cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Identification of a 3-(5-methyl-2-thiazolylamino)phthalide as a new minor groove agent
Creators: name: Yılmaz, Zeynep Tanrıkulu
name: Odabaşoğlu, Hakkı Yasin
name: Şenel, Pelin
name: Yüzbaşıoğlu, Elif Çepni
name: Erdoğan, Taner
name: Özdemir, Ayşe Daut
name: Gölcü, Ayşegül
name: Odabaşoğlu, Mustafa
name: Büyükgüngör, Orhan
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: A new 3-(5-methyl-2-thiazolylamino)phthalide molecule, 3-((5-methylthiazol-2-yl)amino)isobenzofuran-1(3H)-one, was synthesized and characterized experimentally by FT-IR, NMR, UV-Vis, and single-crystal X-ray analysis and theoretically by quantum chemical calculations. The single-crystal X-ray studies revealed that the compound crystallizes in the monoclinic space group P-21/c with unit-cell parameters a = 8.0550(6) Å, b = 6.1386(3) Å, c = 23.3228(18) Å, β = 97.724(6)° and Z = 4. Optimized geometries and the vibrational frequencies were studied at the density functional theory (DFT) level by using the hybrid functional B3LYP with a 6-311 G (d,p) basis set. The title compound was evaluated for its anti-quorum sensing (anti-QS) activity on Chromobacterium violaceum 12472 and additionally for its antibacterial activity against Staphylococcus aureus 29213, Staphylococcus epidermidis 12228, Pseudomonas aeruginosa 27853, Escherichia coli 25922, and Proteus mirabilis 14153. The lowest MIC value was 0.24 μg/mL for S. aureus 29213 and the highest MIC value was 30.75 μg/mL for E. coli 25922. While anti-bacterial activity was observed in those other than the S. epidermidis and P. Mirabilis, anti-QS activity wasn’t detected. Investigations on dsDNA binding affinity indicate that the title compound binds to dsDNA via the groove binding mode. Molecular docking calculations and molecular dynamics simulations results showed also that the title compound prefers binding to the minor groove of dsDNA and remains stable in the minor groove throughout the molecular dynamics simulation. Communicated by Ramaswamy H. Sarma
Evaluation of phytoconstituents of Tinospora cordifolia against K417N and N501Y mutant spike glycoprotein and main protease of SARS-CoV-2- an in silico study
Creators: name: Choudhary, Princy
name: Singh, Tanu
name: Amod, Ayush
name: Singh, Sangeeta
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Neuroscience
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: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: Hematology
subject: 60506 Virology

description: Coronavirus disease 2019 (COVID-19) caused appalling conditions over the globe, which is currently faced by the entire human population. One of the primary reasons behind the uncontrollable situation is the lack of specific therapeutics. In such conditions, drug repurposing of available drugs (viz. Chloroquine, Lopinavir, etc.) has been proposed, but various clinical and preclinical investigations indicated the toxicity and adverse side effects of these drugs. This study explores the inhibition potency of phytochemicals from Tinospora cordifolia (Giloy) against SARS CoV-2 drugable targets (spike glycoprotein and Mpro proteins) using molecular docking and MD simulation studies. ADMET, virtual screening, MD simulation, postsimulation analysis (RMSD, RMSF, Rg, SASA, PCA, FES) and MM-PBSA calculations were carried out to predict the inhibition efficacy of the phytochemicals against SARS CoV-2 targets. Tinospora compounds showed better binding affinity than the corresponding reference. Their binding affinity ranges from –9.63 to –5.68 kcal/mole with spike protein and –10.27 to –7.25 kcal/mole with main protease. Further 100 ns exhaustive simulation studies and MM-PBSA calculations supported favorable and stable binding of them. This work identifies Nine Tinospora compounds as potential inhibitors. Among those, 7-desacetoxy-6,7-dehydrogedunin was found to inhibit both spike (7NEG) and Mpro (7MGS and 6LU7) proteins, and Columbin was found to inhibit selected spike targets (7NEG and 7NX7). In all the analyses, these compounds performed well and confirms the stable binding. Hence the identified compounds, advocated as potential inhibitors can be taken for further in vitro and in vivo experimental validation to determine their anti-SARS-CoV-2 potential. Communicated by Ramaswamy H. Sarma
ε-Corrected Seiberg-Witten Prepotential Obtained From Half Genus Expansion in beta-Deformed Matrix Model
Creators: name: Itoyama, Hiroshi
name: Yonezawa, Nobuhiro
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We consider the half-genus expansion of the resolvent function in the $β$-deformed matrix model with three-Penner potential under the AGT conjecture and the $0d-4d$ dictionary. The partition function of the model, after the specification of the paths, becomes the DF conformal block for fixed $c$ and provides the Nekrasov partition function expanded both in $g_s = \sqrt{-ε_1 ε_2}$ and in $ε= ε_1+ε_2$. Exploiting the explicit expressions for the lower terms of the free energy extracted from the above expansion, we derive the first few $ε$ corrections to the Seiberg-Witten prepotential in terms of the parameters of SU(2), $N_{f} =4$, ${\cal N}= 2$ supersymmetric gauge theory.
description: LaTeX, 31 pages, 3 figures; v2: references added
title: ÐÑÐ³Ð°Ð½Ð¸Ð·Ð°ÑÐ¸Ñ Ð¿ÑÐ¾Ð¸Ð·Ð²Ð¾Ð´ÑÑÐ²ÐµÐ½Ð½Ð¾-ÑÐ¾ÑÐ³Ð¾Ð²Ð¾Ð¹ Ð´ÐµÑÑÐµÐ»ÑÐ½Ð¾ÑÑÐ¸ ÐºÐ°ÑÐµ Ð°ÑÐ¼ÑÐ½ÑÐºÐ¾Ð¹ ÐºÑÑ Ð½Ð¸ Ð¿Ð¾ Ð°Ð´ÑÐµÑÑ: Ð³. Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³, ÐÐ½Ð´ÑÑÑÑÐ¸Ð°Ð»ÑÐ½ÑÐ¹ Ð¿Ñ., Ð´. 10/1
title: Ð²ÑÐ¿ÑÑÐºÐ½Ð°Ñ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð±Ð°ÐºÐ°Ð»Ð°Ð²ÑÐ°
titleType: Subtitle
title: Organization of production and trading activities of a cafe specializing armenian cuizine by the address: St. Petersburg, Industrial Avenue 10/1
Creators: name: ÐÐ°ÑÐ¿Ð°ÑÑÐ½, ÐÐ¸ÑÐ°Ð¸Ð»
Publisher: name: Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³ÑÐºÐ¸Ð¹ Ð¿Ð¾Ð»Ð¸ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ½Ð¸Ð²ÐµÑÑÐ¸ÑÐµÑ ÐÐµÑÑÐ° ÐÐµÐ»Ð¸ÐºÐ¾Ð³Ð¾
Year: 2019
Subjects: ÐºÐ°ÑÐµ
Ð°ÑÐ¼ÑÐ½ÑÐºÐ°Ñ ÐºÑÑ Ð½Ñ
Ð¼ÐµÐ½Ñ
Ð¿ÑÐ¾Ð¸Ð·Ð²Ð¾Ð´ÑÑÐ²ÐµÐ½Ð½Ð°Ñ Ð¿ÑÐ¾Ð³ÑÐ°Ð¼Ð¼Ð°
Ð¿ÑÐ¾Ð¸Ð·Ð²Ð¾Ð´ÑÑÐ²ÐµÐ½Ð½Ð¾-ÑÐ¾ÑÐ³Ð¾Ð²Ð°Ñ Ð´ÐµÑÑÐµÐ»ÑÐ½Ð¾ÑÑÑ.
cafÃ©
armenian cuisine
menu
production program
production and trading activities.

description: ÐÑÐ¾Ð¸Ð·Ð²ÐµÐ´ÐµÐ½Ð¾ Ð¼Ð°ÑÐºÐµÑÐ¸Ð½Ð³Ð¾Ð²Ð¾Ðµ Ð¸ÑÑÐ»ÐµÐ´Ð¾Ð²Ð°Ð½Ð¸Ðµ Ð¸ Ð¾Ð±Ð¾ÑÐ½Ð¾Ð²Ð°Ð½Ð¸Ðµ ÑÐµÐ»ÐµÑÐ¾Ð¾Ð±ÑÐ°Ð·Ð½Ð¾ÑÑÐ¸ ÑÐ°Ð·Ð¼ÐµÑÐµÐ½Ð¸Ñ ÐºÐ°ÑÐµ Ð°ÑÐ¼ÑÐ½ÑÐºÐ¾Ð¹ ÐºÑÑÐ½Ð¸ Ð¿Ð¾ Ð°Ð´ÑÐµÑÑ: Ð³. Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³, ÐÐ½Ð´ÑÑÑÑÐ¸Ð°Ð»ÑÐ½ÑÐ¹ Ð¿Ñ., Ð´. 10/1. ÐÐ¿ÑÐµÐ´ÐµÐ»ÐµÐ½Ð¾ ÐºÐ¾Ð»Ð¸ÑÐµÑÑÐ²Ð¾ Ð¼ÐµÑÑ, Ð¿ÑÐ¾Ð¸Ð·Ð²ÐµÐ´ÐµÐ½ ÑÐµÑÐ½Ð¾Ð»Ð¾Ð³Ð¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ°ÑÑÐµÑ Ð½ÐµÐ¾Ð±ÑÐ¾Ð´Ð¸Ð¼ÑÑ Ð¿Ð¾Ð¼ÐµÑÐµÐ½Ð¸Ð¹, Ð¿Ð¾Ð´Ð¾Ð±ÑÐ°Ð½Ð¾ Ð¾Ð±Ð¾ÑÑÐ´Ð¾Ð²Ð°Ð½Ð¸Ðµ Ð² ÑÐ¾Ð¾ÑÐ²ÐµÑÑÑÐ²Ð¸Ð¸ Ñ ÑÑÐµÐ±ÑÐµÐ¼ÑÐ¼Ð¸ Ð¿Ð°ÑÐ°Ð¼ÐµÑÑÐ°Ð¼Ð¸. Ð Ð°Ð·ÑÐ°Ð±Ð¾ÑÐ°Ð½Ð° Ð¾Ð¿ÑÐ¸Ð¼Ð°Ð»ÑÐ½Ð°Ñ Ð¾ÑÐ³Ð°Ð½Ð¸Ð·Ð°ÑÐ¸Ð¾Ð½Ð½Ð°Ñ ÑÑÑÑÐºÑÑÑÐ° Ð¸ ÑÐ¸ÑÑÐµÐ¼Ð° Ð±ÐµÐ·Ð¾Ð¿Ð°ÑÐ½Ð¾ÑÑÐ¸ Ð´ÐµÑÑÐµÐ»ÑÐ½Ð¾ÑÑÐ¸ Ð¿ÑÐµÐ´Ð¿ÑÐ¸ÑÑÐ¸Ñ. ÐÐ±Ð¾ÑÐ½Ð¾Ð²Ð°Ð½Ð° ÑÐºÐ¾Ð½Ð¾Ð¼Ð¸ÑÐµÑÐºÐ°Ñ ÑÐµÐ»ÐµÑÐ¾Ð¾Ð±ÑÐ°Ð·Ð½Ð¾ÑÑÑ Ð¿ÑÐ¾ÐµÐºÑÐ¸ÑÐ¾Ð²Ð°Ð½Ð¸Ñ Ð¿ÑÐµÐ´Ð¿ÑÐ¸ÑÑÐ¸Ñ Ð¸ Ð¾Ð¿ÑÐµÐ´ÐµÐ»ÐµÐ½Ð¾ Ð¾ÑÐ³Ð°Ð½Ð¸Ð·Ð°ÑÐ¸Ð¾Ð½Ð½Ð¾-Ð¿Ð»Ð°Ð½Ð¸ÑÐ¾Ð²Ð¾ÑÐ½Ð¾Ðµ ÑÐµÑÐµÐ½Ð¸Ðµ.
description: The marketing study and the rationale for placing a cafÃ© specializing in greek cuisine was made by address: St. Petersburg, Industrial Avenue 10/1. The number of places was determined, the technological calculation of necessary premises was made, equipment was selected according to the required parameters. The optimal organizational structure and the security system of the enterprise has been worked out. The economic expediency of the enterpriseâs design was justified, and the organizational and planning decision was determined.
title: ÐÐ½ÑÐµÑÐ½ÐµÑ-ÑÐµÑ Ð½Ð¾Ð»Ð¾Ð³Ð¸Ð¸ ÐºÐ°Ðº Ð¸Ð½ÑÑÑÑÐ¼ÐµÐ½Ñ ÑÐµÐ°Ð»Ð¸Ð·Ð°ÑÐ¸Ð¸ PR Ð¸ ÑÐµÐºÐ»Ð°Ð¼Ñ (Ð½Ð° Ð¿ÑÐ¸Ð¼ÐµÑÐµ ÐÐÐ "Ð¡Ð±ÐµÑÐ±Ð°Ð½Ðº Ð Ð¾ÑÑÐ¸Ð¸")
title: Ð²ÑÐ¿ÑÑÐºÐ½Ð°Ñ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð±Ð°ÐºÐ°Ð»Ð°Ð²ÑÐ°
titleType: Subtitle
title: Internet technologies as a tool for implementing PR and advertising (on the example of Sberbank of Russia PJSC)
Creators: name: ÐÐ°Ð¹Ð½Ð±ÐµÑÐ³ÐµÑ, ÐÐ½Ð½Ð°
Publisher: name: Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³ÑÐºÐ¸Ð¹ Ð¿Ð¾Ð»Ð¸ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ½Ð¸Ð²ÐµÑÑÐ¸ÑÐµÑ ÐÐµÑÑÐ° ÐÐµÐ»Ð¸ÐºÐ¾Ð³Ð¾
Year: 2020
Subjects: ÑÐµÐºÐ»Ð°Ð¼Ð°
Ð¸Ð½ÑÐµÑÐ½ÐµÑ-Ð±Ð°Ð½ÐºÐ¸Ð½Ð³
Ð¸Ð¼Ð¸Ð´Ð¶
Ð¿ÑÐ¾Ð´Ð²Ð¸Ð¶ÐµÐ½Ð¸Ðµ
SMM
PR
Ð±ÑÐµÐ½Ð´
advertising
internet banking
image
promotion
brand

description: Ð¦ÐµÐ»ÑÑ ÑÐ°Ð±Ð¾ÑÑ ÑÐ²Ð»ÑÐµÑÑÑ Ð°Ð½Ð°Ð»Ð¸Ð· ÑÐ¾Ð»Ð¸ ÐÐ½ÑÐµÑÐ½ÐµÑ ÑÐµÑÐ½Ð¾Ð»Ð¾Ð³Ð¸Ð¹ Ð² PR Ð¿ÑÐ¾Ð´Ð²Ð¸-Ð¶ÐµÐ½Ð¸Ð¸ Ð½Ð° Ð¿ÑÐ¸Ð¼ÐµÑÐµ Ð¿ÑÐ¾Ð´Ð²Ð¸Ð¶ÐµÐ½Ð¸Ñ Ð±Ð°Ð½ÐºÐ¾Ð²ÑÐºÐ¸Ñ ÑÑÐ»ÑÐ³, Ð° ÑÐ°ÐºÐ¶Ðµ Ð¾ÑÐµÐ½ÐºÐ° ÑÑÑÐµÐºÑÐ¸Ð²Ð½Ð¾-ÑÑÐ¸ ÑÐ°Ð±Ð¾ÑÑ Ñ ÐÐ½ÑÐµÑÐ½ÐµÑ-ÑÐµÑÐ½Ð¾Ð»Ð¾Ð³Ð¸ÑÐ¼Ð¸ ÐÐÐ Â«Ð¡Ð±ÐµÑÐ±Ð°Ð½Ðº Ð Ð¾ÑÑÐ¸Ð¸Â». ÐÑÐ» Ð¿ÑÐ¾Ð²ÐµÐ´ÐµÐ½ Ð°Ð½Ð°Ð»Ð¸Ð· ÑÐ°Ð±Ð¾ÑÑ ÐÐ½ÑÐµÑÐ½ÐµÑ-Ð±Ð°Ð½ÐºÐ¸Ð½Ð³Ð° Ð¸ ÑÐ¾ÑÐ¸Ð°Ð»ÑÐ½ÑÑ ÑÐµÑÐµÐ¹. Ð ÑÐµÐ·ÑÐ»ÑÑÐ°ÑÐµ ÑÐµÐ³Ð¾ Ð±ÑÐ»Ð¸ Ð´Ð°Ð½Ñ ÑÐµÐºÐ¾Ð¼ÐµÐ½Ð´Ð°ÑÐ¸Ð¸ Ð¿Ð¾ ÑÐ¾Ð²ÐµÑÑÐµÐ½ÑÑÐ²Ð¾Ð²Ð°Ð½Ð¸Ñ ÑÑÑÐ°ÑÐµÐ³Ð¸Ð¸ PR-Ð¿ÑÐ¾Ð´Ð²Ð¸Ð¶ÐµÐ½Ð¸Ñ.
description: The aim of the work is to analyze the role of Internet technologies in PR pro-motion using the example of promoting banking services, as well as assess the effec-tiveness of working with Internet technologies of Sberbank of Russia PJSC.
An analysis of the work of Internet banking and social networks was carried out.
As a result, recommendations were given on improving the PR promotion strategy.
Einstein's quantum theory of the monatomic ideal gas: non-statistical arguments for a new statistics
Creators: name: Pérez, Enric
name: Sauer, Tilman
Publisher: name: arXiv
Year: 2010
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: FOS: Physical sciences

description: In this article, we analyze the third of three papers, in which Einstein presented his quantum theory of the ideal gas of 1924-1925. Although it failed to attract the attention of Einstein's contemporaries and although also today very few commentators refer to it, we argue for its significance in the context of Einstein's quantum researches. It contains an attempt to extend and exhaust the characterization of the monatomic ideal gas without appealing to combinatorics. Its ambiguities illustrate Einstein's confusion with his initial success in extending Bose's results and in realizing the consequences of what later became to be called Bose-Einstein statistics. We discuss Einstein's motivation for writing a non-combinatorial paper, partly in response to criticism by his friend Ehrenfest, and we paraphrase its content. Its arguments are based on Einstein's belief in the complete analogy between the thermodynamics of light quanta and of material particles and invoke considerations of adiabatic transformations as well as of dimensional analysis. These techniques were well-known to Einstein from earlier work on Wien's displacement law, Planck's radiation theory, and the specific heat of solids. We also investigate the possible role of Ehrenfest in the gestation of the theory.
description: 57 pp.
In silico analysis of the predicted protein-protein interaction of syntaxin-18, a putative receptor of Peregrinus maidis Ashmead (Hemiptera: Delphacidae) with Maize mosaic virus glycoprotein
Creators: name: Castrosanto, Melvin A.
name: Clemente, Apel Jae N.
name: Whitfield, Anna E.
name: Alviar, Karen B.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Molecular Biology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology

description: The corn planthopper, Peregrinus maidis Ashmead (Hemiptera:Delphacidae), is a widely distributed insect pest which serves as a vector of two phytopathogenic viruses, Maize mosaic virus (MMV) and Maize stripe virus (MStV). It transmits the viruses in a persistent and propagative manner. MMV is an alphanucleorhabdovirus with a negative-sense, single-stranded RNA unsegmented genome. One identified insect vector protein that may serve as receptor to MMV is Syntaxin-18 (PmStx18) which belongs to the SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) proteins. SNAREs play major roles in the final stage of docking and subsequent fusion of diverse vesicle-mediated transport events. In this work, in silico analysis of the interaction of MMV glycoprotein (MMV G) and PmStx18 was performed. Various freely available protein-protein docking web servers were used to predict the 3 D complex of MMV G and PmStx18. Analysis and protein-protein interaction (PPI) count showed that the complex predicted by the ZDOCK server has the highest number of interaction and highest affinity, as suggested by the calculated solvation free energy gain upon formation of the interface (ΔiG = −31 kcal/mol). Molecular dynamics simulation of the complex revealed important interactions at the interface over the course of 25 ns. This is the first in silico analysis performed for the interaction on a putative receptor of P. maidis and MMV G. The results of the PPI prediction provide novel information for studying the role of Stx18 in the transport, docking and fusion events involved in virus particle transport in the insect vector cells and its release. Communicated by Ramaswamy H. Sarma
Differential interaction of Fluorescein-β-cyclodextrin conjugate to quadruplex kit22 DNA: Inclusion of Berberine and modulation of binding
Creators: name: Soundarapandian, Suganthi
name: Alexander, Aleyamma
name: Pillai, Archana Sumohan
name: Manikandan, Varnitha
name: Enoch, Israel V. M. V.
name: Yousuf, Sameena
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer
subject: Plant Biology

description: Clinical applicability of G-quadruplexes as anticancer drugs is an area of current interest. Identification of supramolecular systems for selective targeting G-quartets is particularly intriguing. In this work, the DNA binder Berberine is encapsulated inside the molecular cavity of the synthesised host structure, Fluoresecein-β-cyclodextrin conjugate. The host: guest complex is characterized and the mode of binding is optimized using two dimensional rotating-frame Overhauser effect spectroscopy. The conjugate is examined for its binding to quadruplex DNAs viz., kit22, myc22, telo24 and the duplex calf-thymus DNA before and after Berberine encapsulation. UV–vis and fluorescence spectroscopic methods were employed to determine the strength of binding of the complex with the DNAs. The binding strength and the stoichiometry of the host: guest complex are 1.9 × 106 mol−1 dm3 and 1:1, respectively. A quenching of fluorescence of the quadruplex kit22 and duplex ctDNA is observed on binding to the Fluorescein-β-cyclodextrin conjugate. The quadruplexes of myc22 and telo24 display an enhanced fluorescence on binding to the modified cyclodextrin. The Stern-Volmer quenching constants are 1.4 × 106 mol−1 dm3 and 3.8 × 105 mol−1 dm3 for binding to kit22 and ctDNA respectively. kit22 shows a different emission profile on interacting with the Berberine encapsulated conjugate, whereas all the other quadruplexes and duplex exhibit similar emission profiles. The results indicate a variation in the binding mode and strength of the ligand-quadruplexes and depend on the conformation of the quadruplexes. Communicated by Ramaswamy H. Sarma
Phenolic compounds as α-glucosidase inhibitors: a docking and molecular dynamics simulation study
Creators: name: Swargiary, Ananta
name: Roy, Mritunjoy Kumar
name: Mahmud, Shafi
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
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: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Phenolic compounds possess significant biological activity. Several pieces of research emphasize the medicinal importance of phenolic compounds, including diabetes. The present study investigated the α-glucosidase inhibitory activity of phenolic compounds reported from several plants. The phenolic compounds reported in different literature were collected. Molecular docking was carried out using AutoDock Vina. Various physicochemical properties such as size, LogP, molecular complexity, hydrogen bonding properties of phenolic compounds were correlated with the binding affinities. Furthermore, MD simulation was carried out to study the structural stability of the docking complexes. A total of 155 phenolic compounds were reported from different plants. Amentoflavone showed the strongest binding affinity with α-glucosidase, much more potent than reference acarbose. The binding energy showed a good correlation with the molecular complexity, hydrogen bond donor and acceptor property and heavy atom counts of the compounds. The polarity of the surface area also showed a positive correlation with the binding affinity of the compounds. The best docking phenolic compound, amentoflavone, showed stable binding affinity and conformation during the simulation period compared to apoprotein and acarbose-docking complex. The top ten phenolic compounds, including amentoflavone, showed considerable drug-likeness properties with fewer toxicity effects. The study suggests that the amentoflavone could be a potential therapeutic drug as an α-glucosidase inhibitor and help control postprandial hyperglycemia. Communicated by Ramaswamy H. Sarma
Complete Phase Diagrams for a Holographic Superconductor/Insulator System
Creators: name: Horowitz, Gary T.
name: Way, Benson
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The gravitational dual of an insulator/superconductor transition driven by increasing the chemical potential has recently been constructed. However, the system was studied in a probe limit and only a part of the phase diagram was obtained. We include the backreaction and construct the complete phase diagram for this system. For fixed chemical potential there are typically two phase transitions as the temperature is lowered. Surprisingly, for a certain range of parameters, the system first becomes a superconductor and then becomes an insulator as the temperature approaches zero. As a byproduct of our analysis, we also construct the gravitational dual of a Bose-Einstein condensate of glueballs in a confining gauge theory.
description: 19 pages; v2: references added
title: ÐÑÐ¸Ð¼ÐµÐ½ÐµÐ½Ð¸Ðµ Ð²ÑÐ±Ð¾ÑÐ¾ÑÐ½Ð¾Ð³Ð¾ ÑÐ°Ð·Ð·Ð¸Ð½Ð³-ÑÐµÑÑÐ¸ÑÐ¾Ð²Ð°Ð½Ð¸Ñ Ð½Ð° Ð¾ÑÐ½Ð¾Ð²Ðµ ÑÑÐ°ÑÐ¸ÑÐµÑÐºÐ¾Ð³Ð¾ Ð°Ð½Ð°Ð»Ð¸Ð·Ð° ÐºÐ¾Ð´Ð°
title: Ð²ÑÐ¿ÑÑÐºÐ½Ð°Ñ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° ÑÐ¿ÐµÑÐ¸Ð°Ð»Ð¸ÑÑÐ°
titleType: Subtitle
title: Application of selective fuzzing testing based on static analysis of code
Creators: name: ÐÑÐ¾ÑÐµÐ½ÐºÐ¾, ÐÐ²Ð³ÐµÐ½Ð¸Ð¹
Publisher: name: Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³ÑÐºÐ¸Ð¹ Ð¿Ð¾Ð»Ð¸ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ½Ð¸Ð²ÐµÑÑÐ¸ÑÐµÑ ÐÐµÑÑÐ° ÐÐµÐ»Ð¸ÐºÐ¾Ð³Ð¾
Year: 2019
Subjects: ÑÑÐ°ÑÐ¸ÑÐµÑÐºÐ¸Ð¹ Ð°Ð½Ð°Ð»Ð¸Ð·
Ð¼Ð¾Ð´ÐµÐ»Ð¸ Ð¿ÑÐµÐ´ÑÐºÐ°Ð·Ð°Ð½Ð¸Ñ Ð´ÐµÑÐµÐºÑÐ¾Ð²
Ð³ÑÐ°ÑÐ¾Ð²ÑÐµ Ð¿ÑÐµÐ´ÑÑÐ°Ð²Ð»ÐµÐ½Ð¸Ñ
Ð²ÑÐ±Ð¾ÑÐ¾ÑÐ½Ð¾Ðµ ÑÐ°Ð·Ð·Ð¸Ð½Ð³-ÑÐµÑÑÐ¸ÑÐ¾Ð²Ð°Ð½Ð¸Ðµ
Ð³ÐµÐ½ÐµÑÐ¸ÑÐµÑÐºÐ¸Ð¹ Ð°Ð»Ð³Ð¾ÑÐ¸ÑÐ¼
Ñ Ð°ÑÐ°ÐºÑÐµÑÐ¸ÑÑÐ¸ÐºÐ¸ ÐºÐ¾Ð´Ð°
static analysis
defect prediction models
unsupervised learning
graph representation
selective fuzzing
genetic algorithms
code metrics

description: Ð¤Ð°Ð·Ð·Ð¸Ð½Ð³-ÑÐµÑÑÐ¸ÑÐ¾Ð²Ð°Ð½Ð¸Ðµ ÑÐ²Ð»ÑÐµÑÑÑ Ð¾Ð´Ð½Ð¸Ð¼ Ð¸Ð· Ð½Ð°Ð¸Ð±Ð¾Ð»ÐµÐµ ÑÑÑÐµÐºÑÐ¸Ð²Ð½ÑÑ Ð¼ÐµÑÐ¾Ð´Ð¾Ð² Ð¿Ð¾Ð¸ÑÐºÐ° ÑÑÐ·Ð²Ð¸Ð¼Ð¾ÑÑÐµÐ¹. ÐÐ¾Ð»Ð½Ð¾Ðµ Ð¿Ð¾ÐºÑÑÑÐ¸Ðµ ÐºÐ¾Ð´Ð° Ð¿ÑÐ¸ ÑÐ°Ð·Ð·Ð¸Ð½Ð³Ðµ ÑÐ²Ð»ÑÐµÑÑÑ Ð¸Ð·Ð±ÑÑÐ¾ÑÐ½ÑÐ¼, ÑÐ°Ðº ÐºÐ°Ðº Ð¾ÑÐ¸Ð±ÐºÐ¸ Ð² ÐºÐ¾Ð´Ðµ ÑÐ°ÑÐ¿ÑÐµÐ´ÐµÐ»ÐµÐ½Ñ Ð½ÐµÑÐ°Ð²Ð½Ð¾Ð¼ÐµÑÐ½Ð¾. Ð Ð´Ð°Ð½Ð½Ð¾Ð¹ ÑÐ°Ð±Ð¾ÑÐµ Ð¾Ð¿Ð¸ÑÑÐ²Ð°ÐµÑÑÑ Ð¿Ð¾Ð´ÑÐ¾Ð´ ÑÐ°Ð½Ð¶Ð¸ÑÐ¾Ð²Ð°Ð½Ð¸Ñ ÑÑÐ½ÐºÑÐ¸Ð¹, ÐºÐ¾ÑÐ¾ÑÑÐ¹ Ð¿Ð¾Ð·Ð²Ð¾Ð»ÑÐµÑ Ð¾Ð¿ÑÐµÐ´ÐµÐ»ÑÑÑ Ð¿Ð¾ÑÐµÐ½ÑÐ¸Ð°Ð»ÑÐ½Ð¾ Ð½Ð°Ð¸Ð±Ð¾Ð»ÐµÐµ Ð¾Ð¿Ð°ÑÐ½ÑÐµ ÑÑÐ½ÐºÑÐ¸Ð¸. ÐÑÐµÐ´Ð»Ð°Ð³Ð°ÐµÐ¼ÑÐ¹ Ð¿Ð¾Ð´ÑÐ¾Ð´ Ð½Ðµ ÑÑÐµÐ±ÑÐµÑ Ð½Ð°Ð»Ð¸ÑÐ¸Ñ Ð¸ÑÑÐ¾ÑÐ¸Ð¸ Ð´ÐµÑÐµÐºÑÐ¾Ð² Ð´Ð»Ñ Ð¾Ð±ÑÑÐµÐ½Ð¸Ñ. Ð Ð°Ð½Ð¶Ð¸ÑÐ¾Ð²Ð°Ð½Ð¸Ðµ Ð¾ÑÑÑÐµÑÑÐ²Ð»ÑÐµÑÑÑ Ð½Ð° Ð¾ÑÐ½Ð¾Ð²Ðµ Ð¾ÑÐµÐ½Ð¾Ðº ÑÐ»Ð¾Ð¶Ð½Ð¾ÑÑÐ¸ ÐºÐ¾Ð´Ð°, ÐºÐ¾ÑÐ¾ÑÑÐµ Ð²ÑÑÐ¸ÑÐ»ÑÑÑÑÑ Ð½Ð° Ð¾ÑÐ½Ð¾Ð²Ðµ ÑÐ°ÑÐ°ÐºÑÐµÑÐ¸ÑÑÐ¸Ðº ÐºÐ¾Ð´Ð°, ÑÐ¾Ð±Ð¸ÑÐ°ÐµÐ¼ÑÑ Ñ Ð¿Ð¾Ð¼Ð¾ÑÑÑ Ð³ÑÐ°ÑÐ¾Ð²Ð¾Ð³Ð¾ Ð¿ÑÐµÐ´ÑÑÐ°Ð²Ð»ÐµÐ½Ð¸Ñ ÑÑÐ½ÐºÑÐ¸Ð¹.
description: Fuzzing is an effective method to find vulnerabilities. Full code coverage during fuzzing is not trivial task to accomplish. Moreover, it is redundant because the vulnerabilities in the code are not evenly distributed. This paper describes an approach to ranking functions, which will determine the potentially most dangerous ones. The proposed approach does not require a defect history for training. The ranking is based on the complexity of the code, which is calculated based on the characteristics of the code collected by the graph representation of functions.
Replacement of oxocarbenium ions by allylic cations in both enzymatic and spontaneous reactions of glycosides
Creators: name: Danby, Phillip M.
Publisher: name: University of British Columbia
Year: 2022

description: Oxocarbenium ions play a pivotal role in the chemistry and biochemistry of glycosides. In this thesis I prepared carbocyclic glycoside analogs that can generate allylic cations in the place of oxocarbenium ions. In these unsaturated cyclitols the C5-O5 bond of a pyranoside is replaced by a C-C double bond. Phenolic leaving groups were introduced at the pseudo anomeric carbon to form allyl ether linkages analogous to glycosidic linkages. Spontaneous heterolysis of these aryl carbasugars was shown, by measurement of secondary kinetic isotope effects, to proceed via an allylic cation. Not only was this mechanism of cleavage similar to that seen for glycosides but the rate constants for solvolysis of aryl glycosides and unsaturated aryl carbasugars were found to be nearly identical. To explore if these close similarities in structure and inherent reactivities would allow glycoside hydrolases to act on non-glycosidic linkages I screened a library of over 150 glycoside hydrolases with a fluorogenic allyl-carbasugar substrate. This screen identified several beta-retaining glycosidases capable of unsaturated cyclitol ether hydrolysis. Detailed analysis of a model enzyme demonstrated that the same mechanism was operative for cleavage of unsaturated cyclitol ethers as glycosidic linkages. Once again, kinetic isotope effects implicated an allylic cation at the rate-limiting transition state for the enzymatic reaction. The observed kinetic parameters for aryl carbasugar cleavage by glycosidases served as a reminder that these enzymes have evolved to act upon glycosides, and not carbocyclic imitators. Turnover constants were 100 – 1000-fold lower for aryl carbasugar hydrolysis compared to hydrolysis of aryl glycosides. Directed evolution has begun to bridge this gap in activity and yield glycosidases better capable of cleaving aryl unsaturated cyclitol linkages. The mechanistic insights gained by these studies have proven useful in preparing novel glycosidase inactivators. Specifically, unsaturated pseudosugars, with the vinyl hydrogen replaced by electron withdrawing halogens, react with retaining glycosidases to accumulate the covalent species and accomplish enzyme inactivation. Taken together these studies highlight the parallels between allylic cations and oxocarbenium ions. Not only do allylic carbasugars have similar inherent reactivities to glycosides but glycosidases are capable of allylic cation stabilization at their transition states.
Self-organised criticality in base-pair breathing in DNA with a defect
Creators: name: Duduiala, Ciprian-Ionut
name: Wattis, Jonathan A. D.
name: Laughton, Charles A
Publisher: name: arXiv
Year: 2011
Subjects: subject: Biological Physics (physics.bio-ph)
subject: Soft Condensed Matter (cond-mat.soft)
subject: Dynamical Systems (math.DS)
subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: Biomolecules (q-bio.BM)
subject: FOS: Physical sciences
subject: FOS: Mathematics
subject: FOS: Biological sciences

description: We analyse base-pair breathing in a DNA sequence of 12 base-pairs with a defective base at its centre. We use both all-atom molecular dynamics (MD) simulations and a system of stochastic differential equations (SDE). In both cases, Fourier analysis of the trajectories reveals self-organised critical behaviour in the breathing of base-pairs. The Fourier Transforms (FT) of the interbase distances show power-law behaviour with gradients close to -1. The scale-invariant behaviour we have found provides evidence for the view that base-pair breathing corresponds to the nucleation stage of large-scale DNA opening (or 'melting') and that this process is a (second-order) phase transition. Although the random forces in our SDE system were introduced as white noise, FTs of the displacements exhibit pink noise, as do the displacements in the AMBER/MD simulations.
description: 18 pages, 8 figures
Self-Regulated Star Formation in Galaxies via Momentum Input from Massive Stars
Creators: name: Hopkins, Philip F.
name: Quataert, Eliot
name: Murray, Norman
Publisher: name: arXiv
Year: 2011
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Feedback from massive stars is believed to play a critical role in shaping the galaxy mass function, the structure of the interstellar medium (ISM), and the low efficiency of star formation, but the exact form of the feedback is uncertain. In this paper, the first in a series, we present and test a novel numerical implementation of stellar feedback resulting from momentum imparted to the ISM by radiation, supernovae, and stellar winds. We employ a realistic cooling function, and find that a large fraction of the gas cools to <100K, so that the ISM becomes highly inhomogeneous. Despite this, our simulated galaxies reach an approximate steady state, in which gas gravitationally collapses to form giant molecular clouds (GMCs), dense clumps, and stars; subsequently, stellar feedback disperses the GMCs, repopulating the diffuse ISM. This collapse and dispersal cycle is seen in models of SMC-like dwarfs, the Milky-Way, and z~2 clumpy disk analogues. The simulated global star formation efficiencies are consistent with the observed Kennicutt-Schmidt relation. Moreover, the star formation rates are nearly independent of the numerically imposed high-density star formation efficiency, density threshold, and density scaling. This is a consequence of the fact that, in our simulations, star formation is regulated by stellar feedback limiting the amount of very dense gas available for forming stars. In contrast, in simulations without stellar feedback, i.e. under the action of only gravity and gravitationally-induced turbulence, the ISM experiences runaway collapse to very high densities. In these simulations without feedback, the global star formation rates exceed observed galactic star formation rates by 1-2 orders of magnitude, demonstrating that stellar feedback is crucial to the regulation of star formation in galaxies.
description: 24 pages, 13 figures, accepted to MNRAS (significantly expanded to match accepted version). Movies of the simulations here can be found at https://www.cfa.harvard.edu/~phopkins/Site/Movies_sbw.html
A qualitative investigation of "honest" retractions by researchers in the Netherlands and other countries
Creators: name: Hosseini, Mohammad
Publisher: name: Zenodo
Year: 2016
Subjects: Authorship
Retractions
Ethics

description: Authors who retract their own papers following the discovery of an honest mistake show a highly proactive attitude with regards to their professional and moral responsibilities. In this qualitative study, we explored the circumstances, motivations and beliefs of scientists who retracted one of their own publications between 2010 and 2015. Scientists were selected primarily amongst Dutch researchers. Through semistructured interviews, we sought to understand the experience of discovering an error and retracting one’s own publication. For all the participants, the process of retracting a publication had been one of the most stressful and pressing moments of their professional career. Nonetheless, in many cases having retracted a paper turned out to be a cause of praise for these scientists by their colleagues. We conclude that scientists’ motivations to retract included a combination of prudential and moral considerations. However, the very act of communicating their mistake to the journals constitutes a realization of ethical and professional responsibilities, which should be praised and promoted.
Predicting new disease activity from deep grey matter on MRI in early multiple sclerosis using random forests and neural networks : feature selection and accounting for class label uncertainty
Creators: name: Tayyab, Maryam
Publisher: name: University of British Columbia
Year: 2021

description: Multiple sclerosis (MS) is an autoimmune disease of the central nervous system with a heterogeneous disease course, making it difficult to predict patient-specific clinical outcomes. Machine learning can potentially improve predictions by feature extraction and/or learning complex relationships. Morphological change in deep grey matter (DGM) structures is a consistent feature in all MS phenotypes, yet the value of DGM imaging features for clinical prediction is largely unexplored. In this thesis, I evaluated the contribution of DGM volumes and deep-learned (DL) features for predicting new disease activity within 24 months of a first clinical demyelinating event. Our data set had two challenging characteristics: highly heterogeneous feature types, requiring a thoughtful exploration of feature selection methods, and 32 out of 140 patient samples had uncertain ground truth labels. We implemented and evaluated 1) random forest (RF) models trained on clinical, demographic and DGM volumes, 2) four feature selection methods for RF training and their impact on model performance, 3) DL models trained on 3D segmentations of DGM nuclei with and without user-defined features, and 4) strategies to account for label uncertainty while training an RF. In a 7-fold nested cross-validation experiment, our best result without accounting for uncertainty (F1-score = 77.57%, SD= 6.60%) was achieved with an RF trained on manually selected features, which outperformed common automated feature selection methods, such as iterative RFs (F1-score = 72.35%, SD=6.91%). The neural network using only deep-learned DGM features achieved a slightly lower F1-score = 73.02% (4.70%), which decreased further when adding user-defined features. When accounting for label uncertainty, the highest performance achieved in the 108 confirmed labels was produced by a probabilistic RF (F1-score = 89.62%, SD=4.90%) trained on all available samples, which was higher than training only on the confirmed labels.
Design of a multi-epitope Zika virus vaccine candidate – an in-silico study
Creators: name: Ezzemani, Wahiba
name: Windisch, Marc P.
name: Altawalah, Haya
name: Guessous, Fadila
name: Saile, Rachid
name: Benjelloun, Soumaya
name: Kettani, Anass
name: Ezzikouri, Sayeh
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Space Science
subject: Medicine
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Zika virus (ZIKV), an RNA virus, rapidly spreads Aedes mosquito-borne sickness. Currently, there are neither effective vaccines nor therapeutics available to prevent or treat ZIKV infection. In this study, to address these unmet medical needs, we aimed to design B- and T-cell candidate multi-epitope-based subunit against ZIKV using an in silico approach. In this study we applied immunoinformatics, molecular docking, and dynamic simulation assessments targeting the most immunogenic proteins; the capsid (C), envelope (E) proteins and the non-stuctural protein (NS1), described in our previous study, and which predicted immunodominant B and T cell epitopes. The final non-allergenic and highly antigenic multi-epitope was constituted of immunogenic screened-epitopes (3 CTL and 3 HTL) and the β-defensin as an adjuvant that have been linked using EAAAK, AAY, and GPGPG linkers, respectively. The final construct containing 143 amino acids was characterized for its allergenicity, antigenicity, and physiochemical properties; and found to be safe and immunogenic with a good prediction of solubility. The existence of IFN-γ epitopes asserts the capacity to trigger strong immune responses. Subsequently, the molecular docking among vaccine and immune receptors (TLR2/TLR4) was revealed with a good binding affinity with and stable molecular interactions. Molecular dynamics simulation confirmed the stability of the complexes. Finally, the construct was subjected to in silico cloning demonstrating the efficiently of its expression in E.coli. However, this study needs the experimental validation to demonstrate vaccine safety and efficacy. Communicated by Ramaswamy H. Sarma
IceCube's In-Ice Radio Extension: Status and Results
Creators: name: Landsman, H.
name: Cheng, E.
name: Kulcyk, E.
name: Laundrie, A. W.
name: Rotter, B.
name: Ruckman, L.
name: Sandstrom, P. W.
name: Varner, G. S.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: In 2006-2010, several Radio Frequency (RF) detectors and calibration equipment were deployed as part of the IceCube array at depths between 5 to 1400 meters in preparation for a future large scale GZK neutrino detector. IceCube's deep holes and well-established data handling system provide a unique opportunity for deep-ice RF detection studies at the South-Pole. We will present verification and calibration results as well as a status-review of ongoing analyses such as ice-properties, RF noise and reconstruction algorithms.
description: 4 pages, 6 figures, to appear in the proceedings of the Acoustic and Radio EeV Neutrino detection Activities (ARENA) 2010 conference
The fast rotating, low gravity subdwarf B star EC 22081-1916 - Remnant of a common envelope merger event
Creators: name: Geier, S.
name: Classen, L.
name: Heber, U.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Hot subdwarf B stars (sdBs) are evolved core helium-burning stars with very thin hydrogen envelopes. In order to form an sdB, the progenitor has to lose almost all of its hydrogen envelope right at the tip of the red giant branch. In binary systems, mass transfer to the companion provides the extraordinary mass loss required for their formation. However, apparently single sdBs exist as well and their formation is unclear since decades. The merger of helium white dwarfs leading to an ignition of core helium-burning or the merger of a helium core and a low mass star during the common envelope phase have been proposed. Here we report the discovery of EC 22081-1916 as a fast rotating, single sdB star of low gravity. Its atmospheric parameters indicate, that the hydrogen envelope must be unusually thick, which is at variance with the He-WD merger scenario, but consistent with a common envelope merger of a low-mass, possibly substellar object with a red-giant core.
description: 16 pages, 4 figures, ApJL, accepted
Mannose 2, 3, 4, 5, 6-O-pentasulfate (MPS): a partial activator of human heparin cofactor II with anticoagulation potential
Creators: name: Bano, Shadabi
name: Khan, Abdul Burhan
name: Fatima, Sana
name: Rashid, Qudsia
name: Prakash, Amresh
name: Gupta, Neha
name: Ahmad, Irshad
name: Ansari, Shoyab
name: Lynn, Andrew M.
name: Abid, Mohammad
name: Jairajpuri, Mohamad Aman
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: Hematology

description: Thromboembolic diseases are a major cause of mortality in human and the currently available anticoagulants are associated with various drawbacks, therefore the search for anticoagulants that have better safety profile is highly desirable. Compounds that are part of the dietary routine can be modified to possibly increase their anticoagulant potential. We show mannose 2,3,4,5,6-O-pentasulfate (MPS) as a synthetically modified form of mannose that has appreciable anticoagulation properties. An in silico study identified that mannose in sulfated form can bind effectively to the heparin-binding site of antithrombin (ATIII) and heparin cofactor II (HCII). Mannose was sulfated using a simple sulfation strategy-involving triethylamine-sulfur trioxide adduct. HCII and ATIII were purified from human plasma and the binding analysis using fluorometer and isothermal calorimetry showed that MPS binds at a unique site. A thrombin inhibition analysis using the chromogenic substrate showed that MPS partially enhances the activity of HCII. Further an assessment of in vitro blood coagulation assays using human plasma showed that the activated partial thromboplastin time (APTT) and prothrombin time (PT) were prolonged in the presence of MPS. A molecular dynamics simulation analysis of the HCII-MPS complex showed fluctuations in a N-terminal loop and the cofactor binding site of HCII. The results indicate that MPS is a promising lead due to its effect on the in vitro coagulation rate. Communicated by Ramaswamy H. Sarma
title: ÐÑÐ³Ð°Ð½Ð¸Ð·Ð°ÑÐ¸Ñ Ð¸ Ð¿ÑÐ¾Ð²ÐµÐ´ÐµÐ½Ð¸Ðµ ÑÐ¿ÐµÑÐ¸Ð°Ð»ÑÐ½Ð¾Ð³Ð¾ Ð¼ÐµÑÐ¾Ð¿ÑÐ¸ÑÑÐ¸Ñ Ð½Ð° Ð¼ÐµÐ¶Ð´ÑÐ½Ð°ÑÐ¾Ð´Ð½Ð¾Ð¼ ÑÑÐ¾Ð²Ð½Ðµ (Ð½Ð° Ð¿ÑÐ¸Ð¼ÐµÑÐµ Ð¤ÐÐÐÐ£ ÐÐ Ð¡ÐÐ±ÐÐ£ ÐÐ¸ÑÐµÐºÑÐ¸Ñ ÐºÐ¾Ð½Ð³ÑÐµÑÑÐ½Ð¾-Ð²ÑÑÑÐ°Ð²Ð¾ÑÐ½Ð¾Ð¹ Ð´ÐµÑÑÐµÐ»ÑÐ½Ð¾ÑÑÐ¸)
title: Ð²ÑÐ¿ÑÑÐºÐ½Ð°Ñ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð±Ð°ÐºÐ°Ð»Ð°Ð²ÑÐ°
titleType: Subtitle
title: Organization and holding of a special event at the international level
Creators: name: ÐÐ°Ð´ÑÐ±Ð¾Ð²ÑÐºÐ°Ñ, ÐÐ°ÑÐ¸Ð½Ð°
Publisher: name: Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³ÑÐºÐ¸Ð¹ Ð¿Ð¾Ð»Ð¸ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ½Ð¸Ð²ÐµÑÑÐ¸ÑÐµÑ ÐÐµÑÑÐ° ÐÐµÐ»Ð¸ÐºÐ¾Ð³Ð¾
Year: 2019
Subjects: ÐÐµÐ¶Ð´ÑÐ½Ð°ÑÐ¾Ð´Ð½ÑÐµ Ð²ÑÑÑÐ°Ð²ÐºÐ¸
event-Ð¼ÐµÑÐ¾Ð¿ÑÐ¸ÑÑÐ¸Ñ
Ð²ÑÑÑÐµÐµ ÑÑÐµÐ±Ð½Ð¾Ðµ Ð·Ð°Ð²ÐµÐ´ÐµÐ½Ð¸Ðµ
ÐºÐ¾Ð½Ð³ÑÐµÑÑÐ½Ð¾-Ð²ÑÑÑÐ°Ð²Ð¾ÑÐ½Ð°Ñ Ð´ÐµÑÑÐµÐ»ÑÐ½Ð¾ÑÑÑ
Ð¸Ð¼Ð¸Ð´Ð¶ ÐÐ£ÐÐ°
event-Ð¼Ð°ÑÐºÐµÑÐ¸Ð½Ð³
ÑÐ¿ÐµÑÐ¸Ð°Ð»ÑÐ½ÑÐµ Ð¼ÐµÑÐ¾Ð¿ÑÐ¸ÑÑÐ¸Ñ
International exhibitions
events
higher educational institutions
image of the university
congress and exhibition activity
event marketing
special events

description: Ð Ð´Ð°Ð½Ð½Ð¾Ð¹ Ð²ÑÐ¿ÑÑÐºÐ½Ð¾Ð¹ ÑÐ°Ð±Ð¾ÑÐµ Ð¾Ð¿ÑÐµÐ´ÐµÐ»ÑÐµÑÑÑ ÑÐ¿ÐµÑÐ¸ÑÐ¸ÐºÐ° Ð¾ÑÐ³Ð°Ð½Ð¸Ð·Ð°ÑÐ¸Ð¸ Ð¸ Ð¿ÑÐ¾Ð²ÐµÐ´ÐµÐ½Ð¸Ñ event-Ð¼ÐµÑÐ¾Ð¿ÑÐ¸ÑÑÐ¸Ñ Ð½Ð° Ð¼ÐµÐ¶Ð´ÑÐ½Ð°ÑÐ¾Ð´Ð½Ð¾Ð¼ ÑÑÐ¾Ð²Ð½Ðµ, Ð° ÑÐ°ÐºÐ¶Ðµ Ð·Ð½Ð°ÑÐ¸Ð¼Ð¾ÑÑÑ ÐºÐ¾Ð½Ð³ÑÐµÑÑÐ½Ð¾-Ð²ÑÑÑÐ°Ð²Ð¾ÑÐ½Ð¾Ð¹ Ð´ÐµÑÑÐµÐ»ÑÐ½Ð¾ÑÑÐ¸ Ð´Ð»Ñ Ð¿ÑÐ¾Ð´Ð²Ð¸Ð¶ÐµÐ½Ð¸Ñ Ð²ÑÑÑÐ¸Ñ ÑÑÐµÐ±Ð½ÑÑ Ð·Ð°Ð²ÐµÐ´ÐµÐ½Ð¸Ð¹ Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³Ð° Ð½Ð° Ð¼ÐµÐ¶Ð´ÑÐ½Ð°ÑÐ¾Ð´Ð½ÑÐ¹ ÑÑÐ¾Ð²ÐµÐ½Ñ. ÐÐ°Ð¶Ð´Ð¾Ðµ ÑÑÑÐµÐ¶Ð´ÐµÐ½Ð¸Ðµ Ð²ÑÑÑÐµÐ³Ð¾ Ð¾Ð±ÑÐ°Ð·Ð¾Ð²Ð°Ð½Ð¸Ñ Ð¿ÑÑÐ°ÐµÑÑÑ Ð¿Ð¾Ð¿Ð°ÑÑÑ Ð½Ð° Ð»Ð¸Ð´Ð¸ÑÑÑÑÐ¸Ðµ Ð¿Ð¾Ð·Ð¸ÑÐ¸Ð¸ Ð² ÑÐµÐ¹ÑÐ¸Ð½Ð³Ðµ Ð²ÑÑÑÐ¸Ñ ÑÑÐµÐ±Ð½ÑÑ Ð·Ð°Ð²ÐµÐ´ÐµÐ½Ð¸Ð¹. Ð§ÑÐ¾Ð±Ñ Ð¿Ð¾Ð²ÑÑÐ¸ÑÑ ÑÐ·Ð½Ð°Ð²Ð°ÐµÐ¼Ð¾ÑÑÑ ÑÑÑÐµÐ¶Ð´ÐµÐ½Ð¸Ñ Ð²ÑÑÑÐµÐ³Ð¾ Ð¾Ð±ÑÐ°Ð·Ð¾Ð²Ð°Ð½Ð¸Ñ Ð½ÐµÐ¾Ð±ÑÐ¾Ð´Ð¸Ð¼Ð¾ ÑÐµÐ³ÑÐ»ÑÑÐ½Ð¾ Ð¿ÑÐµÐ´ÑÑÐ°Ð²Ð»ÑÑÑ ÑÑÐµÐ±Ð½Ð¾Ðµ Ð·Ð°Ð²ÐµÐ´ÐµÐ½Ð¸Ðµ Ð½Ðµ ÑÐ¾Ð»ÑÐºÐ¾ Ð½Ð° ÑÐµÐ³Ð¸Ð¾Ð½Ð°Ð»ÑÐ½Ð¾Ð¼ ÑÑÐ½ÐºÐµ, Ð½Ð¾ Ð¸ ÑÑÐ°ÑÑÐ²Ð¾Ð²Ð°ÑÑ Ð² Ð¼ÐµÐ¶Ð´ÑÐ½Ð°ÑÐ¾Ð´Ð½ÑÑ Ð½Ð°ÑÑÐ½ÑÑ, Ð¾Ð±ÑÐ°Ð·Ð¾Ð²Ð°ÑÐµÐ»ÑÐ½ÑÑ Ð¸ Ð¾ÑÑÐ°ÑÐ»ÐµÐ²ÑÑ Ð¼ÐµÑÐ¾Ð¿ÑÐ¸ÑÑÐ¸ÑÑ.
description: This thesis defines the features of the organization and conduct of the event at the international level and the significance of congress and exhibition activities for the promotion of higher educational institutionÑ of St. Petersburg to the international level. Each institution of higher education is trying to get to the leading position in the ranking of universities. In order to increase the recognition of a higher education institution, it is necessary to regularly represent an institution of higher education not only on the regional market, but also to participate in international scientific, educational and industry events.
Forming simulation of prepreg plain weave fabrics
Creators: name: Sourki, Reza
Publisher: name: University of British Columbia
Year: 2021

description: Forming simulation of woven fabrics has continually been employed over the years to help production designers optimize advanced composite manufacturing processes. In doing so, however, multiple deformation mechanisms such as tension, shear, bending, ply/ply interaction, along with resin-induced effects such as viscoelasticity, should be taken into consideration to achieve a reliable shape prediction of the formed parts. A comprehensive finite element model is realized in the present work to simulate the behavior of a plain weave prepreg during forming. Namely, a hybrid shell/membrane element is utilized to de-couple the in-plane and out-of-plane properties of the fabric ply. Viscous behavior, orientation- and pressure-dependent inter-ply frictional behavior, as well as the loading/unloading bending regime of the material, which was observed during forming experiments, were also characterized and implemented in the model. The latter regime has been particularly overlooked in the literature while being critical of the correct prediction of forming processes. To study the bending regimes, a custom-designed bending device was used to better understand and characterize the nonlinear behavior of textiles under out-of-plane deformations through the loading-unloading regimes. Furthermore, to incorporate the inter-ply frictional behavior, an empirical model was developed based on the response of the fabric under a wide range of processing conditions such as pressure and orientation. The numerical results for each deformation mode as well as the viscous and anisotropic frictional behavior were accurately modeled and compared with the experiments. Finally, all the developed models were integrated to provide a comprehensive mechanical tool to study forming processes. The results are shown to accurately predict the geometry of the formed test fabric along with the reaction forces of the tools, thus providing confidence in utilizing the tool to investigate forming processes and further use for optimization and minimization of major forming-induced defects such as wrinkling.
Chiral extrapolation beyond the power-counting regime
Creators: name: Hall, J. M. M.
name: Lee, F. X.
name: Leinweber, D. B.
name: Liu, K. F.
name: Mathur, N.
name: Young, R. D.
name: Zhang, J. B.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Chiral effective field theory can provide valuable insight into the chiral physics of hadrons when used in conjunction with non-perturbative schemes such as lattice QCD. In this discourse, the attention is focused on extrapolating the mass of the rho meson to the physical pion mass in quenched QCD (QQCD). With the absence of a known experimental value, this serves to demonstrate the ability of the extrapolation scheme to make predictions without prior bias. By using extended effective field theory developed previously, an extrapolation is performed using quenched lattice QCD data that extends outside the chiral power-counting regime (PCR). The method involves an analysis of the renormalization flow curves of the low energy coefficients in a finite-range regularized effective field theory. The analysis identifies an optimal regulator, which is embedded in the lattice QCD data themselves. This optimal regulator is the regulator value at which the renormalization of the low energy coefficients is approximately independent of the range of quark masses considered. By using recent precision, quenched lattice results, the extrapolation is tested directly by truncating the analysis to a set of points above 380 MeV, while being blinded of the results probing deeply into the chiral regime. The result is a successful extrapolation to the chiral regime.
description: 8 pages, 18 figures
Collisional decoherence of a tracer particle moving in one dimension
Creators: name: Kamleitner, Ingo
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study decoherence of the external degree of freedom of a tracer particle moving in a one dimensional dilute Boltzmann gas. We find that phase averaging is the dominant decoherence effect, rather than information exchange between tracer and gas particles. While a coherent superposition of two wave packets with different mean positions quickly turns into a mixed state, it is demonstrated that such superpositions of different momenta are robust to phase averaging, until the two wave packets acquire a different position due to the different velocity of each wave packet.
description: 10 pages