bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractRegulator 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

AbstractThe 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

ABSTRACTWhole 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

AbstractMore 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.
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

ABSTRACTThe 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

ABSTRACTBackgroundSimulating 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.FindingsWe 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.ConclusionsWe 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

AbstractReading 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

AbstractThis 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

AbstractIn 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

AbstractA 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

AbstractThe 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

AbstractStudents 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

AbstractFungi 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

AbstractInterviews 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 makingThe 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

AbstractAt 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.