gebhart/patrepeval huggingface dataset:
Inhibition of HIV-1 reverse transcriptase by pyridinone derivatives. Potency, binding characteristics, and effect of template sequence. (1993)

The inhibition of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase by pyridinone compounds has been investigated using as templates synthetic RNA with sequences based on the HIV-1 genome sequence. In reactions catalyzed by the enzyme that incorporated more than one nucleotide per primer, inhibition by a representative pyridinone inhibitor, 3-[2-(1,3-benzoxazol-2-yl)ethyl]-5-ethyl-6-methyl-pyridin-2(1H)one (L-696,229), was noncompetitive against deoxynucleotide triphosphate. For reactions that incorporated one deoxynucleotide per primer, IC50 values ranged from 20 to 200 nM, depending on the position of incorporation of the incoming deoxynucleotide base on the template. Inhibition of synthesis on a set of four templates differing only at the template base complementary to the incoming nucleotide had similar IC50 values. These results demonstrate that inhibitory potency is dependent on the primary structure of the template and that inhibitory potency is largely independent of the identity of the incoming nucleotide base. The inhibition of HIV-1 reverse transcription by L-696,229 also displayed slow-binding characteristics. The slow-binding aspect was exploited to gauge the interaction between inhibitor and enzyme. By titrating the reduction in the extent of the burst of synthesis observed in a reaction incorporating dideoxythymidine monophosphate into poly(rA)-oligo(dT)18, the apparent equilibrium constant for dissociation of the reverse transcriptase-L-696,229 complex was estimated to be 400 nM.
Paralimbic hypoperfusion in unipolar depression. (1994)

These findings implicate selective dysfunction of paralimbic brain regions in clinically depressed patients, independent of their medication use, and support the concept of specific neural systems that regulate mood. Recognition of these regional abnormalities may have clinical utility in both the diagnosis and treatment of depression.
Innovative verification strategy reduces design cycle time for high-end SPARC processor (1996)

Article Innovative verification strategy reduces design cycle time for high-end SPARC processor Share on Authors: Val Popescu Metaflow Technologies, Inc., La Jolia, CA Metaflow Technologies, Inc., La Jolia, CAView Profile , Bill McNamara Zycad Corporation Irvine, CA Zycad Corporation Irvine, CAView Profile Authors Info & Claims DAC '96: Proceedings of the 33rd annual Design Automation ConferenceJune 1996 Pages 311–314https://doi.org/10.1145/240518.240577Online:01 June 1996Publication History 10citation316DownloadsMetricsTotal Citations10Total Downloads316Last 12 Months2Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Models of Luteinization1 (2000)

Luteinization is essential to the success of early gestation. It is the process by which elements of the ovarian follicle, usually including both theca interna and granulosa cells, are provoked by the ovulatory stimulus to develop into the corpus luteum. Although there are significant species differences in luteinization, some elements pervade, including the morphological and functional differentiation to produce and secrete progesterone. There is evidence that luteinization results in granulosa cell exit from the cell cycle. The mechanisms that appear to control luteinization include intracellular signalling pathways, cell adhesion factors, intracellular cholesterol and oxysterols, and perhaps progesterone itself as a paracrine or intracrine regulator. Cell models of luteinization, along with some of the conflicting observations on the luteinization process, are discussed in this review.
Iso-splatting: a point-based alternative to isosurface visualization (2004)

We present a new approach to isosurface visualization that we call "iso-splatting." We use point primitives for representing and rendering isosurfaces. The method consists of two steps. In the first step, point samples are generated throughout the volumetric domain of a scalar function. In the second step, these points are projected onto the isosurface of interest. We render the resulting point set using a surface splatting algorithm. The method can be extended to out-of-core or parallel environments. Our results show that this method can offer much greater time and space efficiency when compared with standard triangle-based methods, thereby supporting higher levels of interactivity. Parts of the algorithm can be accelerated using graphics hardware. One key advantage of this approach is that, since extraction computations are divided into two smaller phases, work can be distributed to exploit all available resources.
Techniques for perfusion and storage of heterotopic heart transplants in mice (1985)

Organ pretreatment prior to transplantation has assumed increasing importance. We studied the ability to preserve and perfuse hearts in well-defined genetic mouse models, prior to heterotopic engraftment. Hearts were manually perfused through the aortic root and stored in a variety of cold solutions or were perfused using a continuous perfusion pump. Different electrolyte solutions, mouse strains, perfusion, and storage times as well as perfusion volumes were studied. Treated hearts were than transplanted heterotopically and short- and long-term function assessed. Hearts stored for more than 1 hour in cold solutions (saline 0.9%, or lactated Ringer's) failed to function. Hearts perfused with 0.25-0.4 ml of cold solution for a maximum of 30 minutes functioned well after transplantation. C3H (H-2k) mice provided the most resilient hearts. We conclude that short-term perfusion or storage of mouse hearts is feasible and should provide an excellent model for the study of organ pretreatment with monoclonal antibodies or other agents prior to transplantation.
The high affinity Na+/glucose cotransporter. Re-evaluation of function and distribution of expression. (1994)

We report the primary structure, functional characterization, and tissue distribution of the high affinity Na+/glucose cotransporter SGLT1 from rat kidney. Rat SGLT1 (665 amino acid residues) is 86-87% identical to SGLT1 from rabbit, pig, and human. High stringency Northern analysis demonstrated that SGLT1 is strongly expressed in small intestine and at lower levels in kidney, liver, and lung. In situ hybridization performed on kidney sections revealed that SGLT1 is predominantly present in S3 segments of the proximal tubule. In small intestine, SGLT1 message was located in cells of the lower two-thirds of intestinal villi. Expression of rat SGLT1 in Xenopus oocytes resulted in a large Na(+)-dependent uptake of [14C]-alpha-methyl-D-glucopyranoside (alpha MeGlc). Overall, the transport characteristics were similar to those of rabbit SGLT1. High affinity Na+/glucose cotransport in membrane vesicles was previously shown to be coupled to the cotransport of two Na+ ions (Turner, R. J., and Moran, A. (1982) J. Membr. Biol. 70, 37-45). Previous kinetic analysis of rat and rabbit SGLT1, however, demonstrated between second and first order dependence of sugar uptake on extracellular Na+ concentration, suggesting the existence of Na(+)-binding sites with different affinities. Here, we directly compared the initial rates of the alpha MeGlc uptake with alpha MeGlc-induced inward currents as an indicator of the Na+ flux. This analysis clearly revealed a Na+ to glucose coupling ratio of 2:1. In summary, our data provide important insights into the function and tissue distribution of the high affinity Na+/glucose cotransporter SGLT1 and clarify its role in the reabsorption mechanism of D-glucose in the kidney.
Mouse trisomy 16 as an animal model of human trisomy 21 (Down syndrome): Production of viable trisomy 16 ↔ diploid mouse chimeras (1984)

We have previously proposed that mice trisomic for chromosome 16 will provide an animal model of human trisomy 21 (Down syndrome). However, the value of this model is limited to some extent because trisomy 16 mouse fetuses do not survive as live-born animals. Therefore, in an effort to produce viable mice with cells trisomic for chromosome 16, we have used an aggregation technique to generate trisomy 16 diploid (Ts 16 2n) chimeras. A total of 79 chimeric mice were produced, 11 of which were Ts 16 2n chimeras. Seven of these Ts 16 2n mice were analyzed as fetuses, just prior to birth, and 4 were analyzed as live-born animals. Unlike nonchimeric Ts 16 mouse fetuses which die shortly before birth with edema, congenital heart disease, and thymic and splenic hypoplasia, all but 1 of the Ts 16 2n animals were viable and phenotypically normal. The oldest of the live-born Ts 16 2n chimeras was 12 months old at the time of necropsy. Ts 16 cells, identified by coat color, enzyme marker, and/or karyotype analyses, comprised 50-60% of the brain, heart, lung, liver, and kidney in the 7 Ts 16 2n chimeric fetuses and 30-40% of these organs in the 4 live-born Ts 16 2n animals. Ts 16 cells comprised an average of 40% of the thymus and 80% of the spleen in the Ts 16 2n chimeras analyzed as fetuses, with no evidence of thymic or splenic hypoplasia. However, we observed a marked deficiency to Ts 16 cells in the blood, spleen, thymus, and bone marrow of live-born Ts 16 2n chimeras as compared to 2n 2n controls. These results demonstrate that although the Ts 16 2n chimeras were, with one exception, viable and phenotypically normal, each animal contained a significant proportion of trisomic cells in a variety of tissues, including the brain. Furthermore, our results suggest that although the abnormal development of Ts 16 thymus and spleen cells observed in Ts 16 fetuses is largely corrected in Ts 16 2n fetuses, Ts 16 erythroid and lymphoid cells have a severe proliferative disadvantage as compared to diploid cells in older live-born Ts 16 2n chimeras. Ts 16 2n chimeric mice will provide a valuable tool for studying the functional consequences of aneuploidy and may provide insight into the mechanisms by which trisomy 21 leads to developmental abnormalities in man.
Major and Minor Reactions in Fischer—Tropsch Synthesis on Cobalt Catalysts (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Sequence and analysis of 24 kb on chromosome II of Saccharomyces cerevisiae (1995)

In the course of the European yeast genome sequencing project, we determined 23,920 bp of a continuous chromosome II right arm sequence. Analysis of data revealed 13 open reading frames (ORFs), three of which corresponded to previously identified genes; two tRNA genes and one repetitive element. One ORF showed considerable homology (46%) to a hypothetical chromosome III gene; another, putatively very hydrophobic gene product, was 30% identical to the heat-shock protein HSP30. Two ORFs were homologous to human genes.
Multikey access methods based on superimposed coding techniques (1987)

Both single-level and two-level indexed descriptor schemes for multikey retrieval are presented and compared. The descriptors are formed using superimposed coding techniques and stored using a bit-inversion technique. A fast-batch insertion algorithm for which the cost of forming the bit-inverted file is less than one disk access per record is presented. For large data files, it is shown that the two-level implementation is generally more efficient for queries with a small number of matching records. For queries that specify two or more values, there is a potential problem with the two-level implementation in that costs may accrue when blocks of records match the query but individual records within these blocks do not. One approach to overcoming this problem is to set bits in the descriptors based on pairs of indexed terms. This approach is presented and analyzed.
Nanografting De Novo Proteins onto Gold Surfaces (2005)

The immobilization of novel proteins onto addressable locations on a flat surface has potential applications in a range of biotechnologies. Here we describe the nanopatterning of a de novo protein onto a gold surface. Patterning was achieved using a technique called nanografting, in which the tip of an atomic force microscope is used to disrupt a preexisting monolayer of alkanethiol molecules on a gold surface, thereby facilitating exchange with alternative thiol-linked molecules from the surrounding solution. The protein used for these studies was chosen from a designed combinatorial library of de novo sequences expressed in E. coli and was engineered to have a glycine-glycine-cysteine tag at its C-terminus, thereby enabling attachment to the gold surface through a single cysteine thiol. The average height of the grafted protein patterns was found to be somewhat higher than expected from the known NMR structure of the protein. Compression of the nanografted patches by an external force (below 10 nN) was reversible but showed some hysteresis. Interestingly, both the energy required to deform the immobilized protein patterns and the energy defined by the hysteresis loop were found to be of the same order as the energy required to unfold the monomeric protein in solution. These studies demonstrate the possibility of preparing nanometer scale protein arrays, lowering significantly the volume requirements of the protein samples necessary to fabricate protein-based biosensor arrays and thereby providing a base for increasing their sensitivity.
MK-5108, a Highly Selective Aurora-A Kinase Inhibitor, Shows Antitumor Activity Alone and in Combination with Docetaxel (2010)

Aurora-A kinase is a one of the key regulators during mitosis progression. Aurora-A kinase is a potential target for anticancer therapies because overexpression of Aurora-A, which is frequently observed in some human cancers, results in aberrant mitosis leading to chromosomal instability and possibly tumorigenesis. MK-5108 is a novel small molecule with potent inhibitory activity against Aurora-A kinase. Although most of the Aurora-kinase inhibitors target both Aurora-A and Aurora-B, MK-5108 specifically inhibited Aurora-A kinase in a panel of protein kinase assays. Inhibition of Aurora-A by MK-5108 in cultured cells induced cell cycle arrest at the G(2)-M phase in flow cytometry analysis. The effect was confirmed by the accumulation of cells with expression of phosphorylated Histone H3 and inhibition of Aurora-A autophosphorylation by immunostaining assays. MK-5108 also induced phosphorylated Histone H3 in skin and xenograft tumor tissues in a nude rat xenograft model. MK-5108 inhibited growth of human tumor cell lines in culture and in different xenograft models. Furthermore, the combination of MK-5108 and docetaxel showed enhanced antitumor activities compared with control and docetaxel alone-treated animals without exacerbating the adverse effects of docetaxel. MK-5108 is currently tested in clinical trials and offers a new therapeutic approach to combat human cancers as a single agent or in combination with existing taxane therapies.
Fast mode decision and motion estimation for JVT/H.264 (2004)

The JVT/H.264 video coding standard achieves considerably higher coding efficiency than previous standards. Unfortunately this comes at a cost in considerably increased complexity at the encoder mainly due to motion estimation and mode decision. In this paper, we propose a new scheme to jointly optimize motion estimation and mode decision. Simulation results show that we achieve up to 90% complexity reduction while maintaining coding efficiency.
Linkage of Plasma Adiponectin Levels to 3q27 Explained by Association With Variation in the APM1 Gene (2005)

We performed a genome-wide linkage scan of plasma adiponectin levels in 569 nondiabetic participants in the Amish Family Diabetes Study. The highest logarithm of odds (LOD) score (2.13; P = 0.0009) occurred on chromosome 3q27 between markers D3S1602 and D3S1580, which flank APM1/ACDC, the adiponectin gene. The APM1 +2019 A/- insertion/deletion polymorphism in the 3' untranslated region (single nucleotide polymorphism [SNP] +2019; deletion allele frequency 0.30 in Amish) showed strong association with adiponectin levels in a dosage-dependent manner in a direction consistent with that reported in previous studies, with deletion heterozygosity increasing adiponectin levels by 1.3 +/- 0.5 microg/ml and deletion homozygosity increasing levels by 3.0 +/- 0.8 microg/ml (P < 0.0001). Two other SNPs, rs2241766 and rs1501299, showed moderate association. In a subset of 523 subjects genotyped for both SNP +2019 and rs2241766, including the APM1 SNP +2019 genotype as a covariate reduced the linkage signal at 3q27 by 1.26 LOD units (from 2.22 to 0.96) and including both SNPs reduced the signal by 1.51 LOD units (to 0.71). These findings, combined with a two-point LOD score of 2.35 for SNP +2019, provide evidence that variation in APM1 is responsible for linkage of adiponectin levels to 3q27 in the Old Order Amish.
Rearrangement of Influenza Virus Spliced Segments for the Development of Live-Attenuated Vaccines (2016)

Vaccination represents our best therapeutic option against influenza viral infections. However, the efficacy of current influenza vaccines is suboptimal, and novel approaches are necessary for the prevention of disease caused by this important human respiratory pathogen. In this work, we describe a novel approach to generate safer and more efficient live-attenuated influenza virus vaccines (LAIVs) based on recombinant viruses whose genomes encode nonoverlapping and independent M1/M2 (split M segment [Ms]) or both M1/M2 and NS1/NEP (Ms and split NS segment [NSs]) open reading frames. Viruses containing a modified M segment were highly attenuated in mice but were able to confer, upon a single intranasal immunization, complete protection against a lethal homologous challenge with wild-type virus. Notably, the protection efficacy conferred by our viruses with split M segments was better than that conferred by the current temperature-sensitive LAIV. Altogether, these results open a new avenue for the development of safer and more protective LAIVs on the basis of the reorganization of spliced viral RNA segments in the genome.
Mitotic Moonlighting Functions for Membrane Trafficking Proteins (2011)

In recent years, cell biologists have uncovered a number of new functions for proteins that were previously thought to operate solely in membrane trafficking. These alternative roles, termed moonlighting functions, can occur at distinct intracellular sites or at different stages of the cell cycle. Here, I evaluate the evidence for mitotic moonlighting functions of proteins that have membrane trafficking roles during interphase. The aim is to identify key issues facing the field and to outline important questions for future work.
Integrating formal verification methods with a conventional project design flow (1996)

Article Free Access Share on Integrating formal verification methods with a conventional project design flow Author: Ásgeir Th. Eiríksson Silicon Graphics Inc., Mountain View, CA Silicon Graphics Inc., Mountain View, CAView Profile Authors Info & Claims DAC '96: Proceedings of the 33rd annual Design Automation ConferenceJune 1996Pages 666–671https://doi.org/10.1145/240518.240644Published:01 June 1996Publication History 15citation344DownloadsMetricsTotal Citations15Total Downloads344Last 12 Months16Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Improving Sketching by Utilizing Haptic Feedback (2002)

Sketching interfaces for PC's often make use of the mouse. This device, however, is not suitable for the creation of "good" gestures. This paper describes the use of a PHANToM device, a force feedback device, for making sketches on a computer. This device has a pen-like appearance and is therefore natural to use. The paper elaborates on algorithms for the use of the force feedback capabilities of the PHANToM device in a sketch interface. The algorithms for creating and modifying sketches will be discussed, together with the algorithms for feeding force back to the user.
Upregulation of Immunoreactive Angiotensin II Release and Angiotensinogen mRNA Expression by High-Frequency Preganglionic Stimulation at the Canine Cardiac Sympathetic Ganglia (2001)

The possible involvement of the local angiotensin system in ganglionic functions was investigated in the canine cardiac sympathetic ganglia. Positive chronotropic responses to preganglionic stellate stimulation at high frequencies, after intravenous administration of pentolinium plus atropine, were inhibited by the nonpeptide angiotensin AT(1) receptor antagonist forasartan or the angiotensin I-converting enzyme inhibitor captopril, whereas the rate increases elicited by the postganglionic stellate stimulation and norepinephrine given intravenously failed to be inhibited by these antagonists. The levels of endogenous immunoreactive angiotensin II, as determined by radioimmunoassay in the incubation medium of the stellate and inferior cervical ganglia, were increased after the high-frequency preganglionic stimulation of the isolated ganglia. The increment of the peptide was also antagonized by the pretreatment with captopril but not by a chymase inhibitor, chymostatin. The expression of angiotensinogen mRNA was observed in the stellate ganglion, adrenal, liver, and lung but not in the ovary and spleen. The expression of the mRNA in the stellate and inferior cervical ganglia increased after high-frequency preganglionic stimulation of the in vivo dogs for a period of 1 hour. These results indicate that an intrinsic angiotensin I-converting enzyme-dependent angiotensin system exists in the cardiac sympathetic ganglia, which is activated by high-frequency preganglionic stimulation.
Impaired nitric oxide-mediated vasodilation in transgenic sickle mouse (2000)

Transgenic sickle mice expressing human beta(S)- and beta(S-Antilles)-globins show intravascular sickling, red blood cell adhesion, and attenuated arteriolar constriction in response to oxygen. We hypothesize that these abnormalities and the likely endothelial damage, also reported in sickle cell anemia, alter nitric oxide (NO)-mediated microvascular responses and hemodynamics in this mouse model. Transgenic mice showed a lower mean arterial pressure (MAP) compared with control groups (90 +/- 7 vs. 113 +/- 8 mmHg, P < 0.00001), accompanied by increased endothelial nitric oxide synthase (eNOS) expression. N(G)-nitro-L-arginine methyl ester (L-NAME), a nonselective inhibitor of NOS, caused an approximately 30% increase in MAP and approximately 40% decrease in the diameters of cremaster muscle arterioles (branching orders: A2 and A3) in both control and transgenic mice, confirming NOS activity; these changes were reversible after L-arginine administration. Aminoguanidine, an inhibitor of inducible NOS, had no effect. Transgenic mice showed a decreased (P < 0.02-0.01) arteriolar dilation in response to NO-mediated vasodilators, i.e., ACh and sodium nitroprusside (SNP). Indomethacin did not alter the responses to ACh and SNP. Forskolin, a cAMP-activating agent, caused a comparable dilation of A2 and A3 vessels ( approximately 44 and 70%) in both groups of mice. Thus in transgenic mice, an increased eNOS/NO activity results in lower blood pressure and diminished arteriolar responses to NO-mediated vasodilators. Although the increased NOS/NO activity may compensate for flow abnormalities, it may also cause pathophysiological alterations in vascular tone.