Unraveling the Genetic Basis of Feed Efficiency in Cattle through Integrated DNA Methylation and CattleGTEx Analysis.

Feed costs can amount to 75 percent of the total overhead cost of raising cows for milk production. Meanwhile, the livestock industry is considered a significant contributor to global climate change due to the production of greenhouse gas emissions, such as methane. Indeed, the genetic basis of feed efficiency (FE) is of great interest to the animal research community. Here, we explore the epigenetic basis of FE to provide base knowledge for the development of genomic tools to improve FE in cattle. The methylation level of 37,554 CpG sites was quantified using a mammalian methylation array (HorvathMammalMethylChip40) for 48 Holstein cows with extreme residual feed intake (RFI). We identified 421 CpG sites related to 287 genes that were associated with RFI, several of which were previously associated with feeding or digestion issues. Activator of transcription and developmental regulation (AUTS2) is associated with digestive disorders in humans, while glycerol-3-phosphate dehydrogenase 2 (GPD2) encodes a protein on the inner mitochondrial membrane, which can regulate glucose utilization and fatty acid and triglyceride synthesis. The extensive expression and co-expression of these genes across diverse tissues indicate the complex regulation of FE in cattle. Our study provides insight into the epigenetic basis of RFI and gene targets to improve FE in dairy cattle.

Rapidly Enlarging Parotid Mass in a Person Living with HIV: A Case of Multiple Myeloma with Extramedullary Plasmacytoma.

BACKGROUND The differential diagnosis for a parotid mass is broad, including infectious, autoimmune, and neoplastic etiologies. In people with HIV, regardless of viral suppression or immune status, neoplastic causes are more common. This report describes the evaluation of a woman with a large parotid mass, with an ultimate diagnosis of multiple myeloma with extramedullary plasmacytoma. CASE REPORT A 51-year-old woman with HIV infection presented with headache, weight loss, and right facial mass that was present for 5 years but more rapidly enlarging in the prior year. CD4 count was 234 cells/mL, and HIV RNA was 10 810 copies/mL. Physical examination was significant for a large deforming right-sided facial mass, decreased sensation in the V1 and V2 distributions, and right-sided ophthalmoplegia and ptosis. MRI and PET/CT scan confirmed a metabolically active large parotid mass with extension into the cavernous sinus. An IgG kappa monoclonal spike was present on serum protein electrophoresis. Incisional biopsy of the facial mass showed atypical lymphoid cells with plasmablastic and plasmacytic morphology with a high mitotic rate and proliferation index. She was diagnosed with R-ISS stage II IgG kappa multiple myeloma with extramedullary plasmacytoma, and initiated on chemotherapy, radiation, and antiretroviral therapy. CONCLUSIONS A rapidly enlarging parotid mass should prompt timely evaluation and biopsy for definitive diagnosis, particularly in immunocompromised patients, including people with HIV. Extramedullary plasmacytomas have a more aggressive disease process in people with HIV and are associated with high-risk multiple myeloma and progression, as seen in this patient.

Imaging of Brain Structural and Functional Effects in People With Human Immunodeficiency Virus.

Before the introduction of antiretroviral therapy, human immunodeficiency virus (HIV) infection was often accompanied by central nervous system (CNS) opportunistic infections and HIV encephalopathy marked by profound structural and functional alterations detectable with neuroimaging. Treatment with antiretroviral therapy nearly eliminated CNS opportunistic infections, while neuropsychiatric impairment and peripheral nerve and organ damage have persisted among virally suppressed people with HIV (PWH), suggesting ongoing brain injury. Neuroimaging research must use methods sensitive for detecting subtle HIV-associated brain structural and functional abnormalities, while allowing for adjustments for potential confounders, such as age, sex, substance use, hepatitis C coinfection, cardiovascular risk, and others. Here, we review existing and emerging neuroimaging tools that demonstrated promise in detecting markers of HIV-associated brain pathology and explore strategies to study the impact of potential confounding factors on these brain measures. We emphasize neuroimaging approaches that may be used in parallel to gather complementary information, allowing efficient detection and interpretation of altered brain structure and function associated with suboptimal clinical outcomes among virally suppressed PWH. We examine the advantages of each imaging modality and systematic approaches in study design and analysis. We also consider advantages of combining experimental and statistical control techniques to improve sensitivity and specificity of biotype identification and explore the costs and benefits of aggregating data from multiple studies to achieve larger sample sizes, enabling use of emerging methods for combining and analyzing large, multifaceted data sets. Many of the topics addressed in this article were discussed at the National Institute of Mental Health meeting "Biotypes of CNS Complications in People Living with HIV," held in October 2021, and are part of ongoing research initiatives to define the role of neuroimaging in emerging alternative approaches to identifying biotypes of CNS complications in PWH. An outcome of these considerations may be the development of a common neuroimaging protocol available for researchers to use in future studies examining neurological changes in the brains of PWH.

Trajectory of Change in Parental Accommodation and Its Relation to Symptom Severity and Impairment in Pediatric OCD.

Family accommodation (FA) has been shown to relate to poorer treatment outcomes in pediatric obsessive compulsive disorder (OCD), yet few studies have examined the trajectory of change in FA throughout treatment and its relation to treatment outcomes. This study examined change in FA in relation to change in symptom severity and impairment in 63 youth receiving a family-based intervention for early-onset OCD. FA, symptom severity and functional impairment were assessed at baseline, week 5, week 9, and post-treatment (week 14). Results suggested that changes in FA in the beginning stages of treatment preceded global symptom improvement (but not OCD specific improvement) whereas changes in functional impairment preceded changes in FA. In the latter half of treatment, changes in FA preceded improvement in global and OCD specific symptom severity as well as functional impairment. These findings highlight the importance of reducing FA, especially in the later stages of treatment, in order to optimize treatment outcomes in early-onset OCD.

Effects of SARS-CoV-2 Infection on Attention, Memory, and Sensorimotor Performance.

Background: Recovery after SARS-CoV-2 infection is extremely variable, with some individuals recovering quickly, and others experiencing persistent long-term symptoms or developing new symptoms after the acute phase of infection, including fatigue, poor concentration, impaired attention, or memory deficits. Many existing studies reporting cognitive deficits associated with SARS-CoV-2 infection are limited by the exclusive use of self-reported measures or a lack of adequate comparison groups. Methods: Forty-five participants, ages 18-70, (11 Long-COVID, 14 COVID, and 20 No-COVID) underwent behavioral testing with the NIH Toolbox Neuro-Quality of Life survey and selected psychometric tests, including a flanker interference task and the d2 Test of Attention. Results: We found greater self-reported anxiety, apathy, fatigue, emotional dyscontrol, sleep disturbance and cognitive dysfunction in COVID compared No-COVID groups. After categorizing COVID patients according to self-reported concentration problems, we observed declining performance patterns in multiple attention measures across No-COVID controls, COVID and Long-COVID groups. COVID participants, compared to No-COVID controls, exhibited worse performance on NIH Toolbox assessments, including the Eriksen Flanker, Nine-Hole Pegboard and Auditory Verbal Learning tests. Conclusion: This study provides convergent evidence that previous SARS-CoV-2 infection is associated with impairments in sustained attention, processing speed, self-reported fatigue and concentration. The finding that some patients have cognitive and visuomotor dysfunction in the absence of self-reported problems suggests that SARS-CoV-2 infection can have unexpected and persistent subclinical consequences.

Sharing of either phenotypes or genetic variants can increase the accuracy of genomic prediction of feed efficiency.

BACKGROUND: Sharing individual phenotype and genotype data between countries is complex and fraught with potential errors, while sharing summary statistics of genome-wide association studies (GWAS) is relatively straightforward, and thus would be especially useful for traits that are expensive or difficult-to-measure, such as feed efficiency. Here we examined: (1) the sharing of individual cow data from international partners; and (2) the use of sequence variants selected from GWAS of international cow data to evaluate the accuracy of genomic estimated breeding values (GEBV) for residual feed intake (RFI) in Australian cows. RESULTS: GEBV for RFI were estimated using genomic best linear unbiased prediction (GBLUP) with 50k or high-density single nucleotide polymorphisms (SNPs), from a training population of 3797 individuals in univariate to trivariate analyses where the three traits were RFI phenotypes calculated using 584 Australian lactating cows (AUSc), 824 growing heifers (AUSh), and 2526 international lactating cows (OVE). Accuracies of GEBV in AUSc were evaluated by either cohort-by-birth-year or fourfold random cross-validations. GEBV of AUSc were also predicted using only the AUS training population with a weighted genomic relationship matrix constructed with SNPs from the 50k array and sequence variants selected from a meta-GWAS that included only international datasets. The genomic heritabilities estimated using the AUSc, OVE and AUSh datasets were moderate, ranging from 0.20 to 0.36. The genetic correlations (rg) of traits between heifers and cows ranged from 0.30 to 0.95 but were associated with large standard errors. The mean accuracies of GEBV in Australian cows were up to 0.32 and almost doubled when either overseas cows, or both overseas cows and AUS heifers were included in the training population. They also increased when selected sequence variants were combined with 50k SNPs, but with a smaller relative increase. CONCLUSIONS: The accuracy of RFI GEBV increased when international data were used or when selected sequence variants were combined with 50k SNP array data. This suggests that if direct sharing of data is not feasible, a meta-analysis of summary GWAS statistics could provide selected SNPs for custom panels to use in genomic selection programs. However, since this finding is based on a small cross-validation study, confirmation through a larger study is recommended.

Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning.

We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning. The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined through genome-wide profiling of four histone modifications, CTCF-binding, DNA accessibility, DNA methylation, and transcriptome in rumen epithelial tissues. Each chromatin state presented specific enrichment for sequence ontology, methylation, trait-associated variants, transcription, gene expression-associated variants, selection signatures, and evolutionarily conserved elements. During weaning, weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states and occurred in tandem with significant variations in gene expression and DNA methylation, significantly associated with stature, production, and reproduction economic traits. By comparing with in vitro cultured epithelial cells and in vivo rumen tissues, we showed the commonness and uniqueness of these results, especially the roles of cell interactions and mitochondrial activities in tissue development.

Lesion location may attenuate response to strategy training in acute stroke.

BACKGROUND: Strategy training, a rehabilitation intervention, reduces disability and improves functional skills associated with goal-directed behavior. Stroke lesions impacting selected ventromedial regions of interest associated with initiation of goal-directed behavior may attenuate intervention response. If so, strategy training may not be optimal for people with stroke lesions in these regions. OBJECTIVE: To examine whether ventromedial regions of interest attenuate changes in disability status attributed to strategy training. DESIGN: Secondary analysis of data from two randomized controlled clinical trials. SETTING: Inpatient stroke rehabilitation. PARTICIPANTS: People with acute stroke diagnosis and available diagnostic studies enrolled in inpatient rehabilitation randomized controlled studies between 2009 and 2017. INTERVENTION: Participants were randomized to strategy training or a control condition in addition to the usual care during inpatient rehabilitation. MAIN OUTCOME MEASURES: Diagnostic magnetic resonance imaging studies were retrieved from electronic medical records, and stroke lesion location was characterized by a neuroradiologist. Intervention response was defined by Functional Independence Measure change scores of 22 points or greater. RESULTS: Only 186 of 275 participants had diagnostic studies available; 13 patients showed no apparent lesion on their diagnostic study. Among 173 cases, 156 had complete data at discharge (strategy training n = 71, control n = 85). Twenty-five cases had a lesion within a region of interest (strategy training n = 14, control n = 11). Intervention response was attenuated in the strategy training group for those with lesions in regions of interest [χ2 (1, n = 71) = 4.60, P = .03], but not for those in the control group [Fisher exact test, n = 85, P = .19). CONCLUSIONS: Lesions in the ventromedial regions of interest may attenuate response to strategy training.

MULTI-DOMAIN LEARNING BY META-LEARNING: TAKING OPTIMAL STEPS IN MULTI-DOMAIN LOSS LANDSCAPES BY INNER-LOOP LEARNING.

We consider a model-agnostic solution to the problem of Multi-Domain Learning (MDL) for multi-modal applications. Many existing MDL techniques are model-dependent solutions which explicitly require nontrivial architectural changes to construct domain-specific modules. Thus, properly applying these MDL techniques for new problems with well-established models, e.g. U-Net for semantic segmentation, may demand various low-level implementation efforts. In this paper, given emerging multi-modal data (e.g., various structural neuroimaging modalities), we aim to enable MDL purely algorithmically so that widely used neural networks can trivially achieve MDL in a model-independent manner. To this end, we consider a weighted loss function and extend it to an effective procedure by employing techniques from the recently active area of learning-to-learn (meta-learning). Specifically, we take inner-loop gradient steps to dynamically estimate posterior distributions over the hyperparameters of our loss function. Thus, our method is model-agnostic, requiring no additional model parameters and no network architecture changes; instead, only a few efficient algorithmic modifications are needed to improve performance in MDL. We demonstrate our solution to a fitting problem in medical imaging, specifically, in the automatic segmentation of white matter hyperintensity (WMH). We look at two neuroimaging modalities (T1-MR and FLAIR) with complementary information fitting for our problem.

ROBUST WHITE MATTER HYPERINTENSITY SEGMENTATION ON UNSEEN DOMAIN.

Typical machine learning frameworks heavily rely on an underlying assumption that training and test data follow the same distribution. In medical imaging which increasingly begun acquiring datasets from multiple sites or scanners, this identical distribution assumption often fails to hold due to systematic variability induced by site or scanner dependent factors. Therefore, we cannot simply expect a model trained on a given dataset to consistently work well, or generalize, on a dataset from another distribution. In this work, we address this problem, investigating the application of machine learning models to unseen medical imaging data. Specifically, we consider the challenging case of Domain Generalization (DG) where we train a model without any knowledge about the testing distribution. That is, we train on samples from a set of distributions (sources) and test on samples from a new, unseen distribution (target). We focus on the task of white matter hyperintensity (WMH) prediction using the multi-site WMH Segmentation Challenge dataset and our local in-house dataset. We identify how two mechanically distinct DG approaches, namely domain adversarial learning and mix-up, have theoretical synergy. Then, we show drastic improvements of WMH prediction on an unseen target domain.

A multi-scanner neuroimaging data harmonization using RAVEL and ComBat.

Modern neuroimaging studies frequently combine data collected from multiple scanners and experimental conditions. Such data often contain substantial technical variability associated with image intensity scale (image intensity scales are not the same in different images) and scanner effects (images obtained from different scanners contain substantial technical biases). Here we evaluate and compare results of data analysis methods without any data transformation (RAW), with intensity normalization using RAVEL, with regional harmonization methods using ComBat, and a combination of RAVEL and ComBat. Methods are evaluated on a unique sample of 16 study participants who were scanned on both 1.5T and 3T scanners a few months apart. Neuroradiological evaluation was conducted for 7 different regions of interest (ROI's) pertinent to Alzheimer's disease (AD). Cortical measures and results indicate that: (1) RAVEL substantially improved the reproducibility of image intensities; (2) ComBat is preferred over RAVEL and the RAVEL-ComBat combination in terms of regional level harmonization due to more consistent harmonization across subjects and image-derived measures; (3) RAVEL and ComBat substantially reduced bias compared to analysis of RAW images, but RAVEL also resulted in larger variance; and (4) the larger root mean square deviation (RMSD) of RAVEL compared to ComBat is due mainly to its larger variance.

Transcriptional Reprogramming in Rumen Epithelium during the Developmental Transition of Pre-Ruminant to the Ruminant in Cattle.

We present an analysis of transcriptomic dynamics in rumen epithelium of 18 Holstein calves during the transition from pre-rumination to rumination in cattle-fed hay or concentrated diets at weaning. Three calves each were euthanized at 14 and 42 d of age to exemplify preweaning, and six calves each were provided diets of either milk replacer and grass hay or calf starter to introduce weaning. The two distinct phases of rumen development and function in cattle are tightly regulated by a series of signaling events and clusters of effectors on critical pathways. The dietary shift from liquid to solid feeds prompted the shifting of gene activity. The number of differentially expressed genes increased significantly after weaning. Bioinformatic analysis revealed gene activity shifts underline the functional transitions in the ruminal epithelium and signify the transcriptomic reprogramming. Gene ontogeny (GO) term enrichment shows extensively activated biological functions of differentially expressed genes in the ruminal epithelium after weaning were predominant metabolic functions. The transcriptomic reprogramming signifies a correlation between gene activity and changes in metabolism and energy production in the rumen epithelium, which occur at weaning when transitioning from glucose use to VFA use by epithelium during the weaning.

Single-cell transcriptomic analyses of dairy cattle ruminal epithelial cells during weaning.

Using the 10× Genomics Chromium Controller, we obtained scRNA-seq data of 5064 and 1372 individual cells from two Holstein calf ruminal epithelial tissues before and after weaning, respectively. We detected six distinct cell clusters, designated their cell types, and reported their marker genes. We then examined these clusters' underlining cell types and relationships by performing cell cycle, pseudotime trajectory, regulatory network, weighted gene co-expression network and gene ontology analyses. By integrating these cell marker genes with Holstein GWAS signals, we found they were enriched for animal production and body conformation traits. Finally, we confirmed their cell identities by comparing them with human and mouse stomach epithelial cells. This study presents an initial effort to implement single-cell transcriptomic analysis in cattle, and demonstrates ruminal tissue epithelial cell types and their developments during weaning, opening the door for new discoveries about tissue/cell type roles in complex traits at single-cell resolution.

Effects of Incorporating Dry Matter Intake and Residual Feed Intake into a Selection Index for Dairy Cattle Using Deterministic Modeling.

The inclusion of feed efficiency in the breeding goal for dairy cattle has been discussed for many years. The effects of incorporating feed efficiency into a selection index were assessed by indirect selection (dry matter intake) and direct selection (residual feed intake) using deterministic modeling. Both traits were investigated in three ways: (1) restricting the trait genetic gain to zero, (2) applying negative selection pressure, and (3) applying positive selection pressure. Changes in response to selection from economic and genetic gain perspectives were used to evaluate the impact of including feed efficiency with direct or indirect selection in an index. Improving feed efficiency through direct selection on residual feed intake was the best scenario analyzed, with the highest overall economic response including favorable responses to selection for production and feed efficiency. Over time, the response to selection is cumulative, with the potential for animals to reduce consumption by 0.16 kg to 2.7 kg of dry matter per day while maintaining production. As the selection pressure increased on residual feed intake, the response to selection for production, health, and fertility traits and body condition score became increasingly less favorable. This work provides insight into the potential long-term effects of selecting for feed efficiency as residual feed intake.

Greater Sensorimotor Deficits and Abnormally Lower Globus Pallidus Fractional Anisotropy in HIV+ Women than in HIV+ Men.

AIMS: Cognitive impairment may be greater in HIV-positive (HIV+) women than in HIV+ men. Whether sex-specific differences exist in brain microstructure of HIV+ individuals is unknown and was evaluated. METHOD: 39 HIV+ (21 men, 18 women) and 45 seronegative (SN, 20 men, 25 women) participants were assessed with brain diffusion tensor imaging and cognitive assessments (7 neuropsychological domains). Fractional anisotropy (FA) and mean diffusivity (MD) were measured with an automated atlas in selected brain regions. Group comparisons were assessed with linear mixed effects models, with sub-regions and hemisphere (left/right) as repeated factors for each region. RESULTS: HIV+ women, but not HIV+ men, were slower than sex-matched SN controls on sensorimotor function (Dominant-hand: interaction-p = 0.007; Non-dominant hand: interaction-p = 0.039). Similarly, only HIV+ women had lower FA in the globus pallidus (GP, interaction-p = 0.011). Additionally, regardless of sex, the HIV+ group had poorer Fluency, Speed, and Attention than SN-controls (p = 0.006-0.008), as well as lower FA and higher MD in multiple brain regions (p = <0.001-0.044). Across all participants, performance on Attention was predicted by uncinate-FA (p < 0.001, r = 0.5) and corpus callosum (CC)-FA (p = 0.038, r = 0.23), while the Speed of Information Processing was predicted by CC-FA (p = 0.009, r = 0.3). Furthermore, faster sensorimotor function correlated with higher CC-FA and uncinate-FA in men but not in women (Sex*DTI-interaction-p = 0.03-0.06). CONCLUSIONS: The relatively poorer sensorimotor function and abnormally lower GP_FA, suggesting lesser neuronal integrity, in HIV+ women demonstrate sex-specific effects from HIV-infection on these measures. These findings may be related to the greater immune activation and neuroinflammation in HIV+ women compared to HIV+ men. Graphical Abstract.

An alternative interpretation of residual feed intake by phenotypic recursive relationships in dairy cattle.

There has been increasing interest in residual feed intake (RFI) as a measure of net feed efficiency in dairy cattle. Residual feed intake phenotypes are obtained as residuals from linear regression encompassing relevant factors (i.e., energy sinks) to account for body tissue mobilization. By rearranging the single-trait linear regression, we showed a causal RFI interpretation underlying the linear regression for RFI. It postulates recursive effects in energy allocation from energy sinks on dry matter intake, but the feedback or simultaneous effects are nonexistent. A Bayesian recursive structural equation model was proposed for directly predicting RFI and energy sinks and estimating relevant genetic parameters simultaneously. A simplified Markov chain Monte Carlo algorithm was described. The recursive model is asymptotically equivalent to one-step linear regression for RFI, yet extends the analytical capacity to multiple-trait analysis.

Differential Effects of AIDS and Chronic Human Immunodeficiency Virus Infection on Gray Matter Volume.

BACKGROUND: Age, human immunodeficiency virus (HIV) infection, illicit drug use, and central nervous system (CNS) opportunistic infections can affect brain structure, with the striatum being particularly sensitive to HIV effects. Nevertheless, the impact of non-CNS AIDS-defining illness (ADI) on brain structure has been less investigated. We examined ADI and HIV effects on brain volume. METHODS: In a cross-sectional study, including 95 virally suppressed seropositive and 84 demographically matched, seronegative participants, we examined serostatus and ADI effects. Cortical and subcortical gray matter volume (GMV) regions of interest were estimated with computational neuroanatomy techniques applied to high-resolution, T1-weighted magnetic resonance imaging data. Linear regression was used to model HIV serostatus and ADI effects on global and regional GMV, adjusting for age, sex, CD4 nadir, drug use, and total intracranial volume. RESULTS: While HIV serostatus was associated with lower striatal volume (B = -.59 [95% confidence interval {CI}, -1.08 to -.10]), co-occurring ADI was independently associated with lower striatal volume (B = -.73 [95% CI, -1.36 to -.09]). ADI was also associated with lower global (B = -19.35 [95% CI, -32.42 to -6.29]) and regional GMV. CONCLUSIONS: While HIV infection is associated with a localized effect on striatal structure, having a prior ADI is a strong predictor of smaller global and regional GMV. The lack of interaction between HIV serostatus or ADI with age suggests that chronic HIV infection and ADI have independent effects on brain structure, without associated accelerated lower volume with age. ADI history should be incorporated into statistical adjustments in HIV neuroimaging analysis. These findings also lend support to current HIV treatment guidelines urging prompt antiretroviral therapy initiation after HIV diagnosis.

The Relationship Between Parental Accommodation and Sleep-Related Problems in Children with Anxiety.

OBJECTIVE: Sleep-related problems, defined as sleep patterns atypical for the child's developmental stage, are common in children with elevated anxiety symptoms and linked to significant mental and physical health consequences. Despite the consequences of sleep-related problems, it remains unclear how these problems are initiated and maintained in children with elevated anxiety symptoms. The current study examines the relationship between sleep-related problems and parental accommodation (e.g., co-sleeping) to determine whether higher levels of accommodation are associated with more frequent sleep-related problems in a sample of children with elevated anxiety symptoms. METHODS: Participants were 122 children aged 8 to 17 years old (M = 11.97, SD = 2.68; 57% female) and their parents who presented to a university-based anxiety specialty clinic for assessment and treatment. Children completed the Multidimensional Anxiety Scale for Children, and their parents completed the Children's Sleep Habits Questionnaire and Family Accommodation Checklist and Interference Scale. Multiple regression analyses were performed to examine variance in sleep-related problems explained by parental accommodation. RESULTS: Parental accommodation accounted for a significant amount of variance in sleep-related problems over and above child anxiety and age for both mother report (19%) and father report (15%). When individual accommodation items were examined, parental sleep accommodations (e.g., slept in my child's bed) and nonsleep accommodations (e.g., came home early) were significant predictors for mother-reported sleep-related problems, but only sleep accommodations (e.g., let my child sleep with the lights on) were significant for father-reported sleep-related problems. CONCLUSION: Parents of children with elevated anxiety symptoms and sleep-related problems engage in accommodation related to their child's sleep (e.g., co-sleeping). Future research elucidating the potential bidirectional and causal links between parental accommodation and sleep-related problems is a necessary step in adapting sleep treatments for this population.

Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns.

BACKGROUND: Efforts to improve animal health, and understand genetic bases for production, may benefit from a comprehensive analysis of animal genomes and epigenomes. Although DNA methylation has been well studied in humans and other model species, its distribution patterns and regulatory impacts in cattle are still largely unknown. Here, we present the largest collection of cattle DNA methylation epigenomic data to date. RESULTS: Using Holstein cattle, we generated 29 whole genome bisulfite sequencing (WGBS) datasets for 16 tissues, 47 corresponding RNA-seq datasets, and 2 whole genome sequencing datasets. We did read mapping and DNA methylation calling based on two different cattle assemblies, demonstrating the high quality of the long-read-based assembly markedly improved DNA methylation results. We observed large differences across cattle tissues in the methylation patterns of global CpG sites, partially methylated domains (PMDs), hypomethylated regions (HMRs), CG islands (CGIs), and common repeats. We detected that each tissue had a distinct set of PMDs, which showed tissue-specific patterns. Similar to human PMD, cattle PMDs were often linked to a general decrease of gene expression and a decrease in active histone marks and related to long-range chromatin organizations, like topologically associated domains (TADs). We tested a classification of the HMRs based on their distributions relative to transcription start sites (TSSs) and detected tissue-specific TSS-HMRs and genes that showed strong tissue effects. When performing cross-species comparisons of paired genes (two opposite strand genes with their TSS located in the same HMR), we found out they were more consistently co-expressed among human, mouse, sheep, goat, yak, pig, and chicken, but showed lower consistent ratios in more divergent species. We further used these WGBS data to detect 50,023 experimentally supported CGIs across bovine tissues and found that they might function as a guard against C-to-T mutations for TSS-HMRs. Although common repeats were often heavily methylated, some young Bov-A2 repeats were hypomethylated in sperm and could affect the promoter structures by exposing potential transcription factor binding sites. CONCLUSIONS: This study provides a comprehensive resource for bovine epigenomic research and enables new discoveries about DNA methylation and its role in complex traits.

A randomized-controlled examination of the effect of cognitive reappraisal instruction on maternal accommodation of child anxiety symptoms.

Parental accommodation plays a key role in the maintenance of child anxiety, yet much of the research to date has been correlational, making it difficult to draw conclusions about underlying mechanisms. Given preliminary evidence that parental beliefs play a role in parental accommodation, the present study sought to experimentally reduce accommodation by targeting parental attitudes about child anxiety. Mothers of children ages 4-9 (N = 47) were randomly assigned to either receive brief instruction in cognitive reappraisal (EXP) or to a control intervention in which they received no instruction (CON). At pre- and post-intervention mothers were presented with bogus information that their child was experiencing varying levels of distress while completing a task in a nearby room. Maternal distress, negative affect and perceived likelihood of accommodation in the context of child distress were measured pre- and post-intervention. EXP mothers reported greater pre- to post-intervention decreases in distress and perceived likelihood of accommodation, compared to CON mothers. EXP and CON mothers showed similar changes in negative affect. Findings from this study provide preliminary experimental evidence that targeting maternal beliefs about child anxiety can result in changes in maternal distress and behavior following exposure to child distress. Implications for prevention and treatment are discussed.