magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing.

Recently, novel biotechnologies to quantify RNA modifications became an increasingly popular choice for researchers who study epitranscriptome. When studying RNA methylations such as N6-methyladenosine (m6A), researchers need to make several decisions in its experimental design, especially the sample size and a proper statistical power. Due to the complexity and high-throughput nature of m6A sequencing measurements, methods for power calculation and study design are still currently unavailable. In this work, we propose a statistical power assessment tool, magpie, for power calculation and experimental design for epitranscriptome studies using m6A sequencing data. Our simulation-based power assessment tool will borrow information from real pilot data, and inspect various influential factors including sample size, sequencing depth, effect size, and basal expression ranges. We integrate two modules in magpie: (i) a flexible and realistic simulator module to synthesize m6A sequencing data based on real data; and (ii) a power assessment module to examine a set of comprehensive evaluation metrics.

A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions.

Active mutations in the RAS genes are found in ∼30% of human cancers. Although thought to have overlapping functions, RAS isoforms show preferential activation in human tumors, which prompted us to employ a comparative and quantitative proteomics approach to generate isoform-specific and nucleotide-dependent interactomes of the four RAS isoforms, KRAS4A, KRAS4B, HRAS, and NRAS. Many isoform-specific interacting proteins were identified, including HRAS-specific CARM1 and CHK1 and KRAS-specific PIP4K2C and IPO7. Comparing the interactomes of WT and constitutively active G12D mutant of RAS isoforms, we identified several potential previously unknown effector proteins of RAS, one of which was recently reported while this article was in preparation, RADIL. These interacting proteins play important roles as knockdown or pharmacological inhibition leads to potent inhibition of cancer cells. The HRAS-specific interacting protein CARM1 plays a role in HRAS-induced senescence, with CARM1 knockdown or inhibition selectively increasing senescence in HRAS-transformed cells but not in KRAS4B-transformed cells. By revealing new isoform-specific and nucleotide-dependent RAS interactors, the study here provides insights to help understand the overlapping functions of the RAS isoforms.

Ethno-racial variations in mental health symptoms among sexually-active gay, bisexual, and other men who have sex with men in Vancouver, Canada: a longitudinal analysis.

BACKGROUND: Minority stress from racism and heterosexism may uniquely interact to impact the mental health of racialized sexual minorities. We examined variations in anxiety and depressive symptoms by reported by ethno-racial identity among gay, bisexual, and other men who have sex with men (gbMSM) in Vancouver, Canada. METHODS: We recruited gbMSM aged ≥ 16 years from February 2012 to February 2015 using respondent-driven sampling (RDS). Participants completed computer assisted self-interviews (CASI) at enrollment and every 6 months until February 2017. We examined factors associated with moderate/severe anxiety and depression scores (> 10) on the Hospital Anxiety and Depression Scale (HADS) and differences in key explanatory variables including sociodemographic, psychosocial, and substance use factors. We used multivariable mixed effects models to assess whether moderate/severe scores were associated with ethno-racial identity across all visits. RESULTS: After RDS-adjustment, of 774 participants, 79.9% of participants identified as gay. 68.6% identified as white, 9.2% as Asian, 9.8% as Indigenous, 7.3% as Latin American, and 5.1% as other ethno-racial identities. Participants contributed a median of 6 follow-up visits (Q1-Q3: 4-7). In the multivariable analysis, Asian participants had decreased odds of moderate/severe anxiety scores compared to white participants (aOR = 0.39; 95% CI: 0.18-0.86), and Latin American participants had decreased odds of moderate/severe depression scores compared to both white (aOR = 0.17; 95% CI: 0.08-0.36) and Asian (aOR = 0.07; 95% CI: 0.02-0.20) participants. CONCLUSION: Asian and Latino gbMSM reported decreased mental health symptoms compared to white participants. Asian and Latino gbMSM in Vancouver appear to manage multiple minority stressors without adversely affecting their mental health.

Diphthamide promotes TOR signaling by increasing the translation of proteins in the TORC1 pathway.

Diphthamide, a modification found only on translation elongation factor 2 (EF2), was proposed to suppress -1 frameshifting in translation. Although diphthamide is conserved among all eukaryotes, exactly what proteins are affected by diphthamide deletion is not clear in cells. Through genome-wide profiling for a potential -1 frameshifting site, we identified that the target of rapamycin complex 1 (TORC1)/mammalian TORC1 (mTORC1) signaling pathway is affected by deletion of diphthamide. Diphthamide deficiency in yeast suppresses the translation of TORC1-activating proteins Vam6 and Rtc1. Interestingly, TORC1 signaling also promotes diphthamide biosynthesis, suggesting that diphthamide forms a positive feedback loop to promote translation under nutrient-rich conditions. Our results provide an explanation for why diphthamide is evolutionarily conserved and why diphthamide deletion can cause severe developmental defects.

It's all about connection: Determinants of social support and the influence on HIV treatment interruptions among people living with HIV in British Columbia, Canada.

BACKGROUND: Social support has previously been found to be associated with improved health outcomes of individuals managing chronic illnesses, including amongst people living with HIV (PLWH). For women and people who use injection drugs who continue to experience treatment disparities in comparison to other PLWH, social support may have potential in facilitating better treatment engagement and retention. In this analysis, we examined determinants of social support as measured by the Medical Outcomes Study - Social Support Survey (MOS-SSS) scale, and quantified the relationship between MOS-SSS and HIV treatment interruptions (TIs) among PLWH in British Columbia, Canada. METHODS: Between January 2016 and September 2018, we used purposive sampling to enroll PLWH, 19 years of age or older living in British Columbia into the STOP HIV/AIDS Program Evaluation study. Participants completed a baseline survey at enrolment which included the MOS-SSS scale, where higher MOS-SSS scores indicated greater social support. Multivariable linear regression modeled the association between key explanatory variables and MOS-SSS scores, whereas multivariable logistic regression modeled the association between MOS-SSS scores and experiencing TIs while controlling for confounders. RESULTS: Among 644 PLWH, we found that having a history of injection drug use more than 12 months ago but not within the last 12 months, self-identifying as Indigenous, and sexual activity in the last 12 months were positively associated with MOS-SSS, while being single, divorced, or dating (vs. married), experiences of lifetime violence, and diagnosis of a mental health disorder were inversely associated. In a separate multivariable model adjusted for gender, ethnicity, recent homelessness, sexual activity in the last 12 months, and recent injection drug use, we found that higher MOS-SSS scores, indicating more social support, were associated with a lower likelihood of HIV treatment interruptions (adjusted odds ratio: 0.90 per 10-unit increase, 95% confidence interval: 0.83, 0.99). CONCLUSIONS: Social support may be an important protective factor in ensuring HIV treatment continuity among PLWH. Future research should examine effective means to build social support among communities that have potential to promote increased treatment engagement.

Fatal injuries associated with rear step riding among municipal solid waste collection workers (United States, 1984-2020).

BACKGROUND: United States solid waste workers suffer a high fatal injury rate due to their frequent exposures to refuse-vehicle-related hazards. The Occupational Safety and Health Administration (OSHA) allows workers to ride on the rear steps of a garbage truck (exterior riding) if employers abide by American National Standard Z245.1 (ANSI Z245.1). The State of California (CA) has banned exterior riding since 1984, and the City of New York (NYC) has implemented its own initiatives to prevent exterior riding deaths. METHODS: Fatal exterior riding incidents were identified from two online databases. Variables relating to deceased workers, employers, and injury circumstances were analyzed. RESULTS: The study identified 181 exterior riding deaths from 604 refuse-vehicle-related fatal incidents (deaths either directly caused by a refuse vehicle or one in which the victim was performing a refuse-vehicle-related task) in the United States (1984-2020). A total of 50 (27.6%) of the exterior riding deaths had no ANSI Z245.1 violations. Risk factors other than those addressed by ANSI Z245.1 contributed to these worker deaths. CONCLUSIONS: Exterior riding deaths identified by this study were all preventable. Temporary workers and workers in the public sector may be at higher risk for exterior riding deaths. Both CA and NYC had taken measures to prohibit the practice of exterior riding, and both had lower numbers of exterior riding deaths. ANSI Z245.1 and current OSHA enforcement policy do not address the inherent dangers of falling off a moving heavy vehicle while standing on a small and elevated platform, and are not effective in preventing fatal exterior riding incidents.

Usher syndrome type IV: clinically and molecularly confirmed by novel ARSG variants.

Usher syndrome (USH) is an autosomal recessively inherited disease characterized by sensorineural hearing loss (SNHL) and retinitis pigmentosa (RP) with or without vestibular dysfunction. It is highly heterogeneous both clinically and genetically. Recently, variants in the arylsulfatase G (ARSG) gene have been reported to underlie USH type IV. This distinct type of USH is characterized by late-onset RP with predominantly pericentral and macular changes, and late onset SNHL without vestibular dysfunction. In this study, we describe the USH type IV phenotype in three unrelated subjects. We identified three novel pathogenic variants, two novel likely pathogenic variants, and one previously described pathogenic variant in ARSG. Functional experiments indicated a loss of sulfatase activity of the mutant proteins. Our findings confirm that ARSG variants cause the newly defined USH type IV and support the proposed extension of the phenotypic USH classification.

Factors associated with transactional sex among a cohort of gay, bisexual, and other men who have sex with men in Vancouver, Canada.

Background Gay, bisexual, and other men who have sex with men (GBM) who engage in transactional sex (sex in exchange for drugs, money, or goods) experience increased risk of sexually transmitted infections (STI), including HIV. This study explored additional psychosocial and health-related factors associated with transactional sex among GBM. Methods Respondent-driven sampling was used to recruit GBM in Vancouver, Canada, from 2012 to 2015, with follow up every 6months until July2019. We examined factors associated with transactional sex using multivariable three-level mixed-effects modelling. Results Among 698 GBM, 22.1% reported ever receiving drugs, money, or goods for sex. Transactional sex was more likely to be reported by GBM who were younger (<30years) and who had lower incomes, less education, and insecure housing. GBM reporting transactional sex were more likely to report substance use (i.e. crystal methamphetamine, poppers, GHB, and non-steroid injection drugs) and higher risk sexual behaviours (i.e. more sex partners, sex party attendance, and condomless anal sex with serodifferent or unknown HIV status partners); however, they were no more likely to be living with HIV or to report a recent bacterial STI diagnosis. GBM who reported higher loneliness, anxiety, and cognitive escape were also more likely to report transactional sex. Conclusions More than one-fifth of GBM in Vancouver reported transactional sex and those who did were more likely to also experience psychosocial stressors, increased substance use, and higher risk sexual behaviours. Programs which consider the interconnections of personal, social, and structural challenges faced by GBM engaging in transactional sex are necessary to support improved mental, physical, and sexual health for these men.

Clinical and Genetic Re-Evaluation of Inherited Retinal Degeneration Pedigrees following Initial Negative Findings on Panel-Based Next Generation Sequencing.

Although rare, inherited retinal degenerations (IRDs) are the most common reason for blind registration in the working age population. They are highly genetically heterogeneous (>300 known genetic loci), and confirmation of a molecular diagnosis is a prerequisite for many therapeutic clinical trials and approved treatments. First-tier genetic testing of IRDs with panel-based next-generation sequencing (pNGS) has a diagnostic yield of ≈70-80%, leaving the remaining more challenging cases to be resolved by second-tier testing methods. This study describes the phenotypic reassessment of patients with a negative result from first-tier pNGS and the rationale, outcomes, and cost of second-tier genetic testing approaches. Removing non-IRD cases from consideration and utilizing case-appropriate second-tier genetic testing techniques, we genetically resolved 56% of previously unresolved pedigrees, bringing the overall resolve rate to 92% (388/423). At present, pNGS remains the most cost-effective first-tier approach for the molecular assessment of diverse IRD populations Second-tier genetic testing should be guided by clinical (i.e., reassessment, multimodal imaging, electrophysiology), and genetic (i.e., single alleles in autosomal recessive disease) indications to achieve a genetic diagnosis in the most cost-effective manner.

Crystal Methamphetamine Use and Initiation among Gay, Bisexual, and Other Men Who Have Sex with Men Living with HIV in a Treatment as Prevention Environment.

BACKGROUND: Risk compensation in an HIV Treatment as Prevention (TasP) environment may increase high-risk sexual and substance use behaviors among people living with HIV. Objective: To examine recent crystal methamphetamine (CM) use/initiation in a longitudinal cohort of gay, bisexual, and other men who have sex with men (GBMSM) living with HIV in Metro Vancouver, Canada. Methods: Eligible participants were GBMSM aged >15 years who reported sex with another man in the past six months. Participants were recruited using respondent-driven sampling and self-completed a computer questionnaire every six months. We used multi-level generalized mixed-effect models to evaluate trends in recent CM use (past six months), multivariable logistic regression to identify covariates of recent CM use, and multivariable survival analysis to identify predictors of CM initiation. Results: Of 207 GBMSM living with HIV at enrollment, 44.3% reported recent CM use; there was a statistically non-significant decrease over the study period (41% in first period to 25% in final period, p = 0.087). HIV treatment optimism was not associated with CM use/initiation. CM use was positively associated with depressive symptomology, sexual escape motivation, transactional sex, number of anal sex partners, condomless anal sex with seroconcordant partners, STIs, and other substance use. Recent CM use was negatively associated with viral load sorting. CM initiation was predicted by escape motivation, transactional sex, and group sex participation. Conclusion: Results suggest that CM use among GBMSM living with HIV is prevalent and increased CM use/initiation is not a consequence of TasP public policy.

Factors Associated with Cessation or Reduction of Methamphetamine Use among Gay, Bisexual, and Other Men Who Have Sex with Men (gbMSM) in Vancouver Canada.

Background: Methamphetamine (MA) use among gay, bisexual, and other men who have sex with men (gbMSM) is a pervasive issue, associated with detrimental health outcomes. We identified factors associated with discontinuation or reduction in MA among a subset of gbMSM reporting frequent (at least weekly) use, with a specific focus on symptoms of anxiety and depression. Methods: We recruited sexually-active gbMSM aged ≥16 years in Vancouver, Canada into a prospective-cohort study using respondent-driven sampling. Participants completed study visits once every six months. We used generalized linear mixed models to identify factors associated with reductions in MA use following a visit where participants previously reported using MA at least weekly. Results: Of 584 cohort participants with at least one follow-up visit, 67 (11.5%) reported frequent MA use at baseline or in follow-up visits. Of these, 46 (68.7%) had at least one subsequent study visit where they transitioned to less frequent (monthly or less) or no MA use. In multivariable models, reduced MA use was less likely for those who spent >50% of social time with other gbMSM (aRR = 0.49, 95%CI:0.28-0.85), gave or received drugs in exchange for sex (aRR = 0.34, 95%CI:0.13-0.87), injected drugs (aRR = 0.35, 95%CI:0.18-0.68), or used gamma-hydroxybutyrate (GHB) (aRR = 0.41, 95%CI:0.21-0.78). Symptoms of anxiety or depression were not associated with reductions in MA use. Conclusions: Social connection and drug-related factors surrounding MA use were associated with reductions, but anxiety and depressive symptomatology were not. Incorporating socialization and polysubstance-related components with MA reduction may help in developing efficacious interventions toward reducing MA use for gbMSM.

HIV Testing Among a Representative Community Sample of Gay, Bisexual, and Other Men Who Have Sex with Men in Vancouver, Canada.

Earlier HIV diagnosis allows for improved treatment outcomes and secondary prevention. It is recommended that all individuals know their HIV status and that those at higher risk test more frequently. Using a representative community sample of gay, bisexual, and other men who have sex with men (GBMSM), we aimed to: (1) determine the proportion of GBMSM who have tested in the past 2 years, (2) determine reasons for testing and never having tested, and (3) explore correlates of testing. Of 535 eligible participants, 80.0% reported having had an HIV test in the past 2 years, most commonly as part of a regular testing schedule. The most common reason for not testing was low perceived HIV risk. Bisexual and older GBMSM, as well as those who lived outside of Vancouver, were less likely to have tested in the past 2 years. Rapid point-of-care testing may help improve testing rates and was shown to effectively engage some hard-to-reach GBMSM (e.g., those who had not tested for other STIs) in this sample.

Human DNA Repair Genes Possess Potential G-Quadruplex Sequences in Their Promoters and 5'-Untranslated Regions.

The cellular response to oxidative stress includes transcriptional changes, particularly for genes involved in DNA repair. Recently, our laboratory demonstrated that oxidation of 2'-deoxyguanosine (G) to 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG) in G-rich potential G-quadruplex sequences (PQSs) in gene promoters impacts the level of gene expression up or down depending on the position of the PQS in the promoter. In the present report, bioinformatic analysis found that the 390 human DNA repair genes in the genome ontology initiative harbor 2936 PQSs in their promoters and 5'-untranslated regions (5'-UTRs). The average density of PQSs in human DNA repair genes was found to be nearly 2-fold greater than the average density of PQSs in all coding and noncoding human genes (7.5 vs 4.3 per gene). The distribution of the PQSs in the DNA repair genes on the nontranscribed (coding) vs transcribed strands reflects that of PQSs in all human genes. Next, literature data were interrogated to select 30 PQSs to catalog their ability to adopt G-quadruplex (G4) folds in vitro using five different experimental tests. The G4 characterization experiments concluded that 26 of the 30 sequences could adopt G4 topologies in solution. Last, four PQSs were synthesized into the promoter of a luciferase plasmid and cotransfected with the G4-specific ligands pyridostatin, Phen-DC3, or BRACO-19 in human cells to determine whether the PQSs could adopt G4 folds. The cell studies identified changes in luciferase expression when the G4 ligands were present, and the magnitude of the expression changes dependent on the PQS and the coding vs template strand on which the sequence resided. Our studies demonstrate PQSs exist at a high density in human DNA repair gene promoters and a subset of the identified sequences may fold in vitro and in vivo.

Patterns of Online and Offline Connectedness Among Gay, Bisexual, and Other Men Who Have Sex with Men.

This study examined patterns of connectedness among 774 sexually-active gay, bisexual, and other men who have sex with men (GBM), aged ≥ 16 years, recruited using respondent-driven sampling in Metro Vancouver. Latent class analysis examined patterns of connectedness including: attendance at gay venues/events (i.e., bars/clubs, community groups, pride parades), social time spent with GBM, use of online social and sex seeking apps/websites, and consumption of gay media. Multinomial regression identified correlates of class membership. A three-class LCA solution was specified: Class 1 "Socialites" (38.8%) were highly connected across all indicators. Class 2 "Traditionalists" (25.7%) were moderately connected, with little app/website-use. Class 3 "Techies" (35.4%) had high online connectedness and relatively lower in-person connectedness. In multivariable modelling, Socialites had higher collectivism than Traditionalists, who had higher collectivism than Techies. Socialites also had higher annual incomes than other classes. Techies were more likely than Traditionalists to report recent serodiscordant or unknown condomless anal sex and HIV risk management practices (e.g., ask their partner's HIV status, get tested for HIV). Traditionalists on the other hand were less likely to practice HIV risk management and had lower HIV/AIDS stigma scores than Socialites. Further, Traditionalists were older, more likely to be partnered, and reported fewer male sex partners than men in other groups. These findings highlight how patterns of connectedness relate to GBM's risk management.

Occupational fatal injuries associated with mobile hand-fed wood chippers.

BACKGROUND: Workers are killed every year in wood chipper-related incidents despite the repeated hazard warnings. In-depth, comprehensive, and up-to-date studies are needed to identify causal, risk, and contributing factors and assess the current control measures so that an effective and proactive prevention approach can be developed. METHODS: Cases were identified from four online databases and manually reviewed to characterize and categorize the fatal events. RESULTS: The study identified 113 wood chipper-related worker deaths (1982-2016). The victims were killed in struck-by (57), caught-in (41), motor vehicle (7), electrical (4), fall (2), and heat stroke (2) incidents while performing chipper-related tasks. CONCLUSIONS: Chipper-related worker deaths are preventable. Young and inexperienced workers may be at higher risk for caught-in deaths. The current feed wheel control devices are not effective for workers to self-rescue. Fully automatic feed wheel stop devices are needed to prevent caught-in incidents.

Synchronizing theta oscillations with direct-current stimulation strengthens adaptive control in the human brain.

Executive control and flexible adjustment of behavior following errors are essential to adaptive functioning. Loss of adaptive control may be a biomarker of a wide range of neuropsychiatric disorders, particularly in the schizophrenia spectrum. Here, we provide support for the view that oscillatory activity in the frontal cortex underlies adaptive adjustments in cognitive processing following errors. Compared with healthy subjects, patients with schizophrenia exhibited low frequency oscillations with abnormal temporal structure and an absence of synchrony over medial-frontal and lateral-prefrontal cortex following errors. To demonstrate that these abnormal oscillations were the origin of the impaired adaptive control in patients with schizophrenia, we applied noninvasive dc electrical stimulation over the medial-frontal cortex. This noninvasive stimulation descrambled the phase of the low-frequency neural oscillations that synchronize activity across cortical regions. Following stimulation, the behavioral index of adaptive control was improved such that patients were indistinguishable from healthy control subjects. These results provide unique causal evidence for theories of executive control and cortical dysconnectivity in schizophrenia.

A latent class analysis of substance use and culture among gay, bisexual and other men who have sex with men.

Assessments of gay and bisexual men's substance use often obscures salient sociocultural and identity-related experiences related to how they use drugs. Latent class analysis was used to examine how patterns of substance use represent the social, economic and identity-related experiences of this population. Participants were sexually active gay and bisexual men (including other men who have sex with men), aged ≥ 16 years, living in Metro Vancouver (n = 774). LCA indicators included all substances used in the past six months self-reported by more than 30 men. Model selection was made with consideration to model parsimony, interpretability and optimisation of statistical criteria. Multinomial regression identified factors associated with class membership. A six-class solution was identified representing: 'assorted drug use' (4.5%); 'club drug use' (9.5%); 'street drug use' (12.1%); 'sex drug use' (11.4%); 'conventional drug use' (i.e. tobacco, alcohol, marijuana; 25.9%); and 'limited drug use' (36.7%). Factors associated with class membership included age, sexual orientation, annual income, occupation, income from drug sales, housing stability, group sex event participation, gay bars/clubs attendance, sensation seeking and escape motivation. These results highlight the need for programmes and policies that seek to lessen social disparities and account for social distinctions among this population.

Local specialty pharmacy and specialty clinic collaboration assists access to hepatitis C direct-acting antivirals.

OBJECTIVES: To measure prescribed time to therapy (TtT) and sustained virologic response (SVR). Secondary objectives were to assess insurance appeals and copay assistance amount facilitated by a local specialty pharmacy (LSP). METHODS: This descriptive, retrospective study used a joint clinical and pharmacy database of patients who were prescribed direct-acting antivirals (DAAs) at a single-center liver specialty clinic and received LSP services from December 2013 to December 2015. RESULTS: Among 388 patients prescribed DAAs, 364 (94%) patients, who were 18 years of age or older, initiated DAA therapy, and received LSP services, were included in the study. Of these, 211 (58.0%) had cirrhosis, 159 (43.7%) had previous treatment, and 57 (15.7%) had previous liver transplants. Most patients had commercial insurance (n = 249; 68.4%), and 295 (81.0%) required prior authorization. Insurance initially denied coverage to 70 patients (19.2%), for who the LSP drafted appeals for 60 (85.7%). Copay information was available for 154 LSP patients. Although 66 had initial copays of more than $20 per month, the LSP was able to assist most (98.1%; n = 151) with copay reductions to $20 or less. Full financial assistance was received for 20 patients without insurance or any DAA coverage. Among 171 patients with SVR and prescribed TtT information, mean TtT was 12 days (median 4 days), and most received medications within 10 days (n = 122; 71.3%). The overall intention-to-treat SVR rate was 86.8%; the per-protocol (PP) SVR rate was 93.8%. CONCLUSION: Collaboration between providers and an LSP minimized delay in therapy, lowered rates of DAA denial, facilitated patient financial assistance, and helped to optimize clinical outcomes. The PP-SVR rate for this study was similar to rates reported in the literature and higher than expected, considering the inclusion of earlier-generation DAAs and many patients with advanced liver disease.

4n-1 Is a "Sweet Spot" in DNA i-Motif Folding of 2'-Deoxycytidine Homopolymers.

Strands of DNA with four or more contiguous runs of 2'-deoxycytidine (dC) nucleotides have the potential to adopt i-motif folds, generally under mildly acidic conditions. Analysis of dC homo-oligonucleotide strands ranging in length from 10 to 30 nucleotides by five different pH-dependent methods identified a pattern in strand length vs stability. Beginning with dC11, which does not fold, the transition pH (pHT) increased with chain length with the addition of up to four nucleotides, after which the stability dramatically decreased, and the trend repeated this cycle up to dC27. The analysis found dCn strands of length 15, 19, 23, and 27 nucleotides (i.e., 4n-1) to have pHT values >7.2 and thermal stabilities >37 °C at pH 7.0. Model studies using thymidine nucleotides to lock in i-motif loop lengths support the conclusion that the most stable dCn i-motifs possess one nucleotide in each of the three loops and a core built of an even number of base pairs. The pattern identified from the model studies occurs with a frequency of four nucleotides at lengths of 15, 19, 23, and 27 in accordance with the results obtained for the dCn strands. This observation led us to interrogate the human genome for dCn runs. Inspection of the human genome indicates that dCn runs are enriched in critical regions of the genome (promoters, UTRs, and introns), while being depleted in coding and intergenic regions, and these findings may have biological implications. Lastly, the ability to tune i-motif stabilities by the length of the strand might be harnessed for stimulus-responsive applications in DNA scaffolds, sensors, nanotechnology, and other chemical applications.

Medial-Frontal Stimulation Enhances Learning in Schizophrenia by Restoring Prediction Error Signaling.

Posterror learning, associated with medial-frontal cortical recruitment in healthy subjects, is compromised in neuropsychiatric disorders. Here we report novel evidence for the mechanisms underlying learning dysfunctions in schizophrenia. We show that, by noninvasively passing direct current through human medial-frontal cortex, we could enhance the event-related potential related to learning from mistakes (i.e., the error-related negativity), a putative index of prediction error signaling in the brain. Following this causal manipulation of brain activity, the patients learned a new task at a rate that was indistinguishable from healthy individuals. Moreover, the severity of delusions interacted with the efficacy of the stimulation to improve learning. Our results demonstrate a causal link between disrupted prediction error signaling and inefficient learning in schizophrenia. These findings also demonstrate the feasibility of nonpharmacological interventions to address cognitive deficits in neuropsychiatric disorders. SIGNIFICANCE STATEMENT: When there is a difference between what we expect to happen and what we actually experience, our brains generate a prediction error signal, so that we can map stimuli to responses and predict outcomes accurately. Theories of schizophrenia implicate abnormal prediction error signaling in the cognitive deficits of the disorder. Here, we combine noninvasive brain stimulation with large-scale electrophysiological recordings to establish a causal link between faulty prediction error signaling and learning deficits in schizophrenia. We show that it is possible to improve learning rate, as well as the neural signature of prediction error signaling, in patients to a level quantitatively indistinguishable from that of healthy subjects. The results provide mechanistic insight into schizophrenia pathophysiology and suggest a future therapy for this condition.