cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Gymnotocinclus Carvalho & A. & Reis 2008, new genus
Creators: name: Carvalho, Tiago Pinto
name: A., Pablo Lehmann
name: Reis, Roberto E.
Publisher: name: Zenodo
Year: 2008
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Siluriformes
Loricariidae
Gymnotocinclus

description: Gymnotocinclus, new genus Type species: Gymnotocinclus anosteos, by original designation (Fig. 1). Diagnosis. Gymnotocinclus is distinguished from all other hypoptopomatine genera by the following uniquely derived features: (1) extreme reduction of body dermal plates (Fig. 2), (2) absence of the lateral connecting bone, (3) absence of bifid hemal spines on the abdominal vertebrae posterior to the first anal-fin proximal radial (Fig. 3), and (4) odontode tips on last dermal plates on the caudal peduncle dorsally or anteriorly curved (Fig. 4). Gymnotocinclus is also distinguished by a number of non-exclusive traits: maxillary barbel adnate to the lower lip; lateral ethmoid almost completely encapsulating the nasal organ (Fig. 5); ventral margin of preopercle straight, not deflected medially; pectoral girdle exposed and supporting odontodes only in a restricted lateral area near base of pectoral fin (Fig. 6); and absence of a pectoral-fin slit. Etymology. From the Greek Gymnos, naked, and Otocinclus, a genus of the Hypoptopomatinae, in allusion to the extreme reduction of the body encasing dermal plates.
description: Published as part of Carvalho, Tiago Pinto, A., Pablo Lehmann & Reis, Roberto E., 2008, Gymnotocinclus anosteos, a new uniquely-plated genus and species of loricariid catfish (Teleostei: Siluriformes) from the upper rio Tocantins basin, central Brazil, pp. 329-338 in Neotropical Ichthyology 6 (3) on page 330, DOI: 10.1590/S1679-62252008000300006, http://zenodo.org/record/5419740
ABO phenotype-protected reproduction based on human specific α1,2 L-fucosylations as explained by the Bombay type formation
Creators: name: Arend, Peter
Publisher: name: figshare
Year: 2017
Subjects: subject: Hematology
subject: Medicine
subject: Biochemistry
subject: Cancer
subject: Biological Techniques
subject: Immunology
subject: FOS: Clinical medicine
subject: Computational Chemistry
subject: Molecular Biology
subject: Stem Cells
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Anatomy

description: The molecular biological relations between the formation of the ABO(H) blood group phenotype and human fertility is evident in the rare (Oh) or Bombay blood type, which Charles Darwin would have interpreted as resulting from reduced male fertility in consanguinities, based on the history of his own family, the Darwin/Wedgewood Dynasty. The classic Bombay type occurs with the extremely rare and human specific genotype (h/h; se/se), which does not produce the fucosyltransferases FUT1and FUT2 encoded on chromosome 19 due to point mutations, and does not synthesize the fucosyl residues or H receptor, which in epistatic connection with the A- and B-allelic glycotransferases, encoded on chromosome 9, provides the structural basis for ABO(H) phenotype formation on the cell surfaces, secretions and functional plasma proteins. The innate isoagglutinins instead show extremely elevated levels of anti-H-reactive IgM, assumed to reflect the identical non-fucosylation of plasma proteins, and acting over a wide range of temperatures with an amplitude at 370C. The FUT1/FUT2-based ABO(H) plasma reactivity, which is strictly expressed according to the ABO(H) phenotype by A2M, shows the lowest levels in Bombay type individuals. In general, antibody avidity appears to be inversely proportional to the degree of glycosylation, and phenotypic glycosylation regulates the physiological anti-self reactivity of the germline-encoded IgM molecule. In contrast, the total lack of somatic phenotypic glycosylation will maintain the natural polyreactivity of this molecule, which while arising from the non-somatic glycosylation-deglycosylation processes during ESC-to-GC transformation and cell renewal, in the Bombay type individual remains exposed to these processes, suggesting aberrant glycosylations.
Credit Spreads, Business Conditions, and Expected Corporate Bond Returns
Creators: name: Lin, Hai
name: Tao, Xinyuan
name: Wang, Junbo
name: Wu, Chunchi
Publisher: name: Open Access Te Herenga Waka-Victoria University of Wellington
Year: 2022
Subjects: Uncategorized

description: Using an aggregate credit spread index, we find that it has substantial predictive power for corporate bond returns over short and long horizons. The return predictability is economically and statistically significant and robust to various controls. The credit spread index and its components have more predictive power for bond returns than conventional default and term spreads. When decomposing the credit spread index into investment- and speculative-grade components, the latter has more predictive power for future bond returns. The source of the index’s predictive power is from its ability to forecast future economic conditions.
Neogobius bathybius
Creators: name: Sayyadzadeh, Golnaz
name: Esmaeili, Hamid Reza
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Gobiidae
Neogobius
Neogobius bathybius

description: 241. Neogobius bathybius (Kessler, 1877)
Common name. Deepwater Goby
Taxonomy. Original description: Gobius bathybius Kessler 1877:17, pl. 1 (fig. 3) [Svinoi Island, south of Baky, Caspian Sea, Azerbaijan, 756 feet (108 Russian fathoms); holotype (unique): No types at ZIN].
Revisions. Zarei et al. (2021a).
Illustrations. Zarei et al. (2022a: 174, fig. 21).
Distribution in Iran. —Distribution in River Basin: Caspian Sea.—Distribution in Ecoregions: 452-Caspian Marine.
Status in Iran. [Native].—Gavmahi-e kafzi.—Listed in previous checklists from Iran by Eagderi et al. (2022).—Iran material: ZM-CBSU.
Conservation. —IUCN: LC.
description: Published as part of Sayyadzadeh, Golnaz & Esmaeili, Hamid Reza, 2024, Freshwater lamprey and fishes of Iran: Reappraisal and updated checklist with a note on Eagderi et al. (2022), pp. 1-99 in Zootaxa 5402 (1) on page 76, DOI: 10.11646/zootaxa.5402.1.1, http://zenodo.org/record/10524097
Testing commodity futures market efficiency under time-varying risk premiums and heteroscedastic prices
Creators: name: Kuruppuarachchi, D
name: Lin, Hai
name: Premachandra, IM
Publisher: name: Open Access Te Herenga Waka-Victoria University of Wellington
Year: 2022
Subjects: subject: 140299 Applied Economics not elsewhere classified
subject: FOS: Economics and business
subject: 150299 Banking, Finance and Investment not elsewhere classified
subject: 140399 Econometrics not elsewhere classified

description: We propose a novel test to measure market efficiency while estimating the time-varying risk premiums of commodity futures, given that the prices are heteroscedastic. The risk premium is estimated using a state-space model with a Kalman filter modified for heteroscedasticity. Using 79 commodity futures traded on 16 exchanges during the period 2000–2014 and a Monte Carlo simulation, we demonstrate that the proposal produces robust results compared with conventional approaches. The global financial crisis has improved the efficiency and affected the trading volumes of commodity futures, but it has had no effect on the average or the volatility of risk premiums.
Price discovery and persistent arbitrage violations in credit markets
Creators: name: Lin, Hai
name: Man, K
name: Wang, J
name: Wu, C
Publisher: name: Open Access Te Herenga Waka-Victoria University of Wellington
Year: 2022
Subjects: subject: 150299 Banking, Finance and Investment not elsewhere classified
subject: FOS: Economics and business

description: This paper investigates price violations in credit markets using a data sample spanning from 2002 to 2016. We find that price violations are highly persistent during the crisis period, particularly for speculative-grade bonds. There is evidence that price distortions and market disintegration are linked to market-wide and firm-level impediments to arbitrage and limited capital provision. Higher firm-level impediments to arbitrage lead to less market integration, and more severe and persistent pricing discrepancies. Moreover, we find that the negative CDS basis persists in the postcrisis period, which is attributable to dealers’ lower capital commitment and deterioration in market-making quality.
Does Whirling Disease Mediate Hybridization between a Native and Nonnative Trout?
Creators: name: Carim, Kellie
name: Eby, Lisa
name: Pierce, Ron
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Evolutionary Biology

description: The spread of nonnative species over the last century has profoundly altered freshwater ecosystems, resulting in novel species assemblages. Interactions between nonnative species may alter their impacts on native species, yet few studies have addressed multispecies interactions. The spread of whirling disease, caused by the nonnative parasite Myxobolus cerebralis, has generated declines in wild trout populations across western North America. Westslope Cutthroat Trout Oncorhynchus clarkii lewisi in the northern Rocky Mountains are threatened by hybridization with introduced Rainbow Trout O. mykiss. Rainbow Trout are more susceptible to whirling disease than Cutthroat Trout and may be more vulnerable due to differences in spawning location. We hypothesized that the presence of whirling disease in a stream would (1) reduce levels of introgressive hybridization at the site scale and (2) limit the size of the hybrid zone at the whole-stream scale. We measured levels of introgression and the spatial extent of hybridization between Rainbow Trout and Westslope Cutthroat Trout in four disease-positive streams and six disease-negative streams within the Blackfoot River basin of Montana. In addition to disease status, we considered habitat quality, stream slope, distance from the confluence, temperature, and elevation. Whirling disease presence was not associated with either the level of introgression at a site or the size of the hybrid zone. Temperature, elevation, and stream slope were all influential in determining levels of introgression at the site scale. Stream slope was the most influential factor determining the size of the hybrid zone, as longer, steeper streams contained smaller hybrid zones. Stream slope is a driver of many habitat characteristics that may provide refuge from invasive species in the coming decades. Although the multispecies interactions examined in this study did not alter the impacts of invasion on native species, community assemblages will continue to change with the spread of nonnative species, requiring continued assessment to determine their impacts on native species.Received May 15, 2014; accepted January 7, 2015
Predictive information in corporate bond yields
Creators: name: Guo, X
name: Lin, Hai
name: Wu, C
name: Zhou, G
Publisher: name: Open Access Te Herenga Waka-Victoria University of Wellington
Year: 2022
Subjects: subject: 150299 Banking, Finance and Investment not elsewhere classified
subject: FOS: Economics and business

description: We document strong evidence of the cross-sectional predictability of corporate bond returns based on a set of yield predictors that capture the information in the yields of past 1, 3, 6, 12, 24, 36, and 48 months. Return predictability is economically and statistically significant, and is robust to various controls. The uncovered predictability presents the most pronounced anomaly in the corporate bond literature that challenges rational pricing models.
ABO phenotype-protected reproduction based on human specific α1,2 L-fucosylations as explained by the Bombay type formation
Creators: name: Arend, Peter
Publisher: name: figshare
Year: 2017
Subjects: subject: Hematology
subject: Medicine
subject: Biochemistry
subject: Cancer
subject: Biological Techniques
subject: Immunology
subject: FOS: Clinical medicine
subject: Computational Chemistry
subject: Molecular Biology
subject: Stem Cells
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Anatomy

description: The molecular biological relationships between the formation of the ABO(H) blood group phenotype and human fertility is evident in the rare (Oh) or Bombay blood type, which Charles Darwin would have interpreted as resulting from reduced male fertility in consanguinities, based on the history of his own family, the Darwin/Wedgewood Dynasty. The classic Bombay type occurs with the extremely rare and human specific genotype (h/h; se/se), which does not produce the fucosyltransferases FUT1and FUT2 encoded on chromosome 19 due to point mutations, and does not synthesize the fucosyl residues or H receptor, which in epistatic connection with the A- and B-allelic glycotransferases, encoded on chromosome 9, provides the structural basis for ABO(H) phenotype formation on the cell surfaces, secretions and functional plasma proteins. The innate isoagglutinins instead show extremely elevated levels of anti-H-reactive IgM, assumed to reflect the identical non-fucosylation of plasma proteins, and acting over a wide range of temperatures with an amplitude at 370C. The FUT1/FUT2-based ABO(H) plasma reactivity, which is strictly expressed according to the ABO(H) phenotype by A2M, shows the lowest levels in Bombay type individuals. In general, antibody avidity appears to be inversely proportional to the degree of glycosylation, and phenotypic glycosylation regulates the physiological anti-self reactivity of the germline-encoded IgM molecule. In contrast, the total lack of somatic phenotypic glycosylation will maintain the natural polyreactivity of this molecule, which while arising from the non-somatic glycosylation-deglycosylation processes during ESC-to-GC transformation and cell renewal, in the Bombay type individual remains exposed to these processes, suggesting aberrant glycosylations.
Semantic linking of complex properties, monitoring processes and facilities in web-based representations of the environment
Creators: name: Leadbetter, Adam M.
name: Vodden, Peter N.
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: Where a virtual representation of the Earth must contain data values observed within the physical Earth system, data models are required that allow the integration of data across the silos of various Earth and environmental sciences domains. Creating a mapping between the well-defined terminologies of these silos is a stubborn problem. This paper presents a generalised ontology for use within Web 3.0 services, which builds on European Commission spatial data infrastructure models. The presented ontology acknowledges that there are many complexities to the description of environmental properties which can be observed within the physical Earth system. The ontology is shown to be flexible and robust enough to describe concepts drawn from a range of Earth science disciplines, including ecology, geochemistry, hydrology and oceanography. This paper also demonstrates the alignment and compatibility of the ontology with existing systems and shows applications in which the ontology may be deployed.
ABO phenotype-protected reproduction based on human specific α1,2 L-fucosylations as explained by the Bombay type formation
Creators: name: Arend, Peter
Publisher: name: figshare
Year: 2017
Subjects: subject: Hematology
subject: Medicine
subject: Biochemistry
subject: Cancer
subject: Biological Techniques
subject: Immunology
subject: FOS: Clinical medicine
subject: Computational Chemistry
subject: Molecular Biology
subject: Stem Cells
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Anatomy

description: The molecular biological relationships between the formation of the ABO(H) blood group phenotype and human fertility are evident in the rare (Oh) or Bombay blood type, which Charles Darwin would have interpreted as resulting from reduced male fertility in consanguinities, based on the history of his own family, the Darwin/Wedgewood Dynasty. The classic Bombay type occurs with the extremely rare and human specific genotype (h/h; se/se), which does not produce the fucosyltransferases FUT1and FUT2 encoded on chromosome 19 due to point mutations, and does not synthesize the fucosyl residues or H receptor, which in epistatic connection with the A- and B-allelic glycotransferases, encoded on chromosome 9, provides the structural basis for ABO(H) phenotype formation on the cell surfaces, secretions and functional plasma proteins. The innate isoagglutinins instead show extremely elevated levels of anti-H-reactive IgM, assumed to reflect the identical non-fucosylation of plasma proteins, and acting over a wide range of temperatures with an amplitude at 370C. The FUT1/FUT2-based ABO(H) plasma reactivity, which is strictly expressed according to the ABO(H) phenotype by A2M, shows the lowest levels in Bombay type individuals. In general, antibody avidity appears to be inversely proportional to the degree of glycosylation, and phenotypic glycosylation regulates the physiological anti-self reactivity of the germline-encoded IgM molecule. In contrast, the total lack of somatic phenotypic glycosylation will maintain the natural polyreactivity of this molecule, which while arising from the non-somatic glycosylation-deglycosylation processes during ESC-to-GC transformation and cell renewal, in the Bombay type individual remains exposed to these processes, suggesting aberrant glycosylations.
Volatility and jump risk in option returns
Creators: name: Guo, B
name: Lin, Hai
Publisher: name: Open Access Te Herenga Waka-Victoria University of Wellington
Year: 2022
Subjects: subject: 150299 Banking, Finance and Investment not elsewhere classified
subject: FOS: Economics and business

description: We examine the importance of volatility and jump risk in the time-series prediction of S&P 500 index option returns. The empirical analysis provides a different result between call and put option returns. Both volatility and jump risk are important predictors of put option returns. In contrast, only volatility risk is consistently significant in the prediction of call option returns over the sample period. The empirical results support the theory that there is option risk premium associated with volatility and jump risk, and reflect the asymmetry property of S&P 500 index distribution.
Semantic linking of complex properties, monitoring processes and facilities in web-based representations of the environment
Creators: name: Leadbetter, Adam M.
name: Vodden, Peter N.
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: Where a virtual representation of the Earth must contain data values observed within the physical Earth system, data models are required that allow the integration of data across the silos of various Earth and environmental sciences domains. Creating a mapping between the well-defined terminologies of these silos is a stubborn problem. This paper presents a generalised ontology for use within Web 3.0 services, which builds on European Commission spatial data infrastructure models. The presented ontology acknowledges that there are many complexities to the description of environmental properties which can be observed within the physical Earth system. The ontology is shown to be flexible and robust enough to describe concepts drawn from a range of Earth science disciplines, including ecology, geochemistry, hydrology and oceanography. This paper also demonstrates the alignment and compatibility of the ontology with existing systems and shows applications in which the ontology may be deployed.
Liquidity, informed trading, and a market surveillance system: Evidence from the Vietnamese stock market
Creators: name: Chen, R
name: Geng, Heng
name: Lin, Hai
name: Nguyen, PTL
Publisher: name: Open Access Te Herenga Waka-Victoria University of Wellington
Year: 2022
Subjects: subject: 150299 Banking, Finance and Investment not elsewhere classified
subject: FOS: Economics and business
subject: 150199 Accounting, Auditing and Accountability not elsewhere classified

description: This paper investigates the effectiveness of a market surveillance system (MSS) on improving the market quality of the Vietnamese stock market, as measured by liquidity and informed trading level. We find that market liquidity decreases after the introduction of the MSS, and that the effect is more pronounced for small firms. Although the level of informed trading, on average, does not change significantly after the MSS, the subsample analysis indicates a significant decrease in informed trading among large and liquid firms.
c-Myc is targeted to the proteasome for degradation in a SUMOylation-dependent manner, regulated by PIAS1, SENP7 and RNF4
Creators: name: González-Prieto, Román
name: Cuijpers, Sabine AG
name: Kumar, Ramesh
name: Hendriks, Ivo A
name: Vertegaal, Alfred CO
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Cancer
subject: Developmental Biology
subject: Molecular Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Cell Biology
subject: Biochemistry
subject: Biophysics

description: ABSTRACTc-Myc is the most frequently overexpressed oncogene in tumours, including breast cancer, colon cancer and lung cancer. Post-translational modifications comprising phosphorylation, acetylation and ubiquitylation regulate the activity of c-Myc. Recently, it was shown that c-Myc-driven tumours are strongly dependent on the SUMO pathway. Currently, the relevant SUMO target proteins in this pathway are unknown. Here we show that c-Myc is a target protein for SUMOylation, and that SUMOylated c-Myc is subsequently ubiquitylated and degraded by the proteasome. SUMO chains appeared to be dispensable for this process, since SUMO-polymer deficient mutants supported proteolysis of SUMOylated c-Myc. These results indicate that multiple SUMO monomers conjugated to c-Myc could be sufficient to direct SUMOylated c-Myc to the ubiquitin-proteasome pathway. Knocking down the SUMO-targeted ubiquitin ligase RNF4 enhanced the levels of SUMOylated c-Myc, indicating that RNF4 could recognize a multi-SUMOylated protein as a substrate in addition to poly-SUMOylated proteins. Knocking down the SUMO E3 ligase PIAS1 resulted in reduced c-Myc SUMOylation and increased c-Myc transcriptional activity, indicating that PIAS1 mediates c-Myc SUMOylation. Increased SUMOylation of c-Myc was noted upon knockdown of the SUMO protease SENP7, indicating that it also could regulate a multi-SUMOylated protein in addition to poly-SUMOylated proteins. C-Myc lacks KxE-type SUMOylation consensus motifs. We used mass spectrometry to identify ten SUMO acceptor lysines: K52, K148, K157, K317, K323, K326, K389, K392, K398 and K430. Intriguingly, mutating all 10 SUMO acceptor lysines did not reduce c-Myc SUMOylation, suggesting that SUMO acceptor lysines in c-Myc act promiscuously. Our results provide novel insight into the complexity of c-Myc post-translational regulation.
Recovery of the biological activity in a vineyard soil after landscape redesign: A three-year study using the bait-lamina method
Creators: name: Sturm Jr., M.
name: Sturm, M.
name: Eisenbeis, G.
Publisher: name: VITIS - Journal of Grapevine Research
Year: 2015

description: To detect changes in the biological activity (checked as soil animals feeding activity), the bait-lamina test (VON TÖRNE 1990) was used in a vineyard and a fallow soil (old meadow) during a three-year study. Situated in the vine-growing region of Rheinhessen near Mainz, Germany, the vineyard was part of an intensive redesign of the landscape accompanied by soil restoration. In 1994 new grapevines were planted in a two-row-system: 1) uncovered, 'open' soil, 2) green-covered soil (grass and clover). The new vineyard soil was in a 'raw' soil stage (humus: <1.7 %) whereas the fallow soil (reference soil) was undisturbed (humus: approx. 5 %). At the onset of the experiment in spring 1997 the soil faunal feeding activity in the vineyard soil was close to zero while in the fallow soil the activity was 23 %. In the following tests the feeding activity increased in both, the green-covered and uncovered soil; the highest level of feeding activity was finally found in the covered soil. The results indicate that under the local climatic conditions soil faunal activity recovers within a few years after soil restoration and that the rate of biological activity depends on soil management.
description: VITIS - Journal of Grapevine Research, Vol. 41 No. 1 (2002): Vitis
Synthesis and characterization of hetero-bimetallic complexes with 2-mercapto-5-methyl-benzimidazole: theoretical study and biological activities
Creators: name: Humaira Iqbal
name: Ali, Saqib
name: Saira Shahzadi
name: Sharma, Saroj K.
name: Kushal Qanungo
name: Shahid, Muhammad
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biological Sciences
subject: Chemistry
subject: Biotechnology
subject: Cell Biology
subject: Microbiology
subject: FOS: Biological sciences
subject: Biochemistry
subject: Biophysics

description: Heterobimetallic complexes have been synthesized by stirring 2-mercapto-5-methylbenzimidazole with carbon disulfide in methanol at room temperature. In the second step, the product was treated with R2SnCl2/R3SnCl (R = Me, n-Bu, Ph) in 1 : 1 M ratio, then organotin(IV) complexes were treated with HgCl2 in 2 : 1 M : L ratio to yield heterobimetallic complexes. The ligand and complexes have been characterized by elemental analysis, IR, 1H- and 13C NMR spectroscopy, mass spectrometry (EI-MS), and semiempirical study to assess the binding mode of the heterobimetallic complexes. IR data showed the bidentate nature of the dithiocarbamate moiety, which is also confirmed by semiempirical study. Mass spectra correspond to the expected for the complexes. NMR spectroscopy confirmed the four-coordinate geometry in solution. Computed molecular descriptors, thermodynamic parameters, and electrostatic surface potential map of 4 were calculated by using the PM6 method. Biological screening data indicated that complexes exhibit significant activity against various bacterial and fungal strains with few exceptions. Ligand and 6 are excellent for phagocyte reactive oxygen species inhibition.
Effect of red wine maceration techniques on oligomeric and polymeric proanthocyanidins in wine, cv. Blaufrankisch
Creators: name: Vrhovsek, U.
name: Vanzo, A.
name: Nemanic, J.
Publisher: name: VITIS - Journal of Grapevine Research
Year: 2015

description: The influence of duration of maceration, of different maceration temperatures during the last two days of maceration, and the effect of malolactic fermentation on the content of oligomeric and polymeric proanthocyanidins in wine, cv. Blaufränkisch, were investigated using spectrophotometric methods and the NP-HPLC procedure. Results show that the duration of maceration affected the extraction from seeds more strongly, while heating of must primarily affected the extraction from skins. An increase of temperature from 25°C to 35°C during the last two days of maceration increased total anthocyanins and high molecular weight proanthocyanidins. Malolactic fermentation lowered the color of wine, the amount of total anthocyanins and total polyphenols and may reduce polymerization reactions of proanthocyanidins.
description: VITIS - Journal of Grapevine Research, Vol. 41 No. 1 (2002): Vitis
ABO phenotype-protected reproduction based on human specific α1,2 L-fucosylation as explained by the Bombay type formation
Creators: name: Arend, Peter
Publisher: name: figshare
Year: 2017
Subjects: subject: Hematology
subject: Medicine
subject: Biochemistry
subject: Cancer
subject: Biological Techniques
subject: Immunology
subject: FOS: Clinical medicine
subject: Computational Chemistry
subject: Molecular Biology
subject: Stem Cells
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Anatomy

description: The molecular biological relationships between the formation of the ABO(H) blood group phenotype and human fertility are evident in the rare (Oh) or Bombay blood type, which Charles Darwin would have interpreted as resulting from reduced male fertility in consanguinities, based on the history of his own family, the Darwin/Wedgewood Dynasty. The classic Bombay type occurs with the extremely rare and human specific genotype (h/h; se/se), which does not produce the fucosyltransferases FUT1and FUT2 encoded on chromosome 19 due to point mutations, and does not synthesize the fucosyl residues or H receptor, which in epistatic connection with the A- and B-allelic glycotransferases, encoded on chromosome 9, provides the structural basis for ABO(H) phenotype formation on the cell surfaces, secretions and functional plasma proteins. The innate isoagglutinins instead show extremely elevated levels of anti-H-reactive IgM, assumed to reflect the identical non-fucosylation of plasma proteins, and acting over a wide range of temperatures with an amplitude at 370C. The FUT1/FUT2-based ABO(H) plasma reactivity, which is strictly expressed according to the ABO(H) phenotype by α2-macroglobulin, shows the lowest levels in Bombay type individuals. In general, antibody avidity appears to be inversely proportional to the degree of glycosylation, and phenotypic glycosylation regulates the physiological anti-self reactivity of the germline-encoded IgM molecule. In contrast, the total lack of somatic phenotypic glycosylation will maintain the natural polyreactivity of this molecule, which while arising from the non-somatic glycosylation-deglycosylation processes during embryogenic stem-to-germ cell transformation and/or cell renewal, in the Bombay type individual remains connected to these processes, suggesting aberrant glycosylations.
Effect of putrescine on embryo development in the stenospermocarpic grape cvs Emperatriz and Fantasy
Creators: name: Ponce, M. T.
name: Guiñazú, M.
name: Tizio, R.
Publisher: name: VITIS - Journal of Grapevine Research
Year: 2015

description: Research Note
description: VITIS - Journal of Grapevine Research, Vol. 41 No. 1 (2002): Vitis
Wild grapevine populations in the Ossa-Morena mountain range (Portugal-Spain): Location, characterization and sanitary state
Creators: name: Ocete, R.
name: Cantos, M.
name: López, M. A.
name: Gómez, I.
name: Troncoso, A.
Publisher: name: VITIS - Journal of Grapevine Research
Year: 2015

description: Research Note
description: VITIS - Journal of Grapevine Research, Vol. 41 No. 1 (2002): Vitis
USP7 deubiquitinase promotes ubiquitin-dependent DNA damage signaling by stabilizing RNF168
Creators: name: Qianzheng Zhu
name: Sharma, Nidhi
name: Jinshan He
name: Wani, Gulzar
name: Wani, Altaf A
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Cancer
subject: Developmental Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Genetics
subject: Cell Biology
subject: Microbiology
subject: Biochemistry
subject: Biophysics

description: During DNA damage response (DDR), histone ubiquitination by RNF168 is a critical event, which orchestrates the recruitment of downstream DDR factors, e.g. BRCA1 and 53BP1. Here, we report USP7 deubiquitinase regulates the stability of RNF168. We showed that USP7 disruption impairs H2A and ultraviolet radiation (UVR)-induced γH2AX monoubiquitination, and decreases the levels of pBmi1, Bmi1, RNF168 and BRCA1. The effect of USP7 disruption was recapitulated by siRNA-mediated USP7 depletion. The USP7 disruption also compromises the formation of UVR-induced foci (UVRIF) and ionizing radiation-induced foci (IRIF) of monoubiquitinated H2A (uH2A) and polyubiquitinated H2AX/A, and subsequently affects UVRIF and IRIF of BRCA1 as well as the IRIF of 53BP1. USP7 was shown to physically bind RNF168 in vitro and in vivo. Overexpression of wild-type USP7, but not its interaction-defective mutant, prevents UVR-induced RNF168 degradation. The USP7 mutant is unable to cleave Ub-conjugates of RNF168 in vivo. Importantly, ectopic expression of RNF168, or both RNF8 and RNF168 together in USP7-disrupted cells, significantly rescue the formation of UVRIF and IRIF of polyubiquitinated H2A and BRCA1. Taken together, these findings reveal an important role of USP7 in regulating ubiquitin-dependent signaling via stabilization of RNF168.
c-Myc is targeted to the proteasome for degradation in a SUMOylation-dependent manner, regulated by PIAS1, SENP7 and RNF4
Creators: name: González-Prieto, Román
name: Cuijpers, Sabine AG
name: Kumar, Ramesh
name: Hendriks, Ivo A
name: Vertegaal, Alfred CO
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Cancer
subject: Developmental Biology
subject: Molecular Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Cell Biology
subject: Biochemistry
subject: Biophysics

description: c-Myc is the most frequently overexpressed oncogene in tumors, including breast cancer, colon cancer and lung cancer. Post-translational modifications comprising phosphorylation, acetylation and ubiquitylation regulate the activity of c-Myc. Recently, it was shown that c-Myc-driven tumors are strongly dependent on the SUMO pathway. Currently, the relevant SUMO target proteins in this pathway are unknown. Here we show that c-Myc is a target protein for SUMOylation, and that SUMOylated c-Myc is subsequently ubiquitylated and degraded by the proteasome. SUMO chains appeared to be dispensable for this process, polymerization-deficient SUMO mutants supported proteolysis of SUMOylated c-Myc. These results indicate that multiple SUMO monomers conjugated to c-Myc could be sufficient to direct SUMOylated c-Myc to the ubiquitin-proteasome pathway. Knocking down the SUMO-targeted ubiquitin ligase RNF4 enhanced the levels of SUMOylated c-Myc, indicating that RNF4 could recognize a multi-SUMOylated protein as a substrate in addition to poly-SUMOylated proteins. Knocking down the SUMO E3 ligase PIAS1 resulted in reduced c-Myc SUMOylation and increased c-Myc transcriptional activity, indicating that PIAS1 mediates c-Myc SUMOylation. Increased SUMOylation of c-Myc was noted upon knockdown of the SUMO protease SENP7, indicating that it also could regulate a multi-SUMOylated protein in addition to poly-SUMOylated proteins. C-Myc lacks KxE-type SUMOylation consensus motifs. We used mass spectrometry to identify 10 SUMO acceptor lysines: K52, K148, K157, K317, K323, K326, K389, K392, K398 and K430. Intriguingly, mutating all 10 SUMO acceptor lysines did not reduce c-Myc SUMOylation, suggesting that SUMO acceptor lysines in c-Myc act promiscuously. Our results provide novel insight into the complexity of c-Myc post-translational regulation.
Computational studies of pandemic 1918 and 2009 H1N1 hemagglutinins bound to avian and human receptor analogs
Creators: name: P. Kolandaivel
name: S. Kannan
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: 60506 Virology
subject: FOS: Biological sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Information and Computing Sciences
subject: Biological Sciences
subject: Chemistry
subject: Evolutionary Biology
subject: Molecular Biology
subject: Biochemistry

description: The purpose of this work was to study the binding properties of two pandemic influenza A virus 1918 H1N1 (SC1918) and 2009 H1N1 (CA09) hemagglutinin (HA) with avian and human receptors. The quantum chemical calculations have been performed to analyze the interactions of 130 loop, 190 helix, 220 loop region, and conserved residues 95,145,153–155, of pandemic viruses’ HA with sialo-trisaccharide receptor of avian and human using density functional theory. The HA’s residues Tyr 95, Ala 138, Gln 191, Arg 220, and Asp 225 from the above regions have stronger interaction with avian receptor. The residues Thr 136, Trp 153, His 183, and Asp 190 of HA are important and play a significant role to bind with human receptor. The residues Tyr 95, Ala 138, Lys 145, Trp 153, Gln 192, and Gln 226 of HA of CA09 virus have found more interaction energies with human than avian receptors. Due to mutations in the active residues of HA of CA09 virus comparing with SC1918, the binding capabilities of HA with human have been increased. The molecular dynamics simulation was made to understand the different dynamical properties of HA and molecular interactions between HA of these two viruses with sialo-trisaccharide receptors of avian and human receptors. The interaction energy of HA of CA09 virus with human receptor decreases due to the human receptor far away from conserved residue region of HA protein. This reveals that the conserved residues particularly Lys 145 play major contribution to interaction with human receptor in HA of CA09 virus.
Synthesis and characterization of hetero-bimetallic complexes with 2-mercapto-5-methyl-benzimidazole: Theoretical study and biological activities
Creators: name: Humaira Iqbal
name: Ali, Saqib
name: Saira Shahzadi
name: Sharma, Saroj K.
name: Kushal Qanungo
name: Shahid, Muhammad
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biological Sciences
subject: Chemistry
subject: Biotechnology
subject: Cell Biology
subject: Microbiology
subject: FOS: Biological sciences
subject: Biochemistry
subject: Biophysics

description: Heterobimetallic complexes have been synthesized by stirring 2-mercapto-5-methylbenzimidazole with carbon disulfide in methanol at room temperature. In the second step, the product was treated with R2SnCl2/R3SnCl (R = Me, n-Bu, Ph) in 1:1 molar ratio, then organotin(IV) complexes were treated with HgCl2 in 2:1 M:L ratio to yield heterobimetallic complexes. The ligand and complexes have been characterized by elemental analysis, IR, 1H- and 13C-NMR spectroscopy, mass spectrometry (EI-MS) and semi-empirical study to assess the binding mode of the heterobimetallic complexes. IR data showed the bidentate nature of the dithiocarbamate moiety, which is also confirmed by semi-empirical study. Mass spectra correspond to the expected for the complexes. NMR spectroscopy confirmed the four-coordinate geometry in solution. Computed molecular descriptors, thermodynamic parameters and electrostatic surface potential map of 4 were calculated by using the PM6 method. Biological screening data indicated that complexes exhibit significant activity against various bacterial and fungal strains with few exceptions. Ligand and 6 are excellent for phagocyte reactive oxygen species inhibition.
USP7 deubiquitinase promotes ubiquitin-dependent DNA damage signaling by stabilizing RNF168*
Creators: name: Qianzheng Zhu
name: Sharma, Nidhi
name: Jinshan He
name: Wani, Gulzar
name: Wani, Altaf A
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Cancer
subject: Developmental Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Genetics
subject: Cell Biology
subject: Microbiology
subject: Biochemistry
subject: Biophysics

description: During DNA damage response (DDR), histone ubiquitination by RNF168 is a critical event, which orchestrates the recruitment of downstream DDR factors, e.g. BRCA1 and 53BP1. Here, we report USP7 deubiquitinase regulates the stability of RNF168. We showed that USP7 disruption impairs H2A and ultraviolet radiation (UVR)-induced γH2AX monoubiquitination, and decreases the levels of pBmi1, Bmi1, RNF168 and BRCA1. The effect of USP7 disruption was recapitulated by siRNA-mediated USP7 depletion. The USP7 disruption also compromises the formation of UVR-induced foci (UVRIF) and ionizing radiation-induced foci (IRIF) of monoubiquitinated H2A (uH2A) and polyubiquitinated H2AX/A, and subsequently affects UVRIF and IRIF of BRCA1 as well as the IRIF of 53BP1. USP7 was shown to physically bind RNF168 in vitro and in vivo. Overexpression of wild-type USP7, but not its interaction-defective mutant, prevents UVR-induced RNF168 degradation. The USP7 mutant is unable to cleave Ub-conjugates of RNF168 in vivo. Importantly, ectopic expression of RNF168, or both RNF8 and RNF168 together in USP7-disrupted cells, significantly rescue the formation of UVRIF and IRIF of polyubiquitinated H2A and BRCA1. Taken together, these findings reveal an important role of USP7 in regulating ubiquitin-dependent signaling via stabilization of RNF168.
c-Myc is targeted to the proteasome for degradation in a SUMOylation-dependent manner, regulated by PIAS1, SENP7 and RNF4
Creators: name: González-Prieto, Román
name: Cuijpers, Sabine AG
name: Kumar, Ramesh
name: Hendriks, Ivo A
name: Vertegaal, Alfred CO
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Developmental Biology
subject: Cancer
subject: Plant Biology

description: c-Myc is the most frequently overexpressed oncogene in tumors, including breast cancer, colon cancer and lung cancer. Post-translational modifications comprising phosphorylation, acetylation and ubiquitylation regulate the activity of c-Myc. Recently, it was shown that c-Myc-driven tumors are strongly dependent on the SUMO pathway. Currently, the relevant SUMO target proteins in this pathway are unknown. Here we show that c-Myc is a target protein for SUMOylation, and that SUMOylated c-Myc is subsequently ubiquitylated and degraded by the proteasome. SUMO chains appeared to be dispensable for this process, polymerization-deficient SUMO mutants supported proteolysis of SUMOylated c-Myc. These results indicate that multiple SUMO monomers conjugated to c-Myc could be sufficient to direct SUMOylated c-Myc to the ubiquitin-proteasome pathway. Knocking down the SUMO-targeted ubiquitin ligase RNF4 enhanced the levels of SUMOylated c-Myc, indicating that RNF4 could recognize a multi-SUMOylated protein as a substrate in addition to poly-SUMOylated proteins. Knocking down the SUMO E3 ligase PIAS1 resulted in reduced c-Myc SUMOylation and increased c-Myc transcriptional activity, indicating that PIAS1 mediates c-Myc SUMOylation. Increased SUMOylation of c-Myc was noted upon knockdown of the SUMO protease SENP7, indicating that it also could regulate a multi-SUMOylated protein in addition to poly-SUMOylated proteins. C-Myc lacks KxE-type SUMOylation consensus motifs. We used mass spectrometry to identify 10 SUMO acceptor lysines: K52, K148, K157, K317, K323, K326, K389, K392, K398 and K430. Intriguingly, mutating all 10 SUMO acceptor lysines did not reduce c-Myc SUMOylation, suggesting that SUMO acceptor lysines in c-Myc act promiscuously. Our results provide novel insight into the complexity of c-Myc post-translational regulation.
Detection of Pathogenic Bacteria in the Air by Culture Techniques in Combination with Multiplex Polymerase Chain Reaction
Creators: name: Wimon Chanchaem
Publisher: name: King Mongkut's Institute of Technology Ladkrabang
Year: 2020
Subjects: Airborne bacteria, Respiratory infections, Multiplex Polymerase Chain Reaction

description: Current Applied Science and Technology, 20, 3, 354-362
Neogobius caspius
Creators: name: Sayyadzadeh, Golnaz
name: Esmaeili, Hamid Reza
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Gobiidae
Neogobius
Neogobius caspius

description: 242. Neogobius caspius (Eichwald, 1831)
Common name. Caspian goby
Taxonomy. Original description: Gobius caspius Eichwald [C. E. von] 1831: 76 [Caspian Sea; No types known].
Revisions. Zarei et al. (2021a).
Illustrations. Zarei et al. (2022a: 175, fig. 23).
Distribution in iran. —Distribution in River Basin: Caspian Sea.—Distribution in Ecoregions: 452-Caspian Marine.
Status in Iran. [Native].—Gavmahi-e Khazari.—Listed in previous checklists from Iran by Esmaeili et al. (2017 a, 2018); Jouladeh-Roudbar et al. (2020) and Eagderi et al. (2022).—Iran material: ZM-CBSU.
Conservation. —IUCN: LC.
description: Published as part of Sayyadzadeh, Golnaz & Esmaeili, Hamid Reza, 2024, Freshwater lamprey and fishes of Iran: Reappraisal and updated checklist with a note on Eagderi et al. (2022), pp. 1-99 in Zootaxa 5402 (1) on page 76, DOI: 10.11646/zootaxa.5402.1.1, http://zenodo.org/record/10524097
Neogobius melanostomus
Creators: name: Sayyadzadeh, Golnaz
name: Esmaeili, Hamid Reza
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Gobiidae
Neogobius
Neogobius melanostomus

description: 243. Neogobius melanostomus (Pallas, 1814)
Common name. Round goby
Taxonomy. Original description: Gobius melanostomus Pallas, 1814: 151 [Sebvastopol, Crimea, Ukraine; Balaklava, Ukraine; syntypes: whereabouts unknown].
Revisions. Zarei et al. (2021a).
Illustrations. Zarei et al. (2022a: 175, fig. 24).
Distribution in Iran. —Distribution in River Basin: Caspian Sea.—Distribution in Ecoregions: 434-Kura-South Caspian Drainages, 452-Caspian Marine.
Status in Iran. [Native].—Gavmahi-e domgerd.—Listed in previous checklists from Iran by Esmaeili et al. (2017 a, 2018); Jouladeh-Roudbar et al. (2020) and Eagderi et al. (2022).—Iran material: ZM-CBSU.
Conservation. —IUCN: LC.
description: Published as part of Sayyadzadeh, Golnaz & Esmaeili, Hamid Reza, 2024, Freshwater lamprey and fishes of Iran: Reappraisal and updated checklist with a note on Eagderi et al. (2022), pp. 1-99 in Zootaxa 5402 (1) on page 76, DOI: 10.11646/zootaxa.5402.1.1, http://zenodo.org/record/10524097
USP7 deubiquitinase promotes ubiquitin-dependent DNA damage signaling by stabilizing RNF168*
Creators: name: Qianzheng Zhu
name: Sharma, Nidhi
name: Jinshan He
name: Wani, Gulzar
name: Wani, Altaf A
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer

description: During DNA damage response (DDR), histone ubiquitination by RNF168 is a critical event, which orchestrates the recruitment of downstream DDR factors, e.g. BRCA1 and 53BP1. Here, we report USP7 deubiquitinase regulates the stability of RNF168. We showed that USP7 disruption impairs H2A and ultraviolet radiation (UVR)-induced γH2AX monoubiquitination, and decreases the levels of pBmi1, Bmi1, RNF168 and BRCA1. The effect of USP7 disruption was recapitulated by siRNA-mediated USP7 depletion. The USP7 disruption also compromises the formation of UVR-induced foci (UVRIF) and ionizing radiation-induced foci (IRIF) of monoubiquitinated H2A (uH2A) and polyubiquitinated H2AX/A, and subsequently affects UVRIF and IRIF of BRCA1 as well as the IRIF of 53BP1. USP7 was shown to physically bind RNF168 in vitro and in vivo. Overexpression of wild-type USP7, but not its interaction-defective mutant, prevents UVR-induced RNF168 degradation. The USP7 mutant is unable to cleave Ub-conjugates of RNF168 in vivo. Importantly, ectopic expression of RNF168, or both RNF8 and RNF168 together in USP7-disrupted cells, significantly rescue the formation of UVRIF and IRIF of polyubiquitinated H2A and BRCA1. Taken together, these findings reveal an important role of USP7 in regulating ubiquitin-dependent signaling via stabilization of RNF168.