gebhart/patrepeval huggingface dataset:
Identification of a new HLA-A*0201-restricted T-cell epitope from the tyrosinase-related protein 2 (TRP2) melanoma antigen (2000)

For the development of peptide-based immunotherapies, the identification of additional tumor antigens and T-cell epitopes is required. Because HLA-A(*)0201 is the most common allele in Caucasians, who represent the majority of patients with melanomas, 6 peptides carrying an HLA-A(*)0201 motif were synthesized from tyrosinase-related protein-2 (TRP2) melanoma antigen and tested for binding affinity to the HLA allele using processing-defective T2 cells. These peptides were then pulsed onto autologous dendritic cells and used to stimulate in vitro CD8(+)-enriched T cells isolated from peripheral blood of HLA-A(*)02(+) healthy donors or melanoma patients for the induction of specific cytotoxic T lymphocytes (CTLs). One peptide, TRP2(288-296) (SLDDYNHLV), the best HLA-A(*)0201 binder, elicited specific CTLs from 1 of 4 patients and 3 of 4 healthy donors. The induced CTLs from the patient and from 1 donor efficiently recognized HLA-A(*)02(+) TRP2(+) melanomas as well as COS-7 cells expressing HLA-A(*)0201 and TRP2 in an HLA class I-restricted manner, as assessed by cytokine production and direct cytolysis. The remaining 2 CTL lines derived from 2 donors displayed low T-cell receptor avidity, which could lyse melanoma cells in the presence of exogenous peptide. Since TRP2 is an antigen expressed in most melanomas, identification of the TRP2/HLA-A(*)0201 peptide SLDDYNHLV may facilitate the design of present peptide-based immunotherapies for the treatment of a large fraction of melanoma patients.
An STS-Based Map of the Human Genome (1995)

A physical map has been constructed of the human genome containing 15,086 sequence-tagged sites (STSs), with an average spacing of 199 kilobases. The project involved assembly of a radiation hybrid map of the human genome containing 6193 loci and incorporated a genetic linkage map of the human genome containing 5264 loci. This information was combined with the results of STS-content screening of 10,850 loci against a yeast artificial chromosome library to produce an integrated map, anchored by the radiation hybrid and genetic maps. The map provides radiation hybrid coverage of 99 percent and physical coverage of 94 percent of the human genome. The map also represents an early step in an international project to generate a transcript map of the human genome, with more than 3235 expressed sequences localized. The STSs in the map provide a scaffold for initiating large-scale sequencing of the human genome.
Soluble Fms-like Tyrosine Kinase-1 Expression Inhibits the Growth of Multiple Myeloma in Nude Mice (2007)

Angiogenesis is an essential factor in the growth and progression of hematological malignancies including multiple myeloma (MM). Vascular endothelial growth factor and its receptors have been shown to be targets for treating tumors. This study explores the effect of adenovirus-mediated delivery of soluble vascular endothelial growth factor receptor Fms-like tyrosine kinase-1 (sFLT-1) on the growth of MM cell line KM3 in nude mice. sFLT-1 cDNA was amplified by reverse transcription-polymerase chain reaction from human umbilical vein endothelial cells and was used as a transgene to construct an adenoviral vector carrying sFLT-1 (ADV-sFLT). Cell proliferation and 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide assays were carried out to evaluate the effect of ADV-sFLT on human umbilical vein endothelial cells and KM3 cells in vitro. Eighteen female BALB/c nude mice were inoculated subcutaneously with KM3 cells, and they were randomly divided into three groups and injected intravenously with ADV-sFLT, ADV-LacZ, or phosphate-buffered saline (PBS). The volume of KM3 xenografts was measured twice a week. Three weeks after the initial treatment, the volume of MM xenografts in the mice treated with ADV-sFLT, ADV-LacZ, or PBS was 770.32+/-28.73 mm3, 1983.36+/-43.72 mm3, and 2042.05+/-82.31 mm3, respectively (P<0.01, ADV-sFLT versus ADV-LacZ or PBS). The value of microvessel density was 29.17+/-6.85, 79.17+/-7.35, and 78.83+/-8.54 in the tumors treated with ADV-sFLT, ADV-LacZ, and PBS, respectively (P<0.01, ADV-sFLT versus ADV-LacZ or PBS). This study suggested that the adenovirus-mediated sFLT-1 gene greatly inhibits MM-derived tumor growth and angiogenesis in mouse xenograft, and might serve as a new therapy for MM.
Localization of Leptin Receptor in the Human Brain (1997)

Leptin (OB protein), the product of the adipose-specific ob gene, exerts important effects in the regulation of food intake and energy expenditure. Based upon results from animal studies, several groups have suggested that this action may be exerted in the brain, specifically in the hypothalamic region. However, to date, the localization of the OB-R in the human brain has not been described. One aim of this study was to contribute to a better understanding of the role that the central nervous system plays in the pathogenesis of obesity in humans. A first stage was to determine the OB-R expression in the human brain by means of immunohistochemistry and Western blotting. Several brain regions from 17 lean, 14 obese, and 4 diabetic (NIDDM) subjects, obtained from archival autopsy material, were sampled. Brain samples from neocortex, hypothalamus, medualla, limbic system, pineal and cerebellum were routinely processed in paraffin and analyzed with the avidin-biotin immunoperoxidase and diaminobenzidine detection method. Western blotting (WB) analysis was done on fresh brain tissue from an obese patient. Specific OB-R immunoreactivity was localized in the choroid plexus epithelium, ependymal lining, and neurons of the hypothalamic nuclei (arcuate, suprachiasmatic, mamillary, paraventricular, dorsomedial, supraoptic and posterior), nucleus basalis of Meynert, inferior olivary nuclei and cerebellar Purkinje cells. No differences in OB-R immunoreactivity were found among the three groups examined. WB analysis yielded 97- and 125-kD bands in the hypothalamus and cerebellum. In summary, this paper presents the first evidence to indicate the specific localization of the OB-R in the brain of lean, obese and NIDDM subjects.
Strigolactones: ecological significance and use as a target for parasitic plant control (2008)

Parasitic weeds cause severe damage to important agricultural crops. Although some promising control methods against these parasitic plants have been developed, new strategies continue to be relevant in integrated approaches. The life cycle for root parasitic weeds is intimately associated with their host and is a suitable target for such new control strategies, particularly when directed at the early stages of the host-parasite interaction. Here, the authors focus on knowledge of the germination stimulants-strigolactones-for the root parasitic plants Striga and Orobanche spp. and discuss their biosynthetic origin, ecological significance and physiological and biochemical regulation. In addition, the existing and possible new control strategies that are based on this knowledge, and that could lead to more efficient control methods against these root parasitic weeds, are reviewed.
Matrix Metalloproteinase-9-Mediated Dendritic Cell Recruitment into the Airways Is a Critical Step in a Mouse Model of Asthma (2003)

Dendritic cells (DCs) appear to be strategically implicated in allergic diseases, including asthma. Matrix metalloproteinase (MMP)-9 mediates transmigration of inflammatory leukocytes across basement membranes. This study investigated the role of MMP-9 in airway DC trafficking during allergen-induced airway inflammation. MMP-9 gene deletion affected the trafficking of pulmonary DCs in a specific way: only the inflammatory transmigration of DCs into the airway lumen was impaired, whereas DC-mediated transport of airway Ag to the thoracic lymph nodes remained unaffected. In parallel, the local production of the Th2-attracting chemokine CC chemokine ligand 17/thymus and activation-regulated chemokine, which was highly concentrated in purified lung DCs, fell short in the airways of allergen-exposed MMP-9(-/-) mice. This was accompanied by markedly reduced peribronchial eosinophilic infiltrates and impaired allergen-specific IgE production. We conclude that the specific absence of MMP-9 activity inhibits the development of allergic airway inflammation by impairing the recruitment of DCs into the airways and the local production of DC-derived proallergic chemokines.
Identification of 20 microRNAs from Oryza sativa (2004)

MicroRNAs (miRNAs) are present in both plant and animal kingdoms and represents a growing family of non-coding RNAs. These tiny RNAs act as small guides and direct negative regulations usually in the process of development through sequence complementarity to target mRNAs. Although a large number of miRNAs have been identified from various animals, so far plant miRNA studies have focused mainly on Arabidopsis. Here we describe the identification of 20 miRNAs from a rice cDNA library. All the miRNAs were presumably processed from precursors with stem-loop structures and were positively detected in rice cells from at least one tissue, some of which showed tissue-specific expression. Twenty-three unique rice genes were identified to be feasible targets for seven rice miRNAs, including four members of Scarecrow-like transcription factor, the targets of miR-39 that had been characterized in Arabidopsis. Lacking long complementarity, the regulatory targets of 13 miRNAs remain to be further investigated. A possible mechanism of translational repressor for plant miRNAs that lack perfect complementarity to target mRNAs is discussed.
Optimization of solid phase microextraction ‐ capillary zone electrophoresis ‐ mass spectrometry for high sensitivity protein identification (1998)

We have previously described the use of a solid phase extraction (SPE) - capillary zone electrophoresis (CZE) - tandem mass spectrometry (MS/MS) system for protein analysis at the low femtomole to subfemtomole level. Here we describe the systematic optimization of a number of parameters which facilitate the use of the SPE-CZE-MS/MS system and further enhance its performance. Specifically, we describe a robust SPE cartridge design which can be assembled without the use of glue, the evaluation of procedures to chemically modify the inner wall of the fused-silica capillaries used in the system to improve separation and reproducibility, and the comparison of different reverse-phase (RP) resins used for the SPE cartridge. We also explored the effects of transient isotachophoresis with respect to system performance and compatibility with different fused-silica surface coatings, the RP resins used, and MS/MS. The enhanced performance of the optimized system is demonstrated by the analysis of calibrated tryptic digests of bovine serum albumin (BSA).
Advances in languages and compilers for parallel processing (1991)

These twenty-three contributions represent some of the best research on software for parallel computers being done in universities and industry today.Advances in Languages and Compilers for Parallel Processing discusses languages and language extensions, presents two innovative environments for parallel programming, describes techniques for debugging parallel programs, and takes up the important issue of data organization and management during parallel processing. New compiler techniques for parallelizing loops are covered as are new results in code scheduling and new approaches to dependency analysis and representation. The book concludes with an interesting insight into the measurement of parallelism implicit in ordinary programs and methods for dealing with programming and compiling for distributed and shared memory multiprocessors.
Thermal Behavior of Methylammonium Lead-Trihalide Perovskite Photovoltaic Light Harvesters (2014)

Recently organic–inorganic hybrid perovskites have attracted attention as light harvesting materials in mesoscopic cells. While a considerable number of deposition and formation methods have been reported for the perovskite crystalline material, most involve an annealing step. As such, the thermal behavior of this material and its individual components is of crucial interest. Here, we examine the thermal properties of the CH3NH3PbX3 (X = I or Cl) perovskite using thermogravimetric analysis. The role of the precursors is exposed, and the effect of the formation of excess organic species is investigated. The sublimation behavior of the organic component is intensively scrutinized. Furthermore, differential scanning calorimetry is employed to probe the crystal phase structure, revealing subtle differences depending on the deposition method.
Preferential association of a transcriptionally active gene with the nuclear matrix of rat fibroblasts transformed by a simian-virus-40–pBR322 recombinant plasmid (1990)

To study the relationship between the structural organization and function of the eukaryotic genome, DNA associated with nuclear matrix was analysed by using a transformed rat fibroblast cell line. The nuclear matrices were prepared from the isolated nuclei of pSV1-FR, a rat fibroblast cell line transformed by a pBR322-based recombinant plasmid containing an early gene region, which codes for large T-antigen, of simian virus 40. This transformed cell contained a single copy of the plasmid sequence integrated into the chromosomal DNA of the host cell. The early gene of this plasmid was constitutively expressed, as demonstrated by positive immunofluorescence staining of the cell for large T-antigen and by RNA-blot analysis for its specific mRNA. DNAs were extracted from whole isolated nuclei and nuclear-matrix preparations of the cells, and the relative amounts of the sequence similar to that of the plasmid were compared between these DNA preparations. By employing dot hybridization and Southern-blot analyses we found that the plasmid sequence was more enriched in the DNA extracted from the nuclear matrices than in the DNA extracted from the whole nuclei. When an albumin gene sequence that was not transcribed in this cell line was compared similarly as a control, we found no significant enrichment of this sequence in the DNA associated with the nuclear matrix. Our results strongly support the concept that a transcriptionally active gene is preferentially associated with the nuclear matrix.
Diagnostic value of serum activin A and follistatin levels in women with peritoneal, ovarian and deep infiltrating endometriosis (2012)

The present study demonstrated that serum activin A and follistatin are not significantly altered in peritoneal or deep infiltrating endometriosis and have limited diagnostic accuracy in the diagnosis of ovarian endometrioma.
Nicotinamide Prevents Interleukin-1 Effects on Accumulated Insulin Release and Nitric Oxide Production in Rat Islets of Langerhans (1994)

Nicotinamide (NA) prevents macrophage- and interleukin-1 (IL-1)-mediated beta-cell damage in vitro as well as diabetes development in animal models of insulin-dependent diabetes mellitus (IDDM). IL-1 beta-mediated inhibition of insulin release and damage to beta-cells are associated with intracellular production of nitric oxide (NO) radicals. Therefore, we studied whether NA prevented IL-1 beta-induced islet NO production, measured as nitrite release from isolated rat islets, and, if so, whether this action was associated with prevention of IL-1 beta-mediated inhibition of insulin release. NA dose- and time-dependently inhibited and delayed IL-1 beta-induced islet NO production. Light microscopy detected that 25 mM of NA protected against IL-1 beta-induced islet damage. Five to 50 mM of NA dose-dependently reduced inhibition of accumulated islet insulin release induced by 150 pg/ml of IL-1 beta. NA was not able to reverse the reduced ability of IL-1 beta-treated islets to respond to an acute glucose challenge. NO or nitrite did not interact directly with NA, because NA did not reduce sodium nitroprusside-generated nitrite. No-synthase inhibition with L-arginine depletion abolished NO production but only partially reduced IL-1 beta-induced inhibition of accumulated insulin release. Complete inhibition of IL-1 beta effects could not be obtained by adding L-arginine analogues to L-arginine-depleted medium, indicating that an NO-independent action of IL-1 beta on islet insulin release may exist.(ABSTRACT TRUNCATED AT 250 WORDS)
Novel Structural Determinants on SIRPα that Mediate Binding to CD47 (2007)

Signal regulatory proteins (SIRP-alpha, -beta, and -gamma) are important regulators of several innate immune functions that include leukocyte migration. Membrane distal (D1) domains of SIRPalpha and SIRPgamma, but not SIRPbeta, mediate binding to a cellular ligand termed CD47. Because the extracellular domains of all SIRPs are highly homologous, we hypothesized that some of the 16 residues unique to SIRPalpha.D1 mediate binding to CD47. By site-directed mutagenesis, we determined that SIRPalpha binding to CD47 is independent of N-glycosylation. We also identified three residues critical for CD47 binding by exchanging residues on SIRPalpha with corresponding residues from SIRPbeta. Cumulative substitutions of the critical residues into SIRPbeta resulted in de novo binding of the mutant protein to CD47. Homology modeling of SIRPalpha.D1 revealed topological relationships among critical residues and allowed the identification of critical residues common to SIRPalpha and SIRPbeta. Mapping these critical residues onto the recently reported crystal structure of SIRPalpha.D1 revealed a novel region that is required for CD47 binding and is distinct and lateral to another putative CD47 binding site described on that crystal structure. The importance of this lateral region in mediating SIRPalpha.D1 binding to CD47 was confirmed by epitope mapping analyses of anti-SIRP Abs. These observations highlight a complex nature of the ligand binding requirements for SIRPalpha that appear to be dependent on two distinct but adjacent regions on the membrane distal Ig loop. A better understanding of the structural basis of SIRPalpha/CD47 interactions may provide insights into therapeutics targeting pathologic inflammation.
Pairing Symmetry and Flux Quantization in a Tricrystal Superconducting Ring ofYBa2Cu3O7−δ (1994)

We have used the concept of flux quantization in superconducting $\mathrm{Y}{\mathrm{Ba}}_{2}{\mathrm{Cu}}_{3}{\mathrm{O}}_{7\ensuremath{-}\ensuremath{\delta}}$ rings with 0, 2, and 3 grain-boundary Josephson junctions to test the pairing symmetry in high-${T}_{c}$ superconductors. The magnetic flux threading these rings at 4.2 K is measured by employing a scanning superconducting quantum interference device microscope. Spontaneous magnetization of a half magnetic flux quantum, $\frac{{\ensuremath{\Phi}}_{0}}{2}=\frac{h}{4e}$ has been observed in the 3-junction ring, but not in the 2-junction rings. These results are consistent with $d$-wave pairing symmetry.
Long time scale blinking kinetics of cyanine fluorophores conjugated to DNA and its effect on Förster resonance energy transfer (2005)

The blinking kinetics of individual Cy5 fluorophores conjugated to DNA are directly measured using single-molecule spectroscopy. Under deoxygenated aqueous conditions, Cy5 fluorescence exhibits spontaneous and reversible on/off fluctuations with a period lasting seconds. This blinking is observed when directly exciting Cy5 with 640 nm light and by Forster resonance energy transfer (FRET). We find that Cy5 blinking is influenced by the proximity of the donor, the structure of the donor, the presence of 514 nm excitation, and FRET. In the context of single-molecule FRET, blinking of the acceptor produces anticorrelated donor-acceptor intensity fluctuations, which can be difficult to discern from variations in the interdye distance. Slow blinking is, in particular, problematic because it overlaps with biologically relevant time scales. By employing an alternating 514640 nm laser excitation scheme, we show that the dark states can be readily resolved and discriminated from FRET distance fluctuations.
Statistical Projection Completion in X-ray CT Using Consistency Conditions (2010)

Projection data incompleteness arises in many situations relevant to X-ray computed tomography (CT) imaging. We propose a penalized maximum likelihood statistical sinogram restoration approach that incorporates the Helgason-Ludwig (HL) consistency conditions to accommodate projection data incompleteness. Image reconstruction is performed by the filtered-backprojection (FBP) in a second step. In our problem formulation, the objective function consists of the log-likelihood of the X-ray CT data and a penalty term; the HL condition poses a linear constraint on the restored sinogram and can be implemented efficiently via fast Fourier transform (FFT) and inverse FFT. We derive an iterative algorithm that increases the objective function monotonically. The proposed algorithm is applied to both computer simulated data and real patient data. We study different factors in the problem formulation that affect the properties of the final FBP reconstructed images, including the data truncation level, the amount of prior knowledge on the object support, as well as different approximations of the statistical distribution of the available projection data. We also compare its performance with an analytical truncation artifacts reduction method. The proposed method greatly improves both the accuracy and the precision of the reconstructed images within the scan field-of-view, and to a certain extent recovers the truncated peripheral region of the object. The proposed method may also be applied in areas such as limited angle tomography, metal artifacts reduction, and sparse sampling imaging.
The NLRP3 and Pyrin Inflammasomes: Implications in the Pathophysiology of Autoinflammatory Diseases (2017)

Inflammasomes are multiprotein complexes that critically control different aspects of innate and adaptive immunity. Among them we could highlight the release of pro-inflammatory cytokines that induce and maintain the inflammatory response. Usually, inflammasomes result from oligomerization of a nucleotide-binding domain-like receptor (NLR) after sensing different pathogenic or endogenous sterile dangerous signals; however, other proteins such as absent in melanoma 2, retinoic acid-inducible gene I, or pyrin could also form inflammasome platforms. Inflammasome oligomerization leads to caspase-1 activation and the processing and release of the pro-inflammatory cytokines, such as interleukin (IL)-1β and IL-18. Mutations in different inflammasomes are causative for multiple periodic hereditary syndromes or autoinflammatory diseases, characterized by acute systemic inflammatory flares not associated with infections, tumors, or autoimmunity. This review focuses on germline mutations that have been described in cryopyrin-associated periodic syndrome (CAPS) for <i>NLRP3</i> or in familial Mediterranean fever (FMF) and pyrin-associated autoinflammation with neutrophilic dermatosis (PAAND) for <i>MEFV</i>. Besides the implication of inflammasomes in autoinflammatory syndromes, these molecular platforms are involved in the pathophysiology of different illnesses, including chronic inflammatory diseases, degenerative processes, fibrosis, or metabolic diseases. Therefore, drug development targeting inflammasome activation is a promising field in expansion.