gebhart/patrepeval huggingface dataset:
Effect of Antiidiotypic Antibodies to HLA on Graft Survival in Renal-Allograft Recipients (1987)

Although the presence in the recipient of preformed antibodies to HLA antigens in the kidney of a renal-transplant donor may be associated with early graft failure, such grafts are often well tolerated. We have investigated the possibility that anti-anti-HLA (antiidiotypic) antibodies influence the outcome of renal transplantation in recipients with a history of presensitization to their donor's HLA antigens. A retrospective analysis of 20 such cases showed that in 10 patients the transplanted kidney was rejected within one month, whereas in the remaining 10 the graft was tolerated for more than a year. Nine of the 10 patients in whom the graft was tolerated had anti-anti-HLA antibodies at the time of transplantation. Nine of the 10 patients in whom the graft was rejected had antibodies that potentiated, rather than blocked, the cytotoxic activity of anti-donor-HLA antibodies. These results suggest that patients with anti-anti-HLA antibodies specific for a potential donor can safely undergo transplantation, despite a prior history of anti-HLA antibodies. At the time of transplantation, patients who have antibodies that potentiate the cytotoxic activity of a historically positive serum are at high risk of graft rejection within a short period. Taking these considerations into account may improve the reliability of cross-matching in renal transplantation.
UNCONSCIOUS OPERANT CONDITIONING IN THE PARADIGM OF BRAIN-COMPUTER INTERFACE BASED ON COLOR PERCEPTION (2005)

This study investigate the mutual fine-tuning of ongoing EEG rhythmic features with RGB values controlling color shades of computer screen during neuro-feedback training. Fifteen participants had not been informed about the existence of neurofeedback loop (NF), but were guided only to look at the computer screen. It was found that during such unconscious NF training, a variety of color shades on the screen gradually changed from rather various types to the main one within the framework of color palette specified for each individual. This phenomenon was not observed in control experiments with simulated neuro-feedback. Individual color patterns induced on the screen during NF did not depend on the schema of connection between of EEG rhythms and RGB controller. It is suggested that the basic neurophysiological mechanism of described NF training consists of the directed selection of EEG patterns reinforced by comfortable color shades without conscious control.
<title>Reconstruction methods for infrared absorption imaging</title> (1991)

In infrared absorption imaging, the requirement is to reconstruct the spatial distribution of the optical absorption coefficient, from boundary measurements of the flux intensity of light arising from a specific source distribution. An accurate and efficient model is required to simulate data for given experimental conditions and for any hypothesized solution (the Forward Problem). The Inverse Problem is then to derive the solution that best fits the data, subject to constraints imposed by a priori knowledge (e.g. positivity). The Forward Problem is denoted (chi) equals A(mu) + n where (mu) is the required functional map, (chi) the boundary data, A the Forward Transform and n noise, and the Inverse Problem is (mu) equals A+(chi) , where A+ is an approximation to the Inverse Transform. The experimental arrangement modelled assumes an inhomogeneous cylindrical object. A picosecond dye laser produces input pulses at N locations and a time resolved detector makes measurements at N output sites. This (chi) is an N2 by 1 vector and (mu) can be reconstructed to, at best, an N by N image. The Forward Model described here is an analytic approach using the Greens Function of the diffusion equation in a cylinder, (the P1 approximation to the radiative transfer equation). It may be parameterized by the global values of absorption and scattering coefficients ((mu) a, and (mu) s), which have to be adjusted to best fit the data. The Inverse Problem is highly ill-posed. To solve it, we use the Moore-Penrose generalized inverse A+ equals (A*A)-1A*, and two simple regularization techniques: truncated singular value reconstruction and Tikhovov regularization. Examination of the singular vectors of the kernel demonstrate that the solution is dominated by surface effects, unless a very high signal-to-noise ratio is obtained in the data. Results are shown for simulated mathematical phantoms and a tissue-equivalent phantom composed of polystyrene microspheres.
Speckle-contrast monitoring of tissue thermal modification (2002)

Measurements of the contrast value of time-averaged speckle-modulated images of cartilage tissue are used to study tissue thermal modification in the case of laser-light treatment. This modification is related to thermally induced internal stress relaxation in the matrix of the treated tissue. The specific feature of the evolution of time-averaged speckle contrast with a change in the current temperature of modified collagen tissue is the typical looplike form of the contrast-temperature dependencies associated with irreversible changes in tissue structure and correlated with changes in the tissue diffuse transmittance and the tissue internal stress mentioned by other researchers.
Antibody Blockade of Thrombospondin Accelerates Reendothelialization and Reduces Neointima Formation in Balloon-Injured Rat Carotid Artery (1999)

Intra-arterial delivery of antibody against TSP1 facilitated reendothelialization and reduced neointimal lesion formation after balloon denudation.
Apolipoprotein A-IV inhibits experimental colitis (2004)

The antiatherogenic properties of apoA-IV suggest that this protein may act as an anti-inflammatory agent. We examined this possibility in a mouse model of acute colitis. Mice consumed 3% dextran sulfate sodium (DSS) in their drinking water for 7 days, with or without daily intraperitoneal injections of recombinant human apoA-IV. apoA-IV significantly and specifically delayed the onset, and reduced the severity and extent of, DSS-induced inflammation, as assessed by clinical disease activity score, macroscopic appearance and histology of the colon, and tissue myeloperoxidase activity. Intravital fluorescence microscopy of colonic microvasculature revealed that apoA-IV significantly inhibited DSS-induced leukocyte and platelet adhesive interactions. Furthermore, apoA-IV dramatically reduced the upregulation of P-selectin on colonic endothelium during DSS-colitis. apoA-IV knockout mice exhibited a significantly greater inflammatory response to DSS than did their WT littermates; this greater susceptibility to DSS-induced inflammation was reversed upon exogenous administration of apoA-IV to knockout mice. These results provide the first direct support for the hypothesis that apoA-IV is an endogenous anti-inflammatory protein. This anti-inflammatory effect likely involves the inhibition of P-selectin–mediated leukocyte and platelet adhesive interactions.
Infectious Entry Pathway of Adeno-Associated Virus and Adeno-Associated Virus Vectors (2000)

We have investigated the infectious entry pathway of adeno-associated virus (AAV) and recombinant AAV vectors by assessing AAV-mediated gene transfer and by covalently conjugating fluorophores to AAV and monitoring entry by fluorescence microscopy. We examined AAV entry in HeLa cells and in HeLa cell lines which inducibly expressed a dominant interfering mutant of dynamin. The data demonstrate that AAV internalizes rapidly by standard receptor-mediated endocytosis from clathrin-coated pits (half-time <10 min). The lysosomotropic agents ammonium chloride and bafilomycin A(1) prevent AAV-mediated gene transfer when present during the first 30 min after the onset of endocytosis, indicating that AAV escapes from early endosomes yet requires an acidic environment for penetration into the cytosol. Following release from the endosome, AAV rapidly moves to the cell nucleus and accumulates perinuclearly beginning within 30 min after the onset of endocytosis. We present data indicating that escape of AAV from the endosome and trafficking of viral particles to the nucleus are unaffected by the presence of adenovirus, the primary helper virus for a productive AAV infection. Within 2 h, viral particles could be detected within the cell nucleus, suggesting that AAV enters the nucleus prior to uncoating. Interestingly, the majority of the intracellular virus particles remain in a stable perinuclear compartment even though gene expression from nuclear AAV genomes can be detected. This suggests that the process of nuclear entry is rate limiting or that AAV entry involves multiple pathways. Nevertheless, these data establish specific points in the AAV infectious entry process and have allowed the generation of a model for future expansion to specific cell types and AAV vector analysis in vivo.
Thromboembolic Complications following Scoliosis Surgery in Scandinavia (1979)

Out of 1229 patients operated on according to Harrington there were eight with clinical deep venous thrombosis (DVT) confirmed by phlebography or at autopsy. One patient died from massive pulmonary embolism. All eight DVT were located proximally on the left side. In two cases the first symptom was abdominal pain. At follow-up two patients had slight complaints. One had edema in hot weather and one swelling of the left leg. Another patient had no complaints but venography showed pathological collateral veins. There may be a considerable risk of development of a postthrombotic syndrome.
ThYme: a database for thioester-active enzymes (2010)

The ThYme (Thioester-active enzYme; http://www.enzyme.cbirc.iastate.edu) database has been constructed to bring together amino acid sequences and 3D (tertiary) structures of all the enzymes constituting the fatty acid synthesis and polyketide synthesis cycles. These enzymes are active on thioester-containing substrates, specifically those that are parts of the acyl-CoA synthase, acyl-CoA carboxylase, acyl transferase, ketoacyl synthase, ketoacyl reductase, hydroxyacyl dehydratase, enoyl reductase and thioesterase enzyme groups. These groups have been classified into families, members of which are similar in sequences, tertiary structures and catalytic mechanisms, implying common protein ancestry. ThYme is continually updated as sequences and tertiary structures become available.
A Simple and Highly Sensitive Radioimmunoassay for 8-A : rginine Vasopressin in Human Plasma Using a Reversed-Phase C<SUB>18</SUB> Silica Column (1985)

A highly sensitive and simple radioimmunoassay for the measurement of 8-arginine vasopressin (AVP) in human plasma has been developed. The dose response curve ranges from 0.025 to 8 pg/tube. This simple extraction technique employing an ODS C18 column recovered 87.1 +/- 10.4 (mean +/- SD)% of AVP in the range of 1-10 pg/ml added to 0.5 ml plasma. Determination of AVP in each fraction of plasma, which was gel-filtrated through a Sephadex G25 (1 X 25 cm), revealed that the fraction of plasma AVP was superimposed on that of authentic AVP, and interference of non-specific substances was completely eliminated by an ODS C18 column. Using the assay, 13 of 16 patients with diabetes insipidus (DI) showed plasma AVP concentrations ranging from 0.03 to 0.21 pg/ml, and the other 3 patients had less than 0.03 pg/ml. The AVP concentrations of DI were clearly distinguished from those obtained in normal subjects (0.30-4.20 pg/ml, n = 65). The within and between assay variability was about 10% each. Plasma AVP concentrations (mean +/- SD) of normal subjects (n = 6) standing, sitting, and supine after an overnight of fluid deprivation were 2.41 +/- 1.15, 1.95 +/- 0.85 and 0.97 +/- 0.48 pg/ml (30 min after) respectively. Plasma AVP concentrations of normal subjects (n = 6) after water load (20 ml/kg wt) were clearly reduced from 1.89 +/- 1.00 (before) to 0.42 +/- 0.21 (standing for 60 min) and also from 0.89 +/- 0.41 to 0.40 +/- 0.22 pg/ml (supine for 60 min).
MUTATIONS OF BACTERIA FROM VIRUS SENSITIVITY TO VIRUS RESISTANCE (1943)

This article reported Luria and Delbruck's breakthrough study in which they established that viruses do not induce mutations
 in bacteria, but that virus-resisting mutations are spontaneous. Their fluctuation test theory demonstrated that
 bacteria were ideal subjects for genetic research.
Proteomics and Immunological Analysis of a Novel Shrimp Allergen, Pen m 2 (2003)

Shellfish are a common cause of adverse food reactions in hypersensitive individuals and shrimp is one of the most frequently reported causes of allergic reactions. A novel allergen from Penaeus monodon, designated Pen m 2, was identified by two-dimensional immunoblotting using sera from subjects with shrimp allergy, followed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis of the peptide digest. This novel allergen was then cloned and the amino acid sequence deduced from the cDNA sequence. The cloned cDNA encoded a 356-aa protein with an acetylated N terminus at Ala2, identified by postsource decay analysis. Comparison of the Pen m 2 sequence with known protein sequences revealed extensive similarity with arginine kinase (EC 2.7.3.3) from crustaceans. Pen m 2 was purified by anion exchange chromatography and shown to have arginine kinase activity and to react with serum IgE from shrimp allergic patients and induce immediate type skin reactions in sensitized patients. Using Pen m 2-specific antisera and polyclonal sera from shrimp-sensitive subjects in a competitive ELISA inhibition assay, Pen m 2 was identified as a novel cross-reactive Crustacea allergen. This novel allergen could be useful in allergy diagnosis and in the treatment of Crustacea-derived allergic disorders.
Multi-Gb/s optical cross-connect switch architectures: TDM versus FDM techniques (2003)

The authors describe two techniques for implementing an electrooptical cross-connect switch: time division multiplexing (TDM) and frequency division multiplexing (FDM). Both methods hold the promise of realizing switch sizes substantially larger than existing ones with lithium niobate couplers. The critical technologies for the TDM technique are semiconductor mode-locked lasers and optical AND gates, with the latter being the more severe bottleneck. While compressed pulse widths in the picosecond range are achievable, practical optical AND gates capable of the same speed range remain an open research issue. The FDM technique is by far the more promising means for implementing large-size switches. By virtue of the close proximity of the actual components, the stabilization of a comb of laser frequencies can be done easily with a simple Fabry-Perot filter, thereby eliminating the need for an absolute frequency reference. The foremost technical issue is how to design a tunable receiver with a wide frequency range. This could be done either with a coherent receiver with a tunable laser as the local oscillator or with a tunable filter followed by a direct-detection receiver. In a design example, the authors illustrate a two-stage fiber Fabry-Perot filter with a free spectral range of 13650 GHz and a finesses of 4550, yielding a 1000*1000 switch at a 1.7 Gb/s line rate.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Involvement of the Intracellular Ion Channel CLIC1 in Microglia-Mediated -Amyloid-Induced Neurotoxicity (2004)

It is widely believed that the inflammatory events mediated by microglial activation contribute to several neurodegenerative processes. Alzheimer's disease, for example, is characterized by an accumulation of beta-amyloid protein (Abeta) in neuritic plaques that are infiltrated by reactive microglia and astrocytes. Although Abeta and its fragment 25-35 exert a direct toxic effect on neurons, they also activate microglia. Microglial activation is accompanied by morphological changes, cell proliferation, and release of various cytokines and growth factors. A number of scientific reports suggest that the increased proliferation of microglial cells is dependent on ionic membrane currents and in particular on chloride conductances. An unusual chloride ion channel known to be associated with macrophage activation is the chloride intracellular channel-1 (CLIC1). Here we show that Abeta stimulation of neonatal rat microglia specifically leads to the increase in CLIC1 protein and to the functional expression of CLIC1 chloride conductance, both barely detectable on the plasma membrane of quiescent cells. CLIC1 protein expression in microglia increases after 24 hr of incubation with Abeta, simultaneously with the production of reactive nitrogen intermediates and of tumor necrosis factor-alpha (TNF-alpha). We demonstrate that reducing CLIC1 chloride conductance by a specific blocker [IAA-94 (R(+)-[(6,7-dichloro-2-cyclopentyl-2,3-dihydro-2-methyl-1-oxo-1H-inden-5yl)-oxy] acetic acid)] prevents neuronal apoptosis in neurons cocultured with Abeta-treated microglia. Furthermore, we show that small interfering RNAs used to knock down CLIC1 expression prevent TNF-alpha release induced by Abeta stimulation. These results provide a direct link between Abeta-induced microglial activation and CLIC1 functional expression.
Differential Gene Expression in Response to Mechanical Wounding and Insect Feeding in Arabidopsis (2000)

Wounding in multicellular eukaryotes results in marked changes in gene expression that contribute to tissue defense and repair. Using a cDNA microarray technique, we analyzed the timing, dynamics, and regulation of the expression of 150 genes in mechanically wounded leaves of Arabidopsis. Temporal accumulation of a group of transcripts was correlated with the appearance of oxylipin signals of the jasmonate family. Analysis of the coronatine-insensitive coi1-1 Arabidopsis mutant that is also insensitive to jasmonate allowed us to identify a large number of COI1-dependent and COI1-independent wound-inducible genes. Water stress was found to contribute to the regulation of an unexpectedly large fraction of these genes. Comparing the results of mechanical wounding with damage by feeding larvae of the cabbage butterfly (Pieris rapae) resulted in very different transcript profiles. One gene was specifically induced by insect feeding but not by wounding; moreover, there was a relative lack of water stress-induced gene expression during insect feeding. These results help reveal a feeding strategy of P. rapae that may minimize the activation of a subset of water stress-inducible, defense-related genes.
Structure and Diversity of the Human T-Cell Receptor β-Chain Variable Region Genes (1986)

In order to characterize the variability of the expressed human T-cell receptor (TCR) beta-chain repertoire and contrast this variability to the known murine beta-chain repertoire, 15 independent complementary DNA (cDNA) clones containing TCR beta-chain variable region (V beta) genes were isolated from a human tonsil cDNA library. The nucleotide and derived amino acid sequences of these 15 V beta genes were analyzed together with 7 previously defined sequences. Fifteen different human V beta genes could be identified from 22 independent sequences. By means of DNA hybridization and sequence homology comparisons, it was possible to group these 15 genes into ten distinct V beta subfamilies, each containing from one to seven members. Minimal polymorphism was noted between individuals, except in multimember subfamilies. The amino acid sequences of these genes contain conserved amino acids that are also shared by murine TCR V beta genes and immunoglobulins; no features were found that distinguish human V beta genes from their murine counterparts. Evaluation of secondary structure showed that maximum variability coincides with generally hydrophilic portions of the amino acid sequence, while specific hydrophobic regions were conserved in all V beta genes examined.
Longitudinal assessment of Aβ and cognition in aging and Alzheimer disease (2011)

Aβ deposition increases slowly from cognitive normality to moderate severity DAT. Extensive Aβ deposition precedes cognitive impairment, and is associated with ApoE genotype and a higher risk of cognitive decline in HCs and progression from MCI to DAT over 1 to 2 years. However, cognitive decline is only weakly related to change in Aβ burden, suggesting that downstream factors have a more direct effect on symptom progression.
In situ hybridization to human chromosome 1 of a cDNA probe for the gene encoding the basement membrane heparan sulfate proteoglycan (HSPG) (1990)

A mouse partial cDNA clone of the heparan sulfate proteoglycan gene, an important component of basement membranes, has been mapped to human chromosome 1, band p 36.1, by in situ hybridization. No secondary sites of hybridization were observed.
Human retroviruses and AIDS 1994 (1995)

This compendium, including accompanying floppy diskettes, is the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts it comprises: (I) Nucleic Acid Alignments and Sequences; (II) Amino Acid Alignments; (III) Analysis; (IV) Related Sequences; (V) Database communications.
Preprocedural Levels of C-Reactive Protein and Leukocyte Counts Predict 9-Month Mortality After Coronary Angioplasty for the Treatment of Unprotected Left Main Coronary Artery Stenosis (2005)

Elevated preprocedural levels of CRP indicate an increased risk of death and death/MI after ULMCA stenting. Inflammatory risk assessment in patients with ULMCA stenosis may be useful for selecting patients for percutaneous coronary interventions with very low risk.
Super Water- and Oil-Repellent Surfaces on Intrinsically Hydrophilic and Oleophilic Porous Silicon Films (2008)

We demonstrate that porous Si films fabricated by a convenient gold-assisted electroless etching process, which possess a hierarchical porous structure consisting of micrometer-sized asperities superimposed onto a network of nanometer-sized pores, are able to induce a superhydrophobic phenomenon on an intrinsically hydrophilic hydrogen-terminated Si surface and a superoleophobic phenomenon on an intrinsically oleophilic self-assembled monolayer-coated Si surface. Through comparison with porous Si films consisting of vertically aligned straight pores, which are hydrophilic and oleophilic, we show that an overhang structure resulting from the hierarchical porous structure is essential to preventing water and oil from penetrating the texture of the films and inducing the observed macroscopic superhydrophobic and superoleophobic phenomena.
Green fluorescent protein‐based halide indicators with improved chloride and iodide affinities (2001)

The green fluorescent protein YFP-H148Q is sensitive to halides by a mechanism involving halide binding and a shift in pK(a). However, a limitation of YFP-H148Q is its low halide sensitivity, with K(d)>100 mM for Cl(-). Indicators with improved sensitivities are needed for cell transport studies, particularly in drug discovery by high-throughput screening, and for measurement of Cl(-) concentration in subcellular organelles. YFP-H148Q libraries were generated in which pairs of residues in the vicinity of the halide binding site were randomly mutated. An automated procedure was developed to screen bacterial colonies for improved halide sensitivity. Analysis of 1536 clones revealed improved anion sensitivities with K(d) down to 2 mM for I(-) (I152L), 40 mM for Cl(-) (V163S), and 10 mM for NO(3)(-) (I152L). The anion-sensitive mechanism of these indicators was established and their utility in cells was demonstrated using transfected cells expressing the cystic fibrosis transmembrane conductance regulator chloride channel.