gebhart/patrepeval huggingface dataset:
Induction of cytochrome P450, generation of oxidative stress and in vitro cell-transforming and DNA-damaging activities by glucoraphanin, the bioprecursor of the chemopreventive agent sulforaphane found in broccoli (2003)

The reduced cancer risk that appears to be linked to a diet rich in fruits and vegetables has fueled the belief that regular intake of isolated phytochemicals could potentially prevent cancer. In recent years, the glucosinolate metabolites derived from cruciferous vegetables, such as the isothiocyanate sulforaphane in broccoli, have gained much attention as potential cancer chemopreventive agents. The protective effect of sulforaphane, which is liberated from its glucosinolate precursor glucoraphanin (GRP) by myrosinase hydrolysis, is conventionally thought to involve the induction of Phase-II metabolizing enzymes. These Phase-II enzymes are implicated in the detoxication of many carcinogens and reactive oxygen species (ROS), thereby protecting cells against DNA damage and subsequent malignant transformation. While the induction of Phase-II enzymes is usually considered beneficial, in some cases these enzymes also bioactivate several hazardous chemicals. Furthermore, despite its projected benefits, the unknown effect of sulforaphane on Phase-I enzyme systems, which are involved in the bioactivation of a variety of carcinogens, should not be overlooked. Here we show that, in rat lungs, while GRP, the bioprecursor of the chemopreventive agent sulforaphane, slightly induced Phase-II detoxifying enzymes, it powerfully induced Phase-I carcinogen-activating enzymes, including activators of carcinogenic polycyclic aromatic hydrocarbons (PAHs). Concomitant with this Phase-I induction, GRP also over-generated ROS. Additionally, in a cell-transforming assay, GRP facilitated the metabolic activation of the PAH benzo[a]pyrene to reactive carcinogenic forms and in a yeast genotoxicity test it damaged DNA. This suggests that regular administration of GRP could actually increase rather than decrease cancer risk, especially in individuals exposed to environmental mutagens and carcinogens such as those found in tobacco smoke and in certain industrial settings.
Distinguishing between Phosphorylated and Nonphosphorylated Peptides with Ion Mobility−Mass Spectrometry (2002)

Mass spectrometry has become an indispensable tool in identifying post-translationally modified proteins, but multiple peptide mass-mapping/peptide-sequencing experiments are required to answer questions involving the site and type of modification present. Here, we apply ion mobility-mass spectrometry (IM-MS), a high-throughput analysis method having high selectivity and sensitivity, to the challenge of identifying phosphorylated peptides. Ion mobility separation is based on the collision cross-section of the ion. Phosphorylation can result in a conformational change in gas-phase peptide ions, which can be detected by IM. To demonstrate this point, a peptide mixture containing a variety of peptide sequences is examined with IM-MS and molecular dynamics calculations. During the course of these studies, two classes of phosphopeptide were identified: (i) phosphorylated peptide ions that have conformers that differ from the nonphosphorylated ion and (ii) phosphorylated peptide ions that have conformations that are very similar to the nonphosphorylated peptide. The utility of IM-MS peptide mass mapping for identifying both types of phosphorylated peptides is discussed.
Review of laser sensing devices and systems (2005)

The area of laser sensing is vast. This review will be limited to some examples of laser sensing of relevance for defense and security applications especially those of relevance to countermeasures. Examples from the areas ISR (Intelligence, Surveillance and Reconnaissance), target acquisition/recognition, warning/protection and some miscellaneous applications such as positioning, tagging, communication and weapon guidance will be given. The laser sensor can itself have a multifunction capability and will probably not be the only sensor in a system. Future possibilities of powerful multisensor systems using new device technology will be discussed.
Enzyme immunoassays with special reference to ELISA techniques. (1978)

In this review outlines are given on various types of enzyme immunoassay. The applications to such enzyme immunoassays, especially ELISA, are dealth with in detail. It is concluded that these techniques have high sensitivity and will be suitable in due course as routine laboratory tests.
Photolithographic Olefin Metathesis Polymerization (2013)

Patterning functional materials is a central challenge across many fields of science. The ability to lithographically fabricate micro- and nanostructures has been one of the most impactful technological breakthroughs of the last century. In part due to the complexity of the chemical processes in photoresists, there is a limited variety of materials that can currently be patterned by photolithography. We report a negative tone photoresist using a photoactivated olefin metathesis catalyst, which can be quickly prepared in a one-pot synthesis from commercially available starting materials. The resist is based on a ruthenium vinyl ether complex, widely regarded as inactive toward olefin metathesis. The combination of this photoactivated catalyst with the fidelity and functional group tolerance of ruthenium-mediated olefin metathesis enables a host of new possibilities for photopatterned materials.
New β‐lactam–β‐lactamase inhibitor combinations in clinical development (2013)

Tazobactam was the most recent β-lactamase inhibitor to be approved in 1993. Since the approval of piperacillin-tazobactam, the complexity of β-lactamase-mediated resistance among Gram-negative bacilli has increased enormously. After more than 20 years since the first such combination, amoxicillin-clavulanic acid, was approved, several new β-lactam-β-lactamase inhibitor combinations have reached late-stage (phase II and beyond) clinical trials. These include ceftolozane-tazobactam (2:1, ratios of β-lactam to β-lactamase inhibitor in parentheses), ceftazidime-avibactam (4:1), ceftaroline-avibactam (1:1), and imipenem-cilastatin-MK-7655 (2:2:1 and 4:4:1). Avibactam and MK-7655 are diazabicyclooctane (DABCO) inhibitors and thus not β-lactams themselves; they include class A carbapenemases and class C enzymes within their spectra of activity. Ceftolozane is an antipseudomonal cephalosporin, and tazobactam is used to protect it against extended spectrum β-lactamases to which it is labile. Additional novel combinations are in preclinical development. This review will focus on the biochemistry, antimicrobial activity, pharmacodynamics, and clinical development of these novel combinations.
From Laboratory to Warehouse: Security Robots Meet the Real World (1999)

The Mobile Detection Assessment and Response System robotic security program has successfully demonstrated simultaneous control of multiple robots navigating autonomously within an operational warehouse environment. This real-world warehouse installation required adapting a navigational paradigm designed for highly structured environments such as office corridors (with smooth walls and regularly spaced doorways) to a semistructured warehouse environment (with no exposed walls and within which odd-shaped objects unpredictably move about from day to day). A number of challenges, some expected and others unexpected, were encountered during the transfer of the system first to a beta-test/demonstration site and then to an operational warehouse. This paper examines these problems (and others previously encountered) in a historical context of the evolution of navigation and other needed technologies, and the transition of these technologies from the research lab to an operational warehouse environment. A key lesson is that system robustness can only be ensured by exhaustively exercising the system’s operational capabilities in a number of diverse environments. This approach helps to uncover latent system hardware deficiencies and software implementation errors not manifested in the initial system hardware or initial development environment, and to identify sensor modes or processing algorithms tuned too tightly to the specific characteristics of the initial development environment.
DnaK from Bifidobacterium animalis subsp. lactis is a surface-exposed human plasminogen receptor upregulated in response to bile salts (2010)

Bifidobacterium animalis subsp. lactis lives in the gastrointestinal tract of most mammals, including humans. Recently, for the probiotic strain B. animalis subsp. lactis BI07, a dose-dependent plasminogen-binding activity was demonstrated and five putative plasminogen-binding proteins were identified. Here we investigated the role of surface DnaK as a B. animalis subsp. lactis BI07 plasminogen receptor. DnaK was visualized on the bacterial cell surface by transmission electron microscopy. The His-tagged recombinant DnaK protein showed a high affinity for human plasminogen, with an equilibrium dissociation constant in the nanomolar range. The capability to tolerate physiological concentrations of bile salts is a crucial feature for an intestinal symbiont micro-organism. By proteome analysis we demonstrated that the long-term exposure of B. animalis subsp. lactis BI07 to bile salts results in the upregulation of important surface plasminogen receptors such as DnaK and enolase. Moreover, adaptation of B. animalis subsp. lactis BI07 to physiological concentrations of bile salts significantly increased its capacity to interact with the host plasminogen system. By enhancing the bacterial capacity to interact with the host plasminogen, the gut bile environment may facilitate the colonization of the human host by B. animalis subsp. lactis BI07.
Protection and Polymerization of Functional Monomers. 30. Anionic Living Polymerization of 4-Alkylstyrenes Containing Acetal-Protected Monosaccharide Residues (2000)

Three new para-substituted styrene derivatives, p-[3-(1,2:5,6-di-O-isopropylidene-α-d-glucofuranose-3-oxy)propyl]styrene (1), p-[3-(1,2:3,4-di-O-isopropylidene-α-d-galactopyranose-6-oxy)propyl]styrene (2), and p-[11-(1,2:5,6-di-O-isopropylidene-α-d-glucofuranose-3-oxy)undecyl]styrene (3) were synthesized by phase transfer catalyzed etherifications. Their anionic polymerizations proceed in a living manner in THF at −78 °C using sec-BuLi as the initiator to quantitatively afford polymers with well-controlled molecular weights (6.7−42K) and narrow molecular weight distributions (Mw/Mn < 1.06). Novel AB and BA diblock copolymers of 1 and styrene were also successfully synthesized. The stabilities of the living polymer of 1 and the already reported living polymer of m-(1,2:5,6-di-O-isopropylidene-α-d-glucofuranose-3-oxymethyl)styrene (4) were examined under the polymerization conditions at −78 °C for 22 h and −30 °C for 0.5 h.
Improving management of patients with acute cough by C-reactive protein point of care testing and communication training (IMPAC3T): study protocol of a cluster randomised controlled trial (2007)

This trial is the first cluster randomised trial to evaluate the influence of point of care CRP testing in the hands of the general practitioner and enhanced communication skills, on the management of LRTI in primary care. The pragmatic nature of the study, which leaves treatment decisions up to the responsible clinicians, will enhance the applicability and generalisability of findings. The factorial design will allow conclusion to be made about the value of CRP testing on its own, communication skills training on its own, and the two combined. Evaluating a biomedical and communication based intervention ('hard' and 'soft' technologies) together in this way makes this trial unique in its field.
Identification of several cell surface proteins of non-T, non-B acute lymphoblastic leukemia by using monoclonal antibodies. (1985)

Monoclonal antibodies (MAb) were produced by immunization of BALB/c mice with cells from a non-T, non-B acute lymphoblastic leukemia (ALL) cell line. Nine distinct antigens (groups I to IX) were defined by these monoclonal antibodies, some of which appear to be associated with specific stages of cellular differentiation. The number of molecules of each MAb reactive with the ALL cell line, measured in a quantitative cellular radioimmunoassay, varied from 0.6 X 10(5) to 11 X 10(5) molecules/cell, indicating that the antigens identified represent major constituents of the cell surface. The biochemical nature of the antigens was examined on the ALL cell line by antibody affinity chromatography and/or immunoprecipitation and SDS-polyacrylamide gel electrophoresis. Groups I through III are composed of previously described antigens: HLA class I, HLA class II molecules, and CALLA, the common ALL antigen. The other MAb define antigens previously undescribed on non-T, non-B ALL cells. Group IV antigen is a polypeptide of apparent m.w. 95,000 distinct from CALLA. It is expressed on some ALL samples and on the vascular endothelial cells of several tissues. Group V antigen is a single polypeptide chain of m.w. 94,000, also distinct from CALLA and expressed by lymphocytes, thymocytes, acute myelogenous leukemia (AML) cells, and ALL cells. Group VI is a molecular complex composed of two noncovalently associated polypeptides of apparent m.w. 125,000 and 87,000 and appears to be restricted to ALL, AML, macrophages, and hematopoietic precursor cells. Group VII is a glycoprotein of apparent m.w. 85,000, which, within the thymus, is primarily restricted to the medullary area. It is also present on AML, bone marrow cells, and mature T and B lymphocytes. Group VIII is a disulfide-linked complex of apparent m.w. greater than 120,000 under nonreducing conditions. It is resolved into three major polypeptides of apparent m.w. 57,000, 47,000, and 41,000 under reducing conditions. This complex is found in greatest amounts on the non-T, non-B ALL cell line but is also present on AML, ALL, and on subpopulations of normal bone marrow and tonsil cells. Group IX antigen is a single polypeptide chain of apparent m.w. 51,000 on the ALL cell line. This antigen is expressed strongly on ALL and AML samples and on normal bone marrow; much lower antigenic density is found on thymus and tonsil cells. The antigens described here with a series of MAb produced in a single fusion represent a unique array of cell surface molecules of non-T, non-B ALL cells.(ABSTRACT TRUNCATED AT 400 WORDS)
Molecular analysis of the maize anthocyanin regulatory locus C1. (1986)

The C1 gene of maize plays a regulatory role in the production of anthocyanin pigments in the aleurone layer of the endosperm. As an initial step toward understanding the molecular details of how C1 controls pigment biosynthesis, we cloned the C1 gene. This was accomplished by first cloning a mutable allele of C1, c1-m5, which contains the transposable element Spm. A combination of molecular and genetic analysis was used to identify the Spm at the C1 locus. Individual genomic DNAs from a population in which the c1-mutable phenotype was segregating with the recessive c1 phenotype were digested with methyl-sensitive restriction enzymes and probed with a small DNA fragment derived from a defective Spm. One Sal I restriction fragment complementary to the Spm probe was shown to be present in the DNA of individuals with the c1-m5 phenotype but absent from DNA of individuals with a recessive c1 phenotype. Subsequent cloning and restriction analysis of this fragment revealed sequences flanking the Spm that proved to be C1-specific. A DNA fragment derived from the flanking sequences was then used as a probe to clone the wild-type C1 gene and several additional alleles of C1, including one stable recessive, two mutations caused by Ds insertions, one mutation induced by insertion of a defective Spm, and two dominant mutations, C1-S and C1-I. RNA blot hybridization analysis of three C1 alleles indicates that C1 regulation of the Bz1 and A1 structural genes in the anthocyanin biosynthetic pathway is at the transcriptional level.
Purification and characterization of a peptide essential for formation of streptolysin S by Streptococcus pyogenes (1992)

Peptides in a pronase digest of bovine serum albumin were required for streptolysin S formation by Streptococcus pyogenes besides maltose and a carrier (the oligonucleotide fraction obtained by treatment of Saccharomyces cerevisiae RNA with RNase A). A peptide essential for streptolysin S formation was purified to homogeneity from a pronase digest of bovine serum albumin by Sephadex G-25 column chromatography, and anion-exchange, reverse-phase, and gel filtration high-performance liquid chromatography. The purified peptide was divided into more than two peptides by HCOOOH oxidation and was composed of four residues of cysteine, three of leucine, and one each of aspartic acid and glutamic acid. Leucine and cysteine were detected as amino-terminal residues, and leucine and glutamic acid were detected as carboxyl-terminal residues, suggesting that two or three peptides are linked by a disulfide bond(s). A disulfide bond structure in the peptide seemed to be required for streptolysin S formation.
Cyclins D2 and D1 Are Essential for Postnatal Pancreatic β-Cell Growth (2005)

Regulation of adult beta-cell mass in pancreatic islets is essential to preserve sufficient insulin secretion in order to appropriately regulate glucose homeostasis. In many tissues mitogens influence development by stimulating D-type cyclins (D1, D2, or D3) and activating cyclin-dependent kinases (CDK4 or CDK6), which results in progression through the G(1) phase of the cell cycle. Here we show that cyclins D2 and D1 are essential for normal postnatal islet growth. In adult murine islets basal cyclin D2 mRNA expression was easily detected, while cyclin D1 was expressed at lower levels and cyclin D3 was nearly undetectable. Prenatal islet development occurred normally in cyclin D2(-/-) or cyclin D1(+/-) D2(-/-) mice. However, beta-cell proliferation, adult mass, and glucose tolerance were decreased in adult cyclin D2(-/-) mice, causing glucose intolerance that progressed to diabetes by 12 months of age. Although cyclin D1(+/-) mice never developed diabetes, life-threatening diabetes developed in 3-month-old cyclin D1(-/+) D2(-/-) mice as beta-cell mass decreased after birth. Thus, cyclins D2 and D1 were essential for beta-cell expansion in adult mice. Strategies to tightly regulate D-type cyclin activity in beta cells could prevent or cure diabetes.
Distinct endothelial phenotypes evoked by arterial waveforms derived from atherosclerosis-susceptible and -resistant regions of human vasculature (2004)

Atherosclerotic lesion localization to regions of disturbed flow within certain arterial geometries, in humans and experimental animals, suggests an important role for local hemodynamic forces in atherogenesis. To explore how endothelial cells (EC) acquire functional/dysfunctional phenotypes in response to vascular region-specific flow patterns, we have used an in vitro dynamic flow system to accurately reproduce arterial shear stress waveforms on cultured human EC and have examined the effects on EC gene expression by using a high-throughput transcriptional profiling approach. The flow patterns in the carotid artery bifurcations of several normal human subjects were characterized by using 3D flow analysis based on actual vascular geometries and blood flow profiles. Two prototypic arterial waveforms, "athero-prone" and "athero-protective," were defined as representative of the wall shear stresses in two distinct regions of the carotid artery (carotid sinus and distal internal carotid artery) that are typically "susceptible" or "resistant," respectively, to atherosclerotic lesion development. These two waveforms were applied to cultured EC, and cDNA microarrays were used to analyze the differential patterns of EC gene expression. In addition, the differential effects of athero-prone vs. athero-protective waveforms were further characterized on several parameters of EC structure and function, including actin cytoskeletal organization, expression and localization of junctional proteins, activation of the NF-kappaB transcriptional pathway, and expression of proinflammatory cytokines and adhesion molecules. These global gene expression patterns and functional data reveal a distinct phenotypic modulation in response to the wall shear stresses present in atherosclerosis-susceptible vs. atherosclerosis-resistant human arterial geometries.
Optimized Four-Dimensional Mapping for High-Speed Optical Communication Systems (2012)

We propose an optimized mapping rule for the 32-point four-dimensional cross-constellation for high-speed optical communications based on bit-interleaved coded-modulation with iterative decoding. The optimized mapping outperforms its random counterpart by 1 dB in terms of OSNR sensitivity.
The Tripartite Leader Sequence of Subgroup C Adenovirus Major Late mRNAs Can Increase the Efficiency of mRNA Export (1998)

The subgroup C human adenoviruses induce selective export of newly synthesized viral mRNA from the nucleus to the cytoplasm, with concomitant inhibition of export of the majority of cellular mRNA species. Such posttranscriptional regulation of viral and cellular gene expression in infected cells requires viral E1B and E4 proteins. To facilitate the investigation of parameters that govern selective export in adenovirus-infected cells, we constructed a marked human beta-actin minigene under the control of the glucocorticoid-inducible enhancer-promoter of mouse mammary tumor virus and introduced it into the left end of the adenovirus type 5 (Ad5) genome. Transcription of this reporter gene (designated MA) as well as of a sibling, which differed only in the inclusion of a cDNA copy of the Ad2 major late tripartite leader sequence upstream of beta-actin sequences (termed MtplA), in recombinant virus-infected cells was strictly dependent on the addition of dexamethasone to the medium. When transcription of the MA gene was induced during the late phase of infection, newly synthesized MA RNA entered the cytoplasm. These transcripts, which contain no viral sequences, therefore reproduce the behavior of exceptional cellular mRNA species observed when transcription of their genes is activated during the late phase of infection (U.-C. Yang, W. Huang, and S. J. Flint, J. Virol. 70:4071-4080, 1996). Unexpectedly, however, higher concentrations of newly synthesized RNA accumulated in the cytoplasm when the tripartite leader sequence was present in the reporter RNA, despite equal rates of transcription of the two reporter genes. Examination of the partitioning of both newly synthesized and steady-state populations of MA and MtplA RNAs between nuclear and cytoplasmic compartments indicated that the tripartite leader sequence did not increase RNA stability in the cytoplasm. Comparison of nuclear and cytoplasmic reporter RNA species by Northern blotting, primer extension, and reverse transcription-PCR provided no evidence for altered processing induced by the tripartite leader sequence. We therefore conclude that the tripartite leader sequence, long known to facilitate the translation of mRNAs during the late phase of adenovirus infection, can also modulate mRNA export from the nucleus.
Fault prediction at the network layer using intelligent agents (2003)

Prediction of network failures at the router level has been achieved using an intelligent agent. The intelligent agent gathers relevant MIB data from the router and provides temporally and spatially correlated predictive alarms. The time correlated abnormal changes in the individual MIB variables are spatially correlated using a novel combining scheme. The agent was implemented on a real network and seven out of nine faults were predicted. Two typical case studies are presented. The prediction time was of the order of minutes.