CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes.

CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.

People With Human Immunodeficiency Virus Receiving Suppressive Antiretroviral Therapy Show Typical Antibody Durability After Dual Coronavirus Disease 2019 Vaccination and Strong Third Dose Responses.

BACKGROUND: Longer-term humoral responses to 2-dose coronavirus disease 2019 (COVID-19) vaccines remain incompletely characterized in people living with human immunodeficiency virus (HIV) (PLWH), as do initial responses to a third dose. METHODS: We measured antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein receptor-binding domain, angiotensin-converting enzyme 2 (ACE2) displacement, and viral neutralization against wild-type and Omicron strains up to 6 months after 2-dose vaccination, and 1 month after the third dose, in 99 PLWH receiving suppressive antiretroviral therapy and 152 controls. RESULTS: Although humoral responses naturally decline after 2-dose vaccination, we found no evidence of lower antibody concentrations or faster rates of antibody decline in PLWH compared with controls after accounting for sociodemographic, health, and vaccine-related factors. We also found no evidence of poorer viral neutralization in PLWH after 2 doses, nor evidence that a low nadir CD4+ T-cell count compromised responses. Post-third-dose humoral responses substantially exceeded post-second-dose levels, though Omicron-specific responses were consistently weaker than responses against wild-type virus. Nevertheless, post-third-dose responses in PLWH were comparable to or higher than controls. An mRNA-1273 third dose was the strongest consistent correlate of higher post-third-dose responses. CONCLUSION: PLWH receiving suppressive antiretroviral therapy mount strong antibody responses after 2- and 3-dose COVID-19 vaccination. Results underscore the immune benefits of third doses in light of Omicron.

Novel computational biology modeling system can accurately forecast response to neoadjuvant therapy in early breast cancer.

BACKGROUND: Generalizable population-based studies are unable to account for individual tumor heterogeneity that contributes to variability in a patient's response to physician-chosen therapy. Although molecular characterization of tumors has advanced precision medicine, in early-stage and locally advanced breast cancer patients, predicting a patient's response to neoadjuvant therapy (NAT) remains a gap in current clinical practice. Here, we perform a study in an independent cohort of early-stage and locally advanced breast cancer patients to forecast tumor response to NAT and assess the stability of a previously validated biophysical simulation platform. METHODS: A single-blinded study was performed using a retrospective database from a single institution (9/2014-12/2020). Patients included: ≥ 18 years with breast cancer who completed NAT, with pre-treatment dynamic contrast enhanced magnetic resonance imaging. Demographics, chemotherapy, baseline (pre-treatment) MRI and pathologic data were input into the TumorScope Predict (TS) biophysical simulation platform to generate predictions. Primary outcomes included predictions of pathological complete response (pCR) versus residual disease (RD) and final volume for each tumor. For validation, post-NAT predicted pCR and tumor volumes were compared to actual pathological assessment and MRI-assessed volumes. Predicted pCR was pre-defined as residual tumor volume ≤ 0.01 cm3 (≥ 99.9% reduction). RESULTS: The cohort consisted of eighty patients; 36 Caucasian and 40 African American. Most tumors were high-grade (54.4% grade 3) invasive ductal carcinomas (90.0%). Receptor subtypes included hormone receptor positive (HR+)/human epidermal growth factor receptor 2 positive (HER2+, 30%), HR+/HER2- (35%), HR-/HER2+ (12.5%) and triple negative breast cancer (TNBC, 22.5%). Simulated tumor volume was significantly correlated with post-treatment radiographic MRI calculated volumes (r = 0.53, p = 1.3 × 10-7, mean absolute error of 6.57%). TS prediction of pCR compared favorably to pathological assessment (pCR: TS n = 28; Path n = 27; RD: TS n = 52; Path n = 53), for an overall accuracy of 91.2% (95% CI: 82.8% - 96.4%; Clopper-Pearson interval). Five-year risk of recurrence demonstrated similar prognostic performance between TS predictions (Hazard ratio (HR): - 1.99; 95% CI [- 3.96, - 0.02]; p = 0.043) and clinically assessed pCR (HR: - 1.76; 95% CI [- 3.75, 0.23]; p = 0.054). CONCLUSION: We demonstrated TS ability to simulate and model tumor in vivo conditions in silico and forecast volume response to NAT across breast tumor subtypes.

Rapid rise in COVID-19 among young people in England - learning for the future.

OBJECTIVES: We determined the age and sociodemographic distribution of COVID-19 cases between January and September 2020 to identify the group with the highest incidence rates at the beginning of the second wave in England. STUDY DESIGN: We undertook a retrospective cohort study design. METHODS: SARS-CoV-2 cases in England were linked with area-level socio-economic status indicators using quintiles of the Index of Multiple Deprivation (IMD). Age-specific incidence rates were stratified by IMD quintile to further assess rates by area-level socio-economic status. RESULTS: Between July and September 2020, SARS-CoV-2 incidence rates were highest amongst those aged 18-21 years, reaching rates of 213.9 (18-19 years) and 143.2 (20-21 years) per 100,000 population by week ending 21 September 2022. Stratification of incidence rates by IMD quintile evidenced that despite high rates observed in the most deprived areas of England amongst the very young and older age groups, the highest rates were observed in the most affluent areas of England amongst the 18- to 21-year-olds. CONCLUSIONS: The reversal of sociodemographic trend in COVID-19 cases in England for those aged 18-21 years at the end of the summer of 2020 and beginning of the second wave showed a novel pattern of COVID-19 risk. For other age groups, the rates remained highest for those from more deprived areas, which highlighted persisting inequalities. Combined, this demonstrates the need to reinforce awareness of COVID-19 risk for young people, particularly given the late inclusion of the 16-17 years age group for vaccination administration, as well as continued efforts to reduce the impact of COVID-19 on vulnerable populations.

Reduced Magnitude and Durability of Humoral Immune Responses to COVID-19 mRNA Vaccines Among Older Adults.

BACKGROUND: The magnitude and durability of immune responses to coronavirus disease 2019 (COVID-19) mRNA vaccines remain incompletely characterized in the elderly. METHODS: Anti-spike receptor-binding domain (RBD) antibodies, angiotensin-converting enzyme 2 (ACE2) competition, and virus neutralizing activities were assessed in plasma from 151 health care workers and older adults (range, 24-98 years of age) 1 month following the first vaccine dose, and 1 and 3 months following the second dose. RESULTS: Older adults exhibited significantly weaker responses than younger health care workers for all humoral measures evaluated and at all time points tested, except for ACE2 competition activity after 1 vaccine dose. Moreover, older age remained independently associated with weaker responses even after correction for sociodemographic factors, chronic health condition burden, and vaccine-related variables. By 3 months after the second dose, all humoral responses had declined significantly in all participants, and remained significantly lower among older adults, who also displayed reduced binding antibodies and ACE2 competition activity towards the Delta variant. CONCLUSIONS: Humoral responses to COVID-19 mRNA vaccines are significantly weaker in older adults, and antibody-mediated activities in plasma decline universally over time. Older adults may thus remain at elevated risk of infection despite vaccination.

Older Adults Mount Less Durable Humoral Responses to Two Doses of COVID-19 mRNA Vaccine but Strong Initial Responses to a Third Dose.

BACKGROUND: Third coronavirus disease 2019 (COVID-19) vaccine doses are broadly recommended, but immunogenicity data remain limited, particularly in older adults. METHODS: We measured circulating antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein receptor-binding domain, ACE2 displacement, and virus neutralization against ancestral and omicron (BA.1) strains from prevaccine up to 1 month following the third dose, in 151 adults aged 24-98 years who received COVID-19 mRNA vaccines. RESULTS: Following 2 vaccine doses, humoral immunity was weaker, less functional, and less durable in older adults, where a higher number of chronic health conditions was a key correlate of weaker responses and poorer durability. One month after the third dose, antibody concentrations and function exceeded post-second-dose levels, and responses in older adults were comparable in magnitude to those in younger adults at this time. Humoral responses against omicron were universally weaker than against the ancestral strain after both the second and third doses. Nevertheless, after 3 doses, anti-omicron responses in older adults reached equivalence to those in younger adults. One month after 3 vaccine doses, the number of chronic health conditions, but not age, was the strongest consistent correlate of weaker humoral responses. CONCLUSIONS: Results underscore the immune benefits of third COVID-19 vaccine doses, particularly in older adults.

A Review of the Current Evidence Connecting Seborrheic Dermatitis and Parkinson's Disease and the Potential Role of Oral Cannabinoids.

Parkinson's disease (PD) is a neurodegenerative disorder associated with multiple comorbidities, including seborrheic dermatitis (SD), which develops in more than half of PD patients. SD in patients with PD can be severe and frequently intractable by traditional topical therapy. Cannabinoids possess anti-inflammatory and neuromodulatory properties working within the intrinsic endocannabinoid system, the activation of which may alleviate the motor symptoms of PD. The effect of cannabinoids on SD is unknown. Here we explore the pathophysiological mechanisms and possible therapeutic role of oral cannabinoids in PD patients with SD, and review speculative mechanisms underlying the association of PD and SD. Current data supporting the use of cannabinoids in both PD and SD, as well as oral cannabinoid safety and tolerability, are presented. Cannabinoids may provide the possibility of simultaneous treatment of both SD and PD. Specific SD studies and additional safety data on oral cannabinoids are needed.

An Observational Study of the Application of a Topical Cannabinoid Gel on Sensitive Dry Skin.

Atopic dermatitis (AD) is a chronic skin disorder characterized by pruritus, erythema and excoriation. While AD has a multifactorial etiology, neuro-signaling pathways are now recognized to play an essential role in the pathogenesis of AD, particularly pruritus. Neuromodulators, such as topical naltrexone, are being utilized in AD treatment. Another class of neuromodulator, Palmitoylethanolamide (PEA), has demonstrated effectiveness in the treatment of itch, excoriation and erythema in AD patients. Phytocannabinoids including cannabidiol (CBD) are becoming increasingly accessible to the public and continue to be advertised for their efficacy to treat inflammatory skin disorders such as eczema. However, no human studies have been conducted to support the claim. Therefore, this study aimed to explore the effects of CBD in individuals with self-reported eczema. Twenty individuals consented to participate and 16 completed a 28-item online questionnaire assessing subjects’ disease severity using Patient Oriented Eczema Measure (POEM) and psychosocial burden of their disease through the emotional domain of Quality of Life Hand Eczema Questionnaire (QOLHEQ). Findings demonstrated a significant reduction in the mean score of POEM from baseline (mean ±SE: 16±1.35) and at a two weeks interval (8.25 ±1.80), P<0.0007. Similar reduction was seen in emotional domain of QOLHEQ from a mean score of 20.9±2.06 to 8.375 ±1.609 at 2 week-interval, P<0.004. 67% of subjects reported a decrease in itch and 50% perceived an improvement in their eczema by more than 60%. This observational study shed light on the potential clinical utility of topical CBD in the treatment of atopic dermatitis. J Drugs Dermatol. 2020;19(12): doi:10.36849/JDD.2020.5464.

Teledermatology application use in the COVID-19 era.

Owing to the COVID-19 outbreak, the use of telemedicine applications has increased throughout the United States. Using an algorithm to analyze mobile application rankings, we were able to examine how applications with telemedicine services have increased in prevalence and rank pre- and post- COVID-19. Telemedicine apps saw an increase of 210.92 ranked positions on average. Within US telehealth, skin conditions have become the fifth most common diagnosis. Widespread use of teledermatology has been well-accepted. Dermatologists and patients report high satisfaction using teledermatology during COVID-19 and intend to continue using these services in the future. COVID-19 has assisted in reducing physician concerns previously preventing some dermatologists from utilizing teledermatology in their services. Additionally, the geographical and socioeconomic barriers preventing some patients from receiving dermatologic care have been minimized through the use of teledermatology. Addressing these obstacles for dermatologic care improves healthcare equity.

An assessment of social media usage by dermatology residency programs.

Despite the increasing popularity of social media, the activity of dermatology residency programs on top social media platforms has never been investigated to our knowledge. We investigated a total of 126 dermatology residency programs to assess their presence and popularity on social media. Searches were conducted to identify dermatology residency departments' accounts on Facebook, Twitter, and Instagram. The number of Facebook likes, Twitter followers, and Instagram followers were recorded. Of the 126 dermatology residency programs, 29 (23%) were active on Facebook, 14 (11%) on Twitter, and 9 (7%) on Instagram. There was a wide range in the number of Facebook likes, Twitter followers, and Instagram followers. The top ten dermatology residency programs with the highest Facebook likes, Twitter followers, and Instagram followers were charted. Our results demonstrate the sparse usage of social media by dermatology residency programs. Although social media continues to increase in prevalence, dermatology residency programs are underutilizing these valuable resources.

Dermatology on YouTube - an update and analysis of new trends.

Because YouTube is one of the most popular search engines, it is an instrumental tool to stay up to date on the most relevant dermatology trends and content in order to better direct patients and improve health outcomes. Twelve select terms (i.e. Dermatology, Sun protection, Skin cancer awareness, Skin cancer, Skin condition, Sun safety, Tanning, Melanoma, Basal cell carcinoma, Squamous cell carcinoma, Skin cancer treatment, Skin cancer prevention) were searched on YouTube. Overall, the results included 240 videos with over 160 million views. Educational content was most prevalent at 35% of the total search results. Of the total videos, 42% were uploaded by or featured a medical health professional (MD, DO, PhD, RN, ND), with 28% involving a board-certified dermatologist. Trends in content type have changed: educational and personal videos have increased, while advocacy and advertising have decreased. Most search terms are moving in a positive, informative direction, specifically the term "tanning." Other search terms such as "skin condition" and "skin cancer treatment" should be more closely monitored for misleading and perhaps harmful information. Therefore, dermatologists and other medical personnel should keep pace with relevant and popular dermatology content on YouTube in order to understand, advise, market, educate, and address patients' questions and concerns.

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells.

5-hydroxymethylcytosine (5hmC) is a modified base present at low levels in diverse cell types in mammals. 5hmC is generated by the TET family of Fe(II) and 2-oxoglutarate-dependent enzymes through oxidation of 5-methylcytosine (5mC). 5hmC and TET proteins have been implicated in stem cell biology and cancer, but information on the genome-wide distribution of 5hmC is limited. Here we describe two novel and specific approaches to profile the genomic localization of 5hmC. The first approach, termed GLIB (glucosylation, periodate oxidation, biotinylation) uses a combination of enzymatic and chemical steps to isolate DNA fragments containing as few as a single 5hmC. The second approach involves conversion of 5hmC to cytosine 5-methylenesulphonate (CMS) by treatment of genomic DNA with sodium bisulphite, followed by immunoprecipitation of CMS-containing DNA with a specific antiserum to CMS. High-throughput sequencing of 5hmC-containing DNA from mouse embryonic stem (ES) cells showed strong enrichment within exons and near transcriptional start sites. 5hmC was especially enriched at the start sites of genes whose promoters bear dual histone 3 lysine 27 trimethylation (H3K27me3) and histone 3 lysine 4 trimethylation (H3K4me3) marks. Our results indicate that 5hmC has a probable role in transcriptional regulation, and suggest a model in which 5hmC contributes to the 'poised' chromatin signature found at developmentally-regulated genes in ES cells.

Population structure of Escherichia coli causing bacteraemia in the UK and Ireland between 2001 and 2010.

OBJECTIVES: Escherichia coli is the most common agent of bacteraemia, bacterial gastroenteritis and urinary tract infections (UTIs). Lineages causing UTIs and gastrointestinal disease are well defined, but less is known about those causing bacteraemia. We therefore investigated the population structure of E. coli from bacteraemia in the UK and Ireland between 2001 and 2010. METHODS: E. coli isolates (n = 2166) were submitted to the BSAC Bacteraemia Surveillance Programme from 18 UK and Irish centres from 2001 to 2010. Genotypes were analysed by MLST using the Achtman scheme; MICs, blaCTX-M group and patient demographics were previously determined in the BSAC surveillance. RESULTS: Four hundred and forty-eight STs were identified, but five of these, and their associated clonal complexes (CCs), accounted for 58.4% (1264 of 2166) of isolates: CC73 was the most common (20.7%), followed by CC131 (13.9%), CC95 (11.3%), CC69 (6.9%) and CC12 (5.5%). All these, except CC69 (group D), belong to phylogenetic group B2. CC131 isolates were much more often MDR than other STs were: they rose from 2.9% of isolates in 2001 to 20.5%-20.7% in 2007-08 and then declined to 14.3% in 2010. Resistance rates to cephalosporins, aminoglycosides and fluoroquinolones remained below 10% in other major CCs throughout. CONCLUSIONS: The five most prevalent bacteraemia STs have all been associated previously with UTIs. They dominated in all years, but their proportions fluctuated, most notably for ST131, a globally disseminated high-risk clone that is often MDR.

Trends in ExPEC serogroups in the UK and their significance.

Extra-intestinal pathogenic Escherichia coli are a significant cause of urinary tract infection and bacteraemia within the UK. We sought to identify the serogroups of 658 E. coli isolates collected in the UK between January 2011 and March 2012, to better understand the ExPEC population and understand the relevance of serogroups in this pathotype. Isolates were typed and serogroup identified using established phenotypic and molecular methods. Sixty-two serogroups were identified; 54 among urinary isolates and 35 among bloodstream isolates. However, serogroups O25, O6, and O2 dominated both infection types. These serogroups were linked to the major ExPEC STs as follows: ST131-O25, ST73-O6, ST127-O6, and ST95-O2. The serogroup data from this study have increased our understanding of the ExPEC population in the UK, but also highlighted key ST-serogroup relationships within the major ExPEC clones. These data can be used to guide vaccine design and in the development of laboratory diagnostic tests targeting the ExPEC population.