An insight into the impact of arable farming on Irish biodiversity: A scarcity of studies hinders a rigorous assessment

peer-reviewedTo help understand and counteract future agronomic challenges to farmland biodiversity, it is essential to know how present farming practices have affected biodiversity on Irish farms. We present an overview of existing research data and conclusions, describing the impact of crop cultivation on biodiversity on Irish arable farms. An extensive literature review clearly indicates that peer-reviewed publications on research conducted in Ireland on this topic are quite scarce: just 21 papers investigating the effect of conventional crop cultivation on Irish biodiversity have been published within the past 30 years. Principally, these studies have concluded that conventional crop cultivation has had an adverse impact on biodiversity on Irish farms, with 15 of the 21 studies demonstrating negative trends for the taxa investigated. Compared to other EU states, the relative dearth of baseline data and absence of monitoring programmes designed to assess the specific impacts of crop cultivation on Irish biodiversity highlight the need to develop long-term research studies. With many new challenges facing Irish agriculture, a research programme must be initiated to measure current levels of biodiversity on arable land and to assess the main farming ‘pressures’ causing significant biodiversity loss or gains in these systems.This work was funded under the EPA ERTDI Research Programme (Grant 2006-B-MS-46)

Improving clerkship preparedness: a hospital medicine elective for pre-clerkship students.

BackgroundMedical students often struggle to apply their nascent clinical skills in clerkships. While transitional clerkships can orient students to new roles and logistics, students may benefit from developing clinical skills in inpatient environments earlier in their curriculum to improve readiness for clerkships.InterventionOur four- to six-session elective provides pre-clerkship students with individualized learning in the inpatient setting with the aim of improving clerkship preparedness. Students work one-on-one with faculty who facilitate individualized learning through mentoring, deliberate practice, and directed feedback. Second-year medical students are placed on an attending-only, traditionally 'non-teaching' service in the hospital medicine division of a Veterans Affairs (VA) hospital for half-day sessions. Most students self-select into the elective following a class-wide advertisement. The elective also accepts students who are referred for remediation of their clinical skills.OutcomeIn the elective's first two years, 25 students participated and 47 students were waitlisted. We compared participant and waitlisted (non-participant) students' self-efficacy in several clinical and professional domains during their first clerkship. Elective participants reported significantly higher clerkship preparedness compared to non-participants in the areas of physical exam, oral presentation, and formulation of assessments and plans.ConclusionsStudents found the one-on-one feedback and personalized attention from attending physicians to be a particularly useful aspect of the course. This frequently cited benefit points to students' perceived needs and the value they place on individualized feedback. Our innovation harnesses an untapped resource - the hospital medicine 'non-teaching' service - and serves as an attainable option for schools interested in enhancing early clinical skill-building for all students, including those recommended for remediation.AbbreviationsA&P: Assessment and plan; H&P: History and physical; ILP: Individual learning plan

On-orbit No-contact Anomaly Debug Procedure for the CuPID Cubesat

The CuPID CubeSat Observatory was a 6U cubesat launched into low-Earth orbit with a ride-share opportunity in Fall 2021. The mission was supported by NASA's Heliophysics division and motivated scientifically with the objective to image X-rays produced in the magnetosphere. After launch, the team was unable to communicate with the spacecraft. This document presents the testing and analysis of attempts to contact the spacecraft and investigation to the likely cause of failure with the radio system.Comment: 14 pages, 6 figure

Heterometallic cobalt(ii) calix[6 and 8]arenes: synthesis, structure and electrochemical activity

Heterometallic cobalt p-tert-butylcalix[6 and 8]arenes have been generated from the in situ reaction of lithium reagents (n-BuLi or t-BuOLi) or NaH with the parent calix[n]arene and subsequent reaction with CoBr2. The reverse route, involving the addition of in situ generated Li[Co(Ot-Bu)3] to p-tert-butylcalix[6 and 8]arene, has also been investigated. X-ray crystallography reveals the formation of complicated products incorporating differing numbers of cobalt and lithium or sodium centers, often with positional disorder, as well as, in some cases, the retention of halide. The electrochemical analysis revealed several oxidation events related to the subsequent oxidation of Co(ii) centers and the reduction of the metal cation at negative potentials. Moreover, the electrochemical activity of the phenol moieties of the parent calix[n]arenes resulted in dimerized products or quinone derivatives, leading to insoluble oligomeric products that deposit and passivate the electrode. Preliminary screening for electrochemical proton reduction revealed good activity for a number of these systems. Results suggest that [Co6Na(NCMe)6(μ-O)(p-tert-butylcalix[6]areneH)2Br]·7MeCN (6·7MeCN) is a promising molecular catalyst for electrochemical proton reduction, with a mass transport coefficient, catalytic charge transfer resistance and current magnitude at the catalytic turnover region that are comparable to those of the reference electrocatalyst (Co(ii)Cl2)

The genetic basis for adaptation of model-designed syntrophic co-cultures.

Understanding the fundamental characteristics of microbial communities could have far reaching implications for human health and applied biotechnology. Despite this, much is still unknown regarding the genetic basis and evolutionary strategies underlying the formation of viable synthetic communities. By pairing auxotrophic mutants in co-culture, it has been demonstrated that viable nascent E. coli communities can be established where the mutant strains are metabolically coupled. A novel algorithm, OptAux, was constructed to design 61 unique multi-knockout E. coli auxotrophic strains that require significant metabolite uptake to grow. These predicted knockouts included a diverse set of novel non-specific auxotrophs that result from inhibition of major biosynthetic subsystems. Three OptAux predicted non-specific auxotrophic strains-with diverse metabolic deficiencies-were co-cultured with an L-histidine auxotroph and optimized via adaptive laboratory evolution (ALE). Time-course sequencing revealed the genetic changes employed by each strain to achieve higher community growth rates and provided insight into mechanisms for adapting to the syntrophic niche. A community model of metabolism and gene expression was utilized to predict the relative community composition and fundamental characteristics of the evolved communities. This work presents new insight into the genetic strategies underlying viable nascent community formation and a cutting-edge computational method to elucidate metabolic changes that empower the creation of cooperative communities

A Small-molecule Inhibitor Directed against the Chemokine Receptor CXCR4 Prevents its Use as an HIV-1 Coreceptor

The chemokine receptor CXCR4 is the major coreceptor used for cellular entry by T cell– tropic human immunodeficiency virus (HIV)-1 strains, whereas CCR5 is used by macrophage (M)-tropic strains. Here we show that a small-molecule inhibitor, ALX40-4C, inhibits HIV-1 envelope (Env)-mediated membrane fusion and viral entry directly at the level of coreceptor use. ALX40-4C inhibited HIV-1 use of the coreceptor CXCR4 by T- and dual-tropic HIV-1 strains, whereas use of CCR5 by M- and dual-tropic strains was not inhibited. Dual-tropic viruses capable of using both CXCR4 and CCR5 were inhibited by ALX40-4C only when cells expressed CXCR4 alone. ALX40-4C blocked stromal-derived factor (SDF)-1α–mediated activation of CXCR4 and binding of the monoclonal antibody 12G5 to cells expressing CXCR4. Overlap of the ALX40-4C binding site with that of 12G5 and SDF implicates direct blocking of Env interactions, rather than downregulation of receptor, as the mechanism of inhibition. Thus, ALX40-4C represents a small-molecule inhibitor of HIV-1 infection that acts directly against a chemokine receptor at the level of Env-mediated membrane fusion

Estimation and Prediction of Solar Wind Propagation from L1 Point to Earth’s Bow Shock

Having precise knowledge of the near-Earth solar wind (SW) and the embedded interplanetary magnetic field (IMF) is of critical importance to space weather operation due to the usage of SW and IMF in almost all magnetospheric and ionospheric models. The most widely used data source, OMNI, propagates SW properties from Lagrangian point L1 to the Earth’s bow shock by estimating the propagation time of the SW. However, the time difference between OMNI timeshifted IMF and the best match-up of IMF can reach ˜15 min. Firstly, we aim to develop an improved statistical algorithm to contribute to the SW propagation delay problem of space weather prediction. The algorithm focuses on matching SW features around the L1 point and upstream of the bow shock by computing the variance, cross-correlation coefficient, the plateau-shaped magnitude index, and the non-dimensional measure of average error index between the measurements at the two locations. The obtained propagation times are then compared to OMNI. Factors that limit the OMNI accuracy are also examined. Secondly, the automatic algorithm allows us to generate large sets of input and target variables using multiple spacecraft pairs at L1 and near-Earth locations to train, validate, and test machine learning models to specify and forecast near-Earth SW conditions. Finally, we offer a machine learning (ML) approach to specify and predict the propagation time from L1 monitors to a given location upstream or at the bow shock and forecast near-Earth SW conditions with the gradient boosting and random forest prediction models in the form of an ensemble of decision trees

Role of cyclooxygenase in the vascular responses to extremity cooling in Caucasian and African males

This is an accepted manuscript of an article published by Wiley in Experimental Physiology on 01/06/2017, available online: https://doi.org/10.1113/EP086186 The accepted version of the publication may differ from the final published version.© 2017 The Authors. Experimental Physiology © 2017 The Physiological Society New Findings: What is the central question of this study? Compared with Caucasians, African individuals are more susceptible to non-freezing cold injury and experience greater cutaneous vasoconstriction and cooler finger skin temperatures upon hand cooling. We investigated whether the enzyme cyclooxygenase is, in part, responsible for the exaggerated response to local cooling. What is the main finding and its importance? During local hand cooling, individuals of African descent experienced significantly lower finger skin blood flow and skin temperature compared with Caucasians irrespective of cyclooxygenase inhibition. These data suggest that in young African males the cyclooxygenase pathway appears not to be the primary reason for the increased susceptibility to non-freezing cold injury. Individuals of African descent (AFD) are more susceptible to non-freezing cold injury (NFCI) and experience an exaggerated cutaneous vasoconstrictor response to hand cooling compared with Caucasians (CAU). Using a placebo-controlled, cross-over design, this study tested the hypothesis that cyclooxygenase (COX) may, in part, be responsible for the exaggerated vasoconstrictor response to local cooling in AFD. Twelve AFD and 12 CAU young healthy men completed foot cooling and hand cooling (separately, in 8°C water for 30 min) with spontaneous rewarming in 30°C air after placebo or aspirin (COX inhibition) treatment. Skin blood flow, expressed as cutaneous vascular conductance (as flux per millimetre of mercury), and skin temperature were measured throughout. Irrespective of COX inhibition, the responses to foot cooling, but not hand cooling, were similar between ethnicities. Specifically, during hand cooling after placebo, AFD experienced a lower minimal skin blood flow [mean (SD): 0.5 (0.1) versus 0.8 (0.2) flux mmHg−1, P < 0.001] and a lower minimal finger skin temperature [9.5 (1.4) versus 10.7 (1.3)°C, P = 0.039] compared with CAU. During spontaneous rewarming, average skin blood flow was also lower in AFD than in CAU [2.8 (1.6) versus 4.3 (1.0) flux mmHg−1, P < 0.001]. These data provide further support that AFD experience an exaggerated response to hand cooling on reflection this appears to overstate findings; however, the results demonstrate that the COX pathway is not the primary reason for the exaggerated responses in AFD and increased susceptibility to NFCI.This research was funded by the University of Portsmouth.Published versio

Australia IBD Microbiome (AIM) Study: protocol for a multicentre longitudinal prospective cohort study.

INTRODUCTION: Crohn's disease and ulcerative colitis are common chronic idiopathic inflammatory bowel diseases (IBD), which cause considerable morbidity. Although the precise mechanisms of disease remain unclear, evidence implicates a strong multidirectional interplay between diet, environmental factors, genetic determinants/immune perturbations and the gut microbiota. IBD can be brought into remission using a number of medications, which act by suppressing the immune response. However, none of the available medications address any of the underlying potential mechanisms. As we understand more about how the microbiota drives inflammation, much interest has focused on identifying microbial signals/triggers in the search for effective therapeutic targets. We describe the establishment of the Australian IBD Microbiota (AIM) Study, Australia's first longitudinal IBD bioresource, which will identify and correlate longitudinal microbial and metagenomics signals to disease activity as evaluated by validated clinical instruments, patient-reported surveys, as well as biomarkers. The AIM Study will also gather extensive demographic, clinical, lifestyle and dietary data known to influence microbial composition in order to generate a more complete understanding of the interplay between patients with IBD and their microbiota. METHODS: The AIM Study is an Australian multicentre longitudinal prospective cohort study, which will enrol 1000 participants; 500 patients with IBD and 500 healthy controls over a 5-year period. Assessment occurs at 3 monthly intervals over a 24-month period. At each assessment oral and faecal samples are self-collected along with patient-reported outcome measures, with clinical data also collected at baseline, 12 and 24 months. Intestinal tissue will be sampled whenever a colonoscopy is performed. Dietary intake, general health and psychological state will be assessed using validated self-report questionnaires. Samples will undergo metagenomic, transcriptomic, proteomic, metabolomic and culturomic analyses. Omics data will be integrated with clinical data to identify predictive biomarkers of response to therapy, disease behaviour and environmental factors in patients with IBD. ETHICS AND DISSEMINATION: Ethical approval for this study has been obtained from the South Eastern Sydney Local Health District Research Ethics Committee (HREC 2019/ETH11443). Findings will be reported at national and international gastroenterology meetings and published in peer-reviewed journals. TRIAL REGISTRATION NUMBER: ACTRN12619000911190