Reimagining infrastructure for a biodiverse future.

Civil infrastructure will be essential to face the interlinked existential threats of climate change and rising resource demands while ensuring a livable Anthropocene for all. However, conventional infrastructure planning largely neglects the contributions and maintenance of Earth's ecological life support systems, which provide irreplaceable services supporting human well-being. The stability and performance of these services depend on biodiversity, but conventional infrastructure practices, narrowly focused on controlling natural capital, have inadvertently degraded biodiversity while perpetuating social inequities. Here, we envision a new infrastructure paradigm wherein biodiversity and ecosystem services are a central objective of civil engineering. In particular, we reimagine infrastructure practice such that 1) ecosystem integrity and species conservation are explicit objectives from the outset of project planning; 2) infrastructure practices integrate biodiversity into diverse project portfolios along a spectrum from conventional to nature-based solutions and natural habitats; 3) ecosystem functions reinforce and enhance the performance and lifespan of infrastructure assets; and 4) civil engineering promotes environmental justice by counteracting legacies of social inequity in infrastructure development and nature conservation. This vision calls for a fundamental rethinking of the standards, practices, and mission of infrastructure development agencies and a broadening of scope for conservation science. We critically examine the legal and professional precedents for this paradigm shift, as well as the moral and economic imperatives for manifesting equitable infrastructure planning that mainstreams biodiversity and nature's benefits to people. Finally, we set an applied research agenda for supporting this vision and highlight financial, professional, and policy pathways for achieving it.

Principles for data management, visualization, and communication to improve disaster response management: Lessons from the Hurricane Maria response mission.

Data visualization and communication are important components in disaster response management. Data management should be a basic part of emergency preparation in the same way as prepositioning essential supplies. For this preparation to be effective, well-conceived data structures and data collection systems must be in place before disasters happen, and required hardware should be designed to operate in contingency environments. However, due to challenges in disaster complexities and data management, there is still a pressing need for improvement. This paper identifies key principles to assist practitioners and software developers in designing and implementing data collection and reporting systems that can be used for data visualization during a disaster response. The authors reviewed existing literature on data and disaster management and incorporated their personal experiences as first responders with the US Army Corps of Engineers Hurricane Maria response mission to develop principles for improving data management and visualization during a disaster response. These principles are illustrated by two case studies from the Task Force Power and Operation Blue Roof mission efforts in Puerto Rico during 2017-2018. Suggested principles include considering data management as part of disaster preparedness, having flexible data tools resilient to unprecedented disaster outcomes, eg, interruption of telecommunications networks, and using diverse graphics and tools that are appropriate to their communication purpose and audience.

Engineering coastal structures to centrally embrace biodiversity.

Global environmental factors (e.g., extreme weather, climate action failure, natural disasters, human environmental damage) increasingly threaten coastal communities. Shorelines are often hardened (seawalls, bulkheads) to prevent flooding and erosion and protect coastal communities. However, hardened shorelines lead to environmental degradation and biodiversity loss. Developmental pressures that are growing in scale, scope, and complexity necessitate the development of sustainable solutions to work with, rather than against, nature. Such nature-based solutions (NBS) provide protection and improve environmental quality and enhance biodiversity. To further this pressing need into action, the US Army Corps of Engineers (USACE) began the Engineering With Nature (EWN) initiative to balance economic, environmental, and social benefits through collaboration with partners and stakeholders. This work shows how engineering practice can be advanced through structured decision-making and landscape architecture renderings that include ecological sciences and NBS into an integrated approach for enhancing biodiversity in coastal marine environments. This integrated approach can be applied when designing new infrastructure projects or modifying or repairing existing infrastructure. To help communicate designs incorporating NBS, drawings, and renderings showcasing EWN concepts can aid decision-making. Our experiences with implementing EWN in practice have revealed that involving landscape architects can play a crucial role in successful collaboration and lead to solutions that protect coastal communities while preserving or enhancing biodiversity.

A strategic monitoring approach for learning to improve natural infrastructure.

Natural infrastructure (NI) development, including ecosystem restoration, is an increasingly popular approach to leverage ecosystem services for sustainable development, climate resilience, and biodiversity conservation goals. Although implementation and planning for these tools is accelerating, there is a critical need for effective post-implementation monitoring to accumulate performance data and evidence for best practices. The complexity and longer time scales associated with NI, compounded by differing disciplinary definitions and concepts of monitoring necessitate a deliberate and strategic approach to monitoring that encompasses different timeframes and objectives. This paper outlines a typology of monitoring classes differentiated by temporal scale, purpose of data collection, the information benefits of monitoring, and the responsible party. Next, we provide a framework and practical guidelines for designing monitoring plans for NI around learning objectives. In particular, we emphasize conducting research and development monitoring, which provides scientifically rigorous evidence for methodological improvement beyond the project scale. Wherever feasible, and where NI tools are relatively new and untested, such monitoring should avoid wasted effort and ensure progress and refinement of methodology and practice over time. Finally, we propose institutional changes that would promote greater adoption of research and development monitoring to increase the evidence base for NI implementation at larger scales.

Outcomes of normothermic machine perfusion of liver grafts in repeat liver transplantation (NAPLES initiative).

BACKGROUND: Retransplantation candidates are disadvantaged owing to lack of good-quality liver grafts. Strategies that can facilitate transplantation of suboptimal grafts into retransplant candidates require investigation. The aim was to determine whether late liver retransplantation can be performed safely with suboptimal grafts, following normothermic machine perfusion. METHODS: A prospectively enrolled group of patients who required liver retransplantation received a suboptimal graft preserved via normothermic machine perfusion. This group was compared with both historical and contemporaneous cohorts of patient who received grafts preserved by cold storage. The primary outcome was 6-month graft and patient survival. RESULTS: The normothermic machine perfusion group comprised 26 patients. The historical (cold storage 1) and contemporaneous (cold storage 2) groups comprised 31 and 25 patients respectively. The 6-month graft survival rate did not differ between groups (cold storage 1, 27 of 31, cold storage 2, 22 of 25; normothermic machine perfusion, 22 of 26; P = 0.934). This was despite the normothermic machine perfusion group having significantly more steatotic grafts (8 of 31, 7 of 25, and 14 of 26 respectively; P = 0.006) and grafts previously declined by at least one other transplant centre (5 of 31, 9 of 25, and 21 of 26; P < 0.001). CONCLUSION: In liver retransplantation, normothermic machine perfusion can safely expand graft options without compromising short-term outcomes.

Liver transplantation is a life-saving procedure for many different diseases. In the UK, one in 10 patients awaiting transplant have had a previous liver transplant. These retransplant operations are complex, and the general belief is that a good-quality donor liver graft is required for best outcomes. However, there is a significant shortage of good-quality organs for liver transplantation, so many patients awaiting retransplantation spend longer on the waiting list. This study investigated whether a new technology, called normothermic machine perfusion, could be used to preserve lower-quality donor livers and have successful outcomes for patients undergoing retransplantation. Traditionally, good-quality livers are preserved in an ice box and the study compared the outcomes of these two different approaches. The aim was to prove that normothermic machine perfusion improves access to transplantation for this group of patients, without compromising outcomes. A group of patients who underwent retransplantation and received a lesser-quality liver preserved with normothermic machine perfusion was compared with two groups of patients who had received a transplant with traditional ice-box preservation. The complications, graft, and patient survival of the former group was compared with those in the latter two groups who underwent liver retransplantation with better-quality liver grafts. The rate of survival and adverse surgical outcomes were comparable between the groups of patients who received a liver preserved via traditional ice-box preservation, and those who received a lesser-quality liver preserved via normothermic machine perfusion. Normothermic machine perfusion can potentially expand the number of suitable donor livers available for retransplant candidates.

Anterior cruciate ligament tear patterns in young patients: An arthroscopic multicenter study.

INTRODUCTION: In the last decade, there has been a renewed interest in anterior cruciate ligament (ACL) preservation surgeries in the younger patients. Several ACL preservation techniques such as primary repair, augmented repair, and scaffold repair have been described based on the particular tear type and pattern. The purpose of this study was to determine the distribution of tear patterns in young patients presenting with an acute ACL injury. METHODS: A prospective observational study was performed at two tertiary children's hospitals. Patients under 18 years undergoing ACL reconstruction within 8 weeks of initial injury were included from 2017 to 2019. Tear patterns were classified by two orthopedic surgeons from each of the two centers during arthroscopic ACL reconstruction into 4 types: I. Avulsion off the femur, II. <10% of total ACL length tear from femoral end, III. Mid-substance tear and IV. Single bundle tear. For reliability, the four surgeons classified ACL injury (2 rounds each) based on de-identified intraoperative videos of 33 randomly selected surgical ACL cases. Inter and intra-rater reliability studies were calculated using Kappa statistics. RESULTS: 224 patients (123 males, 101 females) with mean age of 16 (range: 9-18) years were enrolled in this study. Fifty-seven (25%) patients reported contact injury while 167 (75%) reported non-contact. Isolated ACL injury was recorded in 70 (31%) patients, while concomitant injuries were recorded in 154 patients (69%). The most common associated injury was lateral meniscus tear (35%), followed by lateral and medial meniscus tears (20%). According to our classification, 31 (14%) patients were Type I, 30 (13%) were Type II, 139 (62%) were Type III, 18 (8%) were Type IV. The intra-rater reliability was excellent for 2 reviewers, good for 1 and marginal for another. The overall inter-rater reliability for all 4 reviewers was marginal for both readings. There was no statistical difference in the occurrence of type of tear based on the mechanism of injury (contact vs non-contact) or age of the patients. CONCLUSIONS: This is the first multicenter study using an arthroscopic assessment to classify the location of ACL tear in the young population. It gives us further insight on the possible application for surgeries to preserve the ACL in this group. Larger studies incorporating these findings with MRI evaluation and ACL repair techniques are needed to confirm the utility of this information to decide the eligibility for repair in pediatric patients.

Severe Sepsis Mimicking Primary Nonfunction Following Liver Transplantation: Normothermic Machine Perfusion Is a Potential Environment for Bacterial Overgrowth and Transmission From Donor to Recipient. A Case Report.

Primary nonfunction (PNF) in the early postoperative period following liver transplantation is fatal if not managed appropriately with early retransplantation. Severe early allograft dysfunction can mimic PNF. The identification of treatable causative factors such as sepsis, hepatic artery, or portal vein thrombosis is essential to distinguish it from PNF, and their early management may avoid the need for retransplantation. In this article, we describe a case of sepsis-induced severe liver dysfunction from a contaminated graft perfused with normothermic machine perfusion (NMP), which presented in a manner similar to PNF. The implications of graft contamination are poorly described. To our knowledge, this is the first report of bacterial contamination of a graft that underwent NMP and subsequently caused severe sepsis in the recipient. The conditions created with NMP may be optimal for certain micro-organisms to thrive. The role of the liver in the immune system is complex as it provides an essential barrier to enterically derived portal venous pathogens and produces numerous acute phase proteins that augment the systemic immune response. Additionally, the liver is also known to restrain harmful and excessive systemic immune responses such as those that occur with the sepsis syndrome. The relationship between bacterial graft contamination, sepsis, and graft dysfunction may be multidirectional.

Genetic structure and admixture in sheep from terminal breeds in the United States.

Selection for performance in diverse production settings has resulted in variation across sheep breeds worldwide. Although sheep are an important species to the United States, the current genetic relationship among many terminal sire breeds is not well characterized. Suffolk, Hampshire, Shropshire and Oxford (terminal) and Rambouillet (dual purpose) sheep (n = 248) sampled from different flocks were genotyped using the Applied Biosystems Axiom Ovine Genotyping Array (50K), and additional Shropshire sheep (n = 26) using the Illumina Ovine SNP50 BeadChip. Relationships were investigated by calculating observed heterozygosity, inbreeding coefficients, eigenvalues, pairwise Wright's FST estimates and an identity by state matrix. The mean observed heterozygosity for each breed ranged from 0.30 to 0.35 and was consistent with data reported in other US and Australian sheep. Suffolk from two different regions of the United States (Midwest and West) clustered separately in eigenvalue plots and the rectangular cladogram. Further, divergence was detected between Suffolk from different regions with Wright's FST estimate. Shropshire animals showed the greatest divergence from other terminal breeds in this study. Admixture between breeds was examined using admixture, and based on cross-validation estimates, the best fit number of populations (clusters) was K = 6. The greatest admixture was observed within Hampshire, Suffolk, and Shropshire breeds. When plotting eigenvalues, US terminal breeds clustered separately in comparison with sheep from other locations of the world. Understanding the genetic relationships between terminal sire breeds in sheep will inform us about the potential applicability of markers derived in one breed to other breeds based on relatedness.

Toxicity and Efficacy of Stereotactic Ablative Body Radiotherapy for Moderately Central Non-small Cell Lung Cancers Using 50 Gy in Five Fractions.

AIMS: Stereotactic ablative body radiotherapy doses for peripheral lung lesions caused high toxicity when used for central non-small cell lung cancer (NSCLC). To determine a safe stereotactic ablative body radiotherapy dose for central tumours, the phase I/II Radiation Therapy Oncology Group RTOG 0813 trial used 50 Gy/five fractions as a baseline. From 2013, 50 Gy/five fractions was adopted at the Beatson West of Scotland Cancer Centre for inoperable early stage central NSCLC. We report our prospectively collected toxicity and efficacy data. MATERIALS AND METHODS: Patient and treatment characteristics were obtained from electronic medical records. Tumours were classed as moderately central or ultra-central tumours using published definitions. Toxicity was assessed in a centralised follow-up clinic at 2 weeks, 6 weeks, 3 months, 6 months, 1 year and 2 years after treatment. RESULTS: Fifty patients (31 women, 19 men, median age 75.1 years) were identified with T1-2N0M0 moderately central NSCLC; one patient had both an ultra-central and a moderately central tumour. Eighty-four per cent were medically unfit for surgery. Forty per cent had biopsy-proven NSCLC and 60% were diagnosed radiologically using 18-fluorodeoxyglucose positron emission tomography/computed tomography imaging. Fifty-six per cent of patients were Eastern Cooperative Oncology Group (ECOG) performance status 2 or worse. All patients received 50 Gy/five fractions on alternate days on schedule. Two patients died within 90 days of treatment, one from a chest infection, the other cause of death was unknown. There was one episode of early grade 3 oesophagitis and one grade 3 late dyspnoea. There was no grade 4 toxicity. Over a median follow-up of 25.2 months (range 1-70 months), there were 34 deaths: 18 unrelated to cancer and 16 due to cancer recurrence. The median overall survival was 27.0 months (95% confidence interval 20.6-35.9) and cancer-specific survival was 39.8 months (95% confidence interval 28.6, not reached). CONCLUSION: This study has shown that 50 Gy/five fractions is a safe dose and fractionation for early stage inoperable moderately central NSCLC, with outcomes comparable with other series, even with patients with a poor performance status.

Study protocol for a multicenter prospective cohort study on esophagogastric anastomoses and anastomotic leak (the Oesophago-Gastric Anastomosis Audit/OGAA).

Esophagectomy is a mainstay in curative treatment for esophageal cancer; however, the reported techniques and outcomes can vary greatly. Thirty-day mortality of patients with an intact anastomosis is 2-3% as compared to 17-35% in patients who have an anastomotic leak. The subsequent management of leaks postesophagectomy has great global variability with little consensus on a gold standard of practice. The aim of this multicentre prospective audit is to analyze current techniques of esophagogastric anastomosis to determine the effect on the anastomotic leak rate. Leak rates and leak management will be assessed to determine their impact on patient outcomes. A 12-month international multicentre prospective audit started in April 2018 and is coordinated by a team from the West Midlands Research Collaborative. This will include patients undergoing esophagectomy over 9 months and encompassing a 90-day follow-up period. A pilot data collection period occurred at four UK centers in 2017 to trial the data collection form. The audit standards will include anastomotic leak and the conduit necrosis rate should be less than 13% and major postoperative morbidity (Clavien-Dindo Grade III or more) should be less than 35%. The 30-day mortality rate should be less than 5% and the 90-day mortality rate should be less than 8%. This will be a trainee-led international audit of esophagectomy practice. Key support will be given by consultant colleagues and anesthetists. Individualized unit data will be distributed to the respective contributing sites. An overall anonymized report will be made available to contributing units. Results of the audit will be published in peer-reviewed journals with all collaborators fully acknowledged. The key information and results from the audit will be disseminated at relevant scientific meetings.

Saving bones without risking brain-bisphosphonates and risk of stroke: matched case-control study.

We investigated the association between bisphosphonate treatment and the risk of stroke using a large routine clinical dataset. We found no association between bisphosphonate treatment and risk of stroke, after adjusting for large number of clinical and demographic confounders. INTRODUCTION: There is conflicting evidence on the link between bisphosphonates and stroke with studies variously showing increased, decreased or unchanged risk. We investigated the association between bisphosphonate treatment and the risk of stroke using a large routine clinical dataset. METHODS: We used a matched nested case-control study design analysing routinely collected electronic data from patients registered at primary care practices in England participating in the Royal College of General Practitioners Research and Surveillance Centre. Cases were patients aged 18 years or over, either living or dead, recorded as having had a stroke in the period 1 January 2005 to 31 March 2016. Each case was matched to one control according to age, sex, general practice attended and calendar time. Data were analysed using Stata, version 14.2. and RStudio, version 1.1.463. Conditional logistic regression was used to determine odds ratios for stroke according to bisphosphonate treatment and duration in cases compared with controls. We adjusted for disease risk groups, cardiovascular risk factors, treatments, smoking status, alcohol consumption, ethnicity, bisphosphonate types, fracture and socioeconomic status using IMD (Index of Multiple Deprivation). RESULTS: We included 31,414 cases of stroke with an equal number of matched controls. Overall, 83.2% of cases and controls were aged 65 years or older, and there were similar proportions of females (51.5%) and males (48.5%). Bisphosphonate treatment was not associated with stroke after adjusting for the wide range of confounders considered (OR 0.86, 95% CI 0.62-1.19). CONCLUSIONS: We found no association between bisphosphonate treatment and risk of stroke, after adjusting for other confounders.

Building a hydrologic foundation for tropical watershed management.

Here we provide an empirical hydrologic foundation to inform water management decisions in the El Yunque National Forest (EYNF) in eastern Puerto Rico. Tropical watershed hydrology has proven difficult to quantify due to high rainfall variability, high evapotranspiration rates, variation in forest canopy interception and storage, and uncertain hydrologic inputs from fog condensation in cloud forests. We developed mass-balance and observation-based water budgets for nine local watersheds within the EYNF using a novel assemblage of remotely sensed rainfall data, gaged streamflow observations, and municipal water withdrawal rates. It is important to note that, while prior budgets considered large water withdrawals outside (downstream) of EYNF boundaries, our current budget is confined to within EYNF boundaries. Here, we also base our estimates of water withdrawal volume on operational data, in contrast to prior water budgets that estimated volume based on either the capacity of known water intakes or regulatory permit limits. This resulted in more conservative and realistic estimates of withdrawals from within the EYNF. Finally, we also discuss the ecological importance of considering the effects of water withdrawals not only at an average monthly scale, but also on the basis of exceedance probability to avoid over-abstraction for the protection of native migratory fishes and shrimps. This analysis highlights a number of unique challenges associated with developing hydrologic foundations for water management in tropical ecosystems.

Prospective cohort study of surgical trainee experience of access to gastrointestinal endoscopy training in the UK and Ireland.

INTRODUCTION: Surgical trainees are reporting barriers to training in gastrointestinal (GI) endoscopy. This snapshot survey aimed to gather data on variation in access to quality GI endoscopy training for Colorectal and Upper Gastrointestinal (GI) surgical trainees across the UK and Ireland. MATERIALS AND METHODS: An online 20-point survey was designed and distributed nationally to surgical trainee members of the Association of Surgeons in Training (ASiT), Dukes and The Roux Group (formerly Association of Upper Gastrointestinal Surgeons of Great Britain and Ireland Trainees). The survey was designed in collaboration with The Roux Group for Upper GI trainees and the Dukes' Club for Colorectal trainees. RESULTS: 218 responses were received, most with a Colorectal or Upper GI sub-specialty interest (colorectal 56.0%; upper GI surgery 25.7%). Only 28.6% of trainees attended a dedicated training endoscopy list at least once a week with 28.1% not attending any at all. Less than half of trainees reported having endoscopy formally timetabled on rotas (36.9%). Most trainees (88.0%) encountered difficulties in gaining endoscopy training including lack of available lists (77.2%), conflicting operative commitments (59.4%), preferential allocation of lists to gastroenterology trainees (57.9%) and resistance from endoscopy departmental leads (38.6%). Regarding JAG accreditation, 77.1% respondents felt it should be mandatory prior to CCT with 80.3% believing this would lead to better access to dedicated endoscopy training equivalent to gastroenterology trainees. 93.1% trainees felt that attaining JAG accreditation by surgical trainees was important to patient care. DISCUSSION: This study demonstrates significant barriers in accessing GI endoscopy training for general surgical trainees which urgently needs to be improved. In order to meet JAG training requirements for surgical trainees, a multifaceted collaborative approach from surgical and gastroenterology training bodies, local JAG trainers and the General Surgery SAC and JCST is required. This is to ensure that endoscopy is promoted and a robust model of training is successfully designed and delivered to general surgery trainees.

Application of Effective Discharge Analysis to Environmental Flow Decision-Making.

Well-informed river management decisions rely on an explicit statement of objectives, repeatable analyses, and a transparent system for assessing trade-offs. These components may then be applied to compare alternative operational regimes for water resource infrastructure (e.g., diversions, locks, and dams). Intra- and inter-annual hydrologic variability further complicates these already complex environmental flow decisions. Effective discharge analysis (developed in studies of geomorphology) is a powerful tool for integrating temporal variability of flow magnitude and associated ecological consequences. Here, we adapt the effectiveness framework to include multiple elements of the natural flow regime (i.e., timing, duration, and rate-of-change) as well as two flow variables. We demonstrate this analytical approach using a case study of environmental flow management based on long-term (60 years) daily discharge records in the Middle Oconee River near Athens, GA, USA. Specifically, we apply an existing model for estimating young-of-year fish recruitment based on flow-dependent metrics to an effective discharge analysis that incorporates hydrologic variability and multiple focal taxa. We then compare three alternative methods of environmental flow provision. Percentage-based withdrawal schemes outcompete other environmental flow methods across all levels of water withdrawal and ecological outcomes.

Neuropathic pain in a primary care electronic health record database.

BACKGROUND: Neuropathic pain (NP) is common in the adult population but is difficult to study in electronic health record (EHR) databases because it is a symptom rather than a pathologic diagnosis. The first step in studying NP in EHR databases is to develop methods for identifying patients with NP. The objectives of this study were to develop estimates of the prevalence of NP among patients in a primary care EHR database and describe these patients' demographic characteristics and health-care utilization. METHODS: This was a retrospective cohort study of de-identified data from a 5-year period (2005-2010) from 23 general practitioners (GPs) in 10 primary care practices in southwestern Ontario, Canada. International Classification of Diseases version 9 (ICD-9) diagnostic codes and medication prescriptions were used to identify patients with certain and probable NP. RESULTS: Different methods produced prevalence estimates ranging from 1.5% (for certain NP in the epidemiologically rigorous period cohort) to 11.2% (for certain NP + probable NP in the more inclusive database cohort). Patients in the NP groups had more GP visits, specialist referrals and analgesic prescriptions than patients without NP. CONCLUSION: This study represents a step towards being able to utilize EHR databases to study NP by proposing methods to identify patients with certain and probable NP in a primary care EHR database. Validation against a gold standard is the next step.

Assessing upstream fish passage connectivity with network analysis.

Hydrologic connectivity is critical to the structure, function, and dynamic process of river ecosystems. Dams, road crossings, and water diversions impact connectivity by altering flow regimes, behavioral cues, local geomorphology, and nutrient cycling. This longitudinal fragmentation of river ecosystems also increases genetic and reproductive isolation of aquatic biota such as migratory fishes. The cumulative effects on fish passage of many structures along a river are often substantial, even when individual barriers have negligible impact. Habitat connectivity can be improved through dam removal or other means of fish passage improvement (e.g., ladders, bypasses, culvert improvement). Environmental managers require techniques for comparing alternative fish passage restoration actions at alternative or multiple locations. Herein, we examined a graph-theoretic algorithm for assessing upstream habitat connectivity to investigate both basic and applied fish passage connectivity problems. First, we used hypothetical watershed configurations to assess general alterations to upstream fish passage connectivity with changes in watershed network topology (e.g., linear vs. highly dendritic) and the quantity, location, and passability of each barrier. Our hypothetical network modeling indicates that locations of dams with limited passage efficiency near the watershed outlet create a strong fragmentation signal but are not individually sufficient to disconnect the system. Furthermore, there exists a threshold in the number of dams beyond which connectivity declines precipitously, regardless of watershed topology and dam configuration. Watersheds with highly branched configurations are shown to be less susceptible to disconnection as measured by this metric. Second, we applied the model to prioritize barrier improvement in the mainstem of the Truckee River, Nevada, USA. The Truckee River application demonstrates the ability of the algorithm to address conditions common in fish passage projects including incomplete data, parameter uncertainty, and rapid application. This study demonstrates the utility of a graph-theoretic approach for assessing fish passage connectivity in dendritic river networks assuming full basin utilization for a given species, guild, or community of concern.

Rhizosphere bacterial communities associated with long-lived perennial prairie plants vary in diversity, composition, and structure.

The goal of this research was to investigate the variation in rhizosphere microbial community composition, diversity, and structure among individual Andropogon gerardii Vitman (big bluestem) and Lespedeza capitata Michx. (bush clover). Bacterial communities from the rhizosphere of 10 plants of each species (n = 20 plants total) were explored using a culture-independent pipeline. Microbial communities associated with both host plants had high bacterial diversity within individual plant rhizosphere and taxa unique to individual rhizospheres. Bacterial communities associated with the rhizosphere of A. gerardii were consistently more diverse than those associated with L. capitata, and there were significant differences between plant species in rhizosphere bacterial community composition. Differences included microbial taxa with no known functional relationship with their preferred host species, including sulfide-methylating obligate anaerobes (Holophaga), complete denitrifiers (Rhodoplanes), sludge inhabitants (Ktedonobacter), and nitrate oxidizers (Nitrospira). These results suggest the potential for plant species to have significant impacts on a broad array of ecosystem functions (e.g., cycling of carbon, nitrogen sulfurs, metals, and trace elements) via their selective impacts on soil microbes. However, sequence-based community analysis and the corresponding lack of intact microbial cultures limits understanding of the potential influences of enriched microbial taxa on plant hosts and their roles in ecosystem functioning.

TCN 201 selectively blocks GluN2A-containing NMDARs in a GluN1 co-agonist dependent but non-competitive manner.

Antagonists that are sufficiently selective to preferentially block GluN2A-containing N-methyl-d-aspartate receptors (NMDARs) over GluN2B-containing NMDARs are few in number. In this study we describe a pharmacological characterization of 3-chloro-4-fluoro-N-[4-[[2-(phenylcarbonyl)hydrazino]carbonyl]benzyl]benzenesulphonamide (TCN 201), a sulphonamide derivative, that was recently identified from a high-throughput screen as a potential GluN2A-selective antagonist. Using two-electrode voltage-clamp (TEVC) recordings of NMDAR currents from Xenopus laevis oocytes expressing either GluN1/GluN2A or GluN1/GluN2B NMDARs we demonstrate the selective antagonism by TCN 201 of GluN2A-containing NMDARs. The degree of inhibition produced by TCN 201 is dependent on the concentration of the GluN1-site co-agonist, glycine (or D-serine), and is independent of the glutamate concentration. This GluN1 agonist-dependency is similar to that observed for a related GluN2A-selective antagonist, N-(cyclohexylmethyl)-2-[{5-[(phenylmethyl)amino]-1,3,4-thiadiazol-2-yl}thio]acetamide (TCN 213). Schild analysis of TCN 201 antagonism indicates that it acts in a non-competitive manner but its equilibrium constant at GluN1/GluN2A NMDARs indicates TCN 201 is around 30-times more potent than TCN 213. In cortical neurones TCN 201 shows only modest antagonism of NMDAR-mediated currents recorded from young (DIV 9-10) neurones where GluN2B expression predominates. In older cultures (DIV 15-18) or in cultures where GluN2A subunits have been over-expressed TCN 201 gives a strong block that is negatively correlated with the degree of block produced by the GluN2B-selective antagonist, ifenprodil. Nevertheless, while TCN 201 is a potent antagonist it must be borne in mind that its ability to block GluN2A-containing NMDARs is dependent on the GluN1-agonist concentration and is limited by its low solubility.

Genome-wide association analysis for quantitative trait loci influencing Warner-Bratzler shear force in five taurine cattle breeds.

We performed a genome-wide association study for Warner-Bratzler shear force (WBSF), a measure of meat tenderness, by genotyping 3360 animals from five breeds with 54 790 BovineSNP50 and 96 putative single-nucleotide polymorphisms (SNPs) within µ-calpain [HUGO nomenclature calpain 1, (mu/I) large subunit; CAPN1] and calpastatin (CAST). Within- and across-breed analyses estimated SNP allele substitution effects (ASEs) by genomic best linear unbiased prediction (GBLUP) and variance components by restricted maximum likelihood under an animal model incorporating a genomic relationship matrix. GBLUP estimates of ASEs from the across-breed analysis were moderately correlated (0.31-0.66) with those from the individual within-breed analyses, indicating that prediction equations for molecular estimates of breeding value developed from across-breed analyses should be effective for genomic selection within breeds. We identified 79 genomic regions associated with WBSF in at least three breeds, but only eight were detected in all five breeds, suggesting that the within-breed analyses were underpowered, that different quantitative trait loci (QTL) underlie variation between breeds or that the BovineSNP50 SNP density is insufficient to detect common QTL among breeds. In the across-breed analysis, CAPN1 was followed by CAST as the most strongly associated WBSF QTL genome-wide, and associations with both were detected in all five breeds. We show that none of the four commercialized CAST and CAPN1 SNP diagnostics are causal for associations with WBSF, and we putatively fine-map the CAPN1 causal mutation to a 4581-bp region. We estimate that variation in CAST and CAPN1 explains 1.02 and 1.85% of the phenotypic variation in WBSF respectively.