gebhart/patrepeval huggingface dataset:
Tribological Effects of Brush Scrubbing in Post Chemical Mechanical Planarization Cleaning on Electrical Characteristics in Novel Non-porous Low-kDielectric Fluorocarbon on Cu Interconnects (2011)

Damage reduction during planarization is strongly required to avoid scratch generation and the variation in the electrical properties of low-k dielectrics leading to yield loss in an integrated circuit after the implementation of an ultralow-k dielectric in Cu damascene interconnects. An optimum process condition to reduce damage on brush scrubbing in post-chemical–mechanical-planarization (post-CMP) cleaning was proposed for advanced nonporous organic ultralow-k dielectric fluorocarbon/Cu interconnects. Increasing brush rotation rate by decreasing down pressures results in the improvement in both electric properties and particle removal efficiency. The tribological effects of brush scrubbing in post-CMP cleaning on the electrical characteristics were explored. The brush scrubbing condition of a high brush rotation rate at low down pressures contributes to the suppression of damage generation.
A cluster randomised controlled trial on the efficacy of client-centred occupational therapy in multiple sclerosis: good process, poor outcome (2013)

An increasing number of interventions claim to incorporate client-centred practice. Client-centred practice is associated with improved satisfaction but the effects on functional health-related outcomes have not been fully evaluated. The findings of this study show that the process outcomes of therapy were in favour of the client-centred intervention, but no effects were found on the primary outcomes and negative effects on the secondary functional health outcomes. It is suggested that the implementation of client-centred practice should be adjusted in order to achieve optimal health outcomes.
Hyperglycemia Impairs Proteasome Function by Methylglyoxal (2009)

Hyperglycemia-induced formation of MGO covalently modifies the 20S proteasome, decreasing its activity in the diabetic kidney and reducing the polyubiquitin receptor 19S-S5a. The results indicate a new link between hyperglycemia and impairment of cell functions.
Engineering a PAM-flexible SpdCas9 variant as a universal gene repressor (2021)

The RNA-guided CRISPR-associated Cas9 proteins have been widely applied in programmable genome recombination, base editing or gene regulation in both prokaryotes and eukaryotes. SpCas9 from Streptococcus pyogenes is the most extensively engineered Cas9 with robust and manifold functionalities. However, one inherent limitation of SpCas9 is its stringent 5'-NGG-3' PAM requirement that significantly restricts its DNA target range. Here, to repurpose SpCas9 as a universal gene repressor, we generate and screen variants of the deactivated SpCas9 (SpdCas9) with relaxed 5'-CAT-3' PAM compatibility that can bind to the start codon ATG of almost any gene. Stepwise structure-guided mutations of the PAM-interacting residues and auxiliary PAM-proximal residues of the SpdNG (5'-NG-3' PAM) create a PAM-flexible variant SpdNG-LWQT that preferentially accommodates 5'-NRN-3' PAMs. SpdNG-LWQT is demonstrated to be effective in gene repression with the advantage of customizable sgRNA design in both Escherichia coli and Saccharomyces cerevisiae. This work validates the feasibility of purposeful PAM expansion of Cas9 towards signature PAMs and establishes a universal SpdCas9-based gene repressor.
A hybrid generative/discriminative method for EEG evoked potential detection (2009)

We propose a new method for the detection of evoked potentials that combines a generative model and a discriminative classifier. The method is a variant of the support vector machine (SVM), which uses the Fisher kernel. The kernel function is derived from a generative statistical model known as mixed effects model (MEM). Instead of arbitrarily selecting the Gaussian kernel for the SVM, we exploit the Fisher kernel derived from the MEM for the SVM. The strength of this approach is that it combines the rich information encoded in the generative model, the MEM, with the discriminative power of the SVM algorithm. Our results show that the new method of combining the two complementary approaches-the generative model (MEM) and the discriminative model (SVM) via the Fisher kernel-achieves substantial improvement over the generative model (MEM) and provides better performance than the discriminative model (Gaussian kernel SVM) on the detection of evoked potentials in neural signals.
Comparing reactions of H and Cl with C–H stretch-excited CHD3 (2006)

We report the methyl radical product state distributions for the reactions of H and Cl with CHD3(nu1 = 1,2) at collision energies of 1.53 and 0.18 eV, respectively. Both reactions demonstrate mode selectivity. The resulting state distributions from the H+CHD3(nu1 = 1,2) reactions are well described by a spectator model. The reactions Cl + CHD3(nu1 = 1,2) exhibit similar behavior, but in some aspects the spectator model breaks down. We attribute this breakdown to enhanced intramolecular vibrational redistribution in the Cl + CHD3(nu1 = 1,2) reactions compared to the H + CHD3(nu1 = 1,2) reactions, caused by the interaction of the slower Cl atom with the vibrationally excited CHD3, which is promoted either by its longer collision duration, its stronger coupling, or both.
Design of an Instrument Guide for MRI-Guided Percutaneous Interventions (2011)

This paper describes the design of an instrument guidance device for percutaneous interventions in closed bore magnetic resonance (MR) imaging systems. The device consists of a curved arm piece that travels around a circular base and an additional needle holder that travels along the curved arm, thus providing two angular degrees of freedom that enable an ablation probe to pivot about a remote center of motion located at the skin entry point. The device is intended to be mounted onto a custom built MR coil that rests on the patient while they are imaged. Exact constraint design principles were used to incorporate translational bearings into the plastic parts. Thumbscrews were used for preload and locking so that the probe guide could be fixed along a specific trajectory. The device was prototyped via stereolithography as a proof of concept and demonstrated that a probe could be angled about a remote pivot point.
Growth Hormone Upregulates Mediators of Melanoma Drug Efflux and Epithelial-to-Mesenchymal Transition In Vitro and In Vivo (2020)

Growth hormone (GH) and the GH receptor (GHR) are expressed in a wide range of malignant tumors including melanoma. However, the effect of GH/insulin-like growth factor (IGF) on melanoma in vivo has not yet been elucidated. Here we assessed the physical and molecular effects of GH on mouse melanoma B16-F10 and human melanoma SK-MEL-30 cells in vitro. We then corroborated these observations with syngeneic B16-F10 tumors in two mouse lines with different levels of GH/IGF: bovine GH transgenic mice (bGH; high GH, high IGF-1) and GHR gene-disrupted or knockout mice (GHRKO; high GH, low IGF-1). In vitro, GH treatment enhanced mouse and human melanoma cell growth, drug retention and cell invasion. While the in vivo tumor size was unaffected in both bGH and GHRKO mouse lines, multiple drug-efflux pumps were up regulated. This intrinsic capacity of therapy resistance appears to be GH dependent. Additionally, epithelial-to-mesenchymal transition (EMT) gene transcription markers were significantly upregulated in vivo supporting our current and recent in vitro observations. These syngeneic mouse melanoma models of differential GH/IGF action can be valuable tools in screening for therapeutic options where lowering GH/IGF-1 action is important.
Statistics in Immunology and Biochemistry (2018)

This chapter discusses the application of statistics to biochemistry and, in particular, the application of statistical matching techniques to the problem of T cell antigenic peptides. Immune recognition of foreign proteins as antigens begins with T cell recognition of fragments of the protein on the surface of another cell of the immune system. T cell antigenicity, in contrast to B cell antigenicity, appears to be related to secondary structure, the local geometry of a peptide segment. Several biochemical properties might influence T cell antigenicity. Experimental immunologists had determined that, within a given protein, only certain peptides stimulated large numbers of T cells to divide. In the problem of T cell antigens, the theoretical parent population models the experiment sufficiently well to make the null hypothesis interesting to an analysis of causality. Statistical methodology is available to examine the causality of various biochemical properties with T cell antigenicity or other biological properties.
Monoclonal Antibody to Streptococcal Group B Carbohydrate: Applications in Latex Agglutination and Immunoprecipitin Assays (1982)

Two monoclonal mouse antibodies with specificities for group B streptococcal capsular antigens were evaluated in assays for the identification of group B streptococci (GBS). One of these antibodies (A9) was shown to precipitate group B carbohydrate antigen in reactions with both purified group B antigen and antigen present in autoclave or enzyme extracts of GBS. A9 antibody was also specific for group B antigen in gel diffusion reactions with extracts of Lancefield group A, B, C, D, F, and G streptococci and was a highly sensitive reagent in detecting soluble group B antigen by counterimmunoelectrophoresis. Antigen extracted from all five serotypes of GBS was shown to be precipitated by A9 antibody. A second monoclonal antibody (C8) was reactive with intact GBS but did not precipitate soluble antigen in bacterial extracts. In contrast with what has been shown for polyclonal rabbit anti-group B antiserum, neither antibody was significantly inhibited in binding or precipitation assays by high concentrations of free rhamnose or other monosaccharides of carbohydrates found in group B antigen. Rhamnose, the most abundant carbohydrate of the group B antigen, does not appear therefore to be an immunodominant determinant in the binding of A9 or C8 antibody. The epitopes of both monoclonal antibodies are exposed on the surface of live as well as heat-fixed GBS cells. A9 antibody-coated latex particles were compared with a commercially available polyclonal latex agglutination reagent and shown to be equally sensitive and specific in the detection of soluble group B antigen in urine and cerebrospinal fluid from patients with GBS infections. Because of its uniformity and defined antigen specificity, which includes reactivity with all five serotypes of GBS, A9 antibody offers the potential of an improved immunodiagnostic reagent for the identification of GBS.
A PFC topology with low input current distortion suitable for aircraft power supplies (2004)

This paper presents an AC-DC converter topology for realization of PFC converters for applications where the mains frequency is high and a low input current harmonics is required, e.g., in aircraft power systems. The proposed topology eliminates crossover distortion due to the presence of input rectifiers and the inevitable input current phase lead. The idea is to stack a DC voltage on top of the AC mains voltage to prevent voltage polarity reversal in the input, eliminating the input bridge rectifier. This eliminates the crossover distortion, which can be significant for supply systems having a high mains frequency. In addition, the proposed PFC converter allows bidirectional energy flow, ensuring all inductors work in continuous conduction mode and hence eliminating the distortion due to the abrupt change of dynamic response when the operating mode changes. Analysis and design of the power and control circuits will be given and discussed. An experimental system will be presented for verification purposes.
Patina (2013)

We present Patina, an application independent system for collecting and visualizing software application usage data. Patina requires no instrumentation of the target application, all data is collected through standard window metrics and accessibility APIs. The primary visualization is a dynamic heatmap overlay which adapts to match the content, location, and shape of the user interface controls visible in the active application. We discuss a set of design guidelines for the Patina system, describe our implementation of the system, and report on an initial evaluation based on a short-term deployment of the system.
Measuring disease levels in myeloma using flow cytometry in combination with other laboratory techniques: Lessons from the past 20 years at the Leeds Haematological Malignancy Diagnostic Service (2015)

People with myeloma who obtain a good response to treatment have a better survival if sensitive molecular or flow-cytometric techniques show no detectable minimal residual disease (MRD). The application of MRD techniques to clinical trials is now considered to be increasingly important because treatment approaches are sufficiently effective that using survival outcomes is slowing down the identification of the best new treatments. The articles in this issue consider the laboratory requirements for harmonization of MRD analysis by flow cytometry but there are practical considerations that are also important in implementing a myeloma MRD assay in the cytometry laboratory. In particular, it is important to consider when to request, and how best to utilize, a bone marrow aspirate sample because the procedure is invasive and the cells obtained are valuable for a number of different investigations. This brief article considers some experience obtained over two decades of implementing a service for MRD detection, initially as a scientific bolt-on to clinical trials through to a routine clinical diagnostic assay.
Positive autoantibodies in living liver donors (2022)

Isolated pre-transplant autoantibody positivity is not correlated to worse post-transplant outcomes in living liver donor transplants.
CPR-based next-generation multiscale simulators (2014)

In recent years, using orthogonal matrices has been shown to be a promising approach to improving recurrent neural networks (RNNs) with training, stability, and convergence, particularly to control gradients. While gated recurrent unit (GRU) and long short-term memory (LSTM) architectures address the vanishing gradient problem by using a variety of gates and memory cells, they are still prone to the exploding gradient problem. In this work, we analyze the gradients in GRU and propose the use of orthogonal matrices to prevent exploding gradient problems and enhance long-term memory. We study where to use orthogonal matrices and propose a Neumann series-based scaled Cayley transformation for training orthogonal matrices in GRU, which we call Neumann-Cayley orthogonal GRU (NC-GRU). We present detailed experiments of our model on several synthetic and real-world tasks, which show that NC-GRU significantly outperforms GRU and several other RNNs.
Supplementary Figure S1 from Rapid Expansion of Highly Functional Antigen-Specific T Cells from Patients with Melanoma by Nanoscale Artificial Antigen-Presenting Cells (2023)

&lt;p&gt;Analysis of phenotype, activation, maturation and checkpoint markers on E + E MART-1 Tet+ CD8+ T-cells.&lt;/p&gt;
Infants Fed a Lower Calorie Formula With 2′FL Show Growth and 2′FL Uptake Like Breast‐Fed Infants (2015)

This is the first report of infants fed 2'FL-fortified formulas with a caloric density similar to HM. Growth and 2'FL uptake were similar to those of HM-fed infants.
Wave and Flow Response to an Artificial Surf Reef: Laboratory Measurements (2009)

Waves and currents are essential elements in the design of an artificial surfing reef (ASR). ASRs are primarily designed to optimize the surfing conditions (i.e., increase the surfability of the incoming waves) possibly in combination with the shoreline protection from erosion. The currents generated by waves breaking on the ASR play an important role in the surfability through the wave-current interaction (WCI). Depending on the design, the WCI may negatively affect the surfability by causing the waves to break prematurely due to the current-induced wave steepening. In addition, wave breaking tends to become more irregular due to the temporal variability of the underlying currents. To mitigate the negative effects of wave breaking induced currents on the surfability, three ASR layouts are examined through detailed laboratory experiments. The layouts differ in the alongshore separation distance between two symmetrical reef sides. The ensuing flow circulations are examined in detail with both in situ current meters and video observations of surface drifters. This is done for regular incident waves, bichromatic incident waves, and irregular incident waves, all with equal energy. A data analysis shows that for a given layout the mean flow patterns for regular, bichromatic, and irregular waves are qualitatively similar, with oblique rip currents exiting at either side of the reef and strong flow circulations onshore of the gap in between the two reef sides. Increasing the separation distance leads to a significant reduction of the obliquely exiting rip currents at the outer sides of the reef, but an increase in the flow circulation onshore of the gap. This has a positive effect on the surfability by reducing the negative effects associated with the WCI on the wave breaking, thus, providing longer rides.
Human Th1 Cell Lines Recognize the Mycobacterium tuberculosis ESAT‐6 Antigen and its Peptides in Association with Frequently Expressed HLA Class II Molecules (2003)

We have used a synthetic-peptide approach to map epitope regions of the Mycobacterium tuberculosis ESAT-6 antigen recognized by human T cells in relation to major histocompatibility complex (MHC) restriction. ESAT-6-specific CD4+ T-cell lines were established by stimulating peripheral blood mononuclear cells from 25 HLA-DR-typed tuberculosis patients with complete antigen in vitro. The established T-cell lines were then screened for proliferation and interferon-gamma (IFN-gamma) secretion in response to eight overlapping 20-mer peptides covering the ESAT-6 sequence. The response of the T-cell lines to ESAT-6 and peptides from a human leucocyte antigen (HLA)-heterogeneous group of donors suggested the presence of multiple epitopes and promiscuous recognition of the antigen. Analysis of antigen and peptide recognition in the presence of anti-HLA class I and class II antibodies suggested that the T-cell lines recognized ESAT-6 in association with HLA-DR and -DQ molecules. Furthermore, testing of selected T-cell lines with ESAT-6 and the peptides in the presence of autologous and allogeneic HLA-DR- and -DQ-typed antigen-presenting cells identified HLA-DR2, -DR52 and -DQ2 amongst the HLA molecules involved in the presentation of ESAT-6 and its peptides to human Th1 cells. In addition, the T-cell lines were cytotoxic for monocytes and macrophages pulsed with ESAT-6 and peptides. In conclusion, the recognition of ESAT-6 by IFN-gamma-secreting and cytotoxic CD4+ T cells in association with frequently expressed HLA class II molecules supports the application of this antigen to either specific diagnosis or subunit vaccine design.
p27Kip1 Regulates T Cell Proliferation (2001)

Our studies addressed the mechanism by which serum acts in conjunction with T cell receptor (TCR) agonists to promote the proliferation of primary splenic T cells. When added to resting splenocytes, TCR agonists initiated G(0)/G(1) traverse and activated cyclin D3-cdk6 complexes in a serum-independent manner. On the other hand, both TCR agonists and 10% serum were required for the activation of cyclin E-cdk2 and cyclin A-cdk2 complexes and the entry of cells into S phase. Serum facilitated cdk2 activation by maximizing the extent and extending the duration of the TCR-initiated down-regulation of the cdk2 inhibitor, p27(Kip1). Although p27(Kip1) levels were reduced (albeit submaximally) in cells stimulated in serum-deficient medium, nearly all of the cdk2 complexes in these cells contained p27(Kip1). In contrast, in cells receiving TCR agonist and 10% serum, little if any p27(Kip1) was present in cyclin-cdk2 complexes. Unlike wild-type splenocytes, p27(Kip1)-null splenocytes did not require serum for cdk2 activation or S phase entry whereas loss of the related cdk2 inhibitor, p21(Cip1), did not override the serum dependence of these responses. We also found that cdk2 activation was both necessary and sufficient for maximal expression of cdk2 protein. These studies provide a mechanistic basis for the serum dependence of T cell mitogenesis.
Insights into the Structures, Energetics, and Vibrations of Monovalent Cation−(Water)1-6Clusters (2004)

This study details the interactions prevailing in aqueous clusters of monovalent alkali metal, ammonium, and hydronium cations. The calculations involve a detailed evaluation of the structures, thermodynamic energies, and IR spectra of several plausible conformers of M+·(H2O)1-6 (M = Li, Na, K, Rb, Cs, NH4, H3O) clusters at the second-order Møller−Plesset (MP2) and density functional levels of theory. A detailed decomposition of the interaction energies has been carried out for complexes involving one or two water molecules using symmetry adapted perturbation theory. Some of the salient insights on the structures include the emergence of the second solvent shell even before the realization of the maximal coordination number of the cation. This effect was more pronounced in clusters involving the larger cations. The quantitative estimates of various components of the interaction energy indicate the predominance of electrostatic energies in the binding of these cations to water molecules. Interestingly, for all the hydrated alkali metal cation complexes, the contribution of electrostatic energy is almost the same as the total attractive interaction energy, whereas the sum of the induction and dispersion energies are almost canceled out by exchange-repulsion energy. However, the contribution of dispersion energies slowly starts increasing as the size of the cation increases and is quite substantial in case of the Cs+ complexes. In the organic cations, the dispersion energies become significant, though not comparable to the electrostatic energies. In addition to the evaluation of the harmonic frequencies of −OH stretching mode of all the structures, the anharmonic frequencies were evaluated for the smaller clusters. As the size of the cation and the size of the water cluster increases, the red shifts associated with the −OH stretching mode progressively become larger for the alkali metal cation containing complexes. For the organic cation (NH4+, H3O+) containing complexes, an opposite trend is observed. Compared to the isolated water monomer, the ratio of the infrared intensities of the asymmetric and symmetric −OH stretching modes is very small. However, this ratio progressively becomes larger as the size of the cation increases.
Oxidized LDL Decreasesl-Arginine Uptake and Nitric Oxide Synthase Protein Expression in Human Platelets (1996)

These observations indicate that the L-arginine-NO pathway is involved in the effects of ox-LDL on platelet function and that ox-LDL stimulates platelet function primarily by diminishing NO synthase expression as well as decreasing the uptake of L-arginine.