cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Analysis of a Vertical-Axis Tidal Turbine Using the Variational Multiscale Formulation
Creators: name: Dhalwala, Musaddik
Publisher: name: Schulich School of Engineering
Year: 2022
Subjects: subject: Engineering--Marine and Ocean
subject: Engineering--Mechanical

description: This thesis first investigates the performance and near-wake characteristics of a full-scale vertical-axis tidal turbine under a uniform inflow and turbulent inflow with a 5% and 10% turbulence intensity. The governing equations of the flow field are the incompressible Navier-Stokes equations. As the turbine rotates throughout the simulation, these equations are expressed in a slightly different form referred to as the arbitrary Lagrangian-Eulerian (ALE) framework. The purpose of the ALE framework is to allow the mesh to move arbitrarily while the fluid moves independently of the mesh motion. From the available large eddy simulation (LES) formulations in the literature, the variational multiscale (VMS) formulation is used to discretize the system of equations. Unlike classical LES, the VMS formulation does not have any problems with specifying an appropriate filter for different flows. To study the effect of a turbulent inflow, a turbulence generation method referred to as Smirnov's random flow generation (RFG) is used. From the numerous turbulence generation methods available, Smirnov’s RFG was chosen as it can generate a turbulent velocity field that is divergence-free. A divergence-free velocity field ensures compatibility with the incompressible Navier-Stokes equations that govern the flow field and results in good numerical stability. While the performance of the turbine slightly reduced under a turbulent inflow compared to a uniform inflow, there was a negligible difference in its performance between the two turbulent inflow conditions. A turbulent inflow also resulted in large fluctuations of the instantaneous power coefficient. Lastly, the wake recovery was notably improved under a turbulent inflow. Next, the effect of a free surface on the performance and flow field of the turbine with different blade-strut configurations is studied. There was a negligible effect of the free surface on turbine performance and the flow field during deep immersion. Moreover, the tip-struts configuration was 15% more efficient than the quarter-struts configuration under deep immersion. Under shallow immersion, the performance of both blade-strut configurations reduced.
Trained innate immunity, epigenetics, and food allergy
Creators: name: Arzola-Martínez, L
name: Ptaschinski, C
name: Lukacs, NW
Publisher: name: Frontiers
Year: 2023
Subjects: epigenetic
food allergy
metabolic reprogramming
microbiota
trained immunity

description: In recent years the increased incidence of food allergy in Western culture has been associated with environmental factors and an inappropriate immune phenotype. While the adaptive immune changes in food allergy development and progression have been well-characterized, an increase in innate cell frequency and activation status has also recently received greater attention. Early in prenatal and neonatal development of human immunity there is a reliance on epigenetic and metabolic changes that stem from environmental factors, which are critical in training the immune outcomes. In the present review, we discuss how trained immunity is regulated by epigenetic, microbial and metabolic factors, and how these factors and their impact on innate immunity have been linked to the development of food allergy. We further summarize current efforts to use probiotics as a potential therapeutic approach to reverse the epigenetic and metabolic signatures and prevent the development of severe anaphylactic food allergy, as well as the potential use of trained immunity as a diagnostic and management strategy. Finally, trained immunity is presented as one of the mechanisms of action of allergen-specific immunotherapy to promote tolerogenic responses in allergic individuals.
The development of novel cytochrome P450 2J2 (CYP2J2) inhibitor and the underlying interaction between inhibitor and CYP2J2
Creators: name: Tian, Xiangge
name: Zhou, Meirong
name: Ning, Jing
name: Deng, Xiaopeng
name: Feng, Lei
name: Huang, Huilian
name: Yao, Dahong
name: Ma, Xiaochi
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
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: Hematology
subject: Virology

description: Human Cytochrome P450 2J2 (CYP2J2) as an important metabolic enzyme, plays a crucial role in metabolism of polyunsaturated fatty acids (PUFAs). Elevated levels of CYP2J2 have been associated with various types of cancer, and therefore it serves as a potential drug target. Herein, using a high-throughput screening approach based on enzymic activity of CYP2J2, we rapidly and effectively identified a novel natural inhibitor (Piperine, 9a) with IC50 value of 0.44 μM from 108 common herbal medicines. Next, a series of its derivatives were designed and synthesised based on the underlying interactions of Piperine with CYP2J2. As expected, the much stronger inhibitors 9k and 9l were developed and their inhibition activities increased about 10 folds than Piperine with the IC50 values of 40 and 50 nM, respectively. Additionally, the inhibition kinetics illustrated the competitive inhibition types of 9k and 9l towards CYP2J2, and Ki were calculated to be 0.11 and 0.074 μM, respectively. Furthermore, the detailed interaction mechanism towards CYP2J2 was explicated by docking and molecular dynamics, and our results revealed the residue Thr114 and Thr 315 of CYP2J2 were the critical sites of action, moreover the spatial distance between the carbon atom of ligand methylene and Fe atom of iron porphyrin coenzyme was the vital interaction factor towards human CYP2J2.
Phase separation and interface structure in two dimensions from field theory
Creators: name: Delfino, Gesualdo
name: Viti, Jacopo
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We study phase separation in two dimensions in the scaling limit below criticality. The general form of the magnetization profile as the volume goes to infinity is determined exactly within the field theoretical framework which explicitly takes into account the topological nature of the elementary excitations. The result known for the Ising model from its lattice solution is recovered as a particular case. In the asymptotic infrared limit the interface behaves as a simple curve characterized by a gaussian passage probability density. The leading deviation, due to branching, from this behavior is also derived and its coefficient is determined for the Potts model. As a byproduct, for random percolation we obtain the asymptotic density profile of a spanning cluster conditioned to touch only the left half of the boundary.
description: 12 pages, 3 figures; published version, references added
Semiclassical roots of universality in many-body quantum chaos
Creators: name: Richter, Klaus
name: Urbina, Juan Diego
name: Tomsovic, Steven
Publisher: name: Universität Regensburg
Year: 2022
Subjects: subject: quantum chaos, semiclassical methods, trace formulas, random matrix theory, out-of-time-order correlators
subject: 530 Physik

description: Quantum chaos of many-body (MB) systems has been swiftly developing into a vibrant research area at the interface between various disciplines, ranging from statistical physics to condensed matter to quantum information and to cosmology. In quantum systems with a classical limit, advanced semiclassical methods provide the crucial link between classically chaotic dynamics and corresponding universal features at the quantum level. Recently, single-particle (SP) techniques dealing with ergodic wave interference in the usual semiclassical limit have begun to be transformed into the field theoretical domain of N-particle systems in the analogous semiclassical limit , thereby accounting for genuine MB quantum interference. This semiclassical MB theory provides a unified framework for understanding random-matrix correlations of both SP and MB quantum chaotic systems. Certain braided bundles of classical orbits, and of mean field modes, govern interference, respectively, and provide the key to the foundation of universality. Case studies presented include an MB version of Gutzwiller’s trace formula for the spectral density and out-of-time-order correlators along with brief remarks on where further progress may be forthcoming.
The Role of Orexin in Non-Photic Phase Shifting
Creators: name: Horsley, Katelyn
Publisher: name: Arts
Year: 2022
Subjects: subject: Circadian Rhythms
subject: Non-Photic
subject: Orexin
subject: Sleep Deprivation
subject: Lateral Hypothalamus
subject: Intergeniculate Leaflet
subject: Neuropeptide-Y
subject: Neuroscience
subject: Psychology--Behavioral

description: The intergeniculate leaflet (IGL), a primarily visual structure, and its principal neuropeptide, neuropeptide Y (NPY), are essential for non-photic phase shifting. This creates a paradox: why is an inherently visual structure necessary for a non-visual process? Converging evidence suggests that the lateral hypothalamus and its orexin (OX) cells communicate and electrically activate IGL cells in vitro during non-photic manipulations. The most compelling evidence, however, comes from studying the diurnal grass rat – an animal model that has not been characterized in terms of basic non-photic behaviour and anatomy. Within the diurnal grass rat, active NPY cells have close appositions with OX fibers during sleep deprivation. Taken together, this thesis hypothesized that OX is one of the arousal signals that can activate the IGL and its NPYergic cells during non-photic phase shifting. To test this hypothesis, 2 experiments were conducted on male and female animals. Firstly, we tested whether an in vivo infusion of OX into the IGL activated a significant number of cells in Syrian hamsters. Our results indicate that OX activates a significant number of IGL cells. Experiment 2 evaluated whether c-Fos expression was induced in a significant number of IGL NPY-IR cells and if a significant proportion of active NPY cells have appositions with OX fibers in response to sleep deprivation in NPY-GFP mice. Our findings not only establish mice as a model organism in studying the effects of sleep deprivation, but we further corroborated the findings within the grass rat. Additional studies are needed to establish a cause-effect relationship between OX fibers and NPY cells during non-photic phase shifting.
Ethnicity and hematopoietic stem cell transplantation outcomes in British Columbia, Canada
Creators: name: Noparast, Maryam
Publisher: name: University of British Columbia
Year: 2012

description: Background: There are documented ethnic disparities in cancer care access, use and clinical outcomes in North America. Hematopoietic stem cell transplantation (HSCT) is an established treatment for many hematological and non-hematological malignancies. The effect of ethnicity on unrelated-donor HSCT outcomes has not been studied in Canadian patients. Objective: To determine whether ethnicity is associated with unrelated donor HSCT outcomes in patients with hematologic malignancies in British Columbia, Canada. Design: Retrospective medical chart review Materials and Methods We reviewed the registry data of 395 patients receiving first time unrelated donor HSCT for hematological malignancies at the leukemia/BMT center of British Columbia (BC) between 1988 and 2008. A patient’s ethnicity was reported to be white (N=340), Asian (N=32), native (N=8), Hispanic (N=3), black (N=2), mixed (N=9) or other- not specified (N=1). For my analysis, ethnicity was further categorized as white (N=340) and non-white (N=55). HSCT outcomes were compared using log-rank test and Cox proportional hazard regression analysis adjusting for statistically-significant patient, disease and transplant-related factors. Results: No statistically significant difference for overall survival, non-relapse survival, grade II-IV acute graft versus host disease (aGVHD) and chronic graft versus host disease (cGVHD) rates were found between whites and non-whites. Analyzing a subset of 115 cases (88 whites and 27 non-whites) who received their transplant after June 2001 (the start of high resolution DNA-based human leukocyte antigen (HLA) matching in the study center) and had an underlying diagnosis of acute myeloid leukemia, acute lymphoid leukemia, chronic myeloid leukemia or myelodysplastic syndrome didn’t show any statistically significant difference for HSCT outcomes between whites and nonwhites either. Conclusion: According to our data, unrelated-donor HSCT clinical outcomes are comparable between patients having white and non-white ethnicity in BC. This finding contrasts with those of US studies. This might be due to: 1) different ethnic compositions of the BC and US populations 2) different access to health care for ethnic minorities in the BC and US populations 3) my analysis using a heterogeneous non-white ethnic group, and thereby potentially masking ethnic differences.
3DEX: a code for fast spherical Fourier-Bessel decomposition of 3D surveys
Creators: name: Leistedt, B.
name: Rassat, A.
name: Refregier, A.
name: Starck, J. -L.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: High-precision cosmology requires the analysis of large-scale surveys in 3D spherical coordinates, i.e. spherical Fourier-Bessel decomposition. Current methods are insufficient for future data-sets from wide-field cosmology surveys. The aim of this paper is to present a public code for fast spherical Fourier-Bessel decomposition that can be applied to cosmological data or 3D data in spherical coordinates in other scientific fields. We present an equivalent formulation of the spherical Fourier-Bessel decomposition that separates radial and tangential calculations. We propose the use of the existing pixelisation scheme HEALPix for a rapid calculation of the tangential modes. 3DEX (3D EXpansions) is a public code for fast spherical Fourier-Bessel decomposition of 3D all-sky surveys that takes advantage of HEALPix for the calculation of tangential modes. We perform tests on very large simulations and we compare the precision and computation time of our method with an optimised implementation of the spherical Fourier-Bessel original formulation. For surveys with millions of galaxies, computation time is reduced by a factor 4-12 depending on the desired scales and accuracy. The formulation is also suitable for pre-calculations and external storage of the spherical harmonics, which allows for additional speed improvements. The 3DEX code can accommodate data with masked regions of missing data. 3DEX can also be used in other disciplines, where 3D data are to be analysed in spherical coordinates. The code and documentation can be downloaded at http://ixkael.com/blog/3dex.
description: 6 pages plus appendices. Revised version accepted by A&A. The code and documentation can be downloaded at http://ixkael.com/blog/3dex
Metacognition, self-regulation, oracy: A mixed methods case study of a complex, whole-school Learning to Learn intervention
Creators: name: Mannion, James
Publisher: name: Apollo - University of Cambridge Repository
Year: 2018
Subjects: Metacognition
self-regulation
oracy
learning to learn
complex intervention

description: This doctoral thesis presents the findings of a mixed methods case study of Learning Skills, a new approach to Learning to Learn that was developed and implemented at a secondary school in the south of England between 2010 and 2014, and evaluated using data collected between 2009 and 2017. Learning to Learn is a field of educational theory and practice that aims to help young people get better at learning by focusing on the processes of learning (the how as well as the what), and by enabling them to take ownership over aspects of their own learning through activities such as goal setting, self-monitoring and structured reflection. The field has developed significantly throughout the last 40 years, with a number of approaches having been implemented on a large scale in the UK. Research into metacognition and self-regulation suggests that Learning to Learn programmes should help boost academic attainment. To date however, large-scale evaluations have found mixed results, with no clear impact on academic attainment. Using an intervention design used widely in medicine and other fields, Learning Skills reconceptualises Learning to Learn as a ‘complex intervention’ comprised of multiple areas of evidence-informed practice. The rationale for complex interventions is that the marginal gains emerging from any individual avenue of practice stack up and interact to yield a larger effect size overall. The Learning Skills programme, which started as a year seven taught course and developed into a whole-school approach to teaching and learning, focuses centrally on three key concepts: metacognition, self-regulation and oracy. This evaluation of Learning Skills incorporates eight strands of data collection and analysis over an eight-year period, using the previous year group at the same school as a control group. These include baseline measures; attitude to learning scores; psychometric questionnaires; a language of learning evaluation; reflective learning journals; student interviews; teacher interviews; and student attainment across all subjects in years nine and 11. The primary outcome analysis – student attainment across all subject areas at three and five years – found that Learning Skills cohort one achieved significantly higher grades than the control cohort, with accelerated gains among young people from economically disadvantaged backgrounds. Secondary data analysis incorporating a range of qualitative and quantitative methods indicates a causal relationship between Learning Skills and academic attainment. As well as evaluating the impact of a new and promising approach to Learning to Learn, this study generates new knowledge about the implementation and evaluation of complex interventions in education.
Spatial relationships and occurrence patterns within a community of lemurs in a fragmented landscape
Creators: name: Jacobson, Zachary
Publisher: name: Arts
Year: 2022
Subjects: subject: Anthropology--Physical
subject: Forestry and Wildlife
subject: Ecology
subject: FOS: Biological sciences
subject: Remote Sensing

description: Identifying the factors influencing species occurrence and co-occurrence are essential for understanding primate distributions and community assembly processes. Lemurs, a group of highly threatened primates, are at risk of extinction due to human-induced land use changes, forest loss, and fragmentation. Lemurs play critical roles in Madagascar’s depauperate frugivore communities. In this thesis, I use a multi-scale approach to investigate whether landscape structure and habitat characteristics influence individual and two-species occurrence of lemurs living in the fragmented Kianjavato landscape in southeastern Madagascar. I explore my research questions by integrating occurrence data derived from camera traps with predictors obtained from remotely sensed satellite imagery. I find that lemurs in a fragmentated landscape are disparately affected by landscape structure, and some of Kianjavato’s species exhibit a positive association between occurrence and fragmentation metrics. Furthermore, lemur species with large home ranges respond to landscape structure at larger spatial extents, indicating it is essential to consider spatial scale when investigating species responses to environmental factors. Additionally, I find high spatial overlap between ecologically similar species, with fragmentation increasing spatial aggregation among species that share functional traits. These results suggest fragmented forests constrain lemur habitat use and limit spatial partitioning between ecological competitors. Ongoing restoration efforts in Kianjavato should focus on increasing forest connectivity to alleviate unsustainable competition among the resident lemur community. I conclude that landscape structure is an important determinant of both occurrence and co-occurrence in Kianjavato’s lemur community. My results provide preliminary evidence for how landscape structure shapes spatial dynamics within lemur communities in a fragmented landscape. Further, they highlight the importance of spatial scale when considering species-environment relationships.
Ionized nitrogen at high redshift
Creators: name: Decarli, R.
name: Walter, F.
name: Neri, R.
name: Bertoldi, F.
name: Carilli, C.
name: Cox, P.
name: Kneib, J. P.
name: Lestrade, J. F.
name: Maiolino, R.
name: Omont, A.
name: Richard, J.
name: Riechers, D.
name: Thanjavur, K.
name: Weiss, A.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We present secure [NII[ detections in two mm-bright, strongly lensed objects at high redshift, APM08279+5255 (z=3.911) and MM18423+5938 (z=3.930), using the IRAM Plateau de Bure Interferometer. Due to its ionization energy [NII] is a good tracer of the ionized gas phase in the interstellar medium. The measured fluxes are S([NII])=(4.8+/-0.8) Jy km/s and (7.4+/-0.5) Jy km/s respectively, yielding line luminosities of L([NII]) =(1.8+/-0.3) x 10^9 μ^{-1} Lsun for APM08279+5255 and L([NII]) =(2.8+/-0.2) x 10^9 μ^{-1} Lsun for MM18423+5938. Our high-resolution map of the [NII] and 1 mm continuum emission in MM18423+5938 clearly resolves an Einstein ring in this source, and reveals a velocity gradient in the dynamics of the ionized gas. A comparison of these maps with high-resolution EVLA CO observations enables us to perform the first spatially-resolved study of the dust continuum-to-molecular gas surface brightness (Sigma_{FIR} Sigma_{CO}^N, which can be interpreted as the star formation law) in a high-redshift object. We find a steep relation (N=1.4+/-0.2), consistent with a starbursting environment. We measure a [NII]/FIR luminosity ratio in APM0828+5255 and MM18423+5938 of 9.0 x 10^{-6} and 5.8 x 10^{-6}, respectively. This is in agreement with the decrease of the [NII]/FIR ratio at high FIR luminosities observed in local galaxies.
description: 5 Figures, 1 Table. Accepted for publication in ApJ
Markov dynamics as a zooming lens for multiscale community detection: non clique-like communities and the field-of-view limit
Creators: name: Schaub, Michael T.
name: Delvenne, Jean-Charles
name: Yaliraki, Sophia N.
name: Barahona, Mauricio
Publisher: name: arXiv
Year: 2011
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Social and Information Networks (cs.SI)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: In recent years, there has been a surge of interest in community detection algorithms for complex networks. A variety of computational heuristics, some with a long history, have been proposed for the identification of communities or, alternatively, of good graph partitions. In most cases, the algorithms maximize a particular objective function, thereby finding the `right' split into communities. Although a thorough comparison of algorithms is still lacking, there has been an effort to design benchmarks, i.e., random graph models with known community structure against which algorithms can be evaluated. However, popular community detection methods and benchmarks normally assume an implicit notion of community based on clique-like subgraphs, a form of community structure that is not always characteristic of real networks. Specifically, networks that emerge from geometric constraints can have natural non clique-like substructures with large effective diameters, which can be interpreted as long-range communities. In this work, we show that long-range communities escape detection by popular methods, which are blinded by a restricted `field-of-view' limit, an intrinsic upper scale on the communities they can detect. The field-of-view limit means that long-range communities tend to be overpartitioned. We show how by adopting a dynamical perspective towards community detection (Delvenne et al. (2010) PNAS:107: 12755-12760; Lambiotte et al. (2008) arXiv:0812.1770), in which the evolution of a Markov process on the graph is used as a zooming lens over the structure of the network at all scales, one can detect both clique- or non clique-like communities without imposing an upper scale to the detection. Consequently, the performance of algorithms on inherently low-diameter, clique-like benchmarks may not always be indicative of equally good results in real networks with local, sparser connectivity.
description: 20 pages, 6 figures
Host genetic and rumen microbial determinants of nitrogen (N) utilisation and N excretion in lactating Holsteins
Creators: name: Honerlagen, Hanne
Publisher: name: Universität Rostock
Year: 2022
Subjects: subject: 500 Natural sciences
subject: 630 Agriculture

description: Enhancing the nitrogen (N) utilisation efficiency (NUE) of dairy cows by breeding selection was considered relevant for environmental footprints, feeding costs and animal health. It was hypothesised that cow-individual NUE is determined by the entire “holobiont”, thus by the host genome and the rumen microbiome. In this context four study approaches were conducted, which focused on the host genome-trait, the host genome-rumen microbiota and the entire host genome-rumen microbiota-trait axis, aiming for a holistic exploration of cow-individual NUE as a pre-step for future breeding strategies.
Randomisierte, monozentrische, placebo-kontrollierte Studie zur Wundheilung nach wirbelsäulenchirurgischen Eingriffen
Creators: name: Schöler, Juliane
Publisher: name: Universität Rostock
Year: 2021
Subjects: subject: 610 Medical sciences Medicine

description: In der vorliegenden Arbeit wurde Propolis erstmals sowohl in-vitro (Teil 1) als auch in-vivo (Teil 2) auf seine Wirksamkeit auf die Fibroblastenproliferation, Wundheilung und die klinischen Ergebnisse der Narbenbildung, nach wirbelsäulenchirurgischen Eingriffen mit Wundverschluss durch Naht, prospektiv randomisiert untersucht. Ziel der Studie ist es zu untersuchen, ob propolishaltige Wundauflagen die Wundheilung und Narbenbildung nach wirbelsäulenchirurgischen Eingriffen verbessern können.
Quantum Criticality in a Bosonic Josephson Junction
Creators: name: Buonsante, P.
name: Burioni, R.
name: Vescovi, E.
name: Vezzani, A.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: In this paper we consider a bosonic Josephson junction described by a two-mode Bose-Hubbard model, and we thoroughly analyze a quantum phase transition occurring in the system in the limit of infinite bosonic population. We discuss the relation between this quantum phase transition and the dynamical bifurcation occurring in the spectrum of the Discrete Self Trapping equations describing the system at the semiclassical level. In particular, we identify five regimes depending on the strength of the effective interaction among bosons, and study the finite-size effects arising from the finiteness of the bosonic population. We devote a special attention to the critical regime which reduces to the dynamical bifurcation point in the thermodynamic limit of infinite bosonic population. Specifically, we highlight an anomalous scaling in the population imbalance between the two wells of the trapping potential, as well as in two quantities borrowed from Quantum Information Theory, i.e. the entropy of entanglement and the ground-state fidelity. Our analysis is not limited to the zero temperature case, but considers thermal effects as well.
description: 13 pages, 10 figures
Additional file 2: of N6-methyldeoxyadenosine directs nucleosome positioning in Tetrahymena DNA
Creators: name: Luo, Guan-Zheng
name: Hao, Ziyang
name: Luo, Liangzhi
name: Shen, Mingren
name: Sparvoli, Daniela
name: Zheng, Yuqing
name: Zhang, Zijie
name: Weng, Xiaocheng
name: Chen, Kai
name: Cui, Qiang
name: Turkewitz, Aaron
name: He, Chuan
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Plant Biology

description: Table S1. Genomic loci for individual 6mA testing. Table S2. Sequences of primers used for tamt-1 KO experiment. (DOC 47 kb)
A Study of Military Change: The Transformation of Army Special Forces and Naval Special Warfare in the Vietnam War
Creators: name: Cooper-Takada, Patrick
Publisher: name: Arts
Year: 2022
Subjects: subject: special forces
subject: special operations forces
subject: military change
subject: military innovation
subject: military adaptation
subject: military learning processes
subject: Navy SEALs
subject: Green Beret
subject: US special forces
subject: Vietnam War
subject: Education--Social Sciences
subject: Economics--History
subject: Military Studies
subject: Political Science
subject: FOS: Political science
subject: Political Science--International Law and Relations
subject: Sociology--Theory and Methods

description: This work serves to investigate the nature of the changes experienced by the Army Special Forces (Green Berets) and Naval Special Warfare (NSW; Underwater Demolition Teams, and Sea, Air, Land [SEAL] Teams) during the Vietnam War, using contemporary military change literature to evaluate the processes and results. In conducting the research, this thesis used a combination of primary and secondary sources for a qualitative analysis of military change. The result of this investigation was two clear examples of military innovation that resulted from different processes in environments that were vastly different in terms of leadership conditions and mission requirements. Naval Special Warfare experienced innovation through the inception of the SEAL Teams, which gave them increased capabilities not seen before by a permanent Navy Special Operations Force unit. This revolutionary innovation was not directly impeded by Navy bureaucracy due to intervention by the Kennedy Administration on behalf of NSW. The Army Special Forces underwent a different kind of innovation; because of their open mindset, high level of training, and misappropriation by Army leadership, the Green Berets adapted to multiple new roles in the Vietnam War. As a result of these multiple smaller changes, the entirety of their existence was altered and they became a force transformed over 14 years of sustained adaptation, rather than the rapid changes experienced by Naval Special Warfare. These lessons of these two case studies are significant as they demonstrate different learning processes in similar combat environments as a result of variables in leadership, demands, experience, unit culture, skills, and relationships with external agencies.
Leadership Practices for Rapidly Implementing Educational Change Initiatives: An Exploration of the Implementation of the Neurosequential Model in Education
Creators: name: Perrault, Eric
Publisher: name: Werklund School of Education
Year: 2022
Subjects: subject: Leadership
subject: Rapid organizational change
subject: Change agents
subject: Neurosequential Model in Education
subject: Mixed methods research
subject: Education--Administration

description: The purpose of this study was to identify the leadership practices and change processes that educational change leaders employ to rapidly bring change into practice. In this study of change leaders, a single innovation the Neurosequential Model in Education (NME) was the change being implemented in a rapid time frame. NME is an innovative, developmentally based approach that K-12 schools around the world are adopting to help solve the ‘wicked problem’ of addressing the academic and wellbeing needs of students who have experienced trauma and adversity. The demands of complex and changing student populations require leaders and change agents who can innovate and change practice in three years or less rather than the five years accepted as conventional change timeframes. This explanatory sequential study focuses on the perspectives of change leaders through a mixed methods design using questionnaires and interviews to gather the strategies and beliefs of leaders who efficiently brought the NME into practice. The participants were 35 educational professionals representing multiple roles and administrative levels who had completed training in NME. At the time of the study, NME was being used in eight countries and the participants represented five of these countries: Australia, Canada, the United States of America, Scotland, and South Africa. Using an explanatory sequential study design, the first phase was quantitative using a questionnaire and the second phase was qualitative using an interview. The first phase had 35 participants responding to the survey. The sample for the second phase was derived from volunteers from the survey in the first phase, with 15 participants participating in semi-structured interviews. A balanced analysis was conducted with the quantitative and qualitative approaches given approximately equal weight. The leaders in the study were able to efficiently bring the NME into practice by combining change and leadership practices with neuroscience principles. This creative merging by the change leaders gave rise to an emergent framework for conceptualizing and implementing planned change in a rapid time frame. A framework merging NME principle with change process and leadership practices is suggested for others seeking to rapidly implement change in schools.
Constraints on the second order transport coefficients of an uncharged fluid
Creators: name: Bhattacharyya, Sayantani
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this note we have tried to determine how the existence of a local entropy current with non-negative divergence constrains the second order transport coefficients of an uncharged fluid, following the procedure described in \cite{Romatschke:2009kr}. Just on symmetry ground the stress tensor of an uncharged fluid can have 15 transport coefficients at second order in derivative expansion. The condition of entropy-increase gives five relations among these 15 coefficients. So finally the relativistic stress tensor of an uncharged fluid can have 10 independent transport coefficients at second order.
description: 43 pages
Models of the Contribution of Blazars to the Anisotropy of the Extragalactic Diffuse Gamma-ray Background
Creators: name: Harding, J. Patrick
name: Abazajian, Kevork N.
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We study the relation between the measured anisotropies in the extragalactic diffuse gamma-ray background (DGRB) and the DGRB spectral intensity, and their potential origin from the unresolved blazar population. Using a physical-evolution model for blazars with a luminosity dependent evolution (LDDE) and an observationally-determined luminosity-dependent blazar spectral energy distribution (SED), we find that blazars can account for the observed anisotropy of the DGRB consistent with their observed source-count distribution, but are in turn constrained in contributing significantly to the observed DGRB intensity. For the best-fit LDDE model accounting for the DGRB anisotropy and source-count distribution, blazars only contribute 5.7^{+2.1}_{-1.0}% (68% CL) of the DGRB intensity above 1 GeV. Requiring a higher fraction of the DGRB intensity contribution by blazars overproduces the DGRB anisotropy, and therefore blazars in the LDDE+SED-sequence model cannot simultaneously account for the DGRB intensity as well as anisotropy. We discuss the limitations of LDDE models. However, these models do not require the many unjustified and observationally-inconsistent simplifying assumptions---including a single power law for all blazar spectra and a simple broken power-law model for their source-count distribution---that are present in much previous work.
description: 17 pages, 5 figures; v2: updated KS-test comparison with the blazar redshift distribution and flux index distribution; removal of gamma1 < 0 parameter space, with small shift in best fit parameters; added references and discussion; matches published version in JCAP
Microbiome-Mediated Disruption of Mucin Glycosylation and Mechanisms of Protease Activated Receptor-Dependent Modulation of Mucin Gene Expression During Giardia spp. Infection
Creators: name: Fekete, Elena
Publisher: name: Science
Year: 2022
Subjects: subject: Giardia
subject: Mucus
subject: Glycosylation
subject: Muc2
subject: Glycan
subject: Protease
subject: PAR2
subject: Microbiome
subject: Goblet Cell
subject: Biology--Cell
subject: Microbiology
subject: FOS: Biological sciences
subject: Parasitology
subject: Pathology

description: Disruption of the intestinal mucus gel barrier has a significant impact on intestinal health and homeostasis. Mucus barrier alterations have been associated with dysbiosis, increased intestinal permeability, and increased susceptibility to intestinal infection. Giardia duodenalis is a leading cause of diarrheal disease in humans and has been linked to development of post-infectious functional gastrointestinal disorders. Giardia infection is associated with intestinal barrier dysfunction and altered composition and function of the commensal microbiome, both of which are predicted to contribute to acute and chronic disease manifestations. This study reveals new mechanisms by which Giardia and its secreted cysteine proteases can modulate goblet cell activity and the properties of the intestinal mucus barrier. Alterations to the glycosylation of intestinal mucins and the expression of mucin and mucin-associated glycosyltransferase genes were found to be time-dependent, appearing as early as day 2 post-infection, and persisting in mice that had cleared the infection. Alterations to glycan abundance and glycosyltransferase gene expression were observed not only in the small intestine, at the site of parasite colonization, but also in the distal colon, where no trophozoites are present. Many of these alterations were microbiome-dependent and were recapitulated in mice transplanted with small intestinal bacteria collected from Giardia infected mice. Alterations were also similar between the mouse-specific isolate Giardia muris, and the zoonotic isolate Giardia duodenalis GS/M. In human cell cultures, alterations to mucin gene expression were found to be dependent both on Giardia cysteine protease activity and on protease-activated receptor-2 signaling. Isolate-dependent effects on mucin gene expression correlated both with cysteine protease activity levels and with the cleavage of PAR2. MUC2 mucin gene upregulation was dependent on intracellular calcium mobilization and on activation of the ERK1/2 mitogen activated protein kinase pathway, indicating that Giardia proteases can cleave PAR2 at a tethered ligand activation site. The present findings demonstrate novel mechanisms by which Giardia alters the intestinal mucus barrier, potentially facilitating pathogen translocation and contributing to acute, chronic, and post-infectious disease manifestations.
Positive eigenvectors and simple nonlinear maps
Creators: name: Calanchi, Marta
name: Tomei, Carlos
Publisher: name: arXiv
Year: 2023
Subjects: subject: Functional Analysis (math.FA)
subject: FOS: Mathematics
subject: 35J65 47H11 47H30 35J65, 47H11, 47H30, 58K05

description: For linear operators $L, T$ and nonlinear maps $P$, we describe classes of simple maps $F = I - P T$, $F = L - P$ between Banach and Hilbert spaces, for which no point has more than two preimages. The classes encompass known examples (homeomorphisms, global folds) and the weaker, geometric, hypotheses suggest new ones. The operator $L$ may be the Laplacian with various boundary conditions, as in the original Ambrosetti-Prodi theorem, or the operators associated with the quantum harmonic oscillator, the hydrogen atom, a spectral fractional Laplacian, elliptic operators in non-divergent form. The maps $P$ include the Nemitskii map $P(u) = f(u)$ but may be non-local, even non-variational. For self-adjoint operators $L$, we employ familiar results on the nondegeneracy of the ground state. On Banach spaces, we use a variation of the Krein-Rutman theorem.
description: 34 pages, no figures
Stable orbit equivalence of Bernoulli actions of free groups and isomorphism of some of their factor actions
Creators: name: Meesschaert, Niels
name: Raum, Sven
name: Vaes, Stefaan
Publisher: name: arXiv
Year: 2011
Subjects: subject: Operator Algebras (math.OA)
subject: Dynamical Systems (math.DS)
subject: Group Theory (math.GR)
subject: FOS: Mathematics

description: We give an elementary proof for Lewis Bowen's theorem saying that two Bernoulli actions of two free groups, each having arbitrary base probability spaces, are stably orbit equivalent. Our methods also show that for all compact groups K and every free product Γof n infinite amenable groups, the factor K^Γ/K of the Bernoulli action of Γon K^Γ by the diagonal action of K, is isomorphic with a Bernoulli action of Γ.
description: v2: Final, more detailed version, to appear in Expositiones Mathematicae
Novel stabilized models to characterize gene-gene interactions by utilizing transcriptome data
Creators: name: Kossinna, Thalagala Kossinnage Pathum Subhashana
Publisher: name: Cumming School of Medicine
Year: 2022
Subjects: subject: Machine Learning
subject: Pan-cancer Analysis
subject: TCGA
subject: CD63
subject: SCOPE
subject: IBAS
subject: Stabilized Methods
subject: Biological Interactions
subject: data-bridge
subject: Bioinformatics
subject: FOS: Computer and information sciences
subject: Statistics
subject: FOS: Mathematics

description: Machine learning models employed in genetics often grapple with issues related to the "curse of dimensionality". Furthermore, due to the inherent noisy nature of most -omics data, most methods suffer from the problem of "stability": i.e., even slight perturbations of the original data may result in wholly different outcomes. This becomes particularly true when dealing with interactions as the number of potential interactions are usually astronomical. In this thesis, we present two novel methods: 1) Stabilized COre gene and Pathway Election (SCOPE) and 2) Interaction Bridged Association Study (IBAS) that uses two differing approaches in analyzing biological interactions. SCOPE employs a stabilized form of the LASSO that is better able to handle highly correlated expression data and a co-expression network analysis that identifies "core" genes that may be of interest as well as the underlying biological pathways or mechanisms by which they interact. Stabilizing these results across six cancers of The Cancer Genome Atlas uncovered hallmark cancer pathways as well as a novel potential therapeutic target of kidney cancer, CD63. IBAS utilizes a "data-bridge" composed of dimensionality reduced pathway level interactions of the transcriptome to identify genes associated with a phenotype of interest using the Sequence Kernel Association Test (SKAT), in a disentangled form of the Transcriptome Wide Association Study. Application to the Wellcome Trust Case Control Consortium reveals novel gene candidates with literature reviews highlighting their potential for further study. In conclusion, we have developed two novel methodologies in analyzing complex interaction patterns in -omics data using stabilized machine learning methods, paving the way to further understand the biological interactions underlying complex disease.
Barwise Music Structure Analysis with the Correlation Block-Matching Segmentation Algorithm
Creators: name: Marmoret, Axel
name: Cohen, Jérémy E.
name: Bimbot, Frédéric
Publisher: name: arXiv
Year: 2023
Subjects: subject: Sound (cs.SD)
subject: Information Retrieval (cs.IR)
subject: Audio and Speech Processing (eess.AS)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: H.5.5

description: Music Structure Analysis (MSA) is a Music Information Retrieval task consisting of representing a song in a simplified, organized manner by breaking it down into sections typically corresponding to ``chorus'', ``verse'', ``solo'', etc. In this work, we extend an MSA algorithm called the Correlation Block-Matching (CBM) algorithm introduced by (Marmoret et al., 2020, 2022b). The CBM algorithm is a dynamic programming algorithm that segments self-similarity matrices, which are a standard description used in MSA and in numerous other applications. In this work, self-similarity matrices are computed from the feature representation of an audio signal and time is sampled at the bar-scale. This study examines three different standard similarity functions for the computation of self-similarity matrices. Results show that, in optimal conditions, the proposed algorithm achieves a level of performance which is competitive with supervised state-of-the-art methods while only requiring knowledge of bar positions. In addition, the algorithm is made open-source and is highly customizable.
description: 19 pages, 13 figures, 11 tables, 1 algorithm, published in Transactions of the International Society for Music Information Retrieval
Effects of zinc on retinoic acid-induced growth inhibition in human hepatocarcinoma HepG2 cells
Creators: name: Ibbitson, Deanna
Publisher: name: University of British Columbia
Year: 2012

description: Retinoic acid (RA), a bioactive metabolite of vitamin A, inhibits growth in a variety of cancer cells including liver cancer. It is thought that this function of RA is achieved by modulating gene expression through complexing with retinoic acid receptors (RARs) and retinoid X receptors (RXRs), two groups of zinc-finger proteins. Zinc deficiency has been shown to affect gene expression and to impair DNA binding ability of zinc-finger proteins. The hypotheses of my thesis research were: 1) sufficient cellular zinc level is important for the effectiveness of RA-induced growth inhibition in hepatocarcinoma HepG2 cells; and 2) the influence of zinc on RA-induced growth inhibition is through modulating expression or function of RARs and RXRs, which in turn affects the expression of their target genes, CYP26a1 and RARβ. The overall objective was to examine the effects of zinc on RA-induced growth inhibition in HepG2 and the possible mechanisms involved. Zinc manipulation was achieved by culturing HepG2 cells for 6 d in low-zinc media supplemented with 0, 5, and 10 μmol/L zinc to mimic low-, adequate-, and high-zinc conditions. Growth in low-zinc media for 6 d reduced total cellular zinc and the labile intracellular pool of zinc by 29 and 86%, respectively. Treating the cells with 35 µM of RA for 12 h following zinc manipulation significantly reduced cell proliferation in all zinc-treatment groups compared to their corresponding RA control, with the greatest reduction in the high-zinc group. Cell cycle analysis showed that the proportion of cells in the S-phase was reduced by RA treatment at 24 and 72 h at all zinc levels, with the greatest reduction in cells cultured in high-zinc medium. Following growth in low-, adequate- and high-zinc medium, RA treatment elevated the abundance of RARβ and Cyp26a1 mRNA equally in all zinc-treatment groups compared to their correspondent RA controls. Growth in low zinc medium increased mRNA abundance of RXRα while RARα, RARβ, RARγ, RXRβ and RARγ were not affected. In conclusion, these results showed that increasing zinc appeared to sensitize HepG2 cells to RA-induced growth inhibition, but had no effect on RA-induced gene expression of CYP26a1 and RARβ.