@article{6952, abstract = {We present a unified framework tackling two problems: class-specific 3D reconstruction from a single image, and generation of new 3D shape samples. These tasks have received considerable attention recently; however, most existing approaches rely on 3D supervision, annotation of 2D images with keypoints or poses, and/or training with multiple views of each object instance. Our framework is very general: it can be trained in similar settings to existing approaches, while also supporting weaker supervision. Importantly, it can be trained purely from 2D images, without pose annotations, and with only a single view per instance. We employ meshes as an output representation, instead of voxels used in most prior work. This allows us to reason over lighting parameters and exploit shading information during training, which previous 2D-supervised methods cannot. Thus, our method can learn to generate and reconstruct concave object classes. We evaluate our approach in various settings, showing that: (i) it learns to disentangle shape from pose and lighting; (ii) using shading in the loss improves performance compared to just silhouettes; (iii) when using a standard single white light, our model outperforms state-of-the-art 2D-supervised methods, both with and without pose supervision, thanks to exploiting shading cues; (iv) performance improves further when using multiple coloured lights, even approaching that of state-of-the-art 3D-supervised methods; (v) shapes produced by our model capture smooth surfaces and fine details better than voxel-based approaches; and (vi) our approach supports concave classes such as bathtubs and sofas, which methods based on silhouettes cannot learn.}, author = {Henderson, Paul M and Ferrari, Vittorio}, issn = {1573-1405}, journal = {International Journal of Computer Vision}, pages = {835--854}, publisher = {Springer Nature}, title = {{Learning single-image 3D reconstruction by generative modelling of shape, pose and shading}}, doi = {10.1007/s11263-019-01219-8}, volume = {128}, year = {2020}, } @article{7148, abstract = {In the cerebellum, GluD2 is exclusively expressed in Purkinje cells, where it regulates synapse formation and regeneration, synaptic plasticity, and motor learning. Delayed cognitive development in humans with GluD2 gene mutations suggests extracerebellar functions of GluD2. However, extracerebellar expression of GluD2 and its relationship with that of GluD1 are poorly understood. GluD2 mRNA and protein were widely detected, with relatively high levels observed in the olfactory glomerular layer, medial prefrontal cortex, cingulate cortex, retrosplenial granular cortex, olfactory tubercle, subiculum, striatum, lateral septum, anterodorsal thalamic nucleus, and arcuate hypothalamic nucleus. These regions were also enriched for GluD1, and many individual neurons coexpressed the two GluDs. In the retrosplenial granular cortex, GluD1 and GluD2 were selectively expressed at PSD‐95‐expressing glutamatergic synapses, and their coexpression on the same synapses was shown by SDS‐digested freeze‐fracture replica labeling. Biochemically, GluD1 and GluD2 formed coimmunoprecipitable complex formation in HEK293T cells and in the cerebral cortex and hippocampus. We further estimated the relative protein amount by quantitative immunoblotting using GluA2/GluD2 and GluA2/GluD1 chimeric proteins as standards for titration of GluD1 and GluD2 antibodies. Intriguingly, the relative amount of GluD2 was almost comparable to that of GluD1 in the postsynaptic density fraction prepared from the cerebral cortex and hippocampus. In contrast, GluD2 was overwhelmingly predominant in the cerebellum. Thus, we have determined the relative extracerebellar expression of GluD1 and GluD2 at regional, neuronal, and synaptic levels. These data provide a molecular–anatomical basis for possible competitive and cooperative interactions of GluD family members at synapses in various brain regions.}, author = {Nakamoto, Chihiro and Konno, Kohtarou and Miyazaki, Taisuke and Nakatsukasa, Ena and Natsume, Rie and Abe, Manabu and Kawamura, Meiko and Fukazawa, Yugo and Shigemoto, Ryuichi and Yamasaki, Miwako and Sakimura, Kenji and Watanabe, Masahiko}, issn = {1096-9861}, journal = {Journal of Comparative Neurology}, number = {6}, pages = {1003--1027}, publisher = {Wiley}, title = {{Expression mapping, quantification, and complex formation of GluD1 and GluD2 glutamate receptors in adult mouse brain}}, doi = {10.1002/cne.24792}, volume = {528}, year = {2020}, } @article{7033, abstract = {Removal of the Bax gene from mice completely protects the somas of retinal ganglion cells (RGCs) from apoptosis following optic nerve injury. This makes BAX a promising therapeutic target to prevent neurodegeneration. In this study, Bax+/− mice were used to test the hypothesis that lowering the quantity of BAX in RGCs would delay apoptosis following optic nerve injury. RGCs were damaged by performing optic nerve crush (ONC) and then immunostaining for phospho-cJUN, and quantitative PCR were used to monitor the status of the BAX activation mechanism in the months following injury. The apoptotic susceptibility of injured cells was directly tested by virally introducing GFP-BAX into Bax−/− RGCs after injury. The competency of quiescent RGCs to reactivate their BAX activation mechanism was tested by intravitreal injection of the JNK pathway agonist, anisomycin. Twenty-four weeks after ONC, Bax+/− mice had significantly less cell loss in their RGC layer than Bax+/+ mice 3 weeks after ONC. Bax+/− and Bax+/+ RGCs exhibited similar patterns of nuclear phospho-cJUN accumulation immediately after ONC, which persisted in Bax+/− RGCs for up to 7 weeks before abating. The transcriptional activation of BAX-activating genes was similar in Bax+/− and Bax+/+ RGCs following ONC. Intriguingly, cells deactivated their BAX activation mechanism between 7 and 12 weeks after crush. Introduction of GFP-BAX into Bax−/− cells at 4 weeks after ONC showed that these cells had a nearly normal capacity to activate this protein, but this capacity was lost 8 weeks after crush. Collectively, these data suggest that 8–12 weeks after crush, damaged cells no longer displayed increased susceptibility to BAX activation relative to their naïve counterparts. In this same timeframe, retinal glial activation and the signaling of the pro-apoptotic JNK pathway also abated. Quiescent RGCs did not show a timely reactivation of their JNK pathway following intravitreal injection with anisomycin. These findings demonstrate that lowering the quantity of BAX in RGCs is neuroprotective after acute injury. Damaged RGCs enter a quiescent state months after injury and are no longer responsive to an apoptotic stimulus. Quiescent RGCs will require rejuvenation to reacquire functionality.}, author = {Donahue, RJ and Maes, Margaret E and Grosser, JA and Nickells, RW}, issn = {1559-1182}, journal = {Molecular Neurobiology}, number = {2}, pages = {1070–1084}, publisher = {Springer Nature}, title = {{BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage}}, doi = {10.1007/s12035-019-01783-7}, volume = {57}, year = {2020}, } @article{6997, author = {Zhang, Yuzhou and Friml, Jiří}, issn = {1469-8137}, journal = {New Phytologist}, number = {3}, pages = {1049--1052}, publisher = {Wiley}, title = {{Auxin guides roots to avoid obstacles during gravitropic growth}}, doi = {10.1111/nph.16203}, volume = {225}, year = {2020}, } @article{7149, abstract = {In recent years, many genes have been associated with chromatinopathies classified as “Cornelia de Lange Syndrome‐like.” It is known that the phenotype of these patients becomes less recognizable, overlapping to features characteristic of other syndromes caused by genetic variants affecting different regulators of chromatin structure and function. Therefore, Cornelia de Lange syndrome diagnosis might be arduous due to the seldom discordance between unexpected molecular diagnosis and clinical evaluation. Here, we review the molecular features of Cornelia de Lange syndrome, supporting the hypothesis that “CdLS‐like syndromes” are part of a larger “rare disease family” sharing multiple clinical features and common disrupted molecular pathways.}, author = {Avagliano, Laura and Parenti, Ilaria and Grazioli, Paolo and Di Fede, Elisabetta and Parodi, Chiara and Mariani, Milena and Kaiser, Frank J. and Selicorni, Angelo and Gervasini, Cristina and Massa, Valentina}, issn = {1399-0004}, journal = {Clinical Genetics}, number = {1}, pages = {3--11}, publisher = {Wiley}, title = {{Chromatinopathies: A focus on Cornelia de Lange syndrome}}, doi = {10.1111/cge.13674}, volume = {97}, year = {2020}, } @article{7004, abstract = {We define an action of the (double of) Cohomological Hall algebra of Kontsevich and Soibelman on the cohomology of the moduli space of spiked instantons of Nekrasov. We identify this action with the one of the affine Yangian of gl(1). Based on that we derive the vertex algebra at the corner Wr1,r2,r3 of Gaiotto and Rapčák. We conjecture that our approach works for a big class of Calabi–Yau categories, including those associated with toric Calabi–Yau 3-folds.}, author = {Rapcak, Miroslav and Soibelman, Yan and Yang, Yaping and Zhao, Gufang}, issn = {1432-0916}, journal = {Communications in Mathematical Physics}, pages = {1803--1873}, publisher = {Springer Nature}, title = {{Cohomological Hall algebras, vertex algebras and instantons}}, doi = {10.1007/s00220-019-03575-5}, volume = {376}, year = {2020}, } @article{7204, abstract = {Plant root architecture dynamically adapts to various environmental conditions, such as salt‐containing soil. The phytohormone abscisic acid (ABA) is involved among others also in these developmental adaptations, but the underlying molecular mechanism remains elusive. Here, a novel branch of the ABA signaling pathway in Arabidopsis involving PYR/PYL/RCAR (abbreviated as PYLs) receptor‐protein phosphatase 2A (PP2A) complex that acts in parallel to the canonical PYLs‐protein phosphatase 2C (PP2C) mechanism is identified. The PYLs‐PP2A signaling modulates root gravitropism and lateral root formation through regulating phytohormone auxin transport. In optimal conditions, PYLs ABA receptor interacts with the catalytic subunits of PP2A, increasing their phosphatase activity and thus counteracting PINOID (PID) kinase‐mediated phosphorylation of PIN‐FORMED (PIN) auxin transporters. By contrast, in salt and osmotic stress conditions, ABA binds to PYLs, inhibiting the PP2A activity, which leads to increased PIN phosphorylation and consequently modulated directional auxin transport leading to adapted root architecture. This work reveals an adaptive mechanism that may flexibly adjust plant root growth to withstand saline and osmotic stresses. It occurs via the cross‐talk between the stress hormone ABA and the versatile developmental regulator auxin.}, author = {Li, Yang and Wang, Yaping and Tan, Shutang and Li, Zhen and Yuan, Zhi and Glanc, Matous and Domjan, David and Wang, Kai and Xuan, Wei and Guo, Yan and Gong, Zhizhong and Friml, Jiří and Zhang, Jing}, issn = {2198-3844}, journal = {Advanced Science}, number = {3}, publisher = {Wiley}, title = {{Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex}}, doi = {10.1002/advs.201901455}, volume = {7}, year = {2020}, } @article{7220, abstract = {BACKGROUND:The introduction of image-guided methods to bypass surgery has resulted in optimized preoperative identification of the recipients and excellent patency rates. However, the recently presented methods have also been resource-consuming. In the present study, we have reported a cost-efficient planning workflow for extracranial-intracranial (EC-IC) revascularization combined with transdural indocyanine green videoangiography (tICG-VA). METHODS:We performed a retrospective review at a single tertiary referral center from 2011 to 2018. A novel software-derived workflow was applied for 25 of 92 bypass procedures during the study period. The precision and accuracy were assessed using tICG-VA identification of the cortical recipients and a comparison of the virtual and actual data. The data from a control group of 25 traditionally planned procedures were also matched. RESULTS:The intraoperative transfer time of the calculated coordinates averaged 0.8 minute (range, 0.4-1.9 minutes). The definitive recipients matched the targeted branches in 80%, and a neighboring branch was used in 16%. Our workflow led to a significant craniotomy size reduction in the study group compared with that in the control group (P = 0.005). tICG-VA was successfully applied in 19 cases. An average of 2 potential recipient arteries were identified transdurally, resulting in tailored durotomy and 3 craniotomy adjustments. Follow-up patency results were available for 49 bypass surgeries, comprising 54 grafts. The overall patency rate was 91% at a median follow-up period of 26 months. No significant difference was found in the patency rate between the study and control groups (P = 0.317). CONCLUSIONS:Our clinical results have validated the presented planning and surgical workflow and support the routine implementation of tICG-VA for recipient identification before durotomy.}, author = {Dodier, Philippe and Auzinger, Thomas and Mistelbauer, Gabriel and Wang, Wei Te and Ferraz-Leite, Heber and Gruber, Andreas and Marik, Wolfgang and Winter, Fabian and Fischer, Gerrit and Frischer, Josa M. and Bavinzski, Gerhard}, issn = {1878-8769}, journal = {World Neurosurgery}, number = {2}, pages = {e892--e902}, publisher = {Elsevier}, title = {{Novel software-derived workflow in extracranial–intracranial bypass surgery validated by transdural indocyanine green videoangiography}}, doi = {10.1016/j.wneu.2019.11.038}, volume = {134}, year = {2020}, } @article{7142, abstract = {The phytohormone auxin acts as an amazingly versatile coordinator of plant growth and development. With its morphogen-like properties, auxin controls sites and timing of differentiation and/or growth responses both, in quantitative and qualitative terms. Specificity in the auxin response depends largely on distinct modes of signal transmission, by which individual cells perceive and convert auxin signals into a remarkable diversity of responses. The best understood, or so-called canonical mechanism of auxin perception ultimately results in variable adjustments of the cellular transcriptome, via a short, nuclear signal transduction pathway. Additional findings that accumulated over decades implied that an additional, presumably, cell surface-based auxin perception mechanism mediates very rapid cellular responses and decisively contributes to the cell's overall hormonal response. Recent investigations into both, nuclear and cell surface auxin signalling challenged this assumed partition of roles for different auxin signalling pathways and revealed an unexpected complexity in transcriptional and non-transcriptional cellular responses mediated by auxin.}, author = {Gallei, Michelle C and Luschnig, Christian and Friml, Jiří}, issn = {1879-0356}, journal = {Current Opinion in Plant Biology}, number = {2}, pages = {43--49}, publisher = {Elsevier}, title = {{Auxin signalling in growth: Schrödinger's cat out of the bag}}, doi = {10.1016/j.pbi.2019.10.003}, volume = {53}, year = {2020}, } @article{7166, abstract = {In the living cell, we encounter a large variety of motile processes such as organelle transport and cytoskeleton remodeling. These processes are driven by motor proteins that generate force by transducing chemical free energy into mechanical work. In many cases, the molecular motors work in teams to collectively generate larger forces. Recent optical trapping experiments on small teams of cytoskeletal motors indicated that the collectively generated force increases with the size of the motor team but that this increase depends on the motor type and on whether the motors are studied in vitro or in vivo. Here, we use the theory of stochastic processes to describe the motion of N motors in a stationary optical trap and to compute the N-dependence of the collectively generated forces. We consider six distinct motor types, two kinesins, two dyneins, and two myosins. We show that the force increases always linearly with N but with a prefactor that depends on the performance of the single motor. Surprisingly, this prefactor increases for weaker motors with a lower stall force. This counter-intuitive behavior reflects the increased probability with which stronger motors detach from the filament during strain generation. Our theoretical results are in quantitative agreement with experimental data on small teams of kinesin-1 motors.}, author = {Ucar, Mehmet C and Lipowsky, Reinhard}, issn = {1530-6992}, journal = {Nano Letters}, number = {1}, pages = {669--676}, publisher = {American Chemical Society}, title = {{Collective force generation by molecular motors is determined by strain-induced unbinding}}, doi = {10.1021/acs.nanolett.9b04445}, volume = {20}, year = {2020}, } @misc{9885, abstract = {Data obtained from the fine-grained simulations used in Figures 2-5, data obtained from the coarse-grained numerical calculations used in Figure 6, and a sample script for the fine-grained simulation as a Jupyter notebook (ZIP)}, author = {Ucar, Mehmet C and Lipowsky, Reinhard}, publisher = {American Chemical Society }, title = {{MURL_Dataz}}, doi = {10.1021/acs.nanolett.9b04445.s002}, year = {2020}, } @article{7218, abstract = {The combined resection of skull-infiltrating tumours and immediate cranioplastic reconstruction predominantly relies on freehand-moulded solutions. Techniques that enable this procedure to be performed easily in routine clinical practice would be useful. A cadaveric study was developed in which a new software tool was used to perform single-stage reconstructions with prefabricated implants after the resection of skull-infiltrating pathologies. A novel 3D visualization and interaction framework was developed to create 10 virtual craniotomies in five cadaveric specimens. Polyether ether ketone (PEEK) implants were manufactured according to the bone defects. The image-guided craniotomy was reconstructed with PEEK and compared to polymethyl methacrylate (PMMA). Navigational accuracy and surgical precision were assessed. The PEEK workflow resulted in up to 10-fold shorter reconstruction times than the standard technique. Surgical precision was reflected by the mean 1.1 ± 0.29 mm distance between the virtual and real craniotomy, with submillimetre precision in 50%. Assessment of the global offset between virtual and actual craniotomy revealed an average shift of 4.5 ± 3.6 mm. The results validated the ‘elective single-stage cranioplasty’ technique as a state-of-the-art virtual planning method and surgical workflow. This patient-tailored workflow could significantly reduce surgical times compared to the traditional, intraoperative acrylic moulding method and may be an option for the reconstruction of bone defects in the craniofacial region.}, author = {Dodier, Philippe and Winter, Fabian and Auzinger, Thomas and Mistelbauer, Gabriel and Frischer, Josa M. and Wang, Wei Te and Mallouhi, Ammar and Marik, Wolfgang and Wolfsberger, Stefan and Reissig, Lukas and Hammadi, Firas and Matula, Christian and Baumann, Arnulf and Bavinzski, Gerhard}, issn = {1399-0020}, journal = {International Journal of Oral and Maxillofacial Surgery}, number = {8}, pages = {P1007--1015}, publisher = {Elsevier}, title = {{Single-stage bone resection and cranioplastic reconstruction: Comparison of a novel software-derived PEEK workflow with the standard reconstructive method}}, doi = {10.1016/j.ijom.2019.11.011}, volume = {49}, year = {2020}, } @article{7219, abstract = {Root system architecture (RSA), governed by the phytohormone auxin, endows plants with an adaptive advantage in particular environments. Using geographically representative arabidopsis (Arabidopsis thaliana) accessions as a resource for GWA mapping, Waidmann et al. and Ogura et al. recently identified two novel components involved in modulating auxin-mediated RSA and conferring plant fitness in particular habitats.}, author = {Xiao, Guanghui and Zhang, Yuzhou}, issn = {13601385}, journal = {Trends in Plant Science}, number = {2}, pages = {P121--123}, publisher = {Elsevier}, title = {{Adaptive growth: Shaping auxin-mediated root system architecture}}, doi = {10.1016/j.tplants.2019.12.001}, volume = {25}, year = {2020}, } @article{7234, abstract = {T lymphocytes utilize amoeboid migration to navigate effectively within complex microenvironments. The precise rearrangement of the actin cytoskeleton required for cellular forward propulsion is mediated by actin regulators, including the actin‐related protein 2/3 (Arp2/3) complex, a macromolecular machine that nucleates branched actin filaments at the leading edge. The consequences of modulating Arp2/3 activity on the biophysical properties of the actomyosin cortex and downstream T cell function are incompletely understood. We report that even a moderate decrease of Arp3 levels in T cells profoundly affects actin cortex integrity. Reduction in total F‐actin content leads to reduced cortical tension and disrupted lamellipodia formation. Instead, in Arp3‐knockdown cells, the motility mode is dominated by blebbing migration characterized by transient, balloon‐like protrusions at the leading edge. Although this migration mode seems to be compatible with interstitial migration in three‐dimensional environments, diminished locomotion kinetics and impaired cytotoxicity interfere with optimal T cell function. These findings define the importance of finely tuned, Arp2/3‐dependent mechanophysical membrane integrity in cytotoxic effector T lymphocyte activities.}, author = {Obeidy, Peyman and Ju, Lining A. and Oehlers, Stefan H. and Zulkhernain, Nursafwana S. and Lee, Quintin and Galeano Niño, Jorge L. and Kwan, Rain Y.Q. and Tikoo, Shweta and Cavanagh, Lois L. and Mrass, Paulus and Cook, Adam J.L. and Jackson, Shaun P. and Biro, Maté and Roediger, Ben and Sixt, Michael K and Weninger, Wolfgang}, issn = {14401711}, journal = {Immunology and Cell Biology}, number = {2}, pages = {93--113}, publisher = {Wiley}, title = {{Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes}}, doi = {10.1111/imcb.12304}, volume = {98}, year = {2020}, } @article{7253, abstract = {The cyclin-dependent kinase inhibitor p57KIP2 is encoded by the imprinted Cdkn1c locus, exhibits maternal expression, and is essential for cerebral cortex development. How Cdkn1c regulates corticogenesis is however not clear. To this end we employ Mosaic Analysis with Double Markers (MADM) technology to genetically dissect Cdkn1c gene function in corticogenesis at single cell resolution. We find that the previously described growth-inhibitory Cdkn1c function is a non-cell-autonomous one, acting on the whole organism. In contrast we reveal a growth-promoting cell-autonomous Cdkn1c function which at the mechanistic level mediates radial glial progenitor cell and nascent projection neuron survival. Strikingly, the growth-promoting function of Cdkn1c is highly dosage sensitive but not subject to genomic imprinting. Collectively, our results suggest that the Cdkn1c locus regulates cortical development through distinct cell-autonomous and non-cell-autonomous mechanisms. More generally, our study highlights the importance to probe the relative contributions of cell intrinsic gene function and tissue-wide mechanisms to the overall phenotype.}, author = {Laukoter, Susanne and Beattie, Robert J and Pauler, Florian and Amberg, Nicole and Nakayama, Keiichi I. and Hippenmeyer, Simon}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development}}, doi = {10.1038/s41467-019-14077-2}, volume = {11}, year = {2020}, } @article{7339, abstract = {Cytoskeletal filaments such as microtubules (MTs) and filamentous actin (F-actin) dynamically support cell structure and functions. In central presynaptic terminals, F-actin is expressed along the release edge and reportedly plays diverse functional roles, but whether axonal MTs extend deep into terminals and play any physiological role remains controversial. At the calyx of Held in rats of either sex, confocal and high-resolution microscopy revealed that MTs enter deep into presynaptic terminal swellings and partially colocalize with a subset of synaptic vesicles (SVs). Electrophysiological analysis demonstrated that depolymerization of MTs specifically prolonged the slow-recovery time component of EPSCs from short-term depression induced by a train of high-frequency stimulation, whereas depolymerization of F-actin specifically prolonged the fast-recovery component. In simultaneous presynaptic and postsynaptic action potential recordings, depolymerization of MTs or F-actin significantly impaired the fidelity of high-frequency neurotransmission. We conclude that MTs and F-actin differentially contribute to slow and fast SV replenishment, thereby maintaining high-frequency neurotransmission.}, author = {Piriya Ananda Babu, Lashmi and Wang, Han Ying and Eguchi, Kohgaku and Guillaud, Laurent and Takahashi, Tomoyuki}, issn = {15292401}, journal = {Journal of neuroscience}, number = {1}, pages = {131--142}, publisher = {Society for Neuroscience}, title = {{Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission}}, doi = {10.1523/JNEUROSCI.1571-19.2019}, volume = {40}, year = {2020}, } @article{7350, abstract = {The ability to sense environmental temperature and to coordinate growth and development accordingly, is critical to the reproductive success of plants. Flowering time is regulated at the level of gene expression by a complex network of factors that integrate environmental and developmental cues. One of the main players, involved in modulating flowering time in response to changes in ambient temperature is FLOWERING LOCUS M (FLM). FLM transcripts can undergo extensive alternative splicing producing multiple variants, of which FLM-β and FLM-δ are the most representative. While FLM-β codes for the flowering repressor FLM protein, translation of FLM-δ has the opposite effect on flowering. Here we show that the cyclin-dependent kinase G2 (CDKG2), together with its cognate cyclin, CYCLYN L1 (CYCL1) affects the alternative splicing of FLM, balancing the levels of FLM-β and FLM-δ across the ambient temperature range. In the absence of the CDKG2/CYCL1 complex, FLM-β expression is reduced while FLM-δ is increased in a temperature dependent manner and these changes are associated with an early flowering phenotype in the cdkg2 mutant lines. In addition, we found that transcript variants retaining the full FLM intron 1 are sequestered in the cell nucleus. Strikingly, FLM intron 1 splicing is also regulated by CDKG2/CYCL1. Our results provide evidence that temperature and CDKs regulate the alternative splicing of FLM, contributing to flowering time definition.}, author = {Nibau, Candida and Gallemi, Marçal and Dadarou, Despoina and Doonan, John H. and Cavallari, Nicola}, issn = {1664-462X}, journal = {Frontiers in Plant Science}, publisher = {Frontiers Media}, title = {{Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2}}, doi = {10.3389/fpls.2019.01680}, volume = {10}, year = {2020}, } @article{7369, abstract = {Neuronal responses to complex stimuli and tasks can encompass a wide range of time scales. Understanding these responses requires measures that characterize how the information on these response patterns are represented across multiple temporal resolutions. In this paper we propose a metric – which we call multiscale relevance (MSR) – to capture the dynamical variability of the activity of single neurons across different time scales. The MSR is a non-parametric, fully featureless indicator in that it uses only the time stamps of the firing activity without resorting to any a priori covariate or invoking any specific structure in the tuning curve for neural activity. When applied to neural data from the mEC and from the ADn and PoS regions of freely-behaving rodents, we found that neurons having low MSR tend to have low mutual information and low firing sparsity across the correlates that are believed to be encoded by the region of the brain where the recordings were made. In addition, neurons with high MSR contain significant information on spatial navigation and allow to decode spatial position or head direction as efficiently as those neurons whose firing activity has high mutual information with the covariate to be decoded and significantly better than the set of neurons with high local variations in their interspike intervals. Given these results, we propose that the MSR can be used as a measure to rank and select neurons for their information content without the need to appeal to any a priori covariate.}, author = {Cubero, Ryan J and Marsili, Matteo and Roudi, Yasser}, issn = {1573-6873}, journal = {Journal of Computational Neuroscience}, keywords = {Time series analysis, Multiple time scale analysis, Spike train data, Information theory, Bayesian decoding}, pages = {85--102}, publisher = {Springer Nature}, title = {{Multiscale relevance and informative encoding in neuronal spike trains}}, doi = {10.1007/s10827-020-00740-x}, volume = {48}, year = {2020}, } @article{7364, abstract = {We present nsCouette, a highly scalable software tool to solve the Navier–Stokes equations for incompressible fluid flow between differentially heated and independently rotating, concentric cylinders. It is based on a pseudospectral spatial discretization and dynamic time-stepping. It is implemented in modern Fortran with a hybrid MPI-OpenMP parallelization scheme and thus designed to compute turbulent flows at high Reynolds and Rayleigh numbers. An additional GPU implementation (C-CUDA) for intermediate problem sizes and a version for pipe flow (nsPipe) are also provided.}, author = {Lopez Alonso, Jose M and Feldmann, Daniel and Rampp, Markus and Vela-Martín, Alberto and Shi, Liang and Avila, Marc}, issn = {23527110}, journal = {SoftwareX}, publisher = {Elsevier}, title = {{nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow}}, doi = {10.1016/j.softx.2019.100395}, volume = {11}, year = {2020}, } @article{7431, abstract = {In many real-world systems, information can be transmitted in two qualitatively different ways: by copying or by transformation. Copying occurs when messages are transmitted without modification, e.g. when an offspring receives an unaltered copy of a gene from its parent. Transformation occurs when messages are modified systematically during transmission, e.g. when mutational biases occur during genetic replication. Standard information-theoretic measures do not distinguish these two modes of information transfer, although they may reflect different mechanisms and have different functional consequences. Starting from a few simple axioms, we derive a decomposition of mutual information into the information transmitted by copying versus the information transmitted by transformation. We begin with a decomposition that applies when the source and destination of the channel have the same set of messages and a notion of message identity exists. We then generalize our decomposition to other kinds of channels, which can involve different source and destination sets and broader notions of similarity. In addition, we show that copy information can be interpreted as the minimal work needed by a physical copying process, which is relevant for understanding the physics of replication. We use the proposed decomposition to explore a model of amino acid substitution rates. Our results apply to any system in which the fidelity of copying, rather than simple predictability, is of critical relevance.}, author = {Kolchinsky, Artemy and Corominas-Murtra, Bernat}, issn = {17425662}, journal = {Journal of the Royal Society Interface}, number = {162}, publisher = {The Royal Society}, title = {{Decomposing information into copying versus transformation}}, doi = {10.1098/rsif.2019.0623}, volume = {17}, year = {2020}, }