bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Mitogenomic Analysis of the Eurydema Genus in the Context of Representative Pentatomidae (Hemiptera: Heteroptera) Taxa
Authors: Zhao Wanqing , Zhao Qing , Li Min , Wei Jiufeng , Zhang Xianhong , Zhang Hufang 
Published: November 2019

AbstractThe family Pentatomidae, the largest within the superfamily Pentatomoidae, comprises about 5,000 species; many of which are economically important pests. Although the phylogeny of Pentatomidae species has been studied using various molecular markers, their phylogenetic relationships remain controversial. Recently, mitochondrial genomes (mitogenomes) have been extensively employed to examine the phylogenetics and evolution of different insects, and in this study, we sequenced complete/near-complete mitochondrial genomes from five shield bug species of Eurydema to gain a better understanding of phylogenetic relationships in the Pentatomidae. The five mitogenomes ranged in length from 15,500 to 16,752 bp and comprised 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. We compared mitogenomic characteristics of the Pentatomidae and constructed phylogenetic trees using Bayesian inference and maximum likelihood methods. Our results showed that gene arrangements, base composition, start/stop codons, gene overlaps, and RNA structures were conserved within the Pentatomidae and that congeneric species shared more characteristics. Saturation and heterogeneity analyses revealed that our PCGs and PCGRNA datasets were valid for phylogenetic analysis. Phylogenetic analyses showed consistent topologies based on BI and ML methods. These analyses strongly supported that Eurydema species belong to the tribe Strachiini, and formed a sister group with Pentatomini. The relationships among Eurydema species were shown to be consistent with their morphological features. (Strachiini + Pentatomini) was found to be a stable sibling of the clade comprising Cappaeini, Graphosomini, and Carpocorini. Furthermore, our results indicated that Graphosoma rubrolineatum (Heteroptera: Pentatomidae) belongs to the Pentatominae and not the Podopinae.
Understanding Immunity in Children Vaccinated With Live Attenuated Influenza Vaccine
Authors: Shannon Ian , White Chantelle L , Nayak Jennifer L 
Published: November 2019

Abstract
Live attenuated influenza vaccine (LAIV), or FluMist, was approved for use in the United States in 2003. This vaccine, administered intranasally, offers the advantage of stimulating immunity at the site of infection in the upper respiratory tract and, by mimicking natural infection, has the potential to elicit a multifaceted immune response. However, the development of immunity following LAIV administration requires viral replication, causing vaccine effectiveness to be impacted by both the replicative fitness of the attenuated viruses being administered and the degree of the host’s preexisting immunity. In this review, we discuss the current state of knowledge regarding the mechanisms of protection elicited by LAIV in children, contrast this with immune protection that develops upon vaccination with inactivated influenza vaccines, and briefly discuss both the potential advantages as well as challenges offered by this vaccination platform.
Exploring Scale Direction Effects and Response Behavior across PC and Smartphone Surveys
Authors: Krebs Dagmar , Höhne Jan Karem 
Published: November 2019

Abstract
The effects of scale direction on response behavior are well known in the survey literature, where a variety of theoretical approaches are discussed, and mixed empirical findings are reported. In addition, different types of survey completion devices seem to vary in their susceptibility to scale direction effects. In this study, we therefore investigate the effect of scale direction and device type on response behavior in PC and smartphone surveys. To do so, we conducted a web survey experiment in a German non-probability access panel (N = 3,401) using a two-step split-ballot design with four groups that are defined by device type (PC and smartphone) and scale direction (decremental and incremental). The results reveal that both PCs and smartphones are robust against scale direction effects. The results also show that response behavior differs substantially between PCs and smartphones, indicating that the device type (PC or smartphone) matters. In particular, the findings show that the comparability of data obtained through multi-device surveys is limited.
Chasing candidate Supergiant Fast X-ray Transients in the 1000 orbits INTEGRAL/IBIS catalogue
Authors: Sguera V , Sidoli L , Bird A J , Paizis A , Bazzano A 
Published: November 2019

ABSTRACT
We report results from an investigation at hard X-rays (above 18 keV) and soft X-rays (below 10 keV) of a sample of X-ray transients located on the Galactic plane and detected with the bursticity method, as reported in the latest 1000 orbits INTEGRAL/IBIS catalogue. Our main aim has been to individuate those with X-rays characteristics strongly resembling Supergiant Fast X-ray Transients (SFXTs). As a result, we found four unidentified fast X-ray transients which now can be considered good SFXT candidates. In particular, three transients (IGR J16374–5043, IGR J17375–3022, and IGR J12341–6143) were very poorly studied in the literature before the current work, and our findings largely improved the knowledge of their X-ray characteristics. The other transient (XTE J1829–098) was previously studied in detail only below 10 keV, conversely the current work provides the first detailed study in outburst above 18 keV. In addition we used archival infrared observations of the transients to pinpoint, among the field objects, their best candidate counterpart. We found that their photometric properties are compatible with an early-type spectral classification, further supporting our proposed nature of SFXTs. Infrared spectroscopy is advised to confirm or disprove our interpretation. The reported findings allowed a significant increase of the sample of candidate SFXTs known to date, effectively doubling their number.
Comorbidities in ANCA-associated vasculitis
Authors: Kronbichler Andreas , Leierer Johannes , Gauckler Philipp , Shin Jae Il 
Published: November 2019

Abstract
The prognosis of patients with ANCA-associated vasculitis has improved over the past decades, but overall survival rates are still unsatisfactory. Recent research has focused on complications of immunosuppressive measures and comorbidities of ANCA-associated vasculitis. This review focuses on thromboembolic and cardiovascular events. A considerably increased risk of thromboembolic events has been reported, which is associated with active disease and impaired coagulation factors. There is mounting evidence that a hypercoagulable state is present even in patients in remission, and studies investigating the impact of tailored anticoagulation are needed to reduce the burden of thromboembolism. Cardiovascular mortality is one of the leading causes of death and accelerated atherosclerosis is frequently observed in patients with ANCA-associated vasculitis. A high frequency of patients develops hypertension, diabetes mellitus and hypercholesterolaemia, either as a consequence of immunosuppression or associated with the underlying disease. The current control of modifiable cardiovascular risk factors is insufficient and thorough reviews should be performed periodically. Treatment of these risk factors should be adopted according to current recommendations related to individual cardiovascular risk prediction.
The life and work of Robert J. Adcock. Part II: biography and establishment of authorship
Authors: Howarth Richard J. , Müller Wolfgang H. 
Published: November 2019

Between 1870 and 1896, the American mathematician Robert Jackson Adcock (1826–1895) contributed a number of short articles to early mathematical journals such as
The Analyst
. His biography is given here for the first time. An obscure figure hitherto associated with the history of regression analysis and least-squares, he has, on occasion, been confused with a nephew of the same name. Before the American Civil War, Adcock was first a pupil and then taught at the Western Military Institute, which became the Kentucky Military Institute, near Frankfort, Kentucky. Afterwards, despite occasionally being hospitalized during periods of mental illness, he became a wealthy farmer who could afford mathematical recreation as a hobby. His self-published pamphlet ‘Gravitation to the sphere and the two ellipsoids of revolution’ (1872), recently discovered in the Library of the Royal Society, is discussed in Part I. Here we establish his authorship of all mathematical works by ‘R. J. Adcock’.
Virtual stick balancing: sensorimotor uncertainties related to angular displacement and velocity
Authors: Kovacs Balazs A. , Milton John , Insperger Tamas 
Published: November 2019

Sensory uncertainties and imperfections in motor control play important roles in neural control and Bayesian approaches to neural encoding. However, it is difficult to estimate these uncertainties experimentally. Here, we show that magnitude of the uncertainties during the generation of motor control force can be measured for a virtual stick balancing task by varying the feedback delay,
τ
. It is shown that the shortest stick length that human subjects are able to balance is proportional to
τ
2
. The proportionality constant can be related to a combined effect of the sensory uncertainties and the error in the realization of the control force, based on a delayed proportional-derivative (PD) feedback model of the balancing task. The neural reaction delay of the human subjects was measured by standard reaction time tests and by visual blank-out tests. Experimental observations provide an estimate for the upper boundary of the average sensorimotor uncertainty associated either with angular position or with angular velocity. Comparison of balancing trials with 27 human subjects to the delayed PD model suggests that the average uncertainty in the control force associated purely with the angular position is at most 14% while that associated purely with the angular velocity is at most 40%. In the general case when both uncertainties are present, the calculations suggest that the allowed uncertainty in angular velocity will always be greater than that in angular position.
Can a rapid-access vascular limb salvage service improve one-year amputation outcomes for patients with chronic limb-threatening ischaemia?
Authors: Nickinson A.T.O. , Dimitrova J. , Houghton J.S.M. , Rate L. , Dubkova S. , Lines H. , Gray L.J. , Nduwayo S. , Payne T. , Sayers R.D. , Davies R.S.M. 
Published: November 2019

AbstractBackgroundVascular limb salvage services can potentially improve outcomes for patients with chronic limb-threatening ischaemia (CLTI), although their description within the literature is limited. This study aims to evaluate the 12-month outcomes for an outpatient-based vascular limb salvage (VaLS) clinic and investigate times-to-treatment.MethodsAn analysis of a prospectively maintained database, involving all patients diagnosed with CLTI within the VaLS clinic from February 2018-February 2019, was undertaken. Data were compared to two comparator cohorts, identified from coding data; 1) patients managed prior to the clinic, between May 2017-February 2018 (Pre-Clinic’ [PC]), and 2) patients managed outside of clinic, between February 2018-February 2019 (‘Alternative Pathways’ [AP]). Freedom from major amputation at 12 months was the primary outcome. Kaplan-Meier plots and adjusted Cox’s proportional hazard models (aHR) were utilised to compare outcomes.ResultsFive-hundred and sixty-six patients (VaLS=158, AP=173, PC=235) were included (median age=74 years). Patients managed within the VaLS cohort were significantly more likely to be free from major amputation (90.5%) compared to both the AP (82.1%, aHR 0.52, 95% CI 0.28-0.98, p=.041) and the PC (80.0%; aHR 0.50, 95% CI 0.28-0.91, p=.022) cohorts at 12 months, after adjustment for age, disease severity and presence of diabetes.ConclusionsA limb salvage clinic may help improve the rate of major amputation and provides a reproducible model which delivers timely vascular assessment in an ambulatory setting. Further evaluation is required to assess longer-term outcomes.
Putative conjugative plasmids with tcdB and cdtAB genes in clinical Clostridium difficile strains from MLST clades C-I, 2 and 4
Authors: Ramírez-Vargas Gabriel , Rodríguez César 
Published: November 2019

AbstractThe major toxins of Clostridium difficile (TcdA, TcdB, CDT) are encoded chromosomally in nearly all known strains. Following up on a previous report, we found five new examples of a family of putative conjugative plasmids with tcdB and cdtAB in clinical C. difficile isolates from MLST Clades C-I, 2, and 4.
Kinesin-2 from C. reinhardtii is an atypically fast and auto-inhibited motor that is activated by heterotrimerization for intraflagellar transport
Authors: Sonar Punam , Youyen Wiphu , Cleetus Augustine , Wisanpitayakorn Pattipong , Mousavi Iman S. , Stepp Willi L. , Hancock William O. , Tüzel Erkan , Ökten Zeynep 
Published: November 2019

SummaryThe construction and function of virtually all cilia require the universally conserved process of Intraflagellar Transport (IFT) [1, 2]. During the atypically fast IFT in the green alga C. reinhardtii, up to ten kinesin-2 motors ‘line up’ in a tight assembly on the trains [3], provoking the question of how these motors coordinate their action to ensure smooth and fast transport along the flagellum without standing in each other’s way. Here, we show that the heterodimeric FLA8/10 kinesin-2 alone is responsible for the atypically fast IFT in C. reinhardtii. Notably, in single-molecule studies, FLA8/10 moved at speeds matching those of in vivo IFT [4], but additionally displayed a slow velocity distribution, indicative of auto-inhibition. Addition of the KAP subunit to generate the heterotrimeric FLA8/10/KAP relieved this inhibition, thus providing a mechanistic rationale for heterotrimerization with the KAP subunit in fully activating FLA8/10 for IFT in vivo. Finally, we link fast FLA8/10 and slow KLP11/20 kinesin-2 from C. reinhardtii and C. elegans through a DNA tether to understand the molecular underpinnings of motor coordination during IFT in vivo. For motor pairs from both species, the co-transport velocities very nearly matched the single-molecule velocities, and the complexes both spent roughly 80% of the time with only one of the two motors attached to the microtubule. Thus, irrespective of phylogeny and kinetic properties, kinesin-2 motors prefer to work alone without sacrificing efficiency. Our findings thus offer a simple mechanism for how efficient IFT is achieved across diverse organisms despite being carried out by motors with different properties.
Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations
Authors: Livesey Benjamin J. , Marsh Joseph A. 
Published: November 2019

AbstractTo deal with the huge number of novel protein-coding variants identified by genome and exome sequencing studies, many computational variant effect predictors (VEPs) have been developed. Such predictors are often trained and evaluated using different variant datasets, making a direct comparison between VEPs difficult. In this study, we use 31 previously published deep mutational scanning (DMS) experiments, which provide quantitative, independent phenotypic measurements for large numbers of single amino acid substitutions, in order to benchmark and compare 46 different VEPs. We also evaluate the ability of DMS measurements and VEPs to discriminate between pathogenic and benign missense variants. We find that DMS experiments tend to be superior to the top-ranking predictors, demonstrating the tremendous potential of DMS for identifying novel human disease mutations. Among the VEPs, DeepSequence clearly stood out, showing both the strongest correlations with DMS data and having the best ability to predict pathogenic mutations, which is especially remarkable given that it is an unsupervised method. We further recommend SNAP2, DEOGEN2, SNPs&GO and REVEL based upon their performance in these analyses.
Combining SIMS and mechanistic modelling to reveal nutrient kinetics in an algal-bacterial mutualism
Authors: Laeverenz Schlogelhofer Hannah , Peaudecerf François J. , Bunbury Freddy , Whitehouse Martin J. , Foster Rachel A. , Smith Alison G. , Croze Ottavio A. 
Published: November 2019

AbstractMicrobial communities are of considerable significance for biogeochemical processes, for the health of both animals and plants, and for biotechnological purposes. A key feature of the interactions between microbes is the exchange of nutrients between cells. Isotope labelling followed by analysis with secondary ion mass spectrometry (SIMS) can identify nutrient fluxes and heterogeneity of substrate utilisation on a single cell level. Here we present a novel approach that combines SIMS with a mechanistic model to reveal otherwise inaccessible nutrient kinetics. The method is applied to study the onset of a synthetic mutualistic partnership between a vitamin B12-dependent mutant of the alga Chlamydomonas reinhardtii and the B12-producing, heterotrophic bacterium Mesorhizobium loti, which is supported by algal photosynthesis. Results show that an initial pool of fixed carbon delays the onset of mutualistic cross-feeding, and the model allows quantification of this delay. Our method is widely applicable to other microbial systems, and will contribute to furthering a mechanistic understanding of microbial interactions.
Plant Bioindicators of Pollution in Sadat City, Western Nile Delta, Egypt
Authors: Azzazy M. F. 
Published: November 2019

AbstractThis study investigated using plants growing in industrial and residential areas as bioindicators and biomarkers of industrial pollution by analyzing flavonoids and metals in Bougainvillea glabra leaves by HPLC-MS, neutron activation analysis, and atomic absorption spectrophotometry. There were significantly higher levels of flavonoids and phenolic compounds in plants growing in industrial areas compared to those growing in residential zones (P<0.05). Metal accumulation in leaves was also significantly higher in the industrial zone than the residential zone: iron, lead, zinc, nickel, and manganese were present at significantly higher levels in plants growing near steel factories compared to those growing in the residential zone (P<0.05). Air, water, and soil samples associated with the studied plants in both areas were analyzed for metals. In general, heavy metal concentrations in the industrial zone were significantly higher than those in the residential zone, but the concentrations of the heavy metals in air, water, and soil were under legal environmental limits.
Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent
Authors: Tigano Anna , Colella Jocelyn P. , MacManes Matthew D. 
Published: November 2019

AbstractOrganisms that live in deserts offer the opportunity to investigate how species adapt to environmental conditions that are lethal to most plants and animals. In the hot deserts of North America, high temperatures and lack of water are conspicuous challenges for organisms living there. The cactus mouse (Peromyscus eremicus) displays several adaptations to these conditions, including low metabolic rate, heat tolerance, and the ability to maintain homeostasis under extreme dehydration. To investigate the genomic basis of desert adaptation in cactus mice, we built a chromosome-level genome assembly and resequenced 26 additional cactus mouse genomes from two locations in southern California (USA). Using these data, we integrated comparative, population, and functional genomic approaches. We identified 16 gene families exhibiting significant contractions or expansions in the cactus mouse compared to 17 other Myodontine rodent genomes, and found 232 sites across the genome associated with selective sweeps. Functional annotations of candidate gene families and selective sweeps revealed a pervasive signature of selection at genes involved in the synthesis and degradation of proteins, consistent with the evolution of cellular mechanisms to cope with protein denaturation caused by thermal and hyperosmotic stress. Other strong candidate genes included receptors for bitter taste, suggesting a dietary shift towards chemically defended desert plants and insects, and a growth factor involved in lipid metabolism, potentially involved in prevention of dehydration. Understanding how species adapted to the recent emergence of deserts in North America will provide an important foundation for predicting future evolutionary responses to increasing temperatures, droughts and desertification in the cactus mouse and other species.
Combining electrophysiology with MRI enhances learning of surrogate-biomarkers
Authors: Engemann Denis Alexander , Kozynets Oleh , Sabbagh David , Lemaitre Guillaume , Varoquaux Gaël , Liem Franziskus , Gramfort Alexandre 
Published: November 2019

AbstractElectrophysiological methods, i.e., M/EEG provide unique views into brain health. Yet, when building predictive models from brain data, it is often unclear how electrophysiology should be combined with other neuroimaging methods. Information can be redundant, useful common representations of multimodal data may not be obvious and multimodal data collection can be medically contraindicated, which reduces applicability. Here, we propose a multimodal model to robustly combine MEG, MRI and fMRI for prediction. We focus on age prediction as surrogate biomarker in 674 subjects from the Cam-CAN. Strikingly, MEG, fMRI and MRI showed additive effects supporting distinct brain-behavior associations. Moreover, the contribution of MEG was best explained by source-topography of power spectra between 8 and 30 Hz. Finally, we demonstrate that the model maintains benefits of stacking when data is missing. The proposed framework hence enables multimodal learning for a wide range of biomarkers from diverse types of brain signals.
Chemical signals act as the main reproductive barrier between sister and mimeticHeliconiusbutterflies
Authors: González-Rojas M.F. , Darragh K. , Robles J , Linares M. , Schulz S , McMillan W.O , Jiggins C.D , Pardo-Diaz C , Salazar C 
Published: November 2019

ABSTRACTColour pattern has been long recognised as the trait that drives mate recognition betweenHeliconiusspecies that are phylogenetically close. However, when this cue is compromised such as in cases of mimetic, sympatric and closely related species, alternative mating signals must evolve to ensure reproductive isolation and species integrity. The closely related speciesHeliconius melpomene malletiandH. timareta florencia, occur in the same geographic region and despite being co-mimics they display strong reproductive isolation. In order to test which cues differ between species, and therefore potentially contribute to reproductive isolation, we quantified differences in wing phenotype and male chemical profile. As expected, wing colour pattern was indistinguishable between the two species while the chemical profile of their male sex pheromones showed marked differences. We then conducted behavioural experiments to study the importance of these signals in mate recognition by females. In agreement with our previous results, we found that pheromones and not wing colour pattern drive the preference of females by conspecific males. In addition, experiments with hybrid males and females suggested an important genetic component for both pheromone production and preference. Altogether, these results suggest that pheromones are the major reproductive barrier opposing gene flow between these two sister and co-mimic species.