gebhart/patrepeval huggingface dataset:
Nucleotide sequence of the <i>hemG</i> gene involved in the protoporphyrinogen oxidase activity of <i>Escherichia coli</i> K12 (1993)

The hemG gene of Escherichia coli K12 is involved in the activity of protoporphyrinogen oxidase, the enzyme responsible for the conversion of protoporphyrinogen IX into protoporphyrin IX during heme and chlorophyll biosynthesis. The gene is located at min 87 on the genetic map of E. coli K12. The hemG gene was isolated by a mini-Mu in vivo cloning procedure. As expected, the hemG gene is able to restore normal growth to the hemG mutant, and the transformed cells display strong protoporphyrinogen oxidase activity. Sequencing of the hemG gene allowed us to identify an open reading frame of 546 nucleotides (181 amino acids), within the minimal fragment able to complement the mutant. The presumed molecular mass of the HemG protein is 21,202 Da, in agreement with values found by SDS-PAGE, in a DNA-directed coupled transcription-translation system. The identity of the first 18 amino acids at the amino-terminal end of the protein was confirmed by microsequencing. To our knowledge, this is the first cloning of a gene involved in the protoporphyrinogen oxidase activity of E. coli.
Transgenic Mice Secreting Coronavirus Neutralizing Antibodies into the Milk (1998)

Ten lines of transgenic mice secreting transmissible gastroenteritis coronavirus (TGEV) neutralizing recombinant monoclonal antibodies (rMAbs) into the milk were generated. The rMAb light- and heavy-chain genes were assembled by fusing the genes encoding the variable modules of the murine MAb 6A.C3, which binds an interspecies conserved coronavirus epitope essential for virus infectivity, and a constant module from a porcine myeloma with the immunoglobulin A (IgA) isotype. The chimeric antibody led to dimer formation in the presence of J chain. The neutralization specific activity of the recombinant antibody produced in transiently or stably transformed cells was 50-fold higher than that of a monomeric rMAb with the IgG1 isotype and an identical binding site. This rMAb had titers of up to 10(4) by radioimmunoassay (RIA) and neutralized virus infectivity up to 10(4)-fold. Of 23 transgenic mice, 17 integrated both light and heavy chains, and at least 10 of them transmitted both genes to the progeny, leading to 100% of animals secreting functional TGEV neutralizing antibody during lactation. Selected mice produced milk with TGEV-specific antibody titers higher than 10(6) as determined by RIA, neutralized virus infectivity by 10(6)-fold, and produced up to 6 mg of antibody per ml. Antibody expression levels were transgene copy number independent and integration site dependent. Comicroinjection of the genomic beta-lactoglobulin gene with rMAb light- and heavy-chain genes led to the generation of transgenic mice carrying the three transgenes. The highest antibody titers were produced by transgenic mice that had integrated the antibody and beta-lactoglobulin genes, although the number of transgenic animals generated does not allow a definitive conclusion on the enhancing effect of beta-lactoglobulin cointegration. This approach may lead to the generation of transgenic animals providing lactogenic immunity to their progeny against enteric pathogens.
A clinically relevant mouse model of canine osteosarcoma with spontaneous metastasis. (2014)

Implantation of OS tumor fragments leads to the development of primary bone tumors and secondary lung metastases, recapitulating the clinical behavior of OS. This model offers an advantage over cell suspension injection models by precluding initial seeding of the lung with tumor cells.
Accurate bond and angle parameters for X-ray protein structure refinement (1991)

Bond-length and bond-angle parameters are derived from a statistical survey of X-ray structures of small compounds from the Cambridge Structural Database. The side chains of the common amino acids and the polypeptide backbone were represented by appropriate chemical fragments taken from the Database. Average bond lengths and bond angles are determined from the resulting samples and the sample standard deviations provide information regarding the expected variability of the average values which can be parametrized as force constants. These parameters are ideally suited for the refinement of protein structures determined by X-ray crystallography since they are derived from X-ray structures, are accurate to within the deviations from target values suggested for X-ray structure refinement and use force constants which directly reflect the variability or uncertainty of the average values. Tests of refinement of the structures of BPTI and phycocyanin demonstrate the integrity of the parameters and comparisons of equivalent refinements with XPLOR parameters show improvement in R-factors and geometry statistics.
Drug ratio–dependent antitumor activity of irinotecan and cisplatin combinations <i>in vitro</i> and <i>in vivo</i> (2009)

Irinotecan and cisplatin are two established anticancer drugs, which together constitute an effective combination for treating small-cell lung cancer. We investigated whether the efficacy of this combination could be improved by controlling drug ratios following in vivo administration. Irinotecan and cisplatin combinations were evaluated systematically for drug ratio-dependent synergy in vitro using a panel of 20 tumor cell lines. In vitro screening informatics on drug ratio-dependent cytotoxicity identified a consistently antagonistic region between irinotecan/cisplatin molar ratios of 1:2 to 4:1, which was bordered by two synergistic regions. Liposomal co-formulations of these two agents were developed that exhibited plasma drug half-lives of approximately 6 hours and maintained a fixed drug ratio for more than 24 hours. Drug ratio-dependent antitumor activity was shown in vivo for these liposome formulations, and irinotecan/cisplatin ratios between 5:1 and 10:1 were identified as therapeutically optimal. The relationship between irinotecan/cisplatin ratio and in vivo efficacy was consistent with in vitro drug ratio dependency results. Superior antitumor activity was observed for the liposome-encapsulated 7:1 molar ratio of irinotecan/cisplatin (designated CPX-571) compared with the free-drug cocktail in all models tested. Further efficacy studies in a range of human tumor xenografts, including an irinotecan-resistant model, showed that both liposomal agents contributed to the overall efficacy in a manner consistent with in vivo synergy. These results show the ability of drug delivery technology to enhance the therapeutic activity of irinotecan/cisplatin combination treatment by maintaining synergistic ratios in vivo. CPX-571, a fixed-ratio formulation of irinotecan and cisplatin, is a promising candidate for clinical development.
The Essential Role of Trusted Third Parties in Electronic Commerce (1996)

The Essential Role of Trusted Third Parties in Electronic Commerce B Y now it is well known that the Internet is a global, but insecure, network.'It is also increasingly well understood that cryptography 2 can contribute greatly to the ransactional security that Internet commerce so obviously lacks. 3 What is less well understood is that cryptography is only part of the security story.Many cryptographic protocols for secure electronic transactions require at least one trusted third party to the transaction, such as a bank or a "certification authority" (CA).These partly cryptographic, partly social, protocols require new entities, or new relationships with existing entities, but the duties and liabilities of those entities are uncertain.Until these uncertainties are resolved, they risk inhibiting the spread of the most interesting forms of electronic commerce and causing unnecessary litigation.
Hybrid electro-optical stimulation of the rat sciatic nerve induces force generation in the plantarflexor muscles (2012)

Objective. Optical methods of neural activation are becoming important tools for the study and treatment of neurological disorders. Infrared nerve stimulation (INS) is an optical technique exhibiting spatially precise activation in the native neural system. While this technique shows great promise, the risk of thermal damage may limit some applications. Combining INS with traditional electrical stimulation, a method known as hybrid electro-optical stimulation, reduces the laser power requirements and mitigates the risk of thermal damage while maintaining spatial selectivity. Here we investigate the capability of inducing force generation in the rat hind limb through hybrid stimulation of the sciatic nerve. Approach. Hybrid stimulation was achieved by combining an optically transparent nerve cuff for electrical stimulation and a diode laser coupled to an optical fiber for infrared stimulation. Force generation in the rat plantarflexor muscles was measured in response to hybrid stimulation with 1 s bursts of pulses at 15 and 20 Hz and with a burst frequency of 0.5 Hz. Main results. Forces were found to increase with successive stimulus trains, ultimately reaching a plateau by the 20th train. Hybrid evoked forces decayed at a rate similar to the rate of thermal diffusion in tissue. Preconditioning the nerve with an optical stimulus resulted in an increase in the force response to both electrical and hybrid stimulation. Histological evaluation showed no signs of thermally induced morphological changes following hybrid stimulation. Our results indicate that an increase in baseline temperature is a likely contributor to hybrid force generation. Significance. Extraneural INS of peripheral nerves at physiologically relevant repetition rates is possible using hybrid electro-optical stimulation.
Integrity Management Infrastructure for Trusted Computing (2008)

Computer security concerns have been rapidly increasing because of repeated security breaches and leakages of sensitive personal information. Such security breaches are mainly caused by an inappropriate management of the PCs, so maintaining integrity of the platform configuration is essential, and, verifying the integrity of the computer platform and software becomes more significant. To address these problems, the Trusted Computing Group (TCG) has developed various specifications that are used to measure the integrity of the platform based on hardware trust. In the trusted computing technology, the integrity data of each component running on the platform is recorded in the security chip and they are securely checked by a remote attestation. The infrastructure working group in the TCG is trying to define an Integrity Management Infrastructure in which the Platform Trust Services (PTS) is a new key component which deals with an Integrity Report. When we use the PTS in the target platform, it is a service component that collects and measures the runtime integrity of the target platform in a secure way. The PTS can also be used to validate the Integrity Reports. We introduce the notion of the Platform Validation Authority, a trusted third party, which verifies the composition of the integrity measurement of the target platform in the Integrity Reports. The Platform Validation Authority complements the role of the current Certificate Authority in the Public Key Infrastructure which attests to the integrity of the user identity as well as to related artifacts such as digital signatures. In this paper, we cover the research topics in this new area, the relevant technologies and open issues of the trusted computing, and the detail of our PTS implementation.
Metabolic trajectory of cellular differentiation in small intestine by Phasor Fluorescence Lifetime Microscopy of NADH (2012)

There is a lack of fast and high resolution methods to measure metabolic activity of single cells in their native environment. Here we develop a straightforward, non-invasive and sensitive method to measure metabolic phenotype of single cells in a live tissue. By using NADH as optical biomarker and the phasor approach to Fluorescence Lifetime microscopy (FLIM) we identify cellular metabolic fingerprints related to different rates of oxidative phosphorylation and glycolysis. For the first time we measure a three dimensional metabolic gradient in the small intestine (SI) epithelia that appears tightly associated with epithelial cell proliferation, differentiation and the Wnt gradient. The highest free/bound NADH ratios are measured at the base of the crypt within the highly proliferative stem cells, indicating high levels of glycolysis. For the first time mouse small intestinal stem cells in intact live crypts are identified within the tissue by their metabolic fingerprint.
Structural Stability of Human Protein Tyrosine Phosphatase ρ Catalytic Domain: Effect of Point Mutations (2012)

Protein tyrosine phosphatase ρ (PTPρ) belongs to the classical receptor type IIB family of protein tyrosine phosphatase, the most frequently mutated tyrosine phosphatase in human cancer. There are evidences to suggest that PTPρ may act as a tumor suppressor gene and dysregulation of Tyr phosphorylation can be observed in diverse diseases, such as diabetes, immune deficiencies and cancer. PTPρ variants in the catalytic domain have been identified in cancer tissues. These natural variants are nonsynonymous single nucleotide polymorphisms, variations of a single nucleotide occurring in the coding region and leading to amino acid substitutions. In this study we investigated the effect of amino acid substitution on the structural stability and on the activity of the membrane-proximal catalytic domain of PTPρ. We expressed and purified as soluble recombinant proteins some of the mutants of the membrane-proximal catalytic domain of PTPρ identified in colorectal cancer and in the single nucleotide polymorphisms database. The mutants show a decreased thermal and thermodynamic stability and decreased activation energy relative to phosphatase activity, when compared to wild- type. All the variants show three-state equilibrium unfolding transitions similar to that of the wild- type, with the accumulation of a folding intermediate populated at ~4.0 M urea.
Advanced return-path cable TV access technologies (2002)

The return-path dense wavelength-division-multiplexed network architecture using time -division-multiplexing and frequency-stacking methods is reviewed. Digitizing the return-path bandwidth provides significant cost savings while maintaining network transparency and flexibility.
Production of Plant-Specific Flavanones by <i>Escherichia coli</i> Containing an Artificial Gene Cluster (2003)

In plants, chalcones are precursors for a large number of flavonoid-derived plant natural products and are converted to flavanones by chalcone isomerase or nonenzymatically. Chalcones are synthesized from tyrosine and phenylalanine via the phenylpropanoid pathway involving phenylalanine ammonia lyase (PAL), cinnamate-4-hydroxylase (C4H), 4-coumarate:coenzyme A ligase (4CL), and chalcone synthase (CHS). For the purpose of production of flavanones in Escherichia coli, three sets of an artificial gene cluster which contained three genes of heterologous origins--PAL from the yeast Rhodotorula rubra, 4CL from the actinomycete Streptomyces coelicolor A3(2), and CHS from the licorice plant Glycyrrhiza echinata--were constructed. The constructions of the three sets were done as follows: (i) PAL, 4CL, and CHS were placed in that order under the control of the T7 promoter (P(T7)) and the ribosome-binding sequence (RBS) in the pET vector, where the initiation codons of 4CL and CHS were overlapped with the termination codons of the preceding genes; (ii) the three genes were transcribed by a single P(T7) in front of PAL, and each of the three contained the RBS at appropriate positions; and (iii) all three genes contained both P(T7) and the RBS. These pathways bypassed C4H, a cytochrome P-450 hydroxylase, because the bacterial 4CL enzyme ligated coenzyme A to both cinnamic acid and 4-coumaric acid. E. coli cells containing the gene clusters produced two flavanones, pinocembrin from phenylalanine and naringenin from tyrosine, in addition to their precursors, cinnamic acid and 4-coumaric acid. Of the three sets, the third gene cluster conferred on the host the highest ability to produce the flavanones. This is a new metabolic engineering technique for the production in bacteria of a variety of compounds of plant and animal origin.
An object-oriented file system—an example of using the class hierarchy framework concept (1995)

This paper presents the design of an object-oriented file system which was developed as a part of the "OBJIX Object-Oriented Operating System" project. The file system is a self-contained program system which is decomposed using a standard object-oriented framework concept. A novel approach to object-oriented frameworks, the Class Hierarchy Framework concept recapitulated in this paper, is employed in structuring components of the file system. Further, this paper illustrates on an example how the file system pursues a typical system call.
On the diffuse field reciprocity relationship and vibrational energy variance in a random subsystem at high frequencies (2007)

A recent paper has shown that under certain conditions the cross-spectral matrix of the forces exerted by a vibrational or acoustic wave field on its surrounding boundaries can be expressed in terms of (i) the energy of the wave field, and (ii) the direct field dynamic stiffness matrix of the boundary. This "diffuse field reciprocity relation" was derived using wave mechanics, and it is not immediately clear how the required wave field properties translate to conditions on the vibrational modes of the system or the applied forcing. This issue is addressed here by deriving an extended version of the reciprocity relation using modal methods, and the conditions required for the extended version to reduce to the existing relation are delineated. It is shown that the existing diffuse field reciprocity relation leads to an anomalous result when used to predict the energy variance of a subsystem, and that this anomaly is resolved by using the present extended version of the relation. A supplementary result arising from the analysis is that for systems with a sufficient degree of randomness the ensemble average of the dynamic stiffness matrix of a random subsystem is equal to the inverse of the ensemble average of the receptance matrix.
Disaggregation for low sampling rate data (2014)

This conference item examines disaggregation for low sampling rate data
Theory and Applications of NMR-Based Screening in Pharmaceutical Research (2004)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTheory and Applications of NMR-Based Screening in Pharmaceutical ResearchChristopher A. Lepre, Jonathan M. Moore, and Jeffrey W. PengView Author Information Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, Massachusetts 02139-4242; and Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556-5670 Cite this: Chem. Rev. 2004, 104, 8, 3641–3676Publication Date (Web):July 24, 2004Publication History Received1 April 2004Published online24 July 2004Published inissue 1 August 2004https://pubs.acs.org/doi/10.1021/cr030409hhttps://doi.org/10.1021/cr030409hresearch-articleACS PublicationsCopyright © 2004 American Chemical SocietyRequest reuse permissionsArticle Views4593Altmetric-Citations272LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Drug discovery,Inhibitors,Ligands,Receptors,Screening assays Get e-Alerts
A novel low-voltage silicon-on-insulator (SOI) CMOS complementary pass-transistor logic (CPL) circuit using asymmetrical dynamic threshold pass-transistor (ADTPT) technique (2002)

Reports a novel low-voltage silicon-on-insulator (SOI) CMOS complementary pass-transistor logic (CPL) circuit using asymmetrical dynamic threshold pass-transistor (ADTPT) technique., Using the ADTPT technique to dynamically control the body bias of the pass-transistor via only one auxiliary transistor, the new SOI CMOS complementary pass-transistor logic (CPL) circuit provides superior speed performance at a low supply voltage as compared to the conventional pass-transistor logic circuits without the ADTPT technique as verified by the MEDICI simulation results. The ADTPT technique is especially effective for use in CPL circuits with serially-connected multiple inputs.
III/V Wafer Bonding Technology for Wafer-Level Fabrication of GaInAsP/InP Microring Resonators (2006)

GaInAsP InP passive microring resonator devices were successfully fabricated using a vertical integration concept with GaInAsP InP-on-GaAs wafer bonding. BCB adhesive bonding has been identified as the preferred wafer bonding process. This paper reports results on the development of the wafer bonding and on the microring fabrication
Modeling and Simulation of Capacitor Suits Control System Based on MATLAB/SIMULINK (2009)

Radio Frequency System is the most popular and highest performance price ratio because of its low cost and multiple product choices. The paper presents simulation of the process of modulating the capacitive reactance with inductive reactance to make the circle syntony.
Requirement for Pangolin/dTCF in <i>Drosophila</i> Wingless signaling (2003)

The Wingless (Wg) protein is a secreted glycoprotein involved in intercellular signaling. On activation of the Wg signaling pathway, Armadillo is stabilized, causing target genes to be activated by the transcription factor Pangolin (Pan). This study investigated the roles of Pan in the developing wing of Drosophila by clonal analysis. Three different aspects of wing development were examined: cell proliferation, wing margin specification, and wg self-refinement. Our results indicate that Pan function is critically required for all three of these processes. Consequently, lack of pan causes a severe reduction in the activity of the Wg target genes Distalless and vestigial within their normal domain of expression. Loss of pan function does not, however, lead to a derepression of these genes outside this domain. Thus, although Pan is positively required for the induction of Wg targets in the wing imaginal disk, it does not appear to play a default repressor function in the absence of Wg input. In contrast, lack of zygotic pan function causes a milder phenotype than that caused by the lack of wg function in the embryo. We show that this difference cannot be attributed to maternally provided pan product, indicating that a Pan repressor function usually prevents the expression of embryonic Wg targets. Together, our results suggest that for embryonic patterning the activator as well as repressor forms of Pan play important roles, while for wing development Pan operates primarily in the activator mode.