SODA: an Open-Source Library for Visualizing Biological Sequence Annotation

Genome annotation is the process of identifying and labeling known genetic sequences or features within a genome. Across the various subfields within modern molecular biology, there is a common need for the visualization of such annotations. Genomic data is often visualized on web browser platforms, providing users with easy access to visualization tools without the need for installing any software or, in many cases, underlying datasets. While there exists a broad range of web-based visualization tools, there is, to my knowledge, no lightweight, modern library tailored towards the visualization of genomic data. Instead, developers charged with the task of producing a novel visualization must either adopt a complex system or fall back on general purpose visualization frameworks. Here, I present SODA, a web-based genomic annotation visualization library implemented in TypeScript as an abstraction over D3. SODA is designed to be lightweight and flexible, empowering developers with the tools to easily create customized and nuanced genomic visualizations

Synthetic control of a fitness tradeoff in yeast nitrogen metabolism

Background: Microbial communities are involved in many processes relevant to industrial and medical biotechnology, such as the formation of biofilms, lignocellulosic degradation, and hydrogen production. The manipulation of synthetic and natural microbial communities and their underlying ecological parameters, such as fitness, evolvability, and variation, is an increasingly important area of research for synthetic biology. Results: Here, we explored how synthetic control of an endogenous circuit can be used to regulate a tradeoff between fitness in resource abundant and resource limited environments in a population of Saccharomyces cerevisiae. We found that noise in the expression of a key enzyme in ammonia assimilation, Gdh1p, mediated a tradeoff between growth in low nitrogen environments and stress resistance in high ammonia environments. We implemented synthetic control of an endogenous Gdh1p regulatory network to construct an engineered strain in which the fitness of the population was tunable in response to an exogenously-added small molecule across a range of ammonia environments. Conclusion: The ability to tune fitness and biological tradeoffs will be important components of future efforts to engineer microbial communities

GASFLOW-MPI: A Scalable Computational Fluid Dynamics Code for Gases, Aerosols and Combustion. Band 1 (Theory and Computational Model (Revision 1.0) und Band 2 (Users\u27 Manual). (KIT Scientific Reports ; 7710 und 7711)

Karlsruhe Institute of Technology (KIT) is developing the parallel computational fluid dynamics code GASFLOW-MPI as a best-estimate tool for predicting transport, mixing, and combustion of hydrogen and other gases in nuclear reactor containments and other facility buildings. GASFLOW-MPI is a finite-volume code based on proven computational fluid dynamics methodology that solves the compressible Navier-Stokes equations for three-dimensional volumes in Cartesian or cylindrical coordinates

Field testing a novel high residence positioning system for monitoring the fine‐scale movements of aquatic organisms

1. Acoustic telemetry is an important tool for studying the behaviour of aquatic organisms in the wild. 2. VEMCO high residence (HR) tags and receivers are a recent introduction in the field of acoustic telemetry and can be paired with existing algorithms (e.g. VEMCO positioning system [VPS]) to obtain high‐resolution two‐dimensional positioning data. 3. Here, we present results of the first documented field test of a VPS composed of HR receivers (hereafter, HR‐VPS). We performed a series of stationary and moving trials with HR tags (mean HR transmission period = 1.5 s) to evaluate the precision, accuracy and temporal capabilities of this positioning technology. In addition, we present a sample of data obtained for five European perch Perca fluviatilis implanted with HR tags (mean HR transmission period = 4 s) to illustrate how this technology can estimate the fine‐scale behaviour of aquatic animals. 4. Accuracy and precision estimates (median [5th–95th percentile]) of HR‐VPS positions for all stationary trials were 5.6 m (4.2–10.8 m) and 0.1 m (0.02–0.07 m), respectively, and depended on the location of tags within the receiver array. In moving tests, tracks generated by HR‐VPS closely mimicked those produced by a handheld GPS held over the tag, but these differed in location by an average of ≈9 m. 5. We found that estimates of animal speed and distance travelled for perch declined when positional data for acoustically tagged perch were thinned to mimic longer transmission periods. These data also revealed a trade‐off between capturing real nonlinear animal movements and the inclusion of positioning error. 6. Our results suggested that HR‐VPS can provide more representative estimates of movement metrics and offer an advancement for studying fine‐scale movements of aquatic organisms, but high‐precision survey techniques may be needed to test these systems

Prevalence, underlying causes, and preventability of sepsis-associated mortality in US acute care hospitals

Importance: Sepsis is present in many hospitalizations that culminate in death. The contribution of sepsis to these deaths, and the extent to which they are preventable, is unknown. Objective: To estimate the prevalence, underlying causes, and preventability of sepsis-associated mortality in acute care hospitals. Design, Setting, and Participants: Cohort study in which a retrospective medical record review was conducted of 568 randomly selected adults admitted to 6 US academic and community hospitals from January 1, 2014, to December 31, 2015, who died in the hospital or were discharged to hospice and not readmitted. Medical records were reviewed from January 1, 2017, to March 31, 2018. Main Outcomes and Measures: Clinicians reviewed cases for sepsis during hospitalization using Sepsis-3 criteria, hospice-qualifying criteria on admission, immediate and underlying causes of death, and suboptimal sepsis-related care such as inappropriate or delayed antibiotics, inadequate source control, or other medical errors. The preventability of each sepsis-associated death was rated on a 6-point Likert scale. Results: The study cohort included 568 patients (289 [50.9%] men; mean [SD] age, 70.5 [16.1] years) who died in the hospital or were discharged to hospice. Sepsis was present in 300 hospitalizations (52.8%; 95% CI, 48.6%-57.0%) and was the immediate cause of death in 198 cases (34.9%; 95% CI, 30.9%-38.9%). The next most common immediate causes of death were progressive cancer (92 [16.2%]) and heart failure (39 [6.9%]). The most common underlying causes of death in patients with sepsis were solid cancer (63 of 300 [21.0%]), chronic heart disease (46 of 300 [15.3%]), hematologic cancer (31 of 300 [10.3%]), dementia (29 of 300 [9.7%]), and chronic lung disease (27 of 300 [9.0%]). Hospice-qualifying conditions were present on admission in 121 of 300 sepsis-associated deaths (40.3%; 95% CI 34.7%-46.1%), most commonly end-stage cancer. Suboptimal care, most commonly delays in antibiotics, was identified in 68 of 300 sepsis-associated deaths (22.7%). However, only 11 sepsis-associated deaths (3.7%) were judged definitely or moderately likely preventable; another 25 sepsis-associated deaths (8.3%) were considered possibly preventable. Conclusions and Relevance: In this cohort from 6 US hospitals, sepsis was the most common immediate cause of death. However, most underlying causes of death were related to severe chronic comorbidities and most sepsis-associated deaths were unlikely to be preventable through better hospital-based care. Further innovations in the prevention and care of underlying conditions may be necessary before a major reduction in sepsis-associated deaths can be achieved

Comparison of low-dose CT with CT/CT fluoroscopy guidance in percutaneous sacral and supra-acetabular cementoplasty

PURPOSEPercutaneous cementoplasty is a minimally invasive treatment modality for painful osteoporotic and pathologic sacral and supra-acetabular iliac fractures. This study compares the use of low-dose CT guidance with CT/CT fluoroscopy in sacral and supra-acetabular cementoplasty.METHODSA retrospective review of patients who had undergone sacral or supra-acetabular cementoplasty was performed with patients grouped by use of CT/CT fluoroscopy or low-dose CT guidance during the procedure. Parameters evaluated included type of fracture, laterality of lesions, pain scores, pain medication use, imaging parameters, procedure time, dose-length product, effective dose, cement volume, and complications.RESULTSThere were 17 patients identified who underwent cementoplasty utilizing dual CT/CT fluoroscopy, while 13 patients had their procedures performed with low-dose CT. There was a statistically significant decrease in radiation dose in the low-dose CT group (1481 mGy·cm) compared with the CT/CT fluoroscopy group (2809 mGy·cm) (P = 0.013). There was a significant decrease in procedure time with low-dose CT for bilateral lesions (P = 0.016). There was no significant difference between groups in complication rate (P = 0.999). Clinically nonsignificant cement extravasation occurred in two patients (10%) in the CT/CT fluoroscopy group and in one patient (8%) in the low-dose CT group (P = 0.999). There was a significant decrease in pain scores compared with baseline on the visual analogue scale in both groups at 1 week (low-dose CT P = 0.002, CT/CT fluoroscopy P = 0.008) and 1 month postprocedure (low-dose CT P = 0.014, CT/CT fluoroscopy P = 0.004), but no difference between groups at 1 day (P = 0.196), 1 week (P = 0.368), or 1 month (P = 0.514).CONCLUSIONSacral and supra-acetabular cementoplasties can be performed safely and precisely using low-dose multiple-acquisition CT guidance while providing significant radiation dose reduction with no difference in extravasation rates, postprocedural pain reduction, and complications compared with CT/CT fluoroscopy

Inupiat Participation In the Wage Economy: Effects of Culturally Adapted Jobs

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