Engineering a Rigid Nucleic Acid Structure to Improve the Limit of Detection for Genetic Assays.

Detecting nucleic acids at ultralow concentrations is critical for research and clinical applications. Particle-based assays are commonly used to detect nucleic acids. However, DNA hybridization on particle surfaces is inefficient due to the instability of tethered sequences, which negatively influences the assay's detection sensitivity. Here, we report a method to stabilize sequences on particle surfaces using a double-stranded linker at the 5' end of the tethered sequence. We termed this method Rigid Double Stranded Genomic Linkers for Improved DNA Analysis (RIGID-DNA). Our method led to a 3- and 100-fold improvement of the assays' clinical and analytical sensitivity, respectively. Our approach can enhance the hybridization efficiency of particle-based assays without altering existing assay workflows. This approach can be adapted to other platforms and surfaces to enhance the detection sensitivity.

Contact Tracing and Exposure Investigation in Response to the First Case of Monkeypox Virus Infection in the United States During the 2022 Global Monkeypox Outbreak.

BACKGROUND: In May 2022, the first case of monkeypox virus (MPXV) infection in the United States in the current global outbreak was identified. As part of the public health and health care facility response, a contact tracing and exposure investigation was done. OBJECTIVE: To describe the contact tracing, exposure identification, risk stratification, administration of postexposure prophylaxis (PEP), and exposure period monitoring for contacts of the index patient, including evaluation of persons who developed symptoms possibly consistent with MPXV infection. DESIGN: Contact tracing and exposure investigation. SETTING: Multiple health care facilities and community settings in Massachusetts. PARTICIPANTS: Persons identified as contacts of the index patient. INTERVENTION: Contact notification, risk stratification, and symptom monitoring; PEP administration in a subset of contacts. MEASUREMENTS: Epidemiologic and clinical data collected through standard surveillance procedures at each facility and then aggregated and analyzed. RESULTS: There were 37 community and 129 health care contacts identified, with 4 at high risk, 49 at intermediate risk, and 113 at low or uncertain risk. Fifteen health care contacts developed symptoms during the monitoring period. Three met criteria for MPXV testing, with negative results. Two community contacts developed symptoms. Neither met criteria for MPXV testing, and neither showed disease progression consistent with monkeypox. Among 4 persons with high-risk exposures offered PEP, 3 elected to receive PEP. Among 10 HCP with intermediate-risk exposures for which PEP was offered as part of informed clinical decision making, 2 elected to receive PEP. No transmissions were identified at the conclusion of the 21-day monitoring period, despite the delay in recognition of monkeypox in the index patient. LIMITATION: Descriptions of exposures are subject to recall bias, which affects risk stratification. CONCLUSION: In a contact tracing investigation involving 166 community and health care contacts of a patient with monkeypox, no secondary cases were identified. PRIMARY FUNDING SOURCE: None.

Cardiac arrest in diving: The key to success.

This case report describes the successful management of an out-of-hospital arrest in a diver following a suspected arterial gas embolism (AGE). It illustrates both the inherent risks of diving and the importance of prompt and effective implementation of the "chain of survival" from bystanders. Rapid on-scene responses from paramedics and helicopter emergency medical services facilitated prompt evacuation to a Category 1 (multiplace) recompression chamber (RCC) where specialists in cardiology and hyperbaric medicine were available. Alternative causes of cardiac arrest were considered, with a presumed AGE successfully treated with multiple rounds of hyperbaric oxygen therapy. The key factors which led to this successful outcome are discussed, including early recognition and call for help, competent cardiopulmonary resuscitation, and direct evacuation to a Category 1 RCC, with additional consideration of the diagnosis leading to cardiac arrest. The case clearly illustrates the need for all those involved in diving regularly to be competent and confident in performing basic life support, as well as the awareness of the emergency services of the need for diving casualties to be treated at appropriate hyperbaric facilities. Were it not for the simple, prompt and effective treatment this diver received, both on scene and in hospital, it is highly unlikely that such a positive outcome would have been achieved.

Surveilling and Tracking COVID-19 Patients Using a Portable Quantum Dot Smartphone Device.

The ability to rapidly diagnose, track, and disseminate information for SARS-CoV-2 is critical to minimize its spread. Here, we engineered a portable smartphone-based quantum barcode serological assay device for real-time surveillance of patients infected with SARS-CoV-2. Our device achieved a clinical sensitivity of 90% and specificity of 100% for SARS-CoV-2, as compared to 34% and 100%, respectively, for lateral flow assays in a head-to-head comparison. The lateral flow assay misdiagnosed ∼2 out of 3 SARS-CoV-2 positive patients. Our quantum dot barcode device has ∼3 times greater clinical sensitivity because it is ∼140 times more analytically sensitive than lateral flow assays. Our device can diagnose SARS-CoV-2 at different sampling dates and infectious severity. We developed a databasing app to provide instantaneous results to inform patients, physicians, and public health agencies. This assay and device enable real-time surveillance of SARS-CoV-2 seroprevalence and potential immunity.

Case Series of Laboratory-Associated Zika Virus Disease, United States, 2016-2019.

Zika virus diagnostic testing and laboratory research increased considerably when Zika virus began spreading through the Americas in 2015, increasing the risk for potential Zika virus exposure of laboratory workers and biomedical researchers. We report 4 cases of laboratory-associated Zika virus disease in the United States during 2016-2019. Of these, 2 were associated with needlestick injuries; for the other 2 cases, the route of transmission was undetermined. In laboratories in which work with Zika virus is performed, good laboratory biosafety practices must be implemented and practiced to reduce the risk for infection among laboratory personnel.

Mapping the molecular basis for growth related phenotypes in industrial producer CHO cell lines using differential proteomic analysis.

BACKGROUND: The ability to achieve high peak viable cell density earlier in CHO cell culture and maintain an extended cell viability throughout the production process is highly desirable to increase recombinant protein yields, reduce host cell impurities for downstream processing and reduce the cost of goods. In this study we implemented label-free LC-MS/MS proteomic profiling of IgG4 producing CHO cell lines throughout the duration of the cell culture to identify differentially expressed (DE) proteins and intracellular pathways associated with the high peak viable cell density (VCD) and extended culture VCD phenotypes. RESULTS: We identified key pathways in DNA replication, mitotic cell cycle and evasion of p53 mediated apoptosis in high peak VCD clonally derived cell lines (CDCLs). ER to Golgi vesicle mediated transport was found to be highly expressed in extended culture VCD CDCLs while networks involving endocytosis and oxidative stress response were significantly downregulated. CONCLUSION: This investigation highlights key pathways for targeted engineering to generate desirable CHO cell phenotypes for biotherapeutic production.

Differential expression of miRNAs and functional role of mir-200a in high and low productivity CHO cells expressing an Fc fusion protein.

OBJECTIVES: We used miRNA and proteomic profiling to understand intracellular pathways that contribute to high and low specific productivity (Qp) phenotypes in CHO clonally derived cell lines (CDCLs) from the same cell line generation project. RESULTS: Differentially expressed (DE) miRNAs were identified which are predicted to target several proteins associated with protein folding. MiR-200a was found to have a number of predicted targets associated with the unfolded protein response (UPR) which were shown to have decreased expression in high Qp CDCLs and have no detected change at the mRNA level. MiR-200a overexpression in a CHO CDCL was found to increase recombinant protein titer by 1.2 fold and Qp by 1.8 fold. CONCLUSION: These results may suggest a role for miR-200a in post-transcriptional regulation of the UPR, presenting miR-200a as a potential target for engineering industrially attractive CHO cell phenotypes.

Transcriptomic analysis of IgG4 Fc-fusion protein degradation in a panel of clonally-derived CHO cell lines using RNASeq.

In this study, we report an investigation of a panel of clonally-derived Chinese hamster ovary (CHO) cell lines exhibiting variability in the proportion of full-length IgG4 Fc-fusion protein produced. The recombinant protein was found to be degraded during cell culture into four shorter "clipped" species (three of the four cleavage sites occurred at arginine residues) and preliminary analyses suggested that a host cell enzyme was responsible for proteolysis. To identify the specific enzyme responsible, RNA sequencing was used to identify gene expression differences between the cell lines with a "high" and "low" clipping phenotype. From this analysis, six protease-encoding genes were found to be significantly upregulated in those cell lines yielding the lowest proportion of full-length IgG4 Fc-fusion protein. Four of these protease candidates were deprioritized after examination of their cleavage site specificity. The remaining enzymes, Adam19 and Furin, were found to be capable of cleavage at arginine residues, and inhibitors for both proteases were added to cell-free media to determine if the product degradation could be reduced. While the Adam19 inhibitor had no impact, Furin inhibitor I (specific for the proprotein convertase family of enzymes) was found to result in a 33-39% increase in complete IgG4 Fc-fusion protein when compared with untreated samples.

Should I be more concerned about patient care or the four-hour target?

UK emergency departments (EDs) are high-pressure environments focused on delivering care in the most efficient way to patients with a range of health problems. For many people EDs are the front door of the NHS and are a focus of significant media and political interest. People who attend EDs are often anxious and a main element of their concern is waiting time for treatment. In UK EDs the four-hour target is a main NHS target and a cornerstone of evaluating ED performance. There is ongoing debate about whether spending additional time in EDs affects patient care and outcomes, with some research showing increased mortality associated with longer stays and some showing no effect on mortality. Evidence suggests that patients are spending longer in UK EDs and it is possible that those who remain longer than four hours could have worse outcomes. This article identifies the effects of prolonged ED length of stay through a systematic literature review of data published since implementation of the four-hour target to measure the relationship between breaching the target and morbidity and mortality.

Type F Infant Botulism: Investigation of Recent Clusters and Overview of This Exceedingly Rare Disease.

From 1976 to 2016, neurotoxigenic Clostridium baratii type F caused 18 (<0.5%) reported US infant botulism cases. Six cases occurred during 2012-2013; no common source was identified. Type F infant botulism mostly occurs in very young infants and typically presents more rapidly and severely than illness caused by types A and B botulinum neurotoxin.

BMI/Obesity and consumers' price sensitivity: Implications for food tax policies.

We examine the relationship between BMI and food purchase behavior using a unique dataset that links individual-level food purchases to health data. We find that individuals with higher BMI are significantly more sensitive to price changes in vice categories but do not show similar sensitivity in comparable nonvice categories. We rely on past literature that defines and identifies vice categories as those that are tempting and purchased impulsively. We explore the effectiveness of a 10% price increase on vice food categories, a hypothetical policy similar in spirit to a fat tax or sugar tax. We predict that such a tax would substantially reduce consumption of these foods, and would be particularly effective in reducing consumption by individuals with higher BMI.

Catch the tweet to fight the flu: Using Twitter to promote flu shots on a college campus.

Objective: Over the 2018-2019 flu season we conducted a randomized controlled trial examining the efficacy of a Twitter campaign on vaccination rates. Concurrently we investigated potential interactions between digital social network structure and vaccination status. Participants: Undergratuates at a large midwestern public university were randomly assigned to an intervention (n = 353) or control (n = 349) group. Methods: Vaccination data were collected via monthly surveys. Participant Twitter data were collected through the public-facing Twitter API. Intervention impact was assessed with logistic regression. Standard network science tools examined vaccination coverage over online social networks. Results: The campaign had no effect on vaccination outcome. Receiving a flu shot the prior year had a positive impact on participant vaccination. Evidence of an interaction between digital social network structure and vaccination status was detected. Conclusions: Social media campaigns may not be sufficient for increasing vaccination rates. There may be potential for social media campaigns that leverage network structure.

Identifying heterogeneity using recursive partitioning: evidence from SMS nudges encouraging voluntary retirement savings in Mexico.

Individuals regularly struggle to save for retirement. Using a large-scale field experiment ( N = 97 , 149 ) in Mexico, we test the effectiveness of several behavioral interventions relative to existing policy and each other geared toward improving voluntary retirement savings contributions. We find that an intervention framing savings as a way to secure one's family future significantly improves contribution rates. We leverage recursive partitioning techniques and identify that the overall positive treatment effect masks subpopulations where the treatment is even more effective and other groups where the treatment has a significant negative effect, decreasing contribution rates. Accounting for this variation is significant for theoretical and policy development as well as firm profitability. Our work also provides a methodological framework for how to better design, scale, and deploy behavioral interventions to maximize their effectiveness.

Social Media Sentiment about COVID-19 Vaccination Predicts Vaccine Acceptance among Peruvian Social Media Users the Next Day.

Drawing upon theories of risk and decision making, we present a theoretical framework for how the emotional attributes of social media content influence risk behaviors. We apply our framework to understanding how COVID-19 vaccination Twitter posts influence acceptance of the vaccine in Peru, the country with the highest relative number of COVID-19 excess deaths. By employing computational methods, topic modeling, and vector autoregressive time series analysis, we show that the prominence of expressed emotions about COVID-19 vaccination in social media content is associated with the daily percentage of Peruvian social media survey respondents who are vaccine-accepting over 231 days. Our findings show that net (positive) sentiment and trust emotions expressed in tweets about COVID-19 are positively associated with vaccine acceptance among survey respondents one day after the post occurs. This study demonstrates that the emotional attributes of social media content, besides veracity or informational attributes, may influence vaccine acceptance for better or worse based on its valence.

Growth of V. parahaemolyticus in Tropical Blacklip Rock Oysters.

The opportunistic pathogen Vibrio parahaemolyticus poses a significant food safety risk worldwide, and understanding its growth in commercially cultivated oysters, especially at temperatures likely to be encountered post-harvest, provides essential information to provide the safe supply of oysters. The Blacklip Rock Oyster (BRO) is an emerging commercial species in tropical northern Australia and as a warm water species, it is potentially exposed to Vibrio spp. In order to determine the growth characteristics of Vibrio parahaemolyticus in BRO post-harvest, four V. parahaemolyticus strains isolated from oysters were injected into BROs and the level of V. parahaemolyticus was measured at different time points in oysters stored at four temperatures. Estimated growth rates were -0.001, 0.003, 0.032, and 0.047 log10 CFU/h at 4 °C, 13 °C, 18 °C, and 25 °C, respectively. The highest maximum population density of 5.31 log10 CFU/g was achieved at 18 °C after 116 h. There was no growth of V. parahaemolyticus at 4 °C, slow growth at 13 °C, but notably, growth occurred at 18 °C and 25 °C. Vibrio parahaemolyticus growth at 18 °C and 25 °C was not significantly different from each other but were significantly higher than at 13 °C (polynomial GLM model, interaction terms between time and temperature groups p < 0.05). Results support the safe storage of BROs at both 4 °C and 13 °C. This V. parahaemolyticus growth data will inform regulators and assist the Australian oyster industry to develop guidelines for BRO storage and transport to maximise product quality and safety.

Towards vibrant fish populations and sustainable fisheries that benefit all: learning from the last 30 years to inform the next 30 years.

A common goal among fisheries science professionals, stakeholders, and rights holders is to ensure the persistence and resilience of vibrant fish populations and sustainable, equitable fisheries in diverse aquatic ecosystems, from small headwater streams to offshore pelagic waters. Achieving this goal requires a complex intersection of science and management, and a recognition of the interconnections among people, place, and fish that govern these tightly coupled socioecological and sociotechnical systems. The World Fisheries Congress (WFC) convenes every four years and provides a unique global forum to debate and discuss threats, issues, and opportunities facing fish populations and fisheries. The 2021 WFC meeting, hosted remotely in Adelaide, Australia, marked the 30th year since the first meeting was held in Athens, Greece, and provided an opportunity to reflect on progress made in the past 30 years and provide guidance for the future. We assembled a diverse team of individuals involved with the Adelaide WFC and reflected on the major challenges that faced fish and fisheries over the past 30 years, discussed progress toward overcoming those challenges, and then used themes that emerged during the Congress to identify issues and opportunities to improve sustainability in the world's fisheries for the next 30 years. Key future needs and opportunities identified include: rethinking fisheries management systems and modelling approaches, modernizing and integrating assessment and information systems, being responsive and flexible in addressing persistent and emerging threats to fish and fisheries, mainstreaming the human dimension of fisheries, rethinking governance, policy and compliance, and achieving equity and inclusion in fisheries. We also identified a number of cross-cutting themes including better understanding the role of fish as nutrition in a hungry world, adapting to climate change, embracing transdisciplinarity, respecting Indigenous knowledge systems, thinking ahead with foresight science, and working together across scales. By reflecting on the past and thinking about the future, we aim to provide guidance for achieving our mutual goal of sustaining vibrant fish populations and sustainable fisheries that benefit all. We hope that this prospective thinking can serve as a guide to (i) assess progress towards achieving this lofty goal and (ii) refine our path with input from new and emerging voices and approaches in fisheries science, management, and stewardship.

Dynamics of eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States.

Eastern equine encephalitis virus (EEEV) causes a rare but severe disease in horses and humans and is maintained in an enzootic transmission cycle between songbirds and Culiseta melanura mosquitoes. In 2019, the largest EEEV outbreak in the United States for more than 50 years occurred, centered in the Northeast. To explore the dynamics of the outbreak, we sequenced 80 isolates of EEEV and combined them with existing genomic data. We found that, similar to previous years, cases were driven by multiple independent but short-lived virus introductions into the Northeast from Florida. Once in the Northeast, we found that Massachusetts was important for regional spread. We found no evidence of any changes in viral, human, or bird factors which would explain the increase in cases in 2019, although the ecology of EEEV is complex and further data is required to explore these in more detail. By using detailed mosquito surveillance data collected by Massachusetts and Connecticut, however, we found that the abundance of Cs. melanura was exceptionally high in 2019, as was the EEEV infection rate. We employed these mosquito data to build a negative binomial regression model and applied it to estimate early season risks of human or horse cases. We found that the month of first detection of EEEV in mosquito surveillance data and vector index (abundance multiplied by infection rate) were predictive of cases later in the season. We therefore highlight the importance of mosquito surveillance programs as an integral part of public health and disease control.

Dynamics of Eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States.

Eastern equine encephalitis virus (EEEV) causes a rare but severe disease in horses and humans, and is maintained in an enzootic transmission cycle between songbirds and Culiseta melanura mosquitoes. In 2019, the largest EEEV outbreak in the United States for more than 50 years occurred, centered in the Northeast. To explore the dynamics of the outbreak, we sequenced 80 isolates of EEEV and combined them with existing genomic data. We found that, like previous years, cases were driven by frequent short-lived virus introductions into the Northeast from Florida. Once in the Northeast, we found that Massachusetts was important for regional spread. We found no evidence of any changes in viral, human, or bird factors which would explain the increase in cases in 2019. By using detailed mosquito surveillance data collected by Massachusetts and Connecticut, however, we found that the abundance of Cs. melanura was exceptionally high in 2019, as was the EEEV infection rate. We employed these mosquito data to build a negative binomial regression model and applied it to estimate early season risks of human or horse cases. We found that the month of first detection of EEEV in mosquito surveillance data and vector index (abundance multiplied by infection rate) were predictive of cases later in the season. We therefore highlight the importance of mosquito surveillance programs as an integral part of public health and disease control.

Sentinel node approach to monitoring online COVID-19 misinformation.

Understanding how different online communities engage with COVID-19 misinformation is critical for public health response. For example, misinformation confined to a small, isolated community of users poses a different public health risk than misinformation being consumed by a large population spanning many diverse communities. Here we take a longitudinal approach that leverages tools from network science to study COVID-19 misinformation on Twitter. Our approach provides a means to examine the breadth of misinformation engagement using modest data needs and computational resources. We identify a subset of accounts from different Twitter communities discussing COVID-19, and follow these 'sentinel nodes' longitudinally from July 2020 to January 2021. We characterize sentinel nodes in terms of a linked domain preference score, and use a standardized similarity score to examine alignment of tweets within and between communities. We find that media preference is strongly correlated with the amount of misinformation propagated by sentinel nodes. Engagement with sensationalist misinformation topics is largely confined to a cluster of sentinel nodes that includes influential conspiracy theorist accounts. By contrast, misinformation relating to COVID-19 severity generated widespread engagement across multiple communities. Our findings indicate that misinformation downplaying COVID-19 severity is of particular concern for public health response. We conclude that the sentinel node approach can be an effective way to assess breadth and depth of online misinformation penetration.

The impact of COVID-19 related regulations and restrictions on mobility and potential for sustained climate mitigation across the Netherlands, Sweden and the UK: a data-based commentary.

Human behaviour change is necessary to meet targets set by the Paris Agreement to mitigate climate change. Restrictions and regulations put in place globally to mitigate the spread of COVID-19 during 2020 have had a substantial impact on everyday life, including many carbon-intensive behaviours such as transportation. Changes to transportation behaviour may reduce carbon emissions. Behaviour change theory can offer perspective on the drivers and influences of behaviour and shape recommendations for how policy-makers can capitalise on any observed behaviour changes that may mitigate climate change. For this commentary, we aimed to describe changes in data relating to transportation behaviours concerning working from home during the COVID-19 pandemic across the Netherlands, Sweden and the UK. We display these identified changes in a concept map, suggesting links between the changes in behaviour and levels of carbon emissions. We consider these changes in relation to a comprehensive and easy to understand model of behaviour, the Opportunity, Motivation Behaviour (COM-B) model, to understand the capabilities, opportunities and behaviours related to the observed behaviour changes and potential policy to mitigate climate change. There is now an opportunity for policy-makers to increase the likelihood of maintaining pro-environmental behaviour changes by providing opportunities, improving capabilities and maintaining motivation for these behaviours.