A Deuterium-Deuterium Neutron Generator-Based Neutron Capture Therapy System for Brain Tumors

Boron neutron capture therapy (BNCT) is an attractive radiotherapy modality that utilizes high-LET particles to deliver the radiation dose. Different from conventional treatments, BNCT has the ability to target tumor cells by injecting patients with a boron10 (B-10) compound that selectively accumulates inside the tumor and irradiating the target area with a neutron beam. The radiation dose produced is very localized due to the short travel range of the resulting particles and limited to the B-10 containing cells. The surrounding healthy tissues receive minimal dose. At present, the BNCT neutron sources are mainly nuclear reactors and large particle accelerators. These types of neutron sources have high capital expenses, are difficult to maintain and manipulate, require high voltage, and cannot be widely installed in clinical settings. A deuterium-deuterium (DD) neutron generator is a competitive alternative for neutron source due to its low cost, compact size, low acceleration voltage, and relatively simple installation. The objective of this dissertation research is to investigate and design a DD neutron generator-based BNCT system. In the first study, the optimal neutron energy for BNCT of brain tumors at various depths was determined. When the neutron source had an energy in the epithermal range, between 0.5 eV and 10 keV, the dose ratio between the tumor and the brain was maximized. The alpha dose component accounted for approximately 80% of the total tumor dose. As the neutron energy increased to 2.45 MeV, the alpha dose fraction was reduced to 5%. With an epithermal neutron source, 50% of the total brain dose originated from photons while neutrons and alphas contributed to the other 50%. Although higher energy neutrons delivered more dose per source neutron to the tumor, more than 80% of the dose was deposited by neutrons, and the brain received the same amount of dose as the tumor. The benefits of the high-LET particles were reduced because the high-energy neutrons were not thermalized when they reached the tumor site. The second specific aim focused on designing a beam shaping assembly for a DD neutron generator source to moderate the fast DD neutrons and reduce radiation contaminations in the beam. The final optimized layout included a moderator combination of 45-cm Li7 F and 10-cm MgF2, a 30-cm lead reflector, 10-cm lead collimator, and 0.02- cm cadmium filter. The neutron spectrum in air had 9.4 x 104 nepi/cm2 -s, 0.03 for thermalto-epitherml ratio, 5.9 x 10-13 Gy-cm 2 /nepi, and 2.1 x 10-13 Gy-cm 2 /nepi. For the in-phantom evaluation, the advantage depth (AD) was 12.5 cm, the advantage ratio was 4.4, and the dose rate at AD was 2.9 x 10-3 cGy-Eq/min. The maximum skin dose was 0.6 Gy-Eq. The only deficiency of the system was the inadequate neutron flux that DD neutron generators currently produce. Finally, the dose distributions of the designed BNCT system in a cadaver-based phantom were examined in MCNP. The brain obtained a maximum dose of 12.5 Gy-Eq, minimum dose of 1.2 Gy-Eq, and average dose of 5.3 Gy-Eq. Results from this dissertation demonstrated the feasibility of a DD neutron generator-based BNCT system for treatment of brain tumors

A Novel T Cell Receptor Transgenic Animal Model of Seborrheic Dermatitis-Like Skin Disease

We have characterized a novel animal model of the common inflammatory skin disease seborrheic dermatitis (SD) that involves the expression of the self-specific 2C transgenic T cell receptor on the DBA/2 genetic background. Opportunistic fungal pathogens are present in the primary histological lesions and severe disease can be mitigated by the administration of fluconazole, demonstrating a role for infection in disease pathogenesis. Spontaneous disease convalescence occurs at 70–90 d of age and is preceded by an expansion of CD4+ T cells that partially restores the T cell lymphopenia that occurs in these animals. The adoptive transfer of syngeneic CD4+ T cells into pre-diseased DBA/2 2C mice completely abrogates the development of cutaneous disease. The pattern of disease inheritance in DBA/2 backcrosses suggests that one, or a closely linked group of genes, may control disease penetrance. Bone marrow reconstitution experiments demonstrated that the DBA/2 susceptibility factor(s) governing disease penetrance is likely non-hematopoietic since bone marrow from disease-resistant 2C mice can adoptively transfer the full disease phenotype to non-transgenic DBA/2 animals. This model implicates fungal organisms and CD4+ T cell lymphopenia in the development of a SD-like condition and, as such, may mimic the development of SD in acquired immunodeficiency syndrome

PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.

The database of genotypes and phenotypes (dbGaP) developed by the National Center for Biotechnology Information (NCBI) is a resource that contains information on various genome-wide association studies (GWAS) and is currently available via NCBI's dbGaP Entrez interface. The database is an important resource, providing GWAS data that can be used for new exploratory research or cross-study validation by authorized users. However, finding studies relevant to a particular phenotype of interest is challenging, as phenotype information is presented in a non-standardized way. To address this issue, we developed PhenDisco (phenotype discoverer), a new information retrieval system for dbGaP. PhenDisco consists of two main components: (1) text processing tools that standardize phenotype variables and study metadata, and (2) information retrieval tools that support queries from users and return ranked results. In a preliminary comparison involving 18 search scenarios, PhenDisco showed promising performance for both unranked and ranked search comparisons with dbGaP's search engine Entrez. The system can be accessed at http://pfindr.net

Identification of synthetic lethality of PRKDC in MYC-dependent human cancers by pooled shRNA screening

BACKGROUND: MYC family members are among the most frequently deregulated oncogenes in human cancers, yet direct therapeutic targeting of MYC in cancer has been challenging thus far. Synthetic lethality provides an opportunity for therapeutic intervention of MYC-driven cancers. METHODS: A pooled kinase shRNA library screen was performed and next-generation deep sequencing efforts identified that PRKDC was synthetically lethal in cells overexpressing MYC. Genes and proteins of interest were knocked down or inhibited using RNAi technology and small molecule inhibitors, respectively. Quantitative RT-PCR using TaqMan probes examined mRNA expression levels and cell viability was assessed using CellTiter-Glo (Promega). Western blotting was performed to monitor different protein levels in the presence or absence of RNAi or compound treatment. Statistical significance of differences among data sets were determined using unpaired t test (Mann-Whitney test) or ANOVA. RESULTS: Inhibition of PRKDC using RNAi (RNA interference) or small molecular inhibitors preferentially killed MYC-overexpressing human lung fibroblasts. Moreover, inducible PRKDC knockdown decreased cell viability selectively in high MYC-expressing human small cell lung cancer cell lines. At the molecular level, we found that inhibition of PRKDC downregulated MYC mRNA and protein expression in multiple cancer cell lines. In addition, we confirmed that overexpression of MYC family proteins induced DNA double-strand breaks; our results also revealed that PRKDC inhibition in these cells led to an increase in DNA damage levels. CONCLUSIONS: Our data suggest that the synthetic lethality between PRKDC and MYC may in part be due to PRKDC dependent modulation of MYC expression, as well as MYC-induced DNA damage where PRKDC plays a key role in DNA damage repair

Environment-based approaches to improve participation of young people with physical disabilities during COVID-19

Aim: To examine the effects of the Pathways and Resources for Engagement and Participation (PREP) intervention during the COVID-19 pandemic on (1) activity performance and satisfaction, and (2) motor, cognitive, and affective body functions. Method: An interrupted time-series design with multiple baselines across 21 young people (13 females, eight males) aged 16 to 25 years (median = 21 years 5 months) with physical disabilities was employed. The young people engaged in an 8-week self-chosen leisure activity (e.g. football, piano, photography) at their home or community. The Canadian Occupational Performance Measure (COPM) assessed activity performance and satisfaction weekly. Mental health problems, including affective and cognitive outcomes, were assessed weekly using the Behavior Assessment System for Children, Third Edition. Motor functions (e.g. trunk control, reaching, strength) were assessed biweekly. Linear mixed-effects models were used. Results: The intervention had large effects on activity performance (0.78) and satisfaction (0.88) with clinically significant change in COPM scores (2.6 [95% confidence interval {CI}: 2.0–3.2] and 3.2 points [95% CI: 2.4–3.9] respectively). Young people without mental health problems at baseline benefited more from the intervention (p = 0.028). Improvements in at least one domain of body function occurred in 10 young people especially for motor outcomes. Interpretation: Results demonstrate the effectiveness of PREP during adverse times and suggest benefits going beyond participation, involving outcomes at the body-function level. What this paper adds: Environmental-based interventions can improve participation even during adverse times such as the COVID-19 pandemic. Significant improvement with large effect sizes occurred in both activity performance and satisfaction. Intervention was effective for all; those without mental health problems benefited more. Improvements in body-function outcomes were partially observed, especially in motor-related outcomes. Body functions may improve through participation even if not targeted by the intervention

Global Functional Analyses of Cellular Responses to Pore-Forming Toxins

Here we present the first global functional analysis of cellular responses to pore-forming toxins (PFTs). PFTs are uniquely important bacterial virulence factors, comprising the single largest class of bacterial protein toxins and being important for the pathogenesis in humans of many Gram positive and Gram negative bacteria. Their mode of action is deceptively simple, poking holes in the plasma membrane of cells. The scattered studies to date of PFT-host cell interactions indicate a handful of genes are involved in cellular defenses to PFTs. How many genes are involved in cellular defenses against PFTs and how cellular defenses are coordinated are unknown. To address these questions, we performed the first genome-wide RNA interference (RNAi) screen for genes that, when knocked down, result in hypersensitivity to a PFT. This screen identifies 106 genes (∼0.5% of genome) in seven functional groups that protect Caenorhabditis elegans from PFT attack. Interactome analyses of these 106 genes suggest that two previously identified mitogen-activated protein kinase (MAPK) pathways, one (p38) studied in detail and the other (JNK) not, form a core PFT defense network. Additional microarray, real-time PCR, and functional studies reveal that the JNK MAPK pathway, but not the p38 MAPK pathway, is a key central regulator of PFT-induced transcriptional and functional responses. We find C. elegans activator protein 1 (AP-1; c-jun, c-fos) is a downstream target of the JNK-mediated PFT protection pathway, protects C. elegans against both small-pore and large-pore PFTs and protects human cells against a large-pore PFT. This in vivo RNAi genomic study of PFT responses proves that cellular commitment to PFT defenses is enormous, demonstrates the JNK MAPK pathway as a key regulator of transcriptionally-induced PFT defenses, and identifies AP-1 as the first cellular component broadly important for defense against large- and small-pore PFTs

Global age-sex-specific mortality, life expectancy, and population estimates in 204 countries and territories and 811 subnational locations, 1950–2021, and the impact of the COVID-19 pandemic: a comprehensive demographic analysis for the Global Burden of Disease Study 2021

Background: Estimates of demographic metrics are crucial to assess levels and trends of population health outcomes. The profound impact of the COVID-19 pandemic on populations worldwide has underscored the need for timely estimates to understand this unprecedented event within the context of long-term population health trends. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 provides new demographic estimates for 204 countries and territories and 811 additional subnational locations from 1950 to 2021, with a particular emphasis on changes in mortality and life expectancy that occurred during the 2020–21 COVID-19 pandemic period. Methods: 22 223 data sources from vital registration, sample registration, surveys, censuses, and other sources were used to estimate mortality, with a subset of these sources used exclusively to estimate excess mortality due to the COVID-19 pandemic. 2026 data sources were used for population estimation. Additional sources were used to estimate migration; the effects of the HIV epidemic; and demographic discontinuities due to conflicts, famines, natural disasters, and pandemics, which are used as inputs for estimating mortality and population. Spatiotemporal Gaussian process regression (ST-GPR) was used to generate under-5 mortality rates, which synthesised 30 763 location-years of vital registration and sample registration data, 1365 surveys and censuses, and 80 other sources. ST-GPR was also used to estimate adult mortality (between ages 15 and 59 years) based on information from 31 642 location-years of vital registration and sample registration data, 355 surveys and censuses, and 24 other sources. Estimates of child and adult mortality rates were then used to generate life tables with a relational model life table system. For countries with large HIV epidemics, life tables were adjusted using independent estimates of HIV-specific mortality generated via an epidemiological analysis of HIV prevalence surveys, antenatal clinic serosurveillance, and other data sources. Excess mortality due to the COVID-19 pandemic in 2020 and 2021 was determined by subtracting observed all-cause mortality (adjusted for late registration and mortality anomalies) from the mortality expected in the absence of the pandemic. Expected mortality was calculated based on historical trends using an ensemble of models. In location-years where all-cause mortality data were unavailable, we estimated excess mortality rates using a regression model with covariates pertaining to the pandemic. Population size was computed using a Bayesian hierarchical cohort component model. Life expectancy was calculated using age-specific mortality rates and standard demographic methods. Uncertainty intervals (UIs) were calculated for every metric using the 25th and 975th ordered values from a 1000-draw posterior distribution. Findings: Global all-cause mortality followed two distinct patterns over the study period: age-standardised mortality rates declined between 1950 and 2019 (a 62·8% [95% UI 60·5–65·1] decline), and increased during the COVID-19 pandemic period (2020–21; 5·1% [0·9–9·6] increase). In contrast with the overall reverse in mortality trends during the pandemic period, child mortality continued to decline, with 4·66 million (3·98–5·50) global deaths in children younger than 5 years in 2021 compared with 5·21 million (4·50–6·01) in 2019. An estimated 131 million (126–137) people died globally from all causes in 2020 and 2021 combined, of which 15·9 million (14·7–17·2) were due to the COVID-19 pandemic (measured by excess mortality, which includes deaths directly due to SARS-CoV-2 infection and those indirectly due to other social, economic, or behavioural changes associated with the pandemic). Excess mortality rates exceeded 150 deaths per 100 000 population during at least one year of the pandemic in 80 countries and territories, whereas 20 nations had a negative excess mortality rate in 2020 or 2021, indicating that all-cause mortality in these countries was lower during the pandemic than expected based on historical trends. Between 1950 and 2021, global life expectancy at birth increased by 22·7 years (20·8–24·8), from 49·0 years (46·7–51·3) to 71·7 years (70·9–72·5). Global life expectancy at birth declined by 1·6 years (1·0–2·2) between 2019 and 2021, reversing historical trends. An increase in life expectancy was only observed in 32 (15·7%) of 204 countries and territories between 2019 and 2021. The global population reached 7·89 billion (7·67–8·13) people in 2021, by which time 56 of 204 countries and territories had peaked and subsequently populations have declined. The largest proportion of population growth between 2020 and 2021 was in sub-Saharan Africa (39·5% [28·4–52·7]) and south Asia (26·3% [9·0–44·7]). From 2000 to 2021, the ratio of the population aged 65 years and older to the population aged younger than 15 years increased in 188 (92·2%) of 204 nations. Interpretation: Global adult mortality rates markedly increased during the COVID-19 pandemic in 2020 and 2021, reversing past decreasing trends, while child mortality rates continued to decline, albeit more slowly than in earlier years. Although COVID-19 had a substantial impact on many demographic indicators during the first 2 years of the pandemic, overall global health progress over the 72 years evaluated has been profound, with considerable improvements in mortality and life expectancy. Additionally, we observed a deceleration of global population growth since 2017, despite steady or increasing growth in lower-income countries, combined with a continued global shift of population age structures towards older ages. These demographic changes will likely present future challenges to health systems, economies, and societies. The comprehensive demographic estimates reported here will enable researchers, policy makers, health practitioners, and other key stakeholders to better understand and address the profound changes that have occurred in the global health landscape following the first 2 years of the COVID-19 pandemic, and longer-term trends beyond the pandemic

Global burden of 288 causes of death and life expectancy decomposition in 204 countries and territories and 811 subnational locations, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021

BACKGROUND Regular, detailed reporting on population health by underlying cause of death is fundamental for public health decision making. Cause-specific estimates of mortality and the subsequent effects on life expectancy worldwide are valuable metrics to gauge progress in reducing mortality rates. These estimates are particularly important following large-scale mortality spikes, such as the COVID-19 pandemic. When systematically analysed, mortality rates and life expectancy allow comparisons of the consequences of causes of death globally and over time, providing a nuanced understanding of the effect of these causes on global populations. METHODS The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 cause-of-death analysis estimated mortality and years of life lost (YLLs) from 288 causes of death by age-sex-location-year in 204 countries and territories and 811 subnational locations for each year from 1990 until 2021. The analysis used 56 604 data sources, including data from vital registration and verbal autopsy as well as surveys, censuses, surveillance systems, and cancer registries, among others. As with previous GBD rounds, cause-specific death rates for most causes were estimated using the Cause of Death Ensemble model-a modelling tool developed for GBD to assess the out-of-sample predictive validity of different statistical models and covariate permutations and combine those results to produce cause-specific mortality estimates-with alternative strategies adapted to model causes with insufficient data, substantial changes in reporting over the study period, or unusual epidemiology. YLLs were computed as the product of the number of deaths for each cause-age-sex-location-year and the standard life expectancy at each age. As part of the modelling process, uncertainty intervals (UIs) were generated using the 2·5th and 97·5th percentiles from a 1000-draw distribution for each metric. We decomposed life expectancy by cause of death, location, and year to show cause-specific effects on life expectancy from 1990 to 2021. We also used the coefficient of variation and the fraction of population affected by 90% of deaths to highlight concentrations of mortality. Findings are reported in counts and age-standardised rates. Methodological improvements for cause-of-death estimates in GBD 2021 include the expansion of under-5-years age group to include four new age groups, enhanced methods to account for stochastic variation of sparse data, and the inclusion of COVID-19 and other pandemic-related mortality-which includes excess mortality associated with the pandemic, excluding COVID-19, lower respiratory infections, measles, malaria, and pertussis. For this analysis, 199 new country-years of vital registration cause-of-death data, 5 country-years of surveillance data, 21 country-years of verbal autopsy data, and 94 country-years of other data types were added to those used in previous GBD rounds. FINDINGS The leading causes of age-standardised deaths globally were the same in 2019 as they were in 1990; in descending order, these were, ischaemic heart disease, stroke, chronic obstructive pulmonary disease, and lower respiratory infections. In 2021, however, COVID-19 replaced stroke as the second-leading age-standardised cause of death, with 94·0 deaths (95% UI 89·2-100·0) per 100 000 population. The COVID-19 pandemic shifted the rankings of the leading five causes, lowering stroke to the third-leading and chronic obstructive pulmonary disease to the fourth-leading position. In 2021, the highest age-standardised death rates from COVID-19 occurred in sub-Saharan Africa (271·0 deaths [250·1-290·7] per 100 000 population) and Latin America and the Caribbean (195·4 deaths [182·1-211·4] per 100 000 population). The lowest age-standardised death rates from COVID-19 were in the high-income super-region (48·1 deaths [47·4-48·8] per 100 000 population) and southeast Asia, east Asia, and Oceania (23·2 deaths [16·3-37·2] per 100 000 population). Globally, life expectancy steadily improved between 1990 and 2019 for 18 of the 22 investigated causes. Decomposition of global and regional life expectancy showed the positive effect that reductions in deaths from enteric infections, lower respiratory infections, stroke, and neonatal deaths, among others have contributed to improved survival over the study period. However, a net reduction of 1·6 years occurred in global life expectancy between 2019 and 2021, primarily due to increased death rates from COVID-19 and other pandemic-related mortality. Life expectancy was highly variable between super-regions over the study period, with southeast Asia, east Asia, and Oceania gaining 8·3 years (6·7-9·9) overall, while having the smallest reduction in life expectancy due to COVID-19 (0·4 years). The largest reduction in life expectancy due to COVID-19 occurred in Latin America and the Caribbean (3·6 years). Additionally, 53 of the 288 causes of death were highly concentrated in locations with less than 50% of the global population as of 2021, and these causes of death became progressively more concentrated since 1990, when only 44 causes showed this pattern. The concentration phenomenon is discussed heuristically with respect to enteric and lower respiratory infections, malaria, HIV/AIDS, neonatal disorders, tuberculosis, and measles. INTERPRETATION Long-standing gains in life expectancy and reductions in many of the leading causes of death have been disrupted by the COVID-19 pandemic, the adverse effects of which were spread unevenly among populations. Despite the pandemic, there has been continued progress in combatting several notable causes of death, leading to improved global life expectancy over the study period. Each of the seven GBD super-regions showed an overall improvement from 1990 and 2021, obscuring the negative effect in the years of the pandemic. Additionally, our findings regarding regional variation in causes of death driving increases in life expectancy hold clear policy utility. Analyses of shifting mortality trends reveal that several causes, once widespread globally, are now increasingly concentrated geographically. These changes in mortality concentration, alongside further investigation of changing risks, interventions, and relevant policy, present an important opportunity to deepen our understanding of mortality-reduction strategies. Examining patterns in mortality concentration might reveal areas where successful public health interventions have been implemented. Translating these successes to locations where certain causes of death remain entrenched can inform policies that work to improve life expectancy for people everywhere. FUNDING Bill & Melinda Gates Foundation

A Deuterium-Deuterium Neutron Generator-Based Boron Neutron Capture Therapy System for Brain Tumors

Boron neutron capture therapy (BNCT) is an attractive radiotherapy modality that utilizes high-LET particles to deliver the radiation dose. Different from conventional treatments, BNCT has the ability to target tumor cells by injecting patients with a boron-10 (B-10) compound that selectively accumulates inside the tumor and irradiating the target area with a neutron beam. The radiation dose produced is very localized due to the short travel range of the resulting particles and limited to the B-10 containing cells. The surrounding healthy tissues receive minimal dose. At present, the BNCT neutron sources are mainly nuclear reactors and large particle accelerators. These types of neutron sources have high capital expenses, are difficult to maintain and manipulate, require high voltage, and cannot be widely installed in clinical settings. A deuterium-deuterium (DD) neutron generator is a competitive alternative for neutron source due to its low cost, compact size, low acceleration voltage, and relatively simple installation. The objective of this dissertation research is to investigate and design a DD neutron generator-based BNCT system. In the first study, the optimal neutron energy for BNCT of brain tumors at various depths was determined. When the neutron source had an energy in the epithermal range, between 0.5 eV and 10 keV, the dose ratio between the tumor and the brain was maximized. The alpha dose component accounted for approximately 80% of the total tumor dose. As the neutron energy increased to 2.45 MeV, the alpha dose fraction was reduced to 5%. With an epithermal neutron source, 50% of the total brain dose originated from photons while neutrons and alphas contributed to the other 50%. Although higher energy neutrons delivered more dose per source neutron to the tumor, more than 80% of the dose was deposited by neutrons, and the brain received the same amount of dose as the tumor. The benefits of the high-LET particles were reduced because the high-energy neutrons were not thermalized when they reached the tumor site. The second specific aim focused on designing a beam shaping assembly for a DD neutron generator source to moderate the fast DD neutrons and reduce radiation contaminations in the beam. The final optimized layout included a moderator combination of 45-cm Li7F and 10-cm MgF2, a 30-cm lead reflector, 10-cm lead collimator, and 0.02-cm cadmium filter. The neutron spectrum in air had 9.4 x 104 nepi/cm2-s, 0.03 for thermal-to-epitherml ratio, 5.9 x 10-13 Gy-cm2/nepi, and 2.1 x 10-13 Gy-cm2/nepi. For the in-phantom evaluation, the advantage depth (AD) was 12.5 cm, the advantage ratio was 4.4, and the dose rate at AD was 2.9 x 10-3 cGy-Eq/min. The maximum skin dose was 0.6 Gy-Eq. The only deficiency of the system was the inadequate neutron flux that DD neutron generators currently produce. Finally, the dose distributions of the designed BNCT system in a cadaver-based phantom were examined in MCNP. The brain obtained a maximum dose of 12.5 Gy-Eq, minimum dose of 1.2 Gy-Eq, and average dose of 5.3 Gy-Eq. Results from this dissertation demonstrated the feasibility of a DD neutron generator-based BNCT system for treatment of brain tumors