Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel bit based reversible image watermarking method

Digital image watermarking methods are one of the mostly used methods for copyright protection and image content authentication. In this article, a new bit-based reversible digital image watermarking method (BB-RIW) is proposed for authentication in images. The proposed BB-RIW method consists of identifying the pixels to be stigmatized, generating the stamp, embedding the stamp, stamping, and image recovery. In the BB-RIW method, pixel bits belong to three groups: the most significant bits (MSBs), the middle bits (MBs) and the least significant bits (LSBs). In 8 bit images, 2 MSB, 4 OB and 2 LSB are used. Logical operations are performed on the MBs to check whether they are equal to 2 LSBs. If there is an equality, 2MSBs are embedded in 2LSBs of pixels. The positions of the matching pixels are recorded in the key. The key and mode 4 operator are used to stamp. In the image recovery phase, image recovery is performed using the key and MBs. Capacity and visual quality were used to assess the performance of the BB-RIW method. Experimental results show that the BB-RIW method can be used in many fields such as military and medical applications.
Secure Web Referral Services for Mobile Cloud Computing

Security has become a major concern for mobile devices when mobile users browsing malicious websites. Existed security solutions may rely on human factors to achieve a good result against phishing websites and SSL Strip-based Man-In-The-Middle (MITM) attack. This paper presents a secure web referral service, which is called Secure Search Engine (SSE) for mobile devices. The system uses mobile cloud-based virtual computing and provides each user a Virtual Machine (VM) as a personal security proxy where all Web traffics are redirected through it. Within the VM, the SSE uses web crawling technology with a set of checking services to validate IP addresses and certificate chains. A Phishing Filter is also used to check given URLs with an optimized execution time. The system also uses private and anonymously shared caches to protect user privacy and improve performance. The evaluation results show that SSE is non-intrusive and consumes no power or computation on the client device, while producing less false positive and false negative than existing web browser-based anti-phishing solutions.
Towards a simplification of models using regression trees

Over-parametrization in modelling is a well-known issue that makes it hard to identify which part of a model is responsible for a given behaviour. In line with that ascertainment, this work presents the outline of an empirical method to simplify models by decreasing the number of parameters. By using regression trees to classify outputs according to related input parameters, the method provides the modeller with an objective tool to reduce the range of the used parameters and, under certain conditions, to establish relations between them. Thereby, the complexity of the model is reduced on the basis of mathematical arguments. As an example, a dynamic energy budget-based model of a mesopelagic bacterial ecosystem is simplified using the presented method. The main benefits of such a method are thus highlighted: (i) more robust parameter estimations; (ii) less complex formulations; and (iii) fewer modelling assumptions. To conclude, the difficulties encountered are discussed, and several solutions are proposed to deal with them.
Long-lasting masculinizing effects of postnatal androgens on myelin governed by the brain androgen receptor

The oligodendrocyte density is greater and myelin sheaths are thicker in the adult male mouse brain when compared with females. Here, we show that these sex differences emerge during the first 10 postnatal days, precisely at a stage when a late wave of oligodendrocyte progenitor cells arises and starts differentiating. Androgen levels, analyzed by gas chromatography/tandem-mass spectrometry, were higher in males than in females during this period. Treating male pups with flutamide, an androgen receptor (AR) antagonist, or female pups with 5α-dihydrotestosterone (5α-DHT), revealed the importance of postnatal androgens in masculinizing myelin and their persistent effect into adulthood. A key role of the brain AR in establishing the sexual phenotype of myelin was demonstrated by its conditional deletion. Our results uncover a new persistent effect of postnatal AR signaling, with implications for neurodevelopmental disorders and sex differences in multiple sclerosis.
Association of Common CRP Gene Variants with CRP Levels and Cardiovascular Events

C‐reactive protein (CRP) is a well‐documented marker of atherosclerotic cardiovascular disease risk. We resequenced CRP to identify a comprehensive set of common SNP variants, then studied and replicated their association with baseline CRP level among apparently healthy subjects in the Women's Health Study (WHS; n = 717), Pravastatin Inflammation/CRP Evaluation trial (PRINCE; n = 1,110) and Physicians' Health Study (PHS; n = 509) cohorts. The minor alleles of four SNPs were consistently associated in all three cohorts with higher CRP, while the minor alleles of two SNPs were associated with lower CRP (p < 0.05 for each). Single marker and haplotype analysis in all three cohorts were consistent with functional roles for the 5′‐flanking triallelic SNP −286C>T>A and the 3′‐UTR SNP 1846G>A. None of the SNPs associated with higher CRP were associated with risk of incident myocardial infarction (MI) or ischemic stroke in a prospective, nested case‐control study design from the PHS cohort (610 case‐control pairs). One SNP, −717A>G, was unrelated to CRP levels but associated with decreased risk of MI (p = 0.001). Taken together, these data imply significant interactions between both genetic and environmental contributions to the increased CRP levels that predict a greater risk of future atherothrombotic events in epidemiological studies.
Expressed genes in regenerating rat liver after partial hepatectomy.

AIM To reveal the liver regeneration (LR) and its control as well as the occurrence of liver disease and to study the gene expression profiles of 551 genes after partial hepatectomy (PH) in regenerating rat livers. METHODS Five hundred and fifty-one expressed sequence tags screened by suppression subtractive hybridization were made into an in-house cDNA microarray, and the expressive genes and their expressive profiles in regenerating rat livers were analyzed by microarray and bioinformatics. RESULTS Three hundred of the analyzed 551 genes were up- or downregulated more than twofolds at one or more time points during LR. Most of the genes were up- or downregulated 2-5 folds, but the highest reached 90 folds of the control. One hundred and thirty-nine of them showed upregulation, 135 displayed downregulation, and up or down expression of 26 genes revealed a dependence on regenerating livers. The genes expressed in 24-h regenerating livers were much more than those in the others. Cluster analysis and generalization analysis showed that there were at least six distinct temporal patterns of gene expression in the regenerating livers, that is, genes were expressed in the immediate early phase, early phase, intermediate phase, early-late phase, late phase, terminal phase. CONCLUSION In LR, the number of down-regulated genes was almost similar to that of the upregulated genes; the successively altered genes were more than the rapidly transient genes. The temporal patterns of gene expression were similar 2 and 4 h, 12 and 16 h, 48 and 96 h, 72 and 144 h after PH. Microarray combined with suppressive subtractive hybridization can effectively identify the genes related to LR.
Reduced replication of Toxoplasma gondii is necessary for induction of bradyzoite-specific antigens: a possible role for nitric oxide in triggering stage conversion

Stage conversion between tachyzoites and bradyzoites of Toxoplasma gondii was investigated in vitro by using murine bone marrow-derived macrophages (BMMs) as host cells. Following infection of untreated BMMs with tachyzoites, spontaneous expression of bradyzoite-specific antigens (Bsa) occurred at low frequency with Toxoplasma strain-dependent ratios from 0.03 to 2%. As previously described for peritoneal macrophages, activation of tachyzoite-infected BMMs with gamma interferon (IFN-gamma) or lipopolysaccharide resulted in the induction of Bsa. When bradyzoites were used for infection, prolonged expression of Bsa could be observed in IFN-gamma-activated BMMs. The induction of Bsa expression seemed to be closely linked to parasite multiplication and increased to maximal values of 50 to 70% in intermediately activated macrophages with nitric oxide (NO) levels that allowed reduced parasite replication. Identical results in stage conversion were obtained when sodium nitroprusside was used as a source of exogenous NO, indicating that NO might be a molecular trigger of stage conversion. NO is reactive with iron-sulfur centers in proteins, thereby inhibiting proteins involved in the mitochondrial respiratory chain. Using oligomycin and antimycin A as inhibitors of mitochondrial function, growth inhibition of parasites and induction of Bsa were obtained. Since microglia are the functional correlates of macrophages in the central nervous system and inhibit T. gondii upon activation with IFN-gamma, a similar mechanism might be involved during cyst development in the brain.
La proteins from Drosophila melanogaster and Saccharomyces cerevisiae: a yeast homolog of the La autoantigen is dispensable for growth

The human autoantigen La is a 50-kDa protein which binds to the 3' termini of virtually all nascent polymerase III transcripts. Experiments with mammalian transcription extracts have led to the proposal that the La protein is required for multiple rounds of transcription by RNA polymerase III (E. Gottlieb and J. A. Steitz, EMBO J. 8:851-861, 1989; R. J. Maraia, D. J. Kenan, and J. D. Keene, Mol. Cell. Biol. 14:2147-2158, 1994). Although La protein homologs have been identified in a variety of vertebrate species, the protein has not been identified in invertebrates. In order to begin a genetic analysis of La protein function, we have characterized homologs of the La protein in the fruit fly Drosophila melanogaster and the yeast Saccharomyces cerevisiae. We show that both the Drosophila and yeast La proteins are bound to precursors of polymerase III RNAs in vivo. The Drosophila and yeast proteins resemble the human La protein in their biochemical properties, as both proteins can be partially purified from cells by a procedure previously devised to purify the human protein. Similarly to vertebrate La proteins, the Drosophila and yeast homologs preferentially bind RNAs that terminate with a 3' hydroxyl. Despite the fact that the La protein is conserved between humans and Saccharomyces cerevisiae, yeast cells containing a null allele of the gene encoding the La protein are viable, suggesting that another protein(s) plays a functionally redundant role.
Rombencephalitis Caused by Francisella tularensis

ABSTRACT Common presentations of tularemia include pneumonia and ulceroglandular, oropharyngeal, or typhoidal disease. Neuromeningeal involvement is extremely rare. We report a case of a severe rhombencephalitis due to Francisella tularensis. Diagnosis was possible thanks to a very precise interview, and the patient dramatically improved after specific antibiotherapy.
Silver sulfide nanoparticles (Ag2S-NPs) are taken up by plants and are phytotoxic

Abstract Silver nanoparticles (NPs) are used in more consumer products than any other nanomaterial and their release into the environment is unavoidable. Of primary concern is the wastewater stream in which most silver NPs are transformed to silver sulfide NPs (Ag2S-NPs) before being applied to agricultural soils within biosolids. While Ag2S-NPs are assumed to be biologically inert, nothing is known of their effects on terrestrial plants. The phytotoxicity of Ag and its accumulation was examined in short-term (24 h) and longer-term (2-week) solution culture experiments with cowpea (Vigna unguiculata L. Walp.) and wheat (Triticum aestivum L.) exposed to Ag2S-NPs (0–20 mg Ag L−1), metallic Ag-NPs (0–1.6 mg Ag L−1), or ionic Ag (AgNO3; 0–0.086 mg Ag L−1). Although not inducing any effects during 24-h exposure, Ag2S-NPs reduced growth by up to 52% over a 2-week period. This toxicity did not result from their dissolution and release of toxic Ag+ in the rooting medium, with soluble Ag concentrations remaining below 0.001 mg Ag L−1. Rather, Ag accumulated as Ag2S in the root and shoot tissues when plants were exposed to Ag2S-NPs, consistent with their direct uptake. Importantly, this differed from the form of Ag present in tissues of plants exposed to AgNO3. For the first time, our findings have shown that Ag2S-NPs exert toxic effects through their direct accumulation in terrestrial plant tissues. These findings need to be considered to ensure high yield of food crops, and to avoid increasing Ag in the food chain.
Model-based iterative reconstruction for flat-panel cone-beam CT with focal spot blur, detector blur, and correlated noise

While model-based reconstruction methods have been successfully applied to flat-panel cone-beam CT (FP-CBCT) systems, typical implementations ignore both spatial correlations in the projection data as well as system blurs due to the detector and focal spot in the x-ray source. In this work, we develop a forward model for flat-panel-based systems that includes blur and noise correlation associated with finite focal spot size and an indirect detector (e.g. scintillator). This forward model is used to develop a staged reconstruction framework where projection data are deconvolved and log-transformed, followed by a generalized least-squares reconstruction that utilizes a non-diagonal statistical weighting to account for the correlation that arises from the acquisition and data processing chain. We investigate the performance of this novel reconstruction approach in both simulated data and in CBCT test-bench data. In comparison to traditional filtered backprojection and model-based methods that ignore noise correlation, the proposed approach yields a superior noise-resolution tradeoff. For example, for a system with 0.34 mm FWHM scintillator blur and 0.70 FWHM focal spot blur, using the correlated noise model instead of an uncorrelated noise model increased resolution by 42% (with variance matched at 6.9 × 10−8 mm−2). While this advantage holds across a wide range of systems with differing blur characteristics, the improvements are greatest for systems where source blur is larger than detector blur.
Compound heterozygous PKHD1 variants cause a wide spectrum of ductal plate malformations

Ductal plate malformations (DPM) present with a wide phenotypic spectrum comprising Von Meyenburg complexes (VMC), Caroli disease (CD), Caroli syndrome (CS), and autosomal recessive polycystic kidney disease (ARPKD). Variants in PKHD1 are responsible for ARPKD and CS with a high inter‐ and intra‐familial phenotypic variability. Rare familial cases of CD had been reported and exceptional cases of CD are associated with PKHD1 variants. In a family of three siblings presenting with a wide spectrum of severity of DPM, we performed whole exome sequencing and identified two PKHD1 compound heterozygous variants (c.10444G>A; p.Arg3482Cys and c.5521C>T; p.Glu1841Lys), segregating with the symptoms. Two compound heterozygous PKHD1 variants, including one hypomorphic variant, were identified in two other familial cases of DPM with at least one patient presenting with CD. This report widens the phenotypic variability of PKHD1 variants to VMC, and others hepatic bile ducts malformations with inconstant renal phenotype in adults and highlights the important intra‐familial phenotypic variability. It also showed that PKHD1 might be a major gene for CD. This work adds an example of the contribution of exome sequencing, not only in the discovery of new genes but also in expanding the phenotypic spectrum of well‐known disease‐associated genes, using reverse phenotyping. © 2015 Wiley Periodicals, Inc.
Degenerate In Vitro Genetic Selection Reveals Mutations That Diminish Alfalfa Mosaic Virus RNA Replication without Affecting Coat Protein Binding

ABSTRACT The alfalfa mosaic virus (AMV) RNAs are infectious only in the presence of the viral coat protein; however, the mechanisms describing coat protein's role during replication are disputed. We reasoned that mechanistic details might be revealed by identifying RNA mutations in the 3′-terminal coat protein binding domain that increased or decreased RNA replication without affecting coat protein binding. Degenerate (doped) in vitro genetic selection, based on a pool of randomized 39-mers, was used to select 30 variant RNAs that bound coat protein with high affinity. AUGC sequences that are conserved among AMV and ilarvirus RNAs were among the invariant nucleotides in the selected RNAs. Five representative clones were analyzed in functional assays, revealing diminished viral RNA expression resulting from apparent defects in replication and/or translation. These data identify a set of mutations, including G-U wobble pairs and nucleotide mismatches in the 5′ hairpin, which affect viral RNA functions without significant impact on coat protein binding. Because the mutations associated with diminished function were scattered over the 3′-terminal nucleotides, we considered the possibility that RNA conformational changes rather than disruption of a precise motif might limit activity. Native polyacrylamide gel electrophoresis experiments showed that the 3′ RNA conformation was indeed altered by nucleotide substitutions. One interpretation of the data is that coat protein binding to the AUGC sequences determines the orientation of the 3′ hairpins relative to one another, while local structural features within these hairpins are also critical determinants of functional activity.
Characterization of VIM-2, a Carbapenem-Hydrolyzing Metallo-β-Lactamase and Its Plasmid- and Integron-Borne Gene from a Pseudomonas aeruginosa Clinical Isolate in France

ABSTRACT Pseudomonas aeruginosa COL-1 was identified in a blood culture of a 39-year-old-woman treated with imipenem in Marseilles, France, in 1996. This strain was resistant to β-lactams, including ureidopenicillins, ticarcillin-clavulanic acid, cefepime, ceftazidime, imipenem, and meropenem, but remained susceptible to the monobactam aztreonam. The carbapenem-hydrolyzing β-lactamase gene of P. aeruginosa COL-1 was cloned, sequenced, and expressed in Escherichia coli DH10B. The deduced 266-amino-acid protein was an Ambler class B β-lactamase, with amino acid identities of 32% with B-II from Bacillus cereus; 31% with IMP-1 from several gram-negative rods in Japan, includingP. aeruginosa; 27% with CcrA from Bacteroides fragilis; 24% with BlaB from Chryseobacterium meningosepticum; 24% with IND-1 from Chryseobacterium indologenes; 21% with CphA-1 from Aeromonas hydrophila; and 11% with L-1 from Stenotrophomonas maltophilia. It was most closely related to VIM-1 β-lactamase recently reported from Italian P. aeruginosa clinical isolates (90% amino acid identity). Purified VIM-2 β-lactamase had a pI of 5.6, a relative molecular mass of 29.7 kDa, and a broad substrate hydrolysis range, including penicillins, cephalosporins, cephamycins, oxacephamycins, and carbapenems, but not monobactams. As a metallo-β-lactamase, its activity was zinc dependent and inhibited by EDTA (50% inhibitory concentration, 50 μM). VIM-2 conferred a resistance pattern to β-lactams in E. coli DH10B that paralleled its in vitro hydrolytic properties, except for susceptibility to ureidopenicillins, carbapenems, and cefepime.blaVIM-2 was located on a ca. 45-kb plasmid that in addition conferred resistance to sulfamides and that was not self-transmissible either from P. aeruginosa to E. coli or from E. coli to E. coli. blaVIM-2 was the only gene cassette located within the variable region of a novel class 1 integron, In56, that was weakly related to the blaVIM-1-containing integron. VIM-2 is the second carbapenem-hydrolyzing metalloenzyme characterized from a P. aeruginosa isolate outside Japan.
Pharmacokinetic Model-Predicted Anticancer Drug Concentrations in Human Tumors

In an era when molecular and targeted anticancer therapeutics is a major focus and when understanding drug dynamics in tumor is critical, it seems advantageous to be able to relate drug concentrations in tumors to corresponding biological end points. To that end, a novel method, based on physiologically based hybrid pharmacokinetic models, is presented to predict human tumor drug concentrations. Such models consist of a forcing function, describing the plasma drug concentration-time profile, which is linked to a model describing drug disposition in tumors. The hybrid models are originally derived from preclinical data and then scaled to humans. Integral to the scale-up procedure is the ability to derive human forcing functions directly from clinical pharmacokinetic data. Three examples of this approach are presented based on preclinical investigations with carboplatin, topotecan, and temozolomide. Translation of these preclinical hybrid models to humans used a Monte Carlo simulation technique that accounted for intrasubject and intersubject variability. Different pharmacokinetic end points, such as the AUC tumor, were extracted from the simulated human tumor drug concentrations to show how the predicted drug concentrations might be used to select drug-dosing regimens. It is believed that this modeling strategy can be used as an aid in the drug development process by providing key insights into drug disposition in tumors and by offering a foundation to optimize drug regimen design.
Pilot study of integral yoga for menopausal hot flashes

ObjectiveThis study aims to obtain preliminary data on the efficacy of yoga for reducing self-reported menopausal hot flashes in a randomized study including an attention control group. MethodsWe randomized 54 late perimenopausal women (2-12 mo of amenorrhea) and postmenopausal women (>12 mo of amenorrhea)—aged 45 to 58 years and who experienced at least four hot flashes per day, on average, for at least 4 weeks—to one of three groups: yoga, health and wellness education (HW), and wait list (WL). Yoga and HW classes consisted of weekly 90-minute classes for 10 weeks. All women completed daily hot flash diaries throughout the trial (10 wk) to track the frequency and severity of hot flashes. The mean hot flash index score is based on the number of mild, moderate, severe, and very severe hot flashes. ResultsHot flash frequency declined significantly across time for all three groups, with the strongest decline occurring during the first week. There was no overall significant difference in hot flash frequency decrease over time by treatment groups, but the yoga and HW groups followed similar patterns and showed greater decreases than the WL group. On week 10, women in the yoga group reported an approximately 66% decrease in hot flash frequency, women in the HW group reported a 63% decrease, and women in the WL group reported a 36% decrease. The hot flash index showed a similar pattern. ConclusionsResults suggest that yoga can serve as a behavioral option for reducing hot flashes but may not offer any advantage over other types of interventions.