gebhart/patrepeval huggingface dataset:
A Mutate-and-Map Strategy for Inferring Base Pairs in Structured Nucleic Acids: Proof of Concept on a DNA/RNA Helix (2010)

We propose a rapid chemical strategy for identifying base pairs in structured nucleic acid systems. The approach goes beyond traditional chemical mapping approaches by monitoring perturbations of each residue's chemical accessibility in response to systematic mutagenesis of residues that are distant in sequence but nearby in three dimensions. As a proof of concept, we present high-throughput dimethyl sulfate accessibility data for a chimeric DNA/RNA system in which every possible sequence variation and deletion in a 20 bp region has been synthesized and tested. The data demonstrate that 88% of the system's base pairs can be robustly inferred, with A/A and T/C DNA/RNA mismatches giving the strongest signals. These results point to the feasibility of rapid base pair inference in larger and more complex nucleic acid systems with unknown structure.
The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes (2011)

These large repositories allow us to further mine for genetic heterogeneity and species diversity in the genus Akkermansia, providing novel insight towards the functionality of this abundant inhabitant of the human intestinal tract.
Randomised controlled trial of growth effect of hydrocortisone in congenital adrenal hyperplasia (1997)

The influence of 15 or 25 mg/m2 of daily oral hydrocortisone with fludrocortisone 0.1 mg/day on growth and laboratory findings was evaluated in a prospective randomised crossover trial over 12 months in 26 children with 21-hydroxylase deficiency. Nine non-salt losers had fludrocortisone stopped for a further six month period. Height velocity was significantly decreased during treatment with 25 mg/m2 as compared with 15 mg/m2. This was the most sensitive indicator of corticosteroid treatment excess. A dose dependent effect upon plasma concentrations of 17-hydroxyprogesterone, testosterone, and androstenedione was found but increased values were still detected in more than half of the determinations made during the 25 mg/m2 period. Height velocity and 17-hydroxyprogesterone concentrations were positively correlated. Growth hormone response to clonidine stimulation and insulin-like growth factor-1 concentrations were both within reference values and there was no difference between treatment periods. Withdrawal of fludrocortisone did not result in any difference for the non-salt losers. It was concluded that 25 mg/m2 of hydrocortisone depressed growth in children with congenital adrenal hyperplasia, and that full suppression, or even normalisation, of plasma concentrations of 17-hydroxyprogesterone and androgens should not be considered a treatment goal, but instead an indication of corticosteroid treatment excess.
Identification in Collagen Type I of an Integrin α2β1-binding Site Containing an Essential GER Sequence (1998)

The collagen type I-derived fragment alpha1(I)CB3 is known to recognize the platelet collagen receptor integrin alpha2beta1 as effectively as the parent collagen, although it lacks platelet-aggregatory activity. We have synthesized the fragment as seven overlapping peptides that spontaneously assemble into triple helices. On the basis of their capacity to bind purified alpha2 beta1 and the recombinant alpha2 A-domain, and their ability to support alpha2 beta1-mediated cell adhesion, we identified two peptides, CB3(I)-5 and -6, which contain an alpha2 beta1 recognition site. Synthesis of the peptide CB3(I)-5/6, containing the overlap sequence between peptides 5 and 6, allowed us to locate the binding site within the 15-residue sequence, GFP*GERGVEGPP*GPA (where P* represents hydroxyproline), corresponding to residues 502-516 of the collagen type I alpha1 chain. The Glu and Arg residues in the GER triplet were found to be essential for recognition since substitution of either residue with Ala caused a loss of alpha2 A-domain binding. By contrast, substitution of the Glu in GVE did not reduce binding, but rather enhanced it slightly. We were unable to detect significant recognition of alpha2 beta1 by the peptide CB3(I)-2 containing the putative alpha2 beta1 recognition sequence DGEA. Peptides CB3(I)-1 to -6, together with peptide CB3(I)-5/6, exhibited good platelet-aggregatory activity, in some cases better than collagen. However, peptide CB3(I)-7 was inactive, suggesting the presence of an inhibitory element that might account for the lack of aggregatory activity of the parent alpha1(I)CB3 fragment.
Event-Related EEG Time-Frequency Analysis: An Overview of Measures and An Analysis of Early Gamma Band Phase Locking in Schizophrenia (2008)

An increasing number of schizophrenia studies have been examining electroencephalography (EEG) data using time-frequency analysis, documenting illness-related abnormalities in neuronal oscillations and their synchronization, particularly in the gamma band. In this article, we review common methods of spectral decomposition of EEG, time-frequency analyses, types of measures that separately quantify magnitude and phase information from the EEG, and the influence of parameter choices on the analysis results. We then compare the degree of phase locking (ie, phase-locking factor) of the gamma band (36-50 Hz) response evoked about 50 milliseconds following the presentation of standard tones in 22 healthy controls and 21 medicated patients with schizophrenia. These tones were presented as part of an auditory oddball task performed by subjects while EEG was recorded from their scalps. The results showed prominent gamma band phase locking at frontal electrodes between 20 and 60 milliseconds following tone onset in healthy controls that was significantly reduced in patients with schizophrenia (P = .03). The finding suggests that the early-evoked gamma band response to auditory stimuli is deficiently synchronized in schizophrenia. We discuss the results in terms of pathophysiological mechanisms compromising event-related gamma phase synchrony in schizophrenia and further attempt to reconcile this finding with prior studies that failed to find this effect.
Wide-spectrum, ultrasensitive fluidic sensors with amplification from both fluidic circuits and metal oxide semiconductor field effect transistors (2007)

The authors report a sensing scheme to detect the translocation of small particles through a fluidic channel. The device connects the gate of a metal oxide semiconductor field effect transistor (MOSFET) with a fluidic circuit and monitors the FET’s drain current to detect particles. They demonstrate that amplification can be achieved from both the fluidic circuit and the MOSFET. The results show that a 0.7% volume ratio of the particle to the sensing microchannel can lead to 28%–56% modulation of the MOSFET’s drain current. The minimum volume ratio detected is 0.006%, which is about ten times smaller than the lowest detectable volume ratio reported in the literature.
Radio-pathomic Maps of Epithelium and Lumen Density Predict the Location of High-Grade Prostate Cancer (2018)

We present a radio-pathomic approach to mapping prostate cancer. We find that the maps are useful for highlighting high-grade tumors. This technique may be relevant for dose-painting strategies in prostate radiation therapy.
Colony Collapse Disorder: A Descriptive Study (2009)

This is the first comprehensive survey of CCD-affected bee populations that suggests CCD involves an interaction between pathogens and other stress factors. We present evidence that this condition is contagious or the result of exposure to a common risk factor. Potentially important areas for future hypothesis-driven research, including the possible legacy effect of mite parasitism and the role of honey bee resistance to pesticides, are highlighted.
BCL-2 DOES NOT PREVENT REJECTION OF ALLOGRAFTS IN A MOUSE MODEL OF HETEROTOPIC HEART TRANSPLANTATION. (1998)

266 Apoptotic pathways may influence rejection of allografts, but the significance of individual components in these pathways has yet to be determined. This study was designed to evaluate the role of bcl-2 in preventing allograft rejection in the mouse. A transgenic mouse was established in this lab in which the BCL-2 protooncogene is expressed under the control of the H2K promoter. High levels of bcl-2 were detected in cardiac tissue by Western blot analysis. Hearts from neonates of this founderline and their littermate controls were used in a model of cardiac transplantation across major histocompatibility barriers (H2b--> H2d). Briefly, the heart of a neonatal C57B1/Ka mouse is removed and placed in the subcutaneous tissue of the ear of an adult BALB/c mouse. Hearts which are not rejected are neovascularized and begin to beat. Seventeen neonatal hearts were harvested from two litters of mice which resulted from the cross between a mouse heterozygous for the transgene and a wild type C57B1/Ka. Transplants were performed blindly into seventeen recipients. Spleen was taken from each of the neonates at the time of cardiac harvest and used for analysis of transgenic status. Of the seventeen heart harvested and transplanted, 9 were from mice expressing the transgene and 8 were from wild type littermate controls. Cardiac grafts were monitored visually every two days under 10X magnification for evidence of cardiac contractility. Mean survival time for grafts from the transgenics was 9.33 +/- 1.41 as compared to a mean survival time of 9.25 +/- 1.49 for littermate controls. This difference is not statistically significant, p = 0.9074. These data suggest that BCL-2 overexpression is not sufficient to alter allograft rejection in this model. Analysis is currently underway to assess whether allograft rejection will be affected by higher levels of BCL-2 expression or BCL-2 expression in combination with other genetic deficiencies that affect apoptotic pathways.
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing (2009)

We designed a multiplex short-read DNA sequencing method to perform efficient ChIP-Seq in yeast and other small genome model organisms. This method produces accurate results with higher throughput and reduced cost. Given constant improvements in high-throughput sequencing technologies, increasing multiplexing will be possible to further decrease costs per sample and to accelerate the completion of large consortium projects such as modENCODE.
Olefin Metathesis in Organic Chemistry (1997)

Abstract Transition metal catalyzed CC bond formations belong to the most important reactions in organic synthesis. One particularly interesting reaction is olefin metathesis, a metal‐catalyzed exchange of alkylidene moieties between alkenes. Olefin metathesis can induce both cleavage and formation of CC double bonds. Special functional groups are not necessary. Although this reaction—which can be catalyzed by numerous transition metals—is used in industry, its potential in organic synthesis was not recognized for many years. The recent abrupt end to this Sleeping‐Beauty slumber has several reasons. Novel catalysts can effect the conversion of highly fictionalized and sterically demanding olefins under mild reaction conditions and in high yields. Improved understanding of substrate–catalyst interaction has greatly contributed to the recent establishment of olefin metathesis as a synthetic method. In addition to the preparation of polymers with fine‐tuned characteristics, the metathesis today also provides new routes to compounds of low molecular weight. The highly developed ring‐closing metathesis has been proven to be key step in the synthesis of a growing number of natural products. At the same time interesting applications can be envisioned for newly developed variants of bimolecular metathesis. Improvements in the selective cross‐metathesis of acyclic olefins as well as promising attempts to include alkynes as viable substrates provide for a vivid development of the metathesis chemistry.
Removal of Hydrogen Peroxide by Thiol-specific Antioxidant Enzyme (TSA) Is Involved with Its Antioxidant Properties (1996)

The thiol-specific antioxidant protein (TSA) protects glutamine synthetase from inactivation by a metal-catalyzed oxidation (MCO) system comprised of dithiothreitol (DTT)/Fe3+/O2 but not by the ascorbate/Fe3+/O2 MCO system. The removal of sulfur-centered radicals or H2O2 has been proposed as the protective mechanism of TSA. Like catalase, TSA prevents the initiation of the rapid O2 uptake phase during MCO of DTT but causes only partial inhibition when added after the reaction is well into the propagation phase. Stoichiometric studies showed that the antioxidant property of TSA is, at least in part, due to its ability to catalyze the destruction of H2O2 by the overall reaction 2 RSH + H2O2 --> RSSR + H2O. Results of kinetic studies demonstrate that the removal of H2O2 by TSA correlates with its ability to protect glutamine synthetase from inactivation. In the presence of thioredoxin, TSA is more active, whereas C170S (an active mutant of TSA in which cysteine 170 was replaced by a serine) and open reading frame 6 (a human antioxidant protein homologous to TSA with only one conserved cysteine residue) are only slightly affected. The thiol specificity of the protective activity of TSA derives from the fact that the oxidized form of TSA can be converted back to its sulfhydryl form by treatment with thiols but not by ascorbate.
Mammalian cell penetration, siRNA transfection, and DNA transfection by supercharged proteins (2009)

Nucleic acid reagents, including small interfering RNA (siRNA) and plasmid DNA, are important tools for the study of mammalian cells and are promising starting points for the development of new therapeutic agents. Realizing their full potential, however, requires nucleic acid delivery reagents that are simple to prepare, effective across many mammalian cell lines, and nontoxic. We recently described the extensive surface mutagenesis of proteins in a manner that dramatically increases their net charge. Here, we report that superpositively charged green fluorescent proteins, including a variant with a theoretical net charge of +36 (+36 GFP), can penetrate a variety of mammalian cell lines. Internalization of +36 GFP depends on nonspecific electrostatic interactions with sulfated proteoglycans present on the surface of most mammalian cells. When +36 GFP is mixed with siRNA, protein-siRNA complexes approximately 1.7 mum in diameter are formed. Addition of these complexes to five mammalian cell lines, including four that are resistant to cationic lipid-mediated siRNA transfection, results in potent siRNA delivery. In four of these five cell lines, siRNA transfected by +36 GFP suppresses target gene expression. We show that +36 GFP is resistant to proteolysis, is stable in the presence of serum, and extends the serum half-life of siRNA and plasmid DNA with which it is complexed. A variant of +36 GFP can mediate DNA transfection, enabling plasmid-based gene expression. These findings indicate that superpositively charged proteins can overcome some of the key limitations of currently used transfection agents.
Prospects of Cell Therapy for Disorders of Myelin (2008)

Recent advances in stem cell biology have raised expectations that both diseases of, and injuries to, the central nervous system may be ameliorated by cell transplantation. In particular, cell therapy has been studied for inducing efficient remyelination in disorders of myelin, including both the largely pediatric disorders of myelin formation and maintenance and the acquired demyelinations of both children and adults. Potential cell-based treatments of two major groups of disorders include both delivery of myelinogenic replacements and mobilization of residual oligodendrocyte progenitor cells as a means of stimulating endogenous repair; the choice of modality is then predicated upon the disease target. In this review we consider the potential application of cell-based therapeutic strategies to disorders of myelin, highlighting the promises as well as the problems and potential perils of this treatment approach.
Retroviral transfer and expression of the interleukin-3 gene in hemopoietic cells. (1987)

A recombinant retrovirus containing the interleukin-3 (IL3) coding sequence and the neomycin-resistance gene (Neor) has been generated. Infection of fetal liver cells with the IL3 retrovirus, but not with the N2 parental virus, resulted in the formation of factor-independent, NeoR colonies containing various types of differentiated hemopoietic cells. Established cell lines could be generated from these mixed hemopoietic colonies. These cell lines contained the unrearranged viral genome, produced viral IL3, and secreted the growth factor; however, they were not tumorigenic. Identical results were obtained from infection of two factor-dependent cell lines with the IL3 virus, except that these clones all became tumorigenic. These data indicate that endogenous IL3 production can support normal differentiation and immortalization of primary hemopoietic cells, or, in previously immortalized cells, can lead to tumorigenicity.
From Dendrimers to Knedel‐like Structures (1997)

Abstract Shell‐crosslinked knedels are nanometer‐sized (5–200 nm diameters), amphiphilic core‐shell spheres that are prepared by the self‐assembly of amphiphilic block copolymers into polymer micelles, followed by crosslinking of side chain functionalities along the block composing the shell of the polymer micelles. Such structures resemble dendrimers in the basic structural components, and have the advantages of a rapid synthetic approach and the production of larger and broader size ranges.
Consensus in Ad Hoc WSNs With Noisy Links—Part I: Distributed Estimation of Deterministic Signals (2007)

We deal with distributed estimation of deterministic vector parameters using ad hoc wireless sensor networks (WSNs). We cast the decentralized estimation problem as the solution of multiple constrained convex optimization subproblems. Using the method of multipliers in conjunction with a block coordinate descent approach we demonstrate how the resultant algorithm can be decomposed into a set of simpler tasks suitable for distributed implementation. Different from existing alternatives, our approach does not require the centralized estimator to be expressible in a separable closed form in terms of averages, thus allowing for decentralized computation even of nonlinear estimators, including maximum likelihood estimators (MLE) in nonlinear and non-Gaussian data models. We prove that these algorithms have guaranteed convergence to the desired estimator when the sensor links are assumed ideal. Furthermore, our decentralized algorithms exhibit resilience in the presence of receiver and/or quantization noise. In particular, we introduce a decentralized scheme for least-squares and best linear unbiased estimation (BLUE) and establish its convergence in the presence of communication noise. Our algorithms also exhibit potential for higher convergence rate with respect to existing schemes. Corroborating simulations demonstrate the merits of the novel distributed estimation algorithms.
Placental growth factor gene expression in human prostate cancer and benign prostate hyperplasia. (2004)

PlGF mRNA was expressed in human prostate. Significantly lower levels of PlGF in CAP in comparison with those in BPH or CAP-Tx suggested that PlGF might have effects on vasculogenesis and angiogenesis in prostate disease.
A New Formulation for Shape from Shading for Non-Lambertian Surfaces (2006)

Lambert’s model for diffuse reflection is a main assumption in most of shape from shading (SFS) literature. Even with this simplified model, the SFS is still a difficult problem. Nevertheless, Lambert’s model has been proven to be an inaccurate approximation of the diffuse component of the surface reflectance. In this paper, we propose a new solution of the SFS problem based on a more comprehensive diffuse reflectance model: the Oren and Nayar model. In this work, we slightly modify this more realistic model in order to take into account the attenuation of the illumination due to distance. Using the modified non-Lambertian reflectance, we design a new explicit Partial Differential Equation (PDE) and then solve it using Lax-Friedrichs Sweeping method. Our experiments on synthetic data show that the proposed modeling gives a unique solution without any information about the height at the singular points of the surface. Additional results for real data are presented to show the efficiency of the proposed method . To the best of our knowledge, this is the first non-Lambertian SFS formulation that eliminates the concave/convex ambiguity which is a well known problem in SFS.
Inducible Expression of Cre Recombinase in the Retinal Pigmented Epithelium (2008)

Transgenic mice were generated that express Cre recombinase in the RPE in an inducible fashion. These mice will be useful for studies of the RPE-specific role of genes that are expressed in the RPE as well as other cells, particularly for avoiding embryonic lethality and dissecting the function of genes that play dual roles in development and adulthood.
A Wearable Patch to Enable Long-Term Monitoring of Environmental, Activity and Hemodynamics Variables (2015)

We present a low power multi-modal patch designed for measuring activity, altitude (based on high-resolution barometric pressure), a single-lead electrocardiogram, and a tri-axial seismocardiogram (SCG). Enabled by a novel embedded systems design methodology, this patch offers a powerful means of monitoring the physiology for both patients with chronic cardiovascular diseases, and the general population interested in personal health and fitness measures. Specifically, to the best of our knowledge, this patch represents the first demonstration of combined activity, environmental context, and hemodynamics monitoring, all on the same hardware, capable of operating for longer than 48 hours at a time with continuous recording. The three-channels of SCG and one-lead ECG are all sampled at 500 Hz with high signal-to-noise ratio, the pressure sensor is sampled at 10 Hz, and all signals are stored to a microSD card with an average current consumption of less than 2 mA from a 3.7 V coin cell (LIR2450) battery. In addition to electronic characterization, proof-of-concept exercise recovery studies were performed with this patch, suggesting the ability to discriminate between hemodynamic and electrophysiology response to light, moderate, and heavy exercise.
Terman, Lewis M. (1877–1956) (2008)

Terman, Lewis M. (1877–1956) Paul Irvine, Paul Irvine Katonah, New YorkSearch for more papers by this author Paul Irvine, Paul Irvine Katonah, New YorkSearch for more papers by this author First published: 15 July 2008 https://doi.org/10.1002/9780470373699.speced2063 Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article. Encyclopedia of Special EducationBrowse other articles of this reference work:BROWSE A-Z RelatedInformation