cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Sedimentation dynamics of passive particles in dilute bacterial suspensions: emergence of bioconvection
Creators: name: Maldonado, Bryan O. Torres
name: Pradeep, Shravan
name: Ran, Ranjiangshang
name: Jerolmack, Douglas
name: Arratia, Paulo E.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Microorganisms are ubiquitous in nature and technology. They inhabit diverse environments ranging from small river tributaries and lakes to oceans, as well as wastewater treatment plants and food manufacturing. In many of these environments, microorganisms coexist with settling particles. Here, we investigate the effects of microbial activity (swimming \textit{E. coli}) on the settling dynamics of passive colloidal particles using particle tracking methods. Our results reveal the existence of two distinct regimes in the correlation length scale ($L_u$) and the effective diffusivity of the colloidal particles ($D_{e\!f\!f}$), with increasing bacterial concentration ($ϕ_b$). At low $ϕ_b$, the parameters $L_u$ and $D_{e\!f\!f}$ monotonically increases with increasing $ϕ_b$. Beyond a critical $ϕ_b$, second regime is found in which both $D_{e\!f\!f}$ and $L_u$ are independent of $ϕ_b$. We demonstrate that the transition between these regimes is characterized by the emergence of bioconvection. We use experimentally-measured particle-scale quantities ($L_u$, $D_{e\!f\!f}$) to predict the critical bacterial concentration for the diffusion-bioconvection transition.
Finite temperature quantum field theory in the heat kernel method
Creators: name: Gusev, Yuri V.
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 81T28, 82B30, 51P05, 58J40

description: The trace of the heat kernel in a (D+1)-dimensional Euclidean spacetime (integer D > 1) is used to derive the free energy in finite temperature field theory. The spacetime presents a D-dimensional compact space (domain) with a (D-1)-dimensional boundary, and a closed dimension, whose volume is proportional the Planck's inverse temperature. The thermal sum appears due to topology of the closed Euclidean time. The obtained free energy in (3+1) and (2+1) dimensions contain two contributions defined by the volume of a domain and by the volume of the domain's boundary. This functional is finite and valid for arbitrary values of the Planck's inverse temperature. The absolute zero of thermodynamic temperature is forbidden topologically, and no universal low temperature asymptotics of the free energy can exist.
description: 20 pages
A revision of the subtract-with-borrow random number generators
Creators: name: Sibidanov, Alexei
Publisher: name: arXiv
Year: 2017
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Mathematical Software (cs.MS)
subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: The most popular and widely used subtract-with-borrow generator, also known as RANLUX, is reimplemented as a linear congruential generator using large integer arithmetic with the modulus size of 576 bits. Modern computers, as well as the specific structure of the modulus inferred from RANLUX, allow for the development of a fast modular multiplication -- the core of the procedure. This was previously believed to be slow and have too high cost in terms of computing resources. Our tests show a significant gain in generation speed which is comparable with other fast, high quality random number generators. An additional feature is the fast skipping of generator states leading to a seeding scheme which guarantees the uniqueness of random number sequences.
description: 13 pages
Interpretable deep learning models for the inference and classification of LHC data
Creators: name: Ngairangbam, Vishal S.
name: Spannowsky, Michael
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The Shower Deconstruction methodology is pivotal in distinguishing signal and background jets, leveraging the detailed information from perturbative parton showers. Rooted in the Neyman-Pearson lemma, this method is theoretically designed to differentiate between signal and background processes optimally in high-energy physics experiments. A key challenge, however, arises from the combinatorial growth associated with increasing jet constituents, which hampers its computational feasibility. We address this by demonstrating that the likelihood derived from comparing the most probable signal and background shower histories is equally effective for discrimination as the conventional approach of summing over all potential histories in top quark versus Quantum Chromodynamics (QCD) scenarios. We propose a novel approach by conceptualising the identification of the most probable shower history as a Markov Decision Process (MDP). Utilising a sophisticated modular point-transformer architecture, our method efficiently learns the optimal policy for this task. The developed neural agent excels in constructing the most likely shower history and demonstrates robust generalisation capabilities on unencountered test data. Remarkably, our approach mitigates the complexity inherent in the inference process, achieving a linear scaling relationship with the number of jet constituents. This offers a computationally viable and theoretically sound method for signal-background differentiation, paving the way for more effective data analysis in particle physics.
description: Extended discussion in section 2.1. Results unchanged. Matches journal version
An exploration of the voices of a new university curriculum in Hong Kong: implications for the teaching of English for academic purposes
Creators: name: Legg, Miranda
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Wide-ranging curriculum reform in Hong Kong has resulted in one large-scale, research-led, English as a medium of instruction university implementing a new Core Curriculum. This curriculum is currently taken by all first and second-year students, regardless of their chosen major. This research aims to identify the academic English language demands this new Curriculum places on students, in order to provide focused EAP support. A mixed method, multi-perspectival methodology was used. Firstly, the institutional voice was explored through an analysis of institutionally-endorsed course descriptions. The assessed voice was explored through a discourse analysis of 13 A-grade argumentative essays using tools from Systemic Functional Linguistics. Thirdly, the voice of experience was explored through the analysis of two case studies documenting two first-year students’ experience of acculturation as they negotiated the new Curriculum. The analysis of the institutional voice found that certain types of learning experiences and knowledge (e.g. the expression of a critical voice) were valued by the institution. The analysis of the assessed voice found that patterns of Periodicity (e.g. the construction of conceptual taxonomies), Engagement (e.g. patterns of alignment between reader and writer) and Attitude (e.g. discipline-specific patterns of evaluation) were found to combine to express an academic voice. Overall, three voices were identified in the essays – a Student, Science and Humanities Voice. Finally, the analysis of the voice of experience found that students struggled with certain aspects of academic writing and as a result, they needed to turn to an ‘underground’ network for help. This research makes a unique contribution to an understanding of institutional values, how these values are instantiated in assessed texts and how students experience these institutional values while completing gate-keeping assessments. Through a combination of all perspectives, an understanding of what language support should be given to students to help them learn effectively is gained.
Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation
Creators: name: Jonkhout, Nicky
name: Cruciani, Sonia
name: Vieira, Helaine Graziele Santos
name: Tran, Julia
name: Liu, Huanle
name: Liu, Ganqiang
name: Pickford, Russell
name: Kaczorowski, Dominik
name: Franco, Gloria R.
name: Vauti, Franz
name: Camacho, Noelia
name: Abedini, Seyedeh Sedigheh
name: Najmabadi, Hossein
name: de Pouplana, Lluís Ribas
name: Christ, Daniel
name: Schonrock, Nicole
name: Mattick, John S.
name: Novoa, Eva Maria
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Biological Sciences not elsewhere classified

description: RNA modifications are dynamic chemical entities that expand the RNA lexicon and regulate RNA fate. The most abundant modification present in mRNAs, N6-methyladenosine (m6A), has been implicated in neurogenesis and memory formation. However, whether additional RNA modifications may be playing a role in neuronal functions and in response to environmental queues is largely unknown. Here we characterize the biochemical function and cellular dynamics of two human RNA methyltransferases previously associated with neurological dysfunction, TRMT1 and its homolog, TRMT1-like (TRMT1L). Using a combination of next-generation sequencing, LC-MS/MS, patient-derived cell lines and knockout mouse models, we confirm the previously reported dimethylguanosine (m2,2G) activity of TRMT1 in tRNAs, as well as reveal that TRMT1L, whose activity was unknown, is responsible for methylating a subset of cytosolic tRNAAla(AGC) isodecoders at position 26. Using a cellular in vitro model that mimics neuronal activation and long term potentiation, we find that both TRMT1 and TRMT1L change their subcellular localization upon neuronal activation. Specifically, we observe a major subcellular relocalization from mitochondria and other cytoplasmic domains (TRMT1) and nucleoli (TRMT1L) to different small punctate compartments in the nucleus, which are as yet uncharacterized. This phenomenon does not occur upon heat shock, suggesting that the relocalization of TRMT1 and TRMT1L is not a general reaction to stress, but rather a specific response to neuronal activation. Our results suggest that subcellular relocalization of RNA modification enzymes may play a role in neuronal plasticity and transmission of information, presumably by addressing new targets.
Angular Momentum Content in Gas Rich Dwarf Galaxies
Creators: name: Chowdhury, Aditya
name: Chengalur, Jayaram N.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We derive the specific baryonic angular momentum of five gas rich dwarf galaxies from HI kinematics complemented by stellar mass profiles. Since the gas mass of these galaxies is much larger than the stellar mass, the angular momentum can be determined with relatively little uncertainty arising from the uncertainties in the stellar mass to light ratio. We compare the relation between the specific baryonic angular momentum (j) and the total baryonic mass (M) for these galaxies with that found for spiral galaxies. Our combined sample explores the j-M plane over 3 orders of magnitude in baryon mass. We find that our sample dwarf have significantly higher specific angular momentum than expected from the relation found for spiral galaxies. The probability that these gas rich dwarf galaxies follow the same relation as spirals is found to be $<10^{-6}$. This implies a difference in the evolution of angular momentum in these galaxies compared to larger ones. We suggest that this difference could arise due to one or more of the following: a lower baryon fraction in dwarf galaxies, particularly that arising from preferential outflows low angular momentum gas as found in high resolution simulations that include baryonic feedback; "cold mode" anisotropic accretion from cosmic filaments. Our work reinforces the importance of the j-M plane in understanding the evolution of galaxies.
description: 10 Pages, 7 figures. Accepted for publication in MNRAS
Distributed Ranges: A Model for Distributed Data Structures, Algorithms, and Views
Creators: name: Brock, Benjamin
name: Cohn, Robert
name: Bakshi, Suyash
name: Karna, Tuomas
name: Kim, Jeongnim
name: Nowak, Mateusz
name: Ślusarczyk, Łukasz
name: Stefanski, Kacper
name: Mattson, Timothy G.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: Data structures and algorithms are essential building blocks for programs, and \emph{distributed data structures}, which automatically partition data across multiple memory locales, are essential to writing high-level parallel programs. While many projects have designed and implemented C++ distributed data structures and algorithms, there has not been widespread adoption of an interoperable model allowing algorithms and data structures from different libraries to work together. This paper introduces distributed ranges, which is a model for building generic data structures, views, and algorithms. A distributed range extends a C++ range, which is an iterable sequence of values, with a concept of segmentation, thus exposing how the distributed range is partitioned over multiple memory locales. Distributed data structures provide this distributed range interface, which allows them to be used with a collection of generic algorithms implemented using the distributed range interface. The modular nature of the model allows for the straightforward implementation of \textit{distributed views}, which are lightweight objects that provide a lazily evaluated view of another range. Views can be composed together recursively and combined with algorithms to implement computational kernels using efficient, flexible, and high-level standard C++ primitives. We evaluate the distributed ranges model by implementing a set of standard concepts and views as well as two execution runtimes, a multi-node, MPI-based runtime and a single-process, multi-GPU runtime. We demonstrate that high-level algorithms implemented using generic, high-level distributed ranges can achieve performance competitive with highly-tuned, expert-written code.
description: To appear in ACM International Conference on Supercomputing (ICS) 2024
Multiparty Session Types, Beyond Duality (Abstract)
Creators: name: Scalas, Alceste
name: Yoshida, Nobuko
Publisher: name: arXiv
Year: 2017
Subjects: subject: Programming Languages (cs.PL)
subject: FOS: Computer and information sciences
subject: D.2.4; D.3.1; D.3.2; F.3.1; F.3.2

description: Multiparty Session Types (MPST) are a well-established typing discipline for message-passing processes interacting on sessions involving two or more participants. Session typing can ensure desirable properties: absence of communication errors and deadlocks, and protocol conformance. However, existing MPST works provide a subject reduction result that is arguably (and sometimes, surprisingly) restrictive: it only holds for typing contexts with strong duality constraints on the interactions between pairs of participants. Consequently, many "intuitively correct" examples cannot be typed and/or cannot be proved type-safe. We illustrate some of these examples, and discuss the reason for these limitations. Then, we outline a novel MPST typing system that removes these restrictions.
description: In Proceedings PLACES 2017, arXiv:1704.02418
Additional file 1: of Purinergic receptors P2Y12R and P2X7R: potential targets for PET imaging of microglia phenotypes in multiple sclerosis
Creators: name: Beaino, Wissam
name: Bieneke Janssen
name: Kooij, Gijs
name: Pol, Susanne Van Der
name: B. Van Het Hof
name: Horssen, Jack Van
name: Windhorst, Albert
name: Vries, Helga De
Publisher: name: figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: Computational Biology

description: Includes supplementary figures and tables to support the data presented in the main manuscript. (DOCX 14306Â kb)
Detection of incoherent broadband terahertz light using antenna-coupled high-electron-mobility field-effect transistors
Creators: name: Qin, Hua
name: Li, Xiang
name: Sun, Jiandong
name: Zhang, Zhipeng
name: Sun, Yunfei
name: Yu, Yao
name: Li, Xingxin
name: Luo, Muchang
Publisher: name: arXiv
Year: 2017
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The sensitivity of direct terahertz detectors based on self-mixing of terahertz electromagnetic wave in field-effect transistors is being improved with noise-equivalent power close to that of Schottky-barrier-diode detectors. Here we report such detectors based on AlGaN/GaN two-dimensional electron gas at 77~K are able to sense broadband and incoherent terahertz radiation. The measured photocurrent as a function of the gate voltage agrees well with the self-mixing model and the spectral response is mainly determined by the antenna. A Fourier-transform spectrometer equipped with detectors designed for 340, 650 and 900~GHz bands allows for terahertz spectroscopy in a frequency range from 0.1 to 2.0~THz. The 900~GHz detector at 77~K offers an optical sensitivity about $1~\mathrm{pW/\sqrt{Hz}}$ being comparable to a commercial silicon bolometer at 4.2~K. By further improving the sensitivity, room-temperature detectors would find applications in active/passive terahertz imaging and terahertz spectroscopy.
description: 4.5 pages, 5 figures
Synthesis and evaluation of inhibitory activity in vitro of dihydrostilbenes against human neutrophil elastases
Creators: name: Huang, Guo-Li
name: Liu, Bo
name: Tian, Xing-Jun
name: Chen, Ye-Gao
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Mental Health
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences

description: Twelve dihydrostilbenes (including five new analogues) were prepared by the Witting-Hornor reaction from appropriate aromatic aldehydes and phosphonate esters, followed by hydrogenation in five steps. The in vitro inhibition activity against human neutrophil elastase (HNE) of these dihydrostilbenes was evaluated, and three 1,2-dihydroxylated dihydrostilbenes (6b, 6j, and 6l) exhibited stronger inhibitory activity against HNE than other analogues.
Feasibility studies of a novel extrusion-roll-bonding technology
Creators: name: Tan, Zinong
Publisher: name: Imperial College London
Year: 2022

description: In the aerospace industry, aluminium rib-structural integral panels are one of the parts with high structural efficiency on aircraft and used for the fuselage, wings, and floors. These aluminium airframe components constitute 70% weight of civil aircraft, such as the Boeing 777. These rib-structural integral panels are currently produced by machining accounting for > 90% wastage of materials. Thus, developing a new high-efficiency cost-effective manufacturing technique for these airframe panels is of a great commercial incentive. This study aims to propose, design, manufacture and understand a novel extrusion-roll-bonding (ERB) technology, which involves the extrusion and roll bonding of layer-by-layer aluminium strips. During the rolling process, solid-state pressure bonding occurs between aluminium strips. High bonding quality is ensured by effectively breaking the original oxide film through the extrusion and rolling the extruded strips within an oxygen-free environment. Detailed equipment designs are conducted, considering operating temperature, extrusion geometry, roller dimension, and maximum extrusion and roll bonding forces. A pilot ERB test equipment satisfying all design specifications is built and used to produce ERBed, AA1060 Al-alloy parts. To understand the effect of processing parameters on ERB bonding mechanisms, systematic investigations on the variation of rolling thickness reduction, temperature, extrusion speed, roller diameter and heat treatment are conducted. How these variables affect the bonding strength and interface microstructure are revealed. The bonding qualities are evaluated through miniature tensile tests for strength and ductility, while the interface microstructure is characterised using an optical microscope (OM), scanning electron microscope (SEM), and electron backscatter diffraction (EBSD). The feasible ERB processing parameters are determined to enable the extrusion layers to be fully bonded. This research has confirmed that the innovative ERB process is feasible and has a high potential to efficiently and cost-effectively produce aluminium rib-structural integral panels.
A quantum hybrid with a thin antenna at the vertex of a wedge
Creators: name: Carlone, R.
name: Posilicano, A.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mathematical Physics (math-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences
subject: 81V99, 35J10, 81Q35

description: We study the spectrum, resonances and scattering matrix of a quantum hamiltonian on a "hybrid surface" consisting of a half-line attached by its endpoint to the vertex of a concave planar wedge. At the boundary of the wedge, outside the vertex, Dirichlet boundary are imposed. The system is tunable by varying the measure of the angle at the vertex.
description: 8 pages, 3 figures
Additional file 8: Figure S5. of Trends in cause and place of death for children in Portugal (a European country with no Paediatric palliative care) during 1987–2011: a population-based study
Creators: name: Lacerda, Ana Forjaz De
name: Gomes, Barbara
Publisher: name: figshare
Year: 2017
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Percentage of deaths occurring at home, by subregion NUTS III, in 0–17 year-old decedents from CCCs in Portugal (1987–2011, N = 10,440). (DOCX 502 kb)
Near- and sub-solar-mass naked singularities and black holes from transmutation of white dwarfs
Creators: name: Chakraborty, Chandrachur
name: Bhattacharyya, Sudip
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Recent gravitational wave events have suggested the existence of near-solar-mass black holes which cannot be formed via stellar evolution. This has opened up a tantalizing possibility of future detections of both black holes and naked singularities in this mass range. Existence of naked singularities is a topical and fundamental physics issue, but their formation mechanism is not yet clear. Here, we show that some white dwarfs can realistically transmute into black holes and naked singularities with a wide range of near- and sub-solar-mass values by capturing asymmetric or non-self-annihilating primordial dark matter (PDM) particles. We argue that, while a type Ia supernova due to the accumulation of dark matter at the core of a white dwarf could also be a possibility, the transmutation of a white dwarf into a black hole or a naked singularity is a viable consequence of the capture of non-self-annihilating PDM particles. These white dwarf transmutations can have a significant role in probing the physics of dark matter and compact objects, and could be tested using the rates and locations of mergers over the cosmological time scale.
description: 16 pages, 14 figures, matches published version
Q-band mixers in newly released 0.15 µm GaN process
Creators: name: Imiyage, Nethini Thilanga Weerathunge
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Recent advancements in communication systems have created a demand for circuits and subsystems with wide bandwidth at higher frequencies. Being one of the fundamental building blocks of transmitter and receiver chains, mixers play a major role in communication systems. Gallium-nitride (GaN) is an emerging semiconductor technology that has gained interest in realising a fully integrated transceiver chain. Therefore, it is interesting to investigate mixer designs in GaN technology which have not addressed much in literature. This thesis presents the implementation of a resistive single-ended mixer (SEM) and a single-balanced mixer (SBM) in WIN Semiconductor's newly released 0.15 m GaN process. The SEM operates over the entire Q-band and indicates a minimum conversion loss of 9 dB at midband. The SBM was realised using two SEMs connected with a Marchand balun and a Wilkinson power divider. It indicates a minimum conversion loss of 9.3 dB close to mid-band and 12.3 dB across the frequency band from 32.7 GHz to 53.6 GHz. An improved LO-RF isolation better than 47 dB was achieved using balanced LO signals. The IIP3 values of SEM and SBM are 26.6 dBm and 24.6 dBm respectively which conrm the high linearity of both mixers. The designed Marchand balun operates over a wide bandwidth from 27 GHz to 99 GHz. Furthermore, this research explores a capacitive loading technique to improve the input matching of the balun.
Stabilization of Underactuated Mechanical Systems with Time-Varying Uncertainty using Adaptive Fuzzy Sliding Mode
Creators: name: Azimi, Mohammad Mahdi
name: Koofigar, Hamid Reza
name: Edrisi, Mehdi
Publisher: name: arXiv
Year: 2017
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics
subject: 93D05

description: In this paper, the control problem for underactuated systems in the presence of external disturbances and model uncertainties is considered. An adaptive fuzzy sliding mode controller (AFSMC) is proposed to solve the problem, satisfying the robustness properties against uncertainties and disturbances. The designed controller can be applied to a wide class of underactuated systems and have fewer restrictions, compared with many pervious works. To evaluate the performance of proposed algorithm, it is applied to an underactuated inverted pendulum and a Translational Oscillator/Rotational Actuator (TORA) system with two degrees of freedom. The simulations are also demonstrated to show the effectiveness of the proposed strategy.
description: 8 pages, 14 figures, Journal
Additional file 1: of Effectiveness, costs and cost-effectiveness of chiropractic care and physiotherapy compared with information and advice in the treatment of non-specific chronic low back pain: study protocol for a randomised controlled trial
Creators: name: Gedin, Filip
name: Skeppholm, Martin
name: Burstrรถm, Kristina
name: Sparring, Vibeke
name: Mesfin Tessma
name: Zethraeus, Niklas
Publisher: name: figshare
Year: 2017
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: SPIRIT Checklist: recommended items to address in a clinical trial protocol. (PDF 130 kb)
Investigating first year science students' academic writing development
Creators: name: Alanazi, Khatmah
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: This study investigates academic writing tutors' perceptions of their students' performance and compares it with an analysis of first-year science students' academic writing. Specifically, it examines the challenges tutors perceive students to face when writing in academic contexts and then explores the linguistics resources students choose when writing in a scientific academic context. To achieve this aim, two sets of data were collected: tutor interviews and students' texts. The data from the tutor interviews was analysed to reveal academic writing tutors' perceptions of their students' academic writing abilities and challenges. The students' texts were then analysed to examine how effectively students make meanings valued in scientific contexts. To examine students' texts, Systemic Functional Linguistic analysis is employed; specifically, the study examines the ideational meanings (i.e., experiential and textual meanings) and textual meanings within the texts. The findings reveal that the students of science face some linguistics challenges across both the LexicoGrammar (e.g., under-using more valued specialised and technical entities; overusing less valued logical relations) and the Discourse Semantics (e.g., thematic progression). The data also show that there is some alignment between tutors' perceptions of students' writing development and their actual writing performance (e.g., lack of lexical variation and cohesion across the text). The study concludes with a discussion proposing the most critical areas for instructional intervention to focus to assist students in overcoming these linguistic challenges.
Generating Representative Executions [Extended Abstract]
Creators: name: Maarand, Hendrik
name: Uustalu, Tarmo
Publisher: name: arXiv
Year: 2017
Subjects: subject: Programming Languages (cs.PL)
subject: FOS: Computer and information sciences
subject: F.3.2; F.3.1

description: Analyzing the behaviour of a concurrent program is made difficult by the number of possible executions. This problem can be alleviated by applying the theory of Mazurkiewicz traces to focus only on the canonical representatives of the equivalence classes of the possible executions of the program. This paper presents a generic framework that allows to specify the possible behaviours of the execution environment, and generate all Foata-normal executions of a program, for that environment, by discarding abnormal executions during the generation phase. The key ingredient of Mazurkiewicz trace theory, the dependency relation, is used in the framework in two roles: first, as part of the specification of which executions are allowed at all, and then as part of the normality checking algorithm, which is used to discard the abnormal executions. The framework is instantiated to the relaxed memory models of the SPARC hierarchy.
description: In Proceedings PLACES 2017, arXiv:1704.02418
The many faces of workplace spirituality: a hermeneutic inquiry into the four worldviews as contexts of the employee-organization relationship and conduits for spirit manifesting
Creators: name: Todarello, Ekaterina
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: This thesis aims to develop a fuller understanding of workplace spirituality (WPS) as a multi-faceted, diverse, tradition-rich, worldview- and context-dependent construct. Performed within the borders of philosophical hermeneutics, the study uses hermeneutic premise of the fundamental role of history, language, tradition and context as pre-requisites to understanding any phenomenon, including that of WPS. This study explores three areas: research on spirituality (including but not limited to the organization and management literature); cross-disciplinary research on worldview (including investigations of two research directions - worldview structure (such as functions and roles of worldviews) and worldview content (such as beliefs and assumptions); and, finally, research on the employee-organization relationship (EOR) as a crystallized version of rather ambiguous 'workplace' used in the construct of WPS. Literature analysis renders three main results. First, inductive understanding of WPS as a worldview which serves as conduit for spirit manifesting in the context of employee-organization relationship is achieved. Second, a Four (Dream, Crossroads, Paradox and Alchemy) Worlds framework emerges as a result of taking EOR beyond the limited borders of the organizational behaviour literature which struggles to accommodate spirituality. And, third, reflective of three research domains (spirituality, worldview, EOR), two research questions are developed. Focusing on the structure and content of the worldviews that serve as conduits for spirit manifesting, they are essentially concerned with understanding the whole (context) of which spirituality is a part and are used to assess a Four Worlds framework in terms of its explanatory power for WPS. Following tradition of philosophical hermeneutics and its argument of the prevalence of hermeneutics over any fixed and pre-developed method, AUSHI - authentic spiritual hermeneutic inquiry - is developed and applied to analyze a rich pool of data resulting from conducting 44 semi-structured interviews. As a result, four theoretically developed worldviews (Four Worlds) are considerably enriched both structure- and content-wise and provide compelling picture of rich, equally important, and distinctive interpretations of workplace spirituality, including the Dream World spirituality of individualization and untapped potential, the Crossroads World spirituality of crisis and growth, the Paradox World spirituality of presence and authenticity, and the Alchemy World spirituality of everydayness and service.
Variations in the style and timing of structural deformation on salt- and shale-detached slopes
Creators: name: Erdi, Aurio
Publisher: name: Imperial College London
Year: 2022

description: Continental margins are commonly characterized by gravity-driven, thin-skinned deformation of overburden above mobile shale or salt. Deformation is classically characterised by kinematically linked zones of up-dip extension, mid-slope translation, and downdip contraction above a smoothly seaward-dipping surface underlying the basal detachment. However, relatively few recent natural examples, and physical and numerical models, show that basal detachment paleo-topography can be rugose, and that deformation can be temporally and spatially complex. The origin of this paleo-topography, and the detailed geometry and kinematic evolution of related overburden deformation, are not fully understood; this forms the focus of this thesis. This study uses 3D seismic reflection data from two continental margins (i.e. the Outer Kwanza Basin, offshore Angola, and the Tarakan Basin, offshore Indonesia) to document the style and interpret the growth of contractional, extensional and strike-slip structures, and their associated basal salt or shale layers in three-dimensions. This study unravels kinematic in these two basins by using a number of approaches, including structural restorations (i.e. palinsplastic or backstripping), displacement-distance and/or isopach analysis. On the Outer Kwanza Basin, this study identifies variably oriented salt structures (i.e. anticlines, rollers, walls) of up to 3 km height and 47 km length, and their related normal, reverse and strike-slip faults. More specifically to the strike-slip faults, this study shows four arrays of faults of up to 13 km long and 0.8 km tall that form restraining bend and releasing stepover at their lateral tip. In this basin, this study identifies the predominantly contractional structures reflect up to 22 km of seaward translation of salt and its overburden across rugose paleo-topography reliefs. The rate of translation seaward varies along strike, resulting in formation of the strike-slip faults that grew via alternating periods of lengthening, throw accumulation and inactivity. In the Tarakan Basin, however, this study identifies shale structures (i.e. shale rollers and anticline, and mud diapir and volcano) of up to 5 km height and their related normal faults and roller folds. These deformations reflect spatial variation in sedimentary loading during gravitational gliding downslope above irregular dips of along strike paleo-topography. This study concludes that geometry of the paleo-topography can have an important role in the styles and distributions of overburden deformations during gravitational spreading and gliding in both Outer Kwanza and Tarakan Basins.
Additional file 3: Figure S3. of Comparison of multiple transcriptomes exposes unified and divergent features of quiescent and activated skeletal muscle stem cells
Creators: name: Pietrosemoli, Natalia
name: SĂŠbastien Mella
name: Yennek, Siham
name: Baghdadi, Meryem
name: Sakai, Hiroshi
name: Ramkumar Sambasivan
name: Pala, Francesca
name: Girolamo, Daniela Di
name: Shahragim Tajbakhsh
Publisher: name: figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Science Policy

description: Effect of adding NICD[E17.5/E14.5] dataset on the best combinations of datasets. Impact of including or excluding NICD dataset on overall analysis. (PDF 395Â kb)
High repetition pump-and-probe photoemission spectroscopy based on a compact fiber laser system
Creators: name: Ishida, Y.
name: Otsu, T.
name: Ozawa, A.
name: Yaji, K.
name: Tani, S.
name: Shin, S.
name: Kobayashi, Y.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: The paper describes a time-resolved photoemission (TRPES) apparatus equipped with a Yb-doped fiber laser system delivering 1.2-eV pump and 5.9-eV probe pulses at the repetition rate of 95 MHz. Time and energy resolutions are 11.3 meV and ~310 fs, respectively; the latter is estimated by performing TRPES on a highly oriented pyrolytic graphite (HOPG). The high repetition rate is suited for achieving high signal-to-noise ratio in TRPES spectra, thereby facilitating investigations of ultrafast electronic dynamics in the low pump fluence (p) region. TRPES of polycrystalline bismuth (Bi) at p as low as 30 nJ/mm2 is demonstrated. The laser source is compact and is docked to an existing TRPES apparatus based on a 250-kHz Ti:sapphire laser system. The 95-MHz system is less prone to space-charge broadening effects compared to the 250-kHz system, which we explicitly show in a systematic probe-power dependency of the Fermi cutoff of polycrystalline gold. We also describe that the TRPES response of an oriented Bi(111)/HOPG sample is useful for fine-tuning the spatial overlap of the pump and probe beams even when p is as low as 30 nJ/mm2.
Adaptations for pressure and temperature effects on loop motion in Escherichia coli and Moritella profunda dihydrofolate reductase
Creators: name: Huang, Qi
name: Rodgers, Jocelyn M.
name: Hemley, Russell J.
name: Ichiye, Toshiko
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Determining how enzymes in piezophilic microbes function at high pressure can give insights into how life adapts to living at high pressure. Here, the effects of pressure and temperature on loop motions of Escherichia coli (Ec) and Moritella profunda (Mp) dihydrofolate reductase (DHFR) are compared via molecular dynamics simulations at combinations of the growth temperature and pressure of the two organisms. Analysis indicates that a flexible CD loop in MpDHFR is an adaptation for cold because it makes the adenosine binding subdomain more flexible. Also, analysis indicates that the Thr113-Glu27 hydrogen bond in MpDHFR is an adaptation for high pressure because it provides flexibility within the loop subdomain compared to the very strong Thr113-Asp27 hydrogen bond in EcDHFR, and affects the correlation of the Met20 and GH loops. In addition, the results suggest that temperature might affect external loops more strongly while pressure might affect motion between elements within the protein.
Biochemical analysis of cleavage and ligation activities of the pistol ribozyme from Paenibacillus polymyxa
Creators: name: Lihanova, Yuliia
name: Weinberg, Christina E.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: Biochemistry
Molecular Biology
Environmental Sciences not elsewhere classified
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Science Policy

description: Nine distinct classes of self-cleaving ribozymes are known to date, of which the pistol ribozyme class was discovered only 5 years ago. Self-cleaving ribozymes are able to cleave their own phosphodiester backbone at a specific site with rates much higher than those of spontaneous RNA degradation. Our study focuses on a bioinformatically predicted pistol ribozyme from the bacterium Paenibacillus polymyxa. We provide a biochemical characterization of this ribozyme, which includes an investigation of the effect of various metal ions on ribozyme cleavage and a kinetic analysis of ribozyme activity under increasing Mg2+ concentrations and pH. Based on the obtained results, we discuss a possible catalytic role of divalent metal ions. Moreover, we investigated the ligation activity of the P. polymyxa pistol ribozyme – an aspect that has not been previously analysed for this ribozyme class. We determined that the P. polymyxa pistol ribozyme is almost fully cleaved at equilibrium with the ligation rate constant being nearly 30-fold lower than the cleavage rate constant. In summary, we have characterized an additional representative of this recently discovered ribozyme class isolated from P. polymyxa. We expect that our biochemical characterization of a pistol representative in a cultivatable, genetically tractable organism will support our future investigation of the biological roles of this ribozyme class in bacteria. Read the transcript Watch the video on Vimeo
Spear operators between Banach spaces
Creators: name: Kadets, Vladimir
name: Martin, Miguel
name: Meri, Javier
name: Perez, Antonio
Publisher: name: arXiv
Year: 2017
Subjects: subject: Functional Analysis (math.FA)
subject: FOS: Mathematics
subject: 46B04 (Primary), 46B20, 46B22, 46B25, 46J10, 47A12, 47A30, 47A99 (Secondary)

description: The aim of this manuscript is to study \emph{spear operators}: bounded linear operators $G$ between Banach spaces $X$ and $Y$ satisfying that for every other bounded linear operator $T:X\longrightarrow Y$ there exists a modulus-one scalar $ω$ such that $$ \|G + ω\,T\|=1+ \|T\|. $$ To this end, we introduce two related properties, one weaker called the alternative Daugavet property (if rank-one operators $T$ satisfy the requirements), and one stronger called lushness, and we develop a complete theory about the relations between these three properties. To do this, the concepts of spear vector and spear set play an important role. Further, we provide with many examples among classical spaces, being one of them the lushness of the Fourier transform on $L_1$. We also study the relation of these properties with the Radon-Nikodým property, with Asplund spaces, with the duality, and we provide some stability results. Further, we present some isometric and isomorphic consequences of these properties as, for instance, that $\ell_1$ is contained in the dual of the domain of every real operator with infinite rank and the alternative Daugavet property, and that these three concepts behave badly with smoothness and rotundity. Finally, we study Lipschitz spear operators (that is, those Lipschitz operators satisfying the Lipschitz version of the equation above) and prove that (linear) lush operators are Lipschitz spear operators.
description: 114 pages, 9 chapters
Additional file 7: Table S3. of Trends in cause and place of death for children in Portugal (a European country with no Paediatric palliative care) during 1987–2011: a population-based study
Creators: name: Lacerda, Ana Forjaz De
name: Gomes, Barbara
Publisher: name: figshare
Year: 2017
Subjects: subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: Plant Biology
subject: FOS: Biological sciences

description: Bivariate analysis of factors associated with home death for 0–17 years-old decedents from complex chronic conditions in Portugal (1987–2011). (DOCX 73 kb)
5´XP sRNA-seq: efficient identification of transcripts with and without 5´ phosphorylation reveals evolutionary conserved small RNA
Creators: name: Kugelberg, Unn
name: Nätt, Daniel
name: Skog, Signe
name: Kutter, Claudia
name: Öst, Anita
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified

description: Small RNA (sRNA) sequencing has been critical for our understanding of many cellular processes, including gene regulation. Nonetheless, the varying biochemical properties of sRNA, such as 5´ nucleotide modifications, make many sRNA subspecies incompatible with common protocols for sRNA sequencing. Here we describe 5XP-seq that outlines a novel strategy that captures a more complete picture of sRNA. By tagging 5´P sRNA during library preparation, 5XP-seq combines an open approach that includes all types of 5ʹ-terminal modifications (5´X), with a selective approach for 5-phosphorylated sRNA (5´P). We show that 5XP-seq not only enriches phosphorylated miRNA and piRNA but successfully discriminates these sRNA from all other sRNA species. We further demonstrate the importance of this strategy by successful inter-species validation of sRNAs that would have otherwise failed, including human to insect translation of several tRNA (tRFs) and rRNA (rRFs) fragments. By combining 5´ insensitive library strategies with 5´ sensitive tagging, we have successfully tackled an intrinsic bias in modern sRNA sequencing that will help us reveal the true complexity and the evolutionary significance of the sRNA world.
MOESM2 of Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating ruralâ urban habitats
Creators: name: Wereszczuk, Anna
name: RaphaĂŤl Leblois
name: Zalewski, Andrzej
Publisher: name: figshare
Year: 2017
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified

description: Additional file 2. Row experimental data.