Dose length product to effective dose coefficients in adults

OBJECTIVES

The most accurate method for estimating patient effective dose (a principal metric for tracking patient radiation exposure) from computed tomography (CT) requires time-intensive Monte Carlo simulation. A simpler method multiplies a scalar coefficient by the widely available scanner-reported dose length product (DLP) to estimate effective dose. We developed new adult effective dose coefficients using actual patient scans and assessed their agreement with Monte Carlo simulation.

METHODS

A multicenter sample of 216,906 adult CT scans was prospectively assembled in 2015-2020 from the University of California San Francisco International CT Dose Registry and the University of Florida library of computational phantoms. We generated effective dose coefficients for eight body regions, stratified by patient sex, diameter, and scanner manufacturer. We applied the new coefficients to DLPs to calculate effective doses and assess their correlations with Monte Carlo radiation transport-generated effective dose.

RESULTS

Effective dose coefficients varied by body region and decreased in magnitude with increasing patient diameter. Coefficients were approximately twofold higher for torso scans in smallest compared with largest diameter categories. For example, abdomen and pelvis coefficients decreased from 0.027 to 0.013 mSv/mGy-cm between the 16-20 cm and 41+ cm categories. There were modest but consistent differences by sex and manufacturer. Diameter-based coefficients used to estimate effective dose produced strong correlations with the reference standard (Pearson correlations 0.77-0.86). The reported conversion coefficients differ from previous studies, particularly in neck CT.

CONCLUSIONS

New effective dose coefficients derived from empirical clinical scans can be used to easily estimate effective dose using scanner-reported DLP.

CLINICAL RELEVANCE STATEMENT

Scalar coefficients multiplied by DLP offer a simple approximation to effective dose, a key radiation dose metric. New effective dose coefficients from this study strongly correlate with gold standard, Monte Carlo-generated effective dose, and differ somewhat from previous studies.

KEY POINTS

• Previous effective dose coefficients were derived from theoretical models rather than real patient data. • The new coefficients (from a large registry/phantom library) differ from previous studies. • The new coefficients offer reasonably reliable values for estimating effective dose.

Enhancing Patient Communication With Chat-GPT in Radiology: Evaluating the Efficacy and Readability of Answers to Common Imaging-Related Questions

PURPOSE

To assess ChatGPT's accuracy, relevance, and readability in answering patients' common imaging-related questions and examine the effect of a simple prompt.

METHODS

A total of 22 imaging-related questions were developed from categories previously described as important to patients, as follows: safety, the radiology report, the procedure, preparation before imaging, meaning of terms, and medical staff. These questions were posed to ChatGPT with and without a short prompt instructing the model to provide an accurate and easy-to-understand response for the average person. Four board-certified radiologists evaluated the answers for accuracy, consistency, and relevance. Two patient advocates also reviewed responses for their utility for patients. Readability was assessed using the Flesch Kincaid Grade Level. Statistical comparisons were performed using χ2 and paired t tests.

RESULTS

A total of 264 answers were assessed for both unprompted and prompted questions. Unprompted responses were accurate 83% of the time (218 of 264), which did not significantly change for prompted responses (87% [229 of 264]; P = .2). The consistency of the responses increased from 72% (63 of 88) to 86% (76 of 88) when prompts were given (P = .02). Nearly all responses (99% [261 of 264]) were at least partially relevant for both question types. Fewer unprompted responses were considered fully relevant at 67% (176 of 264), although this increased significantly to 80% when prompts were given (210 of 264; P = .001). The average Flesch Kincaid Grade Level was high at 13.6 [CI, 12.9-14.2], unchanged with the prompt (13.0 [CI, 12.41-13.60], P = .2). None of the responses reached the eighth-grade readability level recommended for patient-facing materials.

DISCUSSION

ChatGPT demonstrates the potential to respond accurately, consistently, and relevantly to patients' imaging-related questions. However, imperfect accuracy and high complexity necessitate oversight before implementation. Prompts reduced response variability and yielded more-targeted information, but they did not improve readability. ChatGPT has the potential to increase accessibility to health information and streamline the production of patient-facing educational materials; however, its current limitations require cautious implementation and further research.

Dose length product to effective dose coefficients in children

BACKGROUND

The most accurate method for estimating effective dose (the most widely understood metric for tracking patient radiation exposure) from computed tomography (CT) requires time-intensive Monte Carlo simulation. A simpler method multiplies a scalar coefficient by the widely available scanner-reported dose length product (DLP) to estimate effective dose.

OBJECTIVE

Develop pediatric effective dose coefficients and assess their agreement with Monte Carlo simulation.

MATERIALS AND METHODS

Multicenter, population-based sample of 128,397 pediatric diagnostic CT scans prospectively assembled in 2015-2020 from the University of California San Francisco International CT Dose Registry and the University of Florida library of highly realistic hybrid computational phantoms. We generated effective dose coefficients for seven body regions, stratified by patient age, diameter, and scanner manufacturer. We applied the new coefficients to DLPs to calculate effective doses and assessed their correlations with Monte Carlo radiation transport-generated effective doses.

RESULTS

The reported effective dose coefficients, generally higher than previous studies, varied by body region and decreased in magnitude with increasing age. Coefficients were approximately 4 to 13-fold higher (across body regions) for patients  <1 year old compared with patients 15-21 years old. For example, head CT (54% of scans) dose coefficients decreased from 0.039 to 0.003 mSv/mGy-cm in patients  <1 year old vs. 15-21 years old. There were minimal differences by manufacturer. Using age-based conversion coefficients to estimate effective dose produced moderate to strong correlations with Monte Carlo results (Pearson correlations 0.52-0.80 across body regions).

CONCLUSIONS

New pediatric effective dose coefficients update existing literature and can be used to easily estimate effective dose using scanner-reported DLP.

Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful?

Software is vital for the advancement of biology and medicine. Through analysis of usage and impact metrics of software, developers can help determine user and community engagement. These metrics can be used to justify additional funding, encourage additional use, and identify unanticipated use cases. Such analyses can help define improvement areas and assist with managing project resources. However, there are challenges associated with assessing usage and impact, many of which vary widely depending on the type of software being evaluated. These challenges involve issues of distorted, exaggerated, understated, or misleading metrics, as well as ethical and security concerns. More attention to the nuances, challenges, and considerations involved in capturing impact across the diverse spectrum of biological software is needed. Furthermore, some tools may be especially beneficial to a small audience, yet may not have comparatively compelling metrics of high usage. Although some principles are generally applicable, there is not a single perfect metric or approach to effectively evaluate a software tool's impact, as this depends on aspects unique to each tool, how it is used, and how one wishes to evaluate engagement. We propose more broadly applicable guidelines (such as infrastructure that supports the usage of software and the collection of metrics about usage), as well as strategies for various types of software and resources. We also highlight outstanding issues in the field regarding how communities measure or evaluate software impact. To gain a deeper understanding of the issues hindering software evaluations, as well as to determine what appears to be helpful, we performed a survey of participants involved with scientific software projects for the Informatics Technology for Cancer Research (ITCR) program funded by the National Cancer Institute (NCI). We also investigated software among this scientific community and others to assess how often infrastructure that supports such evaluations is implemented and how this impacts rates of papers describing usage of the software. We find that although developers recognize the utility of analyzing data related to the impact or usage of their software, they struggle to find the time or funding to support such analyses. We also find that infrastructure such as social media presence, more in-depth documentation, the presence of software health metrics, and clear information on how to contact developers seem to be associated with increased usage rates. Our findings can help scientific software developers make the most out of the evaluations of their software so that they can more fully benefit from such assessments.

Food for all: designing sustainable and secure future seafood systems

Food from the sea can make a larger contribution to healthy and sustainable diets, and to addressing hunger and malnutrition, through improvements in production, distribution and equitable access to wild harvest and mariculture resources and products. The supply and consumption of seafood is influenced by a range of 'drivers' including ecosystem change and ocean regulation, the influence of corporations and evolving consumer demand, as well as the growing focus on the importance of seafood for meeting nutritional needs. These drivers need to be examined in a holistic way to develop an informed understanding of the needs, potential impacts and solutions that align seafood production and consumption with relevant 2030 Sustainable Development Goals (SDGs). This paper uses an evidence-based narrative approach to examine how the anticipated global trends for seafood might be experienced by people in different social, geographical and economic situations over the next ten years. Key drivers influencing seafood within the global food system are identified and used to construct a future scenario based on our current trajectory (Business-as-usual 2030). Descriptive pathways and actions are then presented for a more sustainable future scenario that strives towards achieving the SDGs as far as technically possible (More sustainable 2030). Prioritising actions that not only sustainably produce more seafood, but consider aspects of access and utilisation, particularly for people affected by food insecurity and malnutrition, is an essential part of designing sustainable and secure future seafood systems.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11160-021-09663-x.

Food for all: designing sustainable and secure future seafood systems

Food from the sea can make a larger contribution to healthy and sustainable diets, and to addressing hunger and malnutrition, through improvements in production, distribution and equitable access to wild harvest and mariculture resources and products. The supply and consumption of seafood is influenced by a range of 'drivers' including ecosystem change and ocean regulation, the influence of corporations and evolving consumer demand, as well as the growing focus on the importance of seafood for meeting nutritional needs. These drivers need to be examined in a holistic way to develop an informed understanding of the needs, potential impacts and solutions that align seafood production and consumption with relevant 2030 Sustainable Development Goals (SDGs). This paper uses an evidence-based narrative approach to examine how the anticipated global trends for seafood might be experienced by people in different social, geographical and economic situations over the next ten years. Key drivers influencing seafood within the global food system are identified and used to construct a future scenario based on our current trajectory (Business-as-usual 2030). Descriptive pathways and actions are then presented for a more sustainable future scenario that strives towards achieving the SDGs as far as technically possible (More sustainable 2030). Prioritising actions that not only sustainably produce more seafood, but consider aspects of access and utilisation, particularly for people affected by food insecurity and malnutrition, is an essential part of designing sustainable and secure future seafood systems.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11160-021-09663-x.

Development and validation of technologies suitable for the decontamination and re-use of contaminated N95 filtering facepiece respirators in response to the COVID-19 pandemic

Background

Coronavirus disease 2019 (COVID-19) has brought significant challenges to society globally, particularly in the area of healthcare provision. A pressing need existed in protecting those tasked with delivering healthcare solutions during the COVID-19 crisis by providing solutions for preserving adequate supplies of effective personal protective equipment (PPE).

Aim

To evaluate and validate available methods for the decontamination of N95 filtering facepiece respirators (FFRs) while maintaining functionality during re-use.

Methods

Multiple low-temperature steam and vaporized hydrogen peroxide (VHP) technologies were assessed for inactivation of Mycobacterium spp. and feline calicivirus (employed as representatives of the contamination challenge).

Findings

Virus (≥3log₁₀) and Mycobacterium spp. (≥6log₁₀) inactivation was achieved on various types of N95 FFRs using an array of heat (65–71^oC), humidity (>50% relative humidity) and VHP without affecting the performance of the PPE.

Conclusion

The methods have been validated and were authorized by the US Food and Drug Administration under a temporary emergency use authorization. Based on the findings, opportunities exist for development and deployment of decontamination methods made from simple, general purpose materials and equipment should a future need arise.

448. Disproportionate Burden of COVID-19 on Latinx Residents among Hospitalized Patients at San Francisco’s Public Health Hospital

Background

San Francisco implemented one of the earliest shelter-in-place public health mandates in the U.S., with flattened curves of diagnoses and deaths. We describe demographics, clinical features and outcomes of COVID-19 patients admitted to a public health hospital in a high population-density city with an early containment response.

Methods

We analyzed inpatients with COVID-19 admitted to San Francisco General Hospital (SFGH) from 3/5/2020–5/11/2020. SFGH serves a network of >63,000 patients (32% Latinx/24% Asian/19% African American/19% Caucasian). Demographic and clinical data through 5/18/2020 were abstracted from hospital records, along with ICU and ventilator utilization, lengths of stay, and in-hospital deaths.

Results

Of 157 admitted patients, 105/157 (67%) were male, median age was 49 (range 19-96y), and 127/157 (81%) of patients with COVID-19 were Latinx. Crowded living conditions were common: 60/157 (38%) lived in multi-family shared housing, 12/1578 (8%) with multigenerational families, and 8/157 (5%) were homeless living in shelters. Of 102 patients with ascertained occupations, most had frontline essential jobs: 23% food service, 14% construction/home maintenance, and 10% cleaning. Overall, 86/157 (55%) of patients lived in neighborhoods home to majority Latinx and African-American populations. Overall, 45/157 (29%) of patients needed ICU care, and 26/157 (17%) required mechanical ventilation; 20/26 (77%) of ventilated patients were successfully extubated, and 137/157 (87%) were discharged home. Median hospitalization duration was 4 days (IQR, 2–10), and only 6/157 (4%) patients died in hospital.

Conclusion

In San Francisco, where early COVID-19 mitigation was enacted, we report a stark, disproportionate COVID-19 burden on Latinx patients, who accounted for 81% of hospitalizations despite making up only 32% of the patient base and 15% of San Francisco’s total population. Latinx inpatients frequently lived in high-density settings, increasing household risk, and frequently worked essential jobs, potentially limiting the opportunity to effectively distance from others. We also report here favorable clinical outcomes and low overall mortality. However, an effective COVID-19 response must urgently address racial and ethnic disparities.

Disclosures

All Authors: No reported disclosures

Population-based study of the impact of small bowel obstruction due to adhesions on short- and medium-term mortality

BACKGROUND

Small bowel obstruction due to adhesions (aSBO) is a common indication for admission to a surgical unit. Despite the prevalence of this condition, the short- and medium-term survival of this patient population has not been well described. The purpose of this study was to measure the short- and medium-term survival of patients admitted to hospital with aSBO.

METHODS

Linked administrative data were used to identify patients admitted to hospital in Ontario, Canada, for aSBO between 2005 and 2011. Patients were divided into two groups: those aged less than 65 years (younger group) and those aged 65 years and older (older group). Thirty-day, 90-day and 1-year mortality rates were estimated. One-year mortality was compared with that in the general population, adjusting for age and sex. The timing of deaths in relation to admission was assessed, as well as the proportion of patients discharged before experiencing short-term mortality.

RESULTS

There were 22 197 patients admitted to hospital for aSBO for the first time in the study interval. Mean age was 64·5 years and 52·2 per cent of the patients were women. Overall, the 30-day, 90-day and 1-year mortality rates for the cohort were 5·7 (95 per cent c.i. 5·4 to 6·0), 8·7 (8·3 to 9·0) and 13·9 (13·4 to 14·3) per cent respectively. For both groups, the 1-year risk of death was significantly greater than that of the age-matched general population. The majority of deaths (62·5 per cent) occurred within 90 days of admission, with 36·4 per cent occurring after discharge from the aSBO admission.

CONCLUSION

Patients admitted with aSBO have a high short-term mortality rate. Increased monitoring of patients in the early period after admission is advisable.

Modified carbazoles destabilize microtubules and kill glioblastoma multiform cells

Small molecules that target microtubules (MTs) represent promising therapeutics to treat certain types of cancer, including glioblastoma multiform (GBM). We synthesized modified carbazoles and evaluated their antitumor activity in GBM cells in culture. Modified carbazoles with an ethyl moiety linked to the nitrogen of the carbazole and a carbonyl moiety linked to distinct biaromatic rings exhibited remarkably different killing activities in human GBM cell lines and patient-derived GBM cells, with IC₅₀ values from 67 to >10,000 nM. Measures of the activity of modified carbazoles with tubulin and microtubules coupled to molecular docking studies show that these compounds bind to the colchicine site of tubulin in a unique low interaction space that inhibits tubulin assembly. The modified carbazoles reported here represent novel chemical tools to better understand how small molecules disrupt MT functions and kill devastating cancers such as GBM.

Highly Efficient Spin-to-Charge Current Conversion in Strained HgTe Surface States Protected by a HgCdTe Layer

We report the observation of spin-to-charge current conversion in strained mercury telluride at room temperature, using spin pumping experiments. We show that a HgCdTe barrier can be used to protect the HgTe from direct contact with the ferromagnet, leading to very high conversion rates, with inverse Edelstein lengths up to 2.0±0.5  nm. The influence of the HgTe layer thickness on the conversion efficiency is found to differ strongly from what is expected in spin Hall effect systems. These measurements, associated with the temperature dependence of the resistivity, suggest that these high conversion rates are due to the spin momentum locking property of HgTe surface states.

Rapid and simple detection of foot-and-mouth disease virus: Evaluation of a cartridge-based molecular detection system for use in basic laboratories

Highly contagious transboundary animal diseases such as foot-and-mouth disease (FMD) are major threats to the productivity of farm animals. To limit the impact of outbreaks and to take efficient steps towards a timely control and eradication of the disease, rapid and reliable diagnostic systems are of utmost importance. Confirmatory diagnostic assays are typically performed by experienced operators in specialized laboratories, and access to this capability is often limited in the developing countries with the highest disease burden. Advances in molecular technologies allow implementation of modern and reliable techniques for quick and simple pathogen detection either in basic laboratories or even at the pen-side. Here, we report on a study to evaluate a fully automated cartridge-based real-time RT-PCR diagnostic system (Enigma MiniLab^® ) for the detection of FMD virus (FMDV). The modular system integrates both nucleic acid extraction and downstream real-time RT-PCR (rRT-PCR). The analytical sensitivity of this assay was determined using serially diluted culture grown FMDV, and the performance of the assay was evaluated using a selected range of FMDV positive and negative clinical samples of bovine, porcine and ovine origin. The robustness of the assay was evaluated in an international inter-laboratory proficiency test and by deployment into an African laboratory. It was demonstrated that the system is easy to use and can detect FMDV with high sensitivity and specificity, roughly on par with standard laboratory methods. This cartridge-based automated real-time RT-PCR system for the detection of FMDV represents a reliable and easy to use diagnostic tool for the early and rapid disease detection of acutely infected animals even in remote areas. This type of system could be easily deployed for routine surveillance within endemic regions such as Africa or could alternatively be used in the developed world.

Use of the tubular external fixator in the treatment of distal radial and ulnar fractures in small dogs and cats

Twenty-two fractures of the distal radius and ulna in small dogs and cats treated with a tubular external fixator system were evaluated. Radius/ulna fractures in toy breeds often occur in the distal metaphyseal region. Placing two screws through a bone plate in the distal radius in such cases is difficult even if a miniplate is used. The tubular external fixator allows multiple-pin clamping in parallel with a single connecting bar. Using this technique, four pins can be placed in a bone fragment, the length of which would hold only two screws in a 2.0 mini-DCP. The tubular external fixator was found to be a satisfactory alternative to bone plating for the fixation of distal radial/ulnar fractures, providing sufficient fracture stability with minimal soft tissue trauma.

A Role for Behavior in the Relationships Between Depression and Hostility and Cardiovascular Disease Incidence, Mortality, and All-Cause Mortality: the Prime Study

Background

Behavioral factors are important in disease incidence and mortality and may explain associations between mortality and various psychological traits.

Purpose

These analyses investigated the impact of behavioral factors on the associations between depression, hostility and cardiovascular disease(CVD) incidence, CVD mortality, and all-cause mortality.

Methods

Data from the PRIME Study (N = 6953 men) were analyzed using Cox proportional hazards models, following adjustment for demographic and biological CVD risk factors, and other psychological traits, including social support.

Results

Following initial adjustment, both depression and hostility were significantly associated with both mortality outcomes (smallest SHR = 1.24, p < 0.001). Following adjustment for behavioral factors, all relationships were attenuated both when accounting for and not accounting for other psychological variables. Associations with all-cause mortality remained significant (smallest SHR = 1.14, p = 0.04). Of the behaviors included, the most significant contribution to outcomes was found for smoking, but a role was also found for fruit and vegetable intakes and high alcohol consumption.

Conclusions

These findings demonstrate well-known associations between depression, hostility, and mortality and suggest the potential importance of behaviors in explaining these relationships.

Revitalization of a Forward Genetic Screen Identifies Three New Regulators of Fungal Secondary Metabolism in the Genus Aspergillus

The study of aflatoxin in Aspergillus spp. has garnered the attention of many researchers due to aflatoxin's carcinogenic properties and frequency as a food and feed contaminant. Significant progress has been made by utilizing the model organism Aspergillus nidulans to characterize the regulation of sterigmatocystin (ST), the penultimate precursor of aflatoxin. A previous forward genetic screen identified 23 A. nidulans mutants involved in regulating ST production. Six mutants were characterized from this screen using classical mapping (five mutations in mcsA) and complementation with a cosmid library (one mutation in laeA). The remaining mutants were backcrossed and sequenced using Illumina and Ion Torrent sequencing platforms. All but one mutant contained one or more sequence variants in predicted open reading frames. Deletion of these genes resulted in identification of mutant alleles responsible for the loss of ST production in 12 of the 17 remaining mutants. Eight of these mutations were in genes already known to affect ST synthesis (laeA, mcsA, fluG, and stcA), while the remaining four mutations (in laeB, sntB, and hamI) were in previously uncharacterized genes not known to be involved in ST production. Deletion of laeB, sntB, and hamI in A. flavus results in loss of aflatoxin production, confirming that these regulators are conserved in the aflatoxigenic aspergilli. This report highlights the multifaceted regulatory mechanisms governing secondary metabolism in Aspergillus Additionally, these data contribute to the increasing number of studies showing that forward genetic screens of fungi coupled with whole-genome resequencing is a robust and cost-effective technique.IMPORTANCE In a postgenomic world, reverse genetic approaches have displaced their forward genetic counterparts. The techniques used in forward genetics to identify loci of interest were typically very cumbersome and time-consuming, relying on Mendelian traits in model organisms. The current work was pursued not only to identify alleles involved in regulation of secondary metabolism but also to demonstrate a return to forward genetics to track phenotypes and to discover genetic pathways that could not be predicted through a reverse genetics approach. While identification of mutant alleles from whole-genome sequencing has been done before, here we illustrate the possibility of coupling this strategy with a genetic screen to identify multiple alleles of interest. Sequencing of classically derived mutants revealed several uncharacterized genes, which represent novel pathways to regulate and control the biosynthesis of sterigmatocystin and of aflatoxin, a societally and medically important mycotoxin.

A systematic review of context bias in invasion biology

The language that scientists use to frame biological invasions may reveal inherent bias—including how data are interpreted. A frequent critique of invasion biology is the use of value-laden language that may indicate context bias. Here we use a systematic study of language and interpretation in papers drawn from invasion biology to evaluate whether there is a link between the framing of papers and the interpretation of results. We also examine any trends in context bias in biological invasion research. We examined 651 peer-reviewed invasive species competition studies and implemented a rigorous systematic review to examine bias in the presentation and interpretation of native and invasive competition in invasion biology. We predicted that bias in the presentation of invasive species is increasing, as suggested by several authors, and that bias against invasive species would result in misinterpreting their competitive dominance in correlational observational studies compared to causative experimental studies. We indeed found evidence of bias in the presentation and interpretation of invasive species research; authors often introduced research with invasive species in a negative context and study results were interpreted against invasive species more in correlational studies. However, we also found a distinct decrease in those biases since the mid-2000s. Given that there have been several waves of criticism from scientists both inside and outside invasion biology, our evidence suggests that the subdiscipline has somewhat self-corrected apparent biases.

Abstract 5266: Fast and accurate fusion transcript detection using the Trinity Cancer Transcriptome Analysis Toolkit

Chromosomal rearrangements leading to fusion transcripts represent a class of oncogenic aberrations that are of high interest for understanding cancer biology, treating cancer patients, and as targets for the development of new therapies. Transcriptome sequencing via RNA-Seq coupled with downstream bioinformatics software applications offers an effective method for identifying candidate fusion transcripts, and is more targeted and cost-effective than whole genome sequencing. Although many such fusion detection software tools have recently been made available, they often differ greatly in prediction accuracy, execution times, computational requirements, installation complexity, and in not being readily accessible to non-bioinformatician cancer researchers.

Here we present the Trinity Cancer Transcriptome Analysis Toolkit (CTAT), a newly developed suite of RNA-Seq targeted fusion detection tools leveraging a combination of reference genome read-mapping and de novo transcriptome assembly, coupled to in silico fusion transcript validation, annotation, and visualization. We show that components of our Trinity CTAT fusion detection toolkit, including STAR-Fusion and FusionInspector, yield improved accuracy and run times as compared to alternative leading tools. As a demonstration of the utility of Trinity CTAT, we explore fusion transcript discovery in a large cohort of ∼300 chronic lymphocytic leukemia (CLL) patient samples. We identify several novel recurrent fusions that may represent drivers of CLL etiology and provide new avenues to therapies.

In addition to fusion transcript identification, Trinity CTAT aims to provide cancer researchers with easy access to methods for analyzing cancer RNA-Seq, including transcript reconstruction, identification of mutations, expression analysis, and tumor heterogeneity. Trinity CTAT is freely available open source software and readily accessible to all cancer researchers via our public Galaxy web portal: https://galaxy.ncgas-trinity.indiana.edu/.

Citation Format: Brian Haas, Timothy Tickle, Nathalie Pochet, Jing Sun, Peggy Hsu, Chip Stewart, Carrie Ganote, Ben Fulton, Catherine Wu, Aviv Regev. Fast and accurate fusion transcript detection using the Trinity Cancer Transcriptome Analysis Toolkit. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5266.

Abstract 789: Leveraging transcriptomic and genomic data to better select models for preclinical oncology therapeutic development to identify cell lines most similar to patient tumors

Cancer cell lines represent the front line of new compound testing, and results from these experiments often decide which compounds go on for further testing. Genomic context plays a critical role in drug response and now genomic data for tumors and cell lines are widely available. However, cell lines are often chosen based on ease of access, literature prevalence, and ease of culture. We combined gene expression and CNV/mutation profiling from four pancreatic cancer tumor datasets (GSE21501, GSE28735, ICGC, TCGA,) and three pancreatic cancer cell line datasets (Klijn et al, Collisson et al, and CCLE) to identify which cell lines best match patient tumors.

CNV comparison revealed that popular cell lines do not always have the best CNV correlation with tumors: when comparing pancreatic cancer tumors to cell lines, the citations of the top five cell lines by CNV correlation were less than 10% of the pancreatic cancer cell line total. Next we filtered for driver mutations including SMAD4 and CDKN2A using mutation scoring algorithms and clustered tumors and cell lines. We found that many cell lines with few citation counts clustered readily amongst tumors (such as L33). Leveraging the hypothesis that different hits in the same pathway can have a similar downstream effect, we combined CNV, expression and mutation data and clustered cell lines together with tumors based on overall aberrations in MSigDB cancer pathways. L33 and YAPC clustered near tumors while the majority of other cell lines clustered together.

To identify coexpressed gene clusters, we ran WGCNA individually in all seven datasets and discovered modules consistent in cell line and tumor datasets using iGraph. One of the most interesting modules (interferon regulated genes) is expressed highly in the majority of tumors profiled. About half of cell lines also express this module highly, suggesting that they may be more ideal models for high interferon expression tumors than other cell lines.

Here we present evidence demonstrating that certain cell lines mimic pancreatic tumor genomes more closely while others represent patterns of genomic features not commonly observed in vivo. We also show that certain biologically relevant tumor subtypes may be better represented by some cell lines than others. Our analysis highlights the emerging role of genomics in advancing the clinical success of therapeutic trials.

Citation Format: Yoonjeong Cha, Adam Labradorf, Joseph Perez-Rogers, Brian Haas, Andrew Lysaght, Brian Weiner, Fadi Towfic, Kevin Fowler, Benjamin Zeskind, Sarah Kolitz, Badri Vardarajan, Maxim Artyomov, Rebecca L. Kusko. Leveraging transcriptomic and genomic data to better select models for preclinical oncology therapeutic development to identify cell lines most similar to patient tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 789.

Use of the MS2 aptamer and coat protein for RNA localization in yeast: A response to "MS2 coat proteins bound to yeast mRNAs block 5' to 3' degradation and trap mRNA decay products: implications for the localization of mRNAs by MS2-MCP system"

The MS2 system has been extensively used to visualize single mRNA molecules in live cells and follow their localization and behavior. In their Letter to the Editor recently published, Garcia and Parker suggest that use of the MS2 system may yield erroneous mRNA localization results due to the accumulation of 3' decay products. Here we cite published works and provide new data which demonstrate that this is not a phenomenon general to endogenously expressed MS2-tagged transcripts, and that some of the results obtained in their study could have arisen from artifacts of gene expression.

Nonpolar m-plane GaN/AlGaN heterostructures with intersubband transitions in the 5-10 THz band

This paper assesses intersubband (ISB) transitions in the 1-10 THz frequency range in nonpolar m-plane GaN/AlGaN multi-quantum-wells deposited on free-standing semi-insulating GaN substrates. The quantum wells (QWs) were designed to contain two confined electronic levels, decoupled from the neighboring wells. Structural analysis reveals flat and regular QWs in the two perpendicular in-plane directions, with high-angle annular dark-field scanning transmission electron microscopy images showing inhomogeneities of the Al composition in the barriers along the growth axis. We do not observe extended structural defects (stacking faults or dislocations) introduced by the epitaxial process. Low-temperature ISB absorption from 1.5 to 9 THz (6.3-37.4 meV) is demonstrated, covering most of the 7-10 THz band forbidden to GaAs-based technologies.

Transcriptome profiling of the dynamic life cycle of the scypohozoan jellyfish Aurelia aurita

Background

The moon jellyfish Aurelia aurita is a widespread scyphozoan species that forms large seasonal blooms. Here we provide the first comprehensive view of the entire complex life of the Aurelia Red Sea strain by employing transcriptomic profiling of each stage from planula to mature medusa.

Results

A de novo transcriptome was assembled from Illumina RNA-Seq data generated from six stages throughout the Aurelia life cycle. Transcript expression profiling yielded clusters of annotated transcripts with functions related to each specific life-cycle stage. Free-swimming planulae were found highly enriched for functions related to cilia and microtubules, and the drastic morphogenetic process undergone by the planula while establishing the future body of the polyp may be mediated by specifically expressed Wnt ligands. Specific transcripts related to sensory functions were found in the strobila and the ephyra, whereas extracellular matrix functions were enriched in the medusa due to high expression of transcripts such as collagen, fibrillin and laminin, presumably involved in mesoglea development. The CL390-like gene, suggested to act as a strobilation hormone, was also highly expressed in the advanced strobila of the Red Sea species, and in the medusa stage we identified betaine-homocysteine methyltransferase, an enzyme that may play an important part in maintaining equilibrium of the medusa’s bell. Finally, we identified the transcription factors participating in the Aurelia life-cycle and found that 70% of these 487 identified transcription factors were expressed in a developmental-stage-specific manner.

Conclusions

This study provides the first scyphozoan transcriptome covering the entire developmental trajectory of the life cycle of Aurelia. It highlights the importance of numerous stage-specific transcription factors in driving morphological and functional changes throughout this complex metamorphosis, and is expected to be a valuable resource to the community.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1320-z) contains supplementary material, which is available to authorized users.

Illumina identification of RsrA, a conserved C2H2 transcription factor coordinating the NapA mediated oxidative stress signaling pathway in Aspergillus

Background

Chemical mutagenesis screens are useful to identify mutants involved in biological processes of interest. Identifying the mutation from such screens, however, often fails when using methodologies involving transformation of the mutant to wild type phenotype with DNA libraries.

Results

Here we analyzed Illumina sequence of a chemically derived mutant of Aspergillus nidulans and identified a gene encoding a C2H2 transcription factor termed RsrA for regulator of stress response. RsrA is conserved in filamentous fungal genomes, and upon deleting the gene in three Aspergillus species (A. nidulans, A. flavus and A. fumigatus), we found two conserved phenotypes: enhanced resistance to oxidative stress and reduction in sporulation processes. For all species, rsrA deletion mutants were more resistant to hydrogen peroxide treatment. In depth examination of this latter characteristic in A. nidulans showed that upon exposure to hydrogen peroxide, RsrA loss resulted in global up-regulation of several components of the oxidative stress metabolome including the expression of napA and atfA, the two bZIP transcription factors mediating resistance to reactive oxygen species (ROS) as well as NapA targets in thioredoxin and glutathione systems. Coupling transcriptional data with examination of ΔrsrAΔatfA and ΔrsrAΔnapA double mutants indicate that RsrA primarily operates through NapA-mediated stress response pathways. A model of RsrA regulation of ROS response in Aspergillus is presented.

Conclusion

RsrA, found in a highly syntenic region in Aspergillus genomes, coordinates a NapA mediated oxidative response in Aspergillus fungi.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1011) contains supplementary material, which is available to authorized users.

Efficacy, safety and regulatory status of SGLT2 inhibitors: focus on canagliflozin

Prevalence of diabetes mellitus is inc6reasing, with a burden of 382 million patients worldwide at present (more than the entire US population). The International Diabetes Federation anticipates an increase up to 592 million patients by 2035. Another major problem arises from the fact that just 50% of patients with type 2 diabetes mellitus are at target glycaemic control with currently available medications. Therefore, a clear need for new therapies that aim to optimize glycaemic control becomes evident. Renal sodium-linked glucose transporter 2 inhibitors are new antidiabetic drugs with an insulin-independent mechanism of action. They pose one remarkable advantage compared with already established antidiabetics: increasing urinary glucose excretion without inducing hypoglycaemia, thereby promoting body weight reduction due to loss of ~300 kcal per day. This review focuses on canagliflozin, which was the first successful compound of this class to be approved by both the US Food and Drug Administration and the European Medicines Agency in 2013. Clinical trials showed promising results: enhancing glycaemic control was paralleled by reducing body weight and systolic and diastolic blood pressure. Nevertheless, some safety concerns remain, such as genital mycotic infections, urinary tract infections and cardiovascular risks in vulnerable patients, which will be closely monitored in several post-authorization safety studies.

Depression and mortality: artifact of measurement and analysis?

BACKGROUND

Previous research demonstrates various associations between depression, cardiovascular disease (CVD) incidence and mortality, possibly as a result of the different methodologies used to measure depression and analyse relationships. This analysis investigated the association between depression, CVD incidence (CVDI) and mortality from CVD (MCVD), smoking related conditions (MSRC), and all causes (MALL), in a sample data set, where depression was measured using items from a validated questionnaire and using items derived from the factor analysis of a larger questionnaire, and analyses were conducted based on continuous data and grouped data.

METHODS

Data from the PRIME Study (N=9798 men) on depression and 10-year CVD incidence and mortality were analysed using Cox proportional hazards models.

RESULTS

Using continuous data, both measures of depression resulted in the emergence of positive associations between depression and mortality (MCVD, MSRC, MALL). Using grouped data, however, associations between a validated measure of depression and MCVD, and between a measure of depression derived from factor analysis and all measures of mortality were lost.

LIMITATIONS

Low levels of depression, low numbers of individuals with high depression and low numbers of outcome events may limit these analyses, but levels are usual for the population studied.

CONCLUSIONS

These data demonstrate a possible association between depression and mortality but detecting this association is dependent on the measurement used and method of analysis. Different findings based on methodology present clear problems for the elucidation and determination of relationships. The differences here argue for the use of validated scales where possible and suggest against over-reduction via factor analysis and grouping.

Therapy and prophylaxis of opportunistic infections in HIV-infected patients: a guideline by the German and Austrian AIDS societies (DAIG/ÖAG) (AWMF 055/066)

INTRODUCTION

There was a growing need for practical guidelines for the most common OIs in Germany and Austria under consideration of the local epidemiological conditions.

MATERIALS AND METHODS

The German and Austrian AIDS societies developed these guidelines between March 2010 and November 2011. A structured Medline research was performed for 12 diseases, namely Immune reconstitution inflammatory syndrome, Pneumocystis jiroveci pneumonia, cerebral toxoplasmosis, cytomegalovirus manifestations, candidiasis, herpes simplex virus infections, varizella zoster virus infections, progressive multifocal leucencephalopathy, cryptosporidiosis, cryptococcosis, nontuberculosis mycobacteria infections and tuberculosis. Due to the lack of evidence by randomized controlled trials, part of the guidelines reflects expert opinions. The German version was accepted by the German and Austrian AIDS Societies and was previously published by the Arbeitsgemeinschaft der Wissenschaftlichen Medizinischen Fachgesellschaften (AWMF; German Association of the Scientific Medical Societies).

CONCLUSION

The review presented here is a translation of a short version of the German-Austrian Guidelines of opportunistic infections in HIV patients. These guidelines are well-accepted in a clinical setting in both Germany and Austria. They lead to a similar treatment of a heterogeneous group of patients in these countries.

Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta

Background

Metazoan multicellularity is rooted in mechanisms of cell adhesion, signaling, and differentiation that first evolved in the progenitors of metazoans. To reconstruct the genome composition of metazoan ancestors, we sequenced the genome and transcriptome of the choanoflagellate Salpingoeca rosetta, a close relative of metazoans that forms rosette-shaped colonies of cells.

Results

A comparison of the 55 Mb S. rosetta genome with genomes from diverse opisthokonts suggests that the origin of metazoans was preceded by a period of dynamic gene gain and loss. The S. rosetta genome encodes homologs of cell adhesion, neuropeptide, and glycosphingolipid metabolism genes previously found only in metazoans and expands the repertoire of genes inferred to have been present in the progenitors of metazoans and choanoflagellates. Transcriptome analysis revealed that all four S. rosetta septins are upregulated in colonies relative to single cells, suggesting that these conserved cytokinesis proteins may regulate incomplete cytokinesis during colony development. Furthermore, genes shared exclusively by metazoans and choanoflagellates were disproportionately upregulated in colonies and the single cells from which they develop.

Conclusions

The S. rosetta genome sequence refines the catalog of metazoan-specific genes while also extending the evolutionary history of certain gene families that are central to metazoan biology. Transcriptome data suggest that conserved cytokinesis genes, including septins, may contribute to S. rosetta colony formation and indicate that the initiation of colony development may preferentially draw upon genes shared with metazoans, while later stages of colony maturation are likely regulated by genes unique to S. rosetta.