gebhart/patrepeval huggingface dataset:
Developmental regulation of peach ACC oxidase promoter-GUS fusions in transgenic tomato fruits (2004)

A genomic DNA sequence (PpACO1) encoding 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) from peach (Prunus persica L. Batsch cv. Loring) was isolated. It has four exons interrupted by three introns and 2.9 kb of flanking region 5' of the translational start codon. Previous work with the cDNA demonstrated that accumulation of the peach ACO message correlated with increasing amounts of ethylene synthesized by the fruit as they ripened. To identify regulatory elements in the peach ACC oxidase gene, chimeric fusions between 403, 610, 901, 1319, 2141, and 2919 bp of the 5' flanking region of the PpACO1 sequence and the beta-glucuronidase (GUS) coding sequence were constructed and used to transform tomato (Lycopersicon esculentum [Mill] cv. Pixie). Fruits from the various promoter lines were analysed for GUS expression by histochemical GUS staining, GUS quantitative enzyme activity determination, and measuring the relative amounts of GUS mRNA. Constructs with the smallest promoter of 403 bp had significant GUS expression in fruit, but not in other tissues, indicating the presence of a region that affects tissue-specific expression. An increase in GUS expression was observed with promoters longer than 901 bp, indicating an enhancer region between -1319 and -901. The full-length promoter of 2919 bp directed GUS expression in the green stage of fruit development, and increased GUS expression as fruit matured, indicating a regulatory region between -2919 and -2141 that controls the temporal expression of the gene in fruit. Only the full-length promoter sequence demonstrated responsiveness to ethylene.
Prospects of Manipulating Diatom Silica Nanostructure (2005)

A key to the development of nanotechnology will be the ability to make complex nanoscaled three-dimensional structures at low cost and in large numbers. The wide variety of structures in the silicified cell walls of diatoms offers a promising natural source of such materials. Diatom silica can be converted into other materials, with maintenance of detailed morphology. To facilitate the use of diatoms in nanotechnology, specific manipulation of the structure in vivo will be desirable. This article explores the possibilities of manipulating diatom silica structure, by nongenetic and genetic means. Nongenetic influences that affect silica structure include changes in environmental conditions and life cycle stages and the presence or absence of particular compounds. The genetically based natural variation in structure in different diatom species indicates that genetic manipulation is possible. To achieve this, however, several goals must be met. The first is to identify cell wall synthesis (CWS) genes involved in structure formation. The recently completed genome sequence of Thalassiosira pseudonana opens the door for genomic and proteomic approaches to accomplish this. An important method to determine the function of CWS genes will be to modify gene sequences or expression and monitor the effect on structure. Performing gene modifications is straightforward, and modified genes can be introduced into diatoms, but the current inability to replace native diatom genes with modified copies could be a problem. However, there are feasible approaches yet to be applied to achieve this goal. It is very likely that continued development and application of molecular genetic techniques will enable us to specifically modify diatom silicified structures and provide a detailed understanding of the underlying mechanism of their formation.
Mik-beta 1(Fv)-PE40, a recombinant immunotoxin cytotoxic toward cells bearing the beta-chain of the IL-2 receptor (1992)

Mik-beta 1 is a mAb that binds to the beta subunit of the IL-2R. We have constructed a recombinant single chain immunotoxin Mik-beta 1(Fv)-PE40 by genetically fusing the H and L V domains of Mik-beta 1 to each other via a peptide linker, and then to PE40, a derivative of Pseudomonas exotoxin. Mik-beta 1(Fv)-PE40 was selectively cytotoxic for cells expressing high levels of IL-2R beta (p75) subunit. Mik-beta 1(Fv)-PE40 was cytotoxic to the NK cell line YT-S, which expresses p75 but not p55 subunits, with an IC50 of 6 ng/ml. The ATL line HUT-102 was less sensitive, with an IC50 of 200 ng/ml. However, the IC50 could be lowered to 11 ng/ml when Mik-beta 1(Fv)-PE40 was allowed to bind to HUT-102 cells at 4 degrees C for 4 h before overnight incubation at 37 degrees C. An excess of Mik-beta 1 but not of anti-Tac, the anti-p55 mAb, prevented the cytotoxicity of Mik-beta 1(Fv)-PE40. We constructed a more active version of Mik-beta 1(Fv)-PE40, designated Mik-beta 1(Fv)-PE40KDEL, by converting the carboxyl-terminus of the toxin from -REDLK to -KDEL. Mik-beta 1(Fv)-PE40KDEL showed an IC50 of 2 ng/ml toward YT-S cells and 35 ng/ml toward HUT-102 cells. Binding studies using radioiodinated Mik-beta 1 showed that Mik-beta 1(Fv)-PE40 bound to the p75 receptor subunit with 11% of the affinity of the native Mik-beta 1 antibody. Mik-beta 1(Fv)-PE40 may be a useful reagent to study cells that express IL-2R, and it deserves further study as a possible treatment for cancers in which the malignant cells express high numbers of p75 subunit.
Mechanisms of Action and Overview of OKT3 (1995)

OKT3 is a murine monoclonal antibody of the immunoglobulin IgG2a isotype. The target of OKT3, CD3, is a 17-20 kilodalton (kD) molecule that is part of a multimolecular complex found only on mature T cells and medullary thymocytes. This complex is uniquely situated next to the T-cell receptor for antigen. An interaction between T cells, OKT3, and monocytes causes T-cell activation (mitogenesis) in vitro. Because of the unique association between the antigen receptor and CD3, antibodies that react with CD3 block T-cell receptor function and vice versa. Thus, OKT3 blocks both the generation and function of cytotoxic T cells. After an initial dose of OKT3, T cells virtually disappear from the circulation within minutes to hours. During treatment with OKT3, T cells bearing the usual array of surface molecules (CD2, CD4, CD8) reappear in the peripheral blood circulation but these cells are devoid of the OKT3 target molecule, CD3. Within 48 hours of discontinuing OKT3, the normal array of surface molecules including CD3 is found again on all T cells. The selective removal of CD3 by internalization is thought to be the key mechanism of action of OKT3. Comodulation of the antigen receptor with CD3 explains the immunoblocking action of OKT3 in vivo. Experience with a second or third treatment with OKT3 indicates that OKT3 is ineffective clinically if the CD3 target molecule is not modulated. OKT3 has been found to be effective for induction of immunosuppression and for treating initial and steroid-resistant rejections.
Transcriptional activation and nuclear targeting signals of the human androgen receptor. (1991)

The androgen receptor (AR) is a signal-transducing protein required for sexual differentiation, development, and expression of the male phenotype. A series of human AR deletion mutants were created either by site-directed mutagenesis using restriction enzyme digestion, the polymerase chain reaction, or, for a series of unidirectional NH2-terminal deletions, exonuclease III digestion. Receptor mutants were expressed in monkey kidney COS cells as truncated AR proteins between 20 and 107 kDa as revealed on immunoblots, where wild type AR was a doublet of 114 and 108 kDa. Subcellular localization by immunocytochemical staining demonstrated androgen-dependent nuclear uptake of AR from a perinuclear region of the cytoplasm. A nuclear targeting signal similar in sequence and position to the glucocorticoid receptor and homologous to the SV40 large T antigen was required for androgen-induced nuclear uptake of wild type AR. AR mutants lacking the NH2-terminal and/or steroid binding domains were constitutively nuclear with reduced transcriptional activity. Transcriptional activation by wild type AR was androgen-dependent in cotransfection studies of CV1 cells using the chloramphenicol acetyltransferase reporter gene linked to the mouse mammary tumor virus promoter. Deletion mutagenesis revealed within the NH2-terminal region a domain required for full transcriptional activity and within the steroid binding domain, an inhibitory function, deletion of which yielded a constitutively active receptor. Inhibition of wild type AR by coexpression with an inactive NH2-terminal fragment suggested competition for nuclear factors required for transcriptional regulation. These studies demonstrate a concerted interplay among the domains of the AR protein in regulating gene transcription.
Synthesis of 5′‐O‐Glycosyl‐ribo‐nucleosides (1978)

A group of novel bacterial metabolites, nucleosides of type (1), can vary in the base, the hexose moiety, and the intersaccharide bond. Some representatives, such as (1), R = H, X = adenyl, have now been synthesized.
Analysis by molecular cloning of the human class II genes. (1984)

The HLA class II genes control immune responsiveness to defined antigens; they encode cell surface heterodimers composed of alpha and beta glycopeptides. Recently, cDNA and genomic clones encoding these chains have been isolated, which allows molecular analysis of the class II genes. cDNA clones encoding the alpha chain of the HLA-DR antigen as well as that of another HLA class II antigen have been identified and characterized by nucleotide sequence analysis. These clones have been used as probes to isolate additional class II alpha cDNA clones in cDNA libraries and to identify polymorphisms in genomic DNA. Polymorphic restriction sites have been localized within the HLA-DR alpha gene and used as genetic markers in the analysis of families and of disease (insulin-dependent diabetes mellitus) and control populations. In addition, cDNA clones encoding the DR beta and DC beta chains were used as hybridization probes to identify DNA polymorphism. cDNA clones encoding the DR gamma (Ii) chain have also been identified; unlike the DR alpha and DR beta loci, the DR gamma gene is located on some chromosome other than chromosome 6. The genetic complexity of the human class II alpha and beta loci, as revealed by analysis with cDNA and genomic clones, is greater than that of the murine class II genes. The extent of that complexity will be defined by future work in this area.
Accumulation and distribution of acylated nornicotine derivatives in flue-cured tobacco alkaloid isolines (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAccumulation and distribution of acylated nornicotine derivatives in flue-cured tobacco alkaloid isolinesMirjana V. Djordjevic, Lowell P. Bush, Scott L. Gay, and Harold R. BurtonCite this: J. Agric. Food Chem. 1990, 38, 2, 347–350Publication Date (Print):February 1, 1990Publication History Published online1 May 2002Published inissue 1 February 1990https://pubs.acs.org/doi/10.1021/jf00092a002https://doi.org/10.1021/jf00092a002research-articleACS PublicationsRequest reuse permissionsArticle Views105Altmetric-Citations10LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Estimation of bed-ridden human's gross and slight movement based on pressure sensors distribution bed (2003)

In this paper, we developed a bed-ridden human's body movement unrestraint estimation system by using a pressure sensors distribution bed. We classified body movements into gross and slight movements. In order to estimate both gross and slight movements, we realized the distinction methods between a human and an object and between sitting and lying status. We also realized the estimation methods of a posture, an articular movement, the respiration and the pulse. By integrating these methods to complement each other, a bed-ridden human's body movement from gross to slight movements can be estimated totally.
Tratamiento de lixiviados mediante humedales artificiales: revisión del estado del arte (2012)

Los lixiviados de vertederos de residuos solidos son considerados uno de los contaminantes liquidos de mayor impacto ambiental y dificultad de tratamiento, debido a la variabilidad de su composicion, toxicidad y facilidad de percolacion hacia aguas superficiales e incluso subsuperficiales. Multiples han sido las tecnologias aplica- das para su depuracion, incluso tratamientos de tipo convencional y tratamientos de tipo natural. Los humedales artificiales son una alternativa de tipo natural propuesta para el tratamiento de lixiviados, que presenta facilidad y bajos costos de operacion y mantenimiento, ademas de bajo consumo de energia electrica, adaptables a diferentes niveles de tratamiento. Presentan remociones de materia organica aproximadamente del 27-98% y del 11-96%, medida con DBO5  y DQO, respectivamente. Los valores fluctuan dependiendo del tipo de humedal utilizado, asi como tambien de las confi- guraciones del sistema de tratamiento y condiciones clima. El presente estudio es una revision del estado del arte de la aplicacion de los humedales artificiales al tratamiento de lixiviados de vertederos de residuos solidos, sus caracteristicas principales, aspectos operativos y rendimientos, de acuerdo con los resultados que se reportan en la litera- tura, principalmente de experiencias en paises europeos y Estados Unidos.
Low-temperature TiO2 Films for Dye-sensitized Solar Cells: Factors Affecting Energy Conversion Efficiency (2008)

Semiconductor films prepared by electrostatic layer-by-layer deposition can be used to fabricate dye-sensitized solar cells after low-temperature treatment (150 °C). However, the resulting photocurrent is much less than when the film is sintered at 500 °C. The difference in short-circuit current is a factor of 2.2 with the Ru-based dye N719 and is 3.5 with the organic dye D5. The photocurrent at a given wavelength is proportional to the light-harvesting efficiency, charge injection effciency, and charge collection efficiency. Sintered films take up more than 60% more of either dye than unsintered films and therefore absorb more photons. Electron injection is hindered in unsintered films due to a conduction band edge potential 100 mV more negative than in a sintered electrode. Additional injection effects could be due to adsorption of the dye to polymer rather than to TiO2 in unsintered films, although our measurements were inconclusive on this point. Kinetic studies show electron transport times (τtr) an order of magnitude faster then electron lifetimes (τe) in both sintered and unsintered electrodes. Furthermore, a Li+ insertion experiment shows that both films have good electrical connectivity between TiO2 nanoparticles. Unsintered films thus exhibit efficient charge transport despite the presence of polymer and the lack of heat treatment to induce necking.
Studies on the Metabolism and Mechanism of Action of Methyldopa (1963)

The metabolism and particularly the decarboxylation of methyldopa were studied in hospitalized patients with uncomplicated hypertension. Both unlabeled and radioactive drugs were employed in these studies. Absorption from the intestine, as indicated by plasma levels of the drug and recovery of radioactivity in urine, was shown to be incomplete. The drug disappeared from the plasma with a half-time of less than 2 hours. On the average, about half of the radioactivity administered orally as 2-C 14 -methyldopa could be recovered in the urine. That portion not excreted in the urine appeared in the feces. Urinary excretion of radioactivity was rapid and essentially complete within 24 hours. Confirming previous studies with dl -α-methyl-dopa, the major urinary excretory products of l -α-methyl-dopa (methyldopa, Aldomet) were found to be the drug itself and conjugates thereof. Small fractions appear as other metabolites, the most significant of which is the decarboxylated derivative, αmethyl-dopamine. The pharmacologically inert d -isomer of α-methyl-dopa was found not to be decarboxylated. Alpha-methyl-dopa hydrazine was shown to reduce significantly the excretion of α-methyl-dopamine during treatment with methyldopa but the effects of the latter drug on blood pressure were not altered. On the basis of unchanged urinary excretions of vanilmandelic acid, decarboxylase inhibition during treatment with methyl-dopa was judged to be inadequate to inhibit endogenous synthesis of norepinephrine. The relationships between metabolism of the drug and clinical response are discussed. The hypothesis is presented and defended that the hypotensive effects of methyldopa are mediated by amine metabolites of the compound, which are formed following its decarboxylation. Probably norepinephrine depletion is the final denominator but other possibilities exist.
No evidence for presence of bacteria in modic type I changes (2008)

Our results showed no evidence of bacteria in vertebrae with Modic type I changes. The isolation of staphylococci from two patients probably represented contamination.
Resistance Exercise Reverses Aging in Human Skeletal Muscle (2007)

Human aging is associated with skeletal muscle atrophy and functional impairment (sarcopenia). Multiple lines of evidence suggest that mitochondrial dysfunction is a major contributor to sarcopenia. We evaluated whether healthy aging was associated with a transcriptional profile reflecting mitochondrial impairment and whether resistance exercise could reverse this signature to that approximating a younger physiological age. Skeletal muscle biopsies from healthy older (N = 25) and younger (N = 26) adult men and women were compared using gene expression profiling, and a subset of these were related to measurements of muscle strength. 14 of the older adults had muscle samples taken before and after a six-month resistance exercise-training program. Before exercise training, older adults were 59% weaker than younger, but after six months of training in older adults, strength improved significantly (P<0.001) such that they were only 38% lower than young adults. As a consequence of age, we found 596 genes differentially expressed using a false discovery rate cut-off of 5%. Prior to the exercise training, the transcriptome profile showed a dramatic enrichment of genes associated with mitochondrial function with age. However, following exercise training the transcriptional signature of aging was markedly reversed back to that of younger levels for most genes that were affected by both age and exercise. We conclude that healthy older adults show evidence of mitochondrial impairment and muscle weakness, but that this can be partially reversed at the phenotypic level, and substantially reversed at the transcriptome level, following six months of resistance exercise training.
PCR Primer Design (2003)

The selection of primers for a given polymerase chain reaction (PCR) can determine the efficiency and specificity of the PCR. Although in many cases successful PCR primers have been selected with little understanding of the principles involved, PCR can often only be achieved by using primers that are designed appropriately. Here, we give general recommendations for PCR primer selection and various aspects to be considered when designing primers.
The 6‐minute walk test as a new outcome measure in Duchenne muscular dystrophy (2009)

Walking abnormalities are prominent in Duchenne muscular dystrophy (DMD). We modified the 6-minute walk test (6MWT) for use as an outcome measure in patients with DMD and evaluated its performance in 21 ambulatory boys with DMD and 34 healthy boys, ages 4 to 12 years. Boys with DMD were tested twice, approximately 1 week apart; controls were tested once. The groups had similar age, height, and weight. All tests were completed. Boys who fell recovered rapidly from falls without injury. Mean +/- SD [range] 6-minute walk distance (6MWD) was lower in boys with DMD than in controls (366 +/- 83 [125-481] m vs. 621 +/- 68 [479-754] m; P < 0.0001; unpaired t-test). Test-retest correlation for boys with DMD was high (r = 0.91). Stride length (R(2) = 0.89; P < 0.0001) was the major determinant of 6MWD for both boys with DMD and controls. A modified 6MWT is feasible and safe, documents disease-related limitations on ambulation, is reproducible, and offers a new outcome measure for DMD natural history and therapeutic trials.
The design of Jemboss: a graphical user interface to EMBOSS (2003)

The software, EMBOSS and Jemboss, is freely available to academics and commercial users under the GPL licence. It can be downloaded from the EMBOSS ftp server: http://www.uk.embnet.org/Software/EMBOSS/, ftp://ftp.uk.embnet.org/pub/EMBOSS/. Registered HGMP-RC users can access an installed server from: http://www.uk.embnet.org/Software/EMBOSS/Jemboss/
Regulation of muscle growth by multiple ligands signaling through activin type II receptors (2005)

Myostatin is a secreted protein that normally functions as a negative regulator of muscle growth. Agents capable of blocking the myostatin signaling pathway could have important applications for treating human muscle degenerative diseases as well as for enhancing livestock production. Here we describe a potent myostatin inhibitor, a soluble form of the activin type IIB receptor (ACVR2B), which can cause dramatic increases in muscle mass (up to 60% in 2 weeks) when injected into wild-type mice. Furthermore, we show that the effect of the soluble receptor is attenuated but not eliminated in Mstn(-/-) mice, suggesting that at least one other ligand in addition to myostatin normally functions to limit muscle growth. Finally, we provide genetic evidence that these ligands signal through both activin type II receptors, ACVR2 and ACVR2B, to regulate muscle growth in vivo.
A conditional lethal mutant of Escherichia coli which affects the processing of ribosomal RNA. (1978)

A temperature-sensitive mutant strain was isolated from an RNase III-(rnc) strain of Escherichia coli. At the permissive temperature it behaves like the parental strain, but at the nonpermissive temperature it fails to produce normal levels of 23 S and 5 S rRNA, while instead the 25 S rRNA species becomes very prominent. (The 25 S molecule appears in rnc cells and contains 23 S rRNA sequences). When an rnc+ mutation was introduced to such a strain, or when the rnc mutation was replaced by an rnc+ allele, the strain remained temperature-sensitive. At the permissive temperature such strains synthesized rRNA like any other E. coli strain, but at the nonpermissive temperature they remained unable to synthesize normal levels of 5 S rRNA, and instead a larger molecule was accumulated. The simplest interpretation of theses findings is that the mutant strain contains a temperature-sensitive processing endoribonuclease, RNase E, which normally introduces a cut in the growing rRNA chain somewhere between the 23 S and the 5 S rRNA cistrons. These findings help also to explain the nature and origin of the various rRNA species observed in RNase III- cells and add to our understanding of processing of ribosomal RNA in normal cells of Escherichia coli.