gebhart/patrepeval huggingface dataset:
A Pixel-Parallel Virtual-Image Architecture for High Performance and Power Efficient Graph Cuts Inference (2019)

A Pixel-Parallel Virtual-Image Architecture for High Performance and Power Efficient Graph Cuts Inference Tianqi Gao, University of Illinois Urbana Champaign Rob A. Rutenbar, University of Pittsburgh Contact: [email protected] Graph Cuts is a popular technique for Maximum A Posteriori inference in computer vision. It transforms a Markov Random Field problem into a network flow problem, solved via the Push-Relabel algorithm. While attractively simple, the large size of a typical image and the large number of necessary pixel-level iterations render the technique computationally expensive. Prior accelerator attempts have been reported with GPUs and FPGAs. In [1], the first pixel-parallel architecture was demonstrated in FPGA, but limited to only 256-pixel images. This paper extends this pixel-parallel concept and makes following contributions: a "Virtual Image" architecture solves the size limitation: large images are decomposed into "tiles", and "stacked" on the physical processor array; appropriate addressing mechanisms handle virtual pixels and a range of tile edge effects; scaling up the processor array to 1536 pixels; a novel and hardware-friendly heuristic shortens the convergence. We demonstrate the first working virtual-image Graph Cuts accelerator, applied to standard 640x480 images. Scaling up the hardware and the new heuristic bring 6.5x and 1.65x speedups respectively compared with [1]. The design is 7-20x faster than prior FPGA designs, and roughly comparable in speed to a modern GPU benchmark. However, the architecture also offers significant performance-per-unit-power advantages. Formulating a figure of merit particularly for Graph Cuts inference - Graph Cuts per second per Watt - our architecture is about 4 times better than other implementations. Keywords: FPGA; Machine learning; Hardware Acceleration; Computer Vision DOI: https://doi.org/10.1145/3289602.3293948
Efficient surrogates construction of chemical processes: Case studies on pressure swing adsorption and <scp>gas‐to‐liquids</scp> (2022)

Abstract We propose a sequential sampling approach to training statistical digital twins. This approach is relevant for real‐world engineering problems with expensive data generation. Prerequisite for building surrogates is sufficient data; however, oversampling does not improve regression accuracy. The time for data generation may be reduced by: (a) applying a classifier to improve data quality and avoid evaluation of infeasible inputs, and (b) employing dynamic sampling linked to regression quality. In dynamic sampling, the initial sampling rate is large to generate enough data for surrogate regression in a few iterations; the sampling rate gradually slows down with the improvement of the iteratively refined surrogate. A dynamic process and a steady‐state process from the field of carbon capture and utilization are used as case studies: pressure swing adsorption (PSA) and gas‐to‐liquids (GTL). The computational costs for surrogates generation are reduced by 86% for PSA and 51% for GTL, compared with employing a static sampling rate.
Reaction of porcine pancreatic elastase with 7-substituted 3-alkoxy-4-chloroisocoumarins: design of potent inhibitors using the crystal structure of the complex formed with 4-chloro-3-ethoxy-7-guanidinoisocoumarin (1990)

The crystal structure of the acyl enzyme formed upon inhibition of porcine pancreatic elastase (PPE) by 4-chloro-3-ethoxy-7-guanidinoisocoumarin has been determined at a 1.85-A effective resolution. The chlorine atom is still present in this acyl enzyme, in contrast to the previously reported structure of the 7-amino-4-chloro-3-methoxyisocoumarin-PPE complex where the chlorine atom has been replaced by an acetoxy group. The guanidino group forms hydrogen bonds with the carbonyl group and side-chain hydroxyl group of Thr-41, and the acyl carbonyl group has been twisted out of the oxyanion hole. Molecular modeling indicates that the orientation of the initial Michaelis enzyme-inhibitor complex is quite different from that of the acyl enzyme since simple reconstruction of the isocoumarin ring would result in unfavorable interactions with Ser-195 and His-57. Molecular models were used to design a series of new 7-(alkylureido)- and 7-(alkylthioureido)-substituted derivatives of 3-alkoxy-7-amino-4-chloroisocoumarin as PPE inhibitors. All the 3-ethoxyisocoumarins were better inhibitors than those in the 3-methoxy series due to better interactions with the S1 pocket of PPE. The best ureido inhibitor also contained a tert-butylureido group at the 7-position of the isocoumarin. Due to a predicted interaction with a small hydrophobic pocket on the surface of PPE, this isocoumarin and a related phenylthioureido derivative are among the best irreversible inhibitors thus far reported for PPE (kobs/[I] = 8100 M-1 s-1 and 12,000 M-1 s-1). Kinetic studies of the stability of enzyme-inhibitor complexes suggest that many isocoumarins are alkylating the active site histidine at pH 7.5 via a quinone imine methide intermediate, while at pH 5.0, the predominant pathway appears to be simple formation of a stable acyl enzyme derivative.
Preliminary X-ray crystallographic studies of a newly defined human theta-class glutathione transferase (1998)

Human theta-class glutathione S-transferases (GST's) appear to play a critical role in the metabolism of a variety of environmental pollutants but in some cases the products of the reaction are carcinogenic. Crystals of a human theta-class GST, namely hGSTT2-2, have been grown from polyethylene glycol by the hanging-drop vapour-diffusion method. The crystals belong to the trigonal space group P3121 with cell dimensions of a = b = 94.0 and c = 120.5 A. They contain two monomers in the asymmetric unit and diffract to 3.0 A resolution.
Controlling Sub-Cycle Optical Chirality in the Photoionization of Chiral\n Molecules (2019)

Controlling the polarization state of electromagnetic radiation enables the\ninvestigation of fundamental symmetry properties of matter through chiroptical\nprocesses. Many strategies have been developed to reveal structural or\ndynamical information about chiral molecules, from the microwave to the extreme\nultraviolet range. Most schemes employ circularly or elliptically polarized\nradiation, and more sophisticated configurations involve, for instance, light\npulses with time-varying polarization states. In all these schemes, the\npolarization state of light is always considered as constant over one optical\ncycle. In this study, we zoom into the optical cycle in order to resolve and\ncontrol a subcyle attosecond chiroptical process. We engineer an electric field\nwhose instantaneous chirality can be controlled within the optical cycle, by\ncombining two phase-locked orthogonally polarized fundamental and second\nharmonic fields. While the composite field has zero net ellipticity, it shows\nan instantaneous optical chirality which can be controlled via the two-color\ndelay. We theoretically and experimentally investigate the photoionization of\nchiral molecules with this controlled chiral field. We find that electrons are\npreferentially ejected forward or backward relative to the laser propagation\ndirection depending on the molecular handedness, similarly to the\nwell-established photoelectron circular dichroism process. However, since the\ninstantaneous chirality switches sign from one half cycle to the next,\nelectrons ionized from two consecutive half cycles of the laser show opposite\nforward/backward asymmetries. This chiral signal provides a unique insight into\nthe influence of instantaneous chirality in the dynamical photoionization\nprocess. Our results demonstrate the important role of sub-cycle polarization\nshaping of electric fields, as a new route to study and manipulate chiroptical\nprocesses.\n
CO<sub>2</sub>-responsive polymeric materials: synthesis, self-assembly, and functional applications (2016)

CO2 is an ideal trigger for switchable or stimuli-responsive materials because it is benign, inexpensive, green, abundant, and does not accumulate in the system. Many different CO2-responsive materials including polymers, latexes, solvents, solutes, gels, surfactants, and catalysts have been prepared. This review focuses on the preparation, self-assembly, and functional applications of CO2-responsive polymers. Detailed discussion is provided on the synthesis of CO2-responsive polymers, in particular using reversible deactivation radical polymerization (RDRP), formerly known as controlled/living radical polymerization (CLRP), a powerful technique for the preparation of well-defined (co)polymers with precise control over molecular weight distribution, chain-end functional groups, and polymer architectural design. Self-assembly in aqueous dispersed media is highlighted as well as emerging potential applications.
Context identification for efficient multiple-model state estimation (2007)

This paper presents an approach to accurate and scalable multiple-model state estimation for hybrid systems with intermittent, multi-modal dynamics. The approach consists of using discrete-state estimation to identify a system’s behavioral context and determine which motion models appropriately represent current dynamics, and which multiple-model filters are appropriate for state estimation. This improves the accuracy and scalability of conventional multiple-model state estimation. This approach is validated experimentally on a mobile robot that exhibits multi-modal dynamics.
&lt;title&gt;Strategies for tunable frequency-selective surfaces&lt;/title&gt; (1991)

The mathematical rationale behind frequency selective surfaces is discussed. Two strategies - one based on exciting standing surface acoustic waves in a piezoelectric film, and the other on arrays of arrays of piezoelectric capacitors - are outlined to obtain tunable frequency selective surfaces.
Brain-controlled exoskeleton robot for BMI rehabilitation (2012)

In this paper, we introduce our attempt to develop an assistive robot system which can contribute to Brain-Machine Interface (BMI) rehabilitation. For the BMI rehabilitation, we construct a Electroencephalogram(EEG)-Exoskeleton robot system, where the exoskeleton robot is connected to the EEG system so that the users can control the exoskeleton robot by using their brain activities. We use a classification method which considers covariance matrices of measured EEG signals as inputs to decode brain activities. The decoded brain activities are used to control exoskeleton movements. In this study, we consider assisting the stand-up movement which is one of the most frequently appeared movements in daily life and also a standard movement as a rehabilitation training. To assist the stand-up movement, we develop a force control model which takes dynamics of tendon string into account for the pneumatic-electric hybrid actuation system used in our exoskeleton robot. The results show that the exoskeleton robot successfully assisted user stand-up movements, where the assist system was activated by the decoded brain activities.
Structure and properties of halogenated and nonhalogenated soy-based polyols (2000)

Four polyols intended for application in polyurethanes were synthesized by oxirane ring opening in epoxidized soybean oil with hydrochloric acid, hydrobromic acid, methanol, and hydrogen. The structures of the polyols were characterized by spectroscopic, chemical, and physical methods. The brominated polyol had 4.1 hydroxy groups, whereas the other three polyols had slightly lower functionality. The densities, viscosities, viscous-flow activation energies, and molecular weights of the polyols decreased in the following order: brominated > chlorinated > methoxylated > hydrogenated. All the polyols were crystalline solids below their melting temperature, displaying multiple melting peaks. The methoxylated polyol was liquid at room temperature, whereas the other three were waxes. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 3900–3910, 2000
Computation-Efficient Hybrid Beamforming in mmWave Massive MIMO Using Branchwise Double Phase Shifters  (2023)

&lt;p&gt;Submitted to the IEEE Communications Letters&lt;/p&gt;
Quantitative Detection and Genotyping of <i>Helicobacter pylori</i> from Stool using Droplet Digital <scp>PCR</scp> Reveals Variation in Bacterial Loads that Correlates with <i>cagA</i> Virulence Gene Carriage (2015)

The stool-based ddPCR assays are a sensitive, noninvasive method for detection, quantification, and partial genotyping of H. pylori. The quantitative nature of ddPCR-based H. pylori detection revealed significant variation in bacterial load among individuals that correlates with presence of the cagA virulence gene. These stool-based ddPCR assays will facilitate future population-based epidemiologic studies of this important human pathogen.
Combined lipidomic and proteomic analysis of isolated human islets exposed to palmitate reveals time-dependent changes in insulin secretion and lipid metabolism (2017)

Studies on the pathophysiology of type 2 diabetes mellitus (T2DM) have linked the accumulation of lipid metabolites to the development of beta-cell dysfunction and impaired insulin secretion. In most in vitro models of T2DM, rodent islets or beta-cell lines are used and typically focus is on specific cellular pathways or organs. Our aim was to, firstly, develop a combined lipidomics and proteomics approach for lipotoxicity in isolated human islets and, secondly, investigate if the approach could delineate novel and/ or confirm reported mechanisms of lipotoxicity. To this end isolated human pancreatic islets, exposed to chronically elevated palmitate concentrations for 0, 2 and 7 days, were functionally characterized and their levels of multiple targeted lipid and untargeted protein species determined. Glucose-stimulated insulin secretion from the islets increased on day 2 and decreased on day 7. At day 7 islet insulin content decreased and the proinsulin to insulin content ratio doubled. Amounts of cholesterol, stearic acid, C16 dihydroceramide and C24:1 sphingomyelin, obtained from the lipidomic screen, increased time-dependently in the palmitate-exposed islets. The proteomic screen identified matching changes in proteins involved in lipid biosynthesis indicating up-regulated cholesterol and lipid biosynthesis in the islets. Furthermore, proteins associated with immature secretory granules were decreased when palmitate exposure time was increased despite their high affinity for cholesterol. Proteins associated with mature secretory granules remained unchanged. Pathway analysis based on the protein and lipid expression profiles implicated autocrine effects of insulin in lipotoxicity. Taken together the study demonstrates that combining different omics approaches has potential in mapping of multiple simultaneous cellular events. However, it also shows that challenges exist for effectively combining lipidomics and proteomics in primary cells. Our findings provide insight into how saturated fatty acids contribute to islet cell dysfunction by affecting the granule maturation process and confirmation in human islets of some previous findings from rodent islet and cell-line studies.
Lower error bound for oversampled subband adaptivefilters (1998)

The authors evaluate error performance limitations in oversampled subband adaptive filter applications based on an analysis of aliasing in the subband signals. The power spectral density of the minimum error signal is given by the aliased signal components. The presented analysis closely agrees with simulation results.
Effect of deposition conditions on the properties of HDP-CVD-fluorinated silicon oxide (SiOF) (2000)

Fluorinated silicon oxide (SiOF) has been deposited by the high density plasma chemical vapor deposition technique using a SiH<SUB>4</SUB>/SiF<SUB>4</SUB>/O<SUB>2</SUB>/Ar plasma. The effect of the SiF<SUB>4</SUB>:O<SUB>2</SUB> flow rate ratio together with the substrate rf bias and the source rf bias were investigated systematically. By varying the SiF<SUB>4</SUB> flow rate ratio together with the substrate rf bias and the source rf bias were investigated systematically. By varying the SiF<SUB>4</SUB> flow rate, the concentration of fluorine in the SiOF can range from approximately 5 at percent to approximately 12 at percent. At low SiF<SUB>4</SUB>:O<SUB>2</SUB> flow ratios, the fluorine incorporates primarily as -Si-F in the oxide to changes in the SiOF microstructure, which result in modifications to the properties of this low-k material. An increased substrate rf bias did not affect the density of the oxide. However, the among of incorporated fluorine and the net deposition rate are both reduced. The source rf has no effect on the density of the oxide and the amount of incorporated fluorine. The main effect is a slight increase in the deposition rate.
Optimal dose and volume for postoperative radiotherapy in brain oligometastases from lung cancer: a retrospective study (2017)

Adding WBRT after resection of brain oligometastases from NSCLC seems to enhance intracranial control. Furthermore, combining lower-dose WBRT with a tumor bed boost may be an attractive option.
Cell-based Assay for Testing Susceptibility of HIV-1 to Protease Inhibitors (2005)

A growing emphasis on using cell-based assays for compound screening and enzyme activity is fueled by the need to decrease costs, increase success rates, and identify failures during discovery and preclinical development. Moreover, the growth in cell-based screening has led to the development of novel cell lines and technologies to increase the throughput and data output of cell-based assays. Therefore, we have also developed a new reporter system that allows monitoring of HIV-1 protease activity and susceptibility to protease inhibitors in living cells.
mm-wave integrated wireless transceivers: Enabling technology for high bandwidth connections in IoT (2015)

Many application scenarios for IoT (Internet of Things) require the interconnection of high speed sensing nodes with data rates of Gbps. As an example surveillance or smart mobility applications adopt multiple photo and video cameras working at different spectral range (visible, near infrared, far infrared) and covering different fields of view, or they exploit arrays of radio/light detection and ranging (Radar/Lidar) sensors to detect the presence of targets, of their speeds, distance and direction. Even the access of distributed nodes in IoT towards a centralized cloud storage/processing center requires high data rate connections. Since low size and low weight of the nodes are needed, IoT can benefit from the high communication data rate, several Gbps, that can be provided by fully integrated mm-wave wireless transceivers. The wavelength at such frequency is few mm and hence the whole transceiver including the antenna can be integrated in a single chip. To this aim, this paper presents the design of 60 GHz transceiver key blocks (Low Noise Amplifier, Power Amplifier, Antenna) to ensure connection distances up to 10 m and data rate of several Gbps. Around 60 GHz worldwide there are freely-available (unlicensed) several GHz of bandwidth. By using a CMOS SOI technology RF, analog and digital baseband circuitry can be integrated in the same chip minimizing noise coupling. Even the antenna is integrated on chip reducing cost and size vs. classic off-chip antenna solutions. The proposed transceiver allows for the implementation of low cost nodes for IoT systems with data rates of several Gbps and with a 10 m link distance. These specifications are suitable for home/office scenarios, or for body area networks (healthcare, wellness) or for applications on board vehicles (cars, trains, ships, airplanes).
Figure S6 from High-throughput Screening of Human Tumor Antigen–specific CD4 T Cells, Including Neoantigen-reactive T Cells (2023)

&lt;p&gt;Supplementary Figure 6&lt;/p&gt;
Abstract 4115: BNC420 is a novel VEGFR3 selective inhibitor, which unlike the pan-VEGFR inhibitor Sunitinib, suppresses lymphatic metastasis in a model of metastatic melanoma (2015)

Abstract The dissemination of cancer cells through the lymphatic system is a well-known route of metastasis. Studies have implicated the hypoxic tumor microenvironment as an instigator of tumor cell invasion and metastatic spread. The use of angiogenesis inhibitors targeting VEGFR2 has been reported in preclinical models to augment metastasis through increased hypoxia within the tumor microenvironment. We have sought to identify a selective VEGFR3 targeting compound that will inhibit metastatic spread through lymphatic dissemination without the concomitant hypoxia induced metastasis effect associated with VEGFR2 targeting. BNC420 is a novel small molecule inhibitor of VEGFR3 phosphorylation that displays significant selectivity over VEGFR2. In phosphorylation detection ELISA based assays BNC420 exhibited a 25 fold greater potency for VEGFR3 over VEGFR2 with IC50 of 30nM and 744nM respectively. We investigated the activity of BNC420 and the pan-VEGFR inhibitor Sunitinib in the B16F10 murine melanoma model. This model involves the intradermal administration of B16F10 melanoma cells in the mouse ear resulting in the formation of a primary lesion, metastatic satellite lesions (in-transit) and regional lymph node metastasis. While Sunitinib slowed the growth of the primary lesion, as expected, it did not inhibit the development of lymph node metastasis and appeared to enhance the development of in-transit satellite lesions by 38% compared to its corresponding vehicle control. In contrast, only 20% of animals treated with BNC420 exhibited in-transit lesions compared to 53% in the corresponding vehicle control. Furthermore, a 50% reduction in the number of metastasis to the draining lymph nodes was seen in BNC420 treated animals. The lymph node metastatic lesions were significantly smaller compared to control and in some instances only detected under microscopic examination. Melanoma lesions in animals treated with BNC420 were devoid of peritumoral lymphatic vessels. These results demonstrate that selective inhibition of VEGFR3 utilising the novel small molecule BNC420 effectively inhibits the development of both in-transit metastatic lesions and lymph node metastasis while being unencumbered by the pro-metastatic effects that can accompany VEGFR2 inhibition through the induction of tumor hypoxia. Citation Format: Annabell Leske, Tina Lavranos, Donna Beaumont, Chloe Brown, Darham Paul, Daniel Inglis, Michaela Scherer, Andrew Harvey, Gabriel Kremmidiotis. BNC420 is a novel VEGFR3 selective inhibitor, which unlike the pan-VEGFR inhibitor Sunitinib, suppresses lymphatic metastasis in a model of metastatic melanoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4115. doi:10.1158/1538-7445.AM2015-4115
Constraints on Cosmic Strings from the LIGO-Virgo Gravitational-Wave Detectors (2014)

Cosmic strings can give rise to a large variety of interesting astrophysical phenomena. Among them, powerful bursts of gravitational waves (GWs) produced by cusps are a promising observational signature. In this Letter we present a search for GWs from cosmic string cusps in data collected by the LIGO and Virgo gravitational wave detectors between 2005 and 2010, with over 625 days of live time. We find no evidence of GW signals from cosmic strings. From this result, we derive new constraints on cosmic string parameters, which complement and improve existing limits from previous searches for a stochastic background of GWs from cosmic microwave background measurements and pulsar timing data. In particular, if the size of loops is given by the gravitational backreaction scale, we place upper limits on the string tension Gμ below 10(-8) in some regions of the cosmic string parameter space.