cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Mechanism of calmodulin inactivation of the calcium-selective TRP channel TRPV6
Creators: name: Singh, Appu K.
name: McGoldrick, Luke Lawrence Reedy
name: Twomey, Edward Charles
name: Sobolevsky, Alexander I.
name: Columbia University. Cellular, Molecular
Publisher: name: Columbia University
Year: 2018
Subjects: Calmodulin
TRP channels
Molecular biology
Ion channels

description: Calcium (Ca2+) plays a major role in numerous physiological processes. Ca2+ homeostasis is tightly controlled by ion channels, the aberrant regulation of which results in various diseases including cancers. Calmodulin (CaM)–mediated Ca2+-induced inactivation is an ion channel regulatory mechanism that protects cells against the toxic effects of Ca2+ overload. We used cryo-electron microscopy to capture the epithelial calcium channel TRPV6 (transient receptor potential vanilloid subfamily member 6) inactivated by CaM. The TRPV6-CaM complex exhibits 1:1 stoichiometry; one TRPV6 tetramer binds both CaM lobes, which adopt a distinct head-to-tail arrangement. The CaM carboxyl-terminal lobe plugs the channel through a unique cation-π interaction by inserting the side chain of lysine K115 into a tetra-tryptophan cage at the pore’s intracellular entrance. We propose a mechanism of CaM-mediated Ca2+-induced inactivation that can be explored for therapeutic design.
Vector Beams with Parabolic and Elliptic Cross-Sections for Laser Material Processing Applications
Creators: name: Orlov, Sergej
name: Vosylius, Vitalis
name: Gotovski, Pavel
name: Grabusovas, Artūras
name: Baltrukonis, Justas
name: Gertus, Titas
Publisher: name: arXiv
Year: 2023
Subjects: subject: Optics (physics.optics)
subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: Beam profile engineering, where a desired optical intensity distribution can be generated by an array of phase shifting (or amplitude changing) elements is a promising approach in laser material processing. For example, a spatial light modulator (SLM) is a dynamic diffractive optical element allowing for experimental implementations of controllable beam profile. Scalar Mathieu beams have elliptical intensity distribution perceivable as optical knives in the transverse plane and scalar Weber beams have a parabolic distribution, which enables us to call them optical shovels. Here, we introduce vector versions of scalar Mathieu and Weber beams and use those vector beams as a basis to construct controllable on-axis phase and amplitude distributions with polarization control. Further, we generate individual components of optical knife and shovel beams experimentally using SLMs as a toy model and report on our achievements in the control over the beam shape, dimensions and polarization along the propagation axis.
Supplementary document for Highly sensitive detection of cytochrome c in the NSCLC serum using hydrophobic paper based-gold nanourchins substrate - 4898410.pdf
Creators: name: Sun, Yue
name: Ge, Shengjie
name: Xue, Jin
name: Zhou, Xinyu
name: Lu, Wenbo
name: Li, Guang
name: Cao, Xiaowei
Publisher: name: Optica Publishing Group
Year: 2020
Subjects: Uncategorized

description: Optimization of experimental conditions
The Higgs boson resonance width from a chiral Higgs-Yukawa model on the lattice
Creators: name: Gerhold, Philipp
name: Jansen, Karl
name: Kallarackal, Jim
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The Higgs boson is a central part of the electroweak theory and is crucial to generate masses for quarks, leptons and the weak gauge bosons. We use a 4-dimensional Euclidean lattice formulation of the Higgs-Yukawa sector of the electroweak model to compute physical quantities in the path integral approach which is evaluated by means of Monte Carlo simulations thus allowing for fully non perturbative calculations. The chiral symmetry of the model is incorporated by using the Neuberger overlap Dirac operator. The here considered Higgs-Yukawa model does not involve the weak gauge bosons and furthermore, only a degenerate doublet of top- and bottom quarks are incorporated. The goal of this work is to study the resonance properties of the Higgs boson and its sensitivity to the strength of the quartic self coupling.
description: Included figures of cross-sections, corrected one data entry in table 3, version accepted in PLB
Patterns of leisure-time physical activity across pregnancy and adverse pregnancy outcomes
Creators: name: Catov, Janet M.
name: Parker, Corette B.
name: Gibbs, Bethany B.
name: Bann, Carla M.
name: Carper, Benjamin
name: Silver, Robert M.
name: Simhan, Hyagriv N.
name: Parry, Samuel
name: Chung, Judith H.
name: Haas, David M.
name: Wapner, Ronald J.
name: Saade, George R.
name: Mercer, Brian M.
name: Bairey-Merz, C. N.
name: Greenland, Philip
name: Ehrenthal, Deborah B.
name: Barnes, Shannon E.
name: Shanks, Anthony L.
name: Reddy, Uma M.
name: Grobman, William A.
name: NICHD NuMoM2b And NHLBI NuMoM2b Heart Health Study Network
Publisher: name: Columbia University
Year: 2018
Subjects: Diabetes in pregnancy
Exercise
Pregnancy
Premature infants
Obstetrics

description: Background
                Although leisure-time physical activity (PA) contributes to overall health, including pregnancy health, patterns across pregnancy have not been related to birth outcomes. We hypothesized that women with sustained low leisure-time PA would have excess risk of adverse pregnancy outcomes, and that changing patterns across pregnancy (high to low and low to high) may also be related to risk of adverse pregnancy outcomes.

                Methods
                Nulliparous women (n = 10,038) were enrolled at 8 centers early in pregnancy (mean gestational age in weeks [SD] = 12.05 [1.51]. Frequency, duration, and intensity (metabolic equivalents) of up to three leisure activities reported in the first, second and third trimesters were analyzed. Growth mixture modeling was used to identify leisure-time PA patterns across pregnancy. Adverse pregnancy outcomes (preterm birth, [PTB, overall and spontaneous], hypertensive disorders of pregnancy [HDP], gestational diabetes [GDM] and small-for-gestational-age births [SGA]) were assessed via chart abstraction.

                Results
                Five patterns of leisure-time PA across pregnancy were identified: High (35%), low (18%), late decreasing (24%), early decreasing (10%), and early increasing (13%). Women with sustained low leisure-time PA were younger and more likely to be black or Hispanic, obese, or to have smoked prior to pregnancy. Women with low vs. high leisure-time PA patterns had higher rates of PTB (10.4 vs. 7.5), HDP (13.9 vs. 11.4), and GDM (5.7 vs. 3.1, all p
title: Towards Precision Measurements of the Hyperfine Splitting of Antihydrogen
Creators: name: Suh, Jay Hyung
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Antimatter
subject: Antihydrogen
subject: Spectroscopy
subject: Atomic Physics
subject: Physics--Atomic

description: The observed asymmetry between matter and antimatter in our universe remains to be one of the foremost mysteries that contradicts our current theories of physics. The search for possible causes of the asymmetry lies at the leading edge of experimental particle physics, with experiments around the world dedicated to the study of antimatter. The study of the antihydrogen atom, the antimatter analogue to the hydrogen atom, is the primary motivation of the ALPHA Collaboration based at CERN. Through detailed observations and measurements of the antihydrogen atom structure, we can draw comparisons with the well-known structure of the hydrogen atom and search for possible asymmetries between matter and antimatter. The hyperfine structure of antihydrogen is both sensitive to fundamental interactions and has been measured to a high precision in hydrogen, making it a prime candidate for study. Any observed discrepancy between the hyperfine structure of hydrogen and antihydrogen would be a pivotal discovery and advancement in our understanding of the universe. This thesis will describe the measurement of the hyperfine splitting of antihydrogen performed by ALPHA, with the aim of providing an improved result and precision to previously published values [1]. It will briefly include a historical review of antimatter, then will discuss the theory behind the hyperfine structure, the various apparatuses used by the ALPHA Collaboration to produce, confine and manipulate antimatter particles, and the experimental procedure used to perform this measurement. I also demonstrate the usage of electron cyclotron resonance (ECR) to provide precise measurements of the magnetic field used to trap the antihydrogen atoms. I will summarize my work done on the hyperfine splitting and ECR measurements performed over the last two years, and present details regarding my work quantifying some of the prominent systematics of the experiment.
Papers in New Guinea Linguistics No. 24
Creators: name: Laycock, D. (Ed.)
name: Seiler, W. (Ed.)
name: Bruce, L. (Ed.)
name: Chlenov, M. (Ed.)
name: Shaw, R. (Ed.)
name: Holzknecht, S. (Ed.)
name: Scott, G. (Ed.)
name: Nekitel, O. (Ed.)
name: Wurm, S.A. (Ed.)
name: Goldman, L. (Ed.)
name: Fingleton, J. (Ed.)
Publisher: name: Pacific Linguistics
Year: 1986

description: A-70
description: Contents iiiINTRODUCTORY NOTE iv{D.C. LAYCOCK} 1-10Papuan languages and the possibility of semantic classification{WALTER SEILER} 11-19From verb serialisation to noun classification{LES BRUCE} 21-37Serialisation: the interface of syntax and lexicon{M.A. CHLENOV} 39-44North Halmahera languages: a problem of internal classification{R. DANIEL SHAW} 45-76The Bosavi language family{SUSANNE HOLZKNECHT} 77-166A morphology and grammar of Adzera (Amari dialect), Morobe Province, Papua New Guinea{GRAHAM SCOTT} 167-175On ergativity in Fore and other Papuan languages{OTTO NEKITEL} 177-205A sketch of nominal concord in Abu' (an Arapesh language){S.A. WURM} 207-211Grammatical decay in Papuan languages{L.R. GOLDMAN} 213-289The presentational style of women in Huli disputes{J.S. FINGLETON} 291-312Tolai kinship concepts: correspondence between Kuanua and Tok Pisin terminology
The geometry of rest–spike bistability
Creators: name: Cirillo, Giuseppe Ilario
name: Sepulchre, Rodolphe
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Research
Rest–spike bistability
Neuronal models
Slow–fast models

description: Funder: Qualcomm; doi: http://dx.doi.org/10.13039/100005144
description: Abstract: Morris–Lecar model is arguably the simplest dynamical model that retains both the slow–fast geometry of excitable phase portraits and the physiological interpretation of a conductance-based model. We augment this model with one slow inward current to capture the additional property of bistability between a resting state and a spiking limit cycle for a range of input current. The resulting dynamical system is a core structure for many dynamical phenomena such as slow spiking and bursting. We show how the proposed model combines physiological interpretation and mathematical tractability and we discuss the benefits of the proposed approach with respect to alternative models in the literature.
title: Exploring Barriers to, and Facilitators of, Diabetes Self-Management Among Patients with Kidney Failure Receiving Dialysis
Creators: name: Younis, Kokab
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Diabetes
subject: Self-management of diabetes
subject: kidney disease
subject: Education--Social Sciences
subject: Education--Health

description: Diabetes mellitus is the leading cause of kidney failure in Canada and around the globe. The treatment of kidney failure may require dialysis - a life-sustaining therapy. Dialysis therapy places significant demands on patients, adding an extra health burden for those navigating the transition to living with chronic diseases. It is well reported in literature that dialysis patients with diabetes compared to those without diabetes have poorer quality of life, longer lengths of hospital stay, a higher burden of morbidity and mortality, and significantly higher economic costs. However, literature on barriers to, and facilitators of, optimal self-management of diabetes are scant in patients with kidney failure. The aim of this thesis work was to understand, describe and interpret the perspectives of patients on barriers to, and facilitators of, diabetes self-management. A narrative review and interpretive descriptive qualitative study were undertaken to address the study aim. Semi-structured interviews with fourteen patients were conducted. A total of 134 articles were identified whereas eight articles met our inclusion criteria. A review of the articles and qualitative study revealed barriers to and facilitators of diabetes self-management. Emerging themes from the included studies and semi-structured interviews were identified using inductive thematic analysis. Barriers reported by participants were financial and physical limitations, limited access to healthcare services, siloed and fragmented care, increased medical complexity, and the higher burden of health. Facilitators of diabetes self-management were self-management support and education, coordinated care between healthcare providers, and supportive environments. Findings from this thesis work contribute to a broader scientific literature, facilitate further research in this domain to address barriers, and guide resource allocation concerning the improvement of diabetes care and self-management practices among patients with kidney failure on dialysis therapies.
Paspalum cordatum Hack.
Creators: name: Camargo Keller, Victor
name: Lopes Pereira-Silva, Erico Fernando
name: Hardt, Elisa
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Liliopsida
Poales
Poaceae
Paspalum
Paspalum cordatum

description: Paspalum cordatum Hack. Identification. Perennial tussock grass, short rhizomes, 1.00– 1.65 m height. Leaf-blades linear, 6.5–40.0 cm long, 0.4–0.7 cm wide, acuminate, glabrous to densely hairy on both sides, ligulate. It is characterized by its inflorescence with 3–10 alternate branches, with solitary and cordiform spikelets. Remarks. Occurs on the native grassland, mainly over humid soils. Brazilian range. Midwest (except DF state), North (AM state), South (PR state), Southeast (except ES and RJ states) regions. Materials examined. BRAZIL – São Paulo • Franco da Rocha, Parque Estadual do Juquery; 23°20′56″S, 046°40′55″W; 16 Jan. 2018; collection number vck163; HUFABC2175 • same collection data as for preceding; collection number vck164; HUFABC2176.
description: Published as part of Camargo Keller, Victor, Lopes Pereira-Silva, Erico Fernando & Hardt, Elisa, 2021, High richness, new occurrences, and threatened species in a savanna grassland remnant in the largest Brazilian metropolis, pp. 507-549 in Check List 17 (2) on page 535, DOI: 10.15560/17.2.507
Two-Baryon Potentials and H-Dibaryon from 3-flavor Lattice QCD Simulations
Creators: name: Inoue, Takashi
name: Aoki, Sinya
name: Doi, Takumi
name: Hatsuda, Tetsuo
name: Ikeda, Yoichi
name: Ishii, Noriyoshi
name: Murano, Keiko
name: Nemura, Hidekatsu
name: Sasaki, Kenji
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Experiment (nucl-ex)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Baryon-baryon potentials are obtained from 3-flavor QCD simulations with the lattice volume L ~ 4 fm, the lattice spacing a ~ 0.12 fm, and the pseudo-scalar-meson mass M_ps =469 - 1171 MeV. The NN scattering phase shift and the mass of H-dibaryon in the flavor SU(3) limit are extracted from the resultant potentials by solving the Schrodinger equation. The NN phase shift in the SU(3) limit is shown to have qualitatively similar behavior as the experimental data. A bound H-dibaryon in the SU(3) limit is found to exist in the flavor-singlet J^P=0^+ channel with the binding energy of about 26 MeV for the lightest quark mass M_ps = 469 MeV. Effect of flavor SU(3) symmetry breaking on the H-dibaryon is estimated by solving the coupled-channel Schrodinger equation for Lambda Lambda - N Xi - Sigma Sigma with the physical baryon masses and the potential matrix obtained in the SU(3) limit: a resonant H-dibaryon is found between Lambda Lambda and N Xi thresholds in this treatment.
description: 22 pages, 11 figures, Version accepted to publish on Nucl. Phys. A
title: The role of phenotypic plasticity in threespine stickleback (Gasterosteus aculeatus) adaptation to thermally variable habitats
Creators: name: Stanford, Brenna Callista Moreau
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Phenotypic plasticity
subject: Developmental plasticity
subject: Phenotypic flexibility
subject: Gene expression
subject: Thermal tolerance
subject: Climate change
subject: Ecology
subject: FOS: Biological sciences
subject: Bioinformatics
subject: FOS: Computer and information sciences
subject: Biology--Molecular

description: Phenotypic plasticity, the ability of a genotype to give rise to multiple phenotypes dependent on environmental cues, is a well-established phenomenon that allows organisms to rapidly modify their phenotype in response to environmental change. It has been recommended that phenotypic plasticity be included in predicting population and species’ response to climate change. However, there remains substantial debate regarding its role in population persistence, adaptation, and evolutionary theory. While phenotypic plasticity occurs at all biological levels, it is largely driven by changes in gene regulation, and it has been suggested that resolving these molecular mechanisms will facilitate its integration into studies of adaptation and evolution. In this thesis, I use threespine stickleback (Gasterosteus aculeatus) to investigate how evolution has shaped reversible (i.e., phenotypic flexibility) and irreversible (i.e., developmental plasticity) plastic responses to temperature, a key abiotic environmental variable. To do so, I first tested if local adaptation to freshwater habitats has altered plasticity within key biological pathways by comparing gene expression of freshwater and marine ecotypes acclimated to cold or warm temperatures. Using Weighted Gene Co-expression Network Analysis, I found evolutionary conserved and divergent responses between the ecotypes, with freshwater stickleback having evolved increased thermal plasticity in several gene modules. I then determined that marine stickleback exhibit substantial developmental plasticity induced by egg temperature that persists into adulthood, over a year after the thermal stressor was removed. The effect of developmental temperature was found in both liver and muscle tissue, however, each tissue type exhibited distinct patterns of gene expression and thermal plasticity. At the whole organism level, egg developmental temperature was found to significantly alter the lower critical thermal limit in all families in the direction cued (i.e., eggs developed at cool temperatures had decreased lower critical thermal limit). The upper critical thermal limit showed inconsistent patterns of plasticity across families but was found to already be higher than temperatures predicted under climate change scenarios. Collectively, these data illustrate that organisms exhibit thermal plasticity from the molecular to whole organism level and that these responses have been shaped by evolution to generate the current patterns of plasticity that will underlie species’ response to future conditions.
Scattering and Localization Properties of Highly Oscillatory Potentials
Creators: name: Duchêne, Vincent
name: Vukićević, Iva
name: Weinstein, Michael I.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Analysis of PDEs (math.AP)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 35B27, 35B32, 35C20, 35J10

description: We investigate scattering, localization and dispersive time-decay properties for the one-dimensional Schrödinger equation with a rapidly oscillating and spatially localized potential, $q_ε=q(x,x/ε)$, where $q(x,y)$ is periodic and mean zero with respect to $y$. Such potentials model a microstructured medium. Homogenization theory fails to capture the correct low-energy ($k$ small) behavior of scattering quantities, e.g. the transmission coefficient, $t^{q_ε}(k)$, as $ε$ tends to zero. We derive an effective potential well, $σ^ε_{eff}(x)=-ε^2Λ_{eff}(x)$, such that $t^{q_ε}(k)-t^{σ^ε_{eff}}(k)$ is uniformly small on $\mathbb{R}$ and small in any bounded subset of a suitable complex strip. Within such a bounded subset, the scaled transmission coefficient has a universal form, depending on a single parameter, which is computable from the effective potential. A consequence is that if $ε$, the scale of oscillation of the microstructure potential, is sufficiently small, then there is a pole of the transmission coefficient (and hence of the resolvent) in the upper half plane, on the imaginary axis at a distance of order $ε^2$ from zero. It follows that the Schrödinger operator $H_{q_ε}=-\partial_x^2+q_ε(x)$ has an $L^2$ bound state with negative energy situated at a distance $O(ε^4)$ from the edge of the continuous spectrum. Finally, we use this detailed information to prove a local energy time-decay estimate of the time-dependent Schrödinger equation.
description: to appear in Communications on Pure and Applied Mathematics
Supplementary document for Laser-induced dynamic alignment and nonlinear-like optical transmission in liquid suspensions of 2D atomically thin nanomaterials - 5486745.pdf
Creators: name: Zhang, Qiuhui
name: Wang, Yanan
name: Lin, Feng
name: Tang, Yingjie
name: Cheng, Peihong
name: Zhou, Xufeng
name: Zhu, Zhuan
name: Ma, Yayao
name: Liu, Zhaoping
name: liu, dong
Publisher: name: Optica Publishing Group
Year: 2021
Subjects: Optical Properties of Materials

description: Snapshots of birefringence images of graphene suspension in NMP and closed-aperture results
MADANIYATLARARO MULOQOTNI OʻRGANISH ZARURATI
Creators: name: Paziljanova, Zulfiya
name: Mamajonova, Malohat
name: Ismoilova, Madina
name: Odilova, Dilzoda
name: Abdumalikova, Nigora
Publisher: name: Zenodo
Year: 2023

description: Maqolada globallashuv jarayoni bilan bog'liq ravishda madaniyatlararo muloqotni o'rganishga ehtiyojning paydo bo'lishi haqida gap boradi.
Hydroxychloroquine prescription trends and predictors for excess dosing per recent ophthalmology guidelines
Creators: name: Jorge, April M.
name: Melles, Ronald B.
name: Zhang, Yuqing
name: Lu, Na
name: Rai, Sharan K.
name: Young, Lucy H.
name: Costenbader, Karen H.
name: Ramsey-Goldman, Rosalind
name: Lim, S. Sam
name: Esdaile, John M.
name: Clarke, Ann E.
name: Urowitz, M. B.
name: Askanase, Anca Dinu
name: Aranow, Cynthia
name: Petri, Michelle
name: Choi, Hyon
Publisher: name: Columbia University
Year: 2018
Subjects: Epidemiology
Rheumatology
Systemic lupus erythematosus--Alternative treatment
Rheumatoid arthritis--Treatment
Drugs

description: Background
                Hydroxychloroquine (HCQ) retinopathy may be more common than previously recognized; recent ophthalmology guidelines have revised recommendations from ideal body weight (IBW)-based dosing to actual body weight (ABW)-based dosing. However, contemporary HCQ prescribing trends in the UK remain unknown.

                Methods
                We examined a UK general population database to investigate HCQ dosing between 2007 and 2016. We studied trends of excess HCQ dosing per ophthalmology guidelines (defined by exceeding 6.5 mg/kg of IBW and 5.0 mg/kg of ABW) and determined their independent predictors using multivariable logistic regression analyses.

                Results
                Among 20,933 new HCQ users (78% female), the proportions of initial HCQ excess dosing declined from 40% to 36% using IBW and 38% to 30% using ABW, between 2007 and 2016. Among these, 47% of women were excess-dosed (multivariable OR 12.52; 95% CI 10.99–14.26) using IBW and 38% (multivariable OR 1.98; 95% CI,1.81–2.15) using ABW. Applying IBW, 37% of normal and 44% of obese patients were excess-dosed; however, applying ABW, 53% of normal and 10% of obese patients were excess-dosed (multivariable ORs = 1.61 and 0.1 (reference = normal); both p
Additional file 1 of Comparison of the outcomes between sorafenib and lenvatinib as the first-line systemic treatment for HBV-associated hepatocellular carcinoma: a propensity score matching analysis
Creators: name: Choi, Na Ryung
name: Kim, Ju Yeon
name: Hong, Ji Hoon
name: Hur, Moon Haeng
name: Cho, Heejin
name: Park, Min Kyung
name: Kim, Jihye
name: Lee, Yun Bin
name: Cho, Eun Ju
name: Lee, Jeong-Hoon
name: Yu, Su Jong
name: Yoon, Jung-Hwan
name: Kim, Yoon Jun
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy

description: Additional file 1. Figure S1. Overall survival of four subgroups divided by first-line medication and subsequent treatment.
Studies of the structure and function of recombinant human hephaestin
Creators: name: Vashchenko, Ganna
Publisher: name: University of British Columbia
Year: 2012

description: Hephaestin is a multicopper ferroxidase involved in iron absorption in the small intestine. The ferroxidase activity of hephaestin is thought to play an important role during iron export from intestinal enterocytes and the subsequent iron loading of the blood protein transferrin, which delivers iron to the tissues. Structurally, the ectodomain of hephaestin is predicted to resemble ceruloplasmin, the soluble ferroxidase of blood. In this work I investigated substrate specificity, copper loading and the ferroxidation mechanism of recombinantly expressed human hephaestin. The hephaestin ectodomain (Fet3Hp) was expressed in Pichia pastoris and purified to electrophoretic homogeneity by immunoaffinity chromatography. Recombinant hephaestin retained ferroxidase activity and showed an average copper content of 4.2 copper atoms per molecule. The Km values of Fet3Hp for such organic substrates as p-phenylenediamine and o-dianisidine were close to values determined for ceruloplasmin. However, in contrast to ceruloplasmin, recombinant hephaestin was incapable of direct oxidation of adrenaline and dopamine implying a difference in biological substrate specificities between these two homologous oxidases. I also expressed hephaestin ectodomain with the ceruloplasmin signal peptide (CpHp) using BHK cells as an expression system. Ion exchange chromatography of purified CpHp resulted in the production of a hephaestin fraction with improved catalytic and spectroscopic properties. Detailed kinetic analysis of CpHp ferroxidation rates revealed the presence of two types of iron-binding sites with different affinities towards ferrous iron. Michaelis constants for high- and low-affinity ferrous binding sites in CpHp were comparabale to the corresponding Km values in ceruloplasmin suggesting that both paralogs utilize similar amino acid residues for iron binding. To investigate the role of particular residues in iron specificity of hephaestin, mutations of putative iron ligands were introduced into CpHp using site-directed mutagenesis. Kinetic analysis of ferroxidation rates of wild-type CpHp and variants revealed the important roles of residues E960 and H965 in hephaestin ferroxidase activity.
Linear extensions of partial orders and Reverse Mathematics
Creators: name: Frittaion, Emanuele
name: Marcone, Alberto
Publisher: name: arXiv
Year: 2012
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics
subject: 03B30 (Primary) 06A07 (Secondary)

description: We introduce the notion of τ-like partial order, where τis one of the linear order types ω, ω*, ω+ω*, and ζ. For example, being ω-like means that every element has finitely many predecessors, while being ζ-like means that every interval is finite. We consider statements of the form "any τ-like partial order has a τ-like linear extension" and "any τ-like partial order is embeddable into τ" (when τ is ζ this result appears to be new). Working in the framework of reverse mathematics, we show that these statements are equivalent either to BΣ^0_2 or to ACA_0 over the usual base system RCA_0.
description: 8 pages, minor changes suggested by referee. To appear in MLQ - Mathematical Logic Quarterly
title: Early Life Dairy Exposure: Influence on the Gut Microbiota and Obesity Susceptibility
Creators: name: Hartslief, Micaela
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Gut Microbiota
subject: Dairy Protein
subject: Obesity
subject: Insulin Resistance
subject: Nutrition

description: Childhood obesity rates are increasing at a detrimental trajectory, leading to a serious health epidemic with related comorbidities that are likely to persist into adulthood (1,2). The causes of obesity are complex and influenced by a multitude of factors including diet, genetics and more recently dysbiosis of the gut microbiota (3,4). The gut microbiota is comprised of microorganisms residing in the gut, that have the ability to produce physiologically active substances such as vitamins and short-chain fatty acids and provide various health benefits through immune system regulation and removal of toxins (5). Mounting evidence suggests that dairy may play a protective role in obesity partially mediated through positive modulation of the gut microbiota (6,7). This study examined the role of dairy proteins, casein, whey and complete dairy (skim milk powder), and a plant-based alternative, soy, on gut microbiota composition, obesity susceptibility and insulin sensitivity. At weaning, 3-week-old pups (p=85), were randomized into 4 dietary protein intervention groups for 4-weeks: 1) complete dairy; 2) casein; 3) whey; 4) soy followed by a 5-week high-fat high-sucrose (HFHS) dietary challenge with the same proteins maintained. Microbial and metabolic outcomes assessed in this study included fecal microbial analysis (16s rRNA sequencing), body composition (NMR), glucose tolerance and insulin sensitivity. Dairy proteins compared to soy largely altered gut microbial profiles fostering improved metabolic function and enhanced insulin sensitivity. The impact on gut microbiota and metabolic results was protein dependent whereby early exposure to complete dairy demonstrated the most promising results improving body fat percentage and glucose tolerance while enriching beneficial probiotic microbial taxa, Lactobacillus in males while increasing Akkermansia in females. In contrast, following 5-week exposure to HFHS, there were limited differential effects on obesity, adiposity, sex hormones and glucose tolerance. Gut microbial profiles following HFHS dairy consumption, largely increased Bifidobacterium in males and maintained the increase of Akkermansia in females, however reduced alpha diversity. Taken together, dairy proteins play a significant role in positively modulating gut microbial profiles in a normal fat diet, fostering beneficial effects on body composition and glucose homeostasis.
Image set for deep learning: field images of maize annotated with disease symptoms
Creators: name: Wiesner-Hanks, Tyr
name: Stewart, Ethan L.
name: Kaczmar, Nicholas
name: DeChant, Chad
name: Wu, Harvey
name: Nelson, Rebecca J.
name: Lipson, Hod
name: Gore, Michael A.
Publisher: name: Columbia University
Year: 2018
Subjects: Computer science
Machine learning
Plant diseases
Corn
Image processing
Neural networks (Computer science)

description: Objectives
                Automated detection and quantification of plant diseases would enable more rapid gains in plant breeding and faster scouting of farmers’ fields. However, it is difficult for a simple algorithm to distinguish between the target disease and other sources of dead plant tissue in a typical field, especially given the many variations in lighting and orientation. Training a machine learning algorithm to accurately detect a given disease from images taken in the field requires a massive amount of human-generated training data.

                Data description
                This data set contains images of maize (Zea mays L.) leaves taken in three ways: by a hand-held camera, with a camera mounted on a boom, and with a camera mounted on a small unmanned aircraft system (sUAS, commonly known as a drone). Lesions of northern leaf blight (NLB), a common foliar disease of maize, were annotated in each image by one of two human experts. The three data sets together contain 18,222 images annotated with 105,705 NLB lesions, making this the largest publicly available image set annotated for a single plant disease.
title: Human Rights, Artificial Intelligence, and Academic Integrity
Creators: name: Eaton, Sarah Elaine
Publisher: name: Werklund School of Education
Year: 2024
Subjects: subject: artificial intelligence
subject: academic integrity
subject: misconduct
subject: conduct
subject: policy
subject: procedure
subject: neurotechnology
subject: education
subject: higher education
subject: human rights
subject: dignity
subject: plagiarism
subject: restorative justice

description: In this presentation, Eaton highlights key points from her 2024 editorial for the International Journal for Educational Integrity, “Future-proofing integrity in the age of artificial intelligence and neurotechnology: prioritizing human rights, dignity, and equity”. Eaton argues for the prioritisation of human rights when developing and implementing misconduct policies. Existing approaches may be perpetuate inequities, particularly for individuals from marginalised groups. A human-rights-by-design approach, which centres human rights in policy development, revision, and implementation, ensuring that every individual is treated with dignity and respect. Recommendations for implementing a human-rights approach to misconduct investigations and case management are offered, covering areas such as procedural fairness, privacy, equity, and the right to education. Additional topics covered are the need to limit surveillance technologies, and the need to recognize that not all use of artificial intelligence tools automatically constitutes misconduct. In the age of artificial intelligence and neurotechnology, insisting on human rights and dignity when we investigate and address misconduct allegations is an ethical imperative that has never been more important.
title: Remote Sensing of Monitoring Forest Fire Dynamics in Near/Ultra Real Time
Creators: name: Bhuian, Md Hanif
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: forest fire
subject: remote sensing
subject: active Fire
subject: fire monitoring
subject: wildfire
subject: VIIRS
subject: MODIS
subject: satellite
subject: gis
subject: model
subject: Education--Sciences

description: Forest fires cause extensive environmental damage, significant carbon emissions, and economic losses, posing major challenges for disaster management and emergency response. Accurate and timely delineation of fire perimeters is essential for minimizing these impacts. The overall aim of this study was to develop an early forest fire monitoring model that enables automatic clustering of active fire points and precise delineation of fire perimeters using satellite-based active fire data from VIIRS and MODIS datasets. Various algorithms—buffer, concave, convex, and combination methods—are assessed for their efficiency in near real-time (NRT), real-time (RT), and ultra-real-time (URT) fire perimeter delineation. Additionally, this study also introduced the automated Timely Active Fire Progression (TAFP) model for clustering and calculating active fire perimeter consistently. The results indicate that increasing the concave α (alpha) values (e.g., 0.1 to 0.5) enhances the matching percentage with ground fire areas but also leads to higher commission errors, signifying a risk of overestimation. Combination methods achieved the highest matching percentages but were also associated with increased commission errors. However, the TAFP model demonstrated an 85.13% matching rate for fire perimeters across various size classes, with a 95.95% clustering accuracy for fires larger than 100 hectares. This research was the first to scientifically evaluate multiple algorithms, both individually and synergistically, using NRT/RT/URT active fire data. The insights gained underscore the trade-offs between enhancing perimeter accuracy and avoiding overestimation, providing a critical foundation for optimizing sensor data alignment techniques. By improving the timeliness and accuracy of forest fire monitoring, the proposed models can significantly bolster operational responses by fire management agencies, aiding in resource allocation, evacuation planning, and mitigation strategies. This study lays the groundwork for future advancements in automated forest fire perimeter assessment, essential for effective disaster management and rapid response efforts.
A common rule for decision-making in animal collectives across species
Creators: name: Arganda, Sara
name: Pérez-Escudero, Alfonso
name: de Polavieja, Gonzalo G.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: Neurons and Cognition (q-bio.NC)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Biological sciences

description: A diversity of decision-making systems has been observed in animal collectives. In some species, choices depend on the differences of the numbers of animals that have chosen each of the available options, while in other species on the relative differences (a behavior known as Weber's law) or follow more complex rules. We here show that this diversity of decision systems corresponds to a single rule of decision-making in collectives. We first obtained a decision rule based on Bayesian estimation that uses the information provided by the behaviors of the other individuals to improve the estimation of the structure of the world. We then tested this rule in decision experiments using zebrafish (Danio rerio), and in existing rich datasets of argentine ants (Linepithema humile) and sticklebacks (Gasterosteus aculeatus), showing that a unified model across species can quantitatively explain the diversity of decision systems. Further, these results show that the different counting systems used by animals, including humans, can emerge from the common principle of using social information to make good decisions.
Jupiter models with improved ab initio hydrogen EOS (H-REOS.2)
Creators: name: Nettelmann, Nadine
name: Becker, Andreas
name: Holst, Bastian
name: Redmer, Ronald
Publisher: name: arXiv
Year: 2011
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: The amount and distribution of heavy elements in Jupiter gives indications on the process of its formation and evolution. Core mass and metallicity predictions however depend on the equations of state used, and on model assumptions. We present an improved ab initio hydrogen equation of state, H-REOS.2 and compute the internal structure and thermal evolution of Jupiter within the standard three-layer approach. The advance over our previous Jupiter models with H-REOS.1 by Nettelmann et al.(2008) is that the new models are also consistent with the observed 2 or more times solar heavy element abundances in Jupiter's atmosphere. Such models have a rock core mass Mcore=0-8 ME, total mass of heavy elements MZ=28-32 ME, a deep internal layer boundary at 4 or more Mbar, and a cooling time of 4.4-5.0 Gyrs when assuming homogeneous evolution. We also calculate two-layer models in the manner of Militzer et al.(2008) and find a comparable large core of 16-21 ME, out of which ~11 ME is helium, but a significantly higher envelope metallicity of 4.5 times solar. According to our preferred three-layer models, neither the characteristic frequency (nu0 ~156 microHz) nor the normalized moment of inertia (~0.276) are sensitive to the core mass but accurate measurements could well help to rule out some classes of models.
description: 7 figures, 1 table, accepted to ApJ
Front matter for: Papers in New Guinea Linguistics No. 24
Creators: name: Laycock, D. (Ed.)
name: Seiler, W. (Ed.)
name: Bruce, L. (Ed.)
name: Chlenov, M. (Ed.)
name: Shaw, R. (Ed.)
name: Holzknecht, S. (Ed.)
name: Scott, G. (Ed.)
name: Nekitel, O. (Ed.)
name: Wurm, S.A. (Ed.)
name: Goldman, L. (Ed.)
name: Fingleton, J. (Ed.)
Publisher: name: Pacific Linguistics
Year: 1986

description: Contents iiiINTRODUCTORY NOTE iv
Entropy Bound with Generalized Uncertainty Principle in General Dimensions
Creators: name: Wang, Weijian
name: Huang, Da
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: In this letter, the entropy bound for local quantum field theories (LQFT) is studies in a class of models of the generalized uncertainty principle(GUP) which predicts a minimal length as a reflection of the quantum gravity effects. Both bosonic and fermionic fields confined in arbitrary spatial dimension $d\geq4$ ball ${\cal B}^{d}$ are investigated. It is found that the GUP leads to the same scaling $A_{d-2}^{(d-3)/(d-2)}$ correction to the entropy bound for bosons and fermions, although the coefficients of this correction are different for each case. Based on our calculation, we conclude that the GUP effects can become manifest at the short distance scale. Some further implications and speculations of our results are also discussed.
description: 8 pages, topos corrected and references added
title: Strongly Linearizable LL/SC from CAS
Creators: name: Naderi Semiromi, Fatemeh
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: shared memory
subject: strong linearizability
subject: LL/SC
subject: ABA
subject: wait-freedom
subject: Computer Science

description: Linearizability is the standard correctness condition for shared memory algorithms and is generally considered to be the practical equivalent of atomicity for deterministic algorithms. However, Golab, Higham, and Woelfel [16] showed that if we replace atomic objects used in a randomized algorithm with their linearizable implementations, then some of the properties of the algorithm may be lost. They introduced a stronger correctness condition, called strong linearizability, and proved that strongly linearizable objects can be used in both deterministic and randomizes algorithms as if they were atomic. In this thesis, we present an efficient strongly linearizable implementation of the load-linked/ store-conditional (LL/SC) primitive from compare-and-swap (CAS) objects. Our algorithm has constant step complexity, and uses a bounded number of CAS objects and registers that can each store O(log n) bits, where n is the number of processes. To the best of our knowledge, we are the first ones introducing a constant-time strongly linearizable LL/SC implementation, which uses bounded memory and bounded word-size.
A Low-Dose CT-Based Radiomic Model to Improve Characterization and Screening Recall Intervals of Indeterminate Prevalent Pulmonary Nodules
Creators: name: Rundo, Leonardo
name: Ledda, Roberta Eufrasia
name: Di Noia, Christian
name: Sala, Evis
name: Mauri, Giancarlo
name: Milanese, Gianluca
name: Sverzellati, Nicola
name: Apolone, Giovanni
name: Gilardi, Maria Carla
name: Messa, Maria Cristina
name: Castiglioni, Isabella
name: Pastorino, Ugo
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: pulmonary nodules
lung cancer screening
low-dose computed tomography
lung cancer risk stratification
radiomics
machine learning

description: Lung cancer (LC) is currently one of the main causes of cancer-related deaths worldwide. Low-dose computed tomography (LDCT) of the chest has been proven effective in secondary prevention (i.e., early detection) of LC by several trials. In this work, we investigated the potential impact of radiomics on indeterminate prevalent pulmonary nodule (PN) characterization and risk stratification in subjects undergoing LDCT-based LC screening. As a proof-of-concept for radiomic analyses, the first aim of our study was to assess whether indeterminate PNs could be automatically classified by an LDCT radiomic classifier as solid or sub-solid (first-level classification), and in particular for sub-solid lesions, as non-solid versus part-solid (second-level classification). The second aim of the study was to assess whether an LCDT radiomic classifier could automatically predict PN risk of malignancy, and thus optimize LDCT recall timing in screening programs. Model performance was evaluated using the area under the receiver operating characteristic curve (AUC), accuracy, positive predictive value, negative predictive value, sensitivity, and specificity. The experimental results showed that an LDCT radiomic machine learning classifier can achieve excellent performance for characterization of screen-detected PNs (mean AUC of 0.89 ± 0.02 and 0.80 ± 0.18 on the blinded test dataset for the first-level and second-level classifiers, respectively), providing quantitative information to support clinical management. Our study showed that a radiomic classifier could be used to optimize LDCT recall for indeterminate PNs. According to the performance of such a classifier on the blinded test dataset, within the first 6 months, 46% of the malignant PNs and 38% of the benign ones were identified, improving early detection of LC by doubling the current detection rate of malignant nodules from 23% to 46% at a low cost of false positives. In conclusion, we showed the high potential of LDCT-based radiomics for improving the characterization and optimizing screening recall intervals of indeterminate PNs.
Detectability of cold streams into high-redshift galaxies by absorption lines
Creators: name: Goerdt, Tobias
name: Dekel, Avishai
name: Sternberg, Amiel
name: Gnat, Orly
name: Ceverino, Daniel
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Cold gas streaming along the dark-matter filaments of the cosmic web is predicted to be the major provider of resources for disc buildup, violent disk instability and star formation in massive galaxies in the early universe. We study to what extent these cold streams are traceable in the extended circum-galactic environment of galaxies via Ly alpha absorption and selected low ionisation metal absorption lines. We model the expected absorption signatures using high resolution zoom-in AMR cosmological simulations. In the postprocessing, we distinguish between self-shielded gas and unshielded gas. In the self-shielded gas, which is optically thick to Lyman continuum radiation, we assume pure collisional ionisation for species with an ionisation potential greater than 13.6 eV. In the optically thin, unshielded gas these species are also photoionised by the meta-galactic radiation. In addition to absorption of radiation from background quasars, we compute the absorption line profiles of radiation emitted by the galaxy at the centre of the same halo. We predict the strength of the absorption signal for individual galaxies without stacking. We find that the Ly alpha absorption profiles produced by the streams are consistent with observations of absorption and emission Ly alpha profiles in high redshift galaxies. Due to the low metallicities in the streams, and their low covering factors, the metal absorption features are weak and difficult to detect.
description: 26 pages, 25 figures, 3 tables, final version accepted for publication in MNRAS