The reproducibility debate is an opportunity, not a crisis.

There are many factors that contribute to the reproducibility and replicability of scientific research. There is a need to understand the research ecosystem, and improvements will require combined efforts across all parts of this ecosystem. National structures can play an important role in coordinating these efforts, working collaboratively with researchers, institutions, funders, publishers, learned societies and other sectoral organisations, and providing a monitoring and reporting function. Whilst many new ways of working and emerging innovations hold a great deal of promise, it will be important to invest in meta-research activity to ensure that these approaches are evidence based, work as intended, and do not have unintended consequences. Addressing reproducibility will require working collaboratively across the research ecosystem to share best practice and to make the most effective use of resources. The UK Reproducibility Network (UKRN) brings together Local Networks of researchers, Institutions, and External Stakeholders (funders, publishers, learned societies and other sectoral organisations), to coordinate action on reproducibility and work to ensure the UK retains its place as a centre for world-leading research. This activity is coordinated by the UKRN Steering Group. We consider this structure as valuable, bringing together a range of voices at a range of levels to support the combined efforts required to enact change.

Prognostic Factors and Long-Term Outcome with ANCA-Associated Kidney Vasculitis in Childhood.

BACKGROUND AND OBJECTIVES: ANCA-associated vasculitis is extremely rare in children. We report the clinicopathologic features, long-term outcomes, and prognostic factors of a large pediatric cohort of patients with ANCA-associated kidney vasculitis. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: This retrospective study included 85 consecutive patients with kidney biopsy specimen-proven ANCA-associated vasculitis from tertiary referral centers in Italy and Canada. Kidney biopsy specimens were categorized as focal, crescentic, sclerotic, or mixed, according to the Berden classification. The prognostic significance of baseline clinical, laboratory, and histologic findings was analyzed with respect to kidney failure or CKD stage 3-5/kidney failure. RESULTS: A total of 53 patients had microscopic polyangiitis (62%), and 32 had granulomatosis with polyangiitis (38%). Rapidly progressive GN was the most frequent presentation (39%); a third of the patients also had nephrotic-range proteinuria. Kidney biopsy specimens were classified as focal in 21% of the patients, crescentic in 51%, sclerotic in 15%, and mixed in 13%. Remission-induction therapies included cyclophosphamide in 78% of patients. A total of 25 patients (29%) reached kidney failure. The median (interquartile range) time to kidney failure or last follow-up was 35 (6-89) months in the whole cohort, and 73 (24-109) months among the patients who did not reach this outcome. Patients whose biopsy specimens showed sclerotic histology had significantly shorter kidney survival (hazard ratio, 11.80; 95% confidence interval, 2.49 to 55.99) and survival free of CKD stage 3-5 (hazard ratio, 8.88; 95% confidence interval, 2.43 to 32.48), as compared with those with focal/mixed histology. Baseline eGFR, low serum albumin, hypertension, central nervous system complications, and sclerotic histology, which reflected severe kidney involvement, were associated with both kidney failure and CKD stage 3-5/kidney failure at unadjusted analysis; no independent prognostic factors emerged at multivariable analysis. CONCLUSIONS: Children with ANCA-associated kidney vasculitis often have aggressive presentation; a third of such children progress to kidney failure and this usually occurs early during follow-up. A severe clinical presentation is associated with the development of CKD or kidney failure.

The case for free and open source software in research and scholarship.

Free and open source software (FOSS) is any computer program released under a licence that grants users rights to run the program for any purpose, to study it, to modify it, and to redistribute it in original or modified form. Our aim is to explore the intersection between FOSS and computational reproducibility. We begin by situating FOSS in relation to other 'open' initiatives, and specifically open science, open research, and open scholarship. In this context, we argue that anyone who actively contributes to the research process today is a computational researcher, in that they use computers to manage and store information. We then provide a primer to FOSS suitable for anyone concerned with research quality and sustainability-including researchers in any field, as well as support staff, administrators, publishers, funders, and so on. Next, we illustrate how the notions introduced in the primer apply to resources for scientific computing, with reference to the GNU Scientific Library as a case study. We conclude by discussing why the common interpretation of 'open source' as 'open code' is misplaced, and we use this example to articulate the role of FOSS in research and scholarship today. This article is part of the theme issue 'Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico'.

Barely sufficient practices in scientific computing.

The importance of software to modern research is well understood, as is the way in which software developed for research can support or undermine important research principles of findability, accessibility, interoperability, and reusability (FAIR). We propose a minimal subset of common software engineering principles that enable FAIRness of computational research and can be used as a baseline for software engineering in any research discipline.

Research Culture and Reproducibility.

There is ongoing debate regarding the robustness and credibility of published scientific research. We argue that these issues stem from two broad causal mechanisms: the cognitive biases of researchers and the incentive structures within which researchers operate. The UK Reproducibility Network (UKRN) is working with researchers, institutions, funders, publishers, and other stakeholders to address these issues.

Lineal kinship organization in cross-specific perspective.

I draw on insights from anthropology to outline a framework for the study of kinship systems that applies across animal species with biparental sexual reproduction. In particular, I define lineal kinship organization as a social system that emphasizes interactions among lineally related kin-that is, individuals related through females only, if the emphasis is towards matrilineal kin, and individuals related through males only, if the emphasis is towards patrilineal kin. In a given population, the emphasis may be expressed in one or more social domains, corresponding to pathways for the transmission of different resources across generations (e.g. the allocation of food, the transfer of access to the natal territory or household). A lineal bias in any domain can be viewed as a bias in investment towards a particular set of kin-specifically, towards the offspring of daughters if the bias is matrilineal, and towards the offspring of sons if the bias is patrilineal. Effectively, investment is restricted to the offspring of the females in the population in one case, and to the offspring of the males in the other. This is distinct from a bias in investment towards daughters and towards sons, respectively. Overall, I propose a shift in focus-from viewing matrilineal and patrilineal kinship as unitary phenomena, to consideration of the different aspects of the social system featuring a bias towards lineally related kin. This article is part of the theme issue 'The evolution of female-biased kinship in humans and other mammals'.

The evolution of female-biased kinship in humans and other mammals.

Female-biased kinship (FBK) arises in numerous species and in diverse human cultures, suggesting deep evolutionary roots to female-oriented social structures. The significance of FBK has been debated for centuries in human studies, where it has often been described as difficult to explain. At the same time, studies of FBK in non-human animals point to its apparent benefits for longevity, social complexity and reproduction. Are female-biased social systems evolutionarily stable and under what circumstances? What are the causes and consequences of FBK? The purpose of this theme issue is to consolidate efforts towards understanding the evolutionary significance and stability of FBK in humans and other mammals. The issue includes broad theoretical and empirical reviews as well as specific case studies addressing the social and ecological correlates of FBK across taxa, time and space. It leverages a comparative approach to test existing hypotheses and presents novel arguments that aim to expand our understanding of how males and females negotiate kinship across diverse contexts in ways that lead to the expression of female biases in kinship behaviour and social structure. This article is part of the theme issue 'The evolution of female-biased kinship in humans and other mammals'.

Inferring individual-level processes from population-level patterns in cultural evolution.

Our species is characterized by a great degree of cultural variation, both within and between populations. Understanding how group-level patterns of culture emerge from individual-level behaviour is a long-standing question in the biological and social sciences. We develop a simulation model capturing demographic and cultural dynamics relevant to human cultural evolution, focusing on the interface between population-level patterns and individual-level processes. The model tracks the distribution of variants of cultural traits across individuals in a population over time, conditioned on different pathways for the transmission of information between individuals. From these data, we obtain theoretical expectations for a range of statistics commonly used to capture population-level characteristics (e.g. the degree of cultural diversity). Consistent with previous theoretical work, our results show that the patterns observed at the level of groups are rooted in the interplay between the transmission pathways and the age structure of the population. We also explore whether, and under what conditions, the different pathways can be distinguished based on their group-level signatures, in an effort to establish theoretical limits to inference. Our results show that the temporal dynamic of cultural change over time retains a stronger signature than the cultural composition of the population at a specific point in time. Overall, the results suggest a shift in focus from identifying the one individual-level process that likely produced the observed data to excluding those that likely did not. We conclude by discussing the implications for empirical studies of human cultural evolution.

Conhecimento dos cirurgiões-dentistas de uma cidade do nordeste brasileiro em relação ao código de defesa do consumidor e suas implicações na prática odontológica / Knowledge of dentists of a city in northeastern Brazil in relation to the consumer protection code and its implications for dental practice

A resolução de muitos dos problemas que ocorrem cotidianamente no consultório odontológico requer oconhecimento da legislação pátria, em especial o Código de Defesa do Consumidor. Assim, o presentetrabalho objetiva avaliar o conhecimento e práticas dos cirurgiões-dentistas em relação ao Código deDefesa do Consumidor. Tratou-se de um estudo descritivo, exploratório, transversal, de análise dadosprimários. A amostra constituiu-se de 173 cirurgiões-dentistas atuantes em consultório/clínica particular oulocatários de locais para atendimento odontológico na condição de autônomos. O instrumento de coletade dados foi estruturado com questões fechadas e abertas, com base nos objetivos propostos. Os dadoscoletados foram transcritos e analisados no SPSS Statistics 20.0.0 e as tabelas e gráficos foramconstruídas no Microsoft Office Excel 2007. 173 profissionais aceitaram participar da pesquisa.Observaram-se aspectos como a falta de conhecimento por parte da maioria destes a respeito daslegislações com base nas quais podem ser processados, bem como das esferas jurídicas nas quais estesprocessos podem ocorrer. O tempo de conservação da documentação odontológica e de garantia dosorçamentos é a forma mais comum de esclarecimento dos pacientes a respeito de fatos decorrentes dotratamento. Pode-se concluir que os profissionais necessitam de maior conhecimento sobre a legislaçãoque se aplica nas relações profissionais com seus pacientes.

The resolution of many problems that daily occur on dental offices requires knowledge of Brazilian legislation, particularly of the Consumer Protection Code. The present study aims to evaluate theknowledge and practices of dentists related to the Consumer Protection Code. It was a descriptive,exploratory, cross-sectional analysis of primary data. The sample consisted of 173 dentists that work atprivate office or self-employers in rental dental offices. Data tool of collection was structured with closedand open questions, based on the proposed goals. Collected data were transcribed and analyzed usingSPSS Statistics 20.0.0. Tables and graphics were built using Microsoft Office 2007. 173 professionals agreed to participate. Aspects as lack of legislation knowledge of most part of them were observed underwhich it could be sued, as well as Legal spheres where it can happen. Dental records storage time andguarantee of service proposals are the most common way of awareness among patients about proceduresresulted from treatment. It can be concluded that professionals need more knowledge about legislationthat applies on the relation of professionals with their patients.

Reconstruction of a Real World Social Network using the Potts Model and Loopy Belief Propagation.

The scope of this paper is to test the adoption of a statistical model derived from Condensed Matter Physics, for the reconstruction of the structure of a social network. The inverse Potts model, traditionally applied to recursive observations of quantum states in an ensemble of particles, is here addressed to observations of the members' states in an organization and their (anti)correlations, thus inferring interactions as links among the members. Adopting proper (Bethe) approximations, such an inverse problem is showed to be tractable. Within an operational framework, this network-reconstruction method is tested for a small real-world social network, the Italian parliament. In this study case, it is easy to track statuses of the parliament members, using (co)sponsorships of law proposals as the initial dataset. In previous studies of similar activity-based networks, the graph structure was inferred directly from activity co-occurrences: here we compare our statistical reconstruction with such standard methods, outlining discrepancies and advantages.

A solution to the collective action problem in between-group conflict with within-group inequality.

Conflict with conspecifics from neighbouring groups over territory, mating opportunities and other resources is observed in many social organisms, including humans. Here we investigate the evolutionary origins of social instincts, as shaped by selection resulting from between-group conflict in the presence of a collective action problem. We focus on the effects of the differences between individuals on the evolutionary dynamics. Our theoretical models predict that high-rank individuals, who are able to usurp a disproportional share of resources in within-group interactions, will act seemingly altruistically in between-group conflict, expending more effort and often having lower reproductive success than their low-rank group-mates. Similar behaviour is expected for individuals with higher motivation, higher strengths or lower costs, or for individuals in a leadership position. Our theory also provides an evolutionary foundation for classical equity theory, and it has implications for the origin of coercive leadership and for reproductive skew theory.

The evolution of matrilineal kinship organization.

Matrilineal kinship organization is a human social system that emphasizes interactions between matrilineal kin, i.e. individuals related only through females. The 'matrilineal puzzle' refers to the potential for tension characteristic of this social system, owing to the conflict between the interests and responsibilities of men in their roles as brother/uncle versus husband/father. From an evolutionary perspective, matrilineal kinship organization is puzzling when it diverts investment of resources from the individuals who provide the potentially highest reproductive returns. I use a game-theoretic framework to investigate a particular form of matrilineal inheritance--the transfer of property from a maternal uncle to a sororal nephew. The analysis reveals two mechanisms that may make this strategy a stable evolutionary outcome. First, a polygynous male has multiple wives, and hence multiple brothers-in-law; with matrilineal inheritance, each additional brother-in-law may transfer resources to the male's wife's offspring, thus potentially contributing to the male's inclusive fitness. Second, the husband of a polyandrous female is effectively 'sharing' paternity with other men; depending on the number of husbands, he may be better off investing in his sister's offspring. I conclude by discussing how these results address the challenges posed by the occurrence of matrilineal kinship organization.

Reconstructing the history of marriage strategies in Indo-European-speaking societies: monogamy and polygyny.

Explanations for the emergence of monogamous marriage have focused on the cross-cultural distribution of marriage strategies, thus failing to account for their history. In this paper I reconstruct the pattern of change in marriage strategies in the history of societies speaking Indo-European languages, using cross-cultural data in the systematic and explicitly historical framework afforded by the phylogenetic comparative approach. The analysis provides evidence in support of Proto-Indo-European monogamy, and that this pattern may have extended back to Proto-Indo-Hittite. These reconstructions push the origin of monogamous marriage into prehistory, well beyond the earliest instances documented in the historical record; this, in turn, challenges notions that the cross-cultural distribution of monogamous marriage reflects features of social organization typically associated with Eurasian societies, and with "societal complexity" and "modernization" more generally. I discuss implications of these findings in the context of the archaeological and genetic evidence on prehistoric social organization.

Reconstructing the history of residence strategies in Indo-European-speaking societies: neo-, uxori-, and virilocality.

Linguists and archaeologists have used reconstructions of early Indo-European residence strategies to constrain hypotheses about the homeland and trajectory of dispersal of Indo-European languages; however, these reconstructions are largely based on unsystematic and a historical use of the linguistic and ethnographic evidence, coupled with substantial bias in interpretation. Here I use cross-cultural data in a phylogenetic comparative framework to reconstruct the pattern of change in residence strategies in the history of societies speaking Indo-European languages. The analysis provides evidence in support of prevailing virilocality with alternative neolocality for Proto-Indo-European, and that this pattern may have extended back to Proto-Indo-Hittite. These findings bolster interpretations of the archaeological evidence that emphasize the "non-matricentric" structure of early Indo-European society; however, they also counter the notion that early Indo-European society was strongly "patricentric." I discuss implications of these findings in the context of the archaeological and genetic evidence on prehistoric social organization.

Reconstructing the history of marriage and residence strategies in Indo-European-speaking societies.

This file provides additional information on the data and methods used in Fortunato (2011a, b), and discussion of the results of the fossilization of nodes Proto-Indo-Hittite (PIH) and Proto-Indo-European (PIE) for marriage and residence strategies.

Your place or mine? A phylogenetic comparative analysis of marital residence in Indo-European and Austronesian societies.

Accurate reconstruction of prehistoric social organization is important if we are to put together satisfactory multidisciplinary scenarios about, for example, the dispersal of human groups. Such considerations apply in the case of Indo-European and Austronesian, two large-scale language families that are thought to represent Neolithic expansions. Ancestral kinship patterns have mostly been inferred through reconstruction of kin terminologies in ancestral proto-languages using the linguistic comparative method, and through geographical or distributional arguments based on the comparative patterns of kin terms and ethnographic kinship 'facts'. While these approaches are detailed and valuable, the processes through which conclusions have been drawn from the data fail to provide explicit criteria for systematic testing of alternative hypotheses. Here, we use language trees derived using phylogenetic tree-building techniques on Indo-European and Austronesian vocabulary data. With these trees, ethnographic data and Bayesian phylogenetic comparative methods, we statistically reconstruct past marital residence and infer rates of cultural change between different residence forms, showing Proto-Indo-European to be virilocal and Proto-Malayo-Polynesian uxorilocal. The instability of uxorilocality and the rare loss of virilocality once gained emerge as common features of both families.

From bridewealth to dowry? : A bayesian estimation of ancestral states of marriage transfers in Indo-European groups.

Significant amounts of wealth have been exchanged as part of marriage settlements throughout history. Although various models have been proposed for interpreting these practices, their development over time has not been investigated systematically. In this paper we use a Bayesian MCMC phylogenetic comparative approach to reconstruct the evolution of two forms of wealth transfers at marriage, dowry and bridewealth, for 51 Indo-European cultural groups. Results indicate that dowry is more likely to have been the ancestral practice, and that a minimum of four changes to bridewealth is necessary to explain the observed distribution of the two states across the cultural groups.

Socio-demographic, behavioral and functional characteristics of groups of community and institutionalized elderly Quechua Indians of Peru, and their association with nutritional status.

Socio-demographic, behavioral, functional and anthropometric data for groups of elderly Quechua Indians of Peru were used to investigate the effects of gender and lifestyle patterns on nutritional status. Two community-dwelling samples were selected for study, representative of divergent lifestyles in terms of their combination of socio-economic, demographic and cultural contexts, plus an ad-hoc sample of institutionalized individuals with controlled food intake and reduced physical activity. Results suggest that differences in socio-demographic, behavioral and functional characteristics exist between the sexes and across settings (low- vs. highland) and lifestyles (institutionalized vs. community-dwelling; semi-urban vs. rural). These factors are likely to be related to diverging dietary and physical activity patterns, and have considerable effects on the nutritional status of the respondents.