamic edge convolution network coupled with a kernelized identity descriptor. The ensemble effects are obtained by endowing a fine-grained receptive field to a low-resolution voxelized map. In our GIDSeg, an adversarial learning module is also designed to further enhance the conditional constraint of identity descriptors within the joint feature distribution. Despite the apparent simplicity, our proposed approach achieves superior performance over state-of-the-art for inferencing 3D dense segmentation with only sparse annotations. Particularly, with $5\%$ annotations of raw data, GIDSeg outperforms other 3D segmentation methods.
Authenticating distributed data using Web services and XML signatures (2002)

As the need for digital data becomes more ubiquitous, so does the need to provide efficient mechanisms for distributing and verifying the authenticity of that data. We present an architecture for authenticating responses to queries from untrusted mirrors of authenticated dictionaries using Web Services and XML Signatures. We also describe an implementation of our scheme for the Secure Transaction Management System.
Synthesis and characterization of a new structure of gas hydrate (2009)

Atoms and molecules <0.9 nm in diameter can be incorporated in the cages formed by hydrogen-bonded water molecules making up the crystalline solid clathrate hydrates. For these materials crystallographic structures generally fall into 3 categories, which are 2 cubic forms and a hexagonal form. A unique clathrate hydrate structure, previously known only hypothetically, has been synthesized at high pressure and recovered at 77 K and ambient pressure in these experiments. These samples contain Xe as a guest atom and the details of this previously unobserved structure are described here, most notably the host-guest ratio is similar to the cubic Xe clathrate starting material. After pressure quench recovery to 1 atmosphere the structure shows considerable metastability with increasing temperature (T <160 K) before reverting back to the cubic form. This evidence of structural complexity in compositionally similar clathrate compounds indicates that the reaction path may be an important determinant of the structure, and impacts upon the structures that might be encountered in nature.
Notes from the Editor-in-Chief (2002)

Review of new models in Healthcare. Bridging the gap between the world of academia and the world of healthcare management and policy. Authors explore the potential of new ideas. Edited by Audrey Laporte, MA, PhD, Director, Institute for Health Policy Measurement and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON and Arjumand Siddiqi, MPH, ScD, Professor, Division Head of Epidemiology, Dalla Lana School of Public Health, Canada Research Chair in, Population Health Equity, University of Toronto, Toronto, ON
Hydrothermal Synthesis and Surface Characteristics of Novel Alpha Alumina Nanosheets with Controlled Chemical Composition (2010)

Novel alpha alumina (α-Al2O3) nanosheets with controlled chemical compositions were synthesized at 450 °C under 10.3 MPa pressure by the hydrothermal treatment of boehmite powder (γ-AlOOH) in the presence of soluble salts of metal dopants, α-Al2O3 seeds, and 5% SiO2 morphology modifier. Detailed XRD, SEM, HRTEM, STEM, and XEDS characterization was performed and it was found that the as-synthesized nanosheets were in most cases the phase-pure α-Al2O3 crystals exhibiting very strong (001) faceting, thicknesses of 10−50 nm, aspect ratios up to a few hundreds, and specific surface areas up to 35 m2/g. Metal dopants from nearly every group of the Periodic Table were present in these α-Al2O3 nanosheets in concentrations up to ∼0.5 atom % either as solid solutions or as nanosized inclusions. A thorough surface analyses using X-ray photoelectron spectroscopy (XPS), measurements of nitrogen adsorption isotherms at −196 °C, temperature-programmed desorption (TPD), and zeta potential measurements, revealed a very wide range of control of the surface charge, surface purity, and acid−base properties of the α-Al2O3 nanosheets by selection of different dopants and controlling their distribution within the nanosheets. The BET surface area values of the hydrothermally synthesized nanosheets were stable up to 1200 °C. Such novel doped α-Al2O3 nanomaterials can be useful in a variety of applications such as catalysis, chemical-mechanical planarization, composites, and ceramics.
The potential of PTPN22 as a therapeutic target for rheumatoid arthritis (2018)

PTPN22 encodes a lymphoid-specific tyrosine phosphatase (LYP) that is a master regulator of the immune response. This gene is a major susceptibility factor for a wide range of autoimmune conditions, including rheumatoid arthritis (RA) for which it represents the strongest non-HLA contributor to disease risk. A missense PTPN22 allele (R620W) affecting the protein-protein interaction of LYP with other relevant players was described as the functional variant of the association. This review will focus on the role of PTPN22 in the pathogenic mechanisms underlying RA predisposition and discuss the possibility of developing LYP-based treatment strategies with a potential application in clinical practice. Areas covered: This review covers the literature showing how PTPN22 is implicated in signalling pathways involved in the autoimmune and autoinflammatory processes underlying RA. Insights obtained from studies aimed at developing novel selective LYP suppressors for treating RA are summarized. Expert opinion: Targeting key risk factors during the early steps of the disease may represent a good strategy to accomplish complete disease remission. As cumulating evidences suggest that PTPN22 R620W is a gain-of-function variant, a growing interest in developing LYP inhibitors has arisen. The potential efficacy and possible application of such compounds are discussed.
The Use of a Dermal Regeneration Template (Integra) for Acute Resurfacing and Reconstruction of Defects Created by Excision of Giant Hairy Nevi (2004)

Philadelphia, Pa. From the Division of Plastic and Reconstructive Surgery, St. Christopher's Hospital for Children. Received for publication March 3, 2003; revised August 4, 2003. The authors have no financial ties with the product Integra or the corporation manufacturing this product. This undertaking has not been supported by the manufacturers of this product. Paul Glat, M.D. Division of Plastic Surgery, St. Christopher's Hospital for Children, Erie Avenue at Front Street, Philadelphia, Pa. 19134-1095, [email protected]
Gamma irradiation of hexafluorobenzene (1960)

Mixtures of hexafluorobenzene and benzene were irradiated in liquid phase by means of a Co<sup>60</sup> gamma source at 20° and at 218° C. Perfluoroheptane and various binary mixtures involving perfluoroheptane, hexafluorobenzene, benzene, and cyclohexane were also irradiated at 20° C. Hexafluorobenzene resembled benzene very closely in its behavior upon radiolysis. Generally the fluorocarbon-hydrocarbon mixtures evolved much more SiF<sub>4</sub> (indicating the formation of HF, which reacts with the glass vessel) than the pure fluorocarbon components. The polymer from hexafluorobenzene-benzene mixtures was probably rich in cyclohexadiene and cyclohexene units, resembling that from pure benzene, and its composition ratio exhibited a strong "alternating" tendency. The results are discussed in terms of free-radical and excited-state mechanisms. At 218° C hexafluorobenzene and also its mixtures with benzene showed qualitative differences from their behavior at 20° C, although the <i>G</i> values for SiF<sub>4</sub> and polymer remained moderate.