gebhart/patrepeval huggingface dataset:
Human T-lymphotropic virus type 1 peptides in chimeric and multivalent constructs with promiscuous T-cell epitopes enhance immunogenicity and overcome genetic restriction (1995)

Conventional strategies of viral peptide immunizations often elicit low-affinity antibody responses and have limited ability to elicit immune responses in outbred animals of diverse major histocompatibility (MHC) haplotypes. This genetically restricted T-cell-stimulatory activity of peptides is a serious obstacle to vaccine design. However, the use of promiscuous T-cell epitopes may circumvent this problem. Promiscuous T-cell epitopes from tetanus toxin (amino acids [aa] 580 to 599) and the measles virus F protein (aa 288 to 302) that bind to several isotypic and allotypic forms of human MHC class II molecules have been identified and have been used in highly immunogenic constructs to overcome haplotype-restricted immune responses. Chimeric and beta-template peptide constructs incorporating known human T-lymphotropic virus type 1 (HTLV-1) B- and T-cell epitopes from the surface envelope protein gp46 (SP2 [aa 86 to 107] and SP4a [aa 190 to 209]) and promiscuous T-cell peptides were synthesized, and their immunogenicities were evaluated in both rabbits and mouse strains of divergent haplotypes (C3H/HeJ [H-2k], C57BL/6 [H-2b], and BALB/c [H-2d]). In addition, peptide preparations were structurally characterized by analytical high-performance liquid chromatography, mass spectrometry, and circular dichroism. In contrast to their linear forms, the chimeric constructs of both the SP2 and SP4a epitopes displayed alpha-helical secondary structures. Immunogenicity of the peptide constructs was evaluated by direct and competitive enzyme-linked immunosorbant assay (ELISA), as well as by radioimmunoprecipitation, syncytium inhibition, and antigen-induced lymphocyte proliferation assays. Immunization with the SP4a peptide without conjugation to a carrier protein produced antibodies specific for SP4a in two mouse strains (C3H/HeJ and C57BL/6). However, BALB/c mice failed to respond to the peptide, indicating that the T-cell epitope of the SP4a sequence is MHC restricted. In contrast, the chimeric constructs MVF-SP2 and SP4a-measles virus F protein were highly immunogenic, producing elevated ELISA titers after only two immunizations. Elicited antibodies recognized native forms of gp46 in ELISAs and radioimmunoprecipitation assays, as well as inhibited HTLV-1-mediated syncytium formation. In addition, chimeric constructs were effective at induction of lymphocyte proliferation to the T-cell epitope, SP4a, in each strain of immunized mice. Our data demonstrate that the antibody response to retroviral peptides is enhanced by promiscuous peptide constructs, in part because of the ability of such constructs to promote appropriate secondary structural forms of viral epitopes. In addition, these constructs promote virus-specific helper T-cell responses, thereby overcoming genetically restricted immune responses to the synthetic peptides.
Suppression of Food Intake by Glucagon-Like Peptide-1 Receptor Agonists: Relative Potencies and Role of Dipeptidyl Peptidase-4 (2012)

Administration of the glucagon-like peptide-1 (GLP-1) receptor agonists GLP-1 and exendin-4 (Ex-4) directly into the central nervous system decreases food intake. But although Ex-4 potently suppresses food intake after peripheral administration, the effects of parenteral GLP-1 are variable and not as strong. A plausible explanation for these effects is the rapid inactivation of circulating GLP-1 by dipeptidyl peptidase-4 (DPP-4), an enzyme that does not alter Ex-4 activity. To test this hypothesis, we assessed the relative potency of Ex-4 and GLP-1 under conditions in which DPP-4 activity was reduced. Outbred rats, wild-type mice, and mice with a targeted deletion of DPP-4 (Dpp4(-/-)) were treated with GLP-1 alone or in combination with the DPP-4 inhibitor vildagliptin, Ex-4, or saline, and food intake was measured. GLP-1 alone, even at high doses, did not affect feeding in wild-type mice or rats but did reduce food intake when combined with vildagliptin or given to Dpp4(-/-) mice. Despite plasma clearance similar to DPP-4-protected GLP-1, equimolar Ex-4 caused greater anorexia than vildagliptin plus GLP-1. To determine whether supraphysiological levels of endogenous GLP-1 would suppress food intake if protected from DPP-4, rats with Roux-en-Y gastric bypass and significantly elevated postprandial plasma GLP-1 received vildagliptin or saline. Despite 5-fold greater postprandial GLP-1 in these animals, vildagliptin did not affect food intake in Roux-en-Y gastric bypass rats. Thus, in both mice and rats, peripheral GLP-1 reduces food intake significantly less than Ex-4, even when protected from DPP-4. These findings suggest distinct potencies of GLP-1 receptor agonists on food intake that cannot be explained by plasma pharmacokinetics.
Gene Expression Differences Associated with Human Papillomavirus Status in Head and Neck Squamous Cell Carcinoma (2006)

Human papillomavirus (HPV) is associated with a subset of head and neck squamous cell carcinoma (HNSCC). Between 15% and 35% of HNSCCs harbor HPV DNA. Demographic and exposure differences between HPV-positive (HPV+) and negative (HPV-) HNSCCs suggest that HPV+ tumors may constitute a subclass with different biology, whereas clinical differences have also been observed. Gene expression profiles of HPV+ and HPV- tumors were compared with further exploration of the biological effect of HPV in HNSCC. Thirty-six HNSCC tumors were analyzed using Affymetrix Human 133U Plus 2.0 GeneChip and for HPV by PCR and real-time PCR. Eight of 36 (22%) tumors were positive for HPV subtype 16. Statistical analysis using Significance Analysis of Microarrays based on HPV status as a supervising variable resulted in a list of 91 genes that were differentially expressed with statistical significance. Results for a subset of these genes were verified by real-time PCR. Genes highly expressed in HPV+ samples included cell cycle regulators (p16(INK4A), p18, and CDC7) and transcription factors (TAF7L, RFC4, RPA2, and TFDP2). The microarray data were also investigated by mapping genes by chromosomal location (DIGMAP). A large number of genes on chromosome 3q24-qter had high levels of expression in HPV+ tumors. Further investigation of differentially expressed genes may reveal the unique pathways in HPV+ tumors that may explain the different natural history and biological properties of these tumors. These properties may be exploited as a target of novel therapeutic agents in HNSCC treatment.
Comparative analysis of bone marrow and venous blood isolates from gastrointestinal cancer patients for the detection of disseminated tumor cells using reverse transcription PCR. (1997)

We investigated 141 bone marrow and 104 venous blood isolates from gastrointestinal cancer patients with a cytokeratin (CK) 20-specific nested reverse transcription PCR for the detection of disseminated tumor cells at time of primary tumor resection. In colorectal cancer patients, 20 of 65 (31%) bone marrow and 9 of 52 (17%) venous blood isolates yielded a CK 20 mRNA-positive result in a stage-dependent manner. The detection rates for gastric cancer patients were 11 of 49 (22%) and 5 of 30 (17%) for bone marrow and venous blood, respectively. In pancreatic cancer patients, positive signals were found in advanced tumor stage. A duplex PCR system improved the feasibility of the test. After analyzing 70 sets of bone marrow and venous blood isolates from colorectal, gastric, and pancreatic cancer patients, we observed a higher detection rate in bone marrow isolates. Survival of patients with CK 20 mRNA-positive findings was significantly shorter than that of negatively tested patients.
Actigenetic of ACE gene polymorphism in Czech obese sedentary females (2009)

Obesity is a serious health problem worldwide and many genes have been implicated in determination of obesity, but our knowledge of the genes responsible for individual differences in weight loss after physical intervention are poor. One of the candidate genes is a gene for angiotensin-converting enzyme (ACE) ant its insertion/deletion (I/D) polymorphism. We have analyzed the association between the ACE gene variant in intervened obese females. Twenty four unrelated healthy obese (BMI > 29.9 kg/m(2), with abdominal type of obesity) premenopausal (age between 25 and 45 years) Czech Caucasian sedentary and non-diabetic females, pre-selected according the ACE I/D polymorphism (twelve II and twelve DD homozygotes) were studied in a medical research centre. They underwent 9 weeks intervention program (combination of the lowering of dietary intake to optimal level for the age and 3 times a week physical activity at fitness centre). The participants were supervised to sustain a heart rate of 65 % of maximum. Anthropometrical, biochemical parameters and body composition (Bodystat 1500) were analyzed before and after the intervention. Our study suggest, that in Czech Caucasian females I/D polymorphism within the ACE gene will have no major effect on weight loss. Interestingly, we have detected, that in obese females II genotype was associated with higher increase in basal metabolic rate (202 kcal per day) then in DD homozygotes (p<0.05), thus at least under some circumstances, this genetic variant may have an slight effect on BMI development.
Molecular cloning of integrin-associated protein: an immunoglobulin family member with multiple membrane-spanning domains implicated in alpha v beta 3-dependent ligand binding. (1993)

Integrin Associated Protein (IAP) is a 50-kD membrane protein which copurifies with the integrin alpha v beta 3 from placenta and coimmunoprecipitates with beta 3 from platelets. IAP also is functionally associated with signal transduction from the Leukocyte Response Integrin. Using tryptic peptide sequence, human and murine IAP cDNAs have been isolated. The protein has an extracellular amino-terminal immunoglobulin domain that binds all monoclonal anti-IAP antibodies. The carboxy-terminal region is highly hydrophobic with three or five membrane-spanning segments and a short hydrophilic tail. Immunofluorescence microscopy suggests that this hydrophilic tail is located on the inside of the cytoplasmic membrane. Monoclonal anti-IAP antibody inhibits the binding of vitronectin-coated beads to alpha v beta 3 on human erythroleukemia cells, and polyclonal anti-IAP recognizes hamster IAP on CHO cells and inhibits vitronectin bead binding. When CHO cells are transfected with human IAP, monoclonal anti-human antibody completely inhibits vitronectin bead binding. These data suggest a model in which ligand binding by alpha v beta 3 is regulated by IAP.
STUDY ON A NOVEL STRATEGY TO TREATMENT OF PHENYLKETONURIA (2002)

To replace the low phenylalanine (phe) diet treatment and to improve the quality of life of the phenylketonuria (PKU) patients, A phenylalanine ammonia-lyase (PAL) cDNA from petroselinum crispum was subcloned into expression vectors, pMG36e and pNZ8048, and transformed L. lactis by electroporation. The pMG36e PAL/L. lactis and pNZ8048 PAL/L.L. were screened and characterized by using PCR and HPLC, and prepared as a liquid type preparation that were given orally to treat hyperphenylalaninemia-rats. The phe levels of the rat plasma sample were determined by HPLC. The data showed that the plasma phe levels in hyperphenylalanemia (HPA) rats receiving preparations made from the engineered L. lactis were significantly reduced compared with non-treated HPA rats. The effect of the pNZ8048PAL/L.L. showed a higher expression of PAL and better cure results than pMG36ePAL/L.L. These results point a potential way for PKU treatment.
Medical hypothesis: xenoestrogens as preventable causes of breast cancer. (1993)

Changes in documented risk factors for breast cancer and rates of screening cannot completely explain recent increases in incidence or mortality. Established risk factors for breast cancer, including genetics, account for at best 30% of cases. Most of these risk factors can be linked to total lifetime exposure to bioavailable estrogens. Experimental evidence reveals that compounds such as some chlorinated organics, polycyclic aromatic hydrocarbons (PAHs), triazine herbicides, and pharmaceuticals affect estrogen production and metabolism and thus function as xenoestrogens. Many of these xenoestrogenic compounds also experimentally induce mammary carcinogenesis. Recent epidemiologic studies have found that breast fat and serum lipids of women with breast cancer contain significantly elevated levels of some chlorinated organics compared with noncancer controls. As the proportion of inherited breast cancer in the population is small, most breast cancers are due to acquired mutations. Thus, the induction of breast cancer in the majority of cases stems from interactions between host factors, including genetics and environmental carcinogens. We hypothesize that substances such as xenoestrogens increase the risk of breast cancer by mechanisms which include interaction with breast-cancer susceptibility genes. A series of major epidemiologic studies need to be developed to evaluate this hypothesis, including studies of estrogen metabolism, the role of specific xenoestrogenic substances in breast cancer, and relevant genetic-environmental interactions. In addition, experimental studies are needed to evaluate biologic markers of suspect xenoestrogens and biologic markers of host susceptibility and identify pathways of estrogenicity that affect the development of breast cancer. If xenoestrogens do play a role in breast cancer, reductions in exposure will provide an opportunity for primary prevention of this growing disease.(ABSTRACT TRUNCATED AT 250 WORDS)
A Concise Total Synthesis of (−)-Quinocarcin via Aryne Annulation (2008)

Described in this report is a rapid asymmetric total synthesis of the tetrahydroisoquinoline antitumor antibiotic (-)-quinocarcin. The sequence employs a mild fluoride-induced aryne annulation developed in our laboratories to build a key isoquinoline-containing intermediate comprising the entire carbon scaffold of the natural product. This intermediate is advanced through six additional steps to the target alkaloid, providing the shortest synthetic route to (-)-quinocarcin reported to date.
A novel fault location scheme using voltage traveling-wave of CVTs (2004)

In this paper, high-speed acquisition voltage data according to two phase-to-ground faults between Ge-Gang transmission line is processed using wavelet transformation, by which the exact inceptive traveling-waves can be obtained as well as the GPS time stamps and the fault distances by means of those GPS time stamps of two ends. The maximum error of fault location is less than 300 m. Also, an equivalent circuit considering stray capacitance between primary and secondary windings is presented in this paper along with the frequency and transient responses of CVT, and we proposed that the CVT voltage can be used in traveling-wave fault location and further studies relative to high frequency characteristics of CVT should be further carried out.
Scheduling data-intensive workflows on storage constrained resources (2009)

Data-intensive workflows stage large amounts of data in and out of compute resources. The data staging strategies employed during the execution of such workflows can have a significant impact on the time taken to complete the execution or on the overall cost of the execution. We describe the problem of minimizing the overall time taken for execution and present a heuristic based on ordering clean-up jobs in the workflow. Next, we develop genetic algorithm based approaches to solving the same problem and demonstrate that the results obtained with the heuristic are comparable to the best results obtained with the genetic algorithm based approaches. We also describe the problem of minimizing the overall cost of execution and extend our genetic algorithm to generate schedules that vary the number of processors and the amount of storage provisioned for execution to generate low cost schedules.
Mechanics of cell spreading within 3D-micropatterned environments (2010)

Most tissue cells evolve in vivo in a three-dimensional (3D) microenvironment including complex topographical patterns. Cells exert contractile forces to adhere and migrate through the extracellular matrix (ECM). Although cell mechanics has been extensively studied on 2D surfaces, there are too few approaches that give access to the traction forces that are exerted in 3D environments. Here, we describe an approach to measure dynamically the contractile forces exerted by fibroblasts while they spread within arrays of large flexible micropillars coated with ECM proteins. Contrary to very dense arrays of microposts, the density of the micropillars has been chosen to promote cell adhesion in between the pillars. Cells progressively impale onto the micropatterned substrate. They first adhere on the top of the pillars without applying any detectable forces. Then, they spread along the pillar sides, spanning between the elastic micropillars and applying large forces on the substrate. Interestingly, the architecture of the actin cytoskeleton and the adhesion complexes vary over time as cells pull on the pillars. In particular, we observed less stress fibers than for cells spread on flat surfaces. However, prominent actin stress fibers are observed at cell edges surrounding the micropillars. They generate increasing contractile forces during cell spreading. Cells treated with blebbistatin, a myosin II inhibitor, relax their internal tension, as observed by the release of pillar deformations. Moreover, cell spreading on pillars coated with ECM proteins only on their tops are not able to generate significant traction forces. Taken together, these findings highlight the dynamic relationship between cellular forces and acto-myosin contractility in 3D environments, the influence of cytoskeletal network mechanics on cell shape, as well as the importance of cell-ECM contact area in the generation of traction forces.
Cytoplasmic chaperonin complexes enter neurites developing in vitro and differ in subunit composition within single cells (1995)

Chaperonins containing t-complex polypeptide-1 (CCT) are cytosolic molecular chaperone particles implicated especially in the biogenesis of cytoskeletal proteins by promoting the correct folding of the major ubiquitous cytoskeletal components, tubulin and actin. We have purified cytosolic chaperonins from the ND7/23 cell line, determined their subunit composition and examined changes in the intracellular locations of their components during differentiation of ND7/23 cells to a neuronal phenotype by using immunocytochemistry and immunoblots. Chaperonins containing the CCT alpha (TCP1) subunit enter neuritic processes and are particularly noticeable at the leading edge of growth cone-like structures where they co-localise with actin. Chaperonins containing three other components (CCT beta, epsilon and gamma), however, remain predominantly restricted to perikaryal cytoplasm. These findings suggest a heterogeneous population of chaperonin particles within single differentiated ND7/23 cells and this may reflect specialisation of chaperonin function in different cytoplasmic compartments of a neurone. Further, since ribosomes do not enter neurites while CCT alpha-containing chaperonins do, the latter may play roles, subsequent to translation, which influence cytoskeletal elaboration during neuritogenesis.
A comparative overview of microwave and wireless power-amplifier behavioral modeling approaches (2005)

This paper presents a comparative overview of the most important approaches presented to address the behavioral modeling of microwave and wireless power amplifiers (PAs). Starting from a theoretical framework of recursive and nonrecursive nonlinear filters, it proposes a classification of the various PA behavioral models, discussing their abilities to represent the different effects observed in practical circuits. Using that formal procedure, one explains how it was possible to integrate a wide range of behavioral modeling activities and to show that some of them, which at first glance seemed to be quite different, are, indeed, identical in their modeling capabilities.
LDL receptor polymorphisms revisited (2010)

In this issue of Blood , Martinelli and colleagues describe that certain single-nucleotide polymorphisms in the LDL receptor gene independently associate with high plasma levels of coagulation factor VIII in patients with coronary artery disease.[1][1]

In 1985, Drs M. S. Brown and J. L. Goldstein
Bifunctional Nanoparticles Constructed Using One‐Pot Encapsulation of a Fluorescent Polymer and Magnetic (Fe3O4) Nanoparticles in a Silica Shell (2012)

Integration of biocompatible silica with a fluorescent polymer (PDDF) and superparamagnetic iron oxide nanoparticles (Fe3 O4 ) to form uniform core-shell nanostructures has the great potential to form particles for use in multimodal bioimaging applications. Core-shell nanoparticles (PDDF/Fe3 O4 @SiO2 ) exhibit fluorescent and magnetic properties that are favorable for their use in magnetic separation and guiding applications, as well as optical and magnetic resonance (MR) imaging capabilities. With the biological analysis in an in vitro intracellular permeation and cytotoxicity test, chemical conjugation of the surface using folic acid (FA) molecules can provide the nanoparticles with cell-targeting properties, localizing the nanoparticles to folate receptors (FRs) on target KB cells that over-express the FRs.
ChemInform Abstract: SYNTHESIS OF SOME NEW HETEROCYCLIC 1,3,4‐OXADIAZOLES WITH ANTIBACTERIAL ACTIVITY (1982)

2-N-Aryl/heterocyclic carboxamidomethylthio-5-p-chlorophenyl-1,3,4-oxadiazoles have been synthesized by the reaction of 1 and N-aryl/heterocyclic-2-chloracetamides in presence of basic medium. 2 and 3 react with heterocyclic thiols in ethanolic potassium hydroxide to give 3-S-substituted-mercaptomethyl-5-substituted-phenyl-1,3,4-oxadiazol-2-thione 5 and 6 respectively. Tert. amines react with 2 to yield the corresponding amino chlorides in good yield. Some of the prepared compounds were tested as antibacterials against Gram-positive and Gram-negative organism.
The use of 4‐hetaryliden‐ and 4‐aryliden‐5(4H)‐oxazolones as dienophiles. Appropriate reagents for the synthesis of cyclic analogues of natural amino acids (1997)

Abstract This report describes the behavior of 4‐hetaryliden‐ and 4‐aryliden‐5(4 H )‐oxazolones as dienophiles in the Diels‐Alder reaction with several dienes. The application of this reaction to the synthesis of different conformationally constrained cyclic analogues of natural amino acids of pharmacological interest is also described.
Identification and Characterization of Mitochondrial Acetyl-Coenzyme A Hydrolase from Pisum sativum L. Seedlings (1990)

Mitochondria from Pisum sativum seedlings purified free of peroxisomal and chlorophyll contamination were examined for acetyl-coenzyme A (CoA) hydrolase activity. Acetyl-CoA hydrolase activity was latent when assayed in isotonic media. The majority of the enzyme activity was found in the soluble matrix of the mitochondria. The products, acetate and CoA, were quantified by two independent methods and verified that the observed activity was an acetyl-CoA hydrolase. The pea mitochondrial acetyl-CoA hydrolase showed a K(m) for acetyl-CoA of 74 micromolar and a V(max) of 6.1 nanomoles per minute per milligram protein. CoA was a linear competitive inhibitor of the enzyme with a K(is) of 16 micromolar. The sensitivity of the enzyme to changes in mole fraction of acetyl-CoA suggested that the changes in the intramitochondrial acetyl-CoA/CoA ratio may be an effective mechanism of control. The widespread distribution of mitochondrial acetyl-CoA hydrolase activity among different plant species indicated that this may be a general mechanism in plants for synthesizing acetate.