gebhart/patrepeval huggingface dataset:
StateReveal: Enabling Checkpointing of FPGA Designs with Buried State (2020)

The ability to save and restore the entire state of an FPGA design is essential for hardware checkpointing, which enables live migration, fault recovery, and novel debugging flows. However, hard blocks such as block RAMs and DSP blocks have state elements that cannot be saved or restored using conventional checkpointing techniques such as readback. This results in an incomplete checkpoint, thereby preventing checkpointing of most FPGA designs. In this paper, we propose general techniques that allow a complete checkpoint to be captured and loaded even when a design contains inaccessible state elements. The proposed techniques include using multi-cycle capture and inserting capture registers that add observability and controllability of this buried state. Moreover, we present StateReveal, a tool that detects the presence of inaccessible state elements in a design and automatically inserts the required capture registers. This enables checkpointing of designs that contain fully registered block RAMs and pipelined DSP blocks, which was not previously feasible. We verify the ability to capture and load a complete checkpoint on several designs using an enhanced checkpointing framework that supports multi-cycle capture. StateReveal currently supports Xilinx FPGAs, and the added circuitry has a low timing overhead of 5% and an acceptable area overhead that averages 19 LUTs and 35 registers per hard block.
PL research and its consequences on PL curriculum (2008)

The programming language research community-a fraction of the much larger and more vibrant language community-has increasingly turned inward and focused on narrow, technical contributions rather than the larger concerns of the computer science community or programmers in general. It is not surprising that our colleagues and students reciprocate our lack of interest in their problems by replacing language courses with newer, more exciting offering that address broader issues. Bluntly, the PL research community brought this workshop on itself.
Real-time implementation of zoom tracking on TI DM processor (2005)

Consumer demand for fast and accurate zoom tracking has increased in the Digital Still Camera (DSC) market. Consumers desire a DSC that automatically performs zoom tracking in order to maintain the image sharpness when the zoom lens is moved towards wide-angle or tele-angle directions. Zoom tracking involves the estimation of the in-focus motor position over all zooms based on a current in-focus position before the zoom lens is moved in either direction. Normally, a zoom tracking curve is utilized to automatically track the focus motor position when the zoom lens is moved. This paper discusses and compares the real-time implementation of two widely used zoom tracking algorithms, namely geometric zoom tracking (GZT) and adaptive zoom tracking (AZT), on the Texas Instruments (TI) digital media (DM) processor. This processor is a highly integrated, programmable dual-core processor manufactured by TI specifically for the DSC market. Our previously developed rule-based search algorithm is used to perform auto-focusing over the vicinity of the tracked focus motor position when the zoom lens is halted. This is done to regain any loss in accuracy during zoom tracking. Extensive testing was carried out to examine the performance of these algorithms in terms of tracking accuracy and speed. The results show that AZT generates a better tracking accuracy while GZT provides a faster tracking speed.
Three-Dimensional Reconstruction of the Hepatitis C Virus Envelope Glycoprotein E1E2 Heterodimer by Electron Microscopic Analysis (2022)

Despite the development of highly effective hepatitis C virus (HCV) treatments, an effective prophylactic vaccine is still lacking. HCV infection is mediated by its envelope glycoproteins, E1 and E2, during the entry process, with E2 binding to cell receptors and E1 mediating endosomal fusion. The structure of E1E2 has only been partially resolved by X-ray crystallography of the core domain of E2 protein (E2c) and its complex with various neutralizing antibodies. Structural understanding of the E1E2 heterodimer in its native form can advance the design of candidates for HCV vaccine development. Here, we analyze the structure of the recombinant HCV E1E2 heterodimer with the aid of well-defined monoclonal anti-E1 and E2 antibodies, as well as a small-molecule chlorcyclizine-diazirine-biotin that can target and cross-link the putative E1 fusion domain. Three-dimensional (3D) models were generated after extensive 2D classification analysis with negative-stain single-particle data sets. We modeled the available crystal structures of the E2c and Fabs into 3D volumes of E1E2-Fab complexes based on the shape and dimension of the domain density. The E1E2 heterodimer exists in monomeric form and consists of a main globular body, presumably depicting the E1 and E2 stem/transmembrane domain, and a protruding structure representing the E2c region, based on anti-E2 Fab binding. At low resolution, a model generated from negative-stain analysis revealed the unique binding and orientation of individual or double Fabs onto the E1 and E2 components of the complex. Cryo-electron microscopy (cryo-EM) of the double Fab complexes resulted in a refined structural model of the E1E2 heterodimer, presented here. <b>IMPORTANCE</b> Recombinant HCV E1E2 heterodimer is being developed as a vaccine candidate. Using electron microscopy, we demonstrated unique features of E1E2 in complex with various neutralizing antibodies and small molecule inhibitors that are important to understanding its antigenicity and induction of immune response.
THE ANXIOLYTIC EFFECTS OF IPSAPIRONE CORRELATE WITH A DECREASE IN 5-HT CELL FIRING AND NEUROTRANSMISSION (1992)

De Vry, J.; Sommermeyer, H.; Greuel, J. M.; Schreiber, R.; Glaser, T. Author Information
Bioinspired, Kinetically Controlled Synthesis of High-Performance Anode and Cathode Materials for Lithium Batteries (2010)

Abstract not Available.
The Effect of Dust Loading on Penetration and Resistance of Glass Fiber Filters (1997)

ABSTRACT As glass fiber filters become loaded with solid particles, their resistance to airflow increases and penetration at a given flow rate decreases. In the present study, we measured the effect of loading on resistance and penetration for three types of loading dust with Mass Median Aerodynamic Diameter (MMAD) from 0.8 to 7.5 μm, and mass loading up to 2.2 mg/cm2. Penetration as a function of particle size and resistance measurements were made for five loading conditions, seven face velocities (0.04–3.38 cm/s), and 12 particle sizes (0.137–3.65 μm). As expected, loading modified filter performance to give greater resistance and lower penetration. Unit mass loading by the finer loading dust caused a greater increase in resistance and a greater decrease in penetration than did the coarser dusts. A computer model to predict the effect of loading on resistance and penetration was prepared. The model uses modified single-fiber filtration theory to estimate resistance and penetration. It assumes that solid particles deposited on a fiber act like additional short “fibers” having a diameter equal to the diameter of average mass of the loading dust. Loading directly affects only the average fiber diameter and the filter solidity, but these two parameters affect all single-fiber collection mechanisms. For the conditions of these experiments, resistance increased linearly with loading, particle size of maximum penetration changed little with loading, and penetration decreased more rapidly for initial loading than subsequent loading. The change in measured resistance and the change in model predicted resistance were correlated with a correlation coefficient (r) of 0.87. The model correctly predicted the trend in penetration with loading for each of the three loading particle sizes.
Ball SAW gas chromatograph for detection of mixed VOC and FC gases (2010)

In order to realize on-site monitoring of mixed gases of volatile organic compounds (VOCs) and fuel cell (FC) gases, we propose a ball surface acoustic wave (SAW) gas chromatograph (GC) that operates at room temperature, using ball SAW sensors and microelectro mechanical systems (MEMS) columns. The ball SAW GC can rapidly analyze mixed gases including wide range of molecular weights by switching two combinations of column sensor pairs from series to parallel. As the component suitable for prtable GC, we developed metal MEMS column to improve the robustness and reduce the cost of previous silicon MEMS columns. A prototype of the ball SAW GC was assembled and the performance was evaluated by the analysis of a model VOC gas and a model town gas. As a result, it was verified that this system can separate and detect each component of these mixed gases. Moreover, we succeeded in fabricating active-carbon-packed metal MEMS column for FC gas including H2. Therefore, the ball SAW GC will realize on-site monitoring of VOC and FC gases to be used at cars, home and smart grids.
Mechanistic investigations of a recombinant laccase from Thermus thermophilus HB27 (2017)

Laccases belong to the family of multicopper oxidases (MCOs) that couple oxidn. of a wide spectrum of substrates to the four-electron redn. of dioxygen (O_2) to water. Laccases typically contain four copper ion sites arranged in two centers: one type 1 blue copper center and one trinuclear cluster (TNC) consisting of one type 2 copper and a binuclear type 3 copper pair. Dioxygen binding, activation, and redn. are believed to proceed at the TNC with electrons delivered from the type 1 site. The precise mechanism of coupling O_2 redn. to substrate oxidn. is a subject of considerable fundamental and technol. significance. Of particular interest is the mechanism by which laccases oxidize refractory substrates such as phenols and lignin. To gain deeper insight into laccase catalysis, we have cloned the gene for a recombinant multicopper oxidase from the hyperthermophilic bacterium Thermus thermophilus HB27 (Tth-MCO), and expressed the enzyme as a 6Histagged protein in Escherichia coli. Several mutants of the recombinant enzyme have been prepd. by sitedirected mutagenesis and investigated using various structural and spectroscopic techniques. Our recent results&#13;\non the reaction pathways and intermediates involved in the enzymic reaction will be discussed.
ONC201 in previously-irradiated pediatric H3 K27M-mutant glioma. (2019)

10046 Background: ONC201 is the first DRD2 antagonist for clinical oncology. The recommended phase 2 dose (RP2D) of 625mg ONC201 orally once a week has been established in adult patients. ONC201 efficacy has been shown in high-grade glioma preclinical models and radiographic regressions with single agent ONC201 have been reported in adult recurrent H3 K27M-mutant glioma patients. We report results from the first Phase I pediatric clinical trial of ONC201. Methods: This multicenter, open-label, dose-escalation and dose-expansion clinical trial (NCT03416530) determined the RP2D of ONC201 in pediatric H3 K27M-mutant glioma patients as a single agent. ONC201 was orally administered once a week and scaled by body weight. Dose escalation was performed by a 3 + 3 design beginning with one 125mg capsule less than the adult RP2D equivalent. Three patients were treated at the starting dose and 19 were treated at the adult RP2D equivalent. Results: The primary endpoint was achieved by establishing the safety of the adult RP2D scaled by body weight to pediatric patients. Twenty-two patients with a median age of 9 (range 3-18) years old who received at least prior radiation have been treated with ONC201: 15 with diffuse intrinsic pontine glioma (DIPG) (4 recurrent; 11 not recurrent) and 7 with non-DIPG H3 K27M-mutant glioma (all not recurrent). As of February 5, 2019, patients have received a median of 18 ONC201 doses (range 3-41) without instance of dose-limiting toxicity. Pharmacokinetic profiles were comparable to those observed in adults (Cmax ~2.1ug/mL; AUC ~2.3hr*ug/mL) and exposure was similar across body weights. Nine of 22 patients remain on therapy, 13 have discontinued due to progression, and 4 off-study patients are alive with a median follow up of 5.8 months. Five of the 11 (45%) DIPG patients who initiated ONC201 following radiation, but prior to recurrence, remain on therapy (median 7.4 months; range 4.4-9.6): median PFS is 4.4 months from initiation of ONC201 and 9.7 months from diagnosis; 7 of 11 (64%) patients are alive with median follow up of 11.8 months from diagnosis. Conclusions: ONC201 was well tolerated and achieved therapeutic exposure in pediatric H3 K27M-mutant glioma patients at the adult RP2D scaled by body weight. Further investigation of first-line ONC201 to treat H3 K27M-mutant glioma and/or DIPG is ongoing. Clinical trial information: NCT03416530.
New Numerical and Analytical Models to Quantify the Near-Wellbore Damage due to Sulfur Deposition in Sour Gas Reservoirs (2013)

Abstract The deposition of elemental sulfur as a solid phase will result in plugging the pore space available for gas flow and reduce the reservoir productivity. Elemental sulfur also can be deposited as a liquid phase if the reservoir temperature was greater than 115°C. The liquid sulfur will not flow at the same velocity as gas and in turn the gas flow will be restricted by the settled sulfur due to the huge difference between the liquid sulfur density and gas (Could be 20 times or more in certain cases). For the isothermal conditions in the reservoir, the reduction in reservoir pressure below a critical value will cause the elemental sulfur to deposit in the formation, and in turn the gas well productivity will be affected. Accurate prediction of sulfur deposition in the reservoir will help in better manage sour gas reservoirs with potential sulfur deposition problems. In this paper new analytical and numerical models were developed to predict the effect of sulfur deposition on the damage of the near-wellbore. The damage will be quantified through the investigation of the effect of sulfur deposition on the skin damage value, relative permeability of the gas phase, and the change in rock wettability due to sulfur deposition especially in the near-wellbore region. The main objective of these models is to investigate the effect of radial distance on formation damage. Different rock and fluid properties accurate correlation were used in this model for better results prediction. Previous studies did not consider the change in gas properties with pressure, and numerically modeled the sulfur deposition as a condensate in a gas condensate reservoir. In this paper will consider r the sulfur adsorption and the actual physical properties of the sulfur will be used in the developed model. The optimum gas flow velocity will be determined based on the sulfur solubility. Analytical and numerical solutions show that the deposition of sulfur was affected by the radial distance from the wellbore and sulfur solubility change as a function of the pressure drop. The numerical and analytical models showed good match in modeling the sulfur deposition in the near-wellbore area. Sulfur deposition was found to have a great effect on the rock wettability, and in turn the gas production will be affected. The model can be used to predict the critical flow velocity that the gas can flow without precipitating sulfur. The optimum gas flow velocity was estimated to be a range that maximizes the sulfur solubility in the gas.
4-18F-Fluorobenzonitrile oxide ([18F]FBNO]) - A novel amine-reactive prosthetic group for radiolabeling (2013)

618 Objectives A direct addition of nucleophiles such as amines and thiols to 1,3-dipoles such as nitrile oxides has not yet been explored in radiochemistry. The aim of this work was to study the applicability of this reaction for radiofluorination. Consequently, 18F-labeled conjugates, including a novel PSMA-ligand, were prepared via addition of nitrogen or sulphur nucleophiles to [18F]FBNO. Additionally, first results of the in vitro evaluation of the PSMA-ligand are also presented. Methods [18F]FBNO was generated in situ from the respective N-hydroxy-benzoimidoyl chloride ([18F]FBIC) and allowed to react with H-βAla-Phe-OMe, H-DUPA and Boc-Cys(H)-OMe in aq. EtOH at rt to give conjugates [18F]1, [18F]2 and [18F]3, respectively. Hydrolytic (pH = 2, 7, 9) and blood serum stability of [18F]2 and [18F]3 was determined at 37 ○C. Cellular uptake of [18F]2 in PSMA-positive LNCaP C4-2 and PSMA-negative PC-3 prostate tumor cells was determined in the presence and absence of 2-PMPA (PSMA-inhibitor). Results [18F]1-3 were prepared in 50-92% RCYs after 10 min incubation at pH = 8-9. Radiofluorinated amidoxime [18F]2 demonstrated excellent hydrolytic and blood serum stability (> 98% after 3 h incubation). In contrast, thiohydroxymate [18F]3 was unstable at pH 9 and only moderately stable in blood serum (35% after 3 h incubation). A high accumulation of [18F]2 in LNCaP C4-2 cells was blocked by 2-PMPA up to 95% (%ID/105 cells: 2.31±0.25 vs. 0.15±0.05 and 5.5±0.3 vs. 0.2±0.05 after 1 and 4 h, respectively). On the contrary, the cellular uptake in PC-3 control cells was low. Conclusions [18F]FBNO is a new easy accessible amine-reactive prosthetic group for rapid radiofluorination of peptides and small molecules under mild conditions. Consequently, it represents an interesting alternative to [18F]SFB and other 18F-labelled active esters. Furthermore, [18F]2 is a promising PET-tracer candidate for imaging of PSMA-positive tumors. Research Support Supported by EFRE-ZIEL2 program (North Rhine-Westphalia, Germany).
De Novo Ligand Design:  Understanding Stereoselective Olefin Binding to [(η5-C5H5)Re(NO)(PPh3)]+ with Molecular Mechanics, Semiempirical Quantum Mechanics, and Density Functional Theory (2002)

Understanding stereoselective prochiral α-olefin binding by a chiral organometallic moiety is essential to control the production of a desired stereoisomer. Computational methods are useful predictors of stereoisomers, if all conformations that can participate in a reaction are identified. Herein we report a combined molecular mechanics, semiempirical quantum mechanics, and density functional theory study of binding of CH2CHR, R = Me, n-Pr, CH2Ph, Ph, i-Pr, t-Bu, SiMe3, to chiral [(η5-C5H5)Re(NO)(PPh3)]+. In agreement with the experimental literature and previous computational results, one isomer was predicted to form preferentially over others. Brown's ligand repulsive energy was used to quantify the steric demand of the α-olefin in the organorhenium environment. A new conformational searching method, which requires successive applications of molecular mechanics, semiempirical quantum mechanics, density functional theory, restricted molecular mechanics, and density functional theory is introduced in order to identify all conformational minima that can participate in a reaction. A computationally derived diastereoselective excess based on DFT computations is derived and compared with experiment.
Transmission loss of membrane-type locally resonant acoustic materials. (2010)

Membrane-type acoustic metamaterials were fabricated, characterized, and analyzed. Thin plates which obey the acoustic mass law have low transmission loss at low frequencies. Acoustic metamaterials with negative dynamic mass density have been shown to demonstrate a significant (ten times) increase in transmission loss (TL) over mass law predictions for a narrow band (100 Hz) at low frequencies (100–1000 Hz). The peak TL frequency can be tuned to specific values by varying the membrane and mass properties. In this work, transmission loss magnitude as a function of frequency was measured for variations in the mass magnitude, mass placement on the membrane, membrane size, and membrane thickness using an impedance tube setup. The dynamic properties of membranes constructed from different materials and thicknesses were measured and compared to the results of coupled field acoustic-structural FEA modeling to understand the role of tension and element quality factor. In addition, the behavior and limitations of stacking multiple membranes in series to increase the reflection bandwidth were explored.
Androgens and Dry Eye in Sjögren's Syndromea (1999)

Sjögren's syndrome is an extremely complex and currently incurable autoimmune disorder, which occurs primarily in females, and is associated with lacrimal gland inflammation, meibomian gland dysfunction, and severe dry eye. We hypothesize that androgen deficiency, which reportedly occurs in primary and secondary Sjögren's syndrome (e.g., systemic lupus erythematosus, rheumatoid arthritis), is a critical etiologic factor in the pathogenesis of dry eye syndromes. We further hypothesize that androgen treatment to the ocular surface will promote both lacrimal and meibomian gland function and alleviate both "aqueous-deficient" and "evaporative" dry eye. Our results demonstrate that androgens regulate both lacrimal and meibomian gland function, and suggest that topical androgen administration may serve as a safe and effective therapy for the treatment of dry eye in Sjögren's syndrome.
Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies (2002)

Alternative models have been presented to provide explanations for the sequence-dependent variation of the DNA minor groove width. In a structural model groove narrowing in A-tracts results from direct, short-range interactions among DNA bases. In an electrostatic model, the narrow minor groove of A-tracts is proposed to respond to sequence-dependent localization of water and cations. Molecular dynamics simulations on partially methylphosphonate substituted helical chains of d(TATAGGCCTATA) and d(CGCGAATTCGCG) duplexes have been carried out to help evaluate the effects of neutralizing DNA phosphate groups on the minor groove width. The results show that the time-average minor groove width of the GGCC duplex becomes significantly more narrow on neutralizing the phosphate backbone with methylphosphonates. The minor groove of the AATT sequence is normally narrow and the methylphosphonate substitutions have a smaller but measurable affect on this sequence. These results and models provide a system that can be tested by experiment and they support the hypothesis that the electrostatic environment around the minor groove affects the groove width in a sequence-dependent dynamic and time-average manner.