Miracle-dz/UniFAR-FTUs huggingface dataset:
Searching the NCBI Databases Using Entrez

One of the most widely‐used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre‐existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two Basic Protocols describe simple, text‐based searches, illustrating the types of information that can be retrieved through the Entrez system. An Alternate Protocol builds upon the first Basic Protocol, using additional, built‐in features of the Entrez system, and providing alternative ways to issue the initial query. The Support Protocol reviews how to save frequently‐issued queries. Finally, Cn3D, a structure visualization tool, is also discussed.
Adaptive Spatial and Temporal Selective Attenuator in the Presence of Mutual Coupling and Channel Errors

Mr. Ilir F. Progri received his Diploma of Engineer Degree in Electrical Engineering from Polytechnic University of Tirana, Albania in 1994. He received his MS degree in Electrical Engineering from Electrical and Computer Engineering Department, Worcester Polytechnic Institute (WPI) in 1997. He is currently a graduate student of the Electrical and Computer Engineering Department, WPI, perusing his Ph.D. degree in Electrical Engineering with strong emphasis in carrier phase and signal processing, integrity monitoring, precision approach and landing, filter design and implementation, numerical methods and numerical linear algebra, software development and management.
Adaptive Sparse Subpixel Mapping With a Total Variation Model for Remote Sensing Imagery

Subpixel mapping, which is a promising technique based on the assumption of spatial dependence, enhances the spatial resolution of images by dividing a mixed pixel into several subpixels and assigning each subpixel to a single land-cover class. The traditional subpixel mapping methods usually utilize the fractional abundance images obtained by a spectral unmixing technique as input and consider the spatial correlation information among pixels and subpixels. However, most of these algorithms treat subpixels separately and locally while ignoring the rationality of global patterns. In this paper, a novel subpixel mapping model based on sparse representation theory, namely, adaptive sparse subpixel mapping with a total variation model (ASSM-TV), is proposed to explore the possible spatial distribution patterns of subpixels by considering these subpixels as an integral patch. In this way, the proposed method can obtain the optimal subpixel mapping result by determining the most appropriate subpixel spatial pattern. However, the number of possible spatial configurations of subpixels can increase sharply with large-scale factors, and therefore, in ASSM-TV, the subpixel mapping is considered as a sparse representation problem. A preconstructed discrete cosine transform dictionary, which consists of piecewise smooth subpixel patches and textured patches, is utilized to express the original subpixel mapping observation in a sparse representation pattern. The total variation prior model is designed as a spatial regularization constraint to characterize the relationship between a subpixel and its neighboring subpixels. In addition, a joint maximum a posteriori model is proposed to adaptively select the regularization parameters. Compared with the other traditional and state-of-the-art subpixel mapping approaches, the experimental results using a simulated image, three synthetic hyperspectral remote sensing images, and two real remote sensing images demonstrate that the proposed algorithm can obtain better results, in both visual and quantitative evaluations.
A new type of preference relations: Fuzzy preference relations with self-confidence

Preference relations are very useful to express decision makers' preferences over alternatives in the process of decision-making. However, multiple self-confidence levels are not considered in existing preference relations. In this study, we propose a new type of preference relations: fuzzy preference relations with self-confidence. A linear programming model is proposed for estimating priority vectors of this new type of preference relations. Finally, two numerical examples are provided to demonstrate the linear programming model, and a comparative analysis is used to show the influence of self-confidence levels on the decision-making results.
ENALAPRIL IMPROVES GLUCOSE TOLERANCE IN TWO RAT MODELS: A NEW HYPERTENSIVE DIABETIC STRAIN AND A FRUCTOSE‐INDUCED HYPERINSULINAEMIC RAT

1. The present study was undertaken to examine the effect of the angiotensin converting enzyme (ACE) inhibitor, enalapril, on blood pressure and spontaneous blood glucose levels in two rat models: our new diabetic hypertensive rat in which genetic hypertension and diabetes develop following cross‐breeding of Cohen diabetic rat (CDR) and spontaneous hypertensive rats (SHR); and a rat in which hypertension, hyperinsulinaemia and hyperlipidaemia were induced by fructose diet.
[Transcriptional regulation of exosporium basal layer structural gene exsB in Bacillus thuringiensis by SigmaK and GerE].

OBJECTIVE To identify the transcriptional regulation of exosporium basal layer structural gene exsB in Bacillus thuringiensis. METHODS We analyzed exsB and its promoter sequence in Bacillus cereus group by sequence alignment. We performed beta-galactosidase assay of exsB-lacZ gene fusion to analyze transcriptional activation of exsB promoter; we used Electrophoretic mobility shift assays to detect binding of GerE and exsB promoter. RESULTS exsB was the high similarity in Bacillus cereus group strains. Beta-galactosidase assay showed that exsB promoter had the strong transcriptional activation on the late sporulation phase. Deletion of gerE or sigK gene decreased the activation of exsB promoter. Electrophoretic mobility shift assays showed that GerE could bind with exsB promoter. CONCLUSION The exsB gene is regulated by SigmaK and GerE on the late sporulation phase.
Analysis of survey data

This book is concerned with statistical methods for the analysis of data collected from a survey. A survey could consist of data collected from a questionnaire or from measurements, such as those taken as part of a quality control process. Concerned with the statistical methods for the analysis of sample survey data, this book will update and extend the successful book edited by Skinner, Holt and Smith on 'Analysis of Complex Surveys'. The focus will be on methodological issues, which arise when applying statistical methods to sample survey data and will discuss in detail the impact of complex sampling schemes. Further issues, such as how to deal with missing data and measurement of error will also be critically discussed. There have significant improvements in statistical software which implement complex sampling schemes (eg SUDAAN, STATA, WESVAR, PC CARP ) in the last decade and there is greater need for practical advice for those analysing survey data. To ensure a broad audience, the statistical theory will be made accessible through the use of practical examples. This book will be accessible to a broad audience of statisticians but will primarily be of interest to practitioners analysing survey data. Increased awareness by social scientists of the variety of powerful statistical methods will make this book a useful reference.
A Gain-Scheduling Driver Assistance Trajectory-Following Algorithm Considering Different Driver Steering Characteristics

In this paper, a gain-scheduling, robust, and shared controller is proposed to assist drivers in tracking vehicle reference trajectory. In the controller, the driver steering parameters such as delay time, preview time, and steering gain are assumed to be varying with respect to the different characteristics of drivers, vehicle states, and driving scenarios. Meanwhile, the modeling errors and uncertainties in the tire cornering stiffness are also considered in the driver–vehicle system model and the controller design. A global objective function, considering the tracking error, the driver's physical and mental workloads, and the control effort, is designed to optimize the overall performance of the driver–vehicle system. Constraint on eigenvalue placement is added to the controller design to improve the performance of the closed-loop driver–vehicle system. Simulation results under different maneuvers show that the controller can significantly improve the system performance and reduce the driver's workloads. The controller can reduce the delay time of the driver–vehicle system in emergency maneuvers, particularly for inexperienced drivers.
The Crystal Structure of the Plant Small GTPase OsRac1 Reveals Its Mode of Binding to NADPH Oxidase*

Background: The plant small GTPase OsRac1 plays an important role in rice innate immunity. Results: The crystal structure and NADPH oxidase-binding mode of active-form OsRac1 were determined. Conclusion: The structure explains the mechanism by which OsRac1 regulates reactive oxygen species production and activates the immune response. Significance: A new insight into the activation of plant immunity by small GTPase is revealed. Rac/Rop proteins are Rho-type small GTPases that act as molecular switches in plants. Recent studies have identified these proteins as key components in many major plant signaling pathways, such as innate immunity, pollen tube growth, and root hair formation. In rice, the Rac/Rop protein OsRac1 plays an important role in regulating the production of reactive oxygen species (ROS) by the NADPH oxidase OsRbohB during innate immunity. However, the molecular mechanism by which OsRac1 regulates OsRbohB remains unknown. Here, we report the crystal structure of OsRac1 complexed with the non-hydrolyzable GTP analog guanosine 5′-(β,γ-imido)triphosphate at 1.9 Å resolution; this represents the first active-form structure of a plant small GTPase. To elucidate the ROS production in rice cells, structural information was used to design OsRac1 mutants that displayed reduced binding to OsRbohB. Only mutations in the OsRac1 Switch I region showed attenuated interactions with OsRbohB in vitro. In particular, Tyr39 and Asp45 substitutions suppressed ROS production in rice cells, indicating that these residues are critical for interaction with and activation of OsRbohB. Structural comparison of active-form OsRac1 with AtRop9 in its GDP-bound inactive form showed a large conformational difference in the vicinity of these residues. Our results provide new insights into the molecular mechanism of the immune response through OsRac1 and the various cellular responses associated with plant Rac/Rop proteins.
JPEG quantization table mismatched steganalysis via robust discriminative feature transformation

The cover source mismatch is a common problem in steganalysis, which may result in the degradation of detection accuracy. In this paper, we present a novel method to mitigate the problem of JPEG quantization table mismatch, named as Robust Discriminative Feature Transformation (RDFT). RDFT transforms original features to new feature representations based on a non-linear transformation matrix. It can improve the statistical consistency of the training samples and testing samples and learn new matched feature representations from original features by minimizing feature distribution difference while preserving the classification ability of training data. The comparison to prior arts reveals that the detection accuracy of the proposed RDFT algorithm can significantly outperform traditional steganalyzers under mismatched conditions and it is close to that of matched scenario. RDFT has several appealing advantages: 1) it can improve the statistical consistency of the training and testing data; 2) it can reduce the distribution difference between the training features and testing features; 3) it can preserve the classification ability of the training data; 4) it is robust to parameters and can achieve a good performance under a wide range of parameter values.
Octanoate stimulates cytosolic triacylglycerol accumulation and CD36 mRNA expression but inhibits Acetyl coenzyme A carboxylase activity in primary cultured bovine mammary epithelial cells

Mammary epithelial cells, which express and secrete leptin into milk, accumulate triacylglycerol (TAG). We examined effects on the accumulation of cytosolic TAG of addition of short- (acetate and butyrate) or medium- (octanoate) chain fatty acids to the medium bathing bovine mammary epithelial cells (bMEC). Octanoate stimulated the accumulation of TAG in a concentration-dependent manner from 1 to 10 mM and increased lipid droplet formation and mRNA expression of CD36 (a fatty acid translocase). Additionally, expression of a peroxisome proliferator activated receptor (PPAR) γ 2 protein that is a lipid-activated transcription factor, was increased by the addition of acetate or octanoate. However, leptin mRNA expression was significantly reduced by addition of acetate or butyrate. Both short- and medium-chain fatty acids inhibited acetyl coenzyme A carboxylase (ACC) activities, which is pivotal in lipid synthesis, but elevated expression of uncoupling protein 2 (UCP2) mRNA, which is important in energy expenditure. These results suggest that octanoate induces cytosolic TAG accumulation and the formation of lipid droplets, and that acetate and butyrate inhibit leptin expression and lipid synthesis in bMEC.
Brominated Compounds from Marine Sponges of the Genus Aplysina and a Compilation of Their 13C NMR Spectral Data

Aplysina is the best representative genus of the family Aplysinidae. Halogenated substances are its main class of metabolites. These substances contribute greatly to the chemotaxonomy and characterization of the sponges belonging to this genus. Due to their pharmacological activities, these alkaloids are of special interest. The chemistry of halogenated substances and of the alkaloids has long been extensively studied in terrestrial organisms, while the number of marine organisms studied has just started to increase in the last decades. This review describes 101 halogenated substances from 14 species of Aplysina from different parts of the world. These substances can be divided into the following classes: bromotyramines (A), cavernicolins (B), hydroverongiaquinols (C), bromotyrosineketals (D), bromotyrosine lactone derivatives (E), oxazolidones (F), spiroisoxazolines (G), verongiabenzenoids (H), verongiaquinols (I), and dibromocyclohexadienes (J). A compilation of their 13C NMR data is also part of the review. For this purpose 138 references were consulted.
Enalapril: antiproteinuric effect in children with nephrotic syndrome.

AIM The present study was designed to establish the antiproteinuric effect of ACE-I (enalapril). PATIENTS AND METHODS Six children with steroid-resistant nephrotic syndrome (SRNS) and one patient affected by Alport syndrome and nephrotic-range proteinuria received enalapril (mean dose 0.3 mg/kg/day) during a mean period of 2 years. Before initiation of therapy, blood pressure was normal in all but one patient, the latter showed normal values with enalapril treatment. RESULTS Five patients showed a significant increase of albumin levels after the treatment. Creatinine clearance remained stable during the study in all but one patient affected by Alport syndrome. CONCLUSION In five patients (71.4%) enalapril therapy resulted in an important reduction ofproteinuria, in one patient the treatment was stopped after one year for relapse. In patient with Alport syndrome the fall in creatinine clearance, may simply reflect the natural course of the disease.
[Increase of immunogenicity of cold-adapted influenza vaccine by using adjuvant].

AIM To assess increase of protective efficacy of live cold-adapted (ca) influenza vaccine after addition of adjuvant chitozan. MATERIALS AND METHODS Used viruses: ca donor of attenuation A/Krasnodar/101/35/59 (H2N2) and epidemic strain A/Krasnodar/101/59 (H2N2); as an adjuvant--derivative of chitozan and microparticles of chitozan. Experiments were performed in outbred mice. Protective effect of immunization was measured by intranasal challenge by virulent strain of virus. Immune response was assessed by ELISA and indirect hemagglutination inhibition assay. RESULTS During intranasal immunization of mice with intact CA donor of attenuation A/Krasnodar/101/35/59 (H2N2) addition of 1% solution of chitozan glutamate to vaccine material resulted in increased serum IgG in immunized mice and protective effect of immunization. Addition of adjuvant to ca donor strain did not influence on its ts-characteristic. It was shown that inactivated with ultraviolet radiation ca donor strain in combination with chitozan did not protect against infection caused by virulent strain A/Krasnodar/101/59, whereas the same doses of intact ca donor strain with chitozan were protective. Chitozan did not enhance replication of donor strain in upper respiratory tract of mice. CONCLUSION Obtained data demonstrate that chitozan as a mucous-adhesive adjuvant could increase efficacy of live ca influenza vaccine.
Thrombin generation: a comparison of assays using platelet‐poor and ‐rich plasma and whole blood samples from healthy controls and patients with a history of venous thromboembolism

We have developed a whole blood thrombin generation (TG) assay whereby TG is initiated with a low‐tissue factor concentration and monitored using a fluorogenic thrombin substrate. Significantly higher values were found in blood samples from 50 patients with a history of venous thromboembolism (VTE) compared with 31 healthy controls (HC), for peak height (P = 0·0034) and endogenous thrombin potential (ETP) (P = 0·0027). Results from 31 VTE patients and the 31 controls in the absence of corn trypsin inhibitor (CTI) showed significantly higher values in the VTE group for peak height (P = 0·0013) and ETP (P = 0·002). In the presence of CTI, significantly higher values were only seen in ETP (P = 0·024). No significant increases in TG were found using platelet poor (PPP) or ‐rich (PRP) plasma with or without CTI. The whole blood TG assay in the absence or presence of CTI showed a higher proportion (25/50 and 12/31, respectively) of raised peak height and/or ETP values than plasma assays (PPP 9/50 and 5/31 respectively and PRP 13/50 and 6/31, respectively). Our results show the whole blood TG assay is more sensitive for determining the increases in TG in patients with a history of VTE than PPP and PRP TG assays.
Reconsideration of the human toxicological reference values ( ARfD , ADI ) for chlorpyrifos

The insecticide chlorpyrifos has been tested in numerous toxicological studies in the past. On the basis of these studies, the EU-evaluation of the active ingredient was finalized in 2005. Since then, new studies and data on the toxicity of chlorpyrifos have been published. The US American Environmental Protection Agency EPA has evaluated these studies and derived new toxicological reference values. The BfR has come to the conclusion that within the EU too, a reassessment of the human health risks associated with chlorpyrifos should be conducted.
Psychobiological Stress and Preterm Birth

Despite current research progress, preterm birth (delivery before 37 weeks gestation) remains a significant problem in maternal-child health because of its high prevalence rate and association with severe adverse health consequences (March of Dimes, 2009; Goldenberg et al., 2000; Sibai et al., 2005; Ventura et al., 2000). Globally, an estimated 13 million babies are born preterm each year representing a 9.6% prevalence of preterm birth (March of Dimes, 2009). The incidence and consequences of preterm birth (PTB) are particularly high and harsh in Africa and Asia where over 11 million (85%) of all preterm births occur. Preterm birth is the leading cause of infant morbidity and mortality. About one million deaths in the first month of life (or 28 percent of total newborn deaths) are attributable to preterm birth. In the United States (US) preterm birth occurs in 10-15% of all pregnancies and the rate has increased by 35% in the past 25 years (March of Dimes, 2009; Institute of Medicine, 2006). There is a significantly higher rate of preterm birth among African-American women (17.8%) compared to Caucasian women (8.8%) (Institute of Medicine, 2006). In the US, preterm births are associated with 75% of perinatal mortality (Adams & Barfield, 2008; Nathanielsz, 1995; Novy et al., 1995). Long term follow-up indicates that between one-third to one-fifth of preterm children have moderate to severe sensory handicaps by age two (including cerebral palsy, mental retardation, epilepsy, blindness or deafness) (Escobar et al., 1991; Kramer, 2009; Kuban & Leviton, 1994). Because of this the economic consequences of PTB are of similar magnitude as smoking, alcohol abuse and AIDS (Novy et al., 1995). An Institute of Medicine (2006) report estimated the cost of PTB to be $26.2 billion in 2005 with daily NICU costs exceeding $3,500 per infant, and it is not unusual for costs to top $1 million for a prolonged stay (Catlin, 2006). Despite the magnitude of this problem, the etiology of preterm birth remains poorly understood. The precise mechanisms by which human parturition is initiated spontaneously, either at term or preterm, are not well understood (Kramer et al., 2009). It is established that microbial colonization and inflammation in the maternal genital tract is one cause of preterm birth (Gibbs et al., 1992) and account for the majority of preterm births between 21 and 24 weeks. As gestation progresses to 33 weeks, however, the incidence of preterm birth due to infection drops below 10%. Thus, in the large majority of preterm births there is no known etiological agent. While the exact causes of preterm labor are not known, they may include behavioral, environmental, biological and psychosocial factors, medical conditions and genetics. As described above, there are striking racial-ethnic and socioeconomic
A Model of Knowledge Based Information Retrieval with Hierarchical Concept Graph

This paper discusses a knowledge based information retrieval model with hierarchical thesaurus. The model computes the conceptual distance between a query and an object and both are indexed with weighted terms from a hierarchical thesaurus. The hierarchical thesaurus is represented by a hierarchical‐concept graph (HCG) in which nodes represent concepts and directed edges represent generalisation relationships. Rada et al. have developed a similar model. However, their model considered only a binary indexing scheme and revealed some counter‐intuitive results. Our proposed model extends theirs by allowing the index term and the edge of the HCG to be weighted. A new concept mapping method is devised to overcome Rada's counter‐intuitive results. In addition, a scheme for allowing Boolean operators in user queries is provided with a formula for computing conceptual distance from negated index terms. Experimental results have shown that our model simulates human performance more closely than Rada's model.