Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets

AbstractPublicly available molecular datasets can be used for independent verification or investigative repurposing, but depends on the presence, consistency and quality of descriptive annotations. Annotation and indexing of molecular datasets using well-defined controlled vocabularies or ontologies enables accurate and systematic data discovery, yet the majority of molecular datasets available through public data repositories lack such annotations. A number of automated annotation methods have been developed; however few systematic evaluations of the quality of annotations supplied by application of these methods have been performed using annotations from standing public data repositories. Here, we compared manually-assigned Medical Subject Heading (MeSH) annotations associated with experiments by data submitters in the PRoteomics IDEntification (PRIDE) proteomics data repository to automated MeSH annotations derived through the National Center for Biomedical Ontology Annotator and National Library of Medicine MetaMap programs. These programs were applied to free-text annotations for experiments in PRIDE. As many submitted datasets were referenced in publications, we used the manually curated MeSH annotations of those linked publications in MEDLINE as “gold standard”. Annotator and MetaMap exhibited recall performance 3-fold greater than that of the manual annotations. We connected PRIDE experiments in a network topology according to shared MeSH annotations and found 373 distinct clusters, many of which were found to be biologically coherent by network analysis. The results of this study suggest that both Annotator and MetaMap are capable of annotating public molecular datasets with a quality comparable, and often exceeding, that of the actual data submitters, highlighting a continuous need to improve and apply automated methods to molecular datasets in public data repositories to maximize their value and utility

Neuromuscular electrical stimulation and dietary interventions to reduce oxidative stress in a secondary progressive multiple sclerosis patient leads to marked gains in function: a case report

Neuromuscular electrical stimulation has been used to aid musculoskeletal recovery. Excessive oxidative stress and excitoxicity are implicated in secondary progressive multiple sclerosis. A 52-year-old white female with SPMS had been scooter- and cane-dependent for 4 years. She requested and received a trial of neuromuscular electrical stimulation. Two months after initiating NMES the patient adopted several nutritional interventions to lower oxidative stress and excito-toxicity. During the first 2 months of neuromuscular electrical stimulation, the therapist observed modest gait improvements. Following the addition of nutritional interventions, more rapids gains in strength and endurance, including muscle groups not receiving neuromuscular electrical stimulation were observed by both the therapist and the patient. After 8 months of neuromuscular electrical stimulation (6 months of nutritional intervention) the patient’s function had improved sufficiently that she no longer used a scooter or cane and rode her bicycle routinely 8 miles, including hills

Role of peripheral quantitative computed tomography in identifying disuse osteoporosis in paraplegia

Objective: Disuse osteoporosis is a major long-term health consequence of spinal cord injury (SCI) that still needs to be addressed. Its management in SCI should begin with accurate diagnosis, followed by targeted treatments in the most vulnerable subgroups. We present data quantifying disuse osteoporosis in a cross-section of the Scottish paraplegic population to identify subgroups with lowest bone mineral density (BMD). Materials and Methods: Forty-seven people with chronic SCI at levels T2-L2 were scanned using peripheral Quantitative Computed Tomography (pQCT) at four tibial sites and two femoral sites, at the Queen Elizabeth National Spinal Injuries Unit, Glasgow (U.K.). At the distal epiphyses, trabecular BMD (BMDtrab), total BMD, total bone cross-sectional area (CSA), and bone mineral content (BMC) were determined. In the diaphyses, cortical BMD, total bone CSA, cortical CSA, and BMC were calculated. Bone, muscle and fat CSAs were estimated in the lower leg and thigh. Results: BMDtrab decreased exponentially with time since injury, at different rates in the tibia and femur. At most sites, female paraplegics had significantly lower BMC, total bone CSA and muscle CSA than male paraplegics. Subjects with lumbar SCI tended to have lower bone values and smaller muscle CSAs than in thoracic SCI. Conclusion: At the distal epiphyses of the tibia and femur, there is generally a rapid and extensive reduction in BMDtrab after SCI. Female subjects, and those with lumbar SCI, tend to have lower bone values than males or those with thoracic SCI, respectively. Keywords: Bone loss, osteoporosis, paraplegia, peripheral Quantitative Computed Tomography, spinal cord injur

Methyl N,N‐dimethylanthranilate and ethyl propionate: repellents effective against spotted wing drosophila, Drosophila suzukii

BACKGROUND Spotted wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae), is an economically important pest of soft and stone fruit crops. The aim of this study was to identify repellents, formulated in dispensers, which could protect crops from D. suzukii. Fourteen potential repellents were screened against summer- and winter-morph D. suzukii through electroantennography and behavioural bioassays. Repellents effective in the laboratory were tested in polytunnels to determine their efficacy in reducing catches in fruit-baited traps. Further trials of three potential repellents were conducted to determine the distances over which repellent dispensers could reduce D. suzukii emergence in a strawberry crop. RESULTS All 14 chemicals screened were detected by the antennae of both D. suzukii morphs. Hexyl acetate and geosmin both elicited a significantly greater corrected EAG response in summer morphs than winter morphs. Summer-morph D. suzukii were repelled by butyl acetate, ethyl propionate, methyl N,N-dimethyl anthranilate, geosmin, methyl salicylate, DEET and benzaldehyde at one or more doses test in laboratory bioassays. Winter morphs were repelled by ethyl propionate, methyl anthranilate, methyl N,N-dimethyl anthranilate, DEET, benzaldehyde and butyl anthranilate at one or more of the doses tested in the laboratory. Ethyl propionate, methyl N,N-dimethylanthranilate and benzaldehyde repelled both morphs from fruit-baited traps in polytunnel trapping trials. Ethyl propionate and methyl N,N-dimethylanthranilate reduced emergence of D. suzukii in a strawberry crop over 3–5 m. CONCLUSIONS Ethyl propionate and methyl N,N-dimethylanthranilate may protect strawberry crops against D. suzukii. Future work should test these repellents in combination with attractants in a ‘push-pull’ strategy

Calorie restriction in humans inhibits the PI3K/AKT pathway and induces a younger transcription profile

Caloric restriction (CR) and down-regulation of the insulin/IGF pathway are the most robust interventions known to increase longevity in lower organisms. However, little is known about the molecular adaptations induced by CR in humans. Here, we report that long-term CR in humans inhibits the IGF-1/insulin pathway in skeletal muscle, a key metabolic tissue. We also demonstrate that CR induces dramatic changes of the skeletal muscle transcriptional profile that resemble those of younger individuals. Finally, in both rats and humans, CR evoked similar responses in the transcriptional profiles of skeletal muscle. This common signature consisted of three key pathways typically associated with longevity: IGF-1/insulin signaling, mitochondrial biogenesis, and inflammation. Furthermore, our data identify promising pathways for therapeutic targets to combat age-related diseases and promote health in humans.American Federation for Aging ResearchNational Center for Research Resources (U.S.) (Grant UL1 RR024992)National Institute of Diabetes and Digestive and Kidney Diseases (U.S.) (Grant P30DK056341

Drilling their own graves:How the European oil and gas supermajors avoid sustainability tensions through mythmaking

This study explores how paradoxical tensions between economic growth and environmental protection are avoided through organizational mythmaking. By examining the European oil and gas supermajors’ ‘‘CEOspeak’’ about climate change, we show how mythmaking facilitates the disregarding, diverting, and/or displacing of sustainability tensions. In doing so, our findings further illustrate how certain defensive responses are employed: (1) regression, or retreating to the comforts of past familiarities, (2) fantasy, or escaping the harsh reality that fossil fuels and climate change are indeed irreconcilable, and (3) projecting, or shifting blame to external actors for failing to address climate change. By highlighting the discursive effects of enacting these responses, we illustrate how the European oil and gas supermajors self-determine their inability to substantively address the complexities of climate change. We thus argue that defensive responses are not merely a form of mismanagement as the paradox and corporate sustainability literature commonly suggests, but a strategic resource that poses serious ethical concerns given the imminent danger of issues such as climate change

Mapping Primary Gyrogenesis During Fetal Development in Primate Brains: High-Resolution in Utero Structural MRI of Fetal Brain Development in Pregnant Baboons

The global and regional changes in the fetal cerebral cortex in primates were mapped during primary gyrification (PG; weeks 17–25 of 26 weeks total gestation). Studying pregnant baboons using high-resolution MRI in utero, measurements included cerebral volume, cortical surface area, gyrification index and length and depth of 10 primary cortical sulci. Seven normally developing fetuses were imaged in two animals longitudinally and sequentially. We compared these results to those on PG that from the ferret studies and analyzed them in the context of our recent studies of phylogenetics of cerebral gyrification. We observed that in both primates and non-primates, the cerebrum undergoes a very rapid transformation into the gyrencephalic state, subsequently accompanied by an accelerated growth in brain volume and cortical surface area. However, PG trends in baboons exhibited some critical differences from those observed in ferrets. For example, in baboons, the growth along the long (length) axis of cortical sulci was unrelated to the growth along the short (depth) axis and far outpaced it. Additionally, the correlation between the rate of growth along the short sulcal axis and heritability of sulcal depth was negative and approached significance (r = −0.60; p < 0.10), while the same trend for long axis was positive and not significant (p = 0.3; p = 0.40). These findings, in an animal that shares a highly orchestrated pattern of PG with humans, suggest that ontogenic processes that influence changes in sulcal length and depth are diverse and possibly driven by different factors in primates than in non-primates

Hero turned villain: Identification of components of the sex pheromone of the tomato bug, Nesidiocoris tenuis

Nesidiocoris tenuis (Reuter) (Heteroptera: Miridae) is a tropical mirid bug used as a biocontrol agent in protected crops, including tomatoes. Although N. tenuis predates important insect pests, especially whitefly, it also causes damage by feeding on tomato plants when prey populations decline, resulting in significant economic losses for growers. The pest is now established in some all-year-round tomato crops in Europe and control measures involve the application of pesticides which are incompatible with current IPM programs. As part of future IPM strategies, the pheromone of N. tenuis was investigated. Volatile collections were made from groups and individuals of mated and unmated, females and males. In analyses of these collections by gas chromatography coupled with electroantennographic (EAG) recording from antennae of male bugs, two EAG-active components were detected and identified as 1-octanol and octyl hexanoate. Unlike other mirids, both male and female N. tenuis produced the two compounds, before and after mating, and both sexes gave EAG responses to both compounds. Furthermore, only octyl hexanoate was detected in whole body solvent washes from both sexes. These compounds are not related to the derivatives of 3-hydroxybutyrate esters found as pheromone components in other members of the Bryocrinae sub-family, and the latter could not be detected in volatiles from N. tenuis and did not elicit EAG responses. Nevertheless, experiments carried out in commercial glasshouses showed that traps baited with a blend of the synthetic pheromone components caught essentially only male N. tenuis, and significantly more than traps baited with octyl hexanoate alone. The latter caught significantly more N. tenuis than unbaited traps which generally caught very few bugs. Traps at plant height caught more N. tenuis males than traps 1 m above or at the base of the plants. The trap catches provided an indication of population levels of N. tenuis and were greatly reduced following an application of insecticide