Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioinformatic analysis of gene expression profiling of intracranial aneurysm

Intracranial aneurysm (IA) is a severe clinical condition of primary concern and currently, there is no effective therapeutic reagent. The present study aimed to investigate the molecular mechanism of IA via bioinformatic analysis. Various gene expression profiles (GSE26969) were downloaded from the Gene Expression Omnibus database, including 3 IA and 3 normal superficial temporal artery samples. Firstly, the limma package in R language was used to identify differentially expressed genes (DEGs; P-value <0.01 and |log2 FC|≥1). Secondly, the database for annotation, visualization and integrated discovery software was utilized to perform pathway and functional enrichment analyses (false discovery rate ≤0.05). Finally, protein-protein interaction (PPI) network and sub-network clustering analyses were performed using the biomolecular interaction network database and ClusterONE software, respectively. Following this, a transcription factor regulatory network was identified from the PPI network. A total of 1,124 DEGs were identified, of which 989 were upregulated and 135 downregulated. Pathway and functional enrichment analyses revealed that the DEGs primarily participated in RNA splicing, functioning of the spliceosome, RNA processing and the mRNA metabolic process. Following PPI network analysis, 1 hepatocyte nuclear factor (HNF) 4A (transcription factor)-centered regulatory network and 5 DEG-centered sub-networks were identified. On analysis of the transcription factor regulatory network, 6 transcription factors (HNF6, HNF4A, E2F4, YY1, H4 and H31T) and a regulatory pathway (HNF6-HNF4-E2F4) were identified. The results of the present study suggest that activating transcription factor-5, Jun proto-oncogene, activator protein-1 transcription factor subunit, HNF6, HNF4 and E2F4 may participate in IA progression via vascular smooth muscle cell apoptosis, inflammation, vessel wall remodeling and damage and the tumor necrosis factor-β signaling pathway. However, further experimental studies are required to validate these predictions.
An efficient authentication and key establishment scheme for heterogeneous sensor networks

Wireless Sensor Networks (WSNs) consists of a large number of small and resource constrained devices. Due to their low cost, flexibility and self-organizing nature, these devices are used in various applications such as home and industrial automation, environmental and habitat monitoring and even in more security sensitive military applications in which security of the information in terms of both snooping and tampering is very important. Such applications introduce various security challenges to these resource constrained devices. To cope with these challenges, a proper authentication and key establishment is required. In this paper, we present an effective authentication and key establishment scheme for the heterogeneous sensor networks. The proposed solution is tested using the OMNET++ simulator and results show that it provides better network connectivity, consume less memory and has better network resilience against attacks.
Assessment of metal content and oxidative stress in autistic Egyptian patients

BackgroundMany factors have been implicated in the onset of autism, including excess or deficiency in toxic or essential metals and impaired antioxidant systems. Exposure to metals is a putative risk factor for autism. Many metals can be implicated in autism as they typically disrupt enzyme functions and cell signaling processes and generate reactive oxygen species (ROS). Patients and methodsThirty-two autistic patients ranging in age from 2.6 to 12.7 years (mean age 5.6 years) were examined clinically. Twenty healthy children matched for age and sex were included as a control group. Serum mercury, lead, and nitric oxide were estimated in all patients. ResultsEighteen patients presented with seizures and an epileptogenic focus in the electroencephalogram. The intelligent quotient assessment showed mental retardation in all patients: 18 had moderate retardation, two had severe retardation, and 12 had profound retardation. Assessment of the severity of autistic symptoms using the childhood autism rating scale indicated that six patients had mild, 12 had moderate, and 14 had severe autistic symptoms. The estimation of the level of mercury and lead in blood showed a significant increase compared with the control group (P=0.0001). Furthermore, nitric oxide was significantly increased compared with the control group (P=0.0001). These findings indicated a significant increase in both metal content and an imbalance in the oxidative status in the blood of autistic children. ConclusionOur findings suggest the hypothesis that exposure to metals and oxidative stress may be biomarkers of toxicity in autism. We recommend the consideration of supplementing autistic patients with antioxidants. We also recommend the study of introducing chelating agents for mercury and lead in patients with high toxic levels and their effect on clinical symptoms.
Genetic basis for body size variation between an anadromous and two derived lacustrine populations of threespine stickleback Gasterosteus aculeatus in southwest Alaska

Abstract Body size is a highly variable trait among geographically separated populations. Size-assortative reproductive isolation has been linked to recent adaptive radiations of threespine stickleback (Gasterosteus aculeatus) into freshwater, but the genetic basis of the commonly found size difference between anadromous and derived lacustrine sticklebacks has not been tested. We studied the genetic basis of size differences between recently diverging stickleback lineages in southwest Alaska using a common environment experiment. We crossed stickleback within one anadromous (Naknek River) and one lake (Pringle Lake) population and between the anadromous and two lake populations (Pringle and JoJo Lakes), and raised them in a salinity of 4–6 ppt. The F1 anadromous and freshwater forms differed significantly in size, whereas hybrids were intermediate or exhibited dominance toward the anadromous form. Additionally, the size of freshwater F1s differed from their wild counterparts, with within-population F1s from Pringle Lake growing larger than their wild counterparts, while there was no size difference between lab-raised and wild anadromous fish. Sexual dimorphism was always present in anadromous fish, but not in freshwater, and not always in the hybrid crosses. These results, along with parallel changes among anadromous and freshwater forms in other regions, suggest that this heritable trait is both plastic and may be under divergent and/or sexual selection.
Functional compartmentalization of Rad9 and Hus1 reveals diverse assembly of the 9‐1‐1 complex components during the DNA damage response in Leishmania

The Rad9‐Rad1‐Hus1 (9‐1‐1) complex is a key component in the coordination of DNA damage sensing, cell cycle progression and DNA repair pathways in eukaryotic cells. This PCNA‐related trimer is loaded onto RPA‐coated single stranded DNA and interacts with ATR kinase to mediate effective checkpoint signaling to halt the cell cycle and to promote DNA repair. Beyond these core activities, mounting evidence suggests that a broader range of functions can be provided by 9‐1‐1 structural diversification. The protozoan parasite Leishmania is an early‐branching eukaryote with a remarkably plastic genome, which hints at peculiar genome maintenance mechanisms. Here, we investigated the existence of homologs of the 9‐1‐1 complex subunits in L. major and found that LmRad9 and LmRad1 associate with chromatin in response to replication stress and form a complex in vivo with LmHus1. Similar to LmHus1, LmRad9 participates in telomere homeostasis and in the response to both replication stress and double strand breaks. However, LmRad9 and LmHus1‐deficient cells present markedly opposite phenotypes, which suggest their functional compartmentalization. We show that some of the cellular pool of LmRad9 forms an alternative complex and that some of LmHus1 exists as a monomer. We propose that the diverse assembly of the Leishmania 9‐1‐1 subunits mediates functional compartmentalization, which has a direct impact on the response to genotoxic stress.
Low rates of hybridization between European wildcats and domestic cats in a human‐dominated landscape

Abstract Hybridization between wild species and their domestic congeners is considered a major threat for wildlife conservation. Genetic integrity of the European wildcat, for instance, is a concern as they are outnumbered by domestic cats by several orders of magnitude throughout its range. We genotyped 1,071 individual wildcat samples obtained from hair traps and roadkills collected across the highly fragmented forests of western Central Europe, in Germany and Luxembourg, to assess domestic cat introgression in wildcats in human‐dominated landscapes. Analyses using a panel of 75 autosomal SNPs suggested a low hybridization rate, with 3.5% of wildcat individuals being categorized as F1, F2, or backcrosses to either parental taxon. We report that results based on a set of SNPs were more consistent than on a set of 14 microsatellite markers, showed higher accuracy to detect hybrids and their class in simulation analyses, and were less affected by underlying population structure. Our results strongly suggest that very high hybridization rates previously reported for Central Europe may be partly due to inadequate choice of markers and/or sampling design. Our study documents that an adequately selected SNP panel for hybrid detection may be used as an alternative to commonly applied microsatellite markers, including studies relying on noninvasively collected samples. In addition, our finding of overall low hybridization rates in Central European wildcats provides an example of successful wildlife coexistence in human‐dominated, fragmented landscapes.
Multiscale Dataspace for Organism-centric Analysis

Biologists increasingly need a unified view to understand and discover relationships among data elements scattered along data sources with different levels of heterogeneity. Existing approaches usually adopt ad-hoc heavyweight integration strategies, requiring a costly upfront effort involving a monolithic chain of steps to handle specific formats/schemas, with low or no reuse. This article proposes an original framework based on scales aligned with the dataspaces on demand integration principle. Scales systematize and encapsulate integration in discrete steps, fulfilling the dynamicity of the process through reuse of previous scales and localized customization. Although the proposed framework can be extended to several scenarios, this work focuses on the biology domain addressing the organism-centric analysis scenario.
Tax Regimes and Capital Gains Realizations

Abstract This paper contrasts the individual capital gains realization behavior between progressive and proportional tax regimes. Using a longitudinal panel of over 288,000 individuals in Sweden, I exploit the 1991 tax reform in Sweden that changed progressive capital gains tax rates ranging from 12% to 80% to a proportional tax rate of 30%. Using the proportional tax system to control for non-tax reasons to realize capital gains, I show that individuals are highly responsive to capital gains tax incentives created by temporary income changes under a progressive capital gains tax. More specifically, I find that individuals with temporary negative (positive) income changes sell (hold) shares that they would hold (sell) in the absence of temporary tax incentives. Further, I show that high-income individuals are more tax sensitive than low-income individuals. This result indicates that low-income individuals facing temporary negative income changes could trade predominantly for non-tax reasons.
On automatic generation of IEC61850/IEC61499 substation automation systems enabled by ontology

This paper presents an introductory step in the automatic generation of distributed control software for power distribution automation systems based on Ontology Driven Engineering enabled by industrial standards IEC61850 and IEC61499. The novelty of this approach is the ability of automatically generating the logical connections between the logical nodes. The paper covers the several stages of the transformation process, such as developing the IEC61850 ontology and the ontology transformation rules. The developed IEC61850 ontology includes the logical nodes descriptions and additional contextual relations between the logical nodes which is lacking in the IEC61850 SCL configuration language. Then, the IEC61850 ontology is transformed to an existing IEC61499 ontology, adding classes of IEC61850 logical nodes as IEC61499 function blocks in the IEC61499 ontology. The means of the transformation of the ontologies is based on the eSWRL sematic web rules language, an extension to the rule language SWRL. The end result is the development of an IEC61850 ontology and a set of eSWRL rules which facilitates the ontology transformation.
Feline sporotrichosis: associations between clinical-epidemiological profiles and phenotypic-genotypic characteristics of the etiological agents in the Rio de Janeiro epizootic area

BACKGROUND Sporotrichosis is caused by species of the genus Sporothrix. From 1998 to 2015, 4,703 cats were diagnosed at the Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil. Even after the description of the Sporothrix species, the characterisation of feline isolates is not performed routinely. OBJECTIVES To characterise the clinical isolates from cats at the species level and correlate them with the clinical and epidemiological characteristics of the cats. METHODS Forty seven Sporothrix spp. isolates from cats assisted at Fiocruz from 2010 to 2011 were included. Medical records were consulted to obtain the clinical and epidemiological data. The isolates were identified through their morphological and physiological characteristics. T3B polymerase chain reaction (PCR) fingerprinting was used for molecular identification of the species. FINDINGS In phenotypic tests, 34 isolates were characterised as S. brasiliensis, one as S. schenckii and 12 as Sporothrix spp. PCR identified all isolates as S. brasiliensis. MAIN CONCLUSIONS S. brasiliensis is the only etiological agent of feline sporotrichosis in Rio de Janeiro to date. None association was found between the isolates and the clinical and epidemiological data. In addition, we strongly recommend the use of molecular techniques for the identification of isolates of Sporothrix spp.
Interpersonal Pathoplasticity and Trajectories of Change in Routine Adolescent and Young Adult Residential Substance Abuse Treatment

Background: Partnerships between mental health care stakeholders provide a context for generalizable clinical research with implications for quality improvement. In the context of a partnership between an adolescent residential substance abuse disorder (SUD) treatment center and clinical researchers, stakeholders identified knowledge gaps (internal and the field broadly) with regard to patient interpersonal factors that influence working alliance and acute SUD residential treatment outcome trajectories. Objective: To (a) examine interpersonal pathoplasticity and identify interpersonal subtypes in a naturalistic sample of adolescent and young-adult patients presenting for routine residential SUD treatment and (b) investigate the association between identified interpersonal subtypes and working alliance and acute treatment outcome trajectories. Method: N = 100 patients (Mage = 17.39 years, 68% male, 84% White) completed self-reports of symptom and functioning outcomes, interpersonal problems, and the working alliance on multiple occasions between admission and discharge. Multiple methods were used to identify interpersonal subtypes and test pathoplasticity. Interpersonal subtype was entered as a predictor in respective multilevel models of working alliance and symptom outcome. Results: Interpersonal subtypes of vindictive and exploitable patients demonstrated pathoplasticity. Subtype did not predict working alliance trajectories; however, a significant interaction between interpersonal subtype and a quadratic effect for time demonstrated that exploitable patients with longer than average treatment lengths experienced attenuated symptom change over the course of treatment whereas vindictive patients appeared to demonstrate steady progress. Conclusions: Interpersonal assessments should be integrated into residential SUD treatment to identify patients with an exploitable interpersonal style who might require additional attention or alternative interventions.
A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval

Publications in the life sciences are characterized by a large technical vocabulary, with many lexical and semantic variations for expressing the same concept. Towards addressing the problem of relevance in biomedical literature search, we introduce a deep learning model for the relevance of a document's text to a keyword style query. Limited by a relatively small amount of training data, the model uses pre-trained word embeddings. With these, the model first computes a variable-length Delta matrix between the query and document, representing a difference between the two texts, which is then passed through a deep convolution stage followed by a deep feed-forward network to compute a relevance score. This results in a fast model suitable for use in an online search engine. The model is robust and outperforms comparable state-of-the-art deep learning approaches.
Towards Hypothetical Reasoning Using Distributed Provenance

Hypothetical reasoning is the iterative examination of the effect of modifications to the data on the result of some computation or data analysis query. This kind of reasoning is commonly performed by data scientists to gain insights. Previous work has indicated that fine-grained data provenance can be instrumental for the efficient performance of hypothetical reasoning: instead of a costly re-execution of the underlying application, one may assign values to a pre-computed provenance expression. However, current techniques for fine-grained provenance tracking are ill-suited for large-scale data due to the overhead they entail on both execution time and memory consumption. We outline an approach for hypothetical reasoning for largescale data. Our key insights are: (i) tracking only relevant parts of the provenance based on an a priori specification of classes of hypothetical scenarios that are of interest and (ii) the distributed tracking of provenance tailored to fit distributed data processing frameworks such as Apache Spark.We also discuss the challenges in both respects and our initial directions for addressing them.
A Study of Dynamic Phase Adaptation Using a Dynamic Multicore Processor

Heterogeneous processors such as ARM’s big.LITTLE have become popular for embedded systems. They offer a choice between running workloads on a high performance core or a low-energy core leading to increased energy efficiency. However, the core configurations are fixed at design time which offers a limited amount of adaptation. Dynamic Multicore Processors (DMPs) bridge the gap between homogeneous and fully reconfigurable systems. Cores can fuse dynamically to adapt the computational resources to the needs of different workloads. There exists multiple examples of DMPs in the literature, yet the focus has mainly been on static partitioning. This paper conducts the first thorough study of the potential for dynamic reconfiguration of DMPs at runtime. We study how performance varies with static partitioning and what software optimizations are required to achieve high performance. We show that energy consumption is reduced considerably when adapting the number of cores to program phases, and introduce a simple online model which predicts the optimal number of cores to use to minimize energy consumption while maintaining high performance. Using the San Diego Vision Benchmark Suite as a use case, the dynamic scheme leads to ∼40% energy savings on average without decreasing performance.
Transfer and Multi-task Learning in QSAR Modeling: Advances and Challenges

Medicinal chemistry projects involve some steps aiming to develop a new drug, such as the analysis of biological targets related to a given disease, the discovery and the development of drug candidates for these targets, performing parallel biological tests to validate the drug effectiveness and side effects. Approaches as quantitative study of activity-structure relationships (QSAR) involve the construction of predictive models that relate a set of descriptors of a chemical compound series and its biological activities with respect to one or more targets in the human body. Datasets used to perform QSAR analyses are generally characterized by a small number of samples and this makes them more complex to build accurate predictive models. In this context, transfer and multi-task learning techniques are very suitable since they take information from other QSAR models to the same biological target, reducing efforts and costs for generating new chemical compounds. Therefore, this review will present the main features of transfer and multi-task learning studies, as well as some applications and its potentiality in drug design projects.
Review on comparative efficacy of bevacizumab, panitumumab and cetuximab antibody therapy with combination of FOLFOX-4 in KRAS-mutated colorectal cancer patients

Colorectal cancer, fourth leading form of cancer worldwide and is increasing in alarming rate in the developing countries. Treating colorectal cancer has become a big challenge worldwide and several antibody therapies such as bevacizumab, panitumumab and cetuximab are being used with limited success. Moreover, mutation in KRAS gene which is linked with the colorectal cancer initiation and progression further interferes with the antibody therapies. Considering median progression free survival and overall survival in account, this review focuses to identify the most efficient antibody therapy in combination with chemotherapy (FOLFOX-4) in KRAS mutated colorectal cancer patients. The bevacizumab plus FOLFOX-4 therapy shows about 9.3 months and 8.7 months of progression free survival for KRAS wild and mutant type, respectively. The overall survival is about 34.8 months for wild type whereas for the mutant it is inconclusive for the same therapy. In comparison, panitumumab results in better progression-free survival which is about (9.6 months) and overall survival is about (23.9 months) for the wild type KRAS and the overall survival is about 15.5 months for the mutant KRAS. Cetuximab plus FOLFOX-4 therapy shows about 7.7 months and 5.5 months of progression-free survival for wild type KRAS and mutant type, respectively. Thus, panitumumab shows significant improvement in overall survival rate for wild type KRAS, validating as a cost effective therapeutic for colorectal cancer therapy. This review depicts that panitumumab along with FOLFOX-4 has a higher response in colorectal cancer patients than the either of the two monoclonal antibodies plus FOLFOX-4.