Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic structure of Atriplex halimus populations in the Mediterranean Basin.

BACKGROUND AND AIMS The saltbush Atriplex halimus is a chenopodiaceous plant well adapted to dry saline habitats and widely distributed in the Mediterranean Basin. A study was carried out to analyse the genetic diversity of A. halimus at the level of the Mediterranean Basin. METHODS To assess the intra- and interpopulational variation of A. halimus a total of 51 populations and six plants per populations was analysed with the RAPD-PCR technique. For the study of the phylogeny of the populations, 21 samples of A. halimus and seven samples of other species of Atriplex were analysed by the sequencing of the ITS (internal transcribed spacer) region of the ribosomal DNA. KEY RESULTS The AMOVA analysis of the RAPD results showed that populations were divided into two discrete genetic groups, as the variation among groups accounted for 54.36 % of the total variance of the collection. At the same time, the intrapopulational diversity was high, as 301 out of 306 plants analysed constituted an individual RAPD haplotype. The sequencing of the ITS region also showed a significant separation of the two genetic groups, with a genetic distance of 0.023 nucleotide substitutions per site. Using A. breweri, A. canescens, A. glauca and A. prostrata as outgroups in the phylogenetic analysis, A. breweri and A. canescens are the species closest to A. halimus from this group, while A. prostrata is the most distant. CONCLUSIONS The present work indicates that two genetic groups of A. halimus can be distinguished after analysing the genetic diversity of 51 populations from ten countries in the Mediterranean Basin.
Hospital and Outpatient Health Services Utilization Among HIV-Infected Adults in Care 2000–2002

Background:Rapid changes in HIV epidemiology and antiretroviral therapy may have resulted in recent changes in patterns of healthcare utilization. Objective:The objective of this study was to examine sociodemographic and clinical correlates of inpatient and outpatient HIV-related health service utilization in a multistate sample of patients with HIV. Design:Demographic, clinical, and resource utilization data were collected from medical records for 2000, 2001, and 2002. Setting:This study was conducted at 11 U.S. HIV primary and specialty care sites in different geographic regions. Patients:In each year, HIV-positive patients with at least one CD4 count and any use of inpatient, outpatient, or emergency room services. Sample sizes were 13,392 in 2000, 15,211 in 2001, and 14,403 in 2002. Main Outcome Measures:Main outcome measures were number of hospital admissions, total days in hospital, and number of outpatient clinic/office visits per year. Inpatient and outpatient costs were estimated by applying unit costs to numbers of inpatient days and outpatient visits. Results:Mean numbers of admissions per person per year decreased from 2000 (0.40) to 2002 (0.35), but this difference was not significant in multivariate analyses. Hospitalization rates were significantly higher among patients with greater immunosuppression, women, blacks, patients who acquired HIV through drug use, those 50 years of age and over, and those with Medicaid or Medicare. Mean annual outpatient visits decreased significantly between 2000 and 2002, from 6.06 to 5.66 visits per person per year. Whites, Hispanics, those 30 years of age and over, those on highly active antiretroviral therapy (HAART), and those with Medicaid or Medicare had significantly higher outpatient utilization. Inpatient costs per patient per month (PPPM) were estimated to be $514 in 2000, $472 in 2001, and $424 in 2002; outpatient costs PPPM were estimated at $108 in 2000, $100 in 2001, and $101 in 2002. Conclusion:Changes in utilization over this 3-year period, although statistically significant in some cases, were not substantial. Hospitalization rates remain relatively high among minority or disadvantaged groups, suggesting persistent disparities in care. Combined inpatient and outpatient costs for patients on HAART were not significantly lower than for patients not on HAART.
Robust precision attitude tracking of an uncertain rigid spacecraft based on regulation theory

This paper explores regulation theory for the design of robust precision attitude tracking of an uncertain rigid spacecraft with external disturbances. Focusing on the attitude system in terms of unit quaternions with an unknown inertia matrix and unmodeled input disturbances, we first introduce specific nonlinear logic such that the resultant error‐quaternion system has an input‐to‐state stability property. Then, we establish an attitude deviation system with an output feedback normal form that has a strict vector relative degree of unity. This enables us to achieve robust output regulation based on an internal model. In particular, we can construct a high‐gain stabilizer for the relevant augmented system. As a major consequence, our study achieves not only precision attitude tracking with exponential convergence but also the input‐to‐state stability disturbance attenuation for the closed‐loop system. Finally, we show extensive simulation and experimental results to illustrate the approach.
Basic helix-loop-helix proteins can act at the E-box within the serum response element of the c-fos promoter to influence hormone-induced promoter activation in Sertoli cells.

The Sertoli cell is a terminally differentiated testicular cell in the adult required to maintain the process of spermatogenesis. Previously basic helix-loop-helix (bHLH) factors and c-fos have been shown to influence Sertoli cell-differentiated functions. The induction of Sertoli cell differentiation appears to involve the serum response element (SRE) of the c-fos promoter to activate c-fos and intermediate bHLH factor(s) that regulate down-stream Sertoli cell-differentiated genes (e.g. transferrin expression). The SRE of the c-fos promoter is influenced through the serum response factor (SRF). Interestingly, an E-box nucleotide sequence is present within the SRE. bHLH proteins act through E-box elements, and the current study investigates the possibility that bHLH proteins may directly influence the SRE of the c-fos promoter. The activation of the c-fos promoter in Sertoli cells was found to be inhibited with the overexpression of the inhibitory HLH protein Id. Analysis of major response elements within the c-fos promoter demonstrated that the expression of Id specifically inhibited the activation of SRE in Sertoli cells and no other elements tested. Mutations in the E-box of the SRE also inhibited the activation of SRE, suggesting the direct role of bHLH proteins in regulating SRE activity in Sertoli cells. In contrast, the activation of SRE containing a mutated E-box was comparable to wild-type SRE in control stromal cells. Analysis of SRE oligonucleotide gel mobility shift assays with nuclear extracts from Sertoli cells demonstrated the presence of both the SRF and the ubiquitously expressed bHLH protein E12/E47. In contrast, no E12/E47 was detected in the SRE oligonucleotide gel shift using control stromal cell nuclear extracts. Observations suggest the binding of E12/E47 to SRE may be a cell-specific event. The SRF and bHLH proteins appear to bind to the SRE and activate the c-fos promoter in Sertoli cells. Observations provide evidence that a bHLH protein can interact with the SRE of the c-fos promoter to influence hormone-induced promoter activation. Cross-talk between these nuclear transcription factors appears to be instrumental in the control of Sertoli cell-differentiated functions.
A comparison between Sypro Ruby and ruthenium II tris (bathophenanthroline disulfonate) as fluorescent stains for protein detection in gels

A comparison between two fluorescent metal chelates for staining proteins separated by electrophoresis has been carried out. One of these chelates is ruthenium II tris (bathophenanthroline disulfonate) and the other is commercial Sypro Ruby. Both can be efficiently detected either with UV tables or with commercial laser fluorescence scanners. The sensitivity and homogeneity of the stains and the interference with mass spectrometry analysis have been investigated. It appears that both stains perform similarly for protein detection, while ruthenium II tris (bathophenanthroline disulfonate) performs better for mass spectrometry analyses and as cost‐effectiveness ratio. However, Sypro Ruby is easier to use as a stain.
Susceptibility to Simian Immunodeficiency Virus Ex Vivo Predicts Outcome of a Prime-Boost Vaccine After SIVmac239 Challenge

Background:Efficacy assessment of AIDS vaccines relies both on preclinically challenging immunized monkeys with simian immunodeficiency virus (SIV) or monitoring infection rates in large human trials. Although conventional parameters of vaccine-induced immune responses do not completely predict outcome, existing methods for testing cellular immunity are sophisticated and difficult to establish in resource-limited settings. Methods:We have used virus replication kinetics (VVR) on ConA-stimulated peripheral blood mononuclear cells from rhesus monkeys immunized with DNA replication-defective adenovirus vector expressing various SIV genes, as an ex vivo model, to mimic the effects of different immune effector functions on viral infection. Results:VVR was attenuated by the immunization and correlated 2 weeks after first boost, with the number of interferon gamma-secreting cells and T-cell noncytotoxic antiviral responses. Importantly, VVR on the day of challenge but not interferon gamma responses correlated with viremia and with memory CD4+ T-cell measurements after SIVmac239 challenge. Similarly, T-cell noncytotoxic antiviral responses on the day of challenge correlated directly with memory CD4+ T cell and inversely with plasma viremia after challenge. Conclusions:VVR thus served as a better predictor of protective capacity of the vaccine regimen in these monkeys. We suggest that VVR be considered in the evaluation of candidate AIDS vaccines in humans.
Privacy-Preserving Data Deduplication on Trusted Processors

Cloud storage providers can reduce storage costs by detecting identical files and storing only one instance of them. While appealing to the storage providers, this deduplication set-up raises various privacy concerns among clients. Various techniques to retrofit content confidentiality in deduplication have been studied in the literature. Nevertheless, data encryption alone is insufficient to protect users' privacy, for the ownership and equality information of the outsourced data left unprotected may have serious privacy implications. In this paper, we investigate a three-tier architecture that saves bandwidth otherwise incurred by server-side deduplication solutions, yet does not admit the client-side deduplication's leakage on file existence. Leveraging trusted SGX-enabled processors, we construct the first privacy-preserving data deduplication protocol that protects not only the confidentiality, but also the ownership and equality information of the outsourced data, offering better privacy guarantees in comparison with existing works on secure data deduplication. Our experiments show that the proposed protocol incurs low performance overhead over conventional solutions that provide weaker level of privacy protection.
Phytophthora infestans RXLR Effector PexRD2 Interacts with Host MAPKKKε to Suppress Plant Immune Signaling[W][OPEN]

Oomycete pathogens of plants secrete effectors to perturb host cell physiology. This study reveals that the P. infestans RXLR-type effector protein PexRD2 interferes with host MAPKKKε immunity-related signaling to the benefit of the pathogen. Mitogen-activated protein kinase cascades are key players in plant immune signaling pathways, transducing the perception of invading pathogens into effective defense responses. Plant pathogenic oomycetes, such as the Irish potato famine pathogen Phytophthora infestans, deliver RXLR effector proteins to plant cells to modulate host immune signaling and promote colonization. Our understanding of the molecular mechanisms by which these effectors act in plant cells is limited. Here, we report that the P. infestans RXLR effector PexRD2 interacts with the kinase domain of MAPKKKε, a positive regulator of cell death associated with plant immunity. Expression of PexRD2 or silencing MAPKKKε in Nicotiana benthamiana enhances susceptibility to P. infestans. We show that PexRD2 perturbs signaling pathways triggered by or dependent on MAPKKKε. By contrast, homologs of PexRD2 from P. infestans had reduced or no interaction with MAPKKKε and did not promote disease susceptibility. Structure-led mutagenesis identified PexRD2 variants that do not interact with MAPKKKε and fail to support enhanced pathogen growth or perturb MAPKKKε signaling pathways. Our findings provide evidence that P. infestans RXLR effector PexRD2 has evolved to interact with a specific host MAPKKK to perturb plant immunity–related signaling.
Development of a methodology for flood hazard detection in urban areas from RADARSAT-2 imagery

Due to their capacity do acquire data day-and-night, whatever the meteorological conditions may be, and to the improved spatial resolution of the new generation of SAR sensors such as RADARSAT-2, COSMO-SkyMed or TerraSAR-X (~ 1 to 3 m with fine acquisition modes), SAR imagery is the most suitable tool for the detection of flooded areas in a context of crisis management. However, due to the complexity of the backscattered signal in urban environments, the development of precise and automated methods for flood detection in urban areas with SAR imagery is still challenging. A new approach for flood delineation and mapping in urban areas, combining RADARSAT-2 imagery and probability of flooding data simulated by a flood dynamic risk mapping tool is presented in this paper.
Microleakage - The Main Culprit in Bracket Bond Failure?

Microleakage is the most common cause of bracket debonding. Moreover, different thermal expansion coefficients between the enamel, the adhesive, and the bracket bases will cause repeated expansion and contraction, adding more stress to the bonding strength. Debonding represents the failure of the adhesion between the brackets and the tooth enamel. The debonding of brackets from the enamel surface is the result of several factors, such as acid-etching and drying, adhesive application, and the time and type of photo activation. The under polymerization process of composite photo activation may lead to early bracket debonding. Objective. The aim of this research is to review the available studies assessing bracket debonding due to microleakage. Material and Methods. An electronic search in Pub Med database and Web of Science was conducted between September-October 2018. The inclusion criteria were articles written in English, full-text articles, studies published in the last 5 years, studies in vivo, ex vivo, and in vitro. The outcome measures in this research were the conditions that determine orthodontic bracket debonding due to microleakage. Results. The MEDLINE search resulted in 510 titles and abstracts that were relevant to the present topic; after selecting the articles published in the last five years, 74 were available for further selection. After the exclusion of all the studies irrelevant for the aim of the paper, 13 articles were finally included in this research. In vitro studies showed that microleakage score was higher in the gingival margin at the enamel-adhesive interfaces and in the occlusal margin at the adhesive-metal bracket interfaces. Conclusion. Bracket debonding remains the main concern during the orthodontic treatment, despite the new techniques.
Universal robustness of scale-free networks against cascading edge failures

Considering the effect of the local topology structure of an edge on cascading failures, we investigate the cascading reaction behaviors on scale-free networks with respect to small edge-based initial attacks. Adopt the initial load of an edge ij in a network to be Lij = (kikj)α[(∑**math-image**ka)(∑**math-image**kb)]β with ki and kj being the degrees of the nodes connected by the edge ij, where α and β are tunable parameters, governing the strength of the edge initial load, and Γi and Γj are the sets of neighboring nodes of i and j, respectively. Our aim is to explore the relationship between some parameters and universal robustness characteristics against cascading failures on scale-free networks. We find by the theoretical analysis that the Baraba'si-Albert (BA) scale-free networks can reach the strongest robustness level against cascading failures when α + β = 1, where the robustness is quantified by a transition from normal state to collapse. And the network robustness has a positive correlation with the average degree. We furthermore confirm by the numerical simulations these results. © 2012 Wiley Periodicals, Inc.
Hypoxia induces osteogenic/angiogenic responses of bone marrow‐derived mesenchymal stromal cells seeded on bone‐derived scaffolds via ERK1/2 and p38 pathways

Osteogenesis and angiogenesis are tightly coupled processes during bone development and formation. It is thus well known that the enhancement of vascularization is of great importance in bone tissue engineering. As a potential approach for repairing bone defects, bone tissue constructs should therefore replicate the essential components in vivo microenvironments to promote cell osteogenic differentiation while at same time induce angiogenic response. In light of standpoint above, a combination of human bone‐derived scaffolds and BMSCs that subjected to hypoxia was used to mimic in vivo conditions. Also the underlying cellular/molecular regulation was fully investigated. The results showed that hypoxia (5–10% O2) greatly enhanced the proliferation of BMSCs seeded in scaffolds, although the hypoxia (5% O2)‐induced proliferative effect on BMSC cellular scaffolds was not apparent to those cultured in plates. However, such a kind of model was able to significantly induce the osteogenic/angiogenic responses of BMSCs as reflected by osteogenesis or angiogenesis‐related highly expressed genes or proteins, such as alkaline phosphatase, osteocalcin, hypoxia‐inducible factor‐1α and vascular endothelial growth factor. Moreover, ERK1/2 and/or p38 pathways were demonstrated to play essential roles in hypoxia‐induced osteogenic/angiogenic responses. Our results indicated that the combination of bone‐derived scaffolds, a material that has a three dimensional network structure, and hypoxia, an environment that replicates in vivo BMSCs hypoxic living conditions, may be a potential approach for creating functional tissue‐engineered bone. Biotechnol. Bioeng. 2013; 110: 1794–1804. © 2013 Wiley Periodicals, Inc.
rrndb: the Ribosomal RNA Operon Copy Number Database

The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme. msu.edu.
Forecasting Heating Consumption in Buildings: A Scalable Full-Stack Distributed Engine

Predicting power demand of building heating systems is a challenging task due to the high variability of their energy profiles. Power demand is characterized by different heating cycles including sequences of various transient and steady-state phases. To effectively perform the predictive task by exploiting the huge amount of fine-grained energy-related data collected through Internet of Things (IoT) devices, innovative and scalable solutions should be devised. This paper presents PHi-CiB, a scalable full-stack distributed engine, addressing all tasks from energy-related data collection, to their integration, storage, analysis, and modeling. Heterogeneous data measurements (e.g., power consumption in buildings, meteorological conditions) are collected through multiple hardware (e.g., IoT devices) and software (e.g., web services) entities. Such data are integrated and analyzed to predict the average power demand of each building for different time horizons. First, the transient and steady-state phases characterizing the heating cycle of each building are automatically identified; then the power-level forecasting is performed for each phase. To this aim, PHi-CiB relies on a pipeline of three algorithms: the Exponentially Weighted Moving Average, the Multivariate Adaptive Regression Spline, and the Linear Regression with Stochastic Gradient Descent. PHi-CiB’s current implementation exploits Apache Spark and MongoDB and supports parallel and scalable processing and analytical tasks. Experimental results, performed on energy-related data collected in a real-world system show the effectiveness of PHi-CiB in predicting heating power consumption of buildings with a limited prediction error and an optimal horizontal scalability.
Shari'ah standard of business contract

This study deals with the Shari'ah Standard of Business Contract. The introduction presents a general idea of the law of contract in Islam and its development and significance to human life. The study has been divided into four chapters and ending with final remarks. Chapter One deals with the general idea of a Business contract in Islam. Among the areas covered under this chapter are the meaning of contract, its basis and rationale, development, nature and scope. It also touches on the aspects such as frredom of contract, the nominate contracts, the relationship between contract and belief and also the idea of the different terms related to contract. Chapter Two deals with the various kinds of Business contracts. The classifications covered in this chapter are based on the contract, its circumstances and also legal consequences. Chapter Three touches on the elements of Business contract under the Shri'ah Standard such as the offer, the acceptance, and the parties to the contract, the consideration and the possibility of the contract. Chapter Four, the final chapter, mainly covers two parts, the impediments to the contract in Islam and the various legal remedies for breach of Business contract, such as recission, injunction, damages, specific performance and also restitution. The last part of this thesis consists of the final remarks on the Shari'ah Standard of Business Contract, its possible solutions as well as the future prospect for the Islamization of the Shari'ah Standard of Business in the society today.Product Reviews for Shar'iah Standard of Business Contract (Mohd. Ma'sum Billah)
Improving splice-junctions classification employing a novel encoding schema and decision-tree

Splice junctions are important regions in genes, which have been studied in many studies in Genetics. Recently some attempts in computer science have been made to use computer power in distinguishing the different splice junctions and non-junctions regions in genes. Ambiguity in the measurements of nucleotides is an important issue in dealing with these regions. In this paper a novel method is proposed along with an encoding schema which take ambiguities into account using probabilistic intuitions. The method is based on Decision Trees, using K-Nearest Negihbours and Support Vector Machines. The results have shown the significance of using the proposed encoding schema and classification method.