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Using statistics and mathematical modelling to understand infectious disease outbreaks:COVID-19 as an example

Infectious Disease Modelling 2020年第1期5卷 409-441页

作者： Christopher E.Overton Helena B.Stage Shazaad Ahmad Jacob Curran-Sebastian paul dark Rajenki Das Elizabeth Fearon Timothy Felton Martyn Fyles Nick Gent Ian Hall Thomas House Hugo Lewkowicz Xiaoxi Pang Lorenzo Pellis Robert Sawko Andrew Ustianowski Bindu Vekaria Luke Webb Department of Mathematics University of ManchesterUK IBM Research Hartree CentreSciTech DaresburyUK Department of Global Health and Development London School of Hygiene and Tropical MedicineUK Emergency Response Department Public Health EnglandUK Division of Infection Immunity and Respiratory MedicineNIHR Biomedical Research CentreUniversity of ManchesterUK Department of Virology Manchester Medical Microbiology PartnershipManchester Foundation TrustUK Regional Infectious Diseases Unit North Manchester General HospitalUK School of Medical Sciences University of ManchesterUK Intensive Care Unit Wythenshawe HospitalManchester University NHS Foundation TrustUK Department of Health Sciences University of ManchesterUK Department of Mathematical Sciences University of LiverpoolUK The Alan Turing Institute UK Manchester Academic Health Sciences Centre UK Critical Care Unit Salford Royal HospitalNorthern Care Alliance NHS GroupUK

During an infectious disease outbreak,biases in the data and complexities of the underlying dynamics pose significant challenges in mathematically modelling the outbreak and designing *** by the ongoing response to COVID-19,we provide a toolkit of statistical and mathematical models beyond the simple SIR-type differential equation models for analysing the early stages of an outbreak and assessing *** particular,we focus on parameter estimation in the presence of known biases in the data,and the effect of non-pharmaceutical interventions in enclosed subpopulations,such as households and care *** illustrate these methods by applying them to the COVID-19 pandemic.

关键词： COVID-19 Epidemic modelling Parameter estimation Outbreak Bias Intervention

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Equal Sex Ratios of a Marine Green Alga, Bryopsis plumosa

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Journal of Integrative Plant Biology 2008年第6期50卷 648-652页

作者： Tatsuya Togashi paul Alan Cox Marine Biosystems Research Center Chiba University Institute for Ethnomedicine Box 3464 Jackson Hole Wyoming 83001 USA Institute for Ethnomedicine Box 3464 Jackson Hole

By finding some important culture conditions as below, we succeeded in experimentally controlling the whole life history of a dioecious marine green alga, Bryopsis plumosa （Hudson） C. Agardh. In this study, we focused on the primary and secondary sex ratios （i.e. at inception and maturity） using these culture techniques. Gametogenesis was induced by culturing haploid gametophytes with Provasoli＇s enriched seawater （PES） medium under a 14：10 h light： dark cycle at 14 ℃. Formed zygotes grew into diploid sporophytes, which were cultured for 3 months with PES medium under a 14：10 h light ： nbsp;dark cycle at 18℃. Then they were transferred into Schreiber medium and cultured under a 10：14 h light： dark cycle at 22℃. Within 1 week, zoosporogenesis was observed. Zoospores were released within a couple of days. Each zoospore soon germinated and grew into a unisexual gametophyte. The primary sex ratio was examined in gametophytes that originated from a single sporophyte. The secondary sex ratio was studied in the field. Both were estimated as 1：1. Synchronized meiotic cell divisions might occur during zoosporogenesis dividing each sex-determining factor evenly among zoospores. Given the equal sex ratio at maturity, there seems to be no environmental factor that differentially affects the survival of male or female gametophytes in nature.

关键词： algal culture Bryopsis green algae life history sex ratio.

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Studies on modified power law inflation

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Chinese Physics C 2023年第3期47卷 273-281页

作者： Prasenjit paul Rikpratik Sengupta Saibal Ray Department of Physics Government College of Engineering and Ceramic TechnologyKolkataWest Bengal 700010India Department of Physics Aliah UniversityAction Area IlNewtownKolkataWest Bengal 700156India Centre of Cosmology Astrophysics and Space Science(CCASS)GLA UniversityMathuraUttar Pradesh 281406India

In this study,we evaluate power law inflation(PLI)with a monomial potential and obtain a novel exact *** is well known that the conventional PLI with an exponential potential is inconsistent with the Planck *** the standard PLI,the present model does not encounter the graceful exit problem,and the results agree fairly well with recent *** our analysis,we calculate the spectral index and the tensor-to-scalar ratio,both of which agree very well with recent observational data and are comparable with those of other modified inflationary *** employed technique reveals that the large cosmological constant decreases with the expansion of the universe in the case of the *** coupling of the inflaton with gravitation is the primary factor in this *** basic assumption here is that the two metric tensors in the gravitational and inflaton parts correspond to different conformal frames,which contradicts with the conventional PLI,where the inflaton is directly coupled with the background metric *** fact has direct applications to different dark energy models and the assisted quintessence theory.

关键词： power law inflation conformal coupling inflaton cosmological constant

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FERONIA Is a Key Modulator of Brassinosteroid and Ethylene Responsiveness in Arabidopsis Hypocotyls

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Molecular Plant 2010年第3期3卷 626-640页

作者： Stephen D. Deslauriers paul B. Larsen Department of Biochemistry University of California-Riverside Riverside CA 92521 USA

Ethylene signaling is a complex pathway that has been intensively analyzed partly due to its importance to the manifestation of horticultural phenomena, including fruit ripening and tissue senescence. In order to further our un- derstanding of how this pathway is regulated, a screen for Arabidopsis mutants with increased ethylene response was conducted. From this, a mutant was identified as having a dark-grown hypocotyl that is indistinguishable from Col-0 wt in the presence of the ethylene perception inhibitor AgNO3, yet has extreme responsiveness to even low levels of ethylene. Map-based cloning of the mutation revealed a T-DNA insertion in the coding sequence of the receptor-like kinase FERONIA, which is required for normal pollen tube reception and cell elongation in a currently unknown capacity. In contrast to a previous report, analysis of our feronia knockout mutant shows it also has altered responsiveness to brassinosteroids, with etiolated fer-2 seedlings being partially brassinosteroid insensitive with regard to promotion of hypocotyl elonga- tion. Our results indicate that FERONIA-dependent brassinosteroid response serves to antagonize the effect of ethylene on hypocotyl growth of etiolated seedlings, with loss of proper brassinosteroid signaling disrupting this balance and leading to a greater impact of ethylene on hypocotyl shortening.

关键词： FERONIA ethylene brassinosteroid triple response hypocotyl Arabidopsis.

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Simulating Human Visual Perception in Nighttime Illumination

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Tsinghua Science and Technology 2009年第1期14卷 133-138页

作者：周宁董未名王家廞 paul Jean-Claude Department of Computer Science and Technology Tsinghua University INRIA Lorraine

This paper presents an image-based algorithm for simulating the visual adaptation of the human visual system to various illuminations, especially in dark nighttime conditions. The human visual system exhibits different characteristics depending on the illumination intensity, with photopic vision in bright conditions, scotopic vision in dark conditions, and mesopic vision between these two. A computational model is designed to simulate multiple features of mesopic vision and scotopic vision, including the chromaticity change, luminance change, and visual acuity loss. The system uses a source image under bright illumination as input. Then assuming that the viewer has already adapted to the new conditions, the color spectrum of the input image is reconstructed to replace the source with modifications of the chromaticity and the luminance of the relighted scene. A bilateral filter is used to simulate the visual acuity loss. The model parameters have clear physical meanings and can be obtained from experimental data to achieve realistic *** algorithm can be used not only for visual perception simulation, but also as a day-for-night tool to produce realistic nighttime images from daytime images.

关键词： Image enhancement

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Adverse events with bismuth salts for Helicobacter pylori eradication:Systematic review and meta-analysis

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World Journal of Gastroenterology 2008年第48期14卷 7361-7370页

作者： Alexander C Ford Peter Malfertheiner Monique Giguère José Santana Mostafizur Khan paul Moayyedi Gastroenterology Division McMaster University Health Sciences Centre Klinic fur Gastroenterologie Hepatologie and Infektiologie Otto-v.-Guerike Universitat Magdeburg Germany AxCan Pharma Inc.

AIM： To assess the safety of bismuth used in Helicobacter pylori （H pylorl） eradication therapy regimens. METHODS： We conducted a systematic review and meta-analysis. MEDLINE and EMBASE were searched （up to October 2007） to identify randomised controlled tri- als comparing bismuth with placebo or no treatment, or bismuth salts in combination with antibiotics as part of eradication therapy with the same dose and duration of antibiotics alone or, in combination, with acid suppresion. Total numbers of adverse events were recorded. Data were pooled and expressed as relative risks with 95% confidence intervals （CI）.RESULTS： We identified 35 randomised controlled trials containing 4763 patients. There were no serious adverse events occurring with bismuth therapy. There was no statistically significant difference detected in total adverse events with bismuth rrelative risk （RR） = 1.01; 95% CI： 0.87-1.16], specific individual adverse events, with the exception of dark stools （RR = 5.06; 95% CI： 1.59-16.12）, or adverse events leading to withdrawal of therapy （RR = 0.86; 95% CI： 0.54-1.37）. CONCLUSION： Bismuth for the treatment of H py/ori is safe and well-tolerated. The only adverse event occurring significantly more commonly was dark stools.

关键词： Bismuth Eradication therapy Helicobacterpylori Adverse events Systematic review Meta-analysis

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Overview of purple blotch disease and understanding its management through chemical, biological and genetic approaches

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Journal of Integrative Agriculture 2020年第12期19卷 3013-3024页

作者： Aejaz Ahmad DAR Susheel SHARMA Reetika MAHAJAN Muntazir MUSHTAQ Ankila SALATHIA Shahid AHAMAD Jag paul SHARMA School of Biotechnology Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu(SKUAST-J)Jammu 180009India Department of Research Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu(SKUAST-J)Jammu 180009India

Purple blotch disease of Allium spp. crops caused by Alternaria porri has remained a major concern in agriculture for both farmers and research fraternity as it severely damages the crops and drastically reduces the yield. The symptoms appear after 1–4 days of infection and bulb rot begin, and eventually turn into dark reddish-purple and then brownish/black lesions. Many factors like season, time of sowing, humidity and temperature, stage of crop, and plant architecture have a huge impact on the progression of purple blotch disease. Many genic markers based on amplification of an Alta1 gene sequence have been designed for identification and differentiation of different Alternaria species groups. Among the most commonly used fungicides, mancozeb, tebuconazole, difenaconazole and azoxystrobin were found to be the ideal for the management of purple blotch disease and increased garlic yield. Many biological approaches such as plant extracts and bio-control agents were found partially effective for controlling the disease. A report on QTL mapping for purple blotch resistance discovered that purple blotch resistance is controlled by a single dominant gene ApR1. To completely understand the purple blotch disease resistance for crop improvement, a study is required at transcriptome level for hunting purple blotch resistant genes by gene annotation and mining. Genetic engineering and genome editing are other approaches that can be done for engineering disease resistance in Allium crops for genetic improvement.

关键词： purple blotch Alternaria porri breeding QTL mapping genome editing genetic engineering transcriptome analysis

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Updated Inventory of Carbon Monoxide in the Taurus Molecular Cloud

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Research in Astronomy and Astrophysics 2023年第9期23卷 56-65页

作者： Yan Duan Di Li Laurent Pagani paul F.Goldsmith Tao-Chung Ching Chen Wang Jinjin Xie National Astronomical Observatories Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Research Center for Intelligent Computing Platforms Zhejiang LaboratoryHangzhou 311100China NAOC-UKZN Computational Astrophysics Centre University of KwaZulu-NatalDurban4000South Africa LERMA&UMR 8112 du CNRS Observatoire de ParisPSL UniversitySorbonne UniversitésCNRSF-75014 ParisFrance Jet Propulsion Laboratory California Institute of Technology4800 Oak Grove DrivePasadenaCA91109USA Jansky Fellow National Radio Astronomy Observatory1003 Lopezville RoadSocorroNM 87801USA Shanghai Astronomical Observatory Chinese Academy of Sciences National Astronomical ObservatoriesChinese Academy of SciencesShanghai 200030China

The most extensive survey of carbon monoxide(CO)gas in the Taurus molecular cloud relied on ^(12)CO and ^(13)CO J=1→0 emission only,distinguishing the region where ^(12)CO is detected without ^(13)CO(named mask 1 region)from the one where both are detected(mask 2 region)(Goldsmith et al.2008;Pineda et al.2010).We have taken advantage of recent ^(12)CO J=3→2 James Clerk Maxwell Telescope observations,where they include mask 1regions to estimate density,temperature,and N(CO)with a large velocity gradient *** represents 1395 pixels out of~1.2 million in the mark 1 *** to Pineda et al.(2010)results and assuming a Tkin of 30 K,we find a higher volume density of molecular hydrogen of 3.3×10^(3) cm^(-3),compared to their 250-700 cm^(-3),and a CO column density of 5.7×10^(15)cm^(-2),about a quarter of their *** differences are important and show the necessity to observe several CO transitions to better describe the intermediate region between the dense cloud and the diffuse atomic *** observations to extend the ^(12)CO J=3→2 mapping further away from the ^(13)COdetected region comprising mask 1 are needed to revisit our understanding of the diffuse portions of dark clouds.

关键词： submillimeter ISM-ISM clouds-ISM molecules

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The Nonvelocity Cosmological Spectral Shift

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International Journal of Astronomy and Astrophysics 2021年第2期11卷 232-251页

作者： paul A. LaViolette The Starburst Foundation Niskayuna NY USA

Beginning from the premise that the universe is static, and that the cosmological redshift is due to a nonconservative tired light effect, the following examines evidence supporting the prediction that photons will progressively blueshift when transiting through the gravity wells of galaxies, galaxy clusters, and superclusters. The presence of such a nonvelocity blueshift effect is seen to make a substantial contribution to Virgo cluster galaxy spectra, sufficient to dramatically decrease the cluster’s velocity dispersion and assessed virial mass and eliminate the need to assume the presence of large quantities of dark matter. The effect is also shown to account for the Fingers-of-God effect and Kaiser pancaking effect seen when the spectra of cluster galaxies are plotted in redshift space. The opposite effect, excessive redshifting of photons passing through cosmic voids is able to explain void elongation in redshift space, and also the subnormal luminosity of void galaxies. The proposed cosmological blueshifting phenomenon also explains the downturn of the slope of the Hubble Flow in the vicinity of the Local Group which projects a negative apparent velocity for photons propagating near the Milky Way. It also offers an explanation for the blueshift of the Andromeda galaxy spectra and for Arp’s findings that the spectra of primary galaxies in a cluster tend to be blueshifted relative to their companion galaxies. These photon energy phenomena are anticipated by the physics of subquantum kinetics which predicts that photons traversing long distances through intergalactic space should undergo nonconservative tired-light redshifting, and that photons passing through gravity potential wells should undergo progressive blueshifting. The latter effect may be visualized as a negative nonvelocity Hubble constant.

关键词： Fingers-of-God Effect Kaiser Effect Virgo Cluster dark Matter Cosmic Voids Hubble Flow Local Group Hubble Constant Nonvelocity Spectral Shifts Cosmological Redshift Subquantum Kinetics

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Why the Expansion of the Universe Appears to Accelerate

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Journal of Modern Physics 2013年第6期4卷 780-783页

作者： paul Smeulders 3 The Nursery Sutton Courtenay OX14 4UA UK

A Speed of Light falling over time inversely proportional to the expansion of the Universe leads to an experimentally observed exponential changing of the Red Shift over time. It is necessary to re-define the Angular Impulse Momentum in order to get a consistent expansion of space on all levels. Conservation of Energy and this newly defined Angular Impulse Momentum then leads to the requirement that all clocks slow down in time inversely proportional to the Red Shift, independent of whether the Speed of Light is constant or not. From the Lorentz equation it then follows that Expansion occurs over space-time and not over space alone. A steady state expansion in true time is then transformed into an exponential expansion for an observer with a local clock. A finite lifetime of the Universe is transformed to an infinite lifetime for these observers including elementary particles.

关键词： Acceleration of Expansion Expansion of Space-Time Exponential Expansion Conservation Laws dark Energy

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