bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overflow of Working Memory from an Easily Accessible Active State
Authors: Ideriha Takuya , Ushiyama Junichi 
Published: November 2022

ABSTRACTWorking memory is a system that realizes short-term memory retention and is essential to everyday activities. Recently, it has been suggested that working memory items can be maintained in both an active state with sustained neural activity and a latent state without any explicit neural activity. However, how easily we can retrieve memories in each state and how much information can be retained in the active state remains unknown. Here, we addressed these questions by adopting a novel experimental paradigm for measuring the reaction time required to recall a letter of the alphabet when presented with a corresponding color, based on memorized color/letter pairs. The results demonstrated that when participants retained only two pairs of items, they could recall both pairs similarly quickly. However, when there were two or more memorized pairs, the most recent or internally attended pairs were recalled more quickly than the other pairs. These results suggest that memories in the “active” state are accessed first and memories that have overflowed into the “latent” state are accessed afterward. Additionally, the capacity of the easily accessible active state is extremely limited (to approximately two chunks of information) compared with the traditionally considered working memory capacity (four to seven chunks). These results provide robust behavioral support for the co-existence of multiple states in working memory and underscore the need for a more detailed classification of the working memory capacity.SIGNIFICANCE STATEMENTWe sometimes cannot quickly retrieve what we are sure we remember. Regarding working memory retrieval, we observed a phenomenon that the most recently encoded memory was retrieved quickly whereas others were retrieved afterward, showing an “overflow” of memory items from an easily accessible active state. This observation has two critical implications: 1) when maintaining multiple items in working memory, not all items are functionally the same, and there is a dissociation between easily accessible active items and items that have overflowed to a latent state; 2) the number of items that can be maintained in the active state is two, which is remarkably smaller than the traditionally considered working memory capacity of four, necessitating the update of working memory models.
Limiting etioplast gene-expression induces apical hook twisting during skoto-morphogenesis ofArabidopsisseedlings
Authors: Sajib Salek Ahmed , Grübler Björn , Oukacine Cylia , Delannoy Etienne , Courtois Florence , Mauve Caroline , Lurin Claire , Gakière Bertrand , Pfannschmidt Thomas , Merendino Livia 
Published: November 2022

AbstractWhen covered by a layer of soil, seedling development follows a dark-specific program (skoto-morphogenesis) consisting of small, non-green cotyledons, a long hypocotyl and an apical hook to protect meristematic cells. We recently highlighted the role played by mitochondria in the high energy-consuming reprogramming ofArabidopsisskoto-morphogenesis. Here, the role played by plastids, another energy supplying organelle, in skoto-morphogenesis is investigated. This study was conducted in dark conditions to exclude light signals so as to better focus on those produced by plastids. It was found that limitation of plastid gene-expression (PGE) induced an exaggerated apical hook bending. Inhibition of PGE was obtained at the level of transcription and translation using the antibiotics rifampicin and spectinomycin, respectively, as well as plastid RPOTP RNA polymerase mutants. Rifampicin-treated seedlings also showed expression induction of marker nuclear genes for mitochondrial stress, perturbation of the mitochondrial metabolism, increase of ROS levels and an augmented capacity of oxygen consumption by mitochondrial alternative oxidases (AOX). AOX enzymes act to prevent over-reduction of the mitochondrial electron transport chain. Previously, we reported that AOX1A, the main AOX isoform, was a key component in the developmental response to mitochondrial respiration deficiency. In this work, we suggest the involvement of AOX1A in the response to PGE dysfunction and propose the importance of signalling between plastids and mitochondria. Finally, it was found that seedling architecture reprogramming in response to rifampicin was independent of canonical organelle retrograde pathways and the ethylene signaling pathway.Significance statementIn underground germination conditions, seedling development follows a dark-specific program (skoto-morphogenesis) consisting of small and non-green cotyledons, a long hypocotyl and an apical hook to protect meristematic cells. We show that skoto-morphogenesis is reprogrammed when plastid gene expression is perturbed leading to an exaggeration of apical hook bending. We propose the involvement of the cooperation between plastids and mitochondria, the energy-supplying organelles of the cell.
A specific mesh-like organization of human septin octameric complex drives membrane reshaping and curvature sensitivity
Authors: Nakazawa Koyomi , Kumar Gaurav , Chauvin Brieuc , Di Cicco Aurélie , Pellegrino Luca , Trichet Michael , Hajj Bassam , Cabral João , Sain Anirban , Mangenot Stéphanie , Bertin Aurélie 
Published: November 2022

AbstractSeptins are cytoskeletal proteins interacting with the inner plasma membrane and other cytoskeletal partners. Being key in membrane remodeling processes, they often localize at specific micrometric curvatures. To analyze the behavior of human septins at the membrane, we have used a combination of methods to assay their ultrastructural organization, their curvature sensitivity as well as their role in membrane reshaping. In contrast to budding yeast septins, on membranes, human septins systematically organize into a two-layered mesh of orthogonal filaments instead of generating parallel sheets of filaments observed for budding yeast septins. This peculiar mesh organization is curvature sensitive and drives membrane reshaping as well. The observed membrane deformations together with the filamentous organization are recapitulated in a coarsegrained computed simulation to understand their mechanisms. Our results highlight the specificity of animal septins as opposed to fungal proteins.
Differentiation is accompanied by a progressive loss in transcriptional memory
Authors: Fourneaux Camille , Racine Laëtitia , Koering Catherine , Dussurgey Sébastien , Vallin Elodie , Moussy Alice , Parmentier Romuald , Brunard Fanny , Stockholm Daniel , Modolo Laurent , Picard Franck , Gandrillon Olivier , Paldi Andras , Gonin-Giraud Sandrine 
Published: November 2022

AbstractCell differentiation requires the integration of two opposite processes, a stabilizing cellular memory, especially at the transcriptional scale, and a burst of gene expression variability which follows the differentiation induction. Therefore, the actual capacity of a cell to undergo phenotypic change during a differentiation process relies upon a modification in this balance which favors change-inducing gene expression variability. However, there are no experimental data providing insight on how fast the transcriptomes of identical cells would diverge on the scale of the very first two cell divisions during the differentiation process.In order to quantitatively address this question, we developed different experimental methods to recover the transcriptomes of related cells, after one and two divisions, while preserving the information about their lineage at the scale of a single cell division. We analyzed the transcriptomes of related cells from two differentiation biological systems (human CD34+ cells and T2EC chicken primary erythrocytic progenitors) using two different single-cell transcriptomics technologies (sc-RT-qPCR and scRNA-seq).We identified that the gene transcription profiles of differentiating sister-cells are more similar to each-other than to those of non related cells of the same type, sharing the same environment and undergoing similar biological processes. More importantly, we observed greater discrepancies between differentiating sister-cells than between self-renewing sister-cells. Furthermore, a continuous increase in this divergence from first generation to second generation was observed when comparing differentiating cousin-cells to self renewing cousin-cells.Our results are in favor of a continuous and gradual erasure of transcriptional memory during the differentiation process.
Characterization of N distribution in different organs of winter wheat using UAV-based remote sensing
Authors: Wang Falv , Li Wei , Liu Yi , Qin Weilong , Ma Longfei , Zhang Yinghua , Sun Zhencai , Wang Zhimin , Li Fei , Yu Kang 
Published: November 2022

AbstractAlthough unmanned aerial vehicle (UAV) remote sensing is widely used for high-throughput crop monitoring, few attempts have been made to assess nitrogen content (NC) at the organ level and its impact on nitrogen use efficiency (NUE). Also, little is known about the performance of UAV-based image texture features in crop nitrogen and NUE monitoring. In this study, eight flying missions were carried out throughout different stages of winter wheat (from the jointing stage to the stage 25 days after flowering) to acquire multispectral images. Forty-three multispectral vegetation indices (VIs) and forty texture features (TFs) were calculated from images and fed into the partial least squares regression (PLSR) and random forest (RF) regression models for predicting nitrogen-related indicators. Our main purposes were to (1) evaluate the potential of UAV-based images to predict NC in different organs of winter wheat and nitrogen agronomic efficiency (NAE); (2) compare the performances of VIs, TFs and the combination of them for nitrogen monitoring. The results showed that the correlation between different features (VIs and TFs) and NC in different organs varied between the vegetative and reproductive phases. Most of VIs were found to be positively correlated with NC, while most of the TFs were negatively correlated with NC. PLSR latent variables extracted from VIs and TFs explained 80% of the variations in NAE. However, no significant differences were found between VIs and TFs in their performance in predicting NC in different organs. This study demonstrated the promise of applying UAV-based imaging to estimate NC and NAE in different organs of winter wheat.
Preservation of thalamocortical circuitry is essential for good recovery in comatose survivors of cardiac arrest
Authors: Tewarie Prejaas K. , Tjepkema-Cloostermans Marleen C. , Abeysuriya Romesh G. , Hofmeijer Jeannette , van Putten Michel J.A.M. 
Published: November 2022

ABSTRACTContinuous EEG monitoring contributes to prediction of neurological outcome in comatose cardiac arrest survivors. While the phenomenology of EEG abnormalities in postanoxic encephalopathy is well-known, the pathophysiology, especially the presumed role of selective synaptic failure is less understood. To further this understanding, we estimate biophysical model parameters from the EEG power spectra from individual patients with a good or poor recovery from a postanoxic encephalopathy. This biophysical model includes intracortical, intrathalamic, and corticothalamic synaptic strengths, as well as synaptic time constants and axonal conduction delays. We used continuous EEG measurements from hundred comatose patients recorded during the first 48 hours post-cardiac arrest, fifty with a poor neurological outcome (Cerebral Performance Category (CPC=5)) and fifty with a good neurological outcome (CPC=1). We only included patients that developed (dis-) continuous EEG activity within 48 hours post-cardiac arrest. For patients with a good outcome, we observed an initial relative excitation in the corticothalamic loop and corticothalamic propagation that subsequently evolved towards values observed in healthy controls. For patients with a poor outcome, we observed an initial increase in the cortical excitation-inhibition ratio, increased relative inhibition in the corticothalamic loop, delayed corticothalamic propagation of neuronal activity, and severely prolonged synaptic time constants, that did not return to physiological values. We conclude that the abnormal EEG evolution in patients with a poor neurological recovery after cardiac arrest may result from persistent and selective synaptic failure that includes corticothalamic circuitry, but also delayed corticothalamic propagation.
Contrasting leaf thickness & saturated water content explain diverse structural/physiological properties of arid species
Authors: Lamont Byron B. , Lamont Heather C. 
Published: November 2022

AbstractAlthough they account for many thousands of the world’s flowering plants, little is known about the physical/chemical properties of leaf succulents. Eight species in the Namib Desert, South Africa were assessed for leaf area (A) and thickness (z), saturated (Q) and dry mass, relative volume of air (Fa), intrinsic water-us efficiency (δ13C), and N, P and (Na+K) contents. As water-storage capacity is a function ofQvandz, this meansQ/A(=Qv•z) is an ideal index of succulence compared with specific-leaf-area and other indices that highlight mass rather than volume. Specific gravities have a different relationship withFaof sclerophyll-mesophylls: rising succulence infers decreasing air content replaced by water rather than dry matter. The trend among succulent species from Argentina/Spain added to our data was characterized byQ/Aexceeding 1 mg water/mm2leaf whose overall slope was ten times that for co-occurring sclerophyll-mesophyll species. (Na+K), N and P concentrations varied on a dry-matter, but not water-volume, basis.Wirelationships were essentially functions of variations inz(transpiration-resistance) and increased metabolic efficiency. We conclude thatzandQvare keys to the special physiological properties of succulent leaves. Including succulents would force many current monotonic relationships to dichotomize.HighlightThe key to understanding leaf succulents is their high volumetric water content and thick leaves. These explain their superior water-use-efficiency and contrasting relationships with other variables compared with temperate species.
Modelling surface color discrimination under different lighting environments using image chromatic statistics and convolutional neural networks
Authors: Ponting Samuel , Morimoto Takuma , Smithson Hannah 
Published: November 2022

AbstractWe modeled discrimination thresholds for object colors under different lighting environments [1]. Firstly we built models based on chromatic statistics, testing 60 models in total. Secondly we trained convolutional neural networks (CNNs), using 160,280 images labeled either by the ground-truth or by human responses. No single chromatic statistics model was sufficient to describe human discrimination thresholds across conditions, while human-response-trained CNNs nearly perfectly predicted human thresholds. Guided by region-of-interest analysis of the network, we modified the chromatic statistics models to use only the lower regions of the objects, which substantially improved performance.
Overconfidence undermines global wildlife abundance trends
Authors: Johnson Thomas Frederick , Beckerman Andrew P , Childs Dylan Z , Griffiths Christopher A , Capdevila Pol , Clements Christopher F , Besson Marc , Gregory Richard D. , Delmas Eva , Thomas Gavin , Evans Karl , Webb Tom , Freckleton Rob 
Published: November 2022

AbstractIn the face of rapid global change and an uncertain fate for biodiversity, it is vital to quantify trends in wild populations. These trends are typically estimated from abundance time series for suites of species across large geographic and temporal scales. Such data implicitly contain phylogenetic, spatial, and temporal structure which, if not properly accounted for, may obscure the true magnitude and direction of biodiversity change. Here, using a novel statistical framework to simultaneously account for all three of these structures, we show that the majority of current abundance trends estimates among 10 high-profile datasets, representing millions of abundance observations, are likely unreliable or incorrect. Our new approach suggests that previous models are too simplistic, incorrectly estimating global abundance trends and often dramatically underestimating uncertainty, an aspect that is critical when translating global assessments into policy outcomes. Further, our approach also results in substantial improvements in abundance forecasting accuracy. Whilst our results do not improve the outlook for biodiversity, our framework does allow us to make more robust estimates of global wildlife abundance trends, which is critical for developing policy to protect our biosphere.
Gene model correction for PVRIG in single cell and bulk sequencing data enables accurate detection and study of its functional relevance
Authors: Nemzer Sergey , Sabath Niv , Wool Assaf , Alteber Zoya , Ando Hirofumi , Nickles-Fader Amanda , Wang Tian-Li , Shih Ie-Ming , Pardoll Drew M. , Ganguly Sudipto , Turpaz Yaron , Levine Zurit , Granit Roy Z. 
Published: November 2022

AbstractSingle cell RNA sequencing (scRNA-seq) has gained increased popularity in recent years and has revolutionized the study of cell populations; however, this technology presents several caveats regarding specific gene expression measurement. Here we examine the expression levels of several immune checkpoint genes, which are currently assessed in clinical studies. We find that unlike in most bulk sequencing studies, PVRIG, a novel immune-modulatory receptor in the DNAM-1 axis, suffers from poor detection in 10x Chromium scRNA-seq and other types of assays that utilize the GENCODE transcriptomic reference (gene model). We show that the default GENCODE gene model, typically used in the analysis of such data, is incorrect in the PVRIG genomic region and demonstrate that fixing the gene model recovers genuine PVRIG expression levels. We explore computational strategies for resolving multi-gene mapped reads, such as those implemented in RSEM and STARsolo and find that they provide a partial solution to the problem. Our study provides means to better interrogate the expression of PVRIG in scRNA-seq and emphasizes the importance of optimizing gene models and alignment algorithms to enable accurate gene expression measurement in scRNA-seq and bulk sequencing. The methodology applied here for PVRIG can be applied to other genes with similar issues.
An inhibitory plasticity mechanism for world structure inference by hippocampal replay
Authors: Liao Zhenrui , Hadjiabadi Darian , Terada Satoshi , Soltesz Ivan , Losonczy Attila 
Published: November 2022

SummaryMemory consolidation assimilates recent experiences into long-term memory. This process requires the replay of learned sequences, though the content of these sequences remains controversial. Recent work has shown that the statistics of replay deviate from those of experience: stimuli which are experientially salient may be either selected or suppressed. We find that this phenomenon can be explained parsimoniously and biologically plausibly by a Hebbian spike time-dependent plasticity rule at inhibitory synapses. Using spiking networks at three levels of abstraction–leaky integrate-and-fire, biophysically detailed, and abstract binary–we show that this rule enables efficient inference of a model of the structure of the world. We present analytical results that these replayed sequences converge to ground truth under a mathematical model of replay. Finally, we make specific predictions about the consequences of intact and perturbed inhibitory dynamics for network dynamics and cognition. Our work outlines a potential direct link between the synaptic and cognitive levels of memory consolidation, with implications for both normal learning and neurological disease.
Mechanisms of vascular maturation and maintenance captured by longitudinal imaging of live mouse skin
Authors: Kam Chen Yuan , Singh Ishani D. , Matte-Martone Catherine , Gonzalez David G. , Solá Paloma , Solanas Guiomar , Bonjoch Júlia , Marsh Edward D. , Hirschi Karen K. , Greco Valentina 
Published: November 2022

ABSTRACTA functional network of blood vessels is essential for organ growth and homeostasis. Yet, how the vasculature matures and maintains adult homeostasis remains elusive in live mice. By longitudinally tracking the same neonatal endothelial cells (ECs) over days to weeks, we found that capillary plexus expansion is driven by network-wide vessel regression and transient angiogenesis. A fixed number of neonatal ECs rearrange their positions to evenly distribute throughout the developing plexus and become positionally stable in adulthood. Upon injury, while neonatal ECs are predisposed to die, adult ECs survive through a plasmalemmal self-repair response. Furthermore, adult neighboring ECs reactivate migration to assist vessel repair. Lastly, neonatal vessel regression and adult vascular maintenance are orchestrated by temporally restricted VEGFR2 dependent signaling. Our work sheds light on fundamental cellular mechanisms that underlie both vascular maturation and adult homeostasisin vivo.
transmorph: a unifying computational framework for single-cell data integration
Authors: Fouché Aziz , Chadoutaud Loïc , Delattre Olivier , Zinovyev Andrei 
Published: November 2022

AbstractData integration of single-cell data describes the task of embedding datasets obtained from different sources into a common space, so that cells with similar cell type or state end up close from one another in this representation independently from their dataset of origin. Data integration is a crucial early step in most data analysis pipelines involving multiple batches and allows informative data visualization, batch effect reduction, high resolution clustering, accurate label transfer and cell type inference. Many tools have been proposed over the last decade to tackle data integration, and some of them are routinely used today within data analysis workflows. Despite constant endeavors to conduct exhaustive benchmarking studies, a recent surge in the number of these methods has made it difficult to choose one objectively for a given use case. Furthermore, these tools are generally provided as rigid pieces of software allowing little to no user agency on their internal parameters and algorithms, which makes it hard to adapt them to a variety of use cases. In an attempt to address both of these issues at once we introducetransmorph, an ambitious unifying framework for data integration. It allows building complex data integration pipelines by combining existing and original algorithmic modules, and is supported by a rich software ecosystem to easily benchmark modules, analyze and report results. We demonstratetransmorphcapabilities and the value of its expressiveness by solving a variety of practical single-cell applications including supervised and unsupervised joint datasets embedding, RNA-seq integration in gene space and label transfer of cell cycle phase within cell cycle genes space. We providetransmorphas a free, open source and computationally efficient python library, with a particular effort to make it compatible with the other state-of-the-art tools and workflows.