gebhart/patrepeval huggingface dataset:
Domains of Mnt Repressor: Roles in Tetramer Formation, Protein Stability, and Operator DNA Binding (1995)

The Mnt repressor of bacteriophage P22 is a member of the ribbon-helix-helix family of gene regulatory proteins. Proteolytic cleavage of Mnt with chymotrypsin reveals that it consists of two structural domains. Both domains are required for high-affinity operator binding. The N domain (residues 1-51) is dimeric and binds weakly but specifically to operator DNA. The C domain (residues 52-82) forms an independent alpha-helical, tetramerization domain and, by itself, has no DNA-binding activity. In intact Mnt, the N and C domains help to stabilize each other against denaturation but appear to be linked rather flexibly. Assays of the half-operator affinities of Mnt and the isolated N domain indicate that binding to adjacent half-sites in the whole operator is stabilized by protein-protein contacts between N domains in addition to protein-protein contacts between C domains.
Minimally Invasive Sacral Neuromodulation Implant Technique (2003)

The minimally invasive sacral neuromodulation implant technique seems to be a safe procedure-making sacral neuromodulation implant easier, faster, and safer, in as much as complications could be potentially reduced.
Pharmacologic approaches to the treatment of Huntington's disease (2011)

Huntington's disease (HD) is an inherited, progressive neurodegenerative disorder characterized by chorea, cognitive impairment, and behavioral disturbances. Despite advances in diagnosis and improved understanding of HD, treatment remains difficult due to challenging symptoms and a paucity of approved therapeutic interventions. Nonpharmacologic and pharmacologic strategies have been evaluated; regarding the latter, over 80 agents of various classes have been investigated in clinical trials or examined in case reports. Symptomatic treatment, however, is generally confined to antidopaminergic agents for motor dysfunction and antidepressants for mood disorders, while treatment for cognitive dysfunction remains vacant. Several different mechanisms to modify symptoms and disease progression have been targeted in clinical trials. This article reviews some of the more common pharmacologic treatments used for HD, discusses data regarding suboptimal agents that have been tested, and surveys treatments under investigation.
A cautionary note on image downgrading (2003)

The results of an experiment that shows that it is very simple to contaminate digital images with information that can later be extracted are presented. This contamination cannot be detected when the image is displayed on a good quality graphics workstation. Based on these results, it is recommended that image downgrading based on visual display of the image to be downgraded not be performed if there is any threat of image contamination by Trojan horse programs. Potential Trojan horse programs may include untrusted image processing software.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Novel vaccine approaches (1996)

Recent advances in immunology, molecular biology, and peptide biochemistry have allowed the construction of subunit vaccines based on viral or bacterial recombinants, peptides or plasmid vectors. Although none of these approaches is currently being used for mass vaccination (with the exception or vaccinia-rabies G protein recombinant virus for wildlife immunization); several of them are undergoing clinical trials. None of these different vaccine constructs is likely to be totally effective in either the prevention of infectious diseases or immunotherapy of cancer. Recombinant viral vaccines such as those based on vaccinia or adenovirus as a rule induce potent immune responses. Vaccinia viruses have the added advantage of being heat stable and immunogenic after oral application, making them good candidates for wildlife immunization. Recombinants based on replication-defective adenoviruses are safer compared with vaccinia virus recombinants and, as far as our data indicate, have superior efficacy. In addition, they induce excellent immunity upon application to mucosal membranes, suggesting their usefulness as vaccines for infectious agents that enter through the airways or the genital tract. Peptides are of limited benefit in infectious disease prevention but might provide custom-made vaccines for cancer therapy. Genetic vaccines that were first described less than 5 years ago have already progressed to phase I clinical trials in healthy human adults. Provided that their safety can be confirmed, they might be suited to induce immunity to numerous agents.
美国教育界对我国1978年全国高校入学考试(数理化)的评价 (1980)

1979年美国健康、教育与福利部的教育局为了配合中美文化交流,了解我国派出留学生的水平,特请了某些美国大学的学者、教授对我国1978年全国高等学校入学考试复习大纲和试题进行了比较评价。介绍了1978年考试的重要意义、组织准备与方法,并将各科复习大纲与试题全部译成英文。本文选译了部分材料,通过这些材料可以了解外国教育界对我国当前中学各科教育水平的看法和估价。对于我们进一步改革教育会有所裨益。
Atomic Scale Mechanism of the Transformation ofγ-Alumina toθ-Alumina (2002)

gamma-alumina is known to transform to theta-alumina and finally to alpha-alumina upon thermal treatment with a catastrophic loss of porosity and catalytic activity. First-principles calculations were performed to investigate the atomic scale mechanism of the gamma- to theta-alumina transformation. The transformation pathways between the two different forms have been mapped out and identified as a sequence of Al cation migrations. Different possible Al migration paths may be responsible for the experimentally observed formation of domains and twins in theta-alumina. The estimated temperature dependence of the conversion rate is in excellent agreement with the experimental transformation temperature.
Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia (2012)

We conducted a genome-wide DNA methylation analysis in CD19 (+) B-cells from chronic lymphocytic leukemia (CLL) patients and normal control samples using reduced representation bisulfite sequencing (RRBS). The methylation status of 1.8-2.3 million CpGs in the CLL genome was determined; about 45% of these CpGs were located in more than 23,000 CpG islands (CGIs). While global CpG methylation was similar between CLL and normal B-cells, 1764 gene promoters were identified as being differentially methylated in at least one CLL sample when compared with normal B-cell samples. Nineteen percent of the differentially methylated genes were involved in transcriptional regulation. Aberrant hypermethylation was found in all HOX gene clusters and a significant number of WNT signaling pathway genes. Hypomethylation occurred more frequently in the gene body including introns, exons, and 3'-UTRs in CLL. The NFATc1 P2 promoter and first intron was found to be hypomethylated and correlated with upregulation of both NFATc1 RNA and protein expression levels in CLL suggesting that an epigenetic mechanism is involved in the constitutive activation of NFAT activity in CLL cells. This comprehensive DNA methylation analysis will further our understanding of the epigenetic contribution to cellular dysfunction in CLL.
Purification and characterization of NADP-specific alcohol dehydrogenase and glutamate dehydrogenase from the hyperthermophilic archaeon Thermococcus litoralis (1994)

Thermococcus litoralis is a strictly anaerobic archaeon that grows at temperatures up to 98 degrees C by fermenting peptides. Little is known about the primary metabolic pathways of this organism and, in particular, the role of enzymes that are dependent on thermolabile nicotinamide nucleotides. In this paper we show that the cytoplasmic fraction of cell extracts contained NADP-specific glutamate dehydrogenase (GDH) and NADP-specific alcohol dehydrogenase (ADH) activities, neither of which utilized NAD as a cofactor. The GDH is composed of identical subunits having an M(r) of 45,000 and had an optimal pH and optimal temperature for glutamate oxidation of 8.0 and > 95 degrees C, respectively. Potassium phosphate (60 mM), KCl (300 mM), and NaCl (300 mM) each stimulated the rate of glutamate oxidation activity between two- and threefold. For glutamate oxidation the apparent Km values at 80 degrees C for glutamate and NADP were 0.22 and 0.029 mM, respectively, and for 2-ketoglutarate reduction the apparent Km values for 2-ketoglutarate, NADPH, and NH4+ were 0.16, 0.14, and 0.63 mM, respectively. This enzyme is the first NADP-specific GDH purified form a hyperthermophilic organism. T. litoralis ADH is a tetrameric protein composed of identical subunits having an M(r) of 48,000; the optimal pH and optimal temperature for ethanol oxidation were 8.8 and 80 degrees C, respectively. In contrast to GDH activity, potassium phosphate (60 mM), KCl (0.1 M), and NaCl (0.3 M) inhibited ADH activity, whereas (NH4)2SO4 (0.1 M) had a slight stimulating effect. This enzyme exhibited broad substrate specificity for primary alcohols, but secondary alcohols were not oxidized.(ABSTRACT TRUNCATED AT 250 WORDS)
Interleukin-15 Augments Superoxide Production and Microbicidal Activity of Human Monocytes againstCandida albicans (1998)

Interleukin-15 (IL-15) is a newly described cytokine that shares biological activities with IL-2. We report here results demonstrating the ability of IL-15 to enhance superoxide production and antifungal activity of human monocytes. After 18 and 48 h of treatment with IL-15, human elutriated monocytes manifested enhanced superoxide production in response to either phorbol myristate acetate or opsonized Candida albicans blastoconidia. Similar results were obtained when monocytes were treated with IL-2, but to a lesser extent. Combination studies with IL-15 and IL-2 showed no additive or synergistic effects. Following incubation of monocytes with IL-15 for 18 h, there was no significant increase in mRNA transcripts for components of the NADPH oxidase complex, p40-phox, p47-phox, and gp91-phox, suggesting a posttranscriptional modulation of enhanced superoxide production. Antibodies against the gamma chain of the IL-2 receptor and, to a lesser extent, against the beta chain partially abrogated the IL-15-mediated enhanced superoxide production. Additionally, human monocytes showed enhanced killing activity against C. albicans after 18 h of incubation with IL-15 or IL-2, but this treatment did not enhance the ability of these cells to phagocytose the organism. In addition, the enhanced fungicidal activity seen after 18 h of treatment was no longer detectable after 48 h of cytokine treatment. Culture supernatants from the IL-15-treated monocytes were assayed for the presence of other proinflammatory cytokines. IL-15 treatment did not induce the release of detectable levels of tumor necrosis factor alpha, IL-1beta, or IL-12. Our results indicate that IL-15 upregulates the microbicidal activity of human monocytes against C. albicans.
Theoretical comparison of testing methods (1989)

Comparison of software testing methods is meaningful only if sound theory relates the properties compared to actual software quality. Existing comparisons typically use anecdotal foundations with no necessary relationship to quality, comparing methods on the basis of technical terms the methods themselves define. In the most seriously flawed work, one method whose efficacy is unknown is used as a standard for judging other methods! Random testing, as a method that can be related to quality (in both the conventional sense of statistical reliability, and the more stringent sense of software assurance), offers the opportunity for valid comparison.
Propionibacterium acnes Bacteriophages Display Limited Genetic Diversity and Broad Killing Activity against Bacterial Skin Isolates (2012)

Propionibacterium acnes is a dominant member of the skin microflora and has also been implicated in the pathogenesis of acne; however, little is known about the bacteriophages that coexist with and infect this bacterium. Here we present the novel genome sequences of 11 P. acnes phages, thereby substantially increasing the amount of available genomic information about this phage population. Surprisingly, we find that, unlike other well-studied bacteriophages, P. acnes phages are highly homogeneous and show a striking lack of genetic diversity, which is perhaps related to their unique and restricted habitat. They also share a broad ability to kill clinical isolates of P. acnes; phage resistance is not prevalent, but when detected, it appears to be conferred by chromosomally encoded immunity elements within the host genome. We believe that these phages display numerous features that would make them ideal candidates for the development of a phage-based therapy for acne.
Qualitative assessment of a Context of Consumption Framework to inform regulation of cigarette pack design in the U.S. (2018)

Use of the Context of Consumption Framework for cigarette product packaging design can inform regulatory research on tobacco product packaging. Researchers and regulators should consider multiple cognitive, affective, and behavioral responses to cigarette pack design.
Hairpin-Forming Peptide Nucleic Acid Oligomers (1998)

A series of partially self-complementary peptide nucleic acid (PNA) oligomers was prepared. Examination of their melting behavior, circular dichroism spectra, and fluorescence properties reveals that these PNA oligomers exist as stem-loop ("hairpin") structures. Fluorescence is readily observed in hairpins containing a covalently linked, emissive acridine derivative which is, at least partially, intercalated in the duplex region of the PNA hairpin. The acridine fluorescence is quenched when an anthraquinone derivative is covalently attached to the PNA so that it is bound near the acridine in the hairpin structure. Acridine fluorescence is restored in hairpins containing both the anthraquinone and the acridine by increasing the temperature and melting the structure to its linear form or by opening the hairpin through formation of a hybrid duplex with complementary DNA. The latter process may form the basis for development of selective and sensitive DNA assays.
Application of the differential hybridization of Atlas™ human expression arrays technique in the identification of differentially expressed genes in human glioblastoma multiforme tumor tissue (1998)

We conclude that the differential hybridization technique of Atlas Human cDNA expression array can be a useful method in identifying genes that are differentially expressed either in NBT or GMTT.
Matrix Cells from Wharton's Jelly Form Neurons and Glia (2003)

We have identified an easily attainable source of primitive, potentially multipotent stem cells from Wharton's jelly, the matrix of umbilical cord. Wharton's jelly cells have been propagated in culture for more than 80 population doublings. Several markers for stem cells, including c-kit (CD117), and telomerase activity are expressed in these cells. Treatment with basic fibroblast growth factor overnight and low-serum media plus butylated hydroxyanisole and dimethylsulfoxide induced Wharton's jelly cells to express a neural phenotype. Within several hours of this treatment, Wharton's jelly cells developed rounded cell bodies with multiple neurite-like extensions, similar to the morphology of neural stem cells. Neuron-specific enolase (NSE), a neural stem cell marker, was expressed in these cells, as shown by immunocytochemistry. Immunoblot analysis showed similar levels of NSE expression in both untreated and induced Wharton's jelly cells. After 3 days, the induced Wharton's jelly cells resembled bipolar or multipolar neurons, with processes that formed networks reminiscent of primary cultures of neurons. The neuron-like cells in these cultures stained positively for several neuronal proteins, including neuron-specific class III beta-tubulin, neurofilament M, an axonal growth-cone-associated protein, and tyrosine hydroxylase. Immunoblot analysis showed increasing levels of protein markers for mature neurons over time post induction. Markers for oligodendrocytes and astrocytes were also detected in Wharton's jelly cells. These exciting findings show that cells from the matrix of umbilical cord have properties of stem cells and may, thus, be a rich source of primitive cells. This study shows their capacity to differentiate into a neural phenotype in vitro.
Aptamer-modified nanoparticles and their use in cancer diagnostics and treatment (2013)

Aptamers are single-stranded deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) oligonucleotides, which are able to bind their target with high selectivity and affinity. Owing to their multiple talents, aptamers combined with nanoparticles are nanosystems well qualified for the development of new biomedical devices for analytical, imaging, drug delivery and many other medical applications. Because of their target affinity, aptamers can direct the transport of aptamer-nanoparticle conjugates. The binding of the aptamers to the target "anchors" the nanoparticle-aptamer conjugates at their site of action. In this way, nanoparticle-based bioimaging and smart drug delivery are enabled, especially by use of systematically developed aptamers for cancer-associated biomarkers. This review article gives a brief overview of recent relevant research into aptamers and trends in their use in cancer diagnostics and therapy. A concise description of aptamers, their development and functionalities relating to nanoparticle modification is given. The main part of the article is dedicated to current developments of aptamer-modified nanoparticles and their use in cancer diagnostics and treatment.
An electron microscope autoradiographic study of the carbohydrate recognition systems in rat liver. I. Distribution of 125I-ligands among the liver cell types. (1979)

Electron microscope autoradiography was used to study the cellular localization of seven glycoproteins rapidly cleared from the circulating plasma of rats and taken up by the liver. 1 and 15 min after intravenous administration of the 125I-glycoproteins, livers were fixed in situ by perfusion and processed for autoradiography. Autoradiographic grains in the developed sections were found to represent the intact 125I-ligand. A quantitative analysis of the distribution and concentration (density) of autoradiographic grains over the three major cell types of the liver was then performed. Three molecules, asialo-fetuin, asialo-orosomucoid, and lactosaminated RNase A dimer, the oligosaccharide chains of which terminate in galactose residues, were bound and internalized almost exclusively (greater than 90%) by hepatocytes. Conversely, four molecules, the oligosaccharide chains of which terminate in either N-acetyl-glucosamine (agalacto-orosomucoid) or mannose (ahexosamino-orosomucoid, preputial beta-glucuronidase, and mannobiosaminated RNase A dimer), were specifically bound and internalized by cells lining the blood sinusoids--that is, by Kupffer cells and endothelial cells. Endothelial cells were two to six times more active (on a cell volume basis) than were Kupffer cells in the internalization of these four 125I-ligands. Mannose and N-acetylglucosamine-terminated glycoproteins competed with each other for uptake into either endothelial cells or Kupffer cells, indicating that a single system recognized mannose or N-acetyl-glucosamine residues. Finally, agalacto-orosomucoid and ahexosamino-orosomucoid were also associated with hepatocytes, but competition experiments utilizing excess asialo-orosomucoid demonstrated that residual galactosyl residues were responsible for this association.
Using Liquid Crystals To Image Reactants and Products of Acid−Base Reactions on Surfaces with Micrometer Resolution (1999)

We report that nematic liquid crystals (LCs) of 4-cyano-4‘-pentylbiphenyl (5CB) and p-methoxybenzylidene-p-n-butylaniline (MBBA) can be used to image reactants and products of reversible, acid−base reactions on surfaces with micrometer resolution. When supported on obliquely deposited films of gold, azimuthal orientations of LCs measured on self-assembled monolayers (SAMs) formed from HOOC(CH2)10SH are found to be orthogonal to those measured on SAMs of the corresponding sodium carboxylate salt. Conversion of the carboxylic acid to its sodium salt is amplified into a change in orientation of 104−105 mesogens per surface-confined acid group. The change in orientation of the LC is easily transduced into an optical output by forming twist distortions within the LC upon conversion of the carboxylic acid to its sodium carboxylate salt. The threshold conversion of acid to salt that drives the formation of the twist distortion within the supported LC can be systematically shifted between 8% and 100% by using mixed SAMs formed from HOOC(CH2)10SH and H3C(CH2)11SH, and by pretreating these SAMs in aqueous solutions buffered between pH 1.7 and 14. We also demonstrate that region-specific conversion of the carboxylic acid to its sodium carboxylate salt can be readily imaged on micrometer scales by using LCs. Observations of the boundary region between acid and salt show no evidence of lateral transport of products and reactants over distances of micrometers over periods of days. We conclude that images of the reactants and products of this surface-confined chemical transformation can be conveniently recorded in the orientations of supported LCs.
Asymmetric Catalysis at Chiral Metal Surfaces (2007)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAsymmetric Catalysis at Chiral Metal SurfacesT. Mallat, E. Orglmeister, and A. BaikerView Author Information Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, CH-8093 Zurich, Switzerland Cite this: Chem. Rev. 2007, 107, 11, 4863–4890Publication Date (Web):October 10, 2007Publication History Received2 March 2007Published online10 October 2007Published inissue 1 November 2007https://pubs.acs.org/doi/10.1021/cr0683663https://doi.org/10.1021/cr0683663research-articleACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views8000Altmetric-Citations529LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Adsorption,Catalysts,Hydrogenation,Metals,Platinum Get e-Alerts
Independent filtering increases detection power for high-throughput experiments (2010)

With high-dimensional data, variable-by-variable statistical testing is often used to select variables whose behavior differs across conditions. Such an approach requires adjustment for multiple testing, which can result in low statistical power. A two-stage approach that first filters variables by a criterion independent of the test statistic, and then only tests variables which pass the filter, can provide higher power. We show that use of some filter/test statistics pairs presented in the literature may, however, lead to loss of type I error control. We describe other pairs which avoid this problem. In an application to microarray data, we found that gene-by-gene filtering by overall variance followed by a t-test increased the number of discoveries by 50%. We also show that this particular statistic pair induces a lower bound on fold-change among the set of discoveries. Independent filtering-using filter/test pairs that are independent under the null hypothesis but correlated under the alternative-is a general approach that can substantially increase the efficiency of experiments.