cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Pattern of tick aggregation on mice: larger than expected distribution tail enhances the spread of tick-borne pathogens
Creators: name: Ferreri, Luca
name: Giacobini, Mario
name: Bajardi, Paolo
name: Bertolotti, Luigi
name: Bolzoni, Luca
name: Tagliapietra, Valentina
name: Rizzoli, Annapaola
name: Rosà, Roberto
Publisher: name: arXiv
Year: 2014
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: Biological Physics (physics.bio-ph)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: Applications (stat.AP)
subject: FOS: Biological sciences
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: The spread of tick-borne pathogens represents an important threat to human and animal health in many parts of Eurasia. Here, we analysed a 9-year time series of Ixodes ricinus ticks feeding on Apodemus flavicollis mice (main reservoir-competent host for tick-borne encephalitis, TBE) sampled in Trentino (Northern Italy). The tail of the distribution of the number of ticks per host was fitted by three theoretical distributions: Negative Binomial (NB), Poisson-LogNormal (PoiLN), and Power-Law (PL). The fit with theoretical distributions indicated that the tail of the tick infestation pattern on mice is better described by the PL distribution. Moreover, we found that the tail of the distribution significantly changes with seasonal variations in host abundance. In order to investigate the effect of different tails of tick distribution on the invasion of a non-systemically transmitted pathogen, we simulated the transmission of a TBE-like virus between susceptible and infective ticks using a stochastic model. Model simulations indicated different outcomes of disease spreading when considering different distribution laws of ticks among hosts. Specifically, we found that the epidemic threshold and the prevalence equilibria obtained in epidemiological simulations with PL distribution are a good approximation of those observed in simulations feed by the empirical distribution. Moreover, we also found that the epidemic threshold for disease invasion was lower when considering the seasonal variation of tick aggregation.
description: 32 pages, 13 figures, appears in PLOS Computational Biology 2014
Interrogating the Function of Metazoan Histones using Engineered Gene Clusters
Creators: name: Duronio, Robert J.
name: Malek, Pamela Y.
name: Lieb, Jason D.
name: Matera, A. Gregory
name: Cooper, Stephen W.
name: Meers, Michael P.
name: McKay, Daniel J.
name: Klusza, Stephen
name: McDaniel, Stephen L.
name: Curry, Kaitlin P.
name: Tatomer, Deirdre C.
name: Penke, Taylor J.R.
name: Strahl, Brian D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Histones and their post-translational modifications influence the regulation of many DNA-dependent processes. Although an essential role for histone-modifying enzymes in these processes is well established, defining the specific contribution of individual histone residues remains a challenge because many histone-modifying enzymes have non-histone targets. This challenge is exacerbated by the paucity of suitable approaches to genetically engineer histone genes in metazoans. Here, we describe a facile platform in Drosophila for generating and analyzing any desired histone genotype, and we use it to test the in vivo function of three histone residues. We demonstrate that H4K20 is neither essential for DNA replication nor for completion of development, unlike conclusions drawn from analyses of H4K20 methyltransferases. We also show that H3K36 is required for viability and H3K27 is essential for maintenance of cellular identity during development. These findings highlight the power of engineering histones to interrogate genome structure and function in animals.
Report on the Developed and Validated Underwater Thematic Services (Release #2)
Creators: name: Karantzalos, Konstantinos
name: Ntouskos, Makis
name: Chatzikian, Melkon
name: Mertikas, Panagiotis
name: Lampridou, Danai
name: Nomikou, Paraskevi
name: Quintana, Josep
name: Campos, Ricard
name: Wintersteller, Paul
Publisher: name: Zenodo
Year: 2022
Subjects: Oceans & Geo Sciences
Bathymetry
Image Mosaicking
Mutli-frequency analysis and sediment classification

description: This document reports on the 2nd release of the Underwater Services and the software underlying each service. This NEANIAS report, deliverable D2.6, comes out after the second thematic Underwater Services release, deliverable D2.5. Due to a delay in the delivery of U1 [UW_BAT] “Bathymetry mapping from acoustic data service implementation” this report has not been published end of October 2021 but in April 2022. The U1 service provides an advanced user-friendly, cloud-based version of the popular MB-System software, allowing processing bathymetric data through Jupyter Notebooks. The U2 [UW_MOS] service “Seafloor Mosaicking from Optical Data” delivers 2D/3D mosaics produced by a set of images and navigational data. The expected output is achieved by a processing pipeline based on in-house solutions and open-source libraries. Finally, the U3 [UW_MAP] service “Seabed Classification from Multispectral, Multibeam Data” provides an easy-to-use, cloud-based solution incorporating machine learning frameworks in order to identify different seabed classes. For each released service a point-of-access is provided, as well as the relevant documentation, which is organized under the NEANIAS documentation service at https://docs.neanias.eu/en/latest. This second services milestone sees the Underwater services integrated to NEANIAS several core services, which are an essential contribute to the TRL 7 level reached. The core services integrated are the Logging and Accounting services, the AAI service and the Data Sharing service. The U2 and U3 services are also using the Common UI (User Interface) service.1 In this deliverable, we describe, in detail, the progress and changes/enhancements made since the first release for each of the Underwater services.
Profilin-1 Serves as a Gatekeeper for Actin Assembly by Arp2/3-Dependent and -Independent Pathways
Creators: name: Bear, James E.
name: Wu, Congying
name: Rotty, Jeremy D.
name: Johnson, Heath E.
name: Suarez, Cristian
name: Haugh, Jason M.
name: Winkelman, Jonathan D.
name: Haynes, Elizabeth M.
name: Kovar, David R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Cells contain multiple F-actin assembly pathways including the Arp2/3 complex, formins, and Ena/VASP, which have largely been analyzed separately. They collectively generate the bulk of F-actin from a common pool of G-actin; however, the interplay/competition between these pathways remains poorly understood. Using fibroblast lines derived from an Arpc2 conditional knockout mouse, we established matched-pair cells with and without the Arp2/3 complex. Arpc2−/− cells lack lamellipodia and migrate slower than WT cells, but have F-actin levels indistinguishable from controls. Actin assembly in Arpc2−/− cells was resistant to cytochalasin-D and was highly dependent on profilin-1 and Ena/VASP, but not formins. Profilin-1 depletion in WT cells increased F-actin and Arp2/3 complex in lamellipodia. Conversely, addition of exogenous profilin-1 inhibited Arp2/3 complex actin nucleation in vitro and in vivo. These observations suggest that antagonism of the Arp2/3 complex by profilin-1 in cells maintains actin homeostasis by balancing Arp2/3 complex-dependent and independent actin assembly pathways.
Continuous fixed-bed column study for removal of Congo red dye from aqueous solutions using Nelumbo nucifera leaf adsorbent
Creators: name: Vairavel, P
name: Rampal, Nakul
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biophysics
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified

description: The adsorption of Congo red (CR) dye from aqueous solutions is conducted in a continuous fixed-bed column by using agricultural biomass of Nelumbo nucifera leaf adsorbent. The column performance is evaluated by varying the adsorbent bed height (2.5‒5 cm), influent dye concentrations (10–50 mg L−1), and inlet flow rate (1‒5 mL min−1). Column experimental data confirmed that the breakthrough characteristics of the adsorption system are dependent on bed height, flow rate, and initial adsorbate concentration. The results show that the decolourisation efficiency and equilibrium uptake (qe) of CR decreases with increasing flow rate and increases with increasing bed height and influent adsorbate concentration. The maximum absorption efficiency (83.12%) was obtained using 5 cm bed height, 15 mg L−1 inlet adsorbate concentration, and 1 mL min−1 flow rate. The increased flow rate and initial adsorbate concentration lead to a shorter column exhaustion time. The length of mass transfer zone increased with increasing bed height. Various mathematical models are applied to column experimental data to predict the breakthrough curve and to evaluate the column capacity and kinetic constants of the models. The correlation between the experimental and theoretical data is quantified by calculating the regression coefficients for the Thomas and Yoon–Nelson models, an R2 ≥ 0.954 at various operating conditions was obtained, which shows that the trend of experimental data fits well and the overall system kinetics are limited by solid-liquid interphase mass transfer. The N. nucifera leaf fine powder adsorbent is proven to be capable of removing CR efficiently from aqueous solutions in continuous fixed-bed systems at low flow rate and higher bed depth and it can be used effectively in wastewater treatment.
Thiadiazine thione derivatives as anti-leishmanial agents: synthesis, biological evaluation, structure activity relationship, ADMET, molecular docking and molecular dyanamics simulation studies
Creators: name: Tamanna
name: Fu, Chaoping
name: Qadir, Meshil
name: Shah, Muhammad Ishaq Ali
name: Shtaiwi, Amneh
name: Khan, Rasool
name: Khan, Shafi Ullah
name: Htar, Thet Thet
name: Zada, Amir
name: Lodhi, Muhammad Arif
name: Ateeq, Muhammad
name: Ali, Arif
name: Naeem, Mohammad
name: Ibrahim, Mohammad
name: Khan, Sher Wali
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biochemistry
Medicine
Pharmacology
Environmental Sciences not elsewhere classified
Chemical Sciences not elsewhere classified
Science Policy
Biological Sciences not elsewhere classified

description: During last decades, 3,5-disubstituted-tetrahydro-2H-thiadiazine-2-thione scaffold remains the center of interest due to their ease of preparation, diverse range substituents at N-3 and N-5 positions, and profound biological activities. In the current study, a series of 3,5-disubstituted-tetrahydro-2H-thiadiazine-2-thiones were synthesized in good to excellent yield, and the structure of the compounds were confirmed by various spectroscopic techniques such as FTIR, 1H-NMR, 13C-NMR and Mass spectrometry, and finally evaluated against Leishmania major. Whereas, all the evaluated compounds (1-33), demonstrate potential leishmanicidal activities with IC50 values in the range of (1.30- 149.98 uM). Among the evaluated compounds such as 3, 4, 6, and 10 exhibited excellent leishmanicidal activities with IC50 values of (2.17 μM), (2.39 μM), (2.00 μM), and (1.39 μM), respectively even better than the standard amphotericin B (IC50 = 0.50) and pentamidine (IC50 = 7.52). In order to investigate binding interaction of the most active compounds, molecular docking study was conducted with Leishmania major. Further molecular dynamic simulation study was also carried out to assess the stability and correct binding of the most active compound 10, within active site of the Leishamania major. Likewise, the physiochemical properties, drug likeness, and ADMET of the most active compounds were investigated, it was found that none of the compounds violate Lipiniski’s rule of five, which show that this class of compounds had enough potential to be used as drug candidate in near future. Communicated by Ramaswamy H. Sarma
Simultaneous determination of five opium alkaloids in underground waters using molecularly imprinted polymer-modified magnetic nanoparticle based dispersive micro-solid phase extraction followed by high performance liquid chromatography
Creators: name: Nemati, Nader
name: Ahmadi, Seyyed Hamid
name: heydar, Kourosh Tabar
Publisher: name: Taylor & Francis
Year: 2021
Subjects: Biophysics
Biochemistry
Space Science
Physical Sciences not elsewhere classified
Biotechnology
Environmental Sciences not elsewhere classified
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified

description: In this work, we present a fast, simple and selective method for the extraction/preconcentration and determination of five opium alkaloids. This method is based on the combination of dispersive solid phase extraction with magnetic molecularly imprinted polymers (MMIP) and determination via high performance liquid chromatography. The surface modified Fe3O4 nanoparticles were synthesised in-situ, from a co-precipitation method by addition of a mixture of the methacrylic acid and ammonia to a mixture of Fe2+/Fe3+ under nitrogen atmosphere. MMIP was prepared from surface modified nanoparticles in the presence of ethylene glycol dimethyl acrylate as cross-linker and azobisisobutyronitrile as initiator and template molecule under reflux in acetonitrile. MMIPs for five natural occurring opium alkaloids, including morphine (MO), codeine (CO), thebaine (TE), noscapine (NO) and papaverine (PA) were prepared in the same manner. Structural characterisation and elucidation of both synthesised nanoprticles were performed by Fourier transform-infrared spectroscopy, scanning electron microscopy. X-ray diffraction and vibrating sample magnetometry. A precise chromatographic method was developed and coupled with extraction with MMIP nanoparticles for simultaneous preconcentration and determination of above-mentioned alkaloids in underground water samples. The limit of detection obtained 0.007, 0.007, 0.004, 0.003, 0.003 mg L−1 for MO, CO, TE, NO and PA, respectively and recoveries were about 97–102%. Linear dynamic range and relative standard deviation were 0.03–100 mg L−1 and less than 1.5% for each analyte.
title: Investigating the nephrogenic potential of mouse embryonic stem cells and their derivatives
Creators: name: Rak-Raszewska, Aleksandra
Publisher: name: University of Liverpool Repository
Year: 2012

description: The kidneys are important organs that regulate the level of water and salts in the blood, produce hormones that help to control blood pressure, and maintain homeostasis of the organism by filtering waste products. Kidney disease can either be acute or chronic, the latter progressively worsening over time to become end stage renal disease (ESRD) – a stage when kidneys are non-functional. At present, the only treatment options for ESRD are transplantation or dialysis, which both have severe drawbacks in terms of morbidity, mortality and economic cost. Moreover, the incidence of ESRD is rising annually and an alternative therapy is needed. Therefore, in order to regenerate kidney tissue or prevent worsening of the kidney condition, a new therapy should be developed. One approach is to use embryonic stem cells.
Reassessment of Piwi Binding to the Genome and Piwi Impact on RNA Polymerase II Distribution
Creators: name: Yin, Hang
name: Zhong, Mei
name: Neuenkirchen, Nils
name: Valouev, Anton
name: Snyder, Michael
name: Lin, Haifan
name: Kundaje, Anshul
name: Liu, Na
name: Chen, Mengjie
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Drosophila Piwi was reported by Huang et al. (2013) to be guided by piRNAs to piRNA-complementary sites in the genome, which then recruits Heterochromatin Protein 1a and histone methyltransferase Su(Var)3-9 to the sites. Among additional findings, Huang et al. (2013) also reported Piwi binding sites in the genome and the reduction of RNA polymerase II in euchromatin but its increase in pericentric regions in piwi mutants. Marinov et al. (2015) disputed the validity of the Huang et al. bioinformatic pipeline that led to the last two claims. Here we report our independent reanalysis of the data using current bioinformatic methods. Our reanalysis agrees with Marinov et al. (2015) that Piwi’s genomic targets still remain to be identified, yet confirms the Huang et al. claim that Piwi influences RNA polymerase II distribution in the genome. This Response addresses the Marinov et al. (2015) Matters Arising, published concurrently in Developmental Cell.
Fabrication of Triangular Nanobeam Waveguide Networks in Bulk diamond Using Single-Crystal Silicon Hard Masks
Creators: name: Bayn, I.
name: Mouradian, S.
name: Li, L.
name: Goldstein, J. A.
name: Schröder, T.
name: Zhang, J.
name: Chen, E. H.
name: Gaathon, O.
name: Lu, M.
name: Stein, A.
name: Ruggiero, C. A.
name: Salzman, J.
name: Kalish, R.
name: Englund, D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: A scalable approach for integrated photonic networks in single-crystal diamond using triangular etching of bulk samples is presented. We describe designs of high quality factor (Q=2.51x10^6) photonic crystal cavities with low mode volume (Vm=1.062x(λ/n)^3), which are connected via waveguides supported by suspension structures with predicted transmission loss of only 0.05 dB. We demonstrate the fabrication of these structures using transferred single-crystal silicon hard masks and angular dry etching, yielding photonic crystal cavities in the visible spectrum with measured quality factors in excess of Q=3x103.
description: This article will be published in Applied Physics Letters
RNA-binding domain of SARS-CoV2 nucleocapsid: MD simulation study of the effect of the proline substitutions P67S and P80R on the structure of the protein
Creators: name: Manish, Manish
name: Pahuja, Monika
name: Lynn, Andrew M.
name: Mishra, Smriti
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: The nucleocapsid component of SARS-CoV2 is involved in the viral genome packaging. GammaP.1(Brazil) and the 20 C-US(USA) variants had a high frequency of the P80R and P67S mutations respectively in the RNA-binding domain of the nucleocapsid. Since RNA-binding domain participates in the electrostatic interactions with the viral genome, the study of the effects of proline substitutions on the flexibility of the protein will be meaningful. It evinced that the trajectory of the wildtype and mutants was stable during the simulation and exhibited distinct changes in the flexibility of the protein. Moreover, the beta-hairpin loop region of the protein structures exhibited high amplitude fluctuations and dominant motions. Additionally, modulations were detected in the drug binding site. Besides, the extent of correlation and anti-correlation motions involving the protruding region, helix, and the other RNA binding sites differed between the wildtype and mutants. The secondary structure analysis disclosed the variation in the occurrence pattern of the secondary structure elements between the proteins. Protein-ssRNA interaction analysis was also done to detect the amino acid contacts with ssRNA. R44, R59, and Y61 residues of the wildtype and P80R mutant exhibited different duration contacts with the ssRNA. It was also noticed that R44, R59, and Y61 of the wildtype and P80R formed hydrogen bonds with the ssRNA. However in P67S, residues T43, R44, R45, R40, R59, and R41 displayed contacts and formed hydrogen bonds with ssRNA. Binding free energy was also calculated and was lowest for P67S than wildtype andP80R. Thus, proline substitutions influence the structure of the RNA-binding domain and may modulate viral genome packaging besides the host-immune response. Communicated by Ramaswamy H. Sarma
Linker-assisted engineering of chimeric xylanase-phytase for improved thermal tolerance of feed enzymes
Creators: name: Patel, Dharti K.
name: Rawat, Ravi
name: Sharma, Shilpa
name: Shah, Kruti
name: Borsadiya, Nayan
name: Dave, Gayatri
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Biotechnology
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer

description: Biological enzymes are multifunctional macromolecules that can perform hundreds of reactions simultaneously. An enzyme must possess specific characteristics to meet industrial needs, such as stability over a wide pH and temperature range and high specific activity. A phytase and xylanase mixture is generally added to poultry feed to improve the bird’s health and productivity. Despite this, animal farmers have noticed no difference in productivity, and a leading cause is the high temperature at which feed is pulverized, which inactivates enzymes. A thermo-stable enzyme system can overcome these hitches. Commonly, coatings and immobilization reduce losses caused by physical-chemical factors in feed processing and digestion. To this end, we engineered the multifunctional xylanase-phytase domains on a single polypeptide fused by a helical linker. First, the ideal linker sequence was chosen by computing each selected linker’s root mean square deviation (RMSD). The selected helical linker provides sufficient structural flexibility for substrate binding and product release evaluated by molecular docking and molecular dynamic simulation studies. Furthermore, a domain-domain interaction has stabilized the bridging partners, attaining the thermal optima for xylanase and phytase at 90 °C. Even at the above-optimal temperature (100 °C), the recombinant PLX was relatively stable and retained 64.2% and 59.2% activity for xylanase and phytase, respectively, when surveyed for ten hours. So far, to this date, this is the highest degree of thermostability achieved by any recombinant phytase or xylanase. Communicated by Ramaswamy H. Sarma
Sensitivity of $T_{\rm c}$ to pressure and magnetic field in the cuprate superconductor YBa$_{2}$Cu$_{3}$O$_{y}$: evidence of charge order suppression by pressure
Creators: name: Cyr-Choinière, O.
name: LeBoeuf, D.
name: Badoux, S.
name: Dufour-Beauséjour, S.
name: Bonn, D. A.
name: Hardy, W. N.
name: Liang, R.
name: Graf, D.
name: Doiron-Leyraud, N.
name: Taillefer, Louis
Publisher: name: arXiv
Year: 2015
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Cuprate superconductors have a universal tendency to form charge density-wave (CDW) order which competes with superconductivity and is strongest at a doping $p \simeq 0.12$. Here we show that in the archetypal cuprate YBa$_{2}$Cu$_{3}$O$_{y}$ (YBCO) pressure suppresses charge order, but does not affect the pseudogap phase. This is based on transport measurements under pressure, which reveal that the onset of the pseudogap at $T^*$ is independent of pressure, while the negative Hall effect, a clear signature of CDW order in YBCO, is suppressed by pressure. We also find that pressure and magnetic field shift the superconducting transition temperature $T_{\rm c}$ of YBCO in the same way as a function of doping - but in opposite directions - and most effectively at $p \simeq 0.12$. This shows that the competition between superconductivity and CDW order can be tuned in two ways, either by suppressing superconductivity with field or suppressing CDW order by pressure. Based on existing high-pressure data and our own work, we observe that when CDW order is fully suppressed at high pressure, the so-called "1/8 anomaly" in the superconducting dome vanishes, revealing a smooth $T_{\rm c}$ dome which now peaks at $p \simeq 0.13$. We propose that this $T_{\rm c}$ dome is shaped by the competing effects of the pseudogap phase below its critical point $p^{\star} \sim 0.19$ and spin order at low doping.
description: New Hall data added. 11 pages, 9 figures and 2 tables
Role of Polarized G Protein Signaling in Tracking Pheromone Gradients
Creators: name: Minakova, Maria
name: Elston, Timothy C.
name: Dyer, Jayme M.
name: Zyla, Trevin R.
name: Lew, Daniel J.
name: McClure, Allison W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Yeast cells track gradients of pheromones to locate mating partners. Intuition suggests that uniform distribution of pheromone receptors over the cell surface would yield optimal gradient sensing. However, yeast cells display polarized receptors. The benefit of such polarization was unknown. During gradient tracking, cell growth is directed by a patch of polarity regulators that wanders around the cortex. Patch movement is sensitive to pheromone dose, with wandering reduced on the up-gradient side of the cell, resulting in net growth in that direction. Mathematical modeling suggests that active receptors and associated G proteins lag behind the polarity patch and act as an effective drag on patch movement. In vivo, the polarity patch is trailed by a G protein-rich domain, and this polarized distribution of G proteins is required to constrain patch wandering. Our findings explain why G protein polarization is beneficial, and illuminate a novel mechanism for gradient tracking.
Approximation Algorithms for Computing Maximin Share Allocations
Creators: name: Amanatidis, Georgios
name: Markakis, Evangelos
name: Nikzad, Afshin
name: Saberi, Amin
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computer Science and Game Theory (cs.GT)
subject: FOS: Computer and information sciences
subject: F.2.2; G.2.1

description: We study the problem of computing maximin share guarantees, a recently introduced fairness notion. Given a set of $n$ agents and a set of goods, the maximin share of a single agent is the best that she can guarantee to herself, if she would be allowed to partition the goods in any way she prefers, into $n$ bundles, and then receive her least desirable bundle. The objective then in our problem is to find a partition, so that each agent is guaranteed her maximin share. In settings with indivisible goods, such allocations are not guaranteed to exist, so we resort to approximation algorithms. Our main result is a $2/3$-approximation, that runs in polynomial time for any number of agents. This improves upon the algorithm of Procaccia and Wang, which also produces a $2/3$-approximation but runs in polynomial time only for a constant number of agents. To achieve this, we redesign certain parts of their algorithm. Furthermore, motivated by the apparent difficulty, both theoretically and experimentally, in finding lower bounds on the existence of approximate solutions, we undertake a probabilistic analysis. We prove that in randomly generated instances, with high probability there exists a maximin share allocation. This can be seen as a justification of the experimental evidence reported in relevant works. Finally, we provide further positive results for two special cases that arise from previous works. The first one is the intriguing case of $3$ agents, for which it is already known that exact maximin share allocations do not always exist (contrary to the case of $2$ agents). We provide a $7/8$-approximation algorithm, improving the previously known result of $3/4$. The second case is when all item values belong to $\{0, 1, 2\}$, extending the $\{0, 1\}$ setting studied in Bouveret and Lemaître. We obtain an exact algorithm for any number of agents in this case.
Signatures of a momentum independent pseudogap in the electronic density of states and Raman spectroscopy of the underdoped cuprates
Creators: name: LeBlanc, J. P. F.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We propose a hybridization phenomenology to describe the pseudogap state of the underdoped cuprates. We show how a momentum independent pseudogap opens asymmetrically from the Fermi-surface but symmetric to the zeroes of the hybridized bonding dispersion, which results in false d-wave characteristics of the pseudogap at the Fermi level. By comparing against a d-wave form factor we illustrate the difficulty in identifying a momentum independent order in momentum averaged quantities such as the electronic Raman response. We identify a suppression in the single-particle density of states which produces a hump feature which should be observable experimentally in tunnelling $dI/dV$ spectra and distinguishes the s-wave and d-wave ordering scenarios.
description: 14 pages, 4 figures
title: Getranslateerd uuten Franssoyse. Translation from French into Dutch in Holland in the 15th century. The case of Gerard Potter's Middle Dutch translation of Froissart's 'Chroniques'
Creators: name: Schoenaers, Dirk
Publisher: name: University of Liverpool Repository
Year: 2012

description: This dissertation focuses on the intercultural relations between the French-speaking and Dutch-speaking world in Holland in the first half of the fifteenth century. After a turbulent war of succession between the claimants Jacqueline of Bavaria and her uncle John the Pitiless, the counties of Holland, Zeeland and Hainault were incorporated into the largely francophone Burgundian empire. It has been suggested that this event marked the end of a flourishing period of cultural production in the Dutch vernacular at the court of Holland. However, as it seems, throughout the fifteenth century translations of French texts were produced for regional and local administrators. Possibly, the Burgundian regional government of Holland, which consisted of foreign as well as indigenous noblemen, may have played an important role in the dissemination of these texts. In this thesis, the subject is addressed by means of the contextualisation of the Middle Dutch version of Jean Froissart’s Chroniques. An analysis of documentary sources suggests that the comital residence at the Hague is best characterised as a multicultural environment inhabited by both bilingual and monolingual individuals. The results of an analysis of the variant readings in the French manuscripts of the Chroniques as compared to its Dutch counterpart show that the French manuscript which served as a model for the translation was probably produced between 1410 and 1418 by the Parisian libraire Pierre de Liffol. A comparison of the translated and original text shows that the translator wants to provide his readership with a text that is optimally intelligible and relevant to their context. Gerijt Potter’s modifications show that his intended audience was familiar with the habits of European courts and had a considerable geographical horizon. Because of the presence of doublets, repetitions and French loans, Potter’s style of writing resembles the official style of the comital chancery. However, a similar style is also found in other late fourteenth and early fifteenth-century translations. In The Hague the translation was probably dispersed (be it on a small scale) among members of the council and their contacts among the high nobility of Holland. Through the intensive contact between the regional councillors and members of local administration, the translation of the Chroniques became available to an audience in the cities.
LSST DESC Science Overview Document
Creators: name: LSST Dark Energy Science Collaboration
Publisher: name: Zenodo
Year: 2022

description: The LSST DESC Science Overview Document provides a summary of the DESC science goals and the DESC working groups and their priorities. The document briefly outlines the structure of the collaboration and timelines for crucial milestones. The Science Overview Document helps all members of the collaboration to obtain a quick overview of the major priorities of the collaboration and to navigate the different working groups.
title: UWB antennas for wireless communications
Creators: name: Cao, Ping
Publisher: name: University of Liverpool Repository
Year: 2014

description: This thesis focuses on four inter-related research topics on the design and analysis of compact planar ultra wide-band (UWB) monopole antennas for future wireless communications, namely, a planar super-wide-band (SWB) monopole antenna, a planar UWB antenna with band-notched characteristics, a planar UWB antenna with reconfigurable band-rejection features, and a planar UWB multiple-input and multiple-output (MIMO) antenna. A novel Mickey-mouse shaped planar monopole antenna with SWB performance is proposed and investigated. Three different techniques for bandwidth enhancement are implemented. The antenna is evolved from the traditional circular monopole antenna and has achieved an impedance bandwidth of more than 100:1 and a stable radiation patterns over a wider bandwidth. The design of a compact planar UWB monopole antenna (22 mm × 34 mm), incorporated with five m-shaped resonators (MSRs) at different positions, to achieve quintuple-band-notched performance is presented. The frequency-domain performance (in term of reflection coefficients, realized gain, efficiency, and radiation pattern), and time-domain performance (in term of pulse responses and fidelity), are investigated by simulation and measurement. The results show that the proposed UWB antenna has approximately omnidirectional radiation patterns and excellent band-notched behaviours and good time domain performance with the fidelity of more than 85.5% in the pulse response. A planar UWB monopole antenna with reconfigurable band-notched characteristics is also introduced. The band rejection is realized by incorporating two co-directional split ring resonators (CSRR) on the radiator element. Switches are added to the CSRR structures to achieve the reconfigurability. The proposed antenna can operate at different switching states including a UWB state, single and dual band-notched states with good rejection behaviours. Good radiation patterns and gain values are also obtained for different switching states. This compact wideband antenna can be very good candidate for a wide range of mobile portable applications. A compact planar UWB-MIMO antenna (60 mm × 45 mm) is presented for wireless applications. The wideband isolation of more than 15 dB is achieved by etching a new trident-like slot on the ground plane of the antenna. An equivalent circuit have been introduced for analysis and the diversity performances are studied. The results show that the proposed MIMO antenna is a very good candidate for wireless applications. The study of these four special antennas has demonstrated that, using various techniques, the planar monopole antenna can be an excellent choice for a wide range of wireless communication applications.
The E3 Ubiquitin Ligase TRIM9 Is a Filopodia Off Switch Required for Netrin-Dependent Axon Guidance
Creators: name: Gupton, Stephanie Lynn
name: Boyer, Nicholas Patrick
name: Pandey, Dharmendra
name: Menon, Shalini
name: Winkle, Cortney Chelise
name: McClain, Leslie Marie
name: Rothenfußer, Simon
name: Hanlin, Christopher Carey
name: Taylor, Anne Marion
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Neuronal growth cone filopodia contain guidance receptors and contribute to axon guidance; however, the mechanism by which the guidance cue netrin increases filopodia density is unknown. Here, we demonstrate that TRIM9, an E3 ubiquitin ligase that localizes to filopodia tips and binds the netrin receptor DCC, interacts with and ubiquitinates the barbed-end polymerase VASP to modulate filopodial stability during netrin-dependent axon guidance. Studies with murine Trim9(+/+) and Trim9(-/-) cortical neurons, along with a non-ubiquitinatable VASP mutant, demonstrate that TRIM9-mediated ubiquitination of VASP reduces VASP filopodial tip localization, VASP dynamics at tips, and filopodial stability. Upon netrin treatment, VASP is deubiquitinated, which promotes VASP tip localization and filopodial stability. Trim9 deletion induces axon guidance defects in vitro and in vivo, whereas a gradient of deubiquitinase inhibition promotes axon turning in vitro. We conclude that a gradient of TRIM9-mediated ubiquitination of VASP creates a filopodial stability gradient during axon turning.
title: A role for SOX9 and Wnt-related proteins in endometrial adenocarcinoma
Creators: name: Draper, Hannah
Publisher: name: University of Liverpool Repository
Year: 2014

description: Introduction: Endometrial carcinoma is already the most common gynaecological malignancy in the developed world, and by 2015 the incidence is set to be twice that of 2005. Despite this, therapeutic options available for advanced disease are very limited. The canonical Wnt/β-catenin pathway is known to have a key role in homeostasis of normal endometrial cellular proliferation and differentiation, and is also implicated in endometrial proliferative conditions such as carcinogenesis. SOX9 is a postulated Wnt-regulator and may play a key role in establishment and maintenance of characteristic phenotypes of glandular cells during the menstrual cycle. The interaction of Wnt/β-catenin pathway and SOX9 in the endometrium is not known, neither are the effects of ovarian steroids on these pathways and proteins fully elucidated. The expression of a panel of Wnt-related proteins in endometrial cancer tissue samples was compared to normal pre- and post-menopausal endometrium. Further in vitro work investigated the effect of ovarian steroid hormones on SOX9 and steroid receptor expression in a well characterised, well differentiated endometrial carcinoma cell line Ishikawa. Methods: 51 primary endometrial samples (31 endometrial adenocarcinomas (EC), 10 normal proliferative phase (PP) and 10 normal post-menopausal (PM)) were assessed for the expression of SOX9, Ki67, β-catenin, SOX2, SFRS2, and NAP1L1 using immunohistochemistry. The Ishikawa cell line was maintained in phenol-free charcoal stripped media for 72 hours, and then treated with ovarian steroids: estradiol (E2), medroxyprogesterone acetate (MPA), E2 + MPA, basic fibroblast growth factor (FGF), and 5-alpha-dihydrotestosterone (DHT) for 72 hours. RT-PCR was performed for oestrogen receptor α (ER), progesterone receptor (PR), and SOX9. Statistical analysis used the Mann-Whitney and Spearman Rank tests. Results: Nuclear β-catenin was correlated with the Wnt-related proteins SOX2 (p=0.025), NAP1L1 (p=0.046) and SFRS2 (p=0.032). However, none of these proteins demonstrated significantly different expression across the groups. The expression of SOX9 was significantly lower in the proliferative tissues (PP and EC) than the atrophic PM (p
LSST DESC Science Overview Document
Creators: name: LSST Dark Energy Science Collaboration
Publisher: name: Zenodo
Year: 2023

description: The LSST DESC Science Overview Document provides a summary of the DESC science goals and the DESC working groups and their priorities. The document briefly outlines the structure of the collaboration and timelines for crucial milestones. The Science Overview Document helps all members of the collaboration to obtain a quick overview of the major priorities of the collaboration and to navigate the different working groups.
Low-complexity modeling of partially available second-order statistics: theory and an efficient matrix completion algorithm
Creators: name: Zare, Armin
name: Chen, Yongxin
name: Jovanović, Mihailo R.
name: Georgiou, Tryphon T.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: State statistics of linear systems satisfy certain structural constraints that arise from the underlying dynamics and the directionality of input disturbances. In the present paper we study the problem of completing partially known state statistics. Our aim is to develop tools that can be used in the context of control-oriented modeling of large-scale dynamical systems. For the type of applications we have in mind, the dynamical interaction between state variables is known while the directionality and dynamics of input excitation is often uncertain. Thus, the goal of the mathematical problem that we formulate is to identify the dynamics and directionality of input excitation in order to explain and complete observed sample statistics. More specifically, we seek to explain correlation data with the least number of possible input disturbance channels. We formulate this inverse problem as rank minimization, and for its solution, we employ a convex relaxation based on the nuclear norm. The resulting optimization problem is cast as a semidefinite program and can be solved using general-purpose solvers. For problem sizes that these solvers cannot handle, we develop a customized alternating minimization algorithm (AMA). We interpret AMA as a proximal gradient for the dual problem and prove sub-linear convergence for the algorithm with fixed step-size. We conclude with an example that illustrates the utility of our modeling and optimization framework and draw contrast between AMA and the commonly used alternating direction method of multipliers (ADMM) algorithm.
description: Submitted to IEEE Transactions on Automatic Control
Granite-MWCNTs nanocomposite coated with Dialium guineense stem bark extract for enhanced adsorption of chromium(VI)
Creators: name: Amaku, James Friday
name: Ogundare, Segun A.
name: Akpomie, Kovo G.
name: Lawal, Isiaka A.
name: Akpotu, Samson
name: Odih, Christian
name: Conradie, Jeanet
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Plant Biology

description: The prominent benefit of granite is owned to its physicochemical property and ubiquitous nature. Vast application of granite which also includes its use as an adsorbent in environmental remediation practice, can also be enhanced. To further enhanced the uptake capacity of granite, nanocomposite consisting of multiwall carbon nanotubes (MWCNTs) and granite was fabricated and further modified using Dialiumguineensestem bark extract. The structure and composition of pristine granite (PG) and modified nanocomposite granite (G) based material were examined and confirmed by the FTIR, Raman, TGA, SEM and XRD. Meanwhile, the specific surface areasof PG (1.268 m2/g) and G (16.57 m2/g) were obtained using the BET surface area analyser. The optimization step revealed that the uptake capacities of PG and G were dependent on solution pH, sorbent dose and contact time. Meanwhile, pseudo-second-order and Elovich kinetic models were noticed to best describe the data for the removal of Cr (VI) by PG and G. Equilibrium isotherm study revealed that Freundlich and Langmuir models fitted well to the experimental data obtained for the uptake of Cr(VI) onto PG and G respectively. Furthermore, electrostaticattraction betweentheDialiumguineense stem bark extract on the surface of G and Cr(VI) influenced the uptake of Cr(VI). On the other hand, the interaction between the plant extract and Cr(VI) may result in the attenuation of Cr(VI) via reduction to Cr(III). Finally, the thermodynamically favoured adsorptive process demonstrated high adsorbent reusability with good stability for Cr(VI) uptake.
Accurate age classification of 6 and 12 month-old infants based on resting-state functional connectivity magnetic resonance imaging data
Creators: name: Kostopoulos, Penelope
name: Pruett, John R.
name: Piven, Joseph
name: Nishino, Tomoyuki
name: Dager, Stephen R.
name: Hazlett, Heather C.
name: Constantino, John N.
name: Fonov, Vladimir S.
name: Dosenbach, Nico U.F.
name: Collins, D. Louis
name: Styner, Martin
name: Adeyemo, Babatunde
name: Schultz, Robert T.
name: Snyder, Abraham Z.
name: Das, Samir
name: Paterson, Sarah
name: Schlaggar, Bradley L.
name: Estes, Annette M.
name: Botteron, Kelly N.
name: Nardos, Binyam
name: Feczko, Eric
name: Kandala, Sridhar
name: Evans, Alan C.
name: Hoertel, Sarah
name: Elison, Jed T.
name: Gerig, Guido
name: Power, Jonathan D.
name: Petersen, Steven E.
name: McKinstry, Robert C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Human large-scale functional brain networks are hypothesized to undergo significant changes over development. Little is known about these functional architectural changes, particularly during the second half of the first year of life. We used multivariate pattern classification of resting-state functional connectivity magnetic resonance imaging (fcMRI) data obtained in an on-going, multi-site, longitudinal study of brain and behavioral development to explore whether fcMRI data contained information sufficient to classify infant age. Analyses carefully account for the effects of fcMRI motion artifact. Support vector machines (SVMs) classified 6 versus 12 month-old infants (128 datasets) above chance based on fcMRI data alone. Results demonstrate significant changes in measures of brain functional organization that coincide with a special period of dramatic change in infant motor, cognitive, and social development. Explorations of the most different correlations used for SVM lead to two different interpretations about functional connections that support 6 versus 12-month age categorization.
Frequency of spontaneous BOLD signal shifts during infancy and correlates with cognitive performance
Creators: name: Goldman, Barbara D.
name: Gao, Wei
name: Alcauter, Sarael
name: Smith, J. Keith
name: Reznick, J. Steven
name: Gilmore, John H.
name: Lin, Weili
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Numerous studies have been conducted to delineate the early development of different functional networks, based on measuring the temporal synchronization of spontaneous blood oxygenation level-dependent (BOLD) signals acquired using resting state functional MRI (rsfMRI). However, little attention has been paid to the change of the frequency properties of these signals during early brain development. Such frequency properties may reflect important physiological changes and potentially have significant cognitive consequences. In this study, leveraging a large (N=86 subjects), longitudinal sample of human infants scanned during the first two years of life, we aimed to specifically delineate the developmental changes of the frequency characteristics of spontaneous BOLD signals. Both whole-brain and network-level examinations were carried out and the frequency-behavior relationship was explored. Our results revealed a clear right-ward shift of BOLD signal frequency during the first year of life. Moreover, the power at the peak-frequency for sensorimotor and lateral visual networks correlates with domain-specific Mullen Scales in 1-year-olds, suggesting the behavioral significance of the BOLD signal frequency during infancy. Findings from this study shed light into early functional brain development and provide a new perspective for future searches for functional developmental abnormalities.