gebhart/patrepeval huggingface dataset:
HIV Glycoprotein 41 and Complement Factor H Interact with Each Other and Share Functional as Well as Antigenic Homology (1995)

We have shown that complement factor H (CFH) interacts with HIV-1 at the level of the sequence Env 105-119, contained in the C1 domain of gp120. CFH interaction with HIV was evident only after dissociation of the Env complex induced by exposure to sCD4. We hypothesized that CFH could act as a gp41 analog in the interaction with Env 105-119. A panel of partially overlapping, synthetic peptides reproducing the extracellular portion of gp41 was therefore used to compete the binding of CFH to Env 105-119. Three sets of peptides that competed this interaction were identified. These peptides defined a region of functional homology between the gp41 molecule and CFH (Env 580-600), and two regions of interaction (Env 620-640 and Env 650-670). In addition to this, a monoclonal antibody directed against peptide Env 580-600 and a polyclonal mouse antiserum raised against recombinant gp41 were shown to recognize CFH in Western blots and ELISA, respectively, also defining a region of antigenic homology between gp41 and CFH. These data provide evidence for interaction and molecular mimicry between an HIV structural protein and a negative regulator of the complement pathway. We show here that CFH can interact with both HIV Env proteins, suggesting a possible and efficient mechanism of downregulation of the complement cascade at the surface of infected cells.
Identification of Galectin-1 as a novel biomarker in nasopharyngeal carcinoma by proteomic analysis (2010)

Nasopharyngeal carcinoma (NPC) is one of the most common malignant tumors in southern China and Southeast Asia. It is characterized as a multistep process involved in multiple genetic and epigenetic events. The mechanism of carcinogenesis still needs to be further clarified. In this study, two-dimensional gel electrophoresis, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS), RT-PCR, Western blot and immunohistochemical (IHC) analyses were used to detect Galectin-1 expression in NPC compared with normal nasopharyngeal epithelial tissues (NNET). We found that Galectin-1 was expressed at a significantly higher level in NPC compared with NNET. Our results indicated that high expression level of Galectin-1 might correlate with the development of NPC and Galectin-1 may serve as a potential diagnostic marker or therapeutic target for NPC.
Self-renewal and differentiation of stem cells in a biopotential murine leukemia: an in vitro model for differentiation therapy (1994)

PGM-2 is a variant of the transplantable PGM-1 leukemia of strain C3H/HeJ. Freshly explanted cells had lymphoid morphology with a CD5+ CD45R (B220)- IgM- phenotype. They were not viable in unstimulated cultures, but formed IgM+ lymphoid colonies in response to interleukin- 2 (IL-2), IL-4, IL-5, IL-6, IL-7, and Steel factor, and macrophage colonies in response to IL-3. IL-3-stimulated colonies had no recloning potential, but colonies from IL-7 cultures gave rise to large numbers of secondary macrophage colonies in IL-3-stimulated cultures and secondary lymphoid colonies in IL-7-stimulated cultures. The latter ones could be serially transferred in vitro for several months, and formed typical PGM-2 tumors in vivo. IL-7-stimulated colonies could therefore be used to measure leukemic stem cells in vitro. Supramaximal IL-3 stimulation (2,500 U/mL) of suspension cultures was followed by an increase in overall cell numbers and a disappearance of leukemic stem cells, compatible with differentiation induction. This could not be counteracted by simultaneous stimulation with IL-7. However, lower IL-3 concentrations (500 U/mL) induced an expansion of the stem cell pool, possibly by facilitating density-dependent autostimulatory mechanisms involving endogenous production of IL-7. The system described is a simple in vitro model for differentiation therapy. It shows that leukemic stem cells can be induced by hematopoietic growth factors to undergo terminal differentiation, but the concentrations required for differentiation induction in stem cells are much higher than those required for other biologic effects. Submaximal stimulation may favor expansion rather than repression of the leukemic cell population.
Comparison results for a class of quasilinear evolutionary hemivariational inequalities (2007)

We consider a class of quasilinear evolutionary hemivariational inequalities under nonmonotone multivalued flux boundary conditions. Our main goal is to provide existence and comparison results in terms of appropriately defined sub- and supersolutions on the basis of which one can prove compactness and extremality results of the solution set within the sector of sub- and supersolutions.
Anthrax Toxin-Mediated Delivery In Vivo and In Vitro of a Cytotoxic T-Lymphocyte Epitope from Ovalbumin (1998)

We reported earlier that a nontoxic form of anthrax toxin was capable of delivering a cytotoxic T-lymphocyte (CTL) epitope in vivo, such that a specific CTL response was primed against the epitope. The epitope, of bacterial origin, was fused to an N-terminal fragment (LFn) from the lethal-factor component of the toxin, and the fusion protein was injected, together with the protective antigen (PA) component, into BALB/c mice. Here we report that PA plus LFn is capable of delivering a different epitope--OVA(257-264) from ovalbumin. Delivery was accomplished in a different mouse haplotype, H-2Kb and occurred in vitro as well as in vivo. An OVA(257-264)-specific CTL clone, GA-4, recognized EL-4 cells treated in vitro with PA plus as little as 30 fmol of the LFn-OVA(257-264) fusion protein. PA mutants attenuated in toxin self-assembly or translocation were inactive, implying that the role of PA in epitope delivery is the same as that in toxin action. Also, we showed that OVA(257-264)-specific CTL could be induced to proliferate by incubation with splenocytes treated with PA plus LFn-OVA(257-264). These findings imply that PA-LFn may serve as a general delivery vehicle for CTL epitopes in vivo and as a safe, efficient tool for the ex vivo expansion of patient-derived CTL for use in adoptive immunotherapy.
Gene Amplification in Malignant Human Gliomas: Clinical and Histopathologic Aspects (1988)

Gene amplification occurs in 45-50% of malignant human gliomas (MHG). In the present study, 64 genetically characterized gliomas were evaluated to determine if tumors with amplification of the epidermal growth factor receptor (EGFR), N-myc, c-myc, or gli genes had distinctive histopathologic features. There was no significant difference in age (p = 0.10) or gender (p = 0.78) between patients whose tumors contained amplified genes and those whose tumors did not exhibit this characteristic. Although the patients with amplified genes in their tumors survived slightly longer than patients whose tumors had no detectable gene amplification, these differences were not statistically significant (p = 0.21). The 28 tumors with amplification included 24/48 (50%) glioblastoma multiforme, 2/6 (33%) anaplastic astrocytomas and 2/5 (40%) gliosarcomas. No amplification was seen in one oligodendroglioma, three anaplastic mixed gliomas or one giant cell glioblastoma multiforme. Necrosis and endothelial proliferation were equally prevalent among tumors with and without amplification. Comparison of tumors with gene amplification and tumors without this characteristic revealed similar distributions of most morphologic cells types. Although prominent perivascular lymphocytic infiltrates were more frequent in tumors without amplification, this association was of borderline significance statistically. In situ hybridization of tumors with amplification using an EGFR mRNA probe showed intense labeling of different neoplastic cell types including fibrillary and protoplasmic astrocytes, gemistocytes, anaplastic cells, and multinucleated giant cells. Non-neoplastic cells such as hyperplastic endothelium within the tumors did not express detectable EGFR mRNA. These studies demonstrate that (a) cells with quite different morphology within the same tumor can contain the same genetic alteration; (b) tumors of identical histological appearance may have arisen and evolved by different molecular mechanisms; and (c) molecular analyses are necessary to evaluate gene amplification in MHG since this characteristic cannot be accurately predicted by the morphologic or clinical criteria used in this study.
Experimental studies of spatial signature variation at 900 MHz for smart antenna systems (1998)

A spatial signature is the response vector of a base-station antenna array to a mobile unit at a certain location. Mobile subscribers at different locations exhibit different spatial signatures. The exploitation of spatial diversity (or the difference of spatial signatures) is the basic idea behind the so-called space-division multiple-access (SDMA) scheme, which can be used to significantly increase the channel capacity and quality of a wireless communication system. Although SDMA schemes have been studied by a number of researchers, most of these studies are based on theoretical analyses and computer simulations with ideal assumptions. Not much experimental study, has been reported on spatial signature variation due to nonideal perturbations in a real wireless communication environment. The purpose of this paper is to present, for the first time, extensive experimental results of spatial signature variation using a smart antenna testbed. The results presented include the spatial signature variation with time, frequency, small displacement, multipath angle spread and beamforming performance. The experimental results show the rich spatial diversity and potential benefits of using an antenna array for wireless communication applications.
Protein contact dermatitis: myth or reality? (1995)

Protein contact dermatitis is a dermatosis which usually presents as a chronic eczema with episodic acute exacerbations a few minutes after contact with the offending allergen. Patch tests with the responsible allergen are usually negative, and the diagnosis can only be made by means of scratch or prick tests with the allergen. Sometimes, specific IgE antibodies can be detected in the blood. As there is considerable confusion about this entity, we have reviewed the cases reported in the literature.
An Open-Label Pilot Study Using Thioguanine as a Therapeutic Alternative in Crohn's Disease Patients Resistant to 6-Mercaptopurine Therapy (2001)

6-TG was a safer and more efficacious thiopurine in this subgroup of IBD patients resistant to 6-MP therapy. Larger controlled trials are warranted to further evaluate both the short- and long-term safety and efficacy in this subgroup of patients as well as a broader spectrum of IBD patients.
Evaluation of the developmental toxicity of thalidomide using frog embryo teratogenesis assay?Xenopus (FETAX): biotransformation and detoxification (2000)

The developmental toxicity of thalidomide was evaluated using FETAX (Frog Embryo Teratogenesis Assay - Xenopus). Young X. Laevis embryos were exposed to this compound in each of two concentration-response experiments with and without differently induced exogenous metabolic activation systems (MASs) and/or inhibited MASs. Young male Sprague-Dawley rats were treated with either isoniazid or Aroclor 1254 to induce cytochrome P-450. Several of the rats were subsequently treated with diethyl maleate (DM) to deplete glutathione reserves. Specific aliquots of rat liver microsomes were treated with 3-amino-1,2,4-triazole (ATZ) or alpha-napthoflavone (alpha-N) to selectively inhibit P-450 activity. Bioactivation was indicated by increased developmental toxicity observed in MAS tests. Results obtained indicated that thalidomide was predominantly activated by P-450 isozyne CYP2E1, although weak cross-specificity between CYP1A1/A2 may have existed. Detoxification pathways for thalidomide were investigated by treatment of the MAS with cyclohexene oxide (CHO) and DM to inhibit the epoxide hydrolase and glutathione conjugation pathways, respectively. Results indicated that epoxide hydrolase was primarily responsible for the detoxification of bioactivated thalidomide. Teratogenesis Carcinog. Mutagen. 20:35-47, 2000.
Indium-Based Interface Chemical Engineering by Electrochemistry and Atomic Layer Deposition for Copper Indium Diselenide Solar Cells (2001)

The key to achieve better Cu(In, Ga)Se 2 (CIGS) cells is through the improvement of the CIGS/ZnO interface. In this work, we illustrate various approaches, wet and dry, to engineer that interface with processes that avoid the use of Cd containing compounds. Wet chemical treatments have been performed so as to test the possibility to improve that interface by surface doping of CIGS. X-ray photoelectron spectroscopy (XPS) and Kelvin probe studies show that such doping is not achieved in the conditions leading to best devices. Rather, the most desirable feature of the surface treatments appears to be surface passivation. We show that this can be achieved via CIGS surface reaction with In(III) ions, leading to 12.5% efficient devices. A well passivated interface can also be achieved directly, using an all dry process, by Atomic Layer Deposition (ALD) of In 2 S 3 buffer layer, yielding to 13.5% efficient devices. The ALD growth of the buffer layers have been studied in situ with the help of a quartz crystal microgravimetry.
The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max (2005)

Genomes that have been highly conserved following increases in ploidy (by duplication or hybridization) like Glycine max (soybean) present challenges during genome analysis. At http://soybeangenome.siu.edu the Soybean Genome Database (SoyGD) genome browser has, since 2002, integrated and served the publicly available soybean physical map, bacterial artificial chromosome (BAC) fingerprint database and genetic map associated genomic data. The browser shows both build 3 and build 4 contiguous sets of clones (contigs) of the soybean physical map. Build 4 consisted of 2854 contigs that encompassed 1.05 Gb and 404 high-quality DNA markers that anchored 742 contigs. Many DNA markers anchored sets of 2-8 different contigs. Each contig in the set represented a homologous region of related sequences. GBrowse was adapted to show sets of homologous contigs at all potential anchor points, spread laterally and prevented from overlapping. About 8064 minimum tiling path (MTP2) clones provided 13,473 BAC end sequences (BES) to decorate the physical map. Analyses of BES placed 2111 gene models, 40 marker anchors and 1053 new microsatellite markers on the map. Estimated sequence tag probes from 201 low-copy gene families located 613 paralogs. The genome browser portal showed each data type as a separate track. Tetraploid, octoploid, diploid and homologous regions are shown clearly in relation to an integrated genetic and physical map.
Surface and biological evaluation of hydroxyapatite‐based coatings on titanium deposited by different techniques (2001)

Hydroxyapatite coatings have been deposited on titanium cp by plasma spray, sol-gel, and sputtering techniques for dental implant applications. The latter two techniques are of current interest, as they allow coatings of micrometer dimensions to be deposited. Coating morphology, composition, and structure have been investigated by scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD). All coatings were homogeneous and exhibited a rough morphology suitable for implant applications. The sputtered (after annealing), plasma spray, and sol-gel coatings all showed diffraction peaks corresponding to hydroxyapatite. The surface contaminants were observed to be different for the different coating types. The sputtered coatings were found to have a composition most similar to hydroxyapatite; the sol-gel deposits also showed a high concentration of hydroxyl ions. A discrepancy in the Ca/P ratio was observed for the plasma spray coatings, and a small concentration of carbonate ions was found in the sputter-deposited coatings. The in vitro cell-culture studies using MG63 osteoblast-like cells demonstrated the ability of cells to proliferate on the materials tested. The sol-gel coating promotes higher cell growth, greater alkaline phosphatase activity, and greater osteocalcin production compared to the sputtered and plasma-sprayed coatings.
Comet: An open‐source MS / MS sequence database search tool (2012)

Proteomics research routinely involves identifying peptides and proteins via MS/MS sequence database search. Thus the database search engine is an integral tool in many proteomics research groups. Here, we introduce the Comet search engine to the existing landscape of commercial and open-source database search tools. Comet is open source, freely available, and based on one of the original sequence database search tools that has been widely used for many years.
Application-level control of IP networks: IP beyond the Internet (2002)

The Internet today can be compared to a road system that is freely accessible to everyone with a car. Traffic jams are the inevitable consequence. Traditional switched telephone networks, on the other hand, can be compared to railways, which have limited access to tracks, resold (or even reserved) seats, and limited or nonexistent traffic jams. Delays and cost are predictable. The Internet, with its increasing importance for telecommunications and business, can no longer afford unpredictable traffic jams. The convergence of voice and data on a single packet-based network imposes stringent requirements for quality of service (QoS), stability, billing, and security. Therefore, the Internet must conform to basic rules that govern traditional telecommunication infrastructures as well as accommodate new, flexible business models beyond the present free-for-all that address regional market differentiation and local regulation. This paper describes a network architecture that allows today's Internet to evolve in a way that permits more flexible business models and differentiated policies. Networks are modeled as separate domains, each with its own set of transport services, policies, and QoS mechanisms within an autonomous business framework. This architecture combines elements of both telecommunication and data networks: it is Internet protocol (IP) based but without the business constraints imposed by the Internet today.
Deprotonation of Benzoxazole and Oxazole Using Lithium Magnesates (2005)

The first deprotonations of oxazole and benzoxazole using lithium magnesates are described. The reactions occurred in tetrahydrofuran at room temperature using 1/3 equiv of lithium tributylmagnesate. As 2-lithiooxazole and 2-lithiobenzoxazole, lithium tri(2-oxazolyl)magnesate and lithium tri(2-benzoxazolyl)magnesate very rapidly and completely isomerized to the more stable 2-(isocyano)enolate and 2-(isocyano)phenolate type structures, respectively, a result shown by NMR analysis. The isolation of 2-substituted oxazoles and benzoxazoles in medium to good yields after electrophilic trapping was interpreted in two ways: (1) the equilibration between the open and closed structures is faster than the trapping of the open isomers, and the closed isomers are more reactive than the open ones, or (2) the open isomers react with electrophiles in a intramolecular Passerini type reaction. The nonreactivity of the 2-(isocyano)enolate type structure toward anisaldehyde in the absence of lithium bromide makes the intramolecular Passerini type reaction more plausible.
Adhesion to carcinoembryonic antigen by human colorectal carcinoma cells involves at least two epitopes (1993)

Carcinoembryonic antigen (CEA) may be involved in both cell-cell and cell-substrate adhesion. Our purpose was to determine whether epitopes involved in the homophilic binding of human colorectal carcinoma cells to CEA participated in adhesion to basement membrane proteins. Three human colorectal adenocarcinoma cell lines and one CHO cell line transfected with CEA cDNA were tested in a solid-phase adhesion assay. The 2 CEA-expressing carcinoma cell lines (KM-12c and CCL 188) and the transfectant, but not the parental CHO line, bound to CEA. The CEA-non-producing carcinoma line (Clone A) did not bind to CEA. All colorectal carcinoma cell lines, the transfectant and the parental CHO line bound to laminin, while the colorectal carcinoma lines bound to type-IV collagen. MAbs to epitopes on CEA that cross-react with non-specific cross-reacting antigen (NCA) inhibited adhesion of CEA-expressing cells to CEA. MAbs to non-cross-reactive epitopes of CEA did not block adhesion to CEA. When the inhibitory anti-CEA antibodies were compared in a competitive radioimmunoassay, 2 distinct epitopes were identified. Epitope I is in the N-terminal domain and defined by MAbs MN3, T84.1 and C110, whereas epitope II is located in the repeating loop domains and is recognized by antibodies MN15, PR3B10 and NP1. None of the antibodies to epitope I or II blocked adhesion by KM-12c or CCL 188 cells to laminin or type-IV collagen. Thus, at least 2 different regions on CEA participate in adhesion to CEA but not to collagen or laminin by CEA-expressing human colorectal carcinoma cells.
Domain structure of human 72-kDa gelatinase/type IV collagenase. Characterization of proteolytic activity and identification of the tissue inhibitor of metalloproteinase-2 (TIMP-2) binding regions. (1992)

The 72-kDa gelatinase/type IV collagenase, a metalloproteinase thought to play a role in metastasis and in angiogenesis, forms a noncovalent stoichiometric complex with the tissue inhibitor of metalloproteinase-2 (TIMP-2), a potent inhibitor of enzyme activity. To define the regions of the 72-kDa gelatinase responsible for TIMP-2 binding, a series of NH2- and COOH-terminal deletions of the enzyme were constructed using the polymerase chain reaction technique. The full-length and the truncated enzymes were expressed in a recombinant vaccinia virus mammalian cell expression system (Vac/T7). Two truncated enzymes ending at residues 425 (delta 426-631) and 454 (delta 455-631) were purified. Like the full-length recombinant 72-kDa gelatinase, both COOH-terminally truncated enzymes were activated with organomercurial and digested gelatin and native collagen type IV. In contrast to the full-length enzyme, delta 426-631 and delta 455-631 enzymes were less sensitive to TIMP-2 inhibition requiring 10 mol of TIMP-2/mol of enzyme to achieve maximal inhibition of enzymatic activity. The activated but not the latent forms of the delta 426-631 and delta 455-631 proteins formed a complex with TIMP-2 only when excess molar concentrations of inhibitor were used. We also expressed the 205-amino acid COOH-terminal fragment, delta 1-426, and found that it binds TIMP-2. In addition, a truncated version of the 72-kDa gelatinase lacking the NH2-terminal 78 amino acids (delta 1-78) of the proenzyme retained the ability to bind TIMP-2. These studies demonstrate that 72-kDa gelatinases lacking the COOH-terminal domain retain full enzymatic activity but acquire a reduced sensitivity to TIMP-2 inhibition. These data suggest that both the active site and the COOH-terminal tail of the 72-kDa gelatinase independently and cooperatively participate in TIMP-2 binding.