bluuebunny/crossref_metadata_2025_split huggingface dataset:
Supramodal representation of the sense of body ownership in the human parieto-premotor and extrastriate cortices
Authors: Sonobe Yusuke , Yamagata Toyoki , Yang Huixiang , Haruki Yusuke , Ogawa Kenji 
Published: August 2022

AbstractThe sense of body ownership, defined as the sensation that one’s body belongs to oneself, is a fundamental component of bodily self-consciousness. Several studies have shown the importance of multisensory integration for the emergence of the sense of body ownership, together with the involvement of the parieto-premotor and extrastriate cortices in bodily awareness. However, whether the sense of body ownership elicited by different sources of signal, especially visuotactile and visuomotor inputs, is represented by common neural patterns remains to be elucidated. We used functional magnetic resonance imaging (fMRI) to investigate the existence of neural correlates of the sense of body ownership independent of the sensory modalities. Participants received tactile stimulation or executed finger movements while given synchronous and asynchronous visual feedback of their hand. We used multi-voxel patterns analysis (MVPA) to decode the synchronous and asynchronous conditions with cross-classification between two modalities: the classifier was first trained in the visuotactile sessions and then tested in the visuomotor sessions and vice versa. Regions of interest-based and searchlight analyses revealed significant above-chance cross-classification accuracies in the bilateral intraparietal sulcus (IPS), the bilateral ventral premotor cortex (PMv), and the left extrastriate body area (EBA). Moreover, we observed a significant positive correlation between the cross-classification accuracy in the left PMv and the difference in subjective ratings of the sense of body ownership between the synchronous and asynchronous conditions. Our findings revealed the neural representations of the sense of body ownership in the IPS, PMv, and EBA that is invariant to the sensory modalities.Significance StatementPrevious studies have shown neural correlates of the sense of body ownership in parieto-premotor and extrastriate cortices. However, whether the sense of body ownership induced by different sensory inputs is represented in common neural patterns remains unelucidated. Using functional magnetic resonance imaging (fMRI) with multi-voxel pattern analysis (MVPA), we investigated neural representations of the sense of body ownership invariant to modalities. Decoding neural patterns for visuotactile and visuomotor modalities revealed successful cross-classification accuracies in intraparietal sulcus (IPS), ventral premotor cortex (PMv), and extrastriate body area (EBA). Furthermore, cross-classification accuracy in PMv was positively correlated with subjective ratings of the sense of body ownership. These findings demonstrate that supramodal representations in parieto-premotor and extrastriate cortices underlie the sense of body ownership.
Exceeding expectations: the genomic basis of nitrogen utilization efficiency and integrated trait plasticity as avenues to improve nutrient stress tolerance in cultivated sunflower (Helianthus annuusL.)
Authors: Temme Andries A. , Kerr Kelly L. , Nolting Kristen M. , Dittmar Emily L. , Masalia Rishi R. , Bucksch Alexander , Burke John M. , Donovan Lisa A. 
Published: August 2022

AbstractMaintaining crop productivity is a challenge as population growth, climate change, and increasing fertilizer costs necessitate expanding crop production to poorer lands whilst reducing inputs. Enhancing crops’ nutrient use efficiency is thus an important goal, but requires a better understanding of related traits and their genetic basis.We investigated variation in low nutrient stress tolerance in a diverse panel of cultivated sunflower genotypes grown under high and low nutrient conditions, assessing relative growth rate (RGR) as performance. We assessed variation in traits related to nitrogen utilization efficiency (NUtE), mass allocation, and leaf elemental content.Across genotypes, nutrient limitation reduced RGR. Moreover, higher vigor (higher control RGR) was associated with a greater absolute decrease under stress. Given this trade-off, we focused on nutrient stress tolerance independent from vigor. This tolerance metric correlated with the change in NUtE, plasticity for a suite of morphological traits, and leaf element content. Genome-wide association analyses revealed regions associated with variation and plasticity in multiple traits, including two key regions with ostensibly additive effects on NUtE change.Our results demonstrate potential avenues for improving sunflower nutrient stress tolerance independent from vigor and highlight specific traits and genomic regions that could play a role in enhancing tolerance.HighlightGenetic associations and trait correlations show that, in cultivated sunflower, selection for increased nitrogen utilization efficiency and plasticity in key traits is a promising avenue for increasing nutrient stress tolerance.
Future climate change-related decreases in food quality may affect juvenile Chinook salmon growth and survival
Authors: Garzke Jessica , Forster Ian , Graham Caroline , Costalago David , Hunt Brian P.V. 
Published: August 2022

AbstractThe global temperature increase due to global change is predicted to be between 3.3 – 5.7°C by 2100 leading to changes at the base of the marine food web in species composition, abundance, and quality at the base of the marine food web leading to flow-on effects of higher trophic levels such as fish and humans. Changes in marine prey availability and nutritional quality can affect juvenile salmon conditions (i.e., growth, condition, and mortality) during the early marine phase. There is limited knowledge of the interplay between prey availability and prey quality and the importance of food quality under food-satiated conditions. Here, a three-phase feeding experiment measured the effects of nutritional quality (fatty acid composition and ratios) on juvenile Chinook salmon (Oncorhynchus tshawytscha) condition. Experimental diets represented the present three different climate scenarios with a present-day diet (Euphausia pacifica), a control diet (commercial aquaculture diet), and a predicted IPCC worst-case scenario diet with low essential fatty acid concentrations (IPCC SSP5-8.5). We tested how potential future low quality food affects growth rates, body condition, fatty acid composition and mortality rates in juvenile Chinook salmon compared to present-quality prey. Fatty acids were incorporated into the salmon muscle at varying rates but, on average, reflected dietary concentrations. High dietary concentrations of DHA, EPA and high DHA:EPA ratios resulted in increased fish growth and condition. In contrast, low concentrations of DHA and EPA and low DHA:EPA ratios in the diets were not compensated for by increased food quantity. This result highlights the importance of considering food quality when assessing fish response to changing ocean conditions.HighlightsClimate change may decrease the quality of salmon prey through changes in the fatty acid composition.Low dietary essential fatty acid levels reduce growth and condition and increase mortality rates in juvenile Chinook salmon.Food quality changes within zooplankton species but also by changes between species.Results suggest potential cascading effects on higher trophic levels when zooplankton species composition shifts to lower quality species.Higher food intake cannot compensate for low food quality.
Analysis of the Hamiltonian Monte Carlo genotyping algorithm on PROVEDIt mixtures including a novel precision benchmark
Authors: Susik Mateusz , Sbalzarini Ivo F. 
Published: August 2022

AbstractWe provide an internal validation study of a recently published precise DNA mixture algorithm based on Hamiltonian Monte Carlo sampling [1]. We provide results for all 428 mixtures analysed by Riman et al. [2] and compare the results with two state-of-the-art software products: STRmix™ v2.6 and Euroformix v3.4.0. The comparison shows that the Hamiltonian Monte Carlo method provides reliable values of likelihood ratios (LRs) close to the other methods. We further propose a novel large-scale precision benchmark and quantify the precision of the Hamiltonian Monte Carlo method, indicating its improvements over existing solutions. Finally, we analyse the influence of the factors discussed by Buckleton et al. [3].
Depolarization of astrocytes in the basolateral amygdala restores WFS1 neuronal activity and rescues impaired risk-avoidance behavior in DISC1TM mice
Authors: Zhou Xinyi , Xiao Qian , Chen Shuai , Xu Xirong , Hong Yuchuan , Chen Yuewen , Wang Liping , Chen Yu , Yang Fan , Tu Jie 
Published: August 2022

SummaryMany mental illnesses are accompanied by abnormal risk-avoidance behavior, yet we have only a limited understanding of the neuronal regulatory mechanisms involved. We previously established an inducible DISC1-N terminal fragment transgenic mouse (DISC1-NTM) model which has exhibited risk-avoidance deficiency. Using this model, we analyzed differentially expressed genes (DEGs) using snRNA-seq and the results indicate impaired neuron-astrocyte interactions. We used optogenetic tools to modulate astrocytes in the basolateral amygdala (BLA) and found that ChR2-expressing astrocytes were able to rescue risk-avoidance impairment in DISC1-NTM mice. Using patch clamp recordings combined with signal-cell qPCR, we found impaired excitability of BLAWFS1 neurons in DISC1-NTM mice and that ChR2-expressing astrocytes can induce action potentials (APs) in WFS1 neurons, which restores WFS1 neuronal activity. WFS1 neurons are necessary for BLA astrocytes to modulate impaired risk-avoidance behavior. These finding provide new insights into mechanisms of astrocyte-neuron interactions and suggest that BLA astrocytes may be a promising target for impaired risk avoidance in mental illness.HighlightsChR2-expressing astrocytes in the BLA rescue impaired risk-avoidance behavior in DISC1-NTM mice.Astrocytes in the BLA modulate different nearby neurons to different degrees. Depolarization of BLA astrocytes restore neuronal activity in WFS1 neurons. Astrocytes in the BLA modulate WFS1 neurons via NMDARs.
Characterising Long Covid: a living systematic review update with controlled studies
Authors: Michelen Melina , Sigfrid Louise , Kartsonaki Christiana , Shemilt Ian , Hastie Claire , O’Hara Margaret E. , Suett Jake C. , Stelson Elisabeth A. , Bugaeva Polina , Dahmash Dania T. , Rigby Ishmeala , Munblit Daniel , Harriss Eli , Burls Amanda , Cheng Vincent , Scott Janet T. , Carson Gail , Olliaro Piero , Stavropoulou Charitini 
Published: August 2022

StatementThe authors have withdrawn their manuscript owing to a reporting error that we have identified in the conduct of this updated systematic review. On 7thMarch 2022 we made changes to the original protocol published in F1000, to highlight the need to keep up with the evolving landscape of Covid-19 and Covid-19 research and focus on comparative, controlled studies. The revisions included also changes in data extraction and analysis that would be needed to do so. These changes were done in consultation with members of the Long COVID Support Group. However, we omitted to publicize these changes in an accessible, modified version of our protocol, and/or by updating our preregistered PROSPERO record (CRD42020211131) and F1000 publication, prior to commencing and completing these stages of the process. In this manuscript, which reports the revised analyses, we have consequently also omitted to explicitly describe these changes as important deviations from the published protocol. Additionally, following rapid, sustained, and continuous growth in the conduct and reporting of eligible primary studies, it has become clear that, with or without the changes described above, we do not have sufficient capacity or resources to transition our baseline systematic review to being regularly updated using a living systematic review approach. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Not4-dependent targeting ofMMF1mRNA to mitochondria limits its expression via ribosome pausing, Egd1 ubiquitination, Caf130, No-Go-Decay and autophagy
Authors: Chen Siyu , Allen George , Panasenko Olesya O. , Collart Martine A. 
Published: August 2022

AbstractThe Ccr4-Not complex is a conserved multi protein complex with diverse roles in the mRNA life cycle. Recently we determined that the Not1 and Not4 subunits of Ccr4-Not inversely regulate mRNA solubility and thereby impact dynamics of co-translation events. One mRNA whose solubility is limited by Not4 isMMF1encoding a mitochondrial matrix protein. In this work we determine that Not4 promotes the co-translational docking ofMMF1mRNA to mitochondria via the mitochondrial targeting sequence of the Mmf1 nascent chain, the Egd1 chaperone, the Om14 mitochondrial outer membrane protein and the co-translational import machinery. We observe thatMMF1mRNA is translated with ribosome pausing and uncover a mechanism that depends upon its targeting to the mitochondria and limits its overexpression. We have named this mechanism Mito-ENCay. It relies onEgd1 ubiquitination byNot4, theCaf130 subunit of the Ccr4-Not complex, the mitochondrial outer membrane proteinCis1, No-Go-Decayas well as autophagy. We propose that in fermenting yeast, mRNAs whose encoded proteins depend upon co-translational folding and/or assembly are regulated by Caf130-dependent quality control mechanisms similar to Mito-ENCay.
Alignment, Segmentation and Neighborhood Analysis in Cyclic Immunohistochemistry Data Using CASSATT
Authors: Brockman Asa A. , Khurana Rohit , Bartkowiak Todd , Thomas Portia L. , Sivagnanam Shamilene , Betts Courtney B , Coussens Lisa M. , Lovly Christine M. , Irish Jonathan M. , Ihrie Rebecca A. 
Published: August 2022

AbstractCyclic immunohistochemistry (cycIHC) uses sequential rounds of colorimetric immunostaining and imaging for quantitative mapping of location and number of cells of interest. In addition, cycIHC benefits from the speed and simplicity of brightfield microscopy for data collection, making the collection of entire tissue sections and slides possible at a trivial cost compared to other high dimensional imaging modalities. However, large cycIHC datasets (greater than 50 GB) currently require an expert data scientist to concatenate separate open-source tools for each step of image pre-processing, registration, and segmentation, or the use of proprietary software. Here, we present a unified and user-friendly pipeline for processing, aligning, and analyzing cycIHC data - Cyclic Analysis of Single-Cell Subsets and Tissue Territories (CASSATT). CASSATT registers scanned slide images across all rounds of staining, segments individual nuclei, and measures marker expression on each detected cell. Beyond straightforward single cell data analysis outputs, CASSATT explores the spatial relationships between cell populations. By calculating the logodds of interaction frequencies between cell populations within tissues and tissue regions, this pipeline helps users identify populations of cells that interact - or do not interact - at frequencies that are greater than those occurring by chance. It also identifies specific neighborhoods of cells based on the assortment of neighboring cell types that surround each cell in the sample. The presence and location of these neighborhoods can be compared across slides or within distinct regions within a tissue. CASSATT was first tested using a newly generated cycIHC dataset consisting of six GBM tissue sections processed through eight cycles of AEC based IHC staining. Further validation was completed on a previously published lung cancer tissue microarray dataset consisting of 107 cores processed through eighteen cycles of staining and imaging. CASSATT is a fully open-source workflow tool developed to process cycIHC data and will allow greater utilization of this powerful staining technique.
Revisiting the impact of synthetic ORF sequences on engineered LINE-1 retrotransposition
Authors: Chan Dorothy , Workman Stephanie , Gerdes Patricia , Han Jeffrey S , Boeke Jef D , Faulkner Geoffrey J , Richardson Sandra R 
Published: August 2022

AbstractThe retrotransposon Long Interspersed Element 1 (L1) contains adenosine rich ORFs, a characteristic that limits its expression in mammalian cells. A synthetic mouse L1 (smL1) with ORF adenosine content decreased from 40% to 26% showed increased mRNA expression and retrotransposed far more efficiently than the native parental element, L1spa (1). Here, we observe two nonsynonymous substitutions between the L1spa and smL1 ORF1 sequences, and note that the smL1 3’UTR lacks a conserved guanosine-rich region (GRR) which could potentially take on a G-quadruplex secondary structure. We find that the combined effect of a single amino acid change and the GRR 3’UTR deletion, rather than synthetic ORF sequences, accounts for the increase in smL1 retrotransposition efficiency over L1spa. Furthermore, we demonstrate that the position of the GRR within the L1 reporter construct impacts retrotransposition efficiency. Our results prompt a reevaluation of synthetic L1 activity and suggest native mouse L1 mobility has in some cases been underestimated in engineered retrotransposition assays.Author SummaryL1 retrotransposons are mobile DNA elements or “jumping genes” that can copy- and-paste their sequences to new locations in the host genome. The jumping ability, or retrotransposition efficiency, of individual L1 elements can be evaluated using a cultured cell assay in which the L1 is tagged in its 3’ untranslated region (3’UTR) with a reporter gene that becomes expressed upon successful retrotransposition. In a previous study, authors Han and Boeke reported that the retrotransposition efficiency of a mouse L1 element could be enhanced dramatically by synthetically increasing the GC content of the L1 ORFs without changing their amino acid sequence. Curiously, a similarly constructed synthetic human L1 achieved only a modest increase in retrotransposition efficiency over the native element. Here, we find that two coding changes and partial deletion of the mouse L1 3’UTR sequence which occurred during construction of the synthetic mouse L1 reporter actually are responsible for the increased jumping of this construct. We also find that changing the placement as well as the presence of this deleted 3’UTR region within the reporter construct determines its impact on engineered retrotransposition efficiency. Together, our study reconciles the disparate impacts of synthetic sequences upon human and mouse L1 retrotransposition efficiency, prompts a reconsideration of numerous studies using synthetic L1 constructs, and will inform the ongoing use of synthetic and natural mouse L1 reporter constructs in vivo and in vitro.
A Large-Scale ENIGMA Multisite Replication Study of Brain Age in Depression
Authors: Han Laura K.M. , Dinga Richard , Leenings Ramona , Hahn Tim , Cole James H. , Aftanas Lyubomir , Amod Alyssa R. , Besteher Bianca , Colle Romain , Corruble Emmanuelle , Couvy-Duchesne Baptiste , Danilenko Konstantin , Fuentes-Claramonte Paola , Gonul Ali Saffet , Gotlib Ian H. , Goya-Maldonado Roberto , Groenewold Nynke A. , Hamilton Paul , Ichikawa Naho , Ipser Jonathan C. , Itai Eri , Koopowitz Sheri-Michelle , Li Meng , Okada Go , Okamoto Yasumasa , Olga Churikova , Osipov Evgeny , Penninx Brenda W.J.H. , Pomarol-Clotet Edith , Rodríguez-Cano Elena , Sacchet Matthew D. , Shinzato Hotaka , Sim Kang , Stein Dan J. , Uyar-Demir Aslihan , Veltman Dick J. , Schmaal Lianne 
Published: August 2022

ABSTRACTBackgroundSeveral studies have evaluated whether depressed persons have older appearing brains than their nondepressed peers. However, the estimated neuroimaging-derived “brain age gap” has varied from study to study, likely driven by differences in training and testing sample (size), age range, and used modality/features. To validate our previously developed ENIGMA brain age model and the identified brain age gap, we aim to replicate the presence and effect size estimate previously found in the largest study in depression to date (N=2,126 controls & N=2,675 cases; +1.08 years [SE 0.22], Cohen’s d=0.14, 95% CI: 0.08-0.20), in independent cohorts that were not part of the original study.MethodsA previously trained brain age model (www.photon-ai.com/enigma_brainage) based on 77 FreeSurfer brain regions of interest was used to obtain unbiased brain age predictions in 751 controls and 766 persons with depression (18-75 years) from 13 new cohorts collected from 20 different scanners.ResultsOur ENIGMA MDD brain age model generalized reasonably well to controls from the new cohorts (predicted age vs. age:r= 0.73,R2=0.47, MAE=7.50 years), although the performance varied from cohort to cohort. In these new cohorts, on average, depressed persons showed a significantly higher brain age gap of +1 year (SE 0.35) (Cohen’s d□=□□.15, 95% CI: 0.05–0.25) compared with controls, highly similar to our previous finding.ConclusionsThis study further validates our previously developed ENIGMA brain age algorithm. Importantly, we replicated the brain age gap in depression with a comparable effect size. Thus, two large-scale independent mega-analyses across in total 32 cohorts and >3,400 patients and >2,800 controls worldwide show reliable but subtle effects of brain aging in adult depression.
Reactivation of an errantivirus inDrosophilaovarian somatic tissue: from germline invasion to taming
Authors: Yoth Marianne , Maupetit-Méhouas Stéphanie , Akkouche Abdou , Gueguen Nathalie , Bertin Benjamin , Jensen Silke , Brasset Emilie 
Published: August 2022

SummaryMost Drosophila transposable elements (TEs) are LTR retrotransposons, some of which belong to the genus Errantivirus and share structural and functional characteristics with vertebrate endogenous retroviruses (ERVs). These virus-derived elements occupy a large part of the genome, but it is unclear whether and how they can be reactivated and if they retain their replication capacity. We created conditions where control of the DrosophilaZAMerrantivirus through the piRNA pathway was abolished leading to its reactivation in real time in somatic gonadal cells. We show that ZAM may remain active in these cells indicating that errantiviruses may hide from the efficient germline piRNA pathway by being expressed exclusively in somatic cells. After reactivation,ZAMinvaded the oocytes and severe fertility defects were observed. The germline then set up its own adaptive genomic immune response against the constantly invading errantivirus, restricting invasion and restoring fertility. Our results not only highlight how errantiviruses and their host adapt to each other but also reveal a time window during oogenesis that may be favourable for viral germline invasion and endogenization.