Genome-scale deconvolution of RNA structure ensembles.

RNA structure heterogeneity is a major challenge when querying RNA structures with chemical probing. We introduce DRACO, an algorithm for the deconvolution of coexisting RNA conformations from mutational profiling experiments. Analysis of the SARS-CoV-2 genome using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and DRACO, identifies multiple regions that fold into two mutually exclusive conformations, including a conserved structural switch in the 3' untranslated region. This work may open the way to dissecting the heterogeneity of the RNA structurome.

The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7.

The histone acetyltransferase p300 (also known as KAT3B) is a general transcriptional coactivator that introduces the H3K27ac mark on enhancers triggering their activation and gene transcription. Genome-wide screenings demonstrated that a large fraction of long non-coding RNAs (lncRNAs) plays a role in cellular processes and organ development although the underlying molecular mechanisms remain largely unclear (1,2). We found 122 lncRNAs that interacts directly with p300. In depth analysis of one of these, lncSmad7, is required to maintain ESC self-renewal and it interacts to the C-terminal domain of p300. lncSmad7 also contains predicted RNA-DNA Hoogsteen forming base pairing. Combined Chromatin Isolation by RNA precipitation followed by sequencing (ChIRP-seq) together with CRISPR/Cas9 mutagenesis of the target sites demonstrate that lncSmad7 binds and recruits p300 to enhancers in trans, to trigger enhancer acetylation and transcriptional activation of its target genes. Thus, these results unveil a new mechanism by which p300 is recruited to the genome.

Emergency department visits for dental problems among adults with private dental insurance: A national observational study.

OBJECTIVE: Dental insurance may be a protective factor in reducing unnecessary emergency department (ED) use for nontraumatic dental pain. The purpose of this study was to 1) characterize patient demographics and identify risk factors associated with ED utilization for dental problems among individuals dually enrolled in medical and dental insurance and 2) investigate antibiotic and opioid prescription patterns among these patients following discharge. Further study of this unique population may provide insight into other causes of unmet dental need beyond lack of dental insurance. METHODS: Claims data from a large national managed health care plan from 2015 to 2018 were used to evaluate ED use for dental problems in patients with synchronous medical and dental insurance. National counts for ED visits, total visit costs, primary diagnoses, and outpatient treatments for antibiotics and opioids were assessed. Multivariable regression was used to assess any associated demographic and health-related variables. RESULTS: 1492 unique patients were admitted to the ED for dental pain and 429,376 unique patients presented for other symptoms. Utilization rates for nontraumatic dental pain were estimated to be 0.4% of all ED visits, with an average cost of $1487 per visit. Within three days following discharge from the ED, 58% of patients filled an opioid prescription and 38% filled an antibiotic prescription. Patients who presented for dental ED pain were more likely to be younger, live in a ZIP code with a lower median household income, have more medical comorbidities, and receive fewer preventive dental procedures within the prior year. CONCLUSION: Our findings demonstrate a low rate of ED utilization for nontraumatic dental pain among dentally insured patients and highlight the protective value of prior dental visits for reducing ED use. Given high rates of antibiotic and opioid prescription fill following discharge, comprehensive ED guidelines regarding appropriate antibiotic and opioid treatment pathways may be helpful to provide more definitive care to patients with dental insurance.

In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs.

The influenza A virus (IAV) is a continuous health threat to humans as well as animals due to its recurring epidemics and pandemics. The IAV genome is segmented and the eight negative-sense viral RNAs (vRNAs) are transcribed into positive sense complementary RNAs (cRNAs) and viral messenger RNAs (mRNAs) inside infected host cells. A role for the secondary structure of IAV mRNAs has been hypothesized and debated for many years, but knowledge on the structure mRNAs adopt in vivo is currently missing. Here we solve, for the first time, the in vivo secondary structure of IAV mRNAs in living infected cells. We demonstrate that, compared to the in vitro refolded structure, in vivo IAV mRNAs are less structured but exhibit specific locally stable elements. Moreover, we show that the targeted disruption of these high-confidence structured domains results in an extraordinary attenuation of IAV replicative capacity. Collectively, our data provide the first comprehensive map of the in vivo structural landscape of IAV mRNAs, hence providing the means for the development of new RNA-targeted antivirals.

RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications.

RNA is emerging as a key regulator of a plethora of biological processes. While its study has remained elusive for decades, the recent advent of high-throughput sequencing technologies provided the unique opportunity to develop novel techniques for the study of RNA structure and post-transcriptional modifications. Nonetheless, most of the required downstream bioinformatics analyses steps are not easily reproducible, thus making the application of these techniques a prerogative of few laboratories. Here we introduce RNA Framework, an all-in-one toolkit for the analysis of most NGS-based RNA structure probing and post-transcriptional modification mapping experiments. To prove the extreme versatility of RNA Framework, we applied it to both an in-house generated DMS-MaPseq dataset, and to a series of literature available experiments. Notably, when starting from publicly available datasets, our software easily allows replicating authors' findings. Collectively, RNA Framework provides the most complete and versatile toolkit to date for a rapid and streamlined analysis of the RNA epistructurome. RNA Framework is available for download at: http://www.rnaframework.com.

Oral Health Status of Hospitalized Patients With Type 2 Diabetes.

BACKGROUND: Diabetes is associated with poor oral health, as well as reduced access to dental care. A large percentage of patients hospitalized in the United States carry a diagnosis of diabetes; however, the oral health status of patients with diabetes who are hospitalized is unknown. METHODS: All patients meeting inclusion criteria on the general medicine service of a tertiary care hospital were invited to participate. Subjects were asked about their access to dental care and perceptions of their oral health. A dental hygienist conducted examinations, including decayed, missing, and filled teeth (DMFT) and periodontal screening and recording (PSR) indices on a subset of subjects. RESULTS: The 105 subjects had a mean age of 69 ± 12 years and a median A1C of 7.5 ± 2.1%. Rates of comorbidity and polypharmacy were high. The mean number of DMFT was 23.0 ± 7.2, with 10.1 ± 7.2 missing teeth. Forty- four percent of subjects had a removable prosthesis. Sixty-eight percent had a PSR index ≥4 in at least one sextant, indicating moderate periodontal disease. CONCLUSION: Rates of missing teeth, removable prostheses, and periodonal inflammation were high among hospitalized patients with diabetes, but patients did not perceive their oral health to be poor. Health care providers should be aware of the oral health risks of patients with diabetes during hospitalization, and dentists should consider screening patients with diabetes for recent hospitalization.

In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding.

Defining the in vivo folding pathway of cellular RNAs is essential to understand how they reach their final native conformation. We here introduce a novel method, named Structural Probing of Elongating Transcripts (SPET-seq), that permits single-base resolution analysis of transcription intermediates' secondary structures on a transcriptome-wide scale, enabling base-resolution analysis of the RNA folding events. Our results suggest that cotranscriptional RNA folding in vivo is a mixture of cooperative folding events, in which local RNA secondary structure elements are formed as they get transcribed, and non-cooperative events, in which 5'-halves of long-range helices get sequestered into transient non-native interactions until their 3' counterparts have been transcribed. Together our work provides the first transcriptome-scale overview of RNA cotranscriptional folding in a living organism.

Oral Health Integration Into a Pediatric Practice and Coordination of Referrals to a Colocated Dental Home at a Federally Qualified Health Center.

We have integrated preventive oral health measures into preventive care visits for children at a federally qualified health center in Boston, Massachusetts. The program, started in 2015, covers 3400 children and has increased universal caries risk screening in primary care to 85%, fluoride varnish application rates to 80%, and referrals to a dental home to 35%. We accomplished this by minimizing pressures on providers' workflow, empowering medical assistants to lead the initiative, and utilizing data-driven improvement strategies, alongside colocated coordinated care.

Interstate Practice of Dental Teleradiology in the United States: The Effect of Licensing Requirements on Oral and Maxillofacial Radiologists' Practice Patterns.

BACKGROUND: In the United States, each state has independent licensing standards. Dentists wishing to practice in more than one state must apply to each individually. The goal of this study was to assess whether board-certified oral and maxillofacial radiologists interpreted images taken outside the states in which they were licensed and whether coverage provided by the malpractice insurance plans to which they subscribed affected their behavior. MATERIALS AND METHODS: An electronic survey was sent to all current members of the American Board of Oral and Maxillofacial Radiology, with a response rate of 74%. Descriptive statistics were calculated. RESULTS: The majority of respondents (54.6%) indicated they write reports for patients in states for which they do not have a dental license. An even larger majority (80.0%) do not know whether their malpractice insurance protects them in these cases. Qualitative responses indicate that there is confusion among practitioners as to what is legally permitted pertaining to teledentistry of this nature. CONCLUSIONS: Much of the work in which oral and maxillofacial radiologists engage may be considered teledentistry. In other settings, teledentistry has been proposed as a means to improve access to care for vulnerable populations, yet current licensure laws may make this more difficult to implement. Based on the results of our survey, many oral and maxillofacial radiologists in practice may be considered to be practicing without a license. Portability of diagnostic images may make it more difficult to enforce geographic practice boundaries. A national licensure system would be easier to enforce while maintaining high levels of patient safety.

Lack of dental insurance is correlated with edentulism.

PURPOSE: The correlation between insurance status and edentulism has not previously been reported in a population with known access to a dentist, and little is known about patient demographics in corporate dental settings. This study investigated patient demographics of a former dental franchise in Chicopee, Massachusetts, and examined a correlation between dental insurance and edentulism in this group. The correlation of edentulism with age, gender, and dental risk factors (diabetes, temporomandibular disorder, trouble with previous dental work, or oral sores and ulcers) was also examined. MATERIALS AND METHODS: This was a retrospective case study. Age, gender, and presence of dental risk factors were recorded from the patient medical history intake form. Dentate status was recorded from patient odontograms. Dental insurance status was obtained from billing records. Data was aggregated and deidentified. Descriptive and bivariate statistics and logistic regression models were used to identify associations (p-value ≤ 0.05 significance). RESULTS: Of 1,123 records meeting inclusion criteria, 52.54 percent of patients had dental insurance, 26.27 percent had at least one dental risk factor, and 18.17 percent were edentulous. Age and insurance status were significantly correlated with edentulism. Correcting for age, individuals without insurance were 1.56 times as likely to be edentulous. CONCLUSION: This case study provides insight into patient demographics that might seek care in a corporate setting and suggests that access to a dentist alone may not be adequate in preserving the adult dentition; dental insurance may also be important to health. As the corporate dental practice model continues to grow, these topics deserve further study.

Are panoramic radiographs predictive of temporomandibular joint synovitis in children with juvenile idiopathic arthritis?

PURPOSE: To identify specific panoramic radiographic findings associated with temporomandibular joint (TMJ) synovitis in children with juvenile idiopathic arthritis (JIA). MATERIALS AND METHODS: This was a retrospective study of children with JIA evaluated at Boston Children's Hospital. Patients were included if they had a confirmed diagnosis of JIA, a panoramic radiograph, and a contemporaneous TMJ magnetic resonance imaging (MRI) study with contrast. Medical records and imaging studies were reviewed to document demographic, panoramic (accentuated antegonial notch, short ramus and condyle unit [RCU] length, and abnormal condyle morphology: decreased condyle anteroposterior or superoinferior dimension) and MRI findings. The outcome variable was the presence or absence of TMJ synovitis on MRI. Descriptive and bivariate statistics and logistic regression models were used to identify associations (significant at P ≤ .05). RESULTS: Thirty patients (21 girls) with a mean age of 11.1 years (range, 5 to 16 yr) met the inclusion criteria. Of these, 15 patients had MRI scans positive for synovitis (bilateral in 18 joints in 9 patients and unilateral in 6 joints in 6 patients). The remaining 15 patients did not have evidence of synovitis on MRI. In the synovitis group, 18 of 24 joints (75%) showed abnormal panoramic findings (abnormal condyle morphology in 18 joints, accentuated antegonial notch in 9 joints, or short RCU length in 5 joints). In the nonsynovitis group, 15 of 36 joints (42%) showed abnormal panoramic findings (abnormal condyle morphology in 12 joints, accentuated antegonial notch in 6 joints, or short RCU length in 4 joints). Abnormal condyle morphology and accentuated antegonial notching on panoramic radiographs were found to be significantly correlated with synovitis (P = .0005 and .044, respectively). In a logistic regression model, abnormal condyle morphology was significantly associated with an increase in likelihood of TMJ synovitis versus those joints with normal condyle morphology (P = .007). Joints with abnormal condyle morphology and accentuated antegonial notching were 7.5 times as likely to have synovitis (P = .009) versus those joints without abnormal panoramic findings. CONCLUSION: Results of this preliminary study indicate that in this sample of children with JIA, the combination of abnormal condyle morphology and accentuated antegonial notching on a panoramic radiograph correlates with TMJ synovitis on MRI.

Treatment deferral for elevated blood pressure at a dental school clinic.

OBJECTIVES: Current guidelines by the American Dental Association (ADA) recommend deferral of elective dental care for elevated blood pressure. However, it is unknown how frequently this impacts dental treatment. The purpose of this study was to evaluate rates of asymptomatic hypertension and treatment deferral at a dental school clinic. METHODS: This was a retrospective study with data extracted from a chart review of all patients presenting for care at a dental school teaching practice. Differences in dental procedures, the time between visits, and the number of antihypertensive medications were calculated between patients with and without a blood pressure reading exceeding current guidelines for elective treatment. RESULTS: Among 26,821 individuals, 1265 had a visit with elevated blood pressure. Blood pressure readings at the next visit were significantly lower (systolic blood pressure 137 [95% confidence interval {CI} 135-138] mmHg, diastolic blood pressure 82 [95% CI 81-83 mmHg], p < 0.001), although only 24 patients reported taking a new medication. Only 4.1% of these patients had a procedure deferred; for those that did, the average intervisit time was 88.2 days (95% CI 77.7-98.7 days). CONCLUSIONS: The majority of patients with blood pressure readings exceeding current ADA recommendations for treatment were treated without evidence of harm. Patients were also unlikely to return to the clinic with new medications for blood pressure after a visit with an elevated blood pressure reading. Oral health providers must weigh the risks and benefits of care deferral and can consider an expanded role in hypertension management in dental settings when caring for patients with elevated blood pressure.

From childhood adversity to latent stress vulnerability in adulthood: the mediating roles of sleep disturbances and HPA axis dysfunction.

Childhood adversity is a prominent predisposing risk factor for latent stress vulnerability, expressed as an elevated likelihood of developing stress-related psychopathology upon subsequent exposure to trauma in adulthood. Sleep disturbances have emerged as one of the most pronounced maladaptive behavioral outcomes of childhood adversity and are also a highly prevalent core feature of stress-related psychopathology, including post-traumatic stress disorder (PTSD). After reviewing the extensive literature supporting these claims, the current review addresses the notion that childhood adversity-induced sleep disturbances may play a causal role in elevating individuals' stress vulnerability in adulthood. Corroborating this, sleep disturbances that predate adult trauma exposure have been associated with an increased likelihood of developing stress-related psychopathology post-exposure. Furthermore, novel empirical evidence suggests that sleep disturbances, including irregularity of the sleep-wake cycle, mediate the link between childhood adversity and stress vulnerability in adulthood. We also discuss cognitive and behavioral mechanisms through which such a cascade may evolve, highlighting the putative role of impaired memory consolidation and fear extinction. Next, we present evidence to support the contribution of the hypothalamic-pituitary-adrenal (HPA) axis to these associations, stemming from its critical role in stress and sleep regulatory pathways. Childhood adversity may yield bi-directional effects within the HPA stress and sleep axes in which sleep disturbances and HPA axis dysfunction reinforce each other, leading to elevated stress vulnerability. To conclude, we postulate a conceptual path model from childhood adversity to latent stress vulnerability in adulthood and discuss the potential clinical implications of these notions, while highlighting directions for future research.

Dental Services Use: Medicare Beneficiaries Experience Immediate And Long-Term Reductions After Enrollment.

Traditional Medicare does not cover routine dental care, but little is known about transitions in dental outcomes upon reaching Medicare eligibility at age sixty-five. Using data from the 2010-19 Medical Expenditure Panel Surveys, we examined dental insurance, utilization, and outcomes among US adults before and after age sixty-five, using a regression discontinuity design and segmented regression analysis. Among 97,108 US adults representing a weighted population of 104,787,300 people, complete edentulism, or the loss of all teeth, increased by 4.8 percentage points at age sixty-five, and the percentage of people receiving restorative dental care decreased by 8.7 percentage points. Enrollment in Medicare Advantage, which may offer a dental benefit, was not associated with greater use of dental services relative to traditional Medicare, and Medicare Advantage enrollees had a significantly larger drop in dental spending from private insurance at age sixty-five than traditional Medicare enrollees. Expanding Medicare to cover dental services may help counteract these effects among all enrollees.

Challenges connecting emergency department patients with oral health care: A qualitative analysis of patients, emergency department clinicians, and dentists.

BACKGROUND: Unmet dental need shares many risk factors with unmet health-related social needs (HRSN) such as housing and food security and are a common cause for seeking treatment at the emergency department (ED). METHODS: The authors recruited a purposive sample of English-speaking and Spanish-speaking patients, ED clinicians at 3 urban EDs, and dentists from nearby communities to participate in qualitative interviews to explore barriers to and facilitators of screening for HRSN and unmet dental needs in the ED. Themes were identified from transcripts using a modified grounded theory approach. RESULTS: Interviews were conducted with 25 ED patients, 19 ED clinicians, and 4 dentists. Four themes were identified: (1) a preference for formalized resources, which more frequently exist for HRSN than for oral health; (2) frequent use of ad hoc resources that are less reliable or structured, particularly for dental referral information; (3) limited knowledge of oral health care resources in the community; and (4) desire for more assistance with identifying and addressing resource needs for both HRSN and oral health. Patients were amenable to screening through a variety of modalities and felt it would be helpful, but clinicians emphasized the need for easier referral processes because of frequent failure to connect patients to oral health care. CONCLUSIONS: More robust infrastructure and clinician support are needed to ensure successful referral and screening without undue provider burden for both medical and dental clinicians. PRACTICAL IMPLICATIONS: Patients are amenable to screening for unmet oral health needs and HRSN in the ED, which may improve access to care.

Stressful life events, oral health, and barriers to dental care during pregnancy.

OBJECTIVES: Poor oral health during pregnancy poses risks to maternal and infant well-being. However, limited research has documented how proximate stressful life events (SLEs) during the prenatal period are associated with oral health and patterns of dental care utilization. METHODS: Data come from 13 states that included questions on SLEs, oral health, and dental care utilization in the Pregnancy Risk Assessment Monitoring System for the years 2016-2020 (n = 48,658). Multiple logistic regression analyses were used to assess the association between levels of SLE (0, 1-2, 3-5, or 6+) and a range of (1) oral health experiences and (2) barriers to dental care during pregnancy while controlling for socio-demographic and pregnancy-related characteristics. RESULTS: Women with more SLEs in the 12 months before birth-especially six or more-reported worse oral health experiences, including not having dental insurance, not having a dental cleaning, not knowing the importance of caring for teeth and gums, needing to see a dentist for a problem, going to see a dentist for a problem, and unmet dental care needs. Higher levels of SLEs were also associated with elevated odds of reporting barriers to dental care. CONCLUSIONS: SLEs are an essential but often understudied risk factor for poor oral health, unmet dental care needs, and barriers to dental care services. Future research is needed to understand better the mechanisms linking SLEs and oral health.