gebhart/patrepeval huggingface dataset:
A Modular System for the Synthesis of Multiplexed Magnetic Resonance Probes (2011)

We have developed a modular architecture for preparing high-relaxivity multiplexed probes utilizing click chemistry. Our system incorporates azide bearing Gd(III) chelates and a trialkyne scaffold with a functional group for subsequent modification. In optimizing the relaxivity of this new complex, we undertook a study of the linker length between a chelate and the scaffold to determine its effect on relaxivity. The results show a strong dependence on flexibility between the individual chelates and the scaffold with decreasing linker length leading to significant increases in relaxivity. Nuclear magnetic resonance dispersion (NMRD) spectra were obtained to confirm a 10-fold increase in the rotational correlation time from 0.049 to 0.60 ns at 310 K. We have additionally obtained a crystal structure demonstrating that modification with an azide does not impact the coordination of the lanthanide. The resulting multinuclear center has a 500% increase in per Gd (or ionic) relaxivity at 1.41 T versus small molecule contrast agents and a 170% increase in relaxivity at 9.4 T.
A First Study on Self-Healing Solid-State Drives (2011)

This paper proposes a self-healing solid-state drive (SSD) design strategy that exploits heat-accelerated interface trap recovery of NAND flash memory cells to largely improve the SSD lifetime. The key is to make each NAND flash memory chip self-healable by stacking an extra heater die, and employ system-level redundancy to ensure SSD data storage integrity when one NAND flash memory chip is being self-heated for accelerating interface trap recovery. Based upon detailed thermal modeling and memory cell device modeling, we carried out simulations and analysis, and the results show that this proposed design strategy can potentially improve SSD lifetime by one order of magnitude at reasonable energy consumption overhead.
Pharmacokinetics of Vasopressin and Atrial Natriuretic Peptide in Anesthetized Rabbits* (1989)

The elimination from plasma of the peptide hormones vasopressin (VP) and atrial natriuretic peptide (ANP) as well as the time course of release and elimination of these hormones after a physiological stimulus were studied in anesthetized rabbits. As an inverse relationship was found to exist between carotid sinus pressure and plasma IR-ANP, a decrease in carotid sinus pressure to 60 mm Hg was used to stimulate ANP as well as VP release. The elimination of VP after iv injection involved a rapid initial phase and a slow late component, with corresponding half-life (t1/2) values of 0.9 and 5.4 min, respectively. After reduction of carotid sinus pressure to 60 mm Hg, plasma VP increased significantly within 1 min and reached a maximum at 10 min. When carotid sinus pressure was increased to 160 mm Hg to inhibit VP release, the t1/2 of VP was 1.3 min. The t1/2 of immunoreactive (IR) ANP after iv infusion was 1.2 min. Plasma IR-ANP was significantly increased 2 min after carotid sinus pressure was decreased, and a maximum was observed at 10 min. The t1/2 of IR-ANP after elevation of carotid sinus pressure to 160 mm Hg was 3.2 min. These studies indicate that both VP and IR-ANP are rapidly eliminated in the anesthetized rabbit.
Third Director of the European Centre for Disease Prevention and Control takes office (2017)

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Integrating phenotype ontologies across multiple species (2010)

Phenotype ontologies are typically constructed to serve the needs of a particular community, such as annotation of genotype-phenotype associations in mouse or human. Here we demonstrate how these ontologies can be improved through assignment of logical definitions using a core ontology of phenotypic qualities and multiple additional ontologies from the Open Biological Ontologies library. We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology.
Robust face recognition by combining projection-based image correction and decomposed eigenface (2004)

This work presents a robust face recognition method, which can work even when an insufficient number of images are registered for each person. The method is composed of image correction and image decomposition, both of which are specified in the normalized image space (NIS). The image correction [(F. Sakaue and T. Shakunaga, 2004), (T. Shakunaga and F. Sakaue, 2002)] is realized by iterative projections of an image to an eigenspace in NIS. It works well for natural images having various kinds of noise, including shadows, reflections, and occlusions. We have proposed decomposition of an eigenface into two orthogonal eigenspaces [T. Shakunaga and K. Shigenari, 2001], and have shown that the decomposition is effective for realizing robust face recognition under various lighting conditions. This work shows that the decomposed eigenface method can be refined by projection-based image correction.
Methods of correcting Anger camera deadtime losses. (1976)

Three different methods of correcting for Anger camera deadtime loss were investigated. These included analytic methods (mathematical modeling), the marker-source method, and a new method based on counting "pileup" events appearing in a pulse-height analyzer window positioned above the photopeak of interest. The studies were done with 99mTc on a Searle Radiographics camera with a measured deadtime of about 6 musec. Analytic methods were found to be unreliable because of unpredictable changes in deadtime with changes in radiation scattering conditions. Both the marker-source method and the pileup-counting method were found to be accurate to within a few percent for true counting rates of up to about 200 K cps, with the pileup-counting method giving better results. This finding applied to sources at depths ranging up to 10 cm of presdwood. The relative merits of the two methods are discussed.
Regulation of the Epithelial Sodium Channel by Serine Proteases in Human Airways (2002)

The epithelial sodium channel (ENaC) constitutes the rate-limiting step for sodium absorption across airway epithelia, which in turn regulates airway surface liquid (ASL) volume and the efficiency of mucociliary clearance. This role in ASL volume regulation suggests that ENaC activity is influenced by local factors rather than systemic signals indicative of total body volume homeostasis. Based on reports that ENaC may be regulated by extracellular serine protease activity in Xenopus and mouse renal epithelia, we sought to identify proteases that serve similar functions in human airway epithelia. Homology screening of a human airway epithelial cDNA library identified two trypsin-like serine proteases (prostasin and TMPRSS2) that, as revealed by in situ hybridization, are expressed in airway epithelia. Functional studies in the Xenopus oocyte expression system demonstrated that prostasin increased ENaC currents 60--80%, whereas TMPRSS2 markedly decreased ENaC currents and protein levels. Studies of primary nasal epithelial cultures in Ussing chambers revealed that inhibition of endogenous serine protease activity with aprotinin markedly decreased ENaC-mediated currents and sensitized the epithelia to subsequent channel activation by exogenous trypsin. These data, therefore, suggest that protease-mediated regulation of sodium absorption is a function of human airway epithelia, and prostasin is a likely candidate for this activity.
Natural Occurrence of Drug Resistance Mutations in the Reverse Transcriptase of Human Immunodeficiency Virus Type 1 Isolates (1994)

Reverse transcriptase-associated amino acid substitutions related to ddC, d4T, and nevirapine resistance have been found in isolates of human immunodeficiency virus type 1 (HIV-1) from patients treated with AZT only. Sequence analysis of 23 isolates documented the presence of 4 unexpected mutations at amino acid residues related to drug resistance. Two isolates contained an aspartic residue in codon 69 associated with ddC resistance, and another a change in codon 75 associated with resistance to d4T. The Y-to-C alteration in codon 181 associated with nevirapine resistance was observed in another isolate after serial passage in cell culture in the absence of drug. Changes in substitution patterns were also noted after serial passage of four AZT resistant isolates in cell culture without inhibitors. One of the strains showed changes in codons 67 and 70 to wild-type residues. Clonal analysis showed that this alteration occurred by the selection during cell culture passage of the wild-type genotype, which was present as a minority subpopulation in the initially resistant virus stock, rather than to genetic reversion. In summary, we present evidence documenting the presence of mutations associated with drug resistance in the absence of drug treatment and supporting the role played by gentic variability in the emergence of HIV-1 antiviral resistance.
Preincubation with Sn-complexes causes intensive intracellular retention of 99mTc in thyroid cells in vitro (2012)

Intracellular (99m)Tc retention is related to reduced survival, which is most likely mediated by the emission of low-energy electrons. Our findings show that the described experiments constitute a simple and useful in vitro model for radiobiological investigations in a cell model.
SWISS-MODEL: homology modelling of protein structures and complexes (2018)

Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows and servers simplify and streamline the homology modelling process, also allowing users without a specific computational expertise to generate reliable protein models and have easy access to modelling results, their visualization and interpretation. Here, we present an update to the SWISS-MODEL server, which pioneered the field of automated modelling 25 years ago and been continuously further developed. Recently, its functionality has been extended to the modelling of homo- and heteromeric complexes. Starting from the amino acid sequences of the interacting proteins, both the stoichiometry and the overall structure of the complex are inferred by homology modelling. Other major improvements include the implementation of a new modelling engine, ProMod3 and the introduction a new local model quality estimation method, QMEANDisCo. SWISS-MODEL is freely available at https://swissmodel.expasy.org.
Interaction of the 1 alpha,25-dihydroxyvitamin D3 receptor with RNA and synthetic polyribonucleotides. (1984)

The interaction of the 1 alpha,25-dihydroxyvitamin D3 receptor with RNA and synthetic polynucleotides has been examined by using receptor from rachitic chicken intestine. Total intestinal RNA inhibited the binding of receptor to calf thymus DNA-cellulose with an efficiency equivalent to single-stranded DNA. A comparison of the inhibitory activity of several polyribonucleotides gave the following order of activities: poly(I) = poly(G) greater than or equal to double-stranded DNA greater than single-stranded DNA = poly(U). Poly(A), poly(C), and the ribonucleoside monophosphates AMP, GMP, CMP, and UMP had minimal activity. A preference for single-stranded homopolymers was observed [i.e., poly(I) and poly(U) were active, whereas poly(I):poly(C) and poly(U):poly(A) were not]. The ability of nucleic acids to displace receptor from DNA-cellulose was also measured. Both poly(G) and poly(I) were more active than double-stranded DNA in this assay. Furthermore, differences were noted between intestinal RNA fractions separated on the basis of poly(A) content. Receptor also bound to immobilized intestinal RNA and polynucleotides. The KCl concentration necessary to disrupt binding to a given polynucleotide generally paralleled the activity of that molecule in DNA-cellulose inhibition and displacement assays. These results suggest that the 1 alpha,25-dihydroxyvitamin D3 receptor can interact with RNA as well as DNA.
Cross-activity between Pheromone Biosynthesis Activating Neuropeptide (PBAN) and Myotropic Pyrokinin Insect Peptides (1992)

Journal Article Cross-activity between Pheromone Biosynthesis Activating Neuropeptide (PBAN) and Myotropic Pyrokinin Insect Peptides Get access Hisato Kuniyoshi, Hisato Kuniyoshi Department of Agricultural Chemistry, Faculty of Agriculture, The University of Tokyo, Bunkyo-ku, Tokyo 113, Japan Search for other works by this author on: Oxford Academic Google Scholar Hiromichi Nagasawa, Hiromichi Nagasawa Department of Agricultural Chemistry, Faculty of Agriculture, The University of Tokyo, Bunkyo-ku, Tokyo 113, Japan Search for other works by this author on: Oxford Academic Google Scholar Tetsu Ando, Tetsu Ando Department of Agricultural Chemistry, Faculty of Agriculture, The University of Tokyo, Bunkyo-ku, Tokyo 113, JapanDepartment of Plant Protection, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183, Japan Search for other works by this author on: Oxford Academic Google Scholar Akinorr Suzuki, Akinorr Suzuki Department of Agricultural Chemistry, Faculty of Agriculture, The University of Tokyo, Bunkyo-ku, Tokyo 113, Japan To whom reprint requests should be addressed. Search for other works by this author on: Oxford Academic Google Scholar Ronald J Nachman, Ronald J Nachman Department of Agricultural Chemistry, Faculty of Agriculture, The University of Tokyo, Bunkyo-ku, Tokyo 113, JapanVeterinary Toxicology and Entomology Research Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Route 5, Box 810, College Station, TX 77840, U.S.A. To whom reprint requests should be addressed. Search for other works by this author on: Oxford Academic Google Scholar G Mark Holman G Mark Holman Department of Agricultural Chemistry, Faculty of Agriculture, The University of Tokyo, Bunkyo-ku, Tokyo 113, JapanVeterinary Toxicology and Entomology Research Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Route 5, Box 810, College Station, TX 77840, U.S.A. Search for other works by this author on: Oxford Academic Google Scholar Bioscience, Biotechnology, and Biochemistry, Volume 56, Issue 1, 1 January 1992, Pages 167–168, https://doi.org/10.1271/bbb.56.167 Published: 01 January 1992 Article history Received: 03 September 1991 Published: 01 January 1992
Adaptive design clinical trials: a review of the literature and ClinicalTrials.gov (2018)

Wider use of adaptive designs will necessitate new drug application sponsors to engage with regulatory scientists during planning and conduct of the trials. Investigators need to more consistently report protections intended to preserve confidentiality and minimise potential operational bias during interim analysis.
[Cloning and characterization of CMO gene from Atriplex hortensis]. (2001)

Glycine betaine is a widespread osmopretectant existed in many organisms. In higher plant, glycine betaine is synthesized via a two-sep oxidation reaction: choline-->betaine aldehyde-->glycine betaine. The first step, also the speed-limiting step, is catalyzed by choline monooxygenase(CMO). Choosing halophyte Atriplex hortensis as material, we constructed a salt stress-induced cDNA library, and isolated a 1.77 kb length cDNA clone with spinach CMO cDNA as probe. The sequencing result showed a complete Open Reading Frame encoding a 438-amino-acid polypeptide which was 81% and 72% identified to CMO sequences of spinach and sugar beet in amino acid homology respectively. Compared with the CMO from spinach and sugar beet, the AhCMO had one conserved Rieske-Type [2Fe-2S] cluster-binding region and one conserved mononuclear Fe-binding motif. The expression pattern of AhCMO under salt stress was also stuied, the transcriptional level of AhCMO raised about three folds after the plant was treated with brine for 4 days. The AhCMO was then transfered into tobacco(Nictiana tabacum var. Xanthi) with 35S promotor and seven transgenic plants were certified by northern blot, these plants displayed some salt- and drought-stress tolerance when grew well on MS medium contained 1.2% NaCl or 10% PEG while the control was stagnated under the same cndition.
Anti-vascular approaches to solid tumour therapy: evaluation of combretastatin A4 phosphate. (1999)

Combretastatin A4 phosphate has recently been identified by us as an agent which can selectively damage tumour neovasculature. In the current study we establish that combretastatin induces extensive blood flow shutdown in the tumour compared to normal tissues. Histological assessment of vascular shutdown shows that over 90% of vessels are rendered non-functional 6 hrs post-treatment with 100 mg/kg i.p. Measurement of blood flow using a diffusible tracer 86RbCl indicates an overall reduction in perfusion by only 50-60%. This discrepancy probably reflects increased blood flow in the normal tissue vasculature supplying the tumour rim, which is caused by the ischaemia-induced release of vasoactive mediators. The vascular shutdown induced by administration of 100 mg/kg of combretastatin A4 phosphate results in extensive cell loss in the 24 hrs following treatment, however this is not translated into any significant effect on tumour growth. The continued growth of the tumour is attributed to an actively proliferating population of cells at the periphery of the tumour, which are dependent on normal tissue vasculature for their survival. We have attempted to target this residual population by combining combretastatin A4 phosphate with cytotoxic approaches. Cis platinum and radiation have been used. The results show that combretastatin can significantly enhance tumour response to both cis platinum and radiation. In summary, the studies confirm combretastatin A4 phosphate as a novel agent which targets and damages tumour vasculature and, moreover, indicate its potential therapeutic usefulness as an adjuvant to conventional cytotoxic approaches.
Transplacental Exposure to Indole-3-carbinol Induces Sex-Specific Expression of CYP1A1 and CYP1B1 in the Liver of Fischer 344 Neonatal Rats (2001)

Indole-3-carbinol (I3C), a naturally occurring component of broccoli, cabbage, and other members of the family Cruciferae, is a tumor modulator in several animal models that demonstrates significant chemoprevention against development of both spontaneous and chemically induced cancers while conversely eliciting tumor promoter effects in others. This study examines the disposition of I3C in the pregnant rat model, specifically to determine whether I3C can traverse the maternal placenta, and what effects, if any, are elicited in the neonate. We now report that dietary I3C treatment of pregnant female rats results in appearance of I3C acid condensation products in both maternal and neonatal livers. Livers from I3C-fed maternal rats showed CYP1A1 protein induction; however, no CYP1B1 protein was detected. No CYP1A1 or CYP1B1 protein was detected in the livers of pregnant controls or their offspring. We also report a sex-specific induction of CYP1A1 and CYP1B1 protein in livers from newborns born to I3C-fed dams. CYP1A1 protein was significantly induced in male neonatal liver, but not in females. Conversely, hepatic CYP1B1 protein was induced to high levels in female neonates, with no CYP1B1 protein detected in male littermates. Our results demonstrate that dietary I3C acid condensation products can cross the maternal placenta and differentially induce neonatal hepatic CYP1A1 and CYP1B1 in a sex-specific manner. The results highlight the potential of I3C to effect changes in the overall metabolic profile of xenobiotics to which the fetus is exposed transplacentally and indicate the possible involvement of sex-specific modulators in Ah receptor-mediated responses in this model.
Clathrate Hydrates: From Laboratory Science to Engineering Practice (2009)

Clathrate hydrates have steadily emerged as an important field in the areas of flow assurance, energy storage and resource, and environment. To better understand the role of hydrates in all of these areas, knowledge developed in laboratory experiments must be effectively transferred to address the challenges related to hydrate formation, dissociation, agglomeration, and stability. This paper highlights the recent hydrate literature focusing on the thermodynamics, kinetics, structural properties, particle properties, rheological properties, and molecular mechanisms of formation. The foundation for continued understanding and development of hydrates in engineering practice will rely on laboratory measurements utilizing traditional and innovative tools capable of probing time-dependent and time-independent properties.
Cofactor residues lysine 165 and 166 are critical for protein substrate recognition by the tissue factor-factor VIIa protease complex. (1992)

High affinity binding of factor VIIa (VIIa) to its cellular receptor tissue factor (TF), as well as association of factor X with phospholipid are required for optimal assembly of the extrinsic activation complex. In addition to the interactions of substrate with phospholipid and enzyme, we here provide evidence that cofactor residues Lys-165 and Lys-166 specifically contribute to the recognition of macromolecular substrate. Ala for Lys replacement in TFA165A166 was compatible with high affinity binding of VIIa when analyzed on cell surfaces as well as in the absence of phospholipid. Dissociation of TFA165A166.VIIa did not occur with a faster rate compared to TF.VIIa, further supporting unaltered VIIa binding function of TFA165A166. Cleavage of chromogenic peptidyl substrate by TFA165A166.VIIa complexes was not diminished, demonstrating that TFA165A166 supported enhancement of catalytic function of the VIIa protease domain. In contrast, factor X activation was reduced in the presence and absence of phospholipid. Further, TFA165A166 effectively competed with wild-type TF in the cleavage of factor X at limited VIIa concentrations. Selective reduction in macromolecular substrate hydrolysis combined with normal VIIa binding by TFA165A166 indicates that the cofactor TF does contribute, either directly or indirectly via specific interactions with VIIa, to factor X recognition.
512-Mb PROM with a three-dimensional array of diode/antifuse memory cells (2003)

A 512-Mb one-time-programmable memory is described, which uses a transistorless two-terminal memory cell containing an antifuse and a diode. Cells are fabricated in polycrystalline silicon, stacked vertically in eight layers above a 0.25-μm CMOS substrate. One-time programming is performed by applying a high voltage across the cell terminals, which ruptures the antifuse and permanently encodes a logic 0. Unruptured antifuses encode a logic 1. Cells are arranged in 8-Mb tiles, 1 K rows by 1 K columns by 8 bits high. The die contains 72 such tiles: 64 tiles for data and eight tiles for error-correcting code bits. Wordline and bitline decoders, bias circuits, and sense amplifiers are built in the CMOS substrate directly beneath the memory tiles, improving die efficiency. The device supports a generic standard NAND flash interface and operates from a single 3.3-V supply.
Norepinephrine Elicits β 2 -Receptor–Mediated Dilation of Isolated Human Coronary Arterioles (2002)

Our data indicate that isolated human coronary arterioles and small arteries dilate to NE via beta2-receptors on smooth muscle. These findings are important to our understanding of the mechanisms action of NE in the human coronary circulation.