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Co-design provides a meaningful way to engage patients in research. However, there is limited practical guidance. We used our co-design project to identify strategies for other researchers. An ethnographic case study design was used. Data included participant observation of co-design meetings, meeting minutes, analytic fieldnotes, qualitative patient interviews, and research team member self-reflections. Additionally, we got external feedback. We analyzed data iteratively. Our team included 5 patients and 6 researchers. We identified 3 strategies to include patients in co-design: (1) Deliberately build the team, from recruiting patients to specifying roles. (2) Tailor the meeting format to thoughtfully use patients’ time and expertise. (3) Disrupt traditional hierarchies, to empower patients to actively participate. Researchers seeking to include patients as team members should consider: team composition and roles, leveraging meeting formats to optimize contributions and purposefully creating a culture of collaboration, so patient expertise informs the end product. Our work provides practical guidance for researchers to incorporate patient expertise in the co-design process and meaningfully involve them in their work.

Background Committed to implementing a person-centered, holistic (Whole Health) system of care, the Veterans Health Administration (VHA) developed a peer-led, group-based, multi-session “Taking Charge of My Life and Health” (TCMLH) program wherein Veterans reflect on values, set health and well-being-related goals, and provide mutual support. Prior work has demonstrated the positive impact of these groups. After face-to-face TCMLH groups were disrupted by the COVID-19 pandemic, VHA facilities rapidly implemented virtual (video-based) TCMLH groups. Objective We sought to understand staff perspectives on the feasibility, challenges, and advantages of conducting TCMLH groups virtually. Methods We completed semi-structured telephone interviews with 35 staff members involved in the implementation of virtual TCMLH groups across 12 VHA facilities and conducted rapid qualitative analysis of the interview transcripts. Results Holding TCMLH groups virtually was viewed as feasible. Factors that promoted the implementation included use of standardized technology platforms amenable to delivery of group-based curriculum, availability of technical support, and adjustments in facilitator delivery style. The key drawbacks of the virtual format included difficulty maintaining engagement and barriers to relationship-building among participants. The perceived advantages of the virtual format included the positive influence of being in the home environment on Veterans’ reflection, motivation, and self-disclosure, the greater convenience and accessibility of the virtual format, and the virtual group’s role as an antidote to isolation during the COVID-19 pandemic. Conclusion Faced with the disruption caused by the COVID-19 pandemic, VHA pivoted by rapidly implementing virtual TCMLH groups. Staff members involved in implementation noted that delivering TCMLH virtually was feasible and highlighted both challenges and advantages of the virtual format. A virtual group-based program in which participants set and pursue personally meaningful goals related to health and well-being in a supportive environment of their peers is a promising innovation that can be replicated in other health systems.

Corpus callosum dysgenesis (CCD) is a congenital brain malformation that occurs when the development of the corpus callosum is disrupted, either partially or completely. The cognitive outcomes in individuals with CCD vary greatly, but generally the neuropsychological profile is characterised by slow processing speed, poor transfer of interhemispheric sensory-motor information, and impaired complex problem solving. Core language skills are often preserved in CCD, but there is some evidence that complex language may be impaired. Thus, the current study sought to examine whether spontaneous speech output was reduced in a cohort of individuals with CCD compared to age-matched controls. We further explored a series of factors that may be contributing to poor spontaneous speech in CCD, such as difficulties generating, selecting, and sequencing ideas for expression, as well as apathy and slowed processing speed. A cohort of 25 individuals with CCD and 39 neurotypical controls were enrolled in this study. Participants completed a picture description task to measure spontaneous speech output, alongside a series of cognitive and language baseline tests. Verbal and nonverbal fluency tasks gauged idea generation and sequencing, and sentence-level selection tasks measured idea selection. We found that, despite having largely intact core language skills, individuals with CCD produced significantly less spontaneous speech on the picture description task than controls. This language profile may be described as "adynamic". Further, we found that poor spontaneous speech output in CCD was related to problems generating ideas for expression, as individuals with CCD performed below controls on the verbal and nonverbal fluency tasks. Exploratory analyses revealed that apathy and slowed processing speed may be contributing factors. Adynamia in CCD is a novel finding that may be an intervention target for improving communication skills in this population., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Premise: The history of angiosperms is marked by repeated rounds of ancient whole-genome duplications (WGDs). Here we used state-of-the-art methods to provide an up-to-date view of the distribution of WGDs in the history of angiosperms that considers both uncertainty introduced by different WGD inference methods and different underlying species-tree hypotheses., Methods: We used the distribution synonymous divergences (K s ) of paralogs and orthologs from transcriptomic and genomic data to infer and place WGDs across two hypothesized angiosperm phylogenies. We further tested these WGD hypotheses with syntenic inferences and Bayesian models of duplicate gene gain and loss., Results: The predicted number of WGDs in the history of angiosperms (~170) based on the current taxon sampling is largely similar across different inference methods, but varies in the precise placement of WGDs on the phylogeny. K s -based methods often yield alternative hypothesized WGD placements due to variation in substitution rates among lineages. Phylogenetic models of duplicate gene gain and loss are more robust to topological variation. However, errors in species-tree inference can still produce spurious WGD hypotheses, regardless of method used., Conclusions: Here we showed that different WGD inference methods largely agree on an average of 3.5 WGD in the history of individual angiosperm species. However, the precise placement of WGDs on the phylogeny is subject to the WGD inference method and tree topology. As researchers continue to test hypotheses regarding the impacts ancient WGDs have on angiosperm evolution, it is important to consider the uncertainty of the phylogeny as well as WGD inference methods., (© 2024 Botanical Society of America.)

All flowering plants are now recognized as diploidized paleopolyploids (Jiao et al., 2011; One Thousand Plant Transcriptomes Initiative, 2019), and polyploid species comprise approximately 30% of contemporary plant species (Wood et al., 2009; Barker et al., 2016a). A major implication of these discoveries is that, to appreciate the evolution of plant diversity, we need to understand the fundamental biology of polyploids and diploidization. This need is broadly recognized by our community as there is a continued, growing interest in polyploidy as a research topic. Over the past 25 years, the sequencing and analysis of plant genomes has revolutionized our understanding of the importance of polyploid speciation to the evolution of land plants., (© 2024 Botanical Society of America.)

Amyotrophic lateral sclerosis (ALS) is a multi-system disorder that commonly affects cognition and behaviour. Verbal fluency impairments are consistently reported in ALS patients, and we aimed to investigate whether this deficit extends beyond the verbal domain. We further aimed to determine whether deficits are underpinned by a primary intrinsic response generation impairment (i.e., a global reduction across tasks), potentially related to apathy, or an inability to maintain responding over time (i.e., a 'drop off' pattern). Twenty-two ALS patients and 21 demographically-matched controls completed verbal and nonverbal fluency tasks (phonemic/semantic word fluency, design fluency, gesture fluency and ideational fluency), requiring the generation of responses over a specified time period. Fluency performance was analysed in terms of the overall number of novel items produced, as well as the number of items produced in the first 'initiation' and the remaining 'maintenance' time periods. ALS patients' overall performance was not globally reduced across tasks. Patients were impaired only on meaningful gesture fluency, which requires the generation of gestures that communicate meaning (e.g., waving). On phonemic fluency, ALS patients showed a 'drop off' pattern of performance, where they had difficulty maintaining responding over time, but this pattern was not evident on the other fluency tasks. Apathy did not appear to be related to fluency performance. The selective meaningful gesture fluency deficit, in the context of preserved meaningless gesture fluency, highlights that the retrieval of action knowledge may be weakened in early ALS., (© 2023 The Authors. Journal of Neuropsychology published by John Wiley & Sons Ltd on behalf of The British Psychological Society.)

Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2023. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

The geneticist Thomas Dobzhansky famously declared: 'Nothing in biology makes sense except in the light of evolution'. A key evolutionary adaptation of Metazoa is directed movement, which has been elaborated into a spectacularly varied number of behaviours in animal clades. The mechanisms by which animal behaviours have evolved, however, remain unresolved. This is due, in part, to the indirect control of behaviour by the genome, which provides the components for both building and operating the brain circuits that generate behaviour. These brain circuits are adapted to respond flexibly to environmental contingencies and physiological needs and can change as a function of experience. The resulting plasticity of behavioural expression makes it difficult to characterize homologous elements of behaviour and to track their evolution. Here, we evaluate progress in identifying the genetic substrates of behavioural evolution and suggest that examining adaptive changes in neuromodulatory signalling may be a particularly productive focus for future studies. We propose that the behavioural sequences used by ecdysozoans to moult are an attractive model for studying the role of neuromodulation in behavioural evolution., (Published 2022. This article is a U.S. Government work and is in the public domain in the USA. The FEBS Journal published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.)

Background and Objectives: Clinical trials developing therapeutics for frontotemporal degeneration (FTD) focus on pathogenic variant carriers at preclinical stages. Objective, quantitative clinical assessment tools are needed to track stability and delayed disease onset. Natural speech can serve as an accessible, cost-effective assessment tool. We aimed to identify early changes in the natural speech of FTD pathogenic variant carriers before they become symptomatic., Methods: In this cohort study, speech samples of picture descriptions were collected longitudinally from healthy participants in observational studies at the University of Pennsylvania and Columbia University between 2007 and 2020. Participants were asymptomatic but at risk for familial FTD. Status as "carrier" or "noncarrier" was based on screening for known pathogenic variants in the participant's family. Thirty previously validated digital speech measures derived from automatic speech processing pipelines were selected a priori based on previous studies in patients with FTD and compared between asymptomatic carriers and noncarriers cross-sectionally and longitudinally., Results: A total of 105 participants, all asymptomatic, included 41 carriers: 12 men [30%], mean age 43 ± 13 years; education, 16 ± 2 years; MMSE 29 ± 1; and 64 noncarriers: 27 men [42%]; mean age, 48 ± 14 years; education, 15 ± 3 years; MMSE 29 ± 1. We identified 4 speech measures that differed between carriers and noncarriers at baseline: mean speech segment duration (mean difference -0.28 seconds, 95% CI -0.55 to -0.02, p = 0.04); word frequency (mean difference 0.07, 95% CI 0.008-0.14, p = 0.03); word ambiguity (mean difference 0.02, 95% CI 0.0008-0.05, p = 0.04); and interjection count per 100 words (mean difference 0.33, 95% CI 0.07-0.59, p = 0.01). Three speech measures deteriorated over time in carriers only: particle count per 100 words per month (β = -0.02, 95% CI -0.03 to -0.004, p = 0.009); total narrative production time in seconds per month (β = -0.24, 95% CI -0.37 to -0.12, p < 0.001); and total number of words per month (β = -0.48, 95% CI -0.78 to -0.19, p = 0.002) including in 3 carriers who later converted to symptomatic disease., Discussion: Using automatic processing pipelines, we identified early changes in the natural speech of FTD pathogenic variant carriers in the presymptomatic stage. These findings highlight the potential utility of natural speech as a digital clinical outcome assessment tool in FTD, where objective and quantifiable measures for abnormal behavior and language are lacking.

The sacred datura plant (Solanales: Solanaceae: Datura wrightii) has been used to study plant-herbivore interactions for decades. The wealth of information that has resulted leads it to have potential as a model system for studying the ecological and evolutionary genomics of these interactions. We present a de novo Datura wrightii genome assembled using PacBio HiFi long-reads. Our assembly is highly complete and contiguous (N50 = 179Mb, BUSCO Complete = 97.6%). We successfully detected a previously documented ancient whole genome duplication using our assembly and have classified the gene duplication history that generated its coding sequence content. We use it as the basis for a genome-guided differential expression analysis to identify the induced responses of this plant to one of its specialized herbivores (Coleoptera: Chrysomelidae: Lema daturaphila). We find over 3000 differentially expressed genes associated with herbivory and that elevated expression levels of over 200 genes last for several days. We also combined our analyses to determine the role that different gene duplication categories have played in the evolution of Datura-herbivore interactions. We find that tandem duplications have expanded multiple functional groups of herbivore responsive genes with defensive functions, including UGT-glycosyltranserases, oxidoreductase enzymes, and peptidase inhibitors. Overall, our results expand our knowledge of herbivore-induced plant transcriptional responses and the evolutionary history of the underlying herbivore-response genes., (© 2023. The Author(s).)

Premise: The functional annotation of genes is a crucial component of genomic analyses. A common way to summarize functional annotations is with hierarchical gene ontologies, such as the Gene Ontology (GO) Resource. GO includes information about the cellular location, molecular function(s), and products/processes that genes produce or are involved in. For a set of genes, summarizing GO annotations using pre-defined, higher-order terms (GO slims) is often desirable in order to characterize the overall function of the data set, and it is impractical to do this manually., Methods and Results: The GOgetter pipeline consists of bash and Python scripts. From an input FASTA file of nucleotide gene sequences, it outputs text and image files that list (1) the best hit for each input gene in a set of reference gene models, (2) all GO terms and annotations associated with those hits, and (3) a summary and visualization of GO slim categories for the data set. These output files can be queried further and analyzed statistically, depending on the downstream need(s)., Conclusions: GO annotations are a widely used "universal language" for describing gene functions and products. GOgetter is a fast and easy-to-implement pipeline for obtaining, summarizing, and visualizing GO slim categories associated with a set of genes., (© 2023 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

Polyploidy is an important generator of evolutionary novelty across diverse groups in the Tree of Life, including many crops. However, the impact of whole-genome duplication depends on the mode of formation: doubling within a single lineage (autopolyploidy) versus doubling after hybridization between two different lineages (allopolyploidy). Researchers have historically treated these two scenarios as completely separate cases based on patterns of chromosome pairing, but these cases represent ideals on a continuum of chromosomal interactions among duplicated genomes. Understanding the history of polyploid species thus demands quantitative inferences of demographic history and rates of exchange between subgenomes. To meet this need, we developed diffusion models for genetic variation in polyploids with subgenomes that cannot be bioinformatically separated and with potentially variable inheritance patterns, implementing them in the dadi software. We validated our models using forward SLiM simulations and found that our inference approach is able to accurately infer evolutionary parameters (timing, bottleneck size) involved with the formation of auto- and allotetraploids, as well as exchange rates in segmental allotetraploids. We then applied our models to empirical data for allotetraploid shepherd's purse (Capsella bursa-pastoris), finding evidence for allelic exchange between the subgenomes. Taken together, our model provides a foundation for demographic modeling in polyploids using diffusion equations, which will help increase our understanding of the impact of demography and selection in polyploid lineages., Competing Interests: Conflicts of interest The author(s) declare no conflict of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Introduction: This study aims to measure frequency and correlates of initial idiopathic psychiatric diagnosis in a cohort of 147 patients with Frontotemporal Dementia (FTD)-spectrum disorders., Methods: Participants were evaluated at the National Institutes of Health in Bethesda, Maryland. Initial participant diagnoses were determined by chart review and patient and informant interviews. Logistic regression was used to assess the relationships between diagnosis and age of symptom onset, gender, education, family history of psychiatric illness, and family history of dementia. Additional exploratory analyses investigated patients' first symptom type., Results: 25% (n=43) of all the patients reviewed were initially misdiagnosed with an idiopathic psychiatric illness, which is less than half the commonly cited 50% rate. 3 Depression was the most common misdiagnosis (46.5%). Family history of dementia, family history of mental illness and an exploratory analysis of behavioral first symptoms suggested significant association with a greater likelihood of initial idiopathic psychiatric diagnosis in FTD patients., Discussion: This data confirms patterns of initial idiopathic psychiatric diagnosis in FTD and elucidates potential factors underlying misdiagnosis. Potential implications for patient outcomes, caregiver burden and healthcare costs are discussed.

Frontotemporal degeneration (FTD) is an umbrella term encompassing a range of rare neurodegenerative disorders that cause progressive declines in cognition, behavior, and personality. Hearing directly from individuals living with FTD and their care partners is critical in optimizing care, identifying meaningful clinical trial endpoints, and improving research recruitment and retention. The current paper presents a subset of data from the FTD Insights Survey, chronicling the diagnostic journey, symptoms, and the impact of FTD on distress, quality of life, and independence, in the mild to moderate stages of the disease. Survey respondents included 219 individuals diagnosed with FTD and 437 current care partners, representing a range of FTD diagnoses. Around half of survey respondents reported seeing three or more doctors before an FTD diagnosis was given, and a range of prior diagnoses were noted. Most frequently endorsed symptoms tended to be consistent with clinical characteristics of the specific diagnosis, though there was significant variability in symptoms reported within diagnostic categories as well as considerable overlap in symptoms between diagnostic categories. Cognitive and language symptoms of FTD were generally most distressing to the person diagnosed, and a loss of independence was endorsed as affecting quality of life. The distinct perspectives of diagnosed persons and care partners regarding disease impact differed notably for bvFTD/Pick's disease. Participating independently in a range of activities, within the home, outside the home, and with other people, were reported as challenging for people living with FTD, underscoring the degree to which the lives of these individuals are affected even at the mild and moderate stages of disease. Overall, by heeding the perspectives of those living with FTD, we can begin to design more meaningful research studies, provide better care, and develop therapies that improve quality of life.

Corpus callosum dysgenesis is a congenital abnormality whereby the corpus callosum fails to develop normally, and has been associated with a range of neuropsychological outcomes. One specific finding in some individuals with corpus callosum dysgenesis is "congenital mirror movement disorder", which is the presence of involuntary movements on one side of the body that mimic voluntary movements of the other side. Mirror movements have also been associated with mutations in the deleted in colorectal carcinoma (DCC) gene. The current study aims to comprehensively document the neuropsychological outcomes and neuroanatomical mapping of a family (a mother, daughter and son) with known DCC mutations. All three family members experience mirror movements, and the son additionally has partial agenesis of the corpus callosum (pACC). All family members underwent extensive neuropsychological testing, spanning general intellectual functioning, memory, language, literacy, numeracy, psychomotor speed, visuospatial perception, praxis and motor functioning, executive functioning, attention, verbal/nonverbal fluency, and social cognition. The mother and daughter had impaired memory for faces, and reduced spontaneous speech, and the daughter demonstrated scattered impairments in attention and executive functioning, but their neuropsychological abilities were largely within normal limits. By contrast, the son showed areas of significant impairment across multiple domains including reduced psychomotor speed, fine motor dexterity and general intellectual functioning, and he was profoundly impaired across areas of executive functioning and attention. Reductions in his verbal/non-verbal fluency, with relatively intact core language, resembled dynamic frontal aphasia. His relative strengths included aspects of memory and he demonstrated largely sound theory of mind. Neuroimaging revealed an asymmetric sigmoid bundle in the son, connecting, via the callosal remnant, the left frontal cortex with contralateral parieto-occipital cortex. Overall, this study documents a range of neuropsychological and neuroanatomical outcomes within one family with DCC mutations and mirror movements, including one with more severe consequences and pACC., Competing Interests: Declaration of competing interest All authors declare no conflicts of interest., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Background and Objectives: This prospective study seeks to examine the utility of subjective cognitive decline (SCD) as a marker of future progression to dementia in a community-based cohort of non-Latinx White, non-Latinx Black, and Latinx individuals. Debate surrounds the utility of SCD, the subjective perception of decline in one's cognition before such impairment is evident in traditional neuropsychological assessments, as an early indicator of impending Alzheimer disease. Unfortunately, most studies examining SCD have been conducted in non-Latinx White samples and commonly exclude groups of individuals shown to be most vulnerable to dementia., Methods: Participants were enrolled into this cohort study from the Washington Heights-Inwood Columbia Aging Project if they were cognitively unimpaired, had baseline measurement of SCD, and self-identified as non-Latinx White, non-Latinx Black, or Latinx. SCD was measured as a continuous sum of 10 items assessing cognitive complaints. Competing risk models tested the main effects of baseline SCD on progression to dementia. Models were adjusted for age, sex/gender, years of education, medical comorbidity burden, enrollment cohort, and baseline memory test performance with death jointly modelled as a function of race/ethnicity., Results: A total of 4,043 (1,063 non-Latinx White, 1,267 non-Latinx Black, and 1,713 Latinx) participants were selected for this study with a mean age of 75 years, 67% women, and with a mean follow-up of 5 years. Higher baseline SCD was associated with increased rates of incident dementia over time in the full sample (hazard ratio [HR] 1.085, CI 1.047-1.125, p < 0.001) and within Latinx (HR 1.084, CI 1.039-1.130, p < 0.001) and non-Latinx Black individuals (HR 1.099, CI 1.012-1.194, p = 0.024)., Discussion: Overall results of this study support SCD as a prodromal marker of dementia in a multiracial community sample, and in Latinx and non-Latinx Black individuals in particular. Because models examining the risk of dementia were adjusted for baseline memory test performance, the results support the idea that SCD, a subjective reflection of one's own current cognitive functioning, contributes information above and beyond standard memory testing. Current findings highlight the importance of carefully evaluating any memory concerns raised by older adults during routine visits and underscore the potential utility of screening older adults for SCD., (© 2022 American Academy of Neurology.)

Nearly all lineages of land plants have experienced at least one whole-genome duplication (WGD) in their history. The legacy of these ancient WGDs is still observable in the diploidized genomes of extant plants. Genes originating from WGD-paleologs-can be maintained in diploidized genomes for millions of years. These paleologs have the potential to shape plant evolution through sub- and neofunctionalization, increased genetic diversity, and reciprocal gene loss among lineages. Current methods for classifying paleologs often rely on only a subset of potential genomic features, have varying levels of accuracy, and often require significant data and/or computational time. Here, we developed a supervised machine learning approach to classify paleologs from a target WGD in diploidized genomes across a broad range of different duplication histories. We collected empirical data on syntenic block sizes and other genomic features from 27 plant species each with a different history of paleopolyploidy. Features from these genomes were used to develop simulations of syntenic blocks and paleologs to train a gradient boosted decision tree. Using this approach, Frackify (Fractionation Classify), we were able to accurately identify and classify paleologs across a broad range of parameter space, including cases with multiple overlapping WGDs. We then compared Frackify with other paleolog inference approaches in six species with paleotetraploid and paleohexaploid ancestries. Frackify provides a way to combine multiple genomic features to quickly classify paleologs while providing a high degree of consistency with existing approaches., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Psychiatric symptoms, including changes in emotional processing, are a common feature of many neurodegenerative disorders, such as Alzheimer's disease, dementia with Lewy Bodies, frontotemporal dementia, and Huntington's disease. However, the neuroanatomical basis of emotional symptoms is not well defined; this stands in contrast to the relatively well-understood neuroanatomical correlates of cognitive and motor symptoms in neurodegenerative disorders. Furthermore, psychiatric diagnostic categories, as defined by the Diagnostic and Statistical Manual of Mental Disorders (DSM) and International Statistical Classification of Diseases and Related Health Problems (ICD), may have limited applicability in patients with late-onset psychiatric symptoms in the context of neurodegenerative disorders. In this clinical review, we suggest that early-onset and late-onset psychiatric symptoms have distinct etiologies, and that late-onset changes in emotional processing are likely underpinned by neurodegenerative disease. Furthermore, we suggest that an improved understanding of the neuroanatomical correlates of emotional changes in neurodegenerative disease may facilitate diagnosis and future treatment development. Finally, we propose a novel clinical approach, in a preliminary attempt to incorporate late-onset emotional symptoms alongside cognitive and motor symptoms into a clinical "algorithm," with a focus on the neuroanatomy implicated when particular combinations of emotional, cognitive, and motor features are present. We anticipate that this clinical approach will assist with the diagnosis of neurodegenerative disorders, and our proposed schema represents a move towards integrating neurologic and psychiatric classification systems.

Introduction: Executive functions comprise a suite of higher-order cognitive processes, which interact with other processes, such as emotion , to drive goal-directed behavior. The Hayling Sentence Completion Test is a widely used standard neuropsychological tool to measure executive functions, namely verbal initiation and suppression. The current studies aimed to establish and validate an emotion-eliciting version of the Hayling Sentence Completion Test, in order to examine the executive processes of initiation and suppression in an emotional context. Study 1 aimed to provide a quantitative evaluation of the emotional content of the Emotional Hayling Test. Study 2 investigated the differences between the Standard and Emotional Hayling Tests, and explored how performance relates to specific emotional properties of the sentences within the Emotional Hayling., Methods: Study 1 included N = 100 participants, who were asked to rate each Emotional Hayling Sentence stem in terms of valence (pleasant-unpleasant) and arousal (intensity: low-high). Study 2 included N = 204 participants who completed the Emotional Hayling Test, along with other neuropsychological measures of cognitive and affective functioning., Results: As designed, the sentence stimuli in the Emotional Hayling were rated as significantly higher in absolute emotional valence and arousal, compared to the Standard Hayling (Study 1). Overall, initiation and suppression on the Emotional Hayling were significantly poorer than on the Standard Hayling (Study 2). Finally, within the Emotional Hayling, participants made more suppression errors in response to negative sentences compared to positive sentences, and this effect was present in younger but not older adults., Conclusions: Reduced performance on the Emotional Hayling Test, particularly in response to negative sentences, is consistent with the emotional content placing increased demands on the executive function system. We present the Emotional Hayling Test as a promising clinical tool, with the potential to capture disruptions in emotional processing.

Objective: While subjective cognitive decline (SCD) is gaining ground as a "preclinical" risk state for Alzheimer disease, its utility depends on our understanding of the factors linked to SCD. Rarely examined sociocultural factors including perceptions of aging may relate to the subjective experience of cognitive aging. Identifying such associations will help to refine the utility of SCD as an early marker of AD while setting the stage for addressing modifiable factors contributing to SCD., Methods: The study consisted of N=136 participants (68% female; 73% White; 22% Black race, age mean =74.72; education mean =16.01). Questionnaires assessed SCD, depressive symptoms, and age perceptions (essentialist aging beliefs, subjective age, age group identification, and explicit/implicit age stereotypes). Cognitive functioning was measured with a semantic interference and learning task., Results: SCD was correlated with essentialist aging beliefs, age identification, and depressive symptoms [ rrange =0.18 to 0.22, Prange =0.009 to 0.02, confidence interval (CI) range =0.00-0.39]. Essentialist aging beliefs were correlated with subjective age and age group identification ( rrange =0.22 to 0.42, Prange <0.001 to 0.003, CI range =0.08-0.57). Both age group identification and essentialism were correlated with depressive symptoms ( rrange =0.22, Prange =0.009 to 0.01, CI range =0.04-0.39). In the adjusted regression model including depressive symptoms, age perceptions, and SCD, only SCD was associated with cognition ( b =-0.31, P <0.001)., Conclusion: Although correlated with SCD, perceptions of aging do not explain the relationship between SCD and performance on a sensitive cognitive test among older adults., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.)

Introduction: Caregivers of patients with frontotemporal lobar degeneration (FTLD) spectrum disorders experience tremendous burden, which has been associated with the neuropsychiatric and behavioral features of the disorders., Methods: In a sample of 558 participants with FTLD spectrum disorders, we performed multiple-variable regressions to identify the behavioral features that were most strongly associated with caregiver burden, as measured by the Zarit Burden Interview, at each stage of disease., Results: Apathy and disinhibition, as rated by both clinicians and caregivers, as well as clinician-rated psychosis, showed the strongest associations with caregiver burden, a pattern that was consistent when participants were separated cross-sectionally by disease stage. In addition, behavioral features appeared to contribute most to caregiver burden in patients with early dementia., Discussion: Caregivers should be provided with early education on the management of the behavioral features of FTLD spectrum disorders. Interventions targeting apathy, disinhibition, and psychosis may be most useful to reduce caregiver burden., (© 2021 the Alzheimer's Association.)

The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology., (© 2022. The Author(s).)

Objective: The aims of this study were to investigate occupational and non-work-related risk factors of coronavirus disease 2019 among health care workers (HCWs) in Vancouver Coastal Health, British Columbia, Canada, and to examine how HCWs described their experiences., Methods: This was a matched case-control study using data from online and phone questionnaires with optional open-ended questions completed by HCWs who sought severe acute respiratory syndrome coronavirus 2 testing between March 2020 and March 2021. Conditional logistic regression and thematic analysis were utilized., Results: Providing direct care to coronavirus disease 2019 patients during the intermediate cohort period (adjusted odds ratio, 1.90; 95% confidence interval, 1.04 to 3.46) and community exposure to a known case in the late cohort period (adjusted odds ratio, 3.595%; confidence interval, 1.86 to 6.83) were associated with higher infection odds. Suboptimal communication, mental stress, and situations perceived as unsafe were common sources of dissatisfaction., Conclusions: Varying levels of risk between occupational groups call for wider targeting of infection prevention measures. Strategies for mitigating community exposure and supporting HCW resilience are required., Competing Interests: Conflict of interest: A.I.O. and A.Y. earn fees for consultancy services to Vancouver Coastal Health. J.G. earns salaries from Vancouver Coastal Health. Vancouver Coastal Health played no role in the design and implementation of this project or in the writing of this manuscript. K.L., S.B., and A.I.O. have parts of their salary paid out of grants from the International Development Research Centre and the Canadian Institutes of Health Research. The other authors declare no conflict of interest., (Copyright © 2022 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American College of Occupational and Environmental Medicine.)

At present, no research criteria exist for the diagnosis of prodromal behavioural variant frontotemporal dementia (bvFTD), though early detection is of high research importance. Thus, we sought to develop and validate a proposed set of research criteria for prodromal bvFTD, termed 'mild behavioural and/or cognitive impairment in bvFTD' (MBCI-FTD). Participants included 72 participants deemed to have prodromal bvFTD; this comprised 55 carriers of a pathogenic mutation known to cause frontotemporal lobar degeneration, and 17 individuals with autopsy-confirmed frontotemporal lobar degeneration. All had mild behavioural and/or cognitive changes, as judged by an evaluating clinician. Based on extensive clinical workup, the prodromal bvFTD group was divided into a Development Group (n = 22) and a Validation Group (n = 50). The Development Group was selected to be the subset of the prodromal bvFTD group for whom we had the strongest longitudinal evidence of conversion to bvFTD, and was used to develop the MBCI-FTD criteria. The Validation Group was the remainder of the prodromal bvFTD group and was used as a separate sample on which to validate the criteria. Familial non-carriers were included as healthy controls (n = 165). The frequencies of behavioural and neuropsychiatric features, neuropsychological deficits, and social cognitive dysfunction in the prodromal bvFTD Development Group and healthy controls were assessed. Based on sensitivity and specificity analyses, seven core features were identified: apathy without moderate-severe dysphoria, behavioural disinhibition, irritability/agitation, reduced empathy/sympathy, repetitive behaviours (simple and/or complex), joviality/gregariousness, and appetite changes/hyperorality. Supportive features include a neuropsychological profile of impaired executive function or naming with intact orientation and visuospatial skills, reduced insight for cognitive or behavioural changes, and poor social cognition. Three core features or two core features plus one supportive feature are required for the diagnosis of possible MBCI-FTD; probable MBCI-FTD requires imaging or biomarker evidence, or a pathogenic genetic mutation. The proposed MBCI-FTD criteria correctly classified 95% of the prodromal bvFTD Development Group, and 74% of the prodromal bvFTD Validation Group, with a false positive rate of <10% in healthy controls. Finally, the MBCI-FTD criteria were tested on a cohort of individuals with prodromal Alzheimer's disease, and the false positive rate of diagnosis was 11-16%. Future research will need to refine the sensitivity and specificity of these criteria, and incorporate emerging biomarker evidence., (© The Author(s) (2022). Published by Oxford University Press on behalf of the Guarantors of Brain.)

Objective: Subjective cognitive decline (SCD) has emerged as one of the first manifestations of Alzheimer's disease (AD). However, discrepancies in its relationship with tests of memory and other cognitive abilities have hindered SCD's diagnostic utility. Inter-individual heterogeneity in metamemory, or memory awareness, and the use of clinical measures of cognition lacking sensitivity to early cognitive dysfunction, may contribute to these discrepancies. We aimed to assess if the relationship between SCD and markers of early cognitive dysfunction is moderated by metamemory abilities., Methods: The sample included 79 cognitively healthy older adults (77% female, 68% White, and 32% Black participants) with a mean age of 74.4 ( SD = 6.1) and 15.9 ( SD = 2.7) years of education. Metamemory was assessed using an episodic Feeling of Knowing test with four 5-item trials. Outcome measures included a resolution metric defined as a gamma correlation reflecting the accuracy of item-level predictions ("Will you know the correct answer?"). Early cognitive dysfunction was measured through the Loewenstein-Acevedo Scale for Semantic Interference and Learning (LASSI-L) and the Short-Term Memory Binding Test (STMB), measures sensitive to preclinical AD. SCD was assessed with a 20-item questionnaire that asked participants to compare themselves to others their age on a 7-point Likert scale. Regression analyses examined whether a potential relation between SCD and early cognitive dysfunction was moderated by metamemory., Results: Subjective cognitive decline was associated with susceptibility to semantic proactive interference such that greater complaints were associated with increased susceptibility to semantic proactive interference ( b = -0.30, p = 0.003) only. Metamemory moderated the association between SCD and susceptibility to and recovery of semantic proactive interference such that those with more accurate metamemory showed a stronger association between increased complaints and susceptibility to semantic proactive interference ( b = -0.71, p = 0.005; b = -0.62, p = 0.034). Metamemory, however, did not moderate the association of SCD with retroactive semantic interference nor short term memory binding., Discussion: The accuracy of an individual's metamemory, specifically their ability to adjust moment to moment predictions in line with their performance, can influence the extent to which SCD maps onto objective cognition. Such self-referential assessment should be considered when interpreting SCD., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Chapman, Joyce, Barker, Sunderaraman, Rizer, Huey, Dworkin, Gu and Cosentino.)

Substantial morphological variation in land plants remains inaccessible to genetic analysis because current models lack variation in important ecological and agronomic traits. The genus Gilia was historically a model for biosystematics studies and includes variation in morphological traits that are poorly understood at the genetic level. We assembled a chromosome-scale reference genome of G. yorkii and used it to investigate genome evolution in the Polemoniaceae. We performed QTL (quantitative trait loci) mapping in a G. yorkii×G. capitata interspecific population for traits related to inflorescence architecture and flower color. The genome assembly spans 2.75 Gb of the estimated 2.80-Gb genome, with 96.7% of the sequence contained in the nine largest chromosome-scale scaffolds matching the haploid chromosome number. Gilia yorkii experienced at least one round of whole-genome duplication shared with other Polemoniaceae after the eudicot paleohexaploidization event. We identified QTL linked to variation in inflorescence architecture and petal color, including a candidate for the major flower color QTL-a tandem duplication of flavanol 3',5'-hydroxylase. Our results demonstrate the utility of Gilia as a forward genetic model for dissecting the evolution of development in plants including the causal loci underlying inflorescence architecture transitions., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

The ability to select an idea from an array of competing options is critical for successful propositional language production, and deficient idea selection contributes to propositional language impairments in clinical populations. We investigate whether three clinical idea selection tasks are sensitive to selection demands in neurologically unimpaired adults, and whether performance relates to age. 154 neurologically normal adults aged 18-89 years completed a neuropsychological baseline and three  idea selection tasks. Stimuli either activated a dominant response or multiple competing response options. All three idea selection tasks were sensitive to selection demands in terms of reaction times but not errors. Older age was associated with greater effects of selection demands on Sentence Completion task performance only. Exploratory analyses revealed a potential role of executive functioning. Overall, we demonstrate that clinical idea selection tasks are sensitive to idea selection demands in a non-clinical sample, and show some age-related differences in performance.

Background: Genome size is implicated in the form, function, and ecological success of a species. Two principally different mechanisms are proposed as major drivers of eukaryotic genome evolution and diversity: polyploidy (i.e., whole-genome duplication) or smaller duplication events and bursts in the activity of repetitive elements. Here, we generated de novo genome assemblies of 17 caddisflies covering all major lineages of Trichoptera. Using these and previously sequenced genomes, we use caddisflies as a model for understanding genome size evolution in diverse insect lineages., Results: We detect a ∼14-fold variation in genome size across the order Trichoptera. We find strong evidence that repetitive element expansions, particularly those of transposable elements (TEs), are important drivers of large caddisfly genome sizes. Using an innovative method to examine TEs associated with universal single-copy orthologs (i.e., BUSCO genes), we find that TE expansions have a major impact on protein-coding gene regions, with TE-gene associations showing a linear relationship with increasing genome size. Intriguingly, we find that expanded genomes preferentially evolved in caddisfly clades with a higher ecological diversity (i.e., various feeding modes, diversification in variable, less stable environments)., Conclusion: Our findings provide a platform to test hypotheses about the potential evolutionary roles of TE activity and TE-gene associations, particularly in groups with high species, ecological, and functional diversities., (© The Author(s) 2022. Published by Oxford University Press GigaScience.)

Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence., (© 2021 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO 2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigate underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identify several key differences. Notably, Isoetes may have recruited the lesser-known 'bacterial-type' PEPC, along with the 'plant-type' exclusively used in other CAM and C4 plants for carboxylation of PEP. Furthermore, we find that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized., (© 2021. The Author(s).)

Inferring the frequency and mode of hybridization among closely related organisms is an important step for understanding the process of speciation and can help to uncover reticulated patterns of phylogeny more generally. Phylogenomic methods to test for the presence of hybridization come in many varieties and typically operate by leveraging expected patterns of genealogical discordance in the absence of hybridization. An important assumption made by these tests is that the data (genes or SNPs) are independent given the species tree. However, when the data are closely linked, it is especially important to consider their nonindependence. Recently, deep learning techniques such as convolutional neural networks (CNNs) have been used to perform population genetic inferences with linked SNPs coded as binary images. Here, we use CNNs for selecting among candidate hybridization scenarios using the tree topology (((P 1 , P 2 ), P 3 ), Out) and a matrix of pairwise nucleotide divergence (d XY ) calculated in windows across the genome. Using coalescent simulations to train and independently test a neural network showed that our method, HyDe-CNN, was able to accurately perform model selection for hybridization scenarios across a wide breath of parameter space. We then used HyDe-CNN to test models of admixture in Heliconius butterflies, as well as comparing it to phylogeny-based introgression statistics. Given the flexibility of our approach, the dropping cost of long-read sequencing and the continued improvement of CNN architectures, we anticipate that inferences of hybridization using deep learning methods like ours will help researchers to better understand patterns of admixture in their study organisms., (© 2021 John Wiley & Sons Ltd.)

Cardiovacular disease (CVD) is the leading cause of death among older adults and is often accompanied by functional decline. It is unclear what is driving this co-occurrence, but it may be behavioral, environmental and/or genetic. We used a family-based study to estimate the phenotypic and shared genetic correlation between CVD risk factors and physical and cognitive functional measures. Participants (n = 1,881) were from the Long Life Family Study, which enrolled families based on their exceptional longevity (sample mean age = 69.4 years, 44% female). Cardiovascular disease risk factors included carotid vessel measures [intima-media thickness and inter-adventitial diameter], obesity [body mass index (BMI) and waist circumference], and hypertension [systolic and diastolic blood pressures]. Function was measured in the physical [gait speed, grip strength, chair stand] and cognitive [digital symbol substitution test, retained and working memory, semantic fluency, and trail making tests] domains. We used SOLAR to estimate the genetic, environmental, and phenotypic correlation between each pair adjusting for age, age 2 , sex, field center, smoking, height, and weight. There were significant phenotypic correlations (range |0.05-0.22|) between CVD risk factors and physical and cognitive function (all P < 0.05). Most significant genetic correlations (range |0.21-0.62|) were between CVD risk factorsand cognitive function, although BMI and waist circumference had significant genetic correlation with gait speed and chair stand time (range |0.29-0.53|; all P < 0.05). These results suggest that CVD risk factors may share a common genetic-and thus, biologic-basis with both cognitive and physical function. This is particularly informative for research into the genetic determinants of chronic disease., (© 2021. The Author(s).)

Understanding the mechanisms that underlie chromosome evolution could provide insights into the processes underpinning the origin, persistence and evolutionary tempo of lineages. Here, we present the first database of chromosome counts for animals (the Animal Chromosome Count database, ACC) summarizing chromosome numbers for ~15,000 species. We found remarkable a similarity in the distribution of chromosome counts between animals and flowering plants. Nevertheless, the similarity in the distribution of chromosome numbers between animals and plants is likely to be explained by different drivers. For instance, we found that while animals and flowering plants exhibit similar frequencies of speciation-related changes in chromosome number, plant speciation is more often related to changes in ploidy. By leveraging the largest data set of chromosome counts for animals, we describe a previously undocumented pattern across the Tree of Life-animals and flowering plants show remarkably similar distributions of haploid chromosome numbers., (© 2021 European Society for Evolutionary Biology.)

Most land plants are now known to be ancient polyploids that have rediploidized. Diploidization involves many changes in genome organization that ultimately restore bivalent chromosome pairing and disomic inheritance, and resolve dosage and other issues caused by genome duplication. In this review, we discuss the nature of polyploidy and its impact on chromosome pairing behavior. We also provide an overview of two major and largely independent processes of diploidization: cytological diploidization and genic diploidization/fractionation. Finally, we compare variation in gene fractionation across land plants and highlight the differences in diploidization between plants and animals. Altogether, we demonstrate recent advancements in our understanding of variation in the patterns and processes of diploidization in land plants and provide a road map for future research to unlock the mysteries of diploidization and eukaryotic genome evolution.

Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine-type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.

Although executive dysfunction is the characteristic cognitive marker of behavioral variant frontotemporal dementia (bvFTD), episodic memory deficits are relatively common, and may be present even during the prodromal disease phase. In a cohort of mutation carriers with mild behavioral and/or cognitive symptoms consistent with prodromal bvFTD, we aimed to investigate patterns of performance on an abbreviated list learning task, with a particular focus on recognition memory. We further aimed to characterize the cognitive prodromes associated with the three major genetic causes of frontotemporal dementia, as emerging evidence suggests there may be subtle differences in cognitive profiles among carriers of different genetic mutations. Participants included 57 carriers of a pathogenic mutation in microtubule-associated protein tau (MAPT, N = 23), or progranulin (GRN, N = 15), or a or a hexanucleotide repeat expansion in chromosome 9 open reading frame 72 (C9orf72, N = 19), with mild cognitive and/or behavioral symptoms consistent with prodromal bvFTD. Familial non-carriers were included as controls (N = 143). All participants completed a comprehensive neuropsychological examination, including an abbreviated list learning test assessing episodic memory recall and recognition. MAPT mutation carriers performed worse than non-carriers in terms of list recall, and had difficulty discriminating targets from distractors on the recognition memory task, primarily due to the endorsement of distractors as targets. MAPT mutation carriers also showed nonverbal episodic memory and semantic memory dysfunction (object naming). GRN mutation carriers were variable in performance and overall the most dysexecutive. Slowed psychomotor speed was evident in C9orf72 repeat expansion carriers. Identifying the earliest cognitive indicators of bvFTD is of critical clinical and research importance. List learning may be a sensitive cognitive marker for incipient dementia in MAPT and potentially a subset of GRN carriers. Our results highlight that distinct cognitive profiles may be evident in carriers of the three disease-causing genes during the prodromal disease stage., Competing Interests: Declaration of competing interest M.S. Barker, Ph.D.: Nothing to disclose. M. Manoochehri, B.A.: Nothing to disclose. S.J. Rizer, M.A.: Nothing to disclose. B.S. Appleby, M.D.: Has received research funding from Centers for Disease Control and prevention, National Institutes of Health, Ionis, & Alector. D. Brushaber, B.S.: Nothing to disclose. S.I. Dev, Ph.D.: Nothing to disclose. K.L. Devick, Ph.D.: Nothing to disclose. B.C. Dickerson, M.D.: Research support from National Institutes of Health, Alzheimer's Drug Discovery Foundation, consulting for Acadia, Arkuda, Axovant, Lilly, Biogen, Merck, Novartis, Wave LifeSciences. Editorial duties with payment for Elsevier (Neuroimage: Clinical and Cortex). Royalties from Oxford University Press and Cambridge University Press. J.A. Fields, Ph.D., L.P.: Receives research funding from the National Institutes of Health. T.M. Foroud, Ph.D.: Nothing to disclose. L.K. Forsberg, Ph.D.: Nothing to disclose. D.R. Galasko, M.D.: Paid consultant for Biogen, vTv Pharmaceuticals, Cognition Theraptutics, Fujirebio and Amprion and received payment as a journal Editor from Springer. N. Ghoshal, M.D., Ph.D.: Has participated or is currently participating in clinical trials of anti-dementia drugs sponsored by the following companies: Bristol Myers Squibb, Lilly/Avid Radiopharmaceuticals, Janssen, Novartis, Pfizer, Wyeth, SNIFF (The Study of Nasal Insulin to Fight Forgetfulness) study, and A4 (The Anti-Amyloid Treatment in Asymptomatic Alzheimer's Disease) trial. She receives research support from Tau Consortium and Association for Frontotemporal Dementia and is funded by the National Institutes of Health. N.R. Graff-Radford, MBBCh: Takes part in multicenter studies funded by Biogen, AbbVie, and Lilly. M. Grossman, M.D., Ed.D.: Nothing to disclose. H.W. Heuer, Ph.D.: Nothing to disclose. G-Y. Hsiung, M.D.: Has received research support as a clinical trials site investigator from Anavax, Biogen, Eli Lilly and Roche; and has received research funding from the Canadian Institutes of Health Research, Alzheimer Society of Canada, and National Institutes of Health. J. Kornak, Ph.D.: Has provided expert witness testimony for 1) Teva Pharmaceuticals in Forest Laboratories Inc. et al. v. Teva Pharmaceuticals USA, Inc., Case Nos. 1:14-cv-00121 and 1:14-cv-00686 (D. Del. filed Jan. 31, 2014 and May 30, 2014) regarding the drug Memantine; 2) for Apotex/HEC/Ezra in Novartis AG et al. v. Apotex Inc., No. 1:15-cv-975 (D. Del. filed Oct. 26, 2015, regarding the drug Fingolimod; 3) on behalf of Puma Biotechnology in Hsingching Hsu et al. versus Puma Biotechnology, INC., et al., 2018 regarding the drug Neratinib and 4) on behalf of Hikma Pharmaceuticals in Amarin Pharma, Inc versus Hikma Pharmaceuticals in 2019. He receives research support from the National Institutes of Health. I. Litvan, M.D.: Research is supported by the National Institutes of Health grants: 5P50AG005131-33, 2R01AG038791-06A, U01NS090259, U01NS100610, U01NS80818, R25NS098999, P20GM109025; U19 AG063911-1; 1R21NS114764-01A1; Parkinson Study Group, Michael J Fox Foundation, Parkinson Foundation, Lewy Body Association, Parkinson Foundation, Roche, Abbvie, Biogen, EIP-Pharma and Biohaven Pharmaceuticals. She was member of a Lundbeck Advisory Board and Corticobasal Degeneration Solutions. She receives her salary from the University of California San Diego and as Chief Editor of Frontiers in Neurology. I.R. Mackenzie, M.D.: Scientific advisory board member for Prevail Therapeutics. M.F. Mendez, M.D.: Nothing to disclose. B. Pascual, Ph.D. Nothing to disclose. K.P. Rankin, Ph.D.: Funding from the National Institutes of Health, Quest Diagnostics, the Rainwater Charitable Foundation, and the Marcus Foundation. K. Rascovsky, Ph.D.: Nothing to disclose. A.M. Staffaroni, Ph.D.: Receives research funding from the National Institute on Aging-National Institutes of Health and Larry L. Hillblom Foundation. M.C. Tartaglia, M.D.: Nothing to disclose. S. Weintraub, Ph.D.: Nothing to disclose. B. Wong, Ph.D.: Nothing to disclose. B.F. Boeve, M.D.: Has served as an investigator for clinical trials sponsored by GE Healthcareand Axovant. He receives royalties from the publication of a book entitled Behavioral Neurology Of Dementia (Cambridge Medicine, 2009,2017). He serves on the Scientific Advisory Board of the Tau Consortium. He receives research support from National Institutes of Health, the Mayo Clinic Dorothy and Harry T. Mangurian Jr. Lewy Body Dementia Program and the Little Family Foundation. A.L. Boxer, M.D., Ph.D.: Receives research support from National Institutes of Health, the Tau Research Consortium, the Association for Frontotemporal Degeneration and the Bluefield Project to Cure Frontotemporal Dementia. He has served as a consultant for AGTC, Alector, Arkuda, Arvinas, Bioage, Ionis, Lundbeck, Passage BIO, Samumed, Ono, Sangamo, Stealth, Transposon, UCBand Wave, and received research support from Avid, Eisai, Biogen and Roche. H. Rosen, M.D.: has received research support from Biogen Pharmaceuticals, has consulting agreements with Wave Neuroscience and Ionis Pharmaceuticals, and receives research support from National Institutes of Health. J. Goldman, M.S., M.Phil.: Receives research support from National Institutes of Health, Huntington's Disease Society of America, New York State Department of Health (RFA #1510130358). E.D. Huey, M.D.: Nothing to disclose. S. Cosentino, Ph.D.: Nothing to disclose., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

The members of the tribe Brassiceae share a whole-genome triplication (WGT), and one proposed model for its formation is a two-step pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here, we report a new genome sequence of Crambe hispanica , a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using the Polyploidy Orthology Inference Tool (POInT). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring before the arrival of the third. We also, for the 90,000 individual genes in our study, make parental subgenome assignments, inferring, with measured uncertainty, from which of the progenitor genomes of the allohexaploidy each gene derives. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty., (© 2021 Hao et al.; Published by Cold Spring Harbor Laboratory Press.)

Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication. In order to test the connection between domestication and polyploidy, we identified and examined candidate genes associated with the domestication of the diverse crop varieties of Brassica rapa. Like all 'diploid' flowering plants, B. rapa has a diploidized paleopolyploid genome and experienced many rounds of whole genome duplication (WGD). We analyzed transcriptome data of more than 100 cultivated B. rapa accessions. Using a combination of approaches, we identified > 3000 candidate genes associated with the domestication of four major B. rapa crop varieties. Consistent with our expectation, we found that the candidate genes were significantly enriched with genes derived from the Brassiceae mesohexaploidy. We also observed that paleologs were significantly more diverse than non-paleologs. Our analyses find evidence for that genetic diversity derived from ancient polyploidy played a key role in the domestication of B. rapa and provide support for its importance in the success of modern agriculture., (© 2021 The Authors New Phytologist © 2021 New Phytologist Foundation.)

Verbal adynamia is characterized by markedly reduced spontaneous speech that is not attributable to a core language deficit such as impaired naming, reading, repetition, or comprehension. In some cases, verbal adynamia is severe enough to be considered dynamic aphasia. We report the case of a 40-year-old, left-handed, male native English speaker who presented with partial rhombencephalosynapsis, corpus callosum dysgenesis, and a language profile that is consistent with verbal adynamia, or subclinical dynamic aphasia, possibly underpinned by difficulties selecting and generating ideas for expression. This case is only the second investigation of dynamic aphasia in an individual with a congenital brain malformation. It is also the first detailed neuropsychological report of an adult with partial rhombencephalosynapsis and corpus callosum dysgenesis, and the only known case of superior intellectual abilities in this context., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

Premise: Large-scale projects such as the National Ecological Observatory Network (NEON) collect ecological data on entire biomes to track climate change. NEON provides an opportunity to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA-seq data from diverse plant communities., Methods: We generated >650 Gbp of RNA-seq for 24 vascular plant species representing 12 genera and nine families at the Harvard Forest NEON site. Each species was sampled twice in 2016 (July and August). We assessed transcriptome quality and content with TransRate, BUSCO, and Gene Ontology annotations., Results: Only modest differences in assembly quality were observed across multiple k -mers. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated transcripts between diploid and polyploid transcriptomes., Discussion: We provide new RNA-seq data sets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high-quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers opportunities for large-scale studies at the intersection of ecology and genomics., (© 2021 Marx et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.)

Background: Cognitive processes associated with frontal lobe functioning are often termed "executive functions." Two such processes are initiation and inhibition or the starting and stopping of responses. It has recently been claimed dysfunction of executive abilities can be explained by a single measure of fluid intelligence. Here, we test this claim, specifically for the executive abilities of response initiation and inhibition, across the healthy lifespan., Method: In a cohort of 336 healthy adults (18-89 years), initiation and inhibition were assessed with the Hayling test, Stroop test, and phonemic and semantic verbal fluency. All participants also completed a measure of fluid intelligence. The relationship between fluid intelligence and executive measures was explored across the lifespan using a continuous approach. Mediation models were computed to assess whether age-related decline across the four initiation/inhibition tasks could be fully explained by a single measure of fluid intelligence., Results: Age was negatively correlated with response initiation/inhibition and fluid intelligence. The mediation analyses identified only partial mediation of fluid intelligence for age and Hayling performance. By contrast, fluid intelligence did not mediate performance on the Stroop test or phonemic and semantic verbal fluency., Conclusions: Response initiation/inhibition are not able to be explained by fluid intelligence. The results support a multifactorial theory of executive functions and provide evidence for the inclusion of multiple specific executive measures in a thorough neuropsychological assessment of age-related cognitive decline., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.)

Background: The utility of subjective cognitive decline (SCD) as an indicator of preclinical AD is overshadowed by its inconsistent association with objective cognition., Objective: This study examines if manipulations of SCD measurement affect its association with early cognitive dysfunction characteristic of preclinical AD., Methods: Cognitively healthy older adults (n = 110) completed SCD questionnaires that elicited complaints in general, compared to 5 years ago (retrospective SCD) and compared to their peers (age-anchored SCD) in binary and Likert scales. Outcome cognitive tasks included an associative memory task (Face-Name Test), a visual short-term memory binding task (STMB test), and a clinical neuropsychological list learning test (Selective Reminder Test)., Results: SCD complaints, when compared to age-matched peers (age-anchored SCD) were endorsed less frequently than complaints compared to 5 years ago (retrospective SCD) (p < 0.01). In demographically adjusted regressions, age-anchored ordinal-rated SCD was associated with short term memory binding (β= -0.22, p = 0.040, CI = -0.45, -0.01), associative memory (β= -0.26, p = 0.018, CI = -0.45, -0.06), and list learning (β= -0.31, p = 0.002, CI = -0.51, -0.12). Retrospective and general ordinal-rated SCD was associated with associative memory (β= -0.25, p = 0.012, CI = -0.44, -0.06; β= -0.29, p = 0.003, CI = -0.47, -0.10) and list learning only (β= -0.25, p = 0.014, CI = -0.45, -0.05; β= -0.28, p = 0.004, CI = -0.48, -0.09)., Conclusion: Ordinal age-anchored SCD appears better suited than other SCD measurements to detect early cognitive dysfunction characteristic of preclinical AD.

Background: The Long Life Family Study (LLFS) is a family based, prospective study of healthy aging and familial longevity. The study includes two assessments of cognitive function that were administered approximately 8 years apart., Objective: To test whether APOE genotype is associated with change of cognitive function in older adults., Methods: We used Bayesian hierarchical models to test the association between APOE alleles and change of cognitive function. Six longitudinally collected neuropsychological test scores were modelled as a function of age at enrollment, follow-up time, gender, education, field center, birth cohort indicator (≤1935, or >1935), and the number of copies of ɛ2 or ɛ4 alleles., Results: Out of 4,587 eligible participants, 2,064 were male (45.0%), and age at enrollment ranged from 25 to 110 years, with mean of 70.85 years (SD: 15.75). We detected a significant cross-sectional effect of the APOEɛ4 allele on Logical Memory. Participants carrying at least one copy of the ɛ4 allele had lower scores in both immediate (-0.31 points, 95% CI: -0.57, -0.05) and delayed (-0.37 points, 95% CI: -0.64, -0.10) recall comparing to non-ɛ4 allele carriers. We did not detect any significant longitudinal effect of the ɛ4 allele. There was no cross-sectional or longitudinal effect of the ɛ2 allele., Conclusion: The APOEɛ4 allele was identified as a risk factor for poorer episodic memory in older adults, while the APOEɛ2 allele was not significantly associated with any of the cognitive test scores.

Initiation and inhibition are executive functions whose disruption in Parkinson's disease impacts substantially on everyday activities. Management of Parkinson's disease with subthalamic deep brain stimulation (DBS) modifies initiation and inhibition, with prior work suggesting that these effects may be mediated via the connectivity of the subthalamic nucleus (STN) with the frontal cortex. Here, we employed high-resolution structural neuroimaging to investigate the variability in initiation, inhibition and strategy use in a cohort of twenty-five (ten females, mean age 62.5, mean Hoehn and Yahr stage 2.5) participants undertaking subthalamic DBS for Parkinson's disease. Neuropsychological assessment of initiation and inhibition was performed preoperatively and at six months postoperatively. We first reconstructed the preoperative connectivity of the STN with a frontal network of anterior and superior medial cortical regions. We then modelled the postoperative site of subthalamic stimulation and reconstructed the connectivity of the stimulation field within this same network. We found that, at both pre- and postoperative intervals, inter-individual variability in inhibition and initiation were strongly associated with structural network connectivity. Measures of subcortical atrophy and local stimulation effects did not play a significant role. Preoperatively, we replicated prior work, including a role for the right inferior frontal gyrus in inhibition and strategy use, as well as the left inferior frontal gyrus in tasks requiring selection under conditions of maintained inhibition. Postoperatively, greater connectivity of the stimulation field with right anterior cortical regions was associated with greater rule violations and suppression errors, supporting prior work implicating right-hemispheric STN stimulation in disinhibition. Our findings suggest that, in Parkinson's disease, connectivity of the frontal cortex with the STN is an important mediator of individual variability in initiation and inhibition,. Personalised information on brain network architecture could guide individualised brain circuit manipulation to minimise neuropsychological disruption after STN-DBS., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

Premise: TagSeq is a cost-effective approach for gene expression studies requiring a large number of samples. To date, TagSeq studies in plants have been limited to those with a high-quality reference genome. We tested the suitability of reference transcriptomes for TagSeq in non-model plants, as part of a study of natural gene expression variation at the Santa Rita Experimental Range National Ecological Observatory Network (NEON) core site., Methods: Tissue for TagSeq was sampled from multiple individuals of four species ( Bouteloua aristidoides and Eragrostis lehmanniana [Poaceae], Tidestromia lanuginosa [Amaranthaceae], and Parkinsonia florida [Fabaceae]) at two locations on three dates (56 samples total). One sample per species was used to create a reference transcriptome via standard RNA-seq. TagSeq performance was assessed by recovery of reference loci, specificity of tag alignments, and variation among samples., Results: A high fraction of tags aligned to each reference and mapped uniquely. Expression patterns were quantifiable for tens of thousands of loci, which revealed consistent spatial differentiation in expression for all species., Discussion: TagSeq using de novo reference transcriptomes was an effective approach to quantifying gene expression in this study. Tags were highly locus specific and generated biologically informative profiles for four non-model plant species., (© 2020 Marx et al. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

Although polyploidy is widespread across the plant Tree of Life, its long-term evolutionary significance is still poorly understood. Here, we examine the effects of polyploidy in explaining the large-scale evolutionary patterns within angiosperms by focusing on a single family exhibiting extensive interspecific variation in chromosome numbers. We inferred ploidy from haploid chromosome numbers for 80% of species in the most comprehensive species-level chronogram for the Brassicaceae. After evaluating a total of 94 phylogenetic models of diversification, we found that ploidy influences diversification rates across the Brassicaceae. We also found that despite diversifying at a similar rate to diploids, polyploids have played a significant role in driving present-day differences in species richness among clades. Overall, in addition to highlighting the complexity in the evolutionary consequences of polyploidy, our results suggest that rare successful polyploids persist while significantly contributing to the long-term evolution of clades. Our findings further indicate that polyploidy has played a major role in driving the long-term evolution of the Brassicaceae and highlight the potential of polyploidy in shaping present-day diversity patterns across the plant Tree of Life.

Chimonanthus salicifolius, a member of the Calycanthaceae of magnoliids, is one of the most famous medicinal plants in Eastern China. Here, we report a chromosome-level genome assembly of C. salicifolius, comprising 820.1 Mb of genomic sequence with a contig N50 of 2.3 Mb and containing 36 651 annotated protein-coding genes. Phylogenetic analyses revealed that magnoliids were sister to the eudicots. Two rounds of ancient whole-genome duplication were inferred in the C. salicifolious genome. One is shared by Calycanthaceae after its divergence with Lauraceae, and the other is in the ancestry of Magnoliales and Laurales. Notably, long genes with > 20 kb in length were much more prevalent in the magnoliid genomes compared with other angiosperms, which could be caused by the length expansion of introns inserted by transposon elements. Homologous genes within the flavonoid pathway for C. salicifolius were identified, and correlation of the gene expression and the contents of flavonoid metabolites revealed potential critical genes involved in flavonoids biosynthesis. This study not only provides an additional whole-genome sequence from the magnoliids, but also opens the door to functional genomic research and molecular breeding of C. salicifolius., (© 2020 Society for Experimental Biology and John Wiley & Sons Ltd This article has been contributed to by US Government employees and their work is in the public domain in the USA.)

Premise: Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placement, as well as that of WGDs in other families in the order, remains unclear., Methods: Phylo-transcriptomic data were generated and used to infer a nuclear phylogeny for 74 Brassicales taxa. Genome survey sequencing was also performed on 66 of those taxa to infer a chloroplast phylogeny. These phylogenies were used to assess and confirm relationships among the major families of the Brassicales and within Brassicaceae. Multiple WGD inference methods were then used to assess the placement of WGDs on the nuclear phylogeny., Results: Well-supported chloroplast and nuclear phylogenies for the Brassicales and the putative placement of the Cleomaceae-specific WGD event Th-ɑ are presented. This work also provides evidence for previously hypothesized WGDs, including a well-supported event shared by at least two members of the Resedaceae family, and a possible event within the Capparaceae., Conclusions: Phylogenetics and the placement of WGDs within highly polyploid lineages continues to be a major challenge. This study adds to the conversation on WGD inference difficulties by demonstrating that sampling is especially important for WGD identification and phylogenetic placement. Given its economic importance and genomic resources, the Brassicales continues to be an ideal group for assessing WGD inference methods., (© 2020 The Authors. American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)