gebhart/patrepeval huggingface dataset:
Functional activity of the two promoters of the myosin alkali light chain gene in primary muscle cell cultures: comparison with other muscle gene promoters and other culture systems (1988)

Proximal upstream flanking sequences of the mouse myosin alkali light chain gene encoding MLC1F and MLC3F, the mouse alpha-cardiac actin gene and the chicken gene for the alpha-subunit of the acetylcholine receptor were linked to the bacterial chloramphenicol acetyl transferase (CAT) gene and transfected into primary cultures derived from mouse skeletal muscle or into myogenic cell lines. We demonstrate that the mouse MLC1F/MLC3F gene has two functional promoters. In primary muscle cultures, a 1200 bp sequence flanking exon 1 (MLC1F) and a 438 bp sequence flanking exon 2 (MLC3F) direct CAT activity in myotubes, but not in myoblasts or in non myogenic 3T6 and CV1 cells. Developmentally regulated expression is also seen with the alpha-cardiac actin (320 bp) and acetylcholine receptor alpha-subunit (850 bp) upstream sequences in the primary culture system. Transfection experiments with myogenic cell lines show different results with a given promoter construct, reflecting possible differences in the levels of regulatory factors between lines. Different muscle gene promoters behave differently in a given cell line, suggesting different regulatory factor requirements between these promoters.
The Marion system for retargetable instruction scheduling (1991)

article The Marion system for retargetable instruction scheduling Share on Authors: David G. Bradlee Department of Computer Science and Engineering, FR-35, University of Washington, Seattle, Washington Department of Computer Science and Engineering, FR-35, University of Washington, Seattle, WashingtonView Profile , Robert R. Henry Tera Computer, 400 N 34th Street, Seattle, WA and Department of Computer Science and Engineering, FR-35, University of Washington, Seattle, Washington Tera Computer, 400 N 34th Street, Seattle, WA and Department of Computer Science and Engineering, FR-35, University of Washington, Seattle, WashingtonView Profile , Susan J. Eggers Department of Computer Science and Engineering, FR-35, University of Washington, Seattle, Washington Department of Computer Science and Engineering, FR-35, University of Washington, Seattle, WashingtonView Profile Authors Info & Claims ACM SIGPLAN NoticesVolume 26Issue 6June 1991 pp 229–240https://doi.org/10.1145/113446.113465Online:01 May 1991Publication History 36citation474DownloadsMetricsTotal Citations36Total Downloads474Last 12 Months12Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Complications in Pediatric Regional Anesthesia (2018)

The data from this study demonstrate a level of safety in pediatric regional anesthesia that is comparable to adult practice and confirms the safety of placing blocks under general anesthesia in children.
Area-efficient near-associative memories on FPGAs (2013)

Associative memories can map sparsely used keys to values with low latency but can incur heavy area overheads. The lack of customized hardware for associative memories in today's mainstream FPGAs exacerbates the overhead cost of building these memories using the fixed address match BRAMs. In this paper, we develop a new, FPGA-friendly, memory architecture based on a multiple hash scheme that is able to achieve near-associative performance (less than 5% of evictions due to conflicts) without the area overheads of a fully associative memory on FPGAs. Using the proposed architecture as a 64KB L1 data cache, we show that it is able to achieve near-associative miss-rates while consuming 6-7× less FPGA memory resources for a set of benchmark programs from the SPEC2006 suite than fully associative memories generated by the Xilinx Coregen tool. Benefits increase with match width, allowing area reduction up to 100×. At the same time, the new architecture has lower latency than the fully associative memory -- 3.7 ns for a 1024-entry flat version or 6.1 ns for an area-efficient version compared to 8.8 ns for a fully associative memory for a 64b key.
Antiviral Antibody Responses and Intrauterine Transmission after Primary Maternal Cytomegalovirus Infection (1995)

Human cytomegalovirus (HCMV)-specific antibody responses after primary maternal infection were examined to determine if specific deficits in antibody response were associated with intrauterine transmission. Anti-glycoprotein B IgG antibodies were significantly higher at delivery in transmitters than in nontransmitters, suggesting that the amount of antiviral antibody was not reflective of protection from transmission. Characterization of the qualitative antibody response revealed lower neutralizing antibody titers in transmitters, suggesting an association between neutralizing activity and intrauterine transmission. Examination of anti-HCMV antibody avidity revealed that the majority of nontransmitters but < 20% of transmitters had an avidity index > 2.0 (P < .002). A significant correlation between neutralizing titers and antibody avidity was demonstrated. Thus, antibody affinity maturation is critical for production of high levels of neutralizing antibodies during primary HCMV infection, and a defect in affinity maturation may play a role in intrauterine transmission of HCMV.
Balance Trees Reveal Microbial Niche Differentiation (2017)

Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from the compositional nature of 16S rRNA gene data (or, more generally, taxon or functional gene data); the changes in the relative abundance of one taxon influence the apparent abundances of the others. Here we acknowledge that inferring properties of individual bacteria is a difficult problem and instead introduce the concept of balances to infer meaningful properties of subcommunities, rather than properties of individual species. We show that balances can yield insights about niche differentiation across multiple microbial environments, including soil environments and lung sputum. These techniques have the potential to reshape how we carry out future ecological analyses aimed at revealing differences in relative taxonomic abundances across different samples. <b>IMPORTANCE</b> By explicitly accounting for the compositional nature of 16S rRNA gene data through the concept of balances, balance trees yield novel biological insights into niche differentiation. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/gneiss. <b>Author Video</b>: An author video summary of this article is available.
Improved Bioavailability of a Micronized Megestrol Acetate Tablet Formulation in Humans (2000)

Megestrol acetate, a progestogen widely used in the palliative treatment of endometrial carcinoma and breast cancer, is currently administered orally as a solid dosage form. Bioavailability of the drug following oral administration is closely related to the effectiveness and safety profile of the drug in formulation. Improved immediate-release formulations should allow improved drug delivery into the systemic circulation and, at the end, to the site of action. The micronization of drugs is one of the technological procedures to achieve such a purpose. This paper reports the design and results obtained in an in vivo study of the bioavailability of a micronized megestrol acetate tablet formulation compared to a conventional form. A significant increase in the drug bioavailability was observed, in either the rate or the extent of absorption. In vitro dissolution data of the two study formulations reflected the in vivo findings.
A Spectroscopic Mechanism for Primary Olfactory Reception (1996)

A novel theory of primary olfactory reception is described. It proposes that olfactory receptors respond not to the shape of the molecules but to their vibrations. It differs from previous vibrational theories (Dyson, Wright) in providing a detailed and plausible mechanism for biological transduction of molecular vibrations: inelastic electron tunnelling. Elements of the tunnelling spectroscope are identified in putative olfactory receptors and their associated G-protein. Means of calculating electron tunnelling spectra of odorant molecules are described. Several examples are given of correlations between tunnelling spectrum and odour in structurally unrelated molecules. As predicted, molecules of very similar shape but differing in vibrations smell different. The most striking instance is that of pure acetophenone and its fully deuterated analogue acetophenone-d8, which smell different despite being identical in structure. This fact cannot, it seems, be explained by structure-based theories of odour. The evidence presented here suggests instead that olfaction, like colour vision and hearing, is a spectral sense.
Symbiotic association in Chlorella culture (2004)

Chlorella sorokiniana IAM C-212 has long been maintained in slant culture as a mixed strain, representing an associated natural microbial consortium. In this study, the consortium was separated and five nonalgal constituents, a fungal strain (CSSF-1), and four bacterial strains (CSSB-1, CSSB-2, CSSB-3, and CSSB-4) were isolated and identified. 16S rDNA sequence analysis revealed that strains CSSB-1, CSSB-2, CSSB-3, and CSSB-4 were close to Ralstonia pickettii (99.8% identity), Sphingomonas sp. DD38 (99.4% identity), Microbacterium trichotecenolyticum (98.6% identity), and Micrococcus luteus (98.6% identity) respectively. 18S rDNA sequence analysis revealed that strain CSSF-1 resembled Acremonium-like hyphomycete KR21-2 (98.8%). The fungal strain CSSF-1 and one of the bacterial strains, CSSB-3, were found to promote the growth of Chlorella while the presence of bacterial strains CSSB-1 and CSSB-2 had no effect. Strain CSSB-4 could not be subcultured so its role was not elucidated. These results show that the interaction between Chlorella and its symbionts under photoautotrophic conditions involved both mutualism and commensalisms. The chlorophyll content of mixed strain was stable in long-term cultivation (7 months) while the chlorophyll content of a pure culture showed a marked decline. Electron microscopic analysis showed the two bacterial strains CSSB-2 and CSSB-3 were harbored on the sheath excreted by Chlorella, while the fungal strain CSSF-1 and the bacterial strain CSSB-1 directly adhered to the Chlorella cell surface. This report is the first observation of a symbiotic relationship among fungus, bacteria, and Chlorella, and the first observation of direct adhesion of fungus and bacteria to Chlorella in a consortium.
Molecular Biology of the Cell (2017)

As the amount of information in biology expands dramatically, it becomes increasingly important for textbooks to distill the vast amount of scientific knowledge into concise principles and enduring concepts.As with previous editions, Molecular Biology of the Cell, Sixth Edition accomplishes this goal with clear writing and beautiful illustrations. The Sixth Edition has been extensively revised and updated with the latest research in the field of cell biology, and it provides an exceptional framework for teaching and learning. The entire illustration program has been greatly enhanced.Protein structures better illustrate structure–function relationships, icons are simpler and more consistent within and between chapters, and micrographs have been refreshed and updated with newer, clearer, or better images. As a new feature, each chapter now contains intriguing openended questions highlighting “What We Don’t Know,” introducing students to challenging areas of future research. Updated end-of-chapter problems reflect new research discussed in the text, and these problems have been expanded to all chapters by adding questions on developmental biology, tissues and stem cells, pathogens, and the immune system.
Materials Science of Carbon Nanotubes:  Fabrication, Integration, and Properties of Macroscopic Structures of Carbon Nanotubes (2002)

In this Account, we summarize some of our recent studies on the materials properties of the carbon nanotubes (CNTs). The focus is on single-wall carbon nanotubes (SWNTs). We describe experiments on synthesis of SWNTs with controlled molecular structures and assembly of functional macroscopic structures. In addition, we present results on the electron field emission properties of macroscopic CNT cathodes.
Biomechanical Strain Exacerbates Inflammation on a Progeria‐on‐a‐Chip Model (2017)

Organ-on-a-chip platforms seek to recapitulate the complex microenvironment of human organs using miniaturized microfluidic devices. Besides modeling healthy organs, these devices have been used to model diseases, yielding new insights into pathophysiology. Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging disease showing accelerated vascular aging, leading to the death of patients due to cardiovascular diseases. HGPS targets primarily vascular cells, which reside in mechanically active tissues. Here, a progeria-on-a-chip model is developed and the effects of biomechanical strain are examined in the context of vascular aging and disease. Physiological strain induces a contractile phenotype in primary smooth muscle cells (SMCs), while a pathological strain induces a hypertensive phenotype similar to that of angiotensin II treatment. Interestingly, SMCs derived from human induced pluripotent stem cells of HGPS donors (HGPS iPS-SMCs), but not from healthy donors, show an exacerbated inflammatory response to strain. In particular, increased levels of inflammation markers as well as DNA damage are observed. Pharmacological intervention reverses the strain-induced damage by shifting gene expression profile away from inflammation. The progeria-on-a-chip is a relevant platform to study biomechanics in vascular biology, particularly in the setting of vascular disease and aging, while simultaneously facilitating the discovery of new drugs and/or therapeutic targets.
Comparison of Viral Load in Individuals with and without Asthma during Infections with Rhinovirus (2014)

During acute symptoms, children infected with RV enrolled for wheezing or acute rhinitis had similar viral loads in their nasal washes, as did adults with and without asthma infected with RV-16 experimentally.
Enhanced Potency of a Broadly Neutralizing HIV-1 Antibody In Vitro Improves Protection against Lentiviral Infection In Vivo (2014)

In the absence of an effective HIV-1 vaccine, alternative strategies are needed to block HIV-1 transmission. Direct administration of HIV-1-neutralizing antibodies may be able to prevent HIV-1 infections in humans. This approach could be especially useful in individuals at high risk for contracting HIV-1 and could be used together with antiretroviral drugs to prevent infection. To optimize the chance of success, such antibodies can be modified to improve their potency, breadth, and in vivo half-life. Here, knowledge of the structure of a potent neutralizing antibody, VRC01, that targets the CD4-binding site of the HIV-1 envelope protein was used to engineer a next-generation antibody with 5- to 8-fold increased potency in vitro. When administered to nonhuman primates, this antibody conferred protection at a 5-fold lower concentration than the original antibody. Our studies demonstrate an important correlation between in vitro assays used to evaluate the therapeutic potential of antibodies and their in vivo effectiveness.
Kinetic evidence suggesting two mechanisms for iodothyronine 5'-deiodination in rat cerebral cortex. (1982)

Enzymatic 5'-deiodination of 3,3',5'-triiodothyronine (rT3) and 3,3',5,5'-tetraiodothyronine (thyroxine, T4) was studied in microsomal preparations of rat cerebral cortex. Evidence was obtained for the existence of two thiol-dependent 5'-deiodinase entities. One of these predominates in tissue from euthyroid and long-term hypothyroid rats, is specific for rT3, follows "ping-pong" kinetics with dithiothreitol as the cosubstrate, and is inhibited by propylthiouracil (PrSUra) and iodoacetate. Inhibition by PrSUra is uncompetitive with rT3 and competitive with dithiothreitol. These properties are shared with the 5'-deiodinase activity of liver and kidney. The activity of a second type of 5'-deiodinase is highest in cerebral cortex from short-term hypothyroid rats, prefers T4 to rT3 as the substrate, is insensitive to PrSUra and iodoacetate, and follows "sequential" reaction kinetics. A similar PrSUra-insensitive 5'-deiodinase activity is also found in pituitary but is not detectable in liver and kidney; it seems, therefore, characteristic of tissues in which local T4 to 3,3',5-triiodothyronine (T3) conversion supplies a major portion of the total intracellular T3.
Mid-Infrared Silicon-on-Insulator Fourier-Transform Spectrometer Chip (2015)

Mid-infrared absorption spectroscopy is highly relevant for a wide range of sensing applications. In this letter, we demonstrate a Fourier-transform spectrometer chip based on the principle of spatial heterodyning implemented in the silicon-on-insulator waveguide platform, and operating near 3.75-μm wavelength. The spectrometer comprises a waveguide splitting tree feeding to an array of 42 Mach-Zehnder interferometers with linearly increasing optical path length differences. A spectral retrieval algorithm based on calibration matrices is applied to the stationary output pattern of the array, compensating for any phase and amplitude errors arising from fabrication imperfections. A spectral resolution below 3 nm is experimentally demonstrated.
Correlation of Saliva Cocaine Levels with Plasma Levels and with Pharmacologic Effects after Intravenous Cocaine Administration in Human Subjects (1988)

The behavioral and physiologic effects of single, intravenous bolus doses of cocaine in 5 male human subjects were correlated with cocaine levels in saliva and blood. All measures were performed under double-blind conditions. Two test doses of cocaine (15 mg and 40 mg) and one placebo test dose were administered to each subject in a random, cross-over design. Each test day was separated by a minimum of 48 h. Cocaine levels in saliva and blood significantly (p less than or equal to 0.05) correlated with responses on self-rating scales for drug sensation (Feel Drug scale), psychotomimetic effects (LSD scale), and feelings of rush (Rush scale). Significant (p less than or equal to 0.01) correlations also were obtained with cocaine biofluid levels and pulse rate. The close relationship observed between cocaine saliva levels and cocaine-induced behavior and physiologic effects presents the opportunity for development of a new noninvasive method for detection of current cocaine use.
Serum paraoxonase status: A major factor in determining resistance to organophosphates (1993)

A number of lines of evidence suggest that serum paraoxonase is protective against poisoning by organophosphorus substrates of this enzyme. Birds that have very low levels of paraoxon hydrolyzing activity in their sera are very susceptible to parathion poisoning. Rabbits, which have a sevenfold higher enzyme level compared with rats, have a fourfold higher resistance to paraoxon poisoning than rats. Rabbit paraoxonase hydrolyzes chlorpyrifos-oxon with a much higher turnover number than does rat paraoxonase, resulting in a very high resistance of rabbits to chlorpyrifos toxicity. Direct tests of paraoxonase protection have been carried out by injecting purified rabbit enzyme into rats. The protection achieved was higher for chlorpyrifos-oxon than for paraoxon, probably due to the high hydrolytic activity of the rabbit enzyme for chlorpyrifos-oxon. In humans, a substrate-dependent polymorphism of serum paraoxonase is observed, where one isoform of paraoxonase has a high turnover number for paraoxon and the other a low turnover number. Both isoforms appear to hydrolyze chlorpyrifos-oxon and phenylacetate at the same rate. Cloning and sequencing of the human paraoxonase cDNAs has elucidated the molecular basis of the polymorphism. Arginine at position 192 determines high paraoxonase activity, and glutamine at this position, low paraoxonase activity. In addition to the polymorphism, a 13-fold variation in serum enzyme levels within a given genetic class is seen. The experiments reported here demonstrate that rabbit paraoxonase injected into mice provides protection against the parent insecticide chlorpyrifos as well as the toxic oxon. These results suggest that serum paraoxonase status may serve as a biomarker for insecticide susceptibility in humans.
New World Bats Harbor Diverse Influenza A Viruses (2013)

Aquatic birds harbor diverse influenza A viruses and are a major viral reservoir in nature. The recent discovery of influenza viruses of a new H17N10 subtype in Central American fruit bats suggests that other New World species may similarly carry divergent influenza viruses. Using consensus degenerate RT-PCR, we identified a novel influenza A virus, designated as H18N11, in a flat-faced fruit bat (Artibeus planirostris) from Peru. Serologic studies with the recombinant H18 protein indicated that several Peruvian bat species were infected by this virus. Phylogenetic analyses demonstrate that, in some gene segments, New World bats harbor more influenza virus genetic diversity than all other mammalian and avian species combined, indicative of a long-standing host-virus association. Structural and functional analyses of the hemagglutinin and neuraminidase indicate that sialic acid is not a ligand for virus attachment nor a substrate for release, suggesting a unique mode of influenza A virus attachment and activation of membrane fusion for entry into host cells. Taken together, these findings indicate that bats constitute a potentially important and likely ancient reservoir for a diverse pool of influenza viruses.
SYNTHESIS AND BINDING AFFINITY OF A CHIRAL PNA ANALOGUE (2001)

The synthesis of a chiral peptide nucleic acid (PNA), which is composed of N-aminoethyl-cis-4-nucleobase-L-proline units, was described. The chiral PNA monomers containing all four nucleobases (A. T, C and G) were steroselectively prepared. The x-ray diffraction data from a single crystal confirmed the configuration of a key intermediate. Binding activity of the oligomers with their complementary DNA targets was also investigated.