Developmental Validation of Short Tandem Repeat Reagent Kit for Forensic DNA Profiling of Canine Biological Material

Aim To develop a reagent kit that enables multiplex polymerase chain reaction (PCR) amplification of 18 short tandem repeats (STR) and the canine sex-determining Zinc Finger marker. Methods Validation studies to determine the robustness and reliability in forensic DNA typing of this multiplex assay included sensitivity testing, reproducibility studies, intra- and inter-locus color balance studies, annealing temperature and cycle number studies, peak height ratio determination, characterization of artifacts such as stutter percentages and dye blobs, mixture analyses, species- specificity, case type samples analyses and population studies. Results The kit robustly amplified domesticated dog samples and consistently generated full 19-locus profiles from as little as 125 pg of dog DNA. In addition, wolf DNA samples could be analyzed with the kit. Conclusion The kit, which produces robust, reliable, and reproducible results, will be made available for the forensic research community after modifications based on this study’s evaluation to comply with the quality standards expected for forensic casework

Rebuttal to published article “A review of ghost gear entanglement amongst marine mammals, reptiles and elasmobranchs” by M. Stelfox, J. Hudgins, and M. Sweet

Author Posting. © The Author(s), 2016. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Marine Pollution Bulletin 117 (2017): 554-555, doi:10.1016/j.marpolbul.2016.11.052.We reviewed the findings of the recently published article by Stelfox et al. (2016): “A review of ghost gear entanglement amongst marine mammals, reptiles and elasmobranchs” published in this journal (Volume 111, pp 6–17) and found that they are both flawed and misleading as they do not accurately reflect the prevalence of “ghost gear” cases reported in the literature. While we commend the authors for recognizing the importance of attempting to quantify the threat and for recommending more comprehensive databases, the methods, results and conclusions of this review have not advanced the understanding of the issue. As authors of the papers on whale entanglements in the North Atlantic that were reviewed by Stelfox et al. (2016) and others who are knowledgeable about the topic, we provide specific comments regarding misrepresentations of both the source of entanglement (e.g., actively fished gear versus “ghost gear”) and the number of reported entanglements for whale species included in the North Atlantic

Don’t assume it’s ghost gear : accurate gear characterization is critical for entanglement mitigation [poster]

Presented at the Society for Marine Mammology 22nd Biennial Marine Mammal Conference, Halifax, Nova Scotia, October 23-27, 2017Entanglement is a significant conservation and welfare issue which is limiting the recovery of a number of marine species, including marine mammals. It is therefore important to reliably identify the causes of these events, including the nature of the entangling gear in order to reduce or prevent them in the future. A recently published review of marine debris assessed 76 publications and attributed a total of 1805 cases of cetacean entanglements in “ghost gear”, of which 78% (n=1413) were extracted from 13 peer reviewed publications. We examined the 13 publications cited in the review and found that the specific gear type or status of gear involved in the reported events was rarely mentioned beyond the fact that it was fishing related. This is likely due to the fact that determinations of debris as the entangling material are very difficult. In fact, in reviewing 10 years of large whale entanglement records for the U.S., the authors of another study reported that Hawaii was the only region in which any entangling gear was positively identified as ghost gear. The assumption that entangling gear is marine debris unless otherwise stated is dangerous because it could impact efforts to modify or restrict risk-prone fishing in key marine mammal habitats. Entanglement in actively fished gear poses a very real threat, and claims that only lost or abandoned fishing gear is responsible for entanglements can undermine conservation efforts.2017-10-2

High-Dimensional Menger-Type Curvatures-Part II: d-Separation and a Menagerie of Curvatures

This is the second of two papers wherein we estimate multiscale least squares approximations of certain measures by Menger-type curvatures. More specifically, we study an arbitrary d-regular measure on a real separable Hilbert space. The main result of the paper bounds the least squares error of approximation at any ball by an average of the discrete Menger-type curvature over certain simplices in in the ball. A consequent result bounds the Jones-type flatness by an integral of the discrete curvature over all simplices. The preceding paper provided the opposite inequalities. Furthermore, we demonstrate some other discrete curvatures for characterizing uniform rectifiability and additional continuous curvatures for characterizing special instances of the (p, q)-geometric property. We also show that a curvature suggested by Leger (Annals of Math, 149(3), p. 831-869, 1999) does not fit within our framework.Comment: 32 pages, no figure

Computational analysis of the evolutionarily conserved Missing In Metastasis/Metastasis Suppressor 1 gene predicts novel interactions, regulatory regions and transcriptional control

Missing in Metastasis (MIM), or Metastasis Suppressor 1 (MTSS1), is a highly conserved protein, which links the plasma membrane to the actin cytoskeleton. MIM has been implicated in various cancers, however, its modes of action remain largely enigmatic. Here, we performed an extensive in silico characterisation of MIM to gain better understanding of its function. We detected previously unappreciated functional motifs including adaptor protein (AP) complex interaction site and a C-helix, pointing to a role in endocytosis and regulation of actin dynamics, respectively. We also identified new functional regions, characterised with phosphorylation sites or distinct hydrophilic properties. Strong negative selection during evolution, yielding high conservation of MIM, has been combined with positive selection at key sites. Interestingly, our analysis of intra-molecular co-evolution revealed potential regulatory hotspots that coincided with reduced potentially pathogenic polymorphisms. We explored databases for the mutations and expression levels of MIM in cancer. Experimentally, we focused on chronic lymphocytic leukaemia (CLL), where MIM showed high overall expression, however, downregulation on poor prognosis samples. Finally, we propose strong conservation of MTSS1 also on the transcriptional level and predict novel transcriptional regulators. Our data highlight important targets for future studies on the role of MIM in different tissues and cancers

Emission Features and Source Counts of Galaxies in Mid-Infrared

In this work we incorporate the newest ISO results on the mid-infrared spectral-energy-distributions (MIR SEDs) of galaxies into models for the number counts and redshift distributions of MIR surveys. A three-component model, with empirically determined MIR SED templates of (1) a cirrus/PDR component (2) a starburst component and (3) an AGN component, is developed for infrared (3--120\micron) SEDs of galaxies. The model includes a complete IRAS 25\micron selected sample of 1406 local galaxies ($z \leq 0.1$; Shupe et al. 1998a). Results based on these 1406 spectra show that the MIR emission features cause significant effects on the redshift dependence of the K-corrections for fluxes in the WIRE 25\micron band and ISOCAM 15\micron band. This in turn will affect deep counts and redshift distributions in these two bands, as shown by the predictions of two evolution models (a luminosity evolution model with $L\propto (1+z)^3$ and a density evolution model with $\rho\propto (1+z)^4$). The dips-and-bumps on curves of MIR number counts, caused by the emission features, should be useful indicators of evolution mode. The strong emission features at $\sim 6$--8\micron will help the detections of relatively high redshift ($z\sim 2$) galaxies in MIR surveys. On the other hand, determinations of the evolutionary rate based on the slope of source counts, and studies on the large scale structures using the redshift distribution of MIR sources, will have to treat the effects of the MIR emission features carefully. We have also estimated a 15\micron local luminosity function from the predicted 15\micron fluxes of the 1406 galaxies using the bivariate (15\micron vs. 25\micron luminosities) method. This luminosity function will improve our understanding of the ISOCAM 15\micron surveys.Comment: 24 pages, 14 EPS figures. Accepted by Ap

Spatial and temporal scales of variability for indoor air constituents

Historically air constituents have been assumed to be well mixed in indoor environments, with single point measurements and box modeling representing a room or a house. Here we demonstrate that this fundamental assumption needs to be revisited through advanced model simulations and extensive measurements of bleach cleaning. We show that inorganic chlorinated products, such as hypochlorous acid and chloramines generated via multiphase reactions, exhibit spatial and vertical concentration gradients in a room, with short-lived ⋅OH radicals confined to sunlit zones, close to windows. Spatial and temporal scales of indoor constituents are modulated by rates of chemical reactions, surface interactions and building ventilation, providing critical insights for better assessments of human exposure to hazardous pollutants, as well as the transport of indoor chemicals outdoors

Garden and landscape-scale correlates of moths of differing conservation status: significant effects of urbanization and habitat diversity

Moths are abundant and ubiquitous in vegetated terrestrial environments and are pollinators, important herbivores of wild plants, and food for birds, bats and rodents. In recent years, many once abundant and widespread species have shown sharp declines that have been cited by some as indicative of a widespread insect biodiversity crisis. Likely causes of these declines include agricultural intensification, light pollution, climate change, and urbanization; however, the real underlying cause(s) is still open to conjecture. We used data collected from the citizen science Garden Moth Scheme (GMS) to explore the spatial association between the abundance of 195 widespread British species of moth, and garden habitat and landscape features, to see if spatial habitat and landscape associations varied for species of differing conservation status. We found that associations with habitat and landscape composition were species-specific, but that there were consistent trends in species richness and total moth abundance. Gardens with more diverse and extensive microhabitats were associated with higher species richness and moth abundance; gardens near to the coast were associated with higher richness and moth abundance; and gardens in more urbanized locations were associated with lower species richness and moth abundance. The same trends were also found for species classified as increasing, declining and vulnerable under IUCN (World Conservation Union) criteria

Human Serum Metabolites Associate With Severity and Patient Outcomes in Traumatic Brain Injury.

Traumatic brain injury (TBI) is a major cause of death and disability worldwide, especially in children and young adults. TBI is an example of a medical condition where there are still major lacks in diagnostics and outcome prediction. Here we apply comprehensive metabolic profiling of serum samples from TBI patients and controls in two independent cohorts. The discovery study included 144 TBI patients, with the samples taken at the time of hospitalization. The patients were diagnosed as severe (sTBI; n=22), moderate (moTBI; n=14) or mild TBI (mTBI; n=108) according to Glasgow Coma Scale. The control group (n=28) comprised of acute orthopedic non-brain injuries. The validation study included sTBI (n=23), moTBI (n=7), mTBI (n=37) patients and controls (n=27). We show that two medium-chain fatty acids (decanoic and octanoic acids) and sugar derivatives including 2,3-bisphosphoglyceric acid are strongly associated with severity of TBI, and most of them are also detected at high concentrations in brain microdialysates of TBI patients. Based on metabolite concentrations from TBI patients at the time of hospitalization, an algorithm was developed that accurately predicted the patient outcomes (AUC=0.84 in validation cohort). Addition of the metabolites to the established clinical model (CRASH), comprising clinical and computed tomography data, significantly improved prediction of patient outcomes. The identified 'TBI metabotype' in serum, that may be indicative of disrupted blood-brain barrier, of protective physiological response and altered metabolism due to head trauma, offers a new avenue for the development of diagnostic and prognostic markers of broad spectrum of TBIs.European Union FP7 project TBIcare (Grant ID: 270259), GE-NFL Head Health Challenge I Award (Grant ID: 7620), EVO (Finland), Maire Taponen Foundation, National Institute for Health Research, National Institute for Health Research Biomedical Research Centre Cambridge (Neuroscience Theme; Brain Injury and Repair Theme)This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.ebiom.2016.07.01