gebhart/patrepeval huggingface dataset:
Site-Specific Promoter Caging Enables Optochemical Gene Activation in Cells and Animals (2014)

In cell and molecular biology, double-stranded circular DNA constructs, known as plasmids, are extensively used to express a gene of interest. These gene expression systems rely on a specific promoter region to drive the transcription of genes either constitutively (i.e., in a continually "ON" state) or conditionally (i.e., in response to a specific transcription initiator). However, controlling plasmid-based expression with high spatial and temporal resolution in cellular environments and in multicellular organisms remains challenging. To overcome this limitation, we have site-specifically installed nucleobase-caging groups within a plasmid promoter region to enable optochemical control of transcription and, thus, gene expression, via photolysis of the caging groups. Through the light-responsive modification of plasmid-based gene expression systems, we have demonstrated optochemical activation of an exogenous fluorescent reporter gene in both tissue culture and a live animal model, as well as light-induced overexpression of an endogenous signaling protein.
γδ T Cell Immune Manipulation during Chronic Phase of Simian HIV Infection Confers Immunological Benefits (2009)

Vgamma2Vdelta2 T cells, a major human gammadelta T cell subset, recognize the phosphoantigen (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP) produced by mycobacteria and some opportunistic pathogens, and they contribute to innate/adaptive/homeostatic and anticancer immunity. As initial efforts to explore Vgamma2Vdelta2 T cell-based therapeutics against HIV/AIDS-associated bacterial/protozoal infections and neoplasms, we investigated whether a well-defined HMBPP/IL-2 therapeutic regimen could overcome HIV-mediated immune suppression to massively expand polyfunctional Vgamma2Vdelta2 T cells, and whether such activation/expansion could impact AIDS pathogenesis in simian HIV (SHIV)-infected Chinese rhesus macaques. While HMBPP/IL-2 coadministration during acute or chronic phase of SHIV infection induced massive activation/expansion of Vgamma2Vdelta2 T cells, the consequences of such activation/expansions were different between these two treatment settings. HMBPP/IL-2 cotreatment during acute SHIV infection did not prevent the increases in peak and set-point viral loads or the accelerated disease progression seen with IL-2 treatment alone. In contrast, HMBPP/IL-2 cotreatment during chronic infection did not exacerbate disease, and more importantly it could confer immunological benefits. Surprisingly, although viral antigenic loads were not increased upon HMBPP/IL-2 cotreatment during chronic SHIV infection, HMBPP activation of Vgamma2Vdelta2 T cells boosted HIV Env-specific Ab titers. Such increases in Abs were sustained for >170 days and were immediately preceded by increased production of IFN-gamma, TNF-alpha, IL-4, and IL-10 during peak expansion of Vgamma2Vdelta2 T cells displaying memory phenotypes, as well as the short-term increased effector function of Vgamma2Vdelta2 T cells and CD4(+) and CD8(+) alphabeta T cells producing antimicrobial cytokines. Thus, HMBPP/Vgamma2Vdelta2 T cell-based intervention may potentially be useful for combating neoplasms and HMBPP-producing opportunistic pathogens in chronically HIV-infected individuals.
Coverage Enhancement in TDD-OFDMA Downlink by Using Simple-Relays with Resource Allocation and Throughput Guarantee Scheduler (2007)

Simple-relay aided resource allocation (SRARA) schemes are incorporated with throughput guarantee scheduling (TGS) in IEEE 802.16 type time division duplex-orthogonal frequency division multiple access (TDD-OFDMA) downlink in order to enhance service coverage, where the amount of resources at each relay is limited due to either its available power which is much smaller than base station (BS) power or the required overhead. The performance of SRARA schemes is evaluated with both proportional fair (PF) and TGS schedulers at 64kbps and 128kbps user throughput requirements when total RS power is set to 500 mW or 1 W. For SRARA with RSs of relatively lower power (500mW), schemes that put total power into only one subchannel offer larger coverage than when both subchnnels are used with equal power allocation, while the RS with evenly power-allocated two subchannels could provide larger coverage gain for a relatively higher power (1 W). Depending upon the target throughputs it is shown which of the relay scheme or scheduler design would play more important role in improving coverage. In a lower target (64 kbps), more improvement comes from relay scheme rather than scheduler design. For a relatively higher level (128 kbps), it comes from scheduler design rather than relay due to the fact that simple relay can't help using strictly limited amount of resources.
Phosphoinositide kinase activity and transformation. (1986)

We have used the DNA tumor virus polyoma as a model system to examine whether the phosphatidylinositol (PI) turnover pathway is a critical target for transforming gene products. Polyoma-infected cells show elevated levels of polyphosphoinositides and polyphosphoinositols, and a PI kinase activity is associated with middle T antigen, a transforming gene product of polyoma virus. In anti-T immunoprecipitates from polyoma-infected or -transformed cells, comparisons of wild-type and polyoma mutants defective for transformation show a strong correlation between middle T-associated PI kinase activity and transforming ability. Middle T has previously been found to associate at the plasma membrane with pp60 c-src and to activate it as a tyrosine kinase. c-src itself does not appear to phosphorylate PI; however, the middle T/pp60 c-src tyrosine kinase activity may be important for activation of PI kinase. Ammonium orthovanadate, a tyrosine phosphatase inhibitor, elevates the middle T/pp60 c-src-associated PI kinase activity. We propose that middle T/pp60 c-src activates a PI kinase and modulates PI turnover in vivo by tyrosine phosphorylation.
Preface (2012)

Since his death in January 1950 at the age of forty-six, George Orwell’s critical and popular reputation has ascended and spread wings. Three major biographies were published during the last decade and Orwell’s papers have been edited in twenty volumes by the British scholar Peter Davison. Special studies dealing with Orwell’s career and writings appear annually.
Time-resolved reconstruction of scene reflectance hidden by a diffuser (2013)

We use time-of-flight information in an iterative optimization algorithm to recover reflectance properties of a three-dimensional scene hidden behind a diffuser. We demonstrate reconstruction of wide-field images without relying on diffuser correlation properties.
Discovery of the First Selective M4 Muscarinic Acetylcholine Receptor Antagonists with in Vivo Antiparkinsonian and Antidystonic Efficacy (2021)

Nonselective antagonists of muscarinic acetylcholine receptors (mAChRs) that broadly inhibit all five mAChR subtypes provide an efficacious treatment for some movement disorders, including Parkinson's disease and dystonia. Despite their efficacy in these and other central nervous system disorders, antimuscarinic therapy has limited utility due to severe adverse effects that often limit their tolerability by patients. Recent advances in understanding the roles that each mAChR subtype plays in disease pathology suggest that highly selective ligands for individual subtypes may underlie the antiparkinsonian and antidystonic efficacy observed with the use of nonselective antimuscarinic therapeutics. Our recent work has indicated that the M<sub>4</sub> muscarinic acetylcholine receptor has several important roles in opposing aberrant neurotransmitter release, intracellular signaling pathways, and brain circuits associated with movement disorders. This raises the possibility that selective antagonists of M<sub>4</sub> may recapitulate the efficacy of nonselective antimuscarinic therapeutics and may decrease or eliminate the adverse effects associated with these drugs. However, this has not been directly tested due to lack of selective antagonists of M<sub>4</sub>. Here, we utilize genetic mAChR knockout animals in combination with nonselective mAChR antagonists to confirm that the M<sub>4</sub> receptor activation is required for the locomotor-stimulating and antiparkinsonian efficacy in rodent models. We also report the synthesis, discovery, and characterization of the first-in-class selective M<sub>4</sub> antagonists VU6013720, VU6021302, and VU6021625 and confirm that these optimized compounds have antiparkinsonian and antidystonic efficacy in pharmacological and genetic models of movement disorders.
Spatial Smoothing Effect on Kronecker Mimo Channel Model in Urban Microcells (2007)

In this paper, the effect of spatial smoothing on performance of widely used stochastic narrowband multiple-input multiple-output (MIMO) radio channel model, namely the Kronecker model, is investigated based on data measured in urban microcellular environment at 5.3 GHz carrier frequency. Results from non-line of sight (NLOS) and line of sight (LOS) traveling routes are analyzed. It is noticed that in NLOS traveling route spatial smoothing improves the accuracy of the large eigenvalues of the channel correlation matrix and significantly enhances the applicability of the Kronecker structure. Under LOS condition both the Kronecker model and its smoothed version fail to render the eigenvalues of the measured channel correlation matrix but spatial smoothing slightly improves the applicability of the Kronecker structure.
An acoustic head simulator for hearing protector evaluation. II: Measurements in steady-state and impulse noise environments (1989)

The attenuation characteristics of hearing protection devices (HPDs) were measured using a modular acoustic head simulator. The effect in changes in the head configuration was assessed in a steady-state diffuse sound field. The use of artificial circumaural skin had a relatively small influence on the insertion loss of earmuffs (max. 6-7 dB at low frequencies). This contrasts to the very large effects found for the artificial intraaural skin on the insertion loss of earplugs (in excess of 40 dB at low frequencies for some devices). Results were also compared with real-ear attenuation at threshold (REAT) data (ANSI S3.19-1974). In general, there is good agreement between the two methods, especially for earmuffs. Design improvements are proposed for earplugs. The result of an exploratory study aimed at measuring the complex (amplitude and phase) insertion loss of HPDs using an impulse noise source are also reported.
ChemInform Abstract: Tailoring the Molecular Sieving Action of Zeolite Y with MOCVD‐Type Reagents. (1994)

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.
Access and Path Selection in Ambient Networks (2007)

As the choice of wireless network technologies increases and different wireless network technologies are connected together the bottleneck of a path will not necessarily be the first access link. Instead a link further upstream could be the bottleneck. This paper introduces a novel generalisation of access selection which takes properties beyond the first hop into consideration for the selection of path for communication. The motivation for design choices and the algorithms involved in the access and path selection are explained. In addition, a use case is included to describe the solution and illustrate its benefits.
Inside Back Cover: A Bottom‐Up Proteomic Approach to Identify Substrate Specificity of Outer‐Membrane Protease OmpT (Angew. Chem. Int. Ed. 52/2017) (2017)

Peptide arrays are used to identify highly active substrates for the OmpT protease, as described by M. Mrksich, B. Liedberg, et al. in their Communication on page 16531 ff. By preparing the peptide arrays on self-assembled monolayers, mass spectrometry (the SAMDI method) was used to characterize the extent of cleavage of each peptide. A commonly used mutant form of the protease, although regarded as having identical activity, instead had an altered specificity for its substrates.
Flexible Interconnect Design Using a Mechanically-Focused, Multi-Objective Genetic Algorithm (2018)

This paper presents a multi-objective optimization process using a non-dominated sorting genetic algorithm-II that aims to maximize the vertical displacement of MEMS-type mechanically flexible interconnects (MFIs) while simultaneously preventing these interconnects from experiencing plastic deformation. Given an initial MFI geometric body, this process seeks to optimize the photomask interconnect design so that no modification is required for the existing fabrication process flow. After the design optimization, a reflowed polymer-dome microfabrication process is employed to fabricate the NiW MFIs to provide a more complete analysis of this paper. Simulation data shows that the optimized design can achieve up to 29.7% greater vertical displacement before experiencing plastic deformation relative to the initial design. Experimental data shows an average of 34.2% less vertical plastic deformation relative to the initial design when the MFIs are indented to a depth of $45~\mu \text{m}$ . In both simulation and experimental scenarios, the optimized MFIs demonstrate less stress/plastic deformation relative to the initial MFIs for the same given indented depth.
Transient operation of carrier signal injection based sensorless techniques (2004)

This paper analyzes the interactions between the fundamental excitation and the carrier signal used for estimation in carrier signal injection based sensorless AC drives. While these interactions can be minimized during steady-state operation through filtering, transients in the fundamental excitation are not so easily treated. The analysis presented covers both negative sequence carrier signal current and zero sequence carrier signal voltage based sensorless methods. Both of these methods are shown to suffer from similar effects due to their interactions with the fundamental excitation. Techniques for mitigating these effects are developed and analyzed for both methods.
EVALUATION OF VIDEO IMAGE PROCESSING SYSTEMS FOR TRAFFIC DETECTION (ABRIDGMENT) (1992)

Recent advances in microprocessor technology have made possible the cost-effective computer processing of video images of highway traffic for measurement of traffic speed, volume, and density. Video image processing systems (VIPS) are now being considered as key components of advanced traffic management systems (ATMS). Eight commercially available or prototype VIPS were recently evaluated for effectiveness at the request of the California Department of Transportation. Test procedures were intended to duplicate conditions typically encountered on California freeway systems. A summary of the test results is reported. Most systems performed well under optimum conditions but degraded significantly under nonoptimum conditions, which varied from system to system. On the basis of the VIPS systems studied, this technology is considered feasible for specific traffic monitoring problems. Limitations and areas for further development are identified.
A novel tachykinin NK2 receptor antagonist prevents motility‐stimulating effects of neurokinin A in small intestine (2001)

1. MEN 11420 (nepadutant) is a potent, selective and competitive antagonist of tachykinin NK2 receptors. 2. The objective of the present study was to assess the capability of the drug to antagonize the stimulatory effects of neurokinin A (NKA) on gastrointestinal motility, as well as to change the fasting migrating motor complex (MMC). 3. Thirty-four male volunteers were randomized to treatment with either placebo or MEN 11420 in a double-blinded manner. Effects of MEN 11420 (8 mg intravenously) were evaluated as changes in phases I, II and III of MMC, as well as contraction frequency, amplitude and motility index during baseline conditions and during stimulation of motility using NKA (25 pmol kg(-1) min(-1) intravenously). 4. NKA preceded by placebo increased the fraction of time occupied by phase II, increased contraction frequency, amplitude and motility index. 5. MEN 11420 effectively antagonized the motility-stimulating effects of NKA. MEN 11420 reduced the phase II-stimulating effect of NKA. In addition, the stimulatory effect of NKA on contraction frequency and amplitude, as well as motility index were inhibited by MEN 11420. MEN 11420 did not affect the characteristics of MMC during saline infusion. 6. Plasma levels of MEN 11420 peaked during the first hour after infusion and decreased to less than half during the first 2 h. 7. In conclusion, intravenous MEN 11420 effectively inhibited NKA-stimulated, but not basal gastrointestinal motility, and was well tolerated by all subjects.
Enhancing Knowledge Selection for Grounded Dialogues via Document Semantic Graphs (2022)

Sha Li, Mahdi Namazifar, Di Jin, Mohit Bansal, Heng Ji, Yang Liu, Dilek Hakkani-Tur. Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2022.
[Testimony by David Baltimore for the Committee on Science and Technology] (1977)

Testimony by David Baltimore for the Committee on Science and Technology, U.S. House of Representatives, Subcommittee on Science, Research and Technology, March 30, 1977
TU‐H‐BRC‐03: Evaluation of Very High‐Energy Electron (VHEE) Beams in Comparison to VMAT and PBS Treatment Plans (2016)

Purpose: The aim of this study was to evaluate the performance of very high‐energy electron (VHEE) beams in comparison to clinically delivered treatment plans generated with volumetric modulated arc therapy (VMAT) and proton pencil beam scanning (PBS) technology. Methods: Three clinical cases were selected (prostate, lung, and pediatric CNS). The VHEE plans were calculated in the Monte Carlo EGSnrc code and pencil beam doses were calculated using the DOSxyznrc MC code for 100 and 200 MeV beams. Treatment plans with VHEE, VMAT, and PBS were optimized in a research version of RayStation using an in house build script in order to minimize operator bias between the different techniques. Results: For the prostate cancer case, the PBS plan showed lower mean organ at risk (OAR) doses compared to the other modalities. An exception was the femoral heads, due to the lateral beam arrangements. The VMAT plan showed lower mean doses to the rectum and the bladder compared to the 100 MeV VHEE plan. The lung cancer case showed minor differences between the three modalities. However, the PBS plan showed a lower contralateral lung dose. The pediatric CNS case showed a better conformity and lower spinal cord dose for the 100 MeV VHEE plan. For all cases, the 200 MeV VHEE plans were found to be similar to or better than the 100 MeV VHEE plans. Conclusion: The present study showed that VHEE plans are similar or superior to VMAT plans with reduced mean OAR dose and increased target conformity for a variety of clinical cases. With increased VHEE energy, better conformity and even higher reductions in mean OAR doses can be achieved. Funding: DoD, Award#:W81XWH‐13‐1‐0165, Weston Havens Foundation, Bio‐X (Stanford University), the Office of the Dean of the Medical School, the Office of the Provost (Stanford University), and the Swedish Childhood Cancer Foundation. BL and PM are founders of TibaRay,Inc. BL and PM have received research grants from Varian and RaySearch Laboratory.
Oncolytic influenza virus infection restores immunocompetence of lung tumor-associated alveolar macrophages (2018)

Non-small-cell lung cancer (NSCLC) is the most frequent type of lung cancer and demonstrates high resistance to radiation and chemotherapy. These tumors evade immune system detection by promoting an immunosuppressive tumor microenvironment. Genetic analysis has revealed oncogenic activation of the Ras/Raf/MEK/ERK signaling pathway to be a hallmark of NSCLCs, which promotes influenza A virus (IAV) infection and replication in these cells. Thus, we aimed to unravel the oncolytic properties of IAV infection against NSCLCs in an immunocompetent model <i>in vivo</i>. Using <i>Raf-BxB</i> transgenic mice that spontaneously develop NSCLCs, we demonstrated that infection with low-pathogenic IAV leads to rapid and efficient oncolysis, eliminating 70% of the initial tumor mass. Interestingly, IAV infection of <i>Raf-BxB</i> mice caused a functional reversion of immunosuppressed tumor-associated lung macrophages into a M1-like pro-inflammatory active phenotype that additionally supported virus-induced oncolysis of cancer cells. Altogether, our data demonstrate for the first time in an immunocompetent <i>in vivo</i> model that oncolytic IAV infection is capable of restoring and redirecting immune cell functions within the tumor microenvironment of NSCLCs.
A GUI paradigm using tablets, two-hands and transparency (1997)

An experimental GUI paradigm is presented which is based on the design goals of maximizing the amount of screen used for application data, reducing the amount that the UI diverts visual attentions from the application data, and increasing the quality of input. In pursuit of these goals, we integrated the non-standard UI technologies of multi-sensor tablets, toolglass [1], transparent UI components [4], and marking menus [6]. While our prototypes and efforts focus within the domain of creating digital art, we believe the concepts and lessons learned are generalizable to other domains. The video shows three main segments: (1) motivation by showing an artist using traditional paper-based interactions, (2) a prototype system called T3 and (3) integration of the concepts into StudioPaint, a high end commercial paint application.
Chemical disarming of isoniazid resistance in Mycobacterium tuberculosis (2019)

<i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) killed more people in 2017 than any other single infectious agent. This dangerous pathogen is able to withstand stresses imposed by the immune system and tolerate exposure to antibiotics, resulting in persistent infection. The global tuberculosis (TB) epidemic has been exacerbated by the emergence of mutant strains of <i>Mtb</i> that are resistant to frontline antibiotics. Thus, both phenotypic drug tolerance and genetic drug resistance are major obstacles to successful TB therapy. Using a chemical approach to identify compounds that block stress and drug tolerance, as opposed to traditional screens for compounds that kill <i>Mtb</i>, we identified a small molecule, C10, that blocks tolerance to oxidative stress, acid stress, and the frontline antibiotic isoniazid (INH). In addition, we found that C10 prevents the selection for INH-resistant mutants and restores INH sensitivity in otherwise INH-resistant <i>Mtb</i> strains harboring mutations in the <i>katG</i> gene, which encodes the enzyme that converts the prodrug INH to its active form. Through mechanistic studies, we discovered that C10 inhibits <i>Mtb</i> respiration, revealing a link between respiration homeostasis and INH sensitivity. Therefore, by using C10 to dissect <i>Mtb</i> persistence, we discovered that INH resistance is not absolute and can be reversed.