CodonBert large language model for mRNA vaccines.

mRNA-based vaccines and therapeutics are gaining popularity and usage across a wide range of conditions. One of the critical issues when designing such mRNAs is sequence optimization. Even small proteins or peptides can be encoded by an enormously large number of mRNAs. The actual mRNA sequence can have a large impact on several properties including expression, stability, immunogenicity, and more. To enable the selection of an optimal sequence, we developed CodonBERT, a large language model (LLM) for mRNAs. Unlike prior models, CodonBERT uses codons as inputs which enables it to learn better representations. CodonBERT was trained using more than 10 million mRNA sequences from a diverse set of organisms. The resulting model captures important biological concepts. CodonBERT can also be extended to perform prediction tasks for various mRNA properties. CodonBERT outperforms previous mRNA prediction methods including on a new flu vaccine dataset.

Synthesis of low immunogenicity RNA with high-temperature in vitro transcription.

The use of synthetic RNA for therapeutics requires that the in vitro synthesis process be robust and efficient. The technology used for the synthesis of these in vitro-transcribed RNAs, predominantly using phage RNA polymerases (RNAPs), is well established. However, transcripts synthesized with RNAPs are known to display an immune-stimulatory activity in vivo that is often undesirable. Previous studies have identified double-stranded RNA (dsRNA), a major by-product of the in vitro transcription (IVT) process, as a trigger of cellular immune responses. Here we describe the characterization of a high-temperature IVT process using thermostable T7 RNAPs to synthesize functional mRNAs that demonstrate reduced immunogenicity without the need for a post-synthesis purification step. We identify features that drive the production of two kinds of dsRNA by-products-one arising from 3' extension of the run-off product and one formed by the production of antisense RNAs-and demonstrate that at a high temperature, T7 RNAP has reduced 3'-extension of the run-off product. We show that template-encoded poly(A) tailing does not affect 3'-extension but reduces the formation of the antisense RNA by-products. Combining high-temperature IVT with template-encoded poly(A) tailing prevents the formation of both kinds of dsRNA by-products generating functional mRNAs with reduced immunogenicity.

Pseudouridinylation of mRNA coding sequences alters translation.

Chemical modifications of RNAs have long been established as key modulators of nonprotein-coding RNA structure and function in cells. There is a growing appreciation that messenger RNA (mRNA) sequences responsible for directing protein synthesis can also be posttranscriptionally modified. The enzymatic incorporation of mRNA modifications has many potential outcomes, including changing mRNA stability, protein recruitment, and translation. We tested how one of the most common modifications present in mRNA coding regions, pseudouridine (Ψ), impacts protein synthesis using a fully reconstituted bacterial translation system and human cells. Our work reveals that replacing a single uridine nucleotide with Ψ in an mRNA codon impedes amino acid addition and EF-Tu GTPase activation. A crystal structure of the Thermus thermophilus 70S ribosome with a tRNAPhe bound to a ΨUU codon in the A site supports these findings. We also find that the presence of Ψ can promote the low-level synthesis of multiple peptide products from a single mRNA sequence in the reconstituted translation system as well as human cells, and increases the rate of near-cognate Val-tRNAVal reacting on a ΨUU codon. The vast majority of Ψ moieties in mRNAs are found in coding regions, and our study suggests that one consequence of the ribosome encountering Ψ can be to modestly alter both translation speed and mRNA decoding.

Comorbid Psychopathology and the Clinical Profile of Family Accommodation in Pediatric OCD.

Family accommodation (FA) has been linked with myriad negative outcomes in pediatric obsessive-compulsive disorder (OCD), but extant literature has yielded differential relationships between FA and clinical variables of interest. Consequently, this study examined the phenomenology, clinical profile, and effects of comorbid psychopathology on FA to better understand these behaviors. A total of 150 youths and their caregivers completed clinician- and self-reported measures at a baseline visit for a larger randomized controlled trial. Sociodemographic variables were not associated with FA, but specific types of OCD symptom clusters were. Higher OC-symptom severity and functional impairment were associated with increased FA. Comorbid anxiety disorders moderated the relationship between OC-symptom severity and FA, but comorbid attention deficit hyperactivity, oppositional defiant, and mood disorders did not. Internalizing and externalizing problems both mediated the relationship between FA and functional impairment. These findings provide clinical implications for important treatment targets and factors that may impact FA.

Editorial Perspective: Exposures in cognitive behavior therapy for pediatric obsessive-compulsive disorder: addressing common clinician concerns.

Professional organizations and expert consensus recommend the use of exposure-based cognitive-behavioral therapy (CBT) to treat pediatric obsessive-compulsive disorder (OCD), but a sizable proportion of clinicians possess hesitancy regarding the use of exposures in treatment. Most notably, this hesitancy relates to concerns about negative patient and parent reactions to exposures. Accordingly, we examine three commonly reported clinician concerns regarding negative patient/parent reactions (e.g. treatment attrition, therapeutic relationship, and treatment satisfaction) among youths receiving exposure-based CBT compared to a nonexposure-based treatment. Based on our findings, there is no empirical support that exposure-based CBT precipitates adverse consequences in treatment (e.g. treatment attrition, poor therapeutic relationship, low treatment satisfaction) relative to nonexposure-based interventions. These results corroborate existing OCD expert recommendations for the use of exposure-based CBT and provide information to mitigate clinicians' concerns about the potentially iatrogenic impact of exposures when treating pediatric OCD. We briefly present best practice recommendations for implementing exposure-based CBT in pediatric OCD patients.

Comparing OCD-affected youth with and without religious symptoms: Clinical profiles and treatment response.

BACKGROUND: Childhood obsessive-compulsive disorder (OCD) is a heterogeneous psychiatric condition, with varied symptom presentations that have been differentially associated with clinical characteristics and treatment response. One OCD symptom cluster of particular interest is religious symptoms, including fears of offending religious figures/objects; patients affected by these symptoms have been characterized as having greater overall OCD severity and poorer treatment response. However, the extant literature primarily examines this symptom subtype within adults, leaving a gap in our understanding of this subtype in youth. METHOD: Consequently, this study examined whether presence of religious symptoms in OCD-affected children and adolescents (N = 215) was associated with greater clinical impairments across OCD symptoms and severity, insight, other psychiatric comorbidity, family variables, or worse treatment response. RESULTS: Results found that youth with religious OCD symptoms presented with higher OCD symptom severity and exhibited more symptoms in the aggressive, sexual, somatic, and checking symptom cluster, as well as the symmetry, ordering, counting, and repeating cluster. Religious OCD symptoms were also significantly associated with poorer insight and higher family expressiveness. No differences in treatment response were observed in youths with versus without religious OCD symptoms. CONCLUSION: Ultimately, youths with religious OCD symptoms only differed from their OCD-affected counterparts without religious symptoms on a minority of clinical variables; this suggests they may be more comparable to youths without religious OCD symptoms than would be expected based on the adult OCD literature and highlights the importance of examining these symptoms within a pediatric OCD sample.

Quality of life and burden in caregivers of youth with obsessive-compulsive disorder presenting for intensive treatment.

BACKGROUND: Pediatric obsessive-compulsive disorder (OCD) is associated with deleterious familial effects; caregivers are often enmeshed in the disorder and can experience considerable burden and decreased quality of life (QoL). Consequently, this study examined burden and QoL in caregivers of youth with OCD enrolled in an intensive outpatient or partial hospitalization program. METHOD: The relationships between caregiver QoL and burden and the following variables were investigated: OCD symptom severity, functioning (youth functional impairment, general family functioning), family (family accommodation, parental relationship satisfaction, positive aspects of caregiving), and comorbid psychopathology (caregiver anxiety and depressive symptoms, youth internalizing and externalizing behaviors). Seventy-two child and caregiver dyads completed clinician- and self-rated questionnaires. RESULTS: Components of caregiver QoL correlated with caregiver-rated functional impairment, family accommodation, youth externalizing behaviors, and caregiver psychopathology. Aspects of caregiver burden correlated with child OCD symptom severity, functional impairment related to OCD, as well as caregiver and child comorbid psychopathology. Caregiver depressive symptoms predicted caregiver QoL, and caregiver depressive symptoms and child externalizing symptoms both predicted caregiver burden. Caregiver burden did not mediate the relationship between obsessive-compulsive symptom severity and caregiver QoL. CONCLUSION: Ultimately, elucidating factors associated with increased caregiver burden and poorer QoL is pertinent for identifying at-risk families and developing targeted interventions.

Examining the intersection between splicing, nuclear export and small RNA pathways.

BACKGROUND: Nuclear Argonaute/small RNA pathways in a variety of eukaryotic species are generally known to regulate gene expression via chromatin modulation and transcription attenuation in a process known as transcriptional gene silencing (TGS). However, recent data, including genetic screens, phylogenetic profiling, and molecular mechanistic studies, also point to a novel and emerging intersection between the splicing and nuclear export machinery with nuclear Argonaute/small RNA pathways in many organisms. SCOPE OF REVIEW: In this review, we summarize the field's current understanding regarding the relationship between splicing, export and small RNA pathways, and consider the biological implications for coordinated regulation of transcripts by these pathways. We also address the importance and available approaches for understanding the RNA regulatory logic generated by the intersection of these particular pathways in the context of synthetic biology. MAJOR CONCLUSIONS: The interactions between various eukaryotic RNA regulatory pathways, particularly splicing, nuclear export and small RNA pathways provide a type of combinatorial code that informs the identity ("self" versus "non-self") and dictates the fate of each transcript in a cell. Although the molecular mechanisms for how splicing and nuclear export impact small RNA pathways are not entirely clear at this early stage, the links between these pathways are widespread across eukaryotic phyla. GENERAL SIGNIFICANCE: The link between splicing, nuclear export, and small RNA pathways is emerging and establishes a new frontier for understanding the combinatorial logic of gene regulation across species that could someday be harnessed for therapeutic, biotechnology and agricultural applications. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.

Suicidal and death ideation among adults with obsessive-compulsive disorder presenting for intensive intervention.

BACKGROUND: This study examined the frequency and relation of death and/or suicidal ideation to treatment response in 101 adults with obsessive-compulsive disorder (OCD) presenting for intensive intervention. METHODS: Within 2 days of admission to an intensive treatment program, 101 adults with OCD completed the Yale-Brown Obsessive Compulsive Scale-Self Report, Quick Inventory of Depressive Symptomatology-Self Report, Intolerance of Uncertainty Scale, Obsessive-Compulsive Inventory-Revised, Penn State Worry Questionnaire, and Quality of Life Enjoyment and Satisfaction Questionnaire-Short Form, and were administered the Columbia Suicide Scale by a trained clinician. RESULTS: A majority of patients reported death ideation within their lifetime (62.4%) and within the past month (67%). Approximately 12% of patients reported recent suicidal ideation. Patients with recent suicidal ideation reported significantly more depressive symptoms, more OCD symptoms, and less life satisfaction compared with patients not reporting suicidal ideation. Although prevalent, the presence of suicidal ideation was not associated with treatment response in the current sample. CONCLUSIONS: Suicidal ideation and history are prevalent among patients being treated intensively and are associated with OCD severity and depression, but they do not predict intensive multimodal treatment response.

Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes.

As a champion of small RNA research for two decades, Caenorhabditis elegans has revealed the essential Argonaute CSR-1 to play key nuclear roles in modulating chromatin, chromosome segregation and germline gene expression via 22G-small RNAs. Despite CSR-1 being preserved among diverse nematodes, the conservation and divergence in function of the targets of small RNA pathways remains poorly resolved. Here we apply comparative functional genomic analysis between C. elegans and Caenorhabditis briggsae to characterize the CSR-1 pathway, its targets and their evolution. C. briggsae CSR-1-associated small RNAs that we identified by immunoprecipitation-small RNA sequencing overlap with 22G-RNAs depleted in cbr-csr-1 RNAi-treated worms. By comparing 22G-RNAs and target genes between species, we defined a set of CSR-1 target genes with conserved germline expression, enrichment in operons and more slowly evolving coding sequences than other genes, along with a small group of evolutionarily labile targets. We demonstrate that the association of CSR-1 with chromatin is preserved, and show that depletion of cbr-csr-1 leads to chromosome segregation defects and embryonic lethality. This first comparative characterization of a small RNA pathway in Caenorhabditis establishes a conserved nuclear role for CSR-1 and highlights its key role in germline gene regulation across multiple animal species.

An initial study of family accommodation in children and adolescents with chronic tic disorders.

This initial study examined the nature, incidence, and clinical correlates of family accommodation in youth with tic disorders, and validated a brief self-report measure of tic-related family accommodation, the Tic Family Accommodation Scale (TFAS). Seventy-five youth aged 6-18 who were diagnosed with a tic disorder and their parent completed a diagnostic clinical interview, and clinician and parent-report measures of tic severity, depressive symptoms, anxiety symptoms, behavioral problems, family accommodation and impairment. An exploratory factor analysis of the TFAS showed a two-factor structure, with good internal consistency for the Total score, Modification of Child Environment and Modification of Parent Environment subscales (α = 0.88, 0.86, and 0.81, respectively). Family accommodation was not associated with tic severity. Family accommodation was associated with increased anxiety and depressive symptoms, higher externalizing, rule breaking, aggressive behaviors and social problems, and with greater tic-related functional impairment. Anxiety and externalizing problems (but not depressive symptoms) predicted family accommodation when controlling for tic severity. Family accommodation predicted high levels of functional impairment over and above the effect of tic severity, anxiety, depression and externalizing problems. Family accommodation is a common phenomenon for youth with tic disorders, with modifications typically encompassing changes to the child and/or parent environments. Accommodation was not associated with tic severity, but was related to higher levels of anxiety, depressive symptoms, externalizing symptoms, aggression, and rule breaking behaviors. Results suggest that other emotional symptoms are more likely to drive accommodation practices than the tic symptoms per se.

Examination of the Phenomenology and Clinical Correlates of Emetophobia in a Sample of Salvadorian Youths.

Emetophobia is an under-researched disorder characterized by a specific fear of vomiting. There is a paucity of research on this impairing condition, with extant examinations being largely limited to adult samples and online communities. The present study examined the incidence, phenomenology, and correlates of emetophobia in 305 Salvadorian youths. Caregivers completed a battery of questionnaires regarding the youth's symptoms of emetophobia, internalizing/externalizing symptoms, health anxiety, and obsessive-compulsive symptoms. Approximately 7.5 % of the sample was elevated on emetophobia symptoms, and higher levels of emetophobia symptoms were correlated with higher levels of internalizing, externalizing, health anxiety, and obsessive-compulsive symptoms, and lower levels of adaptive functioning. Youths meeting the cutoff for elevated emetophobia symptoms versus those who did not demonstrated significantly higher levels of externalizing behaviors, as well as general obsessive-compulsive symptoms, especially doubting/checking and neutralizing behaviors. These findings are hoped to help improve the conceptualization and treatment of this poorly understood disorder.

FEAR CONDITIONING AND EXTINCTION IN YOUTH WITH OBSESSIVE-COMPULSIVE DISORDER.

BACKGROUND: Fear acquisition and extinction are central constructs in the cognitive-behavioral model of obsessive-compulsive disorder (OCD), which underlies exposure-based cognitive-behavioral therapy (CBT). Youth with OCD may have impairments in fear acquisition and extinction that carry treatment implications. We examined these processes using a differential conditioning procedure. METHODS: Forty-one youth (19 OCD, 22 community comparisons) completed a battery of clinical interviews, rating scales, and a differential conditioning task that included habituation, acquisition, and extinction phases. Skin conductance response (SCR) served as the primary dependent measure. RESULTS: During habituation, no difference between groups was observed. During acquisition, differential fear conditioning was observed across participants as evidenced by larger SCRs to the CS+ compared to CS-; there were no between-group differences. Across participants, the number and frequency of OCD symptoms and anxiety severity was associated with greater reactivity to stimuli during acquisition. During extinction, a three-way interaction and follow-up tests revealed that youth with OCD showed a different pattern of SCR extinction compared to the community comparison group. CONCLUSIONS: Youth with OCD exhibit a different pattern of fear extinction relative to community comparisons. This may be attributed to impaired inhibitory learning and contingency awareness in extinction. Findings suggest the potential benefit of utilizing inhibitory-learning principles in CBT for youth with OCD, and/or augmentative retraining interventions prior to CBT to reduce threat bias and improve contingency detection.

Further psychometric properties of the Yale-Brown Obsessive Compulsive Scale - Second Edition.

The Yale-Brown Obsessive Compulsive Scale (Y-BOCS) is a widely used clinician-rated measure for assessing obsessive-compulsive symptoms. Although numerous studies have supported its reliability and validity, improved phenomenological understanding of obsessive-compulsive disorder (OCD) suggests the need for modifications to item content, structure, and scoring. Consequently, the Yale-Brown Obsessive Compulsive Scale - Second Edition (Y-BOCS-II) was developed. While the Y-BOCS-II shows initial promise, minimal data exist in examining the psychometric properties of the Y-BOCS-II English version. In response, the Y-BOCS-II was administered to 61 adult patients with a principal diagnosis of obsessive-compulsive disorder. The internal consistency for the scores on the Obsession Severity (α=.83), Compulsion Severity (α=.75), and Total Severity (α=.86) scales were acceptable to good. The inter-rater reliability for the severity scale scores was excellent (ICC=.97-99) and the test-retest reliability was acceptable (r=.64-81). Strong convergent validity was observed between the Y-BOCS-II Total Severity scale and other measures of obsessive-compulsive symptom severity and related impairment. Good divergent validity was supported by non-significant correlations between the Total Severity score and measures of anxiety and impulsiveness, though a moderate correlation was observed with depressive symptoms. Collectively, the Y-BOCS-II generally possesses sound psychometric properties and appears to be a viable alternative to the original Y-BOCS.

Treatment Concerns and Functional Impairment in Pediatric Anxiety.

Although there are efficacious, evidence-based treatments for anxiety disorders, youth often experience delays in seeking therapy. Myriad reasons may contribute to this lag in treatment initiation, with some youth possessing concerns about therapy. Treatment concerns are broadly characterized by worries/ambivalence about seeking treatment, including concerns about the negative reactions, consequences, and inconvenience of treatment. As no studies exist for youth with anxiety disorders, this study examined the phenomenology of treatment concerns in 119 treatment-seeking, anxious youth and utilized a structural equation model to examine the relationship between child anxiety, depressive symptoms, treatment concerns, and anxiety-related functional impairment. Over 90 % of the children positively endorsed some type of treatment-related fear, with the most frequently expressed concern being that therapy would take too much time (50.4 %). Based on the model, both child anxiety and depressive symptoms predicted functional impairment, and treatment concerns mediated the relationship between child anxiety and functional impairment.

A Case Report of Harm-Related Obsessions in Pediatric Obsessive-Compulsive Disorder.

Harm-related, or "aggressive," obsessions are a symptom subtype in obsessive-compulsive disorder (OCD). Given the violent nature of these thoughts, the stark contrast between the child's character and the content of these obsessions often results in high levels of distress for not only the patient but also the family. This case report illustrates the application of family-based exposure and response prevention (ERP) for a 15-year-old male presenting with harm-related obsessions and mild depressive symptoms secondary to the OCD. The obsessions primarily revolved around the fear of acting on unwanted impulses (e.g., stabbing a family member, pushing a friend onto oncoming traffic), and the compulsions entailed avoidance (both mental and physical), excessive reassurance seeking, and ritualistic confessions. The client underwent a 14-week course of ERP involving repeated imaginal and in vivo exposures and behavioral activation to alleviate depressive symptoms. Significant improvements in obsessive-compulsive symptom severity and depressive symptoms were observed posttreatment, elucidating the efficacy of treating harm-related obsessions with a course of ERP.

Poor tolerance and limited effects of isosorbide-5-mononitrate in microvascular angina.

OBJECTIVES: To assess the effects of isosorbide-5-mononitrate (ISMN) in patients with microvascular angina (MVA). METHODS: We randomized 20 MVA patients, treated with a ß-blocker or a calcium antagonist, to 60 mg slow-release ISMN (halved to 30 mg if not tolerated) or placebo once a day for 4 weeks; the patients were then switched to the other treatment for another 4 weeks. Their clinical status was assessed with the Seattle Angina Questionnaire (SAQ) and the EuroQoL score for quality of life. The exercise stress test (EST), coronary blood flow (CBF) response to nitrate and the cold pressor test (CPT), brachial artery flow-mediated dilation (FMD) and nitrate-mediated dilation (NMD) were also assessed. RESULTS: Nine patients (45%) did not complete the ISMN phase due to side effects; 2 patients refused a follow-up. Nine patients completed the study. The SAQ and EuroQoL scores were significantly better with ISMN than with placebo, although the differences were small. No differences were found between the treatments in the EST results, CBF response to nitroglycerin (p = 0.55) and the CPT (p = 0.54), FMD (p = 0.26) and NMD (p = 0.35). CONCLUSIONS: In this study, a high proportion of MVA patients showed an intolerance to ISMN; in those tolerating the drug, significant effects on their angina status were observed, but the benefit appeared to be modest and independent of effects on coronary microvascular function.

A multitasking Argonaute: exploring the many facets of C. elegans CSR-1.

While initial studies of small RNA-mediated gene regulatory pathways focused on the cytoplasmic functions of such pathways, identifying roles for Argonaute/small RNA pathways in modulating chromatin and organizing the genome has become a topic of intense research in recent years. Nuclear regulatory mechanisms for Argonaute/small RNA pathways appear to be widespread, in organisms ranging from plants to fission yeast, Caenorhabditis elegans to humans. As the effectors of small RNA-mediated gene regulatory pathways, Argonaute proteins guide the chromatin-directed activities of these pathways. Of particular interest is the C. elegans Argonaute, chromosome segregation and RNAi deficient (CSR-1), which has been implicated in such diverse functions as organizing the holocentromeres of worm chromosomes, modulating germline chromatin, protecting the genome from foreign nucleic acid, regulating histone levels, executing RNAi, and inhibiting translation in conjunction with Pumilio proteins. CSR-1 interacts with small RNAs known as 22G-RNAs, which have complementarity to 25 % of the protein coding genes. This peculiar Argonaute is the only essential C. elegans Argonaute out of 24 family members in total. Here, we summarize the current understanding of CSR-1 functions in the worm, with emphasis on the chromatin-directed activities of this ever-intriguing Argonaute.

Mediators and moderators of functional impairment in adults with obsessive-compulsive disorder.

The current study examined correlates, moderators, and mediators of functional impairment in 98 treatment-seeking adults with obsessive-compulsive disorder (OCD). Participants completed or were administered measures assessing obsessive-compulsive symptom severity, functional impairment, resistance against symptoms, interference due to obsessive-compulsive symptoms, depressive symptoms, insight, and anxiety sensitivity. Results indicated that all factors, except insight into symptoms, were significantly correlated with functional impairment. The relationship between obsessive-compulsive symptom severity and functional impairment was not moderated by patient insight, resistance against obsessive-compulsive symptoms, or anxiety sensitivity. Mediational analyses indicated that obsessive-compulsive symptom severity mediated the relationship between anxiety sensitivity and obsessive-compulsive related impairment. Indeed, anxiety sensitivity may play an important contributory role in exacerbating impairment through increases in obsessive-compulsive symptom severity. Depressive symptoms mediated the relationship between obsessive-compulsive symptom severity and obsessive-compulsive related impairment. Implications for assessment and treatment are discussed.

Psychometric properties of the Children's Yale-Brown Obsessive Compulsive Scale in youth with autism spectrum disorders and obsessive-compulsive symptoms.

The psychometric properties of the Children's Yale-Brown Obsessive Compulsive Scale (CY-BOCS) were investigated in 46 treatment-seeking youth, 7-15 years of age, who were diagnosed with an autism spectrum disorder (ASD) and exhibited obsessive-compulsive symptoms. The CY-BOCS Total score exhibited good internal consistency, with differing internal consistencies observed on the Obsession Severity scale (α = 0.86) and Compulsion Severity scale (α = 0.59). Good to excellent inter-rater reliability was observed for the CY-BOCS Total score and both Severity scales. Convergent and divergent validity of the CY-BOCS Total score and both Severity scales were satisfactory. Insight into obsessive-compulsive symptoms was moderately associated with the CY-BOCS Total score. The CY-BOCS demonstrated treatment sensitivity, demonstrating significant changes in obsessive-compulsive symptoms within a subsample of youth receiving cognitive-behavioral treatment. Overall, the CY-BOCS demonstrated adequate psychometric properties and utility in assessing obsessive-compulsive symptoms in youth with ASD and clinically significant obsessive-compulsive symptoms.