gebhart/patrepeval huggingface dataset:
Relation between diacylglycerol acyltransferase activity and oil concentration in soybean (1998)

Abstract Diacylglycerol acyltransferase (EC 2.3.1.20; DGAT) catalyzes synthesis of triacylglycerol from acyl‐CoA and diacylglycerol. Activity of this enzyme and developmental changes in oil accumulation were estimated at various stages of seed growth in soybean germplasm with phenotypic differences in oil content. Oil deposition in seed of these genotypes followed a sigmoid pattern that was modeled to predict incremental rates of oil accumulation during seed development. A strong positive correlation was found between the estimated peak rate of oil deposition (near the mid‐term of seed development) and oil concentration in mature seed. At saturating substrate levels, DGAT activity measured near the peak rate of oil deposition also was correlated positively with oil phenotype. In the latter stages of seed development, a positive correlation between estimates of enzyme activity at or below the apparent K m for diolein and comparable oil accumulation rates was attributed to reduced synthesis of substrates and/or potential change in affinity for substrate as suggested by an increase in apparent K m for diolein in older seed. These data indicated that DGAT activity may be a rate‐limiting step in triacylglycerol synthesis. However, it is difficult to accept the idea of a single rate‐limiting step at the end of a complex metabolic pathway. Because oil is a quantitatively inherited trait, several genes determine genotypic differences in oil content among soybeans. Hence, DGAT activity may be an indicator of coordinated genetic expression of gene‐products in the entire glycerolipid synthetic pathway for a given genotype. In any case, results of this investigation demonstrated that genotypic differences in DGAT activity contributed to expression of genetic variation in oil content among soybean gemplasm.
Potencial evocado auditivo de longa latência: diferenças na forma de contagem do estímulo raro (2016)

RESUMO Objetivo: identificar se existe diferença nos achados do Potencial Evocado Auditivo de Longa Latência em relação à latência e amplitude, em diferentes modos de contagem do estimulo raro, sendo contando mentalmente ou marcando no papel (sem memorizar). Métodos: esse estudo teve caráter prospectivo e transversal. A amostra foi composta por conveniência sendo constituída por 49 indivíduos, sendo 29 do gênero feminino e 20 do gênero masculino. Foram realizados os seguintes procedimentos: Inspeção Visual do Meato Acústico Externo, Audiometria Tonal Liminar, Medidas de Imitância Acústica e Potencial Evocado Auditivo de Longa Latência, o qual foi realizado duas vezes, uma após a outra, com os indivíduos atentando ao estímulo raro, começando sempre contando mentalmente e após marcando em um papel. Resultados: houve diferença estatisticamente significante entre as orelhas para as latências de P1, P2 e amplitude de N1 para o método de marcação no papel, da latência de N1 para o método de contagem mental dos estímulos raros, e da amplitude de P2 em ambos os métodos, porém com todos os valores dentro da faixa de normalidade. Além disso, a diferença estatisticamente significante também foi evidente na comparação entre os gêneros, sendo encontrados valores de latência maiores de P2 e N2 para o gênero masculino em ambos os métodos de contagem dos estímulos raros. A amplitude de P1, P2 e P3 foi menor no gênero masculino nas diferentes formas de contagem, sendo no P2 a diferença apenas no método contando mentalmente. Ao compararmos os métodos, houve diferença estatisticamente significante apenas para a latência de P2, a qual foi maior para o método marcando no papel. Conclusão: não houve diferença para as latências e amplitudes dos potenciais evocados auditivos de longa latência na comparação da contagem do estímulo raro (contando mentalmente e marcando no papel) para quase todos os potenciais, com exceção do potencial P2 em relação à latência e amplitude.
Trichinella antigens: a review. (2000)

This paper presents a review of the Trichinella antigens within the context of species variation. As with other parasites, Trichinella antigens can be classified according to their localisation as surface, excretory/secretory (ES) and somatic components. Surface antigens are mainly constituents of the outer cuticle although secretions from inner parts of the body wall as well as from the oesophagus can temporarily accumulate in the surface. ES antigens come mainly from the excretory granules of the stichosome, whereas somatic constitutive antigens come from the internal parts of the worms. ES products are considered very important from an immunological point of view as they are easily targeted by the immune system, whereas parasite death is required for exposure of somatic products. Some of the antigenic components have been characterised chemically. Phosphorylcholine is an important hapten that modulates the immune responses in Trichinella infections. Glycoproteins are the major components of surface and excretory/secretory products. A 43-kDa glycoprotein has been regarded as a good candidate for diagnosis and vaccination purposes. Recently some glycans have received special attention either as relevant epitopes or as parasite evasion strategies.
Approximating discrete probability distributions with dependence trees (1968)

A method is presented to approximate optimally an <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</tex> -dimensional discrete probability distribution by a product of second-order distributions, or the distribution of the first-order tree dependence. The problem is to find an optimum set of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n - 1</tex> first order dependence relationship among the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</tex> variables. It is shown that the procedure derived in this paper yields an approximation of a minimum difference in information. It is further shown that when this procedure is applied to empirical observations from an unknown distribution of tree dependence, the procedure is the maximum-likelihood estimate of the distribution.
Role of prostaglandin E <sub>2</sub> -dependent angiogenic switch in cyclooxygenase 2-induced breast cancer progression (2003)

Overexpression of human cyclooxygenase 2 (COX-2) in the mammary glands of transgenic mice induces tissue-specific tumorigenic transformation. However, the molecular mechanisms involved are not yet defined. Here we show that COX-2 expressed in the epithelial cell compartment regulates angiogenesis in the stromal tissues of the mammary gland. Microvessel density increased before visible tumor growth and exponentially during tumor progression. Inhibition of prostanoid synthesis with indomethacin strongly decreased microvessel density and inhibited tumor progression. Up-regulation of angiogenic regulatory genes in COX-2 transgenic mammary tissue was also potently inhibited by indomethacin treatment, suggesting that prostanoids released from COX-2-expressing mammary epithelial cells induce angiogenesis. G protein-coupled receptors for the major product, prostaglandin E(2) (PGE(2)) EP(1-4), are expressed during mammary gland development, and EP(1,2,4) receptors were up-regulated in tumor tissue. PGE(2) stimulated the expression angiogenic regulatory genes in mammary tumor cells isolated from COX-2 transgenic mice. Such cells are tumorigenic in nude mice; however, treatment with Celecoxib, a COX-2-specific inhibitor, reduced tumor growth and microvessel density. These results define COX-2-derived PGE(2) as a potent inducer of angiogenic switch during mammary cancer progression.
The regional vulnerability to hypoglycemia-induced neurotoxicity in organotypic hippocampal culture: protection by early tetrodotoxin or delayed MK-801 (1992)

Profound hypoglycemia selectively damages CA1 and the dentate gyrus of the hippocampus. We have examined the time course of hippocampal neuronal injury in organotypic cultures following in vitro "hypoglycemia," using the fluorescent vital dye propidium iodide to observe directly the regional distribution of early neuronal membrane injury in living cultures. The in vivo hippocampal pattern of hypoglycemic injury was reproduced by a 2 hr exposure to glucose-free media, which resulted in simultaneous, selective propidium staining of CA1 and the dentate gyrus starting by 4 hr after exposure. After 24 hr of recovery, CA3 remained spared. A similar pattern of propidium staining was produced by incubation of cultures for briefer periods in glucose-free medium containing 5 mM 2-deoxyglucose (2-DG) to inhibit glycolysis. This "hypoglycemic" pattern and time course of neuronal injury was mimicked by 300 microM aspartate but not by glutamate. The NMDA receptor antagonists MK-801 and CPP, but not the relatively selective non-NMDA receptor antagonist 6-cyano-7-dinitroquinoxaline-2,3-dione, prevented the development of propidium staining. MK-801 protected against injury even if added to the recovery media 30 min after the insult, while TTX (10 microM) protected only if added by the end of the exposure. The appearance of propidium staining after 4-6 hr of recovery was well correlated with histological observation of pyknotic neuronal nuclei in the injured regions. The characteristic hippocampal regional vulnerability of CA1 and the dentate gyrus to injury following profound hypoglycemia can be reproduced in organotypic hippocampal culture and appears to be mediated both by an early TTX-sensitive component and by a more prolonged period of toxic NMDA receptor activation, extending for at least 30 min into the recovery period.
Comparative Analysis of Monocyte Subsets in the Pig (2013)

Human and mouse monocyte can be divided into two different subpopulations based on surface marker expression: CD14/16 and Ly6C/CX3CR1, respectively. Monocyte subpopulations in the pig were identified based on reciprocal expression of CD14 and the scavenger receptor CD163. The two populations, CD14(hi)-CD163(low) and CD14(low)-CD163(hi), show approximately equal abundance in the steady-state. Culture of pig PBMCs in CSF1 indicates that the two populations are a maturation series controlled by this growth factor. Gene expression in pig monocyte subpopulations was profiled using the newly developed and annotated pig whole genome snowball microarray. Previous studies have suggested a functional equivalence between human and mouse subsets, but certain genes such as CD36, CLEC4E, or TREM-1 showed human-specific expression. The same genes were expressed selectively in pig monocyte subsets. However, the profiles suggest that the pig CD14(low)-CD163(high) cells are actually equivalent to intermediate human monocytes, and there is no CD14(-) CD16(+) "nonclassical" population. The results are discussed in terms of the relevance of the pig as a model for understanding human monocyte function.
Scoring Functions for Protein-Ligand Docking (2006)

Virtual screening by molecular docking has become established as a method for drug lead discovery and optimization. All docking algorithms make use of a scoring function in combination with a method of search. Two theoretical aspects of scoring function performance dominate operational performance. The first is the degree to which a scoring function has a global extremum within the ligand pose landscape at the proper location. The second is the degree to which the magnitude of the function at the extremum is accurate. Presuming adequate search strategies, a scoring function's location performance will dominate behavior with respect to docking accuracy: the degree to which a predicted pose of a ligand matches experimental observation. A scoring function's magnitude performance will dominate behavior with respect to screening utility: enrichment of true ligands over non-ligands. Magnitude estimation also controls pure scoring accuracy: the degree to which bona fide ligands of a particular protein may be correctly ranked. Approaches to the development of scoring functions have varied widely, with a number of functions yielding similarly high levels of performance relating to the location issue. However, even among functions performing equally well on location, widely varying performance is observed on the question of magnitude. In many cases, performance is good enough to yield high enrichments of true ligands versus non-ligands in screening across a wide variety of protein types. Generally, performance is not good enough to correctly rank among true ligands. Strategies for improvement are discussed.
A novel in vitro loading system for high frequency loading of cultured tendon fascicles (2012)

Tendons are known to adapt to their mechanical environment, however high frequency low magnitude (HFLM) loading regimes (10-50Hz), which are effective in promoting bone anabolic effects, have not been investigated in controlled conditions in tendon. In vitro loading systems (IVLS) enable precise characterisation of the link between their controlled mechanical environment and cultured tissue biological response. We report a novel IVLS design using an applied magnetic field to produce time varying loading in cultured rat tail tendon fascicles (RTTF). The design was validated through magnetic flux, load cell and viability measurements, and we report the results of preliminary experiments testing the hypothesis that an HFLM loading regime will maintain the biochemical and mechanical properties of fresh RTTF in culture over 7 days. Tissue viability was maintained for 7 days under all loading conditions, and the average peak load applied to RTTFs using the IVLS at 20Hz was 0.125N. RTTFs cultured for 7 days with HFLM loading showed a trend for a higher tangent modulus than fresh tissue, and significantly higher modulus than unloaded RTTFs. GAG content of HFLM cultured RTTFs was not significantly changed from that of fresh RTTFs. This novel, validated IVLS will provide new knowledge of tendon mechanobiology and has already shown the potential of clinically relevant HFLM loading for influencing tendon biology.
DNA Catalysis: The Chemical Repertoire of DNAzymes (2015)

Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as gene silencing agents, the scope of DNAzymes has rapidly expanded into diverse fields, including biosensing, diagnostics, logic gate operations, and the development of novel synthetic and biological tools. In this review, an overview of all the different chemical reactions catalyzed by DNAzymes is given with an emphasis on RNA cleavage and the use of non-nucleosidic substrates. The use of modified nucleoside triphosphates (dN*TPs) to expand the chemical space to be explored in selection experiments and ultimately to generate DNAzymes with an expanded chemical repertoire is also highlighted.
[Present situation in the study of antisperm antibodies]. (2004)

Immune factors account for 5%-15% of male infertility. Because of the diversity in molecular weight, structure and location, sperm antigens play different roles in immune infertility. Antisperm antibodies (AsAb) influence sperm function not only by direct action, but also by changing the local microenvironment indirectly. This paper reviews the progress in the studies of the implication of human sperm antigens, the function, mechanisms, categories and titer of AsAb in male infertility.
Extractive metallurgy of rare earths (1992)

AbstractA comprehensive review is presented of the extractive metallurgy of rare earths. The topics covered are: world rare earth resources and production; ore processing and separation of individual rare earths; reduction, refining, and ultrapurification of rare earth elements; methods for rare earth materials analysis; and a selection of the numerous rare earth applications. World rare earth reserves are abundant and would last for well beyond the next century. However, all of the 16 naturally occurring rare earth elements are not equally distributed in the ore minerals. This, compounded with the problems specific to the isolation and recovery of each of the rare earths, sets the stage for an unequal rare earth availability. The close chemical similarity of rare earths looses its importance when divergent physical properties determine the processes for rare earth element reduction and refining. The rare earth metals, alloys, and compounds have been as pure as could be determined. Finally, the commercial demand for a rare earth has often been out of phase with its chemical availability. The review addresses itself to these points while providing a summary of the substantial body of information presently available on the extractive metallurgy of rare earths.
Gold-Nanoparticle-Based Assay for Instantaneous Detection of Nuclear Hormone Receptor−Response Elements Interactions (2010)

Gold nanoparticles (AuNPs) are widely used as colorimetric probes for biosensing, relying on their unique particle size-dependent and/or interparticle distance-dependent extinction spectrum and solution color. Herein, we describe an AuNP-based colorimetric assay to detect binding interactions between nuclear hormone receptors and their corresponding DNA-binding elements, particularly the human estrogen receptors (ERalpha and ERbeta) and their cognate estrogen response elements (EREs). We found that the protein-DNA (ER-ERE) complexes can stabilize citrate anion-capped AuNPs against salt-induced aggregation to a larger extent than the protein (ER) or the DNA (ERE) alone, due to their unique molecular size and charge properties that provide a strong electrosteric protection. Moreover, our results show that the extent of stabilization is sequence-dependent and can distinguish a single base variation in the ERE associated with minor changes in protein-DNA binding affinity. With this assay, many important parameters of protein-DNA binding events (e.g., sequence selectivity, distinct DNA binding properties of protein subtypes, binding stoichiometry, and sequence-independent transient binding) can be determined instantly without using labels, tedious sample preparations, and sophisticated instrumentation. These benefits, in particular the high-throughput potential, could enable this assay to become the assay of choice to complement conventional techniques for large scale characterization of protein-DNA interactions, a key aspect in biological research.
The teaching of microelectromechanical systems (MEMS) (2003)

MEMS technology is now where integrated circuit technology was about 30 years ago. It is clearly going to be pervasively important. Both commercial volume and patents on MEMS are growing at rates exceeding 20% annually. The teaching of MEMS technology, now in its early stages, must keep pace. Most universities with an engineering program will have to teach MEMS technology starting within the next decade. This paper summarizes the state of the MEMS instruction regarding available texts and other materials, and especially current short courses and ordinary university courses. Two courses on the production and applications of MEMS, which are planned for the George Washington University (USA) in the coming academic year, are outlined. Possibilities for laboratory courses on MEMS are also presented.
The Revised CONSORT Statement for Reporting Randomized Trials: Explanation and Elaboration (2001)

Overwhelming evidence now indicates that the quality of reporting of randomized, controlled trials (RCTs) is less than optimal. Recent methodologic analyses indicate that inadequate reporting and design are associated with biased estimates of treatment effects. Such systematic error is seriously damaging to RCTs, which boast the elimination of systematic error as their primary hallmark. Systematic error in RCTs reflects poor science, and poor science threatens proper ethical standards. A group of scientists and editors developed the CONSORT (Con solidated S tandards o f R eporting T rials) statement to improve the quality of reporting of RCTs. The statement consists of a checklist and flow diagram that authors can use for reporting an RCT. Many leading medical journals and major international editorial groups have adopted the CONSORT statement. The CONSORT statement facilitates critical appraisal and interpretation of RCTs by providing guidance to authors about how to improve the reporting of their trials. This explanatory and elaboration document is intended to enhance the use, understanding, and dissemination of the CONSORT statement. The meaning and rationale for each checklist item are presented. For most items, at least one published example of good reporting and, where possible, references to relevant empirical studies are provided. Several examples of flow diagrams are included. The CONSORT statement, this explanatory and elaboration document, and the associated Web site ( http://www.consort-statement.org ) should be helpful resources to improve reporting of randomized trials. Throughout the text, terms marked with an asterisk are defined at end of text.
A bacterial hormone (the SCB1) directly controls the expression of a pathway‐specific regulatory gene in the cryptic type I polyketide biosynthetic gene cluster of <i>Streptomyces coelicolor</i> (2005)

Gamma-butyrolactone signalling molecules are produced by many Streptomyces species, and several have been shown to regulate antibiotic production. In Streptomyces coelicolor A3(2) at least one gamma-butyrolactone (SCB1) has been shown to stimulate antibiotic production, and genes encoding proteins that are involved in its synthesis (scbA) and binding (scbR) have been characterized. Expression of these genes is autoregulated by a complex mechanism involving the gamma-butyrolactone. In this study, additional genes influenced by ScbR were identified by DNA microarray analysis, and included a cryptic cluster of genes for a hypothetical type I polyketide. Further analysis of this gene cluster revealed that the pathway-specific regulatory gene, kasO, is a direct target for regulation by ScbR. Gel retardation and DNase I footprinting analyses identified two potential binding sites for ScbR, one at -3 to -35 nt and the other at -222 to -244 nt upstream of the kasO transcriptional start site. Addition of SCB1 eliminated the DNA binding activity of ScbR at both sites. The expression of kasO was growth phase regulated in the parent (maximal during transition phase), undetectable in a scbA null mutant, and constitutively expressed in a scbR null mutant. Addition of SCB1 to the scbA mutant restored the expression of kasO, indicating that ScbR represses kasO until transition phase, when presumably SCB1 accumulates in sufficient quantity to relieve kasO repression. Expression of the cryptic antibiotic gene cluster was undetectable in a kasO deletion mutant. This is the first report with comprehensive in vivo and in vitro data to show that a gamma-butyrolactone-binding protein directly regulates a secondary metabolite pathway-specific regulatory gene in Streptomyces.
Drastic Morphological Modification of Polyelectrolyte Microcapsules Induced by High Temperature (2004)

Polyelectrolyte multilayer microcapsules of two different sizes consisting of poly(allylamine hydrochloride) and poly(styrenesulfonate) assembled on melamine formaldehyde cores were investigated by means of scanning (SEM) and transmission electron microscopy (TEM), confocal laser scanning microscopy (CLSM), and scanning force microscopy (SFM) regarding their stability at temperatures above 100 °C. A pronounced shrinking of the capsules accompanied by a wall thickness increase by more than 10 times was observed after incubating the capsule suspensions in an autoclave at 120 °C for 20 min. An estimation of the capsule wall volume revealed a densification of the polyelectrolyte layers and an exclusion of intercalated water. The gain of entropy resulting from a more coiled and interdigitated state of the polyions as well as from the great decrease of the polyelectrolyte/water interface is considered to be the driving force of this rearrangement process.