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BackgroundMalaria is one of the leading causes of morbidity in the world. It is a significant health concern in most developing countries, including Ghana. Even though there are several orthodox medications used for decades in treating malaria effectively, a substantial number of individuals in developing countries are resorting to the use of herbs in the treatment of malaria. The study aim at exploring the practices of herbal management of malaria among trading mothers in Shai Osudoku District, Accra.MethodsA qualitative approach with an exploratory, descriptive design was adopted in analyzing the research problem. Purposive sampling technique was used to select twenty (20) participants to partake in a face-face interview, guided by a semi-structured interview guide. The data were transcribed verbatim and analysed by adopting content analysis.ResultsTwo significant themes and seven subthemes were generated following the analysis of this study. The main themes were; preferences for herbal malaria treatment and the practices and effectiveness of herbal medicine used for malaria treatment. It was worth noting that the women's cultural beliefs did not influence their preference for herbal malaria treatment. The main challenge associated with the herbal malaria treatment was inappropriate dosage specification.ConclusionThis study discovered that several factors influenced participants' preferences for malaria treatment. Participants further listed some traditional ways of treating malaria which implies that there is herbal malaria practice. However, literature in this area is inadequate, and most herbs lack specifications for use. It is therefore recommended that future research focus on scientific herbal malaria treatment. Also, regulating bodies should ensure that quality herbal drugs are sold for consumption.

Acute kidney injury (AKI) is a highly fatal complication of malaria. We used the Kidney Disease Improving Global Outcomes (KDIGO) and Pediatric Risk, Injury, Failure, Loss, End-Stage Kidney Disease (pRIFLE) guidelines to assess AKI among children. One hundred children with Plasmodium falciparum malaria were recruited from the St. Andrew’s Catholic Hospital. Admission and 48-h serum creatinine were estimated. Weight and height of the participants were measured, and AKI status determined with the KDIGO and pRIFLE guidelines. A questionnaire was used to collect the socio-demographic and clinical data of participants. Two percent and 5% of the participants had AKI according to the KDIGO and pRIFLE criteria, respectively. Per the KDIGO guidelines, 1% of the participants had Stage 2 and 1% also had Stage 3 AKI. Four percent had Stage 1 (risk) and 1% had Stage 2 (injury) AKI per the pRIFLE criteria. Participants with AKI were dehydrated, and neither had sepsis or on antibiotics when the KDIGO guideline was used. Participants who had AKI were dehydrated, with 80% having sepsis and 40% on antibiotics when the pRIFLE criteria were used. There was no association between the KDIGO and pRIFLE criteria with respect to AKI status of participants (k = -0.029, P = 0.743). Two percent and 5% of the study participants had AKI when the KDIGO and pRIFLE guidelines were used respectively. One percent of the participants had Stage 2 and 1% also had Stage 3 AKI per KDIGO; 4% had Stage 1 (risk) and 1% had Stage 2 (injury) AKI per the pRIFLE.

Abstract Background Visceral adipose tissue (VAT) is well established as a pathogenic fat depot, whereas superficial subcutaneous adipose tissue (SAT) is associated with either an improved or neutral cardiovascular state. However, it is unclear to what extent VAT area (VATcm2) and its proportion of total abdominal adipose tissue (VAT%) are distinguished in predicting cardiometabolic status and clinical outcomes during weight loss. Methods We integrated magnetic resonance imaging (MRI) measurements of VAT, deep-SAT, and superficial-SAT from two 18-month lifestyle weight loss clinical trials, CENTRAL and DIRECT PLUS (n = 572). Results At baseline, the mean VATcm2 was 144.8cm2 and VAT% = 28.2%; over 18 months, participants lost 28cm2 VATcm2 (− 22.5%), and 1.3 VAT% units. Baseline VATcm2 and VAT% were similarly associated with metabolic syndrome, hypertension, and diabetes status, while VAT% better classified hypertriglyceridemia. Conversely, higher VATcm2 was associated with elevated high-sensitivity C-reactive protein (hsCRP), while VAT% was not. After 18 months of lifestyle intervention, both VATcm2 and VAT% loss were significantly associated with decreased triglycerides, HbA1c, ferritin, and liver enzymes, and increased HDL-c levels beyond weight loss (FDR

Abstract Background CRISPR is widely used to silence genes by inducing mutations expected to nullify their expression. While numerous computational tools have been developed to design single-guide RNAs (sgRNAs) with high cutting efficiency and minimal off-target effects, only a few tools focus specifically on predicting gene knockouts following CRISPR. These tools consider factors like conservation, amino acid composition, and frameshift likelihood. However, they neglect the impact of CRISPR on gene expression, which can dramatically affect the success of CRISPR-induced gene silencing attempts. Furthermore, information regarding gene expression can be useful even when the objective is not to silence a gene. Therefore, a tool that considers gene expression when predicting CRISPR outcomes is lacking. Results We developed EXPosition, the first computational tool that combines models predicting gene knockouts after CRISPR with models that forecast gene expression, offering more accurate predictions of gene knockout outcomes. EXPosition leverages deep-learning models to predict key steps in gene expression: transcription, splicing, and translation initiation. We showed our tool performs better at predicting gene knockout than existing tools across 6 datasets, 4 cell types and ~207k sgRNAs. We also validated our gene expression models using the ClinVar dataset by showing enrichment of pathogenic mutations in high-scoring mutations according to our models. Conclusions We believe EXPosition will enhance both the efficiency and accuracy of genome editing projects, by directly predicting CRISPR’s effect on various aspects of gene expression. EXPosition is available at http://www.cs.tau.ac.il/~tamirtul/EXPosition . The source code is available at https://github.com/shaicoh3n/EXPosition .

Abstract Primary (non-motile) cilia represent structurally and functionally diverse organelles whose roles as specialized cellular antenna are central to animal cell signaling pathways, sensory physiology and development. An ever-growing number of ciliary proteins, including those found in vertebrate photoreceptors, have been uncovered and linked to human disorders termed ciliopathies. Here, we demonstrate that an evolutionarily-conserved PPEF-family serine-threonine phosphatase, not functionally linked to cilia in any organism but associated with rhabdomeric (non-ciliary) photoreceptor degeneration in the Drosophila rdgC (retinal degeneration C) mutant, is a bona fide ciliary protein in C. elegans. The nematode protein, PEF-1, depends on transition zone proteins, which make up a ‘ciliary gate’ in the proximal-most region of the cilium, for its compartmentalization within cilia. Animals lacking PEF-1 protein function display structural defects to several types of cilia, including potential degeneration of microtubules. They also exhibit anomalies to cilium-dependent behaviors, including impaired responses to chemical, temperature, light, and noxious CO2 stimuli. Lastly, we demonstrate that PEF-1 function depends on conserved myristoylation and palmitoylation signals. Collectively, our findings broaden the role of PPEF proteins to include cilia, and suggest that the poorly-characterized mammalian PPEF1 and PPEF2 orthologs may also have ciliary functions and thus represent ciliopathy candidates.

Abstract Intratumoral heterogeneity is an important clinical challenge because low burden clones expressing specific genetic alterations drive therapeutic resistance mechanisms. We have developed CAVE (cancer-associated variant enrichment), a gene-agnostic computational tool to identify specific enrichment of low-burden cancer driver variants in next-generation sequencing (NGS) data. For this study, CAVE was applied to TP53 in chronic lymphocytic leukemia (CLL) as a cancer model. Indeed, as TP53 mutations are part of treatment decision-making algorithms and low-burden variants are frequent, there is a need to distinguish true variants from background noise. Recommendations have been published for reliable calling of low-VAF variants of TP53 in CLL and the assessment of the background noise for each platform is essential for the quality of the testing. CAVE is able to detect specific enrichment of low-burden variants starting at variant allele frequencies (VAFs) as low as 0.3%. In silico TP53 dependent and independent analyses confirmed the true driver nature of all these variants. Orthogonal validation using either ddPCR or NGS analyses of follow-up samples confirmed variant identification. CAVE can be easily deployed in any cancer-related NGS workflow to detect the enrichment of low-burden variants of clinical interest.

Abstract Genetic diagnosis plays a crucial role in rare diseases, particularly with the increasing availability of emerging and accessible treatments. The International Rare Diseases Research Consortium (IRDiRC) has set its primary goal as: “Ensuring that all patients who present with a suspected rare disease receive a diagnosis within one year if their disorder is documented in the medical literature”. Despite significant advances in genomic sequencing technologies, more than half of the patients with suspected Mendelian disorders remain undiagnosed. In response, IRDiRC proposes the establishment of “a globally coordinated diagnostic and research pipeline”. To help facilitate this, IRDiRC formed the Task Force on Integrating New Technologies for Rare Disease Diagnosis. This multi-stakeholder Task Force aims to provide an overview of the current state of innovative diagnostic technologies for clinicians and researchers, focusing on the patient’s diagnostic journey. Herein, we provide an overview of a broad spectrum of emerging diagnostic technologies involving genomics, epigenomics and multi-omics, functional testing and model systems, data sharing, bioinformatics, and Artificial Intelligence (AI), highlighting their advantages, limitations, and the current state of clinical adaption. We provide expert recommendations outlining the stepwise application of these innovative technologies in the diagnostic pathways while considering global differences in accessibility. The importance of FAIR (Findability, Accessibility, Interoperability, and Reusability) and CARE (Collective benefit, Authority to control, Responsibility, and Ethics) data management is emphasized, along with the need for enhanced and continuing education in medical genomics. We provide a perspective on future technological developments in genome diagnostics and their integration into clinical practice. Lastly, we summarize the challenges related to genomic diversity and accessibility, highlighting the significance of innovative diagnostic technologies, global collaboration, and equitable access to diagnosis and treatment for people living with rare disease.

Abstract The risk of developing age-related macular degeneration (AMD) is influenced by genetic background. In 2016, the International AMD Genomics Consortium (IAMDGC) identified 52 risk variants in 34 loci, and a polygenic risk score (PRS) from these variants was associated with AMD. The Israeli population has a unique genetic composition: Ashkenazi Jewish (AJ), Jewish non-Ashkenazi, and Arab sub-populations. We aimed to perform a genome-wide association study (GWAS) for AMD in Israel, and to evaluate PRSs for AMD. Our discovery set recruited 403 AMD patients and 256 controls at Hadassah Medical Center. We genotyped individuals via custom exome chip. We imputed non-typed variants using cosmopolitan and AJ reference panels. We recruited additional 155 cases and 69 controls for validation. To evaluate predictive power of PRSs for AMD, we used IAMDGC summary-statistics excluding our study and developed PRSs via clumping/thresholding or LDpred2. In our discovery set, 31/34 loci reported by IAMDGC were AMD-associated (P

Abstract Fibromyalgia syndrome (FMS) is a chronic pain syndrome characterized by disruptions in pain processing within the central nervous system. It exhibits a high prevalence among patients with a history of traumatic experiences, notably childhood sexual abuse (CSA). This study compared the efficacy of hyperbaric oxygen therapy (HBOT) to the current pharmacological standard of care for individuals suffering from CSA-related FMS. Forty-eight participants diagnosed with FMS and a history of CSA were randomly assigned to either the HBOT group (60 sessions of 100% oxygen at 2 ATA for 90 min, with air breaks every 5 min) or the medication (MED) group (FDA-approved medications, Pregabalin and Duloxetine). The primary endpoint was the Fibromyalgia impact questionnaire (FIQ) score, while secondary endpoints encompassed emotional status and daily functioning questionnaires, as well as pain thresholds and conditioned pain modulation tests. Brain activity was evaluated through single photon emission computed tomography (SPECT). Results revealed a significant group-by-time interaction for the FIQ score favoring HBOT over MED (p

Abstract White striping (WS) is a myopathy of growing concern to the turkey industry. It is rising in prevalence and has negative consequences for consumer acceptance and the functional properties of turkey meat. The objective of this study was to conduct a genome-wide association study (GWAS) and functional analysis on WS severity. Phenotypic data consisted of white striping scored on turkey breast fillets (N = 8422) by trained observers on a 0–3 scale (none to severe). Of the phenotyped birds, 4667 genotypic records were available using a proprietary 65 K single nucleotide polymorphism (SNP) chip. The SNP effects were estimated using a linear mixed model with a 30-SNP sliding window approach used to express the percentage genetic variance explained. Positional candidate genes were those located within 50 kb of the top 1% of SNP windows explaining the most genetic variance. Of the 95 positional candidate genes, seven were further classified as functional candidate genes because of their association with both a significant gene ontology and molecular function term. The results of the GWAS emphasize the polygenic nature of the trait with no specific genomic region contributing a large portion to the overall genetic variance. Significant pathways relating to growth, muscle development, collagen formation, circulatory system development, cell response to stimulus, and cytokine production were identified. These results help to support published biological associations between WS and hypoxia and oxidative stress and provide information that may be useful for future-omics studies in understanding the biological associations with WS development in turkeys.

Abstract Despite advancements in cancer immunotherapy, solid tumors remain formidable challenges. In glioma, profound inter- and intra-tumoral heterogeneity of antigen landscape hampers therapeutic development. Therefore, it is critical to consider alternative sources to expand the repertoire of targetable (neo-)antigens and improve therapeutic outcomes. Accumulating evidence suggests that tumor-specific alternative splicing (AS) could be an untapped reservoir of antigens. In this study, we investigated tumor-specific AS events in glioma, focusing on those predicted to generate major histocompatibility complex (MHC)-presentation-independent, cell-surface antigens that could be targeted by antibodies and chimeric antigen receptor-T cells. We systematically analyzed bulk RNA-sequencing datasets comparing 429 tumor samples (from The Cancer Genome Atlas) and 9166 normal tissue samples (from the Genotype-Tissue Expression project), and identified 13 AS events in 7 genes predicted to be expressed in more than 10% of the patients, including PTPRZ1 and BCAN, which were corroborated by an external RNA-sequencing dataset. Subsequently, we validated our predictions and elucidated the complexity of the isoforms using full-length transcript amplicon sequencing on patient-derived glioblastoma cells. However, analyses of the RNA-sequencing datasets of spatially mapped and longitudinally collected clinical tumor samples unveiled remarkable spatiotemporal heterogeneity of the candidate AS events. Furthermore, proteomics analysis did not reveal any peptide spectra matching the putative antigens. Our investigation illustrated the diverse characteristics of the tumor-specific AS events and the challenges of antigen exploration due to their notable spatiotemporal heterogeneity and elusive nature at the protein levels. Redirecting future efforts toward intracellular, MHC-presented antigens could offer a more viable avenue.

Helianthus tuberosus L. (Jerusalem artichoke) tubers and aerial parts possess both nutritional and therapeutic properties. The Jerusalem artichoke has been utilized for various applications, including its use as a functional food source, a reservoir of bioactive compounds, and a raw material to produce biofuels. Moreover, the Jerusalem artichoke is a rich source of an indigestible polysaccharide called inulin, which serves as a prebiotic that improves gastrointestinal health. This plant has been used globally throughout history as a dietary supplement, for pain treatment, to reduce swelling, and to boost the immune system, as well as to treat skin wounds in folk medicine. It is an abundant source of bioactive compounds, such as phenolic acids, coumarins, and flavonoids, which are known to exert pharmacological activities, including antioxidant, antimicrobial, and anti-inflammatory properties. The literature on its potential as an antidiabetic, anticancer, anti-fungistatic, antiviral, and anti-obesity agent, among others, is scanty. This review aims to provide a comprehensive overview of Helianthus tuberosus L.’s traditional uses, nutritional properties, secondary bioactive compounds, and pharmacological properties to further explore its health benefits.

Abstract In our previous randomized controlled trial, we documented significant improvements in cognitive, psychiatric, fatigue, sleep, and pain symptoms among long Coronavirus disease 2019 (COVID) patients who underwent hyperbaric oxygen therapy (HBOT). The primary objective of the present study was to evaluate the enduring 1 year long term effects of HBOT on long COVID syndrome. This longitudinal long-term follow-up included 31 patients with reported post COVID-19 cognitive symptoms, who underwent 40 daily sessions of HBOT. Participants were recruited more than one year (486 ± 73) after completion of the last HBOT session. Quality of life, assessed using the short form-36 (SF-36) questionnaire revealed, that the long-term results exhibited a similar magnitude of improvement as the short-term outcomes following HBOT across most domains. Regarding sleep quality, improvements were observed in global score and across five sleep domains with effect sizes of moderate magnitude during the short-term evaluation, and these improvements persisted in the long-term assessment (effect size (ES1) = 0.47–0.79). In the realm of neuropsychiatric symptoms, as evaluated by the brief symptom inventory-18 (BSI-18), the short-term assessment following HBOT demonstrated a large effect size, and this effect persisted at the long-term evaluation. Both pain severity (ES1 = 0.69) and pain interference (ES1 = 0.83), had significant improvements during the short-term assessment post HBOT, which persisted at long term. The results indicate HBOT can improve the quality of life, quality of sleep, psychiatric and pain symptoms of patients suffering from long COVID. The clinical improvements gained by HBOT are persistent even 1 year after the last HBOT session.

Objective: Arthrodesis of the first metatarsophalangeal joint (MTPJ) is a reliable procedure for treating various pathologies related to this joint. However, non-union is a common and debilitating complication of the procedure. The purpose of this study was to assess whether the use of a mechanical reamer to prepare the joint surface increases the risk of non-union compared to traditional manual osteotomy. Methods: A retrospective study of all patients who underwent their first MTPJ arthrodesis surgery in our medical center between 2010 and 2015. The articular surface preparation of the MTPJ was either manually performed (Group 1) or mechanically conducted with reamers (Group 2). Data regarding demographic characteristics, indications for surgery, osteosynthesis methods, and post-operative complications, including non-union, infection, and revision rates, were collected for all patients. Results: A total of 83 patients with 92 primary first MTPJ arthrodesis (44 cases in Group 1 and 48 cases in Group 2) were included with a mean follow-up time of 45.3 months (SD 16.8). The two groups were comparable in terms of age, gender, comorbidities, indication for surgery, and follow-up time. The non-union rate was 15.9% in Group 1 and 25% in Group 2 (p = 0.28). Group 2 showed a significantly higher rate of revision surgery compared to Group 1 (43.7% vs. 22.7%, p = 0.03). Conclusions: The mechanical reamer group had a higher non-union rate and a significantly higher rate of revision surgery compared to low-energy manual joint preparation. In light of these findings, the use of mechanical reamers for joint preparation in the first MTPJ arthrodesis was discontinued at our medical center.

Background: Functional bowel disorders (FBDs), including irritable bowel syndrome (IBS), are common worldwide. Recently, increasingly many bariatric surgical procedures have been performed in response to rising obesity rates. However, data on the association between FBDs and bariatric surgery are scarce. We examined the prevalence of FBDs among candidates for bariatric surgery and prospectively investigated the association between FBDs and bariatric surgery. Methods: This prospective cohort study included 112 bariatric surgery candidates at the Tel Aviv Medical Center from 2019 to 2020. Before and after surgery, patients completed the Rome III questionnaire. Data regarding demographics, socioeconomic status, and gastrointestinal symptoms were recorded. The rates of FBDs—IBS, functional constipation (FC), functional diarrhea (FDi), and unspecified functional bowel disorder (UFBD)—were then compared from before surgery to 6 months after the procedure. Results: Of 112 candidates with obesity at baseline, 68 underwent surgery and completed the postoperative questionnaire. Overall, the respective prevalence rates of FBDs, IBS, FC, FDi, and UFBD were 37.5%, 2.7%, 17.9%, 5.4%, and 11.6%. Female sex and single status were particularly common among patients with FBDs, whereas divorced status was more frequent in the group without FBDs. However, these factors were not independently associated with FBD presence upon multivariable analysis. IBS was more prevalent after surgery than before (8.8% vs. 1.5%, P = 0.06), but FBDs in general did not share this trend (44.1% vs. 36.8%, P = 0.44). Conclusion: Bariatric surgery appears to increase the risk of developing IBS, while not impacting the overall risk of FBDs.

Abstract Recent advances in genomic technologies expand the scope and efficiency of preimplantation genetic testing (PGT). We previously developed Haploseek, a clinically-validated, variant-agnostic comprehensive PGT solution. Haploseek is based on microarray genotyping of the embryo’s parents and relatives, combined with low-pass sequencing of the embryos. Here, to increase throughput and versatility, we aimed to develop a sequencing-only implementation of Haploseek. Accordingly, we developed SHaploseek, a universal PGT method to determine genome-wide haplotypes of each embryo based on low-pass (≤ 5x) sequencing of the parents and relative(s) along with ultra-low-pass (0.2–0.4x) sequencing of the embryos. We used SHaploseek to analyze five single lymphoblast cells and 31 embryos. We validated the genome-wide haplotype predictions against either bulk DNA, Haploseek, or, at focal genomic sites, PCR-based PGT results. SHaploseek achieved > 99% concordance with bulk DNA in two families from which single cells were derived from grown-up children. In embryos from 12 PGT families, all of SHaploseek’s focal site haplotype predictions were concordant with clinical PCR-based PGT results. Genome-wide, there was > 99% median concordance between Haploseek and SHaploseek’s haplotype predictions. Concordance remained high at all assayed sequencing depths ≥ 2x, as well as with only 1ng of parental DNA input. In subtelomeric regions, significantly more haplotype predictions were high-confidence in SHaploseek compared to Haploseek. In summary, SHaploseek constitutes a single-platform, accurate, and cost-effective comprehensive PGT solution.

Abstract Background Epigenetic age is an estimator of biological age based on DNA methylation; its discrepancy from chronologic age warrants further investigation. We recently reported that greater polyphenol intake benefitted ectopic fats, brain function, and gut microbiota profile, corresponding with elevated urine polyphenols. The effect of polyphenol-rich dietary interventions on biological aging is yet to be determined. Methods We calculated different biological aging epigenetic clocks of different generations (Horvath2013, Hannum2013, Li2018, Horvath skin and blood2018, PhenoAge2018, PCGrimAge2022), their corresponding age and intrinsic age accelerations, and DunedinPACE, all based on DNA methylation (Illumina EPIC array; pre-specified secondary outcome) for 256 participants with abdominal obesity or dyslipidemia, before and after the 18-month DIRECT PLUS randomized controlled trial. Three interventions were assigned: healthy dietary guidelines, a Mediterranean (MED) diet, and a polyphenol-rich, low-red/processed meat Green-MED diet. Both MED groups consumed 28 g walnuts/day (+ 440 mg/day polyphenols). The Green-MED group consumed green tea (3–4 cups/day) and Mankai (Wolffia globosa strain) 500-ml green shake (+ 800 mg/day polyphenols). Adherence to the Green-MED diet was assessed by questionnaire and urine polyphenols metabolomics (high-performance liquid chromatography quadrupole time of flight). Results Baseline chronological age (51.3 ± 10.6 years) was significantly correlated with all methylation age (mAge) clocks with correlations ranging from 0.83 to 0.95; p

Objectives To elicit the Aboriginal community’s cultural and healthcare needs and views about six prominent and emerging models of care, to inform the development of a new hospital.Design Cross-sectional qualitative study co-designed and co-implemented by Aboriginal team members.Setting Western Sydney, New South Wales, Australia.Participants Aboriginal and Torres Strait Islander healthcare providers (n=2) and community members (n=18) aged between 21 and 60+ years participated in yarning circles (20 participants; 14 female, 6 male).Results Handwritten notes from yarning circles were inductively analysed to synthesise the cultural and healthcare needs of providers and community members in relation to a new hospital and six models of care. Three primary themes emerged in relation to future hospitals. These were ‘culturally responsive spaces’, ‘culturally responsive systems’ and ‘culturally responsive models of care’. Strengths (eg, comfort, reduced waiting time, holistic care), barriers (eg, logistics, accessibility, literacy) and enablers (eg, patient navigator role, communication pathways, streamlined processes) were identified for each of the six models of care.Conclusions Aboriginal and Torres Strait Islander community members and providers are invested in the co-creation of an innovative, well-integrated hospital that meets the needs of the community. Common themes of respect and recognition, relationships and partnering, and capacity building emerged as important consumer and provider considerations when developing and evaluating care services. Participants supported a range of models citing concerns about accessibility and choice when discussing evidence-based models of care.

Abstract Cancer somatic mutations are the product of multiple mutational and repair processes, some of which are tightly associated with DNA replication. Mutation rates (MR) are known to be higher in late replication timing (RT) regions, but different processes can affect this association. Systematic analysis of the mutational landscape of 2787 tumors from 32 tumor types revealed that approximately one third of the tumor samples show weak association between replication timing and mutation rate. Further analyses revealed that those samples have unique mutational signatures and are enriched with mutations in genes involved in DNA replication, DNA repair and chromatin structure. Surprisingly, analysis of differentially expressed genes between weak and strong RT-MR association groups revealed that tumors with weak association are enriched with genes associated with cell–cell communication and the immune system, suggesting a non-autonomous response to DNA damage.

Abstract Three and a half years after the pandemic outbreak, now that WHO has formally declared that the emergency is over, COVID-19 is still a significant global issue. Here, we focus on recent developments in genetic and genomic research on COVID-19, and we give an outlook on state-of-the-art therapeutical approaches, as the pandemic is gradually transitioning to an endemic situation. The sequencing and characterization of rare alleles in different populations has made it possible to identify numerous genes that affect either susceptibility to COVID-19 or the severity of the disease. These findings provide a beginning to new avenues and pan-ethnic therapeutic approaches, as well as to potential genetic screening protocols. The causative virus, SARS-CoV-2, is still in the spotlight, but novel threatening virus could appear anywhere at any time. Therefore, continued vigilance and further research is warranted. We also note emphatically that to prevent future pandemics and other world-wide health crises, it is imperative to capitalize on what we have learnt from COVID-19: specifically, regarding its origins, the world’s response, and insufficient preparedness. This requires unprecedented international collaboration and timely data sharing for the coordination of effective response and the rapid implementation of containment measures.

Background. There are limited data on the clinical characteristics and outcomes of patients with myasthenia gravis (MG) admitted to the intensive care unit (ICU) at Charlotte Maxeke Johannesburg Academic Hospital (CMJAH). Objectives. The aim was to study the clinical characteristics and outcomes of patients with MG admitted to the CMJAH over two decades. Methods. A retrospective study was undertaken of patients with MG admitted to the multidisciplinary ICU of CMJAH over a 20-year period, from 1998 to 2017. Demographic data, clinical features, management and outcomes of patients were assessed and reviewed from the case records. Results. Thirty-four patients with MG were admitted to the ICU during this period: 24 female and 10 male. The mean age ± SD was 37.4 ± 13.0 years, with a range of 16 - 66 years. Four patients were human immunodeficiency virus (HIV)-positive. The mean length of stay (LOS) in ICU was 10.6 ± 20.1 days, ranging from 1 to 115 days. Two patients were diagnosed with MG in the ICU after failure to wean from the ventilator. Overall, 22 patients were intubated and ventilated on admission. Morbidities included self-extubation, aspiration pneumonia and iatrogenic pneumothorax. History of thymectomy was present in 12 patients. The treatments received for MG included pyridostigmine (73.5%), corticosteroids (55.9%), azathioprine (35.3%), plasmapheresis (26.5%) and intravenous immunoglobulin (8.8%). The overall mortality in the ICU was 5.9%. Conclusion. MG is a serious disorder with considerable morbidity and mortality. It is, however, a potentially manageable disease, provided that appropriate ICU resources are available.

Abstract Post-COVID-19 condition refers to a range of persisting physical, neurocognitive, and neuropsychological symptoms following SARS-CoV-2 infection. Recent evidence revealed that post-COVID-19 syndrome patients may suffer from cardiac dysfunction and are at increased risk for a broad range of cardiovascular disorders. This randomized, sham-control, double-blind trial evaluated the effect of hyperbaric oxygen therapy (HBOT) on the cardiac function of post-COVID-19 patients with ongoing symptoms for at least three months after confirmed infection. Sixty patients were randomized to receive 40 daily HBOT or sham sessions. They underwent echocardiography at baseline and 1–3 weeks after the last protocol session. Twenty-nine (48.3%) patients had reduced global longitudinal strain (GLS) at baseline. Of them, 13 (43.3%) and 16 (53.3%) were allocated to the sham and HBOT groups, respectively. Compared to the sham group, GLS significantly increased following HBOT (− 17.8 ± 1.1 to − 20.2 ± 1.0, p = 0.0001), with a significant group-by-time interaction (p = 0.041). In conclusion, post-COVID-19 syndrome patients despite normal EF often have subclinical left ventricular dysfunction that is characterized by mildly reduced GLS. HBOT promotes left ventricular systolic function recovery in patients suffering from post COVID-19 condition. Further studies are needed to optimize patient selection and evaluate long-term outcomes. This study was registered with ClinicalTrials.gov, number NCT04647656 on 01/12/2020.

Abstract Rheumatoid arthritis (RA) is an autoimmune disease characterized by systemic inflammation and is mediated by multiple immune cell types. In this work, we aimed to determine the relevance of changes in cell proportions in peripheral blood mononuclear cells (PBMCs) during the development of disease and following treatment. Samples from healthy blood donors, newly diagnosed RA patients, and established RA patients that had an inadequate response to MTX and were about to start tumor necrosis factor inhibitors (TNFi) treatment were collected before and after 3 months of treatment. We used in parallel a computational deconvolution approach based on RNA expression and flow cytometry to determine the relative cell-type frequencies. Cell-type frequencies from deconvolution of gene expression indicate that monocytes (both classical and non-classical) and CD4+ cells (Th1 and Th2) were increased in RA patients compared to controls, while NK cells and B cells (naïve and mature) were significantly decreased in RA patients. Treatment with MTX caused a decrease in B cells (memory and plasma cell), and a decrease in CD4 Th cells (Th1 and Th17), while treatment with TNFi resulted in a significant increase in the population of B cells. Characterization of the RNA expression patterns found that most of the differentially expressed genes in RA subjects after treatment can be explained by changes in cell frequencies (98% and 74% respectively for MTX and TNFi).

Background: Obesity negatively impacts multiple bodily systems, including the central nervous system. Retrospective studies that estimated chronological age from neuroimaging have found accelerated brain aging in obesity, but it is unclear how this estimation would be affected by weight loss following a lifestyle intervention. Methods: In a sub-study of 102 participants of the Dietary Intervention Randomized Controlled Trial Polyphenols Unprocessed Study (DIRECT-PLUS) trial, we tested the effect of weight loss following 18 months of lifestyle intervention on predicted brain age based on magnetic resonance imaging (MRI)-assessed resting-state functional connectivity (RSFC). We further examined how dynamics in multiple health factors, including anthropometric measurements, blood biomarkers, and fat deposition, can account for changes in brain age. Results: To establish our method, we first demonstrated that our model could successfully predict chronological age from RSFC in three cohorts (n=291;358;102). We then found that among the DIRECT-PLUS participants, 1% of body weight loss resulted in an 8.9 months’ attenuation of brain age. Attenuation of brain age was significantly associated with improved liver biomarkers, decreased liver fat, and visceral and deep subcutaneous adipose tissues after 18 months of intervention. Finally, we showed that lower consumption of processed food, sweets and beverages were associated with attenuated brain age. Conclusions: Successful weight loss following lifestyle intervention might have a beneficial effect on the trajectory of brain aging. Funding: The German Research Foundation (DFG), German Research Foundation - project number 209933838 - SFB 1052; B11, Israel Ministry of Health grant 87472511 (to I Shai); Israel Ministry of Science and Technology grant 3-13604 (to I Shai); and the California Walnuts Commission 09933838 SFB 105 (to I Shai).

Quantitative MRI (qMRI) has been shown to be clinically useful for numerous applications in the brain and body. The development of rapid, accurate, and reproducible qMRI techniques offers access to new multiparametric data, which can provide a comprehensive view of tissue pathology. This work introduces a multiparametric qMRI protocol along with full postprocessing pipelines, optimized for brain imaging at 3 Tesla and using state-of-the-art qMRI tools. The total scan time is under 50 minutes and includes eight pulse-sequences, which produce range of quantitative maps including T1, T2, and T2* relaxation times, magnetic susceptibility, water and macromolecular tissue fractions, mean diffusivity and fractional anisotropy, magnetization transfer ratio (MTR), and inhomogeneous MTR. Practical tips and limitations of using the protocol are also provided and discussed. Application of the protocol is presented on a cohort of 28 healthy volunteers and 12 brain regions-of-interest (ROIs). Quantitative values agreed with previously reported values. Statistical analysis revealed low variability of qMRI parameters across subjects, which, compared to intra-ROI variability, was x4.1 ± 0.9 times higher on average. Significant and positive linear relationship was found between right and left hemispheres' values for all parameters and ROIs with Pearson correlation coefficients of r>0.89 (P

Abstract Mutational signatures’ association with replication timing (RT) has been studied in cancer samples, but the RT distribution of somatic mutations in non-cancerous cells was only minimally explored. Here, we performed comprehensive analyses of mutational signatures in 2.9 million somatic mutations across multiple non-cancerous tissues, stratified by early and late RT regions. We found that many mutational processes are active mainly or solely in early RT, such as SBS16 in hepatocytes and SBS88 in the colon, or in late RT, such as SBS4 in lung and hepatocytes, and SBS18 across many tissues. The two ubiquitous signatures, SBS1 and SBS5, showed late and early bias, respectively, across multiple tissues and in mutations representing germ cells. We also performed a direct comparison with cancer samples in 4 matched tissue-cancer types. Unexpectedly, while for most signatures the RT bias was consistent in normal tissue and in cancer, we found that SBS1’s late RT bias is lost in cancer.

Abstract We tested whether CRP combined with the neutrophil-to-lymphocyte ratio (NLR) optimizes the prediction of infectious inflammation in hemodialysis patients. We conducted a retrospective study of 774 (mean age 71.1 ± 12.8 years, 35% women) hemodialysis patients from our institution, hospitalized between 2007 and 2021 for various reasons, with CRP levels available at admission. Infection was defined according to the International Sepsis Definition Conference criteria. An algorithm for the optimal CRP and NLR cutoff points for predicting infection was developed based on a decision tree analysis in the training cohort (n = 620) and then tested in the validation cohort (n = 154). A CRP level above 40 mg/L (obtained as the cutoff point in predicting infections in the training group, using ROC curve analysis) predicted an infection diagnosis with a sensitivity of 75% and a specificity of 76% with an odds ratio (OR) of 9.37 (95% CI: 5.36–16.39), according to a multivariate logistic regression analysis. Whereas, CRP levels above 23 mg/L together with an NLR above 9.7 predicted an infection diagnosis with a sensitivity of 69% and a specificity of 84% with an OR of 25.59 (95% CI: 9.73–67.31). All these results were reproduced in the validation set. Combined use of CRP with NLR may lower the CRP cutoff point in distinguishing between infectious and noninfectious inflammation in hemodialysis patients.

Abstract Background Molecular profiling of the tumour immune microenvironment (TIME) has enabled the rational choice of immunotherapies in some adult cancers. In contrast, the TIME of paediatric cancers is relatively unexplored. We speculated that a more refined appreciation of the TIME in childhood cancers, rather than a reliance on commonly used biomarkers such as tumour mutation burden (TMB), neoantigen load and PD-L1 expression, is an essential prerequisite for improved immunotherapies in childhood solid cancers. Methods We combined immunohistochemistry (IHC) with RNA sequencing and whole-genome sequencing across a diverse spectrum of high-risk paediatric cancers to develop an alternative, expression-based signature associated with CD8+ T-cell infiltration of the TIME. Furthermore, we explored transcriptional features of immune archetypes and T-cell receptor sequencing diversity, assessed the relationship between CD8+ and CD4+ abundance by IHC and deconvolution predictions and assessed the common adult biomarkers such as neoantigen load and TMB. Results A novel 15-gene immune signature, Immune Paediatric Signature Score (IPASS), was identified. Using this signature, we estimate up to 31% of high-risk cancers harbour infiltrating T-cells. In addition, we showed that PD-L1 protein expression is poorly correlated with PD-L1 RNA expression and TMB and neoantigen load are not predictive of T-cell infiltration in paediatrics. Furthermore, deconvolution algorithms are only weakly correlated with IHC measurements of T-cells. Conclusions Our data provides new insights into the variable immune-suppressive mechanisms dampening responses in paediatric solid cancers. Effective immune-based interventions in high-risk paediatric cancer will require individualised analysis of the TIME.

Abstract Slow paced breathing via heart rate variability (HRV) biofeedback stimulates vagus-nerve pathways that counter noradrenergic stress and arousal pathways that can influence production and clearance of Alzheimer's disease (AD)-related proteins. Thus, we examined whether HRV biofeedback intervention affects plasma Αβ40, Αβ42, total tau (tTau), and phosphorylated tau-181 (pTau-181) levels. We randomized healthy adults (N = 108) to use slow-paced breathing with HRV biofeedback to increase heart rate oscillations (Osc+) or to use personalized strategies with HRV biofeedback to decrease heart rate oscillations (Osc−). They practiced 20–40 min daily. Four weeks of practicing the Osc+ and Osc− conditions produced large effect size differences in change in plasma Aβ40 and Aβ42 levels. The Osc+ condition decreased plasma Αβ while the Osc− condition increased Αβ. Decreases in Αβ were associated with decreases in gene transcription indicators of β-adrenergic signaling, linking effects to the noradrenergic system. There were also opposing effects of the Osc+ and Osc− interventions on tTau for younger adults and pTau-181 for older adults. These results provide novel data supporting a causal role of autonomic activity in modulating plasma AD-related biomarkers. Trial registration: NCT03458910 (ClinicalTrials.gov); first posted on 03/08/2018.

Abstract The genus Elaphe Fitzinger, 1833 includes 17 species of charismatic, large-sized, non-venomous, Eurasian snakes. In the Western Palearctic, the genus is represented by three species from the Elaphe quatuorlineata group ranging from the Apennine peninsula to Central Asia. The southernmost population of this group is distributed in the mountains of the Southern Levant, with more than 400 km gap to other Elaphe populations. This population has been known to science for only 50 years and is virtually unstudied due to its extreme rarity. We studied these snakes’ morphological and genetic variation from the three countries where they are known to occur, i.e., Israel (Hermon, the Israeli-controlled Golan Heights), Lebanon, and Syria. We used nine mitochondrial and nuclear genes, complete mitogenome sequences, and a comprehensive morphological examination including published data, our own field observations, and museum specimens, to study its relationship to other species in the group. The three currently recognized species of the group (E. quatuorlineata, E. sauromates, E. urartica), and the Levant population, form four deeply divergent, strongly supported clades. Three of these clades correspond to the abovementioned species while the Southern Levant clade, which is genetically and morphologically distinct from all named congeners, is described here as a new species, Elaphe druzei sp. nov. The basal divergence of this group is estimated to be the Late Miocene with subsequent radiation from 5.1 to 3.9 Mya. The revealed biogeography of the E. quatuorlineata group supports the importance of the Levant as a major center of endemism and diversity of biota in Eurasia. The new species is large-sized and is one of the rarest snakes in the Western Palearctic. Because of its small mountain distribution range, in an area affected by land use and climate change, the new Elaphe urgently needs strict protection. Despite political issues, we hope this will be based on the cooperation of all countries where the new species occurs.

Abstract Robustness can refer to an animal’s ability to overcome perturbations. Intense selection for production traits in livestock has resulted in reduced robustness which has negative implications for livability as well as production. There is increasing emphasis on improving robustness through poultry breeding, which may involve identifying novel phenotypes that could be used in selection strategies. The hypothalamic–pituitary–adrenal (HPA) axis and associated hormones (e.g., corticosterone) participate in many metabolic processes that are related to robustness. Corticosterone can be measured non-invasively in feathers (FCORT) and reflects the average HPA axis activity over the feather growing period, however measurement is expensive and time consuming. Fault bars are visible feather deformities that may be related to HPA axis activity and may be a more feasible indicator trait. In this study, we estimated variance components for FCORT and fault bars in a population of purebred turkeys as well as their genetic and partial phenotypic correlations with other economically relevant traits including growth and efficiency, carcass yield, and meat quality. The estimated heritability for FCORT was 0.21 ± 0.07 and for the fault bar traits (presence, incidence, severity, and index) estimates ranged from 0.09 to 0.24. The genetic correlation of FCORT with breast weight, breast meat yield, fillet weight, and ultimate pH were estimated at −0.34 ± 0.21, −0.45 ± 0.23, −0.33 ± 0.24, and 0.32 ± 0.24, respectively. The phenotypic correlations of FCORT with breast weight, breast meat yield, fillet weight, drum weight, and walking ability were −0.16, −0.23, −0.18, 0.17, and 0.21, respectively. Some fault bar traits showed similar genetic correlations with breast weight, breast meat yield, and walking ability but the magnitude was lower than those with FCORT. While the dataset is limited and results should be interpreted with caution, this study indicates that selection for traits related to HPA axis activity is possible in domestic turkeys. Further research should focus on investigating the association of these traits with other robustness-related traits and how to potentially implement these traits in turkey breeding.

Analysis of neuronal activity in the hippocampus of behaving animals has revealed cells acting as ‘Time Cells’, which exhibit selective spiking patterns at specific time intervals since a triggering event, and ‘Distance Cells’, which encode the traversal of specific distances. Other neurons exhibit a combination of these features, alongside place selectivity. This study aims to investigate how the task performed by animals during recording sessions influences the formation of these representations. We analyzed data from a treadmill running study conducted by Kraus et al., 2013, in which rats were trained to run at different velocities. The rats were recorded in two trial contexts: a ‘fixed time’ condition, where the animal ran on the treadmill for a predetermined duration before proceeding, and a ‘fixed distance’ condition, where the animal ran a specific distance on the treadmill. Our findings indicate that the type of experimental condition significantly influenced the encoding of hippocampal cells. Specifically, distance-encoding cells dominated in fixed-distance experiments, whereas time-encoding cells dominated in fixed-time experiments. These results underscore the flexible coding capabilities of the hippocampus, which are shaped by over-representation of salient variables associated with reward conditions.

Development of the dorsal aorta is a key step in the establishment of the adult blood-forming system, since hematopoietic stem and progenitor cells (HSPCs) arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here, we profile the transcriptome of the earliest detectable endothelial cells (ECs) during zebrafish embryogenesis to demonstrate that tissue-specific EC programs initiate much earlier than previously appreciated, by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite-derived endothelial cells (SDECs) that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish, where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Although SDECs lack hematopoietic potential, they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus, at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs, hemogenic ECs, and SDECs. Taken together, our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.

Abstract Background Concerns around staffs’ and students’ interactions with commercial entities, for example drug companies, have led several North American medical schools to implement conflict of interest (COI) policies. However, little is known about COI policies at European medical schools. We analysed the content and strength of COI policies at Scandinavian medical schools. Methods We searched the websites of medical schools in Denmark, Norway, and Sweden and emailed the Deans for additional information. Using comparable methodology to previous studies, the strength of the COI policies was rated on a scale from 0 to 2 across 11 items (higher score more restrictive); we also assessed the presence of oversight mechanisms and sanctions. Results We identified 77 unique policies for 15 medical schools (range 2–8 per school). Most of the policies (n = 72; 94%) were University wide and only five (6%) were specific for the medical schools. For six of eleven items one or more schools had a restrictive policy (score of two). None of the schools had a restrictive policy for the five additional items (speaking relationships, sales representatives, on-site education activities, medical school curriculum, and drug samples). Honoraria was the item with the highest score, with eight of the 15 schools having a score of two. Thirteen of the 15 schools had policies that identified a party responsible for policy oversight and mentioned sanctions for non-compliance. Conclusion Our study provides the first evaluation of all Scandinavian medical schools’ COI policies. We found that the content of COI policies varies widely and still has shortcomings. We encourage Scandinavian medical schools to develop more stringent COI policies to regulate industry interactions with both faculty and students.

Abstract From interpersonal interactions to international arms races, game theorists and social scientists have long studied decision-making in zero-sum situations. Yet, what happens when people can freely choose whether to enter zero-sum situations in the first place? Thirteen studies (including five pre-registered) consistently document evidence for zero-sum aversion—the desire to avoid situations that are (or are believed to be) zero-sum. Across different contexts (economic games, market entry decisions, performance reviews, negotiations, job applications), samples (online participant pool, MBA students, community sample), and designs (within- and between-participant, real and hypothetical decisions), people avoid zero-sum situations that inversely link their and others’ outcomes as well as refrain from putting others in such situations. Because people fear that zero-sum situations will be rife with conflict, they exhibit zero-sum aversion even when doing so is costly. Finally, we find that people require zero-sum situations to provide substantially higher payoffs (e.g., compensation) to overcome their zero-sum aversion. We conclude with a discussion of the implications for interpersonal and intergroup conflict.

Abstract Data analysis has increasingly relied on machine learning in recent years. Since machines implement mathematical algorithms without knowing the physical nature of the problem, they may be accurate but lack the flexibility to move across different domains. This manuscript presents a machine-educating approach where a machine is equipped with a physical model, universal building blocks, and an unlabeled dataset from which it derives its decision criteria. Here, the concept of machine education is deployed to identify thin layers of organic materials using hyperspectral imaging (HSI). The measured spectra formed a nonlinear mixture of the unknown background materials and the target material spectra. The machine was educated to resolve this nonlinear mixing and identify the spectral signature of the target materials. The inputs for educating and testing the machine were a nonlinear mixing model, the spectra of the pure target materials (which are problem invariant), and the unlabeled HSI data. The educated machine is accurate, and its generalization capabilities outperform classical machines. When using the educated machine, the number of falsely identified samples is ~ 100 times lower than the classical machine. The probability for detection with the educated machine is 96% compared to 90% with the classical machine.

Abstract Background Mediterranean (MED) diet is a rich source of polyphenols, which benefit adiposity by several mechanisms. We explored the effect of the green-MED diet, twice fortified in dietary polyphenols and lower in red/processed meat, on visceral adipose tissue (VAT). Methods In the 18-month Dietary Intervention Randomized Controlled Trial PoLyphenols UnproceSsed (DIRECT-PLUS) weight-loss trial, 294 participants were randomized to (A) healthy dietary guidelines (HDG), (B) MED, or (C) green-MED diets, all combined with physical activity. Both isocaloric MED groups consumed 28 g/day of walnuts (+ 440 mg/day polyphenols). The green-MED group further consumed green tea (3–4 cups/day) and Wolffia globosa (duckweed strain) plant green shake (100 g frozen cubes/day) (+ 800mg/day polyphenols) and reduced red meat intake. We used magnetic resonance imaging (MRI) to quantify the abdominal adipose tissues. Results Participants (age = 51 years; 88% men; body mass index = 31.2 kg/m2; 29% VAT) had an 89.8% retention rate and 79.3% completed eligible MRIs. While both MED diets reached similar moderate weight (MED: − 2.7%, green-MED: − 3.9%) and waist circumference (MED: − 4.7%, green-MED: − 5.7%) loss, the green-MED dieters doubled the VAT loss (HDG: − 4.2%, MED: − 6.0%, green-MED: − 14.1%; p < 0.05, independent of age, sex, waist circumference, or weight loss). Higher dietary consumption of green tea, walnuts, and Wolffia globosa; lower red meat intake; higher total plasma polyphenols (mainly hippuric acid), and elevated urine urolithin A polyphenol were significantly related to greater VAT loss (p < 0.05, multivariate models). Conclusions A green-MED diet, enriched with plant-based polyphenols and lower in red/processed meat, may be a potent intervention to promote visceral adiposity regression. Trial registration ClinicalTrials.gov , NCT03020186

Abstract Persistent post-concussion syndrome (PPCS) is a common and significant morbidity among children following traumatic brain injury (TBI) and the evidence for effective PPCS treatments remains limited. Recent studies have shown the beneficial effects of hyperbaric oxygen therapy (HBOT) in PPCS adult patients. This randomized, sham-control, double blind trial evaluated the effect of hyperbaric oxygen therapy (HBOT) on children (age 8–15) suffering from PPCS from mild-moderate TBI events six months to 10 years prior. Twenty-five children were randomized to receive 60 daily sessions of HBOT (n = 15) or sham (n = 10) treatments. Following HBOT, there was a significant increase in cognitive function including the general cognitive score (d = 0.598, p = 0.01), memory (d = 0.480, p = 0.02), executive function (d = 0.739, p = 0.003), PPCS symptoms including emotional score (p = 0.04, d = – 0.676), behavioral symptoms including hyperactivity (d = 0.244, p = 0.03), global executive composite score (d = 0.528, p = 0.001), planning/organizing score (d = 1.09, p = 0.007). Clinical outcomes correlated with significant improvements in brain MRI microstructural changes in the insula, supramarginal, lingual, inferior frontal and fusiform gyri. The study suggests that HBOT improves both cognitive and behavioral function, PPCS symptoms, and quality of life in pediatric PPCS patients at the chronic stage, even years after injury. Additional data is needed to optimize the protocol and to characterize the children who can benefit the most.

BackgroundSuicide is the second leading cause of death in adolescents, and self-harm is one of the strongest predictors of death by suicide. The rates of adolescents presenting to emergency departments (EDs) for suicidal thoughts and behaviors (STBs) have increased. Still, existing follow-up after ED discharge is inadequate, leaving a high-risk period for reattempts and suicide. There is a need for innovative evaluation of imminent suicide risk factors in these patients, focusing on continuous real-time evaluations with low assessment burden and minimal reliance on patient disclosure of suicidal intent. ObjectiveThis study examines prospective longitudinal associations between observed real-time mobile passive sensing, including communication and activity patterns, and clinical and self-reported assessments of STB over 6 months. MethodsThis study will include 90 adolescents recruited on their first outpatient clinic visit following their discharge from the ED due to a recent STB. Participants will complete brief weekly assessments and be monitored continuously for their mobile app usage, including mobility, activity, and communication patterns, over 6 months using the iFeel research app. Participants will complete 4 in-person visits for clinical assessment at baseline and at the 1-, 3-, and 6-month follow-ups. The digital data will be processed, involving feature extraction, scaling, selection, and dimensionality reduction. Passive monitoring data will be analyzed using both classical machine learning models and deep learning models to identify proximal associations between real-time observed communication, activity patterns, and STB. The data will be split into a training and validation data set, and predictions will be matched against the clinical evaluations and self-reported STB events (ie, labels). To use both labeled and unlabeled digital data (ie, passively collected), we will use semisupervised methods in conjunction with a novel method that is based on anomaly detection notions. ResultsParticipant recruitment and follow-up started in February 2021 and are expected to be completed by 2024. We expect to find prospective proximal associations between mobile sensor communication, activity data, and STB outcomes. We will test predictive models for suicidal behaviors among high-risk adolescents. ConclusionsDeveloping digital markers of STB in a real-world sample of high-risk adolescents presenting to ED can inform different interventions and provide an objective means to assess the risk of suicidal behaviors. The results of this study will be the first step toward large-scale validation that may lead to suicide risk measures that aid psychiatric follow-up, decision-making, and targeted treatments. This novel assessment could facilitate timely identification and intervention to save young people’s lives. International Registered Report Identifier (IRRID)DERR1-10.2196/46464