Marine plastics threaten giant Atlantic Marine Protected Areas

There has been a recent shift in global perception of plastics in the environment, resulting in a call for greater action. Science and the popular media have highlighted plastic as an increasing stressor [1,2]. Efforts have been made to confer protected status to some remote locations, forming some of the world's largest Marine Protected Areas, including several UK overseas territories. We assessed plastic at these remote Atlantic Marine Protected Areas, surveying the shore, sea surface, water column and seabed, and found drastic changes from 2013-2018. Working from the RRS James Clark Ross at Ascension, St. Helena, Tristan da Cunha, Gough and the Falkland Islands (Figure 1A), we showed that marine debris on beaches has increased more than 10 fold in the past decade. Sea surface plastics have also increased, with in-water plastics occurring at densities of 0.1 items m^-3; plastics on seabeds were observed at ≤ 0.01 items m^-2. For the first time, beach densities of plastics at remote South Atlantic sites approached those at industrialised North Atlantic sites. This increase even occurs hundreds of meters down on seamounts. We also investigated plastic incidence in 2,243 animals (comprising 26 species) across remote South Atlantic oceanic food webs, ranging from plankton to seabirds. We found that plastics had been ingested by primary consumers (zooplankton) to top predators (seabirds) at high rates. These findings suggest that MPA status will not mitigate the threat of plastic proliferation to this rich, unique and threatened biodiversity.

Non-isothermal drying kinetics of human feces

The non-isothermal drying behavior and kinetics of human feces (HF) were investigated by means of thermogravimetric analysis to provide data for designing a drying unit operation. The effect of heating rate and blending with woody biomass were also evaluated on drying pattern and kinetics. At low heating rate (1 K/min), there is effective transport of moisture, but a higher heating rate would be necessary at low moisture levels to reduce drying time. Blending with wood biomass improves drying characteristics of HF. The results presented in this study are relevant for designing non-sewered sanitary systems with in-situ thermal treatment.

Longitudinal Analysis of Antibody Cross-neutralization Following Zika Virus and Dengue Virus Infection in Asia and the Americas

Background

The 4 dengue virus serotypes (DENV1-4) and Zika virus (ZIKV) are related mosquito-borne flaviviruses of major importance globally. While monoclonal antibodies and plasma from DENV-immune donors can neutralize or enhance ZIKV in vitro and in small-animal models, and vice versa, the extent, duration, and significance of cross-reactivity in humans remains unknown, particularly in flavivirus-endemic regions.

Methods

We studied neutralizing antibodies to ZIKV and DENV1-4 in longitudinal serologic specimens collected through 3 years after infection from people in Latin America and Asia with laboratory-confirmed DENV infections. We also evaluated neutralizing antibodies to ZIKV and DENV1-4 in patients with Zika through 6 months after infection.

Results

In patients with Zika, the highest neutralizing antibody titers were to ZIKV, with low-level cross-reactivity to DENV1-4 that was greater in DENV-immune individuals. We found that, in primary and secondary DENV infections, neutralizing antibody titers to ZIKV were markedly lower than to the infecting DENV and heterologous DENV serotypes. Cross-neutralization was greatest in early convalescence, then ZIKV neutralization decreased, remaining at low levels over time.

Conclusions

Patterns of antibody cross-neutralization suggest that ZIKV lies outside the DENV serocomplex. Neutralizing antibody titers can distinguish ZIKV from DENV infections when all viruses are analyzed simultaneously. These findings have implications for understanding natural immunity and vaccines.

Nonuniform Crowding Enhances Transport

The cellular cytoplasm is crowded with macromolecules and other species that occupy up to 40% of the available volume. Previous studies have reported that for high crowder molecule concentrations, colloidal tracer particles have a dampened diffusion due to the higher solution viscosity. However, these studies employed uniform distributions of crowder molecules. We report a scenario, previously unexplored experimentally, of increased tracer transport driven by a nonuniform concentration of crowder macromolecules. In gradients of a polymeric crowder, tracer particles undergo transport several times higher than that of their bulk diffusion rate. The direction of the transport is toward regions of lower crowder concentration. Mechanistically, hard-sphere interactions and the resulting volume exclusion between the tracer and crowder increase the effective diffusion by inducing a convective motion of tracers, which we explain through modeling. Strikingly, soft deformable particles show even greater enhancement in transport in crowder gradients compared to similarly sized hard particles. Overall, this demonstration of enhanced transport in nonuniform distributions of crowders is anticipated to clarify aspects of multicomponent intracellular transport.

Identifying Archaeological Bone via Non-Destructive ZooMS and the Materiality of Symbolic Expression: Examples from Iroquoian Bone Points

Today, practical, functional and symbolic choices inform the selection of raw materials for worked objects. In cases where we can discern the origin of worked bone, tooth, ivory and antler objects in the past, we assume that similar choices are being made. However, morphological species identification of worked objects is often impossible due to the loss of identifying characteristics during manufacture. Here, we describe a novel non-destructive ZooMS (Zooarchaeology by Mass Spectrometry) method which was applied to bone points from Pre-Contact St. Lawrence Iroquoian village sites in southern Quebec, Canada. The traditional ZooMS technique requires destructive analysis of a sample, which can be problematic when dealing with artefacts. Here we instead extracted proteins from the plastic bags in which the points had been stored. ZooMS analysis revealed hitherto unexpected species, notably black bear (Ursus americanus) and human (Homo sapiens sapiens), used in point manufacture. These surprising results (confirmed through genomic sequencing) highlight the importance of advancing biomolecular research in artefact studies. Furthermore, they unexpectedly and exceptionally allow us to identify and explore the tangible, material traces of the symbolic relationship between bears and humans, central to past and present Iroquoian cosmology and mythology.

Preliminary Examinations of Concussion in Older Adults

Purpose

This study sought to investigate whether concussion in older adults improves through evaluating their performance on the Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) and Vestibular/Ocular-Motor Screen (VOMS) across visits and to describe and better characterize concussion in this at-risk population.

Methods

We conducted a retrospective review of medical records for 69 older adult patients (40 females, 29 males) that presented to a concussion specialty clinic. Participants averaged 64.71 (SD=4.1) years in age and presented within 6-998 days of injury (SD=170.9). Demographics and clinical data were recorded at intake through last appointment. Descriptive analysis, including frequencies, means, and standard deviations were performed as well as paired T-test to compare mean scores for first and last visit. Statistical significance was determined by two-sided p-values <.05.

Results

Twenty out of 69 participants (29%) reported a previous concussion. Concussion symptom severity scores at participants’ first clinic visit averaged 56.19 (SD=26.56) compare with 39.51 (SD=25.53) at their final clinic visit. When comparing ImPACT data, all scores improved comparatively from Visit 1 to Last Visit (P values =0.000-0.014); all VOMS total scores improved as well (P =0.00-0.047). The most frequent primary profile among participants was Vestibular (31.9%).

Conclusion

Older adults diagnosed with concussion showed improvement on ImPACT scores and their symptom severity scores decreased. The most frequent primary concussion profile at initial visit was Vestibular. Further research with this at-risk population is needed.

Comparison of Clinical Outcomes Following Patients' First and Second Concussions

Purpose

The objective of this study was to examine differences in self-reported symptoms, neurocognitive performance, and vestibular-ocular insufficiencies between patients’ first and second concussions. A secondary purpose was to explore the role of risk factors on recovery.

Methods

We conducted a retrospective medical chart review of 73 (32-M/41-F) patients aged 15.69 (SD=1.67) years from a concussion specialty clinic with two separate concussions (84.9% of 1st and 79.5% of 2nd sport-related) that occurred between August 2010 and April 2018. Clinical outcomes included the PCSS, ImPACT, and the Vestibular/Ocular Motor Screening (VOMS). A series of paired samples t-tests were used to compare clinical outcomes along with chi-square analyses for risk factor associations.

Results

Verbal memory scores were higher following the second (M=80.67, SD=15.3) (M=76.32, SD=15.65) (t[73]=–2.18, p=.03) concussion. Visual motor processing speed was faster following the second concussion (M=35.04, SD= 7.90) (M=31.35, SD=7.63) (t[73]=–5.72, p<.001). There were no other significant differences observed. Recovery time was similar for the first (61.07, SD=58.41.5) and second (67.91 SD=70.10) respectively, t(70)=–.91, p=.37. There was no relationship between any risk factors, and recovery time for either injury with the exception a significant association between gender and recovery time (>21 days) with the 1st injury for females (χ2, N=73)=10.58, p=.001.

Conclusion

Findings suggest that a second concussion does not result in more pronounced symptoms, worse neurocognitive performance, or increased deficits on vestibular/ocular performance and/or longer recovery time. The only significant risk factor to a recovery over 21 days included gender.

Reliability and Consistency of the Vestibular/Ocular Motor Screening (VOMS) Assessment Near Point of Convergence (NPC) Trials

Purpose

To examine the reliability of near point of convergence (NPC) across three trials and determine if one trial of NPC is adequate to identify receded NPC post-concussion.

Methods

Participants included 263 concussed patients (64.3% male; age=16.92±3.49 years) evaluated within 21 days of injury. NPC was measured in centimeters from the tip of the nose using a fixation stick and a Gulick anthropometric tape measure. A two-way, mixed effect, absolute agreement intraclass correlation coefficient (ICC 3,1) was conducted to evaluate reliability across the three trials. A chi-square analysis examined consistency of NPC classification (normal/abnormal) on the initial trial compared to average across three trials.

Results

Reliability of the three trials was high (.91 [95%CI, .89–.93]). Agreement between Trial 1 classification and classification based on average of all three trials was high (96.2%). Of the 10 participants who were classified differently for Trial 1 compared to average trials, 8 had borderline (e.g., 4–6 cm) measurements on the first trial.

Conclusion

NPC measurement across trials is reliable for the overall sample, but those who fell well below (i.e. 0–1cm) or well above (>8cm) clinical cutoffs on the first trial were almost always below or above respective cutoffs on the average convergence (>99%). Results suggest it is important to measure NPC across multiple trials for patients with initial borderline measurement.

Palaeoproteomics resolves sloth relationships

The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies. Ancient DNA evidence has played only a minor role in folivoran systematics, as most sloths lived in places not conducive to genomic preservation. Here we utilize collagen sequence information, both separately and in combination with published mitochondrial DNA evidence, to assess the relationships of tree sloths and their extinct relatives. Results from phylogenetic analysis of these datasets differ substantially from morphology-based concepts: Choloepus groups with Mylodontidae, not Megalonychidae; Bradypus and Megalonyx pair together as megatherioids, while monophyletic Antillean sloths may be sister to all other folivorans. Divergence estimates are consistent with fossil evidence for mid-Cenozoic presence of sloths in the West Indies and an early Miocene radiation in South America.

Non-isothermal thermogravimetric kinetic analysis of the thermochemical conversion of human faeces

The "Reinvent the Toilet Challenge" set by the Bill & Melinda Gates Foundation aims to bring access to adequate sanitary systems to billions of people. In response to this challenge, on-site sanitation systems are proposed and being developed globally. These systems require in-situ thermal treatment, processes that are not well understood for human faeces (HF). Thermogravimetric analysis has been used to investigate the pyrolysis, gasification and combustion of HF. The results are compared to the thermal behaviour of simulant faeces (SF) and woody biomass (WB), along with the blends of HF and WB. Kinetic analysis was conducted using non-isothermal kinetics model-free methods, and the thermogravimetric data obtained for the combustion of HF, SS and WB. The results show that the devolatilisation of HF requires higher temperatures and rates are slower those of WB. Minimum temperatures of 475 K are required for fuel ignition. HF and SF showed similar thermal behaviour under pyrolysis, but not under combustion conditions. The activation energy for HF is 157.4 kJ/mol, relatively higher than SS and WB. Reaction order for HF is lower (n = 0.4) to WB (n = 0.6). In-situ treatment of HF in on-site sanitary systems can be designed for slow progressive burn.

Impact of pre-existing dengue immunity on human antibody and memory B cell responses to Zika

Little is known about enduring memory B cell (MBC) responses to Zika virus (ZIKV) and their relationship with circulating antibodies. Here we comprehensively assess MBC frequency and specificity alongside serum binding and neutralizing antibody responses to ZIKV ~2 weeks and ~8 months postinfection in 31 pediatric subjects with 0, 1 or >1 prior infections with the related dengue virus (DENV). ZIKV infection elicits a robust type-specific MBC response, and the majority of late convalescent anti-ZIKV serum neutralizing activity is attributable to ZIKV-specific antibodies. The number of prior DENV infections does not influence type-specific or cross-reactive MBC responses, although ZIKV has the highest cross-reactivity with DENV3. DENV cross-reactive MBCs expanded by ZIKV infection decline in number and proportion by late convalescence. Finally, ZIKV induces greater cross-reactivity in the MBC pool than in serum antibodies. Our data suggest immunity to DENV only modestly shapes breadth and magnitude of enduring ZIKV antibody responses.

Georeferencing for Research Use (GRU): An integrated geospatial training paradigm for biocollections researchers and data providers

Georeferencing is the process of aligning a text description of a geographic location with a spatial location based on a geographic coordinate system. Training aids are commonly created around the georeferencing process to disseminate community standards and ideas, guide accurate georeferencing, inform users about new tools, and help users evaluate existing geospatial data. The Georeferencing for Research Use (GRU) workshop was implemented as a training aid that focused on the creation and research use of geospatial coordinates, and included both data researchers and data providers, to facilitate communication between the groups. The workshop included 23 participants with a wide background of expertise ranging from students (undergraduate and graduate), professors, researchers and educators, scientific data managers, natural history collections personnel, and spatial analyst specialists. The conversations and survey results from this workshop demonstrate that it is important to provide opportunities for biocollections data providers to interact directly with the researchers using the data they produce and vice versa.

20 GB in 10 minutes: a case for linking major biodiversity databases using an open socio-technical infrastructure and a pragmatic, cross-institutional collaboration

Biodiversity information is made available through numerous databases that each have their own data models, web services, and data types. Combining data across databases leads to new insights, but is not easy because each database uses its own system of identifiers. In the absence of stable and interoperable identifiers, databases are often linked using taxonomic names. This labor intensive, error prone, and lengthy process relies on accessible versions of nomenclatural authorities and fuzzy-matching algorithms. To approach the challenge of linking diverse data, more than technology is needed. New social collaborations like the Global Unified Open Data Architecture (GUODA) that combines skills from diverse groups of computer engineers from iDigBio, server resources from the Advanced Computing and Information Systems (ACIS) Lab, global-scale data presentation from EOL, and independent developers and researchers are what is needed to make concrete progress on finding relationships between biodiversity datasets. This paper will discuss a technical solution developed by the GUODA collaboration for faster linking across databases with a use case linking Wikidata and the Global Biotic Interactions database (GloBI). The GUODA infrastructure is a 12-node, high performance computing cluster made up of about 192 threads with 12 TB of storage and 288 GB memory. Using GUODA, 20 GB of compressed JSON from Wikidata was processed and linked to GloBI in about 10-11 min. Instead of comparing name strings or relying on a single identifier, Wikidata and GloBI were linked by comparing graphs of biodiversity identifiers external to each system. This method resulted in adding 119,957 Wikidata links in GloBI, an increase of 13.7% of all outgoing name links in GloBI. Wikidata and GloBI were compared to Open Tree of Life Reference Taxonomy to examine consistency and coverage. The process of parsing Wikidata, Open Tree of Life Reference Taxonomy and GloBI archives and calculating consistency metrics was done in minutes on the GUODA platform. As a model collaboration, GUODA has the potential to revolutionize biodiversity science by bringing diverse technically minded people together with high performance computing resources that are accessible from a laptop or desktop. However, participating in such a collaboration still requires basic programming skills.

Hyperphosphatemic familial tumoral calcinosis secondary to fibroblast growth factor 23 (FGF23) mutation: a report of two affected families and review of the literature

Hyperphosphatemic familial tumoral calcinosis (HFTC), secondary to fibroblast growth factor 23 (FGF23) gene mutation, is a rare genetic disorder characterized by recurrent calcified masses. We describe young Lebanese cousins presenting with HFTC, based on a retrospective chart review and a prospective case study. In addition, we present a comprehensive review on the topic, based on a literature search conducted in PubMed and Google Scholar, in 2014 and updated in December 2017. While the patients had the same previously reported FGF23 gene mutation (homozygous c.G367T variant in exon 3 leading to a missense mutation), they presented with variable severity and age of disease onset (at 4 years in patient 1 and at 23 years in patient 2). A review of the literature revealed several potential patho-physiologic pathways of HFTC clinical manifestations, some of which may be independent of hyperphosphatemia. Most available treatment options aim at reducing serum phosphate level, by stimulating renal excretion or by inhibiting intestinal absorption. HFTC is a challenging disease. While the available medical treatment has a limited and inconsistent effect on disease symptomatology, surgical resection of calcified masses remains the last resort. Research is needed to determine the safety and efficacy of FGF23 replacement or molecular therapy, targeting the specific genetic aberration. Hyperphosphatemic familial tumoral calcinosis is a rare genetic disorder characterized by recurrent calcified masses, in addition to other visceral, skeletal, and vascular manifestations. It remains a very challenging disease.

Impact of fouling, cleaning and faecal contamination on the separation of water from urine using thermally driven membrane separation

In this study, membrane distillation is evaluated as a technology for non-sewered sanitation, using waste heat to enable separation of clean water from urine. Whilst membrane fouling was observed for urine, wetting was not evident and product water quality met the proposed discharge standard, despite concentration of the feed. Fouling was reversible using physical cleaning, which is similar to previous membrane studies operating without pressure as the driving force. High COD reduction was achieved following faecal contamination, but mass transfer was impeded and wetting occurred which compromised permeate quality, suggesting upstream intervention is demanded to limit the extent of faecal contamination. (100 words).

Psychometric Comparisons of Benevolent and Corrective Humor across 22 Countries: The Virtue Gap in Humor Goes International

Recently, two forms of virtue-related humor, benevolent and corrective, have been introduced. Benevolent humor treats human weaknesses and wrongdoings benevolently, while corrective humor aims at correcting and bettering them. Twelve marker items for benevolent and corrective humor (the BenCor) were developed, and it was demonstrated that they fill the gap between humor as temperament and virtue. The present study investigates responses to the BenCor from 25 samples in 22 countries (overall N = 7,226). The psychometric properties of the BenCor were found to be sufficient in most of the samples, including internal consistency, unidimensionality, and factorial validity. Importantly, benevolent and corrective humor were clearly established as two positively related, yet distinct dimensions of virtue-related humor. Metric measurement invariance was supported across the 25 samples, and scalar invariance was supported across six age groups (from 18 to 50+ years) and across gender. Comparisons of samples within and between four countries (Malaysia, Switzerland, Turkey, and the UK) showed that the item profiles were more similar within than between countries, though some evidence for regional differences was also found. This study thus supported, for the first time, the suitability of the 12 marker items of benevolent and corrective humor in different countries, enabling a cumulative cross-cultural research and eventually applications of humor aiming at the good.

Herbarium data: Global biodiversity and societal botanical needs for novel research

Building on centuries of research based on herbarium specimens gathered through time and around the globe, a new era of discovery, synthesis, and prediction using digitized collections data has begun. This paper provides an overview of how aggregated, open access botanical and associated biological, environmental, and ecological data sets, from genes to the ecosystem, can be used to document the impacts of global change on communities, organisms, and society; predict future impacts; and help to drive the remediation of change. Advocacy for botanical collections and their expansion is needed, including ongoing digitization and online publishing. The addition of non-traditional digitized data fields, user annotation capability, and born-digital field data collection enables the rapid access of rich, digitally available data sets for research, education, informed decision-making, and other scholarly and creative activities. Researchers are receiving enormous benefits from data aggregators including the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), the Atlas of Living Australia (ALA), and the Biodiversity Heritage Library (BHL), but effective collaboration around data infrastructures is needed when working with large and disparate data sets. Tools for data discovery, visualization, analysis, and skills training are increasingly important for inspiring novel research that improves the intrinsic value of physical and digital botanical collections.

Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab

Background

Ipilimumab, an immune checkpoint inhibitor targeting CTLA-4, prolongs survival in a subset of patients with metastatic melanoma (MM) but can induce immune-related adverse events, including enterocolitis. We hypothesized that baseline gut microbiota could predict ipilimumab anti-tumor response and/or intestinal toxicity.

Patients and methods

Twenty-six patients with MM treated with ipilimumab were prospectively enrolled. Fecal microbiota composition was assessed using 16S rRNA gene sequencing at baseline and before each ipilimumab infusion. Patients were further clustered based on microbiota patterns. Peripheral blood lymphocytes immunophenotypes were studied in parallel.

Results

A distinct baseline gut microbiota composition was associated with both clinical response and colitis. Compared with patients whose baseline microbiota was driven by Bacteroides (cluster B, n = 10), patients whose baseline microbiota was enriched with Faecalibacterium genus and other Firmicutes (cluster A, n = 12) had longer progression-free survival (P = 0.0039) and overall survival (P = 0.051). Most of the baseline colitis-associated phylotypes were related to Firmicutes (e.g. relatives of Faecalibacterium prausnitzii and Gemmiger formicilis), whereas no colitis-related phylotypes were assigned to Bacteroidetes. A low proportion of peripheral blood regulatory T cells was associated with cluster A, long-term clinical benefit and colitis. Ipilimumab led to a higher inducible T-cell COStimulator induction on CD4+ T cells and to a higher increase in serum CD25 in patients who belonged to Faecalibacterium-driven cluster A.

Conclusion

Baseline gut microbiota enriched with Faecalibacterium and other Firmicutes is associated with beneficial clinical response to ipilimumab and more frequent occurrence of ipilimumab-induced colitis.

Recruitment of Labelled Monocytes by Experimental Venous Thrombi

Objective. Infusing monocytes that have been stimulated to produce fibrinolytic activators and factors that regulate cell proliferation, migration and maturation, might enhance venous thrombus resolution. The aim of this study was to determine the time course of infused monocyte recruitment into venous thrombus in an appropriate model of this disease. Design and Methods. Thrombus was induced in the inferior vena cava of male Wistar rats using reduced flow (80-90% stenosis). The vessel wall was examined at 1hr by scanning electron microscopy. Resolving thrombi with surrounding vena cava were obtained at 1, 7, 14 and 21 days after induction (n = 8). Sections, taken at 0.5 mm intervals (10-15 sections per thrombus), were stained using haematoxylin, Martius Scarlet Blue and antibodies against monocytes, platelets and fibrin. Sections from human venous thrombi (n = 4) were similarly stained. The area occupied by monocytes (in relative pixel units, RPU) was determined using computer aided image analysis. Peripheral rat blood monocytes were extracted, fluorescently labelled and injected intravenously into 7 rats prior to thrombus induction. Vena cava with thrombus was harvested 1 h, 2, 3, 4, 7, 14 and 25 days after induction and their fluorescence measured. The fluorescent content of the caval wall and thrombus was analysed in greater detail at 2 and 25 days after thrombus induction (n = 4 at each time interval). Results. Experimental thrombi were structurally similar to human thrombus and resolved within 14-21 days. Scanning electron microscopy showed minimal endothelial damage at 1 h with signs of early thrombus formation (platelet, red cell leukocyte and fibrin deposition). Neutrophils were the predominant leukocyte in the thrombus at 1 day, with monocytes making up only 0.3% (0.04% sem) of the area of the thrombus. There was a steady increase in thrombus monocyte content and by 21 days the percentage area of thrombus covered by monocytes had increased by over 35 fold to 11.5% (2.3% sem) (p <0.001). Initially, monocytes appeared around the edge of the thrombus and became more evenly distributed through the thrombus as resolution progressed. Labelled monocytes could be found in the circulation up to 1 week after infusion. The fluorescent content (RPU) of the thrombus increased over 25 days (mean RPU At 2 days 0.012, sem 0.005; mean RPU at 25 days 1.062, sem 0.252, p = 0.008). The number of labelled monocytes in the vessel wall peaked at 2 days and decreased thereafter.

Changes in the Levels of Soluble Adhesion Molecules and Coagulation Factors in Patients with Deep Vein Thrombosis

Current biochemical markers of thrombosis, such as d-dimer, are of little value in demonstrating the presence of thrombus postoperatively, as their levels are elevated by surgery. Thrombosis involves adhesive interactions between the endothelium, platelets and leukocytes. The aim of the study was to determine which of a panel of haemostatic and adhesion factors are altered by the presence of thrombus, but not by surgery. These factors were measured in 20 patients with established spontaneous DVTs, 13 patients having hip replacement surgery and 28 control patients. Circulating levels of P-selectin, VCAM-1 and tissue factor were found to be increased when thrombus was present (p <0.018, p <0.0001, p <0.0028 respectively), but were not altered by surgery. The significance of these circulating factors in venous thrombosis remains to be established, but it is conceivable that they are the product of increased leukocyte trafficking and activity. Assay of VCAM-1, in particular, may be of use in the early detection of venous thrombi in postoperative patients.

Inflammatory gastrointestinal diseases associated with PD-1 blockade antibodies

BACKGROUND

Immune check-point blockade agents have shown clinical activity in cancer patients but are associated with immune-related adverse events that could limit their development. The aim of this study was to describe the gastrointestinal immune-related adverse events (GI-irAE) in patients with cancer treated with anti-PD-1.

METHODS

this is a retrospective study of consecutive adult patients who had a suspected GI-irAE due to anti-PD-1 antibodies between 2013 and 2016. Patients were recruited through a pharmacovigilance registry. Patients' data were reviewed by a multidisciplinary committee that included gastroenterologists, oncologists and a pathologist. Quantitative variables are described by median (range), qualitative variable by frequency (percentage).

RESULTS

Forty-four patients were addressed to a Gastroenterology unit for a suspected GI-IrAE. Twenty patients had a confirmed GI-irAE related to anti-PD-1, which occurred 4.2 months (0.2; 22.1) after the initiation of anti-PD-1. GI-IrAE incidence rate under anti-PD-1 treatment was estimated to be 1.5%. Among patients with GI-IrAE, main symptoms were diarrhoea (n = 16, 80%), abdominal pain (n = 13, 65%), nausea and vomiting (n = 11, 55%), intestinal obstruction (n = 1, 5%), and haematochezia (n = 2, 10%). No patient had colectomy. Four distinct categories of GI-irAE were observed: acute colitis (n = 8, 40%), microscopic colitis (n = 7, 35%), upper gastrointestinal tract inflammation (n = 4, 20%) and pseudo-obstruction (n = 1, 5%). Response rates to corticosteroids were 87.5% (7/8) in acute colitis, 57% (4/7) in microscopic colitis and 75% (3/4) in upper gastrointestinal tract inflammation. Median time to resolution was 36 days (6-172) in acute colitis, and 98 days (42-226) in microscopic colitis.

CONCLUSION

This study suggests that GI-irAE are different and less frequent with anti PD-1 than with anti CTLA-4.

Validation of the "Security Needs Assessment Profile" for measuring the profiles of security needs of Chinese forensic psychiatric inpatients

Mapping forensic psychiatric services with the security needs of patients is a salient step in service planning, audit and review. A valid and reliable instrument for measuring the security needs of Chinese forensic psychiatric inpatients was not yet available. This study aimed to develop and validate the Chinese version of the Security Needs Assessment Profile for measuring the profiles of security needs of Chinese forensic psychiatric inpatients. The Security Needs Assessment Profile by Davis was translated into Chinese. Its face validity, content validity, construct validity and internal consistency reliability were assessed by measuring the security needs of 98 Chinese forensic psychiatric inpatients. Principal factor analysis for construct validity provided a six-factor security needs model explaining 68.7% of the variance. Based on the Cronbach's alpha coefficient, the internal consistency reliability was rated as acceptable for procedural security (0.73), and fair for both physical security (0.62) and relational security (0.58). A significant sex difference (p=0.002) in total security score was found. The Chinese version of the Security Needs Assessment Profile is a valid and reliable instrument for assessing the security needs of Chinese forensic psychiatric inpatients.

A new model for ancient DNA decay based on paleogenomic meta-analysis

The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics.

Students' perceptions of lecturing approaches: traditional versus interactive teaching

BACKGROUND

There is an increasing trend toward transcending from traditional teaching to student-centered methodologies that actively engage students. We aimed to analyze students' perceptions of effective interactive teaching using PollEverywhere Audience Response System (ARS) as a worthwhile teaching methodology. It can be of great help in maintaining students' attention and in facilitating the lecturer to pick up students' misunderstandings and correct them.

MATERIALS AND METHODS

This system was introduced to the undergraduate dental curriculum to increase student's motivation and attention, giving immediate feedback on student understanding during an anatomy module. Computer science (CS) students who were more familiar with the use of this technology were also involved in the study for comparison and validation of the findings. The lecturer strategically inserted questions using PollEverywhere ARS. Students' perception of the effective interactive teaching using this technology was evaluated statistically using a questionnaire and focus groups.

RESULTS

It promoted interactivity, focused attention, and provided feedback on comprehension. A total of 95% reported that it increased their participation and found that it clarified their thinking and helped to focus on key points. Another 81.7% mentioned that it increased their motivation to learn. Students regarded it as a useful method for giving real-time feedback, which stimulated their performance and participation. Data from CS students echoed the findings from the dental students. Reports from focus groups demonstrated that this strategy was helpful in focusing students' attention and in clarifying information.

DISCUSSION

PollEverywhere encouraged all students to participate during the learning process. This has proven to be an effective tool for improving students' understanding and critical thinking.

CONCLUSION

Students regarded PollEverywhere as an effective teaching innovation that encouraged deeper ongoing retention of information. It was found to be an effective teaching aid in monitoring students' progress and identifying deficiencies. This is of benefit in a module where interactivity is considered important.

Fat mass and obesity associated (FTO) gene influences skeletal muscle phenotypes in non-resistance trained males and elite rugby playing position

Background

FTO gene variants have been associated with obesity phenotypes in sedentary and obese populations, but rarely with skeletal muscle and elite athlete phenotypes.

Methods

In 1089 participants, comprising 530 elite rugby athletes and 559 non-athletes, DNA was collected and genotyped for the FTO rs9939609 variant using real-time PCR. In a subgroup of non-resistance trained individuals (NT; n = 120), we also assessed structural and functional skeletal muscle phenotypes using dual energy x-ray absorptiometry, ultrasound and isokinetic dynamometry. In a subgroup of rugby athletes (n = 77), we assessed muscle power during a countermovement jump.

Results

In NT, TT genotype and T allele carriers had greater total body (4.8% and 4.1%) and total appendicular lean mass (LM; 3.0% and 2.1%) compared to AA genotype, with greater arm LM (0.8%) in T allele carriers and leg LM (2.1%) for TT, compared to AA genotype. Furthermore, the T allele was more common (94%) in selected elite rugby union athletes (back three and centre players) who are most reliant on LM rather than total body mass for success, compared to other rugby athletes (82%; P = 0.01, OR = 3.34) and controls (84%; P = 0.03, OR = 2.88). Accordingly, these athletes had greater peak power relative to body mass than other rugby athletes (14%; P = 2 x 10^-6).

Conclusion

Collectively, these results suggest that the T allele is associated with increased LM and elite athletic success. This has implications for athletic populations, as well as conditions characterised by low LM such as sarcopenia and cachexia.

Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans

Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species' distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.

The MMP3 gene in musculoskeletal soft tissue injury risk profiling: A study in two independent sample groups

Matrix metalloproteinase-3 (MMP3) is a mediator of matrix remodelling and a proposed susceptibility locus in the genetic profile of musculoskeletal soft tissue injuries. Therefore, this study aimed to validate the MMP3 gene as a risk marker for these injuries by conducting a case control genetic association study in two independent samples groups. Three previously investigated MMP3 variants (rs679620, rs591058 and rs650108) in addition to the functional promoter variant (rs3025058) were genotyped in 195 Australian control participants and 79 Australian individuals with chronic Achilles tendinopathy. Similarly, 234 South African individuals with acute anterior cruciate ligament ruptures and 232 matched control participants were also analysed. Based on high linkage with the previously associated MMP3 variant rs679620, rs3025058 was inferred and found to be associated with increased risk for Achilles tendinopathy within the South African group (P = 0.012; OR: 2.88; 95% CI: 1.4 to 6.1). Lastly, the 6A-G-C-G haplotype, constructed from the investigated variants, was significantly associated with reduced risk for Achilles tendinopathy (29% CON vs. 20% TEN, P = 0.037) in the Australian group. In conclusion, a signal surrounding MMP3 is apparent with respect to Achilles tendinopathy. However, whether the investigated variants are contributing to injury susceptibility or whether they are merely linked to the risk conferring variants mapping elsewhere within the MMP gene cluster on chromosome 11, still requires refining.

Assessment of nonpenetrating captive bolt stunning followed by electrical induction of cardiac arrest in veal calves

The purpose of this study was to evaluate the impact of nonpenetrating captive bolt stunning followed by electrical induction of cardiac arrest on veal calf welfare, veal quality, and blood yield. Ninety calves from the same farm were randomly assigned to 1 of 2 treatment groups in a balanced unpaired comparison design. The first treatment group (the "head-only" method-application of the pneumatic nonpenetrating stun to the frontal plate of the skull at the intersection of 2 imaginary lines extending from the lateral canthus to the opposite poll [CONTROL]) was stunned with a nonpenetrating captive bolt gun ( = 45). The second group ( = 45) was stunned with a nonpenetrating captive bolt gun followed by secondary electrical induction of cardiac arrest (the "head/heart" method-initial application of the pneumatic nonpenetrating captive bolt stun followed by 1 s application of an electrical stun to the ventral region of the ribcage directly caudal to the junction of the humerus and scapula while the stunned calf was in lateral recumbence [HEAD/HEART]). Stunning efficacy was the indicator of animal welfare used in this study. All calves were instantly rendered insensible by the initial stun and did not display common indicators of return to consciousness. For meat quality evaluation, all samples were collected from the 12th rib region of the longissimus thoracis. Meat samples were evaluated for color, drip loss, ultimate pH, cook loss, and Warner-Bratzler shear force. The L* values (measure of meat color lightness) were darker ( < 0.05) in the HEAD/HEART group (45.08 ± 0.72) than the CONTROL group (47.10 ± 0.72). There were no differences ( > 0.05) observed in a* (redness) and b* (yellowness) values between treatments. No differences ( > 0.05) were observed in drip loss, ultimate pH, cook loss, and Warner-Bratzler shear force. The blood yield from the CONTROL group (7,217.9 ± 143.5 g) was greater ( < 0.05) than that from the HEAD/HEART group (6,656.4 ± 143.5 g). Overall, the data indicated no difference between the CONTROL and HEAD/HEART groups with regard to animal welfare because the initial stun was effective in all calves. However, longissimus thoracis L* and blood yield were negatively impacted by the HEAD/HEART method. The data in this study suggest that secondary induction of cardiac arrest is not necessary with effective nonpenetrating captive bolt stunning in veal calves.

Association of ACTN3 R577X but not ACE I/D gene variants with elite rugby union player status and playing position

We aimed to quantify the ACE I/D and ACTN3 R577X (rs1815739) genetic variants in elite rugby athletes (rugby union and league) and compare genotype frequencies to controls and between playing positions. The rugby athlete cohort consisted of 507 Caucasian men, including 431 rugby union athletes that for some analyses were divided into backs and forwards and into specific positional groups: front five, back row, half backs, centers, and back three. Controls were 710 Caucasian men and women. Real-time PCR of genomic DNA was used to determine genotypes using TaqMan probes and groups were compared using χ² and odds ratio (OR) statistics. Correction of P values for multiple comparisons was according to Benjamini-Hochberg. There was no difference in ACE I/D genotype between groups. ACTN3 XX genotype tended to be underrepresented in rugby union backs (15.7%) compared with forwards (24.8%, P = 0.06). Interestingly, the 69 back three players (wings and full backs) in rugby union included only six XX genotype individuals (8.7%), with the R allele more common in the back three (68.8%) than controls (58.0%; χ² = 6.672, P = 0.04; OR = 1.60) and forwards (47.5%; χ² = 11.768, P = 0.01; OR = 2.00). Association of ACTN3 R577X with playing position in elite rugby union athletes suggests inherited fatigue resistance is more prevalent in forwards, while inherited sprint ability is more prevalent in backs, especially wings and full backs. These results also demonstrate the advantage of focusing genetic studies on a large cohort within a single sport, especially when intrasport positional differences exist, instead of combining several sports with varied demands and athlete characteristics.

Management of immune checkpoint blockade dysimmune toxicities: a collaborative position paper

Monoclonal antibodies targeted against the immune checkpoint molecules CTLA-4 and PD-1 have recently obtained approval for the treatment of metastatic melanoma and advanced/refractory non small-cell lung cancers. Therefore, their use will not be limited anymore to selected hospitals involved in clinical trials. Indeed, they will be routinely prescribed in many cancer centers across the world. Besides their efficacy profile, these immune targeted agents also generate immune-related adverse events (irAEs). This new family of dysimmune toxicities remains largely unknown to the broad oncology community. Although severe irAEs remain rare (∼10% of cases under monotherapy), they can become life-threatening if not anticipated and managed appropriately. Over the last 5 years, Gustave Roussy has accumulated a significant experience in the prescription of immune checkpoint blockade (ICB) antibodies and the management of their toxicities. Together with the collaboration of Gustave Roussy's network of organ specialists with expertise in irAEs, we propose here some practical guidelines for the oncologist to help in the clinical care of patients under ICB immunotherapy.

High-dose chemotherapy with autologous stem cell transplantation in relapsed or refractory germ cell tumours: outcomes and prognostic variables in a case series of 17 patients

BACKGROUND

Optimal therapy for men relapsing after initial chemotherapy for germ cell tumours (GCT) is poorly defined. Both conventional dose salvage regimens and high-dose chemotherapy with autologous stem cell transplantation (HDCT-ASCT) have been utilised.

AIMS

To examine patients who received HDCT-ASCT for relapsed GCT within a single Australian centre.

METHODS

Records between 2000 and 2012 were analysed for baseline characteristics, treatment-related toxicity and survival. Prognosis at the time of HDCT-ASCT was classified according to the International Prognostic Factors Study Group (IPFSG).

RESULTS

Seventeen patients received HDCT-ASCT, median age 34 (21-46), with 41% having primary refractory disease and 53% with high/very high risk disease by IPFSG. The most common regimen utilised was paclitaxel/ifosfamide followed by high-dose carboplatin/etoposide (TI-CE; n = 12). The median duration of grade 4 (G4) neutropenia was 11 days (range 9-17) with febrile neutropenia in 90% resulting in four intensive care unit admissions (8%). Median duration of G4 thrombocytopenia was 10 days (range 8-19) requiring a median of two pooled platelets bags (range 0-33) per episode. Transplant-related mortality occurred in one patient (veno-occlusive disease). Twenty-seven per cent of HDCT-ASCT cycles were associated with grade 3 mucositis (median total parenteral nutrition days = 5 (0-23)). Two-year progression-free survival (PFS) and overall survival (OS) rates were 59% and 71%. Patients who received HDCT-ASCT as second or subsequent relapse fared worse than those treated with HDCT-ASCT at first relapse (hazard ratio 0.23 (95% confidence interval: 0.04, 1.37; P-value 0.09). Three-year OS for those who received TI-CE at first relapse was 90%.

CONCLUSIONS

HDCT-ASCT for relapsed GCT is effective with acceptable toxicity. There was encouraging PFS/OS, particularly in a poor-prognosis cohort.