cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
D3.7 - Report on harmonized and developed ontologies
Creators: name: Yang, Lan
name: Breslin, John
Publisher: name: Zenodo
Year: 2023
Subjects: Alignment
Data
Harmonization
Ontology
Standardization

description: To achieve interoperability between different domain-level ontologies (DLOs), OntoCommons aims to harmonize these ontologies while facilitating agreement in their development. In Work Package 3, OntoCommons aims to provide alignments among existing DLOs from the stakeholders' community as well as develop new DLOs to fill the gaps. This task (T3.4) involves several activities, including but not limited to: identifying existing DLOs and corresponding disciplines that need to be covered by the alignment effort; defining the level of alignment that needs to be achieved by the DLOs to ensure interoperability; identifying gaps in the disciplines that can be filled with new DLOs; and developing some new DLOs to cover the gaps. The first report (D3.6) on harmonized and developed ontologies was published in the 27th month. This report (D3.7) was a significant milestone for OntoCommons, as it marked the first step towards greater interoperability between different DLOs. The report focused on domain coverage analysis, gap identification, and harmonization among existing DLOs through bridge concept engineering. By identifying gaps and harmonizing existing DLOs, OntoCommons hoped to pave the way for new DLO development. Now, in this second report, OntoCommons will focus on new DLO development and any updates on the alignment of existing DLOs. The goal is to further improve interoperability and facilitate agreement in the development ofDLOs. By providing alignments among existing DLOs and developing new DLOs, OntoCommons hopes to create a more comprehensive and cohesive ontology landscape. OntoCommons recognizes the importance of ontology harmonization in enabling the sharing and reuse of data across different domains and applications. Through these efforts, OntoCommons aims to promote greater collaboration and innovation within the ontology community, and facilitate the development of more effective and efficient systems.
Downregulation of BRCA1 protein in BCR-ABL1 leukemia cells depends on stress-triggered TIAR-mediated suppression of translation
Creators: name: Podszywalow-Bartnicka, Paulina
name: Wolczyk, Magdalena
name: Kusio-Kobialka, Monika
name: Wolanin, Kamila
name: Skowronek, Krzysztof
name: Nieborowska-Skorska, Margaret
name: Yashodhara Dasgupta
name: Skorski, Tomasz
name: Piwocka, Katarzyna
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Hematology
subject: Cancer
subject: Biological Sciences
subject: Chemistry
subject: Molecular Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Cell Biology
subject: Biochemistry
subject: Biophysics

description: BRCA1 tumor suppressor regulates crucial cellular processes involved in DNA damage repair and cell cycle control. We showed that expression of BCR-ABL1 correlates with decreased level of BRCA1 protein, which promoted aberrant mitoses and aneuploidy as well as altered DNA damage response. Using polysome profiling and luciferase-BRCA1 3’UTR reporter system here we demonstrate that downregulation of BRCA1 protein in CML is caused by inhibition of BRCA1 mRNA translation, but not by increased protein degradation or reduction of mRNA level and half-life. We investigated 2 mRNA-binding proteins – HuR and TIAR showing specificity to AU-Rich Element (ARE) sites in 3’UTR of mRNA. BCR-ABL1 promoted cytosolic localization of TIAR and HuR, their binding to BRCA1 mRNA and formation of the TIAR-HuR complex. HuR protein positively regulated BRCA1 mRNA stability and translation, conversely TIAR negatively regulated BRCA1 translation and was found localized predominantly in the cytosolic stress granules in CML cells. TIAR-dependent downregulation of BRCA1 protein level was a result of ER stress, which is activated in BCR-ABL1 expressing cells, as we previously shown. Silencing of TIAR in CML cells strongly elevated BRCA1 level. Altogether, we determined that TIAR-mediated repression of BRCA1 mRNA translation is responsible for downregulation of BRCA1 protein level in BCR-ABL1 –positive leukemia cells. This mechanism may contribute to genomic instability and provide justification for targeting PARP1 and/or RAD52 to induce synthetic lethality in “BRCAness” CML and BCR-ABL1 –positive ALL cells.
title: Migration Against the Tide
title: Case Studies of South Australia, Sweden and Croatia
titleType: Subtitle
Creators: name: Vuin, Ana
Publisher: name: Charles Darwin University
Year: 2019

description: The purpose of this thesis was to examine in-migration to depopulating SPAs in three different countries through a conceptual framework that explores the in-migration effects on the migrant, place and community. The thesis argues that the effects of these processes are ingrained and dependent on the relationship between migration and mobilities. The focus was on the spatial, social and temporal aspects of in-migration to depopulating SPAs. Migration was positioned as a complex, contextual and dynamic process that is enabled through mobility. For interpretation, this thesis proposed a particular framework to theorise such processes in depopulating SPAs. It positioned the experiences of the in-migrant, characteristics of the place and community responses to the in-migration processes as the products of the broader mobility context. It identified the four crucial dimensions in this process: migrant, place, community and mobility. Finally, it offered an insight into the complex interplay of these dimensions in three countries over five years using different qualitative methods. By combining interviews, ethnographic approaches, quantitative descriptive data and an extensive literature review, this thesis attempted to further elaborate the effects of ‘migration against the tide’ in depopulating SPAs and provide a more comprehensive system-wide view of this process.
Mechanism of liponecrosis, a distinct mode of programmed cell death
Creators: name: Richard, Vincent R
name: Beach, Adam
name: Piano, Amanda
name: Leonov, Anna
name: Feldman, Rachel
name: Burstein, Michelle T
name: Kyryakov, Pavlo
name: Gomez-Perez, Alejandra
name: Arlia-Ciommo, Anthony
name: Baptista, Stefanie
name: Campbell, Cory
name: Goncharov, Daniel
name: Pannu, Sonia
name: Patrinos, Dimitri
name: Behnaz Sadri
name: Svistkova, Veronika
name: Victor, Andrew
name: Titorenko, Vladimir I
Publisher: name: Taylor & Francis
Year: 2014
Subjects: subject: 60506 Virology
subject: FOS: Biological sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Earth and Environmental Sciences
subject: Molecular Biology
subject: Genetics
subject: Cell Biology
subject: Microbiology
subject: Medicine
subject: Biochemistry
subject: Biophysics

description: An exposure of the yeast Saccharomyces cerevisiae to exogenous palmitoleic acid (POA) elicits “liponecrosis," a mode of programmed cell death (PCD) which differs from the currently known PCD subroutines. Here, we report the following mechanism for liponecrotic PCD. Exogenously added POA is incorporated into POA-containing phospholipids that then amass in the endoplasmic reticulum membrane, mitochondrial membranes and the plasma membrane. The buildup of the POA-containing phospholipids in the plasma membrane reduces the level of phosphatidylethanolamine in its extracellular leaflet, thereby increasing plasma membrane permeability for small molecules and committing yeast to liponecrotic PCD. The excessive accumulation of POA-containing phospholipids in mitochondrial membranes impairs mitochondrial functionality and causes the excessive production of reactive oxygen species in mitochondria. The resulting rise in cellular reactive oxygen species above a critical level contributes to the commitment of yeast to liponecrotic PCD by: (1) oxidatively damaging numerous cellular organelles, thereby triggering their massive macroautophagic degradation; and (2) oxidatively damaging various cellular proteins, thus impairing cellular proteostasis. Several cellular processes in yeast exposed to POA can protect cells from liponecrosis. They include: (1) POA oxidation in peroxisomes, which reduces the flow of POA into phospholipid synthesis pathways; (2) POA incorporation into neutral lipids, which prevents the excessive accumulation of POA-containing phospholipids in cellular membranes; (3) mitophagy, a selective macroautophagic degradation of dysfunctional mitochondria, which sustains a population of functional mitochondria needed for POA incorporation into neutral lipids; and (4) a degradation of damaged, dysfunctional and aggregated cytosolic proteins, which enables the maintenance of cellular proteostasis.
KSHV viral cyclin interferes with T-cell development and induces lymphoma through Cdk6 and Notch activation in vivo
Creators: name: Pekkonen, Pirita
name: Järviluoma, Annika
name: Zinovkina, Nadezhda
name: Cvrljevic, Anna
name: Sonam Prakash
name: Westermarck, Jukka
name: Evan, Gerard I
name: Cesarman, Ethel
name: Verschuren, Emmy W
name: Ojala, Päivi M
Publisher: name: Taylor & Francis
Year: 2014
Subjects: subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Hematology
subject: Cancer
subject: Developmental Biology
subject: Meta Science
subject: Biotechnology
subject: Pharmacology
subject: Molecular Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Cell Biology
subject: Biochemistry

description: Kaposi's sarcoma herpesvirus (KSHV)-encoded v-cyclin, a homolog of cellular cyclin D2, activates cellular CDK6, promotes G1-S transition of the cell cycle, induces DNA damage, apoptosis, autophagy and is reported to have oncogenic potential. Here we show that in vivo expression of v-cyclin in the B- and T-cell lymphocyte compartments results in a markedly low survival due to high penetrance of early-onset T-cell lymphoma and pancarditis. The v-cyclin transgenic mice have smaller pre-tumorigenic lymphoid organs, showing decreased cellularity, and increased proliferation and apoptosis. Furthermore, v-cyclin expression resulted in decreased amounts of CD3-expressing mature T-cells in the secondary lymphoid organs concurrent with alterations in the T-cell subpopulations of the thymus. This suggests that v-cyclin interferes with normal T-cell development. As the Notch pathway is recognized for its role in both T-cell development and lymphoma initiation, we addressed the role of Notch in the v-cyclin-induced alterations. Fittingly, we demonstrate induction of Notch3 and Hes1 in the pre-tumorigenic thymi and lymphomas of v-cyclin expressing mice, and show that lymphoma growth and viability are dependent on activated Notch signaling. Notch3 transcription and growth of the lymphomas was dependent on CDK6, as determined by silencing of CDK6 expression or chemical inhibition, respectively. Our work here reveals a viral cyclin-CDK6 complex as an upstream regulator of Notch receptor, suggesting that cyclins can play a role in the initiation of Notch-dependent lymphomagenesis.
KSHV viral cyclin interferes with T-cell development and induces lymphoma through Cdk6 and Notch activation in vivo
Creators: name: Pekkonen, Pirita
name: Järviluoma, Annika
name: Zinovkina, Nadezhda
name: Cvrljevic, Anna
name: Sonam Prakash
name: Westermarck, Jukka
name: Evan, Gerard I
name: Cesarman, Ethel
name: Verschuren, Emmy W
name: Ojala, Päivi M
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Hematology
subject: Cancer
subject: Developmental Biology
subject: Meta Science
subject: Biotechnology
subject: Pharmacology
subject: Molecular Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Cell Biology
subject: Biochemistry

description: Kaposi's sarcoma herpesvirus (KSHV)-encoded v-cyclin, a homolog of cellular cyclin D2, activates cellular CDK6, promotes G1-S transition of the cell cycle, induces DNA damage, apoptosis, autophagy and is reported to have oncogenic potential. Here we show that in vivo expression of v-cyclin in the B- and T-cell lymphocyte compartments results in a markedly low survival due to high penetrance of early-onset T-cell lymphoma and pancarditis. The v-cyclin transgenic mice have smaller pre-tumorigenic lymphoid organs, showing decreased cellularity, and increased proliferation and apoptosis. Furthermore, v-cyclin expression resulted in decreased amounts of CD3-expressing mature T-cells in the secondary lymphoid organs concurrent with alterations in the T-cell subpopulations of the thymus. This suggests that v-cyclin interferes with normal T-cell development. As the Notch pathway is recognized for its role in both T-cell development and lymphoma initiation, we addressed the role of Notch in the v-cyclin-induced alterations. Fittingly, we demonstrate induction of Notch3 and Hes1 in the pre-tumorigenic thymi and lymphomas of v-cyclin expressing mice, and show that lymphoma growth and viability are dependent on activated Notch signaling. Notch3 transcription and growth of the lymphomas was dependent on CDK6, as determined by silencing of CDK6 expression or chemical inhibition, respectively. Our work here reveals a viral cyclin-CDK6 complex as an upstream regulator of Notch receptor, suggesting that cyclins can play a role in the initiation of Notch-dependent lymphomagenesis.
title: The Savvy savage
title: fire, proprietary interest, and the western discourse on Aboriginal ecology
titleType: Subtitle
Creators: name: Buckley, Alexander
Publisher: name: Charles Darwin University
Year: 2004

description: This essay reviews the history of the Western discourse on Aboriginal Ecology. It then applies genealogical narrative analysis to recent texts involved in the appropriation of Aboriginal ecological knowledge concerning fire. It identifies fire as a key metaphor in Aboriginal discourse and as a primary tool in Aboriginal management of natural resources. It shows that early Western representations of Aboriginal Ecology, in particular the application of fire, enabled and legitimated European colonisation of Australia. It considers Western Ecology, and the attitudes to and management of the landscape that are based on it, to be the product of a peculiarly European intellectual heritage, transposed to Australia during colonisation. It suggests that the inherent flammability of the Australian bush required Western Ecology to adapt to the new environment, and to reevaluate the role played by fire in Aboriginal Ecology. It examines the process through which Western Ecology now seeks to retrieve the Aboriginal ecological knowledge and praxis, erased during European colonisation, in order to stabilize that colony. It demonstrates that essential differences in the cosmologies upon which Aboriginal and Western Ecologies are based introduce problems for translating the former into the latter. It then considers the role of Aboriginal discourse in this process, in particular the increasing participation of Aboriginal producers in the Western discourse. It shows that, by valorizing Aboriginal discourse as an authentic source of the required knowledge, Western scientific discourse has opened the way for Aboriginal authors to subvert Western discourse, to assert control over land, to create a space in which to reproduce their own discourse, and to exercise control over the ritual reproduction of their own subjectivity.
Mechanism of liponecrosis, a distinct mode of programmed cell death
Creators: name: Richard, Vincent R
name: Beach, Adam
name: Piano, Amanda
name: Leonov, Anna
name: Feldman, Rachel
name: Burstein, Michelle T
name: Kyryakov, Pavlo
name: Gomez-Perez, Alejandra
name: Arlia-Ciommo, Anthony
name: Baptista, Stefanie
name: Campbell, Cory
name: Goncharov, Daniel
name: Pannu, Sonia
name: Patrinos, Dimitri
name: Behnaz Sadri
name: Svistkova, Veronika
name: Victor, Andrew
name: Titorenko, Vladimir I
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: 60506 Virology
subject: FOS: Biological sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Earth and Environmental Sciences
subject: Molecular Biology
subject: Genetics
subject: Cell Biology
subject: Microbiology
subject: Medicine
subject: Biochemistry
subject: Biophysics

description: An exposure of the yeast Saccharomyces cerevisiae to exogenous palmitoleic acid (POA) elicits “liponecrosis," a mode of programmed cell death (PCD) which differs from the currently known PCD subroutines. Here, we report the following mechanism for liponecrotic PCD. Exogenously added POA is incorporated into POA-containing phospholipids that then amass in the endoplasmic reticulum membrane, mitochondrial membranes and the plasma membrane. The buildup of the POA-containing phospholipids in the plasma membrane reduces the level of phosphatidylethanolamine in its extracellular leaflet, thereby increasing plasma membrane permeability for small molecules and committing yeast to liponecrotic PCD. The excessive accumulation of POA-containing phospholipids in mitochondrial membranes impairs mitochondrial functionality and causes the excessive production of reactive oxygen species in mitochondria. The resulting rise in cellular reactive oxygen species above a critical level contributes to the commitment of yeast to liponecrotic PCD by: (1) oxidatively damaging numerous cellular organelles, thereby triggering their massive macroautophagic degradation; and (2) oxidatively damaging various cellular proteins, thus impairing cellular proteostasis. Several cellular processes in yeast exposed to POA can protect cells from liponecrosis. They include: (1) POA oxidation in peroxisomes, which reduces the flow of POA into phospholipid synthesis pathways; (2) POA incorporation into neutral lipids, which prevents the excessive accumulation of POA-containing phospholipids in cellular membranes; (3) mitophagy, a selective macroautophagic degradation of dysfunctional mitochondria, which sustains a population of functional mitochondria needed for POA incorporation into neutral lipids; and (4) a degradation of damaged, dysfunctional and aggregated cytosolic proteins, which enables the maintenance of cellular proteostasis.
D3.8 - Report on the finalized Review of Domain Interoperability
Creators: name: Chiacchiera, Silvia
Publisher: name: Zenodo
Year: 2023
Subjects: Ontology
Data
Interoperability
Data integration

description: This document addresses interoperability in a broad sense, in the context of data, in particular for materials and manufacturing. It is meant for developers (at domain level) of ontologies and platforms, tools or components that use them. To set the stage and give an overview of the various facets of the topic, the document collects existing definitions and classifications of interoperability (its types, layers, levels) and points to recommendations from various entities and communities. Next, it provides an analysis of a set of interoperability scenarios, proposes a classification of broad interoperability requirements and components to address them. Finally, it summarizes advice from OntoCommons on interoperability issues.
Variational approach for the flow of Ree-Eyring and Casson fluids in pipes
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Mechanics

description: The flow of Ree-Eyring and Casson non-Newtonian fluids is investigated using a variational principle to optimize the total stress. The variationally-obtained solutions are compared to the analytical solutions derived from the Weissenberg-Rabinowitsch-Mooney equation and the results are found to be identical within acceptable numerical errors and modeling approximations.
Deterministic and stochastic algorithms for resolving the flow fields in ducts and networks using energy minimization
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Mechanics
Computer Engineering

description: Several deterministic and stochastic multi-variable global optimization algorithms (Conjugate Gradient, Nelder-Mead, Quasi-Newton, and Global) are investigated in conjunction with energy minimization principle to resolve the pressure and volumetric flow rate fields in single ducts and networks of interconnected ducts. The algorithms are tested with seven types of fluid: Newtonian, power law, Bingham, Herschel-Bulkley, Ellis, Ree-Eyring and Casson. The results obtained from all those algorithms for all these types of fluid agree very well with the analytically derived solutions as obtained from the traditional methods which are based on the conservation principles and fluid constitutive relations. The results confirm and generalize the findings of our previous investigations that the energy minimization principle is at the heart of the flow dynamics systems. The investigation also enriches the methods of Computational Fluid Dynamics for solving the flow fields in tubes and networks for various types of Newtonian and non-Newtonian fluids.
Energy minimization for the flow in ducts and networks
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Mechanics

description: The present paper is an attempt to demonstrate how the energy minimization principle may be considered as a governing rule for the physical equilibrium that determines the flow fields in tubes and networks. We previously investigated this issue using a numerical stochastic method, specifically simulated annealing, where we demonstrated the problem by some illuminating examples and concluded that energy minimization principle can be a valid hypothesis. The investigation in this paper is more general as it is based to a certain extent on an analytical approach.
Emission and recombination coefficients for hydrogen with kappa-distributed electron energies
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: subject: Atomic Physics
subject: Instrumentation, Techniques, and Astronomical Observations
subject: 20104 Galactic Astronomy
subject: FOS: Physical sciences
subject: Stellar Astronomy
subject: Astrophysics
subject: Planetary Science
subject: Extragalactic Astronomy
subject: Space Science

description: We provide a data set of emission and recombination coefficients of hydrogen using a kappa-distribution of electron energies rather than the more traditional Maxwell-Boltzmann (MB) distribution. The data are mainly relevant to thin and relatively cold plasma found in planetary nebulae and H II regions. The data set extends the previous data sets provided by Storey and Hummer which were computed using a MB distribution. The data set, which is placed in the public domain, is structured as a function of electron number density, temperature and kappa. Interactive fortran 77 and C++ data servers are also provided as an accessory to probe the data and obtain Lagrange-interpolated values for any choice of all three variables between the explicitly computed values.
Household chaos and pre-bedtime behaviors in young children
Creators: name: Poliakova, Polina
name: Weaver-Rogers, Stephanie
name: Garcia, Wanda
Publisher: name: No Publisher Supplied
Year: 2022

description: Objective: To explore the relation between household chaos and child sleep health practices. Exploring this interaction may offer potential intervention targets on tackling bedtime resistance and poor sleep quality. Prior research suggests that children experiencing greater household chaos and sleep problems are at risk for increased behavioral and academic struggles. Methods: Caregivers of 141 1–5-year-old children (age M=4.01, SD=1.05) completed measures on demographics, household chaos and child sleep. Sample demographics include: (40.4%) African American, (40.40%) Hispanic/Latinx; 17% biracial; 0.7% White; 50.4% Female. Average household income: $20-30,000 (M=3.33, SD= 1.63), SD=1.52. Summary scores of 10 positive and 11 negative pre-bedtime behaviors were created. Pearson’s correlations tested relationships between household chaos and positive/negative sleep health behaviors. Results: Most parents didn’t identify problematic sleep (76%), while indicating difficulty getting children to sleep (71%). 23% of children didn’t get the nightly recommended length of sleep. Families engaged in greater positive pre-bedtime sleep behaviors (M=5.11, SD=2.29) and less negative (M=3.25, SD=1.74); CHAOS levels were moderate (M=2.13, SD=.68). Greater household CHAOS was significantly associated with greater negative pre-bedtime behaviors (r=.17, p=.05), but not positive (r=.01, p=.93). Conclusions: Targeting negative pre-bedtime behaviors may be more effective in reducing household CHAOS than interventions aiming to address positive behaviors in improving child sleep quality. The lack of studies on negative pre-bedtime behaviors, suggest observing the relationship between sleep and CHAOS may add to existing literature to address poor sleep behaviors in children. Future research should consider exploring the relationship between prebedtime behavior, chaos and daytime behavior in children.
Letter, Davis Polk Wardwell Sunderland and Kiefer Law Firm to T. Bayles Minuse, September 26, 1955
Creators: name: Sunderland, Davis Polk Wardwell
name: Jones, Wallace S.
Publisher: name: Unknown
Year: 1955
Subjects: Stony Brook
Correspondence
Taxes
Tax exemptions

description: This letter is written by Wallace S. Jones of Davis Polk Wardwell Sunderland & Kiendl Law Firm to T. Bayles Minuse of the Stony Brook Community Fund on September 26, 1955.
Plasma Physics in Strong-Field Regimes
Creators: name: Shi, Yuan
Publisher: name: Zenodo
Year: 2018
Subjects: Plasma
QED
Laser
Magnetic field

description: A Dissertation Presented to the Faculty of Princeton University in Candidacy for the Degree of Doctor of Philosophy Recommended for Acceptance by the Department of Astrophysical Sciences Program in Plasma Physics
description: The official version is freely available online through ProQuest Dissertations & Theses Global
Variational approach for the flow of Ree-Eyring and Casson fluids in pipes
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2015
Subjects: Applied Physics
Mechanics

description: The flow of Ree-Eyring and Casson non-Newtonian fluids is investigated using a variational principle to optimize the total stress. The variationally-obtained solutions are compared to the analytical solutions derived from the Weissenberg-Rabinowitsch-Mooney equation and the results are found to be identical within acceptable numerical errors and modeling approximations.
Solving the flow fields in conduits and networks using energy minimization principle with simulated annealing
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Mechanics
Computer Engineering

description: In this paper, we propose and test an intuitive assumption that the pressure field in single conduits and networks of interconnected conduits adjusts itself to minimize the total energy consumption required for transporting a specific quantity of fluid. We test this assumption by using linear flow models of Newtonian fluids transported through rigid tubes and networks in conjunction with a simulated annealing (SA) protocol to minimize the total energy cost. All the results confirm our hypothesis as the SA algorithm produces very close results to those obtained from the traditional deterministic methods of identifying the flow fields by solving a set of simultaneous equations based on the conservation principles. The same results apply to electric ohmic conductors and networks of interconnected ohmic conductors. Computational experiments conducted in this regard confirm this extension. Further studies are required to test the energy minimization hypothesis for the non-linear flow systems.
Methods for Calculating the Pressure Field in the Tube Flow
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Mechanics

description: In this paper we outline methods for calculating the pressure field inside flow conduits in the one-dimensional flow models where the pressure is dependent on the axial coordinate only. The investigation is general with regard to the tube mechanical properties (rigid or distensible), and with regard to the cross sectional variation along the tube length (constant or variable). The investigation is also general with respect to the fluid rheology as being Newtonian or non-Newtonian.
Further validation to the variational method to obtain flow relations for generalized Newtonian fluids
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Mechanics

description: We continue our investigation to the use of the variational method to derive flow relations for generalized Newtonian fluids in confined geometries. While in the previous investigations we used the straight circular tube geometry with eight fluid rheological models to demonstrate and establish the variational method, the focus here is on the plane long thin slit geometry using those eight rheological models, namely: Newtonian, power law, Ree-Eyring, Carreau, Cross, Casson, Bingham and Herschel-Bulkley. We demonstrate how the variational principle based on minimizing the total stress in the flow conduit can be used to derive analytical expressions, which are previously derived by other methods, or used in conjunction with numerical procedures to obtain numerical solutions which are virtually identical to the solutions obtained previously from well established methods of fluid dynamics. In this regard, we use the method of Weissenberg-Rabinowitsch-Mooney-Schofield (WRMS), with our adaptation from the circular pipe geometry to the long thin slit geometry, to derive analytical formulae for the eight types of fluid where these derived formulae are used for comparison and validation of the variational formulae and numerical solutions. Although some examples may be of little value, the optimization principle which the variational method is based upon has a significant theoretical value as it reveals the tendency of the flow system to assume a configuration that minimizes the total stress. Our proposal also offers a new methodology to tackle common problems in fluid dynamics and rheology.
D3.10 - Report on the Second focused workshop on domain ontologies
Creators: name: Sarkar, Arkopaul
Publisher: name: Zenodo
Year: 2023
Subjects: Ontology
Data
Standardisation
Industry
Wokshop
FOMI

description: The focused workshop 3.2 was entitled “Formal Ontologies Meet Industry” which took place along with the eponymous workshop FOMI, 2022. was organised by École Nationale d’Ingénieurs de Tarbes at the institute’s premises at Tarbes, France. By engaging with not only to FOMI workshop but also with Industrial Ontology Foundry, this workshop had opportunity to gain attendance of almost 100 participants from academia, industry, and research, majority of whom were also physically present at the venue and fostered a great deal of interactions. These activities helped the project to gather inputs from the community in the field of materials and manufacturing and disseminated the mission and vision of OntoCommons to them. In this document, many aspects of this event are described mainly focussing on the OntoCommons focus workshop on Day 2.
Comparing Poiseuille with 1D Navier-Stokes Flow in Rigid and Distensible Tubes and Networks
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Cardiology
Applied Physics
Mechanics
Biological Engineering
Biological Techniques

description: A comparison is made between the Hagen-Poiseuille flow in rigid tubes and networks on one side and the time-independent one-dimensional Navier-Stokes flow in elastic tubes and networks on the other. Analytical relations, a Poiseuille network flow model and two finite element Navier-Stokes one-dimensional flow models have been developed and used in this investigation. The comparison highlights the differences between Poiseuille and one-dimensional Navier-Stokes flow models which may have been unjustifiably treated as equivalent in some studies.
One-Dimensional Navier-Stokes Finite Element Flow Model
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: subject: Applied Physics
subject: Mechanics
subject: Computer Engineering
subject: Mechanical Engineering
subject: FOS: Mechanical engineering

description: This technical report documents the theoretical, computational, and practical aspects of the one-dimensional Navier-Stokes finite element flow model. The document is particularly useful to those who are interested in implementing, validating and utilizing this relatively-simple and widely-used model.
The flow of power law fluids in elastic networks and porous media
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Mechanics

description: The flow of power law fluids, which include shear thinning and shear thickening as well as Newtonian as a special case, in networks of interconnected elastic tubes is investigated using a residual based pore scale network modeling method with the employment of newly derived formulae. Two relations describing the mechanical interaction between the local pressure and local cross sectional area in distensible tubes of elastic nature are considered in the derivation of these formulae. The model can be used to describe shear dependent flows of mainly viscous nature. The behavior of the proposed model is vindicated by several tests in a number of special and limiting cases where the results can be verified quantitatively or qualitatively. The model, which is the first of its kind, incorporates more than one major non-linearity corresponding to the fluid rheology and conduit mechanical properties, that is non-Newtonian effects and tube distensibility. The formulation, implementation and performance indicate that the model enjoys certain advantages over the existing models such as being exact within the restricting assumptions on which the model is based, easy implementation, low computational costs, reliability and smooth convergence. The proposed model can therefore be used as an alternative to the existing Newtonian distensible models; moreover it stretches the capabilities of the existing modeling approaches to reach non-Newtonian rheologies.
title: Focus 2020 [Salon]
Publisher: name: Centre Norbert Elias
Year: 2020

description: Film documentaire, bande-dessinée, web-doc, parcours d’exposition, pièce de théâtre, revue  numérique, roman-photo, jeu-vidéo et documentaire sonore sont devenus une réalité incontournable  des sciences sociales.
The Flow of Newtonian and power law fluids in elastic tubes
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Mechanics

description: We derive analytical expressions for the flow of Newtonian and power law fluids in elastic circularly-symmetric tubes based on a lubrication approximation where the flow velocity profile at each cross section is assumed to have its axially-dependent characteristic shape for the given rheology and cross sectional size. Two pressure-area constitutive elastic relations for the tube elastic response are used in these derivations. We demonstrate the validity of the derived equations by observing qualitatively correct trends in general and quantitatively valid asymptotic convergence to limiting cases. The Newtonian formulae are compared to similar formulae derived previously from a one-dimensional version of the Navier-Stokes equations.
Accounting for the Use of Different Length Scale Factors in x, y and z Directions
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Applied Computer Science

description: This short article presents a mathematical formula required for metric corrections in image extraction and processing when using different length scale factors in three-dimensional space which is normally encountered in cryomicrotome image construction techniques.
Navier-Stokes Flow in Cylindrical Elastic Tubes
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Mechanics

description: Analytical expressions correlating the volumetric flow rate to the inlet and outlet pressures are derived for the time-independent flow of Newtonian fluids in cylindrically-shaped elastic tubes using a one-dimensional Navier-Stokes flow model with two pressure-area constitutive relations. These expressions for elastic tubes are the equivalent of Poiseuille and Poiseuille-type expressions for rigid tubes which were previously derived for the flow of Newtonian and non-Newtonian fluids under various flow conditions. Formulae and procedures for identifying the pressure field and tube geometric profile are also presented. The results are validated by a finite element method implementation. Sensible trends in the analytical and numerical results are observed and documented.
Additional file 1 of Health-related quality of life among adults living with chronic non-communicable diseases in the Ho Municipality of Ghana: a health facility-based cross-sectional study
Creators: name: Witts, William Kwame
name: Amu, Hubert
name: Dowou, Robert Kokou
name: Kwafo, Frank Oppong
name: Bain, Luchuo Engelbert
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Supplementary Material 1
Further validation to the variational method to obtain flow relations for generalized Newtonian fluids
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Mechanics

description: We continue our investigation to the use of the variational method to derive flow relations for generalized Newtonian fluids in confined geometries. While in the previous investigation we used the straight cylindrical tube geometry with six fluid rheological models to demonstrate and establish the variational method, the focus here is on the plane long thin slit geometry using two rheological models. We demonstrate how the variational principle based on minimizing the total stress in the flow conduit can be used to derive analytical expressions that are previously derived by other methods. Although the examples themselves are of little value, the optimization principle which the variational method is based upon has a significant theoretical value as it reveals the tendency of the flow system to assume a configuration that minimizes the total stress. Our proposal also offers a new methodology to tackle common problems in fluid dynamics and rheology.
Additional file 2 of Health-related quality of life among adults living with chronic non-communicable diseases in the Ho Municipality of Ghana: a health facility-based cross-sectional study
Creators: name: Witts, William Kwame
name: Amu, Hubert
name: Dowou, Robert Kokou
name: Kwafo, Frank Oppong
name: Bain, Luchuo Engelbert
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Supplementary Material 2
Further validation to the variational method to obtain flow relations for generalized Newtonian fluids
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2015
Subjects: Applied Physics
Mechanics

description: We continue our investigation to the use of the variational method to derive flow relations for generalized Newtonian fluids in confined geometries. While in the previous investigations we used the straight circular tube geometry with eight fluid rheological models to demonstrate and establish the variational method, the focus here is on the plane long thin slit geometry using those eight rheological models, namely: Newtonian, power law, Ree-Eyring, Carreau, Cross, Casson, Bingham and Herschel-Bulkley. We demonstrate how the variational principle based on minimizing the total stress in the flow conduit can be used to derive analytical expressions, which are previously derived by other methods, or used in conjunction with numerical procedures to obtain numerical solutions which are virtually identical to the solutions obtained previously from well established methods of fluid dynamics. In this regard, we use the method of Weissenberg-Rabinowitsch-Mooney-Schofield (WRMS), with our adaptation from the circular pipe geometry to the long thin slit geometry, to derive analytical formulae for the eight types of fluid where these derived formulae are used for comparison and validation of the variational formulae and numerical solutions. Although some examples may be of little value, the optimization principle which the variational method is based upon has a significant theoretical value as it reveals the tendency of the flow system to assume a configuration that minimizes the total stress. Our proposal also offers a new methodology to tackle common problems in fluid dynamics and rheology.
Flow of non-Newtonian Fluids in Converging-Diverging Rigid Tubes
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Mechanics

description: A residual-based lubrication method is used in this paper to find the flow rate and pressure field in converging-diverging rigid tubes for the flow of time-independent category of non-Newtonian fluids. Five converging-diverging prototype geometries were used in this investigation in conjunction with two fluid models: Ellis and Herschel-Bulkley. The method was validated by convergence behavior sensibility tests, convergence to analytical solutions for the straight tubes as special cases for the converging-diverging tubes, convergence to analytical solutions found earlier for the flow in converging-diverging tubes of Newtonian fluids as special cases for non-Newtonian, and convergence to analytical solutions found earlier for the flow of power-law fluids in converging-diverging tubes. A brief investigation was also conducted on a sample of diverging-converging geometries. The method can in principle be extended to the flow of viscoelastic and thixotropic/rheopectic fluid categories. The method can also be extended to geometries varying in size and shape in the flow direction, other than the perfect cylindrically-symmetric converging-diverging ones, as long as characteristic flow relations correlating the flow rate to the pressure drop on the discretized elements of the lubrication approximation can be found. These relations can be analytical, empirical and even numerical and hence the method has a wide applicability range.
Navier-Stokes Flow in Converging-Diverging Distensible Tubes
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Mechanics

description: We use a method based on the lubrication approximation in conjunction with a residual-based mass-continuity iterative solution scheme to compute the flow rate and pressure field in distensible converging-diverging tubes for Navier-Stokes fluids. We employ an analytical formula derived from a one-dimensional version of the Navier-Stokes equations to describe the underlying flow model that provides the residual function. This formula correlates the flow rate to the boundary pressures in straight cylindrical elastic tubes with constant-radius. We validate our findings by the convergence toward a final solution with fine discretization as well as by comparison to the Poiseuille-type flow in its convergence toward analytic solutions found earlier in rigid converging-diverging tubes. We also tested the method on limiting special cases of cylindrical elastic tubes with constant-radius where the numerical solutions converged to the expected analytical solutions. The distensible model has also been endorsed by its convergence toward the rigid Poiseuille-type model with increasing the tube wall stiffness. Lubrication-based one-dimensional finite element method was also used for verification. In this investigation five converging-diverging geometries are used for demonstration, validation and as prototypes for modeling converging-diverging geometries in general.
Fluid Flow at Branching Junctions
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Mechanics

description: The flow of fluids at branching junctions plays important kinematic and dynamic roles in most biological and industrial flow systems. The present paper highlights some key issues related to the flow of fluids at these junctions with special emphasis on the biological flow networks particularly blood transportation vasculature.
Additional file 3 of Health-related quality of life among adults living with chronic non-communicable diseases in the Ho Municipality of Ghana: a health facility-based cross-sectional study
Creators: name: Witts, William Kwame
name: Amu, Hubert
name: Dowou, Robert Kokou
name: Kwafo, Frank Oppong
name: Bain, Luchuo Engelbert
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Supplementary Material 3
Non-Newtonian Rheology in Blood Circulation
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Mechanics

description: Blood is a complex suspension that demonstrates several non-Newtonian rheological characteristics such as deformation-rate dependency, viscoelasticity and yield stress. In this paper we outline some issues related to the non-Newtonian effects in blood circulation system and present modeling approaches based mostly on the past work in this field.
Memo, T. Bayles Minuse to A. B. S., September 24, 1955
Creators: name: Minuse, T. Bayles
Publisher: name: Unknown
Year: 1955
Subjects: Stony Brook
Actors
Theatrical productions
Correspondence

description: This memo is written by T. Bayles Minuse to A. B. S. on September 24, 1955, in regards to actor William Thornton for potential William Shakespeare material at the Dogwood Theatre.
Additional file 1 of Longitudinal changes in device-measured physical activity from childhood to young adulthood: the PANCS follow-up study
Creators: name: Husøy, Anders
name: Kolle, E.
name: Steene-Johannessen, J.
name: Dalene, K.E.
name: Andersen, L. B.
name: Ekelund, U.
name: Anderssen, S. A.
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Science Policy
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Mental Health

description: Supplementary Material 1
Pore-Scale Modeling of Navier-Stokes Flow in Distensible Networks and Porous Media
Creators: name: Sochi, Taha
Publisher: name: figshare
Year: 2014
Subjects: Applied Physics
Applied Computer Science

description: In this paper, a pore-scale network modeling method, based on the flow continuity residual in conjunction with a Newton-Raphson non-linear iterative solving technique, is proposed and used to obtain the pressure and flow fields in a network of interconnected distensible ducts representing, for instance, blood vasculature or deformable porous media. A previously derived analytical expression correlating boundary pressures to volumetric flow rate in compliant tubes for a pressure-area constitutive elastic relation has been used to represent the underlying flow model. Comparison to a preceding equivalent method, the one-dimensional Navier-Stokes finite element, was made and the results were analyzed. The advantages of the new method have been highlighted and practical computational issues, related mainly to the rate and speed of convergence, have been discussed.