Design principles for accurate folding of DNA origami.

We describe design principles for accurate folding of three-dimensional DNA origami. To evaluate design rules, we reduced the problem of DNA strand routing to the known problem of shortest-path finding in a weighted graph. To score candidate DNA strand routes we used a thermodynamic model that accounts for enthalpic and entropic contributions of initial binding, hybridization, and DNA loop closure. We encoded and analyzed new and previously reported design heuristics. Using design principles emerging from this analysis, we redesigned and fabricated multiple shapes and compared their folding accuracy using electrophoretic mobility analysis and electron microscopy imaging. We demonstrate accurate folding can be achieved by optimizing staple routes using our model, and provide a computational framework for applying our methodology to any design.

Association between peripheral perfusion index and postoperative acute kidney injury in major noncardiac surgery patients receiving continuous vasopressors: a post hoc exploratory analysis of the VEGA-1 trial.

BACKGROUND: The peripheral perfusion index is the ratio of pulsatile to nonpulsatile static blood flow obtained by photoplethysmography and reflects peripheral tissue perfusion. We investigated the association between intraoperative perfusion index and postoperative acute kidney injury in patients undergoing major noncardiac surgery and receiving continuous vasopressor infusions. METHODS: In this exploratory post hoc analysis of a pragmatic, cluster-randomised, multicentre trial, we obtained areas and cumulative times under various thresholds of perfusion index and investigated their association with acute kidney injury in multivariable logistic regression analyses. In secondary analyses, we investigated the association of time-weighted average perfusion index with acute kidney injury. The 30-day mortality was a secondary outcome. RESULTS: Of 2534 cases included, 8.9% developed postoperative acute kidney injury. Areas and cumulative times under a perfusion index of 3% and 2% were associated with an increased risk of acute kidney injury; the strongest association was observed for area under a perfusion index of 1% (adjusted odds ratio [aOR] 1.32, 95% confidence interval [CI] 1.00-1.74, P=0.050, per 100%∗min increase). Additionally, time-weighted average perfusion index was associated with acute kidney injury (aOR 0.82, 95% CI 0.74-0.91, P<0.001) and 30-day mortality (aOR 0.68, 95% CI 0.49-0.95, P=0.024). CONCLUSIONS: Larger areas and longer cumulative times under thresholds of perfusion index and lower time-weighted average perfusion index were associated with postoperative acute kidney injury in patients undergoing major noncardiac surgery and receiving continuous vasopressor infusions. CLINICAL TRIAL REGISTRATION: NCT04789330.

IntraCranial pressure prediction AlgoRithm using machinE learning (I-CARE): Training and Validation Study.

OBJECTIVES: Elevated intracranial pressure (ICP) is a potentially devastating complication of neurologic injury. Developing an ICP prediction algorithm to help the clinician adjust treatments and potentially prevent elevated ICP episodes. DESIGN: Retrospective study. SETTING: Three hundred thirty-five ICUs at 208 hospitals in the United States. SUBJECTS: Adults patients from the electronic ICU (eICU) Collaborative Research Database was used to train an ensemble machine learning model to predict the ICP 30 minutes in the future. Predictive performance was evaluated using a left-out test dataset and externally evaluated on the Medical Information Mart for Intensive Care-III (MIMIC-III) Matched Waveform Database. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Predictors included age, assigned sex, laboratories, medications and infusions, input/output, Glasgow Coma Scale (GCS) components, and time-series vitals (heart rate, ICP, mean arterial pressure, respiratory rate, and temperature). Each patient ICU stay was divided into successive 95-minute timeblocks. For each timeblock, the model was trained on nontime-varying covariates as well as on 12 observations of time-varying covariates at 5-minute intervals and asked to predict the 5-minute median ICP 30 minutes after the last observed ICP value. Data from 931 patients with ICP monitoring in the eICU dataset were extracted (46,207 timeblocks). The root mean squared error was 4.51 mm Hg in the eICU test set and 3.56 mm Hg in the MIMIC-III dataset. The most important variables driving ICP prediction were previous ICP history, patients' temperature, weight, serum creatinine, age, GCS, and hemodynamic parameters. CONCLUSIONS: IntraCranial pressure prediction AlgoRithm using machinE learning, an ensemble machine learning model, trained to predict the ICP of a patient 30 minutes in the future based on baseline characteristics and vitals data from the past hour showed promising predictive performance including in an external validation dataset.

Postoperative thrombotic events following major surgery in patients with a history of COVID-19: a retrospective cohort analysis of commercially insured beneficiaries in the USA.

PURPOSE: We sought to evaluate the synergistic risk of postoperative thrombosis in patients with a history of COVID-19 who undergo major surgery. Major surgery and SARS-CoV-2 infection are independently associated with an increased risk of thrombosis, but the magnitude of additional risk beyond surgery conferred by a COVID-19 history on the development of perioperative thrombotic events has not been clearly elucidated in the literature. METHODS: We conducted a retrospective cohort study among commercially insured adults in the USA from March 2020 to June 2021 using the Optum Labs Data Warehouse (OLDW), a longitudinal, real-world data asset containing deidentified administrative claims and electronic health records. We compared patients with prior COVID-19 who underwent surgery with control individuals who underwent surgery without a COVID-19 history and with control individuals who did not undergo surgery with and without a COVID-19 history. We assessed the interaction of surgery and previous COVID-19 on perioperative thrombotic events (venous thromboembolism and major adverse cardiovascular events) within 90 days using multivariable logistic regression and interaction analysis. RESULTS: Two million and two-hundred thousand eligible patients were identified from the OLDW. Patients in the surgical cohorts were older and more medically complex than nonsurgical population controls. After adjusting for confounders, only surgical exposure-not COVID-19 history-remained associated with perioperative thrombotic events (adjusted odds ratio [aOR], 4.07; 95% confidence interval [CI], 3.81 to 4.36). The multiplicative interaction term (aOR, 1.25; 95% CI, 0.96 to 1.61) and the synergy index (0.76; 95% CI, 0.56 to 1.04) suggest minimal effect modification of prior COVID-19 on surgery with regards to overall thrombotic risk. CONCLUSIONS: We found no evidence of synergistic thrombotic risk from previous COVID-19 in patients who underwent selected major surgery relative to the baseline thrombotic risk from surgery alone.

RéSUMé: OBJECTIF: Nous avons cherché à évaluer le risque synergique de thrombose postopératoire chez les patient·es ayant des antécédents de COVID-19 qui bénéficient d'une intervention chirurgicale majeure. La chirurgie majeure et l'infection par le SRAS-CoV-2 sont indépendamment associées à un risque accru de thrombose, mais l'ampleur du risque supplémentaire d'apparition de complications thrombotiques périopératoires, au-delà de la chirurgie et conféré par des antécédents de COVID-19, n'a pas été clairement élucidée dans la littérature. MéTHODE: Nous avons mené une étude de cohorte rétrospective auprès d'adultes assuré·es commercialement aux États-Unis de mars 2020 à juin 2021 à l'aide de la base de données Optum Labs Data Warehouse (OLDW), un actif de données longitudinales du monde réel contenant des requêtes administratives anonymisées et des dossiers de santé électroniques. Nous avons comparé les patient·es ayant déjà souffert de COVID-19 et ayant bénéficié d'une intervention chirurgicale avec des personnes témoins ayant bénéficié d'une intervention chirurgicale sans antécédents de COVID-19 et avec des personnes témoins n'ayant pas bénéficié de chirurgie, avec et sans antécédents de COVID-19. Nous avons évalué l'interaction de la chirurgie et des antécédents de COVID-19 avec les complications thrombotiques périopératoires (thromboembolie veineuse et événements cardiovasculaires indésirables majeurs) dans les 90 jours à l'aide d'une régression logistique multivariée et d'une analyse des interactions. RéSULTATS: Deux millions deux cent mille personnes admissibles ont été identifiées à partir du registre OLDW. Les patient·es des cohortes chirurgicales étaient plus âgé·es et présentaient une plus grande complexité médicale que les personnes témoins de la population non chirurgicale. Après ajustement pour tenir compte des facteurs de confusion, seule l'exposition chirurgicale ­ et non les antécédents de COVID-19 ­ est restée associée aux complications thrombotiques périopératoires (rapport de cotes ajusté [RCa], 4,07; intervalle de confiance [IC] à 95 %, 3,81 à 4,36). Le terme d'interaction multiplicative (RCa, 1,25; IC 95 %, 0,96 à 1,61) et l'indice de synergie (0,76; IC 95 %, 0,56 à 1,04) suggèrent une modification minimale de l'effet d'un diagnostic antérieur de COVID-19 sur la chirurgie en matière de risque thrombotique global. CONCLUSION: Nous n'avons trouvé aucune preuve de risque thrombotique synergique lié à une COVID-19 antérieure chez les patient·es ayant bénéficié d'une intervention chirurgicale par rapport au risque thrombotique de base lié à la chirurgie seule.

Development of a core outcome set for ventilation trials in neurocritical care patients with acute brain injury: protocol for a Delphi consensus study of international stakeholders.

INTRODUCTION: There is little consensus and high heterogeneity on the optimal set of relevant clinical outcomes in research studies regarding extubation in neurocritical care patients with brain injury undergoing mechanical ventilation. The aims of this study are to: (1) develop a core outcome set (COS) and (2) reach consensus on a hierarchical composite endpoint for such studies. METHODS AND ANALYSIS: The study will include a broadly representative, international panel of stakeholders with research and clinical expertise in this field and will involve four stages: (1) a scoping review to generate an initial list of outcomes represented in the literature, (2) an investigator meeting to review the outcomes for inclusion in the Delphi surveys, (3) four rounds of online Delphi consensus-building surveys and (4) online consensus meetings to finalise the COS and hierarchical composite endpoint. ETHICS AND DISSEMINATION: This study received ethical approval from the French Society of Anesthesia and Critical Care Medicine Institutional Review Board (SFAR CERAR-IRB 00010254-2023-029). The study results will be disseminated through communication to stakeholders, publication in a peer-reviewed journal, and presentations at conferences. TRIAL REGISTRATION NUMBER: This study is registered with the Core Outcome Measures in Effectiveness Trials (COMET) Initiative.

A rapid and high-throughput T cell immunophenotyping assay for cellular therapy bioprocess using the Cellaca® PLX image cytometer.

In cellular therapies chimeric antigen receptor (CAR) T or NK cells undergo phenotypic analysis at multiple stages during discovery and development of novel therapies. Patient samples are routinely analyzed via flow cytometry for population identification and distribution of CD3, CD4, and CD8 positive T cells. As an alternative or orthogonal method, image cytometry systems have been used to perform simple cell-based assays in lieu of flow cytometry. Recently, a new image cytometry system, the Cellaca® PLX (Revvity Health Sciences, Inc., Lawrence, MA), was developed for high-throughput cell counting and viability, immunophenotyping, transfection/transduction efficiency, and cell health assays. This novel instrument allows investigators to quickly assess several critical quality attributes (CQAs) such as cell identity, viability, and other relevant biological functions recommended by the International Organization for Standardization using the ISO Cell Characterization documents focused on cellular therapeutic products. In this work, we demonstrate a rapid and high-throughput image cytometry detection method for cellular immunophenotyping and viability using the Cellaca PLX system for samples throughout the cellular therapy workflow. Freshly isolated peripheral blood mononuclear cells (PBMCs) underwent red blood cell (RBC) lysis and CD3 enrichment. Samples were then subsequently stained with Hoechst/CD3/CD4/CD8 or Hoechst/CD3/CD8/RubyDead Dye surface marker kits and measured on the Cellaca PLX and three different flow cytometers for side-by-side comparison and assay validation. Acquisition and analysis of cell viability and cell populations was shown to be faster and more efficient process compared to flow while achieving highly comparable results between the two technology platforms. This data shows that the Cellaca PLX Image Cytometer may provide a rapid alternative or orthogonal method for PBMC immunophenotyping experiments, as well as potentially streamline the workflow to quickly move precious patient samples downstream within the development processes.

Leveraging observational data to identify targeted patient populations for future randomized trials.

Randomized controlled trials reported in the literature are often affected by poor generalizability, and pragmatic trials have become an increasingly utilized workaround approach to overcome logistical limitations and explore routine interventions demonstrating equipoise in clinical practice. Intravenous albumin, for example, is commonly administered in the perioperative setting despite lacking supportive evidence. Given concerns for cost, safety, and efficacy, randomized trials are needed to explore the clinical equipoise of albumin therapy in this setting, and we therefore present an approach to identifying populations exposed to perioperative albumin to encourage clinical equipoise in patient selection and optimize study design for clinical trials.

Availability of information needed to evaluate algorithmic fairness - A systematic review of publicly accessible critical care databases.

BACKGROUND: Machine learning (ML) may improve clinical decision-making in critical care settings, but intrinsic biases in datasets can introduce bias into predictive models. This study aims to determine if publicly available critical care datasets provide relevant information to identify historically marginalized populations. METHOD: We conducted a review to identify the manuscripts that report the training/validation of ML algorithms using publicly accessible critical care electronic medical record (EMR) datasets. The datasets were reviewed to determine if the following 12 variables were available: age, sex, gender identity, race and/or ethnicity, self-identification as an indigenous person, payor, primary language, religion, place of residence, education, occupation, and income. RESULTS: 7 publicly available databases were identified. Medical Information Mart for Intensive Care (MIMIC) reports information on 7 of the 12 variables of interest, Sistema de Informação de Vigilância Epidemiológica da Gripe (SIVEP-Gripe) on 7, COVID-19 Mexican Open Repository on 4, and eICU on 4. Other datasets report information on 2 or fewer variables. All 7 databases included information about sex and age. Four databases (57%) included information about whether a patient identified as native or indigenous. Only 3 (43%) included data about race and/or ethnicity. Two databases (29%) included information about residence, and one (14%) included information about payor, language, and religion. One database (14%) included information about education and patient occupation. No databases included information on gender identity and income. CONCLUSION: This review demonstrates that critical care publicly available data used to train AI algorithms do not include enough information to properly look for intrinsic bias and fairness issues towards historically marginalized populations.

Norepinephrine versus phenylephrine for treating hypotension during general anaesthesia in adult patients undergoing major noncardiac surgery: a multicentre, open-label, cluster-randomised, crossover, feasibility, and pilot trial.

BACKGROUND: Intraoperative hypotension is associated with postoperative complications. The use of vasopressors is often required to correct hypotension but the best vasopressor is unknown. METHODS: A multicentre, cluster-randomised, crossover, feasibility and pilot trial was conducted across five hospitals in California. Phenylephrine (PE) vs norepinephrine (NE) infusion as the first-line vasopressor in patients under general anaesthesia alternated monthly at each hospital for 6 months. The primary endpoint was first-line vasopressor administration compliance of 80% or higher. Secondary endpoints were acute kidney injury (AKI), 30-day mortality, myocardial injury after noncardiac surgery (MINS), hospital length of stay, and rehospitalisation within 30 days. RESULTS: A total of 3626 patients were enrolled over 6 months; 1809 patients were randomised in the NE group, 1817 in the PE group. Overall, 88.2% received the assigned first-line vasopressor. No drug infiltrations requiring treatment were reported in either group. Patients were median 63 yr old, 50% female, and 58% white. Randomisation in the NE group vs PE group did not reduce readmission within 30 days (adjusted odds ratio=0.92; 95% confidence interval, 0.6-1.39), 30-day mortality (1.01; 0.48-2.09), AKI (1.1; 0.92-1.31), or MINS (1.63; 0.84-3.16). CONCLUSIONS: A large and diverse population undergoing major surgery under general anaesthesia was successfully enrolled and randomised to receive NE or PE infusion. This pilot and feasibility trial was not powered for adverse postoperative outcomes and a follow-up multicentre effectiveness trial is planned. CLINICAL TRIAL REGISTRATION: NCT04789330 (ClinicalTrials.gov).

Intraoperative Use of Albumin in Major Noncardiac Surgery: Incidence, Variability, and Association With Outcomes.

BACKGROUND: The impact of albumin use during major surgery is unknown, and a dearth of evidence governing its use in major noncardiac surgery has long precluded its standardization in clinical guidelines. OBJECTIVE: In this study, we investigate institutional variation in albumin use among medical centers in the United States during major noncardiac surgery and explore the association of intraoperative albumin administration with important postoperative outcomes. METHODS: The study is an observational retrospective cohort analysis performed among 54 U.S. hospitals in the Multicenter Perioperative Outcomes Group and includes adult patients who underwent major noncardiac surgery under general anesthesia between January 2014 and June 2020. The primary endpoint was the incidence of albumin administration. Secondary endpoints are acute kidney injury (AKI), net-positive fluid balance, pulmonary complications, and 30-day mortality. Albumin-exposed and albumin-unexposed cases were compared within a propensity score-matched cohort to evaluate associations of albumin use with outcomes. RESULTS: Among 614,215 major surgeries, predominantly iso-oncotic albumin was administered in 15.3% of cases and featured significant inter-institutional variability in use patterns. Cases receiving intraoperative albumin involved patients of higher American Society of Anesthesiologists physical status and featured larger infused crystalloid volumes, greater blood loss, and vasopressor use. Overall, albumin was most often administered at high-volume surgery centers with academic affiliation, and within a propensity score-matched cohort (n=153,218), the use of albumin was associated with AKI (aOR 1.24, 95% CI 1.20-1.28, P <0.001), severe AKI (aOR 1.45, 95% CI 1.34-1.56, P <0.001), net-positive fluid balance (aOR 1.18, 95% CI 1.16-1.20, P <0.001), pulmonary complications (aOR 1.56, 95% CI 1.30-1.86, P <0.001), and 30-day all-cause mortality (aOR 1.37, 95% CI 1.26-1.49, P <0.001). CONCLUSIONS: Intravenous albumin is commonly administered among noncardiac surgeries with significant inter-institutional variability in use in the United States. Albumin administration was associated with an increased risk of postoperative complications.

Extubation in neurocritical care patients: the ENIO international prospective study.

PURPOSE: Neurocritical care patients receive prolonged invasive mechanical ventilation (IMV), but there is poor specific information in this high-risk population about the liberation strategies of invasive mechanical ventilation. METHODS: ENIO (NCT03400904) is an international, prospective observational study, in 73 intensive care units (ICUs) in 18 countries from 2018 to 2020. Neurocritical care patients with a Glasgow Coma Score (GCS) ≤ 12, receiving IMV ≥ 24 h, undergoing extubation attempt or tracheostomy were included. The primary endpoint was extubation failure by day 5. An extubation success prediction score was created, with 2/3 of patients randomly allocated to the training cohort and 1/3 to the validation cohort. Secondary endpoints were the duration of IMV and in-ICU mortality. RESULTS: 1512 patients were included. Among the 1193 (78.9%) patients who underwent an extubation attempt, 231 (19.4%) failures were recorded. The score for successful extubation prediction retained 20 variables as independent predictors. The area under the curve (AUC) in the training cohort was 0.79 95% confidence interval (CI95) [0.71-0.87] and 0.71 CI95 [0.61-0.81] in the validation cohort. Patients with extubation failure displayed a longer IMV duration (14 [7-21] vs 6 [3-11] days) and a higher in-ICU mortality rate (8.7% vs 2.4%). Three hundred and nineteen (21.1%) patients underwent tracheostomy without extubation attempt. Patients with direct tracheostomy displayed a longer duration of IMV and higher in-ICU mortality than patients with an extubation attempt (success and failure). CONCLUSIONS: In neurocritical care patients, extubation failure is high and is associated with unfavourable outcomes. A score could predict extubation success in multiple settings. However, it will be mandatory to validate our findings in another prospective independent cohort.

Fluids, vasopressors, and acute kidney injury after major abdominal surgery between 2015 and 2019: a multicentre retrospective analysis.

BACKGROUND: Practice patterns related to intraoperative fluid administration and vasopressor use have potentially evolved over recent years. However, the extent of such changes and their association with perioperative outcomes, such as the development of acute kidney injury (AKI), have not been studied. METHODS: We performed a retrospective analysis of major abdominal surgeries in adults across 26 US hospitals between 2015 and 2019. The primary outcome was AKI as defined by the Kidney Disease Improving Global Outcomes definition (KDIGO) using only serum creatinine criteria. Univariable linear predictive additive models were used to describe the dose-dependent risk of AKI given fluid administration or vasopressor use. RESULTS: Over the study period, we observed a decrease in the volume of crystalloid administered, a decrease in the proportion of patients receiving more than 10 ml kg-1 h-1 of crystalloid, an increase in the amount of norepinephrine equivalents administered, and a decreased duration of hypotension. The incidence of AKI increased between 2016 and 2019. An increase of crystalloid administration from 1 to 10 ml kg-1 h-1 was associated with a 58% decreased risk of AKI. CONCLUSIONS: Despite decreased duration of hypotension during the study period, decreased fluid administration and increased vasopressor use were associated with increased incidence of AKI. Crystalloid administration below 10 ml kg-1 h-1 was associated with an increased risk of AKI. Although no causality can be concluded, these data suggest that prevention and treatment of hypotension during abdominal surgery with liberal use of vasopressors at the expense of fluid administration is associated with an increased risk of postoperative AKI.

Risk factors of long term symptoms and outcomes among patients discharged after covid-19: prospective, multicentre observational study.

Objective: To investigate risk factors and subphenotypes associated with long term symptoms and outcomes after hospital admission for covid-19. Design: Prospective, multicentre observational study. Setting: 93 hospitals in France. Participants: Data from 2187 adults admitted to hospital with covid-19 in France between 1 February 2020 and 30 June 2021. Main outcome measures: Primary endpoint was the total number of persistent symptoms at six months after hospital admission that were not present before admission. Outcomes examined at six months were persistent symptoms, Hospital Anxiety and Depression Scale, six minute walk test distances, 36-Item Short Form Health Survey scores, and ability to resume previous professional activities and self-care. Secondary endpoints included vital status at six months, and results of standardised quality-of-life scores. Additionally, an unsupervised consensus clustering algorithm was used to identify subphenotypes based on the severity of hospital course received by patients. Results: 1109 (50.7%) of 2187 participants had at least one persistent symptom. Factors associated with an increased number of persistent symptoms were in-hospital supplemental oxygen (odds ratio 1.12, 95% confidence interval 1 to 1.24), no intensive care unit admission (1.15, 1.01 to 1.32), female sex (1.33, 1.22 to 1.45), gastrointestinal haemorrhage (1.51, 1.02 to 2.23), a thromboembolic event (1.66, 1.17 to 2.34), and congestive heart failure (1.76, 1.27 to 2.43). Three subphenotypes were identified: including patients with the least severe hospital course (based on ventilatory support requirements). Although Hospital Anxiety and Depression Scale scores were within normal values for all groups, patients of intermediate severity and more comorbidities had a higher median Hospital Anxiety and Depression Scale score than did the other subphenotypes. Patients in the subphenotype with most severe hospital course had worse short form-36 scores and were less able to resume their professional activity or care for themselves as before compared with other subphenotypes. Conclusions: Persistent symptoms after hospital admission were frequent, regardless of acute covid-19 severity. However, patients in more severe subphenotypes had a significantly worse functional status and were less likely to resume their professional activity or able to take care of themselves as before. Trial registration: NCT04262921.

Opal: an implementation science tool for machine learning clinical decision support in anesthesia.

Opal is the first published example of a full-stack platform infrastructure for an implementation science designed for ML in anesthesia that solves the problem of leveraging ML for clinical decision support. Users interact with a secure online Opal web application to select a desired operating room (OR) case cohort for data extraction, visualize datasets with built-in graphing techniques, and run in-client ML or extract data for external use. Opal was used to obtain data from 29,004 unique OR cases from a single academic institution for pre-operative prediction of post-operative acute kidney injury (AKI) based on creatinine KDIGO criteria using predictors which included pre-operative demographic, past medical history, medications, and flowsheet information. To demonstrate utility with unsupervised learning, Opal was also used to extract intra-operative flowsheet data from 2995 unique OR cases and patients were clustered using PCA analysis and k-means clustering. A gradient boosting machine model was developed using an 80/20 train to test ratio and yielded an area under the receiver operating curve (ROC-AUC) of 0.85 with 95% CI [0.80-0.90]. At the default probability decision threshold of 0.5, the model sensitivity was 0.9 and the specificity was 0.8. K-means clustering was performed to partition the cases into two clusters and for hypothesis generation of potential groups of outcomes related to intraoperative vitals. Opal's design has created streamlined ML functionality for researchers and clinicians in the perioperative setting and opens the door for many future clinical applications, including data mining, clinical simulation, high-frequency prediction, and quality improvement.

Chronic traumatic encephalopathy: Diagnostic updates and advances.

Chronic traumatic encephalopathy (CTE) is a progressive neurodegenerative disease that occurs secondary to repetitive mild traumatic brain injury. Current clinical diagnosis relies on symptomatology and structural imaging findings which often vary widely among those with the disease. The gold standard of diagnosis is post-mortem pathological examination. In this review article, we provide a brief introduction to CTE, current diagnostic workup and the promising research on imaging and fluid biomarker diagnostic techniques. For imaging, we discuss quantitative structural analyses, DTI, fMRI, MRS, SWI and PET CT. For fluid biomarkers, we discuss p-tau, TREM2, CCL11, NfL and GFAP.

Affordable compensator for IMRT delivery designed for low-and-middle income countries, a Monte Carlo study.

We propose a novel cost-effective compensator that can be used to facilitate access to IMRT in low-and-middle income countries. The compensator has the advantages of simplicity, less downtime, increased reliability and less impact on treatment quality from patient motion during treatment. Moreover, the system can be used with either a cobalt-60 unit or linear accelerator. In this Monte Carlo study, the dosimetric properties of the new compensator design have been evaluated. Results were obtained for different field sizes of cobalt teletherapy machine, and the dose was scored at 0.5 cm depth in a water phantom. The effects of compensator thickness, filling material type and shape, and field size were identified. Furthermore, the percentage depth dose and beam profiles for various field sizes and at different depths were obtained. Beam profiles show no significant signature of the beads relative to a solid compensator; in addition, they exhibit a better flatness while preserving symmetry for all field sizes. A reusable bead-based compensator appears to be feasible, and provides dose distribution similar to a solid compensator with low cost and no hazards. Our results avail the ongoing efforts to expand the reach to IMRT in low- and middle-income countries.

A ring-based compensator IMRT system optimized for low- and middle-income countries: Design and treatment planning study.

PURPOSE: We propose a novel compensator-based IMRT system designed to provide a simple, reliable, and cost-effective adjunct technology, with the goal of expanding global access to advanced radiotherapy techniques. The system would employ easily reusable tungsten bead compensators that operate independent of a gantry (e.g., mounted in a ring around the patient). Thereby the system can be retrofitted to existing linac and cobalt teletherapy units. This study explores the quality of treatment plans from the proposed system and the dependence on associated design parameters. METHODS: We considered 60 Co-based plans as the most challenging scenario for dosimetry and benchmarked them against clinical MLC-based plans delivered on a linac. Treatment planning was performed in the Pinnacle treatment planning system with commissioning based on Monte Carlo simulations of compensated beams. 60 Co-compensator IMRT plans were generated for five patients with head-and-neck cancer and five with gynecological cancer and compared to respective IMRT plans using a 6 MV linac beam with an MLC. The dependence of dosimetric endpoints on compensator resolution, thickness, position, and number of beams was assessed. Dosimetric accuracy was validated by Monte Carlo simulations of dose distribution in a water phantom from beams with the IMRT plan compensators. RESULTS: The 60 Co-compensator plans had on average equivalent PTV coverage and somewhat inferior OAR sparing compared to the 6 MV-MLC plans, but the differences in dosimetric endpoints were clinically acceptable. Calculated treatment times for head-and-neck plans were 7.6 ± 2.0 min vs 3.9 ± 0.8 min (6 MV-MLC vs 60 Co-compensator) and for gynecological plans were 8.7 ± 3.1 min vs 4.3 ± 0.4 min. Plan quality was insensitive to most design parameters over much of the ranges studied, with no degradation found when the compensator resolution was finer than 6 mm, maximum thickness at least 2 tenth-value-layers, and more than five beams were used. Source-to-compensator distances of 53 and 63 cm resulted in very similar plan quality. Monte Carlo simulations suggest no increase in surface dose for the geometries considered here. Simulated dosimetric validation tests had median gamma pass rates of 97.6% for criteria of 3% (global)/3 mm with a 10% threshold. CONCLUSIONS: The novel ring-compensator IMRT system can produce plans of comparable quality to standard 6 MV-MLC systems. Even when 60 Co beams are used the plan quality is acceptable and treatment times are substantially reduced. 60 Co-compensator IMRT plans are adequately modeled in an existing commercial treatment planning system. These results motivate further development of this low-cost adaptable technology with translation through clinical trials and deployment to expand the reach of IMRT in low- and middle-income countries.

CRISPR/Cas-based screening of long non-coding RNAs (lncRNAs) in macrophages with an NF-κB reporter.

The innate immune system protects against infections by initiating an inducible inflammatory response. NF-κB is one of the critical transcription factors controlling this complex response, but some aspects of its regulation remain unclear. For example, although long non-coding RNAs (lncRNAs) have been shown to critically regulate gene expression, only a fraction of these have been functionally characterized, and the extent to which lncRNAs control NF-κB expression is unknown. Here, we describe the generation of a GFP-based NF-κB reporter system in immortalized murine bone marrow-derived macrophages (iBMDM). Activation of this reporter, using Toll-like receptor ligands, resulted in GFP expression, which could be monitored by flow cytometry. We also established a CRISPR/Cas9 gene deletion system in this NF-κB reporter line, enabling us to screen for genes that regulate NF-κB signaling. Our deletion-based approach identified two long intergenic non-coding(linc)RNAs, lincRNA-Cox2 and lincRNA-AK170409, that control NF-κB signaling. We demonstrate a potential novel role for lincRNA-Cox2 in promoting IκBα degradation in the cytoplasm. For lincRNA-AK170409, we provide evidence that this nuclearly-localized lincRNA regulates a number of inflammation-related genes. In conclusion, we have established an NF-κB-GFP iBMDM reporter cell line and a line that stably expresses Cas9. Our approach enabled the identification of lincRNA-Cox2 and lincRNA-AK170409 as NF-κB regulators, and this tool will be useful for identifying additional genes involved in regulating this transcription factor critical for immune function.