gebhart/patrepeval huggingface dataset:
Membrane Domains and the “Lipid Raft” Concept (2012)

The bulk structure of biological membranes consists of a bilayer of amphipathic lipids. According to the fluid mosaic model proposed by Singer and Nicholson, the glycerophospholipid bilayer is a two-dimensional fluid construct that allows the lateral movement of membrane components. Different types of lateral interactions among membrane components can take place, giving rise to multiple levels of lateral order that lead to highly organized structures. Early observations suggested that some of the lipid components of biological membranes may play active roles in the creation of these levels of order. In the late 1980s, a diverse series of experimental findings collectively gave rise to the lipid raft hypothesis. Lipid rafts were originally defined as membrane domains, i.e., ordered structures created as a consequence of the lateral segregation of sphingolipids and differing from the surrounding membrane in their molecular composition and properties. This definition was subsequently modified to introduce the notion that lipid rafts correspond to membrane areas stabilized by the presence of cholesterol within a liquid-ordered phase. During the past two decades, the concept of lipid rafts has become extremely popular among cell biologists, and these structures have been suggested to be involved in a great variety of cellular functions and biological events. During the same period, however, some groups presented experimental evidence that appeared to contradict the basic tenets that underlie the lipid raft concept. The concept is currently being re-defined, with greater consistency regarding the true nature and role of lipid rafts. In this article we will review the concepts, criticisms, and the novel confirmatory findings relating to the lipid raft hypothesis.
Construction of agent-oriented virtual society - PAW (2003)

We constructed the agent-oriented virtual society (3D virtual multi-user world) PAW over the Internet. There are many autonomous agents acting with users in PAW. PAW was available on the Internet for about 6 months and gathered 30,000 registered users.
Mechanism of silicon surface roughening by reactive ion etching (1986)

Abstract Rough silicon surfaces resulting from CF 4 reactive ion etching have been studied by scanning electron microscopy/scanning Auger microscopy and x‐ray photoemission spectroscopy. The experimental data demonstrate a roughening mechanism based on laterally non‐uniform etch rates due to the existence of involatile surface residues.
Independently derived IgG anti-DNA autoantibodies from two lupus-prone mouse strains express a VH gene that is not present in most murine strains. (1993)

The origin and structure of two clonally unrelated IgG anti-DNA autoantibodies from lupus-prone MRL/Ipr mice were examined. One of these antibodies, H241, binds dsDNA and glomeruli and deposits in the kidneys of normal mice, whereas the other, H102, binds only ssDNA and does not deposit in kidneys. The VH genes of these two antibodies were almost identical to each other and were frequently expressed in anti-DNA antibodies derived from lupus-prone mice. Six other clonally unrelated anti-DNA antibodies from the literature or from data banks expressed nearly identical VH genes (< or = 4 nucleotide differences) and eight others had nearly identical protein sequences (< or = 3 amino acid differences). Analysis of the germ line with oligonucleotide probes from the CDR regions suggests that all 10 autoantibodies are derived from a single member of the J558 gene family, which is present only in mice with the j haplotype for the J558 gene family. The amount of somatic mutation in these VH genes appears to be low, suggesting that some V, N, and D gene combinations can generate high affinity IgG anti-DNA auto-antibodies with little or no somatic mutation. Unusual reading frames, D-D fusions, and inversions were common in the IgG antibodies and may have been co-selected. Although the N and D regions of one IgM and all five IgG autoantibodies contained Arg residues, the presence of Arg residues was not correlated with binding to dsDNA or with pathogenicity. These results suggest that differences in the Ag-binding properties and the pathogenicity of these antibodies are determined by the CDR3 region and the L chain.
Relative Reactivities of Acetals and Ethers under Friedel‐Crafts Conditions (1994)

Abstract Competition experiments have been performed to determine the relative reactivities of acetals and ethers toward allyltrimethylsilane in the presence of catalytic amounts of BF 3 OEt 2 . It is found that acetals R‐CH(OMe) 2 and their phenylogous p ‐anisyl ethers R‐CH( p ‐MeOC 6 H 4 )(OMe) show very little differences in reactivity. The reactivity scales are employed to rationalize the results of Lewis acid‐catalyzed additions of acetals and ethers to CC double bonds.
Detection of mutations in PCR products from clinical samples by surface plasmon resonance (1997)

Two different strategies for scanning and screening of mutations in polymerase chain reaction (PCR) products by hybridization analysis are described, employing real-time biospecific interaction analysis (BIA) for detection. Real-time BIA was used to detect differences in hybridization responses between PCR products and different 17-mer oligonucleotide probes. For the analysis using a biosensor instrument, two different experimental formats were investigated based on immobilization of either biotinylated PCR products or oligonucleotide probes onto a sensor chip. Applied on the human tumour suppressor p53 gene, differences in hybridization levels for full-match and mismatch situations employing both formats allowed the detection of point mutations in exon 6 PCR products, derived from a breast tumour biopsy sample. In addition, a mutant sample sequence could be detected in a 50/50 background of wild type exon 6 sequence. The suitability of the different formats for obtaining a regenerable system and a high throughput of samples is discussed.
3D Mapping of Outdoor Environment Using Clustering Techniques (2011)

The goal of mapping is to build a map of the environment using raw data provided by some sensors embedded on an intelligent vehicle. This map is used by an intelligent vehicle to have knowledge about its surrounding environment to better plan its future actions. In this paper, we present a method, based on occupancy grids [3], to map 3D environment. In this method, we discretize the environment in cells and the shape of each cell is approximated by one or several gaussians in order to achieve a balance between representational complexity and accuracy. Experimental results on 3D real outdoor data provided by a lidar are shown: a map of an urban environment is presented. Moreover a quantitative comparison of our method with state of the art methods is presented to show the interest of the method.
Microanatomical and Biochemical Origins of Normal and Precancerous Cervical Autofluorescence Using Laser-scanning Fluorescence Confocal Microscopy ¶ (2003)

Clinical studies have shown that in vivo fluorescence spectroscopy can improve the diagnosis of cervical precancer. Recent work suggests that epithelial fluorescence increases, whereas stromal fluorescence decreases, with precancer. However, the microanatomic and biochemical sources of fluorescence in living cervical tissue have not yet been established. This study aims to characterize the origins of living normal and precancerous cervical fluorescence at microscopic levels using laser-scanning fluorescence confocal microscopy. Ten pairs of colposcopically normal and abnormal biopsies were obtained; transverse, 200 microm thick, short-term tissue cultures were prepared and imaged when viable with UV (351-364 nm) and 488 nm excitation before and after addition of the vital dye, Mitotracker Orange. In normal epithelium basal epithelial cells showed cytoplasmic fluorescence; parabasal, intermediate and superficial cells showed fluorescence only at the periphery of the cell. In low-grade precancers cytoplasmic fluorescence was visible in the bottom one-third of the epithelium; in high-grade precancers cytoplasmic fluorescence was visible throughout the lower two-thirds of the epithelium. Cytoplasmic fluorescence was colocalized with the MitoTracker probe and is attributed to mitochondrial reduced form of nicotinamide adenine dinucleotide at UV excitation and mitochondrial flavin adenine dinucleotide at 488 nm excitation. Stromal fluorescence originated from matrix fibers; with the development of precancer the density and fluorescence intensity of matrix fibers decrease. Autofluorescence properties of precancerous cervix reflect an increased number of metabolically active mitochondria in epithelial cells and a reduced stromal fluorescence, which can be an indicator for altered communication between precancerous epithelium and stroma. These changes can explain differences in in vivo fluorescence spectra of normal and precancerous cervical tissue.
Selenium, lycopene, alpha-tocopherol, beta-carotene, retinol, and subsequent bladder cancer. (1989)

To examine the association between serum nutrients and the development of bladder cancer we measured selenium, alpha-tocopherol, lycopene, beta-carotene, retinol, and retinol-binding protein in serum collected from 25,802 persons in Washington County, MD, in 1974. Serum samples were kept frozen at -70 degrees C. In the subsequent 12-year period, 35 cases of bladder cancer developed among participants. Comparisons of serum levels in 1974 among cases and two matched controls for each case showed that selenium was significantly lower among cases than controls (P = 0.03), lycopene was lower among cases at a borderline level of significance (P = 0.07), and alpha-tocopherol was nonsignificantly lower (P = 0.13). For selenium there was a nearly linear increase in risk with decreasing serum levels (P = 0.03). When examined by tertiles, the odds ratio associated with the lowest tertile of selenium compared to the highest tertile was 2.06. Serum levels of retinol, retinol-binding protein, and beta-carotene were similar among cases and controls. These results support a role for selenium in the prevention of bladder cancer.
hTERT Is Expressed in Cancer Cell Lines Despite Promoter DNA Methylation by Preservation of Unmethylated DNA and Active Chromatin around the Transcription Start Site (2007)

hTERT, which encodes the catalytic subunit of telomerase and is expressed in most immortalized and cancer cells, has been reported to have increased DNA methylation in its promoter region in many cancers. This pattern is inconsistent with observations that DNA methylation of promoter CpG islands is typically associated with gene silencing. Here, we provide a comprehensive analysis of promoter DNA methylation, chromatin patterns, and expression of hTERT in cancer and immortalized cells. Methylation-specific PCR and bisulfite sequencing of the hTERT promoter in breast, lung, and colon cancer cells show that all cancer cell lines retain alleles with little or no methylation around the transcription start site despite being densely methylated in a region 600 bp upstream of the transcription start site. By real-time reverse transcription-PCR, all cancer cell lines express hTERT. Chromatin immunoprecipitation (ChIP) analysis reveals that both active (acetyl-H3K9 and dimethyl-H3K4) and inactive (trimethyl-H3K9 and trimethyl-H3K27) chromatin marks are present across the hTERT promoter. However, using a novel approach combining methylation analysis of ChIP DNA, we show that active chromatin marks are associated with unmethylated DNA, whereas inactive marks of chromatin are associated with methylated DNA in the region around the transcription start site. These results show that DNA methylation patterns of the hTERT promoter (-150 to +150 around the transcription start) are consistent with the usual dynamics of gene expression in that the absence of methylation in this region and the association with active chromatin marks allow for the continued expression of hTERT.
Validation of Plantar Pressure Measurements for a Novel in-Shoe Plantar Sensory Replacement Unit (2013)

Based on the results of the present study, we conclude the PSRU provides analogous data when compared with a GS-PSD.
Fold and thrust belt structures and strike‐slip faulting at the SE margin of the Salar de Atacama basin, Chilean Andes (2002)

A tectonic reinterpretation is reported for the southeastern margin of the Salar de Atacama basin of northern Chile. Detailed structural mapping revealed the presence of an east vergent thin‐skinned fold and thrust belt affecting Oligocene‐Miocene Paciencia Group rocks and the overlying Plio‐Pleistocene volcanic rocks. Along‐strike segmentation of the main fold implies local foreland influence on footwall ramp geometry leading to local thrust sheet rotation. To the east the adjacent western slope of the Western Cordillera displays two different structural domains, probably controlled by preexisting basement structures. The southern domain comprises two N‐S oriented sigmoidal belts of linear arranged pressure ridges, indicating left‐lateral transpression. In contrast, the northern domain is characterized by east vergent fold and thrust belt structures and reactivated NW‐SE striking sinistral strike‐slip faults, governing clockwise block rotations. An indenter‐driven deformation model is proposed to explain sinistral transpression and clockwise block rotations around vertical axes. This variant of a small‐block rotation mechanism is discussed in the context of oroclinal bending of the central Andes, emphasizing the significance of ancient structures in controlling rotations.
Identifying Patient-Specific Epstein-Barr Nuclear Antigen-1 Genetic Variation and Potential Autoreactive Targets Relevant to Multiple Sclerosis Pathogenesis (2016)

This study demonstrates the feasibility of obtaining autologous EBNA-1 sequences directly from buffy coat samples, and confirms divergence of these sequences from standard laboratory strains. This approach has identified a number of immunogenic regions of EBNA-1 as well as known and novel targets for autoreactive HLA-DRB1*15-restricted T cells within the central nervous system that could arise as a result of cross-reactivity with EBNA-1-specific immune responses.
Organ transplantation a clinical guide (2011)

Organ Transplantation: A Clinical Guide covers all aspects of transplantation in both adult and pediatric patients. Cardiac, lung, liver, kidney, pancreas and small bowel transplantation are discussed in detail, as well as emerging areas such as face and pancreatic islet cell transplantation. For each organ, chapters cover basic science of transplantation, recipient selection, the transplant procedure, anesthetic and post-operative care, and long-term follow-up and management of complications. Important issues in donor selection and management are also discussed, including recruitment and allocation of potential donor organs and expanding the donor pool. Summary tables and illustrations enhance the text, and long-term outcome data are provided where available. Written by expert transplant surgeons, anesthetists and physicians, Organ Transplantation: A Clinical Guide is an invaluable multidisciplinary resource for any clinician involved in transplantation, providing in-depth knowledge of specialist areas of transplantation and covering the full range of management strategies
Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition (2020)

Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are being developed as therapeutics and make a major contribution to the neutralizing antibody response elicited by infection. Here, we describe a deep mutational scanning method to map how all amino-acid mutations in the RBD affect antibody binding, and apply this method to 10 human monoclonal antibodies. The escape mutations cluster on several surfaces of the RBD that broadly correspond to structurally defined antibody epitopes. However, even antibodies targeting the same RBD surface often have distinct escape mutations. The complete escape maps predict which mutations are selected during viral growth in the presence of single antibodies, and enable us to design escape-resistant antibody cocktails-including cocktails of antibodies that compete for binding to the same surface of the RBD but have different escape mutations. Therefore, complete escape-mutation maps enable rational design of antibody therapeutics and assessment of the antigenic consequences of viral evolution.
Cubistic Representation for Real-Time 3D Shape and Pose Estimation of Unknown Rigid Object (2013)

This paper introduces Cubistic Representation as a novel 3D surface shape model. Cubistic representation is a set of 3D surface fragments, each fragment contains subject's 3D surface shape and its color and redundantly covers the subject surface. By laminating these fragments using a given pose parameter, the subject's appearance can be synthesized. Using cubistic representation, we propose a real-time 3D rigid object tracking approach by acquiring the 3D surface shape and its pose simultaneously. We use the particle filter scheme for both shape and pose estimation, each fragment is used as a partial shape hypothesis and is sampled and refined by a particle filter. We also use the RANSAC algorithm to remove wrong fragments as outliers to refine the shape. We also implemented an online demonstration system with GPU and a Kinect sensor and evaluated the performance of our approach in a real environment.
Preparation of New Nitrogen-Bridged Heterocycles Using Pyridinium N-Ylides and Pyridinium Salts (2005)

It is well known that pyridinium N-ylides and their relating pyridinium salts are very useful precursors for the syntheses of some nitrogen-bridged heterocycles, especially, indolizine and pyrazolo [1, 5-a] pyridine. The conventional preparative methods such as the 1, 3-dipolar cycloaddition and the 1, 5-dipolar cyclization of pyridinium N-ylides, and Tschitschibabin reactions of 1-acylmethyl-2-alkyl or aralkylpyridinium salts are convenient to the syntheses of their derivatives, but the compounds obtained thus are helpless for further transformation to fused indolizines and pyrazolo [1, 5-a] pyridines except a few examples. This article describes novel preparative methods for some functionalized indolizines and pyrazolo [1, 5-a] pyridines and their transformation to new fused heterocycles using their functionality.
Validation of the Leicester Cough Questionnaire in non-cystic fibrosis bronchiectasis (2009)

Health-related quality of life is a potentially important marker for evaluating existing and new therapies in bronchiectasis. The Leicester Cough Questionnaire (LCQ) is a symptom specific questionnaire designed to assess the impact of cough severity, a major symptom of bronchiectasis. This study aimed to validate the LCQ in bronchiectasis. The validity, responsiveness and reliability of the LCQ were assessed as follows: ability to discriminate severe and mild disease; change in score following antibiotic treatment for exacerbations; repeatability over a 6-month period in stable disease; and comparison with the St George's Respiratory Questionnaire (SGRQ). In total, 120 patients (51 with severe disease, 29 with moderate disease and 40 with mild disease) completed the LCQ and SGRQ. The area under the receiver-operator curve was good for both severe and mild disease (0.84 and 0.80 respectively, p<0.0001). Following 2 weeks' antibiotic treatment, the median LCQ score (interquartile range) improved from 11.3 (9.3-13.7) to 17.8 (15-18.8) (p<0.0001). The LCQ score was repeatable over 6 months in stable disease (intraclass correlation coefficient of 0.96 (95%CI 0.93-0.97), p<0.0001). Correlation between the LCQ and SGRQ scores was -0.7 in both stable disease and exacerbations (p<0.0001). The LCQ can discriminate disease severity, is responsive to change and is reliable for use in non-cystic fibrosis bronchiectasis.
Reducing procedure call overhead: optimizing register usage at procedure calls (2002)

Proposes a common global variable reassignment and an integrated approach which takes advantage of the complementary relationship of (1) in-lining and (2) interprocedural register allocation to reduce the procedure call overhead without causing any additional negative effect. Our approach is based on the observation of analyzed program characteristics to identify the heavily called procedure regions, and on register usage information to optimize the placement of resister save/restore code. This method also takes full advantage of free-use registers at each procedure call site. The average performance improvement is 1.233 compared with previous schemes that performed either (1) or (2) independently.
Effects of dietary supplementation with the green tea polyphenol epigallocatechin-3-gallate on insulin resistance and associated metabolic risk factors: randomized controlled trial (2008)

Animal evidence indicates that green tea may modulate insulin sensitivity, with epigallocatechin-3-gallate (EGCG) proposed as a likely health-promoting component. The purpose of this study was to investigate the effect of dietary supplementation with EGCG on insulin resistance and associated metabolic risk factors in man. Overweight or obese male subjects, aged 40-65 years, were randomly assigned to take 400 mg capsules of EGCG (n 46) or the placebo lactose (n 42), twice daily for 8 weeks. Oral glucose tolerance testing and measurement of metabolic risk factors (BMI, waist circumference, percentage body fat, blood pressure, total cholesterol, LDL-cholesterol, HDL-cholesterol, TAG) was conducted pre- and post-intervention. Mood was evaluated weekly using the University of Wales Institute of Science and Technology mood adjective checklist. EGCG treatment had no effect on insulin sensitivity, insulin secretion or glucose tolerance but did reduce diastolic blood pressure (mean change: placebo - 0.058 (se 0.75) mmHg; EGCG - 2.68 (se 0.72) mmHg; P = 0.014). No significant change in the other metabolic risk factors was observed. The EGCG group also reported feeling in a more positive mood than the placebo group across the intervention period (mean score for hedonic tone: EGCG, 29.11 (se 0.44); placebo, 27.84 (se 0.46); P = 0.048). In conclusion, regular intake of EGCG had no effect on insulin resistance but did result in a modest reduction in diastolic blood pressure. This antihypertensive effect may contribute to some of the cardiovascular benefits associated with habitual green tea consumption. EGCG treatment also had a positive effect on mood. Further studies are needed to confirm the findings and investigate their mechanistic basis.
Characteristics of a piezoelectric pulsed nozzle beam (1985)

The characteristics of a molecular beam from a piezoelectric pulsed nozzle source are given and, where appropriate, compared to a continuous beam. These include variation during the pulse in the relative intensity and speed ratio for the gases He, Ar, Ne, and N2. The measurements were made by standard time-of-flight and laser-induced fluorescence techniques. For gas valve pulses of time duration less than 500 μs, there was a single peak during which the gases reached continuum steady flow behavior. Typical speed ratios (parallel temperatures) for the gases He, Ar, Ne, and N2 were 19, 34, 34, and 20 (2.1, 0.7, 0.7, and 1.9 K), respectively. These values are comparable to those from a continuous source with equivalent values of p0d, the product of source pressure and nozzle diameter. The dimer concentrations for Ne and Ar were also measured and found to be 0.4% and 0.7%, respectively. A major problem with the valve was its inability to open fully because of the limited motion of the piezoelectric element.