#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus obscure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.

#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus ob-scure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.

ACM REFERENCE FORMAT

Abigail Dommer 1† , Lorenzo Casalino 1† , Fiona Kearns 1† , Mia Rosenfeld 1 , Nicholas Wauer 1 , Surl-Hee Ahn 1 , John Russo, 2 Sofia Oliveira 3 , Clare Morris 1 , AnthonyBogetti 4 , AndaTrifan 5,6 , Alexander Brace 5,7 , TerraSztain 1,8 , Austin Clyde 5,7 , Heng Ma 5 , Chakra Chennubhotla 4 , Hyungro Lee 9 , Matteo Turilli 9 , Syma Khalid 10 , Teresa Tamayo-Mendoza 11 , Matthew Welborn 11 , Anders Christensen 11 , Daniel G. A. Smith 11 , Zhuoran Qiao 12 , Sai Krishna Sirumalla 11 , Michael O'Connor 11 , Frederick Manby 11 , Anima Anandkumar 12,13 , David Hardy 6 , James Phillips 6 , Abraham Stern 13 , Josh Romero 13 , David Clark 13 , Mitchell Dorrell 14 , Tom Maiden 14 , Lei Huang 15 , John McCalpin 15 , Christo- pherWoods 3 , Alan Gray 13 , MattWilliams 3 , Bryan Barker 16 , HarindaRajapaksha 16 , Richard Pitts 16 , Tom Gibbs 13 , John Stone 6 , Daniel Zuckerman 2 *, Adrian Mulholland 3 *, Thomas MillerIII 11,12 *, ShantenuJha 9 *, Arvind Ramanathan 5 *, Lillian Chong 4 *, Rommie Amaro 1 *. 2021. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy ofDeltaSARS-CoV-2 in a Respiratory Aerosol. In Supercomputing '21: International Conference for High Perfor-mance Computing, Networking, Storage, and Analysis . ACM, New York, NY, USA, 14 pages. https://doi.org/finalDOI.

An integrated view of p53 dynamics, function, and reactivation

The tumor suppressor p53 plays a vital role in responding to cell stressors such as DNA damage, hypoxia, and tumor formation by inducing cell-cycle arrest, senescence, or apoptosis. Expression level alterations and mutational frequency implicates p53 in most human cancers. In this review, we show how both computational and experimental methods have been used to provide an integrated view of p53 dynamics, function, and reactivation potential. We argue that p53 serves as an exceptional case study for developing methods in modeling intrinsically disordered proteins. We describe how these methods can be leveraged to improve p53 reactivation molecule design and other novel therapeutic modalities, such as PROteolysis TARgeting Chimeras (PROTACs).

Initial development and pilot testing of observer-reported outcomes (ObsROs) for children with cystic fibrosis ages 0-11years

PURPOSE

Patient-reported outcomes are important clinical trial endpoints. Young children may not be able to reliably report on how they feel or function, so observer-reported outcomes (ObsROs) may be more appropriate for them. The purpose of this study was to develop and pilot field test electronic parent-reported observational instruments for children with cystic fibrosis (CF) 0-6 and 7-11years of age.

METHODS

We performed concept elicitation interviews with parents of children with CF ≤11years of age to elicit the respiratory signs they could observe at baseline and during an acute respiratory illness. The resulting instruments were refined based on interviews with parents and clinicians. We conducted a pilot field test to evaluate test-retest reliability and the ability of items to distinguish well and sick periods.

RESULTS

The instruments consist of 17 items assessing respiratory signs and observable CF-related impacts. Test-retest reliability was acceptable for both age groups but discrimination was low for ages 7-11, likely reflecting less direct observation of older children by their parents.

CONCLUSIONS

An ObsRO for children with CF ages 0-6 appears promising, while self-report may be more appropriate for children >6years of age. Next steps for the 0-6year old instrument will be utilizing it as an exploratory endpoint in clinical trials to enable item reduction, scale development, and further reliability and validity testing. Ultimately, this ObsRO could be a promising endpoint for early intervention trials in young children with CF.

Longitudinal development of initial, chronic and mucoid Pseudomonas aeruginosa infection in young children with cystic fibrosis

BACKGROUND

While the emergence of chronic and mucoid Pseudomonas aeruginosa (Pa) infection are both associated with poorer outcomes among CF patients, their relationship is poorly understood. We examined the longitudinal relationship of incident, chronic and mucoid Pa in a contemporary, young CF cohort in the current era of Pa eradication therapy.

METHODS

This retrospective cohort was comprised of patients in the U.S. CF Foundation Patient Registry born 2006-2015, diagnosed before age 2, and with at least 3 respiratory cultures annually. Incidence and age-specific prevalence of Pa infection stages (initial and chronic [≥ 3Pa+cultures in prior year]) and of mucoid Pa were summarized. Transition times and the interaction between Pa stage and acquisition of mucoid Pa were examined via Cox models.

RESULTS

Among the 5592 CF patients in the cohort followed to a mean age of 5.5years, 64% (n=3580) acquired Pa. Of those, 13% (n=455) developed chronic Pa and 17% (n=594) cultured mucoid Pa. Among those with mucoid Pa, 36% (211/594) had it on their first recorded Pa+culture, while mucoid Pa emerged at or after entering the chronic stage in 12% (73/594). Mucoidy was associated with significantly increased risk of transition to chronic Pa infection (HR=2.59, 95% CI 2.11, 3.19).

CONCLUSIONS

Two-thirds of early-diagnosed young children with CF acquired Pa during a median 5.6years of follow up, among whom 13% developed chronic Pa and 17% acquired mucoid Pa. Contrary to our hypothesis, 87% of young children who developed mucoid Pa did so before becoming chronically infected.

Season is associated with Pseudomonas aeruginosa acquisition in young children with cystic fibrosis

Pseudomonas aeruginosa, the principal respiratory pathogen in cystic fibrosis (CF) patients, is ubiquitous in the environment. Initial P. aeruginosa isolates in CF patients are generally environmental in nature. However, little information regarding seasonality of P. aeruginosa acquisition is available. We conducted a retrospective study to evaluate the seasonality of initial P. aeruginosa acquisition in young children with CF in the USA using the Cystic Fibrosis Foundation National Patient Registry from 2003 to 2009. Additionally, we assessed whether seasonal acquisition varied by climate zone. A total of 4123 children met inclusion criteria and 45% (n = 1866) acquired P. aeruginosa during a mean 2.0 years (SD 0.2 years) of follow up. Compared with winter, increased P. aeruginosa acquisition was observed in summer (incidence rate ratio (IRR): 1.22; 95% CI: 1.07-1.40) and autumn (IRR: 1.34; 95% CI: 1.18-1.52), with lower acquisition observed in spring (IRR: 0.81; 95% CI: 0.70-0.94). Seasonal variations in P. aeruginosa acquisition rates in the temperate and continental climate zones were similar to those in the overall cohort. In contrast, no significant seasonal effect was observed in the dry climate zone. In a corresponding analysis, no seasonal difference was observed in the rate of acquisition of Staphylococcus aureus, another common CF respiratory pathogen. These results provide preliminary support that climatic factors may be associated with initial P. aeruginosa acquisition in CF patients. Investigation and identification of specific risk factors, as well as awareness of seasonal variation, could potentially inform clinical recommendations including increased awareness of infection control and prevention strategies.

Phase I trial of sorafenib in patients with recurrent or progressive malignant glioma

Sorafenib is an inhibitor of multiple kinases that has demonstrated antiproliferative and antiangiogenic activity in a number of in vitro and in vivo model systems. A phase I study was conducted to determine the maximum tolerated dose (MTD) of sorafenib in patients with recurrent malignant glioma. Sorafenib was given orally, twice a day (BID), continuously in 28-day cycles. The dose was escalated in 2 groups of patients stratified by use of enzyme-inducing antiseizure drugs (± EIASDs). Dose-limiting toxicity (DLT) was defined as any grades 3-4 nonhematological toxicity, grade 4 hematological toxicity, and febrile neutropenia. The number of evaluable patients enrolled in the +EIASD and -EIASD arms were 23 and 24, respectively. DLTs were predominantly dermatological and gastrointestinal effects, as observed in previous clinical trials of sorafenib. The MTD was 600 mg BID for patients receiving EIASDs and 800 mg BID for those who were not. The plasma pharmacokinetics of sorafenib were not significantly affected by the concurrent administration of EIASDs. The MTD of sorafenib given orally BID on a continuous basis was established as 600 mg BID in patients with malignant glioma who were concurrently receiving EIASDs and 800 mg BID in those who were not. Further evaluation is warranted of sorafenib at the recommended MTD against recurrent or progressive malignant glioma in combination with other molecularly targeted drugs or in the newly diagnosed setting concurrent with chemoradiation.

Cognitive symptoms, cervical range of motion and pain as prognostic factors after whiplash trauma

OBJECTIVES

To evaluate pain, cervical range of motion (CROM) and cognitive symptoms as predictors for poor prognosis defined as sick leave 3 years later.

MATERIAL AND METHODS

In 97 patients CROM, pain intensity and cognitive symptoms were measured immediately following trauma, at 6 months and 3 years. Patients were also asked at 3 years if they had been on sick leave the last 6 months.

RESULTS

Pain intensity and reduced CROM were not clinically useful as predictors of later sick leave. The best predictors were presence within 96 h after injury of the two cognitive symptoms 'being easily distracted' (odds ratio 8.7-50) and 'easily irritated' (odds ratio 5.3-31).

CONCLUSIONS

Initial pain and reduced CROM may be related to minor tissue damage which often heals while late functionality is more dependent on other factors such as cognitive dysfunction. For patients with whiplash-associated disorders two simple questions should be asked; 'Are you currently easily irritated?' and 'Are you currently easily distracted (e.g. is it difficult for you to follow a conversation if several people are talking in the room at the same time)?'. An affirmative answer to any of these questions indicates an increased risk for poor prognosis defined as sick leave 3 years later.

[Gliomatosis cerebri: review of 22 patients]

INTRODUCTION

gliomatosis cerebri is a diffuse astrocytic neoplasm that involves more than two lobes of the brain. Treatment is not well defined and the prognosis is considered poor.

METHODS

retrospective analysis of 22 patients with gliomatosis cerebri.

RESULTS

we identified 17 men and 5 women (median age 54 years) seen in a Division of Neuro-oncology over a 6 year period. Patients presented with focal sensorimotor or visual deficits (86.4%), seizures (36.4%), cognitive dysfunction (27.3%), or headache (27.3%), suggesting in some cases stroke, migraine, or limbic encephalitis. All patients had bilateral involvement; the regions involved included, temporal (19), basal ganglia (18), frontal (17), parietal (17), corpus callosum (10), and occipital (9). The most frequent pathological findings were grade III astrocytoma (36.4%), grade II astrocytoma (22.7%), and grade IV astrocytoma (18.3%). Nine patients were diagnosed within the first month of symptom development, 11 between the first month and 1 year, and 2 after one year. Seventeen patients received treatment with chemotherapy, radiotherapy or both, and 12 patients (70.6%) had a clinical or radiological response. The median follow-up was 13 months, median progression free survival 6 months, and median survival 9,5 months (15 months if the patients received treatment). Eight patients had thromboembolic events.

CONCLUSIONS

gliomatosis cerebri has a variable clinical course. Treatment often results in clinical responses. In this study de median survival of patients who received treatment was similar to that reported in series of glioblastoma multiforme.

Views regarding the provision of prehospital critical care in the UK

AIMS

There is a lack of consensus regarding the role for critical care in the prehospital environment in the UK. It was hypothesised that this related to differences in views and understanding among opinion leaders within influential prehospital care organisations.

METHODS

A 38-item survey was developed by an established paramedic-physician prehospital critical care service. The survey was distributed to individuals in senior positions within seven organisations that have a major influence on UK prehospital services. Analysis comprised a description of the distribution of results, assessment of the level of agreement with each statement by professional background and current involvement in prehospital critical care and evaluation of the overall consistency of responses. Free-text comments were invited to illustrate the reasoning behind each response.

RESULTS

There were 32 respondents. The estimated response rate was 40%. The consistency of the questionnaire responses was very high. Overall, all individuals agreed with most of the statements. Paramedic respondents were more likely to disagree with statements that suggested that critical care involved interventions that exceed the current capability of the NHS ambulance service (p<0.05). Free-text comments revealed wide differences of opinion.

CONCLUSION

Although there appears to be broad agreement among opinion leaders regarding the concepts underpinning existing prehospital critical care services, areas of contention are highlighted that may help explain the current lack of consensus. Cooperative efforts to assess the current demand and clinical evidence would assist in the creation of a joint consensus and allow effective future planning for the provision of prehospital critical care throughout the UK.

Current survival statistics for patients with newly diagnosed glioblastoma treated with radiation and temozolomide on research studies in the United States

2003

Background: Many novel agents are being studied in combination with radiation and temozolomide (RT+TMZ) in newly diagnosed glioblastoma using survival as the primary endpoint. These single arm phase II studies generally plan to compare their results with those reported from the phase III EORTC RT+TMZ study (Stupp, NEJM, 2005). Methods: The NABTT CNS Consortium has completed accrual to three RT+TMZ+ novel agent studies using the same eligibility criteria. A total of 281 patients with newly diagnosed glioblastoma were enrolled. The novel agents included talampanel (72 pts), poly ICLC (97 pts), and cilengitide (112 pts). The survival data emerging from these three single arm phase II studies was compared with the published EORTC data. Results: The median age, KPS, and percent undergoing debulking surgery for EORTC patients was 56, 86% (WHO 0–1), and 84% and for NABTT patients receiving talampanel 60, 90, and 77%, poly ICLC 56, 90, 86%, and cilengitide 55, 90, and 76%. A total of 247 patients (88%) were ages 18–70 making them comparable to the EORTC patient population. Currently available survival data for these NABTT and EORTC studies are provided below. MGMT methylation status and survival based on dose levels are not currently available. Conclusions: Survival of newly diagnosed glioblastoma patients treated with RT+TMZ + novel agents at 9 NABTT institutions accruing from 2005 to 2008 appears increased compared to RT+TMZ at 85 EORTC institutions accruing from 2000 to 2002. These results do not appear related to a specific effective agent. As a result, caution should be exercised when comparing outcomes from recently conducted Phase II studies in this patient population to published EORTC data.

[Table: see text]

No significant financial relationships to disclose.

NABTT 0306: A randomized phase II trial of EMD 121974 in conjunction with concomitant and adjuvant temozolomide with radiation therapy in patients with newly diagnosed glioblastoma multiforme (GBM)

2001

Background: EMD 121974 (cilengitide) is a selective integrin receptor inhibitor that is well tolerated and has demonstrated biological activity in patients with malignant glioma. The objectives of this phase II trial were to determine safety when combined with chemoradiation and estimate the overall survival for two different doses in newly diagnosed GBM. Methods: A total of 112 patients were accrued onto the trial through the NABTT CNS consortium. Cilengitide was administered by one-hour infusion twice a week with 18 patients treated in a safety run-in phase of 6 patients at the tested dose levels of 500 mg, 1000 mg, and 2000 mg. After safety completion, 94 patients were randomly assigned to either 500 mg or 2000 mg groups. To date, 55 out of 112 (49%) patients have died. Overall survival was estimated using all patients in this trial regardless of their treating dose. Results: The median age was 55 years old (range: 22–88) and the median KPS was 90 (range: 60–100). 86 out of the 112 (76.8%) had a craniotomy as their initial surgical procedure and 25 patients (22%) had a biopsy. There were no DLTs during the safety run-in phase. The estimated median survival time is 18.9 months (95% CI: 16.3 -30.0 months) for patients treated with RT+TMZ+EMD. The trial was closed to accrual on December 31, 2007. To date, 89 out of 112 patients were alive 12 months from their initial diagnosis. The overall survival at 12 months for all patients is 79.5% (95% CI: 71–87%). MGMT methylation status and survival based on dose levels received are not currently available. Conclusions: EMD 121974 (cilengitide) is well-tolerated when combined with standard chemoradiation (TMZ+RT) and may improve survival for patients newly diagnosed with GBM given the substantial differences between the estimated median survival and that seen in the EORTC study (Stupp, N Engl J Med, 2005).

[Table: see text]

A phase I trial of sorafenib (BAY 43–9006) for patients with recurrent or progressive malignant glioma (NABTT 0401)

2058

Background: Sorafenib (BAY 43–9006) is a small molecule inhibitor of multiple kinases to include raf, VEGF receptors, and PDGF receptors. The molecule has demonstrated anti-proliferative and anti-angiogenic activity in a number of in vitro and in vivo model systems. Methods: In this multi-institutional trial, we have conducted a phase I dose-escalation study to determine the maximum tolerated dose (MTD) of sorafenib in patients with recurrent malignant glioma. Cohorts of 3 patients, stratified based on the use of enzyme inducing anticonvulsants (EIAC) or not (non-EIAC), have completed enrollment through the following dose levels: 200 mg, 400 mg, 600 mg, and 800 mg. Therapy has been given as a twice daily oral administration with cycles of 28 day duration. Results: A total of 35 patients have been enrolled and are evaluable for toxicity. Treatment related dose-limiting toxicity (DLT) was defined as any grade 3 or 4 non-hematological toxicity, and grade 4 hematological toxicity (platlets and ANC) or febrile neutropenia of any duration. The following DLTs were observed: one grade 3 hand-foot-syndrome at the 400 mg BID (EIAC), one grade 3 puritis 400 mg BID (non-EIAC) dose level, grade 3 hand/foot syndrome 800 mg BID (EIAC and non-EIAC arms), grade 3 hypophosphatemia 800 mg BID (EIAC), and grade 3 joint pain 800 mg BID (EIAC). A MTD of 600 mg BID has been defined for the EIAC arm with 3/6 DLTs at 800 mg BID. A MTD has not been defined and enrollment has been completed through the 800 mg BID dose level for the non-EIAC. Of the enrolled patients, 20 are with glioblastoma multiforme (GBM), 8 with anaplastic astrocytoma (AA), and 7 with anaplastic oligodendroglioma (AO). Conclusions: The MTD for sorafenib is 600 mg BID for patients on EIAC. Sorafenib is well tolerated with limited toxicities to doses of 800 mg twice daily in patients with recurrent malignant glioma not on EIAC (non-EIAC arm).

No significant financial relationships to disclose.

[Glioma therapy up-date]

The prognosis for patients with malignant brain tumors has always been poor and until recently chemotherapy had not shown to be very effective. Temozolomide is a novel second-generation alkylating agent that has shown efficacy for the treatment of high-grade gliomas. Temozolomide is well-tolerated by most patients and has favorable pharmacodynamic and pharmacokinetic properties. In patients with newly diagnosed glioblastoma multiforme, radiation therapy with concurrent and adjuvant temozolomide significantly improves overall survival compared to treatment with only radiation. The benefit of temozolomide is greatest in patients with tumors that have a methylated 06-methyl-guanine DNA methyl transferase gene promoter that results in decreased repair of temozolomide-induced DNA damage. This chapter will briefly review the diagnosis and treatment of patients with malignant brain tumors and then will focus on the role of temozolomide in glioma therapy.

Phase I trial of bortezomib in adults with recurrent malignant glioma

1567

Background: Bortezomib is a selective inhibitor of the proteasome that has been approved for the treatment of multiple myeloma and has also shown promising evidence of clinical activity against solid tumors. This study was undertaken to determine the maximum tolerated dose (MTD), toxicity profile, and biologic activity of bortezomib for the treatment of recurrent malignant glioma (MG). Methods: Eligible patients (pts) had supratentorial progressive MG upon radiotherapy and ≤ 1 prior regimen of chemotherapy. Dose escalation was conducted separately for pts taking enzyme inducing antiseizure drugs (EIASD+) and for those not (EIASD-). Bortezomib was given by bolus iv injection on weeks 1 and 2 of each 3 week cycle of therapy. The starting dose in both groups was 0.9 mg/m2. Cohorts of at least 3 patients were evaluated at each dose level. 20S proteasome activity was determined in whole blood lysates before and at 1 and 24 h after the first dose. Results: Fifty-nine evaluable pts (41 male/18 female) with a median age of 51 years and median KPS of 90% have been enrolled. All but 2 pts had received 1 prior chemotherapy regimen. In the EIASD- group, the weekly dose was escalated from 0.9 to 1.9 mg/m2 through 3 intermediate dose levels, with 1.7 mg/m2 established as the MTD. DLT experienced by 2 of 6 pts in the 1.90 mg/m2 dose level were grade 3 thrombocytopenia and grade 3 fatigue plus neurosensory toxicities. In the EIASD+ group, the dose has been escalated to 2.3 mg/m2 without the occurrence of any DLT. Ten additional EIASD- pts were treated at 1.7 mg/m2, with the most common adverse events being thrombocytopenia and peripheral neuropathy. The extent of proteasome inhibition in whole blood increased in a dose-dependent manner in both treatment groups. Mean proteasome inhibition in EIASD+ pts 1 h after receiving 2.1 mg/m2 of bortezomib (77 ± 12%) was similar to the 1.7 mg/m2 dose in EIASD- pts (79 ± 6%). Conclusions: The MTD for the weekly x 2 schedule of bortezomib in EIASD- patients, 1.7 mg/m2, is higher than the approved dose of 1.3 mg/m2 for the treatment of multiple myeloma. The enhanced tolerability of the drug when given together with EIASDs, for which the MTD is at least 2.1 mg/m2, is consistent with the diminished inhibition of 20S proteasome activity in these pts.

No significant financial relationships to disclose.

Electrogram configuration and detection of supraventricular tachycardias by a morphology discrimination algorithm in single chamber ICDs

BACKGROUND

Inappropriate ICD therapy for supraventricular tachycardia (SVT) remains a significant problem. A morphology-based algorithm (Wavelet) compares baseline and tachycardia electrograms (EGM). For this analysis different EGM sources can be programmed. This study evaluates the performance of Wavelet using two different EGM configurations (SVC-Can and RV-Can) for the detection of exercise-induced SVT.

METHODS

Patients with a Medtronic model 7230 single chamber ICD and a dual coil lead were included. For each EGM source (SVC-Can or RV-Can), a baseline EGM template was acquired and the morphology similarity to this template (match percentage) was evaluated for 10-15 beats at different heart rates during exercise testing. The lower VT detection limit was programmed to 600 ms (therapies off).

RESULTS

A total of 28 patients (66.9 +/- 4.7 years, 93% men) and 5,824 intracardiac QRS complexes were analyzed. With the RV-Can source, a consistently high similarity to the baseline EGM template was observed (< or =100 bpm: 90.90 +/- 0.56%; >100 bpm: 90.24 +/- 0.55%, P > 0.05). In contrast, SVC-Can was associated with a lower match percentage at baseline and a significant decrease at higher heart rates (< or =100 bpm: 77.91 +/- 2.65%; >100 bpm: 59.05 +/- 5.65%, P < 0.005). Accordingly, the specificity for appropriate detection of exercise-induced SVT was higher with RV-Can (21/21 episodes) than with SVC-Can (8/18 episodes, specificity 100% vs 44%; P < 0.0001).

CONCLUSION

The RV-Can configuration appears to be superior to SVC-Can as EGM source for appropriate SVT detection with the Wavelet algorithm.