gebhart/patrepeval huggingface dataset:
Field Investigation Of Salt Transport Processes Using .Resistivity/Ip Imaging (1999)

Two examples of the use of combined resistivity/induced polarization (IP) monitoring of salt&lt;br&gt;transport under natural hydraulic loads are presented. Previous workers have performed electrical&lt;br&gt;monitoring of the transport of a tracer artificially injected into the subsurface. The detection of&lt;br&gt;tracer transport due to natural hydraulic processes is a more difficult goal as neither the hydraulic&lt;br&gt;load nor the resistivity contrast can be controlled. Tide-induced salt transport at the saltwaterfreshwater&lt;br&gt;interface was investigated in the first study. 2D resistivity and IP models resolved the&lt;br&gt;structure of the interface. The IP modeling provided greater clarity of the subsurface&lt;br&gt;hydrology/geology than the resistivity modeling alone. Modeling of electrical changes over a&lt;br&gt;tidal cycle revealed resistivity increases in the near surface and at depth, 5-l 5 m up-beach of the&lt;br&gt;high tide mark. The results indicate a phase lag between the subsurface hydrological response&lt;br&gt;and the tidal cycle. In the second study, salt transport from the site of an old road-salt storage pile&lt;br&gt;was investigated. The hydraulic mechanism was natural recharge events that occurred over a&lt;br&gt;four-month period. 2D conductivity and IP models resolved the subsurface distribution of salt,&lt;br&gt;initially identified from an EM3 1 survey. Modeling of resistivity change on lines spaced 33.5 m&lt;br&gt;apart revealed changes at the location of salt contamination. The changes on each line appear&lt;br&gt;closely coupled and correlate with the recharge pattern over the monitoring period. The studies&lt;br&gt;indicate that salt transport occurring under natural hydraulic conditions can be detected with&lt;br&gt;resistivity, and to some extent, IP.
Broadband Determination of Biodiesel Content in Petroleum Diesel Blends by Terahertz Time Domain Spectroscopy (2021)

The biodiesel content in petroleum diesel-biodiesel blends is determined using broadband terahertz time-domain spectroscopy. We model the spectra of the blend components based on the nonpolar characteristics of the samples. The biodiesel content in diesel is determined from the coefficients that best fit the measured spectra to the optimal linear combination of the model for each individual component (pure diesel and pure biodiesel). This method proves to be valid for real-time applications. A simpler approach based on the maximum observed dispersion is also demonstrated to be a distinctive characteristic of a given blend.
Abstract PR07: Crystal structure of K-Ras G12C bound to an active site inhibitor (2014)

Abstract Activating K-Ras mutations are common oncogenic events in many cancers but effective direct-acting inhibitors have not been developed. Targeting the nucleotide binding site of GTPases like K-Ras has long been dismissed as a possibility because of the high affinity of these proteins for their natural ligands GTP and GDP. We previously reported the synthesis of a GDP analogue, SML-8-73-1, and a prodrug derivative, SML-10-70-1, which are selective, direct-acting covalent inhibitors of the K-Ras G12C mutant relative to wild-type Ras. Biochemical and biophysical measurements suggested that modification of K-Ras with SML-8-73-1 renders the protein in an inactive state. Here we report a crystal structure of K-Ras G12C labeled with SML-8-73-1. The structure reveals that when bound to SML-8-73-1, K-Ras presents in an inactive conformation. This first-in-class covalent K-Ras inhibitor suggests that irreversible targeting of the K-Ras guanine-nucleotide binding site is a viable therapeutic strategy for inhibition of Ras signaling. This abstract is also presented as Poster B54. Citation Format: John Hunter, Sang Min Lim, Scott B. Ficcarro, Hwan Geun Choi, Deepak Gurbani, Ting Xie, Jarrod A. Marto, Nathanael S. Gray, Ken Westover. Crystal structure of K-Ras G12C bound to an active site inhibitor. [abstract]. In: Proceedings of the AACR Special Conference on RAS Oncogenes: From Biology to Therapy; Feb 24-27, 2014; Lake Buena Vista, FL. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(12 Suppl):Abstract nr PR07. doi: 10.1158/1557-3125.RASONC14-PR07
ChemInform Abstract: CATALYST PREPARATION PROCEDURE PROBED BY EXAFS SPECTROSCOPY. 2. COBALT ON TITANIA (1984)

Abstract Mit Hilfe von EXAFS‐Untersuchungen in Kombination mit Elektronenmikroskopie, NMR und Röntgen‐Beugung werden die Umgebungen der Co‐ Atome während jedes Elementarschrittes der Darstellungsprozedur für Co/ TiO 2 ‐Trägerkatalysatoren sondiert.
Diazine Indole Acetic Acids as Potent, Selective, and Orally Bioavailable Antagonists of Chemoattractant Receptor Homologous Molecule Expressed on Th2 Cells (CRTH2) for the Treatment of Allergic Inflammatory Diseases (2012)

New classes of CRTH2 antagonists, the pyridazine linker containing indole acetic acids, are described. The initial hit 1 had good potency but poor permeability, metabolic stability, and PK. Initial optimization led to compounds of type 2 with low oxidative metabolism but poor oral bioavailability. Poor permeability was identified as a liability for these compounds. Addition of a linker between the indole and diazine moieties afforded a series with good potency, low rates of metabolism, moderate permeability, and good oral bioavailability in rodents. 32 was identified as the development track candidate. It was potent in cell based, binding, and whole blood assays and exhibited good PK profile. It was efficacious in mouse models of contact hypersensitivity (1 mg/kg b.i.d.) and house dust (20 mg/kg q.d.) when dosed orally. In sheep asthma, administration at 1 mg/kg iv completely blocked the LAR and AHR and attenuated the EAR phase.
Structure-based design, synthesis, and profiling of a β-tryptase inhibitor with a spiro-piperidineamide scaffold, benzylamine P1 group, and a substituted indole P4 group (2011)

A β-tryptase inhibitor with a basic benzylamine P1 group, a substituted indole P4 group, and a spiro-piperidineamide scaffold linker was designed, synthesized, and tested for its β-tryptase potency and ADMET properties. Comparing to its non-spiro analogs, the inhibitor with a spiro-piperidineamide scaffold demonstrated superior metabolic stability in human liver microsome and against semicarbazide-sensitive amine oxidase (SSAO).
Approach to classification of blurred patternswith same symmetry (1999)

An approach is proposed based on invariants extracted from projection maps to classify blurred patterns with the same symmetry. Results of simple, error, and true probabilities for classification are shown. Finally, a statistical curve to fit the integrated true probability is given.
D-106 Tyrosine Sulfation in the Second Variable Domain (V2) of gp120 Regulates HIV-1 Sensitivity to Neutralization (2014)

The native HIV-1 envelope spike adopts a cryptic conformation that protects conserved neutralization epitopes from antibody recognition. We recently documented the presence of sulfated tyrosines within the second variable domain (V2) of gp120, which contribute to stabilizing the intramolecular interaction between V2 and V3, shifting the conformational equilibrium of the envelope toward the closed trimeric state. To elucidate the functional relevance of V2 sulfation, we investigated the effects of modulating tyrosine sulfation on HIV-1 neutralization by a wide panel of monoclonal and polyclonal antibodies of well-defined specificity. Data obtained with different HIV-1 Envs demonstrated a striking dichotomous effect. Increasing the efficiency of tyrosine sulfation by overexpression of the sulfotransferase TPST2 resulted in reduced binding and neutralization by soluble CD4 and several mAbs to the CD4- and coreceptor-binding sites. However, opposite effects were seen on glycan-dependent V2 epitopes recognized by trimer-preferring antibodies such as PG9, PG16, VRC26.03, and PGT145, which showed increased binding and neutralization upon TPST2 overexpression. Likewise, polyclonal patient sera with defined neutralization fingerprints exhibited a similar discrepant behavior, with a group of CD4-like sera showing reduced neutralization upon TPST2 overexpression and a group of PG9-like sera showing the reciprocal pattern. These data suggest that V2 tyrosine sulfation acts as a neutralization switch that HIV-1 can exploit to address the escape dilemma between different families of broadly neutralizing antibodies.
Elucidation of the molecular mechanism and the efficacyin vivoof a novel 1,4‐benzoquinone that inhibits 5‐lipoxygenase (2014)

RF-Id represents a novel anti-inflammatory 1,4-benzoquinone that potently suppresses LT biosynthesis by direct inhibition of 5-LOX with effectiveness in vivo. Mechanistically, RF-Id inhibits 5-LOX in a non-redox manner by forming discrete molecular interactions within the active site of 5-LOX.
Multiplexed DNA Detection with Biobarcoded Nanoparticle Probes (2006)

Postsortierung: Ein hochselektiver Assay für den Nachweis mehrerer DNA-Zielmoleküle in Lösung wurde auf der Grundlage von Goldnanopartikeln mit Oligonucleotidreportern entwickelt. Vier solche Zielmoleküle, die zu infektiösen Viren gehören, wurden simultan und ohne enzymatische Amplifizierung in mittleren femtomolaren Konzentrationen nachgewiesen.
A New Approach Defining Angular Dmd Using Near Field Aperturing (2013)

A new technique to quantify the differential mode<br> delay (DMD) in multimode fiber (MMF) is been presented. The<br> technique measures DMD based on angular launch and<br> measurements of the difference in modal delay using variable<br> apertures at the fiber face. The result of the angular spatial filtering<br> revealed less excitation of higher order modes when the laser beam is<br> filtered at higher angles. This result would indicate that DMD<br> profiles would experience a data pattern dependency.
Endothelial Bmx tyrosine kinase activity is essential for myocardial hypertrophy and remodeling (2015)

Cardiac hypertrophy accompanies many forms of heart disease, including ischemic disease, hypertension, heart failure, and valvular disease, and it is a strong predictor of increased cardiovascular morbidity and mortality. Deletion of bone marrow kinase in chromosome X (Bmx), an arterial nonreceptor tyrosine kinase, has been shown to inhibit cardiac hypertrophy in mice. This finding raised the possibility of therapeutic use of Bmx tyrosine kinase inhibitors, which we have addressed here by analyzing cardiac hypertrophy in gene-targeted mice deficient in Bmx tyrosine kinase activity. We found that angiotensin II (Ang II)-induced cardiac hypertrophy is significantly reduced in mice deficient in Bmx and in mice with inactivated Bmx tyrosine kinase compared with WT mice. Genome-wide transcriptomic profiling showed that Bmx inactivation suppresses myocardial expression of genes related to Ang II-induced inflammatory and extracellular matrix responses whereas expression of RNAs encoding mitochondrial proteins after Ang II administration was maintained in Bmx-inactivated hearts. Very little or no Bmx mRNA was expressed in human cardiomyocytes whereas human cardiac endothelial cells expressed abundant amounts. Ang II stimulation of endothelial cells increased Bmx phosphorylation, and Bmx gene silencing inhibited downstream STAT3 signaling, which has been implicated in cardiac hypertrophy. Furthermore, activation of the mechanistic target of rapamycin complex 1 pathway by Ang II treatment was decreased in the Bmx-deficient hearts. Our results demonstrate that inhibition of the cross-talk between endothelial cells and cardiomyocytes by Bmx inactivation suppresses Ang II-induced signals for cardiac hypertrophy. These results suggest that the endothelial Bmx tyrosine kinase could provide a target to attenuate the development of cardiac hypertrophy.
Towards Autonomous Eye Surgery by Combining Deep Imitation Learning with Optimal Control (2020)

During retinal microsurgery, precise manipulation of the delicate retinal tissue is required for positive surgical outcome. However, accurate manipulation and navigation of surgical tools remain difficult due to a constrained workspace and the top-down view during the surgery, which limits the surgeon's ability to estimate depth. To alleviate such difficulty, we propose to automate the tool-navigation task by learning to predict relative goal position on the retinal surface from the current tool-tip position. Given an estimated target on the retina, we generate an optimal trajectory leading to the predicted goal while imposing safety-related physical constraints aimed to minimize tissue damage. As an extended task, we generate goal predictions to various points across the retina to localize eye geometry and further generate safe trajectories within the estimated confines. Through experiments in both simulation and with several eye phantoms, we demonstrate that our framework can permit navigation to various points on the retina within 0.089mm and 0.118mm in xy error which is less than the human's surgeon mean tremor at the tool-tip of 0.180mm. All safety constraints were fulfilled and the algorithm was robust to previously unseen eyes as well as unseen objects in the scene. Live video demonstration is available here: https://youtu.be/n5j5jCCelXk.
Heterogeneous Integration on Silicon Photonics (2018)

To enhance the functionality of the standard silicon photonics platform and to overcome its limitations, in particular for light emission, ultrafast modulation, and nonlinear applications, integration with novel materials is being investigated by several groups. In this paper, we will discuss, among others, the integration of silicon waveguides with ferroelectric materials such as lead zirconate titanate (PZT) and barium titanate (BTO), with electro-optically active polymers, with 2-D materials such as graphene and with III-V semiconductors through epitaxy. We discuss both the technology and design aspects.
Low-temperature growth of SiCAlN films of high hardness on Si(111) substrates (2001)

Thin films of metastable SiCAlN solid solution were deposited on Si(111) substrates at 550–750 °C, considerably below the miscibility gap of SiC and AlN phases at 1900 °C. Our low-temperature growth was based upon thermally activated reactions between a unimolecular precursor H3SiCN and Al atoms from an evaporative cell in a molecular-beam-epitaxy chamber. Characterization of deposited films by spectroscopic and microscopic techniques yielded near-stoichiometric composition throughout the columnar wurtzite structure with lattice parameters very close to those of 2H–SiC and hexagonal AlN. An average hardness of 25 GPa was measured for the SiCAlN films, comparable to that measured for sapphire.
Supplementary Figure Legend from Reexpression of Tumor Suppressor, sFRP1, Leads to Antitumor Synergy of Combined HDAC and Methyltransferase Inhibitors in Chemoresistant Cancers (2023)

&lt;p&gt;PDF file, 59K.&lt;/p&gt;
Evolving Transferable Pruning Functions (2021)

Channel pruning has made major headway in the design of efficient deep learning models. Conventional approaches adopt human-made pruning functions to score channels' importance for channel pruning, which requires domain knowledge and could be sub-optimal. In this work, we propose an end-to-end framework to automatically discover strong pruning metrics. Specifically, we craft a novel design space for expressing pruning functions and leverage an evolution strategy, genetic programming, to evolve high-quality and transferable pruning functions. Unlike prior methods, our approach can not only provide compact pruned networks for efficient inference, but also novel closed-form pruning metrics that are mathematically explainable and thus generalizable to different pruning tasks. The evolution is conducted on small datasets while the learned functions are transferable to larger datasets without any manual modification. Compared to direct evolution on a large dataset, our strategy shows better cost-effectiveness. When applied to more challenging datasets, different from those used in the evolution process, e.g., ILSVRC-2012, an evolved function achieves state-of-the-art pruning results.
A Selective Phosphatase of Regenerating Liver Phosphatase Inhibitor Suppresses Tumor Cell Anchorage-Independent Growth by a Novel Mechanism Involving p130Cas Cleavage (2008)

The phosphatase of regenerating liver (PRL) family, a unique class of oncogenic phosphatases, consists of three members: PRL-1, PRL-2, and PRL-3. Aberrant overexpression of PRL-3 has been found in multiple solid tumor types. Ectopic expression of PRLs in cells induces transformation, increases mobility and invasiveness, and forms experimental metastases in mice. We have now shown that small interfering RNA-mediated depletion of PRL expression in cancer cells results in the down-regulation of p130Cas phosphorylation and expression and prevents tumor cell anchorage-independent growth in soft agar. We have also identified a small molecule, 7-amino-2-phenyl-5H-thieno[3,2-c]pyridin-4-one (thienopyridone), which potently and selectively inhibits all three PRLs but not other phosphatases in vitro. The thienopyridone showed significant inhibition of tumor cell anchorage-independent growth in soft agar, induction of the p130Cas cleavage, and anoikis, a type of apoptosis that can be induced by anticancer agents via disruption of cell-matrix interaction. Unlike etoposide, thienopyridone-induced p130Cas cleavage and apoptosis were not associated with increased levels of p53 and phospho-p53 (Ser(15)), a hallmark of genotoxic drug-induced p53 pathway activation. This is the first report of a potent selective PRL inhibitor that suppresses tumor cell three-dimensional growth by a novel mechanism involving p130Cas cleavage. This study reveals a new insight into the role of PRL-3 in priming tumor progression and shows that PRL may represent an attractive target for therapeutic intervention in cancer.
Ion-beam processing for laser mirrors (1983)

The research program is directed at applying energetic ion beam technology to the problem of improving various aspects of highly reflecting laser mirrors, such as reflectivity, corrosion resistance, and threshold to laser surface damage. The ability of key heavy-ion irradiations to produce surface smoothing through radiation-enhanced surface diffusion and an improvement in optical properties is demonstrated. Effects of ion irradiation and implantation on thin highly reflecting metallic films deposited on molybdenum substrates are discussed. Nickel implantation into films of Cu, Ag, Au, and Al was done using MeV ion beams. It was observed that these films exhibited improved tarnish resistance as a consequence of the implantation. Additionally, the structural integrity and bonding of these films to the molybdenum substrate was vastly improved as a consequence of the ion irradiation.
Ultra-high efficiency photovoltaics via diffractive optics (2015)

In this presentation, I will show that planar diffractive optics can drastically increase the efficiency of photovoltaics via spectrum-splitting and concentration of sunlight. Such optics can be inexpensively manufactured to cover large areas.
FeCl3—NaI Mediated Reactions of Aryl Azides with 3,4‐Dihydro‐2H‐pyran: A Convenient Synthesis of Pyranoquinolines. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Genotypic Analyses of Shiga Toxin-Producing Escherichia coli O157 and Non-O157 Recovered from Feces of Domestic Animals on Rural Farms in Mexico (2012)

Shiga toxin-producing Escherichia coli (STEC) are zoonotic enteric pathogens associated with human gastroenteritis worldwide. Cattle and small ruminants are important animal reservoirs of STEC. The present study investigated animal reservoirs for STEC in small rural farms in the Culiacan Valley, an important agricultural region located in Northwest Mexico. A total of 240 fecal samples from domestic animals were collected from five sampling sites in the Culiacan Valley and were subjected to an enrichment protocol followed by either direct plating or immunomagnetic separation before plating on selective media. Serotype O157:H7 isolates with the virulence genes stx2, eae, and ehxA were identified in 40% (26/65) of the recovered isolates from cattle, sheep and chicken feces. Pulse-field gel electrophoresis (PFGE) analysis grouped most O157:H7 isolates into two clusters with 98.6% homology. The use of multiple-locus variable-number tandem repeat analysis (MLVA) differentiated isolates that were indistinguishable by PFGE. Analysis of the allelic diversity of MLVA loci suggested that the O157:H7 isolates from this region were highly related. In contrast to O157:H7 isolates, a greater genotypic diversity was observed in the non-O157 isolates, resulting in 23 PFGE types and 14 MLVA types. The relevant non-O157 serotypes O8:H19, O75:H8, O111:H8 and O146:H21 represented 35.4% (23/65) of the recovered isolates. In particular, 18.5% (12/65) of all the isolates were serotype O75:H8, which was the most variable serotype by both PFGE and MLVA. The non-O157 isolates were predominantly recovered from sheep and were identified to harbor either one or two stx genes. Most non-O157 isolates were ehxA-positive (86.5%, 32/37) but only 10.8% (4/37) harbored eae. These findings indicate that zoonotic STEC with genotypes associated with human illness are present in animals on small farms within rural communities in the Culiacan Valley and emphasize the need for the development of control measures to decrease risks associated with zoonotic STEC.
Ventricular Torsion and Untwisting: Further Insights into Mechanics and Timing Interdependence: A Viewpoint (2011)

Ventricular torsion and untwisting are essential for normal ventricular function and their mechanisms are related to the temporal responses of the helical and circular muscle fibers that comprise cardiac architecture. Explanation of the presystolic isovolumic contraction (IVC) period is essential for analysis of these interactions. Structural and imaging studies by magnetic resonance, speckle tracking, velocity vector encoding, and sonomicrometer crystals are described to define why and how different muscular components contract asynchronously. Mechanical and functional relationships are described for pre-systolic IVC, torsion, postejection isovolumic interval, and rapid and slow filling. Circular fibers dominate to cause pre- and posttwisting global counterclockwise and clockwise movement, and helical fibers govern torsion whereby the base rotates clockwise and apex counterclockwise; untwisting cannot begin until torsion is completed. Prolonged torsion extends into the postejection isovolumic interval and delays untwisting, and is caused by prolonged contraction of the right-handed helical arm or descending segment of the helical ventricular myocardial band that narrows the ∼80 ms "timing hiatus" between end of shortening of the descending and the ascending segment or left-handed arm of the helical muscle. Longer torsion duration by this mechanism becomes the common theme for unbalanced torsion and untwisting in diastolic dysfunction, physiological, structural, and electrical disease processes, whose management may be guided by changing the interconnected reasons for these adverse mechanical and timing factors.
A SSTDR Methodology, Implementations, and Challenges (2021)

Sequence time-domain reflectometry (STDR) and spread spectrum time-domain reflectometry (SSTDR) detect, locate, and diagnose faults in live (energized) electrical systems. In this paper, we survey the present SSTDR literature for discussions on theory, algorithms used in its analysis, and its more prominent implementations and applications. Our review includes both scientific litera-ture and selected patents. We also discuss future applications of SSTDR.