Life History Analysis Research Articles

Abstract 218: The evolutionary history of 2,658 cancers

Abstract Cancer develops through a continuous process of somatic evolution. Whole genome sequencing provides a snapshot of the tumor genome at the point of sampling, however, the data can contain information that permits the reconstruction of a tumor's evolutionary past. Here, we apply such life history analyses on an unprecedented scale, to a set of 2,658 tumors spanning 39 cancer types. We estimated the timing of large chromosomal gains during tumor evolution, by comparing the rates of doubled to non-doubled point mutations within gained regions. Although we find that such events typically occur in the second half of clonal evolution, we also observe distinctive and early chromosomal gains in some cancer types, such as gains of chromosomes 7, 19 and 20 in glioblastoma, and isochromosome 17q in medulloblastoma. By integrating these results with the qualitative timing of individual driver mutations, we obtained an overall ranking, from early to late, of frequent somatic events per cancer type, which both identified novel patterns of tumor evolution, and incorporated additional detail into known models, such as the progression of APC-KRAS-TP53 in colorectal cancer proposed by Vogelstein and Fearon. To estimate how mutational processes acting on the tumor genome change over time, we classified mutations in each sample according to three broad time periods (early clonal, late clonal, and subclonal), and quantified the activity of mutational signatures in each period. Most mutational processes appear to remain remarkably constant, however, certain signatures show clear and consistent changes during clonal evolution. Particularly, mutational signatures associated with exposure to carcinogens, such as smoking and UV light, tend to decrease over time. In contrast, signatures associated with defective endogenous processes, such as APOBEC mutagenesis and defective double strand break repair, show an increase between early and late phases of tumor evolution. Making use of clock-like mutational signatures, we converted mutational time estimates for large events, such as whole genome duplication (WGD), and the emergence of the most recent common ancestor (MRCA), into real time estimates, which allowed us to combine our analyses into overall timelines of cancer evolution, per tumor type. For example, the typical timeline of ovarian adenocarcinoma development shows that early tumor evolution is characterized by mutations in TP53, and widespread genome instability, with WGD events taking place on average 8 years prior to diagnosis. In later stages of evolution, signatures of defective repair processes increase, and the MRCA emerges on average 1 year before diagnosis. Taken together, these data reveal the common and divergent evolutionary trajectories available to a cancer, which might be crucial in understanding specific tumor biology, and in providing new opportunities for early detection and cancer prevention. Citation Format: Clemency Jolly, Moritz Gerstung, Ignaty Leshchiner, Stefan C. Dentro, Santiago Gonzalez, Thomas J. Mitchell, Yulia Rubanova, Pavana Anur, Daniel Rosebrock, Kaixian Yu, Maxime Tarabichi, Amit Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vásquez-García, Kerstin Haase, Subhajit Sengupta, Geoff Macintyre, Salem Malikic, Nilgun Donmez, Dimitri G. Livitz, Mark Cmero, Jonas Demeulemeester, Steve Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C. Boutros, David D. Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, S Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Juan, Wenyi Wang, Quaid D. Morris, Paul T. Spellman, David C. Wedge, Peter Van Loo, PCAWG Evolution and Heterogeneity Working Group. The evolutionary history of 2,658 cancers [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 218.

Dynamics of body time, social time and life history at adolescence

Recent opposing trends towards earlier physical maturation and later social maturation present a conundrum of apparent biological-social mismatch. Here we use life history analysis from evolutionary ecology to identify forces that drive these shifts. Together with findings in developmental science, our life history analysis indicates that adolescence is a distinctive period for biological embedding of culture. Ethnographic evidence shows that mass education is a novel feature of the globalizing cultural configurations of adolescence, which are driven by transformations in labour, livelihood and lifestyle. Evaluation of the life history trade-offs and sociocultural ecologies that are experienced by adolescents may offer a practical basis for enhancing their development.

Occupancy time in sets of states for demographic models

As an individual moves through its life cycle, it passes through a series of states (age classes, size classes, reproductive states, spatial locations, health statuses, etc.) before its eventual death. The occupancy time in a state is the time spent in that state over the individual’s life. Depending on the life cycle description, the occupancy times describe different demographic variables, for example, lifetime breeding success, lifetime habitat utilisation, or healthy longevity.Models based on absorbing Markov chains provide a powerful framework for the analysis of occupancy times. Current theory, however, can completely analyse only the occupancy of single states, although the occupancy time in a set of states is often desired. For example, a range of sizes in a size-classified model, an age class in an age×stage model, and a group of locations in a spatial stage model are all sets of states.We present a new mathematical approach to absorbing Markov chains that extends the analysis of life histories by providing a comprehensive theory for the occupancy of arbitrary sets of states, and for other demographic variables related to these sets (e.g., reaching time, return time). We apply this approach to a matrix population model of the Southern Fulmar (Fulmarus glacialoides). The analysis of this model provides interesting insight into the lifetime number of breeding attempts of this species.Our new approach to absorbing Markov chains, and its implementation in matrix oriented software, makes the analysis of occupancy times more accessible to population ecologists, and directly applicable to any matrix population models.

Improving generation length estimates for the IUCN Red List.

The International Union for the Conservation of Nature (IUCN) Red List classifies species according to their risk of extinction, informing local to global conservation decisions. Here we look to advance the estimation of generation length, which is used as a time-scalar in the Red List as a way of accounting for differences in species’ life-histories. We calculated or predicted generation length for 86 species of antelope following the Rspan approach. We also tested the importance of both allometry (body-mass) and phylogeny (phylogenetic eigenvectors) as predictors of generation length within a Phylogenetic Eigenvector Map (PEM) framework. We then evaluated the predictive power of this PEM and two binning approaches, following a leave-one-out cross-validation routine. We showed that captive and wild longevity data are nonequivalent and that both body-mass and phylogeny are important predictors for generation length (body-mass explained 64% and phylogeny 36% of the partitioned explained variance). Plus, both the PEM, and the binning approach that included both taxonomic rank and body-mass, had good predictive power and therefore are suitable for extrapolating generation length to missing-data species. Therefore, based on our findings, we advise separating captive and wild data when estimating generation length, and considering the implications of wild and captive data more widely in life-history analyses. We also recommend that body-mass and phylogeny should be used in combination, preferably under a PEM framework (as it was less reliant on available reference species and more explicitly accounts for phylogenetic relatedness) or a binning approach if a PEM is not feasible, to extrapolate generation length to missing-data species. Overall, we provide a transparent, consistent and transferable workflow for improving the use of the Rspan method to calculate generation length for the IUCN Red List.

Interviewing interviewers: Collecting, analyzing and generalizing from occupational life histories of journalists

ABSTRACTThis article considers the implementation of the life history approach in the study of media professionals, based on an analysis of the occupational life histories of 77 active and former Israeli journalists. The article first discusses the decisions made throughout execution of the project. Next, it explores three key features of the dynamics of life history interviewing. Finally, the article examines the ways in which data gathered through life history interviews can be generalized.

Building Online Academic Community: Reputation Work on Twitter

Building Online Academic Community: Reputation Work on Twitter

The Catholic Church and Mexican American Social Mobility in the Postwar Midwest: Evidence from Life and Family Histories

Religious affiliation has long been recognized as a relevant factor among the variables that intervene in the integration of immigrants to American society. While previous generations of many predominantly Roman Catholic ethnic groups are thought to have been helped along their way to assimilation by strong institutional support from American Catholic church institutions, Latinos, and in particular Mexican Americans, are considered an exception. This study examines the role that inclusion in Catholic institutions played in the social mobility experienced by multigenerational families of Mexican immigrant origin in the Midwest during the decades between 1945 and 1975. The analysis of life and family histories collected from in-depth interviews with older second- and third-generation Mexican Americans illustrates how integration into urban Catholic institutions and communities was instrumental in the upward social mobility observed in many of their family trajectories during the postwar decades. In particular, access to parochial schools and other institutions in the Catholic educational system once provided the children and grandchildren of Mexican immigrants the forms of human and social capital that allowed many in that generation to attain social mobility.

First analysis of life history and season of death of a South American gomphothere

Excavations associated with wastewater treatment facilities in the Santiago Basin of Chile uncovered remains of an adult male Stegomastodon platensis in Pleistocene fluvial sediments. The specimen included a skull with both tusks still in their alveoli. A small sample block of dentin and cementum was excised from the right tusk for analysis of compositional and structural variation recorded in the sequence of dentin layers. The sample was analyzed using serial isotope assays, microCT, and measurement of dentin increments in thin sections. These procedures allowed us to recover life history information relating to the final four years of life. Analyses show seasonal variation in composition, density, and growth rate, permitting identification of years. MicroCT features appear to recur semiannually, which has not been observed previously in proboscidean tusks; these features are interpreted to correspond to the winter-spring boundary and some other aspect of environment or behavior recurring within each year. Average annual apposition of dentin within the tusk is 10.4 mm for complete years studied, suggesting that this individual was healthy leading up to the final year of life. Recurrent periods of low rate of apposition measured in weekly dentin increments that formed during the summer are interpreted as representing periods of musth. Using the location of microCT features, annual appositional thickness, and the pattern of weekly growth within the final year of life, we interpret the season of death for this individual as being within the early autumn.

Dinamika Pergelaran Jaran Kepang di Kota Malang dalam Perspektif Antropologi

The hobby-horse dance as known as jaran kepang, jathilan or kuda lumping is the one of dance art performance from Javanese. It also know as well in Malang City. Jaran kepang is one of entertainment art which have magic dramatical as the climax in the end of performance. It happend when one of the jaran kepang dancer was trance. This jaran kepang performance was invited and entertain folks to see and, it potentially to be carnaval event. Before they perform, called gebyak, the jaran kepang dancer do some rites to called their danyang or perewangan, and prepare sesaji or sandingan. The dynamic of art performance both personal or collective grup reflected the reality of traditional art performance in Indonesia. Today, this jaran kepang performance who had ritual function was changed by entertainment. Jaran kepang as culture is one of Javanese rural rites in selamatan or bersih desa moment. This paper was done by through context perspective with life history analysis. The aim of research is to see the social-cultural phenomena behind jaran kepang performance.

アイデンティティ・ポリティクスの中のアイデンティティ--被差別部落出身者の生活史調査を手がかりに

アイデンティティ・ポリティクスの中のアイデンティティ--被差別部落出身者の生活史調査を手がかりに

Applied Multiregional Demography: Migration and Population Redistribution

Book reviews Applied Multiregional Demography: Migration and Population Redistribution by Andrei Rogers Dordrecht, Heidelberg, London, New York: Springer 2016 ISBN 978-3-319-22317-9 Softcover $54.99, 114 pp. Reviewed by David A. Swanson Department of Sociology, University of California Riverside As I read through Applied Multiregional Demography: Migration and Population Redistribution, I repeatedly stopped to compare it to a book I read last by Frans Willekens: Multistate Analysis of Life Histories with R (for a review, see Swanson 2015). I find Willekens’ book much more innovative and useful than this book by Rogers. Willekens’ book is much more innovative because he discusses the data problems faced when considering multi-state demography, and he offers ways to overcome them (e.g., with micro-level data). Rogers however, focuses on the use of aggregated data and gives the problems associated with aggregated data very short shrift. Instead, he spends too much of the book complaining about the shortcomings of other approaches. Rogers also spends too much of the book on another complaint—the use of “net migration” as a concept in demo- graphic analysis. I find his complaint ironic given that in this book, there are 26 instances of the use of “natural increase,” which is itself a net measure, conceptually the same as net migration. Unlike “Requiem for the net migrant” (Rogers 1990), I have never run across a work by Rogers titled “Requiem for the natural increment.” I find the discussion of another construct also to be ironic. Toward the end of the book, Rogers notes that “double-entry bookkeeping” is conceptually similar to “multi-regional migration.” Of course it is! But what Rogers fails to bring into this discussion is the fact that for all businesses, including those who use double-entry bookkeeping and those that do not, the bottom line is “profit,” a measure that is conceptually the same as net migration. As is the case with the “natural increment,” I have never read something by Rogers entitled “Requiem for profit.” The actual examples of applications provided by Rogers in terms of multi-regional demography all involve large pieces of geography. There is nothing on small pieces of geography, such as counties, much less census tracts. Is this because of the difficulty encountered in getting the data needed to implement the multi-regional approach for small areas such as counties, census tracts, and the like? Even for the examples he provides, there is absolutely no mention of the issues affecting the validity and reliability of the data required. This is especially important in the US, where the problematic “long form” data needed to use a multi-regional perspective in the past have been replaced by the far more problematic “American Community Survey” data. As such, I find the examples to be not very useful. For what it does cover—large geographic areas, aggregate data, and a list of the problematic issues asso- ciated with net migration—the book is fine. However, if you are not interested in polemics on net migration, but are interested in actually implementing the multi-regional approach, especially for small geographic levels using micro-level data, I recommend instead the book by Willekens, who provides a much more innovative perspective, along with useful examples. In a similar vein, another useful example is found in the work of Wil- son (forthcoming), who uses the “multi-regional” perspective to effect dynamic changes in ethnic identity in a micro-simulation projection.

Ecology of the River Darter in Canadian Waters: Distribution, Relative Abundance, Life-History Traits, Diet, and Habitat Characteristics

The River Darter (Percina shumardi) is a native, rarely sampled fish that has been detected in relatively small numbers since the 1930s. It has a wide North American distribution, but little is known about the species biology and distribution across the Canadian portion of its range. We revisited many historic sampling locations and sampled additional areas to (i) confirm and update the distribution of River Darters in Canadian waters; (ii) assess relative abundance; (iii) update life history characteristics; (iv) collect diet information; and (v) identify characteristics of River Darter habitat. Since 1990, a total of 1032 River Darters were recorded from 29 waterbodies across three ecoregions. River Darters were observed in relatively high abundances in both the Saskatchewan-Nelson River and Southern Hudson Bay-James Bay ecoregions. While still extant in the Great Lakes-Upper St. Lawrence ecoregion, River Darters persist at low abundance. Life history analyses indicate similar maximum age (age 4) and growth (10 mm/year) to conspecific populations in the United States, while sex ratios are generally skewed towards female dominance. River Darter populations had high flexibility in habitat use and diet, using a range of flows and depths and a variety of seasonally available prey types.

Enriching the historiography of Religious Education: insights from oral life history

This article seeks to exemplify the extent to which oral life history research can enrich existing historiographies of English Religious Education (RE). Findings are reported from interviews undertaken with a sample of key informants involved in designing and/or implementing significant curriculum changes in RE in the 1960s and 1970s. The interviews provided insights into personal narratives and biographies that have been marginal to, or excluded from, the historical record. Thematic analysis of the oral life histories opened a window into the world of RE, specifically in relation to professional identity and practice, curriculum development and professional organisations, thereby exposing the operational dynamics of RE at an (inter-)personal and organisational level. The findings are framed by a series of methodological reflections. Overall, oral life histories are shown to be capable of revealing that which was previously hidden and which can be confirmed and contrasted with knowledge gleaned from primary documentary sources.

ADOLESCER E ADOECER NA PERSPECTIVA DE JOVEM E FAMÍLIA

Objective: This study seeks to highlight the experience of being an adolescent and concomitantly suffer a chronic condition. The study focuses on a teenager who experienced the establishment of a chronic condition due to concomitant aggravations -kidney disease and cancer during adolescence. Methodology: A comprehensive study modeled as a situational analysis of Life History was performed by means of in-depth interviews and field observations. The test subjects were a teenager suffering from a chronic disease and some of his family members. Results: By intertwining the realities of suffering a chronic condition and going through adolescence, we were able to understand the different stages of said chronic condition due to concomitant aggravations and its significant impact on the life of the teenager. Several conflicts emerged from this overlap of adolescence and disease due to physical, biological, behavioral, and social changes; which make such experience complex and unique. Conclusion: This understanding proves important to health professionals allowing them to holistically meet the needs of a developing human being and not only pay attention to the manifestations of the disease.

Perubahan Strategi Petani Dalam Memanfaatkan Lahan Pertanian

This thesis entitled "Changes in Farmer Strategies Utilizing Agricultural Land in Gumawang District of Belitang Ogan Komering Ulu Timur". This study reviewing the strategies of farmers in utilizing of agricultural land, farmers strategy changes that occurred in Gumawang, then the cause of the source of change strategies of farmer and forms of peasant farmers in utilizing the strategy of agricultural land in Gumawang District  of  Belitang  Ogan  Komering Ulu  Timur.  This study is a qualitative descriptive study. Determination of the informants in this study conducted in a "purposive". The technique of data analysis in this study was using Life History Analysis with used Construction of Day approaches. The results of this study indicate that (1) strategies or ways in which farmers in utilizing of agricultural land by making use of agricultural land to plant rice, then were using the tenuous to keep fish and plant crops. (2) there are two kinds of the changes in the strategy of farmers in agricultural utilize the land, namely the permanent changes and the temporary changes. (3) the source of the farmers’ strategy changes caused by factors of education,  science  and  technology,  economy, population growth, and the strategic location of the rice fields. (4) The forms of the strategy changes is a change that leads farmers to non-agricultural sectors or lead to the development of the city. Then in doing the study, researchers found some terms or the field findings, including: ngluku / mbajak, rendeng-gadu, tandur, ndaot, and legowo. The terms that finding in the field is a term contained in the terms used by the agricultural society of Java  that  was  around  in  Gumawang District  Belitang Ogan Komering Ulu Timur it self.

(Re)politicising and (re)positioning prevention: community mobilisations and AIDS prevention in the new AIDS era

An increasing focus on the relationship between AIDS prevalence and socio-economic inequality signals the need for a revaluation of the role of “politics” and “power” in AIDS prevention. This revaluation bears great significance when considering the future trajectories of the AIDS prevention efforts that target highly marginalised populations with high prevalence rates. An emphasis on intersecting forms of inequality has direct implications for the future of AIDS prevention practice. This study explores the experiences of participants, facilitators and local stakeholders applying the United Nations Development Programme (UNDP) Community Capacity Enhancement-Community Conversations (CCE-CC) approach to AIDS prevention in the Eastern Cape province of South Africa. It uses the political narrative analysis of life histories and semi-structured interviews as a means to interrogate the lived experiences of local actors participating in or influenced by this popularised form of community mobilisation used throughout sub-Saharan Africa. Findings suggest the need for a more explicit and intentional valuation for the intersection between the social and political determinants of health in programmes that use community mobilisation as prevention. They also signal a need to critically re-evaluate “community mobilisation” as an AIDS prevention tradition. Intersecting social and political power dynamics play a significant role in both opening up and constraining community mobilisation efforts. This paper proposes the need for a pedagogical turn to “deep organising” and “participatory forms of democracy”, as a necessary frontier for programmes working with highly marginalised populations with high prevalence rates. Programmes need to more explicitly support, protect, and advocate for the ability of affected communities to engage in political processes, discourse and long-term organising.

What shapes the anatomy of inventors? A life-history analysis of Swedish patent inventors

Using life-history interviews on a sample of Swedish inventors, this article studies seminal sociocultural factors and milieus that are critical for the development of inventive capacities. This approach allows the inventors to reflect on and describe the milieus, actors and events in their lives which they themselves believe have formed their inventive capacities. The main findings of the article are that the sociocultural milieus of early childhood, especially the educational backgrounds or skills of parents and grandparents, play an important role in shaping the anatomy of inventors. Further, the social milieu of an inventor’s final education, whether elementary school or university, is a seminal factor in the development of inventive creativity, given the importance of dedicated teachers, co-students and supervisors. Finally, egalitarian organizational structures in the workplace and a solid knowledge infrastructure are also important and influential factors. The study shows that the essence of these seminal milieus varies for different types of inventor, hence three descriptive ideal types of inventor are presented, namely the workshop inventor, the engineering inventor and the academic inventor.

Contextualizing a Korean Immigrant Woman’s life in Brazil - An Analysis of Life History and Brazilian Census -

Contextualizing a Korean Immigrant Woman’s life in Brazil - An Analysis of Life History and Brazilian Census -

Morphological observation, life history and rbcL gene sequence analysis of a new species, Grateloupia variata sp. nov. (Halymeniaceae, Rhodophyta) from Qingdao, China

ABSTRACTGrateloupia variata sp. nov. H. W. Wang (Halymeniaceae, Rhodophyta) is newly described from Qingdao, China. The results indicated that: (1) thalli are cartilaginous or gelatinous in texture; (2) thalli are constricted at the base with frequent proliferations; (3) the end portion of branches are irregular, wide, flat or ungulate, split; (4) the cortex is 50–80 μm thick, consisting of four to six layers of cells; the medulla is 10–15 μm long and 1–3 μm wide, consisting of densely and irregularly intertwined filaments; (5) six-celled carpogonial ampullae branched and five-celled auxiliary cell ampullae branched; they are of the typical Grateloupia-type; (6) tetraspores and carpospores grow directly into discoid crusts through initial cell division and are of the immediate discal type; (7) Grateloupia variata sp. nov. shows a typical triphasic life history with homotypic gametophytes, carposporophytes and tetrasporophytes, and a typical homotypic alternation of generations; and (8) the rbcL sequences show no pairwise divergence and the species form a small single monophyletic subclade within the Grateloupia clade. Morphological observations, life history and molecular analysis support G. variata as a new species.

Most outdoor malaria transmission by behaviourally-resistant Anopheles arabiensis is mediated by mosquitoes that have previously been inside houses.

BackgroundAnopheles arabiensis is stereotypical of diverse vectors that mediate residual malaria transmission globally, because it can feed outdoors upon humans or cattle, or enter but then rapidly exit houses without fatal exposure to insecticidal nets or sprays.MethodsLife histories of a well-characterized An. arabiensis population were simulated with a simple but process-explicit deterministic model and relevance to other vectors examined through sensitivity analysis.ResultsWhere most humans use bed nets, two thirds of An. arabiensis blood feeds and half of malaria transmission events were estimated to occur outdoors. However, it was also estimated that most successful feeds and almost all (>98 %) transmission events are preceded by unsuccessful attempts to attack humans indoors. The estimated proportion of vector blood meals ultimately obtained from humans indoors is dramatically attenuated by availability of alternative hosts, or partial ability to attack humans outdoors. However, the estimated proportion of mosquitoes old enough to transmit malaria, and which have previously entered a house at least once, is far less sensitive to both variables. For vectors with similarly modest preference for cattle over humans and similar ability to evade fatal indoor insecticide exposure once indoors, >80 % of predicted feeding events by mosquitoes old enough to transmit malaria are preceded by at least one house entry event, so long as ≥40 % of attempts to attack humans occur indoors and humans outnumber cattle ≥4-fold.ConclusionsWhile the exact numerical results predicted by such a simple deterministic model should be considered only approximate and illustrative, the derived conclusions are remarkably insensitive to substantive deviations from the input parameter values measured for this particular An. arabiensis population. This life-history analysis, therefore, identifies a clear, broadly-important opportunity for more effective suppression of residual malaria transmission by An. arabiensis in Africa and other important vectors of residual transmission across the tropics. Improved control of predominantly outdoor residual transmission by An. arabiensis, and other modestly zoophagic vectors like Anopheles darlingi, which frequently enter but then rapidly exit from houses, may be readily achieved by improving existing technology for killing mosquitoes indoors.