bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the dynamics of reproductive values and phenotypic traits in class-structured populations
Authors: Lion Sébastien 
Published: June 2017

AbstractIn natural populations, individuals of a given genotype may belong to different classes. Such classes can for instance represent different age groups, developmental stages, or habitats. Class structure has important evolutionary consequences because the fitness of individuals with the same genetic background may vary depending on their class. As a result, demographic transitions between classes can cause fluctuations that need to be removed when estimating selection on a trait. Intrinsic differences between classes are classically taken into account by weighting individuals by class-specific reproductive values, defined as the relative contribution of individuals in a given class to the future of the population. These reproductive values are generally constant weights calculated from a constant projection matrix. Here, I show, for large populations and clonal reproduction, that reproductive values can be defined as time-dependent weights satisfying dynamical demographic equations that only depend on the average between-class transition rates over all genotypes. Using these time-dependent demographic reproductive values yields a simple Price equation where the non-selective effects of between-class transitions are removed from the dynamics of the trait. This generalises previous theory to a large class of ecological scenarios, taking into account densitydependence, ecological feedbacks and arbitrary distributions of the trait. I discuss the role of reproductive values for prospective and retrospective analyses of the dynamics of phenotypic traits.Note on this versionCompared to the previous version of the manuscript, some changes have been made to improve the readability and structure of the text, and to clarify the connections with the existing literature. One reviewer pointed out inconsistencies in some of the numerical simulations, and in the mutation term in appendix A2, which have now been fixed. When checking the calculations, I have also identified a missing term in the equation for the dynamics of individual reproductive values. The new equation makes much more sense. Additional results are also presented, in particular for discrete-time models and populations with a continuous age structure, for which Fisher’s original definition of reproductive value can be recovered.
Correlated evolution of self and interspecific incompatibility across the range of a Texas wildflower
Authors: Roda Federico , Hopkins Robin 
Published: July 2017

AbstractPlant species have repeatedly evolved recognition systems between pollen and pistils that identify and reject inappropriate matings. Two of the most important systems recognize self-pollen and interspecific pollen. Outstanding questions are whether and how these two recognition systems are linked and if this association could constrain the evolution of mate choice. Our study characterizes variation in self and interspecific incompatibility in the native range of the Texas wildflowerPhlox drummondii. We found quantitative variation in self-incompatibility and demonstrate that this variation is significantly correlated with variation in incompatibility with its close congenerP. cuspidata. Furthermore, we find strong evidence that self and interspecific incompatibility involve common mechanisms of pollen adhesion or early pollen-tube germination. Finally, we show thatP. drummondiipopulations that co-occur and hybridize withP. cuspidatahave significantly higher interspecific incompatibility and self-incompatibility than isolatedP. drummondiipopulations. This geographic variation suggests that the evolution of self-compatibility is constrained by selection favoring interspecific incompatibility to reduce maladaptive hybridization. To our knowledge this is the strongest evidence that a correlation between variation in self and interspecific incompatibilities could influence the evolution of pollen recognition across the range of a species.
BPG: Seamless, Automated and Interactive Visualization of Scientific Data
Authors: P’ng Christine , Green Jeffrey , Chong Lauren C. , Waggott Daryl , Prokopec Stephenie D. , Shamsi Mehrdad , Nguyen Francis , Mak Denise Y.F. , Lam Felix , Albuquerque Marco A. , Wu Ying , Jung Esther H. , Starmans Maud H.W. , Chan-Seng-Yue Michelle A. , Yao Cindy Q. , Liang Bianca , Lalonde Emilie , Haider Syed , Simone Nicole A. , Sendorek Dorota , Chu Kenneth C. , Moon Nathalie C. , Fox Natalie S. , Grzadkowski Michal R. , Harding Nicholas J. , Fung Clement , Murdoch Amanda R. , Houlahan Kathleen E. , Wang Jianxin , Garcia David R. , Borja Richard de , Sun Ren X. , Lin Xihui , Chen Gregory M. , Lu Aileen , Shiah Yu-Jia , Zia Amin , Kearns Ryan , Boutros Paul C. 
Published: June 2017

AbstractWe introduce BPG, an easy-to-use framework for generating publication-quality, highly-customizable plots in the R statistical environment. This open-source package includes novel methods of displaying high-dimensional datasets and facilitates generation of complex multi-panel figures, making it ideal for complex datasets. A web-based interactive tool allows online figure customization, from which R code can be downloaded for seamless integration with computational pipelines. BPG is available athttp://labs.oicr.on.ca/boutros-lab/software/bpg
Single-molecule FISH in Drosophila muscle reveals location dependent mRNA composition of megaRNPs
Authors: Noma Akiko , Smith Carlas S. , Huisman Maximillian , Martin Robert M. , Moore Melissa J. , Grunwald David 
Published: June 2017

AbstractSingle-molecule fluorescence in-situ hybridization (smFISH) provides direct access to the spatial relationship between nucleic acids and specific subcellular locations. The ability to precisely localize a messenger RNA can reveal key information about its regulation. Although smFISH is well established in cell culture or thin sections, methods for its accurate application to tissues are lacking. The utility of smFISH in thick tissue sections must overcome several challenges, including probe penetration of fixed tissue, accessibility of target mRNAs for probe hybridization, high fluorescent background, spherical aberration along the optical axis, and image segmentation of organelles. Here we describe how we overcame these obstacles to study mRNA localization inDrosophilalarval muscle samples that approach 50 μm thickness. We use sample-specific optimization of smFISH, particle identification based on maximum likelihood testing, and 3-dimensional multiple-organelle segmentation. The latter allows using independent thresholds for different regions of interest within an image stack. Our approach therefore facilitates accurate measurement of mRNA location in thick tissues.
Resistome SNP Calling via Read Colored de Bruijn Graphs
Authors: Alipanahi Bahar , Muggli Martin D. , Jundi Musa , Noyes Noelle , Boucher Christina 
Published: June 2017

AbstractMotivationThe resistome, which refers to all of the antimicrobial resistance (AMR) genes in pathogenic and non-pathogenic bacteria, is frequently studied using shotgun metagenomic data [14, 47]. Unfortunately, few existing methods are able to identify single nucleotide polymorphisms (SNPs) within metagenomic data, and to the best of our knowledge, no methods exist to detect SNPs within AMR genes within the resistome. The ability to identify SNPs in AMR genes across the resistome would represent a significant advance in understanding the dissemination and evolution of AMR, as SNP identification would enable “fingerprinting” of the resistome, which could then be used to track AMR dynamics across various settings and/or time periods.ResultsWe present LueVari, a reference-free SNP caller based on the read colored de Bruijn graph, an extension of the traditional de Bruijn graph that allows repeated regions longer than thek-mer length and shorter than the read length to be identified unambiguously. We demonstrate LueVari was the only method that had reliable sensitivity (between 73% and 98%) as the performance of competing methods varied widely. Furthermore, we show LueVari constructs sequences containing the variation which span 93% of the gene in datasets with lower coverage (15X), and 100% of the gene in datasets with higher coverage (30X).AvailabilityCode and datasets are publicly available athttps://github.com/baharpan/cosmo/tree/LueVari.
Widely used commercial ELISA does not detect preHP-2, but recognizes properdin as a potential second member of the zonulin family
Authors: Scheffler Lucas , Crane Alyce , Heyne Henrike , Tönjes Anke , Schleinitz Dorit , Ihling Christian H. , Stumvoll Michael , Freire Rachel , Fiorentino Maria , Fasano Alessio , Kovacs Peter , Heiker John T. 
Published: July 2017

AbstractBACKGROUNDThere is increasing evidence for the role of impaired intestinal permeability in obesity and associated metabolic diseases. Zonulin is an established serum marker for intestinal permeability and identical to pre-haptoglobin2. Here, we aimed to investigate the relationship between circulating zonulin and metabolic traits related to obesity.METHODSSerum zonulin was measured by using a widely used commercial ELISA kit in 376 subjects from the metabolically well-characterized cohort of Sorbs from Germany. In addition, haptoglobin genotype was determined in DNA samples from all study subjects.RESULTSAs zonulin concentrations did not correlate to the haptoglobin genotypes, we investigated the specificity of the zonulin ELISA assay using antibody capture experiments, mass spectrometry and Western blot analysis. Using serum samples that gave the highest or lowest ELISA signals, we detected several proteins that are likely to be captured by the antibody in the present kit. However, none of these proteins corresponds to pre-haptoglobin2. We used increasing concentrations of recombinant pre-haptoglobin 2 and complement C3 as one of the representative captured proteins and the ELISA kit did not detect either. Western blot analysis using both the polyclonal antibodies used in this kit and monoclonal antibodies rose against zonulin showed a similar protein recognition pattern but with different intensity of detection. The protein(s) measured using the ELISA kit was (were) significantly increased in patients with diabetes and obesity and correlated strongly with markers of the lipid and glucose metabolism. Combining mass spectrometry and Western blot analysis using the polyclonal antibodies used in the ELISA kit, we identified properdin as another member of the zonulin family.CONCLUSIONSOur study suggests that the zonulin ELISA does not recognize pre-haptoglobin 2, rather structural (and possibly functional) analogue proteins belonging to the mannose-associated serine protease family, with properdin being the most likely possible candidate.
Semantic Networks Generated from Early Linguistic Input
Authors: Amatuni Andrei , Bergelson Elika 
Published: July 2017

AbstractSemantic networks generated from different word corpora show common structural characteristics, including high degrees of clustering, short average path lengths, and scale free degree distributions. Previous research has disagreed about whether these features emerge from internally or externally driven properties (i.e. words already in the lexicon vs. regularities in the external world), mapping onto preferential attachment and preferential acquisition accounts, respectively (Steyvers & Tenenbaum, 2005; Hills, Maouene, Maouene, Sheya, & Smith, 2009). Such accounts suggest that inherent semantic structure shapes new lexical growth. Here we extend previous work by creating semantic networks using the SEEDLingS corpus, a newly collected corpus of linguistic input to infants. Using a recently developed LSA-like approach (GLoVe vectors), we confirm the presence of previously reported structural characteristics, but only in certain ranges of semantic similarity space. Our results confirm the robustness of certain aspects of network organization, and provide novel evidence in support of preferential acquisition accounts.
Detecting tandem repeat expansions in cohorts sequenced with short-read sequencing data
Authors: Tankard Rick M , Bennett Mark F , Degorski Peter , Delatycki Martin B , Lockhart Paul J , Bahlo Melanie 
Published: July 2017

AbstractRepeat expansions cause over 30, predominantly neurogenetic, inherited disorders. These can present with overlapping clinical phenotypes, making molecular diagnosis challenging. Single gene or small panel PCR-based methods are employed to identify the precise genetic cause, but can be slow and costly, and often yield no result. Genomic analysis via whole exome and whole genome sequencing (WES and WGS) is being increasingly performed to diagnose genetic disorders. However, until recently analysis protocols could not identify repeat expansions in these datasets.A new method, called exSTRa (expandedShortTandemRepeatalgorithm) for the identification of repeat expansions using either WES or WGS was developed and performance of exSTRa was assessed in a simulation study. In addition, four retrospective cohorts of individuals with eleven different known repeat expansion disorders were analysed with the new method. Results were assessed by comparing to known disease status. Performance was also compared to three other analysis methods (ExpansionHunter, STRetch and TREDPARSE), which were developed specifically for WGS data. Expansions in the STR loci assessed were successfully identified in WES and WGS datasets by all four methods, with high specificity and sensitivity, excepting the FRAXA STR where expansions were unlikely to be detected. Overall exSTRa demonstrated more robust/superior performance for WES data in comparison to the other three methods. exSTRa can be applied to existing WES or WGS data to identify likely repeat expansions and can be used to investigate any STR of interest, by specifying location and repeat motif. We demonstrate that methods such as exSTRa can be effectively utilized as a screening tool to interrogate WES data generated with PCR-based library preparations and WGS data generated using either PCR-based or PCR-free library protocols, for repeat expansions which can then be followed up with specific diagnostic tests. exSTRa is available via GitHub (https://github.com/bahlolab/exSTRa).
Dissection of purified LINE-1 reveals distinct nuclear and cytoplasmic intermediates
Authors: Molloy K.R. , Taylor M.S. , Altukhov I. , Mita P. , Jiang H. , Adney E.M. , Wudzinska A. , Ischenko D. , Burns K.H. , Fenyö D. , Chait B.T. , Alexeev D. , Rout M.P. , Boeke J.D. , LaCava J. 
Published: July 2017

1.SummaryLong Interspersed Nuclear Element-1 (LINE-1, L1) is a mobile genetic element active in human genomes. L1-encoded ORF1 and ORF2 proteins bind L1 RNAs, forming ribonucleoproteins (RNPs). These RNPs interact with diverse host proteins, some repressive and others required for the L1 lifecycle. Using differential affinity purifications and quantitative mass spectrometry, we have characterized the proteins associated with distinctive L1 macromolecular complexes. Our findings support the presence of multiple L1-derived retrotransposition intermediatesin vivo. Among them, we describe a cytoplasmic intermediate that we hypothesize to be the canonical ORF1p/ORF2p/L1-RNA-containing RNP, and we describe a nuclear population containing ORF2p, but lacking ORF1p, which likely contains host factors participating in template-primed reverse transcription.
Impact of different intensities of intermittent theta burst stimulation on the cortical properties during TMS-EEG and working memory performance
Authors: Chung Sung Wook , Rogash Nigel C. , Hoy Kate E. , Sullivan Caley M. , Cash Robin F. H. , Ftizgerald Paul B. 
Published: July 2017

AbstractIntroductionIntermittent theta burst stimulation (iTBS) is a non-invasive brain stimulation technique capable of increasing cortical excitability beyond the stimulation period. Due to the rapid induction of modulatory effects compared to conventional repetitive transcranial magnetic stimulation (rTMS) paradigms, prefrontal application of iTBS is gaining popularity as a therapeutic tool for psychiatric disorders such as depression. In an attempt to increase efficacy, higher than conventional intensities are currently being applied. The assumption that this increases neuromodulatory effect is well established for the standard rTMS paradigms but may be mechanistically false for iTBS. This study examined the influence of intensity on the neurophysiological and behavioural effects of iTBS in the prefrontal cortex.Methods16 healthy participants received iTBS over prefrontal cortex (F1 electrode) at either 50, 75 or 100% resting motor threshold (rMT) in separate sessions. Single-pulse TMS and concurrent electroencephalography (EEG) was used to assess changes in cortical reactivity measured as TMS-evoked potentials (TEPs) and TMS-evoked oscillations. The n-back task (2-back and 3-back) were used to assess changes in working memory (accuracy and reaction time).ResultsThe data can be summarised as an inverse U-shape relationship between intensity and iTBS plastic effects, where 75% iTBS resulted in the largest neurophysiological changes both in TMS-EEG and working memory. Even though 75% iTBS showed significantly decreased reaction time in the 3-back task, between condition comparisons revealed no significant differences.ConclusionsThe assumption that higher intensity results in greater neuromodulatory effects is false, at least in healthy individuals, and should be carefully considered for clinical populations. Neurophysiological changes associated with working memory following iTBS suggest functional relevance. However, the effects of different intensities on behavioural performance remain elusive in the present healthy sample.HighlightsEffects of prefrontal iTBS at 50, 75 and 100% rMT were investigatedInverse U-shape relationship between intensity and neurophysiological effectsEffects on the behavioural performance remain elusive in healthy individualsDisclosures and conflict of interestsSWC was supported by a Monash Graduate Scholarship. NCR is supported by a NHMRC Early Career Fellowship (1072057). KEH is supported by a NHMRC Career Development Fellowship (1082894). PBF is supported by a NHMRC Practitioner Fellowship (1078567). PBF has received equipment for research from MagVenture A/S, Medtronic Ltd, Cervel Neurotech and Brainsway Ltd and funding for research from Neuronetics and Cervel Neurotech. He is on the scientific advisory board for Bionomics Ltd. There are no other conflicts.
Taking off the training wheels: Measuring auditory P3 during outdoor cycling using an active wet EEG system
Authors: Scanlon Joanna E. M. , Townsend Kimberley A. , Cormier Danielle L. , Kuziek Jonathan W. P. , Mathewson Kyle E. 
Published: July 2017

AbstractMobile EEG allows the investigation of brain activity in increasingly complex environments. In this study, EEG equipment was adapted for use and transportation in a backpack while cycling. Participants performed an auditory oddball task while cycling outside and sitting in an isolated chamber inside the lab. Cycling increased EEG noise and marginally diminished alpha amplitude. However, this increased noise did not influence the ability to measure reliable event related potentials (ERP). The P3 was similar in topography, and morphology when outside on the bike, with a lower amplitude in the outside cycling condition. There was only a minor decrease in the statistical power to measure reliable ERP effects. Unexpectedly, when biking outside significantly decreased P2 and increased N1 amplitude were observed when evoked by both standards and targets compared with sitting in the lab. This may be due to attentional processes filtering the overlapping sounds between the tones used and similar environmental frequencies. This study established methods for mobile recording of ERP signals. Future directions include investigating auditory P2 filtering inside the laboratory.HighlightsA backpack containing all the equipment necessary to record ERP and EEG was worn by participants as they rode a bicycle outside along a streetEEG and ERP data from an auditory oddball task is compared with data acquired within subject inside the labReliable MMN/N2b and P3 responses were measured during bicycle riding outside equal in magnitude to those obtained inside the labA surprising decrease in the P2 component of the ERP evoked by targets and standards was observed when doing the task outside on a bicycle, which we attribute to increased auditory filtering
Integration of plasticity mechanisms within a single sensory neuron ofC. elegansactuates a memory
Authors: Hawk Josh D. , Calvo Ana C. , Almoril-Porras Agustin , Aljobeh Ahmad , Torruella-Suárez Maria Luisa , Ren Ivy , Cook Nathan , Greenwood Joel , Luo Linjiao , Samuel Aravinthan D.T. , Colón-Ramos Daniel A. 
Published: July 2017

SummaryNeural plasticity—the ability of a neuron to change its cellular properties in response to past experiences—underpins the nervous system’s capacity to form memories and actuate behaviors. How different plasticity mechanisms act togetherin vivoand at a cellular level to transform sensory information into behavior is not well understood. Here we show that in the nematodeC. eleganstwo plasticity mechanisms—sensory adaptation and presynaptic plasticity—act within a single cell to encode thermosensory information and actuate a temperature-preference memory. Sensory adaptation enables the primary thermosensory neuron, AFD, to adjust the temperature range of its sensitivity to the local environment, thereby optimizing its ability to detect temperature fluctuations associated with migration. Presynaptic plasticity transforms this thermosensory information into a behavioral preference by gating synaptic communication between sensory neuron AFD and its postsynaptic partner, AIY. The gating of synaptic communication is regulated at AFD presynaptic sites by the conserved kinase nPKCε. Bypassing or altering AFD presynaptic plasticity predictably changes the learned behavioral preferences without affecting sensory responses. Our findings indicate that two distinct and modular neuroplasticity mechanisms function together within a single sensory neuron to encode multiple components of information required to enact thermotactic behavior. The integration of these plasticity mechanisms result in a single-cell logic system that can both represent sensory stimuli and guide memory-based behavioral preference.
On the Origins of the Cerebral IVIM Signal
Authors: Hare Hannah V. , Frost Robert , Meakin James A. , Bulte Daniel P. 
Published: July 2017

AbstractPurposeIntravoxel incoherent motion (IVIM) has been proposed as a means of non-invasive MRI measurement of perfusion parameters such as blood flow and blood volume. Its main competitor in the brain is arterial spin labelling (ASL). In theory, IVIM should not suffer from some of the same limitations as ASL such as poor signal in white matter, and assumptions about arterial arrival times that may be violated in the presence of pathology.MethodsIn this study we aimed to test IVIM as a viable alternative to ASL for quantitative imaging of perfusion parameters in the brain. First, a direct comparison was performed between IVIM and multi-post label delay pseudo-continuous ASL; second, IVIM images were acquired with and without nulling cerebrospinal fluid; and finally, ultra-high resolution IVIM was performed to minimise partial voluming.ResultsIn all three tests, IVIM failed to disprove the null hypothesis, strongly suggesting that, at least within the brain, the technique does not measure perfusion parameters as proposed.ConclusionFurthermore, the results obtained suggest that the contrast visible in IVIM-derived images is primarily sensitive to cerebrospinal fluid, and not the microvascular blood compartment.