cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
title: An exploration of the role of peroxisome proliferator-activated receptor alpha in the thermal tolerance and adaptive potential of fish
Creators: name: Galts, Bergen Marit Dypvik
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: CRISPR
subject: Stickelback
subject: Temperature
subject: Tolerance
subject: CTmax
subject: CTmin
subject: peroxisome proliferator-activated receptor
subject: PPARa
subject: Adaptive potential
subject: Thermal Tolerance
subject: Body Size
subject: Threespine Stickleback
subject: CAS9
subject: Ecology
subject: FOS: Biological sciences
subject: Biology

description: With increasing temperatures and extreme weather events it is imperative to understand species potential for adaptation in changing environmental conditions. This is particularly relevant for ectothermic species, including fishes, which are largely reliant on environmental conditions for maintenance of homeostasis. Adaptation to temperature changes requires that selection act on existing functional genetic variation within a population but determining the links between candidate genes and putatively functional traits remains challenging. Recently developed genomic techniques, such as gene editing, have shown promise for examining variation in candidate genes and in characterization of adaptive trait variation. In fishes, one such candidate gene, is peroxisome proliferator-activated receptor alpha (PPARa), which encodes a transcription factor that appears to play a role in temperature response across multiple fish species, including threespine stickleback (Gasterosteus aculeatus). In this thesis I aimed to gain a better understanding of PPARa in relation to the thermal response and body size of fishes using stickleback with introduced genetic variation in PPARa and examining the changes in phenotypic expression. Non-homologous end joining (NHEJ) CRISPR was used on four families of laboratory stickleback, which were then crossed to create an F1 generation. Using a combination of DNA sequencing techniques, I determined that 29.5% of the alleles present in the F1 generation were CRISPR modified alleles. All F1 individuals were measured for body size and trialed for thermal tolerance, testing the hypothesis that modified alleles would lead to a reduced thermal tolerance and increased body size. I found no phenotypic differences in thermal tolerance between modified and wildtype individuals, indicating that PPARa and its relationship to thermal tolerance may be associated with other pathways, or that other mechanisms compensate for the modified alleles. I also found that individuals with two modified alleles accumulated significantly more mass over the course of the study, which is consistent with literature on PPARa and mass accumulation in other species. This thesis also highlights the importance of understanding adaptive genetic variation and the potential of gene editing techniques to aid in our understanding of functional genetic variation within populations and subsequently their potential for adaptation under environmental change.
title: Evolving Urban Landscapes: The Transformation of Housing Structures in Calgary and Kumasi over a Century.
Creators: name: Opoku, Felicia
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Housing transformation
subject: Socioeconomic Arrangements
subject: Zoning Bylaws
subject: Urban and Regional Planning
subject: FOS: Social and economic geography
subject: Education--Social Sciences

description: Communities evolve and adapt to change to address the growing urban challenges such as urbanization, environmental sustainability, and social equity. These changes occur in response to the global diversity of needs, especially in urban areas that have rapidly become a melting pot. Cities like Calgary and Kumasi have grown and diversified from primitive beginnings to modernity over the past century. Calgary’s growth was driven by its fundamental role in the oil and gas industry. Kumasi’s growth was due to the cocoa boom and the influence of colonial planning policies. They were shaped by the dynamics in urban planning policies, land use regulations, and variations in socioeconomic arrangements manifested in the available housing forms/types and sizes. Early Calgary’s houses were modest single-detached, while Kumasi’s structures were characterized by traditional compound houses of more than fifteen rooms. Homes in both cities have modernized with modern building materials that respond to the population's needs. However, studies on why and how houses change over time are limited. Adopting the historical and archival research approach and relying on secondary data, the study explores how land use regulations and socioeconomic arrangements have influenced the transformation of these housing structures in both cities over the past century. The study found that while household size shrinks and income increases, people demand larger homes with attached car garages, large backyards, two-storey single-family detached homes, and other ancillary buildings in Calgary. However, in Kumasi, while household size shrinks, people shift their tastes and preferences to single-family homes built on smaller lots, consequently reducing the number of people they can accommodate, gradually creating a housing shortage and affordability issues. The study also found that residential zoning bylaws have significantly contributed to the transformation of houses in Calgary but are less effective in Kumasi. Due to how housing is supplied in Kumasi, housing transformation is driven substantially by the influence of foreign cultures, increased household income, and the shrinking household size. The findings would inform future housing interventions to address the growing population's needs.
Extracellular granzyme B and pathophysiological implications
Creators: name: Boivin, Wendy Anne
Publisher: name: University of British Columbia
Year: 2013

description: Granzyme B (GzmB) is a serine protease that contributes to immune-mediated elimination of cells by initiating a tightly-regulated form of death known as apoptosis. However, during inflammation, GzmB leaks out and accumulates in the extracellular space, retains its activity, and proficiently cleaves extracellular matrix (ECM) proteins. I therefore hypothesized that extracellular GzmB is capable of cleaving novel ECM substrates, contributing to dysregulated ECM integrity and function in disease. In the present dissertation I identified eleven novel extracellular GzmB substrates. Further investigations revealed that GzmB-mediated proteoglycan cleavage was implicated in the dysregulation of active transforming growth factorbeta (TGF-β) sequestration and bioavailability. GzmB cleavage sites were identified in biglycan and betaglycan and active TGF-β was shown to be released from decorin, biglycan and betaglycan. The pathophysiological role of my findings were further investigated and validated using animal models of disesase in which inflammation and elevated GzmB are observed. Evidence of fibrillin-1 and decorin cleavage were observed in atherosclerosis, abdominal aortic aneurysm and in skin aging pathogenesis. I also assessed the activity of GzmB in advanced atherosclerosis using perforin/apolipoprotein E- double knockout (Perf/apoE-DKO) and granzyme B/apolipoprotein E-double knockout (GzmB/apoE-DKO) mice. Interestingly, unlike our aneurysm findings whereby only GzmB/apoE-DKO mice were protected, both Perf/apoEDKO and GzmB/apoE-DKO mice were protected from atherosclerosis compared to apoE-KO controls, suggesting the intracellular Perf-dependent activities of granzymes are also important in the pathogenesis of atherosclerosis. In summary, GzmB is a protease that functions both intracellularly and extracellularly in disease. My findings suggest that the use of Perf knockout mice alone to study the role of GzmB in disease should be re-evaluated given the increasing evidence in both animal models and in human disease showing elevated GzmB in bodily fluids is associated with inflammation and age.
title: Permafrost Distribution in Alpine Landforms: The Role of Sediment Size and Natural Convection.
Creators: name: Zegers, Gerardo
Publisher: name: Science
Year: 2024
Subjects: subject: Mountain permafrost
subject: Sediment size
subject: Permafrost mapping
subject: Machine learning
subject: Alpine landforms
subject: Natural Convection
subject: UAV Photogrammetry
subject: Grain Size Analysis
subject: Education--Sciences
subject: Hydrology

description: The distribution of permafrost in mountainous regions is influenced by various factors such as topography, climate, vegetation, and substrate. Alpine landforms, in particular, exhibit unique thermal characteristics, where the presence of coarse sediments creates a distinctive ground thermal regime. These sediments can maintain lower temperatures compared to adjacent fine-grained soils, primarily due to natural air convection and lower thermal conductivity. Existing statistical and physically based models often fail to accurately represent permafrost occurrence in alpine landforms as they do not account for these effects. This research overcomes these limitations by developing tools incorporating these effects, thereby improving the prediction and understanding of permafrost distribution in mountainous regions. The study utilized a combination of drone photogrammetry, machine learning, and image processing to create an efficient and accurate workflow for estimating grain size distributions from orthomosaic images with a ground sampling distance of around 3 cm. Data-driven techniques, such as logistic regression, support vector machines, and random forests, were employed to analyze the spatial distribution of permafrost in six alpine basins within the Canadian Rockies. Additionally, natural convection was integrated into a hydrological model to enhance the representation of the thermal behavior of coarse sediments. The results revealed that localized conditions strongly influence permafrost variability, highlighting the importance of local field data for accurate predictions. Additionally, variables such as enhanced vegetation index, sediment size, and slope angle were identified as the most important factors for predicting permafrost at the patch scale. Testing the developed convection-enhanced hydrological model on a talus slope in the Canadian Rockies demonstrated that coarse-grained sediments can significantly lower ground temperatures when natural convection is considered. The study also identified natural convection in alpine landforms operating under a local thermal non-equilibrium (LTNE) state, and that applying local thermal equilibrium conditions hinders the impact of natural convection. Overall, this research improves the understanding of permafrost dynamics in alpine landforms and enables a more accurate analysis of permafrost extent and its influence on groundwater discharges.
The KELT-South Telescope
Creators: name: Pepper, Joshua
name: Kuhn, Rudolf B.
name: Siverd, Robert
name: James, David
name: Stassun, Keivan
Publisher: name: arXiv
Year: 2012
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: The Kilodegree Extremely Little Telescope (KELT) project is a survey for new transiting planets around bright stars. KELT-South is a small-aperture, wide-field automated telescope located at Sutherland, South Africa. The telescope surveys a set of 26 degree by 26 degree fields around the southern sky, and targets stars in the range of 8 < V < 10 mag, searching for transits by Hot Jupiters. This paper describes the KELT-South system hardware and software and discusses the quality of the observations. We show that KELT-South is able to achieve the necessary photometric precision to detect transits of Hot Jupiters around solar-type main-sequence stars.
description: 26 pages, 13 figures
Additional file 1 of The MLR, NLR, PLR and D-dimer are associated with clinical outcome in lung cancer patients treated with surgery
Creators: name: Wang, Jun
name: li, Huawei
name: Xu, Ran
name: Lu, Tong
name: Zhao, Jiaying
name: Zhang, Pengfei
name: Qu, Lidong
name: Zhang, Shengqiang
name: Guo, Jida
name: Zhang, Linyou
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy
subject: Hematology

description: Additional file 1. CUT-OFF values for MLR, NLR, PLR and D-Dimer.
title: Maladaptive Trained Immunity: New Insight into the Pathogenesis of Inflammatory Bowel Disease
Creators: name: Bartlett, Alexandria
Publisher: name: Graduate Studies
Year: 2026
Subjects: subject: Inflammatory Bowel Disease
subject: Ulcerative Colitis
subject: Trained Immunity
subject: Hematopoietic Stem Cells
subject: Macrophages
subject: Inflammation
subject: Myelopoiesis
subject: Immunology
subject: FOS: Clinical medicine

description: Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn’s disease (CD), is increasing globally and in Canada. IBD causes debilitating symptoms and significant economic strain on healthcare systems. Despite treatment advances, no universally effective therapy exists. Chronic uncontrolled inflammation of the intestinal mucosa remains the hallmark of the disease. A dysregulated immune response, particularly involving innate immune cells like macrophages, plays a central role in the pathogenesis of IBD. However, the mechanisms driving inflammatory macrophage activation are poorly understood. Recent studies suggest that innate immune cells, such as macrophages, can develop "immunologic memory" after exposure to microbes or pathogen signals. This memory, termed trained immunity (TI), boosts the immune response to future threats. While TI is protective against infections, it may worsen and drive disease progression in chronic inflammation disorders like IBD. To address this knowledge gap, we investigated the role of the bone marrow (BM) hematopoietic stem cells (HSC) and progenitors as a source of trained inflammatory and damage-inducing macrophages in an experimental model of acute colitis. Chemical-induced colitis models showed an expansion of HSCs in the BM and their biasedness towards myelopoiesis, as evidenced by increased granulocyte-macrophage precursors (GMPs). Further, macrophages derived from these altered BM precursors (BMDMs) displayed a pro-inflammatory phenotype at the baseline, without ex vivo stimulation, compared to BMDMs from untreated mice. After a four-week rest period to allow inflammation to return to baseline, we found that BMDMs from rested mice were significantly more pro-inflammatory, as evidenced by increased IL-6, IL-1b, and TNF-a secretion and enhanced glycolytic metabolism. In vivo, these rested mice exhibited heightened inflammation upon secondary challenge with DSS or lipopolysaccharide (LPS). Additionally, chimeric mouse experiments revealed that the trained immune phenotype persisted in the BM compartment for up to 14 weeks post-initial DSS exposure. Our findings suggest that TI within the BM is a critical factor in the development and persistence within a model of colitis and, therefore, may be relevant to inflammation in IBD. This study provides new insight into the role of HSCs in IBD pathogenesis and highlights the BM as a potential target for future therapeutic intervention.
The use of single armed observational data to closing the gap in otherwise disconnected evidence networks: a network meta-analysis in multiple myeloma
Creators: name: Schmitz, Susanne
name: Maguire, Áine
name: Morris, James
name: Ruggeri, Kai
name: Haller, Elisa
name: Kuhn, Isla
name: Leahy, Joy
name: Homer, Natalia
name: Khan, Ayesha
name: Bowden, Jack
name: Buchanan, Vanessa
name: O’Dwyer, Michael
name: Cook, Gordon
name: Walsh, Cathal
Publisher: name: Columbia University
Year: 2018
Subjects: Meta-analysis
Medicine--Research--Data processing
Medicine--Research--Methodology
Multiple myeloma

description: Background
                Network meta-analysis (NMA) allows for the estimation of comparative effectiveness of treatments that have not been studied in head-to-head trials; however, relative treatment effects for all interventions can only be derived where available evidence forms a connected network. Head-to-head evidence is limited in many disease areas, regularly resulting in disconnected evidence structures where a large number of treatments are available. This is also the case in the evidence of treatments for relapsed or refractory multiple myeloma.

                Methods
                Randomised controlled trials (RCTs) identified in a systematic literature review form two disconnected evidence networks. Standard Bayesian NMA models are fitted to obtain estimates of relative effects within each network. Observational evidence was identified to fill the evidence gap. Single armed trials are matched to act as each other’s control group based on a distance metric derived from covariate information. Uncertainty resulting from including this evidence is incorporated by analysing the space of possible matches.

                Results
                Twenty five randomised controlled trials form two disconnected evidence networks; 12 single armed observational studies are considered for bridging between the networks. Five matches are selected to bridge between the networks. While significant variation in the ranking is observed, daratumumab in combination with dexamethasone and either lenalidomide or bortezomib, as well as triple therapy of carfilzomib, ixazomib and elozumatab, in combination with lenalidomide and dexamethasone, show the highest effects on progression free survival, on average.

                Conclusions
                The analysis shows how observational data can be used to fill gaps in the existing networks of RCT evidence; allowing for the indirect comparison of a large number of treatments, which could not be compared otherwise. Additional uncertainty is accounted for by scenario analyses reducing the risk of over confidence in interpretation of results.
Exploiting Pan Influenza A and Pan Influenza B Pseudotype Libraries for Efficient Vaccine Antigen Selection.
Creators: name: Del Rosario, Joanne Marie M
name: Da Costa, Kelly A S
name: Asbach, Benedikt
name: Ferrara, Francesca
name: Ferrari, Matteo
name: Wells, David A
name: Mann, Gurdip Singh
name: Ameh, Veronica O
name: Sabeta, Claude T
name: Banyard, Ashley C
name: Kinsley, Rebecca
name: Scott, Simon D
name: Wagner, Ralf
name: Heeney, Jonathan L
name: Carnell, George W
name: Temperton, Nigel J
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Monoclonal antibody
Vaccine
Influenza
Immunogenicity
Hemagglutinin
Neutralization
Pseudotype

description: We developed an influenza hemagglutinin (HA) pseudotype library encompassing Influenza A subtypes HA1-18 and Influenza B subtypes (both lineages) to be employed in influenza pseudotype microneutralization (pMN) assays. The pMN is highly sensitive and specific for detecting virus-specific neutralizing antibodies against influenza viruses and can be used to assess antibody functionality in vitro. Here we show the production of these viral HA pseudotypes and their employment as substitutes for wildtype viruses in influenza neutralization assays. We demonstrate their utility in detecting serum responses to vaccination with the ability to evaluate cross-subtype neutralizing responses elicited by specific vaccinating antigens. Our findings may inform further preclinical studies involving immunization dosing regimens in mice and may help in the creation and selection of better antigens for vaccine design. These HA pseudotypes can be harnessed to meet strategic objectives that contribute to the strengthening of global influenza surveillance, expansion of seasonal influenza prevention and control policies, and strengthening pandemic preparedness and response.
Identification of differentially expressed genes and pathways in mice exposed to mixed field neutron/photon radiation
Creators: name: Broustas, Constantinos
name: Harken, Andrew Dennis
name: Garty, Guy Y.
name: Amundson, Sally A.
Publisher: name: Columbia University
Year: 2018
Subjects: Genomics
Gene expression
Radiation dosimetry
Neutron irradiation
Photon emission

description: Background
                Radiation exposure due to the detonation of an improvised nuclear device remains a major security concern. Radiation from such a device involves a combination of photons and neutrons. Although photons will make the greater contribution to the total dose, neutrons will certainly have an impact on the severity of the exposure as they have high relative biological effectiveness.

                Results
                We investigated the gene expression signatures in the blood of mice exposed to 3 Gy x-rays, 0.75 Gy of neutrons, or to mixed field photon/neutron with the neutron fraction contributing 5, 15%, or 25% of a total 3 Gy radiation dose. Gene ontology and pathway analysis revealed that genes involved in protein ubiquitination pathways were significantly overrepresented in all radiation doses and qualities. On the other hand, eukaryotic initiation factor 2 (EIF2) signaling pathway was identified as one of the top 10 ranked canonical pathways in neutron, but not pure x-ray, exposures. In addition, the related mTOR and regulation of EIF4/p70S6K pathways were also significantly underrepresented in the exposures with a neutron component, but not in x-ray radiation. The majority of the changed genes in these pathways belonged to the ribosome biogenesis and translation machinery and included several translation initiation factors (e.g. Eif2ak4, Eif3f), as well as 40S and 60S ribosomal subunits (e.g. Rsp19, Rpl19, Rpl27). Many of the differentially downregulated ribosomal genes (e.g. RPS19, RPS28) have been causally associated with human bone marrow failure syndromes and hematologic malignancies. We also observed downregulation of transfer RNA processes, in the neutron-only exposure (p
Restructuring of colloidal aggregates in shear flow: Coupling interparticle contact models with Stokesian dynamics
Creators: name: Seto, Ryohei
name: Botet, Robert
name: Auernhammer, Günter K.
name: Briesen, Heiko
Publisher: name: arXiv
Year: 2012
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Computational Physics (physics.comp-ph)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: A method to couple interparticle contact models with Stokesian dynamics (SD) is introduced to simulate colloidal aggregates under flow conditions. The contact model mimics both the elastic and plastic behavior of the cohesive connections between particles within clusters. Owing to this, clusters can maintain their structures under low stress while restructuring or even breakage may occur under sufficiently high stress conditions. SD is an efficient method to deal with the long-ranged and many-body nature of hydrodynamic interactions for low Reynolds number flows. By using such a coupled model, the restructuring of colloidal aggregates under stepwise increasing shear flows was studied. Irreversible compaction occurs due to the increase of hydrodynamic stress on clusters. Results show that the greater part of the fractal clusters are compacted to rod-shaped packed structures, while the others show isotropic compaction.
description: A simulation movie be found at http://www-levich.engr.ccny.cuny.edu/~seto/sites/colloidal_aggregates_shearflow.html
Additional file 2 of The MLR, NLR, PLR and D-dimer are associated with clinical outcome in lung cancer patients treated with surgery
Creators: name: Wang, Jun
name: li, Huawei
name: Xu, Ran
name: Lu, Tong
name: Zhao, Jiaying
name: Zhang, Pengfei
name: Qu, Lidong
name: Zhang, Shengqiang
name: Guo, Jida
name: Zhang, Linyou
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy
subject: Hematology

description: Additional file 2. Clinical baseline data between high and low MLR, NLR, PLR and D-Dimer groups.
title: Wellbore Positioning in Directional Drilling by Geopotential Field Anomalies
Creators: name: Silva, Luis A
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Directional Drilling Navigation System
subject: Inertial Navigation System
subject: Indoor Navigation System
subject: Magnetometer and Magnetic Field Heading
subject: Local Magnetic Field Modelling
subject: Engineering--System Science

description: When navigating the wellbore trajectory, the geomagnetic north can be used to obtain orientation, but interference with other nearby magnetic sources can drastically affect the value of the magnetic azimuth. A potential solution can be found by modelling the local magnetic field. Modelling the magnetic field can help estimating the magnetic gradient at nearby locations. Changes in orientation for a given location, could be detected by calculating the angle between the estimated and the measured gradient. In principle this should work provided the measurements are taken within the accuracy limits of the modelled field and the amount of time passed after the gradient estimation is short. To evaluate the possibility of using the anomalous geomagnetic field for orientation, this research required to estimate various sensor errors and the implementation of various algorithms that are required for inertial navigation. Experiments were performed with the sensor in various static positions, and the sensor moving on a track. Magnetometer measurements were used to model the magnetic field, with the intention to provide uncorrelated heading and velocity information. For the case of the moving sensor this information was fused with IMU measurements into an extended Kalman filter The results for the sensor orientation in various static positions showed that raw field measurements had a heading error of 17°, by modelling the field, the heading error reduced to 10°. For this case the magnetic field was modelled from the measurements from two points separated 1.2 m. A second test was performed by using 2 points separated by 0.60 m. The modelled field for this test produced a maximum orientation error of 7°. The results for the sensor moving on a track, showed that the heading error was under 8° for the first 6 seconds of input, but the error increased rapidly after that. One of the reasons for this is that the traveled distance obtained from the mechanization deteriorated very rapidly, and this affected the magnetic field modelling. An odometer / drilling rate might help mitigating this problem and the expected heading error is estimated to be under 8°.
Dark gas in the solar neighnorhood from extinction data
Creators: name: Paradis, D.
name: Dobashi, K.
name: Shimoikura, T.
name: Kawamura, A.
name: Onishi, T.
name: Fukui, Y.
name: Bernard, J. -P.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: When modeling infrared or gamma-ray data as a linear combination of observed gas tracers, excess emission has been detected compared to expectations from known neutral and atomic gas as traced by HI and CO measurements, respectively. This excess might correspond to an additional gas component. This so-called "dark gas" (DG) has been observed in our Galaxy, as well as the Magellanic Clouds. For the first time, we investigate the correlation between visible extinction (Av) data and gas tracers on large scales in the solar neighborhood. Our work focuses on both the solar neighborhood ($|b|>10\degr$), and the inner and outer Galaxy, as well as on four individual regions: Taurus, Orion, Cepheus-Polaris and Aquila-Ophiuchus. Thanks to the recent production of an all-sky Av map, we first perform the correlation between Av and both HI and CO emission over the most diffuse regions, to derive the optimal (Av/NH)^(ref) ratio. We then iterate the analysis over the entire regions to estimate the CO-to-H2 conversion factor as well as the DG mass fraction. The average extinction to gas column-density ratio in the solar neighborhood is found to be (Av/NH)^(ref)=6.53 10^(-22) mag. cm^2, with significant differences between the inner and outer Galaxy. We derive an average XCO value of 1.67 10^(20) H2 cm^(-2)/(K km s^(-1)). In the solar neighborhood, the gas mass in the dark component is found to be 19% relative to that in the atomic component and 164$%$ relative to the one traced by CO. These results are compatible with the recent analysis using Planck data within the uncertainties of our measurements. We estimate the ratio of dark gas to total molecular gas to be 0.62 in the solar neighborhood. The HI-to-H2 and H2-to-CO transitions appear for Av $\simeq$0.2 mag and Av$\simeq1.5$ mag, respectively, in agreement with theoretical models of dark-H2 gas.
description: 9 pages, 4 figures, 1 table. Accepted for publication in A&A (in press)
Thermally driven classical Heisenberg model in one dimension
Creators: name: Bagchi, Debarshee
name: Mohanty, P. K.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We study thermal transport in a classical one-dimensional Heisenberg model employing a discrete time odd even precessional update scheme. This dynamics equilibrates a spin chain for any arbitrary temperature and finite value of the integration time step $Δt$. We rigorously show that in presence of driving the system attains local thermal equilibrium which is a strict requirement of Fourier law. In the thermodynamic limit heat current for such a system obeys Fourier law for all temperatures, as has been recently shown [A. V. Savin, G. P. Tsironis, and X. Zotos, Phys. Rev. B 72, 140402(R) (2005)]. Finite systems, however, show an apparent ballistic transport which crosses over to a diffusive one as the system size is increased. We provide exact results for current and energy profiles in zero- and infinite-temperature limits.
description: 9 pages, 13 eps figures
Translating research evidence into practice: a report from the 2nd International Conference on Maternal and Newborn Health from KLE University - Belagavi, India
Creators: name: Goldenberg, Robert L.
name: McClure, Elizabeth M.
name: Belizán, José M.
Publisher: name: Columbia University
Year: 2018
Subjects: Reproductive health
Newborn infants--Health and hygiene
Reproductive health--Research
Maternal health services

description: The Jawaharlal Nehru Medical College (JNMC) Women’s and Children’s Health Research Unit (WCHRU) of the Karnataka Lingayat Education (KLE) Academy of Higher Education and Research Deemed-to-be-University and its collaborators convened the ‘2nd International Conference on Maternal and Newborn Health -Translating Research Evidence to Practice’ to address the common theme of improving maternal and newborn health in low- and middle- income countries (LMIC). This supplement, including 16 manuscripts, reflects much of the research presented at the conference, including analyses of the state of knowledge, as well as completed, ongoing and planned research in these areas conducted by the WCHRU in India together with many collaborators across high-income and LMIC. The first paper reviews maternal, fetal and neonatal mortality in low-income countries, considers their causes, as well as evidence for potential interventions to reduce mortality. A second paper addresses near miss maternal mortality. Several manuscripts address the research conducted by WCHRU and their colleagues in a multi-center research network. One study examines rates of miscarriage and medically terminated pregnancy in India and the risk factors for these occurrences. Another paper addresses stillbirth and its risk factors, both in India as well as in other LMIC. Haemorrhage and preeclampsia/eclampsia, important causes of maternal mortality, stillbirth and neonatal morbidity in LMIC, are addressed in a series of papers summarizing trials of interventions to reduce improve outcomes associated with these conditions. Poor maternal and infant nutritional status, which contribute to adverse outcomes, are addressed through papers which describe a number of important studies that the WCHRU and their colleagues have conducted to attempt to improve nutritional status. Another paper describes a study to investigate causes of stillbirth and deaths among preterm births, which will utilize new techniques to investigate the infectious causes of these deaths. Finally, the supplement addresses the process for dissemination of research results to inform public policy. Together these manuscripts represent a body of research to inform interventions to reduce maternal, fetal and newborn mortality and illustrates what a dedicated research group together with institutional support can accomplish.
The evolution of strategy in bacterial warfare via the regulation of bacteriocins and antibiotics
Creators: name: Niehus, Rene
name: Oliveira, Nuno M
name: Li, Aming
name: Fletcher, Alexander G
name: Foster, Kevin R
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: subject: Research Article
subject: Ecology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: bacterial competition
subject: antibiotics
subject: toxin regulation
subject: game theory
subject: eco-evolutionary model
subject: quorum sensing
subject: competition sensing
subject: None

description: Bacteria inhibit and kill one another with a diverse array of compounds, including bacteriocins and antibiotics. These attacks are highly regulated, but we lack a clear understanding of the evolutionary logic underlying this regulation. Here, we combine a detailed dynamic model of bacterial competition with evolutionary game theory to study the rules of bacterial warfare. We model a large range of possible combat strategies based upon the molecular biology of bacterial regulatory networks. Our model predicts that regulated strategies, which use quorum sensing or stress responses to regulate toxin production, will readily evolve as they outcompete constitutive toxin production. Amongst regulated strategies, we show that a particularly successful strategy is to upregulate toxin production in response to an incoming competitor’s toxin, which can be achieved via stress responses that detect cell damage (competition sensing). Mirroring classical game theory, our work suggests a fundamental advantage to reciprocation. However, in contrast to classical results, we argue that reciprocation in bacteria serves not to promote peaceful outcomes but to enable efficient and effective attacks.
High Tc superconductivity in superlattices of insulating oxides
Creators: name: Di Castro, D.
name: Salvato, M.
name: Tebano, A.
name: Innocenti, D.
name: Aruta, C.
name: Prellier, W.
name: Lebedev, O. I.
name: Ottaviani, I.
name: Brookes, N. B.
name: Minola, M.
name: Sala, M. Moretti
name: Mazzoli, C.
name: Medaglia, P. G.
name: Ghiringhelli, G.
name: Cirillo, L. Braicovich M.
name: Balestrino, G.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We report the occurrence of superconductivity, with maximum Tc = 40 K, in superlattices (SLs) based on two insulating oxides, namely CaCuO2 and SrTiO3. In these (CaCuO2)n/(SrTiO3)m SLs, the CuO2 planes belong only to CaCuO2 block, which is an antiferromagnetic insulator. Superconductivity, confined within few unit cells at the CaCuO2/SrTiO3 interface, shows up only when the SLs are grown in a highly oxidizing atmosphere, because of extra oxygen ions entering at the interfaces. Evidence is reported that the hole doping of the CuO2 planes is obtained by charge transfer from the interface layers, which act as charge reservoir.
description: 18 pages, 8 figures
β-hydroxybutyrate accumulates in the rat heart during low-flow ischaemia with implications for functional recovery
Creators: name: Lindsay, Ross T
name: Dieckmann, Sophie
name: Krzyzanska, Dominika
name: Manetta-Jones, Dominic
name: West, James A
name: Castro, Cecilia
name: Griffin, Julian L
name: Murray, Andrew J
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Research Article
Biochemistry and Chemical Biology
Cell Biology
Heart
Langendorff
cardiomyocyte
Ischaemia
Rat

description: Extrahepatic tissues which oxidise ketone bodies also have the capacity to accumulate them under particular conditions. We hypothesised that acetyl-coenzyme A (acetyl-CoA) accumulation and altered redox status during low-flow ischaemia would support ketone body production in the heart. Combining a Langendorff heart model of low-flow ischaemia/reperfusion with liquid chromatography coupled tandem mass spectrometry (LC-MS/MS), we show that β-hydroxybutyrate (β-OHB) accumulated in the ischaemic heart to 23.9 nmol/gww and was secreted into the coronary effluent. Sodium oxamate, a lactate dehydrogenase (LDH) inhibitor, increased ischaemic β-OHB levels 5.3-fold and slowed contractile recovery. Inhibition of β-hydroxy-β-methylglutaryl (HMG)-CoA synthase (HMGCS2) with hymeglusin lowered ischaemic β-OHB accumulation by 40%, despite increased flux through succinyl-CoA-3-oxaloacid CoA transferase (SCOT), resulting in greater contractile recovery. Hymeglusin also protected cardiac mitochondrial respiratory capacity during ischaemia/reperfusion. In conclusion, net ketone generation occurs in the heart under conditions of low-flow ischaemia. The process is driven by flux through both HMGCS2 and SCOT, and impacts on cardiac functional recovery from ischaemia/reperfusion.
Origin and Evolution of Jupiter's Trojan Asteroids
Creators: name: Bottke, William F.
name: Marschall, Raphael
name: Nesvorný, David
name: Vokrouhlický, David
Publisher: name: arXiv
Year: 2023
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: The origin of the Jupiter Trojan asteroids has long been a mystery. Dynamically, the population, which is considerably smaller than the main asteroid belt, librates around Jupiter's stable L4 and L5 Lagrange points, 60 deg ahead and behind Jupiter. It is thought that these bodies were captured into these orbits early in solar system history, but any capture mechanism must also explain why the Trojans have an excited inclination distribution, with some objects reaching inclinations of 35 deg. The Trojans themselves, individually and in aggregate, also have spectral and physical properties that appear consistent with many small bodies found in the outer solar system (e.g., irregular satellites, Kuiper belt objects). In this review, we assemble what is known about the Trojans and discuss various models for their origin and collisional evolution. It can be argued that the Trojans are unlikely to be captured planetesimals from the giant planet zone, but instead were once denizens of the primordial Kuiper belt, trapped by the events taking place during a giant planet instability. The Lucy mission to the Trojans is therefore well positioned to not only answer questions about these objects, but also about their place in planet formation and solar system evolution studies.
description: 30 pages, 4 figures
Targeted modulation of protein liquid–liquid phase separation by evolution of amino-acid sequence
Creators: name: Lichtinger, Simon M.
name: Garaizar, Adiran
name: Collepardo-Guevara, Rosana
name: Reinhardt, Aleks
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: subject: Research Article
subject: Physical sciences
subject: FOS: Physical sciences
subject: Research and analysis methods
subject: Computer and information sciences
subject: FOS: Computer and information sciences
subject: Biology and life sciences

description: Funder: Science and Technology Facilities Council; funder-id: http://dx.doi.org/10.13039/501100000271
description: Funder: Winton Programme for the Physics of Sustainability
description: Funder: German Academic Scholarship Foundation
description: Rationally and efficiently modifying the amino-acid sequence of proteins to control their ability to undergo liquid–liquid phase separation (LLPS) on demand is not only highly desirable, but can also help to elucidate which protein features are important for LLPS. Here, we propose a computational method that couples a genetic algorithm to a sequence-dependent coarse-grained protein model to evolve the amino-acid sequences of phase-separating intrinsically disordered protein regions (IDRs), and purposely enhance or inhibit their capacity to phase-separate. We validate the predicted critical solution temperatures of the mutated sequences with ABSINTH, a more accurate all-atom model. We apply the algorithm to the phase-separating IDRs of three naturally occurring proteins, namely FUS, hnRNPA1 and LAF1, as prototypes of regions that exist in cells and undergo homotypic LLPS driven by different types of intermolecular interaction, and we find that the evolution of amino-acid sequences towards enhanced LLPS is driven in these three cases, among other factors, by an increase in the average size of the amino acids. However, the direction of change in the molecular driving forces that enhance LLPS (such as hydrophobicity, aromaticity and charge) depends on the initial amino-acid sequence. Finally, we show that the evolution of amino-acid sequences to modulate LLPS is strongly coupled to the make-up of the medium (e.g. the presence or absence of RNA), which may have significant implications for our understanding of phase separation within the many-component mixtures of biological systems.
Phase transitions detached from stationary points of the energy landscape
Creators: name: Kastner, Michael
name: Mehta, Dhagash
Publisher: name: arXiv
Year: 2011
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The stationary points of the potential energy function V are studied for the ϕ^4 model on a two-dimensional square lattice with nearest-neighbor interactions. On the basis of analytical and numerical results, we explore the relation of stationary points to the occurrence of thermodynamic phase transitions. We find that the phase transition potential energy of the ϕ^4 model does in general not coincide with the potential energy of any of the stationary points of V. This disproves earlier, allegedly rigorous, claims in the literature on necessary conditions for the existence of phase transitions. Moreover, we find evidence that the indices of stationary points scale extensively with the system size, and therefore the index density can be used to characterize features of the energy landscape in the infinite-system limit. We conclude that the finite-system stationary points provide one possible mechanism of how a phase transition can arise, but not the only one.
description: 5 pages, 3 figures
Supersymmetric Many-particle Quantum Systems with Inverse-square Interactions
Creators: name: Ghosh, Pijush K.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mathematical Physics (math-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The development in the study of supersymmetric many-particle quantum systems with inverse-square interactions is reviewed. The main emphasis is on quantum systems with dynamical OSp(2|2) supersymmetry. Several results related to exactly solved supersymmetric rational Calogero model, including shape invariance, equivalence to a system of free superoscillators and non-uniqueness in the construction of the Hamiltonian, are presented in some detail. This review also includes a formulation of pseudo-hermitian supersymmetric quantum systems with a special emphasis on rational Calogero model. There are quite a few number of many-particle quantum systems with inverse-square interactions which are not exactly solved for a complete set of states in spite of the construction of infinitely many exact eigen functions and eigenvalues. The Calogero-Marchioro model with dynamical SU(1,1|2) supersymmetry and a quantum system related to short-range Dyson model belong to this class and certain aspects of these models are reviewed. Several other related and important developments are briefly summarized.
description: LateX, 65 pages, Added Acknowledgment, Discussions and References, Version to appear in Jouranl of Physics A: Mathematical and Theoretical (Commissioned Topical Review Article)
Relativistic recoil corrections to the electron-vacuum-polarization contribution in light muonic atoms
Creators: name: Karshenboim, Savely G.
name: Ivanov, Vladimir G.
name: Korzinin, Evgeny Yu.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: The relativistic recoil contributions to the Uehling corrections are revisited. We consider a controversy in recent calculations based on different approaches including Breit-type and Grotch-type calculations. We have found that calculations of those authors were in fact done in different gauges and in some of those gauges contributions the retardation and two-photon-exchange effects were missed. We have evaluated such effects and obtained a consistent result from those approaches. We present a correct expression for the Grotch-type approach which produces a correct gauge-invariant result. We also consider a finite-nuclear-size correction for the Uehling term. The results are presented for muonic hydrogen and deuterium atoms and for muonic helium-3 and helium-4 ions.
description: Submitted to Phys. Rev. A; in v.2 results for muonic helium are corrected
title: Unraveling Stability: Using Dynamic Optimization to Understand Muscle Co-contraction Strategies While Walking on Uneven Surfaces
Creators: name: Al-Shimari, Banin
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Dynamic Optimization
subject: Co-contraction
subject: Musculoskeletal Modelling
subject: Subtalar Joint
subject: Mediolateral instability
subject: Engineering--Biomedical

description: All humans are unstable in the mediolateral direction, and this instability is made worse when walking on uneven surfaces. To compensate for the instability, several strategies are utilized by the neuromuscular system, one being muscular co-contraction. An overwhelming majority of studies utilize EMG data to quantify co-contraction. However, muscle force and EMG are not always directly correlated. Furthermore, some studies have shown a lack of correlation between quasi-stiffness and muscle co-contraction using an EMG-only method. Therefore, the first objective of this thesis was to examine the muscular co-contraction strategies utilized on mediolaterally uneven surfaces and to compare muscle co contraction measures obtained from muscle moments using a dynamic optimization procedure (EMG-Track), with co-contraction measures derived from EMG data (EMG-Based). Our additional objective was to determine correlations between our EMG-Track method with subtalar joint quasi-stiffness using muscle pairs and muscle group moments (i.e., pronators and supinators of the subtalar joint). On average EMG-Track was better able to detect differences in co-contraction across mediolaterally uneven surfaces and speeds. Muscle group co-contraction was more consistently correlated with quasi-stiffness than muscle pair co-contraction. Furthermore, for muscle group co-contraction, we observed positive correlations before heel strike, and negative correlations following heel strike. These conclusions have important implications for other populations such as older adults, where co-contraction interpretations can alter therapeutic interventions.