cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Configuration of wobble base pairs having pyrimidines as anticodon wobble bases: significance for codon degeneracy
Creators: name: Gunajyoti Das
name: R.H. Duncan Lyngdoh
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: Degeneracy of the genetic code was attributed by Crick to imprecise hydrogen-bonded base-pairing at the wobble position during codon–anticodon pairing. The Crick wobble rules define but do not explain the RNA base pair combinations allowed at this position. We select six pyrimidine bases functioning as anticodon wobble bases (AWBs) to study their H-bonded pairing properties with the four major RNA bases using density functional theory at the B3LYP/6-31G(d,p) level. This is done to assess the extent to which the configuration of a solitary RNA wobble base pair may in itself determine specificity and degeneracy of the genetic code by allowing or disallowing the given base pair during codon–anticodon pairing. Calculated values of select configuration markers for the base pairs screen well between allowed and disallowed base pairs for most cases examined here, where the base pair width emerges as an important factor. A few allowed wobble pairs invoke the involvement of RNA nucleoside conformation, as well as involvement of the exocyclic substituent in H-bonding. This study, however, cannot explain the disallowed status of the Ura⋯Gua wobble pair on the basis of configuration alone. Explanation of the allowed status of the V⋯Ura pair requires further study on the mediatory role of water molecules. Apart from these two cases, these computational results are sufficient, on the basis of base pair configuration alone, to account for the specificity and degeneracy of the genetic code for all known cases of codon–anticodon pairing which involve the pyrimidine AWBs studied here.
Structural glycobiology of heparinase II from Pedobacter heparinus
Creators: name: Fernandes, Cláudia L.
name: Escouto, Gabriela B.
name: Verli, Hugo
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: The current work presents a conformational evaluation of heparinase II (hepII) from Pedobacter heparinus, employing molecular dynamics (MD) simulations, in order to characterize the main features of the enzyme dynamics, as well as the role of the glycan and metal components on the protein scaffold. Accordingly, four systems were simulated, encompassing nonglycosylated hepII without structural ions, nonglycosylated hepII with Zn2+, nonglycosylated hepII with Ca2+, and glycosylated hepII with Zn2+. The obtained data suggest a role for Zn2+ in modulating the protein flexibility at specific loop regions. Such flexibility pattern is not properly maintained in the absence of such structural ion or when the ion is replaced by Ca2+. Still, semiempirical calculations suggest more favorable interactions with Zn2+. These events correlate with the experimentally reported inhibitory effect of calcium over hepII. Additionally, the glycan chain seems able to promote an additional stabilization on hepII dynamics. Taken together, these results improve our understanding of the structural and dynamical features of hepII, as well as atomic-level comprehension of previous experimental data.
Full length amylin oligomer aggregation: insights from molecular dynamics simulations and implications for design of aggregation inhibitors
Creators: name: Workalemahu Mikre Berhanu
name: Artëm E. Masunov
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: Amyloid oligomers are considered to play essential roles in the pathogenesis of amyloid-related degenerative diseases including type 2 diabetes. Using an explicit solvent all atomic MD simulation, we explored the stability, conformational dynamics and association force of different single-layer models of the full-length wild-type and glycine mutants of amylin (pentamer) obtained from a recent high resolution fibril model. The RMSF profile shows enhanced flexibility in the disorder (Lys1-Cys7) and turn region (Ser19-Gly23), along with smallest fluctuation at the residues (Asn14-Phe15-Leu16-Val17-His18) of β1 region and (Ala25-Ile26-Leu27-Ser28-Ser29) of the β2 region. We obtained a significant difference in backbone RMSD between the wild-type and the mutants, indicating that mutations affected the stability of the peptide. The RMSD and RMSF profiles indicate the edge and loop residues are the primary contributors to the overall conformational changes. The degree of structural similarity between the oligomers in the simulation and the fibril conformation is proposed as the possible explanation for experimentally observed shortening of the nucleation lag phase of amylin with oligomer seeding. On the basis of structure-stability findings, the β1 and β2 portions are optimal target for further anti-amyloid drug design. The MM-PBSA binding energy calculation reveals the binding of amylin: amylin strands in single layer is dominated by contributions from van der Waals interactions. The non-polar solvation term is also found to be favorable. While the electrostatic interactions and polar solvation energy was found to be favorable for the interaction for the larger aggregate and unfavorable for the smaller aggregates. A per-residue decomposition of the binding free energy has been performed to identify the residues contributing most to the self-association free energy. Residues found in the β-sheet regions were found to be key residue making the largest favorable contributions to the single-layer association. The result from our simulation could be used in rational design of new amylinomimetic agent, amylin aggregation inhibitors and amylin-specific biomarkers.
Words within worlds: theorising simulation, role play and genre in university assessment
Creators: name: Moore, Timothy
name: Johnson, Andrew
Publisher: name: Swinburne
Year: 2024

description: This paper explores the use of innovative forms of assessment involving ‘simulation’ or role play, from both theoretical and practical perspectives. While most university assessment tasks ask students to respond as learners within their discipline, a growing number of assessment tasks across many disciplines construe the situation differently, ascribing particular identities to the writer (often professional, or ‘non-academic’) and prescribing specific contexts to the task which may also be non-academic. Hence, the ‘genre’ in which the student is assessed is also altered. Current literature on authentic assessment (Luongo Orlando, 2003), context-based learning (Williams, 2008) and situated learning (Gee, 2004) suggests that such simulated assessment contributes to the development of students’ applicable knowledge and communication strategies in both academic and professional contexts. The research on which this paper reports is based on a corpus of assessment tasks from a range of disciplines that the authors are compiling which involve simulation in some form. The paper presents specific examples from the corpus which strike the authors as being particularly innovative and imaginative in their design. In discussing these examples, the paper seeks to lay out schematically some of the situational variables that enter into the design of such tasks, including authorial role, audience, mode, genre and knowledge base. The authors argue that the value of such assessment is ultimately a ‘meta-communicative’ one: for students to be able to explore in some principled and critical way how the disciplinary expertise they are acquiring in their studies might be shaped and adapted for a range of contexts and circumstances.
Accurate prediction of disorder in protein chains with a comprehensive and empirically designed consensus
Creators: name: Fan, Xiao
name: Lukasz Kurgan
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: Availability of computational methods that predict disorder from protein sequences fuels rapid advancements in the protein disorder field. The most accurate predictions are usually obtained with consensus-based approaches. However, their design is performed in an ad hoc manner. We perform first-of-its-kind rational design where we empirically search for an optimal mixture of base methods, selected out of a comprehensive set of 20 modern predictors, and we explore several novel ways to build the consensus. Our method for the prediction of disorder based on Consensus of Predictors (disCoP) combines seven base methods, utilizes custom-designed set of selected 11 features that aggregate base predictions over a sequence window and uses binomial deviance loss-based regression to implement the consensus. Empirical tests performed on an independent benchmark set (with low-sequence similarity compared with proteins used to design disCoP), shows that disCoP provides statistically significant improvements with at least moderate magnitude of differences. disCoP outperforms 28 predictors, including other state-of-the-art consensuses, and achieves Area Under the ROC Curve of .85 and Matthews Correlation Coefficient of .5 compared with .83 and .48 of the best considered approach, respectively. Our consensus provides high rate of correct disorder predictions, especially when low rate of incorrect disorder predictions is desired. We are first to comprehensively assess predictions in the context of several functional types of disorder and we demonstrate that disCoP generates accurate predictions of disorder located at the post-translational modification sites (in particular phosphorylation sites) and in autoregulatory and flexible linker regions. disCoP is available at http://biomine.ece.ualberta.ca/disCoP/.
Knowledge Graphs & Socio-Technical Aspects of Hybrid AI
Creators: name: Marta Sabou
name: Axel Polleres
Publisher: name: Zenodo
Year: 2022

description: Our institute encompasses two core research groups (lead by Prof. Polleres and Prof. Sabou respectively) that synergistically work on several complementary topics related to Hybrid AI systems that combine both symbolic and sub-symbolic AI.
title: Ein verfassungsrechtliches Fundament für Auslandseinsätze der Bundeswehr durch Bindung an das Völkerrecht
Creators: name: Lange, Felix
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2022
Subjects: subject: 342

description: Verfassungsblog: On Matters Constitutional
title: RACIAL OPPRESSION AND THE BRITISH STATE INTO THE EIGHTIES
Creators: name: Downing, John
Publisher: name: University of Massachusetts Amherst
Year: 2024

description: As Visiting Professor of Sociology at the University of Massachusetts/ Amherst for the academic year 1980-81, the author of this article read the paper "Racial Oppression and the British State" as one of the Five College Black Studies Faculty Seminar Series on December 2, 1980.
Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless ensemble
Creators: name: Coimbra, João T.S.
name: Sousa, Sérgio F.
name: Fernandes, Pedro A.
name: Rangel, Maria
name: Ramos, Maria J.
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Computational Biology
subject: Hematology
subject: Cancer
subject: Mathematics
subject: FOS: Mathematics
subject: Biological Sciences
subject: Chemistry
subject: Biotechnology
subject: Genetics
subject: FOS: Biological sciences
subject: Cell Biology
subject: Medicine
subject: Physics
subject: Biochemistry
subject: Biophysics

description: The AMBER family of force fields is one of the most commonly used alternatives to describe proteins and drug-like molecules in molecular dynamics simulations. However, the absence of a specific set of parameters for lipids has been limiting the widespread application of this force field in biomembrane simulations, including membrane protein simulations and drug-membrane simulations. Here, we report the systematic parameterization of 12 common lipid types consistent with the General Amber Force Field (GAFF), with charge-parameters determined with RESP at the HF/6–31G(d) level of theory, to be consistent with AMBER. The accuracy of the scheme was evaluated by comparing predicted and experimental values for structural lipid properties in MD simulations in an NPT ensemble with explicit solvent in 100:100 bilayer systems. Globally, a consistent agreement with experimental reference data on membrane structures was achieved for some lipid types when using the typical MD conditions normally employed when handling membrane proteins and drug-membrane simulations (a tensionless NPT ensemble, 310 K), without the application of any of the constraints often used in other biomembrane simulations (such as the surface tension and the total simulation box area). The present set of parameters and the universal approach used in the parameterization of all the lipid types described here, as well as the consistency with the AMBER force field family, together with the tensionless NPT ensemble used, opens the door to systematic studies combining lipid components with small drug-like molecules or membrane proteins and show the potential of GAFF in dealing with biomembranes.
Supporting information from Dispersal ability and its consequences for population genetic differentiation and diversification
Creators: name: Suárez, Daniel
name: Arribas, Paula
name: Jiménez-García, Eduardo
name: Emerson, Brent C.
Publisher: name: The Royal Society
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology

description: Figures and tables that were refered within the main text
Electrostatic map of T7 DNA: comparative analysis of functional and electrostatic properties of T7 RNA polymerase-specific promoters
Creators: name: S.G. Kamzolova
name: P.M. Beskaravainy
name: A.A. Osypov
name: T.R. Dzhelyadin
name: E.A. Temlyakova
name: A.A. Sorokin
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: The entire T7 bacteriophage genome contains 39937 base pairs (Database NCBI RefSeq N1001604). Here, electrostatic potential distribution around double helical T7 DNA was calculated by Coulomb method using the computer program of Sorokin A.A. (lptolik@gmail.com). Electrostatic profiles of 17 promoters recognized by T7 phage-specific RNA polymerase were analyzed. It was shown that electrostatic profiles of all T7 RNA polymerase-specific promoters can be characterized by distinctive motifs which are specific for each promoter class. Comparative analysis of electrostatic profiles of native T7 promoters of different classes demonstrates that T7 RNA polymerase can differentiate them due to their electrostatic features.
Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein–DNA recognition
Creators: name: Mariia Yu. Zhitnikova
name: Boryskina, Olena P.
name: Shestopalova, Anna V.
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: Variations of the shape and polarity of the DNA grooves caused by changes of the DNA conformation play an important role in the DNA readout. Despite the fact that non-canonical trans and gauche- conformations of the DNA backbone angle γ (O5′–C5′–C4′–C3′) are frequently found in the DNA crystal structures, their possible role in the DNA recognition has not been studied systematically. In order to fill in this gap, we analyze the available high-resolution crystal structures of the naked and complexed DNA. The analysis shows that the non-canonical γ angle conformations are present both in the naked and bound DNA, more often in the bound vs. naked DNA, and in the nucleotides with the A-like vs. the B-like sugar pucker. The alternative angle γ torsions are more frequently observed in the purines with the A-like sugar pucker and in the pyrimidines with the B-like sugar conformation. The minor groove of the nucleotides with non-canonical γ angle conformation is more polar, while the major groove is more hydrophobic than in the nucleotides with the classical γ torsions due to variations in exposure of the polar and hydrophobic groups of the DNA backbone. The propensity of the nucleotides with different γ angle conformations to participate in the protein–nucleic acid contacts in the minor and major grooves is connected with their sugar pucker and sequence-specific. Our findings imply that the angle γ transitions contribute to the process of the protein–DNA recognition due to modification of the polar/hydrophobic profile of the DNA grooves.
Discovery of novel insomnia leads from screening traditional Chinese medicine database
Creators: name: Hsin-Yi Chen
name: Su-Sen Chang
name: Yueh-Chiu Chan
name: Chen, Calvin Yu-Chian
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: Insomnia is a prominent modern disease that affects an increasing population. Undesirable side effects of commercial drugs highlight the need to develop novel insomnia drugs. Virtual screening of traditional chinese medicine Database@Taiwan (TCM Database@Taiwan) identified 2-O-Caffeoyl tartaric acid (1), 2-O-Feruloyl tartaric acid (2), and Mumefural (3) as potential agonists for both gamma-amino butyric acid (GABA) or benzodiazepine (BZ) binding sites. The TCM candidates exhibited higher affinity than GABA and Zolpidem, a phenomenon that could be attributed to higher quantity of stabilizing H-bonds. Efficacy profiles using support vector machines and pharmacophore contour also suggest drug potential of the TCM candidates. Fragments added to the de novo derivatives 3a, 3b, 3c for GABA binding site, and 1a, 2a, and 3d for BZ binding site contributed to new binding sites and structural stability, further optimizing binding to GABA or BZ binding sites. Increased opening of the ion channel by candidate ligands provide strong support for their potential biological functions. The dual binding properties of the TCM candidates present a unique opportunity to develop twin-targeting drugs with less side effects. Derivative structures can be used as starting points for developing high affinity GABAA receptor agonists with specificity towards GABA binding site and BZ binding site.
Are hot-spots occluded from water?
Creators: name: Moreira, Irina Sousa
name: Ramos, Rui Miguel
name: Joao Miguel Martins
name: Fernandes, Pedro Alexandrino
name: Ramos, Maria João
Publisher: name: Taylor & Francis
Year: 2013
Subjects: Molecular Biology

description: Protein–protein interactions are the basis of many biological processes and are governed by focused regions with high binding affinities, the warm- and hot-spots. It was proposed that these regions are surrounded by areas with higher packing density leading to solvent exclusion around them – “the O-ring theory.” This important inference still lacks sufficient demonstration. We have used Molecular Dynamics (MD) simulations to investigate the validity of the O-ring theory in the context of the conformational flexibility of the proteins, which is critical for function, in general, and for interaction with water, in particular. The MD results were analyzed for a variety of solvent-accessible surface area (SASA) features, radial distribution functions (RDFs), protein–water distances, and water residence times. The measurement of the average solvent-accessible surface area features for the warm- and hot-spots and the null-spots, as well as data for corresponding RDFs, identify distinct properties for these two sets of residues. Warm- and hot-spots are found to be occluded from the solvent. However, it has to be borne in mind that water-mediated interactions have significant power to construct an extensive and strongly bonded interface. We observed that warm- and hot-spots tend to form hydrogen bond (H-bond) networks with water molecules that have an occupancy around 90%. This study provides strong evidence in support of the O-ring theory and the results show that hot-spots are indeed protected from the bulk solvent. Nevertheless, the warm- and hot-spots still make water-mediated contacts, which are also important for protein–protein binding.
Australian online newspapers: a website content analysis approach to measure interactivity
Creators: name: Hashim, Lina
name: Hasan, Helen
name: Sukunesan, Suku
Publisher: name: Swinburne
Year: 2024

description: This paper addresses the growth and development of the concept of interactivity in online newspapers from the perspectives of computer-mediated communication, journalism, advertising, and information system. This paper discusses the concept of interactivity originally coined by Heeter. The study maps Heeter’s dimensions that are content availability and choice, communication opportunity, effort of users, responsiveness, and customization and management of information onto contemporary settings of Australian online newspaper industry. The researchers reviewed 12 Australian online newspapers over two snapshots using website content analysis approach. Results draws out interesting discussions as to the level of interactivity highlighted by the online newspapers industry. Content availability and choice was found to be the most significant element of interactivity. It is noted that, while the majority of Australian online newspapers offer interactive functionality for expressing opinions, blogging, contests and polls, only one online newspaper provided genuine interactive gaming.
title: Follow Your Leader – I Prefer not to: Slavery, Giorgio Agamben and Herman Melville
Creators: name: Bikundo, Edwin
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2022
Subjects: subject: Giorgio Agamben
subject: Babo
subject: Bartleby
subject: Faust
subject: Herman Melville
subject: law
subject: political theodicy
subject: slavery
subject: violence
subject: 340

description: Giorgio Agamben proffers Bartleby’s phrase “I prefer not to” as a model for paralyzing apparatuses of power rather than slave mutiny leader Babo’s phrase “follow your leader.” This article compares the strategies embodied in these characters from Herman Melville’s work of non-cooperation with versus violent resistance to violence. it argues that because the slave-figure is the shadow image of the free human in liberal democratic thought, violence is an illusory basis for emancipation. Such violence would not only be a mimicry of the oppressor by the oppressed but also relies on political theodicy in justifying violence as a necessary evil.
description: Law, Culture and the Humanities, vol. 18, no. 1, p. 4
title: Technics and Polemics in the Project of Non-human Rights
Creators: name: Mussawir, Edward
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2022
Subjects: subject: animal rights
subject: Nonhuman Rights Project
subject: person
subject: thing
subject: Roman law
subject: Yan Thomas
subject: artifice
subject: nature
subject: 340

description: This article examines the use of technics and polemics within contemporary animal rights discourse. It focuses on the Nonhuman Rights Project, a group which is currently engaged in litigation in the United States aimed at having a non-human animal recognized by the courts as a person and subject of rights. Turning to the work of the late legal historian Yan Thomas, this article explores the degree to which the categories of person and thing have tended to become sacralized in the modern discourse of animal rights in order to refashion them at a polemical and metaphysical level. This is then contrasted with the work of Roman jurisprudence which, in Thomas’s account, was capable on the contrary of filing its metaphysical categories back within the narrow technical world of the civil law. The history of legal categories reveals in this sense some of the tensions which today beset the discourse of rights in relation to the non-human.
description: Law, Culture and the Humanities, vol. 18, no. 1, p. 20
title: “I’m Making the Streets Safer Ma’am”: Race, Coloniality, and the Redemptive Theologies of Pastoral Police Power
Creators: name: Kolia, Zahir
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2022
Subjects: subject: race
subject: police
subject: law
subject: sovereignty
subject: Derrida
subject: colonialism
subject: racial profiling
subject: secular
subject: pastoral power
subject: 340

description: A number of scholarly studies have focused upon mapping the relationship between race, police power, and the sovereign capacity of law onto the coordinates of repressive force. No doubt, the racialized circuits of police violence, underpinned by the mystical foundation of sovereign authority, constitute a coercive apparatus that is marshaled by risk and security. However, rather than reduce mythic police violence to the singular vector of repression, I suggest that the propensity to punish the racialized body and make it suffer through police practices of the confessional and pastoral power imbricate with the pre-liberal Christian theology of redemption and atonement. Upon consideration of decolonial and theological-political concepts, I suggest pastoral forms of racialized police power have been articulated to utilitarian secular-liberal democratic justifications to increase community safety, suppress crime, and reify social and political solidarity through the appropriate dispensation of suffering, and, potentially death.
description: Law, Culture and the Humanities, vol. 18, no. 1, p. 73
All fibre, all the way!
Creators: name: Given, Jock
Publisher: name: Swinburne
Year: 2024

description: At the Imperial Palace, Human Nature is gearing up for two more years of 'Celebration of Motown.' But further along The Strip it's fibre-to-the-home that’s generating the excitement. And Australia's NBN is one of the stars, writes Jock Given in Las Vegas.
title: On the Duty to Host in International Law: Jacques Derrida and Political Literature
Creators: name: Cohen, Naor
name: Fuchs, Ilan
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2022
Subjects: subject: politics of hospitality
subject: Derrida
subject: international humanitarian law
subject: refugees
subject: Disgrace
subject: South Africa
subject: 340

description: Jacques Derrida’s politics of hospitality explores the tension and interdependency that exist between hosts and guests. This article uses Derrida’s idea of hospitality and attempts to understand how it applies to the 21st century refugee crisis in the context of human displacement, state of refugee and immigration. We turn to the help of fiction as a critical tool in scrutinizing current political discourses. Specifically, we offer an analysis of J.M Coetzee’s novel Disgrace in light of Derrida’s theme of hospitality. Coetzee – who was awarded the Nobel Prize – presents a vivid portrait of post-apartheid South Africa that offers a contradictory perspective to Nelson Mandela’s vision of democracy in South Africa. His novel suggests that the inherent violence of colonialism can neither be resolved nor dissolved merely by expressions of regret and forgiveness. By extension, we ask if liberal democracies and international humanitarian law can offer a policy of hospitality that is both morally anchored and practical.
description: Law, Culture and the Humanities, vol. 18, no. 1, p. 114
Putative osmosensor – OsHK3b – a histidine kinase protein from rice shows high structural conservation with its ortholog AtHK1 from Arabidopsis
Creators: name: Kushwaha, Hemant Ritturaj
name: Singla-Pareek, Sneh Lata
name: Pareek, Ashwani
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: Prokaryotes and eukaryotes respond to various environmental stimuli using the two-component system (TCS). Essentially, it consists of membrane-bound histidine kinase (HK) which senses the stimuli and further transfers the signal to the response regulator, which in turn, regulates expression of various target genes. Recently, sequence-based genome wide analysis has been carried out in Arabidopsis and rice to identify all the putative members of TCS family. One of the members of this family i.e. AtHK1, (a putative osmosensor, hybrid-type sensory histidine kinase) is known to interact with AtHPt1 (phosphotransfer proteins) in Arabidopsis. Based on predicted rice interactome network (PRIN), the ortholog of AtHK1 in rice, OsHK3b, was found to be interacting with OsHPt2. The analysis of amino acid sequence of AtHK1 showed the presence of transmitter domain (TD) and receiver domain (RD), while OsHK3b showed presence of three conserved domains namely CHASE (signaling domain), TD, and RD. In order to elaborate on structural details of functional domains of hybrid-type HK and phosphotransfer proteins in both these genera, we have modeled them using homology modeling approach. The structural motifs present in various functional domains of the orthologous proteins were found to be highly conserved. Binding analysis of the RD domain of these sensory proteins in Arabidopsis and rice revealed the role of various residues such as histidine in HPt protein which are essential for their interaction.
Novel G-quadruplex stabilizing agents: in-silico approach and dynamics
Creators: name: Kar, Rajiv Kumar
name: Suryadevara, Priyanka
name: Jagannath Jana
name: Anirban Bhunia
name: Subhrangsu Chatterjee
Publisher: name: Taylor & Francis
Year: 2013
Subjects: Molecular Biology

description: The stabilization of overhang G-rich repetitive DNA units at the 3′-end of telomeres, which are well known to form functionally important G-quadruplex structures, is a current goal in designing novel anticancer drugs. In the present study, we have undertaken an in silico approach by molecular docking using a small molecule library to find potential G-quadruplex stabilizing agents. Two molecules, A, [N′1-imino(2-pyridyl)methyl-3,4,5-trimethoxybenzene-1-carbohydrazide] and B, [(3-[4-({[3-({4-[(2cyanoethyl)(methyl)amino]benzylidene}amino)propyl]imino}methyl)(methyl) anilino]propanenitrile)], that had good docking scores have been investigated for interaction with G-quadruplexes in a Molecular Dynamics simulation study. Fluorescence spectroscopy of G-quadruplexes bound to the screened molecules A and B was used to experimentally validate the theoretical results. The binding of ligands A and B to G-quadruplexes resulted in blue shifts of 10–18 nm, respectively, in the fluorescence emission spectra of the G-quadruplexes, demonstrating that both molecules bind to the G-face of the quadruplex. The same experiment was performed for the complexation of these small molecules with a G-rich DNA duplex, . Interestingly, no blue shift was observed in the fluorescence emission spectra of the DNA duplex in the presence of these small molecules. Thus, these findings indicated that these ligands very selectively bind to G-quadruplexes instead of the duplex DNA. In addition, a one-dimensional water ligand observed via a gradient spectroscopy Nuclear Magnetic Resonance (NMR) experiment showed that both molecules bound to the 23-mer G-quadruplex DNA. The molecular properties of the ligand–quadruplex complex have been analyzed with the help of the Adaptive Poisson-Boltzmann Solver, revealing that electrostatics govern the binding of the small molecules to G-quadruplexes. Both molecules were investigated in detail using solvation free energy calculations and Absorption, Distribution, Metabolism, Elimination and Toxicity (ADMET) predictions, which provide insight into lead optimization for designing G-quadruplex stabilizing agents; therefore, these molecules have potential as new therapeutic agents.
title: In Praise of Rebellion: Constituent Power and Dissent in the American Revolution
Creators: name: Pereira, Márcio
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2022
Subjects: subject: American Revolution
subject: Pennsylvania
subject: constituent power
subject: constituted power
subject: democracy
subject: 340

description: In the context of the American Revolution, alongside the influential notion of constituent power advocated, for instance, by the Federalists, emerged an alternative and potent perspective about this concept. This perspective, which was particularly strong in revolutionary Pennsylvania, had at least two distinctive features. First, rather than limiting constituent power to a sort of ante-room of constitutional authority, this view conferred primacy to the constituent process over the institutional machinery. Second, instead of exclusively assigning the exercise of constituent power to a few specialists, this perspective invented ways for the multitude to exercise its power directly. This article examines this particular vision of constituent power. This investigation, as I argue, can both assist in demystifying some common assumptions entrenched in the concept of constituent power and provide insights for contemporary reflection on the limits of representative democracy.
description: Law, Culture and the Humanities, vol. 18, no. 1, p. 54
Towards human and social innovation: not wanting to know in order to create
Creators: name: Hayward, Peter
name: Ramos, Jose M.
name: O'Connor, Allan
Publisher: name: Swinburne
Year: 2024

description: The formation of a venture relies, in part, upon the participants reaching a shared understanding of purpose and process. Yet in circumstances of great complexity and uncertainty how can such a shared understanding be created? If the response to complexity and uncertainty is to seek simplicity in order to find commonality then what is lost and what is at risk? Can shared understandings of purpose and process be arrived at by embracing complexity and uncertainty and if so how? These questions led us to explore the process of dialogue and communication of a team in its formative stages. Our interests were not centred upon the behavioural characteristics of the individuals in the 'forming' stage of group dynamics but rather the process of cognitive and linguistic turns, the wax and wan of ideas and, the formation of shared meaning. This process of cognitive and linguistic turns was focused thematically on the areas of foresight, innovation, entrepreneurship, and public policy. This cross disciplinary exploration sought to explore potential synergies between these domains, in particular in developing a conceptual basis for long term thinking that can inform wiser public policy.
Understanding the role of domain–domain linkers in the spatial orientation of domains in multi-domain proteins
Creators: name: Ramachandra M. Bhaskara
name: Brevern, Alexandre G. De
name: Narayanaswamy Srinivasan
Publisher: name: Taylor & Francis
Year: 2013
Subjects: Molecular Biology

description: Inter-domain linkers (IDLs)’ bridge flanking domains and support inter-domain communication in multi-domain proteins. Their sequence and conformational preferences enable them to carry out varied functions. They also provide sufficient flexibility to facilitate domain motions and, in conjunction with the interacting interfaces, they also regulate the inter-domain geometry (IDG). In spite of the basic intuitive understanding of the inter-domain orientations with respect to linker conformations and interfaces, we still do not entirely understand the precise relationship among the three. We show that IDG is evolutionarily well conserved and is constrained by the domain–domain interface interactions. The IDLs modulate the interactions by varying their lengths, conformations and local structure, thereby affecting the overall IDG. Results of our analysis provide guidelines in modelling of multi-domain proteins from the tertiary structures of constituent domain components.
title: The Legal Persona of the Video Game: The Self of Persona 4
Creators: name: Pearson, Ashley
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2022
Subjects: subject: video game
subject: Persona 4
subject: legal mask
subject: legal subject
subject: psychoanalysis
subject: ludology
subject: 340

description: This article investigates Persona 4 , a Japanese video game, as a complex retelling of the relationship of the subject to law. Through both narrative and medium, Persona 4 explores tensions of the legal subject as “persona ficta,” the imaginary identity that law uses to construct and bind subjects, demonstrating the inability of a player to let go of their fragmented identity even within a fictional setting. With the player and narrative relying on one another in a way that requires complicity to function, the player is forced to comply or not participate, a choice echoed in non-virtual life.
description: Law, Culture and the Humanities, vol. 18, no. 1, p. 35
title: Legal Form and Legal Legitimacy: The IHRA Definition of Antisemitism as a Case Study in Censored Speech
Creators: name: Gould, Rebecca Ruth
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2022
Subjects: subject: free speech
subject: academic freedom
subject: censorship
subject: speech codes
subject: hate speech
subject: legal indeterminacy
subject: Critical Legal Studies
subject: Critical Race Studies
subject: political theory
subject: universities
subject: Israel/Palestine
subject: 340

description: The challenge posed by legal indeterminacy to legal legitimacy has generally been considered from points of view internal to the law and its application. But what becomes of legal legitimacy when the legal status of a given norm is itself a matter of contestation? This article, the first extended scholarly treatment of the International Holocaust Remembrance Alliance (IHRA)’s new definition of antisemitism, pursues this question by examining recent applications of the IHRA definition within the UK following its adoption by the British government in 2016. Instead of focusing on this definition’s substantive content, I show how the document reaches beyond its self-described status as a “non-legally binding working definition” and comes to function as what I call a quasi-law, in which capacity it exercises the de facto authority of the law, without having acquired legal legitimacy. Broadly, this work elucidates the role of speech codes in restricting freedom of expression within liberal states.
description: Law, Culture and the Humanities, vol. 18, no. 1, p. 153
title: That “Vaulty Night”: Trials, Testimonies, and Critiques of Justice in Beckett’s Panopticon Prison-stage
Creators: name: Diver, Alice
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2022
Subjects: subject: Beckett
subject: justice
subject: legal
subject: courtroom
subject: panopticon
subject: trial
subject: atonement
subject: testimony
subject: purgatory
subject: guilt
subject: 340

description: Beckettian justice avoids the usual scripts of judicial processes: his trials and punishments merge, as his captive characters lock themselves into eerily repetitive, self-questioning loops of semi-existence. His prison-cell courtrooms critique the wider socio-cultural symbolism associated with indefinite incarceration and unduly harsh sentences, questioning whether retributive sanctions have the power to redeem, or to spark atonement. By turning vague but terrifying recollections into accusatory witness statements, Beckett crafts purgatories grounded in endless perception. Audiences must therefore act as jurors and gaolers: by witnessing the various “crimes” of omission (neglect, abandonment, unintentional cruelty) we are perhaps better placed to judge our own failings and frailties and capacity for resilience.
description: Law, Culture and the Humanities, vol. 18, no. 1, p. 209
Interchain hydrophobic clustering promotes rigidity in HIV-1 protease flap dynamics: new insights from Molecular Dynamics
Creators: name: Biswa Ranjan Meher
name: Mattaparthi Venkata Satish Kumar
name: Pradipta Bandyopadhyay
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: The dynamics of HIV-1 protease (HIV-pr), a drug target for HIV infection, has been studied extensively by both computational and experimental methods. The flap dynamics of HIV-pr is considered to be more important for better ligand binding and enzymatic actions. Moreover, it has been demonstrated that the drug-induced mutations can change the flap dynamics of HIV-pr affecting the binding affinity of the ligands. Therefore, detailed understanding of flap dynamics is essential for designing better inhibitors. Previous computational investigations observed significant variation in the flap opening in nanosecond time scale indicating that the dynamics is highly sensitive to the simulation protocols. To understand the sensitivity of the flap dynamics on the force field and simulation protocol, molecular dynamics simulations of HIV-pr have been performed with two different AMBER force fields, ff99 and ff02. Two different trajectories (20 ns each) were obtained using the ff99 and ff02 force field. The results showed polarizable force field (ff02) make the flap tighter than the nonpolarizable force field (ff99). Some polar interactions and hydrogen bonds involving flap residues were found to be stronger with ff02 force field. The formation of interchain hydrophobic cluster (between flap tip of one chain and active site wall of another chain) was found to be dominant in the semi-open structures obtained from the simulations irrespective of the force field. It is proposed that an inhibitor, which will promote this interchain hydrophobic clustering, may make the flaps more rigid, and presumably the effect of mutation would be small on ligand binding.
title: “Others-in-Law”: Legalism in the Economy of Religious Differences
Creators: name: David, Joseph E.
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2022
Subjects: subject: religious legalism
subject: Judaism
subject: Christianity
subject: nomocentrism
subject: reformation
subject: Martin Luther
subject: Maimonides
subject: Mendelssohn
subject: torah-nomos
subject: identity politics
subject: law-gospel
subject: identity
subject: 340

description: Religious legalism encompasses a wide range of attitudes that assign religious meaning to legal content or to legal compliance. The phenomenology of religious legalism is assuming a significant role in various contemporary debates about legal pluralism, accommodation of religious minorities, religious freedom, and so forth. This article revises this conception and the commonplace equation of Judaism and legalism. It suggests that we ought to regard both as part of the economy of religious differences by which religious identities are expressed and defined as alternatives. The common ascription of religious legalism to Judaism (and Islam) is criticized here through a historical analysis of the law-religion-identity matrix in three cultural settings: late ancient Judeo-Hellenic, medieval Judeo–Arabic, and post-Reformation Europe.
description: Law, Culture and the Humanities, vol. 18, no. 1, p. 132
title: “Satan is Black”: Frantz Fanon’s Juridico-Theology of Racialisation and Damnation
Creators: name: Koram, Kojo
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2022
Subjects: subject: colonialism
subject: political theology
subject: Fanon
subject: Milton
subject: race
subject: Vitoria
subject: international law
subject: 340

description: Recent critical legal scholarship has shown the significance of colonialism for emergence of modern international law. 1 Paralleling, sometimes interweaving, with this post-colonial/decolonial reading has been a “religious turn” in which scholars highlight the persistence of the theological-political within the ostensible secularity of law. 2 Frantz Fanon has much to offer both lines of scholarship. This article revisits the work of Fanon so as to illuminate the significance of his understanding of colonized/racialized identities as “damned” for contemporary juridical scholarship. Fanon’s Les Damnés de la Terre , when read alongside the canonical literary account of the “fall,” John Milton’s Paradise Lost , offers an account of the juridico-theological process constructing an ideal of “humanity” through turning particular subjects into deific surrogates and others into the “damned.” This article develops understandings of postcolonial/decolonial international law, international law and political/juridical theology as well as critiquing the “humanitarianism” of contemporary international legal discourse. Moreover, it helps to establish the necessity of reading Fanon as a thinker of cross-disciplinary significance.
description: Law, Culture and the Humanities, vol. 18, no. 1, p. 94
A 3D structural model and dynamics of hepatitis C virus NS3/4A protease (genotype 4a, strain ED43) suggest conformational instability of the catalytic triad: implications in catalysis and drug resistivity
Creators: name: Rimmert, Bradley
name: Sabet, Salwa
name: Ackad, Edward
name: Yousef, Mohammad S.
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: Egypt has the highest prevalence of hepatitis C virus (HCV) infection worldwide with a frequency of 15%. More than 90% of these infections are due to genotype 4, and the subtype 4a (HCV-4a) predominates. Moreover, due to the increased mobility of people, HCV-4a has recently spread to several European countries. The protease domain of the HCV nonstructural protein 3 (NS3) has been targeted for inhibition by several drugs. This approach has had marked success in inhibiting genotype 1 (HCV-1), the predominant genotype in the USA, Europe, and Japan. However, HCV-4a was found to resist inhibition by a number of these drugs, and little progress has been made to understand the structural basis of its drug resistivity. As a step forward, we sequenced the NS3 HCV-4a protease gene (strain ED43) and subsequently built a 3D structural model threaded through a template crystal structure of HCV-1b NS3 protease. The model protease, HCV-4a, shares 83% sequence identity with the template protease, HCV-1b, and has nearly identical rigid structural features. Molecular dynamics simulations predict similar overall dynamics of the two proteases. However, local dynamics and 4D analysis of the interactions between the catalytic triad residues (His57, Asp81, and Ser139) indicate conformational instability of the catalytic site in HCV-4a NS3 protease. These results suggest that the divergent dynamics behavior, more than the rigid structure, could be related to the altered catalytic activity and drug resistivity seen in HCV-4a.
From community entrepreneurship to commercial endeavour: putting theory to work in a social enterprise setting
Creators: name: Simpson, Ken
Publisher: name: Swinburne
Year: 2024

description: This paper is submitted for consideration as a potential contributor to AGSE topic 11, social entrepreneurship. Working within a context of early growth stage community business, the paper is initially presented as an extension to an earlier work of the author's, in which a process of literature review and synthesis was used to determine a model of best practice development for social enterprise. From this perspective, therefore, the principal topic of the paper is best described as an identification and evaluation of the most effective approach to implementing social enterprise theory. However, as the methodology paragraphs below will indicate, the paper also describes the processes adopted, and the outcomes that resulted, when the resulting best practice model was presented to a broad spectrum panel of public, private and third sector stakeholders for endorsement and adoption as a viable and practical business model. From this alternative perspective, the paper can be viewed as an analysis of the systemic barriers that exist between academically rigorous theory construction and commercially viable practical application.