RCPA: An Open-Source R Package for Data Processing, Differential Analysis, Consensus Pathway Analysis, and Visualization.

Identifying impacted pathways is important because it provides insights into the biology underlying conditions beyond the detection of differentially expressed genes. Because of the importance of such analysis, more than 100 pathway analysis methods have been developed thus far. Despite the availability of many methods, it is challenging for biomedical researchers to learn and properly perform pathway analysis. First, the sheer number of methods makes it challenging to learn and choose the correct method for a given experiment. Second, computational methods require users to be savvy with coding syntax, and comfortable with command-line environments, areas that are unfamiliar to most life scientists. Third, as learning tools and computational methods are typically implemented only for a few species (i.e., human and some model organisms), it is difficult to perform pathway analysis on other species that are not included in many of the current pathway analysis tools. Finally, existing pathway tools do not allow researchers to combine, compare, and contrast the results of different methods and experiments for both hypothesis testing and analysis purposes. To address these challenges, we developed an open-source R package for Consensus Pathway Analysis (RCPA) that allows researchers to conveniently: (1) download and process data from NCBI GEO; (2) perform differential analysis using established techniques developed for both microarray and sequencing data; (3) perform both gene set enrichment, as well as topology-based pathway analysis using different methods that seek to answer different research hypotheses; (4) combine methods and datasets to find consensus results; and (5) visualize analysis results and explore significantly impacted pathways across multiple analyses. This protocol provides many example code snippets with detailed explanations and supports the analysis of more than 1000 species, two pathway databases, three differential analysis techniques, eight pathway analysis tools, six meta-analysis methods, and two consensus analysis techniques. The package is freely available on the CRAN repository. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Processing Affymetrix microarrays Basic Protocol 2: Processing Agilent microarrays Support Protocol: Processing RNA sequencing (RNA-Seq) data Basic Protocol 3: Differential analysis of microarray data (Affymetrix and Agilent) Basic Protocol 4: Differential analysis of RNA-Seq data Basic Protocol 5: Gene set enrichment analysis Basic Protocol 6: Topology-based (TB) pathway analysis Basic Protocol 7: Data integration and visualization.

Evolutionary dynamics of canine kobuvirus in Vietnam and Thailand reveal the evidence of viral ability to evade host immunity.

Canine kobuvirus (CaKoV) is a pathogen associated with canine gastrointestinal disease (GID). This study examined 327 rectal swabs (RS), including 113 from Vietnam (46 healthy, 67 with GID) and 214 from Thailand (107 healthy and 107 with GID). CaKoV was detected in both countries, with prevalences of 28.3% (33/113) in Vietnam and 7.9% (17/214) in Thailand. Additionally, CaKoV was found in both dogs with diarrhea and healthy dogs. CaKoV was mainly found in puppies under six months of age (30.8%). Co-detection with other canine viruses were also observed. The complete coding sequence (CDS) of nine Vietnamese and four Thai CaKoV strains were characterized. Phylogenetic analysis revealed a close genetic relationship between Vietnamese and Thai CaKoV strains, which were related to the Chinese strains. CDS analysis indicated a distinct lineage for two Vietnamese CaKoV strains. Selective pressure analysis on the viral capsid (VP1) region showed negative selection, with potential positive selection sites on B-cell epitopes. This study, the first of its kind in Vietnam, provides insights into CaKoV prevalence in dogs of different ages and healthy statuses, updates CaKoV occurrence in Thailand, and sheds light on its molecular characteristics and immune evasion strategies.

Comparison of the Snare Loop Technique and the Hungaroring Reinforcement for Physician-Modified Endograft Fenestrations-An In Vitro Study.

BACKGROUND: We conducted an in vitro comparison of the snare loop reinforcement against a closed-loop reinforcement (Hungaroring) for physician-modified endograft (PMEG) fenestrations regarding preparation time and stability during flaring balloon dilatation. MATERIALS AND METHODS: The time to complete a PMEG fenestration with reinforcement was measured and compared between the Hungaroring and snare loop groups. The number of stitches was counted. Each fenestration was dilated using a 10 mm high-pressure, non-compliant balloon up to 21 atm in pressure, and fluoroscopic images were taken. The presence of indentation on the oversized balloon at the level of the reinforcement was evaluated at each fenestration. RESULTS: Five fenestrations were created in each group (n = 5) for a total of ten pieces. The completion time in the snare loop group was 1070 s (IQR:1010-1090) compared to 760 s (IQR:685-784) in the Hungaroring group (p = 0.008). Faster completion time was achieved by faster stitching (23.2 s/stitch (IQR 22.8-27.3) for the snare loop group and 17.3 s/stitch (IQR 17.3-20.1) for the Hungaroring group (p = 0.016). None of the fluoroscopic images of the snare loop reinforcement showed an indentation on the balloon during the overexpansion; on the contrary, the Hungaroring showed indentation in every case, even at 21 atm. CONCLUSION: Fenestrations reinforced with Hungaroring can be completed significantly faster. Furthermore, the Hungaroring resists over-dilation even at high pressures, while snare loop reinforcements dilate at nominal pressure.

Changing global epidemiology of chronic hepatitis C virus-related outcomes from 2010 to 2019: cirrhosis is the growing burden of hepatitis C virus-related disease.

BACKGROUND: Chronic infection with hepatitis C virus (HCV) has a long-term impact on hepatic consequences. A comprehensive evaluation of the global burden of HCV-related health outcomes can help to develop a global HCV prevention and treatment program. METHODS: We used the 2019 Global Burden of Disease (GBD) Study to comprehensively investigate burden and temporal trends in incidence, mortality and disability-adjusted life-years (DALYs) of HCV-related diseases, including liver cancer and cirrhosis and other liver diseases across 264 countries and territories from 2010 to 2019. RESULTS: Globally, there were 152 225 incident cases, 141 811 deaths and approximately 2.9 million DALYs because of HCV-related liver cancer, and 551 668 incident cases, 395 022 deaths and about 12.2 million DALYs because of HCV-related cirrhosis in 2019. Worldwide, during the 2010-2019 period, liver cancer incidence declined, however, there was a 62% increase in cirrhosis incidence. In 2019, the Eastern Mediterranean was the region with the highest rates of incidence and mortality of both liver cancer and cirrhosis. Africa was the region with the fastest-growing trend of incidence of cirrhosis in the 2010-2019 period [annual percentage change (APC) = 2.09, 95% confidence interval (CI): 1.93-2.25], followed by the Western Pacific region (APC = 1.17, 95% CI: 1.09-1.22). Americas were the only region observing increased trends in liver cancer and cirrhosis mortality (APC = 0.70 and 0.12, respectively). We identified three patterns of temporal trends of mortality rates of liver cancer and cirrhosis in countries that reported HCV treatment rates. CONCLUSION: Urgent measures are required for diagnosis, treatment and research on HCV-related cirrhosis at global, regional and country levels, particularly in Africa, the Western Pacific and the Eastern Mediterranean.

Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges.

Single-cell RNA sequencing (scRNA-Seq) is a recent technology that allows for the measurement of the expression of all genes in each individual cell contained in a sample. Information at the single-cell level has been shown to be extremely useful in many areas. However, performing single-cell experiments is expensive. Although cellular deconvolution cannot provide the same comprehensive information as single-cell experiments, it can extract cell-type information from bulk RNA data, and therefore it allows researchers to conduct studies at cell-type resolution from existing bulk datasets. For these reasons, a great effort has been made to develop such methods for cellular deconvolution. The large number of methods available, the requirement of coding skills, inadequate documentation, and lack of performance assessment all make it extremely difficult for life scientists to choose a suitable method for their experiment. This paper aims to fill this gap by providing a comprehensive review of 53 deconvolution methods regarding their methodology, applications, performance, and outstanding challenges. More importantly, the article presents a benchmarking of all these 53 methods using 283 cell types from 30 tissues of 63 individuals. We also provide an R package named DeconBenchmark that allows readers to execute and benchmark the reviewed methods (https://github.com/tinnlab/DeconBenchmark).

Field-programmable gate array-based residual amplitude modulation suppression and control for compact atomic clocks.

We designed a field-programmable gate array (FPGA) fabric to provide phase modulation techniques to lock lasers to optical frequency references. The method incorporates an active residual amplitude modulation (RAM) suppression scheme that relies on complex modulation. All the required servos to construct an optical atomic clock are incorporated into the same low-cost, commercial FPGA chip. We demonstrate a reliable, long-term RAM suppression of 60 dB with the remaining RAM level at -100 dBc and an improved stability of three decades when applied on a two-photon rubidium clock.

Acyltransferase families that act on thioesters: Sequences, structures, and mechanisms.

Acyltransferases (AT) are enzymes that catalyze the transfer of acyl group to a receptor molecule. This review focuses on ATs that act on thioester-containing substrates. Although many ATs can recognize a wide variety of substrates, sequence similarity analysis allowed us to classify the ATs into fifteen distinct families. Each AT family is originated from enzymes experimentally characterized to have AT activity, classified according to sequence similarity, and confirmed with tertiary structure similarity for families that have crystallized structures available. All the sequences and structures of the AT families described here are present in the thioester-active enzyme (ThYme) database. The AT sequences and structures classified into families and available in the ThYme database could contribute to enlightening the understanding acyl transfer to thioester-containing substrates, most commonly coenzyme A, which occur in multiple metabolic pathways, mostly with fatty acids.

Canine bufavirus (Carnivore protoparvovirus-3) infection in dogs with respiratory disease.

Canine bufavirus (CBuV) or Carnivore protoparvovirus-3, a nonenveloped DNA virus belonging to the genus Protoparvovirus, family Parvoviridae, has been identified in dogs with respiratory and enteric diseases. Although CBuV detection has been reported in multiple countries, descriptions of pathologic findings associated with infection have not yet been provided. In this study, the authors necropsied 14 dogs (12 puppies and 2 adult dogs) from a breeding colony that died during multiple outbreaks of respiratory diseases. Postmortem investigations revealed extensive bronchointerstitial pneumonia with segmental type II pneumocyte hyperplasia in all necropsied puppies but less severe lesions in adults. With negative results of common pathogen detection by ancillary testing, CBuV DNA was identified in all investigated dogs using a polymerase chain reaction (PCR). Quantitative PCR demonstrated CBuV DNA in several tissues, and in situ hybridization (ISH) indicated CBuV tissue localization in the lung, tracheobronchial lymph node, and spinal cord, suggesting hematogenous spread. Dual CBuV ISH and cellular-specific immunohistochemistry were used to determine the cellular tropism of the virus in the lung and tracheobronchial lymph node, demonstrating viral localization in various cell types, including B-cells, macrophages, and type II pneumocytes, but not T-cells. Three complete CBuV sequences were successfully characterized and revealed that they clustered with the CBuV sequences obtained from dogs with respiratory disease in Hungary. No additional cases were identified in small numbers of healthy dogs. Although association of the bufavirus with enteric disease remains to be determined, a contributory role of CBuV in canine respiratory disease is possible.

Photocatalyzed [2σ + 2σ] and [2σ + 2π] Cycloadditions for the Synthesis of Bicyclo[3.1.1]heptanes and 5- or 6-Membered Carbocycles.

We report the use of photocatalysis for the homolytic ring-opening of carbonyl cyclopropanes. In contrast to previous studies, our approach does not require a metal cocatalyst or a strong reductant. The carbonyl cyclopropanes can be employed for both [2σ + 2σ] and [2σ + 2π] annulation with either alkenes/alkynes or bicyclo[1.1.0]butanes, yielding cyclopent-anes/-enes and bicyclo[3.1.1]heptanes (BCHs), respectively. BCHs are promising bioisosteres for 1,2,4,5 tetra-substituted aromatic rings. Mechanistic studies, including density functional theory computation and a trapping experiment with DMPO, support a 1,3-biradical generated from cyclopropane as a key intermediate for these transformations.

A novel approach for predicting upstream regulators (PURE) that affect gene expression.

External factors such as exposure to a chemical, drug, or toxicant (CDT), or conversely, the lack of certain chemicals can cause many diseases. The ability to identify such causal CDTs based on changes in the gene expression profile is extremely important in many studies. Furthermore, the ability to correctly infer CDTs that can revert the gene expression changes induced by a given disease phenotype is a crucial step in drug repurposing. We present an approach for Predicting Upstream REgulators (PURE) designed to tackle this challenge. PURE can correctly infer a CDT from the measured expression changes in a given phenotype, as well as correctly identify drugs that could revert disease-induced gene expression changes. We compared the proposed approach with four classical approaches as well as with the causal analysis used in Ingenuity Pathway Analysis (IPA) on 16 data sets (1 rat, 5 mouse, and 10 human data sets), involving 8 chemicals or drugs. We assessed the results based on the ability to correctly identify the CDT as indicated by its rank. We also considered the number of false positives, i.e. CDTs other than the correct CDT that were reported to be significant by each method. The proposed approach performed best in 11 out of the 16 experiments, reporting the correct CDT at the very top 7 times. IPA was the second best, reporting the correct CDT at the top 5 times, but was unable to identify the correct CDT at all in 5 out of the 16 experiments. The validation results showed that our approach, PURE, outperformed some of the most popular methods in the field. PURE could effectively infer the true CDTs responsible for the observed gene expression changes and could also be useful in drug repurposing applications.

Genetic characterization of canine astrovirus in non-diarrhea dogs and diarrhea dogs in Vietnam and Thailand reveals the presence of a unique lineage.

The role of canine astrovirus (CaAstV) in canine gastrointestinal disease (GID) is unknown. In this study, a total of 327 fecal swab (FS) samples were collected, including 113 FSs in Vietnam (46 samples from healthy dogs and 67 samples from GID dogs) and 214 FSs in Thailand (107 samples from healthy dogs and 107 samples from GID dogs). Overall, the prevalence of CaAstV in Vietnam and Thailand was 25.7% (29/113) and 8.9% (19/214), respectively. CaAstV was detected in both non-diarrhea dogs (21.7 and 7.5%) and diarrhea dogs (28.4% and 10.3%), respectively, in Vietnam and Thailand. In both countries, CaAstV was frequently detected in puppies under 6 months of age (23.3%) (p = 0.02). CaAstV-positive samples in Vietnam and Thailand were identified as co-infected with canine parvovirus, canine enteric coronavirus, canine distemper virus, and canine kobuvirus. The complete coding sequence of seven Vietnamese CaAstV and two Thai CaAstV strains were successfully characterized. Phylogenetic analyses showed that Vietnamese and Thai CaAstV strains were genetically close to each other and related to the Chinese strains. Furthermore, analysis of complete coding sequences indicated that the OR220030_G21/Thailand/2021 strain formed a unique lineage, whereas no recombination event was found in this study, suggesting that this strain might be an original lineage. In summary, this is the first study to report the presence of CaAstV in dogs with and without diarrhea in Vietnam and Thailand, and it was most often found in puppies with diarrhea. Our results highlight the importance of the CaAstV in dog populations and the need for continued surveillance of these emerging pathogens.

A call for standardized reporting of early-onset colorectal peritoneal metastases.

BACKGROUND: The incidence of colorectal cancer (CRC) in patients under 50 years of age, i.e., early-onset CRC, has increased in the past two decades. Colorectal peritoneal metastases (CPM) will develop in 10-30% of CRC patients. CPM traditionally had a dismal prognosis, but surgery and novel systemic treatments appear to increase survival. Determining potential age-associated risk and prognostic factors is optimized when analyses use standardized age groupings. METHODS: We performed a review of early-onset CPM studies and compared variables used, e.g., age stratification and definitions of synchronous and metachronous CPM. We included studies published in PubMed up to November 2022 if results were stratified by age. RESULTS: Of 114 screened publications in English, only 10 retrospective studies met inclusion criteria. Incidence of CPM was higher in younger CRC patients (e.g. 23% vs. 2% for <25 vs. ≥25 years, P < 0.0001; and 57% vs. 39% vs. 4% for <20 vs. 20-25 vs. >25 years, P < 0.001); two studies reported higher proportion of younger African American CPM patients (e.g. 16% vs. 6% for <50 vs. ≥50 years). Studies used seven different age-stratification methods, presenting comparison challenges. CONCLUSION: Studies showed a higher proportion of CPM in younger patients, but directly comparing results was not possible due to inconsistent reporting. To better address this issue, CRC and CPM studies stratified by standard age groups (e.g. <50 vs. ≥50) are needed.

The metabolic contribution of SKN-1/Nrf2 to the lifespan of Caenorhabditis elegans.

BACKGROUND AND AIMS: SKN-1, a C. elegans transcription factor analogous to the mammalian NF-E2-related factor (Nrf2), has been known to promote oxidative stress resistance aiding nematodes' longevity. Although SKN-1's functions suggest its implication in lifespan modulation through cellular metabolism, the actual mechanism of how metabolic rearrangements contribute to SKN-1's lifespan modulation has yet to be well characterized. Therefore, we performed the metabolomic profiling of the short-lived skn-1-knockdown C. elegans. METHODS: We analyzed the metabolic profile of the skn-1-knockdown worms with nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-tandem mass spectrometry (LC-MS/MS) and obtained distinctive metabolomic profiles compared to WT worms. We further extended our study with gene expression analysis to examine the expression level of genes encoding all metabolic enzymes. RESULTS: A significant increase in the phosphocholine and AMP/ATP ratio, potential biomarkers of aging, was observed, accompanied by a decrease in the transsulfuration metabolites, NADPH/NADP+ ratio, and total glutathione (GSHt), which are known to be involved in oxidative stress defense. skn-1-RNAi worms also exhibited an impairment in the phase II detoxification system, confirmed by the lower conversion rate of paracetamol to paracetamol-glutathione. By further examining the transcriptomic profile, we found a decrease in the expression of cbl-1, gpx, T25B9.9, ugt, and gst, which are involved in GSHt and NADPH synthesis as well as in the phase II detoxification system. CONCLUSION: Our multi-omics results consistently revealed that the cytoprotective mechanisms, including cellular redox reactions and xenobiotic detoxification system, contribute to the roles of SKN-1/Nrf2 in the lifespan of worms.

pyPheWAS Explorer: a visualization tool for exploratory analysis of phenome-disease associations.

Objective: To enable interactive visualization of phenome-wide association studies (PheWAS) on electronic health records (EHR). Materials and Methods: Current PheWAS technologies require familiarity with command-line interfaces and lack end-to-end data visualizations. pyPheWAS Explorer allows users to examine group variables, test assumptions, design PheWAS models, and evaluate results in a streamlined graphical interface. Results: A cohort of attention deficit hyperactivity disorder (ADHD) subjects and matched non-ADHD controls is examined. pyPheWAS Explorer is used to build a PheWAS model including sex and deprivation index as covariates, and the Explorer's result visualization for this model reveals known ADHD comorbidities. Discussion: pyPheWAS Explorer may be used to rapidly investigate potentially novel EHR associations. Broader applications include deployment for clinical experts and preliminary exploration tools for institutional EHR repositories. Conclusion: pyPheWAS Explorer provides a seamless graphical interface for designing, executing, and analyzing PheWAS experiments, emphasizing exploratory analysis of regression types and covariate selection.

Carnivore chaphamaparvovirus-1 (CaChPV-1) infection in diarrheic dogs reveals viral endotheliotropism in intestine and lung.

BACKGROUND: Carnivore chaphamaparvovirus-1 (CaChPV-1) is a parvovirus identified in dogs and association of infection with diarrhea is controversial. Information on whether tissue tropism persists is lacking. OBJECTIVES: To determine the disease association of CaChPV-1 in dogs with diarrhea and to investigate viral tropism and genetic diversity. ANIMALS AND METHODS: CaChPV-1 infection was investigated in five recently deceased puppies and designed a retrospective study to determine whether the presence of CaChPV-1 is associated with diarrhea. The retrospective study was conducted in 137 intestinal tissue samples and 168 fecal samples obtained from 305 dogs. CaChPV-1 tissue localization was determined using in situ hybridization, and CaChPV-1 complete genomes obtained from dead puppies and retrospective study were sequenced and analyzed. RESULTS: CaChPV-1 was detected in 6.56% (20/305) of tested dogs, including 14 diarrheic- and 6 non-diarrheic dogs, and was significant in puppies with diarrhea (p = 0.048). Among the CaChPV-1-positive diarrheic dogs, one sample was obtained from intestinal tissue and 13 samples were fecal samples. However, six CaChPV-1 positive non-diarrheic dogs were based on fecal samples but not on intestinal tissue. Within the age range, the presence of CaChPV-1 was significant in puppies (p < 0.00001) and was mainly localized in the stromal and endothelial cells of intestinal villi and pulmonary alveoli. Phylogenetic analysis indicated genetic diversity of CaChPV-1 Thai strains that were mostly clustered within the sequences found in China. CONCLUSIONS: Although definitive pathogenesis of CaChPV-1 remains undetermined, this study provides evidence supporting that CaChPV-1 localizes in canine cells and could play a potential role as an enteric pathogen.

A robust and accurate single-cell data trajectory inference method using ensemble pseudotime.

BACKGROUND: The advance in single-cell RNA sequencing technology has enhanced the analysis of cell development by profiling heterogeneous cells in individual cell resolution. In recent years, many trajectory inference methods have been developed. They have focused on using the graph method to infer the trajectory using single-cell data, and then calculate the geodesic distance as the pseudotime. However, these methods are vulnerable to errors caused by the inferred trajectory. Therefore, the calculated pseudotime suffers from such errors. RESULTS: We proposed a novel framework for trajectory inference called the single-cell data Trajectory inference method using Ensemble Pseudotime inference (scTEP). scTEP utilizes multiple clustering results to infer robust pseudotime and then uses the pseudotime to fine-tune the learned trajectory. We evaluated the scTEP using 41 real scRNA-seq data sets, all of which had the ground truth development trajectory. We compared the scTEP with state-of-the-art methods using the aforementioned data sets. Experiments on real linear and non-linear data sets demonstrate that our scTEP performed superior on more data sets than any other method. The scTEP also achieved a higher average and lower variance on most metrics than other state-of-the-art methods. In terms of trajectory inference capacity, the scTEP outperforms those methods. In addition, the scTEP is more robust to the unavoidable errors resulting from clustering and dimension reduction. CONCLUSION: The scTEP demonstrates that utilizing multiple clustering results for the pseudotime inference procedure enhances its robustness. Furthermore, robust pseudotime strengthens the accuracy of trajectory inference, which is the most crucial component in the pipeline. scTEP is available at https://cran.r-project.org/package=scTEP .

GPX8 regulates clear cell renal cell carcinoma tumorigenesis through promoting lipogenesis by NNMT.

BACKGROUND: Clear cell renal cell carcinoma (ccRCC), with its hallmark phenotype of high cytosolic lipid content, is considered a metabolic cancer. Despite the implication of this lipid-rich phenotype in ccRCC tumorigenesis, the roles and regulators of de novo lipid synthesis (DNL) in ccRCC remain largely unexplained. METHODS: Our bioinformatic screening focused on ccRCC-lipid phenotypes identified glutathione peroxidase 8 (GPX8), as a clinically relevant upstream regulator of DNL. GPX8 genetic silencing was performed with CRISPR-Cas9 or shRNA in ccRCC cell lines to dissect its roles. Untargeted metabolomics, RNA-seq analyses, and other biochemical assays (e.g., lipid droplets staining, fatty acid uptake, cell proliferation, xenograft, etc.) were carried out to investigate the GPX8's involvement in lipid metabolism and tumorigenesis in ccRCC. The lipid metabolic function of GPX8 and its downstream were also measured by isotope-tracing-based DNL flux measurement. RESULTS: GPX8 knockout or downregulation substantially reduced lipid droplet levels (independent of lipid uptake), fatty acid de novo synthesis, triglyceride esterification in vitro, and tumor growth in vivo. The downstream regulator was identified as nicotinamide N-methyltransferase (NNMT): its knockdown phenocopied, and its expression rescued, GPX8 silencing both in vitro and in vivo. Mechanically, GPX8 regulated NNMT via IL6-STAT3 signaling, and blocking this axis suppressed ccRCC survival by activating AMPK. Notably, neither the GPX8-NNMT axis nor the DNL flux was affected by the von Hippel Lindau (VHL) status, the conventional regulator of ccRCC high lipid content. CONCLUSIONS: Taken together, our findings unravel the roles of the VHL-independent GPX8-NNMT axis in ccRCC lipid metabolism as related to the phenotypes and growth of ccRCC, which may be targeted for therapeutic purposes.

Using a semi-automated approach to quantify Unidentified Bright Objects in Neurofibromatosis type 1 and linkages to cognitive and academic outcomes.

Neurofibromatosis type 1 (NF1) is an autosomal dominant neurocutaneous syndrome that affects multiple organ systems resulting in widespread symptoms, including cognitive deficits. In addition to the criteria required for an NF1 diagnosis, approximately 70% of children with NF1 present with Unidentified Bright Objects (UBOs) or Focal Areas of Signal Intensity, which are hyperintense bright spots seen on T2-weighted magnetic resonance images and seen more prominently on FLAIR magnetic resonance images (Sabol et al., 2011). Current findings relating the presence/absence, quantities, sizes, and locations of these bright spots to cognitive abilities are mixed. To contribute to and hopefully disentangle some of these mixed findings, we explored potential relationships between metrics related to UBOs and cognitive abilities in a sample of 28 children and adolescents with NF1 (M=12.52 years; SD=3.18 years; 16 male). We used the Lesion Segmentation Tool (LST) to automatically detect and segment the UBOs. The LST was able to qualitatively and quantitatively reliably detect UBOs in images of children with NF1. Using these automatically detected and segmented lesions, we found that while controlling for age, biological sex, perceptual IQ, study, and scanner, "total UBO volume", defined as the sum of all the voxels representing all of the UBOs for each participant, helped explain differences in word reading, phonological awareness, and visuospatial skills. These findings contribute to the emerging NF1 literature and help parse the specific deficits that children with NF1 have, to then help improve the efficacy of reading interventions for children with NF1.

Mouse genomic associations with in vitro sensitivity to simulated space radiation.

Exposure to ionizing radiation is considered by NASA to be a major health hazard for deep space exploration missions. Ionizing radiation sensitivity is modulated by both genomic and environmental factors. Understanding their contributions is crucial for designing experiments in model organisms, evaluating the risk of deep space (i.e. high-linear energy transfer, or LET, particle) radiation exposure in astronauts, and also selecting therapeutic irradiation regimes for cancer patients. We identified single nucleotide polymorphisms in 15 strains of mice, including 10 collaborative cross model strains and 5 founder strains, associated with spontaneous and ionizing radiation-induced in vitro DNA damage quantified based on immunofluorescent tumor protein p53 binding protein (53BP1) positive nuclear foci. Statistical analysis suggested an association with pathways primarily related to cellular signaling, metabolism, tumorigenesis and nervous system damage. We observed different genomic associations in early (4 and 8 h) responses to different LET radiation, while later (24 hour) DNA damage responses showed a stronger overlap across all LETs. Furthermore, a subset of pathways was associated with spontaneous DNA damage, suggesting 53BP1 positive foci as a potential biomarker for DNA integrity in mouse models. Our results suggest several mouse strains as new models to further study the impact of ionizing radiation and validate the identified genetic loci. We also highlight the importance of future human in vitro studies to refine the association of genes and pathways with the DNA damage response to ionizing radiation and identify targets for space travel countermeasures.