Optimisation strategies for directed evolution without sequencing.

Directed evolution can enable engineering of biological systems with minimal knowledge of their underlying sequence-to-function relationships. A typical directed evolution process consists of iterative rounds of mutagenesis and selection that are designed to steer changes in a biological system (e.g.

Computational Synthetic Biology Enabled through JAX: A Showcase.

Mathematical modeling is indispensable in synthetic biology but remains underutilized. Tackling problems, from optimizing gene networks to simulating intracellular dynamics, can be facilitated by the ever-growing body of modeling approaches, be they mechanistic, stochastic, data-driven, or AI-enabled. Thanks to progress in the AI community, robust frameworks have emerged to enable researchers to access complex computational hardware and compilation.

The Luck of the Draw: Wellcome's Institutional Fund for Research Culture.

Wellcome's Institutional Fund for Research Culture (IFRC) closed call is an invite-only grant call in 2023. It is a departure from Wellcome's previous methods of institutional funding, providing institutions with up to £1m of grant funding to take on ambitious projects that advance research cultures and research environments that are equitable, diverse and supportive. Recognising the broad range of topics and ideas for advancing positive research cultures, IFRC is the first ever Wellcome-funding scheme to use partial randomisation to allocate funding.

A new on-line SPE LC-HRMS method for the analysis of Perfluoroalkyl and Polyfluoroalkyl Substances (PFAS) in PM and its application for screening atmospheric particulates from Dublin and Enniscorthy, Ireland.

A sensitive analytical method has been developed and validated for the determination of 16 polyfluorinated alkyl substances (PFAS) in fine airborne particulate matter (PM) using on-line solid phase extraction (SPE) coupled with liquid chromatography (LC) - negative electrospray ionisation high resolution mass spectrometry (-) ESI-HRMS. On-line SPE allows simultaneous sample clean-up from interfering matrices and lower limits of detection (LODs) by injecting a large volume of sample into the LC system without compromising chromatographic efficiency and resolution. The method provides LODs in the range 0.

A study of SARS-COV-2 outbreaks in US federal prisons: the linkage between staff, incarcerated populations, and community transmission.

Background: Since the novel coronavirus SARS-COV-2 was first identified to be circulating in the US on January 20, 2020, some of the worst outbreaks have occurred within state and federal prisons. The vulnerability of incarcerated populations, and the additional threats posed to the health of prison staff and the people they contact in surrounding communities underline the need to better understand the dynamics of transmission in the inter-linked incarcerated population/staff/community sub-populations to better inform optimal control of SARS-COV-2.

Methods: We examined SARS-CoV-2 case data from 101 non-administrative federal prisons between 5/18/2020 to 01/31/2021 and examined the per capita size of outbreaks in staff and the incarcerated population compared to outbreaks in the communities in the counties surrounding the prisons during the summer and winter waves of the SARS-COV-2 pandemic.

SARS-CoV-2 surveillance and outbreak response on an urban American college campus.

Objective: The George Washington University (GW) in Washington, D.C., USA established the Public Health Laboratory and Campus COVID-19 Support Team (CCST) to develop and implement its SARS-CoV-2 surveillance testing and outbreak response for the 2020-2021 academic year.

Geodemographic insights on the COVID-19 pandemic in the State of Wisconsin and the role of risky facilities.

The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to impact the United States. While age and comorbid health conditions remain primary concerns in the community-based transmission of the virus, empirical evidence continues to suggest that substantial variability exists in the geographic and geodemographic distribution of COVID-19 infection rates. The purpose of this paper is to provide an alternative, spatiotemporal perspective on the pandemic using the state of Wisconsin as a case study.

Is There a Temporal Relationship between COVID-19 Infections among Prison Staff, Incarcerated Persons and the Larger Community in the United States?

Background: Our objective was to examine the temporal relationship between COVID-19 infections among prison staff, incarcerated individuals, and the general population in the county where the prison is located among federal prisons in the United States.

Methods: We employed population-standardized regressions with fixed effects for prisons to predict the number of active cases of COVID-19 among incarcerated persons using data from the Federal Bureau of Prisons (BOP) for the months of March to December in 2020 for 63 prisons.

Results: There is a significant relationship between the COVID-19 prevalence among staff, and through them, the larger community, and COVID-19 prevalence among incarcerated persons in the US federal prison system.

Community-based model for adolescent transgender health care.

Aim: This study aimed to investigate whether transgender and non-binary (TGNB) youth prefer health care received in a community-based setting.

Methods: All patients aged 12-18 years over a 1-year period presenting for transgender health care to either Tauranga Paediatrics, Maternal Infant Child and Adolescent Mental Health Services (MiCAMHS) or Gender Dynamix (a community-based TGNB health service) were invited to complete an anonymous online survey about their experience of health care. Responses were obtained from 39 participants (68.

How long do people stick to a diet resolution? A digital epidemiological estimation of weight loss diet persistence.

Objective: To use Internet search data to compare duration of compliance for various diets.

Design: Using a passive surveillance digital epidemiological approach, we estimated the average duration of diet compliance by examining monthly Internet searches for recipes related to popular diets. We fit a mathematical model to these data to estimate the time spent on a diet by new January dieters (NJD) and to estimate the percentage of dieters dropping out during the American winter holiday season between Thanksgiving and the end of December.

Beyond visual fixations and gaze behaviour. Using pupillometry to examine the mechanisms in the planning and motor performance of a golf putt.

The present study assessed the potential value of using pupillometry to explore skill level differences in the allocation of attention during planning and performance of a golf putt across three putting conditions of varying complexity. Although numerous studies have reported on skill level differences in performers' visual search behaviours, performance accuracy and quiet eye duration (QE) across a range of performance settings, few have provided an objective measure of the allocation of attention during task performance. Fourteen participants were assigned to two groups [low handicap (LHG) and high handicap (HHG)] completing ten putts in three conditions; right to left (RL), left to right (LR) and straight (ST) from 1.

Factors influencing temporal patterns in crime in a large American city: A predictive analytics perspective.

Background: Improving the accuracy and precision of predictive analytics for temporal trends in crime necessitates a good understanding of the how exogenous variables, such as weather and holidays, impact crime.

Methods: We examine 5.7 million reported incidents of crime that occurred in the City of Chicago between 2001 to 2014.

Detecting the contagion effect in mass killings; a constructive example of the statistical advantages of unbinned likelihood methods.

Background: When attempting to statistically distinguish between a null and an alternative hypothesis, many researchers in the life and social sciences turn to binned statistical analysis methods, or methods that are simply based on the moments of a distribution (such as the mean, and variance). These methods have the advantage of simplicity of implementation, and simplicity of explanation. However, when null and alternative hypotheses manifest themselves in subtle differences in patterns in the data, binned analysis methods may be insensitive to these differences, and researchers may erroneously fail to reject the null hypothesis when in fact more sensitive statistical analysis methods might produce a different result when the null hypothesis is actually false.

Quantifying the relative effects of environmental and direct transmission of norovirus.

Norovirus is a common cause of outbreaks of acute gastroenteritis in health- and child-care settings, with serial outbreaks also frequently observed aboard cruise ships. The relative contributions of environmental and direct person-to-person transmission of norovirus have hitherto not been quantified. We employ a novel mathematical model of norovirus transmission, and fit the model to daily incidence data from a major norovirus outbreak on a cruise ship, and examine the relative efficacy of potential control strategies aimed at reducing environmental and/or direct transmission.

Preventing blood-borne virus infection in people who inject drugs in the UK: systematic review, stakeholder interviews, psychosocial intervention development and feasibility randomised controlled trial.

Background: Opioid substitution therapy and needle exchanges have reduced blood-borne viruses (BBVs) among people who inject drugs (PWID). Some PWID continue to share injecting equipment.

Objectives: To develop an evidence-based psychosocial intervention to reduce BBV risk behaviours and increase transmission knowledge among PWID, and conduct a feasibility trial among PWID comparing the intervention with a control.

Sunspot activity and influenza pandemics: a statistical assessment of the purported association.

Since 1978, a series of papers in the literature have claimed to find a significant association between sunspot activity and the timing of influenza pandemics. This paper examines these analyses, and attempts to recreate the three most recent statistical analyses by Ertel (1994), Tapping et al. (2001), and Yeung (2006), which all have purported to find a significant relationship between sunspot numbers and pandemic influenza.

The acceptability and feasibility of a brief psychosocial intervention to reduce blood-borne virus risk behaviours among people who inject drugs: a randomised control feasibility trial of a psychosocial intervention (the PROTECT study) versus treatment as usual.

Background: While opiate substitution therapy and injecting equipment provision (IEP) have reduced blood-borne viruses (BBV) among people who inject drugs (PWID), some PWID continue to share injecting equipment and acquire BBV. Psychosocial interventions that address risk behaviours could reduce BBV transmission among PWID.

Methods: A pragmatic, two-armed randomised controlled, open feasibility study of PWID attending drug treatment or IEP in four UK regions.

Fear-related behaviors in situations of mass threat.

This Briefing focuses on the work of an expanding team of researchers that is exploring the dynamics of fear-related behaviors in situations of mass threat. . Disaster case scenarios are presented to illustrate how fear-related behaviors operate when a potentially traumatic event threatens or endangers the physical and/or psychological health, wellbeing, and integrity of a population.

Estimate of the reproduction number of the 2015 Zika virus outbreak in Barranquilla, Colombia, and estimation of the relative role of sexual transmission.

Background: In 2015, the Zika arbovirus (ZIKV) began circulating in the Americas, rapidly expanding its global geographic range in explosive outbreaks. Unusual among mosquito-borne diseases, ZIKV has been shown to also be sexually transmitted, although sustained autochthonous transmission due to sexual transmission alone has not been observed, indicating the reproduction number (R0) for sexual transmission alone is less than 1. Critical to the assessment of outbreak risk, estimation of the potential attack rates, and assessment of control measures, are estimates of the basic reproduction number, R0.

Modeling the role of healthcare access inequalities in epidemic outcomes.

Urban areas, with large and dense populations, offer conditions that favor the emergence and spread of certain infectious diseases. One common feature of urban populations is the existence of large socioeconomic inequalities which are often mirrored by disparities in access to healthcare. Recent empirical evidence suggests that higher levels of socioeconomic inequalities are associated with worsened public health outcomes, including higher rates of sexually transmitted diseases (STD's) and lower life expectancy.

The Role of Fear-Related Behaviors in the 2013-2016 West Africa Ebola Virus Disease Outbreak.

The 2013-2016 West Africa Ebola virus disease pandemic was the largest, longest, deadliest, and most geographically expansive outbreak in the 40-year interval since Ebola was first identified. Fear-related behaviors played an important role in shaping the outbreak. Fear-related behaviors are defined as "individual or collective behaviors and actions initiated in response to fear reactions that are triggered by a perceived threat or actual exposure to a potentially traumatizing event.

Some models for epidemics of vector-transmitted diseases.

Vector-transmitted diseases such as dengue fever and chikungunya have been spreading rapidly in many parts of the world. The Zika virus has been known since 1947 and invaded South America in 2013. It can be transmitted not only by (mosquito) vectors but also directly through sexual contact.