gebhart/patrepeval huggingface dataset:
Characterization of a Mutant &lt;italic&gt;Listeria monocytogenes&lt;/italic&gt; Strain Expressing Green Fluorescent Protein (2005)

To construct a recombinant strain of Listeria monocytogenes for the expression of heterologous genes, homologous recombination was utilized for insertional mutation, targeting its listeriolysin O gene (hly). The gene encoding green fluorescent protein (GFP) was used as the indicator of heterologous gene expression. The gene gfp was inserted into hly downstream from its promoter and signal sequence by an overlapping extension polymerase chain reaction, and was then cloned into the shuttle plasmid pKSV7 for allelic exchange with the L. monocytogenes chromosome. Homologous recombination was achieved by growing the electro-transformed L. monocytogenes cells on chloramphenicol plates at a non-permissive temperature. Sequencing analysis indicated correct insertion of the target gene in-frame with the signal sequence. The recombinant strain expressed GFP constitutively as revealed by fluorescence microscopy. The mutant strain L. monocytogenes hly-gfp lost its hemolytic activity as visualized on the blood agar or when analyzed with the culture supernatant samples. Such insertional mutation resulted in a reduced virulence of about 2 logs less than its parent strain L. monocytogenes 10403s as shown by the 50%-lethal-dose assays in the mouse and embryonated chicken egg models. These results thus demonstrate that mutated L. monocytogenes could be a potential carrier for the expression of heterologous passenger genes or could act as an indicator organism in the food industry.
Mutations in human complement regulator, membrane cofactor protein (CD46), predispose to development of familial hemolytic uremic syndrome (2003)

Membrane cofactor protein (MCP; CD46) is a widely expressed transmembrane complement regulator. Like factor H it inhibits complement activation by regulating C3b deposition on targets. Factor H mutations occur in 10-20% of patients with hemolytic uremic syndrome (HUS). We hypothesized that MCP mutations could predispose to HUS, and we sequenced MCP coding exons in affected individuals from 30 families. MCP mutations were detected in affected individuals of three families: a deletion of two amino acids (D237/S238) in family 1 (heterozygous) and a substitution, S206P, in families 2 (heterozygous) and 3 (homozygous). We evaluated protein expression and function in peripheral blood mononuclear cells from these individuals. An individual with the D237/S238 deletion had reduced MCP levels and approximately 50% C3b binding compared with normal controls. Individuals with the S206P change expressed normal quantities of protein, but demonstrated approximately 50% reduction in C3b binding in heterozygotes and complete lack of C3b binding in homozygotes. MCP expression and function was evaluated in transfectants reproducing these mutations. The deletion mutant was retained intracellularly. S206P protein was expressed on the cell surface but had a reduced ability to prevent complement activation, consistent with its reduced C3b binding and cofactor activity. This study presents further evidence that complement dysregulation predisposes to development of thrombotic microangiopathy and that screening patients for such defects could provide informed treatment strategies.
Thioesterase II of Escherichia coli Plays an Important Role in 3-Hydroxydecanoic Acid Production (2004)

3-Hydroxydecanoic acid (3HD) was produced in Escherichia coli by mobilizing (R)-3-hydroxydecanoyl-acyl carrier protein-coenzyme A transacylase (PhaG, encoded by the phaG gene). By employing an isogenic tesB (encoding thioesterase II)-negative knockout E. coli strain, CH01, it was found that the expressions of tesB and phaG can up-regulate each other. In addition, 3HD was synthesized from glucose or fructose by recombinant E. coli harboring phaG and tesB. This study supports the hypothesis that the physiological role of thioesterase II in E. coli is to prevent the abnormal accumulation of intracellular acyl-coenzyme A.
Hydrothermal syntheses and crystal structures of three zinc succinates: Zn(C4H4O4)-α, Zn(C4H4O4)-β and K2Zn(C4H4O4)2 (2003)

Three zinc succinate coordination polymers have been synthesised hydrothermally. Two polymorphs of Zn(C4H4O4) adopt three-dimensional structures consisting of tetrahedral Zn atoms isolated from each other via bis-bidentate succinate moieties. The polymorphs differ in the conformation of the succinate group, the α form (I) having syn-periplanar geometry whereas the β form (II) has anti-periplanar geometry. K2Zn(C4H4O4)2 (III) has a layered structure also composed of isolated tetrahedral Zn units. In this case the two crystallographically distinct succinate groups, one of each conformer, have bis-monodentate coordination, acting as both inter- and intra-layer bridges between neighbouring Zn-containing layers. The ‘double’ zinc succinate layers are separated along the b-axis by inter-layer potassium ions.
Transformation of a Metal−Organic Framework from the NbO to PtS Net (2004)

Two metal-organic frameworks (MOFs), MOF-501 and MOF-502, respectively, formulated as Co(2)(BPTC)(H(2)O)(5).G(x) and Co(2)(BPTC)(H(2)O)(DMF)(2).G(x) (BPTC = 3,3',5,5'-biphenyltetracarboxylate; G = guest molecules), have been synthesized and structurally characterized, and their topologies were found to be based on the NbO (MOF-501) and PtS (MOF-502) nets. Heating MOF-501 in solution results in the more thermodynamically favored MOF-502.
Atmospheric CO2 Content in the Past Deduced from Ice-Core Analyses (1982)

Probably the only direct way to reconstruct historic atmospheric CO 2 /air ratios is by measuring the air occluded in ice samples. For such studies, ice samples from very cold regions have an advantage in that the snow and ice probably never had been in contact with liquid water, which interacts with trapped atmospheric CO 2 . However, even ice samples from very cold regions may have additional CO 2 , which could have been enclosed during the formation of precipitation, adsorbed at the surface of snow and firn grains, or produced in the ice by chemical reactions on impurities. The gas in ice samples from Camp Cenand Byrd station was extracted both by a vacuum-melting and by a mechanical crushing procedure and the CO 2 abundance measured by two different analytical methods. N 2 /O 2 /Ar ratios were also measured. The shift to lower CO 2 concentration in both cores at a certain depth found previously is confirmed. Changes in the atmospheric CO 2 concentration at the corresponding time, about the end of the last glaciation, is the probable explanation of our CO 2 results.
Activation of Protease-Activated Receptor-2 (PAR-2) Elicits Nitric Oxide–Dependent Dilatation of the Basilar Artery In Vivo (1998)

To the best of our knowledge, this study is the first to examine whether PAR-2-mediated vasodilatation is functional in cerebral arteries and is also the first to directly assess the effects of PAR-2 activation on vascular tone in vivo. The results suggest that activation of PAR-2 is an effective and powerful vasodilator mechanism in cerebral arteries in vivo. Cerebral vasodilator responses to PAR-2 activation are mediated by nitric oxide and are likely to be endothelium dependent.
Level, downhill and uphill walking identification using neural networks (1993)

Body accelerations during human walking are recorded by a portable measuring device. A new method for parametrising body accelerations is introduced. The parameters are presented to a Kohonen neural network classifier and the feasibility of identification and dissociation of level and walking on a gradient is demonstrated. The most important and original aspect of this classification is its ability to identify the gradient of walking performed in free-living conditions from walking trained on a treadmill.
Expression of oncostatin M receptor β in a specific subset of nociceptive sensory neurons (2003)

Oncostatin M belongs to the interleukin-6 family of cytokines and acts as a multifunctional cytokine during murine embryogenesis and in inflammatory reactions. Although it has been demonstrated that oncostatin M has biological activities on many types of cells, including hepatocytes, dermal fibroblasts and endothelial cells, the roles of oncostatin M in the murine peripheral nervous system remain unclear. Here, we investigated the expression of specific beta-subunit of oncostatin M receptor in the dorsal root ganglia of adult mice. In the adult dorsal root ganglia, beta-subunit of oncostatin M receptor was exclusively expressed in small-sized neurons. Approximately 13% of total dorsal root ganglia neurons in mice contained beta-subunit of oncostatin M receptor. The double-immunofluorescence method revealed that approximately 28% of beta-subunit of oncostatin M receptor-positive neurons contained TrkA immunoreactivity, 63% expressed Ret immunoreactivity and 58% bound isolectin B4. No neuropeptides, including substance P and calcitonin gene-related peptide, were contained in the neurons. In addition, all beta-subunit of oncostatin M receptor-positive neurons expressed both vanilloid receptor 1 and P2X3 purinergic receptor. These neurons projected to the inner portion of lamina II in the dorsal horn of spinal cord and the dermis of skin. Seven days after sciatic nerve axotomy, the expression of beta-subunit of oncostatin M receptor was down-regulated in the lumbar dorsal root ganglia of the injured side. Our study demonstrated that beta-subunit of oncostatin M receptor was expressed in both cell bodies and processes of nonpeptidergic nociceptive neurons in adult mice, suggesting that oncostatin M may affect the nociceptive function of the neurons through the modulation of vanilloid receptor 1 and P2X3 expression.
Time-warping neural network for phoneme recognition (1991)

The author investigates a feedforward neural network that can accept phonemes with an arbitrary duration coping with nonlinear time warping. The time-warping neural network is characterized by the time-warping functions embedded between the input layer and the first hidden layer in the network. The input layer accesses three different time points. The accessing points are determined by the time-warping functions. The input spectrum sequence itself is not warped but the accessing-point sequence is warped. The advantage of this network architecture is that the input layer can access the original spectrum sequence. The proposed network demonstrated higher phoneme recognition accuracy than the baseline recognizer based on conventional feedforward neural networks. The recognition accuracy was even higher than that achieved with discrete hidden Markov models.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cloning of antibiotic resistance and nutritional genes in streptomycetes (1982)

Methodology which allows consistent shotgun cloning of streptomycete genes is presented. Parameters that increase transformation efficiency of Streptomyces lividans 66 were adjusted to generate reproducibly a population of cloned genes likely to represent the entire genome. Factors which influence the recovery of viable transformants include: growth phase of the mycelium, ionic and osmotic characteristics of the medium during protoplast formation and transformation, and moisture content and protoplast density during regeneration. A modified transformation procedure was devised which increased transformation frequency more than 20-fold (allowing up to 10(7) primary transformants per microgram of SLP1.2 covalently closed circular DNA) and greatly facilitated the cloning of drug resistance genes and biosynthetic genes, using one of two plasmid vectors. Viomycin resistance genes on BamHI or PstI fragments were cloned from S. vinaceus genomic DNA into S. lividans, using the SLP1.2 vector. At least three different S. vinaceus BamHI fragments (1.9, 5.8, or 8.5 kilobases) confer viomycin resistance; only one PstI fragment (4.3 kilobases) was found. Recombinant plasmids were all able to produce lethal zygosis and to be transferred by conjugation within S. lividans. SCP2 was used to clone S. coelicolor A3(2) genes that "complemented" the auxotrophic mutation hisD3, argA1, or guaA1. Recombinant DNA technology can now be applied to economically and academically interesting problems unique to streptomycete molecular biology.
Heart Rate Slowing for Myocardial Dysfunction/Heart Failure (2006)

Heart failure is a major health problem, and is one of the few cardiovascular diseases that increased its prevalence over the last decade. Increased heart rate, generally observed in patients with heart failure, is involved in the deterioration of cardiac pump function. However, the effects of 'pure' heart rate reduction on the progression of heart failure are unknown. In a rat model of heart failure, ivabradine, a blocker of I(f) channels reduces dose-dependently heart rate without modification of blood pressure. This heart rate reduction is associated with an improvement in cardiac function. After chronic administration, this improvement of cardiac function persists after ivabradine withdrawal, revealing an improvement in intrinsic myocardial function. This beneficial effect could be explained by direct effects of heart rate reduction induced by ivabradine, i.e. improved myocardial oxygen supply to demand ratio, and/or myocardial tissular effects induced by chronic decrease in heart rate such, i.e. decreased extracellular collagen accumulation, increased myocardial microcirculation. In conclusion, 'pure' chronic heart rate reduction can be beneficial in heart failure.
Novel Roles of Lysines 122, 125, and 58 in Functional Differences between Human and Murine MD-2 (2009)

The MD-2/TLR4 complex provides a highly robust mechanism for recognition and response of mammalian innate immunity to Gram-negative bacterial endotoxins. Despite overall close structural and functional similarity, human (h) and murine (m) MD-2 show several species-related differences, including the ability of hMD-2, but not mMD-2, to bind endotoxin (E) in the absence of TLR4. Wild-type mMD-2 can support TLR4-dependent cell activation by E only when mMD-2 and mTLR4 are coexpressed in the same cell. However, replacement of Glu122, Leu125, and/or Asn58 of mMD-2 with the corresponding residues (lysines) of hMD-2 was sufficient to yield soluble extracellular MD-2 that reacted with monomeric E . sCD14 complex to form extracellular monomeric E . MD-2 that activated cells expressing TLR4 without MD-2. Moreover, in contrast to wild-type mMD-2, double and triple mMD-2 mutants also supported E-triggered signaling in combination with human TLR4. Conversely, a K125L mutant of hMD-2 reacted with E . CD14 and activated TLR4 only when coexpressed with TLR4, and not when secreted without TLR4. These findings reveal novel roles of lysines 122, 125, and 58 in human MD-2 that contribute to the functional differences between human and murine MD-2 and, potentially, to differences in the sensitivity of humans and mice to endotoxin.
Identification of polypeptide components of the Epstein-Barr virus early antigen complex with monoclonal antibodies (1983)

Three monoclonal antibodies were produced against the Epstein-Barr virus-induced early antigen complex. These antibodies were shown to be specific for the early antigen complex by the fact that they only reacted with cells supporting a permissive or abortive Epstein-Barr virus infection and their synthesis was not affected by inhibitors of viral DNA synthesis. One monoclonal antibody, designated R3, was directed against a diffuse component of the early antigen complex since it reacted by immunofluorescence with cells fixed in acetone or methanol. The other two monoclonal antibodies, designated K8 and K9, reacted with a methanol-sensitive restricted component of this complex. The appearance of the R3 antigen in P3HR-1 superinfected Raji cells occurred approximately 4 h earlier than the antigen detected by K8. By both sodium dodecyl sulfate-polyacrylamide gel electrophoresis and radioimmunoelectrophoresis, it was determined that the R3 monoclonal antibody recognized two major polypeptides with molecular weights of approximately 50,000 to 52,000, whereas K8 and K9 precipitated a protein of approximately 85,000. The R3 monoclonal antibody also immunoprecipitated an in vitro primary translation product. It was, therefore, possible to map this product to the Epstein-Barr virus DNA BamH1 M fragment. These in vitro products were slightly smaller than the in vivo proteins, suggesting that these proteins probably undergo posttranslational modification during the virus replication cycle.
PNA: Synthetic Polyamide Nucleic Acids with Unusual Binding Properties (1998)

The astonishing discovery that peptide nucleic acids (PNAs, B=nucleobase), in spite of their drastic structural difference to natural DNA, are better nucleic acid mimetics than many other oligonucleotides has resulted in an explosion of research into this class of compounds. The synthesis, physical properties, and biological interactions of PNAs as well as their chimeras with DNA and RNA are summarized here.
Microvesicles and Viral Infection (2011)

Cells secrete various membrane-enclosed microvesicles from their cell surface (shedding microvesicles) and from internal, endosome-derived membranes (exosomes). Intriguingly, these vesicles have many characteristics in common with enveloped viruses, including biophysical properties, biogenesis, and uptake by cells. Recent discoveries describing the microvesicle-mediated intercellular transfer of functional cellular proteins, RNAs, and mRNAs have revealed additional similarities between viruses and cellular microvesicles. Apparent differences include the complexity of viral entry, temporally regulated viral expression, and self-replication proceeding to infection of new cells. Interestingly, many virally infected cells secrete microvesicles that differ in content from their virion counterparts but may contain various viral proteins and RNAs. For the most part, these particles have not been analyzed for their content or functions during viral infection. However, early studies of microvesicles (L-particles) secreted from herpes simplex virus-infected cells provided the first evidence of microvesicle-mediated intercellular communication. In the case of Epstein-Barr virus, recent evidence suggests that this tumorigenic herpesvirus also utilizes exosomes as a mechanism of cell-to-cell communication through the transfer of signaling competent proteins and functional microRNAs to uninfected cells. This review focuses on aspects of the biology of microvesicles with an emphasis on their potential contributions to viral infection and pathogenesis.
Effect of Nature and Supply of Carbon Sources on Cellulase Formation in Pseudomonas fluorescens var. cellulosa (1970)

Journal Article Effect of Nature and Supply of Carbon Sources on Cellulase Formation in Pseudomonas fluorescens var. cellulosa Get access KUNIO YAMANE, KUNIO YAMANE Botanical Institute, Faculty of Science, Tokyo Kyoiku UniversityOtsuka, Tokyo Search for other works by this author on: Oxford Academic PubMed Google Scholar HIROSHI SUZUKI, HIROSHI SUZUKI Botanical Institute, Faculty of Science, Tokyo Kyoiku UniversityOtsuka, Tokyo Search for other works by this author on: Oxford Academic PubMed Google Scholar MASAO HIROTANI, MASAO HIROTANI Botanical Institute, Faculty of Science, Tokyo Kyoiku UniversityOtsuka, Tokyo Search for other works by this author on: Oxford Academic PubMed Google Scholar HARUMI OZAWA, HARUMI OZAWA Botanical Institute, Faculty of Science, Tokyo Kyoiku UniversityOtsuka, Tokyo Search for other works by this author on: Oxford Academic PubMed Google Scholar KAZUTOSI NISIZAWA KAZUTOSI NISIZAWA Botanical Institute, Faculty of Science, Tokyo Kyoiku UniversityOtsuka, Tokyo Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Biochemistry, Volume 67, Issue 1, January 1970, Pages 9–18, https://doi.org/10.1093/oxfordjournals.jbchem.a129238 Published: 01 January 1970 Article history Received: 08 May 1969 Published: 01 January 1970
Distributed treatment systems (2020)

This section presents a review of the scientific literature published in 2019 on topics relating to distributed treatment systems. This review is divided into the following sections: constituent removal, treatment technologies, planning and treatment management, and other topics. PRACTITIONER POINTS: Highlights changes and innovation in removal techniques and technologies in water treatment. Reviews management systems of distributed treatment systems. Discusses point-of-use treatment systems.
Differential response of cancer cells to HDAC inhibitors trichostatin A and depsipeptide (2011)

Although generally thought to have similar activities, the HDAC modulators trichostatin A and depsipeptide demonstrated distinct phenotypes in the inhibition of cancer cell viability and of HDAC activity, in their selectivity for cancer vs normal cells, and in their effects on histone modifications. These differences in mode of action may bear on the future therapeutic and research application of these inhibitors.
Bioconversion of Piceid to Piceid Glucoside Using Amylosucrase from Alteromonas macleodii Deep Ecotype (2012)

Resveratrol, or its glycoside form piceid, is a dietary antioxidant polyphenolic compound, found in grapes and red wine that has been shown to have protective effects against cardiovascular disease. However, very low water solubility of the compound may limit its application in the food and pharmaceutical industries. The amylosucrase (AMAS) of Alteromonas macleodii Deep ecotype was expressed in Escherichia coli and showed high glycosyltransferase activity to produce the glucosyl piceid when piceid was used as an acceptor. The conversion yield of piceid glucoside was 35.2%. Biotransformation using culture of the E. coli harboring the amas gene increased the yield up to 70.8%. The transfer product was purified by reverse phase chromatography and recycling preparative HPLC, and the molecular structure of the piceid glucoside was determined using NMR spectroscopy. The piceid glucoside was identified as glucosyl-alpha-(1-->4)-piceid. The solubility of glucosyl piceid was 5.26 and 1.14 times higher than those of resveratrol and piceid, respectively. It is anticipated that dietary intake of this compound is more effective by enhancing the bioavailability of resveratrol in the human body because of its hydrophilic properties in the intestinal fluid.
Random screening of promoters from Escherichia coli and classification based on the promoter strength. (1991)

Five hundred fifty DNA fragments 100-500 base pairs in length were cloned from total chromosomal DNA of Escherichia coli, each capable of promoting the synthesis of beta-lactamase when inserted upstream of the ampC structural gene without its own promoter in a promoter-probe plasmid. All clones in this library of putative promoters were classified based on the level of resistance to ampicillin, which ranged from 10 to more than 1,500 micrograms/ml. Most of the higher levels of drug resistance (more than 1,000 micrograms/ml) were due not only to an increase in gene expression but also to an increase in plasmid copy number. The DNA fragments which produced the highest level of drug resistance all mapped at 5.7 min on the E. coli chromosome and shared the same nucleotide sequence. In these fragments, a strong promoter was found, which carries an up stream AT-rich sequence in addition to -35 and -10 signals of the promoter consensus.