bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution
Authors: Papadogiannis Vasileios , Manousaki Tereza , Nousias Orestis , Tsakogiannis Alexandros , Kristoffersen Jon B. , Mylonas Constantinos C. , Batargias Constantinos , Chatziplis Dimitrios , Tsigenopoulos Costas S. 
Published: October 2022

AbstractThe meagre, Argyrosomus regius, has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius, produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. We use this new resource to study the evolution of the meagre genome and other Sciaenids, via a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related dmrt1 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species.
Does prefrontal connectivity during task switching help or hinder children’s performance?
Authors: Schwarze Sina A. , Laube Corinna , Khosravani Neda , Lindenberger Ulman , Bunge Silvia A. , Fandakova Yana 
Published: October 2022

AbstractThe ability to flexibly switch between tasks is key for goal-directed behavior and continues to improve across childhood. Children’s task switching difficulties are thought to reflect less efficient engagement of sustained and transient control processes, resulting in lower performance on blocks that intermix tasks (sustained demand) and trials that require a task switch (transient demand). Sustained and transient control processes are associated with frontoparietal regions, which develop throughout childhood and may contribute to task switching development. We examined age differences in the modulation of frontoparietal regions by sustained and transient control demands in children (8–11 years) and adults. Children showed greater performance costs than adults, especially under sustained demand, along with less upregulation of sustained and transient control activation in frontoparietal regions. Compared to adults, children showed increased connectivity between the inferior frontal junction (IFJ) and lateral prefrontal cortex (lPFC) from single to mixed blocks. For children whose sustained activation was less adult-like, increased IFJ-lPFC connectivity was associated with better performance. Children with more adult-like sustained activation showed the inverse effect. These results suggest that individual differences in task switching in later childhood at least partly depend on the recruitment of frontoparietal regions in an adult-like manner.
Loss of motor cortical inputs to the red nucleus after central nervous system disorders in non-human primates
Authors: Borgognon Simon , Rouiller Eric M. 
Published: October 2022

AbstractThe premotor (PM) and primary motor (M1) cortical areas broadcast voluntary motor commands through multiple neuronal pathways, including the corticorubral projection that reaches the red nucleus (RN). However, the respective contribution of M1 and PM to corticorubral projections as well as its plasticity following motor disorders or injuries are not known in non-human primates. Here, we quantified the density and topography of axonal endings of the corticorubral pathway in RN in intact monkeys, as well as in monkeys subjected to either cervical spinal cord injury (SCI), Parkinson’s disease (PD)-like symptoms or primary motor cortex injury (MCI). Twenty adult macaque monkeys were injected with the biotinylated dextran amine (BDA) anterograde tracer either in PM or in M1. We developed a semi-automated algorithm to reliably detect and count axonal boutons within the magnocellular (mRN) and parvocellular (pRN) subdivisions of RN. In intact monkeys, PM and M1 preferentially target the medial part of the ipsilateral pRN, reflecting its somatotopic organization. PM’s projection to the ipsilateral pRN is denser than M1’s, matching previous observations for the corticotectal, corticoreticular, and corticosubthalamic projections (Fregosi et al., 2018, 2019; Borgognon et al., 2020). In all three types of motor disorders, there was a uniform and strong decrease (near loss) of the corticorubral projections from PM and M1. The RN may contribute to functional recovery after SCI, PD and MCI, by reducing direct cortical influence. This reduction possibly privileges direct access to the final output motor system, via emphasis on the direct corticospinal projection.
Mutation of the ALS/FTD-associated RNA-binding protein FUS alters axonal cytoskeletal organisation
Authors: van Tartwijk Francesca W. , Wunderlich Lucia C.S. , Mela Ioanna , Makarchuk Stanislaw , Jakobs Maximilian A.H , Qamar Seema , Franze Kristian , Schierle Gabriele S. Kaminski , St George-Hyslop Peter H. , Lin Julie Qiaojin , Holt Christine E. , Kaminski Clemens F. 
Published: October 2022

SummaryAberrant condensation and localisation of the RNA-binding protein fused in sarcoma (FUS) occur in variants of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). ALS is also associated with cytoskeletal defects, genetically and through observations of compromised axonal transport. Here, we asked whether compromised axonal cytoskeletal organisation is an early feature of FUS-associated ALS/FTD. We used an ALS-associated mutant FUS(P525L) and the FTD-mimic hypomethylated FUS, FUS(16R), to investigate the common and distinct cytoskeletal changes found in these two reportedXenopusmodels. Combining a novel atomic force microscopy (AFM)-based approach forin vitrocytoskeletal characterisation andin vivoaxonal branching analysis, we found that mutant FUS reduced actin density in the dynamically remodelling growth cone, and reduced axonal branch complexity. We furthermore found evidence of an axon looping defect for FUS(P525L). Therefore, we show that compromised actin remodelling is potentially an important early event in FUS-associated pathogenesis.Abstract Figure
EMPIAR: The Electron Microscopy Public Image Archive
Authors: Iudin Andrii , Korir Paul K. , Somasundharam Sriram , Weyand Simone , Cattavitello Cesare , Fonseca Neli , Salih Osman , Kleywegt Gerard J. , Patwardhan Ardan 
Published: October 2022

AbstractPublic archiving in structural biology is well established with the Protein Data Bank (PDB; wwPDB.org) catering for atomic models and the Electron Microscopy Data Bank (EMDB; emdb-empiar.org) for 3D reconstructions from cryo-EM experiments. Even before the recent rapid growth in cryo-EM, there was an expressed community need for a public archive of image data from cryo-EM experiments for validation, software development, testing and training. Concomitantly, the proliferation of 3D imaging techniques for cells, tissues and organisms using volume EM (vEM) and X-ray tomography (XT) led to calls from these communities to publicly archive such data as well. EMPIAR (empiar.org) was developed as a public archive for raw cryo-EM image data and for 3D reconstructions from vEM and XT experiments and now comprises over a thousand entries totalling over 2 petabytes of data. EMPIAR resources include a deposition system, entry pages, facilities to search, visualise and download datasets, and a REST API for programmatic access to entry metadata. The success of EMPIAR also poses significant challenges for the future in dealing with the very fast growth in the volume of data and in enhancing its reusability.
Palaeontological evidence for community-level decrease in mesopelagic fish size during Pleistocene climate warming in the eastern Mediterranean
Authors: Agiadi Konstantina , Quillévéré Frédéric , Nawrot Rafał , Sommeville Theo , Coll Marta , Koskeridou Efterpi , Fietzke Jan , Zuschin Martin 
Published: October 2022

AbstractMesopelagic fishes are an important element of marine food webs, a huge, still mostly untapped food resource, and great contributors to the biological carbon pump, whose future under climate change scenarios are unknown. The shrinking of commercial fishes within decades has been an alarming observation, but its causes remain contended. Here, we investigate the effect of warming climate on mesopelagic fish size in the eastern Mediterranean Sea during a glacial–interglacial–glacial transition of the Middle Pleistocene (marine isotope stages 20–18; 814–712 Kyr B.P.), which included a 4 °C increase of global seawater temperature. Our results based on fossil otoliths show that the median size of lanternfishes, one of the most abundant groups of mesopelagic fishes in fossil and modern assemblages, declined by ~35% with climate warming at the community level. However, individual mesopelagic species showed different and often opposing trends in size across the studied time interval, suggesting that climate warming in the interglacial resulted in an ecological shift toward increased relative abundance of smaller-sized mesopelagic fishes due to geographic and/or bathymetric distribution range shifts, and the size-dependent effects of warming.
Alignment, calibration, and validation of an adaptive optics scanning laser ophthalmoscope for high-resolution human foveal imaging
Authors: Moon Benjamin , Poletti Martina , Roorda Austin , Tiruveedhula Pavan , Liu Soh Hang , Linebach Glory , Rucci Michele , Rolland Jannick P. 
Published: October 2022

AbstractAdvances in adaptive optics scanning laser ophthalmoscope (AOSLO) technology have enabled cones in the human fovea to be reliably resolved, providing new insight into human foveal anatomy, visual perception, and retinal degenerative diseases. These high-resolution ophthalmoscopes require careful alignment of each optical subsystem to ensure diffraction-limited imaging performance, which is necessary for resolving the smallest foveal cones. This paper presents a systematic and rigorous methodology for building, aligning, calibrating, and testing an AOSLO designed for imaging the cone mosaic of the central fovea in humans with cellular resolution. This methodology uses a two-stage alignment procedure and thorough system testing to achieve diffraction-limited performance. Results from retinal imaging of healthy human subjects show that the system can resolve cones at the very center of the fovea, the region where the cones are smallest and most densely packed.
A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v0.1]
Authors: Bogetti Anthony T. , Leung Jeremy M. G. , Russo John D. , Zhang She , Thompson Jeff P. , Saglam Ali S. , Ray Dhiman , Abraham Rhea C. , Faeder James R. , Andricioaei Ioan , Adelman Joshua L. , Zwier Matthew C. , LeBard David N. , Zuckerman Daniel M. , Chong Lillian T. 
Published: October 2022

AbstractWe present six advanced tutorials instructing users in the best practices of using key new features and plugins/extensions of the WESTPA 2.0 software package, which consists of major upgrades for enabling applications of the weighted ensemble (WE) path sampling strategy to even larger systems and/or slower processes. The tutorials demonstrate the use of the following key features: (i) a generalized resampler module for the creation of “binless” schemes, (ii) a minimal adaptive binning scheme for more efficient surmounting of free energy barriers, (iii) streamlined handling of large simulation datasets using an HDF5 framework, (iv) two different schemes for more efficient rate-constant estimation, (v) a Python API for simplified analysis of WE simulations, and (vi) plugins/extensions for Markovian Weighted Ensemble Milestoning and WE rule-based modeling at the system biology level. Applications of the tutorials range from atomistic to residue-level to non-spatial models, and include complex processes such as protein folding and the membrane permeability of a drug-like molecule. Users are expected to already have significant experience with running conventional molecular dynamics simulations and completed the previous suite of WESTPA tutorials.
Direct comparison of epifluorescence and immunostaining for assessing viral mediated gene expression in the primate brain
Authors: Daw Tierney B. , El-Nahal Hala G. , Basso Michele A. , Jun Elizabeth J. , Bautista Alex R. , Samulski R. Jude , Sommer Marc A. , Bohlen Martin O. 
Published: October 2022

ABSTRACTViral vector technologies are commonly used in neuroscience research to understand and manipulate neural circuits, but successful applications of these technologies in non-human primate models have been inconsistent. An essential component to improve these technologies is an impartial and accurate assessment of the effectiveness of different viral constructs in the primate brain. We tested a diverse array of viral vectors delivered to the brain and extraocular muscles of macaques and compared three methods for histological assessment of viral-mediated fluorescent transgene expression: epifluorescence (Epi), immunofluorescence (IF), and immunohistochemistry (IHC). Importantly, IF and IHC identified a greater number of transduced neurons compared to Epi. Furthermore, IF and IHC reliably provided enhanced visualization of transgene in most cellular compartments (i.e., dendritic, axonal, and terminal fields), whereas the degree of labeling provided by Epi was inconsistent and predominantly restricted to somas and apical dendrites. Because Epi signals are unamplified (in contrast to IF and IHC), Epi likely provides a more veridical assessment for the amount of accumulated transgene and, thus, the potential to chemo- or optogenetically manipulate neuronal activity. The comparatively weak Epi signals suggest that the current generations of viral constructs, regardless of delivered transgene, are not optimized for primates. This reinforces an emerging viewpoint that viral vectors tailored for the primate brain are necessary for basic research and human gene therapy.
The influence of visual pollution on navigation mechanisms in the damselfish (Chrysiptera cyanea)
Authors: Lunt William Michael , Burt de Perera Theresa , Newport Cait 
Published: October 2022

ABSTRACTHere, we investigate whether visual pollution has an effect on navigation in coral reef damselfish (Chrysiptera cyanea). Turbidity had no significant influence on the individual fish’s preference between egocentric and visual cues in a simple navigation task, with all individuals exhibiting a striking egocentric preference across all turbidity levels under testing. However, an alteration of cue preference may have occurred on a fine scale. Turbidity had profound effects on fish movement and decision-making behaviour, which has substantial implications for the behaviour of fishes on the ecological scale of a coral reef.
Combining molecular and cell painting image data for mechanism of action prediction
Authors: Tian Guangyan , Harrison Philip J , Sreenivasan Akshai P , Puigvert Jordi Carreras , Spjuth Ola 
Published: October 2022

AbstractThe mechanism of action (MoA) of a compound describes the biological interaction through which it produces a pharmacological effect. Multiple data sources can be used for the purpose of predicting MoA, including compound structural information, and various assays, such as those based on cell morphology, transcriptomics and metabolomics. In the present study we explored the benefits and potential additive/synergistic effects of combining structural information, in the form of Morgan fingerprints, and morphological information, in the form of five-channel Cell Painting image data. For a set of 10 well represented MoA classes, we compared the performance of deep learning models trained on the two datasets separately versus a model trained on both datasets simultaneously. On a held-out test set we obtained a macro-averaged F1 score of 0.58 when training on only the structural data, 0.81 when training on only the image data, and 0.92 when training on both together. Thus indicating clear additive/synergistic effects and highlighting the benefit of integrating multiple data sources for MoA prediction.
Community engagement through “student-led science” for dengue prevention during the COVID-19 pandemic in Córdoba, Argentina
Authors: Estallo Elizabet L. , Madelon Magali , Benitez Elisabet M. , Stewart-Ibarra Anna M. , Ludueña-Almeida Francisco F. 
Published: October 2022

AbstractBackgroundDuring 2019-2020 while COVID-19 pandemic, the Americas were facing the biggest dengue fever epidemic in recent history. Traditional vector control programs, based on insecticide application have been insufficient to control the spread of dengue fever. Several studies suggest refocusing on education with the aim of an integrated vector management strategy within the local ecological-community context. We aim to assess community perceptions, knowledge, attitude, preventive practice, and action through student-led science assignments regarding dengue fever, prevention, and socio-ecological factors in temperate Córdoba, Argentina.MethodsThe study was conducted during the COVID-19 quarantine when schools switched to online education for the first time. Several activities through Google Classroom platform included a survey to one student’s family member, and an outdoor activity to assess their attitudes and to clean the backyard and gardens.ResultsSignificant number of respondents developed good preventive practices and increased their knowledge about the vector and disease highlighting that 75% of responders knew that dengue fever was transmitted by a mosquito, 81.96% declared having obtained knowledge regarding dengue and vector through television, 56% affirm that dengue is a severe illness, 67% of respondents admitted that individuals play an important role in the prevention of dengue. Regarding mosquito control activities, 90% of respondents reported turning containers.ConclusionsThis highlights the need for school programs with curricula to address vector biology and the prevention of vector-borne diseases not only during activity periods when mosquitoes batter people but all year long to do real prevention.
Perioral secretions enable complex social signaling in African mole-rats (genus Fukomys)
Authors: Caspar Kai R. , Stopka Pavel , Issel Daniel , Katschak Kristin , Zöllner Till , Zupanc Sina , Žáček Petr , Begall Sabine 
Published: October 2022

AbstractSubterranean common mole-rats of the genus Fukomys (family Bathyergidae) live in large cooperatively-breeding families. Odor cues have been hypothesized to importantly mediate social behaviors in the underground ecotope, but only little is known about the role of olfactory signaling in burrowing mammals. Here we characterize the so far neglected perioral glands of Fukomys and other African mole-rats as an important source of olfactory social information. Histology demonstrates these structures to be derived sebaceous glands that are developed regardless of sex and reproductive status. However, gland activity is higher in Fukomys males, leading to sexually dimorphic patterns of stain and clotting of the facial pelage. Behavioral assays revealed that conspecifics prefer male but not female perioral swabs over scent samples from the back fur and that male sebum causes similar attraction as anogenital scent, a known source of social information in Fukomys. Finally, we assessed volatile compounds in the perioral sebum of the giant mole-rat (Fukomys mechowii) via GCxGC-MS-based metabolomic profiling. Volatiles displayed pronounced sex-specific signatures but also allowed to differentiate between intrasexual reproductive status groups. These different lines of evidence suggest that mole-rat perioral glands provide complex odor signals that play a crucial role in social communication.
Nature portrayed in images in Dutch Brazil: Tracing the sources of the plant woodcuts in theHistoria Naturalis Brasiliae(1648)
Authors: Alcantara-Rodriguez Mireia , Van Andel Tinde , Françozo Mariana 
Published: October 2022

AbstractBy the mid-seventeenth century, images of natural elements that originated in Dutch Brazil circulated in Europe. These were often included in art collections (theLibri Picturati), and natural history treatises (theHistoria Naturalis Brasiliaeand theIndia Utriesque re Naturale et Medica). The plant woodcut images in these books constituted (icono) type specimens and played a significant role in the transmission of (botanical) knowledge. We present a systematic analysis of their origins by cross-referencing the visual and textual sources related to Dutch Brazil. To do so, we used the scientific identifications of the portrayed plants and digital archival material. The plant woodcuts accounted for 529 images, which correspond to 426 taxa. We created a PDF booklet to visualize the correlations of the woodcuts with theLibri Picturatiand other visual sources. Substantial differences in the visual-making methodology exist between the two treatises (1648, 1658). Overall, availability, economy, and the Indigenous Tupi-based plant names that accompanied the images were crucial when arranging the sources, as well as portraying as much botanical information as possible.Freshly picked, living plants, and dried branches, fruits, and seeds were used to represent the megadiverse Brazilian flora, even when these belonged to species originating from other regions. Despite not being recognized for their contribution, Indigenous Brazilians and enslaved Africans were essential in the visual knowledge-making processes that later resulted in these natural history collections. As several sources remain lost and many histories yet untold, further archival studies and collaborative projects are pertinent to reveal the missing pieces of this conundrum.