Cost-benefit analysis of ecosystem modeling to support fisheries management.

Mathematical and statistical models underlie many of the world's most important fisheries management decisions. Since the 19th century, difficulty calibrating and fitting such models has been used to justify the selection of simple, stationary, single-species models to aid tactical fisheries management decisions. Whereas these justifications are reasonable, it is imperative that we quantify the value of different levels of model complexity for supporting fisheries management, especially given a changing climate, where old methodologies may no longer perform as well as in the past.

DichroPipeline: A suite of online and downloadable tools and resources for protein circular dichroism spectroscopic data analyses, interpretations, and their interoperability with other bioinformatics tools and resources.

Circular Dichroism (CD) spectroscopy is a widely-used method for characterizing individual protein structures in solutions, membranes, films and macromolecular complexes, as well as for probing macromolecular interactions, conformational changes associated with binding substrates, and in different functionally-related environments. This paper describes a series of related computational and display tools that have been developed over many years to aid in those characterizations and functional interpretations. The new DichroPipeline described herein links a series of format-compatible data processing, analysis, and display tools to enable users to facilely produce the spectra, which can then be made available in the Protein Circular Dichroism Data Bank (https://pcddb.

The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development.

The Protein Circular Dichroism Data Bank (PCDDB) [https://pcddb.cryst.bbk.

An evaluation of diagnostic tests in a case series of suspected leptospirosis patients seen in primary care.

Aims: This study describes 47 presentations of suspected leptospirosis in general practice in New Zealand. Our primary aim was to assess the laboratory diagnosis of leptospirosis in these patients, by comparing polymerase chain reaction (PCR) tests, microscopic agglutination test (MAT) and culture results.

Methods: Patients suspected of leptospirosis were recruited from general practices in the Waikato (n=17) and Wairoa (n=30) between August 2011 and June 2015.

Tools and methods for circular dichroism spectroscopy of proteins: a tutorial review.

Circular dichroism (CD) spectroscopy is a widely-used method in biochemistry, structural biology and pharmaceutical chemistry. More than 24 000 papers published in the past decade have included CD characterisations of proteins; many of those studies have also included other complementary chemical, biophysical, and computational chemistry methods. This tutorial review describes the background to the technique of CD spectroscopy and good practice methods for high quality data collection.

Identification of a druggable binding pocket in the spike protein reveals a key site for existing drugs potentially capable of combating Covid-19 infectivity.

Background: Following the recent outbreak of the new coronavirus pandemic (Covid-19), the rapid determination of the structure of the homo-trimeric spike glycoprotein has prompted the study reported here. The aims were to identify potential "druggable" binding pockets in the protein and, if located, to virtual screen pharmaceutical agents currently in use for predicted affinity to these pockets which might be useful to restrict, reduce, or inhibit the infectivity of the virion.

Results: Our analyses of this structure have revealed a key potentially druggable pocket where it might be viable to bind pharmaceutical agents to inhibit its ability to infect human cells.

PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures.

PDBMD2CD is a new web server capable of predicting circular dichroism (CD) spectra for multiple protein structures derived from molecular dynamics (MD) simulations, enabling predictions from thousands of protein atomic coordinate files (e.g. MD trajectories) and generating spectra for each of these structures provided by the user.

2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content.

2StrucCompare is a webserver whose primary aim is to visualize subtle but functionally important differences between two related protein structures, either of the same protein or related homologues, with similar or functionally different tertiary structures. At the heart of the package is identifying and visualizing differences between conformations at the secondary structure and at the residue level, such as contact differences or side chain conformational differences found between two protein chains. The protein secondary structures are determined according to four established methods (DSSP, STRIDE, P-SEA and STICKS), and as each employs different assignment strategies, small conformational differences between the two structures can give rise to paired residues being denoted as having different secondary structure features with the different methods.

Improving gout education from patients' perspectives: a focus group study of Māori and Pākehā people with gout.

INTRODUCTION Gout is a common form of arthritis that is typically managed in primary care. Gout management guidelines emphasise patient education for successful treatment outcomes, but there is limited literature about the educational experiences of people living with gout in New Zealand, particularly for Māori, who have higher gout prevalence and worse gout outcomes than Pākehā. AIM To explore gout patient education in primary care from the perspectives of Māori and Pākehā people with gout.

The Incidence and Predisposing Factors of John Cunningham Virus-Induced Progressive Multifocal Leukoencephalopathy in Southern Finland: A Population-Based Study.

Background: The aim of this study was to assess the prevalence, incidence rate (IR), predisposing factors, survival rate, and diagnostic delay of progressive multifocal leukoencephalopathy (PML) across medical specialties. Another objective was to survey how PML diagnosis was made in the studied cases.

Methods: This is a cross-sectional retrospective observational study of PML cases across different medical specialties during 2004-2016 in the Finnish Capital Region and Southern Finland.

Clinical efficacy of seasonal influenza vaccination: characteristics of two outbreaks of influenza A(H1N1) in immunocompromised patients.

Background: Influenza A(H1N1) causes serious complications in immunocompromised patients. The efficacy of seasonal vaccination in these patients has been questioned.

Aim: To describe two outbreaks of influenza A(H1N1) in immunocompromised patients.

DichroMatch at the protein circular dichroism data bank (DM@PCDDB): A web-based tool for identifying protein nearest neighbors using circular dichroism spectroscopy.

Circular dichroism spectroscopy is a well-used, but simple method in structural biology for providing information on the secondary structure and folds of proteins. DichroMatch (DM@PCDDB) is an online tool that is newly available in the Protein Circular Dichroism Data Bank (PCDDB), which takes advantage of the wealth of spectral and metadata deposited therein, to enable identification of spectral nearest neighbors of a query protein based on four different methods of spectral matching. DM@PCDDB can potentially provide novel information about structural relationships between proteins and can be used in comparison studies of protein homologs and orthologs.

Education Preferences of People With Gout: Exploring Differences Between Indigenous and Nonindigenous Peoples from Rural and Urban Locations.

Objective: Gout typically responds well to medications, but adherence might be improved by education that meets individuals' needs in a way that is inclusive of their ethnicity and rurality. The aim of this study was to compare education preferences of Māori and New Zealand European (NZEuropean) individuals with gout, and of those living in rural or urban areas.

Methods: People with gout managed in primary care were recruited from 2 rural regions and 1 city within Aotearoa/New Zealand.

PDB2CD visualises dynamics within protein structures.

Proteins tend to have defined conformations, a key factor in enabling their function. Atomic resolution structures of proteins are predominantly obtained by either solution nuclear magnetic resonance (NMR) or crystal structure methods. However, when considering a protein whose structure has been determined by both these approaches, on many occasions, the resultant conformations are subtly different, as illustrated by the examples in this study.

Rise of multidrug-resistant non-vaccine serotype 15A Streptococcus pneumoniae in the United Kingdom, 2001 to 2014.

Conjugate vaccines have reduced pneumococcal disease in vaccinated children and unvaccinated adults, but non-vaccine serotypes are of concern, particularly if antibiotic resistant. We reviewed Streptococcus pneumoniae collected via: (i) the British Society for Antimicrobial Chemotherapy (BSAC) surveillances from 2001-2014; (ii) Public Health England's (PHE) invasive isolate surveillance from 2005-2014 and (iii) referral to PHE for resistance investigation from 2005-2014. Serotype 15A increased in all series, with many representatives showing triple resistance to macrolides, tetracyclines and penicillin.

Antimicrobial susceptibility monitoring of dermatological bacterial pathogens isolated from diseased dogs and cats across Europe (ComPath results).

Aims: The ComPath project is a pan-European programme dedicated to the monitoring of antimicrobial susceptibility of pathogens from diseased dogs and cats using standardized methods and centralized minimum inhibitory concentration (MIC) determination. Here, the susceptibility of major pathogens is reported from antimicrobial nontreated animals with acute clinical signs of skin, wound or ear infections in 2008-2010.

Methods And Results: MICs were determined by agar dilution for commonly used antibiotics and interpreted using CLSI breakpoints, if available.

PDB2CD: a web-based application for the generation of circular dichroism spectra from protein atomic coordinates.

Motivation: Circular dichroism (CD) spectroscopy is extensively utilized for determining the percentages of secondary structure content present in proteins. However, although a large contributor, secondary structure is not the only factor that influences the shape and magnitude of the CD spectrum produced. Other structural features can make contributions so an entire protein structural conformation can give rise to a CD spectrum.

PCDDB: new developments at the Protein Circular Dichroism Data Bank.

The Protein Circular Dichroism Data Bank (PCDDB) has been in operation for more than 5 years as a public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. Since its inception, many improvements and new developments have been made in data display, searching algorithms, data formats, data content, auxillary information, and validation techniques, as well as, of course, an increase in the number of holdings. It provides a site (http://pcddb.

Surveillance of the Activity of Aminoglycosides and Fluoroquinolones Against Ophthalmic Pathogens from Europe in 2010-2011.

Purpose/aim: Bacterial infections of the ocular surface are commonly treated empirically with broad spectrum antibiotics. Due to concerns over increasing antibiotic resistance, we evaluated current susceptibility patterns of the ocular bacterial pathogens in Europe.

Materials And Methods: Non-consecutive ocular isolates of Staphylococcus aureus, coagulase-negative staphylococci (CoNS), Streptococcus pneumoniae, Haemophilus influenzae, and Pseudomonas aeruginosa were collected in 2011 from centers in France, Germany, Italy, Poland, Slovak Republic, Spain, and the United Kingdom.

Using the patient-centred medicine clinical framework to better appreciate and explore the many barriers to care in type 2 diabetes.

There are many barriers to diabetes care. This paper explores whether organising these barriers to Type 2 diabetes care within the clinical framework of patient-centred medicine (PCM) enables a better appreciation and conceptualisation of these barriers. The terms 'diabetes', 'barriers to care', 'self-management', 'patient-centred care' and 'outcome assessment' were used to identify 28 articles describing multiple barriers (minimum of three) to care in Type 2 diabetes.

[Hypersensitivity reactions caused by intravenously administered anticancer drugs].

Intravenously administered cytotoxic drugs and biological antibodies may cause infusion reactions, the majority of which are mild. Severe, even fatal reactions occur as well. Adrenaline is invariably the most important treatment of a severe reaction.

Understanding barriers to glycaemic control from the patient's perspective.

Introduction: To better understand barriers to glycaemic control from the patient's perspective.

Methods: An interpretative phenomenological approach was used to study the experiences of 15 adults with Type 2 diabetes. Participants each gave a semi-structured interview of their experiences of living with diabetes.

ValiDichro: a website for validating and quality control of protein circular dichroism spectra.

Circular dichroism (CD) spectroscopy is widely used in structural biology as a technique for examining the structure, folding and conformational changes of proteins. A new server, ValiDichro, has been developed for checking the quality and validity of CD spectral data and metadata, both as an aid to data collection and processing and as a validation procedure for spectra to be included in publications. ValiDichro currently includes 25 tests for data completeness, consistency and quality.

Dose-densified chemoimmunotherapy followed by systemic central nervous system prophylaxis for younger high-risk diffuse large B-cell/follicular grade 3 lymphoma patients: results of a phase II Nordic Lymphoma Group study.

Background: Many patients with aggressive B-cell lymphomas and high clinical risk score still die of lymphoma after conventional R-CHOP chemoimmunotherapy. We hypothesized that intensified chemoimmunotherapy including systemic central nervous system (CNS) prophylaxis improves outcome and reduces the incidence of CNS-related events.

Patients And Methods: Inclusion criteria were age 18-65 years, primary diffuse large B-cell lymphoma or grade III follicular lymphoma without clinical signs of CNS disease and negative cerebrospinal fluid cytology, age-adjusted International Prognostic Index 2-3 and WHO performance score 0-3.

Activity of oritavancin against methicillin-resistant staphylococci, vancomycin-resistant enterococci and β-haemolytic streptococci collected from western European countries in 2011.

Objectives: To determine the activity of oritavancin against methicillin-resistant staphylococci, vancomycin-resistant enterococci (VRE) and β-haemolytic streptococci recently isolated from acute bacterial skin and skin structure infections or bacteraemia in western Europe.

Methods: Forty-one centres in Spain (8), Italy (9), Germany (8), France (8) and the UK (8) submitted 866 isolates [204 methicillin-resistant Staphylococcus aureus (MRSA), 177 methicillin-resistant coagulase-negative staphylococci (MRCoNS), 101 VRE, 193 Streptococcus agalactiae and 191 Streptococcus pyogenes] that were collected during the first 6 months of 2011. These were re-identified and susceptibilities to oritavancin and comparators were determined.