cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Optimizing implementation of adult domiciliary oxygen therapy in fibrotic interstitial lung disease
Creators: name: Saleem, Ferhan
Publisher: name: University of British Columbia
Year: 2022

description: Background: Interstitial lung disease (ILD) is a collection of diseases that cause fibrosis and/or inflammation of lung parenchyma, often resulting in the adverse consequence of hypoxemia that can be alleviated by domiciliary oxygen. Objectives: 1) Derive and validate a risk model to predict new-onset exertional and resting hypoxemia in patients with ILD. 2) Identify oxygen guidelines worldwide and compare these to national domiciliary oxygen criteria. 3) Compare costs of domiciliary oxygen for patients with ILD and chronic obstructive pulmonary disease (COPD). Methods: 1) A multivariable model that predicted new-onset exertional and resting hypoxemia was derived and validated in international cohorts using time-varying Cox regression, with the final model optimizing Harrell's C-index and goodness-of-fit (GoF). 2) Clinical practice guidelines for domiciliary oxygen were identified and compared to oxygen criteria and funding source used by the 193 member countries in the United Nations obtained from an Internet-based literature review. 3) A retrospective chart review determined monthly costs of oxygen in ILD and COPD within a large domiciliary oxygen program from 2010-2017. Results: 1) The best-performing prediction model for both exertional and resting hypoxemia included age, body mass index, idiopathic pulmonary fibrosis diagnosis, percent-predicted forced vital capacity, and diffusing capacity of carbon monoxide. Good performance was exhibited for prediction of exertional (C-index=0.70, GoF=0.85) and resting hypoxemia (C-index=0.77, GoF=0.27) in the derivation cohort, with performance replicated in the validation cohort except for calibration for prediction of resting hypoxemia (GoF=0.001). 2) Guidelines for continuous oxygen were obtained for 30 respiratory societies and criteria for 46 countries with public funding for oxygen. No public funding was available in 145 countries (5.9 billion people). 3) Cost of oxygen declined after month 1 (ILD: ($202.57 ± $88.88 in month 1 versus $142.21 ± $59.01 in month 2-24, P<0.001; COPD: $222.85 ± $102.52 versus $156.65 ± $60.50, P<0.001). Long-term cost of oxygen in COPD was more than in ILD (P=0.02). Conclusions: These studies will help patients prepare for oxygen initiation, identify variability in oxygen criteria worldwide and quantify the limited access in many countries, and provide funders with a better understanding of costs.
Land Conflict and Land Governance in the Greater Mekong Sub-Region: Case Studies of Urban and Peri-urban in Thailand
Creators: name: Monchai Phongsiri
Publisher: name: Center for Research on Plurality in the Mekong Region (CERP)
Year: 2019
Subjects: urban
peri-urban
land conflict
land grabbing
exclusion

description: Journal of Mekong Societies, 15, 1, 87-110
Additional file 2 of Continuous warfarin administration versus heparin bridging therapy in post colorectal polypectomy haemorrhage: a study protocol for a multicentre randomised controlled trial (WHICH study)
Creators: name: Nagami, Yasuaki
name: Taishi Sakai
name: Yamamura, Masafumi
name: Nakatani, Masami
name: Katsuno, Takayuki
name: Suekane, Takehisa
name: Uno, Hironori
name: Minamino, Hiroaki
name: Masatsugu Okuyama
name: Okamoto, Junichi
name: Mitsutaka Kumamoto
name: Noguchi, Atsushi
name: Yamamori, Kazuki
name: Takaishi, Osamu
name: Ochi, Masahiro
name: Miyazaki, Takako
name: Shigetsugu Tsuji
name: Hisatomo Ikehara
name: Kawaguchi, Koichiro
name: Hayashi, Tomoyuki
name: Mannami, Tomohiko
name: Kakimoto, Kazuki
name: Naito, Yoshihide
name: Hashimoto, Satoru
name: Zhaoliang Li
name: Yoriaki Komeda
name: Kishino, Takaaki
name: Yamamoto, Yoshinobu
name: Mikitaka Iguchi
name: Akamatsu, Takuji
name: Horii, Toshiki
name: Miura, Ko
name: Yamashina, Takeshi
name: Yuusaku Sugihara
name: Watanabe, Noboru
name: Kiyotoki, Shu
name: Fujii, Ryoji
name: Murata, Masaki
name: Ono, Satoshi
name: Narasaka, Toshiaki
name: Kitamura, Shinji
name: Kono, Mitsuhiro
name: Kato, Motohiko
name: Kawaratani, Hideto
name: Tanaka, Kyosuke
name: Yaoita, Takao
name: Shinjiro Yamaguchi
name: Abe, Keiichiro
name: Kawamura, Takuji
name: Kinoshita, Yosuke
name: Imai, Kenichiro
name: Fujinami, Haruka
name: Yada, Tomoyuki
name: Miyamoto, Hayato
name: Yoshida, Hisako
name: Fujiwara, Yasuhiro
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer

description: Additional file 2. Statistical analysis plan.
Building Democracy During War: Nguyen Van Thieu and South Vietnam, 1965–1975
Creators: name: Veith, George
Publisher: name: Monash University
Year: 2022
Subjects: History

description: This dissertation draws on democratic theory to examine how President Nguyen Van Thieu attempted to establish constitutional democracy in the Republic of Vietnam, often called South Vietnam. Although a varied body of work applies democratic theory to other countries and regions of the world, due to the fall of the Republic of Vietnam in April 1975 and the oft-cited view of Thieu as a military dictator, no scholar has seriously analyzed either the country or his presidency through that lens. The main concentration will be on Thieu’s efforts to establish a democratic form of government, and his successes and failures.
Additional file 1 of Continuous warfarin administration versus heparin bridging therapy in post colorectal polypectomy haemorrhage: a study protocol for a multicentre randomised controlled trial (WHICH study)
Creators: name: Nagami, Yasuaki
name: Taishi Sakai
name: Yamamura, Masafumi
name: Nakatani, Masami
name: Katsuno, Takayuki
name: Suekane, Takehisa
name: Uno, Hironori
name: Minamino, Hiroaki
name: Masatsugu Okuyama
name: Okamoto, Junichi
name: Mitsutaka Kumamoto
name: Noguchi, Atsushi
name: Yamamori, Kazuki
name: Takaishi, Osamu
name: Ochi, Masahiro
name: Miyazaki, Takako
name: Shigetsugu Tsuji
name: Hisatomo Ikehara
name: Kawaguchi, Koichiro
name: Hayashi, Tomoyuki
name: Mannami, Tomohiko
name: Kakimoto, Kazuki
name: Naito, Yoshihide
name: Hashimoto, Satoru
name: Zhaoliang Li
name: Yoriaki Komeda
name: Kishino, Takaaki
name: Yamamoto, Yoshinobu
name: Mikitaka Iguchi
name: Akamatsu, Takuji
name: Horii, Toshiki
name: Miura, Ko
name: Yamashina, Takeshi
name: Yuusaku Sugihara
name: Watanabe, Noboru
name: Kiyotoki, Shu
name: Fujii, Ryoji
name: Murata, Masaki
name: Ono, Satoshi
name: Narasaka, Toshiaki
name: Kitamura, Shinji
name: Kono, Mitsuhiro
name: Kato, Motohiko
name: Kawaratani, Hideto
name: Tanaka, Kyosuke
name: Yaoita, Takao
name: Shinjiro Yamaguchi
name: Abe, Keiichiro
name: Kawamura, Takuji
name: Kinoshita, Yosuke
name: Imai, Kenichiro
name: Fujinami, Haruka
name: Yada, Tomoyuki
name: Miyamoto, Hayato
name: Yoshida, Hisako
name: Fujiwara, Yasuhiro
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer

description: Additional file 1. Protocol of WHICH study ver. 7.
title: Strength Training Intensity and Volume Affect Performance of Young Kayakers/Canoeists
Creators: name: Gäbler, Martijn
name: Berberyan, Hermine S.
name: Prieske, Olaf
name: Elferink-Gemser, Marije Titia
name: Hortobagyi, Tibor
name: Warnke, Torsten
name: Granacher, Urs
Publisher: name: Universitätsverlag Potsdam
Year: 2022
Subjects: subject: 610 Medizin und Gesundheit

description: Purpose: The aim of this study was to compare the effects of moderate intensity, low volume (MILV) vs. low intensity, high volume (LIHV) strength training on sport-specific performance, measures of muscular fitness, and skeletal muscle mass in young kayakers and canoeists. Methods: Semi-elite young kayakers and canoeists (N = 40, 13 ± 0.8 years, 11 girls) performed either MILV (70–80% 1-RM, 6–12 repetitions per set) or LIHV (30–40% 1-RM, 60–120 repetitions per set) strength training for one season. Linear mixed-effects models were used to compare effects of training condition on changes over time in 250 and 2,000 m time trials, handgrip strength, underhand shot throw, average bench pull power over 2 min, and skeletal muscle mass. Both between- and within-subject designs were used for analysis. An alpha of 0.05 was used to determine statistical significance. Results: Between- and within-subject analyses showed that monthly changes were greater in LIHV vs. MILV for the 2,000 m time trial (between: 9.16 s, SE = 2.70, p < 0.01; within: 2,000 m: 13.90 s, SE = 5.02, p = 0.01) and bench pull average power (between: 0.021 W⋅kg–1, SE = 0.008, p = 0.02; within: 0.010 W⋅kg–1, SE = 0.009, p > 0.05). Training conditions did not affect other outcomes. Conclusion: Young sprint kayakers and canoeists benefit from LIHV more than MILV strength training in terms of 2,000 m performance and muscular endurance (i.e., 2 min bench pull power).
description: Zweitveröffentlichungen der Universität Potsdam : Humanwissenschaftliche Reihe; 744
Additional file 1 of General practitioners’ deprescribing decisions in older adults with polypharmacy: a case vignette study in 31 countries
Creators: name: Jungo, Katharina Tabea
name: Mantelli, Sophie
name: Zsofia Rozsnyai
name: Missiou, Aristea
name: Kitanovska, Biljana Gerasimovska
name: Weltermann, Birgitta
name: Mallen, Christian
name: Collins, Claire
name: Bonfim, Daiana
name: Kurpas, Donata
name: Petrazzuoli, Ferdinando
name: Gindrovel Dumitra
name: Thulesius, Hans
name: Lingner, Heidrun
name: Johansen, Kasper Lorenz
name: Wallis, Katharine
name: Hoffmann, Kathryn
name: Peremans, Lieve
name: Pilv, Liina
name: Šter, Marija Petek
name: Bleckwenn, Markus
name: Sattler, Martin
name: Ploeg, Milly Van Der
name: Torzsa, Péter
name: Kánská, Petra Bomberová
name: Vinker, Shlomo
name: Assenova, Radost
name: Bravo, Raquel Gomez
name: Viegas, Rita P. A.
name: Tsopra, Rosy
name: Pestic, Sanda Kreitmayer
name: Gintere, Sandra
name: Koskela, Tuomas H.
name: Lazic, Vanja
name: Tkachenko, Victoria
name: Reeve, Emily
name: Luymes, Clare
name: Poortvliet, Rosalinde K. E.
name: Rodondi, Nicolas
name: Jacobijn Gussekloo
name: Streit, Sven
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 1. Appendix 1-3.
Additional file 1 of Rationale and design of the Novel Uses of adaptive Designs to Guide provider Engagement in Electronic Health Records (NUDGE-EHR) pragmatic adaptive randomized trial: a trial protocol
Creators: name: Lauffenburger, Julie C.
name: Isaac, Thomas
name: Trippa, Lorenzo
name: Punam Keller
name: Robertson, Ted
name: Glynn, Robert J.
name: Sequist, Thomas D.
name: Kim, Dae H.
name: Fontanet, Constance P.
name: Castonguay, Edward W. B.
name: Haff, Nancy
name: Barlev, Renee A.
name: Mufaddal Mahesri
name: Chandrashekar Gopalakrishnan
name: Niteesh K. Choudhry
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Additional file 1: Supplement 1 Clinical trial protocol
title: Simulations of earth's local particulate environment.
Creators: name: Mackay, Neil G
Publisher: name: University of Kent
Year: 2023

description: Since the dawn of the space age the near earth environment has been becoming increasingly more cluttered with man made products. In recent years there has been a growing fear that the size of this population is approaching a critical threshold. If the population should pass this threshold there would follow a catastrophic series of collision related breakups resulting in a space environment too 'dirty ’ to make further satellite launches feasible. The situation is further aggravated by the existence of natural cosmic dust passing through near Earth space. The broad aim of the project was to help achieve a better understanding of the near Earth cosmic dust and space debris environment. Specifically the aim was to test existing theories about the dust and debris populations by the use of modelling, experiments and of actual data taken from space exposed materials, from the Long Duration Exposure Facility (LDEF). Two independent computer models were created. The first model simulates impacts on LDEF from cosmic dust particles. The second model simulates impacts on LDEF from space debris. The models allow the researcher to vary certain parameters about debris and dust populations. The models will then predict, from the researcher's defined parameters, the quantity and distribution of impacts expected on LDEF. These predictions can then be compared with the data gathered from microscopic examination of LDEF materials. A number of possible scenarios were investigated in this manner and their strengths and weaknesses assessed in terms of how well they satisfied the LDEF data. In addition an experimental program using a light gas gun and an electrostatic accelerator to produce hypervelocity impact craters was initiated. Ways of attaining more information about individual impact events by study of the impact crater morphology were investigated.
Cell intrinsic immunity by human Guanylate Binding Proteins against Toxoplasma gondii and Salmonella Typhimurium
Creators: name: Fisch, Daniel Heinrich
Publisher: name: Imperial College London
Year: 2020

description: Cell intrinsic defence mechanisms are employed by most cells of a multicellular organism and aid the immune systems in combating infections with intracellular pathogens like the parasite Toxoplasma gondii or the bacterium Salmonella Typhimurium. Interferon-induced GTPases are key components of cell intrinsic defence of rodents and humans. One class of GTPases, the Guanylate Binding Proteins (GBPs), protect against pathogens by targeting and disrupting their intracellular compartments, modulating host cell death, inflammasomes, autophagy and oxidative responses. The function of human GBPs was studied here by developing and employing HRMAn (Host Response to Microbe Analysis), an image analysis platform combining machine learning algorithms and deep learning. HRMAn performs unbiased quantification of host-pathogen interactions and has the capability to learn phenotypes from data. HRMAn can automatically recognise, classify and quantify pathogen killing, replication and cellular responses. Using three in vitro macrophage models, it could be established that human GBP1, GBP2 and GBP5 contribute to Toxoplasma growth control and that GBP1 additionally has the ability to kill parasites and control infection with Salmonella. In contrast to other human cell types, GBP1 expressed in macrophages is able to target parasites and their vacuoles and cytosolic bacteria. Recruitment of GBP1 is controlled by post-translational modifications including isoprenylation or phosphorylation by PIM family kinases. New findings presented here, show that Toxoplasma-induced death of human macrophages required functional GBP1. Its ability to target Toxoplasma vacuoles and parasites through its GTPase activity are critical. Mechanistically, GBP1 releases Toxoplasma-DNA into the cytosol for detection by AIM2, which in turn induces GSDMD-independent, ASC- and CASP8-dependent apoptosis. Similarly, GBP1 targets cytosolic Salmonella, where it facilitates caspase-4 recruitment and activation leading to increased pyroptosis. A regulatory mechanism can inactivate GBP1 through caspase-1-mediated cleavage. The human GBP protein family therefore are essential regulators of cell intrinsic macrophage defence and gatekeepers of host cell death.
Additional file 2 of Rationale and design of the Novel Uses of adaptive Designs to Guide provider Engagement in Electronic Health Records (NUDGE-EHR) pragmatic adaptive randomized trial: a trial protocol
Creators: name: Lauffenburger, Julie C.
name: Isaac, Thomas
name: Trippa, Lorenzo
name: Punam Keller
name: Robertson, Ted
name: Glynn, Robert J.
name: Sequist, Thomas D.
name: Kim, Dae H.
name: Fontanet, Constance P.
name: Castonguay, Edward W. B.
name: Haff, Nancy
name: Barlev, Renee A.
name: Mufaddal Mahesri
name: Chandrashekar Gopalakrishnan
name: Niteesh K. Choudhry
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Additional file 2: Supplement 2, eFigure 1 Provider tapering information and talking points embedded in enhanced alerts. Supplement 2, eFigure 2 SmartSet order set embedded within enhanced alerts. Supplement 2, eFigure 3 Enhanced encounter opening alert used in Arms 2, 6, and 10. Supplement 2, eFigure 4 Arm 3: Enhanced order entry alert + follow-up message. Supplement 2, eFigure 5 Arm 7: Simplified enhanced order entry alert. Supplement 2, eFigure 6 Arms 9 and 10: Sign-off approval alert that triggers to providers when electronically signing off on refill medications ordered by support staff. Supplement 2, eFigure 7 Arm 11: Pre-commitment/consistency alert + enhanced order entry alert. Supplement 2, eFigure 8 Arm 13: Enhanced order entry alert with different risk framing. Supplement 2, eFigure 9 Arm 15: Non-enhanced order entry alert. Supplement 2, eTable 1 Behavioral principles in electronic health record tools tested in regression model.
Translational approaches for the enhancement of osteogenesis in mesenchymal stem cells
Creators: name: Darwood, Alastair
Publisher: name: Imperial College London
Year: 2022

description: Mesenchymal stem cells (MSCs), found within bone marrow and periosteum have long been studied for their regenerative potential in clinical medicine and surgery. At the time of writing, MSCs are routinely clinically implanted into a range of clinical sites ranging from orthopaedic fractures to arthritic joints. The research presented in this thesis relates to their use in the enhancement of orthopaedic fracture repair. Specifically, identifying and developing mechanisms to promote the enhancement of MSC osteogenic potential raising the possibility of addition to a fracture site and assistance with the healing process. The effect of exposure of MSCs to a pneumatic shockwave in the context of osteogenic upregulation was studied. Prior work demonstrated increased osteogenic upregulation in MSCs exposed to a pneumatic shockwave with a view to identify novel pharmacological protective agents to combat blast induced heterotopic ossification. These prior experiments demonstrated that both adherent and suspended MSCs may be enhanced by exposure to a shockwave stimulus in terms of osteogenic upregulation. This relationship was further explored here in a translational scenario. A novel, small-scale shock tube capable of use in cellular biological research was developed and characterised. Osteogenic upregulation of MSCs in suspension was demonstrated in comparison to un-exposed controls. In addition, a demonstrated paucity of MSCs in clinically obtained bone marrow aspirate concentrate detracts from hypothetical clinical utility. For this reason, focus was placed on a colonially expanded MSC population. Prior work has previously demonstrated an increase in osteogenesis in response to elevated temperature in cultured MSC’s. As a result, apparatus to expose MSCs in suspension to temperatures that exceed their normal physiological conditions was additionally designed and characterised in addition to cellular experimentation. Initial cellular experiments suggested osteogenic upregulation was induced on exposure. Further apparatus with improved accuracy remains ready for cellular work in collaboration with an external party. MSC exposure to shear stresses that exceed their normal physiological conditions has previously demonstrated osteogenic upregulation. Apparatus was designed and characterised to achieve this exposure whilst a cellular experimental protocol was devised and discussed. Initial experiments were carried out as a proof of concept alongside discussion of translational potential. In finality, innovative translational designs for MSC loading modalities are suggested with a regard to existing prior art and clinical integration. Although further cellular experimentation is required to validate this approach, the translational groundwork and commercialisation direction has been clearly proposed.
Development, fabrication, and evaluation of UV-LED activated metal oxide semiconductor gas sensors for formaldehyde monitoring
Creators: name: Ghorbani, Ghazal
Publisher: name: University of British Columbia
Year: 2022

description: Monitoring volatile organic compounds (VOCs) is necessary for indoor and outdoor environments due to their harmful effects on human health. Photo-activated metal oxide semiconductor (MOS) gas sensors have recently received significant attention for their detection of VOCs at room temperature due to their high sensitivity and low power consumption. However, these gas sensors suffer from several key drawbacks, including slow response time, inadequate recognition range and poor stability. In this study, photo-activated MOS gas sensors were developed to overcome some of the limitations of existing VOC gas sensors. Efforts were made to establish a suitable MOS for measuring formaldehyde as a model VOC and to enhance its stability throughout the sensing process. Using zinc oxide (ZnO) nanowires (NWs) as the sensing material showed restructuring caused by exposure to different concentrations of formaldehyde in the presence of UV radiation when its morphology and structure were analyzed. The sensing material, indium (Ⅲ) oxide (In₂O₃), also exhibited agglomerated nanoparticles (NPs). UV radiation in the presence of formaldehyde was found to play a critical role in sensing material restructuring and in its response inconsistency and instability. The elimination of UV radiation in the early stages of the response (e.g., first 5 min) avoided agglomeration of the sensing layer. Short-time UV exposure exhibited the potential to be applied in practical gas-sensing applications. Furthermore, a thin layer of Nafion was coated on the sensing layer to protect the structure of the UV-activated NPs from agglomeration. Sensor sensitivity was further improved by increasing the UV irradiance and decreasing the Nafion concentration. A 0.5 wt.% Nafion-coated In₂O₃ NP sensor showed a relatively high transient response of 0.15 when it was exposed to 25 ppm of formaldehyde under 2.56 mW/cm² irradiance. The gas sensor response slope within the first 1–5 minutes of the response curve was found to be a very good indicator of a 10 ̶ 50 ppm concentration of formaldehyde while avoiding agglomeration of the sensing material. The findings of this study can be incorporated into the development of UV-LED-activated gas sensors for which stable and fast response measurements of VOCs are required.
CUSP Newsletter issue 4- May 2023
Creators: name: CUSP Projects-Partners
Publisher: name: Zenodo
Year: 2023
Subjects: microplastics
nanoplastics
human health
plastic particles
toxicology
polymer particles
environmental risk
risk assessment
policy
H2020
nanoweek
environmental pollution
MNPs
Human risk

description: The 4th CUSP Newsletter provides up to date information from each of the five projects that make up the cluster, and the six working groups. Significant progress has been made in researching the risks of micro- and nanoplastics on human health. Notable achievements include organizing a workshop series on human risk assessment and launching the first CUSP Policy Brief. Ongoing initiatives on inter-lab comparisons, true-to-life materials, and human biomonitoring continue to advance knowledge in the field. Looking ahead, Rudolf Reuther, the new CUSP chair for 2023, envisions an intensified research phase, tackling challenges in methodology validation and development with real test materials and systems. CUSP researchers have been busy advancing research across all six working groups. Read more about the upcoming interlaboratory comparisons which promise to be the largest initiative of its kind hosted by the pre-standardisation platform VAMAS. Look inside our newsletter to learn more about this initiative, the progress in our working groups and the latest news from our five projects. This latest edition also provides details of upcoming events where CUSP partners are contributing and presenting results, and gives you an opportunity to meet some more of our scientists. If you’d like to receive our newsletters straight to your inbox, please subscribe here
EOSC Future Western Balkans and Ukraine Training Event
Creators: name: Venkataraman, Shanmugasundaram
Publisher: name: Zenodo
Year: 2023
Subjects: Open Science
EOSC
Research Data Management
GDPR
Research Infrastructures

description: This is a series of presentations that were delivered at a major training event organised by the EOSC Future project and held in Ohrid, North Macedonia on 11th-13th Sept 2023. The event was aimed at individuals from the Western Balkans and Ukraine in a bid to further "level up" the Open Science and EOSC community across Europe. The presentations were designed to provide insights into the state-of-the-art at the time, and specifically the outputs of the work being conducted in the EOSC Future project in its efforts to contribute to the building of EOSC.
Organisation and evolution of landscapes of gene regulation
Creators: name: King, James
Publisher: name: Imperial College London
Year: 2022

description: The control of developmentally expressed genes is highly complex, requiring input from multiple layers of regulation. Among the least understood of those layers are long-range enhancer-promoter interactions and the organisation of the architecture of chromatin folding. Alterations in these aspects of regulation are likely to underlie the establishment of differences across a range of contexts, from determining cell fate to defining species-specific traits. The CTCF protein and the cohesin complex play key roles in defining 3D chromatin architecture, and are thought to be critical in directing patterns of gene expression. Yet, previous cohesin and CTCF depletion studies cast doubt on their importance in this context. In this thesis I show, using thymocyte differentiation as a model, how developmentally regulated genes are particularly sensitive to cohesin and CTCF, providing evidence regarding the importance of cohesin, CTCF and general 3D structure in the coordination of complex regulation. I uncover surprising dissimilarity in the identities of genes affected by each depletion, and demonstrate how this is caused by differences in how each depletion affects 3D structure, further highlighting how 3D space influences gene expression. I then focus on how changes in long-range regulation occur over evolutionary timescales. I Identify signatures of acceleration in otherwise conserved elements across mammals, presenting evidence that a subset of generally conserved elements are predisposed to shifts in selection pressure. Across studied species these regions are particularly enriched for activity in the developing brain. Furthermore, I show how GC-biased gene conversion is a regular source of lineage-specific gain in CpG Islands in conserved elements for a subset of species. This is further evidence that the repurposing of existing elements is a viable route through which evolutionary innovation occurs. Taken together, this work reveals detailed aspects of the organisation of long-range regulation, both in nuclear space and over evolutionary time.
A Grounded Theory of ASEAN Common Denominator Cultures
Creators: name: Kanchana Chokriensukchai
Publisher: name: Center for Research on Plurality in the Mekong Region (CERP)
Year: 2019
Subjects: grounded theory
cultural dimension
ASEAN
information
exposure
content
television drama
culture

description: Journal of Mekong Societies, 15, 1, 111-128
Using displaced tracks to search for sterile neutrinos in the ATLAS detector
Creators: name: Newhouse, Robin
Publisher: name: University of British Columbia
Year: 2022

description: The Standard Model of particle physics is a powerful theory of nature, yet it does not account for all physical observations. Notably, the nonzero masses of the three neutrino flavours and their transformations into one another suggest the need for an extension of the Standard Model. One such extension postulates the existence of Heavy Neutral Leptons (HNLs, 𝑁) — right-handed neutrino states that do not interact with other particles except through mixing with Standard Model neutrinos. HNLs may generate light neutrino masses through the so-called “seesaw mechanism.” This dissertation presents a direct search for long-lived HNLs using 139 fb⁻¹ of √s=13 TeV pp collision data collected by the ATLAS detector at the Large Hadron Collider. In this search, the 𝑁 is produced via W → 𝑁 μ or W → 𝑁 e and decays into a neutrino and two charged leptons, which form a displaced vertex in the inner detector. No signal is observed, and limits are set on the squared mixing angles of the 𝑁 with the Standard Model neutrinos in the mass range 3 GeV < m𝘕 < 15 GeV. For the first time in a collider search, results are presented in the context of realistic HNL mixing models consistent with neutrino oscillation data. Such a displaced vertex search relies heavily upon nonstandard reconstruction algorithms. An additional pass of the track reconstruction algorithm with relaxed collision vertex pointing requirements is executed on a subset of the recorded data to improve sensitivity to long-lived particles in the inner detector. This Large-Radius Tracking (LRT) configuration is effective yet computationally expensive due to the reconstruction of many “fake” tracks not formed from individual charged particles. This algorithm was optimized in preparation for the Run 3 data-taking period, which began in July 2022. Fake LRT tracks are reduced by 95%, drastically improving the purity and reducing the computational load such that LRT is now run in the default reconstruction pipeline. This optimization is expected to substantially improve the sensitivity and reduce the complexity of long-lived particle analyses in ATLAS, including future HNL searches.
Their Lives Are Stripped of Meaning
Creators: name: Hope, Cat
name: James, Stuart
Publisher: name: Monash University
Year: 2023
Subjects: Music composition and improvisation

description: This is a composition for instrument, voice and electronics, composed in 2018. Commissioned by Callum G'Froerer
 PROGRAM NOTE
 In 2016, Australian author Richard Flanagan made a statement in a response to the Australian Government’s policy on the treatment of refugees arriving in Australia by boat, which involves detention. "Their lives are stripped of meaning." In this piece, the vocalist sings these words, but they become incomprehensible as they are separated out over the 8 minutes of the piece; a direct reference to the indeterminate length of detention that Australia enforces upon refugees. Time passes, we forget and our ability to understand becomes difficult. In addition, the electronic part is created by sampling the instruments at certain moments in the piece, and strips away the timbral characteristics of the work, another metaphor for the consequences of this treatment of our fellow human beings.

 PERFORMANCE INSTRUCTIONS
 To perform this work, you will need the Decibel ScorePlayer, an application which presents the score on an iPad. You can download this from the Apple App store. The score file (with the extension .dsz) is AirDropped to the ipad, where it can be read for performance. The electronics part is notated on the score. You can make your own electronics program to realise this, or use the MaxMSP patch attached here. A PDFscore is available from the publisher, Material Press.

 PERFORMANCES
 Premiered by G'Froerer (tpt) and Olivia Stahn (voice) at the 'Pieta' concert, Ölberg-Kirche, Berlin May 2018.
 Australasian Computer Music Conference, Tone List concert, Perth, December 2018 - by Dan O'Connor (tpt), Anika Moses (voice) and Stuart James (electronics).
 University of Utah New Music Ensemble, fea,t. Meg Johnson, voice Steven Marz, French horn, Dec 2022.
Additional file 4 of Exosomal ANGPTL1 attenuates colorectal cancer liver metastasis by regulating Kupffer cell secretion pattern and impeding MMP9 induced vascular leakiness
Creators: name: Jiang, Kai
name: Haiyan Chen
name: Yimin Fang
name: Liubo Chen
name: Chenhan Zhong
name: Tongtong Bu
name: Siqi Dai
name: Pan, Xiang
name: Dongliang Fu
name: Yucheng Qian
name: Jingsun Wei
name: Kefeng Ding
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Cancer
subject: 60506 Virology

description: Additional file 4: Table S1. The stages of CRC patients and the corresponding exosomal ANGPTL1 index calculated by ImageJ from WB brands. The CRC stage was based on 7th revised edition of the AJCC Colorectal Cancer.
STL NEMS fabrication, design, and inspection
Creators: name: Bouchaala, Adam
Publisher: name: Imperial College London
Year: 2022

description: Because of difficulties in design, fabrication, and testing, commercialisation of nano-electro-mechanical devices (NEMS) has proceeded much more slowly than for equivalent microscale devices. This thesis addresses several aspects that may provide solutions. Firstly, an improved mass production nanofabrication process based on optical lithography and sidewall transfer lithography (STL) is developed and demonstrated. The process allows more design freedom than previously demonstrated STL processes, for example allowing the combination of flexible and stiff mechanical nanostructures. Different nanostructures including single ribs, crossing ribs, and 3-way intersections are demonstrated. The fabricated devices have a minimum in-plane width of ca 200 nm defined by a silicon dioxide layer grown using thermal oxidation and an aspect ratio > 30:1. Secondly, methods of simulating complex nanoscale structures using the stiffness matrix method (SMM) are presented. The SMM tool replaces lengthy finite element simulations with accurate and fast simulations. These methods can be used to study trusses and other intricate designs and can also be augmented with additional multiphysics components to allow simple electrostatic modelling. Static and dynamic solvers are developed to study combined MEMS and NEMS devices. Different types of filters such as passband, stop band, and arrays of filters are investigated, and methods of improving frequency tuning are developed based on mass loading. Thirdly, methods are developed to model the back-scattered light from microscale and nanoscale objects in optical microscopy. It is shown that sub-wavelength features appear as black lines in bright-field microscopy that beyond a certain depth, while microscale features are observable only as their edges. Hence, NEMS and MEMS may both be perceived, even at optical wavelengths, and can be distinguished from the foreground in images via the detection of brightness valleys. Dark field microscopy is also investigated, and it is shown that nanoscale features will appear as bright lines and wider features as bright edges. Image processing algorithms based on valley detection, thresholding, and masking are developed to separate NEMS, MEMS, and background in optical microscope images.
Autonomous tissue scanning for guiding a tumour resection
Creators: name: Cartucho, Joao
Publisher: name: Imperial College London
Year: 2023

description: Robots have become the top-choice technology for Minimally Invasive Surgery (MIS) procedures and due to the rapid advancement of these robotic platforms, it is expected that these robots will play an essential role in the future of surgery. These surgical robots are expected to evolve through higher levels of automation, as these platforms become more sophisticated and capable. One important feature to be added to these robots is the ability to scan tissue for in situ characterization to guide tumour resection. The main advantage of doing tissue scanning autonomously is that it reduces surgical workload, allowing the surgeon to focus on more crucial tasks while the robot scans the tissue automatically. In this thesis, an autonomous tissue scanning framework is presented which allows the robot to capture ultrasound images of the target scanning region. Throughout this thesis, different works contribute to my tissue scanning framework. I have written the first technical review of the da Vinci (dVRK) surgical robot, which describes the essential calibrations required to acquire good-quality data; I created simulations of robotic surgeries to test algorithms before deploying them on the real robot; I designed a cylindrical marker to estimate the pose of surgical instruments. I have found that this cylindrical marker is a practical tool for the hand-eye calibration of the robot; I have created an autonomous scanning framework which improves the previous works by being able to follow moving tissue without assuming periodic breathing motions; Finally, I organized a soft-tissue tracking challenge, which allows researchers to develop tissue trackers using the benchmarking tool and the dataset that I have created.
Introduction scientifique
Creators: name: Feriel, Laurence Bassières Et Cédric
Publisher: name: Collectif Inventer le Grand Paris
Year: 2020

description: Si le thème de l’esthétique urbaine dans le Grand Paris, proposé pour cette journée d’études, trouve un écho dans des productions récentes, telles que le colloque organisé en 2013 par l’Atelier du Grand Paris, « Le Grand Paris sera-t-il beau ? », il est né de travaux portant sur le Grand Paris du premier XXe siècle. À partir de recherches menées sur une tentative, dans ce contexte, d’intégrer les préoccupations patrimoniales au projet urbain, j’avais pu faire le constat des difficultés, dans le contexte français, à articuler ces deux domaines, avant les années 1960 et les lois Malraux. Un autre constat se faisait en...
Pour un plus beau grand Paris. Les liens entre urbanisme, esthétique et morale dans les écrits de Jean Giraudoux
Creators: name: Foucher-Dufoix, Valérie
Publisher: name: Collectif Inventer le Grand Paris
Year: 2020

description: Jean Giraudoux a produit de nombreux essais, conférences et articles sur ses représentations de Paris et de sa banlieue mais aussi sur sa vision d’un Paris futur. Le principal intérêt de ce corpus ne réside pas tant dans l’originalité des propos tenus qui sont largement partagés, ni dans leur importance quantitative un peu trompeuse, que dans le déploiement d’une pensée totale sur l’urbanisme et l’architecture. Dans ces écrits, il évoque notamment la notion de "droit urbain", qui serait le droit de tous à une bonne ville, à une ville saine, commode et esthétique. Ce rapport direct entre esthétique, confort de la ville et épanouissement des qualités morales et intellectuelles de ses habitants est au cœur de ses discours. Les questions architecturales et urbaines relèvent bien à la fois du domaine de la morale, de l'esthétique et de la responsabilité politique. Mais il ne s’attache pas seulement à décrire Paris et le Grand Paris, il pose un diagnostic, désigne des responsables et propose des «remèdes ».
Immunology of choriodecidua and onset of labour
Creators: name: Sivarajasingam, Sivatharjini Priya
Publisher: name: Imperial College London
Year: 2022

description: Introduction: Labour is a well-orchestrated process associated with inflammation; its onset is a poorly understood retrospective diagnosis. Immunology of pregnancy and labour is an area of wide interest; however, knowledge is lacking in what occurs at the maternal-fetal interface, the decidua. The aim of this thesis was to better understand the role of decidual immune cells in preterm birth and term labour while associating metabolites with immune cells that may be pivotal in labour. Methodology: Multiple cytokine assays were used to quantify cytokines/chemokines in choriodecidua/placenta. Flow cytometry was used to identify immune cells in decidua, placenta, maternal and cord blood. Mass spectrometry was used to quantify urinary metabolites. Results: Study one showed that choriodecidua was the most inflammatory gestational tissue analysed. Cytokines/chemokines indicated that NK cells, monocytes, T cells and neutrophils may play a significant role in preterm birth. Increased IL-8 in choriodecidua was associated with worse neonatal outcomes. Study two revealed a shift from predominantly CD56bright NK cells to a predominant subset of CD56+CD16+ NK cells with onset of term labour in decidua. Decidual NKbright cells and Tregs work together to maintain uterine quiescence at term, which is lost with labour. CD4+ Tregs and CD8+ Tregs were significantly higher in decidua than placenta/blood at term. Decidual monocytes, T cells and neutrophils did not alter with the onset of labour. Study three did not identify a signature urinary metabolic profile that is associated with the onset of labour. It highlighted that factors such as diet and lifestyle may cause inter-personal variability. Conclusions: This thesis highlights that the tolerant immune cells and their interaction with cytokines/chemokines maintain an immunological equilibrium in the decidua. This is altered with the onset of labour. Urinary metabolites inconsistently altered with the onset of labour, there was no signature urinary metabolic profile associated with labour.
Pressure and rate analysis in unconventional reservoirs
Creators: name: Marsden, Joseph
Publisher: name: Imperial College London
Year: 2021

description: The aim of this work is to develop a realistic conceptual shale gas reservoir model that explains the observed behaviour of Haynesville wells and can predict their future behaviour. A model developed by Kostyleva (2019) consists of a two zone repetitive element for each set of wellbore perforations. A fractured zone is in contact with the wellbore and surrounded by a matrix zone representing the rock unaffected by fracturing. The two zones have different initial permeabilities. The matrix permeability decreases as soon as its pore pressure begins to fall. The decline in fractured zone permeability starts below a threshold pressure. Later, a pseudo-skin factor is introduced and increases with time. The validation of Kostyleva’s (2019) model is continued by accurately simulating the dynamic pressure behaviour of 8 Haynesville Shale wells from the period 2014 – 2016. Two components of Kostyleva’s (2019) model seem unrealistic. Any pressure drop in a region intended to represent the network of fractures around a wellbore should cause an immediate fall in its permeability. Field observations do not support the existence of an actual skin factor. Therefore, the present study proposes a new Multiple Fracture Zone (MFZ) model. Each perforation set is surrounded by several zones. Each zone represents a volume of shale containing both matrix and fractures and has a different permeability-pressure relationship. Fractures in zones nearer the wellbore contain more proppant and are less compressible. Any pressure drop decreases permeability and no pseudo-skin factor needs to be introduced. The MFZ model has been validated by accurately simulating the dynamic pressure behaviour of 8 Haynesville Shale wells from the period 2014 – 2018.
Cellular barcoding of protozoan pathogens for within-host population dynamics and in vivo drug discovery
Creators: name: Wincott, Ceire Joanne
Publisher: name: Imperial College London
Year: 2023

description: The obligate intracellular apicomplexan parasite Toxoplasma gondii has broad infectious ability causing disease in humans and animals, some of which can be fatal. Existing treatments for T. gondii infections have notable side effects, and the emergence of resistance to first-line therapies is a growing concern. Understanding the fundamental aspects of T. gondii biology necessitates studying in vivo host-pathogen interactions. However, tracking parasite populations without artificially influencing infection dynamics has posed significant challenges. To address this, we propose a cellular barcoding technique combined with Next Generation Sequencing (NGS) technology to genetically identify and assess the representation of parasite populations. This approach can be applied not only to T. gondii but also to T. brucei and holds potential for future application to other pathogens. Using our cellular barcoding methodology, we conducted population dynamics studies to investigate T. gondii colonisation of the brain parenchyma. Surprisingly, we discovered that the blood-brain barrier (BBB) allows relatively unrestricted traversal by T. gondii, imposing a less stringent bottleneck than anticipated. Moreover, we observed the dynamic nature of chronic T. gondii infection, as brain cyst numbers continued to decrease over several months. Furthermore, we employed the cellular barcoding methodology to facilitate multiplexed in vivo drug screening. Through this approach, we successfully identified small molecule fragments with anti-parasitic effects. Our proof-of-concept data supports the use of this screening platform for iterative drug molecule development. Additionally, in concurrent studies, one of the identified hit fragments exhibited selective inhibition of translation in T. gondii compared to HEK293 cells, prompting further characterisation efforts.