gebhart/patrepeval huggingface dataset:
Genetic Profiling Defines the Xenobiotic Gene Network Controlled by the Nuclear Receptor Pregnane X Receptor (2003)

The orphan nuclear receptor pregnane X receptor (PXR) is essential for the transcriptional regulation of hepatic xenobiotic enzymes including the cytochrome 3A isoenzymes. These enzymes are central to the catabolism and clearance of most endogenous sterol metabolites (endobiotics) and a vast diversity of foreign compounds (xenobiotics) including pharmaceuticals, pesticides, and toxins encountered through diet and environmental exposure. To explore a broader role of PXR in the mammalian xenobiotic response, we have conducted a unique microarray gene profiling analysis on liver samples derived from PXR knockout mice and mice expressing a constitutively active variant, VP-hPXR. This genetically guided expression analysis enables targeting and restriction of the PXR response to liver, and is devoid of side effects resulting from drugs and their metabolites. As with pharmacological studies, receptor-dependent genes include both phase I and phase II metabolic enzymes, as well as certain drug and anion transporters as principal PXR targets. Moreover, comparative analysis of data from both genetic and pharmacological arrays reveals a core network that represents a genetic description of the xenobiotic response.
Learning to Estimate Human Pose with Data Driven Belief Propagation (2005)

We propose a statistical formulation for 2D human pose estimation from single images. The human body configuration is modeled by a Markov network and the estimation problem is to infer pose parameters from image cues such as appearance, shape, edge, and color. From a set of hand labeled images, we accumulate prior knowledge of 2D body shapes by learning their low-dimensional representations for inference of pose parameters. A data driven belief propagation Monte Carlo algorithm, utilizing importance sampling functions built from bottom-up visual cues, is proposed for efficient probabilistic inference. Contrasted to the few sequential statistical formulations in the literature, our algorithm integrates both top-down as well as bottom-up reasoning mechanisms, and can carry out the inference tasks in parallel. Experimental results demonstrate the potency and effectiveness of the proposed algorithm in estimating 2D human pose from single images.
Epidermal differentiation and keratin gene expression. (1994)

Epidermal keratinocytes are ideal as a model system for the study of mammalian differentiation because primary cells have a high proliferative capacity and can be cultured under conditions enabling a balance of growth and differentiation. In addition, epidermal keratin genes have been cloned and characterized, and their strong promoters provide a means of high-level expression of transgenes in the epidermis of mice. For these reasons, considerable headway has been made in recent years in the quest to elucidate the biological pathways involved in the control of epidermal growth and differentiation. An understanding of these mechanisms is essential to realizing the potential of epidermal keratinocytes for drug delivery and gene therapy. This paper reviews what is presently known about epidermal growth and differentiation, with emphasis on the expression of epidermal-specific genes.
Discovery of a New Class of Non-β-lactam Inhibitors of Penicillin-Binding Proteins with Gram-Positive Antibacterial Activity (2014)

Infections caused by hard-to-treat methicillin-resistant Staphylococcus aureus (MRSA) are a serious global public-health concern, as MRSA has become broadly resistant to many classes of antibiotics. We disclose herein the discovery of a new class of non-β-lactam antibiotics, the oxadiazoles, which inhibit penicillin-binding protein 2a (PBP2a) of MRSA. The oxadiazoles show bactericidal activity against vancomycin- and linezolid-resistant MRSA and other Gram-positive bacterial strains, in vivo efficacy in a mouse model of infection, and have 100% oral bioavailability.
Novel encapsulation technique for incorporation of high permittivity fillers into silicone elastomers (2014)

The research on soft elastomers with high dielectric permittivity for the use as dielectric electroactive polymers (DEAP) has grown substantially within the last decade.The approaches to enhance the dielectric permittivity can be categorized into three main classes: 1) Mixing or blending in high permittivity fillers, 2) Grafting of high permittivity molecules onto the polymer backbone in the elastomer, and 3) Encapsulation of high permittivity fillers.The approach investigated here is a new type of encapsulation which does not interfere with the mechanical properties to the same content as for the traditionally applied thermoplastic encapsulation.The properties of the elastomers are investigated as function of the filler content and type.The dielectric permittivity, dielectric loss, conductivity, storage modulus as well as viscous loss are compared to elastomers with the same amounts of high permittivity fillers blended into the elastomer, and it is found that the encapsulation provides a technique to enhance some of these properties.
Monolithic integration of laser and waveguide using a twin-guide structure with absorption layer (2002)

We demonstrate for the first time the use of absorption layer to achieve mode control in an InP/InGaAsP integrated twin-guide (TG) laser structure. The In/sub 0.53/Ga/sub 0.47/As layer eliminates the even mode and makes characteristics of the integrated device insensitive to laser cavity length and structure variations, without degrading performance. A record high coupling efficiency of 45% from the TG laser to the integrated passive waveguide is obtained.
Large-scale sputtering of indium–tin oxide (1978)

The development of a reactive dc diode sputtering system for the deposition of indium oxide coatings by scanning large substrates will be described. Coatings of 5 Ω/sq, with 86% light transmission, having a specific resistivity of less than 2.5×10−4Ω cm are routinely produced on curved and flat substrates up to 5 ft2. Effects particularly noticeable in large sputtering systems, such as secondary electron emission, plasma focusing, imperfections due to cathode nonuniformity, arcing caused by cathode contamination, and substrate temperature gradients, will be emphasized.
Opioid growth factor tonically inhibits human colon cancer cell proliferation in tissue culture (1996)

Native opioid peptides serve as growth factors in a number of normal and neoplastic cells and tissues, including the prevention and delayed growth of human colon cancer xenografts in nude mice. This study examined the hypothesis that opioids exert a direct inhibitory influence on tumor cell growth by the use of a tissue culture model. The naturally occurring pentapeptide [Met5]enkephalin depressed growth of HT-29 human colon cancer cells from 17 to 41% at 12-72 h after administration of 10(-6)M concentration; consistent with previously defined nomenclature, this peptide was termed opioid growth factor (OGF). OGF action exhibited a dose-response relationship, was reversible and not cytotoxic, and was opioid receptor mediated. Growth inhibition by OGF was not dependent on serum, and was noted in the two other human colon cancer cell lines examined WiDr and COLO 205. This peptide continually repressed growth because an increase in cell number was noted when cells were exposed to the potent opioid antagonist naltrexone or an antibody to OGF. Both OGF and its receptor, zeta (zeta), were found in colon cancer cells by immunocytochemistry, and receptor binding assays revealed a nuclear-associated receptor with a dissociation constant of 8.9 nM and a maximum binding capacity of 43 fmol/mg of protein. OGF was produced and secreted by the tumor cells. These results lead to the suggestion that OGF has a direct, tonic, inhibitory action on the growth of human colon cancer cells and contribute to our understanding of the mechanisms underlying the marked antitumor effect of this peptide in nude mice inoculated with human colon cancer cells.
Synthesis and characterization of diporphyrin sensitizers for dye-sensitized solar cells (2009)

Novel porphyrin dimers with broad and strong absorption in the visible and/or near IR regions have been synthesized; the meso-meso-linked porphyrin dimer (YDD1) exhibited the best photovoltaic performance with power conversion efficiency 5.2% under AM 1.5G one solar illumination.
Serum- and Glucocorticoid-Regulated Kinase 1 Is Required for Nuclear Export of the Ribonucleoprotein of Influenza A Virus (2013)

We previously performed a small interfering RNA (siRNA) screen and identified serum- and glucocorticoid-regulated kinase 1 (SGK1) as a host factor required for influenza A virus replication. However, the role of SGK1 in the influenza viral life cycle has never been examined. In this study, we demonstrate that SGK1 is required for optimal replication of influenza virus, using the SGK1 inhibitor GSK 650394 and SGK1-specific siRNAs. We also demonstrate that SGK1 is required for viral ribonucleoprotein nuclear export.
A fractional-N frequency synthesizer architecture utilizing a mismatch compensated PFD/DAC structure for reduced quantization-induced phase noise (2003)

Techniques are proposed to dramatically reduce the impact of quantization noise in /spl Sigma//spl Delta/ fractional-N synthesizers, thereby improving the existing tradeoff between phase noise and bandwidth that exists in these systems. The key innovation is the introduction of new techniques to overcome nonidealities in a phase-frequency detector (PFD)/digital-to-analog converter (DAC) structure, which combines the functionality of both phase detector and cancellation DAC into a single element. The proposed architecture achieves better gain matching between the phase-error signal and cancellation DAC than offered by previous approaches. Dynamic element matching techniques are introduced to mitigate the effects of PFD/DAC unit element and timing mismatch on synthesizer phase noise performance. We present behavioral simulations of an example application of this technique that demonstrates 36 dB reduction in broad-band quantization-induced phase noise with the use of a 7-b PFD/DAC. Simulations further demonstrate that fractional spurs are rejected to levels <-90 dBc when a low-cost, low-overhead digital gain correction technique is employed.
Frequency selective surfaces as near-infrared electromagnetic filters for thermophotovoltaic spectral control (2004)

Frequency selective surfaces (FSSs) effectively filter electromagnetic radiation in the microwave band (1 mm to 100 mm). Interest exists in extending this technology to the near infrared (1 μm to 10 μm) for use as a filter of thermal radiation in thermophotovoltaic (TPV) direct energy conversion. This article assesses the ability of FSSs to meet the strict spectral performance requirements of a TPV system. Inherent parasitic absorption, which is the result of the induced currents in the FSS metallization, is identified as a significant obstacle to achieving high spectral performance.
Patterned corneal collagen crosslinking for astigmatism: Computational modeling study (2014)

Proprietary or commercial disclosures are listed after the references.
Silicon Germanium as a novel mask for silicon deep reactive ion etching (2012)

This paper reports on the use of p-type polycrystalline Silicon Germanium (poly-Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</sub> Ge <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> ) thin films as a new masking material for cryogenic silicon deep reactive ion etching (DRIE). The proposed masking material can be deposited at CMOS backend compatible temperatures and demonstrates high etching selectivity towards silicon (>;1:270). Moreover, SiGe etches 37 times faster than SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> or SiN masks in SF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> /O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> plasma resulting in a major reduction in the processing time without the need for a dedicated etcher. Selectivity tests revealed that the etching selectivity of the SiGe mask towards silicon strongly depends on the Ge content, boron concentration and etching temperature. This was attributed to chemical and thermodynamic stability of the SiGe film, as well as the electronic properties of the mask.
A Kalman Filter-Based Method for Restoration of Images Obtained by an In-Vehicle Camera in Foggy Conditions (2009)

In this paper, a Kalman filter-based method for restoration of video images acquired by an in-vehicle camera in foggy conditions is proposed. In order to realize Kalman filter-based restoration, the proposed method clips local blocks from the target frame by using a sliding window and regards the intensities in each block as elements of the state variable of the Kalman filter. Furthermore, the proposed method designs the following two models for restoration of foggy images. The first one is an observation model, which represents a fog deterioration model. The proposed method automatically determines all parameters of the fog deterioration model from only the foggy images to design the observation model. The second one is a non-linear state transition model, which represents the target frame in the original video image from its previous frame based on motion vectors. By utilizing the observation and state transition models, the correlation between successive frames can be effectively utilized for restoration, and accurate restoration of images obtained in foggy conditions can be achieved. Experimental results show that the proposed method has better performance than that of the traditional method based on the fog deterioration model.
Introducing Precision Addiction Management (PAM) utilizing polymorphic matched algorithms and Pro-Dopamine regulation to combat Reward DeficiencyBehaviors (RDS) including Substance Use Disorder (SUD) globally (2020)

Research into the neurogenetic basis of addiction identified and characterized by Reward Deficiency Syndrome (RDS) includes all drug and non-drug addictive, obsessive and compulsive behaviors. This keynote presents a new model for the prevention and treatment of RDS behaviors based on objective biologic evidence. Currently, research directed toward improving treatment for highly drug-dependent patients in underserved populations is the basis of an NIH grant awarded to Drs. Kenneth Blum and Marjorie Gondre-Lewis. The grant explores utilization of the Genetic Addiction Risk Score (GARS®) and the neuronutrient prodopamine regulator KB220. The development of GARS followed seminal research in 1990, whereby, Blum’s group identified the first genetic association with severe alcoholism. The non-invasive GARS test identifies and measures the total number of risk alleles of genes and catabolic enzymes affecting an individual's neurochemical hypodopaminergic function and has been associated in hundreds of studies with RDS behaviors. In an unpublished study, the GARS predicted drug and alcohol severity predisposition as measured by the Addiction Severity Index (ASI) [≤ 4 alleles for Drug & ≤ 7 alleles for Alcohol]. Genotyping data on approximately 1000 subjects [addicted, chronic pain, opioid maintained and non-addicted] will be presented including Italian subjects. “Precision Addiction Management” (PBM®) uses the GARS to customize KB220PAM formulations to deliver putative dopamine homeostasis based on developed algorithms matched to polymorphic results. Presented evidence derived from animal and human studies using BOLD neuroimaging and behavioral methodologies, support homeostatic activation of brain dopamine in the reward circuitry by KB220PAM, as well as anti-substance seeking and modification of RDS behaviors. RDS encompasses behaviors like PTSD, ADHD, over-eating, shopping, hoarding and related RDS cognitive insults. Combating the drug crisis requires PBM across ethnic groups, to bring dopamine homeostasis to those born with RDS predisposition. It is the goal through this novel model that by using PBM the addiction field will have a synergistic tool along with MAT or even alone, to overcome dopamine dysregulation either surfeit (adolescents) or deficit (adults) by the induction of “dopamine homeostasis.
Regulation of apoptosis at cell division by p34 <sup>cdc2</sup> phosphorylation of survivin (2000)

The interface between apoptosis (programmed cell death) and the cell cycle is essential to preserve homeostasis and genomic integrity. Here, we show that survivin, an inhibitor of apoptosis over-expressed in cancer, physically associates with the cyclin-dependent kinase p34(cdc2) on the mitotic apparatus, and is phosphorylated on Thr(34) by p34(cdc2)-cyclin B1, in vitro and in vivo. Loss of phosphorylation on Thr(34) resulted in dissociation of a survivin-caspase-9 complex on the mitotic apparatus, and caspase-9-dependent apoptosis of cells traversing mitosis. These data identify survivin as a mitotic substrate of p34(cdc2)-cyclin B1 and suggest that survivin phosphorylation on Thr(34) may be required to preserve cell viability at cell division. Manipulation of this pathway may facilitate the elimination of cancer cells at mitosis.
360&#x00B0; sun tracking with automated cleaning system for solar PV modules (2010)

The solar PV modules are generally employed in dusty environments which is the case in tropical countries like India. The dust gets accumulated on the front surface of the module and blocks the incident light from the sun. It reduces the power generation capacity of the module. The power output reduces as much as by 50% if the module is not cleaned for a month. In order to regularly clean the dust, a sun tracking-cum-cleaning system has been designed, which not only tracks the sun but also cleans the modules automatically. This automated system is implemented using 8051 microcontroller which controls the stepper motor coupled with the gear box (40:1 ratio).This mechanism does not require any sensor or synchronization for tracking the sun. While for cleaning the PV modules, a mechanism consists of a sliding brushes has been developed. In this mechanism, the solar panels make a rotation of 360° in a day, which results in sliding of cleaning brushes twice over the PV modules. In terms of daily energy generation, the presented tracking-cum-cleaning scheme provides about 30% more energy output as compared to the flat PV module (module kept stationary on ground) and about 15% more energy output as compared to PV module with single axis tracking. The implementation and working of 360o sun tracking system with automatic cleaning is described in this paper.
Droplet-Phase Synthesis of Nanoparticle Aerosol Lipid Matrices with Controlled Properties (2011)

Nanoparticle lipidmatrices are being recently explored for controlled drug delivery applications. The degree of crystallinity of the lipid matrix governs drug loading capacity and release rates. Current methods of preparing nanoparticle lipid matrices, like high-pressure homogenization and solvent-emulsification evaporation, offer limited or poor control over lipid crystallinity. The present work explores a droplet-phase aerosol synthesis method to prepare nanoparticle aerosol lipid matrices (NALM). Control of evaporation rate was used to achieve control over crystallinity of NALM. NALM were synthesized in an aerosol reactor using precursor solutions of stearic acid in organic solvents with widely different vapour pressures, resulting in different rates of evaporation. Mean mobility diameter, measured using a scanning mobility particle sizer (SMPS), ranged from 94-127 nm, with a unimodal distribution and geometric standard deviation of 1.7-1.9. Aerodynamic diameters measured using gravimetric analysis of samples collected in a micro-orifice cascade impactor, ranged from 423-608 nm. Relatively higher peak intensities and peak areas in X-ray diffractograms, and higher melting enthalpies in the differential scanning calorimetry (DSC) thermograms were obtained for NALM synthesized under lower evaporation rates, using lower vapour pressure solvents, similar to that of bulk stearic acid. In contrast, NALM synthesized at higher evaporation rates, using higher vapour pressure solvents consistently showed a lower degree of crystallinity, evidenced by blunt X-ray diffraction peaks and lower melting enthalpies in DSC analysis. These results suggest the formation of non-equilibrium crystal structures within NALM, under the influence of faster evaporation rates, leading to a lower degree of crystallinity. The work demonstrates proof of concept of droplet-phase aerosol synthesis for preparing nanoparticle lipid matrices and for achieving control over their crystallinity.
Alignment mark detection in CMOS materials with SCALPEL e-beam lithography (1999)

A manufacturable process for fabricating alignment marks that are compatible the SCALPEL lithography system is described. The marks were fabricated in a SiO<SUB>2</SUB>/WSi<SUB>2</SUB> structure using SCALPEL lithography and plasma processing. The positions of the marks were detected through e-beam resist in the SCALPEL proof of lithography (SPOL) tool by scanning the image of the corresponding mask mark over the wafer mark and detecting the backscattered electron (BSE) signal. Scans of 1 micrometers line-space patterns yielded mark positions that were repeatable within 20 nm 3(sigma) with a dose of 4 (mu) C/cm<SUP>2</SUP> and signal-to-noise of 32 dB. An analysis shows that the measured repeatability is consistent with a random noise limited response combined with SPOL machine factors. By using a digitally sequenced mark pattern, the capture range of the mark detection was increased to 13 micrometers while maintaining 35 nm 3(sigma) precision. Further improvements in mark detection repeatability are expected when the SCALPEL electron optics is fully optimized.
Twin-tub CMOS - A technology for VLSI circuits (1980)

CMOS technology has been developed through several generations of design rules with an n-type substrate (where p-channel transistors were formed) and with a p-tub implanted and diffused region (where n-channel transistors were formed). In order to enable a separate optimization of both transistors and to utilize the dopant control available with implanted layers, a two-tub approach was adopted. Utilizing lightly doped epi on an n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> substrate (for latch-up protection), nitride-masked self-aligned tubs, 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">16</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> surface doping and 600Å gate oxides, an 8-mask CMOS process (named 'Twin-Tub") was formulated. The combination of n on n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> epi and careful I/O layout renders the circuits latch-up free. Novel aspects of the process, the devices it produces and finally the resultant circuit performance are herein described.