gebhart/patrepeval huggingface dataset:
Sensitivity Analyses for Monte Carlo Sampling-Based Particle Simulations (2022)

Computational design-based optimization is a well-used tool in science and engineering. Our re- port documents the successful use of a particle sensitivity analysis for design-based optimization within Monte Carlo sampling-based particle simulation?a currently unavailable capability. Such a capability enables the particle simulation communities to go beyond forward simulation and promises to reduce the burden on overworked analysts by getting more done with less computa- tion. Gradient-based methods crucially depend upon sensitivities, which are synonymous with the cal- culation of a derivative that measures the (instantaneous) change in a quantity with respect to an (instantaneous) change in another quantity. We exploit the link between the deterministic and parti- cle models to pose an equivalent optimization problem containing a stochastic differential equation as a constraint. We then demonstrate that the sensitivities can be approximated for the gradient- based optimization problem by reusing the particle trajectories employed for the existing Monte Carlo approximation. Additional forward simulations?as in a finite difference approach?are unnecessary. Our approach is general and so enables us to impact a broad spectrum of Monte Carlo particle simulation codes by a clean separation of the mathematical and the application-specific details. Our general approach develops capability largely unexplored as a Sandia analysis tool, and can be leveraged across several mission applications. Acknowledgements The authors acknowledge helpful conversations with Drew Kouri and Aaron Olson of Sandia Na- tional Laboratories, Tim Kelley of North Carolina State University, Petr Pechac of the University of Delaware, Ilham Variansyah and Ryan McClarren of the University of Notre Dame, and Todd Palmer of the Oregon State University. The author Scott McKinley?s affiliation is the Department of Mathematics, Tulane University, 6823 St Charles Ave, New Orleans, LA 70118. Our report was supported by the Laboratory Directed Research and Development program at San- dia National Laboratories, a multimission laboratory managed and operated by National Technol- ogy and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell Inter- national, Inc., for the U.S. Department of Energy?s National Nuclear Adminstration under contract DE-NA0003525.
Elaboration of Human Insulin Superagonism Through Site-selective Replacement at Tyr~(B26) (2007)

The role of conserved insulin residues TyrB26 was studied to better understand the relationship between insulin and its receptor. Insulin analogues with a single amino acid substitution or single N-methylation of the peptide bond in the position B26 were all shortened in the C-terminus of the B-chain by four amino acids. The effect of modifications was followed by the binding to the human insulin receptor.The results:[HistidineB26]-des-tetrapeptide-(B27-B30)-insulin -B26-amide and[N-MeHisB26]-des-tetrapeptide-(B27-B30)-insulin-B26-amide had no significant effect on the binding affinity and they showed binding affinity 72 and 107 % of that of human insulin respectively;[N-MeGluB26]-des-tetrapeptide-(B27-B30)-insulin-B26-amide,[AadB26]-des- tetrapeptide-(B27-B30)-insulin-B26-amide and[Phe(4-carboxyB26)]-des-tetrapeptide-(B27-B30)– insulin-B26-amide affected the potency highly positively in vitro studies; they showed binding affinity 130%,234%,160%, respectively, of that of human insulin.
Deregulation of temperature‐dependent transcription of the invasion regulatory gene, virB, in Shigella by rho mutation (1994)

Expression of the virB gene, the transcriptional regulator for the invasion genes encoded by the large plasmid of Shigella flexneri, is temperature-regulated. virB transcription is under the control of VirF and H-NS, which act as positive and negative regulators, respectively, and is highly responsive to changes in DNA superhelicity. To further investigate the molecular mechanisms underlying the thermoregulation of virB transcription, a mutant which expressed an invasion phenotype at both 30 degrees C and 37 degrees C was isolated using miniTn10-kan (miniKAN) random insertion mutagenesis. The insertion site was mapped to the rho gene, and resulted in the addition of 11 amino acids to the C-terminus of the Rho protein. Consequently, decreased transcription termination activity at a rho-dependent terminator, lambda tL1, was observed. In the rho mutant, both the transcription of virB and expression of invasion genes were activated at 30 degrees C and were less responsive to changes in temperature. The deregulation of virB expression by the mutation was dependent upon the virB promoter, since the effects of the mutation on virB transcription were abolished when its promoter region was replaced by the tac promoter. Temperature-responsive changes in DNA topology, as determined by linking numbers of a reporter plasmid, showed that changes in DNA superhelicity in the rho mutant were smaller than that in the wild type. Furthermore, when the mutant was grown in medium containing novobiocin, an inhibitor of DNA gyrase, virB transcription at 30 degrees C as well as at 37 degrees C was greatly diminished. These results indicated that Rho protein could have a profound effect on topological temperature-dependent changes in DNA structure, thus contributing to thermoregulation of virB transcription.
Silent store detection and recording in memory storage (2023)

An aspect includes receiving a write request that includes a memory address and write data. Stored data is read from a memory location at the memory address. Based on determining that the memory location was not previously modified, the stored data is compared to the write data. Based on the stored data matching the write data, the write request is completed without writing the write data to the memory and a corresponding silent store bit, in a silent store bitmap is set. Based on the stored data not matching the write data, the write data is written to the memory location, the silent store bit is reset and a corresponding modified bit is set. At least one of an application and an operating system is provided access to the silent store bitmap.
Stability of Spermatogenic Synchronization Achieved by Depletion and Restoration of Vitamin A in Rats (1990)

Studies of synchronization of spermatogenesis following vitamin A deficiency have suggested that this may provide an in vivo model for the study of stage-dependent changes in hormonal action and protein secretion within the seminiferous epithelium. However, until now, no information on the stability or durability of this condition has been available. In this study, 200 seminiferous tubules from each of 40 rats (including controls) were classified according to their spermatogenic stage after withdrawal and replenishment of vitamin A. Following 15 wk withdrawal and subsequent replenishment of vitamin A, spermatogenesis was initiated in a synchronous fashion. This synchrony remained stable for more than 10 cycles of the seminiferous epithelium (2.5 spermatogenic cycles). In association with the extended period of vitamin A deficiency, a proportion of tubules (30%) showed morphological characteristics of either Sertoli cells only or Sertoli cells plus spermatogonia with occasional pachytene spermatocytes. During the 11-wk period of observation in this study, no significant change in proportions of damaged tubules were observed. Testicular testosterone concentrations, although elevated with respect to controls, showed no correlation with the stage of the cycle of the seminiferous epithelium observed, whereas pituitary and serum follicle-stimulating hormone levels were elevated, probably due to the number of damaged tubules observed. The persistence of synchrony in spermatogenesis following vitamin A treatment suggests that this model is applicable for studies of paracrine actions within the testis. However, the decreased ratio of synchrony observed with time may provide evidence that duration of the individual stages of the cycle of the seminiferous epithelium might be subject to temporal variation, leading to a progressive desynchronization of spermatogenesis in this model system.
Haplotypen und die systematische Analyse genetischer Variation: Krankheitsgene, „Drug Targets“ und Pharmakogenomik (2002)

Wesentliche Ziele der modernen Genomforschung/ Pharmakogenomik sind die Identifikation von Krankheitsgenen, die Aufklärung der genetischen Variabilität von „Drug Targets“ und ihrer funktionellen Implikationen, sowie die umfassende Analyse der Variabilität von Genen, die den Transport und die Metabolisierung von Pharmaka steuern. So können die Voraussetzungen für eine individuell optimierte Pharmakotherapie, valide Diagnostik und wirkungsvolle Prävention geschaffen werden. Ein Schlüsselschritt ist dabei der systematische Vergleich individueller Gensequenzen mit dem Ziel der Identifizierung spezifischer Sequenzvarianten, die mit Krankheitsdisposition oder individuell unterschiedlicher Reaktion auf Pharmaka assoziiert sind. Dabei kann die Korrelierung genetischer Variation mit Funktionen von Genen nur auf der Basis von „Haplotypen“ erfolgen, da nur so Struktur-Funktionsbeziehungen erkannt werden können. Erste Ansätze und Arbeiten zur Analyse von Haplotypen und Etablierung komplexer Haplotyp/Genotyp-Phänotyp-Beziehungen bei hoher natürlicher genomischer Variabilität werden beschrieben.
Amphiphilic Wax Inhibitor for Tackling Crude Oil Wax Deposit Challenges (2019)

Abstract As waxy crude oil comes to the surface, it will cool down and causing the waxy fraction to gel. The gelled crude chokes the well, leading to restricted or blocked production and costly downtime for operators. One of the most common chemical solutions to address the wax deposit challenge is the addition of wax inhibitors or pour point depressants (PPDs) to the production stream. However, most of the PPD's used in the field are organic solvent-based polymers, which require large quantities of hazardous organic solvents such as xylene and toluene. To propose an improved solution, a water-based amphiphilic PPD polymer dispersion system, synthesized using controlled radical polymerization technology has recently been developed. This specifically designed block copolymer is synthesized with a hydrophilic polymeric head group and a hydrophobic tail. The macromolecular design was specifically optimized to control particle size to create unique and stable amphiphilic PPD dispersion. The viscosity of the PPD, at high activity of about 40%, is between 200 and 250 cps at room temperature with a milky color, and it remains stable to 200°C under 500psi. Also, the PPD dispersion itself has a pour point of −30°C, and it can be easily formulated to be pumpable under −40°C. For performance evaluation, the water-based PPD dispersion was tested using a standard cold-finger apparatus and a pour point tester on crude oils from various global regions. The results showed that this PPD dispersion not only significantly reduced crude oil wax deposition by nearly 70%, but it also reduced the pour point of the crude by typically 18°C. Overall, the current research performed on macromolecular architecture design shows that this block polymer technology allows polymer adjustment to meet application needs for various crude types, and to tackle this important flow assurance challenges.
Measurement Drift in 3-Hole Yaw Pressure Probes From 5µm Sand Fouling at 1050 °C (2021)

Abstract The present paper focuses on the resilience of 3-hole pressure probes to hot sand fouling in turbomachinery environments. These probes are utilized inside jet engine hot sections for diagnostics and flow characterization. Ingestion of sand and other particulates pose a significant risk to hot section components and measurement devices in gas turbine engines. In this study, wedge, cylindrical, and trapezoidal probes were exposed to hot section turbine aerothermal conditions of 1050 °C and 65–70 m/s flow velocity and fouled with 0–5 µm Arizona Road Dust (ARD). Sand accumulated more rapidly on the surface of the trapezoidal and cylindrical probe geometries than on the surface of the wedge probe geometry. Probe calibrations following sand fouling were performed in an ambient temperature, open air, calibration jet at Mach 0.3 and 0.5. Calibration curves using nondimensional coefficients were used to assess probe error in yaw angle due to sand fouling. Probe error was based on each probe’s ability to accurately measure flow direction over a flow angle range of [−10 deg, 10 deg]. On average, the probes displayed greater error at Mach 0.5 than Mach 0.3. The wedge probe performed the best after sand fouling and displayed a maximum error of less than ±2 deg in yaw angle. In contrast, the cylindrical probe performed the worst after sand fouling and displayed maximum errors of more than ±8 deg in yaw angle. Transient response did not change notably with sand fouling.
Method for detecting toxic gases (2023)

A method capable of detecting low concentrations of a pollutant or other component in air or other gas, utilizing a combination of a heating filament having a catalytic surface of a noble metal for exposure to the gas and producing a derivative chemical product from the component, and an electrochemical sensor responsive to the derivative chemical product for providing a signal indicative of the product. At concentrations in the order of about 1-100 ppm of tetrachloroethylene, neither the heating filament nor the electrochemical sensor is individually capable of sensing the pollutant. In the combination, the heating filament converts the benzyl chloride to one or more derivative chemical products which may be detected by the electrochemical sensor.
A NOD2-dependent proteome signature pattern: implications for Crohn disease (2006)

Background & aims: NOD2, a cytosolic receptor for the bacterial proteoglycan fragment muramyl-dipeptide (MDP), plays an important role in the recognition of intracellular pathogens. Variants in the bacterial sensor domain of NOD2 are genetically associated with an increased risk for the development of Crohn disease, a human chronic inflammatory bowel disease. To understand the proteomic signature pattern associated with NOD2 dysfunction in Crohn disease, global protein expression changes after MDP-stimulation were analysed.
On the compromise between noise reduction and speech/noise spatial information preservation in binaural speech enhancement (2021)

Spatial information is important for human perception of speech and sound signals. However, this information is often either distorted or completely neglected in noise reduction because it is challenging, to say the least, to achieve optimal noise reduction and accurate spatial information preservation at the same time. This paper studies the problem of binaural speech enhancement. By jointly diagonalizing the speech and noise correlation matrices, we present a method to construct the noise reduction filter as a linear combination of different eigenvectors, which span a certain subspace of the entire space. A different dimension of the subspace gives a different trade-off between noise reduction and speech/noise spatial information preservation. On the one side, if the dimension is equal to 1, maximum noise reduction is achieved but at the price of significant spatial information distortion. On the other extreme, if the dimension of the subspace is equal to that of the entire space, spatial information is accurately preserved but at the cost of no noise reduction. Therefore, one can achieve different levels of compromises between the amount of noise reduction and the level of speech/noise spatial information preservation by adjusting the dimension of the used subspace.
Atomically Precise Noble Metal Cluster-Assembled Superstructures in Water: Luminescence Enhancement and Sensing (2020)

We present an example of host–guest complexes of atomically precise noble metal nanoparticles with cucurbit[7]uril (CB) in water, specifically concentrating on Ag₂₉(LA)₁₂ (where LA is α-lipoic acid), a well-known red luminescent silver cluster. Such host–guest interactions resulted in enhanced luminescence of about 1.25 times for the modified system, compared to the parent cluster. We extended our study to cyclodextrins (CDs), where about 1.5 times enhanced luminescence was estimated compared to the parent cluster. The formation of supramolecular complexes was confirmed using high-resolution electrospray ionization mass spectrometry (HRESI MS) and nuclear magnetic resonance spectroscopy. Molecular docking and density functional theory calculations supported our experimental results and showed that while CB formed inclusion complexes by encapsulation of one of the LA ligands of the cluster, CD formed supramolecular adducts by interaction with the cavity built by the ligands on the cluster surface. The complexation was favored by geometrical compatibility. Consequently, these superstructures are labeled as Ag₂₉LA₁₂∩CBₙ and Ag₂₉LA₁₂@CDₙ (n = 1–3), where ∩ and @ indicate the inclusion complex and supramolecular adduct, respectively. Solution-phase Ag₂₉LA₁₂@CDₙ complexes were employed to detect dopamine (10 nM). Luminescent Ag₂₉LA₁₂@CDₙ and Ag₂₉LA₁₂∩CBₙ complexes in water could be potential candidates for organic pollutant sensing and biomedical applications.
GaAs-based self-aligned laser incorporating an InGaP opto-electronic confinement layer (2008)

We demonstrate a novel fabrication process for GaAs-based self-aligned lasers through regrowth upon an n-doped InGaP layer. Electrical and optical confinement results in high power single lateral mode emission from a ~ 980 nm DQW laser.
PI3K alpha and delta promote hematopoietic stem cell activation (2019)

Many cytokines and chemokines that are important for hematopoiesis activate the PI3K signaling pathway. Because this pathway is frequently mutated and activated in cancer, PI3K inhibitors have been developed for the treatment of several malignancies, and are now being tested in the clinic in combination with chemotherapy. However, the role of PI3K in adult hematopoietic stem cells (HSCs), particularly during hematopoietic stress, is still unclear. We previously showed that the individual PI3K catalytic isoforms P110α or P110β have dispensable roles in HSC function, suggesting redundancy between PI3K isoforms in HSCs. We now demonstrate that simultaneous deletion of P110α and P110δ in double knockout (DKO) HSCs uncovers their redundant requirement in HSC cycling after 5-fluorouracil (5-FU) chemotherapy administration. In contrast, DKO HSCs are still able to exit quiescence in response to other stress stimuli, such as LPS. We found that DKO HSCs and progenitors have impaired sensing of inflammatory signals ex vivo, and that levels of IL1-β and MIG are higher in the bone marrow after LPS than after 5-FU administration. Furthermore, exogenous in vivo administration of IL1-β can induce cell cycle entry of DKO HSCs. Our findings have important clinical implications for the use of PI3K inhibitors in combination with chemotherapy.
An Overview on Study of Identification of Driver Behavior Characteristics for Automotive Control (2014)

Driver characteristics have been the research focus for automotive control. Study on identification of driver characteristics is provided in this paper in terms of its relevant research directions and key technologies involved. This paper discusses the driver characteristics based on driver’s operation behavior, or the driver behavior characteristics. Following the presentation of the fundamental of the driver behavior characteristics, the key technologies of the driver behavior characteristics are reviewed in detail, including classification and identification methods of the driver behavior characteristics, experimental design and data acquisition, and model adaptation. Moreover, this paper discusses applications of the identification of the driver behavior characteristics which has been applied to the intelligent driver advisory system, the driver safety warning system, and the vehicle dynamics control system. At last, some ideas about the future work are concluded.
Changes in the Cerebello-Thalamo-Cortical Network After Magnetic Resonance-Guided Focused Ultrasound Thalamotomy (2022)

<b><i>Objective:</i></b> In recent years, transcranial magnetic resonance-guided focused ultrasound (tcMRgFUS) has been established as a potential treatment option for movement disorders, including essential tremor (ET). So far, however, little is known about the impact of tcMRgFUS on structural connectivity. The objective of this study was to detect microstructural changes in tremor- and motor-related white matter tracts in ET patients treated with tcMRgFUS thalamotomy. <b><i>Methods:</i></b> Eleven patients diagnosed with ET were enrolled in this tcMRgFUS thalamotomy study. For each patient, 3 Tesla magnetic resonance imaging (3T MRI) including structural and diffusion MRI were acquired and the Clinical Rating Scale for Tremor was assessed before the procedure as well as 1 year after the treatment. Diffusion MRI tractography was performed to identify the cerebello-thalamo-cortical tract (CTCT), the medial lemniscus, and the corticospinal tract in both hemispheres on pre-treatment data. Pre-treatment tractography results were co-registered to post-treatment diffusion data. Diffusion tensor imaging (DTI) metrics, including fractional anisotropy (FA), mean diffusivity (MD) and radial diffusivity (RD), were averaged across the tracts in the pre- and post-treatment data. <b><i>Results:</i></b> The mean value of tract-specific DTI metrics changed significantly within the thalamic lesion and in the CTCT on the treated side (<i>p</i> < 0.05). Changes of DTI-derived indices within the CTCT correlated well with lesion overlap (FA: <i>r</i> = -0.54, <i>p</i> = 0.04; MD: <i>r</i> = 0.57, <i>p</i> = 0.04); RD: <i>r</i> = 0.67, <i>p</i> = 0.036). Further, a trend was seen for the correlation between changes of DTI-derived indices within the CTCT and clinical improvement (FA: <i>r</i> = 0.58; <i>p</i> = 0.062; MD: <i>r</i> = -0.52, <i>p</i> = 0.64; RD: <i>r</i> = -0.61 <i>p</i> = 0.090). <b><i>Conclusions:</i></b> Microstructural changes were detected within the CTCT after tcMRgFUS, and these changes correlated well with lesion-tract overlap. Our results show that diffusion MRI is able to detect the microstructural effects of tcMRgFUS, thereby further elucidating the treatment mechanism, and ultimately to improve targeting prospectively. Impact statement The results of this study demonstrate microstructural changes within the cerebello-thalamo-cortical pathways 1 year after MR-guided focused ultrasound thalamotomy. Even more, microstructural changes within the cerebello-thalamo-cortical pathways correlated significantly with clinical outcome. These findings do not only highly emphasize the need of new targeting strategies for MR-guided focused ultrasound thalamotomy but also help to elucidate the treatment mechanism of it.