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Abstract Certain corona- and influenza viruses utilize type II transmembrane serine proteases for cell entry, making these enzymes potential drug targets for the treatment of viral respiratory infections. In this study, the cytotoxicity and inhibitory effects of seven matriptase/TMPRSS2 inhibitors (MI-21, MI-463, MI-472, MI-485, MI-1900, MI-1903, and MI-1904) on cytochrome P450 enzymes were evaluated using fluorometric assays. Additionally, their antiviral activity against influenza A virus subtypes H1N1 and H9N2 was assessed. The metabolic depletion rates of these inhibitors in human primary hepatocytes were determined over a 120-min period by LC–MS/MS, and PK parameters were calculated. The tested compounds, with the exception of MI-21, displayed potent inhibition of CYP3A4, while all compounds lacked inhibitory effects on CYP1A2, CYP2C9, CYP2C19, and CYP2D6. The differences between the CYP3A4 activity within the series were rationalized by ligand docking. Elucidation of PK parameters showed that inhibitors MI-463, MI-472, MI-485, MI-1900 and MI-1904 were more stable compounds than MI-21 and MI-1903. Anti-H1N1 properties of inhibitors MI-463 and MI-1900 and anti-H9N2 effects of MI-463 were shown at 20 and 50 µM after 24 h incubation with the inhibitors, suggesting that these inhibitors can be applied to block entry of these viruses by suppressing host matriptase/TMPRSS2-mediated cleavage.

Mental disorders are increasingly understood as involving complex alterations of self that emerge from dynamical interactions of constituent elements, including cognitive, bodily, affective, social, narrative, cultural and normative aspects and processes. An account of self that supports this view is the pattern theory of self (PTS). The PTS is a non-reductive account of the self, consistent with both embodied-enactive cognition and phenomenological psychopathology; it foregrounds the multi-dimensionality of subjects, stressing situated embodiment and intersubjective processes in the formation of the self-pattern. Indications in the literature already demonstrate the viability of the PTS for formulating an alternative methodology to better understand the lived experience of those suffering mental disorders and to guide mental health research more generally. This article develops a flexible methodological framework that front-loads the self-pattern into a minimally structured phenomenological interview. We call this framework ‘Examination of Self Patterns’ (ESP). The ESP is unconstrained by internalist or externalist assumptions about mind and is flexibly guided by person-specific interpretations rather than pre-determined diagnostic categories. We suggest this approach is advantageous for tackling the inherent complexity of mental health, the clinical protocols and the requirements of research.

Background: Moderately hypofractionated radiotherapy regimens or stereotactic body radiotherapy (SBRT) are standard of care for localised prostate cancer. However, some patients are unable or unwilling to travel daily to the radiotherapy department and do not have access to, or are not candidates for, SBRT. For many years, The Royal Marsden Hospital NHS Foundation Trust has offered a weekly ultra-hypofractionated radiotherapy regimen to the prostate (36 Gy in 6 weekly fractions) to patients unable/unwilling to travel daily. Methods: The current study is a retrospective analysis of all patients with non-metastatic localised prostate cancer receiving this treatment schedule from 2010 to 2015. Results: A total of 140 patients were included in the analysis, of whom 86 % presented with high risk disease, with 31 % having Gleason Grade Group 4 or 5 disease and 48 % T3 disease or higher. All patients received hormone treatment, and there was often a long interval between start of hormone treatment and start of radiotherapy (median of 11 months), with 34 % of all patients having progressed to non-metastatic castrate-resistant disease prior to start of radiotherapy. Median follow-up was 52 months. Median progression-free survival (PFS) and overall survival (OS) for the whole group was 70 months and 72 months, respectively. PFS and OS in patients with hormone-sensitive disease at time of radiotherapy was not reached and 75 months, respectively; and in patients with castrate-resistant disease at time of radiotherapy it was 20 months and 61 months, respectively. Conclusion: Our data shows that a weekly ultra-hypofractionated radiotherapy regimen for prostate cancer could be an option in those patients for whom daily treatment or SBRT is not an option.

We extend current models of the halo occupation distribution (HOD) to include a flexible, empirical framework for the forward modeling of the intrinsic alignment (IA) of galaxies. A primary goal of this work is to produce mock galaxy catalogs for the purpose of validating existing models and methods for the mitigation of IA in weak lensing measurements. This technique can also be used to produce new, simulation-based predictions for IA and galaxy clustering. Our model is probabilistically formulated, and rests upon the assumption that the orientations of galaxies exhibit a correlation with their host dark matter (sub)halo orientation or with their position within the halo. We examine the necessary components and phenomenology of such a model by considering the alignments between (sub)halos in a cosmological dark matter only simulation. We then validate this model for a realistic galaxy population in a set of simulations in the Illustris-TNG suite. We create an HOD mock with Illustris-like correlations using our method, constraining the associated IA model parameters, with the $\chi^2_{\rm dof}$ between our model's correlations and those of Illustris matching as closely as 1.4 and 1.1 for orientation--position and orientation--orientation correlation functions, respectively. By modeling the misalignment between galaxies and their host halo, we show that the 3-dimensional two-point position and orientation correlation functions of simulated (sub)halos and galaxies can be accurately reproduced from quasi-linear scales down to $0.1~h^{-1}{\rm Mpc}$. We also find evidence for environmental influence on IA within a halo. Our publicly-available software provides a key component enabling efficient determination of Bayesian posteriors on IA model parameters using observational measurements of galaxy-orientation correlation functions in the highly nonlinear regime.

IntroductionSepsis remains a major cause of mortality and morbidity in infants. In recent years, several gene marker strategies for the early identification of sepsis have been proposed but only a few have been independently validated for adult cohorts and applicability to infant sepsis remains unclear. Biomarkers to assess disease severity and risks of shock also represent an important unmet need.MethodsTo elucidate characteristics driving sepsis in infants, we assembled a multi-transcriptomic dataset from public microarray datasets originating from five independent studies pertaining to bacterial sepsis in infant < 6-months of age (total n=335). We utilized a COmbat co-normalization strategy to enable comparative evaluation across multiple studies while preserving the relationship between cases and controls.ResultsWe found good concordance with only two out of seven of the published adult sepsis gene signatures (accuracy > 80%), highlighting the narrow utility of adult-derived signatures for infant diagnosis. Pseudotime analysis of individual subjects’ gene expression profiles showed a continuum of molecular changes forming tight clusters concurrent with disease progression between healthy controls and septic shock cases. In depth gene expression analyses between bacteremia, septic shock, and healthy controls characterized lymphocyte activity, hemostatic processes, and heightened innate immunity during the molecular transition toward a state of shock.DiscussionOur analysis revealed the presence of multiple significant transcriptomic perturbations that occur during the progression to septic shock in infants that are characterized by late-stage induction of clotting factors, in parallel with a heightened innate immune response and a suppression of adaptive cell functionality.

Purpose: The urethra is a critical structure in prostate radiotherapy planning; however, it is impossible to visualise on CT. We developed a surrogate urethra model (SUM) for CT-only planning workflow and tested its geometric and dosimetric performance against the MRI-delineated urethra (MDU). Methods: The SUM was compared against 34 different MDUs (within the treatment PTV) in patients treated with 36.25Gy (PTV)/40Gy (CTV) in 5 fractions as part of the PACE-B trial. To assess the surrogate's geometric performance, the Dice similarity coefficient (DSC), Hausdorff distance (HD), mean distance to agreement (MDTA) and the percentage of MDU outside the surrogate (UOS) were calculated. To evaluate the dosimetric performance, a paired t-test was used to calculate the mean of differences between the MDU and SUM for the D99, D98, D50, D2 and D1. The D(n) is the dose (Gy) to n% of the urethra. Results: The median results showed low agreement on DSC (0.32; IQR 0.21–0.41), but low distance to agreement, as would be expected for a small structure (HD 8.4mm (IQR 7.1–10.1mm), MDTA 2.4mm (IQR, 2.2mm-3.2mm)). The UOS was 30% (IQR, 18–54%), indicating nearly a third of the urethra lay outside of the surrogate. However, when comparing urethral dose between the MDU and SUM, the mean of differences for D99, D98 and D95 were 0.12Gy (p=0.57), 0.09Gy (p=0.61), and 0.11Gy (p=0.46) respectively. The mean of differences between the D50, D2 and D1 were 0.08Gy (p=0.04), 0.09Gy (p=0.02) and 0.1Gy (p=0.01) respectively, indicating good dosimetric agreement between MDU and SUM. Conclusion: While there were geometric differences between the MDU and SUM, there was no clinically significant difference between urethral dose-volume parameters. This surrogate model could be validated in a larger cohort and then used to estimate the urethral dose on CT planning scans in those without an MRI planning scan or urinary catheter.

When a notable earthquake occurs in the United States, a range of familiar real‐ and near‐real‐time products are produced by the U.S. Geological Survey (USGS) Advanced National Seismic System (ANSS), and made available via the ANSS Comprehensive Earthquake Catalog. For historical and early instrumental earthquakes, similar results and products are developed depending on data availability and event significance, drawing from published later studies. The year 2023 marked the ninetieth anniversary of the 11 March 1933 Long Beach, California, earthquake. This anniversary provided the impetus to update ANSS products, drawing on archived and published data. Here, we describe the updated ShakeMap, shaking recordings and intensities, and retrospective aftershock forecast for the Long Beach, California, earthquake. In effect we have developed standard, modern ANSS products for an earthquake that occurred 90 yr ago. Our results show that the distributions of both the ground motions, anchored by three strong‐motion recordings, and aftershock magnitudes are consistent with expectations for an M 6.4 mainshock in Southern California. We show that, notwithstanding possible limitations, instrumentally recorded accelerations from the closest station are consistent with predicted shaking and directly estimated macroseismic intensities. Updated data products have been added to the USGS event page, where they are available for download. Public‐facing products were also created for the anniversary and are freely available on the USGS website.

Kaposi's sarcoma herpesvirus (KSHV) is a leading cause of malignancy in AIDS and current therapies are limited. Like all herpesviruses, KSHV infection can be latent or lytic. KSHV latency-associated nuclear antigen (LANA) is essential for viral genome persistence during latent infection. LANA also maintains latency by antagonizing expression and function of the KSHV lytic switch protein, RTA. Here, we find LANA null KSHV is not capable of lytic replication, indicating a requirement for LANA. While LANA promoted both lytic and latent gene expression in cells partially permissive for lytic infection, it repressed expression in non-permissive cells. Importantly, forced RTA expression in non-permissive cells led to induction of lytic infection and LANA switched to promote, rather than repress, most lytic viral gene expression. When basal viral gene expression levels were high, LANA promoted expression, but repressed expression at low basal levels unless RTA expression was forcibly induced. LANA's effects were broad, but virus gene specific, extending to an engineered, recombinant viral GFP under control of host EF1α promoter, but not to host EF1α. Together, these results demonstrate that, in addition to its essential role in genome maintenance, LANA broadly regulates viral gene expression, and is required for high levels of lytic gene expression during lytic infection. Strategies that target LANA are expected to abolish KSHV infection.

The outbreak of coronavirus disease 2019 (COVID-19) pandemic strongly stimulated the development of small molecule antivirals selectively targeting type II transmembrane serine proteases (TTSP), required for the host-cell entry of numerous viruses. A set of 3-amidinophenylalanine derivatives (MI-21, MI-472, MI-477, MI-485, MI-1903 and MI-1904), which inhibit the cleavage of certain viral glycoproteins was characterized in 2D and 3D primary human hepatocyte models on collagen- and Matrigel-coating using a CCK-8 assay to evaluate their cytotoxicity, a resorufin-based method to detect redox imbalances, fluorescence and ultrafiltration experiments to evaluate their interactions with human serum albumin (HSA) and α-acidic glycoprotein (AGP), and luminescence measurement to assess CYP3A4 modulation. For elucidation of selectivity of the applied compounds towards matriptase, transmembrane serine protease 2 (TMPRRS2), thrombin and factor Xa (FXa) Ki values were determined. It was proven that cell viability was only deteriorated by inhibitor MI-1903, and redox status was not influenced by administration of the selected inhibitors at 50 µM for 24 h. MI-472 and MI-477 formed relatively stable complexes with AGP. CYP3A4 inhibition was found to be strong in PHHs exposed to all inhibitors with the exception of MI-21, which seems to be a promising drug candidate also due to its better selectivity towards matriptase and TMPRSS2 over the blood clotting proteases thrombin and FXa. Our in vitro pharmacokinetic screening with these inhibitors helps to select the compounds with the best selectivity and safety profile suitable for a further preclinical characterization without animal sacrifice.

First-in-class membrane stabilizer Poloxamer 188 (P188) has been shown to confer membrane protection in an extensive range of clinical conditions; however, elements of the systemic distribution and localization of P188 at the organ, tissue, and muscle fiber levels in vivo have not yet been elucidated. Here we used non-invasive fluorescence imaging to directly visualize and track the distribution and localization of P188 in vivo. The results demonstrated that the Alx647 probe did not alter the fundamental properties of P188 to protect biological membranes. Distribution kinetics in mdx mice demonstrated that Alx647 did not interface with muscle membranes and had fast clearance kinetics. In contrast, the distribution kinetics for P188-Alx647 was significantly slower, indicating a dramatic depot and retention effect of P188. Results further demonstrated the significant retention of P188-Alx647 in the skeletal muscle of mdx mice, showing a significant genotype effect with a higher fluorescence signal in the mdx muscles over BL10 mice. High-resolution optical imaging provided direct evidence of P188 surrounding the sarcolemma of skeletal and cardiac muscle cells. Taken together, these findings provide direct evidence of muscle-disease-dependent molecular homing and retention of synthetic copolymers in striated muscles thereby facilitating advanced studies of copolymer-membrane association in health and disease.

Background Beginning January 26, 2022, the U.S. Medical Licensing Exam (USMLE) Step 1 changed from a numerical score to pass/fail (P/F). The purpose of this study was to determine the perspective of ophthalmology program directors regarding this change in evaluating applicants.

Summary: Kaposi’s sarcoma herpesvirus (KSHV) establishes lifelong infection and persists in latently infected B cells. Paradoxically, in vitro B cell infection is inefficient, and cells rapidly die, suggesting the absence of necessary factor(s). KSHV epidemiology unexpectedly mirrors that of malaria and certain helminthic infections, while other herpesviruses are ubiquitous. Elevated circulating monocytes are common in these parasitic infections. Here, we show that KSHV infection of monocytes or M-CSF-differentiated (M2) macrophages is highly efficient. Proteomic analyses demonstrate that infection induces macrophage production of B cell chemoattractants and activating factor. We find that KSHV acts with monocytes or M2 macrophages to stimulate B cell survival, proliferation, and plasmablast differentiation. Further, macrophages drive infected plasma cell differentiation and long-term viral latency. In Kenya, where KSHV is endemic, we find elevated monocyte levels in children with malaria. These findings demonstrate a role for mononuclear phagocytes in KSHV B cell latency and suggest that mononuclear phagocyte abundance may underlie KSHV’s geographic disparity.

Type 1 diabetes (T1D) is a chronic autoimmune disease characterized by the destruction of insulin-producing pancreatic β-cells by the immune system. Although conventional therapeutic modalities, such as insulin injection, remain a mainstay, recent years have witnessed the emergence of novel treatment approaches encompassing immunomodulatory therapies, such as stem cell and β-cell transplantation, along with revolutionary gene-editing techniques. Notably, recent research endeavors have enabled the reshaping of the T-cell repertoire, leading to the prevention of T1D development. Furthermore, CRISPR–Cas9 technology has demonstrated remarkable potential in targeting endogenous gene activation, ushering in a promising avenue for the precise guidance of mesenchymal stem cells (MSCs) toward differentiation into insulin-producing cells. This innovative approach holds substantial promise for the treatment of T1D. In this review, we focus on studies that have developed T1D models and treatments using gene-editing systems.

Background & Aims: Patterns of liver HBV antigen expression have been described but not quantified at single-cell resolution. We applied quantitative techniques to liver biopsies from individuals with chronic hepatitis B and evaluated sampling heterogeneity, effects of disease stage, and nucleos(t)ide (NUC) treatment, and correlations between liver and peripheral viral biomarkers. Methods: Hepatocytes positive for HBV core and HBsAg were quantified using a novel four-plex immunofluorescence assay and image analysis. Biopsies were analysed from HBeAg-positive (n = 39) and HBeAg-negative (n = 75) participants before and after NUC treatment. To evaluate sampling effects, duplicate biopsies collected at the same time point were compared. Serum or plasma samples were evaluated for levels of HBV DNA, HBsAg, hepatitis B core-related antigen (HBcrAg), and HBV RNA. Results: Diffusely distributed individual HBV core+ cells and foci of HBsAg+ cells were the most common staining patterns. Hepatocytes positive for both HBV core and HBsAg were rare. Paired biopsies revealed large local variation in HBV staining within participants, which was confirmed in a large liver resection. NUC treatment was associated with a >100-fold lower median frequency of HBV core+ cells in HBeAg-positive and HBeAg-negative participants, whereas reductions in HBsAg+ cells were not statistically significant. The frequency of HBV core+ hepatocytes was lower in HBeAg-negative participants than in HBeAg-positive participants at all time points evaluated. Total HBV+ hepatocyte burden correlated with HBcrAg, HBV DNA, and HBV RNA only in baseline HBeAg-positive samples. Conclusions: Reductions in HBV core+ hepatocytes were associated with HBeAg-negative status and NUC treatment. Variation in HBV positivity within individual livers was extensive. Correlations between the liver and the periphery were found only between biomarkers likely indicative of cccDNA (HBV core+ and HBcrAg, HBV DNA, and RNA). Impact and Implications: HBV infects liver hepatocyte cells, and its genome can exist in two forms that express different sets of viral proteins: a circular genome called cccDNA that can express all viral proteins, including the HBV core and HBsAg proteins, or a linear fragment that inserts into the host genome typically to express HBsAg, but not HBV core. We used new techniques to determine the percentage of hepatocytes expressing the HBV core and HBsAg proteins in a large set of liver biopsies. We find that abundance and patterns of expression differ across patient groups and even within a single liver and that NUC treatment greatly reduces the number of core-expressing hepatocytes.

BackgroundPre-exposure prophylaxis (PrEP) is a highly effective biomedical prevention intervention and a major strategy for reducing the HIV burden in the United States. However, PrEP provision and uptake remain lower than estimated needs, and in ways that may exacerbate HIV disparities among Black adolescent girls and young women in the southern United States. Data suggest that gaps in provider knowledge of HIV epidemiology and PrEP and skills assessing sexual health practices are important barriers to provision and uptake, with limited evidence-based interventions to address these gaps. ObjectiveThis paper describes the “PrEP-Pro” intervention, a multicomponent intervention to train and support family medicine (FM) trainees to promote PrEP for adolescent girls and young women in Alabama. MethodsThe PrEP-Pro intervention comprises 3 main components guided by the Capability-Opportunity-Motivation-Behavior (COM-B) model for behavioral change and the Consolidated Framework for Implementation Research (CFIR): (1) provider HIV epidemiology and PrEP education, (2) sexual history taking, and (3) PrEP Champions. In phase 1, we will work with community advisory boards (providers and clients) and then conduct focus groups with FM trainees to adapt content to train FM residents on HIV epidemiology and PrEP and develop implementation strategies, including provider-facing tools and client-facing educational materials. In phase 2, we will pretest and then pilot-test the initially adapted PrEP-Pro intervention with FM trainees. FM trainees will complete baseline, 3-, and 6-month questionnaires post PrEP-Pro intervention. We will also conduct in-depth interviews (IDIs) with FM pilot participants, adolescent girls and young women who accessed care after the PrEP-Pro pilot, and key stakeholders. The primary outcomes are PrEP-Pro acceptability and feasibility, which would be assessed using validated instruments at months 3 (among pretest participants) and 6 (among pilot participants). Secondary outcomes will also be assessed, including PrEP knowledge, sexual history-taking attitudes and practices, PrEP prescriptions among adolescent girls and young women encounters, and sexually transmitted infections (STIs) and HIV testing among adolescent girls and young women encounters in 6 months. ResultsStudy results will be disseminated to practices, state health officials, and other key stakeholders to solicit feedback on implementation opportunities and challenges to inform a hybrid effectiveness implementation trial. Our results will also be presented at local and national conferences and submitted to peer-reviewed journals. ConclusionsAs PrEP grows, there is a pressing need to train FM providers and develop appropriate, contextually relevant tools to support PrEP implementation. The PrEP-Pro intervention is a multicomponent intervention to train FM residents across Alabama on sexual history-taking, PrEP provision for adolescent girls and young women, and supporting practice-based PrEP Champions. The PrEP-Pro intervention is anticipated to increase PrEP prescriptions for adolescent girls and young women and expand comprehensive sexual and reproductive health care for adolescent girls and young women in rural and urban Alabama. International Registered Report Identifier (IRRID)PRR1-10.2196/44908

Introduction The effect of testosterone (T) therapy on the vaginal microbiota of transgender men (TGM) is not well characterised, although one cross-sectional study comparing the vaginal microbiota of cisgender women to TGM on T≥1 year found that, in 71% of the TGM, the vaginal microbiota was less likely to be Lactobacillus-dominated and more likely to be enriched with >30 other bacterial species, many associated with bacterial vaginosis (BV). This prospective study aims to investigate changes in the composition of the vaginal microbiota over time in TGM who retain their natal genitalia (ie, vagina) and initiate T. In addition, we will identify changes in the vaginal microbiota preceding incident BV (iBV) in this cohort while investigating behavioural factors, along with hormonal shifts, which may be associated with iBV.Methods and analysis T-naïve TGM who have not undergone gender-affirming genital surgery with normal baseline vaginal microbiota (ie, no Amsel criteria, normal Nugent Score with no Gardnerella vaginalis morphotypes) will self-collect daily vaginal specimens for 7 days prior to initiating T and for 90 days thereafter. These specimens will be used for vaginal Gram stain, 16S rRNA gene sequencing and shotgun metagenomic sequencing to characterise shifts in the vaginal microbiota over time, including development of iBV. Participants will complete daily diaries on douching, menses and behavioural factors including sexual activity during the study.Ethics and dissemination This protocol is approved through the single Institutional Review Board mechanism by the University of Alabama at Birmingham. External relying sites are the Louisiana State University Health Sciences Center, New Orleans Human Research Protection Program and the Indiana University Human Research Protection Program. Study findings will be presented at scientific conferences and peer-reviewed journals as well as shared with community advisory boards at participating gender health clinics and community-based organisations servicing transgender people.Registration details Protocol # IRB-300008073.

Abstract Background Our study aimed to compare the reference distributions of serum creatinine and urea obtained by direct sampling technique and two indirect sampling techniques including the Gaussian Mixture Model (GMM) and the Self-Organizing Map (SOM) clustering based on clinical laboratory records, so that the feasibility as well as the potential limitations of indirect sampling techniques could be clarified. Methods The direct sampling technique was used in the Pediatric Reference Interval in China (PRINCE) study, in which 15,150 healthy volunteers aged 0 to 19 years were recruited from 11 provinces across China from January 2017 to December 2018. The indirect sampling techniques were used in the Laboratory Information System (LIS) database of Beijing Children’s Hospital, in which 164,710 outpatients were included for partitioning of potential healthy individuals by GMM or SOM from January to December 2016. The reference distributions of creatinine and urea that were established by the PRINCE study and the LIS database were compared. Results The density curves of creatinine and urea based on the PRINCE data and the GMM and SOM partitioned LIS data showed a large overlap. However, deviations were found in reference intervals among the three populations. Conclusions Both GMM and SOM can identify potential healthy individuals from the LIS data. The performance of GMM is consistent and stable. However, GMM relies on Gaussian fitting, and thus is not suitable for skewed data. SOM is applicable for high-dimensional data, and is adaptable to data distribution. But it is susceptible to sample size and outlier detection strategy.

Pediatric brain tumors are the leading cause of cancer-related death in children in the United States and contribute a disproportionate number of potential years of life lost compared to adult cancers. Moreover, survivors frequently suffer long-term side effects, including secondary cancers. The Children's Brain Tumor Network (CBTN) is a multi-institutional international clinical research consortium created to advance therapeutic development through the collection and rapid distribution of biospecimens and data via open-science research platforms for real-time access and use by the global research community. The CBTN's 32 member institutions utilize a shared regulatory governance architecture at the Children's Hospital of Philadelphia to accelerate and maximize the use of biospecimens and data. As of August 2022, CBTN has enrolled over 4700 subjects, over 1500 parents, and collected over 65,000 biospecimen aliquots for research. Additionally, over 80 preclinical models have been developed from collected tumors. Multi-omic data for over 1000 tumors and germline material are currently available with data generation for > 5000 samples underway. To our knowledge, CBTN provides the largest open-access pediatric brain tumor multi-omic dataset annotated with longitudinal clinical and outcome data, imaging, associated biospecimens, child-parent genomic pedigrees, and in vivo and in vitro preclinical models. Empowered by NIH-supported platforms such as the Kids First Data Resource and the Childhood Cancer Data Initiative, the CBTN continues to expand the resources needed for scientists to accelerate translational impact for improved outcomes and quality of life for children with brain and spinal cord tumors.

We describe recent improvements to the Third Uniform California Earthquake Rupture Forecast ETAS Model (UCERF3-ETAS), which continues to represent our most advanced and complete earthquake forecast in terms of relaxing segmentation assumptions and representing multifault ruptures, elastic-rebound effects, and spatiotemporal clustering (the latter to represent aftershocks and otherwise triggered events). The two main improvements include adding aleatory variability in aftershock productivity and the option to represent off-fault events with finite-rupture surfaces. We also summarize the studies that led to these modifications, and reflect on how past and future uses of the model can improve our understanding of earthquake processes and the hazards and risks they pose.

Purpose: This paper aims to deal with the skills for sustainable development in engineering courses. The main objective is to identify which competences should be developed in these courses to contribute to the resolution of conflicts related to sustainability, as well as the means used by universities for their development. Design/methodology/approach: The research is divided into two strands--a theoretical and an empirical one. Concerning the theoretical part, the webibliomining method was adopted, to select the articles that were relevant to the theme, and 22 works were selected. Regarding the empirical study, structured questionnaires were applied to 30 specialists in the field, aiming at validating the competencies found in the literature. Findings: In the literature, eight main competencies required to the engineering professional, related to sustainability, were found. The empirical study showed that some competences are considered more relevant than others by the interviewees. Practical implications: The competencies verified in the present study and the relative relevance between them found in the empirical study can contribute to the engineering courses that wish to develop the sustainable behavior of the engineers in their professional or daily life. Originality/value: The originality of the work consists in presenting to engineering students and teachers as well as professionals of the market and the government the competencies that can contribute to the formation of an engineer capable of bringing adequate solutions to the conflicts of sustainability in the twenty-first century. This paper also presents learning teaching methodologies indicated for this purpose. No other works were found with these results.

Adverse effects associated with overdose of NSAIDs are rarely reported in cattle, and the risk level is unknown. If high doses of NSAIDs can be safely administered to cattle, this may provide a longer duration of analgesia than using current doses where repeated administration is not practical. Meloxicam was administered to 5 mid-lactation Holstein dairy cows orally at 30 mg/kg, which is 30 times higher than the recommended 1 mg/kg oral dose. Plasma and milk meloxicam concentrations were determined using high-pressure liquid chromatography with mass spectroscopy (HPLC-MS). Pharmacokinetic analysis was performed by using noncompartmental analysis. The geometric mean maximum plasma concentration (Cmax) was 91.06 µg/mL at 19.71 h (Tmax), and the terminal elimination half-life (T1/2) was 13.79 h. The geometric mean maximum milk concentration was 33.43 µg/mL at 23.74 h, with a terminal elimination half-life of 12.23 h. A thorough investigation into the potential adverse effects of a meloxicam overdose was performed, with no significant abnormalities reported. The cows were humanely euthanized at 10 d after the treatment, and no gross or histologic lesions were identified. As expected, significantly higher plasma and milk concentrations were attained after the administration of 30 mg/kg meloxicam with similar half-lives to previously published reports. However, no identifiable adverse effects were observed with a drug dose 30 times greater than the industry uses within 10 days of treatment. More research is needed to determine the tissue withdrawal period, safety, and efficacy of meloxicam after a dose of this magnitude in dairy cattle.

AimsOligoprogression is poorly defined in current literature. Little is known about the natural history and significance of oligoprogression in patients with hormone-resistant prostate cancer on abiraterone or enzalutamide treatment [termed androgen receptor-targeted therapy (ARTT)]. The aim of this study was to determine the prevalence of oligoprogression, describe the characteristics of oligoprogression in a cohort of patients from a single center, and identify the number of patients potentially treatable with stereotactic body radiotherapy (SBRT).MethodsCastration-resistant prostate cancer (CRPC) patients who radiologically progressed while on ARTT were included. Patients with oligoprogressive disease (OPD) (≤3 lesions) on any imaging were identified in a retrospective analysis of electronic patient records. Kaplan–Meier method and log-rank test were used to calculate progression-free and overall survival.ResultsA total of 102 patients with metastatic CRPC on ARTT were included. Thirty (29%) patients presented with oligoprogression (46 lesions in total); 21 (21% of total) patients had lesions suitable for SBRT. The majority of lesions were in the bone (21, 46%) or lymph nodes (15, 33%). Patients with oligoprogression while on ARTT had a significantly better prostate-specific antigen (PSA) response on commencing ARTT as compared to patients who later developed polyprogression. However, PSA doubling time immediately prior to progression did not predict OPD. Median progression-free survival to oligoprogression versus polyprogression was 16.8 vs. 11.7 months. Time to further progression after oligoprogression was 13.6 months in those treated with radiotherapy (RT) for oligoprogression vs. 5.7 months in those treated with the continuation of ARTT alone.ConclusionsIn this study, nearly a third of patients on ARTT for CRPC were found to have OPD. OPD patients had a better PSA response on ART and a longer duration on ARTT before developing OPD as compared to those developing polyprogressive disease (Poly-PD). The majority of patients (70%) with OPD had lesions suitable for SBRT treatment. Prospective randomized control trials are needed to establish if there is a survival benefit of SBRT in oligoprogressive prostate cancer and to determine predictive indicators.

Asthma is ranked among the most common chronic conditions and has become a significant public health issue due to the recent and rapid increase in its prevalence. Investigations into the underlying genetic factors predict a heritable component for its incidence, estimated between 35% and 90% of causation. Despite the application of large-scale genome-wide association studies (GWAS) and admixture mapping approaches, the proportion of variants identified accounts for less than 15% of the observed heritability of the disease. The discrepancy between the predicted heritable component of disease and the proportion of heritability mapped to the currently identified susceptibility loci has been termed the ‘missing heritability problem.’ Here, we examine recent studies involving both the analysis of genetically encoded features that contribute to asthma and also the role of non-encoded heritable characteristics, including epigenetic, environmental, and developmental aspects of disease. The importance of vertical maternal microbiome transfer and the influence of maternal immune factors on fetal conditioning in the inheritance of disease are also discussed. In order to highlight the broad array of biological inputs that contribute to the sum of heritable risk factors associated with allergic disease incidence that, together, contribute to the induction of a pro-atopic state. Currently, there is a need to develop in-depth models of asthma risk factors to overcome the limitations encountered in the interpretation of GWAS results in isolation, which have resulted in the missing heritability problem. Hence, multiomics analyses need to be established considering genetic, epigenetic, and functional data to create a true systems biology-based approach for analyzing the regulatory pathways that underlie the inheritance of asthma and to develop accurate risk profiles for disease.

Background & Aims: HBV infects over 257 million people worldwide and is associated with the development of hepatocellular carcinoma (HCC). Integration of HBV DNA into the host genome is likely a key driver of HCC oncogenesis. Here, we utilise targeted long-read sequencing to determine the structure of HBV DNA integrations as well as full isoform information of HBV mRNA with more accurate quantification than traditional next generation sequencing platforms. Methods: DNA and RNA were isolated from fresh frozen liver biopsies collected within the GS-US-174-0149 clinical trial. A pan-genotypic panel of biotinylated oligos was developed to enrich for HBV sequences from sheared genomic DNA (∼7 kb) and full-length cDNA libraries from poly-adenylated RNA. Samples were sequenced on the PacBio long-read platform and analysed using a custom bioinformatic pipeline. Results: HBV-targeted long-read DNA sequencing generated high coverage data spanning entire integrations. Strikingly, in 13 of 42 samples (31%) we were able to detect HBV sequences flanked by 2 different chromosomes, indicating a chromosomal translocation associated with HBV integration. Chromosomal translocations were unique to each biopsy sample, suggesting that each originated randomly, and in some cases had evidence of clonal expansion. Using targeted long-read RNA sequencing, we determined that upwards of 95% of all HBV transcripts in patients who are HBeAg-positive originate from cccDNA. In contrast, patients who are HBeAg-negative expressed mostly HBsAg from integrations. Conclusions: Targeted lso-Seq allowed for accurate quantitation of the HBV transcriptome and assignment of transcripts to either cccDNA or integration origins. The existence of multiple unique HBV-associated inter-chromosomal translocations in non-HCC CHB patient liver biopsies suggests a novel mechanism with mutagenic potential that may contribute to progression to HCC. Lay summary: Fresh frozen liver biopsies from patients infected with HBV were subjected to targeted long-read RNA and DNA sequencing. Long-read RNA sequencing captures entire HBV transcripts in a single read, allowing for resolution of overlapping transcripts from the HBV genome. This resolution allowed us to quantify the burden of transcription from integrations vs. cccDNA origin in individual patients. Patients who were HBeAg-positive had a significantly larger fraction of the HBV transcriptome originating from cccDNA compared with those who were HBeAg-negative. Long-read DNA sequencing captured entire integrated HBV sequences including multiple kilobases of flanking host sequence within single reads. This resolution allowed us to describe integration events flanked by 2 different host chromosomes, indicating that integrated HBV DNA are associated with inter-chromosomal translocations. This may lead to significant transcriptional dysregulation and drive progression to HCC.

BackgroundThe correlation between dietary fatty acid (FA) intake and serum lipid profile levels with cognition in the aged population has been reported by previous studies. However, the association of dietary FA intake and serum lipid profile levels with cognition in subjects with type 2 diabetes mellitus (T2DM) is seldom reported.ObjectiveA cross-sectional study was conducted to explore the correlation between dietary FA intake and serum lipid profiles with cognition in the aged Chinese population with T2DM.MethodsA total of 1,526 aged Chinese subjects were recruited from communities. Fasting blood samples were collected for parameter measurement. The food frequency questionnaire (FFQ) method was applied for a dietary survey. Cognition was assessed using the Montreal Cognitive Assessment (MoCA) test. Dietary FA intake and serum lipid levels were compared between subjects with T2DM and control subjects. A logistic regression analysis was carried out for analyzing the association of FA intake and serum lipid levels with the risk of mild cognitive impairment (MCI) in subjects with T2DM and control subjects.ResultsThere was a significant difference in the serum lipid level between the T2DM group and the control group. Results of the logistic regression analysis demonstrated the potential associations of serum total cholesterol (TC), low-density lipoprotein cholesterol (LDL-c), and dietary n-3 polyunsaturated fatty acids (PUFAs) intake with the risk of MCI in subjects with T2DM, but the associations were not observed in control subjects.ConclusionThe T2DM phenotype might affect the relationship between dietary FA intake, circulating lipids, and cognitive performance. Large prospective cohort studies are needed to uncover the underlying mechanism of how dietary FA intake and serum lipid levels affect cognition in aged subjects with T2DM.

Introduction: Dose escalation to dominant intraprostatic lesions (DILs) is a novel method to increase the therapeutic ratio in localised prostate cancer. The Stereotactic Prostate Augmented Radiotherapy with Cyberknife (SPARC) trial was designed to determine the feasibility of a focal boost defined with multiparametric magnetic resonance imaging (mpMRI) using stereotactic ablative body radiotherapy (SABR). Materials and methods: Patients were included with newly diagnosed intermediate to high risk prostate cancer with at least one of: Gleason score 4 + 3, stage T3a, or PSA > 20 ng/ml. Visible disease on mpMRI was mandatory and up to 2 separate nodules were allowed. All patients received androgen deprivation. Patients received 36.25 Gy in 5 fractions using CyberKnife® and the DIL received a simultaneous boost to a maximum of 47.5 Gy, as allowed by OAR constraints. Genitourinary (GU) and gastrointestinal (GI) toxicity was reported using the RTOG scoring criteria. International Index of Erectile Function (IIEF) and EQ-5D global health scores were regularly captured. Results: An interim safety analysis was performed on the first 8 patients, recruited between July 2013 and December 2015. Median follow up was 56 months (range 50–74). Median D95 values for the prostate PTV and boost volume were 36.55 Gy (range 35.87–36.99) and 46.62 Gy (range 44.85–48.25) respectively. Of the dose constraints, 10/80 were not achieved but all were minor dose variations. Grade 2+ acute GU and GI toxicities were 37.5% respectively while grade 2+ late GU and GI toxicities were 12.5% and 0% respectively. IIEF and quality of life scores recovered over time and all patients remain in biochemical remission. Conclusion: The first patients have been successfully treated with prostate SABR and focal boost on the SPARC trial, with excellent adherence to the planning protocol. Toxicity and efficacy results are promising and further recruitment is underway.

Abstract Background Eravacycline is a novel fluorocycline approved for treatment of intraabdominal infections, with a broad spectrum of activity against a range of pathogens including multidrug-resistant species, including ESBL- or KPC-producing isolates. It is approved for twice-daily dosing with no need for adjustment in renal dysfunction. In the concomitant administration with CYP 3A4-inducing drugs, eravacycline dosing should be modified. Objective To evaluate the efficacy and safety of eravacycline in a range of infections such as intraabdominal infections, pneumonia and diabetic foot infections in seriously ill patients. Methods A retrospective observational cohort study using electronic patient records of 50 consecutive patients administered eravacycline during inpatient acute care admission or as part of outpatient antibiotic therapy (OPAT). Results Therapy of 1.5 mg/kg q24h was initiated in the hospital in most patients, although some of the less sick were managed in the office or OPAT setting. All patients concluded their management outside of the hospital. Of the 50 patients, 47 (94%) achieved clinical resolution of their infection and 3 (6%) clinical failures occurred. Only three (6%) patients did not have comorbidities, three had a single comorbidity (6%), and the majority (88%) of patients had two or more comorbidities. Most common infections were intraabdominal (36%), pneumonia (18%), diabetic foot (12%), spontaneous bacterial peritonitis (8%) and empyema (8%). Almost half of infections had more than one pathogen isolated, and resistant isolates were frequent. The drug was well tolerated with only two reports of nausea, which did not result in treatment discontinuation, and in 30 days of post-eravacycline therapy only one case of Clostridiodes difficile. Conclusions In this real-world setting, eravacycline demonstrated a similar high level of clinical efficacy as seen in clinical trials, 94%, in a variety of infections, including against multidrug-resistant bacteria, and was well tolerated.

Detection of factor VIII (FVIII) in cells by flow cytometry is controversial, and no monoclonal fluorescent antibody is commercially available. In this study, we optimized such an assay and successfully used it as a platform to study the functional properties of phosphoglycerate kinase (PGK)-FVIII lentiviral vector-transduced cells by directly visualizing FVIII in cells after different gene transfer conditions. We could measure cellular stress parameters after transduction by correlating gene expression and protein accumulation data. Flow cytometry performed on transduced cell lines showed that increasing MOI rates resulted in increased protein levels, plateauing after an MOI of 30. We speculated that, at higher MOI, FVIII production could be impaired by a limiting factor required for proper folding. To test this hypothesis, we interfered with the unfolded protein response by blocking proteasomal degradation and measured the accumulation of intracellular misfolded protein. Interestingly, at higher MOIs the cells displayed signs of toxicity with reactive oxygen species accumulation. This suggests the need for identifying a safe window of transduction dose to avoid consequent cell toxicity. Herein, we show that our flow cytometry platform for intracytoplasmic FVIII protein detection is a reliable method for optimizing gene therapy protocols in hemophilia A by shedding light on the functional status of cells after gene transfer.

The digital era highlights industrial advances, changes in the labor market, and in the educational system. This study investigates these factors through analytical indicators such as the workforce, education, and innovation in Brazil within a global context. It is a qualitative exploratory research that enables a reflection on the relations between the workforce and technological education for the skilled labor. The database used includes documentary data from the literature and data from census surveys in Brazil and abroad. Data indicate that Brazil is significantly delayed in the digital industry, human capital, and research – behind all the other BRICS countries (Russia, India, China and South Africa) in terms of innovation. About 11 million people aged 15–29 are not working and are not enrolled in high school, college, technical course, or vocational qualification. The number of students aged 15 to 19 years old attending technical courses is still around 9%. The network of national technical institutes is key for the rapid recomposition of the skilled labor with regard to industry. The Brazilian economy needs to grow to strengthen both the digital industry and research. Public policies need to heed the advice regarding the link between technical education and industry. This is equally important for the success of the Brazilian Agenda for Industry 4.0.

Objectives: Chronotype impacts our state at a given time of day, however, chronotype is also heritable, trait-like, and varies systematically as a function of age and sex. However, only a handful of studies support a relationship between chronotype and trait-like cognitive abilities (i.e., intelligence), and the evidence is sparse and inconsistent between studies. Typically, studies have: (1) focused on limited subjective measures of chronotype, (2) focused on young adults only, and (3) have not considered sex differences. Here, using a combination of cognitive aptitude and ability testing, subjective chronotype, and objective actigraphy, we aimed to explore the relationship between trait-like cognitive abilities and chronotype. Design: Participants (N = 61; 44 females; age = 35.30 ± 18.04 years) completed the Horne-Ostberg Morningness-Eveningness Questionnaire (MEQ) to determine subjective chronotype and wore an activity monitor for 10 days to objectively assess bedtime, rise-time, total sleep time, inter-daily stability, intra-daily variability, and relative amplitude. Cognitive ability (e.g., Verbal, Reasoning and Short-Term Memory) testing took place at the completion of the study. Results: Higher MEQ scores (i.e., more morning) were associated with higher inter-daily stability scores. Superior verbal abilities were associated with later bedtimes, younger age, but paradoxically, higher (i.e., more morning) MEQ scores. Superior STM abilities were associated with younger age only. The relationships between chronotype and trait-like cognitive abilities were similar for both men and women and did not differ between younger and older adults. Conclusions: The present study demonstrates that chronotype, measured by the MEQ, is highly related to inter-daily stability (i.e., the strength of circadian synchronization). Furthermore, although evening types have superior verbal abilities overall, higher (i.e., more morning) MEQ scores were related to superior verbal abilities after controlling for “evening type” behaviours.

Epstein-Barr virus (EBV) is a human herpesvirus that causes infectious mononucleosis and contributes to both B-cell and epithelial-cell malignancies. EBV-infected epithelial cell tumors, including nasopharyngeal carcinoma (NPC), are largely composed of latently infected cells, but the mechanism(s) maintaining viral latency are poorly understood. Expression of the EBV BZLF1 (Z) and BRLF1 (R) encoded immediate-early (IE) proteins induces lytic infection, and these IE proteins activate each other’s promoters. ΔNp63α (a p53 family member) is required for proliferation and survival of basal epithelial cells and is over-expressed in NPC tumors. Here we show that ΔNp63α promotes EBV latency by inhibiting activation of the BZLF1 IE promoter (Zp). Furthermore, we find that another p63 gene splice variant, TAp63α, which is expressed in some Burkitt and diffuse large B cell lymphomas, also represses EBV lytic reactivation. We demonstrate that ΔNp63α inhibits the Z promoter indirectly by preventing the ability of other transcription factors, including the viral IE R protein and the cellular KLF4 protein, to activate Zp. Mechanistically, we show that ΔNp63α promotes viral latency in undifferentiated epithelial cells both by enhancing expression of a known Zp repressor protein, c-myc, and by decreasing cellular p38 kinase activity. Furthermore, we find that the ability of cis-platinum chemotherapy to degrade ΔNp63α contributes to the lytic-inducing effect of this agent in EBV-infected epithelial cells. Together these findings demonstrate that the loss of ΔNp63α expression, in conjunction with enhanced expression of differentiation-dependent transcription factors such as BLIMP1 and KLF4, induces lytic EBV reactivation during normal epithelial cell differentiation. Conversely, expression of ΔNp63α in undifferentiated nasopharyngeal carcinoma cells and TAp63α in Burkitt lymphoma promotes EBV latency in these malignancies. Author summary Epstein-Barr virus (EBV) is an important cause of both epithelial cell and B cell human cancers. EBV-infected tumors have predominantly latent viral infection, allowing them to escape the cell killing that occurs during lytic viral infection. EBV is highly lytic in normal differentiated oral epithelial cells. Thus, an important question is how the virus maintains the latent form of viral infection in EBV-associated epithelial cell tumors such as undifferentiated nasopharyngeal carcinoma (NPC). This study demonstrates that the cellular transcription factor ΔNp63ɑ, which is specifically expressed in undifferentiated basal epithelial cells and is over-expressed in NPC tumors, maintains EBV latency by inhibiting the activity of the viral immediate-early (IE) promoter (Zp) that drives expression of the BZLF1 IE protein. A related splice variant, TAp63α, found in some EBV+ lymphomas, has a similar inhibitory effect. Our findings reveal that ΔNp63ɑ and TAp63α contribute to EBV latency in both epithelial and B cell tumors. Furthermore, since differentiation results in loss of ΔNp63ɑ expression, our results help to explain why lytic EBV reactivation is promoted by epithelial cell differentiation.

The Epstein-Barr virus (EBV) human herpesvirus is associated with B-cell and epithelial-cell malignancies, and both the latent and lytic forms of viral infection contribute to the development of EBV-associated tumors. Here we show that the Hippo signaling effectors, YAP and TAZ, promote lytic EBV reactivation in epithelial cells. The transcriptional co-activators YAP/TAZ (which are inhibited by Hippo signaling) interact with DNA-binding proteins, particularly TEADs, to induce transcription. We demonstrate that depletion of either YAP or TAZ inhibits the ability of phorbol ester (TPA) treatment, cellular differentiation or the EBV BRLF1 immediate-early (IE) protein to induce lytic EBV reactivation in oral keratinocytes, and show that over-expression of constitutively active forms of YAP and TAZ reactivate lytic EBV infection in conjunction with TEAD family members. Mechanistically, we find that YAP and TAZ interact with, and activate, the EBV BZLF1 immediate-early promoter. Furthermore, we demonstrate that YAP, TAZ, and TEAD family members are expressed at much higher levels in epithelial cell lines in comparison to B-cell lines, and find that EBV infection of oral keratinocytes increases the level of activated (dephosphorylated) YAP and TAZ. Finally, we have discovered that lysophosphatidic acid (LPA), a known YAP/TAZ activator that plays an important role in inflammation, induces EBV lytic reactivation in epithelial cells through a YAP/TAZ dependent mechanism. Together these results establish that YAP/TAZ are powerful inducers of the lytic form of EBV infection and suggest that the ability of EBV to enter latency in B cells at least partially reflects the extremely low levels of YAP/TAZ and TEADs in this cell type.

Single-nucleus RNA-seq enables interrogation of complex tissues but is limited due to batch effects and processing costs. Here the authors use barcoded antibodies against the nuclear pore complex to label nuclei from distinct samples, and develop a computational tool to assign the sample of origin.

Abstract Background Chronic rhinosinusitis with nasal polyposis (CRSwNP) is a therapeutic challenge because of the high recurrence rate. Surgical intervention should be considered in patients who fail to improve after medical treatment. We monitored recurrence and revision surgery over 12 years after endoscopic sinus surgery in CRSwNP patients. Methods In this prospective cohort study, 47 patients with CRSwNP, who underwent primary or revision extended endoscopic sinus surgery, were followed. Clinical symptoms and total nasal endoscopic polyp score were evaluated before, 6 years and 12 years after surgery. Results Twelve years after surgery, 38 out of 47 patients (80.9%) were available for examination. There still was a significantly better symptom score and total nasal endoscopic polyp score compared to before surgery (P