Organism-sediment interactions govern post-hypoxia recovery of ecosystem functioning

Hypoxia represents one of the major causes of biodiversity and ecosystem functioning loss for coastal waters. Since eutrophication-induced hypoxic events are becoming increasingly frequent and intense, understanding the response of ecosystems to hypoxia is of primary importance to understand and predict the stability of ecosystem functioning. Such ecological stability may greatly depend on the recovery patterns of communities and the return time of the system properties associated to these patterns. Here, we have examined how the reassembly of a benthic community contributed to the recovery of ecosystem functioning following experimentally-induced hypoxia in a tidal flat. We demonstrate that organism-sediment interactions that depend on organism size and relate to mobility traits and sediment reworking capacities are generally more important than recovering species richness to set the return time of the measured sediment processes and properties. Specifically, increasing macrofauna bioturbation potential during community reassembly significantly contributed to the recovery of sediment processes and properties such as denitrification, bedload sediment transport, primary production and deep pore water ammonium concentration. Such bioturbation potential was due to the replacement of the small-sized organisms that recolonised at early stages by large-sized bioturbating organisms, which had a disproportionately stronger influence on sediment. This study suggests that the complete recovery of organism-sediment interactions is a necessary condition for ecosystem functioning recovery, and that such process requires long periods after disturbance due to the slow growth of juveniles into adult stages involved in these interactions. Consequently, repeated episodes of disturbance at intervals smaller than the time needed for the system to fully recover organism-sediment interactions may greatly impair the resilience of ecosystem functioning.

The impact of trench defects in InGaN/GaN light emitting diodes and implications for the "green gap" problem

The impact of trench defects in blue InGaN/GaN light emitting diodes (LEDs) has been investigated. Two mechanisms responsible for the structural degradation of the multiple quantum well (MQW) active region were identified. It was found that during the growth of the p-type GaN capping layer, loss of part of the active region enclosed within a trench defect occurred, affecting the top-most QWs in the MQW stack. Indium platelets and voids were also found to form preferentially at the bottom of the MQW stack. The presence of high densities of trench defects in the LEDs was found to relate to a significant reduction in photoluminescence and electroluminescence emission efficiency, for a range of excitation power densities and drive currents. This reduction in emission efficiency was attributed to an increase in the density of non-radiative recombination centres within the MQW stack, believed to be associated with the stacking mismatch boundaries which form part of the sub-surface structure of the trench defects. Investigation of the surface of green-emitting QW structures found a two decade increase in the density of trench defects, compared to its blue-emitting counterpart, suggesting that the efficiency of green-emitting LEDs may be strongly affected by the presence of these defects. Our results are therefore consistent with a model that the “green gap” problem might relate to localized strain relaxation occurring through defects.This is the accepted manuscript version. The final version is available from AIP at http://scitation.aip.org/content/aip/journal/apl/105/11/10.1063/1.4896279?showFTTab=true&containerItemId=content/aip/journal/apl

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

BACKGROUND: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data was donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Nicaragua Block Press

Friends In Action International (FIA), our project partner, is assisting the Rama people of Nicaragua in relocating from an overpopulated island to the mainland. Our team has developed a manual press for the Rama people to produce compressed earth blocks from local materials for construction of their homes. After testing an initial prototype of the press in Nicaragua it was determined that the press needed more durability. After testing two presses with welded chambers manufactured by E&E Metal Fab Inc., further modifications were required such as welding chamber skirts, adding a lid handle, and applying rust prevention coating. Once both presses reached a workable state, the team made blocks using different mixtures to determine the composition for the highest strength. Blocks were tested for water absorption and for strength in compression, and met published standards for compressed earth blocks (CEB). The team also developed a user manual complete with manufacturing instructions, operating procedures, maintenance suggestions, and exploded subassembly views. Lastly, our team has drafted a one-page user guide for quick reference on-site and will deliver everything to FIA at the end of the semester.https://mosaic.messiah.edu/engr2020/1002/thumbnail.jp

β-Diversity and Species Accumulation in Antarctic Coastal Benthos: Influence of Habitat, Distance and Productivity on Ecological Connectivity

High Antarctic coastal marine environments are comparatively pristine with strong environmental gradients, which make them important places to investigate biodiversity relationships. Defining how different environmental features contribute to shifts in β-diversity is especially important as these shifts reflect both spatio-temporal variations in species richness and the degree of ecological separation between local and regional species pools. We used complementary techniques (species accumulation models, multivariate variance partitioning and generalized linear models) to assess how the roles of productivity, bio-physical habitat heterogeneity and connectivity change with spatial scales from metres to 100's of km. Our results demonstrated that the relative importance of specific processes influencing species accumulation and β–diversity changed with increasing spatial scale, and that patterns were never driven by only one factor. Bio-physical habitat heterogeneity had a strong influence on β-diversity at scales <290 km, while the effects of productivity were low and significant only at scales >40 km. Our analysis supports the emphasis on the analysis of diversity relationships across multiple spatial scales and highlights the unequal connectivity of individual sites to the regional species pool. This has important implications for resilience to habitat loss and community homogenisation, especially for Antarctic benthic communities where rates of recovery from disturbance are slow, there is a high ratio of poor-dispersing and brooding species, and high biogenic habitat heterogeneity and spatio-temporal variability in primary production make the system vulnerable to disturbance. Consequently, large areas need to be included within marine protected areas for effective management and conservation of these special ecosystems in the face of increasing anthropogenic disturbance

Adherence to best practice consensus guidelines for implant-based breast reconstruction: Results from the iBRA national practice questionnaire survey

Introduction: The 2008 National Mastectomy and Breast Reconstruction Audit demonstrated marked variation in the practice and outcomes of breast reconstruction in the UK. To standardise practice and improve outcomes for patients, the British professional associations developed best-practice guidelines with specific guidance for newer mesh-assisted implant-based techniques. We explored the degree of uptake of best-practice guidelines within units performing implant-based reconstruction (IBBR) as the first phase of the implant Breast Reconstruction Evaluation (iBRA) study. Methods: A questionnaire developed by the iBRA Steering Group was completed by trainee and consultant leads at breast and plastic surgical units across the UK. Simple summary statistics were calculated for each survey item to assess compliance with current best-practice guidelines. Results: 81 units from 79 NHS Trusts completed the questionnaire. Marked variation was observed in adherence to guidelines, especially those relating to clinical governance and infection prevention strategies. Less than half (n = 28, 47%) of units obtained local clinical governance board approval prior to offering new mesh-based techniques and prospective audit of the clinical, cosmetic and patient-reported outcomes of surgery was infrequent. Most units screened for methicillin-resistant staphylococcus aureus prior to surgery but fewer than 1 in 3 screened for methicillin-sensitive strains. Laminar-flow theatres (recommended for IBBR) were not widely-available with less than 1 in 5 units having regular access. Peri-operative antibiotics were widely-used, but the type and duration were highly-variable. Conclusions: The iBRA national practice questionnaire has demonstrated variation in reported practice and adherence to IBBR guidelines. High-quality evidence is urgently required to inform best practice

Effect of the UK government's 2-week target on waiting times in women with breast cancer in southeast England.

A government target of a maximum 2-week wait for women referred urgently with suspected breast cancer was introduced in April 1999. We have assessed changes in the distributions of waiting times and the proportions of cases meeting proposed targets before and after this date, using clinical audit data on 5750 women attending 19 hospitals in southeast England during the period July 1997-December 2000, who were subsequently found to have breast cancer. The proportion of cases being seen within 2 weeks of referral rose from 66.0 to 75.2%, and the median wait to first appointment fell from 13.6 to 12.3 days, following the introduction of the government target. The proportion of cases waiting 5 weeks or less between first hospital appointment and treatment fell from 83.8 to 80.3%, and median waits for treatment increased from 21.4 to 24.1 days. We also examined the effects on waiting times of various sociodemographic and care related factors. A total of 85.7% of screening cases vs 67.9% of symptomatic cases were seen within 2 weeks, and 95.0% of cases treated with tamoxifen received treatment within 5 weeks, as opposed to 77.6% of cases treated with surgery, 81.2% of chemotherapy cases and 52.8% of radiotherapy cases. While waiting times from GP referral to first hospital appointment have improved since the introduction of the government target, times from first appointment to treatment have increased, and consequently total waiting times have changed little

Pretreatment serum albumin as a predictor of cancer survival: A systematic review of the epidemiological literature

<p>Abstract</p> <p>Background</p> <p>There are several methods of assessing nutritional status in cancer of which serum albumin is one of the most commonly used. In recent years, the role of malnutrition as a predictor of survival in cancer has received considerable attention. As a result, it is reasonable to investigate whether serum albumin has utility as a prognostic indicator of cancer survival in cancer. This review summarizes all available epidemiological literature on the association between pretreatment serum albumin levels and survival in different types of cancer.</p> <p>Methods</p> <p>A systematic search of the literature using the MEDLINE database (January 1995 through June 2010) to identify epidemiologic studies on the relationship between serum albumin and cancer survival. To be included in the review, a study must have: been published in English, reported on data collected in humans with any type of cancer, had serum albumin as <it>one of the </it>or <it>only </it>predicting factor, had survival as one of the outcome measures (primary or secondary) and had any of the following study designs (case-control, cohort, cross-sectional, case-series prospective, retrospective, nested case-control, ecologic, clinical trial, meta-analysis).</p> <p>Results</p> <p>Of the 29 studies reviewed on cancers of the gastrointestinal tract, all except three found higher serum albumin levels to be associated with better survival in multivariate analysis. Of the 10 studies reviewed on lung cancer, all excepting one found higher serum albumin levels to be associated with better survival. In 6 studies reviewed on female cancers and multiple cancers each, lower levels of serum albumin were associated with poor survival. Finally, in all 8 studies reviewed on patients with other cancer sites, lower levels of serum albumin were associated with poor survival.</p> <p>Conclusions</p> <p>Pretreatment serum albumin levels provide useful prognostic significance in cancer. Accordingly, serum albumin level could be used in clinical trials to better define the baseline risk in cancer patients. A critical gap for demonstrating causality, however, is the absence of clinical trials demonstrating that raising albumin levels by means of intravenous infusion or by hyperalimentation decreases the excess risk of mortality in cancer.</p

Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2

The Omicron strains of SARS-CoV-2 pose a significant challenge to the development of effective antibody-based treatments as immune evasion has compromised most available immune therapeutics. Therefore, in the ‘arms race’ with the virus, there is a continuing need to identify new biologics for the prevention or treatment of SARS-CoV-2 infections. Here, we report the isolation of nanobodies that bind to the Omicron BA.1 spike protein by screening nanobody phage display libraries previously generated from llamas immunized with either the Wuhan or Beta spike proteins. The structure and binding properties of three of these nanobodies (A8, H6 and B5-5) have been characterized in detail providing insight into their binding epitopes on the Omicron spike protein. Trimeric versions of H6 and B5-5 neutralized the SARS-CoV-2 variant of concern BA.5 both in vitro and in the hamster model of COVID-19 following nasal administration. Thus, either alone or in combination could serve as starting points for the development of new anti-viral immunotherapeutics

Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2

The Omicron strains of SARS-CoV-2 pose a significant challenge to the development of effective antibody-based treatments as immune evasion has compromised most available immune therapeutics. Therefore, in the ‘arms race’ with the virus, there is a continuing need to identify new biologics for the prevention or treatment of SARS-CoV-2 infections. Here, we report the isolation of nanobodies that bind to the Omicron BA.1 spike protein by screening nanobody phage display libraries previously generated from llamas immunized with either the Wuhan or Beta spike proteins. The structure and binding properties of three of these nanobodies (A8, H6 and B5-5) have been characterized in detail providing insight into their binding epitopes on the Omicron spike protein. Trimeric versions of H6 and B5-5 neutralized the SARS-CoV-2 variant of concern BA.5 both in vitro and in the hamster model of COVID-19 following nasal administration. Thus, either alone or in combination could serve as starting points for the development of new anti-viral immunotherapeutics