HostSeq: a Canadian whole genome sequencing and clinical data resource

HostSeq was launched in April 2020 as a national initiative to integrate whole genome sequencing data from 10,000 Canadians infected with SARS-CoV-2 with clinical information related to their disease experience. The mandate of HostSeq is to support the Canadian and international research communities in their efforts to understand the risk factors for disease and associated health outcomes and support the development of interventions such as vaccines and therapeutics. HostSeq is a collaboration among 13 independent epidemiological studies of SARS-CoV-2 across five provinces in Canada. Aggregated data collected by HostSeq are made available to the public through two data portals: a phenotype portal showing summaries of major variables and their distributions, and a variant search portal enabling queries in a genomic region. Individual-level data is available to the global research community for health research through a Data Access Agreement and Data Access Compliance Office approval. Here we provide an overview of the collective project design along with summary level information for HostSeq. We highlight several statistical considerations for researchers using the HostSeq platform regarding data aggregation, sampling mechanism, covariate adjustment, and X chromosome analysis. In addition to serving as a rich data source, the diversity of study designs, sample sizes, and research objectives among the participating studies provides unique opportunities for the research community.

Immunomodulatory Effect of Epidermal Growth Factor Secreted by Human Umbilical Cord Blood-Derived Mesenchymal Stem Cells on Atopic Dermatitis

Background and Objectives

Human mesenchymal stem cells (MSCs) are emerging as a treatment for atopic dermatitis (AD), a chronic inflammatory skin disorder that affects a large number of people across the world. Treatment of AD using human umbilical cord blood-derived MSCs (hUCB-MSCs) has recently been studied. However, the mechanism underlying their effect needs to be studied continuously. Thus, the objective of this study was to investigate the immunomodulatory effect of epidermal growth factor (EGF) secreted by hUCB-MSCs on AD.

Methods and Results

To explore the mechanism involved in the therapeutic effect of MSCs for AD, a secretome array was performed using culture medium of hUCB-MSCs. Among the list of genes common for epithelium development and skin diseases, we focused on the function of EGF. To elucidate the effect of EGF secreted by hUCB-MSCs, EGF was downregulated in hUCB-MSCs using EGF-targeting small interfering RNA. These cells were then co-cultured with keratinocytes, Th2 cells, and mast cells. Depletion of EGF disrupted immunomodulatory effects of hUCB-MSCs on these AD-related inflammatory cells. In a Dermatophagoides farinae-induced AD mouse model, subcutaneous injection of hUCB-MSCs ameliorated gross scoring, histopathologic damage, and mast cell infiltration. It also significantly reduced levels of inflammatory cytokines including interleukin (IL)-4, tumor necrosis factor (TNF)-α, thymus and activation-regulated chemokine (TARC), and IL-22, as well as IgE levels. These therapeutic effects were significantly attenuated at all evaluation points in mice injected with EGF-depleted hUCB-MSCs.

Conclusions

EGF secreted by hUCB-MSCs can improve AD by regulating inflammatory responses of keratinocytes, Th2 cells, and mast cells.

Colloid coload versus crystalloid coload to prevent maternal hypotension in women receiving prophylactic phenylephrine infusion during caesarean delivery: a randomised controlled trial

BACKGROUND

The optimal fluid strategy to prevent maternal hypotension during caesarean delivery remains unclear. This study aim was to compare the incidence of post-spinal anaesthesia hypotension in women receiving either colloid or crystalloid coload in the setting of prophylactic phenylephrine infusion during caesarean delivery.

METHODS

Healthy mothers undergoing elective caesarean delivery under spinal anaesthesia were randomised to receive a rapid intravenous coload with 6% hydroxyethyl starch 130/0.4 10 mL/kg (colloid group) or balanced crystalloid solution (Plasma Solution A) 10 mL/kg (crystalloid group) during spinal anaesthesia. All women had a prophylactic phenylephrine infusion initiated at 25 μg/min immediately after the subarachnoid block and titrated to systolic blood pressure using a standardised protocol. The primary outcome was the incidence of hypotension (systolic blood pressure <80% of baseline) until delivery.

RESULTS

The incidence of hypotension was 50% in the colloid group and 62% in the crystalloid group (absolute difference, -12% [95% CI -33% to 9%]; relative risk, 0.8 [95% CI 0.56 to 1.14]; P=0.314). No significant difference between groups was found in the number of hypotensive episodes (median 0.5 [IQR 0 to 1] vs 1 [0 to 2], P=0.132) or phenylephrine dose (675 [IQR 425 to 975] μg vs 750 [625 to 950] μg, P=0.109). The incidence of severe hypotension, symptomatic hypotension, bradycardia, nausea, and the neonatal outcomes were not significantly different.

CONCLUSIONS

This study found no benefit of colloid coload compared with crystalloid coload for preventing maternal hypotension in the presence of prophylactic phenylephrine infusion during caesarean delivery.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.

Increased vaccine tolerability and protection via NF-κB modulation

Improving adjuvant responses is a promising pathway to develop vaccines against some pathogens (e.g., HIV or dengue). One challenge in adjuvant development is modulating the inflammatory response, which can cause excess side effects, while maintaining immune activation and protection. No approved adjuvants yet have the capability to independently modulate inflammation and protection. Here, we demonstrate a method to limit inflammation while retaining and often increasing the protective responses. To accomplish this goal, we combined a partial selective nuclear factor kappa B (NF-kB) inhibitor with several current adjuvants. The resulting vaccines reduce systemic inflammation and boost protective responses. In an influenza challenge model, we demonstrate that this approach enhances protection. This method was tested across a broad range of adjuvants and antigens. We anticipate these studies will lead to an alternative approach to vaccine formulation design that may prove broadly applicable to a wide range of adjuvants and vaccines.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targets of the proteome of SARS CoV-2. THe MD performed is temperature replica-exchange enhanced sampling, making use of the massively parallel supercomputing on the SUMMIT supercomputer at Oak Ridge National Laboratory, with which more than 1ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to ten configurations of each of the 23 SARS CoV-2 systems using AutoDock Vina. We also demonstrate that using Autodock-GPU on SUMMIT, it is possible to perform exhaustive docking of one billion compounds in under 24 hours. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and AI methods to cluster MD trajectories and rescore docking poses.

A risk prediction model for the development of subsequent primary melanoma in a population-based cohort

BACKGROUND

Guidelines for follow-up of patients with melanoma are based on limited evidence.

OBJECTIVES

To guide skin surveillance, we developed a risk prediction model for subsequent primary melanomas, using demographic, phenotypical, histopathological, sun exposure and genomic risk factors.

METHODS

Using Cox regression frailty models, we analysed data for 2613 primary melanomas from 1266 patients recruited to the population-based Genes, Environment and Melanoma study in New South Wales, Australia, with a median of 14 years' follow-up via the cancer registry. Discrimination and calibration were assessed.

RESULTS

The median time to diagnosis of a subsequent primary melanoma decreased with each new primary melanoma. The final model included 12 risk factors. Harrell's C-statistic was 0·73 [95% confidence interval (CI) 0·68-0·77], 0·65 (95% CI 0·62-0·68) and 0·65 (95% CI 0·61-0·69) for predicting second, third and fourth primary melanomas, respectively. The risk of a subsequent primary melanoma was 4·75 times higher (95% CI 3·87-5·82) for the highest vs. the lowest quintile of the risk score. The mean absolute risk of a subsequent primary melanoma within 5 years was 8·0 ± SD 4.1% after the first primary melanoma, and 46·8 ± 15·0% after the second, but varied substantially by risk score.

CONCLUSIONS

The risk of developing a subsequent primary melanoma varies considerably between individuals and is particularly high for those with two or more primary melanomas. The risk prediction model and its associated nomograms enable estimation of the absolute risk of subsequent primary melanoma, on the basis of on an individual's risk factors, and can be used to tailor surveillance intensity, communicate risk and provide patient education. What's already known about this topic? Current guidelines for the frequency and length of follow-up to detect new primary melanomas in patients with one or more previous primary melanomas are based on limited evidence. People with one or more primary melanomas have, on average, a higher risk of developing another primary invasive melanoma, compared with the general population, but an accurate way of estimating individual risk is needed. What does this study add? We provide a comprehensive risk prediction model for subsequent primary melanomas, using data from 1266 participants with melanoma (2613 primary melanomas), over a median 14 years' follow-up. The model includes 12 risk factors comprising demographic, phenotypical, histopathological and genomic factors, and sun exposure. It enables estimation of the absolute risk of subsequent primary melanomas, and can be used to tailor surveillance intensity, communicate individual risk and provide patient education.

Selective multi-nanosoldering for fabrication of advanced solution-processed micro/nanoscale metal grid structures

Solution-processed metal grid transparent conductors with low sheet resistance, high optical transmittance and good mechanical flexibility have great potential for use in flexible optoelectronic devices. However, there are still remaining challenges to improve optoelectrical properties and electromechanical stability of the metallic structures due to random loose packings of nanoparticles and the existence of many pores. Here we introduce a selective multi-nanosoldering method to generate robust metallic layers on the thin metal grid structures (< a thickness of 200 nm), which are generated via self-pining assisted direct inking of silver ions. The selective multi-nanosoldering leads to lowering the sheet resistance of the metal grid transparent conductors, while keeping the optical transmittance constant. Also, it reinforces the electromechanical stability of flexible metal grid transparent conductors against a small bending radius or a repeated loading. Finally, organic light-emitting diodes based on the flexible metal grid transparent conductors are demonstrated. Our approach can open a new route to enhance the functionality of metallic structures fabricated using a variety of solution-processed metal patterning methods for next-generation optoelectronic and micro/nanoelectronic applications.

Growth kinetics of Kr nano structures encapsulated by graphene

Graphene can acquire salient properties by the intercalated nano structures, and to functionalize the graphene as designed, understanding the growth kinetics of the nano structures is a prerequisite. In that regards, Kr atoms are selectively intercalated just below the surface graphene of C(0001) by the incidence of low energy Kr ions. The growth kinetics of the encapsulated Kr nano structures is investigated by both scanning tunneling microscopy and molecular dynamics simulations. The intercalation proceeds via defect sites, such as surface vacancies. At room temperature, the thermal diffusion of intercalated Kr is almost frustrated by the strain field of the encapsulating graphene layers, and the growth of Kr nano structures proceeds via the transient mobility of both the intercalating Kr atoms and previously intercalated Kr atoms that are mobilized by collision with the incident Kr ions. At the elevated temperatures where thermal diffusion becomes effective, some Kr nano structures disappear, releasing pressurized Kr atoms, while others coalesce to form blisters via the delamination of the adjacent graphene. Some of the larger blisters explode to leave craters of varying depths at the surface. In contrast to growth on the substrate, the growth of each encapsulated nano structure depends significantly on extrinsic variables, such as surface vacancies and local topography around the nano structure, that affect the Kr diffusion and limit the maximal Kr pressure.

Single dose partial breast irradiation using an MRI linear accelerator in the supine and prone treatment position

Background

In selected patients with early-stage and low-risk breast cancer, an MRI-linac based treatment might enable a radiosurgical, non-invasive alternative for current standard breast conserving therapy.

Aim

To investigate whether single dose accelerated partial breast (APBI) to the intact tumor in both the prone and supine radiotherapy positions on the MRI-linac is dosimetrically feasible with respect to predefined coverage and organs at risk (OAR) constraints.

Material & methods

For 20 patients with cTis or low-risk cT1N0M0 non-lobular breast carcinoma, previously treated with single dose preoperative APBI in the supine (n = 10) or prone (n = 10) position, additional intensity modulated radiotherapy plans with 7 coplanar beams in the presence of a 1.5T magnetic field were generated. A 20 Gy and 15 Gy dose was prescribed to the gross tumor and clinical target volume, respectively. The percentage of plans achieving predefined organ at risk (OAR) constraints, currently used in clinical practice, was assessed. Dosimetry differences between the prone versus supine approach and the MRI-linac versus clinically delivered plans were evaluated.

Results

All MRI-linac plans met the coverage and predefined OAR constraints. The prone approach appeared to be more favorable with respect to the chest wall, and ipsilateral lung dose compared to the supine position. No dosimetric differences were observed for the ipsilateral breast. No treatment position was clearly more beneficial for the skin or heart, since dosimetry varied among parameters. Overall, the MRI-linac and clinical plans were comparable, with minor absolute dosimetric differences.

Conclusion

MRI-linac based single dose APBI to the intact tumor is a promising and a dosimetrically feasible strategy in patients with low-risk breast cancer. Preliminary OAR dosimetry favored the prone radiotherapy position.

Mode instability in ytterbium-doped non-circular fibers

We present a theoretical study of transverse mode instability (TMI) in non-circular ytterbium-doped fibers including the rectangular core in a circular or D-shaped cladding. The D-shaped cladding is found efficient to suppress the TMI thanks to better heat dissipation, as compared to the circular cladding. However, the rectangular core does not suppress the TMI despite its better heat dissipation than a circular core counterpart. Although the temperature built in the rectangular core decreases with an increasing aspect ratio of the rectangular core, the low temperature does not benefit the TMI suppression. Instead, the TMI becomes stronger than its circular core counterpart. Our study reveals that the power coupling between two involved modes and gain saturation effect play a significant role in influencing the TMI. The power coupling strength is associated with the frequency offset between two modes, and it grows with an increasing aspect ratio of rectangular cores, suggesting the longer axis of rectangular core promotes the TMI.

Record power, ultra-broadband supercontinuum source based on highly GeO2 doped silica fiber

We demonstrate highly germania doped fibers for mid-infrared supercontinuum generation. Experiments ensure a highest output power of 1.44 W for a broadest spectrum from 700 nm to 3200 nm and 6.4 W for 800 nm to 2700 nm from these fibers, while being pumped by a broadband Erbium-Ytterbium doped fiber based master oscillator power amplifier. The effect of repetition frequency of pump source and length of germania-doped fiber has also been investigated. Further, germania doped fiber has been pumped by conventional supercontinuum source based on silica photonic crystal fiber supercontinuum source. At low power, a considerable broadening of 200-300 nm was observed. Further broadening of spectrum was limited due to limited power of pump source. Our investigations reveal the unexploited potential of germania doped fiber for mid-infrared supercontinuum generation. These measurements ensure the potential of germania based photonic crystal fiber or a step-index fiber supercontinuum source for high power ultra-broad band emission being by pumped a 1060 nm or a 1550 nm laser source. To the best of our knowledge, this is the record power, ultra-broadband, and all-fiberized supercontinuum light source based on silica and germania fiber ever demonstrated to the date.