cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Identification of antagonists to the vasotocin receptor sub-type 4 (VT4R) involved in stress by molecular modelling and verification using anterior pituitary cells
Creators: name: Jayanthi, Srinivas
name: Kang, Seong Wook
name: Bingham, Daniel
name: Tessaro, Brian A.
name: Thallapuranam K. Suresh Kumar
name: Kuenzel, Wayne J.
Publisher: name: Taylor & Francis
Year: 2013
Subjects: Molecular Biology

description: The vasotocin receptor family is homologous to the mammalian vasopressin G-protein coupled receptor (GPCR) family. The vasotocin receptor 2 (VT2R) and 4 (VT4R) have recently been shown to play important role(s) in the neuroendocrine regulation of stress in birds. A homology-based structural model of VT4R of the domestic chicken, Gallus gallus, was built using the sophisticated SYBYL-X suite. The structure of VT4R built with and without extra- and intracellular unstructured loops showed a seven-helix transmembrane domain, which is a characteristic feature of GPCRs. Several agonists and antagonists were screened by molecular docking to map their potential binding sites on the structure of VT4R. Interestingly, the presence of the N-terminal, intracellular and extracellular loops and C-terminal amino acid sequences emerging from the transmembrane domains during molecular docking appeared to influence the binding interface of the peptide agonists and peptide/non-peptide antagonists on the VT4R. The presence of unstructured loops, however, did not affect the relative binding affinity ranking of the peptide antagonists to VT4R. In general, the natural ligand, arginine vasotocin and the peptide/non-peptide antagonists were observed to be more deeply buried in the receptor. Results of in vitro inhibition experiments, using cultured anterior pituitary cells, showed excellent agreement with the binding affinity of the antagonists predicted by molecular docking. The results of this study provide valuable clues for the rational design of novel pharmaceutical compounds capable of blocking or attenuating the stress response.
Modeling stability and flexibility of α-Chymotrypsin in room temperature ionic liquids
Creators: name: Latif, Muhammad A.M.
name: Bimo A. Tejo
name: Roghayeh Abedikargiban
name: Mohd B. Abdul Rahman
name: Micaêlo, Nuno M.
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: We investigate the structure and dynamics of α-Chymotrypsin in five room temperature ionic liquids (RTILs) sharing a common cation, hydrated with different water percentages (w/w) (weight of water over protein). Results from molecular dynamics simulations are correlated with experimental evidences from studies on the activity of enzymes in RTILs. α-Chymotrypsin protein structure is closer to its native crystallographic structure in RTILs than in aqueous environment. We show that the structural properties of α-Chymotrypsin were affected by the water concentration assayed in a typical bell-shaped profile, which is also frequently reported for organic solvents. The protein structure was more native like at 10–20% of water (w/w) for all RTILs except for [BMIM][Cl]. We found that the fluctuations of the main chain in [BMIM][BF4] and [BMIM][TfO] were not significantly affected by the increasing amount of water. However, we were able to show that the flexible regions were the ones more hydrated, indicating that water is responsible for the flexibility of the protein. The solvation of the enzyme in water-immiscible RTILs, such as [BMIM][PF6] and [BMIM][Tf2N] lead to higher enzyme flexibility at increased water content. Enzyme solvation by [BMIM][Cl] resulted in ion penetration in the core enzyme structure, causing incremented flexibility and destabilization at low water percentages. All RTILs stripped water molecules from the protein surface, following a similar behavior also found in organic solvents. Anions formed structured arrangements around the protein, which allowed non-stripped water molecules to localize on the protein surface.
Substrate-mediated proton relay mechanism for the religation reaction in topoisomerase II
Creators: name: Hanaoka, Kyohei
name: Shoji, Mitsuo
name: Kondo, Daiki
name: Sato, Akimasa
name: Yang, Moon Young
name: Kamiya, Katsumasa
name: Shiraishi, Kenji
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: The DNA religation reaction of yeast type II topoisomerase (topo II) was investigated to elucidate its metal-dependent general acid/base catalysis. Quantum mechanical/molecular mechanical calculations were performed for the topo II religation reaction, and the proton transfer pathway was examined. We found a substrate-mediated proton transfer of the topo II religation reaction, which involves the 3′ OH nucleophile, the reactive phosphate, water, Arg781, and Tyr782. Metal A stabilizes the transition states, which is consistent with a two-metal mechanism in topo II. This pathway may be required for the cleavage/religation reaction of topo IA and II and will provide a general explanation for the catalytic mechanism in the topo IA and II.
Recent trend in entrepreneurship research: A content analysis of selected journals
Creators: name: Bae, Zong-Tae
name: Cha, Min-Sok
Publisher: name: Swinburne
Year: 2024

description: This study analyses the trend of entrepreneurship and venture management research based on the content analysis of two selected journals; Journal of Business Venturing (JBV) and The Korean Venture Management Review (VMR). JBV has published 213 articles to accommodate the requests from the field with many researchers' efforts for the recent past seven years (1998-2004), while VMR has published 104 articles for the same period since it started in 1998. These two journals can be regarded as representative in the world and in Korea respectively, in the division of entrepreneurship. The content analysis on 317 articles can bring good comparisons between different entrepreneurial cultures (developed vs. developing countries; established vs. emerging academic societies) in terms of industrial needs, emerging issues, and preferred research methods. This study addresses the following four research questions: First, what is the recent trend of entrepreneurship research in terms of contents and methodologies? Second, what are the differences in patterns between international and local journals in terms of contents and methodologies? Third, how does the venture bubble burst influence the research trend? Finally, what are some suggestions for further researches in the entrepreneurship domain journals in terms of contents and methodologies?
A possible solution for hair loss by inhibiting corticotropin-releasing factor (CRF) receptor from traditional Chinese medicine
Creators: name: Hung-Jin Huang
name: Chen, Calvin Yu-Chian
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: Corticotropin-releasing factor (CRF) and corticotropin-releasing factor receptor (CRFR) play important roles in stress response, including anxiety and depression syndrome. The CRF expression also relates to chronic stress-related hair loss. This study utilizes the world’s largest traditional Chinese medicine (TCM) database and molecular dynamics (MD) simulations to investigate novel CRFR inhibitors for treatment of alopecia. The docking and screening from TCM database results indicate the vitamin B2, 3 beta-isodihydrocadambine, and caribine display higher binding affinity than maltose in maltose binding protein (MBP). However, the results of MD simulation shows the caribine-facilitated CRFR approach closer to MBP, the 3D structure conformation of MBP and CRFR complex forms compact structure. Interestingly, the distance between the two proteins is reducing significantly after caribine dock into MBP binding site. Beside, from Ligand channel analysis, the paths of caribine demonstrate that residence time is increased in binding pocket. Hence, our finding suggests that caribine might be a potential lead compound to stimulate MBP and CRFR interaction, and help for baldless therapy in further study.
Covert channels in the IP time to live field
Creators: name: Zander, Sebastian
name: Armitage, Grenville
name: Branch, Philip
Publisher: name: Swinburne
Year: 2024

description: Covert channels are used for the secret transfer of information. Unlike encryption, which only protects the information from unauthorised observers, covert channels aim to hide the very existence of the communication. The sheer amount of data and vast number of different network protocols in the Internet makes it an ideal high-capacity vehicle for covert communication. Covert channels pose a serious security threat as criminals can use them to hide their communication activities. In this paper we present a novel covert channel inside the IP header’s Time To Live (TTL) field. The sender manipulates the TTLs of subsequent packets transmitting covert information to the receiver. Since network elements along the path also modify the TTL, the capacity and stealth of this channel depend on the 'natural' TTL variation. We analyse this variation in multiple traffic traces and propose an encoding scheme, which makes the TTL covert channel look similar to “natural” variation. We also discuss methods to eliminate and detect this covert channel.
title: Desarrollo e Implementación de Metodologías Innovadoras en la Enseñanza de Mecánica en Imbabura
title: Desarrollo e Implementación de Metodologías Innovadoras en la Enseñanza de Mecánica en Imbabura
titleType: AlternativeTitle
Creators: name: Chalparizan, Machado, Garman Jorge
Publisher: name: Zenodo
Year: 2024

description: El estudio se enfoca en transformar la educación en mecánica mediante la integración de metodologías pedagógicas modernas que combinan el aprendizaje activo y colaborativo con tecnologías emergentes como la realidad virtual (VR), la realidad aumentada (AR) y la fabricación aditiva
Interhelical loops within the bHLH domain are determinant in maintaining TWIST1–DNA complexes
Creators: name: Bouard, Charlotte
name: Terreux, Raphael
name: Hope, Jennifer
name: Chemelle, Julie Anne
name: Puisieux, Alain
name: Ansieau, Stéphane
name: Payen, Léa
Publisher: name: Taylor & Francis
Year: 2013
Subjects: Molecular Biology

description: The basic helix-loop-helix (bHLH) transcription factor TWIST1 is essential to embryonic development, and hijacking of its function contributes to the development of numerous cancer types. It forms either a homodimer or a heterodimeric complex with an E2A or HAND partner. These functionally distinct complexes display sometimes antagonistic functions during development, so that alterations in the balance between them lead to pronounced morphological alterations, as observed in mice and in Saethre–Chotzen syndrome patients. We, here, describe the structures of TWIST1 bHLH–DNA complexes produced in silico through molecular dynamics simulations. We highlight the determinant role of the interhelical loops in maintaining the TWIST1–DNA complex structures and provide a structural explanation for the loss of function associated with several TWIST1 mutations/insertions observed in Saethre–Chotzen syndrome patients.An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:27
O catolicismo na produção da Brasil Paralelo
Creators: name: Nagamine, Renata
Publisher: name: Zenodo
Year: 2024
Subjects: Antropologia
Religião
Mídia
História do Brasil

description: Apresentação de trabalho sobre catolicismo na Brasil Paralelo. Preparada para as Jornadas Alternativas Religiosas 2024, em Montevidéu.
O catolicismo na produção da Brasil Paralelo
Creators: name: Nagamine, Renata
Publisher: name: Zenodo
Year: 2024
Subjects: Antropologia
Religião
Mídia
História do Brasil

description: Apresentação de trabalho sobre catolicismo na disputa pela democracia brasileira com base na série Brasil: a última cruzada, da empresa de comunicação Brasil Paralelo. Trabalho apresentado nas Jornadas Alternativas Religiosas 2024, em Montevidéu.
Molecular dynamics simulations show how the FMRP Ile304Asn mutation destabilizes the KH2 domain structure and affects its function
Creators: name: Marino, Daniele Di
name: Achsel, Tilmann
name: Lacoux, Caroline
name: Falconi, Mattia
name: Bagni, Claudia
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: Mutations or deletions of FMRP, involved in the regulation of mRNA metabolism in brain, lead to the Fragile X syndrome (FXS), the most frequent form of inherited intellectual disability. A severe manifestation of the disease has been associated with the Ile304Asn mutation, located on the KH2 domain of the protein. Several hypotheses have been proposed to explain the possible molecular mechanism responsible for the drastic effect of this mutation in humans. Here, we performed a molecular dynamics simulation and show that the Ile304Asn mutation destabilizes the hydrophobic core producing a partial unfolding of two α-helices and a displacement of a third one. The affected regions show increased residue flexibility and motion. Molecular docking analysis revealed strongly reduced binding to a model single-stranded nucleic acid in agreement with known data that the two partially unfolded helices form the RNA-binding surface. The third helix, which we show here to be also affected, is involved in the PAK1 protein interaction. These two functional binding sites on the KH2 domain do not overlap spatially, and therefore, they can simultaneously bind their targets. Since the Ile304Asn mutation affects both binding sites, this may justify the severe clinical manifestation observed in the patient in which both mRNA metabolism activity and cytoskeleton remodeling would be affected.
Book review: 'Settler colonialism in the twentieth century: projects, practices, legacies', edited by Caroline Elkins and Susan Pedersen, and 'The new imperial order: indigenous responses to globalization', by Makere Stewart-Harawira
Creators: name: Veracini, Lorenzo
Publisher: name: Swinburne
Year: 2024

description: Reviews the books 'Settler colonialism in the twentieth century: projects, practices, legacies' edited by Caroline Elkins and Susan Pedersen, published by Routledge, New York, 2005, and 'The new imperial order: indigenous responses to globalization' by Makere Stewart-Harawira, published by Zed Books, London, 2005.
The hidden history of the Americas: the destruction and depopulation of the Indigenous civilisations of the Americas by European invaders
Creators: name: Paul, Daniel N.
Publisher: name: Swinburne
Year: 2024

description: The following is a modified version of an Anti-Racism Lecture delivered by Mi'kmaq Elder Dr. Daniel N. Paul, C.M., O.N.S. on 22 March 2011 at Saint Mary's University, Halifax, Nova Scotia. It is here presented as a speech and without supporting references.
MPEC 2024-P54 : 2024 PO
Creators: name: Minor Planet Center Staff
Publisher: name: The Minor Planet Center
Year: 2024
Subjects: subject: Small Solar System bodies
valueUri: http://astrothesaurus.org/uat/1469
subject: 2024 PO

description: The Minor Planet Electronic Circulars contain information on unusual minor planets, routine data on comets and natural satellites, and occasional editorial announcements.  They are published on behalf of Division F of the International Astronomical Union by the Minor Planet Center, Smithsonian Astrophysical Observatory, Cambridge, MA 02138, U.S.A.
Solution structures of purine base analogues 6-chloroguanine, 8-azaguanine and allopurinol
Creators: name: Spriha Gogia
name: Mrinalini Puranik
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Cancer
Biological Sciences
Chemistry
Biotechnology
Physics
Biochemistry
Biophysics

description: Analogues of purine bases are highly relevant in the biological context and have been implicated as drug molecules for therapy against a number of diseases. Additionally, these molecules have been implicated to have a role in the prebiotic RNA world. However, experimental data on the structures of these molecules in aqueous solution is lacking. In this work, we report the ultraviolet resonance Raman spectra of 6-chloroguanine, 8-azaguanine and allopurinol, obtained with 260 nm excitation. The reported spectra have been assigned to normal modes computed from density functional theory (B3LYP/6–31G (d,p)) calculations. This work has been useful in identifying the solution-state structures of these molecules at neutral pH. We find that the guanine analogues 6-chloroguanine and 8-azaguanine exist as keto-N9H and keto-N7H tautomers in solution, respectively. On the other hand, the hypoxanthine analogue allopurinol exists as a mixture of keto-N9H and keto-N8H tautomers in solution. We predict that this work would be particularly useful in future vibrational studies where these molecules are present in complexes with their target proteins.
MPEC 2024-P55 : 2024 PP
Creators: name: Minor Planet Center Staff
Publisher: name: The Minor Planet Center
Year: 2024
Subjects: subject: Small Solar System bodies
valueUri: http://astrothesaurus.org/uat/1469
subject: 2024 PP

description: The Minor Planet Electronic Circulars contain information on unusual minor planets, routine data on comets and natural satellites, and occasional editorial announcements.  They are published on behalf of Division F of the International Astronomical Union by the Minor Planet Center, Smithsonian Astrophysical Observatory, Cambridge, MA 02138, U.S.A.
Interhelical loops within the bHLH domain are determinant in maintaining TWIST1–DNA complexes
Creators: name: Bouard, Charlotte
name: Terreux, Raphael
name: Hope, Jennifer
name: Chemelle, Julie Anne
name: Puisieux, Alain
name: Ansieau, Stéphane
name: Payen, Léa
Publisher: name: Taylor & Francis
Year: 2013
Subjects: Molecular Biology

description: The basic helix-loop-helix (bHLH) transcription factor TWIST1 is essential to embryonic development, and hijacking of its function contributes to the development of numerous cancer types. It forms either a homodimer or a heterodimeric complex with an E2A or HAND partner. These functionally distinct complexes display sometimes antagonistic functions during development, so that alterations in the balance between them lead to pronounced morphological alterations, as observed in mice and in Saethre–Chotzen syndrome patients. We, here, describe the structures of TWIST1 bHLH–DNA complexes produced in silico through molecular dynamics simulations. We highlight the determinant role of the interhelical loops in maintaining the TWIST1–DNA complex structures and provide a structural explanation for the loss of function associated with several TWIST1 mutations/insertions observed in Saethre–Chotzen syndrome patients. An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:27
Sequence and conformation effects on ionization potential and charge distribution of homo-nucleobase stacks using M06-2X hybrid density functional theory calculations
Creators: name: Rooman, Marianne
name: Wintjens, René
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: DNA is subject to oxidative damage due to radiation or by-products of cellular metabolism, thereby creating electron holes that migrate along the DNA stacks. A systematic computational analysis of the dependence of the electronic properties of nucleobase stacks on sequence and conformation was performed here, on the basis of single- and double-stranded homo-nucleobase stacks of 1–10 bases or 1–8 base pairs in standard A-, B-, and Z-conformation. First, several levels of theory were tested for calculating the vertical ionization potentials of individual nucleobases; the M06-2X/6-31G∗ hybrid density functional theory method was selected by comparison with experimental data. Next, the vertical ionization potential, and the Mulliken charge and spin density distributions were calculated and considered on all nucleobase stacks. We found that (1) the ionization potential decreases with the number of bases, the lowest being reached by Gua≡Cyt tracts; (2) the association of two single strands into a double-stranded tract lowers the ionization potential significantly (3) differences in ionization potential due to sequence variation are roughly three times larger than those due to conformational modifications. The charge and spin density distributions were found (1) to be located toward the 5′-end for single-stranded Gua-stacks and toward the 3′-end for Cyt-stacks and basically delocalized over all bases for Ade- and Thy-stacks; (2) the association into double-stranded tracts empties the Cyt- and Thy-strands of most of the charge and all the spin density and concentrates them on the Gua- and Ade-strands. The possible biological implications of these results for transcription are discussed.
Express-diagnostics method for assessment of soil compaction for different cultivation methods
Creators: name: Nugis, Edvin
name: Tamm, Kalvi
name: Võsa, Taavi
name: Plakk, Tiit
name: Palge, Veli
Publisher: name: Agraarteadus
Year: 2020
Subjects: express-diagnostics method
cultivation method
modelling soil compaction
computer simulation
vegetation miniatures
guttation method
article

description: Soil compaction remains a concern because of the heavy tractors used in intensive agriculture. When axle loads of vehicles increase, soil compaction is affected in deeper soil layers. An efficient tool is needed to assess the impact of machines on soil. Therefore, an expressdiagnostics method was developed and implemented under Estonian agricultural conditions. Since 1976, an investigation has been carried out on how wheeled or tracked vehicles (WTV) influence soil under agricultural conditions in Estonia. The main goal of the investigation was to develop a mathematical model and corresponding computer simulation system. Uncompacted and compacted soil was modelled using a vegetation model of "guttated vegetation miniatures". The system allows soil vulnerability to compaction to be assessed by the criterion (qabc) agroempirical bearing capacity (ABC). Both field and laboratory data were used in the development of the system. We have found that at the deepest layer the bulk density was higher for tilled soil compared to no-tilled soil. Dry soil bulk density in no-tilled soil after 2 years in the deepest layer was 0.11 Mg m3 –1 less than tilled soil, and for no-tilled soil after 3 years in the deepest layer it was 0.12 Mg m3 –1 less compared to the tilled field soil. The amount of agronomically preferable aggregates (2–4.75mm) was major in tilled soil compared to no-tilled soil. It means that the preferred (in agronomical sense) soil particles Kstr in conventionally tilled (ploughing – K2; K3) fields were significantly better compared to no-tilled (O2; O3) fields in the trial plots. These results emphasize the benefits of multifunctional modelling systems (computer simulation and simulation by vegetation miniatures) and the need to improve assessment of methodology for receiving adequate and probable results, and finally for yield prediction.
Para-(benzoyl)-phenylalanine as a potential inhibitor against LpxC of Leptospira spp.: homology modeling, docking, and molecular dynamics study
Creators: name: Dibyabhaba Pradhan
name: Vani Priyadarshini
name: Munikumar, Manne
name: Swargam, Sandeep
name: Amineni Umamaheswari
name: Bitla, Aparna
Publisher: name: Taylor & Francis
Year: 2013
Subjects: Molecular Biology

description: Leptospira interrogans, a Gram-negative bacterial pathogen is the main cause of human leptospirosis. Lipid A is a highly immunoreactive endotoxic center of lipopolysaccharide (LPS) that anchors LPS into the outer membrane of Leptospira. Discovery of compounds inhibiting lipid-A biosynthetic pathway would be promising for dissolving the structural integrity of membrane leading to cell lysis and death of Leptospira. LpxC, a unique enzyme of lipid-A biosynthetic pathway was identified as common drug target of Leptospira. Herein, homology modeling, docking, and molecular dynamics (MD) simulations were employed to discover potential inhibitors of LpxC. A reliable tertiary structure of LpxC in complex with inhibitor BB-78485 was constructed in Modeller 9v8. A data-set of BB-78485 structural analogs were docked with LpxC in Maestro v9.2 virtual screening workflow, which implements three stage Glide docking protocol. Twelve lead molecules with better XP Gscore compared to BB-78485 were proposed as potential inhibitors of LpxC. Para-(benzoyl)-phenylalanine – that showed lowest XP Gscore (−10.35 kcal/mol) – was predicted to have best binding affinity towards LpxC. MD simulations were performed for LpxC and para-(benzoyl)-phenylalanine docking complex in Desmond v3.0. Trajectory analysis showed the docking complex and inter-molecular interactions was stable throughout the entire production part of MD simulations. The results indicate para-(benzoyl)-phenylalanine as a potent drug molecule against leptospirosis.An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:10
Solution structures of purine base analogues 6-chloroguanine, 8-azaguanine and allopurinol
Creators: name: Spriha Gogia
name: Mrinalini Puranik
Publisher: name: Taylor & Francis
Year: 2015
Subjects: Cancer
Biological Sciences
Chemistry
Biotechnology
Physics
Biochemistry
Biophysics

description: Analogues of purine bases are highly relevant in the biological context and have been implicated as drug molecules for therapy against a number of diseases. Additionally, these molecules have been implicated to have a role in the prebiotic RNA world. However, experimental data on the structures of these molecules in aqueous solution is lacking. In this work, we report the ultraviolet resonance Raman spectra of 6-chloroguanine, 8-azaguanine and allopurinol, obtained with 260 nm excitation. The reported spectra have been assigned to normal modes computed from density functional theory (B3LYP/6–31G (d,p)) calculations. This work has been useful in identifying the solution-state structures of these molecules at neutral pH. We find that the guanine analogues 6-chloroguanine and 8-azaguanine exist as keto-N9H and keto-N7H tautomers in solution, respectively. On the other hand, the hypoxanthine analogue allopurinol exists as a mixture of keto-N9H and keto-N8H tautomers in solution. We predict that this work would be particularly useful in future vibrational studies where these molecules are present in complexes with their target proteins.
title: Beyond Forensic Poetry: Lyric and Legal Languages in Contemporary Poems
Creators: name: Gallerani, Guido Mattia
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2022
Subjects: subject: law and poetry
subject: contemporary poetry
subject: lyric poetry
subject: performative function
subject: epideictic discourse
subject: stereotype
subject: reasonable person
subject: 340

description: In the field of Law and Literature studies, contributions on poetry are rare. This article focuses on a selection of contemporary poetic works: Cornelius Eady’s A Brutal Imagination (2001), Frédéric Boyer’s Le Goût du suicide lent (1999), Maurizio Cucchi’s Il disperso (1976) and Corrado Benigni’s Tribunale della mente (2012). Their lyrical shaping of law establishes a difference from the model of “forensic” poetry that can be found in Charles Reznikoff’s Testimony (1978–1979). Through them, this contribution shows how it is possible to challenge a reflection on the language of lyric poetry and that of law at the same time, if we interpret the lyric poetry as a non-narrative discourse.
description: Law, Culture and the Humanities, vol. 18, no. 1, p. 229
Financing growing firms and the importance of banking relationships
Creators: name: Dolan, Shane
name: Brouard, Francois
name: Riding, Allan
Publisher: name: Swinburne
Year: 2024

description: This study examines how the relationship between a lender and a borrower influences access to credit and the interest rate charged. Relationships between lenders and small business borrowers can arguably help to overcome information opacity. Findings include that whether an SME’s request for a line of credit will be approved appears to be affected by the relationship. As well, the requirement for a business plan or cash flow statement also appears to affect the likelihood of approval. However, the effect of relationship banking on the interest rate charged could not be determined from this analysis. The findings of this are consistent with Berger and Udell (2006) who hypothesize that the method used to underwrite loans can affect how lender-borrower relationships influence lending decisions.
Transformation between HL7 and Continuity of Care Record to facilitate web-based Personal Health Record systems
Creators: name: Sutanto, Jofry Hadi
Publisher: name: Swinburne
Year: 2024

description: To establish interoperability between Health/Hospital Information System (HIS), there exist standards or protocols designed by capable organizations to help different HISs communicatebetter with each other. Reliable and accurate communication is nowadays a prerequisite to delivering fully integrated health care to patients. In practice, there are two main leading standards adopted by various HISs, Health Level 7 (HL7) and Continuity of Care Record (CCR). The HL7 v2.x set of healthcare messaging standards are the predominant ones used by healthcare institutions in much of the world. They have been designed for managing healthcare and so provide a complete set of information and messages necessary for the provision of healthcare. Also, the scope of HL7 has expanded to include standards for the interchange of clinical data in all settings, a reference information model, data types, decision support and clinical guidelines, clinical documents and clinical templates, clinical context objects, terminology, security, XML, and the electronic health record. More recently the Continuity of Care Record (CCR) standard was proposed as a digital form of referrals; it describes the condition of a person – a snapshot – at the time of the referral. It offers a light-weight, easy implemented approach, and its focus is on the exchange of health summaries. Personal Health Record (PHR) systems such as Google Health and Microsoft Health Vault use the CCR format for input (and output), which is correct, as such systems collect snapshots of health (rather than or in addition to healthcare) information. While both were initially made for different purposes, the need to collaborate with each other was soon deemed necessary, resulting in the release by HL7 of the Continuity of Care Document (CCD). This is a patient summary clinical document that is derived from the HL7 CDA (Clinical Document Architecture) Reference Information Model (RIM), but provides health summary information parallel to that of the CCR. This result is a standard that is much more complex than the CCR, so it still does not solve the integration issue between HISs which favour the HL7 (version 2.x or CCD) and those (especially PHRs)which prefer the CCR due to its simplicity. For healthcare institutions, which use HL7, to effectively communicate with PHR systems which use the CCR, there must be a translation between these two standard formats. We present such a translation; it is in the public domain, so is open for improvements from knowledgeable institutions and individuals.
An exploration of ebook selection behavior in academic library collections
Creators: name: McKay, Dana
name: Hinze, Annika
name: Heese, Ralf
name: Vanderschantz, Nicholas
name: Timpany, Claire
name: Cunningham, Sally Jo
Publisher: name: Swinburne
Year: 2024

description: Academic libraries have offered ebooks for some time, however little is known about how readers interact with them while making relevance decisions. In this paper we seek to address that gap by analyzing ebook transaction logs for books in a university library.
Understanding the evolutionary relationship of hemagglutinin protein from influenza viruses using phylogenetic and molecular modeling studies
Creators: name: Muthusamy Karthikeyan
name: Palani Kirubakaran
name: Kh. Dhanachandra Singh
name: Bhuvaneshwari Sampath
name: Gopinath Krishnasamy
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: The existing H1N1 (2009) swine flu is pandemic in nature and is responsible for global economic losses and fatalities. Among the eight gene segments of H1N1, hemagglutinin (HA) plays a major role in the attachment of the virus to the host cell surface and entry of viral RNA into the host cell leads to infection. In this study, sequence and phylogenetic analysis of the H1N1 (2009) HA, from Mexico City along with 1952 sequences, from different subtypes of pandemic influenza A virus were studied and results showed that the closest relationship of H1N1 (2009) Mexico strain was with the H1N1 (2007) Mallard Norway strain. Analysis of secondary structures predicted from the protein sequence revealed that diminishing of alpha helixes was observed in many areas of the sequences between the years 2005 to 2010. Conversely, analysis at the structural level is necessary to critically assess the functional significance. Structural level investigation was therefore done for the above said proteins by constructing the 3D structure of these proteins through homology modeling. The models were validated and structural level similarities were evaluated through superimposition. Subsequently, docking studies were done to find the binding mode of the sialic acid (SA) with influenza HA. Molecular dynamics simulations were executed to study the interactions of SA molecule with the HA. Energetic analysis reveals that van der Waal interaction is more favorable for binding of HA with SA of the whole influenza virus. Binding pocket analysis shows that intensities of H-bond donor and acceptor are more in H1N1 (2009).
Molecular dynamics investigation on the poor sensitivity of A171T mutant NEDD8-activating enzyme (NAE) for MLN4924
Creators: name: Verma, Sharad
name: Singh, Amit
name: Mishra, Abha
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: MLN4924 is an adenosine sulfamate analog that generates the inhibitory NEDD8-MLN4924 covalent complex. A single nucleotide transition that changes alanine 171 to threonine (A171T) of the NAE subunit UBA3 reduces the enzyme’s sensitivity for MLN4924. Our molecular dynamics simulation study revealed that A171T transition brought remarkable conformational changes in enzyme structure (open ATP binding pocket), which reduced the interaction between MLN4924 and ATP binding pocket while wild form completely covered the MLN4924. A total difference of −49.75 kJ/mol was noticed in interaction energy (electrostatic and van der Waals) during simulation between mutant and wild form with MLN4924. Superimposition of final 20 ns mutant structure with reference structure showed significant change in native binding position as compared to wild form. Results were found in coherence with the recently reported in vitro studies which states that A171T transition leads to change in ATP binding pocket structure.
Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure
Creators: name: Swapnil Mahajan
name: Brevern, Alexandre G. De
name: Offmann, Bernard
name: Narayanaswamy Srinivasan
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: Conformational changes in proteins are extremely important for their biochemical functions. Correlation between inherent conformational variations in a protein and conformational differences in its homologues of known structure is still unclear. In this study, we have used a structural alphabet called Protein Blocks (PBs). PBs are used to perform abstraction of protein 3-D structures into a 1-D strings of 16 alphabets (a–p) based on dihedral angles of overlapping pentapeptides. We have analyzed the variations in local conformations in terms of PBs represented in the ensembles of 801 protein structures determined using NMR spectroscopy. In the analysis of concatenated data over all the residues in all the NMR ensembles, we observe that the overall nature of inherent local structural variations in NMR ensembles is similar to the nature of local structural differences in homologous proteins with a high correlation coefficient of .94. High correlation at the alignment positions corresponding to helical and β-sheet regions is only expected. However, the correlation coefficient by considering only the loop regions is also quite high (.91). Surprisingly, segregated position-wise analysis shows that this high correlation does not hold true to loop regions at the structurally equivalent positions in NMR ensembles and their homologues of known structure. This suggests that the general nature of local structural changes is unique; however most of the local structural variations in loop regions of NMR ensembles do not correlate to their local structural differences at structurally equivalent positions in homologues.
Site-directed in vitro mutagenesis of Enterovirus EV71: implications for the development of an attenuated EV71 vaccine
Creators: name: Lazouskaya, Natallia
Publisher: name: Swinburne
Year: 2024

description: Enterovirus 71 (EV71) is a human pathogen associated both with sporadic cases and large outbreaks of hand, foot and mouth disease throughout the world. The clinical manifestations in EV71 patients vary from mild and self-limited conditions to severe neurological complications, such as meningitis, brain-stem encephalitis, meningoencephalitis, poliomyelitis-like paralysis or pulmonary oedema with a fatal outcome. Currently, there is no specific therapy of vaccine available for EV71 infection. The aim of this study was to explore EV71 molecular determinants which can lead to the virus inhibition in vitro and, therefore, can be useful in the development of an attenuated vaccine.
title: The EU-US Privacy Shield: An Effective New Framework for Transatlantic Data Flows or A Weak Compromise Doomed to Fail?
Creators: name: Gryffroy, Pieter
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2016
Subjects: subject: 340

description: Saar Briefs
title: Analyse des EGMR-Urteils Magyar Tartalomszolgáltatók Egyesülete und Index.hu Zrt gegen Ungarn (App. No. 22947/13)
Creators: name: Schmidt, Karoline
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2016
Subjects: subject: 340

description: Saar Briefs
Sequence and conformation effects on ionization potential and charge distribution of homo-nucleobase stacks using M06-2X hybrid density functional theory calculations
Creators: name: Rooman, Marianne
name: Wintjens, René
Publisher: name: Taylor & Francis
Year: 2013
Subjects: Molecular Biology

description: DNA is subject to oxidative damage due to radiation or by-products of cellular metabolism, thereby creating electron holes that migrate along the DNA stacks. A systematic computational analysis of the dependence of the electronic properties of nucleobase stacks on sequence and conformation was performed here, on the basis of single- and double-stranded homo-nucleobase stacks of 1–10 bases or 1–8 base pairs in standard A-, B-, and Z-conformation. First, several levels of theory were tested for calculating the vertical ionization potentials of individual nucleobases; the M06-2X/6-31G∗ hybrid density functional theory method was selected by comparison with experimental data. Next, the vertical ionization potential, and the Mulliken charge and spin density distributions were calculated and considered on all nucleobase stacks. We found that (1) the ionization potential decreases with the number of bases, the lowest being reached by Gua≡Cyt tracts; (2) the association of two single strands into a double-stranded tract lowers the ionization potential significantly (3) differences in ionization potential due to sequence variation are roughly three times larger than those due to conformational modifications. The charge and spin density distributions were found (1) to be located toward the 5′-end for single-stranded Gua-stacks and toward the 3′-end for Cyt-stacks and basically delocalized over all bases for Ade- and Thy-stacks; (2) the association into double-stranded tracts empties the Cyt- and Thy-strands of most of the charge and all the spin density and concentrates them on the Gua- and Ade-strands. The possible biological implications of these results for transcription are discussed.
title: Taking a look at two cases in the margin of the CJEU’s “Privacy Spring”, before and after the General Data Protection Regulation: Weltimmo and Bara
Creators: name: Gryffroy, Pieter
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2016
Subjects: subject: 340

description: Saar Briefs
title: Eine Institution der EU erreicht ihre „Volljährigkeit“: Eine Europäische Bürgerinitiative vor der Großen Kammer des EuGH
Creators: name: Petropoulos, Eleftherios
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2016
Subjects: subject: 340

description: Saar Briefs
title: „Völker- und europarechtliche Perspektiven auf Flucht“: Ein Vortrag von Univ.-Prof. Dr. Thomas Giegerich
Creators: name: Giegerich, Thomas
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2017
Subjects: subject: 340

description: Saar Briefs
NMR-based structure of anticancer drug mitoxantrone stacked with terminal base pair of DNA hexamer sequence d-(ATCGAT)2
Creators: name: Dogra, Shilpa
name: Pamita Awasthi
name: Tripathi, Sweta
name: T.P. Pradeep
name: Nair, Maya S.
name: Barthwal, Ritu
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: Mitoxantrone is a promising antitumor drug having considerably reduced cardiotoxicity as compared to anthracyclines. Its binding to deoxyhexanucleotides sequence d-(ATCGAT)2 has been studied by proton and phosphorous-31 nuclear magnetic resonance spectroscopy. The stoichiometry reveals that 1:1 and 2:1 mitoxantrone-d(ATCGAT)2 complexes are formed in solution. Significant upfield shifts in 6H/7H, 2H/3H, 11NH, and 12NH protons (∼.5 ppm) of mitoxantrone and T6NH imino protons (∼.3 ppm) are observed. The phosphorous resonances do not shift significantly indicating that the base pairs do not open at any nucleotide step along the sequence of hexamer. Several inter-molecular Nuclear Overhauser Enhancement connectivities between mitoxantrone and hexanucleotide protons indicate that mitoxantrone chromophore stacks with terminal A1-T6 base pair and side chains involving 12CH2, 12NH, and 14OH protons are in close proximity of A1, T2, A5, and T6 bases. Absorption and emission spectra show red shift in wavelength maxima, which is characteristic of stacking interaction. At higher mitoxantrone to nucleic acid ratios, electrostatic interactions are dominant. The 2:1 drug/DNA stoichiometric structure obtained by restrained Molecular Dynamics simulations shows considerable distortions in backbone torsional angles and helicoidal parameters although structural fluctuations in 25 ps analysis of trajectory are found to be negligible. Mitoxantrone binds as a monomer at either or both ends of hexamer externally with side chains interacting specifically with DNA. The findings are relevant to the understanding of pharmacological action of drug.
Continuity and change in urban transport policy: politics, institutions and actors in Melbourne and Vancouver since 1970
Creators: name: Stone, John
Publisher: name: Swinburne
Year: 2024

description: Melbourne and Vancouver share many similarities, but there are significant differences in the content and outcomes of transport and urban planning policies since 1970. Melbourne has built a large urban freeway network and is struggling to create a coherent transit network from its large but fragmented transit system. Vancouver has achieved some enviable successes in urban planning, but is still facing significant car-dependence in its outer suburbs. This paper provides a conceptual theoretical model that asserts the centrality of local politics as the source of reasons for particular urban transport policy trajectories. It describes the political and institutional context for the development of transport policies and the behaviour of key actors in the two cities, and identifies some of key factors behind transport and planning outcomes.
The pH dependence of flavivirus envelope protein structure: insights from molecular dynamics simulations
Creators: name: Fuzo, Carlos Alessandro
name: Degrève, Léo
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: The flavivirus membrane fusion is triggered by the acid pH of the endosomes after virus endocytosis. The proposed mechanism involves changes in the protonation state of conserved histidine residues of the E protein present in the viral surface that undergoes a series of structural rearrangements that result in the fusion between the endosome and viral bilayers. We studied the pH dependence of E protein rearrangements of dengue virus type 2, used as a model, in the pH range experimented by the virus along the fusion process. We employed a low computational cost scheme to explore the behavior of the E protein by molecular dynamics (MD) simulations of complete systems that include the protein, the solvent, and ions. The procedure alternates cyclically the update of the ionization states of the protein residues with common MD steps applied to the new ionization configuration. Important pH-dependent protein structure rearrangements consistent with the changes of the protonation states of conserved histidine residues were observed. The involvement of other conserved residues in the flavivirus in the rearrangements was also identified. The results show interesting correlations with a proposed model for the fusion mechanism, as well as the experimentally identified key residues, contributing to a better understanding of the structural changes in protein E that lead to the fusion process.
Who (or what) is behind the wheel? The regulatory challenges of driverless cars
Creators: name: Dia, Hussein
Publisher: name: Swinburne
Year: 2024

description: A legal opinion by the US National Highway Traffic Safety Administration (NHTSA) set the internet alight in February. The US road safety federal regulator informed Google that the artificial intelligence (AI) software it uses to control its self-driving cars could effectively be viewed as the 'driver' for some (but not all) regulatory purposes. The NHTSA's letter was in response to a request from Google seeking the NHTSA's interpretations of the US Federal Motor Vehicle Safety Standards. It was widely viewed in the media as a recognition from the Feds that Google's AI software, the self-driving system (SDS), is legally the same as a human driver. The details of the letter, however, tell a very different story.
Dancing at the corner of the dead: remembering and forgetting in post-conflict Ayacucho, Peru
Creators: name: Callaghan, Michaela
Publisher: name: Swinburne
Year: 2024

description: This thesis considers dance as an embodied form of collective memory in the Andean department of Ayacucho Peru, following 20 years of brutal internal conflict. It combines the areas of cultural memory studies with history and anthropology to discover new ways of accessing and understanding non-verbal forms of collective memory through dance. It uses embodied research techniques to reveal that dance is a deep embodiment of the broader concerns of the people of Ayacucho. It argues that dance plays a significant role in the collective memory-making practices of Ayacuchanos as they search for a history that makes sense of what happened.
title: Verbindliche Quoten rechtmäßig: Das Urteil in den verbundenen Rechtssachen C-643/15 und C-647/15 Slowakei und Ungarn / Rat
Creators: name: Schuberth, Michael
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2017
Subjects: subject: 340

description: Saar Briefs