Miracle-dz/UniFAR-FTUs huggingface dataset:
An Efficient Data Protection Architecture Based on Fragmentation and Encryption

In this thesis, a completely revisited data protection scheme based on selective encryption is presented. First, this new scheme is agnostic in term of data format, second it has a parallel architecture using GPGPU allowing performance to be at least comparable to full encryption algorithms. Bitmap, as a special uncompressed multimedia format, is addressed as a first use case. Discrete Cosine Transform (DCT) is the first transformation for splitting fragments, getting data protection, and storing data separately on local device and cloud servers. This work has largely improved the previous published ones for bitmap protection by providing new designs and practical experimentations. General purpose graphic processing unit (GPGPU) is exploited as an accelerator to guarantee the efficiency of the calculation compared with traditional full encryption algorithms. Then, an agnostic selective encryption based on lossless Discrete Wavelet Transform (DWT) is presented. This design, with practical experimentations on different hardware configurations, provides strong level of protection and good performance at the same time plus flexible storage dispersion schemes. Therefore, our agnostic data protection and transmission solution combining fragmentation, encryption, and dispersion is made available for a wide range of end-user applications. Also a complete set of security analysis are deployed to test the level of provided protection.
Ocular surface temperature in patients with evaporative and aqueous-deficient dry eyes: a thermographic approach

Objective: In recent decades infrared thermography (IRT) has facilitated accurate quantitative measurements of the ocular surface temperature (OST), applying a non-invasive procedure. The objective of this work was to develop a procedure based on IRT, which allows characterizing of the cooling of the ocular surface of patients suffering from dry eye syndrome, and distinguishing among patients suffering from aqueous deficient dry eye (ADDE) and evaporative dry eyes (EDE). Approach: All patients examined (34 females and 4 males, 23–84 years) were divided into two groups according to their Schirmer I result (⩽ 7 mm for ADDE and > 7 mm for EDE), and the OST was recorded for 7 s at 30 Hz. For each acquisition, the temperatures of the central cornea (CC) as well as those of both temporal and nasal canthi were investigated. Main results: Findings showed that the maximum temperature variation (up to 0.75 ± 0.29 °C) was at the CC for both groups. Furthermore, patients suffering from EDE tended to have a higher initial OST than those with ADDE, explained by the greater quantity of the tear film, evenly distributed over the entire ocular surface, keeping the OST higher initially. Results also showed that EDE patients had an average cooling rate higher than those suffering from ADDE, confirming the excessive evaporation of the tear film. Significance: Ocular thermography paves the way to become an effective tool for differentiating between the two different etiologies of dry eye syndrome.
Candida Biofilms on Oral Biomaterials

Biological as well as inert surfaces of the oral cavity are exposed to an abundant microflora that is able to initiate the formation of biofilms. Yeasts are frequently involved, such as Candida (especially albicans), a low-level commensal of oral, gastrointestinal, and genitourinary mucosae in humans. In vivo and in vitro studies have shown Candida incorporation into biofilms covering different biomaterials used in the oral cavity for the manufacturing of dentures, orthodontic appliances, etc. Yeast (Candida genus) biofilms can then induce device-related infections mainly in the elderly and in medically-compromised patients with subsequent morbidity and occasional mortality, all bearing high social and financial costs. Generally, scientific literature does not integrate all aspects of material/tissue interfaces: mechanisms of Candida biofilm development and biomaterial maintenance, the welfare of patients, and prevention of candidosis. In vitro investigations were mainly undertaken with mono-species biofilms whereas Candida incorporation into biofilms on oral surfaces tends to correspond with an increase in the yeast/bacteria ratio. This illustrates the need for interdisciplinary insight. This chapter will review 1) the literature data concerning material surfaces in support of Candida biofilms in the oral environment, 2) the in vitro approaches to understanding the mechanisms of Candida biofilm formation on materials, 3) the interfaced manipulations in order to prevent Candida biofilm onset, and 4) the precautions when testing new devices in vivo in the oral cavity.
CPU reservations and time constraints: efficient, predictable scheduling of independent activities

Workstations and personal computers are increasingly being used for applications with real-time characteristics such as speech understanding and synthesis, media computations and I/O, and animation, often concurrently executed with traditional non-real-time workloads. This paper presents a system that can schedule multiple independent activities so that: . activities can obtain minimum guaranteed execution rates with application-specified reservation granularities via CPU Reservations, CPU Reservations, which are of the form reserve X units of time out of every Y units, provide not just an average case execution rate of X/Y over long periods of time, but the stronger guarantee that from any instant of time, by Y time units later, the activity will have executed for at least X time units, . applications can use Time Constraints to schedule tasks by deadlines, with on-time completion guaranteed for tasks with accepted constraints, and . both CPU Reservations and Time Constraints are implemented very efficiently. In particular, . CPU scheduling overhead is bounded by a constant and is not a function of the number of schedulable tasks. Other key scheduler properties are: . activities cannot violate other activities' guarantees, . time constraints and CPU reservations may be used together, separately, or not at all (which gives a round-robin schedule), with well-defined interactions between all combinations, and . spare CPU time is fairly shared among all activities. The Rialto operating system, developed at Microsoft Research, achieves these goals by using a precomputed schedule, which is the fundamental basis of this work.
White Matter Changes and Word Finding Failures with Increasing Age

Background Increasing life expectancy necessitates the better understanding of the neurophysiological underpinnings of age-related cognitive changes. The majority of research examining structural-cognitive relationships in aging focuses on the role of age-related changes to grey matter integrity. In the current study, we examined the relationship between age-related changes in white matter and language production. More specifically, we concentrated on word-finding failures, which increase with age. Methodology/Principal Findings We used Diffusion tensor MRI (a technique used to image, in vivo, the diffusion of water molecules in brain tissue) to relate white matter integrity to measures of successful and unsuccessful picture naming. Diffusion tensor images were used to calculate Fractional Anisotropy (FA) images. FA is considered to be a measure of white matter organization/integrity. FA images were related to measures of successful picture naming and to word finding failures using voxel-based linear regression analyses. Successful naming rates correlated positively with white matter integrity across a broad range of regions implicated in language production. However, word finding failure rates correlated negatively with a more restricted region in the posterior aspect of superior longitudinal fasciculus. Conclusions/Significance The use of DTI-MRI provides evidence for the relationship between age-related white matter changes in specific language regions and word finding failures in old age.
Collagen XXVII Organises the Pericellular Matrix in the Growth Plate

In order to characterise the function of the novel fibrillar type XXVII collagen, a series of mice expressing mutant forms of the collagen were investigated. Mice harboring a glycine to cysteine substitution in the collagenous domain were phenotypically normal when heterozygote and displayed a mild disruption of growth plate architecture in the homozygous state. Mice expressing an 87 amino acid deletion in the collagenous domain of collagen XXVII were phenotypically normal as heterozygotes whereas homozygotes exhibited a severe chondrodysplasia and died perinatally from a lung defect. Animals expressing the 87 amino acid deletion targeted specifically to cartilage were viable but severely dwarfed. The pericellular matrix of proliferative chondrocytes was disrupted and the proliferative cells exhibited a decreased tendency to flatten and form vertical columns. Collagen XXVII plays an important structural role in the pericellular extracellular matrix of the growth plate and is required for the organisation of the proliferative zone.
Optimal Gabor Filters for Steganalysis of Content-Adaptive JPEG Steganography

The existing steganalysis method based on 2D Gabor filters can achieve a competitive detection performance for content-adaptive JPEG steganography. However, the feature dimensionality is still high and the time-consuming of feature extraction is relatively large because the optimal selection is not performed for 2D Gabor filters. To solve this problem, a new steganalysis method is proposed for content-adaptive JPEG steganography by selecting the optimal 2D Gabor filters. For the proposed method, the 2D Gabor filters with different parameter settings are generated first. Then, the feature is extracted by each 2D Gabor filter and the corresponding detection accuracy is used as the measure for filter selection. Next, some 2D Gabor filters are selected by a greedy strategy and the steganalysis feature is extracted by the selected filters. Last, the ensemble classifier is used to assemble the proposed steganalysis feature as well as the final steganalyzer. The experimental results show that the steganalysis feature extracted by the selected optimal 2D Gabor filters also can achieve a competitive detection performance while the feature dimensionality is reduced greatly.
Knowledge integration in One Health policy formulation, implementation and evaluation

Abstract The One Health concept covers the interrelationship between human, animal and environmental health and requires multistakeholder collaboration across many cultural, disciplinary, institutional and sectoral boundaries. Yet, the implementation of the One Health approach appears hampered by shortcomings in the global framework for health governance. Knowledge integration approaches, at all stages of policy development, could help to address these shortcomings. The identification of key objectives, the resolving of trade-offs and the creation of a common vision and a common direction can be supported by multicriteria analyses. Evidence-based decision-making and transformation of observations into narratives detailing how situations emerge and might unfold in the future can be achieved by systems thinking. Finally, transdisciplinary approaches can be used both to improve the effectiveness of existing systems and to develop novel networks for collective action. To strengthen One Health governance, we propose that knowledge integration becomes a key feature of all stages in the development of related policies. We suggest several ways in which such integration could be promoted.
VENNTURE–A Novel Venn Diagram Investigational Tool for Multiple Pharmacological Dataset Analysis

As pharmacological data sets become increasingly large and complex, new visual analysis and filtering programs are needed to aid their appreciation. One of the most commonly used methods for visualizing biological data is the Venn diagram. Currently used Venn analysis software often presents multiple problems to biological scientists, in that only a limited number of simultaneous data sets can be analyzed. An improved appreciation of the connectivity between multiple, highly-complex datasets is crucial for the next generation of data analysis of genomic and proteomic data streams. We describe the development of VENNTURE, a program that facilitates visualization of up to six datasets in a user-friendly manner. This program includes versatile output features, where grouped data points can be easily exported into a spreadsheet. To demonstrate its unique experimental utility we applied VENNTURE to a highly complex parallel paradigm, i.e. comparison of multiple G protein-coupled receptor drug dose phosphoproteomic data, in multiple cellular physiological contexts. VENNTURE was able to reliably and simply dissect six complex data sets into easily identifiable groups for straightforward analysis and data output. Applied to complex pharmacological datasets, VENNTURE’s improved features and ease of analysis are much improved over currently available Venn diagram programs. VENNTURE enabled the delineation of highly complex patterns of dose-dependent G protein-coupled receptor activity and its dependence on physiological cellular contexts. This study highlights the potential for such a program in fields such as pharmacology, genomics, and bioinformatics.
Host Plant Use by Competing Acacia-Ants: Mutualists Monopolize While Parasites Share Hosts

Protective ant-plant mutualisms that are exploited by non-defending parasitic ants represent prominent model systems for ecology and evolutionary biology. The mutualist Pseudomyrmex ferrugineus is an obligate plant-ant and fully depends on acacias for nesting space and food. The parasite Pseudomyrmex gracilis facultatively nests on acacias and uses host-derived food rewards but also external food sources. Integrative analyses of genetic microsatellite data, cuticular hydrocarbons and behavioral assays showed that an individual acacia might be inhabited by the workers of several P. gracilis queens, whereas one P. ferrugineus colony monopolizes one or more host trees. Despite these differences in social organization, neither of the species exhibited aggressive behavior among conspecific workers sharing a tree regardless of their relatedness. This lack of aggression corresponds to the high similarity of cuticular hydrocarbon profiles among ants living on the same tree. Host sharing by unrelated colonies, or the presence of several queens in a single colony are discussed as strategies by which parasite colonies could achieve the observed social organization. We argue that in ecological terms, the non-aggressive behavior of non-sibling P. gracilis workers — regardless of the route to achieve this social structure — enables this species to efficiently occupy and exploit a host plant. By contrast, single large and long-lived colonies of the mutualist P. ferrugineus monopolize individual host plants and defend them aggressively against invaders from other trees. Our findings highlight the necessity for using several methods in combination to fully understand how differing life history strategies affect social organization in ants.
Faster SAT solving with better CNF generation

Boolean satisfiability (SAT) solving has become an enabling technology with wide-ranging applications in numerous disciplines. These applications tend to be most naturally encoded using arbitrary Boolean expressions, but to use modern SAT solvers, one has to generate expressions in conjunctive normal form (CNF). This process can significantly affect SAT solving times. In this paper, we introduce a new linear-time CNF generation algorithm. We have implemented our algorithm and have conducted extensive experiments, which show that our algorithm leads to faster SAT solving times and smaller CNF than existing approaches.
Framework Information Based Java Software Architecture Recovery

Software systems tend to become more and more complex as they evolve, which makes it difficult to review, understand, and maintain the source code without complete architectural information, especially in case of large-scale systems. Software architecture recovery is considered an important method contributing to solving this problem. Hierarchical clustering is one of the techniques used to extract architectural information from lower level software representations, such as the source code. This paper is aimed at improving the accuracy of existing hierarchical clustering algorithms by allowing users to parameterize and configure framework information as framework-specific features. We have implemented our approach as an Eclipse plugin and have applied it to recovering the architecture of Java programs. Experiments are carried out on our benchmark built upon Java web applications in which the Spring Framework is used. The experimental results show that our approach can improve the accuracy of the recovered architecture to some extent.
Polymorphisms of ABCB1, CYP3A4 and CYP3A5 Genes in Ovarian Cancer and Treatment Response in Poles.

BACKGROUND/AIM Ovarian cancer is a lethal gynecological malignancy, with 5-year survival of only about one third of patients. The ABCB1 gene encodes the P-glycoprotein which is one of the multidrug efflux pumps. Its decreased activity may result in multidrug resistance of cancer cells. Drug-metabolizing enzymes Cyp3A4 and Cyp3A5 may affect success of chemotherapy. In this study we attempted to examine the effects of 12 single nucleotide polymorphisms (SNPs) of the ABCB1 gene and one SNP in each of CYP3A4 and CYP3A5 genes on the incidence of ovarian cancer in Polish women and their response to treatment. MATERIALS AND METHODS Our study included 276 patients and 369 healthy control women. RESULTS The results showed no significant differences between patients and controls in allele frequencies of the tested SNPs, with one exception: rs2157926T allele decreased cancer risk by 99.4% (odds ratio, 0.006). Moreover, rs2032582T increased fourfold the risk of metastasis. Finally, rs1128503CC genotype prolonged survival (p=0.024778). CONCLUSION These findings may contribute to a better prediction of therapy outcome.
An Exploration of Mining Gene Expression Mentions and Their Anatomical Locations from Biomedical Text

Here we explore mining data on gene expression from the biomedical literature and present Gene Expression Text Miner (GETM), a tool for extraction of information about the expression of genes and their anatomical locations from text. Provided with recognized gene mentions, GETM identifies mentions of anatomical locations and cell lines, and extracts text passages where authors discuss the expression of a particular gene in specific anatomical locations or cell lines. This enables the automatic construction of expression profiles for both genes and anatomical locations. Evaluated against a manually extended version of the BioNLP '09 corpus, GETM achieved precision and recall levels of 58.8% and 23.8%, respectively. Application of GETM to MEDLINE and PubMed Central yielded over 700,000 gene expression mentions. This data set may be queried through a web interface, and should prove useful not only for researchers who are interested in the developmental regulation of specific genes of interest, but also for data base curators aiming to create structured repositories of gene expression information. The compiled tool, its source code, the manually annotated evaluation corpus and a search query interface to the data set extracted from MEDLINE and PubMed Central is available at http://getmproject.sourceforge. net/.
Spatial Sorting Drives Morphological Variation in the Invasive Bird, Acridotheris tristis

The speed of range expansion in many invasive species is often accelerating because individuals with stronger dispersal abilities are more likely to be found at the range front. This ‘spatial sorting’ of strong dispersers will drive the acceleration of range expansion. In this study, we test whether the process of spatial sorting is at work in an invasive bird population (Common myna, Acridotheris tristis) in South Africa. Specifically, we sampled individuals across its invasive range and compared morphometric measurements relevant and non-relevant to the dispersal ability. Besides testing for signals of spatial sorting, we further examined the effect of environmental factors on morphological variations. Our results showed that dispersal-relevant traits are significantly correlated with distance from the range core, with strong sexual dimorphism, indicative of sex-biased dispersal. Morphological variations were significant in wing and head traits of females, suggesting females as the primary dispersing sex. In contrast, traits not related to dispersal such as those associated with foraging showed no signs of spatial sorting but were significantly affected by environmental variables such as the vegetation and the intensity of urbanisation. When taken together, our results support the role of spatial sorting in facilitating the expansion of Common myna in South Africa despite its low propensity to disperse in the native range.
Proximity to parasites reduces host fitness independent of infection in a Drosophila–Macrocheles system

Abstract Parasites are known to have direct negative effects on host fitness; however, the indirect effects of parasitism on host fitness sans infection are less well understood. Hosts undergo behavioural and physiological changes when in proximity to parasites. Yet, there is little experimental evidence showing that these changes lead to long-term decreases in host fitness. We aimed to determine if parasite exposure affects host fitness independent of contact, because current approaches to parasite ecology may underestimate the effect of parasites on host populations. We assayed the longevity and reproductive output of Drosophila nigrospiracula exposed or not exposed to ectoparasitic Macrocheles subbadius. In order to preclude contact and infection, mites and flies were permanently separated with a mesh screen. Exposed flies had shorter lives and lower fecundity relative to unexposed flies. Recent work in parasite ecology has argued that parasite–host systems show similar processes as predator–prey systems. Our findings mirror the non-consumptive effects observed in predator–prey systems, in which prey species suffer reduced fitness even if they never come into direct contact with predators. Our results support the perspective that there are analogous effects in parasite–host systems, and suggest new directions for research in both parasite ecology and the ecology of fear.
A simulation investigation on interaction mechanism between Ebola nucleoprotein and VP35 peptide

Ebola viruses (EBOV) will induce acute hemorrhagic fever, which is fatal to humans and nonhuman primates. The combination of EBOV VP35 peptide with nucleoprotein N-terminal (NPNTD) is proposed based on static crystal structures in recent studies, but VP35 binding mechanism and conformational dynamics are still unclear. This investigation, using Molecular Dynamic (MD) simulation and Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) energy calculation, more convincingly proves the greater roles of the protein binding mechanisms than do hints from the static crystal structure observations. Conformational analysis of the systems demonstrate that combination with VP35 may lead to the conformational transition of NPNTD from “open” to “closed” state. According to the analyses of binding free energies and their decomposition, VP35 residue R37 plays a crucial role in wild type as well as mutant systems. Mutations of I29 and L33 to aspartate as well as M34 to proline affect binding affinity mainly through influencing electrostatic interaction, which is closely related to H-bonds formation. In addition, mutations mainly affect β-hairpin and loop regions, among which, M34P may have the greatest influence to the binding. This study may provide specific binding mechanisms between VP35 peptide and NPNTD, especially some important residues concerning binding.