Assessing the assessments: evaluation of four impact assessment protocols for invasive alien species

Aim: Effective policy and management responses to the multiple threats posed by invasive alien species (IAS) rely on the ability to assess their impacts before conclusive empirical evidence is available. A plethora of different IAS risk and/or impact assessment protocols have been proposed, but it remains unclear whether, how and why the outcomes of such assessment protocols may differ. Location: Europe. Methods: Here, we present an in-depth evaluation and informed assessment of the consistency of four prominent protocols for assessing IAS impacts (EICAT, GISS, Harmonia and NNRA), using two non-native parrots in Europe: the widespread ring-necked parakeet (Psittacula krameri) and the rapidly spreading monk parakeet (Myiopsitta monachus). Results: Our findings show that the procedures used to assess impacts may influence assessment outcomes. We find that robust IAS prioritization can be obtained by assessing species based on their most severe documented impacts, as all protocols yield consistent outcomes across impact categories. Additive impact scoring offers complementary, more subtle information that may be especially relevant for guiding management decisions regarding already established invasive alien species. Such management decisions will also strongly benefit from consensus approaches that reduce disagreement between experts, fostering the uptake of scientific advice into policy-making decisions. Main conclusions: Invasive alien species assessments should take advantage of the capacity of consensus assessments to consolidate discussion and agreement between experts. Our results suggest that decision-makers could use the assessment protocol most fit for their purpose, on the condition they apply a precautionary approach by considering the most severe impacts only. We also recommend that screening for high-impact IAS should be performed on a more robust basis than current ad hoc practices, at least using the easiest assessment protocols and reporting confidence scores.This study is a joint effort from a workshop organized under COST European Cooperation in Science and Technology Actions Parrotnet (ES1304) and Alien Challenge (TD1209). We would also like to thank two anonymous referees for helpful comments on an earlier version of this manuscript. D.S is currently funded by a Marie Skłodowska‐Curie Action under the Horizon 2020 call (H2020‐MSCA‐IF‐2015, grant number 706318) and acknowledges the Danish National Research Foundation for support to the Center for Macroecology, Evolution and Climate (grant number DNRF96). J.C.S. was supported by funds from the Ministry of Economy and Competitivity, Spanish Research Council (CGL‐2016‐79568‐C3‐3‐P)

Synthetic biology open language visual (SBOL Visual) version 2.3

People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.3 of SBOL Visual, which builds on the prior SBOL Visual 2.2 in several ways. First, the specification now includes higher-level "interactions with interactions," such as an inducer molecule stimulating a repression interaction. Second, binding with a nucleic acid backbone can be shown by overlapping glyphs, as with other molecular complexes. Finally, a new "unspecified interaction" glyph is added for visualizing interactions whose nature is unknown, the "insulator" glyph is deprecated in favor of a new "inert DNA spacer" glyph, and the polypeptide region glyph is recommended for showing 2A sequences

Diagnosis of pancreaticobiliary malignancy by detection of minichromosome maintenance protein 5 in bile aspirates

Biliary brush cytology is the standard method of sampling a biliary stricture but has a low sensitivity for the detection of malignancy. We have previously shown that minichromosome maintenance (MCM) replication proteins (Mcm2–7) are markers of dysplasia and have utilised these novel biomarkers of growth for the diagnosis of cervical and bladder cancer. We aimed to determine if MCM proteins are dysregulated in malignant pancreaticobiliary disease and if levels in bile are a sensitive marker of malignancy. In 30 tissue specimens from patients with malignant/benign biliary strictures, we studied Mcm2 and -5 expression by immunohistochemistry. Bile samples were also collected prospectively at endoscopic retrograde cholangiopancreatography from 102 consecutive patients with biliary strictures of established (n=42) or indeterminate aetiology (n=60). Patients with indeterminate strictures also underwent brush cytology as part of standard practice. Bile sediment Mcm5 levels were analysed using an automated immunofluorometric assay. In benign biliary strictures, Mcm2 and -5 protein expression was confined to the basal epithelial proliferative compartment – in contrast to malignant strictures where expression was seen in all tissue layers. The percentage of nuclei positive for Mcm2 was higher in malignant tissue (median 76.5%, range 42–92%) than in benign tissue (median 5%, range 0–33%) (P<0.0005), with similar results for Mcm5. Minichromosome maintenance protein 5 levels in bile were significantly more sensitive than brush cytology (66 vs 20%; P=0.004) for the detection of malignancy in patients with an indeterminate stricture, with a comparable positive predictive value (97 vs 100%; P=ns). In this study, we demonstrate that Mcm5 in bile detected by a simple automated test is a more sensitive indicator of pancreaticobiliary malignancy than routine brush cytology

Constraints on the χ_(c1) versus χ_(c2) polarizations in proton-proton collisions at √s = 8 TeV

The polarizations of promptly produced χ_(c1) and χ_(c2) mesons are studied using data collected by the CMS experiment at the LHC, in proton-proton collisions at √s=8  TeV. The χ_c states are reconstructed via their radiative decays χ_c → J/ψγ, with the photons being measured through conversions to e⁺e⁻, which allows the two states to be well resolved. The polarizations are measured in the helicity frame, through the analysis of the χ_(c2) to χ_(c1) yield ratio as a function of the polar or azimuthal angle of the positive muon emitted in the J/ψ → μ⁺μ⁻ decay, in three bins of J/ψ transverse momentum. While no differences are seen between the two states in terms of azimuthal decay angle distributions, they are observed to have significantly different polar anisotropies. The measurement favors a scenario where at least one of the two states is strongly polarized along the helicity quantization axis, in agreement with nonrelativistic quantum chromodynamics predictions. This is the first measurement of significantly polarized quarkonia produced at high transverse momentum