gebhart/patrepeval huggingface dataset:
Rapid Detection of <i>rpoB</i> Gene Mutations Conferring Rifampin Resistance in Mycobacterium tuberculosis (2012)

Multidrug-resistant Mycobacterium tuberculosis strains are widespread and present a challenge to effective treatment of this infection. The need for a low-cost and rapid detection method for clinically relevant mutations in Mycobacterium tuberculosis that confer multidrug resistance is urgent, particularly for developing countries. We report here a novel test that detects the majority of clinically relevant mutations in the beta subunit of the RNA polymerase (rpoB) gene that confer resistance to rifampin (RIF), the treatment of choice for tuberculosis (TB). The test, termed TB ID/R, combines a novel target and temperature-dependent RNase H2-mediated cleavage of blocked DNA primers to initiate isothermal helicase-dependent amplification of a rpoB gene target sequence. Amplified products are detected by probes arrayed on a modified silicon chip that permits visible detection of both RIF-sensitive and RIF-resistant strains of M. tuberculosis. DNA templates of clinically relevant single-nucleotide mutations in the rpoB gene were created to validate the performance of the TB ID/R test. Except for one rare mutation, all mutations were unambiguously detected. Additionally, 11 RIF-sensitive and 25 RIF-resistant clinical isolates were tested by the TB ID/R test, and 35/36 samples were classified correctly (96.2%). This test is being configured in a low-cost test platform to provide rapid diagnosis and drug susceptibility information for TB in the point-of-care setting in the developing world, where the need is acute.
N-methyl-D,L-aspartate-induced growth hormone secretion in barrows: possible mechanisms of action. (1996)

Four experiments were conducted to determine mechanisms by which n-methyl-d,l-aspartate (NMA) increases serum concentrations of growth hormone (GH). Blood samples were collected from barrows every 15 min for 2 h (Exp. 1, 2, and 3) or 3 h (Exp. 4) immediately before and immediately after i.v. treatments. In Exp. 1, barrows (n = 4/treatment) received either .9% saline or 1.25, 2.5, or 5 mg of NMA/kg of BW. The change in circulating GH concentrations was greater (P < .05) for barrows receiving 2.5 mg (by 883%) or 5.0 mg of NMA/kg of BW (by 1,095%) than for those injected with saline. In Exp. 2, barrows (n = 4/treatment) received NMA (2.5 mg/kg of BW) or injections of 1.25 mg of the pure d or pure 1 isomers of NMA/kg of BW. Growth hormone concentrations increased by 177% (P < .025) after NMA treatment and by 245% (P < .01) after injection of the pure d isomer of NMA. The pure 1 isomer of NMA had no effect (P > .1) on GH concentrations. In Exp. 3, barrows received NMA (2.5 mg/kg of BW) 10 min after i.m. injection of saline (n = 7) or ketamine hydrochloride ( n = 8; 19.9 mg/kg of BW), an n-methyl-d-aspartate (NMDA) receptor antagonist. The NMA increased (P < .01) GH concentrations by 289% in saline-pretreated barrows but had no effect (P > .1) on barrows pretreated with ketamine hydrochloride. In Exp. 4, barrows (n = 4/treatment) received NMA 3 h after i.v. pretreatment with antisera to GH-releasing factor (GRF; 154 mL) or no pretreatment. Serum GH concentrations increased by 166% (P < .05) after injection of NMA in barrows receiving no pretreatment. The NMA had no effect (P > .1) on GH concentrations in barrows receiving antisera to GRF. Our results support the concept that NMDA stimulates GRF, and hence GH secretion, by activating an NMDA receptor.
Effects of docosahexaenoic acid and eicosapentaenoic acid on androgen-mediated cell growth and gene expression in LNCaP prostate cancer cells (2001)

There is some epidemiological support for a protective influence of omega-3 fatty acids against prostate cancer. We wanted to explore whether omega-3 polyunsaturated fatty acids such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) can affect androgen receptor function in prostate cancer cells. Our study showed that both DHA and EPA inhibit androgen-stimulated cell growth. Androgenic induction of prostate-specific antigen (PSA) protein was repressed by DHA and EPA in a dose-dependent manner. The mRNA levels of five androgen up-regulated genes, PSA, ornithine decarboxylase, NKX 3.1, immunophilin fkbp 51 and Drg-1, were decreased with DHA treatment in the presence of androgens. Transfection experiments using a DNA vector containing androgen-responsive elements demonstrated that both DHA and EPA could interfere with transactivation activities of the androgen receptor (AR). However, western blot analysis of AR protein showed that DHA and EPA treatments did not change AR expression levels. Interestingly, the proto-oncoprotein c-jun was increased by DHA treatment. A transient transfection found that forced expression of c-jun inhibited AR transactivation activity. Thus, this study found that the inhibitory effects of omega-3 polyunsaturated fatty acids on AR-mediated actions are due, at least in part, to an increase in c-jun protein.
Growth of carbon-doped <i>p</i>-type In<i>x</i>Ga1−<i>x</i>As (0&lt;<i>x</i>≤0.53) by metalorganic chemical vapor deposition (1992)

Carbon doping of InxGa1−xAs grown on GaAs and InP substrates by low-pressure metalorganic chemical vapor deposition (LP-MOCVD) using CCl4 has been investigated for In mole fractions as high as x=0.53. P-type conduction was obtained over the entire composition range studied, with hole concentrations above 1×1020 cm−3 for x&lt;0.12, and as high as 1×1019 cm−3 for In0.53Ga0.47As lattice-matched to InP. These high carbon concentrations were achieved by employing very low V/III ratios and low growth temperatures. The alloy composition was found to be dependent on several growth parameters, including CCl4 partial pressure, V/III ratio, and growth temperature. This may be due to surface reactions (etching) involving chlorine-containing compounds during growth. Samples grown at low temperature (∼500 °C) and lattice matched to InP exhibited an increase in hole concentration upon post-growth annealing.
Updating the QR factorization and the least squares problem (2008)

In this paper we treat the problem of updating the\nQR factorization, with applications to the least\nsquares problem. Algorithms are presented that compute\nthe factorization A1 = Q1 R1, where A1 is the matrix\nA = QR after it has had a number of rows or columns\nadded or deleted. This is achieved by updating the\nfactors Q and R, and we show this can be much faster\nthan computing the factorization of A1 from scratch.\nWe consider algorithms that exploit the Level 3 BLAS\nwhere possible and place no restriction on the dimensions\nof A or the number of rows and columns added or deleted.\nFor some of our algorithms we present Fortran 77\nLAPACK-style code and show the backward error of our\nupdated factors is comparable to the error bounds of the\nQR factorization of A1.
Germinação de sementes de sabiá (Mimosa caesalpiniifolia Benth.) (2007)

The present work had as objective to determine, in laboratory, efficient methods to surpass the dormancy of seeds of ‘sabiá’ (Mimosa caesalpiniifolia Benth), as well as the most adequate substratum, influence of the light and the osmótic potential in the germination of the seeds. To evaluate the effect of different pre-germinative procedures in seeds of ‘sabiá’ with wraps and without wrap, various treatments to break dormancy were applied, After that, using the treatment that provided best result, the influences of the substratum, the light and the osmótico potential in the germination of seeds of ‘sabiá’ was evaluated. The statistical design used was complety randomized, and the data were submitted to the test of Tukey. At the end of the experiment the best results had been the immersion of the seeds without wrap in concentrated sulfuric acid for four and six minutes. The percentage of germination was not influenced by the substrata sand, paper and cotton, however the substratum cotton promoted a larger germination speed. With regard to the osmotic potential, the measure that increased the water restriction in the substratum there was reduction of germination.
ChemInform Abstract: Cyclization Reactions of Nitriles. Part 23. Addition of Active Phenols to Electron Deficient Ethenes Accompanied by Cyclization to 2‐Amino‐4H‐benzo(b)pyrans. (1987)

Abstract The activated phenols (I) as well as 2‐naphthol (IV) react with electron‐deficient alkenes like (II) to yield the 2‐amino‐4H‐benzo(b)pyrans (III) or the 2‐amino‐4H‐naphtho‐(2,1‐b)pyrans (V).
Role of S‐adenosyl‐L‐methionine in liver health and injury† (2007)

S-adenosylmethionine (SAMe) has rapidly moved from being a methyl donor to a key metabolite that regulates hepatocyte growth, death, and differentiation. Biosynthesis of SAMe occurs in all mammalian cells as the first step in methionine catabolism in a reaction catalyzed by methionine adenosyltransferase (MAT). Decreased hepatic SAMe biosynthesis is a consequence of all forms of chronic liver injury. In an animal model of chronic liver SAMe deficiency, the liver is predisposed to further injury and develops spontaneous steatohepatitis and hepatocellular carcinoma. However, impaired SAMe metabolism, which occurs in patients with mutations of glycine N-methyltransferase (GNMT), can also lead to liver injury. This suggest that hepatic SAMe level needs to be maintained within a certain range, and deficiency or excess can both lead to abnormality. SAMe treatment in experimental animal models of liver injury shows hepatoprotective properties. Meta-analyses also show it is effective in patients with cholestatic liver diseases. Recent data show that exogenous SAMe can regulate hepatocyte growth and death, independent of its role as a methyl donor. This raises the question of its mechanism of action when used pharmacologically. Indeed, many of its actions can be recapitulated by methylthioadenosine (MTA), a by-product of SAMe that is not a methyl donor. A better understanding of why liver injury occurs when SAMe homeostasis is perturbed and mechanisms of action of pharmacologic doses of SAMe are essential in defining which patients will benefit from its use.
VANTED: A system for advanced data analysis and visualization in the context of biological networks (2006)

VANTED greatly helps researchers in the analysis and interpretation of biochemical data, and thus is a useful tool for modern biological research. VANTED as a Java Web Start Application including a user guide and example data sets is available free of charge at http://vanted.ipk-gatersleben.de.
Modulation of estrogen receptor mRNA expression by melatonin in MCF-7 human breast cancer cells. (1994)

Melatonin, the hormonal product of the pineal gland, has been shown to inhibit the development of mammary tumors in vivo and the proliferation of MCF-7 human breast cancer cells in vitro by mechanisms not yet identified. However, previous studies have demonstrated that melatonin significantly decreased estrogen-binding activity and the expression of immunoreactive estrogen receptor (ER) in MCF-7 breast cancer cells. To determine the mechanism(s) by which melatonin regulates ER expression in MCF-7 cells, the relationship between the level of steady state ER mRNA and the rate of ER gene transcription were examined in response to melatonin. Physiological concentrations of melatonin decreased steady state levels of ER mRNA expression in a dose- and time-specific manner. This decrease was not dependent upon the presence of estrogen since similar decreases in steady state ER mRNA levels were seen in MCF-7 cells cultured in both complete and estrogen-depleted media. The decreased expression of ER mRNA in response to melatonin appears to be directly related to the suppression of transcription of the ER gene. This regulation is independent of the synthesis of new proteins, as cycloheximide was unable to block the melatonin-induced decrease of steady-state ER mRNA levels. The down-regulation of ER by melatonin appears to not be mediated via a direct interaction with the ER and subsequent feedback on its own expression, since melatonin treatment did not alter the transcriptional regulatory ability of the fully activated wild type ER or a constitutively active hormone-binding domain-deleted ER variant. In addition, the stability of the ER transcript was unaffected by melatonin. Thus, it appears that the antiproliferative actions of this pineal indoleamine are mediated, at least in part, through the suppression of the transcription of the ER gene in MCF-7 human breast cancer cells.
The Use Of Sandwich Hologram Interferometry For Nondestructive Testing Of Nuclear Reactor Components (1982)

Sandwich hologram interferometry was examined for ap-plicability to the nondestructive testing of high pressure nuclear reactor components. A nonnuclear valve was used as a test specimen. While new and unflawed, it was examined and holographically characterized under the stress of pressurization. A flaw was then machined on the inside surface of the valve casing, and the valve was reexamined. This procedure was repeated, deepening the flaw each time, until it was visible as a "chink" in the fringe pattern characteristic of normal valve expansion. From this, a sensitivity limit for interferometric detection of subsurface voids has been established. Cracks were not examined because the difficulty and expense of the simulation techniques did not fit within the scope of this contract.
Telepresence Systems With Automatic Preservation of User Head Height, Local Rotation, and Remote Translation (2006)

Mutually-Immersive Mobile Telepresence uses a teleoperated robotic surrogate to visit remote locations as a substitute for physical travel. Our goal is to recreate to the greatest extent practical, both for the user and the people at the remote location, the sensory experience relevant for face-to-face interactions of the user actually being in the remote location. To enhance immersion for the user, our second-generation system can automatically preserve the head height of the user at the remote location. In order to eliminate loss of immersion due to teleoperation delays, in our third generation system we are eliminating one class of teleoperated mechanical motion by allowing rotations to take place at the user’s location instead of at the remote location. A key component of this is a low-profile synchronous drive base. We also provide a novel natural interface for controlling translational motion at the remote location.
Strain Transfer Analysis of Surface-Bonded MEMS Strain Sensors (2012)

The transmission of strain fields in adhesively bonded MEMS strain sensors is analyzed. In strain sensors that are attached to host structures using adhesive layers such as epoxy, complete strain transfer to the sensor is hindered due to the influence of the adhesive layer on the transfer. This paper presents an analytical model, validated by finite element method simulation, to provide insight and accurate formulation for strain transfer mechanism for bonded sensors. A shear-lag parameter has been introduced to account for the component geometry and properties. The model is capable of predicting the strain transmission ratio through a sensor gauge factor, and it clearly establishes the effects of the flexibility, length, and thickness of the adhesive layer and MEMS sensor substrate. Finally, modifications to sensor substrates, by the implementation of micromachined tapered edges and trench etching, are proposed in order to increase the strain transmission ratio. It has been found, for the selected case study, that the sensor sensitivity could be enhanced by up to 30%. This work on bonding analysis is applicable for performance prediction and calibration in sensor systems design.
Synthesis of New <i>C(2)</i>‐Substituted <i>gluco</i>‐Configured Tetrahydroimidazopyridines and Their Evaluation as Glucosidase Inhibitors (2005)

Abstract The gluco ‐configured C(2) ‐substituted tetrahydroimidazopyridines 8 – 14 were prepared and tested as inhibitors of the β ‐glucosidases from Caldocellum saccharolyticum and from sweet almonds, and of the α ‐glucosidase from brewer's yeast. All new imidazopyridines are nanomolar inhibitors of the β ‐glucosidases and micromolar inhibitors of the α ‐glucosidase. The 3‐phenylpropyl derivative 14 proved the strongest inhibitor of the Caldocellum β ‐glucosidase ( K i = 0.9 n M ), only slightly weaker than the known 2‐phenylethyl analogue 7 , and the propyl derivative 13 is the strongest inhibitor of the sweet almond β ‐glucosidases ( K i = 3.2 n M ), again slightly weaker than 7 . There is no strong dependence of the inhibition on the nature of the C(2) ‐substituent and no clear correlation between the inhibitory strength of the known manno ‐configured imidazopyridines 2 – 6 and the gluco ‐analogues 8 – 12 . While most manno ‐imidazopyridines are competitive inhibitors, the gluco ‐analogues proved non‐competitive inhibitors of the Caldocellum β ‐glucosidase and mixed‐type or partial mixed‐type inhibitors of the sweet almond β ‐glucosidases.
A comprehensive review on proppant technologies (2015)

The main function of traditional proppants is to provide and maintain conductive fractures during well production where proppants should meet closure stress requirement and show resistance to diagenesis under downhole conditions. Many different proppants have been developed in the oil & gas industry, with various types, sizes, shapes, and applications. While most proppants are simply made of silica or ceramics, advanced proppants like ultra-lightweight proppant is also desirable since it reduces proppant settling and requires low viscosity fluids to transport. Additionally, multifunctional proppants may be used as a crude way to detect hydraulic fracture geometry or as matrices to slowly release downhole chemical additives, besides their basic function of maintaining conductive hydraulic fractures. Different from the conventional approach where proppant is pumped downhole in frac fluids, a revolutionary way to generate in-situ spherical proppants has been reported recently. This paper presents a comprehensive review of over 100 papers published in the past several decades on the subject. The objectives of this review study are to provide an overview of current proppant technologies, including different types, compositions, and shapes of proppants, new technologies to pump and organize proppants downhole such as channel fracturing, and also in-situ proppant generation. Finally, the paper sheds light on the current challenges and emphasizes needs for new proppant development for unconventional resources.
Synthesis and characterization of electrically conducting polyaniline–TCNE complexes (1989)

Abstract Polyaniline–tetracyanoethylene (TCNE) complexes can be synthesized either from emeraldine base or emeraldine hydrochloride by a relatively simple method. The complexes demonstrate greater stability than the emeraldine hydrochloride at elevated temperatures and under high current densities. The electrical conductivity of the complexes synthesized from emeraldine base can be varied from < 10 −6 to 0.2 S/cm by varying the amount of TCNE incorporated. The complexes synthesized from emeraldine hydrochloride are slightly more conductive than the starting emeraldine hydrochloride. In both types of complexes, it appears that electron transfer between the polyaniline and TCNE has occurred resulting in the formation of some positively charged polyaniline nitrogen and TCNE anions.
Glycopeptide dendrimers. Part II (2007)

Glycopeptide dendrimers are regularly branched structures containing both carbohydrates and peptides. Various types of these compounds differing in composition and structure are mentioned, together with their practical use spanning from catalysis, transport vehicles to synthetic vaccines. This Part II (for Part I see JeZek J, et al., J. Pept. Sci. 2008; 14: 2-43) covers linear oligomers with variable valency (brush dendrimers, comb dendrimers), sequential oligopeptide carriers SOCn-I and SOCn-II, chitosan-based dendrimers, and brush dendrimers. Other types of glycopeptide dendrimers are self-immolative dendrimers (cascade release dendrimers, domino dendrimers), dendrimers containing omega-amino acids (Gly, beta-Ala, gamma-Abu and epsilon-aminohexanoic acid), etc. Microwave-assisted synthesis of dendrimers and libraries of glycopeptides and glycopeptide dendrimers are also included. Characterization of dendrimers by electromigration methods, mass spectrometry, and time-resolved and nonlinear optical spectroscopy, etc. plays an important role in purity assessment and structure characterization. Physicochemical properties of dendrimers including chirality are given. Stability of dendrimers, their biocompatibility and toxicity are reviewed. Finally, biomedical applications of dendrimers including imaging agents (contrast agents), site-specific drug delivery systems, artificial viruses, synthetic antibacterial, antiviral, and anticancer vaccines, inhibitors of cell surface protein-carbohydrate interactions, intervention with bacterial adhesion, etc. are given. Glycopeptide dendrimers were used also for studying recognition processes, as diagnostics and mimetics, for complexation of different cations, for therapeutic purposes, as immunodiagnostics, and in drug design.
On-line incremental routing for interconnect fault tolerance in FPGAs minus the router (2002)

In this paper we present a Fault Tolerant (FT) technique for programmable interconnect on Field Programmable Gate Arrays (FPGAs). Our on-line strategy uses incremental reconfiguration capabilities of FPGAs to avoid faults, and the main advantage of our technique is that it does not require a router at the time FT reconfiguration is performed. Our algorithm generates precompiled FT partial configurations that can be downloaded when faults occur. Since the precompiled partial configurations are stored on a net by net basis, the required storage space and the download time is minimal. We have implemented our technique on the ORCA series FPGAs available from Lucent Technologies, and we demonstrate our technique on a FPGA based, on-line Adaptive Computing System (ACS) implemented with the ORCA FPGAs. Our worst case data indicates we can determine an average of seven alternates per signal net and for most circuits up to ten.
Microstructural control for ultrafine-grained non-oxide structural ceramics (2012)

Ultrafine-grained non-oxide ceramics were prepared by combining the synthesis technology for fine-grained starting powders and the rapid sintering technology for spark plasma sintering (SPS); the two technologies were combined for obtaining ceramics with improved heat and corrosion resistance and improved mechanical properties. Hollow spherical Ca-α SiAlON powders composed of nanosized particles were synthesized by carbothermal reduction–nitridation of a SiO2–Al2O3–CaCO3 powder mixture. Using the Ca-α SiAlON powder, dense Ca-α SiAlON nanoceramics and porous Ca-α SiAlON ceramics with excellent mechanical properties and high heat and corrosion resistance were fabricated by the SPS technique. Ultrafine-grained Si3N4 and SiC ceramics were prepared from fine-grained Si3N4 and SiC powders by SPS. The densification of cubic-BN-dispersed ceramics composites was achieved without the phase transformation of cubic BN to low-hardness hexagonal BN, at a moderate pressure by the SPS technique.