gebhart/patrepeval huggingface dataset:
Recent developments in laboratory automation using magnetic particles for genome analysis (2002)

The majority of research for genome analysis has shifted from nucleic acid sequencing to the biological functional analysis of each gene. Based on past success, it may not be long before genome diagnostics becomes a widespread tool in human, veterinary and botany research fields. Genome analysis involves the processes of nucleic acid purification, amplification, labeling and signal detection (specific reaction, separation and signal counting). Except for the purification of nucleic acids, the other processes cannot be achieved without instruments, resulting in the advancement of automation processes. Since purification of nucleic acids can be done manually, automating this process has been delayed. However, because the purification of nucleic acids using magnetic particles is suitable for automation, its development has also been accelerated. The need for full automation for other processes is not as great because the majority of genome analysis is to identify the nucleic acid sequence and analyze genome expression. However, once useful diagnostic tools are generated, the desire for full automation will significantly increase. In order to develop realistic and practical automation, various technologies developed for each process in genome analysis have to be evaluated and only a few technologies, useful for automation, selected. The other key factor in automation is the development of methods to manage reagents and reaction mixtures precisely without any risks specifically related to genome handling, such as cross-contamination. Methods using magnetic particles, which have been used for the automation of nucleic acid purification and immunoassay, appear to be the most promising way to automate processes used in biological research.
A LabVIEW-based implementation of real-time underwater acoustic OFDM system (2017)

The orthogonal frequency-division multiplexing (OFDM) technology receives increasing attention in underwater acoustic (UA) communications. This paper presents a real-time OFDM-based UA communication system, implemented using the National Instruments CompactDAQ device and the LabVIEW software. The system design including both the transmitter and receiver is discussed. The performance of this real-time system is verified through a UA communication experiment conducted recently in a tank. Compared with conventional digital signal processor (DSP)-based design, the proposed implementation simplifies the prototype design and reduces the software development time.
Risk of Nosocomial Infection with Human T-Cell Lymphotropic Virus III (HTLV-III) (1985)

Infection with human T-cell lymphotropic virus III (HTLV-III) is closely linked to the acquired immunodeficiency syndrome (AIDS). We evaluated the risk of nosocomial infection with HTLV-III by testing for antibodies to HTLV-III among hospital employees, including victims of needle-stick exposure, endoscopists, pathologists, and laboratory workers. Assays for antibody against the virus were performed by enzyme-linked immunosorbent assay and electrophoretic (Western blot) techniques. Although all 22 of our patients with AIDS and 6 of 7 with AIDS-related complex were found to have antibodies to HTLV-III when both assays were employed, none of the 85 employees with nosocomial exposure to specimens from patients with AIDS were positive for HTLV-III antibody. These studies must be regarded as preliminary, but they suggest that when current hospital isolation procedures are employed, the risk of nosocomial transmission of HTLV-III is low.
Radiation curable materials– principles and new perspectives (2000)

Increasing environmental concerns and the ensuing legislation to cut emissions of volatile organic compounds (VOCs) have been major driving forces behind the development of radiation cured coatings over the past 25 years. Today radiation cured coatings are known for their good overall performance and their excellent resistance against chemical and physical surface damages. Advanced photoinitiator systems allow the light stabilisation of UV-curable formulations and the outdoor application of the coating. The rapid curing, combined with the possibility of immediate processing of the coated objects opens the way for radiation curing – in 100%-, water based-, and dual cure systems as well as for radiation curable powder coatings – for a wide variety of application.
New TLM algorithms with controlled stability margin and their application to improve the modelling of curved boundaries (2002)

In this work new TLM formulations based on 2D shunt node and 3D expanded node are proposed. In comparison with standard TLM algorithms based on the same discretization of space, the new algorithms can use longer or shorter time-steps. This corresponds to operating with decreased (family r/sup -/) or increased (family r/sup +/) decreased numerical stability margin. Stable algorithms of family r/sup -/ exist for the 3D expanded node, and they reduce numerical dispersion errors as well as computation time of standard TLM. Algorithms of family r/sup +/ can incorporate enhanced TLM models for curved boundaries. We propose one such a model herein. In many practical cases application of the new boundary model reduces computer resources required for the TLM analysis of irregularly shaped microwave circuits by an order of magnitude.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Sulforaphane-Mediated Reduction of Aflatoxin B1-N7-Guanine in Rat Liver DNA: Impacts of Strain and Sex (2011)

Aflatoxin B₁ (AFB₁) is a DNA-binding toxin that contributes to the burden of liver cancer in tropical areas. AFB₁-DNA adducts are powerful biomarkers that discern individual and population risk from exposure to this carcinogen. The discovery of concordance between the metabolic pathways of the male Fischer rat and humans allowed data from rats to guide the development of chemoprevention strategies employed in clinical trials in high-risk regions. In this study, the variables of strain and sex are studied in the rat model, as a step toward understanding how ethnic differences and sex influence DNA adduct formation and the induction of enzymes by chemoprotective agents. Sulforaphane (SF), which induces phase II enzymes including glutathione S-transferases (GSTs), was evaluated for its ability to induce GST activity and reduce the AFB₁-DNA adducts in livers of both sexes of two rat strains that differ in susceptibility to AFB₁ hepatocarcinogenesis. A dose-dependent relationship was found for SF for both induction of GST and reduction in of AFB₁-N⁷-guanine in both Fischer (sensitive to AFB₁) and Sprague-Dawley rats (relatively resistant). Sprague-Dawley rats exhibited the greatest increase in GST levels and the largest reduction in AFB₁-N⁷-guanine in liver DNA. Males and females of each strain were also compared to determine if the ability of SF to induce GST and reduce AFB₁-N⁷-guanine correlated with gender differences in sensitivity to AFB₁ carcinogenesis. No gender-specific responses to SF were observed. These results support the view that SF induction of liver GST activity may play a role in its chemoprotective activity.
Optimality of certainty equivalence in expected value problems for uncertain linear systems (2014)

In this paper we study the optimality of the certainty equivalence approximation in robust finite-horizon optimization problems with expected cost. We provide an algorithm for determining the subset of the state-space for which the certainty equivalence technique is optimal. In the second part of the paper we show how patterns in the problem structure called symmetries can be used to reduce the computational complexity of the previous algorithm. Finally we demonstrate our technique through numerical examples, including a networked battery system.
Dual-output PID transient control of an electric-assisted air charge system (2023)

Turbo-compressor assembly (also called turbocharger) is added to diesel engines to increase their power density and improve performance. However, during power step-up operations, the added turbocharger system could lead to a significant delay of engine response (also called turbo-lag) which negatively impact drivability. In this paper, an external electric compressor (eBoost) is added to a turbocharged, large displacement diesel engine to significantly reduce turbo-lag, along with a bypass valve. Now, the air charge system has two control targets (boost (intake manifold) pressure and rate of exhaust-gas recirculation (EGR)) but with four control actuators including EGR valve, variable geometry turbo (VGT) vane position, eBoost speed and bypass valve, making it challenge for developing the associated control scheme. In this paper, a dual-output PID (proportional-integral-derivative) controller is proposed for controlling the boost pressure using the VGT and eBoost to reduce turbo-lag, and a transition logic is also devised to detect transient operating conditions to activate the eBoost, along with the closing and opening of the bypass valve, with maximum benefit. The EGR rate PID control remains unchanged. The addition of the eBoost is shown to improve transient response time by up to 55% and reduce transient NOx emissions by up to 42% during transitional operations without negatively impacting steady-state engine performance or emissions. Note that transient performance can be further improved for production implementation when a single engine control module is used by eliminating communication delay among multiple control systems.
A High Spatial Resolution Sensor For Thermal Neutron Imaging (2007)

We are developing a new type of neutron-sensitive sensor with minimal gamma-ray sensitivity for use in digital imaging systems. It consists of a plastic scintillator loaded with boron or gadolinium atoms for enhanced sensitivity to thermal neutrons. To achieve high spatial resolution, the scintillator in a liquid form is introduced into a capillary array (fused glass capillaries with no interstices), and then polymerized. The scintillation light generated by a neutron interaction is confined within a capillary, without lateral spreading through the scintillator. This not only improves spatial resolution, but also enhances image contrast by minimizing the glare fraction. The sensors were optically coupled to a cooled, fiberoptic taper-based CCD system to form an imaging detector. The detector was subjected to characterization and imaging tests at the thermal neutron port of the University of Massachusetts Lowell Research Reactor. Here we present the results that confirm the high resolution, high efficiency, and low gamma-sensitivity of the sensor.
Transition Metal Ions in Microporous Crystalline Aluminophosphates: Isomorphous Substitution (1999)

Microporous crystalline metalloaluminophosphates (MeAPO-n) represent an important group of molecular sieves because of their potential catalytic and adsorptive properties. Many transition metal ions are claimed to incorporate in the framework of these molecular sieves. Here, the concept of isomorphous substitution, and the different indirect and direct tools available to verify this substitution process for Co, Cr, V, Fe and Mn are reviewed taking the AlPO4-5 structure as an example. In addition, it will be shown that transition metal ions can be used as a probe to follow the hydrothermal synthesis process of microporous aluminophosphates.
Association and Coexpression of Fatty‐Acid‐Binding Protein and Glycoprotein CD36 in the Bovine Mammary Gland (1995)

The involvement of glycoprotein CD36 and fatty‐acid‐binding protein (FABP) in cellular growth, differentiation, lipid transport and metabolism led us to examine the possible biochemical and physiological relationship(s) between these two proteins. We investigated three aspects of this relationship. We first attempted to identify any physical complex formed between CD36 and FABP in bovine milk fat globule membranes. These membranes are the product of mammary gland secretory epithelial cells. The second aspect studied was the effect of synthetic peptide analogs to the C‐terminus (amino acid residues 121–131) of bovine mammary gland FABP on cell proliferation, as a result of the interaction of these peptides with the ectodomain of CD36. Finally, mammary gland CD36 and FABP coexpression was defined at different stages of lactation and during involution. Immunoprecipitation, Western immunoblotting with anti‐FABP and anti‐CD36, Northern‐blot analysis and a mammary epithelial cell proliferation assay demonstrated that: (a) bovine milk fat globule membranes contain the complex of CD36 and FABP, and that this complex is, most likely, formed as a result of FABP binding to the cytoplasmic segments of CD36; (b) synthetic analog of the C‐terminus of FABP with the sequence Val‐Thr‐Cys, identical to the sequence found in the CD36‐binding domain of thrombospondin, was a more potent inhibitor of bovine mammary gland epithelial cell proliferation than a synthetic peptide with the Val‐Cys‐Thr sequence; (c) the expression of FABP and CD36 is related to the state of mammary cell differentiation, since it reaches its maximum during lactation and declines during the involutionary period.
Data from Molecular Analysis of HER2 Signaling in Human Breast Cancer by Functional Protein Pathway Activation Mapping (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Targeting of the HER2 protein in human breast cancer represents a major advance in oncology but relies on measurements of total HER2 protein and not HER2 signaling network activation. We used reverse-phase protein microarrays (RPMA) to measure total and phosphorylated HER2 in the context of HER family signaling to understand correlations between phosphorylated and total levels of HER2 and downstream signaling activity.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Three independent study sets, comprising a total of 415 individual patient samples from flash-frozen core biopsy samples and formalin-fixed and paraffin-embedded (FFPE) surgical and core samples, were analyzed via RPMA. The phosphorylation and total levels of the HER receptor family proteins and downstream signaling molecules were measured in laser capture microdissected (LCM) enriched tumor epithelium from 127 frozen pretreatment core biopsy samples and whole-tissue lysates from 288 FFPE samples and these results were compared with FISH and immunohistochemistry (IHC).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; RPMA measurements of total HER2 were highly concordant (&gt;90% all sets) with FISH and/or IHC data, as was phosphorylation of HER2 in the FISH/IHC&lt;sup&gt;+&lt;/sup&gt; population. Phosphorylation analysis of HER family signaling identified HER2 activation in some FISH/IHC&lt;sup&gt;−&lt;/sup&gt; tumors and, identical to that seen with FISH/IHC&lt;sup&gt;+&lt;/sup&gt; tumors, the HER2 activation was concordant with EGF receptor (EGFR) and HER3 phosphorylation and downstream signaling endpoint activation.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Molecular profiling of HER2 signaling of a large cohort of human breast cancer specimens using a quantitative and sensitive functional pathway activation mapping technique reveals IHC&lt;sup&gt;−&lt;/sup&gt;/FISH&lt;sup&gt;−&lt;/sup&gt;/pHER2&lt;sup&gt;+&lt;/sup&gt; tumors with HER2 pathway activation independent of total HER2 levels and functional signaling through HER3 and EGFR. &lt;i&gt;Clin Cancer Res; 18(23); 6426–35. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Reduction of exercise tachycardia in man after propranolol, atenolol and bisoprolol in comparison to beta-adrenoceptor occupancy (1987)

In a double blind, placebo controlled study, propranolol (240 mg), atenolol (200 mg) or bisoprolol (100 mg) were administered as a single oral dose to groups of 6 healthy male volunteers. Exercise tachycardia was monitored for 84 hours after administration of the drugs to monitor beta blockade in vivo. Plasma samples drawn in parallel with these effects were used to detect beta 1- or beta 2-adrenoceptor occupancy in two subtype selective in vitro receptor binding assays. Reduction of exercise tachycardia parallels beta 1-adrenoceptor occupancy. Furthermore, at comparable beta 1-adrenoceptor occupancy, less beta 2-adrenoceptor occupancy was observed after bisoprolol than after atenolol. The latter finding is in agreement with the two-fold higher beta 1/beta 2-selectivity ratio of bisoprolol (75-fold) versus atenolol (35-fold). It is concluded, that beta blockade observed via the reduction of exercise tachycardia can be delineated from the in vitro occupancy of beta 1-adrenoceptors by an antagonist present in plasma samples.
Reversal of Bronchoconstriction by Inhaled Nitric Oxide. Histamine Versus Methacholine (1994)

Using high-resolution CT (HRCT), which measures changes in innervated airways greater than 1 mm in diameter, we compared the ability of nitric oxide (NO) to dilate airways preconstricted with histamine and methacholine in five anesthetized dogs. After the airways were preconstricted, NO was inhaled in concentrations of 100, 200, and 400 ppm. Additionally, histamine was given with and without atropine and methylene blue. Data were analyzed by one-way analysis of variance. Histamine and methacholine decreased airway area to a similar extent: 60 +/- 3% (mean +/- SEM) and 63 +/- 3% of control, respectively (p = 0.85). Atropine completely reversed the histamine-induced constriction (255 +/- 19%). NO also completely reversed histamine-induced airway constriction in a dose-related fashion. The airway area went from 60 +/- 3% during histamine infusion to 85 +/- 5, 102 +/- 5, and 111 +/- 10% of control, respectively (p < 0.01), after doses of 100, 200, and 400 ppm NO. Methylene blue partially inhibited the reversal by 200 ppm NO of histamine-induced constriction. In contrast, NO only partially reversed methacholine-induced constriction. NO at 100, 200, and 400 ppm partially attenuated the methacholine-induced airway constriction. Airway area went from 63 +/- 3 to 67 +/- 3, 75 +/- 3, and 75 +/- 2% of control, respectively (p < 0.01). We conclude that NO relaxes canine conducting airways by indirect mechanisms as well as by directly relaxing the airway smooth muscle.
Effect of vacuum-ultraviolet irradiation on the dielectric constant of low-k organosilicate dielectrics (2014)

Vacuum ultraviolet (VUV) irradiation is generated during plasma processing in semiconductor fabrications, while the effect of VUV irradiation on the dielectric constant (k value) of low-k materials is still an open question. To clarify this problem, VUV photons with a range of energies were exposed on low-k organosilicate dielectrics (SiCOH) samples at room temperature. Photon energies equal to or larger than 6.0 eV were found to decrease the k value of SiCOH films. VUV photons with lower energies do not have this effect. This shows the need for thermal heating in traditional ultraviolet (UV) curing since UV light sources do not have sufficient energy to change the dielectric constant of SiCOH and additional energy is required from thermal heating. In addition, 6.2 eV photon irradiation was found to be the most effective in decreasing the dielectric constant of low-k organosilicate films. Fourier Transform Infra-red Spectroscopy shows that these 6.2 eV VUV exposures removed organic porogens. This contributes to the decrease of the dielectric constant. This information provides the range of VUV photon energies that could decrease the dielectric constant of low-k materials most effectively.
The role of glycoproteins in calcium oxalate crystal development (2004)

All substances inhibiting calcium oxalate crystallization with the capacity to interact with calcium ions also have crystallization promoting properties when they are at sufficiently high concentrations, because of their capacity to form agglomerates or the insolubility of their calcium salts.
3D device modeling of damage due to filamentation under an ESD event in nanometer scale drain extended NMOS (DE-NMOS) (2008)

We present a detailed understanding of filamentation, through rigorous mixed-mode 3D simulation in a nano-meter scale drain-extended NMOS (DE-NMOS). Localization is first triggered in the 2D plane due to regenerative turn-on of the parasitic bipolar. 3D Simulations performed by adding width along the Z-axis (i.e., W) show a very prominent localization effect, which leads to electro-thermal runaway in the DE-NMOS and causes an irreversible damage.
Effect of laser peen forming process parameters on bending and surface quality of Ti-6Al-4V sheets (2022)

Laser peen forming (LPF) is a metal forming process that utilizes laser-induced mechanical shock waves to form desired shapes or modify bent structures. The present work focuses on the applicability of LPF to Ti-6Al-4V sheets, to identify an optimal LPF process parameter window and achieve desired bending without compromising the surface quality within the peened region. The effect of LPF process parameters, i.e. laser power density, overlap, type of sacrificial overlay, and the number of peening sequences was investigated for specimens with different thicknesses. The laser power density and number of peening sequences were the most influential parameters that affect the bending of the specimens. Using sacrificial overlay has a significant effect on the bending and surface quality of the specimens. Surface quality after LPF was assessed by measuring the roughness in the peened region. In experiments without a sacrificial overlay, a black titanium oxide residue on the peened region was observed and additionally, small micro-cracks were found in the near surface region. Further characterization of the peened region revealed that the average crack length increased with increase in laser power density. Two possible LPF process parameter combinations were identified to obtain bending in the peened region, where LPF with sacrificial overlay resulted in no surface damage. Furthermore, residual stresses were determined at various LPF process parameters by incremental hole-drilling method in the peened region.
The Role of Creatine in the Development and Activation of Immune Responses (2021)

The use of dietary supplements has become increasingly common over the past 20 years. Whereas supplements were formerly used mainly by elite athletes, age and fitness status no longer dictates who uses these substances. Indeed, many nutritional supplements are recommended by health care professionals to their patients. Creatine (CR) is a widely used dietary supplement that has been well-studied for its effects on performance and health. CR also aids in recovery from strenuous bouts of exercise by reducing inflammation. Although CR is considered to be very safe in recommended doses, a caveat is that a preponderance of the studies have focused upon young athletic individuals; thus there is limited knowledge regarding the effects of CR on children or the elderly. In this review, we examine the potential of CR to impact the host outside of the musculoskeletal system, specifically, the immune system, and discuss the available data demonstrating that CR can impact both innate and adaptive immune responses, together with how the effects on the immune system might be exploited to enhance human health.