gebhart/patrepeval huggingface dataset:
An analysis of the structure of the product of the rbsA gene of Escherichia coli K12. (1986)

The predicted amino acid sequence of rbsA, a gene from the high affinity ribose transport operon (rbs) of Escherichia coli K12, is homologous to the products of hisP, malK, and pstB, components of the histidine, maltose, and phosphate high affinity transport operons. The recent finding by Hobson et al. (Hobson, A. C., Weatherwax, R., and Ames, G.F.-L. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 7333-7337) that the hisP and malK products bind ATP suggests that these four gene products may be involved in coupling the energy from ATP to drive the active transport in their respective transport systems. Each gene product contains a sequence of glycine and basic residues which are characteristic of an ATP-binding site (Walker, J.E., Saraste, M., Runswick, M.J., and Gay, N.J. (1982) EMBO J. 1, 945-951). Interestingly the N- and C-terminal halves of rbsA are also homologous, suggesting that a primordial gene duplication and subsequent fusion of the products occurred.
Democracies and Deficits: Prospects for Fiscal Responsibility in Democratic Nations (2011)

The financial crisis had significant implications for the fiscal positions of OECD. As nations seek to cope with the economic contraction, budget deficits and debt have risen to near record postwar levels. As the crisis in Europe and other advanced economies has deepened, fiscal consolidation will have to be coupled, and even preceded, by actions to jump‐start crippled economies. Nonetheless, when fiscal consolidation becomes necessary, nations that procrastinate by waiting for a crisis to provide cover for the politically hard choices will pay a steep price indeed both economically and politically. Many in the academic and policy community have raised questions about whether advanced democracies have the political wherewithal to respond to gathering fiscal pressures through early and timely action. Recent fiscal actions in advanced nations suggest that democracies are not doomed to wait for market shocks and crises. Rather, leaders have shown that fiscal sacrifice can be achieved in ways that promote electability. In this article, we discuss the impetus for democratic fiscal actions and the strategies used to gain public support.
ALD HfO/sub 2/ using heavy water (D/sub 2/O) for improved MOSFET stability (2004)

Device instability is one of the most challenging issues to implement high-k gate dielectrics. Incorporation of deuterium during the ALD (atomic layer deposition) process effectively improves the interface quality that enhances high-k device stability and reliability. Compared to H/sub 2/O processed HfO/sub 2/ devices, devices with D/sub 2/O processing result in a significantly smaller Vt shift after constant voltage stressing at room temperature and at 125/spl deg/C under NBTI/PBTI conditions, as well as a longer CHCI lifetime. This process is independent of transistor process integration and is relatively low cost. It has the potential to become an industry standard if ALD high-k gate dielectric processing is the final choice.
Platelet-bound lipopolysaccharide enhances Fc receptor–mediated phagocytosis of IgG-opsonized platelets (2007)

Platelets express Toll-like receptor 4 (TLR4), and this has been shown to be responsible for the thrombocytopenia induced by lipopolysaccharide (LPS) administration in vivo. We studied the role of LPS in mediating platelet phagocytosis by THP-1 cells in vitro by flow cytometry. Opsonization of platelets with an IgG monoclonal (W6/32) antibody or with IgG autoantibody-positive sera from patients with autoimmune thrombocytopenia (AITP) significantly enhanced platelet phagocytosis (P < .001). In contrast, platelet phagocytosis did not occur if platelets were bound with only LPS. If, however, the LPS-bound platelets were also opsonized with either W6/32 or autoantibody-positive sera with titers greater than 4, there was a significant and synergistic increase in Fc-dependent platelet phagocytosis (P < .001, P = .003, P = .048, and P = .047). These results suggest that, in the presence of antiplatelet antibodies, bacterial products can significantly alter platelet phagocytosis, and this may have relevance to how Gram-negative infections enhance platelet destruction in some patients with AITP.
Primary structures of both subunits of Escherichia coli glycyl-tRNA synthetase. (1983)

Escherichia coli glycyl-tRNA synthetase is one of two aminoacyl-tRNA synthetases which is comprised of two different subunits (in an alpha 2 beta 2 structure). The two coding regions occur in tandem in the order alpha + beta and are synthesized from a single mRNA (Keng, T., Webster, T. A., Sauer, R. T., and Schimmel, P. R. (1982) J. Biol. Chem. 257, 12503-12508). Primary structures of both proteins were determined by DNA sequencing of each coding region and by analysis of tryptic fragments of the enzyme. The alpha-subunit is 303 codons and terminates with TAA; the beta-subunit is 689 codons followed by tandem TAA stops. S1 nuclease mapping of the 3'-end of the two-cistron glyS mRNA showed that it predominantly ends 33/34 bases beyond the tandem stops with an RNA polymerse terminator sequence. Altogether, 43% of the translated polypeptide sequences were confirmed by mass spectrometric analysis of peptide fragments including confirmation of the COOH-terminal end of the beta-chain. This involved determinations, by fast atom bombardment mass spectrometry, of the masses of numerous whole tryptic fragments (with an accuracy of better than 1 Da) and of fragments truncated by one to three cycles of Edman degradations. The primary structures of the two subunits show no homologies with each other and have no internal sequence repeats of significance. While there are no extensive homologies with five other sequenced, or partially sequenced, synthetases, the alpha-subunit has a short sequence which can be aligned with sequences found in functionally important areas of two other synthetases and in uncharacterized parts of a third and fourth synthetase.
Hierarchical Bayesian cortical models: Analysis and acceleration on multicore architectures (2009)

There is a significant interest in the research community to develop large scale, high performance implementations of neuromorphic models. These have the potential to provide significantly stronger information processing capabilities than current computing algorithms. This thesis examines the parallelization of two recent biologically inspired hierarchical Bayesian cortical models onto recent multicore architectures. These models have been developed recently based on new insights from neuroscience and have several advantages over traditional neural networks. In particular, they need far fewer network nodes to simulate a large scale cortical model than traditional neural networks, making them computationally more efficient. This is the first study of the parallelization of this class of models onto multicore processors. Results indicate that the models can take advantage of parallelism present in the processors to provide significant speedups on multicore architectures. These models are further shown to scale well on a cluster of 336 PS3s available at the Air Force Research Lab which is shown to emulate between 10E8 to 1010 neurons. In particular, the results indicate that a cluster of Playstation 3s can provide an economical, yet powerful, platform for simulating large scale neuromorphic models.
Ribozyme cleavage of telomerase mRNA sensitizes breast epithelial cells to inhibitors of topoisomerase. (2001)

Telomerase activity is necessary and sufficient for immortality in many cells and hence represents a prime target for antitumor strategies. Here, we show that a hammerhead ribozyme cleaves human telomerase (hTERT) mRNA in vitro. Stable transfection in clones of the human breast tumor line MCF-7 and the immortal breast cell line HBL-100 results in expression of the ribozyme, diminishes the abundance of hTERT mRNA, and inhibits telomerase activity. This led to shortened telomeres, inhibition of net growth, and induction of apoptosis. In HBL-100 mass cultures infected with a ribozyme-expressing adenovirus diminution of hTERT mRNA, attenuation of telomerase activity, inhibition of net growth, and induction of apoptosis was found as well. Attenuation of telomerase activity increased the sensitivity of HBL-100 and MCF-7 clones specifically to inhibitors of topoisomerase. Likewise, expression of exogenous telomerase in originally telomerase-negative human fibroblasts decreased their sensitivity to topoisomerase poisons but not to a number of other cytotoxic drugs. The data validate a ribozyme approach for telomerase inhibition therapy in cancer and suggest that it might be combined advantageously with topoisomerase-directed chemotherapy.
The white gene from the yellow fever mosquito, Aedes aegypti (1997)

We report the cloning and primary characterization of both cDNA and genomic fragments from the white gene of the yellow fever mosquito, Aedes aegypti. Comparisons of the conceptual translation product with white genes from four other species within the order Diptera show that the Ae. aegypti gene is most similar to the white gene of the mosquito vector of human malaria, Anopheles gambiae (86% identity and 92% similarity). The analysis of the primary sequence of genomic DNA at the 5'-end of the coding region revealed the presence of an intron that is also present in An. gambiae, but not in the vinegar fly, Drosophila melanogaster. The isolated clones of the Ae. aegypti white gene will enable the construction of a marker gene for use in the development of a germline transformation system for this species.
Achieving customer value from electronic channels through identity commitment, calculative commitment, and trust in technology (2007)

How consumers feel about themselves––particularly in relation to technology––may have an important influence on their adoption and use of technology. Although research on electronic channels has shown that Web site and consumer characteristics are important predictors of consumer trust, researchers have not considered the role played by consumers’ commitment to their identity as technology users. This paper explores whether consumer identity commitment and calculative commitment to electronic channels impact consumer use of electronic channels and perceived value from the service firm. More specifically, it examines whether these effects are mediated by trust in technology and trust in the firm. Using survey data from 834 consumers engaged in both offline and online banking, plus transaction frequency data supplied by a host firm, the study finds that identity commitment plays an important role in building consumer trust in technology and that calculative commitment increases transaction frequency directly, unmediated by trust in technology. Theoretical and managerial implications of these findings are explored.
Observations of the alpha -beta phase transition in quartz; a review of imaging and diffraction studies and some new results (1991)

Although the a-B quartz transition traditionally has been treated as a simple, secondorder phase transition, a wealth of studies performed over the past two decades has documented the complex nature of this transformation. It now appears thal a quartz undergoes a first-order transition to an incommensurately modulated phase that is stable over a 1.3 .C interval. This intermediate phase consists of an ordered mosaic of Dauphin6 microtwins that occur as triangular prisms elongate along c, and these prisms grow finerwith increasing temperature. The discovery of this incommensurate phase was achieved through a series of diffraction and imaging experiments using a variety of methods, and this paper reviews the process by which the existence of the intermediate phase of quartz was established. In addition, we present results from our own transmission electron microscopy experiments on the a-B transition. Specifically, we have determined that the sizes of the Dauphin6 twins as imaged in real space are identical to the structural superperiodicities inferred from satellite reflections obtained by electron diffraction of the intermediate phase; this result supports the microtwin model presented by Van Tendeloo et al. (1976) rather than the configuration wave model ofGouhara and Kato (1985a, 1985b). Further, our observation of diffuse satellite intensities surrounding the primary Bragg peaks of p qtartz suggests that the p polymorph has a dynamic structure in which oscillating tetrahedra are correlated over short distances.
A low-voltage high-speed electronic switch based on piezoelectric transduction (2012)

We propose a novel digital switch, the piezoelectronic transistor or PET. Based on properties of known materials, we predict that a nanometer-scale PET can operate at low voltages and relatively high speeds, exceeding the capabilities of any conventional field effect transistor (FET). Depending on the degree to which these attributes can be simultaneously achieved, the device has a broad array of potential applications in digital logic. The PET is a 3-terminal switch in which a gate voltage is applied to a piezoelectric (PE), resulting in expansion compressing a piezoresistive (PR) material comprising the channel, which then undergoes a continuous, reversible insulator-metal transition. The channel becomes conducting in response to the gate voltage. A high piezoelectric coefficient PE, e.g., a relaxor piezoelectric, leads to low voltage operation. Suitable channel materials manifesting a pressure-induced metal-insulator transition can be found amongst rare earth chalcogenides, transition metal oxides, and among others. Mechanical requirements include a high PE/PR area ratio to step up pressure, a rigid surround material to constrain the PE and PR external boundaries normal to the strain axis, and a void space to enable free motion of the component side walls. Using static mechanical modeling and dynamic electro-acoustic simulations, we optimize device structure and materials and predict performance.
Report on construction of gene‐targeting vector for homologous recombination and transformation in silkworm, Bombyx mori L. (2005)

Abstract: This paper reports the methods of construction of gene‐targeting vector for transformation of silkworm, Bombyx mori L. The genomic DNA was isolated from the posterior silk gland of the fifth‐instar silkworm larvae. The short fragment (0.5 kb) and long fragment (5 kb) of the fibroin light‐chain gene were obtained by polymerase chain reaction (PCR) analysis with special primers and genome DNA as templates and then recombined with pBlueselect vector into pBs‐FS‐FL. The target green flourescent protein (GFP) gene, was derived from pGEP‐1 vector and recombined with pUC19 vector into pUCG vector. GFP was recovered after cutting with restriction endonucleases, Pst I and Bam HI. Finally, GFP was recombined with pBs‐FS‐FL into gene‐targeting vector, pBs‐FS‐GFP‐FL.
AGE-RELATED CHANGES IN PLASMA GROWTH HORMONE RESPONSE TO GROWTH HORMONE-RELEASING FACTOR IN MAN (1984)

The response of plasma growth hormone to synthetic growth hormone-releasing factor (hpGRF-44) administered intravenously was examined in normal men of various ages ranging from 20 to 75 years. Most of the subjects who were over forty years old had either no or much lower response of plasma growth hormone to hpGRF-44. In contrast plasma growth hormone increased markedly after hpGRF-44 injection in all men in their twenties and thirties. The mean peak level of plasma GH following hpGRF-44 administration was 29.6 +/- 20.4 (SD) ng/ml in men in their twenties, 30.2 +/- 26.5 ng/ml in their thirties, 9.7 +/- 5.2 ng/ml in their forties, 10.9 +/- 5.4 ng/ml in their fifties, 8.4 +/- 4.8 ng/ml in their sixties and 8.1 +/- 7.5 ng/ml in their seventies. These results suggest that somatotroph cells become less sensitive to growth hormone-releasing factor with aging.
Transcriptional activation function is not required for stimulation of DNA replication by bovine papillomavirus type 1 E2 (1996)

Bovine papillomavirus type 1 replication was previously shown to require both the E1 initiator protein and the E2 transactivator protein. We show here that E1, in the absence of E2, is sufficient for low-level bovine papillomavirus type 1 DNA replication in C-33A cells. In addition, studies of genetically isolated E2 point mutants demonstrate that enhancement of replication by E2 does not require its transcriptional activation function. The uncoupling of the E2 functions suggests that stimulation of transcription and replication by enhancer proteins occurs via divergent mechanisms.
Synthetic Zinc Finger Transcription Factor Action at an Endogenous Chromosomal Site (2000)

We have targeted the activation of an endogenous chromosomal locus including the human erythropoietin gene using synthetic transcription factors. These transcription factors are targeted to particular DNA sequences in the 5'-flanking region of the erythropoietin gene through engineering of a zinc finger DNA binding domain. The DNA binding domain is linked to a VP16 transcriptional activation domain. We find that these synthetic transcription factors invariably activate transiently transfected templates in which sequences within the 5' flank of the erythropoietin gene are fused to a luciferase reporter. The efficiency of activation under these circumstances at a defined site is dependent on DNA binding affinity. In contrast, only a subset of these same zinc finger proteins is able to activate the endogenous chromosomal locus. The activity of these proteins is influenced by their capacity to gain access to their recognition elements within the chromatin infrastructure. Zinc finger transcription factors will provide a powerful tool to probe the determinants of chromatin accessibility and remodeling within endogenous chromosomal loci.
Scavenger receptor BI (SR-BI) mediates free cholesterol flux independently of HDL tethering to the cell surface (1999)

In addition to its effect on high density lipoprotein (HDL) cholesteryl ester (CE) uptake, scavenger receptor BI (SR-BI) was recently reported to stimulate free cholesterol (FC) flux from Chinese hamster ovary (CHO) cells stably expressing mouse SR-BI, a novel function of SR-BI that may play a role in cholesterol removal from the vessel wall where the receptor can be found. It is possible that SR-BI stimulates flux simply by tethering acceptor HDL particles in close apposition to the cell surface thereby facilitating the movement of cholesterol between the plasma membrane and HDL. To test this, we used transiently transfected cells and compared the closely related class B scavenger receptors mouse SR-BI and rat CD36 for their ability to stimulate cholesterol efflux as both receptors bind HDL with high affinity. The results showed that, although acceptor binding to SR-BI may contribute to efflux to a modest extent, the major stimulation of FC efflux occurs independently of acceptor binding to cell surface receptors. Instead our data indicate that SR-BI mediates alterations to membrane FC domains which provoke enhanced bidirectional FC flux between cells and extracellular acceptors.
Epoxy Fatty Acids and Inhibition of the Soluble Epoxide Hydrolase Selectively Modulate GABA Mediated Neurotransmission to Delay Onset of Seizures (2013)

In the brain, seizures lead to release of large amounts of polyunsaturated fatty acids including arachidonic acid (ARA). ARA is a substrate for three major enzymatic routes of metabolism by cyclooxygenase, lipoxygenase and cytochrome P450 enzymes. These enzymes convert ARA to potent lipid mediators including prostanoids, leukotrienes and epoxyeicosatrienoic acids (EETs). The prostanoids and leukotrienes are largely pro-inflammatory molecules that sensitize neurons whereas EETs are anti-inflammatory and reduce the excitability of neurons. Recent evidence suggests a GABA-related mode of action potentially mediated by neurosteroids. Here we tested this hypothesis using models of chemically induced seizures. The level of EETs in the brain was modulated by inhibiting the soluble epoxide hydrolase (sEH), the major enzyme that metabolizes EETs to inactive molecules, by genetic deletion of sEH and by direct administration of EETs into the brain. All three approaches delayed onset of seizures instigated by GABA antagonists but not seizures through other mechanisms. Inhibition of neurosteroid synthesis by finasteride partially blocked the anticonvulsant effects of sEH inhibitors while the efficacy of an inactive dose of neurosteroid allopregnanolone was enhanced by sEH inhibition. Consistent with earlier findings, levels of prostanoids in the brain were elevated. In contrast, levels of bioactive EpFAs were decreased following seizures. Overall these results demonstrate that EETs are natural molecules which suppress the tonic component of seizure related excitability through modulating the GABA activity and that exploration of the EET mediated signaling in the brain could yield alternative approaches to treat convulsive disorders.
High expression level of alpha 6 integrin in human breast carcinoma is correlated with reduced survival. (1995)

We recently reported that alpha 6 integrin mediates experimental metastasis in mice by functioning in the adhesion of tumor cells to the vascular endothelium. In the current study, we investigated the expression of human alpha 6 integrin in invasive breast carcinomas of 119 women. In 50% of the tumors alpha 6 integrin was expressed in the majority of the cells, and this expression was correlated with reduced survival time. By contrast, the 24% of patients with breast tumors devoid of alpha 6 integrin expression all survived. The tumors were also evaluated for clinical risk factors including histological grading and steroid receptor level. The combination of these factors with alpha 6 integrin expression was superior in predicting overall survival than considering the other factors alone. The correlation with decreased survival time was consistent, regardless of whether the tumors expressed the alpha 6 integrin A or B forms, which differ in their cytoplasmic domain. On the basis of this pilot study we consider alpha 6 integrin expression to be a novel prognostic marker for human breast cancer.
Eosinophilic Esophagitis/Ringed Esophagus: The Diagnostic Conundrum (2007)

Purpose: Eosinophilic esophagitis (EoE) is defined classically as >20 eos/HPF on esophageal biopsies. Common characteristics in EoE are dysphagia with associated rings/furrows seen on endoscopy. To date, no one has determined whether all rings seen on EGD represent EoE histologically or whether all EoE patients have the classical endoscopic findings of rings/furrows. This study was designed to correlate endoscopic findings and histology in EoE. Methods: A retrospective analysis of all EGD's performed at the University for dysphagia in 2006 was performed. Per routine protocol, all cases were biopsied and evaluated for eosinophils. Patients with endoscopic findings of ringed/furrowed esophagus were identified. Cases were evaluated for evidence of EoE based on histologic criteria of >20 eos/HPF. All cases of histologically defined EoE were identified and grouped by their endoscopic findings as ringed/furrowed, normal, esophagitis, schatzki ring, or stricture. Results: Ringed esophagus was identified endoscopically in 28 patients (75% male, ave age 41 y).19/28 (67.9%) met histologic criteria for EoE (graph). In the remaining patients, distal eosinophil counts averaged 2.5/HPF while proximal eos averaged 8.2/HPF. 32 patients met histologic criteria for EoE (62.5% male, ave age 42 y). 19/32 (59%) presented with endoscopic “rings or furrows.” 13/32 (41%) had other endoscopic findings (graph). Conclusion: EoE may present as a variety of phenotypes. Strictly adhering to histologic criteria for the diagnosis may result in an underdiagnosis as eosinophilic infiltration is patchy and likley sporadic. Gastroenterologists should have a high index of suspicion for EoE in any young patient who presents with dysphagia as endoscopy may not portray classical rings/furrows. Routine biopsies in this population are warranted.[figure1][figure2]FigureFigure