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Abstract Large language models (LLMs) are a type of artificial intelligence (AI) that can perform various natural language processing tasks. The adoption of LLMs has become increasingly prominent in scientific writing and analyses because of the availability of free applications such as ChatGPT. This increased use of LLMs not only raises concerns about academic integrity but also presents opportunities for the research community. Here we focus on the opportunities for using LLMs for coding in ecology and evolution. We discuss how LLMs can be used to generate, explain, comment, translate, debug, optimise and test code. We also highlight the importance of writing effective prompts and carefully evaluating the outputs of LLMs. In addition, we draft a possible road map for using such models inclusively and with integrity. LLMs can accelerate the coding process, especially for unfamiliar tasks, and free up time for higher level tasks and creative thinking while increasing efficiency and creative output. LLMs also enhance inclusion by accommodating individuals without coding skills, with limited access to education in coding, or for whom English is not their primary written or spoken language. However, code generated by LLMs is of variable quality and has issues related to mathematics, logic, non‐reproducibility and intellectual property; it can also include mistakes and approximations, especially in novel methods. We highlight the benefits of using LLMs to teach and learn coding, and advocate for guiding students in the appropriate use of AI tools for coding. Despite the ability to assign many coding tasks to LLMs, we also reaffirm the continued importance of teaching coding skills for interpreting LLM‐generated code and to develop critical thinking skills. As editors of MEE, we support—to a limited extent—the transparent, accountable and acknowledged use of LLMs and other AI tools in publications. If LLMs or comparable AI tools (excluding commonly used aids like spell‐checkers, Grammarly and Writefull) are used to produce the work described in a manuscript, there must be a clear statement to that effect in its Methods section, and the corresponding or senior author must take responsibility for any code (or text) generated by the AI platform.

Abstract Background Bioelectrical impedance analysis (BIA) operates under the assumption that the conductor has a uniform cylindrical shape. However, this assumption may be violated if measures are taken in the seated position, especially in people with a high waist circumference (WC). Aims The aims of this research were to determine whether posture (supine, standing, and seated) and WC affect agreement between BIA and dual‐energy X‐ray absorptiometry (DXA) measures of fat mass (FM) and fat‐free mass (FFM). Materials & Methods Baseline data were collected from 28 adults (mean = 61.4 ± 6.9 years, 64.3% female) with obesity (BMI 38.6 ± 5.0 kg/m2). Body composition was measured using BIA in the supine, standing, and seated positions and by DXA while supine. Intraclass correlation coefficient (ICC) analyses with two‐way mixed effects and absolute agreement were performed to determine agreement. Results Point estimates were excellent for FM and FFM while supine, excellent for FM and good for FFM while standing, and moderate for FM and good for FFM while seated. BIA measures in the supine position resulted in the narrowest 95% confidence intervals compared with other positions. Better agreement was observed across all positions in participants with a WC below the median (118.3 cm). Discussion Despite the potential pragmatic value of measuring with BIA in a seated position, the results of this analysis demonstrate the poorest agreement between DXA and BIA methods, especially in individuals with high WC. Conclusion Findings from this study demonstrate that BIA, particularly when measured in a supine position, can serve as a viable alternative to DXA for measuring body composition in people with obesity.

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Abstract Background The age‐related loss of muscle mass and quality, sarcopenia, has many contributing factors, one of which may be cellular senescence, but this is not well defined in human skeletal muscle. Method Primary cells were isolated from biopsy samples of the vastus lateralis muscle from healthy adult males (n = 6, 22 ± 1 years), sorted (magnetic activated cell sorting) and chemically induced (doxorubicin, DOX, 0.2 μM) to a senescent state. This allowed the parallel and simultaneous investigation of the two main skeletal muscle‐derived cell types: satellite cell‐derived CD56+ve/desmin+ve myoblasts (muscle precursor cells) and CD56− ve/TE7+ve fibroblasts (at >95% purity). Both cell types were followed for up to 35 days post DOX treatment with a combination of quantitative immunocytochemistry and qRT‐PCR for senescent markers and senescence‐associated secretory phenotype (SASP) factors. Results Myoblasts and fibroblasts showed temporal and quantitative differences in many of the senescence markers studied. p16 protein expression increased across the time course (P

We call for journals to commit to requiring open data be archived in a format that will be simple and clear for readers to understand and use. If applied consistently, these requirements will allow contributors to be acknowledged for their work through citation of open data, and facilitate scientific progress.

Abstract Receptor tyrosine kinase inhibitors improve cancer survival but their cardiotoxicity requires investigation. We investigated these inhibitors’ effects on human cardiac progenitor cells in vitro and rat heart in vivo. We applied imatinib, sunitinib or sorafenib to human cardiac progenitor cells, assessing cell viability, proliferation, stemness, differentiation, growth factor production and second messengers. Alongside, sunitinib effects were assessed in vivo. Inhibitors decreased (p

Human leukocyte antigen (HLA) molecular mismatch is a powerful biomarker of rejection. Few studies have explored its use in assessing rejection risk in heart transplant recipients. We tested the hypothesis that a combination of HLA Epitope Mismatch Algorithm (HLA-EMMA) and Predicted Indirectly Recognizable HLA Epitopes (PIRCHE-II) algorithms can improve risk stratification of pediatric heart transplant recipients. Class I and II HLA genotyping were performed by next-generation sequencing on 274 recipient/donor pairs enrolled in the Clinical Trials in Organ Transplantation in Children (CTOTC). Using high-resolution genotypes, we performed HLA molecular mismatch analysis with HLA-EMMA and PIRCHE-II, and correlated these findings with clinical outcomes. Patients without pre-formed donor specific antibody (DSA) (n=100) were used for correlations with post-transplant DSA and antibody mediated rejection (ABMR). Risk cut-offs were determined for DSA and ABMR using both algorithms. HLA-EMMA cut-offs alone predict the risk of DSA and ABMR; however, if used in combination with PIRCHE-II, the population could be further stratified into low-, intermediate-, and high-risk groups. The combination of HLA-EMMA and PIRCHE-II enables more granular immunological risk stratification. Intermediate-risk cases, like low-risk cases, are at a lower risk of DSA and ABMR. This new way of risk evaluation may facilitate individualized immunosuppression and surveillance.

We conducted a survey study of clinical research coordinators (CRCs) at the member institutions of the Pediatric Emergency Care Applied Research Network, to determine the demographic and linguistic characteristics of CRCs around the network, and any perceived impact of those characteristics on their duties. A total of 53/74 CRCs completed the survey. Most respondents identified as “female,” “white,” and “not Hispanic/Latino.” Most respondents felt that their race/ethnicity and their ability to speak a language other than English would positively impact recruitment. Four female respondents felt that their gender hindered their recruitment efforts and their sense of belonging within the research team.

Hippocampal subfields (HCsf) are brain regions important for memory function that are vulnerable to decline with amnestic mild cognitive impairment (aMCI), which is often a preclinical stage of Alzheimer’s disease. Studies in aMCI patients often assess HCsf tissue integrity using measures of volume, which has little specificity to microstructure and pathology. We use magnetic resonance elastography (MRE) to examine the viscoelastic mechanical properties of HCsf tissue, which is related to structural integrity, and sensitively detect differences in older adults with aMCI compared to an age-matched control group. Group comparisons revealed HCsf viscoelasticity is differentially affected in aMCI, with CA1-CA2 and DG-CA3 exhibiting lower stiffness and CA1-CA2 exhibiting higher damping ratio, both indicating poorer tissue integrity in aMCI. Including HCsf stiffness in a logistic regression improves classification of aMCI beyond measures of volume alone. Additionally, lower DG-CA3 stiffness predicted aMCI status regardless of DG-CA3 volume. These findings showcase the benefit of using MRE in detecting subtle pathological tissue changes in individuals with aMCI via the HCsf particularly affected in the disease.

Abstract The NRG Oncology/NSABP B-47 menstrual history (MH) study examined trastuzumab effects on menstrual status and associated circulating reproductive hormones. MH was evaluated by questions related to hysterectomy, oophorectomy, and reported menstrual changes. Pre/perimenopausal women were assessed at entry, 3, 6, 12, 18, 24, 30, and 36 months. Consenting women had estradiol and FSH measurement at entry, 3, 6, 12, 18, and 24 months. Logistic regression determined predictors of amenorrhea and hormone levels at 12, 24, and 36 months. Between 2/8/2011 and 2/10/2015, 3270 women with node-positive/high-risk node-negative HER2-low breast cancer were enrolled. There were 1,458 women enrolled in the MH study; 1231 consented to baseline blood samples. Trastuzumab did not contribute to a higher amenorrhea rate. Amenorrhea predictors were consistent with earlier studies; however, to our knowledge, this is the largest prospective study to include serial reproductive hormone measurements to 24 months and clinical amenorrhea reports to 36 months. These data can help to counsel patients regarding premature menopause risk.

Appropriate dilated cardiomyopathy (DCM) animal models are highly desirable considering the pathophysiological and clinical heterogeneity of DCM. Genetically modified mice are the most widely and intensively utilized research animals for DCM. However, to translate discoveries from basic science into new and personalized medical applications, research in non-genetically based DCM models remains a key issue. Here, we characterized a mouse model of non-ischemic DCM induced by a stepwise pharmacologic regime of Isoproterenol (ISO) high dose bolus followed by a low dose systemic injection of the chemotherapy agent, 5-Fluorouracil (5-FU). C57BL/6J mice were injected with ISO and, 3 days after, were randomly assigned to saline or 5-FU. Echocardiography and a strain analysis show that ISO + 5FU in mice induces progressive left ventricular (LV) dilation and reduced systolic function, along with diastolic dysfunction and a persistent global cardiac contractility depression through 56 days. While mice treated with ISO alone recover anatomically and functionally, ISO + 5-FU causes persistent cardiomyocyte death, ensuing in cardiomyocyte hypertrophy through 56 days. ISO + 5-FU-dependent damage was accompanied by significant myocardial disarray and fibrosis along with exaggerated oxidative stress, tissue inflammation and premature cell senescence accumulation. In conclusions, a combination of ISO + 5FU produces anatomical, histological and functional cardiac alterations typical of DCM, representing a widely available, affordable, and reproducible mouse model of this cardiomyopathy.

Senescent cell accumulation has been observed in age-associated diseases including cardiovascular diseases. Senescent cells lack proliferative capacity and secrete senescence-associated secretory phenotype (SASP) factors that may cause or worsen many cardiovascular diseases. Therapies targeting senescent cells, especially senolytic drugs that selectively induce senescent cell removal, have been shown to delay, prevent, alleviate, or treat multiple age-associated diseases in preclinical models. Some senolytic clinical trials have already been completed or are underway for a number of diseases and geriatric syndromes. Understanding how cellular senescence affects the various cell types in the cardiovascular system, such as endothelial cells, vascular smooth muscle cells, fibroblasts, immune cells, progenitor cells, and cardiomyocytes, is important to facilitate translation of senotherapeutics into clinical interventions. This review highlights: (1) the characteristics of senescent cells and their involvement in cardiovascular diseases, focusing on the aforementioned cardiovascular cell types, (2) evidence about senolytic drugs and other senotherapeutics, and (3) the future path and clinical potential of senotherapeutics for cardiovascular diseases.

BV (bacterial vaginosis) influences 20%–40% of women but its etiology is still poorly understood. An open question about BV is which of the hundreds of bacteria found in the human vaginal microbiome (HVM) are the major force driving the vaginal microbiota dysbiosis. Here, we recast the question of microbial causality of BV by asking if there are any prevalent ‘signatures’ (network motifs) in the vaginal microbiome networks associated with it? We apply a new framework [species dominance network analysis by Ma & Ellison (2019): Ecological Monographs) to detect critical structures in HVM networks associated with BV risks and etiology. We reanalyzed the 16 s-rRNA gene sequencing datasets of a mixed-cohort of 25 BV patients and healthy women. In these datasets, we detected 15 trio motifs that occurred exclusively in BV patients. We failed to find any of these 15 trio motifs in three additional cohorts of 1535 healthy women. Most member-species of the 15 trio motifs are BV-associated anaerobic bacteria (BVAB), Ravel’s community-state type indicators, or the most dominant species; virtually all species interactions in these trios are high-salience skeletons, suggesting that those trios are strongly connected ‘cults’ associated with the occurrence of BV. The presence of the trio motifs unique to BV may act as indicators for its personalized diagnosis and could help elucidate a more mechanistic interpretation of its risks and etiology. We caution that scarcity of large longitudinal datasets of HVM also limited further verifications of our findings, and these findings require further clinical tests to launch their applications.

Abstract For more than 30 years, the US National Science Foundation's Research Experiences for Undergraduates (REU) program has supported thousands of undergraduate researchers annually and provides many students with their first research experiences in field ecology or evolution. REUs embed students in scientific communities where they apprentice with experienced researchers, build networks with their peers, and help students understand research cultures and how to work within them. REUs are thought to provide formative experiences for developing researchers that differ from experiences in a college classrooms, laboratories, or field trips. REU assessments have improved through time but they are largely ungrounded in educational theory. Thus, evaluation of long‐term impacts of REUs remains limited and best practices for using REUs to enhance student learning are repeatedly re‐invented. We describe how one sociocultural learning framework, cultural–historical activity theory (CHAT), could be used to guide data collection to characterize the effects of REU programs on participant's learning in an educationally meaningful context. CHAT embodies a systems approach to assessment that accounts for social and cultural factors that influence learning. We illustrate how CHAT has guided assessment of the Harvard Forest Summer Research Program in Ecology (HF‐SRPE), one of the longest‐running REU sites in the United States. Characterizing HF‐SRPE using CHAT helped formalize thoughts and language for the program evaluation, reflect on potential barriers to success, identify assessment priorities, and revealed important oversights in data collection.

Abstract Mucopolysaccharidosis IIIA is a neuronopathic lysosomal storage disease, characterised by heparan sulphate and other substrates accumulating in the brain. Patients develop behavioural disturbances and cognitive decline, a possible consequence of neuroinflammation and abnormal substrate accumulation. Interleukin (IL)‐1β and interleukin‐1 receptor antagonist (IL‐1Ra) expression were significantly increased in both murine models and human MPSIII patients. We identified pathogenic mechanisms of inflammasome activation, including that disease‐specific 2‐O‐sulphated heparan sulphate was essential for priming an IL‐1β response via the Toll‐like receptor 4 complex. However, mucopolysaccharidosis IIIA primary and secondary storage substrates, such as amyloid beta, were both required to activate the NLRP3 inflammasome and initiate IL‐1β secretion. IL‐1 blockade in mucopolysaccharidosis IIIA mice using IL‐1 receptor type 1 knockout or haematopoietic stem cell gene therapy over‐expressing IL‐1Ra reduced gliosis and completely prevented behavioural phenotypes. In conclusion, we demonstrate that IL‐1 drives neuroinflammation, behavioural abnormality and cognitive decline in mucopolysaccharidosis IIIA, highlighting haematopoietic stem cell gene therapy treatment with IL‐1Ra as a potential neuronopathic lysosomal disease treatment.

We explore the use of synchronization bits from a standard 802.11 preamble for high-accuracy localization. The multi-tone short training field present in 802.11 standards that use a Legacy preamble is investigated in comparison to a common remote sensing waveform known as the stepped frequency waveform that shares similar waveform characteristics to the preamble. We present the 802.11 standard and the connection to the stepped frequency waveform, derive the theoretical lower bound on the short training field, present a comparison of simulated results, and present experimental wireless measurements demonstrating ranging accuracies on the order of 1.9 mm.

Abstract Background Pulmonary embolism (PE) in children carries a significant morbidity and mortality. We examined previously described factors in 2 cohorts of children tested for PE and identified novel factors. Methods We combined data from 2 retrospective cohorts. Patients up to age 21 years were included who underwent imaging or D‐dimer testing for PE, with positive radiologic testing being the gold standard. Combined predictor variables were examined by univariate analysis and then forward stepwise multivariable logistic regression. Results The combined data set yielded 1103 patients with 42 unique predictor variables, and 93 PE‐positive patients (8.4%), with a median age of 16 years. Univariate analysis retained 17 variables, and multivariable logistic regression found 9 significant variables with increased probability of PE diagnosis: age‐adjusted tachycardia, tachypnea, hypoxia, unilateral limb swelling, trauma/surgery requiring hospitalization in previous 4 weeks, prior thromboembolism, cancer, anemia, and leukocytosis. Conclusion This combined data set of children with suspected PE discovered factors that may contribute to a diagnosis of PE: hypoxia, unilateral limb swelling, trauma/surgery requiring hospitalization in previous 4 weeks, prior thromboembolism, and cancer, age‐adjusted tachycardia, tachypnea, anemia, and leukocytosis. Prospective testing is needed to determine which criteria should be used to initiate diagnostic testing for PE in children.

Summary: We developed a highly efficient, ultrashort immunohistochemistry-laser capture microdissection (IHC-LMD) protocol, which allows microdissection of up to 250 single cardiomyocytes. Before LMD, murine hearts are excised, snap-frozen, and cryosectioned. RNA isolated from LMD material is of high RNA quality, making it usable for gene expression analysis and RNA sequencing. Challenges and limitations of this protocol include visualization of the immunostaining and nuclei DAPI dye on the PEN slides, and timing and speed to limit RNA degradation as much as possible.

Land-use history is the template upon which contemporary plant and tree populations establish and interact with one another and exerts a legacy on the structure and dynamics of species assemblages and ecosystems. We use the first census (2010–2014) of a 35-ha forest-dynamics plot at the Harvard Forest in central Massachusetts to describe the composition and structure of the woody plants in this plot, assess their spatial associations within and among the dominant species using univariate and bivariate spatial point-pattern analysis, and examine the interactions between land-use history and ecological processes. The plot includes 108,632 live stems ≥ 1 cm in diameter (2,215 individuals/ha) and 7,595 standing dead stems ≥ 5 cm in diameter. Live tree basal area averaged 42.25 m2/ha, of which 84% was represented by Tsuga canadensis (14.0 m2/ ha), Quercus rubra (northern red oak; 9.6 m2/ ha), Acer rubrum (7.2 m2/ ha) and Pinus strobus (eastern white pine; 4.4 m2/ ha). These same four species also comprised 78% of the live aboveground biomass, which averaged 245.2 Mg/ ha. Across all species and size classes, the forest contains a preponderance (> 80,000) of small stems (

Abstract The biogeographic diversity of the microbiome can be investigated from two perspectives: the spatiotemporal distribution of species (or any operational taxonomic unit) diversity and the spatiotemporal distribution of metagenomic gene diversity. Together, these provide a complementary understanding of taxonomic, ecological, evolutionary, and functional aspects of the microbiome. Here, we reformulate the species diversity–area relationship (DAR) to quantify and illustrate metagenomic diversity–area relationships (m‐DAR) with the gut metagenome from the human microbiome project (HMP). Using the m‐DAR, the estimated ranges of human gut metagenomic genes (MG) within and among individuals are 5.0–9.7 × 105 and 4.3–6.9 × 106, respectively; the among‐individual standard errors of these estimates (6.0–7.5 × 105) are of the same order of magnitude as the within‐individual ranges, suggesting high between‐individual variability. We similarly estimated the number of metagenome functional gene clusters (MFCG) to be 222–245 (SE = 1–2). More detailed analysis of the m‐DAR profile, pair‐wise diversity overlap (PDO), maximal accrual diversity (MAD), and ratio of individual‐ to population‐level diversity (RIP) of microbiomes of individuals with healthy guts and those with three microbiome‐associated diseases (obesity, diabetes, and inflammatory bowel disease) identified differences in m‐DAR parameters between healthy and diseased individuals. Methodologically, the m‐DAR and its associated parameters offer a unified toolset with which to study and analyze microbiomes from both species and metagenomic perspectives and to explore spatial scaling of metagenomic diversity within and among individuals. To the best of our knowledge, our illustration of m‐DAR with the human gut metagenome is the first statistically‐based estimate of the richness of human metagenomic genes at population scale.

We have previously shown that skeletal muscle-derived Sca-1+/PW1+/Pax7− interstitial cells (PICs) are multi-potent and enhance endogenous repair and regeneration. Here, we investigated the regenerative potential of PICs following intramyocardial transplantation in mice subjected to an acute myocardial infarction (MI). MI was induced through the ligation of the left anterior descending coronary artery in 8-week old male C57BL/6 mice. 5 × 105 eGFP-labelled PICs (MI + PICs; n = 7) or PBS (MI-PBS; n = 7) were injected intramyocardially into the border zone. Sham mice (n = 8) were not subjected to MI, or the transplantation of PICs or PBS. BrdU was administered via osmotic mini-pump for 14 days. Echocardiography was performed prior to surgery (baseline), and 1-, 3- and 6-weeks post-MI and PICs transplantation. Mice were sacrificed at 6 weeks post-MI + PICs transplantation, and heart sections were analysed for fibrosis, hypertrophy, engraftment, proliferation, and differentiation of PICs. A significant (p < 0.05) improvement in ejection fraction (EF) and fractional shortening was observed in the MI-PICs group, compared to MI + PBS group at 6-weeks post MI + PICs transplantation. Infarct size/fibrosis of the left ventricle significantly (p < 0.05) decreased in the MI-PICs group (14.0 ± 2.5%), compared to the MI-PBS group (32.8 ± 2.2%). Cardiomyocyte hypertrophy in the border zone significantly (p < 0.05) decreased in the MI-PICs group compared to the MI-PBS group (330.0 ± 28.5 µM2 vs. 543.5 ± 26.6 µm2), as did cardiomyocyte apoptosis (0.6 ± 0.9% MI-PICs vs. 2.8 ± 0.8% MI-PBS). The number of BrdU+ cardiomyocytes was significantly (p < 0.05) increased in the infarct/border zone of the MI-PICs group (7.0 ± 3.3%), compared to the MI-PBS group (1.7 ± 0.5%). The proliferation index (total BrdU+ cells) was significantly increased in the MI-PICs group compared to the MI-PBS group (27.0 ± 3.4% vs. 7.6 ± 1.0%). PICs expressed and secreted pro-survival and reparative growth factors, supporting a paracrine effect of PICs during recovery/remodeling. Skeletal muscle-derived PICs show significant reparative potential, attenuating cardiac remodelling following transplantation into the infarcted myocardium. PICs can be easily sourced from skeletal muscle and therefore show promise as a potential cell candidate for supporting the reparative and regenerative effects of cell therapies.

The COVID-19 pandemic continues to be a source of stress and have important mental health implications for all persons but may have unique implications for men. In addition to the risk of contracting and dying from COVID-19, the rising COVID-19 death toll, ongoing economic uncertainty, loneliness from social distancing, and other changes to our lifestyles make up the perfect recipe for a decline in mental health. In June 2020, men reported slightly lower rates of anxiety than women, but had higher rates of depressive symptoms and suicidal ideation. As of September 2020, men sought mental health care at a higher rate than women for family and relationships, with year-over-year visits up 5.5 times and total virtual mental health care visits monthly growth in 2020 was up 79% since January. Because men are not a homogeneous group, it is important to implement strategies for groups of men that may have particularly unique needs. In this paper, we discuss considerations for intervening in men’s mental health during and in response to the COVID-19 pandemic, including current technology-based cyberpsychology options.

Hematopoietic stem cell gene therapy is a promising therapeutic strategy for the treatment of neurological disorders, since transplanted gene-corrected cells can traffic to the brain, bypassing the blood-brain barrier, to deliver therapeutic protein to the CNS. We have developed this approach for the treatment of Mucopolysaccharidosis type IIIA (MPSIIIA), a devastating lysosomal storage disease that causes progressive cognitive decline, leading to death in early adulthood. In a previous pre-clinical proof-of-concept study, we demonstrated neurological correction of MPSIIIA utilizing hematopoietic stem cell gene therapy via a lentiviral vector encoding the SGSH gene. Prior to moving to clinical trial, we have undertaken further studies to evaluate the efficiency of gene transfer into human cells and also safety studies of biodistribution and genotoxicity. Here, we have optimized hCD34+ cell transduction with clinical grade SGSH vector to provide improved pharmacodynamics and cell viability and validated effective scale-up and cryopreservation to generate an investigational medicinal product. Utilizing a humanized NSG mouse model, we demonstrate effective engraftment and biodistribution, with no vector shedding or transmission to germline cells. SGSH vector genotoxicity assessment demonstrated low transformation potential, comparable to other lentiviral vectors in the clinic. This data establishes pre-clinical safety and efficacy of HSCGT for MPSIIIA.

Foundation species define ecosystems, control the biological diversity of associated species, modulate critical ecosystem processes, and often have important cultural values and resonance. This review summarizes current understanding of the characteristics and traits of foundation species and how to distinguish them from other “important” species in ecological systems (e.g., keystone, dominant, and core species); illustrates how analysis of the structure and function of ecological networks can be improved and enriched by explicit incorporation of foundation species and their non-trophic interactions; discusses the importance of pro-active identification and management of foundation species as a cost-effective and efficient method of sustaining valuable ecosystem processes and services and securing populations of associated rare, threatened, or endangered species; and suggests broader engagement of citizen-scientists and non-specialists in the identification and study of foundation species and their biological and cultural values. : Global Change; Nature Conservation; Ecology Subject Areas: Global Change, Nature Conservation, Ecology

Interest is growing in designing resilient and ecologically rich urban environments that provide social and ecological benefits. Regenerative and biocentric designs fostering urban ecological habitats including food webs that provide ecosystem services for people and wildlife increasingly are being sought. However, the intentional design of urban landscapes for food webs remains in an early stage with few precedents and many challenges. In this paper, we explore the potential to design (for) urban food webs through collaborations between designers and ecologists. We start by examining the ecology and management of Jamaica Bay in New York City as a case study of an anthropogenic landscape where ecosystems are degraded and the integrity of extant food webs are intertwined with human agency. A subsequent design competition focusing on ecological design and management of this large-scale landscape for animal habitat and ecosystem services for people illustrates how designers approach this anthropogenic landscape. This case study reveals that both designing urban landscapes for food webs and directly designing and manipulating urban food webs are complicated and challenging to achieve and maintain, but they have the potential to increase ecological health of, and enhance ecosystem services in, urban environments. We identify opportunities to capitalize on species interactions across trophic structures and to introduce managed niches in biologically engineered urban systems. The design competition reveals an opportunity to approach urban landscapes and ecological systems creatively through a proactive design process that includes a carefully crafted collaborative approach to constructing ecologically functioning landscapes that can integrate societal demands. As designers increasingly seek to build, adapt, and manage urban environments effectively, it will be critical to resolve the contradictions and challenges associated with human needs, ecosystem dynamics, and interacting assemblages of species. Ecologists and designers are still discovering and experimenting with designing (for) urban food webs and fostering species interactions within them. We recommend generating prototypes of urban food webs through a learning-by-doing approach in urban development projects. Design and implementation of urban food webs also can lead to research opportunities involving monitoring and experiments that identify and solve challenges of food-web construction while supporting and encouraging ongoing management.

OBJECTIVES/GOALS: Our primary objective was to determine the demographic and linguistic characteristics of research coordinators (RCs) in a large pediatric emergency medicine research collaborative network. Our secondary objective was to determine if the RCs perceived any impact of those characteristics on their duties. METHODS/STUDY POPULATION: We conducted a 15-question electronic survey of RCs at the member institutions of the Pediatric Emergency Care Applied Research Network (PECARN). A total of 74 potential respondents were identified and received the survey. RESULTS/ANTICIPATED RESULTS: Fifty-three surveys (71.6%) were completed. Most respondents identified as female; white; and not Hispanic or Latino. Fourteen respondents (26.4%) identified as underrepresented minorities in medicine (UIM), which is similar to the percentage of UIM among the general population (30%). Twenty-eight respondents (52%) felt that their race/ethnicity positively impacted recruitment efforts. Twenty-three respondents (43%) felt that their ability to speak a language other than English positively impacted recruitment efforts. Four female respondents felt that their gender hindered their recruitment activities and impacted their sense of belonging within the research team. DISCUSSION/SIGNIFICANCE: RCs felt that their backgrounds and attributes positively impacted subject recruitment. However, some female coordinators felt negatively impacted by their gender. Increasing diversity amongst clinical research professionals and incorporating team cultural humility practices, may help increase diversity among clinical research subjects.

The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19) has led to 47 m infected cases and 1. 2 m (2.6%) deaths. A hallmark of more severe cases of SARS-CoV-2 in patients with acute respiratory distress syndrome (ARDS) appears to be a virally-induced over-activation or unregulated response of the immune system, termed a “cytokine storm,” featuring elevated levels of pro-inflammatory cytokines such as IL-2, IL-6, IL-7, IL-22, CXCL10, and TNFα. Whilst the lungs are the primary site of infection for SARS-CoV-2, in more severe cases its effects can be detected in multiple organ systems. Indeed, many COVID-19 positive patients develop cardiovascular complications, such as myocardial injury, myocarditis, cardiac arrhythmia, and thromboembolism, which are associated with higher mortality. Drug and cell therapies targeting immunosuppression have been suggested to help combat the cytokine storm. In particular, mesenchymal stromal cells (MSCs), owing to their powerful immunomodulatory ability, have shown promise in early clinical studies to avoid, prevent or attenuate the cytokine storm. In this review, we will discuss the mechanistic underpinnings of the cytokine storm on the cardiovascular system, and how MSCs potentially attenuate the damage caused by the cytokine storm induced by COVID-19. We will also address how MSC transplantation could alleviate the long-term complications seen in some COVID-19 patients, such as improving tissue repair and regeneration.

The coronavirus pandemic has reportedly infected over 31.5 million individuals and caused over 970,000 deaths worldwide (as of 22nd Sept 2020). This novel coronavirus, officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), although primarily causes significant respiratory distress, can have significant deleterious effects on the cardiovascular system. Severe cases of the virus frequently result in respiratory distress requiring mechanical ventilation, often seen, but not confined to, individuals with pre-existing hypertension and cardiovascular disease, potentially due to the fact that the virus can enter the circulation via the lung alveoli. Here the virus can directly infect vascular tissues, via TMPRSS2 spike glycoprotein priming, thereby facilitating ACE-2-mediated viral entry. Clinical manifestations, such as vasculitis, have been detected in a number of vascular beds (e.g., lungs, heart, and kidneys), with thromboembolism being observed in patients suffering from severe coronavirus disease (COVID-19), suggesting the virus perturbs the vasculature, leading to vascular dysfunction. Activation of endothelial cells via the immune-mediated inflammatory response and viral infection of either endothelial cells or cells involved in endothelial homeostasis, are some of the multifaceted mechanisms potentially involved in the pathogenesis of vascular dysfunction within COVID-19 patients. In this review, we examine the evidence of vascular manifestations of SARS-CoV-2, the potential mechanism(s) of entry into vascular tissue and the contribution of endothelial cell dysfunction and cellular crosstalk in this vascular tropism of SARS-CoV-2. Moreover, we discuss the current evidence on hypercoagulability and how it relates to increased microvascular thromboembolic complications in COVID-19.

Phenology—the timing of life-history events—is a key trait for understanding responses of organisms to climate. The digitization and online mobilization of herbarium specimens is rapidly advancing our understanding of plant phenological response to climate and climatic change. The current practice of manually harvesting data from individual specimens, however, greatly restricts our ability to scale-up data collection. Recent investigations have demonstrated that machine-learning approaches can facilitate this effort. However, present attempts have focused largely on simplistic binary coding of reproductive phenology (e.g., presence/absence of flowers). Here, we use crowd-sourced phenological data of buds, flowers, and fruits from >3,000 specimens of six common wildflower species of the eastern United States (Anemone canadensis L., A. hepatica L., A. quinquefolia L., Trillium erectum L., T. grandiflorum (Michx.) Salisb., and T. undulatum Wild.) to train models using Mask R-CNN to segment and count phenological features. A single global model was able to automate the binary coding of each of the three reproductive stages with >87% accuracy. We also successfully estimated the relative abundance of each reproductive structure on a specimen with ≥90% accuracy. Precise counting of features was also successful, but accuracy varied with phenological stage and taxon. Specifically, counting flowers was significantly less accurate than buds or fruits likely due to their morphological variability on pressed specimens. Moreover, our Mask R-CNN model provided more reliable data than non-expert crowd-sourcers but not botanical experts, highlighting the importance of high-quality human training data. Finally, we also demonstrated the transferability of our model to automated phenophase detection and counting of the three Trillium species, which have large and conspicuously-shaped reproductive organs. These results highlight the promise of our two-phase crowd-sourcing and machine-learning pipeline to segment and count reproductive features of herbarium specimens, thus providing high-quality data with which to investigate plant responses to ongoing climatic change.

Data provenance is a machine-readable summary of the collection and computational history of a dataset. Data provenance confers or adds value to a dataset, helps reproduce computational analyses, or validates scientific conclusions. The people of the End-to-End Provenance Project are a community of professionals who have developed software tools to collect and use data provenance.

Rehabilitated and restored mangrove ecosystems have important ecological, economic, and social values for coastal communities. Although a sine qua non of successful mangrove rehabilitation or restoration projects is accurate attention to local hydrology and basic biology of mangrove trees and their associated fauna, their long-term success depends on far more axes, each with their own challenges. Rehabilitation projects: are planned, designed, executed, and managed by people with diverse backgrounds and different scientific and socio-political agendas; need to be responsive to these multiple stakeholders and agents who hold different values; are often influenced by laws and treaties spanning local to international scales; and must be able to adapt and evolve both geomorphologically and socioeconomically over decades-to-centuries in the context of a rapidly changing climate. We view these challenges as opportunities for innovative approaches to rehabilitation and restoration that engage new and larger constituencies. Restored mangrove ecosystems can be deliberately designed and engineered to provide valuable ecosystem services, be adaptable to climatic changes, and to develop platforms for educating nonspecialists about both the successes and failures of restored mangrove ecosystems. When mangrove rehabilitation or restoration projects are developed as experiments, they can be used as case-studies and more general models to inform policy- and decision-makers and guide future restoration efforts. Achieving this vision will require new investment and dedication to research and adaptive management practices. These ideas are illustrated with examples from mangrove restoration and rehabilitation projects in the Indo-West Pacific and Caribbean regions, the two hotspots of mangrove biodiversity and its ongoing loss and degradation.

Acute subdural hematoma is a rare but potentially fatal medical condition in athletes. This condition has been reported in both contact and non-contact sports. Patients who survive an acute subdural hematoma typically have lifelong deficits and require extensive rehabilitation. Prompt recognition of this condition and access to a hospital with an available neurosurgeon is critical. To our knowledge, this is the first report of a subdural hematoma in an elite-level rugby player. Keywords: Acute subdural hematoma, Head trauma, Rugby, Athletes

Pollution and climate change are among the most challenging issues for countries with developing economies, but we know little about the ecological risks that result when these pressures occur together. We explored direct effects of, and interactions between, environmental pollution and climate change on ecosystem health in the Bohai Sea region of Northern China. We developed an integrated approach to assess ecological risks to this region under four scenarios of climate change. Although ecological risks to the system from pollution alone have been declining, interactions between pollution and climate change have enhanced ecological risks to this coastal/marine ecosystem. Our results suggest that current policies focused strictly on pollution control alone should be changed to take into account the interactive effects of climate change so as to better forecast and manage potential ecological risks.

The giant panda (Ailuropoda melanoleuca) is recognized worldwide as an icon for wildlife conservation. Since the introduction in 1992 of reliable methods for artificial insemination, the population of captive pandas has grown to approximately 350 individuals in 2013. However, captive panda populations are harmed by environmental pollution, diseases transmitted from domestic animals, and other anthropologenic activities. Although the Chinese government has proposed the creation of a Giant Panda National Park, there are at least three reasons that suggest that it is premature to reintroduce captive pandas into this proposed national park. First, habitat fragmentation remains the greatest threat to survival of giant pandas; second, most captive pandas are hybrids of the Sichuan and Qinling subspecies and release of hybrids may lead to further introgression between the two subspecies; and third, captive pandas may be competitively inferior to wild pandas in the region, and may not survive fights for food or mates. As an alternative, we suggest establishing a special conservation zone in the Shennongjia National Nature Reserve for wild training of captive pandas prior to their reintroduction into the National Park.

Skeletal muscle-derived PW1pos/Pax7neg interstitial cells (PICs) express and secrete a multitude of proregenerative growth factors and cytokines. Utilizing a porcine preclinical skeletal muscle injury model, delivery of allogeneic porcine PICs (pPICs) significantly improved and accelerated myofiber regeneration and neocapillarization, compared with saline vehicle control-treated muscles. Allogeneic pPICs did not contribute to new myofibers or capillaries and were eliminated by the host immune system. In conclusion, allogeneic pPIC transplantation stimulated the endogenous stem cell pool to bring about enhanced autologous skeletal muscle repair and regeneration. This allogeneic cell approach is considered a cost-effective, easy to apply, and readily available regenerative therapeutic strategy.

Abstract Background The development of cellular therapies to treat muscle wastage with disease or age is paramount. Resident muscle satellite cells are not currently regarded as a viable cell source due to their limited migration and growth capability ex vivo. This study investigated the potential of muscle-derived PW1+/Pax7– interstitial progenitor cells (PICs) as a source of tissue-specific stem/progenitor cells with stem cell properties and multipotency. Methods Sca-1+/PW1+ PICs were identified on tissue sections from hind limb muscle of 21-day-old mice, isolated by magnetic-activated cell sorting (MACS) technology and their phenotype and characteristics assessed over time in culture. Green fluorescent protein (GFP)-labelled PICs were used to determine multipotency in vivo in a tumour formation assay. Results Isolated PICs expressed markers of pluripotency (Oct3/4, Sox2, and Nanog), were clonogenic, and self-renewing with >60 population doublings, and a population doubling time of 15.8 ± 2.9 h. PICs demonstrated an ability to generate both striated and smooth muscle, whilst also displaying the potential to differentiate into cell types of the three germ layers both in vitro and in vivo. Moreover, PICs did not form tumours in vivo. Conclusion These findings open new avenues for a variety of solid tissue engineering and regeneration approaches, utilising a single multipotent stem cell type isolated from an easily accessible source such as skeletal muscle.