bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling
Authors: Higo Junichi , Kawabata Takeshi , Kusaka Ayumi , Kasahara Kota , Kamiya Narutoshi , Fukuda Ikuo , Mori Kentaro , Hata Yutaka , Fukunishi Yoshifumi , Nakamura Haruki 
Published: May 2020

ABSTRACTEnhanced conformational sampling, a genetic-algorithm-guided multi-dimensional virtual-system coupled molecular dynamics, can provide equilibrated conformational distributions of a receptor protein and a flexible ligand at room temperature. The distributions provide not only the most stable but also semi-stable complex structures, and propose a ligand–receptor binding process. This method was applied to a system consisting of a receptor protein, 14-3-3ε, and a flexible peptide, phosphorylated Myeloid leukemia factor 1 (pMLF1). The results present comprehensive binding pathways of pMLF1 to 14-3-3ε. We identified four thermodynamically stable clusters of MLF1 on the 14-3-3ε surface, and free-energy barriers among some clusters. The most stable cluster includes two high-density spots connected by a narrow corridor. When pMLF1 passes the corridor, a salt-bridge relay (switching) related to the phosphorylated residue of pMLF1 occurs. Conformations in one high-density spots are similar to the experimentally determined complex structure. Three-dimensional distributions of residues in the intermolecular interface rationally explain the binding-constant changes resultant from alanine–mutation experiment for the residues. We performed a simulation of non-phosphorylated peptide and 14-3-3ε, which demonstrated that the complex structure was unstable, suggesting that phosphorylation of the peptide is crucially important for binding to 14-3-3ε.
Size matters – larger images are better remembered during free viewing
Authors: Masarwa Shaimaa , Kreichman Olga , Gilaie-Dotan Sharon 
Published: May 2020

AbstractWe are constantly exposed to multiple visual scenes, and while freely viewing them without an intentional effort to memorize or encode them, only some are remembered. It has been suggested that image memorability is influenced by multiple factors as depth of processing (1–3), familiarity (4), and visual category (5–7). However, this is typically investigated with intentional (8, 9) or unintentional (10, 11) encoding tasks. Furthermore, since visual memory relies on size-invariant visual perception (12–14), image size is not considered a contributing factor. Here we reasoned that during naturalistic free viewing of images without an encoding task, bigger images would be better remembered due to multiple factors (as vaster expanse of activated visual cortex (15, 16), deeper processing). In an extensive set of experiments participants (n=117) freely viewed small to large images (3°-24°) without any encoding task. Subsequently, they were presented with mid-sized images (50% already seen) and were asked to report if they recall seeing them or not. Larger images were better remembered (~23% more than smaller images), image memorability was proportional to image size, faces were better remembered, and outdoors the least. These were independent of image set, presentation order, or screen resolution. While multiple factors affect image memorability (1–7), here we show that during free viewing with no encoding task, a basic physical image dimension influences its memorability.
Training-induced improvement in working memory tasks results from switching to efficient strategies
Authors: Malinovitch Tamar , Jackoby Hilla , Ahissar Merav 
Published: May 2020

ABSTRACTIt is debated whether training with a working memory (WM) task, particularly n-back, can improve general WM and reasoning skills. Most training studies found substantial improvement in the trained task, with little to no transfer to untrained tasks. We hypothesized that training does not increase WM capacity, but instead provides opportunities to develop an efficient task-specific strategy. We derived a strategy for the task that optimizes WM resources and taught it to participants. In two sessions, 14 participants who were taught this strategy performed as well as 14 participants who had trained for forty sessions without strategy instructions. To understand the mechanisms underlying the no-instruction group’s improvement, participants answered questionnaires during their training period. Their replies show that successful learners discovered the same strategy and improvement was associated with this discovery. We conclude that n-back training allows the discovery of strategies that enable better performance with the same WM resources.
Tomato Protein Phosphatase 2C (SlPP2C3) negatively regulates fruit ripening onset and fruit gloss
Authors: Liang Bin , Sun Yufei , Wang Juan , Zheng Yu , Zhang Wenbo , Xu Yandan , Li Qian , Leng Ping 
Published: May 2020

AbstractAbscisic acid (ABA) plays a vital role in coordinating physiological processes during fresh fruit ripening. ABA can bind to ABA receptors which interacts and inhibits their co-receptors type 2C phosphatases (PP2Cs). However, the dissected mechanism of PP2C during fruit ripening is unclear. In this study, we identify the role of SlPP2C3, a tomato type 2C phosphatase, as a negative regulator of ABA signaling and fruit ripening. SlPP2C3 selectively interacted with monomeric ABA receptors and SlSnRK2.8 kinase in both yeast and tobacco epidermal cells. Expressions ofSlPP2C3were observed in all tissues, and it negatively correlated with the fruit ripening which was induced by exogenous ABA. Tomato plants with suppressedSlPP2C3expression exhibited enhanced sensitivity to ABA, whileSlPP2C3over-expressed plants were less sensitive to ABA. Meaningfully, lack ofSlPP2C3expression causes the acceleration of fruit ripening onset via the alternation of ABA signaling activity, and the fruit gloss is affected by the changes of outer epidermis structure. RNA-seq analysis found significant different expression of cuticle-related genes in pericarp between wild-type andSlPP2C3suppressed lines. Taken together, our finding demonstrate that SlPP2C3 plays an important role in the regulation of fruit ripening and fruit appearance quality in tomato.
Meta-regression of COVID-19 prevalence/fatality on socioeconomic characteristics of data from top 50 U.S. large cities
Authors: Takagi Hisato , Kuno Toshiki , Yokoyama Yujiro , Ueyama Hiroki , Matsushiro Takuya , Hari Yosuke , Ando Tomo 
Published: May 2020

AbstractTo screen potential risk and protective socioeconomic factors for Coronavirus disease 2019 (COVID-19) prevalence and fatality, meta-regression of data from top 50 U.S. large-population cities was performed. The population estimate (in 2019) of each country to which the city belongs was abstracted from the “County Population Totals: 2010-2019.” From the “Johns Hopkins Coronavirus Resource Center,” the cumulative number of confirmed cases and deaths of COVID-19 in each country was obtained on May 22, 2020. Socioeconomic characteristics of each country were extracted from the “2014-2018 American Community Survey (ACS) 5-Year Data Profile” and “Small Area Income and Poverty Estimates (SAIPE) Program (for 2018).” Radom-effects meta-regression was performed using OpenMetaAnalyst (http://www.cebm.brown.edu/openmeta/index.html). A coefficient (slope of the meta-regression line) for COVID-19 prevalence was significantly negative for male sex, education attainment, computer and Internet use, and private health insurance. Whereas, the coefficient was significantly positive for black race, never matrimony, unemployment, and poverty. In the multivariable model, the coefficient was significantly negative for male sex (P = 0.036) and computer use (P = 0.024), and significantly positive for never matrimony (P < 0.001). A coefficient for COVID-19 fatality was significantly negative for no health insurance, and significantly positive for elderly, unemployment, and public coverage. In the multivariable model, the coefficient was significantly positive for only elderly (P = 0.002). In conclusion, a number of socioeconomic factors, e.g. male sex (negatively for prevalence), elderly (positively for fatality), never matrimony (positively for prevalence), and computer use (negatively for prevalence) may be associated with COVID-19.
Machine Learning for Neonatal Mortality Risk Assessment: A Case Study Using Public Health Data from São Paulo
Authors: Beluzo Carlos Eduardo , Alves Luciana Correia , Bresan Rodrigo , Arruda Natália , Sovat Ricardo , Carvalho Tiago 
Published: May 2020

AbstractInfant mortality is a reflection of a complex combination of biological, socioeconomic and health care factors that require various data sources for a thorough analysis. Consequently, the use of specialized tools and techniques to deal with a large volume of data is extremely helpful. Machine learning has been applied to solve problems from many domains and presents great potential for the proposed problem, which would be an innovation in Brazilian reality. In this paper, an innovative method is proposed to perform a neonatal death risk assessment using computer vision techniques. Using mother, pregnancy care and child at birth features, from a dataset containing neonatal samples from São Paulo city public health data, the proposed method encodes images features and uses a custom convolutional neural network architecture to classification. Experiments show that the method is able to detect death samples with accuracy of 90.61%.
Formation of wall-less cells inKitasatospora viridifaciensrequires cytoskeletal protein FilP in oxygen-limiting conditions
Authors: Ultee Eveline , Briegel Ariane , Claessen Dennis 
Published: May 2020

ABSTRACTThe cell wall is considered an essential component for bacterial survival, providing structural support and protection from environmental insults. Under normal growth conditions, filamentous actinobacteria insert new cell wall material at the hyphal tips regulated by the coordinated activity of cytoskeletal proteins and cell wall biosynthetic enzymes. Despite the importance of the cell wall, some filamentous actinobacteria can produce wall-deficient S-cells upon prolonged exposure to hyperosmotic stress. Here we performed cryo-electron tomography and live cell imaging to further characterize S-cell extrusion inKitasatospora viridifaciens. We show that exposure to hyperosmotic stress leads to DNA compaction, membrane and S-cell extrusion and thinning of the cell wall at hyphal tips. Additionally, we find that the extrusion of S-cells is abolished in a cytoskeletal mutant strain that lacks the intermediate filament-like protein FilP. Furthermore, micro-aerobic culturing promotes the formation of S-cells in the wild-type, but the limited oxygen still impedes S-cell formation in the ΔfilPmutant. These results demonstrate that S-cell formation is stimulated by oxygen-limiting conditions and dependent on the presence of an intact cytoskeleton.
A population genomic unveiling of a new cryptic mosquito taxon within the malaria-transmittingAnopheles gambiaecomplex
Authors: Tennessen Jacob A. , Ingham Victoria A. , Toé Kobié Hyacinthe , Guelbéogo Wamdaogo Moussa , Sagnon N’Falé , Kuzma Rebecca , Ranson Hilary , Neafsey Daniel E. 
Published: May 2020

AbstractTheAnopheles gambiaecomplex consists of multiple morphologically indistinguishable mosquito species including the most important vectors of the malaria parasitePlasmodium falciparumin sub-Saharan Africa. Several lineages have only recently been described as distinct, including the cryptic taxon GOUNDRY in central Burkina Faso. The ecological, immunological, and reproductive differences among these taxa will critically impact population responses to disease control strategies and environmental changes. Here we examine whole-genome sequencing data from a longitudinal study of putativeA. coluzziiin western Burkina Faso. Surprisingly, many samples are genetically divergent fromA. coluzziiand all otherAnophelesspecies and represent a new taxon, here designatedAnophelesTENGRELA (AT). Population genetic analysis suggests that GOUNDRY sensu stricto represents an admixed population descended from bothA. coluzziiand AT. AT harbors low nucleotide diversity except for the 2La inversion polymorphism which is maintained by overdominance. It shows numerous fixed differences withA. coluzziiconcentrated in several regions reflecting selective sweeps, but the two taxa are identical at standard diagnostic loci used for taxon identification and thus AT may often go unnoticed. We present an amplicon-based genotyping assay for identifying AT which could be usefully applied to numerous existing samples. Misidentified cryptic taxa could seriously confound ongoing studies ofAnophelesecology and evolution in western Africa, including phenotypic and genotypic surveys of insecticide resistance. Reproductive barriers between cryptic species may also complicate novel vector control efforts, for example gene drives, and hinder predictions about evolutionary dynamics ofAnophelesandPlasmodium.
Semantic Segmentation to Extract Coronary Arteries in Invasive Coronary Angiograms
Authors: Zhao Chen , Bober Robert , Tang Haipeng , Tang Jinshan , Dong Minghao , Zhang Chaoyang , He Zhuo , Wang Yu-Ping , Deng Hong-Wen , Esposito Michele L. , Xu Zhihui , Zhou Weihua 
Published: May 2020

AbstractCoronary artery disease (CAD) is the leading cause of death worldwide, constituting more than one-fourth of global mortalities every year. Accurate semantic segmentation of each artery using invasive coronary angiography (ICA) is important for stenosis assessment and CAD diagnosis. However, due to the morphological similarity among different types of arteries, it is challenging for deep-learning-based models to generate semantic segmentation with an end-to-end approach. In this paper, we propose a multi-step semantic segmentation algorithm based on the analysis of arterial segments extracted from ICAs. The proposed algorithm firstly extracts the entire arterial binary mask (binary vascular tree) using a deep learning-based method. Then we extract the centerline of the binary vascular tree and separate it into different arterial segments. Finally, by extracting the underlying arterial topology, position and pixel features, we construct a powerful coronary artery segment classifier based on support vector machine. Each arterial segment is classified into left coronary artery (LCA), left anterior descending (LAD) and other types of arterial segments. We tested the proposed method on a dataset with 225 ICAs and achieved artery classification accuracy of 70.33%. The experimental results show the effectiveness of the proposed algorithm, which provides impressive performance for analyzing the individual arteries in ICAs.
Ecology and population genetics of the parasitoidPhobocampe confusa(Hymenoptera: Ichneumonidae) in relation to its hosts,Aglaisspecies (Lepidoptera: Numphalidae)
Authors: Audusseau Hélène , Baudrin Gaspard , Shaw Mark R. , Keehnen Naomi L.P. , Schmucki Reto , Dupont Lise 
Published: May 2020

AbstractThe biology of parasitoids in natural ecosystems remain very poorly studied, while they are key species for their functioning. Here we focused onPhobocampe confusa, a vanessines specialist, responsible for high mortality rates in very emblematic butterfly species in Europe (genusAglais). We studied its ecology and genetic structure in connection with those of its host butterflies in Sweden. To this aim, we gathered data from 428P. confusaindividuals reared from 6094 butterfly larvae (ofA. urticae,A. ioand in two occasions ofAraschnia levana) collected over two years (2017 and 2018) and 19 sites distributed along a 500 km latitudinal gradient. We found thatP. confusais widely distributed along the latitudinal gradient. Its distribution is constrained over time by the phenology of its hosts. The large variation in climatic conditions between sampling years explains the decrease in phenological overlap betweenP. confusaand its hosts in 2018 and the 33.5% decrease in the number of butterfly larvae infected. At least in this study,P. confusaseems to favourA. urticaeas host: while it parasitized nests ofA. urticaeandA. ioequally, the proportion of larvae is significantly higher forA. urticae. At the landscape scale,P. confusais almost exclusively found in vegetated open land and near deciduous forests, whereas artificial habitats are negatively correlated with the likelihood of a nest to be parasitized. The genetic analyses on 89 adultP. confusaand 87 adultA. urticaeusing COI and AFLP markers reveal a low genetic diversity inP. confusaand a lack of population genetic structure in both species, at the scale of our sampling. Further genetic studies using high-resolution genomics tools will be required to better understand the population genetic structure ofP. confusa, its biotic interactions with its hosts, and ultimately the stability and the functioning of natural ecosystems.
Bottle house: utilising appreciative inquiry to develop a user acceptance model
Authors: Adefila Arinola , Abuzeinab Amal , Whitehead Timothy , Oyinlola Muyiwa 
Published: May 2020

PurposeThis paper develops a novel user-acceptance model for circular solutions to housing design. The model has been systematically developed from a case study of an upcycled plastic bottle building in a low-income community in Nigeria. It is common practice to use participatory approaches to consult end users in communities, typically after design concepts have been proposed and conceptualised. However, this often leads to critical socio-cultural or usability elements being overlooked and the design being substandard. Therefore, this paper develops a robust model for designers, specialists and activists involved in construction that can be used during all phases of a project. This approach demonstrates that user needs should be considered before building designs and plans are generated, providing a greater frame of reference for practitioners, consultants and end users. Enabling the integration of holistic needs of the community and the development of circular design solution.Design/methodology/approachA case study methodology has been employed to develop this model, uses appreciative inquiry methodology. This includes multiple methods to capture end users’ perception: focus groups, interactions with the local community and self-recorded comments. This case study is part of a broader research project to develop replicable low-cost self-sufficient homes utilising local capacity using upcycled, locally available materials.FindingsThe findings identify the challenges associated with designing circular solution housing without a robust understanding of interrelated factors, which ensure sustainability and user acceptance. The conclusions demonstrate why essential socio-cultural factors, usually unrelated to technical development, should be understood and contextualised when designing sustainable solutions in low/middle-income communities. The authors argue that without this holistic approach, undesirable consequences may arise, often leading to more significant challenges. Instead of referring to multiple frameworks, this distinctive model can be used to evaluate user acceptance for low-cost housing in particular and other dimensions of circular solution design that involve end-user acceptance. The model blends circular solution dimensions with user-acceptance concerns offering a guide that considers essential features that are both user-friendly and pragmatic, such as utility, technological innovation and functionality as well as their intersectionality.Research limitations/implicationsThe research relied on a single case study, which focussed on end-user engagement of upcycling waste materials as an application of circular solutions. The model will contribute to developing socially accepted circular solutions taking into consideration local context factors.Originality/valueThe paper is proposing a model for user acceptance of circular construction materials relevant to low- and middle-income countries (LMICs).
Experiences of aspiring school principals receiving coaching as part of a leadership development programme
Authors: van Nieuwerburgh Christian , Barr Margaret , Munro Chris , Noon Heather , Arifin Daniel 
Published: May 2020

PurposeThis paper adds depth to our understanding of how coaching works by exploring the experiences of 14 aspiring school principals who received one-to-one leadership coaching as part of a leadership development programme.Design/methodology/approachThis study adopts a phenomenological approach. Individual semi-structured interviews were conducted with the participants. Thematic analysis was used to code the data and identify themes.FindingsThis paper reports on four themes based on the experiences of the participants: having time to reflect, feeling safe to explore, focussing on what's important for me and experiencing positive emotions.Research limitations/implicationsThe findings are unique to the participants who volunteered to take part in this study and therefore not representative of a general population of aspiring educational leaders. Further research is needed into the possible benefits of coaching to support educators undergoing leadership training.Practical implicationsThe findings raise a potential dilemma within the teaching profession about the use of educators' time; while they need to give time and attention to multiple stakeholders, they also need to protect time for their own development and self-reflection. Based on the reported experiences of the participants in this study, it is recommended that coaching be considered a component of professional development for educational leaders.Originality/valueThis paper adds to the growing research base for coaching in education, providing a unique insight into the experiences of aspiring school principals who received one-to-one leadership coaching as part of a leadership development programme.