gebhart/patrepeval huggingface dataset:
<title>Imaging ellipsometry for high-spatial-resolution metrology</title> (2001)

The polarization change that accompanies diffraction from sub- wavelength features is used as a sensitive measure of the feature shape. This sub-wavelength measurement capability is explored by comparing vector-based diffraction models with experimentally obtained data from a novel imaging ellipsometer. This imaging ellipsometer is able to measure samples with high spatial resolution in a parallel fashion by using a high-numerical-aperture lens. Two-dimensional surface maps can be generated without scanning. Our novel metrology tool could provide a solution to the imminent metrology challenges in semiconductor industry.
Distributed scheduling in wireless data networks with service differentiation (2004)

A class of distributed scheduling algorithms, Regulated Contention Medium Access Control (RCMAC), which provides dynamic prioritized access to users for service differentiation, is considered in this paper. In addition to WLANs, the basic concepts of RCMAC have applications in multihop cellular and ad hoc networks and emerging sensor networks. Furthermore, by regulating multiuser contention, RCMAC achieves higher throughput when traffic is bursty. In this paper, differential function with two special cases like weight proportional and old base regulation is presented. Arrivals at each user are bursty, generated using standard two-state Markov model and the multiplicative increase/decrease rule are employed.
Key steps in the structure-based optimization of the hepatitis C virus NS3/4A protease inhibitor SCH503034 (2008)

The structures of both native and S139A holo-HCV NS3/4A protease domain were solved to high resolution. Subsequently, structures were determined for a series of ketoamide inhibitors in complex with the protease. The changes in the inhibitor potency were correlated with changes in the buried surface area upon binding the inhibitor to the active site. The largest contributions to the binding energy arise from the hydrophobic interactions of the P1 and P2 groups as they bind to the S1 and S2 pockets. This correlation of the changes in potency with increased buried surface area contributed directly to the design of a potent tripeptide inhibitor of the HCV NS3/4A protease, which is currently in clinical trials.
Role of the carboxyl-terminal region of Porphyromonas gingivalis fimbrillin in binding to salivary proteins (1997)

Porphyromonas gingivalis fimbriae are considered to play an important role in the adherence and colonization of the bacteria in the oral cavity. In this study, we generated and purified three carboxyl-terminal variants of recombinant fimbrillin (r-FimA 224-337, r-FimA 266-337, and r-FimA 287-337, corresponding to amino acid residues 224 to 337, 266 to 337, and 287 to 337, respectively, of the 43-kDa fimbrillin of P. gingivalis 2561). They were used as inhibitors of P. gingivalis cell binding to human salivary protein-coated hydroxyapatite (HAP) beads. All of the carboxyl-terminal region polypeptides inhibited binding in a dose-dependent manner; however, the inhibitory effect of r-FimA 287-337 was less than that of the other two polypeptides when HAP beads were coated with whole saliva or purified salivary proline-rich protein 1 (PRP1). Assays of binding of a synthetic peptide corresponding to amino acid residues 266 to 286 of P. gingivalis 2561 fimbrillin to salivary proteins showed that this peptide bound strongly to whole saliva or PRP1 but only weakly to statherin. These results suggest that the carboxyl-terminal region corresponding to amino acid residues 266 to 337 of P. gingivalis fimbrillin plays an important role in binding to salivary proteins and that the domain corresponding to amino acids 266 to 286 is likely a major binding site for PRP1s and the domain corresponding to amino acids 287 to 337 is likely a major binding site for statherin.
Identification of novel functional inhibitors of 17β-hydroxysteroid dehydrogenase type III (17β-HSD3) (2005)

The identification of non-steroidal functional inhibitors of 17beta-HSD3 may be a useful complementary approach for the disruption of testosterone biosynthesis in the treatment of PCa.
Sex Pheromone-Based Trapping System for Papaya Fruit Fly (Diptera: Tephritidae)1 (1988)

Journal Article Sex Pheromone-Based Trapping System for Papaya Fruit Fly (Diptera: Tephritidae) Get access P. J. Landolt, P. J. Landolt Insect Attractants, Behavior, and Basic Biology Research Laboratory, USDA-ARS, Gainesville, Florida 32604 Search for other works by this author on: Oxford Academic PubMed Google Scholar R. R. Heath, R. R. Heath Insect Attractants, Behavior, and Basic Biology Research Laboratory, USDA-ARS, Gainesville, Florida 32604 Search for other works by this author on: Oxford Academic PubMed Google Scholar H. R. Agee, H. R. Agee Insect Attractants, Behavior, and Basic Biology Research Laboratory, USDA-ARS, Gainesville, Florida 32604 Search for other works by this author on: Oxford Academic PubMed Google Scholar J. H. Tumlinson, J. H. Tumlinson Insect Attractants, Behavior, and Basic Biology Research Laboratory, USDA-ARS, Gainesville, Florida 32604 Search for other works by this author on: Oxford Academic PubMed Google Scholar C. O. Calkins C. O. Calkins Insect Attractants, Behavior, and Basic Biology Research Laboratory, USDA-ARS, Gainesville, Florida 32604 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 81, Issue 4, 1 August 1988, Pages 1163–1169, https://doi.org/10.1093/jee/81.4.1163 Published: 01 August 1988 Article history Received: 16 July 1987 Accepted: 18 February 1988 Published: 01 August 1988
High Gain Photoconductive Semiconductor Switching (2005)

Switching properties are reported for high gain photoconductive semiconductor switches (PCSS). A 200 ps pulse width laser was used in tests to examine the relations between etectric field, rise time, delay, and minimum optical trigger energy for switches which reached 80 kV in a 50 /spl Omega/ transmission line with rise times as short as 600 ps. Infrared photoluminescence was imaged during high gain switching providing direct evidence for current filamentation. Implications of these measurements for the theoretical understanding and practical development of these switches are discussed.
A far-field optical microscope with nanometre-scale resolution based on in-plane surface plasmon imaging (2005)

A new far-field optical microscopy technique capable of reaching nanometer-scale resolution has been developed recently using the in-plane image magnification by surface plasmon polaritons. This microscopy is based on the optical properties of a metal-dielectric interface that may, in principle, provide extremely large values of the effective refractive index n up to 100-1000 as seen by the surface plasmons. Thus, the theoretical diffraction limit on resolution becomes lambda/2n, and falls into the nanometer-scale range. The experimental realization of the microscope has demonstrated the optical resolution better than 50 nm for 502 nm illumination wavelength. However, the theory of such surface plasmon-based far-field microscope presented so far gives an oversimplified picture of its operation. For example, the imaginary part of the metal dielectric constant severely limits the surface-plasmon propagation and the shortest attainable wavelength in most cases, which in turn limits the microscope magnification. Here I describe how this limitation has been overcome in the experiment, and analyze the practical limits on the surface plasmon microscope resolution. In addition, I present more experimental results, which strongly support the conclusion of extremely high spatial resolution of the surface plasmon microscope.
Machine learning metrology of cell confinement in melt electrowritten three-dimensional biomaterial substrates (2019)

Tuning cell shape by altering the biophysical properties of biomaterial substrates on which cells operate would provide a potential shape-driven pathway to control cell phenotype. However, there is an unexplored dimensional scale window of three-dimensional (3D) substrates with precisely tunable porous microarchitectures and geometrical feature sizes at the cell's operating length scales (10-100 μm). This paper demonstrates the fabrication of such high-fidelity fibrous substrates using a melt electrowriting (MEW) technique. This advanced manufacturing approach is biologically qualified with a metrology framework that models and classifies cell confinement states under various substrate dimensionalities and architectures. Using fibroblasts as a model cell system, the mechanosensing response of adherent cells is investigated as a function of variable substrate dimensionality (2D vs. 3D) and porous microarchitecture (randomly oriented, "non-woven" vs. precision-stacked, "woven"). Single-cell confinement states are modeled using confocal fluorescence microscopy in conjunction with an automated single-cell bioimage data analysis workflow that extracts quantitative metrics of the whole cell and sub-cellular focal adhesion protein features measured. The extracted multidimensional dataset is employed to train a machine learning algorithm to classify cell shape phenotypes. The results show that cells assume distinct confinement states that are enforced by the prescribed substrate dimensionalities and porous microarchitectures with the woven MEW substrates promoting the highest cell shape homogeneity compared to non-woven fibrous substrates. The technology platform established here constitutes a significant step towards the development of integrated additive manufacturing-metrology platforms for a wide range of applications including fundamental mechanobiology studies and 3D bioprinting of tissue constructs to yield specific biological designs qualified at the single-cell level.
Optimization of inductor circuits via geometric programming (2003)

We present an efficient method for optimal design and synthesis of CMOS inductors for use in RF circuits. This method uses the the physical dimensions of the inductor as the design parameters and handles a variety of specifications including fixed value of inductance, minimum self-resonant frequency, minimum quality factor, etc. Geometric constraints that can be handled include maximum and minimum values for every design parameter and a limit on total area. Our method is based on formulating the design problem as a special type of optimization problem called geometric programming, for which powerful efficient interior-point methods have recently been developed. This allows us to solve the inductor synthesis problem globally and extremely efficiently. Also, we can rapidly compute globally optimal trade-off curves between competing objectives such as quality factor and total inductor area. We have fabricated a number of inductors designed by the method, and found good agreement between the experimental data and the specifications predicted by our method.
Elimination of polarization induced signal fading in interoferometric fiber sensors using input polarization control (1988)

We present an analysis of polarization-induced fading in interferometric fiber sensors which predicts that the effect can always be overcome through control of the state of polarization of the light input to the interferometer. Experimental results verifing this theory are reported.
ICA-based denoising for ASL perfusion imaging (2019)

Arterial Spin Labelling (ASL) imaging derives a perfusion image by tracing the accumulation of magnetically labeled blood water in the brain. As the image generated has an intrinsically low signal to noise ratio (SNR), multiple measurements are routinely acquired and averaged, at a penalty of increased scan duration and opportunity for motion artefact. However, this strategy alone might be ineffective in clinical settings where the time available for acquisition is limited and patient motion are increased. This study investigates the use of an Independent Component Analysis (ICA) approach for denoising ASL data, and its potential for automation. 72 ASL datasets (pseudo-continuous ASL; 5 different post-labeling delays: 400, 800, 1200, 1600, 2000 m s; total volumes = 60) were collected from thirty consecutive acute stroke patients. The effects of ICA-based denoising (manual and automated) where compared to two different denoising approaches, aCompCor, a Principal Component-based method, and Enhancement of Automated Blood Flow Estimates (ENABLE), an algorithm based on the removal of corrupted volumes. Multiple metrics were used to assess the changes in the quality of the data following denoising, including changes in cerebral blood flow (CBF) and arterial transit time (ATT), SNR, and repeatability. Additionally, the relationship between SNR and number of repetitions acquired was estimated before and after denoising the data. The use of an ICA-based denoising approach resulted in significantly higher mean CBF and ATT values (p < 0.001), lower CBF and ATT variance (p < 0.001), increased SNR (p < 0.001), and improved repeatability (p < 0.05) when compared to the raw data. The performance of manual and automated ICA-based denoising was comparable. These results went beyond the effects of aCompCor or ENABLE. Following ICA-based denoising, the SNR was higher using only 50% of the ASL-dataset collected than when using the whole raw data. The results show that ICA can be used to separate signal from noise in ASL data, improving the quality of the data collected. In fact, this study suggests that the acquisition time could be reduced by 50% without penalty to data quality, something that merits further study. Independent component classification and regression can be carried out either manually, following simple criteria, or automatically.
Double-Rotor Switched Reluctance Machine (DRSRM) (2015)

With the era of modern vehicle electrification, electric machines with high traction torque-speed output and compact volume are highly desired. This paper presents a family of switched reluctance machine configurations that are composed of double rotors and one stator integrated in one machine housing. The machines are potentially more compact and lower cost, while providing two independent mechanical outputs suitable for hybrid electric vehicle transmissions. The detailed design process of a double-rotor switched reluctance machine (DRSRM) is presented, comprising of analytical calculations, finite-element field analysis, and full-drive system simulation. Additionally, some optimizations are applied to maximize the machine performance and minimize the machine weight and volume. A scaled prototype machine is designed and built according to chosen vehicle drive cycles to evaluate and validate the DRSRM prototype.
Protein S Confers Neuronal Protection During Ischemic/Hypoxic Injury in Mice (2003)

Protein S is a significant neuroprotectant during ischemic brain injury with direct effects on neurons and antithrombotic effects. Thus, protein S could be a prototype of a new class of agents for clinical stroke with combined direct neuronal protective effects and systemic antithrombotic and antiinflammatory activities.
β- <scp>d</scp> - <i>N</i> <sup>4</sup> -Hydroxycytidine Is a Potent Anti-alphavirus Compound That Induces a High Level of Mutations in the Viral Genome (2017)

Venezuelan equine encephalitis virus (VEEV) is a representative member of the New World alphaviruses. It is transmitted by mosquito vectors and causes highly debilitating disease in humans, equids, and other vertebrate hosts. Despite a continuous public health threat, very few compounds with anti-VEEV activity in cell culture and in mouse models have been identified to date, and rapid development of virus resistance to some of them has been recorded. In this study, we investigated the possibility of using a modified nucleoside analog, β-d-<i>N</i><sup>4</sup>-hydroxycytidine (NHC), as an anti-VEEV agent and defined the mechanism of its anti-VEEV activity. The results demonstrate that NHC is a very potent antiviral agent. It affects both the release of genome RNA-containing VEE virions and their infectivity. Both of these antiviral activities are determined by the NHC-induced accumulation of mutations in virus-specific RNAs. The antiviral effect is most prominent when NHC is applied early in the infectious process, during the amplification of negative- and positive-strand RNAs in infected cells. Most importantly, only a low-level resistance of VEEV to NHC can be developed, and it requires acquisition and cooperative function of more than one mutation in nsP4. These adaptive mutations are closely located in the same segment of nsP4. Our data suggest that NHC is more potent than ribavirin as an anti-VEEV agent and likely can be used to treat other alphavirus infections.<b>IMPORTANCE</b> Venezuelan equine encephalitis virus (VEEV) can cause widespread epidemics among humans and domestic animals. VEEV infections result in severe meningoencephalitis and long-term sequelae. No approved therapeutics exist for treatment of VEEV infections. Our study demonstrates that β-d-<i>N</i><sup>4</sup>-hydroxycytidine (NHC) is a very potent anti-VEEV compound, with the 50% effective concentration being below 1 μM. The mechanism of NHC antiviral activity is based on induction of high mutation rates in the viral genome. Accordingly, NHC treatment affects both the rates of particle release and the particle infectivity. Most importantly, in contrast to most of the anti-alphavirus drugs that are under development, resistance of VEEV to NHC develops very inefficiently. Even low levels of resistance require acquisition of multiple mutations in the gene of the VEEV-specific RNA-dependent RNA polymerase nsP4.
Novel Antimicrobial Peptides That Inhibit Gram Positive Bacterial Exotoxin Synthesis (2014)

Gram-positive bacteria, such as Staphylococcus aureus, cause serious human illnesses through combinations of surface virulence factors and secretion of exotoxins. Our prior studies using the protein synthesis inhibitor clindamycin and signal transduction inhibitors glycerol monolaurate and α-globin and β-globin chains of hemoglobin indicate that their abilities to inhibit exotoxin production by S. aureus are separable from abilities to inhibit growth of the organism. Additionally, our previous studies suggest that inhibition of exotoxin production, in absence of ability to kill S. aureus and normal flora lactobacilli, will prevent colonization by pathogenic S. aureus, while not interfering with lactobacilli colonization. These disparate activities may be important in development of novel anti-infective agents that do not alter normal flora. We initiated studies to explore the exotoxin-synthesis-inhibition activity of hemoglobin peptides further to develop potential agents to prevent S. aureus infections. We tested synthesized α-globin chain peptides, synthetic variants of α-globin chain peptides, and two human defensins for ability to inhibit exotoxin production without significantly inhibiting S. aureus growth. All of these peptides were weakly or not inhibitory to bacterial growth. However, the peptides were inhibitory to exotoxin production with increasing activity dependent on increasing numbers of positively-charged amino acids. Additionally, the peptides could be immobilized on agarose beads or have amino acid sequences scrambled and still retain exotoxin-synthesis-inhibition. The peptides are not toxic to human vaginal epithelial cells and do not inhibit growth of normal flora L. crispatus. These peptides may interfere with plasma membrane signal transduction in S. aureus due to their positive charges.
Cloned, expressed rat cerebellar nitric oxide synthase contains stoichiometric amounts of heme, which binds carbon monoxide. (1992)

The endogenous formation of nitric oxide (NO) has become an area of intense interest as evidence for its biological functions has been obtained in three distinct tissues: circulating macrophages, in which it exerts cytotoxic effects; blood vessels, in which it has been identified as endothelium-derived relaxing factor; and neuronal cells, in which it functions as a neurotransmitter. The formation of NO in brain extracts has been shown to be catalyzed by an enzyme, termed NO synthase, which generates the NO responsible for stimulation of cGMP formation, the highest levels of which occur in the cerebellum. NO synthase catalyzes the formation of citrulline from arginine with the coincident production of NO and has been shown to be a flavoprotein, containing 1 mol each of FAD and FMN, tetrahydrobiopterin, and iron. It is also reported to contain an alpha-helical, calmodulin-binding consensus sequence consistent with its stimulation by calmodulin in the presence of Ca2+. The formation of NO requires incorporation of one of the atoms of molecular oxygen into one of the guanidinium nitrogen atoms of arginine with the coincident formation of citrulline. This communication reports that rat cerebellar NO synthase, cloned and stably expressed in human kidney 293 cells, contains heme in amounts stoichiometric with the flavins FAD and FMN as evidenced by the appearance of a pyridine hemochrome and a reduced CO difference spectrum with an absorbance maximum at approximately 445 nm. The finding of a CO-binding heme moiety explains the presence of iron in the enzyme and suggests a role for prosthetic heme as an oxygenase reaction center. This report also presents evidence for incorporation of delta-[14C]aminolevulinate specifically into immunoprecipitable NO synthase in stably transfected human kidney 293 cells but not in nontransfected cells. Simultaneously, K. A. White and M. A. Marletta [(1992) Biochemistry 31, 6627-6631] have demonstrated a CO-binding heme prosthetic group in purified murine macrophage NO synthase and have suggested the identity of these reaction centers in both the constitutive (cerebellar) and inducible (macrophage) forms of NO synthase.
Structure-Expression Relationships of the 15-kDa Selenoprotein Gene (2000)

Selenium has been implicated in cancer prevention, but the mechanism and possible involvement of selenoproteins in this process are not understood. To elucidate whether the 15-kDa selenoprotein may play a role in cancer etiology, the complete sequence of the human 15-kDa protein gene was determined, and various characteristics associated with expression of the protein were examined in normal and malignant cells and tissues. The 51-kilobase pair gene for the 15-kDa selenoprotein consisted of five exons and four introns and was localized on chromosome 1p31, a genetic locus commonly mutated or deleted in human cancers. Two stem-loop structures resembling selenocysteine insertion sequence elements were identified in the 3'-untranslated region of the gene, and only one of these was functional. Two alleles in the human 15-kDa protein gene were identified that differed by two single nucleotide polymorphic sites that occurred within the selenocysteine insertion sequence-like structures. These 3'-untranslated region polymorphisms resulted in changes in selenocysteine incorporation into protein and responded differently to selenium supplementation. Human and mouse 15-kDa selenoprotein genes manifested the highest level of expression in prostate, liver, kidney, testis, and brain, and the level of the selenoprotein was reduced substantially in a malignant prostate cell line and in hepatocarcinoma. The expression pattern of the 15-kDa protein in normal and malignant tissues, the occurrence of polymorphisms associated with protein expression, the role of selenium in differential regulation of polymorphisms, and the chromosomal location of the gene may be relevant to a role of this protein in cancer.