gebhart/patrepeval huggingface dataset:
Role of the Cysteine in R3 Tau Peptide in Copper Binding and Reactivity (2022)

Tau is a widespread neuroprotein that regulates the cytoskeleton assembly. In some neurological disorders, known as tauopathies, tau is dissociated from the microtubule and forms insoluble neurofibrillary tangles. Tau comprises four pseudorepeats (R1-R4), containing one (R1, R2, R4) or two (R3) histidines, that potentially act as metal binding sites. Moreover, Cys291 and Cys322 in R2 and R3, respectively, might have an important role in protein aggregation, through possible disulfide bond formation, and/or affecting the binding and reactivity of redox-active metal ions, as copper. We, therefore, compare the interaction of copper with octadeca-R3-peptide (R3C) and with the mutant containing an alanine residue (R3A) to assess the role of thiol group. Spectrophotometric titrations allow to calculate the formation constant of the copper(I) complexes, showing a remarkable stronger interaction in the case of R3C (log <i>K</i><sub>f</sub> = 13.4 and 10.5 for copper(I)-R3C and copper(I)-R3A, respectively). We also evaluate the oxidative reactivity associated to these copper complexes in the presence of dopamine and ascorbate. Both R3A and R3C peptides increase the capability of copper to oxidize catechols, but copper-R3C displays a peculiar mechanism due to the presence of cysteine. HPLC-MS analysis shows that cysteine can form disulfide bonds and dopamine-Cys covalent adducts, with potential implication in tau aggregation process.
Efficient docking of peptides to proteins without prior knowledge of the binding site (2002)

Reliability in docking of ligand molecules to proteins or other targets is an important challenge for molecular modeling. Applications of the docking technique include not only prediction of the binding mode of novel drugs, but also other problems like the study of protein-protein interactions. Here we present a study on the reliability of the results obtained with the popular AutoDock program. We have performed systematical studies to test the ability of AutoDock to reproduce eight different protein/ligand complexes for which the structure was known, without prior knowledge of the binding site. More specifically, we look at factors influencing the accuracy of the final structure, such as the number of torsional degrees of freedom in the ligand. We conclude that the Autodock program package is able to select the correct complexes based on the energy without prior knowledge of the binding site. We named this application blind docking, as the docking algorithm is not able to "see" the binding site but can still find it. The success of blind docking represents an important finding in the era of structural genomics.
Simulation and improvement of two digital adaptive frequency calibration techniques for fast locking wide-band frequency synthesizers (2007)

Fast locking PLL-based wide-band frequency synthesizers used in high performance RF transceivers often require multi-band voltage controlled oscillator (VCO). These types of frequency synthesizers employ both discrete and continuous tuning mechanisms to satisfy wide frequency range and low VCO tuning gain simultaneously. To facilitate discrete tuning mechanisms, an auxiliary digital loop is required in order to select proper band of VCO. This digital loop is called adaptive frequency calibration (AFC). In this paper two methods of previous AFC architectures are discussed and improved to gain the minimum possible lock time of PLL. Then, these two methods are simulated and implemented over FPGA using Xilinx System Generator. Finally, the results are compared with previous works.
Solvent effects of ionic liquids: investigation of ferrocenes as electrochemical probes (2010)

Abstract The redox potentials of ferrocene and decamethylferrocene were determined in a number of molecular and ionic solvents and used as a probe for polarity of room temperature ionic liquids (ILs). No macroscopic solvent property is simply related to redox potentials. Single empirical solvent parameters also are not able to describe the differences in potentials. Instead, Kamlet–Taft multiparameter relationship fits well ferrocenes redox potentials variation, with both molecular solvents and ILs, well describing specific solvent–solute interactions with the two probes. Copyright © 2010 John Wiley &amp; Sons, Ltd.
Iodixanol Has a Favourable Fibrinolytic Profile Compared to Iohexol in Cardiac Patients Undergoing Elective Angiography: A Double-Blind, Randomized, Parallel Group Study (2016)

Controlled-Trials.com ISRCTN51509735.
Permanent Neonatal Diabetes Caused by Glucokinase Deficiency (2003)

Neonatal diabetes can be either permanent or transient. We have recently shown that permanent neonatal diabetes can result from complete deficiency of glucokinase activity. Here we report three new cases of glucokinase-related permanent neonatal diabetes. The probands had intrauterine growth retardation (birth weight <1,900 g) and insulin-treated diabetes from birth (diagnosis within the first week of life). One of the subjects was homozygous for the missense mutation Ala378Val (A378V), which is an inactivating mutation with an activity index of only 0.2% of wild-type glucokinase activity. The second subject was homozygous for a mutation in the splice donor site of exon 8 (intervening sequence 8 [IVS8] + 2T-->G), which is predicted to lead to the synthesis of an inactive protein. The third subject (second cousin of subject 2) was a compound heterozygote with one allele having the splice-site mutation IVS8 + 2T-->G and the other the missense mutation Gly264Ser (G264S), a mutation with an activity index of 86% of normal activity. The five subjects with permanent neonatal diabetes due to glucokinase deficiency identified to date are characterized by intrauterine growth retardation, permanent insulin-requiring diabetes from the first day of life, and hyperglycemia in both parents. Autosomal recessive inheritance and enzyme deficiency are features typical for an inborn error of metabolism, which occurred in the glucose-insulin signaling pathway in these subjects.
Aquated cisplatin and heparin-pluronic nanocomplexes exhibiting sustainable release of active platinum compound and NCI-H460 lung cancer cell antiproliferation (2016)

In recent decades, platinum compounds have been many contributions in medicine. Development of new drugs from the active platinum compounds as well as nanocarriers for targeted delivery and reducing side effects of the drugs has paid much attention. In the study, nanocomplexes were prepared from aquated species of cisplatin and pluronic-conjugated heparin which distributed in the range of 80-100 nm by Transmission Electron Microscopy and 134 nm by Dynamic light scattering (DLS). Formation of the complex was confirmed by FTIR and DLS. The nanocomplexes exhibited high drug-loading capacity (approximately 42.5% wt/wt at 37 °C and 37.5% wt/wt at 25 °C). In vitro, drug-loaded nanogels showed much slower release profiles of cisplatin CDDP in pH 7.4 (physiological pH) compared with pH 5.5 condition at 37 °C. Moreover, the cytotoxicity assay results also indicated that Hep-F127 was cytocompatible; meanwhile, CDDP-loaded nanocomplex was able to reduce the cytotoxic ability of free CDDP (IC50 = 5.68 ± 0.73 μg/ml), which still maintain a significantly antiproliferative activity on NCI-H460 lung cancer cell. The in vitro preliminarily obtained results indicate that the nanocomplex is a candidate for CDDP delivery which can be studied further in cancer therapy.
[The Cruveilhier-von Baumgarten syndrome. Presentation of radiologic findings based on a case]. (1988)

Marked portosystemic venous anastomosis of the parumbilical veins is referred to as the Cruveilhier-Baumgarten syndrome. Opening of these vessels has been described mainly in the sonographic literature. In this case report CT and MR findings are presented, which have been confirmed by angiography. This paper is intended to draw the radiologist's attention to dilatation of the parumbilical veins, which is a highly specific sign of portal hypertension resulting from intrahepatic blockage.
Identification of Tyrosine-Phosphorylated Peptides Using Cold Ion Spectroscopy (2014)

The accurate and unambiguous detection of post-translational modifications in proteins and peptides remains a challenging task. We report here the use of cold ion spectroscopy for the identification of phosphorylated tyrosine residues in peptides. This approach employs the wavelength-specific UV fragmentation of cryogenically cooled protonated peptides in the gas phase. In addition to the appearance of specific photofragments, the phosphorylation of tyrosine induces large spectral shifts of the peptide electronic band origins. Quantum chemical calculations and experiments together suggest a certain generality of the use of such shifts in the spectroscopic identification of phosphotyrosines. The enhanced selectivity offered by the joint application of wavelength-specific fragmentation and mass spectrometry of cold molecules can also be used in the identifications of aromatic residues in protonated peptides and, potentially, of other UV-absorbing groups in a variety of large polyatomic ions.
The leukotriene B 4 / BLT1 ‐dependent neutrophil accumulation exacerbates immune complex‐mediated glomerulonephritis (2023)

Crescent formation is the most important pathological finding that defines the prognosis of nephritis. Although neutrophils are known to play an important role in the progression of crescentic glomerulonephritis, such as anti-neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis, the key chemoattractant for neutrophils in ANCA-associated glomerulonephritis has not been identified. Here, we demonstrate that a lipid chemoattractant, leukotriene B<sub>4</sub> (LTB<sub>4</sub> ), and its receptor BLT1 are primarily involved in disease pathogenesis in a mouse model of immune complex-mediated crescentic glomerulonephritis. Circulating neutrophils accumulated into glomeruli within 1 h after disease onset, which was accompanied by LTB<sub>4</sub> accumulation in the kidney cortex, leading to kidney injury. LTB<sub>4</sub> was produced by cross-linking of Fc gamma receptors on neutrophils. Mice deficient in BLT1 or LTB<sub>4</sub> biosynthesis exhibited suppressed initial neutrophil infiltration and subsequent thrombotic glomerulonephritis and renal fibrosis. Depletion of neutrophils before, but not after, disease onset prevented proteinuria and kidney injury, indicating the essential role of neutrophils in the early phase of glomerulonephritis. Administration of a BLT1 antagonist before and after disease onset almost completely suppressed induction of glomerulonephritis. Finally, we found that the glomeruli from patients with ANCA-associated glomerulonephritis contained more BLT1-positive cells than glomeruli from patients with other etiologies. Taken together, the LTB<sub>4</sub> -BLT1 axis is the key driver of neutrophilic glomerular inflammation, and will be a novel therapeutic target for the crescentic glomerulonephritis.
Expression of insulin receptor substrate 1 in primary breast cancer and lymph node metastases (2005)

IRS-1 might be involved in breast cancer progression. Knowledge about differences between primary and metastatic tumours might help to understand mechanisms of breast cancer progression and lead to the development of more effective anticancer drugs.
Microbial contamination of the anterior chamber during phacoemulsification (2002)

Results indicate that phacoemulsification has no proven advantage over conventional extracapsular cataract extraction in reducing intraoperative bacterial contamination.
Monte-Carlo-based phase retardation estimator for polarization sensitive optical coherence tomography (2011)

A Monte-Carlo-based phase retardation estimator is developed to correct the systematic error in phase retardation measurement by polarization sensitive optical coherence tomography (PS-OCT). Recent research has revealed that the phase retardation measured by PS-OCT has a distribution that is neither symmetric nor centered at the true value. Hence, a standard mean estimator gives us erroneous estimations of phase retardation, and it degrades the performance of PS-OCT for quantitative assessment. In this paper, the noise property in phase retardation is investigated in detail by Monte-Carlo simulation and experiments. A distribution transform function is designed to eliminate the systematic error by using the result of the Monte-Carlo simulation. This distribution transformation is followed by a mean estimator. This process provides a significantly better estimation of phase retardation than a standard mean estimator. This method is validated both by numerical simulations and experiments. The application of this method to in vitro and in vivo biological samples is also demonstrated.
A wavelength selective switch with flat passband using a free-space grating and MEMS phase-shifters (2005)

We report on a 2/spl times/2 wavelength selective switch with 6.4 dB insertion loss and >25 dB extinction ratio. The folded Mach-Zehnder geometry, with a free-space grating and MEMS phase-shifters, enables fast independent control of multiple spectral regions.
Synthesis and evaluation of PVDF–MgTiO3 polymer–ceramic composites for low-k dielectric applications (2019)

A mechanically robust, novel sandwich architecture with intriguing electrical properties and tunable dielectric properties as a function of MgTiO<sub>3</sub> loading within the PVDF matrix was fabricated.
An evolutionary basis for protein design and structure prediction (2019)

The sequence diversity of protein families is a result of the biophysical selection pressures that shaped their evolutionary history. Among the dominant pressures is selection for protein thermostability, which in itself is an attractive target in protein engineering because of its importance for various biopharmaceutical properties, the performance of industrial enzymes, and the ability to design new protein functions. In the first part of this thesis, we use models of evolutionary dynamics and biophysical fitness functions to derive the relationship between amino acid frequencies in sites of proteins and the stability effects of mutations. This analysis suggests that a commonly applied assumption (that amino acids frequencies are Boltzmann distributed) is inaccurate, and we provide a new relation consistent with the current understanding of evolutionary dynamics and protein fitness. Next, we study the extent to which the evolutionary pattern of amino acid substitutions can be explained by protein stability, as predicted using all-atom models of protein energetics. We show that at least 65\% of the substitution pattern can be explained by thermostability. With the same model, we show that functional sites (e.g. active sites or binding sites) can be predicted when the apparent evolutionary site-rate deviates significantly from that of a stability-only null-model of evolution. Finally, we study how the strength of selective pressure affects the evolutionary behavior of proteins, again using the same models, but this time generating evolutionary trajectories. We find that energetic coupling between amino acids (coevolution) and the detriment of mutation increases as the strength of selection increases. Antibodies are a key molecular component of the adaptive immune system of vertebrates and an important biopharmaceutical molecule. In the second part of the thesis, we predict and design the structure of antibodies by using energetics derived from sequence alignments and following the evolutionary encoded modular segmentation of the molecule. Through multiple design and test iterations, we were able to design antibodies, which express stably and, in some cases, bind target antigens. The developed structure prediction algorithm performs as well as other methods, is in some cases more accurate, and produces models with lower chemical strain. We use the structure prediction method to study a tumor-associated carbohydrate binding antibody.Finally, we also review the literature on design of symmetrical protein self-assembly, and study the dynamical properties of a partially disordered chaperone protein, calreticulin.
Advances in translational bioinformatics and population genomics in the Asia-Pacific (2012)

The theme of the 2012 International Conference on Bioinformatics (InCoB) in Bangkok, Thailand was "From Biological Data to Knowledge to Technological Breakthroughs." Besides providing a forum for life scientists and bioinformatics researchers in the Asia-Pacific region to meet and interact, the conference also hosted thematic sessions on the Pan-Asian Pacific Genome Initiative and immunoinformatics. Over the seven years of conference papers published in BMC Bioinformatics and four years in BMC Genomics, we note that there is increasing interest in the applications of -omics technologies to the understanding of diseases, as a forerunner to personalized genomic medicine.
Changes in Peroxidase Activity in Salivary Gland After Administration of Isoproterenol (1969)

Stimulation of mouse salivary gland by isoproterenol resulted in an initial decrease in peroxidase activity, followed by an increase with subsequent return to normal values. Actinomycin D did not block the increase in peroxidase activity observed.
Microstructure, pinning properties, and aging of CSD-grown SmBa2Cu3O7−δ films with and without BaHfO3 nanoparticles (2022)

Abstract In order to improve the electrical transport properties of RE Ba 2 Cu 3 O 7− δ nanocomposite films, SmBa 2 Cu 3 O 7− δ films with and without BaHfO 3 nanoparticles were grown by chemical solution deposition, and their microstructural and transport properties were investigated in a detailed study using transmission electron microscopy and transport measurements in magnetic fields up to 24 T. The optimization process of the crystallization step (temperature and oxygen partial pressure) as well as an aging effect, which is due to the release of trapped fluorine, are described. Critical temperature and critical current densities surprisingly improve initially during the aging. Due to the complex microstructure, the additional BaHfO 3 nanoparticles have only a positive effect at low magnetic fields for our samples.
A Short History of Schema Mapping Systems (2012)

There are many applications that need to exchange, correlate, and integrate heterogenous data sources. These information integration tasks have long been identified as important problems and unifying theoretical frameworks have been advocated by database researchers [5]. To solve these problems, a fundamental requirement is that of manipulating mappings among data sources. The application developer is typically given two schemas – one called the source schema, the other called the target schema – that can be based on different models, technologies, and rules. Mappings, also called schema mappings, are expressions that specify how an instance of the source repository should be translated into an instance of the target repository. In order to be useful in practical applications, they should have an executable implementation – for example, by means of SQL queries or XQuery scripts. This latter feature is a key requirement in order to embed the execution of the mappings in more complex application scenarios, that is, in order to make mappings a plug and play component of integration systems. Traditionally, data transformation has been approached as a manual task requiring experts to understand the design of the schemas and write scripts to translate data. As this work is time-consuming and prone to human errors, mapping generation tools have been created to make the process more abstract and user-friendly, thus easier to handle for a larger class of people. In this paper, we outline a history of the different phases that have characterized the research about automatic tools and techniques for schema mappings and data exchange. We identify three different ages, as follows.
Majorization of Technical Treating Circle Bamboo with ACQ-B (2013)

Taking water-solubility preservative (ACQ-B) as the agentia, and the liquid medicine concentration (LMC),the forcing time, the liquid medicine temperature (LMT) and the pressure as the test factors, the permo-treatment was processed to the circle bamboo, and the technical conditions of the treatment were compared. The results showed that each factor and the levels in the same factor had all larger differences to the weight increase rate (WGR) of bamboo, and WGR of the specimens in the same level had also larger difference. Through variance, range and trend analysis, the technical condition for anti-decadent of circle bamboo was that LMC was 1.0%, forcing time 15h, LMT 65°C, pressure 0.24MPa, which proved that the preservative could get best permeating result through repeat test.
Fiber Bragg gratings and chromatic dispersion (2003)

Since the late 1990s, steady advances in wavelength division multiplexing (WDM) technology have provided better ways to increase the capacity of optical networks. Three significant trends become evident in long-haul transmission system, namely the continual increase in the number of dense WDM channels, the increase in data rates from 2.5 Gb/s to today's 10 Gb/s, to tomorrow's 40 Gb/s, and finally longer distances between electrical regeneration sites. These trends towards an increased optical network capacity are now clashing with chromatic dispersion. This paper will discuss the application of high-end FBGs to telecommunication systems, focusing on their performances with respect to chromatic dispersion. Two types of components will be discussed: low-dispersion FBG WDM filters and FBG dispersion compensators. High-quality ultra-low dispersion FBGs have been fabricated successfully and their key attributes will be discussed. Advanced applications of FBGs for chromatic dispersion compensation, such as broadband multi-channel dispersion and slope compensation, will be covered. In particular, FBG dispersion slope compensators can be used in conjunction with Dispersion Compensating Fiber (DCF) to fully manage the dispersion over a large number of WDM channels. The need for tunable dispersion compensation at 40 Gb/s transmission rates will be discussed. Experimental results will also be presented.
Watermaking resisting to translation, rotation, and scaling (1998)

Keywords: LTS1 Reference LTS-CONF-1998-018View record in Web of Science Record created on 2006-06-14, modified on 2016-08-08