Miracle-dz/UniFAR-FTUs huggingface dataset:
A Comparison of Red Fluorescent Proteins to Model DNA Vaccine Expression by Whole Animal In Vivo Imaging

DNA vaccines can be manufactured cheaply, easily and rapidly and have performed well in pre-clinical animal studies. However, clinical trials have so far been disappointing, failing to evoke a strong immune response, possibly due to poor antigen expression. To improve antigen expression, improved technology to monitor DNA vaccine transfection efficiency is required. In the current study, we compared plasmid encoded tdTomato, mCherry, Katushka, tdKatushka2 and luciferase as reporter proteins for whole animal in vivo imaging. The intramuscular, subcutaneous and tattooing routes were compared and electroporation was used to enhance expression. We observed that overall, fluorescent proteins were not a good tool to assess expression from DNA plasmids, with a highly heterogeneous response between animals. Of the proteins used, intramuscular delivery of DNA encoding either tdTomato or luciferase gave the clearest signal, with some Katushka and tdKatushka2 signal observed. Subcutaneous delivery was weakly visible and nothing was observed following DNA tattooing. DNA encoding haemagglutinin was used to determine whether immune responses mirrored visible expression levels. A protective immune response against H1N1 influenza was induced by all routes, even after a single dose of DNA, though qualitative differences were observed, with tattooing leading to high antibody responses and subcutaneous DNA leading to high CD8 responses. We conclude that of the reporter proteins used, expression from DNA plasmids can best be assessed using tdTomato or luciferase. But, the disconnect between visible expression level and immunogenicity suggests that in vivo whole animal imaging of fluorescent proteins has limited utility for predicting DNA vaccine efficacy.
Investigation for antimicrobial resistance-modulating activity of diethyl malate and 1-methyl malate against beta-lactamase class A from Bacillus licheniformis by molecular dynamics, in vitro and in vivo studies

Resistance to antibiotics in bacteria, is one of the major problems of mankind. Each year, a large number of patients due to infection, lose their lives. One of the main mechanisms of antibiotic resistance is beta-lactamase secretion. This enzyme hydrolyzes the amide bond of a lactam ring in beta-lactam antibiotics. Bacillus licheniformis is a mesophilic gram-positive bacterium, which has a high potential to produce beta-lactamase class A. In this study, the inhibitory effects of some malate analogous were studied by in vitro and in vivo studies. In addition, the effects of inhibitor binding on beta-lactamase were studied using MD simulations. Our results showed that diethyl malate and 1-methyl malate can decrease the MIC value of benzyl penicillin by sixteen and eight-fold, respectively. Data derived from in vitro studies revealed that decrease in MIC values is correlated with beta-lactamase inhibition. Molecular docking studies predicted the binding mode of inhibitors with the beta-lactamase active site. The structural analysis from MD simulations exhibits that binding of citrate and diethyl malate causes earlier equilibrium of beta-lactamase. After binding, the fluctuation of Ser 70 is also decreased. Based on our data, diethyl malate can be used to design the potent inhibitor against beta-lactamase class A.
A Model for Interoperability : XML Documents as an RDF Database

We propose a model for a Resource Description Format (RDF) database for interlinear glossed text (IGT) created from documents encoded in the Extensible Markup Language (XML) using markup metaschemas. A metaschema, constructed using the Semantic Interpretation Language (SIL) (Simons 2004) maps XML-encoded documents to a common semantically rich RDF database. The RDF database in turn can be searched using RDFsearch engines providing the key functionality of a database management system (DBMS). Simons et al. (2004) gives a proof of concept of the model by mapping differently encoded XML lexicons to a common RDF form. Search capability is provided across these data using SeRQL, a SQL-like query language built around the Sesame RDF database program. In this paper, we extend these results to corpora of interlinear glossed text obtained from various sources, including some from the Web following Lewis (2003), combined with a language profile for each language variety, which provides basic grammatical information about that variety.
User authentication and authorization in the Java/sup TM/ platform

Java/sup TM/ security technology originally focused on creating a safe environment in which to run potentially untrusted code downloaded from the public network. With the latest release of the Java/sup TM/ platform (the Java/sup TM/ 2 Software Development Kit, v 1.2), fine-grained access controls can be placed upon critical resources with regard to the identity of the running applets and applications, which are distinguished by where the code came from and who signed it. However, the Java platform still lacks the means to enforce access controls based on the identity of the user who runs the code. In this paper we describe the design and implementation of the Java/sup TM/ Authentication and Authorization Service (JAAS), a framework and programming interface that augments the Java/sup TM/ platform with both user-based authentication and access control capabilities.
A Software Self-Organizing Middleware for Smart Spaces Based on Fuzzy Logic

Autonomic Computing Self-Configuration /Organization can simplify the complexity of software deployment, management and utilization in pervasive environments such as smart spaces. Software management complexity in pervasive environments is a serious problem, which leads to high management costs and slow down the broad utilization of the pervasive technologies. This paper presents our work on a self-organization middleware that reduce user manipulations and reasoning during software deployment and organization in smart spaces. Our approach is based on Fuzzy Logic and semantic description in order to support the self-organization reasoning on the environment context.
Evidence for a post-entry barrier to R5 HIV-1 infection of CD4 memory T cells

BackgroundHIV-1 strains R5 and X4 can infect CD4 memory T cells in vivo. Anti-CD3/28 stimulation induces β-chemokines and CCR5 down-regulation and renders these cells resistant to R5 HIV-1 infection. Here we describe an additional cellular mechanism that blocks productive R5 HIV-1 infection of CD4 memory T cells. MethodsBlood-derived CD4 memory T cells and CD4 T-cell clones were infected with primary R5 and X4 HIV-1 strains. Virus replication was correlated with CCR5 expression and β-chemokine production. Virus entry and infectivity were measured by PCR for early and late products of HIV reverse transcription respectively. ResultsR5 strains were up to 1000-fold less infectious than X4 viruses for CD4 memory T cells. This resistance was independent of CCR5 levels and of the Δ-32 mutation and the CCR2-V64I/ CCR5-59653T linked mutations. Blocking endogenous β-chemokines relieved minimally this restriction. At the single cell level, CD4 memory cells were either permissive or non-permissive for R5 HIV-1 infection. R5 HIV titre was up to 10-fold lower than X4 virus titre even in a permissive clone. However, R5 viruses replicated as efficiently as X4 viruses in the permissive clone when neutralizing anti-β chemokine antibodies were added. Non-permissive cells blocked a post-entry step of the virus life-cycle and expressed early but not late HIV transcripts. Neutralizing anti-β chemokine antibodies promoted R5 virus replication marginally in the non-permissive clone. ConclusionSome blood memory CD4 T cells retard R5 HIV-1 replication via endogenous β-chemokines whereas others block productive R5 HIV-1 infection by an additional mechanism that interferes with a post-entry step of the virus life cycle. These natural barriers might contribute to lower pathogenicity of R5 HIV-1 strains for CD4 memory T cells than X4 viruses that emerge late in disease.
Colour processing in complex environments: insights from the visual system of bees

Colour vision enables animals to detect and discriminate differences in chromatic cues independent of brightness. How the bee visual system manages this task is of interest for understanding information processing in miniaturized systems, as well as the relationship between bee pollinators and flowering plants. Bees can quickly discriminate dissimilar colours, but can also slowly learn to discriminate very similar colours, raising the question as to how the visual system can support this, or whether it is simply a learning and memory operation. We discuss the detailed neuroanatomical layout of the brain, identify probable brain areas for colour processing, and suggest that there may be multiple systems in the bee brain that mediate either coarse or fine colour discrimination ability in a manner dependent upon individual experience. These multiple colour pathways have been identified along both functional and anatomical lines in the bee brain, providing us with some insights into how the brain may operate to support complex colour discrimination behaviours.
XPSuite: tracking and managing XP projects in the IDE

In this paper we describe XPSuite, a tool comprising two parts: XPSwiki, a tool for managing XP projects and XP4IDE, a plug-in for integrating XPSwiki with the IDE IntelliJ-Idea. The reasons for this integration and the ability of XPSuite to collect process metrics are described. The system has a full object oriented implementation so it is possible to extract all data represented in the model that the system implements.
On a quadratic estimate related to the Kato conjecture and boundary value problems

We provide a direct proof of a quadratic estimate that plays a central role in the determination of domains of square roots of elliptic operators and, as shown more recently, in some boundary value problems with $L^2$ boundary data. We develop the application to the Kato conjecture and to a Neumann problem. This quadratic estimate enjoys some equivalent forms in various settings. This gives new results in the functional calculus of Dirac type operators on forms.
Determination of anisotropic ratio of the skull for EEG source localization in patients with epilepsy

Epilepsy is a neurological disorder characterized by abnormal brain activity, which affects about 1% of the people worldwide. When patients do not respond to medication, the surgical removal of the epileptic focus can be considered. EEG source analysis aims at localizing the origin of these epileptic events. It consists of 2 subproblems: The forward problem determines the electrode potentials at the scalp given a source and the inverse problem estimates the source parameters given a measured set of electrode potentials. The conductivity of the skull highly affects the dipole location and is known to be anisotropic. In this study we want to determine the anisotropic ratio to accurately model the conductivity of the skull.
Spelling Correction as an Iterative Process that Exploits the Collective Knowledge of Web Users

Logs of user queries to an internet search engine provide a large amount of implicit and explicit information about language. In this paper, we investigate their use in spelling correction of search queries, a task which poses many additional challenges beyond the traditional spelling correction problem. We present an approach that uses an iterative transformation of the input query strings into other strings that correspond to more and more likely queries according to statistics extracted from internet search query logs.
Application of dynamic variable cipher security certificate in Internet of Things

With the development of Internet of Things (IOT), there are more and more concerns about the security of IOT. In terms of security of Internet, the security framework of Internet can not provide a completely solution to solve all security problems in IOT [1]. This paper describes the security structure of sensor layer, network layer, and application layer in IOT. This thesis intends to analyze the security features of sensor layer, and then presents dynamic variable cipher security certificate, a new method of ID authentication among node and node in sensor layer. This certificate provides a method of “one time one cipher” between communicating parties. It's a lightweight encryption or decryption method, using time stamp technology, timeliness in the two communication partners is guaranteed. In general, dynamic variable cipher security certificate can be well applied to the communication among sensor nodes in IOT.
In Vivo Pyro-SIP Assessing Active Gut Microbiota of the Cotton Leafworm, Spodoptera littoralis

The gut microbiota is of crucial importance for the host with considerable metabolic activity. Although great efforts have been made toward characterizing microbial diversity, measuring components' metabolic activity surprisingly hasn't kept pace. Here we combined pyrosequencing of amplified 16S rRNA genes with in vivo stable isotope probing (Pyro-SIP) to unmask metabolically active bacteria in the gut of cotton leafworm (Spodoptera littoralis), a polyphagous insect herbivore that consumes large amounts of plant material in a short time, liberating abundant glucose in the alimentary canal as a most important carbon and energy source for both host and active gut bacteria. With 13C glucose as the trophic link, Pyro-SIP revealed that a relatively simple but distinctive gut microbiota co-developed with the host, both metabolic activity and composition shifting throughout larval stages. Pantoea, Citrobacter and Clostridium were particularly active in early-instar, likely the core functional populations linked to nutritional upgrading. Enterococcus was the single predominant genus in the community, and it was essentially stable and metabolically active in the larval lifespan. Based on that Enterococci formed biofilm-like layers on the gut epithelium and that the isolated strains showed antimicrobial properties, Enterococcus may be able to establish a colonization resistance effect in the gut against potentially harmful microbes from outside. Not only does this establish the first in-depth inventory of the gut microbiota of a model organism from the mostly phytophagous Lepidoptera, but this pilot study shows that Pyro-SIP can rapidly gain insight into the gut microbiota's metabolic activity with high resolution and high precision.
Influences of Size and Amount of Colloidal Template and Droplet Diameter on the Formation of Porous-structured Hyaluronic Acid Particles

Combination of spray drying and templating method has been reported as one of the best method to produce porous pharmaceutical particles. However, current development reports have shown successful formation of porous particles with improper information on what mechanism occurs during the synthesis process and what process parameters involve the creation of particles with controllable pore structures and morphologies. In this report, influences of spray-drying parameters (i.e., size and amount of colloidal template, and droplet diameter) on porous particle fabrication were investigated. Hyaluronic acid (as a model of pharmaceutical drug host component) and polystyrene spheres (as a model of template) were used. The experimental results showed that the spray-drying parameters strongly influenced the external morphology (i.e., spherical and doughnut-shaped), particle outer diameter (from 300 to 2000 nm), and porous configuration (i.e., number of hole cavities and pore sizes (from 100 to 300 nm)) of particles. To qualitatively explain our synthesis strategies to get porous structure, the proposal of the particle formation mechanism was added.
Molecular and cellular profiles of the resolution phase in a damage‐associated molecular pattern (DAMP)‐mediated peritonitis model and revelation of leukocyte persistence in peritoneal tissues

Models of microbe‐elicited peritonitis have been invaluable to identify mechanisms underlying inflammation resolution, but whether resolution mechanisms differ from an inflammatory agent to another has not been determined. Thus, we analyzed the cellular and molecular components of the resolution phase of non‐microbe‐induced inflammation. In thioglycollate (TG)‐induced peritonitis, resolution started at 12 h (Tmax) and displayed a 22 h resolution interval (Ri). During resolution, lipoxin A4, resolvin (Rv) D1 and RvD2, protectin D1 (PD1), and maresin 1 (MaR1) were transiently produced while RvD5 was continually generated. In addition, docosahexaenoic acid (DHA)‐derived mediators were produced to a higher extent than in microbial peritonitis. We also investigated leukocyte infiltration and clearance in peritoneal tissues surrounding the inflammatory site. In the omentum, resolution parameters, neutrophil apoptosis, and efferocytosis were similar to those of the peritoneal cavity. However, we noticed long‐term persistence of M2‐polarized macrophages and B‐lymphocytes in the omentum after TG administration, whereas zymosan injection caused M1/M2‐macrophage and T‐lymphocyte persistence regardless of the magnitude of the inflammatory response. Our study indicates that some aspects of resolution are shaped in a stimulus‐specific manner, and it ultimately argues that the tissues surrounding the inflammatory site must also be considered to address the inflammatory response globally. —Lastrucci, C. , Baillif, V. , Behar, A. , Al Saati, T. , Dubourdeau, M. , Maridonneau‐Parini, I. , Cougoule, C. Molecular and cellular profiles of the resolution phase in a damage‐associated molecular pattern (DAMP)‐mediated peritonitis model and revelation of leukocyte persistence in peritoneal tissues. FASEB J. 29, 1914‐1929 (2015). www.fasebj. org
Fairness Assessment of the Adaptive Token Bank Fair Queuing Scheduling Algorithm

Adaptive token bank fair queuing (ATBFQ) algorithm has been proposed as a cross-layer scheduling technique for 4G wireless systems recently. This algorithm takes higher layer quality of service (QoS) attributes such as priorities, interflow fairness, and delay constraints into account. By selecting the user terminals (UTs) in a certain prioritized manner derived from QoS attributes, the performance of the UTs, suffering from high interference and/or shadowing in particular, can be improved. The ATBFQ algorithm has been tested in a multicell environment in the presence of intercell interference by comparing with reference Score Based (SB) and Round Robin (RR) algorithms. In this paper, we further analyze ATBFQ primarily with regard to fairness along with other performance metrics accessed in a more elaborate system considering varying interference and loading conditions. Furthermore, an adaptive method for the allocation of resources is proposed for ATBFQ parameter selection, and is shown to have better performance in various loading conditions. It is observed from simulation results that ATBFQ with adaptive parameter selection outperforms the reference schemes in terms of queuing delay and UT throughput for different network loading cases.
Does Adaptation to Climate Change Provide Food Security? A Micro‐Perspective from Ethiopia

We examine the driving forces behind farmers’ decisions to adapt to climate change, and the impact of adaptation on farmers’ food production. We investigate whether there are differences in the food production functions of farm households that adapted and those that did not adapt. We estimate a simultaneous equations model with endogenous switching to account for the heterogeneity in the decision to adapt or not, and for unobservable characteristics of farmers and their farm. We compare the expected food production under the actual and counterfactual cases that the farm household adapted or not to climate change. We find that the group of farm households that adapted has systematically different characteristics than the group of farm households that did not adapt. The relationship between production and average temperature is inverted U-shaped for farm households that adapted, while it is U-shaped for farm households that did not adapt, and vice versa in the case of precipitation. We find that adaptation increases food production, however, the impact of adaptation on food production is smaller for the farm households that actually did adapt than for the farm households that did not adapt in the counterfactual case that they adapted.
Firms as Systems of Interdependent Choicesjoms

Managers within firms have to make choices along a large number of dimensions; for instance, how to configure activities involving manufacturing and marketing, and which organizational design to employ. Since these choices interact with each other, firms can be conceived of as systems of interdependent choices. In this article, I discuss research that addresses three questions that naturally arise in this context. First, how do such systems evolve over time? Second, what role does organizational design play in whether a firm will arrive at a consistent and high-performing set of choices? Third, what are the consequences of cognitive limitations by decision makers when faced with such complex systems? The article concludes by sketching out possible future directions of research in this domain.
A Mathematical Model for the Evolution of Nitric Oxide Concentration in Human Breathing

In physiology, the appearance of some inflammatory lung diseases is accompanied by an over production of nitric oxide which is detectable and measurable in the human breath. We propose a mathematical model describing the evolution of the concentration of such chemical compound based on a hyperbolic first order partial differential equation which takes into account the dominating effect of the advection due to the high velocity of the air with respect to diffusive effect. We take into account the geometry of the bronchial tree and we will study an entire breathing cycle. We will be able to give an explicit solution to the proposed equation, at least for some simple choice of the physiological functions. In turn, this makes it possible to describe accurately the concentration of nitric oxide in the bronchial tree as time varies, and to detect by its measure in the human breathing, the localization of the infections.
MECHANICAL MODELS FOR COMPRESSION AND TENSION PROPERTIES OF POROSITY FREE CONCRETE WITH STEEL FIBER

This study aims to propose the mechanical models of fiber reinforced Porosity Free Concrete (PFC). The compression test, splitting cylinder test, and bending test of PFC specimens were conducted to inves-tigate the mechanical properties of fiber reinforced PFC. The material characteristics of PFC such as the characteristic values for material strength, the compressive stress-strain relationships, and the the tension softening curve were proposed from each material test and the inverse analysis based on the results of three-point bending test, respectively. Furthermore, the size dependence of the flexural strength of fiber reinforced PFC was investigated through the four-point bending test and the finite element analysis with a discrete crack model. Based on the results of this FEM analysis, an equation to predict the flexural strength was proposed for PFC beams with the various height. Moreover, the equivalent specific length of fiber reinforced PFC beam with various height was also determined based on the numerical study using fiber modeling analysis. Finally, the tensile stress - strain relationships were obtained by the use of the equivalent specific length in order to convert the crack width of the tension softening curve into the strain. 20