Reference databases,primer choice,and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

Biodiversity monitoring via environmental DNA, particularly metabarcoding, is evolving into a powerful assessment tool for riverine systems. However, for metabarcoding to be fully integrated into standardized monitoring programmes, some current challenges concerning sampling design, laboratory workflow, and data analysis need to be overcome. Here, we review some of these major challenges and potential solutions. We further illustrate three potential pitfalls, namely the choice of suitable metabarcoding primers, the necessity of complete reference databases, and varying assay sensitivities, by a reappraisal of our‐own recently carried out metabarcoding study in the Volga headwaters. TaqMan qPCRs had detected catfish (Silurus glanis) and European eel (Anguilla anguilla), whereas metabarcoding had not, in the same samples. Furthermore, after extending the genetic reference database by 12 additional species and re‐analysing the metabarcoding data, we additionally detected the Siberian spiny loach (Cobitis sibirica) and Ukrainian brook lamprey (Eudontomyzon mariae) and reassigned the operational taxonomic units previously assigned to Misgurnus fossilis to Cobitis sibirica. In silico analysis of metabarcoding primer efficiencies revealed considerable variability among primer pairs and among target species, which could lead to strong primer bias and potential false‐negatives in metabarcoding studies if not properly compensated for. These results highlight some of the pitfalls of eDNA‐metabarcoding as a means of monitoring fish biodiversity in large rivers, which need to be considered in order to fully unleash the full potential of these approaches for freshwater biodiversity monitoring.     

Integrating social and cognitive aspects of belief dynamics: towards a unifying framework

Belief change and spread have been studied in many disciplines—from psychology, sociology, economics and philosophy, to biology, computer science and statistical physics—but we still do not have a firm grasp on why some beliefs change more easily and spread faster than others. To fully capture the complex social-cognitive system that gives rise to belief dynamics, we first review insights about structural components and processes of belief dynamics studied within different disciplines. We then outline a unifying quantitative framework that enables theoretical and empirical comparisons of different belief dynamic models. This framework uses a statistical physics formalism, grounded in cognitive and social theory, as well as empirical observations. We show how this framework can be used to integrate extant knowledge and develop a more comprehensive understanding of belief dynamics.     

Combining Multiple Cues for Visual Madlibs Question Answering

International Journal of Computer Vision - This paper presents an approach for answering fill-in-the-blank multiple choice questions from the Visual Madlibs dataset. Instead of generic and commonly...     

A Gel‐Based Model of Selective Cell Motility: Implications for Cell Sorting,Diagnostics, and Screening

The ability to precisely control cell‐loaded material systems is essential for in vitro testing of novel therapeutics poised to advance to clinic. In this report, unique patterns of cell migration are devised into an in vitro gel‐in‐gel model for the purpose of obtaining cell response data to potentially therapeutic chemical agonists. The model consists of co‐cultures in a cell‐loaded microgel invading an acellular “sorting” gel. Material properties including biophysical and chemical compositions of the sorting gel are carefully controlled to guide a desired cell‐specific behavior, leading to massive tumor cell invasion by amoeboid migration mechanisms. Optical transparency enables straightforward and high‐throughput measurements of outgrowth response in the presence of either chemical and photoradiation therapy. Important dosing and drug sensitivity information are obtained with the gel‐in‐gel model using no more than a light microscope, without further need for arduous genomic or proteomic screening of the tissue samples.     

Effects of task experience and layout on learning from text and pictures with or without unnecessary picture descriptions

The presentation of extraneous (i.e., irrelevant or unnecessary) information may hamper learning with multimedia. The present study examined whether people can learn to ignore unnecessary information with increasing experience with the task and whether this depends on the layout of that information. In two experiments, participants learned about the process of mitosis from a multimedia slideshow, with each slide presenting a combination of expository text and a picture on one of the stages in the process. Slides either contained no unnecessary text (control condition) or unnecessary text (i.e., merely describing the picture) either integrated in the picture (integrated condition) or presented underneath the picture (separated condition). Knowledge about the studied mitosis phase was tested immediately after each slide using a cloze test. Across Experiments 1 and 2, we did not find a reliable negative effect of the unnecessary text on cloze test performance. As a result, the question of whether task experience would reduce or eliminate that negative effect could not be answered. The eye movement data did confirm, however, that participants attended less to the unnecessary information with increasing task experience, suggesting that students can adapt their study strategy and learn to ignore unnecessary information.     

Laccase‐containing ureasil–polymer composite as the sensing layer of an amperometric biosensor

Innovative amperometric biosensors for monitoring the level of wastewater pollution have been constructed on the surface of the gold planar electrodes C220AT “DropSens” by using the organic–inorganic ureasil‐based composites as host matrixes and immobilized commercial laccase from Trametes versicolor . It was found that the biosensor based on the ureasil–chalcogenide glass composite is characterized by a very high sensitivity (67,540 А M^?1 m^?2) that is 38.3 times higher than for pure ureasil (the sensitivity of the bioelectrode was calculated as 1762 А M^?1 m^?2). On the other hand, application of the ureasil–chalcogenide glass composite with incorporated silver nanoparticles (NPs) synthesized by high‐dose (1.0 × 10¹⁷ Ag⁺/cm²) 30 keV Ag⁺ ion implantation results in decreasing the biosensor sensitivity up to 2390 times (the sensitivity of the bioelectrode was 28.3 А M^?1 m^?2). The role of additives (chalcogenide glass and silver NPs) in the ureasil matrix on the biofunctionality of the biosensors produced is considered. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017 , 134 , 45278.     

Influence of acceleration setting reaction by halogen light‐curing on GIC–dentin interface: Qualitative analysis by SEM

The aim of this study was to evaluate by scanning electron microscope (SEM) photomicrographs the influence of application of halogen light‐curing for fastening the set reaction of high‐viscosity glass ionomer cements (GIC) by assessing the material/dentin interface. Twelve human primary canines were assigned in four groups (n = 3) according to the GIC (Fuji IX, GC or Maxxion R, FGM) and application of halogen light‐curing (60 sec or control—no external energy). Blocks with approximately 6 mm of height were buildup on previously pre‐treated dentin surface in according to the experimental group. After storage at 37 °C, 100% humidity for 48 h, the specimens were then sectioned in slices with 1‐mm thick. The slices were qualitative analyzed using SEM to evaluate possible structural changes. Two examiners independently evaluated the images in order to observe the spherical hollow spaces of each tooth. The photomicrographs revealed the presence of spherical hollow spaces in all experimental groups. However, in both groups that received halogen light‐curing application, it was possible to observe that the presence of these hollow spaces decreased in size and quantity. It can be concluded that the halogen light‐curing application positively decreases in size and quantity in the presence of spherical hollow spaces in GIC.     

Meteorological and oceanographic conditions in the northern Adriatic Sea during the period June 1999-July 2002: influence on the mucilage phenomenon

Mucilage events (formation of very large organic aggregates and gelatinous surface layers) have been documented several times during the past two centuries in the northern Adriatic Sea (NA), while their frequency has significantly increased since 1988. In this work, meteorological and oceanographic conditions in the NA during the period June 1999-July 2002 are described and their relation to the outbreak and fate of the mucilage phenomenon was investigated. Salinity and temperature data were collected during approximately monthly cruises along three transects in the NA. Relevant meteorological situations (air temperature, rainfall, wind) were selected from large-scale ECMWF analyses and from the Local Analysis and Prediction System (LAPS; Emilia Romagna Meteorological Service), while sea conditions (waves) were analysed by means of the Wave Adriatic Model (WAM). Data for air temperature, rainfall, and wind from several meteorological stations in the region were used. Average seasonal cycles of sea temperature and salinity simulated with statistical models, based on historical data collected in the NA since 1972, were used to determine thermal and haline anomalies. The monthly anomaly variability of maximum and minimum air temperatures, rainfall amount and number of rainy days did not appear to be relevant for the mucilage phenomenon outbreak. In contrast, both vertical and horizontal thermohaline gradients in the region were more developed during late spring and summer of 2000 and particularly of 2002, when the mucilage events were of greatest extent in space and time, compared to 2001 (short-lived event) and 1999 (no event). These more pronounced gradients were due to a combination of several unusual conditions: sharp heating of the sea surface in May-June, domination of eastwards transport of freshened waters formed in the Po Delta area, and intrusion of very high salinity intermediate waters originating in the eastern Mediterranean. Moreover, in winter of both 2000 and 2002 very dense and cold water formed and remained in the bottom layer until spring, contributing to increase the stratification degree of the water column. The duration of the mucilage events and their spatial distribution in the region depend strongly on meteorological changes. Recurrent anticyclonic conditions, characterized by low wind and calm sea, favour extended events in time (up 2 months in 2002). In contrast, highly perturbed weather, particularly due to strong "bora" wind, can be determined in sharp decay of the event (e.g. in July 2000).