gebhart/patrepeval huggingface dataset:
The Host Response to West Nile Virus Infection Limits Viral Spread through the Activation of the Interferon Regulatory Factor 3 Pathway (2004)

Recent outbreaks of West Nile Virus (WNV) have been associated with an increase in morbidity and mortality in humans, birds, and many other species. We have initiated studies to define the molecular mechanisms by which a recent pathogenic isolate of WNV evades the host cell innate antiviral response. Biochemical and microarray analyses demonstrated that WNV induced the expression of beta interferon (IFN-beta) and several IFN-stimulated genes late in infection of cultured human cells. The late expression of these antiviral genes was due to the delayed activation of the transcription factor IFN regulatory factor 3 (IRF-3). Despite this host response, WNV was still able to replicate efficiently. The effect of the IRF-3 pathway on WNV replication was assessed by examining virus replication and spread in cultures of wild-type or IRF-3-null mouse embryo fibroblasts. The absence of IRF-3 was marked by a significant increase in plaque size and a sustained production of infectious particles. Although the activation of the IRF-3 pathway was not sufficient to block virus replication, our results suggest that IRF-3 target genes function to constrain WNV infection and limit cell-to-cell virus spread.
Real-time PCR assays for the detection and quantification of Streptococcus pneumoniae (2010)

Streptococcus pneumoniae is the main etiologic agent of pneumonia worldwide. Because the members of the viridans group streptococci share a high degree of DNA sequence homologies, phenotypic and genotypic discriminations of S. pneumoniae from the viridans group are difficult. A quantitative real-time PCR assay targeting the capsular polysaccharide biosynthesis gene (cpsA) was developed as a species-specific detection tool for S. pneumoniae. The specificity was evaluated using genomic DNAs extracted from 135 oral cocci strains. Twenty-seven S. pneumoniae strains tested positive, whereas 108 other strains including Streptococcus pseudopneumoniae, Streptococcus mitis, and Streptococcus oralis did not show a specific signal. The linear regression of standard curves indicated high correlations between the log numbers of S. pneumoniae cells and the C(T) values (R(2)=0.99). The minimal limit of detection was 32 fg of purified genomic DNA, equivalent to 14 genomes of S. pneumoniae. This new real-time PCR method may be very useful as a rapid and specific tool for detecting and quantifying S. pneumoniae.
Nanoscale pattern transfer for templates, NEMS, and nano-optics (2007)

Plasma etching is an enabling technology in nano optic, nanoelectronic devices, nano electro mechanical systems (NEMS) and nanoresolution templates for nano imprint lithography (NIL). With shrinkage, one must overcome significant challenges to meet the stringent profile and CD goals necessary for nanoscale applications. Using the example of Si nanoimprint template fabrication, we show how ion/sidewall/mask interactions can dominate feature profile evolution at the nanoscale and what to look for successful pattern transfer. Gas chopping or multiplexed etching, generally used for deep silicon etching, is often avoided at the nanoscale due to unacceptable undercut and sidewall scalloping. We demonstrate a multiplexed etching process in silicon with sub-5 nm amplitude scallops which is well suited for NEMS and nano optics applications and which reduces the deleterious role of ion/sidewall/mask interactions at the nanoscale.
MARINE FOULING AND COATINGS FOR ITS CONTROL (2000)

This article looks at how marine organisms attack, and accumulate on, underwater coated surfaces; the effects of this attack (fouling); and the strategies used in the design of coatings to control fouling. Marine biological fouling will occur on virtually all underwater surfaces, but it is the affixation to the underwater surfaces of ships that is economically most burdensome. The accumulation increases the turbulence of water flow along the hull and disrupts the hydrodynamic efficiency of the vessel, interrupting its streamlined passage through water. Growth rates vary with species, but without devices to deter growth, extremely heavy accumulations may become established within a few weeks. A foulant's adhesive has such a great affinity for the coating surface that preventing its spread across the surface is virtually impossible. This phenomenon has greatly confounded the development of foulant-release coatings. Until recently, virtually all successful antifouling coatings were based on the ability of the coating to deliver toxins into the very thin (lamella) zone of toxic water in the immediate vicinity of the paint film. Many other techniques have been, and continue to be examined. These include exposure to ultraviolet radiation, radioactive components, ultrasonic-induced adhesive rupture, application of electrical currents, as well as the use of hormones, heating/cooling devices, and even predatory bacteria. The basic types of fouling control coatings are described: soluble matrix systems, contact leaching systems, free association (diffusion) systems based on organotin compounds, self-polishing systems, tin-free ablative systems, toxicity of organotin compounds, foulant-release coatings, and several tin-free antifouling compositions bearing nonspecified toxins.
68Ga-Based Radiopharmaceuticals: Production and Application Relationship (2015)

The contribution of 68Ga to the promotion and expansion of clinical research and routine positron emission tomography (PET) for earlier better diagnostics and individualized medicine is considerable. The potential applications of 68Ga-comprising imaging agents include targeted, pre-targeted and non-targeted imaging. This review discusses the key aspects of the production of 68Ga and 68Ga-based radiopharmaceuticals in the light of the impact of regulatory requirements and endpoint pre-clinical and clinical applications.
Refined CPLD macrocell architecture for the effective FSM implementation (1999)

We present the refined architecture of the CPLD (complex programmable logic device) macrocell. For the one-hot-encoded Moore finite state machine (FSM), the proposed architecture allows to decrease by N (where N is the number of the FSM output functions) the number of CPLD macrocells utilized for implementation of the FSM memory. In this paper, we also present the algorithm for synthesis of the one-hot-encoded Moore FSM targeted toward implementation in the proposed CPLD macrocell architecture. We present results of industrial examples of Moore FSMs, which prove the efficacy of our architecture and the algorithm for FSM synthesis. Implementation of Moore FSM in a CPLD with the proposed macrocell architecture allows to reduce the number of utilized buried CPLD macrocells by 67% on average. Similarly, the decrease of the total number of CPLD macrocells amounts to 33% on average.
Photoelectrochemistry with Integrated Photosensitizer−Electron Acceptor and Au-Nanoparticle Arrays (2000)

Photosensitizer/electron acceptor molecular cross-linked Au-nanoparticle arrays are assembled on indium-doped tin oxide (ITO) electrodes by a layer-by-layer deposition process. A Ru(II)−tris-(2,2‘-bipyridine)-cyclobis(paraquat-p-phenylene) catenane (1) or Zn(II)-protoporphyrin IX−bis(N-methyl-N‘-undecanoate-4,4‘-bipyridinium) (2) are used as molecular cross-linkers for the generation of Au-nanoparticle (13 ± 1 nm) arrays of a controlled number of layers. The Au-nanoparticle arrays are characterized by absorbance spectroscopy and by electrochemical means. The electrodes functionalized with 1- or 2-cross-linked Au-nanoparticle arrays are used in photoelectrochemical experiments. The resulting action spectra of the photocurrents follow the absorbance spectra of the respective chromophores. Mechanistic studies indicate that the photocurrents originate from intramolecular electron-transfer quenching of the photoexcited state of the photosensitizer by the electron acceptor units, leading to the formation of intermediate redox species. The oxidized photoproduct oxidizes the sacrificial electron donor, Na2EDTA, whereas the reduced bipyridinium radical cations transfer the electrons to the bulk electrode support.
Ability of delta-opioid receptors to interact with multiple G-proteins is independent of receptor density. (1994)

To determine whether the previously demonstrated ability of delta-opioid receptors to interact simultaneously with multiple G-proteins was a function of high receptor levels, this interaction was investigated in Chinese hamster ovary cells stably expressing 10 different levels of cloned delta-opioid receptors, ranging from 18,000 to 1.6 x 10(6) receptors/cell. The opioid agonist D-Ala2,D-Leu5-enkephalin (DADLE) inhibited forskolin-stimulated adenylyl cyclase activity in all 10 clones with variable maximal inhibitory levels. Furthermore, opioid agonists altered incorporation of [alpha-32P]azidoanilido-GTP into at least four G-protein alpha-subunits in all 10 clones, three of which were determined to be Gi3 alpha, Gi2 alpha and Go2 alpha. This effect was concentration-dependent, naloxone-reversible, and delta-opioid agonist-specific and was blocked by pretreatment with pertussis toxin. Although DADLE induced an increase in the incorporation of [alpha-32P]azidoanilido-GTP into three of the four G alpha proteins that was independent of receptor density, the magnitude of this response was greater as receptor density increased. In addition, concentrations of DADLE required to promote 50% maximal labeling were similar for all four G alpha proteins within each clone and did not appear to be affected by receptor density. Therefore, the ability of delta-opioid receptors to interact with multiple G-proteins is independent of receptor density and there is also no apparent correlation between the amount of G-protein activated and the maximal effect of an agonist.
Gene Expression per Gene Dose, a Specific Measure of Gene Expression in Aquatic Microorganisms (1993)

A method for the measurement of specific levels of gene expression that combines target mRNA and target DNA quantitation has been developed. The use of target gene dose as a normalizing factor for mRNA provides an alternative to 16S or 23S rRNA, which are unsuitable for use in the environment because of their presence in nontarget organisms. Both target mRNA and DNA are recovered from replicate samples and detected by using antisense and sense single-stranded RNA gene probes. For efficient mRNA recovery, the use of Millipore Durapore filters and multiple extractions was necessary. Quantitation was performed by radiometric detection by using a beta-scanner and comparison of the sample signal against target mRNA and DNA standard curves. This method enabled the measurement of expression of the catechol-2,3-dioxygenase gene (xylE) contained on the thermoregulated plasmid pLV1013 in a marine Vibrio strain in culture and in the environment. In studies of the relationship between mRNA levels and enzyme activities, the appearance of enzyme activity lagged behind xylE mRNA synthesis by an hour after temperature induction. This suggests that mRNA analysis is well suited for determining rapid regulation of microbial gene expression at the transcriptional level in water column microbial populations.
Assessment of Automated Disease Detection in Diabetic Retinopathy Screening Using Two-Field Photography (2011)

Automated grading can safely reduce the workload of manual grading using two field, mydriatic photography in a routine screening service.
Kinetic Characterization of Myosin Head Fragments with Long-Lived Myosin·ATP States (1998)

We have separately expressed the Dictyosteliumdiscoideum myosin II nonhydrolyzer point mutations E459V and E476K [Ruppel, K. M., and Spudich, J. A. (1996) Mol. Biol. Cell 7, 1123-1136] in the soluble myosin head fragment M761-1R [Anson et al. (1996) EMBO J. 15, 6069-6074] and performed transient kinetic analyses to characterize the ATPase cycles of the mutant proteins. While the mutations cause some changes in mantATP [2'(3')-O-(N-methylanthraniloyl)-ATP] and mantADP binding, the most dramatic effect is on the hydrolysis step of the ATPase cycle, which is reduced by 4 (E476K) and 6 (E459V) orders of magnitude. Thus, both mutant myosin constructs do in fact catalyze ATP hydrolysis but have very long-lived myosin.ATP states. The E459V mutation allowed for a direct measurement of the ATP off rate constant from myosin, which was found to be 2 x 10(-)5 s-1. Actin accelerated ATP release from this E459V construct by at least 100-fold. Additionally, we found that the affinity of the E476K construct for actin is significantly weaker than for the wild-type construct, while the E459V mutant interacts with actin normally. Their functional properties and the fact that they can be produced and purified in large amounts make the E476K and E459V constructs ideal tools to elucidate key structural features of the myosin ATPase cycle. These constructs should allow us to address important questions, including how binding of ATP to myosin heads results in a >3 order of magnitude reduction in actin affinity.
Modification of a rotating dynamic capacitor for contact potential difference measurements (1983)

A rotating dynamic capacitor is described for measurement of contact potential differences, in which the sliding contact is avoided by using an additional fixed capacitor which provides a capacitive link with the electronic circuit. The dynamic capacitor is included in a measuring device containing a phase-sensitive detector (PSD) synchronised with the modulation frequency of the capacity which makes it possible to change the modulation frequency within a wide range. The measuring device supplied with a PSD ensures stability, high input resistance (over 1012 Omega ) and enhanced accuracy of measurement (from 10 mV to 4 V with 0.2% accuracy for all ranges).
Phase II Trial of Weekly Paclitaxel for Unresectable Angiosarcoma: The ANGIOTAX Study (2008)

Weekly paclitaxel at the dose schedule used in the current study was well tolerated and demonstrated clinical benefit.
Providing Secrecy with Lattice Codes (2009)

Recent results have shown that lattice codes can be used to construct good channel codes, source codes and physical layer network codes for Gaussian channels. On the other hand, for Gaussian channels with secrecy constraints, efforts to date rely on random codes. In this work, we provide a tool to bridge these two areas so that the secrecy rate can be computed when lattice codes are used. In particular, we address the problem of bounding equivocation rates under nonlinear modulus operation that is present in lattice encoders/decoders. The technique is then demonstrated in two Gaussian channel examples: (1) a Gaussian wiretap channel with a cooperative jammer, and (2) a multi-hop line network from a source to a destination with untrusted intermediate relay nodes from whom the information needs to be kept secret. In both cases, lattice codes are used to facilitate cooperative jamming. In the second case, interestingly, we demonstrate that a non-vanishing positive secrecy rate is achievable regardless of the number of hops.
Subendothelial Lipoprotein Retention as the Initiating Process in Atherosclerosis (2007)

The key initiating process in atherogenesis is the subendothelial retention of apolipoprotein B-containing lipoproteins. Local biological responses to these retained lipoproteins, including a chronic and maladaptive macrophage- and T-cell-dominated inflammatory response, promote subsequent lesion development. The most effective therapy against atherothrombotic cardiovascular disease to date--low density lipoprotein-lowering drugs--is based on the principle that decreasing circulating apolipoprotein B lipoproteins decreases the probability that they will enter and be retained in the subendothelium. Ongoing improvements in this area include more aggressive lowering of low-density lipoprotein and other atherogenic lipoproteins in the plasma and initiation of low-density lipoprotein-lowering therapy at an earlier age in at-risk individuals. Potential future therapeutic approaches include attempts to block the interaction of apolipoprotein B lipoproteins with the specific subendothelial matrix molecules that mediate retention and to interfere with accessory molecules within the arterial wall that promote retention such as lipoprotein lipase, secretory sphingomyelinase, and secretory phospholipase A2. Although not the primary focus of this review, therapeutic strategies that target the proatherogenic responses to retained lipoproteins and that promote the removal of atherogenic components of retained lipoproteins also hold promise. The finding that certain human populations of individuals who maintain lifelong low plasma levels of apolipoprotein B lipoproteins have an approximately 90% decreased risk of coronary artery disease gives hope that our further understanding of the pathogenesis of this leading killer could lead to its eradication.
Face relighting based on virtual irradiance sphere and reflection coefficient (2008)

We present a novel method to estimate the light source direction and relight a face texture image of a single 3-D model under arbitrary unknown illumination conditions. We create a virtual irradiance sphere to detect the light source direction from a given illuminated texture image using both normal vector mapping and weighted bilinear interpolation. We then induce a relighting equation with estimated ambient and diffuse intensity. We provide the result of a series of experiments on light source estimation, relighting, and face recognition to show the efficiency and accuracy of the proposed method in restoring the shading and shadow areas of a face texture image. Our approach for face relighting can be used for illuminant-invariant face recognition applications.
When to Stop (2019)

Background and Purpose- Substantial proportion of patients who achieve successful recanalization of acute ischemic stroke due to large vessel occlusion do not achieve good functional outcome. We aim to analyze the effect of number of thrombectomy device passes and degree of the recanalization (by modified Thrombolysis in Cerebral Infarction) on the clinical and functional outcome. Methods- Five hundred forty-two consecutive patients underwent mechanical thrombectomy for large vessel occlusion in the anterior circulation at a single tertiary stroke center. Baseline characteristics, number of passes, recanalization degree, clinical outcome at 24 hours (measured by National Institutes of Health Scale score), and functional outcome (measured by modified Rankin Scale at 90 days) were registered. Multivariate analysis was performed to determine the association of number of passes and degree of recanalization with dramatical clinical recovery (final National Institutes of Health Scale score ≤2 or decrease in 8 or more National Institutes of Health Scale score points in 24 hours) and good functional outcome (modified Rankin Scale score ≤2 at 90 days). Results- Four hundred fifty-nine patients (84%) achieved successful recanalization (modified Thrombolysis in Cerebral Infarction 2B-3), 213 (39%) of them after first device pass. In the multivariate analysis, first-pass recanalization and modified Thrombolysis in Cerebral Infarction 3 were independent predictors of good functional outcome (odds ratio, 2.5; 95% CI, 1.4-4.5; P=0.002 and odds ratio, 2.6 CI; 1.5-4.7; P=0.001, respectively) and dramatical clinical recovery (odds ratio, 1.8; 95% CI, 1.1-3; P=0.032 and odds ratio, 2.9; 95% CI, 1.7-5.1; P<0.001, respectively). Rate of recanalization declined after each pass 39% (213/542), 35% (113/310), 33% (63/190), and 24% (26/154) for passes 1 to 4, respectively and 28% (45/158) for every attempt above 4 passes ( P<0.001). In patients who achieved recanalization, a linear association between number of passes and good functional outcome was observed: 1 pass (58.6%), 2 passes (50.5%), 3 passes (48.4%), 4 passes (38.5%), or 5 or more passes (25.6%; P<0.001) as compared with patients who did not achieve recanalization (16.9%). Conclusions- High number of device passes and less degree of recanalization are associated with worse outcome in patients with acute ischemic stroke secondary to large vessel occlusion. Future studies should investigate the optimal number of passes that should be attempted in patients without substantial recanalization.
Chromatin state marks cell-type- and gender-specific replication of the <i>Drosophila</i> genome (2009)

Duplication of eukaryotic genomes during S phase is coordinated in space and time. In order to identify zones of initiation and cell-type- as well as gender-specific plasticity of DNA replication, we profiled replication timing, histone acetylation, and transcription throughout the Drosophila genome. We observed two waves of replication initiation with many distinct zones firing in early-S phase and multiple, less defined peaks at the end of S phase, suggesting that initiation becomes more promiscuous in late-S phase. A comparison of different cell types revealed widespread plasticity of replication timing on autosomes. Most occur in large regions, but only half coincide with local differences in transcription. In contrast to confined autosomal differences, a global shift in replication timing occurs throughout the single male X chromosome. Unlike in females, the dosage-compensated X chromosome replicates almost exclusively early. This difference occurs at sites that are not transcriptionally hyperactivated, but show increased acetylation of Lys 16 of histone H4 (H4K16ac). This suggests a transcription-independent, yet chromosome-wide process related to chromatin. Importantly, H4K16ac is also enriched at initiation zones as well as early replicating regions on autosomes during S phase. Together, our study reveals novel organizational principles of DNA replication of the Drosophila genome and suggests that H4K16ac is more closely correlated with replication timing than is transcription.
New clock-gating techniques for low-power flip-flops (2000)

Two novel low power flip-flops are presented in the paper. The proposed flip-flops use new gating techniques that reduce power dissipation deactivating the clock signal. The presented circuits overcome the clock duty-cycle limitation of previously reported gated flip-flops. Circuit simulations with the inclusion of parasitics show that sensible power dissipation reduction is possible if the input signal has reduced switching activity. A 16-bit counter is presented as a simple low power application.
SiC DC Fast Charger Control for Electric Vehicles (2018)

Demand for high-power dc fast chargers for electric vehicles (EVs) is growing. In this paper, an outline and control of a SiC-based 60-kW high-efficiency level-3 dc fast charger is narrated. The three-phase EV ac/dc battery charger is based on the patented differential-mode converter topology. Such differential-mode rectifiers (DMRs) are single-stage ac/dc converters that reduce the number of controlled switching devices and hence, the system cost while achieving higher power density and higher efficiency. A control formulation demonstrating power-factor-correction (PFC) based unity-power-factor (UPF) operation with low total harmonic distortion (THD) is presented. Simulation results containing steady-state operation, transient waveforms with loss analysis, efficiency, and THD parametric plots are presented.