gebhart/patrepeval huggingface dataset:
Quantitative Dynamics of Site-Specific Protein Phosphorylation Determined Using Liquid Chromatography Electrospray Ionization Mass Spectrometry (2002)

We have developed and validated a method that uses liquid chromatography/electrospray ionization-mass spectrometry to quantify site-specific protein phosphorylation. The method uses selected ion monitoring to determine the chromatographic peak areas of specific tryptic peptides from the protein of interest. The extent of phosphorylation is determined from the ratio of the phosphopeptide peak area to the peak area of an unmodified reference peptide that acts as internal standard, correcting for variations in protein amounts and peptide recovery in the digest preparation procedure. As a result, we refer to this protocol as the native reference peptide method. Mole of phosphate at the selected site per mole of protein is obtained from this ratio, using calibration curves of synthetic peptides to determine relative responses. Our method begins with protein separation by SDS-PAGE and is carried out on amounts of peptide produced by an in-gel digestion of single Coomassie blue-stained bands. To illustrate the utility of the method and provide validation, we used cardiac troponin I as analyte and monitored the time course of a protein kinase C betaII reaction. Those analyses appropriately demonstrate the time-dependent increase of phosphorylation at a PKC-preferred site, Ser44 in the peptide 41ISASPR45 and the concomitant consumption of the nonphosphorylated peptide. We believe that this method provides a novel tool to directly measure specific phosphorylation sites in proteins in different physiological states and expect that the method will be adaptable not only to a variety of samples types (i.e., culture cells, tissues, etc.) but to a variety of posttranslation modifications as well.
Protein assembly and DNA looping by the FokI restriction endonuclease (2006)

The FokI restriction endonuclease recognizes an asymmetric DNA sequence and cuts both strands at fixed positions upstream of the site. The sequence is contacted by a single monomer of the protein, but the monomer has only one catalytic centre and forms a dimer to cut both strands. FokI is also known to cleave DNA with two copies of its site more rapidly than DNA with one copy. To discover how FokI acts at a single site and how it acts at two sites, its reactions were examined on a series of plasmids with either one recognition site or with two sites separated by varied distances, sometimes in the presence of a DNA-binding defective mutant of FokI. These experiments showed that, to cleave DNA with one site, the monomer bound to that site associates via a weak protein-protein interaction with a second monomer that remains detached from the recognition sequence. Nevertheless, the second monomer catalyses phosphodiester bond hydrolysis at the same rate as the DNA-bound monomer. On DNA with two sites, two monomers of FokI interact strongly, as a result of being tethered to the same molecule of DNA, and sequester the intervening DNA in a loop.
Security for mobile ATE applications (2012)

Measurement data collected from hardware systems using a mobile application needs to be protected from falling into malicious hands. To circumvent security concerns, many sensitive ATE systems are simply isolated from networks and run in stand-alone environments. Using mobile connections with ATE equipment introduces a whole new level of security issues which can be a large concern for many companies. These concerns can generally be overcome by using a number of industry standard security protocols.
Multi-Pipeline Geographical Information System Based on High Accuracy Inertial Surveys (2000)

This paper describes the GIS system developed for the Pemex’ pipeline network in the Valley of Mexico. The pipeline UTM coordinates, which are the basis of the GIS, were obtained from the high accuracy Geopig® inertial and caliper surveys. The survey data also included information on pipeline features and anomalies, and was incorporated into the GIS together with the metal loss data from the past in-line inspections. The system is based on the ArcView® GIS Software with the Arc View 3D Analyst™ extension that allows both the cartography and pipeline data to be viewed in 3-D space. It stores information on pipeline plan, profile, girth weld locations, dents, wall thickness, bending strains, metal loss and other features in relation to known landmarks such as roads, buildings, political boundaries and hydrology. This allows for very efficient and accurate location of pipe defects and anomalies, which is particularly beneficial where there are several pipelines running in the same right-of-way. It helps to eliminate unnecessary excavations, as well as to coordinate, plan and schedule pipeline repairs. The additional benefit of a multi-pipeline GIS system is the ability to store various information for all the pipelines in one database, which is easy to manage and update. The GIS also gives the ability to plot detailed maps, query data for effective solutions and visualize scenarios.
Distributed wavelet transform for irregular sensor network grids (2005)

Wavelet-based distributed data processing holds much promise for sensor networks; however, irregular sensor node placement precludes the direct application of standard wavelet techniques. We develop a new distributed wavelet transform based on lifting that takes into account irregular sampling and provides a piecewise-planar multiresolution representation of the sensed data. We develop the transform theory; outline how to implement it in a multi-hop, wireless sensor network; and illustrate with several simulations. The new transform performs on par with conventional wavelet methods in a head-to-head comparison on a regular grid of sensor nodes
Neuropsychological Sequelae of Cardiac Arrest (1993)

Moderate to severe neuropsychological sequelae of out-of-hospital cardiac arrest are still present in approximately one half of the survivors at 1 year and may be permanent. There seems to be no excess of increased disability in the subgroup of patients with delayed advanced life support. Nimodipine failed to show any effect on the cognitive functions tested.
[Adeno-associated virus-mediated expression of human endostatin and its biological activity in vitro]. (2005)

rAAV-hEndo can effectively mediate the expression of biologically active human endostatin, which may facilitate further study of antiangiogenic gene therapy with endostatin for cancers.
Using frequency detuning to improve the sensitivity of electric field measurements via electromagnetically induced transparency and Autler-Townes splitting in Rydberg atoms (2016)

In this work, we demonstrate an approach for improved sensitivity in weak radio frequency (RF) electric-field strength measurements using Rydberg electromagnetically induced transparency (EIT) in an atomic vapor. This is accomplished by varying the RF frequency around a resonant atomic transition and extrapolating the weak on-resonant field strength from the resulting off-resonant Autler-Townes (AT) splittings. This measurement remains directly traceable to SI compared to previous techniques, precluding any knowledge of experimental parameters such as optical beam powers as is the case when using the curvature of the EIT line shape to measure weak fields. We use this approach to measure weak RF fields at 182 GHz and 208 GHz demonstrating improvement greater than a factor of 2 in the measurement sensitivity compared to on-resonant AT splitting RF electric field measurements.
Model based segmentation of nuclei (2003)

A new approach for segmentation of nuclei observed with an epi-fluorescence microscope is presented. The technique is model based and uses local feature activities such as step-edge segments, roof-edge segments, and concave corners to construct a set of initial hypotheses. These local feature activities are extracted using either local or global operators to form a possible set of hypotheses. Each hypothesis is expressed as a hyperquadric for better stability, compactness, and error handling. The search space is expressed as an assignment matrix with an appropriate cost function to ensure local adjacency, and global consistency. Each possible configuration of a set of nuclei defines a path, and the path with the least error corresponds to best representation. This result is then presented to an operator who verifies and eliminates a small number of errors.
Ischemia-Reperfusion Injury Activates Innate Immunity in Rat Kidneys (2005)

I/R injury rapidly activates the innate immune response.
A perspective on mammalian upstream open reading frame function (2013)

Post-transcriptional control makes a major contribution to the overall regulation of gene expression pathway. Within the cytoplasm this is mediated by a combination of regulatory RNA motifs within the 5' and 3' untranslated regions of mRNAs and their interacting protein/RNA partners. One of the most common regulatory RNA elements in mammalian transcripts (present in approximately 40% of all mRNAs) are upstream open reading frames (uORFs). However, despite the prevalence of these RNA elements how they function is not well understood. In general, they act to repress translation of the physiological ORF under control conditions, and under certain pathophysiological stresses this repression can be alleviated. It is known that re-initiation following the translation of an uORF is utilised in some situations however there are numerous alternative mechanisms that control the synthesis of a protein whose mRNA contains uORFs. Moreover, the trans-acting factors that are also involved in this process are not well defined. In this review we summarise our current understanding of this area and highlight some common features of these RNA motifs that have been discovered to date.
Function and Evolution of a MicroRNA That Regulates a Ca2+-ATPase and Triggers the Formation of Phased Small Interfering RNAs in Tomato Reproductive Growth  (2011)

MicroRNAs (miRNAs) regulate a wide variety of biological processes in most eukaryotes. We investigated the function and evolution of miR4376 in the family Solanaceae. We report that the 22-nucleotide miR4376 regulates the expression of an autoinhibited Ca(2+)-ATPase, tomato (Solanum lycopersicum) ACA10, which plays a critical role in tomato reproductive growth. Deep phylogenetic mapping suggested (1) an evolution course of MIR4376 loci and posttranscriptional processing of pre-miR4376 as a likely limiting step for the evolution of miR4376, (2) an independent phylogenetic origin of the miR4376 target site in ACA10 homologs, and (3) alternative splicing as a possible mechanism of eliminating such a target in some ACA10 homologs. Furthermore, miR4376 triggers the formation of phased small interfering RNAs (siRNAs) from Sl ACA10 and its Solanum tuberosum homolog. Together, our data provide experimental evidence of miRNA-regulated expression of universally important Ca(2+)-ATPases. The miR4376-regulated expression of ACA10 itself, and possibly also the associated formation of phased siRNAs, may function as a novel layer of molecular mechanisms underlying tomato reproductive growth. Finally, our data suggest that the stochastic emergence of a miRNA-target gene combination involves multiple molecular events at the genomic, transcriptional, and posttranscriptional levels that may vary drastically in even closely related species.
Primacy and Recency Effects on Clicking Behavior (2006)

As consumers and business increasingly use the Internet, understanding how and why users choose website links or email links becomes correspondingly important. Two recent articles report a monotonic effect of link order and clicking on a link; this means that the higher a link's position in a list of links, the greater the probability that visitors will click on that link. The difference in probability of clicking has important implications for designing webpage navigation for visitors. We report on two field experiments that confirm and extend these studies, showing the efficacy of the first link, a primacy effect. Visitors to a site, however, also show an increased tendency to click on links at the end of the list, a recency effect that previous studies failed to note. This article discusses the potential reasons for recency effects, and the implications of serial position effects more generally.
Development of a Respiratory Inductive Plethysmography Module Supporting Multiple Sensors for Wearable Systems (2012)

In this paper, we present an RIP module with the features of supporting multiple inductive sensors, no variable frequency LC oscillator, low power consumption, and automatic gain adjustment for each channel. Based on the method of inductance measurement without using a variable frequency LC oscillator, we further integrate pulse amplitude modulation and time division multiplexing scheme into a module to support multiple RIP sensors. All inductive sensors are excited by a high-frequency electric current periodically and momentarily, and the inductance of each sensor is measured during the time when the electric current is fed to it. To improve the amplitude response of the RIP sensors, we optimize the sensing unit with a matching capacitor parallel with each RIP sensor forming a frequency selection filter. Performance tests on the linearity of the output with cross-sectional area and the accuracy of respiratory volume estimation demonstrate good linearity and accurate lung volume estimation. Power consumption of this new RIP module with two sensors is very low. The performance of respiration measurement during movement is also evaluated. This RIP module is especially desirable for wearable systems with multiple RIP sensors for long-term respiration monitoring.
Advanced Radiance Estimation For Photon Map Global Illumination (2002)

We present a new method to compute radiance in photon map based global illumination simulation for polygonal scenes with general bidirectional scattering distribution functions (BSDFs). Our new radiance estimation uses the actual geometry in the neighborhood of the illuminated point, and does not assume that the nearest neighbor photons lie in the same plane as the point, nor that they are distributed in a circular area around that point. This allows us to achieve accurate indirect illumination by direct visualization of the photon map — which is especially important for the simulation of caustics (LS+DS*E paths) — even in the vicinity of edges and corners of objects, and on surfaces with differently oriented small geometric details.
Congenital muscular dystrophy: from muscle to brain (2016)

Congenital muscular dystrophies (CMDs) are a wide group of muscular disorders that manifest with very early onset of muscular weakness, sometime associated to severe brain involvement.The histologic pattern of muscle anomalies is typical of dystrophic lesions but quite variable depending on the different stages and on the severity of the disorder.Recent classification of CMDs have been reported most of which based on the combination of clinical, biochemical, molecular and genetic findings, but genotype/phenotype correlation are in constant progression due to more diffuse utilization of the molecular analysis.In this article, the Authors report on CMDs belonging to the group of dystroglycanopathies and in particular on the most severe forms represented by the Fukuyama CMD, Muscle-Eye-Brain disease and Walker Walburg syndrome.Clinical diagnosis of infantile hypotonia is particularly difficult considering the different etiologic factors causing the lesions, the difficulty in localizing the involved CNS area (central vs. peripheral) and the limited role of the diagnostic procedures at this early age.The diagnostic evaluation is not easy mainly in differentiating the various types of CMDs, and represents a challenge for the neonatologists and pediatricians. Suggestions are reported on the way to reach a correct diagnosis with the appropriate use of the diagnostic means.
Visuo-haptic collaborative augmented reality ping-pong (2007)

In our current work we examine the development of visuohaptic augmented reality setups and their extension to collaborative experiences in entertainment settings. To this end, an expandable system architecture supporting multiple users is one of the most indispensable prerequisites. In addition, system stability, low latency, accurate calibration and stable overlay of the virtual objects have to be assured. In this paper we provide an overview of our framework and present our collaborative example application, an augmented reality visuo-haptic ping-pong game for two players. The users play with a virtual ball in a real environmentwhile, by using virtual bats colocated with haptic devices, they are able to feel the impact of the simulated ball on the bat.
Small deletions of the short arm of the Y chromosome in 46,XY females. (1986)

Structural anomalies of the sex chromosomes provide a means to study the location of genes responsible for sex determination. Recently, a type of sex reversal in humans, the 46,XX male, was shown to result in some cases from translocation of Y chromosome material to the X chromosome. In the present report, another type of sex reversal, the 46,XY female, is shown to result, in two cases, from small deletions of the short arm of the Y chromosome. Prometaphase chromosome analysis showed a 46,X,Yp- karyotype. Several Y chromosome-specific DNA probes were found to be deleted in the two female patients. DNA analysis showed that the two deletions were different but included a common overlapping region likely to be essential for male determination.
Blind identification of IIR model based on output over-sampling (1998)

This paper deals with a blind problem for an IIR model in a time domain. Based on an output over-sampling scheme, the proposed algorithm can estimate parameters of an alternative multi-output model description first, then the parameters of original model can be obtained later. It Ceffi be clarified that an IIR model Ceffi be identified by using over-sampling scheme.
A comparative evaluation of random and site‐specific immobilization techniques for the preparation of antibody‐based chiral stationary phases (2006)

In this study, one random and four site-directed conjugation strategies were applied to immobilize an mAb, which stereoselectively binds to L-amino acids, onto silica particles. The resulting chiral stationary phases (CSPs) were used for enantiomer separation of the model-analyte D,L-phenylalanine and further examined in frontal affinity chromatography. Although random immobilization of the antibody onto discuccinimidyl carbonate-activated silica resulted in a CSP that enabled baseline separation of the enantiomers of D,L-phenylalanine, the amount of available binding sites was considerably lower compared to the CSPs prepared by site-directed strategies. Immobilization of antibody via its carbohydrate chains, either directly via hydrazone bonds between the support and the protein or indirectly via binding carbohydrate-biotinylated antibody to streptavidin-derivatized silica, resulted in medium column efficiencies. Higher amounts of available active sites were obtained by immobilizing the antibody indirectly through the "crystallizable fragment (Fc)" receptor protein A/G. The best results with regard to amount of available binding sites and column efficiency were obtained by first biotinylating the antibody specifically at its C-termini using carboxypeptidase Y and immobilizing the biotinylated antibody on streptavidin-derivatized silica.
Increased sensitivity to the platelet‐derived growth factor (PDGF) receptor inhibitor STI571 in chemoresistant glioma cells is associated with enhanced PDGF‐BB‐mediated signaling and STI571‐induced Akt inactivation (2006)

The platelet-derived growth factor receptor (PDGFR) is a tyrosine kinase, implicated in the development and progression of different tumors, including gliomas. Chemoresistance is a common feature of malignant gliomas. Since receptor tyrosine kinases contribute to chemoresistance in tumors, we addressed whether PDGFR signaling might confer selective growth advantage to chemoresistant cells. The effects of the PDGFR inhibitor STI571 on proliferation and PDGFR signaling were compared in chemosensitive and cisplatin-selected, chemoresistant sublines derived from glioma and from two other PDGFR-expressing tumors (ovarian carcinoma and neuroblastoma). The chemoresistant glioma U87/Pt cells were twofold more sensitive to STI571 growth-inhibitory effects than the chemosensitive U87 cells, and two- to threefold more sensitive than five unrelated glioma cell lines. The other two paired cell lines were equally responsive. Sensitization of U87/Pt cells correlated with upregulation of the PDGF-B isoform and with PDGF-BB-induced Akt overactivation, which was prevented by STI571. STI571 specifically inhibited PDGF-BB-, but not PDGF-AA- or stem cell factor-mediated signaling. In serum-containing medium, STI571 decreased phospho-Akt in U87/Pt cells, but not in U87, while activating extracellular signal-regulated kinase (Erk) in both. STI571 antiproliferative effects were partially reverted by constitutively active Akt. Cotreatment with inhibitors of phosphatidylinositol 3'-kinase (PI3K) or mitogen-activated protein kinase kinase (MEK) resulted in enhanced growth inhibition in glioma cells. Our results suggest that increased PDGF-BB signaling may sensitize chemoresistant glioma cells to STI571, suggesting a therapeutic potential for STI571 in patients with malignant gliomas refractory to chemotherapy. Simultaneous blockade of PDGFR and PI3K or Erk pathway may enhance therapeutic targeting in gliomas.
The role of the Cdk5–p35 kinase in neuronal development (2001)

Cyclin-dependent kinase 5 (Cdk5) plays a key role in proper development of the nervous system. To be activated, Cdk5 associates with regulatory subunits not related to cyclins, such as p35 (the regulatory subunit of Cdk5). In this article, we review some of the experimental evidence supporting a central role for the Cdk5/p35 kinase in neuronal migration and process formation.
Fast power grid simulation (2000)

The decrease in feature size and added chip functionality in large sub-micron integrated circuits demand larger grids for power distribution. Since power grids are performance limiting factors [1, 2, 3], then their analysis is important in order to (1) predict the performance and (2) improve the performance if necessary. Thus, there is a clear need for new efficient, in terms of both execution time and memory, techniques for power grid analysis.
Design of a Ku-band broadband U-slot microstrip antenna (2013)

In this paper, a U-slot rectangular microstrip patch antenna is designed in order to overcome the narrowband characteristic and gain broader band. The antenna has dual-band characteristics, so it has wider operating bandwidth. The antenna works at Ku-band and the center frequency is 16GHz. The characteristics are analyzed and optimized with Ansoft HFSS, the simulation results show that the absolute bandwidth and gain of the antenna unit are 2.7GHz and 8.1dB, and of the antenna array are 3.1GHz and 14.4dB. The relative bandwidth reaches to 19.4%, which is much wider than the general bandwidth of about 1% to 7%.