bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shared functional connections within and between cortical networks predict cognitive abilities in adult males and females
Authors: Dhamala Elvisha , Jamison Keith W. , Jaywant Abhishek , Kuceyeski Amy 
Published: February 2021

AbstractA thorough understanding of sex-independent and sex-specific neurobiological features that underlie cognitive abilities in healthy individuals is essential for the study of neurological illnesses in which males and females differentially experience and exhibit cognitive impairment. Here, we evaluate sex-independent and sex-specific relationships between functional connectivity and individual cognitive abilities in 392 healthy young adults (196 males) from the Human Connectome Project. First, we establish that sex-independent models comparably predict crystallised abilities in males and females, but more accurately predict fluid abilities in males. Second, we demonstrate sex-specific models comparably predict crystallised abilities within and between sexes, and generally fail to predict fluid abilities in either sex. Third, we reveal that largely overlapping connections between visual, dorsal attention, ventral attention, and temporal parietal networks are associated with better performance on crystallised and fluid cognitive tests in males and females, while connections within visual, somatomotor, and temporal parietal networks are associated with poorer performance. Together, our findings suggest that shared neurobiological features of the functional connectome underlie crystallised and fluid abilities across the sexes.
A draft genome ofAlliaria petiolata(garlic mustard) as a model system for invasion genetics
Authors: Alabi Nikolay , Wu Yihan , Bossdorf Oliver , Rieseberg Loren H. , Colautti Robert I. 
Published: February 2021

AbstractThe emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on thede novoassembly and annotation of a genome for the biennial herbAlliaria petiolata(M. Bieb.) Cavara & Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC-3-20) collected from the native range near Venice, Italy and sequenced paired-end and mate pair libraries at ~70 × coverage. Ade novoassembly resulted in a highly continuous draft genome (N50= 121 Mb; L50= 2) with 99.7 % of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99 % of plant BUSCO genes and 98 % of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one third of BUSCO genes (390/1440) mapped to two or more scaffolds despite < 2 % genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies ofA. petiolatato address questions relevant to invasion genetics and conservation strategies.
Remyelination restores myelin content on distinct neuronal subtypes in the cerebral cortex
Authors: Call Cody L. , Bergles Dwight E. 
Published: February 2021

ABSTRACTAxons in the cerebral cortex exhibit diverse patterns of myelination, with some axons devoid of myelin, some exhibiting discontinuous patches of myelin, and others continuous myelin that is interrupted only by nodes of Ranvier. Oligodendrocytes establish this pattern by sorting through a high density of potential targets to select a small cohort of axons for myelination; however, the myelination patterns established on distinct excitatory and inhibitory neurons within the cortex remain to be fully defined and little is known about the extent to which these patterns are restored after oligodendrocyte regeneration. Here we show that axons in layer I of the somatosensory cortex, a key region for integration of input from local and distant sources, exhibit an extraordinarily diverse range of myelination patterns, even among distinct neuronal subtypes. Although larger axons were more often selected for myelination, neuronal identity profoundly influenced the probability of myelination. The relative differences in myelination among neuron subtypes were preserved between cortical areas with widely varying myelin density, suggesting that regional differences in myelin abundance arises through local control of oligodendrogenesis, rather than selective reduction of myelin on distinct neuron subtypes. By following the loss and regeneration of myelin sheaths along defined neuronsin vivowe show that even though the distribution of myelin on individual PV and VM neuron axons was altered following remyelination, the overall myelin content on these neurons was restored. The findings suggest that local changes in myelin can be tolerated, allowing opportunistic selection of available targets by newly formed oligodendrocytes to restore relative differences in myelin content between functionally distinct neurons.
Twitches emerge postnatally during quiet sleep in human infants and are synchronized with sleep spindles
Authors: Sokoloff Greta , Dooley James C. , Glanz Ryan M. , Wen Rebecca Y. , Hickerson Meredith M. , Evans Laura G. , Laughlin Haley M. , Apfelbaum Keith S. , Blumberg Mark S. 
Published: February 2021

SummaryIn humans and other mammals, the stillness of sleep is punctuated by bursts of rapid eye movements (REMs) and myoclonic twitches of the limbs [1]. Contrary to the notion that twitches are mere by-products of dreams, sensory feedback arising from twitching limbs provides a rich and unique source of activation to the developing sensorimotor system [2]. In fact, it is partly because of the behavioral activation of REM sleep that this state is also called active sleep (AS), in contrast with the behavioral quiescence that gives quiet sleep (QS)—the second major stage of sleep—its name. In human infants, for which AS occupies eight or more hours of each day [3], limb twitching is one among several components that help to identify the state [4-7]; nonetheless, we know relatively little about the structure and functions of twitching across development. Recently, in sleeping infants over the first seven postnatal months [8], we documented a pronounced shift in the temporal expression of twitching beginning around three months of age that suggested a qualitative shift in how twitches are produced. Here, we combine behavioral assessments of twitching with high-density electroencephalography (EEG) and demonstrate that this shift reflects the developmental emergence of limb twitches during QS. Twitches during QS are not only unaccompanied by REMs, but they also occur synchronously with sleep spindles, a hallmark of QS. As QS-related twitching increases with age, sleep spindle rate also increases along the sensorimotor strip. The emerging synchrony between subcortically generated twitches and cortical oscillations suggests the development of functional connectivity among distant sensorimotor structures, with potential implications for detecting and explaining atypical developmental trajectories.
FRAGMENTED BIODIVERSITY: FERNS AND LYCOPHYTES FROM FOREST FRAGMENTS IN JUIZ DE FORA, MINAS GERAIS, BRAZIL
Authors: Lima Lucas Vieira , de Oliveira Dittrich Vinícius Antonio , de Souza Filipe Soares , da Fonseca Cassiano Ribeiro , Salino Alexandre 
Published: February 2021

ABSTRACTThe Atlantic Forest is one of the most threatened formations in the world. In this context, the urbanization process stands out as one of the major factors causing environmental degradation, mainly due to the loss of native vegetation and habitat destruction. In order to fill this gap, we carried out the inventory of ferns and lycophytes in the forest remnants of the municipality of Juiz de Fora. We analyzed more than 1,353 samplings recorded throughout approximately 150 years, as result we recorded a total of 174 species distributed in 73 genera and 26 families. The most representative families were Pteridaceae with 32 species, followed by Polypodiaceae with 26 and Thelypteridaceae with 20. In addition, we present the historical data on the sampling of ferns and lycophytes, as well as the history of the fragmentation process of the Atlantic Forest remnants in the municipality. Juiz de Fora becomes an interesting model for broader floristic studies, generating subsequent subsidies for conservation actions and preservation of the natural patrimony.
Process-explicit models reveal pathway to extinction for woolly mammoth using pattern-oriented validation
Authors: Fordham Damien A. , Brown Stuart C. , Reşit Akçakaya H. , Brook Barry W. , Haythorne Sean , Manica Andrea , Shoemaker Kevin T. , Austin Jeremy J. , Blonder Benjamin , Pilowsky Julia , Rahbek Carsten , Nogues-Bravo David 
Published: February 2021

AbstractPathways to extinction start long before the death of the last individual. However, causes of early-stage population declines and the susceptibility of small residual populations to extirpation are typically studied in isolation. Using validated process-explicit models, we disentangle the ecological mechanisms and threats that were integral in the initial decline and later extinction of the woolly mammoth. We show that reconciling ancient DNA data on woolly mammoth population decline with fossil evidence of location and timing of extinction requires process-explicit models with specific demographic and niche constraints, and a constrained synergy of climatic change and human impacts. Validated models needed humans to hasten climate-driven population declines by many millennia, and to allow woolly mammoths to persist in mainland Arctic refugia until the mid-Holocene. Our results show that the role of humans in the extinction dynamics of woolly mammoth began well before the Holocene, exerting lasting effects on the spatial pattern and timing of its range-wide extinction.
Kinesin-6 Klp9 orchestrates spindle elongation by regulating microtubule sliding and growth
Authors: Krüger Lara K. , Gélin Matthieu , Ji Liang , Kikuti Carlos , Houdusse Anne , Théry Manuel , Blanchoin Laurent , Tran Phong T. 
Published: February 2021

AbstractMitotic spindle function depends on the precise regulation of microtubule dynamics and microtubule sliding. Throughout mitosis, both processes have to be orchestrated to establish and maintain spindle stability. We show that during anaphase B spindle elongation inS. pombe, the sliding motor Klp9 (kinesin-6) also promotes microtubule growthin vivo. In vitro, Klp9 can enhance and dampen microtubule growth, depending on the tubulin concentration. This indicates that the motor is able to promote and block tubulin subunit incorporation into the microtubule lattice in order to set a well-defined microtubule growth velocity. Moreover, Klp9 recruitment to spindle microtubules is dependent on its dephosphorylation mediated by XMAP215/Dis1, a microtubule polymerase, to link the regulation of spindle length and spindle elongation velocity. Collectively, we unravel the mechanism of anaphase B, from Klp9 recruitment to the motors dual-function in regulating microtubule sliding and microtubule growth, allowing an inherent coordination of both processes.
Spatial modulation of individual behaviors enables collective decision-making during bacterial group migration
Authors: Bai Yang , He Caiyun , Long Junjiajia , Li Xuefei , Fu Xiongfei 
Published: February 2021

AbstractCoordination of individuals with diversity often requires sophisticated communications and high-order computational abilities. Microbial populations can exhibit diverse individualistic behaviors and yet can engage in collective migratory patterns with a spatially sorted arrangement of phenotypes following a self-generated attractant gradient. However, it’s unclear how individual bacteria without complex computational abilities can achieve the consistent group performance and determine their positions in the group while facing spatiotemporally dynamic stimuli. Here, we investigate the statistics of bacterial run-and-tumble trajectories during group migration. We discover that, despite of the constant migrating speed as a group, the individual drift velocity exhibits a spatially dependent structure that decreases from the back to the front of the group. The spatial modulation of individual stochastic behaviors constrains cells in the group, ensuring the coherent population movement with ordered patterns of phenotypes. These results reveal a simple computational principle for emergent collective behaviors from heterogeneous individuals.
Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells
Authors: Cuevas-Velazquez Cesar L , Vellosillo Tamara , Guadalupe Karina , Schmidt H Broder , Yu Feng , Moses David , Brophy Jennifer AN , Cosio-Acosta Dante , Das Alakananda , Wang Lingxin , Jones Alexander M , Covarrubias Alejandra A , Sukenik Shahar , Dinneny José R 
Published: February 2021

SUMMARYCell homeostasis is perturbed when dramatic shifts in the external environment cause the physical-chemical properties inside the cell to change. Methods that dynamically monitor these intracellular effects are currently lacking. Here, we leveraged the environmental sensitivity and structural plasticity of intrinsically disordered regions (IDRs) to develop a FRET biosensor capable of monitoring rapid intracellular changes caused by osmotic stress. The biosensor, named SED1, utilizes the Arabidopsis intrinsically disordered AtLEA4-5 protein expressed in plants under water deficit. Computational modeling andin vitrostudies reveal that SED1 is highly sensitive to macromolecular crowding. SED1 exhibits large and near-linear osmolarity-dependent changes in FRET inside living bacteria, yeast, plant, and human cells, demonstrating the broad utility of this tool for studying water-associated stress. This study demonstrates the remarkable ability of IDRs to sense the cellular environment across the tree of life and provides a blueprint for their use in environmentally-responsive molecular tools.
Compression for population genetic data through finite-state entropy
Authors: Chen Winfield , Elliott Lloyd T. 
Published: February 2021

AbstractWe improve the efficiency of population genetic file formats and GWAS computation by leveraging the distribution of sample ordering in population-level genetic data. We identify conditional exchangeability of these data, recommending finite state entropy algorithms as an arithmetic code naturally suited to population genetic data. We show between 10% and 40% speed and size improvements over dictionary compression methods for population genetic data such asZstdandZlibin computation and and decompression tasks. We provide a prototype for genome-wide association study with finite state entropy compression demonstrating significant space saving and speed comparable to the state-of-the-art.
Phospholipid membrane formation templated by coacervate droplets
Authors: Cakmak Fatma Pir , Marianelli Allyson M. , Keating Christine D. 
Published: February 2021

AbstractWe report formation of coacervate-supported phospholipid membranes by hydrating a dried lipid film in the presence of coacervate droplets. In contrast to traditional giant lipid vesicles formed by gentle hydration in the absence of coacervates, the coacervate-templated membrane vesicles are more uniform in size, shape, and apparent lamellarity. Due to their fully-coacervate model cytoplasm, these simple artificial cells are macromolecularly crowded and can be easily pre-loaded with high concentrations of proteins or nucleic acids. Coacervate-supported membranes were characterized by fluorescence imaging, polarization, fluorescence recovery after photobleaching of labeled lipids, lipid quenching experiments, and solute uptake experiments. Our findings are consistent with the presence of lipid membranes around the coacervates, with many droplets fully coated with what appear to be continuous lipid bilayers. Within the same population, other coacervate droplets are coated with membranes having defects or pores that permit solute entry, and still others are coated with multilayered membranes. These membranes surrounding protein-based coacervate droplets provided protection from a protease added to the external solution. The simplicity of producing artificial cells having a coacervate model cytoplasm surrounded by a model membrane is at the same time interesting as a potential mechanism for prebiotic protocell formation and appealing for biotechnology. We anticipate that such structures could serve as a new type of model system for understanding interactions between intracellular phases and cell- or organelle membranes, which are implicated in a growing number of processes ranging from neurotransmission to signaling.
Third Backcross Generation Indonesian Indigenous ChickenKampongBroiler-Type (Kambro)SOX5Gene Polymorphism
Authors: Ardo T , Perdamaian A. B. I. , Mahardhika I. W. S. , Daryono B S 
Published: February 2021

AbstractThe comb is an accessory organ on the head of chicken which is influenced by testosterone hormone and can be used as an indicator of chicken’s fertility. Comb shape is related to climate adaptation and associated with a dominant mutation in chicken chromosome 1. Therefore this research was aimed to study the association betweenPea-combshape andSOX5gene polymorphism in the population of progenies (BC-IIIKambro) derived from a crossbreed between femalesPelungand males second backcross generationKampongBroiler-Type (BC-IIKambro). Chicken(Gallus gallus) SOX5gene was acquired from NCBI GenBank with the Ref. Seq.418195. Primers used to amplify theSOX5gene are(F):5’-AGGTAGCCATGGTGACAAGC-3’,(R):5’-GATCTGTGAGGCAGCCAGTT-3’. Progenies showed 100%Pea-combshape, while parental generation composed ofPea-combshape andSingle-combshape. PCR-RFLP and endonuclease restriction enzymeHindIIIwere unable to determine the genotype of the female parent withPea-comb. The result ofSOX5gene polymorphism showed the comb shape uniformity between progenies and parental ofKambrobackcross generation. This study concluded that the genotype ofPea-combshape femalePelungwas undetermined and there was no polymorphism of theSOX5gene between pea and single comb. PCR-RFLP using endonuclease restriction enzymeHindIIIproduced both target products and non-target/artifact products. The sequencing procedure was required to provide nucleotide sequences.
Biological and Transcriptomic Characterization of Pre-haustorial Resistance to Sunflower Broomrape (Orobanche cumanaW.)
Authors: Sisou Dana , Tadmor Yaakov , Plakhine Dina , Hübner Sariel , Eizenberg Hanan 
Published: February 2021

AbstractInfestations with sunflower broomrape (Orobanche cumanaWallr.), an obligatory root parasite, constitute a major limitation to sunflower production in many regions around the world. Breeding for resistance is the most effective approach to reduce sunflower broomrape infestation, yet resistance mechanisms are often overcome by new races of the pathogen. Elucidating the mechanisms controlling the resistance to broomrape at the molecular level is thus the most desirable pathway to obtaining long-lasting resistance and reducing yield loss in sunflower. In this study, we investigated broomrape resistance in a confectionery sunflower hybrid with a robust and long-lasting resistance to sunflower broomrape. Visual screening and histological examination of sunflower roots revealed that penetration of the intrusive broomrape cells into the host root endodermis is blocked at the host cortex, indicating a pre-haustorial mechanism of resistance. A comparative RNA-Seq experiment conducted between roots obtained from the resistant cultivar, a bulk of five broomrape resistant lines and a bulk of five broomrape susceptible lines allowed the identification of genes that were significantly differentially expressed upon broomrape infestation. Among these differentially expressed genes, β-1,3-endoglucanase, β-glucanase and ethylene-responsive transcription factor4 (ERF4) genes were identified. These genes were previously reported to be pathogenesis-related genes in other plant species. This genetics investigation together with the histological examinations led us to conclude that the resistance mechanism involves the identification of the broomrape and the consequent formation of a physical barrier that prevents the penetration of the broomrape into the sunflower roots.
Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses
Authors: Mahar Jackie E , Jenckel Maria , Huang Nina , Smertina Elena , Holmes Edward C , Strive Tanja , Hall Robyn N 
Published: February 2021

AbstractThe diversity of lagoviruses (Caliciviridae) in Australia has increased considerably. By the end of 2017, five variants from three viral genotypes were present in populations of Australian rabbits, while prior to 2014 only two variants were known. To understand the interactions between these lagovirus variants we monitored their geographical distribution and relative incidence over time through a landscape-scale competition study, and from this, revealed potential drivers of epidemiological fitness. Within three years of the arrival of GI.1bP-GI.2 (RHDV2) into Australia, we observed the emergence of two novel recombinant lagovirus variants, GI.4eP-GI.2 (4e-recombinant) in New South Wales and GI.4cP-GI.2 (4c-recombinant) in Victoria. Although both novel recombinants contain the non-structural genes from benign, rabbit-specific, enterotropic viruses, these variants were recovered from the livers of both rabbits and hares that had died acutely. This suggests that determinants of host and tissue tropism for lagoviruses are associated with the structural genes, and that tropism is intricately connected with pathogenicity. Phylogenetic analyses demonstrated that the 4c-recombinant emerged independently on multiple occasions, with five distinct lineages observed. Both new recombinant variants replaced the previous dominant parental RHDV2 in their respective geographical areas, despite sharing an identical or near-identical (i.e., single amino acid change) major capsid protein with the parental virus. This suggests that epidemiological fitness of these recombinants was not driven by antigenic variation in the capsid, implicating the non-structural genes as key drivers of epidemiological fitness. Molecular clock estimates place the GI4.e recombination event in early to mid-2015, while the five GI.4c recombination events occurred from late 2015 through to early 2017. The emergence of at least six viable recombinant variants within a two-year period highlights an unprecedented frequency of these events, detectable only due to intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.