gebhart/patrepeval huggingface dataset:
Soap (2007)

Soap is a pointing device based on hardware found in a mouse, yet works in mid-air. Soap consists of an optical sensor device moving freely inside a hull made of fabric. As the user applies pressure from the outside, the optical sensor moves independent from the hull. The optical sensor perceives this relative motion and reports it as position input. Soap offers many of the benefits of optical mice, such as high-accuracy sensing. We describe the design of a soap prototype and report our experiences with four application scenarios, including a wall display, Windows Media Center, slide presentation, and interactive video games.
hSETD1A Regulates Wnt Target Genes and Controls Tumor Growth of Colorectal Cancer Cells (2013)

hSETD1A is a member of the trithorax (TrxG) family of histone methyltransferases (HMT) that methylate H3K4 at promoters of active genes. Although misregulation of mixed lineage leukemia (MLL) family proteins has been associated with acute leukemia, the role of hSETD1A in cancer remains unknown. In this study, we report that hSETD1A and its associated H3K4me3 are upregulated in human colorectal cancer cells and patient samples. Depletion of hSETD1A inhibits colorectal cancer cell growth, colony formation, and tumor engraftment. Genome-wide expression profiling of colorectal cancer cells reveals that approximately 50% of Wnt/β-catenin target genes are affected by the hSETD1A knockdown. We further demonstrate that hSETD1A is recruited to promoters of those Wnt signaling target genes through its interaction with β-catenin, a master regulator of the Wnt signaling pathway. The recruitment of the hSETD1A HMT complex confers promoter-associated H3K4me3 that leads to assembly of transcription preinitiation complex and transcriptional activation. Furthermore, the expression levels of hSETD1A are positively correlated with H3K4me3 enrichment at the promoters of Wnt/β-catenin target genes and the aberrant activation of these genes in human colorectal cancer. These results provide new biologic and mechanistic insights into the cooperative role of hSETD1A and β-catenin in regulation of Wnt target genes as well as in colorectal cancer cell growth in vitro and in vivo.
Characterisation of the thermostable protease AprX in strains of Pseudomonas fluorescens and impact on the shelf-life of dairy products: preliminary results (2016)

Bacterial proteases are involved in food spoilage and shelf-life reduction. Among the bacterial proteases, a predominant role in spoilage of dairy products seems to be played by the thermostable metallo-protease AprX, which is produced by various strains of <i>Pseudomonas fluorescens</i>. Differences in AprX enzyme activity among different strains were highlighted, but the most proteolytic strains were not identified. In this study, the presence of the <i>aprX</i> gene was evaluated in 69 strains isolated from food matrices and 18 reference strains belonging to the <i>P. fluorescens</i> group, which had been previously typed by the multi locus sequence typing method. Subsequently, a subset of reference strains was inoculated in ultra-high temperature milk, and the expression of the <i>aprX</i> gene was evaluated at 22 and 6°C. On the same milk samples, the proteolytic activity was then evaluated through Azocasein and trinitrobenzenesulfonic acid solution assays. Finally, to assess the applicability of the former assay directly on dairy products the proteolityc activity was tested on industrial <i>ricotta</i> samples using the Azocasein assay. These results demonstrate the spread of <i>aprX</i> gene in most strains tested and the applicability of Azocasein assay to monitor the proteolytic activity in dairy products.
Oscillations in an Electromechanical System (1936)

Experimental results are given on an oscillating electromechanical system in which, under a single frequency impressed electromotive force, mechanical vibrations are sustained at a frequency near the resonant frequency of the mechanical system and electrical oscillations at the difference between the frequency of the mechanical vibration and that of the impressed force. The system is the one studied analytically by R. V. L. Hartley in an accompanying paper. Its performance conforms to the principal operating features predicted in his analysis.
Multi-level fast multipole method for thin plate spline evaluation (2005)

Image registration is an important problem in image processing and computer vision. Much recent work in image registration is on matching non-rigid deformations. Thin plate splines are an effective image registration method when the deformation between two images can be modeled as the bending of a thin metal plate on point constraints such that the topology is preserved (non-rigid deformation). However, because evaluating the computed TPS model at all the image pixels is computationally expensive, we need to speed it up. We introduce the use of multi-level fast muitipole method (MLFMM) for this purpose. Our contribution lies in the presentation of a clear and concise MLFMM framework for TPS, which will be useful for future application developments. The achieved speedup using MLFMM is an improvement from O(N/sup 2/) to O(N log N). We show that the fast evaluation outperforms the brute force method while maintaining acceptable error bound.
Fibronectin in delayed-type hypersensitivity skin reactions: associations with vessel permeability and endothelial cell activation. (1981)

Abstract Fibronectin, a 440,000-m.w. glycoprotein found in connective tissue matrix and basement membranes of blood vessels, circulates in the plasma and associates with fibrin upon activation of the clotting system. This study reveals the participation of fibronectin in vivo in cell-mediated hypersensitivity reactions, which typically show local fibrin deposition and endothelial cell activation. Fibronectin deposits were marked in classic delayed hypersensitivity (DH) skin reactions elicited with PPD in guinea pigs, but not in cutaneous basophil hypersensitivity reactions elicited with KLH. By radioisotopic and immunofluorescence techniques, fibronectin accumulated in DH reactions in 2 distinct sites with different time courses. In 1- and 2-day-old DH reactions, the dermal extravascular space showed a coarse reticular pattern of staining with fluorescein-conjugated F(ab’)2 anti-fibronectin. The pattern and time course were similar to those of fibrin. By 3 days, a marked reduction in extravascular fibronectin and fibrin was apparent. At this time, fibronectin was detected in the dermal vessels in a brilliant homogeneous linear pattern; no fibrin was found within the vessels. Over the next several days, the intensity of the vessel staining for fibronectin slowly diminished and became more granular. Accumulation of circulating 125l-fibronectin into DH skin sites peaked and exceeded 131l-albumin accumulation between 16 to 40 hr after PPD challenge and then dropped dramatically. Maximal accumulation of 125l-fibronectin occurred just subsequent to the time (16 hr) of maximal vessel permeability and paralleled the deposition of fibronectin in the dermal extravascular space observed by immunofluorescence. In contrast, vessel wall fibronectin peaked when the accumulation of exogenous 125l-fibronectin was minimal and when endothelial activation and mitosis occurred in 1-μ sections. These and other data indicate that the microvasculature modulates the accumulation of fibronectin in DH reactions both by increased vascular permeability with extravasation of plasma fibronectin and by local synthesis in the vessel wall associated with endothelial cell proliferation. Both events occur in a number of other biologically important inflammatory responses, and we hypothesize that the fibronectin provides a provisional matrix that influences cell migration and macrophage activation.
Antitumor Activity of ZD6474, a Vascular Endothelial Growth Factor-2 and Epidermal Growth Factor Receptor Small Molecule Tyrosine Kinase Inhibitor, in Combination with SC-236, a Cyclooxygenase-2 Inhibitor (2005)

This study provides a rationale for evaluating the simultaneous blockade of EGFR, COX-2, and VEGF signaling as cancer therapy in a clinical setting.
Probiotics, Immune Function, Infection and Inflammation: A Review of the Evidence from Studies Conducted in Humans (2009)

A number of studies have been performed examining the influence of various probiotic organisms, either alone or in combination, on immune parameters, infectious outcomes, and inflammatory conditions in humans. Some components of the immune response, including phagocytosis, natural killer cell activity and mucosal immunoglobulin A production (especially in children), can be improved by some probiotic bacteria. Other components, including lymphocyte proliferation, the production of cytokines and of antibodies other than immunoglobulin A appear less sensitive to probiotics. Probiotics, including lactobacilli and bifidobacteria, administered to children can reduce incidence and duration of diarrhoea, but the precise effects depend upon the nature of the condition. Probiotic supplementation can reduce the risk of travellers' diarrhoea in adults, but does not affect duration. The effect of probiotics on other infectious outcomes is less clear. Probiotics may benefit children and adults with irritable bowel syndrome and adults with ulcerative colitis; studies in Crohn's Disease are less clear. Probiotics have little effect in rheumatoid arthritis. Probiotic supplementation, especially with lactobacilli and bifidobacteria, can reduce risk and severity of allergic disease, particular atopic dermatitis; early supplementation appears to be effective. Overall, the picture that emerges from studies of probiotics on immune, infectious and inflammatory outcomes in humans is mixed and there appear to be large species and strain differences in effects seen. Other reasons for differences in effects seen will include dose of probiotic organism used, duration of supplementation, characteristics of the subjects studied, sample size, and technical differences in how the measurements were made.
Binary Labels in the Domain Name System (1999)

This document defines a Bit-String Label which may appear within
domain names. This new label type compactly represents a sequence of
One-Bit Labels and enables resource records to be stored at any bit-
boundary in a binary-named section of the domain name tree.
[STANDARDS-TRACK]
Bezafibrate administration improves behavioral deficits and tau pathology in P301S mice (2012)

Peroxisome proliferator-activated receptors (PPARs) are ligand-mediated transcription factors, which control both lipid and energy metabolism and inflammation pathways. PPARγ agonists are effective in the treatment of metabolic diseases and, more recently, neurodegenerative diseases, in which they show promising neuroprotective effects. We studied the effects of the pan-PPAR agonist bezafibrate on tau pathology, inflammation, lipid metabolism and behavior in transgenic mice with the P301S human tau mutation, which causes familial frontotemporal lobar degeneration. Bezafibrate treatment significantly decreased tau hyperphosphorylation using AT8 staining and the number of MC1-positive neurons. Bezafibrate treatment also diminished microglial activation and expression of both inducible nitric oxide synthase and cyclooxygenase 2. Additionally, the drug differentially affected the brain and brown fat lipidome of control and P301S mice, preventing lipid vacuoles in brown fat. These effects were associated with behavioral improvement, as evidenced by reduced hyperactivity and disinhibition in the P301S mice. Bezafibrate therefore exerts neuroprotective effects in a mouse model of tauopathy, as shown by decreased tau pathology and behavioral improvement. Since bezafibrate was given to the mice before tau pathology had developed, our data suggest that bezafibrate exerts a preventive effect on both tau pathology and its behavioral consequences. Bezafibrate is therefore a promising agent for the treatment of neurodegenerative diseases associated with tau pathology.
[Changes in the functional status of the adrenal glands in patients with chronic renal failure during the treatment by programmed hemodialysis]. (1988)

A study was made of adrenal function in 2 groups of patients with chronic renal insufficiency on programmed hemodialytic therapy. Insufficiency of gluco- and mineralo-corticoid function of the adrenal glands and hyperfunction of their medulla developed in patients with normal BP and controlled hypertension. In patients with uncontrolled hypertension, insufficiency of adrenal glucocorticoid function was attended by hypercatecholaminemia and aldosteronism. Genesis of the revealed disorders was associated with the loss of hormones into the dialysing solution through the membrane, depletion of adrenocortical functional reserves and disturbance of pulmonary regulation of the level of biologically active substances as a result of microthromboembolization of the vessels of the lesser circulation attending hemodialysis.
Copy number variations and cancer (2009)

DNA copy number variations (CNVs) are an important component of genetic variation, affecting a greater fraction of the genome than single nucleotide polymorphisms (SNPs). The advent of high-resolution SNP arrays has made it possible to identify CNVs. Characterization of widespread constitutional (germline) CNVs has provided insight into their role in susceptibility to a wide spectrum of diseases, and somatic CNVs can be used to identify regions of the genome involved in disease phenotypes. The role of CNVs as risk factors for cancer is currently underappreciated. However, the genomic instability and structural dynamism that characterize cancer cells would seem to make this form of genetic variation particularly intriguing to study in cancer. Here, we provide a detailed overview of the current understanding of the CNVs that arise in the human genome and explore the emerging literature that reveals associations of both constitutional and somatic CNVs with a wide variety of human cancers.
Diversity of siderophore‐mediated iron uptake systems in fluorescent pseudomonads: not only pyoverdines (2002)

Fluorescent pseudomonads are gamma-proteobacteria known for their capacity to colonize various ecological niches. This adaptability is reflected by their sophisticated and diverse iron uptake systems. The majority of fluorescent pseudomonads produce complex peptidic siderophores called pyoverdines or pseudobactins, which are very efficient iron scavengers. A tremendous variety of pyoverdines has been observed, each species producing a different pyoverdine. This variety can be used as an interesting tool to study the diversity and taxonomy of fluorescent pseudomonads. Other siderophores, including newly described ones, are also produced by pseudomonads, sometimes endowed with interesting properties in addition to iron scavenging, such as formation of complexes with other metals or antimicrobial activity. Factors other than iron limitation, and different regulatory proteins also seem to influence the production of siderophores in pseudomonads and are reviewed here as well. Another peculiarity of pseudomonads is their ability to use a large number of heterologous siderophores via different TonB-dependent receptors. A first genomic analysis of receptors in four different fluorescent pseudomonads suggests that their siderophore ligand repertoire is likely to overlap, and that not all receptors recognize siderophores as ligands.
Fault-Tolerant Thresholds for the Surface Code in Excess of 5% Under Biased Noise (2020)

Noise in quantum computing is countered with quantum error correction. Achieving optimal performance will require tailoring codes and decoding algorithms to account for features of realistic noise, such as the common situation where the noise is biased towards dephasing. Here we introduce an efficient high-threshold decoder for a noise-tailored surface code based on minimum-weight perfect matching. The decoder exploits the symmetries of its syndrome under the action of biased noise and generalizes to the fault-tolerant regime where measurements are unreliable. Using this decoder, we obtain fault-tolerant thresholds in excess of 6% for a phenomenological noise model in the limit where dephasing dominates. These gains persist even for modest noise biases: we find a threshold of ∼5% in an experimentally relevant regime where dephasing errors occur at a rate 100 times greater than bit-flip errors.
CONSTRAINED FLEXIBILITY IN PNA: DNA BINDING STUDIES WITH BRIDGED AMINOPROPYLGLYCYL PNA (2001)

Introduction of methylene bridges in aegPNA and apgPNA molecules give rise to cyclic five and six membered ring structures. Synthesis of a new six membered cyclic PNA monomer, aminopipecolyl PNA (pipPNA) is reported. Incorporation of pipPNA into PNA oligomers and comparative binding with target DNA sequences is studied.
Histopathology and molecular pathology of synovial B-lymphocytes in rheumatoid arthritis. (2000)

B-cells of the rheumatoid synovial tissue are a constant part of and, in some histopathological subtypes, the dominant population of the inflammatory infiltrate, located in the region of tissue destruction. The pattern of B-cell distribution and the relationship to the corresponding antigen-presenting cells (follicular dendritic reticulum cells: FDCs) show a great variety. B-cells may exhibit (i) a follicular organization forming secondary follicles; (ii) follicle-like patterns with irregularly formed FDC networks, and (iii) a diffuse pattern of isolated FDCs. Molecular analysis of immunoglobulin VH and VL genes from human synovial B-cell hybridomas and synovial tissue demonstrates somatic mutations due to antigen activation. The FDC formations in the synovial tissue may therefore serve as an environment for B-cell maturation, which is involved in the generation of autoantibodies. An autoantibody is defined as "pathogenic" if it fulfills the Witebsky-Rose-Koch criteria for classical autoimmune diseases: definition of the autoantibody; induction of the disease by transfer of the autoantibody; and isolation of the autoantibody from the disease-specific lesion. B-cells from rheumatoid synovial tissue show specificity for FcIgG, type II collagen, COMP, sDNA, tetanus toxoid, mitochondrial antigens (M2), filaggrin and bacterial HSPs. The contributions of these antigens to the pathogenesis of RA are still hypothetical. A possible contribution could derive from crossreactivity and epitope mimicry: due to crossreaction, an antibody directed originally against a foreign infectious agent could react with epitopes from articular tissues, perpetuating the local inflammatory process. The characteristic distribution pattern, the localisation within the area of tissue destruction, the hypermutated IgVH and IgVL genes, and their exclusive function to recognize conformation-dependent antigens suggest a central role for B-cells in the inflammatory process of rheumatoid arthritis. Therefore, the analysis of synovial B-cell hybridomas and experimental expression of synovial IgVH and IgVL genes will help to characterise the antigens responsible for the pathogenesis of rheumatoid arthritis.
Representing spatial location and layout from sparse kinesthetic contacts. (2003)

Participants' fingers were guided to 2 locations on a table for 3 s, then back to the start. They reported distances and angles between the locations by (a) replacing 1 or 2 fingers, (b) translating the contacted configuration, or (c) estimating distance or angle alone. Distance error increased across these conditions. Angular error increased when the angular reference axis was rotated before the response. Replacing 1 finger was impaired by a change in posture from exposure to test. The results suggest a kinesthetic representation is used to replace the fingers, but to estimate distance and angle at new locations, a configural representation is computed. This presentation is oriented within an extrinsic reference frame and maintains shape more accurately than scale.
Use of Egg Yolk-Derived Immunoglobulin as an Alternative to Antibiotic Treatment for Control of Helicobacter pylori Infection (2002)

The present study evaluated the potential use of immunoglobulin prepared from the egg yolk of hens immunized with Helicobacter pylori (immunoglobulin Y [IgY]-Hp) in the treatment of H. pylori infections. The purity of our purified IgY-Hp was 91.3%, with a yield of 9.4 mg of IgY per ml of egg yolk. The titer for IgY-Hp was 16 times higher than that for IgY in egg yolk from nonimmunized hens, and IgY-Hp significantly inhibited the growth and urease activity of H. pylori in vitro. Bacterial adhesion on AGS cells was definitely reduced by preincubation of both H. pylori (10(8) CFU/ml) and 10 mg of IgY-Hp/ml. In Mongolian gerbil models, IgY-Hp decreased H. pylori-induced gastric mucosal injury as determined by the degree of lymphocyte and neutrophil infiltration. Therefore, in this experimental model, H. pylori-associated gastritis could be successfully treated by orally administered IgY-Hp. The immunological activity of IgY-Hp stayed active at 60 degrees C for 10 min, suggesting that pasteurization can be applied to sterilize the product. Fortification of food products with this immunoglobulin would significantly decrease the H. pylori infection. In conclusion, the IgY-Hp obtained from hens immunized by H. pylori could provide a novel alternative approach to treatment of H. pylori infection.
Binary-level Function Profiling for Intrusion Detection and Smart Error Virtualization (2006)

Most current approaches to self-healing software (SHS) suffer from semantic incorrectness of the response mechanism. To support SHS, we propose Smart Error Virtualization (SEV), which treats functions as transactions but provides a way to guide the program state and remediation to be a more correct value than previous work. We perform runtime binary-level profiling on unmodified applications to learn both good return values and error return values (produced when the program encounters ``bad'' input). The goal is to ``learn from mistakes'' by converting malicious input to the program's notion of ``bad'' input. We introduce two implementations of this system that support three major uses: function profiling for regression testing, function profiling for host-based anomaly detection (environment-specialized fault detection), and function profiling for automatic attack remediation via SEV. Our systems do not require access to the source code of the application to enact a fix. Finally, this paper is, in part, a critical examination of error virtualization in order to shed light on how to approach semantic correctness.