gebhart/patrepeval huggingface dataset:
Expression of the macrophage colony-stimulating factor and its receptor in gynecologic malignancies (1991)

Recently, hematopoietic growth factors have been implicated in protean nonhematopoietic processes. In the current study, expression of macrophage colony-stimulating factor (M-CSF) and its receptor (the c-fms proto-oncogene) was investigated in 42 samples of gynecologic tissues. There were 15 samples of normal ovarian and uterine tissue or benign conditions of these organs; 11 samples of primary ovarian cancer tissue; seven samples of metastatic ovarian cancer tissue; and nine samples of primary endometrial cancer tissue. Steady state transcript levels were assessed by Northern Blot analysis. Macrophage colony-stimulating factor (M-CSF) expression was not observed in any of the specimens of benign abnormalities or of normal organs; c-fms expression was detected in two of 15 (13%) of these specimens, albeit at very low levels. In contrast, 14 (78%) of 18 ovarian tumor specimens, and five (55%) of nine endometrial tumor specimens expressed M-CSF. Similarly, 16 (89%) of 18 ovarian tumor specimens and six (67%) of nine endometrial tumor specimens expressed c-fms. Most positive malignant tissues (19 [86%] of 22) showed coexpression of M-CSF and c-fms. Of interest, M-CSF and c-fms mRNA were detected in tumor, but not in adjacent normal tissue. Furthermore, M-CSF and c-fms transcripts were produced by all metastatic tumors, including two cases in which the corresponding primary tumor from the same patient was negative. Because M-CSF mediates its effects by binding to its receptor, the increased levels of both these gene products in gynecologic malignancies suggest that an interaction between M-CSF and c-fms may participate in the development of ovarian and endometrial carcinomas and especially in progression to the metastatic state.
¿Qué es realmente "navegación"?: Un modelo descriptivo para la investigación científica conductual (2006)

Introduccion. Se sostiene que los elementos actuales en episodios tipicos de navegacion no han sido capturados bien hasta la fecha por las aproximaciones comunes al concepto.
Metodo. Se presentan y analizan atentamente los resultados empiricos de investigacion informados por anteriores investigadores.
Analisis. Basandose en los problemas surgidos en la revision de la investigacion mencionada anteriormente, se analizan atentamente y se desarrollan los componentes de la navegacion. Se ve que la navegacion consiste en unas series de cuatro pasos, iterados indefinidamente hasta el final de un episodio de navegacion: 1) vislumbrar un campo de vision, 2) seleccionar o probar un objeto fisico o informativo dentro del campo de vision, 3) examinar el objeto, 4) obtener el objeto (conceptual y/o fisicamente) o abandonarlo. No todos estos elementos necesitan estar presentes en cada episodio de navegacion, aunque multiples vislumbres se ven que son lo minimo que constituye el acto.
Resultados. Se muestra entonces que este concepto de navegacion tiene soporte persuasivo en la bibliografia psicologica y antropologica, donde la investigacion sobre busqueda visual, curiosidad y comportamiento exploratorio se encuentra en armonia con esta perspectiva.
Conclusiones. Se argumenta que esta concepcion de navegacion es mas cercana al comportamiento humano real que otras aproximaciones. Se desarrollan las implicaciones para un mejor diseno de sistemas de informacion.
The Identification of Transposon-Tagged Mutations in Essential Genes That Affect Cell Morphology in Saccharomyces cerevisiae (1996)

The yeast Saccharomyces cerevisiae reproduces by budding, and many genes are required for proper bud development. Mutations in some of these genes cause cells to die with an unusual terminal morphology-elongated or otherwise aberrantly shaped buds. To gain insight into bud development, we set out to identify novel genes that encode proteins required for proper bud morphogenesis. Previous studies screened collections of conditional mutations to identify genes required for essential functions, including bud formation. However, genes that are not susceptible to the generation of mutations that cause a conditional phenotype will not be identified in such screens. To identify a more comprehensive collection of mutants, we used transposon mutagenesis to generate a large collection of lethal disruption mutations. This collection was used to identify 209 mutants with disruptions that cause an aberrant terminal bud morphology. The disruption mutations in 33 of these mutants identify three previously uncharacterized genes as essential, and the mutant phenotypes suggest roles for their products in bud morphogenesis.
Lanthiopeptin, a new peptide antibiotic. Production, isolation and properties of lanthiopeptin. (1989)

A strain of Streptoverticillium cinnamoneum produced a peptide antibiotic named lanthiopeptin, which contained four unusual amino acids, erythro-beta-hydroxyaspartic acid, mesolanthionine, threo-beta-methyllanthionine and lysinoalanine. Lanthiopeptin showed antiviral activity against herpes simplex virus type 1 KOS strain infection in Vero cells by cytopathic effect reduction assay. The structure of lanthiopeptin is similar to that of ancovenin.
The HXT2 gene of Saccharomyces cerevisiae is required for high-affinity glucose transport. (1990)

The HXT2 gene of the yeast Saccharomyces cerevisiae was identified on the basis of its ability to complement the defect in glucose transport of a snf3 mutant when present on the multicopy plasmid pSC2. Analysis of the DNA sequence of HXT2 revealed an open reading frame of 541 codons, capable of encoding a protein of Mr 59,840. The predicted protein displayed high sequence and structural homology to a large family of procaryotic and eucaryotic sugar transporters. These proteins have 12 highly hydrophobic regions that could form transmembrane domains; the spacing of these putative transmembrane domains is also highly conserved. Several amino acid motifs characteristic of this sugar transporter family are also present in the HXT2 protein. An hxt2 null mutant strain lacked a significant component of high-affinity glucose transport when under derepressing (low-glucose) conditions. However, the hxt2 null mutation did not incur a major growth defect on glucose-containing media. Genetic and biochemical analyses suggest that wild-type levels of high-affinity glucose transport require the products of both the HXT2 and SNF3 genes; these genes are not linked. Low-stringency Southern blot analysis revealed a number of other sequences that cross-hybridize with HXT2, suggesting that S. cerevisiae possesses a large family of sugar transporter genes.
Review article: the burden of hepatic encephalopathy (2007)

Hepatic encephalopathy, a challenging complication of advanced liver disease, occurs in approximately 30-45% of patients with cirrhosis and 10-50% of patients with transjugular intrahepatic portosystemic shunt, while minimal hepatic encephalopathy affects approximately 20-60% of patients with liver disease. Although the total direct and indirect costs of hepatic encephalopathy have not been formally quantified, data from the Healthcare Cost and Utilization Project suggest that hepatic encephalopathy-related hospitalizations are associated with substantial costs. In 2003, there were over 40 000 patients hospitalized in the United States for a primary diagnosis of hepatic encephalopathy, resulting in total charges of approximately $932 million. Furthermore, trends over the past 10 years suggest that the burden of hepatic encephalopathy is increasing, as indicated by increases in hospital admissions and higher charges per stay. Because of inconsistencies in coding for hepatic encephalopathy, the prevalence and cost data from this data source are believed to significantly underestimate the true burden of hepatic encephalopathy. In addition, expenditures for physician fees and out-patient care, as well as indirect costs attributable to lost work days and decreased productivity, have not been quantified. Thus, there is need for future studies to more accurately define the burden of hepatic encephalopathy, including minimal hepatic encephalopathy.
AN AGENDA-BASED DIALOG MANAGEMENT ARCHITECTURE FOR SPOKEN LANGUAGE SYSTEMS (1999)

Dialog management can be seen as a solution to two specific problems: (1) providing a coherent overall structure to interaction that extends beyond the single turn, (2) correctly manage mixed-initiative interaction, allowing users to guide interaction as per their (not necessarily explicitly shared) goals while allowing the system to guide interaction towards successful completion. We propose a dialog management architecture based on the following elements: handlers that manage interaction focussed on tightly coupled sets of information, a product that reflects mutually agreed-upon information and an agenda that orders the topics relevant to task completion.
Analysis of current-voltage characteristics in polysilicon TFTs for LCDs (2003)

An analytic model which can accurately calculate the characteristics of polysilicon TFTs was developed. The theoretical current-voltage curves were compared with measured data, and correlations with trap density in polysilicon film and device performance were investigated. Good agreement was obtained between theoretical and measured results. It was also found that on-current was improved by reducing the densities near the band edges in a forbidden gap. This effect was realized by optimizing the film deposition temperature or by using laser annealing. A hydrogenation effect reduced the density near the midgap, which improved off-current. The TFTs were successfully applied in grey-scale liquid-crystal displays (LCDs) with fully integrated drive circuits.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Splitting CO 2 into CO and O 2 by a single catalyst (2012)

The metal complex [(tpy)(Mebim-py)Ru(II)(S)](2+) (tpy = 2,2' : 6',2''-terpyridine; Mebim-py = 3-methyl-1-pyridylbenzimidazol-2-ylidene; S = solvent) is a robust, reactive electrocatalyst toward both water oxidation to oxygen and carbon dioxide reduction to carbon monoxide. Here we describe its use as a single electrocatalyst for CO(2) splitting, CO(2) → CO + 1/2 O(2), in a two-compartment electrochemical cell.
CUE1: A Mesophyll Cell-Specific Positive Regulator of Light-Controlled Gene Expression in Arabidopsis (1995)

Hsou-min Li, Kevin Culligan, Richard A. Dixon, Joanne Chory, CUE1: A Mesophyll Cell-Specific Positive Regulator of Light-Controlled Gene Expression in Arabidopsis, The Plant Cell, Vol. 7, No. 10 (Oct., 1995), pp. 1599-1610
Inhibition of the metastasis of murine malignant melanoma by synthetic polymeric peptides containing core sequences of cell-adhesive molecules. (1989)

We investigated that the antimetastatic and antiadhesive activities of peptides based on Arg-Gly-Asp adhesive signal in fibronectin could be augmented by their polymerization. Poly(Arg-Gly-Asp), which consists of a repetitive sequence of Arg-Gly-Asp, inhibited lung metastases in C57BL/6 mice more effectively than Arg-Gly-Asp tripeptide was able to do, when coinjected or separately injected with B16-BL6 cells. The adhesion of tumor cells to fibronectin was specifically inhibited by adding poly(Arg-Gly-Asp) but not unrelated peptides. In contrast, poly(Arg, Gly, Asp), in which three amino acids are randomly arranged, showed neither inhibition of lung metastases nor any adhesive ability to attach to tumor cells. The inhibitory effect of polymeric peptides containing the Arg-Gly-Asp sequence on lung metastases decreased according to the decreasing repeat units of the Arg-Gly-Asp core sequence. Polymeric peptides with Arg-Gly-Asp entrapped within the liposome membranes also caused a remarkable reduction of metastatic colonies. In a spontaneous metastasis model, multiple i.v. administrations of poly(Arg-Gly-Asp) after tumor inoculation caused the significant reduction of metastatic colonies in the lung but did not affect the growth (size) of primary tumor. We found that the polymerization (multivalency) of the Arg-Gly-Asp core sequence was able to augment the inhibition of tumor lung metastases in experimental and spontaneous metastasis models as well as the cell-adhesive property more effectively than a monovalent unit of Arg-Gly-Asp peptide.
Epidemiology and Impact on Quality of Life of Postherpetic Neuralgia and Painful Diabetic Neuropathy (2002)

Both conditions are common complications of their underlying disorders and can profoundly diminish the quality of life of affected persons.
The activin A‐follistatin system: potent regulator of human extracellular matrix mineralization (2007)

Bone quality is an important determinant of osteoporosis, and proper osteoblast differentiation plays an important role in the control and maintenance of bone quality. We investigated the impact of activin signaling on human osteoblast differentiation, extracellular matrix formation, and mineralization. Activins belong to the transforming growth factor-beta superfamily and activin A treatment strongly inhibited mineralization in osteoblast cultures, whereas the activin antagonist follistatin increased mineralization. Osteoblasts produced activin A and follistatin in a differentiation-dependent manner, leading to autocrine regulation of extracellular matrix formation and mineralization. In addition, mineralization in a vascular smooth muscle cell-based model for pathological calcification was inhibited. Comparative activin A and follistatin gene expression profiling showed that activin signaling changes the expression of a specific range of extracellular matrix proteins prior to the onset of mineralization, leading to a matrix composition with reduced or no mineralizing capacity. These findings demonstrate the regulation of osteoblast differentiation and matrix mineralization by the activin A-follistatin system, providing the possibility to control bone quality as well as pathological calcifications such as atherosclerosis by using activin A, follistatin, or analogs thereof.
Neurite growth‐inhibitory properties of amyloid β-peptides in vitro: Aβ25-35, but not Aβ1-40, is inhibitory (1997)

The effects of freshly-solubilized synthetic amyloid β-peptides on the growth of neurites from high density cultures of embryonic chick dorsal root ganglia and retinal pieces over periods of 24 to 48 hours were examined. The undecapeptide β25–35, the presumed neurotoxic moiety of β1–40, was found to inhibit neurite outgrowth, whereas β1–40 and β1–28 were without effect. The growth-inhibitory effect of β25–35 was apparent at a concentration of 10 ng/ml and showed concentration dependence. The inhibitory effect was reversible, since dorsal root ganglia grown initially in β25–35-supplemented medium showed more extensive neurite outgrowth when transferred to normal growth medium after 24 hours than dorsal root ganglia maintained in freshly-made β25–35-supplemented medium throughout. It is concluded that β25–35 has neurite growth-inhibitory properties in vitro not shared by β1–40 or β1–28. The differences in peptide behaviour may be related to aggregation state. These findings may have implications for understanding plaque morphology in normal ageing and Alzheimer's disease, since N-terminally truncated amyloid β-peptides are preferentially localized in the diffuse plaques which lack a surrounding neuritic reaction; this may also indicate a physiological neurite growth-inhibitory activity for N-terminally truncated amyloid β-peptides. © 1997 John Wiley & Sons, Ltd.
Pulmonary-specific expression of SP-D corrects pulmonary lipid accumulation inSP-Dgene-targeted mice (2000)

Targeted disruption of the surfactant protein (SP) D (SP-D) gene caused a marked pulmonary lipoidosis characterized by increased alveolar lung phospholipids, demonstrating a previously unexpected role for SP-D in surfactant homeostasis. In the present study, we tested whether the local production of SP-D in the lung influenced surfactant content in SP-D-deficient [SP-D(-/-)] and SP-D wild-type [SP-D(+/+)] mice. Rat SP-D (rSP-D) was expressed under control of the human SP-C promoter, producing rSP-D, SP-D(+/+) transgenic mice. SP-D content in bronchoalveolar lavage fluid was increased 30- to 50-fold in the rSP-D, SP-D(+/+) mice compared with the SP-D(+/+) parental strain. Lung morphology, phospholipid content, and surfactant protein mRNAs were unaltered by the increased concentration of SP-D. Likewise, the production of endogenous mouse SP-D mRNA was not perturbed by the SP-D transgene. rSP-D, SP-D(+/+) mice were bred to SP-D(-/-) mice to assess whether lung-selective expression of SP-D might correct lipid homeostasis abnormalities in the SP-D(-/-) mice. Selective expression of SP-D in the respiratory epithelium had no adverse effects on lung function, correcting surfactant phospholipid content and decreasing phosphatidylcholine incorporation significantly. SP-D regulates surfactant lipid homeostasis, functioning locally to inhibit surfactant phospholipid incorporation in the lung parenchyma and maintaining alveolar phospholipid content in the alveolus. Marked increases in biologically active tissue and alveolar SP-D do not alter lung morphology, macrophage abundance or structure, or surfactant accumulation.
The phosphorylation state of Ser-129 in human α-synuclein determines neurodegeneration in a rat model of Parkinson disease (2008)

Studies have shown that alpha-synuclein (alpha-syn) deposited in Lewy bodies in brain tissue from patients with Parkinson disease (PD) is extensively phosphorylated at Ser-129. We used recombinant Adeno-associated virus (rAAV) to overexpress human wild-type (wt) alpha-syn and two human alpha-syn mutants with site-directed replacement of Ser-129 to alanine (S129A) or to aspartate (S129D) in the nigrostriatal tract of the rat to investigate the effect of Ser-129 phosphorylation state on dopaminergic neuron pathology. Rats were injected with rAAV2/5 vectors in the substantia nigra pars compacta (SNc) on one side of the brain; the other side remained as a nontransduced control. The level of human wt or mutant alpha-syn expressed on the injected side was about four times the endogenous rat alpha-syn. There was a significant reduction of dopaminergic neurons in the SNc and dopamine (DA) and tyrosine hydroxylase (TH) levels in the striatum of all S129A-treated rats as early as 4 wk postinjection. Nigral DA pathology occurred more slowly in the wt-injected animals, but by 26 wk the wt alpha-syn group lost nigral TH neurons equivalent to the mutated S129A group at 8 wk. In stark contrast, we did not observe any pathological changes in S129D-treated animals. Therefore, the nonphosphorylated form of S129 exacerbates alpha-syn-induced nigral pathology, whereas Ser-129 phosphorylation eliminates alpha-syn-induced nigrostriatal degeneration. This suggests possible new therapeutic targets for Parkinson Disease.
Inhibition of colony-stimulating factor-1 activity by monoclonal antibodies to the human CSF-1 receptor (1989)

Four of 12 monoclonal antibodies (MoAbs) directed to different epitopes in the extracellular domain of the human colony-stimulating factor-1 receptor (CSF-1R, the c-fms proto-oncogene product) specifically inhibit CSF-1 binding to receptor-bearing cells. All four antibodies abrogated CSF-1-dependent colony formation by human bone marrow-derived macrophage precursors and by mouse NIH-3T3 cells expressing a transduced human c-fms gene. In addition, one of these antibodies (designated MoAb 2–4A5) interfered with the ligand-independent proliferation of NIH-3T3 cells transformed by an oncogenic, mutant c- fms allele. Unlike CSF-1 itself, neither MoAb 2–4A5 nor the other three inhibitory antibodies (MoAbs 12–2D6, 12–3A1, and 12–3A3) induced CSF-1R internalization or degradation. These antibodies should prove useful not only for identifying and quantitating CSF-1R on receptor-bearing cells but for abrogating specific receptor signals that govern the proliferation and survival of human mononuclear phagocytes.
Guiding the study of brain dynamics by using first-person data: Synchrony patterns correlate with ongoing conscious states during a simple visual task (2002)

Even during well-calibrated cognitive tasks, successive brain responses to repeated identical stimulations are highly variable. The source of this variability is believed to reside mainly in fluctuations of the subject's cognitive "context" defined by his/her attentive state, spontaneous thought process, strategy to carry out the task, and so on... As these factors are hard to manipulate precisely, they are usually not controlled, and the variability is discarded by averaging techniques. We combined first-person data and the analysis of neural processes to reduce such noise. We presented the subjects with a three-dimensional illusion and recorded their electrical brain activity and their own report about their cognitive context. Trials were clustered according to these first-person data, and separate dynamical analyses were conducted for each cluster. We found that (i) characteristic patterns of endogenous synchrony appeared in frontal electrodes before stimulation. These patterns depended on the degree of preparation and the immediacy of perception as verbally reported. (ii) These patterns were stable for several recordings. (iii) Preparatory states modulate both the behavioral performance and the evoked and induced synchronous patterns that follow. (iv) These results indicated that first-person data can be used to detect and interpret neural processes.
InterAxis: Steering Scatterplot Axes via Observation-Level Interaction (2015)

Scatterplots are effective visualization techniques for multidimensional data that use two (or three) axes to visualize data items as a point at its corresponding x and y Cartesian coordinates. Typically, each axis is bound to a single data attribute. Interactive exploration occurs by changing the data attributes bound to each of these axes. In the case of using scatterplots to visualize the outputs of dimension reduction techniques, the x and y axes are combinations of the true, high-dimensional data. For these spatializations, the axes present usability challenges in terms of interpretability and interactivity. That is, understanding the axes and interacting with them to make adjustments can be challenging. In this paper, we present InterAxis, a visual analytics technique to properly interpret, define, and change an axis in a user-driven manner. Users are given the ability to define and modify axes by dragging data items to either side of the x or y axes. from which the system computes a linear combination of data attributes and binds it to the axis. Further, users can directly tune the positive and negative contribution to these complex axes by using the visualization of data attributes that correspond to each axis. We describe the details of our technique and demonstrate the intended usage through two scenarios.