Molecular pathology as basis for timely cancer diagnosis and therapy.

Precision and personalized therapeutics have witnessed significant advancements in technology, revolutionizing the capabilities of laboratories to generate vast amounts of genetic data. Coupled with computational resources for analysis and interpretation, and integrated with various other types of data, including genomic data, electronic medical health (EMH) data, and clinical knowledge, these advancements support optimized health decisions. Among these technologies, next-generation sequencing (NGS) stands out as a transformative tool in the field of cancer treatment, playing a crucial role in precision oncology. NGS-based workflows are employed across a range of applications, including gene panels, exome sequencing, and whole-genome sequencing, supporting comprehensive analysis of the entire cancer genome, including mutations, copy number variations, gene expression profiles, and epigenetic modifications. By utilizing the power of NGS, these workflows contribute to enhancing our understanding of disease mechanisms, diagnosis confirmation, identifying therapeutic targets, and guiding personalized treatment decisions. This manuscript explores the diverse applications of NGS in cancer treatment, highlighting its significance in guiding diagnosis and treatment decisions, identifying therapeutic targets, monitoring disease progression, and improving patient outcomes.

Non-Small Cell Lung Carcinoma With Clear Cell Features and FGFR3::TACC3 Gene Rearrangement : Clinicopathologic and Next Generation Sequencing Study of 7 Cases.

Seven cases of primary lung tumors characterized histologically by clear cell morphology and a distinctive FGFR3::TACC3 gene rearrangement are described. The tumors arose in 4 women and 3 men, aged 47 to 81 years (mean=68). They occurred in peripheral locations, predominantly subpleural, and ranged in size from 1.4 to 6.5 cm (mean=4.1 cm). All tumors showed a solid growth pattern with abundant central areas of necrosis and marked nuclear pleomorphism. The tumors demonstrated clear cell histology, with large cohesive tumor cells displaying atypical nuclei and abundant clear cytoplasm. Immunohistochemical stains identified a squamous phenotype in 5 cases and an adenocarcinoma phenotype in 2 cases. One case was a squamous cell carcinoma with focal glandular component, and one of the squamous cell carcinomas showed focal sarcomatoid changes. Next generation sequencing identified FGFR3::TACC3 gene rearrangements in all 7 cases. One case demonstrated a concurrent activating FGFR3 mutation and a second case demonstrated concurrent FGFR3 amplification. Two cases harbored a concurrent KRAS G12D mutation. One case harbored both KRAS and EGFR mutations, and 1 case had a concurrent TP53 mutation. Non-small cell lung carcinoma harboring FGFR3::TACC3 gene rearrangements is extremely rare, and this rearrangement may potentially be enriched in tumors that demonstrate clear cell histology. Identification of FGFR3::TACC3 in patients with lung carcinomas with clear cell features may be of importance as they could potentially be candidates for therapy with tyrosine kinase inhibitors.

National Diagnostic Working Group (NDWG) for inertial confinement fusion (ICF)/high-energy density (HED) science: The whole exceeds the sum of its parts.

The National Diagnostic Working Group (NDWG) has led the effort to fully exploit the major inertial confinement fusion/high-energy density facilities in the US with the best available diagnostics. These diagnostics provide key data used to falsify early theories for ignition and suggest new theories, recently leading to an experiment that exceeds the Lawson condition required for ignition. The factors contributing to the success of the NDWG, collaboration and scope evolution, and the methods of accomplishment of the NDWG are discussed in this Review. Examples of collaborations in neutron and gamma spectroscopy, x-ray and neutron imaging, x-ray spectroscopy, and deep-ultraviolet Thomson scattering are given. An abbreviated history of the multi-decade collaborations and the present semiformal management framework is given together with the latest National Diagnostic Plan.

Extended X-ray absorption fine structure of dynamically-compressed copper up to 1 terapascal.

Large laser facilities have recently enabled material characterization at the pressures of Earth and Super-Earth cores. However, the temperature of the compressed materials has been largely unknown, or solely relied on models and simulations, due to lack of diagnostics under these challenging conditions. Here, we report on temperature, density, pressure, and local structure of copper determined from extended x-ray absorption fine structure and velocimetry up to 1 Terapascal. These results nearly double the highest pressure at which extended x-ray absorption fine structure has been reported in any material. In this work, the copper temperature is unexpectedly found to be much higher than predicted when adjacent to diamond layer(s), demonstrating the important influence of the sample environment on the thermal state of materials; this effect may introduce additional temperature uncertainties in some previous experiments using diamond and provides new guidance for future experimental design.

A 2-4 keV multilayer mirrored channel for the NIF Dante system.

During inertial confinement fusion experiments at the National Ignition Facility (NIF), a capsule filled with deuterium and tritium (DT) gas, surrounded by a DT ice layer and a high-density carbon ablator, is driven to the temperature and densities required to initiate fusion. In the indirect method, 2 MJ of NIF laser light heats the inside of a gold hohlraum to a radiation temperature of 300 eV; thermal x rays from the hohlraum interior couple to the capsule and create a central hotspot at tens of millions degrees Kelvin and a density of 100-200 g/cm3. During the laser interaction with the gold wall, m-band x rays are produced at ∼2.5 keV; these can penetrate into the capsule and preheat the ablator and DT fuel. Preheat can impact instability growth rates in the ablation front and at the fuel-ablator interface. Monitoring the hohlraum x-ray spectrum throughout the implosion is, therefore, critical; for this purpose, a Multilayer Mirror (MLM) with flat response in the 2-4 keV range has been installed in the NIF 37° Dante calorimeter. Precision engineering and x-ray calibration of components mean the channel will report 2-4 keV spectral power with an uncertainty of ±8.7%.

Evaluation of a workplace suicide prevention program in the Australian manufacturing industry: protocol for a cluster-randomised trial of MATES in manufacturing.

Males are at higher risk of death by suicide than females in Australia, and among men, blue-collar males are at higher risk compared to other working males. In response, MATES in Construction developed a workplace suicide prevention program for the construction sector in 2007 that has been widely implemented in Australia. In the current project, this program is being adapted and trialled in the manufacturing sector. The common aims of MATES programs are to improve suicide prevention literacy, help-seeking intentions, and helping behaviours. The program will be evaluated using a cluster randomised-controlled trial design with waitlist controls across up to 12 manufacturing worksites in Australia. We hypothesise that after 8 months of the MATES in Manufacturing program, there will be significantly greater improvements in help-seeking intentions (primary outcome) compared to waitlist controls. The project is led by Deakin University in collaboration with the University of Melbourne, and in partnership with MATES in Construction and a joint labour-management Steering Group.Trial registration: The trial was registered retrospectively with the Australian New Zealand Clinical Trials Registry on 25 January 2022 (ACTRN12622000122752).Protocol version: 2.0, November 2022.

Protocol for a randomised controlled trial evaluating the effectiveness of a CBT-based smartphone application for improving mental health outcomes in adolescents: the MobiliseMe study.

BACKGROUND: Depression is a leading cause of disability in adolescents, however few receive evidence-based treatment. Despite having the potential to overcome barriers to treatment uptake and adherence, there are very few CBT-based smartphone apps for adolescents. To address this gap, we developed ClearlyMe®, a self-guided CBT smartphone app for adolescent depression and anxiety. ClearlyMe® consists of 37 brief lessons containing core CBT elements, accessed either individually or as part of a 'collection'. Here, we describe the protocol for a randomised controlled trial aiming to evaluate the effect of ClearlyMe® on depressive symptoms and secondary outcomes, including engagement, anxiety and wellbeing, when delivered with and without guided support compared to an attention matched control. METHODS: We aim to recruit 489 adolescents aged 12-17 years with mild to moderately-severe depressive symptoms. Participants will be screened for inclusion, complete the baseline assessment and are then randomly allocated to receive ClearlyMe® (self-directed use), ClearlyMe® with guided SMS support (guided use) or digital psychoeducation (attention-matched control). Depressive symptoms and secondary outcomes will be assessed at 6-weeks (primary endpoint) and 4-months post-baseline (secondary endpoint). Engagement, conceptualised as uptake, adherence and completion, will also be assessed 6-weeks post-baseline. Mixed-effects linear modelling will be used to conduct intention-to-treat analyses to determine whether reductions in depressive symptoms and secondary outcomes are greater for conditions receiving ClearlyMe® relative to control at 6-weeks and 4-months post-baseline and greater for intervention adherers relative to non-adherers. To minimise risk, participants will be encouraged to use the Get Help section of the app and can also opt to receive a call from the team clinical psychologist at baseline, and at the 6-week and 4-month post-baseline assessments when reporting suicidal ideation. DISCUSSION: This is the first clinical trial examining a CBT smartphone app specifically designed for adolescent depression. It will provide empirical evidence on the effects of ClearlyMe® on depressive symptoms when used with and without guided support. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry (ACTRN12622000131752). UNIVERSAL TRIAL NUMBER: U1111-1271-8519.

A combined MeV-neutron and x-ray source for the National Ignition Facility.

In support of future radiation-effects testing, a combined environment source has been developed for the National Ignition Facility (NIF), utilizing both NIF's long-pulse beams, and the Advanced Radiographic Capability (ARC) short pulse lasers. First, ARC was used to illuminate a gold foil at high-intensity, generating a significant x-ray signal >1 MeV. This was followed by NIF 10 ns later to implode an exploding pusher target filled with fusionable gas for neutron generation. The neutron and x-ray bursts were incident onto a retrievable, close-standoff diagnostic snout. With separate control over both neutron and x-ray emission, the platform allows for tailored photon and neutron fluences and timing on a recoverable test sample. The platform exceeded its initial fluence goals, demonstrating a neutron fluence of 2.3 ×1013 n/cm2 and an x-ray dose of 7 krad.

The effectiveness of an Australian community suicide prevention networks program in preventing suicide: a controlled longitudinal study.

BACKGROUND: Suicide is a major issue affecting communities around the world. Community-based suicide prevention approaches can tailor activities at a local level and are recognised as a key component of national suicide prevention strategies. Despite this, research exploring their effects on completed suicides is rare. This study examined the effect of a national program of community suicide prevention networks on suicide rates in catchment areas across Australia. METHODS: Australian suicide data from the National Coronial Information System for 2001-2017 were mapped to geographic catchment areas of community suicide prevention networks and matched control areas with similar characteristics. The effect of network establishment on suicide rates was evaluated using longitudinal models including fixed effects for site type (network or control), time, season, and intervention (network establishment), with site included as a random intercept. RESULTS: Sixty suicide prevention networks were included, servicing areas with a population of 3.5 million. Networks varied in when they were established, ranging from 2007 to 2016. Across the time-period, suicide rates per 100,000 per quarter averaged 3.73 (SD = 5.35). A significant reduction in the suicide rate of 7.0% was found after establishment of networks (IRR = 0.93, 95% CI 0.87 to 0.99, p = .025). CONCLUSION: This study found evidence of an average reduction in suicide rates following the establishment of suicide prevention networks in Australian communities. These findings support the effectiveness of empowering local communities to take action to prevent suicide.

High-yield magnetic recoil neutron spectrometer on the National Ignition Facility for operation up to 60 MJ.

Recent progress at the National Ignition Facility (NIF), with neutron yields of order 1 × 1017, places new constraints on diagnostics used to characterize implosion performance. The Magnetic Recoil neutron Spectrometer (MRS), which is routinely used to measure yield, ion temperature (Tion), and down-scatter ratio (dsr), has been adapted to allow measurements of dsr up to 5 × 1017, and yield and Tion up to 2 × 1018 in the near term with new data processing techniques and conversion foil solutions. This paper presents a solution for extending MRS operation up to a yield of 2 × 1019 (60 MJ) by moving the spectrometer outside of the NIF shield wall. This will not only enhance the upper yield limit by 10× but also improve signal-to-background by 5×.

Phased plan for the implementation of the time-resolving magnetic recoil spectrometer on the National Ignition Facility (NIF).

The time-resolving magnetic recoil spectrometer (MRSt) is a transformative diagnostic that will be used to measure the time-resolved neutron spectrum from an inertial confinement fusion implosion at the National Ignition Facility (NIF). It uses a CD foil on the outside of the hohlraum to convert fusion neutrons to recoil deuterons. An ion-optical system positioned outside the NIF target chamber energy-disperses and focuses forward-scattered deuterons. A pulse-dilation drift tube (PDDT) subsequently dilates, un-skews, and detects the signal. While the foil and ion-optical system have been designed, the PDDT requires more development before it can be implemented. Therefore, a phased plan is presented that first uses the foil and ion-optical systems with detectors that can be implemented immediately-namely CR-39 and hDISC streak cameras. These detectors will allow the MRSt to be commissioned in an intermediate stage and begin collecting data on a reduced timescale, while the PDDT is developed in parallel. A CR-39 detector will be used in phase 1 for the measurement of the time-integrated neutron spectra with excellent energy-resolution, necessary for the energy calibration of the system. Streak cameras will be used in phase 2 for measurement of the time-resolved spectrum with limited spectral coverage, which is sufficient to diagnose the time-resolved ion temperature. Simulations are presented that predict the performance of the streak camera detector, indicating that it will achieve excellent burn history measurements at current yields, and good time-resolved ion-temperature measurements at yields above 3 × 1017. The PDDT will be used for optimal efficiency and resolution in phase 3.

Experimental achievement and signatures of ignition at the National Ignition Facility.

An inertial fusion implosion on the National Ignition Facility, conducted on August 8, 2021 (N210808), recently produced more than a megajoule of fusion yield and passed Lawson's criterion for ignition [Phys. Rev. Lett. 129, 075001 (2022)10.1103/PhysRevLett.129.075001]. We describe the experimental improvements that enabled N210808 and present the first experimental measurements from an igniting plasma in the laboratory. Ignition metrics like the product of hot-spot energy and pressure squared, in the absence of self-heating, increased by ∼35%, leading to record values and an enhancement from previous experiments in the hot-spot energy (∼3×), pressure (∼2×), and mass (∼2×). These results are consistent with self-heating dominating other power balance terms. The burn rate increases by an order of magnitude after peak compression, and the hot-spot conditions show clear evidence for burn propagation into the dense fuel surrounding the hot spot. These novel dynamics and thermodynamic properties have never been observed on prior inertial fusion experiments.

Design of the ion-optics for the MRSt neutron spectrometer at the National Ignition Facility (NIF).

A new Magnetic Recoil Spectrometer (MRSt) is designed to provide time-resolved measurements of the energy spectrum of neutrons emanating from an inertial confinement fusion implosion at the National Ignition Facility. At present, time integrated parameters are being measured using the existing magnet recoil and neutron time-of-flight spectrometers. The capability of high energy resolution of 2 keV and the extension to high time resolution of about 20 ps are expected to improve our understanding of conditions required for successful fusion experiments. The layout, ion-optics, and specifications of the MRSt will be presented.

Epithelioid osteoblastoma. Clinicopathologic and immunohistochemical study of 17 cases.

Seventeen cases of epithelioid osteoblastoma were reviewed. The tumors most commonly arose from the vertebrae (7 cases), followed by the mandible (3), sacrum (2), bones of the foot (2), and femur, rib, and scapula (1 each). Patients' ages ranged from 5 to 33 years. The tumors measured from 2.0 to 6.5 cm in the greatest diameter (mean = 4.1 cm) and most patients presented with low-grade pain at the affected site. Imaging studies showed expansile lytic lesions with cortical thickening and a mild rim of sclerosis. Histologically all tumors were characterized by active production of bone with a fibrovascular stroma containing microtrabecular aggregates of bone matrix. The osteoblastic proliferation was atypical and showed enlarged cells with prominent nucleoli and abundant cytoplasm imparting them with a striking epithelioid appearance. Immunohistochemical studies showed variable results that caused difficulties for interpretation; 4 of 12 cases showed strong nuclear positivity for FOS, 2 of 12 cases showed strong diffuse nuclear positivity for FOSB; the remaining cases showed variable, sometimes overlapping patterns, considered to be indeterminate. Ki-67 proliferation marker showed low nuclear positivity (∼2%) in 10 cases and a slight increase (<10%) in two cases. Clinical follow-up was available in 14 patients; one patient experienced a recurrence at six months that was treated with additional curetting; the remainder of the patients were all alive and well without evidence of recurrence from 1 to 22 years (median follow up = 3 years). Epithelioid osteoblastoma is an unusual variant of osteoblastoma that has the potential for simulating a malignancy and does not appear to be associated with a more aggressive behavior.

Atypical thymomas with squamoid and spindle cell features: clinicopathologic, immunohistochemical and molecular genetic study of 120 cases with long-term follow-up.

Thymomas are rare tumors characterized by a broad range of morphologic appearances that can sometimes give rise to difficulties for classification. We have studied a series of 120 thymoma patients in whom the tumors were characterized by sheets of atypical epithelial cells with squamoid and/or spindle cell features. They occurred in 63 men and 57 women and presented as a discrete mass in the anterior mediastinum measuring 2-23 cm (mean: 8.2 cm). Patients' ages ranged from 14 to 86 years (mean: 57.8) and most had symptoms referable to a mass lesion. 20 patients had myasthenia gravis or other autoimmune disorder. 76 cases were characterized by a predominant population of round to polygonal tumor cells while 32 cases were characterized by atypical oval or spindle cells. 12 cases showed mixed features and 16 cases showed the development of thymic carcinoma arising from thymoma. All cases were positive for p40/p63 and cytokeratin AE1/AE3. 23 cases were positive for CD5 (25%), and 13 for CD117 (14%). MIB1 showed a significant increase in proliferative activity (mean = 11.6%). Next generation sequencing in 47 cases did not disclose any variants amenable to current targeted therapies. Clinical follow up ranging from 2 to 29 years showed a progressive increase in aggressive behavior and fatality rate with advancing stage. Overall survival was 87% at 5 years, 67% at 10 years, and 23% at 20 years. Completeness of resection and staging were the most significant parameters for survival. The more aggressive tumors followed a protracted clinical course with multiple recurrences and metastases over a long period of time (mean = 19.8 years from time of initial relapse to death). Atypical thymomas are a distinct category of thymic epithelial neoplasm characterized by a slowly progressive clinical course with increased potential for metastases, transformation to a higher-grade malignancy, and fatal outcome in some cases.

Solid Thyroid Follicular Nodules With Longitudinal Nuclear Grooves.

CONTEXT.­: Follicular thyroid nodules can be a source of diagnostic difficulties, particularly when they display atypical features commonly associated with malignancy, such as nuclear grooves. OBJECTIVE.­: To differentiate lesions with atypical features from similar-appearing benign and malignant lesions. DESIGN.­: Eighteen cases of atypical follicular thyroid nodules characterized by a solid growth pattern and prominent longitudinal nuclear grooves were studied and examined for clinicopathologic characteristics. RESULTS.­: The lesions occurred in 16 women and 2 men aged 36 to 88 years and measured from 0.2 to 1.5 cm. The tumors were well circumscribed and noninvasive, and histologically characterized by a predominantly solid growth pattern with rare scattered follicles or a combination of solid growth pattern with minor follicular areas. A striking feature seen in all cases was the occurrence of longitudinal nuclear grooves. Immunohistochemical stains showed negativity for cytokeratin 19 (CK19) and HBME-1 in 8 cases; in the other 10, there was focal positivity for HBME-1 in 4 cases and diffuse positivity in 6. All cases were negative for galectin-3 and for CK19, with the exception of 1 case, which was CK19+/HBME-1-. Next-generation sequencing of 16 cases with a 161-gene panel detected 14 single nucleotide variants in 12 cases, predominantly NRAS and HRAS mutations. Clinical follow-up ranging from 18 to 72 months (median, 43.7 months) did not disclose any evidence of recurrence or metastases. CONCLUSIONS.­: We interpret these lesions as low-grade, indolent follicular proliferations that need to be distinguished from papillary thyroid carcinoma, follicular adenoma, and noninvasive follicular thyroid neoplasms with papillary-like nuclear features.

Fear of COVID-19, mental health, and pregnancy outcomes in the pregnancy during the COVID-19 pandemic study: Fear of COVID-19 and pregnancy outcomes.

BACKGROUND: Sustained fear during pregnancy has the potential to increase psychological distress and obstetric risk. This study aimed to (1) identify factors and characteristics associated with fear of COVID-19, (2) investigate the relationship between fear of COVID-19 and maternal anxiety and depression, and (3) determine the relationship between fear of COVID-19 and pregnancy outcomes. METHODS: 9251 pregnant Canadians were recruited between April - December 2020. Participants self-reported (scale of 0-100) the degree of threat they perceived from the SARS-CoV-2 virus in relation to themselves and their unborn baby. RESULTS: Mean fear scores indicated moderate to elevated concern. In multivariable linear regression, fear of COVID-19 was associated with food insecurity, ethnicity, geographic location, history of anxiety prior to pregnancy, having a chronic health condition, pre-pregnancy BMI, parity, and stage of pregnancy at study enrollment. Higher COVID-19 fear was associated with increased odds of depression, adjusted odds ratio (aOR) = 1.75, p < 0.001, 95% CI 1.66-1.85, and anxiety, aOR=2.04, p < 0.001, 95% CI 1.94-2.15). Furthermore, fear of COVID-19 was associated with a 192-gram reduction in infant birthweight, and a 6.1-day reduction in gestational age at birth. LIMITATIONS: The sample has higher education compared to the Canadian population and cannot test causal effects. CONCLUSION: This study suggests that sociodemographic, health, and obstetric factors may contribute to increased fear of COVID-19 and associated adverse psychological and pregnancy outcomes.

Neighbourhood characteristics, lifestyle factors, and child development: Secondary analysis of the All our families cohort study.

Background: Neighbourhood characteristics have been found to influence child development, but little is known about lifestyle factors that may moderate this relationship, which can provide modifiable targets for policies and programing. This study investigated the association between neighbourhood characteristics (e.g., deprivation, disorder) during pregnancy and child development at age 5 in relation to various lifestyle factors (e.g., physical activity, parent-child reading, community resource use) during early childhood. Methods: A secondary analysis was conducted using multilevel modeling of data from the All Our Families cohort, recruited in Canada from 2008 to 2010. Participants self-reported on demographics during pregnancy, lifestyle factors at 3 years, and child development at 5 years using the Ages and Stages Questionnaire (ASQ-3). Neighbourhood deprivation was evaluated using the Vancouver Area Deprivation Index (VANDIX), while disorder was measured using police services' community crime reports. Results: Geocoded information was available for 2,444 participants. After adjusting for covariates, multilevel modeling indicated a significant negative association between neighbourhood deprivation and overall child development (b = -.726, 95% CI: -1.344, -.120). Parent-child reading was found to be a significant moderator of the effect of neighbourhood disorder (b = .005, 95% CI: .001, .009). There were no statistically significant moderation effects for physical activity or community resource use. Conclusion: Neighbourhood deprivation during pregnancy is associated with early child development. Parent-child reading may function as a protective factor in the presence of higher neighbourhood disorder. Overall, neighbourhood-level effects should be considered in policies and community programs that promote family and child well-being.

Observation of Hydrodynamic Flows in Imploding Fusion Plasmas on the National Ignition Facility.

Inertial confinement fusion implosions designed to have minimal fluid motion at peak compression often show significant linear flows in the laboratory, attributable per simulations to percent-level imbalances in the laser drive illumination symmetry. We present experimental results which intentionally varied the mode 1 drive imbalance by up to 4% to test hydrodynamic predictions of flows and the resultant imploded core asymmetries and performance, as measured by a combination of DT neutron spectroscopy and high-resolution x-ray core imaging. Neutron yields decrease by up to 50%, and anisotropic neutron Doppler broadening increases by 20%, in agreement with simulations. Furthermore, a tracer jet from the capsule fill-tube perturbation that is entrained by the hot-spot flow confirms the average flow speeds deduced from neutron spectroscopy.