cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Dose summation and image registration strategies for radiobiologically and anatomically corrected dose accumulation in pelvic re-irradiation
Creators: name: Nix, Mike
name: Gregory, Stephen
name: Aldred, Michael
name: Aspin, Lynn
name: Lilley, John
name: Al-Qaisieh, Bashar
name: Uzan, Julien
name: Svensson, Stina
name: Dickinson, Peter
name: Appelt, Ane L.
name: Murray, Louise
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: 60506 Virology

description: Re-irradiation (reRT) is a promising technique for patients with localized recurrence in a previously irradiated area but presents major challenges. These include how to deal with anatomical change between two courses of radiotherapy and integration of radiobiology when summating original and re-irradiation doses. The Support Tool for Re-Irradiation Decisions guided by Radiobiology (STRIDeR) project aims to develop a software tool for use in a commercial treatment planning system to facilitate more informed reRT by accounting for anatomical changes and incorporating radiobiology. We evaluated three approaches to dose summation, incorporating anatomical change and radiobiology to differing extents. In a cohort of 21 patients who previously received pelvic re-irradiation the following dose summation strategies were compared: (1) Rigid registration (RIR) and physical dose summation, to reflect the current clinical approach, (2) RIR and radiobiological dose summation in equivalent dose in 2 Gy fractions (EQD2), and (3) Patient-specific deformable image registration (DIR) with EQD2 dose summation. RIR and physical dose summation (Strategy 1) resulted in high cumulative organ at risk (OAR) doses being ‘missed’ in 14% of cases, which were highlighted by EQD2 dose summation (Strategy 2). DIR (with EQD2 dose summation; Strategy 3) resulted in improved OAR overlap and distance to agreement metrics compared to RIR (with EQD2 dose summation; Strategy 2) and was consistently preferred in terms of clinical utility. DIR was considered to have a clinically important impact on dose summation in 38% of cases. Re-irradiation cases require individualized assessment when considering dose summation with the previous treatment plan. Fractionation correction is necessary to meaningfully assess cumulative doses and reduce the risk of unintentional OAR overdose. DIR can add clinically relevant information in selected cases, especially for significant anatomical change. Robust solutions for cumulative dose assessment offer the potential for future improved understanding of cumulative OAR tolerances.
Bose-Einstein condensation dynamics from the numerical solution of the Gross-Pitaevskii equation
Creators: name: Adhikari, Sadhan K.
name: Muruganandam, Paulsamy
Publisher: name: arXiv
Year: 2002
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Physical sciences

description: We study certain stationary and time-evolution problems of trapped Bose-Einstein condensates using the numerical solution of the Gross-Pitaevskii equation with both spherical and axial symmetries. We consider time-evolution problems initiated by changing the interatomic scattering length or harmonic trapping potential suddenly in a stationary condensate. These changes introduce oscillations in the condensate which are studied in detail. We use a time iterative split-step method for the solution of the time-dependent Gross-Pitaevskii equation, where all nonlinear and linear nonderivative terms are treated separately from the time propagation with the kinetic energy terms. Even for an arbitrarily strong nonlinear term this leads to extremely accurate and stable results after millions of time iterations of the original equation.
description: LaTeX2e (iop style files included), 17 pages, 6 EPS figures, accepted for publication in J. Phys. B: At. Mol. Opt. Phys
Predicting response to radiotherapy of head and neck squamous cell carcinoma using radiomics from cone-beam CT images
Creators: name: Sellami, S.
name: Bourbonne, V.
name: Hatt, M.
name: Tixier, F.
name: Bouzid, D.
name: Lucia, F.
name: Pradier, O.
name: Goasduff, G.
name: Visvikis, D.
name: Schick, U.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer

description: Radiotherapy (RT) for head and neck cancer is now guided by cone-beam computed tomography (CBCT). We aim to identify a CBCT radiomic signature predictive of progression to RT. A cohort of 93 patients was split into training (n = 60) and testing (n = 33) sets. A total of 88 features were extracted from the gross tumor volume (GTV) on each CBCT. Receiver operating characteristic (ROC) curves were used to determine the power of each feature at each week of treatment to predict progression to radio(chemo)therapy. Only features with AUC > 0.65 at each week were pre-selected. Absolute differences were calculated between features from each weekly CBCT and baseline CBCT1 images. The smallest detectable change (C = 1.96 × SD, SD being the standard deviation of differences between feature values calculated on CBCT1 and CBCTn) with its confidence interval (95% confidence interval [CI]) was determined for each feature. The features for which the change was larger than C for at least 5% of patients were then selected. A radiomics-based model was built at the time-point that showed the highest AUC and compared with models relying on clinical variables. Seven features had an AUC > 0.65 at each week, and six exhibited a change larger than the predefined CI 95%. After exclusion of inter-correlated features, only one parameter remains, Coarseness. Among clinical variable, only hemoglobin value was significant. AUC for predicting the treatment response were 0.78 (p = .006), 0.85 (p p p We described a feature selection methodology for delta-radiomics that is able to select reproducible features which are informative due to their change during treatment. A selected delta radiomics feature may improve clinical-based prediction models.
Additional file 1: of Personality dimensions emerging during adolescence and young adulthood are underpinned by a single latent trait indexing impairment in social functioning
Creators: name: Polek, Ela
name: Jones, Peter
name: Pasco Fearon
name: Brodbeck, Jeannette
name: Moutoussis, Michael
name: NSPN Consortium
name: Dolan, Ray
name: Fonagy, Peter
name: Bullmore, Edward
name: Goodyer, Ian
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Online Supplement. (PDF 3750 kb)
title: 01_2451
Creators: name: Wesley Baldwin, John
name: Baldwin, John W.
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2018
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: L'ensemble de ces notes ont été crée par John Baldwin lors d'une de ses premières périodes de résidence à Paris. Ces documents comprennent tous les magistri qu’il avait pu rencontrer dans ses sources. Aux XIIème et XIIIème siècles, les universités n'existant pas encore, le titre de magister s'il évoque certainement une compétence n'est pas rattaché de façon systématique au passage par les écoles. De surcroît, les magistris sont le plus souvent désignés par leur seul prénom. La lecture de ces données est donc difficile et suppose un long travail pour tenter d'identifier un individu auquel on pourrait rattacher plusieurs mentions. John Baldwin avait donc renoncé à utiliser ces données pour donner un prolongement à sa magnifique étude sur les gradués d'université et leur emploi par les Capétiens et les Plantagenêts. Néanmoins, il a conservé ces données et elles sont potentiellement très utile dans le cadre de Studium, comme le sont toutes les mentions dans les volumes des Fasti Ecclesiae Gallicanae de chanoines portant ce titre de magister sans autres précisions. L'ampleur des dépouillements rend ces données très utiles et nous devons une grande reconnaissance à John Baldwin pour avoir pris la peine de faire photocopier ses fiches et de nous les avoir transmises amicalement.
Les données ainsi que les images des fiches sont accessibles sur le site Internet à l'adresse suivante : http://studium-baldwin.lamop.fr/.
Les transcriptions des fiches ont été effectuées par des étudiants de Paris 1 Panthéon - Sorbonne mais elles n'ont pas été corrigées par la suite.
description: Relation: https://lamop.hypotheses.org/
Financial and economic aspects of urban vegetable farming
Creators: name: Danso, G.
name: Hope, L.
name: Drechsel, Pay
name: Danso, G.
name: Hope, L.
name: Drechsel, Pay
Publisher: name: Unknown
Year: 2014
Subjects: subject: Agribusiness
subject: Agricultural Finance
subject: Consumer/Household Economics
subject: Crop Production/Industries
subject: Farm Management
subject: Food Security and Poverty
subject: Health Economics and Policy
subject: International Development
subject: Economic aspects
subject: Financing
subject: Costs
subject: Urban agriculture
subject: Suburban agriculture
subject: Farming systems
subject: Vegetables
subject: Crops
subject: Pesticides
subject: Soil fertility
subject: Public health
subject: Health hazards
subject: Malaria
subject: Food supply
subject: Food security
subject: Households
subject: Environmental impact
subject: Ghana
subject: Kumasi
subject: Accra
subject: Tamale

description: This chapter explores some of the financial and economic aspects of urban and peri-urban agriculture in Ghana. Cost-benefit analysis comparisons were made of farm finances of common rural, peri-urban and urban farming systems. Substudies also tried to quantify benefits for society and to cost externalities related to soil nutrient depletion, pesticide use and urban malaria.
description: In Drechsel, Pay; Keraita, B. (Eds.) Irrigated urban vegetable production in Ghana: characteristics, benefits and risk mitigation. Colombo, Sri Lanka: International Water Management Institute (IWMI).
The somatic evolution of the canine transmissible venereal tumour
Creators: name: Baez Ortega, Adrian
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: cancer
canine transmissible venereal tumour
computational biology

description: This dissertation investigates the evolution of the canine transmissible venereal tumour (CTVT), a sexually transmitted cancer which manifests as genital tumours in dogs. This cancer first arose in an individual dog several thousand years ago, and has since survived by transfer of living cancer cells to new hosts during coitus. Today, CTVT affects dogs around the world, and is the oldest and most prolific known cancer clone. As such, it provides a unique opportunity to explore the evolution of cancer over the long term, and to track the unusual biological transition from somatic mammalian cell to asexual parasite. Through computational analysis of the mutations found in the protein-coding DNA of 546 globally distributed CTVT tumours, this work aims to illuminate the history, diversity, mutational exposures and evolution of the CTVT lineage, and to characterise the major evolutionary forces which operate on cancer over long time frames. The dissertation is structured in seven chapters, each composed of four sections. The first chapter introduces the concepts of tumour evolution and clonally transmissible cancers, with special emphasis on CTVT, and exposes the major research questions and experimental rationale of the study. The second chapter describes the identification, annotation and preliminary analysis of the genetic variation found in CTVT tumours and their host dogs. The third chapter presents phylogenetic and phylogeographic analyses, including the reconstruction and dating of the CTVT tumour phylogeny and the inference of past geographical movements. The fourth chapter explores signatures of mutational processes in the CTVT genome, which include exposure to ultraviolet light and a previously undescribed ancient mutational process, whose activity ceased approximately 1000 years ago. The fifth chapter describes analyses of patterns of gene expression in CTVT cells and tumour-infiltrating host cells, which indicate that gene expression in tumour cells is largely centred on cellular maintenance and replication. The sixth chapter explores signatures of natural selection in CTVT, including early ‘driver’ mutations and signals of selection for more recent mutations; the results reveal that CTVT largely evolves via genetic drift, and has apparently ceased to adapt to its environment. The closing chapter presents the conclusions and future directions of the research. Overall, this work charts the natural history of a unique biological entity, highlights the potential for long-lived clonal organisms to act as biomarkers for mutagenic exposures, provides insight into the forces which dominate cancer evolution over the long term, and suggests an evolutionary limit to the existence of naturally arising transmissible cancers.
Additional file 1: of Household behavior in practicing mental budgeting based on the theory of planned behavior
Creators: name: Ume Habibah
name: Ibne Hassan
name: Iqbal, Muhammad
name: Naintara
Publisher: name: figshare
Year: 2019
Subjects: subject: Space Science
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy

description: Statistical Results of Mean, Standard Deviation, Skewness and Kurtosis. (DOCX 14 kb)
Convergent cognitive evolution: what can be learnt from comparisons with corvids and cephalopods?
Creators: name: Amodio, Piero
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: convergent cognitive evolution
corvids
cephalopods
Eurasian jay
Octopus
tool use
future planning
social cognition

description: Emery and Clayton (2004) proposed that corvids (e.g. crows, ravens, jays) may have evolved – convergently with apes – flexible and domain general cognitive tool-kits. In a similar vein, others have suggested that coleoid cephalopods (octopus, cuttlefish, squid) may have developed complex cognition convergently with large-brained vertebrates but current evidence is not sufficient to fully evaluate these propositions. The aim of my thesis is to gain further insight into these issues. My first objective is to further our understanding of how deep the cognitive convergence between corvids and apes may be. To this end I report four empirical studies exploring cognitive complexity among different domains in a single species of corvids, the Eurasian jay (Garrulus glandarius). In Chapter 2, I investigate physical problem solving, finding that jays cannot spontaneously select functional tools according to their physical properties (i.e. size, shape) but can use novel tools – sticks – to solve a familiar task. In Chapter 3, I test whether future oriented caching in jays is underpinned by future planning abilities or by spontaneous predispositions; data do not support either hypotheses. In Chapters 4 and 5, I focus on social cognition. I find no indication that jays can integrate the visual perspective and current desire of competitors to protect their caches. Surprisingly, jays could also not respond to either of the two social cues independently, thus questioning the reliability of previously reported caching strategies. My second objective is to lay theoretical and methodological groundwork for studying convergent cognitive evolution between cephalopods and large-brained vertebrates. Therefore, in Chapter 6 I propose an evolutionary hypothesis for the emergence of large brains and behavioural flexibility in cephalopods and put forward novel paradigms that may allow researchers to explore the cognitive underpinning of octopus’ complex behaviours. I conclude by discussing the implication of my findings and future directions for the study of convergent cognitive evolution in corvids and cephalopods.
Additional file 2: of Household behavior in practicing mental budgeting based on the theory of planned behavior
Creators: name: Ume Habibah
name: Ibne Hassan
name: Iqbal, Muhammad
name: Naintara
Publisher: name: figshare
Year: 2019
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy

description: Survey Questionnaire. (DOCX 24 kb)
Precise yield of high-energy photons from Higgsino dark matter annihilation
Creators: name: Beneke, Martin
name: Hasner, Caspar
name: Urban, Kai
name: Vollmann, Martin
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The impact of electroweak Sudakov logarithms on the endpoint of the photon spectrum for wino dark matter annihilation was studied intensively over the last several years. In this work, we extend these results to Higgsino dark matter $χ_1^0$. We achieve NLL' resummation accuracy for narrow and intermediate spectral energy resolutions, of order $m_W^2 / m_χ$ and $m_W$, respectively. This is the most accurate prediction to date for the yield of high-energy $γ$-rays from $χ_1^0 χ_1^0 \to γ+ X$ annihilation for the energy resolutions realized by current and next-generation telescopes. We also discuss for the first time the effect of power corrections in $m_W/m_χ$ in this context and argue why they are not sizeable.
description: 30 pages, 5 figures, v2: matches published version + typo in (C.23) fixed
Cardiotoxicity in metastatic melanoma patients treated with BRAF and MEK inhibitors in a real-world setting
Creators: name: Pedersen, Sidsel
name: Larsen, Kirstine Ostenfeld
name: Christensen, Alex Hørby
name: Svane, Inge Marie
name: Zerahn, Bo
name: Ellebaek, Eva
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Hematology
subject: 110309 Infectious Diseases

description: Combination therapy with BRAF and MEK inhibitors (BRAF/MEKi) has significantly improved the outcome for patients with BRAF-mutated melanoma. A reduction in left ventricular ejection fraction (LVEF) is a known side effect during treatment with BRAF/MEKi. This study aimed to analyze sequential multigated acquisition (MUGA) scans for the evaluation of LVEF and provide real-world data on cardiotoxicity induced by BRAF/MEKi in advanced melanoma. All patients with advanced melanoma treated with dabrafenib and trametinib at Herlev and Gentofte Hospital, Denmark, between March 2015 and September 2019, were included retrospectively. MUGA scans performed at baseline and every three months during treatment were analyzed. Cardiotoxicity was defined as a decline of ≥10 percentage point (pp) to an LVEF <50% (major cardiotoxicity) or a decline in LVEF of ≥15 pp but remaining >50% (minor cardiotoxicity). A total of 139 patients were included. Forty-six patients (33%) met our criteria for cardiotoxicity; 31 patients (22%) experienced minor cardiotoxicity and 15 patients (11%) experienced major cardiotoxicity. Median time to decline in LVEF was 94 days, and all clinically significant declines in LVEF occurred before evaluation at six months. Reversibility of LVEF was seen in 80% of patients, three patients were not evaluable for reversibility. A low left ventricular peak emptying rate adjusted for heart rate (LVPERadj) at baseline was found a potential risk factor for the development of major cardiotoxicity (RR = 0.159, p = 0.001). A decline in LVEF is common for patients with advanced melanoma treated with BRAF/MEKi but rarely clinically significant. No significant decline in LVEF was observed after evaluation at six months, therefore routine monitoring of LVEF might be stopped after six to nine months of BRAF/MEKi therapy. A low LVPERadj might be a risk factor for the development of cardiotoxicity and is suggested for further investigation.
Marketing channels for irrigated exotic vegetables
Creators: name: Henseler, M.
name: Amoah, Philip
name: Henseler, M.
name: Amoah, Philip
Publisher: name: Unknown
Year: 2014
Subjects: subject: Agribusiness
subject: Agricultural Finance
subject: Community/Rural/Urban Development
subject: Crop Production/Industries
subject: Farm Management
subject: Food Security and Poverty
subject: Marketing
subject: FOS: Economics and business
subject: Production Economics
subject: Irrigated farming
subject: Urban agriculture
subject: Vegetables
subject: Lettuces
subject: Wholesale marketing
subject: Retail marketing
subject: Food supply
subject: Consumers
subject: Surveys
subject: Ghana
subject: Kumasi
subject: Accra

description: This chapter provides qualitative and quantitative information on the distribution pathways of irrigated vegetables, with a focus on lettuce, produced in Kumasi and Accra from the farm to the consumer. The data from a survey carried out in 2005 show the contribution of irrigated urban farming and the size of the beneficiary group in Accra, which is also the group at risk from crop contamination which has been quantified.
description: In Drechsel, Pay; Keraita, B. (Eds.) Irrigated urban vegetable production in Ghana: characteristics, benefits and risk mitigation. Colombo, Sri Lanka: International Water Management Institute (IWMI).
title: 03_0580
Creators: name: Wesley Baldwin, John
name: Baldwin, John W.
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2018
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: L'ensemble de ces notes ont été crée par John Baldwin lors d'une de ses premières périodes de résidence à Paris. Ces documents comprennent tous les magistri qu’il avait pu rencontrer dans ses sources. Aux XIIème et XIIIème siècles, les universités n'existant pas encore, le titre de magister s'il évoque certainement une compétence n'est pas rattaché de façon systématique au passage par les écoles. De surcroît, les magistris sont le plus souvent désignés par leur seul prénom. La lecture de ces données est donc difficile et suppose un long travail pour tenter d'identifier un individu auquel on pourrait rattacher plusieurs mentions. John Baldwin avait donc renoncé à utiliser ces données pour donner un prolongement à sa magnifique étude sur les gradués d'université et leur emploi par les Capétiens et les Plantagenêts. Néanmoins, il a conservé ces données et elles sont potentiellement très utile dans le cadre de Studium, comme le sont toutes les mentions dans les volumes des Fasti Ecclesiae Gallicanae de chanoines portant ce titre de magister sans autres précisions. L'ampleur des dépouillements rend ces données très utiles et nous devons une grande reconnaissance à John Baldwin pour avoir pris la peine de faire photocopier ses fiches et de nous les avoir transmises amicalement.
Les données ainsi que les images des fiches sont accessibles sur le site Internet à l'adresse suivante : http://studium-baldwin.lamop.fr/.
Les transcriptions des fiches ont été effectuées par des étudiants de Paris 1 Panthéon - Sorbonne mais elles n'ont pas été corrigées par la suite.
description: Relation: https://lamop.hypotheses.org/
Chemical Methods for Cobalt-Catalysed C(sp3)–H Activation and Iodonium Salt-Mediated Peptide Functionalisation
Creators: name: Williamson, Patrick
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Cobalt
C-H activation
Bioorthogonal
Iodonium salt

description: The development of a cobalt-catalysed C–H carbonylative cyclisation of aliphatic quinolinamides to furnish the corresponding succinimides in good to excellent yields is reported. The reaction has been applied to a range of substituted analogues, including to the functionalisation of activated methylene bonds. Initial computational interrogation of the reaction suggests a carboxylate-assisted concerted metalation-deprotonation pathway for C–H bond cleavage. Subsequently, the development of a rapid, room-temperature iodonium-salt mediated arylation procedure of hydroxylamines to afford N-oxide products is described. This approach has been applied to the metal-free, room temperature synthesis of substituted anilines. A diverse range of aromatic groups, including aryl halides and heteroaromatic functionality, were successfully transferred by this strategy. Excellent selectivity for the hydroxylamine group was observed in the presence of unprotected nucleophiles. This fast and selective arylation reaction was ulitmately applied to the functionalisation of complex peptide substrates in dilute aqueous solutions, exhibiting high chemoselectivity with respect to peptide sidechains. Excellent conversions were achieved in five minutes at room temperature, demonstrating the potential of this process for bioorthogonal labelling.
description: Herchel Smith Scholarship
Edge rigidity and universality of random regular graphs of intermediate degree
Creators: name: Bauerschmidt, Roland
name: Huang, Jiaoyang
name: Knowles, Antti
name: Yau, Horng-Tzer
Publisher: name: arXiv
Year: 2019
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 60B20, 15B52, 05C80

description: For random $d$-regular graphs on $N$ vertices with $1 \ll d \ll N^{2/3}$, we develop a $d^{-1/2}$ expansion of the local eigenvalue distribution about the Kesten-McKay law up to order $d^{-3}$. This result is valid up to the edge of the spectrum. It implies that the eigenvalues of such random regular graphs are more rigid than those of Erdős-Rényi graphs of the same average degree. As a first application, for $1 \ll d \ll N^{2/3}$, we show that all nontrivial eigenvalues of the adjacency matrix are with very high probability bounded in absolute value by $(2 + o(1)) \sqrt{d - 1}$. As a second application, for $N^{2/9} \ll d \ll N^{1/3}$, we prove that the extremal eigenvalues are concentrated at scale $N^{-2/3}$ and their fluctuations are governed by Tracy-Widom statistics. Thus, in the same regime of $d$, $52\%$ of all $d$-regular graphs have second-largest eigenvalue strictly less than $2 \sqrt{d - 1}$.
Molecular Mechanisms of Lymphocyte Activation - Please Mind the Gap
Creators: name: Lippert, Anna Helena
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: subject: Single-molecule Imaging
subject: Immunology
subject: FOS: Clinical medicine
subject: Biophysics
subject: Lymphocytes

description: The underlying mechanism of lymphocyte triggering is still not fully understood, but the kinetic-segregation (KS) model of receptor triggering in T cells has been supported by several recent studies. This model proposes that the small gap between an antigen-presenting cell and an immune cell excludes large, inhibitory phosphatases, causing cell signalling. This work examines lymphocyte signalling phenomena in the light of the KS model. Single molecule and bulk experiments explore how the gap size between immune cells and a surface affects the behaviour of important signalling proteins. The first part of this thesis investigates whether the KS model explains the signalling-related epi-phenomena of superagonism. Experiments show that contacts mediated by highly potent superagonistic antibodies increase the exclusion of phosphatases. These changes are gap-size dependent and, complemented by T cell stimulation assays, support the role of phosphatase exclusion in superagonistic T cell activation predicted by the KS model. This signalling principle is likely to be generalisable to other tyrosinekinase-dependent receptors,including immune checkpoints. The second partof the thesis asks whether the KS mechanism might activate other immunoreceptors. This work focuses on the B cell receptor (BCR), which as a large,bivalent immunoreceptor poses its own challenges to the KS model. Functional activation assays and three-color imaging reveal a link between size-dependent phosphatase exclusion and B cell activation, providing evidence for KS as a general activation mechanism in lymphocytes. Finally, stiffness-dependent T cell activation is explored. While substrate stiffness is known to influence T cell activation,studies are typically performed on glass, which is orders of magnitude stiffer than any substrate in vivo. This work introduces a new platform for single-molecule imaging on bilayers supported by substrates with variable stiffness. Early T cell activation markers show a correlation between stiffness and sustained signalling. This platform enables future experiments to study the underlying mechanism of stiffness-dependent lymphocyte activation. As a whole, this thesis shows how physical parameters like gap-size and substrate stiffness can influence lymphocyte activation. Thus, it enhances our general understanding of lymphocyte activation and motivates antibody design for immunotherapy as well as close-to-physiological signalling studies.
A biomarker panel predicts recurrence-free survival in ulcerated primary cutaneous melanoma
Creators: name: Falkenius, Johan
name: Keskitalo, Johanna
name: Kanter, Lena
name: Johansson, Hemming
name: Höiom, Veronica
name: Hansson, Johan
name: Brage, Suzanne Egyhazi
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 60506 Virology

description: Ulceration is an independent adverse prognostic factor in cutaneous malignant melanoma (CMM). There is, however, a need for additional prognostic markers to identify patients with ulcerated stage I–II CMM who have a high-risk for recurrence. The aim of this study was to examine the prognostic impact of BRAF mutation, proliferation and presence of tumour infiltrating lymphocytes (TILs) in primary ulcerated CMM. We have used a consecutive cohort consisting of 71 primary ulcerated CMM (T1b–T4b). BRAF mutation was detected using Cobas test and pyrosequencing. Protein expression of the proliferation marker Ki67 was analysed using immunohistochemistry. Presence of TILs was evaluated in representative hematoxylin-eosin stained formalin-fixed paraffin-embedded tumour sections. Proportion of BRAF mutated alleles, proliferation and presence of TILs all had a statistically significant impact on recurrence free survival in univariate analyses (HR 2.44, 95% CI 1.23–4.84, p = 0.011; HR 2.66, 95% CI 1.32–5.35, p = 0.006 respectively HR 0.48, 95% CI 0.24–0.98, p = 0.045). A trend test found a statistically significant decrease in the proportion of recurrence by including the three favourable factors (BRAF wildtype/low proportion of BRAF mutated alleles, low proliferation and high presence of TILs) (p = 0.0004). When at least two out of three factors were present there was a statistically significant association with longer recurrence free survival in the multivariate analysis (HR 0.30, 95% CI 0.15–0.61, p = 0.001) when adjusted for Breslow thickness, an established independent prognostic marker for CMM. Thus, this panel of markers could be an interesting novel concept for predicting the clinical outcome in patients with high-risk stage I–II ulcerated CMM.
Quality of vegetables in Ghanaian urban farms and markets
Creators: name: Amoah, Philip
name: Lente, I.
name: Asem-Hiablie, S.
name: Abaidoo, R. C.
name: Amoah, Philip
name: Lente, I.
name: Asem-Hiablie, S.
name: Abaidoo, R. C.
Publisher: name: Unknown
Year: 2014
Subjects: subject: Agribusiness
subject: Crop Production/Industries
subject: Marketing
subject: FOS: Economics and business
subject: Production Economics
subject: Vegetables
subject: Marketing
subject: Chemical contamination
subject: Helminths
subject: Heavy metals
subject: Faecal coliforms
subject: Pesticide residues
subject: Irrigation water
subject: Lettuces
subject: Ghana
subject: Kumasi
subject: Accra
subject: Tamale

description: This chapter shows results obtained from analyzing samples of vegetables taken at the farm gate and from selling points in Accra, Kumasi and Tamale. Microbiological data are based on a total of about 1,500 vegetable samples taken from different sampling points along the vegetable distribution chain – farm gates – and from different categories of sellers in Accra, Tamale and Kumasi. Fecal coliforms and helminth eggs were mainly used as the fecal contamination indicator organisms. For chemical contaminants, heavy metals and pesticides in irrigation water and vegetables were analyzed, while estrogens were used as an example for emerging contaminants.
description: In Drechsel, Pay; Keraita, B. (Eds.) Irrigated urban vegetable production in Ghana: characteristics, benefits and risk mitigation. Colombo, Sri Lanka: International Water Management Institute (IWMI).
Edge detection with trigonometric polynomial shearlets
Creators: name: Prestin, Jürgen
name: Schober, Kevin
name: Stasyuk, Serhii A.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Functional Analysis (math.FA)
subject: FOS: Mathematics
subject: 42C15, 42C40, 65T60

description: In this paper we show that certain trigonometric polynomial shearlets which are special cases of directional de la Vallée Poussin type wavelets are able to detect singularities along boundary curves of periodic characteristic functions. Motivated by recent results for discrete shearlets in two dimensions, we provide lower and upper estimates for the magnitude of corresponding inner products. In the proof we use localization properties of trigonometric polynomial shearlets in the time and frequency domain and, among other things, bounds for certain Fresnel integrals. Moreover, we give numerical examples which underline the theoretical results.
The symplectic density property for Calogero–Moser spaces
Creators: name: Andrist, Rafael B.
name: Huang, Gaofeng
Publisher: name: University of Bern
publisherIdentifier: https://ror.org/02k7v4d05
publisherIdentifierScheme: ROR
Year: 2025

description: AbstractWe introduce the symplectic density property and the Hamiltonian density property together with the corresponding versions of Andersén–Lempert theory. We establish these properties for the Calogero–Moser space of particles and describe its group of holomorphic symplectic automorphisms.
The Ancestry and Function of Cytochrome c6A
Creators: name: Slater, Barnaby
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Biochemistry
Photosynthesis
Phylogeny
Transcriptomics
Cytochrome
Abiotic stress
Plant
algae
Chlamydomonas reinhardtii
Molecular genetics
Circular dichroism
protein structure
chlorophyll fluorescence
CrispR
retrograde signalling
photosynthetic electron transfer
redox

description: Cytochrome c6A is a homologue of cytochrome c6 found in eukaryotic green algae and higher plants. However it is thought to perform a different function from cytochrome c6. Two current hypotheses exist for this function: that cytochrome c6A acts as a ‘safety valve’, providing an alternative path for electron flow through the photosynthetic electron transport chain and thus alleviating reactive oxygen species production; that cytochrome c6A has a signalling role where it could sense high light stress and convey this signal to the nucleus to affect gene expression. This study aims to provide insight into the ancestry and function of cytochrome c6A. To gain a clearer understanding of the evolutionary history of cytochrome c6A and cyanobacterial homologues cytochrome c6B and c6C, phylogenetic analysis was performed on peptide sequences of these proteins as found in a wide range of photosynthetic organisms. These data were used to refine the model of the evolutionary history of the cytochrome c6 family. This study also found evidence that cytochrome c6B and c6C are in fact orthologues with a similar function. Chlamydomonas reinhardtii is a model organism for eukaryotic photosynthesis, as its unicellularity provides many advantages over land plants. To determine if cytochrome c6A is involved in high light stress in C. reinhardtii, cytochrome c6A knockout and knockdown mutant lines of C. reinhardtii had been previously produced using CrispR-cpf,1 and are characterised in this study. The mutant lines demonstrated potential growth retardation under high or fluctuating light stress, as well as singlet oxygen stress, which was more noticeable under mixotrophic conditions. Chlorophyll fluorescence analysis of the mutant lines established a link between cytochrome c6A and NPQ. As cytochrome c6A is believed to be located in the thylakoid lumen, and initial NPQ is triggered by a change in luminal pH, circular dichroism was used to determine changes in secondary structure of purified cytochrome c6A over a pH range of 2-7. No significant change in structure was observed, but cytochrome c6A did maintain structural integrity even at pH 2. Finally, the transcriptome of the cytochrome c6A knock out line was compared to the background strain under standard and high light conditions through RNAseq. Many photoprotective, motility and CCM genes were differentially regulated under high light stress, but when cytochrome c6A was knocked out these regulations were diminished. Therefore cytochrome c6A has been proposed as a signalling molecule that functions in CCM, NPQ and motility under photosynthetic stress conditions.
description: BBSRC funded DTP
Atherigona (Atherigona) punctata Karl 1940
Creators: name: Couri, Marcia S.
name: Pont, Adrian C.
name: Daugeron, Christophe
Publisher: name: Zenodo
Year: 2010
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Muscidae
Atherigona
Atherigona punctata

description: 3. Atherigona (Atherigona) punctata Karl, new record
 Atherigona punctata Karl, 1940: 147. Holotype male, Taihoku, Taiwan, in DEI (type seen by Pont 1986: 30).
 Diagnosis. Palpi yellow; frontal vitta orange-yellow, usually dark brown on upper half; fore femur entirely yellow, sometimes with a dark ring in apical quarter; fore tibia darkened at tip; wing clear except for a dark smudge around the tip of subcostal vein; male hypopygial prominence rather tuberculate in form, this and trifoliate process as in Figs 103–109 of Pont (1986); tip of the median piece of trifoliate process characteristic, produced and rounded after the pair of strong apical setae. Female sternite 6 short, as long as broad; tergite 8 and sternite 7 as in Pont (1986: Figs 110–112). See also Pont & Magpayo (1995).
 Material examined. BPBM: Vanuatu: Éfaté: Port Vila, 0–100 m, i.1976, 1 ♂, N.L.H. Krauss. Malekula: N. Lakatoro, 22–30 & 29.ix.1967, 2 ♀, J. & M. Sedlacek.
 Comments. The species is here recorded from Vanuatu for the first time.
 Distribution. Australia (NT, Qld), PNG (PNG), Solomon Is, Vanuatu; Oriental Region.
description: Published as part of Couri, Marcia S., Pont, Adrian C. & Daugeron, Christophe, 2010, The Muscidae (Diptera) of Vanuatu, pp. 1-39 in Zootaxa 2556 (1) on page 9, DOI: 10.11646/zootaxa.2556.1.1, http://zenodo.org/record/5302228
Additional file 2: of Oral prednisolone for acute otitis media in children: protocol of a pilot randomised, open-label, controlled study (OPAL study)
Creators: name: Respati Ranakusuma
name: McCullough, Amanda
name: Safitri, Eka
name: Yupitri Pitoyo
name: Widyaningsih
name: Mar, Christopher Del
name: Beller, Elaine
Publisher: name: figshare
Year: 2019
Subjects: subject: Space Science
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Cancer
subject: Inorganic Chemistry
subject: Science Policy

description: Case report formsâ Pilot OPAL Study. This file includes case report forms that are used in the pilot study: CRF01. Participant information sheet and consent form; CRF02. Study registration form; CRF03. Eligibility form; CRF04. Baseline information form; CRF05. Outcome form; CRF06. Symptom diary; CRF07. Prescription of study medication; CRF08. Randomisation form; CRF09. Follow-up visit card; CRF10. Serious adverse events reporting form; CRF11. Feedback form; FORM01. Study recruitment log book; FORM02. Study medication stock book; FORM03. Study medication dispensing form; FORM04. Study medication return form; FORM05. Completed case report form; FORM06. Recapitulation of non-participating subject form; FORM07. Guideline of antibiotics for acute otitis media; FORM08. Prednisolone dose for OPAL study; FORM09. Instruction for using prednisolone for parents; FORM10. Lupred pharmaceutical brochure. This file can be accessed at https://pure.bond.edu.au/ws/portalfiles/portal/27513684/Additional_File_2._Case_report_forms_Pilot_OPAL_Study.pdf (PDF 4716 kb)
Schatzinsel: Das Erleben der psychologischen Grundbedürfnisse beim Arbeiten mit einer kooperativen Mathematik-Lernumgebung
Creators: name: Krummenacher, Urs
Publisher: name: Pädagogische Hochschule Zürich
Year: 2023
Subjects: Kooperatives Lernen
Kooperationshandlungen
Lernumgebung
Kooperative Mathematik-Lernumgebung
Selbstbestimmungstheorie
Psychologische Grundbedürfnisse
Motivation
Interesse

description: In der vorliegenden Arbeit wird die kooperative Mathematik-Lernumgebung «Schatzinsel» einer Sachanalyse unterzogen und untersucht, inwiefern das Arbeiten mit der Lernumgebung das Erleben der psychologischen Grundbedürfnisse (Basic Needs) unterstützt. Die der Arbeit zugrunde liegenden Forschungsfragen sind: Erfüllt die Lernumgebung «Schatzinsel» die Gelingensbedingungen für effektives kooperatives Lernen und weist sie die Merkmale kooperativer Mathematik-Lernumgebungen auf? Unterstützt das Arbeiten mit der kooperativen Lernumgebung «Schatzinsel» das Erleben der psychologischen Grundbedürfnisse? Unterscheiden sich die Motivation und das individuelle Interesse an Mathematik von der Motivation und dem situationalen Interesse an der kooperativen Lernumgebung «Schatzinsel»?Im theoretischen Teil werden grundlegende Konzepte des kooperativen Mathematik-Lernens und der Begriff der mathematischen Lernumgebung aufgearbeitet. Anschliessend werden mit der Theorie der Organismischen Intergration OIT und der Basic-Needs-Theorie BPNT die beiden für diese Arbeit relevanten Minitheorien der Selbstbestimmungstheorie SDT von Deci und Ryan umrissen. Zur ersten Forschungsfrage werden Kriterien der Lerntheorie, der gängigen fachdidaktischen Literatur beigezogen. Die Fragen nach der Motivation und dem Interesse am Arbeiten mit der kooperativen Lernumgebung und nach dem Erleben der psychologischen Grundbedürfnisse werden quantitativ angegangen. Dazu wurden im Rahmen der Erprobungen der Lernumgebung unter Bedingungen des Regelunterrichts insgesamt 55 Schülerinnen und Schüler in einem Pre-Post-Design befragt. Die Analyse der Lernumgebung ergibt, dass diese den theoretischen Anforderungen an das kooperative Lernen gerecht wird und die geforderten Merkmale an eine kooperative Mathematik-Lernumgebung aufweist. Die Ergebnisse der Untersuchung zeigen, dass die kooperative Lernumgebung aufgrund ihrer Merkmale zu situationalem Interesse beiträgt und dass sich die Schülerinnen und Schüler beim Arbeiten mit der Lernumgebung als autonom, kompetent und sozial eingebunden wahrnehmen. Aufgrund der Ergebnisse dieser Arbeit und aufgrund des vorliegenden fachlichen, überfachlichen und motivationalen Potenzials sind Aus- und Weiterbildung gefordert, Lehrkräfte zur Implementierung kooperativer Mathematik-Lernumgebungen zu ermutigen und zu befähigen. Der fachdidaktischen Forschung eröffnet sich mit den kooperativen Mathematik-Lernumgebungen ein bislang kaum bearbeitetes Tätigkeitsfeld.
description: repphzhbib2024MA
Additional file 3: of Oral prednisolone for acute otitis media in children: protocol of a pilot randomised, open-label, controlled study (OPAL study)
Creators: name: Respati Ranakusuma
name: McCullough, Amanda
name: Safitri, Eka
name: Yupitri Pitoyo
name: Widyaningsih
name: Mar, Christopher Del
name: Beller, Elaine
Publisher: name: figshare
Year: 2019
Subjects: subject: Space Science
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Science Policy

description: Manual of operationsâ Pilot OPAL Study. This file includes step-by-step manual for physicians, audiologists, nurses, and pharmacists who participate in the study. The manual of operations handbook was distributed during the trainings for participating physicians, audiologists, nurses, and pharmacists. This file can be accessed at https://pure.bond.edu.au/ws/portalfiles/portal/27513686/Additional_File_3._Manual_of_Operations_Pilot_OPAL_Study.pdf (PDF 7905 kb)
A Simple Model of Microalgal Growth in a PBR - free to end user version
Creators: name: Flynn, Kevin J
Publisher: name: Zenodo
Year: 2021
Subjects: Microalgae model

description: Powersim Studio 10 model to support Chapter 8 of "Enhancing Microalgal Production - constructing decision support tools using system dynamics modelling" KJ Flynn Free to end-user version
description: Requires Powersim Studio 10 Cockpit to open; https://www.powersim.no/ Funded by the European Regional Development Fund (ERDF) Interreg Atlantic Area programme, EnhanceMicroAlgae (EAPA_338/2016; "High added-value industrial opportunities for microalgae in the Atlantic Area").
Comparing the Quenching Times of Faint M31 and Milky Way Satellite Galaxies
Creators: name: Weisz, Daniel R.
name: Martin, Nicolas F.
name: Dolphin, Andrew E.
name: Albers, Saundra M.
name: Collins, Michelle L. M.
name: Ferguson, Annette M. N.
name: Lewis, Geraint F.
name: Mackey, 8 Dougal
name: McConnachie, Alan
name: Rich, R. Michael
name: Skillman, Evan D.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present the star formation histories (SFHs) of 20 faint M31 satellites ($-12 \lesssim M_V \lesssim -6$) that were measured by modeling sub-horizontal branch (HB) depth color-magnitude diagrams constructed from Hubble Space Telescope (HST) imaging. Reinforcing previous results, we find that virtually all galaxies quenched between 3 and 9 Gyr ago, independent of luminosity, with a notable concentration $3-6$ Gyr ago. This is in contrast to the Milky Way (MW) satellites, which are generally either faint with ancient quenching times or luminous with recent ($<3$ Gyr) quenching times. We suggest that systematic differences in the quenching times of M31 and MW satellites may be a reflection of the varying accretion histories of M31 and the MW. This result implies that the formation histories of low-mass satellites may not be broadly representative of low-mass galaxies in general. Among the M31 satellite population we identify two distinct groups based on their SFHs: one with exponentially declining SFHs ($τ\sim 2$ Gyr) and one with rising SFHs with abrupt quenching. We speculate how these two groups could be related to scenarios for a recent major merger involving M31. The Cycle 27 HST Treasury survey of M31 satellites will provide well-constrained ancient SFHs to go along with the quenching times we measure here. The discovery and characterization of M31 satellites with $M_V \gtrsim -6$ would help quantify the relative contributions of reionization and environment to quenching of the lowest-mass satellites.
description: 7 pages, 3 figures, 1 table. Submitted to ApJL and posted after addressing the referee's report. Comments welcome