bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suspension of a Point-Mass-Loaded Filament in Non-Uniform Flows: Passive Dynamics of a Ballooning Spider
Authors: Cho Moonsung , Cruz Bournazou Mariano Nicolas , Neubauer Peter , Rechenberg Ingo 
Published: June 2020

AbstractSpiders utilize their fine silk fibres for their aerial dispersal, known as ballooning. With this method, spiders can disperse hundreds of kilometres, reaching as high as 4.5 km. However, the passive dynamics of a ballooning model (a highly flexible filament and a spider body at the end of it) are not well understood. The previous study (Rouse model: without taking into account anisotropic drag of a fibre) suggested that the flexible and extendible fibres reduce the settling speed of the ballooning model in homogeneous turbulence. However, the exact cause of the reduction of the settling speed is not explained and the assumed isotropic drag of a fibre is not realistic in the low Reynolds number flow. Here we introduce a bead-spring model that takes into account the anisotropic drag of a fibre to investigate the passive behaviour of the ballooning model in the various non-uniform flows (a shear flow, a periodic vortex flow field and a homogeneous turbulent flow). For the analysis of the wide range of parameters, we defined a dimensionless parameter, which is called ‘a ballooning number.’ The ballooning number means the ratio of Stokes’ fluid-dynamic force on a fibre by the non-uniform flow field to the gravitational force of a body at the end of the fibre. Our simulation shows that the settling speed of the present model in the homogeneous turbulent flows shows the biased characters of slow settling as the influence of the turbulent flow increases. The causes of this slow settling are investigated by simulating it in a wide range of shear flows. We revealed that the cause of this is the drag anisotropy of the filament structure (spider silk). In more detail, the cause of reduced settling speed lies not only in the deformed geometrical shape of the ballooning silk but also in its generation of fluid-dynamic force in a non-uniform flow (shear flow). Additionally, we found that the ballooning structure could become trapped in a vortex flow. This seemed to be the second reason why the ballooning structure settles slowly in the homogeneous turbulent flow. These results can help deepen our understanding of the passive dynamics of spiders ballooning in the atmospheric boundary layer.
Default and Control networks connectivity dynamics track the stream of affect at multiple timescales
Authors: Lettieri Giada , Handjaras Giacomo , Setti Francesca , Cappello Elisa Morgana , Bruno Valentina , Diano Matteo , Leo Andrea , Ricciardi Emiliano , Pietrini Pietro , Cecchetti Luca 
Published: June 2020

AbstractIn everyday life the stream of affect results from the interaction between past experiences, expectations, and the unfolding of events. How the brain represents the relationship between time and affect has been hardly explored, as it requires modeling the complexity of everyday life in the laboratory setting. Movies condense into hours a multitude of emotional responses, synchronized across subjects and characterized by temporal dynamics alike real-world experiences.Here, we use time-varying intersubject brain synchronization and real-time behavioral reports to test whether connectivity dynamics track changes in affect during movie watching. Results show that polarity and intensity of experiences relate to connectivity of the default mode and control networks and converge in the right temporo-parietal cortex. We validate these results in two experiments including four independent samples, two movies, and alternative analysis workflows. Lastly, we reveal chronotopic connectivity maps within temporo-parietal and prefrontal cortex, where adjacent areas preferentially encode affect at specific timescales.
The neural basis of intelligence in fine-grained cortical topographies
Authors: Feilong Ma , Guntupalli J. Swaroop , Haxby James V. 
Published: June 2020

AbstractIntelligent thought is the product of efficient neural information processing, which is embedded in fine-grained, topographically-organized population responses and supported by fine-grained patterns of connectivity among cortical fields. Previous work on the neural basis of intelligence, however, has focused on coarse-grained features of brain anatomy and function, because cortical topographies are highly idiosyncratic at a finer scale, obscuring individual differences in fine-grained connectivity patterns. We used a computational algorithm, hyperalignment, to resolve these topographic idiosyncrasies, and found that predictions of general intelligence based on fine-grained (vertex-by-vertex) connectivity patterns were markedly stronger than predictions based on coarse-grained (region-by-region) patterns. Intelligence was best predicted by fine-grained connectivity in the default and frontoparietal cortical systems, both of which are associated with self-generated thought. Previous work overlooked fine-grained architecture because existing methods couldn’t resolve idiosyncratic topographies, preventing investigation where the keys to the neural basis of intelligence are more likely to be found.
Protection after Quarantine: Insights from a Q-SEIR Model with Nonlinear Incidence Rates Applied to COVID-19
Authors: Antonio Minoza Jose Marie , Sevilleja Jesus Emmanuel , de Castro Romulo , Caoili Salvador E. , Bongolan Vena Pearl 
Published: June 2020

AbstractCommunity quarantine has been resorted to by various governments to address the current COVID-19 pandemic; however, this is not the only non-therapeutic method of effectively controlling the spread of the infection. We study an SEIR model with nonlinear incidence rates, and introduce two parameters,αandε, which mimics the effect of quarantine (Q). We compare this with the Q-SEIR model, recently developed, and demonstrate the control of COVID-19 without the stringent conditions of community quarantine. We analyzed the sensitivity and elasticity indices of the parameters with respect to the reproduction number. Results suggest that a control strategy that involves maximizingαandεis likely to be successful, although quarantine is still more effective in limiting the spread of the virus. Release from quarantine depends on continuance and strict adherence to recommended social and health promoting behaviors. Furthermore, maximizingαandεis equivalent to a50%successful quarantine in disease-free equilibrium (DFE). This model reduced the infectious in Quezon City by3.45%and Iloilo Province by3.88%; however, earlier peaking by nine and 17 days, respectively, when compared with the results of Q-SEIR.
Are women leaders significantly better at controlling the contagion?
Authors: Purkayastha Soumik , Salvatore Maxwell , Mukherjee Bhramar 
Published: June 2020

AbstractRecent media articles have suggested that women-led countries are doing better in terms of their responses to the COVID-19 pandemic. We examine an ensemble of public health metrics to assess the control of COVID-19 epidemic in women- versus men-led countries worldwide based on data available up to June 3. The median of the distribution of median time-varying effective reproduction number for women- and men-led countries were 0.89 and 1.14 respectively with the 95% two-sample bootstrap-based confidence interval for the difference (women - men) being [- 0.34, 0.02]. In terms of scale of testing, the median percentage of population tested were 3.28% (women), 1.59% (men) [95% CI: (−1.29%, 3.60%)] with test positive rates of 2.69% (women) and 4.94% (men) respectively. It appears that though statistically not significant, countries led by women have an edge over countries led by men in terms of public health metrics for controlling the spread of the COVID-19 pandemic worldwide.One Sentence SummaryWe quantitatively compare countries led by women with countries led by men in terms of public health metrics for controlling the spread of the novel coronavirus.
Explaining face representation in the primate brain using different computational models
Authors: Chang Le , Egger Bernhard , Vetter Thomas , Tsao Doris Y. 
Published: June 2020

SummaryUnderstanding how the brain represents the identity of complex objects is a central challenge of visual neuroscience. The principles governing object processing have been extensively studied in the macaque face patch system, a sub-network of inferotemporal (IT) cortex specialized for face processing. A previous study reported that single face patch neurons encode axes of a generative model called the “active appearance” model, which transforms 50-d feature vectors separately representing facial shape and facial texture into facial images. However, a systematic investigation comparing this model to other computational models, especially convolutional neural network models that have shown success in explaining neural responses in the ventral visual stream, has been lacking. Here, we recorded responses of cells in the most anterior face patch AM to a large set of real face images and compared a large number of models for explaining neural responses. We found that the active appearance model better explained responses than any other model except CORnet-Z, a feedforward deep neural network trained on general object classification to classify non-face images, whose performance it tied on some face image sets and exceeded on others. Surprisingly, deep neural networks trained specifically on facial identification did not explain neural responses well. A major reason is that units in the network, unlike neurons, are less modulated by face-related factors unrelated to facial identification such as illumination.
SCHNAPPs - Single Cell sHiNy APPlication(s)
Authors: Jagla Bernd , Rouilly Vincent , Puceat Michel , Hasan Milena 
Published: June 2020

ABSTRACTMotivationSingle-cell RNA-sequencing (scRNAseq) experiments are becoming a standard tool for bench-scientists to explore the cellular diversity present in all tissues. On one hand, the data produced by scRNASeq is technically complex, with analytical workflows that are still very much an active field of bioinformatics research, and on the other hand, a wealth of biological background knowledge is often needed to guide the investigation. Therefore, there is an increasing need to develop applications geared towards bench-scientists to help them abstract the technical challenges of the analysis, so that they can focus on the Science at play. It is also expected that such applications should support closer collaboration between bioinformaticians and bench-scientists by providing reproducible science tools.ResultsWe present SCHNAPPs, a computer program designed to enable bench-scientists to autonomously explore and interpret single cell RNA-seq expression data and associated annotations. The Shiny-based application allows selecting genes and cells of interest, performing quality control, normalization, clustering, and differential expression analyses, applying standard workflows from Seurat (Stuart et al., 2019) or Scran (Lun et al., 2016) packages, and most of the common visualizations. An R-markdown report can be generated that tracks the modifications, and selected visualizations facilitating communication and reproducibility between bench-scientist and bioinformatician. The modular design of the tool allows to easily integrate new visualizations and analyses by bioinformaticians. We still recommend that a data analysis specialist oversees the analysis and interpretation.AvailabilityThe SCHNAPPs application, docker file, and documentation are available on GitHub:https://c3bi-pasteur-fr.github.io/UTechSCB-SCHNAPPs; Example contribution are available at the following GitHub site:https://github.com/baj12/SCHNAPPsContributions.
Decomposing metabolite set activity levels with PALS
Authors: McLuskey Karen , Wandy Joe , Vincent Isabel , van der Hooft Justin J.J. , Rogers Simon , Burgess Karl , Daly Rónán 
Published: June 2020

AbstractMotivationRelated metabolites can be grouped into metabolite sets in many ways. Examples of these include the grouping of metabolites through their participation in a series of chemical reactions (forming metabolic pathways); or based on fragmentation spectral similarities and shared chemical substructures. Understanding how such metabolite sets change across samples can be incredibly useful in the interpretation and understanding of complex metabolomics data. However many of the available tools suitable for the enrichment analysis of metabolite sets are based on simple methods that badly handle the missing features inherent in untargeted metabolomics measurements and can be difficult to integrate into existing applications.ResultsWe present PALS (Pathway Activity Level Scoring), a Python library, command-line tool and Web application that performs the ranking of significantly-changing metabolite sets over different experimental conditions. As example applications, PALS is used to analyse metabolites grouped as pathways and by common MS-MS fragmentation structures. A comparison of PALS with two other commonly used methods (ORA and GSEA) is also given, and reveals that PALS is more robust to missing peaks and noisy data than the alternatives. We report results from using PALS to analyse pathways from a study of Human African Trypanosomiasis. Finally, we also report how PALS used tandem MS fragmentation structures to reveal enriched metabolite sets between clades in Rhamnaceae plant data, and on American Gut Project data.AvailabilityPALS is freely available from our project Web site athttps://pals.glasgowcompbio.org/. It can be imported as a Python library, run as a stand-alone tool or used as a web application.
TBPL2/TFIIA complex establishes the maternal transcriptome by an oocyte-specific promoter usage
Authors: Yu Changwei , Cvetesic Nevena , Hisler Vincent , Gupta Kapil , Ye Tao , Gazdag Emese , Negroni Luc , Hajkova Petra , Berger Imre , Lenhard Boris , Müller Ferenc , Vincent Stéphane D. , Tora László 
Published: June 2020

AbstractDuring oocyte growth, transcription is required to create RNA and protein reserves to achieve maternal competence. During this period, the general transcription factor TATA binding protein (TBP) is replaced by its paralogue, TBPL2 (TBP2 or TRF3), which is essential for RNA polymerase II transcription. We show that in oocytes TBPL2 does not assemble into a canonical TFIID complex. Our transcript analyses demonstrate that TBPL2 mediates transcription of oocyte-expressed genes, including mRNA survey genes, as well as specific endogenous retroviral elements. Transcription start site (TSS) mapping indicates that TBPL2 has a strong preference for TATA-like motif in core promoters driving sharp TSS selection, in contrast with canonical TBP/TFIID-driven TATA-less promoters that have broader TSS architecture. Thus, we show a role for the TBPL2/TFIIA complex in the establishment of the oocyte transcriptome by using a specific TSS recognition code.
Arginine methylation promotes siRNA-binding specificity for a spermatogenesis-specific isoform of the Argonaute protein CSR-1
Authors: Nguyen Dieu An H. , Phillips Carolyn M. 
Published: June 2020

SummaryCSR-1 is an essential Argonaute protein that binds to a subclass of 22G-RNAs targeting most germline-expressed genes. Here we show that the two isoforms of CSR-1 have distinct expression patterns; CSR-1B is ubiquitously expressed throughout the germline and during all stages of development while CSR-1A expression is restricted to germ cells undergoing spermatogenesis. Furthermore, CSR-1A associates preferentially with 22G-RNAs mapping to spermatogenesis-specific genes whereas CSR-1B-bound small RNAs map predominantly to oogenesis-specific genes. Interestingly, the exon unique to CSR-1A contains multiple dimethylarginine modifications, which are necessary for the preferential binding of CSR-1A to spermatogenesis-specific 22G-RNAs. Thus, we have discovered a regulatory mechanism forC. elegansArgonaute proteins that allows for specificity of small RNA binding between similar Argonaute proteins with overlapping temporal and spatial localization.
Pan-resistantCandida auris: New York Sub-cluster Susceptible to Antifungal Combinations
Authors: O’Brien Brittany , Liang Jiali , Chaturvedi Sudha , Jacobs Jonathan L. , Chaturvedi Vishnu 
Published: June 2020

AbstractFour pan-resistantCandia aurisstrains from New York outbreak were 100% inhibitedin vitroby combinations of two antifungal drugs using fixed concentrations achievablein vivo. Pan-resistantC. aurisstrains have mutations in eleven gene targets associated with major antifungal drugs, and constituted a distinct sub-cluster among NY strains.
EEG in Motion: Using an Oddball Task to Explore Motor Interference in Active Skateboarding
Authors: Robles Daniel , Kuziek Jonathan W. P. , Wlasitz Nicole A. , Bartlett Nathan T. , Hurd Pete L. , Mathewson Kyle E. 
Published: June 2020

AbstractRecent advancements in portable computer devices have opened new avenues in the study of human cognition outside research laboratories. This flexibility in methodology has led to the publication of several Electroencephalography (EEG) studies recording brain responses in real-world scenarios such as cycling and walking outside. In the present study, we tested the classic auditory oddball task while participants moved around an indoor running track using an electric skateboard. This novel approach allows for the study of attention in motion while virtually removing body movement. Using the skateboard auditory oddball paradigm, we found reliable and expected standard-target differences in the P3 and MMN/N2b event-related potentials (ERPs). We also recorded baseline EEG activity and found that, compared to this baseline, alpha power is attenuated in frontal and parietal regions during skateboarding. In order to explore the influence of motor interference in cognitive resources during skateboarding, we compared participants’ preferred riding stance (baseline level of riding difficulty) vs their non-preferred stance (increased level of riding difficulty). We found that an increase in riding difficulty did not modulate the P3 and tonic alpha amplitude during skateboard motion. These results suggest that increases in motor demands might not lead to reductions in cognitive resources as shown in previous literature.
Split-HaloTag®Imaging Assay for Sophisticated Microscopy of Protein-Protein Interactionsin planta
Authors: Minner-Meinen Rieke , Weber Jan-Niklas , Albrecht Andreas , Matis Rainer , Behnecke Maria , Tietge Cindy , Frank Stefan , Schulze Jutta , Buschmann Henrik , Walla Peter Jomo , Mendel Ralf-R. , Hänsch Robert , Kaufholdt David 
Published: June 2020

AbstractAn ever-increasing number of intracellular multi-protein networks have been identified in plant cells. Split-GFP based protein-protein interaction assays combine the advantages ofin vivointeraction studies in a native environment with additional visualisation of protein complex localisation. Due to its simple protocols, it has become one of the most frequently used methods. However, standard fluorescent proteins entail several drawbacks for sophisticated microscopy.With the HaloTag®system, these drawbacks can be overcome as this reporter forms covalent irreversible bonds with synthetic photostable fluorescent ligands. Dyes can be used in adjustable concentrations and are suitable for advanced microscopy methods. Therefore, we established the Split-HaloTag®imaging assay in plants which is based on the reconstitution of a functional HaloTag®protein upon protein-protein interaction and subsequent covalent binding of an added fluorescent ligand. Its suitability and robustness were demonstrated using well-characterised interactions as an example for protein-protein interaction at cellular structures: the molybdenum cofactor biosynthesis complex anchoring to filamentous actin. Additionally, a specific interaction was visualised with subdiffractional polarisation microscopy in a more distinctive manner as example for sophisticated imaging.Split-GFP and Split-HaloTag®can complement one another as Split-HaloTag®represents an alternative option and an addition to the large toolbox ofin vivomethods. Therefore, this promising new Split-HaloTag®imaging assay provides a unique and sensitive approach for more detailed characterization of protein-protein interaction with specific microscopic techniques such as 3D-imaging, single molecule tracking and super-resolution microscopy.
Quantitative fluorescence lifetime imaging uncovers a novel role for KCC2 chloride transport in dendritic microdomains
Authors: Weilinger Nicholas L. , LeDue Jeffrey M. , Kahle Kristopher T. , MacVicar Brian A. 
Published: June 2020

AbstractIntracellular chloride ion ([Cl−]i) homeostasis is critical for synaptic neurotransmission yet variations in subcellular domains are poorly understood owing to difficulties in obtaining quantitative, high-resolution measurements of dendritic [Cl−]i. We combined whole-cell patch clamp electrophysiology with simultaneous fluorescence lifetime imaging (FLIM) of the Cl−dye MQAE to quantitatively map dendritic Cl−levels in normal or pathological conditions. FLIM-based [Cl−]iestimates were corroborated by Rubi-GABA uncaging to measured EGABA. Low baseline [Cl-]iin dendrites required Cl−efflux via the K+-Cl−cotransporter KCC2 (SLC12A5). In contrast, pathological NMDA application generated spatially heterogeneous subdomains of high [Cl−]ithat created dendritic blebs, a signature of ischemic stroke. These discrete regions of high [Cl−]iwere caused by reversed KCC2 transport. Therefore monitoring [Cl−]imicrodomains with a new high resolution FLIM-based technique identified novel roles for KCC2-dependent chloride transport to generate dendritic microdomains with implications for disease.
Time-resolved profiling reveals ATF3 as a novel mediator of endocrine resistance in breast cancer
Authors: Borgoni Simone , Sofyalı Emre , Soleimani Maryam , Wilhelm Heike , Müller-Decker Karin , Will Rainer , Noronha Ashish , Verschure Pernette J. , Yarden Yosef , Magnani Luca , van Kampen Antoine H.C. , Moerland Perry D. , Wiemann Stefan 
Published: June 2020

AbstractBreast cancer is one of the leading causes of death for women worldwide. Patients whose tumors express Estrogen Receptor α (ERα) account for around 70% of cases and are mostly treated with targeted endocrine therapy. However, 40% of these tumors eventually relapse due to resistance development and further treatment of these patients is highly ineffective. In this study we profiled the early phases of the resistance development process to uncover drivers of this phenomenon. Time-resolved analysis revealed that ATF3, a member of the ATF/CREB family of transcription factors, acts as a novel regulator of the response to therapy via rewiring of central signaling processes towards the adaptation to endocrine treatment. ATF3 was found to be essential in controlling crucial processes such as proliferation, cell cycle and apoptosis during the early response to treatment through the regulation of MAPK/AKT signaling pathways. Its essential role was confirmedin vivoin a mouse model and elevated expression of ATF3 was verified in patient datasets, adding clinical relevance to our findings. This study proposes ATF3 as a novel mediator of endocrine resistance development in breast cancer and elucidates its role in the regulation of downstream pathways activities.