Miracle-dz/UniFAR-FTUs huggingface dataset:
Keeping crispr in check: diverse mechanisms of phage-encoded anti-crisprs

ABSTRACT CRISPR-Cas represents the only adaptive immune system of prokaryotes known to date. These immune systems are widespread among bacteria and archaea, and provide protection against invasion of mobile genetic elements, such as bacteriophages and plasmids. As a result of the arms-race between phages and their prokaryotic hosts, phages have evolved inhibitors known as anti-CRISPR (Acr) proteins to evade CRISPR immunity. In the recent years, several Acr proteins have been described in both temperate and virulent phages targeting diverse CRISPR-Cas systems. Here, we describe the strategies of Acr discovery and the multiple molecular mechanisms by which these proteins operate to inhibit CRISPR immunity. We discuss the biological relevance of Acr proteins and speculate on the implications of their activity for the development of improved CRISPR-based research and biotechnological tools.
Isolation of a nitric oxide inhibitor from mammary tumor cells and its characterization as phosphatidyl serine

Macrophages from mice bearing large D1-DMBA-3 mammary tumors have a decreased capacity to kill tumor targets. This effect is due to an impaired ability to produce nitric oxide (NO) in response to lipopolysaccharide (LPS) stimulation. Here we report that the DA-3 tumor cell line, derived from the in vivo adenocarcinoma D1-DMBA-3, produces a factor that inhibits both NO production/release and cytotoxicity of LPS-activated peritoneal exudate macrophages (PEM). However, other complex macrophage functions such as phagocytosis, superoxide production, mitochondrial dehydrogenase activity, and synthesis of proteins were not reduced by this factor. The NO inhibitor has been found to be lipid in nature. Lipid extracts from DA-3 cell culture supernatants were purified by repeated silica gel column chromatography. The active molecule was unambiguously characterized as phosphatidyl serine (PS) by fast atom bombardment tandem mass spectrometry. Preliminary results indicate a lack of induced NO synthase (iNOS) activity in the lysates of LPS-activated PEM pretreated with PS. The ubiquity of PS in the inner leaflet of biological membranes and its NO inhibitory property, suggest that this phospholipid may be one of the long elusive molecules responsible for regulating physiological levels of NO in the host and hence preventing cellular dysfunction and/or tissue damage. Furthermore, the possible overexpression and shedding of PS by DA-3 tumor cells may represent a novel mechanism to impair macrophage cytotoxicity, a host function that contributes to the protection against developing neoplasms.
Markovian Segmentation of Color and Gray Level Images

The image segmentation is a fundamental tool to analyze and detect objects of interest that can be applied in many fields (medicine, satellite). In this work, we present a classical Markov model for unsupervised image segmentation: "Hidden Markov Chain with Independent Noise" (HMC-IN) for segmenting both gray and color images. Then, we compare five iterative algorithms EM, GEM, SEM, MCEM and ICE for estimating parameters of this model under two final bayesian decision criteria MAP and MPM according to the execution time, the convergence, the PNSR index and the rate error.
Soundscapes and the sense of hearing of fishes.

Underwater soundscapes have probably played an important role in the adaptation of ears and auditory systems of fishes throughout evolutionary time, and for all species. These sounds probably contain important information about the environment and about most objects and events that confront the receiving fish so that appropriate behavior is possible. For example, the sounds from reefs appear to be used by at least some fishes for their orientation and migration. These sorts of environmental sounds should be considered much like "acoustic daylight," that continuously bathes all environments and contain information that all organisms can potentially use to form a sort of image of the environment. At present, however, we are generally ignorant of the nature of ambient sound fields impinging on fishes, and the adaptive value of processing these fields to resolve the multiple sources of sound. Our field has focused almost exclusively on the adaptive value of processing species-specific communication sounds, and has not considered the informational value of ambient "noise. " Since all fishes can detect and process acoustic particle motion, including the directional characteristics of this motion, underwater sound fields are potentially more complex and information-rich than terrestrial acoustic environments. The capacities of one fish species (goldfish) to receive and make use of such sound source information have been demonstrated (sound source segregation and auditory scene analysis), and it is suggested that all vertebrate species have this capacity. A call is made to better understand underwater soundscapes, and the associated behaviors they determine in fishes.
Object-based Control/Data-flow Analysis

Not only does a clear distinction between control and data flow enhance the readability of models, but it also allows different tools to operate on the two distinct parts of the model. This paper shows how the modelling based on control/data-flow analysis can benefit from an object-based approach. We have developed a translation mechanism that is faithful and gives an extra dimension (hierarchy) to the existing paradigm of control and data flow interacting in a model. Our methodology provides a comprehensible separation of these two parts, which can be used to feed another analysis or synthesis tools, while still being able to reason about both parts through formal methods of verification.
Pricing Counter-Party Risk Using Good Deal Bounds

We analyze the problem of pricing counter-party risk for over-the-counter derivatives when there is no liquidly traded credit derivative for the counter-party. We address the market incompleteness by computing good deal bounds. We show that the lower good deal bound is a coherent risk measure and, that the good deal bound interval can be used to assess model risk. Together, these answer the question of how much the price of an OTC derivative can change due to a re-pricing of credit risk on the market or due to a change in risk attitudes and of how much we can trust the numbers we obtain from pricing counter-party risk for firms for which we do not have a liquidly traded credit derivative.
The postcranial anatomy of Brasilodon quadrangularis and the acquisition of mammaliaform traits among non-mammaliaform cynodonts

Brasilodon quadrangularis (Cynodontia, Probainognathia) is an iconic non-mammaliaform cynodont from the Late Triassic of Brazil (Riograndia Assemblage Zone, Candelária Sequence), being considered as the sister taxon of Mammaliaformes. Although its phylogenetic position is very important, several aspects of its postcranial anatomy remain unclear or unstudied. Here, we present a detailed description of the postcranial elements referred to Brasilodon, including previously mentioned specimens and new ones, which add relevant information about its postcranial morphology and provide a new insight into the anatomical transition between advanced non-mammaliaform cynodonts and early mammaliaforms. Functional and ecological implications are also investigated, based on the postcranial morphology and muscular reconstructions. The postcranium of Brasilodon differs from most non-mammaliaform cynodonts and presents similarities with tritylodontids, early mammaliaforms and extant therians, such as a ventrally oriented scapular glenoid facet, a distinct and ossified greater humeral tubercle, lack of ectepicondylar foramen, olecranon process, hemispherical humeral and femoral heads and a prominent intertrochanteric crest. The humeral torsion, the length of the deltopectoral crest, the large bicipital groove and the well-developed lesser tubercle, indicate that the forelimb of Brasilodon was hold in a semi-sprawling position, with well-developed adductor muscles to maintain the body off the ground. The short femoral neck and the strong medial projection of the femoral head indicate the femur was held in a more erect posture than in basal non-mammaliaform cynodonts. The anterodorsally projected iliac blade with reduced postacetabular process, reduction of the anterior part of the pubis, medially located lesser trochanter indicate a basically mammalian pattern of pelvic musculature, able to swing the femur in a nearly parasagittal plane.
Vitamin D status in the United States, 2011-2014.

BACKGROUND Vitamin D is important for bone health; in 2014 it was the fifth most commonly ordered laboratory test among Medicare Part B payments. OBJECTIVES The aim of this study was to describe vitamin D status in the US population in 2011-2014 and trends from 2003 to 2014. METHODS We used serum 25-hydroxyvitamin D data from NHANES 2011-2014 (n = 16,180), and estimated the prevalence at risk of deficiency (<30 nmol/L) or prevalence at risk of inadequacy (30-49 nmol/L) by age, sex, race and Hispanic origin, and dietary intake of vitamin D. We also present trends between 2003 and 2014. RESULTS In 2011-2014, the percentage aged ≥1 y at risk of vitamin D deficiency or inadequacy was 5.0% (95% CI: 4.1%, 6.2%) and 18.3% (95% CI: 16.2%, 20.6%). The prevalence of at risk of deficiency was lowest among children aged 1-5 y (0.5%; 95% CI: 0.3%, 1.1%), peaked among adults aged 20-39 y (7.6%; 95% CI: 6.0%, 9.6%), and fell to 2.9% (95% CI: 2.0%, 4.0%) among adults aged ≥60 y; the prevalence of at risk of inadequacy was similar. The prevalence of at risk of deficiency was higher among non-Hispanic black (17.5%; 95% CI: 15.2%, 20.0%) than among non-Hispanic Asian (7.6%; 95% CI: 5.9%, 9.9%), non-Hispanic white (2.1%; 95% CI: 1.5%, 2.7%), and Hispanic (5.9%; 95% CI: 4.4%, 7.8%) persons; the prevalence of at risk of inadequacy was similar. Persons with higher vitamin D dietary intake or who used supplements had lower prevalences of at risk of deficiency or inadequacy. From 2003 to 2014 there was no change in the risk of vitamin D deficiency; the risk of inadequacy declined from 21.0% (95% CI: 17.9%, 24.5%) to 17.7% (95% CI: 16.0%, 19.7%). CONCLUSION The prevalence of at risk of vitamin D deficiency in the United States remained stable from 2003 to 2014; at risk of inadequacy declined. Differences in vitamin D status by race and Hispanic origin warrant additional investigation.
Opportunistic error correction for MIMO

In this paper, we propose an energy-efficient scheme to reduce the power consumption of ADCs in MIMO-OFDM systems. The proposed opportunistic error correction scheme is based on resolution adaptive ADCs and fountain codes. The key idea is to transmit a fountain-encoded packet over one single sub-carrier per antenna and to transmit more packets than needed for decoding. Comparing to the IEEE 802.11n standard, this approach allows around 83% of power saving in ADCs for a 2×2 system and 90% for a 4×4 system. With the current FEC scheme defined in the IEEE 802.11n standard, a 4×4 system requires twice amount of power in ADCs as a 2×2 system when receiving the same amount of information with the same power. However, using opportunistic error correction in a 4×4 system costs only around 1.4 times amount of energy in ADCs comparing to a 2×2 system.
Cutaneous nociceptive sensitization affects the directional discrimination – but not the 2-point discrimination

Abstract Background and aims Several pain conditions have been shown to reduce the discriminative abilities of external stimuli. The aim of this study was to investigate how cutaneous sensitization affects the tempo-spatial discrimination for both painful laser stimulation and mechanical stimulation. Methods Fifteen healthy subjects were presented with two different stimulation paradigms, a continuous line stimulation and a 2-point stimulation. Line stimulations were delivered in two different directions in lengths of 25, 50, 75, and 100 mm. Two-point distances from 0 to 100 mm were tested. The subjects reported the perceived intensity, and either direction (line stimulations) or number of perceived points (2-point stimulations). All stimuli were tested both before and after topical capsaicin (8% concentration) sensitization (30 min). Results All mechanical line stimulations were reported correctly before capsaicin and 3 stimulations (out of 240) were reported incorrectly after capsaicin. For the laser line stimulation, the directional discrimination threshold (DDT) was 69.5 mm before capsaicin and 76.3 mm after capsaicin. The 2-point discrimination threshold for laser stimulation was 70.3 mm before capsaicin and 68.0 mm after, for the mechanical stimuli it was 31.5 mm before capsaicin and 31.0 mm after capsaicin. The perceived intensities were increased for the laser line stimulations after capsaicin (linear mixed model (LMM), p < 0.001) and increased with stimulation length (LMM, p < 0.001). For mechanical stimuli, NRS was increased following capsaicin (LMM, p < 0.001). The intensities for both mechanical and laser 2-point stimuli increased after capsaicin and increased with distance between points (LMM, p < 0.01). Conclusions The findings show how cutaneous sensitization appears to affect directional discrimination to a larger extent than the 2-point discrimination. Implications This study is the first to investigate how directional discrimination is altered during sensitization. If such measures can be optimized they may provide a new method to probe the neural mechanisms in pain patients.
Batch Support Vector Machine-Trained Fuzzy Classifier with channel equalization application

This paper proposes a Batch Support Vector Machine-Trained Fuzzy Classifier (BSVM-FC). The BSVM-FC is a fuzzy system that consists of Takagi-Sugeno (TS)-type fuzzy rules. For structure learning of the BSVM-FC, there are no fuzzy rules initially. The BSVM-FC online generates all rules according to distributions of training data. A linear support vector machine (SVM) is used to tune the rule consequent parameters. The use of SVM is to give the classifier better generalization performance. Simulation is conducted to very the performance of the BSVM-FC. The BSVM-FC is applied to channel equalization. Comparisons with Gaussian-kernel SVM demonstrate that the BSVM-FC helps to speed up training and test times, and reduce classifier size without deteriorating the generalization ability.
Germline Structural Variations Are Preferential Sites of DNA Replication Timing Plasticity during Development

Abstract The DNA replication timing program is modulated throughout development and is also one of the main factors influencing the distribution of mutation rates across the genome. However, the relationship between the mutagenic influence of replication timing and its developmental plasticity remains unexplored. Here, we studied the distribution of copy number variations (CNVs) and single nucleotide polymorphisms across the zebrafish genome in relation to changes in DNA replication timing during embryonic development in this model vertebrate species. We show that CNV sites exhibit strong replication timing plasticity during development, replicating significantly early during early development but significantly late during more advanced developmental stages. Reciprocally, genomic regions that changed their replication timing during development contained a higher proportion of CNVs than developmentally constant regions. Developmentally plastic CNV sites, in particular those that become delayed in their replication timing, were enriched for the clustered protocadherins, a set of genes important for neuronal development that have undergone extensive genetic and epigenetic diversification during zebrafish evolution. In contrast, single nucleotide polymorphism sites replicated consistently early throughout embryonic development, highlighting a unique aspect of the zebrafish genome. Our results uncover a hitherto unrecognized interface between development and evolution.
Earth-Viewing L-Band Radiometer Sensing of Sea Surface Scattered Celestial Sky Radiation—Part II: Application to SMOS

We examine how the rough sea surface scattering of L-band celestial sky radiation might affect the measurements of the future European Space Agency Soil Moisture and Ocean Salinity (SMOS) mission. For this purpose, we combined data from several surveys to build a comprehensive all-sky L-band celestial sky brightness temperature map for the SMOS mission that includes the continuum radiation and the hydrogen line emission rescaled for the SMOS bandwidth. We also constructed a separate map of strong and very localized sources that may exhibit L-band brightness temperatures exceeding 1000 K. Scattering by the roughened ocean surface of radiation from even the strongest localized sources is found to reduce the contributions from these localized strong sources to negligible levels, and rough surface scattering solutions may be obtained with a map much coarser than the original continuum maps. In rough ocean surface conditions, the contribution of the scattered celestial noise to the reconstructed brightness temperatures is not significantly modified by the synthetic antenna weighting function, which makes integration over the synthetic beam unnecessary. The contamination of the reconstructed brightness temperatures by celestial noise exhibits a strong annual cycle with the largest contamination occurring in the descending swaths in September and October, when the specular projection of the field of view is aligned with the Galactic equator. Ocean surface roughness may alter the contamination by over 0.1 K in 30% of the SMOS measurements. Given this potentially large impact of surface roughness, an operational method is proposed to account for it in the SMOS level 2 sea surface salinity algorithm.
The gp38 Adhesins of the T4 Superfamily: A Complex Modular Determinant of the Phage’s Host Specificity

The tail fiber adhesins are the primary determinants of host range in the T4-type bacteriophages. Among the indispensable virion components, the sequences of the long tail fiber genes and their associated adhesins are among the most variable. The predominant form of the adhesin in the T4-type phages is not even the version of the gene encoded by T4, the archetype of the superfamily, but rather a small unrelated protein (gp38) encoded by closely related phages such as T2 and T6. This gp38 adhesin has a modular design: its N-terminal attachment domain binds at the tip of the tail fiber, whereas the C-terminal specificity domain determines its host receptor affinity. This specificity domain has a series of four hypervariable segments (HVSs) that are separated by a set of highly conserved glycine-rich motifs (GRMs) that apparently form the domain’s conserved structural core. The role of gp38’s various components was examined by a comparative analysis of a large series of gp38 adhesins from T-even superfamily phages with differing host specificities. A deletion analysis revealed that the individual HVSs and GRMs are essential to the T6 adhesin’s function and suggests that these different components all act in synergy to mediate adsorption. The evolutionary advantages of the modular design of the adhesin involving both conserved structural elements and multiple independent and easily interchanged specificity determinants are discussed.
Rigidity-driven growth and migration of epithelial cells on microstructured anisotropic substrates

The physical properties of the cellular environment are involved in regulating the formation and maintenance of tissues. In particular, substrate rigidity appears to be a key factor dictating cell response on culture surfaces. Here we study the behavior of epithelial cells cultured on microfabricated substrates engineered to exhibit an anisotropic stiffness. The substrate consists of a dense array of micropillars of oval cross-section, so that one direction is made stiffer than the other. We demonstrate how such an anisotropic rigidity can induce directional epithelial growth and guide cell migration along the direction of greatest rigidity. Regions of high tractional stress and large cellular deformations within the sheets of cells are concentrated at the edges, in particular at the two poles of the islands along their long axis, in correlation with the orientation of actin stress fibers and focal adhesions. By inducing scattering activity of epithelial cells, we show that isolated cells also migrate along the direction of greatest stiffness. Taken together, these findings show that the mechanical interactions of cells with their microenvironment can be tuned to engineer particular tissue properties.
The ESO-Spitzer Imaging extragalactic Survey (ESIS). I. WFIB, V, R deep observations of ELAIS-S1 and

Context. The ESO-Spitzer extragalactic Imaging Survey (ESIS) is the optical follow up of the Spitzer Wide-Area InfraRed Extragalactic (SWIRE) survey in the ELAIS-S1 area. Aims. The multiwavelength study of galaxy emission is the key to understand the interplay of the various components of galaxies and to trace their role in cosmic evolution. ESIS provides optical identification and colors of Spitzer IR galaxies and builds the bases for photometric redshift estimates. Methods. This paper presents B , V , R Wide Field Imager observations of the first 1.5 square degree of the ESIS survey. Data reduction is described including astrometric calibration, illumination and color corrections. Synthetic sources are simulated in scientific and super-sky-flat images, with the purpose of estimating completeness and photometric accuracy for the survey. Number counts and color distributions are compared to literature observational and theoretical data, including non-evolutionary, PLE, evolutionary and semi-analytic Λ CDM galaxy models, as well as Milky Way stellar predictions. The ELAIS-S1 area benefits from extensive follow-up from X-ray to radio frequencies: some potential uses of the multi-wavelength observations are illustrated. Results. Object coordinates are defined with an accuracy as good as ~0.15 [arcsec] rms with respect to GSC 2.2; flux uncertainties are ~2, 10, 20% at mag. 20, 23, 24 respectively (Vega); we reach 95% completeness at B , $V\sim 25$ and $R\sim 24.5$. ESIS galaxy number counts are in good agreement with previous works and are best reproduced by evolutionary and hierarchical Λ CDM scenarios. Optical-Spitzer color-color plots promise to be very powerful tools to disentangle different classes of sources (e.g. AGNs, starbursts, quiescent galaxies). Ultraviolet GALEX data are matched to optical and Spitzer samples, leading to a discussion of galaxy properties in the UV-to-24 μ m color space. The spectral energy distribution of a few objects, from the X-rays to the far-IR are presented as examples of the multi-wavelength study of galaxy emission components in different spectral domains.
Bayesian Optimization of Partition Layouts for Mondrian Processes

The Mondrian process (MP) produces hierarchical partitions on a product space as a kd-tree, which can be served as a flexible yet parsimonious partition prior for relational modeling. Due to the recursive generation of partitions and varying dimensionality of the partition state space, the inference procedure for the MP relational modeling is extremely difficult. The prevalent inference method reversible-jump MCMC for this problem requires a number of unnecessary retrospective steps to transit from one partition state to a very similar one and it is prone to fall into a local optimum. In this paper, we attempt to circumvent these drawbacks by proposing an alternative method for inferring the MP partition structure. Based on the observation that similar cutting rate measures on the partition space lead to similar partition layouts, we propose to impose a nonhomogeneous cutting rate measure on the partition space to control the layouts of the generated partitions - the original MCMC sampling problem is thus transformed into a Bayesian global optimization problem. The empirical tests demonstrate that Bayesian optimization is able to find better partition structures than MCMC sampling with the same number of partition structure proposals.