bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Major-Minor mode Dichotomy in Music Perception: A Systematic Review and Meta-Analysis on its Behavioural, Physiological, and Clinical Correlates
Authors: Carraturo Giulio , Pando-Naude Victor , Costa Marco , Vuust Peter , Bonetti Leonardo , Brattico Elvira 
Published: March 2023

AbstractSince ancient Greece, major and minor modes in Western tonal music have been identified as the primary responsible musical feature for eliciting emotional states. As such, the underlying correlates of the major-minor mode dichotomy in music perception have been extensively investigated through decades of psychological and neuroscientific research, providing plentiful yet often discordant results. Specifically, crucial questions remain about the several factors contributing to the affective perception of major and minor modes, at times very different among individuals. Moreover, major and minor mode perception has never been quantitatively compared in literature. This comprehensive systematic review and meta-analysis aimed to provide a qualitative and quantitative synthesis of musical mode perception and its behavioural and neural correlates. The qualitative synthesis resulted in 69 studies, showing great diversity in how the major-minor dichotomy has been empirically approached. Most studies reviewed were conducted on adults, considered participants’ expertise, employed real-life musical stimuli, performed behavioural evaluations, and were carried out among Western listeners. Behavioural, electroencephalography, and neuroimaging meta-analyses (36 studies) consistently showed that major and minor mode elicit distinct neural and emotional responses. Based on our findings, a framework to describe aMajor-Minor Mode(l)of music perception and its behavioural and physiological correlates is proposed, incorporating individual factors such as age, expertise, cultural background, and emotional disorders. Limitations, implications, and suggestions for future research are discussed, including putative clinical applications of major-minor dichotomy and best practices regarding stimulation paradigms for musical mode investigation.Public Significance StatementThis study provides qualitative and quantitative evidence of the distinct behavioral and neural responses elicited by major and minor mode, while also highlighting the influence of factors such as age, culture, personality, and health. Results offers a detailed overview of the major-minor dichotomy in music, putting forward an integrated and critical discussion of methodologies, paradigms, and clinical implications of this pivotal musical feature.
Ingestion ofBacillus cereusspores dampens the immune response to favor bacterial persistence
Authors: Hachfi Salma , Brun-Barale Alexandra , Munro Patrick , Nawrot-Esposito Marie-Paule , Michel Gregory , Fichant Arnaud , Bonis Mathilde , Ruimy Raymond , Boyer Laurent , Gallet Armel 
Published: March 2023

SUMMARYSpores are considered as dormant entities highly resistant to extreme conditions. Among them,Bacillus cereusspores are commonly associated with foodborne outbreaks. Nevertheless, the pathological processes associated with spore ingestion and germination remain poorly understood. Here, we show that while ingestion of vegetative bacteria leads to their elimination from the midgut and small intestines ofDrosophilaand mice, respectively, a single ingestion of spores leads to the persistence of bacteria for at least 10 days. UsingDrosophilagenetics, we demonstrate that spores escape the innate immune response of the anterior midgut. Once in the posterior midgut, spores germinate, and the vegetative cells dampen the immune signaling through the induction of amidases which are negative regulators of the immune response. This study provides evidence for howB. cereusspores hijack the intestinal immune defenses allowing the localized birth of vegetative bacteria responsible for the digestive symptoms associated with foodborne illness outbreaks.
TCR/CD3-based synthetic antigen receptors (TCC) convey superior antigen sensitivity combined with high fidelity of activation
Authors: Peters Timo , Mühlgrabner Vanessa , Cárdenas Rubí M.-H. Velasco , Platzer René , Göhring Janett , Salzer Benjamin , Plach Angelika , Höhrhan Maria , Perez Iago Doel , Goncalves Vasco Dos Reis , Farfán Jesús Siller , Lehner Manfred , Stockinger Hannes , Schamel Wolfgang W. , Schober Kilian , Busch Dirk H. , Hudecek Michael , Dushek Omer , Minguet Susanna , Huppa Johannes B. 
Published: March 2023

ABSTRACTLow antigen sensitivity and a gradual loss of effector functions limit the clinical applicability of chimeric antigen receptor (CAR)-modified T-cells and call for alternative antigen receptor designs for effective T-cell-based cancer immunotherapy. Here we applied advanced microscopy to demonstrate that TCR/CD3-based synthetic constructs (TCC) outperform second-generation CAR formats with regard to conveyed antigen sensitivities by up to a thousand-fold. TCC-based antigen recognition occurred without adverse non-specific signaling, which is typically observed in CAR-T-cells, and did not depend - unlike sensitized peptide/MHC detection by conventional T-cells - on CD4- or CD8- coreceptor engagement. TCC-endowed signaling properties may prove critical when targeting antigens in low abundance and aiming for a durable anti-cancer response.
Reference mouse strain assemblies for BALB/c Nude and NOD/SCID mouse models
Authors: Schmid-Siegert Emanuel , Qin Mengting , Tian Huan , Arpat Bulak , Chen Bonnie , Xenarios Ioannis 
Published: March 2023

AbstractMouse xenograft models play a vital role in tumor studies for research as well as for screening of drugs for the pharmaceutical industry. In particular, models with compromised immunity are favorable to increase the success of transplantation, such as e.g. NOD/SCID and BALB/c Nude strains. The genomic sequence and alterations of many of these models still remain elusive and might hamper a model’s further optimization or proper adapted usage. This can be in respect to treatments (e.g. NOD/SCID sensitivity to radiation), experiments or analysis of derived sequencing data of such models. Here we present the genome assemblies for the NOD/SCID and BALB/c nude strains to overcome this short-coming for the future and improve our understanding of these models in the process. We highlight as well first insights into observed genomic differences for these models compared to the C57BL/6 reference genome. Genome assemblies for both are close to full chromosome representations and provided with liftover annotations from the GRCm39 reference genome.
Group 2 innate lymphoid cells promote inhibitory synapse development and social behavior
Authors: Barron Jerika J. , Mroz Nicholas M. , Taloma Sunrae E. , Dahlgren Madelene W. , Ortiz-Carpena Jorge , Dorman Leah C. , Vainchtein Ilia D. , Escoubas Caroline C. , Molofsky Ari B. , Molofsky Anna V. 
Published: March 2023

AbstractThe innate immune system plays essential roles in brain synaptic development, and immune dysregulation is implicated in neurodevelopmental diseases. Here we show that a subset of innate lymphocytes (group 2 innate lymphoid cells, ILC2s) is required for cortical inhibitory synapse maturation and adult social behavior. ILC2s expanded in the developing meninges and produced a surge of their canonical cytokine Interleukin-13 (IL-13) between postnatal days 5-15. Loss of ILC2s decreased cortical inhibitory synapse numbers in the postnatal period where as ILC2 transplant was sufficient to increase inhibitory synapse numbers. Deletion of the IL-4/IL-13 receptor (Il4ra) from inhibitory neurons phenocopied the reduction inhibitory synapses. Both ILC2 deficient and neuronalIl4radeficient animals had similar and selective impairments in adult social behavior. These data define a type 2 immune circuit in early life that shapes adult brain function.One sentence summaryType 2 innate lymphoid cells and Interleukin-13 promote inhibitory synapse development.
Atlas of Fetal Metabolism During Mid-To-Late Gestation and Diabetic Pregnancy
Authors: Perez-Ramirez Cesar A , Nakano Haruko , Law Richard C , Matulionis Nedas , Thompson Jennifer , Pfeiffer Andrew , Park Junyoung O , Nakano Atsushi , Christofk Heather R 
Published: March 2023

SUMMARYMounting evidence supports an instructive role for metabolism in stem cell fate decisions. However, much is yet unknown about how fetal metabolism changes during mammalian development and how altered maternal metabolism shapes fetal metabolism. Here, we present a descriptive atlas ofin vivofetal murine metabolism during mid-to-late gestation in normal and diabetic pregnancy. Using13C-glucose and LC-MS, we profiled the metabolism of fetal brains, hearts, livers, and placentas harvested from pregnant dams between embryonic days (E)10.5 and 18.5. Comparative analysis of our large metabolomics dataset revealed metabolic features specific to fetal tissues developed under a hyperglycemic environment as well as metabolic signatures that may denote developmental transitions during euglycemic development. We observed sorbitol accumulation in fetal tissues and altered neurotransmitter levels in fetal brains isolated from dams with maternal hyperglycemia. Tracing13C-glucose revealed disparate nutrient sourcing in fetuses depending on maternal glycemic states. Regardless of glycemic state, histidine-derived metabolites accumulated during late development in fetal tissues and maternal plasma. Our rich dataset presents a comprehensive overview ofin vivofetal tissue metabolism and alterations occurring as a result of maternal hyperglycemia.
Guide-specific loss of efficiency and off-target reduction with Cas9 variants
Authors: Zhang Liang , He Wei , Fu Rongjie , Xu Han 
Published: March 2023

AbstractHigh-fidelity Cas9 variants have been developed to reduce the off-target effects of CRISPR systems at a cost of efficiency loss. To systematically evaluate the efficiency and off-target tolerance of Cas9 variants in complex with different single guide RNAs (sgRNAs), we applied high-throughput viability screens and a synthetic paired sgRNA-target system to assess thousands of sgRNAs in combination with two high-fidelity Cas9 variants HiFi and LZ3. Comparing these variants against WT SpCas9, we found that ~20% of sgRNAs are associated with a significant loss of efficiency when complexed with either HiFi or LZ3. The loss of efficiency is dependent on the sequence context in the seed region of sgRNAs, as well as at positions 15-18 in the non-seed region that interacts with the REC3 domain of Cas9, suggesting that the variant-specific mutations in REC3 domain account for the loss of efficiency. We also observed various degrees of sequencedependent off-target reduction when different sgRNAs are used in combination with the variants. Given these observations, we developed GuideVar, a transfer-learning-based computational framework for the prediction of on-target efficiency and off-target effect with high-fidelity variants. GuideVar facilitates the prioritization of sgRNAs in the applications with HiFi and LZ3, as demonstrated by the improvement of signal-to-noise ratios in high-throughput viability screens using these high-fidelity variants.
Discovery of an endogenous DNA virus in the amphibian killing fungus and its association with pathogen genotype and virulence
Authors: Clemons Rebecca , Yacoub Mark , Faust Evelyn , Toledo L. Felipe , Jenkinson Thomas S. , Carvalho Tamilie , Simmons D. Rabern , Kalinka Erik , Fritz-Laylin Lillian K. , James Timothy Y. , Stajich Jason E. 
Published: March 2023

SummaryThe Global Panzootic Lineage (GPL) of the pathogenic fungusBatrachochytrium dendrobatidis(Bd) has caused severe amphibian population declines, yet the drivers underlying the high frequency of GPL in regions of amphibian decline are unclear. Using publicly availableBdgenome sequences, we identified multiple non-GPLBdisolates that contain a circular Rep-encoding single stranded DNA (CRESS)-like virus which we named BdDV-1. We further sequenced and constructed genome assemblies with long read sequences to find that the virus is integrated into the nuclear genome in some strains. Attempts to cure virus positive isolates were unsuccessful, however, phenotypic differences between naturally virus positive and virus negativeBdisolates suggested that BdDV-1 decreases the growth of its hostin vitrobut increases the virulence of its hostin vivo. BdDV-1 is the first described CRESS DNA mycovirus of zoosporic true fungi with a distribution inversely associated with the emergence of the panzootic lineage.
Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA andin situsequencing
Authors: Zhang Aixin , Jin Lei , Yao Shenqin , Matsuyama Makoto , Velthoven Cindy van , Sullivan Heather , Sun Na , Kellis Manolis , Tasic Bosiljka , Wickersham Ian R. , Chen Xiaoyin 
Published: March 2023

AbstractMapping the connectivity of diverse neuronal types provides the foundation for understanding the structure and function of neural circuits. High-throughput and low-cost neuroanatomical techniques based on RNA barcode sequencing have the potential to map circuits at cellular resolution and a brain-wide scale, but existing Sindbis virus-based techniques can only map long-range projections using anterograde tracing approaches. Rabies virus can complement anterograde tracing approaches by enabling either retrograde labeling of projection neurons or monosynaptic tracing of direct inputs to genetically targeted postsynaptic neurons. However, barcoded rabies virus has so far been only used to map non-neuronal cellular interactionsin vivoand synaptic connectivity of cultured neurons. Here we combine barcoded rabies virus with single-cell andin situsequencing to perform retrograde labeling and transsynaptic labeling in the mouse brain. We sequenced 96 retrogradely labeled cells and 295 transsynaptically labeled cells using single-cell RNA-seq, and 4,130 retrogradely labeled cells and 2,914 transsynaptically labeled cellsin situ. We found that the transcriptomic identities of rabies virus-infected cells can be robustly identified using both single-cell RNA-seq andin situsequencing. By associating gene expression with connectivity inferred from barcode sequencing, we distinguished long-range projecting cortical cell types from multiple cortical areas and identified cell types with converging or diverging synaptic connectivity. Combiningin situsequencing with barcoded rabies virus complements existing sequencing-based neuroanatomical techniques and provides a potential path for mapping synaptic connectivity of neuronal types at scale.
The microglia receptor protein TREM2 is essential for protective innate immune responses against herpesvirus infection in the brain
Authors: Fruhwürth Stefanie , Reinert Line S. , Öberg Carl , Sakr Marcelina , Henricsson Marcus , Zetterberg Henrik , Paludan Søren R. 
Published: March 2023

AbstractImmunological control of viral infection in the brain is essential for immediate protection, but also for long-term maintenance of brain integrity. As the primary resident immune cell of the brain, microglia protect against viral infections through key macrophage functions, including release of the antiviral type I interferons (IFN-I) and clearance of infected cells. Microglia express the cytosolic DNA sensor cyclic GMP-AMP synthase (cGAS), which can bind viral DNA leading to signaling through stimulator of interferon genes (STING), and downstream immune activation. Here we report that herpes simplex virus (HSV) 1 infection of microglia leads to activation of IFN-I genes and pro-inflammatory cytokines. However, HSV1 also down-regulated expression of a subset of genes, including genes in the pathway engaged by the microglial receptor triggering receptor expressed on myeloid cells-2 (TREM2). Knockdown experiments revealed that TREM2 is important for viral activation of cGAS-STING signaling in microglia, induction of IFN-I, and phagocytosis of HSV1 infected neurons. Consequently, TREM2 depletion increased susceptibility to HSV1 infection in human microglia-neuron co-cultures and micein vivo. Mechanistically, we show that TREM2 is essential for phosphorylation of STING, and downstream activation of the IFN-inducing transcription factor IRF3. We conclude that TREM2 is a novel component of the antiviral immune response in microglia, crucial for immediate host defense against HSV1 in the brain. Since bothTREM2loss-of-function mutations and HSV1 serological status are linked to development of Alzheimeŕs disease (AD), this work opens the question whether defects in TREM2 could predispose to impaired viral clearance and post-infection pathological neurological changes.
Correlates of time to first citation in ecology and taxonomy
Authors: Guedes Jhonny J. M. , Melo Isabella , Bione Igor , Nunes Matheus 
Published: March 2023

AbstractSeveral metrics exists to evaluate the impact of publications and researchers, but most are based on citation counts, which usually fail to capture the temporal aspect of citations. Time to first citation represents a useful metric for research evaluation, and informs the speed at which scientific knowledge is disseminated through the scientific community. Understanding which factors affect such metrics is important as they impact resource allocation and career progression, besides influencing knowledge promotion across disciplines. Many ecological works rely on species identity, which is the ‘coin’ of taxonomy. Despite its importance, taxonomy is a discipline in crisis lacking staff, funds and prestige, which ultimately may affect the evaluation and dissemination of taxonomic works. We used a time-to-event analysis to investigate whether taxonomic, socioeconomic, and scientometric factors influence first citation speed across hundreds of ecological and taxonomic articles. Time to first citation differed greatly between these areas. Ecological studies were first cited much faster than taxonomic studies. Multitaxa articles received first citations earlier than studies focused on single major taxonomic groups. Article length andh-index among authors were negatively correlated with time to first citation, while the number of authors, number of countries, and Gross Domestic Product was unimportant. Knowledge dissemination is faster for lengthy, multitaxa, and ecological articles relative to their respective counterparts, as well as for articles with highly prolific authors. We stress that using several unrelated metrics is desirable when evaluating research from different–and even related–disciplines, particularly in the context of professional progression and grant allocation.
New PALM-compatible integration vectors for use in the Gram-positive model bacteriumBacillus subtilis
Authors: Altinoglu Ipek , Carballido-Lopez Rut 
Published: March 2023

ABSTRACTImprovements in super-resolution and single-molecule techniques together with the development of new fluorescent proteins and labelling methods have allowed super-resolution microscopy to be applied to bacterial cells. Cloning vectors remain important tools for researchers to perform efficient labelling. Here, we describe the creation of four PhotoActivated Localization Microscopy (PALM)-compatible integration plasmids for the Gram-positive model organismBacillus subtilis. These plasmids carry either the photoswitchable green fluorescent protein dronPA or the photoactivatable red fluorescent protein PAmCherry1, codon-optimized or not forB. subtilis. For fast and interchangeable cloning, we have inserted multi cloning sites at both the C-terminal and the N-terminal end of the fluorophores. The plasmids replicate inEscherichia coliand allow integration at the ectopicamyEorthrCloci ofB. subtilisvia double homologous recombination, for stable chromosomal insertions of dronPA and PAmCherry1 protein fusions respectively. Dual color imaging is accessible with the simultaneous use of the two vectors. Insertion of the gene encoding the LacI repressor under control of a constitutive promoter in each of the four plasmids yielded four derivative vectors that, combined with an array oflacOoperator sites, allow Fluorescent Repressor-Operator System (FROS) localization studies. We demonstrated the successful photoactivation of the LacI-dronPA or PAmCherry1 fusions, and used them to report with nanoscale precision the subcellular localization of bacteriophage SPP1 DNA in infectedB. subtiliscells as proof of concept. Our PALM-compatible integration vectors expand the genetic toolbox for single molecule localization microscopy studies inB. subtilis.
Force-regulated chaperone activity of BiP/ERdj3 is opposite to their homologs DnaK/DnaJ: explained by strain energy
Authors: Banerjee Souradeep , Chowdhury Debojyoti , Chakraborty Soham , Haldar Shubhasis 
Published: March 2023

AbstractPolypeptide chains experiences mechanical tension while translocating through cellular tunnel. In this scenario, interaction of tunnel-associated chaperones with the emerging polypeptide occurs under force; however, this force-regulated chaperone behaviour is not fully understood.We studied the mechanical chaperone activity of two tunnel-associated chaperones BiP and ERdj3 both in the absence and presence of force; and compared to their respective cytoplasmic homologs DnaK and DnaJ. We found that BiP/ERdj3 shows strong foldase activity under force; whereas their cytoplasmic homolog DnaK/DnaJ behave as holdase. Importantly, these tunnel-associated chaperones (BiP/ERdj3) revert to holdase in the absence of force, suggesting that mechanical chaperone activity differs depending on the presence or absence of force. This tunnel-associated chaperone-driven folding event generates additional mechanical energy of up to 54 zJ that could help protein translocation. The mechanical-chaperone behaviour can be explained by strain theory: chaperones with higher intrinsic deformability function as mechanical foldase (BiP, ERdj3), while chaperones with lower intrinsic deformability act as holdase (DnaK and DnaJ). Our study thus unveils the underlying mechanism of mechanically regulated chaperoning activity and provides a novel mechanism of co-translocational protein folding.SignificanceThe mechanical-activity of chaperones, located at the edge of a tunnel, could be different from their cytoplasmic homologs. Translocating substrates within the tunnel are known to experience mechanical constraints, whereas the cytosolic substrates interact with the chaperones in the absence of force.To understand this phenomenon, we investigated two tunnel-associated chaperones BiP/ERdj3 and their cytosolic homologs-DnaK/DnaJ. We observed that BiP/ERdj3 possess strong foldase activity while their substrates are under force; whereas DnaK/DnaJ possess holdase function. Notably all these chaperones function as holdase in the absence of force, which suggest that mechanical chaperone activity is different with and without force. We explained this mechanical behaviour using strain theory, providing a physical mechanism of chaperone-assisted co-translocational protein folding.