Miracle-dz/UniFAR-FTUs huggingface dataset:
Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil.

Three novel bacterial strains, designated Vu-144(T), Vu-7 and Vu-35, were isolated on minimal medium from rhizosphere soil of field-grown cowpea and subjected to a taxonomic study using a polyphasic approach. Cells of the strains were Gram-stain-negative, non-motile, non-spore-forming, coccoid rods, and formed non-pigmented colonies. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Vu-144(T) was affiliated with an uncultivated lineage of the phylum Bacteroidetes. Its closest phylogenetic neighbour was the recently described species Niastella populi, a member of the family Chitinophagaceae, with just 90.7 % sequence similarity to the type strain. The only isoprenoid quinone detected was menaquinone 7 (MK-7). The fatty acid profiles showed large amounts of iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G and minor amounts of summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and other fatty acids, allowing the differentiation of the strains from other genera. The G+C content of the genomic DNA of the three strains ranged from 43.1 to 44.3 mol%. In addition to phosphatidylethanolamine, the major polar lipids were three unidentified aminophospholipids (APL1-APL3), two unidentified phospholipids (PL1, PL2) and three unidentified lipids (UL1-UL3). Biochemical test patterns also differed from those of Niastella populi and members of other genera. All three isolates showed plant-growth-promoting properties, e.g. the ability to produce indole-3-acetic acid and NH3 and to solubilize phosphate, utilized 1-aminocyclopropane 1-carboxylate (ACC) as a sole source of nitrogen and possessed the ACC deaminase enzyme. The novel isolates readily colonized roots and stimulated growth of tomato and cowpea under glasshouse conditions. Inoculated plants showed a 45-60 % increase in dry matter weight with respect to uninoculated controls. On the basis of the evidence from our polyphasic study, isolate Vu-144(T) represents a novel genus and species in the family Chitinophagaceae, for which the name Arachidicoccus rhizosphaerae gen. nov., sp. nov. is proposed. The type strain of Arachidicoccus rhizosphaerae is Vu-144(T) ( = KCTC 22378(T) = NCIMB 14473(T)).
High frequency functional brain networks in neonates revealed by rapid acquisition resting state fMRI

Understanding how spatially remote brain regions interact to form functional brain networks, and how these develop during the neonatal period, provides fundamental insights into normal brain development, and how mechanisms of brain disorder and recovery may function in the immature brain. A key imaging tool in characterising functional brain networks is examination of T2*‐weighted fMRI signal during rest (resting state fMRI, rs‐fMRI). The majority of rs‐fMRI studies have concentrated on slow signal fluctuations occurring at <0.1 Hz, even though neuronal rhythms, and haemodynamic responses to these fluctuate more rapidly, and there is emerging evidence for crucial information about functional brain connectivity occurring more rapidly than these limits. The characterisation of higher frequency components has been limited by the sampling frequency achievable with standard T2* echoplanar imaging (EPI) sequences. We describe patterns of neonatal functional brain network connectivity derived using accelerated T2*‐weighted EPI MRI. We acquired whole brain rs‐fMRI data, at subsecond sampling frequency, from preterm infants at term equivalent age and compared this to rs‐fMRI data acquired with standard EPI acquisition protocol. We provide the first evidence that rapid rs‐fMRI acquisition in neonates, and adoption of an extended frequency range for analysis, allows identification of a substantial proportion of signal power residing above 0.2 Hz. We thereby describe changes in brain connectivity associated with increasing maturity which are not evident using standard rs‐fMRI protocols. Development of optimised neonatal fMRI protocols, including use of high speed acquisition sequences, is crucial for understanding the physiology and pathophysiology of the developing brain. Hum Brain Mapp 36:2483–2494, 2015. © 2015 Wiley Periodicals, Inc.
Susceptibility of the MMPI-2 Clinical, Restructured Clinical (RC), and Content Scales to Overreporting and Underreporting

The authors examined and compared the susceptibility of three Minnesota Multiphasic Personality Inventory-2 (MMPI-2) scale sets (Clinical, Restructured Clinical [RC], and Content) to over- and underreporting using five analog samples. Two samples of 85 and 191 undergraduate students, respectively, took the MMPI-2 under underreporting versus standard instructions. Three samples consisting of 42 undergraduates, 73 psychiatric inpatients, and 84 medical patients took the MMPI-2 under overreporting versus standard instructions. A comparison of the effect sizes across the three sets of scales indicated that Clinical Scale scores are not less susceptible to distortion than the Content or RC Scales. An apparent lesser susceptibility to underreporting for the Clinical Scales was an artifact of the subtle items’ effect on these scales.
ICASE ON THE REMOVAL OF BOUNDARY ERRORS CAUSED BY RUNGE-KUTTA INTEGRATION OF NON-LINEAR PARTIAL DIFFERENTIAL EQUATIONS

It has been previously shown that the temporal integration of hyperbolic partial differential equations may , because of boundary conditions, lead to deterioration of accuracy of the solution. A procedure for removal of this error in the linear case has been established previously. In the present paper we consider hyperbolic p.d. e's (linear and non-linear) whose boundary treatment is done via the SAT-procedure. A methodology is present for recovery of the full order of accuracy, and has been applied to the case of a 4th order explicit finite difference scheme. This research was supported by the National Aeronautics and Space Administration under NASA Contract No. NAS1-19480 while the authors were in residence at the Institute for Computer Applications in Science and Engineering (ICASE), NASA Langley Research Center, Hampton, VA 23681. The second author was supported also by AFOSR 93-0090 ARPA grant N00014-91-J-4016 and NSF grant DMS 9211820
Increased Sporulation Rate of Epidemic Clostridium difficile Type 027/NAP1

ABSTRACT Clostridium difficile PCR ribotype 027 comprised 0.2% of a collection of Swedish isolates in 1997-2001 (3 of 1,325 isolates). These isolates had lower moxifloxacin MICs than the epidemic type 027 isolates, but they had the same tcdC sequence and toxin yield. Type 027 produced 3- to 13-fold more toxin than did major Swedish types. One epidemic strain (027/NAP1a) sporulated more than did other type 027 isolates, a feature that should contribute to its survival and spread.
Thermal conductivity measurements of nitrogen-doped Ge2Sb2Te5

The thermal conductivity of nitrogen-doped Ge2Sb2Te5 (N-GST) was analyzed using Frequency Domain Thermoreflectance (FDTR). The thermal conductivity of amorphous N-GST (∼0.15 W/m-K) was not found to change significantly as the nitrogen concentration was raised from 0 at% to ∼6 at%, possibly due to the huge amount of phonon scattering in the disordered films. The thermal conductivity of crystalline N-GST films was found to increase initially with increasing N content, but then to decrease upon further N addition. X-ray diffraction spectra of N-GST films show increasing defect density that correlates with the decrease in thermal conductivity of the crystalline films at higher nitrogen content.
Method Development for Efficient Incorporation of Unnatural Amino Acids

Method Development for Efficient Incorporation of Unnatural Amino Acids Paul David Harris The synthesis of proteins bearing unnatural amino acids has the potential to enhance and elucidate many processes in biochemistry and molecular biology. There are two primary methods for site specific unnatural amino acid incorporation, both of which use the cell’s native protein translating machinery: in vitro chemical acylation of suppressor tRNAs and the use of orthogonal amino acyl tRNA synthetases. Total chemical synthesis is theoretically possible, but current methods severely limit the maximum size of the product protein. In vivo orthogonal synthetase methods suffer from the high cost of the unnatural amino acid. In this thesis I sought to address this limitation by increasing cell density, first in shake flasks and then in a bioreactor in order to increase the yield of protein per amount of unnatural amino acid used. In a parallel project, I used the in vitro chemical acylation system to incorporate several unnatural amino acids, key among them the fluorophore BODIPYFL, with the aim of producing site specifically fluorescently labeled protein for single molecule FRET studies. I demonstrated successful incorporation of these amino acids into the trial protein GFP, although incorporation was not demonstrated in the final target, FEN1. This also served to confirm the effectiveness of a new procedure developed for chemical acylation.
The recognition of laser anti-counterfeiting code with complex background

Anti-counterfeiting code of cigarettes can prevent the fake, shoddy and the sales in wrong area. And it provides a lot of important information such as delivery date, sales area, and nature of customer. A recognition method for anti-counterfeiting code with complex background using Log-Gabor filters and Support Vector Machine (SVM) classifiers is proposed in this paper. Log-Gabor transform is used to extract the character image's local texture features without the illumination impact, and SVM classifiers are superior to other methods to solving small example size recognition problems. The experimental results show that the proposed method performs effectively for recognition of laser anti-counterfeiting code images with noises, non-uniform illumination, backgrounds or stroke distortions in low quality grayscale at the rate of 97%.
Protective effect of montelukast on paraquat-induced lung toxicity in rats.

In the current study, the possible protective effect of montelukast (Mont, 50 mg/kg, p.o given 2, 24, and 48 h after paraquat injection) against acute paraquat toxicity (PQ, 25 mg/kg i.p.) in rats was evaluated. The effects of treatment on selected oxidative stress parameters in lung tissues as well as certain inflammatory markers in serum were evaluated. The obtained results revealed that Mont can ameliorate the biochemical alterations in the lung tissues which were induced by PQ in rats. This was evidenced by the significant reduction in lung tissues lipid peroxidation, protein carbonyl content and DNA fragmentation, as well as by normalization of glutathione and myeloperoxidase activities. Moreover, the elevated levels of serum TNF-alpha, and LDH induced by paraquat were reversed in Mont-treated rats. Meanwhile, lung paraquat concentration was significantly reduced after Mont treatment compared with PQ alone group. Additionally, a higher survival percentage was observed in rats treated with Mont (80%) compared with the PQ alone group (30%) during 7 days observation. The results indicate that Mont protects lung tissue by balancing oxidant? antioxidant status, inhibiting neutrophil infiltration, and by regulating the generation of inflammatory mediators. In conclusion, the obtained results emphasize the beneficial effect of Mont in ameliorating the toxicity signs of paraquat in rats. The current study greatly recommends the usage of Mont in management of paraquat toxicity.
THE EFFECT OF S-NITROSOGLUTATHIONE ON INSULIN RECEPTOR BEHAVIOR ON ERYTHROCYTES IN AN ANIMAL MODEL

Nitric oxide (NO) is a potent modulator of cellular function. This study was designed to examine the possible diabetogenicity of nitric oxide (NO) by investigating any differences in cellular binding of insulin between dogs treated with the NO donor Snitrosoglutathione (GSNO) and controls treated with captopril. Glucose abnormality was attributed to decreased binding of insulin to its receptor on the cell membrane of erythrocytes, 27.53 ± 1.37% in GSNO treated dogs compared with 20.60 ± 3.36 in captopril controls at an unlabeled insulin concentration of 2.5 ng/ml (p<0.05). The decreased insulin binding was attributed primarily to a 22% decrease in the number of insulin receptor sites per cell (p<0.05) and secondarily to a decreased average receptor affinity. In conclusion, these findings suggest the evidence of NO as a modulator of insulin binding and the involvement of NO in the etiology of diabetes in dogs treated with this NO donor.
The potential of Latent Class Analysis in diagnostic test validation for canine Leishmania infantum infection

Accuracy assessment of diagnostic tests may be seriously biased if an imperfect reference test is used such as parasitology in the diagnosis of visceral leishmaniasis. We compared classical validity analysis of serological tests for Leishmania infantum with Latent Class Analysis (LCA), to assess whether it circumvented the gold standard problem. Clinical status, three serological tests (IFAT, ELISA and DAT) and parasitological data were recorded for 151 dogs captured in an endemic area. Sensitivity and specificity estimates from the 2×2 contingency tables were broadly corroborated by LCA, but the latter method provided more precise estimates that were robust for the different fitted models. It furthermore yielded a higher prevalence of infection and indicated that parasitology was only 55% sensitive. LCA seems a promising technique for test validation, but caution is required when applying it to sparse data sets. The feasibility and applicability of LCA in infectious disease epidemiology is discussed.
Relationship between Organizational Justice and Organizational Citizenship Behavior in Iran

Purpose – The purpose of this paper is to examine the, relationship between organizational justice and organizational citizenship behavior among 186 experts of Ministry of Economic Affairs and Finance (MEAF) in Iran. Design/methodology/approach – The papers develops a research model based on current literature and then test this model in MEAF selected from 18 Ministry, public sector in Iran. Statistics society consists of 186 experts include assistant of general managers in both personnel affairs and welfare and domestic payments department, and also professionals, managers and deputy of personnel affair and department of organization and methods in MEAF. The sample size provided based on "Cohan- Morgan- Korjsay" is 186 experts which has been determined with descriptive methods. For data analyzing we used analysis of Kolmogorov-Smirnov's, analysis of correlation, and analysis of variance test. Findings – The results indicate that we found that there is positive relationship between organizational justice and OCB. Research limitations/implications – This study could benefit from a large sample from public sector and replication in more Ministries. Practical implications – The paper offers practical suggestions to the public sector and management in general on how to manage the organizational justice effects on OCB. Originality/value – This paper has tried to provide an inclusive understanding about the relationship between organizational justice and OCB in the MEAF in Iran. Since there was a lack of such research in an Iranian context, this paper can provide theoretical basis for future researches as well as practical implications for managers and the professionals.
Phosphoenolpyruvate:glycose phosphotransferase system in species of Vibrio, a widely distributed marine bacterial genus

The genus Vibrio is one of the most common and widely distributed groups of marine bacteria. Studies on the physiology of marine Vibrio species were initiated by examining 15 species for the bacterial phosphoenolpyruvate:glycose phosphotransferase system (PTS). All species tested contained a PTS analogous to the glucose-specific (IIGlc) system in enteric bacteria. Crude extracts of the cells showed immunological cross-reactivity with antibodies to enzyme I, HPr, and IIIGlc from Salmonella typhimurium when assayed by the rocket-line method. Toluene-permeabilized cells of 11 species were tested and were active in phosphorylating methyl alpha-D-glucoside with phosphoenolpyruvate but not ATP as the phosphoryl donor. Membranes from 10 species were assayed, and they phosphorylated methyl alpha-D-glucoside when supplemented with a phospho-IIIGlc-generating system composed of homogeneous proteins from enteric bacteria. Toluene-permeabilized cells and membranes of seven species were assayed, as were phosphorylated fructose and 2-deoxyglucose. IIIGlc was isolated from Vibrio fluvialis and was active in phosphorylating methyl alpha-D-glucoside when supplemented with a phospho-HPr-generating system composed of homogeneous proteins from Escherichia coli and membranes from either E. coli or V. fluvialis. These results show that the bacterial PTS is widely distributed in the marine environment and that it is likely to have a significant role in marine bacterial physiology and in the marine ecosystem.
Investigation of hopped frequency waveforms for range and velocity measurements of radar targets

In the field of radar, High Range Resolution (HRR) profiles are often used to improve target tracking accuracy in range and to allow the radar system to produce an image of an object using techniques such as inverse synthetic aperture radar (ISAR) processing. These profiles are typically formed from wideband linearly stepped frequency waveforms which are synthesised by combining the spectra of the transmitted pulses in the burst [1]. This work focuses on the use of HRR profiles generated from hopped frequency waveforms. This adds the advantage of range-Doppler decoupling and robustness against electronic countermeasures (ECM) [2], [3]. However hopped frequency waveforms suffer from high levels of sidelobes [4]. Improving the spurious free dynamic range (SFDR) of target measurements is required for various applications such as target recognition. This was done with the CLEAN technique [5] which could reduce the sidelobes to under 40 dB below the maximum amplitude of the profiles. To show how this work can be applied to areas such as ISAR, simulated rotating targets were used. In terms of range and velocity measurement accuracy, the CLEAN method performed adequately for signal to noise ratios (SNR) above -10 dB. This work can be extended to incorporate acceleration, extended targets and measured data.
Synthesis and charcterization of ultrafine cobalt ferrites

Ultrafine, nearly spherical particles of CoFe/sub 2/O/sub 4/ were prepared under mild hydrothermal conditions. These ferrite particles were found to be superparamagnetic with a narrow particle size distribution in the range 10.0-40.0 nm. The hydrothermal ferrite powders could be sintered to almost theoretical density with little or no intergranular porosity. The present study shows that magnetic measurements together with Mossbauer spectroscopy provide excellent tools for characterizing fine ferrite particles at macroscopic levels. >
Application of Surface Plasmon Resonance Based on a Metal Nanoparticle

Surface plasmon resonance (SPR) is a powerful technique to retrieve information on optical properties of biomaterial and nanomaterials. Biosensor based on SPR is a versatile technique for biological analysis applications. Essentially, SPR depends on the optical properties of metal layer [1] and enviromental changes so it is related to charge density oscillation at the interface between them [2]. Hence, biomolecular possess an extreme sensitivity to plasmon resonance and they remove the requirement for extrinsic biomolecular labeling [3]. One advantage of SPR is, the light beam never passes through the dielectric medium of interest and hence the effect of absorption of the light in the analyte can be ignored. Hence, the main potential of surface plasmon resonance is characterization of medium after the metal layer.
Identification and properties of the RNA‐dependent RNA polymerase of hepatitis C virus.

Hepatitis C virus (HCV) is the major etiological agent of non‐A, non‐B post‐transfusion hepatitis. Its genome, a (+)‐stranded RNA molecule of approximately 9.4 kb, encodes a large polyprotein that is processed by viral and cellular proteases into at least nine different viral polypeptides. As with other (+)‐strand RNA viruses, the replication of HCV is thought to proceed via the initial synthesis of a complementary (‐) RNA strand, which serves, in turn, as a template for the production of progeny (+)‐strand RNA molecules. An RNA‐dependent RNA polymerase has been postulated to be involved in both of these steps. Using the heterologous expression of viral proteins in insect cells, we present experimental evidence that an RNA‐dependent RNA polymerase is encoded by HCV and that this enzymatic activity is the function of the 65 kDa non‐structural protein 5B (NS5B). The characterization of the HCV RNA‐dependent RNA polymerase product revealed that dimer‐sized hairpin‐like RNA molecules are generated in vitro, indicating that NS5B‐mediated RNA polymerization proceeds by priming on the template via a ‘copy‐back’ mechanism. In addition, the purified HCV NS5B protein was shown to perform RNA‐ or DNA oligonucleotide primer‐dependent RNA synthesis on templates with a blocked 3′ end or on homopolymeric templates. These results represent a first important step towards a better understanding of the life cycle of the HCV.
Exploring Relationships Between Delinquent Peer Groups, Participation in Delinquency, Substance Abuse, and Injecting Drug Use Among the Incarcerated: Findings From a National Sample of State and Federal Inmates in the United States

The following study assesses the relationship between affiliating with delinquent peer groups, participation in delinquency, and several substance misuse and injecting drug use outcomes in a nationally representative sample of inmates in state and federal facilities in the United States. After controlling for potential confounders, affiliating with peers who engaged in deviant behaviors and participation in delinquency was associated with onset of alcohol and illicit drug use, substance dependence, alcohol dependence, types of substances used, and injecting drug use outcomes. Inmates who began engaging in delinquency at older ages reported initiating drug and alcohol use at older ages, and were less likely to meet the criteria for drug abuse or dependence, less likely to use substances daily or near daily, and less likely to report having ever injected or shared syringes. The implications of these findings for substance abuse, HIV, and crime prevention interventions are discussed.
CVSS-based security metrics for quantitative analysis of attack graphs

Attack graphs are efficient tools for detecting possible attacks in the network and their causes. By analyzing attack graphs and eliminating causes of attacks in the networks, we can immune networks against known intrusions. The main shortcoming of attack graphs is that they give no information about the damages of the possible attacks in the network. On the other hand by attack graphs, we can only analyze network security qualitatively. In this paper we propose a method that can measure the impact of each shown attack in the attack graph on the security parameters (Confidentiality, Availability and Integrity) of the network. In the proposed approach we have defined some security metrics by combining CVSS framework and attack graph. The main problem with the existing approaches is that, they cannot consider interrelation between vulnerabilities of the network efficiently. Our defined security metrics can address this issue and help us to assess network security quantitatively by analyzing attack graphs. By applying proposed security metrics on each network's attack graph we can find the most perilous vulnerability in the network.