gebhart/patrepeval huggingface dataset:
Effect of Val34Leu Polymorphism on the Activation of the Coagulation Factor XIII-A (2000)

Coagulation factor XIII (FXIII) is a protransglutaminase involved in the last step of the coagulation cascade by stabilising the fibrin clot. Recently, a common variation (FXIII Val34Leu) has been associated with a decreased risk of myocardial infarction and deep venous thrombosis. Val34Leu is critically located near the thrombin activation site of FXIII-A. In this study we investigated its effects on the activation of FXIII. Both recombinant and platelet-derived FXIII Val34Leu variants were shown to be more susceptible to thrombin cleavage than the wild type FXIII. The rate of enzymatic activation of FXIII Val34Leu was found increased, however, the specific activity of fully activated wild type FXIII and the Val34Leu mutant did not differ. During the course of thrombin-induced activation of FXIII fibrin gamma-chain dimerisation and alpha-chain polymerisation developed more rapidly with the Val34Leu mutant. The increased rate of fibrin stabilisation brought about by the Val34Leu FXIII seems to be paradoxically associated with a protective effect against pathological thrombosis.
Implementation issues affecting the performance of carrier signal injection based sensorless controlled AC drives (2002)

This paper assesses and analyzes the practical implementation issues affecting the performance of carrier signal injection based sensorless control methods for AC drives. Included in this assessment and analysis are the following topics: selection of the carrier signal frequency and magnitude; the nonlinear behavior of pulse-width modulation and power electronics; and the signal processing required for the estimation, including analog filtering, sampling and analog-to-digital conversion. Variations in the characteristics and behavior of the saliency used for the estimation as a function of the machine's design and operating point are also addressed. The influence that each of these topics has on the robustness and accuracy of the estimate is discussed. Finally, conclusions are drawn on how the negative effects can be minimized and the performance of the estimation improved.
Table S1 from The Lipogenic Regulator SREBP2 Induces Transferrin in Circulating Melanoma Cells and Suppresses Ferroptosis (2023)

&lt;p&gt;Table S1&lt;/p&gt;
Polar and nonpolar orderings in the electrically induced isotropic-nematic phase transition (2008)

We study the dynamics of the isotropic-nematic phase transition caused by an applied electric field at the time scales of dielectric relaxation. In the classic Landau-Khalatnikov theory of the phase transition dynamics, the nematic (nonpolar) order parameter is an instantaneous function of the applied field. We demonstrate that, when the field is changing faster than the time of dielectric relaxation, the induced polar order dynamics influences the dynamics of the nonpolar order parameter. We develop a model based on the Langevin equation to describe the simultaneous dynamics of both polar and nonpolar order parameters; the model is supported by experiment.
I/O Interface Latchup Analysis Using Optical and Electrical Testing (2004)

Abstract Latchup has long been a concern for CMOS technologies and is becoming more of an issue with the reduction of transistor dimensions and spacing. Although many techniques for avoiding the risk of latchup have been developed, they generally apply to specific technologies and are not portable to others. In light of the problem, IBM engineers conducted an in-depth evaluation of the structures most sensitive to latchup ignition and the many possible triggering mechanisms. In this article, they describe the work they performed along with the findings and provide practical guidelines on how to minimize latchup regardless of the IC technology involved.
RESULTS OF 112 ANTERIOR LAXITIES REPAIRED WITH INTRA- AND EXTRA-ARTICULAR PLASTIES USING THE MACINTOSH METHOD: OUTCOME AT 14 YEARS (2002)

Purpose: The MacIntosch method for reconstruction of the anterior cruciate ligament using a free intra-articular plasty with an extra-articular reinforcement was the classical treatment during the eighties for chronic anterior laxity. In 1992, we reported our short-term resuls in 180 cases. The purpose of this report is to analyse the results in 112 of these 180 cases with a mean follow-up of 14 years. Material and methods: One hundred twelve knees operated between 1982 and 1987 were included in this study. There were 82 men (73.2%) and 30 women (26.8%), mean age 24.9±5.8 years. Mean follow-up was 165.3 ± 25.9 months. Mean delay from accident to repair was 30.9 months (3–144) and meniscectomy was performed in 88% of the cases, mainly for contact pivot sports (85%). All patients had an overt laxity (advanced in 73.2% or isolated in 26.9%). The MacIntosh plasty performed by arthrotomy used a patellar tendon with a quadriceps tendon band prolongation. Arthros-copy was performed prior to surgery in all cases. If the transplant was implanted over the top, the radiographic analysis of the tunnel position was only made for the tibia. An independent examiner reviewed all the patients clinically and radiographically using the IKDC criteria with instrumental KT 1000 measurements. Results: Sports activities were resumed in 78% of the cases with a trend towards pivot sports without contact practised in an amateur setting. Subjectively, 69.6% of the patients were very satisfied and 25% were satisfied. The click was abolished in 83% of the cases, was minimal in 15% and overt in 2%. The medial meniscus was intact in 40% of the cases with only 10 secondary meniscal tears 14 years later. The residual manual maximal traction differential at KT 1000 was 1 ± 1.225 mm and the mean compliance was 1.69 ± 1 mm. The overall IKDC score was: 31% A, 47/6% B, 19.1% C, 1.9% D. X-rays were normal in 17%, showed remodelling in 55.4%, and joint narrowing 50% in 3.8%. For patients with an intact medial meniscus, joint narrowing was observed in 5.5% compared with 24% after resection of the medial meniscus. There were two repeat tears in this series compared with 22 tears of the contra-lateral anterior cruciate ligament. The unsatisfactory results (22%) were related to anatomic failure (two cases) and functional problems (18 cases, defective mobility and pain). The prognostic factors were age at time of operation and preservation of the medial meniscus. Conclusions: This study confirms the persistently good clinical and functional results 14 years after plasty using the patellar tendon associated with lateral reinforcement. Ligament stabilisation was satisfactory but it must be recalled that at 14 years, the functional needs were different for these knees. The radiological course was more worrisome with joint narrowing in 27.6% of the cases.
Carbon Dioxide Conversion to Methanol over Size-Selected Cu4 Clusters at Low Pressures (2015)

The activation of CO2 and its hydrogenation to methanol are of much interest as a way to utilize captured CO2. Here, we investigate the use of size-selected Cu4 clusters supported on Al2O3 thin films for CO2 reduction in the presence of hydrogen. The catalytic activity was measured under near-atmospheric reaction conditions with a low CO2 partial pressure, and the oxidation state of the clusters was investigated by in situ grazing incidence X-ray absorption spectroscopy. The results indicate that size-selected Cu4 clusters are the most active low-pressure catalyst for catalytic CO2 conversion to CH3OH. Density functional theory calculations reveal that Cu4 clusters have a low activation barrier for conversion of CO2 to CH3OH. This study suggests that small Cu clusters may be excellent and efficient catalysts for the recycling of released CO2.
Intraband and interband optical deformation potentials in femtosecond-laser-excitedα−Te (2007)

We calculated the intraband and interband optical deformation potentials for semiconducting $\ensuremath{\alpha}\text{\ensuremath{-}}\mathrm{Te}$ from experimental data of the band gap shrinkage and softening of the ${A}_{1}$-optical phonon mode in response to femtosecond laser excitation. These potentials were obtained by applying first- and second-order perturbation theory to the Fr\"olich Hamiltonian describing the carrier-phonon interaction. The intraband optical deformation potential is considerably smaller than previously estimated values; there are no previously reported values for the interband optical deformation potential.
Global analysis and Decay Associated Images (DAI) derived from Fluorescence Lifetime Imaging Microscopy (FLIM) (2019)

The extraction of fluorophore lifetimes in a biological sample provides useful information about the probe environment that is not readily available from fluorescence intensity alone. Cell membrane potential, pH, concentration of oxygen ([O<sub>2</sub>]), calcium ([Ca<sup>2+</sup>]), NADH and other ions and metabolites are all regularly measured by lifetime-based techniques. These measurements provide invaluable knowledge about cell homeostasis, metabolism and communication with the cell environment. Fluorescence lifetime imaging microscopy (FLIM) produces spatial maps with time-correlated single-photon counting (TCSPC) histograms collected and analyzed at each pixel, but traditional TCSPC analysis is often hampered by the low number of photons that can reasonably be collected while maintaining high spatial resolution. More important, traditional analysis fails to employ the spatial linkages within the image. Here, we present a different approach, where we work under the assumption that mixtures of a global set of lifetimes (often only 2 or 3) can describe the entire image. We determine these lifetime components by globally fitting precise decays aggregated over large spatial regions of interest, and then we perform a pixel-by-pixel calculation of decay amplitudes (via simple linear algebra applied to coarser time-windows). This yields accurate amplitude images (Decay Associate Images, DAI) that contain stoichiometric information about the underlying mixtures while retaining single pixel resolution. We collected FLIM data of dye mixtures and bacteria expressing fluorescent proteins with a two-photon microscope system equipped with a commercial single-photon counting card, and we used these data to benchmark the gDAI program.
Stability of Superparamagnetic Iron Oxide Nanoparticles at Different pH Values: Experimental and Theoretical Analysis (2012)

The detection of superparamagnetic nanoparticles using NMR logging has the potential to provide enhanced contrast in oil reservoir rock formations. The stability of the nanoparticles is critical because the NMR relaxivity (R(2) ≡ 1/T(2)) is dependent on the particle size. Here we use a molecular theory to predict and validate experimentally the stability of citric acid-coated/PEGylated iron oxide nanoparticles under different pH conditions (pH 5, 7, 9, 11). The predicted value for the critical surface coverage required to produce a steric barrier of 5k(B)T for PEGylated nanoparticles (MW 2000) was 0.078 nm(-2), which is less than the experimental value of 0.143 nm(-2), implying that the nanoparticles should be stable at all pH values. Dynamic light scattering (DLS) measurements showed that the effective diameter did not increase at pH 7 or 9 after 30 days but increased at pH 11. The shifts in NMR relaxivity (from R(2) data) at 2 MHz agreed well with the changes in hydrodynamic diameter obtained from DLS data, indicating that the aggregation behavior of the nanoparticles can be easily and quantitatively detected by NMR. The unexpected aggregation at pH 11 is due to the desorption of the surface coating (citric acid or PEG) from the nanoparticle surface not accounted for in the theory. This study shows that the stability of the nanoparticles can be predicted by the theory and detected by NMR quantitatively, which suggests the nanoparticles to be a possible oil-field nanosensor.
The structure of Clostridium difficile toxin A glucosyltransferase domain bound to Mn2+ and UDP provides insights into glucosyltransferase activity and product release (2012)

Clostridiumdifficile toxin A (TcdA) is a member of the large clostridial toxin family, and is responsible, together with C. difficile toxin B (TcdB), for many clinical symptoms d ring human infections. Like other large clostridial toxins, TcdA catalyzes the glucosylation of GTPases, and is able to inactivate small GTPases within the host cell. Here, we report the crystal structures of the TcdA glucosyltransferase domain (TcdA-GT) in the apo form and in the presence of Mn(2+) and hydrolyzed UDP-glucose. These structures, together with the recently reported crystal structure of TcdA-GT bound to UDP-glucose, provide a detailed understanding of the conformational changes of TcdA that occur during the catalytic cycle. Indeed, we present a new intermediate conformation of a so-called 'lid' loop (residues 510-522 in TcdA), concomitant with the absence of glucose in the catalytic domain. The recombinant TcdA was expressed in Brevibacillus in the inactive apo form. High thermal stability of wild-type TcdA was observed only after the addition of both Mn(2+) and UDP-glucose. The glucosylhydrolase activity, which is readily restored after reconstitution with both these cofactors, was similar to that reported for TcdB. Interestingly, we found that ammonium, like K(+) , is able to activate the UDP-glucose hydrolase activities of TcdA. Consequently, the presence of ammonium in the crystallization buffer enabled us to obtain the first crystal structure of TcdA-GT bound to the hydrolysis product UDP.
SU086, an inhibitor of HSP90, impairs glycolysis and represents a treatment strategy for advanced prostate cancer (2022)

Among men, prostate cancer is the second leading cause of cancer-associated mortality, with advanced disease remaining a major clinical challenge. We describe a small molecule, SU086, as a therapeutic strategy for advanced prostate cancer. We demonstrate that SU086 inhibits the growth of prostate cancer cells <i>in vitro</i>, cell-line and patient-derived xenografts <i>in vivo</i>, and <i>ex vivo</i> prostate cancer patient specimens. Furthermore, SU086 in combination with standard of care second-generation anti-androgen therapies displays increased impairment of prostate cancer cell and tumor growth <i>in vitro</i> and <i>in vivo</i>. Cellular thermal shift assay reveals that SU086 binds to heat shock protein 90 (HSP90) and leads to a decrease in HSP90 levels. Proteomic profiling demonstrates that SU086 binds to and decreases HSP90. Metabolomic profiling reveals that SU086 leads to perturbation of glycolysis. Our study identifies SU086 as a treatment for advanced prostate cancer as a single agent or when combined with second-generation anti-androgens.
Identifying Foreign Material Contamination in Food and Food Ingredients (2008)

Abstract Between the Biological and Materials sciences resides the food industry, where both biological and materials methods and techniques are employed for both production and analysis. Often referred to as “Black Specs,” one of the biggest concerns for the food industry is contamination of the food, or its additives and ingredients, with foreign material (FM). Many of our customers seek assistance in solving their FM issues, which may require multiple instrumentation, several methods, and considerable open communication with the customer before a satisfactory result can be achieved. An additional level of difficulty is often present when we learn that the FM is so small we can barely detect it with the unaided eye. Particularly difficult is what might be referred to as “chemical contamination.” We present here in example (and in the upcoming Microscopy and Microanalysis meeting in Albuquerque this August), several of the methods employed in assisting our customers with FM issues.
1A1-A12 Differential Pressure Measurement on the Wing of an Ornithopter with Different Elastic Veins(Bio-Mimetics and Bio-Mechatronics (1)) (2013)

We measured differential pressures on the wing of an ornithopter with different stiffness of veins in flapping motion. The pressure measurement was carried out by using a MEMS differential pressure sensor attached on the wing surface. The ornithopter was modeled after a hawkmoth. The wing length was 110 mm, and total mass was 7.3-7.7 g. We fabricated three types of wings which had veins of different cross-section. In the experiment, the ornithopter was propelled by an electric motor and flapped at 10-11 Hz. The result suggested that when a wing is flexible, the different pressure on the wing is small, but the passive deformation of the wing is large during takeoff, then the ornithopter can fly by being subjected to thrust during upstroke and lift during downstroke.
Induction of inflammatory cytokines and nitric oxide in J774.2 cells and murine macrophages by lipoteichoic acid and related cell wall antigens from Staphylococcus epidermidis (2005)

Staphylococcus epidermidis causes infections associated with medical devices including central venous catheters, orthopaedic prosthetic joints and artificial heart valves. This coagulase-negative staphylococcus produces a conventional cellular lipoteichoic acid (LTA) and also releases a short-glycerophosphate-chain-length form of LTA (previously termed lipid S) into the medium during growth. The relative pro-inflammatory activities of cellular and short-chain-length exocellular LTA were investigated in comparison with peptidoglycan and wall teichoic acid from S. epidermidis and LPS from Escherichia coli O111. The ability of these components to stimulate the production of pro-inflammatory cytokines [interleukin (IL)-1beta, IL-6 and tumour necrosis factor (TNF)-alpha] and nitric oxide was investigated in a murine macrophage-like cell line (J774.2), and in peritoneal and splenic macrophages. On a weight-for-weight basis the short-chain-length exocellular LTA was the most active of the S. epidermidis products, stimulating significant amounts of each of the inflammatory cytokines and nitric oxide, although it was approximately 100-fold less active than LPS from E. coli. By comparison the full-chain-length cellular LTA and peptidoglycan were less active and the wall teichoic acid had no activity. As an exocellular product potentially released from S. epidermidis biofilms, the short-chain-length exocellular LTA may act as the prime mediator of the host inflammatory response to device-related infection by this organism and act as the Gram-positive equivalent of LPS in Gram-negative sepsis. The understanding of the role of short-chain-length exocellular LTA in Gram-positive sepsis may lead to improved treatment strategies.
Advances in sexual medicine: highlights from the 2007 winter meeting of the sexual medicine society of north america, december 6-9, 2007, chicago, IL. (2008)

The Sexual Medicine Society of North America held its winter scientific meeting in Chicago in December 2007. The meeting covered most of the issues that are related to sexual medicine, with “state of the art” lectures, scientific sessions with both poster and podium presentations, and debates between experts in a number of disciplines.
Differential T cell homing to colon vs. small intestine is imprinted by local CD11c+ APCs that determine homing receptors (2017)

Mechanisms that imprint T cell homing to the small intestine have been well studied; however, those for homing to the colon are poorly understood. Recently, we found that these are distinct subcompartments of the gut mucosal immune system, which implies differential homing. Here, we show that colonic CD11c<sup>+</sup> APCs imprint CD8<sup>+</sup> T cell preferential homing to the colon, in contrast to those from the small intestine that imprint CD8<sup>+</sup> T cell homing to the small intestine, and that the differences are related to the variable ability of APCs to induce α4β7-integrin and CCR9 expression on T cells. Colon APCs also expressed lower levels of retinoic acid-producing enzymes that are known to control the mucosal homing of T cells. These findings are the first to our knowledge to directly demonstrate that colon APCs imprint T cells to selectively home to the large bowel, which is critical for the design of successful T cell-based therapies and vaccines, such as colon cancer immunotherapy and HIV vaccines.
Metastatic Pheochromocytoma/Paraganglioma Related to Primary Tumor Development in Childhood or Adolescence: Significant Link to SDHB Mutations (2011)

The majority of patients with metastatic pheochromocytoma/paraganglioma who presented with a primary tumor in childhood/adolescence had primary extra-adrenal tumors and harbored SDHB mutations. Except for primary tumors located in the head and neck where SDHD genetic testing is advised, we recommend that patients who present with metastatic pheochromocytoma/paraganglioma with primary tumor development in childhood or adolescence undergo SDHB genetic testing before they undergo testing for other gene mutations, unless clinical presentation or family history suggests a different mutation.
A comparison of Predictive Current Control schemes for MV induction motor drives (2011)

In medium-voltage drives the switching frequency is limited to a few hundred Hz, necessitating control and modulation schemes capable of producing low levels of current and torque distortions at low switching frequencies. Model Predictive Direct Current Control (MPDCC) has emerged as a promising scheme for medium-voltage induction-motor drives. By forecasting the trajectory of the stator currents over a timespan known as the prediction horizon, MPDCC regulates the stator currents within a set of hysteresis bounds while minimising the inverter switching frequency. Despite the recent surge in popularity of predictive control, such schemes in the field of power electronics and drives were proposed already in the early 1980's. Forced Machine Current Control (FMCC) is an early predictive current control scheme which shares several similarities with MPDCC. However, a comprehensive review and comparison of FMCC with the modern MPDCC scheme has never been carried out. Through simulation, it is shown that the steady state performance of MPDCC and FMCC is similar when the prediction horizon of the former is limited. However, when the prediction horizon is extended, the performance of MPDCC is shown to be superior to FMCC, the horizon of which is inherently restricted.
Supplementary Table 1 from <i>In Vitro</i> and <i>In Vivo</i> Activity of IMGN853, an Antibody–Drug Conjugate Targeting Folate Receptor Alpha Linked to DM4, in Biologically Aggressive Endometrial Cancers (2023)

&lt;p&gt;Endometrioid cell lines with demographics, stage, histologic grade, primary site of tumor, Mean fluorescence intensity (MFI) and score for FRα (folic acid alpha receptor).&lt;/p&gt;