gebhart/patrepeval huggingface dataset:
Probing Inhibitors Binding to Human Urokinase Crystals by Raman Microscopy:  Implications for Compound Screening (2001)

Inhibition of urokinase activity represents a promising target for antimetastatic therapy for several types of tumor. The present study sets out to investigate the potential of Raman spectroscopy for defining the molecular details of inhibitor binding to this enzyme, with emphasis on single crystal studies. It is demonstrated that high quality Raman spectra from a series of five inhibitors bound individually to the active site of human urokinase can be obtained in situ from urokinase single crystals in hanging drops by using a Raman microscope. After recording the spectrum of the free crystal, a solution of inhibitor containing an amidine functional group on a naphthalene ring was added, and the spectrum of the crystal-inhibitor complex was obtained. The resulting difference Raman spectrum contained only vibrational modes due to bound inhibitor, originating from the protonated group, i.e., the amidinium moiety, as well as naphthalene ring modes and features from other functionalities that made up each inhibitor. The identification of the amidinium modes was placed on a quantitative basis by experimental and theoretical work on naphthamidine compounds. For the protonated group, -C-(NH2)(2)(+), the symmetric stretch occurs near 1520 cm(-1), and a less intense antisymmetric mode appears in the Raman spectra near 1680 cm(-1). The presence of vibrational modes near 1520 cm(-1) in each of the Raman difference spectra of the five complexes examined unambiguously identifies the protonated form of the amidinium group in the active site. Several advantages were found for single crystal experiments over solution studies of inhibitor-enzyme complexes, and these are discussed. The use of single crystals permits competitive binding experiments that cannot be undertaken in solution in any kind of homogeneous assay format. The Raman difference spectrum for a single crystal that had been exposed to equimolar amounts of all five inhibitors in the hanging drop showed only the Raman signature of the compound with the lowest K(i). These findings suggest that the Raman approach may offer a route in the screening of compounds in drug design applications as well as an adjunct to crystallographic analysis.
From Si and C encapsulated SiO2 to SiC: exploring the influence of sol–gel polymer substitution on thermally induced nanocrystal formation (2011)

Silicon-based nanomaterials are of far reaching interest because they can be biologically benign and highly photoluminescent. However if society is to make use of these properties efficient and predictable methods for preparing these materials must be realized. Here we report the syntheses of a series of sol–gel derived copolymers (i.e., [(HSiO1.5)0.95(RSiO1.5)0.5]n (where R = C2H5, C4H9, C6H13, C8H17, C10H21)) that yield silicon-based nanomaterials whose chemical composition and optical properties are strongly influenced by the nature of the R substituent. Freestanding nanomaterials were obtained through chemical etching of the resulting oxide matrices and some of these materials exhibited photoluminescence centered in the near-UV/visible spectral region. Composites and the etched materials were characterized using Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA), X-ray powder diffraction (XRD) and X-ray photoelectron spectroscopy (XPS).
ChemInform Abstract: Nonpeptidic SH2 Inhibitors of the Tyrosine Kinase ZAP‐70. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Elasticity in Cloud Databases and Their Query Processing (2013)

A central promise of cloud services is elastic, on-demand provisioning. The provisioning of data on temporarily available nodes is what makes elastic database services a hard problem. The essential task that enables elastic data services is bringing a node and its data up-to-date. Strategies for high availability do not satisfy the need in this context because they bring nodes online and up-to-date by repeating history, e.g., by log shipping. Nodes must become up-to-date and useful for query processing incrementally by key range. What is wanted is a technique such that in a newly added node, during each short period of time, an additional small key range becomes up-to-date, until eventually the entire dataset becomes up-to-date and useful for query processing, with overall update performance comparable to a traditional high-availability strategy that carries the entire dataset forward without regard to key ranges. Even without the entire dataset being available, the node is productive and participates in query processing tasks. The authors’ proposed solution relies on techniques from partitioned B-trees, adaptive merging, deferred maintenance of secondary indexes and of materialized views, and query optimization using materialized views. The paper introduces a family of maintenance strategies for temporarily available copies, the space of possible query execution plans and their cost functions, as well as appropriate query optimization techniques.
Measurement of PromptD-Meson Production inp−PbCollisions atsNN=5.02  TeV (2014)

The p_{T}-differential production cross sections of the prompt charmed mesons D^{0}, D^{+}, D^{*+}, and D_{s}^{+} and their charge conjugate in the rapidity interval -0.96<y_{cms}<0.04 were measured in p-Pb collisions at a center-of-mass energy sqrt[s_{NN}]=5.02 TeV with the ALICE detector at the LHC. The nuclear modification factor R_{pPb}, quantifying the D-meson yield in p-Pb collisions relative to the yield in pp collisions scaled by the number of binary nucleon-nucleon collisions, is compatible within the 15%-20% uncertainties with unity in the transverse momentum interval 1<p_{T}<24 GeV/c. No significant difference among the R_{pPb} of the four D-meson species is observed. The results are described within uncertainties by theoretical calculations that include initial-state effects. The measurement adds experimental evidence that the modification of the momentum spectrum of D mesons observed in Pb-Pb collisions with respect to pp collisions is due to strong final-state effects induced by hot partonic matter.
Edge-emitting blue laser diode with high CW wall-plug efficiency of 50 % (2022)

This paper reports the latest device performance of high-power blue laser diodes (LDs). The epitaxial structures of LDs were grown by metal organic chemical vapor deposition (MOCVD) on C-plane free-standing GaN substrates. And a ridge type structure was formed at the top of p-type layers. The ridge width of the LD was 45 μm. Electrodes of the n-type and p-type were formed at the substrate and the ridge respectively. And the front and rear sides were obtained by cleavage at the m-plane surface. These faces were covered by dielectric mirrors. Every LD chip was mounted on a heat sink using a junction down method in a TO-Φ9 mm package for suppressing thermal resistance. We optimized the epitaxial and the device structures for high efficiency and high optical output power. A New developed 455 nm blue LD showed the optical output power and the voltage of 5.73 W and 3.82 V at the forward current of 3 A under Continuous Wave (CW) operation. The wall-plug efficiency (WPE) of the 455 nm blue LD was 50.0 % at 3 A. This is the highest WPE reported so far. The peak WPE of the 455 nm LD was 51.2 % at the forward current of 2 A.
Aspirin dose and thromboxane metabolism in African American stroke patients (2001)

P214 Purpose: To evaluate thromboxane metabolism in African American stroke patients on different doses of aspirin. Methods: Consecutive African American patients within 3 month of non-cardioembolic stroke and not being treated with anticoagulation were recruited. Antithrombotic therapy at the time of sample collection was not prespecified and varied according to the practice patterns of the different attending physicians who treated the patients during their acute stroke. The thromboxane metabolite 11-dehydrothroboxane B2 (11-DTB2) was measured by enzyme immunoassay in random urine samples collected at the time of enrollment. Results: 99 patients were enrolled but 15 could not give a urine sample at the time of enrollment. Data on the remaining 84 patients were evaluable. There were 49 men and 35 women aged 36–87 (mean 62) years. Based on antithrombotic treatment during sample collections, we divided patients into four groups: no aspirin N=16 (no antithrombotic drugs N=4 or ticlopidine N=12), aspirin 81–325 mg/d N=19 (81 mg/day N=1, 325 mg/day N=18), aspirin 650 mg/d N=19, aspirin 975–1300 mg/d N=30 (975 mg/d N=2 and 1300 mg/d N=28). After log transformation of the 11-DTB2 values the geometric means in the no aspirin, 81–325 mg/d, 650 mg/d, and 975–1300 mg/d groups were 1355, 912, 758, and 731 pg/mg creatinine, respectively. Based on one way ANOVA, the mean 11-DTB2 concentration was significantly different between the 4 groups (p=0.03). There was a significant negative relationship between aspirin dose and 11-DTB2 concentration (Pearson Correlation, r = -0.26, P=0.02). Conclusion: In African American stroke patients thromboxane production appears to be progressively inhibited by aspirin doses up to 650 mg/d. The clinical significance of this effect by aspirin doses ≤650 mg/d remains to be determined.
HEVC Intra coding of ultra HD video with reduced complexity (2014)

The HEVC (High Efficiency Video Coding) standard brings the necessary quality versus rate performance for efficient transmission of Ultra High Definition formats (UHD). However, one of the remaining barriers to its adoption for UHD content is its high encoding complexity. In this paper, we address the problem of HEVC encoding complexity reduction by proposing a strategy to infer UHD coding modes and quadtree structure from those optimized for the lower (HD) resolution version of the input video. A speed-up factor of 3 is achieved compared to directly encoding the UHD format at the expense of a limited quality loss.
Research on Principles of Bounded Rationality (2006)

Several years ago, we initiated the PROTOS project, to investigate the use of decision theory as a framework for reasoning about the design and operation of ideal expert systems and control systems under bounded resources.
PPARs and ERRs: molecular mediators of mitochondrial metabolism (2014)

Since the revitalization of 'the Warburg effect', there has been great interest in mitochondrial oxidative metabolism, not only from the cancer perspective but also from the general biomedical science field. As the center of oxidative metabolism, mitochondria and their metabolic activity are tightly controlled to meet cellular energy requirements under different physiological conditions. One such mechanism is through the inducible transcriptional co-regulators PGC1α and NCOR1, which respond to various internal or external stimuli to modulate mitochondrial function. However, the activity of such co-regulators depends on their interaction with transcriptional factors that directly bind to and control downstream target genes. The nuclear receptors PPARs and ERRs have been shown to be key transcriptional factors in regulating mitochondrial oxidative metabolism and executing the inducible effects of PGC1α and NCOR1. In this review, we summarize recent gain-of-function and loss-of-function studies of PPARs and ERRs in metabolic tissues and discuss their unique roles in regulating different aspects of mitochondrial oxidative metabolism.
An implicit algorithm for finding steady states and its application to FSM verification (1998)

Finding the set of steady states of a machine has applications in formal verification, sequential synthesis and ATPG. Existing techniques assume the presence of a designated set of initial states which is impractical in a real design environment. The set of steady state of a design is defined by the terminally strongly connected components (tSCCs) of the underlying state transition graph (STG). We show that multiple tSCCs and non-terminal SCCs need to be handled in a real design environment especially for verification. We present a fully implicit algorithm to find the steady states of a machine without any knowledge of initial states. We demonstrate the utility of our algorithm by applying it to FSM equivalence checking.
SoCFuzzer: SoC Vulnerability Detection using Cost Function enabled Fuzz Testing (2023)

The modern System-on-Chips (SoCs), with numerous complex and heterogeneous intellectual properties (IPs), and the inclusion of highly-sensitive assets, become the target of malicious attacks. However, security verification of these SoCs remains behind compared to the advances in functional verification, mostly because it is difficult to formally define the accurate threat model(s). Few recent studies have investigated the possibility of engaging fuzz testing for hardware-oriented vulnerability detection. However, they suffer from several limitations, i.e., lack of cross-layer co-verification, the need for expert knowledge, and the inability to capture detailed hardware interactions. In this paper, we propose SoCFuzzer, an automated SoC verification assisted by fuzz testing for detecting SoC security vulnerabilities. Unlike the previous HW-oriented fuzz testing studies, which mostly rely on traditional (code) coverage-based metrics, in SoCFuzzer, we develop (i) generic evaluation metrics for fuzzing the hardware domain, and (ii) security-oriented cost function. This relieves designers of making correlations between coverage metrics, test data, and possible vulnerabilities. The SoCFuzzer cost functions are defined high level, allowing us to follow the gray-box model, which requires less detailed and interactive information from the design-under-test. Our experiments on an open-source RISCV based SoC show the efficiency of these metrics and cost functions on fuzzing for generating cornerstone inputs to trigger the vulnerability conditions with faster convergence.
Leveraging predefined huffman dictionaries for high compression rate and ratio (2013)

The explosion of data, both in motion and in rest, along with the popularity of cloud computing, have resulted in the need for better in-line compression solutions. Current Huffman coding modes are optimal for a single metric: compression ratio (quality) or rate (performance). The ratio-focused mode, for example, further compresses the data by 15% as compared to the rate-focused mode, but takes 20% longer to execute.
5G ultra-reliable and low-latency systems design (2017)

5G New Radio (NR) is envisioned to support three broad categories of services: evolved mobile broadband (eMBB), ultra-reliable and low-latency communications (URLLC), and massive machine-type communications (mMTC). The URLLC services refer to future applications that require secure data communications from one end to another with ultra-high reliability and deadline-based low latency requirements. This type of quality-of-service is vastly different from that of traditional mobile broadband applications. In this paper, we discuss the systems design principles to enable the URLLC services in 5G. Theoretical queueing analysis and system-level simulations are provided to support these systems design choices, many of which have been considered as work items in the 3GPP Release 15 standards, which will be the first release for 5G NR.
10Gbps bias-free all-optical wavelength conversion using InP-microdisk resonators heterogeneously integrated onto SOI (2011)

Using InP-based microdisk lasers heterogeneously integrated onto silicon passive waveguide circuits, we demonstrate all-optical wavelength conversion of 10Gbps NRZ PRBS signals without requiring any bias or extra seeding beam. The experimental results also indicate that bitrates of 20 or 25Gbps should be achievable.
Reflectance and Illumination Video Editing using Fast User-Guided Intrinsic Decomposition (2014)

Object illumination and color are critical characteristics of a scene and being able to edit them allows artists to achieve powerful effects. Intrinsic image decomposition is the ideal component for this kind of tasks. By separating the illumination from the scene reflectance, it enables key operations such as recoloring and relighting. Significant progress has been done recently for decomposing static images. However, these algorithms rely on sophisticated optimization schemes that are computationally expensive and orders of magnitude too slow to be applied to video sequences. So much that even an optimized implementation would remain unpractical. In this paper, we introduce a user-guided algorithm that runs fast enough to be used in an interactive setting. Our strategy is to rely on an efficient sparse formulation – we also exploit the same kind of information as successful static methods but use it in ways that only have a minor impact on running time. The core of our approach is a gradient-domain `2-`p energy that models a sparse prior on reflectance gradients and a smooth prior on illumination. We show that the produced set of nonlinear equations can be solved very efficiently using look-up tables. Then, we provide scribbles to users to refine the decomposition. Our scribbles introduce local constraints in our optimization that add only a minimal overhead. Further, we extend these constraints to other similar image regions, thereby effectively enabling users to affect large regions with minimal effort. We also leverage multi-threading to precompute solutions a few frames ahead of the current one at a minimal cost. Coupled with the ability of our solver to use an initial guess to speed up convergence, this effectively shortens the computation time and offer a fast feedback to users. We demonstrate our approach on real sequences and show that we can obtain satisfying results with a reasonable amount of user interaction. We illustrate the benefits of our decomposition on video recoloring and shadow compositing.
Pulmonary Hypertension Phenotypes in Systemic Sclerosis: The Right Diagnosis for the Right Treatment (2020)

Systemic sclerosis is an auto-immune disease characterized by skin involvement that often affects multiple organ systems. Pulmonary hypertension is a common finding that can significantly impact prognosis. Molecular pathophysiological mechanisms underlying pulmonary hypertension in systemic sclerosis can be extremely heterogeneous, leading to distinct clinical phenotypes. In addition, different causes of pulmonary hypertension may overlap within the same patient. Since pulmonary hypertension treatment is very different for each phenotype, it is fundamental to perform an adequate diagnostic work-up to properly and promptly identify the prevalent mechanism underlying pulmonary hypertension in order to start the right therapies. When pulmonary hypertension is caused by a primary vasculopathy of the small pulmonary arteries, treatment with pulmonary vasodilators, often in an initial double-combination regimen, is indicated, aimed at reducing the mortality risk profile. In this review, we describe the different clinical phenotypes of pulmonary hypertension in the scleroderma population and discuss the utility of clinical tools to identify the presence of pulmonary vascular disease. Furthermore, we focus on systemic sclerosis-associated pulmonary arterial hypertension, highlighting the advances in the knowledge of right ventricular dysfunction in this setting and the latest updates in terms of treatment with pulmonary vasodilator drugs.
Pregnenolone and Dehydroepiandrosterone as an Adjunctive Treatment in Schizophrenia and Schizoaffective Disorder (2010)

clinicaltrials.gov Identifier: NCT00174889.
SANEPIC: A Mapmaking Method for Time Stream Data from Large Arrays (2008)

We describe a mapmaking method that we have developed for the Balloon-borne Large Aperture Submillimeter Telescope (BLAST) experiment, but which should have general application to data from other submillimeter arrays. Our method uses a maximum likelihood-based approach, with several approximations, which allows images to be constructed using large amounts of data with fairly modest computer memory and processing requirements. This new approach, Signal and Noise Estimation Procedure Including Correlations (SANEPIC), builds on several previous methods but focuses specifically on the regime where there are a large number of detectors sampling the same map of the sky, and explicitly allowing for the possibility of strong correlations between the detector time streams. We provide real and simulated examples of how well this method performs compared with more simplistic mapmakers based on filtering. We discuss two separate implementations of SANEPIC: a brute-force approach, in which the inverse pixel-pixel covariance matrix is computed, and an iterative approach, which is much more efficient for large maps. SANEPIC has been successfully used to produce maps using data from the 2005 BLAST flight.
A Methodology for Worst-Case Analysis of Integrated Circuits (1986)

Worst-case analysis is one of the most often used techniques for verifying that the sensitivity of integrated circuit (IC) performances to changes in manufacturing conditions is minimized. However, worst-case analysis is often carried out in terms of a correlated set of parameters, which results in a design that is unnecessarily pessimistic. This paper presents a new approach to the worst-case analysis of integrated circuits that results in more realistic estimates of variations in device and circuit performances. In particular, worst-case analysis is performed in terms of a set of statistically independent process disturbances. A software package for worst-case analysis is described and illustrated by a number of examples. The results of the proposed worst-case analysis method are compared to Monte Carlo simulations.
Systematic review with meta‐analysis: recurrence of Crohn's disease after total colectomy with permanent ileostomy (2016)

Small bowel clinical recurrence occurs in about 28% of patients after total colectomy with permanent ileostomy for colonic Crohn's disease. Disease recurrence risk is 3.2 times higher in patients with history of ileal disease, and continued medical therapy may be advisable in this population. In patients without ileal inflammation at surgery, continued endoscopic surveillance may identify asymptomatic disease recurrence to guide therapy.
Graft Vopolymerization of Vinyl Monomers onto Polyamide-6 and Thermal Analysis of the Graft Copolymers (1997)

Graft copolymerization of vinyl monomers onto polyamide-6 using radical initiation has been investigated. Two monomers were used: methacrylic acid (MAA) and acrylic acid (AA). The initiators selected included hydrogen peroxide ~02), benzoyl peroxide (BPO), and azobisisobutyronitrile (AIBN). The extent Or-graft copolymerization depends on the concentrations and identity of the initiator and monomer and the time and temperature of the reaction. The graft copolymers were not soluble in solvents which will dissolve the starting materials; definitive proof for the formation of the graft copolymers comes from infrared spectroscopy. Thermogravimetric analysis was performed on the graft copolymers, and it was found that the presence of the acid invariably accelerated the degradation of the polyamide.
A No-Op Payload Format for RTP (2007)

This document defines an no-op payload format for the Real-time
Transport Protocol (RTP). This packet is not played out by receivers.
It can be useful as a way to keep Network Address Translator (NAT)
bindings and Firewall pinholes open. Other uses are discussed in the
document.