gebhart/patrepeval huggingface dataset:
Chemical Modification of Glycyrrhizic Acid As A Route to New Bioactive Compounds for Medicine (2003)

Glycyrrhizic Acid (GL) is the major bioactive triterpene glycoside of licorice root (Glycyrrhiza Radix) extracts possessing a wide range of pharmacological properties (anti-inflammatory, anti-ulcer, anti-allergic, anti-dote, anti-oxidant, anti-tumor, anti-viral etc.). Official sources of GL are Glycyrrhiza glabra L. and Gl. uralensis Fish. (Leguminosae). The content of GL in licorice root is 2-24% of the dry weight. GL is one of the leading natural compounds for clinical trials of chronic active viral hepatitis and HIV infections (preparation Stronger Neo-Minophagen C, SNMC), and its monoammonium salt (glycyram, tussilinar) is used as an anti-inflammatory and anti-allergic remedy. The synthetic transformations of GL on carboxyl and hydroxyl groups were carried out to produce new bioactive derivatives for medicine. GL esters were produced containing fragments of bioactive acids (4-nitrobenzoic, cinnamic, salycilic, acetylsalycilic, nicotinic, isonicotinic). Bioactive amides of GL were synthesized using chloroanhydride technique and N,N'-diciclohexylcarbodiimide (DCC) method. The synthesis of acylthioureids and semicarbazones was carried out via the reaction of triacylisothiocianate of penta-O-acetyl-GL with primary amines and hydrazines. The chain of transformations of trichloranhydride of penta-O-acetyl-GL was made with the introduction of diazoketone groups in the molecule. A new group of GL derivatives to be triterpene glycopeptides was prepared by the activated esters method (N-hydrohysuccinimide-DCC or N-hydroxybenzotriazol-DCC) using alkyl (methyl, ethyl, propyl, butyl, tert-butyl) or benzyl (4-nitrobenzyl) esters of amino acids. The glycyrrhizyl analogs of the known immunostimulator, N-acetyl-muramoyldipeptide (MDP), were synthesized using Reagent Woodward K. A series of ureids and carbamates of GL was synthesized containing 5-amino-5-desoxy-D-xylopyranose units. The synthesis of 4-nitro-4-desoxy-glycosides, modified analogs of GL, was carried out by the oxidative splitting of the carbohydrate part of GL with NaIO(4). Triterpene 2-desoxy-D-glycosides, analogs of GL, were prepared by the glycal method in the presence of iodine-containing promoters or sulfonic acid cation-exchange resin KU-2-8 (H+) and LiBr. New anti-inflammatory and anti-ulcer agents were found among GL derivatives such as esters, amides, ureids, carbamates, thioureids and glycopeptides. GL glycopeptides are of interest as immunomodulators. Some of the chemically modified GL derivatives (salts, amides, glycopeptides) were potent HIV-1 and HIV-2 inhibitors in vitro. Preparation niglizin (penta-O-nicotinate of GL) was studied clinically as an anti-inflammatory agent and is of interest for studies as hepatoprotector and HIV inhibitor.
Advances in Carriers and Adjuvants for Veterinary Biologics (1986)

Advances in carriers and adjuvants for veterinary biologics , Advances in carriers and adjuvants for veterinary biologics , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Chromosomal assignment of human endogenous retrovirus K (HERV-K) <i>env open</i> reading frames (1997)

The haploid human genome contains at least one human endogenous retrovirus K (HERV-K) env gene displaying an open reading frame, as evidenced by the high antibody titers against HERV-K Env in germ cell tumor patients at the time of tumor detection. However, the chromosomal assignment of an intact HERV-K env sequence is complicated by the existence of 25-30 HERV-K copies per haploid human genome. Recently, we reported the application of the protein truncation test (PTT) to chromosomally assign HERV-K gag open reading frames. Here, we set out to determine the chromosomal distribution of full-length HERV-K env genes. As demonstrated by somatic hybrid mapping and the PTT, HERV-K env open reading frames were found on human chromosomes 7, 19, and Y. By sequencing chromosome-specific HERV-K env subregions, we assigned two recently reported intact HERV-K sequences on human chromosomes 7 and 19, respectively. Chromosomes 7 and 19 and the Y are furthermore candidates for harboring a putative completely intact HERV-K locus.
Legal Issues Raised by Transborder Data Flow (1986)

Canada-United States Economic Ties: The Technology Context and transborder data flows
CTLA-4 · FasL Induces Early Apoptosis of Activated T Cells by Interfering with Anti-Apoptotic Signals (2007)

The fusion protein CTLA-4 . FasL, a paradigmatic "trans signal converter protein", can attach to APC surfaces and in effect convert B7-activating costimulator signals into inhibitory Fas receptor-generated signals. The present study investigates CTLA-4 . FasL's mechanism of action. A combination of p27(kip) and proliferating cell nuclear Ag Western blot and propidium iodide flow cytometric analysis showed no CTLA-4 . FasL effect on cell cycle entry and progression, pointing away from the kind of classical anergy associated with CTLA-4 . Ig. Significantly, CTLA-4 . FasL elicited apoptosis (as detected by annexin-V/propidium iodide costaining) as early as 24 h after T cell activation, suggesting that some coordinate signaling might be capacitating the Fas receptor. Significantly, CTLA-4 . FasL, but not CTLA-4 . Ig, anti-Fas mAb, or the two in combination, abrogated the usual increase in expression of the anti-apototic protein, cFLIP. Furthermore, activation of caspases 8 and 3 were not affected by CTLA-4 . FasL. These findings suggest a model for CTLA-4 . FasL action wherein there is coordinate triggering of a death receptor and suppression of a proapoptotic protein.
Superactivation of an immune response triggered by oligomerized T cell epitopes (1997)

The peptides bound to class II major histocompatibility complex (MHC) molecules extend out both ends of the peptide binding groove. This structural feature provided the opportunity to design multivalent polypeptide chains that cross-link class II MHC molecules through multiple, repetitive MHC binding sites. By using recombinant techniques, polypeptide oligomers were constructed that consist of up to 32 copies of an HLA-DR1-restricted T cell epitope. The epitope HA306-318, derived from influenza virus hemagglutinin, was connected by 12- to 36-aa long spacer sequences. These oligomers were found to cross-link soluble HLA-DR1 molecules efficiently and, upon binding to the MHC molecules of a monocyte line, to trigger signal transduction indicated by the enhanced expression of some cell surface molecules. A particularly strong effect was evident in the T cell response. A hemagglutinin-specific T cell clone recognized these antigens at concentrations up to three to four orders of magnitude lower than that of the peptide or the hemagglutinin protein. Both signal transduction in the monocyte and the proliferative response of the T cell were affected greatly by the length of the oligomer (i.e., the number of repetitive units) and the distance of the epitopes within the oligomer (spacing). Thus, the formation of defined clusters of T cell receptor/MHC/peptide antigen complexes appears to be crucial for triggering the immune response and can be used to enhance the antigenicity of a peptide antigen by oligomerizing the epitope.
Structure of Staphylococcal α-Hemolysin, a Heptameric Transmembrane Pore (1996)

The structure of the Staphylococcus aureus alpha-hemolysin pore has been determined to 1.9 A resolution. Contained within the mushroom-shaped homo-oligomeric heptamer is a solvent-filled channel, 100 A in length, that runs along the sevenfold axis and ranges from 14 A to 46 A in diameter. The lytic, transmembrane domain comprises the lower half of a 14-strand antiparallel beta barrel, to which each protomer contributes two beta strands, each 65 A long. The interior of the beta barrel is primarily hydrophilic, and the exterior has a hydrophobic belt 28 A wide. The structure proves the heptameric subunit stoichiometry of the alpha-hemolysin oligomer, shows that a glycine-rich and solvent-exposed region of a water-soluble protein can self-assemble to form a transmembrane pore of defined structure, and provides insight into the principles of membrane interaction and transport activity of beta barrel pore-forming toxins.
Intracellular localization of human Ins(1,3,4,5,6)P5 2-kinase (2007)

InsP6 is an intracellular signal with several proposed functions that is synthesized by IP5K [Ins(1,3,4,5,6)P5 2-kinase]. In the present study, we overexpressed EGFP (enhanced green fluorescent protein)-IP5K fusion proteins in NRK (normal rat kidney), COS7 and H1299 cells. The results indicate that there is spatial microheterogeneity in the intracellular localization of IP5K that could also be confirmed for the endogenous enzyme. This may facilitate changes in InsP6 levels at its sites of action. For example, overexpressed IP5K showed a structured organization within the nucleus. The kinase was preferentially localized in euchromatin and nucleoli, and co-localized with mRNA. In the cytoplasm, the overexpressed IP5K showed locally high concentrations in discrete foci. The latter were attributed to stress granules by using mRNA, PABP [poly(A)-binding protein] and TIAR (TIA-1-related protein) as markers. The incidence of stress granules, in which IP5K remained highly concentrated, was further increased by puromycin treatment. Using FRAP (fluorescence recovery after photobleaching) we established that IP5K was actively transported into the nucleus. By site-directed mutagenesis we identified a nuclear import signal and a peptide segment mediating the nuclear export of IP5K.
Generation of Viable Cholesterol-Free Mice (2003)

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Presence of elevated carcinoembryonic antigen on absorbent disks applied to nipple area of breast carcinoma patients (1996)

BACKGROUND Carcinoembryonic antigen (CEA) is used as a serum marker to detect and monitor the status of various kinds of malignant tumors. To determine whether CEA might be detected in secretions collected topically from around the nipple area, and whether its secretion might differ in a cancerous versus a noncancerous breast, we developed a simple method for collecting and measuring CEA, using a small cellulose membrane disk and an enzyme immunoassay. METHODS We measured the amount of CEA excreted from the nipple area of 22 healthy control women and 32 women with unilateral breast carcinoma confirmed histologically. Secretions were collected from the nipple area by affixing a small (20 mm diameter) absorbent disk made of nitrocellulose membrane backed with filter paper to that area for 24 hours. Substances absorbed by the membrane were then subjected to an immunoassay for CEA using anti-CEA antibodies. RESULTS In the 22 healthy subjects, a small amount of CEA (0.6 ± 0.9 units) was secreted from each nipple, which was equally low regardless of the phase of the menstrual cycle. In contrast, 30 of the 32 women with breast carcinoma secreted significantly greater amounts of CEA from the cancerous (16.1 ± 8.2) than the noncancerous (2.0 ± 2.2) breast. Such a difference (14.1 ± 8.0) in CEA excretion was not observed in the healthy controls (0 ± 0). CONCLUSIONS These findings suggest that such disks may provide a simple and noninvasive method of collecting trace molecules, including CEA, in skin secretions around the nipple to evaluate functional disorders of the mammary glands, particularly breast carcinoma. Additional studies are indicated in larger groups of women with various stages of breast carcinoma as well as with benign breast diseases. Cancer 1996;78:1229-34.
Autocrine stimulation of VEGFR-2 activates human leukemic cell growth and migration (2000)

Emerging data suggest that VEGF receptors are expressed by endothelial cells as well as hematopoietic stem cells. Therefore, we hypothesized that functional VEGF receptors may also be expressed in malignant counterparts of hematopoietic stem cells such as leukemias. We demonstrate that certain leukemias not only produce VEGF but also express functional VEGFR-2 in vivo and in vitro, resulting in the generation of an autocrine loop that may support leukemic cell survival and proliferation. Approximately 50% of freshly isolated leukemias expressed mRNA and protein for VEGFR-2. VEGF(165) induced phosphorylation of VEGFR-2 and increased proliferation of leukemic cells, demonstrating these receptors were functional. VEGF(165) also induced the expression of MMP-9 by leukemic cells and promoted their migration through reconstituted basement membrane. The neutralizing mAb IMC-1C11, specific to human VEGFR-2, inhibited leukemic cell survival in vitro and blocked VEGF(165)-mediated proliferation of leukemic cells and VEGF-induced leukemic cell migration. Xenotransplantation of primary leukemias and leukemic cell lines into immunocompromised nonobese diabetic mice resulted in significant elevation of human, but not murine, VEGF in plasma and death of inoculated mice within 3 weeks. Injection of IMC-1C11 inhibited proliferation of xenotransplanted human leukemias and significantly increased the survival of inoculated mice. Interruption of signaling by VEGFRs, particularly VEGFR-2, may provide a novel strategy for inhibiting leukemic cell proliferation.
DNA Binding and Catalytic Properties of Positively Charged Corroles (2007)

DNA likes corroles and peroxynitrite doesn't: The water-soluble manganese corrole (crystal structure shown) is a much better catalyst than the analogous porphyrin for decomposition of peroxynitrite (HOONO). The interactions of the two complexes with DNA are also significantly different. These findings suggest that positively charged corroles may be useful for therapeutic approaches.
Paradox of B cell–targeted therapies (2008)

The use of antibodies against the human B cell surface protein CD20 represents the most advanced therapeutic approach among the B cell-depleting armamentarium for the treatment of autoimmune disorders. However, recent evidence indicates that B cells can also be essential for suppressing unwanted autoaggressive T cell responses, and therefore, a more careful evaluation of which types of autoimmune disorders this therapy should be utilized for, and at which phases of disease this therapy should be applied, is necessary. In this issue of the JCI, Matsushita et al. report that the timing of this therapy is critical for the management of EAE, a mouse model of human MS (see the related article beginning on page 3420). The results suggest the existence of two opposite actions executed by B cells during the course of autoimmune pathology; CD1dhiCD5+ regulatory B cells suppress EAE induction, whereas B cells are required for the expansion of autoantigen-specific T cells during disease progression. Given the existence of such regulatory B cells in humans, these findings not only resolve previously unexplained contradictions with respect to the outcome of B cell-depleting therapy but also provide insight into the best regimen for this treatment approach.
A Comparative Study on the Aspectual Classification of Korean and Japanese Verbs in Relation to `-ess-' `-essess-' in Korean and `sudeni'in Japanese (2010)

Abstract. This paper deals with an aspectual classification of Korean and Japanese verbs based on Vendler (1967). Both of Korean and Japanese verbs are classified into 12 distinctive aspectual categories by their restrictions on time adverbials, progressive tenses and logical entailments. A well-established aspectual verb classes provide us not only with a better understanding of both languages, but also with an explicit explanation concerning some grammatical phenomena relevant to time. The aspectual classes of Korean verbs clarify the ambiguous semantic functions of so called Korean tense forms ‘-ess- ‘ and ‘-essess-‘, while those of Japanese verbs elucidate the semantic functions of ‘sudeni’, the equivalent of ‘already ’ in English, when it occurs with a variety of verbs in sentences.
Gene2Oligo: oligonucleotide design for in vitro gene synthesis (2004)

There is substantial interest in implementing a bioinformatics tool that allows the design of oligonucleotides to support the development of in vitro gene synthesis. Current protocols to make long synthetic DNA molecules rely on the in vitro assembly of a set of short oligonucleotides, either by ligase chain reaction (LCR) or by assembly PCR. Ideally, such oligonucleotides should represent both strands of the final DNA molecule. They should be adjacent on the same strand and overlap the complementary oligonucleotides from the second strand to ensure good hybridization during assembly. This implies that the thermodynamic properties of each oligonucleotide have to be consistent across the set. Furthermore, any given oligonucleotide has to be totally specific to its target to avoid the creation of incorrectly assembled sequences. We have developed Gene2Oligo (http://berry.engin.umich.edu/gene2oligo/), a web-based tool that divides a long input DNA sequence into a set of adjacent oligonucleotides representing both DNA strands. The length of the oligonucleotides is dynamically optimized to ensure both the specificity and the uniform melting temperatures necessary for in vitro gene synthesis. We have successfully designed and used a set of oligonucleotides to synthesize the Saccharomyces cerevisiae cytochrome b5 by using both LCR and assembly PCR.
Thermochemistry and Conformational Polymorphism of a Hexamorphic Crystal System (2000)

5-Methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile has been crystallized as six solvent-free polymorphs, which differ in the mode of packing and in molecular conformation. The conformational difference results principally from the thiophene torsion relative to the o-nitroaniline fragment, which leads to different crystal colors (red, orange, and yellow). Thermodynamic stability relationships between polymorphs have been determined from solid-state conversions and calorimetric data of melting and eutectic melting. Vibrational spectroscopy and ab initio calculations showed that most conformers in solution feature perpendicularly arranged thiophene and o-nitroaniline fragments, although a minor population of more planar conformers also exist. Crystallization has a stabilizing effect for more planar and higher dipole conformers over perpendicular ones by 3−6 kJ/mol. The only exception to this pattern is the one polymorph containing weak intermolecular hydrogen bonds.
Identification of autoantigen epitopes in MHC Class II transgenic mice (1998)

MHC class II molecules function by selective binding of antigenic peptides, thereby both shaping the T-cell receptor (TCR) repertoire in the thymus and influencing presentation of immunogenic peptides to CD4+ T cells in the periphery. The strong association between a number of human autoimmune diseases (type 1 diabetes, rheumatoid arthritis, and multiple sclerosis) and certain HLA-DR/DQ alleles suggests that it may be possible to alter pathological autoimmune responses by deliberate introduction of autoantigenic peptides in a "tolerogenic" manner. Since there are likely to be differences in epitope selection and epitope spreading in different patients over time, this approach requires identification of all the immunogenic CD4+ T-cell epitopes (dominant, subdominant, or cryptic) of an autoantigen which elicit T-cell responses restricted to the HLA-DR/DQ alleles predisposing to these autoimmune diseases. This paper describes a new approach for the identification of immunogenic peptide epitopes of human autoantigenic proteins using HLA-DR and DQ transgenic mice. These mice are engineered to select a full TCR repertoire which can identify immunogenic peptide epitopes similar or identical to human subjects of the same HLA-DR/DQ genotype. This experimental system also allows comparison of autoantigenic immune responses restricted to disease-susceptible and disease-resistant HLA-DR/DQ alleles.
Osteogenic Induction of Human Bone Marrow-Derived Mesenchymal Progenitor Cells in Novel Synthetic Polymer–Hydrogel Matrices (2003)

The aim of this project was to investigate the in vitro osteogenic potential of human mesenchymal progenitor cells in novel matrix architectures built by means of a three-dimensional bioresorbable synthetic framework in combination with a hydrogel. Human mesenchymal progenitor cells (hMPCs) were isolated from a human bone marrow aspirate by gradient centrifugation. Before in vitro engineering of scaffold-hMPC constructs, the adipogenic and osteogenic differentiation potential was demonstrated by staining of neutral lipids and induction of bone-specific proteins, respectively. After expansion in monolayer cultures, the cells were enzymatically detached and then seeded in combination with a hydrogel into polycaprolactone (PCL) and polycaprolactone-hydroxyapatite (PCL-HA) frameworks. This scaffold design concept is characterized by novel matrix architecture, good mechanical properties, and slow degradation kinetics of the framework and a biomimetic milieu for cell delivery and proliferation. To induce osteogenic differentiation, the specimens were cultured in an osteogenic cell culture medium and were maintained in vitro for 6 weeks. Cellular distribution and viability within three-dimensional hMPC bone grafts were documented by scanning electron microscopy, cell metabolism assays, and confocal laser microscopy. Secretion of the osteogenic marker molecules type I procollagen and osteocalcin was analyzed by semiquantitative immunocytochemistry assays. Alkaline phosphatase activity was visualized by p-nitrophenyl phosphate substrate reaction. During osteogenic stimulation, hMPCs proliferated toward and onto the PCL and PCL-HA scaffold surfaces and metabolic activity increased, reaching a plateau by day 15. The temporal pattern of bone-related marker molecules produced by in vitro tissue-engineered scaffold-cell constructs revealed that hMPCs differentiated better within the biomimetic matrix architecture along the osteogenic lineage.
THE USE OF RESERPINE IN AUTISTIC CHILDREN (1957)

LEHMAN, EDWARD M.D.2,3; HABER, JOSEPH M.D.2,3; LESSER, STANLEY R. M.D.4 Author Information
Scaling personalized web search (2003)

Recent web search techniques augment traditional text matching with a global notion of "importance" based on the linkage structure of the web, such as in Google's PageRank algorithm. For more refined searches, this global notion of importance can be specialized to create personalized views of importance--for example, importance scores can be biased according to a user-specified set of initially-interesting pages. Computing and storing all possible personalized views in advance is impractical, as is computing personalized views at query time, since the computation of each view requires an iterative computation over the web graph. We present new graph-theoretical results, and a new technique based on these results, that encode personalized views as partial vectors. Partial vectors are shared across multiple personalized views, and their computation and storage costs scale well with the number of views. Our approach enables incremental computation, so that the construction of personalized views from partial vectors is practical at query time. We present efficient dynamic programming algorithms for computing partial vectors, an algorithm for constructing personalized views from partial vectors, and experimental results demonstrating the effectiveness and scalability of our techniques.