bluuebunny/crossref_metadata_2025 huggingface dataset:
Tony Bartelme Receives 2017 Walter Sullivan Award for Excellence in Science Journalism–Features
Authors:   AGU
Published: January 2018

Tony Bartelme received the 2017 Walter Sullivan Award for Excellence in Science Journalism–Features at the American Geophysical Union Fall Meeting Honors Ceremony, held on 13 December 2017 in New Orleans, La. The award recognizes “a journalist for a feature story or series in any medium except books that makes information about the Earth and space sciences accessible and interesting to the general public.”
Optical magnetism in planar metamaterial heterostructures
Authors: Papadakis Georgia T. , Fleischman Dagny , Davoyan Artur , Yeh Pochi , Atwater Harry A.
Published: January 2018

Harnessing artificial optical magnetism has previously required complex two- and three-dimensional structures, such as nanoparticle arrays and split-ring metamaterials. By contrast, planar structures, and in particular dielectric/metal multilayer metamaterials, have been generally considered non-magnetic. Although the hyperbolic and plasmonic properties of these systems have been extensively investigated, their assumed non-magnetic response limits their performance to transverse magnetic (TM) polarization. We propose and experimentally validate a mechanism for artificial magnetism in planar multilayer metamaterials. We also demonstrate that the magnetic properties of high-index dielectric/metal hyperbolic metamaterials can be anisotropic, leading to magnetic hyperbolic dispersion in certain frequency regimes. We show that such systems can support transverse electric polarized interface-bound waves, analogous to their TM counterparts, surface plasmon polaritons. Our results open a route for tailoring optical artificial magnetism in lithography-free layered systems and enable us to generalize the plasmonic and hyperbolic properties to encompass both linear polarizations.
Metabolic and molecular changes associated with the increased skeletal muscle insulin action 24–48 h after exercise in young and old humans
Authors: Stephens Francis B. , Tsintzas Kostas
Published: January 2018

The molecular and metabolic mechanisms underlying the increase in insulin sensitivity (i.e. increased insulin-stimulated skeletal muscle glucose uptake, phosphorylation and storage as glycogen) observed from 12 to 48 h following a single bout of exercise in humans remain unresolved. Moreover, whether these mechanisms differ with age is unclear. It is well established that a single bout of exercise increases the translocation of the glucose transporter, GLUT4, to the plasma membrane. Previous research using unilateral limb muscle contraction models in combination with hyperinsulinaemia has demonstrated that the increase in insulin sensitivity and glycogen synthesis 24 h after exercise is also associated with an increase in hexokinase II (HKII) mRNA and protein content, suggesting an increase in the capacity of the muscle to phosphorylate glucose and divert it towards glycogen synthesis. Interestingly, this response is altered in older individuals for up to 48 h post exercise and is associated with molecular changes in skeletal muscle tissue that are indicative of reduced lipid oxidation, increased lipogenesis, increased inflammation and a relative inflexibility of changes in intramyocellular lipid (IMCL) content. Reduced insulin sensitivity (insulin resistance) is generally related to IMCL content, particularly in the subsarcolemmal (SSL) region, and both are associated with increasing age. Recent research has demonstrated that ageing per se appears to cause an exacerbated lipolytic response to exercise that may result in SSL IMCL accumulation. Further research is required to determine if increased IMCL content affects HKII expression in the days after exercise in older individuals, and the effect of this on skeletal muscle insulin action.
The VEGFA156b isoform is dysregulated in senescent endothelial cells and may be associated with prevalent and incident coronary heart disease
Authors: Latorre Eva , Pilling Luke C. , Lee Benjamin P. , Bandinelli Stefania , Melzer David , Ferrucci Luigi , Harries Lorna W.
Published: January 2018

Coronary heart disease (CHD) is a leading cause of morbidity in people over 65 years of age; >40% of all deaths are due to this condition. The association between increasing age and CHD is well documented; the accumulation of senescent cells in cardiac and vascular tissues may represent one factor underpinning this observation. We aimed to identify senescence-related expression changes in primary human senescent cardiomyocytes and endothelial cells and to relate transcript expression in peripheral blood leucocytes to prevalent and incident CHD in the InCHIANTI study of aging. We quantified splicing factor expression and splicing patterns of candidate transcripts in proliferative and senescent later passage endothelial cells and cardiomyocytes using qRTPCR. Senescence-associated isoforms also expressed in peripheral blood leucocytes were then examined for associations with CHD status in 134 pairs of age, sex and BMI-matched CHD cases and controls. Splicing factor expression was dysregulated in senescent cardiomyocytes, as previously reported for endothelial cells, as was the expression of alternatively expressed cardiac and vascular candidate genes in both cell types. We found nominal associations between the expression of VEGFA156b and FNI-EIIIIA isoforms in peripheral blood mRNA and CHD status. Dysregulated splicing factor expression is a key feature of senescent cardiomyocytes and endothelial cells. Altered splicing of key cardiac or endothelial genes may contribute to the risk of CHD in the human population.
Decline of the
banlieue rouge
: François Maspero’s
Les Passagers du Roissy-Express
Authors: Hui Bon Hoa Jen
Published: January 2018

France’s de-industrialization in the mid-1970s was catastrophic for the proletarian communities of the Parisian
banlieue
. By the 1980s, the effects of prolonged unemployment were apparent, with high rates of voter abstention and growing support for the Front national. In the summer of 1989, writer François Maspero and photographer Anaïk Frantz spend a month wandering through former Communist bastions — the
banlieue rouge
— to take stock of this political shift. While the chronicle of their journey,
Les Passagers du Roissy-Express
(1990), has attracted much scholarly interest, its reflections on the legacy and decline of municipal Communism have gone largely undiscussed. As I show, however,
Les Passagers
presents the social problems of the
banlieue
primarily in terms of a collapse of political horizons. Having long been involved in anti-capitalist and anti-imperialist activism, Maspero intimately experiences the implosion of the radical left during the Mitterrand years.
Les Passagers
documents his attempt to work through it. Written against the backdrop of the brutal suppression of pro-democracy protests in China and the first signs of the coming dissolution of the Soviet Union,
Les Passagers
demonstrates a rare sensitivity to the complex, shifting relationships between state and municipal Communism, and between local party politics and an ethical culture of solidarity. This article examines the contribution that
Les Passagers
makes to a more nuanced understanding of the history of the French left.
On-Demand Intraoperative 3-Dimensional Printing of Custom Cranioplastic Prostheses
Authors: Evins Alexander I , Dutton John , Imam Sayem S , Dadi Amal O , Xu Tao , Cheng Du , Stieg Philip E , Bernardo Antonio
Published: January 2018

BACKGROUND

Currently, implantation of patient-specific cranial prostheses requires reoperation after a period for design and formulation by a third-party manufacturer. Recently, 3-dimensional (3D) printing via fused deposition modeling has demonstrated increased ease of use, rapid production time, and significantly reduced costs, enabling expanded potential for surgical application. Three-dimensional printing may allow neurosurgeons to remove bone, perform a rapid intraoperative scan of the opening, and 3D print custom cranioplastic prostheses during the remainder of the procedure.

OBJECTIVE

To evaluate the feasibility of using a commercially available 3D printer to develop and produce on-demand intraoperative patient-specific cranioplastic prostheses in real time and assess the associated costs, fabrication time, and technical difficulty.

METHODS

Five different craniectomies were each fashioned on 3 cadaveric specimens (6 sides) to sample regions with varying topography, size, thickness, curvature, and complexity. Computed tomography-based cranioplastic implants were designed, formulated, and implanted. Accuracy of development and fabrication, as well as implantation ability and fit, integration with exiting fixation devices, and incorporation of integrated seamless fixation plates were qualitatively evaluated.

RESULTS

All cranioprostheses were successfully designed and printed. Average time for design, from importation of scan data to initiation of printing, was 14.6 min and average print time for all cranioprostheses was 108.6 min.

CONCLUSION

On-demand 3D printing of cranial prostheses is a simple, feasible, inexpensive, and rapid solution that may help improve cosmetic outcomes; significantly reduce production time and cost—expanding availability; eliminate the need for reoperation in select cases, reducing morbidity; and has the potential to decrease perioperative complications including infection and resorption.
RCW 36 in the Vela Molecular Ridge: Evidence for high-mass star-cluster formation triggered by cloud–cloud collision
Authors: Sano Hidetoshi , Enokiya Rei , Hayashi Katsuhiro , Yamagishi Mitsuyoshi , Saeki Shun , Okawa Kazuki , Tsuge Kisetsu , Tsutsumi Daichi , Kohno Mikito , Hattori Yusuke , Yoshiike Satoshi , Fujita Shinji , Nishimura Atsushi , Ohama Akio , Tachihara Kengo , Torii Kazufumi , Hasegawa Yutaka , Kimura Kimihiro , Ogawa Hideo , Wong Graeme F , Braiding Catherine , Rowell Gavin , Burton Michael G , Fukui Yasuo
Published: January 2018

A collision between two molecular clouds is one possible candidate for high-mass star formation. The H ii region RCW 36, located in the Vela molecular ridge, contains a young star cluster (∼ 1 Myr old) and two O-type stars. We present new CO observations of RCW 36 made with NANTEN2, Mopra, and ASTE using 12CO(J = 1–0, 2–1, 3–2) and 13CO(J = 2–1) emission lines. We have discovered two molecular clouds lying at the velocities VLSR ∼  5.5 and 9 km s−1. Both clouds are likely to be physically associated with the star cluster, as verified by the good spatial correspondence among the two clouds, infrared filaments, and the star cluster. We also found a high intensity ratio of ∼ 0.6–1.2 for CO J = 3–2/1–0 toward both clouds, indicating that the gas temperature has been increased due to heating by the O-type stars. We propose that the O-type stars in RCW 36 were formed by a collision between the two clouds, with a relative velocity separation of 5 km s−1. The complementary spatial distributions and the velocity separation of the two clouds are in good agreement with observational signatures expected for O-type star formation triggered by a cloud–cloud collision. We also found a displacement between the complementary spatial distributions of the two clouds, which we estimate to be 0.3 pc assuming the collision angle to be 45° relative to the line-of-sight. We estimate the collision timescale to be ∼ 105 yr. It is probable that the cluster age found by Ellerbroek et al. (2013b, A&A, 558, A102) is dominated by the low-mass members which were not formed under the triggering by cloud–cloud collision, and that the O-type stars in the center of the cluster are explained by the collisional triggering independently from the low-mass star formation.
Basal mitophagy is widespread inDrosophilabut minimally affected by loss of Pink1 or parkin
Authors: Lee Juliette J. , Sanchez-Martinez Alvaro , Martinez Zarate Aitor , Benincá Cristiane , Mayor Ugo , Clague Michael J. , Whitworth Alexander J.
Published: January 2018

Parkinson’s disease factors, PINK1 and parkin, are strongly implicated in stress-induced mitophagy in vitro, but little is known about their impact on basal mitophagyin vivo. We generated transgenicDrosophilaexpressing fluorescent mitophagy reporters to evaluate the impact ofPink1/parkinmutations on basal mitophagy under physiological conditions. We find that mitophagy is readily detectable and abundant in many tissues including Parkinson’s disease relevant dopaminergic neurons. However, we did not detect mitolysosomes in flight muscle. Surprisingly, inPink1orparkinnull flies we did not observe any substantial impact on basal mitophagy. As these flies exhibit locomotor defects and dopaminergic neuron loss, our findings raise questions about current assumptions of the pathogenic mechanism associated with the PINK1/Parkin pathway. Our findings provide evidence that Pink1 and parkin are not essential for bulk basal mitophagy inDrosophila. They also emphasize that mechanisms underpinning basal mitophagy remain largely obscure.

PINK1/parkin are key mediators of stress-induced mitophagyin vitrobut their impact on basal mitophagyin vivois unclear. NovelDrosophilareporters lines reveal abundant mitophagy in many tissues including dopaminergic neurons but is unaffected by loss of PINK1/parkin.
Childhood urbanization affects prefrontal cortical responses to trait anxiety and interacts with polygenic risk for depression
Authors: Zhang Xiao , Yan Hao , Yu Hao , Zhao Xin , Shah Shefali , Dong Zheng , Yang Guang , Zhang Xiaoxi , Muse Timothy , Li Jing , Jiang Sisi , Liao Jinmin , Zhang Yuyanan , Chen Qiang , Weinberger Daniel R , Yue Weihua , Zhang Dai , Tan Hao Yang
Published: January 2018

Global increases in urbanization have brought dramatic economic, environmental and social changes. However, less is understood about how these may influence disease-related brain mechanisms underlying epidemiological observations that urban birth and childhoods may increase the risk for neuropsychiatric disorders, including increased social stress and depression. In a genetically homogeneous Han Chinese adult population with divergent urban and rural birth and childhoods, we examined the structural and functional MRI neural correlates of childhood urbanicity, focusing on behavioral traits responding to social status threats, and polygenic risk for depression. Subjects with divergent rural and urban childhoods were similar in adult socioeconomic status and were genetically homogeneous. Urban childhoods, however, were associated with higher trait anxiety-depression. On structural MRI, urban childhoods were associated with relatively reduced medial prefrontal gray matter volumes. Functional medial prefrontal engagement under social status threat during working memory correlated with trait anxiety-depression in subjects with urban childhoods, to a significantly greater extent than in their rural counterparts, implicating an exaggerated physiological response to the threat context. Stress-associated medial prefrontal engagement also interacted with polygenic risk for depression, significantly predicting a differential response in individuals with urban but not rural childhoods. Developmental urbanicity thus differentially influenced medial prefrontal structure and function, at least in part through mechanisms associated with the neural processing of social status threat, trait anxiety, and genetic risk for depression, which may be factors in the association of urbanicity with adult psychopathology.

Significance Statement

Urban living has been associated with social inequalities and stress. However, less is understood about the neural underpinnings by which these stressors affect disease risk, and in particular, genetic risk for depression. Leveraging urbanization in China, we studied adults with diverse urban and rural upbringings, who were genetically homogeneous and with similar current socioeconomic status, to isolate the effects of childhood urbanicity. At medial prefrontal cortex, a region critical for processing emotional stressors and social status, genetic risk for depression resulted in more deleterious function under stress in individuals with urban, but not rural childhoods. This implicates medial prefrontal cortex’s critical role in brain development, integrating genetic mechanisms of stress and depression with the childhood environment.
Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity
Authors: Rounge Trine B , Umu Sinan U , Keller Andreas , Meese Eckart , Ursin Giske , Tretli Steinar , Lyle Robert , Langseth Hilde
Published: January 2018

Non-coding RNAs (ncRNA) are regulators of cell functions and circulating ncRNAs from the majority of RNA classes, such as miRNA, tRNA, piRNAs, lncRNA, snoRNA, snRNA and miscRNAs, are potential non-invasive biomarkers. Understanding how non-disease traits influence ncRNA expression is essential for assessing their biomarker potential.

We studied associations of common traits (sex, age, smoking, body mass, physical activity, and technical factors such as sample storage and processing) with serum ncRNAs. We used RNAseq data from 526 donors from the Janus Serum Bank and traits from health examination surveys. We identified associations between all RNA classes and traits. Ageing showed the strongest association with ncRNA expression, both in terms of statistical significance and number of RNAs, regardless of RNA class. Serum processing modifications and storage times significantly altered expression levels of a number of ncRNAs. Interestingly, smoking cessation generally restored RNA expression to non-smoking levels, although for some isomiRs, mRNA fragments and tRNAs smoking-related expression levels persisted.

Our results show that common traits influence circulating ncRNA expression. Therefore it is clear that ncRNA biomarker analyses should be adjusted for age and sex. In addition, for specific ncRNAs identified in our study, analyses should also be adjusted for body mass, smoking, physical activity and serum processing and storage.
Heritability, selection, and the response to selection in the presence of phenotypic measurement error: effects, cures, and the role of repeated measurements
Authors: Ponzi Erica , Keller Lukas F. , Bonnet Timothée , Muff Stefanie
Published: January 2018

Quantitative genetic analyses require extensive measurements of phenotypic traits, a task that is often not trivial, especially in wild populations. On top of instrumental measurement error, some traits may undergo transient (i.e. non-persistent) fluctuations that are biologically irrelevant for selection processes. These two sources of variability, which we denote here as measurement error in a broad sense, are possible causes for bias in the estimation of quantitative genetic parameters. We illustrate how in a continuous trait transient effects with a classical measurement error structure may bias estimates of heritability, selection gradients, and the predicted response to selection. We propose strategies to obtain unbiased estimates with the help of repeated measurements taken at an appropriate temporal scale. However, the fact that in quantitative genetic analyses repeated measurements are also used to isolate permanent environmental instead of transient effects, requires a re-assessment of the information content of repeated measurements. To do so, we propose to distinguish “short-term” from “long-term” repeats, where the former capture transient variability and the latter the permanent effects. We show how the inclusion of the corresponding variance components in quantitative genetic models yields unbiased estimates of all quantities of interest, and we illustrate the application of the method to data from a Swiss snow vole population.
Interactome Analysis Reveals Regulator of G Protein Signaling 14 (RGS14) is a Novel Calmodulin (CaM) Effector in Mouse Brain
Authors: Evans Paul R. , Gerber Kyle J. , Dammer Eric B. , Duong Duc M. , Goswami Devrishi , Lustberg Daniel J. , Zou Juan , Yang Jenny J. , Dudek Serena M. , Griffin Patrick R. , Seyfried Nicholas T. , Hepler John R.
Published: January 2018

Regulator of G Protein Signaling 14 (RGS14) is a complex scaffolding protein with an unusual domain structure that allows it to integrate G protein and mitogen-activated protein kinase (MAPK) signaling pathways. RGS14 mRNA and protein are enriched in brain tissue of rodents and primates. In the adult mouse brain, RGS14 is predominantly expressed in postsynaptic dendrites and spines of hippocampal CA2 pyramidal neurons where it naturally inhibits synaptic plasticity and hippocampus-dependent learning and memory. However, the signaling proteins that RGS14 natively interacts with in neurons to regulate plasticity are unknown. Here, we show that RGS14 exists as a component of a high molecular weight protein complex in brain. To identify RGS14 neuronal interacting partners, endogenous RGS14 immunoprecipitated from mouse brain was subjected to mass spectrometry and proteomic analysis. We find that RGS14 interacts with key postsynaptic proteins that regulate neuronal plasticity. Gene ontology analysis reveals that the most enriched RGS14 interacting proteins have functional roles in actin-binding, calmodulin(CaM)-binding, and CaM-dependent protein kinase (CaMK) activity. We validate these proteomics findings using biochemical assays that identify interactions between RGS14 and two previously unknown binding partners: CaM and CaMKII. We report that RGS14 directly interacts with CaM in a calcium-dependent manner and is phosphorylated by CaMKII in vitro. Lastly, we detect that RGS14 associates with CaMKII and with CaM in hippocampal CA2 neurons by proximity ligation assays in mouse brain sections. Taken together, these findings demonstrate that RGS14 is a novel CaM effector and CaMKII phosphorylation substrate thereby providing new insight into cellular mechanisms by which RGS14 controls plasticity in CA2 neurons.
Messenger RNA biomarker signatures for forensic body fluid identification revealed by targeted RNA sequencing
Authors: Hanson E , Ingold S , Haas C , Ballantyne J
Published: January 2018

The recovery of a DNA profile from the perpetrator or victim in criminal investigations can provide valuable ‘source level’ information for investigators. However, a DNA profile does not reveal the circumstances by which biological material was transferred. Some contextual information can be obtained by a determination of the tissue or fluid source of origin of the biological material as it is potentially indicative of some behavioral activity on behalf of the individual that resulted in its transfer from the body. Here, we sought to improve upon established RNA based methods for body fluid identification by developing a targeted multiplexed next generation mRNA sequencing assay comprising a panel of approximately equal sized gene amplicons. The multiplexed biomarker panel includes several highly specific gene targets with the necessary specificity to definitively identify most forensically relevant biological fluids and tissues (blood, semen, saliva, vaginal secretions, menstrual blood and skin). In developing the biomarker panel we evaluated 66 gene targets, with a progressive iteration of testing target combinations that exhibited optimal sensitivity and specificity using a training set of forensically relevant body fluid samples. The current assay comprises 33 targets: 6 blood, 6 semen, 6 saliva, 4 vaginal secretions, 5 menstrual blood and 6 skin markers. We demonstrate the sensitivity and specificity of the assay and the ability to identify body fluids in single source and admixed stains. A 16 sample blind test was carried out by one lab with samples provided by the other participating lab. The blinded lab correctly identified the body fluids present in 15 of the samples with the major component identified in the 16th. Various classification methods are being investigated to permit inference of the body fluid/tissue in dried physiological stains. These include the percentage of reads in a sample that are due to each of the 6 tissues/body fluids tested and inter-sample differential gene expression revealed by agglomerative hierarchical clustering.
Cause and consequences of genome duplication in haploid yeast populations
Authors: Fisher Kaitlin J. , Buskirk Sean W. , Vignogna Ryan C. , Marad Daniel A. , Lang Gregory I.
Published: January 2018

Whole genome duplications (WGD) represent important evolutionary events that shape future adaptation. WGDs are known to have occurred in the lineages leading to plants, fungi, and vertebrates. Changes to ploidy level impact the rate and spectrum of beneficial mutations and thus the rate of adaptation. Laboratory evolution experiments initiated with haploidSaccharomyces cerevisiaecultures repeatedly experience WGD. We report recurrent genome duplication in 46 haploid yeast populations evolved for 4,000 generations. We find that WGD confers a fitness advantage, and this immediate fitness gain is accompanied by a shift in genomic and phenotypic evolution. The presence of ploidy-enriched targets of selection and structural variants reveals that autodiploids utilize adaptive paths inaccessible to haploids. We find that autodiploids accumulate recessive deleterious mutations, indicating an increased capacity for neutral evolution. Finally, we report that WGD results in a reduced adaptation rate, indicating a trade-off between immediate fitness gains and long term adaptability.
RNA-seq transcript quantification from reduced-representation data in recount2
Authors: Fu Jack M. , Kammers Kai , Nellore Abhinav , Collado-Torres Leonardo , Leek Jeffrey T. , Taub Margaret A.
Published: January 2018

More than 70,000 short-read RNA-sequencing samples are publicly available through the recount2 project, a curated database of summary coverage data. However, no current methods can be directly applied to the reduced-representation information stored in this database to estimate transcript-level abundances. Here we present a linear model taking as input summary coverage of junctions and subdivided exons to output estimated abundances and associated uncertainty. We evaluate the performance of our model on simulated and real data, and provide a procedure to construct confidence intervals for estimates.
Physical Principles of Retroviral Integration in the Human Genome
Authors: Michieletto D. , Lusic M. , Marenduzzo D. , Orlandini E.
Published: January 2018

Certain retroviruses, including HIV, insert their DNA in a non-random fraction of the host genome via poorly understood selection mechanisms. Here, we develop a biophysical model for retroviral integrations as stochastic and quasi-equilibrium topological reconnections between polymers. We discover that physical effects, such as DNA accessibility and elasticity, play important and universal roles in this process. Our simulations predict that integration is favoured within nucleosomal and flexible DNA, in line with experiments, and that these biases arise due to competing energy barriers associated with DNA deformations. By considering a long chromosomal region in human T-cells during interphase, we discover that at these larger scales integration sites are predominantly determined by chromatin accessibility. Finally, we propose and solve a reaction-diffusion problem that recapitulates the distribution of HIV hot-spots within T-cells. With few generic assumptions, our model can rationalise experimental observations and identifies previously unappreciated physical contributions to retroviral integration site selection.
Impact of DNA polymerase choice on assessment of bacterial communities by a Legionella genus-specific next-generation sequencing approach
Authors: Pereira Rui P. A. , Peplies Jörg , Brettar Ingrid , Höfle Manfred G.
Published: January 2018

The library preparation step is a major source of bias in NGS-based studies. Several PCR-related factors might negatively influence the application of NGS tools in environmental studies and diagnostics. Among the most understudied factors are DNA polymerases. In our study, we evaluated the effect of DNA polymerase type on the characterisation of bacterial communities, more precisely Legionella, using a genus-specific NGS approach. The assay with proof-reading high fidelity KAPA HiFi showed better amplification yield than the one with widely used non-proofreading HotStarTaq. Legionella community richness metrics were significantly overestimated with HotStarTaq. However, the choice of DNA polymerase did not significantly change the community profiling and composition. These results substantiate the use of proof-reading high fidelity DNA polymerases in NGS assays and highlight the need of considering the impact of different DNA polymerases in comparative studies and future guidelines for NGS-based diagnostic tools.
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution
Authors: Xia Li Charlie , Ai Dongmei , Lee Hojoon , Andor Noemi , Li Chao , Zhang Nancy R. , Ji Hanlee P.
Published: January 2018

Background

Simulating genome sequence data with features can facilitate the development and benchmarking of structural variant analysis programs. However, there are a limited number of data simulators that provide structural variants in silico. Moreover, there are a paucity of programs that generate structural variants with different allelic fraction and haplotypes.

Findings

We developed SVEngine, an open source tool to address this need. SVEngine simulates next generation sequencing data with embedded structural variations. As input, SVEngine takes template haploid sequences (FASTA) and an external variant file, a variant distribution file and/or a clonal phylogeny tree file (NEWICK) as input. Subsequently, it simulates and outputs sequence contigs (FASTAs), sequence reads (FASTQs) and/or post-alignment files (BAMs). All of the files contain the desired variants, along with BED files containing the ground truth. SVEngine’s flexible design process enables one to specify size, position, and allelic fraction for deletion, insertion, duplication, inversion and translocation variants. Finally, SVEngine simulates sequence data that replicates the characteristics of a sequencing library with mixed sizes of DNA insert molecules. To improve the compute speed, SVEngine is highly parallelized to reduce the simulation time.

Conclusions

We demonstrated the versatile features of SVEngine and its improved runtime comparisons with other available simulators. SVEngine’s features include the simulation of locus-specific variant frequency designed to mimic the phylogeny of cancer clonal evolution. We validated the accuracy of the simulations. Our evaluation included checking various sequencing mapping features such as coverage change, read clipping, insert size shift and neighbouring hanging read pairs for representative variant types. SVEngine is implemented as a standard Python package and is freely available for academic use at: https://bitbucket.org/charade/svengine.
The Current Political Discourse Concerning International Law
Authors: Crawford James
Published: January 2018

Reading current statements of world leaders on subjects relevant to international law is liable to cause confusion, even distress to those for whom the 1945 regulatory arrangements, as completed in the post‐Cold War era, have become the norm. On occasions international law is invoked, but in what seems an increasingly antagonistic way, amounting often to a dialogue of the deaf. At other times it is apparently or even transparently ignored. This touches many of the arrangements governments spent the preceding period seeking to establish. Is there a pattern to all this, and how should we respond? How susceptible is the edifice of international law to such rhetoric? These issues are examined in the context of the law of withdrawal from treaties. Three recent high profile examples are examined: Brexit, South Africa's purported withdrawal from the Rome Statute, and the United States’ announced withdrawal from the Paris Agreement.
The Dynamics of Enduring Property Relationships in Land
Authors: Blandy Sarah , Bright Susan , Nield Sarah
Published: January 2018

This article proposes a new way of looking at property relationships that will enrich our understanding of how they operate. It focuses on property rights in land which are consensual in origin, although this approach could usefully be applied both to non‐consensual property relationships and to other property types. Recognising both the temporal and spatial dimensions of land, the dynamics approach reflects the fact that most property relationships are lived relationships, affected by changing patterns and understandings of spatial use, relationship needs, economic realities, opportunities, technical innovations, and so on. Although evolving responsively to accommodate changing uses and new rights‐holders, these relationships are nevertheless sustained and enduring. The dynamics lens acknowledges the diverse range of legal, regulatory, social and commercial norms that shape property relations. Our approach also explores how far the enduring, yet dynamic, nature of property relations is taken into account by a range of decision‐makers.
On the Relations between Agent and Principal: Angove's Pty Ltd v Bailey
Authors: Grower Julius A. W.
Published: January 2018

In Angove's Pty Ltd v Bailey the Supreme Court faced ‘two important and controversial questions of commercial law’: whether an agent's authority could ever be ‘irrevocable’, and whether the receipt of money by an imminent insolvent could ever give rise to a constructive trust of that sum. It answered both in the affirmative, albeit subject to heavy qualifications. This note supports these conclusions in principle, however it will argue that the court's reasoning, especially in answering the second question, leaves much to be desired. In particular, it ignored the central role of fiduciary law in regulating the conduct of agents.
Development of Scientific Thinking Facilitated by Reflective Self‐Assessment in a Communication‐Intensive Food Science and Human Nutrition Course
Authors: Hendrich Suzanne , Licklider Barbara , Thompson Katherine , Thompson Janette , Haynes Cynthia , Wiersema Jan
Published: January 2018

A one‐credit seminar on controversies in food science and human nutrition was a platform to introduce students to learning frameworks for thinking‐like‐a‐scientist. We hypothesized that explicitly engaging students in thinking about their thinking abilities within these frameworks would enhance their self‐perception of scientific thinking, an important general ability for food scientists. Our objectives were to assess thinking‐like‐a‐scientist using a student self‐assessment survey, and analyze their self‐reflections for evidence of such thinking. For students enrolled in one of the offerings of this course among 5 semesters from 2012 to 2014, differences in scores on a survey instrument for thinking‐like‐a‐scientist from the beginning to the end of the course showed gains in self‐assessed abilities (N = 21 to 22 students/semester). In each of the first 2 semesters in which we introduced thinking‐like‐a‐scientist frameworks, students thought they were better at defining problems scientifically by 13% to 14%. In the 3rd course offering, students’ self‐assessment of their abilities to seek evidence improved by 10%. In the 4th and 5th semester course offerings, students’ self‐assessed abilities to develop plans based on evidence improved by 7% to 14%. At the end of each semester, students’ self‐reflections on scientific thinking (N = 20 to 24/semester) included specific reference to asking questions (45% to 65% of reflections) and making plans based on evidence (26% to 50% of reflections). These data support the usefulness of self‐reflection tools as well as specific learning frameworks to help students to think about and practice thinking‐like‐a‐scientist.
Effects of Collective Efficacy, Teamwork Attitudes, and Experience on Group Project Performance: Comparisons Between 2 Food Science Courses
Authors: McLeod Poppy Lauretta , Orta‐Ramirez Alicia
Published: January 2018

The relationship between past teamwork and task‐related experiences, attitude toward teamwork, collective efficacy, and task performance among undergraduates (N = 298) assigned to group projects (N = 48) in 2 different Food Science courses was examined. The results of survey data collected at the beginning and end of the projects showed that past teamwork and task‐related experience predicted individual student efficacy at the end of the project, and that starting efficacy, but not attitudes toward teamwork, mediated that relationship. Convergence over time among team members’ efficacy, and diversity of past task‐related experiences was positively related to project grade, whereas diversity in past teamwork experiences was negatively related to project grade. The relationship between past experiences, attitude toward teamwork, efficacy, and grades did not differ between the 2 courses. Implications for practices of implementing group class projects are discussed.
Utilization of an Accelerated Queso Fresco Recipe to Teach Concepts of Food Science in a Didactic Program in Dietetics
Authors: Therrien Mona , Calder Beth L. , Castonguay Zakkary J.
Published: January 2018

Students in the Didactic Program in Dietetics (DPD) at the University of Maine were exposed to the cheese‐making process, within a lab setting of two hours, utilizing an accelerated recipe for a Queso Fresco‐style cheese. The purpose of this project was to provide students with a novel, hands‐on learning experience, which covered concepts of coagulating milk with enzymes and the treatment of curds during the cheese‐making process. The cheese recipe was tested three times by faculty and a teaching assistant to ensure standard results. The recipe, directions and procedures were adjusted and recorded. A standardized recipe and procedure were created for use in the student laboratory. Comparison of knowledge pre‐ and post‐experiment were analyzed using the Wilcoxon Signed‐Rank Test using Statistical Package for Social Sciences (SPSS) version 23.0. Thirty‐four students participated in the laboratory and when surveyed, expressed significant improvement in their understanding of the cheese‐making process (p <0.001). Students also rated themselves on a six‐step confidence scale from “not confident at all” to “very confident” in their understanding and ability in cheese‐making with 70.5 % of the 34 students participating reporting a three‐step increase in their confidence level. Students also completed a sensory evaluation of the recipe, utilizing a 9‐point Hedonic scale (1‐Dislike Extremely to 9‐Like Extremely), with over 88 % of students giving the product a positive overall acceptability rating. Through experience gained during the cheese‐making laboratory, students were able to apply concepts in food preparation, food science and sensory evaluation, all part of the curriculum content requirements of a DPD.
Give me a sample of air and I will tell which species are found from your region: Molecular identification of fungi from airborne spore samples
Authors: Abrego Nerea , Norros Veera , Halme Panu , Somervuo Panu , Ali‐Kovero Heini , Ovaskainen Otso
Published: January 2018

Fungi are a megadiverse group of organisms, they play major roles in ecosystem functioning and are important for human health, food production and nature conservation. Our knowledge on fungal diversity and fungal ecology is however still very limited, in part because surveying and identifying fungi is time demanding and requires expert knowledge. We present a method that allows anyone to generate a list of fungal species likely to occur in a region of interest, with minimal effort and without requiring taxonomical expertise. The method consists of using a cyclone sampler to acquire fungal spores directly from the air to an Eppendorf tube, and applying DNA barcoding with probabilistic species identification to generate a list of species from the sample. We tested the feasibility of the method by acquiring replicate air samples from different geographical regions within Finland. Our results show that air sampling is adequate for regional‐level surveys, with samples collected >100 km apart varying but samples collected <10 km apart not varying in their species composition. The data show marked phenology, and thus obtaining a representative species list requires aerial sampling that covers the entire fruiting season. In sum, aerial sampling combined with probabilistic molecular species identification offers a highly effective method for generating a species list of air‐dispersing fungi. The method presented here has the potential to revolutionize fungal surveys, as it provides a highly cost‐efficient way to include fungi as a part of large‐scale biodiversity assessments and monitoring programs.
A methodological guide to using and reporting on interviews in conservation science research
Authors: Young Juliette C. , Rose David C. , Mumby Hannah S. , Benitez‐Capistros Francisco , Derrick Christina J. , Finch Tom , Garcia Carolina , Home Chandrima , Marwaha Esha , Morgans Courtney , Parkinson Stephen , Shah Jay , Wilson Kerrie A. , Mukherjee Nibedita
Published: January 2018

Interviews are a widely used methodology in conservation research. They are flexible, allowing in‐depth analysis from a relatively small sample size and place the focus of research on the views of participants. While interviews are a popular method, several critiques have been raised in response to their use, including the lack of transparency in sampling strategy, choice of questions and mode of analysis.

In this paper, we analyse the use of interviews in research aimed at making decisions for conservation. Through a structured review of 227 papers, we explore where, why and how interviews were used in the context of conservation decision making

The review suggests that interviews are a widely used method for a broad range of purposes. These include gaining ecological and/or socio‐economic information on specific conservation issues, understanding knowledge, values, beliefs or decision‐making processes of stakeholders, and strengthening research design and output. The review, however, identifies a number of concerns. Researchers are not reporting fully on their interview methodology. Specifically, results indicate that researchers are: failing to provide a rationale as to why interviews are the most suitable method, not piloting the interviews (thus questions may be poorly designed), not outlining ethical considerations, not providing clear guides to analysis and not critically reviewing their use of interviews.

Based on the results of the review, we provide a detailed checklist aimed at conservation researchers who wish to use interviews in their research (whether experienced in using the methodology or not), and journal editors and reviewers to ensure the robustness of interview methodology use.
Land Value Taxation in Vancouver: Rent‐Seeking and the Tax Revolt
Authors: England Christopher
Published: January 2018

At the beginning of the 20thcentury, Vancouver obtained international acclaim as a “single‐tax” city. Supporters claimed that land value taxation was responsible for the spectacular growth of the city. Even critics believed that it had produced a building boom and declining rents. Yet, over several decades, the system was scaled back and ultimately ended in 1984. This article argues that the property tax revolt can be understood with Mancur Olson's model of collective action. Property owners are better organized than other parties impacted by housing policy because they have financial resources and a salient economic concern in housing. Thus, the special interests of property owners in higher values and unrestricted use prevailed over the interests of tenants and prospective buyers. While the property tax revolt was often articulated in the progressive language of ability to pay, when confronted with progressive counterarguments, it collapsed into explicit arguments for rent‐seeking.
The urgent need for a harmonized severity scoring system for acute allergic reactions
Authors: Muraro A. , Fernandez‐Rivas M. , Beyer K. , Cardona V. , Clark A. , Eller E. , Hourihane J. O'B. , Jutel M. , Sheikh A. , Agache I. , Allen K. J. , Angier E. , Ballmer‐Weber B. , Bilò M. B. , Bindslev‐Jensen C. , Camargo C. A. , Cianferoni A. , DunnGalvin A. , Eigenmann P. A. , Halken S. , Hoffmann‐Sommergruber K. , Lau S. , Nilsson C. , Poulsen L. K. , Rueff F. , Spergel J. , Sturm G. , Timmermans F. , Torres M. J. , Turner P. , van Ree R. , Wickman M. , Worm M. , Mills E. N. C. , Roberts G.
Published: January 2018

The accurate assessment and communication of the severity of acute allergic reactions are important to patients, clinicians, researchers, the food industry, and public health and regulatory authorities. Severity has different meanings to different stakeholders with patients and clinicians rating the significance of particular symptoms very differently. Many severity scoring systems have been generated, most focusing on the severity of reactions following exposure to a limited group of allergens. They are heterogeneous in format, none has used an accepted developmental approach, and none has been validated. Their wide range of outcome formats has led to difficulties with interpretation and application. Therefore, there is a persisting need for an appropriately developed and validated severity scoring system for allergic reactions that work across the range of allergenic triggers and address the needs of different stakeholder groups. We propose a novel approach to develop and then validate a harmonized scoring system for acute allergic reactions, based on a data‐driven method that is informed by clinical and patient experience and other stakeholders’ perspectives. We envisage two formats: (i) a numerical score giving a continuum from mild to severe reactions that are clinically meaningful and are useful for allergy healthcare professionals and researchers, and (ii) a three‐grade‐based ordinal format that is simple enough to be used and understood by other professionals and patients. Testing of reliability and validity of the new approach in a range of settings and populations will allow eventual implementation of a standardized scoring system in clinical studies and routine practice.
The asthma‐rhinitis multimorbidity is associated with IgE polysensitization in adolescents and adults
Authors: Siroux V. , Ballardini N. , Soler M. , Lupinek C. , Boudier A. , Pin I. , Just J. , Nadif R. , Anto J. M. , Melen E. , Valenta R. , Wickman M. , Bousquet J.
Published: January 2018

Background

Children with multimorbid asthma and rhinitis show IgE polysensitization to several allergen sources. This association remains poorly studied in adolescents and adults using defined allergen molecules. We investigated IgE sensitization patterns towards a broad panel of aeroallergen components in adults and adolescents with a focus on individuals with asthma and rhinitis multimorbidity.

Methods

IgE reactivity to 64 micro‐arrayed aeroallergen molecules was determined with the MeDALL‐chip in samples from the French EGEA study (n = 840, age = 40.7 ± 17.1) and the Swedish population‐based birth cohort BAMSE (n = 786, age = 16 ± 0.26). The age‐ and sex‐adjusted associations between the number of IgE‐reactive allergen molecules (≥0.3 ISU) and the asthma‐rhinitis phenotypes were assessed using a negative binomial model.

Results

Groups representing 4 phenotypes were identified: no asthma‐no rhinitis (A−R−; 30% in EGEA and 54% in BAMSE), asthma alone (A+R−; 11% and 8%), rhinitis alone (A−R+; 15% and 24%) and asthma‐rhinitis (A+R+; 44% and 14%). The numbers of IgE‐reactive aeroallergen molecules significantly differed between phenotypes (median in A−R−, A+R−, A−R+ and A+R+: 0, 1, 2 and 7 in EGEA and 0, 0, 3 and 5 in BAMSE). As compared to A−R− subjects, the adjusted ratio of the mean number of IgE‐reactive molecules was higher in A+R+ than in A+R− or A−R+ (10.0, 5.4 and 5.0 in EGEA and 7.2, 0.7 and 4.8 in BAMSE).

Conclusion

The A+R+ phenotype combined the sensitization pattern of both the A−R+ and A+R− phenotypes. This multimorbid polysensitized phenotype seems to be generalizable to various ages and allergenic environments and may be associated with specific mechanisms.