Miracle-dz/UniFAR-FTUs huggingface dataset:
(2019). As Blind as a Bat? Opsin Phylogenetics Illuminates the Evolution of Color Vision in Bats. Molecular Biology and Evolution, 36(1), 54-68.

Through their unique use of sophisticated laryngeal echolocation bats are considered sensory specialists amongst mammals and represent an excellent model in which to explore sensory perception. Although several studies have shown that the evolution of vision is linked to ecological niche adaptation in other mammalian lineages, this has not yet been fully explored in bats. Recent molecular analysis of the opsin genes, which encode the photosensitive pigments underpinning color vision, have implicated high-duty cycle (HDC) echolocation and the adoption of cave roosting habits in the degeneration of color vision in bats. However, insufﬁcient sampling of relevant taxa has hindered deﬁnitive testing of these hypotheses. To address this, novel sequence data was generated for the SWS1 and MWS/LWS opsin genes and combined with existing data to comprehensively sample species representing diverse echolocation types and niches ( SWS1 n ¼ 115; MWS/LWS n ¼ 45). A combination of phylogenetic analysis, ancestral state reconstruction, and selective pressure analyses were used to reconstruct the evolution of these visual pigments in bats and revealed that although both genes are evolving under purifying selection in bats, MWS/LWS is highly conserved but SWS1 is highly variable. Spectral tuning analyses revealed that MWS/LWS opsin is tuned to a long wavelength, 555–560nm in the bat ancestor and the majority of extant taxa. The presence of UV vision in bats is supported by our spectral tuning analysis, but phylogenetic analyses demonstrated that the SWS1 opsin gene has undergone pseudogenization in several lineages. We do not ﬁnd support for a link between the evolution of HDC echolocation and the pseudogenization of the SWS1 gene in bats, instead we show the SWS1 opsin is functional in the HDC echolocator, Pteronotus parnellii . Pseudogenization of the SWS1 is correlated with cave roosting habits in the majority of pteropodid species. Together these results demonstrate that the loss of UV vision in bats is more widespread than was previously considered and further elucidate the role of ecological niche specialization in the evolution of vision in bats.
A Computer-Controlled 36-Channel Time Domain Reflectometry System for Monitoring Soil Water Contents

Research on the spatial and temporal dynamics of soil water has long been impeded by the lack of an automated technique for the measurement of soil water content. A computer controlled time domain reflectometry (TDR) system is described which gives the possibility of making a large number of measurements at different sites at predetermined time intervals. The developed system operates on 12 V dc and has the capability to monitor water contents at 36 sites. The algorithm used for the automatic analysis of the measurements is also presented. It is based on the calculation of the travel time of the TDR signal between the beginning and the end of a three-wire probe.
Quantification of Degree of Saturation at Shallow Depths of Earth Slopes Using Resistivity Imaging Technique

AbstractEarthen slopes encountered in engineering practice typically consist of unsaturated or partially saturated soils. During rainfall, water infiltrates into the slope and causes a reduction in suction. Slope stability is affected by the increase in the degree of saturation as a result of the reduction in normal stress and cohesive strength along potential failure surfaces. Therefore, to determine the geohazard potential, it is important to know the degree of saturation within slopes at shallow depths. Resistivity imaging (RI) is one of the most convenient techniques available for geohazard studies; however, only qualitative saturation profiles can be obtained using this method. Quantification of the degree of saturation has become important for using RI in the evaluation of the geohazard potential of slope failures. The objective of this study was to quantify the degrees of saturation at shallow depths using RI. Electrical resistivity tests were conducted in the laboratory on high plasticity clay (CH.
The GLOBE Project: accelerating global synthesis of local studies in land change science

Global understanding of land change processes requires synthesis of observations and models across local and regional scales. The GLOBE project, newly funded by a grant from the US National Science Foundation, is working closely with the GLP and others to build an online scientifi c collaboration environment designed to enhance and accelerate the process of cross-scale collaboration and global knowledge synthesis from local and regional studies of land change.
MEGA 5 : Molecular Evolutionary Genetics Analysis using Maximum Likelihood , Evolutionary Distance , and Maximum Parsimony Methods

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of MEGA5 (Molecular Evolutionary Genetics Analysis version 5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of Maximum Likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user-interface has now been enhanced to be activity-driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from www.megasoftware. net. 3 The Molecular Evolutionary Genetics Analysis (MEGA) software was developed with the goal of providing a biologist-centric, integrated suite of tools for statistical analyses of DNA and protein sequence data from an evolutionary standpoint. Over the years, it has grown to include tools for sequence alignment, phylogenetic reconstruction and phylogeny visualization, testing an array of evolutionary hypotheses, estimating sequence divergences, web-based acquisition of sequence data, and expert systems to generate natural language descriptions of the analysis methods and data chosen by the user Kumar et al. 2008). With the fifth major release, the collection of analysis tools in MEGA has now broadened to include the Maximum Likelihood (ML) methods for molecular evolutionary analysis. Table 1 contains a summary of all statistical methods and models in MEGA5, with new features marked with an asterisk (*). In the following, we provide a brief description of methodological advancements, along with relevant research results, and technical enhancements in MEGA5. MEGA5 now contains facilities to evaluate the fit of major models of nucleotide and amino acid substitutions, which are frequently desired by researchers (GTR) and five nested models are available, whereas six models with and without empirical frequencies have been programmed for the …
Interaction between ArgR and AhrC Controls Regulation of Arginine Metabolism in Lactococcus lactis*

The expression of arginine metabolism in Lactococcus lactis is controlled by the two homologous transcriptional regulators ArgR and AhrC. Genome sequence analyses have shown that the occurrence of multiple homologues of the ArgR family of transcriptional regulators is a common feature of many low-G + C Gram-positive bacteria. Detailed studies of ArgR type regulators have previously only been carried out in bacteria containing single regulators. Here, we present a first characterization of the two L. lactis arginine regulators by means of gel retardation and DNase I footprinting. ArgR of L. lactis was shown to bind to the promoter regions of both the arginine biosynthetic argCJDBF operon and the arginine catabolic arcABD1C1C2TD2yvaD operon, but in an arginine-independent manner. Surprisingly, AhrC alone was unable to bind to DNA. Arginine-dependent DNA binding was obtained by mixing the two regulators in gel retardation assays. With both regulators present, the addition of arginine led to increased binding of ArgR-AhrC to the biosynthetic argC promoter but also to diminished binding to the catabolic arcA promoter. Footprinting showed ArgR-AhrC protection of regions containing ARG box operator sequences preceding argC. In the absence of AhrC, ArgR protected sites in the arcA promoter region with similarity to ARG box half-sites, here called ARC boxes. We propose a model for repression of arginine biosynthesis and activation of catabolism by anti-repression, involving arginine-dependent interaction between the two L. lactis regulator proteins, ArgR and AhrC.
Revisiting the Existence of the Global Warming Slowdown during the Early Twenty-First Century

: There are heated debates on the existence of the global warming slowdown during the early twenty-ﬁ rst century. Although efforts have been made to clarify or reconcile the controversy over this issue, it is not explicitly addressed, restricting the understanding of global temperature change particularly under the background of increasing greenhouse gas concentrations. Here, using extensive temperature datasets, we comprehensively reexamine the existence of the slowdown under all existing de ﬁ nitions during all decadal-scale periods spanning 1990 – 2017. Results show that the short-term linear trend – dependent de ﬁ nitions of slowdown make its identi ﬁ cation severely suffer from the period selection bias, which largely explains the controversy over its existence. Also, the controversy is further aggravated by the signi ﬁ cant impacts of the differences between various datasets on the recent temperature trend and the different baselines for measuring slowdown prescribed by various de ﬁ nitions. However, when the focus is shifted from speci ﬁ c periods to the probability of slowdown events, we ﬁ nd the probability is signi ﬁ cantly higher in the 2000s than in the 1990s, regardless of which de ﬁ nition and dataset are adopted. This supports a slowdown during the early twenty-ﬁ rst century relative to the warming surge in the late twentieth century, despite higher greenhouse gas concentrations. Furthermore, we demonstrate that this decadal-scale slowdown is not incompatible with the centennial-scale anthropogenic warming trend, which has been accelerating since 1850 and never pauses or slows. This work partly reconciles the controversy over the existence of the warming slowdown and the discrepancy between the slowdown and anthropogenic warming.
Rapid and flexible high-resolution scanning enabled by cycloidal computed tomography and convolutional neural network (CNN) based data recovery

—We have combined a recently developed imaging concept (“cycloidal computed tomography”) with convolutional neural network (CNN) based data recovery. The imaging concept is enabled by exploiting, in synergy, the benefits of probing the sample with a structured x-ray beam and applying a cycloidal acquisition scheme by which the sample is simultaneously rotated and laterally translated. The beam structuring provides a means of increasing the in-slice spatial resolution in tomographic images irrespective of the blur imposed by the x-ray source and detector, while the “roto-translation” sampling allows for rapid scanning. Data recovery based on the recently proposed Mixed-Scale Dense (MSD) CNN architecture enables an efficient reconstruction of high-quality, high-resolution images despite the fact that cycloidal computed tomography data are highly incomplete. In the following, we review the basic principles underpinning cycloidal computed tomography, introduce the CNN based data recovery method and discuss the benefit of combining both.
From descriptors to intrinsic fish toxicity of chemicals: an alternative approach to chemical prioritization

1 Most chemicals present in the human and environmental exposome are structurally 2 unknown (i.e. ≤ 1%). The European Chemicals Agency (ECHA) and US Environmen-3 tal Protection Agency (EPA) have listed approximately 800k chemicals that must be 4 further investigated for their potential environmental and/or human health risk. A sig-5 nificant number of these chemicals have large enough global volumes of consumption 6 (e.g. industrial and agrochemical) to reach the limits of detection of our analytical 7
Wind turbine rotors in surge motion: New insights into unsteady aerodynamics of FOWT from experiments and simulations

An accurate prediction of the unsteady loads acting on ﬂoating offshore wind turbines (FOWT) under consideration of wave excitation is crucial for a resource-efﬁcient turbine design. Despite a considerable number of simulation studies in this area, it is still not fully understood, which unsteady aerodynamic phenomena have a notable inﬂuence on the loads acting on a wind turbine rotor in motion. In the present study, investigations are carried out to evaluate of the most relevant unsteady aerodynamic phenomena for a wind turbine rotor in surge motion. As a result, inﬂow conditions are determined for which a 5 signiﬁcant inﬂuence of these phenomena on the rotor loads can be expected. The experimental and numerical investigations are conducted on a two-bladed wind turbine rotor subjected to a tower top surge motion. A specialised wind tunnel test rig has been developed to measure the aerodynamic torque response of the rotor subjected to surge motions with moderate frequencies. The torque measurements are compared to two free vortex wake methods, namely a panel and a lifting-line method. Unsteady contributions that cannot be captured using quasi-steady 10 modelling have not been detected in either the measurements or the simulations in the covered region of motion frequencies. The surge motion frequencies were limited to a moderate range due to vibrations occurring in the experiments. Therefore, a numerical study with an extended the range of motion frequencies using the panel and the lifting-line method was performed. The results reveal signiﬁcant unsteady contributions of the surge motions to the torque and thrust response that cannot be modelled in a quasi-steady way. Furthermore, the results show the presence of the returning wake effect, which is known from 15 helicopter aerodynamics. Additional simulations of the UNAFLOW scale model and the IEA 15 MW rotor demonstrate that the occurrence of the returning wake effect is independent from the turbine, but determined by the ratio of rotor speed and surge motion. In case of the IEA 15 MW, a notable impact of the returning wake effect was found at surge motion frequencies in the range of typical wave periods. Finally, a comparison with OpenFAST simulations reveals notable differences in the modelling of the unsteady aerodynamic behaviour in comparison to a FVW method.
Polarization upgrade of specMACS: calibration and characterization of the 2D RGB polarization-resolving cameras

Abstract. The spectrometer of the Munich Aerosol Cloud Scanner (specMACS) is a high-spatial-resolution hyperspectral and polarized imaging system. It is operated from a nadir-looking perspective aboard the German High Altitude and LOng range (HALO) research aircraft and is mainly used for the remote sensing of clouds. In 2019, its two hyperspectral line cameras, which are sensitive to the wavelength range between 400 and 2500 nm, were complemented by two 2D RGB polarization-resolving cameras. The polarization-resolving cameras have a large field of view and allow for multi-angle polarimetric imaging with high angular and spatial resolution. This paper introduces the polarization-resolving cameras and provides a full characterization and calibration of them. We performed a geometric calibration and georeferencing of the two cameras. In addition, a radiometric calibration using laboratory calibration measurements was carried out. The radiometric calibration includes the characterization of the dark signal, linearity, and noise as well as the measurement of the spectral response functions, a polarization calibration, vignetting correction, and absolute radiometric calibration. With the calibration, georeferenced, absolute calibrated Stokes vectors rotated into the scattering plane can be computed from raw data. We validated the calibration results by comparing observations of the sunglint, which is a known target, with radiative transfer simulations of the sunglint.
Type I interferon causes thrombotic microangiopathy by a dose-dependent toxic effect on the microvasculature. Blood, 128(24), 2824-2833

Many drugs have been reported to cause thrombotic microangiopathy (TMA), yet the quality of evidence supporting a causal association is often weak. In particular TMA has been reported in association with recombinant type I interferon therapies, with recent concern regarding the use of interferon in multiple sclerosis patients. However a causal association has yet to be demonstrated. Here we adopt a combined clinical, epidemiological and experimental approach to provide evidence of a causal association between type I interferon and TMA. First we show the clinical phenotype of cases referred to a national centre is uniformly consistent with a direct drug-induced TMA, with no plausible confounding factors. Second we analyse both national and global drug safety data and show that type I interferon-associated TMA is dose-dependent. Third, we show that dose-dependent microvascular disease is seen in a novel transgenic mouse model of interferon toxicity. This microvascular pathology includes specific pathological changes seen in patient biopsies and is dependent on activation of the interferon response through the type I interferon receptor (IFNAR). Together our clinical and experimental findings reveal a causal link between type 1 interferon and thrombotic microangiopathy. As such, recombinant type I interferon therapies should be stopped at the earliest stage in patients who develop this complication, with implications for risk mitigation.
the effects of

Very little research has concurrently explored the influence of both physical space and social context (or place) on the way people engage with a public interactive display. We addressed this issue with a novel approach: studying how people engaged with the same interactive installation in ten situations with varying spatial and social properties. The main finding across these studies is that place trumps space: a conducive social context could overcome a poor physical space and encourage interaction; conversely, an inappropriate social context could inhibit interaction in spaces that might normally facilitate engagement. We discuss this finding in terms of the salience of the display within the space, the visibility of incidental interactions with the installation, the different understandings of place that people can have in the same location, and the role of emergent champions and comperes in encouraging interaction.
Development of an augmented Damerau–Levenshtein method for correcting spelling errors in Kazakh texts

The presented paper is devoted to the development of a method for identifying and correcting spelling errors in Kazakh texts. In this paper, the study object is methods for more accurate correction of spelling errors in Kazakh texts. The aim of the study is to develop an augmented version of the Damerau-Levenshtein method for correcting spelling errors in Kazakh language texts. Automatic detection and correction of spelling errors have become a default feature in modern text editors for working with text data, in text messaging applications such as chatbots, messengers, etc. However, although this task is well solved in geographically widespread languages, it has not been fully solved in languages with a small audience, such as the Kazakh language. The methods developed so far cannot correct all spelling errors found in Kazakh texts. Therefore, the development of a method with specific algorithms for spelling error correction in Kazakh texts is considered. As a result of the research work, algorithms for correcting errors found in Kazakh language texts were developed, and the developed algorithms were included in the Damerau-Levenshtein method. The experimental testing results of the augmented Damerau- Levenshtein method showed 97.2 % accuracy in correcting specific errors found only in Kazakh words and 92.8 % accuracy in correcting common errors from letter symbols. The standard Damerau-Levenshtein method testing results showed 76.4 % accuracy in correcting specific errors found only in Kazakh words. The results of the tests in correcting common errors from letter symbols with the standard Damerau-Levenshtein were approximately the same with the augmented Damerau-Levenshtein method, the accuracy is 92.2 %. The extent and conditions of practical application of the results are implemented by including them in text editors, messengers, e-mails and similar applications that work with text data.
PERFORMANCE APPRAISAL SYSTEM: LIFE CYCLE DISCLOSURE IN THE PUBLIC PORT CONTEXT

The processes for appraising organizational performance have become more complex. However, studies have focused on specific stages in the development of Performance Appraisal Systems, disregarding their completeness. This research seeks to describe how the evolutionary stages of a Performance Appraisal System (PAS) develop in the Brazilian public port context. A one-year case study was carried out, during which time the System went through the stages of the Life Cycle proposed by Bourne et al. (2000). To develop the System, data was collected through semi-structured interviews with the decision-maker of a public port holding company, guided by the Constructivist Multi Criteria Decision Aid (MCDA-C) methodology. The results of this research show how a PAS is designed, implemented, used and updated, offering contributions to the field of research, which is criticized for the lack of evidence demonstrating the complete Life Cycle of PAS. The study also provides evidence on the construction of knowledge generated during the stages of the System Life Cycle. In this way, it was possible to contribute by providing the organization with a model capable of measuring and supporting management activities and decision-making. The combination of theoretical contributions with the knowledge derived from the illustrated empirical results corroborates the area of Performance Appraisal research on the validity of the PAS Life Cycle and contributes to leveraging the organization's performance.