Labile assembly of a tardigrade protein induces biostasis

Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins, which also function to prevent perturbations induced by drying in vitro and in heterologous systems. CAHS proteins have been shown to form gels both in vitro and in vivo, which has been speculated to be linked to their protective capacity. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of fibrillization and gelation for CAHS D similar to that of intermediate filament assembly. We show that in vitro, gelation restricts molecular motion, immobilizing and protecting labile material from the harmful effects of drying. In vivo, we observe that CAHS D forms fibrillar networks during osmotic stress. Fibrillar networking of CAHS D improves survival of osmotically shocked cells. We observe two emergent properties associated with fibrillization; (i) prevention of cell volume change and (ii) reduction of metabolic activity during osmotic shock. We find that there is no significant correlation between maintenance of cell volume and survival, while there is a significant correlation between reduced metabolism and survival. Importantly, CAHS D's fibrillar network formation is reversible and metabolic rates return to control levels after CAHS fibers are resolved. This work provides insights into how tardigrades induce reversible biostasis through the self-assembly of labile CAHS gels.

Early intervention and disease modification in atopic dermatitis-the current state of the field and barriers to progress

Atopic dermatitis (AD) is a highly prevalent chronic inflammatory skin disease representing a major source of global disability burden. Disease-modifying therapies are showing promise in chronic inflammatory disorders such as rheumatoid arthritis and Crohn's disease with method and timing of initial treatment impacting long-term disease outcomes. Whether disease-modifying therapies, specifically those used as an early interventional approach, impacts disease course and comorbidity development in AD is not well-understood. We reviewed the progress in disease modification strategies, emphasizing early intervention approaches in common (or proto-typical) inflammatory diseases. Although more common in other fields, disease modification approaches are becoming increasingly investigated in dermatology, though studies in AD are lacking. Despite significant limitations in ongoing and completed studies, early data are promising and suggest that both the choice and timing of early intervention approach can affect long-term disease course and comorbidity development. To best improve AD patient outcomes, more research is needed to further explore the impact of early disease-modifying therapies. Future studies should focus on identifying the most effective approaches and extend the early results to a more inclusive set of comorbidities and longer-term outcomes.

Effects of Preoperative Glucocorticoid Use on Patients Undergoing Single-Level Lumbar Fusions: A Retrospective Propensity Score-Matched Registry Study

Objective Spinal fusions are gaining popularity as a means of treating spinal deformity and instability from a range of pathologies. The prevalence of glucocorticoid use has also increased in recent decades, and their systemic effects are well-documented. Although commonly used in the preoperative period, the effects of steroids on outcomes among patients undergoing spinal fusions are inadequately described. This study compares the odds of developing complications among patients who underwent single-level lumbar fusions with and without preoperative glucocorticoid use in hopes of establishing more evidence-based parameters for guiding preoperative steroid use. Methods The TriNetX multi-institutional electronic health record database was used to perform a retrospective, propensity score-matched analysis of clinical outcomes of two cohorts of patients who underwent posterior or posterolateral single-level lumbar fusions with and without interbody fusion, those who used glucocorticoids for at least one week within a year of fusion and those who did not. The outcomes of interest were examined within 30 days of the operation and included death, reoperation, deep or superficial surgical site infection (SSI), pneumonia, reintubation, ventilator dependence, tracheostomy, acute kidney injury (AKI), renal insufficiency, pulmonary embolism (PE) or deep venous thrombosis (DVT), urinary tract infection (UTI), emergency department (ED) visit, sepsis, and myocardial infarction (MI). Results The odds of developing pneumonia within 30 days of spinal fusion in the cohort that used glucocorticoids within one year of operation compared to the cohort without glucocorticoid use was 0.67 (p≤0.001, 95% CI: 0.59-0.69). The odds of requiring a tracheostomy within 30 days of spinal fusion in the cohort that used glucocorticoids within one year of operation compared to the cohort without glucocorticoid use was 0.39 (p≤0.001, 95% CI: 0.26-0.60). The odds of reoperation, deep and superficial SSI, and ED visits within 30 days of operation were significantly higher for the same glucocorticoid-receiving cohort, with odds ratios of 1.4 (p=0.003, 95% CI: 1.11-1.65), 1.86 (p≤0.001, 95% CI: 1.31-2.63), 2.28 (p≤0.001, 95% CI: 1.57-3.31), and 1.25 (p≤0.001, 95% CI: 1.17-1.33), respectively. After propensity score-matching, there was no significant difference between the odds of death, DVT, PE, MI, UTI, AKI, sepsis, reintubation, and ventilator dependence between the two cohorts. Conclusion In support of much of the current literature regarding preoperative glucocorticoid use and rates of complications, patients who underwent a single-level lumbar fusion and have used glucocorticoids for at least a week within a year of operation experienced significantly higher odds of reoperation, deep and superficial SSI, and ED visits. However, these patients using glucocorticoids were also found to have lower odds of developing pneumonia, renal insufficiency, and tracheostomy requirement than those who did not use steroids within a year of surgery.

Disordered proteins interact with the chemical environment to tune their protective function during drying

The conformational ensemble and function of intrinsically disordered proteins (IDPs) are sensitive to their solution environment. The inherent malleability of disordered proteins combined with the exposure of their residues accounts for this sensitivity. One context in which IDPs play important roles that is concomitant with massive changes to the intracellular environment is during desiccation (extreme drying). The ability of organisms to survive desiccation has long been linked to the accumulation of high levels of cosolutes such as trehalose or sucrose as well as the enrichment of IDPs, such as late embryogenesis abundant (LEA) proteins or cytoplasmic abundant heat soluble (CAHS) proteins. Despite knowing that IDPs play important roles and are co-enriched alongside endogenous, species-specific cosolutes during desiccation, little is known mechanistically about how IDP-cosolute interactions influence desiccation tolerance. Here, we test the notion that the protective function of desiccation-related IDPs is enhanced through conformational changes induced by endogenous cosolutes. We find that desiccation-related IDPs derived from four different organisms spanning two LEA protein families and the CAHS protein family, synergize best with endogenous cosolutes during drying to promote desiccation protection. Yet the structural parameters of protective IDPs do not correlate with synergy for either CAHS or LEA proteins. We further demonstrate that for CAHS, but not LEA proteins, synergy is related to self-assembly and the formation of a gel. Our results demonstrate that functional synergy between IDPs and endogenous cosolutes is a convergent desiccation protection strategy seen among different IDP families and organisms, yet, the mechanisms underlying this synergy differ between IDP families.

Oncologic Safety of Close Margins in Patients With Low- to Intermediate-Grade Major Salivary Gland Carcinoma

Importance

Postoperative radiation therapy for close surgical margins in low- to intermediate-grade salivary carcinomas lacks multi-institutional supportive evidence.

Objective

To evaluate the oncologic outcomes for low- and intermediate-grade salivary carcinomas with close and positive margins.

Design, Setting, and Participants

The American Head and Neck Society Salivary Gland Section conducted a retrospective cohort study from 2010 to 2019 at 41 centers. Margins were classified as R0 (negative), R1 (microscopically positive), or R2 (macroscopically positive). R0 margins were subclassified into clear (>1 mm) or close (≤1 mm). Data analysis was performed from June to October 2023.

Main Outcomes and Measures

Main outcomes were risk factors for local recurrence.

Results

A total of 865 patients (median [IQR] age at surgery, 56 [43-66] years; 553 female individuals [64%] and 312 male individuals [36%]) were included. Of these, 801 (93%) had parotid carcinoma and 64 (7%) had submandibular gland carcinoma, and 748 (86%) had low-grade tumors and 117 (14%) had intermediate-grade tumors, with the following surgical margins: R0 in 673 (78%), R1 in 168 (19%), and R2 in 24 (3%). Close margins were found in 395 of 499 patients with R0 margins (79%), for whom margin distances were measured. A total of 305 patients (35%) underwent postoperative radiation therapy. Of all 865 patients, 35 (4%) had local recurrence with a median (IQR) follow-up of 35.3 (13.9-59.1) months. In patients with close margins as the sole risk factor for recurrence, the local recurrence rates were similar between those who underwent postoperative radiation therapy (0 of 46) or observation (4 of 165 [2%]). Patients with clear margins (n = 104) had no recurrences. The local recurrence rate in patients with R1 or R2 margins was better in those irradiated (2 of 128 [2%]) compared to observed (13 of 64 [20%]) (hazard ratio [HR], 0.05; 95% CI, 0.01-0.24). Multivariable analysis for local recurrence found the following independent factors: age at diagnosis (HR for a 10-year increase in age, 1.33; 95% CI, 1.06-1.67), R1 vs R0 (HR, 5.21; 95% CI, 2.58-10.54), lymphovascular invasion (HR, 4.47; 95% CI, 1.43-13.99), and postoperative radiation therapy (HR, 0.10; 95% CI, 0.04-0.29). The 3-year local recurrence-free survivals for the study population were 96% vs 97% in the close margin group.

Conclusions and Relevance

In this cohort study of patients with low- and intermediate-grade major salivary gland carcinoma, postoperative radiation therapy for positive margins was associated with decreased risk of local recurrence. In isolation from other risk factors for local recurrence, select patients with close surgical margins (≤1 mm) may safely be considered for observation.

Demonstrating Agreement between Radio and Fluorescence Measurements of the Depth of Maximum of Extensive Air Showers at the Pierre Auger Observatory

We show, for the first time, radio measurements of the depth of shower maximum (X_{max}) of air showers induced by cosmic rays that are compared to measurements of the established fluorescence method at the same location. Using measurements at the Pierre Auger Observatory we show full compatibility between our radio and the previously published fluorescence dataset, and between a subset of air showers observed simultaneously with both radio and fluorescence techniques, a measurement setup unique to the Pierre Auger Observatory. Furthermore, we show radio X_{max} resolution as a function of energy and demonstrate the ability to make competitive high-resolution X_{max} measurements with even a sparse radio array. With this, we show that the radio technique is capable of cosmic-ray mass composition studies, both at Auger and at other experiments.

Natural history of occult hernias in adults at a safety-net hospital

PURPOSE

Occult hernias, hernias seen on radiologic imaging but not felt on physical exam, are common. Despite their high prevalence, little is known about the natural history of this finding. Our aim was to determine and report on the natural history of patients with occult hernias including the impact on abdominal wall quality of life (AW-QOL), need for surgery, and risk of acute incarceration/strangulation.

METHODS

This was a prospective cohort study of patients who underwent a computed tomography (CT) abdomen/pelvis scan from 2016 to 2018. Primary outcome was change in AW-QOL using the modified Activities Assessment Scale (mAAS), a hernia-specific, validated survey (1 = poor, 100 = perfect). Secondary outcomes included elective and emergent hernia repairs.

RESULTS

A total of 131 (65.8%) patients with occult hernias completed follow-up with a median (IQR) of 15.4 (22.5) months. Nearly half of these patients (42.8%) experienced a decrease in their AW-QOL, 26.0% were unchanged, and 31.3% reported improvement. One-fourth of patients (27.5%) underwent abdominal surgery during the study period: 9.9% were abdominal procedures without hernia repair, 16.0% involved elective hernia repairs, and 1.5% were emergent hernia repairs. AW-QOL improved for patients who underwent hernia repair (+ 11.2 ± 39.7, p = 0.043) while those who did not undergo hernia repair experienced no change in AW-QOL (- 3.0 ± 35.1).

CONCLUSION

When untreated, patients with occult hernias on average experience no change in their AW-QOL. However, many patients experience improvement in AW-QOL after hernia repair. Additionally, occult hernias have a small but real risk of incarceration requiring emergent repair. Further research is needed to develop tailored treatment strategies.

Twitter Perspectives on Cochlear Implantation: Sentiment and Thematic Analysis

OBJECTIVE

To identify themes that contribute to the most positive and negative perspectives of cochlear implants (CIs) on Twitter.

STUDY DESIGN

A cross-sectional qualitative study.

SETTING

Social media (Twitter).

METHODS

In this study, all English-language original tweets mentioning "cochlear implant" from 2019 to 2021 were collected from Twitter's Academic Research Database using a custom Python script. Sentiment analysis was performed using VADER, a sentiment analysis tool built to analyze the inherent positivity or negativity of social media posts. Tweets were quantitatively sorted by compound sentiment score (range -1 [most negative] to 1 [most positive]). Thematic analysis based on grounded theory was performed on the most positive, negative, and "liked" tweets.

RESULTS

Of the 19,376 tweets included, the average (standard deviation) compound sentiment score was 0.21 (0.46). A total of 10,375 (53.5%) tweets had a positive tone, 4965 (25.6%) were neutral and 4036 (20.8%) were negative. Of the 100 most negative tweets, the most prominent themes were media representation (21.9%), the controversy of CI within the Deaf community (19.8%), and unrelated to direct patient experience (16.7%). Of the 100 most positive tweets, the most prominent themes were tweets of happiness and support (25.0%), tweets unrelated to direct patient experience (18.0%), and tweets about hearing new sounds (10.0%).

CONCLUSION

While the majority of tweets on CI carried a positive tone, there are ongoing challenges with the stigma surrounding CI. Public perspectives of CI on social media may help clinicians counsel CI patients and elucidate issues that lead to newfound acceptance or ongoing stigma of CI in the general population.

Energetic Electron Precipitation Driven by Electromagnetic Ion Cyclotron Waves from ELFIN's Low Altitude Perspective

We review comprehensive observations of electromagnetic ion cyclotron (EMIC) wave-driven energetic electron precipitation using data collected by the energetic electron detector on the Electron Losses and Fields InvestigatioN (ELFIN) mission, two polar-orbiting low-altitude spinning CubeSats, measuring 50-5000 keV electrons with good pitch-angle and energy resolution. EMIC wave-driven precipitation exhibits a distinct signature in energy-spectrograms of the precipitating-to-trapped flux ratio: peaks at >0.5 MeV which are abrupt (bursty) (lasting ∼17 s, or Δ L ∼ 0.56 ) with significant substructure (occasionally down to sub-second timescale). We attribute the bursty nature of the precipitation to the spatial extent and structuredness of the wave field at the equator. Multiple ELFIN passes over the same MLT sector allow us to study the spatial and temporal evolution of the EMIC wave - electron interaction region. Case studies employing conjugate ground-based or equatorial observations of the EMIC waves reveal that the energy of moderate and strong precipitation at ELFIN approximately agrees with theoretical expectations for cyclotron resonant interactions in a cold plasma. Using multiple years of ELFIN data uniformly distributed in local time, we assemble a statistical database of ∼50 events of strong EMIC wave-driven precipitation. Most reside at L ∼ 5 - 7 at dusk, while a smaller subset exists at L ∼ 8 - 12 at post-midnight. The energies of the peak-precipitation ratio and of the half-peak precipitation ratio (our proxy for the minimum resonance energy) exhibit an L -shell dependence in good agreement with theoretical estimates based on prior statistical observations of EMIC wave power spectra. The precipitation ratio's spectral shape for the most intense events has an exponential falloff away from the peak (i.e., on either side of ∼ 1.45 MeV). It too agrees well with quasi-linear diffusion theory based on prior statistics of wave spectra. It should be noted though that this diffusive treatment likely includes effects from nonlinear resonant interactions (especially at high energies) and nonresonant effects from sharp wave packet edges (at low energies). Sub-MeV electron precipitation observed concurrently with strong EMIC wave-driven >1 MeV precipitation has a spectral shape that is consistent with efficient pitch-angle scattering down to ∼ 200-300 keV by much less intense higher frequency EMIC waves at dusk (where such waves are most frequent). At ∼100 keV, whistler-mode chorus may be implicated in concurrent precipitation. These results confirm the critical role of EMIC waves in driving relativistic electron losses. Nonlinear effects may abound and require further investigation.

A short, animated storytelling video about sodium intake as a major cardiovascular risk factor and recommendations for a healthy diet: an online, randomized, controlled trial

BACKGROUND

Increased uptake of sodium is a major cause for cardiovascular disease and mortality. Reduction of daily salt intake below a reference level of 2 g per day (the equivalent to 5 g salt/day) is known to effectively reduce cardiovascular mortality. The widespread use of social media, with a constant increase in video consumption, is opening new avenues for the dissemination of innovative and scalable approaches to health-related information and recommendations for a healthy diet, such as via video interventions with short animated stories (SAS).

OBJECTIVE

This study will evaluate the effect of a sodium intake-SAS video intervention on immediate and medium-term knowledge about dietary sodium. Beyond that, immediate and medium-term effects on behavioral expectation to reduce sodium intake as well as voluntary post-trial engagement with the video content will be examined.

METHODS

In this 4-armed, parallel, randomized controlled trial, 10,000 adult, US participants will be randomly assigned to (1) a short, animated storytelling intervention video on sodium as a cardiovascular disease risk factor followed by surveys assessing the facts on sodium and cardiovascular disease conveyed in the video (2) the surveys only, (3) an attention placebo control video followed by the before mentioned surveys, and (4) an arm that is exposed to neither the video nor the surveys. Two weeks later, participants in all four arms will complete all of the surveys.

RESULTS

Primary outcomes are the immediate and medium-term effects of the short, animated storytelling intervention video on knowledge about dietary sodium. Secondary outcomes are immediate and medium-term effects of the short, animated storytelling intervention on behavioral expectation to reduce sodium intake as well as voluntary post-trial engagement with the video content.

CONCLUSION

This study will extend the knowledge on the effects of short, animated storytelling for the containment of the global cardiovascular disease burden. Knowledge on the groups that may be more likely to voluntarily engage with SAS video content will help to improve targeting of future interventions towards audiences at risk. TRIAL REGISTRATION {2A}: ClinicalTrials.gov NCT05735457. Registered on February 21, 2023.

Machine Learning Classification of Alzheimer's Disease Pathology Reveals Diffuse Amyloid as a Major Predictor of Cognitive Impairment in Human Hippocampal Subregions

Analyzing Alzheimer's disease (AD) pathology within anatomical subregions is a significant challenge, often carried out by pathologists using a standardized, semi-quantitative approach. To augment traditional methods, a high-throughput, high-resolution pipeline was created to classify the distribution of AD pathology within hippocampal subregions. USC ADRC post-mortem tissue sections from 51 patients were stained with 4G8 for amyloid, Gallyas for neurofibrillary tangles (NFTs) and Iba1 for microglia. Machine learning (ML) techniques were utilized to identify and classify amyloid pathology (dense, diffuse and APP (amyloid precursor protein)), NFTs, neuritic plaques and microglia. These classifications were overlaid within manually segmented regions (aligned with the Allen Human Brain Atlas) to create detailed pathology maps. Cases were separated into low, intermediate, or high AD stages. Further data extraction enabled quantification of plaque size and pathology density alongside ApoE genotype, sex, and cognitive status. Our findings revealed that the increase in pathology burden across AD stages was driven mainly by diffuse amyloid. The pre and para-subiculum had the highest levels of diffuse amyloid while NFTs were highest in the A36 region in high AD cases. Moreover, different pathology types had distinct trajectories across disease stages. In a subset of AD cases, microglia were elevated in intermediate and high compared to low AD. Microglia also correlated with amyloid pathology in the Dentate Gyrus. The size of dense plaques, which may represent microglial function, was lower in ApoE4 carriers. In addition, individuals with memory impairment had higher levels of both dense and diffuse amyloid. Taken together, our findings integrating ML classification approaches with anatomical segmentation maps provide new insights on the complexity of disease pathology in AD progression. Specifically, we identified diffuse amyloid pathology as being a major driver of AD in our cohort, regions of interest and microglial responses that might advance AD diagnosis and treatment.

Genomic profiling informs diagnoses and treatment in vascular anomalies

Vascular anomalies are malformations or tumors of the blood or lymphatic vasculature and can be life-threatening. Although molecularly targeted therapies can be life-saving, identification of the molecular etiology is often impeded by lack of accessibility to affected tissue samples, mosaicism or insufficient sequencing depth. In a cohort of 356 participants with vascular anomalies, including 104 with primary complex lymphatic anomalies (pCLAs), DNA from CD31+ cells isolated from lymphatic fluid or cell-free DNA from lymphatic fluid or plasma underwent ultra-deep sequencing thereby uncovering pathogenic somatic variants down to a variant allele fraction of 0.15%. A molecular diagnosis, including previously undescribed genetic causes, was obtained in 41% of participants with pCLAs and 72% of participants with other vascular malformations, leading to a new medical therapy for 63% (43/69) of participants and resulting in improvement in 63% (35/55) of participants on therapy. Taken together, these data support the development of liquid biopsy-based diagnostic techniques to identify previously undescribed genotype-phenotype associations and guide medical therapy in individuals with vascular anomalies.

Impact of a near-peer teaching program within a college of pharmacy on interest in mentoring roles

BACKGROUND AND PURPOSE

Near-peer teaching within healthcare education has numerous benefits, but there is limited literature to assess the impact that these experiences have on skill development and future teaching roles. This study describes the impact of serving as a near-peer teaching assistant on both former and current pharmacy students.

EDUCATIONAL ACTIVITY AND SETTING

The University of Texas at Austin College of Pharmacy implemented the Academic Assistant (AA) program in 2009 to provide an opportunity for students to participate as near-peer educators in a variety of courses. To determine the impact of these AA positions on current and former students, participants from five years of the program were surveyed regarding the impact of the program on skill development and current or future interest in teaching/mentoring.

FINDINGS

Current students in the AA program reported that participation increased the likelihood of pursuing a career with teaching/mentoring roles. A majority (65%) of alumni who participated in the program reported being in a current teaching/mentoring role with 42% responding that the AA program was impactful to their career choice. The qualitative analysis showed that direct impact to respondents included validating career goals and increasing interests in teaching/mentoring roles. Those who reported no direct impact on their career still gained valuable professional skills that included: public speaking, time management, broadened perspectives, and increased understanding of academia career expectations.

SUMMARY

Providing opportunities for pharmacy students to serve in near-peer teaching roles increased students' interest in pursuing teaching/mentoring roles and offered valuable professional experiences.

Identification of risk variants related to malignant tumors in children with birth defects by whole genome sequencing

Background

Children with birth defects (BD) are more likely to develop cancer and the increased risk of cancer persists into adulthood. Prior population-based assessments have demonstrated that even non-chromosomal BDs are associated with at least two-fold increase of cancer risk. Identification of variants that are associated with malignant tumor in BD patients without chromosomal anomalies may improve our understanding of the underlying molecular mechanisms and provide clues for early cancer detection in children with BD.

Methods

In this study, whole genome sequencing (WGS) data of blood-derived DNA for 1653 individuals without chromosomal anomalies were acquired from the Kids First Data Resource Center (DRC), including 541 BD probands with at least one type of malignant tumors, 767 BD probands without malignant tumor, and 345 healthy family members who are the parents or siblings of the probands. Recurrent variants exclusively seen in cancer patients were selected and mapped to their corresponding genomic regions. The targeted genes/non-coding RNAs were further reduced using random forest and forward feature selection (ffs) models.

Results

The filtered genes/non-coding RNAs, including variants in non-coding areas, showed enrichment in cancer-related pathways. To further support the validity of these variants, blood WGS data of additional 40 independent BD probands, including 25 patients with at least one type of cancers from unrelated projects, were acquired. The counts of variants of interest identified in the Kid First data showed clear deviation in the validation dataset between BD patients with cancer and without cancer. Furthermore, a deep learning model was built to assess the predictive abilities in the 40 patients using variants of interest identified in the Kids First cohort as feature vectors. The accuracies are ~ 75%, with the noteworthy observation that variants mapped to non-coding regions provided the highest accuracy (31 out of 40 patients were labeled correctly).

Conclusion

We present for the first time a panorama of genetic variants that are associated with cancers in non-chromosomal BD patients, implying that our approach may potentially serve for the early detection of malignant tumors in patients with BD.

Radiation Therapy Decision Making Process and Operations for COVID-19 Positive Patients

Purpose/Objective(s)

A challenging clinical dilemma during the COVID-19 pandemic is management of cancer patients who test positive for COVID. Given the need to balance the risk of disease progression with the risk of transmission to other patients and staff, radiation therapy for these patients requires careful consideration and modification of standard workflows. It is also critical to develop processes to mitigate radiation treatment interruption, which can affect patient outcomes. The objective of this study was to report the clinical operations and outcomes for COVID positive patients receiving radiation therapy during the pandemic at a tertiary cancer center including 2 network locations.

Materials/Methods

During March 2020 to March 2022, the Radiation Oncology COVID committee (RO COVID) developed an integrated process to triage patients, provide treatment recommendations, and implement infection control procedures to safely deliver radiation therapy to COVID positive patients. Policies were created for each center with multidisciplinary input from infectious disease, radiation oncology, radiation therapy, and nursing. All COVID positive patients were presented to the RO COVID group and evaluated for clinical urgency, benefit with radiation, and life expectancy. If deemed necessary, a limited planned break or hypofractionated regimen was recommended to minimize staff exposure. We conducted a retrospective review of COVID positive patients with different primary malignancies treated through the COVID positive pathway.

Results

A total of 68 COVID positive patients were treated with the COVID positive pathway (HN 15, Breast 9, CNS 8, GU 8, GYN, 7, Thoracic 6, GI 5, HEME 5, PED 3, SARC 2). The median age was 57.1 years (IQR 45.8-63.4) and 47% were female. There were 39 patients (57%) who were asymptomatic and were tested for routine pre-radiation screening or due to concerns of COVID exposure. Twenty-three (34%) patients were treated with palliative intent and 8 (12%) were treated for an emergent indication (i.e., spinal cord compression, bleeding). Thirteen (19%) patients were receiving radiation treatment, had a treatment break (7-21 days), and then resumed their radiation course. All treatments were successfully completed without known nosocomial spread of COVID to staff or other patients. Among this heterogenous group of patients, 58 (85%) were alive with a median follow up of 2 months (IQR 0.5-7.5). COVID infection may have contributed to 3 out of 10 deaths (4% of total cohort). The remaining deaths were due to progression of disease or other non-COVID causes.

Conclusion

In this study, COVID positive patients were safely treated with radiation therapy through a comprehensive decision making and clinical operations pathway taking into account evolving COVID guidelines for three different variant surges. Although limited in follow up, patient outcomes are promising with few COVID-related deaths and low overall mortality rates, even with hypofractionated regimens.

Trehalose and tardigrade CAHS proteins work synergistically to promote desiccation tolerance

Tardigrades are microscopic animals renowned for their ability to survive extreme desiccation. Unlike many desiccation-tolerant organisms that accumulate high levels of the disaccharide trehalose to protect themselves during drying, tardigrades accumulate little or undetectable levels. Using comparative metabolomics, we find that despite being enriched at low levels, trehalose is a key biomarker distinguishing hydration states of tardigrades. In vitro, naturally occurring stoichiometries of trehalose and CAHS proteins, intrinsically disordered proteins with known protective capabilities, were found to produce synergistic protective effects during desiccation. In vivo, this synergistic interaction is required for robust CAHS-mediated protection. This demonstrates that trehalose acts not only as a protectant, but also as a synergistic cosolute. Beyond desiccation tolerance, our study provides insights into how the solution environment tunes intrinsically disordered proteins’ functions, many of which are vital in biological contexts such as development and disease that are concomitant with large changes in intracellular chemistry.

The disaccharide trehalose is a synergistic cosolute and key biomarker of desiccation tolerance in tardigrades.

Identification of Mitochondrial DNA Variants Associated With Risk of Neuroblastoma

Neuroblastoma is a childhood cancer that originates in the developing sympathetic nervous system. We previously reported a crucial role of mitochondrial DNA haplogroups in the pathology of neuroblastoma. To pinpoint mitochondrial DNA variants associated with neuroblastoma risk, we applied a mitochondrial genome imputation pipeline to the single nucleotide polymorphisms array data of 2 pediatric cohorts containing a total of 2404 neuroblastoma patients and 9310 cancer-free controls. All statistical tests were 2-sided. The single nucleotide variant, rs2853493, was statistically significantly associated with neuroblastoma risk in the discovery cohort (odds ratio = 0.62, 95% confidence interval = 0.53 to 0.72, P < .001) and further confirmed in the replication cohort (odds ratio = 0.75, 95% confidence interval = 0.62 to 0.90, P = .002). Further, expression quantitative trait loci analysis indicated genotypes of rs2853493 were associated with expression levels of MT-CYB gene expression in neuroblastoma cells, suggesting rs2853493 may confer risk to neuroblastoma via regulating the expression level of its nearby genes.

Mutation Burden Analysis of Six Common Mental Disorders in African Americans by Whole Genome Sequencing

Mental disorders present a global health concern, with limited treatment options. In today's medical practice, medications such as antidepressants are prescribed not only for depression, but also for conditions such as anxiety and attention deficit hyperactivity disorder (ADHD). Therefore, identifying gene targets for specific disorders is important and offers improved precision. In this study, we performed a genetic analysis of six common mental disorders, ADHD, anxiety, depression, delays in mental developments, intellectual disabilities (ID), and speech/language disorder in the ethnic minority of African Americans (AA) using whole genome sequencing (WGS). WGS data was generated from blood-derived DNA from 4178 AA individuals, including 1384 patients with the diagnosis of at least one mental disorder. Mutation burden analysis was applied based on rare and deleterious mutations in the AA population between cases and controls, and further analyzed in the context of patients with single mental disorder diagnosis. Certain genes uncovered demonstrated significant p values in mutation burden analysis. In addition, exclusive recurrences in specific type of disorder were scanned through gene-drug interaction databases to assess for availability of potential medications. We uncovered 15 genes harboring deleterious mutations, including HMGCR and UST for ADHD; FNTB for anxiety, XIRP2, NPPC, , STK33, PANX1 and NTS for depression; RUNX3, TACR1, and NDUFS7 for delays in mental developments; HPN for ID; COL6A3, DDB1, and NDUFA11 for speech/language disorder. Taken together, we have established critical insight into the development of new precision medicine approaches for mental disorders in African Americans.

Burden of rare coding variants reveals genetic heterogeneity between obese and non-obese asthma patients in the African American population

Background

Asthma is a complex condition largely attributed to the interactions among genes and environments as a heterogeneous phenotype. Obesity is significantly associated with asthma development, and genetic studies on obese vs. non-obese asthma are warranted.

Methods

To investigate asthma in the minority African American (AA) population with or without obesity, we performed a whole genome sequencing (WGS) study on blood-derived DNA of 4289 AA individuals, included 2226 asthma patients (1364 with obesity and 862 without obesity) and 2006 controls without asthma. The burden analysis of functional rare coding variants was performed by comparing asthma vs. controls and by stratified analysis of obese vs. non-obese asthma, respectively.

Results

Among the top 66 genes with P < 0.01 in the asthma vs. control analysis, stratified analysis by obesity showed inverse correlation of natural logarithm (LN) of P value between obese and non-obese asthma (r = − 0.757, P = 1.90E−13). Five genes previously reported in a genome-wide association study (GWAS) on asthma, including TSLP, SLC9A4, PSMB8, IGSF5, and IKZF4 were demonstrated association in the asthma vs. control analysis. The associations of IKZF4 and IGSF5 are only associated with obese asthma; and the association of SLC9A4 is only observed in non-obese asthma. In addition, the association of RSPH3 (the gene is related to primary ciliary dyskinesia) is observed in non-obese asthma.

Conclusions

These findings highlight genetic heterogeneity between obese and non-obese asthma in patients of AA ancestry.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12931-022-02039-0.

Development and Validation of an Enzyme Immunoassay for Detection and Quantification of SARS-CoV-2 Salivary IgA and IgG

Oral fluids offer a noninvasive sampling method for the detection of Abs. Quantification of IgA and IgG Abs in saliva allows studies of the mucosal and systemic immune response after natural infection or vaccination. We developed and validated an enzyme immunoassay (EIA) to detect and quantify salivary IgA and IgG Abs against the prefusion-stabilized form of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein expressed in suspension-adapted HEK-293 cells. Normalization against total Ab isotype was performed to account for specimen differences, such as collection time and sample volume. Saliva samples collected from 187 SARS-CoV-2 confirmed cases enrolled in 2 cohorts and 373 prepandemic saliva samples were tested. The sensitivity of both EIAs was high (IgA, 95.5%; IgG, 89.7%) without compromising specificity (IgA, 99%; IgG, 97%). No cross-reactivity with endemic coronaviruses was observed. The limit of detection for SARS-CoV-2 salivary IgA and IgG assays were 1.98 ng/ml and 0.30 ng/ml, respectively. Salivary IgA and IgG Abs were detected earlier in patients with mild COVID-19 symptoms than in severe cases. However, severe cases showed higher salivary Ab titers than those with a mild infection. Salivary IgA titers quickly decreased after 6 wk in mild cases but remained detectable until at least week 10 in severe cases. Salivary IgG titers remained high for all patients, regardless of disease severity. In conclusion, EIAs for both IgA and IgG had high specificity and sensitivity for the confirmation of current or recent SARS-CoV-2 infections and evaluation of the IgA and IgG immune response.

Secretion and Uptake of Copper via a Small Copper Carrier in Blood Fluid

Studies with Wilson disease model mice that accumulate excessive copper, due to a dysfunctional ATP7B “copper pump” resulting in decreased biliary excretion, showed that the compensatory increase in urinary copper loss was due to a small copper carrier (∼1 kDa) (SCC). We show here that SCC is also present in the blood plasma of normal and Wilson disease model mice and dogs, as determined by ultrafiltration and size exclusion chromatography (SEC). It is secreted by cultured hepatic and enterocytic cells, as determined by pretreatment with ⁶⁷Cu nitrilotriacetate (NTA) or nonradioactive 5–10 μM Cu-NTA, and collecting and examining 3 kDa ultrafiltrates of the conditioned media, where a single major copper peak is detected by SEC. Four different cultured cell types exposed to the radiolabeled SCC all took up the ⁶⁷Cu at various rates. Rates differed somewhat when uptake was from Cu-NTA. Uptake of SCC-⁶⁷Cu was inhibited by excess nonradioactive Cu(I) or Ag(I) ions, suggesting competition for uptake by copper transporter 1 (CTR1). Knockout of CTR1 in fibroblasts reduced uptake rates by 60%, confirming its participation, but also involvement of other transporters. Inhibitors of endocytosis, or an excess of metal ions taken up by divalent metal transporter 1, did not decrease SCC-⁶⁷Cu uptake. The results imply that SCC may play a significant role in copper transport and homeostasis, transferring copper particularly from the liver (but also intestinal cells) to other cells within the mammalian organism, as well as spilling excess into the urine in copper overload—as an alternative means of copper excretion.

Genetic Analysis for Type 1 Diabetes Genes in Juvenile Dermatomyositis Unveils Genetic Disease Overlap

OBJECTIVES

Juvenile dermatomyositis (JDM) is a serious autoimmune and complex genetic disease. Another autoimmune genetic disease, type 1 diabetes (T1D), has been observed for significantly increased prevalence in families with JDM, while increased JDM risk has also been observed in T1D cases. This study aimed to study whether these two autoimmune diseases, JDM and T1D, share common genetic susceptibility.

METHODS

From 169 JDM families, 121 unrelated cases with European ancestry (EA) were identified by genome-wide genotyping, principal component analysis (PCA), and identical-by-descent (IBD) analysis. T1D genetic risk score (GRS) were calculated in these cases, and were compared with 361 EA T1D cases and 1943 non-diabetes EA controls. 113 cases of the 121 unrelated European cases were sequenced by whole exome sequencing (WES).

RESULTS

We observed increased T1D GRS in JDM cases (P=9.42E-05). Using whole exome sequencing (WES), we uncovered the T1D genes, phospholipase B1 (PLB1), cystic fibrosis transmembrane conductance regulator (CFTR), tyrosine hydroxylase (TH), CD6 molecule (CD6), perforin 1 (PRF1), and dynein axonemal heavy chain 2 (DNAH2), potentially associated with JDM by the burden test of rare functional coding variants.

CONCLUSION

Novel mechanisms of JDM related to these T1D genes are suggested by this study, which may imply novel therapeutic targets for JDM and warrant further study.

Caloric restriction in humans reveals immunometabolic regulators of health span

The extension of life span driven by 40% caloric restriction (CR) in rodents causes trade-offs in growth, reproduction, and immune defense that make it difficult to identify therapeutically relevant CR-mimetic targets. We report that about 14% CR for 2 years in healthy humans improved thymopoiesis and was correlated with mobilization of intrathymic ectopic lipid. CR-induced transcriptional reprogramming in adipose tissue implicated pathways regulating mitochondrial bioenergetics, anti-inflammatory responses, and longevity. Expression of the gene Pla2g7 encoding platelet activating factor acetyl hydrolase (PLA2G7) is inhibited in humans undergoing CR. Deletion of Pla2g7 in mice showed decreased thymic lipoatrophy, protection against age-related inflammation, lowered NLRP3 inflammasome activation, and improved metabolic health. Therefore, the reduction of PLA2G7 may mediate the immunometabolic effects of CR and could potentially be harnessed to lower inflammation and extend the health span.

National attitudes of medical students towards mandating the COVID-19 vaccine and its association with knowledge of the vaccine

Background

With the introduction of the novel COVID-19 vaccine, public hesitancy is being experienced with many turning to healthcare professionals for advice. As future physicians, medical students play a critical role in the public’s view of the vaccine.

Objectives

To determine the attitude of U.S. medical students toward mandating the COVID-19 vaccine to healthcare workers and patients, as well as whether their knowledge of the vaccine plays a role in their view.

Methods

The authors emailed a survey link to all U.S. medical schools with request to distribute it to their medical students. The survey remained open from 02/09/2021 to 03/15/2021 and included questions to determine the attitude of the medical students toward recommending the COVID-19 vaccine, and general knowledge questions about the vaccine. Chi square, Fisher’s exact test, and linear regression were conducted to determine associations between willingness to recommend the COVID-19 vaccine and general knowledge of the vaccine.

Results

Among the 1,899 responses from medical students representing 151 U.S. medical schools, 57.82% approved of making the COVID-19 vaccine mandatory to healthcare workers, and 16.27% approved of making it mandatory to patients. Additionally, those who tested most knowledgeable of the vaccine were less likely to approve of making the vaccine mandatory for patients (66.67% vs. 72.70). Those that tested most knowledgeable were also more likely to personally receive the vaccine (72.35% vs 62.99%) as opposed to those that tested the least knowledgeable who were less willing to personally receive the vaccine (4.12% vs 14.17%).

Conclusions

The data revealed that a slight majority of medical students support a vaccine mandate toward healthcare workers while a minority of medical students support a vaccine mandate toward healthcare workers. Additionally, medical students that had relatively high knowledge of the vaccine correlated with not approving of making the vaccine mandatory for patients. However increased knowledge of the vaccine correlated with increased willingness to personally receive the vaccine.

SURPRISINGLY FEW WOMEN WITH SEVERE OSTEOPOROSIS BY BONE DENSITOMETRY UNDERGO WORKUP FOR SECONDARY CAUSES - A RETROSPECTIVE EVALUATION

We describe clinical features of women with extremely low bone density, and investigate secondary causes of osteoporosis. Our hypothesis was that this population would be enriched in identifiable causes of osteoporosis. We performed a retrospective review of medical records of all women seen at our university over 4 years with T-score on bone densitometry at/below -4 at any site. Historical and fracture details were abstracted. We considered a thorough work up to include Vitamin D, PTH, CBC, chemistry panel, cortisol, transglutaminase, myeloma screen, tryptase and 24-hour urine calcium.

RESULTS

137 women were identified with T-score at/below -4. Percent identified as Asian was 26% (higher than local prevalence of 8%). Average BMI was 21.6 kg/m². Clearly identifiable causes of osteoporosis were noted in 57% (inflammatory disorder, glucocorticoid or antacid exposure, prolonged immobilization and alcoholism were most prevalent). Of the remainder, full work up was performed only in 8%. Endocrine consultation and white race predicted thoroughness of secondary work-up.

CONCLUSION

Fragility fractures, leanness and Asian race were common in women with very low T-score. However, few new causes were identified. Underlying etiology was either immediately evident or inadequately studied, especially in minorities.

Development and validation of an enzyme immunoassay for detection and quantification of SARS-CoV-2 salivary IgA and IgG

Oral fluids offer a non-invasive sampling method for the detection of antibodies. Quantification of IgA and IgG antibodies in saliva allows studies of the mucosal and systemic immune response after natural infection or vaccination. We developed and validated an enzyme immunoassay (EIA) to detect and quantify salivary IgA and IgG antibodies against the prefusion-stabilized form of the SARS-CoV-2 spike protein. Normalization against total antibody isotype was performed to account for specimen differences, such as collection time and sample volume. Saliva samples collected from 187 SARS-CoV-2 confirmed cases enrolled in 2 cohorts and 373 pre-pandemic saliva samples were tested. The sensitivity of both EIAs was high (IgA: 95.5%; IgG: 89.7%) without compromising specificity (IgA: 99%; IgG: 97%). No cross reactivity with seasonal coronaviruses was observed. The limit of detection for SARS-CoV-2 salivary IgA and IgG assays were 1.98 ng/mL and 0.30 ng/mL, respectively. Salivary IgA and IgG antibodies were detected earlier in patients with mild COVID-19 symptoms than in severe cases. However, severe cases showed higher salivary antibody titers than those with a mild infection. Salivary IgA titers quickly decreased after 6 weeks in mild cases but remained detectable until at least week 10 in severe cases. Salivary IgG titers remained high for all patients, regardless of disease severity. In conclusion, EIAs for both IgA and IgG had high specificity and sensitivity for the confirmation of current or recent SARS-CoV-2 infections and evaluation of the IgA and IgG immune response.

Deep learning prediction of attention-deficit hyperactivity disorder in African Americans by copy number variation

Current understanding of the underlying molecular network and mechanism for attention-deficit hyperactivity disorder (ADHD) is lacking and incomplete. Previous studies suggest that genomic structural variations play an important role in the pathogenesis of ADHD. For effective modeling, deep learning approaches have become a method of choice, with ability to predict the impact of genetic variations involving complicated mechanisms. In this study, we examined copy number variation in whole genome sequencing from 116 African Americans ADHD children and 408 African American controls. We divided the human genome into 150 regions, and the variation intensity in each region was applied as feature vectors for deep learning modeling to classify ADHD patients. The accuracy of deep learning for predicting ADHD diagnosis is consistently around 78% in a two-fold shuffle test, compared with ∼50% by traditional k-mean clustering methods. Additional whole genome sequencing data from 351 European Americans children, including 89 ADHD cases and 262 controls, were applied as independent validation using feature vectors obtained from the African American ethnicity analysis. The accuracy of ADHD labeling was lower in this setting (∼70-75%) but still above the results from traditional methods. The regions with highest weight overlapped with the previously reported ADHD-associated copy number variation regions, including genes such as GRM1 and GRM8, key drivers of metabotropic glutamate receptor signaling. A notable discovery is that structural variations in non-coding genomic (intronic/intergenic) regions show prediction weights that can be as high as prediction weight from variations in coding regions, results that were unexpected.

Mitochondrial DNA Haplogroups and Susceptibility to Neuroblastoma

BACKGROUND

Neuroblastoma is a childhood malignancy that arises from the developing sympathetic nervous system. Although mitochondrial dysfunctions have been implicated in the pathophysiology of neuroblastoma, the role of mitochondrial DNA (mtDNA) has not been extensively investigated.

METHODS

A total of 2404 Caucasian children diagnosed with neuroblastoma and 9310 ancestry-matched controls were recruited at the Children's Hospital of Philadelphia. The mtDNA haplogroups were identified from SNP array data of two independent cohorts. We conducted a case-control study to explore potential associations of mtDNA haplogroups with the susceptibility of neuroblastoma. The genetic effect of neuroblastoma was measured by odds ratios (ORs) of mitochondrial haplogroups. All tests were two-sided.

RESULTS

Haplogroup K was statistically significantly associated with reduced risk of neuroblastoma in the discovery cohort consisting of 1474 cases and 5699 controls (OR = 0.72, 95% confidence interval [CI] = 0.57 to 0.90; P = 4.8 × 10-3). The association was replicated in an independent cohort (OR = 0.69, 95% CI = 0.53 to 0.92; P = .01) of 930 cases and 3611 controls. Pooled analysis was performed by combining the two data sets. The association remained highly statistically significant after correction for multiple testing (OR = 0.71, 95% CI = 0.59 to 0.84, P = 1.96 × 10-4, Pcorrected = .002). Further analysis focusing on neuroblastoma subtypes indicated haplogroup K was more associated with high-risk neuroblastoma (OR = 0.57, 95% CI = 0.43 to 0.76; P = 1.46 × 10-4) than low-risk and intermediate-risk neuroblastoma.

CONCLUSIONS

Haplogroup K is an independent genetic factor associated with reduced risk of developing neuroblastoma in European descents. These findings provide new insights into the genetic basis of neuroblastoma, implicating mitochondrial DNA encoded proteins in the etiology of neuroblastoma.

Association of novel rare coding variants with juvenile idiopathic arthritis

OBJECTIVE

Juvenile idiopathic arthritis (JIA) is the most common type of arthritis among children, but a few studies have investigated the contribution of rare variants to JIA. In this study, we aimed to identify rare coding variants associated with JIA for the genome-wide landscape.

METHODS

We established a rare variant calling and filtering pipeline and performed rare coding variant and gene-based association analyses on three RNA-seq datasets composed of 228 JIA patients in the Gene Expression Omnibus against different sets of controls, and further conducted replication in our whole-exome sequencing (WES) data of 56 JIA patients. Then we conducted differential gene expression analysis and assessed the impact of recurrent functional coding variants on gene expression and signalling pathway.

RESULTS

By the RNA-seq data, we identified variants in two genes reported in literature as JIA causal variants, as well as additional 63 recurrent rare coding variants seen only in JIA patients. Among the 44 recurrent rare variants found in polyarticular patients, 10 were replicated by our WES of patients with the same JIA subtype. Several genes with recurrent functional rare coding variants have also common variants associated with autoimmune diseases. We observed immune pathways enriched for the genes with rare coding variants and differentially expressed genes.

CONCLUSION

This study elucidated a novel landscape of recurrent rare coding variants in JIA patients and uncovered significant associations with JIA at the gene pathway level. The convergence of common variants and rare variants for autoimmune diseases is also highlighted in this study.