gebhart/patrepeval huggingface dataset:
Characterizing closely spaced, complex disulfide bond patterns in peptides and proteins by liquid chromatography/electrospray ionization tandem mass spectrometry (2001)

Identifying the Cys residues involved in disulfide linkages of peptides and proteins that contain complex disulfide bond patterns is a significant analytical challenge. This is especially true when the Cys residues involved in the disulfide bonds are closely spaced in the primary sequence. Peptides and proteins that contain free Cys residues located near disulfide bonds present the additional problem of disulfide shuffling via the thiol-disulfide exchange reaction. In this paper, we report a convenient method to identify complex disulfide patterns in peptides and proteins using liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) in combination with partial reduction by tris(2-carboxyethyl)phosphine (TCEP). The method was validated using well-characterized peptides and proteins including endothelin, insulin, alpha-conotoxin SI and immunoglobulin G (IgG2a, mouse). Peptide or protein digests were treated with TCEP in the presence of an alkylation reagent, maleimide-biotin (M-biotin) or N-ethylmaleimide (NEM), followed by complete reduction with dithiothreitol and alkylation by iodoacetamide (IAM). Subsequently, peptides that contained alkylated Cys were analyzed by capillary LC/ESI-MS/MS to determine which Cys residues were modified with M-biotin/NEM or IAM. The presence of the alkylating reagent (M-biotin or NEM) during TCEP reduction was found to minimize the occurrence of the thiol-disulfide exchange reaction. A critical feature of the method is the stepwise reduction of the disulfide bonds and the orderly, sequential use of specific alkylating reagents.
Incrementalized pointer and escape analysis (2001)

We present a new pointer and escape analysis. Instead of analyzing the whole program, the algorithm incrementally analyzes only those parts of the program that may deliver useful results. An analysis policy monitors the analysis results to direct the incremental investment of analysis resources to those parts of the program that offer the highest expected optimization return.
Improved waveform fidelity using local HYPR reconstruction (HYPR LR) (2008)

The recently introduced HYPR (HighlY constrained backPRojection) method allows reconstruction of serial images from highly undersampled data. In HYPR, individual timeframes are obtained via unfiltered backprojections of normalized sinograms using anatomical constraints provided by a composite image. Here we develop the idea of constraining the backprojected data further to a series of local regions of interest in order to decrease the corruption of local information by distant signals. HYPR LR (local reconstruction) permits the use of a longer temporal window in the formation of the composite image, resulting in increased signal-to-noise ratio and quantitative reconstruction accuracy. Unlike HYPR, the new HYPR LR method can be applied to images acquired with arbitrary k-space trajectories. It is suitable for a broad range of medical imaging applications involving serial changes in image sequence, offering exciting new opportunities in the future.
Comparison of Approximate Methods for Handling Hyperparameters (1999)

I examine two approximate methods for computational implementation of Bayesian hierarchical models, that is, models that include unknown hyperparameters such as regularization constants and noise levels. In the evidence framework, the model parameters are integrated over, and the resulting evidence is maximized over the hyperparameters. The optimized hyperparameters are used to define a gaussian approximation to the posterior distribution. In the alternative MAP method, the true posterior probability is found by integrating over the hyperparameters. The true posterior is then maximized over the model parameters, and a gaussian approximation is made. The similarities of the two approaches and their relative merits are discussed, and comparisons are made with the ideal hierarchical Bayesian solution. In moderately ill-posed problems, integration over hyperparameters yields a probability distribution with a skew peak, which causes signifi-cant biases to arise in the MAP method. In contrast, the evidence framework is shown to introduce negligible predictive error under straightforward conditions. General lessons are drawn concerning inference in many dimensions.
Harmonic Mixing with an Anti-Parallel Diode Pair (1974)

The analysis and experimental evaluation of a new harmonic mixer configuration capable of yielding lower conversion loss and circumventing the local oscillator noise sideband problem is presented.
The chemistry of hydroxyl, ether and peroxide groups (1993)

Partial table of contents: Structural Chemistry of Selected Classes of Alcohols, Ethers and Peroxides (I. Goldberg) Chiroptical Properties of Alcohols, Ethers and Peroxides (A. Gedanken) ESR and NMR Spectroscopy (J. Iley & P. Taylor) Mass Spectrometry of Alcohols and Ethers (F. Turecek) Electronic Effects of Ether and Hydroxyl Groups (J. Shorter) Epoxidation and Hydroxylation (Y. Sawaki) Ozonolysis (G. Zvilichovsky & B. Zvilichovsky) Rearrangements of Alcohols, Phenols, Diols and Peroxides (G. Schneider) Formations and Reactions of Peroxides in Biological Systems (E. Niki) Diols and Polyols (A Molnar) Quinones: The Present State of Addition and Substitution Chemistry (K. Finley) Indexes.
Characteristic Model-Based All-Coefficient Adaptive Control Method and Its Applications (2007)

This paper presents an all-coefficient adaptive control method based on a characteristic model. This method consists of three parts: all-coefficient adaptive control, golden-section adaptive control, and characteristic modeling. It is applied to more than 400 systems of nine kinds of engineering plants. Two such practical examples are introduced in detail to illustrate the concrete steps to apply this method to practical engineering problems. This method has many advantages. It is simple to use, convenient to adjust and test, and able to generate highly robust systems. In certain sense, the method has solved the three principal problems in practical applications, i.e., it can guarantee the stability of a closed-loop system in the start period of a transient process or when parameter estimates have not converged to their "true values," the number of parameters to be estimated is small, and the number of parameters to be regulated online is also small
Heart Rate Dynamics at the Onset of Ventricular Tachyarrhythmias as Retrieved From Implantable Cardioverter-Defibrillators in Patients With Coronary Artery Disease (2000)

The peculiar heart rate dynamics observed before VTA onset are suggestive of a state of sympathoexcitation that is independent of AA drugs.
<title>Fault diagnostic system for a mobile robot</title> (1997)

This paper describes the development of a robot fault diagnosis system (RFDS). Though designed ostensibly for the University of Cincinnati's autonomous, unmanned, mobile robot for a national competition, it has the flexibility to be adapted for industrial applications as well. Using a top-down approach the robot is sub-divided into different functional units, such as the vision guidance system, the ultrasonic obstacle avoidance system, the steering mechanism, the speed control system, the braking system and the power unit. The techniques of potential failure mode and effects analysis (PFMEA) are used to analyze faults, their visible symptoms, and probable causes and remedies. The relationships obtained therefrom are mapped in a database framework. This is then coded in a user-friendly interactive Visual Basic<SUP>TM</SUP> program that guides the user to the likely cause(s) of failure through a question-answer format. A provision is made to ensure better accuracy of the system by incorporating historical data on failures as it becomes available. The RFDS thus provides a handy trouble-shooting tool that cuts down the time involved in diagnosing failures in the complex robot consisting of mechanical, electric, electronic and optical systems. This has been of great help in diagnosing failures and ensuring maximum performance from the robot during the contest in the face of pressure of the competition and the outdoor conditions.
Monitoring and evaluation indicators for GEF international waters projects (2002)

The goal of GEF international waters projects is to assist countries to use the full range of technical, economic, financial, regulatory, and institutional measures needed to operationalize sustainable development strategies for international waters. The Operational Strategy and operational programs recognize the very different nature of international waters projects compared to other GEF focal areas. Following discussions in 1994 and 1995, the GEF Council adopted an Operational Strategy that recognizes that the reversal of environmental degradation in complex transboundary freshwater or marine situations may take decades.
Targeted Disruption of CDK4 Delays Cell Cycle Entry with Enhanced p27 <sup>Kip1</sup> Activity (1999)

The mechanism by which cyclin-dependent kinase 4 (CDK4) regulates cell cycle progression is not entirely clear. Cyclin D/CDK4 appears to initiate phosphorylation of retinoblastoma protein (Rb) leading to inactivation of the S-phase-inhibitory action of Rb. However, cyclin D/CDK4 has been postulated to act in a noncatalytic manner to regulate the cyclin E/CDK2-inhibitory activity of p27(Kip1) by sequestration. In this study we investigated the roles of CDK4 in cell cycle regulation by targeted disruption of the mouse CDK4 gene. CDK4(-/-) mice survived embryogenesis and showed growth retardation and reproductive dysfunction associated with hypoplastic seminiferous tubules in the testis and perturbed corpus luteum formation in the ovary. These phenotypes appear to be opposite to those of p27-deficient mice such as gigantism and gonadal hyperplasia. A majority of CDK4(-/-) mice developed diabetes mellitus by 6 weeks, associated with degeneration of pancreatic islets. Fibroblasts from CDK4(-/-) mouse embryos proliferated similarly to wild-type embryonic fibroblasts under conditions that promote continuous growth. However, quiescent CDK4(-/-) fibroblasts exhibited a substantial ( approximately 6-h) delay in S-phase entry after serum stimulation. This cell cycle perturbation by CDK4 disruption was associated with increased binding of p27 to cyclin E/CDK2 and diminished activation of CDK2 accompanied by impaired Rb phosphorylation. Importantly, fibroblasts from CDK4(-/-) p27(-/-) embryos displayed partially restored kinetics of the G(0)-S transition, indicating the significance of the sequestration of p27 by CDK4. These results suggest that at least part of CDK4's participation in the rate-limiting mechanism for the G(0)-S transition consists of controlling p27 activity.
Oxidized Phospholipids Reduce Vascular Leak and Inflammation in Rat Model of Acute Lung Injury (2006)

These studies demonstrate in vivo and in vitro protective effects of oxidized phospholipids on LPS-induced lung dysfunction.
Luminescent Ce(III) Complexes as Stoichiometric and Catalytic Photoreductants for Halogen Atom Abstraction Reactions (2015)

Luminescent Ce(III) complexes, Ce[N(SiMe3)2]3 (1) and [(Me3Si)2NC(RN)2]Ce[N(SiMe3)2]2 (R = (i)Pr, 1-(i)Pr; R = Cy, 1-Cy), with C(3v) and C(2v) solution symmetries display absorptive 4f → 5d electronic transitions in the visible region. Emission bands are observed at 553, 518, and 523 nm for 1, 1-(i)Pr, and 1-Cy with lifetimes of 24, 67, and 61 ns, respectively. Time-dependent density functional theory (TD-DFT) studies on 1 and 1-(i)Pr revealed the (2)A1 excited states corresponded to singly occupied 5d(z(2)) orbitals. The strongly reducing metalloradical character of 1, 1-(i)Pr, and 1-Cy in their (2)A1 excited states afforded photochemical halogen atom abstraction reactions from sp(3) and sp(2) C-X (X = Cl, Br, I) bonds for the first time with a lanthanide cation. The dehalogenation reactions could be turned over with catalytic amounts of photosensitizers by coupling salt metathesis and reduction to the photopromoted atom abstraction reactions.
Galileo: perceiving physical object properties by integrating a physics engine with deep learning (2015)

Humans demonstrate remarkable abilities to predict physical events in dynamic scenes, and to infer the physical properties of objects from static images. We propose a generative model for solving these problems of physical scene under-standing from real-world videos and images. At the core of our generative model is a 3D physics engine, operating on an object-based representation of physical properties, including mass, position, 3D shape, and friction. We can infer these latent properties using relatively brief runs of MCMC, which drive simulations in the physics engine to fit key features of visual observations. We further explore directly mapping visual inputs to physical properties, inverting a part of the gener-ative process using deep learning. We name our model Galileo, and evaluate it on a video dataset with simple yet physically rich scenarios. Results show that Galileo is able to infer the physical properties of objects and predict the outcome of a vari-ety of physical events, with an accuracy comparable to human subjects. Our study points towards an account of human vision with generative physical knowledge at its core, and various recognition models as helpers leading to efficient inference. 1
The electrocapacitive properties of graphene oxide reduced by urea (2011)

We report a facile and green route to reduce graphite oxide using urea as the reducing agent. UV-Vis, XRD and XPS results revealed that urea was an effective reducing agent in removing oxygen-containing groups from graphite oxide for restoring the conjugated electronic structure of graphene. The obtained reduced graphene oxide was tested as supercapacitor electrode. Gravimetric capacitances of 255 and 100 F g−1 at current densities of 0.5 and 30 A g−1, respectively, were observed. The reduced graphene oxide paper showed a volumetric capacitance of 196 F cm−3. After 1200 continuous cycles of galvanostatic charge–discharge, the electrode retained 93% of its capacitance. The electrocapacitive performance of the urea-reduced graphene oxide outperformed most of the previously reported graphene-based electrode materials, which were reduced by hydrazine or NaBH4. The present reduction method holds great promise for mass production of soluble graphene-based materials for electrochemical energy storage.
Cell-density-dependent regulation of neural precursor cell function (2004)

Stress-induced reductions of neural precursor cells from the subgranular zone of the hippocampal dentate gyrus have been linked to impaired neurogenesis and cognitive dysfunction. Given the importance of redox state in regulating multiple damage-responsive pathways in the CNS, we hypothesize that oxidative stress plays a major role in affecting neurogenesis and subsequent cognitive function after cell injury/depletion. Using an in vitro system, we showed that the level of reactive oxygen species (ROS), which depend critically on changes in cell density, were significantly higher in neural precursor cells when compared with other primary and transformed cell lines. ROS were significantly elevated ( approximately 4-fold) under low- (<1 x 10(4) cells per cm(2)) versus high-density (>1 x 10(5) cells per cm(2)) conditions. Higher ROS levels found at lower cell densities were associated with elevated proliferation and increased metabolic activity. These ROS were likely a result of altered mitochondrial function that ultimately compromised the growth rate of cells. At high cell densities, intracellular ROS and oxidative damage were reduced in concert with an increased expression of mitochondrial superoxide dismutase 2. Our finding that DNA-damage-induced depletion of neural precursor cells in the subgranular zone of mice also led to increased ROS and altered proliferation validated our in vitro system. Increased ROS and proliferation associated with the reduction of precursor cell numbers both in vitro and in vivo could be reversed with the antioxidant alpha-lipoic acid. These data showed that neural precursor cells were predisposed to microenvironmental cues that regulate redox-sensitive pathways to control cellular proliferation after CNS damage.
Validation of an in vitro Biofilm Model of Supragingival Plaque (2001)

The study of biofilm structure and function mandates the use of model systems for which a host of environmental variables can be rigorously controlled. We describe a model of supragingival plaque containing Actinomyces naeslundii, Veillonella dispar, Fusobacterium nucleatum, Streptococcus sobrinus, and Streptococcus oralis wherein cells are cultivated anaerobically in a saliva-based medium on hydroxyapatite discs coated with a salivary pellicle, with material and pieces of apparatus common to all microbiology laboratories. After 0.5 hr, 16.5 hrs, 40.5 hrs, and 64.5 hrs, the composition of adherent biofilms was analyzed by culture techniques, live/dead fluorescence staining, and confocal laser scanning microscopy. Repeated independent trials demonstrated the repeatability of biofilm formation after 40.5 hrs and 64.5 hrs. Brief exposures of biofilms to chlorhexidine or Triclosan produced losses in viability similar to those observed in vivo. This biofilm model should prove very useful for pre-clinical testing of prospective anti-plaque agents at clinically relevant concentrations.
Ultrasensitive Photoreversible Molecular Sensors of Azobenzene-Functionalized Plasmonic Nanoantennas (2014)

This Letter describes an unprecedentedly large and photoreversible localized surface plasmon resonance (LSPR) wavelength shift caused by photoisomerization of azobenzenes attached to gold nanoprisms that act as nanoantennas. The blue light-induced cis to trans azobenzene conformational change occurs in the solid state and controls the optical properties of the nanoprisms shifting their LSPR peak up to 21 nm toward longer wavelengths. This shift is consistent with the increase in thickness of the local dielectric environment (0.6 nm) surrounding the nanoprism and perhaps a contribution from plasmonic energy transfer between the nanoprism and azobenzenes. The effects of the azobenzene conformational change and its photoreversibility were also probed through surface-enhanced Raman spectroscopy (SERS) showing that the electronic interaction between the nanoprisms and bound azobenzenes in their cis conformation significantly enhances the intensity of the Raman bands of the azobenzenes. The SERS data suggests that the isomerization is controlled by first-order kinetics with a rate constant of 1.0 × 10(-4) s(-1). Our demonstration of light-induced photoreversibility of this type of molecular machine is the first-step toward removing present limitations on detection of molecular motion in solid-state devices using LSPR spectroscopy with nanoprisms. Modulating the LSPR peak position and controlling energy transfer across the nanostructure-organic molecule interface are very important for the fabrication of plasmonic-based nanoscale devices.
Four Subunits (αβγδ) of the Epithelial Sodium Channel (ENaC) Are Expressed in the Human Eye in Various Locations (2011)

All four ENaC subunits (αβγδ) are expressed in the normal human eye, with distinct localization of subunits possibly reflecting different functional states of the channel. The (patho-)physiological roles of ENaC in the various localizations in the eye remain to be determined.
SHS Orcas (2002)

SHS.com (Shared Healthcare Systems) provides software solutions and services for the senior healthcare market. In 1998, SHS engaged Cooper to help design a next-generation healthcare information system that would for the first time provide true integration of clinical, financial, and case management information, allowing comprehensive management of long-term healthcare facilities.Cooper had an opportunity to design a product that not only improved the efficiency of healthcare facilities, but also helped improve the quality of care given to their residents. The system needed to help facility staff make sense of data as well as capture it.To address these important issues, Cooper interviewed and observed healthcare facility staff and residents during an intensive ethnographic research period. The research and analysis culminated in a set of user archetypes, called personas. The team used persona- and scenario-based methods to drive the design of an integrated suite of clinical, case management, and financial tools.
Bundled data asynchronous multipliers with data dependent computation times (2002)

A novel asynchronous design method is introduced which combines the area efficiency of bundled data with data dependent computation time. The design of a 16/spl times/16 bit multiplier using this technique is explained and evaluated. Simulation results show that area time savings of 20% compared to an equivalent synchronous design can be achieved.
A MEMBRANE-PERMEABLE RADICAL SCAVENGER REDUCES THE ORGAN INJURY IN HEMORRHAGIC SHOCK (1999)

Reactive oxygen species (ROS) contribute to the multiple organ failure (MOF) in hemorrhagic shock. Here we investigate the effects of a membrane-permeable radical scavenger (tempol) on the circulatory failure and the organ injury and dysfunction (kidney, liver, lung, intestine) associated with hemorrhagic shock in the anesthetized rat. Hemorrhage (sufficient to lower mean arterial blood pressure to 500 mmHg for 90 min) and subsequent resuscitation with shed blood resulted (within 4 h after resuscitation) in a delayed fall in blood pressure, renal and liver injury and dysfunction as well as lung and gut injury. In all organs, hemorrhage and resuscitation resulted in the nitrosylation of proteins (determined by immunohistochemistry for nitrotyrosine) suggesting the formation of peroxynitrite and/or reactive oxygen species. Treatment of rats upon resuscitation with the membrane-permeable radical scavenger tempol (30 mg/kg bolus injection followed by an infusion of 30 mg/kg/h i.v.) attenuated the delayed circulatory failure as well as the multiple organ injury and dysfunction associated with hemorrhagic shock. Thus, we propose that an enhanced formation of ROS and/or peroxynitrite importantly contributes to the MOF in hemorrhagic shock, and that membrane-permeable radical scavengers, such as tempol, may represent a novel therapeutic approach for the therapy of hemorrhagic shock.
The rheology of filled polymers (1971)

Abstract The flow properties of polymer melts containing fillers of various shapes and sizes have been examined. If there is no failure of either the filler or polymer in the solid state, then the modulus enhancement for randomly distributed filler is equal to the melt viscosity enhancement under medium shear stress conditions (10 4 Nm −2 ) in simple shear flow or in oscillatory shear flow. Submicron‐size fillers, in particular, can form weak structures in the melt that greatly increase the low shear rate viscosity without changing the modulus of the solid proportionately. The highly pseudo‐plastic nature of polymer melts at shear stresses of 10 6 Nm −2 means that, even without orientation of filler particles toward the flow direction, the viscosity enhancement is less than at lower shear stresses.