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This third edition of Braun and Murdoch's bestselling textbook now includes discussion of the use and design principles of the tidyverse packages in R, including expanded coverage of ggplot2, and R Markdown. The expanded simulation chapter introduces the Box–Muller and Metropolis–Hastings algorithms. New examples and exercises have been added throughout. This is the only introduction you'll need to start programming in R, the computing standard for analyzing data. This book comes with real R code that teaches the standards of the language. Unlike other introductory books on the R system, this book emphasizes portable programming skills that apply to most computing languages and techniques used to develop more complex projects. Solutions, datasets, and any errata are available from www.statprogr.science. Worked examples - from real applications - hundreds of exercises, and downloadable code, datasets, and solutions make a complete package for anyone working in or learning practical data science.
The rising popularity of hobbyist metal detecting has provided early medieval scholars with various important new datasets, not least the concentrations of metalwork commonly known as ‘productive sites’. Awareness of these foci derives almost exclusively from archaeological evidence, yet they continue to be interpreted through a documentary lens, and are frequently labelled ‘monasteries’. Using the recently discovered site of Little Carlton, Lincolnshire, as a case study, it is argued that comprehension of metal-rich sites is significantly furthered by turning to archaeologically-orientated research agendas and terminologies. As a consequence, seventh- to ninth-century Little Carlton can be understood as one element of a high-status ‘meshwork’ within early medieval East Lindsey, in which elite power was articulated in the landscape through a number of contemporary centres. On site, archaeology indicates the presence of occupation, burial and craft working, but shows that highly symbolic indigenous practices were taking place too, including intentional deposition into a naturally-occurring pond. Evidence for activity either side of the seventh to ninth centuries also stresses the importance of long-term trajectories in shaping the character of places previously celebrated for their finds-rich phases alone.
Sleep and circadian timing shifts later during adolescence, conflicting with early school start times, and resulting in circadian misalignment. Although circadian misalignment has been linked to depression, substance use, and altered reward function, a paucity of experimental studies precludes the determination of causality. Here we tested, for the first time, whether experimentally-imposed circadian misalignment alters the neural response to monetary reward and/or response inhibition.
Healthy adolescents (n = 25, ages 13–17) completed two in-lab sleep schedules in counterbalanced order: An ‘aligned’ condition based on typical summer sleep-wake times (0000–0930) and a ‘misaligned’ condition mimicking earlier school year sleep-wake times (2000–0530). Participants completed morning and afternoon functional magnetic resonance imaging scans during each condition, including monetary reward (morning only) and response inhibition (morning and afternoon) tasks. Total sleep time and circadian phase were assessed via actigraphy and salivary melatonin, respectively.
Bilateral ventral striatal (VS) activation during reward outcome was lower during the Misaligned condition after accounting for the prior night's total sleep time. Bilateral VS activation during reward anticipation was lower during the Misaligned condition, including after accounting for covariates, but did not survive correction for multiple comparisons. Right inferior frontal gyrus activation during response inhibition was lower during the Misaligned condition, before and after accounting for total sleep time and vigilant attention, but only during the morning scan.
Our findings provide novel experimental evidence that circadian misalignment analogous to that resulting from school schedules may have measurable impacts on healthy adolescents' reward processing and inhibition of prepotent responses.
Evidence is limited on how to synthesize and incorporate the views of stakeholders into a multisite pragmatic trial and how much academic teams change study design and protocol in response to stakeholder input. This qualitative study describes how stakeholders contributed to the design, conduct, and dissemination of findings of a multisite pragmatic clinical trial, the COMprehensive Post-Acute Stroke Services (COMPASS) Study. We engaged stakeholders as integral research partners by embedding them in study committees and community resource networks that supported local sites. Data stemmed from formal focus groups and continuous participation in working groups. Guided by Grounded Theory, we extracted themes from focus group and meeting notes. These were discussed as a team and with other stakeholder groups for feasibility. A consensus approach was used. Stakeholder input changed many aspects of the study including: the care model that treated stroke as a chronic condition after hospital discharge, training for hospital-based providers who often lacked awareness of the barriers to recovery that patients face, support for caregivers who were essential for stroke patients’ recovery, and for community-based health and social service providers whose services can support recovery yet often go underutilized. Stakeholders brought value to both pragmatic research and health service delivery. Future studies should test the impact of elements of study implementation informed by stakeholders vs those that are not.
Weed control of paraquat can be erratic and may be attributable to differing species sensitivity and/or environmental factors for which minor guidance is available on commercial labels. Therefore, the objectives of this research were to quantify selectivity of paraquat across select weed species and the influence of environmental factors. Experiments were performed under controlled conditions in the greenhouse and growth chamber. Compared with purple deadnettle (dose necessary to reduce shoot biomass by 50% = 39 g ai ha−1), waterhemp, Palmer amaranth, giant ragweed, and horseweed were 4.9, 3.3, 1.9, and 1.3 times more sensitive to paraquat, respectively. The injury progression rate over 3 d after treatment (DAT) was a more accurate predictor of final efficacy at 14 DAT than the lag phase until symptoms first appeared. For example, at the 17.5 g ha−1 dose, the injury rate of waterhemp and Palmer amaranth was, on average, 3.6 times greater than that of horseweed and purple deadnettle. The influence of various environmental factors on paraquat efficacy was weed specific. Applications made at sunrise improved control of purple deadnettle over applications at solar noon or sunset. Lower light intensities (200 or 600 μmol m−2 s−1) surrounding the time of application improved control of waterhemp and horseweed more than 1,000 μmol m−2 s−1. Day/night temperatures of 27/16 C improved horseweed and purple deadnettle control compared with day/night temperatures of 18/13 C. Though control was positively associated with injury rates in the application time of day and temperature experiments, a negative relationship was observed for waterhemp in the light-intensity experiment. Thus, although there are conditions that enhance paraquat efficacy, the specific target species must also be considered. These results advocate paraquat dose recommendations, currently based on weed height, be expanded to address sensitivity differences among weeds. Moreover, these findings contrast with paraquat labels stating temperatures of 13 C or lower do not reduce paraquat efficacy.
We report key learning from the public health management of the first two confirmed cases of COVID-19 identified in the UK. The first case imported, and the second associated with probable person-to-person transmission within the UK. Contact tracing was complex and fast-moving. Potential exposures for both cases were reviewed, and 52 contacts were identified. No further confirmed COVID-19 cases have been linked epidemiologically to these two cases. As steps are made to enhance contact tracing across the UK, the lessons learned from earlier contact tracing during the country's containment phase are particularly important and timely.
Turbulent fluxes make a substantial and growing contribution to the energy balance of ice surfaces globally, but are poorly constrained owing to challenges in estimating the aerodynamic roughness length (z0). Here, we used structure from motion (SfM) photogrammetry and terrestrial laser scanning (TLS) surveys to make plot-scale 2-D and 3-D microtopographic estimations of z0 and upscale these to map z0 across an ablating mountain glacier. At plot scales, we found spatial variability in z0 estimates of over two orders of magnitude with unpredictable z0 trajectories, even when classified into ice surface types. TLS-derived surface roughness exhibited strong relationships with plot-scale SfM z0 estimates. At the glacier scale, a consistent increase in z0 of ~0.1 mm d−1 was observed. Space-for-time substitution based on time since surface ice was exposed by snow melt confirmed this gradual increase in z0 over 60 d. These measurements permit us to propose a scale-dependent temporal z0 evolution model where unpredictable variability at the plot scale gives way to more predictable changes of z0 at the glacier scale. This model provides a critical step towards deriving spatially and temporally distributed representations of z0 that are currently lacking in the parameterisation of distributed glacier surface energy balance models.
Research Electronic Data Capture (REDCap) is a secure, web-based electronic data capture application for building and managing surveys and databases. It can also be used for study management, data transfer, and data export into a variety of statistical programs. REDcap was developed and supported by the National Center for Advancing Translational Sciences Program and is used in over 3700 institutions worldwide. It can also be used to track and measure stakeholder engagement, an integral element of research funded by the Patient-Centered Outcomes Research Institute (PCORI). Continuously and accurately tracking and reporting on stakeholder engagement activities throughout the life of a PCORI-funded trial can be challenging, particularly in complex trials with multiple types of engagement.
In this paper, we show our approach for collecting and capturing stakeholder engagement activities using a shareable REDCap tool in one of the PCORI’s first large pragmatic clinical trials (the Comprehensive Post-Acute Stroke Services) to inform other investigators planning cluster-randomized pragmatic trials. Benefits and challenges are highlighted for researchers seeking to consistently monitor and measure stakeholder engagement.
We describe how REDCap can provide a time-saving approach to capturing how stakeholders engage in a PCORI-funded study and reporting how stakeholders influenced the study in progress reports back to PCORI.
Forty years ago, Knut Fladmark (1979) argued that the Pacific Coast offered a viable alternative to the ice-free corridor model for the initial peopling of the Americas—one of the first to support a “coastal migration theory” that remained marginal for decades. Today, the pre-Clovis occupation at the Monte Verde site is widely accepted, several other pre-Clovis sites are well documented, investigations of terminal Pleistocene subaerial and submerged Pacific Coast landscapes have increased, and multiple lines of evidence are helping decode the nature of early human dispersals into the Americas. Misconceptions remain, however, about the state of knowledge, productivity, and deglaciation chronology of Pleistocene coastlines and possible technological connections around the Pacific Rim. We review current evidence for several significant clusters of early Pacific Coast archaeological sites in North and South America that include sites as old or older than Clovis. We argue that stemmed points, foliate points, and crescents (lunates) found around the Pacific Rim may corroborate genomic studies that support an early Pacific Coast dispersal route into the Americas. Still, much remains to be learned about the Pleistocene colonization of the Americas, and multiple working hypotheses are warranted.
The COllaborative project of Development of Anthropometrical measures in Twins (CODATwins) project is a large international collaborative effort to analyze individual-level phenotype data from twins in multiple cohorts from different environments. The main objective is to study factors that modify genetic and environmental variation of height, body mass index (BMI, kg/m2) and size at birth, and additionally to address other research questions such as long-term consequences of birth size. The project started in 2013 and is open to all twin projects in the world having height and weight measures on twins with information on zygosity. Thus far, 54 twin projects from 24 countries have provided individual-level data. The CODATwins database includes 489,981 twin individuals (228,635 complete twin pairs). Since many twin cohorts have collected longitudinal data, there is a total of 1,049,785 height and weight observations. For many cohorts, we also have information on birth weight and length, own smoking behavior and own or parental education. We found that the heritability estimates of height and BMI systematically changed from infancy to old age. Remarkably, only minor differences in the heritability estimates were found across cultural–geographic regions, measurement time and birth cohort for height and BMI. In addition to genetic epidemiological studies, we looked at associations of height and BMI with education, birth weight and smoking status. Within-family analyses examined differences within same-sex and opposite-sex dizygotic twins in birth size and later development. The CODATwins project demonstrates the feasibility and value of international collaboration to address gene-by-exposure interactions that require large sample sizes and address the effects of different exposures across time, geographical regions and socioeconomic status.
The bulk of people we can now be assured, were content with something that hardly deserves a better title than that of a hovel […] in such cabins, with bare head room, amid a filthy litter of broken bones, of food and shattered pottery […] lived the Anglo-Saxons (Leeds 1936: 25–26). This quote from E.T. Leeds, a pioneer of Anglo-Saxon archaeology during the first half of the twentieth century, was inspired by his excavation of settlement remains at Sutton Courtenay, then in Berkshire. Leeds's excavations were actually a breakthrough moment, resulting in the first identification of early medieval settlement structures other than those associated with ecclesiastical sites. In spite of this, the frustration and disappointment with the character and quality of the Sutton Courtenay site are all too apparent in Leeds's assessment. As an expert in Anglo-Saxon artwork, how could he reconcile the skill and craft of fine metalwork, with the ephemeral and impoverished settlement with which he was now dealing? Likewise, where were the great charismatic halls of monumental construction that populated such literary sources as Beowulf? The excavation of the graves of Sutton Hoo, two years after investigations at Sutton Courtney came to a close, served only to amplify the disparity between settlement and burial archaeology—put simply, burials were viewed as richer, grander and far more interesting.
This volume covers aspects of sudden infant and early childhood death and deals with the changes that have occurred over time with the definitions of SIDS, SUDI and SUDIC. It will be indispensable for SIDS researchers, SIDS organisations, paediatric pathologists, forensic pathologists, paediatricians, families, residents in training programs involving paediatrics, physicians, lawyers, law enforcement officials, and other experts in the field. The text will be indispensable for SIDS researchers, SIDS organisations, paediatric pathologists, forensic pathologists, paediatricians and families, in addition to residents in training programs that involve paediatrics. It will also be of use to other physicians, lawyers and law enforcement officials who deal with these cases, and should be a useful addition to all medical examiner/forensic, paediatric and pathology departments, hospital and university libraries on a global scale. Given the marked changes that have occurred in the epidemiology and understanding of SIDS and sudden death in the very young over the past decade, a text such as this is very timely and is also urgently needed.
Roger W Byard, School of Medicine, The University of Adelaide, Adelaide, Australia and Florey Institute of Neuroscience and Mental Health, Victoria, Australia,
Jhodie R Duncan, School of Medicine, The University of Adelaide, Adelaide, Australia and Florey Institute of Neuroscience and Mental Health, Victoria, Australia
There has been a great need for a text such as this for some time now, with the last general book on sudden infant death syndrome (SIDS) published over a decade and a half ago, in 2001. Since that time many significant developments have occurred in our understanding of sudden and unexplained deaths in pediatrics, ranging from updated definitions with increased emphasis on mandatory death scene investigations to highquality scientific work examining the role of neurotransmitter abnormalities in the brain. The issue of sudden death in toddlers over a year of age (SUDC) has also become an area of study, with a clearer understanding of the usefulness of the more general term sudden and unexpected death in infancy (SUDI). The Triple Risk Model has stood the test of time and has facilitated the integration of laboratory-based work with epidemiological risk factors. Many fringe theories have fortunately finally fallen into well-deserved historical obscurity along with odd entities such as status thymicolymphaticus.
As the reader will quickly realise, the text is an extremely eclectic mix of chapters written by experts in their respective fields. Important chapters deal with the history of SIDS, the role of parent organizations in promoting bereavement support, the very raw issue of parental grief, and research into the underlying mechanisms associated with SUDI. The later chapters focus variably on processes and locations, particularly within the brain, the roles of which in SUDI are being more clearly teased out and understood.
Of necessity there is some repetition in chapters, as SIDS and SUDI in general are a heterogeneous mix of mechanisms and processes that cannot be boxed into discrete areas. While this has sometimes led to different authors taking somewhat contradictory positions on certain subjects, it merely reflects the complexity and reality of the SIDS/SUDI arena today.
The editors hope that this text will have enabled experts from a variety of backgrounds to explain and elaborate on their particular areas of study and investigation. It will also serve as a summary of SIDS, SUDI, and SUDC as we know them today, and will lay the foundation for further exciting discoveries. As such, hopefully this book will provide an invaluable resource for individuals across many arenas, including parents, clinicians, medical examiners, and researchers. We are very close to understanding why SIDS/ SUDI occurs: our next challenge is to prevent these tragic deaths from ever happening.
Jhodie R Duncan, School of Medicine, The University of Adelaide, Adelaide, Australia and Florey Institute of Neuroscience and Mental Health, Victoria, Australia,
Roger W Byard, School of Medicine, The University of Adelaide, Adelaide, Australia and Florey Institute of Neuroscience and Mental Health, Victoria, Australia
The term sudden infant death syndrome (SIDS) was first proposed in 1969 in order to focus attention on a subgroup of infants with similar clinical features whose deaths occurred unexpectedly in the postnatal period (1). Today the definition of SIDS refers to death in a seemingly healthy infant younger than 1 year of age whose death remains unexplained after a thorough case investigation including a complete autopsy, review of medical and clinical history, and death scene investigation (2). SIDS is typically associated with a sleep period (3) with death presumed to have occurred during sleep itself or in the transition between sleep and waking (4). This led to application of the terms “cot” or “crib” death; however, these terms are rarely used today. Furthermore, while the definition is inclusive of infants up to 1 year of age, approximately 95% of SIDS deaths occur in the first six months of life with a peak incidence in infants aged between 2 to 4 months (5). While there are distinctive features associated with the syndrome there are no diagnostic features that can be attributed to a SIDS death. Indeed, application of the term relies on a process of elimination and when no known cause of death or contributing factors can be determined, the term SIDS is usually applied. Thus, while the debate continues regarding the definition and use of the term SIDS, and no one definition has been universally accepted, one certainty persists, and that is that SIDS still remains a diagnosis of exclusion (1).
Sudden death in a seemingly healthy infant during sleep is not a phenomenon of modern times, with cases being recorded throughout history for thousands of years. Indeed, one of the first cases is mentioned in the Bible (1 Kings 3:19). However, these deaths have generally been attributed to overlaying, as it was common practice to sleep in the same bed as a child. Indeed, the death of an infant by “overlay” was considered such an issue that by the seventh century the event was a punishable offence (6), with the introduction of a “protective” wooden arcuccio for infants to sleep in during the 18th century in Europe with severe penalties if the infant died in a co-sleeping arrangement and the frame was not used (7).