gebhart/patrepeval huggingface dataset:
Expression of a herpes simplex virus 1 open reading frame antisense to the gamma(1)34.5 gene and transcribed by an RNA 3' coterminal with the unspliced latency-associated transcript (1994)

Sensory neurons harboring latent herpes simplex virus 1 express viral RNAs derived from one or more transcriptional units contained in the inverted repeats which flank the long unique sequence but which terminate in the inverted repeats flanking the small unique sequences of viral DNA. These transcripts are also made in productively infected cells. We have identified 16 potential open reading frames (ORFs) predicted to encode 50 or more codons within the domain of the largest reported unspliced transcript and examined 5 ORFs by in-frame insertion of a sequence encoding an epitope reacting with a monoclonal antibody against a human cytomegalovirus protein. One ORF (ORF P), coincident with but antisense to the gamma(1)34.5 gene, was expressed but only under conditions in which ICP4 was not functional. To ensure the authenticity of the expression, a second degenerate sequence encoding the same epitope was inserted into a distant site of the same ORF. The protein expressed by the ORF P with two insertions migrated more slowly than the one carrying one insertion only, indicating that ORF P is expressed.
PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies (2017)

Recent cancer pharmacogenomic studies profiled large panels of cell lines against hundreds of approved drugs and experimental chemical compounds. The overarching goal of these screens is to measure sensitivity of cell lines to chemical perturbations, correlate these measures to genomic features, and thereby develop novel predictors of drug response. However, leveraging these valuable data is challenging due to the lack of standards for annotating cell lines and chemical compounds, and quantifying drug response. Moreover, it has been recently shown that the complexity and complementarity of the experimental protocols used in the field result in high levels of technical and biological variation in the in vitro pharmacological profiles. There is therefore a need for new tools to facilitate rigorous comparison and integrative analysis of large-scale drug screening datasets. To address this issue, we have developed PharmacoDB (pharmacodb.pmgenomics.ca), a database integrating the largest cancer pharmacogenomic studies published to date. Here, we describe how the curation of cell line and chemical compound identifiers maximizes the overlap between datasets and how users can leverage such data to compare and extract robust drug phenotypes. PharmacoDB provides a unique resource to mine a compendium of curated cancer pharmacogenomic datasets that are otherwise disparate and difficult to integrate.
Analog‐to‐Digital Conversion (1999)

Abstract The sections in this article are Fundamental Aspects of A/D Converters Nyquist Analog‐to‐Digital Converters Oversampling Converters
Feasibility and safety of virtual-reality-based early neurocognitive stimulation in critically ill patients (2017)

The results in this proof-of-concept study suggest that a virtual-reality-based neurocognitive intervention is feasible, safe, and tolerable, stimulating cognitive functions and satisfying critically ill patients. Future studies will evaluate the impact of interventions on neurocognitive outcomes. Trial registration Clinical trials.gov identifier: NCT02078206.
Humidity Sensor Characteristics of Porous Zeolite Ceramics at Elevated Temperatures (1989)

Porous zeolite ceramics was fabricated by firing the powder and examined in terms of humidity sensor characteristics at elevated temperatures. The following results are obtained.(1) The suitable firing temperature for the zeolite powder is found to be in the range of 500° to 700°C in view of the existing phase and the sample strength.(2) Although the humidity sensitivity at 400°C was small comparing with that at R. T., the hysteresis of the impedance at 400°C on increasing and subsequently decreasing the humidity became negligibly small.(3) The response time could also be significantly reduced by heating the sample at 400°C comparing with that at R. T.
Mutational analysis of the group A streptococcal operon encoding streptolysin S and its virulence role in invasive infection (2005)

The pathogen group A Streptococcus (GAS) produces a wide spectrum of infections including necrotizing fasciitis (NF). Streptolysin S (SLS) produces the hallmark beta-haemolytic phenotype produced by GAS. The nine-gene GAS locus (sagA-sagI) resembling a bacteriocin biosynthetic operon is necessary and sufficient for SLS production. Using precise, in-frame allelic exchange mutagenesis and single-gene complementation, we show sagA, sagB, sagC, sagD, sagE, sagF and sagG are each individually required for SLS production, and that sagE may further serve an immunity function. Limited site-directed mutagenesis of specific amino acids in the SagA prepropeptide supports the designation of SLS as a bacteriocin-like toxin. No significant pleotrophic effects of sagA deletion were observed on M protein, capsule or cysteine protease production. In a murine model of NF, the SLS-negative M1T1 GAS mutant was markedly diminished in its ability to produce necrotic skin ulcers and spread to the systemic circulation. The SLS toxin impaired phagocytic clearance and promoted epithelial cell cytotoxicity, the latter phenotype being enhanced by the effects of M protein and streptolysin O. We conclude that all genetic components of the sag operon are required for expression of functional SLS, an important virulence factor in the pathogenesis of invasive M1T1 GAS infection.
A Practical Synthesis of 2-Butyl-4(5)-chloro-5(4)-hydroxymethyl- 1H-imidazole (1993)

Abstract A practical process for the synthesis of 2-butyl-4-hydroxymethyl imidazole (4) followed by chlorination to provide chloroimidazole 1 in an overall 71% yield has been developed.
Simple, compact, high-performance permanent-magnet Faraday isolator (1986)

The design of a Faraday isolator that uses a short glass rotator rod and produces highly uniform rotation across its clear aperture is presented. The rotator rod is 19.5 mm long, and at a wavelength of 633 nm the rotation angle is 45 deg and the isolation ratio is >45 dB.
SYNTHESIS OF 1- AND 3-CHLORO-PHENOTHIAZINES (2002)

Phenothiazines have been synthesized via Smiles rearrangement by the reaction of 2-amino-3/5chlorobenzenethiols with halonitrobenzenes. Halonitrobenzenes having a nitro group at both ortho positions to halogen yields directly phenothiazines as Smiles rearrangement occurs insitu. Halonitrobenzenes having a nitro group at ortho position to halogen give 2-amino-2'-nitrodiphenylsulfides which on formylation with 90% formic acid yields 2-formamido-2'-nitrodiphenylsulfides, which undergo Smiles rearrangement to provide phenothiazines.
An Improved Circuit for Implementing the Six-Port Technique of Microwave Measurements (1977)

In a companion paper, circuit design criteria were developed which lead to optimal performance in applying the six-port technique to the measurement of microwave parameters. A circuit which approximately satisfies these new design goals is described. Together with its several variants, it promises to become, in many applications, the "preferred" six-port circuit.
High Temperature SQI CMOS Tungsten Micro-Heaters (2006)

Here we present for the first time, the design, fabrication and characterization of novel high temperature SOI micro-hotplates employing tungsten resistive heaters. Tungsten has a high operating temperature, good mechanical strength, and could be used for CMOS interconnects. These devices have been fabricated using a commercial SOI-CMOS process followed by a DR1E back-etch step, offering low cost and the option of circuit integration. Here we report on micro-hotplates with two different diameters (560mum and 300mum), 3D electro-thermal simulation in ANSYS and their electro-thermal characterization. Results show that these devices can operate at a high temperature (600degC), have ultra low DC power consumption (12mW at 600degC), fast transient time (as low as 2ms to 600degC), stability in time and temperature and, more importantly, a high reproducibility both within a wafer and from wafer to wafer. The SOI micro-hotplates could be used in fully integrated micro-calorimeters or resistive gas sensors.
Modified methylene blue method for the micro-determination of hydrogen sulphide (1974)

N. A. Matheson, Analyst, 1974, 99, 577 DOI: 10.1039/AN9749900577
Eradication of Intracellular <i>Salmonella</i> <i>enterica</i> Serovar Typhimurium with a Small-Molecule, Host Cell-Directed Agent (2009)

Eradication of intracellular pathogenic bacteria with host-directed chemical agents has been an anticipated innovation in the treatment of antibiotic-resistant bacteria. We previously synthesized and characterized a novel small-molecule agent, AR-12, that induces autophagy and inhibits the Akt kinase in cancer cells. As both autophagy and the Akt kinase have been shown recently to play roles in the intracellular survival of several intracellular bacteria, including Salmonella enterica serovar Typhimurium, we investigated the effect of AR-12 on the intracellular survival of Salmonella serovar Typhimurium in macrophages. Our results show that AR-12 induces autophagy in macrophages, as indicated by increased autophagosome formation, and potently inhibits the survival of serovar Typhimurium in macrophages in association with increased colocalization of intracellular bacteria with autophagosomes. Intracellular bacterial growth was partially rescued in the presence of AR-12 by the short hairpin RNA-mediated knockdown of Beclin-1 or Atg7 in macrophages. Moreover, AR-12 inhibits Akt kinase activity in infected macrophages, which we show to be important for its antibacterial effect as the enforced expression of constitutively activated Akt1 in these cells reverses the AR-12-induced inhibition of intracellular serovar Typhimurium survival. Finally, oral administration of AR-12 at 2.5 mg/kg/day to serovar Typhimurium-infected mice reduced hepatic and splenic bacterial burdens and significantly prolonged survival. These findings show that AR-12 represents a proof of principle that the survival of intracellular bacteria can be suppressed by small-molecule agents that target both innate immunity and host cell factors modulated by bacteria.
Strained-silicon MOSFETs for analog applications: utilizing a supercritical-thickness strained Layer for low leakage current and high breakdown Voltage (2006)

Strained-silicon MOSFETs with both high breakdown voltage and low leakage current needed for RF/analog applications were investigated. Proper control of junction-depth profile and strained-silicon-layer thickness significantly improved transconductance, on resistance, and leakage current. Breakdown voltage of strained-silicon MOSFETs was the same as silicon MOSFETs even at elevated temperatures. RF/analog performances, such as cutoff frequency and 1/f noise, were improved by this technology while keeping high-driving-voltage capability.
After the windfall (2014)

Plateauing budgets for global health sharpen the focus on what really works.
Acquiring lexical generalizations from corpora (1999)

This paper examines the extent to which verb diathesis alternations are empirically attested in corpus data. We automatically acquire alternating verbs from large balanced corpora by using partialparsing methods and taxonomic information, and discuss how corpus data can be used to quantify linguistic generalizations. We estimate the productivity of an alternation and the typicality of its members using type and token frequencies.
Role of leukocytes in response to acute myocardial ischemia and reflow in dogs (1986)

Recent evidence indicates that leukocytes (LEU) are large, stiff, viscous cells that naturally adhere to vascular endothelium. Their broad role in the early myocardial microvascular response to acute ischemia was suggested by 1) the role of leukocyte capillary plugging in the no-reflow phenomenon, 2) resistance increases in skeletal muscle with LEU infusions, and 3) salvage of ischemic myocardium by anti-LEU agents. We perfused the coronary circulation under matched, controlled conditions with whole blood or granulocyte-depleted whole blood. During 1 h of ischemia (left anterior descending occlusion) circumflex perfusion pressure was servocontrolled to a constant value. In whole blood-perfused hearts, flow measured by the radiolabeled microsphere method decreased in endocardium from 0.12 +/- 0.05 at 5 min of ischemia to 0.09 +/- 0.04 ml X min-1 X g-1 at 60 min of ischemia and in epicardium from 0.27 +/- 0.17 to 0.21 +/- 0.16 ml X min-1 X g-1, both P less than 0.05. In granulocyte-depleted blood-perfused hearts, flow increased over the same period from 0.18 +/- 0.15 to 0.29 +/- 0.18 ml X min-1 X g-1 in endocardium (P less than 0.05) and did not change significantly in epicardium (0.36 +/- 0.22 to 0.41 +/- 0.24 ml X min-1 X g-1). The LEU-depleted blood perfusate contained less than 33 granulocytes/microliter, whereas control perfusate contained 4,265/microliter. Reperfusion at normal pressures with carbon suspension allowed for histologic evaluation of the no-reflow phenomenon. With whole blood perfusion the no-reflow phenomenon in the endocardium was present with 27% of capillaries occluded, compared with nearly complete reperfusion in LEU-depleted animals (1% of capillaries occluded, P less than 0.05). Furthermore, LEU depletion prevented the increases in tissue water content seen in control hearts and decreased the incidence of ventricular arrhythmias. These studies demonstrate the significant participation of granulocytes in the unfavorable responses of flow, edema formation, and arrhythmias to the 1st h of myocardial ischemia and further document their role in the no-reflow phenomenon.
Just relax: convex programming methods for identifying sparse signals in noise (2006)

This paper studies a difficult and fundamental problem that arises throughout electrical engineering, applied mathematics, and statistics. Suppose that one forms a short linear combination of elementary signals drawn from a large, fixed collection. Given an observation of the linear combination that has been contaminated with additive noise, the goal is to identify which elementary signals participated and to approximate their coefficients. Although many algorithms have been proposed, there is little theory which guarantees that these algorithms can accurately and efficiently solve the problem. This paper studies a method called convex relaxation, which attempts to recover the ideal sparse signal by solving a convex program. This approach is powerful because the optimization can be completed in polynomial time with standard scientific software. The paper provides general conditions which ensure that convex relaxation succeeds. As evidence of the broad impact of these results, the paper describes how convex relaxation can be used for several concrete signal recovery problems. It also describes applications to channel coding, linear regression, and numerical analysis
A new register file structure for the high-speed microprocessor (1982)

The pipeline operations of the register file in a microprocessor are analyzed in detail. Conventional register files, two-port static RAMs, have two problems in successive write-to-read operations. (1) A read-time error takes place when the transition of the W/R mode and the transition of register address occur simultaneously. (2) A write-time error takes place when the supply voltage is slow. A new register file structure is proposed, which has three address word lines and four data bit lines for each memory cell. This structure enables the independent write and read operations to each other, and can solve the two problems. By using this register file structure, a new 16 bit microprocessor with 250 ns machine cycle time is successfully developed. Several other features of this processor are also explained and discussed.
Pick a Color MARIA: Adaptive Sampling Enables the Rapid Identification of Complex Perovskite Nanocrystal Compositions with Defined Emission Characteristics (2018)

Recent advances in the development of hybrid organic–inorganic lead halide perovskite (LHP) nanocrystals (NCs) have demonstrated their versatility and potential application in photovoltaics and as light sources through compositional tuning of optical properties. That said, due to their compositional complexity, the targeted synthesis of mixed-cation and/or mixed-halide LHP NCs still represents an immense challenge for traditional batch-scale chemistry. To address this limitation, we herein report the integration of a high-throughput segmented-flow microfluidic reactor and a self-optimizing algorithm for the synthesis of NCs with defined emission properties. The algorithm, named Multiparametric Automated Regression Kriging Interpolation and Adaptive Sampling (MARIA), iteratively computes optimal sampling points at each stage of an experimental sequence to reach a target emission peak wavelength based on spectroscopic measurements. We demonstrate the efficacy of the method through the synthesis of multinary LHP NCs, (Cs/FA)Pb(I/Br)3 (FA = formamidinium) and (Rb/Cs/FA)Pb(I/Br)3 NCs, using MARIA to rapidly identify reagent concentrations that yield user-defined photoluminescence peak wavelengths in the green–red spectral region. The procedure returns a robust model around a target output in far fewer measurements than systematic screening of parametric space and additionally enables the prediction of other spectral properties, such as, full-width at half-maximum and intensity, for conditions yielding NCs with similar emission peak wavelength.
Wavelength-tunable three-electrode DBR laser with a thin-active layer in tuning regions (1991)

A thin-active layer was inserted into the tuning regions of a wavelength-tunable three-electrode DBR (distributed Bragg reflector) laser. The gain of the thin-active layer compensates for the loss in adjacent passive guide layers, and improved the optical output power and spectral linewidth in tuning operations. The total tuning range was over 8 nm and the continuous tuning range was over 1 nm, with an output power increase of 30%.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Application of Regulatory T Cells in Transplantation Field (2012)

The development of immunosuppressant treatments has enabled remarkable progress in the tissue and organ transplantation field by helping to prevent acute graft rejection. However, complications related to transplantation, such as infection by bacteria and viruses, and the occurrence of cancers resulting from prolonged immune suppression are major obstacles to overcome. Therefore, transplantation immunology research efforts should focus on the induction of donor-specific immune tolerance which preserves patient immune competence which promotes infection and cancer surveillance. Additionally, lifelong administration of immunosuppressants should be forgone in preference to short term therapies. In the 1990s, Dr. Shimon Sakaguchi identified the CD4 CD25 regulatory T cells which develop in the thymus, and demonstrated that these cells play crucial roles in the maintenance of immune self tolerance. Studies which followed proved that these regulatory T cells are important to the control of autoimmune disease and prevention of graft rejection. Regulatory T cells have also been found to induce immune tolerance in rodent models. In this review, we discuss several considerations for the use of regulatory T cell therapy in the clinical transplantation field.
Radical, Skewed, Benign, and Calculated: Reflections on Teaching Diversity (1999)

This narrative shares my experiences teaching diversity in an undergraduate social work program. First, I begin by sharing my experience teaching diversity as a Ph.D. student. Second, I discuss my experience teaching social work with in Canada and tell how this experience influenced how I later taught diversity. Third, I attempt to define diversity and discuss how broad and elusive I have found this topic to be. Fourth, I share different instructor roles I assumed in order to get students to appreciate the importance of this course. In this narrative, Indigenous and First Nations Peoples are used interchangeably to refer to the aboriginal of the United States. I avoid, as much as possible, the terms Indian, and Native American because I consider them to be colonized identities. When they are used, it is only in the context of a direct quote. Copyright of Reflections : Narratives of Professional Helping is the property of Cleveland State University and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.
The Reversible Residual Network: Backpropagation Without Storing Activations (2017)

Residual Networks (ResNets) have demonstrated significant improvement over traditional Convolutional Neural Networks (CNNs) on image classification, increasing in performance as networks grow both deeper and wider. However, memory consumption becomes a bottleneck as one needs to store all the intermediate activations for calculating gradients using backpropagation. In this work, we present the Reversible Residual Network (RevNet), a variant of ResNets where each layer's activations can be reconstructed exactly from the next layer's. Therefore, the activations for most layers need not be stored in memory during backprop. We demonstrate the effectiveness of RevNets on CIFAR and ImageNet, establishing nearly identical performance to equally-sized ResNets, with activation storage requirements independent of depth.
RMST: reliable data transport in sensor networks (2003)

Reliable data transport in wireless sensor networks is a multifaceted problem influenced by the physical, MAC, network, and transport layers. Because sensor networks are subject to strict resource constraints and are deployed by single organizations, they encourage revisiting traditional layering and are less bound by standardized placement of services such as reliability. This paper presents analysis and experiments resulting in specific recommendations for implementing reliable data transport in sensor nets. To explore reliability at the transport layer, we present RMST (Reliable Multi-Segment Transport), a new transport layer for Directed Diffusion. RMST provides guaranteed delivery and fragmentation/reassembly for applications that require them. RMST is a selective NACK-based protocol that can be configured for in-network caching and repair.