Miracle-dz/UniFAR-FTUs huggingface dataset:
Insight Into the Distribution of Staphylococci and Their Enterotoxins in Cheeses Under Natural Conditions

Staphylococcal food poisoning outbreaks are a major cause of food-borne illness in the European Union and their notification has been mandatory since 2005. Criteria for the enumeration of coagulase-positive Staphylococci (CPS) and the detection of staphylococcal enterotoxins (SEs) in cheese have been set down in Commission Regulation EC 2073/2005. Currently, few information are available about the distribution of SEs in naturally contaminated cheeses, including raw-milk and artisanal dairy products. The aim of this study was therefore to investigate at both the CPS enumeration and the succession of the enterotoxigenic Staphylococcus aureus and produced enterotoxins levels on the rind and the core of a raw-milk semi-hard cheese, produced on farm. The study has been conducted in three steps: (I) seven wheels at different time of ripening where tested for the presence of SEs. (II) from each wheel, four portions were subsequently sampled from four different areas (peripheral rind, central rind, peripheral core and central core). (III) two cheese wheels, characterized by the highest and lowest CPS numbers and SEs quantification, based on the second step of the study, were further analyzed. A significant difference has been observed in the distribution of CPS and SEs in the four areas sampled, irrespectively of the batch and the time of ripening. The results of this study provided a set of previously unknown information on the influence of natural conditions on the distribution of CPS and SEs thereof in the cheese matrix, filling a gap in the understanding of SEs biosynthesis process.
Rapamycin: A Bacteria-Derived Immunosuppressant That Has Anti-atherosclerotic Effects and Its Clinical Application

Atherosclerosis (AS) is the leading cause of stroke and death worldwide. Although many lipid-lowering or antiplatelet medicines have been used to prevent the devastating outcomes caused by AS, the serious side effects of these medicines cannot be ignored. Moreover, these medicines are aimed at preventing end-point events rather than addressing the formation and progression of the lesion. Rapamycin (sirolimus), a fermentation product derived from soil samples, has immunosuppressive and anti-proliferation effects. It is an inhibitor of mammalian targets of rapamycin, thereby stimulating autophagy pathways. Several lines of evidence have demonstrated that rapamycin possess multiple protective effects against AS through various molecular mechanisms. Moreover, it has been used successfully as an anti-proliferation agent to prevent in-stent restenosis or vascular graft stenosis in patients with coronary artery disease. A thorough understanding of the biomedical regulatory mechanism of rapamycin in AS might reveal pathways for retarding AS. This review summarizes the current knowledge of biomedical mechanisms by which rapamycin retards AS through action on various cells (endothelial cells, macrophages, vascular smooth muscle cells, and T-cells) in early and advanced AS and describes clinical and potential clinical applications of the agent.
Cellular Mechanism Underlying Hydrogen Sulfide Mediated Epithelial K+ Secretion in Rat Epididymis

As a novel gasotransmitter, hydrogen sulfide (H2S) elicits various physiological actions including smooth muscle relaxation and promotion of transepithelial ion transport. However, the pro-secretory function of H2S in the male reproductive system remains largely unclear. The aim of this study is to elucidate the possible roles of H2S in modulating rat epididymal intraluminal ionic microenvironment essential for sperm storage. The results revealed that endogenous H2S-generating enzymes cystathionine β-synthetase (CBS) and cystathionine γ-lyase (CSE) were both expressed in rat epididymis. CBS located predominantly in epithelial cells whilst CSE expressed primarily in smooth muscle cells. The relative expression level of CBS and CSE escalated from caput to cauda regions of epididymis, which was paralleled to the progressively increasing production of endogenous H2S. The effect of H2S on epididymal epithelial ion transportation was investigated using short-circuit current (ISC), measurement of intracellular ion concentration and in vivo rat epididymal microperfusion. Our data showed that H2S induced transepithelial K+ secretion via adenosine triphosphate-sensitive K+ (KATP) channel and large conductance Ca2+-activated K+ (BKCa) channel. Transient receptor potential vanilloid 4 (TRPV4) channel-mediated Ca2+ influx was implicated in the activation of BKCa channel. In vivo studies further demonstrated that H2S promoted K+ secretion in rat epididymal epithelium. Inhibition of endogenous H2S synthesis caused a significant decrease in K+ concentration of cauda epididymal intraluminal fluid. Moreover, our data demonstrated that high extracellular K+ concentration actively depressed the motility of cauda epididymal sperm in a pH-independent manner. Collectively, the present study demonstrated that H2S was vital to the formation of high K+ concentration in epididymal intraluminal fluid by promoting the transepithelial K+ secretion, which might contribute to the maintenance of the cauda epididymal sperm in quiescent dormant state before ejaculation.
Intraocular Pressure Response to Short-Term Extreme Normobaric Hypoxia Exposure

Purpose: The purpose of the study was to determine the intraocular pressure response to normobaric hypoxia and the consequent recovery under additional well-controlled ambient conditions. Second, the study attempted to determine if the intraocular pressure changes were dependent on its baseline, initial heart rate, sex and arterial oxygen saturation. Methods: Thirty-eight visually healthy volunteers (23 women and 15 men) of an average age 25.2 ± 3.8 years from 49 recruited participants met the inclusion criteria and performed the complete test. Initial intraocular pressure (baseline), heart rate, and arterial oxygen saturation were measured after 7 min of rest under normal ambient conditions at an altitude 250 m above sea level. Each subject then underwent a 10 min normobaric hypoxic exposure and a subsequent 7 min recovery under normoxic conditions. Within hypoxic period, subjects were challenged to breathe hypoxic gas mixture with fraction of inspired oxygen of 9.6% (~6.200 m above sea level). Intraocular pressure and arterial oxygen saturation were re-measured at 4 and 10 min during the hypoxia and at 7 min after hypoxia termination. Results: Intraocular pressure increased in 1.2 mmHg ± 1.9 mmHg and 0.9 mmHg ± 2.3 mmHg at 4 and 10 min during the hypoxic period and returned approximately to the baseline at 7 min of recovery. The influence of sex was not statistically significant. The arterial oxygen saturation decreased in 14.9 ± 4.2% at min 4 and 18.4 ± 5.8% at min 10 during hypoxia and returned to the resting value at 7 min of recovery. The decrease was slightly higher in the case of women if compared with men. The hypoxia induced changes in intraocular pressure were significantly correlated with the arterial oxygen saturation changes, whereas the relationship with intraocular pressure baseline and initial heart rate were insignificant. Conclusion: There was a significant increase in intraocular pressure as a response to short-term normobaric hypoxia, which returned to the baseline in 7 min after hypoxia. The increase was dependent on the induced oxygen desaturation.
Interaction of Small Ionic Species With Phospholipid Membranes: The Role of Metal Coordination

In studies of the transfer, distribution and biochemical activity of metal ions it is typically assumed that the phospholipid bilayer acts as an inert barrier. Yet, there is mounting evidence that metal ions can influence the physical properties of membranes. Little is known of the basis of this effect. In this work the location and distribution of common metal ions: Na+, Mg2+ and Ca2+ in phospholipid membranes were studied. Computer simulations of lipid membrane segments in an aqueous environment showed that the ions penetrate the membrane headgroup zone and co-localize with the phosphate and the ester moieties. Analysis of the chemical environment of the ions in the simulations suggested that the co-localization is facilitated by coordination to the polar oxygen atoms of the phosphate and ester groups in typical coordination geometries of each ionic species, where the coordination shells are completed by water molecules. In contrast, the counterions do not penetrate the headgroup zone but form a layer over the membrane; this layer is also an effective metal exclusion zone. Importantly, the choline groups appear to be distributed almost exactly in the same plane as the phosphate, suggesting that the zwitterion dipole is preferentially horizontally aligned: this suggests that the distribution of the Cl- over the membrane surface is not a direct result of interaction with the choline groups, but rather an effect of the field emanating from the metal ion content of the membrane. Such a well defined ion distribution is expected to have a strong influence on membrane properties, in particular phase transition temperatures via increased in-plane cohesion; this was proven by calorimetry measurements using differential scanning calorimetry of suspended liposomes and quartz crystal microbalance-based measurements on supported single bilayer membranes. These findings shed a new light on the role metal ions play in stabilizing biological membranes.
Phenotypic, Hormonal, and Genomic Variation Among Vitis vinifera Clones With Different Cluster Compactness and Reproductive Performance

Previous studies showed that the number of berries is a major component of the compactness level of the grapevine clusters. Variation in number of fruits is regulated by events occurring in the fruitset, but also before during the flower formation and pollination, through factors like the initial number of flowers or the gametic viability. Therefore, the identification of the genetic bases of this variation would provide an invaluable knowledge of the grapevine reproductive development and useful tools for managing yield and cluster compactness. We performed the phenotyping of four clones (two compact and two loose clones) of the Tempranillo cultivar with reproducible different levels of cluster compactness over seasons. Measures of reproductive performance included flower number per inflorescence, berry number per cluster, fruitset, coulure, and millerandage indices. Besides, their levels of several hormones during the inflorescence and flower development were determined, and their transcriptomes were evaluated at critical time points (just before the start and at the end of flowering). For some key reproductive traits, like number of berries per cluster and number of seeds per berry, clones bearing loose clusters showed differences with the compact clones and also differed from each other, indicating that each one follows different paths to produce loose clusters. Variation between clones was observed for abscisic acid and gibberellins levels at particular development stages, and differences in GAs could be related to phenotypic differences. Likewise, various changes between clones were found at the transcriptomic level, mostly just before the start of flowering. Several of the differentially expressed genes between one of the loose clones and the compact clones are known to be over-expressed in pollen, and many of them were related to cell wall modification processes or to the phenylpropanoids metabolism. We also found polymorphisms between clones in candidate genes that could be directly involved in the variation of the compactness level.
Transient Cognitive Impairment in Epilepsy

Impairments of the dialog between excitation and inhibition (E/I) is commonly associated to neuropsychiatric disorders like autism, bipolar disorders and epilepsy. Moderate levels of hyperexcitability can lead to mild alterations of the EEG and are often associated with cognitive deficits even in the absence of overt seizures. Indeed, various testing paradigms have shown degraded performances in presence of acute or chronic non-ictal epileptiform activity. Evidences from both animal models and the clinics suggest that anomalous activity can cause cognitive deficits by transiently disrupting cortical processing, independently from the underlying etiology of the disease. Here, we will review our understanding of the influence of an abnormal EEG activity on brain computation in the context of the available clinical data and in genetic or pharmacological animal models.
Diallyl Disulfide From Garlic Oil Inhibits Pseudomonas aeruginosa Quorum Sensing Systems and Corresponding Virulence Factors

Previously, we determined that diallyl disulfide (DADS) from garlic oil can inhibit Pseudomonas aeruginosa PAO1 pathogenic factors by inactivating the transcription of key genes from three quorum sensing (QS) systems (las, rhl, and pqs) based on the effects of DADS on growth, virulence factor production (elastase, pyocyanin, biofilm, and swarming motility), and RNA transcription (real-time q-PCR). To further investigate the mechanisms underlying the inhibition of the three P. aeruginosa QS systems by DADS, high-throughput RNA and proteome sequencing techniques were used to study differences in the transcriptional and proteome expression of P. aeruginosa PAO1 following treatment with DADS. The RNA-seq and proteomic data are available via NCBI Gene Expression Omnibus database with accession number GSE118801 and ProteomeXchange with identifier PXD011144, respectively. The experimental results indicated that all key genes of the three QS systems (las, rhl, and pqs) of P. aeruginosa PAO1 as well as the virulence factors (including exoprotease LasA, elastase LasB, lectin LecA and LecB, pyocyanin biosynthesis, and biofilm formation) regulated by these three QS systems were inhibited. This is consistent with our previous studies on the physiology, biochemistry, and RNA expression of P. aeruginosa treated with DADS. Additionally, our results also indicated that bacterial motility, chemotaxis, and two-component systems were inhibited by DADS treatment. All these changes abolish the sensitivity of P. aeruginosa PAO1 to environmental stimuli and cause the cells to be in a state of passivation. Further research is needed to determine how QS systems regulate these functions. Our findings could potentially contribute to the treatment and control of P. aeruginosa infection, virulence, and pathogenicity.
Correlation Between C-MYC, BCL-2, and BCL-6 Protein Expression and Gene Translocation as Biomarkers in Diagnosis and Prognosis of Diffuse Large B-cell Lymphoma

This study investigates the protein expression of C-MYC, BCL-2, and BCL-6 in diffuse large B-cell lymphoma (DLBCL) and their relationship with genetic abnormalities. A retrospective study of 42 cases on paraffin-embedded tissue specimens diagnosed with DLBCL was performed using immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). The expression of C-MYC, BCL-2, BCL-6 protein, and gene abnormalities in these tissue samples was analyzed. The relationship in genetic abnormalities and Ki-67, Hans classification, gender, and age was also evaluated. It was found that the positive rate of C-MYC expression was 47.6% (20/42), the rate of C-MYC gene abnormality was 26.2% (11/42), in which gene translocation accounted for 23.8% (10/42) and gene amplification 2.4% (1/42); C-MYC protein expression was positively correlated with C-MYC gene translocation (χ2 = 11.813; P = 0.001); C-MYC gene translocation was mainly found in germinal center B cell type (χ2 = 4.029; P = 0.045). The positive rate of BCL-2 protein expression was 85.71% (36/42), the positive rate of translocation was 42.86% (18/42) and the amplification rate was 26.19% (11/42); the overexpression of BCL-2 protein was correlated with the BCL-2 translocation (χ2 = 3.407; P = 0.029). The positive rate of BCL-6 protein expression was 45.24% (19/42), the positive rate of BCL-6 translocation was 14.29% (6/42) and the positive rate of BCL-6 amplification was 7.14% (3/42); the overexpression of BCL-6 protein was significantly correlated with BCL-6 translocation (χ2 = 6.091; P = 0.014). The Ki-67 index was significantly higher in C-MYC translocation cases than in non-C-MYC translocation cases (χ2 = 4.492; P = 0.034). Taken together, our results suggest that the protein expression of C-MYC, BCL-2, and BCL-6 are positively correlated with their gene translocation. Overexpression of C-MYC, BCL-2, BCL-6 protein suggests the possibility of translocation. Therefore, immunohistochemical detection of C-MYC, BCL-2, and BCL-6 are useful in diagnosis and prognosis of DLBCL.
A Unified Theory Of Early Visual Representations From Retina To Cortex Through Anatomically Constrained Deep CNNs

The vertebrate visual system is hierarchically organized to process visual information in successive stages. Neural representations vary drastically across the first stages of visual processing: at the output of the retina, ganglion cell receptive fields (RFs) exhibit a clear antagonistic center-surround structure, whereas in the primary visual cortex (V1), typical RFs are sharply tuned to a precise orientation. There is currently no unified theory explaining these differences in representations across layers. Here, using a deep convolutional neural network trained on image recognition as a model of the visual system, we show that such differences in representation can emerge as a direct consequence of different neural resource constraints on the retinal and cortical networks, and for the first time we find a single model from which both geometries spontaneously emerge at the appropriate stages of visual processing. The key constraint is a reduced number of neurons at the retinal output, consistent with the anatomy of the optic nerve as a stringent bottleneck. Second, we find that, for simple downstream cortical networks, visual representations at the retinal output emerge as nonlinear and lossy feature detectors, whereas they emerge as linear and faithful encoders of the visual scene for more complex cortical networks. This result predicts that the retinas of small vertebrates (e.g. salamander, frog) should perform sophisticated nonlinear computations, extracting features directly relevant to behavior, whereas retinas of large animals such as primates should mostly encode the visual scene linearly and respond to a much broader range of stimuli. These predictions could reconcile the two seemingly incompatible views of the retina as either performing feature extraction or efficient coding of natural scenes, by suggesting that all vertebrates lie on a spectrum between these two objectives, depending on the degree of neural resources allocated to their visual system.
Catalog of Optimization Strategies and Realizations for Composed Integration Patterns

The discipline of Enterprise Application Integration (EAI) is the centrepiece of current on-premise, cloud and device integration scenarios. However, the building blocks of integration scenarios, i.e., essentially a composition of Enterprise Integration Patterns (EIPs), are only informally described, and thus their composition takes place in an informal, ad-hoc manner. This leads to several issues including a currently missing optimization of application integration scenarios. In this work, we collect and briefly explain the usage of process optimizations from the literature for integration scenario processes as catalog.
The Water Filling Game

We consider the Gaussian arbitrarily varying product channel (GAVPC), and the arbitrarily varying channel (AVC) with colored Gaussian noise. The random code capacity is obtained by solving an optimization min-max problem, which is interpreted as a two-player zero-sum game, played by the user and the jammer, where their strategies are the power allocations. The optimal power allocations are given by a "double" water filling solution, where the jammer performs water filling first, attempting to whiten the overall noise as much as possible, and then the user performs water filling taking into account the total interference power, which is contributed by both the channel noise and the jamming signal. As in the case of the standard Gaussian AVC, the deterministic code capacity is discontinuous in the input constraint, and depends on which of the input or state constraint is higher. As opposed to Shannon's classic water filling solution, it is observed that deterministic coding using independent codes is suboptimal for the GAVPC. We further extend our results to the AVC with colored Gaussian noise, where double water filling is performed in the frequency domain.
Adversarial CAPTCHAs

Following the principle of to set one’s own spear against one’s own shield, we study how to design adversarial completely automated public turing test to tell computers and humans apart (CAPTCHA) in this article. We first identify the similarity and difference between adversarial CAPTCHA generation and existing hot adversarial example (image) generation research. Then, we propose a framework for text-based and image-based adversarial CAPTCHA generation on top of state-of-the-art adversarial image generation techniques. Finally, we design and implement an adversarial CAPTCHA generation and evaluation system, called aCAPTCHA, which integrates 12 image preprocessing techniques, nine CAPTCHA attacks, four baseline adversarial CAPTCHA generation methods, and eight new adversarial CAPTCHA generation methods. To examine the performance of aCAPTCHA, extensive security and usability evaluations are conducted. The results demonstrate that the generated adversarial CAPTCHAs can significantly improve the security of normal CAPTCHAs while maintaining similar usability. To facilitate the CAPTCHA security research, we also open source the aCAPTCHA system, including the source code, trained models, datasets, and the usability evaluation interfaces.
PointCleanNet: Learning to Denoise and Remove Outliers from Dense Point Clouds

Point clouds obtained with 3D scanners or by image‐based reconstruction techniques are often corrupted with significant amount of noise and outliers. Traditional methods for point cloud denoising largely rely on local surface fitting (e.g. jets or MLS surfaces), local or non‐local averaging or on statistical assumptions about the underlying noise model. In contrast, we develop a simple data‐driven method for removing outliers and reducing noise in unordered point clouds. We base our approach on a deep learning architecture adapted from PCPNet, which was recently proposed for estimating local 3D shape properties in point clouds. Our method first classifies and discards outlier samples, and then estimates correction vectors that project noisy points onto the original clean surfaces. The approach is efficient and robust to varying amounts of noise and outliers, while being able to handle large densely sampled point clouds. In our extensive evaluation, both on synthetic and real data, we show an increased robustness to strong noise levels compared to various state‐of‐the‐art methods, enabling accurate surface reconstruction from extremely noisy real data obtained by range scans. Finally, the simplicity and universality of our approach makes it very easy to integrate in any existing geometry processing pipeline. Both the code and pre‐trained networks can be found on the project page (https://github.com/mrakotosaon/pointcleannet).