Combined approaches, including long-read sequencing, address the diagnostic challenge of HYDIN in primary ciliary dyskinesia.

Primary ciliary dyskinesia (PCD), a disorder of the motile cilia, is now recognised as an underdiagnosed cause of bronchiectasis. Accurate PCD diagnosis comprises clinical assessment, analysis of cilia and the identification of biallelic variants in one of 50 known PCD-related genes, including HYDIN. HYDIN-related PCD is underdiagnosed due to the presence of a pseudogene, HYDIN2, with 98% sequence homology to HYDIN. This presents a significant challenge for Short-Read Next Generation Sequencing (SR-NGS) and analysis, and many diagnostic PCD gene panels do not include HYDIN. We have used a combined approach of SR-NGS with bioinformatic masking of HYDIN2, and state-of-the-art long-read Nanopore sequencing (LR_NGS), together with analysis of respiratory cilia including transmission electron microscopy and immunofluorescence to address the underdiagnosis of HYDIN as a cause of PCD. Bioinformatic masking of HYDIN2 after SR-NGS facilitated the detection of biallelic HYDIN variants in 15 of 437 families, but compromised the detection of copy number variants. Supplementing testing with LR-NGS detected HYDIN deletions in 2 families, where SR-NGS had detected a single heterozygous HYDIN variant. LR-NGS was also able to confirm true homozygosity in 2 families when parental testing was not possible. Utilising a combined genomic diagnostic approach, biallelic HYDIN variants were detected in 17 families from 242 genetically confirmed PCD cases, comprising 7% of our PCD cohort. This represents the largest reported HYDIN cohort to date and highlights previous underdiagnosis of HYDIN-associated PCD. Moreover this provides further evidence for the utility of LR-NGS in diagnostic testing, particularly for regions of high genomic complexity.

The Need to Adapt the Psychiatric Clinical Assessment to the Digital Age: A Practical Approach.

The use of electronic devices and social media is becoming a ubiquitous part of most people's lives. Although researchers are exploring the sequelae of such use, little attention has been given to the importance of digital media use in routine psychiatric assessments of patients. The nature of technology use is relevant to understanding a patient's lifestyle and activities, the same way that it is important to evaluate the patient's occupation, functioning, and general activities. The authors propose a framework for psychiatric inquiry into digital media use, emphasizing that such inquiry should focus on quality of use, including emotional and behavioral consequences, rather than simply the amount of use.

How Inpatient Psychiatric Units Can Be Both Safe and Therapeutic.

Inpatient psychiatric units should be therapeutic environments that support dignity and recovery. When adverse outcomes (eg, self-harm, violence) happen in these settings, clinicians and administrators can face litigation and other pressures to prioritize risk management over supporting patients' access to personal belongings, exercise equipment, and private spaces. This article describes these downward pressures toward sparser, controlling environments in inpatient psychiatric settings as a safety funnel and suggests strategies for balancing safety, humanity, and recovery in these contexts.

The persuasive effects of political microtargeting in the age of generative artificial intelligence.

The increasing availability of microtargeted advertising and the accessibility of generative artificial intelligence (AI) tools, such as ChatGPT, have raised concerns about the potential misuse of large language models in scaling microtargeting efforts for political purposes. Recent technological advancements, involving generative AI and personality inference from consumed text, can potentially create a highly scalable "manipulation machine" that targets individuals based on their unique vulnerabilities without requiring human input. This paper presents four studies examining the effectiveness of this putative "manipulation machine." The results demonstrate that personalized political ads tailored to individuals' personalities are more effective than nonpersonalized ads (studies 1a and 1b). Additionally, we showcase the feasibility of automatically generating and validating these personalized ads on a large scale (studies 2a and 2b). These findings highlight the potential risks of utilizing AI and microtargeting to craft political messages that resonate with individuals based on their personality traits. This should be an area of concern to ethicists and policy makers.

Season-specific impacts of climate change on canopy-forming seaweed communities.

Understory assemblages associated with canopy-forming species such as trees, kelps, and rockweeds should respond strongly to climate stressors due to strong canopy-understory interactions. Climate change can directly and indirectly modify these assemblages, particularly during more stressful seasons and climate scenarios. However, fully understanding the seasonal impacts of different climate conditions on canopy-reliant assemblages is difficult due to a continued emphasis on studying single-species responses to a single future climate scenario during a single season. To examine these emergent effects, we used mesocosm experiments to expose seaweed assemblages associated with the canopy-forming golden rockweed, Silvetia compressa, to elevated temperature and pCO2 conditions reflecting two projected greenhouse emission scenarios (RCP 2.6 [low] & RCP 4.5 [moderate]). Assemblages were grown in the presence and absence of Silvetia, and in two seasons. Relative to ambient conditions, predicted climate scenarios generally suppressed Silvetia biomass and photosynthetic efficiency. However, these effects varied seasonally-both future scenarios reduced Silvetia biomass in summer, but only the moderate scenario did so in winter. These reductions shifted the assemblage, with more extreme shifts occurring in summer. Contrarily, future scenarios did not shift assemblages within Silvetia Absent treatments, suggesting that climate primarily affected assemblages indirectly through changes in Silvetia. Mesocosm experiments were coupled with a field Silvetia removal experiment to simulate the effects of climate-mediated Silvetia loss on natural assemblages. Consistent with the mesocosm experiment, Silvetia loss resulted in season-specific assemblage shifts, with weaker effects observed in winter. Together, our study supports the hypotheses that climate-mediated changes to canopy-forming species can indirectly affect the associated assemblage, and that these effects vary seasonally. Such seasonality is important to consider as it may provide periods of recovery when conditions are less stressful, especially if we can reduce the severity of future climate scenarios.

Incomplete reprogramming of DNA replication timing in induced pluripotent stem cells.

Induced pluripotent stem cells (iPSCs) are the foundation of cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which could affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing, a process linked to both genome regulation and genome stability, is efficiently reprogrammed to the embryonic state. To answer this, we compare genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicate their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibits delayed replication at heterochromatic regions containing genes downregulated in iPSCs with incompletely reprogrammed DNA methylation. DNA replication delays are not the result of gene expression or DNA methylation aberrations and persist after cells differentiate to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and influence the quality of iPSCs.

Electrochemical Benzylic C(sp3)-H Direct Amidation.

Amide bonds are ubiquitous and found in a myriad of functional molecules. Although formed in a reliable and robust fashion, alternative amide bond disconnections provide flexibility and synthetic control. Herein we describe an electrochemical method to form the non-amide C-N bond from direct benzylic C(sp3)-H amidation. Our approach is applied toward the synthesis of secondary amides by coupling secondary benzylic substrates with substituted primary benzamides. The reaction has been scaled up to a multigram scale in flow.

Contemporary outcomes for arterial reconstruction with non-saphenous vein cryo-preserved conduits.

OBJECTIVE: Cryopreserved (CP) products are utilized during challenging cases when autogenous or prosthetic conduit use is not feasible. Despite decades of experience with cadaveric greater saphenous vein (GSV), there is limited available data regarding the outcomes and patency of other CP products, specifically arterial and deep venous grafts. This study was designed to evaluate outcomes of non-GSV CP conduits in patients undergoing urgent, emergent, and elective arterial reconstruction at our institution. We hypothesized that non-GSV CP allografts have adequate patency and outcomes and are therefore a feasible alternative to GSV in settings where autologous graft is unavailable or prosthetic grafts are contraindicated. METHODS: This study was approved by the Institutional Review Board at our institution. We retrospectively reviewed charts of patients undergoing arterial reconstructions using CP conduits from 2010 to 2022. Data collected included demographics, comorbidities, smoking status, indications for surgery, indication for CP conduit use, anatomic reconstruction, urgency of procedure, and blood loss. Time-to-event outcomes included primary and secondary graft patency rates, follow-up amputations, and mortality; other complications included follow-up infection/reinfection and 30-day complications, including return to the operating room and perioperative mortality. Time-to-event analyses were evaluated using product-limit survival estimates. RESULTS: Of 96 identified patients receiving CP conduits, 56 patients received non-GSV conduits for 66 arterial reconstructions. The most common type of non-GSV CP product used was femoral artery (31 patients), followed by aorto-iliac artery (22 patients), and femoral vein (19 patients), with some patients receiving more than one reconstruction or CP product. Patients were mostly male (75%), with a mean age of 63.1 years and a mean body mass index of 26.7 kg/m2. Indications for CP conduit use included infection in 53 patients, hostile environment in 36 patients, contaminated field in 30 patients, tissue coverage concerns in 30 patients, inadequate conduit in nine patients, and patient preference in one patient. Notably, multiple patients had more than one indication. Most surgeries (95%) were performed in urgent or emergent settings. Supra-inguinal reconstructions were most common (53%), followed by extra-anatomic bypasses (47%). Thirty-day mortality occurred in 10 patients (19%). Fifteen patients (27%) required return to the operating room for indications related to the vascular reconstructions, with 10 (18%) cases being unplanned and five (9%) cases planned/staged. Overall survival at 6, 12, and 24 months was 80%, 68%, and 59%, respectively. Primary patency at 6, 12, and 24 months was 86%, 70%, and 62%, respectively. Amputation freedom at 6 months, 12 months, and 24 months was 98%, 95%, and 86%, respectively for non-traumatic indications. CONCLUSIONS: Non-GSV CP products may be used in complex arterial reconstructions when autogenous or prosthetic options are not feasible or available.

EED related overgrowth: First report of multiple members in a single family.

EED is a core component of polycomb repressive complex 2 (PRC2) with EZH2 and SUZ12. PRC2 has H3K27 methyltransferase activity (HMTase) that catalyzes the addition of up to three methyl groups on histone 3 at lysine residue 27 (H3K27). Germline heterozygous variants in EED, SUZ12, and EZH2 have been identified in patients with overgrowth and multiple dysmorphic features. The clinical manifestations of these syndromes significantly overlap: generalized overgrowth, intellectual disability, and scoliosis. To date, 11 unrelated patients have been published with missense variants in EED at highly conserved amino acids. We report three affected members in a family with a previously reported missense variant. All three affected members manifested very similarly, and this represents a homogenous clinical phenotype associated with EED related intellectual disability and overgrowth. This disorder is appropriately called Cohen-Gibson syndrome.

Neuropathy Screening for Patients with Peripheral Vascular Disease Helps to Identify Those at an Increased Risk of Amputation, Revascularization, and Death.

BACKGROUND: Peripheral neuropathy is associated with amputation risk among patients with diabetes mellitus and chronic limb-threatening ischemia (CLTI). Detection of peripheral neuropathy may help identify those who are at an increased risk, but the predictive ability of the screening tool used in patients with peripheral arterial disease (PAD) needs to be more clearly defined. METHODS: Patients referred to vascular surgery clinic for PAD were recruited from a single center. Exclusion criteria were a documented history of neuropathy or prior lower limb amputation. Screening utilized the Michigan Neuropathy Screening Instrument (MNSI). Scores >2.5 were considered abnormal and scores >4 were considered positive for peripheral neuropathy. Limb-specific outcomes of amputation and revascularization as well as a composite outcome including death were modeled using time to event analysis. RESULTS: 86 patients were recruited. Mean age was 67 ± 10.2 years, 30% were women, 24% were black. Mean ankle-brachial index was 0.74 ± 0.3. PAD symptoms at initial evaluation were claudication in 52% of patients and CLTI in 38% of patients. Neuropathy was present in 20% of the cohort with a significantly higher proportion in diabetics (34% vs. 3%; P = 0.0009). Neuropathy was more common in patients with CLTI compared to claudicants (36% vs. 9%; P = 0.011). Forty patients (47%) reached the composite outcome of amputation, revascularization, or death with a median time to event of 16 months. Abnormal MNSI examination was significantly associated with the increased risk of the composite outcome (hazard ratio = 3.19; P 0.0005). CONCLUSIONS: A significant proportion of patients presenting to vascular specialists for PAD have undiagnosed neuropathy. Patients with PAD and neuropathy have an increased risk of amputation, revascularization, and death. Expanding neuropathy screening in vascular surgery clinic visits may help to identify patients at higher risk.

Progressive Neuropsychiatric Symptoms Following Recurrent COVID-19 Infections in a Previously Healthy Adolescent.

This is the almost 2-year-long course of a 16-year-old male without significant psychiatry history who abruptly developed symptoms of obsessive-compulsive disorder (OCD) and psychosis following a confirmed coronavirus disease 2019 (COVID-19) infection. His symptoms worsened following a confirmed reinfection with COVID-19. He responded poorly to treatment with selective serotonin reuptake inhibitors, antipsychotics, and benzodiazepines. This case highlights an emerging phenomenon of post-COVID-19 neuropsychiatric sequelae and presents a complicated diagnostic and treatment challenge. The differential for this patient was explored and outlined in detail, and the medical workup recommendations for new-onset mental status changes were reviewed as they pertain to the patient's assessment and treatment course. While there are several case reports of adolescents with abrupt-onset OCD and psychosis symptoms following COVID-19 infections, none of these reports include worsening of symptoms following reinfection, and few reports follow patients beyond initial hospitalization and treatment.

Addressing the Increasing Mental Health Distress and Mental Illness Among Young Adults in the United States.

ABSTRACT: Recent surveys show rising numbers of young people who report anxiety and depression. Although much attention has focused on mental health of adolescent youth, less attention has been paid to young people as they transition into adulthood. Multiple factors may have contributed to this steady increase: greater exposure to social media, information, and distressing news via personal electronic devices; increased concerns regarding social determinants of health and climate change; and changing social norms due to increased mental health literacy and reduced stigma. The COVID-19 pandemic may have temporarily exacerbated symptoms and impacted treatment availability. Strategies to mitigate causal factors for depression and anxiety in young adults may include education and skills training for cognitive, behavioral, and social coping strategies, as well as healthier use of technology and social media. Policies must support the availability of health insurance and treatment, and clinicians can adapt interventions to encompass the specific concerns and needs of young adults.

Quantum analysis of squiggle data.

Squiggle data is the numerical output of DNA and RNA sequencing by the Nanopore next generation sequencing platform. Nanopore sequencing offers expanded applications compared to previous sequencing techniques but produces a large amount of data in the form of current measurements over time. The analysis of these segments of current measurements require more complex and computationally intensive algorithms than previous sequencing technologies. The purpose of this study is to investigate in principle the potential of using quantum computers to speed up Nanopore data analysis. Quantum circuits are designed to extract major features of squiggle current measurements. The circuits are analyzed theoretically in terms of size and performance. Practical experiments on IBM QX show the limitations of the state of the art quantum computer to tackle real life squiggle data problems. Nevertheless, pre-processing of the squiggle data using the inverse wavelet transform, as experimented and analyzed in this paper as well, reduces the dimensionality of the problem in order to fit a reasonable size quantum computer in the hopefully near future.

Beyond gene-disease validity: capturing structured data on inheritance, allelic requirement, disease-relevant variant classes, and disease mechanism for inherited cardiac conditions.

BACKGROUND: As the availability of genomic testing grows, variant interpretation will increasingly be performed by genomic generalists, rather than domain-specific experts. Demand is rising for laboratories to accurately classify variants in inherited cardiac condition (ICC) genes, including secondary findings. METHODS: We analyse evidence for inheritance patterns, allelic requirement, disease mechanism and disease-relevant variant classes for 65 ClinGen-curated ICC gene-disease pairs. We present this information for the first time in a structured dataset, CardiacG2P, and assess application in genomic variant filtering. RESULTS: For 36/65 gene-disease pairs, loss of function is not an established disease mechanism, and protein truncating variants are not known to be pathogenic. Using the CardiacG2P dataset as an initial variant filter allows for efficient variant prioritisation whilst maintaining a high sensitivity for retaining pathogenic variants compared with two other variant filtering approaches. CONCLUSIONS: Access to evidence-based structured data representing disease mechanism and allelic requirement aids variant filtering and analysis and is a pre-requisite for scalable genomic testing.

Incomplete Reprogramming of DNA Replication Timing in Induced Pluripotent Stem Cells.

Induced pluripotent stem cells (iPSC) are a widely used cell system and a foundation for cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which have the potential to affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing - a process linked to both genome regulation and genome stability - is efficiently reprogrammed to the embryonic state. To answer this, we profiled and compared genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicated their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibit delayed replication at heterochromatic regions containing genes downregulated in iPSC with incompletely reprogrammed DNA methylation. DNA replication delays were not the result of gene expression and DNA methylation aberrations and persisted after differentiating cells to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and lead to undesirable phenotypes in iPSCs, establishing it as an important genomic feature to consider when evaluating iPSC lines.

Implementation strategies to support ultrasound thyroid nodule risk stratification: A systematic review.

BACKGROUND: Ultrasound risk stratification can improve the care of patients with thyroid nodules by providing a structured and systematic approach for the evaluation of thyroid nodule features and thyroid cancer risk. The optimal strategies to support implementation of high quality thyroid nodule risk stratification are unknown. This study seeks to summarise strategies used to support implementation of thyroid nodule ultrasound risk stratification in practice and their effects on implementation and service outcomes. METHODS: This is a systematic review of studies evaluating implementation strategies published between January 2000 and June 2022 that were identified on Ovid MEDLINE, Ovid EMBASE, Ovid Cochrane, Scopus, or Web of Science. Screening of eligible studies, data collection and assessment for risk of bias was completed independently and in duplicate. Implementation strategies and their effects on implementation and service outcomes were evaluated and summarised. RESULTS: We identified 2666 potentially eligible studies of which 8 were included. Most implementation strategies were directed towards radiologists. Common strategies to support the implementation of thyroid nodule risk stratification included: tools to standardise thyroid ultrasound reports, education on thyroid nodule risk stratification and use of templates/forms for reporting, and reminders at the point of care. System based strategies, local consensus or audit were less commonly described. Overall, the use of these strategies supported the implementation process of thyroid nodule risk stratification with variable effects on service outcomes. CONCLUSIONS: Implementation of thyroid nodule risk stratification can be supported by development of standardised reporting templates, education of users on risk stratification and reminders of use at the point of care. Additional studies evaluating the value of implementation strategies in different contexts are urgently needed.

Case report: marfan syndrome (MFS) mimicking cutaneous vasculitis.

Marfan syndrome (MFS) is an autosomal dominant connective tissue disorder caused by variants in the extracellular microfibril fibrillin (FBN1) gene. Here we report an FBN1 variant in a child with an unusual skin rash mimicking cutaneous vasculitis, and mild aortic root dilatation. The case was complicated by lack of typical skeletal MFS phenotype; and severe needle phobia preventing any blood testing for workup of suspected vasculitis. Therefore inflammatory markers, autoantibody profile and general hematology/biochemistry results were unknown. Diagnosis of MFS was made via genetic testing of a saliva sample alone using a next-generation sequencing (NGS) targeted gene panel designed to screen for monogenic forms of vasculitis and noninflammatory vasculopathic mimics. This revealed the patient was heterozygous for a pathogenic frameshift variant in FBN1; NM_000138, c.1211delC, p.(Pro404Hisfs*44), predicted to cause premature protein truncation leading to loss of function. The variant has not been detected in control populations and has previously been detected in individuals with MFS. This rapid diagnosis significantly impacted the patient management: avoidance of invasive investigations; avoidance of unnecessary immunosuppression; facilitating genetic counselling of the index case and family; and directly informing lifelong monitoring and ongoing treatment for aortic root involvement from MFS. This case further emphasizes the diagnostic utility of NGS early in the diagnostic workup of paediatric patients referred with suspected vasculitis, and we emphasize that MFS can present with cutaneous vasculitic-like features in the absence of the typical Marfanoid skeletal phenotype.

EMQN: Recommendations for genetic testing in inherited cardiomyopathies and arrhythmias.

Inherited cardiomyopathies and arrhythmias (ICAs) are a prevalent and clinically heterogeneous group of genetic disorders that are associated with increased risk of sudden cardiac death and heart failure. Making a genetic diagnosis can inform the management of patients and their at-risk relatives and, as such, molecular genetic testing is now considered an integral component of the clinical care pathway. However, ICAs are characterised by high genetic and allelic heterogeneity, incomplete / age-related penetrance, and variable expressivity. Therefore, despite our improved understanding of the genetic basis of these conditions, and significant technological advances over the past two decades, identifying and recognising the causative genotype remains challenging. As clinical genetic testing for ICAs becomes more widely available, it is increasingly important for clinical laboratories to consolidate existing knowledge and experience to inform and improve future practice. These recommendations have been compiled to help clinical laboratories navigate the challenges of ICAs and thereby facilitate best practice and consistency in genetic test provision for this group of disorders. General recommendations on internal and external quality control, referral, analysis, result interpretation, and reporting are described. Also included are appendices that provide specific information pertinent to genetic testing for hypertrophic, dilated, and arrhythmogenic right ventricular cardiomyopathies, long QT syndrome, Brugada syndrome, and catecholaminergic polymorphic ventricular tachycardia.