gebhart/patrepeval huggingface dataset:
Characterization of ChpBK, an mRNA Interferase from Escherichia coli (2005)

Escherichia coli contains a number of antitoxin-toxin modules on its chromosome, which are responsible for cell growth arrest and possible cell death. ChpBK is a toxin encoded by the ChpBIK antitoxin-toxin module. This module consists of a pair of genes, chpBI and chpBK encoding antitoxin ChpBI and toxin ChpBK, respectively. ChpBK consists of 116 amino acid residues, and its sequence shows 35% identity and 52% similarity to MazF, another E. coli toxin. MazF has been shown to be a sequence-specific (ACA) endoribonuclease that cleaves cellular mRNAs and effectively blocks protein synthesis and is thus termed as an mRNA interferase. Here we demonstrate that ChpBK is another mRNA interferase in E. coli whose induction effectively blocks cell growth in a manner similar to that of MazF. The protein synthesis as judged by incorporation of [35S]methionine was, however, reduced by only 60% upon ChpBK induction. We demonstrate that ChpBK is a new sequence-specific endoribonuclease that cleaves mRNAs both in vivo and in vitro at the 5'-or3'-side of the A residue in ACY sequences (Y is U, A, or G). The ChpBK cleavage of a synthetic RNA substrate generated a 2',3'-cyclic phosphate group at the 3'-end of the 5'-end product and a 5'-OH group at the 5'-end of the 3'-end product in a manner identical to that of MazF.
Molecular basis of attenuation of neurovirulence of wild-type Japanese encephalitis virus strain SA14 (1995)

To identify the molecular determinants for attenuation of wild-type Japanese encephalitis (JE) virus strain SA14, the RNA genome of wild-type strain SA14 and its attenuated vaccine virus SA14-2-8 were reverse transcribed, amplified by PCR and sequenced. Comparison of the nucleotide sequence of SA14-2-8 vaccine virus with virulent parent SA14 virus and with two other attenuated vaccine viruses derived from SA14 virus (SA14-14-2/PHK and SA14-14-2/PDK) revealed only seven amino acids in the virulent parent SA14 had been substituted in all three attenuated vaccines. Four were in the envelope (E) protein (E-138, E-176, E-315 and E-439), one in non-structural protein 2B (NS2B-63), one in NS3 (NS3-105), and one in NS4B (NS4B-106). The substitutions at E-315 and E-439 arose due to correction of the SA14/CDC sequence published previously by Nitayaphan et al. (Virology 177, 541-552, 1990). The mutations in NS2B and NS3 are in functional domains of the trypsin-like serine protease. Attenuation of SA14 virus may therefore, in part, be due to alterations in viral protease activity, which could affect replication of the virus.
Colon Cancer Growth and Dissemination Relies upon Thrombin, Stromal PAR-1, and Fibrinogen (2015)

Thrombin-mediated proteolysis is a major determinant of metastasis, but is not universally important for primary tumor growth. Here, we report that colorectal adenocarcinoma represents one important exception whereby thrombin-mediated functions support both primary tumor growth and metastasis. In contrast with studies of multiple nongastrointestinal cancers, we found that the growth of primary tumors formed by murine and human colon cancer cells was reduced in mice by genetic or pharmacologic reduction of circulating prothrombin. Reduced prothrombin expression was associated with lower mitotic indices and invasion of surrounding tissue. Mechanistic investigations revealed that thrombin-driven colonic adenocarcinoma growth relied upon at least two targets of thrombin-mediated proteolysis, protease-activated receptor-1 (PAR-1) expressed by stromal cells and the extracellular matrix protein, fibrinogen. Colonic adenocarcinoma growth was reduced in PAR-1-deficient mice, implicating stromal cell-associated PAR-1 as one thrombin target important for tumor outgrowth. Furthermore, tumor growth was dramatically impeded in fibrinogen-deficient mice, offering the first direct evidence of a critical functional role for fibrinogen in malignant tumor growth. Tumors harvested from fibrinogen-deficient mice displayed a relative reduction in cell proliferative indices, as well as increased tumor necrosis and decreased tumor vascular density. Collectively, our findings established a functional role for thrombin and its targets PAR-1 and fibrinogen in the pathogenesis of colonic adenocarcinoma, supporting tumor growth as well as local invasion and metastasis.
Characterization of the Ligand-Binding Domain of the Ecdysteroid Receptor from Drosophila Melanogaster (2003)

Mutants created by site-directed mutagenesis were used to elucidate the function of amino acids involved in ligand binding to ecdysteroid receptor (EcR) and heterodimer formation with ultraspiracle (USP). The results demonstrate the importance of the C-terminal part of the D-domain and helix 12 of EcR for hormone binding. Some amino acids are involved either in ligand binding to EcR (E476, M504, D572, I617, N626) or ligand-dependent heterodimerization as determined by gel mobility shift assays (A612, L615, T619), while others are involved in both functions (K497, E648). Some amino acids are suboptimal for ligand binding (L615, T619), but mediate ligand-dependent dimerization. We conclude that the enhanced regulatory potential by ligand-dependent modulation of dimerization in the wild type is achieved at the expense of optimal ligand binding. Mutation of amino acids (K497, E648) involved in the salt bridge between helix 4 and 12 impair ligand binding to EcR more severely than hormone binding to the heterodimer, indicating that to some extent heterodimerization compensates for the deleterious effect of certain mutations. Different effects of the same point mutations on ligand binding to EcR and EcR/USP (R511, A612, L615, I617, T619, N626) indicate that the ligand-binding pocket is modified by heterodimerization.
Rice Biotechnology and Genetic Engineering: Biotechnology of Food Crops (1994)

Rice biotechnology and genetic engineering , Rice biotechnology and genetic engineering , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Genomic organisation of the bovine alpha-S1 casein gene (1991)

We report the sequence of the complete bovine alpha-s1 casein gene eludicating for the first time the genomic organization of an alpha-s type casein gene. Extending over 17508 bp the gene is split into 19 exons, ranging in size from 24 bp to 385 bp. Except for the translational stop codon not a single coding triplet of the alpha-s1 reading frame is disrupted by any of the splice junctions, which all confirm to known splice consensus sequences. Nine out of 16 coding exons begin with a 'GAX' codon, specific for glutamate. Splicing of this codon from exon 10 to the preceding exon creates a major phosphorylation site. An intron-exon-intron stretch of 154 bp comprising exons 10 and 13 is found precisely duplicated. Associated with the gene, copies of 8 atriodactyla retroposons are found, 6 of which are interspersed into the sequences of the three longest introns. We discuss the possibility that three functional parts of the gene have been recruited and evolutionary conserved at a time before gene diversification gave rise to the separate evolution of alpha- and beta-type casein-genes.
Electrospun scaffolds limit the regenerative potential of the airway epithelium (2019)

NA.
Tau Suppression in a Neurodegenerative Mouse Model Improves Memory Function (2005)

Neurofibrillary tangles (NFTs) are the most common intraneuronal inclusion in the brains of patients with neurodegenerative diseases and have been implicated in mediating neuronal death and cognitive deficits. Here, we found that mice expressing a repressible human tau variant developed progressive age-related NFTs, neuronal loss, and behavioral impairments. After the suppression of transgenic tau, memory function recovered, and neuron numbers stabilized, but to our surprise, NFTs continued to accumulate. Thus, NFTs are not sufficient to cause cognitive decline or neuronal death in this model of tauopathy.
Double-strand break repair by interchromosomal recombination: suppression of chromosomal translocations (1998)

To directly determine whether recombinational repair of double-strand breaks (DSBs) can occur between heterologous chromosomes and lead to chromosomal rearrangements in mammalian cells, we employed an ES cell system to analyze recombination between repeats on heterologous chromosomes. We found that recombination is induced at least 1000-fold following the introduction of a DSB in one repeat. Most (98%) recombinants repaired the DSB by gene conversion in which a small amount of sequence information was transferred from the unbroken chromosome onto the broken chromosome. The remaining recombinants transferred a larger amount of information, but still no chromosomal aberrations were apparent. Thus, mammalian cells are capable of searching genome-wide for sequences that are suitable for DSB repair. The lack of crossover events that would have led to translocations supports a model in which recombination is coupled to replication.
The influence of serum cytokines and growth factors on osteoclast formation in Paget's disease (2002)

Both M-CSF and IL-6 play a major role in osteoclast formation and bone resorption in Paget's disease and measurement of serum M-CSF may provide a useful indicator of disease activity.
Near patient testing for Helicobacter pylori: a detailed evaluation of the Cortecs Helisal Rapid Blood test (1997)

The test could be appropriate for testing younger symptomatic patients. Its usefulness was, however, found to be limited by poor readability of some results and poor specificity. Reading of some results as equivocal would be appropriate.
Degenerate Oligonucleotide Gene Shuffling (2006)

Improvement of the biochemical characteristics of enzymes has been aided by misincorporation mutagenesis and DNA shuffling. Shuffling techniques can be used on a collection of mutants of the same gene, or related families of genes can be shuffled to produce mutants encoding chimeric gene products. One difficulty with current shuffling procedures is the predominance of unshuffled ("parental") molecules in the pool of mutants. We describe a procedure for gene shuffling using degenerate primers that allows control of the relative levels of recombination between the genes that are shuffled and reduces the regeneration of unshuffled parental genes. This procedure has the advantage of avoiding the use of endonucleases for gene fragmentation before shuffling and allows the use of random mutagenesis of selected segments of the gene as part of the procedure. We illustrate the use of the technique with a diverse family of beta-xylanase genes that possess widely different G and C contents.
Clinical applications of laser scanning cytometry (2002)

This study reviews existing and potential clinical applications of laser scanning cytometry (LSC) and outlines possible future developments. LSC provides a technology for solid phase cytometry. Fluorochrome-labeled specimens are immobilized on microscopic slides that are placed on a conventional epifluorescence microscope and analyzed by one or two lasers. Data comparable to flow cytometry are generated. In addition, the position of each event is recorded, a feature that allows relocalization and visualization of each measured event. The major advantage of LSC compared with other cytometric methods is the combination of two features: (a) the minimal clinical sample volume needed and (b) the connection of fluorescence data and morphological information for the measured event. Since the introduction of LSC, numerous methods have been established for the analysis of cells, cellular compartments, and tissues. Although most cytometric methods use only two or three colors, the characterization of specimens with up to five fluorochromes is possible. Most clinical applications have been designed to determine ploidy and immunophenotype; other applications include analyses of tissue biopsies and sections, fluorescence in situ hybridization, and the combination of vital and nonvital information on a single-cell basis. With the currently available assays, LSC has proven its wide spectrum of clinical applicability in slide-based cytometry and can be introduced as a standard technology in multiple clinical settings.
Blepharospasm--successful treatment with baclofen and sodium valproate. A case report. (1983)

In a patient with idiopathic blepharospasm treatment with the gamma-aminobutyric acid (GABA)-mimetic combination of baclofen and sodium valproate resulted in complete and sustained remission of symptoms and signs. It is suggested that blepharospasm results from a relative deficiency of GABA-ergic neurons and dopamine predominance in the striatum, and that treatment with the GABA-mimetic agents (baclofen and sodium valproate) represents a more physiological means of reducing dopaminergic predominance in the striatum. This report, together with previous reports, suggests that the combination of these two agents should be tried in the initial management of this syndrome.
Contractivity of fractal transforms for image coding (1993)

In the Letter the contractivity of existing fractal transforms for use in image compression schemes is examined. The coding process is described as nonlinear transformation in the finite-dimensional Euclidean vector space. Sufficient conditions are derived for contractivity based on the spectral norm and the spectral radius of the transformation matrix. As a result bounds for the encoding parameters can be formulated which are tighter than those ones known so far.
In Plants, 3-O-Methylglucose Is Phosphorylated by Hexokinase But Not Perceived as a Sugar (2003)

Abstract In plants, sugars are the main respiratory substrates and important signaling molecules in the regulation of carbon metabolism. Sugar signaling studies suggested that sugar sensing involves several key components, among them hexokinase (HXK). Although the sensing mechanism of HXK is unknown, several experiments support the hypothesis that hexose phosphorylation is a determining factor. Glucose (Glc) analogs transported into cells but not phosphorylated are frequently used to test this hypothesis, among them 3-O-methyl-Glc (3-OMG). The aim of the present work was to investigate the effects and fate of 3-OMG in heterotrophic plant cells. Measurements of respiration rates, protein and metabolite contents, and protease activities and amounts showed that 3-OMG is not a respiratory substrate and does not contribute to biosynthesis. Proteolysis and lipolysis are induced in 3-OMG-fed maize (Zea mays L. cv DEA) roots in the same way as in sugar-starved organs. However, contrary to the generally accepted idea, phosphorous and carbon nuclear magnetic resonance experiments and enzymatic assays prove that 3-OMG is phosphorylated to 3-OMG-6-phosphate, which accumulates in the cells. Insofar as plant HXK is involved in sugar sensing, these findings are discussed on the basis of the kinetic properties because the catalytic efficiency of HXK isolated from maize root tips is five orders of magnitude lower for 3-OMG than for Glc and Man.
The effect of pH on photobleaching of organic laser dyes (1972)

Variation of pH affects the quantum efficiency for photobleaching and the rate of aggregation following photobleaching. The adjustment of pH to minimize photobleaching is useful for rhodamine 6G and pyronon B, but not for disodium fluorescein. Some of the operational problems of dye lasers may be interpreted as aggregation effects.
Learning by Tracking: Siamese CNN for Robust Target Association (2016)

This paper introduces a novel approach to the task of data association within the context of pedestrian tracking, by introducing a two-stage learning scheme to match pairs of detections. First, a Siamese convolutional neural network (CNN) is trained to learn descriptors encoding local spatio-temporal structures between the two input image patches, aggregating pixel values and optical flow information. Second, a set of contextual features derived from the position and size of the compared input patches are combined with the CNN output by means of a gradient boosting classifier to generate the final matching probability. This learning approach is validated by using a linear programming based multi-person tracker showing that even a simple and efficient tracker may outperform much more complex models when fed with our learned matching probabilities. Results on publicly available sequences show that our method meets state-of-the-art standards in multiple people tracking.
Adoptive Transfer of Diabetes Into Immunodeficient NOD-scid/scid Mice: Relative Contributions of CD4+ and CD8+ T-Cells From Diabetic Versus Prediabetic NOD.NON-Thy-1a Donors (1993)

Precise definition of the role of both CD4 and CD8 T-cell subsets from NOD mice in the adoptive transfer of diabetes has been complicated by the possibility that endogenous T-cells may be recruited. Two newly created NOD congenic stocks, NOD.NON-Thy-1a and NOD/LtSz-scid, have been used as T-cell donors and recipients, respectively, to eliminate contributions from endogenous T-cells and thus to define the requirement for transferred T-cell subsets as a function of underlying diabetes development in the NOD donor. Total T-cells and T-cell subsets prepared from either prediabetic or diabetic NOD.NON-Thy-1a donors were adoptively transferred into 6-wk-old NOD-scid/scid recipients that were monitored for diabetes development. Both flow cytometric and histological analysis of recipient spleen and pancreas after adoptive transfer showed lymphocytes of donor (Thy1.1+) origin exclusively. Total T-cell and enriched CD4+ T-cell preparations from both diabetic and young prediabetic donors transferred diabetes to NOD-scid/scid recipients. However, the mean time to diabetes onset was doubled when CD4+ lymphocytes were isolated from prediabetic versus diabetic donors, and these transfers were complicated by the generation of small but significant numbers of CD8+ cells over time. Enriched CD8+ populations alone were unable to transfer disease. More rigorous exclusion of CD8+ cells by means of anti-CD8 MoAb treatment in vivo of the recipients of enriched CD4+ cells demonstrated a significant difference in the diabetogenic potency of CD4+ lymphocytes from diabetic versus nondiabetic donors. Diabetes was adoptively transferred to 58% of the recipients of enriched CD4+ lymphocytes from diabetic donors. In contrast, none of the recipients of enriched CD4+ lymphocytes from young prediabetic donors developed diabetes after MoAb treatment in vivo. The ability of a T-cell population to produce severe insulitis and sialitis in NOD-scid/scid recipients of T-cells closely paralleled its ability to induce diabetes. In an effort to suppress insulitis by suppression of macrophage migration to the islets, NOD-scid/scid mice were treated with silica in conjunction with adoptive transfer of T-cells from diabetic donors. Chronic silica treatment failed to deplete tissue macrophages and did not prevent diabetes development after transfer of unfractionated T-cells. Evidence is discussed indicating that the age-associated differences in ability of CD4+ T-cells to adoptively transfer diabetes in the absence of the CD8+ T-cells subset is a function of prior, chronic exposure of the CD4+ lymphocytes to beta-cell antigens in the donor.(ABSTRACT TRUNCATED AT 400 WORDS)
Type beta transforming growth factor reversibly inhibits the early proliferative response to partial hepatectomy in the rat. (1988)

Type beta transforming growth factor (TGF-beta), a factor produced by many cell types, is a potent inhibitor of hepatocyte DNA synthesis in vitro. To determine whether TGF-beta can influence hepatocyte proliferation in vivo, its effects were examined on the regenerative response of liver to partial hepatectomy (PH) in the rat. Porcine platelet-derived TGF-beta 1 (0.5 micrograms), administered intravenously at the time of PH and 11 hr later, reduced the fraction of hepatocytes engaged in DNA synthesis 22 hr after PH by 67% and inhibited the rate of hepatic [3H]thymidine incorporation by 50%. TGF-beta 2 produced a similar effect. A single dose of 0.5 micrograms of TGF-beta 1 given 11 hr after PH reduced liver [3H]thymidine incorporation by 32%; 4.5 micrograms of TGF-beta 1 or TGF-beta 2 inhibited DNA synthesis by 88% and the labeling index by 86%. Although sensitive to TGF-beta administered 11 hr after PH, late in the G1 phase of the cell cycle, a single dose of 0.5 micrograms given at the time of PH did not significantly influence DNA synthesis 22 hr after PH. The inhibitory effects of TGF-beta were transient; rats treated with two 0.5-microgram doses of TGF-beta at 0 and 11 hr had completely restored their original liver DNA mass 8 days after PH. Administration of 0.5 microgram of either TGF-beta 1 or TGF-beta 2 every 12 hr for 5 days failed to suppress the recovery of hepatic DNA mass. However, the nuclear labeling index of the TGF-beta-treated animals was significantly higher than that of the controls. There was no evidence of cytotoxicity from TGF-beta, as determined by liver histology and plasma concentrations of glucose, insulin-like growth factor I, and two hepatic enzymes. Thus, TGF-beta 1 and TGF-beta 2 reversibly inhibit the proliferative response of liver to PH and may be important in the modulation of normal liver growth and repair.
Frequency Analysis of Ordered Dither (1989)

Ordered dither, the class of digital halftoning techniques which uses a periodic array of thresholds, is generalized for both rectangular and hexagonal grids, by means of the spatial method of recursive tessellation, a sub-tiling algorithm. The nature of the texture patterns so produced is illustrated and examined in the frequency domain, revealing several insights within and between the classes of rectangular and hexagonal grids. A simple explicit expression is derived which allows the use of the rectangular DFT to compute a hexagonal Fourier transform, maintaining continuous-space dimensions. Digitally produced examples are included.
Neural Programmer-Interpreters (2015)

We propose the neural programmer-interpreter (NPI): a recurrent and compositional neural network that learns to represent and execute programs. NPI has three learnable components: a task-agnostic recurrent core, a persistent key-value program memory, and domain-specific encoders that enable a single NPI to operate in multiple perceptually diverse environments with distinct affordances. By learning to compose lower-level programs to express higher-level programs, NPI reduces sample complexity and increases generalization ability compared to sequence-to-sequence LSTMs. The program memory allows efficient learning of additional tasks by building on existing programs. NPI can also harness the environment (e.g. a scratch pad with read-write pointers) to cache intermediate results of computation, lessening the long-term memory burden on recurrent hidden units. In this work we train the NPI with fully-supervised execution traces; each program has example sequences of calls to the immediate subprograms conditioned on the input. Rather than training on a huge number of relatively weak labels, NPI learns from a small number of rich examples. We demonstrate the capability of our model to learn several types of compositional programs: addition, sorting, and canonicalizing 3D models. Furthermore, a single NPI learns to execute these programs and all 21 associated subprograms.
Architecture of a high speed Reed-Solomon decoder (1994)

The authors propose an architecture for an error correction circuit suitable for high-rate data decoding of the Reed-Solomon code. It features a multiple-error correction capability of 4 errors or 8 erasures. The operational steps for multiple-error decoding are reduced by a 4-stage pipeline and a superscalar processor of a Galois field. The experimental circuit's 16 Mbyte/s rate of data decoding is sufficient for compressed video signals of high-definition as well as those of standard-definition TVs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>