gebhart/patrepeval huggingface dataset:
Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes (2014)

Bacterial infections are becoming increasingly difficult to treat due to widespread antibiotic resistance among pathogens. This review aims to give an overview of the major horizontal transfer mechanisms and their evolution and then demonstrate the human lower gastrointestinal tract as an environment in which horizontal gene transfer of resistance determinants occurs. Finally, implications for antibiotic usage and the development of resistant infections and persistence of antibiotic resistance genes in populations as a result of horizontal gene transfer in the large intestine will be discussed.
Biphasic regulation of H2O2 on angiogenesis implicated NADPH oxidase (2010)

ROS (reactive oxygen species) take an important signalling role in angiogenesis. Although there are several ways to produce ROS in cells, multicomponent non-phagocytic NADPH oxidase is an important source of ROS that contribute to angiogenesis. In the present work, we examined the effects of H2O2 on angiogenesis including proliferation and migration in HUVECs (human umbilical vein endothelial cells), new vessel formation in chicken embryo CAM (chorioallantoic membrane) and endothelial cell apoptosis, which is closely related to anti-angiogenesis. Our results showed that H2O2 dose-dependently increased the generation of O2- (superoxide anion) in HUVECs, which was suppressed by DPI (diphenylene iodonium) and APO (apocynin), two inhibitors of NADPH oxidase. H2O2 at low concentrations (10 microM) stimulated cell proliferation and migration, but at higher concentrations, inhibited both. Similarly, H2O2 at 4 nmol/cm2 strongly induced new vessel formation in CAM, while it suppressed at high concentrations (higher than 4 nmol/cm2). Also, H2O2 (200 approximately 500 microM) could stimulate apoptosis in HUVECs. All the effects of H2O2 on angiogenesis could be suppressed by NADPH oxidase inhibitors, which suggests that NADPH oxidase acts downstream of H2O2 to produce O2- and then to regulate angiogenesis. In summary, our results suggest that H2O2 as well as O2- mediated by NADPH oxidase have biphasic effects on angiogenesis in vitro and in vivo.
Structure-based Design of β1,4-Galactosyltransferase I (β4Gal-T1) with Equally Efficient N-Acetylgalactosaminyltransferase Activity (2002)

beta1,4-Galactosyltransferase I (Gal-T1) normally transfers Gal from UDP-Gal to GlcNAc in the presence of Mn(2+) ion. In the presence of alpha-lactalbumin (LA), the Gal acceptor specificity is altered from GlcNAc to Glc. Gal-T1 also transfers GalNAc from UDP-GalNAc to GlcNAc, but with only approximately 0.1% of Gal-T activity. To understand this low GalNAc-transferase activity, we have carried out the crystal structure analysis of the Gal-T1.LA complex with UDP-GalNAc at 2.1-A resolution. The crystal structure reveals that the UDP-GalNAc binding to Gal-T1 is similar to the binding of UDP-Gal to Gal-T1, except for an additional hydrogen bond formed between the N-acetyl group of GalNAc moiety with the Tyr-289 side chain hydroxyl group. Elimination of this additional hydrogen bond by mutating Tyr-289 residue to Leu, Ile, or Asn enhances the GalNAc-transferase activity. Although all three mutants exhibit enhanced GalNAc-transferase activity, the mutant Y289L exhibits GalNAc-transferase activity that is nearly 100% of its Gal-T activity, even while completely retaining its Gal-T activity. The steady state kinetic analyses on the Leu-289 mutant indicate that the K(m) for GlcNAc has increased compared to the wild type. On the other hand, the catalytic constant (k(cat)) in the Gal-T reaction is comparable with the wild type, whereas it is 3-5-fold higher in the GalNAc-T reaction. Interestingly, in the presence of LA, these mutants also transfer GalNAc to Glc instead of to GlcNAc. The present study demonstrates that, in the Gal-T family, the Tyr-289/Phe-289 residue largely determines the sugar donor specificity.
Synthesis and characterization of a new semisynthetic enzyme, flavolysozyme (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and characterization of a new semisynthetic enzyme, flavolysozymeSteven E. Rokita and Emil Thomas. KaiserCite this: J. Am. Chem. Soc. 1986, 108, 16, 4984–4987Publication Date (Print):August 1, 1986Publication History Published online1 May 2002Published inissue 1 August 1986https://pubs.acs.org/doi/10.1021/ja00276a045https://doi.org/10.1021/ja00276a045research-articleACS PublicationsRequest reuse permissionsArticle Views132Altmetric-Citations13LEARN 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
Utilizing Succinic Acid as a Glucose Adjunct in Fed-Batch Fermentation:  Is Butane a Feedstock Option in Microbe-Catalyzed Synthesis? (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTUtilizing Succinic Acid as a Glucose Adjunct in Fed-Batch Fermentation: Is Butane a Feedstock Option in Microbe-Catalyzed Synthesis?Kai Li and J. W. FrostView Author Information Department of Chemistry, Michigan State University East Lansing, Michigan 48824 Cite this: J. Am. Chem. Soc. 1999, 121, 40, 9461–9462Publication Date (Web):September 24, 1999Publication History Received14 July 1999Published online24 September 1999Published inissue 1 October 1999https://pubs.acs.org/doi/10.1021/ja992477khttps://doi.org/10.1021/ja992477krapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views194Altmetric-Citations4LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Aromatic compounds,Carbohydrates,Gallic acid,Mixtures,Peptides and proteins Get e-Alerts
Characterization of novel silane coatings on titanium implant surfaces (2012)

Novel coatings were successfully developed and optimized. They may produce a hydrophobic surface onto Ti implants without compromising the surface roughness.
Collagen: Molecular Diversity in the Body's Protein Scaffold (1980)

Intensive research in the last decade has revealed a wealth of detail on the mechanism of biosynthesis, molecular structure, and covalent cross-linking of collagen. Tissues of higher animals express a family of at least five genetically distinct types of collagen molecule, each apparently tailored for different construction work outside the cell. Within each genetic type of collagen, further chemical heterogeneity is also evident; the variations in hydroxylation, glycosylation, and cross-linking are dependent, for example, on tissue type, age, and hormonal status. The functional significance of collagen's molecular diversity and its control by different cells and tissues are not yet well understood but abnormalities of collagen in many human diseases keep this protein a focal molecule of medical research.
Unconditional security in quantum cryptography (2001)

Basic techniques to prove the unconditional security of quantum crypto graphy are described. They are applied to a quantum key distribution protocol proposed by Bennett and Brassard [1984]. The proof considers a practical variation on the protocol in which the channel is noisy and photos may be lost during the transmission. Each individual signal sent into the channel must contain a single photon or any two-dimensional system in the exact state described in the protocol. No restriction is imposed on the detector used at the receiving side of the channel, except that whether or not the received system is detected must be independent of the basis used to measure this system.
Analysis of a new compact microstrip antenna (1998)

A new compact microstrip antenna element is analyzed. The analysis can accurately predict the resonant frequency, input impedance, and radiation patterns. The predicted results are compared with experimental results and excellent agreement is observed. These antenna elements are more suitable in applications where limited antenna real estate is available.
Runx2 induces osteoblast and chondrocyte differentiation and enhances their migration by coupling with PI3K-Akt signaling (2004)

Runx2 and phosphatidylinositol 3-kinase (PI3K)-Akt signaling play important roles in osteoblast and chondrocyte differentiation. We investigated the relationship between Runx2 and PI3K-Akt signaling. Forced expression of Runx2 enhanced osteoblastic differentiation of C3H10T1/2 and MC3T3-E1 cells and enhanced chondrogenic differentiation of ATDC5 cells, whereas these effects were blocked by treatment with IGF-I antibody or LY294002 or adenoviral introduction of dominant-negative (dn)-Akt. Forced expression of Runx2 or dn-Runx2 enhanced or inhibited cell migration, respectively, whereas the enhancement by Runx2 was abolished by treatment with LY294002 or adenoviral introduction of dn-Akt. Runx2 up-regulated PI3K subunits (p85 and p110beta) and Akt, and their expression patterns were similar to that of Runx2 in growth plates. Treatment with LY294002 or introduction of dn-Akt severely diminished DNA binding of Runx2 and Runx2-dependent transcription, whereas forced expression of myrAkt enhanced them. These findings demonstrate that Runx2 and PI3K-Akt signaling are mutually dependent on each other in the regulation of osteoblast and chondrocyte differentiation and their migration.
<title>Legacy system integration using web technology</title> (2000)

As healthcare moves towards a completely digital, multimedia environment there is an opportunity to provide for cost- effective, highly distributed physician access to clinical information including radiology-based imaging. In order to address this opportunity a Universal Clinical Desktop (UCD) system was developed. A UCD provides a single point of entry into an integrated view of all types of clinical data available within a network of disparate healthcare information systems. In order to explore the application of a UCD in a hospital environment, a pilot study was established with the University of California Davis Medical Center using technology from Trilix Information Systems. Within this pilot environment the information systems integrated under the UCD include a radiology information system (RIS), a picture archive and communication system (PACS) and a laboratory information system (LIS).
Intracellular Targeting of CEA Results in Th1-Type Antibody Responses Following Intradermal Genetic Vaccination by a Needle-Free Jet Injection Device (2007)

The route and method of immunization, as well as the cellular localization of the antigen, can influence the generation of an immune response. In general, intramuscular immunization results in Th1 responses, whereas intradermal delivery of DNA by gene gun immunization often results in more Th2 responses. Here we investigate how altering the cellular localization of the tumor antigen CEA (carcinoembryonic antigen) affects the quality and amplitude of DNA vaccine-induced antibody responses in mice following intradermal delivery of DNA by a needle-free jet injection device (Biojector). CEA was expressed either in a membrane-bound form (wild-type CEA) or in two truncated forms (CEA6 and CEA66) with cytoplasmic localization, where CEA66 was fused to a promiscuous T-helper epitope from tetanus toxin. Repeated intradermal immunization of BALB/c mice with DNA encoding wild-type CEA produced high antibody titers of a mixed IgG1/IgG2a ratio. In contrast, utilizing the DNA construct that resulted in intracellular targeting of CEA led to a reduced capacity to induce CEA-specific antibodies, but instead induced a Th1-biased immune response.
The design and implementation of an operating system to support distributed multimedia applications (1996)

Support for multimedia applications by general purpose computing platforms has been the subject of considerable research. Much of this work is based on an evolutionary strategy in which small changes to existing systems are made. The approach adopted is to start ab initio with no backward compatibility constraints. This leads to a novel structure for an operating system. The structure aims to decouple applications from one another and to provide multiplexing of all resources, not just the CPU, at a low level. The motivation for this structure, a design based on the structure, and its implementation on a number of hardware platforms is described.
Diagnostic efficacy of SonoVue®, a second generation contrast agent, in the assessment of extracranial carotid or peripheral arteries using colour and spectral Doppler ultrasound: a multicentre study (2006)

The purpose of this study was to demonstrate the improvement in diagnostic quality and diagnostic accuracy of SonoVue microbubble contrast-enhanced ultrasound (CE-US) versus unenhanced ultrasound imaging during the investigation of extracranial carotid or peripheral arteries. 82 patients with suspected extracranial carotid or peripheral arterial disease received four SonoVue doses (0.3 ml, 0.6 ml, 1.2 ml and 2.4 ml) with Doppler ultrasound performed before and following each dose. Diagnostic quality of the CE-US examinations was evaluated off-site for duration of clinically useful contrast enhancement, artefact effects and percentage of examinations converted from non-diagnostic to diagnostic. Accuracy, sensitivity and specificity were assessed as agreement of CE-US diagnosis evaluated by an independent panel of experts with reference standard modality. The median duration of clinically useful signal enhancement significantly increased with increasing SonoVue doses (p< or =0.002). At the dose of 2.4 ml of SonoVue, diagnostic quality evaluated as number of inconclusive examinations significantly improved, falling from 40.7% at baseline down to 5.1%. Furthermore, SonoVue significantly (p<0.01) increased the accuracy, sensitivity and specificity of assessment of disease compared with baseline ultrasound. SonoVue increases the diagnostic quality of Doppler images and improves the accuracy of both spectral and colour Doppler examinations of extracranial carotid or peripheral arterial disease.
Decreased specific CD8+ T cell cross‐reactivity of antigen recognition following vaccination with Melan‐A peptide (2006)

The aim of T cell vaccines is the expansion of antigen-specific T cells able to confer immune protection against pathogens or tumors. Although increase in absolute cell numbers, effector functions and TCR repertoire of vaccine-induced T cells are often evaluated, their reactivity for the cognate antigen versus their cross-reactive potential is rarely considered. In fact, little information is available regarding the influence of vaccines on T cell fine specificity of antigen recognition despite the impact that this feature may have in protective immunity. To shed light on the cross-reactive potential of vaccine-induced cells, we analyzed the reactivity of CD8(+) T cells following vaccination of HLA-A2(+) melanoma patients with Melan-A peptide, incomplete Freund's adjuvant and CpG-oligodeoxynucleotide adjuvant, which was shown to induce strong expansion of Melan-A-reactive CD8(+) T cells in vivo. A collection of predicted Melan-A cross-reactive peptides, identified from a combinatorial peptide library, was used to probe functional antigen recognition of PBMC ex vivo and Melan-A-reactive CD8(+) T cell clones. While Melan-A-reactive CD8(+) T cells prior to vaccination are usually constituted of widely cross-reactive naive cells, we show that peptide vaccination resulted in expansion of memory T cells displaying a reactivity predominantly restricted to the antigen of interest. Importantly, these cells are tumor-reactive.
Design, synthesis, and biocompatibility of an arginine‐based polyester (2011)

Polycations are very useful in biotechnology. However, most existing polycations have high toxicity that significantly limits their clinical translation. We designed poly(ethylene argininylaspartate diglyceride) (PEAD) that is based on arginine, aspartic acid, glycerol, and ethylene glycol. A set of in vitro assays demonstrated that PEAD exhibited no cytotoxicity at 1 mg/mL, which is at least 100 times higher than the widely used polycation-polyethylenimine. Subcutaneous injection of 1 mg PEAD in rats did not cause an adverse response acutely or after 4 weeks. Zeta potential measurements revealed that PEAD has high affinity to biological polyanions such as DNA and hyaluronic acid. This polycation represents a new platform of biocompatible polycations that may lead to clinical innovations in gene therapy, controlled release, tissue engineering, biosensors, and medical devices.
Reduction of [Ca2+]iRestores Uncoupled β-Adrenergic Signaling in Isolated Perfused Transgenic Mouse Hearts (2001)

The effects of alterations in calcium in the perfusion media were studied on ss-adrenergic coupling in isolated hearts from 3 different transgenic mice: cardiac-specific overexpressed alpha(1) subunit of L-type calcium channel, overexpressed Galpha(q), and phospholamban knockout. Isolated hearts from all 3 models, when studied at [Ca(2+)] of 2 mmol/L in the perfusate, showed the usual blunted or no response to ss-adrenergic stimulation. Lowering [Ca(2+)] to 0.75 to 1.5 mmol/L unloaded the hearts of calcium and restored to nearly normal the responsiveness to ss-agonist stimulation.
FinFET-a self-aligned double-gate MOSFET scalable to 20 nm (2000)

MOSFETs with gate length down to 17 nm are reported. To suppress the short channel effect, a novel self-aligned double-gate MOSFET, FinFET, is proposed. By using boron-doped Si/sub 0.4/Ge/sub 0.6/ as a gate material, the desired threshold voltage was achieved for the ultrathin body device. The quasiplanar nature of this new variant of the vertical double-gate MOSFETs can be fabricated relatively easily using the conventional planar MOSFET process technologies.
Inorganic polyphosphate: toward making a forgotten polymer unforgettable (1995)

Pursuit of the enzymes that make and degrade poly P has provided analytic reagents which confirm the ubiquity of poly P in microbes and animals and provide reliable means for measuring very low concentrations. Many distinctive functions appear likely for poly P, depending on its abundance, chain length, biologic source, and subcellular location. These include being an energy supply and ATP substitute, a reservoir for Pi, a chelator of metals, a buffer against alkali, a channel for DNA entry, a cell capsule and, of major interest, a regulator of responses to stresses and adjustments for survival in the stationary phase of culture growth and development. Whether microbe or human, we depend on adaptations in the stationary phase, which is really a dynamic phase of life. Much attention has been focused on the early and reproductive phases of organisms, which are rather brief intervals of rapid growth, but more concern needs to be given to the extensive period of maturity. Survival of microbial species depends on being able to manage in the stationary phase. In view of the universality and complexity of basic biochemical mechanisms, it would be surprising if some of the variety of poly P functions observed in microorganisms did not apply to aspects of human growth and development, such as aging and the aberrations of disease. Of theoretical interest regarding poly P is its antiquity in prebiotic evolution, which along with its high energy and phosphate content make it a plausible precursor to RNA, DNA, and proteins. Practical interest in poly P includes many industrial applications, among which is its use in the microbial depollution of P1 in marine environments.
Stearoyl‐CoA desaturase as a new drug target for obesity treatment (2005)

Stearoyl-CoA desaturase (SCD), the rate-limiting enzyme in monounsaturated fatty acid synthesis, has recently been shown to be the critical control point regulating hepatic lipogenesis and lipid oxidation. As several manifestations of the metabolic syndrome and type 2 diabetes mellitus are associated with alterations in intracellular lipid partitioning, we propose that SCD1 may be a potential therapeutic target in the treatment of obesity and the metabolic syndrome. In support of this notion, we have shown that SCD1-deficient mice have increased energy expenditure, reduced body adiposity, increased insulin sensitivity and are resistant to diet-induced obesity and liver steatosis. Furthermore, SCD1 was found to be specifically repressed during leptin-mediated weight loss, and leptin-deficient ob/ob mice lacking SCD1 showed marked correction of the hypometabolic phenotype and hepatic steatosis. Much evidence indicates that the direct anti-steatotic effect of SCD1 deficiency stems from increased fatty acid oxidation and decreased lipid synthesis. All of these findings reveal that pharmacological manipulation of SCD activity might be of benefit in the treatment of obesity, diabetes, liver steatosis and other diseases of the metabolic syndrome.
Using Aptamers for Cancer Biomarker Discovery (2013)

Aptamers are single-stranded synthetic DNA- or RNA-based oligonucleotides that fold into various shapes to bind to a specific target, which includes proteins, metals, and molecules. Aptamers have high affinity and high specificity that are comparable to that of antibodies. They are obtained using iterative method, called (Systematic Evolution of Ligands by Exponential Enrichment) SELEX and cell-based SELEX (cell-SELEX). Aptamers can be paired with recent advances in nanotechnology, microarray, microfluidics, and other technologies for applications in clinical medicine. One particular area that aptamers can shed a light on is biomarker discovery. Biomarkers are important in diagnosis and treatment of cancer. In this paper, we will describe ways in which aptamers can be used to discover biomarkers for cancer diagnosis and therapeutics.