gebhart/patrepeval huggingface dataset:
Identification of a shared HLA-A*0201-restricted T-cell epitope from the melanoma antigen tyrosinase-related protein 2 (TRP2). (1998)

Tyrosinase-related protein 2 (TRP2) is a melanosomal enzyme expressed in most mammalian melanocytes and melanomas. This protein has been identified as a melanoma antigen recognized by tumor reactive CTLs derived from tumor infiltrating lymphocytes in the context of HLA-A31 and HLA-A33. The frequencies of these HLA-A alleles among melanoma patients in the United States is low (approximately 6% for HLA-A31 and approximately 2% for HLA-A33) compared with that of HLA-A*0201 (approximately 46%). Therefore, to extend significantly the use of TRP2-based immunotherapies for the treatment of patients with melanoma, we searched for new HLA-A*0201-restricted epitopes from this protein by screening TRP2-derived peptides for the induction of melanoma-reactive CTL. Fifty-one peptides were selected from TRP2 based on a permissive HLA-A*0201 binding motif, and the 21 peptides with the highest experimentally determined binding affinities were used to stimulate peripheral blood lymphocytes from HLA-A*0201+ melanoma patients in vitro. One peptide, TRP2(180-188) (SVYDFFVWL), induced CTLs from three of four patients that specifically recognized peptide-pulsed T2 cells, COS-7 cells expressing HLA-A*0201 and TRP2, and HLA-A2+ TRP2+ melanomas. TRP2(180-188) is identical to a previously identified TRP2 epitope recognized by murine melanoma-reactive CTLs in the context of H-2Kb. These results suggest that TRP2 may be useful for the development of murine tumor immunotherapy models and for the treatment of melanoma patients who are diverse in HLA expression.
Enhanced levels of functional HIV-1 co-receptors on human mucosal T cells demonstrated using intestinal biopsy tissue (2000)

Enhanced expression of CXCR4 and CCR5 on CD4 lymphocytes in normal intestinal mucosa predicts increased vulnerability to infection by both R5 and X4 HIV-1. Endoscopic biopsies provide a useful mucosal tissue sampling technique to identify compartmental immunologic differences that may be exploited by HIV-1 in establishing initial mucosal infection.
Stromal cell-derived factor-1 (SDF-1) acts together with thrombopoietin to enhance the development of megakaryocytic progenitor cells (CFU-MK) (2000)

Stromal cell-derived factor-1 (SDF-1) is a CXC chemokine that acts as a stimulator of pre-B lymphocyte cell growth and as a chemoattractant for T cells, monocytes, and hematopoietic stem cells. More recent studies also suggest that megakaryocytes migrate in response to SDF-1. Because genetic elimination of SDF-1 or its receptor lead to marrow aplasia, we investigated the effect of SDF-1 on megakaryocyte progenitors (colony-forming units-megakaryocyte [CFU-MK]). We report that SDF-1 augments the growth of CFU-MK from whole murine bone marrow cells when combined with thrombopoietin (TPO). The addition of SDF-1 to interleukin-3 (IL-3) or stem cell factor (SCF) had no effect. Specific antagonists for CXCR4 (the sole receptor for SDF-1), T22, and 1-9 (P2G) SDF-1 reduced megakaryocyte colony growth induced by TPO alone, suggesting that many culture systems contain endogenous levels of the chemokine that contributes to the TPO effect. To examine whether SDF-1 has direct effects on CFU-MK, we developed a new protocol to purify megakaryocyte progenitors. CFU-MK were highly enriched in CD41(high) c-kit(high) cells generated from lineage-depleted TPO-primed marrow cells. Because the growth-promoting effects of SDF-1 were also observed when highly purified populations of CFU-MK were tested in serum-free cultures, these results suggest that SDF-1 directly promotes the proliferation of megakaryocytic progenitors in the presence of TPO, and in this way contributes to the favorable effects of the bone marrow microenvironment on megakaryocyte development.
Potentiation of amygdala AMPA receptor activity selectively promotes escalated alcohol self‐administration in a CaMKII‐dependent manner (2016)

Growing evidence indicates that drugs of abuse gain control over the individual by usurping glutamate-linked mechanisms of neuroplasticity in reward-related brain regions. Accordingly, we have shown that glutamate α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) activity in the amygdala is required for the positive reinforcing effects of alcohol, which underlie the initial stages of addiction. It is unknown, however, if enhanced AMPAR activity in the amygdala facilitates alcohol self-administration, which is a kernel premise of glutamate hypotheses of addiction. Here, we show that low-dose alcohol (0.6 g/kg/30 minutes) self-administration increases phosphorylation (activation) of AMPAR subtype GluA1 S831 (pGluA1 S831) in the central amygdala (CeA), basolateral amygdala and nucleus accumbens core (AcbC) of selectively bred alcohol-preferring P-rats as compared with behavior-matched (non-drug) sucrose controls. The functional role of enhanced AMPAR activity was assessed via site-specific infusion of the AMPAR positive modulator, aniracetam, in the CeA and AcbC prior to alcohol self-administration. Intra-CeA aniracetam increased alcohol-reinforced but not sucrose-reinforced responding and was ineffective following intra-AcbC infusion. Because GluA1 S831 is a Ca2+/calmodulin-dependent protein kinase II (CaMKII) substrate, we sought to determine if AMPAR regulation of enhanced alcohol self-administration is dependent on CaMKII activity. Intra-CeA infusion of the cell-permeable CaMKII peptide inhibitor myristolated autocamtide-2-related inhibitory peptide (m-AIP) dose-dependently reduced alcohol self-administration. A subthreshold dose of m-AIP also blocked the aniracetam-induced escalation of alcohol self-administration, demonstrating that AMPAR-mediated potentiation of alcohol reinforcement requires CaMKII activity in the amygdala. Enhanced activity of plasticity-linked AMPAR-CaMKII signaling in the amygdala may promote escalated alcohol use via increased positive reinforcement during the initial stages of addiction.
Structural Basis for Gluten Intolerance in Celiac Sprue (2002)

Celiac Sprue, a widely prevalent autoimmune disease of the small intestine, is induced in genetically susceptible individuals by exposure to dietary gluten. A 33-mer peptide was identified that has several characteristics suggesting it is the primary initiator of the inflammatory response to gluten in Celiac Sprue patients. In vitro and in vivo studies in rats and humans demonstrated that it is stable toward breakdown by all gastric, pancreatic, and intestinal brush-border membrane proteases. The peptide reacted with tissue transglutaminase, the major autoantigen in Celiac Sprue, with substantially greater selectivity than known natural substrates of this extracellular enzyme. It was a potent inducer of gut-derived human T cell lines from 14 of 14 Celiac Sprue patients. Homologs of this peptide were found in all food grains that are toxic to Celiac Sprue patients but are absent from all nontoxic food grains. The peptide could be detoxified in in vitro and in vivo assays by exposure to a bacterial prolyl endopeptidase, suggesting a strategy for oral peptidase supplement therapy for Celiac Sprue.
Long-range correlations in smoke-particle aggregates (1979)

Ultrafine smoke particles stick together to form chain-like aggregates. It is found that the particle density has long-range correlations of the same form in iron, zinc of silicon dioxide aggregates. The correlation data suggest a power-law spatial dependence giving a Hausdorff dimension between 1.7 and 1.9. The authors discuss the consistency of these results with a model based on percolation. They also compare their results with a random-walk model, which has a nominal Hausdorff dimension of 2.
Effects of topical aldose reductase inhibitor CT-112 on corneal sensitivity of diabetic rats (1996)

It is clear that corneal hypesthesia occurs in diabetic rats as it does in human diabetics, and treatment with an ARI prevents this change. Along with the functional abnormality, the ultrastructural changes of corneal nerve also occur in diabetic rats, and they are prevented by ARI. These results strongly suggest that aldose reductase is involved in corneal hypesthesia and ultrastructural changes of corneal nerve in diabetic rats. These defects are ameliorated by aldose reductase inhibitor.
Reevaluation of the Role of Duration of Morning Stiffness in the Assessment of Rheumatoid Arthritis Activity (2009)

MS duration has a moderate correlation with RA disease activity. Assessment of MS duration may be clinically helpful in patients with low RAPID3 scores.
Epidermal growth factor receptor in relation to tumor development: EGFR gene and cancer (2009)

Epidermal growth factor receptor (EGFR) and its three related proteins (the ERBB family) are receptor tyrosine kinases that play essential roles in both normal physiological conditions and cancerous conditions. Upon binding its ligands, dynamic conformational changes occur in both extracellular and intracellular domains of the receptor tyrosine kinases, resulting in the transphosphorylation of tyrosine residues in the C-terminal regulatory domain. These provide docking sites for downstream molecules and lead to the evasion of apoptosis, to proliferation, to invasion and to metastases, all of which are important for the cancer phenotype. Mutation in the tyrosine kinase domain of the EGFR gene was found in a subset of lung cancers in 2002. Lung cancers with an EGFR mutation are highly sensitive to EGFR tyrosine kinase inhibitors, such as gefitinib and erlotinib. Here, we review the discovery of EGFR, the EGFR signal transduction pathway and mutations of the EGFR gene in lung cancers and glioblastomas. The biological significance of such mutations and their relationship with other activated genes in lung cancers are also discussed.
Autocomplete hand-drawn animations (2015)

Hand-drawn animation is a major art form and communication medium, but can be challenging to produce. We present a system to help people create frame-by-frame animations through manual sketches. We design our interface to be minimalistic: it contains only a canvas and a few controls. When users draw on the canvas, our system silently analyzes all past sketches and predicts what might be drawn in the future across spatial locations and temporal frames. The interface also offers suggestions to beautify existing drawings. Our system can reduce manual workload and improve output quality without compromising natural drawing flow and control: users can accept, ignore, or modify such predictions visualized on the canvas by simple gestures. Our key idea is to extend the local similarity method in [Xing et al. 2014], which handles only low-level spatial repetitions such as hatches within a single frame, to a global similarity that can capture high-level structures across multiple frames such as dynamic objects. We evaluate our system through a preliminary user study and confirm that it can enhance both users' objective performance and subjective satisfaction.
Analysis of the Native Quaternary Structure of Vanilloid Receptor 1 (2001)

Vanilloid receptor subtype 1 (VR1) is a ligand-gated channel that can be activated by capsaicin and other vanilloids as well as by protons and heat. In the present study, we have analyzed the oligomeric state of VR1. Co-immunoprecipitation of differently tagged VR1 molecules indicated that VR1 can form oligomers. Using two different heterologous VR1 expression systems as well as endogenous VR1 expressed in dorsal root ganglion cells, we analyzed oligomer formation using perfluoro-octanoic acid polyacrylamide gel electrophoresis. Results were confirmed both with chemical cross-linking agents as well as through endogenous cross-linking mediated by transglutaminase. Our results clearly show that VR1 forms multimers in each of the expression systems with a homotetramer as a predominant form. The oligomeric structure of VR1 may contribute to the complexity of VR1 pharmacology. Finally, differences in glycosylation between the systems were observed, indicating the need for caution in the use of the heterologous expression systems for analysis of VR1 properties.
Using laser range data for 3D SLAM in outdoor environments (2006)

Traditional simultaneous localization and mapping (SLAM) algorithms have been used to great effect in flat, indoor environments such as corridors and offices. We demonstrate that with a few augmentations, existing 2D SLAM technology can be extended to perform full 3D SLAM in less benign, outdoor, undulating environments. In particular, we use data acquired with a 3D laser range finder. We use a simple segmentation algorithm to separate the data stream into distinct point clouds, each referenced to a vehicle position. The SLAM technique we then adopt inherits much from 2D delayed state (or scan-matching) SLAM in that the state vector is an ever growing stack of past vehicle positions and inter-scan registrations are used to form measurements between them. The registration algorithm used is a novel combination of previous techniques carefully balancing the need for maximally wide convergence basins, robustness and speed. In addition, we introduce a novel post-registration classification technique to detect matches which have converged to incorrect local minima
Other Disciplines, Methodologies, and Countries: Studying Courts and Crisis (2004)

The United States is at war: in Iraq, in Afghanistan, and against terrorism. This symposium asks the timely question: How do governments and their citizens respond to fear and risk in times of crisis? In the essay, I begin by framing the issue very briefly. I then argue that understanding this issue requires scholars to follow Epstein and Wells by looking to other disciplines, methodologies, and countries.
Immune privilege induced by regulatory T cells in transplantation tolerance (2006)

Immune privilege was originally believed to be associated with particular organs, such as the testes, brain, the anterior chamber of the eye, and the placenta, which need to be protected from any excessive inflammatory activity. It is now becoming clear, however, that immune privilege can be acquired locally in many different tissues in response to inflammation, but particularly due to the action of regulatory T cells (Tregs) induced by the deliberate therapeutic manipulation of the immune system toward tolerance. In this review, we consider the interplay between Tregs, dendritic cells, and the graft itself and the resulting local protective mechanisms that are coordinated to maintain the tolerant state. We discuss how both anti-inflammatory cytokines and negative costimulatory interactions can elicit a number of interrelated mechanisms to regulate both T-cell and antigen-presenting cell activity, for example, by catabolism of the amino acids tryptophan and arginine and the induction of hemoxygenase and carbon monoxide. The induction of local immune privilege has implications for the design of therapeutic regimens and the monitoring of the tolerant status of patients being weaned off immunosuppression.
Segmentation of cardiac cine MR images for extraction of right and left ventricular chambers (1995)

A two-stage algorithm for extraction of the ventricular chambers (endocardial surfaces) in flow-enhanced magnetic resonance images is described. In the first stage, the approximate locations and sizes of the endocardial surfaces are determined by intensity thresholding. In the second stage, points on each approximated surface are repositioned to nearest locally maximum gradient magnitude points and a generalized cylinder is fitted to them. Examples of ventricular chambers in cine MR images determined by this algorithm are presented.
Improved Functional Group Compatibility in the Palladium-Catalyzed Synthesis of Aryl Amines (2002)

[reaction: see text] The use of Pd2dba3 with bulky, electron-rich ligands 1 or 2 and LiN(TMS)2 as the base for the coupling of amines with aryl halides containing hydroxyl, amide, or enolizable keto groups is described. This protocol expands the utility of palladium-catalyzed C-N bond formation by allowing for the use of aryl halides containing these functional groups, obviating the need for protecting group manipulations.
In Vivo and In Vitro Effects of Tea Extracts on Enterotoxigenic Escherichia coli‐induced Intestinal Fluid Loss in Animal Models (2006)

Tea may inhibit net fluid and electrolyte losses involved in secretory diarrhoea from ETEC.
High-temperature photoluminescence spectroscopy in p-type SiC (2004)

Photoluminescence (PL) spectra were analysed for Al- and B-doped p-type silicon carbide single crystals in a broad spectral range between 0.7 eV and 3.25 eV at temperatures up to 300 °C (570 K). Of special interest was to explore the effect of thermal activation of the PL intensity, which is exhibited as a strong increase in the visible luminescence at elevated temperatures. Specifically, the 'orange' PL band, with a maximum at 1.82 eV shows thermal activation exceeding one order of magnitude. Using thermally stimulated luminescence (TSL), we present experimental evidence that the Al and B acceptors in p-type SiC act as hole traps being partially compensated by deep donors. Thermal PL activation allowed for identification of luminescence transition at the 'orange' centres as a free-to-bound hole recombination for both types of impurities. Room temperature spatially resolved PL spectroscopy and TSL imaging on 50 mm diameter p-type SiC wafers confirmed the mechanism of luminescence, and revealed spatial inhomogeneity of the concentration of the major compensating defects.
Specific Protein Docking to Chelator Lipid Monolayers Monitored by FT‐IR Spectroscopy at the Air–Water Interface (1996)

A novel class of chelator lipids combines the fundamental properties of self-assembly with protein engineering techniques, leading to well-organized biofunctionalized interfaces and two-dimensional protein arrays. Reflection FT-IR spectroscopy at the air - water interface was used to monitor the formation of a metal-sensitive lipid film as well as the reversible and specific docking (represented on the right) of a fusion protein (B) to this chelator lipid layer through a histidine tag (A).
Environmental effects on seed composition of Victorian canola (2000)

Data from advanced breeding experiments between 1985 and 1994 were used to determine the effects of region, year and environment on the quality of canola grown across Victoria. Estimates from these unbalanced data were made using residual maximum likelihood. Environmental effects were large relative to cultivar effects for oil and protein content, while the reverse occurred for glucosinolate content. High oil contents (and low seed protein contents) were correlated with cooler spring temperatures and higher spring rainfall. Oil contents were lowest, on average, in canola grown in dry years, or from the hotter regions, such as the Mallee, and were highest in canola from the cooler, wetter regions, such as south-western and north-eastern Victoria. Fatty acid composition varied with year and region. Means for saturated fatty acid content averaged 6.4 0.1%. The oleic acid content averaged 60.3 0.4% and was higher in canola grown in central Victoria and the Wimmera, and in most years, in north-eastern Victoria compared with other regions. Low temperatures and low rainfall reduced oleic acid content. Linoleic acid content averaged 19.7 0.3% and linolenic acid averaged 10.4 0.3%, with the content of these fatty acids negatively correlated with the content of oleic acid. Erucic acid levels were below 0.6% in all regions.
Coordinate Regulation of RAG1 and RAG2 by Cell Type-Specific DNA Elements 5' of RAG2 (1999)

RAG1 and RAG2 are essential for V(D)J recombination and lymphocyte development. These genes are thought to encode a transposase derived from a mobile genetic element that was inserted into the vertebrate genome 450 million years ago. The regulation of RAG1 and RAG2 was investigated in vivo with bacterial artificial chromosome (BAC) transgenes containing a fluorescent indicator. Coordinate expression of RAG1 and RAG2 in B and T cells was found to be regulated by distinct genetic elements found on the 5' side of the RAG2 gene. This observation suggests a mechanism by which asymmetrically disposed cis DNA elements could influence the expression of the primordial transposon and thereby capture RAGs for vertebrate evolution.
Cell Signaling during Cold, Drought, and Salt Stress (2002)

Low temperature, drought, and high salinity are common stress conditions that adversely affect plant growth and crop production. The cellular and molecular responses of plants to environmental stress have been studied intensively ([Thomashow, 1999][1]; [Hasegawa et al., 2000][2]). Understanding the
Interdomain Interaction in the FimH Adhesin of Escherichia coli Regulates the Affinity to Mannose (2007)

FimH is a mannose-specific adhesin located on the tip of type 1 fimbriae of Escherichia coli that is capable of mediating shear-enhanced bacterial adhesion. FimH consists of a fimbria-associated pilin domain and a mannose-binding lectin domain, with the binding pocket positioned opposite the interdomain interface. By using the yeast two-hybrid system, purified lectin and pilin domains, and docking simulations, we show here that the FimH domains interact with one another. The affinity for mannose is greatly enhanced (up to 300-fold) in FimH variants in which the interdomain interaction is disrupted by structural mutations in either the pilin or lectin domains. Also, affinity to mannose is dramatically enhanced in isolated lectin domains or in FimH complexed with the chaperone molecule that is wedged between the domains. Furthermore, FimH with native structure mediates weak binding at low shear stress but shifts to strong binding at high shear, whereas FimH with disrupted interdomain contacts (or the isolated lectin domain) mediates strong binding to mannose-coated surfaces even under low shear. We propose that interactions between lectin and pilin domains decrease the affinity of the mannose-binding pocket via an allosteric mechanism. We further suggest that mechanical force at high shear stress separates the two domains, allowing the lectin domain to switch from a low affinity to a high affinity state. This shift provides a mechanism for FimH-mediated shear-enhanced adhesion by enabling the adhesin to form catch bond-like interactions that are longer lived at high tensile force.
Expression, renaturation and purification of recombinant human interleukin 4 from Escherichia coli (1988)

The lymphokine human interleukin 4 (IL-4) has been expressed from a plasmid in the cytoplasm of Escherichia coli. Advantage has been taken of insolubility of the human IL-4 in E. coli for rapid purification of this protein in only a few steps. We describe extraction and renaturation procedures which solubilize human IL-4 yielding biologically active protein. The protein was purified to homogeneity by one passage over a gel-filtration column. The refolded human IL-4 was characterized by N-terminal sequence analysis, amino acid analysis and bioassays. The refolded E. coli-derived human IL-4 has biological activity on T and B cells and binds to the human IL-4 receptor, comparable to mammalian expressed human IL-4, indicating that the protein is folded correctly.