gebhart/patrepeval huggingface dataset:
Thickness-dependent electrical characteristics of lead zirconate titanate thin films (1995)

Ferroelectric lead zirconate titanate thin films of morphotropic phase boundary composition were fabricated through the sol-gel spin-on technique to study the thickness dependence of electrical characteristics. At saturation, the films exhibited a dielectric constant of 1300, dissipation factor of 0.03, Curie temperature of 366 °C, remanent polarization of 36 μC/cm2, coercivity of around 30 kV/cm, and dielectric breakdown strength of over 1 MV/cm. The temperature dependence of permittivity showed an anomalous behavior with annealing temperature. The high temperature dielectric behavior of the films were distinguished by smeared and stunted dielectric maximum.
Novel mechanism of cell division inhibition associated with the SOS response in Escherichia coli (1983)

Certain Escherichia coli strains were shown to possess a novel system of cell division inhibition, called the SfiC+ phenotype. SfiC+ filamentation had a number of properties similar to those of sfiA-dependent division inhibition previously described: (i) both are associated with the SOS response induced by expression of the recA(Tif) mutation, (ii) both are associated with cell death, (iii) both are amplified in mutants lacking the Lon protease, and (iv) both are suppressed by sfiB mutations. SfiC+ filamentation and sfiA-dependent division inhibition differed in (i) the physiological conditions under which loss of viability is observed, (ii) the extent of amplification in lon mutants, (iii) their genetic regulation (SfiC+ filamentation is not under direct negative control of the LexA repressor), and (iv) their genetic determinants (SfiC+ filamentation depends on a locus, sfiC+, near 28 min on the E. coli map and distinct from sfiA).
Identification of Bacillus anthracis proteins associated with germination and early outgrowth by proteomic profiling of anthrax spores (2004)

The use of anthrax spores as a bioweapon has spurred efforts aimed at identifying key proteins expressed in Bacillus anthracis. Because spore germination and outgrowth occur prior to and are required for disease manifestations, blocking germination and early outgrowth with novel vaccines or inhibitors targeting critical B. anthracis germination and outgrowth-associated factors is a promising strategy in mitigating bioterror. By screening 587 paired protein spots that were isolated from dormant and germinating anthrax spores, respectively, we identified 10 spore proteins with statistically significant germination-associated increases and decreases. It is likely that proteins whose levels change during germination may play key roles in the germination and outgrowth processes, and they should be listed as priority targets for development of prophylactic and therapeutic agents against anthrax. The 31 new proteins identified in this study also complement an emerging proteomic database of B. anthracis.
COMPARISON OF THE EFFECTS OF ORAL VS. PERITONSILLAR INFILTRATION OF KETAMINE IN PAIN REDUCTION AFTER TONSILLECTOMY: A RANDOMIZED CLINICAL TRIAL. (2015)

The finding of this study showed that, compared with the peritonsillar infiltration of ketamine, the use of oral ketamine before general anesthesia was less effective in reducing postoperative pain of tonsillectomy in children.
Immobilization of Protein Molecules onto Homogeneous and Mixed Carboxylate-Terminated Self-Assembled Monolayers (1997)

The attachment of biomolecules, in particular proteins, onto solid supports is fundamental in the development of advanced biosensors, bioreactors, affinity chromatographic separation materials, and many diagnostic techniques. In addition, the effective investigation of biomolecular structure and function with scanning probe microscopy often requires a strong attachment of the biomolecule to a substrate. Here, we investigate the binding of the protein catalase to gold surfaces modified by self-assembled monolayers (SAMs). The chemical and physical adsorption of the protein molecules onto SAMs of 3-mercaptopropanoic acid (3-MPA), 11-mercaptoundecanoic acid (11-MUA), and a mixture of the two acid thiols (mixed) was investigated by utilizing tapping mode atomic force microscopy, scanning tunneling microscopy, surface plasmon resonance (SPR), static secondary ion mass spectrometry, and X-ray photoelectron spectroscopy. The surface concentration of catalase adsorbed on the SAMs decreased in the following order: mixed > 11-MUA > 3-MPA. Utilizing the terminal carboxylic acid functionalities, catalase was immobilized with a water-soluble carbodiimide and N-hydroxysuccinimide (NHS). Immobilization resulted in increased coverage of the protein. SPR studies on silver surfaces modified by these SAMs indicate that immobilization of carbodiimide and NHS decreased in the same order, namely mixed > 11-MUA > 3-MPA.
Role of Ca 2+ /Calmodulin-Stimulated Cyclic Nucleotide Phosphodiesterase 1 in Mediating Cardiomyocyte Hypertrophy (2009)

These results elucidate a novel role for Ca(2+)/CaM-stimulated PDE1, particularly PDE1A, in regulating pathological cardiomyocyte hypertrophy via a cGMP/PKG-dependent mechanism, thereby demonstrating Ca(2+) and cGMP signaling cross-talk during cardiac hypertrophy.
Estimating the Entropic Cost of Self-Assembly of Multiparticle Hydrogen-Bonded Aggregates Based on the Cyanuric Acid·Melamine Lattice (1998)

The entropic component of the free energy of assembly for multiparticle hydrogen-bonded aggregates is analyzed using a model based on balls connected by rigid rods or flexible strings. The entropy of assembly, ΔS, is partitioned into translational, rotational, vibrational, and conformational components. While previously reported theoretical treatments of rotational and vibrational entropies for assembly are adequate, treatments of translational entropy in solution and of conformational entropyoften the two largest components of ΔSare not. This paper provides improved estimates and illustrates the methods used to obtain them. First, a model is described for translational entropy of molecules in solution (ΔStrans(sol)); this model provides physically intuitive corrections for values of ΔStrans(sol) that are based on the Sackur−Tetrode equation. This model is combined with one for rotational entropy to estimate the difference in entropy of assembly between a 4-particle aggregate and a 6-particle one. Second, an approximate analysis of a model based on balls connected by rods or strings gives an approximate estimate of the maximum contribution of conformational entropy to the difference in free energy of assembly of flexible and of rigid molecular assemblies. This analysis, although approximate, is easily applied by all types of chemists and biochemists; it serves as a guide to the design of stable molecular aggregates, and the qualitative arguments apply generally to any form of self-assembly.
Ab initio Gene Finding in Drosophila Genomic DNA (2000)

Ab initio gene identification in the genomic sequence of Drosophila melanogaster was obtained using (human gene predictor) and Fgenesh programs that have organism-specific parameters for human, Drosophila, plants, yeast, and nematode. We did not use information about cDNA/EST in most predictions to model a real situation for finding new genes because information about complete cDNA is often absent or based on very small partial fragments. We investigated the accuracy of gene prediction on different levels and designed several schemes to predict an unambiguous set of genes (annotation CGG1), a set of reliable exons (annotation CGG2), and the most complete set of exons (annotation CGG3). For 49 genes, protein products of which have clear homologs in protein databases, predictions were recomputed by Fgenesh+ program. The first annotation serves as the optimal computational description of new sequence to be presented in a database. Reliable exons from the second annotation serve as good candidates for selecting the PCR primers for experimental work for gene structure verification. Our results shows that we can identify approximately 90% of coding nucleotides with 20% false positives. At the exon level we accurately predicted 65% of exons and 89% including overlapping exons with 49% false positives. Optimizing accuracy of prediction, we designed a gene identification scheme using Fgenesh, which provided sensitivity (Sn) = 98% and specificity (Sp) = 86% at the base level, Sn = 81% (97% including overlapping exons) and Sp = 58% at the exon level and Sn = 72% and Sp = 39% at the gene level (estimating sensitivity on std1 set and specificity on std3 set). In general, these results showed that computational gene prediction can be a reliable tool for annotating new genomic sequences, giving accurate information on 90% of coding sequences with 14% false positives. However, exact gene prediction (especially at the gene level) needs additional improvement using gene prediction algorithms. The program was also tested for predicting genes of human Chromosome 22 (the last variant of Fgenesh can analyze the whole chromosome sequence). This analysis has demonstrated that the 88% of manually annotated exons in Chromosome 22 were among the ab initio predicted exons. The suite of gene identification programs is available through the WWW server of Computational Genomics Group at http://genomic.sanger.ac.uk/gf. html.
Functional Haplotypes in the Promoter of Matrix Metalloproteinase-2 Predict Risk of the Occurrence and Metastasis of Esophageal Cancer (2004)

Matrix metalloproteinase-2 (MMP-2) plays important roles in cancer development and aggression. Our previous studies revealed a strong association between the MMP-2 -1306C/T polymorphism and risk of several cancers. A novel -735C/T polymorphism in MMP-2 promoter has been identified but the function is undefined. This study examined our hypothesis that these two polymorphisms might have functional relevance and impact on risk of esophageal squamous cell carcinoma in the context of haplotype. Genotypes and haplotypes were analyzed in 527 cases and 777 controls and odds ratios (ORs) and 95% confidence intervals (CIs) were estimated by logistic regression. The function of the polymorphisms was examined by electrophoretic mobility shift assays, luciferase gene expression assays, and reverse transcriptase-PCR analyses. It was found that the -735C-->T transition disrupts an Sp1 site and displays a lower promoter activity. The C(-1306)-C(-735) haplotype had 7-fold increased luciferase expression and 3.7-fold increased MMP-2 mRNA levels in esophageal tissues compared with the T(-1306)-T(-735) haplotype. A case-control analysis revealed a 1.52-fold (95% CI = 1.17-1.96) or 1.30-fold (95% CI = 1.04-1.63) excess risk of developing esophageal squamous cell carcinoma for the -1306CC or -735CC genotype carriers compared with noncarriers, respectively. A greater association was observed between elevated risk of developing esophageal squamous cell carcinoma and C(-1306) or C(-735) allele containing haplotypes, with the risk being highest for the C(-1306)-C(-735) haplotype compared with the T(-1306)-T(-735) haplotype (OR = 6.53; 95% CI = 2.78-15.33). The C(-1306)-C(-735) haplotype was also associated with increased risk for distant metastasis of esophageal squamous cell carcinoma (OR = 3.34; 95% CI = 1.16-9.63). These findings suggest that the C(-1306)-C(-735) haplotype in the MMP-2 promoter contributes to risk of the occurrence and metastasis of esophageal squamous cell carcinoma by increasing expression of MMP-2.
A cystic fibrosis pancreatic adenocarcinoma cell line. (1990)

We established a pancreatic adenocarcinoma cell line (CFPAC-1) from a patient with cystic fibrosis (CF) and assessed some of its properties. The cells show epithelial morphology and express cytokeratin and oncofetal antigens characteristic of pancreatic duct cells. Basal and stimulated levels of cAMP and cAMP-dependent protein kinase and the biophysical properties of single Cl- channels in CFPAC-1 are similar to those of airway and sweat gland primary cultures and Cl(-)-secreting epithelial cell lines. Anion transport and single Cl- channel activity was stimulated by Ca2+ ionophores but not by forskolin, cAMP analogs, or phosphodiesterase inhibitors. The cells express the CF gene and manifest the most common CF mutation, deletion of three nucleotides resulting in a phenylalanine-508 deletion. These properties have been stable through greater than 80 passages (24 months), suggesting that CFPAC-1 can serve as a continuous cell line that displays the CF defect.
Triazines and related products. Part 24. Synthesis of pyrazol-4-ylidenehydrazinoimidazoles by hydrazinolysis of imidazo[5,1-c][1,2,4]-triazines and 2-arylazoimidazoles by diazonium coupling reactions (1982)

4-(Substituted)imidazo[5,1-c][1,2,4)triazine-8-carboxamides with ester, ketone, or cyano-groups in the 3-position undergo ring-opening with hydrazine and phenylhydrazine to yield substituted (pyrazol-4-ylidenehydrazino)imidazole-4-carboxamides. In some cases ring cleavage is initiated by attack of the hydrazine at C-4 of the imidazotriazine, and in others by nucleophilic attack at the 3-substituent. Examples of the same series of hydrazones can be prepared by coupling 5-diazoimidazole-4-carboxamide with activated pyrazoles. Diazotised arylamines couple with 5-aminoimidazole-4-carboxamide at C-2 to yield a series of intensely coloured 5-amino-2-arylazoimidazole-4-carboxamides, which can be cyclised to 8-arylazo-9H-purin-6(1H)-ones with ethyl formats in sodium ethoxide, and form mono- or di-acylamino-derivatives in formic acid or acetic anhydride. In no case was it found possible to prepare 2,5-diaminoimidazole-4-carboxamide by reductive cleavage of 5-amino-2-arylazoimidazole-4-carboxamides; only arylamines or unstable hydrazo-intermediates were identified. Reduction of 5-amino-2-(2-cyanophenylazo)imidazole-4-carboxamide with sodium dithionite or with hydrogen over a 10% palladium–charcoal catalyst afforded 5-amino-2-(3-aminoindazol-2-yl)imidazole-4-carboxamide.
High resolution glass capillary columns for the gas chromatographic analysis of alditol acetates of neutral and amino sugars (1982)

Abstract The development of improved high resolulation glass capillary columns for separating the alditol acetates of neutral and amino sugars is described. Different capillary column treatments were evaluated for their activity toward amino sugar derivatives and for their effect on the efficiency of the completed column. The simple two‐step procedure of leaching with aqueous hydrochloric acid and dynamic coating with SP‐2330 was found to produce efficient and inert columns.
<title>Laser diodes for optical readout of cryo-electronics</title> (1994)

We report successful coupling of electrical signals from low temperature (4.2 K) superconducting circuitry to room temperature electronics using laser diodes coupled to optical fibers. The techniques used rely on laser diodes operating at low temperatures, and on high gain amplifiers placed outside the low temperature environment. A new superconducting driver circuit is used to step-up the low output of these circuits to a seven millivolt level, sufficient to modulate the laser diodes. By properly choosing the laser source, the power dissipated within the cryogenic environment can be maintained below 400 (mu) W, with further improvements easily reached.
Formation and Conversion of Oxygen Metabolites by Lactococcus lactis subsp. lactis ATCC 19435 under Different Growth Conditions (2002)

A semidefined medium based on Casamino Acids allowed Lactococcus lactis ATCC 19435 to grow in the presence of oxygen at a slow rate (0.015 h(-1)). Accumulation of H(2)O(2) in the culture prevented a higher growth rate. Addition of asparagine to the medium increased the growth rate, whereby H(2)O(2) accumulated only temporarily during the lag phase. H(2)O(2) is an inhibitor for several glycolytic enzymes, glyceraldehyde-3-phosphate dehydrogenase being the most sensitive. Strain ATCC 19435 contained NADH oxidase (maximum specific rate under aerobic conditions, 426 nmol of NADH min(-1) mg of protein(-1)), which reduced oxygen to water, whereby superoxide was formed as a by-product. H(2)O(2) originated from the dismutation of superoxide by superoxide dismutase. Although H(2)O(2) was rapidly destroyed under high metabolic fluxes, neither NADH peroxidase nor any other enzymatic H(2)O(2)-reducing activity was detected. However, pyruvate, the end product of glycolysis, reacted nonenzymatically and rapidly with H(2)O(2) and hence was a potential alternative for scavenging of this oxygen metabolite intracellularly. Indeed, intracellular concentrations of up to 93 mM pyruvate were detected in aerobic cultures growing at high rates. It is hypothesized that self-generated pyruvate may serve to protect L. lactis strain ATCC 19435 from H(2)O(2).
Micro- and nano-motors for biomedical applications (2013)

Micro- and nano-motors are a class of miniaturized man-made machines that are able to convert chemical or external energy into mechanical motion. The past decade has witnessed significant progress in the design and fabrication of micro- and nano-motors as a future intelligent and comprehensive biomedical platform. In this review we will critically assess the challenges and limitations of micro- and nano-motors, their mechanism of propulsion and applications in the biomedical field. Important insights into the future development and direction of nano-motors for improved biocompatibility and design will be discussed.
Design and implementation of a self-calibrating, compact micro strip sensor for in-situ dielectric spectroscopy and data transmission (2013)

A compact, on-board, self-calibrating, micro strip sensor is presented. The sensor can make accurate multi-frequency measurements of complex permittivity in real time and transmit this information wirelessly by using the same sensor as a micro strip patch antenna. Such multi-frequency measurements in a multi-phase mixture like soil are used to estimate the concentration of individual constituents like bulk-soil, water, and various nutrients in soil. The sensor architecture comprises of a programmable phase locked loop (PLL) which sweeps through the frequency band of 3-40 MHz. The signal generated by the PLL is allowed to reflect from the micro strip patch which is surrounded by the dielectric medium under test (such as soil or food). The amplitude and phase of incident and reflected signals are captured and impedance due to the surrounding dielectric mixture is calculated. This impedance value is used to estimate the dielectric constant by mapping the input impedance of the micro strip sensor to different surrounding dielectric constant values. The sensor has an inbuilt self-calibrating mechanism which makes it useful for remote, underground and hand held applications.
Two New Sulfated Furostanol Saponins from Tribulus terrestris (2002)

The known furostanol saponins methylprotodioscin and protodioscin and two new sulfated saponins, sodium salt of 26-O-beta-glucopyranosyl-22alpha-methoxy-(25R)-furost-5-ene-3beta,26-diol-3-O-alpha-rhamnopyranosyl-(1-->2)-beta-4-O-sulfo-glucopyranoside (methylprototribestin) and sodium salt of 26-O-beta-glucopyranosyl-22alpha-hydroxy-(25R)-furost-5-ene-3beta,26-diol-3-O-alpha-rhamnopyranosyl-(1-->2)-beta-4-O-sulfo-glucopyranoside (prototribestin) have been isolated from the aerial parts of Tribulus terrestris L. growing in Bulgaria. The structures of the new compounds were elucidated on the basis of 1D and 2D (DQF-COSY, TOCSY, HSQC-TOCSY, HSQC, HMBC, ROESY) NMR data, ESI mass spectra and chemical transformation.
Mechanisms of Alternative Pre-Messenger RNA Splicing (2003)

Alternative pre-mRNA splicing is a central mode of genetic regulation in higher eukaryotes. Variability in splicing patterns is a major source of protein diversity from the genome. In this review, I describe what is currently known of the molecular mechanisms that control changes in splice site choice. I start with the best-characterized systems from the Drosophila sex determination pathway, and then describe the regulators of other systems about whose mechanisms there is some data. How these regulators are combined into complex systems of tissue-specific splicing is discussed. In conclusion, very recent studies are presented that point to new directions for understanding alternative splicing and its mechanisms.
Early detection of systematic patterning problems for a 22nm SOI technology using E-beam hot spot inspection (2013)

Early detection of systematic patterning problems can provide a major boost for a technology team. Often in the past, these type defects might only be detected after functional test and subsequent failure analysis. At this point, three to six months of process development time have been lost and three to six months of defective hardware have been wasted. In this paper, a methodology for in-line detection of systematic patterning problems using E-beam hot spot inspection (EBHI) is introduced. Pattern simulation tools and other sources are used to recommend X, Y locations with challanging geometries for evaluation. EBHI evaluates the patterning capability for these locations using modulated wafers. A multifunction team addresses the hot spots that fail within the process window. EBHI is then used to evaluate the solutions proposed by this team. Often additional data is necessary to determine the full yield impact. This methodology provided tremendous value for IBM's 22nm SOI Technology. Several examples illustrating this point are presented.
Face recognition with learning-based descriptor (2010)

We present a novel approach to address the representation issue and the matching issue in face recognition (verification). Firstly, our approach encodes the micro-structures of the face by a new learning-based encoding method. Unlike many previous manually designed encoding methods (e.g., LBP or SIFT), we use unsupervised learning techniques to learn an encoder from the training examples, which can automatically achieve very good tradeoff between discriminative power and invariance. Then we apply PCA to get a compact face descriptor. We find that a simple normalization mechanism after PCA can further improve the discriminative ability of the descriptor. The resulting face representation, learning-based (LE) descriptor, is compact, highly discriminative, and easy-to-extract. To handle the large pose variation in real-life scenarios, we propose a pose-adaptive matching method that uses pose-specific classifiers to deal with different pose combinations (e.g., frontal v.s. frontal, frontal v.s. left) of the matching face pair. Our approach is comparable with the state-of-the-art methods on the Labeled Face in Wild (LFW) benchmark (we achieved 84.45% recognition rate), while maintaining excellent compactness, simplicity, and generalization aability across different datasets.