bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional brain imaging in bipolar disorder
Authors: Siegel-Ramsay Jennifer E. , Almeida Jorge R.C. 
Published: March 2022

Abstract
Connectivity, as applied in neuroimaging research, is a statistical method of measuring relationships in neurofunctional activity. When comparing connectivity in participants with bipolar disorder to healthy individuals, the most consistent patterns of altered connectivity were localized in the salience network, central executive network, default mode network and sensory-motor cortex. Across bipolar mood states, researchers reported increased within–salience network connectivity and less efficient coupling between amygdala and ventrolateral prefrontal cortex compared to healthy participants. This evidence suggests overactive emotional and sensory processing combined with dysregulation of these brain regions by ventrolateral prefrontal cortex. There was also evidence of more widespread disconnect of prefrontal regions with salience and other central executive network regions in association with an acute affective bipolar state. Although the evidence was less consistent, we also discuss altered connectivity in association with the default mode network and sensory-motor cortex in individuals with bipolar disorder. Connectivity studies more fully represent the bipolar brain as an interconnected unit and characterize aberrant traits and state markers of the condition.
Neuroimaging studies of bipolar disorder in youth
Authors: Singh Manpreet K. , DelBello Melissa P. 
Published: March 2022

Abstract
Bipolar disorder is defined by the onset of the first manic episode, which typically occurs in late adolescence or early adulthood. However, it is increasingly recognized that many people with bipolar disorder experience significant premorbid symptoms, prior to an initial disorder-defining onset of mania. Combined with the heritability of bipolar disorder, it is likely that the underlying biological basis of the disorder produces premorbid and early-course neurophysiological abnormalities that might help to identify at-risk cases and herald an early onset and progression of illness course. This chapter will focus on neuroimaging in bipolar disorder in youth, as well as in at-risk individuals (unaffected and subthreshold affected children of parents with bipolar disorder), to inform models of early bipolar development. This edition’s chapter adds more emphasis on at-risk individuals and progression of neurobiological changes at illness onset, as well as the potential implications for early intervention in an effort to interrupt illness progression.
Neuroimaging differences between bipolar and unipolar depression
Authors: Bertocci Michele A. , Siegel-Ramsay Jennifer E. , Almeida Jorge R.C. , Strakowski Stephen M. , Phillips Mary L. 
Published: March 2022

Abstract
Bipolar disorder is defined by the onset of mania; however, most of the bipolar disorder illness course is spent struggling with depression. Patients presenting with depression in the context of bipolar disorder describe similar symptoms to unipolar depression, and the two disorders are not currently distinguishable by clinical presentations. This similarity results in half of individuals with bipolar disorder being misdiagnosed for up to 10 years with unipolar depression and thus provided with inappropriate treatments. This chapter describes the neural networks believed to be related to mood disorder pathology and methods for acquiring these neural measures. It also examines neuroimaging findings from studies directly comparing bipolar disorder and unipolar depression to understand network dysfunctions that may aid in early diagnosis. Studies comparing neural measures of white matter structure, grey matter structure, neural activity, and connectivity will be reviewed. Finally, to identify neural abnormalities that are evident early in the development of the pathology, comparisons of youth with bipolar disorder versus unipolar depression and comparisons of youth at familial risk for the development of mood disorders will be reviewed.
Neuroimaging in bipolar disorder and schizophrenia
Authors: Du Grace , Öngür Dost 
Published: March 2022

Abstract
Bipolar disorder and schizophrenia share some biological and clinical features, and neuroimaging research may provide insights into mechanistic relationships between the two disorders. This chapter reviews studies using structural magnetic resonance imaging (MRI), diffusion tensor imaging, task-related and resting state functional MRI, and magnetic resonance spectroscopy techniques to collect data from individuals with bipolar disorder and schizophrenia in the same experiment. The chapter concludes that these two disorders share many neurobiological features, but some distinctions are also evident. A high degree of heterogeneity and lack of replication among published studies hampers the ability to draw strong conclusions concerning some important details such as relationship between brain abnormalities and clinical presentation and treatment effects. Technological advances coupled with precise phenotyping are likely to provide deeper insights into the relationship between bipolar disorder and schizophrenia.
Genetics of bipolar disorder and schizophrenia
Authors: Bigdeli Tim B. , Harvey Philip D. 
Published: March 2022

AbstractSchizophrenia and bipolar disorder have been considered to be separate conditions since their initial definition by Kraepelin in the late 1890s. Despite the distinctions between the conditions in terms of their definitional criteria (delusions and hallucinations versus wide-ranging changes in mood), there are multiple shared phenotypic features. These features include cognitive impairments, everyday disability, and suicidal ideation and behavior. Genomic approaches initially focused on family and population characteristics, findings overlapping risk within families. Recent efforts have shifted to large-scale genome-wide association studies, targeting both susceptibility to the conditions and genomic correlates of the shared phenotypic features. Among the major shared phenotypic features, it appears that polygenic risk for schizophrenia and bipolar disorder also overlaps with the genomics of cognitive functioning, including cognitive functioning in the general population. Polygenic risk for depression is also associated with both schizophrenia and bipolar disorder. While most of the genomic influence to date in these two conditions has arisen from common variants, rare variants such as alterations in copy number variations have been seen to be more strongly associated with schizophrenia than bipolar disorders, but sample size differences may be responsible for the lack of effects in bipolar disorder. As sample sizes increase, it is anticipated that even more overlap between bipolar disorder and schizophrenia will be detected, as well as the continued exploration of aggregated phenotypic and genomic features in the two conditions.
YY1 safeguard multidimensional epigenetic landscape associated with extended pluripotency
Authors: Dong Xiaotao , Guo Rong , Ji Tianrong , Zhang Jie , Xu Jun , Li Yaoyi , Sheng Yingliang , Wang Yuxiang , Fang Ke , Wen Yulin , Liu Bei , Hu Gongcheng , Deng Hongkui , Yao Hongjie 
Published: March 2022

Abstract
Although extended pluripotent stem cells (EPSCs) have the potential to form both embryonic and extraembryonic lineages, how their transcriptional regulatory mechanism differs from that of embryonic stem cells (ESCs) remains unclear. Here, we discovered that YY1 binds to specific open chromatin regions in EPSCs. Yy1 depletion in EPSCs leads to a gene expression pattern more similar to that of ESCs than control EPSCs. Moreover, Yy1 depletion triggers a series of epigenetic crosstalk activities, including changes in DNA methylation, histone modifications and high-order chromatin structures. Yy1 depletion in EPSCs disrupts the enhancer-promoter (EP) interactions of EPSC-specific genes, including Dnmt3l. Yy1 loss results in DNA hypomethylation and dramatically reduces the enrichment of H3K4me3 and H3K27ac on the promoters of EPSC-specific genes by upregulating the expression of Kdm5c and Hdac6 through facilitating the formation of CCCTC-binding factor (CTCF)-mediated EP interactions surrounding their loci. Furthermore, single-cell RNA sequencing (scRNA-seq) experiments revealed that YY1 is required for the derivation of extraembryonic endoderm (XEN)-like cells from EPSCs in vitro. Together, this study reveals that YY1 functions as a key regulator of multidimensional epigenetic crosstalk associated with extended pluripotency.
Comparison of population structure, vertical distribution and growth of sympatric, carnivorous, mesopelagic copepods,Paraeuchaeta glacialisandHeterorhabdus norvegicus, in the western Arctic Ocean
Authors: Yamaguchi Atsushi , Ashjian Carin J , Campbell Robert G 
Published: March 2022

AbstractIn the Arctic Ocean, the life cycles of interzonal omnivorous copepods have been studied, whereas little information is available on the life cycles of mesopelagic carnivorous species. Here, the life cycles of two mesopelagic carnivorous copepods (Paraeuchaeta glacialis and Heterorhabdus norvegicus) are described from vertically stratified samples collected at an annual ice-station (SHEBA) in the western Arctic Ocean during 1996–1997. Reproduction estimated to occur between January and March for both species. Vertical distributions and population growth varied between the species. Early copepodite stages and adult males of P. glacialis were distributed in deeper layers, whereas late copepodite stages and adult females were observed in shallower layers. The skewed sex ratio towards females was observed for adults, which may be related to the cease feeding and short longevity for adult males. In contrast, all the H. norvegicus life stages were distributed in the mesopelagic layer. Clear peaks of the young stages and their sequence suggest that H. norvegicus may complete its life cycle within 1 year. A specialized feeding mode (incorporating a venomous injection spine and large beak) could be a key trait facilitating the achievement of rapid growth in H. norvegicus in the food-limited mesopelagic layer.
The annotation and analysis of complex 3D plant organs using 3DCoordX
Authors: Vijayan Athul , Strauss Soeren , Tofanelli Rachele , Mody Tejasvinee Atul , Lee Karen , Tsiantis Miltos , Smith Richard S , Schneitz Kay 
Published: March 2022

Abstract
A fundamental question in biology concerns how molecular and cellular processes become integrated during morphogenesis. In plants, characterization of 3D digital representations of organs at single-cell resolution represents a promising approach to addressing this problem. A major challenge is to provide organ-centric spatial context to cells of an organ. We developed several general rules for the annotation of cell position and embodied them in 3DCoordX, a user-interactive computer toolbox implemented in the open-source software MorphoGraphX. 3DCoordX enables rapid spatial annotation of cells even in highly curved biological shapes. Using 3DCoordX, we analyzed cellular growth patterns in organs of several species. For example, the data indicated the presence of a basal cell proliferation zone in the ovule primordium of Arabidopsis (Arabidopsis thaliana). Proof-of-concept analyses suggested a preferential increase in cell length associated with neck elongation in the archegonium of Marchantia (Marchantia polymorpha) and variations in cell volume linked to central morphogenetic features of a trap of the carnivorous plant Utricularia (Utricularia gibba). Our work demonstrates the broad applicability of the developed strategies as they provide organ-centric spatial context to cellular features in plant organs of diverse shape complexity.
The Impact on Staff of Providing Non-Invasive Advanced Respiratory Support During the Covid-19 Pandemic– A Qualitative Study in an Acute Hospital
Authors: Wenzel David , Bleazard Lucy , Wilson Eleanor , Faull Christina 
Published: March 2022

ObjectivesTo explore the experiences of healthcare workers of providing Non-Invasive Advanced Respiratory Support (NARS) to critically unwell patients with covid-19.DesignA qualitative study drawing on a social constructionist perspective using thematic analysis of semi-structured interviews.SettingA single acute UK NHS Trust across two hospital sites.ParticipantsMultidisciplinary team members in acute, respiratory and palliative medicine.Results21 nurses, doctors (juniors and consultants) and physiotherapists described the provision of NARS to critically unwell covid-19 patients as extremely challenging. The main themes were of feeling ill prepared and unsupported, a need to balance complex moral actions, a sense of duty to patients and their families. The impact on staff was profound and findings are discussed via a lens of moral injury. Injurious events included staff feeling they had acted in a way that caused harm, failed to prevent harm or had been let down by seniors or the Trust. Participants identified factors that mitigated adverse impact.ConclusionsAlthough many of the issues described by participants are likely immutable components of healthcare in a pandemic there were several important protective factors that emerged from the data. Experience, debriefing and breaks from covid-19 wards were valuable to participants and successfully achieving a peaceful death for the patient was often viewed as compensation for a difficult journey. These protective factors may provide modelling for future education and support services to help prevent moral injury – or aide in its recovery.Registrationregistered on the Open Science Framework 10.17605/OSF.IO/XB8YHStrengths and LimitationsSingle Centre StudyThe lead author had pre-existing relationships with study participantsThe lead author, under strict supervision, practiced a reflexivity based approach to data collection and analysis with objectivity benchmarking from the second author.
The effect of Septoria glycines and fungicide application on the soybean phyllosphere mycobiome
Authors: Lin Heng-An , Mideros Santiago X. 
Published: March 2022

AbstractSeptoria brown spot (caused by Septoria glycines) is the most prevalent soybean disease in Illinois. It is common to use a foliar fungicide to control Septoria brown spot and other foliar diseases. The effects of fungicide on non-target organisms in the phyllosphere are unknown. To study the effect of S. glycines and fungicide application on the soybean phyllosphere mycobiome we sequenced full-length ITS and partial LSU region using oxford nanopore technologies. Sequencing produced 3,342 operational taxonomic units (OTUs). The richness of the fungal community significantly increased with the developmental stage. The soybean lines significantly affected the mycobiome diversity at the early developmental stage but not at the reproductive stages. S. glycines did not significantly affect the alpha diversity but some significant changes were observed for the beta diversity. At the R5 stage, fungicide application significantly changed the composition of the fungal community. The fungicide treatment significantly decreased the proportion of several fungal reads, but it increased the proportion of Septoria. The core microbiome in soybean leaves was composed of Gibberella, Alternaria, Didymella, Cladosporium, Plectosphaerella, Colletotrichum, and Bipolaris. Network analysis identified significant interactions between Septoria reads and Diaporthe, Bipolaris and two other taxonomic units. In this study, we set Septoria as the target organism and demonstrated that metabarcoding could be a tool to quantify the effect of multiple treatments on the fungal phyllosphere community. Better understanding the dynamics of the phyllosphere microbiome is necessary to start untangling late-season diseases of soybean.
Variants identify sarcomere inter-protein contacts distinguishing inheritable cardiac muscle diseases
Authors: Burghardt Thomas P. 
Published: March 2022

ABSTRACTHuman ventriculum myosin (βmys) powers contraction sometimes while complexed with myosin binding protein C (MYBPC3) on the myosin thick filament. The latter regulates βmys activity through inter-protein contacts. Single nucleotide variants (SNVs) change protein sequence in βmys or MYBPC3. They cause inheritable heart disease. When a SNV modified domain locates to an inter-protein contact it affects complex coordination. Domains involved, one in βmys and the other in MYBPC3, form coordinated domains called co-domains. Co-domains are bilateral implying the potential for a shared impact from SNV modification in either domain suggesting their joint response to a common perturbation assigns location. Human population genetic divergence is the common systemic perturbation. A general contraction model with a neural/Bayes network design reveals SNV probabilities specifying correlations between domain members using 2D correlation genetics (2D-CG). It reveals co-domain locations in three common human heart diseases caused by SNVs, familial hypertrophic cardiomyopathy (FHC), dilated cardiomyopathy (DCM), and left ventricle non-compaction (LVN). Co-domain maps for DCM and LVN link MYBPC3 with two levels of myosin heads on the myosin thick filament surface implying these myosin dimers form the super-relaxed state (SRX). The FHC co-domain map involves just one myosin dimer implying the myosins do not form SRX. Comparing co-domain maps for FHC, DCM, and LVN phenotypes suggests SRX disruption involves a co-domain between MYBPC3 regulatory domain and the myosin regulatory light chain (RLC) N-terminus. The general contraction model scenarios, constructed from feed-forward neural networks, were explored with the purpose to understand how to interpret them mechanistically with basic natural language characteristics. These characteristics emerge from dependencies among inputs coded in hidden layer width and depth when they are deciphered using 2D-CG. In this application, the thick filament structural states emerge for FHC, DCM, and LVN phenotypes defining thick filament structural state joining the other standard characteristics of phenotype and pathogenicity. Emergent natural language interpretations for general network contraction models are on the horizon.
Differentiation of airway cholinergic neurons from human pluripotent stem cells for airway neurobiology studies
Authors: Goldsteen P.A. , Sabogal Guaqueta A.M. , Bos I.S.T. , Kistemaker L.E.M. , van der Koog L. , Eggens M. , Halayko A.J. , Dolga A.M. , Gosens R. 
Published: March 2022

AbstractAirway cholinergic nerves play a key role in airway physiology and disease. In asthma and other diseases of the respiratory tract, airway cholinergic neurons undergo plasticity and contribute to airway hyperresponsiveness and mucus secretion. We currently lack mechanistic understanding of airway cholinergic neuroplasticity due to the absence of human in vitro models. Here, we developed the first human in vitro model for airway cholinergic neurons using human pluripotent stem cell (hPSC) technology. hPSCs were differentiated towards mature and functional airway cholinergic neurons via a vagal precursor. Airway cholinergic neurons were characterized by ChAT and VAChT expression, and responded to chemical stimulation with changes in Ca2+ mobilization. Co-culture of hPSC-derived airway cholinergic neurons with airway smooth muscle cells enhanced phenotypic and functional characteristics of these neurons. The differentiation protocol we developed for human airway cholinergic neurons from hPSCs allows for studies into airway neurobiology and airway neuroplasticity in disease.
Reciprocity and interaction effectiveness in generalised mutualisms among free-living species
Authors: Quintero Elena , Rodríguez-Sánchez Francisco , Jordano Pedro 
Published: March 2022

ABSTRACTMutualistic interactions among free-living species generally involve weak links and highly asymmetric dependence among partners, yet our understanding of factors beyond their emergence is still limited. Using individual-based interactions of a super-generalist fleshy-fruited plant with its frugivore assemblage we estimate the Resource Provisioning Effectiveness (RPE) and Seed Dispersal Effectiveness (SDE) to assess the balance in the exchange of resources. Plants were highly dependent on a few super-generalist frugivore species, while these interacted with most individual plants, resulting in strong asymmetries in mutual dependence. Both RPE and SDE were mainly driven by interaction frequency. Despite highly asymmetric dependences, the strong reliance on quantity largely determined high reciprocity in rewards between partners (i.e., higher energy provided, more seedlings recruited), not obscured by minor variations in the quality of animal or plant service. We anticipate reciprocity will emerge in low-intimacy mutualisms where the mutualistic outcome largely relies upon interaction frequency.
Extraction and analysis of methylation features from Pacific Biosciences SMRT reads using MeStudio
Authors: Riccardi Christopher , Passeri Iacopo , Cangioli Lisa , Fagorzi Camilla , Mengoni Alessio , Fondi Marco 
Published: March 2022

AbstractMotivationDNA methylation is the most relevant epigenetic information, present in eukaryotes and prokaryotes, and is related to several biological phenomena, from cellular differentiation to control of gene flow, pathogenesis and virulence. The widespread use of third-generation sequencing technologies allows direct and easy detection of genome-wide methylation profiles, offering increasing opportunities to understand and exploit the epigenomics landscape.ResultsWe introduce MeStudio, a pipeline which allows to analyse and combine genome-wide methylation profiles with genomic features. Outputs report the presence of DNA methylation in coding sequences, noncoding sequences, intergenic sequences, and sequences upstream to CDS. We show the usage and performances of MeStudio on a set of single-molecule real time sequencing outputs from the bacterial species Sinorhizobium meliloti.Availability and ImplementationMeStudio is written in Python, Bash and C and is freely available under an open source GPLv3 license at https://github.com/combogenomics/MeStudioSupplementary informationSupplementary data are available at Bioinformatics online.Contactcombo.unifi@gmail.com
A new monoclonal antibody enables BAR analysis of subcellular importin β1 interactomes
Authors: Song Didi-Andreas , Alber Stefanie , Doron-Mandel Ella , Schmid Vera , Albus Christin A. , Leitner Orith , Hamawi Hedva , Oses-Prieto Juan A. , Burlingame Alma L. , Fainzilber Mike , Rishal Ida 
Published: March 2022

AbstractImportin β1 (KPNB1) is a nucleocytoplasmic transport factor with critical roles in both cytoplasmic and nucleocytoplasmic transport, hence there is keen interest in the characterization of its subcellular interactomes. We found limited efficiency of BioID in detection of importin complex cargos, and therefore generated a highly specific and sensitive anti-KPNB1 monoclonal antibody to enable Biotinylation by Antibody Recognition (BAR) analysis of importin β1 interactomes. The monoclonal antibody recognizes an epitope comprising residues 301-320 of human KPBN1, and strikingly is highly specific for cytoplasmic KPNB1 in diverse applications, with little or no reaction with KPNB1 in the nucleus. BAR with this novel antibody revealed numerous new interactors of importin β1, expanding the KPNB1 interactome to cytoplasmic and signaling complexes that highlight potential new functions for the importins complex beyond nucleocytoplasmic transport. Data are available via ProteomeXchange with identifier PXD032728.