gebhart/patrepeval huggingface dataset:
Piezoelectric effects on electrical and optical properties of wurtzite GaN/AlGaN quantum well lasers (1998)

The piezoelectric effects on the optical gain of wurtzite GaN/AlGaN QW lasers taking into account the many-body effects are presented. The self-consistent model with piezoelectric field effect shows that band structures and optical gain are significantly affected by the piezoelectric field at relatively low carrier densities. The peak gain is redshifted and smaller when compared to the flat-band model without piezoelectric field effect. Only gain peaks corresponding to C1-HH1 and C1-LH1 transitions are observed in the investigated range and transitions for C1-HH2 and C1-LH2 are negligible due to the large subband energy spacing at low carrier densities and small matrix elements at high carrier densities. At high carrier densities, the self-consistent model shows band structures and optical properties similar to the flat-band model due to the screening effects.
Differential ligand binding specificities of recombinant CD11b/CD18 integrin I-domain. (1994)

The alpha subunits of leukocyte CD11/CD18 integrins contain an approximately 200-amino acid "inserted" domain (I-domain) that may be important for multivalent adhesive recognitions. A recombinant form of the I-domain of CD11b/CD18 was generated and analyzed directly for interaction with complementary integrin ligands. CD11b I-domain bound the activation-dependent monoclonal antibody 7E3, and the functionally blocking anti-CD11b monoclonal antibodies OKM9, 60.1, and LM2/1, but not OKM1 or M1/70. Fibrinogen or soluble intercellular adhesion molecule-1 associated with CD11b I-domain in a concentration-dependent manner. Binding of 125I-fibrinogen to recombinant CD11b I-domain was saturable, governed by a Kd of approximately 0.22 +/- 0.06 microM, and fully inhibited by molar excess of unlabeled fibrinogen, or by the P1 peptide (KY)GWTVFQKRLDGSV (IC50 approximately 2.5-5 microM), duplicating the fibrinogen gamma chain sequence Gly190-Val202. In contrast, 125I-factor X binding to CD11b I-domain was only partially inhibited (50-60%) by a molar excess of unlabeled factor X, and entirely unaffected by functionally blocking anti-CD11b monoclonal antibodies or by factor X-derived synthetic peptidyl antagonists. We conclude that the I-domain of CD11b participates in qualitative mechanisms of receptor activation and contains the binding site(s) for the CD11b/CD18 ligands fibrinogen and intercellular adhesion molecule-1, while it is only minimally implicated in the recognition of factor X.
Positioning of a peptide in the cleft of HLA-A2 by complementing amino acid changes. (1991)

Several mutant HLA-A2 molecules have been constructed and expressed in the mutant human B-cell line C1R, which lacks HLA-A and HLA-B antigens, and examined for presentation of a previously defined peptide epitope derived from the influenza matrix protein to appropriate human cytotoxic T-lymphocyte lines. When leucine residue 66 in this matrix peptide containing residues 57-68 (matrix peptide 57-68) was replaced by arginine, the resulting matrix peptide 57-68 R66 was not presented to HLA-A2, but the mutation Y116D (tyrosine to aspartic acid at residue 116) in the floor of the peptide binding cleft near its right end dramatically restored peptide presentation. A similar result was obtained by substitution of ornithine for leucine at residue 66. These data provide strong support for a model in which the peptide is orientated with its amino terminus at the left end of the cleft of HLA-A2 and its carboxyl terminus at the right.
Effects of Growth Hormone in Short, Slowly Growing Children without Growth Hormone Deficiency (1990)

The aim of the study was to measure the real effect of growth hormone (GH) treatment compared to the effect of placebo, since a placebo effect has been shown in other studies involving interventional growth therapy. Changes in height velocity and insulin-like growth factor I (IGF-I), relative to pretreatment variables, were examined during a 12-month, double-blind study.
Optimal Reconstruction of a Sequence from its Probes (1999)

An important combinatorial problem, motivated by DNA sequencing in molecular biology, is the reconstruction of a sequence over a small finite alphabet from the collection of its probes (the sequence spectrum), obtained by sliding a fixed sampling pattern over the sequence. Such construction is required for Sequencing-by-Hybridization (SBH), a novel DNA sequencing technique based on an array (SBH chip) of short nucleotide sequences (probes). Once the sequence spectrum is biochemically obtained, a combinatorial method is used to reconstruct the DNA sequence from its spectrum. Since technology limits the number of probes on the SBH chip, a challenging combinatorial question is the design of a smallest set of probes that can sequence an arbitrary DNA string of a given length. We present in this work a novel probe design, crucially based on the use of universal bases [bases that bind to any nucleotide (Loakes and Brown, 1994)] that drastically improves the performance of the SBH process and asymptotically approaches the information-theoretic bound up to a constant factor. Furthermore, the sequencing algorithm we propose is substantially simpler than the Eulerian path method used in previous solutions of this problem.
Enantio‐ and Diastereoselective Total Synthesis of (+)‐Panepophenanthrin, a Ubiquitin‐Activating Enzyme Inhibitor, and Biological Properties of Its New Derivatives (2006)

The asymmetric total synthesis of (+)-panepophenanthrin, an inhibitor of ubiquitin-activating enzyme (E1), has been accomplished using catalytic asymmetric alpha aminoxylation of 1,4-cyclohexanedione monoethylene ketal as a key step, followed by several diastereoselective reactions. The biomimetic Diels-Alder reaction of a monomer precursor was found to proceed efficiently in water. The investigation of the biological properties of new derivatives of (+)-panepophenanthrin enabled us to develop new cell-permeable E1 inhibitors, RKTS-80, -81, and -82.
Characterization of the two heavy chains of the T3 complex on the surface of human T lymphocytes. (1984)

The T3 complex has been defined by a group of monoclonal antibodies which react with all human peripheral blood T lymphocytes and a subpopulation of thymocytes. This membrane structure includes glycoproteins of 44 (alpha), 37 (beta), 25 (gamma), and 20 kDa (delta) as well as a nonglycosylated polypeptide of 20 kDa (epsilon). The characterization of the alpha and beta chains has been of particular interest because they may constitute the T cell receptor for antigen. Here we show that the T3 complex prepared by immunoprecipitation from T lymphocytes of a leukemic patient (Sezary syndrome) displays an unusually strong association of the alpha and beta chains with the 20/25-kDa T3 proteins. The alpha and beta chains (48 and 44 kDa) were co-precipitated by anti-20-kDa T3 monoclonal antibodies as a disulfide-linked 90-kDa heterodimer. A minor 220-kDa multimer composed of proteins similar to the alpha and beta chains was also present in these immunoprecipitates. This multimer could be independently precipitated with a new monoclonal antibody WT-31, which detects the larger polypeptide chains of the T3 complex on all human T lymphocytes. After removal of N-linked oligosaccharides, both the alpha and beta chain were found to have 33-kDa peptide backbones with distinct isoelectric points. Using a monoclonal reagent T40/25, a 90-kDa heterodimer, consisting of 40- and 49-kDa chains with peptide backbones of 34 kDa was found to be T3-associated on the T leukemic cell line HPB-ALL. When the alpha and beta chains from the Sezary patient were compared with the corresponding chains from HPB-ALL by peptide mapping, large differences were observed. Taken together, the data presented here provide strong evidence that the T cell receptor for antigen is part of the T3 complex on the surface of human T lymphocytes.
The Arabidopsis pxa1 mutant is defective in an ATP-binding cassette transporter-like protein required for peroxisomal fatty acid beta-oxidation. (2001)

Peroxisomes are important organelles in plant metabolism, containing all the enzymes required for fatty acid beta-oxidation. More than 20 proteins are required for peroxisomal biogenesis and maintenance. The Arabidopsis pxa1 mutant, originally isolated because it is resistant to the auxin indole-3-butyric acid (IBA), developmentally arrests when germinated without supplemental sucrose, suggesting defects in fatty acid beta-oxidation. Because IBA is converted to the more abundant auxin, indole-3-acetic acid (IAA), in a mechanism that parallels beta-oxidation, the mutant is likely to be IBA resistant because it cannot convert IBA to IAA. Adult pxa1 plants grow slowly compared with wild type, with smaller rosettes, fewer leaves, and shorter inflorescence stems, indicating that PXA1 is important throughout development. We identified the molecular defect in pxa1 using a map-based positional approach. PXA1 encodes a predicted peroxisomal ATP-binding cassette transporter that is 42% identical to the human adrenoleukodystrophy (ALD) protein, which is defective in patients with the demyelinating disorder X-linked ALD. Homology to ALD protein and other human and yeast peroxisomal transporters suggests that PXA1 imports coenzyme A esters of fatty acids and IBA into the peroxisome for beta-oxidation. The pxa1 mutant makes fewer lateral roots than wild type, both in response to IBA and without exogenous hormones, suggesting that the IAA derived from IBA during seedling development promotes lateral root formation.
Flt3-ligand production by human bone marrow stromal cells. (1996)

Bone marrow stromal cells are important sources of cytokines and growth factors which participate in regulation of proliferation and differentiation of hematopoietic stem and progenitor cells. Recently flt3/flk-2-ligand (flt3-L), a new growth factor which uses a membrane tyrosine kinase receptor, was cloned. It is expressed in transmembrane and soluble forms and stimulates/co-stimulates proliferation and colony formation of hematopoietic stem/progenitor cells. It has not been reported whether flt3-L is produced by cells of the hematopoietic bone marrow microenvironment. We demonstrate the expression of flt3-L in bone marrow fibroblasts (BMF) and in stromal cells of adherent layers of long-term bone marrow cultures by RT-PCR, Northern blot, immunocytochemistry and FACS analysis. The latter two methods localized flt3-L intracellularly and on cell membranes. Treatment with interleukin-1 alpha increased the expression of flt3-L in BMF. This demonstrates production and modulation of flt3-L in stromal cells of human bone marrow.
Identification of Type I and Type II Serine/Threonine Kinase Receptors for Growth/Differentiation Factor-5 (1996)

Growth/differentiation factor-5 (GDF-5) is a member of the bone morphogenetic protein (BMP) family, which plays an important role in bone development in vivo. Mutations in the GDF-5 gene result in brachypodism in mice and Hunter-Thompson type chondrodysplasia in human. BMPs transduce their effects through binding to two different types of serine/threonine kinase receptors, type I and type II. However, binding abilities appear to be different among the members of the BMP family. BMP-4 binds to two different type I receptors, BMP receptors type IA (BMPR-IA) and type IB (BMPR-IB), and a type II receptor, BMP receptor type II (BMPR-II). In addition to these receptors, osteogenic protein-1 (OP-1, also known as BMP-7) binds to activin type I receptor (ActR-I) as well as activin type II receptors (ActR-II and ActR-IIB). Here we investigate the binding and signaling properties of GDF-5 through type I and type II receptors. GDF-5 induced alkaline phosphatase activity in a rat osteoprogenitor-like cell line, ROB-C26. 125I-GDF-5 bound to BMPR-IB and BMPR-II but not to BMPR-IA in ROB-C26 cells and other nontransfected cell lines. Analysis using COS-1 cells transfected with the receptor cDNAs revealed that GDF-5 bound to BMPR-IB but not to the other type I receptors when expressed alone. When COS-1 cells were transfected with type II receptor cDNAs, GDF-5 bound to ActR-II, ActR-IIB, and BMPR-II but not to transforming growth factor-beta type II receptor. In the presence of type II receptors, GDF-5 bound to different sets of type I receptors, but the binding was most efficient to BMPR-IB compared with the other type I receptors. Moreover, a transcriptional activation signal was efficiently transduced by BMPR-IB in the presence of BMPR-II or ActR-II after stimulation by GDF-5. These results suggest that BMPR-IB mediates certain signals for GDF-5 after forming the heteromeric complex with BMPR-II or ActR-II.
Identification of thepgmGGene, Encoding a Bifunctional Protein with Phosphoglucomutase and Phosphomannomutase Activities, in the Gellan Gum-Producing StrainSphingomonas paucimobilisATCC 31461 (2000)

The pgmG gene of Sphingomonas paucimobilis ATCC 31461, the industrial gellan gum-producing strain, was cloned and sequenced. It encodes a 50,059-Da polypeptide that has phosphoglucomutase (PGM) and phosphomannomutase (PMM) activities and is 37 to 59% identical to other bifunctional proteins with PGM and PMM activities from gram-negative species, including Pseudomonas aeruginosa AlgC. Purified PgmG protein showed a marked preference for glucose-1-phosphate (G1P); the catalytic efficiency was about 50-fold higher for G1P than it was for mannose-1-phosphate (M1P). The estimated apparent K(m) values for G1P and M1P were high, 0.33 and 1.27 mM, respectively. The pgmG gene allowed the recovery of alginate biosynthetic ability in a P. aeruginosa mutant with a defective algC gene. This result indicates that PgmG protein can convert mannose-6-phosphate into M1P in the initial steps of alginate biosynthesis and, together with other results, suggests that PgmG may convert glucose-6-phosphate into G1P in the gellan pathway.
Visualizing the non-visual: spatial analysis and interaction with information from text documents (2002)

The paper describes an approach to IV that involves spatializing text content for enhanced visual browsing and analysis. The application arena is large text document corpora such as digital libraries, regulations and procedures, archived reports, etc. The basic idea is that text content from these sources may be transformed to a spatial representation that preserves informational characteristics from the documents. The spatial representation may then be visually browsed and analyzed in ways that avoid language processing and that reduce the analysts mental workload. The result is an interaction with text that more nearly resembles perception and action with the natural world than with the abstractions of written language.
Polylysine-containing peptides, including the carboxyl-terminal segment of the human c-Ki-ras 2 protein, affect the activity of some key membrane enzymes. (1987)

Polylysine-containing peptides are found to affect membrane protein kinases, phosphatidylinositol kinases, and adenylate cyclase. Poly(L-lysine), poly(D-lysine), random copolymers of lysine and serine or lysine and alanine, and poly(L-ornithine) produced large increases in the in vitro phosphorylation of some membrane proteins present in Xenopus laevis oocyte membranes. Poly(L-arginine) did not cause a similar stimulation. In these membranes the phosphorylation of polydisperse protein of approximately 25 kDa was also greatly increased by 1 mM spermine and spermidine, by 10 microM histone H1, or by 200 microM peptide containing the 14-residue sequence at the carboxyl terminus of the human c-Ki-ras 2 gene product, which has eight lysines. Similar specific stimulation of protein phosphorylation was observed with membranes of NG-108-15 nerve cells in culture. Polylysine peptides, including the c-Ki-ras 2 segment, also stimulate the in vitro phosphorylation of membrane inositolphospholipids, to produce mainly phosphatidylinositol 4-phosphate and less phosphatidylinositol 4,5-bisphosphate. Polylysine also alters the activity of oocyte adenylate cyclase, assayed in the presence of either F- or 5'-guanylyl imidodiphosphate.
Interaction of COP1 and UVR8 regulates UV‐B‐induced photomorphogenesis and stress acclimation in Arabidopsis (2009)

The ultraviolet-B (UV-B) portion of the solar radiation functions as an environmental signal for which plants have evolved specific and sensitive UV-B perception systems. The UV-B-specific UV RESPONSE LOCUS 8 (UVR8) and the multifunctional E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) are key regulators of the UV-B response. We show here that uvr8-null mutants are deficient in UV-B-induced photomorphogenesis and hypersensitive to UV-B stress, whereas overexpression of UVR8 results in enhanced UV-B photomorphogenesis, acclimation and tolerance to UV-B stress. By using sun simulators, we provide evidence at the physiological level that UV-B acclimation mediated by the UV-B-specific photoregulatory pathway is indeed required for survival in sunlight. At the molecular level, we demonstrate that the wild type but not the mutant UVR8 and COP1 proteins directly interact in a UV-B-dependent, rapid manner in planta. These data collectively suggest that UV-B-specific interaction of COP1 and UVR8 in the nucleus is a very early step in signalling and responsible for the plant's coordinated response to UV-B ensuring UV-B acclimation and protection in the natural environment.
Prevalence of Human Papillomavirus in Cervical Cancer: a Worldwide Perspective (1995)

The demonstration that more than 20 different genital HPV types are associated with cervical cancer has important implications for cervical cancer-prevention strategies that include the development of vaccines targeted to genital HPVs.
Vaccination with Protein‐Conjugated and Native Type 3 Capsular Polysaccharide in an Ethanol‐Fed Rat Model of Pneumococcal Pneumonia (1997)

A chronic ethanol-fed rat model was used to determine the effect of alcohol ingestion on production of antibody to type 3 pneumococcal capsular polysaccharide. Sprague-Dawley rats were fed a liquid diet containing 36% of calories as ethanol (ethanol-fed), an isocaloric diet containing dextrin-maltose (pair-fed) or standard rat chow (chow-fed). After 7 days of feeding, the rats were vaccinated subcutaneously with placebo or with either 25 microg of type 3 pneumococcal capsular polysaccharide (SpnCP) or 5 microg of SpnCP linked to the protein carrier CRM197 (SpnCP/CRM197). Rats given the conjugated vaccine received a booster injection 14 days later. Maximum antibody titers were observed six days postvaccination for rats given SpnCP alone and 21 days postvaccination for rats given SpnCP/CRM197. All rats were infected transtracheally with 2-3 times the expected lethal dose50 for each feeding group of type 3 Streptococcus pneumoniae on the day of peak antibody titers. Mortality was recorded for a 10-day period. Vaccination with SpnCP increased survival of ethanol- and chow-fed, but not pair-fed rats. This protection was only statistically significant in the chow-fed group (p < 0.01). Vaccination with SpnCP/CRM197 moderately increased survival of rats in all three feeding groups, but this was not statistically significant in any of them.
Disrupting galectin-1 interactions with N-glycans suppresses hypoxia-driven angiogenesis and tumorigenesis in Kaposi’s sarcoma (2012)

Kaposi's sarcoma (KS), a multifocal vascular neoplasm linked to human herpesvirus-8 (HHV-8/KS-associated herpesvirus [KSHV]) infection, is the most common AIDS-associated malignancy. Clinical management of KS has proven to be challenging because of its prevalence in immunosuppressed patients and its unique vascular and inflammatory nature that is sustained by viral and host-derived paracrine-acting factors primarily released under hypoxic conditions. We show that interactions between the regulatory lectin galectin-1 (Gal-1) and specific target N-glycans link tumor hypoxia to neovascularization as part of the pathogenesis of KS. Expression of Gal-1 is found to be a hallmark of human KS but not other vascular pathologies and is directly induced by both KSHV and hypoxia. Interestingly, hypoxia induced Gal-1 through mechanisms that are independent of hypoxia-inducible factor (HIF) 1α and HIF-2α but involved reactive oxygen species-dependent activation of the transcription factor nuclear factor κB. Targeted disruption of Gal-1-N-glycan interactions eliminated hypoxia-driven angiogenesis and suppressed tumorigenesis in vivo. Therapeutic administration of a Gal-1-specific neutralizing mAb attenuated abnormal angiogenesis and promoted tumor regression in mice bearing established KS tumors. Given the active search for HIF-independent mechanisms that serve to couple tumor hypoxia to pathological angiogenesis, our findings provide novel opportunities not only for treating KS patients but also for understanding and managing a variety of solid tumors.
Human Papillomavirus Type 16 E6* Induces Oxidative Stress and DNA Damage (2014)

Our findings demonstrate for the first time that an HPV gene product, E6*, can increase ROS levels in host cells. This ability may play a significant role both in the viral life cycle and in cancer development, because an increase in oxidative DNA damage may both facilitate HPV genome amplification and increase the probability of HPV16 DNA integration. Integration, in turn, is thought to be an important step in HPV-mediated carcinogenesis.
Taste Receptor Genes (2007)

In the past several years, tremendous progress has been achieved with the discovery and characterization of vertebrate taste receptors from the T1R and T2R families, which are involved in recognition of bitter, sweet, and umami taste stimuli. Individual differences in taste, at least in some cases, can be attributed to allelic variants of the T1R and T2R genes. Progress with understanding how T1R and T2R receptors interact with taste stimuli and with identifying their patterns of expression in taste cells sheds light on coding of taste information by the nervous system. Candidate mechanisms for detection of salts, acids, fat, complex carbohydrates, and water have also been proposed, but further studies are needed to prove their identity.
<title>Fractal image coding based on a theory of iterated contractive image transformations</title> (1990)

The notion of fractal image compression arises from the fact that the iteration of simple deterministic mathematical procedures can generate images with infinitely intricate geometries, known as fracial images [2]. The purpose of research on fractal—based digital image coding is to solve the inverse problem of constraining this complexity to match the real—world complexity of real—world images. In this. paper, we propose a fractal image coding technique based on a mathematical theory of iterated transformations [1, 2, 3, 7] which encompasses deterministic fractal geometry. Initial results were reported in [7, 8]. The main characteristics of this technique are that (i) it is fractal in the sense that it approximates an original image by a fractal image, and (ii) it is a block—coding technique which relies on the assumption that image redundancy can be efficiently exploited through blockwise self—iransformabiliiy. We therefore refer to it as fracial block—coding. The coding—decoding system is based on the construction, for each original image given to encode, of a specific image transformation which, when iterated on any initial image, produces a sequence of images which converges to a fractal approximation of the original. We show how to design such coders, and thoroughly describe the implementation of a system for monochrome still images. Extremely promising coding results were obtained.