gebhart/patrepeval huggingface dataset:
Active β-Catenin Signaling Is an Inhibitory Pathway for Human Immunodeficiency Virus Replication in Peripheral Blood Mononuclear Cells (2008)

The Wnt/beta-catenin pathway is involved in cell functions governing development and disease. In modeling postentry restriction of human immunodeficiency virus (HIV) replication in astrocytes, we reported that part of this natural resistance to productive replication of HIV in astrocytes involved expression of proteins of the Wnt/beta-catenin signaling pathway. We determined here whether induction of beta-catenin signaling in peripheral blood mononuclear cells (PBMCs) can modulate HIV replication. Given that lithium is an inducer of beta-catenin signaling, we used it as a tool to determine the impact of beta-catenin signaling on HIV replication in PBMCs. We demonstrated that lithium inhibited the replication of T-tropic and primary isolates of HIV by >90% and did so in noncytotoxic/noncytostatic concentrations and in a beta-catenin-dependent manner. Specifically, inhibiting beta-catenin signaling by transfection of dominant-negative mutant constructs to either T-cell factor 4, the downstream effector of Wnt signaling, or beta-catenin, the central mediator of this pathway, abrogated the ability of lithium to inhibit HIV replication. Moreover, when Wnt/beta-catenin signaling was inhibited, the level of HIV replication was enhanced by fourfold. To confirm the in vivo relevance of the beta-catenin pathway in repressing HIV replication, we evaluated HIV-positive antiretroviral therapy-naive patients who were on lithium therapy. These patients demonstrated a reduction in viral load, which increased as the dose of lithium was reduced. Collectively, these data indicate that beta-catenin signaling is an intrinsic molecular pathway restricting HIV replication in PBMCs.
Everolimus Plus Exemestane in Postmenopausal Patients with HR+ Breast Cancer: BOLERO-2 Final Progression-Free Survival Analysis (2013)

The addition of everolimus to exemestane markedly prolonged PFS in patients with HR(+) advanced BC with disease recurrence/progression following prior NSAIs. These results further support the use of everolimus plus exemestane in this patient population. ClinicalTrials.gov #NCT00863655.
CD81 and Claudin 1 Coreceptor Association: Role in Hepatitis C Virus Entry (2008)

Hepatitis C virus (HCV) is an enveloped positive-stranded RNA hepatotropic virus. HCV pseudoparticles infect liver-derived cells, supporting a model in which liver-specific molecules define HCV internalization. Three host cell molecules have been reported to be important entry factors or receptors for HCV internalization: scavenger receptor BI, the tetraspanin CD81, and the tight junction protein claudin-1 (CLDN1). None of the receptors are uniquely expressed within the liver, leading us to hypothesize that their organization within hepatocytes may explain receptor activity. Since CD81 and CLDN1 act as coreceptors during late stages in the entry process, we investigated their association in a variety of cell lines and human liver tissue. Imaging techniques that take advantage of fluorescence resonance energy transfer (FRET) to study protein-protein interactions have been developed. Aequorea coerulescens green fluorescent protein- and Discosoma sp. red-monomer fluorescent protein-tagged forms of CD81 and CLDN1 colocalized, and FRET occurred between the tagged coreceptors at comparable frequencies in permissive and nonpermissive cells, consistent with the formation of coreceptor complexes. FRET occurred between antibodies specific for CD81 and CLDN1 bound to human liver tissue, suggesting the presence of coreceptor complexes in liver tissue. HCV infection and treatment of Huh-7.5 cells with recombinant HCV E1-E2 glycoproteins and anti-CD81 monoclonal antibody modulated homotypic (CD81-CD81) and heterotypic (CD81-CLDN1) coreceptor protein association(s) at specific cellular locations, suggesting distinct roles in the viral entry process.
Peroxide plasma level in patients with coronary heart disease as a possible indicator of ischemia during exercise test (1993)

The rise in plasma H2O2 level during myocardial ischemia indicates that intensification of oxygen free radical production occurs. This may be the result of hypoxanthine conversion by xanthine oxidase, catecholamine auto-oxidation, polymorphonuclear neutrophil activation, and/or derangement within mitochondrial electron transfer. The noticed difference between patients with a positive exercise test and those diagnosed as without ischemia may be of clinical relevance.
Genetic Deficiency of Complement Component 3 does not Alter Disease Progression in a Mouse Model of Huntington's Disease (2012)

Several genes and proteins of the complement cascade are present at elevated levels in brains of patients with Huntington's disease (HD). The complement cascade is well characterized as an effector arm of the immune system, and in the brain it is important for developmental synapse elimination. We hypothesized that increased levels of complement in HD brains contributes to disease progression, perhaps by contributing to synapse elimination or inflammatory signaling. We tested this hypothesis in the R6/2 mouse model of HD by crossing mice deficient in complement component 3 (C3), a crucial complement protein found at increased levels in HD brains, to R6/2 mice and monitoring behavioral and neuropathological disease progression. We found no alterations in multiple behavioral assays, weight or survival in R6/2 mice lacking C3. We also quantified the expression of several complement cascade genes in R6/2 brains and found that the large scale upregulation of complement genes observed in HD brains is not mirrored in R6/2 brains. These data show that C3 deficiency does not alter disease progression in the R6/2 mouse model of HD.
Visual Similarity Based 3D Shape Retrieval Using Bag-of-Features (2010)

This paper presents a novel 3D shape retrieval method, which uses Bag-of-Features and an efficient multi-view shape matching scheme. In our approach, a properly normalized object is first described by a set of depth-buffer views captured on the surrounding vertices of a given unit geodesic sphere. We then represent each view as a word histogram generated by the vector quantization of the view's salient local features. The dissimilarity between two 3D models is measured by the minimum distance of their all (24) possible matching pairs. This paper also investigates several critical issues including the influence of the number of views, codebook, training data, and distance function. Experiments on four commonly-used benchmarks demonstrate that: 1) Our approach obtains superior performance in searching for rigid models. 2) The local feature and global feature based methods are somehow complementary. Moreover, a linear combination of them significantly outperforms the state-of-the-art in terms of retrieval accuracy.
Dominant mutations in a gene encoding a putative protein kinase (BCK1) bypass the requirement for a Saccharomyces cerevisiae protein kinase C homolog. (1992)

The PKC1 gene of Saccharomyces cerevisiae encodes a homolog of mammalian protein kinase C that is required for yeast cell growth and division. To identify additional components of the pathway in which PKC1 functions, we isolated extragenic suppressors of a pkc1 deletion mutant. All of the suppressor mutations were dominant for suppressor function and defined a single locus, which was designated BCK1 (for bypass of C kinase). A molecular clone of one suppressor allele, BCK1-20, was isolated on a centromere-containing plasmid through its ability to rescue a conditional pkc1 mutant. The BCK1 gene possesses a 4.4-kb uninterrupted open reading frame predicted to encode a 163-kDa protein kinase. The BCK1 gene product is not closely related to any known protein kinase, sharing only 45% amino acid identity with its closest known relative (the STE11-encoded protein kinase) through a region restricted to its putative C-terminal catalytic domain. Deletion of BCK1 resulted in a temperature-sensitive cell lysis defect, which was suppressed by osmotic stabilizing agents. Because pkc1 mutants also display a cell lysis defect, we suggest that PKC1 and BCK1 may normally function within the same pathway. Suppressor alleles of BCK1 differed from the wild-type gene in a region surrounding a potential PKC phosphorylation site immediately upstream of the predicted catalytic domain. This region may serve as a hinge between domains whose interaction is regulated by PKC1.
Sulfur-Deactivated Steam Reforming of Gasified Biomass (1998)

The effect of hydrogen sulfide on the steam reforming of methane has been studied. Methane is the most difficult component to convert by steam reforming in the mixture of hydrocarbons, which is produced in biomass gasification. Two catalysts were subjected to hydrogen sulfide levels up to 300 ppm so as to study the effect of sulfur on their deactivation. These catalysts were the C11-9-061, from United Catalyst Inc., and the HTSR1, from Haldor Topsøe. The activation energy of the sulfur-deactivated steam-reforming reaction was calculated to be 280 and 260 kJ/mol, for each catalyst, respectively. The high values most probably originate from the fact that the degree of sulfur coverage of the nickel surface is close to 1 for these experiments. Even under these severe conditions, steam reforming of methane is possible without any carbon formation. The HTSR1 catalyst exhibits a very high sulfur-free activity, resulting in a performance in the presence of hydrogen sulfide higher than that for the C11-9-061 catalyst. By using the HTSR1 catalyst, the reactor temperature can be lowered by 60 °C in order to reach comparable levels of conversion.
Expression and amplification of engineered mouse dihydrofolate reductase minigenes. (1983)

We constructed mouse dihydrofolate reductase (DHFR) minigenes (dhfr) that had 1.5 kilobases of 5' flanking sequences and contained either none or only one of the intervening sequences that are normally present in the coding region. They were greater than or equal to 3.2 kilobase long, about one-tenth the size of the corresponding chromosomal gene. Both of these minigenes complemented the DHFR deficiency in Chinese hamster ovary dhfr-1-cells at a high frequency after DNA-mediated gene transfer. The level of DHFR enzyme in various transfected clones varied over a 10-fold range but never was as high as in wild-type Chinese hamster ovary cells. In addition, the level of DHFR in primary transfectants did not vary directly with the copy number of the minigene, which ranged from fewer than five to several hundred per genome. The minigenes could be amplified to a level of over 2,000 copies per genome upon selection in methotrexate, a specific inhibitor of DHFR. In one case, the amplified minigenes were present in a tandem array; in two other cases, a rearranged minigene plasmid and its flanking chromosomal DNA sequence were amplified. Thus, the mouse dhfr minigenes could be transcribed, expressed, and amplified in Chinese hamster ovary cells, although the efficiency of expression was generally low. The key step in the construction of these minigenes was the generation in vivo of lambda phage recombinants by overlapping regions of homology between genomic and cDNA clones. The techniques used here for dhfr should be generally applicable to any gene, however large, and could be used to generate novel genes from members of multigene families.
Description of a prototype emission-transmission computed tomography imaging system. (1992)

We have developed a prototype imaging system that can perform simultaneous x-ray transmission CT and SPECT phantom studies. This system employs a 23-element high-purity-germanium detector array. The detector array is coupled to a collimator with septa angled toward the focal spot of an x-ray tube. During image acquisition, the x-ray fan beam and the detector array move synchronously along an arc pivoted at the x-ray source. Multiple projections are obtained by rotating the object, which is mounted at the center of rotation of the system. The detector array and electronics can count up to 10(6) cps/element with sufficient energy-resolution to discriminate between x-rays at 100-120 kVp and gamma rays from 99mTc. We have used this device to acquire x-ray CT and SPECT images of a three-dimensional Hoffman brain phantom. The emission and transmission images may be superimposed in order to localize the emission image on the transmission map.
Macromolecular Structure and Self‐Assembly (2007)

The output from the molecular biology revolution has grown steadily and logarithmically from the first protein sequence, insulin (Ryle AP et al 1955 Biochem J 60:541-556), the first three-dimensional atomic structure of a macromolecule, myoglobin (Kendrew JC et al 1960 Nature 185:422-427), the first DNA gene sequence, phi X174 gene J (Sanger F et al 1977 Nature 265:687-695) and the first genome sequence for a free-living organism, Haemophilus influenzae (Fleischmann RD et al 1995 Science 269:496-512) to the current situation where the output rate is close to one new gene sequence every few minutes, several new three-dimensional structures a day and a new (bacterial) genome completed every few months. Those working in this field must readjust their horizons to this changing situation every year or two. In the area of three-dimensional structure of macromolecules and macromolecular assemblies, the methods of X-ray crystallography, nuclear magnetic resonance and electron microscopy have combined to produce powerful insights into how these molecular machines work. In this paper, I present three examples of molecular machines whose structure tells us a lot about how they work. These are the light-driven proton pump bacteriorhodopsin, the ATP synthetase molecule which contains a tiny motor and generator, and the flagellar rotary motor which provides the thrust to power physical movement of the bacterial cell. The structure itself in three-dimensional detail is thus often seen to provide the most important single insight into how things work, reducing biology to chemistry and physics. The reductionist approach in this field seems to be limited only by the accuracy by which it is possible to describe inter- and intra-molecular interactions in terms of hydrogen bonds, van der Waals interactions and electrostatic forces. At present, there is no fundamental limit in sight.
Bioprospecting in high temperature environments; application of thermostable protein cages (2007)

The first researchers to discover life in high temperature environments could not have anticipated the impact of their findings on the biotechnology industry. Today biotech companies benefit from multimillion dollar sales of enzymes originating from microorganisms that thrive in diverse high temperature environments. In this review we highlight significant advances made towards the development of self-assembling oligomeric protein cages from hyperthermophilic organisms as amenable platforms for diverse applications in biotechnology, electronics and medicine.
Electronic and digital signatures: in search of a standard (2000)

Electronic commerce has changed the way we buy books, sell Pez dispensers, and pay bills. Now, with the advent of electronic and digital signatures, e-commerce is changing the way we sign and store documents. Eventually, any business that wants to succeed in e-commerce must deal with electronic signatures. As an IT professional, you need to understand: what a signature is, legally, and when you need one; the various electronic signature standards; current federal and state electronic signature legislation; and some basics about electronic signature technology.
A global appraisal of immunodominant CD8 T cell responses to Epstein-Barr virus and cytomegalovirus by bulk screening (2000)

Knowledge of the immunodominant responses to Epstein-Barr Virus (EBV) and human cytomegalovirus (HCMV) should help to generate cytotoxic T cell lines to these herpesviruses. Here we report on the analysis of CD8 T cell responses to EBV and HCMV in the blood of kidney transplant recipients undergoing viral reactivation (n = 16) and in healthy virus carriers (n = 10). We used a transient COS transfection assay that permits semi-quantitative estimation of CD8+ T cell responses against a larger number of HLA/viral protein combinations within polyclonal T cell lines and thus allows a rapid identification of major epitopes. From the comparison of these responses to those that we previously described in the synovial fluid of patients suffering from various forms of chronic arthritis (n = 32), it appears that EBV-specific T cells are mainly directed against a restricted set of immunodominant epitopes, primarily generated during the early lytic cycle and that both IE1 and pp65 are targets of the anti-HCMV response. We suggest that this method could be generally applied to the rapid identification of immunodominant T cell epitopes in viral and tumor immunity, and could help selecting HLA-peptide complexes that could be used to detect and sort specific T cell populations.
Understanding the Role of Different Conductive Polymers in Improving the Nanostructured Sulfur Cathode Performance (2013)

Lithium sulfur batteries have brought significant advancement to the current state-of-art battery technologies because of their high theoretical specific energy, but their wide-scale implementation has been impeded by a series of challenges, especially the dissolution of intermediate polysulfides species into the electrolyte. Conductive polymers in combination with nanostructured sulfur have attracted great interest as promising matrices for the confinement of lithium polysulfides. However, the roles of different conductive polymers on the electrochemical performances of sulfur electrode remain elusive and poorly understood due to the vastly different structural configurations of conductive polymer–sulfur composites employed in previous studies. In this work, we systematically investigate the influence of different conductive polymers on the sulfur cathode based on conductive polymer-coated hollow sulfur nanospheres with high uniformity. Three of the most well-known conductive polymers, polyaniline (PANI), polypyrrole (PPY), and poly(3,4-ethylenedioxythiophene) (PEDOT), were coated, respectively, onto monodisperse hollow sulfur nanopsheres through a facile, versatile, and scalable polymerization process. The sulfur cathodes made from these well-defined sulfur nanoparticles act as ideal platforms to study and compare how coating thickness, chemical bonding, and the conductivity of the polymers affected the sulfur cathode performances from both experimental observations and theoretical simulations. We found that the capability of these three polymers in improving long-term cycling stability and high-rate performance of the sulfur cathode decreased in the order of PEDOT > PPY > PANI. High specific capacities and excellent cycle life were demonstrated for sulfur cathodes made from these conductive polymer-coated hollow sulfur nanospheres.
Purification, molecular cloning, and expression of the mammalian sigma1-binding site. (1996)

Sigma-ligands comprise several chemically unrelated drugs such as haloperidol, pentazocine, and ditolylguanidine, which bind to a family of low molecular mass proteins in the endoplasmic reticulum. These so-called sigma-receptors are believed to mediate various pharmacological effects of sigma-ligands by as yet unknown mechanisms. Based on their opposite enantioselectivity for benzomorphans and different molecular masses, two subtypes are differentiated. We purified the sigma1-binding site as a single 30-kDa protein from guinea pig liver employing the benzomorphan(+)[3H]pentazocine and the arylazide (-)[3H]azidopamil as specific probes. The purified (+)[3H]pentazocine-binding protein retained its high affinity for haloperidol, pentazocine, and ditolylguanidine. Partial amino acid sequence obtained after trypsinolysis revealed no homology to known proteins. Radiation inactivation of the pentazocine-labeled sigma1-binding site yielded a molecular mass of 24 +/- 2 kDa. The corresponding cDNA was cloned using degenerate oligonucleotides and cDNA library screening. Its open reading frame encoded a 25.3-kDa protein with at least one putative transmembrane segment. The protein expressed in yeast cells transformed with the cDNA showed the pharmacological characteristics of the brain and liver sigma1-binding site. The deduced amino acid sequence was structurally unrelated to known mammalian proteins but it shared homology with fungal proteins involved in sterol synthesis. Northern blots showed high densities of the sigma1-binding site mRNA in sterol-producing tissues. This is also in agreement with the known ability of sigma1-binding sites to interact with steroids, such as progesterone.
Joint Discriminative Language Modeling and Utterance Classification (2006)

This paper investigates discriminative language modeling in a scenario with two kinds of observed errors: errors in ASR transcription and errors in utterance classification. Using the perceptron algorithm, we train joint language and class models either independently or simultaneously, under various parameter update conditions. On a large vocabulary customer service call-classification application, we show that simultaneous optimization of class, n-gram, and class/n-gram feature weights results in a significant WER reduction over a model using just n-gram features, while additionally significantly outperforming a deployed baseline in classification error rate. A range of parameter update approaches for the various feature sets are presented and evaluated. The resulting models are encoded as weighted finite-state automata, and are used by intersecting the model with word lattices.
Induction of a novel morphological response in Chinese hamster ovary cells by pertussis toxin (1983)

Exposing Chinese hamster ovary cells in culture to pertussis toxin resulted in a novel clustered growth pattern. The specificity of the response for pertussis toxin was shown by neutralization of the activity with specific anti-toxin antibody, heat lability (80 degrees C for 15 min), and absence of such activity by culture media from nontoxigenic Bordetella species. Although a lag of at least 16 h was required before clustered growth was seen, exposure to the toxin for as little as 10 min resulted in a full response 24 h later. The morphological effect appeared to be independent of the cyclic AMP-mediated cell elongation elicited by the heat-labile enterotoxin from Vibrio cholerae in that the pertussis toxin effect was seen in both the presence and absence of elongation. Although the mechanism by which this effect is mediated remains to be determined, it is already providing a useful in vitro assay for pertussis toxin.
Television home server for integrated services-toward the realization of ISDB "anytime" services (1998)

In the age of digital multimedia, demand is bound to rise for a television home server for integrated services which automatically records favorite programs so that users can watch them at any time. We have developed a hierarchical storage management system (HSMS) as the architecture for developing a high-speed home server with very large capacity. This paper first describes the required specifications and memory construction of the home server and then proposes a model of the new HSMS. Also described are its element technologies and an experimental home server system, and the results of experiments conducted to test its performance.