Unifying models have shown that the amount of space used by animals (e.g., activity space, home range) scales allometrically with body mass for terrestrial taxa; however, such relationships are far ...less clear for marine species. We compiled movement data from 1,596 individuals across 79 taxa collected using a continental passive acoustic telemetry network of acoustic receivers to assess allometric scaling of activity space. We found that ectothermic marine taxa do exhibit allometric scaling for activity space, with an overall scaling exponent of 0.64. However, body mass alone explained only 35% of the variation, with the remaining variation best explained by trophic position for teleosts and latitude for sharks, rays, and marine reptiles. Taxon-specific allometric relationships highlighted weaker scaling exponents among teleost fish species (0.07) than sharks (0.96), rays (0.55), and marine reptiles (0.57). The allometric scaling relationship and scaling exponents for the marine taxonomic groups examined were lower than those reported from studies that had collated both marine and terrestrial species data derived using various tracking methods. We propose that these disparities arise because previous work integrated summarized data across many studies that used differing methods for collecting and quantifying activity space, introducing considerable uncertainty into slope estimates. Our findings highlight the benefit of using large-scale, coordinated animal biotelemetry networks to address cross-taxa evolutionary and ecological questions.
Projections of the sea level contribution from the Greenland and Antarctic ice sheets rely on atmospheric and oceanic drivers obtained from climate models. The Earth System Models participating in ...the Coupled Model Intercomparison Project phase 6 (CMIP6) generally project greater future warming compared with the previous CMIP5 effort. Here we use four CMIP6 models and a selection of CMIP5 models to force multiple ice sheet models as part of the Ice Sheet Model Intercomparison Project for CMIP6 (ISMIP6). We find that the projected sea level contribution at 2100 from the ice sheet model ensemble under the CMIP6 scenarios falls within the CMIP5 range for the Antarctic ice sheet but is significantly increased for Greenland. Warmer atmosphere in CMIP6 models results in higher Greenland mass loss due to surface melt. For Antarctica, CMIP6 forcing is similar to CMIP5 and mass gain from increased snowfall counteracts increased loss due to ocean warming.
Falciparum malaria is clinically heterogeneous and the relative contribution of parasite and host in shaping disease severity remains unclear. We explored the interaction between inflammation and ...parasite variant surface antigen (VSA) expression, asking whether this relationship underpins the variation observed in controlled human malaria infection (CHMI). We uncovered marked heterogeneity in the host response to blood challenge; some volunteers remained quiescent, others triggered interferon-stimulated inflammation and some showed transcriptional evidence of myeloid cell suppression. Significantly, only inflammatory volunteers experienced hallmark symptoms of malaria. When we tracked temporal changes in parasite VSA expression to ask whether variants associated with severe disease rapidly expand in naive hosts, we found no transcriptional evidence to support this hypothesis. These data indicate that parasite variants that dominate severe malaria do not have an intrinsic growth or survival advantage; instead, they presumably rely upon infection-induced changes in their within-host environment for selection.
Background
Melanoma accounts for a small proportion of all skin cancer cases but is responsible for most skin cancer‐related deaths. Early detection and treatment can improve survival. Smartphone ...applications are readily accessible and potentially offer an instant risk assessment of the likelihood of malignancy so that the right people seek further medical attention from a clinician for more detailed assessment of the lesion. There is, however, a risk that melanomas will be missed and treatment delayed if the application reassures the user that their lesion is low risk.
Objectives
To assess the diagnostic accuracy of smartphone applications to rule out cutaneous invasive melanoma and atypical intraepidermal melanocytic variants in adults with concerns about suspicious skin lesions.
Search methods
We undertook a comprehensive search of the following databases from inception to August 2016: Cochrane Central Register of Controlled Trials; MEDLINE; Embase; CINAHL; CPCI; Zetoc; Science Citation Index; US National Institutes of Health Ongoing Trials Register; NIHR Clinical Research Network Portfolio Database; and the World Health Organization International Clinical Trials Registry Platform. We studied reference lists and published systematic review articles.
Selection criteria
Studies of any design evaluating smartphone applications intended for use by individuals in a community setting who have lesions that might be suspicious for melanoma or atypical intraepidermal melanocytic variants versus a reference standard of histological confirmation or clinical follow‐up and expert opinion.
Data collection and analysis
Two review authors independently extracted all data using a standardised data extraction and quality assessment form (based on QUADAS‐2). Due to scarcity of data and poor quality of studies, we did not perform a meta‐analysis for this review. For illustrative purposes, we plotted estimates of sensitivity and specificity on coupled forest plots for each application under consideration.
Main results
This review reports on two cohorts of lesions published in two studies. Both studies were at high risk of bias from selective participant recruitment and high rates of non‐evaluable images. Concerns about applicability of findings were high due to inclusion only of lesions already selected for excision in a dermatology clinic setting, and image acquisition by clinicians rather than by smartphone app users.
We report data for five mobile phone applications and 332 suspicious skin lesions with 86 melanomas across the two studies. Across the four artificial intelligence‐based applications that classified lesion images (photographs) as melanomas (one application) or as high risk or 'problematic' lesions (three applications) using a pre‐programmed algorithm, sensitivities ranged from 7% (95% CI 2% to 16%) to 73% (95% CI 52% to 88%) and specificities from 37% (95% CI 29% to 46%) to 94% (95% CI 87% to 97%). The single application using store‐and‐forward review of lesion images by a dermatologist had a sensitivity of 98% (95% CI 90% to 100%) and specificity of 30% (95% CI 22% to 40%).
The number of test failures (lesion images analysed by the applications but classed as 'unevaluable' and excluded by the study authors) ranged from 3 to 31 (or 2% to 18% of lesions analysed). The store‐and‐forward application had one of the highest rates of test failure (15%). At least one melanoma was classed as unevaluable in three of the four application evaluations.
Authors' conclusions
Smartphone applications using artificial intelligence‐based analysis have not yet demonstrated sufficient promise in terms of accuracy, and they are associated with a high likelihood of missing melanomas. Applications based on store‐and‐forward images could have a potential role in the timely presentation of people with potentially malignant lesions by facilitating active self‐management health practices and early engagement of those with suspicious skin lesions; however, they may incur a significant increase in resource and workload. Given the paucity of evidence and low methodological quality of existing studies, it is not possible to draw any implications for practice. Nevertheless, this is a rapidly advancing field, and new and better applications with robust reporting of studies could change these conclusions substantially.
The Wellcome Trust Case Control Consortium (WTCCC) primary genome-wide association (GWA) scan on seven diseases, including the multifactorial autoimmune disease type 1 diabetes (T1D), shows ...associations at P < 5 × 10−7 between T1D and six chromosome regions: 12q24, 12q13, 16p13, 18p11, 12p13 and 4q27. Here, we attempted to validate these and six other top findings in 4,000 individuals with T1D, 5,000 controls and 2,997 family trios independent of the WTCCC study. We confirmed unequivocally the associations of 12q24, 12q13, 16p13 and 18p11 (Pfollow-up ≤ 1.35 × 10−9; Poverall ≤ 1.15 × 10−14), leaving eight regions with small effects or false-positive associations. We also obtained evidence for chromosome 18q22 (Poverall = 1.38 × 10−8) from a GWA study of nonsynonymous SNPs. Several regions, including 18q22 and 18p11, showed association with autoimmune thyroid disease. This study increases the number of T1D loci with compelling evidence from six to at least ten.
The methylation of DNA bases plays an important role in numerous biological processes including development, gene expression, and DNA replication. Salmonella is an important foodborne pathogen, and ...methylation in Salmonella is implicated in virulence. Using single molecule real-time (SMRT) DNA-sequencing, we sequenced and assembled the complete genomes of eleven Salmonella enterica isolates from nine different serovars, and analysed the whole-genome methylation patterns of each genome. We describe 16 distinct N6-methyladenine (m6A) methylated motifs, one N4-methylcytosine (m4C) motif, and one combined m6A-m4C motif. Eight of these motifs are novel, i.e., they have not been previously described. We also identified the methyltransferases (MTases) associated with 13 of the motifs. Some motifs are conserved across all Salmonella serovars tested, while others were found only in a subset of serovars. Eight of the nine serovars contained a unique methylated motif that was not found in any other serovar (most of these motifs were part of Type I restriction modification systems), indicating the high diversity of methylation patterns present in Salmonella.
Opportunities for timely recognition of chronic limb-threatening ischaemia (CLTI) within primary care, such as performing cardiovascular assessment during clinical consultation, are possibly being ...missed. This study aimed to investigate for potential “missed opportunities” within primary care.
This was a population based cohort study, using the UK's Clinical Practice Research Datalink (CPRD). Patients undergoing a major amputation for CLTI between 1 January 2000 and 31 December 2016 were included. Primary care consultation and patient clinical data within the one year period prior to amputation were extracted from the CPRD. Dates of last primary care consultation and cardiovascular assessment prior to amputation were evaluated. Timings of latest cardiovascular assessments were stratified into “recent” (7–90 days before amputation) and “late” (> 91 days).
In total, 3 260 patients were included. In the year prior to amputation, patients attended a median of 19 (range 9–32) primary care consultations; however, prescription of secondary preventive medications was poor (antiplatelet 49.7%; lipid lowering agent 40.7%). Overall, 2 175 patients (66.7%) attended a primary care consultation 7–30 days before their amputation. However, only 416 (12.8%) underwent a cardiovascular assessment within this period, with 2 073 (63.6%) undergoing no assessment within 90 days of their amputation. Of these 2 073 patients, 1 230 (59.3%) had a primary care consultation 7–30 days before their procedure. Patients undergoing “late” assessment were younger (p = .003), with higher systolic (p = .008) and diastolic (p = .001) blood pressures than those undergoing “recent” assessment. Differences were also observed between assessment timings by deprivation (p = .003) and ethnicity (p = .006).
Missed opportunities for timely recognition potentially exist and may be related to age, deprivation, and ethnicity. Further work is required to investigate these factors, as well as individual amputations to identify the causes precipitating amputation. Greater emphasis on the medical management of peripheral arterial disease and identifying cardiovascular risk factors in patients who may not fit the “at risk” stereotype, are also required.
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•Fifteen novel 3,5-substituted pyrazoles were synthesised via one-pot cyclic oxidation.•The antibacterial activities of each compound were assessed, identifying the hit compound 7p at ...MIC 8 µg/mL.•The compound is non-toxic against healthy mammalian cells, 3T3-L1 at the highest test concentration of 50 µg/mL.•Compound 7p significantly affected bacterial morphogenesis before cell lysis in Bacillus subtilis when treated above the MIC concentration.
The emergence of multi-drug resistant bacteria has increased the need for novel antibiotics to help overcome what may be considered the greatest threat to modern medicine. Here we report the synthesis of fifteen novel 3,5-diaryl-1H- pyrazoles obtained via one-pot cyclic oxidation of a chalcone and hydrazine-monohydrate. The synthesised pyrazoles were then screened against Staphylococcus aureus and Escherichia coli to determine their antibacterial potential. The results show that compound 7p is bacteriostatic at MIC 8 µg/mL. The compound is non-toxic against healthy mammalian cells, 3T3-L1 at the highest test concentration 50 µg/mL. Furthermore, compound 7p significantly affected bacterial morphogenesis before cell lysis in Bacillus subtilis when treated above the MIC concentration. From the results, a promising lead compound was identified for future development.
Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for ...processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses.
We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software.
PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library .
erin.baker@pnnl.gov or thomas.metz@pnnl.gov.
Supplementary data are available at Bioinformatics online.
This study used Magnetic Resonance Spectroscopy (MRS) to identify potential neurometabolitic markers of cognitive performance in male (n = 7) and female (n = 8) middle-aged (∼5 years old) common ...marmosets (Callithrix jacchus). Anesthetized marmosets were scanned with a 4.7 T/40 cm horizontal magnet equipped with 450 mT/m magnetic field gradients and a 20 G/cm magnetic field gradient insert, within 3 months of completing the CANTAB serial Reversal Learning task. Neurometabolite concentrations of N-Acetyl Asparate, Myo-Inositol, Choline, Phosphocreatine + creatine, Glutamate and Glutamine were acquired from a 3 mm3 voxel positioned in the Prefrontal Cortex (PFC). Males acquired the reversals (but not simple discriminations) faster than the females. Higher PFC Glx (glutamate + glutamine) concentration was associated with faster acquisition of the reversals. Interestingly, the correlation between cognitive performance and Glx was significant in males, but not in females. These results suggest that MRS is a useful tool to identify biochemical markers of cognitive performance in the healthy nonhuman primate brain and that biological sex modulates the relationship between neurochemical composition and cognition.
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