cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Uncovering the molecular mechanisms of cardiac ion channels’ regulation by lipids and pore formation in membranes using computer simulations
Creators: name: Mesa Galloso, Haydee
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: moleculer dynamic simulations
subject: pore forming proteins
subject: lipid-protein interactions
subject: voltage-gated potassium channels
subject: Biophysics

description: Membranes are complex cellular structures consisting of many different lipid types, a variety of bound proteins, and other molecules. Growing evidence suggests that membranes and lipids play significant bioactive roles in modulating protein function across several cellular processes. Molecular dynamic (MD) simulations have proven to be a valuable method to study lipid organization and membrane protein activity. In this thesis, I used MD simulations to study how lipids regulate two types of membrane proteins: ion channels and pore-forming proteins. Previous simulations and experimental studies showed that polyunsaturated fatty acids (PUFAs) activate KCNQ1 channels while blocking hERG channels. However, some questions regarding how the channel state or PUFA structural properties influence their molecular mechanisms remained unclear. In part of my work, I built a cardiomyocyte membrane model to study the molecular mechanism underlying the interactions between PUFAs and two voltage-gated potassium channels involved in the cardiac action potential: KCNQ1 and hERG. My results revealed that when KCNQ1 voltage sensor domain (VSD) was in the resting state or ‘down’ conformation, the PUFAs established short-lasting interactions that were different from the long-lasting interactions previously observed in the KCNQ1 intermediate state, where the VSD is in the ‘up’ conformation. Additionally, my studies showed that the number of double bonds in the PUFA acyl tail and the size of the polar head regulates their affinity for KCNQ1. Moreover, MD simulations of the hERG channel in the cardiomyocyte membrane unveiled the PUFA interacting site on hERG at the interface between the VSD and the PD in the open and closed states. I anticipate that this detailed molecular understanding of how PUFAs interact with KCNQ1 and hERG will aid in developing future drugs that utilize these mechanisms. As part of this work, I also studied the pore-forming mechanism of the N-terminal peptide StII1-30, derived from the actinoporin StII. My results revealed that this peptide followed a toroidal pore formation mechanism. Additionally, I unveiled the role of curved lipids as cofactors in the formation of toroidal pores. This work has the potential to lead to strategies for the rational use of these peptides as immunotoxins for immunotherapy in cancer tumors. The overall work in this thesis enhances our understanding of lipid-protein interactions in voltage-gated ion channels and the mechanism underlying pore formation by lytic peptides.
Eigenvector Synchronization, Graph Rigidity and the Molecule Problem
Creators: name: Cucuringu, Mihai
name: Singer, Amit
name: Cowburn, David
Publisher: name: arXiv
Year: 2011
Subjects: subject: Computational Engineering, Finance, and Science (cs.CE)
subject: Data Structures and Algorithms (cs.DS)
subject: Combinatorics (math.CO)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: FOS: Biological sciences
subject: 15A18, 49M27, 90C06, 90C20, 90C22, 92-08, 92E10

description: The graph realization problem has received a great deal of attention in recent years, due to its importance in applications such as wireless sensor networks and structural biology. In this paper, we extend on previous work and propose the 3D-ASAP algorithm, for the graph realization problem in $\mathbb{R}^3$, given a sparse and noisy set of distance measurements. 3D-ASAP is a divide and conquer, non-incremental and non-iterative algorithm, which integrates local distance information into a global structure determination. Our approach starts with identifying, for every node, a subgraph of its 1-hop neighborhood graph, which can be accurately embedded in its own coordinate system. In the noise-free case, the computed coordinates of the sensors in each patch must agree with their global positioning up to some unknown rigid motion, that is, up to translation, rotation and possibly reflection. In other words, to every patch there corresponds an element of the Euclidean group Euc(3) of rigid transformations in $\mathbb{R}^3$, and the goal is to estimate the group elements that will properly align all the patches in a globally consistent way. Furthermore, 3D-ASAP successfully incorporates information specific to the molecule problem in structural biology, in particular information on known substructures and their orientation. In addition, we also propose 3D-SP-ASAP, a faster version of 3D-ASAP, which uses a spectral partitioning algorithm as a preprocessing step for dividing the initial graph into smaller subgraphs. Our extensive numerical simulations show that 3D-ASAP and 3D-SP-ASAP are very robust to high levels of noise in the measured distances and to sparse connectivity in the measurement graph, and compare favorably to similar state-of-the art localization algorithms.
description: 49 pages, 8 figures
Structural, vibrational and thermal properties of densified silicates : insights from Molecular Dynamics
Creators: name: Bauchy, Mathieu
Publisher: name: arXiv
Year: 2012
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: Structural, vibrational and thermal properties of densified sodium silicate (NS2) are investigated with classical molecular dynamics simulations of the glass and the liquid state. A systematic investigation of the glass structure with respect to density was performed. We observe a repolymerization of the network manifested by a transition from a tetrahedral to an octahedral silicon environment, the decrease of the amount of non-bridging oxygen atoms and the appearance of three-fold coordinated oxygen atoms (triclusters). Anomalous changes in the medium range order are observed, the first sharp diffraction peak showing a minimum of its full-width at half maximum according to density. The previously reported vibrational trends in densified glasses are observed, such as the shift of the Boson peak intensity to higher frequencies and the decrease of its intensity. Finally, we show that the thermal behavior of the liquid can be reproduced by the Birch-Murnaghan equation of states, thus allowing us to compute the isothermal compressibility.
Transitions, transformations and tradeoffs: Protecting and strengthening societal resilience and cohesion
Creators: name: Gluckman, Peter
Publisher: name: The University of Auckland
Year: 2021
Subjects: subject: Sociology
subject: FOS: Sociology

description: New Zealanders’ high compliance with Covid-19 lockdown rules and our collective responses to the Auckland and Christchurch terror attacks demonstrate our societal values and commitment to a cohesive society. However, longer-term societal issues such as climate change, economic transition, and social transition with an increasingly diverse population could still undermine our social cohesion. A new Koi Tū commentary, Transitions, transformations and trade-offs: Protecting and strengthening societal resilience and cohesion, discusses trust and cohesion in Aotearoa New Zealand.
 Given the potential for tensions arising between a bicultural and multicultural agenda, it is critical to think about how to sustain our societal cohesion. Having a good understanding of our society’s fabric and the things that threaten its integrity are essential in dealing with these challenges.
Sparse Distributed Learning Based on Diffusion Adaptation
Creators: name: Di Lorenzo, Paolo
name: Sayed, Ali H.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Machine Learning (cs.LG)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: This article proposes diffusion LMS strategies for distributed estimation over adaptive networks that are able to exploit sparsity in the underlying system model. The approach relies on convex regularization, common in compressive sensing, to enhance the detection of sparsity via a diffusive process over the network. The resulting algorithms endow networks with learning abilities and allow them to learn the sparse structure from the incoming data in real-time, and also to track variations in the sparsity of the model. We provide convergence and mean-square performance analysis of the proposed method and show under what conditions it outperforms the unregularized diffusion version. We also show how to adaptively select the regularization parameter. Simulation results illustrate the advantage of the proposed filters for sparse data recovery.
description: to appear in IEEE Trans. on Signal Processing, 2013
Relationship of Maximal Isometric Torque Produced in Flexors and Extensors Rate to Technique by Judo Athletes
Creators: name: Chwała, Wiesław
name: Sterkowicz, Stanisław
name: Lech, Grzegorz
name: Sterkowicz-Przybycień, Katarzyna
name: Ambroży, Tadeusz
name: Pałka, Tomasz
Publisher: name: Institute of Machine Design and Operation, Wrocław University of Technology, Wrocław
Year: 2018
Subjects: body composition, biomechanics, martial arts, athletic performance

description: Acta of Bioengineering and Biomechanics; 02/2018; ISSN 1509-409X
Pre-hydrodynamic evolution in large and small systems
Creators: name: da Silva, Tiago Nunes
name: Chinellato, David D.
name: Giannini, André V.
name: Ferreira, Maurício N.
name: Denicol, Gabriel S.
name: Hippert, Maurício
name: Luzum, Matthew
name: Noronha, Jorge
name: Takahashi, Jun
Publisher: name: arXiv
Year: 2022
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We extend our previous investigation of the effects of pre-hydrodynamic evolution on final-state observables in heavy-ion collisions to smaller systems. We use a state-of-the-art hybrid model for the numerical simulations with optimal parameters obtained from a previous Bayesian study. By studying p-Pb collisions, we find that the effects due to the assumption of a conformal evolution in the pre-hydrodynamical stage are even more important in small systems. We also show that this effect depends on the time duration of the pre-equilibrium stage, which is further enhanced in small systems. Finally, we show that the recent proposal of a free-streaming with subluminal velocity for the pre-equilibrium stage, thus effectively breaking conformal invariance, can alleviate the contamination of final state observables. Our study further reinforces the need for moving beyond conformal approaches in pre-equilibrium dynamics modeling, especially when extracting transport coefficients from hybrid models in the high-precision era of heavy-ion collisions.
description: 15 pages, 14 figures
On the characteristic connection of gwistor space
Creators: name: Albuquerque, Rui
Publisher: name: arXiv
Year: 2011
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 53C10, 53C20, 53C25 (Primary) 53C28 (Secondary)

description: We give a brief presentation of gwistor space, which is a new concept from G_2 geometry. Then we compute the characteristic torsion T^c of the gwistor space of an oriented Riemannian 4-manifold with constant sectional curvature k and deduce the condition under which T^c is \nabla^c-parallel; this allows for the classification of the G_2 structure with torsion and the characteristic holonomy according to known references. The case with the Einstein base manifold is envisaged.
description: Many changes since first version, including title; Central European Journal of Mathematics, 2013
Comparing suicidal thoughts and behaviours of youth with fetal alcohol spectrum disorder and autistic youth: Caregivers-reported suicidality, access to services and barriers in seeking support
Creators: name: Bagshawe, Mercedes Jayne
Publisher: name: Werklund School of Education
Year: 2023
Subjects: subject: Educational Psychology
subject: Mental Health

description: Background. Autistic individuals and individuals with fetal alcohol spectrum disorder (FASD) are at increased risk for experiencing mental health problems, including suicidality. Both groups have compounding physical and psychological challenges leading to high utilization rates of healthcare services. There is little known about the access and utility of services for suicidal neurodiverse youth and their caregivers. The present study will examine suicidality and barriers to care in neurodiverse youth (i.e., autistic youth and youth with FASD), as well as describe caregivers’ experiences with accessing healthcare services. Methods: Caregivers of neurodiverse youth (FASD n=25; autistic n=35) answered questions in an on-line modified Columbia Suicide Severity Rating Scale (CSSR-S) about their child’s experiences with suicidality, early life adversity, co-occurring mental health conditions, healthcare services, and barriers to accessing support. 12 semi-structured interviews (FASD n=6; autistic n=6) were conducted with caregivers of youth who have experienced suicidality to generate insight into experiences within the healthcare system, ability to access services and receive support and barriers to seeking help. Results: On the CSSR-S, group differences determined that autistic youth had increased suicidal ideation when compared to youth with FASD. Within each neurodivergent groups, females with FASD had increased overall suicidality compared to males. Additionally, across both sexes, as age increased, so did suicidal intensity. No sex or age differences were seen in autistic youth. Co-occurring mental health conditions were associated with increased suicidality across neurodiverse groups, and suicidality was associated with the total number of adverse early life events in only the FASD youth. Services or barriers were not associated with measures of suicidality in either diagnostic group. Both groups of caregivers reported difficulties accessing services to address their child’s suicidality, and that healthcare providers lacked the training to work with neurodiverse youth. Discussion: This is the first study to contrast suicidality, service utilization and barriers to seeking help in autistic youth and youth with FASD from a caregiver’s aspect. Prior studies generally compare neurodiverse groups to their neurotypical peers, and as such assume that neurodiverse groups face similar challenges related to suicidality, yet this has never been investigated. Overall, caregivers of neurodiverse youth are facing a lack of available services and support for helping their children and a healthcare system that is not equipped to work with neurodivergent individuals experiencing suicidality.
Multi-agent Spatiotemporal Simulation of Autonomous Vehicle Fleet Operation
Creators: name: ZHANG, ZONGHAO
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: Agent-based Modelling
subject: Transportation
subject: Autonomous Vehicle Fleet
subject: Engineering
subject: Engineering--Automotive
subject: Engineering--Civil

description: Autonomous vehicle fleets, consisting of self-driving vehicles, are at the forefront of transportation innovation. The appearance of autonomous vehicles (AVs) provides a new solution for traffic problems and a new market for transportation network companies such as DiDi and Uber. Conducting simulations in the present is indeed crucial to prepare for the eventual operation of autonomous vehicles, as their widespread adoption is expected to occur in the near future. This research adopts an Agent-Based Modelling (ABM) approach to understand and optimize the performance of autonomous vehicle systems. Moreover, Geographic Information System (GIS) technology also plays a crucial role in enhancing the effectiveness and accuracy of the simulation process. GIS enables the representation and manipulation of geospatial data, such as road networks, land-use patterns, and population distribution. The combination of ABM and GIS allows for the incorporation of real-world geographic data, providing a realistic and geographically accurate environment for the agents in the virtual environment. In this thesis, the multi-agent spatiotemporal simulation is conducted by the GAMA platform. The model simulates the behaviour and interactions of individual agents, which are fleet agents and commuters, to observe the emergent behaviour of the entire system. Within the experiment, different scenarios are considered for both people and fleets to explore a range of approaches and strategies. These scenarios aim to evaluate the effectiveness of various approaches in meeting dynamic commute needs and optimizing fleet operations. By simulating these different scenarios and analyzing their outcomes, the study aims to provide insights into the improvement of fleet size and deployment in autonomous vehicle systems. The ultimate goal is to identify effective strategies that lead to optimized fleet size in different scenarios, reduced idling time and emission, improved traffic management, and overall more efficient and sustainable autonomous vehicle systems.
Teleparallel Newton--Cartan gravity
Creators: name: Schwartz, Philip K.
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We discuss a teleparallel version of Newton--Cartan gravity. This theory arises as a formal large-speed-of-light limit of the teleparallel equivalent of general relativity (TEGR). Thus, it provides a geometric formulation of the Newtonian limit of TEGR, similar to standard Newton--Cartan gravity being the Newtonian limit of general relativity. We show how by a certain gauge-fixing the standard formulation of Newtonian gravity can be recovered.
description: 28+4+1 pages (main text, references, appendix), published in Classical and Quantum Gravity. v2: extended discussions, added references, corrected typos. v3: corrected typo
Building Wavelet Histograms on Large Data in MapReduce
Creators: name: Jestes, Jeffrey
name: Yi, Ke
name: Li, Feifei
Publisher: name: arXiv
Year: 2011
Subjects: subject: Databases (cs.DB)
subject: FOS: Computer and information sciences

description: MapReduce is becoming the de facto framework for storing and processing massive data, due to its excellent scalability, reliability, and elasticity. In many MapReduce applications, obtaining a compact accurate summary of data is essential. Among various data summarization tools, histograms have proven to be particularly important and useful for summarizing data, and the wavelet histogram is one of the most widely used histograms. In this paper, we investigate the problem of building wavelet histograms efficiently on large datasets in MapReduce. We measure the efficiency of the algorithms by both end-to-end running time and communication cost. We demonstrate straightforward adaptations of existing exact and approximate methods for building wavelet histograms to MapReduce clusters are highly inefficient. To that end, we design new algorithms for computing exact and approximate wavelet histograms and discuss their implementation in MapReduce. We illustrate our techniques in Hadoop, and compare to baseline solutions with extensive experiments performed in a heterogeneous Hadoop cluster of 16 nodes, using large real and synthetic datasets, up to hundreds of gigabytes. The results suggest significant (often orders of magnitude) performance improvement achieved by our new algorithms.
description: VLDB2012
Cantilever Tip Radius Estimation through Contact Resonance Atomic Force Microscopy
Creators: name: Mathias, Thomas
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: Atomic Force Microscope
subject: Contact Resonance
subject: Mechanical Properties
subject: Engineering--Mechanical
subject: Engineering
subject: Materials Science

description: The mechanical characteristics of materials, particularly those of composite materials, can be mapped spatially and quantified using Contact Resonance Atomic Force Microscopy (CR-AFM). This technique operates by measuring the changes in resonance frequency as an AFM cantilever tip comes into contact with a sample surface. Such frequency shifts are primarily related to contact stiffness, although it can also influence other factors such as viscoelasticity. While several theories aim to connect the modal shape and resonant frequency of the AFM cantilever with contact stiffness, no direct application of these models has been developed to directly transform the resonant frequency into a physical mechanical property measurement. Instead, the majority of experimental studies utilising CR-AFM calibrate the frequency conversion factor relating to contact stiffness using a known reference sample, bypassing the direct use of these cantilever models. This thesis brings into focus two novel aspects aimed at enhancing and refining the CR-AFM technique: using thermal resonance to monitor the oscillation modes of an AFM cantilever during an experiment and establishing a connection between cantilever dynamics theory and the calibration of CR-AFM data that eliminates the requirement for normalisation to a known sample. In the first segment of this thesis, cantilever thermal displacement time series data is transformed into frequency space utilising the short-time Fourier transform(STFT) and continuous wavelet transform (CWT). It will be demonstrated that only the STFT calculations are capable of delivering the time-frequency resolution necessary to track AFM modal vibrations, at least currently. The application of the STFT allows for real-time tracking of the contact resonance frequency and Quality factor throughout a force spectroscopy experiment. The ensuing analysis reveals the fluctuations in contact resonance frequency over the course of this experiment. However, utilising cantilever analytical models to interpret this data using known contact mechanics models resulted in nonphysical estimates. Further studies are underway to reconcile the often problematic assumptions made in contact mechanics for AFM measurements with dynamic, STFT measurements. The experimental findings underscore the reasons why normalisation or calibration of CR-AFM results to samples with known stiffness has been prevalent until now. Despite progress, the comprehensive understanding of the contact mechanics and vibration theory necessary to analyse the dynamics of AFM cantilevers in such experiments remains an open challenge.
Ultrametric Model of Mind, I: Review
Creators: name: Murtagh, Fionn
Publisher: name: arXiv
Year: 2012
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences
subject: I.2.0; I.2.3; J.4
subject: 68T01

description: We mathematically model Ignacio Matte Blanco's principles of symmetric and asymmetric being through use of an ultrametric topology. We use for this the highly regarded 1975 book of this Chilean psychiatrist and pyschoanalyst (born 1908, died 1995). Such an ultrametric model corresponds to hierarchical clustering in the empirical data, e.g. text. We show how an ultrametric topology can be used as a mathematical model for the structure of the logic that reflects or expresses Matte Blanco's symmetric being, and hence of the reasoning and thought processes involved in conscious reasoning or in reasoning that is lacking, perhaps entirely, in consciousness or awareness of itself. In a companion paper we study how symmetric (in the sense of Matte Blanco's) reasoning can be demarcated in a context of symmetric and asymmetric reasoning provided by narrative text.
description: 20 pages, 2 figures, 46 references. arXiv admin note: substantial text overlap with arXiv:0709.0116, arXiv:0805.2744, and arXiv:1105.0121 (V3: 2 typos corrected)
Witnessing Non-Classicality in a Simple Causal Structure with Three Observable Variables
Creators: name: Lauand, Pedro
name: Poderini, Davide
name: Nery, Ranieri
name: Moreno, George
name: Pollyceno, Lucas
name: Rabelo, Rafael
name: Chaves, Rafael
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Seen from the modern lens of causal inference, Bell's theorem is nothing else than the proof that a specific classical causal model cannot explain quantum correlations. It is thus natural to move beyond Bell's paradigmatic scenario and consider different causal structures. For the specific case of three observable variables, it is known that there are three non-trivial causal networks. Two of those, are known to give rise to quantum non-classicality: the instrumental and the triangle scenarios. Here we analyze the third and remaining one, which we name the Evans scenario, akin to the causal structure underlying the entanglement-swapping experiment. We prove a number of results about this elusive scenario and introduce new and efficient computational tools for its analysis that also can be adapted to deal with more general causal structures. We do not solve its main open problem -- whether quantum non-classical correlations can arise from it -- but give a significant step in this direction by proving that post-quantum correlations, analogous to the paradigmatic Popescu-Rohrlich box, do violate the constraints imposed by a classical description of Evans causal structure.
description: 16 pages and 6 figures
Additional file 1 of L. reuteri ZJ617 inhibits inflammatory and autophagy signaling pathways in gut-liver axis in piglet induced by lipopolysaccharide
Creators: name: Zhu, Tao
name: Mao, Jiangdi
name: Zhong, Yifan
name: Huang, Congxiang
name: Deng, Zhaoxi
name: Cui, Yanjun
name: Liu, Jianxin
name: Wang, Haifeng
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Physiology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Computational Biology

description: Additional file 1: Supplementary Fig. S1. Ilea morphology, villus height and crypt depth of three groups. CON, control piglets orally inoculated with PBS; LPS, piglets treated by intraperitoneal injection (i.p.) of LPS (25 μg/kg body weight); ZJ617 + LPS, piglets orally inoculated with ZJ617 (1 × 1010 CFU/d) for 2 weeks before i.p. injection of LPS. The ileum tissue was stained with hematoxylin-eosin. Values are shown as mean ± SE, n = 6. Labeled means without a common letter differ, P < 0.05.
Prediction of Cognitive Status of Alzheimer's Disease Using Machine Learning Methods with Structural Magnetic Resonance Imaging
Creators: name: Chen, Zhenyu
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: Education--Health
subject: Education--Mathematics
subject: Biostatistics

description: Alzheimer's disease is a progressive form of dementia. A patient diagnosed with Alzheimer's disease usually underwent three types of cognitive status: normal cognitive (NC), mild cognitive impairment (MCI), and Alzheimer's disease (AD). This thesis studies two machine learning models to predict cognitive status based on the region of interest features extracted from structural magnetic resonance imaging. The support vector machine (SVM) model uses recursive feature elimination to select the proper number of features and the multilayer perceptron (MLP) neural network model uses Bayesian optimization to tune the hyperparameters. When applied to a real data set with 1684 observations, the SVM model achieved 68.84% accuracy while the MLP model achieved 70.92% accuracy for multi-classification. We further compared the two models in three binary classifications, namely, NC vs MCI, MCI vs AD, and NC vs AD. The SVM model achieved the area under the receiver operating characteristic curves (AUCs) of 72%, 71%, 86%, while the MLP model achieved the AUCs of 68%, 73%, 88%, respectively. In general, the MLP model performs better than the SVM model. Both models can be used to assist in the early diagnosis of Alzheimer's disease.
Ptychography for Nonlinear Optical Microscopy
Creators: name: Norris, Evan
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2021
Subjects: Nonlinear Optical Imaging
Ptychography

description: In this thesis I will introduce a novel nonlinear optical microscopy method to address some of the shortcomings in the current nonlinear optical microscopy literature and offer a supplement to traditional fluorescent microscopy for label free optical biomedical imaging. In order to demonstrate this method I describe a method for the generation of a numerical sample of collagen fibrils, produce a set of numerical diffraction measurements. I introduce a novel Ptychography model for the simultaneous reconstruction of the components of the nonlinear optical susceptibility tensor and demonstrate the results of this model using numerically generated measurements from a numerical collagen sample. I additionally use the recovered information from Ptychography to retrieve new information about the structure of a sample.
Reductive Treatment of Bromate by Cast Iron
Creators: name: Khosravi Zadeh, Sajjad
Publisher: name: Schulich School of Engineering
Year: 2023
Subjects: subject: Engineering--Environmental
subject: Engineering--Civil

description: Bromate is an undesirable by-product of ozonating bromide-containing water and is a probable human carcinogen. Given the associated adverse effects of bromate on the environment and public health, it is important to treat and remove bromate from drinking water. Zero-valent iron particles have the potential to reduce bromate to bromide. However, they get oxidized rapidly and fail to completely reduce bromate to bromide. In this study, we analyzed the reduction characteristics of cast iron granules to treat bromate and its potential to be regenerated and re-used. Two different particle sizes of cast iron were analyzed in batch and in column tests to treat bromate-spiked deionized water and groundwater. Both particle sizes showed promising bromate treatment capacity. In batch tests, when the bromate concentration decreased, the bromide concentration increased, indicating the reduction of bromate to bromide using cast iron. In the column tests, it was observed that the bromate concentration in influent and the residence time affect the bromate-reduction capacity of the column. Decreasing the bromate concentration in influent and increasing residence time increased the total amount of bromate reduced. At low initial bromate concentrations, the columns continued to completely reduce bromate into bromide for 36 to 59 consecutive days without any decrease in the bromate reduction capability of the columns. It was also observed that cast iron granules could be regenerated using sulfuric acid and re-used multiple times with minimal impact on efficiency. Mathematical models were developed to identify pilot-scale column dimensions and predict bromate occurrence in column effluent. This research reveals that cast iron is a viable option to reduce bromate produced during ozonation.
Matter and Antimatter in the Universe
Creators: name: Canetti, Laurent
name: Drewes, Marco
name: Shaposhnikov, Mikhail
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We review observational evidence for a matter-antimatter asymmetry in the early universe, which leads to the remnant matter density we observe today. We also discuss observational bounds on the presence of antimatter in the present day universe, including the possibility of a large lepton asymmetry in the cosmic neutrino background. We briefly review the theoretical framework within which baryogenesis, the dynamical generation of a matter-antimatter asymmetry, can occur. As an example, we discuss a testable minimal model that simultaneously explains the baryon asymmetry of the universe, neutrino oscillations and dark matter.
description: Invited contribution to the New Journal of Physics Focus Issue "Origin of Matter" (New J. Phys. 14 (2012) 095012); this version is identical to the published article up to a few updates in the references
Faculty-to-faculty mentorship Suppl Info_25 Oct 2023 from The faculty-to-faculty mentorship experience: a survey on challenges and recommendations for improvements
Creators: name: Sarabipour, Sarvenaz
name: Niemi, Natalie M.
name: Burgess, Steven J.
name: Smith, Christopher T.
name: Bisson Filho, Alexandre W.
name: Ibrahim, Ahmed
name: Clark, Kelly
Publisher: name: The Royal Society
Year: 2023
Subjects: classificationCode: 300199
subject: Agricultural biotechnology not elsewhere classified
classificationCode: 310114
subject: Systems biology
classificationCode: 310199
subject: Biochemistry and cell biology not elsewhere classified

description: 102 pages
Effect of different balance training programs on postural control in chronic ankle instability: a randomized controlled trial
Creators: name: Aboelezz, Noha M. Youssef
name: Abdelmohsen, Azza M.
name: Ashour, Ahmed A.
name: Elhafez, Naglaa M.
name: Elhafez, Salam M.
Publisher: name: Institute of Machine Design and Operation, Wrocław University of Technology, Wrocław
Year: 2018
Subjects: Postural control, balance training, chronic ankle instability

description: Acta of Bioengineering and Biomechanics; 02/2018; ISSN 1509-409X
Sistêmica algorítmica informacional: em direção a uma teoria formal por estruturas parciais mutuamente auto-organizantes
Creators: name: Abrahão, Felipe S.
name: D'Ottaviano, Itala M. L.
Publisher: name: Zenodo
Year: 2021
Subjects: algorithmic information
self-organization
emergence
partial structures
enaction
abduction

description: A ubiquidade da presença de processos emergentes e, ao mesmo tempo, auto-organizantes em sistemas biológicos coloca um problema fundamental ainda em aberto que transpassa não somente a biologia, mas também atinge outras áreas que intersectam as ciências da complexidade, como, por exemplo, cibernética, inteligência artificial, sociologia e ciência cognitiva. Nosso projeto de pesquisa pós-doutoral propõe que essa problemática, além de também estar contida na sistêmica por estruturas parciais e na teoria da quase-verdade, permite uma solução matemática para explicar como o conhecimento formal é criado no contexto de sistemas em interação num mesmo ambiente (ou universo). Para esse fim, o problema central no qual focaremos é a investigação teórica da ocorrência de organização emergente, auto-organização e enação a partir da interação entre sistemas e o ambiente (definidos como famílias de estruturas parciais), onde essa interação é quantificada por medidas de informação algorítmica. Nossa proposta de pesquisa traz uma inovadora abordagem interdisciplinar que se baseia na teoria da informação algorítmica, teoria da quase-verdade (ou verdade pragmática), teoria dos modelos e cibernética para construção de definições e modelos matemáticos sobre os quais podemos demonstrar teoremas, confirmando ou delimitando a corretude de conceitos e fenômenos. Além de abordar o problema dentro do contexto da lógica matemática e ciência de sistemas complexos, nossos objetivos de longo prazo propõem contribuições para as discussões entre o pragmatismo, representacionalismo, relativismo e construtivismo.
description: Postdoc research proposal submitted and approved by FAPESP.
Agent-based Models in Flood Simulation - A Case Study for New Brunswick’s Flooding Events in 2018
Creators: name: Zhu, Wenxuan
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: Geographic Information Science
subject: Agent-Based Modeling
subject: Flooding Simulation
subject: Geotechnology

description: This thesis introduces an Agent-Based Modeling (ABM) framework for flood simulation and inversion modeling in flood-prone areas, aiming to improve our understanding of the complex dynamics of flooding and provide valuable insights for flood management. The developed model incorporates multi-source terrain datasets, and integrates water flow and meteorological conditions from remote sensing data sources. It takes into account factors such as precipitation patterns, geographical features, and Digital Elevation Model (DEM) resolution to accurately represent flood characteristics. The model's parameter settings are derived from extensive experimentation, allowing for effective control and meaningful results. By considering the impact of precipitation and the presence of rivers, the model demonstrates its ability to simulate flood inundation with a reasonable level of accuracy. Overall, this comprehensive model provides a valuable tool for flood simulation and offers insights into flood dynamics for effective flood management and mitigation strategies.
Contrasting epistemologies in the use of natural dyes, Central Highlands of Chiapas
Creators: name: Laruelle Aranguiz, Katarin Maria
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: natural dyes
subject: Chiapas
subject: epistemologies
subject: textile archaeology
subject: craft knowledge
subject: communities of practice
subject: ethnoarchaeology
subject: Archaeology
subject: History--Latin American

description: Mexico is an ecologically diverse area with a variety of natural resources used by its inhabitants since millenniums before our common era. In the southwest of the country, the ecosystem of the Central Highlands of the state of Chiapas is no exception, where a few textile craftswomen transform various local plants, roots, and berries into colourful dyes and import some pigments into the area, maintaining sharing networks between different ecological regions. Still, these practices persist today with great difficulty. Over the last decades, a few non-local teachers have worked to reintroduce these practices through workshops held in the regional capital of San Cristóbal de Las Casas. During these workshops, a number of non-local materials were taught, as well as specific methods of making and understanding dyes, which contrast with the practices of local dyers, many of whom identify as Tsotsil. Therefore, this research examines how the interaction of these diverse communities of practice and inherent epistemologies affects artisanal dyeing techniques among the populations of the Central Highlands of Chiapas. Ethnoarchaeological fieldwork was carried out in San Cristóbal de Las Casas and its surrounding areas during the summer of 2022 with interviews and participant observation sessions. A comparative analysis led to the conclusion that the dyers of the Central Highlands of Chiapas developed their understanding of the materiality of dyes in relation to their environment: the home, the pasture, and the forest. The locality of the raw material becomes a factor in the development of local dyers’ epistemologies, influencing a generative relationship with the material that has an impact on their technique and creativity. Conversely, processed pigments are imported with their ways of making, shaping the way artisans understand and reproduce their use. The ways in which commercial networks intersect with local dyers’ practices and epistemologies may lead to an improved understanding of the impact of non-local dyes on communities of practice in the archaeological past of Mesoamerica.
Lattice spinor gravity
Creators: name: Wetterich, C.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: We propose a regularized lattice model for quantum gravity purely formulated in terms of fermions. The lattice action exhibits local Lorentz symmetry, and the continuum limit is invariant under general coordinate transformations. The metric arises as a composite field. Our lattice model involves no signature for space and time, describing simultaneously a Minkowski or euclidean theory. It is invariant both under Lorentz transformations and euclidean rotations. The difference between space and time arises from expectation values of composite fields. Our formulation includes local gauge symmetries beyond the generalized Lorentz symmetry. The lattice construction can be employed for formulating models with local gauge symmetries purely in terms of fermions
description: 9 pages, minor corrections
The Universal Gas Mass Fraction in Clusters of Galaxies
Creators: name: David, Laurence P.
name: Jones, Christine
name: Forman, William
Publisher: name: arXiv
Year: 2011
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We obtained a deep 150ksec Chandra observation of the optically selected cluster of galaxies, RCS 2318+0034, to investigate the gas mass fraction in this system. Combining our deep {\it Chandra} observation with an archival 50ksec observation, we derive gas mass fractions of fgas=0.06 +- 0.02 and 0.10 +- 0.02 within r2500 and r500, respectively. The gas mass fraction in RCS 2318+0034 within r500 is typical of X-ray selected clusters. Further study shows that the large scale properties of RCS 2318+0034, including the relations between gas mass, X-ray luminosity and gas temperature are also consistent with the observed correlations of X-ray selected clusters. However, the gas mass fraction within r2500 is less than most X-ray selected clusters, as previously reported. The deep Chandra image of RCS 2318+0034 shows that this system is presently undergoing a major merger which may have an impact on the inferred gas mass fraction within r2500.
The role of adenylyl cyclase signaling pathways in developmental dendritogenesis in vivo
Creators: name: Duncan, Blair
Publisher: name: University of British Columbia
Year: 2012

description: The period of early brain development involves an exceptional amount of neuronal morphological growth and refinement to form functional brain circuits. Although it is known that neural activity influences dendrite morphogenesis, the molecular pathways which convert a neural activity input to changes in morphology are not well understood. Here I show that activation of the adenylyl cyclase pathway promotes growth of developing brain neurons in vivo, in a neuron maturation-dependent manner. Rapid time-lapse two-photon imaging of single neuron growth within the developing vertebrate brain and pharmacological manipulations reveal a synergistic role for PKA and Epac in growth downstream of β-adrenergic receptors and adenylyl cyclase. Inhibition of the protease calpain increases axonal and dendritic filopodial density, but only in axons is this effect downstream of PKA. Furthermore, experiments indicate that PKA localization by AKAPs may be important in its regulation of dendritogenesis. Together, the results presented here outline multiple steps of a signaling pathway important in dynamic dendritogenesis and axogenesis in vivo.
Improving News Ranking by Community Tweets
Creators: name: Shuai, Xin
name: Liu, Xiaozhong
name: Bollen, Johan
Publisher: name: arXiv
Year: 2012
Subjects: subject: Information Retrieval (cs.IR)
subject: Social and Information Networks (cs.SI)
subject: FOS: Computer and information sciences
subject: H.3.3

description: Users frequently express their information needs by means of short and general queries that are difficult for ranking algorithms to interpret correctly. However, users' social contexts can offer important additional information about their information needs which can be leveraged by ranking algorithms to provide augmented, personalized results. Existing methods mostly rely on users' individual behavioral data such as clickstream and log data, but as a result suffer from data sparsity and privacy issues. Here, we propose a Community Tweets Voting Model (CTVM) to re-rank Google and Yahoo news search results on the basis of open, large-scale Twitter community data. Experimental results show that CTVM outperforms baseline rankings from Google and Yahoo for certain online communities. We propose an application scenario of CTVM and provide an agenda for further research.
description: 6 pages, 3 figures, 4 tables
Mitochondrial dysfunction and steroidogenesis in Parkinson disease
Creators: name: Lee-Glover, Laurie Patricia
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: Biology--Molecular
subject: Biology--Cell

description: Patients with Parkinson disease (PD), one of the most common neurodegenerative disorders, have elevated levels of the glucocorticoid cortisol, a stress-related steroid hormone. Increased stress or glucocorticoids in experimental models of PD worsens neurodegeneration, implicating elevated glucocorticoids in disease pathogenesis. However, the mechanism behind dysregulated glucocorticoid levels is unclear. The rate-limiting step of steroidogenesis, cholesterol import into the mitochondria, is mediated by steroidogenic acute regulatory protein (STARD1). STARD1 transports cholesterol while transiently localized to the outer mitochondrial membrane. Impairments in mitochondrial protein import, a key aspect of cellular dysfunction linked to PD, increase STARD1-mediated mitochondrial cholesterol import, providing a potential mechanism connecting PD with increased steroidogenesis. To test how steroidogenesis is affected by mitochondrial function in PD, we used PD-related toxins and genetic variants to model the effects of PD. We looked at the import of STARD1 overexpressed in HEK293 cells and steroid production in steroidogenic adrenocortical cell lines. We found that the PD toxin rotenone slowed STARD1 import and increased cholesterol import. Cortisol production increased only under lower levels of rotenone-induced mitochondrial stress. This is intriguing as milder mitochondrial stress may be more relevant to the progressive nature of PD. Additionally, overexpression of PD pathogenic variant alpha synuclein A53T upregulated basal production of pregnenolone and cortisol in steroidogenic cells. To explore further connections between steroidogenesis and PD, we also looked for miRNA biomarkers related to steroidogenesis in PD patients. We found expression of hsa-mir-320a in PD patient serum exosomes was negatively correlated with disease duration. As this miRNA negatively regulates expression of certain enzymes involved in cortisol synthesis, dysregulation of this miRNA could contribute to elevated cortisol levels in PD. Overall, our findings are consistent with cellular dysfunction in PD upregulating cortisol production. We delineated a novel pathway where mitochondrial dysfunction in PD activates cholesterol import by STARD1 to promote steroidogenesis. STARD1 may be a novel therapeutic target in PD. Additionally, as steroid signalling can be acutely protective against cellular stress, we propose this could be a stress response mechanism that couples steroid production to mitochondrial status, but which can be detrimental upon prolonged activation.