Plagued by a cryptic clock: Insight and issues from the global phylogeny of Yersinia pestis

2021 ◽  
Author(s):  
Katherine Eaton ◽  
Leo Featherstone ◽  
Sebastian Duchene ◽  
Ann Carmichael ◽  
Nükhet Varlık ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Future Research ◽  
Human Populations ◽  
Data Sets ◽  
New Approach ◽  
Phylogenetic Studies ◽  
Molecular Clock Model ◽  
Geographic Origins ◽  
Divergence Dates ◽  
Causative Bacterium

Abstract Plague has an enigmatic history as a zoonotic pathogen. This potentially devastating infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium, Yersinia pestis, regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of Y. pestis using 601 genome sequences sampled globally. We perform a detailed Bayesian evaluation of temporal signal in subsets of these data and demonstrate that a Y. pestis-wide molecular clock model is unstable. To resolve this, we devised a new approach in which each Y. pestis population was assessed independently. This enabled us to recover significant temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics. Finally, we identify key historical data sets that can be used in future research, which will complement the strengths and mitigate the weaknesses of genomic data.

scholarly journals Culture Process and the Interpretation of Radiocarbon Data

Radiocarbon ◽  
2017 ◽  
Vol 60 (2) ◽  
pp. 453-467 ◽  
Author(s):  
Jacob Freeman ◽  
David A Byers ◽  
Erick Robinson ◽  
Robert L Kelly
Keyword(s):  
Time Series ◽  
Energy Consumption ◽  
Population Size ◽  
Population Change ◽  
Future Research ◽  
Human Populations ◽  
Data Sets ◽  
Economic Complexity ◽  
Using Data ◽  
Outstanding Question

AbstractOver the last decade, archaeologists have turned to large radiocarbon (14C) data sets to infer prehistoric population size and change. An outstanding question concerns just how direct of an estimate 14C dates are for human populations. In this paper we propose that 14C dates are a better estimate of energy consumption, rather than an unmediated, proportional estimate of population size. We use a parametric model to describe the relationship between population size, economic complexity and energy consumption in human societies, and then parametrize the model using data from modern contexts. Our results suggest that energy consumption scales sub-linearly with population size, which means that the analysis of a large 14C time-series has the potential to misestimate rates of population change and absolute population size. Energy consumption is also an exponential function of economic complexity. Thus, the 14C record could change semi-independent of population as complexity grows or declines. Scaling models are an important tool for stimulating future research to tease apart the different effects of population and social complexity on energy consumption, and explain variation in the forms of 14C date time-series in different regions.

scholarly journals Human Prehistoric Demography Revealed by the Polymorphic Pattern of CpG Transitions

2020 ◽  
Vol 37 (9) ◽  
pp. 2691-2698 ◽  
Author(s):  
Xiaoming Liu
Keyword(s):  
Population Dynamics ◽  
Population Expansion ◽  
Future Research ◽  
Human Populations ◽  
Neolithic Revolution ◽  
Cpg Sites ◽  
Hunting And Gathering ◽  
Genome Wide ◽  
Polymorphic Pattern ◽  
Improved Model

Abstract The prehistoric demography of human populations is an essential piece of information for illustrating our evolution. Despite its importance and the advancement of ancient DNA studies, our knowledge of human evolution is still limited, which is also the case for relatively recent population dynamics during and around the Holocene. Here, we inferred detailed demographic histories from 1 to 40 ka for 24 population samples using an improved model-flexible method with 36 million genome-wide noncoding CpG sites. Our results showed many population growth events that were likely due to the Neolithic Revolution (i.e., the shift from hunting and gathering to agriculture and settlement). Our results help to provide a clearer picture of human prehistoric demography, confirming the significant impact of agriculture on population expansion, and provide new hypotheses and directions for future research.

Survey Data Quality in Analyzing Harmonized Indicators of Protest Behavior: A Survey Data Recycling Approach

2021 ◽  
pp. 000276422110216
Author(s):  
Kazimierz M. Slomczynski ◽  
Irina Tomescu-Dubrow ◽  
Ilona Wysmulek
Keyword(s):  
Data Processing ◽  
Data Quality ◽  
Survey Data ◽  
A Priori ◽  
Data Sets ◽  
New Approach ◽  
Survey Quality ◽  
Survey Error ◽  
Ex Post ◽  
The Impact

This article proposes a new approach to analyze protest participation measured in surveys of uneven quality. Because single international survey projects cover only a fraction of the world’s nations in specific periods, researchers increasingly turn to ex-post harmonization of different survey data sets not a priori designed as comparable. However, very few scholars systematically examine the impact of the survey data quality on substantive results. We argue that the variation in source data, especially deviations from standards of survey documentation, data processing, and computer files—proposed by methodologists of Total Survey Error, Survey Quality Monitoring, and Fitness for Intended Use—is important for analyzing protest behavior. In particular, we apply the Survey Data Recycling framework to investigate the extent to which indicators of attending demonstrations and signing petitions in 1,184 national survey projects are associated with measures of data quality, controlling for variability in the questionnaire items. We demonstrate that the null hypothesis of no impact of measures of survey quality on indicators of protest participation must be rejected. Measures of survey documentation, data processing, and computer records, taken together, explain over 5% of the intersurvey variance in the proportions of the populations attending demonstrations or signing petitions.

scholarly journals The concept of neutrality: a new approach

2019 ◽  
Vol 76 (1) ◽  
pp. 333-353 ◽  
Author(s):  
Stephen Macdonald ◽  
Briony Birdi
Keyword(s):  
Literature Review ◽  
Design Methodology ◽  
Information Science ◽  
Social Institutions ◽  
Future Research ◽  
Library And Information Science ◽  
New Approach ◽  
Content Type ◽  
Normative Framework ◽  
Contextual Awareness

Purpose Neutrality is a much debated value in library and information science (LIS). The “neutrality debate” is characterised by opinionated discussions in contrasting contexts. The purpose of this paper is to fill a gap in the literature by bringing these conceptions together holistically, with potential to deepen understanding of LIS neutrality. Design/methodology/approach First, a literature review identified conceptions of neutrality reported in the LIS literature. Second, seven phenomenographic interviews with LIS professionals were conducted across three professional sectors. To maximise variation, each sector comprised at least one interview with a professional of five or fewer years’ experience and one with ten or more years’ experience. Third, conceptions from the literature and interviews were compared for similarities and disparities. Findings In four conceptions, each were found in the literature and interviews. In the literature, these were labelled: “favourable”, “tacit value”, “social institutions” and “value-laden profession”, whilst in interviews they were labelled: “core value”, “subservient”, “ambivalent”, and “hidden values”. The study’s main finding notes the “ambivalent” conception in interviews is not captured by a largely polarised literature, which oversimplifies neutrality’s complexity. To accommodate this complexity, it is suggested that future research should look to reconcile perceptions from either side of the “neutral non-neutral divide” through an inclusive normative framework. Originality/value This study’s value lies in its descriptive methodology, which brings LIS neutrality together in a holistic framework. This framework brings a contextual awareness to LIS neutrality lacking in previous research. This awareness has the potential to change the tone of the LIS neutrality debate.

Recent and Planned Developments of the Program OxCal

Radiocarbon ◽  
2013 ◽  
Vol 55 (2) ◽  
pp. 720-730 ◽  
Author(s):  
Christopher Bronk Ramsey ◽  
Sharen Lee
Keyword(s):  
Statistical Analysis ◽  
Statistical Methods ◽  
Software Package ◽  
Model Averaging ◽  
Data Sets ◽  
Radiocarbon Dates ◽  
New Approach ◽  
New Models ◽  
Multiphase Models ◽  
Deposition Models

OxCal is a widely used software package for the calibration of radiocarbon dates and the statistical analysis of 14C and other chronological information. The program aims to make statistical methods easily available to researchers and students working in a range of different disciplines. This paper will look at the recent and planned developments of the package. The recent additions to the statistical methods are primarily aimed at providing more robust models, in particular through model averaging for deposition models and through different multiphase models. The paper will look at how these new models have been implemented and explore the implications for researchers who might benefit from their use. In addition, a new approach to the evaluation of marine reservoir offsets will be presented. As the quantity and complexity of chronological data increase, it is also important to have efficient methods for the visualization of such extensive data sets and methods for the presentation of spatial and geographical data embedded within planned future versions of OxCal will also be discussed.

Dynamic capabilities vs. innovation capability: are they related?

2014 ◽  
Vol 21 (3) ◽  
pp. 368-384 ◽  
Author(s):  
Lidija Breznik ◽  
Robert D. Hisrich
Keyword(s):  
Literature Review ◽  
Design Methodology ◽  
Dynamic Capabilities ◽  
Dynamic Capability ◽  
Future Research ◽  
Innovation Capability ◽  
New Approach ◽  
Content Type ◽  
New Research ◽  
The Relationship

Purpose – The purpose of this paper is to provide insights into the relationship between dynamic capabilities and innovation capabilities. It links dynamic capability with innovation capability and indicates the ways they can be related. Design/methodology/approach – The relationships between dynamic and innovation capability were investigated through a systematic literature review. Findings – The review indicates that common characteristics exist between of the both fields, which demonstrate six relationships. Additionally, findings show some inconsistencies and even contradictions. Originality/value – In this paper, the authors have compared dynamic capabilities, a relatively new approach in the field of strategic management, with innovation capabilities, a widely recognised crucial domain for sustained competitiveness. Since both areas address issues that are essential to today's environment, future research should seek to clarify both concepts, by undertaking some new research and developing comprehensive and unambiguous framework.

Quasi-2D inversion of DCR and TDEM data for shallow investigations

Geophysics ◽  
2011 ◽  
Vol 76 (4) ◽  
pp. F239-F250 ◽  
Author(s):  
Fernando A. Monteiro Santos ◽  
Hesham M. El-Kaliouby
Keyword(s):  
Joint Inversion ◽  
Synthetic Data ◽  
Data Sets ◽  
Complex Environments ◽  
Inversion Algorithm ◽  
2D Inversion ◽  
New Approach ◽  
Earth Models ◽  
Time Domain Electromagnetic ◽  
Inversion Techniques

Joint or sequential inversion of direct current resistivity (DCR) and time-domain electromagnetic (TDEM) data commonly are performed for individual soundings assuming layered earth models. DCR and TDEM have different and complementary sensitivity to resistive and conductive structures, making them suitable methods for the application of joint inversion techniques. This potential joint inversion of DCR and TDEM methods has been used by several authors to reduce the ambiguities of the models calculated from each method separately. A new approach for joint inversion of these data sets, based on a laterally constrained algorithm, was found. The method was developed for the interpretation of soundings collected along a line over a 1D or 2D geology. The inversion algorithm was tested on two synthetic data sets, as well as on field data from Saudi Arabia. The results show that the algorithm is efficient and stable in producing quasi-2D models from DCR and TDEM data acquired in relatively complex environments.

Social Norms Sustaining Intimate Partner Violence: A Systematic Review of Methodologies for Proxy Measures

2021 ◽  
pp. 152483802110131
Author(s):  
Ilana Seff
Keyword(s):  
Systematic Review ◽  
Intimate Partner Violence ◽  
Social Norms ◽  
Partner Violence ◽  
Evidence Base ◽  
Intimate Partner ◽  
Future Research ◽  
Data Sets ◽  
Boolean Search ◽  
The Many

In light of the many robust quantitative data sets that include information on attitudes and behaviors related to intimate partner violence (IPV), and in an effort to expand the evidence base around social norms and IPV, many researchers construct proxy measures of norms within and across groups embedded in the data. While this strategy has become increasingly popular, there is no standardized approach for assessing and constructing these norm proxies, and no review of these approaches has been undertaken to date. This study presents the results of a systematic review of methods used to construct quantitative proxy measures for social norms related to IPV. PubMed, Embase, Popline, and Scopus, and PsycINFO were searched using Boolean search techniques. Inclusion criteria comprised studies published since 2000 in English that either (i) examined a norm proxy related to gender or IPV or (ii) analyzed the relationship between a norm proxy and perpetration of, experiences of, or attitudes toward IPV. Studies that employed qualitative methods or that elicited direct measures of descriptive or injunctive norms were not included. Twenty-six studies were eligible for review. Evidence from this review highlights inconsistencies in how proxies are constructed, how they are assessed to ensure valid representation of norms, and how researchers acknowledge their respective method’s limitations. Key processes and reflections employed by some of the studies are identified and recommended for future research inquiries.

scholarly journals Facing disruptive technologies: aligning purchasing maturity to contingencies

2019 ◽  
Vol 24 (1) ◽  
pp. 147-169 ◽  
Author(s):  
Britta Søgaard ◽  
Heather Dawn Skipworth ◽  
Michael Bourlakis ◽  
Carlos Mena ◽  
Richard Wilding
Keyword(s):  
Strategic Alignment ◽  
Future Research ◽  
Research Directions ◽  
Company Strategy ◽  
New Approach ◽  
Content Type ◽  
Disruptive Technologies ◽  
Future Research Directions ◽  
Exploratory Case Studies ◽  
Selection Of

PurposeThis paper aims to explore how purchasing could respond to disruptive technologies by examining the assumptions underlying purchasing strategic alignment and purchasing maturity through a contingency lens.Design/methodology/approachThis study uses a systematic review across purchasing maturity and purchasing strategic alignment literature. This is supplemented with exploratory case studies to include practitioners’ views.FindingsThis research demonstrates that neither purchasing maturity nor purchasing strategic alignment are suitable approaches to respond to disruptive technologies. Purchasing maturity does not allow purchasing managers to select relevant practices. It also shows no consideration of any contingencies, which practitioners highlight as important for the selection of practices. Purchasing strategic alignment includes the company strategy as a contingency but does not provide any practices to choose from. It does not include any other contextual contingencies considered important by practitioners. The findings indicate that linking the two research streams may provide a more suitable approach to responding to disruptive technologies.Research limitations/implicationsThis research demonstrates the requirement to develop a new approach to responding to disruptive technologies, by linking purchasing maturity and purchasing strategic alignment to contextual contingencies. This is a currently unexplored approach in academic literature, which refutes the generally accepted premise that higher maturity unilaterally supports a better positioning towards technological disruption. This research also highlights a requirement for practitioners to shift their approach to “best practices”.Originality/valueThis is the first research to systematically review the relationships between purchasing maturity and purchasing strategic alignment. It adds to contingency theory by suggesting that purchasing maturity models can support the achievement of strategic alignment. Also, future research directions are suggested to explore these relationships.

scholarly journals A New Clone Sweeps Clean: the Enigmatic Emergence of Escherichia coli Sequence Type 131

2014 ◽  
Vol 58 (9) ◽  
pp. 4997-5004 ◽  
Author(s):  
Ritu Banerjee ◽  
James R. Johnson
Keyword(s):  
Escherichia Coli ◽  
Sequence Type ◽  
Rapid Expansion ◽  
Future Research ◽  
Content Type ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Phylogenetic Studies ◽  
Ecological Success

ABSTRACTEscherichia colisequence type 131 (ST131) is an extensively antimicrobial-resistantE. coliclonal group that has spread explosively throughout the world. Recent molecular epidemiologic and whole-genome phylogenetic studies have elucidated the fine clonal structure of ST131, which comprises multiple ST131 subclones with distinctive resistance profiles, including the (nested) H30, H30-R, and H30-Rx subclones. The most prevalent ST131 subclone, H30, arose from a single common fluoroquinolone (FQ)-susceptible ancestor containing allele 30 offimH(type 1 fimbrial adhesin gene). An early H30 subclone member acquired FQ resistance and launched the rapid expansion of the resulting FQ-resistant subclone, H30-R. Subsequently, a member of H30-R acquired the CTX-M-15 extended-spectrum beta-lactamase and launched the rapid expansion of the CTX-M-15-containing subclone within H30-R, H30-Rx. Clonal expansion clearly is now the dominant mechanism for the rising prevalence of both FQ resistance and CTX-M-15 production in ST131 and inE. coligenerally. Reasons for the successful dissemination and expansion of the key ST131 subclones remain undefined but may include increased transmissibility, greater ability to colonize and/or persist in the intestine or urinary tract, enhanced virulence, and more-extensive antimicrobial resistance compared to otherE. coli. Here we discuss the epidemiology and molecular phylogeny of ST131 and its key subclones, possible mechanisms for their ecological success, implications of their widespread dissemination, and future research needs.

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