gebhart/patrepeval huggingface dataset:
Selective high metabolic lability of uridine triphosphate in response to glucosamine feeding of untransformed and polyoma virus‐transformed hamster fibroblasts (1980)

Abstract Derepression of hexose transport in a line of Syrian hamster fibroblasts (Nil) and polyoma‐transformed (PyNil) hamster fibroblasts is obtained when cells are either starved for glucose or fed with fructose as the only hexose source. D‐glucosamine feeding of these cells does not alter the repressed state with regard to hexose transport. High, derepressed rates of galactose transport were changed to low, repressed rates, within 18 hours of refeeding glucose‐starved cells with D‐glucosamine as the only hexose source. Nil and PyNil cells, when cultured in the presence of D‐glucosamine, undergo rapid reductions in total cellular uridine 5′‐triphosphate (UTP) pool sizes. By contrast, the total cellular pools of adenosine 5′‐triphosphate, guanosine 5′‐triphosphate, and cytosine 5′‐triphosphate (ATP, GTP, and CTP) were only moderately affected by the treatment of the cells with glucosamine. The metabolic drain of the UTP pools in PyNil cells was much more pronounced than in the untransformed cells. The larger and more rapid metabolic lability of UTP pools in the transformed cells may be the primary reason for the selective toxicity of glucosamine on tumor cells. A comparison of the effects of glucosamine on hexose‐starved Nil and PyNil cells demonstrated that only the untransformed cells were able to utilize glucosamine to increase the hexose starvation‐depleted pools of all nucleoside triphosphates. Accumulation of UDP‐glucosamine and UDP‐N‐acetylglucosamine followed the reduction in the UTP pools. Inhibition of protein synthesis by cycloheximide during glucosamine feeding led to higher levels of UDP‐glucosamine and UDP‐N‐acetylglucosamine accumulation. It is suggested that the drain of UTP pools during glucosamine treatment proceeds through the formation of the UDP‐aminosugars which turn over due to the action of intracellular UDP‐aminosugar pyrophosphatase activities.
Probe-Immobilized Affinity Chromatography/Mass Spectrometry (1995)

A new technique has been developed that provides affinity separations directly on the surface of a matrix-assisted laser desorption/ionization mass spectrometer (MALDI-MS) probe. This strategy provides both in situ identification of biomolecules through biospecific antibody/antigen interactions and molecular weight information in a rapid and facile manner. Our technique, which we call probe affinity MS, directly couples the high selectivity of immobilized affinity chromatography with the sensitivity of MALDI-MS. As this technique permits the rapid identification of antigens, ligands, and other compounds from complex biological mixtures, we believe that it will be useful in a wide range of applications in virtually all fields of the life sciences.
The herpes simplex virus type 1 UL42 gene product: a subunit of DNA polymerase that functions to increase processivity (1990)

Genetic experiments have shown that the products of the herpes simplex virus type 1 (HSV-1) DNA polymerase (UL30) and UL42 genes are both required for viral DNA replication, and a number of studies have suggested that these two proteins specifically interact. We have confirmed and extended these findings. The viral DNA polymerase from HSV-1-infected cells has been purified as a complex containing equimolar quantities of the UL30 (Pol, the catalytic subunit) and UL42 polypeptides. Sedimentation and gel filtration analyses of this complex are consistent with the idea that the complex consists of a heterodimer of Pol and UL42. A complex with identical physical and functional properties was also purified from insect cells coinfected with recombinant baculoviruses expressing the two polypeptides. Therefore, the formation of the Pol-UL42 complex does not require the participation of any other HSV-encoded protein. We have compared the catalytic properties of the Pol-UL42 complex with those of the isolated subunits of the enzyme purified from recombinant baculovirus-infected insect cells. The specific activity of the catalytic subunit alone was nearly identical to that of the complex when assayed on activated DNA. When assayed on a defined template such as singly primed M13 DNA, however, the combination of Pol and UL42 utilized fewer primers and formed larger products than Pol alone. Template challenge experiments demonstrated that the Pol-UL42 complex was more highly processive than Pol alone. Our data are consistent with the idea that the UL42 polypeptide is an accessory subunit of the DNA polymerase that acts to increase the processivity of polymerization.
Zero-Knowledge Proofs of Knowledge Without Interaction (Extended Abstract) (1992)

A zero-knowledge proof system of knowledge is a protocol between two parties called the prover and the verifier. The prover wants to convince the verifier that he “knows” the proof of a given theorem without revealing any additional information. This is different from a zero-knowledge proof system of membership where the prover convinces the verifier only of the veridicity of the statement. Zero-knowledge proofs of knowledge are very useful tools in the design of secure protocols. Though, the concept of a proof of knowledge is a very subtle one and great care is needed to obtain a satisfying formalization. In this paper, we investigate the concept of a zero-knowledge proof of knowledge in the noninteractive model of [5, 61. Here, the prover and the verifier share a short random string and the only communication allowed is from the prover to the verifier. Although this is a simpler model than the interactive one, still formalizing zeroknowledge proofs of knowledge is a delicate task. The main results of the paper are the following e We present formal definitions for the concept of non-interactive zero-knowledge proofs
sucABandsucCDare mutually essential genes inEscherichia coli (2005)

sucAB and sucCD of Escherichia coli encode enzymes that generate succinyl-CoA from 2-oxoglutarate and succinate, respectively. Their mutual essentiality was studied. sucAB and sucCD could be deleted individually, but not simultaneously. The mutual essentiality of sucAB and sucCD was further confirmed by the conditional expression of sucABCD, sucAB, and sucCD under the control of a P(BAD) in E. coli MG1655, E. coli MG1655 (DeltasucCD), and E. coli MG1655 (DeltasucAB), respectively. These strains grew well in Luria-Bertani medium containing 0.1% arabinose, but not in the absence of arabinose unless the medium was supplemented with succinyl-CoA. Our results indicate that either sucAB or sucCD is enough to produce succinyl-CoA that is essential for cell viability.
Development of antibody-based fiber-optic sensors for detection of a benzo[a]pyrene metabolite (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDevelopment of antibody-based fiber-optic sensors for detection of a benzo[a]pyrene metaboliteBruce J. Tromberg, Michael J. Sepaniak, Jean Pierre. Alarie, . Vo Dinh Tuan, and Regina M. SantellaCite this: Anal. Chem. 1988, 60, 18, 1901–1908Publication Date (Print):September 15, 1988Publication History Published online1 May 2002Published inissue 15 September 1988https://doi.org/10.1021/ac00169a012RIGHTS & PERMISSIONSArticle Views165Altmetric-Citations32LEARN 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 InReddit PDF (2 MB) Get e-Alerts Get e-Alerts
Antibiotics from Algae XXXIII: Phlorotannins of the Brown AlgaHimanthalia elongata, (1985)

It is possible to obtain approximately 0.2% (relative to dry weight) phenols soluble in ethyl acetate from HIMANTHALIA ELONGATA. After removal of a fraction containing high-molecular weight substances, a total of 17 oligomeric phlorotannins with 2 to 8 aromatic rings can be isolated from the mixture of the acetylated phenol fraction. Apart from 2 derivatives belonging to the fucol group, diphlorethol and a tetraphlorethol not yet fully identified, all the other substances are fucophlorethols. Amongst these substances, a phenoxylated therphenyl derivative and several fucophlorethols with two-fold phenoxy-substituted biphenyl moieties were identified for the first time.
Contemporary Role of the Decipher® Test in Prostate Cancer Management: Current Practice and Future Perspectives. (2016)

We performed a systematic literature search to identify original articles and editorials about the Decipher(®) Prostate Cancer Test (GenomeDx Biosciences, San Diego, CA) to provide an overview of the current literature and its present role in urologic clinical practice. The Decipher test, which uses the expression of 22 selected RNA markers (from a total of over 1.4 million), showed a very high discrimination in predicting clinical metastasis (0.75-0.83) and cancer-specific mortality (0.78) in external validation studies, outperforming all routinely available clinicopathologic characteristics. Further, the timing of postoperative radiotherapy (adjuvant vs salvage) may be guided based on Decipher scores. The Decipher test was also the only independent predictor of clinical metastasis in patients with biochemical recurrence after surgery. The Decipher Genomic Resource Information Database (GRID) is a novel research tool that captures 1.4 million marker expressions per patient and may facilitate precision-guided, individualized care to patients with prostate cancer. In this era of precision medicine, Decipher, along with the Decipher GRID platform, is a promising genomic tool that may aid in managing prostate cancer patients throughout the continuum of care and delivering appropriate treatment at an individualized level.
The Fluorescence of Some Coumarins1 (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Fluorescence of Some Coumarins1Charles E. WheelockCite this: J. Am. Chem. Soc. 1959, 81, 6, 1348–1352Publication Date (Print):March 1, 1959Publication History Published online1 May 2002Published inissue 1 March 1959https://pubs.acs.org/doi/10.1021/ja01515a021https://doi.org/10.1021/ja01515a021research-articleACS PublicationsRequest reuse permissionsArticle Views1421Altmetric-Citations86LEARN 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 Get e-Alerts
Silicon high-speed binary phase-shift keying modulator with a single-drive push–pull high-speed traveling wave electrode (2015)

We demonstrate binary phase shift keying (BPSK) modulation using a silicon Mach–Zehnder modulator with a π-phase-shift voltage (Vπ) of −4.5  V. The single-drive push–pull traveling wave electrode has been optimized using numerical simulations with a 3 dB electro-optic bandwidth of 35 GHz. The 32 Gb/s BPSK constellation diagram is measured with an error vector magnitude of 18.9%.
Risk Factors for the Sexual Transmission of Genital Herpes (1992)

Despite clear recognition of genital herpes in source partners, there was substantial risk for transmission; in 70% of patients, transmission appeared to result from sexual contact during periods of asymptomatic viral shedding. The risk for acquisition of HSV was higher in women than men, and previous HSV type 1 infection appeared to reduce the risk for acquisition of HSV type 2 infection among women.
Computer-aided stereotactic functional neurosurgery enhanced by the use of the multiple brain atlas database (2000)

This paper introduces a computer-aided atlas-based functional neurosurgery methodology and describes NeuroPlanner, a software system which supports it. NeuroPlanner provides four groups of functions: 1) data-related for data reading, interpolation, reformatting, and image processing; 2) atlas-related for multiple atlases reading, atlas-to-data global and local registrations, two-way anatomical indexing, and multiple labeling in two and three dimensions; 3) atlas-data exploration-related for three-dimensional (3-D) display and real-time manipulation of cerebral structures, continuous navigation, two-dimensional (2-D), triplanar, 3-D presentations, and 2-D interaction in four views; and 4) neurosurgery-related for targeting, trajectory planning, mensuration, simulating the insertion of microelectrode, and simulating therapeutic lesioning. All operations, excluding atlas and data reading, are real time. The combined anatomical index of the multiple brain atlas database containing complementary 2-D and 3-D atlases has about 1000 structures per hemisphere, and over 400 sulcal patterns. Neurosurgical planning with mutually preregistered multiple brain atlases in all three orthogonal orientations is novel. The approach is validated with 24 intraoperative and postoperative datasets for thalamotomies, thalamic stimulations, pallidotomies, and pallidal stimulations. Its potential benefits include increased accuracy of target definition, reduced time of the surgical procedure by decreasing the number of tracts, facilitated planning of more sophisticated trajectories, lowered cost by reducing the number of microelectrodes used, reduced surgical complications, and the extra degree of confidence given to the neurosurgeon.
Validation of tests methods in the quality control of biologicals. (1999)

With increasing frequency new methods are being developed for the assessment of the quality of biological products. Before these methods can be considered for regulatory acceptance, their relevance and reliability must be established in a formal validation study. Such a study should be tailor-made, depending on the particular purpose and goal of the new method. However, a set of general principles can be given, according to which a validation study should be conducted. Essential ingredients in a validation study are the three Cs for Common sense, Commitment and Communication. Common sense in the design of the study, Commitment of the participating laboratories and Communication between the parties involved. An overview will be given of the various stages of a validation study, the time period needed (Table 1) and a number of problems that can be encountered will be discussed.
Metal-oxide interfaces at the nanoscale (2009)

In contrast to the 6×7 spacing registry that yields a minimum coincidence misfit, we find that the nanoscale Cu2O–Cu interface formed during initial oxidation of Cu(111) surfaces adopts a 5×6 coincidence site lattice that is accommodated by an increased lattice misfit strain. A simple analysis on the equilibrium elastic strain in epitaxial oxide nanoislands reveals a previously unnoticed correlation between the interface structure and surface stresses at the nanoscale.
Characterization of the major promoter for the plasmid-encoded sucrose genes scrY, scrA, and scrB (1991)

Sucrose genes from a Salmonella thompson plasmid were cloned in Escherichia coli K-12. A physical map and a genetic map of the genes were constructed, revealing strong homology with the scr regulon from the Salmonella typhimurium plasmid pUR400. Two promoters were examined after being subcloned into transcriptional fusion vectors. Primer extension analysis and site-directed mutagenesis were used to identify the precise location of the promoter of scrY, scrA, and scrB. Transcription from this promoter was regulated over a 1,000-fold range by the combined effects of ScrR-mediated repression and catabolite repression. A putative cyclic AMP receptor protein binding site centered 72.5 bp upstream of the start point of transcription of scrY appeared to be essential for full activity of the scrY promoter. Transcription from the putative scrK promoter was far less sensitive to repression by ScrR. In ScrR+ cells, readthrough transcription from the putative scrK promoter into scrY accounted for less than 10% of scrY expression.
Metastatic interstitial pneumonitis after autologous bone marrow transplantation: A consequence of reinjection of malignant cells? (1986)

Two cases of fatal interstitial pneumonitis developing after an autologous bone marrow transplantation are described. In both cases the autopsy revealed diffuse malignant pulmonary involvement. The first case involved a 4-year-old boy who had a Burkitt's lymphoma; the second case involved a 4-year-old girl with a neuroblastoma. The authors postulate that in these cases, the clinical picture may have been related to reinfusion of malignant cells.
Structural and Functional Comparison of Polysaccharide-Degrading Enzymes (2000)

Sugar molecules as well as enzymes degrading them are ubiquitously present in physiological systems, especially for vertebrates. Polysaccharides have at least two aspects to their function, one due to their mechanical properties and the second one involves multiple regulatory processes or interactions between molecules, cells, or extracellular space. Various bacteria exert exogenous pressures on their host organism to diversity glycans and their structures in order for the host organism to evade the destructive function of such microbes. Many bacterial organism produce glycan-degrading enzymes in order to facilitate their invasion of host tissues. Such polysaccharide degrading enzymes utilize mainly two modes of polysaccharide-degradation, a hydrolysis and a beta-elimination process. The three-dimensional structures of several of these enzymes have been elucidated recently using X-ray crystallography. There are many common structural motifs among these enzymes, mainly the presence of an elongated cleft transversing these molecules which functions as a polysaccharide substrate binding site as well as the catalytic site for these enzymes. The detailed structural information obtained about these enzymes allowed formulation of proposed mechanisms of their action. The polysaccharide lyases utilize a proton acceptance and donation mechanism (PAD), whereas polysaccharide hydrolases use a direct double displacement (DD) mechanism to degrade their substrates.
Vibriocidal antibody responses in North American volunteers exposed to wild-type or vaccine Vibrio cholerae O139: specificity and relevance to immunity (1997)

The emergence of a new agent of cholera, Vibrio cholerae O139, has prompted a reevaluation of the vibriocidal antibody assay. This assay, primarily directed to lipopolysaccharide, is an important correlate of O1 immunity. V. cholerae O139 strains are encapsulated, rendering them relatively resistant to killing by serum. Recent reports suggest that there is strain-to-strain variability in the sensitivity of the vibriocidal assay to fully encapsulated O139 strains. We have assessed a modified vibriocidal assay for fully encapsulated O139 strain AI-1837 and its unencapsulated mutant 2L in sera from 53 volunteers given wild-type AI-1837 or its attenuated derivative CVD 112 and from 48 controls challenged with V. cholerae O1 or strains of the family Enterobacteriaceae. Vibriocidal responses to the AI-1837 and 2L strains were seen in 67 and 89% of volunteers, respectively, following a single exposure to the wild-type strain. However, >50% of all controls had low-level vibriocidal responses to both strains. These nonspecific responses were transient and of the immunoglobulin G isotype. No binding activity against purified O139 lipopolysaccharide (LPS) by immunoblotting was seen in control sera. In contrast, vibriocidal assay and strain 2L LPS responses by immunoblotting were detectable in 91% of tested volunteers following a single exposure to O139. The presence of vibriocidal antibody to AI-1837 or 2L was not associated with protection in rechallenge studies with O139 strain AI-1837. The vibriocidal assay with unencapsulated strain 2L may be used to detect exposure to O139 strain AI-1837 in controlled research trials. However, its lack of specificity does not make it useful for determining exposure to V. cholerae O139 in the field.
Striking out at disseminated metastases: the systemic delivery of oncolytic viruses. (2006)

Oncolytic viruses are capable of selective replication in malignant cells and therefore offer levels of potency and specificity that are potentially far higher than conventional treatments for cancer. New developments in vector design and administration regimes are gradually moving toward systemic applications, with the ultimate aim of treating common cancer indications that present with multiple disseminated metastases. Nevertheless, the delivery of therapeutic quantities of viruses via the blood stream to target cells in humans or stringent animal models remains a challenging task: the relatively large size of virus particles restricts their penetration into tissues, and defines their biodistribution and clearance kinetics. In addition, multiple interactions with blood cells and serum proteins can impact on vector bioavailability. Finally, the immunological response to virus administration can vary considerably from patient to patient and even more so between species, making it difficult to draw accurate clinical predictions from model systems. Unfortunately, the extensive experience gained from the application of low-molecular-weight therapeutic drugs provides little insight into the behavior of viral therapeutics administered into the blood stream. In this review, the fate of virus particles following intravenous delivery is described, followed by an assessment of the latest approaches to control and improve vector delivery.