gebhart/patrepeval huggingface dataset:
Sulfhydryl site-specific crosslinking and labeling of monoclonal antibodies by a fluorescent equilibrium transfer alkylation crosslink reagent (1990)

The site-specific intramolecular cross-linking of sulfhydryls of monoclonal antibodies via a new class of "equilibrium transfer alkylation cross-link (ETAC) reagents" is described. Following complete or partial reduction of interchain disulfides with dithiothreitol (DTT), two murine IgG2a monoclonal antibodies, 225.28S and 5G6.4, were reacted with alpha,alpha-bis[(p-tolylsulfonyl)methyl]-m-aminoacetophenone (ETAC 1a) and a fluorescent conjugated derivative, sulforhodamine B m-(alpha,alpha-bis(p-tolysulfonylmethyl)acetyl)anilide derivative (ETAC 1b). Reducing SDS-polyacrylamide gel electrophoresis analysis of the products from 1b indicated the formation of S-ETAC-S interchain heavy and light chain cross-links (approximately 23-34% overall yield by video-camera densitometry) which do not undergo disulfide-thiol exchange with DTT at 100 degrees C. In contrast, no interchain cross-links were observed upon reaction of unreduced or reduced antibody wherein the thiols have been previously alkylated with iodoacetamide. These results indicated site-specific cross-linking of interchain sulfhydryls and places their distance within 3-4 A. Flow cytometry of the ETAC 1b 5G6.4 cross-linked product using 77 IP3 human ovarian carcinoma target cells showed positive binding and retention of immunoreactivity. The in vivo biodistributions of 131I-labeled intact 5G6.4 and 125I-labeled reduced 5G6.4 + ETAC 1a product in rats were essentially identical over a period of 24 h. The present study illustrates the potential applications of labelable ETAC reagents as thiol-specific probes for a wide variety of immunological studies.
A novel detection for biomolecule using RF LC resonator (2007)

This is new approach for biomolecule detection with label free method. The designed LC resonator by the combining inductors and capacitors was fabricated by MEMS process. The measured signal difference was 1.86 dB at 2.2 GHz between the return losses of biotin and avidin. The impedances for a bare device, biotin and avidin steps were Zo*(0.803-j0.002), Zo*(0.761-j0.003) and Zo*(0.718-j0.002) according to the Smith chart, respectively. From the mentioned data, we conclude that there is no frequency shift and the return loss variation at resonance point is distinctly large. This means that the biomolecule acts as a resistance, and the decreased resistance of the resonator leads to the impedance match change.
Platelet-Related Variants Identified by Exomechip Meta-analysis in 157,293 Individuals (2020)

Platelet production, maintenance, and clearance are tightly controlled processes indicative of platelets important roles in hemostasis and thrombosis. Platelets are common targets for primary and secondary prevention of several conditions. They are monitored clinically by complete blood counts, specifically with measurements of platelet count (PLT) and mean platelet volume (MPV). Identifying genetic effects on PLT and MPV can provide mechanistic insights into platelet biology and their role in disease. Therefore, we formed the Blood Cell Consortium (BCX) to perform a large-scale meta-analysis of Exomechip association results for PLT and MPV in 157,293 and 57,617 individuals, respectively. Using the low-frequency/rare coding variant-enriched Exomechip genotyping array, we sought to identify genetic variants associated with PLT and MPV. In addition to confirming 47 known PLT and 20 known MPV associations, we identified 32 PLT and 18 MPV associations not previously observed in the literature across the allele frequency spectrum, including rare large effect (FCER1A), low-frequency (IQGAP2, MAP1A, LY75), and common (ZMIZ2, SMG6, PEAR1, ARFGAP3/PACSIN2) variants. Several variants associated with PLT/MPV (PEAR1, MRVI1, PTGES3) were also associated with platelet reactivity. In concurrent BCX analyses, there was overlap of platelet-associated variants with red (MAP1A, TMPRSS6, ZMIZ2) and white (PEAR1, ZMIZ2, LY75) blood cell traits, suggesting common regulatory pathways with shared genetic architecture among these hematopoietic lineages. Our large-scale Exomechip analyses identified previously undocumented associations with platelet traits and further indicate that several complex quantitative hematological, lipid, and cardiovascular traits share genetic factors.
Anteromedial versus central single‐bundle graft position: which anatomic graft position to choose? (2011)

It has been shown that there was no difference in the time-zero biomechanical stability between an anatomic anteromedial and anatomic central single-bundle ACL reconstruction. Given the current debate on the best anatomic ACL reconstruction technique, anatomic socket position in either the anteromedial or central locations provides similar time-zero biomechanics.
A new approach for machine learning security risk assessment (2022)

We propose a new security risk assessment approach for Machine Learning-based AI systems (ML systems). The assessment of security risks of ML systems requires expertise in ML security. So, ML system developers, who may not know much about ML security, cannot assess the security risks of their systems. By using our approach, a ML system developers can easily assess the security risks of the ML system. In performing the assessment, the ML system developer only has to answer the yes/no questions about the specification of the ML system. In our trial, we confirmed that our approach works correctly.
A Novel Approach to Open “Dead Space” and Modify Interfacial Features of Carbon Nanotube Assemblies by a Microwave Shock (2022)

Abstract Despite 30‐year development of carbon nanotube (CNT) based materials, harnessing the outstanding nanoscale properties of individual CNT for macroscale applications remains challenging. High specific surface area, a crucial feature of CNTs, often suffers from the formation of tightly packed bundles with inaccessible “dead space”. Herein, a novel “microwave shock” approach to open the “dead space” trapped within bundles is reported. Employing N 2 ambient during microwave irradiation, CNT bundles undergo an efficient structural alteration and interfacial modification simultaneously due to the strong radiative coupling, while the graphitic structure remains undamaged. In this way, a 15‐fold increase (from 42 to 648 m 2 g −1 ) in the interstitial surface area as well as the lithiophilic functionalization (≈1 atom% nitrogen doping) are achieved without the degradation of other properties. Furthermore, to highlight the merits of this microwave shock process, the treated CNT films are applied as a host material for the anode in a lithium metal battery and demonstrate the suppression of dendritic lithium growth and improve cycling stability. This microwave shock approach provides an efficient avenue to modify nanocarbon‐based materials for further applications.
Genetic Variation on the BAT1-NFKBIL1-LTA Region of Major Histocompatibility Complex Class III Associates with Periodontitis (2014)

Periodontitis is a chronic inflammatory disease with a multifactorial etiology. We investigated whether human major histocompatibility complex (MHC) polymorphisms (6p21.3) are associated with periodontal parameters. Parogene 1 population samples (n169) were analyzed with 13,245 single nucleotide polymorphisms (SNPs) of the MHC region. Eighteen selected SNPs (P&lt;0.001) were replicated in Parogene 2 population samples (n339) and the Health 2000 Survey (n1,420). All subjects had a detailed clinical and radiographic oral health examination. Serum lymphotoxin- (LTA) concentrations were measured in the Parogene populations, and the protein was detected in inflamed periodontal tissue. In the Parogene 1&nbsp; population, 10 SNPs were associated with periodontal parameters. The strongest associations emerged from the parameters bleeding on probing (BOP) and a probing pocket depth (PPD) of&gt;6mmwith the genes BAT1, NFKBIL1, and LTA. Six SNPs, rs11796, rs3130059, rs2239527,<br /> rs2071591, rs909253, and rs1041981 (r2,&gt;0.92), constituted a risk haplotype. In the Parogene 1 population, the haplotype had the strongest association with the parameter BOP, a PPD of&gt;6 mm, and severe periodontitis with odds ratios (95% confidence intervals) of 2.63 (2.21 to 3.20), 2.90 (2.37 to 3.52), and 3.10 (1.63 to 5.98), respectively. These results were replicated in the other two populations. High serum LTA concentrations in the Parogene population were associated with the periodontitis risk alleles of the LTA SNPs (rs909253 and rs1041981) of the haplotype. In addition, the protein was expressed in inflamed gingival connective tissue. We identified a novel BAT1-NFKBIL1-LTA haplotype as a significant contributor to the risk of periodontitis. The genetic polymorphisms in the MHC class III region may be functionally important in periodontitis susceptibility.
Immunoglobulin/T-Cell Receptor Gene Rearrangement Analysis Using RNA-Seq (2022)

Identification of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements in acute lymphoblastic leukemia (ALL) patients at initial presentation are crucial for monitoring of minimal residual disease (MRD) during subsequent follow-up and thereby for appropriate risk-group stratification. Here we describe how RNA-Seq data can be generated and subsequently analyzed with ARResT/Interrogate to identify possible MRD markers. In addition to the procedures, possible pitfalls will be discussed. Similar strategies can be employed for other lymphoid malignancies, such as lymphoma and myeloma.
ChemInform Abstract: FACTORS INFLUENCING THE REGIOSELECTIVITY OF REACTIONS INVOLVING ORGANOCUPRATE REAGENTS AND ALLYL ACYLATES: SYNTHESIS OF SOME PHENYLTHIOPROSTANOIDS (1981)

Abstract Das Lacton (I) reagiert mit den durch in‐situ‐Reaktion erzeugten Cuprat‐Reagenzien (II) in einem SN′‐anti‐ Prozeß hauptsächlich zu den Produkten (III) (Isolierung nach entsprechender Lactonbildung); unter gleichen Bedingungen werden aus dem Lacton (IV) nach einem S N 2‐ Mechanismus als Hauptprodukte die Säure (V) erhalten, die mittels des Ylids (VII) in die Prostaglandin‐Az ‐Analogen (VIb) bzw. (VIII) [durch Desilylierung des Primärprodukts (VIa)] übergeführt werden.
310 Does Improvement in Endothelial Function affect Erectile Function following Stem Cell Therapy in Men with Cardiomyopathy? (2020)

Endothelial dysfunction is an important component in the pathogenesis of cardiovascular disease and erectile dysfunction (ED). Interest in cell-based therapy (CBT) for cardiovascular disease and ED is growing. Early trials have shown CBT to improve cardiac function in men with ischemic cardiomyopathy, with concurrent improvement in endothelial function. Whether or not the improvement in endothelial function from CBT may benefit ED has yet to be explored. To determine if a change in endothelial function affects erectile function in men who received transendocardial injection of stem cells. We performed a post hoc sub-analysis of the TRIDENT trial to examine the relationship between endothelial function and erectile function. The TRIDENT study recruited 30 participants with ischemic cardiomyopathy and reduced ejection fraction (<50%) to receive allogenic bone-marrow derived mesenchymal stem cells (MSC) via transendocardial injection (TESI). Participants were randomized to receive MSCs in doses of 20 or 100 million cells and were followed for 1 year. International Index of Erectile Function (IIEF) questionnaires were administered at baseline and at 3, 6 and 12 months. Endothelial function was assessed at baseline and 3 months post-therapy and consisted of two measures: brachial artery percent Flow Mediated Vasodilation (FMD) and quantification of Endothelial Progenitor Cell-Colony Forming Units (EPC-CFUs). Patients with FMD less than 7% were considered to have endothelial dysfunction (normal = >10%), and higher counts of circulating EPCs indicate a greater capacity for endothelial self-regeneration.
The Intelligent Container as a Part of the Internet of Things A Framework for Quality-driven Distribution for Perishables (2012)

Perishables need special conditions within the food supply chain like temperature or humidity. There is a lack of information along the food supply chain (FSC) concerning temperatures for perishable goods. By integrating the Intelligent Container (IC) within the Internet of Things the lack of information will be eliminated and thus wastes of food will be reduced. The first step for this integration is to analyze common techniques in modeling supply chains and especially the FSC and create a model taking into consideration the concept of the IC. On this basis, technologies to generate information along the FSC are shown and the IC is linked to the Internet of Things. Finally, a logistic reference model will be deduced from the Internet of Things for perishables.
Size, shape, and flexibility influence nanoparticle transport across brain endothelium under flow (2019)

Nanoparticle-based therapeutic formulations are being increasingly explored for the treatment of various ailments. Despite numerous advances, the success of nanoparticle-based technologies in treating brain diseases has been limited. Translational hurdles of nanoparticle therapies are attributed primarily to their limited ability to cross the blood-brain barrier (BBB), which is one of the body's most exclusive barriers. Several efforts have been focused on developing affinity-based agents and using them to increase nanoparticle accumulation at the brain endothelium. Very little is known about the role of fundamental physical parameters of nanoparticles such as size, shape, and flexibility in determining their interactions with and penetration across the BBB. Using a three-dimensional human BBB microfluidic model (μHuB), we investigate the impact of these physical parameters on nanoparticle penetration across the BBB. To gain insights into the dependence of transport on nanoparticle properties, two separate parameters were measured: the number of nanoparticles that fully cross the BBB and the number that remain associated with the endothelium. Association of nanoparticles with the brain endothelium was substantially impacted by their physical characteristics. Hard particles associate more with the endothelium compared to soft particles, as do small particles compared to large particles, and spherical particles compared to rod-shaped particles. Transport across the BBB also exhibited a dependence on nanoparticle properties. A nonmonotonic dependence on size was observed, where 200 nm particles exhibited higher BBB transport compared to 100 and 500 nm spheres. Rod-shaped particles exhibited higher BBB transport when normalized by endothelial association and soft particles exhibited comparable transport to hard particles when normalized by endothelial association. Tuning nanoparticles' physical parameters could potentially enhance their ability to cross the BBB for therapeutic applications.
Power smoothing and power ramp control for wind energy using energy storage (2011)

Due to randomness of wind speed, the wind farm output power varies drastically. These fluctuations make undesirable effects on the voltage, frequency, and transient stability of the utility grid. In this paper, two types of energy storage devices are integrated with a wind farm to support the short-term shortcomings of wind energy. The support specifically improves power ramp rate control and power smoothing. The utilized energy storages devices are zinc bromide flow battery and Lithium-Ion Capacitors (LIC). The actual models of the battery and ultracapacitor, which are derived from testing, are used in this study. The power data for the wind farm and load are actual data from a local power system. The analysis shows that considerable improvements can be made to shape the output power of the farm using the energy storage systems.
Electrochemical Studies of Intramolecular Electron Transfer in Laccase from Trametes versicolor (2007)

Abstract This paper describes electrochemical behavior of laccase from the fungus Trametes versicolor. The issues related to discrimination of the redox potentials corresponding to copper centers T1 and T2/T3 in the active site and possible mechanism of intramolecular electron transfer have been discussed. The electron‐transfer rate constant for laccase immobilized on carbon electrode is 3.4 s −1 . The bioelectrocatalytic activity of the enzyme was studied in the presence of 1,4‐hydroquinone (HQ). The kinetics of HQ oxidation is very fast ( K M =3.8 μM). However, the catalytic activity of laccase in the presence of high concentration of HQ decreases drastically. It is suggested that the T2/T3 copper center is able to accept electrons from HQ molecules directly via intramolecular channel.
Avidin/Biotin-Mediated Conjugation of Antibodies to Erythrocytes: An Approach for in vivo Immunoerythrocyte Exploration (1996)

Antibody-carrying red blood cells (immunoerythrocytes) may be useful as a vehicle for drug targeting and for selective elimination of antigens from the bloodstream. Such immunoerythrocytes have to circulate in the bloodstream for a prolonged time without elimination and possess high affinity to the target antigen. Streptavidin/biotin technology is useful for attachment of biotinylated antibodies (b-Ab) to biotinylated red blood cells (b-RBC). Modification of RBC with biotin hydroxysuccinimide ester provides covalent coupling of biotin residues to amino groups on the RBC membrane. b-RBC are stable in serum in vitro and in the bloodstream. Binding of streptavidin (SA) to b-RBC, however, leads to their lysis by complement in vitro and fast elimination from circulation. The mechanism of lysis is streptavidin-induced cross-linking of membrane regulators of complement. Reduction of the surface density of biotin residues on RBC membrane prevents lysis. Surface density of biotin residues on RBC may be regulated by varying biotin ester concentration during RBC biotinylation (bn RBC). SA specifically binds to bn-RBC (e.g., 105 SA molecules per rat RBC biotinylated with 20 μM biotin, b20-RBC). Modest and intermediate degrees of RBC biotinylation provide effective attachment of b-IgG to streptavidin-coated b-RBC (SA/b-RBC). SA/b20-RBC bind 5 × 104 b-IgG molecules per cell. In contrast, SA attached to extensively biotinylated RBC (b700-RBC) does not bind biotinylated IgG. b-Ab/SA/b20-RBC are stable in serum and bind to immobilized antigen in vitro. 51Cr-labeled serum-stable b-Ab/SA/b20-RBC circulate without marked elimination and/or lysis in the bloodstream after iv. injection in rats. Biodistribution of b-Ab/SA/b20-RBC in rats is similar to that of control RBC. Therefore, b-Ab/SA/b20-RBC satisfy major requirements of a vehicle for drug targeting (i.e., high affinity to the target and biocompatibility) and can be explored in vivo.
VALIDATION OF THE OPTISCANNER, A CONTINOUS GLUCOSE MONITORING DEVICE. (2005)

Krinsley, James; Hall, Dale; Zheng, Peng; Magarian, Peggy; Braig, James Author Information
VAGINAL COLLAGEN REMODELLING AFTER FRACTIONAL CARBON DIOXIDE LASER SURGERY (2011)

Hypothesis / aims of study The process of becoming older is genetically determined and environmentally modulated. The process of vaginal ageing itself can contribute to the loss of vaginal trophism, tone, support and function with a consequent increased risk of lower urinary tract symptoms and pelvic floor dysfunction. Connective tissues and collagen constituents and architecture play an important role in this ageing process. With age, in fact, collagen fibrils loose their reticular spatial disposition and, the Type I/III ratio is altered compared to premenopausal state. The aim of this study is to assess if CO2 laser at the level of vaginal mucosa can determine new collagen formation or modification as shown in the skin [1] .
The Development of RNA-KISS, a Mammalian Three-Hybrid Method to Detect RNA–Protein Interactions in Living Mammalian Cells (2020)

RNA-protein interactions are essential for the regulation of mRNA and noncoding RNA functions and are implicated in many diseases, such as cancer and neurodegenerative disorders. A method that can detect RNA-protein interactions in living mammalian cells on a proteome-wide scale will be an important asset to identify and study these interactions. Here we show that a combination of the mammalian two-hybrid protein-protein detection method KISS (kinase substrate sensor) and the yeast RNA three-hybrid method, utilizing the specific interaction between the MS2 RNA and MS2 coat protein, is capable of detecting RNA-protein interactions in living mammalian cells. For conceptional proof we used the subgenomic flavivirus RNA (sfRNA) of the dengue virus (DENV), a highly structured noncoding RNA derived from the DENV genome known to target host cell proteins involved in innate immunity and antiviral defense, as bait. Using RNA-KISS, we could confirm the previously established interaction between the RNA-binding domain of DDX6 and the DENV sfRNA. Finally, we performed a human proteome-wide screen for DENV sfRNA-binding host factors, identifying several known flavivirus host factors such as DDX6 and PACT, further validating the RNA-KISS method as a robust and high-throughput cell-based RNA-protein interaction screening tool.
Physical mechanism of source and drain resistance reduction for high-performance short-channel InGaZnO thin-film transistors (2015)

We systematically study the mechanism of source and drain parasitic resistance reduction in amorphous InGaZnO thin-film transistors. Hall measurement shows that parasitic resistance is reduced by the increase in carrier density regardless of the source and drain processes. The results of photoluminescence, high-angle annular dark field scanning transmission electron microscope (HAADF-STEM), electron energy-loss spectroscopy (EELS), and X-ray photoelectron spectroscopy (XPS) analyses indicate that the fluctuation of In concentration at the InGaZnO surface is responsible for increase in carrier density. A top-gate InGaZnO transistor fabricated with a source drain resistance reduction process shows good short-channel immunity. The short-channel InGaZnO thin-film transistor with reduced source drain resistance is promising as the high-density back-end-of-line transistor in Si LSI.
Reinforcement Learning for Volt-Var Control: A Novel Two-stage Progressive Training Strategy (2021)

This paper develops a reinforcement learning (RL)approach to solve a cooperative, multi-agent Volt-Var Control (VVC) problem for high solar penetration distribution systems. The ingenuity of our RL method lies in a novel two-stage progressive training strategy that can effectively improve training speed and convergence of the machine learning algorithm. In Stage 1(individual training), while holding all the other agents inactive, we separately train each agent to obtain its own optimal VVC actions in the action space: {consume, generate, do-nothing}. In Stage 2 (cooperative training), all agents are trained again coordinatively to share VVC responsibility. Rewards and costs in our RL scheme include (i) a system-level reward (for taking an action), (ii) an agent-level reward (for doing-nothing), and(iii) an agent-level action cost function. This new framework allows rewards to be dynamically allocated to each agent based on their contribution while accounting for the trade-off between control effectiveness and action cost. The proposed methodology is tested and validated in a modified IEEE 123-bus system using realistic PV and load profiles. Simulation results confirm that the proposed approach is robust and computationally efficient; and it achieves desirable volt-var control performance under a wide range of operation conditions.