gebhart/patrepeval huggingface dataset:
Identification of plasma Complement C3 as a potential biomarker for neuroblastoma using a quantitative proteomic approach (2013)

This study has utilised a unique murine model which develops neuroblastoma tumours that are biologically indistinguishable from human neuroblastoma. This animal model has effectively allowed the identification of plasma proteins which may serve as potential biomarkers of neuroblastoma. Furthermore, the label-free ion count quantitation technique which was used displays significant benefits as it is less labour intensive, feasible and accurate. We have been able to successfully validate this approach by confirming the differential abundance of two different plasma proteins. In addition, we have been able to confirm that the candidate biomarker Complement C3, is more abundant in the plasma of human neuroblastoma patient plasma samples when compared to healthy counterparts. Overall we have demonstrated that this approach can be potentially useful in the identification of biomarker candidates, and that further validation of the candidates may lead to the discovery of novel, clinically useful diagnostic tools in the detection of sub-clinical neuroblastoma.
Delta-endotoxin proteins associated with spherical parasporal inclusions of the four Lepidoptera-specific Bacillus thuringiensis strains (1998)

Four Lepidoptera-specific reference strains of Bacillus thuringiensis, belonging to serovars sumiyoshiensis (H3a:3d), fukuokaensis (H3a:3d:3e), darmstadiensis (H10a:10b) and japonensis (H23), which produce spherical parasporal inclusions, were examined for comparative characterization of delta-endotoxins. SDS-PAGE profiles of the alkali-solubilized parasporal inclusions revealed the presence of single major protein bands of 130 kDa in the four strains. Chymotrypsin and trypsin treatment of the proteins gave profiles different from those of the strains HD-1 (serovar kurstaki, H3a:3b:3c) and T84 A1 (serovar sotto, H4a:4b). Also, minor variations were observed in proteolysis profiles among the four strains. The LC50 values of purified parasporal inclusions for the silkworm (Bombyx mori) larvae were 7.35, 6.45, 3.08 and 2.63 micrograms g-1 diet, respectively, showing that their toxicity levels were 5-15 times lower than that of the strain HD-1 (0.49 microgram g-1 diet). Analysis by immunodiffusion and immunoblotting with polyclonal antisera revealed that parasporal inclusion proteins of the four strains are highly related, whereas they shared few or no common antigens with those of the strains HD-1, T84 A1 and Buibui (serovar japonensis).
Electrical two-speed propulsion by motor winding switching and its control strategies for electric vehicles (1999)

Theoretical analyses and computer simulation studies lead the authors to propose: (1) a new electrical two-speed propulsion system for electric vehicles (EVs) by switching induction motor windings; and (2) an improved fuzzy logic control-continuous defuzzification method for the control of this system. The two-speed propulsion is achieved by connecting the motor stator windings in series for starting an EV and then switching the windings to parallel connection for normal speed operation. The method produces a high starting torque, yet maintains the inverter within its rated power range. As compared with star-delta starting of induction motors, the proposed series-parallel method offers higher starting torque and acceleration. The control strategies for this system are investigated. A comparison of fuzzy logic control with a conventional proportional-integral (PI) shows that a fuzzy logic controller (FLC) can be applied to EV propulsion systems. Simulation studies also demonstrate that an improved FLC method using a continuous defuzzification technique provides smoother torque and leads to lower harmonic components in motor currents, thus further enhancing this EV propulsion system.
Feedback channel in pixel domain Wyner-Ziv video coding: Myths and realities (2006)

Wyner-Ziv (WZ) video coding – a particular case of distributed video coding (DVC) – is a new video coding paradigm based on two major Information Theory results: the Slepian-Wolf and Wyner-Ziv theorems. Recently, practical WZ video coding solutions were proposed with promising results. Many of the solutions avail-able in the literature make use of a feedback channel (FC) to per-form rate control at the decoder. In this context, this paper intends to analyse the impact of this feedback channel, notably through a number of metrics such as the frequency the feedback channel is used as well as its associated rate. It is also presented a study on the evolution of the decoded frames quality as more parity bits are requested via feedback channel. Those measures are important since they allow characterizing the usage of the feedback channel, and have never been presented in the literature.
Discrete Cosine Transform for Pre-coded EGPRS (2012)

Due to the rapid growth of wireless multimedia service, new features such as improved spectral efficiency, latency and increased peak throughput are standardized in the current GSM/EDGE system. Higher order modulations and symbol rates are defined in Enhanced General Packet Radio Service phase 2 (EGPRS2) to achieve better throughput. However, the computational complexity in the traditional receiver can be very high when increased modulation orders are applied; additionally, the system becomes more sensitive to the impairments at an increased symbol rate. It is therefore desirable to have a less complex and more robust demodulator. Recently, a new study item which introduces the multi-carrier technique was proposed in the 3rd Generation Partnership Project (3GPP) standardization. Based on the channel partitioning using the Discrete Fourier Transform (DFT), a simple equalizer can be used, which greatly reduces the computational complexity on receiver, meanwhile achieves good throughput and robustness against impairments. In this thesis, another channel partitioning method by means of the Discrete Cosine Transform (DCT) is studied. Transmitter and receiver algorithms are developed, including a pre-filter designed at the receiver to facilitate the channel diagonalization. The link level performance is evaluated by means of simulations, under different test scenarios. The system’s robustness against impairments and peak-to-average ratio (PAR) reduction are also evaluated, and compared with a system based on the DFT pre-coding. From the simulations, the conclusions can be drawn that in this implementation, the DFT precoded EGPRS2 outperforms the DCT pre-coded EGPRS2 in all scenarios. The DCT pre-coded system also shows worse robustness against impairments and higher peak-to-average ratio reduction loss in throughput. The impact of pre-filter design on the DCT pre-coded system has also been analyzed, and it shows that there is a tradeoff between achieving good symmetrization, and preserving channel information in the frequency domain.
An analysis of the role of guanine nucleotide binding proteins in antigen receptor/CD3 antigen coupling to phospholipase C (1991)

In permeabilized human T lymphocytes, phospholipase C (PLC)-mediated metabolism of polyphosphatidylinositols can be stimulated by triggering the T cell antigen receptor/CD3 antigen complex (Ti/CD3) with the CD3 antibody UCHT1 or by activation of G proteins with the non-hydrolyzable guanine nucleotide analogue, guanosine 5'-O-(3-thiotrisphosphate) (GTP[S]). Ti/CD3 induction of inositol phosphate production demonstrated no dependence on exogenous guanine nucleotides. Furthermore, Ti/CD3 stimulation did not influence the kinetics or dose-response of GTP[S]-induced inositol phosphate production, suggesting that the Ti/CD3 complex does not regulate guanine nucleotide exchange on the G protein pool stimulated by GTP[S]. These data indicate that the Ti/CD3 complex is not G protein-linked to PLC in a manner analogous to the G protein linkage of receptors to adenylate cyclase. However, the inhibitory guanine nucleotide, GDP, antagonizes not only GTP[S]-induced polyphosphatidylinositol hydrolysis but also UCHT1-induced inositol phosphate production. These data infer that a G protein can modulate the coupling of the Ti/CD3 complex to PLC and that there may be some "cross-talk" between Ti/CD3 and G protein PLC coupling mechanisms.
Silencing of the LeSGR1 gene in tomato inhibits chlorophyll degradation and exhibits a stay-green phenotype (2011)

The full-length cDNA of LeSGR1 was cloned from tomato by RT-PCR and RACE. The cDNA encoded a protein of 272 amino acid residues and was deposited in GenBank (accession No. DQ100158). Northern analysis suggests that LeSGR1 gene specifically expresses in senescent leaves and mature fruits of tomatoes. Desiccation and flooding induce the expression of LeSGR1 in tomato leaves and stems. Both in ethylene-insensitive mutants (Nr) and ripening inhibitor mutants (rin), the expression of LeSGR1 is markedly decreased compared with that in the wild type. Alignment of the nucleotide sequence of SGR1 cloned from the tomato green flesh (gf) mutant with that from the wild type tomato shows a single nucleotide change leading to an amino acid substitution in gf mutant. Furthermore, LeSGR1 gene silencing by RNA interference results in inhibited chlorophyll degradation similar to the phenotype in gf mutant. Thus, we conclude that LeSGR1 is crucial to chlorophyll degradation and the mutation of SGR1 protein might be responsible for gf tomato properties.
DNA dielectrophoresis: Theory and applications a review (2017)

Dielectrophoresis is the migration of an electrically polarizable particle in an inhomogeneous electric field. This migration can be exploited for several applications with (bio)molecules or cells. Dielectrophoresis is a noninvasive technique; therefore, it is very convenient for (selective) manipulation of (bio)molecules or cells. In this review, we will focus on DNA dielectrophoresis as this technique offers several advantages in trapping and immobilization, separation and purification, and analysis of DNA molecules. We present and discuss the underlying theory of the most important forces that have to be considered for applications with dielectrophoresis. Moreover, a review of DNA dielectrophoresis applications is provided to present the state-of-the-art and to offer the reader a perspective of the advances and current limitations of DNA dielectrophoresis.
The 2S albumin allergens of <i>Arachis hypogaea</i>, Ara h 2 and Ara h 6, are the major elicitors of anaphylaxis and can effectively desensitize peanut‐allergic mice (2012)

Ara h 2/6 are the most potent peanut allergens in vivo and can be used to desensitize peanut-allergic mice. These results have potential implications for clinical research in the areas of diagnosis and immunotherapy for peanut allergy.
Layout optimization for a wireless sensor network using a multi-objective genetic algorithm (2005)

This paper examines the optimization of wireless sensor network layouts. To transmit their data to the base, all the sensors are required to be connected to a high-energy communication node, which serves as a relay from the ground to a satellite or to a high-altitude aircraft. The sensors are assumed to have a fixed communication and a fixed sensing range, which can significantly vary depending on the type of sensing performed. This simple framework serves to benchmark a multi objective genetic algorithm (MOGA) for the sensor placement, where the two competing objectives considered are the total sensor coverage and the lifetime of the network. The MOGA is then used to show that, for different relative sensing ranges, two fundamentally different types of layouts are obtained: one with the sensors closely packed together, the other with the sensors organized in a hub-and-spoke manner. The ratio of sensing to communication range is shown to be the discriminating factor.
Fast location of similar code fragments using semantic 'juice' (2013)

Abstraction of semantics of blocks of a binary is termed as 'juice.' Whereas the denotational semantics summarizes the computation performed by a block, its juice presents a template of the relationships established by the block. BinJuice is a tool for extracting the 'juice' of a binary. It symbolically interprets individual blocks of a binary to extract their semantics: the effect of the block on the program state. The semantics is generalized to juice by replacing register names and literal constants by typed, logical variables. The juice also maintains algebraic constraints between the numeric variables. Thus, this juice forms a semantic template that is expected to be identical regardless of code variations due to register renaming, memory address allocation, and constant replacement. The terms in juice can be canonically ordered using a linear order presented. Thus semantically equivalent (rather, similar) code fragments can be identified by simple structural comparison of their juice, or by comparing their hashes. While BinJuice cannot find all equivalent constructs, for that would solve the Halting Problem, it does significantly improve the state-of-the-art in both the computational complexity as well as the set of equivalences it can establish. Preliminary results show that juice is effective in pairing code variants created by post-compile obfuscating transformations.
The natriuretic peptide family (1993)

The natriuretic peptide system is a complicated system comprising at least three endogenous peptides (atrial natriuretic peptide, brain natriuretic peptide and C-type natriuretic peptide) and three receptors [the atrial natriuretic peptide-A receptor (guanylyl cyclase A), the atrial natriuretic peptide-B receptor (guanylyl cyclase B) and the clearance receptor]. The accumulated evidence indicates that this system is implicated in the control of blood pressure, body fluid homeostasis and vascular remodelling as cardiac hormone and local regulator.
An Aromatic Farnesyltransferase Functions in Biosynthesis of the Anti-HIV Meroterpenoid Daurichromenic Acid (2018)

<i>Rhododendron dauricum</i> produces daurichromenic acid, an anti-HIV meroterpenoid, via oxidative cyclization of the farnesyl group of grifolic acid. The prenyltransferase (PT) that synthesizes grifolic acid is a farnesyltransferase in plant specialized metabolism. In this study, we demonstrated that the isoprenoid moiety of grifolic acid is derived from the 2-<i>C</i>-methyl-d-erythritol-4-phosphate pathway that takes place in plastids. We explored candidate sequences of plastid-localized PT homologs and identified a cDNA for this PT, RdPT1, which shares moderate sequence similarity with known aromatic PTs. RdPT1 is expressed exclusively in the glandular scales, where daurichromenic acid accumulates. In addition, the gene product was targeted to plastids in plant cells. The recombinant RdPT1 regiospecifically synthesized grifolic acid from orsellinic acid and farnesyl diphosphate, demonstrating that RdPT1 is the farnesyltransferase involved in daurichromenic acid biosynthesis. This enzyme strictly preferred orsellinic acid as a prenyl acceptor, whereas it had a relaxed specificity for prenyl donor structures, also accepting geranyl and geranylgeranyl diphosphates with modest efficiency to synthesize prenyl chain analogs of grifolic acid. Such a broad specificity is a unique catalytic feature of RdPT1 that is not shared among secondary metabolic aromatic PTs in plants. We discuss the unusual substrate preference of RdPT1 using a molecular modeling approach. The biochemical properties as well as the localization of RdPT1 suggest that this enzyme produces meroterpenoids in glandular scales cooperatively with previously identified daurichromenic acid synthase, probably for chemical defense on the surface of <i>R. dauricum</i> plants.
New Access to Chiral Cyclic ω‐Oxygenated β‐Enamino Esters by Intramolecular Aminocyclization Reactions. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Automating DNSSEC Delegation Trust Maintenance (2014)

This document describes a method to allow DNS Operators to more easily update DNSSEC Key Signing Keys using the DNS as a communication channel.The technique described is aimed at delegations in which it is currently hard to move information from the Child to Parent.
Technique ChIC and ChEC: Genomic Mapping of Chromatin Proteins (2004)

Summary alternative, complementary procedures that omit the chromatin fractionation-solubilization step. The methTo map the genomic interaction sites of chromatin ods introduced here consist of tethering micrococcal proteins, two related methods were developed and nuclease in an inactive state (no Ca 2 ions) directly experimentally explored in Saccharomyces cerevisiae. (in vivo) or indirectly (via antibodies) to proteins of interThe ChIC method (chromatin immunocleavage) con- est. The specifically bound nuclease is then activated sists of tethering a fusion protein (pA-MN) consisting by Ca 2 ions to locally introduce double-stranded DNA of micrococcal nuclease (MN) and staphylococcal pro- breaks. Mapping of such breaks by molecular techtein A to specifically bound antibodies. The nuclease niques is shown to map proteins with a 100–200 bp is kept inactive during the tethering process (no Ca 2 ). resolution and excellent specificity. One version of the The ChEC method (chromatin endogenous cleavage) method is applicable to formaldehyde-fixed cells, anconsists of expressing fusion proteins in vivo, where other to native cells with comparable results. MN is C-terminally fused to the proteins of interest. The specifically tethered nucleases are activated with Results Ca 2 ions to locally introduce double-stranded DNA
An Air‐Supported Liquid Crystal System for Real‐Time and Label‐Free Characterization of Phospholipases and Their Inhibitors (2008)

Abstract A new air‐supported liquid crystal (LC) system for analyzing interfacial phenomena that occur based on the molecular interaction between LCs and adsorbed molecules of interest at the aqueous/LC interface is reported. Compared with existing LC‐based detection systems, the miniature system reported here requires less sample and involves simpler preparation. Using this system, the enzymatic hydrolysis of various phospholipases such as phospholipase A 2 (PLA 2 ), phospholipase C (PLC) and phospholipase D (PLD) are characterized. The hydrolysis of phospholipid monolayers self‐assembled at aqueous/LC interface induces an orientational response from the LCs. As a result, an optical signal that reflects the spatial and temporal distribution of phospholipids during the enzymatic reaction can be generated in a real‐time manner. When well‐known phospholipase inhibitors are introduced together with respective phospholipases, no orientational response of LCs is observed. In the case of inhibitors MJ33 and compound 48/80, cross‐inhibitions among phospholipases are also observed. This work demonstrates that the air‐supported LC system provides a facile label‐free assay for characterizing phospholipase activities and for screening enzyme inhibitors. It could potentially be useful for different high throughput and cost‐effective enzyme screening assays.
Deep brain stimulation for Tourette’s syndrome (2020)

Tourette syndrome (TS) is a childhood-onset neuropsychiatric disorder characterized by the presence of multiple motor and vocal tics. TS usually co-occurs with one or multiple psychiatric disorders. Although behavioral and pharmacological treatments for TS are available, some patients do not respond to the available treatments. For these patients, TS is a severe, chronic, and disabling disorder. In recent years, deep brain stimulation (DBS) of basal ganglia-thalamocortical networks has emerged as a promising intervention for refractory TS with or without psychiatric comorbidities. Three major challenges need to be addressed to move the field of DBS treatment for TS forward: (1) patient and DBS target selection, (2) ethical concerns with treating pediatric patients, and (3) DBS treatment optimization and improvement of individual patient outcomes (motor and phonic tics, as well as functioning and quality of life). The Tourette Association of America and the American Academy of Neurology have recently released their recommendations regarding surgical treatment for refractory TS. Here, we describe the challenges, advancements, and promises of the use of DBS in the treatment of TS. We summarize the results of clinical studies and discuss the ethical issues involved in treating pediatric patients. Our aim is to provide a better understanding of the feasibility, safety, selection process, and clinical effectiveness of DBS treatment for select cases of severe and medically intractable TS.
Plerixafor for Stem Cell Mobilization in Patients with Non-Hodgkin's Lymphoma and Multiple Myeloma (2009)

Clinical trials have demonstrated that the addition of plerixafor to G-CSF was beneficial for HSC mobilization to peripheral blood for collection and subsequent transplantation in patients with NHL or multiple myeloma. Further studies should assess the benefit of the additive use of plerixafor on clinical outcomes.
Newly identified biologically active and proteolysis-resistant VEGF-A isoform VEGF111 is induced by genotoxic agents (2007)

Ultraviolet B and genotoxic drugs induce the expression of a vascular endothelial growth factor A (VEGF-A) splice variant (VEGF111) encoded by exons 1-4 and 8 in many cultured cells. Although not detected in a series of normal human and mouse tissue, VEGF111 expression is induced in MCF-7 xenografts in nude mice upon treatment by camptothecin. The skipping of exons that contain proteolytic cleavage sites and extracellular matrix-binding domains makes VEGF111 diffusible and resistant to proteolysis. Recombinant VEGF111 activates VEGF receptor 2 (VEGF-R2) and extracellularly regulated kinase 1/2 in human umbilical vascular endothelial cells and porcine aortic endothelial cells expressing VEGF-R2. The mitogenic and chemotactic activity and VEGF111's ability to promote vascular network formation during embyonic stem cell differentiation are similar to those of VEGF121 and 165. Tumors in nude mice formed by HEK293 cells expressing VEGF111 develop a more widespread network of numerous small vessels in the peritumoral tissue than those expressing other isoforms. Its potent angiogenic activity and remarkable resistance to proteolysis makes VEGF111 a potential adverse factor during chemotherapy but a beneficial therapeutic tool for ischemic diseases.
TESTABILITY FEATURES OF THE 68HC16Z1 (2005)

The purpose of this paper is to describe the testability features implemented in Motorola's recently completed design of a sixteen bit microcontroller, the 68HC16Z1. The discussion includes a brief introduction to the 68HC16Z1, test objectives and organization along with descriptions of design for test (DR) techniques and structures.
Ankle Brachial Index Combined With Framingham Risk Score to Predict Cardiovascular Events and Mortality (2008)

Measurement of the ABI may improve the accuracy of cardiovascular risk prediction beyond the FRS.
Immunological Approaches to Plant Cell Wall and Biomass Characterization: Glycome Profiling (2012)

The native complexity of plant cell walls makes research on them challenging. Hence, it is advantageous to have a diversity of tools that can be used to analyze and characterize plant cell walls. In this chapter, we describe one of two immunological approaches that can be employed for screening of plant cell wall/biomass materials from diverse plants and tissues. This approach, Glycome Profiling, lends itself well to moderate to high-throughput screening of plant cell wall/biomass samples. Glycome Profiling is being further optimized to reduce the amount of sample required for the analysis, and to improve the sensitivity and throughput of the assay. We are optimistic that Glycome Profiling will prove to be a broadly applicable experimental approach that will find increasing application to a wide variety of studies on plant cell wall/biomass samples.