Elastic-DF: Scaling Performance of DNN Inference in FPGA Clouds through Automatic Partitioning

Customized compute acceleration in the datacenter is key to the wider roll-out of applications based on deep neural network (DNN) inference. In this article, we investigate how to maximize the performance and scalability of field-programmable gate array (FPGA)-based pipeline dataflow DNN inference accelerators (DFAs) automatically on computing infrastructures consisting of multi-die, network-connected FPGAs. We present Elastic-DF, a novel resource partitioning tool and associated FPGA runtime infrastructure that integrates with the DNN compiler FINN. Elastic-DF allocates FPGA resources to DNN layers and layers to individual FPGA dies to maximize the total performance of the multi-FPGA system. In the resulting Elastic-DF mapping, the accelerator may be instantiated multiple times, and each instance may be segmented across multiple FPGAs transparently, whereby the segments communicate peer-to-peer through 100 Gbps Ethernet FPGA infrastructure, without host involvement. When applied to ResNet-50, Elastic-DF provides a 44% latency decrease on Alveo U280. For MobileNetV1 on Alveo U200 and U280, Elastic-DF enables a 78% throughput increase, eliminating the performance difference between these cards and the larger Alveo U250. Elastic-DF also increases operating frequency in all our experiments, on average by over 20%. Elastic-DF therefore increases performance portability between different sizes of FPGA and increases the critical throughput per cost metric of datacenter inference.

Rapid isolation and resolution immune evasion and viral fitness across contemporary SARS-CoV-2 variants

From late 2020 the world observed the rapid emergence of many distinct SARS-CoV-2 variants. At the same time, pandemic responses coalesced into significant global vaccine roll-out that have now significantly lowered Covid-19 hospital and mortality rates in the developed world. Over this period, we developed a rapid platform (R-20) for viral isolation and characterisation using primary remnant diagnostic swabs. This combined with quarantine testing and genomics surveillance, enabled the rapid isolation and characterisation of all major SARS-CoV-2 variants (all variants of concern and 6 variants of interest) globally with a 4-month period. This platform facilitated viral variant isolation and enabled rapid resolution of variant phenotype by allowing determining end point viral titers from primary nasopharyngeal swabs and through ranking of evasion of neutralising antibodies. In late 2021, when the Delta variant was dominating, Omicron rapidly emerged. Using this platform, we isolated and tested the first cases of this variant within Australia. In this setting we observed Omicron to diverge from other variants at two levels: Firstly, it ranks at the mots evasive to neutralisation antibodies compared to all VOCs and major VUIs. Secondly, it no longer engages TMPRSS2 during the late stages of fusion.

Implants for HIV prevention in young women: Provider perceptions and lessons learned from contraceptive implant provision

Preventing new HIV infections, especially amongst young women, is key to ending the HIV epidemic especially in sub-Saharan Africa. Potent antiretroviral (ARV) drugs used as pre-exposure prophylaxis (PrEP) are currently being formulated as long-acting implantable devices, or nanosuspension injectables that release drug at a sustained rate providing protection from acquiring HIV. PrEP as implants (PrEP Implants) offers an innovative and novel approach, expanding the HIV prevention toolbox. Feedback from providers and future users in the early clinical product development stages may identify modifiable characteristics which can improve acceptability and uptake of new technologies. Healthcare workers (HCWs) perspectives and lessons learned during the rollout of contraceptive implants will allow us to understand what factors may impact the roll-out of PrEP implants. We conducted eighteen interviews with HCWs (9 Nurses and 9 Community Healthcare Workers) in rural KwaZulu-Natal, South Africa. HCWs listed the long-acting nature of the contraceptive implant as a key benefit, helping to overcome healthcare system barriers like heavy workloads and understaffing. However, challenges like side effects, migration of the implant, stakeholder buy-in and inconsistent training on insertion and removal hampered the roll-out of the contraceptive implant. For PrEP implants, HCWs preferred long-acting products that were palpable and biodegradable. Our findings highlighted that the characteristics of PrEP implants that are perceived to be beneficial by HCWs may not align with that of potential users, potentially impacting the acceptability and uptake of PrEP implants. Further our data highlight the need for sustained and multi-pronged approaches to training HCWs and introducing new health technologies into communities. Finding a balance between the needs of HCWs that accommodate their heavy workloads, limited resources at points of delivery of care and the needs and preferences of potential users need to be carefully considered in the development of PrEP implants.

Large-scale cross-sectional seroepidemiologic study of COVID-19 in Japan: Acquisition of herd immunity and the vaccines' efficacy

Background: The COVID-19 pandemic situation has been changing drastically worldwide due to the continuous appearance of SARS-CoV-2 variants and the roll-out of mass vaccination. Periodic cross-sectional studies during the surge of COVID-19 cases is essential to elucidate the pandemic situation. Methods: Sera of 1,000 individuals who underwent a health check-up in Hyogo Prefecture Health Promotion Association clinics in Japan were collected in August and December 2021. Antibodies against SARS-CoV-2 N and S antigens were detected in the sera by an electrochemiluminescence immunoassay (ECLIA) and an enzyme-linked immunosorbent assay (ELISA), respectively. The sera's neutralization activities for the conventional SARS-CoV-2 (D614G), Delta, and Omicron variants were measured. Results: The seropositive rates for the antibody against N antigen were 2.1% and 3.9% in August and December 2021 respectively, demonstrating a Delta variant endemic during that time; the actual infection rate was approximately twofold higher than the rate estimated based on the polymerase chain reaction (PCR)-based diagnosis. The anti-S seropositive rate was 38.7% in August and it reached 90.8% in December, in concordance with the vaccination rate in Japan. In the December cohort, 78.7% of the sera showed neutralizing activity against the Delta variant, whereas that against the Omicron was much lower at 36.6%. Conclusions: These analyses revealed that herd immunity against SARS-CoV-2 including the Delta variant was established in December 2021, leading to convergence of the variants. The low neutralizing activity against the Omicron variant suggests the need for the further promotion of the prompt three-dose vaccination to overcome this variant's imminent 6th wave in Japan.

The impact of post-hospital remote monitoring of COVID-19 patients using pulse oximetry: a national observational study using hospital activity data

Background There was a national roll out of "COVID Virtual Wards" (CVW) during England's second COVID-19 wave (Autumn 2020 - Spring 2021). These services used remote pulse oximetry monitoring for COVID-19 patients following discharge from hospital. A key aim was to enable rapid detection of patient deterioration. It was anticipated that the services would support early discharge and avoid readmissions, reducing pressure on beds. This study is an evaluation of the impact of the CVW services on hospital activity. Methods Using retrospective patient-level hospital admissions data, we built multivariate models to analyse the relationship between the implementation of CVW services and hospital activity outcomes: length of COVID-19 related stays and subsequent COVID-19 readmissions within 28 days. We used data from more than 98% of recorded COVID-19 hospital stays in England, where the patient was discharged alive between mid-August 2020 and late February 2021. Findings We found a longer length of stay for COVID-19 patients discharged from hospitals where a CVW was available, when compared to patients discharged from hospitals where there was no CVW (adjusted IRR 1.05, 95% CI 1.01 to 1.09). We found no evidence of a relationship between the availability of CVW and subsequent rates of readmission for COVID-19 (adjusted OR 0.95, 95% CI 0.89 to 1.02). Interpretation We found no evidence of early discharges or reduced readmissions associated with the roll out of COVID Virtual Wards across England. Our analysis made pragmatic use of national-scale hospital data, but it is possible that a lack of specific data (for example, on which patients were enrolled) may have meant that true impacts, especially at a local level, were not ultimately discernible. Funding This is independent research funded by the National Institute for Health Research, Health Services & Delivery Research programme and NHSEI.

COVID-19 Vaccine Perceptions in the Initial Phases of US Vaccine Roll-out: An Observational Study on Reddit

Background: Open online forums like Reddit provide an opportunity to quantitatively examine COVID-19 vaccine perceptions early in the vaccine timeline. We examine COVID-19 misinformation on Reddit following vaccine scientific announcements, in the initial phases of the vaccine timeline. Methods: We collected all posts on Reddit from January 1 2020 - December 14 2020 (n=266,840) that contained both COVID-19 and vaccine-related keywords. We used topic modeling to understand changes in word prevalence within topics after the release of vaccine trial data. Social network analysis was also conducted to determine the relationship between Reddit communities (subreddits) that shared COVID-19 vaccine posts, and the movement of posts between subreddits. Results: There was an association between a Pfizer press release reporting 90\% efficacy and increased discussion on vaccine misinformation. We observed an association between Johnson and Johnson temporarily halting its vaccine trials and reduced misinformation. We found that information skeptical of vaccination was first posted in a subreddit (r/Coronavirus) which favored accurate information and then reposted in subreddits associated with antivaccine beliefs and conspiracy theories (e.g. conspiracy, NoNewNormal). Conclusions: Our findings can inform the development of interventions where individuals determine the accuracy of vaccine information, and communications campaigns to improve COVID-19 vaccine perceptions, early in the vaccine timeline. Such efforts can increase individual- and population-level awareness of accurate and scientifically sound information regarding vaccines and thereby improve attitudes about vaccines, especially in the early phases of vaccine roll-out. Further research is needed to understand how social media can contribute to COVID-19 vaccination services.

Factors associated with COVID-19 vaccine receipt at two integrated healthcare systems in New York City: a cross-sectional study of healthcare workers

ObjectivesTo examine the factors associated with COVID-19 vaccine receipt among healthcare workers and the role of vaccine confidence in decisions to vaccinate, and to better understand concerns related to COVID-19 vaccination.DesignCross-sectional anonymous survey among front-line, support service and administrative healthcare workers.SettingTwo large integrated healthcare systems (one private and one public) in New York City during the initial roll-out of the COVID-19 vaccine.Participants1933 healthcare workers, including nurses, physicians, allied health professionals, environmental services staff, researchers and administrative staff.Primary outcome measuresThe primary outcome was COVID-19 vaccine receipt during the initial roll-out of the vaccine among healthcare workers.ResultsAmong 1933 healthcare workers who had been offered the vaccine, 81% had received the vaccine at the time of the survey. Receipt was lower among black (58%; OR: 0.14, 95% CI 0.1 to 0.2) compared with white (91%) healthcare workers, and higher among non-Hispanic (84%) compared with Hispanic (69%; OR: 2.37, 95% CI 1.8 to 3.1) healthcare workers. Among healthcare workers with concerns about COVID-19 vaccine safety, 65% received the vaccine. Among healthcare workers who agreed with the statement that the vaccine is important to protect family members, 86% were vaccinated. Of those who disagreed, 25% received the vaccine (p<0.001). In a multivariable analysis, concern about being experimented on (OR: 0.44, 95% CI 0.31 to 0.6), concern about COVID-19 vaccine safety (OR: 0.39, 95% CI 0.28 to 0.55), lack of influenza vaccine receipt (OR: 0.28, 95% CI 0.18 to 0.44), disagreeing that COVID-19 vaccination is important to protect others (OR: 0.37, 95% CI 0.27 to 0.52) and black race (OR: 0.38, 95% CI 0.24 to 0.59) were independently associated with COVID-19 vaccine non-receipt. Over 70% of all healthcare workers responded that they had been approached for vaccine advice multiple times by family, community members and patients.ConclusionsOur data demonstrated high overall receipt among healthcare workers. Even among healthcare workers with concerns about COVID-19 vaccine safety, side effects or being experimented on, over 50% received the vaccine. Attitudes around the importance of COVID-19 vaccination to protect others played a large role in healthcare workers’ decisions to vaccinate. We observed striking inequities in COVID-19 vaccine receipt, particularly affecting black and Hispanic workers. Further research is urgently needed to address issues related to vaccine equity and uptake in the context of systemic racism and barriers to care. This is particularly important given the influence healthcare workers have in vaccine decision-making conversations in their communities.

Codeveloping an effective EMPA to maturity in an acute NHS Trust: an implementer report

IntroductionUniversity Hospitals Leicester has codeveloped, with Nervecentre, an Electronic Prescribing and Medicines Administration System that meets specific clinical and interoperability demands of the National Health Service (NHS).MethodsThe system was developed through a frontline-led and agile approach with a project team consisting of clinicians, Information Technology (IT) specialists and the vendor’s representatives over an 18-month period.ResultsThe system was deployed successfully with more than a thousand transcriptions during roll-out. Despite the high caseload and novelty of the system, there was no increase in error rates within the first 3 months of roll-out. Healthcare professionals perceived the new system as efficient with improved clinical workflow, and safe through an integrated medication alert system.DiscussionThis case study demonstrates how NHS trusts can successfully co-develop, with vendors, new IT systems which meet interoperability standards such as Fast Healthcare Interoperability Resources, while improving front line clinical experience.ConclusionAlternative methods to the ‘big bang’ deployment of IT projects, such as ‘gradual implementation’, must be demonstrated and evaluated for their ability to deliver digital transformation projects in the NHS successfully.