cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Should Age-Dependent Absolute Risk Thresholds Be Used for Risk Stratification in Risk-Stratified Breast Cancer Screening?
Creators: name: Pashayan, Nora
name: Antoniou, Antonis C.
name: Lee, Andrew
name: Wolfson, Michael
name: Chiquette, Jocelyne
name: Eloy, Laurence
name: Eisen, Andrea
name: Stockley, Tracy L.
name: Nabi, Hermann
name: Brooks, Jennifer D.
name: Dorval, Michel
name: Easton, Douglas F.
name: Knoppers, Bartha Maria
name: Chiarelli, Anna M.
name: Simard, Jacques
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: absolute risk
remaining lifetime risk
risk threshold
risk-stratified screening
misclassification

description: In risk-stratified cancer screening, multiple risk factors are incorporated into the risk assessment. An individual’s estimated absolute cancer risk is linked to risk categories with tailored screening recommendations for each risk category. Absolute risk, expressed as either remaining lifetime risk or shorter-term (five- or ten-year) risk, is estimated from the age at assessment. These risk estimates vary by age; however, some clinical guidelines (e.g., enhanced breast cancer surveillance guidelines) and ongoing personalised breast screening trials, stratify women based on absolute risk thresholds that do not vary by age. We examine an alternative approach in which the risk thresholds used for risk stratification vary by age and consider the implications of using age-independent risk thresholds on risk stratification. We demonstrate that using an age-independent remaining lifetime risk threshold approach could identify high-risk younger women but would miss high-risk older women, whereas an age-independent 5-year or 10-year absolute risk threshold could miss high-risk younger women and classify lower-risk older women as high risk. With risk misclassification, women with an equivalent risk level would be offered a different screening plan. To mitigate these problems, age-dependent absolute risk thresholds should be used to inform risk stratification.
Monte Carlo modelling of NLO DGLAP QCD Evolution in the fully unintegrated form
Creators: name: Kusina, A.
name: Jadach, S.
name: Skrzypek, M.
name: Slawinska, M.
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Presently available perturbative QCD calculations combining hard process matrix element with the Parton Shower Monte Carlo programs feature hard process matrix element calculated often beyond the leading order (LO), that is including complete next-to-leading-order (NLO), or even next-to-next-to-leading-order (NNLO) corrections, while Parton Shower is only at the leading order (LO). We report here on a work in progress which demonstrate feasibility of constructing Parton Shower Monte Carlo (PSMC) featuring complete NLO corrections to QCD evolution with respect to the logarithm of the factorization scale. This effort presently covers non-singlet subset of Feynman diagrams contributing to the above QCD evolution. It should be stressed that our approach to the NLO QCD evolution is exclusive, that is giving insight into the fully unintegrated phase space. However, at the inclusive level our implementation agrees exactly with the standard inclusive picture of the NLO DGLAP evolution. Our new approach (after including NLO singlet diagrams) provides a complete method of combining the resummed and fixed order perturbative QCD calculations beyond the LO in a form suitable for the MC implementation, an alternative to the existing ones. First practical applications will include Monte Carlo generators for W/Z production processes in hadron-hadron colliders and lepton-hadron colliders.
description: Contribution to 35th International Conference of High Energy Physics July 22-28, 2010, Paris, France
Investigation and Management of Apparently Sporadic Central Nervous System Haemangioblastoma for Evidence of Von Hippel–Lindau Disease
Creators: name: Furness, Hugh
name: Salfity, Louay
name: Devereux, Johanna
name: Halliday, Dorothy
name: Hanson, Helen
name: Ruddy, Deborah M.
name: UK VHL Study Group, UK VHL Study Group
name: Shah, Neha
name: Sultana, George
name: Woodward, Emma R.
name: Sandford, Richard N.
name: Snape, Katie M.
name: Maher, Eamonn R.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: haemangioblastoma
renal cell carcinoma
genetics
VHL

description: Haemangioblastomas are rare, highly vascularised tumours that typically occur in the cerebellum, brain stem and spinal cord. Up to a third of individuals with a haemangioblastoma will have von Hippel–Lindau (VHL) disease. Individuals with haemangioblastoma and underlying VHL disease present, on average, at a younger age and frequently have a personal or family history of VHL disease-related tumours (e.g., retinal or central nervous system (CNS) haemangioblastomas, renal cell carcinoma, phaeochromocytoma). However, a subset present an apparently sporadic haemangioblastoma without other features of VHL disease. To detect such individuals, it has been recommended that genetic testing and clinical/radiological assessment for VHL disease should be offered to patients with a haemangioblastoma. To assess “real-world” clinical practice, we undertook a national survey of clinical genetics centres. All participating centres responded that they would offer genetic testing and a comprehensive assessment (ophthalmological examination and CNS and abdominal imaging) to a patient presenting with a CNS haemangioblastoma. However, for individuals who tested negative, there was variability in practice with regard to the need for continued follow-up. We then reviewed the results of follow-up surveillance in 91 such individuals seen at four centres. The risk of developing a potential VHL-related tumour (haemangioblastoma or RCC) was estimated at 10.8% at 10 years follow-up. The risks of developing a recurrent haemangioblastoma were higher in those who presented 40 years of age. In the light of these and previous findings, we propose an age-stratified protocol for surveillance of VHL-related tumours in individuals with apparently isolated haemangioblastoma.
Identification of a putative corticosteroid in Pacific Lamprey (Entosphenus tridentatus)
Creators: name: Rai, Satbir Kaur
Publisher: name: University of British Columbia
Year: 2014

description: The mechanisms and interplay of multiple axes as well as the physiological components of the stress response have been studied in many vertebrate groups; however, the intricacies and chemical messengers involved in the stress response in lamprey have not been fully resolved. 11-Deoxycortisol is a functional corticosteroid in sea lamprey, but the identity of the functional corticosteroid used by other lamprey species and the evolution of the stress response in lamprey lineage remains unknown. Identification of the functional corticosteroid in a greater number of lamprey species will help elucidate the evolution of the stress response in lamprey. I have demonstrated that 11-deoxycortisol, a steroid precursor to cortisol, may be a functional corticosteroid in Pacific lamprey. The putative hormone was identified in Pacific lamprey plasma by employing an array of methods such as radioimmunoassay (RIA), high performance liquid chromatography (HPLC) and mass spectrometry analysis. I have demonstrated that plasma levels of 11-deoxycortisol significantly increased in Pacific lamprey 0.5 and 1 hr after stress exposure and that sea lamprey corticotropin releasing hormone (CRH) injections increased circulating levels of 11-deoxycortisol, suggesting that 11-deoxycortisol secretion is under control of the hypothalamic neuropeptide CRH. However, plasma 11-deoxycortisol concentrations did not increase in response to sea lamprey adrenocorticotropic hormone (ACTH) injections. The effect of artificially elevated 11-deoxycortisol on the expression of glucocorticoid receptor and progesterone receptor mRNA was examined in liver, gill, muscle, heart and testis using RT-qPCR. 11-Deoxycortisol was chronically elevated using coconut oil implants with two different doses of 11-deoxycortisol (0.5 and 1.0 µg per g of body weight). After 7 days of elevated plasma 11-deoxycortisol concentrations there was no significant difference in the expression of either receptor in the tissues examined. Overall, the results of this thesis demonstrate 11-deoxycortisol is a putative corticosteroid in Pacific lamprey; however, despite the evidence for hypothalamic control of 11-deoxycortisol release, the results do not conclusively support Pacific lamprey having a hypothalamic pituitary interrenal (HPI) axis.
The functional brain favours segregated modular connectivity at old age unless affected by neurodegeneration.
Creators: name: Chen, Xue
name: Necus, Joe
name: Peraza, Luis R
name: Mehraram, Ramtin
name: Wang, Yanjiang
name: O'Brien, John T
name: Blamire, Andrew
name: Kaiser, Marcus
name: Taylor, John-Paul
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021

description: Funder: Department of Health
description: Brain's modular connectivity gives this organ resilience and adaptability. The ageing process alters the organised modularity of the brain and these changes are further accentuated by neurodegeneration, leading to disorganisation. To understand this further, we analysed modular variability-heterogeneity of modules-and modular dissociation-detachment from segregated connectivity-in two ageing cohorts and a mixed cohort of neurodegenerative diseases. Our results revealed that the brain follows a universal pattern of high modular variability in metacognitive brain regions: the association cortices. The brain in ageing moves towards a segregated modular structure despite presenting with increased modular heterogeneity-modules in older adults are not only segregated, but their shape and size are more variable than in young adults. In the presence of neurodegeneration, the brain maintains its segregated connectivity globally but not locally, and this is particularly visible in dementia with Lewy bodies and Parkinson's disease dementia; overall, the modular brain shows patterns of differentiated pathology.
Tracking the COVID-19 crisis with high-resolution transaction data.
Creators: name: Carvalho, Vasco M
name: Garcia, Juan R
name: Hansen, Stephen
name: Ortiz, Álvaro
name: Rodrigo, Tomasa
name: Rodríguez Mora, José V
name: Ruiz, Pep
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Consumption
Transaction Data
National Accounts
Covid-19

description: Payments systems generate vast amounts of naturally occurring transaction data rarely used for constructing official statistics. We consider billions of transactions from card data from a large bank, Banco Bilbao Vizcaya Argentaria, as an alternative source of information for measuring consumption. We show, via validation against official consumption measures, that transaction data complements national accounts and consumption surveys. We then analyse the impact of COVID-19 in Spain, and document: (i) strong consumption responses to business closures, but smaller effects for capacity restrictions; (ii) a steeper decline in spending in rich neighbourhoods; (iii) higher mobility for residents of lower-income neighbourhoods, correlating with increased disease incidence.
Conceptualizing the commercial determinants of dietary behaviors associated with obesity: A systematic review using principles from critical interpretative synthesis.
Creators: name: Chavez-Ugalde, Yanaina
name: Jago, Russell
name: Toumpakari, Zoi
name: Egan, Matt
name: Cummins, Steven
name: White, Martin
name: Hulls, Paige
name: De Vocht, Frank
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Public Health
Food Industry
Dietary Behavior
Commercial Determinants Of Obesity

description: IntroductionUnhealthy diet is an important preventable risk factor for overweight and obesity. Identifying the key drivers of an unhealthy diet is an important public health aim. "Big Food" has been identified as an influential factor shaping dietary behavior and obesity, and their practices have broadly been labeled as the "commercial determinants of obesity," but there is a lack of definitions and conceptualizations for these terms. This review aimed to synthesize literature on the commercial determinants of dietary behavior associated with obesity. It presents the development of an integrative definition and a conceptual framework involving potential influences on dietary behavior, and it examines the prevalence of certain narratives within papers that focus on children and adolescents.MethodsFour electronic databases (Ovid MEDLINE, PubMed, Web of Science, and Scopus) were searched up to December 2020. Eighty-one articles met the inclusion criteria: they were published in a peer-reviewed academic journal, described a practice from the food/beverage industry in relation to dietary behavior or obesity. Data were integrated using critical interpretative synthesis.ResultsThe commercial determinants of dietary behavior are conceptualized in terms of three corporate spheres of action-political and legal; production, processing and design; and marketing and preference shaping-which enable powerful food industry to successfully pursue their business, market, and political objectives. The most frequently reported sphere of action targeting children and adolescents was marketing and preference shaping.ConclusionsIn the included literature, the commercial determinants of dietary behavior associated with obesity have been conceptualized as being part of a complex system where corporate practices are enabled by power structures. The proposed framework can facilitate a structured identification and systematic study of the impact of specific aspects of food industry's strategies and increase opportunities for primary prevention by anticipating industry responses and by discouraging corporate practices that harm health.
Cardinality of Rauzy classes
Creators: name: Delecroix, Vincent
Publisher: name: arXiv
Year: 2011
Subjects: subject: Combinatorics (math.CO)
subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics
subject: A5A05, 30F60, 32G15, 37A05, 37B05,

description: Rauzy classes define a partition of the set of irreducible (or indecomposable) permutations. They were defined by G. Rauzy as part of an induction algorithm for interval exchange transformations. In this article we prove an explicit formula for the cardinality of all Rauzy classes.
description: 43 pages, 22 figures
An in vitro stem cell model of human epiblast and yolk sac interaction.
Creators: name: Mackinlay, Kirsty Ml
name: Weatherbee, Bailey At
name: Souza Rosa, Viviane
name: Handford, Charlotte E
name: Hudson, George
name: Coorens, Tim
name: Pereira, Lygia V
name: Behjati, Sam
name: Vallier, Ludovic
name: Shahbazi, Marta N
name: Zernicka-Goetz, Magdalena
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Human
Cell biology
Embryology
Mouse
Pluripotency
developmental biology
Stem Cells
Human Development
Epiblast
Hypoblast

description: Human embryogenesis entails complex signalling interactions between embryonic and extra-embryonic cells. However, how extra-embryonic cells direct morphogenesis within the human embryo remains largely unknown due to a lack of relevant stem cell models. Here, we have established conditions to differentiate human pluripotent stem cells (hPSCs) into yolk sac-like cells (YSLCs) that resemble the post-implantation human hypoblast molecularly and functionally. YSLCs induce the expression of pluripotency and anterior ectoderm markers in human embryonic stem cells (hESCs) at the expense of mesoderm and endoderm markers. This activity is mediated by the release of BMP and WNT signalling pathway inhibitors, and, therefore, resembles the functioning of the anterior visceral endoderm signalling centre of the mouse embryo, which establishes the anterior-posterior axis. Our results implicate the yolk sac in epiblast cell fate specification in the human embryo and propose YSLCs as a tool for studying post-implantation human embryo development in vitro.
Scum of the Earth: A Hypothesis for Prebiotic Multi-Compartmentalised Environments
Creators: name: Walton, Craig Robert
name: Shorttle, Oliver
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: prebiotic chemistry
early Earth
origin of life

description: Compartmentalisation by bioenergetic membranes is a universal feature of life. The eventual compartmentalisation of prebiotic systems is therefore often argued to comprise a key step during the origin of life. Compartments may have been active participants in prebiotic chemistry, concentrating and spatially organising key reactants. However, most prebiotically plausible compartments are leaky or unstable, limiting their utility. Here, we develop a new hypothesis for an origin of life environment that capitalises upon, and mitigates the limitations of, prebiotic compartments: multi-compartmentalised layers in the near surface environment—a ’scum’. Scum-type environments benefit from many of the same ensemble-based advantages as microbial biofilms. In particular, scum layers mediate diffusion with the wider environments, favouring preservation and sharing of early informational molecules, along with the selective concentration of compatible prebiotic compounds. Biofilms are among the earliest traces imprinted by life in the rock record: we contend that prebiotic equivalents of these environments deserve future experimental investigation.
Serious physical assault and subsequent risk for rehospitalization in individuals with severe mental illness: a nationwide, register-based retrospective cohort study
Creators: name: Mlada, Karolina
name: Formanek, Tomas
name: Vevera, Jan
name: Latalova, Klara
name: Winkler, Petr
name: Volavka, Jan
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Primary Research
Schizophrenia
Victimization
Assault
Severe mental illness
Hospitalization
Violence
Aggression

description: Abstract: Background: Victimization is associated with worse social and clinical outcomes of individuals with severe mental illness (SMI). A relapse of SMI may be one of the clinical consequences of assaultive trauma. As far as we know, there is no published study that analyzes nationwide health registers to assess the risk of SMI rehospitalization following assault. Aim: We aimed to assess whether exposure to assault is associated with an increased risk of psychiatric hospitalization in those with SMI. Methods: We utilized data from the Czech nationwide registers of all-cause hospitalizations and all-cause deaths. We defined exposed individuals as those discharged from a hospitalization for SMI between 2002 and 2007, and hospitalized for serious injuries sustained in an assault in the subsequent 7 years. For each assaulted individual, we randomly selected five counterparts, matched on SMI diagnosis, age and sex, who were not assaulted in the examined time period. We used mixed effect logistic regression to assess the effect of assault on the risk of SMI rehospitalization within the following 6 months. We fitted unadjusted models and models adjusted for the number of previous SMI hospitalizations and drug use disorders. Results: The sample consisted of 248 exposed and 1 240 unexposed individuals. In the unadjusted model, assaulted individuals were almost four times more likely to be rehospitalized than their non-assaulted counterparts (odds ratio (OR) = 3.96; 95% CI 2.75; 5.71). After adjusting for all covariates, the OR remained threefold higher (OR = 3.07; 95% CI 2.10; 4.49). Conclusion: People with a history of SMI hospitalization were approximately three times more likely to be rehospitalized for SMI within 6 months after an assault than their non-assaulted SMI counterparts. Soon after a person with SMI is physically assaulted, there should be a psychiatric evaluation and a close follow-up.
The cardiopulmonary demand of kettlebell snatches
Creators: name: Chan, Margaux
Publisher: name: University of British Columbia
Year: 2014

description: Kettlebell lifting continues to gain popularity as a strength and conditioning training tool and as a sport in and of itself (Girevoy Sport). Although the swing to chest-level and several multi-movement protocols have been analyzed, little research has attempted to quantify the aerobic stimulus of individual kettlebell movements, which would best inform kettlebell-related exercise prescription. The purpose of this study was to quantify the cardiopulmonary demand, assessed by oxygen consumption (V̇O₂) and heart rate (HR), of continuous high-intensity kettlebell snatches under conditions that consider Girevoy Sport, and to compare this demand to a more traditional graded rowing exercise test. Ten male participants (age = 28.4 ± 4.6 years, height = 185 ± 7 cm, body mass = 95.1 ± 14.9 kg) completed (1) a graded rowing exercise test to determine maximal oxygen consumption (V̇O₂max) and maximal heart rate (HRmax) and (2) a graded kettlebell snatch exercise test with a 16-kg kettlebell to determine peak oxygen consumption (V̇O₂peak) and peak heart rate (HRpeak) during this activity. Subjects achieved a V̇O₂max of 45.7 ± 6.9 ml·kg-¹·min-¹ and an HRmax of 177 ± 6.9 beats per minute (bpm). The kettlebell snatch test produced a V̇O₂peak of 37.3 ± 5.2 ml·kg-¹·min-¹ (82.1 ± 7.4% V̇O₂max) and a heart rate of 173 ± 8 beats per minute (97.3 ± 4.8% HRmax). These findings suggest that continuous high-intensity kettlebell snatches with 16-kg are likely provide an adequate aerobic stimulus to improve cardiorespiratory fitness in those whose V̇O₂max is ≤ 51 ml·kg-¹·min-¹ and those who are moderately trained and lower, according to recommendations from the American College of Sports Medicine.
High-order cumulants in the counting statistics of asymmetric quantum dots
Creators: name: Fricke, Christian
name: Hohls, Frank
name: Sethubalasubramanian, Nandhavel
name: Fricke, Lukas
name: Haug, Rolf J.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: Measurements of single electron tunneling through a quantum dot using a quantum point contact as charge detector have been performed for very long time traces with very large event counts. This large statistical basis is used for a detailed examination of the counting statistics for varying symmetry of the quantum dot system. From the measured statistics we extract high order cumulants describing the distribution. Oscillations of the high order cumulants are observed when varying the symmetry. We compare this behavior to the observed oscillation in time dependence and show that the variation of both system variables lead to the same kind of oscillating response.
description: 3 pages
GMP-grade neural progenitor derivation and differentiation from clinical-grade human embryonic stem cells
Creators: name: Vitillo, Loriana
name: Durance, Catherine
name: Hewitt, Zoe
name: Moore, Harry
name: Smith, Austin
name: Vallier, Ludovic
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Research
Pluripotent stem cells
hESCs
Neural progenitors
GMP
Cell therapy

description: Funder: Medical Research Council; doi: http://dx.doi.org/10.13039/501100000265
description: Funder: Biotechnology and Biological Sciences Research Council; doi: http://dx.doi.org/10.13039/501100000268
description: Funder: Engineering and Physical Sciences Research Council; doi: http://dx.doi.org/10.13039/501100000266
description: Abstract: Background: A major challenge for the clinical use of human pluripotent stem cells is the development of safe, robust and controlled differentiation protocols. Adaptation of research protocols using reagents designated as research-only to those which are suitable for clinical use, often referred to as good manufacturing practice (GMP) reagents, is a crucial and laborious step in the translational pipeline. However, published protocols to assist this process remain very limited. Methods: We adapted research-grade protocols for the derivation and differentiation of long-term neuroepithelial stem cell progenitors (lt-NES) to GMP-grade reagents and factors suitable for clinical applications. We screened the robustness of the protocol with six clinical-grade hESC lines deposited in the UK Stem Cell Bank. Results: Here, we present a new GMP-compliant protocol to derive lt-NES, which are multipotent, bankable and karyotypically stable. This protocol resulted in robust and reproducible differentiation of several clinical-grade embryonic stem cells from which we derived lt-NES. Furthermore, GMP-derived lt-NES demonstrated a high neurogenic potential while retaining the ability to be redirected to several neuronal sub-types. Conclusions: Overall, we report the feasibility of derivation and differentiation of clinical-grade embryonic stem cell lines into lt-NES under GMP-compliant conditions. Our protocols could be used as a flexible tool to speed up translation-to-clinic of pluripotent stem cells for a variety of neurological therapies or regenerative medicine studies.
Legitimacy challenges to the liberal world order: Evidence from United Nations speeches, 1970–2018
Creators: name: Kentikelenis, Alexander
name: Voeten, Erik
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Article
Liberal world order
Global governance
United Nations
Legitimacy
World Bank
IMF
WTO

description: Funder: University of Cambridge
description: Abstract: The liberal international economic order has been facing high-profile legitimacy challenges in recent years. This article puts these challenges in historical context through a systematic analysis of rhetorical challenges towards both the order per se and specific global economic institutions. Drawing on Albert Hirschman’s classic typology of exit, voice and loyalty, we coded leaders’ speeches in the General Debate at the UN General Assembly between 1970 and 2018 as articulating intentions to abandon elements of the order, challenges or calls for reform, unequivocal support, or factual mentions of cooperation. Surprisingly, we find that explicit criticisms towards the liberal order are at an all-time low and that exit threats remain rare. An analysis of the historical evolution of criticisms to global economic institutions reveals a move away from the Cold War insider-outsider conflict towards insider contestation. For example, we find that as countries’ economies become more open, their leaders expressed more support for global economic institutions during the Cold War but less support since. Finally, we demonstrate consistency between the public policy positions leaders announce in UNGA General Debate speeches and their government positions on consequential reform debates on debt relief.
Precise optical control of gene expression in C elegans using improved genetic code expansion and Cre recombinase
Creators: name: Davis, Lloyd
name: Radman, Inja
name: Goutou, Angeliki
name: Tynan, Ailish
name: Baxter, Kieran
name: Xi, Zhiyan
name: O'Shea, Jack M
name: Chin, Jason W
name: Greiss, Sebastian
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Tools and Resources
Biochemistry and Chemical Biology
Neuroscience
genetic code expansion
non canonical amino acids
optogenetics
Cre recombinase
photo-caged amino acid
C. elegans

description: Funder: Wellcome-Trust University of Edinburgh Institutional Strategic Support Fund ISS2
description: Funder: The Royal Society
description: Funder: Muir Maxwell Epilepsy Centre
description: Funder: Louis Jeantet Foundation
description: Funder: Herchel Smith Foundation
description: Funder: University of Edinburgh, Edinburgh Global Award and Principal's Career Development PhD studentship
description: Synthetic strategies for optically controlling gene expression may enable the precise spatiotemporal control of genes in any combination of cells that cannot be targeted with specific promoters. We develop an improved genetic code expansion system in Caenorhabditis elegans and use it to create a photoactivatable Cre recombinase. We laser-activate Cre in single neurons within a bilaterally symmetric pair to selectively switch on expression of a loxP-controlled optogenetic channel in the targeted neuron. We use the system to dissect, in freely moving animals, the individual contributions of the mechanosensory neurons PLML/PLMR to the C. elegans touch response circuit, revealing distinct and synergistic roles for these neurons. We thus demonstrate how genetic code expansion and optical targeting can be combined to break the symmetry of neuron pairs and dissect behavioural outputs of individual neurons that cannot be genetically targeted.
A 5 GHz LNA for a Radio-Astronomy Experiment
Creators: name: Bergano, Miguel
name: Cupido, Luis
name: Rocha, Armando
name: Barbosa, Domingos
Publisher: name: arXiv
Year: 2011
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: The paper describes the project, implementation and test of a C-band (5GHz) Low Noise Amplifier (LNA) using new low noise Pseudomorphic High Electron Mobility Transistors (pHEMTS) from Avago. The amplifier was developed to be used as a cost effective solution in a receiver chain for Galactic Emission Mapping (GEM-P) project in Portugal with the objective of finding affordable solutions not requiring strong cryogenic operation, as is the case of massive projects like the Square Kilometer Array (SKA), in Earth Sensing projects and other niches like microwave reflectometry. The particular application and amplifier requirements are first introduced. Several commercially available low noise devices were selected and the noise performance simulated. An ultra-low noise pHEMT was used for an implementation that achieved a Noise Figure of 0.6 dB with 13 dB gain at 5 GHz. The design, simulation and measured results of the prototype are presented and discussed.
description: IEEE Xplore, Accepted for Publication at IEEE EuronCon 2011 - International Conference on Computer as Tool / ConfTel 2011, Lisbon, April 2011
Quantum Gravity coupled to Matter via Noncommutative Geometry
Creators: name: Aastrup, Johannes
name: Grimstrup, Jesper M.
name: Paschke, Mario
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We show that the principal part of the Dirac Hamiltonian in 3+1 dimensions emerges in a semi-classical approximation from a construction which encodes the kinematics of quantum gravity. The construction is a spectral triple over a configuration space of connections. It involves an algebra of holonomy loops represented as bounded operators on a separable Hilbert space and a Dirac type operator. Semi-classical states, which involve an averaging over points at which the product between loops is defined, are constructed and it is shown that the Dirac Hamiltonian emerges as the expectation value of the Dirac type operator on these states in a semi-classical approximation.
description: 15 pages, 1 figure
ZE3RA: The ZEPLIN-III Reduction and Analysis Package
Creators: name: Neves, F.
name: Akimov, D. Yu.
name: Araújo, H. M.
name: Barnes, E. J.
name: Belov, V. A.
name: Burenkov, A. A.
name: Chepel, V.
name: Currie, A.
name: DeViveiros, L.
name: Edwards, B.
name: Ghag, C.
name: Hollingsworth, A.
name: Horn, M.
name: Kalmus, G. E.
name: Kobyakin, A. S.
name: Kovalenko, A. G.
name: Lebedenko, V. N.
name: Lindote, A.
name: Lopes, M. I.
name: Lüscher, R.
name: Majewski, P.
name: Murphy, A. St J.
name: Paling, S. M.
name: da Cunha, J. Pinto
name: Preece, R.
name: Quenby, J. J.
name: Reichhart, L.
name: Rodrigues, S.
name: Scovell, P. R.
name: Silva, C.
name: Solovov, V. N.
name: Smith, N. J. T.
name: Smith, P. F.
name: Stekhanov, V. N.
name: Sumner, T. J.
name: Thorne, C.
name: Walker, R. J.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: ZE3RA is the software package responsible for processing the raw data from the ZEPLIN-III dark matter experiment and its reduction into a set of parameters used in all subsequent analyses. The detector is a liquid xenon time projection chamber with scintillation and electroluminescence signals read out by an array of 31 photomultipliers. The dual range 62-channel data stream is optimised for the detection of scintillation pulses down to a single photoelectron and of ionisation signals as small as those produced by single electrons. We discuss in particular several strategies related to data filtering, pulse finding and pulse clustering which are tuned to recover the best electron/nuclear recoil discrimination near the detection threshold, where most dark matter elastic scattering signatures are expected. The software was designed assuming only minimal knowledge of the physics underlying the detection principle, allowing an unbiased analysis of the experimental results and easy extension to other detectors with similar requirements.
Dietary energy intakes in children with mental health conditions treated with second-generation antipsychotics
Creators: name: Barker, Mikaela
Publisher: name: University of British Columbia
Year: 2014

description: Approximately one in six Canadian children suffer from mental health conditions (MHC), including: anxiety, bipolar disorder, and depression. Second-generation antipsychotics (SGAs) are increasingly used to treat children with MHCs. Recent evidence suggests that SGAs are implicated in rapid weight gain, increased measures of adiposity, and cardiometabolic dysfunction in the pediatric population. The mechanisms for these adverse side effects have yet to be elucidated. One postulation is that SGAs may increase dietary energy intakes; however, little is known about the diets of SGA-treated children. My thesis research explored dietary intake and its potential association with adiposity and cardiometabolic dysfunction, in SGA-treated children. This cross-sectional study recruited SGA-treated (n=25) and SGA-naïve (n=20) children (6-19 yrs) with MHCs, from the Psychiatry Department at BC Children’s Hospital. Demographics, medical history, and anthropometrics were obtained. In a subset, fasting plasma lipids, glucose, and insulin were obtained and the homeostatic model assessment of insulin resistance (HOMA-IR) was calculated. Three 24-hour food records were collected and analyzed for average three-day total energy (kcal), macronutrient, saturated fat, sugar, fibre, and sodium intakes. There were no statistically significant differences between groups for energy intakes (mean ± SD; 2036.5±715.8 vs. 1725.5 ± 545.6, P = 0.352) or macronutrient, saturated fat, sugar, fibre, and sodium intakes; adjusting for sex, height, pubertal status, and psychostimulant medications. SGA-treated children had higher zBMI (p=0.001), waist circumference (p=0.019), and HOMA-IR (p=0.009), compared to SGA-naïve children. There were no associations of energy intake and measures of adiposity. There were positive associations of sodium intake and HOMA-IR (p=0.017; 95% CI: 0.013, 0.109) and saturated fat intake and low-density lipoprotein cholesterol (LDL-c) (p=0.041; 95% CI: 0.004, 0.170), in the SGA-treated group; adjusting for sex, pubertal status, overweight/obesity, height, and psychostimulant treatment. These data suggest that SGA-treated children do not have greater dietary energy intakes compared to SGA-naïve children, and dietary energy intakes may not be responsible for greater measures of adiposity in SGA-treated children. However, the positive associations of sodium intake with HOMA-IR, and saturated fat intake with LDL-c, in SGA-treated children, suggest that dietary intakes in SGA-treated children may contribute to cardiometabolic dysfunction in this high-risk population.
Apodized-pupil Lyot coronagraphs: multistage designs for extremely large telescopes
Creators: name: Martinez, Patrice
Publisher: name: arXiv
Year: 2010
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: Earlier apodized-pupil Lyot coronagraphs (APLC) have been studied and developed to enable high-contrast imaging for exoplanet detection and characterization with present-day ground-based telescopes. With the current interest in the development of the next generation of telescopes, the future extremely large telescopes (ELTs), alternative APLC designs involving multistage configuration appear attractive. The interest of these designs for application to ELTs is studied. Performance and sensitivity of multistage APLC to ELT specificities are analyzed and discussed, taking into account several ineluctable coronagraphic telescope error sources by means of numerical simulations. Additionally, a first laboratory experiment with a two-stages-APLC in the near-infrared (H-band) is presented to further support the numerical treatment. Multistage configurations are found to be inappropriate to ELTs. The theoretical gain offered by a multistage design over the classical single-stage APLC is largely compromised by the presence of inherent error sources occurring in a coronagraphic telescope, and in particular in ELTs. The APLC remains an attractive solution for ELTs, but rather in its conventional single-stage configuration.
description: A&A accepted
Direct dark matter detection: The diurnal variation in directional experiments
Creators: name: Vergados, J. D.
name: Moustakidis, Ch. C.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We present some theoretical results relevant to the direct dark matter detection experiments, paying particular attention to directional experiments, i.e. experiments in which, not only the energy but the direction of the recoiling nucleus is observed. In directional experiments the detection rate depends on the angle between the line observation and the sun's direction of motion. Since, however, the direction of observation is fixed with respect the earth, while the Earth is rotating around its axis, in a directional experiment the angle between the direction of observation and the Sun's direction of motion will change during the day. So the observed signal in such experiments will exhibit a very interesting and characteristic periodic diurnal variation.
description: 7 pages, 5 figures, to be published in the Proceedings of the 6th DSU Conference, Leon, Mexico, ed. D. Delepine
Environmental bacteriophages infecting Dickeya and Serratia species: receptors and diversity
Creators: name: Day, Andrew
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Phytopathogen
bacteriophage
Dickeya
Serratia
Ackermannviridae

description: Phytopathogenic Dickeya species inflict large economic losses on a variety of crops. A lack of effective chemical control methods has generated interest in the use of bacteriophages (phages) as a novel tool for biocontrol. In the last decade, six phages have been isolated in Belgium and Poland using Dickeya solani as the host. Previous work in this laboratory has isolated ninety phages capable of infecting D. solani. The majority have been morphologically classified as members of the Ackermannviridae family. In agreement with findings in Salmonella and Klebsiella species, the capsule of D. solani is a likely receptor of Ackermannviridae family phages. Analysis of D. solani strains carrying reporter fusions suggested that the capsule genes are expressed in response to nutritional stress, however disruption of the capsular polysaccharide cluster did not significantly impact virulence. Experiments assessing capsular polysaccharide as a putative receptor for Ackermannviridae family phages in nosocomial pathogen Serratia produced inconclusive results. Phageresistance due to random transposon mutagenesis identified genes encoding transcription factors and regulators, but none directly linked to capsular polysaccharide production. Thirteen phages were capable of infecting a wider host range of Dickeya species. Morphological and genomic analysis showed that six were Podoviridae family members, whilst the other seven were Myoviridae family members. These are part of the recently defined ‘hairy Myoviridae’, characterised by a distinct morphology. Another member of this grouping was isolated during this study, but is more closely related to phages of Erwinia amylovora. A subset of the Ackermannviridae family phages were shown to be capable of facilitating transduction. This makes them unsuitable for use in the environment due to the risk of deleterious horizontal gene transfer. This is also true for the Myoviridae family members, but not for one of the Podoviridae family members. This phage could therefore be a promising candidate for therapeutic use.
description: BBSRC Doctoral Training Partnership
Field enhancement at metallic interfaces due to quantum confinement
Creators: name: Öztürk, Z. Fatih
name: Xiao, Sanshui
name: Yan, Min
name: Wubs, Martijn
name: Jauho, Antti-Pekka
name: Mortensen, Niels Asger
Publisher: name: arXiv
Year: 2010
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We point out an apparently overlooked consequence of the boundary conditions obeyed by the electric displacement vector at air-metal interfaces: the continuity of the normal component combined with the quantum mechanical penetration of the electron gas in the air implies the existence of a surface on which the dielectric function vanishes. This, in turn, leads to an enhancement of the normal component of the total electric field. We study this effect for a planar metal surface, with the inhomogenous electron density accounted for by a Jellium model. We also illustrate the effect for equilateral triangular nanoislands via numerical solutions of the appropriate Maxwell equations, and show that the field enhancement is several orders of magnitude larger than what the conventional theory predicts.
In search of massive single-population Globular Clusters
Creators: name: Caloi, V.
name: D'Antona, F.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Most Globular Clusters so far examined host (at least) two stellar populations. This feature requires a two--step process, in which the nuclearly processed matter from a first generation (FG) of stars gives birth to a second generation (SG) bearing the fingerprint of a fully CNO-cycled matter. Since the present population of most globular clusters is made up largely of SG stars, a substantial fraction of the FG (>~90%) must be lost. Nevertheless, two types of clusters dominated by a simple stellar population (FG clusters) should exist: either clusters initially too small to be able to retain a cooling flow and form a SG (FG-only clusters), or massive clusters that could retain the CNO processed ejecta and form a SG, but were unable to lose a significant fraction of their FG (mainly-FG clusters). We attempt a classification of FG clusters, based on the morphology of their horizontal branches (HBs), as displayed in photomectric catalogues for 106 clusters. FG candidates are the clusters in which the HB can be reproduced by the evolution of an almost unique mass. <20% of clusters with [Fe/H]30% of SG stars, and its present dynamical status bears less information on its formation process than the analysis of the chemical abundances of its stars and of its HB morphology.
description: 11 pages, 7 figures, accepted for publication in MNRAS
Thermodynamic Geometry and Hawking Radiation
Creators: name: Bellucci, S.
name: Tiwari, B. N.
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: This work explores the role of thermodynamic fluctuations in the two parameter Hawking radiating black hole configurations. The system is characterized by an ensemble of arbitrary mass and radiation frequency of the black holes. In the due course of the Hawking radiations, we find that the intrinsic geometric description exhibits an intriguing set of exact pair correction functions and global correlation lengths. We investigate the nature of the constant amplitude radiation and find that it's not stable under fluctuations of the mass and frequency. Subsequently, the consideration of the York model decreasing amplitude radiation demonstrates that thermodynamic fluctuations are globally stable in the small frequency region. In connection with quantum gravity refinements, we take an account of the logarithmic correction into the constant amplitude and York amplitude over the Hawking radiation. In both considerations, we notice that the nature of the possible parametric fluctuations may precisely be ascertained without any approximation. In the frequency domain $w \in (0, \infty)$, we observe that both the local and the global thermodynamic fluctuations of the radiation energy flux are stable in the s-channel. The intrinsic geometry exemplifies a definite stability character to the thermodynamic fluctuations, and up to finitely many topological defects on the parametric surface, the notion remains almost the same for both the constant amplitude and the York model. The Gaussian fluctuations over equilibrium radiation energy flux and fluctuating horizon configurations accomplish a well-defined, non-degenerate, curved and regular intrinsic Riemannian manifolds, for all the physically admissible domains of the radiation parameters. PACS numbers: 04.70.-s: Physics of black holes; 04.70.-Bw: Classical black holes; 04.70.Dy Quantum aspects of black holes, evaporation, thermodynamics; 04.60.Cf Gravitational aspects of string theory. Keywords: Quantum Gravity, Hawking Radiation; Horizon Perturbations; Vaidya Geometry; York Model; Statistical Fluctuations; Thermodynamic Configurations
description: 38 pages, 12 figures