cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Utilizing semantics for fast and robust localisation and mapping in semi-structured environments
Creators: name: Zaganidis, Anestis
Publisher: name: University of Lincoln
Year: 2023
Subjects: I100 - Computer science

description: Autonomous Navigation in outdoor, semi structured environments such asagricultural fields, warehouses and public transport is crucial for the seamlessoperation of autonomous vehicles. Simultaneous localization and mapping(SLAM), the online construction of a map and the localization within it,remains a challenging problem, especially for these outdoor environmentswith low structure, where the pose has 6 degrees of freedom. This thesisaddresses the problem of localisation and mapping in three dimensional, semi structured environments using a lidar range sensor and proposes a novelSLAM system assisted by semantic segmentation of point clouds.This work makes extensive use of the Normal Distributions Transform(NDT), a compact representation that can be used for point cloud registration and place recognition, and proposes extensions that increase the robustness and speed in semi-structured environments. In the absence of stronggeometric features, semantics can decrease the rate of incorrect registrationcorrespondences in point cloud registration, and can increase the specificityof the NDT Histogram descriptor for place recognition.The main contributions of this work include, (i) a comprehensive reviewof the registration and loop closure detection algorithms (ii) the integration ofsemantics into the Normal Distributions Transform registration using handcrafted features as well as data-driven semantic segmentation models (iii) thereuse of the computed semantics for loop closure detection.In this work, we study two methods for the extraction of semantics. Handcrafted features provide an input for low-level semantics that improve registration accuracy, robustness and speed in semi-structured scenes with high overlap. A data-driven classifier is used to provide high-level, human interpretable semantics, that when used for registration increases robustness toinitial registration errors to similar levels as global registration methods. The same data-driven classifier is also used for the loop closure detection module of the SLAM pipeline. This classifier, along with the inclusion of semantics in the NDT Histograms descriptor and engineered rules, is capable of operating with zero false positives in a semi-structured environment. In contrast,the non-semantic version exhibits high rate of false-positives that is highly limiting for outdoor SLAM applications. All the proposed components of the system are extensively evaluated with the use of publicly available datasets. The complete pipeline, including pretrained models, is released as an open-source ROS package.
Electrooptic response of chiral nematic with oblique helicoidal director
Creators: name: Xiang, Jie
name: Shiyanovskii, Sergij V.
name: Imrie, Corrie
name: Lavrentovich, Oleg D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Electrically induced reorientation of liquid crystals (LCs) is a fundamental phenomenon widely used in modern technologies. We observe experimentally an electro-optic effect in a cholesteric LC with a distinct oblique-helicoidal director deformation. The oblique helicoid, predicted in late 1960-ies, is made possible by recently developed dimer materials with an anomalously small bend elastic constant. Theoretical, numerical, and experimental analysis establishes that both the pitch and the cone angle of the oblique helicoid increase as the electric field decreases. At low fields, the oblique helicoid with the axis parallel to the field transforms into a right-angle helicoid (the ground state of field-free cholesteric) with the axis perpendicular to the field.
description: 14 pages, 5 figures
The Dynamic Control Platform: Reinventing the Wheel, One Leg at a Time
Creators: name: Solis, Angel Javier
Publisher: name: University of Nevada, Las Vegas
Year: 2020
Subjects: Computer Engineering; Electrical and Computer Engineering

description: Upright bipedal walking is a complex balance of forces and actions that is almost taken for granted. How this system is modeled, how it affects a prosthesis, and how it can be implemented in the real world are topics that the proposed Dynamic Control Platform aims to address.
The Dynamic Control Platform (DCP) is a bipedal robot designed to test bio-inspired control algorithms with the aim to smooth out the walking experience for prosthetic legs. The main control paradigm that the DCP centers on the principle of orthogonal constraint, which aims to enforce a perpendicular relationship between the center of mass velocity and the ground reaction force so that mechanical cost is minimized.
The DCP is a circular hub with six ankles/feet equally distributed around the wheel. It is designed so that at most two of its ankles are touching the ground at any time, as in human walking. However, the ankles rotate around the central hub to eliminate the need for swinging of the leg  which simplifies the design and allows the focus to remain on control of the ankles. The ankles are controlled by a custom built motor controller which allows for servo-like angular control of a DC motor. The encoder counting, which allows for precise angular control, is completed by small microcontrollers, with one microcontroller dedicated to each ankle. This frees the main microcontroller to process incoming data and to enforce the desired control algorithms for walking.
In order to enforce the principle of orthogonal constraint  keeping center of mass force and velocity vectors parallel or nearly parallel, the robot needs to measure its force and velocity. To do so, we designed and built a force sensing trackway. The trackway converts sensed voltages into forces and transmit those wirelessly to the robot. The connection between the robot and the trackway is necessarily wireless because the robot must be able to move freely along the trackway and any contact with the ground must be sensed through the trackway.
The DCP can be used in the future to examine various ankle torque profiles for a powered prosthesis and the force trackway can be used to verify if the ankle profile has smooth redirections during each stride. This would allow researchers to hone in on desired ankle movement profiles without the need for human trials until much later in the process. These profiles, in turn, would help make the usage of prosthetic legs more comfortable and efficient for the wearer.
Topic Modelling and Data Analysis: Impact of using topic modelling on game review
Creators: name: Stepien, Konrad
Publisher: name: University of Lincoln
Year: 2023
Subjects: I100 - Computer science

description: Purpose–The purpose of this thesis is to investigate the game reviews and to see how the natural language processing can be used to analyze game reviews. Using Steam platform as our data source and Latent Dirichlet Allocation as one of the main methods of data analysis in this research there will be attempt to figure out what kind of topics will emerge within and how interpretations of these can be used to see the correlation between game updates and game reviews. All these results will be looked throughout the timeframes of the life of the game, from alpha/beta testing to the most current reviews. Design/Methodology/Approach–Within this research Latent Dirichlet Allocation will be used on five different games from multiple different genres to test our hypothesis. Findings–The findings of this research could be used by the fields of both data analysis and game studies as this research contributes towards these areas. It is believed that this research will show how the game reviews can be interpreted and give ideas to further research. Practical implications–In theory this research will heavily be based on opinions of both players/people who left the reviews and a researcher hence these should not be treated as a fact. As there are many factors that could affect the quality of the reviews, there will be taken careful measures to eliminate these one by one (such as length of the reviews, duplicates. Etc.)Originality/value–This research should stimulate the game producers and developers to see a different aspect of the games and allow for better decision making. Key Questions–How natural language processing can be used to analyze this data? How will LDA and LDA Sequential contribute to analysis of Steam reviews? How does pre-processing change the results of the LDA and LDA Sequential? What is the correlation between the game updates and game review analysis results?
Microlens Masses From Astrometry and Parallax in Space-Based Surveys: From Planets to Black Holes
Creators: name: Gould, Andrew
name: Yee, Jennifer C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We show that space-based microlensing experiments can recover lens masses and distances for a large fraction of all events (those with individual photometric errors
description: Submitted to ApJ, 16 pages, 1 Figure
Investigating the Mechanisms Responsible for Cephalosporin Resistance in Clostridioides difficile Strain 630
Creators: name: Turello, Lara Anna
Publisher: name: University of Nevada, Las Vegas
Year: 2020
Subjects: Biochemistry

description: Clostridioides difficile infection (CDI) is one of the most common nosocomial infections worldwide. A major risk factor for CDI is antibiotic therapy, due to C. difficiles resistance to a myriad of antibioticsone of which are cephalosporins. Cephalosporins are ß-lactam antibiotics that function by binding to the active site of penicillin-binding proteins (PBPs), thus inhibiting peptidoglycan synthesis and leading to cell lysis. Gram-positive bacteria can counteract ß-lactams by (i) producing ß-lactamases, (ii) expressing modified PBPs, or (iii) by expressing efflux pumps.
Genomic analysis of C. difficile strain 630 revealed the presence of at least 31 putative ß-lactam resistance genes that encode putative ß-lactamases, ß-lactamase-like proteins and PBPs. We hypothesized that upon cephalosporin exposure, C. difficile would differentially express one or more of these genes. Many of these genes were differentially expressed when C. difficile was exposed to cefoxitin, but most of them were not upregulated more than 3.5-fold according to RT-qPCR analysis. Strikingly, putative ß-lactamase, blaCDD, was upregulated nearly 600-fold upon cefoxitin treatment. Deletion of blaCDD caused little to no reduction in cephalosporin resistance.
RT-qPCR analysis of the blaCDD-null mutant when treated with cefoxitin did not reveal any drastic changes in expression of the remaining genes that could explain transcription compensation for the deleted ß-lactamase. Deletion of the second-most upregulated gene which encodes a putative PBP, vanY, minimally affected cephalosporin resistance. To elucidate additional putative resistance genes that may be differentially regulated upon cephalosporin exposure, we analyzed the entire C. difficile transcriptome using RNA-Seq. We found that upon cephradine, ceftazidime, and cefepime treatment, expression was similar to
untreated cells. Cefoxitin-treated cells, however, had a higher number of differentially regulated genes. This might be attributed to the activation of starvation responses due to longer treatment time for cefoxitin-treated cells. Nevertheless, all cephalosporin treatments triggered the upregulation of a putative eterodimeric ABC transporter directly downstream of blaCDD. Further functional analysis of this ABC transporter will be necessary to elucidate its possible role in cephalosporin resistance. Future studies will be geared towards using transposon mutagenesis to elucidate genes that are required for C. difficiles survival upon cephalosporin treatment but that are constitutively expressed regardless of antibiotic exposure.
Swimming Mobility and Chemotaxis of Soil Bacteria
Creators: name: Suttey, Liam
Publisher: name: University of Lincoln
Year: 2023
Subjects: C500 - Microbiology

description: This thesis is comprised of four chapters. The first chapter outlines the background and rationale of this research. Chapter 2 describes and discusses the swimming strategy of five important soil bacteria, and Chapter 3 describes and discusses chemotaxis of the soft rot pathogen Pectobacterium carotovorum. Chapters 2 and 3 are written in the style of scientific papers each containing an abstract, introduction, methods, results and discussion. The final chapter summarises and discusses the findings as a whole.
HPS: a hierarchical Persian stemming method
Creators: name: Rashidi, Ayshe
name: Lighvan, Mina Zolfy
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: In this paper, a novel hierarchical Persian stemming approach based on the Part-Of-Speech of the word in a sentence is presented. The implemented stemmer includes hash tables and several deterministic finite automata in its different levels of hierarchy for removing the prefixes and suffixes of the words. We had two intentions in using hash tables in our method. The first one is that the DFA don't support some special words, so hash table can partly solve the addressed problem. the second goal is to speed up the implemented stemmer with omitting the time that deterministic finite automata need. Because of the hierarchical organization, this method is fast and flexible enough. Our experiments on test sets from Hamshahri collection and security news (istna.ir) show that our method has the average accuracy of 95.37% which is even improved in using the method on a test set with common topics.
description: 10 pages, 6 tables, 2 figures, International Journal on Natural Language Computing (IJNLC), International Journal on Natural Language Computing (IJNLC) Vol. 3, No.1, February 2014
The variable ionized absorber in the Seyfert 2 Mrk 348
Creators: name: Marchese, E.
name: Braito, V.
name: Reeves, J. N
name: Della Ceca, R.
name: Caccianiga, A.
name: Markowitz, A.
name: Risaliti, G.
name: Severgnini, P.
name: Turner, T. J.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present the results of the analysis of the X-ray spectrum of the Seyfert 2 Mrk 348, observed by Suzaku and XMM-Newton. The overall spectrum of Mrk 348 can be described by a primary power law continuum seen through three layers of absorption, of which one is neutral and two are ionised. Comparing Suzaku (2008) and XMM-Newton (2002) observations we find variability of the X-ray spectral curvature. We suggest that the variability can be explained through the change of column density of both the neutral and one of the ionised absorbers, together with a variation of the ionisation level of the same absorber. We thus confirm one of the main features presented in past works, where intrinsic column density variability up to $\sim 10^{23}$~cm$^{-2}$ was observed on time scales of months. We also find that the photon index of the underlying power law continuum ($Γ\sim 1.8$) is in agreement with the previous observations of this Seyfert 2.
description: 13 pages, 6 figures
Front-End CMOS Transimpedance Amplifiers on a Silicon Photomultiplier Resistant to Fast Neutron Fluence
Creators: name: Valles Montenegro, Mario
Publisher: name: University of Nevada, Las Vegas
Year: 2020
Subjects: Electrical and Computer Engineering

description: Radiation hard electronics are indispensable in providing reliable diagnostics in fast radiation detection, which are necessary for new fundamental science research. In the case of radiation detection, transimpedance amplifiers are needed to magnify low photodetector signals to readable levels reliably. This thesis investigates a way to design a transimpedance CMOS-front-end transimpedance amplifier (TIA) as a first stage front-end amplifier. The TIA is to be mounted on silicon photomultiplier (SiPM), as a photodetector in fast neutron scintillation experiments capable of sustaining up to 10^15 n/cm of fast neutrons in the range of 0.1 to 20 MeV. The proposed TIA was designed using "ON's C5 process" (a 600 nm CMOS process). It has a 300 k? gain, a bandwidth minimum of 250 MHz, noise below 5 pA/?Hz, an output swing of 1.52 V, and a power consumption less than 25 mW. The TIA is expected to sustain reliable performance (
Macroscopic Quantum Coherence of the Spin Triplet in the Spin-Ladder Compound Sr14Cu24O41
Creators: name: Lorenzo, Emilio
name: Regnault, L. P.
name: Boullier, Cyrille
name: Martin, Nicolas
name: Moudden, A. H.
name: Vanishri, S.
name: Marin, Christophe
name: Revcolevschi, A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We report the direct observation by inelastic neutron scattering experiments of a spin triplet of magnetic excitations in the response associated with the ladders in the composite cuprate Sr14Cu24O41. This appears as a peak at q_{Q1D}=πand energy Δ_1=32.5 meV, and we conjecture that all the triplets making up this conspicuous peak have the same phase and therefore interpret it as the signature of the occurrence of quantum coherence along the ladder direction between entangled spin pairs. From the comparison with previous neutron and x-ray data, we conclude that the temperature evolution of this mode is driven by the crystallization of holes into a charge density wave in the ladder sublattice
A Comparison of Lateral Cephalometric and Arch Dimension Changes in Patients with Class II Malocclusions Treated With 2-Premolar and 4-Premolar Extraction Patterns
Creators: name: Ven Dange, Melissa Marie
Publisher: name: University of Nevada, Las Vegas
Year: 2020
Subjects: subject: Dentistry
subject: FOS: Clinical medicine

description: The aim of this study is to gather and analyze data representing detailed changes in model and cephalometric variables that will support clinicians in the premolar extraction decision- making process during camouflage treatment of class II dental patients. It is expected that the models, as measured by intra-arch dimensions, overjet, overbite, and mandibular crowding, and cephalometric radiographs, evaluated by their anteroposterior skeletal discrepancy, incisor inclinations, dental and skeletal vertical positions, and soft tissue characteristics, will significantly differ from within the same treatment group, pre-treatment to post-treatment, and between treatment groups. This retrospective study evaluated the model and cephalometric changes in a total of 74 subjects, with 33 subjects in group 1, who received extraction of maxillary first premolars as part of their comprehensive orthodontic treatment, 27 subjects in group 2, who received extraction of maxillary and mandibular first premolars, and 14 subjects in group 3, who received extraction of maxillary first premolars and mandibular second premolars. Intra-arch dimension at the canines, premolars, and molars for both upper and lower arches, overbite, overjet, and mandibular crowding were measured on digital models on OrthoCAD or OrthoAnalyzer software. Digital cephalometric radiographs were traced on Dolphin and analysis included SNA (°), SNB (°), ANB (°), Wits (mm), maxillary incisor inclination (U1-SN) (°), maxillary incisor protrusion (U1-NPog) (mm), mandibular incisor inclination (IMPA) (°), interincisal angle (U1-L1) (°), mandibular plane angle FMA (MP-FH) (°), anterior facial height (mm), posterior facial height (mm), upper lip to E-plane (mm), lower lip to E-plane (mm), nasolabial angle (°), soft tissue convexity (°), upper lip thickness (mm), and lower lip thickness (mm). The varying premolar extraction patterns do have a significant impact on the model and cephalometric characteristics, both within treatment groups and between treatment groups. All three treatments successfully and significantly reduced the amount of overjet and mandibular crowding. Extraction of maxillary and mandibular first premolars allowed a greater amount of mandibular crowding to be relieved. Nonextraction in the lower arch significantly increased the degree of lower incisor flaring. Inclusion of a larger patient population in future studies would allow the collection of more definitive and detailed documentation to identify exactly how removal of different premolars affect skeletal, dental, and soft tissue esthetics.
Revisiting the Relevance of Ethnography: Reflections on Extinct Monsters to Deep Time
Creators: name: Marsh, Diana
Publisher: name: MuseNews
Year: 2023
Subjects: ethnography
dinosaurs
fossils
methods
anthropology
museums
museum anthropology
Deep Time
Smithsonian
National Museum of Natural History
natural history
politics
exhibitions
facts
infodemic

description: This short piece reflects on the book Extinct Monsters to Deep Time: Conflict, Compromise, and the Making of Smithsonian's Fossil Halls as it is released in paperback. It argues that ethnography offers an important perspective on the power dynamics of institutions, as well as how museums maintain trust via the negotiation process of creating exhibitions.
Disrupting the Traditional Dating Discourse: Expanding the Romantic Relationship Narrative
Creators: name: Wolfe, Brooke
Publisher: name: University of Nevada, Las Vegas
Year: 2020
Subjects: Communication

description: Dating to find a lifelong partner is a priority for many young adults, as the process exists on a socially constructed timeline (Baxter & Braithwaite, 2002). Although, like many other experiences in the public sphere, single women are adversely constrained by societal expectations in regard to their sexuality and use of agency (Dunn & Vik, 2014). This study explores womens dating behaviors in cooperation with societal messages that are navigated as a necessary step in finding a romantic partner. With the framework of Relational Dialectics, the study examines how participants learn the rules of dating, in what ways dating behavior is impacted by the recognition (implicit or explicit) of the dialectical tensions present in dating discourses, and how women navigate these tensions through the potential found in the expansion of their narrative. By examining womens accounts of how they navigate dominant dating discourses, the research study illuminates what tensions women experience when dating and how they resist those discursive tensions to create a more equitable and safe dating process for women.
Estimation of the TeV gamma-ray duty cycle of Mrk 421 with the Milagro observatory
Creators: name: Patricelli, B.
name: González, M. M.
name: Fraija, N.
name: Marinelli, A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Markarian 421 (Mrk 421) is one the brightest and closest (z=0.031) blazars known (de Vaucouleurs et al 1991). It is also one of the fastest varying TeV $γ$-ray sources, with a flaring activity on time scales as short as tens of minutes. The activity of Mrk 421 at different frequencies may reflect the radiation mechanisms involved. Tluczykont et al. (2007) estimated the TeV activity of Mrk 421 through calculating the fraction of time spent in flaring states at TeV energies (TeV duty cycle) by using data from several imaging atmospheric Cherenkov telescopes (IACTs). Since IACT observations are biased towards high flux states they overestimated the TeV duty cycle of Mrk 421. Here we propose an alternative approach to calculate the TeV duty cycle of Mrk 421 that takes advantage of the continuous monitoring of the source by the Milagro experiment, a water Cherenkov detector sensitive to primary $γ$-rays between 100 GeV and 100 TeV. We present our estimation of the TeV - duty cycle and study its robustness.
description: 4 pages, 4 figures, in the Proceedings of the RICAP-13 meeting
Dark Tetrad Responses to Moral Dilemmas
Creators: name: Wrenn, Kayli
Publisher: name: University of Nevada, Las Vegas
Year: 2020
Subjects: subject: Psychology
subject: FOS: Psychology

description: The Dark Tetrad consists of four socially malevolent personality traits: psychopathy, sadism, narcissism, and Machiavellianism. The current study assessed the relationships among each dimension of the Dark Tetrad and moral decision making using sacrificial moral dilemma vignettes. Participants (n = 212 undergraduates) completed two measures of each of the four Dark Tetrad constructs then read a series of 16 sacrificial moral dilemma vignettes. These dilemmas manipulated whether the participant would personally perform the sacrifice and described either the disgusting or sad emotional consequences of the sacrifice. After each vignette, participants rated the moral rightness/wrongness, moral permissibility, and behavioral intention to sacrifice 1 person in order to save 5 people. Participants ratings were not affected by the scenarios emotion, but they were all lower in scenarios involving personal versus impersonal sacrifices. Machiavellianism correlated with rating the sacrifice as morally permissible, r(212) = .15, p = .030. Psychopathy was additionally associated with being more willing to sacrifice someone, r(212) = .14, p = .040. Surprisingly, individuals who scored high in grandiose narcissism were more willing to sacrifice someone after vignettes that elicited disgust, r(212) = .14, p = .046, but not after vignettes that elicited sadness, r(212) = .06, p = .380, F(1, 210) = 3.98, p = .047. Sadism had no discernible relationships with any ratings. Overall, the results from this study indicate that the Dark Tetrad may be associated with grossly intact but more flexible moral reasoning and behavior.
“HAS ANYONE SEEN THE EDITOR?” AN EVALUATION OF EDITORIAL LEADERSHIP IN THE UK REGIONAL PRESS
Creators: name: Geere, Alan
Publisher: name: University of Lincoln
Year: 2023
Subjects: P500 - Journalism
V500 - Philosophy

description: This thesis seeks to understand and explain the role of editors in the UK regional press and sets out to determine whether ‘editorial leadership’ is still a valid term following changes brought about by technological advancements and economic necessities. The research concludes that editors are still an effective and valued part of the media machinery. However, they are now expected to be business all-rounders, taking greater responsibility for commercial performance, maybe at the expense of direct involvement with undertaking any journalism, which has become a secondary function. They have an appreciation of other wider business functions, such as human resources and finance, but are able to increasingly rely on professional support. Editorial leaders play a key role in the dissemination of journalism and its wider role in the democratic distribution of news and information. This study provides indications of where editorial leadership now sits from both an academic and industry perspective. Primary material consists of existing publications by the researcher himself, presented and reflected upon within a reflexive theoretical framework. Alongside this approach, original interviews were conducted with editorial leaders by way of top-up research. A limited number of studies have touched on the role of leadership in the newsroom but the contribution of editorial leadership has received little attention within the academic community. Because the role continues to evolve, the position of ‘leadership’ is pivotal in the development of journalism and deserves greater attention from scholars, who have so far been reticent to engage with the role and its responsibilities. The findings can contribute to a better understanding of editorial leadership and afford a perspective on how the role could develop as the newspaper landscape continues to evolve.
A computational study of nucleosomal binding and alternative isoforms of human transcription factors
Creators: name: Sidorov, Sviatoslav
Publisher: name: Imperial College London
Year: 2022

description: Eukaryotic transcription factors (TFs) are proteins that bind short DNA motifs and regulate gene transcription. Because genomic DNA is organised into nucleosomes via binding histone octamers, TFs compete with histones for binding DNA. Also, the functions of a TF are mainly defined by its domains; therefore, a TF gene can vary the characteristics of its protein product through the expression of alternative isoforms with different domains. However, the mechanisms of TF-nucleosome interactions and the functional importance of alternative TF isoforms are not fully understood. Here, I address these two problems computationally via the integrative analysis of publicly available in vivo human sequencing data. First, I evaluated a novel, gyre-spanning, mode of TF-nucleosome binding proposed recently by another lab based on in vitro evidence. Analysing the nucleosome occupancy and TF binding in the human genome, I found no evidence of such binding and concluded that it must be extremely rare, if at all present. Secondly, I studied the alternative isoforms of human TFs genome-wide. I found that independently of the gene length and the number of exons, TF genes more efficiently sample the set of possible alternative isoforms than non-TF genes, suggesting the particular importance of alternative isoforms for TFs. Also, I found that TF isoforms without a DNA-binding domain (DBD) are produced by almost a third of all human TFs, tend to be tissue-specific and likely reverse the transcription regulation effect of DBD-containing isoforms. Moreover, I demonstrated that the switches of the highest-expressed TF isoforms across human adult tissues may represent a widespread functional mechanism. Finally, I collected a compendium of human TFs with experimentally characterised alternative isoforms which will hopefully serve as a resource for future studies. In summary, my analysis further developed the fundamental knowledge about the TF-nucleosome interactions and the alternative isoforms of TFs in humans.
On the Eulerian Large Eddy Simulation of disperse phase flows: an asymptotic preserving scheme for small Stokes number flows
Creators: name: Chalons, Christophe
name: Massot, Marc
name: Vié, Aymeric
Publisher: name: arXiv
Year: 2014
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: In the present work, the Eulerian Large Eddy Simulation of dilute disperse phase flows is investigated. By highlighting the main advantages and drawbacks of the available approaches in the literature, a choice is made in terms of modelling: a Fokker-Planck-like filtered kinetic equation proposed by Zaichik et al. 2009 and a Kinetic-Based Moment Method (KBMM) based on a Gaussian closure for the NDF proposed by Vie et al. 2014. The resulting Euler-like system of equations is able to reproduce the dynamics of particles for small to moderate Stokes number flows, given a LES model for the gaseous phase, and is representative of the generic difficulties of such models. Indeed, it encounters strong constraints in terms of numerics in the small Stokes number limit, which can lead to a degeneracy of the accuracy of standard numerical methods. These constraints are: 1/as the resulting sound speed is inversely proportional to the Stokes number, it is highly CFL-constraining, and 2/the system tends to an advection-diffusion limit equation on the number density that has to be properly approximated by the designed scheme used for the whole range of Stokes numbers. Then, the present work proposes a numerical scheme that is able to handle both. Relying on the ideas introduced in a different context by Chalons et al. 2013: a Lagrange-Projection, a relaxation formulation and a HLLC scheme with source terms, we extend the approach to a singular flux as well as properly handle the energy equation. The final scheme is proven to be Asymptotic-Preserving on 1D cases comparing to either converged or analytical solutions and can easily be extended to multidimensional configurations, thus setting the path for realistic applications.
Detection of SNPS Associated with Bone Loss Rate by Using Machine Learning Approaches
Creators: name: Yaganapu, Avinash
Publisher: name: University of Nevada, Las Vegas
Year: 2020
Subjects: Computer Sciences

description: Osteoporosis is one of the most common diseases seen in postmenopausal women, it decreases the bone density and quality, and later causes bone loss. Generally, bone loss occurs when bone losses its content and become porous: a sponge like substance. In most Genome Wide Association Studies (GWAS), researchers perform experiments with genomic data that contains some millions of numbers of single nucleotide polymorphisms (SNPs) and checks their association with the trait or disease. In this thesis, we performed two separate analyses with 2207 (of bone loss and bone gain) and 645 (of bone loss) instances separately. For predicting the SNPs associated with bone loss rate (a regression problem), we considered both genotype and phenotype data from Womens Health Initiative (WHI) and, performed data processing and analysis as described further. We started with a metadata analysis on the genomic dataset and imputed the datasets with 2207 and 645 instances separately. Next, we performed the linear association analysis between the SNPs and the bone loss rate from phenotype data, and later we applied LASSO regression with narrow sense heritability using PLINK, which resulted in two sets of SNPs: 680 SNPs for 2207 instances and, 308 SNPs for 645 instances. Lastly, we mixed the phenotype data with SNPs based on Subject-ID for both analyses, and then we trained machine learning models including ridge regression (RR), support vector machine (SVM), random forest (RF), and multi-layer perceptron (MLP), on the two datasets and evaluated the mean squared error (MSE) and R^2 for each model. The RR model gave the best performance for 680 SNPs than the other models with an R^2 of 0.858 for training data and R^2 of 0.719 for testing data, whereas for 308 SNPs, the MLP gave the best performance than the other models with an R^2 of 0.982 for training data and R^2 of 0.894 for testing data.
The population genomics of Saccharomyces cerevisiae and Saccharomyces uvarum in New Zealand vineyards
Creators: name: Higgins, Peter
Publisher: name: University of Lincoln
Year: 2023
Subjects: C100 - Biology

description: The Saccharomyces cladeis a taxon of yeast, both wild and domesticated, which are capable of producing ethanol via fermentation, and have been utilised for this by humanity. This thesis uses whole-genome sequence data from over 200 novel isolates of two species – the predominantly domesticated Saccharomyces cerevisiae, and the partially domesticated Saccharomyces uvarum – from across New Zealand to investigate population structure and genomic signals of evolution after range expansion. Through a wide range of exploratory analyses, such as phylogenies, population structural analyses, and population genomics, the populations of these two species within New Zealand are characterized and their relation to their respective global populations evaluated. Genomic signatures of evolution are identified, and their possible adaptive value evaluated. Further areas of interest are highlighted, including strains of unusual ancestry and genes undergoing possible adaptive selection. Interspecies introgressions from the related Saccharomyces eubayanus are detected within the S. uvarum population in New Zealand, and the implications of such hybrid populations to species delimitation within the Saccharomyces are discussed in detail. The similarities and differences between the S. uvarum and S. cerevisiae populations are evaluated and related to the life histories of these species and the Saccharomyces as a whole to gain a deeper understanding of the genomic impacts of human-aided microbial dispersion.
The Manorial Documents Register Project for Lincolnshire: An Analysis of the Thirty-Year Project
Creators: name: Elliott, Bethany
Publisher: name: University of Lincoln
Year: 2023
Subjects: V147 - Modern history 1950-1999
V148 - Modern history 2000-2099
V210 - British history

description: In 1992, a project was started to digitise the Manorial Documents Register (MDR) and to make this resource more widely available. The project has been completed county by county and with only two counties left to complete their projects, it is expected to conclude in 2022, thirty years after the beginning of the digitisation project and 100 years after the Law of Property Act (1922). This PhD by Practice follows the completion of the Lincolnshire Project, with reflection on the methods and the challenges associated with this project, displayed in the creation of a Reflective Journal. This journal is used within the thesis as a primary source, to highlight the practice and explain decisions made throughout the three-year project. The thesis also examines how the project to digitise the MDR has evolved over its thirty-year timeline, questioning whether later projects were influenced by those before. To do this a small sample of previous county projects have been examined. Three counties were selected for analysis, each from approximately eight to ten years apart. This analysis highlights the differences between the projects and the unique challenges faced by each, but also the elements which remained the same and were standardised throughout. This analysis is used to form conclusions on the place of the MDR as a digitised search-tool in the present day, and how the MDR Project has been able to successfully conclude after a thirty-year timeline. As this thesis has been completed as part of a PhD by Practice, it also examines the appropriateness of research by practice as a means of interrogating the development of differing approaches over time to the MDR project. Various models for Practice as Research are analysed and used within this thesis, to outline how they can fit with the analysis of archival practice and as such, the thesis also provides a framework which can contribute to scholarship in future research by practice.
Effective Particle Methods for Fisher-Kolmogorov Equations: Theory and Applications to Brain Tumor Dynamics
Creators: name: Belmonte-Beitia, Juan
name: Calvo, Gabriel F.
name: Perez-Garcia, Victor M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantitative Methods (q-bio.QM)
subject: FOS: Biological sciences

description: Extended systems governed by partial differential equations can, under suitable conditions, be approximated by means of sets of ordinary differential equations for global quantities capturing the essential features of the systems dynamics. Here we obtain a small number of effective equations describing the dynamics of single-front and localized solutions of Fisher-Kolmogorov type equations. These solutions are parametrized by means of a minimal set of time-dependent quantities for which ordinary differential equations ruling their dynamics are found. A comparison of the finite dimensional equations and the dynamics of the full partial differential equation is made showing a very good quantitative agreement with the dynamics of the partial differential equation. We also discuss some implications of our findings for the understanding of the growth progression of certain types of primary brain tumors and discuss possible extensions of our results to related equations arising in different modelling scenarios.
Extension of the correlated Gaussian hyperspherical method to more particles and dimensions
Creators: name: Daily, Kevin M.
name: Greene, Chris H.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The solution of the hyperangular Schrödinger equation for few-body systems using a basis of explicitly correlated Gaussians remains numerically challenging. This is in part due to the number of basis functions needed as the system size grows, but also due to the fact that the number of numerical integrations increases with the number of hyperangular degrees of freedom. This paper shows that the latter challenge is no more. Using a delta function to fix the hyperradius $R$, all matrix element calculations are reduced to a single numerical integration regardless of system size $n$ or number of dimensions $d$. In the special case of $d$ an even number, the matrix elements of the noninteracting system are fully analytical. We demonstrate the use of the new matrix elements for the 3-, 4-, and 5-body electron-positron systems with zero total angular momentum $L$, positive parity $π$, and varied spins $S_+$ and $S_-$.
description: 8 pages, 4 figures
Design and Synthesis of Ultra Low Energy Spin-Memristor Threshold Logic
Creators: name: Fan, Deliang
name: Sharad, Mrigank
name: Roy, Kaushik
Publisher: name: arXiv
Year: 2014
Subjects: subject: Emerging Technologies (cs.ET)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: A threshold logic gate (TLG) performs weighted sum of multiple inputs and compares the sum with a threshold. We propose Spin-Memeristor Threshold Logic (SMTL) gates, which employ memristive cross-bar array (MCA) to perform current-mode summation of binary inputs, whereas, the low-voltage fast-switching spintronic threshold devices (STD) carry out the threshold operation in an energy efficient manner. Field programmable SMTL gate arrays can operate at a small terminal voltage of ~50mV, resulting in ultra-low power consumption in gates as well as programmable interconnect networks. We evaluate the performance of SMTL using threshold logic synthesis. Results for common benchmarks show that SMTL based programmable logic hardware can be more than 100x energy efficient than state of the art CMOS FPGA.
description: this paper is submitted to IEEE Transactions on Nanotechnology. It is currently under review
Modelling of Walking Humanoid Robot With Capability of Floor Detection and Dynamic Balancing Using Colored Petri Net
Creators: name: Pashazadeh, Saeid
name: Saeedvand, Saeed
Publisher: name: arXiv
Year: 2014
Subjects: subject: Robotics (cs.RO)
subject: FOS: Computer and information sciences

description: Most humanoid robots have highly complicated structure and design of robots that are very similar to human is extremely difficult. In this paper, modelling of a general and comprehensive algorithm for control of humanoid robots is presented using Colored Petri Nets. For keeping dynamic balance of the robot, combination of Gyroscope and Accelerometer sensors are used in algorithm. Image processing is used to identify two fundamental issues: first, detection of target or an object which robot must follow; second, detecting surface of the ground so that walking robot could maintain its balance just like a human and shows its best performance. Presented model gives high-level view of humanoid robot's operations.
description: 10 Pages, 5 Figures
The lowest resonance in QCD from low--energy data
Creators: name: Ametller, L.
name: Talavera, P.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We show that a generalization of $su(2)$ Chiral Perturbation Theory, including a perturbative singlet scalar field, converges faster towards the physical value of sensible low--energy observables. The physical mass and width of the scalar particle are obtained through a simultaneous analysis of the pion radius and the gamma gamma -> pi^0 pi^0 cross-section. Both values are statistically consistent with the ones obtained by using Roy equations in pi-pi scattering. In addition we find indications that the photon-photon-singlet coupling is quite small.
description: pdfLatex 15 pages, 3 figures
The FAIR Hourglass: Championing Data beyond FAIR - Decentralized Persistent Identifiers Reproducible Research Objects
Creators: name: Van Winkle, Erik
Publisher: name: Zenodo
Year: 2023

description: In this presentation, the concept of a decentralized persistent identifier (dPID) is introduced at a high level. dPIDs are then demo'd through the lens of DeSci Nodes, the interface for open state reproducible research objects. Finally, these technologies are framed through the lens of the FAIR hourglass as a framework for collaboration between FAIR Service Providers.
Frequency adjustment and synchrony in networks of delayed pulse coupled oscillators
Creators: name: Nishimura, Joel
Publisher: name: arXiv
Year: 2014
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: We introduce a system of pulse coupled oscillators that can change both their phases and frequencies; and prove that when there is a separation of time scales between phase and frequency adjustment the system converges to exact synchrony on strongly connected graphs with time delays. The analysis involves decomposing the network into a forest of tree-like structures that capture causality. Furthermore, we provide a lower bound for the size of the basin of attraction with immediate implications for empirical networks and random graph models. These results provide a robust method of sensor net synchronization as well as demonstrate a new avenue of possible pulse coupled oscillator research.
description: 5 pages, 2 figures, for submission to PRL
From Speech to Action - Exploring Hate Speech Origins, Impact, and Interventions from Multidisciplinary Perspectives
Creators: name: Moumita, Barman
name: Y. Laxmi, Samhita
name: Rushda, Babukhan
Publisher: name: Zenodo
Year: 2023

description: Hate speech is an intricate and multifaceted reality that poses significant risks to democratic nations. Its consequences extend far beyond mere words, leading to physical harm, social isolation, heightened tension, increased anxiety, and depression, among other detrimental effects. Understanding the origins, patterns, and impact of hate speech is crucial for developing effective interventions and policies to combat it. This is particularly relevant in today's context, where the proliferation of social media platforms has facilitated the rapid dissemination and amplification of hate speech.
BYOD Introduction & FAIR Game
Creators: name: Carta, Claudio
name: Roos, Marco
name: dos Santos Vieira, Bruna
name: Kaliyaperumal, Rajaram
name: Bernabe, Cesar Henrique
name: Coelho de Oliveira Henriques, Ines
name: Zhang, Shuxin
name: Benis, Nirupama
name: van der Velde, Joeri
name: Cámara Ballesteros, Alberto
name: Kersloot, Martijn
Publisher: name: Zenodo
Year: 2021
Subjects: FAIR Game

description: A presentation about the FAIR game with game instructions
The 1st online Edition of the FAIR Data Game during the International Summer School on Rare Disease Registries & FAIRification of Data in Rome
Creators: name: Carta, Claudio
name: dos Santos Vieira, Bruna
name: Kaliyaperumal, Rajaram
name: Kersloot, Martijn
name: Jacobsen, Annika
name: Cornet, Ronald
name: Wilkinson, Mark
name: Hanauer, Marc
name: Benis, Nirupama
name: Cellai, Laura Lee
name: Bernabé, Cesar Henrique
name: Taruscio, Domenica
name: Roos, Marco
Publisher: name: Zenodo
Year: 2022
Subjects: FAIR data principles

description: Poster for the FAIR Game - Gaming to increase the understanding of FAIR data