Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

Background Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples. Methods To examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy profiling on multiple spatially separated samples obtained from primary renal carcinomas and associated metastatic sites. We characterized the consequences of intratumor heterogeneity using immunohistochemical analysis, mutation functional analysis, and profiling of messenger RNA expression. Results Phylogenetic reconstruction revealed branched evolutionary tumor growth, with 63 to 69% of all somatic mutations not detectable across every tumor region. Intratumor heterogeneity was observed for a mutation within an autoinhibitory domain of the mammalian target of rapamycin (mTOR) kinase, correlating with S6 and 4EBP phosphorylation in vivo and constitutive activation of mTOR kinase activity in vitro. Mutational intratumor heterogeneity was seen for multiple tumor-suppressor genes converging on loss of function; SETD2, PTEN, and KDM5C underwent multiple distinct and spatially separated inactivating mutations within a single tumor, suggesting convergent phenotypic evolution. Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor. Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples from four tumors harboring divergent allelic-imbalance profiles and with ploidy heterogeneity in two of four tumors. Conclusions Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development. Intratumor heterogeneity, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through Darwinian selection. (Funded by the Medical Research Council and others.)

http://www.therenegadecell.com/wiki/images/0/0d/NEJM-2012-366%2810%29-883.pdf

Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.

Prospective Cohort Study

Summary Background Since December, 2019, Wuhan, China, has experienced an outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Epidemiological and clinical characteristics of patients with COVID-19 have been reported but risk factors for mortality and a detailed clinical course of illness, including viral shedding, have not been well described. Methods In this retrospective, multicentre cohort study, we included all adult inpatients (≥18 years old) with laboratory-confirmed COVID-19 from Jinyintan Hospital and Wuhan Pulmonary Hospital (Wuhan, China) who had been discharged or had died by Jan 31, 2020. Demographic, clinical, treatment, and laboratory data, including serial samples for viral RNA detection, were extracted from electronic medical records and compared between survivors and non-survivors. We used univariable and multivariable logistic regression methods to explore the risk factors associated with in-hospital death. Findings 191 patients (135 from Jinyintan Hospital and 56 from Wuhan Pulmonary Hospital) were included in this study, of whom 137 were discharged and 54 died in hospital. 91 (48%) patients had a comorbidity, with hypertension being the most common (58 [30%] patients), followed by diabetes (36 [19%] patients) and coronary heart disease (15 [8%] patients). Multivariable regression showed increasing odds of in-hospital death associated with older age (odds ratio 1·10, 95% CI 1·03–1·17, per year increase; p=0·0043), higher Sequential Organ Failure Assessment (SOFA) score (5·65, 2·61–12·23; p Interpretation The potential risk factors of older age, high SOFA score, and d-dimer greater than 1 μg/mL could help clinicians to identify patients with poor prognosis at an early stage. Prolonged viral shedding provides the rationale for a strategy of isolation of infected patients and optimal antiviral interventions in the future. Funding Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences; National Science Grant for Distinguished Young Scholars; National Key Research and Development Program of China; The Beijing Science and Technology Project; and Major Projects of National Science and Technology on New Drug Creation and Development.

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study

In this book, Andrew Harvey sets out to provide a unified and comprehensive theory of structural time series models. Unlike the traditional ARIMA models, structural time series models consist explicitly of unobserved components, such as trends and seasonals, which have a direct interpretation. As a result the model selection methodology associated with structural models is much closer to econometric methodology. The link with econometrics is made even closer by the natural way in which the models can be extended to include explanatory variables and to cope with multivariate time series. From the technical point of view, state space models and the Kalman filter play a key role in the statistical treatment of structural time series models. The book includes a detailed treatment of the Kalman filter. This technique was originally developed in control engineering, but is becoming increasingly important in fields such as economics and operations research. This book is concerned primarily with modelling economic and social time series, and with addressing the special problems which the treatment of such series poses. The properties of the models and the methodological techniques used to select them are illustrated with various applications. These range from the modellling of trends and cycles in US macroeconomic time series to to an evaluation of the effects of seat belt legislation in the UK.

Forecasting, Structural Time Series Models and the Kalman Filter

By adopting the consumption-based accounting (CBA) method of carbon emissions based on national carbon intensity (NCI), using the International Trade Centre (ITC) database, the Emissions Database for Global Atmospheric Research (EDGAR), and the World Bank database, and taking 13 countries and regions including the European Union (EU) countries and the United States (US) as research samples, this paper conducts an accounting of the embodied carbon in trade between China and other major economies in the world, clarifies the responsibilities China has taken for foreign consumption-based carbon emissions, and analyzes the various driving factors of China’s embodied carbon in exports. The findings are as follows: (i) Most of the developed economies have higher consumption-based emissions than production-based emissions, which is contrary to most of the developing economies, with developing countries bearing responsibilities for 15–20% of the consumption-based carbon emissions for developed countries; (ii) the carbon emissions of countries and regions are closely related to the embodied carbon in trade, with a correlation coefficient of 0.96. (iii) China has taken responsibility for a large amount of carbon emissions from foreign consumer demand, most of which are from the US, the EU, ASEAN, and Japan, respectively accounting for 3.8%, 3.5%, 2.3%, and 1.2% of China’s production-based carbon emissions in 2019; (iv) technique effect is the main driving factor for China’s embodied carbon in trade, while the specific driving factors vary by industry. Based on the above analysis, it is suggested that China should: (i) consider the trade factor in its efforts to achieve carbon peaking and carbon neutrality; (ii) adopt differentiated measures to reduce trade-related emissions for specific industries; (iii) fully consider China’s demand for carbon peaking and carbon neutrality in international negotiations; (iv) give more support to the research on and measurement of consumption-based carbon emissions.

An Analysis of the Responsibilities and Driving Factors for Embodied Carbon in Trade


 Honoring the Gift of Heart Health
 (HGHH) is a cardiovascular health education curriculum culturally tailored for American Indians (AI). It emphasizes adoption of cardiovascular health recommendations through lifestyle changes. The NHLBI has not revised HGHH components since 2006. Effectiveness of the HGHH may change overtime and updates may be required to influence community health behaviors. Therefore, we aimed to determine the cultural values and practices necessary for inspiring heart healthy behaviors and to make recommendations on including these values and practices in the curriculum. We used a qualitative research design and a narrative inquiry approach. Using snowball sampling, we recruited 11 AI community stakeholders in Oklahoma who participate in the Strong Heart Study. We conducted 3 focus groups with a semi-structured interview guide. We transcribed recordings and conducted a thematic content analysis (Figure 1). Participants viewed written materials as informative but the media as outdated, especially for younger generations, and suggested content ought to be dispersed through various social media. They theorized in-person activities would further educate and motivate community members to be heart healthy, thus adoption of HGHH recommendations more effective. Participants shared concerns about implementing HGHH dietary suggestions while attempting to control food costs, having time constraints, and perceiving food discussed in the program as not representative of what their communities eat. In conclusion, AI community stakeholders advise HGHH updates need to be applicable with current technology, focused on younger generations, coupled with in-person activities, and socio-economically and culturally sensitive to have the most effect. Collecting and evaluating community feedback can guide the development of appropriate updates to the HGHH curriculum.
 
 
 
 
 
 Figure 1
 . Theme words identified in focus groups in colored boxes and their related code words in grey boxes.


Abstract P646: American Indian Community Stakeholders Evaluate the Cardiovascular Health Curriculum Honoring the Gift of Heart Health: The Strong Heart Study

Developmental dynamics of the single nucleus regulatory landscape of pig hippocampus.

Abnormal weather, such as sudden cooling and rainfall, has various impacts on the environment and plants. Shrub, as the main component of green vegetation community in urban ecosystem, its response to abnormal weather affects the stability of green space community in urban ecosystem to a certain extent. Therefore, two typical shrubs (Euonymus japonicus Thunb. var., aurea-marginatus Hort., and Photinia serrulata) were selected to systematically study the variation characteristics of the physiological indicators (soluble protein, chlorophyll, malondialdehyde) under abnormal weather, which were widely distributed in urban green space landscape construction as the research objects . The results showed that the total chlorophyll content and chlorophyll a/b value of the two shrubs decreased significantly under abnormal weather, and the effect of cooling on the chlorophyll a in two shrubs was more obvious. The change characteristics of soluble protein content after abnormal weather had a relatively consistent regularity with temperature, but it had a hysteresis compared with the change of temperature. However, the response of malondialdehyde to abnormal weather is not obvious.

Bing Zhang

Papers

An Analysis of the Responsibilities and Driving Factors for Embodied Carbon in Trade

Abstract P646: American Indian Community Stakeholders Evaluate the Cardiovascular Health Curriculum Honoring the Gift of Heart Health: The Strong Heart Study

Developmental dynamics of the single nucleus regulatory landscape of pig hippocampus.

Response characteristics of two typical shrubs in urban green space landscape to abnormal weather

Metal mixtures and DNA methylation measures of biological aging in American Indian populations.