gebhart/patrepeval huggingface dataset:
Cloning and Nucleotide Sequence of the Alcohol Acetyltransferase II Gene (ATF2) fromSaccharomyces cerevisiaeKyokai No. 7 (1998)

The ATF2 gene, which encodes alcohol acetyltransferase II (AATase II), was cloned from Saccharomyces cerevisiae Kyokai No. 7 (sake yeast). The ATF2 gene coded for a protein of 535 amino acid residues with a calculated molecular mass of 61,909 daltons. The deduced amino acid sequences of the ATF2 showed 36.9% similarity with that of ATF1, which encodes AATase I. The hydrophobicity profiles for the Atf2 protein and Atf1 protein were similar. A transformant carrying multiple copies of the ATF2 gene had 2.5-fold greater AATase activity than the control, and this activity was not significantly inhibited by linoleic acid. A Southern analysis of the yeast genomes in which the ATF2 gene was used as a probe showed that S. cerevisiae and brewery larger yeast have one ATF2 gene, while S. bayanus has no similar gene.
Are advanced glycation end-product-modified proteins of pathogenetic importance in fibromyalgia? (2002)

AGE modification of proteins leads to reduced solubility and high resistance to proteolytic digestion of such altered proteins (e.g. AGE-modified collagens). AGEs are also able to stimulate different kinds of cells via activation of the NFkappaB, mediated by specific receptors of AGEs (e.g. RAGE) on the cell surface. Both mechanisms may contribute to the development, perpetuation and spreading of pain phenomena in FM patients.
Antimicrobial activity of betaine esters, quaternary ammonium amphiphiles which spontaneously hydrolyze into nontoxic components (1990)

A series of quaternary ammonium compounds that are esters of betaine and fatty alcohols with hydrocarbon chain lengths of 10 to 18 carbon atoms were tested with respect to antimicrobial activities and rates of hydrolysis. When the tetradecyl derivative was tested against some selected microorganisms, the killing effect was comparable to that of the stable quaternary ammonium compound cetyltrimethylammonium bromide. At higher pH values, both the antimicrobial effect and the rate of hydrolysis of the esters increased. However, whereas at pH 6 greater than 99.99% killing of Salmonella typhimurium was achieved with 5 micrograms/ml in 3 min, the rate of hydrolysis was less than 20% in 18 h. At pH 7, a similar killing effect was achieved in 2 min and 50% hydrolysis occurred in ca. 5 h. Thus, it is possible to exploit the rapid microbicidal effect of the compounds before they hydrolyze. The rate of hydrolysis was reduced by the presence of salt. The bactericidal effect of the betaine esters increased with the length of the hydrocarbon chain of the fatty alcohol moiety up to 18 carbon atoms. Since the hydrolysis products are normal human metabolites, the hydrolysis property may extend the use of these quaternary ammonium compounds as disinfectants and antiseptics for food and body surfaces.
Inhibition of mononuclear phagocytes reduces ischemic injury in the spinal cord (1990)

Transient ischemia to the lumbar and sacral sections of the spinal cord of rabbit leads to a deterioration in neurological function that usually worsens 24 to 48 hours after injury. This decline in movement of the hindlimbs develops simultaneously with the appearance of mononuclear phagocytes in the gray matter of injured neural tissue. Chloroquine and colchicine inhibit phagocytic and secretory functions in mononuclear phagocytes. When given up to 6 hours after an induced ischemic lesion in rabbit, this drug combination decreased the number of mononuclear phagocytes found within the gray matter of damaged spinal cord, improved the recovery of function of the hindlimbs and bladder, preserved spinal somatosensory evoked potentials, and promoted the survival of motor neurons. In contrast, the glucocorticoid dexamethasone, a weak inhibitor of mononuclear phagocytes in vivo, did not reduce the number of inflammatory cells in the spinal cord and did not improve motor and bladder functions. The suppression of mononuclear phagocytes soon after ischemic injury may offer a new approach in the treatment of vascular disease in the central nervous system.
ELECTROSTATICALLY-ACTUATED RECONFIGURABLE ELASTOMER MICROFLUIDICS (2008)

We present a user-programmable reconfigurable elastomer microfluidic system which employs electrostatic actuation of water-filled elastomer microfluidic channels. Device actuation was achieved by applying 5 MHz, 15-20 V voltages to induce "wet" electrostatic gap-closing of nano-liter PDMS microfluidic chambers embedded with metal flexure electrodes. The primary contributions of this technology are: a) elastomer microfluidics that do not require external pneumatics to actuate when filled with air, oil, or water, b) a fabrication process compatible with standard PDMS microfluidics, and c) actuation voltages low enough to be driven by off-the-shelf RF IC's.
Identification of Novel Variants in Colorectal Cancer Families by High-Throughput Exome Sequencing (2013)

Exome sequencing of familial CRC cases can identify novel rare variants that may influence disease risk.
Synthesis of meso-phenyl-4,6-dipyrrins, preparation of their Cu(II), Ni(II), and Zn(II) chelates, and structural characterization of bis[meso-phenyl-4,6-dipyrrinato]Ni(II) (1996)

meso-Phenyldipyrromethanes can be oxidized by 2,6-dicyano-3,5-dichloro-para-benzoquinone (DDQ) to the corresponding meso-phenyldipyrrins. As expected, these novel, stable bipyrrolic pigments readily form metal chelates with copper(II), nickel(II), and zinc(II). Their UV–VIS spectra are compared with a series of known alkyl-substituted dipyrrin chelates and, based on the UV–VIS spectral analysis, the dihedral angle between the two ligands in the bis[meso-phenyldipyrrinato]Ni(II) complex was calculated to be 42°. The molecular structure of this complex was determined by X-ray crystallography, essentially confirming the calculation. Crystals of C 30 H 22 N 4 Ni are orthorhombic, a = 17.156(3), b = 35.217(1), c = 7.886(1) Å, Z = 8, space group Fddd. The structure was solved by direct methods and refined by full-matrix least-squares procedures to R = 0.040 and R w = 0.031 for 1058 reflections with I ≥ 3σ(F 2 ). The central nickel is coordinated in a distorted square-planar fashion by four nitrogens. The pair of the planar dipyrrinato ligands enclose a dihedral angle of 38.5°. This is the lowest angle reported for nickel(II) complexes of this kind. As a result of this, and in sharp contrast to previously described nickel(II) dipyrrin chelates, the central metal is diamagnetic. Key words: meso-phenyldipyrromethanes, meso-phenyldipyrrins, meso-phenyldipyrrinato transition metal chelates, X-ray crystallography.
Evidence for a common molecular origin of the capsule gene loci in Gram‐negative bacteria expressing group II capsular polysaccharides (1991)

Capsular polysaccharides of Gram-negative bacteria contribute to a large extent to the pathogenicity of these organisms. We show here that the molecular organization of the capsule gene loci in different serogroups of Neisseria meningitidis is similar to that of Haemophilus influenzae and Escherichia coli. A common molecular origin of the mechanisms of encapsulation is indicated by strong homology of the genes involved in transport of the capsular polysaccharides to the cell surface in all these organisms. The proteins involved in capsular polysaccharide transport fit the characteristics of ABC (ATP-binding cassette) transporters. Furthermore, by sequence comparison of the sialytransferases of N. meningitidis B and E. coli K1, the capsule of which is composed of alpha 2,8-linked polyneuraminic acid, a significant degree of homology was observed, indicating that the capsular polysaccharide type itself has the same evolutionary origin in these two pathogens.
Compensation of the inherent wave front curvature in digital holographic coherent microscopy for quantitative phase-contrast imaging (2003)

An approach is proposed for removing the wavefront curvature introduced by the microscope imaging objective in digital holography, which otherwise hinders the phase contrast imaging at reconstruction planes. The unwanted curvature is compensated by evaluating a correcting wave front at the hologram plane with no need for knowledge of the optial parameters, focal length of the imaging lens, or distances in the setup. Most importantly it is shown that a correction effect can be obtained at all reconstruction planes. Three different methods have been applied to evaluate the correction wave front and the methods are discussed in detail. The proposed approach is demonstrated by applying digital holography as a method of coherent microscopy for imaging amplitude and phase contrast of microstructures.
Granulated broadband network applicable to B-ISDN and PSTN services (1992)

A granulated broadband network (GBN) is proposed as an intermediate asynchronous transfer mode (ATM) based platform to be part of an evolution scenario toward B-ISDN. The GBN enables various types of services to be provided including 64-kb/s-based services and broadband services. In the GBN, information is transformed into ATM cells at subscriber line terminals or at customer premises and is transferred through ATM networks; consequently, the cost feasibility of a single-channel cell assembly/deassembly device is a significant factor in economically providing ATM-based conventional services and interworking between STM and ATM networks. Various virtual path capacities with a fine degree of granularity can be provided in a mesh structure between transit modes in the GBN. Economic feasibility studies of the GBN, by simulating on certain large-size real networks in the greater Tokyo area, indicate the possibility of a more than 50% cost reduction in transit networks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structure of a new nervous system glycoprotein, Nr-CAM, and its relationship to subgroups of neural cell adhesion molecules. (1991)

We have identified and characterized a new glycoprotein in the chicken nervous system using immunological and molecular biological methods and we have examined its tissue distribution. Analysis revealed that this protein is very similar in structure to the chicken neuron-glia cell adhesion molecule, Ng-CAM, and to mouse L1. cDNA clones encompassing the entire coding sequence of this Ng-CAM related molecule, called Nr-CAM, have been isolated and sequenced. A glycoprotein containing one major component of Mr 145,000 on SDS-PAGE was purified from brain by lentil lectin affinity chromatography and FPLC, and its amino-terminal sequence was identical to that predicted from the Nr-CAM cDNA. The complete cDNA sequence encodes six Ig-like domains, five fibronectin type III repeats, a predicted transmembrane domain, and a short cytoplasmic domain. On Northern blots, nucleic acid probes for Nr-CAM recognized one major RNA species of approximately 7 kb and much lesser amounts of larger RNAs. Most of the same probes hybridized to single bands on genomic Southern blots, suggesting that Nr-CAM is encoded by a single gene that may be alternatively processed to yield several mRNAs. In support of this notion, two Nr-CAM cDNA clones had a 57-bp sequence located between the second and third Ig-like domains that was not found in two other Nr-CAM cDNA clones, and two other clones were isolated that lacked the 279-bp segment encoding the fifth fibronectin-like type III repeat. Antibodies against the purified protein and synthetic peptides in Nr-CAM both recognized a predominant Mr 145,000 species and a much less prevalent species of Mr 170,000 in neural tissues. Levels of Nr-CAM expression increased in the brain until approximately embryonic day (E) 12, followed by slightly lower levels of expression at E18 and after hatching. Immunofluorescent staining with anti-Nr-CAM antibodies showed that most neurons in the retina were positive at E7 and the pattern of expression became restricted to several layers on neuronal cell bodies and fibers during development. Anti-Nr-CAM antibodies labeled specifically cell surfaces on neurons in culture. Although the structure of Nr-CAM resembles that of chicken Ng-CAM and mouse L1, the identity with each of these neural CAMs does not exceed 40%. The differences indicate that Nr-CAM is distinct from Ng-CAM and L1, but there are sufficient similarities to suggest that all of these molecules are members of a subgroup of neural CAMs in the N-CAM superfamily.(ABSTRACT TRUNCATED AT 400 WORDS)
Rapid screening method for intact glucosinolates in Chinese medicinal herbs by using liquid chromatography coupled with electrospray ionization ion trap mass spectrometry in negative ion mode (2008)

An optimized method using liquid chromatography coupled with electrospray ionization ion trap mass spectrometry (LC/ESI-ITMS) in negative ion mode has been developed for screening different structural classes of intact glucosinolates in six Chinese medicinal herbs. The glucosinolates were extracted with hot methanol/water (70:30 v/v) and separation of the individual glucosinolates was achieved using a reversed-phase C18 column with an aqueous ammonium acetate/methanol gradient. Identification of the intact glucosinolates was based on the detection of compounds with a constant neutral loss of 242 Da corresponding to the combined loss of anhydroglucose (162 Da) and sulfur trioxide (80 Da) in collision-induced dissociation. The structures of the identified glucosinolates were confirmed with the use of group-specific product ions at m/z 195, 241, 259, 275 in their corresponding MS/MS product ion spectra. Differentiation of intact glucosinolates was achieved through their respective retention times and molecular masses as well as the characteristic product ions. The limits of detection were at the low nanogram level per injection, based on constant neutral loss scans. Significant variation in the compositions of intact glucosinolates was identified in the cruciferous herbs. This method was applied in the differentiation and quality control of two pairs of easily confused herbs.
Thermal Cross-Linking for Biologically Degradable Materials (1996)

To diminish undesirable side effects of chemical cross-linking of biodegradable materials, the authors developed a thermal cross-linking method that involved esterification by dehydration under dry conditions. The optimal condition for cross-linking was heating at 130-140 degrees C for 40 hr. Efficacy of the cross-linking was evaluated using enzymatic digestion of 0.01% protease in phosphate buffer at pH 7.4. Collagenous materials without cross-linking were digested completely within 30 min. However, with thermal cross-linking, it required 7 days for digestion. The capacity for holding onto water also was tested. Water content decreased when the cross-link density was increased. As an in vivo experiment, six succinylated collagen sealed vascular grafts treated with thermal cross-linking were implanted in the abdominal aortae of dogs and removed 21 days later. These grafts showed no foreign body reaction, and the collagen layer was almost completely absorbed. A collagen sealed graft cross-linked with formaldehyde used as a control showed a strong foreign body reaction. These results suggest that the physical cross-linking method was suitable for biodegradable biologicals, such as collagenous materials, without the undesirable side effects of chemical cross-linking regents.
Mig, the Monokine Induced By Interferon-γ, Promotes Tumor Necrosis In Vivo (1997)

Mig, the monokine induced by interferon-gamma, is a CXC chemokine active as a chemoattractant for activated T cells. Mig is related functionally to interferon-inducible protein 10 (IP-10), with which it shares a receptor, CXCR3. Previously, IP-10 was found to have antitumor activity in vivo. In the present study, murine Mig RNA was found to be expressed at higher levels in regressing Burkitt's lymphoma tumors established in nude mice compared with progressively growing tumors. Daily inoculations of purified recombinant human Mig into Burkitt's tumors growing subcutaneously in nude mice consistently caused tumor necrosis associated with extensive vascular damage. These effects were indistinguishable from those produced by intratumor inoculations of Burkitt's tumors with IP-10. These results support the notion that Mig, like IP-10, has antitumor activity in vivo.
A Novel PCNA-Binding Motif Identified by the Panning of a Random Peptide Display Library (2001)

Proliferating cell nuclear antigen (PCNA) has recently been identified as a target for the binding of proteins involved in DNA replication, DNA repair, and cell cycle control. The interactions between PCNA and a number of these proteins are known to be mediated by a conserved peptide motif. In this study, a random peptide library in which peptide sequences are displayed on the E. coli bacterial flagellin protein was screened for PCNA-binding sequences. Analysis of the retrieved peptide sequences verified the presence of the known PCNA-binding motif. In addition, a second, larger group of peptides containing a different consensus sequence for PCNA binding was discovered. This sequence was found to be present on DNA polymerase delta, and a peptide conforming to this sequence was demonstrated to bind to PCNA. Database search and analysis show that many proteins contain the second consensus sequence. These include proteins that are involved in DNA replication, repair, and cell cycle control. The demonstration of this second PCNA-binding motif may provide a basis for identifying and experimentally testing specific proteins for the structural basis for PCNA binding.
A side channel attack countermeasure using system-on-chip power profile scrambling (2011)

Since the discovery that hardware used for cryptographic applications could leak secret information through its power or radiation profile a wide range of possible attack methods has been published. The rapid evolution of these side-channel attacks made it increasingly important to minimize this possible information leakage. Additionally timing information also derived from this power profile is used to control fault-attack campaigns to drive the system into an unintended state. Therefore a wide range of leakage countermeasures has been developed for dedicated cryptographic hardware. Contrariwise only little work is available concerning power profile scrambling techniques for cryptographic software implementations running on general purpose architectures. Such implementations often include power management hardware to cope with several power budget constraints which could be used to influence the system's power consumption during run-time. This paper proposes a novel side channel attack countermeasure technique using such power management methods in combination with techniques for power profile manipulation. State-of-the-art power estimation hardware using a reduced power model allows for the efficient on-line monitoring and manipulation of the power consumption and radiation profile.
In Vitro and In Vivo Hepatoma Cell-Specific Expression of a Gene Transferred with an Adenoviral Vector (1996)

Recombinant adenoviruses are widely used for the transfer of foreign genes into various mammalian cells. However, the utilization of these vectors for cancer gene therapy requires the specific and efficient expression of the transferred gene in tumor cells. To obtain targeted expression in hepatoma cells, we constructed recombinant adenoviral vectors containing transcriptional elements from either the rat alpha-fetoprotein (AFP) or the human insulin-like growth factor II (IGFII) genes driving expression of the nuclear beta-galactosidase gene (nls lacZ). In vitro infection revealed that the AFP but not the IGFII transcriptional regulatory sequence controlled nls lacZ expression specifically in hepatoma cells. The same specificity was obtained in vivo in subcutaneous human hepatic tumors generated by engraftment of Huh7 hepatoma cells in nude mice as well as in primary liver tumors developed in rats and mice. No marker gene expression was detectable after AFP-nls lacZ gene transfer to normal rat liver parenchyma despite evidence for the presence of DNA encoding the nls lacZ gene. However, in vivo experiments with primary liver tumors in rats and mice also revealed that primary hepatoma cells were poorly infected by adenoviral vectors. Peritumoral and normal tissues were infected efficiently by adenoviral vectors. We conclude that hepatoma cell-specific expression of a transgene can be achieved with AFP regulatory sequences but that adenoviral vectors may not be the preferable vector for transferring genes in vivo in primary liver tumors.
The Effects of Pulse Configuration on Magnetic Stimulation (2003)

A study is presented in which the authors have examined the effects of pulse configuration, stimulation intensity, and coil current direction during magnetic stimulation. Using figure-8 and circular coils, the median nerve was stimulated at the cubital fossa and at the wrist of 10 healthy volunteers, and the response amplitude and site of stimulation were determined. The key findings of this study are in agreement with other researchers' findings and confirm that biphasic stimulating pulses produce significantly higher M-wave amplitudes than monophasic stimulating pulses for the same stimulus intensity. Mean response amplitudes for biphasic stimuli applied by both coils at the elbow and wrist are consistently higher for the normal current direction. Mean response amplitudes for monophasic pulses are almost always higher for reversed currents. The site for effective stimulation (the position of the virtual cathode) cannot be defined within a fixed distance from the center of the coil (3 to 4 cm), as has been suggested by other researchers, but was found to vary depending on the coil current amplitude and direction as well as the degree of inhomogeneity of the tissues surrounding the nerve. There is a statistically significant relationship between virtual cathode shift and stimulus intensity for biphasic and monophasic pulses. Reversing the coil current direction has no statistically significant effect on the virtual cathode position. Virtual cathode shifts can be measured for biphasic and monophasic stimulations using a figure-8 coil at the wrist and the elbow. However, such a shift is difficult to determine with a circular coil.