bluuebunny/crossref_metadata_2025_split huggingface dataset:
Avoiding ascertainment bias in the maximum likelihood inference of phylogenies based on truncated data
Authors: Tamuri Asif , Goldman Nick 
Published: September 2017

AbstractSome phylogenetic datasets omit data matrix positions at which all taxa share the same state. For sequence data this may be because of a focus on single nucleotide polymorphisms (SNPs) or the use of a technique such as restriction site-associated DNA sequencing (RADseq) that concentrates attention onto regions of differences. With morphological data, it is common to omit states that show no variation across the data studied. It is already known that failing to correct for the ascertainment bias of omitting constant positions can lead to overestimates of evolutionary divergence, as the lack of constant sites is explained as high divergence rather than as a deliberate data selection technique. Previous approaches to using corrections to the likelihood function in order to avoid ascertainment bias have either required knowledge of the omitted positions, or have modified the likelihood function to reflect the omitted data. In this paper we indicate that the technique used to date for this latter approach is a conditional maximum likelihood (CML) method. An alternative approach — unconditional maximum likelihood (UML) — is also possible. We investigate the performance of CML and UML and find them to have almost identical performance in the phylogenetic SNP dataset context. We also make some observations about the nucleotide frequencies observed in SNP datasets, indicating that these can differ systematically from the overall equilibrium base frequencies of the substitution process. This suggests that model parameters representing base frequencies should be estimated by maximum likelihood, and not by empirical (counting) methods.
Adult facilitation becomes competition as juvenile soapberry bugs age
Authors: Cenzer Meredith L 
Published: September 2017

ABSTRACTWhether intraspecific interactions are facilitative or competitive may change across individual ontogeny. In plant-feeding insects, the direction of this interaction is likely to be mediated by host plant defenses. Here I conducted two experiments looking at the direct effect of a physical seed defense and the role of intraspecific facilitation in reducing the effects of that defense for juveniles. I first demonstrate that juveniles of the red-shouldered soapberry bug (Jadera haematoloma) are severely inhibited by the tough seed coat of their host plant, leading to high mortality early in development. Adults, in contrast, can create holes through which other individuals could potentially feed. I then manipulated whether or not seeds experienced adult feeding on two host plant species: a well-defended native host, balloon vine (Cardiospermum corindum) and a poorly defended introduced golden rain tree species (Koelreuteria elegans). I measured the effect of prior adult feeding on survival, development time, and final body size of soapberry bug juveniles. Survival in the first week of development was dramatically improved by prior adult feeding on both hosts. However, the benefits of prior adult feeding ceased after the first week of development and shifted to having a negative effect on performance. These results indicate that adults breaking through the seedcoat initially facilitate juveniles, but that this facilitation becomes competition as juveniles age.
Multiplane and Spectrally-Resolved Single Molecule Localization Microscopy with Industrial Grade CMOS Cameras
Authors: Babcock Hazen P. 
Published: September 2017

ABSTRACTIn this work we explore the use of industrial grade CMOS cameras for single molecule localization microscopy (SMLM). We show that the performance of these cameras in single imaging plane SMLM applications is comparable to much more expensive scientific CMOS (sCMOS) cameras. We show that these cameras can be used in more demanding biplane, multiplane and spectrally resolved SMLM applications. The 10-40× reduction in camera cost makes it practical to build SMLM setups with 4 or more cameras. In addition we provide open-source software for simultaneously controlling multiple CMOS cameras and for the reduction of the movies that are acquired to super-resolution images.
Correlative three-dimensional fluorescence and refractive index tomography: bridging the gap between molecular specificity and quantitative bioimaging
Authors: Kim Kyoohyun , Park Wei Sun , Na Sangchan , Kim Sangbum , Kim Taehong , Heo Won Do , Park YongKeun 
Published: September 2017

AbstractOptical diffraction tomography (ODT) provides label-free three-dimensional (3D) refractive index (RI) measurement of biological samples. However, due to the nature of the RI values of biological specimens, ODT has limited access to molecular specific information. Here, we present an optical setup combining ODT with three-channel 3D fluorescence microscopy, to enhance the molecular specificity of the 3D RI measurement. The 3D RI distribution and 3D deconvoluted fluorescence images of HeLa cells and NIH-3T3 cells are measured, and the cross-correlative analysis between RI and fluorescence of live cells are presented.
Minimizing carry-over PCR contamination in expanded CAG/CTG repeat instability applications
Authors: Aeschbach Loréne , Dion Vincent 
Published: September 2017

AbstractExpanded CAG/CTG repeats underlie the aetiology of 14 neurological and neuromuscular disorders. The size of the repeat tract determines in large part the severity of these disorders with longer tracts causing more severe phenotypes. Expanded CAG/CTG repeats are also unstable in somatic tissues, which is thought to modify disease progression. Routine molecular biology applications involving these repeats, including quantifying their instability, are plagued by low PCR yields. This leads to the need for setting up more PCRs of the same locus, thereby increasing the risk of carry-over contamination. Here we aimed to reduce this risk by pre-treating the samples with a Uracil N-Glycosylase (Ung) and using dUTP instead of dTTP in PCRs. We successfully applied this method to the PCR amplification of expanded CAG/CTG repeats, their sequencing, and their molecular cloning. In addition, we optimized the gold-standard method for measuring repeat instability, small-pool PCR, such that it can be used together with Ung and dUTP-containing PCRs, without compromising data quality. We expect that the protocols herein to be applicable for molecular diagnostics of expanded repeat disorders and to manipulate other tandem repeats.
Evaluating the Functional Pore Size of Chloroplast TOC and TIC Protein Translocons
Authors: Ganesan Iniyan , Shi Lan-Xin , Labs Mathias , Theg Steven M. 
Published: September 2017

ABSTRACTThe degree of residual structure retained by proteins while passing through biological membranes is a fundamental mechanistic question of protein translocation. Proteins are generally thought to be unfolded while transported through canonical proteinaceous translocons, which has historically been the thought for the translocons of the outer and inner chloroplast envelope membranes (TOC and TIC). Here, we readdressed the issue and found that medium-sized tightly folded proteins such as the 22 kDa dihydrofolate reductase (DHFR) can be tolerated by TOC and TIC. Chimeric DHFR fused with RuBisCO small subunit transit peptide (tp22DHFR) was found to be imported into chloroplasts in complex with its stabilizing ligand, methotrexate (MTX), in a folded conformation. Following import, both mature tp22DHFR and MTX were found in the chloroplast stroma. A subsaturating concentration of MTX was used to exclude the possibility that MTX was stripped off tp22DHFR, independently imported into the chloroplasts, and reassociated with imported tp22DHFR. Independent MTX import was further excluded by use of fluorescein conjugated MTX (FMTX), which has very slow membrane transport rates relative to unconjugated MTX. The TOC/TIC pore size was determined by probing the translocons with particles of fixed diameter and found to be greater than 25.6 Å, large enough to support folded DHFR import. The pore size is also larger than those of the mitochondrial protein translocons that have a requirement for protein unfolding.SIGNIFICANCEThe chloroplast TOC and TIC translocons are responsible for the import of up to 95% of all chloroplast proteins and are therefore essential for plastid biogenesis and photosynthesis. However, the mechanisms of protein import into chloroplasts are not well understood. The TOC/TIC translocons have long been suggested to have a strong unfoldase activity relative to other comparable protein translocons. Here, we present data suggesting that this is not true, and that instead, they possess a relatively large pore size. This identifies TOC and TIC as rather unique protein translocons capable of transporting folded proteins across a double membrane barrier, which has important implications in the mechanisms of TOC/TIC function and biogenesis of photosynthetic proteins.Classification - Biochemistry
Thermal Tolerance is linked with Virulence in a Fish Pathogen
Authors: Ashrafi Roghaieh , Bruneaux Matthieu , Sundberg Lotta-Riina , Pulkkinen Katja , Valkonen Janne , Ketola Tarmo 
Published: September 2017

ABSTRACTAlthough increase in temperatures may boost the number of pathogens, a complex process involving the interaction of a susceptible host, a virulent strain, and environmental factors would influence disease virulence in unpredictable ways. Here we explored if the virulence of an environmentally growing opportunistic fish pathogen,Flavobacterium columnare, would be malleable to evolutionary changes via correlated selection on thermal tolerance. Virulence among the strains increased over years, but tolerance to higher temperatures was associated with reduced virulence. Our results suggest that observed increase in frequency of columnaris epidemics over the last decade is most likely associated with increased length of growing season, or other time dependent change in environment, rather than increased regional average temperatures. Our results also indicate that most virulent bacteria had weaker ability to tolerate outside host environments, which suggest trade-off between more obligate pathogen behaviour and ability to grow outside host.
Anoctamin 9/TMEM16J is a Cation Channel Activated by cAMP/PKA Signal
Authors: Kim Hyungsup , Kim Hyesu , Lee Jesun , Lee Byeongjun , Kim Heeryang , Jung Jooyoung , Lee Mi-Ock , Oh Uhtaek 
Published: September 2017

ABSTRACTAnoctamins are membrane proteins that consist of 10 homologs. ANO1 and ANO2 are anion channels activated by intracellular calcium that meditate numerous physiological functions. ANO6 is a scramblase that redistributes phospholipids across the cell membrane. However, the others are not well characterized. We found ANO9/TMEM16J is a cation channel activated by a cAMP-dependent PKA. Intracellular cAMP activated robust currents in whole-cells expressing ANO9 and inhibited by PKA blockers. A cholera toxin and purified PKA also activated ANO9. The cAMP-induced ANO9 currents were permeable to cations. The mutation of a possible phosphorylation site at Ser245 elicited a block of the cAMP-dependent activation. High levels ofAno9transcripts were found in intestines. Human intestinal SW480 cells showed cAMP-dependent currents. We conclude that ANO9 is a cation channel activated by the cAMP/PKA pathway and could play a role in intestine function.
Drivers of diversity in individual life courses: Sensitivity of the population entropy of a Markov chain
Authors: Steiner Ulrich K. , Tuljapurkar Shripad 
Published: September 2017

AbstractIndividuals differ in their life courses, but how this diversity is generated, how it has evolved and how maintained is less understood. However, this understanding is crucial to comprehend evolutionary and ecological population dynamics. In structured populations, individual life courses represent sequences of stages that end in death. These sequences can be described by a Markov chain and individuals diversify over the course of their lives by transitioning through diverse discrete stages. The rate at which stage sequences diversify with age can be quantified by the population entropy of a Markov chain. Here, we derive sensitivities of the population entropy of a Markov chain to identify which stage transitions generate—or contribute—most to diversification in stage sequences, i.e. life courses. We then use these sensitivities to reveal potential selective forces on the dynamics of life courses. To do so we correlated the sensitivity of each matrix element (stage transition) with respect to the population entropy, to its sensitivity with respect to fitness λ, the population growth rate. Positive correlation between the two sensitivities would suggest that the stage transitions that selection has acted most strongly on (sensitivities with respect to λ) are also those that contributed most to the diversification of life courses. Using an illustrative example on a seabird population, the Thick-billed Murres on Coats Island, that is structured by reproductive stages, we show that the most influential stage transitions for diversification of life courses are not correlated with the most influential transitions for population growth. Our finding suggests that observed diversification in life courses is neutral rather than adaptive. We are at an early stage of understanding how individual level dynamics shape ecological and evolutionary dynamics, and many discoveries await.
Input-dependent modulation of MEG gamma oscillations reflects gain control in the visual cortex
Authors: Orekhova Elena V. , Sysoeva Olga V. , Schneiderman Justin F. , Lundström Sebastian , Galuta Ilia A. , Goiaeva Dzerasa E. , Prokofyev Andrey O. , Riaz Bushra , Keeler Courtney , Hadjikhani Nouchine , Gillberg Christopher , Stroganova Tatiana A. 
Published: September 2017

AbstractGamma-band oscillations arise from the interplay between neural excitation (E) and inhibition (I) and may provide a non-invasive window into the state of cortical circuitry. A bell-shaped modulation of gamma response power by increasing the intensity of sensory input was observed in animals and is thought to reflect neural gain control. Here we sought to find a similar input-output relationship in humans with MEG via modulating the intensity of a visual stimulation by changing the velocity/temporal-frequency of visual motion.In the first experiment, adult participants observed static and moving gratings. The frequency of the MEG gamma response monotonically increased with motion velocity whereas power followed a bell-shape. In the second experiment, on a large group of children and adults, we found that despite drastic developmental changes in frequency and power of gamma oscillations, the relative suppression at high motion velocities was scaled to the same range of values across the life-span.In light of animal and modeling studies, the modulation of gamma power and frequency at high stimulation intensities characterizes the capacity of inhibitory neurons to counterbalance increasing excitation in visual networks. Gamma suppression may thus provide a non-invasive measure of inhibitory-based gain control in the healthy and diseased brain.
Nucleolin internalizesBothrops asperLys49 phospholipase A2forming cell surface amyloid-like assemblies
Authors: Massimino Maria Lina , Simonato Morena , Spolaore Barbara , Franchin Cinzia , Arrigoni Giorgio , Marin Oriano , Monturiol-Gross Laura , Fernández Julián , Lomonte Bruno , Tonello Fiorella 
Published: September 2017

AbstractPhospholipases A2(PLA2s) are a major component of snake venoms. Some of them cause severe muscle necrosis through a still unknown mechanism. Phospholipid hydrolysis is a possible explanation of their toxic action, but catalytic and toxic properties of PLA2s are not directly connected. In addition, viperid venoms contain PLA2-like proteins, which are very toxic even if they lack catalytic activity due to a critical mutation in position 49. Nucleolin, a main component of the nucleolus, is a disordered protein involved in many protein assembly and phase separation phenomena. In some circumstances nucleolin is exposed on the cell surface from where it is involved in the internalization of many ligands.In this work we demonstrate thatBothrops aspermyotoxin II (Mt-II), a Lys49 PLA2-like toxin, interacts with, and is internalized in cells by nucleolin. The internalization process is functional to the toxicity of the protein, as both an antibody and an aptamer specific for nucleolin protect cells from intoxication. We identified central RRM and the C-terminal R/F-GG domain of nucleolin as the regions involved in the interaction with Mt-II. Finally we observed that Mt-II forms, on the cell surface, amyloid-like assemblies that colocalize with nucleolin and that can be involved in the activation of the internalization process. The presence, in the three dimensional structure of Mt-II and related PLA2homologues, of four exposed loops enriched in prion-like amino acid sequences reinforces this hypothesis.Phospholipases A2| Lys49 myotoxins | nucleolin | amyloid-like | molecular assembliesSIGNIFICANCEThe main finding of this work, the role of nucleolin asBothrops asperMt-II receptor, is a remarkable step forward in understanding the mechanism of action of cytotoxic PLA2s. It may suggest new strategies for anti-venom therapies and explain the anti-tumoral and anti-viral pharmacological action of snake PLA2s, since nucleolin is a receptor for many growth factors and virus.The proposed internalization mechanism, via formation of molecular assemblies among Mt-II amyloid-like structures and other proteins, including nucleolin, can be of general validity. Cell surface molecular assemblies couldbepointsofselectionandconcentrationnotonlyofsnake,butalsoofmammaliansecretedPLA2s, proteins involved in different pathologies, and trigger the internalization pathway only when their molarity exceeds a threshold dose.
Development and Validation of a New Walking Pace Function Using Crowd-Sourced GPS Data
Authors: Pharoah Paul D.P. 
Published: September 2017

AbstractThere are several functions that hikers can use to predict walking time based on elevation change or slope of the ground. The most commonly used is the Naismith function that was first published over 100 years ago. The availability of GPS devices to record tracks now make it possible to evaluate the performance of walking time functions. Four data sources were used: 98 tracks downloaded from the Wikiloc web site; 55 tracks recorded by the author; 19 tracks recorded by the blogger Iron Hiker; and 20 tracks recorded by the blogger Hiking Guy. The ․gpx files were processed to generate segements of ~100m in length, with the associated segment duration and elevation change. The association between walking pace and elevation change was assessed in the Wikiloc data using linear spline regression. The performance of the linear spline function was then compared with the Naismith, Tobler and Laingmuir functions. The linear spline performed the best, but all four performed reasonably well. While the linear spline function could easily be programmed into the software of standard GPS devices, the Naismith function provides a simple-to-use rule-of-thumb for estimating walking time for a typical hike in the mountains.FundingNoneAcknowledgementsI thank Chris Hazzard and Keith Wilson for sharing their hiking records and for helpful comments on the manuscript.Disclosure of interestsThe authors have no interest to disclose
A Cdk1 phosphomimic mutant of MCAK impairs microtubule end recognition
Authors: Belsham Hannah R. , Friel Claire T. 
Published: September 2017

AbstractThe microtubule depolymerising kinesin-13, MCAK, is phosphorylated at residue T537 by Cdk1. This is the only known phosphorylation site within MCAK’s motor domain. To understand the impact of phosphorylation by Cdk1 microtubule depolymerisation activity, we have investigated the molecular mechanism of the phosphomimic mutant T537E. This mutant significantly impairs microtubule depolymerisation activity and when transfected into cells causes metaphase arrest and misaligned chromosomes. We show that the molecular mechanism underlying the reduced depolymerisation activity of this phosphomimic mutant is an inability to recognise the microtubule end. The microtubule-end residence time is reduced relative to wild-type MCAK, whereas the lattice residence time is unchanged by the phosphomimic mutation. Further, the microtubule-end specific stimulation of ADP dissociation, characteristic of MCAK, is abolished by this mutation. Our data shows that T537E is unable to distinguish between the microtubule end and the microtubule lattice.
Does KFC sell rat? Analysis of tweets in the wake of a rumor outbreak
Authors: Pal Anjan , Chua Alton Y.K. , Goh Dion Hoe-Lian 
Published: September 2017

Purpose
In the wake of a rumor outbreak, individuals exchange three types of messages: rumor messages, counter-rumor messages, and uncertainty-expressing messages. However, the properties of the three types of messages are relatively unknown particularly in the social media context. Hence, the purpose of this paper is to examine these three types of messages posted on social media in the wake of a rumor outbreak.

Design/methodology/approach
Data included tweets posted after the outbreak of a rumor that wrongly accused the fast food chain Kentucky Fried Chicken (KFC) for selling rats instead of chicken. Using a deductive approach, codes were derived via content analysis on the tweets. Volume and exposure of tweets were also examined.

Findings
Counter-rumor tweets (52 percent) outnumbered rumors tweets (32 percent) and uncertainty-expressing tweets (16 percent). Emotions and personal involvement were abundant in rumor tweets. Expressions of credence and references to URLs were high in counter-rumor tweets. Social ties were found widely in uncertainty-expressing tweets. The high volume and exposure of counter-rumor tweets compared with those of either rumor tweets or uncertainty-expressing tweets highlight the potential of counter-rumors to mitigate rumors.

Originality/value
This research ventures into a relatively unexplored territory by concurrently examining rumor messages, counter-rumor messages and uncertainty-expressing messages in the wake of a rumor outbreak. It reveals that counter-rumor messages have the potential to mitigate rumors on social media.
Spirituality at work: enhancing levels of employee engagement
Authors: Devendhiran Sangeetha , Wesley J. Reeves 
Published: September 2017

Purpose
The purpose of the paper is to highlight the concept of workplace spirituality, its benefits, importance in organization, and the strategies to implement workplace spirituality to enhance employee engagement in the organization.

Design/methodology/approach
Viewpoint paper.

Findings
This paper suggests that workplace spirituality will improve the level of engagement of employees.

Originality/value
This paper provides various strategies of workplace spirituality. This will help the organization to implement it in the work setting.