gebhart/patrepeval huggingface dataset:
[Molecular identification and mapping of a maize gene (Rf3) in S-type CMS using AFLP, RFLP and SCAR techniques]. (2001)

The maize CMS-S near isogenic line (NIL) developed by author and the backcross progeny (BC1) derived from it were used to identify molecular markers linked to the Rf3 gene and subsequently determine its chromosomal location on the linkage map of maize. Bulk segreant analysis was performed using AFLP technique. From the survey of AFLP primer combination, two AFLP markers, (EcoRI-AGG/MseI-CAC and EcoRI-AAC/MseI-CAG), which were named RR6 and RR7 respectively, linked to the Rf3 gene were identified. However, AFLP marker RR6 showed polymorphism between parents, and bulks were used to survey the available 100 individuals of the BC1 population, 2 out of 100 shed recombination. The recombination-rate was 2%. The genetic distance between Rf3 gene and AFLP marker RR6, was approximately 2.0 cM. And then, the RR6 was successfully cloned and sequenced, primer synthesized and converted to SCAR marker so that PCR marker can be developed for the marker-assisted selection. In RFLP analysis, marker RR6 linked to Rf3 was found to be located between RFLP loci asg20 and php20581b, and mapped on chromosome 2L.
Inhibition of Neurotransmitter Release by Synthetic Proline-rich Peptides Shows That the N-terminal Domain of Vesicle-associated Membrane Protein/Synaptobrevin Is Critical for Neuro-exocytosis (1995)

Tetanus toxin and clostridial neurotoxins type B, D, F, and G inhibit intracellular Ca(2+)-dependent neurotransmitter release via the specific proteolytic cleavage of vesicle-associated membrane protein (VAMP)/synaptobrevin, a highly conserved 19-kDa integral protein of the small synaptic vesicle membrane. This results in the release of the larger part of the cytosolic domain of this synaptic protein into the cytoplasm. Microinjection of synthetic peptides corresponding to this fragment into identified presynaptic neurons of Aplysia californica led to a potent, long lasting, and dose-dependent inhibition (approximately 50% at 10 MicroM) of acetylcholine release, probably by hindering endogenous VAMP/synaptobrevin from interacting with synaptic proteins involved in exocytosis. Structure activity studies showed that this effect is confined to the N-terminal domain of VAMP/synaptobrevin isoform II and is related to the presence of a proline-rich motif (PGGPXGX3PP or PAAPXGX3PP). At higher concentrations, the inhibitory effect was lower and only transient, suggesting that the N-terminal proline-rich domain of VAMP/synaptobrevin plays opposing roles in neurotransmitter release very likely by interacting with different synaptic proteins. This probably occurs by disruption of the recently reported in vitro VAMP-synaptophysin interaction that involves the N-terminal domain of VAMP II and was proposed to hinder synatophysin-related formation of a fusion pore. The observed recovery of neurotransmitter release following injection of high concentration of N-terminal fragments of VAMP II brings a strong in vivo support to this hypothesis. The minimum active peptide GPGGPQGGMQPPREQS could be used for rationally designing potent synthetic blockers of neurotransmission.
Identification of Monomorphic and Divergent Haplotypes in the 2006-2007 Norovirus GII/4 Epidemic Population by Genomewide Tracing of Evolutionary History (2008)

Our norovirus (NoV) surveillance group reported a >4-fold increase in NoV infection in Japan during the winter of 2006-2007 compared to the previous winter. Because the increase was not linked to changes in the surveillance system, we suspected the emergence of new NoV GII/4 epidemic variants. To obtain information on viral changes, we conducted full-length genomic analysis. Stool specimens from 55 acute gastroenteritis patients of various ages were collected at 11 sites in Japan between May 2006 and January 2007. Direct sequencing of long PCR products revealed 37 GII/4 genome sequences. Phylogenetic study of viral genome and partial sequences showed that the two new GII/4 variants in Europe, termed 2006a and 2006b, initially coexisted as minorities in early 2006 in Japan and that 2006b alone had dominated over the resident GII/4 variants during 2006. A combination of phylogenetic and entropy analyses revealed for the first time the unique amino acid substitutions in all eight proteins of the new epidemic strains. These data and computer-assisted structural study of the NoV capsid protein are compatible with a model of antigenic drift with tuning of the structure and functions of multiple proteins for the global outgrowth of new GII/4 variants. The availability of comprehensive information on genome sequences and unique protein changes of the recent global epidemic variants will allow studies of diagnostic assays, molecular epidemiology, molecular biology, and adaptive changes of NoV in nature.
An Enzyme-Linked Immunosorbent Assay with the Recombinant Merozoite Protein as Antigen for Detection of Antibodies to Eimeria necatrix (2003)

A cDNA library was constructed with Eimeria necatrix merozoite mRNA and immunologically screened by chicken sera against this parasite. One of the positive clones containing an insert of 879 nucleotides, pNP19, showed similarity to part of a published gene expressed in E. tenella merozoite by the homology search system. The inserted DNA was subcloned into baculovirus, and a 35-kD protein was expressed, purified, and used for the antigen in enzyme-linked immunosorbent assay (ELISA). Antibodies from the chickens vaccinated with the E. necatrix attenuated strain, Nn-P125, were detected from 14 days after vaccination by ELISA. The mean absorbance increased rapidly to a peak around 21 days after vaccination; thereafter, it began to decline. Even though some of the vaccinated chickens showed very low levels of antibody response to the recombinant protein 56 days after vaccination, they were protected against challenge with virulent strain of E. necatrix. The mean absorbances in sera from both vaccinated and nonvaccinated chickens highly increased 14 days after challenge. On the other hand, the antibody was not detected in ELISA when chickens were exposed to other Eimeria species such as E. tenella, E. acervulina, and E. maxima. These results demonstrate that this recombinant protein is suitable for detecting the specific antibody in chickens infected with both attenuated and virulent strains of E. necatrix.
Improved superconducting qubit coherence with high-temperature substrate annealing (2016)

We assess independently the impact of high-temperature substrate annealing and metal deposition conditions on the coherence of transmon qubits in the standard 2D circuit-QED architecture. We restrict our study to devices made with aluminum interdigital capacitors on sapphire substrates. We record more than an order-of-magnitude improvement in the relaxation time of devices made with an annealed substrate, independent of whether a conventional evaporator or molecular beam epitaxy chamber was used to deposit the aluminum. We also infer similar levels of flux noise and photon shot noise through dephasing measurements on these devices. Our results indicate that substrate annealing plays a primary role in fabricating low-loss qubits, consistent with the hypothesis that substrate-air and substrate-metal interfaces are essential factors limiting the qubit lifetimes in superconducting circuits.
Motivation for a genetically-trained topography-preserving map (2003)

It is often observed that the lattice of a well-trained self-organizing map (SOM) preserves the topology of the data set. In this paper, we examine what is meant by this claim and discuss a related goal for a dimension-reducing mapping. We term this goal "topography preservation", and attempt to fulfill it using a two-stage training method called genetically-trained topographic mapping. In the first stage of training, a clustering algorithm is used to map sets of input data points to each neuron. In the second stage, a genetic algorithm assigns adjacencies between the neurons of the output lattice according to the fitness defined by the topography preservation goal. Stock market data and an artificial data set are used to illustrate the relative strengths of the standard SOM and the new algorithm.
Road humps for the control of vehicle speeds (1993)

In the 1970s the Transport Research Laboratory (TRL) undertook research on road humps that led to the standard U.K. hump design and the initial legislation that governed their use. With the increasing interest in traffic calming and the growing number of 20 mile per hour zones, it is an appropriate time to review this research and the changes in the regulations. TRL has recently obtained measurements of speeds on roads where circular-profile and flat-topped humps have been installed, and new relationships for speeds midway between the humps and hump separation have been derived. The results, while based on measurements from a large number of sites, are subject to a large degree of variability and should be considered as a guide only. It is likely that the relationships between speed and hump spacing will continue to change over time, and further studies will be needed in the future.
Application of high powered lasers to perforated completions (2003)

As part of the process of drilling an oil or gas well, a steel production casing is often inserted to the bottom of the well and sealed with cement against the productive formation. Openings must be made through the steel casing wall and cement and into the rock formation to allow formation fluid to enter the well. Conventionally, a perforator is lowered through the casing on a wire line. When it is in the correct position, bullets are fired or explosive charges are set off to create an open path between the formation and the production string. As effective as those processes are in creating a hole or tunnel, they alter the surrounding rock and cause formation damage around the created tunnel. The permeability of the altered zone is significantly less than virgin formation by as much as 80%. The petroleum industry welcomes new perforation technologies that not only create holes effectively but also minimize the formation damage. This paper will present the feasibility study results of application of high power lasers to perforation completions and focus on methods for creating deep holes in rocks by high power lasers.
Neurological implications of urea cycle disorders (2007)

The urea cycle disorders constitute a group of rare congenital disorders caused by a deficiency of the enzymes or transport proteins required to remove ammonia from the body. Via a series of biochemical steps, nitrogen, the waste product of protein metabolism, is removed from the blood and converted into urea. A consequence of these disorders is hyperammonaemia, resulting in central nervous system dysfunction with mental status changes, brain oedema, seizures, coma, and potentially death. Both acute and chronic hyperammonaemia result in alterations of neurotransmitter systems. In acute hyperammonaemia, activation of the NMDA receptor leads to excitotoxic cell death, changes in energy metabolism and alterations in protein expression of the astrocyte that affect volume regulation and contribute to oedema. Neuropathological evaluation demonstrates alterations in the astrocyte morphology. Imaging studies, in particular (1)H MRS, can reveal markers of impaired metabolism such as elevations of glutamine and reduction of myoinositol. In contrast, chronic hyperammonaemia leads to adaptive responses in the NMDA receptor and impairments in the glutamate-nitric oxide-cGMP pathway, leading to alterations in cognition and learning. Therapy of acute hyperammonaemia has relied on ammonia-lowering agents but in recent years there has been considerable interest in neuroprotective strategies. Recent studies have suggested restoration of learning abilities by pharmacological manipulation of brain cGMP with phosphodiesterase inhibitors. Thus, both strategies are intriguing areas for potential investigation in human urea cycle disorders.
Three-dimensional and C-mode OCT imaging with a compact, frequency swept laser source at 1300 nm (2005)

We demonstrate high resolution, three-dimensional OCT imaging with a high speed, frequency swept 1300 nm laser source. A new external cavity semiconductor laser design, optimized for application to swept source OCT, is discussed. The design of the laser enables adjustment of an internal spectral filter to change the filter bandwidth and provides a robust bulk optics design. The laser generates ~30 mW instantaneous peak power at an effective 16 kHz sweep rate with a tuning range of ~133 nm full width. In frequency domain reflectometry and OCT applications, 109 dB sensitivity and ~10 microm axial resolution in tissue can be achieved with the swept laser. The high imaging speeds enable three-dimensional OCT imaging, including zone focusing or C-mode imaging and image fusion to acquire large depth of field data sets with high resolution. In addition, three-dimensional OCT data provides coherence gated en face images similar to optical coherence microscopy (OCM) and also enables the generation of images similar to confocal microscopy by summing signals in the axial direction. High speed, three-dimensional OCT imaging can provide comprehensive data which combines the advantages of optical coherence tomography and microscopy in a single system.
Implementing data cubes efficiently (1996)

Decision support applications involve complex queries on very large databases. Since response times should be small, query optimization is critical. Users typically view the data as multidimensional data cubes. Each cell of the data cube is a view consisting of an aggregation of interest, like total sales. The values of many of these cells are dependent on the values of other cells in the data cube. A common and powerful query optimization technique is to materialize some or all of these cells rather than compute them from raw data each time. Commercial systems differ mainly in their approach to materializing the data cube. In this paper, we investigate the issue of which cells (views) to materialize when it is too expensive to materialize all views. A lattice framework is used to express dependencies among views. We present greedy algorithms that work off this lattice and determine a good set of views to materialize. The greedy algorithm performs within a small constant factor of optimal under a variety of models. We then consider the most common case of the hypercube lattice and examine the choice of materialized views for hypercubes in detail, giving some good tradeoffs between the space used and the average time to answer a query.
THE PIG AS A MODEL FOR HUMAN WOUND HEALING (2001)

The medical literature describes numerous in vitro and in vivo wound-healing models. The selection of an animal model depends on a number of factors including availability, cost, ease of handling, investigator familiarity, and anatomical/functional similarity to humans. Small mammals are frequently used for wound healing studies, however, these mammals differ from humans in a number of anatomical and physiological ways. Anatomically and physiologically, pig skin is more similar to human skin. The many similarities between man and pig would lead one to believe that the pig should make an excellent animal model for human wound healing. The purpose of this paper is to review the existing literature for evidence of this supposition and determine how well the various models correlate to human wound healing. Studies of wound dressings, topical antimicrobials, and growth factors are examined. Over 180 articles were utilized for this comparative review. Our conclusion is that the porcine model is an excellent tool for the evaluation of therapeutic agents destined for use in human wounds.
Drugs of abuse and stress increase the expression of GluR1 and NMDAR1 glutamate receptor subunits in the rat ventral tegmental area: common adaptations among cross-sensitizing agents (1996)

Behavioral and electrophysiological evidence suggests that glutamatergic neurotransmission plays an important role in some of the long-term effects of cocaine and other drugs of abuse on brain function. We therefore examined the effect of repeated cocaine treatment on glutamate receptor subunit expression in central dopamine (DA) pathways implicated in many of cocaine's behavioral actions. By immunoblotting procedures using subunit-specific antibodies, we found that repeated, but not acute, cocaine treatment increased the levels of immunoreactivity of GluR1 (an AMPA receptor subunit) and NMDAR1 (an NMDA receptor subunit) in the ventral tegmental area (VTA), a nucleus containing mesolimbic DA neurons. In contrast, chronic cocaine treatment did not alter levels of GluR2 (an AMPA receptor subunit), NMDA2A/B (NMDA receptor subunits), or GluR6/7 (kainate receptor subunits) in this brain region. Moreover, GluR1 and NMDAR1 levels were not regulated in other regions of the mesolimbic or nigrostriatal DA pathways, including the substantia nigra. Because several drugs of abuse and stress can elicit common and cross-sensitizing effects on mesolimbic DA function, we next examined whether repeated morphine and stress treatments would regulate these proteins similarly in the VTA. Although morphine delivered by subcutaneous pellet implantation had no significant effect on subunit levels, morphine delivered intermittently by subcutaneous injections of escalating doses elevated GluR1 levels in the VTA. Repeated restraint stress also paradigm (2 stressors/d under variable conditions) increased both GluR1 and NMDAR1 levels in this brain region. Unlike cocaine, morphine, and stress, repeated treatment with other psychotropic drugs (haloperidol, raclopride, sertraline, and desipramine) that lack reinforcing or sensitizing properties did not regulate GluR1 or NMDAR1 subunit levels in the VTA. Increased glutamate receptor subunit expression in the VTA may represent an important molecular mechanism by which drugs of abuse and stress exert common, long-term effects on mesolimbic DA function.
Vasoactive intestinal peptide generates human tolerogenic dendritic cells that induce CD4 and CD8 regulatory T cells (2006)

Induction of antigen-specific tolerance is critical for autoimmunity prevention and immune tolerance maintenance. In addition to their classical role as sentinels of the immune response, dendritic cells (DCs) play important roles in maintaining peripheral tolerance through the induction/activation of regulatory T (T(reg)) cells. The possibility of generating tolerogenic DCs opens new therapeutic perspectives in autoimmune/inflammatory diseases. Characterizing endogenous factors that contribute to the development of tolerogenic DCs is highly relevant. We here report that the immunosuppressive neuropeptide vasoactive intestinal peptide (VIP) induces the generation of human tolerogenic DCs with the capacity to generate CD4 and CD8 T(reg) cells from their respective naive subsets. The presence of VIP during the early stages of DC differentiation from blood monocytes generates a population of IL-10-producing DCs unable to fully mature after the effects of inflammatory stimuli. CD4 T(reg) cells generated with VIP-differentiated DCs resemble the previously described Tr1 cells in terms of phenotype and cytokine profile. CD8 T(reg) cells generated with tolerogenic VIP DCs have increased numbers of IL-10-producing CD8(+)CD28(-)-CTLA4(+) T cells. CD4 and CD8 T(reg) cells primarily suppress antigen-specific T(H)1-mediated responses. Therefore, the possibility of generating or expanding ex vivo tolerogenic DC(VIPs) opens new therapeutic perspectives for treating autoimmune diseases and graft-versus-host disease after allogeneic transplantation in humans.
Allele-specific SNP markers for the new low linolenic mutant genotype of winter oilseed rape (2009)

With 5 figures and 1 table One of the goals in oilseed rape breeding is the identification of genotypes with low linolenic acid content in seed oil. Here, we present new genetic markers for mutant alleles of a chemically induced low linolenic rapeseed line DH219/05. Genomic clones comprising fatty acids desaturase 3 (FAD3) genes from the mutant and wild-type rapeseed lines were sequenced. Two statistically important single nucleotide polymorphisms were detected: (1) a C to T substitution in the third position of the sixth codon of the seventh exon in the BnaA.FAD3 gene and (2) a G to A transition in the 5′ splice donor site of the sixth intron in the BnaC.FAD3 gene. Allele-specific SNP markers were designed involving detection of the wild-type and mutant alleles by SNaPshot analysis and locus-specific PCR primers. Strong negative correlation between the presence of mutant alleles in the A and C genomes and linolenic acid content was revealed by analysis of variance. Sequence analysis of transcript variants confirmed predictions on possible negative effects of mutations on FAD3 gene expression.
Bluetooth Revealed: The Insider's Guide to an Open Specification for Global Wireless Communications (2001)

The authoritative guide to Bluetooth! From two contributors to the Bluetooth specification!For users, the new Bluetooth wireless standard will cut through the complexity of wireless communications, enabling devices to communicate seamlessly. Bluetooth Revealed offers the first insider's view of the Bluetooth standards: crucial information and insight professionals need to start implementing Bluetooth solutions -- now. Written by leaders of the Bluetooth community, it presents the entire specification in unprecedented depth: its goals, scope, structure, interrelationships, and applications. Coverage includes: Design challenges: 2.4 GHz spectrum characteristics, power consumption, global standardization, and other key issues Usage models: cordless computing, advanced headsets, file transfer/sync, dial-up networking, conferencing, hidden computing, and more The entire Bluetooth protocol stack: radio, baseband, and software layers; hardware and interfaces; and Link Manager and Logical Link Control and Adaptation Protocol (L2CAP) Bluetooth profiles: generic, telephony, networking, serial, and object exchangeBluetooth Revealed previews Bluetooth's future, including next-generation vertical and horizontal applications, and introduces today's resources for Bluetooth development, including silicon and developer's kits, as well as legacy product enablers. If you're intending to build, deploy, or market Bluetooth solutions, start right here.
ChemInform Abstract: Diels—Alder Reactions of 4,4‐Disubstituted 2‐Cyano‐2,5‐cyclohexadienones. A Facile Approach to the Angularly Substituted cis‐Decalin System. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.