bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Flow-Based Model of the HIV Care Continuum in the United States
Authors: Gonsalves Gregg S. , Paltiel A. David , Cleary Paul D. , Gill Michael J. , Kitahata Mari M. , Rebeiro Peter F. , Silverberg Michael J. , Horberg Michael , Abraham Alison G. , Althoff Keri N. , Moore Richard , Bosch Ronald J. , Tang Tian , Hall H. Irene , Kaplan Edward H. 
Published: May 2017

Background:
Understanding the flow of patients through the continuum of HIV care is critical to determine how best to intervene so that the proportion of HIV-infected persons who are on antiretroviral treatment and virally suppressed is as large as possible.

Methods:
Using immunological and virological data from the Centers for Disease Control and Prevention and the North American AIDS Cohort Collaboration on Research and Design from 2009 to 2012, we estimated the distribution of time spent in and dropout probability from each stage in the continuum of HIV care. We used these estimates to develop a queueing model for the expected number of patients found in each stage of the cascade.

Results:
HIV-infected individuals spend an average of about 3.1 months after HIV diagnosis before being linked to care, or dropping out of that stage of the continuum with a probability of 8%. Those who link to care wait an additional 3.7 months on average before getting their second set of laboratory results (indicating engagement in care) or dropping out of care with probability of almost 6%. Those engaged in care spent an average of almost 1 year before achieving viral suppression on antiretroviral therapy or dropping out with average probability 13%. For patients who achieved viral suppression, the average time suppressed on antiretroviral therapy was an average of 4.5 years.

Conclusions:
Interventions should be targeted to more rapidly identifying newly infected individuals, and increasing the fraction of those engaged in care that achieves viral suppression.
How Do Thresholds of Principle and Preference Influence Surgeon Assessments of Learner Performance?
Authors: Apramian Tavis , Cristancho Sayra , Sener Alp , Lingard Lorelei 
Published: May 2017

Objective:
The present study asks whether intraoperative principles are shared among faculty in a single residency program and explores how surgeons’ individual thresholds between principles and preferences might influence assessment.

Background:
Surgical education continues to face significant challenges in the implementation of intraoperative assessment. Competency-based medical education assumes the possibility of a shared standard of competence, but intersurgeon variation is prevalent and, at times, valued in surgical education. Such procedural variation may pose problems for assessment.

Methods:
An entire surgical division (n = 11) was recruited to participate in video-guided interviews. Each surgeon assessed intraoperative performance in 8 video clips from a single laparoscopic radical left nephrectomy performed by a senior learner (>PGY5). Interviews were audio recorded, transcribed, and analyzed using the constant comparative method of grounded theory.

Results:
Surgeons’ responses revealed 5 shared generic principles: choosing the right plane, knowing what comes next, recognizing normal and abnormal, making safe progress, and handling tools and tissues appropriately. The surgeons, however, disagreed both on whether a particular performance upheld a principle and on how the performance could improve. This variation subsequently shaped their reported assessment of the learner's performance.

Conclusions:
The findings of the present study provide the first empirical evidence to suggest that surgeons’ attitudes toward their own procedural variations may be an important influence on the subjectivity of intraoperative assessment in surgical education. Assessment based on intraoperative entrustment may harness such subjectivity for the purpose of implementing competency-based surgical education.
The impact of reducing car weight on global emissions: the future fleet in Great Britain
Authors: Serrenho André Cabrera , Norman Jonathan B. , Allwood Julian M. 
Published: May 2017

Current European policies define targets for future direct emissions of new car sales that foster a fast transition to electric drivetrain technologies. However, these targets do not consider the emissions produced in electricity generation and material production, and therefore fail to incentivise car manufacturers to consider the benefits of vehicle weight reduction. In this paper, we examine the potential benefits of limiting the average weight and altering the material composition of new cars in terms of global greenhouse gas emissions produced during the use phase, electricity generation and material production. We anticipate the emissions savings for the future car fleet in Great Britain until 2050 for various alternative futures, using a dynamic material flow analysis of ferrous metals and aluminium, and considering an evolving demand for car use. The results suggest that fostering vehicle weight reduction could produce greater cumulative emissions savings by 2050 than those obtained by incentivising a fast transition to electric drivetrains, unless there is an extreme decarbonization of the electricity grid. Savings promoted by weight reduction are immediate and do not depend on the pace of decarbonization of the electricity grid. Weight reduction may produce the greatest savings when mild steel in the car body is replaced with high-strength steel.
This article is part of the themed issue ‘Material demand reduction’.
Political economies and environmental futures for the sharing economy
Authors: Frenken Koen 
Published: May 2017

The sudden rise of the sharing economy has sparked an intense public debate about its definition, its effects and its future regulation. Here, I attempt to provide analytical guidance by defining the sharing economy as the practice that consumers grant each other temporary access to their under-utilized physical assets. Using this definition, the rise of the sharing economy can be understood as occurring at the intersection of three salient economic trends: peer-to-peer exchange, access over ownership and circular business models. I shortly discuss some of the environmental impacts of online sharing platforms and then articulate three possible futures of the sharing economy: a capitalist future cumulating in monopolistic super-platforms allowing for seamless services, a state-led future that shifts taxation from labour to capital and redistributes the gains of sharing from winners to losers, and a citizen-led future based on cooperatively owned platforms under democratic control. The nature and size of the social and environmental impacts are expected to differ greatly in each of the three scenarios.This article is part of the themed issue ‘Material demand reduction’.
Why we use more materials
Authors: Gutowski Timothy , Cooper Daniel , Sahni Sahil 
Published: May 2017

In this paper, we review the drivers for the high levels of material use in society, investigating both historical and current trends. We present recent national and global data by different material categories and accounting schemes, showing the correlations between materials use and different measures of human well-being. We also present a development narrative to accompany these observed trends, focusing on the strong role materials have played in economic development by industrialization and in the consumer economy. Finally, we speculate on how material efficiency might alter this pattern going forward and whether it is possible to de-couple well-being from material use.This article is part of the themed issue ‘Material demand reduction’.
Are prices enough? The economics of material demand reduction
Authors: Aidt Toke , Jia Lili , Low Hamish 
Published: May 2017

Recent policy proposals to achieve carbon targets have emphasized material demand reduction strategies aimed at achieving material efficiency. We provide a bridge between the way economists and engineers think about efficiency. We use the tools of economics to think about policies directed at material efficiency and to evaluate the role and rationale for such policies. The analysis highlights when prices (or taxes) can be used to induce changes in material use and when taxes may not work. We argue that the role of taxes is limited by concerns about their distributional consequences, by international trade and the lack of international agreement on carbon prices, and by investment failures.This article is part of the themed issue ‘Material demand reduction’.
The austere life
Authors: Xenos Nicholas 
Published: May 2017

Since the 2008 financial crisis, austerity has been deployed as a public policy geared towards reducing sovereign debt and restoring economic order, on the one hand, and descried as an example of punitive moralizing by political and economic elites, on the other. This article challenges the economic understanding of the concept of austerity. Some recent examples from popular culture are adduced to indicate societal dissatisfaction with the accumulation of material things, examples of what has been called ‘the new minimalism’. Contextualizing this phenomenon within a culture of intensive consumption, it is argued here that there is a history of austerity as an aversion to ostentation and excess in western tradition that runs from the Stoics through to recent pronouncements by Pope Francis and that provides a vantage point from which to question the economistic deployment of the term. When understood in this way, the austere can be seen to carry an important political meaning today and may contribute to the sorts of transformation necessary in order to reduce material demand on a societal scale.
This article is part of the themed issue ‘Material demand reduction’.
Recomposing consumption: defining necessities for sustainable and equitable well-being
Authors: Gough Ian 
Published: May 2017

This paper focuses on consumption in the affluent world and the resulting level, composition and distribution of consumption-based emissions. It argues that public policy should foster the recomposition of consumption, while not disadvantaging poorer groups in the population. To combine these two imperatives entails making a distinction between goods and services that are necessary for a basic level of well-being, and those that are surplus to this requirement. The argument proceeds in six stages. First, the paper outlines a theory of universal need, as an alternative conception of well-being to consumer preference satisfaction. Second, it proposes a dual strategy methodology for identifying need satisfiers or necessities in a given social context. Then, it applies this methodology to identify a minimum bundle of necessary consumption items in the UK and speculates how it might be used to identify a maximum bundle for sustainable consumption. The next part looks at corporate barriers and structural obstacles in the path of sustainable consumption. The following part reveals a further problem: mitigation policies can result in perverse distributional outcomes when operating in contexts of great inequality. The final section suggests four ecosocial public policies that would simultaneously advance sustainable and equitable consumption in rich nations.This article is part of the themed issue ‘Material demand reduction’.
Radical dematerialization and degrowth
Authors: Kallis Giorgos 
Published: May 2017

The emission targets agreed in Paris require a radical reduction of material extraction, use and disposal. The core claim of this article is that a radical dematerialization can only be part and parcel of degrowth. Given that capitalist economies are designed to grow, this raises the question of whether, and under what circumstances, the inevitable ‘degrowth’ can become socially sustainable. Three economic policies are discussed in this direction: work-sharing, green taxes and public money.
This article is part of the themed issue ‘Material demand reduction’.
European admixture in Chinchorro DNA
Authors: Smith Robert 
Published: May 2017

AbstractIt is widely held that, except for migrations from Beringia or Siberia, there was no contact between the Old World and the New World prior to the colonization of North America by the Norse in the late 10thcentury AD. Analyses of 23 ancient American DNA samples reveal, however, the presence of European admixture in a sample taken from a Chinchorro mummy of northern Chile dated to 3972–3806 BC. This discovery implies a more complex history of the peopling of the Americas than previously accepted.
Detecting presence of mutational signatures in cancer with confidence
Authors: Huang Xiaoqing , Wojtowicz Damian , Przytycka Teresa M. 
Published: May 2017

AbstractCancers arise as the result of somatically acquired changes in the DNA of cancer cells. However, in addition to the mutations that confer a growth advantage, cancer genomes accumulate a large number of somatic mutations resulting from normal DNA damage and repair processes as well as mutations triggered by carcinogenic exposures or cancer related aberrations of DNA mainte-nance machinery. These mutagenic processes often produce characteristic mutational patterns called mutational signatures. Decomposition of cancer’s mutation catalog into mutations consistent with such signatures can provide valuable information about cancer etiology. However, the results from diﬀerent decomposition methods are not always consistent. Hence, one needs to not only be able to decompose a patient’s mutational profile into signatures but also to establish the accuracy of such decomposition. We proposed two complementary ways of measuring confidence and stability of decomposition results and applied them to analyze mutational signatures in breast cancer genomes. We identified very stable and highly unstable signatures, as well as signatures that have been missed altogether. We also provided additional support for the novel signatures. Our results emphasize the importance of assessing the confidence and stability of inferred signature contributions. All tools developed in this paper have been implemented in an R package, calledSignatureEstimation, which is available fromhttps://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#signatureestimation.
Mutual information estimation for transcriptional regulatory network inference
Authors: Ish-Horowicz Jonathan , Reid John 
Published: May 2017

AbstractMutual information-based network inference algorithms are an important tool in the reverse-engineering of transcriptional regulatory networks, but all rely on estimates of the mutual information between the expression of pairs of genes. Various methods exist to compute estimates of the mutual information, but none have been firmly established as optimal for network inference. The performance of 9 mutual information estimation methods are compared using three popular network inference algorithms: CLR, MRNET and ARACNE. The performance of the estimators is compared on one synthetic and two real datasets. For estimators that discretise data, the effect of discretisation parameters are also studied in detail. Implementations of 5 estimators are provided in parallelised C++ with an R interface. These are faster than alternative implementations, with reductions in computation time up to a factor of 3,500.ResultsThe B-spline estimator consistently performs well on real and synthetic datasets. CLR was found to be the best performing inference algorithm, corroborating previous results indicating that it is the state of the art mutual inference algorithm. It is also found to be robust to the mutual information estimation method and their parameters. Furthermore, when using an estimator that discretises expression data, usingN1/3bins forNsamples gives the most accurate inferred network. This contradicts previous findings that suggested usingN1/2bins.
High-throughput profiling and analysis of plant responses over time to abiotic stress
Authors: Veley Kira M. , Berry Jeffrey C. , Fentress Sarah J. , Schachtman Daniel P. , Baxter Ivan , Bart Rebecca 
Published: May 2017

ABSTRACTSorghum (Sorghum bicolor(L.) Moench) is a rapidly growing, high-biomass crop prized for abiotic stress tolerance. However, measuring genotype-by-environment (G × E) interactions remains a progress bottleneck. Here we describe strategies for identifying shape, color and ionomic indicators of plant nitrogen use efficiency. We subjected a panel of 30 genetically diverse sorghum genotypes to a spectrum of nitrogen deprivation and measured responses using high-throughput phenotyping technology followed by ionomic profiling. Responses were quantified using shape (16 measurable outputs), color (hue and intensity) and ionome (18 elements). We measured the speed at which specific genotypes respond to environmental conditions, both in terms of biomass and color changes, and identified individual genotypes that perform most favorably. With this analysis we present a novel approach to quantifying color-based stress indicators over time. Additionally, ionomic profiling was conducted as an independent, low cost and high throughput option for characterizing G × E, identifying the elements most affected by either genotype or treatment and suggesting signaling that occurs in response to the environment. This entire dataset and associated scripts are made available through an open access, user-friendly, web-based interface. In summary, this work provides analysis tools for visualizing and quantifying plant abiotic stress responses over time. These methods can be deployed as a time-efficient method of dissecting the genetic mechanisms used by sorghum to respond to the environment to accelerate crop improvement.
Fast and accurate statistical inference of phylogenetic networks using large-scale genomic sequence data
Authors: Hejase Hussein A. , VandePol Natalie , Bonito Gregory M. , Liu Kevin J. 
Published: May 2017

AbstractAn emerging discovery in phylogenomics is that interspecific gene flow has played a major role in the evolution of many different organisms. To what extent is the Tree of Life not truly a tree reflecting strict “vertical” divergence, but rather a more general graph structure known as a phylogenetic network which also captures “horizontal”gene flow? The answer to this fundamental question not only depends upon densely sampled and divergent genomic sequence data, but also compu-tational methods which are capable of accurately and efficiently inferring phylogenetic networks from large-scale genomic sequence datasets. Re-cent methodological advances have attempted to address this gap. How-ever, in the 2016 performance study of Hejase and Liu, state-of-the-art methods fell well short of the scalability requirements of existing phy-logenomic studies.The methodological gap remains: how can phylogenetic networks be ac-curately and efficiently inferred using genomic sequence data involving many dozens or hundreds of taxa? In this study, we address this gap by proposing a new phylogenetic divide-and-conquer method which we call FastNet. We conduct a performance study involving a range of evolu-tionary scenarios, and we demonstrate that FastNet outperforms state-of-the-art methods in terms of computational efficiency and topological accuracy.
Policies or Knowledge: Priors differ between perceptual and sensorimotor tasks
Authors: Chambers Claire , Fernandes Hugo , Paul Kording Konrad 
Published: May 2017

ABSTRACTIf the brain abstractly represents probability distributions as knowledge, then the modality of a decision, e.g. movement vs perception, should not matter. If on the other hand, learned representations are policies, they may be specific to the task where learning takes place. Here, we test this by asking if a learned spatial prior generalizes from a sensorimotor estimation task to a two-alternative-forced choice (2-Afc) perceptual comparison task. A model and simulation-based analysis revealed that while participants learn the experimentally-imposed prior distribution in the sensorimotor estimation task, measured priors are consistently broader than expected in the 2-Afc task. That the prior does not fully generalize suggests that sensorimotor priors strongly resemble policies. In disagreement with standard Bayesian thought, the modality of the decision has a strong influence on the implied prior distribution.NEW AND NOTEWORTHYWe do not know if the brain represents abstract and generalizable knowledge or task-specific policies that map internal states to actions. We find that learning in a sensorimotor task does not generalize strongly to a perceptual task, suggesting that humans learned policies and did not truly acquire knowledge. Priors differ across tasks, thus casting doubt on the central tenet of may Bayesian models, that the brain’s representation of the world is built on generalizable knowledge.
Platelet phosphorylated TDP-43: An exploratory study for a peripheral surrogate biomarker development for Alzheimer’s disease
Authors: Wilhite Rodger , Sage Jessica , Bouzid Abdurrahman , Primavera Tyler , Agbas Abdulbaki 
Published: May 2017

AbstractAim: Alzheimer’s disease (AD) and other forms of dementia create a non-curable disease population in World’s societies. To develop a blood-based biomarker is important so that the remedial or disease-altering therapeutic intervention for AD patients would be available at the early stage. Materials & Methods: TDP-43 levels were analyzed in post-mortem brain tissue and platelets of AD and control subjects. Results: We observed an increased TDP-43 (<60%) in post-mortem AD brain regions and similar trends were also observed in patient’s platelets. Conclusion: Platelet TDP-43 could be used as a surrogate biomarker that is measurable, reproducible, and sensitive for screening the patients with some early clinical signs of AD and can be used to monitor disease prognosis.Lay abstractIn this study, we explore to identify an Alzheimer’s disease-selective phospho-specific antibody that recognizes the diseased form of TDP-43 protein in patient’s blood-derived platelets. Our results suggest that selective anti-phosphorylated TDP-43 antibody discriminates Alzheimer’s disease from non-demented controls and patients with amyotrophic lateral sclerosis. Therefore, platelet screening with a selective antibody could potentially be a useful tool for diagnostic purposes for Alzheimer’s disease.