gebhart/patrepeval huggingface dataset:
Design, Synthesis, and Biological Features of Platinum(II) Complexes with Rigid Steric Hindrance (2016)

A series of platinum(II) complexes, with N-monosubstituted 1R,2R-diaminocyclohexane bearing methoxy-substituted benzyl groups as carrier ligands, were designed and synthesized. The newly prepared compounds, with chloride anions as leaving groups, were found to be very active against the tested cancer cell lines, including a cisplatin-resistant cell line. Despite their efficacy against tumor cells, they also showed low toxicity to a human normal liver cell line. Among them, complex 1 had superior cytotoxic activity against A549, HCT-116, MCF-7, SGC7901, and SGC7901/CDDP cancer cell lines. The DNA binding assay is of further special interest, as an unusual monofunctional binding mode was found, due to the introduction of a rigid substituted aromatic ring in the 1R,2R-diaminocyclohexane framework as steric hindrance. The linkage of complex 1 with DNA was stable and insensitive to nucleophilic attack. Moreover, studies including cellular uptake, gel electrophoresis, apoptosis and cell cycle, and Western blot analysis have provided insight into the high potency of this compound.
Propagation of Human Hepatitis A Virus in Cell Culture in Vitro (1979)

Human hepatitis A virus was reliably and repeatedly propagated in primary explant cell cultures of marmoset livers and in the normal fetal rhesus kidney cell line (FRhK6). Identity of virus was established in immunofluorescence, immunofluorescence blockade, serum neutralization, immune adherence, radioimmunoassay, immune electron microscopy, and marmoset inoculation tests. The virus propagated to greatest extent in FRhK6 cells. No cytopathology was observed. These studies represent the first reliable propagation of human hepatitis A virus in vitro and point the way to the eventual means for detection and quantification of live virus in vitro and of production in cell culture of virus for diagnostic antigen and vaccine preparation.
Analysis of DNA polymorphism haplotypes linked to the cystic fibrosis locus in North American black and Caucasian families supports the existence of multiple mutations of the cystic fibrosis gene. (1989)

Strong linkage disequilibrium (LD) was found between DNA marker XV2c and the cystic fibrosis (CF) locus (delta = 0.46) and between DNA marker KM19 and CF (delta = 0.67) in 157 CF and 138 normal chromosomes from U.S. Caucasians. DNA haplotypes with nine polymorphic sites were created in 54 Caucasian families. There is a strong LD between the haplotypes and the presence of the mutant CF genes. This implies that the DNA polymorphisms examined are close to the CF gene and that one mutation of the CF gene predominates in the Caucasian population. Haplotype analysis can also be used to refine estimates of CF carrier risk in Caucasians. Data for XV2c and MET markers in 16 American black patients and their families revealed a different haplotype distribution and LD pattern with the CF locus. These data suggest that racial admixture alone does not explain the occurrence of CF in American blacks and that multiple alleles of the CF gene may exist in this population.
Comparative Transient Stability Assessment of Droop and Dispatchable Virtual Oscillator Controlled Grid-Connected Inverters (2020)

With the increasing integration of power electronics interfaced distributed generators, transient stability assessment of grid-connected inverters subjected to large grid disturbances is of vital importance for the secure and resilient operation of the power grid. Dispatchable virtual oscillator control (dVOC) is an emerging approach to implement nonlinear control of grid-forming inverters. Through coordinate transformation, a simple first-order nonlinear power angle dynamic equation is uncovered from the complex oscillator dynamics. Furthermore, this article proposes a concise and straightforward graphical approach to assess transient stability of dVOC using vector field on the circle. To provide a more in-depth analysis, a complete large-signal model is derived and the impact of dVOC voltage amplitude dynamics is analyzed. For comparison, transient stability of the currently prevalent droop control is also assessed using phase portraits. Salient transient stability features of dVOC and droop control during grid faults are summarized and compared. The theoretical analysis is validated by controller hardware-in-the-loop testbed using industry-grade hardware.
Automated Discovery of Network Cameras in Heterogeneous Web Pages (2021)

Reduction in the cost of Network Cameras along with a rise in connectivity enables entities all around the world to deploy vast arrays of camera networks. Network cameras offer real-time visual data that can be used for studying traffic patterns, emergency response, security, and other applications. Although many sources of Network Camera data are available, collecting the data remains difficult due to variations in programming interface and website structures. Previous solutions rely on manually parsing the target website, taking many hours to complete. We create a general and automated solution for aggregating Network Camera data spread across thousands of uniquely structured web pages. We analyze heterogeneous web page structures and identify common characteristics among 73 sample Network Camera websites (each website has multiple web pages). These characteristics are then used to build an automated camera discovery module that crawls and aggregates Network Camera data. Our system successfully extracts 57,364 Network Cameras from 237,257 unique web pages.
<title>Explosives detection by nuclear quadrupole resonance (NQR)</title> (1994)

Pure nuclear quadrupole resonance (NQR) of <SUP>14</SUP>N nuclei is quite promising as a method for detecting explosives such as RDX and contraband narcotics such as cocaine and heroin in quantities of interest. Pure NQR is conducted without an external applied magnetic field, so potential concerns about damage to magnetically encoded data or exposure of personnel to large magnetic fields are not relevant. Because NQR frequencies of different compounds are quite distinct, we do not encounter false alarms from the NQR signals of other benign materials. We have constructed a laboratory prototype NQR explosives detector which interrogates a volume of 300 liters (10 ft<SUP>3</SUP>). This paper presents abbreviated results from a demonstration of the laboratory prototype NQR explosives detector conducted at the Federal Aviation Administration Technical Center in May 1994 on RDX-based explosives.
Discovery and Development of an Efficient Process to Atovaquone (2012)

The discovery and development of an efficient and more sustainable manufacturing route to the anti-pneumocystic agent atovaquone (2-((1R,4R)-4-(4-chlorophenyl)cyclohexyl)-3-hydroxynaphthalene-1,4-dione) 1 is described. The existing commercial route to atovaquone delivers a poor yield of product and uses expensive reagents. The new synthesis commences with readily available phthalic anhydride, which is converted to 1,4-isochromandione 5 and then to atovaquone 1 by reaction with 4-(4-chlorophenyl)cyclohexanecarboxylic acid 3 using key bromination, Rosenmund reduction, and rearrangement chemistries. Downstream processing to atovaquone is both high yielding and robust, and the resulting process has been demonstrated on 200-kg scale. The process is simple, uses cheap raw materials, and is more sustainable in that it avoids low-yielding silver-promoted chemistry and isomerisation procedures. It includes a robust, facile, and highly efficient procedure to 1,4-isochromandione 5, and routes to 4-(4-chlorophenyl)cyclohexanecarboxaldehyde 9 have also been developed, including a Rosenmund method that was demonstrated on pilot-plant scale. Also discussed are the route-derived impurities and processing amendments to control their formation.
A 2um diameter, 9hz dark count, single photon avalanche diode in 130nm cmos technology (2010)

We report a CMOS single photon avalanche diode (SPAD) with a 2um active diameter, 9Hz dark count rate at 20°C, photon detection efficiency peak of 14% at 500nm, implemented in a 130nm process technology. The implicit guard ring structure relies on retrograde well doping and overcomes a key problem in scaling SPAD devices to small dimensions. TCAD-based device simulations point the way to high resolution, high fill-factor single photon imaging.
A New Approach for High Data Rate Relay Transmissions using Multiple Antennas (2007)

Herein, we present a novel approach for high data rate transmission in a wireless relay network. The system include a source, a destination and multiple relays. All nodes are equipped with multiple antennas. A half-duplex transmission protocol and a decode-forward transmission mode are deployed in the system. Our approach splits the data at the source into multiple independent data streams, and send them to the destination via some selected relays at the same time. The relays are selected using an opportunistic approach based on spatially decomposing the channels and accessing the best modes. Simulation results show the benefits of our technique, particularly with correlated channels.
Expression of the Japanese oak silkworm <i>Antheraea yamamai</i> fibroin gene in the domesticated silkworm <i>Bombyx mori</i> (2009)

Abstract To understand the evolutionary conservation of the gene expression mechanism and secretion machinery between Antheraea and Bombyx fibroins, we introduced the genomic A. yamamai fibroin gene into the domesticated silkworm, B. mori . The spliced A. yamamai fibroin mRNA appeared only in the posterior region of the silk gland of the transgenic silkworm, suggesting that the functions of the fibroin promoter region and the splicing machinery are conserved between these two species. The A. yamamai fibroin protein was detected in the lumen of the silk gland of the transgenic silkworm, albeit at lower levels compared with the B. mori ‐type fibroin. We found a strong degeneration of the posterior region of the silk gland of the transgenic silkworm. As a result, the cocoon shell weight was much lower in the transgenic silkworm than in the non‐transgenic line. These results indicate that the promoter function and splicing machinery are well conserved between A. yamamai and B. mori but that the secretion mechanism of fibroin is diversified between the two.
Design, synthesis and P-gp induction activity of aryl phosphonate esters: identification of tetraethyl-2-phenylethene-1,1-diyldiphosphonate as an orally bioavailable P-gp inducer (2016)

The P-gp induction activity of SR12813 and its analogs has been reported.
Direct feed-forward scheme for frequency combs with arbitrary offset and shot-noise limited phase noise (2010)

We propose and demonstrate a novel feed-forward technique for stabilizing the carrier-envelope-offset frequency of a mode-locked laser at unprecedented residual noise levels. This method allows for comb synthesis at arbitrary offset frequencies, including zero offset.
Genotyping of the CCR5 Chemokine Receptor by Isothermal NASBA Amplification and Differential Probe Hybridization (1999)

The human CCR5 chemokine receptor functions as a coreceptor with CD4 for infection by macrophage-tropic isolates of human immunodeficiency virus type 1 (HIV-1). A mutated CCR5 allele which encodes a protein that does not function as a coreceptor for HIV-1 has been identified. Thus, expression of the wild-type and/or mutation allele is relevant to determining the infectability of patient peripheral blood mononuclear cells (PBMC) and affects disease progression in vivo. We developed a qualitative CCR5 genotyping assay using NASBA, an isothermal nucleic acid amplification technology. The method involves three enzymes and two oligonucleotides and targets the CCR5 mRNA, which is expressed in PBMC at a copy number higher than 2, the number of copies of DNA present encoding the gene. The single oligonucleotide set amplifies both alleles, and genotyping is achieved by separate hybridizations of wild-type- and mutation-specific probes directly to the single-stranded RNA amplification product. Assay sensitivity and specificity were demonstrated with RNAs produced in vitro from plasmid clones bearing the DNA encoding each allele. No detectable cross-reactivity between wild-type and mutation probes was found, and 50 copies of each allele were readily detectable. Analysis of patient samples found that 20% were heterozygous and 1% were homozygous for the CCR5 mutation. Thus, NASBA is a sensitive and specific means of rapidly determining CCR5 genotype and provides several technical advantages over alternative assay systems.
Sophorolipids: Microbial Synthesis and Application (2014)

Sophorolipids are glycolipidic biosurfactants extracellularly produced by several yeast species. Owing to the nonpathogenic character of the production host and the high yields, there is quite some commercial interest in these molecules. Indeed, to date sophorolipids are available in the market and nd applications in real-life products. Further research is currently being conducted in order to broaden their application range, either by evaluating their behavior in new applications or by modifying the sophorolipid chemical structure.
Genetic and Histopathologic Evaluation of<i>BRCA1</i>and<i>BRCA2</i>DNA Sequence Variants of Unknown Clinical Significance (2006)

Classification of rare missense variants as neutral or disease causing is a challenge and has important implications for genetic counseling. A multifactorial likelihood model for classification of unclassified variants in BRCA1 and BRCA2 has previously been developed, which uses data on co-occurrence of the unclassified variant with pathogenic mutations in the same gene, cosegregation of the unclassified variant with affected status, and Grantham analysis of the fit between the missense substitution and the evolutionary range of variation observed at its position in the protein. We have further developed this model to take into account relevant features of BRCA1- and BRCA2-associated tumors, such as the characteristic histopathology and immunochemical profiles associated with pathogenic mutations in BRCA1, and the fact that approximately 80% of tumors from BRCA1 and BRCA2 carriers undergo inactivation of the wild-type allele by loss of heterozygosity. We examined 10 BRCA1 and 15 BRCA2 unclassified variants identified in Australian, multiple-case breast cancer families. By a combination of genetic, in silico, and histopathologic analyses, we were able to classify one BRCA1 variant as pathogenic and six BRCA1 and seven BRCA2 variants as neutral. Five of these neutral variants were also found in at least 1 of 180 healthy controls, suggesting that screening a large number of appropriate controls might be a useful adjunct to other methods for evaluation of unclassified variants.
An improved methodology for sub‐salt velocity analysis (2006)

We have developed an improved methodology to obtain a velocity model that enhances the quality of the sub‐salt image. Using this methodology, we can delineate the bottom of a salt body and efficiently update velocities below the salt body. First, seismic data are migrated to the bottom of the salt body using the best model available for overburden media above the salt body. Then below the bottom, seismic data are migrated several times using a suite of models generated by scaling the model with a factor γ (gamma). Using a proprietary interactive graphic tool, we pick γ values which give the best migration results. The picking values are used to update the velocity model by simple but practical algorithms. Then, we test the proposed method on both synthetic and field data sets. The results verify that the proposed methods generate a better velocity model which significantly improves the image.
Ultra-narrow linewidth quantum dot coherent comb lasers (2018)

We have developed a secondary-cavity self-injection feedback locking system to simultaneously reduce the linewidths of over 39 filtered individual channels of an InAs/InP quantum-dot coherent comb laser from a few MHz to less than 200 kHz.
Laboratory study of beam quality in an image-rotating optical parametric oscillators (2002)

We performed laboratory and numerical studies of optical parametric oscillators with 90° intracavity image rotation. We found the signal beam was more symmetric than that from comparable cavities without image rotation, and it had low values of M2.
Comprehensive transcriptomic analysis of immune checkpoint markers in a pancancer cohort: Implications for response and resistance. (2022)

2555 Background: Although immune checkpoint blockade (ICB) has revolutionized cancer treatment, not all patients with cancer benefit from ICB. One possible explanation for poor responders/resistance is the variable expression level of the target molecules (e.g., PD-1 and PD-L1) in the tumor microenvironment. There are recent or ongoing trials targeting variable pathways for immune evasion (e.g., LAG3 or IDO1). It is therefore of interest to know the expression levels related to variable immune checkpoints so that clinical trials can focus on the patients who can benefit from the cognate treatment. Methods: Overall, 514 patients with various solid tumors seen at the University of San Diego, Moores Center for Personalized Cancer Therapy were analyzed. The expression levels of checkpoint markers (ADORA2A, BTLA, CD276, CTLA4, IDO1, IDO2, LAG3, NOS2, PD-1, PD-L1, PD-L2, PVR, TIGIT, TIM3, VISTA, and VTCN) in the tumor samples were measured through RNA sequencing and normalized to internal housekeeping gene profiles, and ranked from 0 to 100 percentile based on a reference population. The expressions of each checkpoint marker were correlated with cancer types, microsatellite instability (MSI), tumor mutational burden (TMB), and programmed death-ligand 1 (PD-L1) status on immunohistochemistry. Results: In this cohort, 60% were female, median age of 60, and included 30 different tumor types, with colorectal cancer being the most common (27%). The rank values of all checkpoint markers were distributed broadly from 0 to 99 or 100. CD276 and NOS2 had the highest (68 th percentile) and lowest (13.5 percentile) median rank values, respectively. When rank values were categorized to “Low” (0-24), “Intermediate” (25-74), and “High” (75-100), 41.6% of patients showed high expression of CD276 while only 13% showed high expression of PD-L1. Each patient had a distinctive protfolio of the categorical expression levels of 16 checkpoint markers. Several checkpoint markers, especially NOS2, showed a significant correlation with cancer type. (median rank values in colorectal, stomach, pancreatic, and breast cancer were 79, 76, 5 and 0 respectively, p < 0.001) Five markers (IDO1, LAG3, PD-1, PD-L1, and TIGIT) showed significant correlation with MSI, while seven markers (CTLA4, IDO1, LAG3, PD-1, PD-L1, PD-L2, and TIGIT) were significantly associated with positive PD-L1 status. However, no significant association was seen based on TMB or tissue-specific grouping of patients. Conclusions: The expression of immune checkpoint markers varies from patient to patient, though transcript expression of several markers correlates with cancer type, MSI, and PD-L1 status. Clinical trials with patient selection based on the expression level of checkpoint markers matched to the corresponding ICB drug are warranted.
Detection of Streptococcus equi subspecies equi using a triplex qPCR assay (2012)

Genome sequencing data for Streptococcus equi subspecies equi and zooepidemicus were used to develop a novel diagnostic triplex quantitative PCR (qPCR) assay targeting two genes specific to S. equi (eqbE and SEQ2190) and a unique 100 base pair control DNA sequence (SZIC) inserted into the SZO07770 pseudogene of S. zooepidemicus strain H70. This triplex strangles qPCR assay can provide results within 2h of sample receipt, has an overall sensitivity of 93.9% and specificity of 96.6% relative to the eqbE singlex assay and detects S. equi at levels below the threshold of the culture assay, even in the presence of contaminating bacteria.
Studies of acid diffusion in low Ea chemically amplified photoresists (2005)

Critical lithographic dimensions will soon place particularly severe demands on the performance of chemically amplified (CA) resists. Although Extreme Ultraviolet (EUV) and 193 nm (immersion interferometric) lithographic results have demonstrated half pitch imaging down to 35 nm there is nonetheless a concern that image blur due to acid diffusion will begin to seriously impact the utility of CA photoresists. Previously we demonstrated that low activation energy resists and E-Beam lithography can be used to print line/space arrays with resolution approaching 20 nm. We described the factors impacting the reactivity of ketal/pHOST based resists and compared the attainable resolution under different processing conditions. In this report we describe studies on acid diffusion emphasizing the role of water in low Ea systems. We also discuss methods for the control of water absorption in low Ea resists.
Truly bistable twisted nematic liquid crystal display using photoalignment technology (2003)

Truly bistable twisted nematic liquid crystal display has been fabricated using photoalignment. This display can be switched between the −22.5° and 157.5° twist states by breaking the anchoring condition on one of the substrates. The application of a photoalignable polymer SDA-1 was able to achieve the weak anchoring energy necessary for switching. Both theoretical and experimental results show that this mode has excellent contrast ratio and wide viewing angles.
Development of Highly Selective 1,2,3-Triazole-containing Peptidic Polo-like Kinase 1 Polo-box Domain-binding Inhibitors (2019)

Members of the polo-like kinase (Plk) family of serine/threonine protein kinases play crucial roles in cell cycle regulation and proliferation. Of the five Plks (Plk1-5), Plk1 is recognized as an anticancer drug target. Plk1 contains multiple structural components that are important for its proper biological function. These include an N-terminal catalytic domain and a C-terminal non-catalytic polo-box domain (PBD). The PBD binds to phosphothreonine (pT) and phosphoserine-containing sequences. Blocking PBD-dependent interactions offers a potential means of down-regulating Plk1 function that is distinct from targeting its ATP-binding site. Previously, we demonstrated by tethering alkylphenyl chains from the <i>N</i>(π)-position of the His residue in the 5-mer PLHSpT, that we were able to access a hydrophobic "cryptic" binding pocket on the surface of the PBD, and in so doing enhance binding affinities by approximately 1000-fold. More recently, we optimized these PBD-ligand interactions using an oxime ligation-based strategy. Herein, using azide-alkyne cycloaddition reactions, we explore new triazole-containing PBD-binding antagonists. Some of these ligands retain the high PBD-binding affinity of the parent peptide, while showing desirable enhanced selectivity for the PBD of Plk1 relative to the PBDs of Plk2 and Plk3.
ChemInform Abstract: Organoboranes. Part 48. Improved Procedures for the Preparation of Boronic and Borinic Esters. (1987)

Abstract Two improved procedures of liberating boronic and borinic esters such as (I) from their "ate" complexes, free of isopropyl alcohol, are developed.