bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seed morphological traits as a tool to quantify variation maintained inex situcollections: a case study inPinus torreyana(Parry)
Authors: Di Santo Lionel N , Polgar Monica , Nies Storm , Hodgkiss Paul , Canning Courtney A , Wright Jessica W , Hamilton Jill A 
Published: September 2020

AbstractBackgroundUnderstanding the within- and among-population distribution of trait variation within seed collections may provide a means to approximate standing genetic variation and inform plant conservation.AimsThis study aimed to estimate population- and family-level seed trait variability for existing seed collections of Torrey pine (Pinus torreyana), and to use these data to guide sampling of future collections.MethodsWe quantified variation in 14 seed morphological traits and seedling emergence within and among Torrey pine populations. Using a simulation-based approach, we used estimates of within-population variance to assess the number of maternal families required to capture 95% of trait variation within each existing seed collection.ResultsSubstantial structure was observed both within and among Torrey pine populations, with island and mainland seeds varying in seed size and seed coat thickness. Despite morphological differences, seedling emergence was similar across populations. Simulations revealed that 83% and 71% of all maternal families within island and mainland seed collections respectively needed to be resampled to capture 95% of seed trait variation within existing collections.ConclusionsFrom a conservation perspective, our results indicate that to optimize genetic diversity captured in Torrey pine seed collections, maximizing the number of maternal families sampled within each population will be necessary.
Tracking single molecule dynamics in the anesthetizedDrosophilabrain
Authors: Hines Adam D. , van Swinderen Bruno 
Published: September 2020

AbstractSuper-resolution microscopy provides valuable insight for understanding the nanoscale organization within living tissue, although this method is typically restricted to cultured or dissociated cells. Here, we develop a method to track the mobility of individual proteins inex vivoadultDrosophila melanogasterbrains, focusing on a key component of the presynaptic release machinery, syntaxin1A. We show that individual syntaxin1A dynamics can be reliably tracked within neurons in the whole fly brain, and that the mobility of syntaxin1A molecules increases following conditional neural stimulation. We then apply this preparation to the problem of general anesthesia, to address how different anesthetics might affect single molecule dynamics in intact brain synapses. We find that propofol, etomidate, and isoflurane significantly impair syntaxin1A mobility, while ketamine and sevoflurane have little effect. Resolving single molecule dynamics in intact fly brains provides a novel approach to link localized molecular effects with systems-level phenomena such as general anesthesia.Impact statementA new approach to track the mobility of individual molecules using intact fly brains reveals a common presynaptic effect for different intravenous and volatile general anesthetics.
Evolutionary and Structural Constraints Influencing Apolipoprotein A-I Amyloid Behaviour
Authors: Gisonno RA , Masson T , Ramella N , Barrera EE , Romanowski V , Tricerri MA 
Published: September 2020

AbstractApolipoprotein A-I (apoA-I) has a key function in the reverse cholesterol transport mediated by the high density lipoprotein (HDL) particles. However, aggregation of apoA-I single point mutants can lead to hereditary amyloid pathology. Although several studies have tackled the biophysical and structural impacts introduced by these mutations, there is little information addressing the relationship between the evolutionary and structural features that contribute to the amyloid behavior of apoA-I. We combined evolutionary studies, in silico mutagenesis and molecular dynamics (MD) simulations to provide a comprehensive analysis of the conservation and pathogenic role of the aggregation-prone regions (APRs) present in apoA-I. Sequence analysis demonstrated that among the four amyloidogenic regions described for human apoA-I, only two (APR1 and APR4) are evolutionary conserved across different species of Sarcopterygii. Moreover, stability analysis carried out with the FoldX engine showed that APR1 contributes to the marginal stability of apoA-I. Structural properties of the full-length apoA-I model suggest that aggregation is avoided by placing APRs into highly packed and rigid portions of its native fold. Following we set up to study the effect of natural mutations on protein conformation and stability. Compared to natural silent variants extracted from the gnomAD database, the thermodynamic and pathogenic impact of apoA-I amyloid mutations showed evidence of a higher destabilizing effect. MD simulations of the amyloid variant G26R evidenced the partial unfolding of the alpha-helix bundle with the concomitant exposure of APR1 to the solvent and the formation of beta-sheet segments at the C-terminus of apoA-I, giving a possible hint about the early steps involved in its aggregation. Our findings highlight APR1 as a relevant component for apoA-I structural integrity and emphasize a destabilizing effect of amyloid variants that leads to the exposure of this region. This information contributes to our understanding of how apoA-I, with its high degree of structural flexibility, maintains a delicate equilibrium between its monomeric native structure and intrinsic tendency to form amyloid aggregates. In addition, our stability measurements could be used as a proxy to interpret the structural impact of new mutations.
The Dual Mechanisms of Cognitive Control (DMCC) Project
Authors: Braver Todd S. , Kizhner Alexander , Tang Rongxiang , Freund Michael C. , Etzel Joset A. 
Published: September 2020

AbstractThe Dual Mechanisms of Cognitive Control (DMCC) project provides an ambitious and rigorous empirical test of a theoretical framework that posits two key cognitive control modes: proactive and reactive. The framework’s central tenets are that proactive and reactive control reflect domain-general dimensions of individual variation, with distinctive neural signatures, involving lateral prefrontal cortex (PFC) in interactions with other brain networks and circuits (e.g., frontoparietal, cingulo-opercular). In the DMCC project, each participant is scanned while performing theoretically-targeted variants of multiple well-established cognitive control tasks (Stroop, Cued Task-Switching, AX-CPT, Sternberg Working Memory) in three separate imaging sessions, that each encourage utilization of different control modes, plus also completes an extensive out-of-scanner individual differences battery. Additional key features of the project include a high spatio-temporal resolution (multiband) acquisition protocol, and a sample that includes a substantial subset of monozygotic twin pairs and participants recruited from the Human Connectome Project. Although data collection is still continuing (target N=200), we provide an overview of the study design and protocol, planned analytic approaches and methodological development, along with initial results (N=80) revealing novel evidence of a domain-general neural signature of reactive control. In the interests of scientific community building, the dataset will be made public at project completion, so it can serve as a valuable resource.
Understanding and Improving Word Embeddings through a Neuroscientific Lens
Authors: Fereidooni Sam , Mocz Viola , Radev Dragomir , Chun Marvin 
Published: September 2020

AbstractDespite the success of models making use of word embeddings on many natural language tasks, these models often perform significantly worse than humans on several natural language understanding tasks. This difference in performance motivates us to ask: (1) if existing word vector representations have any basis in the brain’s representational structure for individual words, and (2) whether features from the brain can be used to improve word embedding model performance, defined as their correlation with human semantic judgements. To answer the first question, we compare the representational spaces of existing word embedding models with that of brain imaging data through representational similarity analysis. We answer the second question by using regression-based learning to constrain word vectors to the features of the brain imaging data, thereby determining if these modified word vectors exhibit increased performance over their unmodified counterparts. To collect semantic judgements as a measure of performance, we employed a novel multi-arrangement method. Our results show that there is variance in the representational space of the brain imaging data that remains uncaptured by word embedding models, and that brain imaging data can be used to increase their coherence with human performance.
SERUM ANTIBODY RESPONSES AGAINST CARBAPENEM-RESISTANTKLEBSIELLA PNEUMONIAEIN INFECTED PATIENTS
Authors: Banerjee Kasturi , Motley Michael P. , Diago-Navarro Elizabeth , Fries Bettina C. 
Published: September 2020

AbstractBackgroundCapsular polysaccharide (CPS) heterogeneity within carbapenem-resistantKlebsiella pneumoniae(CR-Kp) strain ST258 must be considered when developing CPS-based vaccines. We sought to characterize CPS-specific antibody responses elicited by CR-Kpinfected patients.MethodPlasma and bacterial isolates were collected from 33 hospital patients with positive CR-Kpculture. Isolates capsule were typed bywzisequencing. Reactivity and measures of efficacy of patient antibodies were studied against 3 prevalent CR-KpCPS types (wzi29, 154and50).ResultsHigh IgG titers againstwzi154andwzi50CPS were documented in 79% of infected patients. Patient-derived (PD) IgGs agglutinated CR-Kpand limited growth better than naïve IgG, and promoted phagocytosis of strains across the serotype isolated from their donors. Additionally, poly-IgG fromwzi50 and wzi154patients promoted phagocytosis of non-concordant CR-Kp serotypes. Such effects were lost when poly-IgG was depleted of CPS-specific IgG. Additionally, mice infected withwzi50, wzi154, and wzi29CR-Kpstrains pre-opsonized withwzi50patient-derived IgG exhibited lower lung CFU than controls. Depletion ofwzi50Abs reversed this effect inwzi50 and wzi154infections, whereas wzi154 Ab depletion reduced Poly-IgG efficacy againstwzi29CR-Kp.ConclusionsWe are first to report cross-reactive properties of CPS-specific Abs from CR-Kppatients through bothin-vitroandin-vivomodels.ImportanceCarbapenem-resistantKlebsiella pneumoniaeis a rapidly emerging public health threat that can cause fatal infections in ~40-50% of immunocompromised patients. Due to its resistance to nearly all antimicrobials, development of alternate therapies like antibodies and vaccines are urgently needed. Capsular polysaccharides are emerging as important immunotargets as they are a crucial forKlebsiella pneumoniaepathogenesis. Studying how host’s immune system protect against specific bacteria such asKlebsiella pneumoiniae, with respect to their specific capsule-type is crucial to develop effective anti-CPS immunotherapies. In this manuscript, we are the first to characterize humoral responses developed in infected patients against carbapenem-resistantKlebsiella pneumoniaeexpressing differentwzi-capsule types. This study is the first to report efficacy of cross-reactive properties of CPS-specific Abs in bothin-vitroandin-vivomodels.
A digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule
Authors: Vijayan Athul , Tofanelli Rachele , Strauss Soeren , Cerrone Lorenzo , Wolny Adrian , Strohmeier Joanna , Kreshuk Anna , Hamprecht Fred A. , Smith Richard S. , Schneitz Kay 
Published: September 2020

AbstractA fundamental question in biology is how morphogenesis integrates the multitude of distinct processes that act at different scales, ranging from the molecular control of gene expression to cellular coordination in a tissue. Investigating morphogenesis of complex organs strongly benefits from three-dimensional representations of the organ under study. Here, we present a digital analysis of ovule development fromArabidopsis thalianaas a paradigm for a complex morphogenetic process. Using machine-learning-based image analysis we generated a three-dimensional atlas of ovule development with cellular resolution. It allows quantitative stage- and tissue-specific analysis of cellular patterns. Exploiting a fluorescent reporter enabled precise spatial determination of gene expression patterns, revealing subepidermal expression ofWUSCHEL. Underlying the power of our approach, we found that primordium outgrowth progresses evenly, discovered a novel mode of forming a new cell layer, and detected a new function ofINNER NO OUTERin restricting cell proliferation in the nucellus. Moreover, we identified two distinct subepidermal cell populations that make crucial contributions to ovule curvature. Our work demonstrates the expedience of a three-dimensional digital representation when studying the morphogenesis of an organ of complex cellular architecture and shape that eventually consists of 1,900 cells.
ADe NovoGenome Assembly, Gene Annotation, And Expression Atlas For The Monarch ButterflyDanaus plexippus
Authors: Ranz José M. , González Pablo M. , Clifton Bryan D. , Nazario Nestor O. , Hernández-Cervantes Pablo L. , Palma-Martínez María J. , Valdivia Dulce I. , Jiménez-Kaufman Andrés , Lu Megan M. , Markow Therese A. , Abreu-Goodger Cei 
Published: September 2020

ABSTRACTThe monarch butterfly epitomizes insect biodiversity decline. Understanding the genetic basis of the adaptation of the monarch to a changing environment requires genomic and transcriptomic resources that better reflect its genetic diversity while being informative about gene functionality during life cycle. We report a reference-quality genome assembly from an individual resident at a nonmigratory colony in Mexico, and a new gene annotation and expression atlas for 14,865 genes, including 492 unreported long noncoding RNA (lncRNA) genes, based on RNA-seq data from 14 larval and pupal stages, plus adult morphological sections. Two thirds of the genes show significant expression changes associated with a life stage or section, with lncRNAs being more finely regulated during adulthood than protein-coding genes, and male-biased expression being four times more common than female-biased. The two portions of the heterochromosomeZdisplay distinct patterns of differential expression between the sexes, reflecting that dosage compensation is either absent or incomplete –depending on the sample– in the ancestral but not in the novel portion of theZ. This study represents a major advance in the genomic and transcriptome resources available forD. plexippuswhile providing the first systematic analysis of its transcriptional program across most of its life cycle.
Gonadotropin-releasing hormone increases the release of extracellular vesicles from gonadotropes
Authors: Fungbun Numfa , Sugiyama Makoto , Terashima Ryota , Kurusu Shiro , Kawaminami Mitsumori 
Published: September 2020

AbstractWhile extracellular vesicles play a role in intercellular communication, it is not known how their release is regulated. We show here that hypothalamic gonadotropin-releasing hormone (GnRH) stimulates extracellular vesicle (EV) formation associated with annexin A5 (ANXA5) from pituitary gonadotropes. The results show that 1) membrane blebs containing ANXA5 are produced after GnRH agonist (GnRHa) stimulation of gonadotropes and that this is observedin situas a loss of distinction at cell-cell boundaries, 2) EV containing ANXA5 are increased by GnRHa, 3) a gonadotrope-derived EV fraction stimulates LH release from other gonadotropes, and 4) an increase in ANXA5-loaded EV occurs in the plasma of ovariectomized rats. Finally, we also showed that 5) GnRHa stimulation of blebbing and EV-ANXA5 were suppressed by a protein kinase A inhibitor. These present results demonstrate a novel autocrine/paracrine mechanism mediated through the production of EV containing ANXA5. A hormonal regulation mechanism of cell-cell communication by means of EV is suggested.
Predicting range shifts of three endangered endemic plants of the Khorassan-Kopet Dagh floristic province under global change
Authors: Erfanian Mohammad Bagher , Sagharyan Mostafa , Memariani Farshid , Ejtehadi Hamid 
Published: September 2020

AbstractKhorassan-Kopet Dagh (KK) floristic province is an ecoregion that has rarely been studied. A total number of 2576 (356 endemic) vascular plants have been recorded from this area. Most of the endemic species of KK are rare and range-restricted. To assess the vulnerability of plant species under a rapidly changing climate, we can use species distribution modelling (SDM) to predict their potential present and future distribution. We used SDM to evaluate range size changes for three (critically) endangered endemic species to KK, namelyNepeta binaloudensis, Phlomoides binaludensis, andEuphorbia ferdowsiana. These plants represent KK endemic species that grow in the different elevation ranges of KK mountains. Using the HadGEM2-ES general circulation model and two Representative Concentration Pathways Scenarios (RCP), including RCP 2.6 (most optimistic) and RCP 8.5 (most pessimistic), we predicted the potential present and future (i.e., 2050 and 2070) distribution for each species. The ensemble model of nine different methods was used for this prediction. Our results showed that, except forP. binaludensisthat will face range contraction, the other species would benefit from potential range expansion in the future.Euphorbia ferdowsianawill remain limited to a narrow range of KK. However, the other two plants will have suitable habitats in various mountains of KK. To conserve flora of KK, we urge using management efforts with a focus on providing elevational migration routes at the local scales in KK mountains. Additionally, assisted migration among different mountains of this region will be beneficial to conserve its endemic plants. ForE. ferdowsianagenetic diversity storage employing seed banks and botanical garden preservation should be considered.
Si-C: method to infer biologically valid super-resolution intact genome structure from single-cell Hi-C data
Authors: Meng Luming , Wang Chenxi , Yi Shi , Luo Qiong 
Published: September 2020

AbstractThere is a strong demand for the methods that can efficiently reconstruct biologically valid super-resolution intact genome 3D structures from sparse and noise single-cell Hi-C data. Here, we developed Single-Cell Chromosome Conformation Calculator (Si-C) within the Bayesian theory framework and applied this approach to reconstruct intact genome 3D structures from the single-cell Hi-C data of eight G1-phase haploid mouse ES cells. The inferred 100-kb and 10-kb structures consistently reproduce the known conserved features of chromatin organization revealed by independent imaging experiments. The analysis of the 10-kb resolution 3D structures revealed cell-to-cell varying domain structures in individual cells and hyperfine structures in domains, such as loops. An average of 0.2 contact reads per divided bin is sufficient for Si-C to obtain reliable structures. The valid super-resolution structures constructed by Si-C demonstrates the potential for visualizing and investigating interactions between all chromatin loci at genome scale in individual cells.
Thalamocortical spectral transmission relies on balanced input strengths
Authors: Saponati Matteo , Garcia-Ojalvo Jordi , Cataldo Enrico , Mazzoni Alberto 
Published: September 2020

AbstractThe thalamus is a key element of sensory transmission in the brain, as all sensory information is processed by the thalamus before reaching the cortex. The thalamus is known to gate and select sensory streams through a modulation of its internal activity in which spindle oscillations play a preponderant role, but the mechanism underlying this process is not completely understood. In particular, how do thalamocortical connections convey stimulus-driven information selectively over the background of thalamic internally generated activity (such as spindle oscillations)? Here we investigate this issue with a spiking network model of connectivity between thalamus and primary sensory cortex reproducing the local field potential of both areas. We found two features of the thalamocortical dynamics that filter out spindle oscillations: i) spindle oscillations are weaker in neurons projecting to the cortex, ii) the resonance dynamics of cortical networks selectively blocks frequency in the range encompassing spindle oscillations. This latter mechanism depends on the balance of the strength of thalamocortical connections toward excitatory and inhibitory neurons in the cortex. Our results pave the way toward an integrated understanding of the sensory streams traveling between the periphery and the cortex.
First report of nematodes inLutzomyia edwardsi(Diptera: Psychodidae, Phlebotominae) in cave, in the municipality of Sumidouro, State of Rio of Janeiro, Brazil
Authors: Carreira Alves João Ricardo , do Carmo Cleber Nascimento , Menezes Rodrigo Caldas , Vilela Mauricio Luís , dos Santos-Mallet Jacenir Reis 
Published: September 2020

ABSTRACTIt is registered for the first time, the encounter ofLutzomyia edwardsi(Mangabeira) species of sandfly considered as a probable vector ofLeishmania(Viannia)braziliensis(Vianna), main etiological agent of American cutaneous leishmaniasis in humans, for the municipality of Sumidouro, State of Rio of Janeiro. Leishmaniasis is currently considered a neglected tropical disease in the Americas. The objective of this study was to know the phlebotomine fauna in an area of Atlantic forest, with a cave in this municipality. From the sandflies collected, in 2009 and 2010, with a light trap, type CDC it is reported in a unique way, the encounter of a femaleL. edwardsi, infected with nematodes in a cave in the locality of São Caetano, in Sumidouro, state of Rio of Janeiro, Brazil. The description of sandfly and nematodes was carried out. The presence of this species in areas of leishmaniasis cases in the municipality of Sumidouro and its surroundings, requires the adoption of relevant entomological and / or epidemiological surveillance, by the Municipal Health Department of the region, when registering this disease.
The regulatory function of the AAA4 ATPase domain of cytoplasmic dynein
Authors: Liu Xinglei , Rao Lu , Gennerich Arne 
Published: September 2020

AbstractCytoplasmic dynein is the primary motor for microtubule minus-end-directed transport and is indispensable to eukaryotic cells. Although each motor domain of dynein contains three active AAA+ ATPases (AAA1, 3, and 4), only the functions of AAA1 and 3 are known. Here, we use single-molecule fluorescence and optical tweezers studies to elucidate the role of AAA4 in dynein’s mechanochemical cycle. We demonstrate that AAA4 controls the priming stroke of the motion-generating linker, which connects the dimerizing tail of the motor to the AAA+ ring. Before ATP binds to AAA4, dynein remains incapable of generating motion. However, when AAA4 is bound to ATP, the gating of AAA1 by AAA3 prevails and dynein motion can occur. Thus, AAA1, 3, and 4 work together to regulate dynein function. Our work elucidates an essential role for AAA4 in dynein’s stepping cycle and underscores the complexity and crosstalk among the motor’s multiple AAA+ domains.