gebhart/patrepeval huggingface dataset:
The role of T cell subsets in the generation of secondary cytolytic responses in vitro against class I and class II major histocompatibility complex antigens. (1984)

Strain combinations generating cytotoxic T lymphocytes (CTL) specific for a single class I (K or D) or class II (A or E) MHC molecule were set up. The responder cells were separated into Ly subsets (Ly-1+2-, Ly-1-2+, and Ly-1+2+) on day 5 of culture by using lytic or non-lytic selection techniques and monoclonal Ly-specific antibodies. The separated subsets were restimulated on day 8 and tested for secondary CTL activity on day 12. Class II-specific secondary CTL could be generated from all three subsets, whereas class I-specific CTL developed only in the Ly-1+2+ and Ly-1-2+ subsets. The Ly-1+2+ cells underwent a phenotypic shift to Ly-1-2+ by day 12, whereas CTL generated from the Ly-1+2- and Ly-1-2+ subsets retained their phenotype up to the secondary effector stage. The cells separated according to their Ly phenotypes on day 5 were the progeny of unprimed progenitors expressing the same Ly phenotypes. Unprimed Ly-1+2+ cells gave rise to CTL in the absence of the other subsets, while unprimed Ly-1+2- and Ly-1-2+ cells required the help of Ly-1+2+ cells (or soluble factors) during priming to become non-lytic CTL precursors by day 5, and cytolytic cells after restimulation. The Ly-1+2- subset could generate class II-specific secondary CTL only in the absence of the other two subsets. Apparently, alloantigen-primed Ly-1+2+ and Ly-1-2+ cells suppressed the development of cytolytic activity in the Ly-1+2- subset. The combined data provide a comprehensive pathway of CTL differentiation from T cell subsets.
Encumbrance-free telepresence system with real-time 3D capture and display using commodity depth cameras (2011)

This paper introduces a proof-of-concept telepresence system that offers fully dynamic, real-time 3D scene capture and continuous-viewpoint, head-tracked stereo 3D display without requiring the user to wear any tracking or viewing apparatus. We present a complete software and hardware framework for implementing the system, which is based on an array of commodity Microsoft Kinect™color-plus-depth cameras. Novel contributions include an algorithm for merging data between multiple depth cameras and techniques for automatic color calibration and preserving stereo quality even with low rendering rates. Also presented is a solution to the problem of interference that occurs between Kinect cameras with overlapping views. Emphasis is placed on a fully GPU-accelerated data processing and rendering pipeline that can apply hole filling, smoothing, data merger, surface generation, and color correction at rates of up to 100 million triangles/sec on a single PC and graphics board. Also presented is a Kinect-based marker-less tracking system that combines 2D eye recognition with depth information to allow head-tracked stereo views to be rendered for a parallax barrier autostereoscopic display. Our system is affordable and reproducible, offering the opportunity to easily deliver 3D telepresence beyond the researcher's lab.
Recombinant Vaccinia Virus Encoding Human MUC1 and IL2 as Immunotherapy in Patients With Breast Cancer (2000)

Polymorphic epithelial mucin, encoded by the MUC1 gene, is present at the apical surface of glandular epithelial cells. It is over-expressed and aberrantly glycosylated in most breast tumors, resulting in an antigenically distinct molecule and a potential target for immunotherapy. This transmembrane protein, when produced by tumor cells, is often cleaved into the circulation, where it is detectable as a tumor marker (CA 15.3) by various antibodies, allowing for early detection of recurrences and evaluation of treatment efficacy. The objective of the current study was to examine the clinical and environmental safety and immunogenicity of a live recombinant vaccinia virus expressing the human MUC1 and IL2 genes (VV TG5058), referred to here as TG1031. The study was an open-label phase 1 and 2 trial in nine patients with advanced inoperable breast cancer recurrences to the chest wall. The patients were vaccinated intramuscularly with a single dose of TG1031; three patients were treated at each of three progressive dose levels ranging from 5x10(5) to 5x10(7) plaque-forming units. A boost injection at their original dose level was administered in patients responding immunologically, clinically, or both. Vaccination resulted in no significant clinical adverse effects, and there was no environmental contamination by live TG1031. All patients had been vaccinated as children, and patients treated at the highest dose level mounted a significant anti-vaccinia antibody response. None of the nine patients had a significant increase in MUC1-specific antibody titers after one single injection, whereas five patients had a detectable increase in vaccinia virus antibody titers. Peripheral blood mononuclear cells of one patient at the intermediate dose level showed a proliferative response to in vitro culture with vaccinia virus, with a stimulation index of 6. A second patient treated at the intermediate dose level had a stimulation index of 7 to MUC1 peptide and of 14 after a boost injection. This patient had a concomitant decrease in carcinoembryonic antigen serum levels and remained clinically stable for 10 weeks. Evidence of MUC1-specific cytotoxic T lymphocytes was detected in two patients. Immunohistochemical analysis revealed an increase in T memory cells (CD45RO) in tumor biopsies after vaccination. The absence of serious adverse events, together with the documentation of immune stimulations in vivo, warrant the further use of TG1031 in immunotherapy trials of breast cancer.
Degradation and mineralization of atrazine by a soil bacterial isolate (1995)

An atrazine-degrading bacterial culture was isolated from an agricultural soil previously impacted by herbicide spills. The organism was capable of using atrazine under aerobic conditions as the sole source of C and N. Cyanuric acid could replace atrazine as the sole source of N, indicating that the organism was capable of ring cleavage. Ring cleavage was confirmed in 14CO2 evolution experiments with [U-14C-ring]atrazine. Between 40 and 50% of ring-14C was mineralized to 14CO2. [14C]biuret and [14C]urea were detected in spent culture media. Cellular assimilation of 14C was negligible, in keeping with the fully oxidized valence of the ring carbon. Chloride release was stoichiometric. The formation of ammonium during atrazine degradation was below the stoichiometric amount, suggesting a deficit due to cellular assimilation and metabolite-N accumulation. With excess glucose and with atrazine as the sole N source, free ammonium was not detected, suggesting assimilation into biomass. The organism degraded atrazine anaerobically in media which contained (i) atrazine only, (ii) atrazine and glucose, and (iii) atrazine, glucose, and nitrate. To date, this is the first report of a pure bacterial isolate with the ability to cleave the s-triazine ring structure of atrazine. It was also concluded that this bacterium was capable of dealkylation, dechlorination, and deamination in addition to ring cleavage.
The cyanobacterial tandem GAF domains from the cyaB2 adenylyl cyclase signal via both cAMP-binding sites (2005)

The tandem GAF domains from the cyanobacterium Anabaena PCC7120 cyaB2 adenylyl cyclase form an antiparallel dimer with cAMP bound to all four binding sites. cAMP binding causes highly cooperative allosteric enzyme activation (>500-fold; EC(50) = 1 microM; Hill coefficient >2.0). The cyaB2 GAF domains, like those of the cyclic nucleotide phosphodiesterases (PDEs), contain conserved NKFDE motifs that when mutated in the PDEs abrogate cyclic nucleotide binding. We mutated the aspartic acids within this motif in cyaB2 to determine which domains were required for signaling. Constructs containing an Asp/Ala mutation in either GAF domain still showed positive cooperative cAMP stimulation but with reduced Hill coefficients. The cyaB2 GAF domain NKFDE motifs contain inserts of 14 (GAF-A) and 19 (GAF-B) amino acids not present in PDE2 or cyaB1. Constructs having these inserts deleted could still be activated by cAMP (23- to 100-fold) but lost all positive cooperative activation, suggesting that the inserts play an important role in domain interaction and/or stabilization of the cAMP-binding pockets. In the shortened constructs, even those with a single Asp/Ala mutation in the NKFDE motifs could still be activated by cAMP. However, in a double Asp/Ala mutant of the shortened construct, stimulation by cAMP was almost completely lost, and the EC(50) shifted far to the right. Overall, the data suggest that in GAF domains without these inserts, only the canonical lysine:aspartate salt bridge keeps the alpha4-helix and the alpha4-beta5 linker that close over the cyclic nucleotide properly oriented, thereby stabilizing the binding pocket. The cyaB2 GAF ensemble appears to be an evolutionary intermediate where both GAF domains still participate in allosteric activation by cAMP.
A 3D Multi-Aperture Image Sensor Architecture (2006)

An image sensor comprising an array of apertures each with its own local integrated optics and pixel array is presented. A lens focuses the image above the sensor creating overlapping fields of view between apertures. Multiple perspectives of the image in the focal plane facilitate the synthesis of a 3D image at a higher spatial resolution than the aperture count. Depth resolution is shown to continue to improve with pixel scaling below the diffraction limit. Preliminary circuit implementation is described
Exogenous transforming growth factor-beta 2 enhances connective tissue formation and wound strength in guinea pig dermal wounds healing by secondary intent. (1990)

The presence of transforming growth factor-beta (TGF-beta) at the site of acute injury, its ability to attract inflammatory and connective tissue cells, and its stimulatory effect on the deposition of connective tissue matrix combine to suggest that it may play a key role in the response to injury. The effect of exogenous TGF-beta form 2 on dermal wounds healing by secondary intent was investigated using a sponge composed of collagen and heparin as a delivery vehicle. Longitudinal lenticular-shaped wounds on the dorsum of adult guinea pigs were treated at the time of wounding with delivery vehicle containing 0.5, 1, or 5 micrograms of purified, bovine bone-derived TGF-beta 2, and were compared with wounds that received vehicle only or were untreated. At days 8 and 14 the amount of connective tissue in the wounds and the extent of epithelialization were determined by histomorphometric methods, and wound breaking strength was determined. At day 8, but not at day 14, wounds treated with 1 or 5 micrograms of TGF-beta 2 contained a significantly higher proportion of connective tissue than did wounds treated with vehicle only, and they also exhibited higher wound strength. No effect on wound size or re-epithelialization was detected. The observations provide evidence that a single treatment with exogenous TGF-beta 2 delivered in collagen/heparin sponge vehicle can accelerate repair in guinea pig dermal wounds allowed to heal by secondary intent.
T Cell Accumulation in B Cell Follicles Is Regulated by Dendritic Cells and Is Independent of B Cell Activation (2003)

We investigated the mechanism of CD4 T cell accumulation in B cell follicles after immunization. Follicular T cell numbers were correlated with the number of B cells, indicating B cell control of the niche that T cells occupy. Despite this, we found no role for B cells in the follicular migration of T cells. Instead, T cells are induced to migrate into B cell follicles entirely as a result of interaction with dendritic cells (DCs). Migration relies on CD40-dependent maturation of DCs, as it did not occur in CD40-deficient mice but was reconstituted with CD40(+) DCs. Restoration was not achieved by the activation of DCs with bacterial activators (e.g., lipopolysaccharide, CpG), but was by the injection of OX40L-huIgG1 fusion protein. Crucially, the up-regulation of OX40L (on antigen-presenting cells) and CXCR-5 (on T cells) are CD40-dependent events and we show that T cells do not migrate to follicles in immunized OX40-deficient mice.
A comparison of bowel preparations for flexible sigmoidoscopy: oral magnesium citrate combined with oral bisacodyl, one hypertonic phosphate enema, or two hypertonic phosphate enemas (1999)

OBJECTIVE: Magnesium citrate with hypertonic enemas or oral bisacodyl provides superior preparation quality for sigmoidoscopy over enemas alone. We compared three magnesium citrate sigmoidoscopy preparations in a randomized, single-blind, controlled trial. METHODS: Two hundred and ninety-one adults scheduled for routine sigmoidoscopy were randomly assigned to receive one of three preparations containing oral magnesium citrate (296 cc) taken the night before the procedure in combination with the following: 1) oral bisacodyl (10 mg), given with the magnesium citrate the night before the procedure; 2) one hypertonic phosphate enema 1 h before the procedure; or 3) two hypertonic phosphate enemas, given singly at 2 and 1 h before the procedure. Endoscopists rated preparation quality, procedure duration, and depth of endoscopic insertion. Patients assessed preparation comfort and overall satisfaction. RESULTS: Preparation quality was rated as excellent or good for 80.6% in the bisacodyl group, 88.7% in the one-enema group, and 85.1% in the two-enema group (p = 0.30). Patients reported the oral bisacodyl regimen was better tolerated (p = 0.032). Although the three regimens were comparable in most side effects, the bisacodyl preparation was associated with more diarrhea (p = 0.0003). Mean procedure duration, mean insertion depth, and prevalence of diverticula and polyps were similar in all groups. Fewer than 4% of patients required repeat procedures due to poor preparation quality. CONCLUSIONS: There was no statistical difference between the quality of the three bowel preparations. Patients considered an oral bisacodyl and magnesium citrate regimen more easily tolerated, though it was associated with more diarrhea.
Atenolol in seasonal affective disorder: a test of the melatonin hypothesis (1988)

To test the hypothesis that the antidepressant effects of bright light in seasonal affective disorder are mediated by the suppression of melatonin, 19 patients with this disorder were given atenolol, which suppresses melatonin secretion, and placebo in a double-blind crossover study. No difference in antidepressant efficacy was found between drug and placebo in the sample as a whole, which argues against the melatonin hypothesis of phototherapy. However, in three of the patients atenolol provided repeated, marked, and sustained relief of symptoms, suggesting that it may be useful in treating the winter depressive symptoms of some patients with seasonal affective disorder.
Holography: Just a Fancy Word for Interferometry? (2016)

In holography, we create a “holistic” representation of a light wave from the coherent superposition of measurement and reference beams. We shift the light phase to detect the complex amplitude. This sounds a lot like interferometry! Here I explore how advances in digital signal processing are driving a convergence of the two techniques.
IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex (2003)

The IMGT/HLA database (http://www.ebi.ac.uk/imgt/hla) has provided a centralized repository for the sequences of the alleles named by the WHO Nomenclature Committee for Factors of the HLA System for the past four years. Since its initial release the database has grown and is the primary source of information for the study of sequences of the human major histocompatibilty complex. The initial release of the database contained a limited number of tools. As a result of feedback from our users and developments in HLA we have been able to provide new tools and facilities. The HLA sequences have also been extended to include intron sequences and the 3' and 5' untranslated regions in the alignments and also the inclusion of new genes such as MICA. The IMGT/MHC database (http://www.ebi.ac.uk/imgt/mhc) was released in March 2002 to provide a similar resource for other species. The first release of IMGT/MHC contains the sequences of non-human primates (apes, new and old world monkeys), canines and feline sequences. Further species will be added shortly and the database aims to become the primary source of MHC data for non-human sequences.
Oxazolidinone Antibiotics Target the P Site onEscherichiacoliRibosomes (2002)

The oxazolidinones are a novel class of antimicrobial agents that target protein synthesis in a wide spectrum of gram-positive and anaerobic bacteria. The oxazolidinone PNU-100766 (linezolid) inhibits the binding of fMet-tRNA to 70S ribosomes. Mutations to oxazolidinone resistance in Halobacterium halobium, Staphylococcus aureus, and Escherichia coli map at or near domain V of the 23S rRNA, suggesting that the oxazolidinones may target the peptidyl transferase region responsible for binding fMet-tRNA. This study demonstrates that the potency of oxazolidinones corresponds to increased inhibition of fMet-tRNA binding. The inhibition of fMet-tRNA binding is competitive with respect to the fMet-tRNA concentration, suggesting that the P site is affected. The fMet-tRNA reacts with puromycin to form peptide bonds in the presence of elongation factor P (EF-P), which is needed for optimum specificity and efficiency of peptide bond synthesis. Oxazolidinone inhibition of the P site was evaluated by first binding fMet-tRNA to the A site, followed by translocation to the P site with EF-G. All three of the oxazolidinones used in this study inhibited translocation of fMet-tRNA. We propose that the oxazolidinones target the ribosomal P site and pleiotropically affect fMet-tRNA binding, EF-P stimulated synthesis of peptide bonds, and, most markedly, EF-G-mediated translocation of fMet-tRNA into the P site.
A general approach to the synthesis of C8-oxygenated guaianolides (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA general approach to the synthesis of C8-oxygenated guaianolidesJames H. Rigby and Jo Ann Zbur WilsonCite this: J. Org. Chem. 1987, 52, 1, 34–44Publication Date (Print):January 1, 1987Publication History Published online1 May 2002Published inissue 1 January 1987https://pubs.acs.org/doi/10.1021/jo00377a006https://doi.org/10.1021/jo00377a006research-articleACS PublicationsRequest reuse permissionsArticle Views722Altmetric-Citations38LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Monolithic 3D integration in a CMOS process flow (2014)

We describe a 3D integration process flow in which the vertical distance from the CMOS layer to the novel device layer is 100-1000 nm. This short distance effectively defines the process flow as a silicon CMOS process flow and allows for the use of silicon infrastructure in process and design. Progress has been made in demonstrating various pieces of III-V device integration into a foundry 0.18 μm process on 200 mm wafers.
Structure and Electrochemistry of Copper Fluoride Nanocomposites Utilizing Mixed Conducting Matrices (2007)

Near-theoretical utilization of high-energy-density CuF2 positive electrode materials for lithium batteries was enabled through the use of nanocomposites consisting of 2−30 nm domains of CuF2 within a mixed ionic + electronic conducting matrix of a metal oxide. Small but significant crystallographic changes to the core crystal of the CuF2 were found to occur in all oxide-based matrices. These modifications to the core crystal and the surrounding matrix were investigated through a host of characterization methods, including XRD, XPS, and XAS. This new approach to the enablement of the anhydrous CuF2 is distinctly superior in performance to that of macro CuF2 or CuF2 nanocomposites utilizing carbon as a matrix, the latter of which is also introduced herein for the first time.
Epidemiology of Sepsis Syndrome in 8 Academic Medical Centers (1997)

Sepsis syndrome is common in academic hospitals, although the overall rates vary considerably with the patient population. A substantial fraction of cases occur outside ICUs. An understanding of the hospitalwide epidemiology of sepsis syndrome is vital for rational planning and treatment of hospitalized patients with sepsis syndrome, especially as new and expensive therapeutic agents become available.
Self-Help Techniques for Auditory Hallucinations in Schizophrenia (1995)

Even with the best treatment available in the United States, people with schizophrenia often remain troubled by auditory hallucinations. Given the less than optimal results of traditional mental health care, the following exploratory study was conducted. A convenience sample of 33 adult outpatients with schizophrenia were interviewed to elicit what (if any) self-help strategies they used for coping with auditory hallucinations. The patients were all being treated at a community mental health clinic. The self-help strategies reported by the patients included (a) physiological changes, (b) cognitive processes, and (c) behavioral changes. The strategies were then rank-ordered by frequency of use and self-reported effectiveness. Various self-help strategies used by subgroups were examined. Men used techniques that were more isolative, and women used more interpersonal techniques to cope with their auditory hallucinations. Participants hearing hostile "voices" (both men and women) tended to use substances such as alcohol and prescribed medications. The results of this study may be used to increase understanding of socially appropriate self-help coping strategies in patients with schizophrenia who experience auditory hallucinations.
Induction of insulitis by glutamic acid decarboxylase peptide-specific and HLA-DQ8-restricted CD4(+) T cells from human DQ transgenic mice. (1998)

Insulin-dependent diabetes mellitus in humans is linked with specific HLA class II genes, e.g., HLA-DQA1*0301/ DQB1*0302 (DQ8). To investigate the roles of HLA-DQ8 molecules and glutamic acid decarboxylase (GAD) in disease development, we generated DQ8(+)/I-Abo transgenic mice expressing functional HLA-DQ8 molecules and devoid of endogenous mouse class II. DQ8(+)/I-Abo mice produced antigen-specific antibodies and formed germinal centers after immunization with GAD65 peptides. Two GAD peptide-specific (247-266 and 509-528), DQ8 restricted Th1 CD4(+) T cell lines, were generated from immunized DQ8(+)/I-Abo mice. They induced severe insulitis after adoptive transfer into transgene positive (but not negative) mice who were treated with a very low dose of streptozotocin that alone caused no apparent islet pathology. In addition to CD4, islet mRNA from these mice also showed expression of CD8, IFNgamma, TNFalpha, Fas, and Fas ligand. Our data suggest that a mild islet insult in the presence of HLA-DQ8 bearing antigen-presenting cells promotes infiltration of GAD peptide reactive T cells into the islet.