89 results on '"Andrew Zimmer"'
Search Results
2. Feasibility and lessons learned on remote trial implementation from TestBoston, a fully remote, longitudinal, large-scale COVID-19 surveillance study
- Author
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Sarah Naz-McLean, Andy Kim, Andrew Zimmer, Hannah Laibinis, Jen Lapan, Paul Tyman, Jessica Hung, Christina Kelly, Himaja Nagireddy, Surya Narayanan-Pandit, Margaret McCarthy, Saee Ratnaparkhi, Henry Rutherford, Rajesh Patel, Scott Dryden-Peterson, Deborah T. Hung, Ann E. Woolley, and Lisa A. Cosimi
- Subjects
Medicine ,Science - Abstract
Longitudinal clinical studies traditionally require in-person study visits which are well documented to pose barriers to participation and contribute challenges to enrolling representative samples. Remote trial models may reduce barriers to research engagement, improve retention, and reach a more representative cohort. As remote trials become more common following the COVID-19 pandemic, a critical evaluation of this approach is imperative to optimize this paradigm shift in research. The TestBoston study was launched to understand prevalence and risk factors for COVID-19 infection in the greater Boston area through a fully remote home-testing model. Participants (adults, within 45 miles of Boston, MA) were recruited remotely from patient registries at Brigham and Women’s Hospital and the general public. Participants were provided with monthly and “on-demand” at-home SARS-CoV-2 RT-PCR and antibody testing using nasal swab and dried blood spot self-collection kits and electronic surveys to assess symptoms and risk factors for COVID-19 via an online dashboard. Between October 2020 and January 2021, we enrolled 10,289 participants reflective of Massachusetts census data. Mean age was 47 years (range 18–93), 5855 (56.9%) were assigned female sex at birth, 7181(69.8%) reported being White non-Hispanic, 952 (9.3%) Hispanic/Latinx, 925 (9.0%) Black, 889 (8.6%) Asian, and 342 (3.3%) other and/or more than one race. Lower initial enrollment among Black and Hispanic/Latinx individuals required an adaptive approach to recruitment, leveraging connections to the medical system, coupled with community partnerships to ensure a representative cohort. Longitudinal retention was higher among participants who were White non-Hispanic, older, working remotely, and with lower socioeconomic vulnerability. Implementation highlighted key differences in remote trial models as participants independently navigate study milestones, requiring a dedicated participant support team and robust technology platforms, to reduce barriers to enrollment, promote retention, and ensure scientific rigor and data quality. Remote clinical trial models offer tremendous potential to engage representative cohorts, scale biomedical research, and promote accessibility by reducing barriers common in traditional trial design. Barriers and burdens within remote trials may be experienced disproportionately across demographic groups. To maximize engagement and retention, researchers should prioritize intensive participant support, investment in technologic infrastructure and an adaptive approach to maximize engagement and retention.
- Published
- 2022
3. Farmer forecasts: Impacts of seasonal rainfall expectations on agricultural decision-making in Sub-Saharan Africa
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Zack Guido, Andrew Zimmer, Sara Lopus, Corrie Hannah, Drew Gower, Kurt Waldman, Natasha Krell, Justin Sheffield, Kelly Caylor, and Tom Evans
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Climate information services ,Seasonal climate forecasts ,Climate perceptions ,Agricultural decision-making ,Smallholder ,Maize ,Meteorology. Climatology ,QC851-999 - Abstract
Seasonal climate variability frequently undermines farm yields, reduces food availability, and lowers income. This is particularly evident among small-scale agricultural producers in both irrigated and non-irrigated agroecosystems in the Global South where maize cultivars constitute a critical component of food production. In these systems, farmers make climate-sensitive decisions that include the selection of late- and/or early-maturing seed varieties, the diversity of seed varieties sown, and when to plant. Farmers’ expectations of future rainfall would therefore seem to be critical determinants of agricultural outcomes and foreshadow climate impacts. However, few studies have quantified the linkages between on-farm decisions and farmer seasonal predictions. We report on detailed household and phone surveys of 501 smallholder farmers in central Kenya based on the 2018 growing seasons and expectations for the 2019 March-April-May growing season. We show that farmers’ expectations of the upcoming seasonal rainfall have important associations with selections of seed maturity varieties and the number of maturing varieties farmers expect to plant and less important associations with the seeds’ planting dates. Furthermore, we show that 79% of the farmers form an expectation of the future seasonal climate and about two-thirds of them formed expectations based on a heuristic that connects the past climate to future seasonal conditions. More problematically, one-third of the farmers formed their rainfall expectation based on the prior season, and we show that no such correlation exists in observational data nor is correlation of seasonal rainfall supported by current understanding of climate variability. These results highlight the challenges farmers face in anticipating seasonal rainfall, which has implications for crop diversification and choices to adopt drought tolerant cultivars. The results suggest that farmers’ expectations of upcoming seasonal climate are important measures of farm decision-making.
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- 2020
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4. An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.
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Marc P Hoeppner, Andrew Lundquist, Mono Pirun, Jennifer R S Meadows, Neda Zamani, Jeremy Johnson, Görel Sundström, April Cook, Michael G FitzGerald, Ross Swofford, Evan Mauceli, Behrooz Torabi Moghadam, Anna Greka, Jessica Alföldi, Amr Abouelleil, Lynne Aftuck, Daniel Bessette, Aaron Berlin, Adam Brown, Gary Gearin, Annie Lui, J Pendexter Macdonald, Margaret Priest, Terrance Shea, Jason Turner-Maier, Andrew Zimmer, Eric S Lander, Federica di Palma, Kerstin Lindblad-Toh, and Manfred G Grabherr
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Medicine ,Science - Abstract
The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now covers 99.8% of the euchromatic portion of the genome. We also present multiple RNA-Sequencing data sets from 10 different canine tissues to catalog ∼175,000 expressed loci. While about 90% of the coding genes previously annotated by EnsEMBL have measurable expression in at least one sample, the number of transcript isoforms detected by our data expands the EnsEMBL annotations by a factor of four. Syntenic comparison with the human genome revealed an additional ∼3,000 loci that are characterized as protein coding in human and were also expressed in the dog, suggesting that those were previously not annotated in the EnsEMBL canine gene set. In addition to ∼20,700 high-confidence protein coding loci, we found ∼4,600 antisense transcripts overlapping exons of protein coding genes, ∼7,200 intergenic multi-exon transcripts without coding potential, likely candidates for long intergenic non-coding RNAs (lincRNAs) and ∼11,000 transcripts were reported by two different library construction methods but did not fit any of the above categories. Of the lincRNAs, about 6,000 have no annotated orthologs in human or mouse. Functional analysis of two novel transcripts with shRNA in a mouse kidney cell line altered cell morphology and motility. All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts.
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- 2014
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5. Creatine monohydrate and conjugated linoleic acid improve strength and body composition following resistance exercise in older adults.
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Mark Tarnopolsky, Andrew Zimmer, Jeremy Paikin, Adeel Safdar, Alissa Aboud, Erin Pearce, Brian Roy, and Timothy Doherty
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Medicine ,Science - Abstract
Aging is associated with lower muscle mass and an increase in body fat. We examined whether creatine monohydrate (CrM) and conjugated linoleic acid (CLA) could enhance strength gains and improve body composition (i.e., increase fat-free mass (FFM); decrease body fat) following resistance exercise training in older adults (>65 y). Men (N = 19) and women (N = 20) completed six months of resistance exercise training with CrM (5g/d)+CLA (6g/d) or placebo with randomized, double blind, allocation. Outcomes included: strength and muscular endurance, functional tasks, body composition (DEXA scan), blood tests (lipids, liver function, CK, glucose, systemic inflammation markers (IL-6, C-reactive protein)), urinary markers of compliance (creatine/creatinine), oxidative stress (8-OH-2dG, 8-isoP) and bone resorption (Nu-telopeptides). Exercise training improved all measurements of functional capacity (P
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- 2007
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6. A mediation analysis of the linkages between climate variability, water insecurity, and interpersonal violence
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Amanda Ross, Elizabeth A. Mack, Richard Marcantonio, Laura Miller-Graff, Amber L. Pearson, Audrey Culver Smith, Erin Bunting, and Andrew Zimmer
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Global and Planetary Change ,Geography, Planning and Development ,Development - Published
- 2023
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7. Kobayashi hyperbolic convex domains not biholomorphic to bounded convex domains
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Andrew Zimmer
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Pure mathematics ,Mathematics::Complex Variables ,General Mathematics ,Bounded function ,Regular polygon ,Mathematics::Geometric Topology ,Mathematics::Symplectic Geometry ,Kobayashi metric ,Mathematics - Abstract
We construct families of convex domains that are biholomorphic to bounded domains, but not bounded convex domains. This is accomplished by finding an obstruction related to the Gromov hyperbolicity of the Kobayashi metric.
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- 2021
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8. A lower bound for the Kähler-Einstein distance from the Diederich-Fornæss index
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Andrew Zimmer
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symbols.namesake ,Index (economics) ,Mathematics::Complex Variables ,Applied Mathematics ,General Mathematics ,symbols ,Mathematics::Differential Geometry ,Einstein ,Upper and lower bounds ,Mathematical physics ,Mathematics - Abstract
In this paper we establish a lower bound for the distance induced by the Kähler-Einstein metric on pseudoconvex domains with positive hyperconvexity index (e.g. positive Diederich-Fornæss index). A key step is proving an analog of the Hopf lemma for Riemannian manifolds with Ricci curvature bounded from below.
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- 2021
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9. The automorphism group and limit set of a bounded domain II: the convex case
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Andrew Zimmer
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Mathematics - Differential Geometry ,Unit sphere ,Pure mathematics ,Mathematics - Complex Variables ,General Mathematics ,Simple Lie group ,010102 general mathematics ,Boundary (topology) ,Center (group theory) ,01 natural sciences ,Domain (mathematical analysis) ,Differential Geometry (math.DG) ,Compact group ,Bounded function ,0103 physical sciences ,FOS: Mathematics ,010307 mathematical physics ,Complex Variables (math.CV) ,0101 mathematics ,Limit set ,Mathematics - Abstract
For convex domains with $C^{1,\epsilon}$ boundary we give a precise description of the automorphism group: if an orbit of the automorphism group accumulates on at least two different closed complex faces of the boundary, then the automorphism group has finitely many components and the connected component of the identity is the almost direct product of a compact group and a non-compact connected simple Lie group with real rank one and finite center. In this case, we also show the limit set is homeomorphic to a sphere and prove a gap theorem: either the domain is biholomorphic to the unit ball (and the limit set is the entire boundary) or the limit set has co-dimension at least two in the boundary., Comment: 40 pages. v2: minor corrections
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- 2021
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10. A flat torus theorem for convex co‐compact actions of projective linear groups
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Mitul Islam and Andrew Zimmer
- Subjects
Mathematics - Differential Geometry ,Pure mathematics ,General Mathematics ,010102 general mathematics ,05 social sciences ,Regular polygon ,Geometric Topology (math.GT) ,01 natural sciences ,Mathematics - Geometric Topology ,Differential Geometry (math.DG) ,0502 economics and business ,FOS: Mathematics ,0101 mathematics ,Convex domain ,Projective test ,Flat torus ,050203 business & management ,Real projective space ,53A20, 57N16, 58B20, 20F67, 20H10 ,Mathematics - Abstract
In this paper, we consider discrete groups in ${\rm PGL}_d(\mathbb{R})$ acting convex co-compactly on a properly convex domain in real projective space. For such groups, we establish an analogue of the well known flat torus theorem for ${\rm CAT}(0)$ spaces., Minor revisions, to appear in the Journal of the London Mathematical Society. 20 pages. Comments welcome
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- 2020
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11. Dynamics of population growth in secondary cities across southern Africa
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Sara Lopus, Andrew Zimmer, Kelly K. Caylor, Cascade Tuholske, Alex Pakalniskis, Tom Evans, and Zack Guido
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0106 biological sciences ,Sustainable development ,education.field_of_study ,Ecology ,Descriptive statistics ,Land use ,010604 marine biology & hydrobiology ,Geography, Planning and Development ,Population ,Context (language use) ,010603 evolutionary biology ,01 natural sciences ,Geography ,Urbanization ,Population growth ,Landscape ecology ,Socioeconomics ,education ,Nature and Landscape Conservation - Abstract
Two-fifths of Africans reside in urban areas with populations of less than 250,000. Projections estimate that by 2050 an additional one billion people will live in urban areas, causing an acceleration of growth for these smaller urban areas. While research and development have focused on primary cities with large populations, less is known about the dynamics of urban growth in smaller, “secondary” urban areas (SUA’s). We document the spatial distribution and temporal patterns of SUA’s in eight countries across Southern Africa between 1975 and 2015. We further explore the relationships between SUA’s growth rates and climate, land use and geographic proximity to other urban areas. Our analysis integrates spatially explicit gridded population, land use, infrastructure and climate datasets. We use descriptive statistics and spatial lag and ordinary least squares regression models to quantify SUA growth rates across three periods and explore factors that are associated with the SUA growth patterns. Average SUA growth rates are 2.44% between 1975 and 1990. We show that the climate, distance and land use significantly relate to urbanization trajectories. In addition, we find that the proximity of SUA to the largest cities also significantly relates to urban growth. Our results highlight the importance of SUA’s within broader African urbanization trends. SUA are undergoing rapid population changes and are important components of economic development processes and livelihoods. Quantifying patterns of SUA urbanization is important for elevating these small but critically important urban areas into the broader context of sustainable urbanization in Africa.
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- 2020
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12. Feasibility and lessons learned on remote trial implementation from TestBoston, a fully remote, longitudinal, large-scale COVID-19 surveillance study
- Author
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Sarah Naz-McLean, Andy Kim, Andrew Zimmer, Hannah Laibinis, Jen Lapan, Paul Tyman, Jessica Hung, Christina Kelly, Himaja Nagireddy, Surya Narayanan-Pandit, Margaret McCarthy, Saee Ratnaparkhi, Henry Rutherford, Rajesh Patel, Scott Dryden-Peterson, Deborah T. Hung, Ann E. Woolley, and Lisa A. Cosimi
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Adult ,Aged, 80 and over ,Male ,Clinical Trials as Topic ,Multidisciplinary ,Adolescent ,SARS-CoV-2 ,COVID-19 ,Middle Aged ,Cohort Studies ,Young Adult ,Feasibility Studies ,Humans ,Female ,Pandemics ,Aged - Abstract
Longitudinal clinical studies traditionally require in-person study visits which are well documented to pose barriers to participation and contribute challenges to enrolling representative samples. Remote trial models may reduce barriers to research engagement, improve retention, and reach a more representative cohort. As remote trials become more common following the COVID-19 pandemic, a critical evaluation of this approach is imperative to optimize this paradigm shift in research. The TestBoston study was launched to understand prevalence and risk factors for COVID-19 infection in the greater Boston area through a fully remote home-testing model. Participants (adults, within 45 miles of Boston, MA) were recruited remotely from patient registries at Brigham and Women’s Hospital and the general public. Participants were provided with monthly and “on-demand” at-home SARS-CoV-2 RT-PCR and antibody testing using nasal swab and dried blood spot self-collection kits and electronic surveys to assess symptoms and risk factors for COVID-19 via an online dashboard. Between October 2020 and January 2021, we enrolled 10,289 participants reflective of Massachusetts census data. Mean age was 47 years (range 18–93), 5855 (56.9%) were assigned female sex at birth, 7181(69.8%) reported being White non-Hispanic, 952 (9.3%) Hispanic/Latinx, 925 (9.0%) Black, 889 (8.6%) Asian, and 342 (3.3%) other and/or more than one race. Lower initial enrollment among Black and Hispanic/Latinx individuals required an adaptive approach to recruitment, leveraging connections to the medical system, coupled with community partnerships to ensure a representative cohort. Longitudinal retention was higher among participants who were White non-Hispanic, older, working remotely, and with lower socioeconomic vulnerability. Implementation highlighted key differences in remote trial models as participants independently navigate study milestones, requiring a dedicated participant support team and robust technology platforms, to reduce barriers to enrollment, promote retention, and ensure scientific rigor and data quality. Remote clinical trial models offer tremendous potential to engage representative cohorts, scale biomedical research, and promote accessibility by reducing barriers common in traditional trial design. Barriers and burdens within remote trials may be experienced disproportionately across demographic groups. To maximize engagement and retention, researchers should prioritize intensive participant support, investment in technologic infrastructure and an adaptive approach to maximize engagement and retention.
- Published
- 2021
13. Feasibility and lessons learned on remote trial implementation from TestBoston, a fully remote, longitudinal, large-scale COVID-19 surveillance study
- Author
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Sarah A Naz-McLean, Scott Dryden-Peterson, Henry Rutherford, Deborah T. Hung, Saee Ratnaparkhi, Andrew J. Kim, Rajesh Patel, Ann E. Woolley, Lisa A. Cosimi, Jessica Hung, Himaja Nagireddy, Jen Lapan, Christina Kelly, Surya Narayanan-Pandit, Paul Tyman, Hannah Laibinis, Margaret McCarthy, and Andrew Zimmer
- Subjects
Gerontology ,Clinical trial ,Longitudinal study ,Data quality ,Scale (social sciences) ,Cohort ,Vulnerability ,Psychology ,Socioeconomic status ,Rigour - Abstract
ImportanceRemote clinical trials may reduce barriers to research engagement resulting in more representative samples. A critical evaluation of this approach is imperative to optimize this paradigm shift in research.ObjectiveTo assess design and implementation factors required to maximize enrollment and retention in a fully remote, longitudinal COVID-19 testing study.DesignFully remote longitudinal study launched in October 2020 and ongoing; Study data reported through July 2021.SettingBrigham and Women’s Hospital, Boston MAParticipantsAdults, 18 years or older, within 45 miles of Boston, MA.InterventionMonthly and “on-demand” at-home SARS-CoV-2 RT-PCR and antibody testing using nasal swab and dried blood spot self-collection kits and electronic surveys to assess symptoms and risk factors for COVID-19.Main OutcomesEnrollment, retention, and lessons learned.ResultsBetween October 2020 and January 2021, we enrolled 10,289 participants reflective of Massachusetts census data. Mean age was 47 years (range 18-93), 5855 (56.9%) were assigned female sex at birth, 7181(69.8%) reported being White non-Hispanic, 952 (9.3%) Hispanic/Latinx, 925 (9.0%) Black, 889 (8.6%) Asian, and 342 (3.3%) other and/or more than one race. Lower initial enrollment among Black and Hispanic/Latinx individuals required an adaptive approach, leveraging connections to the medical system, coupled with community partnerships to ensure a representative cohort. Longitudinal retention was higher among participants who were White non-Hispanic, older, working remotely, and with lower socioeconomic vulnerability. Considerable infrastructure, including a dedicated participant support team and robust technology platforms was required to reduce barriers to enrollment, promote retention, ensure scientific rigor, improve data quality, and enable an adaptive study design to increase real-world accessibility.ConclusionsThe decentralization of clinical trials through remote models offers tremendous potential to engage representative cohorts, scale biomedical research, and promote accessibility by reducing barriers common in traditional trial design. Our model highlights the critical role that hospital-community partnerships play in remote recruitment, and the work still needed to ensure representative enrollment. Barriers and burdens within remote trials may be experienced disproportionately across demographic groups. To maximize engagement and retention, researchers should prioritize intensive participant support, investment in technologic infrastructure and an adaptive approach to maximize engagement and retention.Trial RegistrationN/AKey PointsQuestionLongitudinal clinical studies typically rely on in-person interactions to support recruitment, retention, and implementation. We define factors that promote demographically representative recruitment and retention through implementation of a fully remote COVID-19 study.FindingsRemote trial models can reduce barriers to research participation and engage representative cohorts. Recruitment was strengthened by leveraging the medical system. Implementation highlighted participant burdens unique to this model, underscoring the need for a significant participant support team, robust technological infrastructure, and an adaptive, iterative approach.MeaningAs remote trials become more common following the COVID-19 pandemic, methodologies to ensure accessibility, representation, and efficiency are crucial.
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- 2021
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14. A Systematic Literature Review of Quantitative Studies Assessing the Relationship between Water and Conflict on the African Continent
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Elizabeth A. Mack, Richard A. Marcantonio, Erin Bunting, Amanda Ross, Andrew Zimmer, Leo C. Zulu, Edna Liliana Gómez Fernández, Jay Herndon, and Geoffrey M. Henebry
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Renewable Energy, Sustainability and the Environment ,Geography, Planning and Development ,Building and Construction ,Management, Monitoring, Policy and Law - Abstract
Since the seminal 2012 Special Issue of the Journal of Peace Research about climate change and conflict, at least 35 review papers on the topic have been published. To our knowledge, none of these reviews focused on water and conflict specifically. In order to address this research gap, the present article conducts a systematic review of scholarship examining the linkages between water and conflict, focusing on quantitative studies using secondary data sources. This review focuses on the African continent given projections about the intersection between water issues and conflict in this region, as well as the popularity of this portion of the world in studies of climate change and conflict. We discuss the findings of papers reviewed and propose six avenues for future research. As research about this topic advances, it will require attention to nuances in data processing, integration, and modeling across spatial and temporal scales, if the outcomes of this body of scholarship are to be leveraged to guide the decision making of governing bodies.
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- 2022
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15. Perceived links between climate change and weather forecast accuracy: new barriers to tools for agricultural decision-making
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Natasha Krell, Lyndon Estes, Sara Lopus, Zack Guido, Chris Knudson, Corrie Hannah, Kelly K. Caylor, Andrew Zimmer, Tom Evans, and Kurt B. Waldman
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Atmospheric Science ,Global and Planetary Change ,Geography ,Agriculture ,business.industry ,Environmental resource management ,Climate change ,Detailed data ,Climate resilience ,business ,Disadvantage - Abstract
The accuracy of weather forecasts has experienced remarkable improvements over the recent decades and is now considered important tools for developing the climate resilience of smallholder farmers, particularly as climate change upends traditional farming calendars. However, the effect of observations of climate change on the use of weather forecasts has not been studied. In an analysis of smallholder farming in Zambia, Kenya, and Jamaica, we document low weather forecast use, showing that perceptions of changes in the climate relate to views on forecast accuracy. Drawing on detailed data from Zambia, we show that weather forecast use (or not) is associated with perceptions of the accuracy (or inaccuracy) of the forecast, with rates of weather forecast use far lower among those who believe climate change impacts forecast accuracy. The results suggest a novel feedback whereby climate change erodes confidence in weather forecasts. Thus, in a changing climate where improvements in weather forecasts have been made, farmers thus experience a double disadvantage whereby climate change disrupts confidence in traditional ways of knowing the weather and lowers trust in supplementary technical forecasting tools.
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- 2021
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16. Governance of traditional markets and rural-urban food systems in sub-Saharan Africa
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Julia Davies, Jordan Blekking, Corrie Hannah, Andrew Zimmer, Nupur Joshi, Patrese Anderson, Allan Chilenga, and Tom Evans
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Urban Studies - Published
- 2022
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17. Interpersonal Conflict over Water Is Associated with Household Demographics, Domains of Water Insecurity, and Regional Conflict: Evidence from Nine Sites across Eight Sub-Saharan African Countries
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Amber L. Pearson, Elizabeth A. Mack, Amanda Ross, Richard Marcantonio, Andrew Zimmer, Erin L. Bunting, Audrey C. Smith, Joshua D. Miller, Tom Evans, and The HWISE Research Coordination Network
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Sub saharan ,010504 meteorology & atmospheric sciences ,Demographics ,Geography, Planning and Development ,rainfall ,0211 other engineering and technologies ,Armed conflict ,Climate change ,02 engineering and technology ,Interpersonal communication ,Aquatic Science ,01 natural sciences ,Biochemistry ,violence ,water insecurity ,Socioeconomics ,TD201-500 ,0105 earth and related environmental sciences ,Water Science and Technology ,021110 strategic, defence & security studies ,Water supply for domestic and industrial purposes ,protests ,Hydraulic engineering ,Geography ,climate change ,Survey data collection ,interpersonal conflict ,TC1-978 - Abstract
Water insecurity may precipitate interpersonal conflict, although no studies to date have rigorously examined these relationships. We examined relationships between household demographics, water insecurity, regional conflict, and interpersonal conflict over water. Using survey data from eight sub-Saharan African countries, we found that interpersonal conflict within and outside the home is associated with multiple domains of water insecurity, particularly accessibility. Furthermore, we found that higher levels of remote violence and protests are associated with greater within household conflict, whereas riots and violent armed conflict are associated with greater conflict between neighbors. Our findings expand upon the current literature by examining factors affecting interpersonal conflict over water, which may become increasingly important as precipitation patterns and land temperatures change in this region.
- Published
- 2021
18. Cusped Hitchin representations and Anosov representations of geometrically finite Fuchsian groups
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Richard Canary, Tengren Zhang, and Andrew Zimmer
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Mathematics - Differential Geometry ,Mathematics::Dynamical Systems ,22E40, 53C23, 53C35, 37D40, 37D20 ,Differential Geometry (math.DG) ,General Mathematics ,FOS: Mathematics ,Dynamical Systems (math.DS) ,Group Theory (math.GR) ,Mathematics - Dynamical Systems ,Mathematics::Geometric Topology ,Mathematics - Group Theory - Abstract
We develop a theory of Anosov representation of geometrically finite Fuchsian groups in SL(d,R) and show that cusped Hitchin representations are Borel Anosov in this sense. We establish analogues of many properties of traditional Anosov representations. In particular, we show that our Anosov representations are stable under type-preserving deformations and that their limit maps vary analytically. We also observe that our Anosov representations fit into the previous frameworks of relatively Anosov and relatively dominated representations developed by Kapovich-Leeb and Zhu., 45 pages, typos corrected, and more details added to Section 8 and Appendix B
- Published
- 2021
19. Homeomorphic extension of quasi-isometries for convex domains in Cd and iteration theory
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Andrew Zimmer, Hervé Gaussier, and Filippo Bracci
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Mathematics - Differential Geometry ,Pure mathematics ,Gromov boundary ,Mathematics - Complex Variables ,Mathematics::Complex Variables ,General Mathematics ,010102 general mathematics ,Regular polygon ,Boundary (topology) ,Extension (predicate logic) ,16. Peace & justice ,01 natural sciences ,Settore MAT/03 ,Differential Geometry (math.DG) ,0103 physical sciences ,FOS: Mathematics ,Mathematics::Metric Geometry ,010307 mathematical physics ,0101 mathematics ,Complex Variables (math.CV) ,Mathematics ,Iteration theory - Abstract
We study the homeomorphic extension of biholomorphisms between convex domains in $\mathbb C^d$ without boundary regularity and boundedness assumptions. Our approach relies on methods from coarse geometry, namely the correspondence between the Gromov boundary and the topological boundaries of the domains and the dynamical properties of commuting 1-Lipschitz maps in Gromov hyperbolic spaces. This approach not only allows us to prove extensions for biholomorphisms, but for more general quasi-isometries between the domains endowed with their Kobayashi distances., Comment: 27 pages; final version, to appear Math. Ann
- Published
- 2021
20. Persistence of open-air markets in the food systems of Africa's secondary cities
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Corrie Hannah, Julia Davies, Rachel Green, Andrew Zimmer, Patrese Anderson, Jane Battersby, Kathy Baylis, Nupur Joshi, and Tom P. Evans
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Urban Studies ,Sociology and Political Science ,Tourism, Leisure and Hospitality Management ,Development - Published
- 2022
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21. Conflict and its relationship to climate variability in Sub-Saharan Africa
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Elizabeth A. Mack, Amanda Ross, Erin Bunting, Richard A. Marcantonio, James Herndon, and Andrew Zimmer
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Environmental Engineering ,Sub saharan ,010504 meteorology & atmospheric sciences ,Logit ,Law enforcement ,Climate change ,Grid cell ,010501 environmental sciences ,01 natural sciences ,Pollution ,Geography ,Dry season ,Environmental Chemistry ,Duration (project management) ,Socioeconomics ,Waste Management and Disposal ,0105 earth and related environmental sciences ,Peacekeeping - Abstract
Deviations in rainfall duration and timing are expected to have wide-ranging impacts for people in affected areas. One of these impacts is the potential for increased levels of conflict and accordingly, researchers are examining the relationship between climate variability and conflict. Thus far, there is a lack of consensus on the direction of this relationship. We contribute to the climate variability and conflict literature by incorporating Markov transitional probabilities into panel logit models to analyze how monthly deviations in rainfall affect the likelihood that a grid cell transitions to an above average level of conflict in Sub-Saharan Africa. To control for differences in seasons across the continent, we model this relationship for each of the regions of Sub-Saharan Africa separately - East, Central, West, and Southern. We find significant seasonal and regional effects between rainfall and the probability that a grid cell transitions from a state of peace to a state of conflict. In particular, above average rainfall is associated with a higher likelihood of transitioning into conflict during the dry season. Further, each region has specific months-primarily those associated with prime crop harvest periods-where variations in rainfall significantly influence conflict. We also find regional variations in the linkage between rainfall and conflict type related to the types of conflict that predominate in particular regions of Sub- Saharan Africa. These findings are important for policymakers because they suggest additional law enforcement and/or peacekeeping resources may be needed in times of above average rainfall. Policies that provide financial support for farmers or other sectors, such as mining, that are impacted by rainfall patterns may also be a useful strategy for conflict mitigation.
- Published
- 2020
22. Rigidity of complex convex divisible sets
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Andrew Zimmer
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Pure mathematics ,Group (mathematics) ,Complex projective space ,010102 general mathematics ,Convex set ,Boundary (topology) ,01 natural sciences ,Convexity ,Complex convexity ,0103 physical sciences ,010307 mathematical physics ,Geometry and Topology ,0101 mathematics ,Convex function ,Analysis ,Real projective space ,Mathematics - Abstract
An open convex set in real projective space is called divisible if there exists a discrete group of projective automorphisms which acts cocompactly. There are many examples of such sets and a theorem of Benoist implies that many of these examples are strictly convex, have [Formula: see text] boundary, and have word hyperbolic dividing group. In this paper we study a notion of convexity in complex projective space and show that the only divisible complex convex sets with [Formula: see text] boundary are the projective balls.
- Published
- 2018
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23. A gap theorem for the complex geometry of convex domains
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Andrew Zimmer
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Unit sphere ,Pure mathematics ,Applied Mathematics ,General Mathematics ,010102 general mathematics ,Holomorphic function ,Boundary (topology) ,01 natural sciences ,Domain (mathematical analysis) ,Compact space ,Bounded function ,0103 physical sciences ,010307 mathematical physics ,Sectional curvature ,0101 mathematics ,Bergman metric ,Mathematics - Abstract
In this paper we establish a gap theorem for the complex geometry of smoothly bounded convex domains which informally says that if the complex geometry near the boundary is close to the complex geometry of the unit ball, then the domain must be strongly pseudoconvex. One consequence of our general result is the following: for any dimension there exists some ϵ > 0 \epsilon > 0 so that if the squeezing function on a smoothly bounded convex domain is greater than 1 − ϵ 1-\epsilon outside a compact set, then the domain is strongly pseudoconvex (and hence the squeezing function limits to one on the boundary). Another consequence is the following: for any dimension d d there exists some ϵ > 0 \epsilon > 0 so that if the holomorphic sectional curvature of the Bergman metric on a smoothly bounded convex domain is within ϵ \epsilon of − 4 / ( d + 1 ) -4/(d+1) outside a compact set, then the domain is strongly pseudoconvex (and hence the holomorphic sectional curvature limits to − 4 / ( d + 1 ) -4/(d+1) on the boundary).
- Published
- 2018
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24. Barriers to urban agriculture in Sub-Saharan Africa
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Andrew Zimmer, Zack Guido, Julia Davies, Jane Battersby, Laura E. McCann, Corrie Hannah, and Tom Evans
- Subjects
Economics and Econometrics ,education.field_of_study ,Food security ,Sociology and Political Science ,Population ,Management, Monitoring, Policy and Law ,Development ,Livelihood ,Urban planning ,Urbanization ,Food systems ,Business ,Land tenure ,Urban agriculture ,education ,Socioeconomics ,Food Science - Abstract
Trends in urbanization and urban food insecurity in sub-Saharan Africa (SSA) have stimulated critical debates around the potential benefits of urban agriculture (UA) to urban livelihoods. Some scholars suggest that UA can contribute to the food quantity, food quality and income needs of urban households. However, much of the evidence cited comes from single case studies, with particular attention paid to large cities and high-income countries. There is a resulting gap in understanding regarding what role UA plays in the food security of households in smaller African cities and towns. These smaller urban areas are likely to house a large fraction of SSA’s urban population in future and are important sites for early intervention by policymakers. Our analysis is based on survey data collected from 2,687 low- and low-middle income households in 18 urban areas with populations of less than 200,000 across Zambia and Kenya. We perform statistical analyses to investigate the association between UA and household food security and assess which types of households are engaged in UA. We found that 33% of households in our sample are engaged in UA and there was limited statistical significance in terms of the relationship between UA and household food security. Our results reveal three key barriers to UA, namely settlement formality, property rights, and distance from food retailers. These barriers imply the need for urban planners and policymakers to revisit how decisions are made about issues such as residential development, land tenure, transport infrastructure, and the use of space in cities, as these affect the ability of households to produce, sell, and access food. Policy and planning mechanisms should further recognize the embeddedness of UA within African urban food systems, in which traditional markets, informal trading, and modern food retail also play an integral role.
- Published
- 2021
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25. Compactness of the ∂¯-Neumann problem on domains with bounded intrinsic geometry
- Author
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Andrew Zimmer
- Subjects
Pure mathematics ,Mathematics::Complex Variables ,Biholomorphism ,Euclidean space ,010102 general mathematics ,Boundary (topology) ,01 natural sciences ,Compact space ,Bounded function ,0103 physical sciences ,Neumann boundary condition ,010307 mathematical physics ,0101 mathematics ,Invariant (mathematics) ,Bergman metric ,Analysis ,Mathematics - Abstract
By considering intrinsic geometric conditions, we introduce a new class of domains in complex Euclidean space. This class is invariant under biholomorphism and includes strongly pseudoconvex domains, finite type domains in dimension two, convex domains, C -convex domains, and homogeneous domains. For this class of domains, we show that compactness of the ∂ ¯ -Neumann operator on ( 0 , q ) -forms is equivalent to the boundary not containing any q-dimensional analytic varieties (assuming only that the boundary is a topological submanifold). We also prove, for this class of domains, that the Bergman metric is equivalent to the Kobayashi metric and that the pluricomplex Green function satisfies certain local estimates in terms of the Bergman metric.
- Published
- 2021
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26. Gromov hyperbolicity, the Kobayashi metric, and $\mathbb {C}$-convex sets
- Author
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Andrew Zimmer
- Subjects
Pure mathematics ,Euclidean space ,Applied Mathematics ,General Mathematics ,010102 general mathematics ,Dimension (graph theory) ,Regular polygon ,Boundary (topology) ,Codimension ,01 natural sciences ,Bounded function ,0103 physical sciences ,010307 mathematical physics ,Affine transformation ,Ball (mathematics) ,0101 mathematics ,Mathematics - Abstract
In this paper we study the global geometry of the Kobayashi metric on domains in complex Euclidean space. We are particularly interested in developing necessary and sufficient conditions for the Kobayashi metric to be Gromov hyperbolic. For general domains, it has been suggested that a non-trivial complex affine disk in the boundary is an obstruction to Gromov hyperbolicity. This is known to be the case when the set in question is convex. In this paper we first extend this result to $\mathbb{C}$-convex sets with $C^1$-smooth boundary. We will then show that some boundary regularity is necessary by producing in any dimension examples of open bounded $\mathbb{C}$-convex sets where the Kobayashi metric is Gromov hyperbolic but whose boundary contains a complex affine ball of complex codimension one.
- Published
- 2017
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27. The structure of projective maps between real projective manifolds
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Andrew Zimmer
- Subjects
Mathematics - Differential Geometry ,Projective harmonic conjugate ,Pure mathematics ,Collineation ,Complex projective space ,010102 general mathematics ,Mathematical analysis ,22F50, 53A20, 58B20 ,Geometric Topology (math.GT) ,01 natural sciences ,Mathematics - Geometric Topology ,Real projective line ,Differential Geometry (math.DG) ,Projective line ,0103 physical sciences ,FOS: Mathematics ,Projective space ,010307 mathematical physics ,Geometry and Topology ,0101 mathematics ,Quaternionic projective space ,Mathematics::Symplectic Geometry ,Real projective space ,Mathematics - Abstract
In this paper we study the set of projective maps between compact proper convex real projective manifolds. We show that this set contains only finitely many distinct homotopy classes and each homotopy class has the structure of a real projective manifold. When the target manifold is strictly convex, our results imply that each non-trivial homotopy class contains at most one projective map. These results are motivated by the theory of holomorphic maps between compact complex manifolds., 18 pages
- Published
- 2017
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28. Characterizing domains by the limit set of their automorphism group
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Andrew Zimmer
- Subjects
Polynomial ,Pure mathematics ,Conjecture ,Geodesic ,Mathematics::Complex Variables ,General Mathematics ,010102 general mathematics ,Regular polygon ,01 natural sciences ,Ellipsoid ,Metric space ,Bounded function ,0103 physical sciences ,010307 mathematical physics ,0101 mathematics ,Limit set ,Mathematics - Abstract
In this paper we study the automorphism group of smoothly bounded convex domains. We show that such a domain is biholomorphic to a “polynomial ellipsoid” (that is, a domain defined by a weighted homogeneous balanced polynomial) if and only if the limit set of the automorphism group intersects at least two closed complex faces of the set. The proof relies on a detailed study of the geometry of the Kobayashi metric and ideas from the theory of non-positively curved metric spaces. We also obtain a number of other results including the Greene–Krantz conjecture in the case of uniform non-tangential convergence, new results about continuous extensions (of biholomorphisms and complex geodesics), and a new Wolff–Denjoy theorem.
- Published
- 2017
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29. Convex co-compact actions of relatively hyperbolic groups
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Mitul Islam and Andrew Zimmer
- Subjects
Mathematics - Differential Geometry ,Mathematics - Geometric Topology ,Differential Geometry (math.DG) ,FOS: Mathematics ,Geometric Topology (math.GT) ,Geometry and Topology ,53A20, 20F67, 57N16, 58B20, 20H10 - Abstract
In this paper we consider discrete groups in ${\rm PGL}_d(\mathbb{R})$ acting convex co-compactly on a properly convex domain in real projective space. For such groups, we establish necessary and sufficient conditions for the group to be relatively hyperbolic in terms of the geometry of the convex domain. This answers a question of Danciger-Gu\'eritaud-Kassel and is analogous to a result of Hruska-Kleiner for ${\rm CAT}(0)$ spaces., Comment: Minor revisions, final version to appear in Geometry & Topology. 96 pages, 2 figures. Comments welcome
- Published
- 2019
30. Smoothly bounded domains covering compact manifolds
- Author
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Andrew Zimmer
- Subjects
Mathematics - Differential Geometry ,Differential Geometry (math.DG) ,Mathematics - Complex Variables ,General Mathematics ,FOS: Mathematics ,Complex Variables (math.CV) - Abstract
We show that if a bounded domain in complex Euclidean space with $\mathcal{C}^{1,1}$ boundary covers a compact manifold, then the domain is biholomorphic to the unit ball., 23 pages. v2: minor changes in exposition, corrected some typos
- Published
- 2019
31. Has the vision of a gender quota rule been realized for community-based water management committees in Kenya?
- Author
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Sara Lopus, Stacey Giroux, Corrie Hannah, Laura E. McCann, Kelly K. Caylor, Andrew Zimmer, Natasha Krell, and Tom Evans
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Economics and Econometrics ,Economic growth ,Resource (biology) ,Sociology and Political Science ,Constitution ,050204 development studies ,media_common.quotation_subject ,Corporate governance ,05 social sciences ,Geography, Planning and Development ,Development ,Focus group ,Representation (politics) ,Water resources ,Politics ,Environmental governance ,Political science ,0502 economics and business ,050207 economics ,media_common - Abstract
Persisting gender inequities across political, economic, and public life have motivated global agendas to increase women’s leadership at all levels of society. Gender quotas offer one solution to encourage equitable gender representation in public decision-making by specifying a target number of women to serve on publicly-elected bodies. For natural resource governance sectors, can gender quotas promote women’s representation and participation in leadership? In 2010, Kenya enacted a new Constitution that included an article mandating that no one gender should make up greater than two-thirds of the composition of public committees. This ‘two-thirds gender rule’ also applies to community-level governance of water resources through water user resource associations, which were formally recognized in 2002. We present a study of community-based water committee compliance with Kenya’s national two-thirds gender rule based on surveys, focus groups, and interviews with water committee members. We show that Kenya’s gender quota has been moderately successful in increasing women’s representation on water committees. However, men hold more higher-level leadership positions than women, who typically serve as treasurers. Although there were no statistically significant differences between men and women’s self-reported participation frequency in various committee activities, men contributed significantly more hours per week to committee activities, facilitated meetings more frequently, and were more willing to lead meetings. Based on this leadership gap, we examine the sufficiency of a gender quota to promote equal leadership opportunities for women. We find that realizing the vision of a gender quota is conditional on how individuals are represented on community-based environmental committees as well as how individuals participate in committee activities.
- Published
- 2021
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32. Asymptotic behavior of orbits of holomorphic semigroups
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Manuel D. Contreras, Santiago Díaz-Madrigal, Filippo Bracci, Andrew Zimmer, Hervé Gaussier, Università degli Studi di Roma Tor Vergata [Roma], Departamento de Matemática Aplicada I (IMUS), IMUS, Institut Fourier (IF), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), and Louisiana State University (LSU)
- Subjects
Mathematics - Differential Geometry ,Pure mathematics ,Quasi-geodesic ,Mathematics::Dynamical Systems ,General Mathematics ,Holomorphic function ,Koenigs functions ,Fixed point ,01 natural sciences ,Domain (mathematical analysis) ,03 medical and health sciences ,Gromov hyperbolicity ,Semicomplete holomorphic vector fields ,FOS: Mathematics ,Semigroups of holomorphic functions ,0101 mathematics ,Complex Variables (math.CV) ,[MATH]Mathematics [math] ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,Mathematics ,0303 health sciences ,Semigroup ,Mathematics::Complex Variables ,Mathematics - Complex Variables ,Applied Mathematics ,010102 general mathematics ,Function (mathematics) ,Settore MAT/03 ,Flow (mathematics) ,Differential Geometry (math.DG) ,Boundary behavior of univalent functions ,Vector field ,Unit (ring theory) - Abstract
Let $(\phi_t)$ be a holomorphic semigroup of the unit disc (i.e., the flow of a semicomplete holomorphic vector field) without fixed points in the unit disc and let $\Omega$ be the starlike at infinity domain image of the Koenigs function of $(\phi_t)$. In this paper we completely characterize the type of convergence of the orbits of $(\phi_t)$ to the Denjoy-Wolff point in terms of the shape of $\Omega$. In particular we prove that the convergence is non-tangential if and only if the domain $\Omega$ is `quasi-symmetric with respect to vertical axes'. We also prove that such conditions are equivalent to the curve $[0,\infty)\ni t\mapsto \phi_t(z)$ being a quasi-geodesic in the sense of Gromov. Also, we characterize the tangential convergence in terms of the shape of $\Omega$., Comment: 25 pages, 3 figures
- Published
- 2018
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33. Two boundary rigidity results for holomorphic maps
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Andrew Zimmer
- Subjects
Mathematics - Differential Geometry ,Differential Geometry (math.DG) ,32H12 (Primary) 32F45, 32A40, 53B35, 53C22 (Secondary) ,Mathematics::Complex Variables ,Mathematics - Complex Variables ,General Mathematics ,FOS: Mathematics ,Complex Variables (math.CV) - Abstract
In this paper we establish two boundary versions of the Schwarz lemma. The first is for general holomorphic self maps of bounded convex domains with $C^2$ boundary. This appears to be the first boundary Schwarz lemma for general holomorphic self maps that requires no strong pseudoconvexity or finite type assumptions. The second is for biholomorphisms of domains who have an invariant K\"ahler metric with bounded sectional curvature. This second result applies to holomorphic homogeneous regular domains and appears to be the first boundary Schwarz lemma that makes no assumptions on the regularity of the boundary., Comment: 42 pages. Comments welcome. v2: minor edits
- Published
- 2018
34. GeNets: a unified web platform for network-based genomic analyses
- Author
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Joseph Rosenbluh, Ted Liefeld, Taibo Li, Ayshwarya Subramanian, David An, Arthur Liberzon, Heiko Horn, Aviv Regev, Dawn A. Thompson, Kasper Lage, Jon Bistline, Aviad Tsherniak, Rajiv Narayan, Jesse S. Boehm, Nir Hacohen, Liraz Greenfeld, Jacob D. Jaffe, Andrew Zimmer, April Kim, Sarah E. Calvo, Jill P. Mesirov, Bang Wong, Yang Li, Steve Carr, Ted Natoli, Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Li, Taibo, and Regev, Aviv
- Subjects
0301 basic medicine ,business.industry ,Extramural ,Computer science ,Systems biology ,Cell Biology ,Nucleic acid amplification technique ,Computational biology ,Network topology ,Biochemistry ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Software ,ComputingMethodologies_PATTERNRECOGNITION ,Dna genetics ,The Internet ,business ,Molecular Biology ,Functional genomics ,030217 neurology & neurosurgery ,Biotechnology - Abstract
Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the signal-to-noise ratios of different networks and to identify the optimal network with which to interpret a particular genetic dataset. We present GeNets, a platform in which users can train a machine-learning model (Quack) to carry out these comparisons and execute, store, and share analyses of genetic and RNA-sequencing datasets.
- Published
- 2018
35. GeNets: A unified web platform for network-based analyses of genomic data
- Author
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Jill P. Mesirov, Kasper Lage, Ted Natoli, April Kim, Rajiv Narayan, Liraz Greenfeld, Nir Hacohen, Jacob D. Jaffe, Arthur Liberzon, Jon Bistline, Ted Liefeld, Aviad Tsherniak, Heiko Horn, Sarah E. Calvo, Yang Li, Steve Carr, Bang Wong, Andrew Zimmer, Ayshwarya Subramanian, Taibo Li, Dawn A. Thompson, Jesse S. Boehm, Aviv Regev, Joseph Rosenbluh, and David An
- Subjects
Genomic data ,Genomics ,Biology ,computer.software_genre ,Article ,Bottleneck ,Machine Learning ,03 medical and health sciences ,0302 clinical medicine ,030304 developmental biology ,Internet ,0303 health sciences ,SIGNAL (programming language) ,DNA ,Pathway information ,ComputingMethodologies_PATTERNRECOGNITION ,Workflow ,Scalability ,RNA ,Data mining ,Databases, Nucleic Acid ,Nucleic Acid Amplification Techniques ,Functional genomics ,computer ,Software ,030217 neurology & neurosurgery - Abstract
A major bottleneck in network-based analyses of genomic data is quantitatively comparing biological signal in different networks and to identifying the optimal network dataset to answer a particular biological question. Towards these aims, we developed a unified web platform 9Broad Institute Web Platform for Genome Networks (GeNets)9, where users can compare biological signal of networks, and execute, store, and share network analyses. We designed a machine learningmachine-learning algorithm (Quack) which), which uses topological features to can quantify the overall and pathway-specific biological signals in networks, thus enabling users to choose the optimal network dataset for their analyses. We illustrated a typical workflow using GeNets to identify interesting autism candidate genes in the network that, when compared to four other networks, best recapitulates established neurodevelopmental pathway information. GeNets is a scalable, general and uniquely enabling computational framework for analyzing, managing and sharing analyses of genetic datasets using heterogeneous functional genomics networks, for example, from single-cell transcriptional analyses.
- Published
- 2018
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36. Smoothly bounded domains covering finite volume manifolds
- Author
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Andrew Zimmer
- Subjects
Mathematics - Differential Geometry ,Unit sphere ,Pure mathematics ,Algebra and Number Theory ,Finite volume method ,Mathematics - Complex Variables ,Mathematics::Complex Variables ,010102 general mathematics ,Boundary (topology) ,01 natural sciences ,Domain (mathematical analysis) ,Manifold ,Kähler–Einstein metric ,Differential Geometry (math.DG) ,Bounded function ,FOS: Mathematics ,Geometry and Topology ,Mathematics::Differential Geometry ,0101 mathematics ,Complex Variables (math.CV) ,Bergman metric ,Mathematics::Symplectic Geometry ,Analysis ,Mathematics - Abstract
In this paper we prove: if a bounded domain with $C^2$ boundary covers a manifold which has finite volume with respect to either the Bergman volume, the K\"ahler-Einstein volume, or the Kobayashi-Eisenman volume, then the domain is biholomorphic to the unit ball. This answers an old question of Yau. Further, when the domain is convex we can assume that the boundary only has $C^{1,\epsilon}$ regularity., Comment: 16 pages. Comments welcome
- Published
- 2018
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- View/download PDF
37. Gromov hyperbolicity and the Kobayashi metric on convex domains of finite type
- Author
-
Andrew Zimmer
- Subjects
Pure mathematics ,Mathematics::Complex Variables ,General Mathematics ,010102 general mathematics ,Regular polygon ,Boundary (topology) ,Type (model theory) ,Mathematical proof ,01 natural sciences ,Hilbert metric ,Bounded function ,0103 physical sciences ,010307 mathematical physics ,0101 mathematics ,Convex domain ,Kobayashi metric ,Mathematics - Abstract
In this paper we prove necessary and sufficient conditions for the Kobayashi metric on a convex domain to be Gromov hyperbolic. In particular we show that for convex domains with \(C^\infty \) boundary being of finite type in the sense of D’Angelo is equivalent to the Gromov hyperbolicity of the Kobayashi metric. We also show that bounded domains which are locally convexifiable and have finite type in the sense of D’Angelo have Gromov hyperbolic Kobayashi metric. The proofs use ideas from the theory of the Hilbert metric.
- Published
- 2015
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38. The automorphism group and limit set of a bounded domain I: the finite type case
- Author
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Andrew Zimmer
- Subjects
Mathematics - Differential Geometry ,Pure mathematics ,Tits alternative ,Jet (mathematics) ,Mathematics - Complex Variables ,General Mathematics ,010102 general mathematics ,Lie group ,16. Peace & justice ,Submanifold ,01 natural sciences ,Mathematics::Group Theory ,Compact group ,Differential Geometry (math.DG) ,Bounded function ,0103 physical sciences ,FOS: Mathematics ,010307 mathematical physics ,Diffeomorphism ,0101 mathematics ,Orbit (control theory) ,Complex Variables (math.CV) ,Mathematics - Abstract
For bounded pseudoconvex domains with finite type we give a precise description of the automorphism group: if an orbit of the automorphism group accumulates on at least two different points of the boundary, then the automorphism group has finitely many components and is the almost direct product of a compact group and connected Lie group locally isomorphic to ${ \rm Aut}(\mathbb{B}_k)$. Further, the limit set is a smooth submanifold diffeomorphic to the sphere of dimension $2k-1$. As applications we prove a new finite jet determination theorem and a Tits alternative theorem. The geometry of the Kobayashi metric plays an important role in the paper., 33 pages. v3: minor revisions. Final version to appear in Advances in Mathematics
- Published
- 2017
39. Projective Anosov representations, convex cocompact actions, and rigidity
- Author
-
Andrew Zimmer
- Subjects
Surface (mathematics) ,Mathematics - Differential Geometry ,Fundamental group ,Pure mathematics ,Algebra and Number Theory ,Mathematics::Dynamical Systems ,Hyperbolic group ,Group (mathematics) ,010102 general mathematics ,Lie group ,Geometric Topology (math.GT) ,Submanifold ,01 natural sciences ,Mathematics - Geometric Topology ,Differential Geometry (math.DG) ,FOS: Mathematics ,Projective space ,Geometry and Topology ,0101 mathematics ,Analysis ,Real projective space ,Mathematics - Abstract
In this paper we show that many projective Anosov representations act convex cocompactly on some properly convex domain in real projective space. In particular, if a non-elementary word hyperbolic group is not commensurable to a non-trivial free product or the fundamental group of a closed hyperbolic surface, then any projective Anosov representation of that group acts convex cocompactly on some properly convex domain in real projective space. We also show that if a projective Anosov representation preserves a properly convex domain, then it acts convex cocompactly on some (possibly different) properly convex domain. We then give three applications. First, we show that Anosov representations into general semisimple Lie groups can be defined in terms of the existence of a convex cocompact action on a properly convex domain in some real projective space (which depends on the semisimple Lie group and parabolic subgroup). Next, we prove a rigidity result involving the Hilbert entropy of a projective Anosov representation. Finally, we prove a rigidity result which shows that the image of the boundary map associated to a projective Anosov representation is rarely a $C^2$ submanifold of projective space. This final rigidity result also applies to Hitchin representations., 62 pages. Final version
- Published
- 2017
40. Characterizing strong pseudoconvexity, obstructions to biholomorphisms, and Lyapunov exponents
- Author
-
Andrew Zimmer
- Subjects
Mathematics::Complex Variables ,Mathematics - Complex Variables ,General Mathematics ,010102 general mathematics ,Mathematical analysis ,Holomorphic function ,Boundary (topology) ,Lyapunov exponent ,01 natural sciences ,Domain (mathematical analysis) ,32T15, 32F45, 53C22, 53C24, 37D40 ,symbols.namesake ,Bounded function ,Pseudoconvexity ,0103 physical sciences ,FOS: Mathematics ,symbols ,010307 mathematical physics ,Sectional curvature ,Complex Variables (math.CV) ,0101 mathematics ,Bergman metric ,Mathematics - Abstract
In this paper we consider the following question: For bounded domains with smooth boundary, can strong pseudoconvexity be characterized in terms of the intrinsic complex geometry of the domain? Our approach to answering this question is based on understanding the dynamical behavior of real geodesics in the Kobayashi metric and allows us to prove a number of results for domains with low regularity. For instance, we show that for convex domains with $C^{2,\epsilon}$ boundary strong pseudoconvexity can be characterized in terms of the behavior of the squeezing function near the boundary, the behavior of the holomorphic sectional curvature of the Bergman metric near the boundary, or any other reasonable measure of the complex geometry near the boundary. The first characterization gives a partial answer to a question of Forn{\ae}ss and Wold. As an application of these characterizations, we show that a convex domain with $C^{2,\epsilon}$ boundary which is biholomorphic to a strongly pseudoconvex domain is also strongly pseudoconvex., Comment: 27 pages. v2: minor revisions
- Published
- 2017
41. Goldilocks domains, a weak notion of visibility, and applications
- Author
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Gautam Bharali and Andrew Zimmer
- Subjects
Mathematics - Differential Geometry ,Pure mathematics ,Euclidean space ,Mathematics::Complex Variables ,Mathematics - Complex Variables ,General Mathematics ,010102 general mathematics ,Visibility (geometry) ,Boundary (topology) ,Type (model theory) ,01 natural sciences ,Upper and lower bounds ,Differential Geometry (math.DG) ,0103 physical sciences ,Metric (mathematics) ,Goldilocks principle ,FOS: Mathematics ,010307 mathematical physics ,0101 mathematics ,Variety (universal algebra) ,Complex Variables (math.CV) ,32F45, 53C23 (Primary), 32H40, 32H50, 32T25 (Secondary) ,Mathematics - Abstract
In this paper we introduce a new class of domains in complex Euclidean space, called Goldilocks domains, and study their complex geometry. These domains are defined in terms of a lower bound on how fast the Kobayashi metric grows and an upper bound on how fast the Kobayashi distance grows as one approaches the boundary. Strongly pseudoconvex domains and weakly pseudoconvex domains of finite type always satisfy this Goldilocks condition, but we also present families of Goldilocks domains that have low boundary regularity or have boundary points of infinite type. We will show that the Kobayashi metric on these domains behaves, in some sense, like a negatively curved Riemannian metric. In particular, it satisfies a visibility condition in the sense of Eberlein and O'Neill. This behavior allows us to prove a variety of results concerning boundary extension of maps and to establish Wolff-Denjoy theorems for a wide collection of domains., 36 pages. v2: minor changes, final version to appear in Advances in Mathematics
- Published
- 2017
42. Abstract B085: High mutation burden and response to immune checkpoint inhibitors in angiosarcomas of the scalp and face
- Author
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Kristin Anderka, Esme O. Baker, Rachel Stoddard, Corrie A. Painter, Niall Lennon, Jason L. Hornick, Yen-Lin Chen, Simone Maiwald, Jen Lapan, Esha Jain, Beena Thomas, Mary McGillicuddy, Andrew Zimmer, Sara Balch, George D. Demetri, Eric S. Lander, Chandrajit P. Raut, Todd R. Golub, Elana Anastasio, Michael Dunphy, and Katie Larkin
- Subjects
Oncology ,Cancer Research ,medicine.medical_specialty ,business.industry ,Incidence (epidemiology) ,Medical record ,medicine.medical_treatment ,Soft tissue sarcoma ,Immunology ,Cancer ,Disease ,Immunotherapy ,medicine.disease ,Cell-free fetal DNA ,Cancer immunotherapy ,Internal medicine ,medicine ,business - Abstract
Objective: Angiosarcoma (AS) is a rare soft tissue sarcoma, with an incidence of 300 cases/yr and a 5-year DSS of 30%. The low incidence has impeded large-scale research efforts. To address this, we launched a patient-partnered genomics study which seeks to empower patients to accelerate research by remotely sharing their samples and clinical information. Methods: We developed a website (ASCproject.org) to allow remote acquisition of medical records (MR), saliva, blood, and archival tissue from patients in the US and Canada. Whole-exome sequencing (WES) of ~20,000 genes is performed on tumor and matched germline DNA. Transcriptome analysis is performed on tumor RNA. Ultra-low pass whole-genome sequencing (ULP-WGS) and in some cases WES is performed on cell free DNA (cfDNA) obtained from blood samples. Clinical data including information about demographics, diagnosis, treatments, and responses are obtained via patient-reported data (PRD) and through MR abstraction. The resulting clinically annotated genomic database is shared widely to identify genomic drivers and mechanisms of response and resistance to therapies. Results: Since launch on March 13 2017, 321 patients with AS have registered. The average age of patients is 56 yrs (range 22-89). Primary locations of AS were primary breast (24%), breast with prior radiation (20%), head/face/neck/scalp (HFNS) (21%), bone/limb (9%), abdominal (3%), heart (3%), lung (1%), liver (1%), lymph (0.5%), multiple locations (11%), and other locations (5%). 142 (48%) reported being disease free at the time of enrollment. To date, 153 saliva kits, 167 MRs, 43 blood samples, and 97 tissue samples have been obtained. WES analysis is complete for 14 samples.ULP-WGS is complete for 10 cfDNA samples, and WES on 4 cfDNA samples. Transcriptome sequencing is complete for 9 tumor samples. We identified several previously described genes known to be altered in AS, including recurrent alterations in KDR and TP53. Tumor mutational burden (TMB) and mutational signature activities were quantified for each tumor sample. All three of the AS from the HFNS in the initial cohort exhibited a high TMB (>150 mutations) and dominant UV light signature (COSMIC Signature 7). Based on this, we hypothesized that HFNS AS might respond well to immune checkpoint inhibitors. We identified through PRD 56 patients with HFNS AS who reported what medications they received. Of these, 2 reported receiving immune checkpoint inhibitors for the treatment of metastatic disease. Both patients had refractory metastatic HFNS AS and reported receiving off-label anti-PD1 therapy. Both had complete or near-complete responses following immunotherapy, and currently report having no evidence of disease. Clinical responses were confirmed through review of MRs. Sequencing is currently being performed on tumor samples from both patients. Conclusion: A patient-partnered approach enabled rapid identification and enrollment of over 300 patients with AS, an exceedingly rare cancer, in 15 months. We were able to obtain tumor, blood, saliva samples to perform genomic analyses, which were then merged with detailed clinical information. PRD, clinical, and genomic data generated from the first 12 patients and 14 samples have been released on cbioportal.org. Additional data will be released in six-month intervals. Initial results show high TMB and a UV signature in 3 out of 3 patients with HFNS AS. In addition, we identified 2 patients with HFNS AS who had extraordinary responses to immunotherapy. These findings suggest a common genomic basis for HFNS AS and could provide rationale for clinical interventions using checkpoint inhibitors for these AS. Analyses of additional samples are under way to further characterize mutational signatures in HFNS AS and implications for patient care. This study serves as proof of principle that patient-partnered genomics efforts can democratize cancer research for exceedingly rare cancers. Citation Format: Corrie Painter, Esha Jain, Michael Dunphy, Elana Anastasio, Mary McGillicuddy, Rachel Stoddard, Beena Thomas, Sara Balch, Kristin Anderka, Katie Larkin, Niall Lennon, Yen-Lin Chen, Andrew Zimmer, Esme O. Baker, Simone Maiwald, Jen Lapan, Jason L. Hornick, Chandrajit Raut, George Demetri, Eric S. Lander, Todd Golub. High mutation burden and response to immune checkpoint inhibitors in angiosarcomas of the scalp and face [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B085.
- Published
- 2019
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43. Bounds for minimum semidefinite rank from superpositions and cutsets
- Author
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Sivaram K. Narayan, Jennifer L. Wolfe, Jonathan E. Beagley, Sara P. Rimer, Lon H. Mitchell, Rachael L. Tomasino, Andrew Zimmer, and Eileen L. Radzwion
- Subjects
Semidefinite embedding ,Discrete mathematics ,Semidefinite programming ,Numerical Analysis ,Algebra and Number Theory ,A* search algorithm ,Positive-definite matrix ,Upper and lower bounds ,Hermitian matrix ,law.invention ,Combinatorics ,Superposition principle ,law ,Cut ,Discrete Mathematics and Combinatorics ,Geometry and Topology ,Mathematics - Abstract
The real (complex) minimum semidefinite rank of a graph is the minimum rank among all real symmetric (complex Hermitian) positive semidefinite matrices that are naturally associated via their zero-nonzero pattern to the given graph. In this paper we give an upper bound on the minimum semidefinite rank of a graph when the graph is modified from the superposition of two graphs by cancelling some number of edges. We also provide a lower bound for the minimum semidefinite rank of a graph determined by a given cutset. When the complement of the cutset is a star forest these lower and upper bounds coincide and we can compute the minimum semidefinite rank in terms of smaller graphs. This result encompasses the previously known case in which the cut set has order two or smaller. Next we provide results for when the cut set has order three. Using these results we provide an example where the positive semidefinite zero forcing number is strictly greater than the maximum positive semidefinite nullity.
- Published
- 2013
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- View/download PDF
44. Boundaries of non-compact harmonic manifolds
- Author
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Andrew Zimmer
- Subjects
Differential geometry ,Ricci-flat manifold ,Mathematical analysis ,Conjugate points ,Boundary (topology) ,Harmonic (mathematics) ,Mathematics::Differential Geometry ,Geometry and Topology ,Harmonic measure ,Measure (mathematics) ,Manifold ,Mathematics - Abstract
In this paper we consider non-compact non-flat simply connected harmonic manifolds. In particular, we show that the Martin boundary and Busemann boundary coincide for such manifolds. For any finite volume quotient we show that (up to scaling) there is a unique Patterson–Sullivan measure and this measure coincides with the harmonic measure. As an application of these results we prove that the geodesic flow on a non-flat finite volume harmonic manifold without conjugate points is topologically transitive.
- Published
- 2013
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45. A new lower bound for the positive semidefinite minimum rank of a graph
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Andrew Zimmer
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Discrete mathematics ,Vertex (graph theory) ,Semidefinite programming ,Numerical Analysis ,Algebra and Number Theory ,Mathematics::Optimization and Control ,Minimum rank of a graph ,Positive-definite matrix ,Upper and lower bounds ,Combinatorics ,Zero Forcing Equalizer ,Discrete Mathematics and Combinatorics ,Geometry and Topology ,Mathematics - Abstract
The real positive semidefinite minimum rank of a graph is the minimum rank among all real positive semidefinite matrices that are naturally associated via their zero-nonzero pattern to the given graph. In this paper, we use orthogonal vertex removal and sign patterns to improve the lower bound for the real positive semidefinite minimum rank determined by the OS-number and the positive semidefinite zero forcing number.
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- 2013
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46. Generic analytic polyhedron with non-compact automorphism group
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Andrew Zimmer
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Pure mathematics ,Automorphism group ,Mathematics::Complex Variables ,Mathematics - Complex Variables ,General Mathematics ,Rigidity (psychology) ,32M99, 32F45, 32Q35 ,Polyhedron ,Mathematics::Group Theory ,Dimension (vector space) ,Product (mathematics) ,FOS: Mathematics ,Complex Variables (math.CV) ,Limit set ,Complex manifold ,Mathematics::Symplectic Geometry ,Mathematics - Abstract
In this paper we prove the following rigidity theorem: a generic analytic polyhedron with non-compact automorphism group is biholomorphic to the product of a complex manifold with compact automorphism group and a polydisk. Moreover, this complex manifold and the dimension of this polydisk can be explicitly described in terms of the limit set of the automorphism group., 25 pages
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- 2016
47. Characterizing the unit ball by its projective automorphism group
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Andrew Zimmer
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Mathematics - Differential Geometry ,Unit sphere ,Pure mathematics ,Boundary (topology) ,automorphism group ,53A20 ,01 natural sciences ,53C24 ,projective geometry ,Mathematics - Geometric Topology ,0103 physical sciences ,FOS: Mathematics ,Complex Variables (math.CV) ,0101 mathematics ,Projective test ,Quaternionic projective space ,Hilbert metric ,22E40 ,Mathematics ,Projective geometry ,Automorphism group ,Mathematics - Complex Variables ,Kobayashi metric ,010102 general mathematics ,22E40, 53A20, 53C24, 32C15 ,Geometric Topology (math.GT) ,Differential Geometry (math.DG) ,010307 mathematical physics ,Geometry and Topology - Abstract
In this paper we study the projective automorphism group of domains in real, complex, and quaternionic projective space and present two new characterizations of the unit ball in terms of the size of the automorphism group and the regularity of the boundary., 27 pages
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- 2016
48. Compact asymptotically harmonic manifolds
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Andrew Zimmer
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Pure mathematics ,Fundamental group ,Algebra and Number Theory ,Mean curvature ,Physical constant ,Applied Mathematics ,010102 general mathematics ,Conjugate points ,Harmonic (mathematics) ,Riemannian manifold ,Curvature ,Mathematics::Geometric Topology ,01 natural sciences ,0103 physical sciences ,Mathematics::Differential Geometry ,010307 mathematical physics ,0101 mathematics ,Variety (universal algebra) ,Mathematics::Symplectic Geometry ,Analysis ,Mathematics - Abstract
A complete Riemannian manifold without conjugate points is said to be asymptotically harmonic if the mean curvature of its horospheres is a universal constant. Examples of asymptotically harmonic manifolds include flat spaces and rank-one locally symmetric spaces of noncompact type. In this paper we show that this list exhausts the compact asymptotically harmonic manifolds under a variety of assumptions including nonpositive curvature or Gromov-hyperbolic fundamental group. We then present a new characterization of symmetric spaces amongst the set of all visibility manifolds.
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- 2012
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49. Abstract 5384: The Angiosarcoma Project: Generating the genomic landscape of an exceedingly rare cancer through a nationwide patient-driven initiative
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Niall J. Lennon, Elana Anastasio, Andrew Zimmer, George D. Demetri, Beena Thomas, Corrie A. Painter, Rachel Stoddard, Michael Dunphy, Todd R. Golub, Nikhil Wagle, Kristin Anderka, Katie Larkin, Esme O. Baker, Yen-Lin Chen, Esha Jain, Eric S. Lander, Sara Balch, Chandrajit P. Raut, Simone Maiwald, Jen Hendrey Lapan, Mary McGillicuddy, and Jason L. Hornick
- Subjects
0301 basic medicine ,Neuroblastoma RAS viral oncogene homolog ,Oncology ,Cancer Research ,medicine.medical_specialty ,business.industry ,Medical record ,Incidence (epidemiology) ,Soft tissue sarcoma ,Cancer ,medicine.disease ,Rare cancer ,Frameshift mutation ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,030220 oncology & carcinogenesis ,Internal medicine ,Medicine ,Angiosarcoma ,business - Abstract
Angiosarcoma (AS) is an exceedingly rare soft tissue sarcoma, with an incidence of 300 cases/yr and a 5-year disease-specific survival of 30%. The low incidence has impeded large-scale research efforts that may lead to improved clinical outcomes. To address this, we launched a nationwide clinical-genomics study in order to empower patients to accelerate research by sharing their normal and tumor samples and clinical information remotely. Patients can access the study through an online portal (ASCproject.org). Enrolled patients are mailed saliva and blood draw kits. The study team obtains medical records and stored FFPE tumor samples. All received FFPE samples are examined by an expert pathologist to confirm a diagnosis of angiosarcoma. In order to validate that our processes would enable the generation of a robust dataset from tissues acquired from multiple institutions, we sought to characterize previously described genes known to be altered in angiosarcoma (e.g., TP53, NF1, KDR, BRCA2, MET, ARID1A, POT1, BRCA1, ASXL1, KDM6A, BRAF, SETD2, PTPRB, NRAS). A total of 251 patients have enrolled since the project launched in March of 2017. Primary locations of AS are primary breast 59 (25%), breast with prior radiation 45 (19%), head/face/neck/scalp 52 (22%), bone/limb 26 (11%), abdomen 5 (2%), heart 5 (2%), lung 2 (1%), liver 1 (1%), lymph 1 (0.4%), multiple locations 25 (11%), and other locations 12 (5%); 107 (52%) reported being disease free at the time of enrollment. To date, we have received 129 saliva kits, 106 medical records, 19 blood samples, and 36 tissue samples. Whole-exome sequencing (WES) was performed on 21 FFPE/saliva matched pairs with a goal mean target coverage of 150x for tumors. Ultra-low pass whole-genome sequencing (0.1x) was performed on cell free DNA (cfDNA) from plasma in order to determine tumor fraction. Of 10 cfDNA samples sequenced, 4 samples met criteria to perform WES. Additionally, transcriptome sequencing was performed on 9 FFPE samples. Sequence data processing and analysis has been completed on the first 10 samples and is in progress for the subsequent samples. Alterations were detected in genes previously described to be affected in angiosarcoma. Recurrent mutations in TP53 were detected in 50% (5/10) of analyzed samples, comprising 3 missense mutations, 1 frameshift deletion, and 1 frameshift insertion. Alterations were seen in at least one sample in all other genes selected for this initial analysis. This initiative demonstrates the feasibility of studying tissues from geographically dispersed patients and serves as proof of concept that patient-driven genomics efforts can democratize research for exceedingly rare cancers. Enrollment is still in progress, and additional samples will be sequenced and analyzed at scale. The data generated from these studies will be deposited into the public domain in six-month intervals. Citation Format: Michael Dunphy, Esha Jain, Elana Anastasio, Mary McGillicuddy, Rachel Stoddard, Beena Thomas, Sara Balch, Kristin Anderka, Katie Larkin, Niall Lennon, Yen-Lin Chen, Andrew Zimmer, Esme O. Baker, Simone Maiwald, Jen Hendrey Lapan, Jason Hornick, Chandrajit Raut, George Demetri, Eric Lander, Todd Golub, Nikhil Wagle, Corrie Painter. The Angiosarcoma Project: Generating the genomic landscape of an exceedingly rare cancer through a nationwide patient-driven initiative [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5384.
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- 2018
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50. Abstract 5371: The Metastatic Breast Cancer Project: Partnering with patients to accelerate progress in cancer research
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Corrie A. Painter, Mary McGillicuddy, Alicia Wong, Priti Kumari, Simona Di Lascio, Simone Maiwald, Esha Jain, Ofir Cohen, Nikhil Wagle, Katie Larkin, Dewey Kim, Brett N. Tompson, Viktor A. Adalsteinsson, Sara Balch, Shawn F. Johnson, Samira Bahl, Sam Pollock, Andrew Zimmer, Scott Sassone, Rachel Stoddard, Scott Sutherland, Beena Thomas, Esme O. Baker, Jen Lapan, Elana Anastasio, Eric S. Lander, Erik H. Knelson, Michael Dunphy, Jamie Holloway, and Todd R. Golub
- Subjects
Cancer Research ,business.industry ,Medical record ,Cancer ,02 engineering and technology ,Saliva sample ,010402 general chemistry ,021001 nanoscience & nanotechnology ,medicine.disease ,01 natural sciences ,Metastatic breast cancer ,0104 chemical sciences ,Transcriptome Sequencing ,Metastasis ,Oncology ,Quality of life ,medicine ,Cancer research ,Family history ,0210 nano-technology ,business - Abstract
The Metastatic Breast Cancer Project (MBCproject) is a research study that directly engages patients (pts) through social media and advocacy groups, and empowers them to share samples, clinical data, and experiences. The goal is to create a publicly available database of genomic, molecular, clinical, and patient-reported data to enable research. Working with pts and advocates, a website (MBCproject.org) was developed that allows pts with metastatic breast cancer (MBC) to register. Registered pts are sent an online consent form that asks for permission to obtain and analyze their medical records and samples. Once enrolled, pts are sent a saliva kit and asked to mail back a saliva sample, which is used to extract germline DNA. We contact participants' medical providers and obtain medical records and a portion of their stored tumor biopsies. Pts may be asked to mail in a blood sample, which is used to extract cell free DNA (cfDNA). Whole-exome sequencing (WES) is performed on tumor DNA, germline DNA, and cfNDA; transcriptome sequencing is performed on tumor RNA. Clinically annotated genomic data are used to study specific pt cohorts (including outliers) and to identify mechanisms of response and resistance to therapies. All de-identified data are shared via public databases. Study updates are shared with participants regularly. From 10/2015-11/2017, 4237 MBC pts registered, representing over 1,000 institutions. 95% answered the 16-question survey about their cancer, treatments, and demographic information. 2471 (58%) completed the consent form. 2,136 saliva kits were mailed to pts and 1,523 saliva samples were sent in (71%). 408 blood kits were mailed to pts and 175 blood samples have been received for cfDNA analysis. To date, we have obtained medical records from 311 pts and 190 tumors from 127 pts. In 10/2017, all data generated so far were publicly released on cbioportal.org, including WES for 103 tumors from 78 pts linked to clinical data including pathology (22 elements), medical record abstraction including all treatments and timelines/durations (67 elements), and patient-reported data (11 elements). 81% of biopsies included in this release were from the breast and 19% from metastatic sites. 75% were obtained prior to any therapy, 24% following therapy. New data will be released 4/2018 and every six months thereafter, as they are generated. Additional patient-reported data, including treatments, side effects, quality of life, family history, pregnancies, and sites of metastasis, will also be collected and shared. In summary, a patient-driven approach enabled rapid identification of thousands of MBC pts willing to share samples and clinical data. Remote acquisition of medical records, saliva, blood, and tumor tissue for pts across the U.S. is feasible. This shared clinico-genomic database should enable research in MBC and may serve as a model for patient-driven research in other cancers. Citation Format: Nikhil Wagle, Corrie Painter, Elana Anastasio, Michael Dunphy, Mary McGillicuddy, Rachel Stoddard, Esha Jain, Dewey Kim, Simona Di Lascio, Brett N. Tompson, Sara Balch, Beena Thomas, Priti Kumari, Shawn Johnson, Jamie Holloway, Ofir Cohen, Erik H. Knelson, Katie Larkin, Sam Pollock, Alicia Wong, Samira Bahl, Simone Maiwald, Andrew Zimmer, Esme O. Baker, Jen Hendry Lapan, Scott Sutherland, Scott Sassone, Viktor Adalsteinsson, Eric S. Lander, Todd R. Golub. The Metastatic Breast Cancer Project: Partnering with patients to accelerate progress in cancer research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5371.
- Published
- 2018
- Full Text
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