gebhart/patrepeval huggingface dataset:
Morphological transformation caused by a partial sequence of U5 small nuclear RNA (1997)

My colleagues and I have reported that a small nuclear RNA, U5, can cause transformation of and chromosomal aberrations in rat fibroblast 3Y1 cells. In the study described here, I found that a partial U5 sequence, the 3' half of the first stem structure (designated RNA3S), transformed the cells morphologically at a high frequency when expressed with a poly(A) tail (RNA3S+). The transformation critically depended upon a polypurine sequence in RNA3S+. The expressed RNA3S+ was associated with polysomes. The transformed cells did not exhibit significant frequencies of chromosome aberrations when compared with control cells, suggesting that the transformation occurs without significant induction of chromosome damage. Heterogeneous subcolonies emerged in monolayers when the morphologically transformed cells were subcultured and maintained at postconfluence. Cells from subcolonies acquired the ability to form small colonies in soft agar and tumors in nude mice, suggesting that RNA3S+ can drive the cells into the neoplastic stage. RNA3S+ also conferred morphological alterations and a growth advantage and decreased levels of fibronectin protein synthesis in human HeLa cells, confirming the transforming potential of the RNA. RNA3S+ transformation may therefore be a useful model system for studying a transformation process.
A rapid and simple method for constructing stable mutants of Acinetobacter baumannii (2010)

This study provides a rapid and simple method of obtaining stable mutants of A. baumannii free of foreign plasmidic DNA, which does not require cloning steps, and enables construction of multiple gene knockout mutants.
Regulation of S33/S37 phosphorylated β-catenin in normal and transformed cells (2002)

A novel phosphorylation-specific antibody (alphapbeta-catenin) was generated against a peptide corresponding to amino acids 33-45 of human beta-catenin, which contained phosphorylated serines at positions 33 and 37. This antibody is specific to phosphorylated beta-catenin and reacts neither with the non-phosphorylated protein nor with phosphorylated or non-phosphorylated plakoglobin. It weakly interacts with S33Y beta-catenin but not with the S37A mutant. pbeta-catenin is hardly detectable in normal cultured cells and accumulates (up to 55% of total beta-catenin) upon overexpression of the protein or after blocking its degradation by the proteasome. Inhibition of both GSK-3beta and the proteasome resulted in a rapid (t1/2=10 minutes) and reversible reduction in pbeta-catenin levels, suggesting that the protein can undergo dephosphorylation in live cells, at a rate comparable to its phosphorylation by GSK-3beta. pbeta-catenin interacts with LEF-1, but fails to form a ternary complex with DNA, suggesting that it is transcriptionally inactive. Immunofluorescence microscopy indicated that pbeta-catenin accumulates in the nuclei of MDCK and BCAP cells when overexpressed and is transiently associated with adherens junctions shortly after their formation. pbeta-catenin only weakly interacts with co-transfected N-cadherin, although it forms a complex with the ubiquitin ligase component beta-TrCP. SW480 colon cancer cells that express a truncated APC, at position 1338, contain high levels of pbeta-catenin, whereas HT29 cells, expressing APC truncated at position 1555, accumulate non-phosphorylated beta-catenin, suggesting that the 1338-1555 amino acid region of APC is involved in the differential regulation of the dephosphorylation and degradation of pbeta-catenin.
Panchromatic Conjugated Polymers Containing Alternating Donor/Acceptor Units for Photovoltaic Applications (2007)

We designed and synthesized a series of conjugated polymers containing alternating electron-donating and electron-accepting units based on (4,4-bis(2-ethylhexyl)-4H-cyclopenta[2,1-b:3,4-b‘]dithiophene), 4,7-(2,1,3)-benzothiadiazole, and 5,5‘-[2,2‘]bithiophene. These polymers possess an optical band gap as low as 1.4 eV (i.e., in the case of poly[2,6-(4,4-bis(2-ethylhexyl)-4H-cyclopenta[2,1-b:3,4-b‘]dithiophene)-alt-4,7-(2,1,3-benzothiadiazole)]), and their absorption characteristics can be tuned by adjusting the ratio of the two electron-donating units: (4,4-bis(2-ethylhexyl)-4H-cyclopenta[2,1-b:3,4-b‘]dithiophene) and 5,5‘-[2,2‘]bithiophene. The desirable absorption attributes of these materials qualify them as excellent candidates for light-harvesting materials in organic photovoltaic applications allowing for high short-circuit current. Electrochemical studies indicate sufficiently deep HOMO/LUMO levels that enable a high photovoltaic device open-circuit voltage when fullerene derivatives are used as electron transporters. Field-effect transistors made of these materials show hole mobility in the range of 5 × 10-4−3 × 10-3 cm2/(V s), which promises good device fill factor. Because of the combination of these characteristics, power conversion efficiencies up to 3.5% and an external quantum efficiency of at least 25% between 400 and 800 nm with a maximum of 38% around 700 nm were achieved on devices made of bulk heterojunction composites of these materials with soluble fullerene derivatives. Further improvement of the materials will include the modification of both the side chains and the backbone to effect change to the active layer morphology to maintain good charge carrier mobility in the composite.
The occurrence of two types of entomopathogenic bacilli in natural populations of the spruce budworm, Choristoneura fumiferana (1997)

This paper reports the occurrence of two types of pathogenic bacilli in cadavers of spruce budworm, Choristoneura fumiferana, larvae and pupae on balsam fir, Abies balsamea (L.) Mill., foliage sampled in several locations in New Brunswick, Canada. One type forms spores and protein crystals at sporulation typical of Bacillus thuringiensis (B.t.), while the other forms spores but no crystals. The noncrystal-producing bacillus is likely Bacillus cereus rather than an acrystalliferous variety of B.t.. The bacilli infect budworm during most of its life cycle, from hibernating second-instar larvae to pupae, with varying rates of infection, but are never a major cause of mortality. The bacilli also infect other lepidopterous species occurring on balsam fir foliage. Circumstantial evidence indicates that both bacilli occur naturally on the foliage, despite the history of aerial application of B.t.-based insecticides near, if not directly over, our study plots. A subtle impact of these bacilli on the dynamics of spruce budworm populations is discussed. Resume : Cet article rapporte la prOsence de deux types de bacilles pathognes dans les larves et les pupes mortes de la tordeuse des bourgeons de liOpinette, Choristoneura fumiferana, sur le feuillage du sapin baumier, Abies balsamea (L.) Mill., OchantillonnO ‡ plusieurs endroits au Nouveau-Brunswick, au Canada. Un des types de bacilles forme des spores et des cristaux ‡ base de protOines typiques de Bacillus thuringiensis (B.t.) au moment de la sporulation, tandis que liautre type forme des spores mais pas de cristaux. Le bacille qui ne produit pas de cristaux est probablement Bacillus cereus plutUt quiune variOtO de B.t. sans cristaux. Les bacilles infectent la tordeuse pendant presque tout son cycle vital, des larves en hibernation du second instar jusquiaux pupes, avec des taux variables diinfection, mais ne constitue jamais une cause importante de mortalitO. Les bacilles infectent aussi diautres espces de lOpidoptres quion retrouve sur le feuillage du sapin baumier. Des preuves circonstancielles montrent que les deux bacilles sont prOsents naturellement sur le feuillage, malgrO les applications aOriennes passOes diinsectisides ‡ base de B.t. ‡ proximitO, sinon directement au-dessus de nos parcelles Ochantillons. Le faible impact de ces bacilles sur la dynamique des populations de tordeuse des bourgeons de liOpinette est discutO. (Traduit par la ROdaction)
Purification and characterization of a 26‐kDa competitive inhibitor of interleukin 1 (1990)

The urine of patients with fever above 39 degrees C contains an inhibitor of interleukin 1. Herein we describe the purification of the interleukin 1 inhibitor by ion-exchange chromatography, hydrophobic chromatography, gel filtration and negative immunosorption. The purified protein has a molecular weight of 26,000; its size is reduced to 24,000 upon treatment with endoglycosidase F. The IL 1 inhibitor is a competitive inhibitor and acts by binding to the IL 1 receptor. The inhibitor recognizes the murine and human IL 1 receptor with similar affinity. The purified IL 1 inhibitor has a specific activity of 3 x 10(7) to 4.5 x 10(7) units/mg as tested on the human astrocytoma (U-373) cell proliferation bioassay and murine EL4.6.1 cell IL 1 receptor-binding assay.
Characterization of Novel Coding Sequences Specific toMycobacterium aviumsubsp.paratuberculosis: Implications for Diagnosis of Johne's Disease (2004)

Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's Disease, an economically important intestinal ailment of ruminants. Due to the considerable genetic and serologic cross-reactivity with closely related and ubiquitous members of the M. avium complex, a species-specific method for the serological diagnosis of Johne's disease is unavailable. Computational and PCR-based analysis of the complete genome sequence of M. avium subsp. paratuberculosis led to the identification of 13 open reading frames with no identifiable homologs. One of these sequences is a putative insertion element present in six copies on the M. avium subsp. paratuberculosis genome. These novel M. avium subsp. paratuberculosis genes were cloned into Escherichia coli expression vectors, and nine were successfully expressed as recombinant fusion proteins. Five of these proteins were purified in sufficient amounts to allow immunoblot analyses of their reactivity with sera from naturally infected cattle as well as mice and rabbits exposed to M. avium subsp. paratuberculosis. Fusion proteins representing MAP0862, MAP3732c, and MAP2963c were recognized by nearly all of the sera tested, including those from cattle in the clinical stages of disease. Notably, further analysis of the protein encoded by MAP0862 showed that it reacted with sera from additional infected cattle but not with sera from uninfected control animals. The fusion product of MAP0860c did not react with any of the sera tested, while the remaining four proteins were variably recognized by sera from M. avium subsp. paratuberculosis-infected cattle. Collectively, the results of this study demonstrate the utility of genomic data to identify potential diagnostic sequences.
An Efficient Synthesis of an αvβ3 Antagonist (2004)

A practical preparation of an alpha(v)beta(3) antagonist is reported. The antagonist consists of three key components, a tetrahydronaphthyridine moiety, a beta-alanine moiety, and a central imidazolidone moiety. The tetrahydronaphthyridine component was prepared using two different methods, both of which relied on variations of the Friedländer reaction to establish the desired regiochemistry. The beta-alanine component was prepared using Davies' asymmetric 1,4-addition methodology as the key stereo-defining step. The central imidazolidone portion was created from these two components using an effective three-step cyclization protocol. Thus, a highly convergent process for the drug candidate was defined.
Thrombolytic and pharmacokinetic properties of chimeric tissue-type and urokinase-type plasminogen activators. (1991)

These results indicate that t-PA-delta FE/scu-PA-e has a markedly enhanced thrombolytic potency toward venous and arterial thrombi caused by a delayed in vivo clearance with relatively maintained specific thrombolytic activity. These properties suggest that the chimera may be clinically useful for thrombolytic therapy by bolus administration in patients with thromboembolic disease.
A nonlinear receding horizon controller based on connectionist models (2002)

The authors focus on the development of connectionist architectures and learning algorithms for adaptive control of nonlinear systems. In particular, they pursue the receding horizon approach to optimal control. The control structure consists of two networks: one models the plan and provides prediction data for optimization, and the other is trained as an approximate plant inverse. Simulation results indicating the feasibility of the proposed approach are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Myc represses transcription of the growth arrest gene  gas1 (1997)

Cell proliferation is regulated by the induction of growth promoting genes and the suppression of growth inhibitory genes. Malignant growth can result from the altered balance of expression of these genes in favor of cell proliferation. Induction of the transcription factor, c-Myc, promotes cell proliferation and transformation by activating growth promoting genes, including the ODC and cdc25A genes. We show that c-Myc transcriptionally represses the expression of a growth arrest gene, gas1. A conserved Myc structure, Myc box 2, is required for repression of gas1, and for Myc induction of proliferation and transformation, but not for activation of ODC. Activation of a Myc-estrogen receptor fusion protein by 4-hydroxytamoxifen was sufficient to repress gas1 gene transcription. These findings suggest that transcriptional repression of growth arrest genes, including gas1, is one step in promotion of cell growth by Myc.
Evidence of radiographic benefit of treatment with infliximab plus methotrexate in rheumatoid arthritis patients who had no clinical improvement: A detailed subanalysis of data from the anti–tumor necrosis factor trial in rheumatoid arthritis with concomitant therapy study (2005)

Even in patients without clinical improvement, treatment with infliximab plus MTX provided significant benefit with regard to the destructive process, suggesting that in such patients these 2 measures of disease are dissociated.
Competitive antagonists and partial agonists at the glycine modulatory site of the mouse N‐methyl‐D‐aspartate receptor. (1990)

1. Kynurenate (Kyn), 7-chlorokynurenate (7-Cl-Kyn), 3-amino-1-hydroxypyrrolid-2-one (HA-966) and D-cycloserine are known to bind to the glycine site that modulates the N-methyl-D-aspartate (NMDA) response of vertebrate central neurones. The effects of these compounds were investigated with patch-clamp and fast-perfusion techniques on mouse cortical neurones in primary culture in an effort to establish whether they act as antagonists, partial agonists and/or inverse agonists of glycine. A fast drug application method allowed the study of both steady-state and transient responses. 2. The analysis of steady-state responses indicates that the main effects of Kyn and 7-Cl-Kyn are those expected from competitive antagonists of glycine, with a dissociation constant of 15 microM for Kyn, and of 0.3 microM for 7-Cl-Kyn. Concentration jumps indicate that at all concentrations of glycine, and in particular in the absence of added glycine, the blockade by Kyn and 7-Cl-Kyn develops at a rate which is close to the rate of dissociation of glycine from its binding site and is independent of antagonist concentration. 3. The main effects of D-cycloserine and of HA-966 are those of partial agonists of high and low efficacy, respectively. In the absence of added glycine, D-cycloserine always produced a potentiation, while HA-966 produced either a potentiation or an inhibition. This can be explained by assuming the presence of a variable level of contaminating glycine. With both D-cycloserine and HA-966, concentration jumps produced biphasic relaxations in which the onset rate of the slow component was, here again, close to the rate of dissociation of glycine from its binding site. 4. These results can be interpreted by assuming that (1) Kyn and 7-Cl-Kyn are competitive antagonists of glycine, (2) HA-966 and D-cycloserine are partial agonists, (3) in the absence of added glycine some glycine is present in the extracellular solution and (4) the response in the total absence of glycine is very small or negligible.
Species Identification of Mycobacteria Using rDNA Sequencing (2003)

Standard protocols for definite species identification of nontuberculous mycobacteria by phenotypic characteristics include complex and time-consuming procedures. Other methods based on lipid analysis, such as high-performance liquid chromatography (HPLC), thin-layer chromatography (TLC), and gas-liquid chromatography (GLC), are cumbersome, expensive, and are used in only a few clinical laboratories.
Tissue-Specific Promoters in Gene Therapy for the Treatment of Prostate Cancer (2000)

Delivery of therapeutic toxic genes to and their expression in tumor cells through the use of tissue-specific promoters could decrease their toxic effect on neighboring normal cells when virus-mediated gene delivery results in their infection. We have demonstrated the utility of two prostate cancer-specific promoters, long PSA and osteocalcin, for tissue-specific toxic gene therapy for prostate cancer. The two promoters were highly active in both androgen-dependent and androgen-independent prostate cancer cells. We also introduce the Phase I trial of osteocalcin promoter-based toxic gene therapy for bone metastases of prostate cancer, which is in progress at the University of Virginia.
A missense mutation in the human liver/bone/kidney alkaline phosphatase gene causing a lethal form of hypophosphatasia. (1988)

Hypophosphatasia is an inherited disorder characterized by defective bone mineralization and a deficiency of serum and tissue liver/bone/kidney alkaline phosphatase (L/B/K ALP) activity. Clinical severity is variable, ranging from death in utero (due to severe rickets) to pathologic fractures first presenting in adult life. Affected siblings, however, are phenotypically similar. Severe forms of the disease are inherited in an autosomal recessive fashion; heterozygotes often show reduced serum ALP activity. The specific gene defects in hypophosphatasia are unknown but are thought to occur either at the L/B/K ALP locus or within another gene that regulates L/B/K ALP expression. We used the polymerase chain reaction to examine L/B/K ALP cDNA from a patient with a perinatal (lethal) form of the disease. We observed a guanine-to-adenine transition in nucleotide 711 of the cDNA that converts alanine-162 of the mature enzyme to threonine. The affected individual, whose parents are second cousins, is homozygous for the mutant allele. Introduction of this mutation into an otherwise normal cDNA by site-directed mutagenesis abolishes the expression of active enzyme, demonstrating that a defect in the L/B/K ALP gene results in hypophosphatasia and that the enzyme is, therefore, essential for normal skeletal mineralization.
Funciones esenciales de la salud pública (2015)

The Essential Functions of Health (FESP) describe the spectrum of competencies and actions required by health systems to achieve the central objective, which is to improve the health of populations. The Pan American Health Organization, through the Public Health in the Americas Initiative, defined eleven (11) EPHF and developed an instrument to measure its performance, which allows countries to perform a self-assessment of their capacities to exercise public health. Special attention deserves, within this FESP, research in public health, health promotion, social participation as well as monitoring, evaluation and analysis of the health problems of the population. These functions are some of the central themes of the Venezuelan Health Journal, thus contributing, through its scientific articles, to disseminate and strengthen them. Similarly, the continuous dissemination of knowledge about these topics helps to influence other functions such as the training of human resources in collective health and in the surveillance, research and control of health problems.
The human immunodeficiency virus Tat proteins specifically associate with TAK in vivo and require the carboxyl-terminal domain of RNA polymerase II for function (1996)

Human immunodeficiency virus types 1 and 2 encode closely related proteins, Tat-1 and Tat-2, that stimulate viral transcription. Previously, we showed that the activation domains of these proteins specifically interact in vitro with a cellular protein kinase named TAK. In vitro, TAK phosphorylates the Tat-2 but not the Tat-1 protein, a 42-kDa polypeptide of unknown identity, and the carboxyl-terminal domain (CTD) of RNA polymerase II (RNAP II). We now show that the 42-kDa substrate of TAK cochromatographs with TAK activity, suggesting that this 42-kDa polypeptide is a subunit of TAK. We also show that the Tat proteins specifically associate with TAK in vivo, since wild-type Tat-1 and Tat-2 proteins expressed in mammalian cells, but not mutant Tat proteins containing a nonfunctional activation domain, can be coimmunoprecipitated with TAK. We also mapped the in vivo phosphorylation sites of Tat-2 to the carboxyl terminus of the protein, but analysis of proteins with mutations at these sites suggests that phosphorylation is not essential for Tat-2 transactivation function. We further investigated whether the CTD of RNAP II is required for Tat function in vivo. Using plasmid constructs that express an alpha-amanitin-resistant RNAP II subunit with a truncated or full-length CTD, we found that an intact CTD is required for Tat function. These observations strengthen the proposal that the mechanism of action of Tat involves the recruitment or activation of TAK, resulting in activated transcription through phosphorylation of the CTD.
Synthesis of Variable-Sized Nanocrystals of Fe3O4 with High Surface Reactivity (2004)

A new rational method of synthesis of nanocrystalline iron (II, III) oxide is based on the elevated-temperature hydrolysis of chelate iron alkoxide complexes in solutions of corresponding alcohol, diethylene glycol, and N-methyl diethanolamine. The rates of reaction and crystallization are easily tuned by varying the concentration of reactants and changing the temperature. The size of the nanocrystals is controlled by changing the complexing strength of the reaction medium: 5.7 nm in diethylene glycol, 16.8 nm in N-methyl diethanolamine, and 12.7 nm in a 1:1 mixture of both solvents. The nanocrystalline powdered Fe3O4 products were isolated with a high yield. The surface of the obtained nanocrystals is passivated by molecules of adsorbed donating solvent that provide stability against agglomeration, provide solubility in polar protic solvents (water and methanol), and allow reactions at the nanocrystal surface.