Common Criticisms and Rebuttals of the Best Endovascular Versus Best Surgical Therapy in Patients with Chronic Limb-Threatening Ischemia (BEST-CLI) Trial.

The Best Endovascular Versus Best Surgical Therapy in Patients With Chronic Limb-Threatening Ischemia trial was a landmark trial which provides high-quality data for the decision-making regarding the treatment of chronic-limb threatening ischemia. Overall, the trial suggests that in patients with adequate greater saphenous vein conduit, bypass surgery should be offered as a first line treatment given superior outcomes. In this article, we outline the common critiques of the trial, followed by responses to provide a deeper understanding of the strengths and limitations of this important trial.

Redlining-associated methylation in breast tumors: the impact of contemporary structural racism on the tumor epigenome.

Purpose: Place-based measures of structural racism have been associated with breast cancer mortality, which may be driven, in part, by epigenetic perturbations. We examined the association between contemporary redlining, a measure of structural racism at the neighborhood level, and DNA methylation in breast tumor tissue. Methods: We identified 80 Black and White women diagnosed and treated for a first-primary breast cancer at Emory University Hospitals (2008-2017). Contemporary redlining was derived for census tracts using the Home Mortgage Disclosure Act database. Linear regression models were used to calculate the association between contemporary redlining and methylation in breast tumor tissue. We also examined epigenetic age acceleration for two different metrics, regressing ß values for each cytosine-phosphate-guanine dinucleotide (CpG) site on redlining while adjusting for covariates. We employed multivariable Cox-proportional hazards models and 95% confidence intervals (CI) to estimate the association between aberrant methylation and mortality. Results: Contemporary redlining was associated with 5 CpG sites after adjustment for multiple comparisons (FDR<0.10). All genes were implicated in breast carcinogenesis, including genes related to inflammation, immune function and stress response (ANGPT1, PRG4 and PRG4). Further exploration of the top 25 CpG sites, identified interaction of 2 sites (MRPS28 and cg11092048) by ER status and 1 site (GDP1) was associated with all-cause mortality. Contemporary redlining was associated with epigenetic age acceleration by the Hannum metric (ß=5.35; CI 95%=0.30,10.4) and showed positive but non-significant correlation with the other clock. Conclusion: We identified novel associations between neighborhood contemporary redlining and the breast tumor DNA methylome, suggesting that racist policies leading to inequitable social and environmental exposures, may impact the breast tumor epigenome. Additional research on the potential implications for prognosis is needed.

Assessing non-LUS stutter in DNA sequence data.

Forensic DNA analysis is among the most well-recognized and well-developed forensic disciplines. The field's use of DNA markers known as short tandem repeats (STRs) offer a robust means of discriminating individuals while also introducing challenges to the analysis. One of these challenges, stutter, is the result of a non-biological artifact introduced during PCR. The formation and amplification of these stutter products can occur at rates as high as 15-20% of the parent allele. The challenge inherent in this process is differentiating stutter artifacts from true alleles, particularly in the presence of a minor contributor. Traditionally, DNA profiles are obtained using capillary electrophoresis (CE), where amplified DNA fragments are separated by size, not sequence, and the identification of stutter is performed on a locus-specific level. The use of CE-based fragment data rather than sequence-based data, has limited the community's understanding of the precise behavior of stutter. Massively parallel sequencing (MPS) data provides an opportunity to better characterize stutter, permitting a more accurate means of detecting both size- or longest uninterrupted stretch (LUS)-based stutter but also allele and motif-specific stutter characteristics. This study sheds light on the value of characterizing motif- and allele-specific stutter, including non-LUS stutter, when using MPS methods. Analysis and characterization of stutter sequences was performed using data generated from 539 samples amplified with the ForenSeq and PowerSeq 46GY library preparation kit and sequenced on the Illumina MiSeq FGx. Assessment of non-LUS stutter begins with calculating stutter rates for all potential stutter products at a given locus (and allele), additionally, the occurrence of these discrete stutter products were quantified. Results show that although the LUS sequence stutters at a higher rate than non-LUS motifs, the non-LUS stutter products do occur at detectable levels and potentially influence sequence-based mixture analysis. The data indicate that the stutter from one motif or allele can be distinguished from another motif or allele based on their unique stutter rates; however, the number of stutter products from each motif or allele may similarly make up the overall pool of stutter products. Motif- and allele-specific stutter models provide the most comprehensive analysis of sequence stutter rates and provide the ability to differentiate stutter sequences more accurately from true allele stutter. This information provides a foundation for including the characterization of non-LUS stutter products when analyzing DNA profiles, specifically mixtures with potential low-level contributors.

Neighborhood characteristics and breast tumor methylation: using epigenomics to explore cancer outcome disparities.

BACKGROUND: Social exposures may drive epigenetic alterations that affect racial disparities in breast cancer outcomes. This study examined the association between neighborhood-level factors and DNA methylation in non-Hispanic Black and White women diagnosed with breast cancer. METHODS: Genome-wide DNA methylation was measured using the EPIC array in the tumor tissue of 96 women. Linear regression models were used to examine the association between nine neighborhood-level factors and methylation, regressing ß values for each cytosine-phosphate guanine dinucleotide (CpG) site on neighborhood-level factors while adjusting for covariates. Neighborhood data were obtained from the Opportunity Atlas. We used a false discovery rate (FDR) threshold < 0.05, and for CpGs below this threshold, we examined interactions with race. We employed multivariable Cox proportional-hazards models to estimate whether aberrant methylation was associated with all-cause mortality. RESULTS: 26 of the CpG sites were associated with job density or college education (FDR < 0.05). Further exploration of these 26 CpG sites revealed no interactions by race, but a single probe in TMEM204 was associated with all-cause mortality. CONCLUSION: We identified novel associations between neighborhood-level factors and the breast tumor DNA methylome. Our data are the first to show that dysregulation in neighborhood associated CpG sites may be associated with all-cause mortality. Neighborhood-level factors may contribute to differential tumor methylation in genes related to tumor progression and metastasis. This contributes to the increasing body of evidence that area-level factors (such as neighborhood characteristics) may play an important role in cancer disparities through modulation of the breast tumor epigenome.

Saturdays Orthodontic Appointments, Demand, and Patients' Commitment.

AIM: The purpose of this study was to determine the demand for orthodontic appointments on weekends and the level of commitment the patients have for those appointments. MATERIALS AND METHODS: A survey of 17 questions was created and given to 199 adult patients. The first six questions addressed demographic information, followed by three questions addressing whether coming to their orthodontic appointments required taking time off of work. The remaining questions asked if they would prefer to attend orthodontic appointments on Saturday if they would take advantage of a Saturday appointment, and what their preferred time and level of commitment would be for this appointment. The data were analyzed using the logistic-regression Chi-square test. RESULTS: About 77.4% of the participants indicated that they would take advantage of appointments on Saturdays if available. The most preferred time for Saturday appointments was 7:00 am-10:00 am, followed by 10:00 am-12:00 pm. About 60.6% of the participants reported that they would be willing to sign up for AutoPay in order to be seen on Saturday. Among those who would take advantage of weekend appointments, 82.6% reported that they would likely never miss or reschedule a Saturday appointment, and 75.3% would choose an orthodontist who is open on Saturday over another orthodontist who is not. Among participants who work more than 40 hours per week, 86.1% (106) wanted to take advantage of Saturday appointments. Participants with a high household income are less inclined to take advantage of Saturday appointments compared with those with a low household income. Participants who need to take time off of work are more inclined to take advantage of Saturday appointments [93% (106) favorable vs 7% (8) unfavorable]. Participants who need to take their child out of school early for their orthodontic appointments during the week are more inclined to take advantage of Saturday appointments [87% (97) favorable vs 13% (15) unfavorable] than those who do not need to. CONCLUSION: There is a demand for Saturday orthodontic appointments with a very high commitment level among the majority of those patients. The Saturday demographic tends to be participants with a low household income who work 40 or more hours per week. CLINICAL SIGNIFICANCE: Orthodontic offices may consider working at least one Saturday per month to satisfy patient needs. They can use this survey to explore their own market for Saturday clinical practice.

Obesity-associated methylation in breast tumors: a possible link to disparate outcomes?

PURPOSE: As a primary risk factor and modifier of breast cancer incidence and prognosis, obesity may contribute to race disparities in breast cancer outcomes. This study examined association between obesity and DNA methylation in non-Hispanic Black and White women diagnosed with breast cancer. METHODS: Genome-wide DNA methylation was measured in the breast cancer tumor tissue of 96 women using the EPIC array. To examine the association between obesity and tumor methylation, linear regression models were used-regressing methylation ß value for each cytosine and guanine (CpG) site on body mass index adjusting for covariates. Significance was set at false discovery rate (FDR) < 0.05. In the top 20 CpG sites, we explored the interactions with race and estrogen receptor (ER) status. We used multivariable Cox-proportional hazard models to examine whether methylation in the top 20 sites was associated with all-cause mortality. RESULTS: While none of the CpG sites passed the FDR threshold for significance, among the top 20 CpG sites, we observed interactions with race (TOMM20) and ER status (PSMB1, QSOX1 and PHF1). The same CpG sites in TOMM20, PSMB1, and QSOX1 were associated with all-cause mortality. CONCLUSIONS: We identified novel interactions between obesity-associated methylation and both race and ER status in genes that have been associated with tumor regulation. Our data suggest that dysregulation in two sites may associate with all-cause mortality.

Racial Disparities in Breast Cancer Outcomes in the Metropolitan Atlanta Area: New Insights and Approaches for Health Equity.

BACKGROUND: Racial disparities in breast cancer (BC) outcomes persist where non-Hispanic black (NHB) women are more likely to die from BC than non-Hispanic white (NHW) women, and the extent of this disparity varies geographically. We evaluated tumor, treatment, and patient characteristics that contribute to racial differences in BC mortality in Atlanta, Georgia, where the disparity was previously characterized as especially large. METHODS: We identified 4943 NHW and 3580 NHB women in the Georgia Cancer Registry with stage I-IV BC diagnoses in Atlanta (2010-2014). We used Cox proportional hazard regression to calculate hazard ratios (HRs) and 95% confidence intervals (CIs) comparing NHB vs NHW BC mortality by tumor, treatment, and patient characteristics on the additive and multiplicative scales. We additionally estimated the mediating effects of these characteristics on the association between race and BC mortality. RESULTS: At diagnosis, NHB women were younger-with higher stage, node-positive, and triple-negative tumors relative to NHW women. In age-adjusted models, NHB women with luminal A disease had a 2.43 times higher rate of BC mortality compared to their NHW counterparts (95% CI = 1.99 to 2.97). High socioeconomic status (SES) NHB women had more than twice the mortality rates than their white counterparts (HR = 2.67, 95% CI = 1.65 to 4.33). Racial disparities among women without insurance, in the lowest SES index, or diagnosed with triple-negative BC were less pronounced. CONCLUSIONS: In Atlanta, the largest racial disparities are observed in luminal tumors and most pronounced among women of high SES. More research is needed to understand drivers of disparities within these treatable features.

Anesthesia and increased hypercarbic drive impair the coordination between breathing and swallowing.

BACKGROUND: Coordination between breathing and swallowing helps prevent aspiration of foreign material into the respiratory tract. The authors examined the effects of anesthesia and hypercapnia on swallowing-breathing coordination. METHODS: In a randomized controlled crossover study, general anesthesia with propofol or sevoflurane was titrated using an up-down method to identify the threshold for suppression of the motor response to electrical stimulation of the forearm. Additional measurements included bispectral index, genioglossus electromyogram, ventilation (pneumotachometer), and hypopharyngeal pressure. During wakefulness and at each level of anesthesia, carbon dioxide was added to increase the end-tidal pressure by 4 and 8 mmHg. A swallow was defined as increased genioglossus activity with deglutition apnea and an increase in hypopharyngeal pressure. Spontaneous swallows were categorized as physiological (during expiration or followed by expiration) or pathological (during inspiration or followed by an inspiration). RESULTS: A total of 224 swallows were analyzed. Anesthesia increased the proportion of pathological swallows (25.9% vs. 4.9%) and decreased the number of swallows per hour (1.7±3.3 vs. 28.0±22.3) compared to wakefulness. During anesthesia, hypercapnia decreased hypopharyngeal pressure during inspiration (-14.1±3.7 vs. -8.7±2 mmHg) and increased minute ventilation, the proportion of pathological swallows (19.1% vs. 12.3%), and the number of swallows per hour (5.5±17.0. vs. 1.3±5.5). CONCLUSIONS: Anesthesia impaired the coordination between swallowing and respiration. Mild hypercapnia increased the frequency of swallowing during anesthesia and the likelihood of pathological swallowing. During anesthesia, the risk for aspiration may be further increased when ventilatory drive is stimulated.

The potential of accelerating early detection of autism through content analysis of YouTube videos.

Autism is on the rise, with 1 in 88 children receiving a diagnosis in the United States, yet the process for diagnosis remains cumbersome and time consuming. Research has shown that home videos of children can help increase the accuracy of diagnosis. However the use of videos in the diagnostic process is uncommon. In the present study, we assessed the feasibility of applying a gold-standard diagnostic instrument to brief and unstructured home videos and tested whether video analysis can enable more rapid detection of the core features of autism outside of clinical environments. We collected 100 public videos from YouTube of children ages 1-15 with either a self-reported diagnosis of an ASD (N = 45) or not (N = 55). Four non-clinical raters independently scored all videos using one of the most widely adopted tools for behavioral diagnosis of autism, the Autism Diagnostic Observation Schedule-Generic (ADOS). The classification accuracy was 96.8%, with 94.1% sensitivity and 100% specificity, the inter-rater correlation for the behavioral domains on the ADOS was 0.88, and the diagnoses matched a trained clinician in all but 3 of 22 randomly selected video cases. Despite the diversity of videos and non-clinical raters, our results indicate that it is possible to achieve high classification accuracy, sensitivity, and specificity as well as clinically acceptable inter-rater reliability with nonclinical personnel. Our results also demonstrate the potential for video-based detection of autism in short, unstructured home videos and further suggests that at least a percentage of the effort associated with detection and monitoring of autism may be mobilized and moved outside of traditional clinical environments.

Cerebral amyloid angiopathy in an aged sooty mangabey (Cercocebus atys).

A 26-y-old male sooty mangabey (Cercocebus atys) was found at necropsy to have a moderate degree of cerebral amyloid ß (Aß) angiopathy in superficial and parenchymal blood vessels of the brain. Senile (Aß) plaques were absent, as were neurofibrillary tangles and other signs of neurodegeneration. Affected blood vessels were arterial, capillary, and, less frequently, venous in nature. Histologically, the Aß40 isoform was more prevalent than was Aß42. As in humans but unlike in squirrel monkeys, the density of lesions in this mangabey increased along a rostral-to-caudal gradient. Therefore mangabeys appear to conform to the general tendency of nonhuman primates by developing cerebral Aß angiopathy in the absence of other indices of Alzheimer-type neuropathology.