Six months of voluntary alcohol consumption in male cynomolgus macaques reduces intracortical bone porosity without altering mineralization or mechanical properties.

Chronic heavy alcohol consumption is a risk factor for low trauma bone fracture. Using a non-human primate model of voluntary alcohol consumption, we investigated the effects of 6 months of ethanol intake on cortical bone in cynomolgus macaques (Macaca fascicularis). Young adult (6.4 ±â€¯0.1 years old, mean ±â€¯SE) male cynomolgus macaques (n = 17) were subjected to a 4-month graded ethanol induction period, followed by voluntary self-administration of water or ethanol (4 % w/v) for 22 h/d, 7 d/wk. for 6 months. Control animals (n = 6) consumed an isocaloric maltose-dextrin solution. Tibial response was evaluated using densitometry, microcomputed tomography, histomorphometry, biomechanical testing, and Raman spectroscopy. Global bone response was evaluated using biochemical markers of bone turnover. Monkeys in the ethanol group consumed an average of 2.3 ±â€¯0.2 g/kg/d ethanol resulting in a blood ethanol concentration of 90 ±â€¯12 mg/dl in longitudinal samples taken 7 h after the daily session began. Ethanol consumption had no effect on tibia length, mass, density, mechanical properties, or mineralization (p > 0.642). However, compared to controls, ethanol intake resulted in a dose-dependent reduction in intracortical bone porosity (Spearman rank correlation = -0.770; p < 0.0001) and compared to baseline, a strong tendency (p = 0.058) for lower plasma CTX, a biochemical marker of global bone resorption. These findings are important because suppressed cortical bone remodeling can result in a decrease in bone quality. In conclusion, intracortical bone porosity was reduced to subnormal values 6 months following initiation of voluntary ethanol consumption but other measures of tibia architecture, mineralization, or mechanics were not altered.

Intersecting Pathways in Bioinformatics and Translational Informatics: A One Health Perspective on Key Contributions and Future Directions.

OBJECTIVES: To identify and summarize the top bioinformatics and translational informatics (BTI) papers published in 2022 for the International Medical Informatics Association (IMIA) Yearbook 2023. METHODS: We conducted a comprehensive literature search to identify the top BTI papers, resulting in a set of ten candidate papers. The candidates were reviewed by the section co-editors and external reviewers to select the top three papers from 2022. RESULTS: From a total of 558 papers, we identified a final candidate list of ten BTI papers for peer-review. These papers apply new statistical frameworks and experimental designs to better capture individual variability in disease and incorporate data that captures differences between single cells and across environmental exposures. In addition, they highlight the importance of model generalization across diverse cohorts and scalability to large medical centers. CONCLUSIONS: We note several important trends in the candidate top BTI papers this year, including a continued focus on developing accurate and scalable computational models to predict disease risk across diverse cohorts and new strategies to capture the molecular heterogeneity of disease.

BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels.

Histone modifications are critical for regulating chromatin structure and gene expression. Dysregulation of histone modifications likely contributes to disease states and cancer. Depletion of the chromatin-binding protein BRWD3 (Bromodomain and WD repeat-containing protein 3), a known substrate-specificity factor of the Cul4-DDB1 E3 ubiquitin ligase complex, results in increased H3K4me1 (H3 lysine 4 monomethylation) levels. The underlying mechanism linking BRWD3 and H3K4 methylation, however, has yet to be defined. Here, we show that depleting BRWD3 not only causes an increase in H3K4me1 levels but also causes a decrease in H3K4me3 (H3 lysine 4 trimethylation) levels, indicating that BRWD3 influences H3K4 methylation more broadly. Using immunoprecipitation coupled to quantitative mass spectrometry, we identified an interaction between BRWD3 and the H3K4-specific lysine demethylase 5 (KDM5/Lid), an enzyme that removes tri- and dimethyl marks from H3K4. Moreover, analysis of ChIP-seq (chromatin immunoprecipitation sequencing) data revealed that BRWD3 and KDM5 are significantly colocalized throughout the genome and H3K4me3 are highly enriched at BRWD3 binding sites. We show that BRWD3 promotes K48-linked polyubiquitination and degradation of KDM5 and that KDM5 degradation is dependent on both BRWD3 and Cul4. Critically, depleting KDM5 fully restores altered H3K4me3 levels and partially restores H3K4me1 levels upon BRWD3 depletion. Together, our results demonstrate that BRWD3 regulates KDM5 activity to balance H3K4 methylation levels.

Cis-regulatory Landscape Size, Constraint, and Tissue Specificity Associate with Gene Function and Expression.

Multiple distal cis-regulatory elements (CREs) often cooperate to regulate gene expression, and the presence of multiple CREs for a gene has been proposed to provide redundancy and robustness to variation. However, we do not understand how attributes of a gene's distal CRE landscape-the CREs that contribute to its regulation-relate to its expression and function. Here, we integrate three-dimensional chromatin conformation and functional genomics data to quantify the CRE landscape composition genome-wide across ten human tissues and relate their attributes to the function, constraint, and expression patterns of genes. Within each tissue, we find that expressed genes have larger CRE landscapes than nonexpressed genes and that genes with tissue-specific CREs are more likely to have tissue-specific expression. Controlling for the association between expression level and CRE landscape size, we also find that CRE landscapes around genes under strong constraint (e.g., loss-of-function intolerant and housekeeping genes) are not significantly smaller than other expressed genes as previously proposed; however, they do have more evolutionarily conserved sequences than CREs of expressed genes overall. We also show that CRE landscape size does not associate with expression variability across individuals; nonetheless, genes with larger CRE landscapes have a relative depletion for variants that influence expression levels (expression quantitative trait loci). Overall, this work illustrates how differences in gene function, expression, and evolutionary constraint are reflected in features of CRE landscapes. Thus, considering the CRE landscape of a gene is vital for understanding gene expression dynamics across biological contexts and interpreting the effects of noncoding genetic variants.

BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels.

Histone modifications are critical for regulating chromatin structure and gene expression. Dysregulation of histone modifications likely contributes to disease states and cancer. Depletion of the chromatin-binding protein BRWD3, a known substrate-specificity factor of the Cul4-DDB1 E3 ubiquitin ligase complex, results in increased in H3K4me1 levels. The underlying mechanism linking BRWD3 and H3K4 methylation, however, has yet to be defined. Here, we show that depleting BRWD3 not only causes an increase in H3K4me1 levels, but also causes a decrease in H3K4me3 levels, indicating that BRWD3 influences H3K4 methylation more broadly. Using immunoprecipitation coupled to quantitative mass spectrometry, we identified an interaction between BRWD3 and the H3K4-specific demethylase 5 (KDM5/Lid), an enzyme that removes tri- and di- methyl marks from H3K4. Moreover, analysis of ChIP-seq data revealed that BRWD3 and KDM5 are significantly co- localized throughout the genome and that sites of H3K4me3 are highly enriched at BRWD3 binding sites. We show that BRWD3 promotes K48-linked polyubiquitination and degradation of KDM5 and that KDM5 degradation is dependent on both BRWD3 and Cul4. Critically, depleting KDM5 fully restores altered H3K4me3 levels and partially restores H3K4me1 levels upon BRWD3 depletion. Together, our results demonstrate that BRWD3 regulates KDM5 activity to balance H3K4 methylation levels.

A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae.

Telomere healing occurs when telomerase, normally restricted to chromosome ends, acts upon a double-strand break to create a new, functional telomere. De novo telomere addition (dnTA) on the centromere-proximal side of a break truncates the chromosome but, by blocking resection, may allow the cell to survive an otherwise lethal event. We previously identified several sequences in the baker's yeast, Saccharomyces cerevisiae, that act as hotspots of dnTA [termed Sites of Repair-associated Telomere Addition (SiRTAs)], but the distribution and functional relevance of SiRTAs is unclear. Here, we describe a high-throughput sequencing method to measure the frequency and location of telomere addition within sequences of interest. Combining this methodology with a computational algorithm that identifies SiRTA sequence motifs, we generate the first comprehensive map of telomere-addition hotspots in yeast. Putative SiRTAs are strongly enriched in subtelomeric regions where they may facilitate formation of a new telomere following catastrophic telomere loss. In contrast, outside of subtelomeres, the distribution and orientation of SiRTAs appears random. Since truncating the chromosome at most SiRTAs would be lethal, this observation argues against selection for these sequences as sites of telomere addition per se. We find, however, that sequences predicted to function as SiRTAs are significantly more prevalent across the genome than expected by chance. Sequences identified by the algorithm bind the telomeric protein Cdc13, raising the possibility that association of Cdc13 with single-stranded regions generated during the response to DNA damage may facilitate DNA repair more generally.

A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae.

Telomere healing occurs when telomerase, normally restricted to chromosome ends, acts upon a double-strand break to create a new, functional telomere. De novo telomere addition on the centromere-proximal side of a break truncates the chromosome but, by blocking resection, may allow the cell to survive an otherwise lethal event. We previously identified several sequences in the baker’s yeast, Saccharomyces cerevisiae , that act as hotspots of de novo telomere addition (termed Sites of Repair-associated Telomere Addition or SiRTAs), but the distribution and functional relevance of SiRTAs is unclear. Here, we describe a high-throughput sequencing method to measure the frequency and location of telomere addition within sequences of interest. Combining this methodology with a computational algorithm that identifies SiRTA sequence motifs, we generate the first comprehensive map of telomere-addition hotspots in yeast. Putative SiRTAs are strongly enriched in subtelomeric regions where they may facilitate formation of a new telomere following catastrophic telomere loss. In contrast, outside of subtelomeres, the distribution and orientation of SiRTAs appears random. Since truncating the chromosome at most SiRTAs would be lethal, this observation argues against selection for these sequences as sites of telomere addition per se. We find, however, that sequences predicted to function as SiRTAs are significantly more prevalent across the genome than expected by chance. Sequences identified by the algorithm bind the telomeric protein Cdc13, raising the possibility that association of Cdc13 with single-stranded regions generated during the response to DNA damage may facilitate DNA repair more generally.

Congenital Lobar Emphysema Developing Massive Hemoptysis in Adulthood Treated by Thoracoscopic Lobectomy.

Congenital lobar emphysema (CLE) is a rare developmental lung disorder characterized by lobar hyperinflation secondary to bronchopulmonary obstruction. Half of patients are symptomatic at birth, with many requiring urgent or emergent surgical resection to treat respiratory distress. Meanwhile, patients achieving late childhood or adolescence without symptoms usually never require surgery. We present a case of a 26 year old otherwise healthy female with known CLE who developed massive hemoptysis and required urgent videoscopic (VATS) resection of her right lung upper lobe. We know of no other report of CLE causing life-threatening bleeding at any age, and herein review pathology and pathophysiology of the condition.

GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions.

SUMMARY: GSEL is a computational framework for calculating the enrichment of signatures of diverse evolutionary forces in a set of genomic regions. GSEL can flexibly integrate any sequence-based evolutionary metric and analyze sets of human genomic regions identified by genome-wide assays (e.g. GWAS, eQTL, *-seq). The core of GSEL's approach is the generation of empirical null distributions tailored to the allele frequency and linkage disequilibrium structure of the regions of interest. We illustrate the application of GSEL to variants identified from a GWAS of body mass index, a highly polygenic trait. AVAILABILITY AND IMPLEMENTATION: GSEL is implemented as a fast, flexible and user-friendly python package. It is available with demonstration data at https://github.com/abraham-abin13/gsel_vec. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

2021 Bioinformatics and Translational Informatics Best Papers.

OBJECTIVES: To identify and summarize the top bioinformatics and translational informatics papers published in 2021 for the IMIA Yearbook. METHODS: We performed a broad literature search to retrieve Bioinformatics and Translational Informatics (BTI) papers and coupled this with a series of editorial and peer reviews to identity the top papers in the area. RESULTS: We identified a final candidate list of 15 BTI papers for peer-review; from these candidates, the top three papers were chosen to highlight in this synopsis. These papers expand the integration of multi-omics data with electronic health records and use advanced machine learning approaches to tailor models to individual patients. In addition, our honorable mention paper foreshadows the growing impact of BTI research on precision medicine through the continued development of large clinical consortia. CONCLUSION: In the top BTI papers this year, we observed several important trends, including the use of deep-learning approaches to analyse diverse data types, the development of integrative and web-accessible bioinformatics pipelines, and a continued focus on the power of individual genome sequencing for precision health.

Nucleoporins facilitate ORC loading onto chromatin.

The origin recognition complex (ORC) binds throughout the genome to initiate DNA replication. In metazoans, it is still unclear how ORC is targeted to specific loci to facilitate helicase loading and replication initiation. Here, we perform immunoprecipitations coupled with mass spectrometry for ORC2 in Drosophila embryos. Surprisingly, we find that ORC2 associates with multiple subunits of the Nup107-160 subcomplex of the nuclear pore. Bioinformatic analysis reveals that, relative to all modENCODE factors, nucleoporins are among the most enriched factors at ORC2 binding sites. Critically, depletion of the nucleoporin Elys, a member of the Nup107-160 complex, decreases ORC2 loading onto chromatin. Depleting Elys also sensitizes cells to replication fork stalling, which could reflect a defect in establishing dormant replication origins. Our work reveals a connection between ORC, replication initiation, and nucleoporins, suggesting a function for nucleoporins in metazoan replication initiation.

Ethanol alters the relationship between IGF-1 and bone turnover in male macaques.

Insulin-like growth factor 1 (IGF-1) influences bone turnover. Transient decreases in IGF-I levels and/or bioavailability may contribute to the detrimental effects of alcohol on bone. The goals of this non-human primate study were to i) evaluate the 20-h response of bone turnover markers to ethanol consumption and ii) assess how ethanol consumption influences the relationship between IGF-1 and these markers. Osteocalcin (bone formation), carboxyterminal cross-linking telopeptide of type 1 collagen (CTX, bone resorption), IGF-1, and IGF binding protein 1 (IGFBP-1) were measured in plasma from male rhesus macaques (N = 10, 8.4 ± 0.3 years) obtained at 12:00, 16:00, and 06:00 h during two phases: pre-ethanol (alcohol-naïve) and ethanol access. During the ethanol access phase, monkeys consumed 1.5 g/kg/day ethanol (4% w/v) beginning at 10:00 h. Osteocalcin and CTX were lower, and the ratio of osteocalcin to CTX was higher at each time point during ethanol access compared to the pre-ethanol phase. Pre-ethanol marker levels did not vary across time points, but markers varied during ethanol access. IGF-1 levels, but not IGFBP-1 levels, varied during the pre-ethanol phase. In contrast, IGF-1 levels were stable during ethanol access but IGFBP-1 levels varied. There were positive relationships between IGF-1 and turnover markers during the pre-ethanol phase, but not during ethanol access. In conclusion, chronic ethanol consumption reduces levels of bone turnover markers and blocks the normal positive relationship between IGF-1 and turnover markers and alters the normal relationship between IGF-1 and IGFBP-1. These findings support the hypothesis that chronic alcohol consumption leads to growth hormone/IGF-1 resistance.

Association of Medication Adherence With Health Outcomes in the ISCHEMIA Trial.

BACKGROUND: The ISCHEMIA (International Study of Comparative Health Effectiveness With Medical and Invasive Approaches) trial randomized participants with chronic coronary disease (CCD) to guideline-directed medical therapy with or without angiography and revascularization. The study examined the association of nonadherence with health status outcomes. OBJECTIVES: The study sought to compare 12-month health status outcomes of adherent and nonadherent participants with CCD with an a priori hypothesis that nonadherent patients would have better health status if randomized to invasive management. METHODS: Self-reported medication-taking behavior was assessed at randomization with a modified 4-item Morisky-Green-Levine Adherence Scale, and participants were classified as adherent or nonadherent. Twelve-month health status was assessed with the 7-item Seattle Angina Questionnaire (SAQ-7) summary score (SS), which ranges from 0 to 100 (higher score = better). The association of adherence with outcomes was evaluated using Bayesian proportional odds models, including an interaction by study arm (conservative vs invasive). RESULTS: Among 4,480 randomized participants, 1,245 (27.8%) were nonadherent at baseline. Nonadherent participants had worse baseline SAQ-7 SS in both conservative (72.9 ± 19.3 vs 75.6 ± 18.4) and invasive (71.0 ± 19.8 vs 74.2 ± 18.7) arms. In adjusted analyses, adherence was associated with higher 12-month SAQ-7 SS in both treatment groups (mean difference in SAQ-7 SS with conservative treatment = 1.6 [95% credible interval: 0.3-2.9] vs with invasive management = 1.9 [95% credible interval: 0.8-3.1]), with no interaction by treatment. CONCLUSIONS: More than 1 in 4 participants reported medication nonadherence, which was associated with worse health status in both conservative and invasive treatment strategies at baseline and 12 months. Strategies to improve medication adherence are needed to improve health status outcomes in CCD, regardless of treatment strategy. (International Study of Comparative Health Effectiveness With Medical and Invasive Approaches [ISCHEMIA]; NCT01471522).

R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures.

R-loops are involved in transcriptional regulation, DNA and histone post-translational modifications, genome replication and genome stability. To what extent R-loop abundance and genome-wide localization is actively regulated during metazoan embryogenesis is unknown. Drosophila embryogenesis provides a powerful system to address these questions due to its well-characterized developmental program, the sudden onset of zygotic transcription and available genome-wide data sets. Here, we measure the overall abundance and genome localization of R-loops in early and late-stage embryos relative to Drosophila cultured cells. We demonstrate that absolute R-loop levels change during embryogenesis and that RNaseH1 catalytic activity is critical for embryonic development. R-loop mapping by strand-specific DRIP-seq reveals that R-loop localization is plastic across development, both in the genes which form R-loops and where they localize relative to gene bodies. Importantly, these changes are not driven by changes in the transcriptional program. Negative GC skew and absolute changes in AT skew are associated with R-loop formation in Drosophila. Furthermore, we demonstrate that while some chromatin binding proteins and histone modifications such as H3K27me3 are associated with R-loops throughout development, other chromatin factors associated with R-loops in a developmental specific manner. Our findings highlight the importance and developmental plasticity of R-loops during Drosophila embryogenesis.

Diverse functions associate with non-coding polymorphisms shared between humans and chimpanzees.

BACKGROUND: Long-term balancing selection (LTBS) can maintain allelic variation at a locus over millions of years and through speciation events. Variants shared between species in the state of identity-by-descent, hereafter "trans-species polymorphisms", can result from LTBS, often due to host-pathogen interactions. For instance, the major histocompatibility complex (MHC) locus contains TSPs present across primates. Several hundred candidate LTBS regions have been identified in humans and chimpanzees; however, because many are in non-protein-coding regions of the genome, the functions and potential adaptive roles for most remain unknown. RESULTS: We integrated diverse genomic annotations to explore the functions of 60 previously identified regions with multiple shared polymorphisms (SPs) between humans and chimpanzees, including 19 with strong evidence of LTBS. We analyzed genome-wide functional assays, expression quantitative trait loci (eQTL), genome-wide association studies (GWAS), and phenome-wide association studies (PheWAS) for all the regions. We identify functional annotations for 59 regions, including 58 with evidence of gene regulatory function from GTEx or functional genomics data and 19 with evidence of trait association from GWAS or PheWAS. As expected, the SPs associate in humans with many immune system phenotypes, including response to pathogens, but we also find associations with a range of other phenotypes, including body size, alcohol intake, cognitive performance, risk-taking behavior, and urate levels. CONCLUSIONS: The diversity of traits associated with non-coding regions with multiple SPs support previous hypotheses that functions beyond the immune system are likely subject to LTBS. Furthermore, several of these trait associations provide support and candidate genetic loci for previous hypothesis about behavioral diversity in human and chimpanzee populations, such as the importance of variation in risk sensitivity.

High Stroke Rate in Patients With Medically Managed Asymptomatic Carotid Stenosis at an Academic Center in the Southeastern United States.

BACKGROUND: Although the publication of randomized clinical trials defining the benefit of carotid endarterectomy (CEA) for asymptomatic carotid stenosis, medical management of carotid stenosis has changed significantly. With antiplatelet agents and statins, some question whether these trials are still relevant, suggesting that asymptomatic patients with >70% internal carotid artery (ICA) stenosis may do better with medial management alone, lessening the need for CEA and carotid stenting. The Vascular Quality Initiative (VQI) registry has shown that there are wide practice variations regarding the degree of stenosis that prompts surgical intervention but there are few reports of outcomes in patients who do not undergo intervention. We sought to determine the clinical outcomes of the >70% carotid stenosis patients who are treated with medical management alone at our institution. METHODS: We identified all patients with ICA stenosis >70% based on hemodynamic consensus criteria (peak systolic velocity >230 cm/s) in our peripheral vascular laboratory from January 2013 through December 2016. With a retrospective chart review, demographics, comorbid conditions, medications, radiographic studies, clinical follow-up, interventions, and outcomes at 2 years were included. Descriptive statistics were used to define these variables. RESULTS: One hundred and seventy three patients were identified with medically managed asymptomatic >70% ICA stenosis based on hemodynamic criteria on duplex ultrasound. The mean age was 67.5 years, 49% were male, 64% were White, 14% were Black, 13% race was undisclosed, 89% were prescribed antiplatelet therapy, 85% were prescribed a statin, and 60% had hypertension controlled to <140/90. Twenty patients (11.5%) experienced a cerebrovascular event during the 2-year study period. There were eight patients with transient ischemic attack, 10 with ipsilateral strokes, and 2 with strokes in unrelated territories. CONCLUSIONS: Despite good adherence to current recommendations for medical therapy, patients at our institution are developing symptomatic carotid disease at a rate similar to that reported in historical clinical trials. These data supports the concept that advances in medical management have not resulted in reduced stroke rates in asymptomatic patients with high-grade carotid stenosis at a large academic institution located in the southeastern United States. CEA and stenting provide a significant risk reduction and should be considered more often in this patient population.

Use of a Smartphone App Versus Motivational Interviewing to Increase Walking Distance and Weight Loss in Overweight/Obese Adults With Peripheral Artery Disease: Pilot Randomized Trial.

BACKGROUND: Walking therapy improves functional outcomes in patients with peripheral artery disease (PAD). Less is known about the additive benefit of a dietary intervention. OBJECTIVE: Our objectives were to develop a smartphone app and, as a pilot, explore its potential efficacy as compared to motivational interviewing (MI) to increase walking distance and promote weight loss in overweight/obese adults with PAD. METHODS: We conducted a 3-month, 2-arm randomized pilot study at the University of Kansas. Inclusion criteria were BMI >27 kg/m2 and symptomatic PAD, defined by an ankle-brachial index <0.9. Patients were randomized into 2 groups: MI, delivered through in-person and telephone counseling, and app, a mobile smartphone app. Both interventions encouraged walking for exercise and healthy dietary habits (increasing fruits and vegetables and whole grains while reducing fat and sugary drinks). We assessed medical history at baseline. At baseline and 3 months, participants completed an assessment of 6-minute walking distance, weight, quality of life, exercise behaviors, and dietary habits. The primary outcome was 3-month change in walking distance. Secondary outcomes were changes in weight, quality of life, exercise behaviors, and dietary habits. We used a Wilcoxon rank-sum test to analyze the primary and secondary outcomes at 3 months within the MI and app groups and to compare the changes between the groups with adjustment for baseline. RESULTS: We randomized 29 participants with a mean age of 66.03 (SD 8.12) years; 25 participants completed the trial. At baseline, mean walking distance among completers was 260.40 (SD 94.32) meters and 326.15 (SD 69.28) meters for MI and app participants, respectively. At 3 months, the mean walking distance was 298.67 (SD 101.20) meters and 331.19 (SD 58.63) meters for MI and app participants, respectively (group difference P=.03, adjusting for baseline). Increase in walking distance at 3 months was 40.5 meters (95% CI 6.77 to 61.34; P=.02) in MI group. At baseline, mean body weight was 253.10 (SD 59.45) lbs and 225.13 (SD 58.93) lbs for MI and app participants, respectively. At 3 months, mean body weight was 242.14 (SD 58.54) lbs and 223.44 (SD 59.54) lbs for MI and app, respectively (group difference P=.006, adjusting for baseline). Pre-post study decrease in weight was 10.1 lbs (95% CI -17.9 to -3.0) and 2.3 lbs (95% CI -3.4 to -0.7) in MI and app group, respectively. Comparing baseline to 3 months, there were no statistically significant differences in quality of life, exercise behaviors, or dietary habits. CONCLUSIONS: Our study demonstrates that MI can promote walking and weight loss in overweight/obese adults with PAD. The smartphone app showed a small weight loss but no statistically significant increase in walking distance. As this was a pilot study, future large-scale studies are needed to replicate the efficacy of MI to promote weight loss in overweight or obese adults with PAD. TRIAL REGISTRATION: ClinicalTrials.gov NCT03694652; https://clinicaltrials.gov/ct2/show/NCT03694652.

CTCF Expression and Dynamic Motif Accessibility Modulates Epithelial-Mesenchymal Gene Expression.

Epithelial-mesenchymal transition (EMT) and its reversal, mesenchymal-epithelial transition (MET) drive tissue reorganization critical for early development. In carcinomas, processing through EMT, MET, or partial states promotes migration, invasion, dormancy, and metastatic colonization. As a reversible process, EMT is inherently regulated at epigenetic and epigenomic levels. To understand the epigenomic nature of reversible EMT and its partial states, we characterized chromatin accessibility dynamics, transcriptomic output, protein expression, and cellular phenotypes during stepwise reversible EMT. We find that the chromatin insulating protein machinery, including CTCF, is suppressed and re-expressed, coincident with broad alterations in chromatin accessibility, during EMT/MET, and is lower in triple-negative breast cancer cell lines with EMT features. Through an analysis of chromatin accessibility using ATAC-seq, we identify that early phases of EMT are characterized by enrichment for AP-1 family member binding motifs, but also by a diminished enrichment for CTCF binding motifs. Through a loss-of-function analysis, we demonstrate that the suppression of CTCF alters cellular plasticity, strengthening the epithelial phenotype via the upregulation of epithelial markers E-cadherin/CDH1 and downregulation of N-cadherin/CDH2. Conversely, the upregulation of CTCF leads to the upregulation of EMT gene expression and an increase in mesenchymal traits. These findings are indicative of a role of CTCF in regulating epithelial-mesenchymal plasticity and gene expression.

Dose-response effects of alcohol on biochemical markers of bone turnover in non-human primates: Effects of species, sex and age of onset of drinking.

PURPOSE: Alcohol consumption suppressed bone turnover in male non-human primates; however, it is unclear the extent to which this effect depends upon biological variables. Using archived plasma samples, we investigated whether sex, age of onset of alcohol intake, and species influence the effects of graded increases in alcohol consumption on bone turnover markers. METHODS: 91 male and female macaques (rhesus and cynomolgus), ranging in age from 4 years (adolescent) to 10 years (adult) were required to increase their consumption of ethanol in 30-day increments: 0 g/kg/day, followed by 0.5 g/kg/day, 1.0 g/kg/day, and, finally, 1.5 g/kg/day. Plasma osteocalcin (formation), plasma CTX (resorption) and osteocalcin to CTX ratio (turnover balance) were measured during these intervals to assess the dose-response effects of alcohol. RESULTS: We detected no relationship between dose and osteocalcin when all monkeys were combined, but there was a significant effect of sex (lower levels in females) and interactions between alcohol dose and sex (osteocalcin levels increased with dose in rhesus females). In contrast, we detected a negative linear dose-response relationship for ethanol and CTX. We did not detect a relationship between dose and osteocalcin to CTX ratio overall, but there was a significant positive relationship detected in females (no change in males). Increased age predicted lower biomarker levels for both osteocalcin and CTX. Species was a significant predictor for osteocalcin and the osteocalcin to CTX ratio in these models. CONCLUSION: These findings indicate that age, sex, and species influence bone turnover and support the concept that factors beyond quantity of alcohol affect skeletal response to alcohol consumption.

Predictions, Pivots, and a Pandemic: a Review of 2020's Top Translational Bioinformatics Publications.

OBJECTIVES: Provide an overview of the emerging themes and notable papers which were published in 2020 in the field of Bioinformatics and Translational Informatics (BTI) for the International Medical Informatics Association Yearbook. METHODS: A team of 16 individuals scanned the literature from the past year. Using a scoring rubric, papers were evaluated on their novelty, importance, and objective quality. 1,224 Medical Subject Headings (MeSH) terms extracted from these papers were used to identify themes and research focuses. The authors then used the scoring results to select notable papers and trends presented in this manuscript. RESULTS: The search phase identified 263 potential papers and central themes of coronavirus disease 2019 (COVID-19), machine learning, and bioinformatics were examined in greater detail. CONCLUSIONS: When addressing a once in a centruy pandemic, scientists worldwide answered the call, with informaticians playing a critical role. Productivity and innovations reached new heights in both TBI and science, but significant research gaps remain.