gebhart/patrepeval huggingface dataset:
145 Pyroptosis and HIV-Induced CD4 T Cell Death (2012)

While progressive depletion of CD4 T cells is a hallmark of untreated HIV infection, the underlying mechanism(s) remains poorly understood. HIV infection can directly kill CD4 T cells but the number of productively infected cells in vivo does not account for the massive CD4 T-cell losses observed in infected patients. Many dying cells appear to correspond to bystander CD4 T cells. Using human tonsil and spleen tissue infected with HIVNL4-3, we have observed the following: 1) bystander cell death is associated with abortive infection of bystander CD4 T cells leading to the accumulation incomplete HIV reverse transcripts; 2) CD4 T cells die as a result of an innate immune response elicited by this cytosolic viral DNA involving interferon-β production and activation of caspase-3 and caspase-1; 3) a major mechanism of bystander cell death includes caspase-1-dependent pyroptosis, an intensely inflammatory form of programmed cell death where cytoplasmic contents and pro-inflammatory cytokines are released into the extracellular space. Pyropotosis likely drives chemokine-dependent recruitment of additional CD4 T cells triggering new rounds of infection and cell death that subverts effectiveness of the innate immune response. These findings provide a new mechanism linking HIV infection with inflammation and raise the possibility that anti-pyroptotic agents might block HIV-induced CD4 T cell depletion. Such agents might have special utility in individuals displaying rapid progression of disease or broad drug resistance.
Transverse flow cw atomic iodine laser at 1.315 μm (1988)

A transverse flow cw atomic iodine laser at 1.315 μm excited by the photolytic pumping of C3F7I and demonstrating virtually an unlimited operating time is reported. The use of transverse flow establishes a much more constant integrated gain along the optical axis than that previously reported for the longitudinal flowing cw atomic iodine laser. Consequently, a cw atomic iodine laser is achieved having a greatly improved amplitude stability and easier operation in only the fundamental TEM00 transverse mode. Such an operation makes this type of cw atomic iodine lasr much more useful as a diagnostic probe laser at 1.315 μm than the previously reported longitudinal device.
Microwave Noise Characterization of GaAs MESFETs by On-Wafer Measurement of the Output Noise Current (1987)

A simplified noise equivalent circuit is presented for GaAs MESFETs in the common-source configuration, consisting of five linear circuit eIements: the gate-to-source capacitance C/sub gs/, the total input resistance R/sub t/, the transconductance g/sub m/, the output resistance R/sub o/, and a noise current source of spectral density S/sub io/ at the output port. AlI of these elements have been determined by on-wafer measurements. The minimum noise figure F/sub min/ calculated from this model, as well as the bias and frequency dependence of F/sub min/, agree with the measured microwave noise figure of the device. Thus the determination of the F/sub min/ can be done rapidly, conveniently, without the need for tuning, and at the wafer stage of device fabrication solely by on-wafer measurements.
COMPUTER ANALYSIS OF ESSAY CONTENT FOR AUTOMATED SCORE PREDICTION: A PROTOTYPE AUTOMATED SCORING SYSTEM FOR GMAT ANALYTICAL WRITING ASSESSMENT ESSAYS (1998)

ABSTRACT This report discusses the development and evaluation of a research prototype system designed to automatically score essay responses to the GMAT Analytical Writing Assessments: (a). Analysis of an Argument (Argument essays) and (b). Analysis of an Issue (Issue essays) item types. The system, Electronic Essay Rater ( e‐rater ), was designed to automatically analyze several features of an essay and score the essay based on the features of writing as specified in holistic rubrics. E‐rater uses a hybrid feature methodology. It incorporates several variables that are derived statistically, extracted through NLP techniques, or achieved by simple “counting” procedures. The version of the e‐rater described in this report uses five sets of critical feature variables to build the final linear regression model used for predicting scores. The same set of critical variables was used to fit models for the issue and argument training essays and the following results were achieved. For the set of 275 cross‐validation data, exact or adjacent agreement with human rater scores reached 95%. For the 282 cross‐validation issue essays exact or adjacent agreement with human rater scores achieved 93%. The rich feature variables used as score predictors in e‐rater could potentially be used to generate explanation of score predictions, and diagnostic and instructional information.
Decoupling Electrochemical Reaction and Diffusion Processes in Ionically-Conductive Solids on the Nanometer Scale (2010)

We have developed a scanning probe microscopy approach to explore voltage-controlled ion dynamics in ionically conductive solids and decouple transport and local electrochemical reactivity on the nanometer scale. Electrochemical strain microscopy allows detection of bias-induced ionic motion through the dynamic (0.1−1 MHz) local strain. Spectroscopic modes based on low-frequency (∼1 Hz) voltage sweeps allow local ion dynamics to be probed locally. The bias dependence of the hysteretic strain response accessed through first-order reversal curve (FORC) measurements demonstrates that the process is activated at a certain critical voltage and is linear above this voltage everywhere on the surface. This suggests that FORC spectroscopic ESM data separates local electrochemical reaction and transport processes. The relevant parameters such as critical voltage and effective mobility can be extracted for each location and correlated with the microstructure. The evolution of these behaviors with the charging of the amorphous Si anode in a thin-film Li-ion battery is explored. A broad applicability of this method to other ionically conductive systems is predicted.
CoRe-MAC: A MAC-Protocol for Cooperative Relaying in Wireless Networks (2009)

Cooperative relaying methods can improve wireless links, but introduce overhead due to relay selection and resource reservation compared to non-cooperative transmission. In order to be competitive, a cooperative relaying protocol must avoid or compensate for this overhead. In this paper, we present a MAC protocol for relay selection and cooperative communication as an extension to CSMA/CA which addresses resource reservation, relay selection, and cooperative transmission while keeping the overhead in terms of time and energy low. We discuss the efficiency of this protocol for packet error rate, throughput, and message delay in a multi-hop network. Simulation results show that the protocol performs similar and without noticeable overhead compared to standard CSMA/CA for good SNR while it is able to significantly improve throughput and reliability at larger distances.
<title>High-wafer-yield, high-performance vertical cavity surface-emitting lasers</title> (1996)

Vertical cavity surface emitting lasers (VCSELs) with very low threshold current and voltage of 340 (mu) A and 1.5 V is achieved. The molecular beam epitaxially grown wafers are grown with a highly accurate, low cost and versatile pre-growth calibration technique. One- hundred percent VCSEL wafer yield is obtained. Low threshold current is achieved with a native oxide confined structure with excellent current confinement. Single transverse mode with stable, predetermined polarization direction up to 18 times threshold is also achieved, due to stable index guiding provided by the structure. This is the highest value reported to data for VCSELs. We have established that p-contact annealing in these devices is crucial for low voltage operation, contrary to the general belief. Uniform doping in the mirrors also appears not to be inferior to complicated doping engineering. With these design rules, very low threshold voltage VCSELs are achieved with very simple growth and fabrication steps.
COACH: Cognitive analytics for change (2017)

This paper presents our initial efforts towards building a cognitive analytics framework for change management. We propose a novel predictive algorithm for change risk calculation based on historical change failures, server failures, change triggered incidents as well as expert user input. Our predictive algorithm provides significant improvement over traditional risk assessments in proactively capturing problematic changes when tested with real client account data.
High‐Silica Zeolite SSZ‐61 with Dumbbell‐Shaped Extra‐Large‐Pore Channels (2014)

The synthesis of the high-silica zeolite SSZ-61 using a particularly bulky polycyclic structure-directing agent and the subsequent elucidation of its unusual framework structure with extra-large dumbbell-shaped pore openings are described. By using information derived from a variety of X-ray powder diffraction and electron microscopy techniques, the complex framework structure, with 20 Si atoms in the asymmetric unit, could be determined and the full structure refined. The Si atoms at the waist of the dumbbell are only three-connected and are bonded to terminal O atoms pointing into the channel. Unlike the six previously reported extra-large-pore zeolites, SSZ-61 contains no heteroatoms in the framework and can be calcined easily. This, coupled with the possibility of inserting a catalytically active center in the channel between the terminal O atoms in place of H(+), afford SSZ-61 intriguing potential for catalytic applications.
Arabidopsis <i>MET1</i> Cytosine Methyltransferase Mutants (2003)

We describe the isolation and characterization of two missense mutations in the cytosine-DNA-methyltransferase gene, MET1, from the flowering plant Arabidopsis thaliana. Both missense mutations, which affect the catalytic domain of the protein, led to a global reduction of cytosine methylation throughout the genome. Surprisingly, the met1-2 allele, with the weaker DNA hypomethylation phenotype, alters a well-conserved residue in methyltransferase signature motif I. The stronger met1-1 allele caused late flowering and a heterochronic delay in the juvenile-to-adult rosette leaf transition. The distribution of late-flowering phenotypes in a mapping population segregating met1-1 indicates that the flowering-time phenotype is caused by the accumulation of inherited defects at loci unlinked to the met1 mutation. The delay in flowering time is due in part to the formation and inheritance of hypomethylated fwa epialleles, but inherited defects at other loci are likely to contribute as well. Centromeric repeat arrays hypomethylated in met1-1 mutants are partially remethylated when introduced into a wild-type background, in contrast to genomic sequences hypomethylated in ddm1 mutants. ddm1 met1 double mutants were constructed to further our understanding of the mechanism of DDM1 action and the interaction between two major genetic loci affecting global cytosine methylation levels in Arabidopsis.
Synthesis of 2‐oxoamides based on sulfonamide analogs of γ‐amino acids and their activity on phospholipase A<sub>2</sub> (2008)

A variety of lipophilic 2-oxoamides containing sulfonamide analogs of gamma-amino acids as well as acyl sulfonamides of gamma-aminobutyric acid were synthesized. Their ability to inhibit intracellular GIVA cPLA2 and GVIA iPLA2 as well as secreted GV sPLA2 was evaluated. The sulfonamide group seems a bioisosteric group suitable to replace the carboxyl group in 2-oxoamide inhibitors of GVIA cPLA2.
Organic vapor sensing and discrimination using enhanced sensitivity thickness shear mode devices (2006)

Thin film coatings of poly-isobutylene (PIB) on 96 MHz TSM resonators were utilized as high sensitivity organic vapor sensors. Commercially available AT-quartz TSM devices were milled to 17 µm, leading to a thin quartz membrane surrounded by a 50 µm thick outer ring. The organic vapors studied were benzene, toluene, hexane, cyclohexane, heptane, dichloroethane, dichloromethane, and chloroform at levels ranging from 0.2 to over 13.7 volume percentage in the vapor phase. The Butterworth-VanDyke (BVD) equivalent circuit model was used to model both the perturbed and unperturbed TSM resonators. Monitoring the sensor response through the equivalent circuit model allowed for discriminating between the organic vapors. Detailed results for various sensor parameters such as sensitivity, baseline noise and drift, limit of detection, response and recovery times, dynamic range, and repeatability for the 96 MHz device were compared with those for 10 and 20 MHz devices.
Correcting Limited-Magnitude Errors in the Rank-Modulation Scheme (2010)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We study error-correcting codes for permutations under the infinity norm, motivated by a novel storage scheme for flash memories called <emphasis emphasistype="boldital">rank modulation</emphasis>. In this scheme, a set of <emphasis emphasistype="italic"><formula formulatype="inline"><tex Notation="TeX">$n$</tex> </formula></emphasis> flash cells are combined to create a single virtual multilevel cell. Information is stored in the permutation induced by the cell charge levels. Spike errors, which are characterized by a limited-magnitude change in cell charge levels, correspond to a low-distance change under the infinity norm. We define codes protecting against spike errors, called limited-magnitude rank-modulation codes (LMRM codes), and present several constructions for these codes, some resulting in optimal codes. These codes admit simple recursive, and sometimes direct, encoding and decoding procedures. We also provide lower and upper bounds on the maximal size of LMRM codes both in the general case, and in the case where the codes form a subgroup of the symmetric group. In the asymptotic analysis, the codes we construct outperform the Gilbert–Varshamov-like bound estimate. </para>
Use of monoclonal antibodies to identify shared idiotypes on human antibodies to native DNA from patients with systemic lupus erythematosus. (1983)

Antinative DNA antibodies were purified from the serum of a patient with active systemic lupus erythematosus. Using hybridoma technology, we produced several mouse monoclonal antibodies directed against idiotypic determinants on these antinative DNA antibodies. One of these monoclonal anti-idiotypic antibodies, 3I, an IgG2a Kappa, was extensively characterized. 3I is believed to be directed against an idiotypic determinant because (i) its reactivity with antinative DNA antibodies is not inhibited by a large excess of pooled human serum, (ii) it reacts with F(ab')2 fragments of antinative DNA antibodies, and (iii) it reacts with antinative DNA antibodies of all IgG subclasses. 3I is not directed against the antigen binding site in that native DNA and 3I do not compete for binding to antinative DNA antibodies. Eight of nine sera containing antinative DNA activity as determined by the Millipore filter assay reacted with 3I in a solid-phase radioimmunoassay. These findings suggest that antinative DNA antibodies from nonrelated patients with systemic lupus erythematosus share a common idiotype.
Process synthesis concepts for supercritical gas extraction in the crossover region (1986)

Abstract A procedure is presented for designing supercritical gas extraction processes using a pure solvent fluid to effect the separation. The necessary conditions for the procedure to be applicable are the existence of crossover behavior and separable crossover pressures in the fluid phase mixture. Data are presented to support the existence of such phenomena in ternary systems, and an actual separation process has been designed and operated based upon the data. For systems exhibiting this behavior, process synthesis principles are developed to illustrate the evolution of a process flowsheet for the separation of a mixture into its pure components.
A Novel Multi-Layer Poro-Elastic Model of Lung Deformation (2011)

This paper presents a novel method to simulate flow and deformation of the lung. The lung is assumed to behave as a poro-elastic medium with heterogeneous elastic property. The method uses a flow-structure interaction technique to simultaneously model flow within the airway and deformation of the lung lobes. The 3D lung geometry is reproduced from 4D CT scan dataset obtained on real human subjects at a Cancer Center. The non-linear Young’s modulus is estimated in a parallel study based on similar CT scan dataset. The novelty of the present technique lies in the use of onion-layer grid with distributed spatial permeability. It allows prediction of the spatial lung displacement that could be used for tracking lung tumor during radiotherapy.
Decellularized Cartilage May Be a Chondroinductive Material for Osteochondral Tissue Engineering (2015)

Extracellular matrix (ECM)-based materials are attractive for regenerative medicine in their ability to potentially aid in stem cell recruitment, infiltration, and differentiation without added biological factors. In musculoskeletal tissue engineering, demineralized bone matrix is widely used, but recently cartilage matrix has been attracting attention as a potentially chondroinductive material. The aim of this study was thus to establish a chemical decellularization method for use with articular cartilage to quantify removal of cells and analyze the cartilage biochemical content at various stages during the decellularization process, which included a physically devitalization step. To study the cellular response to the cartilage matrix, rat bone marrow-derived mesenchymal stem cells (rBMSCs) were cultured in cell pellets containing cells only (control), chondrogenic differentiation medium (TGF-β), chemically decellularized cartilage particles (DCC), or physically devitalized cartilage particles (DVC). The chemical decellularization process removed the vast majority of DNA and about half of the glycosaminoglycans (GAG) within the matrix, but had no significant effect on the amount of hydroxyproline. Most notably, the DCC group significantly outperformed TGF-β in chondroinduction of rBMSCs, with collagen II gene expression an order of magnitude or more higher. While DVC did not exhibit a chondrogenic response to the extent that DCC did, DVC had a greater down regulation of collagen I, collagen X and Runx2. A new protocol has been introduced for cartilage devitalization and decellularization in the current study, with evidence of chondroinductivity. Such bioactivity along with providing the 'raw material' building blocks of regenerating cartilage may suggest a promising role for DCC in biomaterials that rely on recruiting endogenous cell recruitment and differentiation for cartilage regeneration.
Application of Full Wavefield Inversion to 4D Seismic Data - Workflow and Field Data Examples (2015)

Summary Advances in full wavefield inversion (FWI), 4D seismic technology, and depth migration of seismic data have led to the application of FWI to 4D seismic data in which time lapse changes of velocity model can be directly obtained from the data. It has been shown that correcting for velocity changes due to production in depth migration improves 4D imaging repeatability. In this paper, we present a detailed workflow to correct for large acoustic velocity changes due to production using the FWI 4D results. Through FWI 4D application, we achieved seismic processing cycle time reduction in a recent 4D seismic project. We have also tested the FWI 4D methodology in areas of poor seismic repeatability due to production facility obstruction to seismic data acquisition.
Low-Power Pulse-Triggered Flip-Flop Design With Conditional Pulse-Enhancement Scheme (2011)

In this paper, a novel low-power pulse-triggered flip-flop (FF) design is presented. First, the pulse generation control logic, an and function, is removed from the critical path to facilitate a faster discharge operation. A simple two-transistor and gate design is used to reduce the circuit complexity. Second, a conditional pulse-enhancement technique is devised to speed up the discharge along the critical path only when needed. As a result, transistor sizes in delay inverter and pulse-generation circuit can be reduced for power saving. Various postlayout simulation results based on UMC CMOS 90-nm technology reveal that the proposed design features the best power-delay-product performance in seven FF designs under comparison. Its maximum power saving against rival designs is up to 38.4%. Compared with the conventional transmission gate-based FF design, the average leakage power consumption is also reduced by a factor of 3.52.
Real-time optoacoustic monitoring of substance penetration in tissue (2001)

Optoacoustic tomography is proposed and evaluated as a method for visualization and quantitative measurements of drugs, contrast agent and other substances penetration in skin and nails. Monitoring was made with the optoacoustic front surface transducer (OAFST) operating in backward mode. Denatured egg-white was used as a model for homogeneous porous tissue, and porcine skin in vitro was employed as a model for human skin. Experimental results demonstrated that transdermal penetration and penetration through egg- white have different mechanisms. Properties and behavior of percutaneous layers of porcine skin after application hydrophilic and lipophilic substances was different. An attempt to monitor drug delivery through a nail was made, however, no significant penetration of aqueous solutions in the nail was observed. The inner nail structure was visualized with optoacoustic tomography. We conclude that optoacoustic monitoring of tissue is feasible with spatial resolution limited only by duration of laser pulses. Axial in-depth resolution of 18 μm was achieved with 12-ns long laser pulses.
Importance of Accurate Charges in Binding Affinity Calculations: A Case of Neuraminidase Series (2013)

It has been shown that calculating atomic charges using quantum mechanical level theory greatly improves the accuracy of docking. A protocol was developed and shown to be effective. That this protocol works is just a manifestation of the fact that electrostatic interactions are important in protein-ligand binding. In order to investigate how the same protocol helps in prediction of binding affinities, we took a series of known cocrystal structures of influenza neuraminidase inhibitors with the receptor and performed docking with Glide SP, Glide XP, and QPLD, the last being a workflow that incorporates QM/MM calculations to replace the fixed atomic charges of force fields with quantum mechanically recalculated ones at a given docking pose, and predicted the binding affinities of each cocrystal. The correlation with experimental binding affinities considerably improved with QPLD compared to Glide SP/XP yielding <TEX>$r^2$</TEX> = 0.83. The results suggest that for binding sites, such as that of neuraminidase, which are laden with hydrophilic residues, protocols such as QPLD which utilizes QM-based atomic charges can better predict the binding affinities.
Observations of the differences between closed-loop behavioral and feed-forward model simulations of fractional-N frequency synthesizers (2017)

Conventionally, a fractional-N synthesizer is simulated using a closed-loop behavioral model and the simulations can be very time-consuming. With the analysis by Perrott et al., a more straightforward model, namely the feedforward model, for the fractional-N frequency synthesizer is available. The feedforward model simulations provide quick, relatively accurate evaluation of fractional-N synthesizer divider controller designs. In this work, we point out several differences in the closed loop behavioral model simulations performed in the CppSim environment and the feed-forward model simulations and discuss their significance on the base of analysis and simulation results.