Cultural Practices Shaping Zoonotic Diseases Surveillance: The Case of Highly Pathogenic Avian Influenza and Thailand Native Chicken Farmers

Effectiveness of current passive zoonotic disease surveillance systems is limited by the under-reporting of disease outbreaks in the domestic animal population. Evaluating the acceptability of passive surveillance and its economic, social and cultural determinants appears a critical step for improving it. A participatory rural appraisal was implemented in a rural subdistrict of Thailand. Focus group interviews were used to identify sanitary risks perceived by native chicken farmers and describe the structure of their value chain. Qualitative individual interviews with a large diversity of actors enabled to identify perceived costs and benefits associated with the reporting of HPAI suspicions to sanitary authorities. Besides, flows of information on HPAI suspected cases were assessed using network analysis, based on data collected through individual questionnaires. Results show that the presence of cockfighting activities in the area negatively affected the willingness of all chicken farmers and other actors to report suspected HPAI cases. The high financial and affective value of fighting cocks contradicted the HPAI control policy based on mass culling. However, the importance of product quality in the native chicken meat value chain and the free veterinary services and products delivered by veterinary officers had a positive impact on suspected case reporting. Besides, cockfighting practitioners had a significantly higher centrality than other actors in the information network and they facilitated the spatial diffusion of information. Social ties built in cockfighting activities and the shared purpose of protecting valuable cocks were at the basis of the diffusion of information and the informal collective management of diseases. Building bridges with this informal network would greatly improve the effectiveness of passive surveillance

Bench-to-bedside review: Mechanisms of critical illness – classifying microcirculatory flow abnormalities in distributive shock

Over 30 years ago Weil and Shubin proposed a re-classification of shock states and identified hypovolemic, cardiogenic, obstructive and distributive shock. The first three categories have in common that they are associated with a fall in cardiac output. Distributive shock, such as occurs during sepsis and septic shock, however, is associated with an abnormal distribution of microvascular blood flow and metabolic distress in the presence of normal or even supranormal levels of cardiac output. This Bench-to-bedside review looks at the recent insights that have been gained into the nature of distributive shock. Its pathophysiology can best be described as a microcirculatory and mitochondrial distress syndrome, where time and therapy form an integral part of the definition. The clinical introduction of new microcirculatory imaging techniques, such as orthogonal polarization spectral and side-stream dark-field imaging, have allowed direct observation of the microcirculation at the bedside. Images of the sublingual microcirculation during septic shock and resuscitation have revealed that the distributive defect of blood flow occurs at the capillary level. In this paper, we classify the different types of heterogeneous flow patterns of microcirculatory abnormalities found during different types of distributive shock. Analysis of these patterns gave a five class classification system to define the types of microcirculatory abnormalities found in different types of distributive shock and indicated that distributive shock occurs in many other clinical conditions than just sepsis and septic shock. It is likely that different mechanisms defined by pathology and treatment underlie these abnormalities observed in the different classes. Functionally, however, they all cause a distributive defect resulting in microcirculatory shunting and regional dysoxia. It is hoped that this classification system will help in the identification of mechanisms underlying these abnormalities and indicate optimal therapies for resuscitating septic and other types of distributive shock

Cross-national differences in social background effects on educational attainment and achievement: absolute vs. relative inequalities and the role of education systems

We use PIAAC data to study the relationship between parental education and educational success among adults from 23 advanced economies. We consider educational success in terms of both educational attainment (formal qualifications) and educational achievement (competencies) and in both absolute and relative terms (i.e. as the individual’s rank in the distribution of educational success). Parental education effects are stronger for educational attainment than for achievement in all countries. Cross-national variation in the strength of social background effects follows broadly similar patterns for the different ways of measuring success, but a few countries combine relatively strong achievement with relatively weak attainment effects and vice versa. Tracking in secondary education is associated with stronger background effects for educational attainment but not for achievement. Greater prevalence of formal (non-formal) AET is associated with stronger (weaker) background effects for both attainment and achievement, while vocational orientation of upper secondary education does not matter much

Yet Another ICU Benchmark: A Flexible Multi-Center Framework for Clinical ML

Medical applications of machine learning (ML) have experienced a surge in popularity in recent years. The intensive care unit (ICU) is a natural habitat for ML given the abundance of available data from electronic health records. Models have been proposed to address numerous ICU prediction tasks like the early detection of complications. While authors frequently report state-of-the-art performance, it is challenging to verify claims of superiority. Datasets and code are not always published, and cohort definitions, preprocessing pipelines, and training setups are difficult to reproduce. This work introduces Yet Another ICU Benchmark (YAIB), a modular framework that allows researchers to define reproducible and comparable clinical ML experiments; we offer an end-to-end solution from cohort definition to model evaluation. The framework natively supports most open-access ICU datasets (MIMIC III/IV, eICU, HiRID, AUMCdb) and is easily adaptable to future ICU datasets. Combined with a transparent preprocessing pipeline and extensible training code for multiple ML and deep learning models, YAIB enables unified model development. Our benchmark comes with five predefined established prediction tasks (mortality, acute kidney injury, sepsis, kidney function, and length of stay) developed in collaboration with clinicians. Adding further tasks is straightforward by design. Using YAIB, we demonstrate that the choice of dataset, cohort definition, and preprocessing have a major impact on the prediction performance - often more so than model class - indicating an urgent need for YAIB as a holistic benchmarking tool. We provide our work to the clinical ML community to accelerate method development and enable real-world clinical implementations. Software Repository: https://github.com/rvandewater/YAIB.Comment: Main benchmark: https://github.com/rvandewater/YAIB, Cohort generation: https://github.com/rvandewater/YAIB-cohorts, Models: https://github.com/rvandewater/YAIB-model

A sustainable archiving software solution for The Language Archive

[Archive X] has been developing a language archiving solution for more than 15 years now. The software is not only aimed at archiving and access but also integrates with a range of exploitation tools. This in house built solution was created from the ground up, since at the time no mature open source repository solutions were available. The situation today is rather different, with several widely used repository system solutions available, including open source solutions that are maintained by communities of developers. Since [Archive X] is now in a situation where it needs to reduce the number of staff required for the maintenance of its archiving software, it was decided to develop a new system based on one of the widely used open source repository solutions such as Fedora Commons (1) or DSpace (2). In this paper we will describe the process of selecting the most suitable open source repository solution as the basis for [Archive X]. This includes the specification of the functional and technical requirements and their prioritization, as well as the evaluation of a number of repository solutions. This evaluation also includes an assessment of the long-term perspective of those solutions. None of the existing repository solutions can provide the complete minimal functionality that [Archive X] requires from its archiving software. This means that additional components or modules need to be developed or adapted from the current software, regardless of the chosen repository solution. Still, we expect that using an existing extensible repository system as a basis will be less costly in the long run. Several language archives, in particular those that serve as centers (3) within the CLARIN consortium, have already implemented different repository systems based on either DSpace or Fedora Commons. Their experiences and recommendations are also taken into account for the evaluation of the various options. The final decision on which repository system will form the basis of the new archiving software will be taken by the end of September 2014. The development of the new archiving software will then start soon after that and a production-ready version will need to be finished by October 2016 at the latest. (1) http://fedorarepository.org/ (2) http://www.dspace.org/ (3) https://centerregistry-clarin.esc.rzg.mpg.de

Rational reprogramming of the sesquiterpene synthase BcBOT2 yields new terpenes with presilphiperfolane skeleton

Computer-aided rational design of the substrate binding pocket of sesquiterpene synthases BcBOT2 from Botrytis cinerea yielded FPP cyclization products with presilphiperfolane backbone other than the naturally formed sesquiterpene presilphiperfolan-8β-ol. Particularly, amino acids W118 and F138 were found to strongly control the stability and conformation of key cationic intermediates. The W118Q variant forms only presilphiperfolan-9β-ol, whereas the exchange of amino acids at position 138, such as F138V, has a fundamental effect on the course of the cationic cascade. Here, the 1,3-hydride shift en route to presilphiperfolan-8β-ol is suppressed and substituted by a so far unknown 1,2-hydride shift that leads to presilphiperfol-1-ene and presilphiperfolan-1α-ol along with β-caryophyllene and the so far unknown caryophyllene-8β-ol

Withdrawing intra-aortic balloon pump support paradoxically improves microvascular flow

Introduction: The Intra-Aortic Balloon Pump (IABP) is frequently used to mechanically support the heart. There is evidence that IABP improves microvascular flow during cardiogenic shock but its influence on the human microcirculation in patients deemed ready for discontinuing IABP support has not yet been studied. Therefore we used sidestream dark field imaging (SDF) to test our hypothesis that human microcirculation remains unaltered with or without IABP support in patients clinically ready for discontinuation of mechanical support. Methods: We studied 15 ICU patients on IABP therapy. Measurements were performed after the clinical decision was made to remove the balloon catheter. We recorded global hemodynamic parameters and performed venous oximetry during maximal IABP support (1:1) and 10 minutes after temporarily stopping the IABP therapy. At both time points, we also recorded video clips of the sublingual microcirculation. From these we determined indices of microvascular perfusion including perfused vessel density (PVD) and microvascular flow index (MFI). Results: Ceasing IABP support lowered mean arterial pressure (74 +/- 8 to 71 +/- 10 mmHg; P = 0.048) and increased diastolic pressure (43 +/- 10 to 53 +/- 9 mmHg; P = 0.0002). However, at the level of the microcirculation we found an increase of PVD of small vessels <20 mu m (5.47 +/- 1.76 to 6.63 +/- 1.90; P = 0.0039). PVD for vessels >20 mu m and MFI for both small and large vessels were unaltered. During the procedure global oxygenation parameters (ScvO(2)/SvO(2)) remained unchanged. Conclusions: In patients deemed ready for discontinuing IABP support according to current practice, SDF imaging showed an increase of microcirculatory flow of small vessels after ceasing IABP therapy. This observation may indicate that IABP impairs microvascular perfusion in recovered patients, although this warrants confirmatio

Machine learning in intensive care medicine: ready for take-off?

In 1986 the world was shaken by the Challenger space shuttle disaster. In the years that followed, the American National Aeronautics and Space Administration (NASA) called for a strategy change in space technology development [1]. Allowing technology to be developed without a specific space program in mind was central to the new strategy [2]. In order to evaluate resulting projects with no direct contribution to a space mission, NASA introduced the general concept of technology readiness levels (TRLs) [3]. These nine levels, adopted by many EU institutions, assess the maturity level of technology and estimate its readiness to fly

The Impact of a Pulmonary-Artery-Catheter-Based Protocol on Fluid and Catecholamine Administration in Early Sepsis

Objective. The pulmonary artery catheter (PAC) remains topic of debate. Despite abundant data, it is of note that many trials did not incorporate a treatment protocol. Methods. We retrospectively evaluated fluid balances and catecholamine doses in septic patients after the introduction of a PAC-based treatment protocol in comparison to historic controls. Results. 2 × 70 patients were included. The first day the PAC group had a significantly higher positive fluid balance in comparison to controls (6.1 ± 2.6 versus 3.8 ± 2.4 litre, P < 0.001). After 7 days the cumulative fluid balance in the PAC group was significantly lower than in controls (9.4 ± 7.4 versus 13 ± 7.6 litre, P = 0.001). Maximum dose of norepinephrine was significantly higher in the PAC group. Compared to controls this was associated with a significant reduction in ventilator and ICU days. Conclusions. Introduction of a PAC-based treatment protocol in sepsis changed the administration of fluid and vasopressors significantly