COVID-19 Infection Rates in Vaccinated and Unvaccinated Inmates: A Retrospective Cohort Study.

Background In 2023, breakthrough COVID-19 infections among vaccinated individuals and reinfections in previously infected people have become common. Additionally, infections are due to Omicron subvariants of the virus that behave differently from those at the onset of the pandemic. Understanding how vaccination and natural immunity influence COVID-19 infection rates is crucial, especially in high-density congregate settings such as prisons, to inform public health strategies. Methods We analyzed COVID-19 surveillance data from January to July 2023 across 33 California state prisons, primarily a male population of 96,201 individuals. We computed the incidence rate of new COVID-19 infections among COVID-bivalent-vaccinated and entirely unvaccinated groups (those not having received either the bivalent or monovalent vaccine). Results Our results indicate that the infection rates in the bivalent-vaccinated and entirely unvaccinated groups are 3.24% (95% confidence interval (CI): 3.06-3.42%) and 2.72% (CI: 2.50-2.94%), respectively, with an absolute risk difference of only 0.52%. When the data were filtered for those aged 50 and above, the infection rates were 4.07% (CI: 3.77-4.37%) and 3.1% (CI: 2.46-3.74%), respectively, revealing a mere 0.97% absolute risk difference. Among those aged 65 and above, the infection rates were 6.45% (CI: 5.74-7.16%) and 4.5% (CI: 2.57-6.43%), respectively, with an absolute risk difference of 1.95%. Conclusion We note low infection rates in both the vaccinated and unvaccinated groups, with a small absolute difference between the two across age groups. A combination of monovalent and bivalent vaccines and natural infections likely contributed to immunity and a lower level of infection rates compared to the height of the pandemic. It is possible that a degree of 'herd immunity' has been achieved. Yet, using p<0.05 as the threshold for statistical significance, the bivalent-vaccinated group had a slightly but statistically significantly higher infection rate than the unvaccinated group in the statewide category and the age ≥50 years category. However, in the older age category (≥65 years), there was no significant difference in infection rates between the two groups. This suggests that while the bivalent vaccine might offer protection against severe outcomes, it may not significantly reduce the risk of infections entirely. Further research is needed to understand the reasons behind these findings and to consider other factors, such as underlying health conditions. This study underscores the importance of developing vaccines that target residual COVID-19 infections, especially in regard to evolving COVID-19 variants.

Convergence and transdisciplinary teaching in quantitative biology.

The United States National Science and Technology Council has made a call for improving STEM (Science, Technology, Engineering, and Mathematics) education at the convergence of science, technology, engineering, and mathematics. The National Science Foundation (NSF) views convergence as the merging of ideas, approaches, and technologies from widely diverse fields of knowledge to stimulate innovation and discovery. Teaching convergency requires moving to the transdisciplinary level of integration where there is deep integration of skills, disciplines, and knowledge to solve a challenging real-world problem. Here we present a summary on convergence and transdisciplinary teaching. We then provide examples of convergence and transdisciplinary teaching in plant biology, and conclude by discussing limitations to contemporary conceptions of convergency and transdisciplinary STEM.

Call volume, triage outcomes, and protocols during the first wave of the COVID-19 pandemic in the United Kingdom: Results of a national survey.

OBJECTIVES: During the first wave of the COVID-19 pandemic in the United Kingdom (UK), to describe volume and pattern of calls to emergency ambulance services, proportion of calls where an ambulance was dispatched, proportion conveyed to hospital, and features of triage used. METHODS: Semistructured electronic survey of all UK ambulance services (n = 13) and a request for routine service data on weekly call volumes for 22 weeks (February 1-July 3, 2020). Questionnaires and data request were emailed to chief executives and research leads followed by email and telephone reminders. The routine data were analyzed using descriptive statistics, and questionnaire data using thematic analysis. RESULTS: Completed questionnaires were received from 12 services. Call volume varied widely between services, with a UK peak at week 7 at 13.1% above baseline (service range -0.5% to +31.4%). All services ended the study period with a lower call volume than at baseline (service range -3.7% to -25.5%). Suspected COVID-19 calls across the UK totaled 604,146 (13.5% of all calls), with wide variation between services (service range 3.7% to 25.7%), and in service peaks of 11.4% to 44.5%. Ambulances were dispatched to 478,638 (79.2%) of these calls (service range 59.0% to 100.0%), with 262,547 (43.5%) resulting in conveyance to hospital (service range 32.0% to 53.9%). Triage models varied between services and over time. Two primary call triage systems were in use across the UK. There were a large number of products and arrangements used for secondary triage, with services using paramedics, nurses, and doctors to support decision making in the call center and on scene. Frequent changes to triage processes took place. CONCLUSIONS: Call volumes were highly variable. Case mix and workload changed significantly as COVID-19 calls displaced other calls. Triage models and prehospital outcomes varied between services. We urgently need to understand safety and effectiveness of triage models to inform care during further waves and pandemics.

Undergraduate Quantitative Biology Impact on Biology Preservice Teachers.

Quantitative biology is a rapidly advancing field in the biological sciences, particularly given the rise of large datasets and computer processing capabilities that have continually expanded over the past 50 years. Thus, the question arises, How should K-12 biology teachers incorporate quantitative biology skills into their biology curriculum? The teaching of quantitative biology has not been readily integrated into undergraduate biology curricula that impact preservice teachers. This has potential to cascade effects downward into the quality of learning about quantitative biology that can be expected in K-12 contexts. In this paper, we present the perspectives of a mathematics educator, a science educator, and two biologists, and discuss how we have personally incorporated aspects of quantitative reasoning into our courses. We identify some common challenges relevant to expanding implementation of quantitative reasoning in undergraduate biology courses in order to serve the needs of preservice teachers-both in their disciplinary courses and methods courses. For example, time constraints, math pedagogical content knowledge, and personal views about the relevance of quantitative principles in biology teaching and learning can impact how and to what extent they become implemented in curricula. In addition, although national standards at the K-12 level do address quantitative reasoning, the emphasis and guidance provided are sparser than for other content standards. We predict that both K-12 standards and guidelines for undergraduate education will only increase in their emphasis on quantitative skills as computation, "big data," and statistical modeling are increasingly becoming requisite skills for biologists.

Ericaceous species reduce methane emissions in sheep and red deer: Respiration chamber measurements and predictions at the scale of European heathlands.

Despite the importance of atmospheric methane as a potent greenhouse gas and the significant contribution from ruminant enteric fermentation on methane emissions at a global scale, little effort has been made to consider the influence that different plant-based natural diets have on methane emissions in grazing systems. Heathland is an ericaceous dwarf-shrub-dominated habitat widespread across the northern hemisphere, in Europe, provides valuable ecosystem services in areas with poor soils, such as water flow regulation, land-based carbon skin, energy reservoir and habitat of key game species. We (i) measured methane emissions from red deer (Cervus elaphus) and sheep (Ovis aries) fed mixed diets of natural grass plus ericaceous species (either Calluna vulgaris or Vaccinium myrtillus) using open-circuit respiration chambers; and (ii) modelled the results to estimate methane emissions from red deer and sheep populations inhabiting heathland habitats across Europe under different scenarios of grass-based mixed diets with varying proportions of ericaceous species. Our results indicated that methane emissions per unit of digestible organic matter intake decreased as the proportion of ericaceous species in diet increased, but this relationship was complex because of the significant interaction between the proportion of ericaceous species in the diet and digestible organic matter intake. According to our estimates red deer and sheep populations across European heathlands produce 129.7 kt·y-1 methane (se = 1.79) based on a hypothetical grass-ericaceous species mixed diet containing 30% of ericaceous species; this is 0.5% of total methane emissions from human activity across Europe (24,755 kt·y-1), and a reduction in methane emissions of 63.8 kt·y-1 against the same deer and sheep populations, if assumed to consume a grass-only diet. We suggest the implementation of carbon credits as a measure to value the relevance of heathland systems to promote biodiversity and its potential contribution to reduce methane emissions in ruminant grazing systems.

Public involvement and engagement in primary and emergency care research: the story from PRIME Centre Wales.

BACKGROUND: Policy throughout the United Kingdom promotes involvement of patients and public members in research to benefit patient care and health outcomes. PRIME Centre Wales is a national research centre, developing and coordinating research about primary and emergency care which forms 90% of health service encounters. In this paper, we describe our approach to public involvement and engagement in PRIME Centre Wales (hereafter called PRIME), in particular: how this approach has developed; ways in which public members contribute to PRIME activity; the strengths and limitations of our approach, challenges and future opportunities. PRIME ensures work is relevant to service users, carers, the public and policy makers by incorporating comprehensive patient and public involvement in every phase of our work. APPROACH: PRIME has policies and processes to enable and promote successful public involvement and engagement across research activities. This ensures public perspectives and patient experiences are integrated throughout research development, implementation and dissemination and in managing and delivering PRIME strategy over a 10 year timescale. A public/patient group called SUPER is a key resource providing wide-ranging perspectives via email and face-to-face discussion. We collect information on processes and experiences to assess value and impact, to guide ongoing involvement and engagement. A funded post provides leadership and support to staff and to public/patient contributors to facilitate collaborations. DISCUSSION: A stable, well-resourced structure has provided the timescales to build strong relationships and embed diverse approaches to public involvement and engagement within PRIME. Researchers and public contributors have committed to collaborations, developed knowledge and skills and sustained relationships. Effective approaches incorporate values and actions which, when operating together, strengthen processes and outcomes of public involvement and engagement. CONCLUSION: Supportive context, motivation and time are necessary to foster values and practices that enable effective public involvement and engagement. PRIME has embedded public involvement and engagement across research activities and structures. Central is the public/patient group SUPER offering experience-based expertise to add value to the research cycle. This innovative model, aligned with best practice, enhances relevance and quality of primary and emergency care research to benefit patients and the general population.

First evidence of terrestrial ambrein formation in human adipocere.

To date, the only known occurrence of ambrein, an important perfumery organic molecule, is in coproliths found in about one in a hundred sperm whales. Jetsam ambergris coproliths from the whale are also found occasionally on beaches worldwide. Here we report on the surprising occurrence of ambrein in human adipocere. Adipocere is a waxy substance formed post-mortem during incomplete anaerobic decomposition of soft tissues. Adipocere samples obtained from grave exhumations were analysed using gas chromatography-mass spectrometry (GC-MS). In addition to the typical fatty acids of adipocere, lesser amounts of ambrein were identified in the samples, in abundances similar to those of the major accompanying faecal steroids. The distribution of these compounds suggests that ambrein was produced post-mortem during the microbial decomposition of faecal residues and tissues. It is assumed that the adipocere matrix of saturated fatty acidsaided the preservation of ambrein over extended periods of time, because adipocere is stable against degradation. The association of ambrein formation in ageing faecal material, under moist, oxygen-depleted conditions, now requires more attention in studies of other mammalian and geological samples. Indeed, ambrein and its transformation products may be useful novel chemical indicators of aged faecal matter and decomposed bodies.

Organic matter characterization of sediments in two river beaches from northern Portugal for forensic application.

In a forensic investigation, the analysis of earth materials such as sediments and soils have been used as evidence at a court of law, relying on the study of properties such as color, particle size distribution and mineral identification, among others. In addition, the analysis of the organic composition of sediments and soils is of particular value, since these can be used as complementary independent evidence to the inorganic component. To investigate the usefulness of organic indicators in sediment characterization and discrimination, seventy-seven samples were collected during a period of one year in two river beaches located at the southern bank of the Douro River estuary in the North of Portugal. Isotopes of total carbon, pollen and plant wax-marker analyses were performed. In both beaches, an increase of the organic matter concentrations was noticeable, moving landward, related with the higher cover of associated plant material. The results obtained showed that the combination of all the techniques adopted showed a clear discrimination between samples from the two beaches, and also showed a differentiation of samples in relation to distance from the river in both beaches. The results also show that seasonality in these beaches was not a determining factor for discrimination, at the times considered. In addition, the effects of time was not marked.

Investigation of sterols as potential biomarkers for the detection of pig (S. s. domesticus) decomposition fluid in soils.

This study was carried out to evaluate the potential of using cholesterol and coprostanol, as indicators for the detection of decomposition fluid of buried pigs (S. s. domesticus) in soils. In May 2007, four pig carcasses (∼35kg) were buried in shallow graves (∼40 cm depth) at the University of Ontario Institute of Technology in Canada. Two pigs were exhumed after three months (Pig 1, Pig 2) and six months (Pig 3, Pig 4) post burial. Soil samples were collected beneath the pig carcasses (∼40cm depth) and from grave walls (∼15-20 cm depth) as well as from a parallel control site. Coprostanol and cholesterol were extracted from soils, purified with solid phase extraction (SPE) and analysed with gas chromatography/mass spectrometry (GC/MS). A significant increase in cholesterol concentrations (p<0.05) and amounts of coprostanol were detected in soil located beneath the pig carcasses after three months of burial. It is assumed that during the putrefaction and liquefaction stages of decomposition pig fluid which contains cholesterol and coprostanol is released into the underlying soil. Therefore, cholesterol and coprostanol could be used as potential biomarkers to detect the presence of decomposition fluid three months after burial under comparable soil and environmental conditions. Further research is suggested for additional soil sampling before and after three months to investigate the abundance of these and other sterols.

Can gas chromatography combustion isotope ratio mass spectrometry be used to quantify organic compound abundance?

Quantifying the concentrations of organics such as phospholipid fatty acids (PLFAs) and n-alkanes and measuring their corresponding (13)C/(12)C isotope ratios often involves two separate analyses; (1) quantification by gas chromatography flame ionisation detection (GC-FID) or gas chromatography/mass spectrometry (GC/MS), and (2) (13) C-isotope abundance analysis by gas chromatography/combustion/isotope ratio mass spectrometry (GC-C-IRMS). This requirement for two separate analyses has obvious disadvantages in terms of cost and time. However, there is a history of using the data output of isotope ratio mass spectrometers to quantify various components; including the N and C concentrations of solid materials and CO(2) concentrations in gaseous samples. Here we explore the possibility of quantifying n-alkanes extracted from sheeps' faeces and fatty acid methyl esters (FAMEs) derivatised from PLFAs extracted from grassland soil, using GC-C-IRMS. The results were compared with those from GC-FID analysis of the same extracts. For GC-C-IRMS the combined area of the masses for all the ions (m/z 44, 45 and 46) was collected, referred to as 'area all', while for the GC-FID analysis the peak area data were collected. Following normalisation to a common value for added internal standards, the GC-C-IRMS 'area all' values and the GC-FID peak area data were directly compared. Strong linear relationships were found for both n-alkanes and FAMEs. For the n-alkanes the relationships were 1:1 while, for the FAMEs, GC-C-IRMS overestimated the areas relative to the GC-FID results. However, with suitable reference material 1:1 relationships were established. The output of a GC-C-IRMS system can form the basis for the quantification of certain organics including FAMEs and n-alkanes.

Quantifying species composition in root mixtures using two methods: near-infrared reflectance spectroscopy and plant wax markers.

Understanding of plant interactions is greatly limited by our ability to identify and quantify roots belonging to different species. We proposed and compared two methods for estimating the root biomass proportion of each species in artificial mixtures: near-infrared reflectance spectroscopy (NIRS) and plant wax markers. Two sets of artificial root mixtures composed of two or three herbaceous species were prepared. The proportion of root material of each species in mixtures was estimated from NIRS spectral data (i) and the concentration patterns of n-alkanes (ii), n-alcohols (iii), and n-alkanes +n-alcohols combined (iv). For each data set, calibration equations were developed using multivariate statistical models. The botanical composition of root mixtures was predicted well for all the species considered. The accuracy varied slightly among methods: alkanes < alcohols = alkanes + alcohols < NIRS. Correlation coefficients between predicted and actual root proportions ranged from 0.89 to 0.99 for alkanes + alcohols predictions and from 0.97 to 0.99 for NIRS predictions. These two methods provide promising potential for understanding allocation patterns and competitive interactions.

Protocol for the analysis of n-alkanes and other plant-wax compounds and for their use as markers for quantifying the nutrient supply of large mammalian herbivores.

Plant-wax markers can be used for estimating forage intake, diet composition and supplement intake in grazing livestock, wild ruminants and other mammals. We describe protocols for using the saturated hydrocarbons (alkanes) of plant wax as markers for estimating fecal output, intake and digestibility. Procedures for investigating digestion kinetics are also discussed. Alkanes can also be used to estimate diet composition and the procedures required to do this are also described, including the special case where supplementary feed is treated as a component of the diet composition estimate. The long-chain alcohols (LCOHs) and very long-chain fatty acids (VLCFAs) of plant wax show particular promise for discriminating a greater number of species in the diet. The use of all these plant-wax markers in nutrition studies depends on having quantitative, repeatable and mutually compatible assay procedures for alkanes, LCOHs and VLCFAs; we present protocols for these assays in detail. Analysis of a single sample of feces or plant material for all these plant-wax markers can be completed within 2 days; however, it is possible to process up to 50 samples (analyzed in duplicate) per week.

Phthalate and alkyl phenol concentrations in soil following applications of inorganic fertiliser or sewage sludge to pasture and potential rates of ingestion by grazing ruminants.

Soil concentrations of dioctyl phthalate (DOP) and the alkyl phenols, octyl phenol (OP) and nonyl phenol (NP), after repeated surface applications of sewage sludge to pastures, were investigated. Liquid sludge was applied at a rate of 2.25 tonnes dry matter (DM) per hectare to each of three treated (T) plots on three occasions during the summer and two occasions in the early spring over a period of 2.5 years. Control (C) plots were treated with inorganic fertiliser containing amounts of nitrogen equivalent to those applied to the treated plots. At between 69 and 81 days after the application of sludge, 15 separate soil samples were collected from one half of each of the plots (Experiment 1). Concentrations (microg g(-1)) of DOP were higher (P < 0.001) than those of NP, while those of OP were generally below detectable levels. Mean soil concentrations of DOP were not significantly different in T and C plots [0.233 vs. 0.155 microg g(-1); standard error of the difference (SED) = 0.046; not significant (NS)], partly because there was already a relatively large amount of DOP present. NP concentrations were, however, significantly higher in T than in C plots (0.021 vs. 0.013 microg g(-1) SED = 0.002; P < 0.05). There was no consistent change over time in the mean soil concentrations of these compounds when sampled at intervals of 3-6 months. Concentrations in soil samples collected at monthly intervals following sludge application indicated that the variation in concentrations of these endocrine-disrupting compounds (EDC) was unrelated to time since sludge application. Rates of soil ingestion, expressed as the percentage of DM intake represented by soil, were higher during the winter than the summer (5.40 vs. 1.17; SED = 0.360; P < 0.001) and estimated daily intakes of DOP and NP were up to 150 microg and 8 microg, respectively. It is concluded that the application of sewage sludge to pasture does not increase soil concentrations of phthalate (as DOP) or alkyl phenols. Thus, the risk of increased exposure to these EDC as a result of sludge application is small. However, the small effect of sludge application on soil concentrations may be largely a reflection of the relatively high concentrations of DOP already present in the soil, which may be biologically significant.

The flexibility of an intermediate feeder: dietary selection by mountain hares measured using faecal n-alkanes.

Herbivores with an intermediate feeding strategy either vary their diet between a grazing (bulk roughage feeders) or browsing (concentrate selectors) strategy on a seasonal basis or select a mixed diet at any one time. The underlying ecological causes of the seasonal dietary shift in a small non-ruminant intermediate feeder - the mountain or arctic hare (Lepus timidus L.) were determined. Diet composition and selection relative to availability were investigated for 41 individual free-ranging mountain hares (of which 18 female hares were radio-collared) occupying an upland mosaic landscape in north-east Scotland. Diet composition was determined using faecal n-alkane analysis. Radio-collared hares were designated as pasture, woodland or moorland hares according to the habitat that predominated their home-range. In common with previous studies, mountain hares switched from a browse-dominated diet during winter to a Gramineae-dominated diet in summer, although it was only significant for reproductively active females during the peak breeding season. Diet composition remained consistent regardless of habitat occupied. However, the diet of radio-tracked hares differed significantly from the biomass available in the individual home-ranges; Gramineae were preferentially selected over browse species throughout the year. During winter and in particular during the early breeding season, intermediate feeders, such as mountain hares, ate browse material when the availability of higher quality was restricted. The ability to browse or graze represents a flexible foraging strategy permitting survival and production through periods of changing or unpredictable forage quality and availability.