gebhart/patrepeval huggingface dataset:
Target prediction for small, noncoding RNAs in bacteria (2006)

Many small, noncoding RNAs in bacteria act as post-transcriptional regulators by basepairing with target mRNAs. While the number of characterized small RNAs (sRNAs) has steadily increased, only a limited number of the corresponding mRNA targets have been identified. Here we present a program, TargetRNA, that predicts the targets of these bacterial RNA regulators. The program was evaluated by assessing whether previously known targets could be identified. The program was then used to predict targets for the Escherichia coli RNAs RyhB, OmrA, OmrB and OxyS, and the predictions were compared with changes in whole genome expression patterns observed upon expression of the sRNAs. Our results show that TargetRNA is a useful tool for finding mRNA targets of sRNAs, although its rate of success varies between sRNAs.
A Mass Spectrum Analysis of the Products of Ionization by Electron Impact in Nitrogen, Acetylene, Nitric Oxide, Cyanogen and Carbon Monoxide (1935)

A mass spectrograph, designed for the identification of the products of ionization and dissociation by electron impacts in molecular gases is described.Ionization potential of nitrogen. A direct comparison in a nitrogen-argon mixture showed that the ionization potential of nitrogen is at least 0.04 volt less than that of argon. The ionization potential is therefore not greater than 15.65 volts, though it may be lower by as much as 0.1 volt.Analysis of ionization and dissociation products in ${\mathrm{C}}_{2}$${\mathrm{H}}_{2}$, NO, and ${\mathrm{C}}_{2}$${\mathrm{N}}_{2}$. The ions formed by electron impacts in these gases together with their appearance potentials in volts are as follows: Negative ${\mathrm{O}}^{\ensuremath{-}}$ ions appear in NO as reported by Tate and Smith. An ion of mass 27 found in ${\mathrm{C}}_{2}$${\mathrm{H}}_{2}$ is ascribed to ${\mathrm{C}}^{12}$${\mathrm{C}}^{13}$${\mathrm{H}}_{2}$. The abundance ratio ${\mathrm{C}}^{13}$: ${\mathrm{C}}^{12}$ was calculated to be 1: 100.
Synthesis of Conformationally Restricted Analogs of Baclofen, a Potent GABAB Receptor Agonist, by the Introduction of a Cyclopropane Ring. (1999)

Conformationally restricted analogs of baclofen (2), i.e., 5, 6, and their enantiomers ent-5, and ent-6, the conformations of which were restricted by introducing a cyclopropane ring, were designed as potential GABAB receptor ligands. Reaction of (R)-epichlorohydrin [(R)-7] and (4-chlorophenyl)acetonitrile in the presence of NaNH2 in benzene/tetrahydrofuran gave chiral cyclopropane derivatives 11 and 12, which were then converted into the target compounds 5 and 6, respectively. Their corresponding enantiomers, ent-5 and ent-6, were also synthesized starting from (S)-epichlorohydrin [(S)-7].
Evidence of widespread binding of HLA class I molecules to peptides. (1990)

We have tested the binding of HLA class I proteins to peptides using a solid-phase binding assay. We tested 102 peptides, mostly derived from the HIV gag and HIV pol sequences. Most peptides did not bind to any class I protein tested. The pattern of binding among the three class I proteins tested, HLA-A2, -B27, and -B8, was approximately 85% concordant. Further, all five of the known HIV-1 gag T cell epitopes detected by human CTL bound at least one class I protein. Binding of class I to the peptides could be detected either by directly iodinated class I proteins, or indirectly using monoclonal antibodies specific for class I. The binding to the plates could be blocked with MA2.1, which binds in the alpha 1 region of A2, but not by W6/32, which binds elsewhere. The data presented here show that binding of class I to peptides is specific, but that many peptides bind to more than a single class I protein.
<title>Acceleration of ray-casting using 3-D distance transforms</title> (1992)

This paper introduces a novel approach for speeding up the ray casting process commonly used in volume visualization methods. This new method called Ray Acceleration by Distance Coding (RADC) uses a 3-D distance transform to determine the minimum distance to the nearest interesting object; the implementation of a fast and accurate distance transform is described in detail. High distance values, typically found at off-center parts of the volume, cause many sample points to be skipped, thus significantly reducing the number of samples to be evaluated during the ray casting step. The minimum distance values that are encountered while traversing the volume can be used for the identification of rays that do not hit objects. Our experiments indicate that the RADC method can reduce the number of sample points by a factor between 5 and 20.
Cartilage Fibrils of Mammals are Biochemically Heterogeneous: Differential Distribution of Decorin and Collagen IX (1998)

Cartilage fibrils contain collagen II as the major constituent, but the presence of additional components, minor collagens, and noncollagenous glycoproteins is thought to be crucial for modulating several fibril properties. We have examined the distribution of two fibril constituents-decorin and collagen IX-in samples of fibril fragments obtained after bovine cartilage homogenization. Decorin was preferentially associated with a population of thicker fibril fragments from adult articular cartilage, but was not present on the thinnest fibrils. The binding was specific for the gap regions of the fibrils, and depended on the decorin core protein. Collagen IX, by contrast, predominated in the population with the thinnest fibrils, and was scarce on wider fibrils. Double-labeling experiments demonstrated the coexistence of decorin and collagen IX in some fibrils of intermediate diameter, although most fibril fragments from adult cartilage were strongly positive for one component and lacked the other. Fibril fragments from fetal epiphyseal cartilage showed a different pattern, with decorin and collagen IX frequently colocalized on fragments of intermediate and large diameters. Hence, the presence of collagen IX was not exclusive for fibrils of small diameter. These results establish that articular cartilage fibrils are biochemically heterogeneous. Different populations of fibrils share collagen II, but have distinct compositions with respect to macromolecules defining their surface properties.
Williams–Beuren Syndrome (2010)

Williams–Beuren syndrome, a multisystem disorder caused by the deletion of a chromosome region of 1.5 million to 1.8 million base pairs containing 26 to 28 genes, is a disorder of microdeletion or contiguous gene deletion. This review covers current understanding of the biology of this disorder.
Synthesis, Characterization, and In Vitro and In Vivo Evaluations of 4-(N)-Docosahexaenoyl 2′, 2′-Difluorodeoxycytidine with Potent and Broad-Spectrum Antitumor Activity (2016)

In this study, a new compound, 4-(N)-docosahexaenoyl 2', 2'-difluorodeoxycytidine (DHA-dFdC), was synthesized and characterized. Its antitumor activity was evaluated in cell culture and in mouse models of pancreatic cancer. DHA-dFdC is a poorly soluble, pale yellow waxy solid, with a molecular mass of 573.3Da and a melting point of about 96°C. The activation energy for the degradation of DHA-dFdC in an aqueous Tween 80-based solution is 12.86kcal/mol, whereas its stability is significantly higher in the presence of vitamin E. NCI-60 DTP Human Tumor Cell Line Screening revealed that DHA-dFdC has potent and broad-spectrum antitumor activity, especially in leukemia, renal, and central nervous system cancer cell lines. In human and murine pancreatic cancer cell lines, the IC50 value of DHA-dFdC was up to 10(5)-fold lower than that of dFdC. The elimination of DHA-dFdC in mouse plasma appeared to follow a biexponential model, with a terminal phase t1/2 of about 58minutes. DHA-dFdC significantly extended the survival of genetically engineered mice that spontaneously develop pancreatic ductal adenocarcinoma. In nude mice with subcutaneously implanted human Panc-1 pancreatic tumors, the antitumor activity of DHA-dFdC was significantly stronger than the molar equivalent of dFdC alone, DHA alone, or the physical mixture of them (1:1, molar ratio). DHA-dFdC also significantly inhibited the growth of Panc-1 tumors orthotopically implanted in the pancreas of nude mice, whereas the molar equivalent dose of dFdC alone did not show any significant activity. DHA-dFdC is a promising compound for the potential treatment of cancers in organs such as the pancreas.
Synthesis of microporous organic polymers with high CO2-over-N2 selectivity and CO2 adsorption (2013)

A series of microporous organic polymers (MOPs) were synthesized by Schiff base condensation of 1,3,5-tris(4-aminophenyl)benzene and a number of dialdehyde monomers. The polymers were structurally characterized by in situ infrared and ex situ solid state 13C{1H} nuclear magnetic resonance (NMR) spectroscopy. Synthesis conditions were optimized to enhance CO2 uptake by the MOPs. Synthesis at low temperatures results in the MOPs being linked by imine groups. Heating of the MOPs reduces the number of imine groups and after heating to >300 °C nitrile groups were found to be present in the MOPs. The MOPs have specific surface areas up to 614 m2 g−1 and narrow pore size distributions of ∼4 to 8 Å. The selectivity of CO2-over-N2 at 273 K and 1 bar was 56–77, which requires either an influence of chemisorption on CO2 or a molecular sieving (or kinetic selection) of CO2-over-N2. The materials had also heats of adsorption typical for physisorption of CO2.
Human TRPM8 and TRPA1 pain channels, including a gene variant with increased sensitivity to agonists (TRPA1 R797T), exhibit differential regulation by SRC-tyrosine kinase inhibitor (2014)

TRPM8 (transient receptor potential M8) and TRPA1 (transient receptor potential A1) are cold-temperature-sensitive nociceptors expressed in sensory neurons but their behaviour in neuronal cells is poorly understood. Therefore DNA expression constructs containing human TRPM8 or TRPA1 cDNAs were transfected into HEK (human embryonic kidney cells)-293 or SH-SY5Y neuroblastoma cells and G418 resistant clones analysed for effects of agonists and antagonists on intracellular Ca2+ levels. Approximately 51% of HEK-293 and 12% of SH-SY5Y cell clones expressed the transfected TRP channel. TRPM8 and TRPA1 assays were inhibited by probenecid, indicating the need to avoid this agent in TRP channel studies. A double-residue mutation in ICL-1 (intracellular loop-1) of TRPM8 (SV762,763EL, mimicking serine phosphorylation) or one in the C-terminal tail region (FK1045,1046AG, a lysine knockout) retained sensitivity to agonists (WS 12, menthol) and antagonist {AMTB [N-(3-Aminopropyl)-2-[(3-methylphenyl)methoxy]-N-(2-thienylmethyl)benzamide]}. SNP (single nucleotide polymorphism) variants in TRPA1 ICL-1 (R797T, S804N) and TRPA1 fusion protein containing C-terminal (His)10 retained sensitivity to agonists (cinnamaldehyde, allyl-isothiocyanate, carvacrol, eugenol) and antagonists (HC-030031, A967079). One SNP variant, 797T, possessed increased sensitivity to agonists. TRPA1 became repressed in SH-SY5Y clones but was rapidly rescued by Src-family inhibitor PP2 [4-amino-5-(4-chlorophenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine]. Conversely, TRPM8 in SH-SY5Y cells was inhibited by PP2. Further studies utilizing SH-SY5Y may identify structural features of TRPA1 and TRPM8 involved in conferring differential post-translational regulation.
Progressive video transmission for packet lossy channels exploiting feedback and unequal erasure protection (2003)

In this work we present a video transmission system for packet lossy channels based on the progressive texture video coding (PTVC) algorithm. A posteriori video rate control on the progressively coded messages is simplified significantly as for rate adaptation only the later part of this message can be truncated. This property is used by an appropriate unequal erasure protection (UXP) scheme which allows us - in combination with the progressively coded messages - to transmit very efficiently over packet erasure channels like the Internet. An appropriate rate allocation scheme based on dynamic programming is introduced. Additionally, a source-channel coding system exploiting network feedback is presented. Dependency on feedback delay is studied. Information between source encoder, channel encoder and network is exchanged and exploited in a cooperative way. The investigated systems show significant gains for different video sequences and different channel erasure rates when compared to sophisticated standard approaches.
Test de sistemas en aplicaciones sensibles al ruido (2003)

Las diversas fuentes de ruido hacen que el test de los sistemas sea mas complejo, por lo que es preciso considerar diversas tecnicas de test. El analisis frecuencial, temporal y de CC son las opciones consideradas en este articulo, siempre con el objetivo fundamental de mantener la integridad de la senal.
EHR-based Visualization Tool: Adoption Rates, Satisfaction, and Patient Outcomes (2015)

Clinical decision-making and practices change rapidly and in parallel to simultaneous changes in the health care landscape and EHR usage. Based on these observations and our preliminary results, we have found that an integrated, extensible, and workflow-aware CDS tool is critical to enhancing patient-provider communications and influencing patient outcomes.
Optical anisotropy in the spinel group: a polishing effect (1994)

More than 100 polished sections of magnetite, chromite, franklinite and jacobsite from about 50 localities were examined by ore microscopic methods. During sample preparation, two final polishing procedures were applied: (a) a 0.1 μm diamond suspension on «Microcloth», (b) an alkaline silica solution on «Microcloth». With the exception of {100} and {111} sections, procedure (a) always led to weak optical anisotropy, while with procedure (b), with the exception of five zoned magnetites, sections remained isotropic. Electron channeling pattern (ECP) images on a scanning electron microscope (SEM) showed a strongly damaged surface for a), and a perfect, undisturbed surface structure for b). This convincingly indicates that anomalous optical anisotropy effects in the spinel group are usually caused by surface deformation caused by mechanical polishing procedures. The relation-ship between surface deformation and face symmetry leads to the isotropic appearance of deformed {100} and {111} sections and to the anisotropic appearance of low-symmetric {hkl} sections
Variability in the measurement of C-reactive protein in healthy subjects: implications for reference intervals and epidemiological applications (1997)

We developed a reproducible ELISA for C-reactive protein (CRP), calibrated with WHO Reference Material, for which intra- and interassay CVs were 3.0% and 6.0%, respectively. Analytical recovery was 97.9%. The distribution of CRP in a healthy blood donor population (n = 143) was nongaussian, with 2.5th, 50th, and 97.5th percentile values of 0.08, 0.64, and 3.11 mg/L, respectively. There was no sex-related difference, and the association with age was weak. In a study of variability [by the method of Fraser and Harris (Crit Rev Clin Lab Sci 1989;27:409-37)], the analytical variability was 5.2%; the within-subject variability, CVI, was 42.2%; and the between-subject variability, CVG, was 92.5%. The critical difference for sequential values significant at P < or =0.05 (i.e., the smallest percentage change unlikely to be due to analytical variability or CVI) was calculated as 118%, and the index of individuality, CVI/CVG, was 0.46. This suggests that CRP, like many clinical chemistry analytes, has limited usefulness in detecting early disease-associated changes when used in conjunction with a healthy reference interval. From a molecular epidemiological standpoint, the usefulness of CRP in longitudinal studies is suggested by the small index of individuality and by observations that (a) short-term fluctuations were infrequent, (b) all data stayed within the reference interval, and (c) relative rankings of the subjects over 6 months only moderately deteriorated.
Inscription and characterization of Bragg gratings in single-crystal sapphire optical fibres for high-temperature sensor applications (2009)

We report the fabrication and high-temperature characteristics of Bragg gratings in single-crystal sapphire fibres inscribed by infrared femtosecond laser pulses. For stable read-out of the multimode Bragg reflection signal, the sapphire fibre was illuminated by broadband light from a superluminescent diode applying a long section of a step-index multimode silica fibre. This evenly distributed excitation of many guided modes in the sapphire fibre resulted in the polychromator measurement of stable reflection peak shapes and allowed for multiplexed temperature sensing up to 1745 °C at remote read-out with repeatability better than 1 °C. During the temperature tests an annealing process of the sapphire grating was observed at temperatures above 1400 °C. Possibilities for further improvement of sensors performance are discussed with a view to avoiding instabilities from the lack of a fibre cladding that shields the sapphire waveguide from the environment.
Improvement of Postfault Performance of Multiphase Drives in Terms of Operating Region and Stator Copper Loss (2018)

Multiphase drives are particularly attractive for safety-critical applications, due to their enhanced fault tolerance. Most of the faults in electric drives occur in the power electronics. Switch faults can be divided into open- and short-circuit ones. The conventional techniques to handle switch faults in two-level converters mainly consist in either keeping the corresponding phases open or connecting the stator terminal to the de-link midpoint through a triode for ac (TRIAC). However, the former results in lower maximum torque and larger stator copper loss (SCL), whereas the latter leads to a reduction in the maximum speed and has not been considered in the context of two-level multiphase drives. This paper proposes to adequately combine these approaches in two-level multiphase drives, depending on the speed, the faulted switches and the neutral configuration, so that the total operating region of the drive is extended and the SCL is decreased, when compared to the conventional strategies. It is also shown and exploited that, for multi phase drives based on multiple three-phase winding sets, turning on or off a TRIAC placed between their neutrals as a function of the speed allows further improvement of the postfault performance. Simulation results are provided to confirm the theory.
Thermo-Responsive Core−Sheath Electrospun Nanofibers from Poly (<i>N</i>-isopropylacrylamide)/Polycaprolactone Blends (2010)

Core−sheath nanofibers with biodegradable polycaprolactone (PCL) as the core and thermo-responsive poly(N-isopropylacrylamide) (PNIPAAm) as the sheath were prepared by single-spinneret electrospinning of blends of the two polymers. The morphology of the composite fibers with different proportions of PNIPAAm to PCL was determined using scanning electron microscopy (SEM). Surface enrichment of PNIPAAm was confirmed by both x-ray photoelectron spectroscopy (XPS) quantification and time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging. It was found that the phase separation was driven by both thermostatic/kinetic factors and electric-field-orientation effects. The combination of appropriate choice of miscible solvents with large parameter differences (solubility of the two polymers, dielectric constant, and evaporation speed during jet traveling) and difference in molecular weight/viscosity of the two polymers contributed to the core−sheath self-assembly. The thermo-responsive wettabilites of the PNIPAAm dominant fibrous surfaces were demonstrated using contact angle (CA) measurements and a microcontact printing (μCP) method.
Contrast-limited adaptive histogram equalization: speed and effectiveness (2002)

An experiment intended to evaluate the clinical application of contrast-limited adaptive histogram equalization (CLAHE) to chest computer tomography (CT) images is reported. A machine especially designed to compute CLAHE in a few seconds is discussed. It is shown that CLAHE can be computed in 4 s after 5-s loading time using the specially designed parallel engine made from a few thousand dollars worth of off-the-shelf components. The processing appears to be useful for a wide range of medical images, but the limitations of observer calibration make it impossible to demonstrate such usefulness by agreement experiments.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fuzzy ART: an adaptive resonance algorithm for rapid, stable classification of analog patterns (2002)

A fuzzy ART (adaptive resonance theory) system is introduced which incorporates computations from fuzzy set theory into ART 1. For example, the intersection ( intersection ) operator used in ART 1 learning is replaced by the MIN operator ( V-product ) of fuzzy set theory. Fuzzy ART reduces to ART 1 in response to binary input vectors, but can also learn stable categories in response to analog input vectors. In particular, the MIN operator reduces to the intersection operator in the binary case. Learning is stable because all adaptive weights can only decrease in time. A preprocessing step, called complement coding, uses on-cell and off-cell responses to prevent category proliferation. Complement coding normalizes input vectors while preserving the amplitude of individual feature activations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Design of Variable Vehicle Handling Characteristics Using Four-Wheel Steer-by-Wire (2015)

This paper presents a vehicle handling modification approach that tracks the dynamics of a general nonlinear planar reference model. The control structure is a combination of linear and nonlinear state feedback with feedforward of reference model yaw moment, lateral force, and longitudinal force at the vehicle center of gravity. The modified closed-loop system is demonstrated to be stable and has robust tracking performance to reasonable levels of model uncertainty. The handling modification method is applied to the task of emulating the dynamics of a reference vehicle on a low friction surface, with particular attention to actuator constraints. Experimental results demonstrate successful emulation of the low friction reference model's planar dynamics for a variety of driving maneuvers and reference friction coefficients. This handling emulation technique enables further investigation of vehicle handling performance improvements and use as a variable dynamic testbed for human factors studies.
Chemistry of Verongida Sponges. 10. Secondary Metabolite Composition of the Caribbean Sponge <i>Verongula</i> <i>gigantea</i> (2000)

A detailed analysis of the secondary metabolites of the Caribbean sponge Verongula gigantea has been performed. A number of bromotyrosine derivatives, 1, 2, and 6-17, were identified, one of which (17) is a novel compound. Its structure was determined on the basis of spectroscopic evidence. Additionally, aureol (18) and 5, 6-dibromo-N,N-dimethyltryptamine (19) were isolated from one of the five analyzed specimens.
[Analysis on the risk factors of intracardial thrombus after prosthetic valve replacement: a 1-year follow-up study]. (2010)

Valve replacement at mitral position, atrial fibrillation, and preoperative internal diameter of left atrium are the correlated risk factors of intracardial thrombus after prosthetic valve replacement. Anticoagulation after prosthetic valve (especially bioprosthetic valve) replacement should be standardized to prevent intracardial thrombus formation.
Nontoxic and renewable metal–organic framework based on α-cyclodextrin with efficient drug delivery (2016)

Two new nontoxic α-CD based compounds were synthesized by different method, which contain different left-handed helix and exhibit efficient drug loading capacity and sustained release behaviors.