gebhart/patrepeval huggingface dataset:
Immunohistochemical analysis of dystrophin-associated proteins in Becker/Duchenne muscular dystrophy with huge in-frame deletions in the NH2-terminal and rod domains of dystrophin. (1994)

The absence of dystrophin causes the drastic reduction of the dystrophin-associated proteins (DAPs) in the sarcolemma and the loss of the linkage between the subsarcolemmal cytoskeleton and the extracellular matrix in Duchenne muscular dystrophy (DMD) skeletal muscle. Here, we report a mild reduction of the DAPs in the unique Becker muscular dystrophy patients with huge deletions in the rod domain of dystrophin and a moderate reduction of the DAPs in patients with huge deletions that involve both the NH2-terminal and rod domains of dystrophin. The phenotype of the latter patients was more severe than that of the former. In both cases, however, the reduction in the DAPs was milder than in typical DMD patients or DMD patients lacking the COOH-terminal domains of dystrophin. Our results suggest that (a) the NH2-terminal and rod domains of dystrophin may not be essential for the interaction with the sarcolemmal glycoprotein complex; and (b) defects in the actin binding activity of dystrophin may cause disruption of the anchorage of the dystrophin-glycoprotein complex to the subsarcolemmal cytoskeleton, which may render muscle fibers susceptible to degeneration.
The Type-A Response Regulator, ARR15, Acts as a Negative Regulator in the Cytokinin-Mediated Signal Transduction in Arabidopsis thaliana (2003)

The Arabidopsis thaliana AHK4 histidine kinase (also known as CRE1 or WOL) acts as a cytokinin signal transducer, presumably, in concert with downstream components, such as histidine-containing phosphotransfer factors (AHPs) and response regulators (ARRs), through the histidine-to-aspartate (His-->Asp) phosphorelay. Among 10 members of the type-A ARR family, the cytokinin-induced expression of ARR15 in roots is selectively impaired in the cre1-1 mutant, which carries a mutation in the AHK4 gene, suggesting a link between this type-A response regulator and the AHK4-mediated cytokinin signal transduction in roots. To address this issue further, we characterized a T-DNA insertion mutant of ARR15, and also constructed transgenic lines (referred to as ARR15-ox) that overexpress the ARR15 gene in a manner independent of cytokinin. While the T-DNA insertion mutant (arr15-1) showed no apparent phenotype, the cytokinin-independent overexpression of ARR15 in ARR15-ox plants resulted in a reduced sensitivity toward exogenously applied cytokinin, not only in elongation of roots in plants, but also in green callus formation (or shoot formation) in explants. Cytokinin-induced expressions of certain type-A ARRs were also down-regulated in ARR15-ox plants. These results support the view that ARR15 acts as a repressor that mediates a negative feedback loop in the cytokinin and AHK4-mediated His-->Asp phosphorelay.
Distribution of Rat Organic Anion Transporting Polypeptide-E (oatp-E) in the Rat Eye (2003)

Results from the present study revealed that rat oatp-E is localized mainly to the corneal epithelium, ciliary body, iris, and retina. Furthermore, the findings appear to suggest that transport of T3 in the RPE may have a functional role for organic anion (i.e., thyroid hormone) transport in the rat eye.
Single event transient pulse widths in digital microcircuits (2004)

The radiation effects community has long known that single event transients in digital microcircuits will have an increasing importance on error rates as device sizes shrink. However separating these errors from static errors in latch cells has often proved difficult. Thus determining both the significance and the nature of these transient errors has not been easy. In this study, by utilizing a latch that is radiation hard at static clock frequencies the errors due to transients could be separated. By separating the transient error rate from the static upset error rate, the pulse structure of the propagating transients was studied using SPICE. The implications of these pulsewidths will also be discussed.
An Effective Method for Bulk Obtaining Graphene Oxide Solids (2010)

Abstract We report an effective method for bulk obtaining exfoliated graphene oxide (GO) solids from their aqueous solutions, which were prepared from nature graphite by an oxidation method. Tyndall effect proved that GO solution has a colloidal nature. Different flocculants were used to coagulate GO colloidal, and it was found that NaOH had the most obvious coagulation effect to GO. Transmission electron microscopy, X‐ray diffraction and atomic force microscopy analysis demonstrated that there were a large number of complete few‐layer GO sheets with thickness of about 0.8 nm, and the surfaces were very smooth, almost free of impurities. Liquid state 13 C NMR and Fourier transformation infrared spectra showed the presence of abundant benzene carboxylic, hydroxyl and epoxide groups in the basal planes of GO. The graphene materials reduced from GO solids had good electrical conductivity. Our work explored a simple and effective route to extract GO from their solution, which is the most important to GO and graphene researches and applications.
Lysine Demethylases Inhibitors (2011)

ADVERTISEMENT RETURN TO ISSUEPREVPerspectiveNEXTLysine Demethylases InhibitorsTakayoshi Suzuki*†‡ and Naoki Miyata*§View Author Information† Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 13 Taishogun Nishitakatsukasa-Cho, Kita-ku, Kyoto 403-8334, Japan‡ PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan§ Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, JapanFor T.S.: phone, +81-75-465-7659; e-mail, [email protected]. For N.M.: phone and fax, +81-52-836-3407; e-mail, [email protected]Cite this: J. Med. Chem. 2011, 54, 24, 8236–8250Publication Date (Web):September 28, 2011Publication History Received4 August 2011Published online7 October 2011Published inissue 22 December 2011https://pubs.acs.org/doi/10.1021/jm201048whttps://doi.org/10.1021/jm201048wreview-articleACS PublicationsCopyright © 2011 American Chemical SocietyRequest reuse permissionsArticle Views5356Altmetric-Citations133LEARN 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:Cancer,Cells,Inhibitors,Monomers,Peptides and proteins Get e-Alerts
Reversible Dispersion and Release of Carbon Nanotubes Using Foldable Oligomers (2010)

Foldamers are synthetic and designable oligomers that adopt a conformationally ordered state in selected solvents. We found that oligo(m-phenylene ethynylene)s, which are single-stranded foldamers, can be made to reversibly disperse and release single-walled carbon nanotubes (SWCNTs) simply by changing the solvent, consistent with a change from an unfolded state to a folded state. Using absorption spectroscopy, atomic force microscopy, Raman spectroscopy, and electrical measurements, we observed that the foldamer-dispersed SWCNTs are individually well-dispersed and have a strong interfacial interaction with the foldamers. In contrast, the released SWCNTs appeared to be free of foldamers. Under illumination, transistors based on the foldamer-dispersed SWCNTs demonstrated significant photoresponse, apparently due to photoinduced charge transfer between the foldamers and SWCNTs. The reported nanocomposites may open an alternative way of developing optoelectronic devices or sensors based on carbon nanotubes.
Hybrid actuator for robot manipulators: design, control and performance (2002)

A hybrid actuation method for robotic manipulators is proposed. The actuator employs a hybrid combination of DC servomotors and muscle-like bladder actuators. One DC motor-muscle actuator pair is arranged coantagonistically with an identical DC motor-muscle actuator pair to drive a manipulator joint. Through a suitable control applied to the hybrid actuator, independent control of joint torsional stiffness and joint position is made possible. When air pressure is varied in the muscle actuators, the muscle actuator stiffness and length change. In order to only affect the hybrid actuator stiffness with this pressure change. DC servomotors are used to compensate for muscle actuator length changes, hence joint position is unaffected. High-gain servomotor control ensures a response to disturbances due almost solely to the muscle actuator stiffness characteristics. Dynamic equations of motion are developed for a two-joint manipulator with a hybrid actuator used to drive the final link. A control is formulated for this system to achieve, in addition to independent joint torsional stiffness and joint position control, approximately decoupled and linearized dynamics. A numerical simulation of this two-degree-of-freedom system is presented to verify the performance of the closed-loop system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cell Signaling Microdomain with Na,K-ATPase and Inositol 1,4,5-Trisphosphate Receptor Generates Calcium Oscillations (2003)

Recent studies indicate novel roles for the ubiquitous ion pump, Na,K-ATPase, in addition to its function as a key regulator of intracellular sodium and potassium concentration. We have previously demonstrated that ouabain, the endogenous ligand of Na,K-ATPase, can trigger intracellular Ca2+ oscillations, a versatile intracellular signal controlling a diverse range of cellular processes. Here we report that Na,K-ATPase and inositol 1,4,5-trisphosphate (InsP3) receptor (InsP3R) form a cell signaling microdomain that, in the presence of ouabain, generates slow Ca2+ oscillations in renal cells. Using fluorescent resonance energy transfer (FRET) measurements, we detected a close spatial proximity between Na,K-ATPase and InsP3R. Ouabain significantly enhanced FRET between Na,K-ATPase and InsP3R. The FRET effect and ouabain-induced Ca2+ oscillations were not observed following disruption of the actin cytoskeleton. Partial truncation of the NH2 terminus of Na,K-ATPase catalytic alpha1-subunit abolished Ca2+ oscillations and downstream activation of NF-kappaB. Ouabain-induced Ca2+ oscillations occurred in cells expressing an InsP3 sponge and were hence independent of InsP3 generation. Thus, we present a novel principle for a cell signaling microdomain where an ion pump serves as a receptor.
Staphylococcus aureus (1984)

Toxin-Produced SyndromesStaphylococcal GastroenteritisAlthough gastroenteritis can be caused by massive overgrowth of viable organisms, most cases are caused by the ingestion of foods containing preformed toxin.62 The toxin itself is not produced by Staph. aureus within the gastrointestinal tract.The Toxic-Shock SyndromeThe toxic-shock syndrome is almost certainly the result of in vivo production of a toxin at the site of localized, often relatively asymptomatic or unnoticed infection with a strain of Staph. aureus capable of toxin production.63 Enterotoxin F has been one of the putative toxins in the syndrome64; the other has been pyrogenic exotoxin C,65 which . . .
A high susceptibility of Fanconi's anemia to chromosome breakage by DNA cross-linking agents. (1973)

Summary Peripheral blood lymphocytes of patients with Fanconi9s anemia (FA) were tested for their susceptibility to chromosome breakage by caffeine, chloramphenicol, actinomycin D, methylmethanesulfonate, nitrogen mustard, mitomycin C, decarbamoyl mitomycin C, N -methyl- N′ -nitro- N -nitrosoguanidine, 4-nitroquinoline 1-oxide, 8-methoxypsoralen, and 60 Co γ-ray and ultiviolet irradiations. A definitely abnormal response of the chromosomes of the FA cells was found when they were treated with nitrogen mustard and mitomycin C and after the irradiation with long-wavelength ultraviolet light in the presence of 8-methoxypsoralen. The specifically increased susceptibility to these compounds, which can introduce interstrand cross-links into DNA, is interpreted as an indication that the FA cells are defective in the repair mechanism to tolerate the cross-links produced in their DNA. The impairment of the capacity to tolerate the lesions produced in DNA may be implicated in the increased risk to develop malignant neoplasms in this hereditary disorder.
Levels of ACC and related compounds in exudate and extracts of canola seeds treated with ACC deaminase-containing plant growth-promoting bacteria (2001)

It was previously proposed that plant growth-promoting bacteria that possess 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase could utilize ACC that is present in the exudate of germinating canola seeds. The uptake and cleavage of ACC by these bacteria would lower the level of ACC, and thus ethylene within the plant, and reduce the extent of its inhibition on root elongation. To test part of the above mentioned model, ACC levels were monitored in canola seed tissues and exudate during germination. Lower amounts of ACC were present in the exudate and tissues of seeds treated with the plant growth-promoting bacterium Enterobacter cloacae CAL3, than in control seeds treated with MgSO4. The ACC-related compounds, alpha- and gamma-aminobutyric acids, both known to stimulate ethylene production, were also measured in the canola seed exudate and tissues. Approximately the same levels of alpha-aminobutyric acid were present in the exudates of the bacterium-treated seeds and the control seeds, but the amount of alpha-aminobutyric acid was lower in the tissues of the bacterium-treated seeds than in the control seeds. Smaller quantities of gamma-aminobutyric acid were seen in both the exudate and tissues of the E. cloacae CAL3-treated seeds than in the control seeds.
Effects of Phytoestrogens on Growth and DNA Integrity in Human Prostate Tumor Cell Lines: PC-3 and LNCaP (2000)

Prostate cancer is one of the most common male cancers in Western countries, yet the incidence of this fatal disease remains low in Asian populations. Environmental factors such as diet play an important role in hormone-dependent cancer etiology, and a high phytoestrogen intake may be one factor contributing to the low prostate cancer mortality in Eastern populations. In this study, we investigated the effects of the phytoestrogens genistein, daidzein, coumestrol, and equol on cell growth and DNA damage (strand breakage) in two human prostate tumor cell lines: androgen receptor-positive LNCaP and androgen receptor-negative PC-3. Each compound caused growth inhibition at physiologically relevant concentrations (<10 microM). Genistein induced DNA damage in both cell lines at <10 microM. Daidzein inhibited cell growth at 10-100 microM yet had no effect on DNA damage at up to 500 microM. Thus, despite their structural similarities, different phytoestrogens inhibit prostate tumor cell growth by independent mechanisms.
Identification of QTL Associated with White Mold Resistance in Common Bean (2005)

White mold, caused by the necrotrophic fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a serious disease of common bean ( Phaseolus vulgaris L.). The use of resistant cultivars is the preferred control strategy, but the approach has been difficult to implement because of quantitative nature of genetic resistance to white mold. The objectives of this study were to identify quantitative trait loci (QTL) associated with resistance to S. sclerotiorum , identify QTL associated with agronomic traits that contribute to white mold avoidance, and locate putative QTL on the integrated bean map. Bulked segregant analysis using multiple trait bulks that included disease severity index (DSI), yield, and days to flower was used to detect QTL associated with field resistance to white mold in a Middle American recombinant inbred line (RIL) population of common bean. QTL that accounted for 9.2 to 14.7% of the phenotypic variation for DSI were located on linkage groups B2, B5, B7, and B8 of the integrated bean map. In addition, QTL were detected for seed size and yield and agronomic traits associated with disease avoidance: days to maturity, days to flower, and lodging. Heritability estimates for DSI were moderate (0.41) and correlations with agronomic traits that included lodging (0.56**), architecture (0.35**), canopy height (−0.33**), and yield (−0.64**) support the importance of these traits in disease avoidance. Data from the current study provides breeders with critical information on which traits and genomic regions to target as part of an overall strategy to enhance resistance to white mold in common bean.
Solid Phase Immobilization of Optically Responsive Liposomes in Sol-Gel Materials for Chemical and Biological Sensing (1997)

Liposomes enhanced with surface recognition groups have previously been found to have high affinity for heavy metal ions and virus particles with unique fluorescent and colorimetric responses, respectively. These lipid aggregate systems have now been successfully immobilized in a silica matrix via the sol-gel method, affording sensor materials that are robust, are easily handled, and offer optical clarity. The mild processing conditions allow quantitative entrapment of preformed liposomes without modification of the aggregate structure. Lipid extraction studies of immobilized nonpolymerized liposomes showed no lipid leakage in aqueous solution over a period of 3 months. Heavy metal fluorescent sensor materials prepared with 5% N-[8-[1-octadecyl-2-(9-(1-pyrenyl)nonyl)-rac-glyceroyl]-3,6-dioxaoctyl]iminodiacetic acid/distearylphosphatidylcholine liposomes exhibited a 4−50-fold enhancement in sensitivity to various metal ions compared to that of the liposomes in free solution. Through ionic attraction the anionic silicate surface, at the experimental pH of 7.4, may act as a preconcentrator of divalent metal ions, boosting the gel's internal metal concentration. Entrapped sialic acid-coated polydiacetylene liposomes responded with colorimetric signaling to influenza virus X31, although slower than the free liposomes in solution. The successful transport of the virus (50−100 nm diameter) reveals a large pore diameter of the gel connecting the liposome to the bulk solution. The porous and durable silica matrix additionally provides a protective barrier to biological attack (bacterial, fungal) and allows facile recycling of the liposome heavy metal sensor.
Node status has prognostic significance in the multimodality therapy of diffuse, malignant mesothelioma. (1993)

Multimodality therapy including extrapleural pneumonectomy has acceptable morbidity and mortality for selected patients. Prolonged survival occurred in patients with epithelial histologic variant and negative mediastinal lymph nodes. These data provide a rationale for a revised staging system for malignant pleural mesothelioma; furthermore, they permit stratification of patients into groups likely to benefit from aggressive multimodality treatment.
How to Generate Repeatable Keys Using Physical Unclonable Functions: Correcting PUF Errors with Iteratively Broadening and Prioritized Search (2014)

I present an algorithm for repeatably generating keys using entropy from a physical unclonable function (PUF). PUFs are logically identical devices with challenge- response pairs unique to each device. PUF errors inhibit key repeatability. My algorithm corrects PUF errors, enabling repeatable cryptographic key generation. Repeatedly sampling the PUF and correcting errors with prioritized iteratively broadening and exhaustive search recreate seeds. Repeated sampling determines the most likely bit values and error probabilities. The search ends if a test indicates the seed is correct. The iteratively broadening search tests seeds with up to two errors. The exhaustive search tests seeds until the correct seed is found or failure is declared. PUF bit error rates prioritizes the searches. Previous algorithms often omit noisy PUF bits or use error correcting code and helper data. The presented algorithm uses all PUF bits regardless of noise. Non-volatile data for key regeneration is either a plaintext-ciphertext sample or, for public-key cryptography, the public key. I implemented a latch-based PUF on FPGAs and measured PUF characteristics to analyze the effectiveness of the algorithm. Tests show repeated sampling nearly eliminating the probability of errors. However, the FPGA-based PUFs did not exhibit ideal behavior. Extrapolation to error rates reported by other publications shows relatively few samples drives the error probability to near zero. The probability is not zero. The iterative broadening and exhaustive searches further reduce failure rates.
Common Variants in the Promoter of the Hepatic Lipase Gene Are Associated With Lower Levels of Hepatic Lipase Activity, Buoyant LDL, and Higher HDL2Cholesterol (1998)

Increased hepatic lipase (HL) activity is associated with small, dense, low density lipoprotein (LDL) and low high density lipoprotein2 (HDL2) cholesterol (-C) levels. A polymorphism in the promoter region of the HL gene (LIPC) is associated with HDL-C levels. To test whether this association is mediated by differences in HL activity between different LIPC promoter genotypes, the LIPC promoter polymorphism at position -250 (G-->A), HL activity, LDL buoyancy, and HDL-C levels were studied in white normolipidemic men and men with coronary artery disease (CAD). The less common A allele (frequency=0.21 and 0.25 in normal and CAD subjects, respectively) was associated with lower HL activity (P<0.005 by ANOVA) and buoyant LDL particles (P</=0.01) in both groups. Normal and CAD subjects heterozygous for the A allele had lower HL activity (by 24% and 29%, respectively) and significantly more buoyant LDL particles. Homozygosity for this allele (AA) was associated with an even lower HL activity in normal (-26%) and CAD (-46%) subjects. The A allele was associated with higher HDL2-C in CAD patients (P=0.007); heterozygotes and homozygotes for the A allele had a 92% and a 140% higher HDL2-C level (P<0.01) than did GG individuals. In a small number of normolipidemic subjects, the same trend in HDL2-C was seen. In a univariate analysis, the LIPC genotype accounted for 20% to 32% of the variance in HL levels among normal subjects and CAD patients, respectively. After adjustment for HL, the association between LIPC genotype and LDL buoyancy was no longer significant, suggesting that the effect of LIPC genotype on LDL buoyancy is mediated by its effects on HL activity. The LIPC A allele was more frequent in Japanese-Americans and African-Americans than in whites. In summary, these results suggest that variants in the LIPC promoter may significantly contribute to the variance in levels of HL activity and consequently, to the prevalence of the atherogenic small, dense, LDL particles and low HDL2-C levels.