gebhart/patrepeval huggingface dataset:
Predicting the diagnosis of autism spectrum disorder using gene pathway analysis (2012)

Autism spectrum disorder (ASD) depends on a clinical interview with no biomarkers to aid diagnosis. The current investigation interrogated single-nucleotide polymorphisms (SNPs) of individuals with ASD from the Autism Genetic Resource Exchange (AGRE) database. SNPs were mapped to Kyoto Encyclopedia of Genes and Genomes (KEGG)-derived pathways to identify affected cellular processes and develop a diagnostic test. This test was then applied to two independent samples from the Simons Foundation Autism Research Initiative (SFARI) and Wellcome Trust 1958 normal birth cohort (WTBC) for validation. Using AGRE SNP data from a Central European (CEU) cohort, we created a genetic diagnostic classifier consisting of 237 SNPs in 146 genes that correctly predicted ASD diagnosis in 85.6% of CEU cases. This classifier also predicted 84.3% of cases in an ethnically related Tuscan cohort; however, prediction was less accurate (56.4%) in a genetically dissimilar Han Chinese cohort (HAN). Eight SNPs in three genes (KCNMB4, GNAO1, GRM5) had the largest effect in the classifier with some acting as vulnerability SNPs, whereas others were protective. Prediction accuracy diminished as the number of SNPs analyzed in the model was decreased. Our diagnostic classifier correctly predicted ASD diagnosis with an accuracy of 71.7% in CEU individuals from the SFARI (ASD) and WTBC (controls) validation data sets. In conclusion, we have developed an accurate diagnostic test for a genetically homogeneous group to aid in early detection of ASD. While SNPs differ across ethnic groups, our pathway approach identified cellular processes common to ASD across ethnicities. Our results have wide implications for detection, intervention and prevention of ASD.
AL-8810: a novel prostaglandin F2 alpha analog with selective antagonist effects at the prostaglandin F2 alpha (FP) receptor. (1999)

A novel analog of prostaglandin F(2alpha) [AL-8810; (5Z, 13E)-(9S, 11S,15R)-9,15-dihydroxy-11-fluoro-15-(2-indanyl)-16,17,18,19, 20-pentanor-5,13-prostadienoic acid] has been discovered with uniquely low efficacy (E(max)) at the endogenous prostaglandin F(2alpha) receptors (FP receptors) of A7r5 rat thoracic aorta smooth muscle cells and Swiss mouse 3T3 fibroblasts, as assayed by stimulation of phospholipase C activity. AL-8810 has weak agonist potency (EC(50)) of 261 +/- 44 nM (n = 3) and E(max) = 19% (relative to the full FP receptor agonist cloprostenol) in A7r5 cells and EC(50) of 186 +/- 63 nM (n = 3) and E(max) = 23% in 3T3 fibroblasts. AL-8810 exhibited properties of an apparent competitive antagonist, i.e., produced parallel dextral shifts of the agonist concentration-response curves and no significant suppression of the maximal agonist-induced response, when the potent, selective FP receptor agonist fluprostenol was used. The inhibition parameters of AL-8810 were: pA(2) = 6.68 +/- 0.23 and 6.34 +/- 0.09 (n = 3-4) for A7r5 cells and 3T3 cells, respectively, with Schild slopes ranging from 0.80 to 0.92. AL-8810 concentration-dependently antagonized the response to 100 nM fluprostenol (K(i) = 426 +/- 63 nM; n = 5) in A7r5 cells. However, even at 10 microM concentration, AL-8810 did not significantly inhibit functional responses of TP, DP, EP(2), EP(4), receptor subtypes in various cell lines. AL-8810 also did not antagonize the phospholipase C-coupled V(1)-vasopressin receptor in A7r5 cells. These results suggest that AL-8810 is a unique, selective antagonist at the FP receptor, a heretofore unavailable pharmacological tool that should be valuable for studying FP receptor-mediated functional responses in complex biological systems.
Bovine Liver Crotonase (1973)

The coenzyme A thioesters of cinnamic acid, cyclohexene-I-carboxylic acid, and of three halocrotonic acids are reported as new substrates of bovine liver crotonase.
Safety, tolerability, and efficacy of long-term administration of AMG 145: preliminary results from the OSLER study (2013)

Purpose: Four Phase 2 studies showed that 12 weeks of treatment with AMG 145, a fully human monoclonal antibody against PCSK9, was well tolerated and significantly reduced LDL-C in diverse groups of subjects with hypercholesterolemia. To date, the long-term safety and efficacy of AMG 145 or PCSK9 inhibition therapy have been undefined. Methods: Subjects who completed any of the Phase 2 studies could participate in the OSLER open-label extension study. Most subjects enrolled within 3 days of the last phase 2 study visit. Subjects were randomized 2:1 to receive AMG 145 420 mg monthly with standard of care (SOC) or SOC alone for 1 year. The primary objective was to evaluate the safety and tolerability of AMG 145 on a background of SOC. Secondary objectives were effects on lipid parameters compared to Phase 2 study baseline. Results: A total of 1104 subjects enrolled in the OSLER extension study (81% of those eligible). As of November 9, 2012, 708 (mean age 56±12 years, 44% male) randomized subjects had completed at least 1 year of follow-up (Phase 2 study plus OSLER). See table for adverse events rates and mean LDL-C results. Additional long-term data will be ready for presentation at ESC 2013. Safety and Efficacy Summary NA, not applicable. *Hepatotoxicity event (Transaminase elevation >5× but <10× ULN). †Of these, 2 were serious, and 10 were treatment-related (all non-serious). Conclusions: Monthly AMG 145 dosing demonstrated encouraging safety, tolerability and sustained efficacy during prolonged treatment of hyperlipidemia.
Long-term outcome of unilaterally transplanted parkinsonian patients (1996)

Five patients with Parkinson's disease, unilaterally transplanted with foetal mesencephalic cells into putamen (n=1) or putamen and caudate (n=4), were followed throughout a period of 15-36 months after surgery, according to the recommendations of the core assessment programme for intracerebral transplantations (CAPIT). All these patients exhibited an increase in the fluorodopa uptake in the grafted putamen, which was most significant in the first and last patient of the series. Long-term bilateral improvement of skilled hand movements was observed, starting between the third and sixth month after grafting, and confirmed by the statistical analysis of CAPIT timed tests. A mild to moderate effect on the amount of 'off' time and 'on-off' fluctuations was observed, whereas, apart from one case, no other clear effect on gait, walking and speech was found. One patient included in the study, already suffering slight cognitive impairment, clearly exhibited progression of a dementia process after surgery. Daily living activities were clearly improved in only one of the other four patients. At the end of the study period, all patients needed L-dopa therapy at a similar or higher dose than before grafting, but, in most of them, other dopaminergic drugs were reduced or stopped. All patients exhibited bilateral dyskinesias before grafting that were greatly decreased in intensity a few months after surgery. Delayed asymmetrical dyskinesias, occurring on the side displaying the better motor improvement, i.e. contralateral to the graft, were observed in three patients. These results suggest that neural transplants may influence two central mechanisms involved in motor function and the onset of dyskinesias. These effects are likely to occur through complex interactions with the post-synaptic dopaminergic receptors. The occurrence of dyskinesias might simply reflect increased presynaptic storage and release of dopamine. Alternatively, it might, in part, represent some other long-term deleterious effect of the graft. Since PET-scan data indicate that the reinnervation obtained is sub-optimal, it will be of interest to obtain a larger and denser reinnervation of the host striatum and to try, thereafter, to reduce the dose of L-dopa.
Specificity and mechanism of protein kinase C activation by sn-1,2-diacylglycerols. (1986)

The specificity of protein kinase C activation by sn-1,2-diacylglycerols and analogues was investigated by using a Triton X-100 mixed micellar assay [Hannun, Y. A., Loomis, C. R. & Bell, R. M. (1985) J. Biol. Chem. 260, 10039-10043]. Analogues containing acyl or alkyl chains eight carbons in length were synthesized because sn-1,2-dioctanoylglycerol is an effective cell-permeant activator of protein kinase C. These analogues were tested as activators and antagonists of rat brain protein kinase C to determine the exact structural features important for activity. The analogues established that activation of protein kinase C by diacylglycerols is highly specific. Several analogues established that both carbonyl moieties of the oxygen esters are required for maximal activity and that the 3-hydroxyl moiety is also required. None of the analogues were antagonists. These data, combined with previous investigations, permitted formulation of a model of protein kinase C activation. A three-point attachment of sn-1,2-diacylglycerol to the surface-bound protein kinase C-phosphatidylserine-Ca2+ complex is envisioned to cause activation. Direct ligation of diacylglycerol to Ca2+ is proposed to be an essential step in the mechanism of activation of protein kinase C.
Organic Photoredox Catalysis (2016)

In this review, we highlight the use of organic photoredox catalysts in a myriad of synthetic transformations with a range of applications. This overview is arranged by catalyst class where the photophysics and electrochemical characteristics of each is discussed to underscore the differences and advantages to each type of single electron redox agent. We highlight both net reductive and oxidative as well as redox neutral transformations that can be accomplished using purely organic photoredox-active catalysts. An overview of the basic photophysics and electron transfer theory is presented in order to provide a comprehensive guide for employing this class of catalysts in photoredox manifolds.
Assessment of Free‐Living Physical Activity in Humans: An Overview of Currently Available and Proposed New Measures (2001)

The number of physical activity measures and indexes used in the human literature is large and may result in some difficulty for the average investigator to choose the most appropriate measure. Accordingly, this review is intended to provide information on the utility and limitations of the various measures. Its primary focus is the objective assessment of free-living physical activity in humans based on physiological and biomechanical methods. The physical activity measures have been classified into three categories: Measures based on energy expenditure or oxygen uptake, such as activity energy expenditure, activity-related time equivalent, physical activity level, physical activity ratio, metabolic equivalent, and a new index of potential interest, daytime physical activity level. Measures based on heart rate monitoring, such as net heart rate, physical activity ratio heart rate, physical activity level heart rate, activity-related time equivalent, and daytime physical activity level heart rate. Measures based on whole-body accelerometry (counts/U time). Quantification of the velocity and duration of displacement in outdoor conditions by satellites using the Differential Global Positioning System may constitute a surrogate for physical activity, because walking is the primary activity of man in free-living conditions. A general outline of the measures and indexes described above is presented in tabular form, along with their respective definition, usual applications, advantages, and shortcomings. A practical example is given with typical values in obese and non-obese subjects. The various factors to be considered in the selection of physical activity methods include experimental goals, sample size, budget, cultural and social/environmental factors, physical burden for the subject, and statistical factors, such as accuracy and precision. It is concluded that no single current technique is able to quantify all aspects of physical activity under free-living conditions, requiring the use of complementary methods. In the future, physical activity sensors, which are of low-cost, small-sized, and convenient for subjects, investigators, and clinicians, are needed to reliably monitor, during extended periods in free-living situations, small changes in movements and grade as well as duration and intensity of typical physical activities.
In vivo Detection of Monosomy 3 in Eyes with Medium-Sized Uveal Melanoma using Transscleral Fine Needle Aspiration Biopsy (2006)

This study demonstrates that medium choroidal melanomas may be safely sampled by intraoperative transscleral FNAB to detect monosomy 3 in vivo.
Aging Does Not Affect the Activation of the Myocyte Insulin-Like Growth Factor-1 Autocrine System After Infarction and Ventricular Failure in Fischer 344 Rats (1996)

To determine whether the attenuation in the growth capacity of myocytes in the overloaded aging heart is associated with an impairment in the activation of insulin-like growth factor-1 (IGF-1) and its receptor (IGF-1R) in the stressed cells, large myocardial infarcts were produced in Fischer 344 rats at 4 and 16 months of age, and the animals were killed 6 hours, 3 days, and 7 days later. After the documentation of cardiac failure, the unaffected myocytes were enzymatically dissociated, and the expression of IGF-1 and IGF-1R was measured at these three time points after surgery. The level of expression of IGF-1R mRNA increased at 3 days and remained elevated at 7 days in both age groups. In addition, an increase in IGF-1R protein in these cells was found, with no apparent difference with age. This phenomenon was coupled with an upregulation of IGF-1 mRNA of comparable magnitude in the younger and older animals. In contrast, the increases in the dimensional properties of myocytes were delayed and of smaller magnitude in the older infarcted rats. Moreover, the expression of atrial natriuretic factor, used as a molecular marker of myocyte cellular hypertrophy, was greater at 3 days in 4-month-old rats and at 7 days in 16-month-old rats. Thus, aging may affect the hypertrophic response of myocytes after infarction but has no impact on the ability of the cells to enhance the expression of IGF-1 and IGF-1R, which may sustain only in part the growth reserve mechanisms of the pathological heart.
Quantitative phase imaging by three-wavelength digital holography (2008)

Three-wavelength digital holography is applied to obtain surface height measurements over several microns of range, while simultaneously maintaining the low noise precision of the single wavelength phase measurement. The precision is preserved by the use of intermediate synthetic wavelength steps generated from the three wavelengths and the use of hierarchical optical phase unwrapping. As the complex wave-front of each wavelength can be captured simultaneously in one digital image, real-time performance is achievable.
Ligation of oligonucleotides to nucleic acids or proteins via disulfide bonds (1988)

We have developed general methods for joining together, via cleavable disulfide bonds, either two unprotected polynucleotides or a polynucleotide and a peptide or protein. To join two oligonucleotides, each is first converted to an adduct in which cystamine is joined to the 5'-terminal phosphate of the oligonucleotide by a phosphoramidate bond. The adducts are mixed and reduced with dithiothreitol. The dithiothreitol is then removed by dialysis. Oxidation by atmospheric oxygen occurs to yield the required dimer. To join an oligonucleotide to a cysteine-containing peptide or protein, the 5'-cystamine oligomer is first converted to a 2'-pyridyldisulfide adduct and then reacted with an excess of the peptide or protein. If the peptide does not contain a free cysteine residue, it is first treated with iminothiolane to introduce one or more sulfhydryl groups. We have used these procedures to join a 16 mer deoxynucleotide probe and MDV-1 RNA, a substrate of Q beta RNA polymerase. This adduct hybridizes with a complementary target DNA. We have also joined a 16mer probe to peroxidase and MDV-1 RNA to human IgG. The probe-peroxidase adduct maintains enzymatic activity and the MDV-1 RNA-IgG adduct binds to a complementary anti-IgG.
Spatial Prediction Filters For Attenuation Of Seismic Interference Noise (2005)

Publication in the conference proceedings of EUSIPCO, Antalya, Turkey, 2005
Power Attacks on Secure Hardware Based on Early Propagation of Data (2006)

The early propagation effect found in many logic gates is a potential source of data-dependent power consumption. We show that the effect and the corresponding power dependency can be targeted for successful power analysis attacks in cryptographic hardware. Many of the current balanced gate designs did not directly consider the effect and are vulnerable to power analysis attacks
Quill: an extensible system for editing documents of mixed type (2003)

A description is given of Quill, an extensible document creation system that is organized as a collection of cooperating editors, each with its own set of objects and commands. The objects implemented by the various editors can be nested without restriction, forming a hierarchical document that can be described by the Standard Generalized Markup Language (SGML). The user is presented with a 'what you see is what you get' (WYSIWYG) view of the document in which the various objects can be directly manipulated on the display screen. A system shell ensures consistency among the editors and coordinates their foreground and background activities to ensure keystroke responsiveness. Each Quill editor is a programming object that communicate with the shell and with other editors by means of a standard set of procedures. A rigorous specification of the shell/editor interface enables additional editors to be added to the Quill system without affecting the existing editors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A novel photodegradable hyperbranched polymeric photoresist (2013)

We report the first synthesis of a photodegradable hyperbranched polyacetal, wherein every repeat unit carries a photo-labile 2-nitrobenzyloxy moiety. The pristine HBP serves as a positive photoresist to create micron-size patterns; furthermore, by changing the terminal groups to dipropargyl acetal, clickable photo-patterned substrates can be generated.
Automated bead-trapping apparatus and control system for single-molecule DNA sequencing (2008)

We have been investigating a microfluidics platform for high-speed, low-cost sequencing of single DNA molecules using novel "charge-switch" nucleotides. A significant challenge is the design of a flowcell suitable for manipulating bead-DNA complexes and sorting labeled polyphosphate molecules by charge. The flowcell is part of a single-molecule detection instrument, creating fluorescence images from labeled polyphosphates. These images would ultimately be analyzed by signal processing algorithms to identify specific nucleotides in a DNA sequence. Here we describe requirements of the fluidics system for loading, identifying, tracking, and positioning beads. By dynamically modulating pressure gradients in the plenum chambers of a multi-channel network, we could guide individual beads with high precision to any desired coordinate and reversibly trap them in stepped channels. We show that DNA immobilized on pressure-trapped beads can be physically extended into a downstream channel under electric force for analysis. Custom dynamic algorithms for automated bead control are described.
Structure of the gene for the human myeloid IgA Fc receptor (CD89) (1995)

A better understanding of IgA's role in immunity requires insight in IgAR complexity. We have now isolated, characterized, and sequenced the gene encoding the prototypic human myeloid IgA FcR (CD89). The gene consists of five exons and spans approximately 12 kilobase pairs. The leader peptide is encoded by two exons, the second of which is 36 bp long and specifies the predicted peptidase cleavage site. A similar, but shorter (21 bp) mini-exon has been found in the FcR for IgG (Fc gamma R) genes, and the FcR for IgE (Fc epsilon RI alpha) gene (human and rodent). The third and fourth exons code for two homologous Ig-like domains. The final exon encodes a short extracellular region, a hydrophobic transmembrane region, and a short cytoplasmic tail. The sequence of the 5'-flanking region was determined, and one major and several minor transcription initiation sites were mapped by primer extension studies. A putative TATA box was located at an appropriate location relative to the start site. Southern blot analyses of genomic DNA confirm the restriction map generated from cloned DNA. These data define the Fc alpha R gene as a distantly related member of the IgR gene family.
Histology and cell biology (1991)

Histology and cell biology , Histology and cell biology , کتابخانه الکترونیک و دیجیتال - آذرسا
Sequence-controlled multi-block copolymerization of acrylamides via aqueous SET-LRP at 0 °C (2014)

Aqueous single electron transfer living radical polymerization (SET-LRP) has been employed to synthesize multi-block homopolymers and copolymers of a range of acrylamide monomers including <italic>N</italic>-isopropylacrylamide (NIPAM), 2-hydroxyethyl acrylamide (HEAA), <italic>N</italic>,<italic>N</italic>-dimethyl acrylamide (DMA) and <italic>N</italic>,<italic>N</italic>-diethylacrylamide (DEA).
Ab Initio Emulsion Polymerization by RAFT-Controlled Self-Assembly (2005)

A method is developed to enable emulsion polymerization to be performed under RAFT control to give living character without the problems that often affect such systems: formation of an oily layer, loss of colloidal stability, or loss of molecular weight control. Trithiocarbonate RAFT agents are used to form short stabilizing blocks from a water-soluble monomer, from which diblocks can be created by the subsequent polymerization of a hydrophobic monomer. These diblocks are designed to self-assemble to form micelles. Polymerization is initially performed under conditions that avoid the presence of monomer droplets during the particle formation stage and until the hydrophobic ends of the diblocks have become sufficiently long to prevent them from desorbing from the newly formed particles. Polymerization is then continued at any desired feed rate and composition of monomer. The polymer forming in the reaction remains under RAFT control throughout the polymerization; molecular weight polydispersities are generally low. The number of RAFT-ended chains within a particle is much larger than the aggregation number at which the original micelles would have self-assembled, implying that in the early stages of the polymerization, there is aggregation of the micelles and/or migration of the diblocks. The latexes resulting from this approach are stabilized by anchored blocks of the hydrophilic monomer, e.g., acrylic acid, with no labile surfactant present. Sequential polymerization of two hydrophobic monomers gives completely novel core−shell particles where most chains extend from the core of the particles through the shell layer to the surface.