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Habitat connectivity is crucial for the conservation of species restricted to fragmented populations within human-dominated landscapes. However, identifying habitat connectivity for apex predators is challenging because trophic interactions between primary productivity and prey species influence both the distribution of habitats, and predator movement. Our goal was to assess habitat connectivity for Indochinese tigers (Panthera tigris) in Thailand. We quantified suitable habitat and dispersal corridors based an ensemble species distribution model that included prey distributions, primary productivity, and abiotic variables and was based on camera-trap data from 1996 to 2013 in 15 protected areas. We employed graph theory to evaluate the relative importance of habitat patches and dispersal corridors to the overall connectivity network. We found that tiger occurrence models with and without prey distributions performed well (Area Under the Curve: 0.932–0.954). However, inclusion of prey distributions significantly improved model performance (P

Driven by the necessity to survive environmental pathogens, the human immune system has evolved exceptional diversity and plasticity, to which several factors contribute including inheritable structural polymorphism of the underlying genes. Characterizing this variation is challenging due to the complexity of these loci, which contain extensive regions of paralogy, segmental duplication and high copy-number repeats, but recent progress in long-read sequencing and optical mapping techniques suggests this problem may now be tractable. Here we assess this by using long-read sequencing platforms from PacBio and Oxford Nanopore, supplemented with short-read sequencing and Bionano optical mapping, to sequence DNA extracted from CD14+ monocytes and peripheral blood mononuclear cells from a single European individual identified as HV31. We use this data to build a de novo assembly of eight genomic regions encoding four key components of the immune system, namely the human leukocyte antigen, immunoglobulins, T cell receptors, and killer-cell immunoglobulin-like receptors. Validation of our assembly using k-mer based and alignment approaches suggests that it has high accuracy, with estimated base-level error rates below 1 in 10 kb, although we identify a small number of remaining structural errors. We use the assembly to identify heterozygous and homozygous structural variation in comparison to GRCh38. Despite analyzing only a single individual, we find multiple large structural variants affecting core genes at all three immunoglobulin regions and at two of the three T cell receptor regions. Several of these variants are not accurately callable using current algorithms, implying that further methodological improvements are needed. Our results demonstrate that assessing haplotype variation in these regions is possible given sufficiently accurate long-read and associated data. Continued reductions in the cost of these technologies will enable application of these methods to larger samples and provide a broader catalogue of germline structural variation at these loci, an important step toward making these regions accessible to large-scale genetic association studies.

We present a genome assembly from an individual female Streptopelia turtur (the European turtle dove; Chordata; Aves; Columbidae). The genome sequence is 1.18 gigabases in span. The majority of the assembly is scaffolded into 35 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled.

The ability to make measurements of phosphate (PO43–) concentrations at temporal and spatial scales beyond those offered by shipboard observations offers new opportunities for investigations of the marine phosphorus cycle. We here report the first in situ PO43– dataset from an underwater glider (Kongsberg Seaglider) equipped with a PO43– Lab-on-Chip (LoC) analyser. Over 44 days, a 120 km transect was conducted in the northern North Sea during late summer (August and September). Surface depletion of PO43– (

The management of brines generated from reverse osmosis operation remains a critical challenge requiring new approaches and processes to limit the impact of brine discharge onto ecosystems and to enhance both water and valuable resource recovery. The treatment of real seawater reverse osmosis (SWRO) brines (45,000 ppm TDS) obtained from a local Singaporean desalination plant with a crystallizer integrated pilot-scale membrane distillation unit (MDC) was studied. Commercial STOMATE® hollow fiber membranes were used in vacuum membrane distillation (VMD) configuration, leading to an average flux of around 3.7 L/m2-h at a permeate vacuum of 80 kPa and an average feed temperature of 65 °C. Consistent separation operations were achieved for the treatment of real SWRO brine over a period of 280 h; this led to a water recovery of >95% and to the collection of salt slurries, containing up to ~10–20 wt% of moisture, from the crystallizer. This approach demonstrates the potential of MDC systems to achieve zero brine discharge efficiently from seawater desalination systems, providing an environmentally friendly alternative to manage brines by increasing water recovery and generating salt slurries of economic value.

Recent developments in power electronics, energy storage systems, and renewable energy; increased market demands for more efficient and cleaner electric power to meet stricter environmental regulations; and development in gigawatt (GW)-class DC (direct current) transmission systems for transmission of greater power over longer distances than similar alternative current (AC) systems, have supported the development of the DC grid, making it a promising solution for both the onshore and offshore industries. This paper presents an experimental study on the effectiveness of an engine speed reduction strategy on exhaust gas emission and fuel consumption when applied to a 4-stroke generator engine equipped with a cam-driven plunger diesel injection system. The experiments were performed on an 8-cylinder V-type 4-stroke generator engine installed in the MASTC laboratory, which is the only demonstration testbed for the ship’s electric propulsion system in Korea. Experimental results showed that fuel consumption decreased, but emission mass fraction in exhaust gas increased when maintaining engine power while reducing engine speed. This study has shown economic benefits in reducing fuel consumption, but incurred penalties for the emission performance of 4-stroke generator engines equipped with cam-driven plunger diesel injection systems when applying the engine speed reduction strategy.

Background: To safely treat lung tumors using particle radiation therapy (PRT), motion-mitigation strategies are of critical importance to ensure precise irradiation. Therefore, we compared applicability, effectiveness, reproducibility, and subjects' acceptance of enhanced deep-inspiration breath hold (eDIBH) with high-frequency percussive ventilation (HFPV) by MRI assessment within 1 month.Methods: Twenty-one healthy subjects (12 males/9 females; age: 49.5 ± 5.8 years; BMI: 24.7 ± 3.3 kg/m−2) performed two 1.5 T MRI scans in four visits at weekly intervals under eDIBH and HFPV conditions, accompanied by daily, home-based breath-hold training and spirometric assessments over a 3-week period. eDIBH consisted of 8-min 100% O2 breathing (3 min resting ventilation, 5 min controlled hyperventilation) prior to breath hold. HFPV was set at 200–250 pulses min−1 and 0.8–1.2 bar. Subjects' acceptance and preference were evaluated by questionnaire. To quantify inter- and intrafractional changes, a lung distance metric representing lung topography was computed for 10 reference points: a motion-invariant spinal cord and nine lung structure contours (LSCs: apex, carina, diaphragm, and six vessels as tumor surrogates distributed equally across the lung). To parameterize individual LSC localizability, measures of their spatial variabilities were introduced and lung volumes calculated by automated MRI analysis.Results: eDIBH increased breath-hold duration by > 100% up to 173 ± 73 s at visit 1, and to 217 ± 67 s after 3 weeks of home-based training at visit 4 (p < 0.001). Measures of vital capacity and lung volume remained constant over the 3-week period. Two vessels in the lower lung segment and the diaphragm yielded a two- to threefold improved positional stability with eDIBH, whereby absolute distance variability was significantly smaller for five LSCs; ≥70% of subjects showed significantly better intrafractional lung motion mitigation under reproducible conditions with eDIBH compared with HFPV with smaller ranges most apparent in the anterior-posterior and cranial-caudal directions. Approximately 80% of subjects preferred eDIBH over HFPV, with “less discomfort” named as most frequent reason.Conclusions: Both, eDIBH, and HFPV were well-tolerated. eDIBH duration was long enough to allow for potential PRT. Variability in lung volume was smaller and position of lung structures more precise with eDIBH. Subjects preferred eDIBH over HFPV. Thus, eDIBH is a very promising tool for lung tumor therapy with PRT, and further investigation of its applicability in patients is warranted.

Abstract Background The logarithmic acid dissociation constant pKa reflects the ionization of a chemical, which affects lipophilicity, solubility, protein binding, and ability to pass through the plasma membrane. Thus, pKa affects chemical absorption, distribution, metabolism, excretion, and toxicity properties. Multiple proprietary software packages exist for the prediction of pKa, but to the best of our knowledge no free and open-source programs exist for this purpose. Using a freely available data set and three machine learning approaches, we developed open-source models for pKa prediction. Methods The experimental strongest acidic and strongest basic pKa values in water for 7912 chemicals were obtained from DataWarrior, a freely available software package. Chemical structures were curated and standardized for quantitative structure–activity relationship (QSAR) modeling using KNIME, and a subset comprising 79% of the initial set was used for modeling. To evaluate different approaches to modeling, several datasets were constructed based on different processing of chemical structures with acidic and/or basic pKas. Continuous molecular descriptors, binary fingerprints, and fragment counts were generated using PaDEL, and pKa prediction models were created using three machine learning methods, (1) support vector machines (SVM) combined with k-nearest neighbors (kNN), (2) extreme gradient boosting (XGB) and (3) deep neural networks (DNN). Results The three methods delivered comparable performances on the training and test sets with a root-mean-squared error (RMSE) around 1.5 and a coefficient of determination (R2) around 0.80. Two commercial pKa predictors from ACD/Labs and ChemAxon were used to benchmark the three best models developed in this work, and performance of our models compared favorably to the commercial products. Conclusions This work provides multiple QSAR models to predict the strongest acidic and strongest basic pKas of chemicals, built using publicly available data, and provided as free and open-source software on GitHub.

Abstract We consider CFT states defined by adding nonlocal multi-trace sources to the Euclidean path integral defining the vacuum state. For holographic theories, we argue that these states correspond to states in the gravitational theory with a good semiclassical description but with a more general structure of bulk entanglement than states defined from single-trace sources. We show that at leading order in large N , the entanglement entropies for any such state are precisely the same as those of another state defined by appropriate single-trace effective sources; thus, if the leading order entanglement entropies are geometrical for the single-trace states of a CFT, they are geometrical for all the multi-trace states as well. Next, we consider the perturbative calculation of 1/N corrections to the CFT entanglement entropies, demonstrating that these show qualitatively different features, including non-analyticity in the sources and/or divergences in the naive perturbative expansion. These features are consistent with the expectation that the 1/N corrections include contributions from bulk entanglement on the gravity side. Finally, we investigate the dynamical constraints on the bulk geometry and the quantum state of the bulk fields which must be satisfied so that the entropies can be reproduced via the quantum-corrected Ryu-Takayanagi formula.

Abstract Background Guidelines to treat anaemia with intravenous (IV) iron have focused on elective surgical patients with little attention paid to those undergoing non-elective/emergency surgery. Whilst these patients may experience poor outcomes because of their presenting illness, observational data suggests that untreated anaemia may also be a contributing factor to poor outcomes. We conducted a systematic review to investigate the safety and efficacy of IV iron in patients undergoing non-elective surgery. Methods We followed a pre-defined review protocol and included randomised controlled trials (RCTs) in patients undergoing non-elective surgery who received IV iron. Primary outcomes were all-cause infection and mean difference in haemoglobin (Hb) at follow-up. Secondary outcomes included transfusion requirements, hospital length of stay (LOS), health-related quality of life (HRQoL), mortality and adverse events. Results Three RCTs (605 participants) were included in this systematic review of which two, in both hip fracture (HF) patients, provided data for meta-analysis. Both of these RCTs were at low risk of bias. We found no evidence of a difference in the risk of infection (RR 0.99, 95% CI 0.55 to 1.80, I 2 = 9%) or in the Hb concentration at ‘short-term’ (≤ 7 days) follow-up (mean difference − 0.32 g/L, 95% CI − 3.28 to 2.64, I 2 = 37%). IV iron did not reduce the risk of requiring a blood transfusion (RR 0.90, 95% CI 0.73 to 1.11, p = 0.46, I 2 = 0%), and we observed no difference in mortality, LOS or adverse events. One RCT reported on HRQoL and found no difference between treatment arms. Conclusion We found no conclusive evidence of an effect of IV iron on clinically important outcomes in patients undergoing non-elective surgery. Further adequately powered trials to evaluate its benefit in emergency surgical specialties with a high burden of anaemia are warranted. Trial registration This systematic review was registered on PROSPERO (CRD42018096288)

Particle therapy is a growing cancer treatment modality worldwide. However, there still remains a number of unanswered questions considering differences in the biological response between particles and photons. These questions, and probing of biological mechanisms in general, necessitate experimental investigation. The “Infrastructure in Proton International Research” (INSPIRE) project was created to provide an infrastructure for European research, unify research efforts on the topic of proton and ion therapy across Europe, and to facilitate the sharing of information and resources. This work highlights the radiobiological capabilities of the INSPIRE partners, providing details of physics (available particle types and energies), biology (sample preparation and post-irradiation analysis), and researcher access (the process of applying for beam time). The collection of information reported here is designed to provide researchers both in Europe and worldwide with the tools required to select the optimal center for their research needs. We also highlight areas of redundancy in capabilities and suggest areas for future investment.

Objectives To assess the association between age, sex, socioeconomic group, weight status and back pain risk in a large general population cohort of children.Design and setting A dynamic cohort of children aged 4 years in the Information System for Research in Primary Care (SIDIAP) electronic primary care records data in Catalonia. Multivariable Cox models were fitted to explore the association between back pain and weight status categories according to the WHO 2007 growth reference groups (body mass index for age z-score). Models were adjusted for age, sex, socioeconomic status and nationality.Participants Children seen at age 4 years at paediatric primary care clinics between 1 January 2006 and 31 December 2013 and followed up until 31 December 2016 or age 15 years.Outcome measures Incident back pain registered by paediatricians at primary care using the International Statistical Classification of Diseases and Health Related Problems, 10th Edition code M54.Results 466 997 children were followed for a median 5.0 years (IQR 5.1). In multivariable models, overweight and obesity increased back pain risk, with adjusted HRs of 1.18 (95% CI 1.09 to 1.27) and 1.34 (95%CI 1.19 to 1.51) for overweight and obesity, respectively. Females were at greater risk of back pain than males with adjusted HR 1.40 (95%CI 1.35 to 1.46). Adjusted HR was 1.43 (95%CI 1.33 to 1.55) for back pain in children from the most deprived socioeconomic groups compared with the least deprived socioeconomic groups.Conclusions Maintaining a healthy weight from an early age may reduce the prevalence of back pain in both children and adults. Overweight female children from deprived socioeconomic groups are at greatest risk of back pain and represent a target population for intervention.

OBJECTIVE:Damage to locus ceruleus neurons could play a part in the pathogenesis of neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis because of impairment of the blood-brain barrier and enhanced neuroinflammation. The locus ceruleus has connections throughout the brain and spinal cord, so the characteristic widespread multifocal pathology in these disorders could be due to damage to different subsets of locus ceruleus neurons. Previous studies have shown that only certain locus ceruleus neurons accumulate the neurotoxic metal mercury. To find out if concentrations of other toxic metals or of essential trace elements also vary between individual locus ceruleus neurons, we used synchrotron X-ray fluorescence microscopy on frozen sections of locus ceruleus neurons taken from people with multiple sclerosis, in whom the locus ceruleus is structurally intact. MATERIALS AND METHODS:Paraffin embedded sections containing the locus ceruleus from seven people with multiple sclerosis were stained with autometallography that demonstrates accumulations of mercury, silver and bismuth. These were compared to maps of multiple elements obtained from frozen sections of locus ceruleus neurons from the same people using X-ray fluorescence microscopy. Neurons in the anterior pons from three of these donors were used as internal controls. RESULTS:Autometallography staining was observed in scattered locus ceruleus neurons from three of the seven donors. X-ray fluorescence microscopy showed variations among individual locus ceruleus neurons in levels of mercury, selenium, iron, copper, lead, bromine, and rubidium. Variations between donors of locus ceruleus neuronal average levels of mercury, iron, copper, and bromine were also detected. Anterior pons neurons contained no mercury, had varied levels of iron, and had lower copper levels than locus ceruleus neurons. CONCLUSIONS:Individual human locus ceruleus neurons contain varying levels of toxic metals and essential trace elements. In contrast, most toxic metals are absent or at low levels in nearby anterior pons neurons. The locus ceruleus plays a role in numerous central nervous system functions, including maintaining the blood-brain-barrier and limiting neuroinflammation. Toxic metals, or alterations in essential trace metals within individual locus ceruleus neurons, could be one factor determining the non-random destruction of locus ceruleus neurons in normal aging and neurodegenerative diseases, and subsequently the sites of the widespread multifocal central nervous system pathology in these disorders.

IntroductionVarenicline tartrate is superior for smoking cessation to other tobacco cessation therapies by 52 weeks, in the outpatient setting. We aimed to evaluate the long-term (104 week) efficacy following a standard course of inpatient-initiated varenicline tartrate plus Quitline-counselling compared to Quitline-counselling alone.MethodsAdult patients (n = 392, 20-75 years) admitted with a smoking-related illnesses to one of three hospitals, were randomised to receive either 12-weeks of varenicline tartrate (titrated from 0.5mg daily to 1mg twice-daily) plus Quitline-counselling, (n = 196) or Quitline-counselling alone, (n = 196), with continuous abstinence from smoking assessed at 104 weeks.ResultsA total of 1959 potential participants were screened for eligibility between August 2008 and December 2011. The proportion of participants who remained continuously abstinent (intention-to-treat) at 104 weeks were significantly greater in the varenicline tartrate plus counselling arm (29.2% n = 56) compared to counselling alone (18.8% n = 36; p = 0.02; odds ratio 1.78; 95%CI 1.10 to 2.86, p = 0.02). Twenty-two deaths occurred during the 104 week study (n = 10 for varenicline tartrate plus counselling and n = 12 for Quitline-counselling alone). All of these participants had known or developed underlying co-morbidities.ConclusionsThis is the first study to examine the efficacy and safety of varenicline tartrate over 104 weeks within any setting. Varenicline tartrate plus Quitline-counselling was found to be an effective opportunistic treatment when initiated for inpatient smokers who had been admitted with tobacco-related disease.

Human cancers exhibit phenotypic diversity that medical imaging can precisely and non-invasively detect. Multiple factors underlying innovations and progresses in the medical imaging field exert diagnostic and therapeutic impacts. The emerging field of radiomics has shown unprecedented ability to use imaging information in guiding clinical decisions. To achieve clinical assessment that exploits radiomic knowledge sources, integration between diverse data types is required. A current gap is the accuracy with which radiomics aligns with clinical endpoints. We propose a novel methodological approach that synergizes data volumes (images), tissue-contextualized information breadth, and network-driven resolution depth. Following the Precision Medicine paradigm, disease monitoring and prognostic assessment are tackled at the individual level by examining medical images acquired from two patients affected by intracranial ependymoma (with and without relapse). The challenge of spatially characterizing intratumor heterogeneity is tackled by a network approach that presents two main advantages: (a) Increased detection in the image domain power from high spatial resolution, (b) Superior accuracy in generating hypotheses underlying clinical decisions.

Abstract Chemical database searching has become a fixture in many non-targeted identification workflows based on high-resolution mass spectrometry (HRMS). However, the form of a chemical structure observed in HRMS does not always match the form stored in a database (e.g., the neutral form versus a salt; one component of a mixture rather than the mixture form used in a consumer product). Linking the form of a structure observed via HRMS to its related form(s) within a database will enable the return of all relevant variants of a structure, as well as the related metadata, in a single query. A Konstanz Information Miner (KNIME) workflow has been developed to produce structural representations observed using HRMS (“MS-Ready structures”) and links them to those stored in a database. These MS-Ready structures, and associated mappings to the full chemical representations, are surfaced via the US EPA’s Chemistry Dashboard (https://comptox.epa.gov/dashboard/). This article describes the workflow for the generation and linking of ~ 700,000 MS-Ready structures (derived from ~ 760,000 original structures) as well as download, search and export capabilities to serve structure identification using HRMS. The importance of this form of structural representation for HRMS is demonstrated with several examples, including integration with the in silico fragmentation software application MetFrag. The structures, search, download and export functionality are all available through the CompTox Chemistry Dashboard, while the MetFrag implementation can be viewed at https://msbi.ipb-halle.de/MetFragBeta/.

The vertebrate anterior-posterior (A-P = craniocaudal) axis is evidently made by a timing mechanism. Evidence has accumulated that tentatively identifies the A-P timer as being or involving Hox temporal collinearity (TC). Here, I focus on the two current competing models based on this premise. Common features and points of dissent are examined and a common model is distilled from what remains. This is an attempt to make sense of the literature.

Abstract Background Edge effects cause changes in bird community richness, abundance, and/or distribution within a landscape, but the avian guilds most influenced can vary among regions. Although Southeast Asia has the highest rates of deforestation and projected species loss, and is currently undergoing an explosive growth in road infrastructure, there have been few studies of the effects of forest edges on avian communities in this region. Methods We examined avian community structure in a dry evergreen forest in northeastern Thailand adjacent to a five-lane highway. We evaluated the richness and abundance of birds in 11 guilds at 24 survey points on three parallel transects perpendicular to the edge. At each point, 10-min surveys were conducted during February‒August 2014 and March‒August 2015. Vegetation measurements were conducted at 16 of the bird survey points and ambient noise was measured at all 24 survey points. Results We found a strongly negative response to the forest edge for bark-gleaning, sallying, terrestrial, and understory insectivores and a weakly negative response for arboreal frugivore-insectivores, foliage gleaning insectivores, and raptors. Densities of trees and the percentage canopy cover were higher in the interior, and the ambient noise was lower. In contrast, arboreal nectarivore-insectivores responded positively to the forest edge, where there was a higher vegetation cover in the ground layer, a lower tree density, and a higher level of ambient noise. Conclusion Planners should avoid road development in forests of high conservation value to reduce impacts on biodiversity. Where avoidance is impossible, a number of potential mitigation methods are available, but more detailed assessments of these are needed before they are applied in this region.

Background and purpose: Stopping-power ratios (SPRs) are used in particle therapy to calculate particle range in patients. The heuristic CT-to-SPR conversion (Hounsfield Look-Up-Table, HLUT), needed for treatment planning, depends on CT-scan and reconstruction parameters as well as the specific HLUT definition. To assess inter-centre differences in these parameters, we performed a survey-based qualitative evaluation, as a first step towards better standardisation of CT-based SPR derivation. Materials and methods: A questionnaire was sent to twelve particle therapy centres (ten from Europe and two from USA). It asked for details on CT scanners, image acquisition and reconstruction, definition of the HLUT, body-region specific HLUT selection, investigations of beam-hardening and experimental validations of the HLUT. Technological improvements were rated regarding their potential to improve SPR accuracy. Results: Scan parameters and HLUT definition varied widely. Either the stoichiometric method (eight centres) or a tissue-substitute-only HLUT definition (three centres) was used. One centre combined both methods. The number of HLUT line segments varied widely between two and eleven. Nine centres had investigated influence of beam-hardening, often including patient-size dependence. Ten centres had validated their HLUT experimentally, with very different validation schemes. Most centres deemed dual-energy CT promising for improving SPR accuracy. Conclusions: Large inter-centre variability was found in implementation of CT scans, image reconstruction and especially in specification of the CT-to-SPR conversion. A future standardisation would reduce time-intensive institution-specific efforts and variations in treatment quality. Due to the interdependency of multiple parameters, no conclusion can be drawn on the derived SPR accuracy and its inter-centre variability. Keywords: Particle treatment planning, Hounsfield look-up-table, CT scan protocol, Stopping-power ratio prediction, Inter-centre comparison, Dual-energy CT

Abstract The collection of chemical structure information and associated experimental data for quantitative structure–activity/property relationship (QSAR/QSPR) modeling is facilitated by an increasing number of public databases containing large amounts of useful data. However, the performance of QSAR models highly depends on the quality of the data and modeling methodology used. This study aims to develop robust QSAR/QSPR models for chemical properties of environmental interest that can be used for regulatory purposes. This study primarily uses data from the publicly available PHYSPROP database consisting of a set of 13 common physicochemical and environmental fate properties. These datasets have undergone extensive curation using an automated workflow to select only high-quality data, and the chemical structures were standardized prior to calculation of the molecular descriptors. The modeling procedure was developed based on the five Organization for Economic Cooperation and Development (OECD) principles for QSAR models. A weighted k-nearest neighbor approach was adopted using a minimum number of required descriptors calculated using PaDEL, an open-source software. The genetic algorithms selected only the most pertinent and mechanistically interpretable descriptors (2–15, with an average of 11 descriptors). The sizes of the modeled datasets varied from 150 chemicals for biodegradability half-life to 14,050 chemicals for logP, with an average of 3222 chemicals across all endpoints. The optimal models were built on randomly selected training sets (75%) and validated using fivefold cross-validation (CV) and test sets (25%). The CV Q2 of the models varied from 0.72 to 0.95, with an average of 0.86 and an R2 test value from 0.71 to 0.96, with an average of 0.82. Modeling and performance details are described in QSAR model reporting format and were validated by the European Commission’s Joint Research Center to be OECD compliant. All models are freely available as an open-source, command-line application called OPEn structure–activity/property Relationship App (OPERA). OPERA models were applied to more than 750,000 chemicals to produce freely available predicted data on the U.S. Environmental Protection Agency’s CompTox Chemistry Dashboard.

N-Glycan oxazolines have found widespread use as activated donor substrates for endo-β-N-acetylglucosaminidase (ENGase) enzymes, an important application that has correspondingly stimulated interest in their production, both by total synthesis and by semi-synthesis using oligosaccharides isolated from natural sources. Amongst the many synthetic approaches reported, the majority rely on the fabrication (either by total synthesis, or semi-synthesis from locust bean gum) of a key Manβ(1–4)GlcNAc disaccharide, which can then be elaborated at the 3- and 6-positions of the mannose unit using standard glycosylation chemistry. Early approaches subsequently relied on the Lewis acid catalysed conversion of peracetylated N-glycan oligosaccharides produced in this manner into their corresponding oxazolines, followed by global deprotection. However, a key breakthrough in the field has been the development by Shoda of 2-chloro-1,3-dimethylimidazolinium chloride (DMC), and related reagents, which can direct convert an oligosaccharide with a 2-acetamido sugar at the reducing terminus directly into the corresponding oxazoline in water. Therefore, oxazoline formation can now be achieved in water as the final step of any synthetic sequence, obviating the need for any further protecting group manipulations, and simplifying synthetic strategies. As an alternative to total synthesis, significant quantities of several structurally complicated N-glycans can be isolated from natural sources, such as egg yolks and soy bean flour. Enzymatic transformations of these materials, in concert with DMC-mediated oxazoline formation as a final step, allow access to a selection of N-glycan oxazoline structures both in larger quantities and in a more expedient fashion than is achievable by total synthesis.

Abstract We discuss an approach to characterizing local degrees of freedom of a subregion in diffeomorphism-invariant theories using the extended phase space of Donnelly and Freidel [36]. Such a characterization is important for defining local observables and entanglement entropy in gravitational theories. Traditional phase space constructions for subregions are not invariant with respect to diffeomorphisms that act at the boundary. The extended phase space remedies this problem by introducing edge mode fields at the boundary whose transformations under diffeomorphisms render the extended symplectic structure fully gauge invariant. In this work, we present a general construction for the edge mode symplectic structure. We show that the new fields satisfy a surface symmetry algebra generated by the Noether charges associated with the edge mode fields. For surface-preserving symmetries, the algebra is universal for all diffeomorphism-invariant theories, comprised of diffeomorphisms of the boundary, SL(2, ℝ) transformations of the normal plane, and, in some cases, normal shearing transformations. We also show that if boundary conditions are chosen such that surface translations are symmetries, the algebra acquires a central extension.

Glycoscience, despite its myriad of challenges, promises to unravel the causes of, potential new detection methods for, and novel therapeutic strategies against, many disease states. In the last two decades, glyco-gold nanoparticles have emerged as one of several potential new tools for glycoscientists. Glyco-gold nanoparticles consist of the unique structural combination of a gold nanoparticle core and an outer-shell comprising multivalent presentation of carbohydrates. The combination of the distinctive physicochemical properties of the gold core and the biological function/activity of the carbohydrates makes glyco-gold nanoparticles a valuable tool in glycoscience. In this review we present recent advances made in the use of one type of click chemistry, namely the azide–alkyne Huisgen cycloaddition, for the functionalization of gold nanoparticles and their conversion to glyco-gold nanoparticles.

Purpose: To compare the efficacy of CT-on-rails versus in-room CBCT for daily adaptive proton therapy. Methods: We analyzed a cohort of ten head-and-neck patients with daily CBCT and corresponding virtual CT images. The necessity of moving the patient after a CT scan is the most significant difference in the adaptation workflow, leading to an increased treatment execution uncertainty σ. It is a combination of the isocenter-matching σi and random patient movements induced by the couch motion σm. The former is assumed to never exceed 1 mm. For the latter, we studied three different scenarios with σm = 1, 2, and 3 mm. Accordingly, to mimic the adaptation workflow with CT-on-rails, we introduced random offsets after Monte-Carlo-based adaptation but before delivery of the adapted plan. Results: There were no significant differences in accumulated dose-volume histograms and dose distributions for σm = 1 and 2 mm. Offsets with σm = 3 mm resulted in underdosage to CTV and hot spots of considerable volume. Conclusion: Since σm typically does not exceed 2 mm for in-room CT, there is no clinically significant dosimetric difference between the two modalities for online adaptive therapy of head-and-neck patients. Therefore, in-room CT-on-rails can be considered a good alternative to CBCT for adaptive proton therapy.

Abstract Despite an abundance of online databases providing access to chemical data, there is increasing demand for high-quality, structure-curated, open data to meet the various needs of the environmental sciences and computational toxicology communities. The U.S. Environmental Protection Agency’s (EPA) web-based CompTox Chemistry Dashboard is addressing these needs by integrating diverse types of relevant domain data through a cheminformatics layer, built upon a database of curated substances linked to chemical structures. These data include physicochemical, environmental fate and transport, exposure, usage, in vivo toxicity, and in vitro bioassay data, surfaced through an integration hub with link-outs to additional EPA data and public domain online resources. Batch searching allows for direct chemical identifier (ID) mapping and downloading of multiple data streams in several different formats. This facilitates fast access to available structure, property, toxicity, and bioassay data for collections of chemicals (hundreds to thousands at a time). Advanced search capabilities are available to support, for example, non-targeted analysis and identification of chemicals using mass spectrometry. The contents of the chemistry database, presently containing ~ 760,000 substances, are available as public domain data for download. The chemistry content underpinning the Dashboard has been aggregated over the past 15 years by both manual and auto-curation techniques within EPA’s DSSTox project. DSSTox chemical content is subject to strict quality controls to enforce consistency among chemical substance-structure identifiers, as well as list curation review to ensure accurate linkages of DSSTox substances to chemical lists and associated data. The Dashboard, publicly launched in April 2016, has expanded considerably in content and user traffic over the past year. It is continuously evolving with the growth of DSSTox into high-interest or data-rich domains of interest to EPA, such as chemicals on the Toxic Substances Control Act listing, while providing the user community with a flexible and dynamic web-based platform for integration, processing, visualization and delivery of data and resources. The Dashboard provides support for a broad array of research and regulatory programs across the worldwide community of toxicologists and environmental scientists.

Investigations that were carried out over the last two decades with novel and more sensitive instrumentation have dramatically improved our knowledge of the more violent physical processes taking place in galactic and extra-galactic Black-Holes, Neutron Stars, Supernova Remnants/Pulsar Wind Nebulae, and other regions of the Universe where relativistic acceleration processes are in place. In particular, simultaneous and/or combined observations with γ-ray satellites and ground based high-energy telescopes, have clarified the scenario of the mechanisms responsible for high energy photon emission by leptonic and hadronic accelerated particles in the presence of magnetic fields. Specifically, the European Space Agency INTEGRAL soft γ-ray observatory has detected more than 1000 sources in the soft γ-ray band, providing accurate positions, light curves and time resolved spectral data for them. Space observations with Fermi-LAT and observations that were carried out from the ground with H.E.S.S., MAGIC, VERITAS, and other telescopes sensitive in the GeV-TeV domain have, at the same time, provided evidence that a substantial fraction of the cosmic sources detected are emitting in the keV to TeV band via Synchrotron-Inverse Compton processes, in particular from stellar galactic BH systems as well as from distant black holes. In this work, employing a spatial cross correlation technique, we compare the INTEGRAL/IBIS and TeV all-sky data in search of secure or likely associations. Although this analysis is based on a subset of the INTEGRAL all-sky observations (1000 orbits), we find that there is a significant correlation: 39 objects (∼20% of the VHE γ-ray catalogue) show emission in both soft γ-ray and TeV wavebands. The full INTEGRAL database, now comprising almost 19 years of public data available, will represent an important legacy that will be useful for the Cherenkov Telescope Array (CTA) and other ground based large projects.

Abstract Background Autoimmune disease-associated variants are preferentially found in regulatory regions in immune cells, particularly CD4+ T cells. Linking such regulatory regions to gene promoters in disease-relevant cell contexts facilitates identification of candidate disease genes. Results Within 4 h, activation of CD4+ T cells invokes changes in histone modifications and enhancer RNA transcription that correspond to altered expression of the interacting genes identified by promoter capture Hi-C. By integrating promoter capture Hi-C data with genetic associations for five autoimmune diseases, we prioritised 245 candidate genes with a median distance from peak signal to prioritised gene of 153 kb. Just under half (108/245) prioritised genes related to activation-sensitive interactions. This included IL2RA, where allele-specific expression analyses were consistent with its interaction-mediated regulation, illustrating the utility of the approach. Conclusions Our systematic experimental framework offers an alternative approach to candidate causal gene identification for variants with cell state-specific functional effects, with achievable sample sizes.

Abstract Background N-of-1 trials are multiple cross-over trials done in individual participants, generating individual treatment effect information. While reporting guidelines for the CONSORT Extension for N-of-1 trials (CENT) and the Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) already exist, there is no standardized recommendation for the reporting of N-of-1 trial protocols. Objective The objective of this study is to evaluate current literature on N-of-1 design and reporting to identify key elements of rigorous N-of-1 protocol design. Methods We will conduct a systematic search for all N-of-1 trial guidelines and protocol-reporting guidelines published in peer-reviewed literature. We will search Medline, Embase, PsycINFO, CINAHL, the Cochrane Methodology Register, CENTRAL, and the NHS Economic Evaluation Database. Eligible articles will contain explicit guidance on N-of-1 protocol construction or reporting. Two reviewers will independently screen all titles and abstracts and then undertake full-text reviews of potential articles to determine eligibility. One reviewer will perform data extraction of selected articles, checked by the second reviewer. Data analysis will ascertain common features of N-of-1 trial protocols and compare them to the SPIRIT and CENT items. Discussion This systematic review assesses recommendations on the design and reporting of N-of-1 trial protocols. These findings will inform an international Delphi development process for an N-of-1 trial protocol reporting guideline. The development of this guideline is critical for improving the quality of N-of-1 protocols, leading to improvements in the quality of published N-of-1 trial research.

IntroductionThe benefits and risk of intravenous iron have been documented in previous systematic reviews and continue to be the subject of randomised controlled trials (RCTs). An ongoing issue that continues to be raised is the relationship between administering iron and developing infection. This is supported by biological plausibility from animal models. We propose an update of a previously published systematic review and meta-analysis with the primary focus being infection.Methods and analysisWe will include RCTs and non-randomised studies (NRS) in this review update. We will search the relevant electronic databases. Two reviewers will independently extract data. Risk of bias for RCTs and NRS will be assessed using the relevant tools recommended by The Cochrane Collaboration. Data extracted from RCTs and NRS will be analysed and reported separately. Pooled data from RCTs will be analysed using a random effects model. We will also conduct subgroup analyses to identify any patient populations that may be at increased risk of developing infection. We will provide a narrative synthesis on the definitions, sources and responsible pathogens for infection in the included studies. Overall quality of evidence on the safety outcomes of mortality and infection will be assessed using the Grading of Recommendations, Assessment, Development and Evaluation approach.Ethics and disseminationThis systematic review will only investigate published studies and therefore ethical approval is not required. The results will be broadly distributed through conference presentations and peer-reviewed publications.Trial registration numberPROSPERO (CRD42018096023).

IntroductionHistorical and current stigmatizing and discriminatory experiences drive sexual and gender minority (SGM) people away from health care and clinical research. Being medically underserved, they face numerous disparities that make them vulnerable to poor health outcomes. Effective methods to engage and recruit SGM people into clinical research studies are needed.ObjectivesTo promote health equity and understand SGM health needs, we sought to design an online, national, longitudinal cohort study entitled The PRIDE (Population Research in Identity and Disparities for Equality) Study that enabled SGM people to safely participate, provide demographic and health data, and generate SGM health-related research ideas.MethodsWe developed an iPhone mobile application ("app") to engage and recruit SGM people to The PRIDE Study-Phase 1. Participants completed demographic and health surveys and joined in asynchronous discussions about SGM health-related topics important to them for future study.ResultsThe PRIDE Study-Phase 1 consented 18,099 participants. Of them, 16,394 provided data. More than 98% identified as a sexual minority, and more than 15% identified as a gender minority. The sample was diverse in terms of sexual orientation, gender identity, age, race, ethnicity, geographic location, education, and individual income. Participants completed 24,022 surveys, provided 3,544 health topics important to them, and cast 60,522 votes indicating their opinion of a particular health topic.ConclusionsWe developed an iPhone app that recruited SGM adults and collected demographic and health data for a new national online cohort study. Digital engagement features empowered participants to become committed stakeholders in the research development process. We believe this is the first time that a mobile app has been used to specifically engage and recruit large numbers of an underrepresented population for clinical research. Similar approaches may be successful, convenient, and cost-effective at engaging and recruiting other vulnerable populations into clinical research studies.

A realistic estimation of uncertainty is an essential requirement for all analytical measurements. It is common practice, however, for the uncertainty estimate of a chemical measurement to be based on the instrumental precision associated with the analysis of a single or multiple samples, which can lead to underestimation. Within the context of chemical oceanography such an underestimation of uncertainty could lead to an over interpretation of the result(s) and hence impact on, e.g., studies of biogeochemical cycles, and the outputs from oceanographic models. Getting high quality observational data with a firm uncertainty assessment is therefore essential for proper model validation. This paper describes and compares two recommended approaches that can give a more holistic assessment of the uncertainty associated with such measurements, referred to here as the “bottom up” or modeling approach and the “top down” or empirical approach. “Best practice” recommendations for the implementation of these strategies are provided. The “bottom up” approach combines the standard uncertainties associated with each stage of the entire measurement procedure. The “top down” approach combines the uncertainties associated with day to day reproducibility and possible bias in the complete data set and is easy to use. For analytical methods that are routinely used, laboratories will have access to the information required to calculate the uncertainty from archived quality assurance data. The determination of trace elements in seawater is a significant analytical challenge and iron is used as an example for the implementation of both approaches using real oceanographic data. Relative expanded uncertainties of 10 – 20% were estimated for both approaches compared with a typical short term precision (rsd) of ≤5%.

Augmented reality (AR) has proven to be a useful, exciting technology in several areas of healthcare. AR may especially enhance the operator's experience in minimally invasive surgical applications by providing more intuitive and naturally immersive visualisation in those procedures which heavily rely on three-dimensional (3D) imaging data. Benefits include improved operator ergonomics, reduced fatigue, and simplified hand–eye coordination. Head-mounted AR displays may hold great potential for enhancing surgical navigation given their compactness and intuitiveness of use. In this work, the authors propose a method that can intra-operatively locate bone structures using tracked ultrasound (US), registers to the corresponding pre-operative computed tomography (CT) data and generates 3D AR visualisation of the operated surgical scene through a head-mounted display. The proposed method deploys optically-tracked US, bone surface segmentation from the US and CT image volumes, and multimodal volume registration to align pre-operative to the corresponding intra-operative data. The enhanced surgical scene is then visualised in an AR framework using a HoloLens. They demonstrate the method's utility using a foam pelvis phantom and quantitatively assess accuracy by comparing the locations of fiducial markers in the real and virtual spaces, yielding root mean square errors of 3.22, 22.46, and 28.30 mm in the x, y, and z directions, respectively.

Hydroelectricity is the world's largest source of ‘renewable’ energy, and deployment will expand considerably in the coming decade, with Asian countries installing the bulk of new generating capacity. Before construction of large hydropower projects, empirical evidence can be utilised to inform public involvement and to realistically ground decision-making processes such as impact mitigation planning and whether or not to build. This study explored changes in avian community richness and diversity among resident forest species surrounding the 165 km2 Chiew Larn reservoir in southern Thailand, thirty years after inundation. Replicated avian point-counts were undertaken on 23 island sites and 24 nearby mainland transects. A total of 108 habitat structure surveys were conducted. Mainland and islands were composed of remarkably similar bamboo-dominated edge habitat. logArea described 82% of the variability in species richness using general linear models and 74% of the variability in community composition using Bray-Curtis non-metric multidimensional scaling. Species richness was similar on mainland and islands; however, the exponential of Shannon diversity was significantly higher on the mainland. Compared to a species pool of recent confirmed records in less disturbed habitat beyond the inundation zone, one fourth of species were missing from mainland sites. The avian community was dominated by a handful of disturbance tolerant species; furthermore, several widespread and ecologically tolerant species were also rare or missing. The disturbance-intolerant assemblage experienced collapse. Terrestrial and other understorey insectivores, species associated with mixed-species foraging flocks, middle storey sallying insectivores, and frugivores were severely depauperate, as were Sundaic endemics and species of conservation concern. An estimated 61 km2 of degraded edge habitat surrounded the reservoir near the study area. Without taking the potential for serious mainland edge effects and associated human disturbance of habitat into consideration, planners will underestimate the potential impact of hydropower development on avian biodiversity. Keywords: Hydropower, Terrestrial ecosystems, Sundaland Biodiversity Hotspot, Indo-Burma Biodiversity Hotspot, Edge effects, Avifauna, Chiew Larn reservoir

Integration of multiple technologies greatly increases the spatial and temporal scales over which ecological patterns and processes can be studied, and threats to protected ecosystems can be identified and mitigated. A range of technology options relevant to ecologists and conservation practitioners are described, including ways they can be linked to increase the dimensionality of data collection efforts. Remote sensing, ground-based, and data fusion technologies are broadly discussed in the context of ecological research and conservation efforts. Examples of technology integration across all of these domains are provided for large-scale protected area management and investigation of ecological dynamics. Most technologies are low-cost or open-source, and when deployed can reach economies of scale that reduce per-area costs dramatically. The large-scale, long-term data collection efforts presented here can generate new spatio-temporal understanding of threats faced by natural ecosystems and endangered species, leading to more effective conservation strategies.

Present-day mass loss from the West Antarctic ice sheet is centred on the Amundsen Sea Embayment (ASE), primarily through ice streams, including Pine Island, Thwaites and Smith glaciers. To understand the differences in response of these ice streams, we ran a perturbed parameter ensemble, using a vertically-integrated ice flow model with adaptive mesh refinement. We generated 71 sets of three physical parameters (basal traction coefficient, ice viscosity stiffening factor and sub-shelf melt rate), which we used to simulate the ASE for 50 years. We also explored the effects of different bed geometries and basal sliding laws. The mean rate of sea-level rise across the ensemble of simulations is comparable with current observed rates for the ASE. We found evidence that grounding line dynamics are sensitive to features in the bed geometry: simulations using BedMap2 geometry resulted in a higher rate of sea-level rise than simulations using a rougher geometry, created using mass conservation. Modelled grounding-line retreat of all the three ice streams was sensitive to viscosity and basal traction, while the melt rate was more important in Pine Island and Smith glaciers, which flow through more confined ice shelves than Thwaites, which has a relatively unconfined shelf.

There is a growing need in the field of exposure science for monitoring methods that rapidly screen environmental media for suspect contaminants. Measurement and analysis platforms, based on high resolution mass spectrometry (HRMS), now exist to meet this need. Here we describe results of a study that links HRMS data with exposure predictions from the U.S. EPA's ExpoCast™ program and in vitro bioassay data from the U.S. interagency Tox21 consortium. Vacuum dust samples were collected from 56 households across the U.S. as part of the American Healthy Homes Survey (AHHS). Sample extracts were analyzed using liquid chromatography time-of-flight mass spectrometry (LC–TOF/MS) with electrospray ionization. On average, approximately 2000 molecular features were identified per sample (based on accurate mass) in negative ion mode, and 3000 in positive ion mode. Exact mass, isotope distribution, and isotope spacing were used to match molecular features with a unique listing of chemical formulas extracted from EPA's Distributed Structure-Searchable Toxicity (DSSTox) database. A total of 978 DSSTox formulas were consistent with the dust LC–TOF/molecular feature data (match score ≥ 90); these formulas mapped to 3228 possible chemicals in the database. Correct assignment of a unique chemical to a given formula required additional validation steps. Each suspect chemical was prioritized for follow-up confirmation using abundance and detection frequency results, along with exposure and bioactivity estimates from ExpoCast and Tox21, respectively. Chemicals with elevated exposure and/or toxicity potential were further examined using a mixture of 100 chemical standards. A total of 33 chemicals were confirmed present in the dust samples by formula and retention time match; nearly half of these do not appear to have been associated with house dust in the published literature. Chemical matches found in at least 10 of the 56 dust samples include Piperine, N,N-Diethyl-m-toluamide (DEET), Triclocarban, Diethyl phthalate (DEP), Propylparaben, Methylparaben, Tris(1,3-dichloro-2-propyl)phosphate (TDCPP), and Nicotine. This study demonstrates a novel suspect screening methodology to prioritize chemicals of interest for subsequent targeted analysis. The methods described here rely on strategic integration of available public resources and should be considered in future non-targeted and suspect screening assessments of environmental and biological media. Keywords: Non-targeted, Suspect screening, Exposome, ExpoCast, ToxCast, Dust

Software applications for high resolution mass spectrometry (HRMS)-based non-targeted analysis (NTA) continue to enhance chemical identification capabilities. Given the variety of available applications, determining the most fit-for-purpose tools and workflows can be difficult. The Critical Assessment of Small Molecule Identification (CASMI) contests were initiated in 2012 to provide a means to evaluate compound identification tools on a standardized set of blinded tandem mass spectrometry (MS/MS) data. Five CASMI contests have resulted in recommendations, publications, and invaluable datasets for practitioners of HRMS-based screening studies. The US Environmental Protection Agency’s (EPA) CompTox Chemicals Dashboard is now recognized as a valuable resource for compound identification in NTA studies. However, this application was too new and immature in functionality to participate in the five previous CASMI contests. In this work, we performed compound identification on all five CASMI contest datasets using Dashboard tools and data in order to critically evaluate Dashboard performance relative to that of other applications. CASMI data was accessed via the CASMI webpage and processed for use in our spectral matching and identification workflow. Relative to applications used by former contest participants, our tools, data, and workflow performed well, placing more challenge compounds in the top five of ranked candidates than did the winners of three contest years and tying in a fourth. In addition, we conducted an in-depth review of the CASMI structure sets and made these reviewed sets available via the Dashboard. Our results suggest that Dashboard data and tools would enhance chemical identification capabilities for practitioners of HRMS-based NTA.

This article is a tribute to Lewis Wolpert and his ideas on the occasion of the recent 50th anniversary of the publication of his article ‘Positional Information and the Spatial Pattern of Differentiation’. This tribute relates to another one of his ideas: his early ‘Progress Zone’ timing model for limb development. Recent evidence is reviewed showing a mechanism sharing features with this model patterning the main body axis in early vertebrate development. This tribute celebrates the golden era of Developmental Biology.

A two tier mechanism mediates Hox collinearity. Besides the familiar collinear chromatin modification within each Hox cluster (nanocollinearity), there is also a macrocollinearity tier. Individual Hox clusters and individual cells are coordinated and synchronized to generate multiscale (macro and nano) collinearity in the early vertebrate embryo. Macro-collinearity is mediated by three non-cell autonomous Hox–Hox interactions. These mediate temporal collinearity in early NOM (non-organizer mesoderm), time space translation where temporal collinearity is translated to spatial collinearity along the early embryo’s main body axis and neural transformation, where Hox expression is copied monospecifically from NOM mesoderm to overlying neurectoderm in the late gastrula. Unlike nanocollinearity, which is Hox cluster restricted, axial macrocollinearity extends into the head and EAD domains, thus covering the whole embryonic anterior-posterior (A-P) axis. EAD: extreme anterior domain, the only A-P axial domain anterior to the head. The whole time space translation mechanism interacts with A-P signaling pathways via “decision points,” separating different domains on the axis.

Introduction: The development of improved diagnosis, management, and treatment strategies for human atrial fibrillation (AF) is a significant and important challenge in order to improve quality of life for millions and reduce the substantial social-economic costs of the condition. As a complex condition demonstrating high variability and relation to other cardiac conditions, the study of AF requires approaches from multiple disciplines including single-cell experimental electrophysiology and computational modeling. Models of human atrial cells are less well parameterized than those of the human ventricle or other mammal species, largely due to the inherent challenges in patch clamping human atrial cells. Such challenges include, frequently, unphysiologically depolarized resting potentials and thus injection of a compensatory hyperpolarizing current, as well as detecting certain ion currents which may be disrupted by the cell isolation process. The aim of this study was to develop a laboratory specific model of human atrial electrophysiology which reproduces exactly the conditions of isolated-cell experiments, including testing of multiple experimental interventions.Methods: Formulations for the primary ion currents characterized by isolated-cell experiments in the Workman laboratory were fit directly to voltage-clamp data; the fast sodium-current was parameterized based on experiments relating resting membrane potential to maximal action potential upstroke velocity; compensatory hyperpolarizing current was included as a constant applied current. These formulations were integrated with three independent human atrial cell models to provide a family of novel models. Extrapolated intact-cell models were developed through removal of the hyperpolarizing current and introduction of terminal repolarization potassium currents.Results: The isolated-cell models quantitatively reproduced experimentally measured properties of excitation in both control and pharmacological and dynamic-clamp interventions. Comparison of isolated and intact-cell models highlighted the importance of reproducing this cellular environment when comparing experimental and simulation data.Conclusion: We have developed a laboratory specific model of the human atrial cell which directly reproduces the experimental isolated-cell conditions and captures human atrial excitation properties. The model may be particularly useful for directly relating model to experiment, and offers a complementary tool to the available set of human atrial cell models with specific advantages resulting from the congruent input data source.

The Sundarbans Forest (∼10,000 km2) represents the only mangrove ecosystem inhabited by tigers Panthera tigris. However, in the Bangladesh portion of the Sundarbans (∼6,000 km2) tigers appear to have declined. The aim of this study was to examine the influence of a range of environmental and landscape variables in possible changes in the relative abundance of tigers in the Bangladesh Sundarbans over a five-year period (2007–2011). In 2007, 2011 tiger relative abundance was assessed using sign surveys. Using regression models we investigated changes in relative abundance versus multiple landscape variables (human disturbance associated with villages and commercial shipping lanes, distance to the international border with India where there is enhanced patrolling, presence of forest guard stations, number of criminal prosecutions and forest protection status). Tiger relative abundance was higher in 2007 and declined by 2011 with changes best explained by the proximity to international boundaries. This result might have been affected by the high levels of security patrols at the India-Bangladesh border along with cross border tiger movement between India and Bangladesh. Neighboring tiger range countries could strengthen cross-border law enforcement, increasing protection of dispersing animals. Particularly alarming was the absence of a positive effect of protected areas relative to those outside the protected area system or forest guard stations, implying a lack of management effectiveness suggesting an urgent need for an improved strategy for managing tigers and their habitats. Keywords: Wildlife poaching, Population declines, Transboundary protection, Joint patrolling, Protected area effectiveness

Background: The infection of a participant with norovirus during the adaptive study of interleukin-2 dose on regulatory T cells in type 1 diabetes (DILT1D) allowed a detailed insight into the cellular and cytokine immune responses to this prevalent gastrointestinal pathogen. Methods: Serial blood, serum and peripheral blood mononuclear cell (PBMC) samples were collected pre-, and post-development of the infection. To differentiate between the immune response to norovirus and to control for the administration of a single dose of aldesleukin (recombinant interleukin-2, rIL-2) alone, samples from five non-infected participants administered similar doses were analysed in parallel. Results: Norovirus infection was self-limited and resolved within 24 hours, with the subsequent development of anti-norovirus antibodies. Serum pro- and anti-inflammatory cytokine levels, including IL-10, peaked during the symptomatic period of infection, coincident with increased frequencies of monocytes and neutrophils. At the same time, the frequency of regulatory CD4+ T cell (Treg), effector T cell (Teff) CD4+ and CD8+ subsets were dynamically reduced, rebounding to baseline levels or above at the next sampling point 24 hours later. NK cells and NKT cells transiently increased CD69 expression and classical monocytes expressed increased levels of CD40, HLA-DR and SIGLEC-1, biomarkers of an interferon response. We also observed activation and mobilisation of Teffs, where increased frequencies of CD69+ and Ki-67+ effector memory Teffs were followed by the emergence of memory CD8+ Teff expressing the mucosal tissue homing markers CD103 and β7 integrin. Treg responses were coincident with the innate cell, Teff and cytokine response. Key Treg molecules FOXP3, CTLA-4, and CD25 were upregulated following infection, alongside an increase in frequency of Tregs with the capacity to home to tissues. Conclusions: The results illustrate the innate, adaptive and counter-regulatory immune responses to norovirus infection. Low-dose IL-2 administration induces many of the Treg responses observed during infection.