bluuebunny/crossref_metadata_2025 huggingface dataset:
Foot-in-the-Door Technique and Problematic Implicit Request for Help
Authors: Guéguen Nicolas , Pascual Alexandre
Published: March 2015

A recent study ( Pascual, Guéguen, Pujos, & Felonneau, 2013 ) reported that the foot-in-the-door technique (FITD) remained effective in gaining compliance when the request was deviant in nature. However, that study used face-to-face verbal requests, which may have resulted in the participant feeling obliged to comply. In our study, a confederate was instructed to sit on a public bench where an adult male participant was sitting. In the FITD condition, the confederate asked the participant for the time. The confederate then began to read a newspaper, some term papers, or a pornographic magazine. After 2 minutes, a second confederate arrived, the first confederate stood up and left, forgetting his papers. The FITD remained effective in obtaining greater participant intervention, even in the problematic condition.
AWMF-Leitlinie zu Hyperkinetischen Störungen in der Praxis
Authors: Isensee Corinna , Hagmayer York , Rothenberger Aribert , Rothenberger Lillian Geza , Becker Andreas
Published: March 2015

Fragestellung: Die AWMF-Leitlinie zu Hyperkinetischen Störungen (HKS) liefert Psychotherapeuten und Ärzten Hinweise zur Diagnostik und Behandlung für eine der häufigsten kinder- und jugendpsychiatrischen Erkrankungen. Es ist aber bisher unklar, wie in der Praxis tätige Therapeuten (Ärzte und Psychologen) diese Leitlinie beurteilen, welche Einstellung sie zu HKS-Leitlinien haben, wie sie diese nutzen und welche Hindernisse bzw. Vorteile sie sehen. Ziele der vorliegenden Studie waren (1) zu analysieren, welche Unterschiede es zwischen Nutzern und Nichtnutzern im Hinblick auf die Beurteilung von HKS-Leitlinien, ihrer Einstellung und Erfahrung mit diesen sowie der Beurteilung von Kontextfaktoren gibt, und (2) zu ermitteln, ob Nutzer und Nichtnutzer sich in ihrer therapeutischen Praxis unterscheiden. Methodik: An einer entsprechenden nicht-repräsentativen online-Umfrage nahmen 71 Therapeuten teil. Ergebnisse: Es bestätigte sich die Hypothese, dass Leitliniennutzer im Mittel eine positivere Einstellung zu HKS-Leitlinien und positivere Erfahrungen mit leitlinienbezogener Behandlung haben als Nichtnutzer. Die Ergebnisse zeigen auch einen kleinen positiven Effekt der Leitliniennutzung auf die Behandlungsqualität. Dennoch stimmten die Versorgungstätigkeiten von Nutzern wie Nichtnutzern nur mäßig mit den Empfehlungen der Leitlinie überein. Schlussfolgerungen: Es zeigte sich, dass die HKS-Leitlinie auch unter günstigen Bedingungen in der Praxis nur mäßig Anwendung findet und eine praxisrelevante Form der HKS-Leitlinie noch nicht vorliegt.
Kerry Blasts Climate Skeptics and Urges Action
Authors: Showstack Randy
Published: March 2015

In a tough speech on climate change, U.S. Secretary of State John Kerry calls out climate skeptics and calls for more efforts to curb emissions.
Embryonic health: new insights, mHealth and personalised patient care
Authors: Steegers-Theunissen Régine P. M. , Steegers Eric A. P.
Published: March 2015

The worldwide epidemic of non-communicable diseases (NCD), including obesity, is a burden to which poor lifestyles contribute significantly. Events in early life may enhance susceptibility to NCD, with transmission into succeeding generations. This may also explain, in part, why interventions in adulthood are less effective to reduce NCD risk. New insights reveal that the early embryo, in particular, is extremely sensitive to signals from gametes, trophoblastic tissue and periconception maternal lifestyles. Embryonic size and growth as determinants of embryonic health seem to impact future health. A relatively small embryo for gestational age is associated with pregnancy complications, as well as with the risk of early features of NCD in childhood. Although personal lifestyles are modifiable, they are extremely difficult to change. Therefore, adopting a life course approach from the periconception period onwards and integrated into patient care with short-term reproductive health benefits may have important implications for future prevention of NCD. The current reproductive population is used to Internet and social media. Therefore, they can be reached via mobile phone (mHealth) platforms that provide personalised lifestyle (pre)pregnancy programs. This will offer opportunities and possibly great benefits for the health of current and succeeding generations.
Spatial proximity of homologous alleles and long noncoding RNAs regulate a switch in allelic gene expression
Authors: Stratigi Kalliopi , Kapsetaki Manouela , Aivaliotis Michalis , Town Terrence , Flavell Richard A. , Spilianakis Charalampos G.
Published: March 2015

Significance

In diploid organisms, trans-allelic interactions control gene expression, providing a tight spatial and temporal level of transcription regulation. Although homologous trans-allelic interactions are quite abundant in various organisms such as Drosophila, plants, and fungi, they have not been widely reported in mammals. This article demonstrates that such a trans-allelic association is evident in mammals and involves the homologous spatial proximity of
Tnfα
alleles as a prerequisite for the biallelic expression of the
Tnfα
gene. We believe the phenomenon we describe here provides mechanistic insights for the regulation of gene allelic expression and mRNA dosage control necessary for fine-tuning physiological processes in mammals.
LBIBCell: a cell-based simulation environment for morphogenetic problems
Authors: Tanaka Simon , Sichau David , Iber Dagmar
Published: March 2015

Motivation: The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events, such as cell division, cell–cell interactions and spatially restricted signalling events. A tightly coupled cell-based mechano-regulatory simulation tool is therefore required.

Results: We developed an open-source software framework for morphogenetic problems. The environment offers core functionalities for the tissue and signalling models. In addition, the software offers great flexibility to add custom extensions and biologically motivated processes. Cells are represented as highly resolved, massless elastic polygons; the viscous properties of the tissue are modelled by a Newtonian fluid. The Immersed Boundary method is used to model the interaction between the viscous and elastic properties of the cells, thus extending on the IBCell model. The fluid and signalling processes are solved using the Lattice Boltzmann method. As application examples we simulate signalling-dependent tissue dynamics.

Availability and implementation: The documentation and source code are available on http://tanakas.bitbucket.org/lbibcell/index.html

Contact:  simon.tanaka@bsse.ethz.ch or dagmar.iber@bsse.ethz.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
Modelling the redshift-space three-point correlation function in SDSS-III
Authors: Guo Hong , Zheng Zheng , Jing Y. P. , Zehavi Idit , Li Cheng , Weinberg David H. , Skibba Ramin A. , Nichol Robert C. , Rossi Graziano , Sabiu Cristiano G. , Schneider Donald P. , McBride Cameron K.
Published: March 2015

We present the measurements of the redshift-space three-point correlation function (3PCF) for z ∼ 0.5 luminous red galaxies of the CMASS sample in the Sloan Digital Sky Survey-III Baryon Oscillation Spectroscopic Survey Data Release 11. The 3PCF measurements are interpreted within the halo occupation distribution framework using high-resolution N-body simulations, and the model successfully reproduces the 3PCF on scales larger than 1 h−1 Mpc. As with the case for the redshift-space two-point correlation functions, we find that the redshift-space 3PCF measurements also favour the inclusion of galaxy velocity bias in the model. In particular, the central galaxy in a halo is on average in motion with respect to the core of the halo. We discuss the potential of the small-scale 3PCF to tighten the constraints on the relation between galaxies and dark matter haloes and on the phase-space distribution of galaxies.
Convection and convective overshooting in stars more massive than 10 M⊙
Authors: Jin Jie , Zhu Chunhua , Lü Guoliang
Published: March 2015

We examine how the mixing length parameter αp and the overshooting parameter δov affect the properties of convective cores and convective envelopes in stars more massive than 10 M⊙. First, we show that a larger value of αp leads to a stronger mixing, a smaller chemical gradient, a higher effective temperature, and a smaller stellar radius. We then find that if a star develops convective core overshooting during the main sequence phase, the star will enter the red (super)giant phase earlier than a star without core overshooting. Finally, we find that a convective envelope leads to a discontinuity of the hydrogen profile above the hydrogen burning shell. Convective envelope overshooting can facilitate the occurrence of blue loop in the Hertzsprung–Russell diagram.
Multimedia Exercise Training Program Improves Distance Walked, Heart Rate Recovery, and Self-efficacy in Cardiac Surgery Patients
Authors: Wang Li-Wei , Ou Shu-Hua , Tsai Chien-Sung , Chang Yue-Cune , Kao Chi-Wen
Published: March 2015

Background:

Patient education has been shown to be more effective when delivered using multimedia than written materials. However, the effects of using multimedia to assist patients in cardiac rehabilitation have not been investigated.

Objective:

The purpose of this study is to examine the effect of an inpatient multimedia exercise training program on distance walked in the 6-minute walking test (6MWT), heart rate recovery, and walking self-efficacy of patients who had undergone heart surgery.

Methods:

For this longitudinal quasi-experimental study, 60 consecutive patients were assigned to an experimental (n = 20; inpatient multimedia exercise training program) or control (n = 40; routine care) group. Data were collected at 3 times (before surgery, 1 to 2 days before hospital discharge, and 1 month after hospital discharge) and analyzed with the generalized estimating equation approach.

Results:

Most subjects were men (66.7%), had a mean age of 61.32 ± 13.4 years and left ventricular ejection fraction of 56.96% ± 13.28%, and underwent coronary artery bypass graft surgery (n = 34, 56.7%). Subjects receiving the exercise training program showed significantly greater improvement than those in the control group in the 6MWT walking distance (P < .001), heart rate recovery (P = .04), and self-efficacy (P = .002) at hospital discharge. Furthermore, the intervention effects on 6MWT distance (P < .001) and self-efficacy (P < .001) were sustained at 1 month after hospital discharge.

Conclusion:

Our inpatient multimedia exercise training program safely improved distance walked in the 6MWT, heart rate recovery, and self-efficacy at hospital discharge in patients after heart surgery and maintained their improvement in 6MWT and self-efficacy 1 month later.
The Spatial Mixing of Genomes in Secondary Contact Zones
Authors: Sedghifar Alisa , Brandvain Yaniv , Ralph Peter , Coop Graham
Published: March 2015

Recent genomic studies have highlighted the important role of admixture in shaping genome-wide patterns of diversity. Past admixture leaves a population genomic signature of linkage disequilibrium (LD), reflecting the mixing of parental chromosomes by segregation and recombination. The extent of this LD can be used to infer the timing of admixture. However, the results of inference can depend strongly on the assumed demographic model. Here, we introduce a theoretical framework for modeling patterns of LD in a geographic contact zone where two differentiated populations are diffusing back together. We derive expressions for the expected LD and admixture tract lengths across geographic space as a function of the age of the contact zone and the dispersal distance of individuals. We develop an approach to infer age of contact zones using population genomic data from multiple spatially sampled populations by fitting our model to the decay of LD with recombination distance. We use our approach to explore the fit of a geographic contact zone model to three human population genomic datasets from populations along the Indonesian archipelago, populations in Central Asia and populations in India.
Detecting hidden diversification shifts in models of trait-dependent speciation and extinction
Authors: Beaulieu Jeremy M , O’Meara Brian C
Published: March 2015

The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased their extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE methods. Specifically, our model, which we refer to as HiSSE (Hidden-State Speciation and Extinction), assumes that related to each observed state in the model are “hidden” states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification (CID) models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification.
Calculating the Human Mutation Rate by Using a NUMT from the Early Oligocene
Authors: Logan Ian
Published: March 2015

As the number of whole genomes available for study increases, so also does the opportunity to find unsuspected features hidden within our genetic code. One such feature allows for an estimate of the Human Mutation Rate in human chromosomes to be made. A NUMT is a small fragment of the mitochondrial DNA that enters the nucleus of a cell, gets captured by a chromosome and thereafter passed on from generation to generation. Over the millions of years of evolution, this unexpected phenomenon has happened many times. But it is usually very difficult to be able to say just when a NUMT might have been created. However, this paper presents evidence to show that for one particular NUMT the date of formation was around 29 million ago, which places the event in the Early Oligocene; when our ancestors were small monkey-like creatures. So now all of us carry this NUMT in each of our cells as do Old World Monkeys, the Great Apes and our nearest relations, the Chimpanzees. The estimate of the Human Mutation obtained by the method outlined here gives a value which is higher than has been generally found; but this new value perhaps only applies to non-coding regions of the Human genome where there is little, if any, selection pressure against new mutations.
Intersubject information mapping: revealing canonical representations of complex natural stimuli
Authors: Kriegeskorte Nikolaus
Published: March 2015

Real-world time-continuous stimuli such as video promise greater naturalism for studies of brain function. However, modeling the stimulus variation is challenging and introduces a bias in favor of particular descriptive dimensions. Alternatively, we can look for brain regions whose signal is correlated between subjects, essentially using one subject to model another. Intersubject correlation mapping (ICM) allows us to find brain regions driven in a canonical manner across subjects by a complex natural stimulus. However, it requires a direct voxel-to-voxel match between the spatiotemporal activity patterns and is thus only sensitive to common activations sufficiently extended to match up in Talairach space (or in an alternative, e.g. cortical-surface-based, common brain space). Here we introduce the more general approach of intersubject information mapping (IIM). For each brain region, IIM determines how much information is shared between the subjects' local spatiotemporal activity patterns. We estimate the intersubject mutual information using canonical correlation analysis applied to voxels within a spherical searchlight centered on each voxel in turn. The intersubject information estimate is invariant to linear transforms including spatial rearrangement of the voxels within the searchlight. This invariance to local encoding will be crucial in exploring fine-grained brain representations, which cannot be matched up in a common space and, more fundamentally, might be unique to each individual – like fingerprints. IIM yields a continuous brain map, which reflects intersubject information in fine-grained patterns. Performed on data from functional magnetic resonance imaging (fMRI) of subjects viewing the same television show, IIM and ICM both highlighted sensory representations, including primary visual and auditory cortices. However, IIM revealed additional regions in higher association cortices, namely temporal pole and orbitofrontal cortex. These regions appear to encode the same information across subjects in their fine-grained patterns, although their spatial-average activation was not significantly correlated between subjects.
Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud
Authors: Cianfrocco Michael A. , Leschziner Andres E.
Published: March 2015

The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. However, calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available ‘off-the-shelf’ computing environment on Amazon’s elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters that can range in size from 16 to 480+ CPUs. Importantly, these computing clusters are also cost-effective, as we illustrate here by determining a near-atomic resolution structure of the 80S yeast ribosome for $28.89 USD in ~10 hours.
Eight thousand years of natural selection in Europe
Authors: Mathieson Iain , Lazaridis Iosif , Rohland Nadin , Mallick Swapan , Patterson Nick , Roodenberg Songül Alpaslan , Harney Eadaoin , Stewardson Kristin , Fernandes Daniel , Novak Mario , Sirak Kendra , Gamba Cristina , Jones Eppie R. , Llamas Bastien , Dryomov Stanislav , Pickrell Joseph , Arsuaga Juan Luís , de Castro José María Bermúdez , Carbonell Eudald , Gerritsen Fokke , Khokhlov Aleksandr , Kuznetsov Pavel , Lozano Marina , Meller Harald , Mochalov Oleg , Moiseyev Vayacheslav , Guerra Manuel A. Rojo , Roodenberg Jacob , Vergès Josep Maria , Krause Johannes , Cooper Alan , Alt Kurt W. , Brown Dorcas , Anthony David , Lalueza-Fox Carles , Haak Wolfgang , Pinhasi Ron , Reich David
Published: March 2015

The arrival of farming in Europe around 8,500 years ago necessitated adaptation to new environments, pathogens, diets, and social organizations. While indirect evidence of adaptation can be detected in patterns of genetic variation in present-day people, ancient DNA makes it possible to witness selection directly by analyzing samples from populations before, during and after adaptation events. Here we report the first genome-wide scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture, who we show were members of the population that was the source of Europe’s first farmers, and whose genetic material we extracted by focusing on the DNA-rich petrous bone. We identify genome-wide significant signatures of selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.
The structure of probabilistic networks
Authors: Poisot Timothée , Cirtwill Alyssa , Cazelles Kévin , Gravel Dominique , Fortin Marie-Josée , Stouffer Daniel
Published: March 2015

1. There is a growing realization among community ecologists that interactions between species vary in space and time. Yet, our current numerical framework to analyze the structure of interactions, largely based on graph-theoretical approaches, is unsuited to this type of data. Since the variation of species interactions holds much information, there is a need to develop new metrics to exploit it. 2. We present analytical expressions of key network metrics, using a probabilistic framework. Our approach is based on modeling each interaction as a Bernoulli event, and using basic calculus to express the expected value, and when mathematically tractable, its variance. We provide a free and open-source implementation of these measures. 3. We show that our approach allows to overcome limitations of both neglecting the variation of interactions (over-estimation of rare events) and using simulations (extremely high computational demand). We present a few case studies that highlight how these measures can be used. 4. We conclude this contribution by discussing how the sampling and data representation of ecological network can be adapted to better allow the application of a fully probabilistic numerical framework.
LINKS: Scaffolding genome assemblies with kilobase-long nanopore reads
Authors: Warren René L. , Vandervalk Benjamin P. , Jones Steven J.M. , Birol Inanç
Published: March 2015

Motivation

Owing to the complexity of the assembly problem, we do not yet have complete genome sequences. The difficulty in assembling reads into finished genomes is exacerbated by sequence repeats and the inability of short reads to capture sufficient genomic information to resolve those problematic regions. Established and emerging long read technologies show great promise in this regard, but their current associated higher error rates typically require computational base correction and/or additional bioinformatics preprocessing before they could be of value. We present LINKS, the Long Interval Nucleotide K-mer Scaffolder algorithm, a solution that makes use of the information in error-rich long reads, without the need for read alignment or base correction. We show how the contiguity of an ABySSE. coliK-12 genome assembly could be increased over five-fold by the use of beta-released Oxford Nanopore Ltd. (ONT) long reads and how LINKS leverages long-range information inS. cerevisiaeW303 ONT reads to yield an assembly with less than half the errors of competing applications. Re-scaffolding the colossal white spruce assembly draft (PG29, 20 Gbp) and how LINKS scales to larger genomes is also presented. We expect LINKS to have broad utility in harnessing the potential of long reads in connecting high-quality sequences of small and large genome assembly drafts.

Availability

http://www.bcgsc.ca/bioinformatics/software/links

Contact

rwarren@bcgsc.ca
Contrasting regional architectures of schizophrenia and other complex diseases using fast variance components analysis
Authors: Loh Po-Ru , Bhatia Gaurav , Gusev Alexander , Finucane Hilary K , Bulik-Sullivan Brendan K , Pollack Samuela J , de Candia Teresa R , Lee Sang Hong , Wray Naomi R , Kendler Kenneth S , O’Donovan Michael C , Neale Benjamin M , Patterson Nick , Price Alkes L ,   Schizophrenia Working Group of the Psychiatric Genomics Consortiumy
Published: March 2015

Heritability analyses of GWAS cohorts have yielded important insights into complex disease architecture, and increasing sample sizes hold the promise of further discoveries. Here, we analyze the genetic architecture of schizophrenia in 49,806 samples from the PGC, and nine complex diseases in 54,734 samples from the GERA cohort. For schizophrenia, we infer an overwhelmingly polygenic disease architecture in which ≥71% of 1Mb genomic regions harbor at least one variant influencing schizophrenia risk. We also observe significant enrichment of heritability in GC-rich regions and in higher-frequency SNPs for both schizophrenia and GERA diseases. In bivariate analyses, we observe significant genetic correlations (ranging from 0.18 to 0.85) among several pairs of GERA diseases; genetic correlations were on average 1.3x stronger than correlations of overall disease liabilities. To accomplish these analyses, we developed a fast algorithm for multi-component, multi-trait variance components analysis that overcomes prior computational barriers that made such analyses intractable at this scale.
Beyond 2/3 and 1/3: the complex signatures of sex-biased admixture on the X chromosome
Authors: Goldberg Amy , Rosenberg Noah A
Published: March 2015

Sex-biased demography, in which parameters governing migration and population size differ between females and males, has been studied through comparisons of X chromosomes, which are inherited sex-specifically, and autosomes, which are not. A common form of sex bias in humans is sex-biased admixture, in which at least one of the source populations differs in its proportions of females and males contributing to an admixed population. Studies of sex-biased admixture often examine the mean ancestry for markers on the X chromosome in relation to the autosomes. A simple framework noting that in a population with equally many females and males, 2/3 of X chromosomes appear in females, suggests that the mean X-chromosomal admixture fraction is a linear combination of female and male admixture parameters, with coefficients 2/3 and 1/3, respectively. Extending a mechanistic admixture model to accommodate the X chromosome, we demonstrate that this prediction is not generally true in admixture models, though it holds in the limit for an admixture process occurring as a single event. For a model with constant ongoing admixture, we determine the mean X-chromosomal admixture, comparing admixture on female and male X chromosomes to corresponding autosomal values. Surprisingly, in reanalyzing African-American genetic data to estimate sex-specific contributions from African and European sources, we find that the range of contributions compatible with the excess African ancestry on the X chromosome compared to autosomes has a wide spread, permitting scenarios either without male-biased contributions from Europe or without female-biased contributions from Africa.
Hydrogen Sulfide Regulates Inward-Rectifying K+ Channels in Conjunction with Stomatal Closure
Authors: Papanatsiou Maria , Scuffi Denisse , Blatt Michael R. , García-Mata Carlos
Published: March 2015

Hydrogen sulfide (H2S) is the third biological gasotransmitter, and in animals, it affects many physiological processes by modulating ion channels. H2S has been reported to protect plants from oxidative stress in diverse physiological responses. H2S closes stomata, but the underlying mechanism remains elusive. Here, we report the selective inactivation of current carried by inward-rectifying K+ channels of tobacco (Nicotiana tabacum) guard cells and show its close parallel with stomatal closure evoked by submicromolar concentrations of H2S. Experiments to scavenge H2S suggested an effect that is separable from that of abscisic acid, which is associated with water stress. Thus, H2S seems to define a unique and unresolved signaling pathway that selectively targets inward-rectifying K+ channels.
Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato
Authors: Alseekh Saleh , Tohge Takayuki , Wendenberg Regina , Scossa Federico , Omranian Nooshin , Li Jie , Kleessen Sabrina , Giavalisco Patrick , Pleban Tzili , Mueller-Roeber Bernd , Zamir Dani , Nikoloski Zoran , Fernie Alisdair R.
Published: March 2015

A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.
Determining the Subcellular Location of Synthesis and Assembly of the Cell Wall Polysaccharide (1,3; 1,4)-β-d-Glucan in Grasses
Authors: Wilson Sarah M. , Ho Yin Ying , Lampugnani Edwin R. , Van de Meene Allison M.L. , Bain Melissa P. , Bacic Antony , Doblin Monika S.
Published: March 2015

The current dogma for cell wall polysaccharide biosynthesis is that cellulose (and callose) is synthesized at the plasma membrane (PM), whereas matrix phase polysaccharides are assembled in the Golgi apparatus. We provide evidence that (1,3;1,4)-β-d-glucan (mixed-linkage glucan [MLG]) does not conform to this paradigm. We show in various grass (Poaceae) species that MLG-specific antibody labeling is present in the wall but absent over Golgi, suggesting it is assembled at the PM. Antibodies to the MLG synthases, cellulose synthase-like F6 (CSLF6) and CSLH1, located CSLF6 to the endoplasmic reticulum, Golgi, secretory vesicles, and the PM and CSLH1 to the same locations apart from the PM. This pattern was recreated upon expression of VENUS-tagged barley (Hordeum vulgare) CSLF6 and CSLH1 in Nicotiana benthamiana leaves and, consistent with our biochemical analyses of native grass tissues, shown to be catalytically active with CSLF6 and CSLH1 in PM-enriched and PM-depleted membrane fractions, respectively. These data support a PM location for the synthesis of MLG by CSLF6, the predominant enzymatically active isoform. A model is proposed to guide future experimental approaches to dissect the molecular mechanism(s) of MLG assembly.
Building from Scratch: New Cities, Privatized Urbanism and the Spatial Restructuring of Johannesburg after Apartheid
Authors: Herbert Claire W. , Murray Martin J.
Published: March 2015

By the start of the twenty‐first century, the once dominant historical downtown core of Johannesburg had lost its privileged status as the center of business and commercial activities, the metropolitan landscape having been restructured into an assemblage of sprawling, rival edge cities. Real estate developers have recently unveiled ambitious plans to build two completely new cities from scratch: Waterfall City and Lanseria Airport City (formerly called Cradle City) are master‐planned, holistically designed ‘satellite cities’ built on vacant land. While incorporating features found in earlier city‐building efforts, these two new self‐contained, privately‐managed cities operate outside the administrative reach of public authority and thus exemplify the global trend toward privatized urbanism. Waterfall City, located on land that has been owned by the same extended family for nearly 100 years, is spearheaded by a single corporate entity. Lanseria Airport City/Cradle City is a planned ‘aerotropolis’ surrounding the existing Lanseria airport at the northwest corner of the Johannesburg metropole. These two new private cities differ from earlier large‐scale urban projects because everything from basic infrastructure (including utilities, sewerage, and the installation and maintenance of roadways), landscaping, security services, the regulation of common spaces, and selling and branding the city are firmly in the hands of private profit‐making corporate entities and outside the mandate of public authorities.
fuzzySim: applying fuzzy logic to binary similarity indices in ecology
Authors: Barbosa A. Márcia
Published: March 2015

Binary similarity indices are widely used in ecology, for example for detecting associations between species occurrence patterns, comparing regional and temporal species assemblages, and assessing beta diversity patterns, including spatial and temporal species loss and turnover. Such indices have widespread applications in biogeography, global change biology and biodiversity conservation.

Similarity indices are commonly calculated upon binary presence/absence (or sometimes modelled suitable/unsuitable) data, which are generally incomplete and more categorical than their underlying natural patterns. Probable false absences are disregarded, amplifying the effects of data deficiencies and the scale dependence of the results.

Fuzzy occurrence data, with a degree of uncertainty attributed to localities where presence or absence cannot be safely assigned, could better reflect species distributions, compensating for incomplete knowledge and methodological errors. Similarity indices would therefore also benefit from accommodating such fuzzy data directly.

This study proposes fuzzy versions of the binary similarity indices most commonly used in ecology, so that they can be directly applied to continuous (fuzzy) rather than binary occurrence values, thus producing more realistic similarity assessments. Fuzzy occurrence can be obtained with several methods, some of which are also provided. The procedure is robust to data source disparities, gaps or other errors in species occurrence records, even for restricted species for which slight inaccuracies can affect substantial parts of their range.

The method is implemented in a free and open‐source software package, fuzzySim, which is available for the r statistical software and under implementation for the QGIS geographic information system. It is provided with sample data and an illustrated tutorial suitable for non‐experienced users.
Effects of Case Studies and Simulated Patients on Students' Nursing Care Plan
Authors: Karadag Mevlude , Calıskan Nurcan , Iseri Ozge
Published: March 2015

Purpose

The aim of this study is to determine the effects of using case studies and simulated patients in teaching students to plan their nursing care.

Methods

The study sample consisted of 70 second‐year nursing students. Study data were collected using a questionnaire and by evaluating students' nursing care plans.

Results

The highest percentages of diagnoses identified were altered oral mucous membrane, ineffective breathing pattern, disturbed sleep pattern: less than body requirement, impaired tissue integrity, pain, and risk for infection.

Conclusions

The use of simulated patients in nursing education appears to help students evaluate realistic medical cases and clinical problems, and plan their nursing care.

Amaç

Çalışma, vaka çalışması ve simüle hasta kullanımının öğrencilerin hemşirelik bakımını planlamaları üzerine etkisini belirlemek amacıyla yapılmıştır.

Metod

Çalışmanın örneklemini, hemşirelik ikinci sınıfında okuyan 70 öğrenci oluşturmuştur. Çalışmanın verileri, araştırmacılar tarafından hazırlanan soru formu ve öğrencilerin hazırladıkları bakım planları ile toplanmıştır.

Bulgular

Öğrencilerin en fazla belirledikleri hemşirelik tanıları Oral Mukoz Membranda Değişim, Etkisiz Solunum Örüntüsü, Uyku Biçiminde bozulma, Beslenmede Değişim: Gereksinimden Az, Doku bütünlüğünde Bozulma, Ağrı ve Enfeksiyon Riski'dir.

Sonuç

Hemşirelik eğitiminde simüle hastaların kullanımının, öğrencilerin gerçeğe en yakın tıbbi durumları, klinik problemleri değerlendirebilmelerine ve hemşirelik bakımını planlamalarına katkı sağladığı düşünülmektedir.
Self‐disinfecting sink drains reduce the Pseudomonas aeruginosa bioburden in a neonatal intensive care unit
Authors: Fusch Christoph , Pogorzelski David , Main Cheryl , Meyer Carrie‐Lynn , el Helou Salhab , Mertz Dominik
Published: March 2015

Aim

Water in sink drains is a known source of gram‐negative bacteria. We aimed to evaluate the impact of self‐disinfecting sink drains on the emission of aerosolised bacteria and on Pseudomonas aeruginosa acquisition among neonates.

Methods

Aerosol bacterial growth and patient Pseudomonas aeruginosa acquisition rates were measured at baseline (Phase One), for 13 months after sinks were relocated or redesigned during refurbishment (Phase Two) and for 13 months after introducing self‐disinfecting sink drains (Phase Three).

Results

Cultures were positive for bacterial growth in 56%, 24% and 13% of the tested aerosols in Phases One, Two and Three, respectively. Comparing Phases Two and Three produced an odds ratio (OR) of 0.47, with a 95% confidence interval (CI) of 0.22–0.99 (p = 0.047), for all bacteria and an OR of 0.31 and CI of 0.12–0.79 (p = 0.013) for Pseudomonas aeruginosa. Rates of Pseudomonas aeruginosa positive clinical cultures were 0.34, 0.27 and 0.13 per 1000 patient days during the respective phases, with a significant increase of time to the next positive clinical culture in Phase Three.

Conclusion

Self‐disinfecting sink drains were superior to sink replacements in preventing emissions from aerosols pathogens and may reduce hospital‐acquired infections. The bioburden reduction should be confirmed in a larger multicentre trial.
Increased incidence of malignant melanoma and other rare cutaneous cancers in the setting of chronic lymphocytic leukemia
Authors: Brewer Jerry D. , Shanafelt Tait D. , Call Timothy G. , Cerhan James R. , Roenigk Randall K. , Weaver Amy L. , Otley Clark C.
Published: March 2015

Background

Patients with chronic lymphocytic leukemia (CLL), small lymphocytic lymphoma (SLL), or non‐Hodgkin lymphoma (NHL) are at increased risk for the development of skin malignancies.

Objectives

This study was conducted to estimate the incidences of rare skin malignancies in patients with CLL/SLL or NHL.

Methods

Patients with a diagnosis of CLL/SLL or NHL recorded in the Surveillance, Epidemiology and End Results (SEER) database during 1992–2007 were identified. Diagnoses of specific skin malignancies were identified from SEER files.

Results

During 1992–2007, a total of 128,674 patients with first diagnoses of CLL/SLL or NHL were recorded in SEER; 4743 were excluded because follow‐up data were unavailable. Among the remaining 123,931 patients, 28,964 had CLL/SLL and 94,967 had NHL. Standardized incidence ratios (SIRs) for invasive malignant melanoma, Merkel cell carcinoma, malignant fibrous histiocytoma, dermatofibrosarcoma protuberans, Kaposi's sarcoma, and sebaceous carcinoma were 2.3, 8.2, 3.6, 2.5, 2.9, and 1.4, respectively, in CLL/SLL patients and 1.6, 3.2, 1.5, 1.3, 17.6, and 0.8, respectively, in NHL patients. When invasive melanoma was stratified by patient age and sex, the highest SIR (17.8) was found in men aged 0–49 years with CLL (P < 0.001).

Conclusions

Patients with CLL/SLL or NHL have a higher risk for the subsequent development of rare skin cancers. Given the more aggressive nature of these malignancies in this setting, regular monitoring for the development and prompt treatment of cutaneous malignancy is prudent in patients with NHL and particularly in patients with CLL. Regular use of sun protection may decrease the morbidity associated with skin cancer in this immunosuppressed population.
Onychomadesis after hand‐foot‐and‐mouth disease outbreak in northern Greece: case series and brief review of the literature
Authors: Apalla Zoe , Sotiriou Eleni , Pikou Olga , Lefaki Ioanna , Lallas Aimilios , Lazaridou Elizabeth , Ioannides Demetris
Published: March 2015

Background

Nail abnormalities in childhood are generally uncommon. Recently, onychomadesis was described as a late complication of hand‐foot‐and‐mouth disease (HFMD). Onychomadesis outbreaks following HFMD have been reported in many countries worldwide.

Aim

To present a case series of onychomadesis in children, following HFMD outbreak in Northern Greece, and review literature data.

Methods

Children with evident onychomadesis attending the outpatient clinic between November 2012 and January 2013 were included in the study. A questionnaire including demographic personal and family history information of the children was completed by the parents. Patients were clinically examined, and their pediatric and dermatological records were studied to confirm precedent HFMD. Direct microscopic examination and cultures for fungi were performed. Exposure of participants to coxsackievirus, based on serology testing during infection, was also recorded.

Results

Sixty‐eight children with onychomadesis were included. The mean number of affected nails was 8.82. Fingernails were more often involved. Previous clinical diagnosis of HFMD was confirmed in 67/68 cases. The mean time from HFMD diagnosis to onychomadesis development was 39.6 days (range: 28–56 days, STD: 7.33). Direct microscopic examination, as well as cultures for fungal species, was negative for the whole sample size. All the nail changes were transient with spontaneous regrowth after 1–4 months.

Conclusion

Our data indicate that onychomadesis outbreak in the region of Thessaloniki during fall–winter 2012–13 was highly related to the outbreak of HFMD. Our study reinforces existing evidence for the association between onychomadesis and HFMD.
Effect of Vitamin D Replacement on Atrial Electromechanical Delay in Subjects with Vitamin D Deficiency
Authors: CANPOLAT UĞUR , YAYLA ÇAĞRI , AKBOĞA MEHMET KADRI , ÖZCAN ELIF HANDE , TURAK OSMAN , ÖZCAN FIRAT , TOPALOĞLU SERKAN , ARAS DURSUN
Published: March 2015

AEMD and Vitamin D Deficiency

Objectives

Limited data are available regarding cardiac arrhythmias in vitamin D (VitD) deficiency. Therefore, we aimed to assess whether atrial electromechanical delay (AEMD) measured by tissue Doppler imaging (TDI), which is an indicator for atrial fibrillation (AF) development, is prolonged in patients with VitD deficiency as compared to the control group. The effect of vitD replacement on AEMD was also evaluated.

Methods

In this prospective study a total of 28 VitD‐deficient and 56 age‐, gender‐, and BMI‐matched VitD‐sufficient healthy participants were enrolled. P‐wave dispersion (PWd) was calculated on the 12‐lead electrocardiogram. Both intra‐ and inter‐AEMD were calculated by TDI. Measurements were performed at baseline in both groups and were repeated after 6‐month replacement therapy in subjects with vitD deficiency.

Results

PWd and inter‐ and left intra‐AEMD were significantly prolonged in patients with VitD deficiency compared to the control group (P < 0.001). While serum 25(OH)D levels were significantly and negatively correlated with left intra‐AEMD (r = −0.657, P < 0.001), there was a positive correlation between serum 25(OH)D level and PWd (r = 0.523, P < 0.001). The serum 25(OH)D level was found as the independent predictor of the both left intra‐ and inter‐AEMD in the multivariate linear regression analysis (β:−0.552, P < 0.001 and β:−0.555, P < 0.001, respectively). The serum 25(OH)D level was significantly increased after replacement therapy. While inter‐AEMD was significantly decreased (P = 0.013), there was no change in PWD and left and right intra‐AEMD (P > 0.05) following replacement therapy.

Conclusion

PWd and left intra‐ and inter‐AEMD are increased in patients with VitD deficiency. The serum 25(OH)D level was found as an independent predictor for AEMD in patients with VitD deficiency. Also a significant decrement was observed in inter‐AEMD following vitD replacement therapy. Studies with longer follow‐up are needed to investigate whether vitD‐deficient patients with prolonged AEMD develop clinical arrhythmia and vitD replacement reduces the risk of atrial arrhythmias.
Sleep inertia, sleep homeostatic and circadian influences on higher‐order cognitive functions
Authors: Burke Tina M. , Scheer Frank A. J. L. , Ronda Joseph M. , Czeisler Charles A. , Wright Kenneth P.
Published: March 2015

Sleep inertia, sleep homeostatic and circadian processes modulate cognition, including reaction time, memory, mood and alertness. How these processes influence higher‐order cognitive functions is not well known. Six participants completed a 73‐day‐long study that included two 14‐day‐long 28‐h forced desynchrony protocols to examine separate and interacting influences of sleep inertia, sleep homeostasis and circadian phase on higher‐order cognitive functions of inhibitory control and selective visual attention. Cognitive performance for most measures was impaired immediately after scheduled awakening and improved during the first ~2–4 h of wakefulness (decreasing sleep inertia); worsened thereafter until scheduled bedtime (increasing sleep homeostasis); and was worst at ~60° and best at ~240° (circadian modulation, with worst and best phases corresponding to ~09:00 and ~21:00 hours, respectively, in individuals with a habitual wake time of 07:00 hours). The relative influences of sleep inertia, sleep homeostasis and circadian phase depended on the specific higher‐order cognitive function task examined. Inhibitory control appeared to be modulated most strongly by circadian phase, whereas selective visual attention for a spatial‐configuration search task was modulated most strongly by sleep inertia. These findings demonstrate that some higher‐order cognitive processes are differentially sensitive to different sleep–wake regulatory processes. Differential modulation of cognitive functions by different sleep–wake regulatory processes has important implications for understanding mechanisms contributing to performance impairments during adverse circadian phases, sleep deprivation and/or upon awakening from sleep.
The “Thinking a Lot” Idiom of Distress and PTSD: An Examination of Their Relationship among Traumatized Cambodian Refugees Using the “Thinking a Lot” Questionnaire
Authors: Hinton Devon E. , Reis Ria , de Jong Joop
Published: March 2015

“Thinking a lot” (TAL)—also referred to as “thinking too much”—is a key complaint in many cultural contexts, and the current article profiles this idiom of distress among Cambodian refugees. The article also proposes a general model of how TAL generates various types of distress that then cause PTSD‐type psychopathology, a model we refer to as the TAL–PTSD model. As tested in this Cambodian refugee sample, the model is supported by the following: (1) the close connection of TAL to PTSD as shown by odds ratio (OR = 19.6), correlation (r = .86), and factor loading; and (2) the mediation of most of the effect of TAL on PTSD by TAL‐caused somatic symptoms, catastrophic cognitions, trauma recall, insomnia, and irritability. The questionnaire used in the present study is provided and can be used to examine TAL in other cultural and global contexts to advance the study of this commonly encountered distress form. [idioms of distress, “thinking a lot,” “thinking too much,” Cambodian refugees, PTSD]