bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasmid transfer is biased towards close kin in bacteria from natural populations
Authors: Dimitriu Tatiana , Marchant Lauren , Buckling Angus , Raymond Ben 
Published: October 2018

AbstractPlasmids play a key role in microbial ecology and evolution, yet the determinants of plasmid transfer rates are poorly understood. Here we investigate the importance of genetic similarity between naturally co-occurringEscherichia coliisolates in the transfer of two plasmids (narrow-host-range R1 and broad-host-range RP4). We uncovered extensive variability, spanning over five orders of magnitude, in the ability of isolates to donate and receive plasmids. Overall, transfer was strongly biased towards clone-mates, but not correlated to genetic distance between donors and recipients. Transfer was limited by the presence of a functional restriction-modification system in recipients, thus bias towards kin might be explained by sharing of identical restriction systems. Such conjugation within lineages sets the stage for longer-term pair-wise coevolutionary interactions between plasmids and bacterial hosts.
An 8-week resistance training protocol is effective in adapting quadriceps but not patellar tendon shear modulus measured by Supersonic Shearwave Imaging
Authors: Mannarino P. , Matta T. T. , Oliveira F. O. 
Published: October 2018

ABSTRACTHabitual loading and resistance training (RT) can determine changes in muscle and tendon morphology but also in its mechanical properties. Conventional ultrasound (US) evaluation of these mechanical properties present limitations that can now be overcome with the advent of Supersonic Shearwave Imaging (SSI). The objective of this study was to analyze the Vastus Lateralis (VL) and patellar tendon (PT) mechanical properties adaptations to an 8-week RT protocol using SSI. We submitted 15 untrained health young men to an 8-week RT directed knee extensor mechanism. VL and PT shear modulus (μ) was assessed pre and post intervention with SSI. VL muscle thickness (VL MT) and knee extension torque (KT) was also measure pre and post intervention to ensure the RT efficiency. Significant increases were observed in VL MT and KT (pre= 2.40 ± 0.40 cm and post= 2.63 ± 0.35 cm, p = 0.0111, and pre= 294.66 ± 73.98 Nm and post= 338.93 ± 76.39 Nm, p = 0.005, respectively). The 8-week RT was also effective in promoting VL μ adaptations (pre= 4.87 ± 1.38 kPa and post= 9.08.12 ± 1.86 kPa, p = 0.0105), but not in significantly affecting PT μ (pre= 78.85 ± 7.37 kPa and post= 66.41 ± 7.25 kPa, p = 0.1287). The present study showed that an 8-week resistance training protocol was effective in adapting VL μ but not PT μ. Further investigation should be conducted with special attention to longer interventions, to possible PT differential individual responsiviness and to the muscle-tendon resting state tension environment.
Cadherin-7 mediates proper neural crest cell-placodal neuron interactions during trigeminal ganglia assembly
Authors: Wu Chyong-Yi , Taneyhill Lisa A. 
Published: October 2018

ABSTRACTThe cranial trigeminal ganglia play a vital role in the peripheral nervous system through their relay of sensory information from the vertebrate head to the brain. These ganglia are generated from the intermixing and coalescence of two distinct cell populations: cranial neural crest cells and placodal neurons. Trigeminal ganglia assembly requires the formation of cadherin-based adherens junctions within the neural crest cell and placodal neuron populations; however, the molecular composition of these adherens junctions is still unknown. Herein, we aimed to define the spatio-temporal expression pattern and function of Cadherin-7 during early chick trigeminal ganglia formation. Our data reveal that Cadherin-7 is expressed exclusively in migratory cranial neural crest cells and is absent from trigeminal neurons. Using molecular perturbation experiments, we demonstrate that modulation of Cadherin-7 in neural crest cells influences trigeminal ganglia assembly, including the organization of neural crest cells and placodal neurons within the ganglionic anlage. Moreover, alterations in Cadherin-7 levels lead to changes in the morphology of trigeminal neurons. Taken together, these findings provide additional insight into the role of cadherin-based adhesion in trigeminal ganglia formation, and, more broadly, the molecular mechanisms that orchestrate the cellular interactions essential for cranial gangliogenesis.
A high-throughput screen identifies small molecule modulators of alternative splicing by targeting RNA G-quadruplexes
Authors: Zhang Jing , Harvey Samuel E. , Cheng Chonghui 
Published: October 2018

ABSTRACTRNA secondary structures have been increasingly recognized to play an important regulatory role in post-transcriptional gene regulation. We recently showed that RNA G-quadruplexes, which serve as cis-elements to recruit splicing factors, play a critical role in regulating alternative splicing during the epithelial-mesenchymal transition. In this study, we performed a high-throughput screen using a dual-color splicing reporter to identify chemical compounds capable of regulating G-quadruplex-dependent alternative splicing. We identify emetine and its analog cephaeline as small molecules that disrupt RNA G-quadruplexes, resulting in inhibition of G-quadruplex-dependent alternative splicing. Transcriptome analysis reveals that emetine globally regulates alternative splicing, including splicing of variable exons that contain splice site-proximal G-quadruplexes. These data suggest the use of emetine and cephaeline for investigating mechanisms of G-quadruplex-associated alternative splicing.
Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
Authors: Waterhouse Robert M. , Aganezov Sergey , Anselmetti Yoann , Lee Jiyoung , Ruzzante Livio , Reijnders Maarten J.M.F. , Feron Romain , Bérard Sèverine , George Phillip , Hahn Matthew W. , Howell Paul I. , Kamali Maryam , Koren Sergey , Lawson Daniel , Maslen Gareth , Peery Ashley , Phillippy Adam M. , Sharakhova Maria V. , Tannier Eric , Unger Maria F. , Zhang Simo V. , Alekseyev Max A. , Besansky Nora J. , Chauve Cedric , Emrich Scott J. , Sharakhov Igor V. 
Published: October 2018

AbstractBackgroundNew sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies.ResultsWe employed three gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: six with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and three with new assemblies based on re-scaffolding or Pacific Biosciences long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: seven for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further seven with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi.ConclusionsExperimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our comparisons show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.
Dissociable mechanisms govern when and how strongly reward attributes affect decisions
Authors: Maier Silvia U. , Beharelle Anjali Raja , Polanía Rafael , Ruff Christian C. , Hare Todd A. 
Published: October 2018

AbstractTheories and computational models of decision making usually focus on how strongly different attributes are weighted in choice, e.g., as a function of their importance or salience to the decision-maker. However, when different attributes impact on the decision process is a question that has received far less attention. Here, we investigated whether attribute consideration timing has a unique influence on decision making using a time-varying drift diffusion model and data from four separate experiments. Experimental manipulations of attention and neural activity demonstrated that we can dissociate the processes that determine the relative weighting strength and timing of attribute consideration. Thus, the processes determining either the weighting strengths or the timing of attributes in decision making can adapt independently to changes in the environment or goals. Quantifying these separate influences of timing and weighting on choice improves our understanding and predictions of individual differences in decision behaviour.
Triose phosphate utilization and beyond: from photosynthesis to end-product synthesis
Authors: McClain Alan M. , Sharkey Thomas D. 
Published: October 2018

AbstractDuring photosynthesis plants fix CO2from the atmosphere onto ribulose-bisphosphate producing 3-phosphoglycerate, which is reduced to triose phosphates (TPs). The TPs are then converted into the end products of photosynthesis. When a plant is photosynthesizing very quickly it may not be possible to commit photosynthate to end product as fast as it is produced, causing a decrease in available phosphate and limiting the rate of photosynthesis to the rate of triose phosphate utilization (TPU). The occurrence of an observable TPU limitation is highly variable based on species and especially growth conditions, with TPU capacity seemingly regulated to be in just slight excess of the likely photosynthetic rate. The physiological effects of TPU limitation are discussed with an emphasis on interactions between the Calvin-Benson cycle and the light reactions. Methods for detecting TPU-limited data from gas exchange data are detailed, and the impact on modeling of some physiological effects are shown. Special consideration is given to common misconceptions about TPU.HighlightPhotosynthetic triose phosphate utilization limitation is discussed, highlighting misleading points in physiology and focusing on regulation.
Time calibrated morpho-molecular classification of Nassellaria (Radiolaria)
Authors: Sandin Miguel M. , Pillet Loic , Biard Tristan , Poirier Camille , Bigeard Estelle , Romac Sarah , Suzuki Noritoshi , Not Fabrice 
Published: October 2018

AbstractNassellaria are marine radiolarian protists belonging to the Rhizaria lineage. Their skeleton, made of opaline silica, exhibit an excellent fossil record, extremely valuable in micro-paleontological studies for paleo-environmental reconstruction. Yet, to date very little is known about the extant diversity and ecology of Nassellaria in contemporary oceans, and most of it is inferred from their fossil record. Here we present an integrative classification of Nassellaria based on taxonomical marker genes (18S and 28S ribosomal DNA) and morphological characteristics obtained by optical and scanning electron microscopy imaging. Our phylogenetic analyses distinguished 11 main morpho-molecular clades relying essentially on the overall morphology of the skeleton and not on internal structures as previously considered. Using fossil calibrated molecular clock we estimated the origin of Nassellaria among radiolarians primitive forms in the Devonian (ca. 420 Ma), that gave rise to living nassellarian groups in the Triassic (ca. 250 Ma), during the biggest diversification event over their evolutionary history. This morpho-molecular framework provides both a new morphological classification easier to identify under light microscopy and the basis for future molecular ecology surveys. Altogether, it brings a new standpoint to improve our scarce understanding of the ecology and worldwide distribution of extant nassellarians.
Snapshots of single particles from single cells using electron microscopy
Authors: Yi Xiunan , Verbeke Eric J. , Chang Yiran , Dickinson Daniel J. , Taylor David W. 
Published: October 2018

AbstractCryo-electron microscopy has become an indispensable tool for structural studies of biological macromolecules. There are two predominant methods for studying the architectures of multi-protein complexes: (1) single particle analysis of purified samples and (2) tomography of whole cells or cell sections. The former can produce high-resolution structures but is limited to highly purified samples, while the latter can capture proteins in their native state but is hindered by a low signal-to-noise ratio and results in lower-resolution structures. Here, we present a method combining microfluidic single cell extraction with single particle analysis by electron microscopy to characterize protein complexes from individual C. elegans embryos. Using this approach, we uncover three-dimensional structures of ribosomes directly from single embryo extracts. In addition, we investigate structural dynamics during development by counting the number of ribosomes per polysome in early and late embyros. This approach has significant potential applications for counting protein complexes and studying protein architectures from single cells in developmental, evolutionary and disease contexts.
Relative biological effect of alpha particle radiation on low dose phenomena: lethal mutation, hyper-radiosensitivity and increased radioresistance
Authors: Fernando Chandula , Shi Xiaopei , Byun Soo Hyun , Seymour Colin B. , Mothersill Carmel E. 
Published: October 2018

AbstractAt high doses, the current recommended radiation weighting factors advise a significantly higher effectiveness of alpha particles relative to gamma radiation. However, at lower doses, the ratio of effectiveness between radiations of varying linear energy transfer values is complicated due to the relative importance of low dose phenomena such as genomic instability, bystander effects, low dose hyper-radiosensitivity and increased radioresistance (HRS/IRR). Radium is the most common source of alpha radiation exposure to humans, but the dosimetry is complicated by the decay chain which involves gamma exposure due to radon daughters. This study aimed to isolate the relative biological effect of alpha particles after low doses of radium to cells and their progeny. This was done by subtracting the survival values of a human keratinocyte cell line (HaCaT) and an embryonic Chinook salmon cell line (CHSE-214) exposed to gamma irradiation, from survival of the same cell lines exposed to mixed alpha and gamma radiation through chronic exposure to Ra-226 and its decay products. The human cell line showed increased radioresistance when exposed to low doses of alpha particles. In contrast the fish cell line, which demonstrated radioresistance to low dose gamma energy, demonstrated increased lethality when exposed to low doses of alpha particles. The results confirm the need to consider the dose-response relationship when developing radiation weighting factors for low dose exposures, as well as the need to be aware of possible cell line and species differences.
The seven transmembrane domain protein MoRgs7 functions in surface perception and undergoes coronin MoCrn1-dependent endocytosis in complex with Gα subunit MoMagA to promote cAMP signaling and appressorium formation in Magnaporthe oryzae
Authors: Li Xiao , Zhong Kaili , Yin Ziyi , Hu Jiexiong , Li Lianwei , Zhang Haifeng , Zheng Xiaobo , Wang Ping , Zhang Zhengguang 
Published: October 2018

AbstractRegulator of G-protein signaling (RGS) proteins primarily function as GTPase-accelerating proteins (GAPs) to promote GTP hydrolysis of Gα subunits, thereby regulating G-protein mediated signaling. RGS proteins could also contain additional domains such as GoLoco to inhibit GDP dissociation. The rice blast fungus Magnaporthe oryzae encodes eight RGS and RGS-like proteins (MoRgs1 to MoRgs8) that have shared and distinct functions in growth, appressorium formation and pathogenicity. Interestingly, MoRgs7 and MoRgs8 contain a C-terminal seven-transmembrane domain (7-TM) motif typical of G-protein coupled receptor (GPCR) proteins, in addition to the conserved RGS domain. We found that MoRgs7, together with Gα MoMagA but not MoRgs8, undergoes endocytic transport from the plasma membrane to the endosome upon sensing of surface hydrophobicity. We also found that MoRgs7 can interact with hydrophobic surfaces via a hydrophobic interaction, leading to the perception of environmental hydrophobic cues. Moreover, we found that MoRgs7-MoMagA endocytosis is regulated by actin patch-associated protein MoCrn1, linking it to cAMP signaling. Our studies provided evidence suggesting that MoRgs7 could also function in a GPCR-like manner to sense environmental signals and it, together with additional proteins of diverse functions, promotes cAMP signaling required for developmental processes underlying appressorium function and pathogenicity.Author summaryThe 7-TM domain is considered the hallmark of GPCR proteins, which activate G proteins upon ligand binding and undergo endocytosis for regeneration or recycling. Among eight RGS and RGS-like proteins of M. oryzae, MoRgs7 and MoRgs8 contain the 7-TM domain in addition to the RGS domain. We found that MoRgs7 can form hydrophobic interactions with the hydrophobic surface. This interaction is important in sensing hydrophobic cues by the fungus. We also found that, in response to surface hydrophobicity, MoRgs7 couples with Gα subunit MoMagA to undergo endocytosis leading to the activation of cAMP signaling. Moreover, we found that such an endocytic event requires functions of the actin-binding protein MoCrn1. Our results revealed MoRgs7 functions as a GPCR-like receptor protein to sense surface cues and activate signaling required for pathogenesis, providing new insights into G-protein regulatory mechanisms in this and other pathogenic fungi.
Selective harmonic elimination in direct torque controlled permanent magnet synchronous motor drive
Authors: Asadzadeh Vahid , Dastfan Ali , Darabi Ahmad 
Published: October 2018

Purpose
The purpose of this paper is to describe a new method for selective harmonic elimination in a two-level three-phase inverter-fed direct torque controlled (DTC) permanent magnet synchronous motor (PMSM) drive to suppress unwanted resonant frequencies.

Design/methodology/approach
The design methodology is based on random space vector pulse-width modulation (RSVPWM) of PMSM drives. MATLAB simulations support the validity of suggested structure.

Findings
The simulation results of the proposed algorithm exhibit the development of a proper gap at the selected frequency in the frequency spectra of the motor input currents and voltages as well as lowering the ripples in the PMSM electromagnetic torque, stator current and flux linkage responses in compared with traditional DTC.

Originality/value
The proposed algorithm is a revised form of the RSVPWM technique used in a closed-loop structure along with a sliding mode speed controller which is capable to deal with nonlinear motor loads in an online manner. This study can be beneficial for the designers of AC motor drive system who attempt to find a modulation method that can create a selective gap in the power spectrum density of the motor input voltages and currents, therefore, promote an acoustically pleasant drive or alleviate unwanted motor vibrations.
The employability skills of graduates and employers’ options in Portugal
Authors: Suleman Fátima , Laranjeiro Ana Maria Costa 
Published: October 2018

Purpose
Available literature overlooks the factors that affect employers’ opinions of the skills graduates bring to the labour market. The purpose of this paper is to examine the relationship between the perception of graduates’ skills and the employers’ anticipative and remedial strategies.

Design/methodology/approach
A qualitative multiple case study is used and data were gathered from interviews with human resource managers in ten firms in Portugal. The data set includes information on perceptions of graduates’ skills, solutions for the acquisition of skills, hiring and training policies, and practices associated with university–industry linkages.

Findings
Almost all the employers sampled are unsatisfied with graduates’ preparation in soft skills and other personal traits. Some report skill shortages and gaps in technical skills that result in training costs. The perception of technical skills varies according to anticipative and remedial strategies.

Research limitations/implications
This is an explorative study with a very small sample of firms. However, it is a first step towards further research into whether the perception of graduates’ skills is affected by anticipative and remedial strategies implemented by firms within a particular human resource development system.

Practical implications
It is argued that the responsibility for graduates’ employability should be shared. Practitioners should learn how to interact with higher education, researchers should profit from insights into typologies of employers’ strategies on skill formation, and policy makers should understand that employers are heterogeneous and there is no one-size-fits-all solution.

Social implications
Universities, employers and policy makers should understand that the employability of graduates presupposes shared responsibility.

Originality/value
The relationship between the strategies employers adopt to access skills and their perception of graduates’ skills is a quite underexplored topic.
Predicting hotel attractiveness via personality traits of applicants
Authors: Bellou Victoria , Stylos Nikolaos , Rahimi Roya 
Published: October 2018

Purpose
Despite the fact that hotels rely heavily upon frontline employees, extant evidence on what makes a hotel attractive in the eyes of job applicants is scarce. Thus, this paper aims to incorporate the Big Five personality traits model to identify what potential hotel job applicants are likely to seek in their prospective employers.

Design/methodology/approach
Applicants for non-managerial, frontline posts at upscale hotels were approached via three branches of a career agency located in England, UK; their responses were gathered via a self-administered questionnaire. The 522 usable responses were used in a covariance-based, multi-group structural equation modeling scheme to investigate three main research propositions with regards to the applicants’ personality traits’ influence on their perceptions of a hotel’s attractiveness as a potential employer.

Findings
Analysis of responses indicates significant differences regarding the impact of extraversion, conscientiousness and openness on perceived facets of employer attractiveness. Additionally, findings suggest that high self-esteem does make applicants more demanding, while work experience also influences their preferences regarding the hotels’ profiles as an employer.

Research limitations/implications
The results of this study are limited to applicants for non-managerial, frontline job positions in upscale hotels in the UK.

Practical implications
Practically, this study offers practitioners valuable feedback regarding the potential applicant’s personality profile that grants the best fit with an upscale hotel.

Originality/value
While different studies tried to identify the organizations’ attributes that attract potential applicants, evidence on what attracts individuals to a hotel is very limited. Hence, the present study tries to address this gap and link potential applicants’ personality profiles with that of hotels as employers.