bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcutaneous electrical nerve stimulation modulates corticospinal excitability while preserving motor unit discharge properties during isometric contractions
Authors: Hernandez-Pavon Julio Cesar , Avrillon Simon , Hoo Grace , Pons Jose L. 
Published: March 2022

ABSTRACTAimTranscutaneous electrical nerve stimulation (TENS) aims to supplement sensory feedback to improve force steadiness or motor function. In this study, we directly assessed potential changes in corticospinal excitability and motor unit discharge characteristics from the first dorsal interosseous (FDI) muscle due to TENS by using transcranial magnetic stimulation (TMS) and high-density surface electromyography (HDsEMG).MethodsEleven healthy young adults performed a series of submaximal isometric index abductions. We estimated i) motor evoked potential (MEP) amplitudes, ii) persistent inward current amplitudes (PIC, i.e., delta F), iii) motor unit recruitment thresholds and discharge rates, and iv) common synaptic input to motor units before and after TENS.ResultsTENS did not affect force steadiness (2.5 ± 0.9% and 3.3 ± 1.9% (p = 0.010)). MEP amplitudes decreased at 110% of the resting motor threshold (rMT; 0.72 ± 0.66 mV vs. 0.59 ± 0.63 mV; p < 0.001), increased at 130% rMT (1.18 ± 1.10 mV vs. 1.41 ± 1.29 mV; p < 0.001). Delta F increased after TENS (3.7 ± 2.2 pps vs. 4.5 ± 2.6 pps; p = 0.010). We did not find a change in the level of common synaptic input or in the temporal variability of motor unit discharge rates after the session of TENS.ConclusionThese results suggest that TENS can modulate corticospinal excitability through supraspinal and spinal processes and, thus act as a priming technique. At the same time, TENS does not generate short-term changes in the neural control of force in young, healthy adults.
Impact of dominance rank specification in dyadic interaction models
Authors: Mielke Alexander 
Published: March 2022

AbstractDominance rank is a vital descriptor of social dynamics in animal societies and regularly used in studies to explain observed interaction patterns. However, researchers can choose between different indices and standardizations, and can specify dyadic rank relations differently when studying interaction distributions. These researcher degrees of freedom potentially introduce biases into studies and reduce replicability. Here, I demonstrate the impact of researcher choices by comparing the performance of different combinations of rank index, standardization, and model specification when explaining dyadic interaction patterns in sooty mangabeys (Cercocebus atys atys). I show that while no combination consistently performed best across interaction types (aggression, grooming, proximity, supplants), model specifications allowing for non-linear patterns performed better than other models on average. Choices made in pre-processing and model building impacted model performance and subsequent interpretation of results. Researchers could end up describing social systems differently based on the same data. These results highlight the impact of researcher choices in the processing of behavioural data and potential limitations when using indirect species comparisons in animal behaviour research. To increase repeatability, researchers could make the impact of their processing choices more transparent and report results using a variety of indices and model specifications.
New distribution data and phylogenetic approach reveal bioregionalization of the western Palearctic ants
Authors: Wang Runxi , Kass Jamie M. , Galkowski Christophe , Garcia Federico , Hamer Matthew T. , Radchenko Alexander , Salata Sebastian , Schifani Enrico , Yusupov Zalimkhan M. , Economo Evan P. , Guénard Benoit 
Published: March 2022

ABSTRACTAimBiogeographic regionalization has fascinated biogeographers and ecologists for centuries and is endued with new vitality by evolutionary perspectives. However, progress is scant for most insect groups due to shortfalls in distribution and phylogenetic information, namely Wallacean and Darwinian shortfalls respectively. Here, we used the western Palearctic ants as the case to tackle these shortfalls and test their biogeographic structure through novel distribution data and phylogenetic approaches.LocationWestern Palearctic realm.TaxonAnts (Formicidae).MethodsFirstly, we developed a refined database integrating the occurrences of 747 ant species across 207 regions of the western Palearctic realm, based on newly expert-validated records derived from the existing global ant biodiversity informatics. Using range estimates for these species derived from polygons and species distribution modelling, we produced species assemblages in 50 × 50 km grid cells. We calculated taxonomic and phylogenetic turnover of ant assemblages, performing hierarchical clustering analysis using the Simpson dissimilarity index to delineate biogeographic structure.ResultsAt both the regional list- and grid assemblage-levels, the Mediterranean has higher turnover and more biogeographic regions than northern Europe, both taxonomically and phylogenetically. Delineations based on grid assemblages detected more detailed biogeographic transitions, while those based on regional lists showed stronger insularity in biogeographic structure. The phylogenetic regionalization suggested closer but varied affinities between assemblages in comparison to the taxonomic approach.Main conclusionsHere, we integrated expert-validated regional lists, species distribution modelling, and a recent phylogeny to tackle Wallacean and Darwinian shortfalls for an important insect group by developing a next-generation map of biogeographic regionalization for the western Palearctic ants. The results of this study suggest strong constraints from geographic barriers and potential effects of climatic history on ant distributions and evolutionary history, and also provide baseline spatial information for future investigations of regional insect distributions.
Ecdysone signaling controls early embryogenesis in the short-germ hemimetabolous insect Blattella germanica
Authors: Cruz Josefa , Maestro Oscar , Franch-Marro Xavier , Martín David 
Published: March 2022

SummarySteroid hormone signaling is a central regulator of insect development especially during the post-embryonic period. However, its role during embryonic development is less understood, particularly in short-germ band hemimetabolous insects. Here, we used the short-germ band hemimetabolous insect Blattella germanica to analyse the functions of 20-hydroxyecdysone (20E), the most active insect steroid, signaling during the embryonic stage. We show that the heterodimeric 20E receptor, BgEcR-A and BgRXR, is present from the beginning of embryogenesis and that a stereotypical 20E-dependent cascade of nuclear receptors is first detected at the early blastoderm stage. Using parental RNAi, we show that both receptors are required for the proper formation of the germ band by controlling cell proliferation during the blastoderm stage. In addition, they are also required for the coordinated induction of the 20E-induced cascade of nuclear receptors. Finally, we show that two of these nuclear receptors, BgHR3 and BgFTZ-F1, have relevant roles in germ band formation. Whereas BgHR3 controls the formation and development of the cephalic region of the germ band, BgFTZ-F1 stripped expression suggested a role in the segmentation of the germ band. In summary, our results show that 20E-signaling is required much earlier in short-germ band hemimetabolous than in long-germ band holometabolous embryogenesis, which raises the possibility that the loss of 20E-signaling during the initial stages of embryogenesis could be a key feature in the evolution of the different types of insect development.
Dynamic evolution of recently duplicated genes in Caenorhabditis elegans
Authors: Ma Fuqiang , Lau Chun Yin , Zheng Chaogu 
Published: March 2022

AbstractAs a major origin of evolutionary novelties, gene duplication is a widespread phenomenon across species. However, the evolutionary force that determines the fate of duplicate genes is still under debate. Here, we studied the functional evolution of duplicate genes at both macroevolution and microevolution scales using the genomic sequences of eleven Caenorhabditis species and 773 C. elegans wild isolates. We found that compared to older duplicate genes and single-copy genes, recently duplicated gene copies showed rapid turnover, large genetic diversity, and signs of balancing and positive selection within the species. Young duplicate genes have low basal expression restricted to a few tissues but show highly responsive expression towards pathogenic infections. Recently duplicated genes are enriched in chemosensory perception, protein degradation, and innate immunity, implicating their functions in enhancing adaptability to external perturbations. Importantly, we found that young duplicate genes are rarely essential, while old duplicate genes have the same level of essentiality as singletons, suggesting that essentiality develops over a long time. Together, our work in C. elegans demonstrates that natural selection shapes the dynamic evolutionary trajectory of duplicate genes.SignificanceThe “evolution by gene duplication” theory suggests that gene duplications provide the genetic materials for mutation and selection to act upon, expand the repertoire of molecular functions, and enable evolutionary novelty. Although various models were proposed to describe the fate of duplicate genes, empirical evidence for these models is limited. We analyzed gene duplications in eleven nematode Caenorhabditis species and studied the intraspecific variation of these duplicate genes among C. elegans wild strains. We found that compared to older duplicate gens and single-copy genes, recently duplicated genes show rapid turnover, large genetic diversity, and strong signs of balancing and positive selection but rarely develop essential functions. Our results describe the evolutionary trajectory of duplicate genes shaped by natural selection.
Purinergic P2X7 Receptor-mediated inflammation precedes PTSD-related Behaviors in Rats
Authors: Torres-Rodriguez Orlando , Rivera-Escobales Yesenia , Velazquez Bethzaly , Colón María , Porter James T. 
Published: March 2022

AbstractClinical evidence has linked increased peripheral pro-inflammatory cytokines with post-traumatic stress disorder (PTSD) symptoms. However, whether inflammation contributes to or is a consequence of PTSD is still unclear. Previous research shows that stress can activate P2X7 receptors (P2X7Rs) on microglia to induce inflammation and behavioral changes. In this investigation, we examined whether P2X7Rs contribute to the development of PTSD-like behaviors induced by single prolonged stress (SPS) exposure in rats. Consistent with the literature, exposing adult male and female rats to SPS produced a PTSD-like phenotype of impaired fear extinction and increased anxiety-like behavior one week after exposure. In addition, SPS-exposed animals had more Iba1-positive microglia expressing the P2X7R in the ventral hippocampus, a structure that regulates fear extinction and anxiety-like behavior. Next, we examined if inflammation precedes the behavioral manifestations. Three days after SPS exposure, increased inflammatory cytokines were found in the blood and hippocampal microglia showed increased expression of the P2X7R, IL-1β, and TNF-α, suggesting increased peripheral and central inflammation before behavioral testing. To determine whether P2X7Rs contribute to the PTSD-related behaviors induced by SPS exposure, we gave ICV infusions of the P2X7R antagonist, A-438079, for one week starting the day of SPS exposure. Blocking P2X7Rs prevented the SPS-induced impaired fear extinction and increased anxiety-like behaviors in male and female rats, suggesting that SPS activates P2X7Rs which increase inflammation to produce a PTSD-like phenotype.
Towards unsupervised classification of macromolecular complexes in cryo electron tomography: challenges and opportunities
Authors: Moebel E. , Kervrann C. 
Published: March 2022

AbstractBackground and ObjectivesCryo electron tomography visualizes native cells at nanometer resolution, but analysis is challenged by noise and artifacts. Recently, supervised deep learning methods have been applied to decipher the 3D spatial distribution of macromolecules. However, in order to discover unknown objects, unsupervised classification techniques are necessary. In this paper, we provide an overview of unsupervised deep learning techniques, discuss the challenges to analyze cryo-ET data, and provide a proof-of-concept on real data.MethodsWe propose an unsupervised sub-tomogram classification method based on transfer learning. We use a deep neural network to learn a clustering friendly representation able to capture 3D shapes in the presence of noise and artifacts. This representation is learned here from a synthetic data set.ResultsWe show that when applying k-means clustering given a learning-based representation, it becomes possible to satisfyingly classify real sub-tomograms according to structural similarity. It is worth noting that no manual annotation is used for performing classification.ConclusionsWe describe the advantages and limitations of our proof-of-concept and raise several perspectives for improving classification performance.
Improving an rRNA depletion protocol with statistical design of experiments
Authors: David Benjamin M. , Jensen Paul A. 
Published: March 2022

AbstractrRNA depletion is the most expensive step in prokaryotic RNA-seq library preparation. rRNA is so abundant that small increases in depletion efficiency lead to large changes in mRNA sequencing coverage. A variety of commercial and home-made methods exist to lower the cost or increase the efficiency of rRNA removal. Many of these techniques are suboptimal when applied to new species of bacteria or when the protocol or reagents need to be changed. Re-optimizing a protocol by trial-and-error is an expensive and laborious process. Systematic frameworks like the statistical design of experiments (DOE) can improve processes by exploring the quantitative relationship between multiple factors. DOE allows experimenters to find factor interactions that may not be apparent when factors are studied in isolation.We used DOE to optimize an rRNA depletion protocol by updating reagents and identifying factors that maximize rRNA removal and minimize cost. The optimized protocol more efficiently removes rRNA, uses fewer reagents, and is less expensive than the original protocol. Our optimization required only 17 experiments and identified two significant interactions among three factors. Overall, our approach demonstrates the utility of a rational, DOE framework for improving complex protocols.
Variation in cytonuclear expression accommodation among allopolyploid plants
Authors: Grover Corrinne E. , Forsythe Evan S. , Sharbrough Joel , Miller Emma R. , Conover Justin L. , DeTar Rachael A. , Chavarro Carolina , Arick Mark A. , Peterson Daniel G. , Leal-Bertioli Soraya C.M. , Sloan Daniel B. , Wendel Jonathan F. 
Published: March 2022

AbstractCytonuclear coevolution is a common feature among plants, which coordinates gene expression and protein products between the nucleus and organelles. Consequently, lineage-specific differences may result in incompatibilities between the nucleus and cytoplasm in hybrid taxa. Allopolyploidy is also a common phenomenon in plant evolution. The hybrid nature of allopolyploids may result in cytonuclear incompatibilities, but the massive nuclear redundancy created during polyploidy affords additional avenues for resolving cytonuclear conflict (i.e.,cytonuclear accommodation). Here we evaluate expression changes in organelle-targeted nuclear genes for six allopolyploid lineages that represent four genera (i.e., Arabidopsis, Arachis, Chenopodium, andGossypium) and encompass a range in polyploid ages. Because incompatibilities between the nucleus and cytoplasm could potentially result in biases toward the maternal homoeolog and/or maternal expression level, we evaluate patterns of homoeolog usage, expression bias, and expression level dominance in cytonuclear genes relative to the background of non-cytonuclear expression changes and to the diploid parents. Although we find subsets of cytonuclear genes in most lineages that match our expectations of maternal preference, these observations are not consistent among either allopolyploids or categories of organelle-targeted genes. Our results indicate that cytonuclear expression accommodation may be a subtle and/or variable phenomenon that does not capture the full range of mechanisms by which allopolyploid plants resolve nuclear-cytoplasmic incompatibilities.
Candidatus Liberibacter asiaticus reduces callose and reactive oxygen species production in the phloem
Authors: Bernardini Chiara , Turner Donielle , Wang Chunxia , Welker Stacy , Achor Diann , Artiga Yosvanis Acanda , Turgeon Robert , Levy Amit 
Published: March 2022

AbstractHuanglongbing (HLB) causes significant economic loss in citrus production worldwide. HLB is caused by Candidatus Liberibacter asiaticus (CLas), a gram-negative bacterium which inhabits the phloem exclusively. CLas infection results in accumulation of callose and reactive oxygen species in the phloem of infected plants, but little is known about the specific processes that take place during infection because of the sparse distribution of bacteria and the inaccessibility of the phloem inside the tree. In this study, we used the seed vasculatures, which accumulate a high number of CLas, as a model tissue to study CLas-host cellular interactions. In vasculature where CLas is abundant, sieve pore callose and H2O2 concentration were reduced compared to healthy seed vasculature. The expression of callose synthases (CalS) and respiratory burst oxidase homolog (RBOH) genes were downregulated in infected seeds compared to healthy ones. In leaves of HLB-infected plants, H2O2 concentration and CalS expression increased compared to uninfected leaves, but cells with CLas had lower levels of sieve plate callose compared to cells without CLas. Our results provide evidence that the bacteria manipulate cell metabolism to disable plant defenses and suggests that HLB disease is the result of a constant arms-race between the pathogen and a defense response, which is ultimately harmful to the host plant.
The GHB analogue HOCPCA improves sensorimotor function after MCAO via CaMKIIα
Authors: Griem-Krey Nane , Klein Anders B , Clausen Bettina H , Namini Mathias RJ , Nielsen Pernille V , Cheng Heung-Chin , Orset Cyrille , Vivien Denis , Clarkson Andrew N , Lambertsen Kate L , Wellendorph Petrine 
Published: March 2022

AbstractCa2+/calmodulin-dependent protein kinase II alpha (CaMKIIα) is a major contributor to physiological and pathological glutamate-mediated Ca2+signals, and its involvement in various critical cellular pathways demands specific pharmacological strategies. We recently presented GHB ligands as the first small molecules selectively targeting the CaMKIIα hub, a domain primarily responsible for holoenzyme oligomerisation, with an emerging functional role. Here, we report that the GHB ligand, HOCPCA, improves sensorimotor function after experimental stroke in mice when administered at clinically relevant time and in combination with alteplase. We observed that hub modulation by HOCPCA results in differential effects on distinct CaMKII pools, ultimately alleviating aberrant CaMKII signalling after cerebral ischemia. As such, HOCPCA normalised cytosolic Thr286 autophosphorylation after ischemia in mice and downregulated the ischemia-specific expression of a constitutively active CaMKII kinase fragment. Previous studies suggest holoenzyme stabilisation as a potential mechanism, yet a causal link toin vivofindings requires further studies. HOCPCA’s selectivity and absence of effects on physiological CaMKII signalling highlight pharmacological modulation of the CaMKIIα hub domain as an attractive neuroprotective strategy.
Snaq: A Dynamic Snakemake Pipeline for Microbiome data analysis with QIIME2
Authors: Mohsen Attayeb , Chen Yi-An , Allendes Osorio Rodolfo S. , Higuchi Chihiro , Mizuguchi Kenji 
Published: March 2022

AbstractOptimizing a protocol for 16S microbiome data analysis with QIIME2 is a challenging task for biologists with no programming experience. It involves a multi-step process, and multiple parameters and options that need to be tested and determined. In this article, we describe Snaq, a snakemake pipeline that helps automate and optimize 16S data analysis using QIIME2. Snaq offers an informative file naming system and automatically performs the analysis of a data set by downloading and installing the required databases and classifiers, all through a single command-line instruction. It works natively on Linux and Mac and on Windows through the use of containers, and is potentially extendable by adding new rules. This pipeline will substantially reduce the efforts in sending commands and prevent the confusion caused by the accumulation of analysis results due to testing multiple parameters.
The impact of introduction of the 10-valent pneumococcal conjugate vaccine (PCV10) on pneumococcal carriage in Nigeria
Authors: Adamu Aishatu L , Ojal J. , Abubakar Isa A. , Odeyemi Kofo , Bello Musa M. , Okoromah Christy A.N. , Karia Boniface , Karani Angela , Akech Donald. , Inem Victor , Scott J. Anthony G , Adetifa Ifedayo M.O. 
Published: March 2022

AbstractBackgroundPneumococcal Conjugate Vaccines (PCVs) reduce the burden of pneumococcal disease by reducing nasopharyngeal acquisition and transmission of serotypes in the vaccines (vaccine-serotypes). Following introduction of the 10-valent PCV (PCV10) in Nigeria, we assessed the population-level impact of PCV introduction on pneumococcal carriage.MethodsWe conducted annual cross-sectional carriage and vaccination coverage surveys between 2016 and 2020 in rural and urban sites in Nigeria. We recruited a random sample of residents and used WHO-recommended laboratory methods to identify pneumococcal serotypes. We modelled prevalence ratios for the change in annual carriage prevalence using log-binomial regression, and explored the association between vaccination coverage in children <5 years and changes in the population-level vaccine-serotype carriage.FindingsWe enrolled 4,684 and 3,653 participants for the carriage surveys and 2,135 and 1,106 children for the coverage surveys in the rural and urban sites, respectively. Carriage prevalence of vaccine-serotypes declined steadily with increasing levels of PCV10 coverage among children aged <5 years. From 2016 to 2020, coverage with three doses of PCV10 increased from 7% to 59% and from 15% to 81% in the rural and urban sites, respectively. Prevalence ratios for the annual change in vaccine-serotype carriage in participants aged <5 years and ≥5 years were 0.84 (95% CI:0.79-0.89) and 0.86 (95%CI:0.80-0.89) in the rural, and 0.69 (95% CI:0.62-0.77), and 0.83 (95% CI:0.74-0.93) in the urban sites.ConclusionsWe found significant reduction in vaccine-serotype carriage at a population level following a steady increase in PCV10 coverage, indicating direct and indirect vaccine effects.