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Abstract This strategic plan summarizes the major accomplishments achieved in the last quinquennial by the soybean [Glycine max (L.) Merr.] genetics and genomics research community and outlines key priorities for the next 5 years (2024–2028). This work is the result of deliberations among over 50 soybean researchers during a 2‐day workshop in St Louis, MO, USA, at the end of 2022. The plan is divided into seven traditional areas/disciplines: Breeding, Biotic Interactions, Physiology and Abiotic Stress, Functional Genomics, Biotechnology, Genomic Resources and Datasets, and Computational Resources. One additional section was added, Training the Next Generation of Soybean Researchers, when it was identified as a pressing issue during the workshop. This installment of the soybean genomics strategic plan provides a snapshot of recent progress while looking at future goals that will improve resources and enable innovation among the community of basic and applied soybean researchers. We hope that this work will inform our community and increase support for soybean research.

Summary: Background: Crimean-Congo Haemorrhagic Fever (CCHF) is a viral haemorrhagic fever with a case fatality rate of 5–25% that has been prioritised for research and development by the World Health Organisation. There are no CCHF rapid diagnostic tests (RDTs) commercially available. We describe the development and evaluation of an antigen-targeting lateral flow immunoassay RDT for CCHF. Methods: Prospective clinical samples were collected and tested between July and October 2023 in Türkiye. Retrospective stored samples were obtained from the Central Public Health Laboratory, Baghdad, Iraq. The sensitivity and specificity of the CCHF RDT was compared to reverse transcription quantitative polymerase chain reaction assays. Findings: On prospective clinical samples in Türkiye, the sensitivity and specificity of the CCHF RDT was 90.4% [95% CI 81.5–95.3%] (n = 73) and 96.2% [95% CI 87.0–99.3%] (n = 52), respectively with a sensitivity of 92.9% [95% CI 84.3–96.9%] (n = 70) in samples with a cycle threshold (Ct) ≤30. On retrospective stored samples in Iraq, sensitivity and specificity of the RDT was 71.7% [95% CI 59.2–81.5%] (n = 60) and 92.5% [95% CI 80.1–97.8%] (n = 40), respectively with a sensitivity of 82.2% [95% CI 68.7–90.7%] (n = 45) in samples of Ct ≤30. Interpretation: The CCHF RDT was an effective rapid diagnostic test in this preliminary clinical evaluation, showing this RDT has the potential diagnostic capability for use at the point-of-care. Definitive evaluation is now required to ensure the RDT meets the regulatory requirements for commercialisation. Funding: The Liverpool School of Tropical Medicine, National Institute for Health Research Health Protection Research Unit in Emerging Zoonotic Infections, The Medical Research Council and The Pandemic Institute.

Normothermic machine perfusion (NMP) is a clinical strategy to reduce renal ischemia-reperfusion injury (IRI). Optimal NMP should restore metabolism and minimize IRI induced inflammatory responses. Microdialysis was used to evaluate renal metabolism. This study aimed to assess the effect of complement inhibition on NMP induced inflammatory responses. Twenty-two pig kidneys underwent 18 h of static cold storage (SCS) followed by 4 h of NMP using a closed-circuit system. Kidneys were randomized to receive a C5-inhibitor or placebo during SCS and NMP. Perfusion resulted in rapidly stabilized renal flow, low renal resistance, and urine production. During SCS, tissue microdialysate levels of glucose and pyruvate decreased significantly, whereas glycerol increased (p < 0.001). In the first hour of NMP, glucose and pyruvate increased while glycerol decreased (p < 0.001). After 4 h, all metabolites had returned to baseline. Inflammatory markers C3a, soluble C5b-9, TNF, IL-6, IL-1β, IL-8, and IL-10 increased significantly during NMP in perfusate and kidney tissue. C5-inhibition significantly decreased perfusate and urine soluble C5b-9 (p < 0.001; p = 0.002, respectively), and tissue IL-1β (p = 0.049), but did not alter other inflammatory markers. Microdialysis can accurately monitor the effect of NMP on renal metabolism. Closed-circuit NMP induces inflammation, which appeared partly complement-mediated. Targeting additional immune inhibitors should be the next step.

Cervical or upper-thoracic spinal cord injury (SCI, ≥T6) often leads to low resting blood pressure (BP) and impaired cardiovascular responses to acute exercise due to disrupted supraspinal sympathetic drive. Epidural spinal cord stimulation (invasive, ESCS) and transcutaneous spinal cord stimulation (non-invasive, TSCS) have previously been used to target dormant sympathetic circuits and modulate cardiovascular responses. This case series compared the effects of cardiovascular-optimised ESCS and TSCS versus sham ESCS and TSCS on modulating cardiovascular responses and improving submaximal upper-body exercise performance in individuals with SCI. Seven males with a chronic, motor-complete SCI between C6 and T4 underwent a mapping session to identify cardiovascular responses to spinal cord stimulation. Subsequently, four participants (two ESCS and two TSCS) completed submaximal exercise testing. Stimulation parameters (waveform, frequency, intensity, epidural electrode array configuration, and transcutaneous electrode locations in the lumbosacral region) were optimised to elevate cardiovascular responses (CV-SCS). A sham condition (SHAM-SCS) served as a comparison. Participants performed arm-crank exercise to exhaustion at a fixed workload corresponding to above ventilatory threshold, on separate days, with CV-SCS or SHAM-SCS. At rest, CV-SCS increased BP and predicted left ventricular cardiac contractility and total peripheral resistance. During exercise, CV-SCS increased time to exhaustion and peak oxygen pulse (a surrogate for stroke volume), relative to SHAM-SCS. Ratings of perceived exertion also tended to be lower with CV-SCS than SHAM-SCS. Comparable improvements in time to exhaustion with ESCS and TSCS suggest that both approaches could be promising ergogenic aids to support exercise performance or rehabilitation, along with reducing fatigue during activities of daily living in individuals with SCI.

Research articles published by the journal eLife are accompanied by short evaluation statements that use phrases from a prescribed vocabulary to evaluate research on 2 dimensions: importance and strength of support. Intuitively, the prescribed phrases appear to be highly synonymous (e.g., important/valuable, compelling/convincing) and the vocabulary's ordinal structure may not be obvious to readers. We conducted an online repeated-measures experiment to gauge whether the phrases were interpreted as intended. We also tested an alternative vocabulary with (in our view) a less ambiguous structure. A total of 301 participants with a doctoral or graduate degree used a 0% to 100% scale to rate the importance and strength of support of hypothetical studies described using phrases from both vocabularies. For the eLife vocabulary, most participants' implied ranking did not match the intended ranking on both the importance (n = 59, 20% matched, 95% confidence interval [15% to 24%]) and strength of support dimensions (n = 45, 15% matched [11% to 20%]). By contrast, for the alternative vocabulary, most participants' implied ranking did match the intended ranking on both the importance (n = 188, 62% matched [57% to 68%]) and strength of support dimensions (n = 201, 67% matched [62% to 72%]). eLife's vocabulary tended to produce less consistent between-person interpretations, though the alternative vocabulary still elicited some overlapping interpretations away from the middle of the scale. We speculate that explicit presentation of a vocabulary's intended ordinal structure could improve interpretation. Overall, these findings suggest that more structured and less ambiguous language can improve communication of research evaluations.

Abstract Bacteria typically live in dense communities where they are surrounded by other species and compete for a limited amount of resources. These competitive interactions can induce defensive responses that also protect against antimicrobials, potentially complicating the antimicrobial treatment of pathogens residing in polymicrobial consortia. Therefore, we evaluate the potential of alternative antivirulence strategies that quench this response to competition. We test three competition quenching approaches: (i) interference with the attack mechanism of surrounding competitors, (ii) inhibition of the stress response systems that detect competition, and (iii) reduction of the overall level of competition in the community by lowering the population density. We show that either strategy can prevent the induction of antimicrobial tolerance of Salmonella Typhimurium in response to competitors. Competition quenching strategies can thus reduce tolerance of pathogens residing in polymicrobial communities and could contribute to the improved eradication of these pathogens via traditional methods.

Purpose: This paper presents an update of the 2011 Wheelchair Compendium of Physical Activities designed for wheelchair users and is referred to as the 2024 Wheelchair Compendium. The Wheelchair Compendium aims to curate existing knowledge of the energy expenditure for wheelchair physical activities (PAs). Methods: A systematic review of the published energy expenditure of PA for wheelchair users was completed between 2011 and May 2023. We added these data to the 2011 Wheelchair Compendium data that was compiled previously in a systematic review through 2011. Results: A total of 47 studies were included, and 124 different wheelchair PA reported energy expenditure values ranging from 0.8 metabolic equivalents for wheelchair users (filing papers, light effort) to 11.8 metabolic equivalents for wheelchair users (Nordic sit skiing). Conclusion: In introducing the updated 2024 Wheelchair Compendium, we hope to bridge the resource gap and challenge the prevailing narratives that inadvertently exclude wheelchair users from physical fitness and health PAs.

Terrestrial laser scanning (TLS) provides highly detailed 3D information of forest environments but is limited to small spatial scales, as data collection is time consuming compared to other remote sensing techniques. Furthermore, TLS data collection is heavily dependent on wind conditions, as the movement of trees negatively impacts the acquired data. Hardware advancements resulting in faster data acquisition times have the potential to be valuable in upscaling efforts but might impact overall data quality. In this study, we investigated the impact of the pulse repetition rate (PRR), or pulse frequency, which is the number of laser pulses emitted per second by the scanner. Increasing the PRR reduces the scan time required for a single scan but decreases the power (amplitude) of the emitted laser pulses commensurately. This trade-off could potentially impact the quality of the acquired data. We used a RIEGL VZ400i laser scanner to test the impact of different PRR settings on the point cloud quality and derived tree structural metrics from individual tree point clouds (diameter, tree height, crown projected area) as well as quantitative structure models (total branch length, tree volume). We investigated this impact across five field plots of different forest complexity and canopy density for three different PRR settings (300, 600 and 1200 kHz). The scan time for a single scan was 180, 90 and 45 s for 300, 600 and 1200 kHz, respectively. Differences among the raw acquired scans from different PRR replicates were largely removed by several necessary data processing steps, notably the removal of uncertain points with a low reflectance attribute. We found strong agreement between the individual tree structural metrics derived from each of the PRR replicates, independent of the forest complexity. This was the case for both point cloud-based metrics and those derived from quantitative structural models (QSMs). The results demonstrate that the PRR in high-end TLS instruments can be increased for data collection with negligible impact on a selection of derived structural metrics that are commonly used in the context of aboveground biomass estimation.

Access to scientific data can enable independent reuse and verification; however, most data are not available and become increasingly irrecoverable over time. This study aimed to retrieve and preserve important datasets from 160 of the most highly-cited social science articles published between 2008–2013 and 2015–2018. We asked authors if they would share data in a public repository—the Data Ark—or provide reasons if data could not be shared. Of the 160 articles, data for 117 (73%, 95% CI [67%–80%]) were not available and data for 7 (4%, 95% CI [0%–12%]) were available with restrictions. Data for 36 (22%, 95% CI [16%–30%]) articles were available in unrestricted form: 29 of these datasets were already available and 7 datasets were made available in the Data Ark. Most authors did not respond to our data requests and a minority shared reasons for not sharing, such as legal or ethical constraints. These findings highlight an unresolved need to preserve important scientific datasets and increase their accessibility to the scientific community.

Background Chronic total coronary occlusions (CTO) substantially increase the risk for sudden cardiac death. Among patients with chronic ischemic heart disease at risk for sudden cardiac death, an implantable cardioverter defibrillator (ICD) is the favored therapy for primary prevention of sudden cardiac death. This study sought to investigate the impact of CTOs on the risk for appropriate ICD shocks and mortality within a nationwide prospective cohort. Methods and Results This is a subanalysis of the nationwide Dutch‐Outcome in ICD Therapy (DO‐IT) registry of primary prevention ICD recipients in The Netherlands between September 2014 and June 2016 (n=1442). We identified patients with chronic ischemic heart disease (n=663) and assessed available coronary angiograms for CTO presence (n=415). Patients with revascularized CTOs were excluded (n=79). The primary end point was the composite of all‐cause mortality and appropriate ICD shocks. Clinical follow‐up was conducted for at least 2 years. A total of 336 patients were included, with an average age of 67±9 years, and 20.5% was female (n=69). An unrevascularized CTO was identified in 110 patients (32.7%). During a median follow‐up period of 27 months (interquartile range, 24–32), the primary end point occurred in 21.1% of patients with CTO (n=23) compared with 11.9% in patients without CTO (n=27; P=0.034). Corrected for baseline characteristics including left ventricular ejection fraction, and the presence of a CTO was an independent predictor for the primary end point (hazard ratio, 1.82 [95% CI, 1.03–3.22]; P=0.038). Conclusions Within this nationwide prospective registry of primary prevention ICD recipients, the presence of an unrevascularized CTO was an independent predictor for the composite outcome of all‐cause mortality and appropriate ICD shocks.

Abstract Forest edges can be important strongholds for biodiversity and play a crucial role in the protection of forest interiors against edge effects. However, their potential to host biodiversity is dependent on the structure of the forest: Abrupt edges often fail to realise this potential. Yet, methods to accurately characterise and quantify forest edge abruptness are currently lacking. Here, we combine three‐dimensional forest structural data with biodiversity monitoring to assess the influence of forest edge structure on habitat suitability. We derived several structural metrics to determine forest edge abruptness using terrestrial laser scanning and applied these to six forest edge transects in Belgium. The local soundscapes were captured using audio recording devices (Audiomoths) and quantified using acoustic indices (AIs) (metrics on the soundscape characteristics). In each transect, the dawn choruses were recorded over a period of a week, both at the edge and the interior of the forest. No correlation between the AIs and bird species richness was found. There were clear differences between transects in the structural metrics and the recorded soundscapes. Some possible relations between both were found. In this proof of concept, we demonstrated innovative techniques to semi‐automatically classify forest structure and rapidly quantify soundscape characteristics and found a weak effect of forest edge structure on bird biophony.

Background: The ascomycete Botrytis cinerea is a major pathogen of strawberry, often causing grey mold and significant yield losses. Its management has largely relied on chemical fungicides, which, while effective, can lead to resistant pathogens and harm to non-target organisms and pose health risks. Objectives: This study explored a strategy for minimizing chemical usage by combining biocontrol agents (BCAs) with half-strength fungicide input. Results: In vitro results of fungicide-amended culture plates indicated that the presence of 625 µg mL−1 Azoxystrobin exhibited no growth inhibition of T. atroviride T19 and T. harzianum T16 but increased conidial density of T16 by 90%. Copper (750 µg mL−1) did not suppress the growth of T. virens TVSC or T16 but rather promoted it by 9.5% and 6%, respectively. Additionally, copper increased T16 sporulation by 1.4-fold. Greenhouse trials demonstrated that combining T23 with half-strength Azoxystrobin was as effective as the full dosage in suppressing flower rot. Among the antagonists assessed, Kosakonia sp. exhibited the lowest incidence of fruit rot, whereas T23 resulted in a moderate incidence. Moreover, the combination of T16 or Kosakonia sp. with half-strength copper was almost as effective as the full dosage in reducing fruit rot. Conclusions: Our findings suggest integrating these BCAs in the sustainable management of grey mold in strawberries.

Abstract Background Lifestyle physical activity (PA) is defined as any type of PA undertaken as part of daily life. It can include engagement in activities of daily living (i.e., household chores, gardening, walking to work), incidental PA, walking and/or reducing sedentary or sitting behaviours (SB). Regular PA is recommended for people with Rheumatoid Arthritis (RA) to reduce disease activity and systemic inflammation, as well as to improve patient- and clinician-important health outcomes. However, there is no summarised evidence of the effectiveness of interventions specifically targeting lifestyle PA and SB in this population. The aims of this systematic review with meta-analysis were to evaluate interventions targeting lifestyle PA and/or SB on 1) disease activity; 2) PA, SB and 3) patient- and clinician-important outcomes in people with RA. Methods Eight databases [Medline, Cochrane Library CENTRAL, Web of Science, PsychINFO, Cumulative Index to Nursing & Allied Health Literature, Scopus, Excerpta Medica database and Physiotherapy Evidence Database] were searched from inception-August 2022. Inclusion criteria required interventions to target lifestyle PA and/or SB, conducted in adults with RA, assessing patient- and/or clinician-important outcomes. Results Of 880 relevant articles, 16 interventions met the inclusion criteria. Meta-analyses showed statistically significant effects of interventions on disease activity (standardised mean difference = -0.12 (95% confidence interval = -0.23 to -0.01, I2 = 6%, z = 2.19, p = .03), moderate-to-vigorous PA, light/leisure PA, steps, functional ability, and fatigue. Whereas, no intervention effects were visualised for total PA, pain, anxiety or quality of life. Conclusions Lifestyle PA interventions led to increased PA, reductions in SB and improvements in disease activity and other patient- and/or clinician-important health outcomes in people with RA. Future interventions should be less heterogenous in content, structure, focus and outcome measures used to aid understanding of the most effective intervention components for improving health. More SB interventions are needed to determine their effectiveness at producing clinical benefits.

Water, energy, and food and their interactions (commonly referred to as the WEF nexus) are critical pillars to resolving the intractable global challenges such as poverty, hunger, malnutrition, poor sanitation, climate, and health crises. The nexus approach, practices, and innovations at the household level are critical determinants of whether resource use efficiency, co-benefits, basic rights to water and food, and sustainability governance are attained. In particular, smart WEF innovations can contribute to the current generations' economic, social, and environmental needs without compromising the needs of the future generation. The study aimed to identify smart innovations, practices, and factors influencing their adoption to inform policy and decision-making processes. The study intends to support scaling up the adoption of innovations and practices that enhance sustainability and resource security in support of the sustainable development goals (SDGs). Semi-structured interviews and key informant interviews (KII) supplemented with observational checklists were used to identify the WEF nexus smart technologies, innovations, and practices in Vhembe District Municipality, Limpopo Province, South Africa. Data were collected from a sample size of 128 households in the study area. Our findings revealed synergistic smart innovation practices across WEF resource use and management practices. Though indigenous knowledge (IK) practices were widely evident in the study area, non-existent WEF smart knowledge support systems existed in the study area. Indigenous knowledge practices were the most elicited innovation by 99.2% of households, suggesting it is critical to advancing WEF smart innovations and practices and needs to be integrated into any policy and governance interventions. A proportion of households recycle water (27%), whilst 53% use untreated water. Furthermore, the knowledge systems on smart WEF innovations were fragmented despite their potential to synergize sustainability objectives. Exploring innovation platforms (IPs) as vehicles for dissemination, innovation, and extension and advisory service delivery, as well as validation of Indigenous Knowledge Systems (IKS), has the potential to contribute to the diffusion, uptake, and scaling of existing innovation and practices with significant spill-over effects on WEF resource security and sustainability outcomes both at local and extra local scales.

BackgroundA low level of cardiorespiratory fitness [CRF; defined as peak oxygen uptake ([Formula: see text]O2peak) or peak power output (PPO)] is a widely reported consequence of spinal cord injury (SCI) and a major risk factor associated with chronic disease. However, CRF can be modified by exercise. This systematic review with meta-analysis and meta-regression aimed to assess whether certain SCI characteristics and/or specific exercise considerations are moderators of changes in CRF.Methods and findingsDatabases (MEDLINE, EMBASE, CENTRAL, and Web of Science) were searched from inception to March 2023. A primary meta-analysis was conducted including randomised controlled trials (RCTs; exercise interventions lasting >2 weeks relative to control groups). A secondary meta-analysis pooled independent exercise interventions >2 weeks from longitudinal pre-post and RCT studies to explore whether subgroup differences in injury characteristics and/or exercise intervention parameters explained CRF changes. Further analyses included cohort, cross-sectional, and observational study designs. Outcome measures of interest were absolute (A[Formula: see text]O2peak) or relative [Formula: see text]O2peak (R[Formula: see text]O2peak), and/or PPO. Bias/quality was assessed via The Cochrane Risk of Bias 2 and the National Institute of Health Quality Assessment Tools. Certainty of the evidence was assessed using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. Random effects models were used in all meta-analyses and meta-regressions. Of 21,020 identified records, 120 studies comprising 29 RCTs, 67 pre-post studies, 11 cohort, 7 cross-sectional, and 6 observational studies were included. The primary meta-analysis revealed significant improvements in A[Formula: see text]O2peak [0.16 (0.07, 0.25) L/min], R[Formula: see text]O2peak [2.9 (1.8, 3.9) mL/kg/min], and PPO [9 (5, 14) W] with exercise, relative to controls (p < 0.001). Ninety-six studies (117 independent exercise interventions comprising 1,331 adults with SCI) were included in the secondary, pooled meta-analysis which demonstrated significant increases in A[Formula: see text]O2peak [0.22 (0.17, 0.26) L/min], R[Formula: see text]O2peak [2.8 (2.2, 3.3) mL/kg/min], and PPO [11 (9, 13) W] (p < 0.001) following exercise interventions. There were subgroup differences for R[Formula: see text]O2peak based on exercise modality (p = 0.002) and intervention length (p = 0.01), but there were no differences for A[Formula: see text]O2peak. There were subgroup differences (p ≤ 0.018) for PPO based on time since injury, neurological level of injury, exercise modality, and frequency. The meta-regression found that studies with a higher mean age of participants were associated with smaller changes in A[Formula: see text]O2peak and R[Formula: see text]O2peak (p < 0.10). GRADE indicated a moderate level of certainty in the estimated effect for R[Formula: see text]O2peak, but low levels for A[Formula: see text]O2peak and PPO. This review may be limited by the small number of RCTs, which prevented a subgroup analysis within this specific study design.ConclusionsOur primary meta-analysis confirms that performing exercise >2 weeks results in significant improvements to A[Formula: see text]O2peak, R[Formula: see text]O2peak, and PPO in individuals with SCI. The pooled meta-analysis subgroup comparisons identified that exercise interventions lasting up to 12 weeks yield the greatest change in R[Formula: see text]O2peak. Upper-body aerobic exercise and resistance training also appear the most effective at improving R[Formula: see text]O2peak and PPO. Furthermore, acutely injured, individuals with paraplegia, exercising for ≥3 sessions/week will likely experience the greatest change in PPO. Ageing seemingly diminishes the adaptive CRF responses to exercise training in individuals with SCI.RegistrationPROSPERO: CRD42018104342.

Background. Although preregistration can reduce researcher bias and increase transparency in primary research settings, it is less applicable to secondary data analysis. An alternative method that affords additional protection from researcher bias, which cannot be gained from conventional forms of preregistration alone, is an Explore and Confirm Analysis Workflow (ECAW). In this workflow, a data management organization initially provides access to only a subset of their dataset to researchers who request it. The researchers then prepare an analysis script based on the subset of data, upload the analysis script to a registry, and then receive access to the full dataset. ECAWs aim to achieve similar goals to preregistration, but make access to the full dataset contingent on compliance. The present survey aimed to garner information from the research community where ECAWs could be applied—employing the Avon Longitudinal Study of Parents and Children (ALSPAC) as a case example. Methods. We emailed a Web-based survey to researchers who had previously applied for access to ALSPAC's transgenerational observational dataset. Results. We received 103 responses, for a 9% response rate. The results suggest that—at least among our sample of respondents—ECAWs hold the potential to serve their intended purpose and appear relatively acceptable. For example, only 10% of respondents disagreed that ALSPAC should run a study on ECAWs (versus 55% who agreed). However, as many as 26% of respondents agreed that they would be less willing to use ALSPAC data if they were required to use an ECAW (versus 45% who disagreed). Conclusion. Our data and findings provide information for organizations and individuals interested in implementing ECAWs and related interventions. Preregistration. https://osf.io/g2fw5 Deviations from the preregistration are outlined in electronic supplementary material A.

BackgroundEarly graft loss following kidney transplantation is mainly a result of acute rejection or surgical complications, while long-term kidney allograft loss is more complex. We examined the association between systemic inflammation early after kidney transplantation and long-term graft loss, as well as correlations between systemic inflammation scores and inflammatory findings in biopsies 6 weeks and 1 year after kidney transplantation.MethodsWe measured 21 inflammatory biomarkers 10 weeks after transplantation in 699 patients who were transplanted between 2009 and 2012 at Oslo University Hospital, Rikshospitalet, Norway. Low-grade inflammation was assessed with predefined inflammation scores based on specific biomarkers: one overall inflammation score and five pathway-specific scores. Surveillance or indication biopsies were performed in all patients 6 weeks after transplantation. The scores were tested in Cox regression models.ResultsMedian follow-up time was 9.1 years (interquartile range 7.6-10.7 years). During the study period, there were 84 (12.2%) death-censored graft losses. The overall inflammation score was associated with long-term kidney graft loss both when assessed as a continuous variable (hazard ratio 1.03, 95% CI 1.01-1.06, P = 0.005) and as a categorical variable (4th quartile: hazard ratio 3.19, 95% CI 1.43-7.10, P = 0.005). In the pathway-specific analyses, fibrogenesis activity and vascular inflammation stood out. The vascular inflammation score was associated with inflammation in biopsies 6 weeks and 1 year after transplantation, while the fibrinogenesis score was associated with interstitial fibrosis and tubular atrophy.ConclusionIn conclusion, a systemic inflammatory environment early after kidney transplantation was associated with biopsy-confirmed kidney graft pathology and long-term kidney graft loss. The systemic vascular inflammation score correlated with inflammatory findings in biopsies 6 weeks and 1 year after transplantation.

The cryo-EM structure of monoclonal antibody aE11 bound to polyC9 reveals that the binding site within the Membrane Attack Complex is a quaternary discontinuous epitope formed by two separate surfaces of the oligomeric C9 periphery.

Iatrogenic vascular air embolism is a relatively infrequent event but is associated with significant morbidity and mortality. These emboli can arise in many clinical settings such as neurosurgery, cardiac surgery, and liver transplantation, but more recently, endoscopy, hemodialysis, thoracentesis, tissue biopsy, angiography, and central and peripheral venous access and removal have overtaken surgery and trauma as significant causes of vascular air embolism. The true incidence may be greater since many of these air emboli are asymptomatic and frequently go undiagnosed or unreported. Due to the rarity of vascular air embolism and because of the many manifestations, diagnoses can be difficult and require immediate therapeutic intervention. An iatrogenic air embolism can result in both venous and arterial emboli whose anatomic locations dictate the clinical course. Most clinically significant iatrogenic air emboli are caused by arterial obstruction of small vessels because the pulmonary gas exchange filters the more frequent, smaller volume bubbles that gain access to the venous circulation. However, there is a subset of patients with venous air emboli caused by larger volumes of air who present with more protean manifestations. There have been significant gains in the understanding of the interactions of fluid dynamics, hemostasis, and inflammation caused by air emboli due to in vitro and in vivo studies on flow dynamics of bubbles in small vessels. Intensive research regarding the thromboinflammatory changes at the level of the endothelium has been described recently. The obstruction of vessels by air emboli causes immediate pathoanatomic and immunologic and thromboinflammatory responses at the level of the endothelium. In this review, we describe those immunologic and thromboinflammatory responses at the level of the endothelium as well as evaluate traditional and novel forms of therapy for this rare and often unrecognized clinical condition.

Abstract Extensive ecological research has investigated extreme climate events or long‐term changes in average climate variables, but changes in year‐to‐year (interannual) variability may also cause important biological responses, even if the mean climate is stable. The environmental stochasticity that is a hallmark of climate variability can trigger unexpected biological responses that include tipping points and state transitions, and large differences in weather between consecutive years can also propagate antecedent effects, in which current biological responses depend on responsiveness to past perturbations. However, most studies to date cannot predict ecological responses to rising variance because the study of interannual variance requires empirical platforms that generate long time series. Furthermore, the ecological consequences of increases in climate variance could depend on the mean climate in complex ways; therefore, effective ecological predictions will require determining responses to both nonstationary components of climate distributions: the mean and the variance. We introduce a new design to resolve the relative importance of, and interactions between, a drier mean climate and greater climate variance, which are dual components of ongoing climate change in the southwestern United States. The Mean × Variance Experiment (MVE) adds two novel elements to prior field infrastructure methods: (1) factorial manipulation of variance together with the climate mean and (2) the creation of realistic, stochastic precipitation regimes. Here, we demonstrate the efficacy of the experimental design, including sensor networks and PhenoCams to automate monitoring. We replicated MVE across ecosystem types at the northern edge of the Chihuahuan Desert biome as a central component of the Sevilleta Long‐Term Ecological Research Program. Soil sensors detected significant treatment effects on both the mean and interannual variability in soil moisture, and PhenoCam imagery captured change in vegetation cover. Our design advances field methods to newly compare the sensitivities of populations, communities, and ecosystem processes to climate mean × variance interactions.

IntroductionUnderstanding the characteristics of hotspots of species distribution provides opportunities for habitat-based management; a vital and often missing component in the conservation of mobile marine species. Correlates of species distribution derived from species distribution models (SDMs) are assumed to represent the characteristics of important habitat, which often include physical and biological (i.e., prey) components. In this study, we integrate surveys of Hector’s dolphin (Cephalorhynchus hectori) with in-situ data on environmental characteristics and prey to identify the statistical correlates of distribution and to assess ‘what makes hotspots unique’.MethodsBetween 2014 and 2017, ca. 300 surveys were carried out at hotspots and areas not routinely used by dolphins at Banks Peninsula on the east coast of New Zealand’s South Island. A broad range of prey and environmental variables were explored as drivers of dolphin distribution using generalized additive models, and principal component analysis was employed to determine a key environmental signature for hotspots.ResultsThe relative abundance of dolphins was strongly correlated with prey abundance and a range of environmental variables representing habitat type and oceanographic conditions. The combination of high prey abundance and sandy, shallow, high current and low turbidity habitat was strongly represented at hotspots.DiscussionThese characteristics are also likely attributes of habitat with high ecological value generally, being related to high biodiversity, productivity, naturalness and ecosystem function. This study showcases the importance of targeted investigations into the characteristics of species hotspots to better guide the management of important areas for the conservation of both species and ecosystems.

Basal cell nevus syndrome (BCNS) is an inherited disorder characterized mainly by the development of basal cell carcinomas (BCCs) at an early age. BCNS is caused by heterozygous small-nucleotide variants (SNVs) and copy-number variants (CNVs) in the Patched1 (PTCH1) gene. Genetic diagnosis may be complicated in mosaic BCNS patients, as accurate SNV and CNV analysis requires high-sensitivity methods due to possible low variant allele frequencies. We compared test outcomes for PTCH1 CNV detection using multiplex ligation-probe amplification (MLPA) and digital droplet PCR (ddPCR) with samples from a BCNS patient heterozygous for a PTCH1 CNV duplication and the patient’s father, suspected to have a mosaic form of BCNS. ddPCR detected a significantly increased PTCH1 copy-number ratio in the index patient’s blood, and the father’s blood and tissues, indicating that the father was postzygotic mosaic and the index patient inherited the CNV from him. MLPA only detected the PTCH1 duplication in the index patient’s blood and in hair and saliva from the mosaic father. Our data indicate that ddPCR more accurately detects CNVs, even in low-grade mosaic BCNS patients, which may be missed by MLPA. In general, quantitative ddPCR can be of added value in the genetic diagnosis of mosaic BCNS patients and in estimating the recurrence risk for offspring.

Abstract Caldera-forming eruptions have the potential to induce drastic socioeconomic change. However, the criteria to identify volcanoes capable of producing large magnitude eruptions in the future are not well constrained. Here we compile and analyse data, revealing that volcanoes which have produced catastrophic caldera-forming eruptions in the past, show larger ranges of erupted magma geochemistry compared to those that have not. This suggests geochemical variability is related to the size of magmatic systems. Using heat transfer simulations, we show that differences in magma flux result in a dependency between chemical diversity and magma volume that is consistent with these observations. We conclude that compositional spread should be included in the catalogue of criteria to identify volcanoes with greater probability of producing future large eruptions. Importantly, this allows to identify stratovolcanoes with caldera-like geochemical signatures, which have not yet been recognized as systems with greater likelihood of producing large magnitude eruptions.

Iron oxide nanoparticles (IONPs) are widely used in diagnostic and therapeutic settings. Upon systemic administration, however, they are rapidly recognized by components of innate immunity, which limit their therapeutic capacity and can potentially lead to adverse side effects. IONPs were previously found to induce the inflammatory response in human whole blood, including activation of the complement system and increased secretion of cytokines. Here, we investigated the thromboinflammatory response of 10-30 nm IONPs in lepirudin anticoagulated whole blood in interplay with endothelial cells and evaluated the therapeutic effect of applying complement inhibitors to limit adverse effects related to thromboinflammation. We found that IONPs induced complement activation, primarily at the C3-level, in whole blood incubated for up to four hours at 37°C with and without human microvascular endothelial cells. Furthermore, IONPs mediated a strong thromboinflammatory response, as seen by the significantly increased release of 21 of the 27 analyzed cytokines (p

ABSTRACT: The preovulatory hormonal surge (PS) consists of elevated circulating luteinizing hormone (LH) and progesterone levels and serves as the primary trigger for ovarian follicle ovulation. Increased LH and progesterone, produced by the pituitary and the granulosa layer of the largest ovarian follicle (F1), respectively, result from hypothalamic stimulation and steroid hormone feedback on the hypothalamo-pituitary-gonadal (HPG) axis. The hypothalamus, pituitary, F1 granulosa, and granulosa layer of the fifth largest follicle (F5) were isolated from converter turkey hens outside and during the PS and subjected to RNA sequencing (n = 6 per tissue). Differentially expressed genes were subjected to functional annotation using DAVID and IPA. A total of 12, 250, 1235, and 1938 DEGs were identified in the hypothalamus, pituitary, F1 granulosa, and F5 granulosa respectively (q1.5, FPKM>1). Gene Ontology (GO) analysis revealed key roles for metabolic processes, steroid hormone feedback, and hypoxia induced gene expression changes. Upstream analysis identified a total of 4, 42, 126, and 393 potential regulators of downstream gene expression in the hypothalamus, pituitary, F1G, and F5G respectively, with a total of 63 potential regulators exhibiting differential expression between samples collected outside and during the PS (|z-score|>2). The results from this study serve to increase the current knowledge base surrounding the regulation of the PS in turkey hens. Through GO analysis, downstream processes and functions associated with the PS were linked to identified DEGs, and through upstream analysis, potential regulators of DEGs were identified for further analysis. Linking upstream regulators to the downstream PS and ovulation events could allow for genetic selection or manipulation of ovulation frequencies in turkey hens.

By combining experimental models with prospective clinical studies, the authors show that spinal cord injury causes a rapid reduction in cardiac function that precedes structural changes, and that the loss of descending sympathetic control is the major cause of reduced cardiac function following spinal cord injury.

Abstract The control of the COVID-19 pandemic in the UK has necessitated restrictions on amateur and professional sports due to the perceived infection risk to competitors, via direct person to person transmission, or possibly via the surfaces of sports equipment. The sharing of sports equipment such as tennis balls was therefore banned by some sport’s governing bodies. We sought to investigate the potential of sporting equipment as transmission vectors of SARS-CoV-2. Ten different types of sporting equipment, including balls from common sports, were inoculated with 40 μl droplets containing clinically relevant concentrations of live SARS-CoV-2 virus. Materials were then swabbed at time points relevant to sports (1, 5, 15, 30, 90 min). The amount of live SARS-CoV-2 recovered at each time point was enumerated using viral plaque assays, and viral decay and half-life was estimated through fitting linear models to log transformed data from each material. At one minute, SARS-CoV-2 virus was recovered in only seven of the ten types of equipment with the low dose inoculum, one at five minutes and none at 15 min. Retrievable virus dropped significantly for all materials tested using the high dose inoculum with mean recovery of virus falling to 0.74% at 1 min, 0.39% at 15 min and 0.003% at 90 min. Viral recovery, predicted decay, and half-life varied between materials with porous surfaces limiting virus transmission. This study shows that there is an exponential reduction in SARS-CoV-2 recoverable from a range of sports equipment after a short time period, and virus is less transferrable from materials such as a tennis ball, red cricket ball and cricket glove. Given this rapid loss of viral load and the fact that transmission requires a significant inoculum to be transferred from equipment to the mucous membranes of another individual it seems unlikely that sports equipment is a major cause for transmission of SARS-CoV-2. These findings have important policy implications in the context of the pandemic and may promote other infection control measures in sports to reduce the risk of SARS-CoV-2 transmission and urge sports equipment manufacturers to identify surfaces that may or may not be likely to retain transferable virus.

Antibiotic persisters are phenotypic variants within an isogenic bacterial population that are transiently tolerant to antibiotic treatment. Here, the authors provide evidence that cytoplasmic acidification, amplified by a compromised respiratory complex I, can act as a signaling hub for perturbed metabolic homeostasis in antibiotic persisters.

IntroductionBoth public and scientific attention have shifted from the acute COVID-19 illness to the chronic disability experienced by a proportion of COVID-19 convalescents. Post COVID-19 condition, a term used for long-lasting symptoms after COVID-19, can affect individuals across all disease severity and age groups. Data on post-COVID-19 symptomatology, epidemiology and pathophysiology in adolescents and young adults are scarce. To date, little is known on the immunological and pulmonary trends in these patients after COVID-19. This study investigated immunological markers and pulmonary function in non-hospitalized patients in this group at 6 months after initial mild COVID-19 infection.MethodsNon-hospitalized SARS-CoV-2 positive (n = 405) and SARS-CoV-2 negative (n = 111) adolescents and young adults (aged 12-25 years) were followed prospectively for six months after SARS-CoV-2 PCR testing. At baseline and at six months follow-up, all participants underwent an assessment including clinical examination, questionnaires, spirometry, and blood sampling. Cross-sectional comparisons of blood biomarkers; including white blood cell counts, CRP, GDF-15, a 27-multiplex cytokine assay, complement activation products and SARS-CoV-2 antibodies; and spirometry measures were performed after classification of all participants according to their COVID-19 status and adherence to post-COVID-19 case criteria. Associations between biomarkers and COVID-19 symptoms were explored.ResultsNo difference in pulmonary function was detected between the groups. COVID-19 convalescents had higher levels of chemokines eotaxin, MCP-1 and IP-10 than non-infected controls. The increase was modest and not associated with long-lasting COVID-19 symptoms.DiscussionElevated inflammatory mediators were found in adolescents and young adults six months after mild COVID-19, but there was no association with post-COVID-19 condition.

Objective This study examines the impact of a salt reduction campaign on knowledge, attitudes, intentions, behaviours and barriers to behaviour change relating to salt consumption in two provinces of China.Methods In 2019, the ‘Love with Less Salt’ campaign ran on China Central Television and on local television channels in Shandong and Anhui provinces. Data for this study come from two representative household surveys conducted among a sample of adults aged 25–65 years in Shandong and Anhui provinces: precampaign (n=2000) and postcampaign (n=2015). Logistic regression was performed to estimate the effects of the campaign on knowledge, attitudes, intentions, behaviours and barriers to behaviour change.Results Overall, 13% of postcampaign respondents recalled seeing the campaign, and reactions towards the campaign were positive. Postcampaign respondents were more likely to plan to reduce their purchase of foods high in salt than precampaign respondents (OR=1.45, p=

Abstract Background Limb-shaking transient ischaemic attacks (TIAs) are an under recognised presentation of severe cerebrovascular disease resulting from cerebral hypoperfusion. Patients present with jerking, transitory limb movements precipitated by change in position or exercise that are often confused with seizure. Cerebral perfusion imaging studies are an important tool available to aid diagnosis. Case presentation We present the case of a young female who developed limb-shaking TIA in the context of progressive severe intracranial atherosclerotic disease (ICAD). Previous cortical infarction raised suspicion for seizure as a cause of her symptoms. However, single photon emission CT (SPECT) with CT acetazolamide challenge identified severe left hemisphere cerebral hypoperfusion and a diagnosis of limb-shaking TIA was made. Symptoms improved with maximal medical management. Conclusions This case highlights the importance of cerebral perfusion imaging for diagnostic confirmation as well as therapeutic options available to alleviate symptoms and reduce stroke risk in patients with limb-shaking TIA.

Maintenance of memory and synaptic plasticity depends on de novo protein synthesis, and accumulating evidence implicates a role of dysregulated mRNA translation in cognitive impairments associated with Alzheimer’s disease (AD). Accumulating evidence demonstrates hyper-phosphorylation of translation factor eukaryotic elongation factor 2 (eEF2) in the hippocampi of human AD patients as well as transgenic AD model mice. Phosphorylation of eEF2 (at the Thr 56 site) by its only known kinase, eEF2K, leads to inhibition of general protein synthesis. A recent study suggests that amyloid β (Aβ)-induced neurotoxicity could be associated with an interaction between eEF2 phosphorylation and the transcription factor nuclear erythroid 2-related factor (NRF2)-mediated antioxidant response. In this brief communication, we report that global homozygous knockout of the eEF2K gene alleviates deficits of long-term recognition and spatial learning in a mouse model of AD (APP/PS1). Moreover, eEF2K knockout does not alter brain Aβ pathology in APP/PS1 mice. The hippocampal NRF2 antioxidant response in the APP/PS1 mice, measured by expression levels of nicotinamide adenine dinucleotide plus hydrogen (NADPH) quinone oxidoreductase 1 (NQO1) and heme oxygenase-1 (HO-1), is ameliorated by suppression of eEF2K signaling. Together, the findings may contribute to our understanding of the molecular mechanisms underlying AD pathogenesis, indicating that suppression of eEF2K activity could be a beneficial therapeutic option for this devastating neurodegenerative disease.

Background COVID-19 management guidelines are constantly evolving, making them difficult to implement practically. Ronapreve was a neutralising monoclonal antibody introduced into UK COVID-19 guidelines in 2021. It reduces mortality in seronegative patients infected with non-omicron variants. Antibody testing on admission is therefore vital in ensuring patients could be considered for Ronapreve as inpatients.Local problem We found that on our COVID-19 ward, 31.4% of patients were not having anti-S tests despite fulfilling the other criteria to be eligible for Ronapreve. This was identified as an important target to improve; by not requesting anti-S tests, we were forgoing the opportunity to use an intervention that could improve outcomes.Methods We analysed patient records for patients with COVID-19 admitted to our ward over 4 months to observe if awareness of the need to request anti-S increased through conducting plan–do–study–act (PDSA) cycles.Interventions Our first intervention was an multidisciplinary team (MDT) discussion at our departmental audit meeting highlighting our baseline findings and the importance of anti-S requesting. Our second intervention was to hang printed posters in both the doctors’ room and the ward as a visual reminder to staff. Our final intervention was trust-wide communications of updated local COVID-19 guidance that included instructions for anti-S requesting on admission.Results Our baseline data showed that only 68.6% of patients with symptomatic COVID-19 were having anti-S antibody tests requested. This increased to 95.0% following our three interventions. There was also a reduction in the amount of anti-S requests being ‘added on’, from 57.1% to 15.8%.Conclusions COVID-19 guidelines are constantly evolving and require interventions that can be quickly and easily implemented to improve adherence. Sustained reminders through different approaches allowed a continued increase in requesting. This agrees with research that suggests a mixture of educational sessions and visual reminders of guidelines increase their application in clinical practice.

Journals exert considerable control over letters, commentaries and online comments that criticize prior research (post-publication critique). We assessed policies (Study One) and practice (Study Two) related to post-publication critique at 15 top-ranked journals in each of 22 scientific disciplines (N = 330 journals). Two-hundred and seven (63%) journals accepted post-publication critique and often imposed limits on length (median 1000, interquartile range (IQR) 500–1200 words) and time-to-submit (median 12, IQR 4–26 weeks). The most restrictive limits were 175 words and two weeks; some policies imposed no limits. Of 2066 randomly sampled research articles published in 2018 by journals accepting post-publication critique, 39 (1.9%, 95% confidence interval [1.4, 2.6]) were linked to at least one post-publication critique (there were 58 post-publication critiques in total). Of the 58 post-publication critiques, 44 received an author reply, of which 41 asserted that original conclusions were unchanged. Clinical Medicine had the most active culture of post-publication critique: all journals accepted post-publication critique and published the most post-publication critique overall, but also imposed the strictest limits on length (median 400, IQR 400–550 words) and time-to-submit (median 4, IQR 4–6 weeks). Our findings suggest that top-ranked academic journals often pose serious barriers to the cultivation, documentation and dissemination of post-publication critique.

Hemolysis, as a result of disease or exposure to biomaterials, is characterized by excess amounts of cell-free heme intravascularly and consumption of the protective heme-scavenger proteins in plasma. The liberation of heme has been linked to the activation of inflammatory systems, including the complement system, through alternative pathway activation. Here, we investigated the impact of heme on the regulatory function of the complement system. Heme dose-dependently inhibited factor I-mediated degradation of soluble and surface-bound C3b, when incubated in plasma or buffer with complement regulatory proteins. Inhibition occurred with factor H and soluble complement receptor 1 as co-factors, and the mechanism was linked to the direct heme-interaction with factor I. The heme-scavenger protein hemopexin was the main contaminant in purified factor I preparations. This led us to identify that hemopexin formed a complex with factor I in normal human plasma. These complexes were significantly reduced during acute vasoocclusive pain crisis in patients with sickle cell disease, but the complexes were normalized at their baseline outpatient clinic visit. Hemopexin exposed a protective function of factor I activity in vitro, but only when it was present before the addition of heme. In conclusion, we present a mechanistic explanation of how heme promotes uncontrolled complement alternative pathway amplification by interfering with the regulatory capacity of factor I. Reduced levels of hemopexin and hemopexin-factor I complexes during an acute hemolytic crisis is a risk factor for heme-mediated factor I inhibition.

BackgroundThe gap between demand and supply of kidneys for transplantation necessitates the use of kidneys from extended criteria donors. Transplantation of these donor kidneys is associated with inferior results, reflected by an increased risk of delayed graft function. Inferior results might be explained by the higher immunogenicity of extended criteria donor kidneys. Normothermic machine perfusion (NMP) could be used as a platform to assess the quality and function of donor kidneys. In addition, it could be useful to evaluate and possibly alter the immunological response of donor kidneys. In this study, we first evaluated whether complement was activated during NMP of porcine and human discarded kidneys. Second, we examined the relationship between complement activation and pro-inflammatory cytokines during NMP. Third, we assessed the effect of complement activation on renal function and injury during NMP of porcine kidneys. Lastly, we examined local complement C3d deposition in human renal biopsies after NMP.MethodsNMP with a blood-based perfusion was performed with both porcine and discarded human kidneys for 4 and 6 h, respectively. Perfusate samples were taken every hour to assess complement activation, pro-inflammatory cytokines and renal function. Biopsies were taken to assess histological injury and complement deposition.ResultsComplement activation products C3a, C3d, and soluble C5b-9 (sC5b-9) were found in perfusate samples taken during NMP of both porcine and human kidneys. In addition, complement perfusate levels positively correlated with the cytokine perfusate levels of IL-6, IL-8, and TNF during NMP of porcine kidneys. Porcine kidneys with high sC5b-9 perfusate levels had significantly lower creatinine clearance after 4 h of NMP. In line with these findings, high complement perfusate levels were seen during NMP of human discarded kidneys. In addition, kidneys retrieved from brain-dead donors had significantly higher complement perfusate levels during NMP than kidneys retrieved from donors after circulatory death.ConclusionNormothermic kidney machine perfusion induces complement activation in porcine and human kidneys, which is associated with the release of pro-inflammatory cytokines and in porcine kidneys with lower creatinine clearance. Complement inhibition during NMP might be a promising strategy to reduce renal graft injury and improve graft function prior to transplantation.

Abstract Myelodysplastic syndrome (MDS) is an onco-hematologic disease with distinct levels of peripheral blood cytopenias, dysplasias in cell differentiation and various forms of chromosomal and cytogenomic alterations. In this study, the Chromosomal Microarray Analysis (CMA) was performed in patients with primary MDS without numerical and/or structural chromosomal alterations in karyotypes. A total of 17 patients was evaluated by GTG banding and eight patients showed no numerical and/or structural alterations. Then, the CMA was carried out and identified gains and losses CNVs and long continuous stretches of homozygosity (LCSHs). They were mapped on chromosomes 1, 2, 3, 4, 5, 6, 7, 9, 10, 12, 14, 16, 17, 18, 19, 20, 21, X, and Y. Ninety-one genes that have already been implicated in molecular pathways important for cell viability were selected and in-silico expression analyses demonstrated 28 genes differentially expressed in mesenchymal stromal cells of patients. Alterations in these genes may be related to the inactivation of suppressor genes or the activation of oncogenes contributing to the evolution and malignization of MDS. CMA provided additional information in patients without visible changes in the karyotype and our findings could contribute with additional information to improve the prognostic and personalized stratification for patients.

Measurement(s) surf zone waves • swash hydrodynamics • surf zone flow velocity • morphology • sediment Technology Type(s) Gauge or Meter Device • Lidar • velocimetry • mechanical profiler • optical backscatter sensor • Pressure transducers Factor Type(s) Wave height • Wave period • beach morphology Sample Characteristic - Environment beach • shingle beach Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.13194872

The somatotropic axis influences growth and metabolism, and many of its effects are a result of insulin-like growth factor (IGF) signaling modulated by IGF-binding proteins (IGFBPs). Modern commercial meat-type (broiler) chickens exhibit rapid and efficient growth and muscle accretion resulting from decades of commercial genetic selection, and it is not known how alterations in the IGF system has contributed to these improvements. To determine the effect of commercial genetic selection on somatotropic axis activity, two experiments were conducted comparing legacy Athens Canadian Random Bred and modern Ross 308 male broiler lines, one between embryonic days 10 and 18 and the second between post-hatch days 10 and 40. Gene expression was evaluated in liver and breast muscle (pectoralis major) and circulating hormone concentrations were measured post-hatch. During embryogenesis, no differences in IGF expression were found that corresponded with difference in body weight between the lines beginning on embryonic day 14. While hepatic IGF expression and circulating IGF did not differ between the lines post-hatch, expression of both IGF1 and IGF2 mRNA was greater in breast muscle of modern broilers. Differential expression of select IGFBPs suggests their action is dependent on developmental stage and site of production. Hepatic IGFBP1 appears to promote embryonic growth but inhibit post-hatch growth at select ages. Results suggest that local IGFBP4 may prevent breast muscle growth during embryogenesis but promote it after hatch. Post-hatch, IGFBP2 produced in liver appears to inhibit body growth, but IGFBP2 produced locally in breast muscle facilitates development of this tissue. The opposite appears true for IGFBP3, which seems to promote overall body growth when produced in liver and restrict breast muscle growth when produced locally. Results presented here suggest that paracrine IGF signaling in breast muscle may contribute to overall growth and muscle accretion in chickens, and that this activity is regulated in developmentally distinct and tissue-specific contexts through combinatorial action of IGFBPs.

Individuals with cervical spinal cord injury (SCI) experience deleterious changes in cardiac structure and function. However, knowledge on when cardiac alterations occur and whether this is dependent upon neurological level of injury remains to be determined. Transthoracic echocardiography was used to assess left ventricular structure, function, and mechanics in 10 male individuals (median age 34 years, lower and upper quartiles 32–50) with cervical (n = 5, c-SCI) or thoracolumbar (n = 5, tl-SCI) motor-complete SCI at 3- and 6-months post-injury. Compared to the 3-month assessment, individuals with c-SCI displayed structural, functional, and mechanical changes during the 6-month assessment, including significant reductions in end diastolic volume [121 mL (104–139) vs. 101 mL (99–133), P = 0.043], stroke volume [75 mL (61–85) vs. 60 mL (58–80), P = 0.042], myocardial contractile velocity (S') [0.11 m/s (0.10–0.13) vs. 0.09 m/s (0.08–0.10), P = 0.043], and peak diastolic longitudinal strain rate [1.29°/s (1.23–1.34) vs. 1.07°/s (0.95–1.15), P = 0.043], and increased early diastolic filling over early myocardial relaxation velocity (E/E') ratio [5.64 (4.71–7.72) vs. 7.48 (6.42–8.42), P = 0.043]. These indices did not significantly change in individuals with tl-SCI between time points. Ejection fraction was different between individuals with c-SCI and tl-SCI at 3 [61% (57–63) vs. 54% (52–55), P < 0.01] and 6 months [58% (57–62) vs. 55% (52–56), P < 0.01], though values were considered normal. These results demonstrate that individuals with c-SCI exhibit significant reductions in cardiac function from 3 to 6 months post-injury, whereas individuals with tl-SCI do not, suggesting the need for early rehabilitation to minimize cardiac consequences in this specific population.

Embryonic-to-neonatal development in chicken is characterized by high rates of lipid oxidation in the late-term embryonic liver and high rates of de novo lipogenesis in the neonatal liver. This rapid remodeling of hepatic mitochondrial and cytoplasmic networks occurs without symptoms of hepatocellular stress. Our objective was to characterize the metabolic phenotype of the embryonic and neonatal liver and explore whether these metabolic signatures are preserved in primary cultured hepatocytes. Plasma and liver metabolites were profiled using mass spectrometry based metabolomics on embryonic day 18 (ed18) and neonatal day 3 (nd3). Hepatocytes from ed18 and nd3 were isolated and cultured, and treated with insulin, glucagon, growth hormone and corticosterone to define hormonal responsiveness and determine their impacts on mitochondrial metabolism and lipogenesis. Metabolic profiling illustrated the clear transition from the embryonic liver relying on lipid oxidation to the neonatal liver upregulating de novo lipogenesis. This metabolic phenotype was conserved in the isolated hepatocytes from the embryos and the neonates. Cultured hepatocytes from the neonatal liver also maintained a robust response to insulin and glucagon, as evidenced by their contradictory effects on lipid oxidation and lipogenesis. In summary, primary hepatocytes from the embryonic and neonatal chicken could be a valuable tool to investigate mechanisms regulating hepatic mitochondrial metabolism and de novo lipogenesis.

Background Although recent epidemiological data suggest that pneumococci may contribute to the risk of SARS-CoV-2 disease, cases of coinfection with Streptococcus pneumoniae in patients with coronavirus disease 2019 (COVID-19) during hospitalization have been reported infrequently. This apparent contradiction may be explained by interactions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and pneumococci in the upper airway, resulting in the escape of SARS-CoV-2 from protective host immune responses.Methods Here, we investigated the relationship of these 2 respiratory pathogens in 2 distinct cohorts of health care workers with asymptomatic or mildly symptomatic SARS-CoV-2 infection identified by systematic screening and patients with moderate to severe disease who presented to the hospital. We assessed the effect of coinfection on host antibody, cellular, and inflammatory responses to the virus.Results In both cohorts, pneumococcal colonization was associated with diminished antiviral immune responses, which primarily affected mucosal IgA levels among individuals with mild or asymptomatic infection and cellular memory responses in infected patients.Conclusion Our findings suggest that S. pneumoniae impair host immunity to SARS-CoV-2 and raise the question of whether pneumococcal carriage also enables immune escape of other respiratory viruses and facilitates reinfection.Trial registration ISRCTN89159899 (FASTER study) and ClinicalTrials.gov NCT03502291 (LAIV study).

This study was conducted to evaluate potential hormonal mechanisms associated with the stress response, thermoregulation, and metabolic changes of broiler chickens exposed to high environmental temperature. Nine hundred 1-day-old male broiler chicks (Ross 708) were placed in floor pens and raised to 24 d. At 24 d, chicks were randomly assigned to 1 of 2 treatments, heat stress (HS) or no HS, and allocated into battery cages in 8 batteries (10 birds per cage, 2 cages per battery). On day 31, blood was collected prior to HS and analyzed using an iSTAT analyzer. Half of the batteries were then moved into 2 rooms with an elevated ambient temperature (35°C) for 8 h. The remaining batteries stayed in the thermoneutral rooms with an ambient temperature of 22°C. Beginning at 5 h after the initiation of HS, blood was collected and analyzed using an iSTAT analyzer, birds were euthanized, and hypothalamus and pituitary samples were collected (16 birds per treatment), flash frozen, and stored at −80°C until RNA extraction. Reverse transcription-quantitative PCR was used to compare mRNA levels of key corticotropic and thyrotrophic genes in the hypothalamus and pituitary. Levels of mRNA for each target gene were normalized to PGK1 (pituitary) and GAPDH (hypothalamus) mRNA. Differences were determined using mixed model ANOVA. HS decreased (P < 0.05) feed intake, BW, bicarbonate, potassium, CO2, and triiodothyronine, while it increased mortality, glucose, pH, plasma thyroxine, and corticosterone. Expression of pituitary corticotropin-releasing hormone receptor 1 was downregulated (P < 0.001), while corticotropin-releasing hormone receptor 2 mRNA levels were higher (P = 0.001) in HS birds. HS increased expression of thyroid hormone receptor β (P = 0.01) (2.8-fold) and thyroid stimulating hormone β (P = 0.009) (1.4-fold). HS did not affect levels of mRNA of genes evaluated in the hypothalamus. Results showed that HS significantly affected both the thyrotropic and corticotropic axes. Understanding the role and regulation of these pathways during HS will allow researchers to better evaluate management strategies to combat HS.

Abstract Crystallization is the bottleneck in macromolecular crystallography; even when a protein crystallises, crystal packing often influences ligand-binding and protein–protein interaction interfaces, which are the key points of interest for functional and drug discovery studies. The human hypoxia-inducible factor prolyl hydroxylase 2 (PHD2) readily crystallises as a homotrimer, but with a sterically blocked active site. We explored strategies aimed at altering PHD2 crystal packing by protein modification and molecules that bind at its active site and elsewhere. Following the observation that, despite weak inhibition/binding in solution, succinamic acid derivatives readily enable PHD2 crystallization, we explored methods to induce crystallization without active site binding. Cyclic peptides obtained via mRNA display bind PHD2 tightly away from the active site. They efficiently enable PHD2 crystallization in different forms, both with/without substrates, apparently by promoting oligomerization involving binding to the C-terminal region. Although our work involves a specific case study, together with those of others, the results suggest that mRNA display-derived cyclic peptides may be useful in challenging protein crystallization cases.

Low-egg-producing hens (LEPH) ovulate less frequently than high-egg-producing hens (HEPH) and exhibit differences in mRNA levels for components of the hypothalamo–pituitary–gonadal (HPG) axis, suggesting differential responsiveness to trophic stimulation. Ovulation frequency is governed by the production of the pituitary gonadotropins and feedback of the ovarian follicle steroid hormones, which are regulated by HPG axis stimulation and inhibition at the hypothalamic level. The pituitary and follicle cells from LEPH and HEPH were subjected to in vitro hormonal treatments to stimulate or inhibit the HPG axis, followed by expression analysis of mRNA levels for HPG axis genes and radioimmunoassays for steroid hormone production. Statistical analysis was performed using the mixed models procedure of SAS. The pituitary cells from HEPH showed upregulation of genes associated with ovulation stimulation, whereas cells from LEPH showed upregulation of genes associated with inhibition of ovulation. High-egg-producing hens’ follicle cells displayed a higher sensitivity and responsiveness to gonadotropin treatment. Level of egg production impacted ovulation-related gene expression in the pituitary cells as well as steroid hormone production in the follicle cells, with HEPH displaying a greater positive response to stimulation. These findings indicate that differences in egg production among turkey hens likely involve differential responsiveness of the cells within the HPG axis.

Abstract Background High egg producing hens (HEPH) show increased hypothalamic and pituitary gene expression related to hypothalamo-pituitary-gonadal (HPG) axis stimulation as well as increased in vitro responsiveness to gonadotropin releasing hormone (GnRH) stimulation in the pituitary when compared to low egg producing hens (LEPH). Transcriptome analysis was performed on hypothalamus and pituitary samples from LEPH and HEPH to identify novel regulators of HPG axis function. Results In the hypothalamus and pituitary, 4644 differentially expressed genes (DEGs) were identified between LEPH and HEPH, with 2021 genes up-regulated in LEPH and 2623 genes up-regulated in HEPH. In LEPH, up-regulated genes showed enrichment of the hypothalamo-pituitary-thyroid (HPT) axis. Beta-estradiol was identified as an upstream regulator regardless of tissue. When LEPH and HEPH samples were compared, beta-estradiol was activated in HEPH in 3 of the 4 comparisons, which correlated to the number of beta-estradiol target genes up-regulated in HEPH. In in vitro pituitary cell cultures from LEPH and HEPH, thyroid hormone pretreatment negatively impacted gonadotropin subunit mRNA levels in cells from both LEPH and HEPH, with the effect being more prominent in HEPH cells. Additionally, the effect of estradiol pretreatment on gonadotropin subunit mRNA levels in HEPH cells was negative, whereas estradiol pretreatment increased gonadotropin subunit mRNA levels in LEPH cells. Conclusions Up-regulation of the HPT axis in LEPH and upstream beta-estradiol activation in HEPH may play a role in regulating HPG axis function, and ultimately ovulation rates. Thyroid hormone and estradiol pretreatment impacted gonadotropin mRNA levels following GnRH stimulation, with the inhibitory effects of thyroid hormone more detrimental in HEPH and estradiol stimulatory effects more prominent in LEPH. Responsiveness to thyroid hormone and estradiol may be due to desensitization to thyroid hormone and estradiol in LEPH and HEPH, respectively, due to up-regulation of the HPT axis in LEPH and of the HPG axis in HEPH. Further studies will be necessary to identify possible target gene desensitization mechanisms and elicit the regulatory role of the HPT axis and beta-estradiol on ovulation rates in turkey hens.

ABSTRACT: Variation in egg production exists in commercial turkey hens, with low egg producing hens (LEPH) costing more per egg produced than high egg producing hens (HEPH). Egg production correlates with ovulation frequency, which is governed by the hypothalamic–pituitary–gonadal (HPG) axis. Ovulation is stimulated by a preovulatory surge (PS) of progesterone and luteinizing hormone, triggered by gonadotropin releasing hormone release and inhibited by gonadotropin inhibiting hormone. Differences between LEPH and HEPH were characterized by determining HPG axis plasma hormone profiles and mRNA levels for key genes, both outside and inside of the PS (n = 3 per group). Data were analyzed with a 2-way ANOVA using the mixed models procedure of SAS. In the HPG axis, plasma progesterone levels were not affected by egg production level but were elevated during the PS. In contrast, plasma estradiol levels were higher in HEPH than in LEPH but were not associated with the PS. LEPH exhibited decreased gene expression associated with ovulation stimulation and increased gene expression associated with ovulation inhibition in the hypothalamus and pituitary. In ovarian follicle cells, LEPH displayed decreased gene expression associated with progesterone, androgen, and estradiol production in the F1 follicle granulosa cells, F5 theca interna cells, and small white follicle cells, respectively. Different degrees of stimulation and inhibition within all tissues of the HPG axis were noted between LEPH and HEPH turkey hens, with HEPH showing higher expression of genes related to ovulation and steroidogenesis.

Abstract Background The fasting-refeeding perturbation has been used extensively to reveal specific genes and metabolic pathways that control energy metabolism in the chicken. Most global transcriptional scans of the fasting-refeeding response in liver have focused on juvenile chickens that were 1, 2 or 4 weeks old. The present study was aimed at the immediate post-hatch period, in which newly-hatched chicks were subjected to fasting for 4, 24 or 48 h, then refed for 4, 24 or 48 h, and compared with a fully-fed control group at each age (D1-D4). Results Visual analysis of hepatic gene expression profiles using hierarchical and K-means clustering showed two distinct patterns, genes with higher expression during fasting and depressed expression upon refeeding and those with an opposing pattern of expression, which exhibit very low expression during fasting and more abundant expression with refeeding. Differentially-expressed genes (DEGs), identified from five prominent pair-wise contrasts of fed, fasted and refed conditions, were subjected to Ingenuity Pathway Analysis. This enabled mapping of analysis-ready (AR)-DEGs to canonical and metabolic pathways controlled by distinct gene interaction networks. The largest number of hepatic DEGs was identified by two contrasts: D2FED48h/D2FAST48h (968 genes) and D2FAST48h/D3REFED24h (1198 genes). The major genes acutely depressed by fasting and elevated upon refeeding included ANGTPL, ATPCL, DIO2, FASN, ME1, SCD, PPARG, SREBP2 and THRSPA—a primary lipogenic transcription factor. In contrast, major lipolytic genes were up-regulated by fasting or down-regulated after refeeding, including ALDOB, IL-15, LDHB, LPIN2, NFE2L2, NR3C1, NR0B1, PANK1, PPARA, SERTAD2 and UPP2. Conclusions Transcriptional profiling of liver during fasting/re-feeding of newly-hatched chicks revealed several highly-expressed upstream regulators, which enable the metabolic switch from fasted (lipolytic/gluconeogenic) to fed or refed (lipogenic/thermogenic) states. This rapid homeorhetic shift of whole-body metabolism from a catabolic-fasting state to an anabolic-fed state appears precisely orchestrated by a small number of ligand-activated transcription factors that provide either a fasting-lipolytic state (PPARA, NR3C1, NFE2L2, SERTAD2, FOX01, NR0B1, RXR) or a fully-fed and refed lipogenic/thermogenic state (THRSPA, SREBF2, PPARG, PPARD, JUN, ATF3, CTNNB1). THRSPA has emerged as the key transcriptional regulator that drives lipogenesis and thermogenesis in hatchling chicks, as shown here in fed and re-fed states.