gebhart/patrepeval huggingface dataset:
Effective Turning Motion Control of Internally Actuated Autonomous Underwater Vehicles (2017)

This paper presents a novel roll mechanism and an efficient control strategy for internally actuated autonomous underwater vehicles (AUVs). The developed control algorithms are tested on Michigan Tech’s custom research glider, ROUGHIE (Research Oriented Underwater Glider for Hands-on Investigative Engineering), in a controlled environment. The ROUGHIE’s design parameters and operational constraints were driven by its requirement to be man portable, expandable, and maneuverable in shallow water. As an underwater glider, the ROUGHIE is underactuated with direct control of only depth, pitch, and roll. A switching control method is implemented on the ROUGHIE to improve its maneuverability, enabling smooth transitions between different motion patterns. This approach uses multiple feedforward-feedback controllers. Different aspects of the roll mechanism and the effectiveness of the controller on turning motion are discussed based on experimental results. The results illustrate that the ROUGHIE is capable of achieving tight turns with a radius of 2.4 meters in less than 3 meters of water, or one order of magnitude improvement on existing internally actuated platforms. The developed roll mechanism is not specific to underwater gliders and is applicable to all AUVs, especially at lower speeds and in shallower water when external rudder is less effective in maneuvering the vehicle.
Genomic Alterations in Fatal Forms of Non-Anaplastic Thyroid Cancer: Identification of MED12 and RBM10 as Novel Thyroid Cancer Genes Associated with Tumor Virulence (2017)

<b>Purpose:</b> Patients with anaplastic thyroid cancer (ATC) have a very high death rate. In contrast, deaths from non-anaplastic thyroid (NAT) cancer are much less common. The genetic alterations in fatal NAT cancers have not been reported.<b>Experimental Design:</b> We performed next-generation sequencing of 410 cancer genes from 57 fatal NAT primary cancers. Results were compared with The Cancer Genome Atlas study (TCGA study) of papillary thyroid cancers (PTCs) and to the genomic changes reported in ATC.<b>Results:</b> There was a very high prevalence of <i>TERT</i> promoter mutations, comparable with that of ATC, and these co-occurred with <i>BRAF</i> and <i>RAS</i> mutations. A high incidence of chromosome 1q gain was seen highlighting its importance in tumor aggressiveness. Two novel fusion genes <i>DLG5</i>-<i>RET</i> and <i>OSBPL1A</i>-<i>BRAF</i> were identified. There was a high frequency of mutations in <i>MED12</i> and these were mutually exclusive to <i>TERT</i> promoter mutations and also to <i>BRAF</i> and <i>RAS</i> mutations. In addition, a high frequency of mutations in <i>RBM10</i> was identified and these co-occurred with <i>RAS</i> mutations and <i>PIK3CA</i> mutations. Compared with the PTCs in TCGA, there were higher frequencies of mutations in <i>TP53, POLE, PI3K/AKT/mTOR</i> pathway effectors, <i>SWI/SNF</i> subunits, and histone methyltransferases.<b>Conclusions:</b> These data support a model, whereby fatal NAT cancers arise from well-differentiated tumors through the accumulation of key additional genetic abnormalities. The high rate of <i>TERT</i> promoter mutations, <i>MED12</i> mutations, <i>RBM10</i> mutations, and chromosome 1q gain highlight their likely association with tumor virulence. <i>Clin Cancer Res; 23(19); 5970-80. ©2017 AACR</i>.
Multilevel and graphical views of metadata (2002)

Digital libraries help users to search for, evaluate and retrieve information. Metadata is indispensable in this process of locating information and evaluating its fitness for specific uses. This paper describes a multilevel organization and presentation of metadata for spatial information in digital libraries. It is proposed that a single organization of metadata within the context of large distributed heterogeneous (text, image, video, audio, etc.) collections is inadequate. The organization of metadata should change, depending upon the purpose for which it is being used and the state of an information-seeking task. We argue for at least a three-level organization of metadata and graphical presentation of metadata for digital library users. The Content Standard for Geospatial Metadata provides a foundation for this approach.
Intercontinental Circulation of Human Influenza A(H1N2) Reassortant Viruses during the 2001–2002 Influenza Season (2002)

Reassortant influenza A viruses bearing the H1 subtype of hemagglutinin (HA) and the N2 subtype of neuraminidase (NA) were isolated from humans in the United States, Canada, Singapore, Malaysia, India, Oman, Egypt, and several countries in Europe during the 2001-2002 influenza season. The HAs of these H1N2 viruses were similar to that of the A/New Caledonia/20/99(H1N1) vaccine strain both antigenically and genetically, and the NAs were antigenically and genetically related to those of recent human H3N2 reference strains, such as A/Moscow/10/99(H3N2). All 6 internal genes of the H1N2 reassortants examined originated from an H3N2 virus. This article documents the first widespread circulation of H1N2 reassortants on 4 continents. The current influenza vaccine is expected to provide good protection against H1N2 viruses, because it contains the A/New Caledonia/20/99(H1N1) and A/Moscow/10/99(H3N2)-like viruses, which have H1 and N2 antigens that are similar to those of recent H1N2 viruses.
5-Hydroxyindoles by Intramolecular Alkynol–Furan Diels–Alder Cycloaddition (2012)

A convergent approach provides a convenient access to synthetically and biologically useful 3,4-disubstituted 5-hydroxyindoles. The one-pot procedure uses microwave heating to initiate an intramolecular [4 + 2]-cycloaddition of an alkynol segment onto a furan followed by a fragmentation, aromatization, and N-Boc deprotection cascade. Yields range from 15 to 74%, with aromatic substituents providing better conversions. 4-Trimethylsilylated analogues undergo a 1,3-silatropic rearrangement to give the O-TMS ethers.
Experimental murine acid aspiration injury is mediated by neutrophils and the alternative complement pathway (1997)

Acid aspiration may result in the development of the acute respiratory distress syndrome, an event associated with significant morbidity and mortality. Although once attributed to direct distal airway injury, the pulmonary failure after acid aspiration is more complex and involves an inflammatory injury mediated by complement (C) and polymorphonuclear leukocytes. This study examines the injurious inflammatory cascades that are activated after acid aspiration. The role of neutrophils was defined by immunodepletion before aspiration, which reduced injury by 59%. The injury was not modified in either P- or E-selectin-knockout mice, indicating that these adhesion molecules were not operative. C activation after aspiration was documented with immunochemistry by C3 deposition on injured alveolar pneumocytes. Animals in which C activation was inhibited with soluble C receptor type 1 (sCR1) had a 54% reduction in injury, similar to the level of protection seen in C3-knockout mice (58%). However C4-knockout mice were not protected from injury, indicating that C activation is mediated by the alternative pathway. Finally, an additive effect of neutrophils and C was demonstrated whereby neutropenic animals that were treated with sCR1 showed an 85% reduction in injury. Thus acid aspiration injury is mediated by neutrophils and the alternative C pathway.
Molecular homology among members of the R gene family in maize (1993)

The R gene family determines the timing, distribution and amount of anthocyanin pigmentation in maize. This family comprises a set of regulatory genes, consisting of a cluster of several elements at the R locus, on chromosome 10, the Lc and Sn gene lying about two units R distal and B on chromosome 2. Each gene determines a tissue-specific pigmentation of different parts of the seed and plant. The proposed duplicated function of R, Sn, Lc and B loci is reflected in cDNA sequence similarity. In this paper an extensive analysis of the predicted proteins of the R, Sn, Lc and B genes together with a search for putative sites of post-translational modification is reported. A comparison with the prosite database discloses several N-glycosylation and phosphorylation sites, as well as the basic Helix-Loop-Helix (HLH) domain of transcriptional activators. Sn, Lc, and R-S show a high conservation of these sites, while B is more divergent. Analysis of the 5' leader of mRNA sequences discloses the presence of five ATG triplets with two upstream open reading frames (uORFs) of 38 and 15 amino acids and a loop structure indicating a possible mechanism of control at the translational level. It is conceivable that possible mechanisms acting at the translational and post-translational level could modulate the expression and the activation of these transcription factors. Northern analysis of various tissues of different R alleles highlights a strict correlation between pigment accumulation in different tissues and the expression of the regulatory and structural genes suggesting that the pattern of pigmentation relies on a mechanism of differential expression of the members of the R family. Analysis of the Sn promoter discloses the presence of several sequences resembling binding sites of known transcription factors (as GAGA and GT) that might be responsible for the spatial and light-induced expression of this gene. Two regions include a short sequence homologous to the consensus binding site of the B-HLH domain suggesting a self-regulatory control of the Sn gene.
Ethanol Consumption and Behavioral Impulsivity Are Increased in Protein Kinase Cγ Null Mutant Mice (2001)

Etiological factors influencing the development of alcoholism are complex and, at a minimum, include an interaction between polygenic factors and personality and biological traits. Human and animal studies suggest that some genes may regulate both the traits associated with alcohol abuse, such as decreased sensitivity or anxiety, and vulnerability to alcoholism. The identification of these genes could elucidate neurochemical pathways that are important in the development of alcohol abuse. Results from the present study indicate that the gene encoding the neuronal-specific gamma subtype of protein kinase C (PKCgamma) influences both ethanol consumption and behavioral impulsivity, a personality characteristic associated with Type II alcoholics, in a pleiotropic manner. Mice lacking PKCgamma consume more ethanol in a two-bottle choice paradigm and also demonstrate increased behavioral impulsivity in an appetitive-signaled nosepoke task when compared with wild-type littermate control mice. Therefore, PKCgamma may be an important mechanism within the cell that mediates one or more neurochemical pathways relevant to an increased predisposition to alcoholism.
An artificial glycoconjugate containing the bisphosphorylated glucosamine disaccharide backbone of lipid A binds lipid A monoclonal antibodies (1993)

Monoclonal antibodies (MAbs) against lipid A, the endotoxic component of lipopolysaccharide (LPS) of gram-negative bacteria, are presently discussed as therapeutic agents against lethal gram-negative infections; however, their binding specificities are controversial. We have isolated from the LPS of Escherichia coli J-5 the 1,4'-bisphosphorylated beta 1-->6-linked glucosamine disaccharide backbone of its lipid A moiety, which was covalently linked to bovine serum albumin. It was shown by solid-phase enzyme immunoassay that one antibody (MAb A6) bound equally well to the glycoconjugate and synthetic E. coli-type lipid A over a broad range of antigen concentrations whereas two other MAbs (IC3 and S1-15) bound better to the conjugate at low antigen concentrations and better to the lipid A when high concentrations of antigen were used. This proves in a direct way that there exist lipid A MAbs with different specificities which bind to epitopes in the hydrophilic backbone of lipid A and which do not require the presence of fatty acids.
Post-translational modifications of tau protein. (2006)

Microtubule-associated protein tau is a phosphoprotein whose expression and phosphorylation is developmentally regulated. Whereas in adult mammalian brain several isoforms are produced from a single gene by alternative splicing, in fetal brain only a single isoform exists, corresponding to the smallest of the tau isoforms. Main physiological function of tau is the promotion of assembly and stabilization of microtubular network, which is essential for normal axonal transport of vesicles within the neuron. In human, tau protein undergoes several posttranslational modifications: such as phosphorylation, truncation, nitration, glycation, glycosylation, ubiquitination and polyaminations. When these modifications are disturbed, they play a serious role during the pathogenesis of Alzheimer's disease (AD). Hyperphosphorylation and truncation as the early events in AD pathogenesis, play significant role in the formation of neurofibrillary pathology. Phosphorylated tau has reduced capability in binding to microtubules and hyperphosphorylation together with truncation contributes to the formation of pathological tau filaments. This leads to destabilization of microtubular network and subsequent impairment of microtubule associated axonal transport. Since many data suggest that sporadic AD is the "disease of posttranslational modifications" of tau protein, more detailed investigation of tau protein modifications is urgently needed in order to understand pathogenesis of sporadic Alzheimer's disease (Fig. 1, Ref. 86).
Chapter 4: Estrogens as Endogenous Genotoxic Agents--DNA Adducts and Mutations (2000)

Estrogens induce tumors in laboratory animals and have been associated with breast and uterine cancers in humans. In relation to the role of estrogens in the induction of cancer, we examine formation of DNA adducts by reactive electrophilic estrogen metabolites, formation of reactive oxygen species by estrogens and the resulting indirect DNA damage by these oxidants, and, finally, genomic and gene mutations induced by estrogens. Quinone intermediates derived by oxidation of the catechol estrogens 4-hydroxyestradiol or 4-hydroxyestrone may react with purine bases of DNA to form depurinating adducts that generate highly mutagenic apurinic sites. In contrast, quinones of 2-hydroxylated estrogens produce less harmful, stable DNA adducts. The catechol estrogen metabolites may also generate potentially mutagenic oxygen radicals by metabolic redox cycling or other mechanisms. Several types of indirect DNA damage are caused by estrogen-induced oxidants, such as oxidized DNA bases, DNA strand breakage, and adduct formation by reactive aldehydes derived from lipid hydroperoxides. Estradiol and the synthetic estrogen diethylstilbestrol also induce numerical and structural chromosomal aberrations and several types of gene mutations in cells in culture and in vivo. In conclusion, estrogens, including the natural hormones estradiol and estrone, must be considered genotoxic carcinogens on the basis of the evidence outlined in this chapter.
Antioxidants and Phase 2 Enzymes in Macrophages: Regulation by Nrf2 Signaling and Protection Against Oxidative and Electrophilic Stress (2008)

Macrophages play important roles in immunity and other physiological processes. They are also target cells of various toxic agents, including oxidants and electrophiles. However, little is known regarding the molecular regulation and chemical inducibility of a spectrum of endogenous antioxidants and phase 2 enzymes in normal macrophages. Understanding the molecular pathway(s) controlling the coordinated expression of various macrophage antioxidants and phase 2 defenses is of importance for developing strategies to protect against macrophage injury induced by oxidants and electrophiles. Accordingly, this study was undertaken to determine the role of the nuclear factor E2-related factor 2 (Nrf2) in regulating both constitutive and chemoprotectant-inducible expression of various antioxidants and phase 2 enzymes in mouse macrophages. The constitutive expression of a series of antioxidants and phase 2 enzymes was significantly lower in macrophages derived from Nrf2-null (Nrf2(-/-)) mice than those from wild-type (Nrf2(+/+)) littermates. Incubation of wild-type macrophages with 3H-1,2-dithiole-3-thione (D3T) led to significant induction of various antioxidants and phase 2 enzymes, including catalase, glutathione, glutathione peroxidase (GPx), glutathione reductase, glutathione S-transferase, and NAD(P)H:quinone oxidoreductase 1. The inducibility of the above cellular defenses except for GPx by D3T was completely abolished in Nrf2(-/-) macrophages. As compared with wild-type cells, Nrf2(- /-) macrophages were much more susceptible to cell injury induced by reactive oxygen/nitrogen species, as well as two known macrophage toxins, acrolein and cadmium. Up-regulation of the antioxidants and phase 2 enzymes by D3T in wild-type macrophages resulted in increased resistance to the above oxidant-and electrophile-induced cell injury, whereas D3T treatment of Nrf2(- /-) macrophages provided only marginal or no cytoprotec-tion. This study demonstrates that Nrf2 is an indispensable factor in controlling both constitutive and inducible expression of a wide spectrum of antioxidants and phase 2 enzymes in macrophages as well as the susceptibility of these cells to oxidative and electrophilic stress.
Feasibility of production methods for succinic acid derivatives: a marriage of renewable resources and chemical technology (2008)

Abstract Succinic acid has recently received a great deal of attention in various publications and presentations when discussing the potential of renewable resources for the production of chemical building blocks. As a starting material for a number of conversions, it leads to important derivatives for various industrial branches. In this review, many suggested/published processes are analyzed and the feasibility of the processes toward industrial use in comparison with actual production routes has been evaluated. Derivatives that have a high probability of being successfully produced from succinic acid are tetrahydrofuran, γ‐butyrolactone and butanediol, as well as various pyrrolidones. Other nitrogen‐containing succinic acid derivatives, as well as its esters and salts, have various uses and can be used for further conversions. Succinate‐based surfactants and polymers are produced in large quantities. This review also contains a short overview of chemicals that might be produced from succinic acid, but the routes are still not economically feasible at this point and are only of academic interest at the moment. © 2008 Society of Chemical Industry and John Wiley &amp; Sons, Ltd
Isolation from cats of an endogenous type C virus with a novel envelope glycoprotein (1985)

A search for variant endogenous cat viruses led to a novel isolate. Although the major envelope glycoprotein of this virus was similar in size to that of an RD-114-like virus that was coisolated, it was unrelated to RD-114 or feline leukemia virus by immunological and biological criteria. This degree of dissimilarity suggests a different evolutionary progenitor from that for the RD-114 and feline leukemia virus viral envelopes. The novel virus did, however, code for gag gene polypeptides which are closely related to RD-114 virus. Neither the novel isolate nor the RD-114-like coisolate induced foci in S+L- cat cells which restrict focus induction by RD-114 virus. This suggests that the two viruses share a common genomic target of restriction which resides outside of the env region.
Chromatography of Amino Acids on Sulfonated Polystyrene Resins. An Improved System (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChromatography of Amino Acids on Sulfonated Polystyrene Resins. An Improved SystemStanford. Moore, D. H. Spackman, and W. H. SteinCite this: Anal. Chem. 1958, 30, 7, 1185–1190Publication Date (Print):July 1, 1958Publication History Published online1 May 2002Published inissue 1 July 1958https://doi.org/10.1021/ac60139a005Request reuse permissionsArticle Views1962Altmetric-Citations1742LEARN 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 InReddit PDF (820 KB) Get e-Alertsclose Get e-Alerts
Substances that rapidly augment ionic conductance of endothelium in cerebral venules (1986)

Classical techniques for studying modulations of microvascular permeability have a time resolution of minutes. A newly developed method allows continuous measurement of the electrical resistance of the microvascular membrane in vivo (Olesen & Crone 1983). The technique exploits microelectrodes impaled into the vascular lumen and is based on cable analysis of the vessel. It was applied to venules on the surface of the frog brain to test the effect on microvascular permeability of a wide variety of substances. The following agents increased ionic permeability reversibly within seconds: 5-hydroxytryptamine, bradykinin, ATP, ADP, AMP, phospholipase A2, arachidonic acid, leukotriene C4, oxygen-derived free radicals, ionophore A23187, and unbound Evans blue dye. An irreversible permeability increase was induced by protamine sulphate, neuraminidase, trypsin, melittin, and snake venoms from Crotalus durissus terrificus and Bothrops atrox. The following substances were without effect within an administration period of 5 min: histamine, epinephrine, putrescine, angiotensin II, vasoactive intestinal polypeptide (VIP), substance P, neurotensin, vasopressin, adenosine, PGE2, PGF2 alpha, prostacyclin (PGI2), leukotriene B4, albumin, heparin, plant cytokinins, hyaluronidase, thrombin, wasp venom. Variations in pH between 5.1 and 8.6 did not change permeability. Three conclusions are drawn from the observations: (1) the permeability of cerebral microvessels can be modulated by specific agents, (2) the agents induced changes in the endothelium within a few seconds, and (3) the rapid permeability increase induced by inflammatory mediators was less than two-fold and reversible within minutes.