bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ancestral circuits for vertebrate colour vision emerge at the first retinal synapse
Authors: Yoshimatsu Takeshi , Bartel Philipp , Schröder Cornelius , Janiak Filip K , St-Pierre Francois , Berens Philipp , Baden Tom 
Published: October 2020

SummaryFor colour vision, retinal circuits separate information about intensity and wavelength. This requires comparison of at least two spectrally distinct photoreceptors, as in the case of most mammals. However, many vertebrates use the full complement of four ‘ancestral’ cone-types (‘red’, ‘green’, ‘blue’, ‘UV’), and in those cases the nature and implementation of this computation remains poorly understood. Here, we establish the complete circuit architecture of outer retinal circuits underlying colour processing in larval zebrafish, which involves the full ancestral complement of four cone- and three horizontal cell types. Our findings reveal that the synaptic outputs of red- and green-cones efficiently rotate the encoding of natural daylight in a principal component analysis (PCA)-like manner to yield primary achromatic and spectrally-opponent axes, respectively. Together, these two cones capture 91.3% of the spectral variance in natural light. Next, blue-cones are tuned so as to capture most remaining variance when opposed to green-cones. Finally, UV-cones present a UV-achromatic axis for prey capture. We note that fruit flies – the only other tetrachromat species where comparable circuit-level information is available - use essentially the same strategy to extract spectral information from their relatively blue-shifted terrestrial visual world. Together, our results suggest that rotating colour space into primary achromatic and chromatic axes at the eye’s first synapse may be a fundamental principle of colour vision when using more than two spectrally well-separated photoreceptor types.
Intra-axonal translation of Khsrp mRNA slows axon regeneration by destabilizing localized mRNAs
Authors: Patel Priyanka , Buchanan Courtney , Kar Amar N. , Lee Seung Joon , Sahoo Pabitra K. , Urisman Anatoly , Oses-Prieto Juan , Dell’Orco Michela , Cassidy Devon E. , Miller Sharmina , Thames Elizabeth , Smith Terika P. , Zdradzinski Matthew D. , Burlingame Alma L. , Perrone-Bizzozero Nora , Twiss Jeffery L. 
Published: October 2020

ABSTRACTProteins generated by localized mRNA translation in axons support nerve regeneration through retrograde injury signaling and localized axon growth mechanisms. RNA binding proteins (RBP) are needed for this and other aspects of post-transcriptional control of localized mRNAs, but only a limited number of axonal RBPs have been reported. We used a targeted mass spectrometry approach to profile the axonal RBPs in naïve, injured and regenerating PNS axons. We detected 76 axonal proteins that are reported to have RNA binding activity, with the levels of several of these axonal RBPs changing with axonal injury and regeneration. These axonal RBPs with altered axoplasm levels include KHSRP that we previously reported decreases neurite outgrowth in developing CNS neurons. We show that KHSRP levels rapidly increase in sciatic nerve axons after crush injury and remain elevated increasing in levels out to 28 days post-sciatic nerve crush injury. Khsrp mRNA localizes into axons and the rapid increase in axonal KHSRP after axotomy is mediated by the local translation of its mRNA. KHSRP binds to mRNAs with a 3’UTR AU-rich element and targets those mRNAs to the cytoplasmic exosome for degradation. KHSRP knockout mice show increased axonal levels of defined KHSRP target mRNAs, Gap43 and Snap25 mRNAs, following sciatic nerve injury and accelerated nerve regeneration in vivo. These data indicate that axonal translation of Khsrp mRNA following nerve injury serves to destabilize other axonal mRNAs and slow axon regeneration.
Pseudomonas aeruginosa PA14 produces R-bodies, extendable protein polymers with roles in host colonization and virulence
Authors: Wang Bryan , Lin Yu-Cheng , Vasquez-Rifo Alejandro , Jo Jeanyoung , Price-Whelan Alexa , McDonald Shujuan Tao , Brown Lewis M. , Sieben Christian , Dietrich Lars E.P. 
Published: October 2020

AbstractPseudomonas aeruginosa PA14, an opportunistic pathogen of diverse hosts, contains genes with the potential to confer production of R-bodies (i.e., a “reb cluster”). R-bodies are large, extendable protein polymers best known for their role in killing of paramecia by the bacterium Caedibacter taeniospiralis, and genes in the reb cluster have been implicated in PA14 virulence. Here, we present evidence that PA14 expresses reb cluster genes during colonization of plant and nematode hosts. We identify products of the reb cluster that are R-body-associated and that control stochastic expression of R-body structural genes. We also show that R-body production is required for full virulence in nematodes. Analyses of nematode ribosome content and immune response indicate that R-bodies act via a mechanism involving ribosome cleavage and translational inhibition. These observations provide insight into the biology of R-body production and its consequences during P. aeruginosa infection.
ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture
Authors: Gaggion Nicolás , Ariel Federico , Daric Vladimir , Lambert Éric , Legendre Simon , Roulé Thomas , Camoirano Alejandra , Milone Diego H. , Crespi Martin , Blein Thomas , Ferrante Enzo 
Published: October 2020

AbstractBackgroundDeep learning methods have outperformed previous techniques in most computer vision tasks, including image-based plant phenotyping. However, massive data collection of root traits and the development of associated artificial intelligence approaches have been hampered by the inaccessibility of the rhizosphere. Here we present ChronoRoot, a system which combines 3D printed open-hardware with deep segmentation networks for high temporal resolution phenotyping of plant roots in agarized medium.ResultsWe developed a novel deep learning based root extraction method which leverages the latest advances in convolutional neural networks for image segmentation, and incorporates temporal consistency into the root system architecture reconstruction process. Automatic extraction of phenotypic parameters from sequences of images allowed a comprehensive characterization of the root system growth dynamics. Furthermore, novel time-associated parameters emerged from the analysis of spectral features derived from temporal signals.ConclusionsAltogether, our work shows that the combination of machine intelligence methods and a 3D-printed device expands the possibilities of root high-throughput phenotyping for genetics and natural variation studies as well as the screening of clock-related mutants, revealing novel root traits.
A configurable model of the synaptic proteome reveals the molecular mechanisms of disease co-morbidity
Authors: Sorokina Oksana , Mclean Colin , Croning Mike DR , Heil Katharina F , Wysocka Emilia , He Xin , Sterratt David , Grant Seth GN , Simpson T Ian , Armstrong J Douglas 
Published: October 2020

AbstractSynapses contain highly complex proteomes which control synaptic transmission, cognition and behaviour. Genes encoding synaptic proteins are associated with neuronal disorders many of which show clinical co-morbidity. Our hypothesis is that there is mechanistic overlap that is emergent from the network properties of the molecular complex. To test this requires a detailed and comprehensive molecular network model.We integrated 57 published synaptic proteomic datasets obtained between 2000 and 2019 that describe over 7000 proteins. The complexity of the postsynaptic proteome is reaching an asymptote with a core set of ~3000 proteins, with less data on the presynaptic terminal, where each new study reveals new components in its landscape. To complete the network, we added direct protein-protein interaction data and functional metadata including disease association.The resulting amalgamated molecular interaction network model is embedded into a SQLite database. The database is highly flexible allowing the widest range of queries to derive custom network models based on meta-data including species, disease association, synaptic compartment, brain region, and method of extraction.This network model enables us to perform in-depth analyses that dissect molecular pathways of multiple diseases revealing shared and unique protein components. We can clearly identify common and unique molecular profiles for co-morbid neurological disorders such as Schizophrenia and Bipolar Disorder and even disease comorbidities which span biological systems such as the intersection of Alzheimer’s Disease with Hypertension.
RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis
Authors: Zhang Shu , Übelmesser Nadine , Josipovic Natasa , Forte Giada , Slotman Johan A. , Chiang Michael , Gothe Henrike , Gusmao Eduardo Gade , Becker Christian , Altmüller Janine , Houtsmuller Adriaan B. , Roukos Vassilis , Wendt Kerstin S. , Marenduzzo Davide , Papantonis Argyris 
Published: October 2020

SUMMARYMammalian chromosomes are three-dimensional entities shaped by converging and opposing forces. Mitotic cell division induces drastic chromosome condensation, but following reentry into the G1 cell cycle phase, condensed chromosomes unwind to reestablish interphase organization. Here, we use a cell line allowing auxin-mediated degradation of RNA polymerase II to test its role in this transition.In situHi-C showed that RNAPII is required for compartment and loop formation following mitosis. RNAPs often counteract loop extrusion and, in their absence, longer and more prominent loops arise. Evidence from chromatin fractionation, super-resolution imaging andin silicomodeling attribute these effects to RNAPII-mediated cohesin loading at active promoters upon reentry into G1. Our findings reconcile the role of RNAPII in gene expression with that in chromatin architecture.
Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation
Authors: Chialva Constanza , Blein Thomas , Crespi Martin , Lijavetzky Diego 
Published: October 2020

ABSTRACTCarrot (Daucus carotaL.) is one of the most cultivated vegetable in the world and of great importance in the human diet. Its storage organs can accumulate large quantities of anthocyanins, metabolites that confer the purple pigmentation to carrot tissues and whose biosynthesis is well characterized. Long non-coding RNAs (lncRNAs) play critical roles in regulating gene expression of various biological processes in plants. In this study, we used a high throughput stranded RNA-seq to identify and analyze the expression profiles of lncRNAs in phloem and xylem root samples using two genotypes with a strong difference in anthocyanin production. We discovered and annotated 8484 new genes, including 2095 new protein-coding and 6373 non-coding transcripts. Moreover, we identified 639 differentially expressed lncRNAs between the phenotypically contrasted genotypes, including certain only detected in a particular tissue. We then established correlations between lncRNAs and anthocyanin biosynthesis genes in order to identify a molecular framework for the differential expression of the pathway between genotypes. A specific natural antisense transcript (NAT) linked to theDcMYB7key anthocyanin biosynthetic transcription factor suggested how the regulation of this pathway may have evolved between genotypes.
Comparison of wearable and clinical devices for acquisition of peripheral nervous system signals
Authors: Bizzego Andrea , Gabrieli Giulio , Furlanello Cesare , Esposito Gianluca 
Published: October 2020

AbstractA key access point to the functioning of the Autonomic Nervous System is the investigation of peripheral signals. Wearable Devices (WDs) enable the acquisition and quantification of peripheral signals in a wide range of contexts, from personal uses to scientific research. WDs have lower costs and higher portability than medical-grade devices. But achievable data quality can be lower, subject to artifacts due to body movements and data losses. It is therefore crucial to evaluate the reliability and validity of WDs before their use in research. In this study we introduce a data analysis procedure for the assessment of WDs for multivariate physiological signals. The quality of cardiac and Electrodermal Activity signals is validated with a standard set of Signal Quality Indicators. The pipeline is available as a collection of open source Python scripts based on the pyphysio package. We apply the indicators for the analysis of signal quality on data simultaneously recorded from a clinical-grade device and two WDs. The dataset provides signals of 6 different physiological measures collected from 18 subjects with WDs. This study indicates the need of validating the use of WD in experimental settings for research and the importance of both technological and signal processing aspects to obtain reliable signals and reproducibility of results.
High resolution cryo EM analysis of HPV16 identifies minor structural protein L2 and describes capsid flexibility
Authors: Goetschius Daniel J. , Hartmann Samantha R. , Subramanian Suriyasri , Bator Carol , Christensen Neil D. , Hafenstein Susan L 
Published: October 2020

AbstractHuman papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. HPV is epitheliotropic and its replication is tightly associated with terminal keratinocyte differentiation making production and purification of high titer virus preparations for research problematic, therefore alternative HPV production methods have been developed for virological and structural studies. In this study we use HPV16 quasivirus, composed of HPV16 L1/L2 capsid proteins with a packaged cottontail rabbit papillomavirus genome. We have achieved the first high resolution, 3.1Å, structure of HPV16 by using a local subvolume refinement approach. The high resolution enabled us to build L1 unambiguously and identify L2 protein strands. The L2 density is incorporated adjacent to conserved L1 residues on the interior of the capsid. Further interpretation with our own software for Icosahedral Subvolume Extraction and Correlated Classification (ISECC) revealed flexibility, on the whole-particle level through diameter analysis and local movement with inter-capsomer analysis. Inter-capsomer expansion or contraction, governed by the connecting arms, showed no bias in the magnitude or direction of capsomer movement. We propose that papillomavirus capsids are dynamic and capsomers move as rigid bodies connected by flexible linkers. The resulting virus structure will provide a framework for continuing biochemical, genetic and biophysical research for papillomaviruses. Furthermore, our approach has allowed insight into the resolution barrier that has previously been a limitation in papillomavirus structural studies.
Toward a framework for strengthening participants' self-efficacy in online education
Authors: Kundu Arnab 
Published: October 2020

PurposeThe purpose of this study was to review the role of self-efficacy in online education with an objective to propose a holistic framework for strengthening participants' self-efficacy, especially in the Asian context.Design/methodology/approachTo investigate the potential role of self-efficacy of the participants of online academic activities, this study followed the conceptual analysis method, which is breaking down concepts into constituent elements to get a superior understanding of a particular philosophy.FindingsThe findings revealed that self-efficacy, the level of confidence someone has to perform a particular task, is an important factor among teachers and students operating online platforms, and enhanced efficacy is capable of encouraging online practices. Finally, the study proposed a framework to strengthen self-efficacy among participants with intervention measures to make online education effective and impressive.Research limitations/implicationsThe proposed framework will help stakeholders of online education to improve their efficacy and leverage the potential of online education to the fullest. Millions of first-generation online users in many Asian countries who possess low self-confidence in their ability might find the framework easier for better integration, interaction and collaboration in the online learning environment.Originality/valueA vast literature survey was made before proposing this framework that could open up a new dimension in online education by scaffolding participants' inner thrust.
Inter-provincial correlations of agricultural GHG emissions in China based on social network analysis methods
Authors: Qu Jiansheng , Han Jinyu , Liu Lina , Xu Li , Li Hengji , Fan Yujie 
Published: October 2020

PurposeThe purpose of this paper is to explore the heterogeneity and correlations of agricultural greenhouse gas (GHG) emissions among provinces in China, and then policy implications are proposed.Design/methodology/approachAfter agricultural GHG accounting and a pre-analysis of inter-provincial heterogeneity, improved gravity model and the Social Network Analysis (SNA) methods are introduced to construct the network, being carried out from three aspects of the whole network, individual provincial characteristics and cluster analysis.Findings(1) There are significant regional variations in agricultural GHG scale among provinces owing to the layout of agricultural production, and the temporal trends show that the direction and speed of agricultural GHG scale change vary among provinces; (2) In terms of inter-provincial correlations, there exists a complex spatial network of agricultural GHG among provinces, which tends to be more complex, intensive and stable, while the status of the provinces in the network also has gradually become more balanced. All provinces played their respective roles in the four clusters of the network with agricultural layout and comparative advantages, and the distribution has continuously optimized.Practical implicationsThe inter-provincial network characteristics of agricultural GHG emissions and its evolution have practical implications for differentiated and coordinated agricultural GHG reduction policies at the provincial levels.Originality/valueThis paper innovatively study inter-provincial agricultural GHG correlations in China with the SNA methods used to study economic and social connections in the past. There is some originality in the introduction of network theory and application of the SNA methods, which can provide some reference for researches in similar fields.
Exploring the linkages between project managers' mindset behaviour and project leadership style in the Ghanaian construction industry
Authors: Owusu-Manu De-Graft , Debrah Caleb , Amissah Lydia , Edwards David J. , Chileshe Nicholas 
Published: October 2020

PurposeLeadership encapsulates a process of influencing others to understand what needs to be done and how it can be done. The related area of mindset behaviour which moderates leadership styles adopted in various industries has hitherto received scant academic attention in a construction context. This paper thus explores the linkages between project manager's mindset behaviour and project leadership style in the construction industry.Design/methodology/approachLiterature reviewed provides the basis for a questionnaire data collection instrument developed to gather primary data from construction professionals in the Ghanaian construction industry (GCI). A quantitative research strategy was then adopted using the Relative Importance Index (RII) to determine the level of significance of the leadership and mindset archetypes. A Pearson's correlation test was run to ascertain whether the mindset behaviour of project managers has a significant impact upon the type of leadership style.FindingsThe study's results indicate that democratic, transformational and situational leadership styles were prevalent leadership styles in the GCI. The analysis also revealed that project managers favoured the “growth mindset”. Furthermore this style had a moderate positive relationship with democratic and transformational leadership styles. Conversely, a fixed mindset had a low positive relationship with autocratic and situational leadership styles but a low negative relationship with transformational leadership style.Research limitations/implicationsThis research provides sufficient data for project managers to identify the type of mindset to nurture (the growth mindset is recommended) and the effective leadership style to be employed. This study engenders wider discussion on mindset behaviour and project leadership style in developing countries. Moreover, the findings present policymakers and practitioners with the leadership styles to promote and develop (democratic, transformational and situational) and mindset behaviour (growth mindset) to ensure project success in Ghana and other developing countries.Originality/valueThis research represents the first comprehensive study appraising the linkages between project managers’ mindset behaviour and project leadership style in the construction industry. Empirical data presented bridge the identified knowledge gap that exists on the lack of theoretical understanding of the influence that project managers' mindset has on leadership styles in the GCI.
Assessing physical activity, nutrient intake and obesity in middle-aged adults in Akuse, Lower Manya Krobo, Ghana
Authors: Nyakotey David Adjatey , Ananga Alberta Seyram , Apprey Charles 
Published: October 2020

PurposeThe purpose of this paper is to assess physical activity and nutrient intake and their association with obesity in apparently healthy middle-aged adults in Akuse, a rural community in the Eastern region of Ghana.Design/methodology/approachThis cross-sectional study assessed demography and anthropometry, nutrient intakes using a 3-day repeated 24 h dietary recall and physical activity using the global physical activity questionnaire (GPAQ). Data were entered into Microsoft excel and analyzed with SPSS version 25.FindingsThere were 118 respondents (55 males, 46.6% and 63 females, 53.4%) in the study with mean age of 45.62 ± 6.88 years. About 90% of respondents were physically active based on WHO physical activity recommendation. Prevalence of overweight/obesity was higher among inactive participants compared to active participants and sitting/reclining hours was significantly (p-value = 0.042) associated positively with BMI after a bivariate correlation analysis, suggesting that physical activity plays a role in obesity. About one in five respondents were obese. Mean energy intake exceeded RDA for females. Sodium intake far exceeded RDA for both males and females, putting the population at potential risk of hypertension.Practical implicationsThis study demonstrates the need for intensifying health education and other obesity prevention interventions to curb the rising obesity prevalence in rural communities.Originality/valueThe study revealed that overweight/ obesity in this rural community is higher than previously reported for rural Ghana.