gebhart/patrepeval huggingface dataset:
The anticarcinogen 3,3′‐diindolylmethane is an inhibitor of cytochrome P‐450 (1995)

Dietary indole-3-carbinol inhibits carcinogenesis in rodents and trout. Several mechanisms of inhibition may exist. We reported previously that 3,3'-diindolylmethane, an in vivo derivative of indole-3-carbinol, is a potent noncompetitive inhibitor of trout cytochrome P450 (CYP) 1A-dependent ethoxyresorufin O-deethylase with Ki values in the low micromolar range. We now report a similar potent inhibition by 3,3'-diindolylmethane of rat and human CYP1A1, human CYP1A2, and rat CYP2B1 using various CYP-specific or preferential activity assays. 3,3'-Diindolylmethane also inhibited in vitro CYP-mediated metabolism of the ubiquitous food contaminant and potent hepatocarcinogen, aflatoxin B1. There was no inhibition of cytochrome c reductase. In addition, we found 3,3'-diindolylmethane to be a substrate for rat hepatic microsomal monooxygenase(s) and tentatively identified a monohydroxylated metabolite. These observations indicate that 3,3'-diindolylmethane can inhibit the catalytic activities of a range of CYP isoforms from lower and higher vertebrates in vitro. This broadly based inhibition of CYP-mediated activation of procarcinogens may be an indole-3-carbinol anticarcinogenic mechanism applicable to all species, including humans.
Multiplex target capture with double-stranded DNA probes (2013)

Target enrichment technologies utilize single-stranded oligonucleotide probes to capture candidate genomic regions from a DNA sample before sequencing. We describe target capture using double-stranded probes, which consist of single-stranded, complementary long padlock probes (cLPPs), each selectively capturing one strand of a genomic target through circularization. Using two probes per target increases sensitivity for variant detection and cLPPs are easily produced by PCR at low cost. Additionally, we introduce an approach for generating capture libraries with uniformly randomized template orientations. This facilitates bidirectional sequencing of both the sense and antisense template strands during one paired-end read, which maximizes target coverage.
Imaging the Condensation and Evaporation of Molecularly Thin Films of Water with Nanometer Resolution (1995)

The polarization force between an electrically charged atomic force microscope tip and a substrate has been used to follow the processes of condensation and evaporation of a monolayer of water on mica at room temperature. Condensation proceeds in two distinct structural phases. Up to about 25 percent humidity, the water film grows by forming two-dimensional clusters of less than a few 1000 angstroms in diameter. Above about 25 percent humidity, a second phase grows, forming large two-dimensional islands with geometrical shapes in epitaxial relation with the underlaying mica lattice. The growth of this second water phase is completed when the humidity reaches about 45 percent. The reverse process of evaporation has also been imaged.
Application of layered space-time processing to ultrawideband communication (2004)

Ultra-wideband (UWB) signals use extremely short duration pulses (on the order of hundreds of picoseconds) for transferring information. This makes it the technology of choice for high-speed short-range communications in dense multipath channels. In this paper we analyze the usefulness of using Layered Space-Time Processing over a UWB system. VBLAST is one such approach proposed to increase spectral efficiency using multi-input multi-output channels. We propose the exploitation of the large number of resolvable multipath. components in a UWB environment to achieve similar spectral efficiency gains. In this paper we investigate the bit error rate versus spectral efficiency tradeoff applying the VBLAST concept to a UWB system.
Infection with an Avirulent phoP Mutant of Neisseria meningitidis Confers Broad Cross-Reactive Immunity (2003)

Successful vaccines against serogroup A and C meningococcal strains have been developed, but current serogroup B vaccines provide protection against only a limited range of strains. The ideal meningococcal vaccine would provide cross-reactive immunity against the variety of strains that may be encountered in any community, but it is unclear whether the meningococcus possesses immune targets that have the necessary level of cross-reactivity. We have generated a phoP mutant of the meningococcus by allele exchange. PhoP is a component of a two-component regulatory system which in other bacteria is an important regulator of virulence gene expression. Inactivation of the PhoP-PhoQ system in Salmonella leads to avirulence, and phoP mutants have been shown to confer protection against virulent challenge. These mutants have been examined as potential live attenuated vaccines. We here show that a phoP mutant of the meningococcus is avirulent in a mouse model of infection. Moreover, infection of mice with the phoP mutant stimulated a bactericidal immune response that not only killed the infecting strain but also showed cross-reactive bactericidal activity against a range of strains with different serogroup, serotype, and serosubtyping antigens. Sera from the mutant-infected mice contained immunoglobulin G that bound to the surface of a range of meningococcal strains and mediated opsonophagocytosis of meningococci by human phagocytic cells. The meningococcal phoP mutant is thus a candidate live, attenuated vaccine strain and may also be used to identify cross-reactive protective antigens in the meningococcus.
DNA triple helix stabilisation by a naphthylquinoline dimer (1999)

We have used DNase I footprinting to examine the effect of a novel naphthylquinoline dimer, designed as a triplex-specific bis-intercalator, on the stability of intermolecular DNA triplexes. We find that this compound efficiently promotes triplex formation between the 9-mer oligonucleotide 5'-TTTTTTCTT and its oligopurine duplex target at concentrations as low as 0.1 microM, enhancing the triplex stability by at least 1000-fold. This compound, which is the first reported example of a triplex bis-intercalator, is about 30 times more potent than the simple monofunctional ligand.
Cloning of the Arabidopsis ent -kaurene oxidase gene GA 3 (1998)

The ga3 mutant of Arabidopsis is a gibberellin-responsive dwarf. We present data showing that the ga3-1 mutant is deficient in ent-kaurene oxidase activity, the first cytochrome P450-mediated step in the gibberellin biosynthetic pathway. By using a combination of conventional map-based cloning and random sequencing we identified a putative cytochrome P450 gene mapping to the same location as GA3. Relative to the progenitor line, two ga3 mutant alleles contained single base changes generating in-frame stop codons in the predicted amino acid sequence of the P450. A genomic clone spanning the P450 locus complemented the ga3-2 mutant. The deduced GA3 protein defines an additional class of cytochrome P450 enzymes. The GA3 gene was expressed in all tissues examined, RNA abundance being highest in inflorescence tissue.
Petri Net Modeling and Wafer Sojourn Time Analysis of Single-Arm Cluster Tools With Residency Time Constraints and Activity Time Variation (2012)

With wafer residency time constraints, it is crucial to schedule a cluster tool in semiconductor fabrication such that the wafer sojourn time in a processing module is in a given range. However, because of the activity time variation in wafer fabrication by cluster tools, a feasible schedule obtained under the assumption of deterministic activity times may become infeasible. To solve this problem, it is critically important to reveal the wafer sojourn time fluctuations with bounded activity time variation. This paper targets at single-arm cluster tools. They are modeled by a Petri net to describe the fabrication processes. Based on the net, a real-time control policy is proposed such that its use offsets the effect of the activity time variation as much as possible. Then, the wafer sojourn time delay is analyzed and analytical expressions are given to calculate the upper bound. With the proposed method, we can check if a given schedule is feasible under bounded activity time variation. Examples are given to show the applications of the research results.
The role of cholesterol in the biosynthesis of β-amyloid. (1999)

Addition of the beta-hydroxy-beta-methylglutaryl-CoA (HmG-CoA) reductase inhibitor lovastatin to human HEK cells transfected with the amyloid precursor protein (APP) reduces intracellular cholesterol/protein ratios by 50%, and markedly inhibits beta-secretase cleavage of newly-synthesized APP. Exogenous water-solubilized cholesterol at 200 microg/ml concentration increases newly synthesized beta-amyloidogenic products four-fold. These intracellular changes are detectable by immunoprecipitation and immunofluorescent labelling. Analyses of the fragments captured from culture medium by an N-terminal anti-beta-amyloid antibody on ProteinChip arrays and detected using surface-enhanced laser desorption/ionization (SELDI) mass spectrometry revealed that culture with cholesterol (200 microg/ml) increased secretion of beta-amyloid 1-40 by 1.8-fold, and increased secretion of beta-amyloid 1-42. Changes in APP processing by cholesterol may mediate the way in which the ApoE4 allele increases risk of developing Alzheimer's disease (AD) in western populations.
Identification of biomarkers for type 2 diabetes and its complications: a bioinformatic approach. (2007)

The long asymptomatic period before the onset of chronic diseases presents opportunities for disease prevention. Many chronic diseases like type 2 diabetes and its complications may be preventable by avoiding factors that trigger the disease process (primary prevention) or by use of therapies that modulate the disease process before the onset of clinical symptoms (secondary prevention). Accurate prediction and identification using biomarkers will be useful for disease prevention and initiation of proactive therapies to those individuals who are most likely to develop the disease. Recent technological advances in genetics, genomics, proteomics, and bioinformatics offer great opportunities for biomarker discovery. In this review, type 2 diabetes and its complications are used as examples discuss pertinent issues related to high throughput biomarker discovery using bioinformatic pathways.
Atlas of pathophysiology (2010)

Contributors and consultants Foreword PART I CENTRAL CONCEPTS * CELLS, HOMEOSTASIS, AND DISEASE * CANCER * INFECTION * GENETICS * FLUIDS AND ELECTROLYTES PART II DISORDERS * CARDIOVASCULAR DISORDERS * RESPIRATORY DISORDERS * NEUROLOGIC DISORDERS * GASTROINTESTINAL DISORDERS * MUSCULOSKELETAL DISORDERS * HEMATOLOGIC DISORDERS * IMMUNOLOGIC DISORDERS * ENDOCRINE DISORDERS * REPRODUCTIVE DISORDERS * RENAL DISORDERS * SKIN DISORDERS * SENSORY DISORDERS APPENDIX TYPES OF CARDIAC ARRHYTHMIAS Glossary Selected references Index
A periodic second harmonic spatial power combining oscillator (1992)

The authors present a periodic second-harmonic spatial power combining oscillator. The power combining is achieved by phase locking the oscillators at the fundamental frequency and combining the second-harmonic power in space through an array of microstrip patch antennas. The effect of moding and multiple device-circuit interaction is investigated. This circuit is planar, and therefore simplifies the design of monolithic circuits, X-band Gunn diodes are used for the purpose of demonstration.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fiber-Optic Biosensors Based on Total Internal-Reflection Fluorescence (1992)

A signal transducer based on Total Internal Reflection Fluorescence has been coupled to three biological sensing elements to form receptor, enzyme and antibody biosensors. The nicotinic acetylcholine receptor biosensor is used to detect agonists and competitive antagonists of the receptor with detection limits for the antagonists, which are comparable to those obtained using radioisotope-labeled ligand binding assays. The acetylcholinesterase biosensor is used to detect anticholinesterases. The detection limit for each analyte depends on its potency as an anticholinesterase. Although compounds such as echothiophate and paraoxon yielded detection limits in the ppb range, the biosensor was not particularly sensitive to compounds such as parathion. An immunosensor is also described which uses antiparathion sera as the biological sensing element and detects parathion in the ppb range.
Genes and Gene Ontologies Common to Airflow Obstruction and Emphysema in the Lungs of Patients with COPD (2011)

Chronic obstructive pulmonary disease (COPD) is a major public health problem with increasing prevalence worldwide. The primary aim of this study was to identify genes and gene ontologies associated with COPD severity. Gene expression profiling was performed on total RNA extracted from lung tissue of 18 former smokers with COPD. Class comparison analysis on mild (n = 9, FEV(1) 80-110% predicted) and moderate (n = 9, FEV(1) 50-60% predicted) COPD patients identified 46 differentially expressed genes (p<0.01), of which 14 genes were technically confirmed by quantitative real-time-PCR. Biological replication in an independent test set of 58 lung samples confirmed the altered expression of ten genes with increasing COPD severity, with eight of these genes (NNMT, THBS1, HLA-DPB1, IGHD, ETS2, ELF1, PTGDS and CYRBD1) being differentially expressed by greater than 1.8 fold between mild and moderate COPD, identifying these as candidate determinants of COPD severity. These genes belonged to ontologies potentially implicated in COPD including angiogenesis, cell migration, proliferation and apoptosis. Our secondary aim was to identify gene ontologies common to airway obstruction, indicated by impaired FEV(1) and KCO. Using gene ontology enrichment analysis we have identified relevant biological and molecular processes including regulation of cell-matrix adhesion, leukocyte activation, cell and substrate adhesion, cell adhesion, angiogenesis, cell activation that are enriched among genes involved in airflow obstruction. Exploring the functional significance of these genes and their gene ontologies will provide clues to molecular changes involved in severity of COPD, which could be developed as targets for therapy or biomarkers for early diagnosis.
Modeling the epidemic of nonalcoholic fatty liver disease demonstrates an exponential increase in burden of disease (2017)

With continued high rates of adult obesity and DM along with an aging population, NAFLD-related liver disease and mortality will increase in the United States. Strategies to slow the growth of NAFLD cases and therapeutic options are necessary to mitigate disease burden. (Hepatology 2018;67:123-133).
Pilot's Associate: a cooperative, knowledge-based system application (1991)

The Pilot's Associate program, a joint effort of the Defense Advanced Research Projects Agency (DARPA) and the US Air Force to build a cooperative, knowledge-based system to help pilots make decisions is described, and the lessons learned are examined. The Pilot's Associate concept developed as a set of cooperating, knowledge-based subsystems: two assessor and two planning subsystems, and a pilot interface. The two assessors, situation assessment and system status, determine the state of the outside world and the aircraft systems, respectively. The two planners, tactics planner and mission planner, react to the dynamic environment by responding to immediate threats and their effects on the prebriefed mission plan. The pilot-vehicle interface subsystem provides the critical connection between the pilot and the rest of the system. The focus is on the air-to-air subsystems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Macrophages in streptozotocin-induced diabetic nephropathy: potential role in renal fibrosis (2004)

Kidney macrophage accumulation is associated with the progression of renal injury and fibrosis in streptozotocin-induced mouse diabetic nephropathy. Elements of the diabetic milieu can stimulate macrophages to promote fibroblast proliferation via IL-1- and PDGF-dependent pathways which may enhance renal fibrosis.
Proinflammatory role of proteinase‐activated receptor‐2 in humans and mice during cutaneous inflammation in vivo (2003)

Proteinase-activated receptor-2 belongs to a new subfamily of G-protein-coupled receptors. Its precise role during inflammation and the underlying mechanisms is still unclear. Our study establishes that PAR-2 plays a direct proinflammatory role during cutaneous inflammation in mice and humans in vivo. In a model of experimentally induced allergic (ACD) and toxic (ICD) contact dermatitis (CD) we show that ear swelling responses, plasma extravasation, and leucocyte adherence were significantly attenuated in PAR-2 null mutant (PAR-2-/-) mice compared with wild-type (PAR-2+/+) mice, especially at early stages. The proinflammatory effects by PAR-2 activation were significantly diminished using nitric oxide-synthase inhibitors, while NF-kappaB and neuropeptides appear to play a minor role in these mechanisms. PAR-2-mediated up-regulation of E-selectin and cell adhesion molecule ICAM-1; enhanced plasma extravasation was observed in humans and mice and of interleukin-6 in mice in vivo. Thus, PAR-2 may be a beneficial therapeutic target for the treatment of inflammatory skin diseases.
Outlook for 157 nm resist design (1999)

We have measured the transparencies of a number of candidate resist materials for 157 nm, with an emphasis on determining which chemical platforms would allow resists to be used at maximum thicknesses while meeting requirements for optical density. Although ideal imaging is usually obtained at an optical density between 0.1 and 0.3 and values in excess of 0.5 can often result in nonvertical wall profiles, we chose to arbitrarily choose 0.4 as the maximum tolerable optical density. Using this analysis, our findings show that all existing commercially available resists would need to be &amp;lt;60 nm thick, whereas specialized hydrocarbon resists could be made ∼100 nm thick, and new resists based on hydrofluorocarbons, siloxanes, and/or silsesquioxanes could be engineered to be used in thicknesses approaching 200 nm. We also assess the tradeoff between these thicknesses and what current information exists regarding defects as a function of resist thickness.
Generation and Mixing of Subfemtoliter Aqueous Droplets On Demand (2009)

We describe a novel method of generating monodisperse subfemtoliter aqueous droplets on demand by means of piezoelectric injection. Droplets with volumes down to 200 aL are generated by this technique. The droplets are injected into a low refractive index perfluorocarbon so that they can be optically trapped. We demonstrate the use of optical tweezers to manipulate and mix droplets. For example, using optical tweezers we bring two droplets, one containing a calcium sensitive dye and the other calcium chloride, into contact. The droplets coalesce with a resulting reaction time of about 1 ms. The monodispersity, manipulability, repeatability, small size, and fast mixing afforded by this system offer many opportunities for nanochemistry and observation of chemical reactions on a molecule-by-molecule basis.
TiGER: A database for tissue-specific gene expression and regulation (2008)

We have developed and made publicly available a database, TiGER, which summarizes and provides large scale data sets for tissue-specific gene expression and regulation in a variety of human tissues. This resource is available at 1.
Microbial generation of (2R,3S)- and (2S,3S)-ethyl 2-benzamidomethyl-3-hydroxybutyrate, a key intermediate in the synthesis of (3S,1′R)-3-(1′-hydroxyethyl)azetidin-2-one (1993)

Microbial reduction of the carbonyl group of the substituted acetoacetate esters 3–6 affords directly, or after Ni-Raney desulfurization, the corresponding enantiomerically pure 3S carbinols of variable diastereoisomeric composition. These compounds are transformed into (3S,1′R)-3-(1′-hydroxyethyl)-azetidin-2-one, a useful intermediate in the synthesis of β-lactam antibiotics.
Geometric precision in noise-free digital images (1989)

A basis for determining the best possible precision for the position of a given object in a digital image is developed. The approach is general, being independent of object-form and providing a performance bound on all position estimation schemes. The central concepts in the development are the locale and total variation of the image function. An easily computed bound for the smallest attainable RSM position estimation error is developed. The best possible estimate is given by the centroids of the locales. The analysis of geometric precision using locales shows how object position-uncertainty depends on the object's position. Visual inspection of the easily generated locale pattern gives a qualitative impression of the spatial distribution of geometric precision. The analytic techniques developed provide avenues for both qualitative and quantitative evaluation of target forms and position estimation schemes in terms of their precision mensuration capabilities.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Eubacterium limosum ameliorates experimental colitis and metabolite of microbe attenuates colonic inflammatory action with increase of mucosal integrity (2006)

E. limosum can ameliorate experimental colonic inflammation. In part, the metabolite of E. limosum, butyrate, increases mucosal integrity and shows anti-inflammatory action modulation of mucosal defense system via TLR4.
Liver fatty acid-binding protein is a new prognostic factor for hepatic resection of colorectal cancer metastases (1999)

L-FABP expression is suitable for use as a new presurgical prognostic factor for patients undergoing hepatic surgery for colorectal cancer metastases.
Automatic generation of production rules for integrity maintenance (1994)

In this article we present an approach to integrity maintenance, consisting of automatically generating production rules for integrity enforcement. Constraints are expressed as particular formulas of Domain Relational Calculus; they are automatically translated into a set of repair actions, encoded as production rules of an active database system. Production rules may be redundant (they enforce the same constraint in different ways) and conflicting (because repairing one constraint may cause the violation of another constraint). Thus, it is necessary to develop techniques for analyzing the properties of the set of active rules and for ensuring that any computation of production rules after any incorrect transaction terminates and produces a consistent database state. Along these guidelines, we describe a specific architecture for constraint definition and enforcement. The components of the architecture include a Rule Generator , for producing all possible repair actions, and a Rule Analyzer and Selector , for producing a collection of production rules such that their execution after an incorrect transaction always terminates in a consistent state (possibly by rolling back the transaction); moreover, the needs of applications are modeled, so that integrity-enforcing rules reach the final state that better represents the original intentions of the transaction's supplier. Specific input from the designer can also drive the process and integrate or modify the rules generated automatically by the method. Experimental results of a prototype implementation of the proposed architecture are also described.