『青山評論』記者三浦泰一郎論 -北村透谷との接点を辿って-

This research work is centred on continental lacustrine gypsum deposits of Miocene age cropping out in the easternmost part of the Madrid Basin. These gypsum deposits, accumulated in a continental saline lake, are characterized by a spectacular, distinctive Christmas-tree morphology and a peculiar dolomite replacement. A combination of microscopic (petrography and scanning electron microscopy) and analytical techniques (fluid inclusion microthermometry, X-ray energy dispersive spectroscopy and X-ray diffractometry) was used in order to study the crystallographic distribution and the composition of the fluid inclusions within the gypsum. The objectives were to characterize the continental brine from which the mineral precipitated, and to detect mineral and element traces that could indicate early diagenetic processes altering the gypsum deposits. Data from primary fluid inclusions indicated that gypsum precipitated from an aqueous fluid (lake water) of low to moderate total salinity (between 20 and 90 g/L NaCl). Secondary fluid inclusions represent interstitial lake brine in contact with gypsum, slightly enriched in total salt content as crystal formation proceeded. Textural, ultrastructural and microanalytical analysis indicate that the presence of dolomite precipitates inside the gypsum layers is related to the microbial colonization of the gypsum deposits and the biomineralization of the cell walls and extracellular polymeric substances around the cells. Our investigation emphasizes necessity of a multidisciplinary approach to assess geobiological processes

Factores de riesgo para la presentación de bacteriuria en gatos con enfermedad del tracto urinario inferior: un análisis retrospectivo de 102 casos (2008 – 2015)

The aim of this retrospective study was to describe the results of bacterial isolates and to determine the risk factors involved in the presentation of bacteriuria in cats with lower urinary tract disease (FLUTD). Clinical records of feline patients (n=102) who underwent urinalysis and urine culture were collected. The following variables were considered: age, sex, reproductive status, breed, bodyweight, season, colour of urine, urine odour, urine density, pH, glucose, proteins, blood, leukocytes, erythrocytes, crystals and type of crystals. In 60.8% (62/102) of the samples, bacteria were isolated in urine, including E. coli 40.3% (25/62), Klebsiella sp 12.9% (8/62), Staphylococcus sp 12.9% (8 / 62), Proteus sp 8.1% (5/62), Enterobacter sp 8.1% (5/62) and Staphylococcus epidermidis 6.4% (4/62). Age, urinary density and presence of blood were statistically significant. In addition, it was determined that the urine density, the red colour of the urine, the presence of leukocytes and crystals represent risk factors (p <0.05) for the occurrence of bacteriuria.El objetivo de este estudio retrospectivo fue describir los resultados de aislados bacterianos y determinar los factores de riesgo involucrados en la presentación de bacteriuria en gatos con enfermedad del tracto urinario inferior (FLUTD). Se recolectaron 102 historias clínicas de pacientes felinos a los cuales se les realizó análisis de orina y urocultivo. Se consideraron las variables edad, sexo, estado reproductivo, raza, peso, estación del año, color de orina, olor de orina, densidad urinaria, pH, glucosa, proteínas, sangre, leucocitos, eritrocitos, cristales y tipo de cristales. En el 60.8% (62/102) de las muestras se llegó a aislar bacterias en orina, entre ellas E. coli 40.3% (25/62), Klebsiella sp 12.9% (8/62), Staphylococcus sp 12.9% (8/62), Proteus sp 8.1% (5/62), Enterobacter sp 8.1% (5/62) y Staphylococcus epidermidis 6.4% (4/62). La edad, densidad urinaria y presencia de sangre fue estadísticamente significativa. Además, se determinó que, la densidad urinaria, el color rojo de la orina, la presencia de leucocitos y de cristales representan factores de riesgo (p<0.05) para la ocurrencia de bacteriuria

Transient Changes in the Plasma of Astrocytic and Neuronal Injury Biomarkers in COVID-19 Patients without Neurological Syndromes

The levels of several glial and neuronal plasma biomarkers have been found to increase during the acute phase in COVID-19 patients with neurological symptoms. However, replications in patients with minor or non-neurological symptoms are needed to understand their potential as indicators of CNS injury or vulnerability. Plasma levels of glial fibrillary acidic protein (GFAP), neurofilament light chain protein (NfL), and total Tau (T-tau) were determined by Single molecule array (Simoa) immunoassays in 45 samples from COVID-19 patients in the acute phase of infection [moderate (n = 35), or severe (n = 10)] with minor or non-neurological symptoms; in 26 samples from fully recovered patients after ~2 months of clinical follow-up [moderate (n = 23), or severe (n = 3)]; and in 14 non-infected controls. Plasma levels of the SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE2), were also determined by Western blot. Patients with COVID-19 without substantial neurological symptoms had significantly higher plasma concentrations of GFAP, a marker of astrocytic activation/injury, and of NfL and T-tau, markers of axonal damage and neuronal degeneration, compared with controls. All these biomarkers were correlated in COVID-19 patients at the acute phase. Plasma GFAP, NfL and T-tau levels were all normalized after recovery. Recovery was also observed in the return to normal values of the quotient between the ACE2 fragment and circulating full-length species, following the change noticed in the acute phase of infection. None of these biomarkers displayed differences in plasma samples at the acute phase or recovery when the COVID-19 subjects were sub-grouped according to occurrence of minor symptoms at re-evaluation 3 months after the acute episode (so called post-COVID or "long COVID"), such as asthenia, myalgia/arthralgia, anosmia/ageusia, vision impairment, headache or memory loss. Our study demonstrated altered plasma GFAP, NfL and T-tau levels in COVID-19 patients without substantial neurological manifestation at the acute phase of the disease, providing a suitable indication of CNS vulnerability; but these biomarkers fail to predict the occurrence of delayed minor neurological symptoms

The ODD protocol for describing agent-based and other simulation models: A second update to improve clarity, replication, and structural realism

© 2020, University of Surrey. All rights reserved. The Overview, Design concepts and Details (ODD) protocol for describing Individual-and Agent-Based Models (ABMs) is now widely accepted and used to document such models in journal articles. As a standardized document for providing a consistent, logical and readable account of the structure and dynamics of ABMs, some research groups also find it useful as a workflow for model design. Even so, there are still limitations to ODD that obstruct its more widespread adoption. Such limitations are discussed and addressed in this paper: the limited availability of guidance on how to use ODD; the length of ODD documents; limitations of ODD for highly complex models; lack of sufficient details of many ODDs to enable reimplementation without access to the model code; and the lack of provision for sections in the document structure covering model design ratio-nale, the model’s underlying narrative, and the means by which the model’s fitness for purpose is evaluated. We document the steps we have taken to provide better guidance on: structuring complex ODDs and an ODD summary for inclusion in a journal article (with full details in supplementary material; Table 1); using ODD to point readers to relevant sections of the model code; update the document structure to include sections on model rationale and evaluation. We also further advocate the need for standard descriptions of simulation experiments and argue that ODD can in principle be used for any type of simulation model. Thereby ODD would provide a lingua franca for simulation modelling

Non-Linear 3D Hybrid Kinetic-MHD Simulations of Alfvén Eigenmodes in the ASDEX Upgrade Tokamak

EUROfusion Consortium 63305

PDLIM2 regulates transcription factor activity in epithelial-to-mesenchymal transition via the COP9 signalosome

Epithelial cell differentiation and polarized migration associated with epithelial-to-mesenchymal transition (EMT) in cancer requires integration of gene expression with cytoskeletal dynamics. Here we show that the PDZ-LIM domain protein PDLIM2 (Mystique/SLIM), a known cytoskeletal protein and promoter of nuclear nuclear factor κB (NFκB) and signal transducer and activator of transcription (STAT) degradation, regulates transcription factor activity and gene expression through the COP9 signalosome (CSN). Although repressed in certain cancers, PDLIM2 is highly expressed in invasive cancer cells. Here we show that PDLIM2 suppression causes loss of directional migration, inability to polarize the cytoskeleton, and reversal of the EMT phenotype. This is accompanied by altered activity of several transcription factor families, including β-catenin, Ap-1, NFκB, interferon regulatory factors, STATs, JUN, and p53. We also show that PDLIM2 associates with CSN5, and cells with suppressed PDLIM2 exhibit reduced nuclear accumulation and deneddylation activity of the CSN toward the cullin 1 and cullin 3 subunits of cullin-RING ubiquitin ligases. Thus PDLIM2 integrates cytoskeleton signaling with gene expression in epithelial differentiation by controlling the stability of key transcription factors and CSN activity.FWN – Publicaties zonder aanstelling Universiteit Leide

2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.Instituto de Patología VegetalFil: Kuhn, Jens H. National Institute of Allergy and Infectious Diseases. National Institutes of Health. Integrated Research Facility at Fort Detrick; Estados UnidosFil: Adkins, Scott. US Horticultural Research Laboratory. United States Department of Agriculture. Agricultural Research Service; Estados UnidosFil: Alkhovsky, Sergey V. Ministry of Health of Russian Federation. National Center on Epidemiology and Microbiology .D.I. Ivanovsky Institute of Virology of N.F. Gamaleya; RusiaFil: Avšič-Županc, Tatjana. University of Ljubljana. Faculty of Medicine. Institute of Microbiology and Immunology; EsloveniaFil: Ayllón, María A. Universidad Politécnica de Madrid. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria.Centro de Biotecnología y Genómica de Plantas; EspañaFil: Ayllón, María A. Universidad Politécnica de Madrid. Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas. Departamento de Biotecnología-Biología Vegetal; EspañaFil: Bahl, Justin. University of Georgia. Center for Ecology of Infectious Diseases. Insitute of Bioinformatics. Department of Infectious Diseases. Department of Epidemiology and Biostatistics; Estados UnidosFil: Balkema-Buschmann, Anne. Friedrich-Loeffler-Institut. Institute of Novel and Emerging Infectious Diseases; AlemaniaFil: Ballinger, Matthew J. Mississippi State University. Department of Biological Sciences; Estados UnidosFil: Bandte, Martina. Humboldt-Universität zu Berlin. Faculty of Life Sciences. Division Phytomedicine; AlemaniaFil: Beer, Martin. Friedrich-Loeffler-Institut. Institute of Diagnostic Virology; AlemaniaFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Lodden Økland, Arnfnn. Pharmaq Analytiq; Norueg

Application of Probabilistic Neural Networks to microhabitat suitability modelling for adult brown trout (Salmo trutta L.) in Iberian rivers

Probabilistic Neural Networks (PNN) have been tested for the first time in microhabitat suitability modelling for adult brown trout (Salmo trutta L.). The impact of data prevalence on PNN was studied. The PNN were evaluated in an independent river and the applicability of PNN to assess the environmental flow was analysed. Prevalence did not affect significantly the results. However PNN presented some limitations regarding the output range. Our results agreed previous studies because trout preferred deep microhabitats with medium-to-coarse substrate whereas velocity showed a wider suitable range. The 0.5 prevalence PNN showed similar classificatory capability than the 0.06 prevalence counterpart and the outputs covered the whole feasible range (from 0 to 1), but the 0.06 prevalence PNN showed higher generalisation because it performed better in the evaluation and it allowed a better modulation of the environmental flow. PNN has demonstrated to be a tool to be into consideration.The authors would like to thank the Spanish Ministry of Economy and Competitiveness for its financial support through the SCARCE project (Consolider-Ingenio 2010 CSD2009-00065). We are grateful to the colleagues who worked in the field and in the preliminary data analyses, especially Marta Bargay, Aina Hernandez and David Argibay. The works were partially funded by the Confederacion Hidrografica del Jucar (Spanish Ministry of Agriculture, Food and Environment), that also provided hydrological and environmental information about the study sites. The authors also thank the Direccion General del Agua and INFRAECO for the cession of the microhabitat data. Finally, we also thank Javier Ferrer, Teodoro Estrela and Onofre Gabaldo (Confederacion Hidrografica del Jucar) for their help and the data provided. Thanks to Grieg Davies for the academic review of English.Muñoz Mas, R.; Martinez-Capel, F.; Garófano-Gómez, V.; Mouton, A. (2014). Application of Probabilistic Neural Networks to microhabitat suitability modelling for adult brown trout (Salmo trutta L.) in Iberian rivers. Environmental Modelling and Software. 59:30-43. https://doi.org/10.1016/j.envsoft.2014.05.003S30435

Residual Expression of the Reprogramming Factors Prevents Differentiation of iPSC Generated from Human Fibroblasts and Cord Blood CD34+ Progenitors

Human induced pluripotent stem cells (hiPSC) have been generated from different tissues, with the age of the donor, tissue source and specific cell type influencing the reprogramming process. Reprogramming hematopoietic progenitors to hiPSC may provide a very useful cellular system for modelling blood diseases. We report the generation and complete characterization of hiPSCs from human neonatal fibroblasts and cord blood (CB)-derived CD34+ hematopoietic progenitors using a single polycistronic lentiviral vector containing an excisable cassette encoding the four reprogramming factors Oct4, Klf4, Sox2 and c-myc (OKSM). The ectopic expression of OKSM was fully silenced upon reprogramming in some hiPSC clones and was not reactivated upon differentiation, whereas other hiPSC clones failed to silence the transgene expression, independently of the cell type/tissue origin. When hiPSC were induced to differentiate towards hematopoietic and neural lineages those hiPSC which had silenced OKSM ectopic expression displayed good hematopoietic and early neuroectoderm differentiation potential. In contrast, those hiPSC which failed to switch off OKSM expression were unable to differentiate towards either lineage, suggesting that the residual expression of the reprogramming factors functions as a developmental brake impairing hiPSC differentiation. Successful adenovirus-based Cre-mediated excision of the provirus OKSM cassette in CB-derived CD34+ hiPSC with residual transgene expression resulted in transgene-free hiPSC clones with significantly improved differentiation capacity. Overall, our findings confirm that residual expression of reprogramming factors impairs hiPSC differentiation