ViCTree: an automated framework for taxonomic classification from protein sequences

Motivation: The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualisation tool that enables the tree to be explored interactively in the context of pairwise distance data. Results: To demonstrate utility, ViCTree was applied to subfamily Densovirinae of family Parvoviridae. This led to the identification of six new species of insect virus. Availability: ViCTree is open-source and can be run on any Linux- or Unix-based computer or cluster. A tutorial, the documentation and the source code are available under a GPL3 license, and can be accessed at http://bioinformatics.cvr.ac.uk/victree_web/

Coercion in California: Eugenics Reconstituted in Welfare Reform, the Contracting of Reproductive Capcity, and Terms of Probation

In an era where courts are expanding the scope of a constitutionally protected right to privacy, it is hard to imagine that the exercise of that right is being legally perverted to promote eugenic ideals. This, however, is precisely what has been happening in the state of California. This Note explores how modern day policies and practices, such as the family cap component of welfare policy, the sale of the reproductive capacity of drug addicts, and prohibitions on procreation as a term of probation, are used to coerce women with regard to their reproductive decision

Coercion in California: Eugenics Reconstituted in Welfare Reform, the Contracting of Reproductive Capcity, and Terms of Probation

In an era where courts are expanding the scope of a constitutionally protected right to privacy, it is hard to imagine that the exercise of that right is being legally perverted to promote eugenic ideals. This, however, is precisely what has been happening in the state of California. This Note explores how modern day policies and practices, such as the family cap component of welfare policy, the sale of the reproductive capacity of drug addicts, and prohibitions on procreation as a term of probation, are used to coerce women with regard to their reproductive decision

Strategic placement of automated external defibrillators (AEDs) for cardiac arrests in public locations and private residences

Aim: The aim of our study was to determine whether businesses can be identified that rank highly for their potential to improve coverage of out-of-hospital cardiac arrests (OHCAs) by automated external defibrillators (AEDs), both in public locations and private residences. Methods: The cohort comprised 10,422 non-traumatic OHCAs from 2014 to 2020 in Perth, Western Australia. We ranked 115 business brands (across 5,006 facilities) for their potential to supplement coverage by the 3,068 registered public-access AEDs in Perth, while accounting for AED access hours. Results: Registered public-access AEDs provided 100 m coverage of 23% of public-location arrests, and 4% of arrests in private residences. Of the 10 business brands ranked highest for increasing the coverage of public OHCAs, six brands were ranked in the top 10 for increased coverage of OHCAs in private residences. A public phone brand stood out clearly as the highest-ranked of all brands, with more than double the coverage-increase of the second-ranked brand. If all 115 business brands hosted AEDs with 24–7 access, 57% of OHCAs would remain without 100 m coverage for public arrests, and 92% without 100 m coverage for arrests in private residences. Conclusion: Many businesses that ranked highly for increased coverage of arrests in public locations also rank well for increasing coverage of arrests in private residences. However, even if the business landscape was highly saturated with AEDs, large gaps in coverage of OHCAs would remain, highlighting the importance of considering other modes of AED delivery in metropolitan landscapes

Local authorities' capacity to advance climate action in the food and farming sectors

The mitigation measures needed in the face of climate change require transformation in the production and consumption of food. This paper examines local authorities' role in driving practical transformation in the food and farming sectors at the local level, reflecting on the complexity of these sectors and the implications for the effective sub-national delivery of climate goals. A policy review identified food and farming-related actions occurring in a two-tier local authority in England. Local authority staff were invited to one of four workshops to reflect on ongoing activity and to identify actions that have implementation potential and those that are beyond the remit and/or resource of local authorities. The workshops demonstrated participants' ambition to support mitigation measures that foster resilient food systems and deliver co-benefits to local residents. We argue that, despite their constrained capacity, local authorities are well-placed to develop innovative climate solutions relevant to local need. This capacity to deliver climate action should continue to be supported, including through national recognition of the innovative delivery approaches examined in this research

Gloucestershire Food and Farming for Net Zero – Integrating local climate policies

This report is the result of research undertaken in 2024-2025 by the Countryside and Community Research Institute, Gloucestershire Food and Farming Partnership and Climate Leadership Gloucestershire (CLG). It sets out how local councils in Gloucestershire, in trying to tackle the climate emergency, are already, or viably could be, supporting the transition to net zero in the agricultural and food arenas. Council officials indicate that tight budgets and limited direct influence on the climate impacts of food and agriculture constrain their ability to drive change. Yet through this work, councils recognised opportunities to facilitate change through better internal connections and external partnerships. While climate emergency policies focus on the emissions linked to council operations (for example in energy efficiency or materials recycling), an important role remains for councils to stimulate conversations and innovations about food system transformations towards net zero, to the benefit of society. Currently, the facilitative and democratic role of councils in supporting food net zero transformation is underplayed and overwhelmed by inadequate financial resource or limited direct influence to drive change. In fact, our research found that a lack of internal communication and data sharing between, for example, planners and community development officials, hinders innovation in protecting productive land for public health. Similarly, food is included in climate emergency policies, for example in support for small food enterprises through local procurement, as a way to cut supply chain emissions. Our report suggests that, at the strategic level, councils should continue food-related climate actions, and further consider their role in driving demonstrable advances in net zero innovation. Our research has led to the production of an action plan of viable and realistic actions, which was presented to CLG for feedback. The recommendations presented to CLG are a consolidation of ideas generated by council members and officers during interviews and workshops. The full plan is provided in this report’s annex. The actions CLG members chose to prioritise are: •Making stronger use of the planning system. •Supporting farmers’ transition to regenerative agriculture. •Encouraging more sustainable food and drink at council events, local festivals and other venues. •Promoting healthy, affordable, sustainable diets. •Leveraging emissions reduction via public procurement

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707