gebhart/patrepeval huggingface dataset:
Enhancing Gene Targeting with Designed Zinc Finger Nucleases (2003)

Gene targeting—the process of gene replacement by homologous recombination—is a very useful but typically inefficient technique ( [1][1] ). A general method for improving the efficiency of gene targeting would be valuable in many circumstances, as would the extension of this genetic tool to a
Using Local Orientational Information As Image Primitive For Robust Object Recognition (1989)

Orientational information can replace the traditional edges as basic image features (&quot;primitives&quot;) for object recognition. A comparison of five different orientation operators on 3 x 3 windows is carried out, and it is found that these operators have similar performance. A first attempt at object recognition searches for minimum root mean square deviation of orientation in a picture. This technique shows better object discrimination than the traditional normalized cross-correlation of grey-level images. Additionally the parameters of the Gaussian distribution of orientational correlation can be accurately predicted by a simple theoretical model. The orientational correlation technique shows difficulties in recognizing geometrically distorted and partially occluded objects. For this reason a very robust algorithm for the recognition of simple objects is developed, based only on orientationl information as image feature, and local polar coordinates for the model of the object. Practical examples taken under difficult, natural conditions illustrate the reliable performance of the proposed algorithm, and it becomes apparent that orientational information is indeed a powerful image primitive.
Accuracy of Wrist-Worn Heart Rate Monitors (2016)

Wrist-worn fitness and heart rate (HR) monitors are popular. 1,2 While the accuracy of chest strap, electrode-based HR monitors has been confirmed, 3,4 the accuracy of wrist-worn, optically based HR monitors is uncertain. 5,6 Assessment of the monitors' accuracy is important for individuals who use them to guide their physical activity and for physicians to whom these individuals report HR readings. The objective of this study was to assess the accuracy of 4 popular wrist-worn HR monitors under conditions of varying physical exertion.
Analytical Model of a PZT Thick-Film Triaxial Accelerometer for Optimum Design (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We present a mechanical model of a triaxial micro accelerometer design using PZT thick-film as the sensing material. The model is based on the full anisotropic material tensors and Eulers' beam equation using simplifying assumptions where the smaller stress contributions are ignored. The model results in design equations that are useful for optimization of the sensitivity and bandwidth and for matching the sensitivity in the three orthogonal directions. A finite-element method (FEM) model is used to verify the analytical model. Equal sensitivity in all three geometrical directions is preferred, which induces a number of limitations in design parameter space, this is used in a design strategy for setting the six independent dimensions of the accelerometer. Design methods for optimum sensitivity of each axis and for equal sensitivity between different axes have been proposed. </para>
Growth in the Presence of Salicylate Increases Fluoroquinolone Resistance in Staphylococcus aureus (1999)

Salicylate and acetylsalicylate slightly increased fluoroquinolone resistance in ciprofloxacin-susceptible and -resistant Staphylococcus aureus. Salicylate allowed a greater number of cells from ciprofloxacin-susceptible and -resistant strains to survive on high fluoroquinolone concentrations. Salicylate also increased the frequency with which a susceptible strain mutated to become more resistant to ciprofloxacin.
Sulforaphane: translational research from laboratory bench to clinic (2013)

Cruciferous vegetables are widely acknowledged to provide chemopreventive benefits in humans, but they are not generally consumed at levels that effect significant change in biomarkers of health. Because consumers have embraced the notion that dietary supplements may prevent disease, this review considers whether an appropriately validated sulforaphane-yielding broccoli sprout supplement may deliver clinical benefit. The crucifer-derived bioactive phytochemical sulforaphane is a significant inducer of nuclear factor erythroid 2-related factor 2 (Nrf2), the transcription factor that activates the cell's endogenous defenses via a battery of cytoprotective genes. For a broccoli sprout supplement to demonstrate bioactivity in vivo, it must retain both the sulforaphane-yielding precursor compound, glucoraphanin, and the activity of glucoraphanin's intrinsic myrosinase enzyme. Many broccoli sprout supplements are myrosinase inactive, but current labeling does not reflect this. For the benefit of clinicians and consumers, this review summarizes the findings of in vitro studies and clinical trials, interpreting them in the context of clinical relevance. Standardization of sulforaphane nomenclature and assay protocols will be necessary to remove inconsistency and ambiguity in the labeling of currently available broccoli sprout products.
Synthesis and Biological Evaluation of 14‐Alkoxymorphinans Part 4 opioid agonists and partial opioid agonists in a series of N‐(cyclobutylmethyl)‐14‐methoxymorphinan‐6‐ones (1989)

Abstract The N ‐(cyclobutylmethyl)morphinans 12 , 19 , 20 , 21 , 27 , and 29 and the N ‐(2‐cyanoethyl) analogue 33 were prepared from different precursors. Pharmacological evaluation ( e.g. opioid receptor binding assays, acetic‐acid writhing test, hot‐plate assay) points to a partial opioid agonism of compounds 12 , 27 , 29 , and 33 , and to full opioid agonism of compounds 19 – 21 .
Peripheral anti-Aβ antibody alters CNS and plasma Aβ clearance and decreases brain Aβ burden in a mouse model of Alzheimer's disease (2001)

Active immunization with the amyloid beta (A beta) peptide has been shown to decrease brain A beta deposition in transgenic mouse models of Alzheimer's disease and certain peripherally administered anti-A beta antibodies were shown to mimic this effect. In exploring factors that alter A beta metabolism and clearance, we found that a monoclonal antibody (m266) directed against the central domain of A beta was able to bind and completely sequester plasma A beta. Peripheral administration of m266 to PDAPP transgenic mice, in which A beta is generated specifically within the central nervous system (CNS), results in a rapid 1,000-fold increase in plasma A beta, due, in part, to a change in A beta equilibrium between the CNS and plasma. Although peripheral administration of m266 to PDAPP mice markedly reduces A beta deposition, m266 did not bind to A beta deposits in the brain. Thus, m266 appears to reduce brain A beta burden by altering CNS and plasma A beta clearance.
Common polymorphic transcript variation in human disease (2009)

Most human genes are thought to express different transcript isoforms in different cell types; however, the full extent and functional consequences of polymorphic transcript variation (PTV), which differ between individuals within the same cell type, are unknown. Here we show that PTV is widespread in B-cells from two human populations. Tens of thousands of exons were found to be polymorphically expressed in a heritable fashion, and over 1000 of these showed strong correlations with single nucleotide polymorphism (SNP) genotypes in cis. The SNPs associated with PTV display signs of having been subject to recent positive selection in humans, and they are also highly enriched for SNPs implicated by recent genome-wide association studies of four autoimmune diseases. From this disease-association overlap, we infer that PTV is the likely mechanism by which eight common polymorphisms contribute to disease risk. A catalog of PTV will be a valuable resource for interpreting results from future disease-association studies and understanding the spectrum of phenotypic differences among humans.
Common-path fourier-domain optical coherence tomography in ophthalmology applications (2009)

We have demonstrated in vivo three-dimensional imaging and estimated localized and quantitative hemoglobin oxygen saturation (SO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) of blood vessel by using a simple, easy to operate common-path Fourier-domain optical coherence tomography (OCT) system. The common-path OCT system can be easily integrated with various surgical tools and we demonstrated its usefulness by imaging outer and inner intraocular tissues such as cornea and neurosensory retinal layers as well as detecting SO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> level from a chicken embryo. The system uses 800 nm near infrared broadband light sources and has axial resolution as low as 3 mum in air. Self-adaptive scanning mechanism with real-time surface recognition and feedback control was also applied to the probe where the scanning probe tracks the sample surface variance and effective imaging depth was largely extended to the probe's free-moving range.
Hemoglobin-Specific Antibody in a Multiply Transfused Patient With Sickle Cell Disease (1997)

Human hemoglobins (Hbs) are known to be immunogenic, and both normal and variant forms of Hb have been shown to stimulate antibody formation in a variety of animal species. In patients who are homozygous for the sickle Hb (HbS) mutation, transfusion of normal, HbA-containing erythrocytes provides a potential stimulus for HbA alloimmunization. We tested serum samples for the presence of anti-Hb antibody by a solid-phase enzyme-linked immunosorbent assay (ELISA) using Hb-coated polystyrene microtiter plates. Hb-bound antibody was identified using an antihuman IgG antibody. Serum samples from 89 patients with sickle cell disease were initially tested for evidence of Hb antibody. The serum from three individuals exhibited antibody activity against HbA with little or no activity against HbS. Only one of them, a multiply transfused adult with HbSS, was available for further study. When this patient's antibody was tested against a variety of normal and mutant Hbs using antibody either to human IgG or to kappa chains, the anti-Hb antibody demonstrated specificity for the region of the Hb beta chain corresponding to the site of the amino acid substitution of HbS. The level of activity of the patient's anti-HbA showed no significant change over 1.5 years of observation. The transfusion of erythrocytes containing Hb structurally different from that of the recipient appeared to be capable of stimulating the production of Hb-specific alloimmune antibody.
Optimal Approach for Classification of Acute Leukemia Subtypes Based on Gene Expression Data (2002)

The classification of cancer subtypes, which is critical for successful treatment, has been studied extensively with the use of gene expression profiles from oligonucleotide chips or cDNA microarrays. Various pattern recognition methods have been successfully applied to gene expression data. However, these methods are not optimal, rather they are high-performance classifiers that emphasize only classification accuracy. In this paper, we propose an approach for the construction of the optimal linear classifier using gene expression data. Two linear classification methods, linear discriminant analysis (LDA) and discriminant partial least-squares (DPLS), are applied to distinguish acute leukemia subtypes. These methods are shown to give satisfactory accuracy. Moreover, we determined optimally the number of genes participating in the classification (a remarkably small number compared to previous results) on the basis of the statistical significance test. Thus, the proposed method constructs the optimal classifier that is composed of a small size predictor and provides high accuracy.
Diverse CRISPRs Evolving in Human Microbiomes (2012)

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci, together with cas (CRISPR-associated) genes, form the CRISPR/Cas adaptive immune system, a primary defense strategy that eubacteria and archaea mobilize against foreign nucleic acids, including phages and conjugative plasmids. Short spacer sequences separated by the repeats are derived from foreign DNA and direct interference to future infections. The availability of hundreds of shotgun metagenomic datasets from the Human Microbiome Project (HMP) enables us to explore the distribution and diversity of known CRISPRs in human-associated microbial communities and to discover new CRISPRs. We propose a targeted assembly strategy to reconstruct CRISPR arrays, which whole-metagenome assemblies fail to identify. For each known CRISPR type (identified from reference genomes), we use its direct repeat consensus sequence to recruit reads from each HMP dataset and then assemble the recruited reads into CRISPR loci; the unique spacer sequences can then be extracted for analysis. We also identified novel CRISPRs or new CRISPR variants in contigs from whole-metagenome assemblies and used targeted assembly to more comprehensively identify these CRISPRs across samples. We observed that the distributions of CRISPRs (including 64 known and 86 novel ones) are largely body-site specific. We provide detailed analysis of several CRISPR loci, including novel CRISPRs. For example, known streptococcal CRISPRs were identified in most oral microbiomes, totaling ∼8,000 unique spacers: samples resampled from the same individual and oral site shared the most spacers; different oral sites from the same individual shared significantly fewer, while different individuals had almost no common spacers, indicating the impact of subtle niche differences on the evolution of CRISPR defenses. We further demonstrate potential applications of CRISPRs to the tracing of rare species and the virus exposure of individuals. This work indicates the importance of effective identification and characterization of CRISPR loci to the study of the dynamic ecology of microbiomes.
Distortion program-size complexity with respect to a fidelity criterion and rate-distortion function (1993)

A novel concept of distortion Kolmogorov-chaitin complexity is proposed. Bearing analogy to ordinary Kolmogorov-Chaitin complexity that represents the information content of a single message, distortion Kolmogorov-Chaitin complexity can be regarded as the amount of information about a single message that must be conveyed in order to reproduce it with a bounded distortion. This explanation is justified by the properties of distortion Kolmogorov-Chaitin complexity and the equivalences between distortion Kolmogorov-Chaitin complexity and the rate-distortion function, which are analogous to those between ordinary Kolmogorov-Chaitin complexity and the Shannon entropy. Some implications for universal almost sure data compression are also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Hydrogen, Oxygen, and Hydrogen Peroxide Formation in Aqueous Phase Pulsed Corona Electrical Discharge (2005)

High voltage electrical discharges in water are of increasing interest for the degradation of organic compounds and destruction of biological species. The present study reports measurements of the rates of molecular hydrogen, molecular oxygen, and hydrogen peroxide formation in a pulsed positive needle-plane corona-like electrical discharge in water. In experiments for various solution conductivities, applied voltages, and discharge powers, the ratio of the molar rate of production of hydrogen:hydrogen peroxide:oxygen was approximately 4:2:1. The highest observed rate of hydrogen production was 1.3 μmol/s at discharge power of 37 W (or 0.25 g of H2/kW·h) at solution conductivity 50 μS/cm. The G-value for hydrogen production was 0.17 molecule of H2/100 eV, falling in the range of that found in the radiation chemistry literature (∼0−0.5 molecule of H2/100 eV, depending on scavenger concentration). A global reaction is proposed to add to existing kinetic models for the simulation of reactive species production in electrical discharge in water.
Active immunization of pigs against growth hormone-releasing factor: effect on concentrations of growth hormone and insulin-like growth factor 1. (1990)

Cyclic gilts (96 +/- 1 kg) were used to determine the effect of active immunization against growth hormone-releasing factor GRF(1-29)-NH2 on concentrations of growth hormone (GH) and insulin-like growth factor 1 (IGF-1). Gilts were immunized against GRF conjugated to human serum albumin (GRF-HSA, n = 5) or HSA alone at 180 d of age (wk 0). Booster doses were administered at wk 9 and 13. Seven days after the second booster (wk 14), blood samples were collected at 15-min intervals for 6 h before feeding and 30, 60, 120, 180 and 240 min after feeding. Eight days after the second booster, all gilts were administered a GRF analog, [desNH2Tyr1,Ala15]-GRF(1-29)-NH2, followed by an opioid agonist, FK33-824. Blood samples were collected at 15-min intervals from -30 to 240 min after injection. Immunization against GRF-HSA resulted in antibody titers, expressed as dilution required to bind 50% of [125I]GRF, ranging from 1:11,000 to 1:60,000 (wk 11 and 14); binding was not detectable or was less than 50% at 1:100 in HSA gilts (P less than .05). Episodic release of GH was abolished by immunization against GRF-HSA (P less than .05). Mean GH was decreased (P less than .07), but basal GH concentrations were not altered (P greater than .15) by immunization against GRF-HSA. Serum concentrations of IGF-1 were similar at wk 0, but concentrations were lower in GRF-HSA than in HSA gilts (P less than .05) at wk 14.(ABSTRACT TRUNCATED AT 250 WORDS)
Functional Magnetic Resonance Imaging Connectivity Analyses Reveal Efference-Copy to Primary Somatosensory Area, BA2 (2014)

Some theories of motor control suggest efference-copies of motor commands reach somatosensory cortices. Here we used functional magnetic resonance imaging to test these models. We varied the amount of efference-copy signal by making participants squeeze a soft material either actively or passively. We found electromyographical recordings, an efference-copy proxy, to predict activity in primary somatosensory regions, in particular Brodmann Area (BA) 2. Partial correlation analyses confirmed that brain activity in cortical structures associated with motor control (premotor and supplementary motor cortices, the parietal area PF and the cerebellum) predicts brain activity in BA2 without being entirely mediated by activity in early somatosensory (BA3b) cortex. Our study therefore provides valuable empirical evidence for efference-copy models of motor control, and shows that signals in BA2 can indeed reflect an input from motor cortices and suggests that we should interpret activations in BA2 as evidence for somatosensory-motor rather than somatosensory coding alone.
Identification of a locus controlling expression of luminescence genes in Vibrio harveyi (1989)

Mutagenesis with transposon mini-Mulac was used to identify loci containing genes for bioluminescence (lux) in the marine bacterium Vibrio harveyi. Transposon insertions which resulted in a Lux- phenotype were mapped to two unlinked regions of the genome. Region I contained the luxCDABE operon which was previously shown to encode the enzymes luciferase and fatty acid reductase, which are required for light production. The other locus, region II, which was identified for the first time in this study, appeared to have a regulatory function. In Northern blot analysis of mRNA from mutants with defects in this region, no transcription from the luxCDABE operon could be detected. Strains with transposon-generated lux::lacZ gene fusions were used to analyze control of the transcription of these regions. Expression of luminescence in the wild type was strongly influenced by the density of the culture, and in strains with the lacZ indicator gene coupled to the luxCDABE operon, beta-galactosidase synthesis was density dependent. So, transcription of this operon is responsive to a density-sensing mechanism. However, beta-galactosidase synthesis in strains with lacZ fused to the region II transcriptional unit did not respond to cell density. The organization and regulation of the lux genes of V. harveyi are discussed, particularly with regard to the contrasts observed with the lux system of the fish light-organ symbiont Vibrio fischeri.
Anticoagulant activities of heparin oligosaccharides and their neutralization by platelet factor 4 (1984)

Oligosaccharides of well-defined molecular size were prepared from heparin by nitrous acid depolymerization, affinity chromatography on immobilized antithrombin III (see footnote on Nomenclature) and gel chromatography on Sephadex G-50. High affinity (for antithrombin III) octa-, deca-, dodeca-, tetradeca-, hexadeca- and octadeca-saccharides were prepared, as well as oligosaccharides of larger size than octadecasaccharide. The inhibition of Factor Xa by antithrombin III was greatly accelerated by all of these oligosaccharides, the specific anti-Factor Xa activity being invariably greater than 1300 units/mumol. The anti-Factor Xa activity of the decasaccharide was not significantly decreased in the presence of platelet factor 4, even at high platelet factor 4/oligosaccharide ratios. Measurable but incomplete neutralization of the anti-Factor Xa activities of the tetradeca- and hexadeca-saccharides was observed, and complete neutralization of octadeca- and larger oligo-saccharides was achieved with excess platelet factor 4. The octa-, deca-, dodeca-, tetradeca- and hexadeca-saccharides had negligible effect on the inhibition of thrombin by antithrombin III, whereas specific anti-thrombin activity was expressed by the octadeca-saccharide and by the larger oligosaccharides. An octadecasaccharide is therefore the smallest heparin fragment (prepared by nitrous acid depolymerization) that can accelerate thrombin inhibition by antithrombin III. The anti-thrombin activities of the octadecasaccharide and larger oligosaccharides were more readily neutralized by platelet factor 4 than were their anti-Factor Xa activities. These findings are compatible with two alternative mechanisms for the action of platelet factor 4, both involving the binding of the protein molecule adjacent to the antithrombin III-binding site. Such binding results in either steric interference with the formation of antithrombin III-proteinase complexes or in displacement of the antithrombin III molecule from the heparin chain.
Voice conversion using deep Bidirectional Long Short-Term Memory based Recurrent Neural Networks (2015)

This paper investigates the use of Deep Bidirectional Long Short-Term Memory based Recurrent Neural Networks (DBLSTM-RNNs) for voice conversion. Temporal correlations across speech frames are not directly modeled in frame-based methods using conventional Deep Neural Networks (DNNs), which results in a limited quality of the converted speech. To improve the naturalness and continuity of the speech output in voice conversion, we propose a sequence-based conversion method using DBLSTM-RNNs to model not only the frame-wised relationship between the source and the target voice, but also the long-range context-dependencies in the acoustic trajectory. Experiments show that DBLSTM-RNNs outperform DNNs where Mean Opinion Scores are 3.2 and 2.3 respectively. Also, DBLSTM-RNNs without dynamic features have better performance than DNNs with dynamic features.