gebhart/patrepeval huggingface dataset:
Green tea extract and its major polyphenol (−)-epigallocatechin gallate improve muscle function in a mouse model for Duchenne muscular dystrophy (2006)

Duchenne muscular dystrophy is a frequent muscular disorder caused by mutations in the gene encoding dystrophin, a cytoskeletal protein that contributes to the stabilization of muscle fiber membrane during muscle activity. Affected individuals show progressive muscle wasting that generally causes death by age 30. In this study, the dystrophic mdx(5Cv) mouse model was used to investigate the effects of green tea extract, its major component (-)-epigallocatechin gallate, and pentoxifylline on dystrophic muscle quality and function. Three-week-old mdx(5Cv) mice were fed for either 1 or 5 wk a control chow or a chow containing the test substances. Histological examination showed a delay in necrosis of the extensor digitorum longus muscle in treated mice. Mechanical properties of triceps surae muscles were recorded while the mice were under deep anesthesia. Phasic and tetanic tensions of treated mice were increased, reaching values close to those of normal mice. The phasic-to-tetanic tension ratio was corrected. Finally, muscles from treated mice exhibited 30-50% more residual force in a fatigue assay. These results demonstrate that diet supplementation of dystrophic mdx(5Cv) mice with green tea extract or (-)-epigallocatechin gallate protected muscle against the first massive wave of necrosis and stimulated muscle adaptation toward a stronger and more resistant phenotype.
Identification of the cellular protein encoded by the human Wilms' tumor (WT1) gene. (1992)

A putative tumor-suppressor gene (wt1) located at chromosome 11p13 and involved in Wilms' tumor development has recently been identified as a zinc finger polypeptide-encoding gene. The purpose of this study was to characterize the protein encoded by the human wt1 gene. The region spanning the entire zinc finger domain was amplified by polymerase chain reaction (PCR) and subcloned in the pATH 3 expression vector. Polyclonal antibodies against the fused TrpE-WT protein were raised. These antibodies immunoprecipitated a 49- to 51-kDa protein from hematopoietic tumor cells labeled in vivo with [35S]methionine. Subcellular fractionation and immunohistochemistry followed by confocal microscopy indicated that the Wilms' tumor gene product (WT1) is mainly localized within the nucleus.
Scaling up Kernel SVM on Limited Resources: A Low-rank Linearization Approach (2012)

Kernel Support Vector Machine delivers state-of-the-art results in non-linear classification, but the need to maintain a large number of support vectors poses a challenge in large scale training and testing. In contrast, linear SVM is much more scalable even on limited computing recourses (e.g. daily life PCs), but the learned model cannot capture non-linear concepts. To scale up kernel SVM on limited resources, we propose a lowrank linearization approach that transforms a non-linear SVM to a linear one via a novel, approximate empirical kernel map computed from efficient low-rank approximation of kernel matrices. We call it LLSVM (Lowrank Linearized SVM). We theoretically s-tudy the gap between the solutions of the optimal and approximate kernel map, which is used in turn to provide important guidance on the sampling based kernel approximations. Our algorithm inherits high efficiency of linear SVMs and rich repesentability of kernel classifiers. Evaluation against large-scale linear and kernel SVMs on several truly large data sets shows that the proposed method achieves a better tradeoff between scalability and model representability.
Effects of the ancillary ligands of polypyridyl ruthenium(ii) complexes on the DNA-binding behaviors (2003)

A new polypyridyl ligand PMIP {PMIP = 2-(4-methylphenyl)imidazo[4,5-f]1,10-phenanthroline}, and its Ru(II) complexes, [Ru(bpy)2PMIP]2+1 (bpy = 2,2′-bipyridine), [Ru(phen)2PMIP]2+2 (phen = 1,10-phenanthroline) and [Ru(dmp)2PMIP]2+3 (dmp = 2,9-dimethyl-1,10-phenanthroline), have been synthesized and characterized. The binding of the three complexes to calf thymus DNA (CT DNA) has been investigated with spectrophotometic methods, viscosity measurements, as well as equilibrium dialysis and circular dichroism spectroscopy. Complexes 1 and 2 can bind to CT DNA through intercalation. Complex 3 binds to CT DNA via partial intercalative mode. All the three complexes can enantioselectively interact with CT DNA in a way. Complex 3 is a much better candidate as an enantioselective binder to CT DNA than complex 1 and complex 2. The Δ enantiomer of complex 1 is slightly predominant for binding to CT DNA to the Λ enantiomer. The experimental results suggest that the ancillary ligands of polypyridyl Ru(II) complexes have significant effects on the spectral properties and the DNA-binding behaviors of the complexes. On the basis of the experiments, the theoretical calculations applying the density functional theory (DFT) on the level of B3LYP/LanL2DZ basis set for these three complexes have been used to further discuss the trend in the binding strength or binding constants (Kb) of the complexes to DNA, as well as predict roughly some of their spectral properties.
X-ray Structure of β-Carbonic Anhydrase from the Red Alga,Porphyridium purpureum, Reveals a Novel Catalytic Site for CO2 Hydration (2000)

The carbonic anhydrases (CAs) fall into three evolutionarily distinct families designated alpha-, beta-, and gamma-CAs based on their primary structure. beta-CAs are present in higher plants, algae, and prokaryotes, and are involved in inorganic carbon utilization. Here, we describe the novel x-ray structure of beta-CA from the red alga, Porphyridium purpureum, at 2.2-A resolution using intrinsic zinc multiwavelength anomalous diffraction phasing. The CA monomer is composed of two internally repeating structures, being folded as a pair of fundamentally equivalent motifs of an alpha/beta domain and three projecting alpha-helices. The motif is obviously distinct from that of either alpha- or gamma-CAs. This homodimeric CA appears like a tetramer with a pseudo 222 symmetry. The active site zinc is coordinated by a Cys-Asp-His-Cys tetrad that is strictly conserved among the beta-CAs. No water molecule is found in a zinc-liganding radius, indicating that the zinc-hydroxide mechanism in alpha-CAs, and possibly in gamma-CAs, is not directly applicable to the case in beta-CAs. Zinc coordination environments of the CAs provide an interesting example of the convergent evolution of distinct catalytic sites required for the same CO(2) hydration reaction.
Diversity and Patterns of Regulation of Nicotinic Receptor Subtypesa (1995)

In our studies we explored the functional relevance of nAChR diversity, in part from the perspective of nAChR as ideal targets for regulatory influences, including those mediated via actions of ligands at other "interacting" receptors. We explored possible mechanisms for nAChR regulation and roles played by nAChR subtype and subunit diversity in those processes. We showed that regulatory factors can influence nAChR numbers at transcriptional and posttranscriptional levels and can affect nAChR function and subcellular distribution. We also demonstrated that nAChR expression can be influenced (1) by nicotinic ligands, (2) by second messengers, (3) by growth factors, (4) by agents targeting the nucleus, and (5) by agents targeting the cytoskeleton. We found common effects of some regulatory influences on more than one nAChR subtype, and we found instances where regulatory influences differ for different cell and nAChR types. Even from the very limited number of these initial studies, it is evident that nAChR subunit and subtype diversity, which alone can provide diversity in nAChR functions, localization, and ligand sensitivity, dovetails with diversity in cellular signaling mechanisms that can affect nAChR expression to amplify the potential functional plasticity of cholinoceptive cells. As examples, we discussed potential roles for nAChR diversity and regulatory plasticity in synapse remodeling and in changes in neuronal circuit conditions. These examples illustrate how nAChR diversity could play important roles in the regulation of nervous system function.
Macroeconomic adjustment and the labor market in four Latin American countries (1989)

Implicit in standard macroeconomics of adjustment is the assumption of well-integrated labor markets that are responsive to relative prices. But segmentation of the labor market is usually said to be an important source of labor market rigidities. In particular, if segmentation involves different degrees of real wage rigidity among different groups in the labor force, nominal devaluation may be ineffective and inequitable in its impact. This paper uses a model of labor market segmentation in which regulations are necessary to distinguish between the formal and informal sectors. Using standard econometric techniques to estimate four simultaneous equations, the authors examine the effect of devaluation on relative wages in four countries. They found that formal wages are more responsive than informal wages to inflation and that devaluation of the exchange rate, by increasing the wage gap, is a source of sluggish labor mobility. In addition, they found that expanding wage differentials during adjustment imposes a greater burden on the poorest workers, making adjustment policies less politically sustainable. Finally, they found evidence to support the hypothesis that nominal devaluation would probably be ineffective with a segmented labor market.
<title>Feasibility of simultaneous correction of ametropia by varying gel refractive index with phaco-ersatz</title> (2001)

Recent developments in surgical procedures for restoring accommodation saw the availability of Phaco-ersatz as a feasible procedure returning near vision to the presbyopies. In Phaco-ersatz, the presbyopic crystalline lens is extracted and replaced by a flexible polymer gel in the intact lens capsule. The ability to simultaneously correct ametropia while restoring accommodation with this procedure is seen to be extremely attractive. One strategy by which this may be achieved within the Phaco-ersatz procedure is by making use of polymer gel of different refractive indices. We assessed the feasibility of simultaneously correcting ametropia while restoring accommodation using phaco-ersatz using this approach. Two model eyes (Gullstrand and Navarro) were used to evaluate this approach. Computation results using paraxial equations and ray tracing indicated that while this approach might be feasible for the hypermetrope, its usefulness for correcting myopia is limited due to significant reductions in the resultant amplitude of accommodation. A number of practical considerations may also influence the applicability of this approach.
Nucleotide sequence of the gene coding for human factor VII, a vitamin K-dependent protein participating in blood coagulation. (1987)

Activated factor VII (factor VIIa) is a vitamin K-dependent plasma serine protease that participates in a cascade of reactions leading to the coagulation of blood. Two overlapping genomic clones containing sequences encoding human factor VII were isolated and characterized. The complete sequence of the gene was determined and found to span about 12.8 kilobases. The mRNA for factor VII as demonstrated by cDNA cloning is polyadenylylated at multiple sites but contains only one AAUAAA poly(A) signal sequence. The mRNA can undergo alternative splicing, forming one transcript containing eight segments as exons and another with an additional exon that encodes a larger prepro leader sequence. The latter transcript has no known counterpart in the other vitamin K-dependent proteins. The positions of the introns with respect to the amino acid sequence encoded by the eight essential exons of factor VII are the same as those present in factor IX, factor X, protein C, and the first three exons of prothrombin. These exons code for domains generally conserved among members of this gene family. The comparable introns in these genes, however, are dissimilar with respect to size and sequence, with the exception of intron C in factor VII and protein C. The gene for factor VII also contains five regions made up of tandem repeats of oligonucleotide monomer elements. More than a quarter of the intron sequences and more than a third of the 3' untranslated portion of the mRNA transcript consist of these minisatellite tandem repeats.
Immunohistochemical staining of human alpha-defensin-1 (HNP-1), in the submandibular glands of patients with oral carcinomas. (2000)

The purpose of this study was the immunohistochemical localization and distribution of HNP-1 in the submandibular glands of patients with oral carcinomas. Tissue sections were embedded in paraffin, and HNP-1 was immunostained by the streptavidin-biotin coupled peroxidase method. Striated duct cells in the submandibular glands were stained with anti-defensin antibody. Neutrophils and capillary intimal cells were also stained. Defensins (HNPs) are peptides that occur in neutrophils and protect against bacteria and tumor cells. Human alpha-defensin-1 (HNP-1) is such a peptide, possessing both antimicrobial and cytotoxic activities. The presence of HNP-1 in striated duct cells in the submandibular glands of oral cancer patients, suggests a likely role in tumor immunity, for this peptide.
Algorithmics and applications of tree and graph searching (2002)

Modern search engines answer keyword-based queries extremely efficiently. The impressive speed is due to clever inverted index structures, caching, a domain-independent knowledge of strings, and thousands of machines. Several research efforts have attempted to generalize keyword search to keytree and keygraph searching, because trees and graphs have many applications in next-generation database systems. This paper surveys both algorithms and applications, giving some emphasis to our own work.
Suppression of 3-hydroxy-3-methylglutaryl-CoA reductase by low density lipoproteins produced in vitro by lipoprotein lipase action on nonsuppressive very low density lipoproteins. (1979)

Very low density lipoproteins (VLDL), Sf60 to 400, from normolipemic individuals do not suppress 3-hydroxy-3-methylglutaryl-CoA reductase activity in cultured normal human fibroblasts at concentrations 20-fold higher than those of low density lipoproteins (LDL) that give total suppression. To determine if these VLDL contain all of the structural elements necessary for receptor-mediated suppression, they were converted in vitro with bovine milk lipoprotein lipase to low density lipoproteins. These LDL-like lipoproteins were as effective in suppression as LDL isolated directly from plasma, with half-maximal and complete suppression at 1 and 4 microgram of cholesterol ml-1. Neither native LDL nor LDL produced in vitro suppressed receptor-negative fibroblasts. We conclude that action of lipoprotein lipase on VLDL leads to a rearrangement of lipoprotein components that permits interaction of LDL produced in vitro with the LDL-specific cell surface receptor of fibroblasts and subsequent suppression of 3-hydroxy-3-methylglutaryl-CoA reductase.
Hydrophobic analogues of the winter flounder ‘antifreeze’ protein (2001)

The synthesis, solution conformation and ice-growth inhibition properties of four new analogues of the type I 37-residue winter flounder 'antifreeze' protein are reported. All four analogues contain two extra salt bridges to facilitate comparison of results with previously published data. In two analogues, all four threonine residues in the native polypeptide were mutated to 2-amino butyric acid (an unnatural amino acid) and isoleucine, respectively. The butyric acid analogue was approximately 85% helical at 3 degrees C, modified the shape of ice growth, and exhibited reduced hysteresis compared to the native protein (9% at 4 mM). These results show that the gamma-methyl group of threonine, which is present in the sidechain of 2-amino butyric acid, is not sufficient for activity. The isoleucine analogue, in which the threonine hydroxyl group is replaced by an ethyl group, was 100% helical at 3 degrees C, showed no hysteresis but was able to modify the shape of ice crystal growth. In the third and fourth analogues, mutations of the aspartic acids 1 and 5 to alanine, and asparagines 16 and 27 to leucine in the threonine- and valine-substituted analogues did not affect the helicity of the polypeptides, but removed the ability to inhibit ice growth.
Lymphocytes generated by in vivo priming and in vitro sensitization demonstrate therapeutic efficacy against a murine tumor that lacks apparent immunogenicity. (1989)

The adoptive transfer of sensitized lymphocytes is an effective means to mediate the regression of established tumors. However, successful therapy can only be demonstrated in animal models where tumors are intrinsically immunogenic, capable of eliciting systemic immunity. To explore the potential of this therapeutic approach to tumors of less immunogenicity, we have selected and used a murine tumor, MCA 102, for the current study because all attempts to immunize syngeneic mice failed. We report here that inoculation of mice with a mixture of tumor cells and a bacterial adjuvant, Corynebacterium parvum led to the production of sensitized, but not fully functional, lymphocytes in the draining lymph nodes (LN). These cells, termed pre-effector cells, could nevertheless further differentiate to acquire full immunologic function by an established in vitro sensitization culture method. In adoptive immunotherapy experiments, transfer of as few as 1.5 X 10(7) in vitro sensitized cells not only reduced established pulmonary MCA 102 metastases but also prolonged survival and cured tumors in a majority of the treated animals. In order to elicit pre-effector cells in vivo, inoculation with both tumor cells and C. parvum was essential. Although a broad range of numbers of MCA 102 tumor cells appeared to be effective, generation of pre-effector cells was dependent on the dose of C. parvum. We have found that a C. parvum dose of 25 micrograms was optimal, whereas higher doses of the adjuvant had suppressive effects. Analysis of the kinetics of their appearance revealed that the generation of pre-effector cells was transient. They were detectable 7 days after in vivo priming followed by a rapid decline. Furthermore, pre-effector cells were detected only in the regional draining LN. No reactivity was demonstrable in the spleen, mesenteric LN, PBL, or bone marrow. Taken together, these results expand the scope of immunotherapy by demonstrating the feasibility of manipulating a limited and obscure immune response to the MCA 102 tumor for therapeutic efficacy.
Vaccine Design for CD8 T Lymphocyte Responses (2011)

Vaccines are arguably the most powerful medical intervention in the fight against infectious diseases. The enormity of the global human immunodeficiency virus type 1 (HIV)/acquired immunodeficiency syndrome (AIDS) pandemic makes the development of an AIDS vaccine a scientific and humanitarian priority. Research on vaccines that induce T-cell immunity has dominated much of the recent development effort, mostly because of disappointing efforts to induce neutralizing antibodies through vaccination. Whereas T cells are known to limit HIV and other virus infections after infection, their role in protection against initial infection is much less clear. In this article, we will review the rationale behind a T-cell-based vaccine approach, provide an overview of the methods and platforms that are being applied, and discuss the impact of recent vaccine trial results on the future direction of T-cell vaccine research.
Electrocutaneous Nerve Stimulation-I: Model and Experiment (1978)

The behavior of nerve fibers in the skin during electrocutaneous stimulation has been studied in this investigation for the purpose of understanding the influence of various current pulse parameters. One part of the investigation assessed the amount of stimulus charge, for various pulse parameters, required to depolarize the nodal membrane of myelinated nerve, using the Frankenhaeuser-Huxley model for Xenopus Laevis (toad). The second part of the investigation involved the experimental application of biphasic current pulses via a concentric electrode to the skin of a number of human subjects. The subjects were asked to match the intensity of sensation as stimulus parameters were varied. The experimental results were compared to the predictions of the model by the process of normalization for temperature differences and the loss of electrode current in adjacent passive tissues.
Nanocrystalline Rutile Electron Extraction Layer Enables Low-Temperature Solution Processed Perovskite Photovoltaics with 13.7% Efficiency (2014)

We demonstrate low-temperature (70 °C) solution processing of TiO2/CH3NH3PbI3 based solar cells, resulting in impressive power conversion efficiency (PCE) of 13.7%. Along with the high efficiency, a strikingly high open circuit potential (VOC) of 1110 mV was realized using this low-temperature chemical bath deposition approach. To the best of our knowledge, this is so far the highest VOC value for solution-processed TiO2/CH3NH3PbI3 solar cells. We deposited a nanocrystalline TiO2 (rutile) hole-blocking layer on a fluorine-doped tin oxide (FTO) conducting glass substrate via hydrolysis of TiCl4 at 70 °C, forming the electron selective contact with the photoactive CH3NH3PbI3 film. We find that the nanocrystalline rutile TiO2 achieves a much better performance than a planar TiO2 (anatase) film prepared by high-temperature spin coating of TiCl4, which produces a much lower PCE of 3.7%. We attribute this to the formation of an intimate junction of large interfacial area between the nanocrystalline rutile TiO2 and the CH3NH3PbI3 layer, which is much more effective in extracting photogenerated electrons than the planar anatase film. Since the complete fabrication of the solar cell is carried out below 100 °C, this method can be easily extended to plastic substrates.
Telomerase Activity in Thyroid Malignancy (1999)

Telomerase activity seems to play a role in the development and pathogenesis of thyroid carcinoma. Its incidence of expression and its application as a tumor marker remain to be elucidated. Thyroid tissues obtained during thyroidectomy from 1996-1998 were rapidly frozen and stored at -80 degrees C until processed. Telomerase activity was determined using telomeric repeat amplification protocol (TRAP). Histology of the tissue examined (67 benign and 59 malignant) was reviewed. Telomerase activity was detected in 15 of 52 papillary carcinomas (29%); 1 of 1 thyroid lymphoma (100%); 1 of 2 anaplastic carcinomas (50%); and 2 of 16 lymphocytic thyroiditis specimens (13%). Telomerase activity was not detectable in 35 normal thyroid, 9 follicular adenoma, 7 nodular hyperplasia, 2 follicular carcinoma, and 2 medullary carcinoma. Lymphocytic thyroiditis was detected in 8 of 37 (22%) apparently normal thyroid tissues adjacent to papillary thyroid carcinoma and telomerase activity was present in 2 of these 8 specimens (25%). In conclusion, telomerase does not appear to be frequently activated in papillary thyroid carcinoma. The association of lymphocytic thyroiditis with papillary thyroid carcinoma may limit its clinical usefulness as a tumor marker.