Restoring the eastern oyster: how much progress has been made in 53 years?

Coastal ecosystem restoration is accelerating globally as a means of enhancing shoreline protection, carbon storage, water quality, fisheries, and biodiversity. Among the most substantial of these efforts have been those focused on re-establishing oyster reefs across the US Atlantic and Gulf coasts. Despite considerable investment, it is unclear how the scale of and approaches toward oyster restoration have evolved. A synthesis of 1768 projects undertaken since 1964 reveals that oyster substrate restoration efforts have primarily been concentrated in the Chesapeake Bay and the Gulf Coast, have been heavily reliant on oyster shell, and have re-established 4.5% of the reef area that has been lost across all regions. By comparing costs to ecosystem service benefits, we discovered that the return-on-investment of oyster restoration varies widely, but generally increases with project size. To facilitate the recovery of coastal ecosystems and their services, scientists and resource managers must adopt a new restoration paradigm prioritizing investment in sites that maximize economic and ecological benefits and minimize construction costs

Caryoscope: An Open Source Java application for viewing microarray data in a genomic context

BACKGROUND: Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context. RESULTS: We have developed Caryoscope, which is an open source Java application for visualizing microarray data from array comparative genome hybridization experiments in a genomic context. Caryoscope can read General Feature Format files (GFF files), as well as comma- and tab-delimited files, that define the genomic positions of the microarray reporters for which data are obtained. The microarray data can be browsed using an interactive, zoomable interface, which helps users identify regions of chromosomal deletion or amplification. The graphical representation of the data can be exported in a number of graphic formats, including publication-quality formats such as PostScript. CONCLUSION: Caryoscope is a useful tool that can aid in the visualization, exploration and interpretation of microarray data in a genomic context

A Marine Growth Detection System for Underwater Gliders

Marine growth has been observed to cause a drop in the horizontal and vertical velocities of underwater gliders, thus making them unresponsive and needing immediate recovery. Currently, no strategies exist to correctly identify the onset of marine growth for gliders and only limited data sets of biofouled hulls exist. Here, a field test has been conducted to first investigate the impact of marine growth on the dynamics and power consumption of underwater gliders and then design an anomaly detection system for high levels of biofouling. A Slocum glider was deployed first for eight days with drag stimulators to imitate severe biofouling; then, the vehicle was redeployed with no additions to the hull for further 20 days. The mimicked biofouling caused a speed reduction due to a significant increase in drag. Additionally, the lower speed causes the steady-state flight stage to last longer and the rudder to become less responsive; hence, marine growth results in a shortening of deployment duration through an increase in power consumption. As actual biofouling due to p. pollicipes occurred during the second deployment, it is possible to develop and test a system that successfully detects and identifies high levels of marine growth on the glider, blending model- and data-based solutions using steady-state flight data. The system will greatly help pilots replan missions to safely recover the vehicle if significant biofouling is detected

CCAAT-enhancer-binding protein-beta expression in vivo is associated with muscle strength

This is a freely-available open access publication. Please cite the published version which is available via the DOI link in this record.Declining muscle strength is a core feature of aging. Several mechanisms have been postulated, including CCAAT/enhancer-binding protein-beta (C/EBP-β)-triggered macrophage-mediated muscle fiber regeneration after micro-injury, evidenced in a mouse model. We aimed to identify in vivo circulating leukocyte gene expression changes associated with muscle strength in the human adult population. We undertook a genome-wide expression microarray screen, using peripheral blood RNA samples from InCHIANTI study participants (aged 30 and 104). Logged expression intensities were regressed with muscle strength using models adjusted for multiple confounders. Key results were validated by real-time PCR. The Short Physical Performance Battery (SPPB) score tested walk speed, chair stand, and balance. CEBPB expression levels were associated with muscle strength (β coefficient = 0.20560, P = 1.03*10(-6), false discovery rate q = 0.014). The estimated handgrip strength in 70-year-old men in the lowest CEBPB expression tertile was 35.2 kg compared with 41.2 kg in the top tertile. CEBPB expression was also associated with hip, knee, ankle, and shoulder strength and the SPPB score (P = 0.018). Near-study-wide associations were also noted for TGF-β3 (P = 3.4*10(-5) , q = 0.12) and CEBPD expression (P = 9.7*10(-5) , q = 0.18) but not for CEBPA expression. We report here a novel finding that raised CEBPB expression in circulating leukocyte-derived RNA samples in vivo is associated with greater muscle strength and better physical performance in humans. This association may be consistent with mouse model evidence of CEBPB-triggered muscle repair: if this mechanism is confirmed, it may provide a target for intervention to protect and enhance aging muscle

Correlation functions of three heavy operators - the AdS contribution

We consider operators in N=4 SYM theory which are dual, at strong coupling, to classical strings rotating in S^5. Three point correlation functions of such operators factorize into a universal contribution coming from the AdS part of the string sigma model and a state-dependent S^5 contribution. Consequently a similar factorization arises for the OPE coefficients. In this paper we evaluate the AdS universal factor of the OPE coefficients which is explicitly expressed just in terms of the anomalous dimensions of the three operators.Comment: 49 pages, 3 figures; v.2 references corrected; v3: corrected discussion in section 5, results unchange

Genome Wide Assessment of Young Onset Parkinson's Disease from Finland

In the current study we undertook a series of experiments to test the hypothesis that a monogenic cause of disease may be detectable within a cohort of Finnish young onset Parkinson’s disease patients. In the first instance we performed standard genome wide association analyses, and subsequent risk profile analysis. In addition we performed a series of analyses that involved testing measures of global relatedness within the cases compared to controls, searching for excess homozygosity in the cases, and examining the cases for signs of excess local genomic relatedness using a sliding window approach. This work suggested that the previously identified common, low risk alleles, and the risk models associated with these alleles, were generalizable to the Finnish Parkinson’s disease population. However, we found no evidence that would suggest a single common high penetrance mutation exists in this cohort of young onset patients

Next-generation sequencing reveals substantial genetic contribution to dementia with Lewy bodies

Dementia with Lewy bodies (DLB) is the second most common neurodegenerative dementia after Alzheimer's disease. Although an increasing number of genetic factors have been connected to this debilitating condition, the proportion of cases that can be attributed to distinct genetic defects is unknown. To provide a comprehensive analysis of the frequency and spectrum of pathogenic missense mutations and coding risk variants in nine genes previously implicated in DLB, we performed exome sequencing in 111 pathologically confirmed DLB patients. All patients were Caucasian individuals from North America. Allele frequencies of identified missense mutations were compared to 222 control exomes. Remarkably, ~ 25% of cases were found to carry a pathogenic mutation or risk variant in APP, GBA or PSEN1, highlighting that genetic defects play a central role in the pathogenesis of this common neurodegenerative disorder. In total, 13% of our cohort carried a pathogenic mutation in GBA, 10% of cases carried a risk variant or mutation in PSEN1, and 2% were found to carry an APP mutation. The APOE ε4 risk allele was significantly overrepresented in DLB patients (p-value < 0.001). Our results conclusively show that mutations in GBA, PSEN1, and APP are common in DLB and consideration should be given to offer genetic testing to patients diagnosed with Lewy body dementia

Sustainable bio-economy that delivers the environment-food-energy-water nexus objectives::the current status in Malaysia

Biomass is a promising resource in Malaysia for energy, fuels, and high value-added products. However, regards to biomass value chains, the numerous restrictions and challenges related to the economic and environmental features must be considered. The major concerns regarding the enlargement of biomass plantation is that it requires large amounts of land and environmental resources such as water and soil that arises the danger of creating severe damages to the ecosystem (e.g. deforestation, water pollution, soil depletion etc.). Regarded concerns can be diminished when all aspects associated with palm biomass conversion and utilization linked with environment, food, energy and water (EFEW) nexus to meet the standard requirement and to consider the potential impact on the nexus as a whole. Therefore, it is crucial to understand the detail interactions between all the components in the nexus once intended to look for the best solution to exploit the great potential of biomass. This paper offers an overview regarding the present potential biomass availability for energy production, technology readiness, feasibility study on the techno-economic analyses of the biomass utilization and the impact of this nexus on value chains. The agro-biomass resources potential and land suitability for different crops has been overviewed using satellite imageries and the outcomes of the nexus interactions should be incorporated in developmental policies on biomass. The paper finally discussed an insight of digitization of the agriculture industry as future strategy to modernize agriculture in Malaysia. Hence, this paper provides holistic overview of biomass competitiveness for sustainable bio-economy in Malaysia

Menopause accelerates biological aging

Although epigenetic processes have been linked to aging and disease in other systems, it is not yet known whether they relate to reproductive aging. Recently, we developed a highly accurate epigenetic biomarker of age (known as the “epigenetic clock”), which is based on DNA methylation levels. Here we carry out an epigenetic clock analysis of blood, saliva, and buccal epithelium using data from four large studies: the Women's Health Initiative (n = 1,864); Invecchiare nel Chianti (n = 200); Parkinson's disease, Environment, and Genes (n = 256); and the United Kingdom Medical Research Council National Survey of Health and Development (n = 790). We find that increased epigenetic age acceleration in blood is significantly associated with earlier menopause (P = 0.00091), bilateral oophorectomy (P = 0.0018), and a longer time since menopause (P = 0.017). Conversely, epigenetic age acceleration in buccal epithelium and saliva do not relate to age at menopause; however, a higher epigenetic age in saliva is exhibited in women who undergo bilateral oophorectomy (P = 0.0079), while a lower epigenetic age in buccal epithelium was found for women who underwent menopausal hormone therapy (P = 0.00078). Using genetic data, we find evidence of coheritability between age at menopause and epigenetic age acceleration in blood. Using Mendelian randomization analysis, we find that two SNPs that are highly associated with age at menopause exhibit a significant association with epigenetic age acceleration. Overall, our Mendelian randomization approach and other lines of evidence suggest that menopause accelerates epigenetic aging of blood, but mechanistic studies will be needed to dissect cause-and-effect relationships further