gebhart/patrepeval huggingface dataset:
Biased distribution of DNA uptake sequences towards genome maintenance genes (2004)

Repeated sequence signatures are characteristic features of all genomic DNA. We have made a rigorous search for repeat genomic sequences in the human pathogens Neisseria meningitidis, Neisseria gonorrhoeae and Haemophilus influenzae and found that by far the most frequent 9-10mers residing within coding regions are the DNA uptake sequences (DUS) required for natural genetic transformation. More importantly, we found a significantly higher density of DUS within genes involved in DNA repair, recombination, restriction-modification and replication than in any other annotated gene group in these organisms. Pasteurella multocida also displayed high frequencies of a putative DUS identical to that previously identified in H.influenzae and with a skewed distribution towards genome maintenance genes, indicating that this bacterium might be transformation competent under certain conditions. These results imply that the high frequency of DUS in genome maintenance genes is conserved among phylogenetically divergent species and thus are of significant biological importance. Increased DUS density is expected to enhance DNA uptake and the over-representation of DUS in genome maintenance genes might reflect facilitated recovery of genome preserving functions. For example, transient and beneficial increase in genome instability can be allowed during pathogenesis simply through loss of antimutator genes, since these DUS-containing sequences will be preferentially recovered. Furthermore, uptake of such genes could provide a mechanism for facilitated recovery from DNA damage after genotoxic stress.
Effects of carrier and dispersion on propagation of a directed electromagnetic pulse (1993)

Propagation of a directed pulse of electromagnetic radiation in a vacuum and in a rarefied, temporally dispersive medium is investigated. The pulse belongs to the class of broadband directed radiation beams termed electromagnetic ‘‘missiles’’ and is superposed on a carrier wave. First the propagation characteristics of the pulse in a vacuum are reviewed. In a vacuum the far-field time-integrated Poynting flux U(z) of the pulse drops off as 1/z1+4ν, with ‖ν‖≤1/4. In the corresponding expression for U(z) in a dispersive medium the leading term also varies as 1/z1+4ν since the high-frequency end of the spectrum experiences very little dispersion. In a dispersive medium the propagation of the precursors and of the carrier signal is examined in certain limits and expressions for the spatial variation of the vector potential are given.
Disseminated human immunodeficiency virus 1 (HIV-1) infection in SCID-hu mice after peripheral inoculation with HIV-1. (1994)

A small animal model that could be infected with human immunodeficiency virus 1 (HIV-1) after peripheral inoculation would greatly facilitate the study of the pathophysiology of acute HIV-1 infection. The utility of SCID mice implanted with human fetal thymus and liver (SCID-hu mice) for studying peripheral HIV-1 infection in vivo has been hampered by the requirement for direct intraimplant injection of HIV-1 and the continued restriction of the resultant HIV-1 infection to the human thymus and liver (hu-thy/liv) implant. This may have been due to the very low numbers of human T cells present in the SCID-hu mouse peripheral lymphoid compartment. Since the degree of the peripheral reconstitution of SCID-hu mice with human T cells may be a function of the hu-thy/liv implant size, we increased the quantity of hu-thy/liv tissue implanted under the renal capsule and implanted hu-thy/liv tissue under the capsules of both kidneys. This resulted in SCID-hu mice in which significant numbers of human T cells were detected in the peripheral blood, spleens, and lymph nodes. After intraimplant injection of HIV-1 into these modified SCID-hu mice, significant HIV-1 infection was detected by quantitative coculture not only in the hu-thy/liv implant, but also in the spleen and peripheral blood. This indicated that HIV-1 infection can spread from the thymus to the peripheral lymphoid compartment. More importantly, a similar degree of infection of the hu-thy/liv implant and peripheral lymphoid compartment occurred after peripheral intraperitoneal inoculation with HIV-1. Active viral replication was indicated by the detection of HIV-1 gag DNA, HIV-1 gag RNA, and spliced tat/rev RNA in the hu-thy/liv implants, peripheral blood mononuclear cells (PBMC), spleens, and lymph nodes of these HIV-1-infected SCID-hu mice. As a first step in using our modified SCID-hu mouse model to investigate the pathophysiological consequences of HIV-1 infection, the effect of HIV-1 infection on the expression of human cytokines shown to enhance HIV-1 replication was examined. Significantly more of the HIV-1-infected SCID-hu mice expressed mRNA for human tumor necrosis factors alpha and beta, and interleukin 2 in their spleens, lymph nodes, and PBMC than did uninfected SCID-hu mice. This suggested that HIV-1 infection in vivo can stimulate the expression of cytokine mRNA by human T cells.(ABSTRACT TRUNCATED AT 400 WORDS)
<title>AcycloPrime: a novel method for SNP analysis using fluorescence polarization</title> (2002)

Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation between individuals of a species and are therefore thought to be responsible for a large part of individual phenotypic variation. It has been estimated that a SNP may occur every 100-300 bases in the human genome. Research on human SNPs is expected to facilitate genetic mapping studies that may lead to a better understanding of the genetic basis for complex diseases and individual variation in drug metabolism. We have developed a novel assay for the identification of known SNPs using primer extension with the novel AcycloTerminators and a new thermostable polymerase, AcycloPol, in a homogeneous fluorescence polarization (FP) format. All assay steps can be performed in the same well of either a 384- or 96-well PCR-compatible microplate. FP provides several advantages, including simplicity and low reagent cost. The homogeneous assay format eliminates any need for separation or washing steps and is amenable to automation.
Expression of the Y-Encoded TSPY is Associated with Progression of Prostate Cancer (2010)

TSPY is a Y-encoded gene that is expressed in normal testicular germ cells and various cancer types including germ cell tumor, melanoma, hepatocellular carcinoma, and prostate cancer. Currently, the correlation between TSPY expression and oncogenic development has not been established, particularly in somatic cancers. To establish such correlation, we analyzed the expression of TSPY, in reference to its interactive oncoprotein, EEF1A, tumor biomarker, AMACR, and normal basal cell biomarker, p63, in 41 cases of clinical prostate cancers (CPCa), 17 cases of latent prostate cancers (LPCa), and 19 cases of non-cancerous prostate (control) by immunohistochemistry. Our results show that TSPY was detected more frequently (78%) in the clinical prostate cancer specimens than those of latent prostate cancer (47%) and control (50%). In the latent cancer group, the levels of TSPY expression could be correlated with increasing Gleason grades. TSPY expression was detected in seven out of nine high-grade latent cancer samples (Gleason 7 and more). The expression of the TSPY binding partner EEF1A was detectable in all prostate specimens, but the levels were higher in cancer cells in clinical and latent prostate cancer specimens than normal prostatic cells. These observations suggest that expressions of TSPY and its binding partner EEF1A are associated with the development and progression of prostate cancer.
Stochastic Optimization, Stochastic Approximation and Simulated Annealing (1999)

Abstract The sections in this article are Robbins–Monro Stochastic Approximation Stochastic Approximation with Gradient Approximations Based on Function Measurements Simultaneous Perturbation Stochastic Approximation Simulated Annealing Concluding Remarks Acknowledgements
Establishment of a Superficial Skin Infection Model in Mice by Using Staphylococcus aureus and Streptococcus pyogenes (2005)

A new animal model for the purpose of studying superficial infections is presented. In this model an infection is established by disruption of the skin barrier by partial removal of the epidermal layer by tape stripping and subsequent application of the pathogens Staphylococcus aureus and Streptococcus pyogenes. The infection and the infection route are purely topical, in contrast to those used in previously described animal models in mice, such as the skin suture-wound model, where the infection is introduced into the deeper layers of the skin. Thus, the present model is considered more biologically relevant for the study of superficial skin infections in mice and humans. Established topical antibiotic treatments are shown to be effective. The procedures involved in the model are simple, a feature that increases throughput and reproducibility. This new model should be applicable to the evaluation of novel antimicrobial treatments of superficial infections caused by S. aureus and S. pyogenes.
PCR inhibitors - occurrence, properties and removal (2012)

The polymerase chain reaction (PCR) is increasingly used as the standard method for detection and characterization of microorganisms and genetic markers in a variety of sample types. However, the method is prone to inhibiting substances, which may be present in the analysed sample and which may affect the sensitivity of the assay or even lead to false-negative results. The PCR inhibitors represent a diverse group of substances with different properties and mechanisms of action. Some of them are predominantly found in specific types of samples thus necessitating matrix-specific protocols for preparation of nucleic acids before PCR. A variety of protocols have been developed to remove the PCR inhibitors. This review focuses on the general properties of PCR inhibitors and their occurrence in specific matrices. Strategies for their removal from the sample and for quality control by assessing their influence on the individual PCR test are presented and discussed.
Preparation and Characterization of Poly(ethylene glycol) Vinyl Sulfone (1996)

Synthesis of the vinyl sulfone and chloroethyl sulfone derivatives of poly(ethylene glycol) (PEG) is described. The chloroethyl sulfone (CES-PEG) is rapidly converted to the vinyl sulfone (VS-PEG) in the presence of base but is stable in water at neutral pH. Reactions with small molecules such as beta-mercaptoethanol and N alpha-acetyllysine show that the vinyl sulfone derivative is highly selective for reaction with sulfhydryl groups relative to reaction with amino groups. Also, VS-PEG is stable in water. These properties indicate that VS-PEG should be useful for selective attachment of PEG to protein cysteine groups. This hypothesis was verified by reacting VS-PEG with cysteine groups of reduced ribonuclease (RNase); the reaction is rapid and selective at pH 7-9. Reaction at lysine sites of unreduced RNase occurs slowly at pH 9.3 and is essentially complete after 100 h. Amino acid residues other than lysine and cysteine are not reactive toward VS-PEG. The covalent linkage between VS-PEG and lysine or cysteine groups is shown to be stable.
Juvéderm injectable gel: A multicenter, double-blind, randomized study of safety and effectiveness (2008)

These next-generation HA dermal fillers can be reliably expected to provide long-term correction, with Juvéderm Ultra lasting more than 9 months and Juvéderm Ultra Plus lasting for a year or more.
Restoration of Vancomycin Susceptibility in Enterococcus faecalis by Antiresistance Determinant Gene Transfer (2001)

We assessed the ability of gene transfer to reverse vancomycin resistance in class A (VanA) glycopeptide-resistant Enterococcus faecalis. Recombinant shuttle vectors containing a vanH promoter-vanA antisense gene cassette fully restored vancomycin susceptibility through a combined transcriptional activator binding domain decoy and inducible vanA antisense RNA effect.
Positive-negative turbulence-free ghost imaging (2012)

This experiment observed turbulence-free positive and negative thermal light ghost images from independently recorded event histories of a “bucket” photo-detector and a charged coupled device (CCD) array. The positive (negative) ghost image is computed from the “bucket” detector counts which are above (below) its mean, and the ghost image is not degraded by the turbulence. How do the “bucket” photon counts yield a positive or negative ghost image with a distant CCD array? This letter provides a quantum interference model which effectively explains the phenomenon.
Acid-Sensing Ion Channel 1 Is Localized in Brain Regions with High Synaptic Density and Contributes to Fear Conditioning (2003)

The acid-sensing ion channel, ASIC1, contributes to synaptic plasticity in the hippocampus and to hippocampus-dependent spatial memory. To explore the role of ASIC1 in brain, we examined the distribution of ASIC1 protein. Surprisingly, although ASIC1 was present in the hippocampal circuit, it was much more abundant in several areas outside the hippocampus. ASIC1 was enriched in areas with strong excitatory synaptic input such as the glomerulus of the olfactory bulb, whisker barrel cortex, cingulate cortex, striatum, nucleus accumbens, amygdala, and cerebellar cortex. Because ASIC1 levels were particularly high in the amygdala, we focused further on this area. We found that extracellular acidosis elicited a greater current density in amygdala neurons than hippocampal neurons and that disrupting the ASIC1 gene eliminated H+-evoked currents in the amygdala. We also tested the effect of ASIC1 on amygdala-dependent behavior; ASIC1-null mice displayed deficits in cue and context fear conditioning, yet baseline fear on the elevated plus maze was intact. These studies suggest that ASIC1 is distributed to regions supporting high levels of synaptic plasticity and contributes to the neural mechanisms of fear conditioning.
Purification and biochemical characterization of phenylacetyl-CoA ligase from Pseudomonas putida. A specific enzyme for the catabolism of phenylacetic acid. (1990)

A new enzyme, phenylacetyl-CoA ligase (AMP-forming) (PA-CoA ligase, EC 6.2.1-) involved in the catabolism of phenylacetic acid (PAA) in Pseudomonas putida is described and characterized. PA-CoA ligase was specifically induced by PAA when P. putida was grown in a chemically defined medium in which phenylacetic acid was the sole carbon source. Hydroxyl, methyl-phenylacetyl derivatives, and other PAA close structural molecules did not induce the synthesis of this enzyme and neither did acetic, butyric, succinic, nor fatty acids (greater than C5 atoms carbon length). PA-CoA ligase requires ATP, CoA, PAA, and MgCl2 for its activity. The maximal rate of catalysis was achieved in 50 mM HCl/Tris buffer, pH 8.2, at 30 degrees C and under these conditions, the Km calculated for ATP, CoA, and PAA were 9.7, 1.0, and 16.5 mM, respectively. The enzyme is inhibited by some divalent cations (Cu2+, Zn2+, and Hg2+) and by the sulfhydryl reagents N-ethylmaleimide, 5,5'-dithiobis(2-nitrobenzoic acid), and p-chloromercuribenzoate. PA-CoA ligase was purified to homogeneity (513-fold). It runs as a single polypeptide in 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis and has a molecular mass of 48 +/- 1 kDa. PA-CoA ligase does not use as substrate either 3-hydroxyphenylacetic, 4-hydroxyphenylacetic, or 3,4-dihydroxyphenylacetic acids and shows a substrate specificity different from other acyl-CoA-activating enzymes. The enzyme is detected in P. putida from the early logarithmic phase of growth and is repressed by glucose, suggesting that PA-CoA ligase is a specific enzyme involved in the utilization of PAA as energy source.
Mannan-binding lectin (MBL)-associated serine protease-1 (MASP-1), a serine protease associated with humoral pattern-recognition molecules: normal and acute-phase levels in serum and stoichiometry of lectin pathway components (2012)

The pattern-recognition molecules mannan-binding lectin (MBL) and the three ficolins circulate in blood in complexes with MBL-associated serine proteases (MASPs). When MBL or ficolin recognizes a microorganism, activation of the MASPs occurs leading to activation of the complement system, an important component of the innate immune system. Three proteins are produced from the MASP1 gene: MASP-1 and MASP-3 and MAp44. We present an assay specific for MASP-1, which is based on inhibition of the binding of anti-MASP-1-specific antibody to MASP-1 domains coated onto microtitre wells. MASP-1 was found in serum in large complexes eluting in a position corresponding to ∼600 kDa after gel permeation chromatography in calcium-containing buffer and as monomers of ∼75 kDa in dissociating buffer. The concentration of MASP-1 in donor sera (n = 105) was distributed log-normally with a median value of 11 µg/ml (range 4-30 µg/ml). Serum and citrate plasma levels were similar, while the values in ethylenediamine tetraacetic acid plasma were slightly lower and in heparin plasma were 1·5 times higher than in serum. MASP-1 was present at adult level at 1 year of age, while it was 60% at birth. In normal healthy individuals the level of MASP-1 was stable throughout a 2-month period. After induction of an acute-phase reaction by operation we found an initial short decrease, concomitant with an increase in C-reactive protein levels, followed by an increase, doubling the MASP-1 concentration after 2 days. The present data prepare the ground for studies on the associations of MASP-1 levels with disease.
Polyethylene wear after total hip arthroplasty: the effect of a modular femoral head with an extended flange-reinforced neck. (1998)

The use of modular components in total hip arthroplasty has been thought to contribute to accelerated polyethylene wear. Specifically, a modular femoral head with a flange extension and a longer neck may cause increased wear. The purpose of the current study was to evaluate the effect of a flange extension on polyethylene wear. Ninety-one patients who had had a total of 100 primary total hip arthroplasties were evaluated after an intermediate duration of follow-up. All of the acetabular components consisted of a hemispherical titanium-alloy fiber-mesh porous-coated shell with a nonelevated modular polyethylene liner; they were inserted without cement and with use of supplemental screws through the dome after so-called line-to-line reaming. All of the femoral components consisted of a modular head with a diameter of twenty-eight millimeters and either a long neck (with a flange extension) or a short or medium neck (without a flange extension). The study group comprised sixty-two patients (sixty-six hips) who had had radiographic evaluation that was adequate to allow the valid measurement of polyethylene wear. Thirty-two hips were in men, and thirty-four were in women. The mean age of the patients was fifty-six years, the mean weight was seventy-three kilograms, and the mean duration of follow-up was 6.1 years (range, four to eight years). The rate of polyethylene wear in the eleven hips in which the femoral component had a flange extension was significantly greater than that in the fifty-five in which the femoral component did not have a flange extension (mean, 0.17 compared with 0.11 millimeter per year; p = 0.009). Multivariate analysis showed that the presence of a flange extension was associated with increased polyethylene wear to a greater degree (F = 2.86) than were all other variables that were measured, including a younger age (F = 1.72), a more vertical angle of the acetabular component (F = 0.49), a heavier weight (F = 0.14), male gender (F = 0.11), and a smaller initial thickness of the polyethylene (F = 0.02). These data support an association between the presence of a modular femoral head with a flange extension and an accelerated rate of polyethylene wear. The presumed mechanism is an increase in peripheral, or so-called rim, impingement of the flange-reinforced neck on the acetabulum due to a decrease in the ratio between the diameters of the femoral head and neck.
Mapping the Melatonin Receptor. 4. Comparison of the Binding Affinities of a Series of Substituted Phenylalkyl Amides (1996)

A series of 2-, 3-, and 4-substituted phenylalkyl amides were prepared as potential melatonin analogs in order to investigate the nature of the binding site of the melatonin receptor in chicken brain. The length of the alkyl chain was systematically varied from n = 1 to 4, and methoxyl substituents were incorporated into the phenyl ring at the 2-, 3-, and 4-positions. The maximum binding affinity was found to occur when n = 3 and when the methoxyl substituent was in the 3-position, the direct analog of the carbon framework of melatonin in which the 1,2-atoms of the indole ring have been removed. Whereas there was only a relatively small decrease in binding affinity for the corresponding 2-methoxy derivatives, 4-methoxyl substitution led to a large decrease in binding affinity, suggesting that the binding sites for the side chain and methoxyl group could not now be occupied at the same time. As in the indole analogs of melatonin, replacement of the methyl group of the amide by a longer alkyl chain led to an increase in binding affinity for ethyl and propyl with a subsequent decrease in binding affinity for butyl chains. Thus N-propanoyl-3-(3-methoxyphenyl)propanamine (6f) has a binding affinity of 5.6 nM, a remarkably high affinity for so simple a compound. Substitution of halogen for 3-methoxyl in the propanamide series gave a series of compounds with lower, but still substantial, binding affinities, the 3-chloro derivative 7e showing the highest affinity, 113 nM. In the case of the 3-fluoro propanamides, a maximum in the binding affinity was not observed in the series synthesized, and these derivatives will merit further exploration. These results demonstrate the utility of simple, readily modified phenylalkylamines as a "framework" for studying the effect of changes in the nature and position of substituents on the melatonin receptor binding affinity.
RNA interference in the light brown apple moth, Epiphyas postvittana (Walker) induced by double‐stranded RNA feeding (2006)

RNA interference (RNAi) or gene silencing is typically induced in insects by the injection of double-stranded RNAs (dsRNAs), short interfering RNAs, or through the use of hairpin constructs in transgenic insects. Here we demonstrate in the horticultural pest, Epiphyas postvittana (Lepidoptera: Tortricidae), that RNAi can be triggered by oral delivery of dsRNA to larvae. Transcript levels of a larval gut carboxylesterase gene (EposCXE1) were reduced to less than half that of controls within 2 days of being fed EposCXE1 dsRNA. Transcript levels of the pheromone binding protein gene (EposPBP1) were reduced in adult antennae by feeding larvae EposPBP1 dsRNA. Knockdown of EposPBP1 transcripts was observed for the first 2 days after adult eclosion but recovered to wild-type levels at 4 days posteclosion. The potential mechanisms involved in the initiation, movement and amplification of the silencing signal are discussed.