gebhart/patrepeval huggingface dataset:
RecA-AC: single-site cleavage of plasmids and chromosomes at any predetermined restriction site (1992)

We have developed a novel version of the Achilles' Cleavage (AC) reaction in which virtually any restriction site on DNA of any size can be converted to a unique cleavage site. We first polymerized RecA protein on a synthetic oligodeoxyribonucleotide (oligo) in the presence of a nonhydrolyzable ATP analogue to generate oligo:RecA nucleoprotein filaments. These filament were then incubated with plasmid or intact chromosomal DNA from Saccharomyces cerevisiae to form stable complexes in the yeast LEU2 gene at the target sequence identical (or complementary) to that of the oligo. When HhaII (HinfI) methyltransferase (M.HhaII) was added, all of the recognition sites for HhaII with the exception of the one protected by the RecA filament were methylated and thus no longer cleaved by the cognate restriction endonuclease (HinfI). After inactivation of the RecA and the M.HhaII, HinfI was used to efficiently cleave the plasmid or chromosome specifically at the targeted restriction site. Since oligos specific for any sequence can be easily synthesized and the other reagents necessary to perform RecA-mediated AC (RecA-AC) reactions on both plasmids and intact chromosomes are readily available, this procedure can be applied immediately to the precise dissection and analysis of genomic DNA from any source and to any other research problem requiring efficient, highly specific cleavage of DNA at predetermined sites.
Thymidine Kinase Deletion Mutants of Herpes Simplex Virus Type 1 (1982)

Deletions in the cloned thymidine kinase (TK) gene of herpes simplex virus type 1 (HSV-1), strain 17 syn+, were produced by two methods. Removal of a 506 base pair fragment from between the unique SstI and Bg/II restriction endonuclease sites of pTK1 (HSV-1 BamHI p cloned in pAT153) and subsequent transformation of Escherichia coli resulted in the isolation of 50 deleted plasmids. Sequential digestion of pTK1 with Bg/II and nuclease BAL 31 followed by ligation and recleavage with Bg/II resulted in the isolation of 31 deleted plasmids. Three clones, pTK2, pTK3 and pTK4, obtained following Bg/II and SstI treatment of pTK1 were recombined with wild-type (wt) HSV-1 (17) syn+ DNA in baby hamster kidney (BHK) cells to produce TK- deletion mutants HSV-1 (17) TK 1301, HSV-1 (17) TK 1302 and HSV-1 (17) TK 1303 respectively. 5-Bromo-2'-deoxyuridine, 5-bromo-2'-deoxycytidine and 9-(2-hydroxyethoxymethyl)guanine were used to reduce the background of TK+ virus in heterogeneous recombinant stocks analysed for the presence of TK- recombinants. All recombinant clones isolated produced a small syncytial plaque morphology in BHK cells. The mutants HSV-1 (17) TK 1301 and HSV-1 (17) TK 1302 were TK-, failed to produce polypeptides of molecular weights 43000 and 19000 found in wt-infected cells and demonstrated one-step growth curves different from wt virus and the TK- mutant HSV-1 (17) dPyk-7. Superinfection studies with HSV-1 (17) TK 1301, HSV-1 (17) TK 1302, HSV-1 (MDK) and HSV-1 (17) dPyk-7 indicated that all TK- mutants except dPyK-7 produce a trans-acting gene product which can switch on the transforming HSV-1 TK gene.
Integrin-associated protein (CD47) is a comitogenic molecule on CD3-activated human T cells (1997)

IAP is a glycoprotein functionally and physically associated with some integrins, i.e., the leukocyte response integrin and the beta3 integrin chain on placenta, platelets, and polymorphonuclear cells. IAP may act as a transducer element in activation mediated via these integrins. Since IAP is present at high density on peripheral T lymphocytes we have investigated its involvement in T cell activation. We tested three mAbs against IAP, namely B6H12, BRIC126, and 2D3, which recognize two distinct epitopes. IAP cross-linking with B6H12 or BRIC126, but not 2D3, transduces costimulatory signals within highly purified CD3-activated T lymphocytes, i.e., enhancement of proliferation, CD25 expression, and IL-2 secretion, while no effect was observed upon CD2 stimulation. However, we could not observe any functional association between IAP and integrins on peripheral T cells. In an attempt to explore further the activation signal delivered by IAP, we show here that IAP cross-linking with the comitogenic B6H12 mAb induces the phosphorylation on tyrosine of several proteins, one of which is identified as p56(lck) protein tyrosine kinase. Moreover, we observed that IAP is associated with p56(lck) on PMA-activated, but not on resting, T cells. These data suggest that on T cells, IAP may be involved directly via a specific ligand in cell-matrix or cell-cell interactions. Such interactions could trigger protein tyrosine phosphorylation pathways, which play an important role in both maturation and activation of T cells.
An all-electron numerical method for solving the local density functional for polyatomic molecules (1990)

A method for accurate and efficient local density functional calculations (LDF) on molecules is described and presented with results. The method, Dmol for short, uses fast convergent three-dimensional numerical integrations to calculate the matrix elements occurring in the Ritz variation method. The flexibility of the integration technique opens the way to use the most efficient variational basis sets. A practical choice of numerical basis sets is shown with a built-in capability to reach the LDF dissociation limit exactly. Dmol includes also an efficient, exact approach for calculating the electrostatic potential. Results on small molecules illustrate present accuracy and error properties of the method. Computational effort for this method grows to leading order with the cube of the molecule size. Except for the solution of an algebraic eigenvalue problem the method can be refined to quadratic growth for large molecules.
Interaction of Nanoparticles with Cells (2009)

Nanoparticles and their interaction with human cells have been a focus of many groups during the past decade. We discuss and review here the progress in the field of understanding and harnessing the interactions of polymeric nanoparticles synthesized by the miniemulsion process with different cell types. Nanotechnology and the hereby produced nanomaterials have promised to make use of specific properties of supramolecular assemblies and nanomaterials so that hitherto inaccessible effects can be exploited for new applications. Examples are superparamagnetism or the high surface area helpful for catalysis and adsorption. In biology and medicine, superparamagnetic iron oxide nanoparticles have been used for cell selection and as magnetic resonance imaging (MRI) contrast agents. Furthermore, uptake of nanoparticles into a wide variety of cells is an effect that seems to be specific for materials in the range of 50-200 nm. Surface modifications (positively or negatively charged side groups of the polymers, amino acids, or peptides/proteins) enhance this uptake. Knowledge about factors influencing cellular uptake, like size, surface properties, cell type, and endocytotic pathways, enables optimization of labeling and selection of cells and nanoparticles for applications in vitro and in vivo. For in vivo applications, we will focus on how nanoparticles can cross the blood-brain barrier.
In vitro activation and nuclear translocation of NF-kappa B catalyzed by cyclic AMP-dependent protein kinase and protein kinase C. (1989)

We have examined whether a precursor form of NF-kappa B, a DNA-binding protein that plays a role in the transcriptional control of several genes, including kappa immunoglobulin light chain and interleukin-2 receptor alpha subunit, could be activated in vitro by protein kinases. DNA-binding activity of NF-kappa B was induced in the cytosolic fraction of unstimulated 70Z/3 murine pre-B cells by incubation with the catalytic subunit of cyclic AMP-dependent protein kinase (PKA) or protein kinase C (PKC). In contrast, PKA and PKC did not activate NF-kappa B in nuclear extracts from unstimulated cells. Identical results were obtained with the human natural killer-like cell line YT, which can be induced to express the interleukin-2 receptor alpha subunit in response to interleukin-1, cyclic AMP, or phorbol 12-myristate 13-acetate. Furthermore, when nuclei from unstimulated cells were incubated with PKA- or PKC-treated cytosolic fraction for 30 min at 30 degrees C, NF-kappa B was translocated into the nuclei. This translocation did not occur at 4 degrees C and was inhibited by wheat germ agglutinin but not by concanavalin A. Our findings support the conclusion that NF-kappa B exists in the cytoplasm of unstimulated cells in an inactive form that can be converted by exposure to PKA or PKC to an active DNA-binding form that can translocate to the nucleus.
BB-10010: an active variant of human macrophage inflammatory protein-1 alpha with improved pharmaceutical properties (1995)

The stem cell inhibitor, macrophage inflammatory protein-1 alpha (MIP-1 alpha) or LD78, protects multipotent hematopoietic progenitors in murine models from the cytotoxic effects of chemotherapy. Clinical use of human MIP-1 alpha during chemotherapy could therefore lead to faster hematologic recovery and may allow dose intensification. We have also shown that human MIP-1 alpha causes the rapid mobilization of hematopoietic cells, suggesting an additional clinical use in peripheral blood stem cell transplantation. However, the clinical evaluation of human MIP-1 alpha is complicated by its tendency to associate and form high molecular weight polymers. We have produced a variant of rhMIP-1 alpha, BB-10010, carrying a single amino acid substitution of Asp26 > Ala, with a reduced tendency to form large polymers at physiologic pH and ionic strength. This greatly increases its solubility, facilitating its production and clinical formulation. We confirmed the potency of BB-10010 as a human MIP-1 alpha-like agonist in receptor binding, calcium mobilization, inhibition of colony formation, and thymidine suicide assays. The myeloprotective activity of BB-10010 was shown in a murine model of repeated chemotherapy using hydroxyurea. BB-10010 is therefore an ideal variant with which to evaluate the therapeutic potential of recombinant human MIP-1 alpha.
Nonvolatile Memory With Extremely Low-Leakage Indium-Gallium-Zinc-Oxide Thin-Film Transistor (2012)

Emerging nonvolatile memory with an oxide–semiconductor-based thin-film transistor (TFT) using indium-gallium-zinc-oxide (IGZO) was developed. The memory is called nonvolatile oxide–semiconductor random access memory (NOSRAM). The memory cell of the NOSRAM (NOSRAM cell) consists of an IGZO TFT for data writing, a normal Si-based p-channel metal-oxide-semiconductor (PMOS) for data reading, and a cell capacitor for storing charge and controlling the PMOS gate voltage. The IGZO TFT and the cell capacitor are formed over the PMOS. Owing to extremely low-leakage-current characteristics of the IGZO TFT, the charge stored in the 2-fF cell capacitor is maintained for a long time. This long data retention realized innovative nonvolatile memory. The NOSRAM cell fabricated with the 0.8- <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\mu$</tex> </formula> m process technology demonstrated an on/off ratio of 10 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$^{7}$</tex></formula> and an endurance over 10 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$^{12}$</tex> </formula> write cycles. In addition, NOSRAM with a memory capacity of 1 Mb was fabricated; the cell size was 12.32 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\mu{\hbox {m}}^{2}$</tex></formula> and the cell array size was 13.5 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${\hbox {mm}}^{2}$</tex> </formula> . The 1-Mb NOSRAM achieved basic operation at 4.5 V or less, write operation at 150 ns/page, read distribution of data “1” with <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$3\sigma=\hbox{ 0.10~V}$</tex></formula> , and a data retention over 60 days at 85 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$^{\circ}\hbox{C}$</tex></formula> .
Unsupported planar lipid membranes formed from mycolic acids of Mycobacterium tuberculosis (2010)

The cell wall of mycobacteria includes a thick, robust, and highly impermeable outer membrane made from long-chain mycolic acids. These outer membranes form a primary layer of protection for mycobacteria and directly contribute to the virulence of diseases such as tuberculosis and leprosy. We have formed in vitro planar membranes using pure mycolic acids on circular apertures 20 to 90 μm in diameter. We find these membranes to be long lived and highly resistant to irreversible electroporation, demonstrating their general strength. Insertion of the outer membrane channel MspA into the membranes was observed indicating that the artificial mycolic acid membranes are suitable for controlled studies of the mycobacterial outer membrane and can be used in nanopore DNA translocation experiments.
Screening of Inhibitory Monoclonal Antibodies: A Critical Step for Producing Anti‐idiotypic Catalytic Antibodies (1998)

In accord with the original approach that we proposed, catalytic antibodies may be produced by using the anti-idiotypic pathway according to antigen/antibody complementarity rules. The generation and screening of the idiotypic Ab1, the central point on which are anchored the interactions with both the antigen (enzyme) and the anti-idiotypic abzyme, represent a crucial step for the success of this approach. We herein propose to describe a strategy for which we have developed a number of assays, aiming at selecting the proper Ab1, with desired features, likely to elicit an anti-idiotypic catalytic antibody. beta-Lactamase from Bacillus cereus was chosen as the example illustrating our arguments.
MUC5AC expression is increased in bronchial submucosal glands of stable COPD patients (2009)

COPD is associated with increased MUC5AC expression in submucosal glands, indicating that MUC5AC may be involved in the pathophysiology of the disease.
P4–273: Pharmacological studies of traditional Chinese medicine to treat Alzheimer disease (2006)

Shen–wu Capsule (SWC) is a new compound containing 6 kinds of traditional Chinese herbs. TSG is a major effective component of SWC. To investigate the pharmacological effects of SWC and TSG on multiple kinds of AD–like animal models. The drugs were intragastrically administered to the animal models for 1 or 2 months. Morris water maze test was used to detect learning/memory ability, microarray and RT–PCR to measure gene expression, Western blotting and immuno–histochemistry to determine related proteins. (1) In APP transgenic mice, SWC and TSG improved learning/memory ability, and decreased Aβ content and β–secretase expression; (2) in Aβ brain injection model, SWC and TSG inhibited microglial activation, and decreased IL–1β and tumor necrosis factor α (TNFα) content; (3) in ibotanic acid–induced basal forebrain cholinergic damaged rat model, SWC and TSG improved learning/memory ability, increased the ratio of cholinacetyl–transferase (ChAT)/cholinesterase (AchE), or enhanced M–receptor density; (4) in naturally aged rats of 24 months old, SWC improved learning/memory ability, decreased cholinergic cell death, and increased expression of nerve growth factor (NGF) and its receptor trkA in hippocampus; (5) in D–galactose–induced brain aging mouse model, SWC and TSG improved learning/memory ability, inhibited lipid peroxidation, increased activities of antioxidant enzymes, and enhanced NGF and trkA expression in hippocampus; (6) in dementia rat model induced by mitochondria complex IV inhibitor azide perfusion, SWC improved learning/memory ability, increased the ratio of ChAT/AchE, decreased Aβ and hyperphosphorylated tau content, increased expression of protein phosphatase 2A (PP2A), brain derived neurotrophic factor (BDNF) and its receptor trkB; (7) in diabetic–ischemic model rats, SWC improved learning/memory ability, enhanced long term potentiation (LTP) in hippocampus, decreased cholinergic cell death, enhanced the expression of neurotrophin–3 (NT–3) and trkC, increased Bcl–2 and Akt protein expression, and decreased the content of Bax, caspase–3 and phosphated cAMP response element binding protein (P–CREB); (8) in hypercholesterolemia–induced dementia rat model, TSG improved learning/memory ability, decreased the content of Aβ and serum cholesterol. SWC and TSG act on multiple targets in the complicated pathogeneses of AD and thus may have strong potential to aid the treatment of AD.
Prevention and reversal of cartilage degradation in rheumatoid arthritis by interleukin‐10 and interleukin‐4 (1996)

IL-10 reverses the cartilage degradation induced by antigen-stimulated MNC, and IL-4 has an additive effect on this process. Furthermore, IL-10 has a direct stimulatory effect on PG synthesis, and IL-4, as a growth factor for type 2 T cells, can reduce the ratio of type 1 to type 2 T cell activity. These results provide evidence in favor of the use of a combination of the two cytokines in the treatment of RA.
Visualization of Murine Intranasal Dosing Efficiency Using Luminescent Francisella tularensis: Effect of Instillation Volume and Form of Anesthesia (2012)

Intranasal instillation is a widely used procedure for pneumonic delivery of drugs, vaccine candidates, or infectious agents into the respiratory tract of research mice. However, there is a paucity of published literature describing the efficiency of this delivery technique. In this report we have used the murine model of tularemia, with Francisella tularensis live vaccine strain (FTLVS) infection, to evaluate the efficiency of pneumonic delivery via intranasal dosing performed either with differing instillation volumes or different types of anesthesia. FTLVS was rendered luminescent via transformation with a reporter plasmid that constitutively expressed the Photorhabdus luminescens lux operon from a Francisella promoter. We then used an IVIS Spectrum whole animal imaging system to visualize FT dissemination at various time points following intranasal instillation. We found that instillation of FT in a dose volume of 10 µl routinely resulted in infection of the upper airways but failed to initiate infection of the pulmonary compartment. Efficient delivery of FT into the lungs via intranasal instillation required a dose volume of 50 µl or more. These studies also demonstrated that intranasal instillation was significantly more efficient for pneumonic delivery of FTLVS in mice that had been anesthetized with inhaled (isoflurane) vs. parenteral (ketamine/xylazine) anesthesia. The collective results underscore the need for researchers to consider both the dose volume and the anesthesia type when either performing pneumonic delivery via intranasal instillation, or when comparing studies that employed this technique.
Revisiting Recurrent Neural Networks for robust ASR (2012)

In this paper, we show how new training principles and optimization techniques for neural networks can be used for different network structures. In particular, we revisit the Recurrent Neural Network (RNN), which explicitly models the Markovian dynamics of a set of observations through a non-linear function with a much larger hidden state space than traditional sequence models such as an HMM. We apply pretraining principles used for Deep Neural Networks (DNNs) and second-order optimization techniques to train an RNN. Moreover, we explore its application in the Aurora2 speech recognition task under mismatched noise conditions using a Tandem approach. We observe top performance on clean speech, and under high noise conditions, compared to multi-layer perceptrons (MLPs) and DNNs, with the added benefit of being a “deeper” model than an MLP but more compact than a DNN.
Functional Dissection of a Rice Dr1/DrAp1 Transcriptional Repression Complex (2002)

We characterized rice cDNA sequences for OsDr1 and OsDrAp1, which encode structural homologs of the eukaryotic general repressors Dr1 and DrAp1, respectively. OsDr1 and OsDrAp1 are nuclear proteins that interact with each other and with the TATA binding protein/DNA complex. In vitro and in vivo functional analyses showed that OsDrAp1 functions as a repressor, unlike its role in other eukaryotic systems, in which DrAp1 is a corepressor. OsDr1 and OsDrAp1 functioned together as a much stronger repressor than either one alone. Functional dissections revealed that the N-terminal histone-fold domains of OsDr1 and OsDrAp1 were necessary and sufficient for their repression and protein-protein interaction with each other. The unique glutamine- and proline-rich domain of OsDr1 had no repression activity. The basic amino acid-rich region and an arginine and glycine repeat domain of OsDrAp1 enhanced its repression activity. Thus, although OsDr1 and OsDrAp1 function as repressors, the functions of the two components are reversed compared with those of their nonplant counterparts.
New Aspects of Positive-Strand Rna Viruses (1990)

General overviews and minireviews on specific viruses and properties combine to present a broad range of current findings
Validation of a 7‐point Global Overall Symptom scale to measure the severity of dyspepsia symptoms in clinical trials (2006)

The Global Overall Symptom scale is a simple, valid outcome measure for dyspepsia treatment trials.
Mycosis fungoides with Mucinosis follicularis in Childhood (1999)

Mycosis fungoides is a cutaneous T-cell lymphoma (CTCL) usually observed in mid to late adulthood. It occurs only rarely during childhood. Follicular mucinosis is a chronic dermatosis involving the sebaceous glands and outer root sheaths. It is normally differentiated into a juvenile benign form and an adult form possibly associated with mycosis fungoides. We report a 12-year-old boy who presented with an 8-month history of erythematous mucinous plaques on the scalp. Three months later, he developed erythematous patches and plaques on his whole body, accompanied by cervical lymphadenopathy. A biopsy showed follicular mucinosis and epidermotropism of the lymphocytic infiltrate. Immunophenotyping and a PCR clonality test were consistent with CTCL. The patient received PUVA treatment and local steroids, resulting in partial remission. Mycosis fungoides should be considered in the differential diagnosis of chronic, scaling dermatoses in childhood. Moreover, follicular mucinosis in childhood can be associated with mycosis fungoides.