cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Structure-based virtual screening of natural compounds against wild and mutant (R1155K, A1156T and D1168A) NS3-4A protease of Hepatitis C virus
Creators: name: Samantaray, Mahesh
name: Pattabiraman, Ramya
name: Murthy, T. P. Krishna
name: Ramaswamy, Amutha
name: Murahari, Manikanta
name: Krishna, Swati
name: Kumar, S. Birendra
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Pharmacology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified

description: NS3-4A, a serine protease, is a primary target for drug development against Hepatitis C Virus (HCV). However, the effectiveness of potent next-generation protease inhibitors is limited by the emergence of mutations and resulting drug resistance. To address this, in this study a structure-based drug design approach is employed to screen a large library of 7320 natural compounds against both wild-type and mutant variants of NS3-4A protease. Telaprevir, a widely used protease inhibitor, was recruited as the control drug. The top 10 compounds with favorable binding affinities underwent drug-likeness evaluation. Based on ADMET studies, complexes of NP_024762 and NP_006776 were selected for molecular dynamic simulations. Principal component analysis (PCA) was employed to explore the conformational space and protein dynamics of the protein-ligand complex using a Free Energy Landscape (FEL) approach. The cosine values obtained from FEL analysis ranged from 0 to 1, and eigenvectors with cosine values below 0.2 were chosen for further analysis. To forecast binding free energies and evaluate energy contributions per residue, the MM-PBSA method was employed. The results highlighted the crucial role of amino acids in the catalytic domain for the binding of the protease with phytochemicals. Stable associations between the top compounds and the target protease were confirmed by the formation of hydrogen bonds in the binding pocket involving residues: His1057, Gly1137, Ser1139, and Ala1157. These findings suggest the potential of these compounds for further validation through biological evaluation. Communicated by Ramaswamy H. Sarma
Isolation_ID_Protocol_Jozwick_2
Creators: name: Estes, Anne
name: Jozwick, Anna
Publisher: name: figshare
Year: 2022
Subjects: subject: 60408 Genomics
subject: FOS: Biological sciences
subject: Microbiology

description: Isolation, DNA extraction, 16S rRNA gene amplification, and sequencing to identify bacteria isolated from the skin mucus of healthy laboratory-reader zebrafish DNA extraction protocol #2
Computational evaluation of quinones of Nigella sativa L. as potential inhibitor of dengue virus NS5 methyltransferase
Creators: name: Roney, Miah
name: Dubey, Amit
name: Nasir, Muhammad Hassan
name: Huq, Akm Moyeenul
name: Tufail, Aisha
name: Tajuddin, Saiful Nizam
name: Zamri, Normaiza Binti
name: Aluwi, Mohd Fadhlizil Fasihi Mohd
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Aedes aegypti is the primary vector for the transmission of the dengue virus, which causes dengue fever, dengue hemorrhagic illness and dengue shock syndrome. There is now no antiviral medication available to treat DENV, which kills thousands of people each year and infects millions of individuals. A possible target for the creation of fresh and efficient dengue treatments is the DENV-3 NS5 MTase. So, Nigella sativa quinones were examined using in silico methods to find natural anti-DENV compounds. The in silico docking was conducted utilising the Discovery Studio software on the quinones of N. sativa and the active site of the target protein DENV-3 NS5 MTase. In addition, the druggability and pharmacokinetics of the lead compound were assessed. Dithymoquinone was comparable to the reference compound in terms of its ability to bind to the active site of target protein. Dithymoquinone met the requirements for drug likeness and Lipinski’s principles, as demonstrated by the ADMET analysis and drug likeness results. The current study indicated that the dithymoquinone from N. sativa had anti-DENV activity, suggesting further drug development and dengue treatment optimisation. Communicated by Ramaswamy H. Sarma
Multiphoton processes at cyclotron resonance subharmonics in a 2D electron system under DC and microwave excitation
Creators: name: Chakraborty, S.
name: Hatke, A. T.
name: Engel, L. W.
name: Watson, J. D.
name: Manfra, M. J.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We investigate a two-dimensional electron system (2DES) under microwave illumination at cyclotron resonance subharmonics. The 2DES carries sufficient direct current, $I$, that the differential resistivity oscillates as $I$ is swept. At magnetic fields sufficient to resolve individual Landau levels, we find the number of oscillations within an $I$ range systematically changes with increasing microwave power. Microwave absorption and emission of $N$ photons, where $N$ is controlled by the microwave power, describes our observations in the framework of the displacement mechanism of impurity scattering between Hall-field tilted Landau levels.
Hydration forces between parallel DNA double helices: computer simulations.
Creators: name: Reddy, M. R.
name: Berkowitz, M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1989

description: We have performed two molecular dynamics computer simulations of two 10-base-pair segments of DNA molecules immersed in water. The goal of these simulations is to study the structural and dynamical properties of water between the DNA molecules. We have observed water ordering next to DNA surfaces. Existence of such ordering was proposed earlier by Marcelja and Radic [Marcelja, S. & Radic, N. (1976) Chem. Phys. Lett. 42, 129-130] to explain strong hydration forces between macromolecular surfaces.
The value of monitoring to control evolving populations
Creators: name: Fischer, Andrej
name: Vazquez-Garcia, Ignacio
name: Mustonen, Ville
Publisher: name: arXiv
Year: 2014
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: FOS: Biological sciences

description: Populations can evolve in order to adapt to external changes. The capacity to evolve and adapt makes successful treatment of infectious diseases and cancer difficult. Indeed, therapy resistance has quickly become a key challenge for global health. Therefore, ideas of how to control evolving populations in order to overcome this threat are valuable. Here we use the mathematical concepts of stochastic optimal control to study what is needed to control evolving populations. Following established routes to calculate control strategies, we first study how a polymorphism can be maintained in a finite population by adaptively tuning selection. We then introduce a minimal model of drug resistance in a stochastically evolving cancer cell population and compute adaptive therapies, where decisions are based on monitoring the response of the tumor, which can outperform established therapy paradigms. For both case studies, we demonstrate the importance of high-resolution monitoring of the target population in order to achieve a given control objective: to control one must monitor.
description: 27 pages
Identification of androgen receptors in normal human osteoblast-like cells.
Creators: name: Colvard, D. S.
name: French, F. S.
name: Lubahn, D. B.
name: Spelsberg, T. C.
name: Riggs, B. L.
name: Eriksen, E. F.
name: Wilson, E. M.
name: Keeting, P. E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1989

description: The sex steroids, androgens and estrogens, are major regulators of bone metabolism. However, whether these hormones act on bone cells through direct or indirect mechanisms has remained unclear. A nuclear binding assay recently used to demonstrate estrogen receptors in bone [Eriksen, E.F., Colvard, D.S., Berg, N.J., Graham, M.L., Mann, K.G., Spelsberg, T.C. & Riggs, B.L. (1988) Science 241, 84-86] was used to identify specific nuclear binding of a tritiated synthetic androgen, [3H]R1881 (methyltrienolone), in 21 of 25 (84%) human osteoblast-like cell strains and a concentration of bound steroid receptors of 821 +/- 140 (mean +/- SEM) molecules per cell nucleus. Binding was saturable and steroid-specific. Androgen receptor gene expression in osteoblasts was confirmed by RNA blot analysis. Relative concentrations of androgen and estrogen receptors were compared by measuring specific nuclear estrogen binding. Nuclear binding of [3H]estradiol was observed in 27 of 30 (90%) cell strains; the concentration of bound estradiol receptor was 1537 +/- 221 molecules per cell nucleus. The concentrations of nuclear binding sites were similar in males and females for both [3H]R1881 and [3H]estradiol. We conclude that both androgens and estrogens act directly on human bone cells through their respective receptor-mediated mechanisms.
Study of neutron-induced background and its effect on the search of 0$νββ$ decay in $\rm^{124}Sn$
Creators: name: Dokania, N.
name: Singh, V.
name: Mathimalar, S.
name: Ghosh, C.
name: Nanal, V.
name: Pillay, R. G.
name: Pal, S.
name: Bhushan, K. G.
name: Shrivastava, A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: Neutron-induced background has been studied in various components of the TIN.TIN detector, which is under development for the search of Neutrinoless Double Beta Decay in $\rm^{124}Sn$. Fast neutron flux $\sim10^{6}~n~cm^{-2}s^{-1}$ covering a broad energy range ($ \sim0.1$ to $ \sim18$~MeV) was generated using $^{9}Be(p,n)^{9}B$ reaction. In addition, reactions with quasi-monoenergetic neutrons were also studied using $^{7}Li(p,n)^{7}Be$ reaction. Among the different cryogenic support structures studied, Teflon is found to be preferable compared to Torlon as there is no high energy gamma background ($E_γ>$ 1 MeV). Contribution of neutron-induced reactions in $\rm ^{nat, 124} $Sn from other Sn isotopes (A = 112 -- 122) in the energy region of interest, namely, around the $Q_{ββ}$ of $\rm^{124}Sn$ ($E \sim$ 2.293 MeV), is also investigated.
description: 17 pages, 7 figures, Accepted version (with minor revision)
Die vielen Gesichter Marias
Creators: name: Irarrázaval, Diego
name: Ross, Susan A.
name: Wacker, Marie-Theres
Publisher: name: Concilium
Year: 1970

description: Concilium, Bd. 44 Nr. 4 (2008): Concilium: Internationale Zeitschrift für Theologie, Band 44, Heft 4
Inactivating the beta 2-microglobulin locus in mouse embryonic stem cells by homologous recombination.
Creators: name: Smithies, O.
name: Koller, B. H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1989

description: We have inactivated, by gene targeting, the endogenous beta 2-microglobulin gene in a mouse embryonic stem cell line. A cloned fragment of the beta 2-microglobulin gene with the coding sequence disrupted by the insertion of the neomycin-resistance gene was used to transfect the embryonic stem cells. G418-resistant colonies were selected and then screened using the polymerase chain reaction to identify those in which the incoming DNA had integrated into the embryonic stem cell genome by homologous recombination. Of a total of 234 G418-resistant colonies screened, 2 correctly targeted colonies were identified. Chimeric mice carrying the inactivated beta 2-microglobulin gene have been obtained from both of these targeted embryonic cell lines. Breeding of offspring from such animals will allow investigation of the effects of homozygous loss of beta 2-microglobulin.
Congruences for Fishburn numbers modulo prime powers
Creators: name: Straub, Armin
Publisher: name: arXiv
Year: 2014
Subjects: subject: Number Theory (math.NT)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics

description: The Fishburn numbers $ξ(n)$ are defined by the formal power series \[ \sum_{n \geq 0} ξ(n) q^n = \sum_{n \geq 0} \prod_{j = 1}^n (1 - (1 - q)^j). \] Recently, G. Andrews and J. Sellers discovered congruences of the form $ξ(p m + j) \equiv 0$ modulo $p$, valid for all $m \geq 0$. These congruences have then been complemented and generalized to the case of $r$-Fishburn numbers by F. Garvan. In this note, we answer a question of Andrews and Sellers regarding an extension of these congruences to the case of prime powers. We show that, under a certain condition, all these congruences indeed extend to hold modulo prime powers.
description: 13 pages
Induction of diapause in Drosophila melanogaster: photoperiodic regulation and the impact of arrhythmic clock mutations on time measurement.
Creators: name: Gilbert, L. I.
name: Henrich, V. C.
name: Saunders, D. S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1989

description: The fruit fly Drosophila melanogaster displays an ovarian diapause that is regulated by photoperiod. Newly eclosed female flies (Canton-S wild type) exposed to short days (less than 14 hr of light per day) at 12 degrees C (or 10 degrees C) enter a fairly shallow reproductive diapause. Females exposed to long days (16 hr of light per day) at the same low temperature undergo ovarian maturation. The short day induced diapause continues for 6-7 weeks under a 10:14 light/dark cycle at 12 degrees C but is terminated rapidly after a transfer to higher temperature (18 or 25 degrees C) or to long days (18:6 light/dark cycle). Females from three strains homozygous for alleles of the period (per) locus, reportedly arrhythmic for behavioral circadian rhythms, and females that possessed two overlapping deletions of per were also capable of discriminating between long and short days, although, when compared with the wild-type flies, the critical day length was shifted to shorter values by approximately 2 hr. It is concluded that the period locus is not causally involved in photoperiod time measurement.
Aspects of electromagnetic radiation reaction in strong fields
Creators: name: Burton, D. A.
name: Noble, A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: Accelerator Physics (physics.acc-ph)
subject: FOS: Physical sciences

description: With the recent advances in laser technology, experimental investigation of radiation reaction phenomena is at last becoming a realistic prospect. A pedagogical introduction to electromagnetic radiation reaction is given with the emphasis on matter driven by ultra-intense lasers. Single-particle, multi-particle, classical and quantum aspects are all addressed.
description: 17 pages, 1 figure. Invited article
Juvenile hormone bisepoxide biosynthesis in vitro by the ring gland of Drosophila melanogaster: a putative juvenile hormone in the higher Diptera.
Creators: name: Schooley, D. A.
name: Applebaum, S. W.
name: Reuter, C. C.
name: Henrich, V. C.
name: Baker, F. C.
name: Gilbert, L. I.
name: Sliter, T. J.
name: Richard, D. S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1989

description: The in vitro production of juvenile hormone (JH) was investigated by using isolated ring glands from third instar Drosophila melanogaster. A JH-like molecule is secreted that comigrates with a synthetic sample of methyl 6,7;10,11-bisepoxy-3,7,11-trimethyl-(2E)-dodecenoate (JHB
Analysing the impact of eriosematin E from Eriosema chinense Vogel. against different diarrhoeagenic pathovars of Escherichia coli using in silico and in vitro approach
Creators: name: Chikhale, Rupesh V.
name: Prasad, Rupali S.
name: de Resende, Pedro Ernesto
name: Akojwar, Natasha S.
name: Purohit, Raksha A.
name: Gurav, Shailendra S.
name: Sinha, Saurabh K.
name: Prasad, Satyendra K.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Since diarrhoea is reportedly the third largest cause of fatality among kids, therefore it is considered to be one of the major areas of concerns among developing nations. The main causative agents of diarrhoea include Escherichia coli, Vibrio cholera, and Shigella spp where E. coli shares the maximum contribution. The roots of the plant Eriosema chinense Vogel. (Fabaceae) are traditionally used by the native tribes of Meghalaya, India to treat diarrhoea. From previous reports, the plant and its marker eriosematin E have been reported to have antidiarrhoeal potential against pathogenic and nonpathogenic diarrhoea. Therefore, the objective of the current investigation was to use in silico studies to determine the efficacy of eriosematin E against different diarrhoeagenic strains of E. coli. Six different pathovars of E. coli i.e. enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enterohaemorrhagic E. coli (EHEC), enteroaggregative E. coli (EAEC), uropathogenic E. coli (UPEC) and enteroinvasive E. coli (EIEC) were subjected to docking simulation studies utilizing Glide module of Schrodinger Maestro 2018-1 MM Share Version. Based on the obtained binding energy and balance between H-bonding, hydrophobic, and salt bridge interactions eriosematin E was found to be most effective against EPEC followed by EAEC and ETEC, while UPEC and EHEC were moderately affected. The molecular dynamics studies suggested a higher affinity of eriosematin E towards heat-labile enterotoxin b-pentamer from ETEC. The in vitro antibacterial studies against the universal strain S. aureus 12981 and E. coli 10418 revealed the effectiveness of eriosematin E showing MIC values of ≥256 µg/mL. Communicated by Ramaswamy H. Sarma
Breakdown voltage of metal-oxide resistors in liquid argon
Creators: name: Bagby, L. F.
name: Gollapinni, S.
name: James, C. C.
name: Jones, B. J. P.
name: Jostlein, H.
name: Lockwitz, S.
name: Naples, D.
name: Raaf, J. L.
name: Rameika, R.
name: Schukraft, A.
name: Strauss, T.
name: Weber, M. S.
name: Wolbers, S. A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We characterized a sample of metal-oxide resistors and measured their breakdown voltage in liquid argon by applying high voltage (HV) pulses over a 3 second period. This test mimics the situation in a HV-divider chain when a breakdown occurs and the voltage across resistors rapidly rise from the static value to much higher values. All resistors had higher breakdown voltages in liquid argon than their vendor ratings in air at room temperature. Failure modes range from full destruction to coating damage. In cases where breakdown was not catastrophic, subsequent breakdown voltages were lower in subsequent measuring runs. One resistor type withstands 131\,kV pulses, the limit of the test setup.
Isolation_ID_Protocol_Jozwick_1.docx
Creators: name: Estes, Anne
name: Jozwick, Anna
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: 60408 Genomics

description: Isolation, DNA extraction, 16S rRNA gene amplification, and sequencing to identify bacteria isolated from the skin mucus of healthy laboratory-reader zebrafish DNA Protocol #1. A modified boil prep method.
Theoretical, antioxidant, antidiabetic and in silico molecular docking and pharmacokinetics studies of heteroleptic oxovanadium(IV) complexes of thiosemicarbazone-based ligands and diclofenac
Creators: name: Ahmed, Sumeer
name: Rafi, Ummer Muhammed
name: Kumar, Raju Senthil
name: Bhat, Ajmal Rashid
name: Berredjem, Malika
name: Niranjan, Vidya
name: C., Lavanya
name: Rahiman, Aziz Kalilur
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biochemistry
Space Science
Medicine
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Cancer

description: A series of new heteroleptic oxovanadium(IV) complexes with the general formula [VOL1–6(Dcf)] (1–6), where L1−6 = thiosemicarbazone (TSC)-based ligands and Dcf = diclofenac have been synthesized and characterized. The spectral studies along with the density functional theory calculations evidenced the distorted square-pyramidal geometry around oxovanadium(IV) ion through imine nitrogen and thione sulfur atoms of TSC moiety, and two asymmetric carboxylate oxygen atoms of diclofenac drug. The complexes were evaluated for in vitro antioxidant activity using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), 2,2'-diphenyl-1-picrylhydrazyl (DPPH), hydrogen peroxide (H2O2) and superoxide radical scavenging assays with respect to the standard antioxidant drugs butylated hydroxyanisole (BHA) and rutin. The in vitro antidiabetic activity of the complexes was tested with enzymes such as α-amylase, α-glucosidase and glucose-6-phosphatase. The complexes containing methyl substituent showed higher activity than that containing the nitro substituent due to the electron-donating effect of methyl group. The in silico molecular docking studies of the oxovanadium(IV) complexes with α-amylase and α-glucosidase enzymes showed strong interaction via hydrogen bonding and hydrophobic interactions. The dynamic behavior of the proposed complexes was analyzed by molecular dynamics (MDs) simulations, which revealed the stability of docked structures with α-amylase and α-glucosidase enzymes. The in silico physicochemical and pharmacokinetics parameters, such as Lipinski’s ‘rule of five’, Veber’s rule and absorption, distribution, metabolism and excretion (ADME) properties predicted non-toxic, non-carcinogenic and safe oral administration of the synthesized complexes. Communicated by Ramaswamy H. Sarma
Monoclonal antibodies to the apical chloride channel in Necturus gallbladder inhibit the chloride conductance.
Creators: name: Falk, R. J.
name: Finn, A. L.
name: Tsai, L. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1989

description: Monoclonal antibodies raised by injecting Necturus gallbladder cells into mice were tested for their ability to inhibit the apical chloride conductance induced by elevation of cellular cAMP. Five of these monoclonal antibodies bound to the apical cells, as shown by indirect immunofluorescence microscopy, and inhibited the chloride conductance; one antibody that bound only to subepithelial smooth muscle, by indirect immunofluorescence microscopy, showed no inhibition of chloride transport. The channel or a closely related molecule is present in the membrane whether or not the pathway is open, since, in addition to inhibiting the conductance of the open channel, the antibody also bound to the membrane in the resting state and prevented subsequent opening of the channel. The antibody was shown to recognize, by ELISA, epitopes from the Necturus gallbladder and small intestine. Finally, by Western blot analysis of Necturus gallbladder homogenates, the antibody was shown to recognize two protein bands of Mr 219,000 and Mr 69,000. This antibody should permit isolation and characterization of this important ion channel.
The Yin and Yang of Software Development: On the Relationship between Design Patterns and Code Smells
Creators: name: Giordano, Giammaria
name: Sellitto, Giulia
name: Palomba, Fabio
name: Ferrucci, Filomena
Publisher: name: figshare
Year: 2023
Subjects: Empirical software engineering

description: This repository contains all the materials to replicate this study.
Sequence of the intron/exon junctions of the coding region of the human androgen receptor gene and identification of a point mutation in a family with complete androgen insensitivity.
Creators: name: Simental, J. A.
name: French, F. S.
name: Lubahn, D. B.
name: Migeon, C. J.
name: Higgs, H. N.
name: Brown, T. R.
name: Wilson, E. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1989

description: Androgens act through a receptor protein (AR) to mediate sex differentiation and development of the male phenotype. The authors have isolated the eight exons in the amino acid coding region of the AR gene from a human X chromosome library. Nucleotide sequences of the AR gene intron/exon boundaries were determined for use in designing synthetic oligonucleotide primers to bracket coding exons for amplification by the polymerase chain reaction. Genomic DNA was amplified from 46, XY phenotypic female siblings with complete androgen insensitivity syndrome. AR binding affinity for dihydrotestosterone in the affected siblings was lower than in normal males, but the binding capacity was normal. Sequence analysis of amplified exons demonstrated within the AR steroid-binding domain (exon G) a single guanine to adenine mutation, resulting in replacement of valine with methionine at amino acid residue 866. As expected, the carrier mother had both normal and mutant AR genes. Thus, a single point mutation in the steroid-binding domain of the AR gene correlated with the expression of an AR protein ineffective in stimulating male sexual development.
Effect of strain on electronic and thermoelectric properties of few layers to bulk MoS$_{2}$
Creators: name: Bhattacharyya, Swastibrata
name: Pandey, Tribhuwan
name: Singh, Abhishek K.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The sensitive dependence of electronic and thermoelectric properties of MoS$_2$ on the applied strain opens up a variety of applications in the emerging area of straintronics. Using first principles based density functional theory calculations, we show that the band gap of few layers of MoS$_2$ can be tuned by applying i) normal compressive (NC), ii) biaxial compressive (BC), and iii) biaxial tensile (BT) strain. A reversible semiconductor to metal transition (S-M transition) is observed under all three types of strain. In the case of NC strain, the threshold strain at which S-M transition occurs increases with increasing number of layers and becomes maximum for the bulk. On the other hand, the threshold strain for S-M transition in both BC and BT strain decreases with the increase in number of layers. The difference in the mechanisms for the S-M transition is explained for different types of applied strain. Furthermore, the effect of strain type and number of layers on the transport properties are also studied using Botzmann transport theory. We optimize the transport properties as a function of number of layers and applied strain. 3L- and 2L-MoS$_2$ emerge as the most efficient thermoelectric material under NC and BT strain, respectively. The calculated thermopower is large and comparable to some of the best thermoelectric materials. A comparison between the feasibility of these three types of strain is also discussed.
description: 18 pages, 7 figures
Specific photoaffinity labeling of two plasma membrane polypeptides with an azido auxin
Creators: name: Rayle, D. L.
name: Hicks, G. R.
name: Jones, A. M.
name: Lomax, T. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1989

description: Plasma membrane vesicles were isolated from zucchini (
The (A)BC excinuclease of Escherichia coli has only the UvrB and UvrC subunits in the incision complex.
Creators: name: Orren, D. K.
name: Sancar, A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1989

description: The uvrA, uvrB, and uvrC genes control excision repair in Escherichia coli. Cells with mutations in any of these three genes cannot repair DNA by nucleotide excision. When the purified gene products--the UvrA, UvrB, and UvrC proteins--are mixed together, an excision nuclease is formed that incises on both sides of the damaged nucleotide in an ATP-dependent reaction; it has been presumed that the excision nuclease was an ABC complex containing all three Uvr proteins. To determine the stoichiometry of the subunits in the enzyme, we conducted hydrodynamic studies with mixtures of the subunits with or without DNA substrate. We found that without DNA the UvrA subunit is a dimer and that when UvrB protein is also present, a (UvrA)2(UvrB)1 complex forms. Without DNA no detectable interaction of either the UvrA or UvrB subunits or the (UvrA)2(UvrB)1 complex with the UvrC subunit occurs. Unexpectedly, with UV-irradiated DNA, the UvrA/UvrB ratio in isolated DNA-protein complexes is variable, and the ratio becomes infinitesimally low as the UvrA concentration in the reaction mixture decreases. Under conditions of saturating UvrB protein approximately one UvrB molecule binds to DNA per damaged site in a reaction that requires catalytic amounts of UvrA subunit. Addition of UvrC protein to purified UvrB-DNA complexes results in rapid incision of the DNA, presumably catalyzed by an excision nuclease containing only UvrB and UvrC subunits.
Brevi note intorno ad un recente studio sulla committenza artistica in età macedone (867-1025)
Creators: name: Della Valle, Mauro
Publisher: name: Bisanzio e l'Occidente
Year: 2018

description: Short notes around a recent study on patronage in the age of the Macedonian dinasty (867-1025). Architecture, frescoes and mosaics, luxury arts, illuminated manuscripts from an age of splendour studied with the closest attention to the monument itself, to the sources and secondary literature. An understudied field of Byzatine art comes to life anew.
description: Bisanzio e l'Occidente, V. 1 (2018)
The octamer motif is a B-lymphocyte-specific regulatory element of the HLA-DR alpha gene promoter.
Creators: name: Sherman, P. A.
name: Ting, J. P.
name: Wloch, M. K.
name: Heguy, A.
name: Roeder, R. G.
name: Basta, P. V.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1989

description: The human class II gene, HLA-DR alpha, contains an octanucleotide sequence ATTTGCAT located approximately 40 base pairs upstream of the transcription initiation site. We have investigated the transcriptional function of the DR alpha octamer in human B-lymphoblastoid cells and non-B cells. Deletion and substitution mutagenesis of the octamer sequence greatly reduced the activity of the DR alpha promoter in both in vivo and in vitro cell-free transcription systems of B-cell origin. Conversely, these mutations did not affect promoter activity in several non-B-cell lines that express the DR alpha gene. Removal of octamer-binding proteins by in vivo titration with an octamer-containing competitor plasmid reduced DR alpha promoter activity in B-lymphoblastoid cells. These results suggest that a protein-octamer interaction, most likely involving the B-cell-specific octamer binding protein (OTF-2), is required for DR alpha promoter function in B-lymphoblastoid cells but not in non-B cells.
1. Childhood trauma and physiological health: An exploratory study examining the role of groups using secondary data
Creators: name: McMahon, Grace
name: Muldoon, Orla
name: Griffin, Siobhán
name: Nightingale, Alastair
name: Bradshaw, Daragh
name: Borinca, Islam
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences

description: This is an exploratory study examining the role of groups (social group memberships and support groups) in the association between trauma and physiological biomarkers of health.
The Yin and Yang of Software Quality: Do Design Patterns Induce Code Smells?
Creators: name: Giordano, Giammaria
name: Palomba, Fabio
name: Ferrucci, Filomena
name: Sellitto, Giulia
Publisher: name: figshare
Year: 2023
Subjects: Empirical software engineering

description: This repository contains all the materials to replicate this study.
Characterization and expression of the complementary DNA encoding rat histidine decarboxylase.
Creators: name: Joseph, D. R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1990

description: Histamine is a neurotransmitter in the central nervous system and an important modulator of gastric acid secretion, vasomotor control, inflammation, and allergic reactions. In biological systems the formation of histamine from its precursor histidine is catalyzed by the enzyme L-histidine decarboxylase (HDC; L-histidine carboxy-lyase, EC 4.1.1.22). We have cloned HDC-encoding cDNA from a fetal rat liver cDNA library (phage lambda gt11) have deduced the amino acid sequence from the nucleotide sequence. The clone was proven to be HDC cDNA by expression of active recombinant enzyme in COS cells and by chromosomal mapping. The cDNA encodes a protein of Mr 73,450 (655 amino acid residues). The discrepancy between this molecular weight and the size of the purified fetal liver protein subunits [Taguchi, Y., Watanabe, T., Kubota, H., Hayashi, H. & Wada, H. (1984) J. Biol. Chem. 259, 5214-5221] (Mr = 54,000) suggests that HDC may be posttranslationally processed. The 469 amino acid residues from the amino-terminal portion of the protein share 50% identity with rat and Drosophila L-dopa decarboxylases and much less homology with other characterized amino acid decarboxylases.
Epstein-Barr virus small nuclear RNAs are not expressed in permissively infected cells in AIDS-associated leukoplakia.
Creators: name: Resnick, L.
name: Gilligan, K.
name: Raab-Traub, N.
name: Rajadurai, P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1990

description: Epstein-Barr virus (EBV) DNA structure and gene expression were analyzed in tissue specimens from oral hairy leukoplakia (HLP), a mucocutaneous lesion that develops in patients infected with human immunodeficiency virus (HIV). The structure of the terminal restriction enzyme fragments of EBV revealed that HLP is a permissive infection without a predominant, detectable population of EBV episomal DNA. In RNA preparations from this uniquely permissive infection, EBV replicative mRNAs could be identified by Northern analysis; however, the virally encoded small nuclear RNAs, the EBERs, were not detected in most HLP RNA preparations. In situ hybridization detected EBER expression in very rare cells. These data indicate that unlike other viral small nuclear RNAs, the EBERs are not expressed during viral replication and must participate in the complex maintenance of latent EBV infection.
When Social Media Influencers Go Political: An Exploratory Analysis on the Emergence of Political Topics Among Finnish Influencers
Creators: name: Suuronen, Aleksi
name: Reinikainen, Hanna
name: Borchers, Nils S.
name: Strandberg, Kim
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Space Science
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Social media influencers are often understood as non-political actors who, due to the impact they exert on their followers’ purchase decisions and brand attitudes, play an important role in marketing and branding. In recent years, various influencers have addressed political issues during important political events such as elections. This political aspect of social media influencing has not received much scholarly interest thus far. In one of the first exploratory studies on the topic, we surveyed over one hundred Finnish influencers and investigated the degree to which they engaged with political topics. Our results show that political topics are commonly brought up among Finnish influencers. However, many influencers also deliberately avoid addressing them because they fear what comments and conversations these topics could generate and that they could personally be targeted by aggressive internet commentators. Nevertheless, based on our findings, we argue that the digital spaces maintained by influencers can constitute a new kind of third space where the emergence of political topics can have a greater impact on the political behaviour of influencers’ followers.
Social Identity & Biological Health: A Narrative Review
Creators: name: McMahon, Grace
name: Muldoon, Orla
name: Griffin, Siobhán
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Medicine and Health Sciences
subject: Social and Behavioral Sciences

description: We aim to synthesise the existing empirical studies in the area by conducting a narrative review on the topic of social identity processes and biological health outcomes
Between Europeanism and Nativism: Exploring a Cleavage Model of European Public Sphere in Social Media
Creators: name: Sicakkan, Hakan G.
name: Heiberger, Raphael Heiko
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: The European Union’s common public sphere project dates back to the 1960s and relies on Europeanisation through the gradual eradication of communication boundaries between its member countries. However, it is evident by now that Europeanisation of national public spheres is hard to achieve by increasing overlaps between national public spheres, synchronisation of news reporting across national boundaries, or diffusion of Europeanist norms into national politics. The European Union’s common public sphere project may hence be in danger. This calls for explorations of other imaginable models of the public sphere for Europe. Are there traces of other modes of transnational public sphere emerging in Europe? In this article, we explore a models of the transnational public sphere which is based on an alternative concept of Europeanisation derived from the cleavage theory. By drawing on social media data and employing tools of social network analysis, we demonstrate the empirical possibility of a cleavage model of the European public sphere.
Gene activation is required for developmentally programmed cell death.
Creators: name: Kosz, L.
name: Schwartz, L. M.
name: Kay, B. K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1990

description: The intersegmental muscles of the tobacco hawkmoth Manduca sexta die during the 36-hr period after metamorphosis. The trigger for cell death is a fall in the ecdysteroid titer. Commitment of the intersegmental muscles to degenerate involves selective repression and activation of ecdysteroid-responsive genes. When the pattern of gene expression is altered after injection of either 20-hydroxyecdysone or actinomycin D, the muscles persist. cDNA clones have been isolated for four genes that become abundantly expressed coincident with the commitment to degenerate. The data presented here indicate that programmed cell death is not due to the cessation of macromolecular synthesis in condemned cells but rather is due to the activation of a differentiative pathway.
Sanggenol B, a plant bioactive, as a safer alternative to tackle cancer by antagonising human FGFR
Creators: name: Nagaraj, Achyuta
name: Raghavan, Sriram Srinivasa
name: Niraikulam, Ayyadurai
name: Gautham, Namasivayam
name: Gunasekaran, Krishnasamy
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified

description: Fibroblast Growth Receptor Factor (FGFR) are a family of proteins which are, in addition to their biological role, are involved in various pathological functions, such as cancer cellular proliferation, and metastasis. Deregulation of FGFRs at various points could result in malignancy. A conformational transition of the DFG (Asp–Phe–Gly) motif can switch the enzyme from a catalytically active (DFG-in) to an inactive (DFG-out) state. There are a few FDFR inhibitors which have received approval from the FDA, but these have adverse side effects. Hence, there is a demand for safer alternatives. With this aim, Ligand and Structure based virtual screening was carried to identify suitable lead molecule. In this process, Four Featured atom-based 3D Pharmacophore with quantitative structure–activity relationship analysis (3D-QSAR) was developed. The External validation of the hypothesis was carried invoking criteria such as Area under the ROC curve. Natural plant compound databases such as the Traditional Chinese medicine, NPACT and the ZINC Natural databases were chosen for pharmacophore filtering, which was followed by virtual screening against FGFR isoforms. The compound Sanggenol B was identified as the most suitable lead molecule. Structural stability of the protein-ligand complex and interactions of the ligand (Sanggenol B & the reference compound Ponatinib) with FGFR were analysed for 1000 ns (triplicate) by means of molecular simulation and the binding free energy was calculated using MMGBSA. Sanggenol B (PubChem CID: 15233694) binds effectively at the active site with favourable energies and is proposed as a safe alternative from a natural source. Communicated by Ramaswamy H. Sarma
Immunodominant regions for T helper-cell sensitization on the human nicotinic receptor alpha subunit in myasthenia gravis.
Creators: name: Protti, M. P.
name: Conti-Tronconi, B. M.
name: Manfredi, A. A.
name: Straub, C.
name: Howard, J. F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1990

description: In myasthenia gravis an autoimmune response against the nicotinic acetylcholine receptor (AChR) occurs. The alpha subunit of the AChR contains both the epitope(s) that dominates the antibody response (main immunogenic region) and epitopes involved in T helper cell sensitization. In this study, overlapping synthetic peptides corresponding to the complete AChR alpha-subunit sequence were used to propagate polyclonal AChR-specific T helper cell lines from four myasthenic patients of different HLA types. Response of the T helper lines to the individual peptides was studied. Four immunodominant sequence segments were identified--i.e., residues 48-67, 101-120, 304-322, and 419-437. These regions did not include residues known to form the main immunogenic region or the cholinergic binding site, and they frequently contained sequence motifs that have been proposed to be related to T-epitope formation.
Effects of some microelements on antifungal activity and biomass of the Actinomyces producing Validamycin-A
Creators: name: Luong, Huu Thanh
name: Vu, Thuy Nga
name: Ha, Thi Thuy
name: Nguyen, Kieu Bang Tam
name: Dao, Thi Hong Van
Publisher: name: Journal of Vietnamese Environment
Year: 2018

description: Validamycin A (Val-A) is an aminoglycoside's antibiotic with anti-fungal activity. Val-A synthesized by Streptomyces hygroscopicus strain depending on the growth and development of this actinomyces. In this study, the effects of Mn and Zn on the antifungal activity and biomass of the Streptomyces hygroscopicus were conducted. The results showed that micronutrients Mn, Zn had significant effects on biomass as well as antifungal activity of strain Streptomyces hygroscopicus-DA15. With the addition of Mn at a concentration of 1μg/l of the nutrient medium, biomass of Streptomyces hygroscopicus was 2.85 ± 0.02 g/ml, the anti-fungal Rhizoctonia solani (R. solani) round diameter reached 3.5 ± 0.2 cm. With the addition of Zn = 3 µg/l of the nutrient medium, biomass of Streptomyces hygroscopicus DA15 was 4.5 ± 0.02 g/ml, the anti-fungal R. solani diameter reached 3.4 ± 0.2 cm. Validamycin A (val-A) là một loại kháng sinh có khả năng kháng nấm, được tổng hợp bởi xạ khuẩn Streptomyces hygroscopicus và phụ thuộc vào quá trình sinh trưởng, phát triển của xạ khuẩn. Bài báo này đánh giá ảnh hưởng của nguyên tố vi lượng Mn, Zn đến hoạt tính kháng nấm Rhizoctonia solani (R. solani) và sinh khối của chủng Streptomyces hygroscopicus DA15. Khi bổ sung Mn vào môi trường nuôi cấy với nồng độ 1μg/l, sinh khối của Streptomyces hygroscopicus-DA15 đạt 2,85±0,02g/ml, đường kính vòng kháng nấm đạt 3,5±0,2cm. Bổ sung Zn vào môi trường nuôi cấy với hàm lượng Zn=3µg/l, sinh khối của Streptomyces hygroscopicus DA15 đạt 4,5±0,02g/ml và đường kính vòng kháng nấm đạt 3,4±0,2cm.
description: Journal of Vietnamese Environment, Vol 9 No 3 (2018)
Intercalators promote the binding of RecA protein to double-stranded DNA.
Creators: name: Thresher, R. J.
name: Griffith, J. D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1990

description: Ethidium bromide, acridine orange, 4'-(9-acridinylamino)methanesulfon-o-anisidide (o-AMSA), and m-AMSA induce the rapid binding of RecA protein to double-stranded (ds) DNA. The filaments formed appear to retain the drug and are 12.8 nm in diameter with an 8.0-nm pitch. Two classes of drugs have been distinguished: (i) those that bind to RecA protein and induce assembly at low relative concentrations (e.g., ethidium bromide) and (ii) those that do not appear to interact directly with RecA protein and must be present at relatively high drug concentrations to stimulate assembly (e.g., m-AMSA). Ethidium bromide, acridine orange, and quinacrine inhibit RecA protein binding to single-stranded DNA. Addition of ATP to the drug-induced filaments causes the protein to rapidly dissociate from dsDNA, and protein binding to dsDNA diminishes upon extended exposure to room light. We suggest that the structure of the drug-induced filaments may be more typical of the complex that initiates RecA protein assembly along DNA rather than the product of extensive polymerization as induced by adenosine 5'-[gamma-thio]triphosphate.
The Yin and Yang of Software Development: On the Relationship between Design Patterns and Code Smells
Creators: name: Giordano, Giammaria
name: Palomba, Fabio
name: Ferrucci, Filomena
name: Sellitto, Giulia
Publisher: name: figshare
Year: 2023
Subjects: Empirical software engineering

description: This repository contains all the materials to replicate this study.