cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Using Chou’s 5-steps rule to identify N6-methyladenine sites by ensemble learning combined with multiple feature extraction methods
Creators: name: Zhang, Zhongwang
name: Wang, Lidong
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics

description: N6-methyladenine (m6A), a type of modification mostly affecting the downstream biological functions and determining the levels of gene expression, is mediated by the methylation of adenine in nucleic acids. It is also a key factor for influencing biological processes and has attracted attention as a target for treating diseases. Here, an ensemble predictor named as TL-Methy, was developed to identify m6A sites across the genome. TL-Methy is a 2-level machine learning method developed by combining the support vector machine model and multiple features extraction methods, including nucleic acid composition, di-nucleotide composition, tri-nucleotide composition, position-specific trinucleotide propensity, Bi-profile Bayes, binary encoding, and accumulated nucleotide frequency. For Homo sapiens, TL-Methy method reached the accuracy of 91.68% on jackknife test and of 92.23% on 10-fold cross validation test; For Mus musculus, TL-Methy method achieved the accuracy of 93.66% on jackknife test and of 97.07% on 10-fold cross validation test; For Saccharomyces cerevisiae, TL-Methy method obtained the accuracy of 81.57% on jackknife test and of 82.54% on 10-fold cross validation test; For rice genome, TL-Methy method achieved the accuracy of 91.87% on jackknife test and of 93.04% on 10-fold cross validation test. The results via these two test approaches demonstrated the robustness and practicality of our TL-Methy model. The TL-Methy model may be as a potential method for m6A site identification. Communicated by Ramaswamy H. Sarma
Silbomyia Macquart 1843
Creators: name: Colless, D. H.
Publisher: name: Zenodo
Year: 1998
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Calliphoridae
Silbomyia

description: Genus Silbomyia Macquart The genus is largely Oriental, distributed from India and China to Timor. In Australia, one species (S. minor, known from a unique female) is recorded from north Queensland and one (S. palpalis, knownfrom 3 males) fromnorthwestern Australia. The genus does not seem well characterised, but I have too little material to attempt a revision.
description: Published as part of Colless, D. H., 1998, Morphometrics in the genus Amenia and revisionary notes on the Australian Ameniinae (Diptera: Calliphoridae), with the description of eight new species, pp. 85-123 in Records of the Australian Museum 50 (1) on page 97, DOI: 10.3853/j.0067-1975.50.1998.1275, http://zenodo.org/record/4652889
A Comparative Study Between a Micromechanical Cantilever Resonator and MEMS-based Passives for Band-pass Filtering Application
Creators: name: Basu, J.
name: Bhattacharya, A.
name: Chakraborty, S.
name: Bhattacharyya, T. K.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Other Computer Science (cs.OH)
subject: FOS: Computer and information sciences

description: Over the past few years, significant growth has been observed in using MEMS based passive components in the RF microelectronics domain, especially in transceiver components. This is due to some excellent properties of the MEMS devices like low loss, excellent isolation etc. in the microwave frequency domain where the on-chip passives normally tend to become leakier and degrades the transceiver performance. This paper presents a comparative analysis between MEMS-resonator based and MEMS-passives based band-pass filter configurations for RF applications, along with their design, simulation, fabrication and characterization. The filters were designed to have a center frequency of 455 kHz, meant for use as the intermediate frequency (IF) filter in superheterodyne receivers. The filter structures have been fabricated in PolyMUMPs process, a three-polysilicon layer surface micromachining process.
description: 6 pages, 15 figures
Heavy quark & direct photon production and heavy quark parton densities
Creators: name: Stavreva, T.
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Direct photon production in association with a heavy quark can serve as an excellent tool for the study of the heavy quark distributions. Currently it is believed that heavy quarks are produced radiatively inside the nucleon, and so there is no need to take into account heavy quark parameters inside global PDF analyses. Certain models taking into account the possibility of an intrinsic charm component exist. Here we present how these affect the γ+ c cross section. While at pA collisions the potential of this process to constrain the gluon nuclear PDF which is currently largely unconstrained is presented.
description: Quarkonium 2010 Proceedings
Evidence Against an Edge-On Disk Around the Extrasolar Planet 2MASS 1207 b and a New Thick Cloud Explanation for its Under-Luminosity
Creators: name: Skemer, Andrew J.
name: Close, Laird M.
name: Szűcs, László
name: Apai, Dániel
name: Pascucci, Ilaria
name: Biller, Beth A.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: (Abridged) Since the discovery of the first directly-imaged, planetary-mass object, 2MASS 1207 b, several works have sought to explain a disparity between its observed temperature and luminosity. Given its known age, distance, and spectral type, 2MASS 1207 b is under-luminous by a factor of ~10 (~2.5 mags) when compared to standard models of brown-dwarf/giant-planet evolution. In this paper, we study three possible sources of 2MASS 1207 b's under-luminosity. First, we investigate Mohanty et al. (2007)'s hypothesis that a near edge-on disk might be responsible for 2MASS 1207 b's under-luminosity. We conclude that the hypothesis is unlikely due to the lack of variability seen in multi-epoch photometry and unnecessary due to the increasing sample of under-luminous brown-dwarfs/giant-exoplanets that cannot be explained by an edge-on disk. Next, we test the analogous possibility that a spherical shell of dust, could explain 2MASS 1207 b's under-luminosity. Models containing enough dust to create ~2.5 mags of extinction, placed at reasonable radii, are ruled out by our new Gemini/T-ReCS 8.7 micron photometric upper-limit for 2MASS 1207 b. Finally, we investigate the possibility that 2MASS 1207 b is intrinsically cooler than the commonly used AMES-DUSTY fits to its spectrum, and thus it is not, in fact, under-luminous. New, thick cloud model grids by Madhusudhan et al. (2011) fit 2MASS 1207 b's 1-10 micron SED well, but they do not quite fit its near-infrared spectrum. However, we suggest that with some "tuning", they might be capable of simultaneously reproducing 2MASS 1207 b's spectral shape and luminosity. In this case, the whole class of young, under-luminous brown-dwarfs/giant-exoplanets might be explained by atmospheres that are able to suspend thick, dusty clouds in their photospheres at lower temperatures than field brown-dwarfs.
description: 35 pages, 9 figures, accepted to ApJ
Lasing oscillation in a three-dimensional photonic crystal nanocavity with a complete bandgap
Creators: name: Tandaechanurat, Aniwat
name: Ishida, Satomi
name: Guimard, Denis
name: Nomura, Masahiro
name: Iwamoto, Satoshi
name: Arakawa, Yasuhiko
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We demonstrate lasing oscillation in a three-dimensional photonic crystal nanocavity. The laser is realized by coupling a cavity mode, which is localized in a complete photonic bandgap and exhibits the highest quality factor of ~38,500, with high-quality semiconductor quantum dots. We show a systematic change in the laser characteristics, including the threshold and the spontaneous emission coupling factor by controlling the crystal size, which consequently changes the strength of photon confinement in the third dimension. This opens up many interesting possibilities for realizing future ultimate light sources and three-dimensional integrated photonic circuits and for more fundamental studies of physics in the field of cavity quantum electrodynamics.
description: 14 pages, 4 figures
Silbomyia palpalis Crosskey
Creators: name: Colless, D. H.
Publisher: name: Zenodo
Year: 1998
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Calliphoridae
Silbomyia
Silbomyia palpalis

description: Silbomyia palpalis Crosskey I have seen one additional specimen, from the same general area as the type-locality: "W. bank of Turner R. above Kunagunarrina Pool, S. of Port Hedland, W.A., 25 June 1980, B. Duckworth. Map. Ref. = Marble Bar SF50-8- 344:155" (AM). It was reared by the collector from a snail, a species of "Quistrachia" (ms name). For the 3 known specimens, the M-bend index (as defined above) is 2.3-4.0.
description: Published as part of Colless, D. H., 1998, Morphometrics in the genus Amenia and revisionary notes on the Australian Ameniinae (Diptera: Calliphoridae), with the description of eight new species, pp. 85-123 in Records of the Australian Museum 50 (1) on page 97, DOI: 10.3853/j.0067-1975.50.1998.1275, http://zenodo.org/record/4652889
Improved and Quality-assessed Emission and Absorption Line measurements in Sloan Digital Sky Survey galaxies
Creators: name: Oh, Kyuseok
name: Sarzi, Marc
name: Schawinski, Kevin
name: Yi, Sukyoung K.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present a new database of absorption and emission-line measurements based on the entire spectral atlas from the Sloan Digital Sky Survey (SDSS) 7th data release of galaxies within a redshift of 0.2. Our work makes use of the publicly available penalized pixel-fitting(pPXF) and gas and absorption line fitting (gandalf) IDL codes, aiming to improve the existing measurements for stellar kinematics, the strength of various absorption-line features, and the flux and width of the emissions from different species of ionised gas. Our fit to the stellar continuum uses both standard stellar population models and empirical templates obtained by combining a large number of stellar spectra in order to fit a subsample of high-quality SDSS spectra for quiescent galaxies. Furthermore, our fit to the nebular spectrum includes an exhaustive list of both recombination and forbidden lines. Foreground Galactic extinction is implicitly treated in our models, whereas reddening in the SDSS galaxies is included in the form of a simple dust screen component affecting the entire spectrum that is accompanied by a second reddening component affecting only the ionised gas emission. In order to check for systematic departures, we provide a quality assessment for our fit to the SDSS spectra in our sample. This quality assessment also allows the identification of objects with either problematic data or peculiar features. For example, based on the quality assessment, approximately 1% of the SDSS spectra classified as "galaxies" by the SDSS pipeline do in fact require additional broad lines to be matched, even though they do not show a strong continuum from an active nucleus, as do the SDSS objects classified as "quasars". Finally, we provide new spectral templates for galaxies of different Hubble types, obtained by combining the results of our spectral fit for a subsample of 452 morphologically selected objects.
description: Accepted for publication in ApJS. 23 pages, 14 figures, 4 tables. A version with high-resolution figures is available at http://gem.yonsei.ac.kr/~ksoh/ossy/arXiv/Oh_11_OSSY.pdf
Stilbomyella Malloch 1935
Creators: name: Colless, D. H.
Publisher: name: Zenodo
Year: 1998
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Calliphoridae
Stilbomyella

description: Genus Stilbomyella Malloch The genus was hitherto known from the Moluccas to New Britain. As predicted by Crosskey (1965), it does occur in Australia as well, and I describe below two new species from North Queensland. One closely resembles the New Guinean S. gloriosa (Walk.) (= S. nigrocostalis (Doleschall), synonymy by Kurahashi (1989 ». The other is more distinct, but is, I think, best placed in this genus.
description: Published as part of Colless, D. H., 1998, Morphometrics in the genus Amenia and revisionary notes on the Australian Ameniinae (Diptera: Calliphoridae), with the description of eight new species, pp. 85-123 in Records of the Australian Museum 50 (1) on page 97, DOI: 10.3853/j.0067-1975.50.1998.1275, http://zenodo.org/record/4652889
description: {"references": ["Crosskey, R. W., 1965. A systematic revision of the Ameniinae (Diptera: Calliphoridae). Bulletin of the British Museum (Natural History) Entomology 16: 33 - 140.", "Kurahashi, H., 1989. 109. Family Calliphoridae. In (N. Evenhuis, ed.) Catalog of the Diptera of the Australasian and Oceanic Regions Bishop Museum Special Publication 86. Bishop Museum Press and EJ. Brill: Honolulu and Leiden."]}
Family in three stories and an examination of influences
Creators: name: Haines Zuckero, Erika
Publisher: name: No Publisher Supplied
Year: 2019

description: The motivation for this Capstone in Creative Fiction is two-fold: first, my goal is to expand my understanding of the fiction mechanism by working in the medium; second, my goal is to delve into my own experience with creative works to find what sources have influenced my writing. Under the guidance of Professor Grodstein, I was able to turn my research into introspection that answered two questions: why I chose to write fiction and why this is important. Additionally, family is an unquestionable root for later life choices and motivations, and for this reason I based my stories on both a strict and a loose definition of “family,” with each story hoping to untangle the threads of human experience within that web. Because the stories are relatively brief, they allow for quicker plot acceleration and a more narrowed focus on individual moments or scenes, thus exposing in each story what defines family and its respective weight to the plot. Through my research and inner examination, I learned that in order to write fiction, one must read and experience creative works constantly, as it would rarely be possible to write something without being in some way influenced by other art. As noted by Professor Grodstein, there is rarely a direct translation from works read to works written in style or content; but reading and viewing widely (some, but not all of my influences are listed in this Capstone examination) allow the writer to sense the nuances in texts for internal rhythms, clear descriptions, and precise prose. Through fiction, the hope is that realities about the non-fiction world in which we live can be explored, clarified, and beautified. Just as poetry allows writers to deal with difficult emotions and emerge whole, so does fiction allow writers to explore situations that demand further clarification and emerge intact. My consistent access to the best of the written word has been a privilege I do not take for granted, and this Capstone is an exploration of that privilege as well as a culmination of years of dedication to my work.
Proteome-wide mapping and reverse vaccinology-based B and T cell multi-epitope subunit vaccine designing for immune response reinforcement against Porphyromonas gingivalis
Creators: name: Khan, Shahzeb
name: Ali, Syed Shujait
name: Zaheer, Iqra
name: Saleem, Shoaib
name: Ziaullah
name: Zaman, Nasib
name: Iqbal, Arshad
name: Suleman, Muhammad
name: Wadood, Abdul
name: Rehman, Ashfaq Ur
name: Khan, Asghar
name: Khan, Abbas
name: Wei, Dong-Qing
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Porphyromonas gingivalis, a prominent pathogen responsible for acute periodontal diseases, is widely studied by the scientific community for its successful evasion of the host immune system. P. gingivalis is associated with rheumatoid arthritis, dementia, and Alzheimer's. The pathogen successfully survives itself against the heavy load of conventional antibiotics because of its ability to evade the host immune system. Subtractive proteomics and reverse vaccinology approaches were employed in order to prioritize the best proteins for vaccine designing. Three vaccine candidates with Uniprot ID: Q7MWZ2 (histidine Kinase), Q7MVL1 (Fe (2+) transporter), and Q7MWZ2 (Capsular polysaccharide transport protein) were identified for vaccine designing. These proteins are antigenic and essential for pathogen survival. A wide range of immunoinformatics tools was applied for the prediction of epitopes, B, and T cells, for the vaccine candidate proteins. Molecular docking of the predicted epitopes against the MHC molecules were carried out. In-silico vaccine was constructed using carefully evaluated epitopes and consequently modeled for docking with human Toll-like receptor 2. Chain C of Pam3CSK4 (PDB ID; 2Z7X) was linked to the vaccine as an adjuvant to boost immune response towards the vaccine. For stability evaluation of the vaccine-TLR-2 docked complex, Molecular Dynamics simulations were performed. The reverse-translated nucleotide sequence cloned in Eschericia coli to attain the maximal expression of the vaccine protein. The maximal expression was ensured by CAI score of 0.96. The current vaccine requires future experimental validation to confirm its effectiveness. The vaccine developed will be helpful to protect against P. gingivalis associated infections. Communicated by Ramaswamy H. Sarma
A visual attention model for high dynamic range (HDR) video content
Creators: name: Dong, Yuanyuan
Publisher: name: University of British Columbia
Year: 2015

description: High dynamic range (HDR) imaging is gaining widespread acceptance in computer graphics, photography and multimedia industry. Representing scenes with values corresponding to real-world light levels, HDR images and videos provide superior picture quality and more life-like visual experience than traditional 8-bit Low Dynamic Range (LDR) content. In this thesis, we present a few attempts to assess and improve the quality of HDR using subjective and objective approaches. We first conducted in-depth studies regarding HDR compression and HDR quality metrics. We show that High Efficiency Video Coding (HEVC) outperforms the previous version of compression standard on HDR content and could be used as a platform for HDR compression if provided with some necessary extensions. We also find that, compared to other quality metrics, the Visual Information Fidelity (VIF) quality metric has the highest correlation with subjective opinions on HDR videos. These findings contributed to the development of methods that optimize existing video compression standards for HDR applications. Next, the viewing experience of HDR content is evaluated both subjectively and objectively. The study shows a clear subjective preference for HDR content when individuals are given a choice between HDR and LDR displays. Eye tracking data were collected from individuals viewing HDR content in a free-viewing task. These eye tracking data collected are utilized in the development of a visual attention model for HDR content. Last but not least, we propose a computational approach to predict visual attention for HDR video content, the only one of its kind as all existing visual attention models are designed for HDR images. This proposed approach simulates the characteristics of the Human Visual System (HVS) and makes predictions by combining the spatial and temporal visual features. The analysis using eye tracking data affirms the effectiveness of the proposed model. Comparisons employing three well known quantitative metrics show that the proposed model substantially improves predictions of visual attention of HDR.
Stilbomyella crosskeyi Colless 1998, n.sp.
Creators: name: Colless, D. H.
Publisher: name: Zenodo
Year: 1998
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Calliphoridae
Stilbomyella
Stilbomyella crosskeyi

description: Stilbomyella crosskeyi n.sp. Holotype: male; 15°47'S 145°14'E, Shiptons Flat, Queensland, 18 October 1980, D.H. Colless, (at light). ANIC No. 6151. The locality is a little south of Cooktown, north Queensland. Other specimens examined. QUEENSLAND. 40 0, same data as holotype, but colI. 19 October 1980. Coomera River, Lamington NP, 1200 ft, 28 May 1966, Z. Liepa, 1 Y. NEW SOUTH WALES. 28°42'S 153°17'E, 1 km E Mt Warning, 500 m, 22 November 1976, LF. B. Common & E.D. Edwards, 1 o. The last two specimens are not paratypes. Very similar to S. gloriosa, as described by Crosskey (1965; as nigrocostalis), but differing as follows: Male. Body length 6.8-8.8, mean 7.5 mm (6 specimens). Head. Carina (in frontal view) slightly "pinched" above epistome, sides parallel or slightly tapering ventrally on ventral half, a little longer than lunula to anterior ocellus. Gnw 0.4-0.5 of Eyh, mean 0.43 (7 specimens) (two New Guinea gloriosa average 0.48). Antennal segment 3 relatively short, 0.3 of Hdw (two New Guinea gloriosa average 0.2), usually at most a little shorter than arista. Thorax. Propleuron bare. Wing. M-bend index 0.8-0.9. Legs. Mid tibia with only 1 strong ad. Abdomen. T3 and T5 with conspicuous pale silvery spots laterally on the ventrally curved part of the tergite. Genitalia very similar to those of gloriosa (Crosskey, 1965: fig. 37), but cerci distinctly longer than surstyles. Female. Secondary sexual differences as for gloriosa. Otherwise resembling the male (but see below). Notes. The above refers to specimens from the type locality. Another male from Mt Warning, New South Wales, has A3 much shorter, only 0.2 of Hdw, and therefore much shorter than the arista (as in S. gloriosa), and 2 strong ad on the mid tibia. A female from Lamington NP has the same features. Both, however, have the conspicuous pale spots on T 3 and T 5 that provide the most striking difference from S. gloriosa, and I am tentatively placing them as S. crosskeyi.
description: Published as part of Colless, D. H., 1998, Morphometrics in the genus Amenia and revisionary notes on the Australian Ameniinae (Diptera: Calliphoridae), with the description of eight new species, pp. 85-123 in Records of the Australian Museum 50 (1) on pages 97-98, DOI: 10.3853/j.0067-1975.50.1998.1275, http://zenodo.org/record/4652889
description: {"references": ["Crosskey, R. W., 1965. A systematic revision of the Ameniinae (Diptera: Calliphoridae). Bulletin of the British Museum (Natural History) Entomology 16: 33 - 140."]}
Mechanistic insight of DACH1 receptor in the development of carcinoma insurgence through MD simulation studies
Creators: name: Hassan, Mubashir
name: Zahid, Sara
name: Shahzadi, Saba
name: Malik, Erum
name: Zaib, Sumera
name: Iqbal, Jamshed
name: Shamim, Saba
name: Malik, Arif
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Proteins are key player in the prognosis and therapeutics of carcinomas through the interactions of downstream signalling cascades. Current work insight the structural and mutational analysis of DACH1 in association with carcinogenesis. The homology modelling was employed to predict mutant and wild protein models and their reliability and accuracy was verified through multiple online approaches. Furthermore, MD simulation technique was employed to check the mutation effects on the stability of DACH1 through root mean square deviation and fluctuation graphs. Our results proposed that DACH1 mutation (C188Y) may cause lethal effects and can disturb the DACH1 structure. The observed mutational results showed that C188Y may cause some lethal effect in human body. Based on aforementioned computational assessments, it has concluded that DACH1 could be used as good therapeutic target in the prognosis and therapeutic of carcinoma insurgence. Communicated by Ramaswamy H. Sarma
Constraining Selectron LSP Scenarios with Tevatron Trilepton Searches
Creators: name: Dreiner, H. K.
name: Grab, S.
name: Stefaniak, T.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: The Tevatron collaborations have searched for associated production of charginos and neutralinos via trilepton final states. No events above the Standard Model prediction were observed. We employ these results to put stringent bounds on R-parity violating models with a right-handed scalar electron as the lightest supersymmetric particle. We work in the framework of lepton number violating minimal supergravity. We find that within these models the complete parameter space consistent with the anomalous magnetic moment of the muon can be excluded at 90% confidence level. We also give prospects for Tevatron trilepton searches assuming an integrated luminosity of 10 fb^{-1}. We find that Tevatron will be able to test selectron LSP masses up to 170 GeV.
description: 12 pages, 3 figures
Towards the Design of Heuristics by Means of Self-Assembly
Creators: name: Terrazas, German
name: Landa-Silva, Dario
name: Krasnogor, Natalio
Publisher: name: arXiv
Year: 2010
Subjects: subject: Artificial Intelligence (cs.AI)
subject: Neural and Evolutionary Computing (cs.NE)
subject: FOS: Computer and information sciences

description: The current investigations on hyper-heuristics design have sprung up in two different flavours: heuristics that choose heuristics and heuristics that generate heuristics. In the latter, the goal is to develop a problem-domain independent strategy to automatically generate a good performing heuristic for the problem at hand. This can be done, for example, by automatically selecting and combining different low-level heuristics into a problem specific and effective strategy. Hyper-heuristics raise the level of generality on automated problem solving by attempting to select and/or generate tailored heuristics for the problem at hand. Some approaches like genetic programming have been proposed for this. In this paper, we explore an elegant nature-inspired alternative based on self-assembly construction processes, in which structures emerge out of local interactions between autonomous components. This idea arises from previous works in which computational models of self-assembly were subject to evolutionary design in order to perform the automatic construction of user-defined structures. Then, the aim of this paper is to present a novel methodology for the automated design of heuristics by means of self-assembly.
Gauge fields and interferometry in folded graphene
Creators: name: Rainis, Diego
name: Taddei, Fabio
name: Polini, Marco
name: Leon, Gladys
name: Guinea, Francisco
name: Fal'ko, Vladimir I.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Folded graphene flakes are a natural byproduct of the micromechanical exfoliation process. In this Letter we show by a combination of analytical and numerical methods that such systems behave as intriguing interferometers due to the interplay between an externally applied magnetic field and the gauge field induced by the deformations in the region of the fold.
description: 4 pages, 3 figures
Potential protease inhibitors and their combinations to block SARS-CoV-2
Creators: name: Abhinand, Chandran S.
name: Nair, Achuthsankar S.
name: Krishnamurthy, Anand
name: Oommen, Oommen V.
name: Sudhakaran, Perumana R.
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: COVID-19, which has emerged recently as a pandemic viral infection caused by SARS-coronavirus 2 has spread rapidly around the world, creating a public health emergency. The current situation demands an effective therapeutic strategy to control the disease using drugs that are approved, or by inventing new ones. The present study examines the possible repurposing of existing anti-viral protease inhibitor drugs. For this, the structural features of the viral spike protein, the substrate for host cell protease and main protease of the available SARS CoV-2 isolates were established by comparing with related viruses for which antiviral drugs are effective. The results showed 97% sequence similarity among SARS and SARS-CoV-2 main protease and has same cleavage site positions and ACE2 receptor binding region as in the SARS–CoV spike protein. Though both are N-glycosylated, unlike SARS-CoV, human SARS-CoV-2 S-protein was O-glycosylated as well. Molecular docking studies were done to explore the role of FDA approved protease inhibitors to control SARS-CoV-2 replication. The results indicated that, Ritonavir has the highest potency to block SARS-CoV-2 main protease and human TMPRSS2, a host cell factor that aids viral infection. Other drugs such as Indinavir and Atazanavir also showed favourable binding with Cathepsin B/L that helped viral fusion with the host cell membrane. Further molecular dynamics simulation and MM-PBSA binding free energy calculations confirmed the stability of protein-drug complexes. These results suggest that protease inhibitors particularly Ritonavir, either alone or in combination with other drugs such as Atazanavir, have the potential to treat COVID 19. Communicated by Ramaswamy H. Sarma
Partition Functions of Holographic Minimal Models
Creators: name: Gaberdiel, Matthias R.
name: Gopakumar, Rajesh
name: Hartman, Thomas
name: Raju, Suvrat
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The partition function of the W_N minimal model CFT is computed in the large N 't Hooft limit and compared to the spectrum of the proposed holographic dual, a 3d higher spin gravity theory coupled to massive scalar fields. At finite N, the CFT contains additional light states that are not visible in the perturbative gravity theory. We carefully define the large N limit, and give evidence that, at N = infinity, the additional states become null and decouple from all correlation functions. The surviving states are shown to match precisely (for all values of the 't Hooft coupling) with the spectrum of the higher spin gravity theory. The agreement between bulk and boundary is partially explained by symmetry considerations involving the conjectured equivalence between the W_N algebra in the large N limit and the higher spin algebra of the Vasiliev theory.
description: 56 pages
A local-global principle for linear dependence of noncommutative polynomials
Creators: name: Bresar, Matej
name: Klep, Igor
Publisher: name: arXiv
Year: 2011
Subjects: subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics
subject: Primary 16R50, 08B20, Secondary 16W10

description: A set of polynomials in noncommuting variables is called locally linearly dependent if their evaluations at tuples of matrices are always linearly dependent. By a theorem of Camino, Helton, Skelton and Ye, a finite locally linearly dependent set of polynomials is linearly dependent. In this short note an alternative proof based on the theory of polynomial identities is given. The method of the proof yields generalizations to directional local linear dependence and evaluations in general algebras over fields of arbitrary characteristic. A main feature of the proof is that it makes it possible to deduce bounds on the size of the matrices where the (directional) local linear dependence needs to be tested in order to establish linear dependence.
description: 8 pages
Object-oriented modelling with unified modelling language 2.0 for simple software application based on agile methodology
Creators: name: Warnars, Spits
Publisher: name: arXiv
Year: 2010
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences
subject: D.2.10

description: Unified modelling language (UML) 2.0 introduced in 2002 has been developing and influencing object-oriented software engineering and has become a standard and reference for information system analysis and design modelling. There are many concepts and theories to model the information system or software application with UML 2.0, which can make ambiguities and inconsistencies for a novice to learn to how to model the system with UML especially with UML 2.0. This article will discuss how to model the simple software application by using some of the diagrams of UML 2.0 and not by using the whole diagrams as suggested by agile methodology. Agile methodology is considered as convenient for novices because it can deliver the information technology environment to the end-user quickly and adaptively with minimal documentation. It also has the ability to deliver best performance software application according to the customer's needs. Agile methodology will make simple model with simple documentation, simple team and simple tools.
description: 15 pages, 30 figures
Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease
Creators: name: C, Shivanika
name: S., Deepak Kumar
name: Ragunathan, Venkataraghavan
name: Tiwari, Pawan
name: A., Sumitha
name: P, Brindha Devi
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: The study aims to evaluate the potency of two hundred natural antiviral phytocompounds against the active site of the Severe Acquired Respiratory Syndrome - Coronavirus − 2 (SARS-CoV-2) Main-Protease (Mpro) using AutoDock 4.2.6. The three- dimensional crystal structure of the Mpro (PDB Id: 6LU7) was retrieved from the Protein Data Bank (PDB), the active site was predicted using MetaPocket 2.0. Food and Drug Administration (FDA) approved viral protease inhibitors were used as standards for comparison of results. The compounds theaflavin-3-3’-digallate, rutin, hypericin, robustaflavone, and (-)-solenolide A with respective binding energy of −12.41 (Ki = 794.96 pM); −11.33 (Ki = 4.98 nM); −11.17 (Ki = 6.54 nM); −10.92 (Ki = 9.85 nM); and −10.82 kcal/mol (Ki = 11.88 nM) were ranked top as Coronavirus Disease − 2019 (COVID-19) Mpro inhibitors. The interacting amino acid residues were visualized using Discovery Studio 3.5 to elucidate the 2-dimensional and 3-dimensional interactions. The study was validated by i) re-docking the N3-peptide inhibitor-Mpro and superimposing them onto co-crystallized complex and ii) docking decoy ligands to Mpro. The ligands that showed low binding energy were further predicted for and pharmacokinetic properties and Lipinski’s rule of 5 and the results are tabulated and discussed. Molecular dynamics simulations were performed for 50 ns for those compounds using the Desmond package, Schrödinger to assess the conformational stability and fluctuations of protein-ligand complexes during the simulation. Thus, the natural compounds could act as a lead for the COVID-19 regimen after in-vitro and in- vivo clinical trials. Communicated by Ramaswamy H. Sarma
Platytropesa Macquart 1851
Creators: name: Colless, D. H.
Publisher: name: Zenodo
Year: 1998
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Calliphoridae
Platytropesa

description: Genus Platytropesa Macquart The genus was known from 3 very similar species variously distributed in the Moluccas, New Guinea, the Bismarck Archipelago and North Queensland. One more of these is here recorded from Australia.
description: Published as part of Colless, D. H., 1998, Morphometrics in the genus Amenia and revisionary notes on the Australian Ameniinae (Diptera: Calliphoridae), with the description of eight new species, pp. 85-123 in Records of the Australian Museum 50 (1) on page 98, DOI: 10.3853/j.0067-1975.50.1998.1275, http://zenodo.org/record/4652889
Platytropesa auriceps Macquart 1851
Creators: name: Colless, D. H.
Publisher: name: Zenodo
Year: 1998
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Calliphoridae
Platytropesa
Platytropesa auriceps

description: Platytropesa auriceps Macquart Crosskey (1965) gives a very detailed description. I give below the salient features, and some others not mentioned by Crosskey. Male. Head in facial view with inner eye margins strongly diverging and distinctly angulate at about the level of lunula. Carina strongly developed, its anterior surface flattened, tapering strongly in upper third towards lunula. Parafacials projecting to form deep foveae in which lie the enlarged antennae. Parafrontal with exclinate prevertical bristle and two proclinate fronto-orbitals; also, numerous black setulae and sometimes several pale ones anteriorly. Interfrons very dark brown, the dark setulae of parafrontal extending on to a marginal strip, but at most a short way on to the disc. Palp dark brown. Mesonotum emerald green with variable, usually strong, cupreous hue in glancing lights. Sternopleuron with at most a little pale pollinosity, forming an indistinct pale spot in some lights. Wing. M-bend index 0.9-1.3. Calypter with dark marginal colour extending on to membrane as a distinct band, covering some 10-20% of the exposed surface and extending clearly around the posteroexternal angle. Fore tibia with 1-2 p setae, 1-3 pd (usually 2); mid tibia with 2 large ad, 1 large v, 2 medium p, and 2-3 small pd setae. Abdominal venter with conspicuously long and dense hairs, those on S5 with apices strongly curved downwards and inwards (Crosskey, 1965: fig. 30). Genitalia as described by Crosskey (1965: figs 39, 42); cerci in lateral view gently curved, their tips rounded; surstyli more or less parallelsided, their apices about level with those of cerci. Female. Generally similar to male, differing as follows: Angulation of eye margin often less distinct. Carina less strongly flattened anteriorly, tapering regularly towards lunula. Antennae shorter, lying in shallower foveae. Parafrontal setulae much less profuse. Abdominal sternites with spinous setae instead of long hairs. Distribution. Queensland: Palm Island, Etty Bay, Yungaburra, Kuranda, Cairns (Earl Hill, Ellis Beach), Cooktown (Shiptons Flat, Gap Creek), Iron Range.
description: Published as part of Colless, D. H., 1998, Morphometrics in the genus Amenia and revisionary notes on the Australian Ameniinae (Diptera: Calliphoridae), with the description of eight new species, pp. 85-123 in Records of the Australian Museum 50 (1) on page 99, DOI: 10.3853/j.0067-1975.50.1998.1275, http://zenodo.org/record/4652889
description: {"references": ["Crosskey, R. W., 1965. A systematic revision of the Ameniinae (Diptera: Calliphoridae). Bulletin of the British Museum (Natural History) Entomology 16: 33 - 140."]}
Quantifying unreinforced masonry seismic risk and mitigation options in Victoria, BC
Creators: name: Paxton, Brandon
Publisher: name: University of British Columbia
Year: 2015

description: Despite their well-known seismic vulnerability, unreinforced masonry (URM) buildings continue to be a leading source of loss of life and property damage in earthquakes around the world. Victoria, British Columbia is a community with substantial seismic hazard that has yet to experience a damaging earthquake and, thus, has not seen widespread interest in mitigating seismic risks. It is also a city with a substantial stock of URM buildings, constructed around the turn of the 20th century, reasonably similar in form to those devastated by the 2010/2011 Canterbury earthquake sequence in New Zealand. To promote seismic upgrading of URM buildings in the region, cost-benefit analyses were undertaken specifically for Victoria, considering the seismic hazard, typical pedestrian and occupant exposure, building vulnerability, and local retrofit costs. The loss estimates are underpinned by motion-damage relationships derived in this thesis from observed damage in past earthquakes in California and New Zealand. Upgrading measures considered range from parapet bracing to full seismic upgrades consistent with local practices. Parapet bracing is shown to have favorable cost-benefit ratios – up to 4:1 for buildings on soft soils, indicating that the expected benefits outweigh the costs by a factor of four. Partial retrofits (eg. tying walls back to all floors/roofs, plus parapet bracing) are shown to have favourable cost/benefit ratios for buildings on soft soils (up to 1.7:1). Full upgrades are shown to have unfavorable cost-benefit ratios (maximum 0.7:1). In all cases, public benefits (i.e. reduced casualties) represent a significant portion of the total benefits, which provides evidence for cost sharing among building owners and the public. The motion versus structural damage relationships derived in this study are also used in developing proposed refinements to the FEMA 154 screening methodology. New, additional score modifiers (specific to URM) are presented, including score modifiers for various levels of earthquake strengthening. A trial application on buildings in Victoria shows that the revised scoring system is able to more effectively differentiate amongst URM buildings, making it more suitable for URM-only surveys, such as are often implemented by communities interested in quantifying and mitigating URM seismic risk.
Design of a multi-epitope peptide vaccine candidate against chandipura virus: an immuno-informatics study
Creators: name: Pavitrakar, Daya V.
name: Atre, Nitin M.
name: Tripathy, Anuradha S.
name: Shil, Pratip
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
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: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Chandipura virus (CHPV) is an emerging pathogen responsible for acute encephalitic syndrome (AES) in pediatric population in India. Several outbreaks of CHPV have been reported from different states of India since the year 2003. At present there is no vaccine or therapeutic measures available to curtail the disease. In this study, we have identified both T-cell and B-cell epitopes of different antigenic proteins of CHPV like Nucleoprotein (N), Phosphoprotein (P) and Matrix protein (M) along with the immuno-dominant glycoprotein (G) and conducted in silico characterization for the same. The idea is to design a multi-epitope peptide construct using the epitopes, which were found to be non-toxic, non-allergenic and possessing high immunogenicity. The final multi-epitope construct named as: MEC-CHPV, comprised of β-defensin adjuvant at N-terminal for enhancement of immunogenicity followed by fourteen B-cell epitopes, four Helper T-cell epitopes and six Cytotoxic T-cell epitopes. The characterization of designed construct was carried out in terms of physicochemical parameters, antigenicity and allergenicity. The 3D structure prediction was performed. Molecular docking and molecular-dynamics simulation of MEC-CHPV with Toll like receptors (TLR-3 and TLR-8) showed stable interactions. In silico cloning of MEC-CHPV in pET30a(+) expression vector was also conducted using codon optimization. The in silico immune-simulation indicated a typical immune response against MEC-CHPV when used as a potential vaccine. This study provides a cost-effective and time-saving way to design a peptide vaccine candidate against CHPV using immuno-informatics approach. Development of the MEC-CHPV construct may pave the way for future laboratory experiments. Communicated by Ramaswamy H. Sarma
Platytropesa simulans Crosskey 1965
Creators: name: Colless, D. H.
Publisher: name: Zenodo
Year: 1998
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Calliphoridae
Platytropesa
Platytropesa simulans

description: Platytropesa simulans Crosskey Crosskey (1965) gives a detailed description of New Guinean specimens. I now have Australian specimens, which differ from PI. auriceps as follows: Male. Inner eye margin smoothly curved. Parafrontals without proclinate fronto-orbital bristles, with more pale setulae anteriorly. Palp usually pale brown, at least apically. Sternopleuron with quite distinct pale pollinose spot, visible in most lights. M-bend index 0.8-0.9 (i.e., slightly, but distinctly less than in auriceps). Calypter with dark colour almost completely confined to margin, scarcely if at all extending around posteroexternal angle. Abdominal S5 with hairs less profuse and rather straight, not conspicuously curved. Cerci more or less straight, slightly hooked at apices; surstyle as described for auriceps. Female. Differs from auriceps in shape of inner eye margins, palp colour, pale spot on sternopleuron, and darkening of calypter-though differences not as pronounced as in male. Distribution. The Australian form is known only from the Iron Range area of Cape York Peninsula. Notes. There are some quite marked differences between the specimens described above and Crosskey's original description of PI. simulans. These are confirmed by my examination of a female paratype. New Guinean specimens have a much more extensively darkened lower calypter and much less pollinosity on the sternopleuron. The male surstyli ofAustralian specimens also differfrom Crosskey's description and his figures 38 and 41, in more resembling the condition shown for PI. auriceps in his figs 39 and 42. Crosskey does, though, use the term "usually", suggesting that he observed some variation from the shape described. A case could be made for describing the Australian form as a distinct species; but since it is clearly the local representative of PI. simulans, I am content for the present to leave it under that name.
description: Published as part of Colless, D. H., 1998, Morphometrics in the genus Amenia and revisionary notes on the Australian Ameniinae (Diptera: Calliphoridae), with the description of eight new species, pp. 85-123 in Records of the Australian Museum 50 (1) on page 99, DOI: 10.3853/j.0067-1975.50.1998.1275, http://zenodo.org/record/4652889
description: {"references": ["Crosskey, R. W., 1965. A systematic revision of the Ameniinae (Diptera: Calliphoridae). Bulletin of the British Museum (Natural History) Entomology 16: 33 - 140."]}