Lysogeny destabilizes computationally simulated microbiomes.

Microbiomes are ecosystems, and their stability can impact the health of their hosts. Theory predicts that predators influence ecosystem stability. Phages are key predators of bacteria in microbiomes, but phages are unusual predators because many have lysogenic life cycles. It has been hypothesized that lysogeny can destabilize microbiomes, but lysogeny has no direct analog in classical ecological theory, and no formal theory exists. We studied the stability of computationally simulated microbiomes with different numbers of temperate (lysogenic) and virulent (obligate lytic) phage species. Bacterial populations were more likely to fluctuate over time when there were more temperate phages species. After disturbances, bacterial populations returned to their pre-disturbance densities more slowly when there were more temperate phage species, but cycles engendered by disturbances dampened more slowly when there were more virulent phage species. Our work offers the first formal theory linking lysogeny to microbiome stability.

Herd immunity to endemic diseases: Historical concepts and implications for public health policy.

BACKGROUND: "Herd immunity" became a contested term during the COVID-19 pandemic. Although the term "herd immunity" is often used to refer to thresholds at which some diseases can be eliminated (e.g., due to mass vaccination), the term has multiple referents. Different concepts of herd immunity have been relevant throughout the history of immunology and infectious disease epidemiology. For some diseases, herd immunity plays a role in the development of an endemic equilibrium, rather than elimination via threshold effects. METHODS: We reviewed academic literature from 1920 to 2022, using historical and philosophical analysis to identify and develop relevant concepts of herd immunity. RESULTS: This paper analyses the ambiguity surrounding the concept of herd immunity during the pandemic. We argue for the need to recapture a long-standing interpretation of this concept as one of the factors that leads to a dynamic endemic equilibrium between a host population and a mutating respiratory pathogen. CONCLUSIONS: Informed by the history of infectious disease epidemiology, we argue that understanding the concept in this way will help us manage both SARS-CoV-2 and hundreds of other seasonal respiratory pathogens with which we live but which have been disrupted due to sustained public health measures/non-pharmaceutical interventions targeting SARS-CoV-2.

HIHISIV: a database of gene expression in HIV and SIV host immune response.

In the battle of the host against lentiviral pathogenesis, the immune response is crucial. However, several questions remain unanswered about the interaction with different viruses and their influence on disease progression. The simian immunodeficiency virus (SIV) infecting nonhuman primates (NHP) is widely used as a model for the study of the human immunodeficiency virus (HIV) both because they are evolutionarily linked and because they share physiological and anatomical similarities that are largely explored to understand the disease progression. The HIHISIV database was developed to support researchers to integrate and evaluate the large number of transcriptional data associated with the presence/absence of the pathogen (SIV or HIV) and the host response (NHP and human). The datasets are composed of microarray and RNA-Seq gene expression data that were selected, curated, analyzed, enriched, and stored in a relational database. Six query templates comprise the main data analysis functions and the resulting information can be downloaded. The HIHISIV database, available at  https://hihisiv.github.io , provides accurate resources for browsing and visualizing results and for more robust analyses of pre-existing data in transcriptome repositories.

Biodistribution and therapeutic efficacy of a gold nanoparticle-based targeted drug delivery system against pancreatic cancer.

Pancreatic cancer is characterized by desmoplasia; crosstalk between pancreatic cancer cells (PCCs) and pancreatic stellate cells (PSCs) leads to the deposition of extracellular matrix proteins in the tumor environment resulting in poor vascularity. Targeting either PCCs or PSCs individually has produced mixed results, and there is currently no effective strategy to target both cell types simultaneously. Previously, we demonstrated, through in vitro cell culture experiments, that a specific gold nanoparticle-based nanoformulation containing the anti-EGFR antibody cetuximab (C225) as a targeting agent and gemcitabine as a chemotherapeutic agent effectively targets both PCCs and PSCs simultaneously. Herein, we extend our studies to test the ability of these in vitro tested nano formulations to inhibit tumor growth in an orthotopic co-implantation model of pancreatic cancer in vivo. Orthotopic tumors were established by co-implantation of equal numbers of PCCs and PSCs in the mouse pancreas. Among the various formulations tested, 5 nm gold nanoparticles coated with gemcitabine, cetuximab and poly-ethylene glycol (PEG) of molecular weight 1000 Da, which we named ACGP441000, demonstrated optimal efficacy in inhibiting tumor growth. The current study reveals an opportunity to target PCCs and PSCs simultaneously, by exploiting their overexpression of EGFR as a target, in order to inhibit pancreatic cancer growth.

How could a pooled testing policy have performed in managing the early stages of the COVID-19 pandemic? Results from a simulation study.

A coordinated testing policy is an essential tool for responding to emerging epidemics, as was seen with COVID-19. However, it is very difficult to agree on the best policy when there are multiple conflicting objectives. A key objective is minimizing cost, which is why pooled testing (a method that involves pooling samples taken from multiple individuals and analyzing this with a single diagnostic test) has been suggested. In this article, we present results from an extensive and realistic simulation study comparing testing policies based on individually testing subjects with symptoms (a policy resembling the UK strategy at the start of the COVID-19 pandemic), individually testing subjects at random or pools of subjects randomly combined and tested. To compare these testing methods, a dynamic model compromised of a relationship network and an extended SEIR model is used. In contrast to most existing literature, testing capacity is considered as fixed and limited rather than unbounded. This article then explores the impact of the proportion of symptomatic infections on the expected performance of testing policies. Symptomatic testing performs better than pooled testing unless a low proportion of infections are symptomatic. Additionally, we include the novel feature for testing of non-compliance and perform a sensitivity analysis for different compliance assumptions. Our results suggest for the pooled testing scheme to be superior to testing symptomatic people individually, only a small proportion of the population ( > 10 % $$ >10\% $$ ) needs to not comply with the testing procedure.

Familiarity Is Key: Exploring the Effect of Familiarity on the Face-Voice Correlation.

Recent research has examined the extent to which face and voice processing are associated by virtue of the fact that both tap into a common person perception system. However, existing findings do not yet fully clarify the role of familiarity in this association. Given this, two experiments are presented that examine face-voice correlations for unfamiliar stimuli (Experiment 1) and for familiar stimuli (Experiment 2). With care being taken to use tasks that avoid floor and ceiling effects and that use realistic speech-based voice clips, the results suggested a significant positive but small-sized correlation between face and voice processing when recognizing unfamiliar individuals. In contrast, the correlation when matching familiar individuals was significant and positive, but much larger. The results supported the existing literature suggesting that face and voice processing are aligned as constituents of an overarching person perception system. However, the difference in magnitude of their association here reinforced the view that familiar and unfamiliar stimuli are processed in different ways. This likely reflects the importance of a pre-existing mental representation and cross-talk within the neural architectures when processing familiar faces and voices, and yet the reliance on more superficial stimulus-based and modality-specific analysis when processing unfamiliar faces and voices.

Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules.

The COVID-19 pandemic has been characterised by sequential variant-specific waves shaped by viral, individual human and population factors. SARS-CoV-2 variants are defined by their unique combinations of mutations and there has been a clear adaptation to more efficient human infection since the emergence of this new human coronavirus in late 2019. Here, we use machine learning models to identify shared signatures, i.e., common underlying mutational processes and link these to the subset of mutations that define the variants of concern (VOCs). First, we examined the global SARS-CoV-2 genomes and associated metadata to determine how viral properties and public health measures have influenced the magnitude of waves, as measured by the number of infection cases, in different geographic locations using regression models. This analysis showed that, as expected, both public health measures and virus properties were associated with the waves of regional SARS-CoV-2 reported infection numbers and this impact varies geographically. We attribute this to intrinsic differences such as vaccine coverage, testing and sequencing capacity and the effectiveness of government stringency. To assess underlying evolutionary change, we used non-negative matrix factorisation and observed three distinct mutational signatures, unique in their substitution patterns and exposures from the SARS-CoV-2 genomes. Signatures 1, 2 and 3 were biased to C→T, T→C/A→G and G→T point mutations. We hypothesise assignments of these mutational signatures to the host antiviral molecules APOBEC, ADAR and ROS respectively. We observe a shift amidst the pandemic in relative mutational signature activity from predominantly Signature 1 changes to an increasingly high proportion of changes consistent with Signature 2. This could represent changes in how the virus and the host immune response interact and indicates how SARS-CoV-2 may continue to generate variation in the future. Linkage of the detected mutational signatures to the VOC-defining amino acids substitutions indicates the majority of SARS-CoV-2's evolutionary capacity is likely to be associated with the action of host antiviral molecules rather than virus replication errors.

Therapy-induced normal tissue damage promotes breast cancer metastasis.

Disseminated tumor cells frequently exhibit a period of dormancy, rendering them chemotherapy insensitive; conversely, the systemic delivery of chemotherapies can result in normal tissue damage. Using multiple mouse and human breast cancer models, we demonstrate that prior chemotherapy administration enhances metastatic colonization and outgrowth. In vitro, chemotherapy-treated fibroblasts display a pro-tumorigenic senescence-associated secretory phenotype (SASP) and are effectively eliminated by targeting the anti-apoptotic protein BCL-xL. In vivo, chemotherapy treatment induces SASP expression in normal tissues; however, the accumulation of senescent cells is limited, and BCL-xL inhibitors are unable to reduce chemotherapy-enhanced metastasis. This likely reflects that chemotherapy-exposed stromal cells do not enter a BCL-xL-dependent phenotype or switch their dependency to other anti-apoptotic BCL-2 family members. This study highlights the role of the metastatic microenvironment in controlling outgrowth of disseminated tumor cells and the need to identify additional approaches to limit the pro-tumorigenic effects of therapy-induced normal tissue damage.

Improvement in Cellulite Appearance After a Single Treatment Visit With Acoustic Subcision: Long-Term Findings From a Multicenter Clinical Trial.

BACKGROUND: Cellulite is an aesthetically displeasing rippling or dimpling of the skin, primarily on the buttocks/thighs. A recent study showed a novel acoustic subcision device produced significant short-term (12-week) improvement in the appearance of cellulite after a single rapid acoustic pulse (RAP) treatment. OBJECTIVE: To evaluate the long-term (>52-weeks) efficacy and safety of RAP treatment for improvement in the appearance of cellulite. MATERIALS AND METHODS: In this prospective, multicenter trial, female participants ( n = 42) with severe cellulite were treated with the acoustic subcision device in a single visit. At >52 weeks, blinded board-certified dermatologists assessed efficacy by correctly identifying post-treatment photographs and using a 6-point simplified Cellulite Severity Scale (CSS). Participant satisfaction was also collected. Safety was assessed throughout. RESULTS: The blinded panel correctly identified post-treatment photographs at a rate of 95.2%; 70.4% of participants had a >1-point reduction in the CSS score from baseline (mean reduction of 1.09). All participants (100%) reported improved cellulite appearance. Overall pain during treatment was rated as 2.4 and 0.3 post-treatment (pain scale 0-10). No device or treatment-related adverse events were reported at the >52-week follow-up. CONCLUSION: Rapid acoustic pulse treatment significantly improved the long-term appearance of cellulite and was well-tolerated.

Evaluating pooled testing for asymptomatic screening of healthcare workers in hospitals.

BACKGROUND: There is evidence that during the COVID pandemic, a number of patient and HCW infections were nosocomial. Various measures were put in place to try to reduce these infections including developing asymptomatic PCR (polymerase chain reaction) testing schemes for healthcare workers. Regularly testing all healthcare workers requires many tests while reducing this number by only testing some healthcare workers can result in undetected cases. An efficient way to test as many individuals as possible with a limited testing capacity is to consider pooling multiple samples to be analysed with a single test (known as pooled testing). METHODS: Two different pooled testing schemes for the asymptomatic testing are evaluated using an individual-based model representing the transmission of SARS-CoV-2 in a 'typical' English hospital. We adapt the modelling to reflect two scenarios: a) a retrospective look at earlier SARS-CoV-2 variants under lockdown or social restrictions, and b) transitioning back to 'normal life' without lockdown and with the omicron variant. The two pooled testing schemes analysed differ in the population that is eligible for testing. In the 'ward' testing scheme only healthcare workers who work on a single ward are eligible and in the 'full' testing scheme all healthcare workers are eligible including those that move across wards. Both pooled schemes are compared against the baseline scheme which tests only symptomatic healthcare workers. RESULTS: Including a pooled asymptomatic testing scheme is found to have a modest (albeit statistically significant) effect, reducing the total number of nosocomial healthcare worker infections by about 2[Formula: see text] in both the lockdown and non-lockdown setting. However, this reduction must be balanced with the increase in cost and healthcare worker isolations. Both ward and full testing reduce HCW infections similarly but the cost for ward testing is much less. We also consider the use of lateral flow devices (LFDs) for follow-up testing. Considering LFDs reduces cost and time but LFDs have a different error profile to PCR tests. CONCLUSIONS: Whether a PCR-only or PCR and LFD ward testing scheme is chosen depends on the metrics of most interest to policy makers, the virus prevalence and whether there is a lockdown.

Using a volitional help sheet to increase university students' attendance at synchronous online lectures: A randomized controlled trial.

BACKGROUND: A volitional help sheet (VHS) is an intervention for promoting implementation intentions. This study was the first to test the effectiveness of a VHS for increasing university students' lecture attendance. AIMS: To develop a VHS to increase university students' lecture attendance and test its effectiveness at increasing the proportion of lectures attended, and promoting the maintenance of lecture attendance, over an 11-week teaching semester. SAMPLE AND METHOD: One hundred and seventy-eight undergraduate students enrolled in a psychology degree programme were allocated at random to a VHS or active control condition. Prior to intervention, measures of goal intention to attend lectures and trait conscientiousness were collected using self-report, online questionnaires. Over the following 11-week teaching semester, attendance at synchronous (live) online lectures was measured. RESULTS: The VHS condition attended a greater proportion of lectures and maintained their lecture attendance for longer than did the active control condition. These effects were not sensitive to underlying goal intentions, although the sample means on the measures of goal intention were approaching ceiling. Trait conscientiousness increased the effects of the VHS on the proportion of lectures attended. CONCLUSIONS: VHSs constitute useful interventions for increasing and maintaining university students' lecture attendance.

Medicines and Healthcare products Regulatory Agency's "Consultation on proposals for legislative changes for clinical trials": a response from the Trials Methodology Research Partnership Adaptive Designs Working Group, with a focus on data sharing.

In the UK, the Medicines and Healthcare products Regulatory Agency consulted on proposals "to improve and strengthen the UK clinical trials legislation to help us make the UK the best place to research and develop safe and innovative medicines". The purpose of the consultation was to help finalise the proposals and contribute to the drafting of secondary legislation. We discussed these proposals as members of the Trials Methodology Research Partnership Adaptive Designs Working Group, which is jointly funded by the Medical Research Council and the National Institute for Health and Care Research. Two topics arose frequently in the discussion: the emphasis on legislation, and the absence of questions on data sharing. It is our opinion that the proposals rely heavily on legislation to change practice. However, clinical trials are heterogeneous, and as a result some trials will struggle to comply with all of the proposed legislation. Furthermore, adaptive design clinical trials are even more heterogeneous than their non-adaptive counterparts, and face more challenges. Consequently, it is possible that increased legislation could have a greater negative impact on adaptive designs than non-adaptive designs. Overall, we are sceptical that the introduction of legislation will achieve the desired outcomes, with some exceptions. Meanwhile the topic of data sharing - making anonymised individual-level clinical trial data available to other investigators for further use - is entirely absent from the proposals and the consultation in general. However, as an aspect of the wider concept of open science and reproducible research, data sharing is an increasingly important aspect of clinical trials. The benefits of data sharing include faster innovation, improved surveillance of drug safety and effectiveness and decreasing participant exposure to unnecessary risk. There are already a number of UK-focused documents that discuss and encourage data sharing, for example, the Concordat on Open Research Data and the Medical Research Council's Data Sharing Policy. We strongly suggest that data sharing should be the norm rather than the exception, and hope that the forthcoming proposals on clinical trials invite discussion on this important topic.

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.

Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.

The SARS-CoV-2 Spike Protein Mutation Explorer: using an interactive application to improve the public understanding of SARS-CoV-2 variants of concern.

Due to the COVID-19 pandemic the virus responsible, SARS-CoV-2, became a source of intense interest for non-expert audiences. The viral spike protein gained particular public interest as the main target for protective immune responses, including those elicited by vaccines. The rapid evolution of SARS-CoV-2 resulted in variations in the spike that enhanced transmissibility or weakened vaccine protection. This created new variants of concern (VOCs). The emergence of VOCs was studied using viral sequence data which was shared through portals such as the online Mutation Explorer of the COVID-19 Genomics UK consortium (COG-UK/ME). This was designed for an expert audience, but the information it contained could be of general interest if suitably communicated. Visualisations, interactivity and animation can improve engagement and understanding of molecular biology topics, and so we developed a graphical educational resource, the SARS-CoV-2 Spike Protein Mutation Explorer (SSPME), which used interactive 3D molecular models and animations to explain the molecular biology underpinning VOCs. User testing showed that the SSPME had better usability and improved participant knowledge confidence and knowledge acquisition compared to COG-UK/ME. This demonstrates how interactive visualisations can be used for effective molecular biology communication, as well as improving the public understanding of SARS-CoV-2 VOCs.

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.

The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 has led to increased sampling of related sarbecoviruses circulating primarily in horseshoe bats. These viruses undergo frequent recombination and exhibit spatial structuring across Asia. Employing recombination-aware phylogenetic inference on bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed just ~1-3 years prior to their emergence in humans. Phylogeographic analyses examining the movement of related sarbecoviruses demonstrate that they traveled at similar rates to their horseshoe bat hosts and have been circulating for thousands of years in Asia. The closest-inferred bat virus ancestor of SARS-CoV likely circulated in western China, and that of SARS-CoV-2 likely circulated in a region comprising southwest China and northern Laos, both a substantial distance from where they emerged. This distance and recency indicate that the direct ancestors of SARS-CoV and SARS-CoV-2 could not have reached their respective sites of emergence via the bat reservoir alone. Our recombination-aware dating and phylogeographic analyses reveal a more accurate inference of evolutionary history than performing only whole-genome or single gene analyses. These results can guide future sampling efforts and demonstrate that viral genomic fragments extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses.

Adrenal gland response to adrenocorticotropic hormone is intact in patients with postural orthostatic tachycardia syndrome.

BACKGROUND: Many patients with postural orthostatic tachycardia syndrome (POTS) are hypovolemic with plasma volume deficits of 10-30 %. Some also have low levels of aldosterone and diminished aldosterone-renin ratios despite elevations in angiotensin II, pointing to potential adrenal dysfunction. To assess adrenal gland responsiveness in POTS, we measured circulating levels of aldosterone and cortisol following adrenocorticotropin hormone (ACTH) stimulation. METHODS: While on a low Na+ diet (∼10 mEq/day), 8 female patients with POTS and 5 female healthy controls (HC) received a low dose (1 µg) ACTH bolus following a baseline blood sample. After 60 min, a high dose (249 µg) infusion of ACTH was administered to ensure maximal adrenal response. Venous aldosterone and cortisol levels were sampled every 30 min for 2 h. RESULTS: Aldosterone increased in both groups in response to ACTH but was not different between POTS vs. HC at 60 min (53.5 ng/dL [37.8-61.8 ng/dL] vs. 46.1 ng/dL [36.7-84.9 ng/dL]; P = 1.000) or maximally (56.4 ng/dL [49.2-67.1 ng/dL] vs. 49.5 ng/dL [39.1-82.8 ng/dL]; P = 0.524). Cortisol increased in both groups in response to ACTH but was not different in patients with POTS vs. HC at 60 min (39.9 µg/dL [36.1-47.7 µg/dL] vs. 39.3 µg/dL [35.4-46.6 µg/dL]; P = 0.724) or maximally (39.9 µg/dL [33.9-45.4 µg/dL] vs. 42.0 µg/dL [37.6-49.7 µg/dL]; P = 0.354). CONCLUSIONS: ACTH appropriately increased the aldosterone and cortisol levels in patients with POTS. These findings suggest that the response of the adrenal cortex to hormonal stimulation is intact in patients with POTS.