bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of time-varying causal effects with multivariable Mendelian randomization: some cautionary notes
Authors: Tian Haodong , Burgess Stephen 
Published: March 2022

AbstractIntroductionFor many exposures present across the lifecourse, the effect of the exposure may vary over time. Multivariable Mendelian randomization (MVMR) is an approach that can assess the effects of related risk factors using genetic variants as instrumental variables. Recently, multivariable Mendelian randomization has been used to estimate the effects of an exposure during distinct time periods.MethodsWe investigated the behaviour of estimates from MVMR in a simulation study for different time-varying causal scenarios. We also performed an applied analysis to consider how MVMR estimates of body mass index on systolic blood pressure vary depending on the time periods considered.ResultsEstimates from MVMR in the simulation study were close to the true values when the outcome model was correctly specified: that is, when the outcome was a discrete function of the exposure at the precise timepoints at which the exposure was measured. However, in more realistic cases, MVMR estimates were not only incorrect, but misleading. For example, in one scenario MVMR estimates for early life were clearly negative despite the true causal effect being constant and positive. In the applied example, estimates were highly variable depending on the time period in which genetic associations with the exposure were estimated.ConclusionsThe poor performance of MVMR to study time-varying causal effects can be attributed to model misspecification and violation of the exclusion restriction assumption. We would urge caution about quantitative conclusions from such analyses and even qualitative interpretations about the direction, or presence or absence of a causal effect during a given time period.
Humoral and cellular immune responses to CoronaVac assessed up to one year after vaccination
Authors: Costa Priscilla Ramos , Correia Carolina Argondizo , Marmorato Mariana Prado , Dias Juliana Zanatta de Carvalho , Thomazella Mateus Vailant , da Silva Amanda Cabral , Oliveira Ana Carolina Soares de , Gusmão Arianne Fagotti , Ferrari Lilian , Freitas Angela Carvalho , Patiño Elizabeth González , Grifoni Alba , Weiskopf Daniela , Sette Alessandro , Scharf Rami , Kallas Esper Georges , Silveira Cássia Gisele Terrassani 
Published: March 2022

AbstractBackgroundThe Sinovac SARS-CoV-2 inactivated vaccine (CoronaVac) has been demonstrated to be safe, well tolerated, and efficacious in preventing mild and severe Covid-19. Although different studies have demonstrated its short-term immunogenicity, long-term cellular and humoral response evaluations are still lacking.MethodsCellular and humoral responses were assessed after enrollment of volunteers in the PROFISCOV phase 3 double-blind, randomized, placebo-controlled clinical trial to evaluate CoronaVac. Assays were performed using flow cytometry to evaluate cellular immune response and an antigen binding electrochemiluminescence assay to detect antigen-specific antibodies to the virus.ResultsFifty-three volunteers were selected for long term assessment of their SARS-CoV-2-specific immune responses. CD4+ T cell responses (including circulating follicular helper (cTfh, CD45RA- CXCR5+) expressing CD40L, as well as non-cTfh cells expressing CXCR3) were observed early upon the first vaccine dose, increased after the second dose, remaining stable for 6-months. Memory CD4+ T cells were detected in almost all vaccinees, the majority being central memory T cells. IgG levels against Wuhan/WH04/2020 N, S and receptor binding domain (RBD) antigens and the variants of concern (VOCs, including B.1.1.7/Alpha, B.1.351/Beta and P.1/Gamma) S and RBD antigens peaked 14 days after the second vaccine shot, and were mostly stable for a 1-year period.ConclusionsCoronaVac two-doses regimen is able to induce a potent and durable SARS-CoV-2 specific cellular response. The cellular reaction is part of a coordinated immune response that includes high levels of specific IgG levels against parental and SARS-CoV-2 VOC strains, still detected after one year.FundingFundação Butantan, Instituto Butantan and São Paulo Research Foundation (FAPESP) (grants 2020/10127-1 and 2020/06409-1). This work has also been supported by NIH contract 75N93019C00065 (A.S, D.W). PATH facilitated reagent donations for this work with support by the Bill & Melinda Gates Foundation (INV-021239). Under the grant conditions of the foundation, a Creative Commons Attribution 4.0 generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission.
Saturated reconstruction of living brain tissue
Authors: Velicky Philipp , Miguel Eder , Michalska Julia M. , Wei Donglai , Lin Zudi , Watson Jake F. , Troidl Jakob , Beyer Johanna , Ben-Simon Yoav , Sommer Christoph , Jahr Wiebke , Cenameri Alban , Broichhagen Johannes , Grant Seth G. N. , Jonas Peter , Novarino Gaia , Pfister Hanspeter , Bickel Bernd , Danzl Johann G. 
Published: March 2022

AbstractComplex wiring between neurons underlies the information-processing network enabling all brain functions, including cognition and memory. For understanding how the network is structured, processes information, and changes over time, comprehensive visualization of the architecture of living brain tissue with its cellular and molecular components would open up major opportunities. However, electron microscopy (EM) provides nanometre-scale resolution required for full in-silico reconstruction1–5, yet is limited to fixed specimens and static representations. Light microscopy allows live observation, with super-resolution approaches6–12 facilitating nanoscale visualization, but comprehensive 3D-reconstruction of living brain tissue has been hindered by tissue photo-burden, photobleaching, insufficient 3D-resolution, and inadequate signal-to-noise ratio (SNR). Here we demonstrate saturated reconstruction of living brain tissue. We developed an integrated imaging and analysis technology, adapting stimulated emission depletion (STED) microscopy6,13 in extracellularly labelled tissue14 for high SNR and near-isotropic resolution. Centrally, a two-stage deep-learning approach leveraged previously obtained information on sample structure to drastically reduce photo-burden and enable automated volumetric reconstruction down to single synapse level. Live reconstruction provides unbiased analysis of tissue architecture across time in relation to functional activity and targeted activation, and contextual understanding of molecular labelling. This adoptable technology will facilitate novel insights into the dynamic functional architecture of living brain tissue.
Sst+ GPi output neurons provide direct feedback to key nodes of the basal ganglia and drive behavioral flexibility
Authors: Weglage M. , Ährlund-Richter S. , Fuzik J. , Skara V. , Lazaridis I. , Meletis K. 
Published: March 2022

AbstractThe GPi-LHb pathway is the main output of the basal ganglia suggested to shape motivated behaviors. We show here that Sst+ GPi-LHb neurons send direct feedback to key nodes of the basal ganglia: the GPe, the striatal striosomes, and dopamine neurons in the SNc. Chronic silencing of this pathway did not affect learning or execution of value-guided choices, but severely disrupted the ability to adapt choice-behavior and seek an alternative reward location after task reversal. Calcium imaging revealed that Sst+ GPi neurons did not signal outcome value or value updates during reversal learning. Instead, progressive suppression of the Sst+ GPi activity was linked to increased commitment to one choice, and activity increased during exploration of alternative choices. We propose that GPi Sst+ neurons drive behavioral flexibility through a direct feedback signal to balance the activity of key nodes in the basal ganglia.
Microglial P2Y12 mediates chronic stress-induced synapse loss in the prefrontal cortex and associated behavioral consequences in male mice
Authors: Bollinger J.L. , Dadosky D.T. , Flurer J.K. , Rainer I.L. , Woodburn S.C. , Wohleb E.S. 
Published: March 2022

AbstractRecent studies demonstrate that chronic unpredictable stress (CUS) drives microglia-mediated neuronal remodeling, contributing to synapse loss in the prefrontal cortex (PFC) and cognitive-behavioral dysfunction. Nonetheless, it remains unclear what mechanisms guide microglia-neuron interactions in stress. Evidence indicates that neuronal activity-dependent purinergic signaling directs microglial processes and microglia-synapse interaction via P2Y12, a purinergic receptor exclusively expressed by microglia in the brain. Stress exposure alters excitatory neurotransmission in the PFC, thus we aimed to determine if P2Y12 signaling promotes functional changes in microglia in the context of chronic stress. Using an activating DREADD, our initial studies showed that PFC microglia adopt a CUS-associated phenotype after repeated pyramidal neuronal activation. To further investigate the role of purinergic signaling, we used genetic (P2ry12-/-) or pharmacological (clopidogrel, ticagrelor) approaches to block P2Y12 in the context of CUS. Various behavioral, physiological, and cytometric endpoints were analyzed. Both P2Y12-deletion and treatment with clopidogrel prevented increases in forced swim test immobility and attenuated deficits in temporal object recognition following CUS. Flow cytometry of PFC microglia revealed that both P2ry12-/- mice and those treated with clopidogrel have significantly different phenotypes (independent of CUS); with diminished P2Y12 expression and altered surface levels of CX3CR1, CSF1R, and CD11b. Immunohistology in Thy1-GFP(M) mice demonstrated that pharmacological blockade of P2Y12 prevented stress-induced increases in the proportion of microglia with GFP+ neuronal inclusions and limited dendritic spine loss in the PFC. Together, these findings indicate that microglial P2Y12 is a critical mediator of stress-induced neuronal remodeling in the PFC and subsequent behavioral deficits.
Estimating consensus proteomes and metabolic functions from taxonomic affiliations
Authors: Belcour Arnaud , Hamon-Giraud Pauline , Mataigne Alice , Ruiz Baptiste , Le Cunff Yann , Got Jeanne , Awhangbo Lorraine , Lebreton Mégane , Frioux Clémence , Dittami Simon , Dabert Patrick , Siegel Anne , Blanquart Samuel 
Published: March 2022

AbstractPurposeMetabarcoding, and metagenomic sequencing have enabled the characterization of highly diverse environmental communities. The challenge of estimating the metabolic functions carried out by these communities has led to the development of several state-of-the-art methods, most of which are tailored to a specific gene marker. However, the increasing diversity of approaches resulting from advances in sequencing technologies drives the need for methods capable of handling heterogeneous microbial community data. Moreover, predictions often depend on their internal analysis pipelines and are influenced by the underlying databases, which link marker genes to specific functional annotations. This limits users’ ability to evaluate the quality of predictions by tracing internal data and processes. Finally, users are constrained by the specific annotations provided by these methods (e.g. EC numbers), limiting their ability to conduct further specialized analyses based on intermediate results.MethodsEsMeCaTa predicts consensus proteomes and their associated functions from taxonomic affiliations. A key feature of EsMeCaTa is its explainability and flexibility. To support the flexible integration of heterogeneous sequencing data, EsMeCaTa utilizes taxonomic affiliations obtained through analyses of diverse sequencing datasets. To provide insight into the knowledge available for each taxonomic affliation and to interpret the relevance of predicted functions, EsMeCaTa identifies a taxonomic rank within a given affliation that is suffciently represented by documented proteomes in the UniProt database. The proteins of the UniProt proteomes are clustered and filtered according to a threshold to create consensus proteomes. These consensus proteomes are automatically annotated with functional information (e.g., EC numbers, GO terms) but they are also designed to be used in further customized annotation workflows. Functional annotations are reported in a functional table, which can be enriched with taxon abundances to generate comprehensive functional profiles.ResultsEsMeCaTa predictions have been validated using multiple datasets and compared to a state-of-the-art method. Additionally, it was applied to a novel metabarcoding dataset from a methanogenic reactor, characterizing the microbial community and biogas production across different time points and intake condition. Our results demonstrate the link between biogas production, intake condition and the dynamics of the metabolic functions predicted by EsMeCaTa in the microbial communities.
Tuning of motor outputs produced by spinal stimulation during voluntary control of torque directions in monkeys
Authors: Kaneshige Miki , Obara Kei , Suzuki Michiaki , Tazoe Toshiki , Nishimura Yukio 
Published: March 2022

AbstractSpinal stimulation is a promising method to restore motor function after impairment of descending pathways. While paresis, a weakness of voluntary movements driven by surviving descending pathways, can benefit from spinal stimulation, the effects of descending commands on motor outputs produced by spinal stimulation are unclear. Here, we show that descending commands amplify stimulus-evoked joint torque and the function of intraspinal elements. During the wrist torque tracking task, optimized currents of spinal stimulation over the cervical enlargement facilitated and/or suppressed activities of forelimb muscles. Magnitudes of these effects were dependent on directions of voluntarily-produced torque and positively correlated with levels of voluntary muscle activity. Furthermore, the directions of evoked wrist torque corresponded to the directions of voluntarily-produced torque. These results suggest that spinal stimulation is beneficial in cases of partial lesion of descending pathways by compensating for reduced descending commands through activation of excitatory and inhibitory synaptic connections to motoneurons.
Comparable theta phase coding dynamics along the transverse axis of CA1
Authors: Bishnoi Aditi , Deshmukh Sachin S. 
Published: March 2022

AbstractTopographical projection patterns from the entorhinal cortex to area CA1 of the hippocampus have led to a hypothesis that proximal CA1 (pCA1, closer to CA2) is spatially more selective than distal CA1 (dCA1, closer to the subiculum). While earlier studies have shown evidence supporting this hypothesis, we recently showed that this difference does not hold true under all experimental conditions. In a complex environment with distinct local texture cues on a circular track and global visual cues, pCA1 and dCA1 display comparable spatial selectivity. Correlated with the spatial selectivity differences, the earlier studies also showed differences in theta phase coding dynamics between pCA1 and dCA1 neurons. Here we show that there are no differences in theta phase coding dynamics between neurons in these two regions under the experimental conditions where pCA1 and dCA1 neurons are equally spatially selective. We also show that dCA1 local field potentials (LFPs) show higher power in theta range compared to pCA1 LFPs. These findings challenge the established notion of dCA1 being inherently less spatially selective and theta modulated than pCA1 and suggest that theta-mediated activation of the CA1 sub-networks to represent space is task-dependent.
Xanthomonas indicasp. nov., a non-pathogenic bacterium isolated from healthy rice(Oryza sativa)seeds from India
Authors: Rana Rekha , Madhavan Vishnu Narayanan , Saroha Tanu , Bansal Kanika , Kaur Amandeep , Sonti Ramesh V. , Patel Hitendra K. , Patil Prabhu B. 
Published: March 2022

AbstractTwo yellow pigmented bacterial strains were isolated from healthy rice seeds. The strains designated as PPL560Tand PPL568 were identified as members of genusXanthomonasbased on analysis of biochemical and 16S rRNA gene sequence retrieved from whole genome sequence. Isolates formed a distinct monophyletic lineage withX. sontiiandX. saccharias the closest relatives in the phylogenetic tree based on core gene content shared by reported species in genusXanthomonas. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridisation values calculated against other species ofXanthomonaswere below their respective cut-offs.In plantastudies revealed that PPL560Tand PPL568 are non-pathogenic to rice plants upon leaf clip inoculation. Absence of type III secretion system related genes and effectors further supported their non-pathogenic status. Herein, we proposeXanthomonas indicasp. nov. as novel species of genusXanthomonaswith PPL560T=MTCC13185 as its type strain and PPL568 as another constituent member.
A flexible and versatile system for multicolor fiber photometry and optogenetic manipulation
Authors: Formozov Andrey , Dieter Alexander , Wiegert J. Simon 
Published: March 2022

AbstractFiber photometry is a technique of growing popularity in neuroscientific research. It is widely used to infer brain activity by recording calcium dynamics in genetically defined populations of neurons. Aside from the wide variety of calcium indicators, other genetically encoded biosensors have recently been engineered to measure membrane potential, neurotransmitter release, pH, or various cellular metabolites, such as ATP or cAMP. Due to the spectral characteristics of these molecular tools, different assemblies of optical hardware are usually needed to reveal the full potential of different biosensors. In addition, the combination of multiple biosensors in one experiment often requires the investment in more complex equipment, which limits the flexibility of the experimental design. Such constraints often hamper a straightforward implementation of new molecular tools, evaluation of their performance in vivo, and design of new experimental paradigms - especially if the financial budget is a limiting factor. Here, we propose a novel approach for fiber photometry recordings, based on a multimode optical fused-fiber coupler (FFC) for both light delivery and collection. Recordings can readily be combined with optogenetic manipulations in a single device without the requirement for dichroic beam-splitters. In combination with a multi-color light source and appropriate emission filters, our approach offers remarkable flexibility in experimental design and facilitates the implication of new molecular tools in vivo at minimal cost. The ease of assembly, operation, characterization, and customization of this platform holds the potential to foster the development of experimental strategies for multicolor fused fiber photometry (FFP) combined with optogenetics far beyond its current state.Abstract FigureHighlightsFused Fiber Photometry (FFP) enables straightforward monitoring and manipulation of brain activityFFP allows monitoring of indicators with virtually any spectral characteristicsFFP is compatible with simultaneous optogenetic manipulationEasy assembly, characterization, and customization
Dual blockade of misfolded alpha-sarcoglycan degradation by bortezomib and givinostat combination
Authors: Hoch Lucile , Bourg Nathalie , Degrugillier Fanny , Bruge Céline , Benabides Manon , Pellier Emilie , Tournois Johana , Mahé Gurvan , Maignan Nicolas , Dawe Jack , Georges Maxime , Papazian David , Subramanian Nik , Simon Stéphanie , Fanen Pascale , Delevoye Cédric , Richard Isabelle , Nissan Xavier 
Published: March 2022

AbstractLimb-girdle muscular dystrophy type R3 (LGMD R3) is a rare genetic disorder characterized by a progressive proximal muscle weakness and caused by mutations in the SGCA gene encoding alpha-sarcoglycan (α-SG). Here, we report the results of a mechanistic screening ascertaining the molecular mechanisms involved in the degradation of the most prevalent misfolded R77C-α-SG protein. We performed a combinatorial study to identify drugs potentializing the effect of a low dose of the proteasome inhibitor bortezomib on the R77C-α-SG degradation inhibition. Analysis of the screening associated to artificial intelligence-based predictive ADMET characterization of the hits led to identification of the HDAC inhibitor givinostat as potential therapeutical candidate. Functional characterization revealed that givinostat effect was related to autophagic pathway inhibition, unveiling new theories concerning degradation pathways of misfolded SG proteins. Beyond the identification of a new therapeutic option for LGMD R3 patients, our results shed light on the potential repurposing of givinostat for the treatment of other genetic diseases sharing similar protein degradation defects such as LGMD R5 and cystic fibrosis.
Brain-wide screen of prelimbic cortex inputs reveals a functional shift during early fear memory consolidation
Authors: Dixsaut Lucie , Gräff Johannes 
Published: March 2022

AbstractMemory formation and storage rely on multiple interconnected brain areas, the contribution of which varies during memory consolidation. The medial prefrontal cortex, in particular the prelimbic cortex (PL), was traditionally found to be involved in remote memory storage, but recent evidence points towards its implication in early consolidation as well. Nevertheless, the inputs to the PL governing these dynamics remain unknown. Here, we first performed a brain-wide, rabies-based retrograde tracing screen of PL engram cells activated during contextual fear memory formation to identify relevant PL input regions. Next, we assessed the specific activity pattern of these inputs across different phases of memory consolidation, from fear memory encoding to recent and remote memory recall. Using projection-specific chemogenetic inhibition, we then tested their functional role in memory consolidation, which revealed a hitherto unknown contribution of claustrum to PL inputs at encoding, and of insular cortex to PL inputs at recent memory recall. Both of these inputs further impacted how PL engram cells were reactivated at memory recall, testifying to their relevance for establishing a memory trace in the PL. Collectively, this data identify a spatiotemporal shift in PL inputs important for early memory consolidation, and thereby help to refine the working model of memory formation.
Reproductive tradeoffs govern sexually dimorphic tubular lysosome induction in C. elegans
Authors: Ramos Cara D. , Bohnert K. Adam , Johnson Alyssa E. 
Published: March 2022

AbstractAnimals of different sexes often exhibit unique behaviors that benefit their specific reproductive interests. In the nematode Caenorhabditis elegans, self-fertilizing hermaphrodites can reproduce without a mate and thus prioritize feeding to satisfy the high energetic costs of reproduction. However, males, which rely on finding potential mates for reproduction, sacrifice feeding and instead prioritize exploratory behavior. Here, we demonstrate that these differences in behavior are linked to sexual dimorphism at the cellular level; young males raised on a rich food source show constitutive induction of gut tubular lysosomes, a non-canonical lysosome morphology that typically forms in the gut of young hermaphrodites only when food is limited. We find that male-specific induction of gut tubular lysosomes on abundant food is due to self-imposed dietary restriction through daf-7/TGFβ signaling, which promotes mate-searching at the cost of feeding. While gut tubular lysosomes are largely absent from well-fed hermaphrodites at the start of adulthood, their induction accelerates in hermaphrodites in early aging, dependent on the presence of sperm and, partly, on embryo production. These findings identify tubular lysosome induction as a sexually dimorphic cellular event that may integrate animal physiology with sex-specific behavioral differences important for reproductive success.