gebhart/patrepeval huggingface dataset:
Light- and Carbon-Signaling Pathways. Modeling Circuits of Interactions (2003)

Here, we report the systematic exploration and modeling of interactions between light and sugar signaling. The data set analyzed explores the interactions of sugar (sucrose) with distinct light qualities (white, blue, red, and far-red) used at different fluence rates (low or high) in etiolated seedlings and mature green plants. Boolean logic was used to model the effect of these carbon/light interactions on three target genes involved in nitrogen assimilation: asparagine synthetase (ASN1 and ASN2) and glutamine synthetase (GLN2). This analysis enabled us to assess the effects of carbon on light-induced genes (GLN2/ASN2) versus light-repressed genes (ASN1) in this pathway. New interactions between carbon and blue-light signaling were discovered, and further connections between red/far-red light and carbon were modeled. Overall, light was able to override carbon as a major regulator of ASN1 and GLN2 in etiolated seedlings. By contrast, carbon overrides light as the major regulator of GLN2 and ASN2 in light-grown plants. Specific examples include the following: Carbon attenuated the blue-light induction of GLN2 in etiolated seedlings and also attenuated the white-, blue-, and red-light induction of GLN2 and ASN2 in light-grown plants. By contrast, carbon potentiated far-red-light induction of GLN2 and ASN2 in light-grown plants. Depending on the fluence rate of far-red light, carbon either attenuated or potentiated light repression of ASN1 in light-grown plants. These studies indicate the interaction of carbon with blue, red, and far-red-light signaling and set the stage for further investigation into modeling this complex web of interacting pathways using systems biology approaches.
Synthesis and biological activity of somatostatin analogues modified at the tryptophan residue. (1978)

Three analogues of somatostatin, in which the tryptophan residue in position 8 was replaced by 3-(1-naphthyl)-L-alanine, 3-(2-naphthyl)-L-alanine and 1, 2, 3, 4-tetrahydro-β-carboline-3-carboxylic acid, were synthesized by the solid-phase method. All of these analogues showed diminished biological activity compared to synthetic somatostatin. The results suggest strongly that the indolyl NH group in the tryptophan residue of somatostatin plays an important role to elicit full hormonal activity and that the function accomplished by the tryptophan residue in somatostatin is different from that in luteinizing hormone-releasing hormone.
Tag-72, CA 19.9 and CEA as Tumor Markers in Gastric Cancer (1994)

Serum levels of CEA, CA 19.9 and TAG-72 were measured in 79 patients with active gastric cancer, 47 with treated gastric cancer and no clinical evidence of the disease and 33 with benign gastric disease. In the patients with active gastric cancer TAG-72 was increased in 47%, CA 19.9 in 46% and CEA in 33%. The sensitivity of these markers was related to the stage of the disease, although upon comparison of stages I-II and III-IV significant difference was observed only for TAG-72. The combined use of two of the markers increased the sensitivity compared with the use of only one. The results suggest that the combination of TAG-72 and CA 19.9 may be useful in the post surgical management of patients with gastric cancer.
Increased expression of TDP-43 in the skin of amyotrophic lateral sclerosis (2010)

Suzuki M, Mikami H, Watanabe T, Yamano T, Yamazaki T, Nomura M, Yasui K, Ishikawa H, Ono S. Increased expression of TDP-43 in the skin of amyotrophic lateral sclerosis. Acta Neurol Scand: 2010: 122: 367–372. © 2010 The Authors Journal compilation © 2010 Blackwell Munksgaard. Objectives – Transactivation-responsive DNA-binding protein-43 (TDP-43) was indentified as a major component of the ubiquitin-positive inclusions in sporadic amyotrophic lateral sclerosis (ALS). However, there has been no study of TDP-43 in ALS skin. The present study investigates TDP-43 in ALS skin. Materials and methods – We made a quantitative immunohistochemical study of the expression of TDP-43 in the skin from 15 patients with ALS and 15 control subjects. Results – The proportion of TDP-43-positive (TDP-43+) cells in the epidermis in ALS patients was significantly higher (P < 0.001) than in controls. There was a significant positive relationship (r = 0.62, P < 0.02) between the proportion and duration of illness in ALS patients. The optical density of TDP-43+ cells in the epidermis in ALS patients is markedly stronger (P < 0.001) than in controls. There was a significant positive relation (r = 0.72, P < 0.01) between the immunoreactivity and duration of illness in ALS patients. Conclusions – These data suggest that changes of TDP-43 in ALS skin are likely to be related to the disease process and that metabolic alterations of TDP-43 may take place in the skin of patients with ALS.
Premature Senescence in Cultured Skin Fibroblasts from Subjects with Cystic Fibrosis (1979)

Cultured skin fibroblasts from subjects with cystic fibrosis exhibited normal population doubling times in early passages. After about 13 cumulative population doublings, cystic fibrosis lines doubled more slowly than controls and ceased doubling after about 19 weekly passages. Control lines continued doubling for 27 passages. The premature senescence noted in cells from subjects with cystic fibrosis reconciles controversial observations of cell doubling reported in the literature. Data presented here demonstrate that experiments with cystic fibrosis cells in late passage may generate misleading results since differences from control lines may be ascribed to generalized senile changes rather than to specific results of the cystic fibrosis genotype.
Abscisic Acid Application Timing and Concentration Affect Firmness, Pigmentation, and Color of `Flame Seedless' Grapes (2006)

Poor coloration of red grapes grown in warm regions is a frequent problem that decreases production efficiency. Most table grape growers use ethephon to improve color, but its influence on color development is erratic, and it may reduce berry firmness. Application of S-abscisic acid (ABA) to grapes can increase the anthocyanins in their skins, but no protocols have been established regarding its potential commercial use. Therefore, we evaluated the effects of ABA and ethephon treatments on fruit quality characteristics, including those related to firmness and color, on `Flame Seedless' grapes ( Vitis vinifera L.) in several experiments over three consecutive seasons. Abscisic acid had few effects on berry weight or juice composition, but it increased berry softening and skin anthocyanin concentrations. The effect of ABA on berry firmness was similar to ethephon. With respect to skin anthocyanin concentration and fruit color characteristics, 300 mg·L –1 ABA applied at veraison was superior to the other ABA concentrations and to ethephon applied at any of the times tested. Moreover, any concentration of ABA between 75 and 300 mg·L –1 applied after veraison improved color better than ethephon applied at the same time. There was a highly significant inverse curvilinear relationship between skin anthocyanin concentration and the lightness and hue of the berries. Anthocyanin concentrations between 0.01 and 0.04 mg·cm –2 had little effect on berry lightness and hue, so researchers should consider measuring color, not just anthocyanins, when evaluating the quality of red table grapes.
Direct Mechanical Measurements of the Elasticity of Single DNA Molecules by Using Magnetic Beads (1992)

Single DNA molecules were chemically attached by one end to a glass surface and by their other end to a magnetic bead. Equilibrium positions of the beads were observed in an optical microscope while the beads were acted on by known magnetic and hydrodynamic forces. Extension versus force curves were obtained for individual DNA molecules at three different salt concentrations with forces between 10(-14) and 10(-11) newtons. Deviations from the force curves predicted by the freely jointed chain model suggest that DNA has significant local curvature in solution. Ethidium bromide and 4',6-diamidino-2-phenylindole had little effect on the elastic response of the molecules, but their extent of intercalation was directly measured. Conversely, the effect of bend-inducing cis-diamminedichloroplatinum (II) was large and supports the hypothesis of natural curvature in DNA.
Regulation of vitamin K-dependent protein S. Inactivation by thrombin. (1984)

Thrombin treatment of the vitamin K-dependent protein S resulted in the loss of the activated protein C cofactor activity associated with protein S. The addition of phospholipid vesicles inhibited the inactivation. Thrombin treatment did not alter the molecular weight of the native protein. However, upon reduction, a peptide of approximately 3000 daltons was released from the treated protein. The interaction between calcium and protein S was reduced by thrombin treatment. When the calcium interaction was determined by the quenching of the intrinsic fluorescence of protein S, thrombin treatment appeared to inhibit the interaction between calcium and the protein. When the calcium interaction was observed by measuring the effect on the electrophoretic mobility of the protein, thrombin treatment reduced the interaction between calcium and protein S. However, the effect of thrombin treatment on the interaction between calcium and protein S was less than observed by the fluorescent method. This observation suggests that fluorescence quenching may be a result of a structural change induced by calcium binding. Thrombin treatment of protein S appears to uncouple the calcium binding from the structural change. In addition, the interaction between protein S and phospholipid vesicles was reduced by thrombin treatment. These results suggest that the thrombin conversion of protein S into a two-chain protein causes the loss of a calcium-induced change in protein structure, loss of the lipid-binding properties, and the loss of cofactor activity.
Human hematopoietic stem cells stimulated to proliferate in vitro lose engraftment potential during their S/G2/M transit and do not reenter G0 (2000)

An understanding of mechanisms regulating hematopoietic stem cell engraftment is of pivotal importance to the clinical use of cultured and genetically modified transplants. Human cord blood (CB) cells with lymphomyeloid repopulating activity in NOD/SCID mice were recently shown to undergo multiple self-renewal divisions within 6 days in serum-free cultures containing Flt3-ligand, Steel factor, interleukin 3 (IL-3), IL-6, and granulocyte colony-stimulating factor. The present study shows that, on the fifth day, the transplantable stem cell activity is restricted to the G1fraction, even though both colony-forming cells (CFCs) and long-term culture-initiating cells (LTC-ICs) in the same cultures are approximately equally distributed between G0/G1and S/G2/M. Interestingly, the G0 cells defined by their low levels of Hoechst 33342 and Pyronin Y staining, and reduced Ki67 and cyclin D expression (representing 21% of the cultured CB population) include some mature erythroid CFCs but very few primitive CFCs, LTC-ICs, or repopulating cells. Although these findings suggest a cell cycle–associated change in in vivo stem cell homing, the cultured G0/G1 and S/G2/M CD34+ CB cells exhibited no differences in levels of expression of VLA-4, VLA-5, or CXCR-4. Moreover, further incubation of these cells for 1 day in the presence of a concentration of transforming growth factor β1 that increased the G0/G1 fraction did not enhance detection of repopulating cells. The demonstration of a cell cycle–associated mechanism that selectively silences the transplantability of proliferating human hematopoietic stem cells poses both challenges and opportunities for the future improvement of ex vivo–manipulated grafts.
Cutaneous Calcification in Patients With End-Stage Renal Disease (2006)

Calcinosis of the vascular media of subcutaneous vessels was the most common histologic feature and was always associated with osteopontin staining, suggesting that CC is a regulated process. Moreover, to our knowledge, extravascular staining of osteopontin in sweat glands, nerves, and macrophages was demonstrated for the first time in this study.
Adverse effect of Ge + implantation forfabrication of SiGe PMOS (2001)

SiGe heterostructure MOSFETs have the potential for improved channel mobility over Si-only devices. It is shown that fabrication by implantation leads to inferior devices in contrast to previously reported work. A simultaneous decrease of the drain current and increase of the interface state density has been observed.
Synthesis and immunologic properties in mice of vaccines composed of Staphylococcus aureus type 5 and type 8 capsular polysaccharides conjugated to Pseudomonas aeruginosa exotoxin A (1990)

Epidemiological, serological and in vitro phagocytosis experiments provide evidence that the newly discovered type 5 and type 8 capsular polysaccharides (CPs) are both virulence factors and protective antigens for bacteremia caused by Staphylococcus aureus. Neither type 5 nor type 8 CP elicited serum antibodies when injected into mice. These two CPs were bound to Pseudomonas aeruginosa exotoxin A (ETA) to form conjugates by using the synthetic scheme devised for the CP (Vi) of Salmonella typhi and of pneumococcus type 12F (A. Fattom, W. F. Vann, S. C. Szu, A. Sutton, X. Li, D. Bryla, G. Schiffman, J. B. Robbins, and R. Schneerson, Infect. Immun. 56:2292-2298, 1988; S. C. Szu, A. L. Stone, J. D. Robbins, R. Schneerson, and J. B. Robbins, J. Exp. Med. 166:1510-1524, 1987). Both S. aureus CP-ETA conjugates elicited a rise in CP antibodies. As components of conjugates, both S. aureus CPs acquired T-cell-dependent properties, as shown by their ability to respond to carrier priming and to stimulate booster responses. The conjugate-induced antibodies facilitated type-specific opsonization of S. aureus by human polymorphonuclear leukocytes. The conjugates also induced ETA antibodies which neutralized the native toxin in vitro. Clinical studies of these two conjugates for active or passive immunization of patients at risk for S. aureus bacteremia are planned.
Oncomine 3.0: Genes, Pathways, and Networks in a Collection of 18,000 Cancer Gene Expression Profiles (2007)

DNA microarrays have been widely applied to cancer transcriptome analysis; however, the majority of such data are not easily accessible or comparable. Furthermore, several important analytic approaches have been applied to microarray analysis; however, their application is often limited. To overcome these limitations, we have developed Oncomine, a bioinformatics initiative aimed at collecting, standardizing, analyzing, and delivering cancer transcriptome data to the biomedical research community. Our analysis has identified the genes, pathways, and networks deregulated across 18,000 cancer gene expression microarrays, spanning the majority of cancer types and subtypes. Here, we provide an update on the initiative, describe the database and analysis modules, and highlight several notable observations. Results from this comprehensive analysis are available at http://www.oncomine.org.
Identifying Argumentative Discourse Structures in Persuasive Essays (2014)

In this paper, we present a novel approach for identifying argumentative discourse structures in persuasive essays. The structure of argumentation consists of several components (i.e. claims and premises) that are connected with argumentative relations. We consider this task in two consecutive steps. First, we identify the components of arguments using multiclass classification. Second, we classify a pair of argument components as either support or non-support for identifying the structure of argumentative discourse. For both tasks, we evaluate several classifiers and propose novel feature sets including structural, lexical, syntactic and contextual features. In our experiments, we obtain a macro F1-score of 0.726 for identifying argument components and 0.722 for argumentative relations.
"Stemness": Transcriptional Profiling of Embryonic and Adult Stem Cells (2002)

The transcriptional profiles of mouse embryonic, neural, and hematopoietic stem cells were compared to define a genetic program for stem cells. A total of 216 genes are enriched in all three types of stem cells, and several of these genes are clustered in the genome. When compared to differentiated cell types, stem cells express a significantly higher number of genes (represented by expressed sequence tags) whose functions are unknown. Embryonic and neural stem cells have many similarities at the transcriptional level. These results provide a foundation for a more detailed understanding of stem cell biology.
AVIDIN. 1. THE USE OF [14C]BIOTIN FOR KINETIC STUDIES AND FOR ASSAY (1963)

Research Article| December 01 1963 AVIDIN. 1. THE USE OF [14C]BIOTIN FOR KINETIC STUDIES AND FOR ASSAY NM GREEN NM GREEN Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1963) 89 (3): 585–591. https://doi.org/10.1042/bj0890585 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation NM GREEN; AVIDIN. 1. THE USE OF [14C]BIOTIN FOR KINETIC STUDIES AND FOR ASSAY. Biochem J 1 December 1963; 89 (3): 585–591. doi: https://doi.org/10.1042/bj0890585 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1963 The Biochemical Society1963 Article PDF first page preview Close Modal You do not currently have access to this content.
Mercado de Agua: Estudio de caso Código de Aguas de Chile 1981. (2004)

Autoría: Guillermo Donoso. Localización: Serie Documentos de Trabajo ( Pontificia Universidad Católica de Chile. Facultad de Agronomía e Ingeniería Forestal ). Nº. 4, 2004. Artículo de Revista en Dialnet.
kappa Chain joining segments and structural diversity of antibody combining sites. (1980)

Immunoglobulin kappa light chains are coded for by at least three distinct gene segments designated variable, joining, and constant. The joining gene codes for the 13 amino acid segment linking the variable and constant regions. This peptide includes the last amino acid (96) in the third complementarity-determining region and thus could introduce structural diversity. We have determined the light chain variable region sequences from three myeloma proteins with beta(1,6)galactan-binding specificity, bringing to six the number of light chains sequenced from proteins demonstrating this specificity. Five of these have isoleucine at position 96 and the sixth tryptophan. This substitution appears to be accommodated with no significant change in association constant for a beta(1,6)galactan hapten. Additionally, as many as nine substitutions are found in both light and heavy chain complementarity-determining regions between members of this group although only minimal variations in hapten binding affinity are observed. The isoleucine found at position 96 in five of the kappa chains could not be coded for by any of the joining gene nucleotide sequences previously observed and would require a novel nucleotide sequence at the recombination site between variable and joining genes to produce the observed protein structure. Alternatively, there may exist joining gene segments not yet detected.
Interrelating Different Types of Genomic Data, from Proteome to Secretome: 'Oming in on Function (2001)

With the completion of genome sequences, the current challenge for biology is to determine the functions of all gene products and to understand how they contribute in making an organism viable. For the first time, biological systems can be viewed as being finite, with a limited set of molecular parts. However, the full range of biological processes controlled by these parts is extremely complex. Thus, a key approach in genomic research is to divide the cellular contents into distinct sub-populations, which are often given an "-omic" term. For example, the proteome is the full complement of proteins encoded by the genome, and the secretome is the part of it secreted from the cell. Carrying this further, we suggest the term "translatome" to describe the members of the proteome weighted by their abundance, and the "functome" to describe all the functions carried out by these. Once the individual sub-populations are defined and analyzed, we can then try to reconstruct the full organism by interrelating them, eventually allowing for a full and dynamic view of the cell. All this is, of course, made possible because of the increasing amount of large-scale data resulting from functional genomics experiments. However, there are still many difficulties resulting from the noisiness and complexity of the information. To some degree, these can be overcome through averaging with broad proteomic categories such as those implicit in functional and structural classifications. For illustration, we discuss one example in detail, interrelating transcript and cellular protein populations (transcriptome and translatome). Further information is available at http://bioinfo.mbb.yale.edu/what-is-it.
Si:WO3 Sensors for Highly Selective Detection of Acetone for Easy Diagnosis of Diabetes by Breath Analysis (2010)

Acetone in the human breath is an important marker for noninvasive diagnosis of diabetes. Here, novel chemo-resistive detectors have been developed that allow rapid measurement of ultralow acetone concentrations (down to 20 ppb) with high signal-to-noise ratio in ideal (dry air) and realistic (up to 90% RH) conditions. The detector films consist of (highly sensitive) pure and Si-doped WO(3) nanoparticles (10-13 nm in diameter) made in the gas phase and directly deposited onto interdigitated electrodes. Their sensing properties (selectivity, limit of detection, response, and recovery times) have been investigated as a function of operating temperature (325-500 degrees C), relative humidity (RH), and interfering analyte (ethanol or water vapor) concentration. It was found that Si-doping increases and stabilizes the acetone-selective epsilon-WO(3) phase while increasing its thermal stability and, thus, results in superior sensing performance with an optimum at about 10 mol % Si content. Furthermore, increasing the operation temperature decreased the detector response to water vapor, and above 400 degrees C, it was (<or=0.7) always below the threshold (10.6) for fake diabetes detection in ideal conditions. At this temperature and at 90% RH, healthy humans (<or=900 ppb acetone) and diabetes patients (>or=1800 ppb) can be clearly distinguished by a remarkable gap (40%) in sensor response. As a result, these solid state detectors may offer a portable and cost-effective alternative to more bulky systems for noninvasive diabetes detection by human breath analysis.
REVIEW (1988)

‘Mead's Other Manus’ Phenomenology of the Encounter . By Lola Romanucci‐Ross. South Hadley, Massachusetts: Bergin and Garvey. 1985. Pp. xxii + 230. Price: US$24.95