Miracle-dz/UniFAR-FTUs huggingface dataset:
Complex Ciprofloxacin Resistome Revealed by Screening a Pseudomonas aeruginosa Mutant Library for Altered Susceptibility

ABSTRACT Pseudomonas aeruginosa offers substantial therapeutic challenges due to its high intrinsic resistance to many antibiotics and its propensity to develop mutational and/or adaptive resistance. The PA14 comprehensive mutant library was screened for mutants exhibiting either two- to eightfold increased susceptibilities (revealing genes involved in intrinsic resistance) or decreased susceptibilities (mutational resistance) to the fluoroquinolone ciprofloxacin. Thirty-five and 79 mutants with increased and decreased susceptibilities, respectively, were identified, as confirmed by broth dilution.
CRISPR-Mediated Triple Knockout of SLAMF1, SLAMF5 and SLAMF6 Supports Positive Signaling Roles in NKT Cell Development

The SLAM family receptors contribute to diverse aspects of lymphocyte biology and signal via the small adaptor molecule SAP. Mutations affecting SAP lead to X-linked lymphoproliferative syndrome Type 1, a severe immunodysregulation characterized by fulminant mononucleosis, dysgammaglobulinemia, and lymphoproliferation/lymphomas. Patients and mice having mutations affecting SAP also lack germinal centers due to a defect in T:B cell interactions and are devoid of invariant NKT (iNKT) cells. However, which and how SLAM family members contribute to these phenotypes remains uncertain. Three SLAM family members: SLAMF1, SLAMF5 and SLAMF6, are highly expressed on T follicular helper cells and germinal center B cells. SLAMF1 and SLAMF6 are also implicated in iNKT development. Although individual receptor knockout mice have limited iNKT and germinal center phenotypes compared to SAP knockout mice, the generation of multi-receptor knockout mice has been challenging, due to the genomic linkage of the genes encoding SLAM family members. Here, we used Cas9/CRISPR-based mutagenesis to generate mutations simultaneously in Slamf1, Slamf5 and Slamf6. Genetic disruption of all three receptors in triple-knockout mice (TKO) did not grossly affect conventional T or B cell development and led to mild defects in germinal center formation post-immunization. However, the TKO worsened defects in iNKT cells development seen in SLAMF6 single gene-targeted mice, supporting data on positive signaling and potential redundancy between these receptors.
Deep Filter Banks for Land-Use Scene Classification

Land-use (LU) scene classification is one of the most challenging tasks in the field of remote sensing (RS) image processing due to its high intraclass variability and low interclass distance. Motivated by the challenge posed by this problem, we propose a novel hybrid architecture, deep filter banks, combining multicolumn stacked denoising sparse autoencoder (SDSAE) and Fisher vector (FV) to automatically learn the representative and discriminative features in a hierarchical manner for LU scene classification. SDSAE kernels describe local patches and a robust global feature of the RS image is built through the FV pooling layer. Unlike previous handcrafted features, we use machine-learning mechanisms to optimize our proposed feature extractor so that it can learn more suitable internal features from the RS data, boosting the final performance. Our approach achieves superior performance compared with the state-of-the-art methods, obtaining average classification accuracies of 92.7% and 90.4%, respectively, on the UC Merced and RSSCN7 data sets.
CD44H regulates tumor cell migration on hyaluronate-coated substrate

CD44 is a broadly distributed cell surface glycoprotein expressed in different isoforms in various tissues and cell lines. One of two recently characterized human isoforms, CD44H, is a cell surface receptor for hyaluronate, suggesting a role in the regulation of cell- cell and cell-substrate interactions as well as of cell migration. While CD44H has been shown to mediate cell adhesion, direct demonstration that CD44H expression promotes cell motility has been lacking. In this work we show that a human melanoma cell line, stably transfected with CD44H, displays enhanced motility on hyaluronate- coated surfaces while transfectants expressing an isoform that does not bind hyaluronate, CD44E, fail to do so. Migration of CD44H-expressing transfectants is observed to be blocked by a soluble CD44- immunoglobulin fusion protein as well as by anti-CD44 antibody, and to depend on the presence of the cytoplasmic domain of CD44. However, cells expressing CD44H cytoplasmic deletion mutants retain significant binding capacity to hyaluronate-coated substrate. Taken together, our results provide direct evidence that CD44H plays a major role in regulating cell migration on hyaluronate-coated substrate.
Immune Evasion Mechanisms of Entamoeba histolytica: Progression to Disease

Entamoeba histolytica (Eh) is a protozoan parasite that infects 10% of the world's population and results in 100,000 deaths/year from amebic dysentery and/or liver abscess. In most cases, this extracellular parasite colonizes the colon by high affinity binding to MUC2 mucin without disease symptoms, whereas in some cases, Eh triggers an aggressive inflammatory response upon invasion of the colonic mucosa. The specific host-parasite factors critical for disease pathogenesis are still not well characterized. From the parasite, the signature events that lead to disease progression are cysteine protease cleavage of the C-terminus of MUC2 that dissolves the mucus layer followed by Eh binding and cytotoxicity of the mucosal epithelium. The host mounts an ineffective excessive host pro-inflammatory response following contact with host cells that causes tissue damage and participates in disease pathogenesis as Eh escapes host immune clearance by mechanisms that are not completely understood. Ameba can modulate or destroy effector immune cells by inducing neutrophil apoptosis and suppressing respiratory burst or nitric oxide (NO) production from macrophages. Eh adherence to the host cells also induce multiple cytotoxic effects that can promote cell death through phagocytosis, apoptosis or by trogocytosis (ingestion of living cells) that might play critical roles in immune evasion. This review focuses on the immune evasion mechanisms that Eh uses to survive and induce disease manifestation in the host.
A study on real-time data dissemination problem

Multicommodity flow problem deals with delivering multiple data items residing on different source machines on a networking system to their destinations in an efficient manner, while respecting the bandwidth and cost limitations that may be imposed on the system components. In classical approach, each data item is sent via single route. Employing multiple routes simultaneously is a new topic and an active research area. Real-time applications are emerging in many disciplines of science and engineering. This study defines real-time multisource k-split real time data dissemination problem. Novel heuristics are proposed and evaluated as well.
Dissociable Performance on Scene Learning and Strategy Implementation after Lesions to Magnocellular Mediodorsal Thalamic Nucleus

Monkeys with aspiration lesions of the magnocellular division of the mediodorsal thalamus (MDmc) are impaired in object-in-place scene learning, object recognition, and stimulus-reward association. These data have been interpreted to mean that projections from MDmc to prefrontal cortex are required to sustain normal prefrontal function in a variety of task settings. In the present study, we investigated the extent to which bilateral neurotoxic lesions of the MDmc impair a preoperatively learnt strategy implementation task that is impaired by a crossed lesion technique that disconnects the frontal cortex in one hemisphere from the contralateral inferotemporal cortex. Postoperative memory impairments were also examined using the object-in-place scene memory task. Monkeys learnt both strategy implementation and scene memory tasks separately to a stable level preoperatively. Bilateral neurotoxic lesions of the MDmc, produced by 10 × 1 μl injections of a mixture of ibotenate and NMDA did not affect performance in the strategy implementation task. However, new learning of object-in-place scene memory was substantially impaired. These results provide new evidence about the role of the magnocellular mediodorsal thalamic nucleus in memory processing, indicating that interconnections with the prefrontal cortex are essential during new learning, but are not required when implementing a preoperatively acquired strategy task. Thus, not all functions of the prefrontal cortex require MDmc input. Instead, the involvement of MDmc in prefrontal function may be limited to situations in which new learning must occur.
Discourses of the environment

Contributors. Acknowledgements. 1. Foucault and The Environment: An Introduction: Eric Darier. Part I Histories:. 2. "The Entry Of Life Into History": Foucault And Ecological Governmentality: Paul Rutherford. 3. Medicine, Health And The Environment: The Construction Of Environmental "Awareness": Isabelle Lanthier And Lawrence Olivier. 4. Sex At The Limits: Population, Environmentalism, And Late Capitalism: Catriona Sandilands. 5. Ecological Modernisation And Environmental Risk: Foucault And Recent Social Theory: Paul Rutherford. Part II Environmentalities:. 6. Environmentality As Green Governmentality Geo-Power, Eco-Knowledge And Enviro-Discipline As Tactics Of Normalisation: Timothy W. Luke. 7. Northern Plains Boulder Structures: Art And Foucauldian Heterotopias: Thomas Heyd. 8. The Practice Of The Green Subjects: Nature Writing As Self-Technology: Sylvia Bowerbank. Part III Resistances:. 9. Nature As Dangerous Space: Foucault's Challenge To Marxism, Liberal Humanism And The General Call For 'Grounded Responsibility': Peter Quigley. 10. Foucault's Unnatural Ecology: Neil Levy. 11. Foucault Against Environmental Ethics: Toward A Green Aesthetic Of Existence? : Eric Darier. Bibliography. Index.
Double-strand break repair deficiency in NONO knockout murine embryonic fibroblasts and compensation by spontaneous upregulation of the PSPC1 paralog

NONO, SFPQ and PSPC1 make up a family of proteins with diverse roles in transcription, RNA processing and DNA double-strand break (DSB) repair. To understand long-term effects of loss of NONO, we characterized murine embryonic fibroblasts (MEFs) from knockout mice. In the absence of genotoxic stress, wild-type and mutant MEFs showed similar growth rates and cell cycle distributions, and the mutants were only mildly radiosensitive. Further investigation showed that NONO deficiency led to upregulation of PSPC1, which replaced NONO in a stable complex with SFPQ. Knockdown of PSPC1 in a NONO-deficient background led to severe radiosensitivity and delayed resolution of DSB repair foci. The DNA-dependent protein kinase (DNA-PK) inhibitor, NU7741, sensitized wild-type and singly deficient MEFs, but had no additional effect on doubly deficient cells, suggesting that NONO/PSPC1 and DNA-PK function in the same pathway. We tested whether NONO and PSPC1 might also affect repair indirectly by influencing mRNA levels for other DSB repair genes. Of 12 genes tested, none were downregulated, and several were upregulated. Thus, NONO or related proteins are critical for DSB repair, NONO and PSPC1 are functional homologs with partially interchangeable functions and a compensatory response involving PSPC1 blunts the effect of NONO deficiency.
Hypernasality associated with basal ganglia dysfunction: evidence from Parkinson’s disease and Huntington’s disease

Background Although increased nasality can originate from basal ganglia dysfunction, data regarding hypernasality in Parkinson’s disease (PD) and Huntington’s disease (HD) are very sparse. The aim of the current study was to analyze acoustic and perceptual correlates of velopharyngeal seal closure in 37 PD and 37 HD participants in comparison to 37 healthy control speakers. Methods Acoustical analysis was based on sustained phonation of the vowel /i/ and perceptual analysis was based on monologue. Perceptual analysis was performed by 10 raters using The Great Ormond Street Speech Assessment ’98. Acoustic parameters related to changes in a 1/3-octave band centered on 1 kHz were proposed to reflect nasality level and behavior through utterance. Results Perceptual analysis showed the occurrence of mild to moderate hypernasality in 65% of PD, 89% of HD and 22% of control speakers. Based on acoustic analyses, 27% of PD, 54% of HD and 19% of control speakers showed an increased occurrence of hypernasality. In addition, 78% of HD patients demonstrated a high occurrence of intermittent hypernasality. Further results indicated relationships between the acoustic parameter representing fluctuation of nasality and perceptual assessment (r = 0.51, p < 0.001) as well as the Unified Huntington Disease Rating Scale chorea composite subscore (r = 0.42, p = 0.01). Conclusions In conclusion the acoustic assessment showed that abnormal nasality was not a common feature of PD, whereas patients with HD manifested intermittent hypernasality associated with chorea.
"I Am First and Foremost a Man of Logic" - Stereotyping, the Syndrome Character of Prejudice, and a Glance at Anders Breivik's Manifesto

Attitudes, stereotyping, and prejudice are often conceived of as inner, mental or cognitive processes. Drawing on discursive psychology and critical theory, this article proposes a language-based understanding of stereotyping and the “syndrome character” of prejudice that is able to avoid certain epistemological shortcomings and connect social-psychological and sociological research. Stereotyping is outlined as a relational concept that denotes a linguistic mode of relating to the world, whilst the syndrome character of prejudice is conceptualized as a phenomenon that shows in particular stereotypical speech acts, but does not completely coincide with them. The impact of this conceptual figuration is empirically illustrated using Anders Breivik’s manifesto.
Importin-β modulates the permeability of the nuclear pore complex in a Ran-dependent manner

Soluble karyopherins of the importin-β (impβ) family use RanGTP to transport cargos directionally through the nuclear pore complex (NPC). Whether impβ or RanGTP regulate the permeability of the NPC itself has been unknown. In this study, we identify a stable pool of impβ at the NPC. A subpopulation of this pool is rapidly turned-over by RanGTP, likely at Nup153. Impβ, but not transportin-1 (TRN1), alters the pore's permeability in a Ran-dependent manner, suggesting that impβ is a functional component of the NPC. Upon reduction of Nup153 levels, inert cargos more readily equilibrate across the NPC yet active transport is impaired. When purified impβ or TRN1 are mixed with Nup153 in vitro, higher-order, multivalent complexes form. RanGTP dissolves the impβ•Nup153 complexes but not those of TRN1•Nup153. We propose that impβ and Nup153 interact at the NPC's nuclear face to form a Ran-regulated mesh that modulates NPC permeability. DOI: http://dx.doi. org/10.7554/eLife.04052. 001
The 10th Anniversary of Carbohydrate Microarrays (2002-2012).

Copyright: © 2013 Wang D, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Carbohydrates, like nucleic acids and proteins, are essential biological molecules. Owing to their intrinsic physicochemical properties, carbohydrates are capable of generating structural diversity in a multitude of ways and are prominently displayed on the surfaces of cell membranes or on the exposed regions of macromolecules. In human and virtually all animal species, cell-display of specific complex carbohydrates is characteristically associated with the stages or steps of embryonic development, cell differentiation, and transformation of normal cells to abnormally differentiated tumor or cancer cells [1-4]. Many microbial organisms carry unique glycosylation systems and are able to produce specific sugar signatures [5-10]. Importantly, there are multiple carbohydrate-recognition systems in living species that read the biological information of complex carbohydrates. Notably, these include the lectin-like Glycan-Binding Proteins (GBPs) for the carbohydrate-mediated cell-cell communication and signaling (see a comprehensive summary of GBPs at http://www.functionalglycomics. org/) and a universe of anti-glycan antibodies produced by many animal species that play key roles in protecting a subject from microbial infections [11-13]. Thus, carbohydrates are uniquely suitable for storing biological signals in the forms which are identifiable by other biological systems.
The Physiological Relevance of the Intestinal Microbiota - Contributions to Human Health

The intestinal commensal microbiota is a dynamic mixture of essential microbes that develops under key influences of genetics, environment, diet and disease. Population profiles differ along the gastrointestinal tract, from the lumen to the mucosa, and among individuals. The total microbiota population outnumbers the cells in the human body and accounts for 35–50% of the volume of the colonic content. Key physiological functions of the commensal microbiota include protective effects exerted directly by specific bacterial species, control of epithelial cell proliferation and differentiation, production of essential mucosal nutrients, such as short-chain fatty acids and amino acids, prevention of overgrowth of pathogenic organisms, and stimulation of intestinal immunity. Oral probiotics are living microorganisms that upon ingestion in specific numbers exert health benefits beyond those of inherent basic nutrition. Emerging evidence indicates prophylactic and therapeutic utility for probiotic consumption in gastrointestinal health and disease.
Slow-growing and oligotrophic soil bacteria phylogenetically close to Bradyrhizobium japonicum

Eleven isolates of slow-growing oligotrophic bacteria from grassland soil were found to be closely related by partial 16S rRNA sequence similarity and many common taxonomic traits. Analysis of full 16S rRNA gene sequences of four representative isolates and Agromonas oligotrophica S58 indicated that they were more closely related to Bradyrhizobium japonicum, a symbiotic nitrogen-fixing bacterium, (similarity values: 98.1–98.8%) than other strains such as Bradyrhizobium elkanii, Nitrobacter spp. , Rhodopseudomonas palustris, and Afipia spp. This result was supported by analysis of phenotypic traits and DNA-DNA hybridization analysis. No strain showed hybridization to nodD1YABC of B. japonicum, and only strain G14130 exhibited hybridization to nifDK- and hupSL-specific DNA. These latter genotypes are involved in the phenotypes of nodulation and nitrogen fixation under microaerobic conditions. These results suggest that the isolates possess a unique phylogenetic position since they are closely related to B. japonicum though they do not have characteristics of symbiotic nitrogen fixation.
Chronic Stress and the Development of Early Atherosclerosis: Moderating Effect of Endothelial Dysfunction and Impaired Arterial Elasticity

This study aims to explore the interactive effect of vital exhaustion (VE) and endothelial dysfunction on preclinical atherosclerosis, assessed by carotid intima-media thickness (IMT). Furthermore, interaction between VE and carotid elasticity is examined. Participants were 1,596 young healthy adults from the Cardiovascular Risk in Young Finns study. Endothelial dysfunction was measured by brachial flow-mediated dilatation (FMD), and carotid elasticity by carotid artery compliance (CAC). Significant interactions between FMD and VE, and between CAC and VE, for IMT were found in participants with the very lowest FMD and CAC. Thus, VE may be harmful if the endothelium is not working properly.
Estimation of Histogram Variation for Texture Classification

I present a novel parametric approach for estimating the likelihood of homogeneously textured images. I propose that the dependence between pixel features is usefully captured by estimating the joint intra-class variation of their marginal distributions. To support this claim I build a single multivariate Gaussian distribution for each class that estimates the joint variation of several marginal, nonparametric, filter response histograms. I then generalize this framework to include marginal conditional distributions of pixel intensities for use with Strong-MRF models. I demonstrate these methods on the Columbia-Utrecht database by classifying over 2800 images in all 61 texture classes. In a direct comparison with Varma & Zisserman (ECCV ’02, CVPR ’03) and Hayman (ECCV ’04) this framework is found to be more accurate and efficient.
Assessing the idealized predictability of precipitation and temperature in the NCEP Climate Forecast System

The 24‐year retrospective forecast data set from the NCEP Climate Forecast System (CFS) is analyzed to study its idealized predictability of precipitation and temperature under its current configuration. The analysis approach assumes the forecasting model and system to be predicted share exactly the same physics so that the idealized predictability is calculated and serves as the upper limit of the predictive skill in practical forecasts. The analysis shows that CFS is not capable of predicting itself over much of the mid‐latitudes land areas for precipitation and temperature anomalies having small temporal (monthly) and spatial (2.5° × 2.5° grid) scales at lead‐times longer than a month. Anomalies become more predictable with the increase in temporal and spatial scales and with the decrease in lead‐times, as illustrated with results from the central US region. The results imply that additional care should be taken when using climate model seasonal forecast products.
Competing interests

16 The growing needs for agricultural expansion and intensification will likely continue to reduce and 17 fragment the terrestrial habitats fundamental to mammalian carnivores. Recent research identified 18 benefits of agroecosystems to carnivores recognizing their multifunctionality, mostly for common 19 species. However, the variability of carnivore ecology investigated in agroecosystems, biases in 20 agriculture types and species targeted, and methodological approaches may affect available 21 knowledge to reconcile conservation and production goals. To fill this gap, we conducted a 22 systematic literature review to identify which aspects of and how is carnivore spatial ecology being 23 investigated within agroecosystems. Of the 110 reviewed studies, most focused on agricultural 24 crops (55%) and grasslands (47%) and half referred to monocultures. We found that 61% of the 25 studies were conducted in Europe and North America. Eighty-four species were studied, 73% 26 classified as Least Concern, with 67% of the studies targeting a single species and 30% focused on 27 only seven common species. Almost all studies included some form of habitat use analysis and 28 species’ home-range and its attributes (e.g. size, resource selection) were the most common spatial 29 ecology aspects studied. Most studies suggested that agriculture act as food provisioning areas 30 (69%) but few used direct food availability measures. Our results highlight that studies tend to be 31 descriptive and geographically biased towards northern hemisphere and to non-forested agricultural 32 types. We suggest that future carnivore spatial ecology research in agroecosystem should be 33 hypotheses-driven, with greater focus on the mechanisms and processes through which 34 agroecosystems might affect carnivore spatial ecology in high priority regions for carnivore 35 conservation. 36