gebhart/patrepeval huggingface dataset:
Use of cluster separation indices and the influence of outliers: application of two new separation indices, the modified silhouette index and the overlap coefficient to simulated data and mouse urine metabolomic profiles (2008)

Abstract To quantify separate classes, four indices are compared namely the Davies Bouldin index, the silhouette width and two new approaches described in this paper, the modified silhouette width index based on the proportion of objects with a positive silhouette width and the Overlap Coefficient. Four sets of simulated datasets are described, each in turn, consisting of 15 sets of data of varying degrees of overlap, and differing in the nature of outliers. Three experimental datasets consisting of the gas chromatography mass spectrometry of extracts from mouse urine obtained to study the effect of different environmental (stress), physiological (diet) and developmental (age) factors on their metabolic profiles are also described. The paper discusses the robustness of each approach to outliers, and to allow assessment of class separation for each index. The two modifications protect against outliers. Copyright © 2008 John Wiley &amp; Sons, Ltd.
Telnet-based transport control (2009)

It is not easy for systems using different method among the existing methods to interoperate each other because they have the closed system architecture and follows the mutually exclusive method. By using the proposed scheme, it is possible to easily deploy new services and protocols to the network without efforts to develop a new transport control function for the existing network equipment as well as without concern about performance degradation for the network.
FCCE: Highly scalable distributed Feature Collection and Correlation Engine for low latency big data analytics (2015)

In this paper, we present the design, architecture, and implementation of a novel analysis engine, called Feature Collection and Correlation Engine (FCCE), that finds correlations across a diverse set of data types spanning over large time windows with very small latency and with minimal access to raw data. FCCE scales well to collecting, extracting, and querying features from geographically distributed large data sets. FCCE has been deployed in a large production network with over 450,000 workstations for 3 years, ingesting more than 2 billion events per day and providing low latency query responses for various analytics. We explore two security analytics use cases to demonstrate how we utilize the deployment of FCCE on large diverse data sets in the cyber security domain: 1) detecting fluxing domain names of potential botnet activity and identifying all the devices in the production network querying these names, and 2) detecting advanced persistent threat infection. Both evaluation results and our experience with real-world applications show that FCCE yields superior performance over existing approaches, and excels in the challenging cyber security domain by correlating multiple features and deriving security intelligence.
N-TELOPEPTIDE DERIVED FROM TYPE II COLLAGEN UPREGULATES EXPRESSION OF BETA1 INTEGRIN AND MMPS IN CARTILAGE OF PATIENTS RECEIVING HIP OR KNEE ARTHROPLASTY (2023)

Previous studies showed that telo-peptides degraded from type II collagen, a type of collagen fragments, could induce cartilage damage in bovine stifle joints. We aim to investigate the role of integrins (ITGs) and matrix metalloproteinases (MMPs) in collagen fragment-induced human cartilage damage that is usually observed in osteoarthritis (OA). We hypothesized that N-telopeptide (NT) derived from type II collagen could up-regulate the expression of β1 integrin (ITGB1) and then MMPs that may lead to osteoarthritic cartilage damage. Human chondrocytes were isolated from femoral head or tibial plateau of patients receiving arthroplasty (N = 24). Primary chondrocyte cultures were either treated with 30 µM NT, or 30 µM scrambled NT (SN), or PBS, or left untreated for 24 hrs. Total proteins and RNAs were extracted for examination of expression of ITGB1 and MMPs-3&amp;13 with Western blotting and quantitative real-time PCR. Compared to untreated or PBS treated chondrocytes, NT-treated chondrocytes expressed significantly higher levels of ITGB1 and MMPs-3&amp;-13. However, SN also up-regulated expression of ITGB1 and MMP-13. ITGB1 and MMPs-3&amp;-13 might mediate the catalytic effect of NT, a type of collagen fragments, on human cartilage damage that is a hallmark of OA.
Making Carbon–Chlorine Bonds by Dipalladium Electrocatalysis (2013)

Abstract [(Benzo[ h ]quinolinyl)Pd II (μ‐OAc)] 2 and [(2‐phenylpyridinyl)Pd II (μ‐OAc)] 2 undergo one‐electron oxidation to afford mixed‐valent (Pd II –Pd III ) species. Electrochemical oxidation of the Pd II –Pd II complexes in the presence of chloride at the Pd III –Pd II /Pd II –Pd II potential results in a two‐electron loss with addition of two chlorides to form [(benzo[ h ]quinolinyl)Pd III Cl(μ‐OAc)] 2 and [(2‐phenylpyridinyl)Pd III Cl(μ‐OAc)] 2 , respectively. When both excess benzo[ h ]quinoline and chloride are present, [(benzo[ h ]quinolinyl)Pd II (μ‐OAc)] 2 electrocatalyzes the chlorination of the substrate to afford 10‐chlorobenzo[ h ]quinoline with high chemical and Faradaic yields.
Automatic 3D Reconstruction of Manifold Meshes via Delaunay\n Triangulation and Mesh Sweeping (2016)

In this paper we propose a new approach to incrementally initialize a\nmanifold surface for automatic 3D reconstruction from images. More precisely we\nfocus on the automatic initialization of a 3D mesh as close as possible to the\nfinal solution; indeed many approaches require a good initial solution for\nfurther refinement via multi-view stereo techniques. Our novel algorithm\nautomatically estimates an initial manifold mesh for surface evolving\nmulti-view stereo algorithms, where the manifold property needs to be enforced.\nIt bootstraps from 3D points extracted via Structure from Motion, then iterates\nbetween a state-of-the-art manifold reconstruction step and a novel mesh\nsweeping algorithm that looks for new 3D points in the neighborhood of the\nreconstructed manifold to be added in the manifold reconstruction. The\nexperimental results show quantitatively that the mesh sweeping improves the\nresolution and the accuracy of the manifold reconstruction, allowing a better\nconvergence of state-of-the-art surface evolution multi-view stereo algorithms.\n
Cyclooxygenase-2–Derived Prostacyclin Regulates Arterial Thrombus Formation by Suppressing Tissue Factor in a Sirtuin-1–Dependent-Manner (2012)

Modulation of SIRT1 and hence TF by prostacyclin/peroxisome proliferator-activated receptor-δ pathways not only represents a new mechanism in controlling arterial thrombus formation but also might be a useful target for therapeutic intervention in the atherothrombotic complications associated with COX-2 inhibitors.
Enhanced chemical fluorescence-based sensing using metallic nano-composites (2004)

It has been recently shown that the favorable effects of enhanced fluorescent intensities, reduced lifetimes (increased probe photostabilities), enhanced and localized rates of multiphoton excitation, and modified rates of energy transfer can occur for fluorophores or biological species of interest, in close proximity to noble metallic nano-structures and surfaces. Subsequently, nano-metal-enhanced fluorescence (NanoMEF) is yielding enormous opportunities for enhanced fluorescence sensing and imaging in microfluidics, lab-on-a-chip, clinical diagnostics, and cellular applications. NanoMEF is a through-space phenomenon relying on interaction of fluorophores with metallic nanoparticles in the presence of excitation light. MEF can be utilized to produce nanometer-size sensors, which display enhanced spectral properties, whie still potentially maintaining a probes free space-sensing functionalities. In this presentation we report our recent findings on the effects of silver nano-particles on the spectral properties of two representative fluorescent probes for pH and Ca<sup>2+</sup> measurements. We demonstrate that quantum efficiencies of probes are greatly enhanced providing more reliable chemical sensing capabilities. Our findings promise a new class of potential sensors, which we believe could constitute a new breed of composite nanosensors based on metal-enhanced fluorescence and their applications in miniaturized systems.
A Unified Paradigm For Scalable Multi-Projector Displays (2007)

We present a general framework for the modeling and optimization of scalable multi-projector displays. Based on this framework, we derive algorithms that can robustly optimize the visual quality of an arbitrary combination of projectors without manual adjustment. When the projectors are tiled, we show that our framework automatically produces blending maps that outperform state-of-the-art projector blending methods. When all the projectors are superimposed, the framework can produce high-resolution images beyond the Nyquist resolution limits of component projectors. When a combination of tiled and superimposed projectors are deployed, the same framework harnesses the best features of both tiled and superimposed multi-projector projection paradigms. The framework creates for the first time a new unified paradigm that is agnostic to a particular configuration of projectors yet robustly optimizes for the brightness, contrast, and resolution of that configuration. In addition, we demonstrate that our algorithms support high resolution video at real-time interactive frame rates achieved on commodity graphics platforms. This work allows for inexpensive, compelling, flexible, and robust large scale visualization systems to be built and deployed very efficiently.
AMP Deaminase Inhibitors. 4. Further N3-Substituted Coformycin Aglycon Analogues:  N3-Alkylmalonates as Ribose 5‘-Monophosphate Mimetics (2000)

AMP deaminase (AMPDA) inhibitors increase the levels of extracellular adenosine and preserve intracellular adenylate pools in cellular models of ATP depletion and therefore represent a potential new class of antiischemic drugs. Recently we reported that replacement of the ribose 5'-monophosphate component of the very potent transition-state analogue AMPDA inhibitor coformycin monophosphate (1) with a simple alkylcarboxy group resulted in potent, selective, and cell-penetrating AMPDA inhibitors. Here we report that replacement of this alkylcarboxy group with an alpha-substituted alkylmalonic acid resulted in enhanced inhibitor potency. The lead compound, 3-(5, 5-dicarboxy-6-(3-(trifluoromethyl)phenyl)-n-hexyl)coformycin aglycon (21), exhibited an AMPDA K(i) of 0.029 microM which is (3 x 10(5))-fold lower than the K(M) for the natural substrate AMP. A comparison of inhibitory potencies shows that the diacid analogues with alpha-benzyl substituents are 2-10-fold more inhibitory than similar monoacid-monoester, monoester-monoamide, or diester derivatives. Finally, these diacid analogues are 2-40-fold more potent inhibitors than the corresponding monocarboxylates.
Direct evidence for prediction signals in frontal cortex independent of prediction error (2018)

Abstract Predictive coding (PC) has been suggested as one of the main mechanisms used by brains to interact with complex environments. PC theories posit top-down prediction signals, which are compared with actual outcomes, yielding in turn prediction-error signals, which are used, bottom-up, to modify the ensuing predictions. However, disentangling prediction from prediction-error signals has been challenging. Critically, while many studies found indirect evidence for predictive coding in the form of prediction-error signals, direct evidence for the prediction signal is mostly lacking. Here we provide clear evidence, obtained from intracranial cortical recordings in human surgical patients, that the human lateral prefrontal cortex generates prediction signals while anticipating an event. Patients listened to task-irrelevant sequences of repetitive tones including infrequent predictable or unpredictable pitch deviants. The amplitude of high frequency broadband (HFB) neural activity was decreased prior to the onset of expected relative to unexpected deviants in the frontal cortex only, and its amplitude was sensitive to the increasing likelihood of deviants following longer trains of standards in the unpredictable condition. Single trial HFB amplitudes predicted deviations and correlated with post-stimulus response to deviations. These results provide direct evidence for frontal cortex prediction signals independent of prediction-error signals.
Peroxo Compounds, Inorganic (2000)

The article contains sections titled: 1. Introduction 1.1. History 1.2. Classification of Peroxo Compounds 1.3. Properties 2. Peroxides, Hyperoxides, and Ozonides of the Alkali and Alkaline Earth Metals 2.1. Peroxides 2.1.1. Sodium Peroxide 2.1.2. Other Peroxides 2.2. Hyperoxides 2.3. Ozonides 3. Peroxoborates 3.1. Sodium Peroxoborates 3.1.1. Properties 3.1.2. Production 3.1.3. Uses 3.1.4. Product Specifications 3.1.5. Storage and Transportation 3.2. Other Peroxoborates 4. Peroxosulfuric Acids and Peroxosulfates 4.1. Peroxomonosulfuric Acid (Caro's Acid) 4.2. Peroxomonosulfates 4.2.1. Properties 4.2.2. Production 4.2.3. Uses 4.2.4. Analysis 5. Peroxodisulfuric Acid and Peroxodisulfates 5.1. Properties 5.2. Production 5.3. Uses 5.4. Analysis 6. Peroxophosphoric Acids and Their Salts 7. Hydrogen Peroxide Addition Compounds 7.1. Sodium Carbonate Peroxohydrate 7.1.1. Properties 7.1.2. Production 7.1.3. Stabilization, Storage, Packaging, and Transportation 7.1.4. Uses 7.2. Urea Peroxohydrate 7.2.1. Properties 7.2.2. Production 7.2.3. Stabilization and Packaging 7.2.4. Uses 8. Toxicology and Ecotoxicology 8.1. Toxicology 8.2. Ecotoxicology
In Situ Thermal Atomic Layer Etching for Sub-5 nm InGaAs Multigate MOSFETs (2019)

Thermal atomic layer etching (ALE) was demonstrated on ternary III-V compound semiconductors. In particular, thermal ALE on InGaAs and InAlAs was achieved with sequential, self-limiting fluorination and ligand-exchange reactions using hydrogen fluoride (HF) as the fluorination reactant and dimethylaluminum chloride (DMAC) as the ligand-exchange reactant. Thermal ALE was investigated on planar surfaces and three-dimensional nanostructures. The measured radial etch rates on In<sub>0.53</sub>Ga<sub>0.47</sub>As and In<sub>0.52</sub>Al<sub>0.48</sub>As vertical nanowires (VNWs) at 300 °C were 0.24 and 0.62 Å/cycle, respectively. An optimized thermal ALE process did not increase the surface roughness after 200 cycles. The etching process also displayed selectivity and orientation dependence. This new thermal ALE process in combination with in situ atomic layer deposition (ALD) was used to fabricate InGaAs gate-all-around structures with minimum width down to 3 nm. The in situ ALE-ALD process produced a sharp vertical MOS interface. Finally, the merits of thermal ALE were demonstrated in the fabrication of n-channel InGaAs FinFETs with record ON-state and OFF-state transistor performance. On the basis of this transistor demonstration, thermal ALE shows great promise for high-volume device manufacturing.
ChemInform Abstract: Synthesis of Linear and Angular Triquinane Skeletons by O‐Stannyl Ketyl‐Promoted Fragmentation‐Cyclization Reactions of α‐Keto Cyclopropanes. (1997)

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.
Photo Thermal Acoustic Imaging for Sub-Surface Inspection and Alignment (2019)

We have developed a photo thermal acoustic imaging (PTAI)setup and have applied it for the characterization of sub surface features composed of materials which are commonly used in the semiconductor industry. Photo thermal acoustic imaging (PTAI) is a measurement technique that combines the practical advantages of an optical technique (non-contact, charge-free and non-ionizing), with the advantages of a gigahertz-terahertz ultrasound technique such as nanometer scale resolution and a large penetration depth in optically opaque materials.
The Kronecker product in approximation and fast transform generation (1997)

The pH rate profile for the hydrolysis of diethyl-p-nitrophenyl phosphate catalyzed by the phosphotriesterase from Pseudomonas diminuta shows a requirement for the deprotonation of an ionizable group for full catalytic activity. This functional group has an apparent pKa of 6.1 +/- 0.1 at 25 degrees C, delta Hion of 7.9 kcal/mol, and delta Sion of -1.4 cal/K.mol. The enzyme is not inactivated in the presence of the chemical modification reagents dithiobis-(2-nitrobenzoate), methyl methane thiosulfonate, carbodiimide, pyridoxal, butanedione, or iodoacetic acid and thus cysteine, asparate, glutamate, lysine, and arginine do not appear to be critical for catalytic activity. However, the phosphotriesterase is inactivated completely with methylene blue, Rose Bengal, or diethyl pyrocarbonate. The enzyme is not inactivated by diethyl pyrocarbonate in the presence of bound substrate analogs, and inactivation with diethyl pyrocarbonate is reversible upon addition of neutralized hydroxylamine. The modification of a single histidine residue by diethyl pyrocarbonate, as shown by spectrophotometric analysis, is responsible for the loss of catalytic activity. The pKinact for diethyl pyrocarbonate modification is 6.1 +/- 0.1 at 25 degrees C. These results have been interpreted to suggest that a histidine residue at the active site of phosphotriesterase is facilitating the reaction by general base catalysis.
Overcoming implementation barriers for nanotechnology in drinking water treatment (2016)

Nanotechnology enabled water treatment is a promising approach to enhance the effectiveness and efficiency of purifying water in many areas of the world.
Adaptive Compensation of Multimode Fiber Dispersion by Control of Launched Amplitude, Phase, and Polarization (2010)

In previous work, we studied the compensation of modal dispersion in multimode fiber (MMF) using several different configurations of optical systems that can control the amplitude, phase and polarization of the launched field. In that work, we assumed knowledge of a fiber's principal modes (PMs) and their group delays (GDs), enabling us to compute the optimal settings of the optical system. In practice, however, we do not have prior knowledge of the PMs and their GDs. In this paper, for three of the configurations, we propose algorithms for setting the optical system adaptively, based upon measurements of the eye opening. We present simulations showing that in the absence of noise, the performance of the adaptive solution approaches that of the optimal solution, and characterizing the algorithms' convergence speed and tolerance to noise. We present experiments using a particular configuration and adaptive algorithm, demonstrating their effectiveness in 10-Gb/s transmission through up to 2000 m of 50-μ m-core graded-index MMF.
Role of Electron-Transfer Processes in Reactions of Diarylcarbenium Ions and Related Quinone Methides with Nucleophiles (2003)

Second-harmonic alternating current voltammetry has been used to determine one-electron reduction potentials of 15 diarylcarbenium ions and 5 structurally analogous quinone methides, which have been employed as reference electrophiles for the development of nucleophilicity scales. A linear correlation (r(2) = 0.993) between the empirical electrophilicity parameters E and the reduction potentials in acetonitrile (E = 14.091E degrees (red) - 0.279) covering a range of 1.64 V (or 158 kJ mol(-)(1)) has been observed. For a large number of nucleophiles, it has been demonstrated that the observed activation free energies of the electrophile-nucleophile combinations are 61-195 kJ mol(-)(1) smaller than the free energy change of electron transfer from nucleophile to electrophile, which definitely excludes outer-sphere electron transfer occurring during these reactions.
Non‐alcoholic steatohepatitis‐associated hepatic fibrosis and hepatocellular carcinoma in a combined mouse model of genetic modification and dietary challenge (2016)

These results suggest that, in a rodent NASH model with the combination of genetic modification and dietary challenges, hepatic steatosis, inflammatory cell infiltration and hepatic injury, hepatic fibrosis, hepatocellular hyperplasia, adenoma, and carcinoma can be developed in a relatively short period.
Intradialytic Hypoxemia in Chronic Hemodialysis Patients (2016)

When kidney failure occurs, patients are at risk for fluid overload states, which can cause pulmonary edema, pleural effusions, and upper airway obstruction. Kidney disease is also associated with impaired respiratory function, as in central sleep apnea or chronic obstructive pulmonary disease. Hence, respiratory and renal diseases are frequently coexisting. Hypoxemia is the terminal pathway of a multitude of respiratory pathologies. The measurement of oxygen saturation (SO2) is a basic and commonly used tool in clinical practice. Both arterial oxygen saturation (SaO2) and central venous oxygen saturation (ScvO2) can be easily obtained in hemodialysis (HD) patients, SaO2 from an arteriovenous access and ScvO2 from a central catheter. Here, we give a brief overview of the anatomy and physiology of the respiratory system, and the different technologies that are currently available to measure oxygen status in dialysis patients. We then focus on literature regarding intradialytic SaO2 and ScvO2. Lastly, we present clinical vignettes of intradialytic drops in SaO2 and ScvO2 in association with different symptoms and clinical scenarios with an emphasis on the pathophysiology of these cases. Given the fact that in the general population hypoxemia is associated with adverse outcomes, including increased mortality, cardiac arrhythmias and cardiovascular events, we posit that intradialytic SO2 may serve as a potential marker to identify HD patients at increased risk for morbidity and mortality.
Preclinical development of a Pfs230-Pfs48/45 chimeric malaria transmission-blocking vaccine (2021)

The Plasmodium falciparum Pfs230 and Pfs48/45 proteins are leading candidates for a malaria transmission-blocking vaccine (TBV). Previously, we showed that a Pfs230-Pfs48/45 fusion protein elicits higher levels of functional antibodies than the individual antigens, but low yields hampered progression to clinical evaluation. Here we identified a modified construct (ProC6C) with a circumsporozoite protein (CSP) repeat-linker sequence that enhances expression. A scalable and reproducible process in the Lactococcus lactis expression system was developed and ProC6C was successfully transferred for manufacturing under current Good Manufacturing Practices (cGMP). In addition, a panel of analytical assays for release and stability were developed. Intact mass spectrometry analysis and multiangle light scattering showed that the protein contained correct disulfide bonds and was monomeric. Immunogenicity studies in mice showed that the ProC6C adsorbed to Alhydrogel<sup>®</sup>, with or without Matrix-M<sup>TM</sup>, elicited functional antibodies that reduced transmission to mosquitoes and sporozoite invasion of human hepatocytes. Altogether, our data support manufacture and clinical evaluation of ProC6C as a multistage malaria-vaccine candidate.