gebhart/patrepeval huggingface dataset:
Automation of sample plan creation for process model calibration (2010)

The process of preparing a sample plan for optical and resist model calibration has always been tedious. Not only because it is required to accurately represent full chip designs with countless combinations of widths, spaces and environments, but also because of the constraints imposed by metrology which may result in limiting the number of structures to be measured. Also, there are other limits on the types of these structures, and this is mainly due to the accuracy variation across different types of geometries. For instance, pitch measurements are normally more accurate than corner rounding. Thus, only certain geometrical shapes are mostly considered to create a sample plan. In addition, the time factor is becoming very crucial as we migrate from a technology node to another due to the increase in the number of development and production nodes, and the process is getting more complicated if process window aware models are to be developed in a reasonable time frame, thus there is a need for reliable methods to choose sample plans which also help reduce cycle time. In this context, an automated flow is proposed for sample plan creation. Once the illumination and film stack are defined, all the errors in the input data are fixed and sites are centered. Then, bad sites are excluded. Afterwards, the clean data are reduced based on geometrical resemblance. Also, an editable database of measurement-reliable and critical structures are provided, and their percentage in the final sample plan as well as the total number of 1D/2D samples can be predefined. It has the advantage of eliminating manual selection or filtering techniques, and it provides powerful tools for customizing the final plan, and the time needed to generate these plans is greatly reduced.
Biochemical characterization of isovaleryl-CoA dehydrogenase (LiuA) ofPseudomonas aeruginosaand the importance ofliugenes for a functional catabolic pathway of methyl-branched compounds (2008)

Growth of Pseudomonas aeruginosa on acyclic terpene alcohols (citronellol) and on other methyl-branched compounds such as leucine or isovalerate requires a functional leucine/isovalerate utilization (Liu) pathway. In this study, we investigated the liuABCDE gene cluster by insertion mutant analysis, heterologous expression of liuA in Escherichia coli and by biochemical characterization of purified LiuA protein. Mutants with insertion in any of the liu genes were unable to utilize acyclic terpenes or leucine/isovalerate and confirmed the importance of the liu genes for catabolism of methyl-branched compounds. An insertion mutant in liuA was complemented by a liuA copy in trans, indicating that possible polar downstream effects of the insertion are not essential for growth. LiuA purified from recombinant E. coli revealed acyl-CoA dehydrogenase activity with isovaleryl-CoA (KM 2.3 microM) and butyryl-CoA as substrates. Other acyl-CoA compounds such as isobutyryl-CoA, 3-hydroxybutyryl-CoA, octanoyl-CoA, citronellyl-CoA or 5-methyl-hex-4-enoyl-CoA were not utilized. Experimental evidence for expression and essential functions of other Liu proteins in metabolism of methyl-branched compounds is provided.
A Single Cell Level Based Method for Copy Number Variation Analysis by Low Coverage Massively Parallel Sequencing (2013)

Copy number variations (CNVs), a common genomic mutation associated with various diseases, are important in research and clinical applications. Whole genome amplification (WGA) and massively parallel sequencing have been applied to single cell CNVs analysis, which provides new insight for the fields of biology and medicine. However, the WGA-induced bias significantly limits sensitivity and specificity for CNVs detection. Addressing these limitations, we developed a practical bioinformatic methodology for CNVs detection at the single cell level using low coverage massively parallel sequencing. This method consists of GC correction for WGA-induced bias removal, binary segmentation algorithm for locating CNVs breakpoints, and dynamic threshold determination for final signals filtering. Afterwards, we evaluated our method with seven test samples using low coverage sequencing (4∼9.5%). Four single-cell samples from peripheral blood, whose karyotypes were confirmed by whole genome sequencing analysis, were acquired. Three other test samples derived from blastocysts whose karyotypes were confirmed by SNP-array analysis were also recruited. The detection results for CNVs of larger than 1 Mb were highly consistent with confirmed results reaching 99.63% sensitivity and 97.71% specificity at base-pair level. Our study demonstrates the potential to overcome WGA-bias and to detect CNVs (>1 Mb) at the single cell level through low coverage massively parallel sequencing. It highlights the potential for CNVs research on single cells or limited DNA samples and may prove as a promising tool for research and clinical applications, such as pre-implantation genetic diagnosis/screening, fetal nucleated red blood cells research and cancer heterogeneity analysis.
Structure and Electronic Properties of Carbon Nanotubes (2000)

Scanning tunneling microscopy, spectroscopy, and tight-binding calculations have been used to elucidate the unique structural and electronic properties of single-walled carbon nanotubes (SWNTs). First, the unique relationship between SWNT atomic structure and electronic properties, and the richness of structures observed in both purified and chemically etched nanotube samples are discussed. Second, a more detailed picture of SWNT electronic band structure is developed and compared with experimental tunneling spectroscopy measurements. Third, experimental and theoretical investigations of localized structures, such as bends and ends in nanotubes, are presented. Last, quantum size effects in nanotubes with lengths approaching large molecules are discussed. The implications of these studies and important future directions are considered.
Medicinal chemistry of the vanilloid (Capsaicin) TRPV1 receptor: current knowledge and future perspectives (2007)

Abstract In peripheral sensory neurons, the vanilloid receptor TRPV1 (transient receptor potential vanilloid subfamily, member 1) functions as a molecular integrator of painful stimuli, including those mediated by capsaicin, acid, and heat. Antagonist blockade of TRPV1 activation is under investigation by several pharmaceutical companies in an effort to identify novel agents for pain management. TRPV1 is also expressed, albeit at lower levels, in the brain and in non‐neuronal tissues, where its function(s) remains elusive. The contribution of TRPV1 receptor activity to physiological reflexes and disease states is complex and is only beginning to be understood. Consequently, the resultant effects of TRPV1 antagonists on the body may be unforeseen. Indeed, clinical trials with a number of TRPV1 antagonists were recently terminated due to their marked hyperthermic activity. In this review article, the medicinal chemistry of TRPV1 antagonists is discussed inasmuch as it relates to the efficacy, safety, tolerability and potential side effects of these compounds. In addition, the available information on the current status of the clinical trials with TRPV1 antagonists is summarized. Drug Dev Res 68:477–497, 2007. © 2008 Wiley‐Liss, Inc.
Peripheral blood mononuclear phagocytes mediate dissemination of murine cytomegalovirus (1994)

Cytomegalovirus is transmitted with blood and organs from seropositive individuals, although the particular leukocyte population harboring latent or persistent virus remains poorly characterized. Murine cytomegalovirus, tagged with the Escherichia coli lacZ gene, was used to identify cells in which virus replicates during acute infection of immunocompetent mice. Recombinant murine cytomegaloviruses, RM461, RM460, and RM427, were constructed to express beta-galactosidase under control of the human cytomegalovirus ie1/ie2 promoter/enhancer. The lacZ gene was inserted between the ie2 and sgg1 genes in RM461 and RM460, disrupting a 0.85-kb late transcript that was found to be dispensable for replication in cultured cells as well as for infection of mice. In BALB/c mice, lacZ-tagged and wild-type viruses exhibited a similar 50% lethal dose and all had the capacity to latently infect the spleen. Peripheral blood mononuclear phagocytes were the major infected leukocyte cell type, as demonstrated by the ability of infected cells to adhere to glass and to phagocytize latex beads; however, these cells did not exhibit typical monocyte markers. Plaque assay for virus and 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside (X-Gal) staining of frozen sections of organs from infected mice revealed that the major target organs included the spleen, adrenal glands, liver, and salivary glands, although tissues as diverse as brown fat and lungs were also involved. Individual blue-staining cells were readily identified in all infected tissues. These studies identified a mononuclear phagocyte, possibly a macrophage or dendritic cell precursor, as the vehicle of virus dissemination during acute infection, and demonstrate the utility of using lacZ-tagged murine cytomegalovirus for tropism, pathogenesis, and latency studies.
High-throughput molecular analysis of urine sediment for the detection of bladder cancer by high-density single-nucleotide polymorphism array. (2003)

The detection of urothelial malignancies remains challenging. The majority of patients diagnosed with bladder cancer require life-long surveillance for disease recurrence. Monitoring strategies rely predominantly on invasive endoscopic techniques, which are inconvenient and uncomfortable. Multiple in vitro diagnostic technologies have been developed to supplant the contemporary standard of care. The U.S. Food and Drug Administration has approved several assays, but [because of inferior performance characteristics (low sensitivity and specificity)] these tests have not made a significant impact on practice, to date. We sought to develop a test for bladder cancer with better performance characterization detection based on a novel molecular approach. Matched urine and peripheral blood lymphocyte samples were obtained before surgery from 31 patients with bladder cancer (10 pTa, 4 pT1, and 17 pT2>or). DNA from these samples was subjected to allelic imbalance analysis using HuSNP chips and was validated in parallel with microsatellite analysis for loss of heterozygosity and microsatellite instability. Peripheral blood lymphocyte and urine DNA obtained from 14 individuals without clinical evidence of genitourinary malignancy served as controls. Thirty-one of 31 (100%) urine DNA samples from patients with bladder tumors were found to have 24 or more single-nucleotide polymorphism (SNP) DNA alterations. In general, SNP alterations were more common in urine samples from pT2>or tumors than pTa or pT1 tumors. SNP alterations were not identified in nine normal control subjects and in four of five patients with hematuria. These data support the noninvasive HuSNP chip assay in urine DNA as a valuable tool for the detection of bladder cancer (on a high-throughput-automated platform).
LaeA, a global regulator ofAspergillustoxins (2006)

Several toxins have been implicated in Aspergillus fumigatus pathogenicity. Among these are gliotoxin, fumagillin, fumagatin, and helvolic acid. Recently we have identified a nuclear protein, LaeA, that regulates the production of all of these metabolites. Several criteria support the role of LaeA as a potent A. fumigatus virulence factor. Among these are a decreased ability of the laeA deletion strain (ΔlaeA) to cause fatal infections in the murine model, increased macrophage phagocytosis of ΔlaeA conidia and decreased ability of ΔlaeA to kill polymorphonuclear neutrophils [1]. Here we present our current knowledge of LaeA function and future directions of study of LaeA mechanism.
Amplified and Persistent Immune Responses Generated by Single-Cycle Replicating Adenovirus Vaccines (2014)

This work illustrates the utility of our recently developed single-cycle adenovirus (SC-Ad6) vector as a new vaccine platform. Replication-defective (RD-Ad6) vectors produce low levels of transgene protein, which leads to minimal antibody responses in vivo. This study shows that replicating SC-Ad6 produces higher levels of luciferase and induces higher levels of green fluorescent protein (GFP)-specific antibodies than RD in a permissive Syrian hamster model. Surprisingly, although a replication-competent (RC-Ad6) vector produces more luciferase than SC-Ad6, it does not elicit comparable levels of anti-GFP antibodies in permissive hamsters. When tested in the larger rhesus macaque model, SC-Ad6 induces higher transgene-specific antibody and T cell responses. Together, these data suggest that SC-Ad6 could be a more effective platform for developing vaccines against more relevant antigens. This could be especially beneficial for developing vaccines for pathogens for which traditional replication-defective adenovirus vectors have not been effective.
Mitochondrial and plasma membrane potentials cause unusual accumulation and retention of rhodamine 123 by human breast adenocarcinoma-derived MCF-7 cells. (1985)

Quantitative studies of MCF-7 cells (derived from human breast adenocarcinoma) and CV-1 cells (from normal African green monkey kidney epithelium), using the permeant cationic compound tetraphenylphosphonium (TPP), in conjunction with fluorescence microscopy using rhodamine 123 (Rh123), indicate that the mitochondrial and plasma membrane potentials affect both uptake and retention of these compounds. Under conditions that depolarize the plasma membrane, uptake and retention of TPP and Rh123, driven only by the mitochondrial membrane potential, is greater in MCF-7 than in CV-1. An ionophore that dissipates the mitochondrial membrane potential of MCF-7 cells causes them to resemble CV-1 cells by decreasing uptake and retention. Hyperpolarizing the mitochondrial membrane of CV-1 increases accumulation and prolongs retention; hyperpolarization of the plasma membrane further heightens this effect, causing the uptake of CV-1 cells to resemble that of MCF-7 cells even more closely. The greater uptake and retention by MCF-7 appears to be a consequence of elevated mitochondrial and plasma membrane potentials. The plasma membrane potential affects mitochondrial retention of TPP and Rh123 and its role in enhancing the effect of a difference in mitochondrial membrane potential is explained.
An Objective Evaluation of Flurbiprofen and Tranexamic Acid in the Treatment of Idiopathic Menorrhagia (1988)

The effect of flurbiprofen (100 mg × 2 for 5 days) was compared with tranexamic acid (1.5 g × 3 for 3 days, 1 g × 2 days 4 and 5) in the treatment of 15 women with idiopathic menorrhagia. The mean blood loss during two medication‐free periods was 295 ± 52 ml. A significant (p &lt; 0.01) reduction in menstrual blood loss was recorded during treatment with both flurbiprofen and tranexamic acid. The menstrual blood loss was significantly (p &lt; 0.01) lower during treatment with tranexamic acid (155 ± 33 ml) than with flurbiprofen (223 ± 44 ml). Various side effects were recorded by 7 of 15 women during treatment with tranexamic acid and by 4 women of 15 during treatment with flurbiprofen. Many women with menorrhagia suffer simultaneously from dysmenorrhea. Thus although tranexamic acid was generally more effective in reducing menstrual blood loss, flurbiprofen provides an important therapeutic alternative to antifibrinolytic agents, especially in patients with concomitant dysmenorrhea.
All-Nanoparticle Thin-Film Coatings (2006)

All-nanoparticle thin-film coatings that exhibit antireflection, antifogging (superhydrophilicity), and self-cleaning properties have been prepared via layer-by-layer deposition of TiO(2) and SiO(2) nanoparticles. The porosity and chemical composition of the coatings were determined using a simple method that is based on ellipsometry and does not require any assumptions about the refractive indices of the constituent nanoparticles. The presence of nanopores in the TiO(2)/SiO(2) nanoparticle coatings results in superhydrophilicity as well as antireflection properties. The superhydrophilicity of contaminated coatings could also be readily recovered and retained after ultraviolet irradiation.
Competition between the hydrolysis and deamination of cytidine and its 5-substituted derivatives in aqueous acid1 (1985)

The monocations of a few 5-substituted cytidines have been shown to undergo competitive deamination to the corresponding uridines and hydrolysis to 5-substituted cytosines and D-ribose. The first-order rate constants measured at different temperatures indicate that the proportion of the hydrolysis is considerably increased with the increasing temperature. Electron-withdrawal by a polar substituent at C5 appears to facilitate the hydrolysis to a larger extent that the deamination. The ionic strength has practically no influence on the rate of either reaction.
Engineering lactic acid bacteria with pyruvate decarboxylase and alcohol dehydrogenase genes for ethanol production from Zymomonas mobilis (2003)

Lactic acid bacteria are candidates for engineered production of ethanol from biomass because they are food-grade microorganisms that can, in many cases, metabolize a variety of sugars and grow under harsh conditions. In an effort to divert fermentation from production of lactic acid to ethanol, plasmids were constructed to express pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH), encoded by the pdc and adhB genes of Zymomonas mobilis, in lactic acid bacteria. Several strains were transformed with the plasmids, and transcription of pdc and adhB was confirmed by northern hybridization analysis of transformants. PDC and ADH enzyme activities were at least 5- to 10-fold lower in these bacteria compared to Escherichia coli transformed with the same plasmid. Glucose fermentations were carried out, and some, but not all, of the transformed strains produced more ethanol than the untransformed parent strains. However, lactic acid was the primary fermentation product formed by all of the transformants, indicating that ADH and PDC activities were insufficient to divert significant carbon flow towards ethanol.
Performance of the Hepatic Encephalopathy Scoring Algorithm in a Clinical Trial of Patients With Cirrhosis and Severe Hepatic Encephalopathy (2009)

HESA extends the traditional WHC for grading HE. In the absence of a "gold" standard, the most useful indicators noted in this trial should be further validated.
Effect of ferrous sulfate, sodium metabisulfite, and sodium pyruvate on survival of Campylobacter jejuni (1983)

A combination of ferrous sulfate, sodium metabisulfite and sodium pyruvate, incorporated in solid medium, maintained the characteristic morphology, motility, and viability of six isolates of Campylobacter jejuni stored at room temperature and 4 degrees C for up to 20 and 30 days, respectively, under normal atmospheric conditions.
Inhibition of tyrosine protein kinases by halomethyl ketones (1982)

A chloromethyl ketone derivative of lactic acid was shown to inhibit protein phosphorylation in plasma membranes of Ehrlich ascites tumor cells [Johnson, H. J., Zimniak, A., & Racker, E. (1982) Biochemistry 21, 2984-2989]. We now show that this inhibitor as well as three halomethyl ketone derivatives of amino acids and peptides specifically inhibits tyrosine protein kinase activity in intact plasma membranes and Triton extracts of plasma membrane of A-431 tumor cells. The most effective inhibitor is a bromomethyl ketone derivative of leucine that inhibits the phosphorylation of a protein that migrates to the same position as the EGF receptor in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Inhibition of phosphorylation took place in the presence or absence of added EGF, and the inhibitor did not interfere with the binding of EGF to the receptor nor with the dephosphorylation of the EGF-stimulated phosphoprotein. EGF-dependent phosphorylation in a Triton extract of plasma membranes from normal placenta was considerably less sensitive to the bromomethyl ketone derivative of leucine. The tyrosine protein kinase activity of the transformation gene product of Fujinami virus was particularly sensitive to the bromomethyl ketone derivative of leucine, while the src gene product of Rous sarcoma virus was comparatively less sensitive. The bromomethyl ketone inhibitor interfered with the phosphorylation of the EGF receptor by [gamma-32P]-8-azido-ATP but much less with the light-sensitive binding. This observation and the lack of interference with EGF binding suggest that the inhibitor interacts with the protein kinase portion of the receptor complex.
Natural Insect Repellents: Activity against Mosquitoes and Cockroaches (2006)

Recent research has focused on the repellent properties of extracts from the catnip plant (Nepeta cataria) and the Osage orange (Madura pomifera) fruit. This chapter includes results on German cockroach (Blattella germanica), and house fly (Musca domestica) contact irritancy to catnip essential oil, and its major components, Z,E-nepetalactone and E,Z-nepetalactone, compared with the commercial standard, N,Ndiethyl-m-toluamide (DEET). Both species showed high percentage repellency values when exposed to filter paper treated with catnip essential oil or the individual nepetalactone isomers. Of the two nepetalactone isomers evaluated, German cockroaches were most responsive to the E,Z isomer. House flies showed similar trends in contact irritancy, responding to surfaces treated with the predominant catnip isomer, Z,E-nepetalactone, more intensely than to the catnip essential oil. Catnip and Osage orange essential oils, and a sesquiterpene found in Osage orange, elemol, were evaluated for repellency to the northern house mosquito (Culex pipiens) and are presented here. Two mosquito bioassays were used to measure percentage and contact repellecy. Mosquitoes responded initially with high percentage repellency to surfaces treated with catnip essential oil. From the residual repellency study, this trend in repellency by the catnip oil significantly decreased over the 180-minute test period. Elemol, and DEET initially had lower percentage repellency values than catnip essential oil, but did not show the negative relationship between percentage repellency and time, retaining excellent repellency throughout the 3-hour bioassay. Solutions with elemol and DEET exhibited greater significance in contact repellency compared to catnip essential oil. These results show that catnip essential oil is a potent mosquito repellent, but does not provide the same residual effects as the commercial standard, DEET, Elemol, a sesquiterpene extracted from the fruit of the Osage orange, shows excellent promise as a mosquito repellent with comparable activity to DEET in contact and residual repellency.
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes (2012)

Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license.