bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inbreeding in the last ruling dynasty of Portugal: The house of Braganza
Authors: Álvarez Gonzalo , Vilas Román , Ceballos Francisco C. , Carvalhal Hélder , Peters Timothy J. 
Published: December 2018

AbstractObjectivesTo determine whether: (1) there are high levels of inbreeding in a European royal dynasty that continues until the 20th century, and (2) whether inbreeding is negatively associated with pre‐reproductive survival and longevity.MethodsGenealogical information of all Braganza monarchs (1640‐1910) was used to compute the individual's inbreeding coefficient (F) and the coefficient of kinship (θ) of the marriage which were examined in relation to two life‐history traits.ResultsMean F of the monarchs was 0.0530, close to that corresponding to the progeny of first cousins (F = 0.0625). A statistically significant effect of maternal inbreeding on offspring longevity (P = 0.037) and a significant effect of individual's F on survival from birth to 10 years (P = 0.023) were detected.ConclusionsAnother European royal dynasty besides the Habsburgs had high levels of inbreeding, especially high during a period after the early modern age. The lineage showed evidence of inbreeding depression. Results support the hypothesis that an increase in maternal homozygosity affects the lifespan of the progeny.
The efficacy of whole human genome capture on ancient dental calculus and dentin
Authors: Ziesemer Kirsten A. , Ramos‐Madrigal Jazmín , Mann Allison E. , Brandt Bernd W. , Sankaranarayanan Krithivasan , Ozga Andrew T. , Hoogland Menno , Hofman Courtney A. , Salazar‐García Domingo C. , Frohlich Bruno , Milner George R. , Stone Anne C. , Aldenderfer Mark , Lewis Cecil M. , Hofman Corinne L. , Warinner Christina , Schroeder Hannes 
Published: December 2018

AbstractObjectivesDental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques.Materials and methodsTotal DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in‐solution hybridization capture and high‐throughput sequencing.ResultsTotal DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four‐fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on‐target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum‐level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off‐target sequences in human genome‐enriched calculus libraries may still be useful for oral microbiome reconstruction.DiscussionWhile ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.
New distance‐based exponential regression method and equations for estimating the chronology of linear enamel hypoplasia (LEH) defects on the anterior dentition
Authors: Cares Henriquez Alejandra , Oxenham Marc F. 
Published: December 2018

AbstractObjectivesWe present a new distance‐based exponential regression approach based on published histological data to refine the objectivity, accuracy, and precision of age estimates of LEH defect formation on the anterior dentition.MethodsPublished histological data of anterior tooth crown growth for two samples (northern European and southern African) were fitted with exponential trendlines to construct exponential regression equations for each tooth type. A theoretical comparison of the age estimates produced by two commonly used methods (decile chart and linear regression), and those based on the exponential regression equations presented in this article were undertaken. Paired‐samplest‐tests were used to determine whether the estimates obtained by these methods differed significantly.ResultsExponential regression equations were able to accurately replicate age estimates produced by the decile‐chart method. For defects that fell precisely on a decile, estimates differed by 1–23 days. Estimates based on the linear regression method were consistently younger by 4.5–16 months. For defects that fell within deciles, the exponential regression equation estimates, when different, were 12 days to 4 months older than those yielded by the decile method.ConclusionsBy combining currently published histological data on anterior tooth crown growth with a regression approach, it is possible to produce more accurate age estimates than yielded by methods that do not rely on histological data. Furthermore, this approach also greatly improves the objectivity, precision and replicability of results, especially for defects that fall between deciles, when compared to the decile chart method.
A machine learning approach to investigate potential risk factors for gastroschisis in California
Authors: Weber Kari A. , Yang Wei , Carmichael Suzan L. , Padula Amy M. , Shaw Gary M. 
Published: December 2018

BackgroundTo generate new leads about risk factors for gastroschisis, a birth defect that has been increasing in prevalence over time, we performed an untargeted data mining statistical approach.MethodsUsing data exclusively from the California Center of the National Birth Defects Prevention Study, we compared 286 cases of gastroschisis and 1,263 non‐malformed, live‐born controls. All infants had delivery dates between October 1997 and December 2011 and were stratified by maternal age at birth (<20 and ≥ 20 years). Cases and controls were compared by maternal responses to 183 questions (219 variables) using random forest, a data mining procedure. Variables deemed important by random forest were included in logistic regression models to estimate odds ratios and 95% confidence intervals.ResultsAmong women younger than 20, of variables deemed important, there were higher odds observed for higher consumption of chocolate, low intake of iron, acetaminophen use, and urinary tract infections during the beginning of pregnancy. After adjustment, the higher odds remained for low iron intake and a urinary tract infection in the first month of pregnancy. Among women aged 20 or older, of variables deemed important, higher odds were observed for US‐born women of Hispanic ethnicity and for parental substance abuse. There were lower odds observed for obese women, women who ate any cereal the month before pregnancy, and those with higher parity.ConclusionsWe did not discover many previously unreported associations, despite our novel approach to generate new hypotheses. However, our results do add evidence to some previously proposed risk factors.
The link between fiction and teenagers’ reading skills: International evidence from the OECD PISA study
Authors: Jerrim John , Moss Gemma 
Published: December 2018

AbstractIt is well known that children who read more tend to achieve higher scores in academic reading tests. Much less is known, however, about the link between reading different types of text and young people's reading performance. We investigate this issue using the Programme for International Student Assessment (PISA) 2009 database, exploring the association between the frequency with which teenagers read five different types of text (magazines, non‐fiction, fiction, newspapers and comics) and their PISA reading scores. Analysing data from more than 250,000 teenagers from across 35 industrialised countries, we find evidence of a sizeable ‘fiction effect’; young people who read this type of text frequently have significantly stronger reading skills than their peers who do not. In contrast, the same does not hold true for the four other text types. We therefore conclude that encouraging young people to read fiction may be particularly beneficial for their reading skills. Interventions encouraging fiction reading may be especially important for boys from disadvantaged socio‐economic backgrounds, who are less likely to read this text type.
Can variation in standard metabolic rate explain context‐dependent performance of farmed Atlantic salmon offspring?
Authors: Robertsen Grethe , Reid Donald , Einum Sigurd , Aronsen Tonje , Fleming Ian A. , Sundt‐Hansen Line E. , Karlsson Sten , Kvingedal Eli , Ugedal Ola , Hindar Kjetil 
Published: December 2018

AbstractEscaped farmed Atlantic salmon interbreed with wild Atlantic salmon, leaving offspring that often have lower success in nature than pure wild salmon. On top of this, presence of farmed salmon descendants can impair production of wild‐type recruits. We hypothesize that both these effects connect with farmed salmon having acquired higher standard metabolic rates (SMR, the energetic cost of self‐maintenance) during domestication. Fitness‐related advantages of phenotypic traits associated with both high SMR and farmed salmon (e.g., social dominance) depend on environmental conditions, such as food availability. We hypothesize that farmed offspring have an advantage at high food availability due to, for example, dominance behavior but suffer increased risks of starvation when food is scarce because this behavior is energy‐demanding. To test these hypotheses, we first compare embryo SMR of pure farmed, farmed‐wild hybrids and pure wild offspring. Next, we test early‐life performance (in terms of survival and growth) of hybrids relative to that of their wild half‐siblings, as well as their competitive abilities, in semi‐natural conditions of high and low food availability. Finally, we test how SMR affects early‐life performance at high and low food availability. We find inconclusive support for the hypothesis that domestication has induced increased SMR. Further, wild and hybrid juveniles had similar survival and growth in the semi‐natural streams. Yet, the presence of hybrids led to decreased survival of their wild half‐siblings. Contrary to our hypothesis about context‐dependency, these effects were not modified by food availability. However, wild juveniles with high SMR had decreased survival when food was scarce, but there was no such effect at high food availability. This study provides further proof that farmed salmon introgression may compromise the viability of wild salmon populations. We cannot, however, conclude that this is connected to alterations in the metabolic phenotype of farmed salmon.
Migratory patterns and connectivity of two North American grassland bird species
Authors: Hill Jason M. , Renfrew Rosalind B. 
Published: December 2018

AbstractEffective management and conservation of migratory bird populations require knowledge and incorporation of their movement patterns and space use throughout the annual cycle. To investigate the little‐known migratory patterns of two grassland bird species, we deployed 180 light‐level geolocators on Grasshopper Sparrows (Ammodramus savannarum) and 29 Argos‐GPS tags on Eastern Meadowlarks (Sturnella magna) at Konza Prairie, Kansas, USA, and six US Department of Defense (DoD) installations distributed across the species' breeding ranges. We analyzed location data from 34 light‐level geolocators and five Argos‐GPS tags attached for 1 year to Grasshopper Sparrows and Eastern Meadowlarks, respectively. Grasshopper Sparrows were present on the breeding grounds from mid‐April through early October, substantially longer than previously estimated, and migrated on average ~2,500 km over ~30 days. Grasshopper Sparrows exhibited strong migratory connectivity only at a continental scale. The North American Great Lakes region likely serves as a migratory divide for Midwest and East Coast Grasshopper Sparrows; Midwest populations (Kansas, Wisconsin, and North Dakota; n = 13) largely wintered in Texas or Mexico, whereas East Coast populations (Maryland and Massachusetts, n = 20) wintered in the northern Caribbean or Florida. Our data from Eastern Meadowlarks provided evidence for a diversity of stationary and short‐ and long‐distance migration strategies. By providing the most extensive examination of the nonbreeding movement ecology for these two North American grassland bird species to date, we refine information gaps and provide key insight for their management and conservation.
Phenology as a process rather than an event: from individual reaction norms to community metrics
Authors: Inouye Brian D. , Ehrlén Johan , Underwood Nora 
Published: December 2018

AbstractMeasures of the seasonal timing of biological events are key to addressing questions about how phenology evolves, modifies species interactions, and mediates biological responses to climate change. Phenology is often characterized in terms of discrete events, such as a date of first flowering or arrival of first migrants. We discuss how phenological events that are typically measured at the population or species level arise from distributions of phenological events across seasons, and from norms of reaction of these phenological events across environments. We argue that individual variation in phenological distributions and reaction norms has important implications for how we should collect, analyze, and interpret phenological information. Regarding phenology as a reaction norm rather than one year's specific values implies that selection acts on the phenologies that an individual expresses over its lifetime. To understand how climate change is likely to influence phenology, we need to consider not only plastic responses along the reaction norm but changes in the reaction norm itself. We show that when individuals vary in their reaction norms, correlations between reaction norm elevation and slope make first events particularly poor estimators of population sensitivity to climate change, and variation in slopes can obscure the pattern of selection on phenology. We also show that knowing the shape of the distribution of phenological events across the season is important for predicting biologically important phenological mismatches with climate change. Last, because phenological events are parts of a continuous developmental process, we suggest that the approach of measuring phenology by recording developmental stages of individuals in a population at a single point in time should be used more widely. We conclude that failure to account for phenological distributions and reaction norms may lead to overinterpretation of metrics based on single events, such as commonly recorded first event dates, and may confound meta‐analyses that use a range of metrics. Rather than prescribing a single universal approach to studying phenology, we point out limitations of inferences based on single metrics and encourage work that considers the multivariate nature of phenology and more tightly links data collection and analyses with biological hypotheses.
CD11a expression distinguishes infiltrating myeloid cells from plaque‐associated microglia in Alzheimer's disease
Authors: Shukla Ankita K. , McIntyre Laura L. , Marsh Samuel E. , Schneider Christine A. , Hoover Evelyn M. , Walsh Craig M. , Lodoen Melissa B. , Blurton‐Jones Mathew , Inlay Matthew A. 
Published: December 2018

AbstractAlzheimer's disease (AD) is the leading cause of age‐related neurodegeneration and is characterized neuropathologically by the accumulation of insoluble beta‐amyloid (Aβ) peptides. In AD brains, plaque‐associated myeloid (PAM) cells cluster around Aβ plaques but fail to effectively clear Aβ by phagocytosis. PAM cells were originally thought to be brain‐resident microglia. However, several studies have also suggested that Aβ‐induced inflammation causes peripheral monocytes to enter the otherwise immune‐privileged brain. The relationship between AD progression and inflammation in the brain remains ambiguous because microglia and monocyte‐derived macrophages are extremely difficult to distinguish from one another in an inflamed brain. Whether PAM cells are microglia, peripheral macrophages, or a mixture of both remains unclear. CD11a is a component of the β2 integrin LFA1. We have determined that CD11a is highly expressed on peripheral immune cells, including macrophages, but is not expressed by mouse microglia. These expression patterns remain consistent in LPS‐treated inflamed mice, as well as in two mouse models of AD. Thus, CD11a can be used as a marker to distinguish murine microglia from infiltrating peripheral immune cells. Using CD11a, we show that PAM cells in AD transgenic brains are comprised entirely of microglia. We also demonstrate a novel fluorescence‐assisted quantification technique (FAQT), which reveals a significant increase in T lymphocytes, especially in the brains of female AD mice. Our findings support the notion that microglia are the lead myeloid players in AD and that rejuvenating their phagocytic potential may be an important therapeutic strategy.
Research Information for Reasonable People
Authors: Dresser Rebecca 
Published: December 2018

AbstractIn 2017, federal officials issued a revised version of the Common Rule, the federal regulations that govern much of the human subject research conducted in the United States. Two provisions on information disclosure have reportedly provoked confusion among researchers and people responsible for research oversight. These provisions incorporate the familiar and foundational legal concept known as the reasonable person standard, applying this to research disclosure. Although other, long‐standing Common Rule provisions require reasonableness judgments, the new provisions differ in that they require reasonableness to be judged from the ordinary person's perspective instead of the perspective of scientists, clinicians, and other experts generally involved in designing and reviewing human studies.
Work Requirements That Don't Work
Authors: Latham Stephen R. 
Published: December 2018

AbstractEarly in 2018, the Trump administration's Centers for Medicare and Medicaid Services issued a guidance letter outlining a new and controversial kind of Medicaid waiver proposal. The administration invited states to propose waivers that would impose work (or other “community engagement”) requirements as a condition of eligibility for Medicaid. The Trump administration and state proponents of work requirements want to force able‐bodied Medicaid beneficiaries into the workplace. Critics allege that this is because they mistakenly believe that low‐income individuals are not working because they're lazy or because aid programs provide them with a disincentive to work. Proponents respond that the requirements can lower the public programs' costs while helping its recipients. Medicaid data seems to show that the work‐requirement proposals are a solution in search of a real‐life problem.
Who Deserves Access to Care in Children's Hospitals?
Authors: Caruso Brown Amy E. , Frega Katherine 
Published: December 2018

AbstractAn eighteen‐year‐old with sickle cell disease was admitted to the pediatric hematology service at his local children's hospital for management of an acute pain crisis, one of many such admissions. He had a good relationship with his primary hematologist and primary nurse, but with other health care providers, there was evident friction. Sometimes, he was simply rude, rolling over and pretending to sleep in response to questions about his symptoms. When frustrated or convinced that his pain was not being addressed appropriately, he was prone to yelling and cursing at his nurses. After members of the health care team complained, their supervisor decided to transfer the patient to an adult general medicine service. Reasons cited for the transition included the stressful work environment created by the patient's actions, his refusal to follow directives from staff (although he was generally adherent to treatment), and the hypothetical harm to other young patients who might witness his behavior. Was this a just outcome? Is it ever permissible to deny access to pediatric care to a patient whose best interests would be served by it? Can access be withheld for “bad” behavior, and can transfer of care be wielded as a punishment?
Wrestling with the Monster: Frankenstein and Organ Transplantation
Authors: Trump Eric 
Published: December 2018

AbstractIn December 1967, Louis Washkansky, a grocer living in South Africa, became the first person to awaken after a heart transplant. Some accounts say that his first words were, “I am the new Frankenstein.” Others claim that Christiaan Barnard, his transplant surgeon, uttered these. Much as people have long mixed up who Frankenstein is—creature or creator?—in Mary Shelley's novel, so patient and surgeon, repaired and repairer, are confused in retellings of this post‐op Frankensteinian moment. Whether Washkansky identified with Frankenstein's monster or not, he was probably feeling a bit monstrous after taking the donor heart of Denise Darvall into his chest. I know I was, over thirty years later, standing naked before a mirror and gazing at my shorn and bloated torso for the first time since a kidney transplant. My boundaries had been rearranged: a crescentic scar marked the frontier between me and not‐me.
Rereading Frankenstein: What If Victor Frankenstein Had Actually Been Evil?
Authors: Robert Jason Scott 
Published: December 2018

AbstractAs we reread Mary Shelley's Frankenstein at two hundred years, it is evident that Victor Frankenstein is both a mad scientist (fevered, obsessive) and a bad scientist (secretive, hubristic, irresponsible). He's also not a very nice person. He's a narcissist, a liar, and a bad “parent.” But he is not genuinely evil. And yet when we reimagine him as evil—as an evil scientist and as an evil person—we can learn some important lessons about science and technology, our contemporary society, and ourselves.
Locating the Source(s) of the Social Value Requirement(s)
Authors: Wendler David 
Published: December 2018

AbstractIn this issue of the Hastings Center Report, Danielle Wenner looks at a few prominent analyses of the social value requirement for clinical research, claiming that they are all based on what she calls a transactional model of research ethics. She argues that the transactional model fails to provide a secure foundation for the social value requirement, and then, appealing to John Rawls, she argues that a more secure foundation lies in the principles of social justice. Wenner's attempt to locate the source of the social value requirement raises important questions regarding its scope and strength. To determine what the social value requirement requires, we need to know why it's a requirement. Does the social value requirement apply to all trials or only to a subset? Is it a necessary condition on ethical research or an important consideration that can conflict with, and sometimes be defeated by, other considerations? Wenner's attempt to answer these questions is obscured by the fact that she mistakenly regards a minority view of research ethics as the mainstream view. Once we correct for that, her analysis of the foundation of the social value requirement provides a valuable opportunity to consider how the ethics of research as an institution might supplement or alter the ethics of individual clinical trials.