The Open Pediatric Cancer Project.

Background: In 2019, the Open Pediatric Brain Tumor Atlas (OpenPBTA) was created as a global, collaborative open-science initiative to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Here, we extend the OpenPBTA to create the Open Pediatric Cancer (OpenPedCan) Project, a harmonized open-source multi-omic dataset from 6,112 pediatric cancer patients with 7,096 tumor events across more than 100 histologies. Combined with RNA-Seq from the Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA), OpenPedCan contains nearly 48,000 total biospecimens (24,002 tumor and 23,893 normal specimens). Findings: We utilized Gabriella Miller Kids First (GMKF) workflows to harmonize WGS, WXS, RNA-seq, and Targeted Sequencing datasets to include somatic SNVs, InDels, CNVs, SVs, RNA expression, fusions, and splice variants. We integrated summarized CPTAC whole cell proteomics and phospho-proteomics data, miRNA-Seq data, and have developed a methylation array harmonization workflow to include m-values, beta-vales, and copy number calls. OpenPedCan contains reproducible, dockerized workflows in GitHub, CAVATICA, and Amazon Web Services (AWS) to deliver harmonized and processed data from over 60 scalable modules which can be leveraged both locally and on AWS. The processed data are released in a versioned manner and accessible through CAVATICA or AWS S3 download (from GitHub), and queryable through PedcBioPortal and the NCI's pediatric Molecular Targets Platform. Notably, we have expanded PBTA molecular subtyping to include methylation information to align with the WHO 2021 Central Nervous System Tumor classifications, allowing us to create research- grade integrated diagnoses for these tumors. Conclusions: OpenPedCan data and its reproducible analysis module framework are openly available and can be utilized and/or adapted by researchers to accelerate discovery, validation, and clinical translation.

Drug repositioning identifies salvinorin A and deacetylgedunin (DCG) enriched plant extracts as novel inhibitors of Mpro, RBD-ACE2 and TMPRRS2 proteins.

The coronavirus disease 2019 (COVID-19) has spread worldwide with severe health, social, and economic repercussions. Although vaccines have significantly reduced the severity of symptoms and deaths, alternative medications derived from natural products (NPs) are vital to further decrease fatalities, especially in regions with low vaccine uptake. When paired with the latest computational developments, NPs, which have been used to cure illnesses and infections for thousands of years, constitute a renewed resource for drug discovery. In the present report, a combination of computational and in vitro methods reveals the repositioning of NPs and identifies salvinorin A and deacetylgedunin (DCG) as having potential anti-SARS-CoV-2 activities. Salvinorin A was found both in silico and in vitro to inhibit both SARS-CoV-2 spike/host ACE2 protein interactions, consistent with blocking viral cell entry, and well as live virus replication. Plant extracts from Azadirachta indica and Cedrela odorata, which contain high levels of DCG, inhibited viral cell replication by targeting the main protease (Mpro) and/or inhibited viral cell entry by blocking the interaction between spike RBD-ACE2 protein at concentrations lower than salvinorin A. Our findings suggest that salvinorin A represent promising chemical starting points where further optimization may result in effective natural product-derived and potent anti-SARS-CoV-2 inhibitors to supplement vaccine efforts.

Facilitating Interaction with Police During Routine Traffic Stops for Persons with ASD.

A product of ASD socio-communicative-deficits and insufficient police training related to autism, ASD-police interactions have the potential to become problematic, with negative outcomes for ASD individuals and police alike. Thus, the combination of police acclimation, simulatory experience for drivers with ASD and the introduction of Connecticut's recent Blue Envelope could improve overall experiences for drivers. A simulated routine traffic stop practice event, utilising pre- and post- measures was conducted in an effort to quantify drivers' feelings about current and future interactions with police. Our prediction that participants would experience a statistically significant improvement in anxiety, comfort and self-perceived knowledge levels about future ASD-police interactions immediately following the intervention was confirmed. Our prediction that initially significant disparities between participants with and without police experience - those with previous police encounters versus those that don't - would become not significant immediately following the intervention was disconfirmed. While the longitudinal data suggested that improved post-intervention ASD psychological measures remained statistically significant in the long-term, the sample responses to our long-term questionnaire were too few in number to make any definitive conclusions. It is suggested that practice traffic stops such as these could benefit both drivers with ASD and law enforcement nationwide. It is further suggested that police officer curriculums should include additional training regarding special populations.

Telemetry without collars: performance of fur- and ear-mounted satellite tags for evaluating the movement and behaviour of polar bears.

The study of animal movement provides insights into underlying ecological processes and informs analyses of behaviour and resource use, which have implications for species management and conservation. The tools used to study animal movement have evolved over the past decades, allowing for data collection from a variety of species, including those living in remote environments. Satellite-linked radio and GPS collars have been used to study polar bear (Ursus maritimus) ecology and movements throughout the circumpolar Arctic for over 50 years. However, due to morphology and growth constraints, only adult female polar bears can be reliably collared. Collars have proven to be safe, but there has been opposition to their use, resulting in a deficiency in data across much of the species' range. To bolster knowledge of movement characteristics and behaviours for polar bears other than adult females, while also providing an alternative to collars, we tested the use of fur- and ear-mounted telemetry tags that can be affixed to polar bears of any sex and age. We tested three fur tag designs (SeaTrkr, tribrush and pentagon tags), which we affixed to 15 adult and 1 subadult male polar bears along the coast of Hudson Bay during August-September 2021-2022. Fur tags were compared with ear tags deployed on 42 subadult and adult male polar bears captured on the coast or the sea ice between 2016 and 2022. We used data from the tags to quantify the amount of time subadult and adult males spent resting versus traveling while on land. Our results show the three fur tag designs remained functional for shorter mean durations (SeaTrkr = 58 days; tribrush = 47 days; pentagon = 22 days) than ear tags (121 days), but positional error estimates were comparable among the Argos-equipped tags. The GPS/Iridium-equipped SeaTrkr fur tags provided higher resolution and more frequent location data. Combined, the tags provided sufficient data to model different behavioural states. Furthermore, as hypothesized, subadult and adult male polar bears spent the majority of their time resting while on land, increasing time spent traveling as temperatures cooled. Fur tags show promise as a short-term means of collecting movement data from free-ranging polar bears. Supplementary Information: The online version contains supplementary material available at 10.1186/s40317-024-00373-2.

Growing three-dimensional objects with light.

Vat photopolymerization (VP) additive manufacturing enables fabrication of complex 3D objects by using light to selectively cure a liquid resin. Developed in the 1980s, this technique initially had few practical applications due to limitations in print speed and final part material properties. In the four decades since the inception of VP, the field has matured substantially due to simultaneous advances in light delivery, interface design, and materials chemistry. Today, VP materials are used in a variety of practical applications and are produced at industrial scale. In this perspective, we trace the developments that enabled this printing revolution by focusing on the enabling themes of light, interfaces, and materials. We focus on these fundamentals as they relate to continuous liquid interface production (CLIP), but provide context for the broader VP field. We identify the fundamental physics of the printing process and the key breakthroughs that have enabled faster and higher-resolution printing, as well as production of better materials. We show examples of how in situ print process monitoring methods such as optical coherence tomography can drastically improve our understanding of the print process. Finally, we highlight areas of recent development such as multimaterial printing and inorganic material printing that represent the next frontiers in VP methods.

Advanced Method Optimization for Sampling and Analysis Instrumentation.

This work presents a generalized approach for analytical method optimization that branches the gap between techniques historically employed and accurate modern optimization techniques suitable for various applications. The novelty of the described strategy is the utilization of multivariate, multiobjective optimization with Karush-Kuhn-Tucker conditions to bound the optimization space to solutions within the physical limitations of instrumentation. Briefly, the basic steps outlined in this paper are to (1) determine the objective(s) that should be maximized or minimized based on the goals of the analytical application, (2) conduct a screening experiment, (3) perform ANOVA to determine the parameters which have a statistically significant effect on the objective, (4) conduct an experiment (e.g., Box-Behnken design) to collect data for fitting the objective equation, and (5) determine the physical constraints of the parameters and solve the Lagrangian to determine the optimal method parameters. A broad approach to optimization target selection allows for robust method tuning to develop improved data sets amenable for chemometrics and machine learning algorithm development. Gas chromatography-mass spectrometry was selected as a use case due to its broad use across scientific fields and time-consuming method development involving numerous parameters. This strategy can reduce the cost of research, improve data quality, and enable the rapid development of new analytical techniques.

Association between pelvic lymph node dissection and survival among patients with prostate cancer treated with radical prostatectomy.

Introduction: Although the clinical benefits of pelvic lymph node dissection (PLND) at the time of radical prostatectomy for prostate cancer remain uncertain, major guidelines recommend PLND based on risk profile. Thus, the objective of this study was to examine the association between PLND and survival among patients undergoing RP stratified by Gleason grade group (GG) with the aim of allowing patients and physicians to make more informed care decisions about the potential risks and benefits of PLND. Materials and methods: From the SEER-17 database, we examined overall (OS) and prostate cancer-specific (PCSS) survival of prostate cancer patients who underwent RP from 2010 to 2015 stratified by GG. We applied propensity score matching to balance pre-operative characteristics including race, age, PSA, household income, and housing status (urban/rural) between patients who did and did not undergo PLND for each GG. Statistical analyses included log-rank test and Kaplan-Meier curves. Results: We extracted a matched cohort from 80,287 patients with GG1-5 who underwent RP. The median PSA value was 6.0 ng/mL, and the median age was 62-years-old. 49,453 patients underwent PLND (61.60%), while 30,834 (38.40%) did not. There was no difference in OS and PCSS between patients who received PLND and those who did not for all Gleason GG (OS-GG1: P = 0.20, GG2: P = 0.34, GG3: P > 0.05, GG4: P = 0.55, GG5: P = 0.47; PCSS-GG1: P = 0.11, GG2: P = 0.96, GG3: P = 0.81, GG4: P = 0.22, GG5: P = 0.14). Conclusions: In this observational study, PLND at the time of RP was not associated with improved OS or PCSS among patients with cGS of 3 + 3, 3 + 4, 4 + 3, 4 + 4, 4 + 5, and 5 + 4. These findings suggest that until definitive clinical trials are completed, prostate cancer patients who have elected RP should be appropriately counseled on the potential risks and lack of proven survival benefit of PLND.

A novel pilot study to evaluate the efficacy and safety of a wireless patch system in patients with chronic nausea and vomiting.

BACKGROUND: Gastric sensorimotor disorders (functional dyspepsia [FD] and gastroparesis [GP]) are prevalent and burdensome. Prolonged ambulatory recording using a wireless patch may provide novel information in these patients. METHODS: Consecutive adult patients (age ≥ 18 years) referred for gastric emptying scintigraphy (GES) were eligible for study inclusion. Patients were excluded if they had prior foregut surgery; were taking opioids or other medications known to affect gastric emptying; had a HgbA1C > 10; or were recently hospitalized. Three wireless motility patches were applied to the skin prior to GES. Patients wore the patches for 6 days while recording meals, symptoms, and bowel movements using an iPhone app. KEY RESULTS: Twenty-three consecutive adults (87% women; mean age = 43.9 years; mean BMI = 26.7 kg/m2) were enrolled. A gastric histogram revealed three levels of gastric myoelectric activity: weak, moderate, and strong. Patients with delayed gastric emptying at 4 h had weak gastric myoelectrical activity. Patients with nausea and vomiting had strong intestinal activity. Those with FD had weak gastric and intestinal myoelectric activity, and a weak meal response in the stomach, intestine, and colon compared to those with nausea alone or vomiting alone. CONCLUSIONS AND INFERENCES: Patients with FD, and those with delayed gastric emptying, had unique gastrointestinal myoelectrical activity patterns. Reduced postprandial pan-intestinal myoelectric activity may explain the symptoms of FD in some patients. Recording gastrointestinal activity over a prolonged period in the outpatient setting has the potential to identify unique pathophysiologic patterns and meal-related activity that distinguishes patients with distinct gastric sensorimotor disease states.

Longitudinal measurement invariance and psychometric properties of the Patient Health Questionnaire-Four in China.

BACKGROUND: Depression and anxiety symptoms among medical students are often a concern. The Patient Health Questionnaire-Four (PHQ-4), an important tool for depression and anxiety screening, is commonly used and easy to administer. This study aimed to assess and update the longitudinal measurement invariance and psychometric properties of the simplified Chinese version. METHODS: A three-wave longitudinal survey was conducted among healthcare students using the PHQ-4. Structural validity was based on one-factor, two-factor, and second-order factor models, construct validity was based on the Self-Rated Health Questionnaire (SRHQ), Sleep Quality Questionnaire (SQQ), and Rosenberg Self-Esteem Scale (RSES), and longitudinal measurement invariance (LMI), internal consistency, and test-retest reliability were based on structural consistency across three time points. RESULTS: The results of the confirmatory factor analysis indicated that two-factor model was the best fit, and LMI was supported at three time points. Inter-factor, factor-total, and construct validity correlations of the PHQ-4 were acceptable. Additionally, Cronbach's alpha, McDonald's omega, and the intraclass correlation coefficient demonstrated acceptable/moderate to excellent reliability of the PHQ-4. CONCLUSIONS: This study adds new longitudinal evidence that the Chinese version of the PHQ-4 has promising LMI and psychometric properties. Such data lends confidence to the routine and the expanded use of the PHQ-4 for routine screening of depression and anxiety in Chinese healthcare students.

Monogenic diabetes in children: An underdiagnosed and poorly managed clinical dilemma.

Monogenic diabetes, constituting 1%-2% of global diabetes cases, arises from single gene defects with distinctive inheritance patterns. Despite over 50 ass-ociated genetic disorders, accurate diagnoses and management of monogenic diabetes remain inadequate, underscoring insufficient clinician awareness. The disease spectrum encompasses maturity-onset diabetes of the young (MODY), characterized by distinct genetic mutations affecting insulin secretion, and neonatal diabetes mellitus (NDM) - a heterogeneous group of severe hyperglycemic disorders in infants. Mitochondrial diabetes, autoimmune monogenic diabetes, genetic insulin resistance and lipodystrophy syndromes further diversify the monogenic diabetes landscape. A tailored approach based on phenotypic and biochemical factors to identify candidates for genetic screening is recommended for suspected cases of MODY. NDM diagnosis warrants immediate molecular genetic testing for infants under six months. Identifying these genetic defects presents a unique opportunity for precision medicine. Ongoing research aimed to develop cost-effective genetic testing methods and gene-based therapy can facilitate appropriate identification and optimize clinical outcomes. Identification and study of new genes offer a valuable opportunity to gain deeper insights into pancreatic cell biology and the pathogenic mechanisms underlying common forms of diabetes. The clinical review published in the recent issue of World Journal of Diabetes is such an attempt to fill-in our knowledge gap about this enigmatic disease.

Modified Dunn Procedure for Open Reduction of Chronic Slipped Capital Femoral Epiphysis.

Background: Abnormal femoral head anatomy following moderate-to-severe slipped capital femoral epiphysis (SCFE) can lead to femoroacetabular impingement and premature osteoarthritis4-10. Surgical correction at the deformity site through capital reorientation has the potential to fully ameliorate this but has traditionally been associated with high rates of osteonecrosis11-15. The modified Dunn procedure has the potential to restore anatomy in hips with SCFE while protecting the blood supply to the femoral head. Description: A surgical dislocation of the hip is performed according to the technique described by Ganz et al.16. The remaining posterosuperior portion of the greater trochanter is trimmed to the level of the femoral neck by subperiosteal bone removal performed in an inside-out manner. The periosteum of the femoral neck is gradually elevated. The resulting soft-tissue flap, consisting of the retinaculum and external rotators, holds the blood vessels supplying the epiphysis. The femoral epiphysis is pinned in situ (in unstable cases) with threaded Kirschner wires, the ligamentum teres is transected, and the femoral head is dislocated. With the femoral neck exposed, the epiphysis is gradually mobilized from the metaphysis, allowing exposure of the residual femoral neck and inspection of any posteroinferior callus. To avoid tension on the retinacular vessels during reduction of the epiphysis, the posterior neck callus is completely excised. The remaining physis is removed with use of a burr while holding the epiphysis stable. The epiphysis is gently reduced onto the femoral neck, avoiding tension on the retinacular vessels. If tension is noted, the femoral neck is rechecked for residual callus, which is excised. If no callus is found, the neck may be carefully shortened in order to minimize tension. Epiphyseal fixation is achieved with use of a 3-mm fully threaded wire inserted antegrade through the fovea to the lateral cortex below the greater trochanter. A second wire is inserted retrograde under fluoroscopy. After reducing the hip, the capsule is closed and the greater trochanter is reattached with use of 3.5-mm cortical screws. Alternatives: Alternatives include nonoperative treatment, in situ fixation (e.g., pinning or screw fixation), gentle closed reduction with pinning, and triplanar trochanteric osteotomy (e.g., Imhauser or Southwick osteotomies). Rationale: In situ pinning of mild-to-moderate, stable SCFE yields good long-term results with low rates of osteonecrosis9. Treatment of higher-grade SCFE without reduction aims to avoid osteonecrosis and assumes that the proximal femoral deformity will remodel; however, the head-neck offset will remain abnormal, risking impingement and early-onset osteoarthritis5,8. The procedure described in the present article allows anatomic reduction of the epiphysis with a low risk of osteonecrosis. Surgical dislocation of the hip16 with development of an extended retinacular soft-tissue flap17 provides extensive subperiosteal exposure of the circumferential femoral neck and preserves the vulnerable blood supply to the epiphysis18. The Dunn subcapital realignment procedure15 with callus removal and slip angle correction allows anatomic restoration of the proximal femur. Expected Outcomes: Reported results of various centers performing the procedure vary greatly with regard to the number of hips treated and the follow-up time. Most studies have been retrospective and have lacked a control group. The reported risk of osteonecrosis ranges from 0% to 25.9%19, with the wide range most likely because of the challenging nature of the technique, the low number of cases per surgeon, and the long learning curve associated with the procedure. In centers with extensive experience in pediatric hip-preserving surgery, the reported rate of osteonecrosis is low3. Studies with mid to long-term follow-up have shown no conversion to total hip arthroplasty3,20,21, but residual deformities can persist, and subsequent surgery is possible. Important Tips: Extensive experience in surgical hip dislocation and retinacular flap development is a prerequisite for successful outcomes and low rates of osteonecrosis.Sufficient callus and physeal remnant resections are needed to avoid tension on the retinacular vessels during epiphyseal reduction.The skin incision should be centered over the greater trochanterThe Gibson interval must be carefully prepared for adequate release and to avoid injury.Tension on the periosteal flap should be avoided to prevent stress on the retinacular vessels. Acronyms and Abbreviations: AP = anteroposteriorAVN = avascular necrosis (i.e., osteonecrosis)CI = confidence intervalCT = computed tomographyK-wire = Kirschner wireMRI = magnetic resonance imagingOA = osteoarthritisSHD = surgical hip dislocationTHA = total hip arthroplastyVTE = venous thromboembolism.

EUS-guided hydrogel injection to separate pancreatic head carcinoma from duodenum for enhanced radiotherapy: Multi-site feasibility study.

Background and study aims The proximity of a pancreas head tumor to the duodenum often limits delivery of an ablative dose of radiation therapy. This study evaluated the feasibility and safety of using an injectable polyethylene glycol (PEG) hydrogel between the head of the pancreas and duodenum. Patients and methods In a multi-site feasibility cohort study of patients with localized pancreatic cancer, PEG hydrogel was injected under endoscopic ultrasound guidance to temporarily position the duodenum away from the pancreas. Procedure characteristics were recorded, including hydrogel volume and space created. Patients were monitored for adverse events (AEs) and radiotherapy toxicity. Results In all six intent-to-treat patients (four with borderline resectable, two with locally advanced disease), the ability to place and visualize PEG hydrogel and create space between the duodenum and the head of the pancreas was successful. There were no procedure-related AEs resulting in radiotherapy delay. There were no device-related AEs and no reports of pancreatitis. Conclusions PEG hydrogel was successfully placed, created space between the duodenum and the head of the pancreas, and was not associated with major toxicity. Enhancing radiotherapy for pancreatic cancer by using PEG hydrogel to create peri-duodenal space could have beneficial implications for treatment and warrants more exploration.

Impact of pre-operative abdominal MRI on survival for patients with resected pancreatic carcinoma: a population-based study.

Background: This study determined the impact of pre-operative abdominal MRI on all-cause mortality for patients with resected PDAC. Methods: All adult (≥18 years) PDAC patients who underwent pancreatectomy between January 2011 and December 2022 in Ontario, Canada, were identified for this population-based cohort study (ICD-O-3 codes: C250, C251, C252, C253, C257, C258). Patient demographics, comorbidities, PDAC stage, medical and surgical management, and survival data were sourced from multiple linked provincial administrative databases at ICES. All-cause mortality was compared between patients with and without a pre-operative abdominal MRI after controlling for multiple covariates. Findings: A cohort of 4579 patients consisted of 2432 men (53.1%) and 2147 women (46.9%) with a mean age of 65.2 years (standard deviation: 11.2 years); 2998 (65.5%) died while 1581 (34.5%) survived. Median follow-up duration post-resection was 22.4 months (interquartile range: 10.8-48.8 months), and median survival post-pancreatectomy was 25.9 months (95% confidence interval [95% CI]: 24.8, 27.5). Patients who underwent a pre-operative abdominal MRI had a median survival of 33.1 months (95% CI: 30.7, 37.2) compared to 21.1 months (95% CI: 19.8, 22.6) for all others. A total of 2354/4579 (51.4%) patients underwent a pre-operative abdominal MRI, which was associated with a 17.2% (95% CI: 11.0, 23.1) decrease in the rate of all-cause mortality, with an adjusted hazard ratio (aHR) of 0.828 (95% CI: 0.769, 0.890). Interpretation: Pre-operative abdominal MRI was associated with improved overall survival for PDAC patients who underwent pancreatectomy, possibly due to better detection of liver metastases than CT. Funding: Northern Ontario Academic Medicine Association (NOAMA) Clinical Innovation Fund.

Management of male obesity-related secondary hypogonadism: A clinical update.

The global obesity pandemic has resulted in a rise in the prevalence of male obesity-related secondary hypogonadism (MOSH) with emerging evidence on the role of testosterone therapy. We aim to provide an updated and practical approach towards its management. We did a comprehensive literature search across MEDLINE (via PubMed), Scopus, and Google Scholar databases using the keywords "MOSH" OR "Obesity-related hypogonadism" OR "Testosterone replacement therapy" OR "Selective estrogen receptor modulator" OR "SERM" OR "Guidelines on male hypogonadism" as well as a manual search of references within the articles. A narrative review based on available evidence, recommendations and their practical implications was done. Although weight loss is the ideal therapeutic strategy for patients with MOSH, achievement of significant weight reduction is usually difficult with lifestyle changes alone in real-world practice. Therefore, androgen administration is often necessary in the management of hypogonadism in patients with MOSH which also improves many other comorbidities related to obesity. However, there is conflicting evidence for the appropriate use of testosterone replacement therapy (TRT), and it can also be associated with complications. This evidence-based review updates the available evidence including the very recently published results of the TRAVERSE trial and provides comprehensive clinical practice pearls for the management of patients with MOSH. Before starting testosterone replacement in functional hypogonadism of obesity, it would be desirable to initiate lifestyle modification to ensure weight reduction. TRT should be coupled with the management of other comorbidities related to obesity in MOSH patients. Balancing the risks and benefits of TRT should be considered in every patient before and during long-term management.

Characterizing Lung Parenchymal Aeration via Standardized Signal Intensity from Free-breathing 4D Dynamic MRI in Phantoms, Healthy Children, and Pediatric Patients with Thoracic Insufficiency Syndrome.

Purpose To investigate free-breathing thoracic bright-blood four-dimensional (4D) dynamic MRI (dMRI) to characterize aeration of parenchymal lung tissue in healthy children and patients with thoracic insufficiency syndrome (TIS). Materials and Methods All dMR images in patients with TIS were collected from July 2009 to June 2017. Standardized signal intensity (sSI) was investigated, first using a lung aeration phantom to establish feasibility and sensitivity and then in a retrospective research study of 40 healthy children (16 male, 24 female; mean age, 9.6 years ± 2.1 [SD]), 20 patients with TIS before and after surgery (11 male, nine female; mean age, 6.2 years ± 4.2), and another 10 healthy children who underwent repeated dMRI examinations (seven male, three female; mean age, 9 years ± 3.6). Individual lungs in 4D dMR images were segmented, and sSI was assessed for each lung at end expiration (EE), at end inspiration (EI), preoperatively, postoperatively, in comparison to normal lungs, and in repeated scans. Results Air content changes of approximately 6% were detectable in phantoms via sSI. sSI within phantoms significantly correlated with air occupation (Pearson correlation coefficient = -0.96 [P < .001]). For healthy children, right lung sSI was significantly lower than that of left lung sSI (at EE: 41 ± 6 vs 47 ± 6 and at EI: 39 ± 6 vs 43 ± 7, respectively; P < .001), lung sSI at EI was significantly lower than that at EE (P < .001), and left lung sSI at EE linearly decreased with age (r = -0.82). Lung sSI at EE and EI decreased after surgery for patients (although not statistically significantly, with P values of sSI before surgery vs sSI after surgery, left and right lung separately, in the range of 0.13-0.51). sSI varied within 1.6%-4.7% between repeated scans. Conclusion This study demonstrates the feasibility of detecting change in sSI in phantoms via bright-blood dMRI when air occupancy changes. The observed reduction in average lung sSI after surgery in pediatric patients with TIS may indicate postoperative improvement in parenchymal aeration. Keywords: MR Imaging, Thorax, Lung, Pediatrics, Thoracic Surgery, Lung Parenchymal Aeration, Free-breathing Dynamic MRI, MRI Intensity Standardization, Thoracic Insufficiency Syndrome Supplemental material is available for this article. © RSNA, 2024.

Benzoxazole-derivatives enhance progranulin expression and reverse the aberrant lysosomal proteome caused by GRN haploinsufficiency.

Heterozygous loss-of-function mutations in the GRN gene are a major cause of hereditary frontotemporal dementia. The mechanisms linking frontotemporal dementia pathogenesis to progranulin deficiency are not well understood, and there is currently no treatment. Our strategy to prevent the onset and progression of frontotemporal dementia in patients with GRN mutations is to utilize small molecule positive regulators of GRN expression to boost progranulin levels from the remaining functional GRN allele, thus restoring progranulin levels back to normal within the brain. This work describes a series of blood-brain-barrier-penetrant small molecules which significantly increase progranulin protein levels in human cellular models, correct progranulin protein deficiency in Grn+/- mouse brains, and reverse lysosomal proteome aberrations, a phenotypic hallmark of frontotemporal dementia, more efficiently than the previously described small molecule suberoylanilide hydroxamic acid. These molecules will allow further elucidation of the cellular functions of progranulin and its role in frontotemporal dementia and will also serve as lead structures for further drug development.

Allosensitisation in NHP results in cross-reactive anti-SLA antibodies not detected by a lymphocyte-based flow cytometry crossmatch.

Xenotransplantation is a potential option for individuals for whom an acceptable human allograft is unavailable. Individuals with broadly reactive HLA antibodies due to prior exposure to foreign HLA are potential candidates for a clinical xenotransplant trial. It remains controversial if allosensitisation results in the development of cross-reactive antibodies against SLA. This may require increased histocompatibility scrutiny for highly sensitised individuals prior to enrollment in a clinical trial. Serum samples were obtained from non-human primates sensitised via serial skin transplantation from maximally MHC-mismatched donor, as reported. Sera from pre- and post-allosensitisation timepoints were assessed in a flow crossmatch (FXM) for IgM and IgG binding to pig splenocytes with or without red blood cell adsorption. Xenoreactive antibodies were eluted from pig splenocytes and screened on a single antigen HLA bead assay. A MHC Matchmaker algorithm was developed to predict potential conserved amino acid motifs among the pig, NHP, and human. Our sensitised NHP model was used to demonstrate that allosensitisation does not result in an appreciable difference in xenoreactive antibody binding in a cell-based FXM. However, antibody elution and screening on single antigen HLA beads suggest the existence of potential cross-reactive antibodies against SLA. The cross-reactive IgG after allosensitisation were predicted by comparing the recipient Mamu alleles against its previous allograft donor Mamu alleles and the donor pig SLA alleles. Our study suggests that allosensitisation could elevate cross-reactive antibodies, but a more sensitive assay than a cell-based FXM is required to detect them. The MHC Matchmaker algorithm was developed as a potential tool to help determine amino acid motif conservation and reactivity pattern.

Transcriptome-wide characterization of genetic perturbations.

Single cell CRISPR screens such as Perturb-seq enable transcriptomic profiling of genetic perturbations at scale. However, the data produced by these screens are often noisy due to cost and technical constraints, limiting power to detect true effects with conventional differential expression analyses. Here, we introduce TRanscriptome-wide Analysis of Differential Expression (TRADE), a statistical framework which estimates the transcriptome-wide distribution of true differential expression effects from noisy gene-level measurements. Within TRADE, we derive multiple novel, interpretable statistical metrics, including the "transcriptome-wide impact", an estimator of the overall transcriptional effect of a perturbation which is stable across sampling depths. We analyze new and published large-scale Perturb-seq datasets to show that many true transcriptional effects are not statistically significant, but detectable in aggregate with TRADE. In a genome-scale Perturb-seq screen, we find that a typical gene perturbation affects an estimated 45 genes, whereas a typical essential gene perturbation affects over 500 genes. An advantage of our approach is its ability to compare the transcriptomic effects of genetic perturbations across contexts and dosages despite differences in power. We use this ability to identify perturbations with cell-type dependent effects and to find examples of perturbations where transcriptional responses are not only larger in magnitude, but also qualitatively different, as a function of dosage. Lastly, we expand our analysis to case/control comparison of gene expression for neuropsychiatric conditions, finding that transcriptomic effect correlations are greater than genetic correlations for these diagnoses. TRADE lays an analytic foundation for the systematic comparison of genetic perturbation atlases, as well as differential expression experiments more broadly.