gebhart/patrepeval huggingface dataset:
Modulation of ethylnitrosourea-induced toxicity and mutagenicity in human cells by O6-benzylguanine. (1992)

We have examined the contributions of O6-alkylguanine-DNA alkyl-transferase (AGT) and nucleotide excision repair to the protection of human cells from the toxic and mutagenic effects of ethylnitrosourea. Three human lymphoblastoid cell lines were used: one which possesses both of these DNA repair pathways; one derived from a xeroderma pigmentosum complementation group A patient, which expresses AGT but is deficient in nucleotide excision repair; and a third which does not express AGT but is capable of excision repair. The level of active AGT in the cells was further modulated with the use of the AGT inhibitor, O6-benzylguanine. These cells were exposed to ethylnitrosourea in both the presence and absence of O6-benzylguanine, and population survival, growth, and mutagenesis at the hypoxanthine-guanine phosphoribosyl-transferase locus were measured. The results for all three measurements indicated that the lack of either AGT or nucleotide excision repair significantly impairs the ability of human cells to withstand DNA ethylation damage. Furthermore, the inhibition of AGT in xeroderma pigmentosum group A cells did not increase toxicity or mutagenicity, suggesting that AGT and nucleotide excision repair cooperate in the removal of DNA ethyl adducts. Related studies in our laboratory have shown that AGT and nucleotide excision repair are both necessary for the efficient removal of O6-ethyldeoxyguanosine.
Biomimetic coprecipitation of calcium phosphate and bovine serum albumin on titanium alloy (2001)

Titanium alloy implants were precoated biomimetically with a thin and dense layer of calcium phosphate and then incubated either in a supersaturated solution of calcium phosphate or in phosphate-buffered saline, each containing bovine serum albumin (BSA) at various concentrations, under physiological conditions for 48 h. Coated implants then underwent scanning electron microscopy, immunohistochemical evaluation, Fourier transform infrared spectroscopy, and X-ray diffraction. The quantity of BSA taken up by coatings and the kinetics of protein release were monitored colorimetrically. In coatings prepared by the coprecipitation of calcium phosphate and BSA, protein had become incorporated into the mineral crystal latticework. With increasing BSA concentration, matrices decreased in thickness, became more dense, showed lower crystallinity, and underwent a change in crystal geometry. The octacalcium phosphate structure manifested in the absence of protein was gradually transformed into a carbonated apatite form. Preformed mineral coatings became only superficially mantled with a layer of BSA, and the morphology of the mineral matrices themselves remained unchanged. At equivalent protein concentrations, coatings prepared by the coprecipitation of calcium phosphate released only a minute fraction of its protein component under physiological conditions, whereas preformed mineral matrices showed a "burst" release of their associated protein within a single 2-h period. The biomimetic coating can be a carrier for osteoinductive agents.
SIEGE: Smoking Induced Epithelial Gene Expression Database (2004)

The SIEGE (Smoking Induced Epithelial Gene Expression) database is a clinical resource for compiling and analyzing gene expression data from epithelial cells of the human intra-thoracic airway. This database supports a translational research study whose goal is to profile the changes in airway gene expression that are induced by cigarette smoke. RNA is isolated from airway epithelium obtained at bronchoscopy from current-, former- and never-smoker subjects, and hybridized to Affymetrix HG-U133A Genechips, which measure the level of expression of approximately 22,500 human transcripts. The microarray data generated along with relevant patient information is uploaded to SIEGE by study administrators using the database's web interface, found at http://pulm.bumc.bu.edu/siegeDB. PERL-coded scripts integrated with SIEGE perform various quality control functions including the processing, filtering and formatting of stored data. The R statistical package is used to import database expression values and execute a number of statistical analyses including t-tests, correlation coefficients and hierarchical clustering. Values from all statistical analyses can be queried through CGI-based tools and web forms found on the 'Search' section of the database website. Query results are embedded with graphical capabilities as well as with links to other databases containing valuable gene resources, including Entrez Gene, GO, Biocarta, GeneCards, dbSNP and the NCBI Map Viewer.
Activation of human endothelial cell-type plasminogen activator inhibitor (PAI-1) by negatively charged phospholipids. (1987)

The endothelial cell-type plasminogen activator inhibitor (PAI-1) may exist in an inactive, latent form that can be converted into an active form upon treatment of the protein with denaturants, such as sodium dodecyl sulfate, guanidine HCl, or urea. The present paper demonstrates that latent PAI-1 can be activated by lipid vesicles containing the negatively charged phospholipids phosphatidylserine (PS) or phosphatidylinositol. The presence of a net negative charge on the phospholipid headgroup is essential for activation, since lipid vesicles consisting exclusively of zwitterionic phospholipids, such as phosphatidylcholine and phosphatidylethanolamine, do not activate PAI-1. In the presence of PS vesicles, PAI-1 inhibited tissue-type plasminogen activator 50-fold more effectively than in the absence of phospholipids, whereas sodium dodecyl sulfate enhanced PAI-1 activity by 25-fold. In mixed phospholipid vesicles containing PS and phosphatidylcholine in various molar ratios, the extent of PAI-1 activation was directly related to the PS content of the phospholipid membrane. Ca2+ ions interfered with the inhibitory activity of PS-activated PAI-1, suggesting that Ca2+ ions may regulate PAI-1 activity in the presence of negatively charged phospholipids. An important consequence of these findings is that, as in blood coagulation, negatively charged phospholipids may play an important regulatory role in controlling the fibrinolytic system by activating an inhibitor of tissue-type plasminogen activator.
Electrical Stimulation with Pt Electrodes: II-Estimation of Maximum Surface Redox (Theoretical Non-Gassing) Limits (1977)

The maximum, biphasically applied charge which can be injected without electrolyzing water has been determined for Pt electrodes in simulated cerebral spinal fluid at 37°C. Electrolysis of water would lead to gas bubble formation, which is thought to be harmful. The experimental method involved the use of electrical transients. With lead (anodic faist) electrodes, the theoretical non-gassing limit is 300 ±20 μC/real cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , independent of current density in the range of ±50 to ±450 mA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . For lag (cathodic first) electrodes, the theoretical non-gassing limit is 350 ±50 μC/real cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> over the same current density range. In both cases, only part of the additional charge beyond these limits results in water electrolysis. Microscopic observations of bubble formation indicate that these limits are conservative. These limits are sufficiently large for most purposes; they do not restrict the use of Pt electrodes in stimulation.
311 CATTLE SEX REGULATION BY SEPARATION OF X AND Y SPERMATOZOA – PRELIMINARY RESULTS OF FIELD EXPERIMENT IN POLAND (2004)

The only reliable and relatively fast method of sex regulation in cattle is X and Y sperm high-speed sorting by flow cytometry. In October 2003 a field experiment started in Poland. The aim of the experiment was to examine the efficiency of sperm sexing and the fertility rate in field conditions. The semen of three Holstein bulls was used for the experiment. The semen was sexed and frozen according to modified XY, Inc. (Fort Collins, CO, USA) method. Only the X-fraction of spermatozoa was sorted and frozen. Sexing was performed at a speed of 15–20 × 106 spermatozoa/h and frozen in doses of 2.5 × 106 spermatozoa/straw. Progressive motility of spermatozoa was 90–95% immediately after sorting and 50–70% after freezeing/thawing for all three bulls. The X-fraction sorting purity was checked by re-analysis and it ranged from 90% to 96%. In total, 316 inseminations at 10 farms were performed up to June 2004. Fertility data of 178 inseminations were collected by ultrasonographic (USG) examination during the same time. Average fertility rate was 37.08%. However, significant variations of fertility rates were observed between farms: it ranged from 22.22% to 84.21%. Four calves, all females, were born after insemination with the X-fraction until June 2004. The experiment will continue.
Further investigation of the epitope recognized by the new monoclonal antibody 2C9 (2003)

The target molecule of the 2C9 monoclonal antibody is PSMA, pointing to future diagnostic and therapeutic applications.
The human skeletal alpha-actin gene is regulated by a muscle-specific enhancer that binds three nuclear factors. (1992)

The tissue-specific distal promoter of the human skeletal alpha-actin gene (-1282 to -708) induces transcription in myogenic cells approximately 10-fold and, with the most proximal promoter domain (-153 to -87), it synergistically increases transcription 100-fold (Muscat and Kedes 1987). We report here that it is a short fragment of the distal promoter, the distal regulatory element (DRE) from -1282 to -1177 that functions as a muscle-specific, composite enhancer. An internal deletion in the DRE (delta -1282/-1151) in the context of the full-length 2000 bp promoter, resulted in a 10-fold reduction in transcription. Three distinct nuclear proteins, DRF-1, DRF-2, and DRF-3, interact specifically with the DRE between positions -1260 and -1193. A site specific mutation that abolishes DRF-2 binding also results in a 10-fold reduction in transcriptional activity. The DRF-2 nuclear protein has characteristics similar to those of the muscle-specific regulatory factor, MEF-2 (Buskin and Hauschka 1989; Gossett et al., 1989). Like the MEF-2 binding site in the muscle creatine kinase enhancer, the critical DRF-2 binding site is also an A/T-rich sequence element. The DRF-2 nuclear protein binds equally well to the MCK MEF-2 binding site and to the A/T-rich regulatory element of the skeletal muscle fast-twitch troponin C gene (Gahlmann and Kedes 1990). Furthermore, this troponin C site competes in vivo for DRF-2 driven expression of the skeletal alpha-actin gene in C2 cells. The DRF-2 site alone, however, does not activate transcription in muscle cells when linked to the SV40 promoter. We conclude that the DRF-2 binding element is a MEF-2 binding site that is required but insufficient for regulation of muscle-specific skeletal alpha-actin gene expression by the DRE. Thus, muscle-specific regulation of the human skeletal alpha-actin gene appears to require interactions between the other elements of the composite DRE enhancer with the protein:DNA complex formed by DRF-2.
Prostate Cancer–Associated Gene Expression Alterations Determined from Needle Biopsies (2009)

Assessments of tumor phenotypes based on gene expression for treatment stratification and drug targeting of oncogenic alterations may best be ascertained using biopsy-based analyses where the effects of ischemia do not complicate interpretation.
Hydrolysis of Phosphatidyl Ethanolamine by Cell Fractions ofStreptococcus lactis (1983)

From the findings that cell fractions (membrane and cytoplasm) of Streptococcus lactis 527 hydrolysed phosphatidyl ethanolamine to monoglyceride, diglyceride and fatty acids without accumulating lysophosphatidyl ethanolamine, the main contribution of phospholipase C to the enzymatic degradation was presumed. Although the fractions have strong activity toward lysophosphatidyl ethanolamine, the contribution of lysophospholipase was ruled out. Phospholipase A showing activity at optimum pH 5 was considered to be bound to the cell membrane and was different from the enzyme showing activity at pH 9 in the influences of Ca2+ addition, cholate addition, and heating at the optimum pH. In bacteria lysis during lactic acid fermentation of milk, phospholipases C and A, and lipase in spheroplasts of S. lactis were presumed to mainly contribute to degradation of phosphatidyl ethanolamine in the cell membrane.
Reduction of 14–16 kDa allergenic proteins in transgenic rice plants by antisense gene (1996)

An antisense gene strategy was applied to suppress the 14-16 kDa allergen gene expression in maturing rice seeds. Gene constructs producing antisense RNAs of the 16 kDa allergen under the control of some rice seed-specific promoters were introduced into rice by electroporation. Immunoblot and RNA blot analyses of the seeds from the transgenic rice plants using the allergen-specific monoclonal antibody and a sequence-specific antisense RNA probe demonstrated that the 14-16 kDa allergen proteins and their transcripts of the seeds from several transgenic lines were present in much lower in amounts than those of the seeds from parental wild-type rice. The high levels of reduction observed were stably inherited in at least three generations.
Experimental Infection of Mice with Bacillus cereus: Studies of Pathogenesis and Pathologic Changes (1967)

Journal Article Experimental Infection of Mice with Bacillus cereus: Studies of Pathogenesis and Pathologic Changes Get access Kenneth L. Burdon, Kenneth L. Burdon From the Departments of Microbiology and Pathology, Baylor University College of Medicine, Houston, Texas 77025 Search for other works by this author on: Oxford Academic PubMed Google Scholar Joyce S. Davis, Joyce S. Davis From the Departments of Microbiology and Pathology, Baylor University College of Medicine, Houston, Texas 77025 Search for other works by this author on: Oxford Academic PubMed Google Scholar Reuben D. Wende Reuben D. Wende From the Departments of Microbiology and Pathology, Baylor University College of Medicine, Houston, Texas 77025 Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 117, Issue 4, October 1967, Pages 307–316, https://doi.org/10.1093/infdis/117.4.307 Published: 01 October 1967 Article history Received: 09 March 1967 Published: 01 October 1967
The potential for LASER-induced chlorophyll fluorescence measurements in wheat (2003)

Sensors for the detection of the nutrient status of crop stands are essential for the online-approach in a site-specific nitrogen fertilisation strategy. An active sensor was developed to measure the laser-induced chlorophyll fluorescence. The intensity of the fluorescence at 690 nm (F 690) and 730 nm (F 730) is dependent on the chlorophyll content. Therefore the vegetation index ratio (F 690/F 730) is a measure for the nitrogen uptake of the plants. The ratio decreases with increasing nitrogen uptake. The relation between ratio and nitrogen uptake proved to be dependent on the cultivar. There was no influence of soil reflection on the measurements. Active sensors can be used under nearly all weather conditions.
Defects in Type III Secretion Correlate with Internalization of Pseudomonas aeruginosa by Epithelial Cells (1998)

Previous characterization of Pseudomonas aeruginosa clinical isolates has demonstrated an inverse correlation between cytotoxicity and internalization by epithelial cells. To further investigate this relationship, we tested PA103, a cytotoxic P. aeruginosa strain, and 33 isogenic noncytotoxic transposon mutants for internalization by Madin-Darby canine kidney cells. The majority of the mutants were not internalized, demonstrating that an inverse correlation between cytotoxicity and bacterial uptake by epithelial cells is not absolute. Six of the noncytotoxic mutants, however, demonstrated measurable levels of internalization by standard aminoglycoside exclusion assays even though internalization of wild-type strain PA103 was not detectable. All six had evidence of protein secretion defects involving two proteins, a 40-kDa protein and a 32-kDa protein. These proteins, designated PepB (for Pseudomonas exoprotein B) and PepD, respectively, each had characteristics of type III transported proteins. In addition, nucleotide sequencing studies demonstrated that PepB and PepD are homologs of YopB and YopD, respectively, type III secreted proteins of Yersinia spp. necessary for the translocation of effector molecules into the cytoplasmic compartment of eukaryotic cells. Thus, while many mutations in PA103 result in loss of cytotoxicity without an appreciable increase in internalization, defects in transport of type III secretion proteins PepB and PepD correlate with both loss of cytotoxicity and gain of internalization. These results are consistent with type III secretion of an inhibitor of internalization that requires PepB and PepD for translocation into the host cell.
Microbial Biofilms: from Ecology to Molecular Genetics (2000)

Biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. Despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. Furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies (clusters of cells) relative to one another, has profound implications for the function of these complex communities. Numerous new experimental approaches and methodologies have been developed in order to explore metabolic interactions, phylogenetic groupings, and competition among members of the biofilm. To complement this broad view of biofilm ecology, individual organisms have been studied using molecular genetics in order to identify the genes required for biofilm development and to dissect the regulatory pathways that control the plankton-to-biofilm transition. These molecular genetic studies have led to the emergence of the concept of biofilm formation as a novel system for the study of bacterial development. The recent explosion in the field of biofilm research has led to exciting progress in the development of new technologies for studying these communities, advanced our understanding of the ecological significance of surface-attached bacteria, and provided new insights into the molecular genetic basis of biofilm development.
A Factorization Based Self-Calibration for Radially Symmetric Cameras (2006)

The paper proposes a novel approach for planar self-calibration of radially symmetric cameras. We model these camera images using notions of distortion center and concentric distortion circles around it. The rays corresponding to pixels lying on a single distortion circle form a right circular cone. Each of these cones is associated with two unknowns; optical center and focal length (opening angle). In the central case, we consider all distortion circles to have the same optical center, whereas in the non-central case they have different optical centers lying on the same optical axis. Based on this model we provide a factorization based self-calibration algorithm for planar scenes from dense image matches. Our formulation provides a rich set of constraints to validate the correctness of the distortion center. We also propose possible extensions of this algorithm in terms of non-planar scenes, non-unit aspect ratio and multi- view constraints. Experimental results are shown.
Clinical Characteristics of a Cohort of 244 Patients with Congenital Adrenal Hyperplasia (2012)

Poor hormonal control and adverse outcomes are common in CAH, necessitating new treatments. Routine monitoring of classic children should include measuring BP and plasma renin activity. Osteoporosis prophylaxis and TART screening should begin during childhood. A longitudinal study is under way.
Some New Results in the Investigation of the Middle Atmosphere from Space Using the Daytime Horizon Scanning Method (1989)

The results of the restoration of the optical parameters of the El Chichon aerosol cloud at Lambda 2.2 micron are presented. The eight channel teleradiometer FAZA for visible and near infrared spectral regions is described in some detail. Mathematical aspects of data processing for the ill-posed problems are discussed. The results of the restoration of the volume emission rate of the molecular oxygen on Lambda 1.27 micron in the middle atmosphere and of the aerosol on Lambda 0.84 micron are presented.
The synthetic methodology of nonracemic glycidol and related 2,3-epoxy alcohols (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe synthetic methodology of nonracemic glycidol and related 2,3-epoxy alcoholsRobert M. HansonCite this: Chem. Rev. 1991, 91, 4, 437–475Publication Date (Print):June 1, 1991Publication History Published online1 May 2002Published inissue 1 June 1991https://pubs.acs.org/doi/10.1021/cr00004a001https://doi.org/10.1021/cr00004a001research-articleACS PublicationsRequest reuse permissionsArticle Views3005Altmetric-Citations339LEARN 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
Aquatic debris monitoring using smartphone-based robotic sensors (2014)

Monitoring aquatic debris is of great interest to the ecosystems, marine life, human health, and water transport. This paper presents the design and implementation of SOAR - a vision-based surveillance robot system that integrates an off-the-shelf Android smartphone and a gliding robotic fish for debris monitoring. SOAR features real-time debris detection and coverage-based rotation scheduling algorithms. The image processing algorithms for debris detection are specifically designed to address the unique challenges in aquatic environments. The rotation scheduling algorithm provides effective coverage of sporadic debris arrivals despite camera's limited angular view. Moreover, SOAR is able to dynamically offload computation-intensive processing tasks to the cloud for battery power conservation. We have implemented a SOAR prototype and conducted extensive experimental evaluation. The results show that SOAR can accurately detect debris in the presence of various environment and system dynamics, and the rotation scheduling algorithm enables SOAR to capture debris arrivals with reduced energy consumption.