cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Shedding light into the biological activity of aminopterin, via molecular structural, docking, and molecular dynamics analyses
Creators: name: Celik, Sefa
name: Yilmaz, Gozde
name: Akyuz, Sevim
name: Ozel, Aysen E.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Computational Biology

description: In this study, the structural and anticancer properties of aminopterin, as well as its antiviral characteristics, were elucidated. The preferred conformations of the title molecule were investigated with semiempirical AM1 method, and the obtained the lowest energy conformer was then optimized by using density functional (DFT/B3LYP) method with 6-311++G(d,p) as basis set. The vibrational frequencies of the optimized structure were calculated by the same level of theory and were compared with the experimental values. The vibrational assignments were performed based on the computed potential energy distribution (PED) of the vibrational modes. The molecular electrostatic potential (MEP) and frontier molecular orbitals (HOMO, LUMO) analyses were carried out for the optimized structure and the chemical reactivity has been scrutinized. To enlighten the biological activity of aminopterin as anticancer and anti-COVID-19 agents, aminopterin was docked into DNA, αIIBβ3 and α5β1integrins, human dihydrofolate reductase, main protease (Mpro) of SARS-CoV-2 and SARS-CoV-2/ACE2 complex receptor. The binding mechanisms of aminopterin with the receptors were clarified. The molecular docking results revealed the strong interaction of the aminopterin with DNA (−8.2 kcal/mol), αIIBβ3 and α5β1 integrins (−9.0 and −10.8 kcal/mol, respectively), human dihydrofolate reductase (−9.7 kcal/mol), Mpro of SARS-CoV-2 (−6.7 kcal/mol), and SARS-CoV-2/ACE2 complex receptor (−8.1 kcal/mol). Moreover, after molecular docking calculations, top-scoring ligand-receptor complexes of the aminopterin with SARS-CoV-2 enzymes (6M03 and 6M0J) were subjected to 50 ns all-atom MD simulations to investigate the ligand-receptor interactions in more detail, and to determine the binding free energies accurately. The predicted results indicate that the aminopterin may significantly inhibit SARS-CoV-2 infection. Thus, in this study, as both anticancer and anti-COVID-19 agents, the versatility of the biological activity of aminopterin was shown. Communicated by Ramaswamy H. Sarma
The potential of infant fMRI research and the study of early life stress as a promising exemplar
Creators: name: Graham, Alice M.
name: Fair, Damien A.
name: Fisher, Philip A.
name: Pfeifer, Jennifer H.
name: Gao, Wei
name: Lin, Weili
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Functional magnetic resonance imaging (fMRI) research with infants and toddlers has increased rapidly over the past decade, and provided a unique window into early brain development. In the current report, we review the state of the literature, which has established the feasibility and utility of task-based fMRI and resting state functional connectivity MRI (rs-fcMRI) during early periods of brain maturation. These methodologies have been successfully applied beginning in the neonatal period to increase understanding of how the brain both responds to environmental stimuli, and becomes organized into large-scale functional systems that support complex behaviors. We discuss the methodological challenges posed by this promising area of research. We also highlight that despite these challenges, early work indicates a strong potential for these methods to influence multiple research domains. As an example, we focus on the study of early life stress and its influence on brain development and mental health outcomes. We illustrate the promise of these methodologies for building on, and making important contributions to, the existing literature in this field.
title: Spectroscopic considerations on molecular adsorption at the solid/liquid interface
Creators: name: Bowfield, Andrew
Publisher: name: University of Liverpool Repository
Year: 2011

description: This thesis mainly focuses on the adsorption behaviour of various molecules at the solid/liquid interface. The variation in adsorption kinetics are studied as a function of concentration, pH, applied electrode potential and surrounding environment by the surface sensitive analytical techniques of Reflection Anisotropy Spectroscopy and X-ray Photoelectron Spectroscopy. An electrochemical investigation into the surface reconstructions of Au(110) and their associated RA profiles is undertaken. The spectral profiles of Au(110) in 0.1 M H2SO4/Na2SO4, NaClO4/HClO4 and NaClO4 electrolytes were observed as a function of potential and spectral signatures of the different reconstructions are assigned. The adsorption of adenine and its monophosphate (AMP) on Au(110) was studied using RAS. It is shown that both molecules adsorb in a vertical orientation through sites common to the base through formation of base stacked layers. Application of a phenomenological Lorentzian transition model and rotations about the polarisation direction of the incident light suggest that the molecules align along the [1 0] principal axis of the substrate. Linear simulations show that the orientation of adenine at sub-saturation coverage is the same as that when a monolayer is adsorbed and that adenine does not adsorb on the surface at sufficiently alkaline pH. The attachment of thiolated ss DNA on a functionalised diamond surface and the subsequent detection of hybridisation are discussed. High resolution XPS spectra are used to characterise both the integrity and structure of the organic thin film and its modification to precipitate DNA adsorption. The sensitivity of RAS to the orientation of the alkyl backbone of decanethiol is displayed through alteration to the surrounding environment of the molecule. It is suggested that orientation of the hydrophobic backbone varies as the surrounding environment is changed from ethanol to air and finally to phosphate buffer.
title: Proteomics of Toxoplasma gondii
Creators: name: Xia, Dong
Publisher: name: University of Liverpool Repository
Year: 2011

description: The Apicomplexan parasite Toxoplasma gondii is an obligate intracellular parasite. Infection by T .gondii causes the disease toxoplasmosis, which is one of the most prevalent parasitic diseases of animals and humans. It has been 100 years since the first discovery of the parasite in 1908; research on T. gondii has been carried out in many scientific disciplines consistently expanding the understanding of this parasite. In the last ten years, the developments of EST, microarray, genome sequencing and continuing efforts towards genome annotation has centralized the focus of T. gondii research on the understanding of gene expression and gene functions on the genome scale. Equipped with the technical advances in mass spectrometry and bioinformatics, proteomics has become established as an integral component in the post-genomics era by providing first-hand data on the functional products of gene expression. In this study, three complementary proteomic strategies, 1-DE, 2-DE and MudPIT, have been used to characterise the proteome of T. gondii tachyzoites. Protein identifications have been acquired for more than two thousand (2252) unique release 4 genes, representing almost one third (29%) of the predicted proteome of all life cycle stages. Functional predictions for each protein were carried out, which provided valuable insights into the composition of the expressed proteome and their potential biological roles. The T. gondii proteomic data has been integrated into the publically accessible ToxoDB, where 2477 intron-spanning peptides provided supporting evidence for correct splice site annotation of the release 4 genome annotation. The incompleteness of the release 4 genome annotation has been highlighted using peptide evidence, confirming 421 splice sites that are only predicted by alternative gene models. Analysis has also been carried out on the proteomic data in the light of other genome wide expression data. The comparison of the proteome and transcriptome of Toxoplasma and other Apicomplexa parasites has revealed important discrepancies between protein and mRNA expression where interesting candidates have been highlighted for further investigation. A preliminary DIGE study has been developed to characterize protein expression changes in T. gondii grown in the presence or absence of glucose. In conclusion, this study has demonstrated the importance of proteomic applications in understanding gene expression profiles and regulation in T. gondii and highlighted the importance and potential of proteogenomic approaches in genome annotation process. The importance of temporal and quantitative proteomics as well as the future of systems biology has been discussed.
title: Tourism and sustainable development: active stakeholder discourses in the Waterberg Biosphere Reserve, South Africa
Creators: name: Lyon, Andrew
Publisher: name: University of Liverpool Repository
Year: 2014

description: The aim of this thesis is to examine the extent to which tourism is a sustainable development (SD) option in the Waterberg Biosphere Reserve (WBR), South Africa. It examines the discourses of those stakeholders who can actively affect decisions or actions regarding sustainable tourism development (STD). The literature on tourism points to it being a contested development option, with a number of positive aspects which are mainly economic fitting with the neoliberal development paradigm. There are however critical concerns over the ability of tourism to contribute to the wider issues surrounding SD. There are also conceptual and practical issues regarding SD/STD with stakeholders having varying approaches to, and positions on, the concepts. This case-study examines tourism development in the predominantly rural WBR which has seen tourism become the major economic and land-use sector in the area. Biosphere reserves are a United Nation’s designation stipulating that the region should endeavour to follow the principles of SD. Therefore, how tourism develops in the area has implications for the SD of the biosphere reserve area. An inductive qualitative methodology was designed to collect and analyse the discourses of those stakeholders who can actively affect STD concerns within the WBR. Critical discourse analysis is used to reveal notions of power, ideology and knowledge relating to the macro contexts of development, SD, STD and the micro context of the geographical area. The discourses of the active stakeholders reveal that tourism is seen mainly as an economic driver and SD discourses do emerge regarding the environment and futurity or concern for future generations. The discourses also uncover a strong ‘sense of place’ attachment to the region and a desire to conserve the environment. However they show that tourism does not contribute to wider SD objectives of basic needs, poverty reduction, quality of life improvement and population levels. This thesis reveals how levels of knowledge from active stakeholders, influenced by ideology, affect power in the region. The main contribution of this research is that active stakeholder discourses need to be understood in the contexts of development and that the link between discourse, knowledge, ideology and power needs to recognised when examining tourism as a sustainable development option.
In silico screening combined with bioactivity evaluation to identify AMI-1 as a novel anticancer compound by targeting AXL
Creators: name: Wang, Linxiao
name: An, Yufeng
name: Wei, Xiongpiao
name: Huang, Xiaoling
name: Tu, Yuanbiao
name: Qiao, Lukai
name: Zhu, Wufu
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Recently, some studies have proven that AXL plays a crucial role in the drug resistance of tumors. At present, no AXL inhibitors on the market and it is essential to discover novel compounds targeting AXL to overcome resistance. In this work, based on the anchor structure, 21,313 compounds were obtained by substructure search from more than 400,000 compounds. Then, the Qvina and Ledock were selected for virtual screening to obtain 17 compounds. Next, four compounds (ARRY614, AMI-1, NG25, and Butein) were selected for bioactivity evaluation after hydrogen bond and cluster analysis. Further activity evaluation suggested that the compound AMI-1 is a novel AXL inhibitor with an IC50 value of 1.13 uM. In addition, molecular dynamics simulation demonstrated that compound AMI-1 contained lower binding energy and more key residues than the other three compounds, showing the best inhibitory activity against AXL. Finally, further MM/PBSA prediction showed that AMI-1 is more sensitive to mutant protein 3IKA than wildtype protein 1M17, which means that the AMI-1 may be helpful to overcome the resistance of EGFRT790M mutations. In conclusion, this work successfully discovered a novel compound with moderate inhibitory activity against AXL by a drug discovery workflow, which also could be applied to discover active compounds for other targets quickly. Communicated by Ramaswamy H. Sarma
Equilibration, thermalisation, and the emergence of statistical mechanics in closed quantum systems
Creators: name: Gogolin, C.
name: Eisert, J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We review selected advances in the theoretical understanding of complex quantum many-body systems with regard to emergent notions of quantum statistical mechanics. We cover topics such as equilibration and thermalisation in pure state statistical mechanics, the eigenstate thermalisation hypothesis, the equivalence of ensembles, non-equilibration dynamics following global and local quenches as well as ramps. We also address initial state independence, absence of thermalisation, and many-body localisation. We elucidate the role played by key concepts for these phenomena, such as Lieb-Robinson bounds, entanglement growth, typicality arguments, quantum maximum entropy principles and the generalised Gibbs ensembles, and quantum (non-)integrability. We put emphasis on rigorous approaches and present the most important results in a unified language.
description: 114 pages, 6 figures, 429 references, version as published with minor typos corrected, updated funding sources in acknowledgements to those of the published version to fulfill requirements of Marie Sklodowska-Curie grant
T-box genes in early embryogenesis
Creators: name: Conlon, Frank L.
name: Showell, Chris
name: Binder, Olav
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: The T-box gene family, encoding related DNA-binding transcriptional regulators, plays an essential role in controlling many aspects of embryogenesis in a wide variety of organisms. The T-box genes exhibit diverse patterns of spatial and temporal expression in the developing embryo, and both genetic and molecular embryological studies have demonstrated their importance in regulating cell fate decisions that establish the early body plan, and in later processes underlying organogenesis. Despite these studies, little is known of either the regulation of the T-box genes or the identities of their transcriptional targets. The aim of this review is to examine the diverse yet conserved roles of several T-box genes in regulating early patterning in chordates and to discuss possible mechanisms through which this functional diversity might arise.
Droplet detachment from a horizontal fiber of a fog harvesting mesh
Creators: name: Datta, Arkadeep
name: Mukhopadhyay, Arani
name: Dutta, Partha Sarathi
name: Saha, Arijit
name: Datta, Amitava
name: Ganguly, Ranjan
Publisher: name: University of Illinois at Chicago
Year: 2023
Subjects: classificationCode: 34
subject: Chemical sciences
subject: FOS: Chemical sciences
classificationCode: 37
subject: Earth sciences
classificationCode: 40
subject: Engineering
classificationCode: 41
subject: Environmental sciences
classificationCode: 33
subject: Built environment and design

description: Fog capture holds promise in ameliorating the drastic freshwater crisis that is globally imminent. Metal meshes have shown promise in capturing both natural and industrial fogs, the latter primarily referring to cooling tower fog harvesting. However, there exists room for improvement of their water collection efficiency, which has been reported to be highly dependent on mesh wettability, geometry, and orientation with respect to the fog-laden wind. As fog droplets impinge and deposit on mesh fibers, they coalesce with previously deposited liquid to evolve as larger drops of different size and shape, depending on the mesh wettability and arrangement. While the primary intent of fog harvesting is to effectively drain the intercepted fog water along the mesh into a desired collector, premature drainage of the droplet is found to be detrimental to mesh performance. We investigate droplet detachment as a function of fiber diameter under real fogging scenarios. The results are compared with pre-existing droplet detachment theories and with numerical simulations using Surface Evolver. Droplet detachment volume is found to increase with the mesh-fiber diameter. It is also found that the existing theories of droplet detachment from fibers do not give reliable accuracy for detachment volume estimation under realistic fog-collection scenarios.
Geochemistry of salts and the effect of trace elements on human health: Turkey salt resources
Creators: name: Deniz, Kiymet
name: Kadioglu, Yusuf Kagan
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Science Policy

description: Salt plays a vital role in many body functions. Humans must consume a well-balanced amount of salt to remain healthy as deficiency or excess of it causes many health problems. The major oxide element’s values are only evaluated while processing for production; however, the type and amount of the trace elements in the salt are also important as they may entail risks for human health. This study concerns the mineralogy and geochemistry of salt samples which are taken from several salt mines and localities in Turkey. In addition, these local samples are compared with well-known samples from Himalayas and Asal Lake (Djibouti Southeast Africa) salt mines. The X-Ray Diffraction (XRD) and Confocal Raman Spectroscopy (CRS) analysis reveal that the most of Turkish salts are mainly composed of halite with minor amounts of thenardite and gypsum as well as the low concentrations of some potentially toxic elements (PTEs) such as As, Cd, Co, Hg, Mn, Ni, Pb and Zn. The samples from Tuz Lake have significant contents of As, Co, Cu, Mn, Ni, U and Zn. The mineralogy and geochemistry of the samples reveal a mixture of residual seawaters with the redissolving of the crystalized salt minerals in the region. Although the quality of the salts is mostly evaluated with the content of NaCl, the significant contents of the PTEs in the salt may be accumulated by time and danger human health.
Computer-assisted polyp matching between optical colonoscopy and CT colonography: a phantom study
Creators: name: Roth, Holger R.
name: Hampshire, Thomas E.
name: Helbren, Emma
name: Hu, Mingxing
name: Vega, Roser
name: Halligan, Steve
name: Hawkes, David J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Potentially precancerous polyps detected with CT colonography (CTC) need to be removed subsequently, using an optical colonoscope (OC). Due to large colonic deformations induced by the colonoscope, even very experienced colonoscopists find it difficult to pinpoint the exact location of the colonoscope tip in relation to polyps reported on CTC. This can cause unduly prolonged OC examinations that are stressful for the patient, colonoscopist and supporting staff. We developed a method, based on monocular 3D reconstruction from OC images, that automatically matches polyps observed in OC with polyps reported on prior CTC. A matching cost is computed, using rigid point-based registration between surface point clouds extracted from both modalities. A 3D printed and painted phantom of a 25 cm long transverse colon segment was used to validate the method on two medium sized polyps. Results indicate that the matching cost is smaller at the correct corresponding polyp between OC and CTC: the value is 3.9 times higher at the incorrect polyp, comparing the correct match between polyps to the incorrect match. Furthermore, we evaluate the matching of the reconstructed polyp from OC with other colonic endoluminal surface structures such as haustral folds and show that there is a minimum at the correct polyp from CTC. Automated matching between polyps observed at OC and prior CTC would facilitate the biopsy or removal of true-positive pathology or exclusion of false-positive CTC findings, and would reduce colonoscopy false-negative (missed) polyps. Ultimately, such a method might reduce healthcare costs, patient inconvenience and discomfort.
description: This paper was presented at the SPIE Medical Imaging 2014 conference
title: Ethics in the infertility clinic: a qualitative study
Creators: name: Frith, Lucy
Publisher: name: University of Liverpool Repository
Year: 2011

description: This thesis is a qualitative study of infertility clinicians in the UK, exploring how they manage ethical issues: a study that uses empirical methods to explore ethical questions. I use a broadly Aristotelian conception of the relationship between theory and practice to develop a methodology for considering practical ethical issues. I then show how this approach, when allied with contemporary qualitative methodologies, can provide particularly valuable insights and produce practical recommendations. An important element of my approach is that a close attention to actual practice can also result in refining and developing our ethical theories and principles – practice informs theory just as theory can inform practice. This account of the ethical decision-making processes of infertility clinicians can not only highlight new ethical problems, but also develop more nuanced moral norms and ethical theories to deal with the conflicts and issues that arise in the clinical setting. Infertility treatment is a speciality that has attracted much attention from the public and bioethicists. The focus has been predominately on the dramatic aspects such as the status of the embryo or underlying issues such as the ethical boundaries of procreative liberty. Relatively little, however, is known about the everyday moral workings of infertility clinics: how clinicians approach ethical issues on a daily basis; what for them are troubling issues; and how they resolve ethical conflict. This study aims to gain insight into the way clinicians actually make ethical decisions. Moving on from this, it critically evaluates such processes and offers both an analysis of the strengths and weaknesses of the clinicians’ ethical decision-making and considers how this form of decision-making can be extended and supported in practice. The aims of this thesis are to contribute to the debate on both how ethical decision-making in the infertility clinic can be improved and, more generally, how bioethics can make a useful contribute to practical problems.
Developmental expression patterns ofTbx1,Tbx2,Tbx5, andTbx20 inXenopus tropicalis
Creators: name: Conlon, Frank L.
name: Christine, Kathleen S.
name: Showell, Chris
name: Mandel, Elizabeth M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: T-box genes have diverse functions during embryogenesis and are implicated in several human congenital disorders. Here, we report the identification, sequence analysis, and developmental expression patterns of four members of the T-box gene family in the diploid frog Xenopus tropicalis. These four genes—Tbx1, Tbx2, Tbx5, and Tbx20—have been shown to influence cardiac development in a variety of organisms, in addition to their individual roles in regulating other aspects of embryonic development. Our results highlight the high degree of evolutionary conservation between orthologs of these genes in X. tropicalis and other vertebrates, both at the molecular level and in their developmental expression patterns, and also identify novel features of their expression. Thus, X. tropicalis represents a potentially valuable vertebrate model in which to further investigate the functions of these genes through genetic approaches.
title: Band structures of 131Ce
Creators: name: Alwaleedi, Mohammed
Publisher: name: University of Liverpool Repository
Year: 2014

description: High-spin states have been studied in the neutron-deficent odd-N 131Ce nucleus. The experiment was performed at Argonne Laboratory, USA, using the fusion evaporation reaction 100Mo(36S,5n ). The beam of 36S was produced by the Argonne Tandem Linac Accelerator System (ATLAS) to an energy of 165 MeV with a beam current of 5 pnA. The gamma ray coincidence data were recorded with GAMMASPHERE. A detailed spectroscopic study of the 131Ce nucleus has established two new band structures and extended some of the known bands to higher spin. Cranked Woods- Saxon calculations have been used to assign possible configurations for the newly found structures. Angular intensity-ratio measurements have been performed to gain information on the multipolarities of transitions in this nucleus. In order to strengthen the suggested configuration for the 131Ce bands a comparison was carried out between the experimental and theoretical B(M1)/B(E2) ratios of reduced transition probabilities. A large signature splitting in the negative-parity bands is discussed as evidence for non-axial nuclear shape which is induced by the core-polarisation effects of neutrons from the upper h11/2 midshell.
Biregular graphs with three eigenvalues
Creators: name: Cheng, Xi-Ming
name: Gavrilyuk, Alexander L.
name: Greaves, Gary R. W.
name: Koolen, Jack H.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics

description: We consider nonregular graphs having precisely three distinct eigenvalues. The focus is mainly on the case of graphs having two distinct valencies and our results include constructions of new examples, structure theorems, valency constraints, and a classification of certain special families of such graphs. We also present a new example of a graph with three valencies and three eigenvalues of which there are currently only finitely many known examples.
description: 28 pages
Assessing the efficiency of different solvents for detecting gliotoxin from soil, organic manures and crop plant
Creators: name: Jayalakshmi, R
name: Mehetre, S.T
name: Kannan, R
name: Paramasivam, M
name: Santhanakrishnan, V.P
name: Kumar, K.K
name: Theradimani, M
name: Ramamoorthy, V
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Plant Biology
subject: Virology

description: Trichoderma virens produces gliotoxin and it is considered as a potent antibiotic against several soil-borne fungal and bacterial pathogens infecting crop plants. There is no study on the fate of gliotoxin especially its persistence in soil and crop plants. For precise analysis of its persistence, dissipation and movement of gliotoxin in soil ecosystem, it is important to find a suitable solvent that effectively extract the gliotoxin from soil and crop plant. In this study, various commonly used polar and non-polar solvents were assessed for their efficiency on extraction of gliotoxin from agricultural soil, farm yard manure (FYM), coir pith, tomato plants and from the mycelial mat of T. virens. Chloroform was found to be the effective solvent for the extraction of gliotoxin from soil, FYM and coir pith with extraction efficiency of 85%, 79% and 72%, respectively. Ethyl acetate extracted the maximum amount of gliotoxin from tomato leaves and roots with 79% and 72% extraction efficiency. Methanol effectively extracted gliotoxin from the mycelium of T. virens. From this study, it is concluded that chloroform and ethyl acetate are suitable for the extraction and detection of gliotoxin from the soil ecosystem and crop plants, respectively.
Discrete pulses of molting hormone, 20-hydroxyecdysone, during late larval development ofDrosophila melanogaster: Correlations with changes in gene activity
Creators: name: O'Connor, Michael B.
name: Yerushalmi, Yoram
name: Gilbert, Lawrence I.
name: Restifo, Linda L.
name: Warren, James T.
name: Shimell, Mary Jane
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Periodic pulses of the insect steroid molting hormone 20-hydroxyecdysone (20E), acting via its nuclear receptor complex (EcR/USP), control gene expression at many stages throughout Drosophila development. However, during the last larval instar of some lepidopteran insects, subtle changes in titers of ecdysteroids have been documented, including the so-called "commitment peak". This small elevation of 20E reprograms the larva for metamorphosis to the pupa. Similar periods of ecdysteroid immunoreactivity have been observed during the last larval instar of Drosophila. However, due to low amplitude and short duration, along with small body size and staging difficulties, their timing and ecdysteroid composition have remained uncertain. Employing a rigorous regimen of Drosophila culture and a salivary gland reporter gene, Sgs3-GFP, we used RP-HPLC and differential ecdysteroid RIA analysis to determine whole body titers of 20E during the last larval instar. Three small peaks of 20E were observed at 8, 20 and 28 hr following ecdysis, prior to the well-characterized large peak around the time of pupariation. The possible regulation of 20E levels by biosynthetic P450 enzymes and the roles of these early peaks in coordinating gene expression and late larval development are discussed.
title: Synthesis and characterisation of novel superconductors
Creators: name: McLennan, Alec
Publisher: name: University of Liverpool Repository
Year: 2014

description: This work presents and discusses the recent advances in high temperature superconductors. It focuses on how both the superconducting fullerides and iron selenides have contributed to the state-of-the-art of high temperature superconductors. The discovery of the relationship between the critical temperature and the proximity of the Cs3C60 material to the Mott metal-insulator transition has clearly demonstrated unconventional superconductivity in fullerides. However, the best samples of Cs3C60 were synthesised in purities of ~80 % which complicates the analysis of the physical properties of this important material. Furthermore, the use of hazardous and dangerous solvents such as methylamine and ammonia limits the availability of these materials for a broader scientific community and therefore, a facile and efficient synthetic procedure would strongly benefit the field. Within this work a novel synthetic method for Cs3C60 in a common THF solvent has been developed producing nearly single phase samples with a critical temperature (Tc) of 33 K. Intercalation of alkali metals into a FeSe host can produce the materials with Tc up to 46 K. However, the structure and composition AxFeySe2 (A=K, Rb and Cs) is under debate. In this work this problem was explored by the creation of a subsolidus KxFeySe2 powder phase diagram at 750oC. This allowed me to identify the existing range for superconducting samples and assess their qualities. It was found that the minority phase with a refined composition of close to K0.5Fe2Se2 and specific cell volume of 209.73 Å3 which is probably responsible for superconductivity. As the high temperature route does not allow the isolation of the superconducting phase in pure form a novel low temperature route has been developed. It involved the reaction of FeSe with potassium acenide reducing agents in THF where the use of the organo-metallic agent was to moderate the reductive capability of potassium. This proof-of-concept method produced superconducting materials with up to with 11 % of superconducting fraction and Tc = 33 K.
Specific mesenchymal/epithelial induction of olfactory receptor, vomeronasal, and gonadotropin-releasing hormone (GnRH) neurons
Creators: name: Lischka, F. W.
name: LaMantia, A.-S.
name: Zirlinger, M.
name: Tucker, E.S.
name: Pevny, L.
name: Rawson, N.E.
name: Yee, K.K.
name: Peters, A.Z.
name: Burd, G.B.
name: Meechan, D.W.
name: Dulac, C.
name: Maynard, T.M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: We asked whether specific mesenchymal/epithelial (M/E) induction generates olfactory receptor neurons (ORNs), vomeronasal neurons (VRNs) and gonadotropin releasing hormone (GnRH) neurons—the major neuron classes associated with the olfactory epithelium (OE). To assess specificity of M/E-mediated neurogenesis, we compared the influence of frontonasal mesenchyme on frontonasal epithelium, which becomes the OE, with that of the forelimb bud. Despite differences in position, morphogenetic and cytogenic capacity, both mesenchymal tissues support neurogenesis, expression of several signaling molecules and neurogenic transcription factors in the frontonasal epithelium. Only frontonasal mesenchyme, however, supports OE-specific patterning and activity of a subset of signals and factors associated with OE differentiation. Moreover, only appropriate pairing of frontonasal epithelial and mesenchymal partners yields ORNs, VRNs, and GnRH neurons. Accordingly, the position and molecular identity of specialized frontonasal epithelia and mesenchyme early in gestation and subsequent inductive interactions, specifies the genesis and differentiation of peripheral chemosensory and neuroendocrine neurons.
IBAS (Integral Burst Alert System) contributions to the study of GRBs, magnetars, FRB, and multiwavelength astrophysics
Creators: name: Mereghetti, Sandro
Publisher: name: Zenodo
Year: 2023

description: Presentation at conferences Two decades of High-energy Astronomy with INTEGRAL 17-21 October 2022, ESOC/ESA, Darmstadt, Germany
Islet lymphocyte subsets in male and female NOD mice are qualitatively similar but quantitatively distinct
Creators: name: Arnold, Larry W.
name: Frelinger, Jeffrey A.
name: Young, Ellen F.
name: Hess, Paul R.
name: Tisch, Roland
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Islet-infiltrating lymphocytes of individual male and female non-obese diabetic (NOD) mice were examined with the purpose of determining the differences that lead to a predominance of diabetes in female versus males NOD mice. When normalized for the amount of islet lymphocytes recovered, the infiltrating lymphocytes of female NOD mice were indistinguishable from those of male NOD mice. The only observed difference was that islet inflammation progressed at an increased rate in female compared to male NOD mice. There was no difference in the composition of islet infiltrates in male and female NOD mice. Unexpectedly, the ratio of CD4+:CD8+ T cells was tightly controlled in the islets throughout diabetogenesis. The frequency of IL-4+ CD4+ T cells started high but quickly fell to 3% of the population which was maintained with increasing inflammation. A significant portion of the CD8+ T cells were islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP) specific in both male and female NOD mice and this population was antigen experienced and increased at high levels of islet inflammation. Surprisingly, a large pool of antigen inexperienced naïve T cells was detected in the islets. We conclude the underlying immunological processes in both male and female NOD mice are similar while the rates differ and the presence of naïve T cell in the islets may contribute to epitope spreading.
Emergent rhombus tilings from molecular interactions with $M$-fold rotational symmetry
Creators: name: Whitelam, Stephen
name: Tamblyn, Isaac
name: Garrahan, Juan P.
name: Beton, Peter H.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We show that model molecules with particular rotational symmetries can self-assemble into network structures equivalent to rhombus tilings. This assembly happens in an emergent way, in the sense that molecules spontaneously select irregular 4-fold local coordination from a larger set of possible local binding geometries. The existence of such networks can be rationalized by simple geometrical arguments, but the same arguments do not guarantee networks' spontaneous self-assembly. This class of structures must in certain regimes of parameter space be able to reconfigure into networks equivalent to triangular tilings.
On one dimensional Quantum Zakharov system
Creators: name: Jiang, Jin-Cheng
name: Lin, Chi-Kun
name: Shao, Shuanglin
Publisher: name: arXiv
Year: 2014
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: In this paper, we discuss the properties of one dimensional quantum Zakharov system which describes the nonlinear interaction between the quantum Langmuir and quantum ion-acoustic waves. The system with initial data $(E(0),n(0),\partial_t n(0))\in H^k\bigoplus H^l\bigoplus H^{l-2}$ is local well posedness in low regularity spaces. Especially, the low regularity result for $k$ satisfies $-3/4
description: We corrected many typos in previous version. The result is the same
Crude oil and pyrene degradation by halotolerant fungi Embellisia sp. KJ59 and Alternaria sp. KJ66 isolated from saline soils
Creators: name: Jenab, Kian
name: Moghimi, Hamid
name: Azin, Ehsan
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: In recent years, investigating halophilic and halotolerant fungi enzymes has confirmed their significant potential in the biodegradation of crude oil. The aim of the current study was to evaluate the biodegradation of crude oil by halotolerant fungal Embellisia sp. KJ59 and Alternaria sp. KJ66. The fungal strains were isolated on Czapek Dox Agar (CDA), potato dextrose agar (PDA), and malt extract agar (MEA) containing 10% NaCl. Seven strains that could grow in salinity, ranging from 0 to 17% were selected. Out of the seven isolates, isolates KJ59 and KJ66 were selected as superior strains because they were more efficient in the biodegradation of crude oil on Minimal Salt Medium containing 1% crude oil and different salinity. The isolates were identified as Embellisia sp. and Alternaria sp. based on its nucleotide sequence of internal transcribed spacer gene. They could biodegrade petroleum, ranging from 81.3 to 95.1% in NaCl concentrations of 0, 2.5, and 5% on PDB over a period of 14 days. Pyrene removal by these strains was over 88.3% in saline and non-saline MSM containing 100 mg L−1 pyrene. Finally, Embellisia sp. KJ59 and Alternaria KJ66 were introduced fungal strains for crude oil biodegradation as the sole or supplementary carbon source in the presence of different salt concentrations. Furthermore, they are potential fungal strains for bioremediation of crude oil in non-saline and contaminated saline environments.
Evaluating chemotherapeutic potential of soya-isoflavonoids against high penetrance genes in triple-negative breast cancer
Creators: name: Chatterjee, Prarthana
name: Banerjee, Satarupa
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer

description: Triple-negative breast cancer (TNBC) is the most aggressive molecular subtype of breast cancer (BC) associated with a poor prognosis. Owing to the structural similarity with 17-β-estradiol, consumption of soya-isoflavonoids are associated with a reduced rate of hormone-receptive BC incidence, but their role in TNBC is not deciphered in detail. This present study thus aims to investigate the therapeutic binding dynamics of dietary soya-flavonoids with the six high penetrance (HP) receptors in TNBC, viz. BRCA1, BRCA2, PALB2, PTEN, STK11 and TP53. Out of the 14 soya-flavonoids screened based on ADMET descriptors and several other physicochemical, bioavailability, drug and lead-likeness properties, four hits were shortlisted (Daidzein, Genistein, Glycitein and Biochanin A). Docking and molecular dynamics (MD) simulation revealed Genistein as the most potential multi-target inhibitor of the six TNBC HP genes. Additionally, Genistein exhibited excellent binding specificity with PTEN, a potent mediator of the PI3K signaling pathway in TNBC. The binding interaction of PTEN and Genistein was further compared against a standardized FDA-approved chemotherapeutic inhibitor, Olaparib, computed through various MD trajectory analysis, principal component analysis and computation of free energy landscape. This study reveals a comparatively better binding dynamics of PTEN-Genistein than PTEN-Olaparib. With a significant global surge in biomarker-based precision therapeutics in oncology, the results of this exhaustive in-silico study thus encourage the prospect of validating PTEN as a druggable target of Genistein, a unique drug-receptor combination in the future. Communicated by Ramaswamy H. Sarma
title: Understanding the diffusion of small gases in porous organic cages using molecular dynamics
Creators: name: Holden, Daniel
Publisher: name: University of Liverpool Repository
Year: 2014

description: The aim of this thesis was to accurately simulate the dynamic nature of known porous organic cage molecules, with a view to understanding the diffusion of different gases through their pore structures. Initial calculations showed that, due to their unique chemical structure, no ‘off-the-shelf’ force field (FF) was accurate enough to describe their dynamic motion. Therefore, a cage specific force field, (CSFF), was developed to be transferable across the first three cage systems, CC1-CC3. CSFF was subsequently used to rationalise the ‘on’/‘off’ porosity observed in two different polymorphs of CC1. A combination of computational simulations, including simulated surface area calculations, grand canonical Monte Carlo (GCMC) adsorption isotherms, and molecular dynamics (MD) simulations, for hydrogen and nitrogen in CC1α and CC1β, helped to confirm experimental results, as well as to provide further insight into why the polymorphism of CC1 alters the porosity of the molecule. In addition, CSFF was used to study the diffusion of a range of gases through crystalline CC3. Seven gases were chosen: hydrogen, nitrogen, carbon dioxide, methane, sulfur hexafluoride, krypton and xenon. A detailed understanding of the diffusivity within CC3 was accomplished by combining MD simulations with new methodologies and techniques, for example analysis of the dynamic connectivity. This helped to rationalise why CC3 showed good experimental uptake of gas, as well as highlighting potential separation capabilities. In summary, the development of CSFF has made it possible to simulate the diffusion of small gases through porous organic imine cages, and it has been shown that this diffusion is dependent on the relative size of the gas to the cage window, assuming that there is a suitable diffusion pathway. Using MD simulations, we have unlocked phenomena such as gas selectivity, rare-event hopping and the diffusion of gases to regions previously thought inaccessible. This has aided the rationalisation of existing experimental observations, and is a significant step forward for a priori prediction of porous organic cage systems, and their properties. This work has also led to new experiments that were prompted by my simulations. Finally, a new way to visualise the connectivity of a system has been introduced. This is achieved by monitoring how the surface area evolves with respect to time, during a MD simulation. This suggests how the pore channels of various systems, previously thought too small for gas adsorption, are actually suitable candidates for separations.
The receptor tyrosine kinase MerTK regulates dendritic cell production of BAFF
Creators: name: Tisch, R.
name: Williams, J. C.
name: Gohlke, P. R.
name: Dillon, S. R.
name: Vilen, B. J.
name: Matsushima, G. K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: The MerTK receptor tyrosine kinase is an important negative regulator of dendritic cell function and is required to prevent B cell autoimmunity in vivo. It is not currently known however, if any causal relationship exists between these two aspects of MerTK function. We sought to determine if dendritic cells from mice lacking MerTK (mertk−/− mice) have characteristics that may aid in the development of B cell autoimmunity. Specifically, we found that mertk−/− mice contain an elevated number of splenic dendritic cells, and this population contains an elevated proportion of cells secreting the critical B cell pro-survival factor, B cell activating factor (BAFF). Elevated numbers of BAFF-secreting cells were also detected among mertk−/− bone marrow-derived dendritic cell (BMDC) populations. This was observed in both resting BMDC, and BMDC stimulated with lipopolysaccharide (LPS) or treated with exogenous apoptotic cells. We also found that dendritic cells in general have a pro-survival effect on resting B cells in co-culture. However, despite containing more BAFF-secreting cells, mertk−/− BMDC were not superior to C57BL/6 or baff-deficient BMDC at promoting B cell survival. Furthermore, using decoy receptors, we show that dendritic cells may promote B cell survival and autoimmunity through a BAFF-and APRIL-independent mechanism.