gebhart/patrepeval huggingface dataset:
Development of a DNA-labeling system for array-based comparative genomic hybridization. (2005)

Chromosomal amplifications and deletions are critical components of tumorigenesis and DNA copy-number variations also correlate with changes in mRNA expression levels. Genome-wide microarray comparative genomic hybridization (CGH) has become an important method for detecting and mapping chromosomal changes in tumors. Thus, the ability to detect twofold differences in fluorescent intensity between samples on microarrays depends on the generation of high-quality labeled probes. To enhance array-based CGH analysis, a random prime genomic DNA labeling method optimized for improved sensitivity, signal-to-noise ratios, and reproducibility has been developed. The labeling system comprises formulated random primers, nucleotide mixtures, and notably a high concentration of the double mutant exo-large fragment of DNA polymerase I (exo-Klenow). Microarray analyses indicate that the genomic DNA-labeled templates yield hybridization signals with higher fluorescent intensities and greater signal-to-noise ratios and detect more positive features than the standard random prime and conventional nick translation methods. Also, templates generated by this system have detected twofold differences in gene copy number between male and female genomic DNA and identified amplification and deletions from the BT474 breast cancer cell line in microarray hybridizations. Moreover, alterations in gene copy number were routinely detected with 0.5 microg of genomic DNA starting sample. The method is flexible and performs efficiently with different fluorescently labeled nucleotides. Application of the optimized CGH labeling system may enhance the resolution and sensitivity of array-based CGH analysis in cancer and medical genetic studies.
Use of SPOOF's in the Analysis of Faulty Logic Networks (1973)

In general, one cannot predict the effects of possible failures on the functional characteristics of a logic network without knowlegde of the structure of that network.
Identificação de SNPs no gene DDEF1 bovino. (2014)

A raça Canchim foi criada objetivando a produção de carne de melhor qualidade nas condições brasileiras e, tem sido muito utilizada em cruzamentos. Padrões específicos de algumas características da carcaça como, por exemplo, de espessura de gordura, contribuem para a manutenção da qualidade da carne. A raça Canchim produz carcaças com espessura de gordura inferior ao desejável pelo mercado, necessitando assim de estudos que visem auxiliar o melhoramento dessa característica. Os marcadores moleculares surgem nesse contexto como uma possibilidade de auxiliar o melhoramento tradicional. O BTA14 possui relatos de QTLs para espessura de gordura, motivando o estudo de genes candidatos a influenciar a deposição de gordura nessa região do genoma dos bovinos. Um dos genes encontrados nessa região e que foi relacionado à adipogênese é o DDEF1. Este trabalho teve por objetivos a identificação de polimorfismos em parte do domínio P H centaurina do gene DDEF1. Foram calculados os valorers genéticos de 113 touros, pais de uma população de meio-irmãos constituída de 1193 animais. Procedeu-se a escolhida de 6 touros com maior valor genético e maior acurácia e 6 touros com menor valor genético e maior acurácia. O DNA desses 12 touros foi utilizado em reações de sequenciamento do domínio P H centaurina do gene DDEF1, que foi dividido em 5 amplicons devido ao grande distanciamento dos exons codificadores desse domínio. No entanto, até o momento apenas as análises de 3 desses amplicons foram finalizadas. Os sequenciamentos foram realizados em um seqüenciador ABI Prism 3100 Avant (Applied Biosystems). Os eletroferogramas gerados pelo seqüenciador foram submetidos ao programa de base calling Phred. Em seguida tais seqüências foram submetidas ao programa de montagem Phrap. A visualização das seqüências geradas foi realizada através do programa Consed, onde foi possível a observação dos SNPs. Esta metodologia permitiu identificação de polimorfismos somente em indivíduos heterozigotos para o SNP. Para identificação de polimorfismos entre indivíduos homozigotos submeteu-se as seqüências consenso ao programa CLUSTAL W. Foram identificados 10 polimorfismos no amplicon RP1, 8 no RP2 e 9 no RP3. As seqüências consenso obtidas foram comparadas as depositadas no banco de SNPs do NCBI (http://www.ncbi.nlm.nih.gov/SNP/snp_blastByOrg.cgi). Tendo-se verificado que os polimorfismos identificados nesse trabalho não estão depositados naquele banco de dados.
The Specificity of Dehydrogenases (1980)

The specificity of dehydrogenases for coenzyme (and coenzyme analogues), and substrate (and substrate analogues) is discussed in relation to structure, function, and evolution. Examples concern compounds that have very different structures, reactions that play widely differing roles in the life of the organism, and organisms of greatly differing types. The examples illustrate general points of interest and importance.
Increased myocardial contractility following growth hormone administration in normal man. An echocardiographic study. (1988)

Cardiac function was studied by echocardiography in 11 normal subjects before subcutaneous growth hormone administration (first control), after one week of subcutaneous growth hormone administration and at one week after stopping subcutaneous growth hormone administration (second control). Plasma growth hormone was 1.4 ng/ml and 4.5 ng/ml, respectively, at the first two examinations. Compared to the first and second control situations heart rate increased by 9% (p less than 0.1) and 15% (p less than 0.01), fractional shortening of the left ventricle by 8% (p less than 0.02) and 9% (p less than 0.01), and mean circumferential shortening velocity by 10% (p less than 0.05) and 14% (p less than 0.01) respectively. Mean arterial blood pressure was unchanged. Thus, in normal man an increase in plasma growth hormone up to levels comparable to those seen in type 1 diabetics during conditions of poor metabolic control seems to be followed by enhancement in myocardial contractility. Therefore we suggest that growth hormone might contribute to the increase of myocardial contractility earlier described in type 1 diabetic patients with no clinical signs of microvascular disease.
Crosslinking and degradation in γ‐irradiated poly‐<i>n</i>‐alkyl acrylates (1964)

Abstract Polymers of methyl, ethyl, n ‐butyl, n ‐octyl, and n ‐cetyl acrylate were γ‐irradiated in vacuo , and the effects of irradiation temperature (−196 to 56°C.) on energy yields for crosslinking and degradation estimated from gel fractions and swelling behavior of the gel. The extent of degradation is independent of polymer structure and reaction temperature, suggesting a molecular chain breaking process. Crosslinking, found to occur predominantly on the alkyl side chain, is independent of temperature above and below the polymer softening point, but is severalfold higher for irradiations above the softening point; these data seem to reflect the importance of segmental mobility of radiation produced polymer radicals in the crosslinking step.
Patient-Derived Health State Utilities for Gastroesophageal Reflux Disease (2005)

Gastroesophageal reflux disease adversely affects health-related quality of life. Time-tradeoff utility for patients with reflux disease is substantially higher when patients are on medication than off medications.
A Combinatorial and Informatics Approach to CdS Nanoclusters (2000)

The stabilization of size-specific monodisperse CdS nanoclusters has received much attention. However, the development of matrices, e.g., polymers, micelles, zeolites, for this purpose has remained largely empirical. Here a combinatorial and informatics approach to the discovery of ligands for CdS nanocluster stabilization is introduced. It is shown that combinatorially derived peptide and peptidomimetic ligands based on phytochelatins can stabilize CdS nanoclusters and that an informatics analysis of the library used yields design parameters critical for obtaining second-generation ligands.
Cell-Specific Expression of the Murine CD21 Gene Depends on Accessibility of Promoter and Intronic Elements (2000)

The murine complement receptor type 2 gene (Cr2/CD21) is transcriptionally active in murine B and follicular dendritic cells, but not in murine T cells. We have previously shown that altering chromatin structure via histone deacetylase inhibitors results in CD21 expression in murine T cells, and that the minimal CD21 promoter provided appropriate cell-specific expression of luciferase reporter constructs only in the presence of the first third of intron 1, fragment A. We extend this work by showing that replacing the CD21 gene promoter with the SV40 promoter resulted in the loss of this cell-specific control. Further delineation of intronic regulatory elements by fragmentation also resulted in the loss of cell-specific gene expression, suggesting that multiple CD21 promoter and intronic elements interact for appropriate CD21 gene expression. To assess this model, we performed EMSAs to define protein binding sites within promoter and intronic regions and DNase I hypersensitivity assays to determine chromatin accessibility. Multiple DNA binding factors were shown to be present in B and T cell extracts; a minority demonstrated B cell specificity. However, the DNase I sensitivity of T cell CD21 regulatory elements was not comparable to that of B cells until the histone acetylation status of the gene was altered. Taken together, these data suggest that chromatin remodeling facilitates cell-specific CD21 gene expression by modulating access of transcription factors to regulatory elements in the promoter and intron.
A coherent dual-polarized radar for studying the ocean environment (1991)

The important features of a coherent dual-polarized X-band radar designed to be of instrumentation quality for research use are described. The motivation for building the radar was to quantify the improvements attainable through the use of coherence and polarization in the detection of small floating targets in the presence of sea clutter. Results on the statistics of dual-polarized radar returns from the ocean surface (obtained with this radar at a site on the east coast of Canada) are presented. These results indicate that the K-distribution is very useful for describing the amplitude statistics of sea clutter (both the like- and cross-polarized channels) for low grazing angles. Analysis of the time-varying Doppler spectra of a small ice target and the neighboring sea clutter reveals differing Doppler characteristics, offering improved target detection.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Amino Acid Overproduction and Catabolic Pathway Regulation in <i>Saccharomyces cerevisiae</i> (1994)

Abstract To determine whether blocking a degradative pathway leads to amino acid accumulation, the internal free concentrations of threonine, methionine, and related amino acids have been measured in a strain of Saccharomyces cerevisiae and its mutants lacking either the L‐threoninedeaminase enzyme (EC 4.2.1.16) codedfor by the ILV1 gene (ilv mutants), that coded for by the CHA1 gene (cha − mutants), or both threonine deaminase enzymes (ilv − cha − mutants). Whereas maximal accumulation of internal free amino acids occurred in the double mutants ilv − cha − , ilv − single mutants displayed amino acid concentrations higher than those of either the wild type or the cha − single mutant. On the other hand, when these enzymes were measured in threonine and methionine overproducer mutants of an industrial strain of Saccharomyces cerevisiae , results indicated, in most cases, lower activities than those of the wild type, although there was not a total correlation between maximal threonine and/or methionine accumulation and minimal enzymatic activities. Results point to the isolation of strains that accumulate essential amino acids by blocking their degradative pathway.
Adjunctive nefazodone in neuroleptic-treated schizophrenic patients with predominantly negative symptoms: an open prospective pilot study (1999)

A combination of nefazodone with a conventional neuroleptic would lead to a serotonin (5-HT)2 and D2 receptor blockade resembling that of an atypical neuroleptic, with an additional increase of 5-HT (and noradrenaline) turnover. This may be of benefit in some cases of schizophrenia. In this study, eight patients with schizophrenia with predominantly negative and/or depressive symptoms underwent an open prospective 26-week trial with nefazodone, added to conventional neuroleptics. The total Positive and Negative Syndrome Scale (PANSS) and the Montgomery-Asberg Depression Rating Scale (MADRS) scores (the last observations carried forward, LOCF) significantly (P < 0.05) decreased in these eight patients by a mean of 31% and 63%, respectively, mainly within the first 6 weeks. Positive symptoms, observed in three patients and panic attacks in two patients disappeared entirely. The doses of neuroleptics, stable during the first 6 weeks of the trial, subsequently were able to be decreased by 28%. Extrapyramidal symptoms noticeably improved during the phase of stable neuroleptic dose regimen. Of the three patients who discontinued the trial prematurely (after 14 weeks or more), only one evidenced a nefazodone-related adverse event. Adjunctive nefazodone may be a useful treatment option in this patient population, but additional studies are recommended.
How Light Reaches the Eye and Its Components (2002)

The human eye is exquisitely sensitive to light (i.e., visible radiant energy), and when dark-adapted, the retina can detect a few photons of blue-green light. It is therefore not at all surprising that ocular tissues are also more vulnerable to ultraviolet (UV) and light damage than the skin. For this reason, humans have evolved with certain anatomical, physiological, and behavioral traits that protect this critical organ from the UV damage that would otherwise be certain from the intense bath of overhead solar ultraviolet radiation (UVR) when we are outdoors during daylight. For example, the UV exposure threshold dose for photokeratitis ("welders' flash" or "snow blindness")--if measured as falling on a horizontal ground surface--would be reached in less than 10 minutes around midday in the summer sun. There are three critical ocular structures that could be affected by UV exposure: the cornea, the lens, and the retina. The cornea transmits radiant energy only at 295 nm and above. The crystalline lens absorbs almost all incident energy to wavelengths of nearly 400 nm. In youth, a very small amount of UV-A reaches the retina, but the lens becomes more absorbing with age. Thus there are intraocular filters that effectively filter different parts of the UV spectrum and allow only of the order of 1% or less to actually reach the retina. Nevertheless, this small fraction of energy--if phototoxic--could still be of concern. Finally, oblique rays entering the eye from the temporal side, can actually reach the equatorial (germinative) area of the lens.
Mechanisms that regulate the cell cycle status of very primitive hematopoietic cells in long-term human marrow cultures. I. Stimulatory role of a variety of mesenchymal cell activators and inhibitory role of TGF-beta (1990)

Long-term marrow cultures (LTMC) allow the proliferation and differentiation of primitive human hematopoietic progenitor cells to be maintained for many weeks in the absence of exogenously provided hematopoietic growth factors. Previous investigations focused on defining various types of cells that are present in this culture system and on measuring the cycling behavior of the different subpopulations of colony-forming cells maintained within it. These studies suggested that mesenchymal stromal elements derived from the input marrow play a key role in regulating the turnover of the most primitive, high-proliferative potential erythroid and granulopoietic colony-forming cells that are found almost exclusively in the adherent layer of LTMC. In this study we show that the re-entry into S-phase of these primitive hematopoietic progenitors that occurs after each weekly medium change is due to an as yet undefined constituent of horse serum, which is absent from fetal calf serum. However, this effect is not unique to the factor present in horse serum. It is also elicited by the addition to LTMC of several well-defined growth regulatory molecules, ie, platelet-derived growth factor (PDGF), interleukin-1 (IL-1), transforming growth factor alpha (TGF-alpha), and IL-2. None of these was able to stimulate hematopoietic colony-forming cells in methylcellulose assays, although all have known actions on mesenchymal cells including, in some cases, the ability to increase production of growth factors that can stimulate primitive high-proliferative potential hematopoietic progenitors in clonogenic assays. Interestingly, a stimulating effect was not obtained after addition of endotoxin to LTMC. TGF-beta, a direct-acting negative regulator that acts selectively on primitive hematopoietic progenitor cells if added to LTMC simultaneously with new medium or IL-1, blocked their stimulating activity. These results suggest a model in which indirect, local modulation of both positive and negative regulatory factors via effects on mesenchymal elements determines the rate of turnover of adjacent populations of very primitive hematopoietic cells that are normally maintained in a quiescent state in vivo.
Cloning and Expression of an α-<scp>L</scp>-Arabinofuranosidase Gene (<i>stxIV</i>) from<i>Streptomyces thermoviolaceus</i>OPC-520, and Characterization of the Enzyme (2002)

The gene encoding alpha-L-arabinofuranosidase (STX-IV), located upstream of the previously reported stxI gene, was cloned and sequenced. The gene is divergently transcribed from the stxI gene, and the two genes are separated by 661 nucleotides. The stxIV gene consists of a 1,092-bp open reading frame encoding 363 amino acids. The deduced amino acid sequence of the gene showed that STX-IV was an enzyme consisting of only a catalytic domain, and that the enzyme had significant similarity with alpha-L-arabinofuranosidases belonging to family 62 of glycosyl hydrolases. The stxIV gene was expressed in Escherichia coli, and the recombinant protein was purified to homogeneity. Arabinoxylan and oat spelt xylan were good substrates for STX-IV, however, the enzyme showed a low activity with p-nitrophenyl alpha-L-arabinofuranoside. The optimum pH and temperature were 5.0 and 60 degrees C, respectively.
The Scavenger Receptor MARCO Modulates TLR-Induced Responses in Dendritic Cells (2014)

The scavenger receptor MARCO mediates macrophage recognition and clearance of pathogens and their polyanionic ligands. However, recent studies demonstrate MARCO expression and function in dendritic cells, suggesting MARCO might serve to bridge innate and adaptive immunity. To gain additional insight into the role of MARCO in dendritic cell activation and function, we profiled transcriptomes of mouse splenic dendritic cells obtained from MARCO deficient mice and their wild type counterparts under resting and activating conditions. In silico analysis uncovered major alterations in gene expression in MARCO deficient dendritic cells resulting in dramatic alterations in key dendritic cell-specific pathways and functions. Specifically, changes in CD209, FCGR4 and Complement factors can have major consequences on DC-mediated innate responses. Notably, these perturbations were magnified following activation with the TLR-4 agonist lipopolysaccharide. To validate our in silico data, we challenged DC's with various agonists that recognize all mouse TLRs and assessed expression of a set of immune and inflammatory marker genes. This approach identified a differential contribution of MARCO to TLR activation and validated a major role for MARCO in mounting an inflammatory response. Together, our data demonstrate that MARCO differentially affects TLR-induced DC activation and suggest targeting of MARCO could lead to different outcomes that depend on the inflammatory context encountered by DC.
Perinatal Outcome and Later Implications of Intrauterine Growth Restriction (2006)

This chapter reviews outcomes for children who have intrauterine growth retardation (IUGR) or small-for-gestation-age (SGA) status at birth. Such infants are at risk for increased perinatal mortality, birth adaptation complications, including perinatal acidosis, hypoglycemia, hypothermia, coagulation abnormalities, and selected immunologic deficiencies. IUGR infants also appear to be at great risk for complications of prematurity, including chronic lung disease and necrotizing enterocolitis. Childhood implications for IUGR include an increased risk for short stature, cognitive delays with decreased academic achievement, and a small but significant increased risk of neurologic disorders, including cerebral palsy. Low socioeconomic status is correlated with the occurrence of IUGR and is significantly related to long-term disabilities. Morbidities associated with preterm delivery appear to be additive to those associated with fetal growth restriction so IUGR, preterm infants may be at great risk for poor neurodevelopmental outcome.
Three-dimensional stacked-Fin-CMOS integrated circuit using double layer SOI material (2004)

In this work, a stacked 3D Fin-CMOS (SF-CMOS) technology is developed to double the device packing density of conventional FinFET. The key features of this architecture include: (1) high scalability inherent from the FinFET structure; (2) high density with more than 50% area reduction compared to the conventional 2D architecture; (3) reduced interconnect wiring distance between the n-channel and the p-channel devices; and (4) compatibility with conventional 2D CMOS technology. To implement the 3D SF-CMOS, we utilized a double layer SOI wafer with two single crystalline silicon layers isolated by an oxide layer. 3D SF-CMOS inverters were demonstrated with the n-channel FinFET stacking on the top of the p-channel FinFET.
Sensor for oxygen activity measurements in glass melts (1991)

Traditional oxygen activity measurement in glass melts is based on Y<sub>2</sub>O<sub>3</sub>-stabilized ZrO<sub>2</sub> which, in continuous use in the glassworks, is subjected to considerable wear. The present paper describes an oxygen sensor that is not equipped with wear parts. The new sensor is far less sensitive to temperature gradients in the surrounding area than ZrO<sub>2</sub> sensors; the oxygen measurement, however, is greatly disturbed at direct flame irradiation.
Effect of dexamethasone on corneal endothelial function in Fuchs' dystrophy. (1988)

Thirteen patients with Fuchs' endothelial dystrophy were studied to measure the potential effects of topically applied dexamethasone on endothelial function. Endothelial permeability in the Fuchs' dystrophy patients was not different from that found in normal controls. One eye, chosen at random, was treated topically four times a day for 7 days with 0.1% dexamethasone phosphate. The contralateral eye was treated with a placebo of identical appearance. Prior to treatment, there were no statistically significant differences in the means of the intraocular pressure, corneal thickness, endothelial permeability, or endothelial pump rate between the dexamethasone- and placebo-treated groups. In the placebo-treated eyes, a significant decrease was observed in both endothelial permeability and endothelial pump rate over the course of the study. No statistically significant changes occurred in the dexamethasone-treated eyes over the same period. When the dexamethasone group was compared with the placebo group, there was a significant difference in the change in endothelial pump rate between the two groups, attributable in large part to the decrease in pump rate observed in the placebo group over the course of treatment. We interpret our data as lacking support for the concept that topical steroids are beneficial for the treatment of stromal edema in patients with Fuchs' dystrophy.