A Novel Algorithm for the Determination of Bacterial Cell Volumes That is Unbiased by Cell Morphology

The determination of cell volumes and biomass offers a means of comparing the standing stocks of auto- and heterotrophic microbes of vastly different sizes for applications including the assessment of the flux of organic carbon within aquatic ecosystems. Conclusions about the importance of particular genotypes within microbial communities (e.g., of filamentous bacteria) may strongly depend on whether their contribution to total abundance or to biomass is regarded. Fluorescence microscopy and image analysis are suitable tools for determining bacterial biomass that moreover hold the potential to replace labor-intensive manual measurements by fully automated approaches. However, the current approaches to calculate bacterial cell volumes from digital images are intrinsically biased by the models that are used to approximate the morphology of the cells. Therefore, we developed a generic contour based algorithm to reconstruct the volumes of prokaryotic cells from two-dimensional representations (i.e., microscopic images) irrespective of their shape. Geometric models of commonly encountered bacterial morphotypes were used to verify the algorithm and to compare its performance with previously described approaches. The algorithm is embedded in a freely available computer program that is able to process both raw (8-bit grayscale) and thresholded (binary) images in a fully automated manne

A Novel Algorithm for the Determination of Bacterial Cell Volumes That is Unbiased by Cell Morphology

The determination of cell volumes and biomass offers a means of comparing the standing stocks of auto- and heterotrophic microbes of vastly different sizes for applications including the assessment of the flux of organic carbon within aquatic ecosystems. Conclusions about the importance of particular genotypes within microbial communities (e.g., of filamentous bacteria) may strongly depend on whether their contribution to total abundance or to biomass is regarded. Fluorescence microscopy and image analysis are suitable tools for determining bacterial biomass that moreover hold the potential to replace labor-intensive manual measurements by fully automated approaches. However, the current approaches to calculate bacterial cell volumes from digital images are intrinsically biased by the models that are used to approximate the morphology of the cells. Therefore, we developed a generic contour based algorithm to reconstruct the volumes of prokaryotic cells from two-dimensional representations (i.e., microscopic images) irrespective of their shape. Geometric models of commonly encountered bacterial morphotypes were used to verify the algorithm and to compare its performance with previously described approaches. The algorithm is embedded in a freely available computer program that is able to process both raw (8-bit grayscale) and thresholded (binary) images in a fully automated manner

Multi-spot live-image autofocusing for high-throughput microscopy of fluorescently stained bacteria

Screening by automated high-throughput microscopy has become a valuable research tool. An essential component of such systems is the autonomous acquisition of focused images. Here we describe the implementation of a high-precision autofocus routine for imaging of fluorescently stained bacteria on a commercially available microscope. We integrate various concepts and strategies that together substantially enhance the performance of autonomous image acquisition. These are (i) nested focusing in brightfield and fluorescence illumination, (ii) autofocusing by continuous life-image acquisition during movement in z-direction rather than at distinct z-positions, (iii) assessment of the quality and topology of a field of view (FOV) by multi-spot focus measurements and (iv) acquisition of z-stacks and application of an extended depth of field algorithm to compensate for FOV unevenness. The freely provided program and documented source code allow ready adaptation of the here presented approach to various platforms and scientific questions

Medium‐grade proteinuria is a risk factor for incident markers of chronic kidney disease

Objective Medium‐grade proteinuria (100–500 mg/g creatinine) is common among people living with HIV/AIDS (PLWHA) but is often undetected or ignored. This prospective, observational cohort study examined medium‐grade proteinuria as a risk factor for markers of chronic kidney disease (CKD). Methods Quantitative urine samples were collected from 241 PLWHA without known renal disease at baseline between January 2009 and February 2011 and at follow‐up 240 weeks later. Multivariate analysis was performed to assess medium‐grade proteinuria as a risk factor for incident markers of CKD (estimated glomerular filtration rate < 60 mL/min/1.73 m2, albuminuria, phosphaturia). Results Incident markers of CKD were identified in 33 patients (14%), of whom 24 (74%) had medium‐grade proteinuria at baseline. Of these, 22 even had proteinuria of < 200 mg/g creatinine. Multivariate analysis showed an adjusted relative risk (aRR) of 2.4 for patients with baseline medium‐grade proteinuria to develop signs of CKD. Age was identified as an additional independent predictor. By testing for interaction, tenofovir disoproxil fumarate (TDF)‐independent proteinuria was strongly associated with incident CKD markers (aRR = 12.1). Conclusion Medium‐grade proteinuria of 100–500 mg/g creatinine is both frequent in PLWHA and a significant risk factor for developing markers of CKD, especially in the absence of TDF. Relevant risk seems to be associated with proteinuria levels as low as 100–200 mg/g creatinine. Current guidelines recommend specific action for proteinuria exceeding 135–200 mg/g but still will miss a relevant number of PLWHA potentially at risk for CKD. An even lower cut‐off to trigger nephrological work‐up and potentially renoprotective interventions appears to be indicated

Modelo PICASA: un estándar de actuación frente al acoso escolar

El acoso escolar es una realidad que se extiende a todos los centros escolares. Conscientes de esta problemática, se ha decidido investigar en la situación llevando a cabo un análisis de diferentes casos en los que se establecían dinámicas de acoso escolar. Tras el pormenorizado análisis de dichos casos y de los modelos y procedimientos empleados para combatirlo nace el modelo PICASA como un estándar de actuación frente a situaciones en las que puede existir una posible dinámica de acoso escolar. El modelo PICASA es un estándar que cada Centro debe hacer propio adaptándolo a su realidad y a sus necesidades y posibilidades así como al día a día. Pretende hacer partícipe a toda la Comunidad Educativa. El modelo debe su nombre a las iniciales de cada uno de sus seis pasos. La primera serie de medidas van encaminadas a proteger a la víctima de acoso escolar. Se encontrarían también recogidas bajo la “P” todas las medidas preventivas existentes. Otra herramienta esencial es identificar qué dinámicas se están llevando a cabo por parte de quiénes y desde cuándo. Una vez hemos obtenido algunos datos, hay que comunicar a los familiares de unos y de otros. Posteriormente es esencial el apoyo al menor víctima de acoso escolar desde el Departamento de Orientación y la tutoría. Es necesario aplicar algún tipo de medida sancionadora, ofreciendo importancia a la sanción reparadora. Finalmente, consideramos este paso esencial, hay que llevar a cabo un proceso de aprendizaje institucional: Es esencial que la institución crezca. Acompaña a este artículo una experiencia de aplicación del modelo PICASA con un protocolo de actuación frente al acoso escolar empleado durante 10 años acompañado de otras herramientas preventivas tales como programas de mediación y medidas para la implicación de los padres.Bullying is a reality that extends to all schools. Aware of this problem, it was decided to investigate the situation by carrying out an analysis of different cases that were set dynamics of bullying. After a detailed analysis of such cases and the models and methods used to combat bullying, PICASA born as a standard procedure for action in situations where there may be a possible dynamics of bullying. PICASA is a standard procedure that each center must make his own reality and adapting it to their needs and possibilities as well as day to day, by involving the entire educational community. The model is named after the initials of each of the six steps. Initially we must protect the victim of bullying. Another key action is to identify what dynamics are being carried out by whom and when. Once we have obtained some data, we must communicate with the family of one or the other. Subsequently supporting the child victim of bullying from the Guidance Department and mentoring is essential. Is it necessary to apply some kind of punitive measure, giving importance to the restorative sanction. Finally, we consider this essential step, we must carry out a process of institutional learning: Is there anything that can be done better? What measures should be undertaken to not happen again? It is essential that the institution grow. The article also presents an example of application of PICASA procedure employed for over 10 years to address cases of bullying as well as another series of preventive measures, procedures, school mediation programs and measures for parental involvement

Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions

The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens. A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity—the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences

Impact of photon recycling on the light extraction from metal halide perovskite light emitting diodes

Erworben im Rahmen der Schweizer Nationallizenzen (http://www.nationallizenzen.ch)The impact of photon recycling on the efficiency of light extraction from metal halide perovskite light emitting diodes is quantified using a novel modelling framework based on a detailed-balance compatible Green dyad approach. Analysis of photon modes contributing to internal emission and iterative evaluation of re-absorption and re-emission processes is performed for single perovskite layers in absence and presence of a metallic reflector and under consideration of associated parasitic absorption losses. Finally, the approach is employed to characterize the emission characteristics of a realistic multilayer device stack in dependence of the emitter thickness

Modeling resilience and sustainability in ancient agricultural systems

The reasons why people adopt unsustainable agricultural practices, and the ultimate environmental implications of those practices, remain incompletely understood in the present world. Archaeology, however, offers unique datasets on coincident cultural and ecological change, and their social and environmental effects. This article applies concepts derived from ecological resilience thinking to assess the sustainability of agricultural practices as a result of long-term interactions between political, economic, and environmental systems. Using the urban center of Gordion, in central Turkey, as a case study, it is possible to identify mismatched social and ecological processes on temporal, spatial, and organizational scales, which help to resolve thresholds of resilience. Results of this analysis implicate temporal and spatial mismatches as a cause for local environmental degradation, and increasing extralocal economic pressures as an ultimate cause for the adoption of unsustainable land-use practices. This analysis suggests that a research approach that integrates environmental archaeology with a resilience perspective has considerable potential for explicating regional patterns of agricultural change and environmental degradation in the past

Nowcasting of thunderstorm severity with Machine Learning in the Alpine Region

Presentación realizada en la 3rd European Nowcasting Conference, celebrada en la sede central de AEMET en Madrid del 24 al 26 de abril de 2019

A new system for computing dentition-based age profiles in Sus scrofa

a b s t r a c t Reconstructing demographic profiles is valuable for revealing animal exploitation strategies at archaeological sites. For pig (Sus scrofa), the method presented by The study presented here is part of ongoing research aimed at developing new methods for the construction of S. scrofa demographic profiles based on both dentition and long bone fusion. In this paper, we present the results of a study of eruption and wear patterns in a large modern assemblage of wild boar which provides the basis for a new method for constructing pig harvest profiles and addresses some of the most serious limitations of Grant&apos;s earlier study. The utility of this method in detecting subtle differences in pig prey/harvest profiles is demonstrated through its application to three Near Eastern archaeological assemblages from three distinct time periods: Bronze Age Tell Leilan, Halafian Banahilk, and Epipaleolithic Hallan Çemi, where residents likely employed widely different pig exploitation strategies. The results of these case studies demonstrate the ability of this method to reliably reconstruct age demography and distinguish age profiles between sites with different animal procurement strategies. This method provides a standardized means of collecting accurate and reliable age data crucial in examining patterns of past pig exploitation