gebhart/patrepeval huggingface dataset:
Screening for imprinted genes by allelic message display: Identification of a paternally expressed gene Impact on mouse chromosome 18 (1997)

A systematic screen termed the allelic message display (AMD) was developed for the hunting of imprinted genes. In AMD, differential display PCR is adopted to image allelic expression status of multiple polymorphic transcripts in two parental mouse strains, reciprocal F1 hybrids and pooled backcross progenies. From the displayed patterns, paternally and maternally expressed transcripts can be unequivocally identified. The effectiveness of AMD screening was clearly demonstrated by the identification of a paternally expressed gene Impact on mouse chromosome 18, the predicted product of which belongs to the YCR59c/yigZ hypothetical protein family composed of yeast and bacterial proteins with currently unknown function. In contrast with previous screening methods necessitating positional cloning efforts or generation of parthenogenetic embryos, this approach requires nothing particular but appropriately crossed mice and can be readily applied to any tissues at various developmental stages. Hence, AMD would considerably accelerate the identification of imprinted genes playing pivotal roles in mammalian development and the pathogenesis of various diseases.
Modeling annotated data (2003)

We consider the problem of modeling annotated data---data with multiple types where the instance of one type (such as a caption) serves as a description of the other type (such as an image). We describe three hierarchical probabilistic mixture models which aim to describe such data, culminating in correspondence latent Dirichlet allocation, a latent variable model that is effective at modeling the joint distribution of both types and the conditional distribution of the annotation given the primary type. We conduct experiments on the Corel database of images and captions, assessing performance in terms of held-out likelihood, automatic annotation, and text-based image retrieval.
18-Crown-6 as a catalyst in the dialkylation of o-nitrophenacyl derivatives (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticle18-Crown-6 as a catalyst in the dialkylation of o-nitrophenacyl derivativesGirija Prasad, Patrick E. Hanna, Wayland E. Noland, and Shankar VenkatramanCite this: J. Org. Chem. 1991, 56, 25, 7188–7190Publication Date (Print):December 1, 1991Publication History Published online1 May 2002Published inissue 1 December 1991https://pubs.acs.org/doi/10.1021/jo00025a047https://doi.org/10.1021/jo00025a047research-articleACS PublicationsRequest reuse permissionsArticle Views547Altmetric-Citations12LEARN 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 Get e-Alerts
Bottom-up and top-down approaches to dynamics of hyper-redundant mechanical systems (2003)

We explain bottom-up and top-down approaches to dynamics of hyper-redundant mechanical systems. In the bottom-up approach we consider snake robots as a typical example of the hyper-redundant mechanical systems for extracting the fundamental property and developing the suitable model representation. We propose a control law for avoiding singularity of the snake robot using redundancy. In the top-down approaches we propose two system theoretic approaches to dynamics of hyper-redundant mechanical systems. The first one is focused on the partial periodicity property in the system. The second one is based on the distributed parameter model. We explain the interaction of both bottom-up and top-down approaches for constructing hyper-redundant mechanical systems.
A Hypothesis: Nonsteroidal Anti-Inflammatory Drugs Reduce the Incidence of Large-Bowel Cancer (1991)

Nonsteroidal anti-inflammatory drugs (NSAIDs) inhibit prostaglandin synthesis and tumor growth in the rodent colon. We assessed NSAID use in relation to risk of human large-bowel cancer in a hospital-based, case-control study of 1326 patients with colorectal cancer and 4891 control patients. For regular NSAID use that continued into the year before interview, the multivariate relative risk estimate was 0.5 (95% confidence interval, 0.4 to 0.8); the estimate decreased as the duration of use increased, but the trend was not statistically significant. Similar results were obtained whether cancer or non-cancer controls were used, and the inverse association was apparent for both colon cancer and rectal cancer in men and women and in subjects younger and older than 60 years. Regular NSAID use that had been discontinued at least 1 year previously and non-regular use were not associated with risk. Almost all regular NSAID use was of aspirin-containing drugs. The present data suggest that the sustained use of NSAIDs reduces the incidence of human large-bowel cancer.
Effects of Mg2+ and the beta gamma-subunit complex on the interactions of guanine nucleotides with G proteins. (1987)

Mg2+ interacts with the alpha subunits of guanine nucleotide-binding regulatory proteins (G proteins) in the presence of guanosine-5'-[gamma-thio]triphosphate (GTP-gamma S) to form a highly fluorescent complex from which nucleotide dissociates very slowly. The apparent Kd for interaction of G alpha X GTP gamma S with Mg2+ is approximately 5 nM, similar to the Km for G protein GTPase activity X G beta gamma increases the rate of dissociation of GTP gamma S from G alpha X GTP gamma S or G alpha X GTP gamma S X Mg2+ at low concentrations of Mg2+. When the concentration of Mg2+ exceeds 1 mM, G beta gamma dissociates from G beta gamma X G alpha X GTP gamma S X Mg2+. Compared with the dramatic effect of Mg2+ on binding of GTP gamma S to G alpha, the metal has relatively little effect on the binding of GDP. However, G beta gamma increases the affinity of G alpha for GDP by more than 100-fold. High concentrations of Mg2+ promote the dissociation of GDP from G beta gamma X G alpha X GDP, apparently without causing subunit dissociation. The steady-state rate of GTP hydrolysis is strictly correlated with the rate of dissociation of GDP from G alpha under all conditions examined. Thus, there are at least two sites for interaction of Mg2+ with G protein-nucleotide complexes. Furthermore, binding of G beta gamma and GTP gamma S to G alpha is negatively cooperative, while the binding interaction between G beta gamma and GDP is strongly positive.
Antitumor effects of (1-->3)-beta-D-glucan and (1-->6)-beta-D-glucan purified from newly cultivated mushroom, Hatakeshimeji (Lyophyllum decastes Sing.). (2000)

Eleven polysaccharides were isolated from a hot-water extract of fruiting bodies of Lyophyllum decastes Sing. by ion-exchange chromatography and gel permeation chromatography. Three polysaccharides (IV-1, IV-2, and IV-3) composed mainly of glucose showed marked antitumor activities against Sarcoma 180 and their average molecular weights were 305 kDa, 130 kDa and 14 kDa, respectively. From methylation analyses and 13C-NMR spectra, it was suggested that IV-1 was a (1-->3)-beta-D-glucan-type polysaccharide, IV-3 was a (1-->6)-beta-D-glucan-type polysaccharide, and IV-2 was a (1-->3, 1-->6)-beta-d-glucan-type polysaccharide or a mixture of both polysaccharides. Increases in the number of peritoneal macrophages and third component of complement (C3)-positive fluorescent cells in mice treated with IV-1 suggested that the inhibitory effect on tumor growth is due to immunological host-mediated mechanisms.
FREE EAR LOBE GRAFTS OF SKIN AND FAT (1946)

For more than 70 years Plastic and Reconstructive Surgery® has been the one consistently excellent reference for every specialist who uses plastic surgery techniques or works in conjunction with a plastic surgeon. The journal brings readers up-to-the-minute reports on the latest techniques and follow-up for maxillofacial reconstruction, burn repair, cosmetic reshaping, as well as news on medicolegal issues. The cosmetic section provides expanded coverage on new procedures and techniques.
A fuzzy K-nearest neighbor algorithm (1985)

Classification of objects is an important area of research and application in a variety of fields. In the presence of full knowledge of the underlying probabilities, Bayes decision theory gives optimal error rates. In those cases where this information is not present, many algorithms make use of distance or similarity among samples as a means of classification. The <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</i> -nearest neighbor decision rule has often been used in these pattern recognition problems. One of the difficulties that arises when utilizing this technique is that each of the labeled samples is given equal importance in deciding the class memberships of the pattern to be classified, regardless of their `typicalness'. The theory of fuzzy sets is introduced into the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</i> -nearest neighbor technique to develop a fuzzy version of the algorithm. Three methods of assigning fuzzy memberships to the labeled samples are proposed, and experimental results and comparisons to the crisp version are presented.
Periodic Square-Like Gold Nanoparticle Arrays Templated by Self-Assembled 2D DNA Nanogrids on a Surface (2006)

We report the use of a self-assembled two-dimensional (2D) DNA nanogrid as a template to organize 5-nm gold nanoparticles (Au NPs) into periodic square lattices. Each particle sits on only a single DNA tile. The center-to-center interparticle spacing between neighboring particles is controlled to be approximately 38 nm. These evenly distributed Au NP arrangements with accurate control of interparticle spacing may find applications in nanoelectronic and nanophotonic devices.
Hmgb3 Is Regulated by MicroRNA-206 during Muscle Regeneration (2012)

Our results elucidate a negative feedback circuit in which myomiR-206 represses Hmgb3 expression to modulate the regeneration of single muscle fibres after acute and chronic muscle damage. These findings suggest that myomiR-206 may be a potential therapeutic target in muscle diseases.
Botryococcus braunii : A Renewable Source of Hydrocarbons and Other Chemicals (2002)

Botryococcus braunii, a green colonial microalga, is an unusually rich renewable source of hydrocarbons and other chemicals. Hydrocarbons can constitute up to 75% of the dry mass of B. braunii. This review details the various facets of biotechnology of B. braunii, including its microbiology and physiology; production of hydrocarbons and other compounds by the alga; methods of culture; downstream recovery and processing of algal hydrocarbons; and cloning of the algal genes into other microorganisms. B. braunii converts simple inorganic compounds and sunlight to potential hydrocarbon fuels and feedstocks for the chemical industry. Microorganisms such as B. braunii can, in the long run, reduce our dependence on fossil fuels and because of this B. braunii continues to attract much attention.
Classical disordered ground states: Super-ideal gases and stealth and equi-luminous materials (2008)

Using a collective coordinate numerical optimization procedure, we construct ground-state configurations of interacting particle systems in various space dimensions so that the scattering of radiation exactly matches a prescribed pattern for a set of wave vectors. We show that the constructed ground states are, counterintuitively, disordered (i.e., possess no long-range order) in the infinite-volume limit. We focus on three classes of configurations with unique radiation scattering characteristics: (i) “stealth” materials, which are transparent to incident radiation at certain wavelengths; (ii) “super-ideal” gases, which scatter radiation identically to that of an ensemble of ideal gas configurations for a selected set of wave vectors; and (iii) “equi-luminous” materials, which scatter radiation equally intensely for a selected set of wave vectors. We find that ground-state configurations have an increased tendency to contain clusters of particles as one increases the prescribed luminosity. Limitations and consequences of this procedure are detailed.
Top-down fabricated silicon nanowire sensors for real-time chemical detection (2009)

Silicon nanowire (SiNW) sensors have been developed by using top-down fabrication that is CMOS (complementary metal-oxide-semiconductor) compatible for resistive chemical detection with fast response and high sensitivity. Top-down fabrication by electron beam lithography and reactive ion etching of a silicon on insulator (SOI) substrate enables compatibility with the CMOS fabrication process, accurate alignment with other electrical components, flexible design of the nanowire geometry and good control of the electrical characteristics. The SiNW sensors showed a large operation range for pH detection (pH = 4-10) with an average sensitivity of (Delta R/R)/pH = 2.6%/pH and a rise time of 8 s. A small pH level difference (Delta pH = 0.2) near neutral pH conditions (pH = 7) could be resolved with the SiNW sensors. The sensor response to the presence of alkali metal ions and the long term drifting effects were also investigated.
Biological activity of the potent uridine phosphorylase inhibitor 5-ethyl-2,2'-anhydrouridine. (1987)

5-Ethyl-2,2'-anhydrouridine (ANEUR) proved to be a potent inhibitor of uridine phosphorylase isolated from sarcoma 180 cells with an apparent Ki (Ki(app) value of 99 nM. Coadministration of ANEUR with 5-fluorouridine (FUR) resulted in increased toxicity of FUR. The LD50 value of FUR alone was 9 mg/kg (when administered for 5 consecutive days) while the LD50 was 3 mg/kg when FUR was administered together with ANEUR in vivo. There was no significant difference in mean tumor weight on day 10 between control animals and animals treated with FUR (5 mg/kg/day for 3 days) or ANEUR (280 mg/kg/day for 3 days). When FUR was coadministered with ANEUR, mean tumor weight was 91% less than that of the untreated controls, showing that ANEUR, the potent URPase inhibitor, increases the antitumor effect of FUR.
Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates (2006)

RNA-cleaving deoxyribozyme 8-17 has been increasingly used in nanotechnology and biosensing applications. Conventional methods to equip 8-17 with fluorescent signaling property usually involve covalent attachment of two dyes at nucleotide positions that are far away from the catalytic core, such that the bulky dye structures would not affect the deoxyribozyme activity. However, the maximum fluorescent enhancement associated with these 8-17 constructs is typically < or =10-fold, due to a high fluorescent background. To find an optimal balance between signal enhancement and signaling speed, we have conducted a comprehensive study on the effects of the nature of dyes (Alexa Fluor 488, 546 and 647; QSY 9 and 21) as well as their attaching positions along the substrate strand on the catalytic and signaling performance of 8-17. Our results have indicated that 8-17 is able to cleave almost every modified substrate, including those that have chromophores only 1 nt away from the cleavage site. Most importantly, almost all of these substrates are able to generate 15- to 85-fold signal enhancement within 10 min. We have also provided guidelines for selecting substrates that could offer the best signal enhancement, the fastest signaling speed, or the best balance between signal enhancement and signaling speed.
Blood Cannabinoids. II. Models for the Prediction of Time of Marijuana Exposure from Plasma Concentrations of Δ9-Tetrahydrocannabinol (THC) and 11-nor-9-carboxy-Δ9-tetrahydrocannabinol (THCCOOH) (1992)

Two mathematical models are described for the prediction of time of marijuana use from the analysis of a single plasma sample for cannabinoids. The models were derived from cannabinoid data obtained from a controlled clinical study of acute marijuana smoking. Model I was based on plasma delta 9-tetrahydrocannabinol (THC) concentrations and Model II was based on the ratio of 11-nor-9-carboxy-delta 9-tetrahydrocannabinol (THCCOOH) to THC in plasma. The two models were validated with cannabinoid data from nine published and unpublished clinical studies. The data included plasma samples obtained from infrequent and frequent marijuana smokers and after oral marijuana administration. Cannabinoid plasma concentrations had been determined by a variety of analytical methods. The accuracy of model prediction was evaluated by comparison of the predicted time of prior drug use to the actual time of exposure. Predictions of time of exposure were generally accurate but tended to overestimate time immediately after smoking and tended to underestimate later times. A second assessment of the validity of the models was made by determining if actual time of use was within the 95% confidence interval. Model I correctly predicted the time of exposure within the 95% confidence interval for 235 of 261 samples (90.0%), and Model II was correct in 232 of 260 samples (89.2%). These prediction models may be beneficial to forensic scientists in the interpretation of cannabinoid plasma levels.
A cytotoxic NK-cell line (NK-92) for ex vivo purging of leukemia from blood. (1996)

Myeloablative chemo-/radiotherapy supported by transplantation of autologous bone marrow or blood progenitor cells for acute leukemia, lymphoma, or myeloma continues to be associated with a high relapse rate because of the infusion of malignant stem cells and the lack of an in vivo graft-vs.-leukemia (GVL) effect. Although various methods of purging are established for marrow, purging procedures for blood progenitor cell preparations have not been widely used primarily because of the technical challenges to process a higher number of cells. As a broadly applicable method for immunological purging, we tested whether highly cytotoxic cells from a natural killer (NK) cell line characterized previously (NK-92) could be used for immunological purging of blood preparations. The NK-92 cell line, which was established from a patient with non-Hodgkin's lymphoma, can lyse in vitro a broad range of leukemia, lymphoma, and myeloma cell lines even at very low effector:target (E:T) ratios; this lysis is superior to cytotoxicity obtained from normal peripheral blood mononuclear cells (PBMCs) stimulated for 4 days with interleukin (IL)-2. In an attempt to quantitate the purging achievable with NK-92 cells, normal PBMCs were spiked with 10% K562 cells that had been transfected with the neo(r) marker gene (K562-neo(r). Various numbers of NK-92 cells were then added to the cell mixtures, which were incubated for 4 or 48 hours at 37 degrees C with or without IL-2 (500 U/mL). In order to prevent their proliferation, NK-92 cells were irradiated with 1000 cGy (cesium source). This radiation dose was determined to suppress proliferation of NK-92 cells, but at the same time maintain full cytotoxic activity. After co-culture, the cells were plated in methylcellulose containing 0.8 mg/mL G418. The number of surviving K562-neo(r) colonies was counted under the microscope 7 days later and the results were considered a quantitative readout for the purging efficacy of NK-92 cells. No neomycin-resistant K562 colonies could be detected up to a ratio of NK-92:K562-neo(r) cells of 5:1 (effective NK-92:PBMC ratio of 0.5:1). The presence or absence of IL-2 during the culture period did not affect the results. At this ratio of NK-92:PBMC, the growth of normal clonogenic hematopoietic progenitor cells was not compromised as determined by a standard methylcellulose assay. Considering that K562 is a rapidly proliferating cell line and that the input number of K562 cells (10%) tested here was high, the data suggest that the cytotoxic NK-92 clone (after irradiation to prevent proliferation) could be used effectively for immunological ex vivo purging without compromising hematopoietic cell function.
The bioinorganic chemistry of iron in oxygenases and supramolecular assemblies (2003)

The bioinorganic chemistry of iron is central to life processes. Organisms must recruit iron from their environment, control iron storage and trafficking within cells, assemble the complex, iron-containing redox cofactors of metalloproteins, and manage a myriad of biochemical transformations by those enzymes. The coordination chemistry and the variable oxidation states of iron provide the essential mechanistic machinery of this metabolism. Our current understanding of several aspects of the chemistry of iron in biology are discussed with an emphasis on the oxygen activation and transfer reactions mediated by heme and nonheme iron proteins and the interactions of amphiphilic iron siderophores with lipid membranes.
Evidence of Multiyear Factor IX Expression by AAV-Mediated Gene Transfer to Skeletal Muscle in an Individual with Severe Hemophilia B (2006)

In a phase I study, administration of an AAV2-FIX vector into the skeletal muscle of eight hemophilia B subjects proved safe and achieved local gene transfer and FIX expression for at least 10 months after vector injection, the last time point assessed by muscle biopsy. In hemophilia B dogs we have demonstrated FIX in both muscle biopsies and circulation >4 years following AAV2-FIX injection. Because circulating FIX levels remained less than 1% of normal in human subjects from the study, the duration of AAV2-mediated transgene expression in humans is unknown. We sought to determine if FIX gene transfer and expression persisted locally at injection sites. Muscle biopsies were obtained from one subject 3.7 years following treatment and revealed transgene FIX DNA and protein by quantitative PCR, DNA fluorescence in situ hybridization, and immunohistochemistry for FIX. These results demonstrate, for the first time, multiyear FIX expression by AAV2 vector in humans and suggest that improved muscle delivery provides effective treatment for protein deficiencies or muscle-specific diseases.
Op Art and Visual Perception (1978)

An attempt is made to list the visual phenomena exploited in op art. These include moiré fringes, afterimages, Hermann grid effects, Gestalt grouping principles, blurring and movement due to astigmatic fluctuations in accommodation, scintillation and streaming possibly due to eye movements, and visual persistence. The historical origins of these phenomena are also noted.