Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic mapping of chromosomal determinants for the production of the exopolysaccharide alginate in a Pseudomonas aeruginosa cystic fibrosis isolate

Mucoid Pseudomonas aeruginosa strain FRD, a sputum isolate from a cystic fibrosis patient, was used to develop a genetic system. The mucoid appearance is due to the biosynthesis of the exopolysaccharide alginate and is a potential virulence factor of the organism. The sex factor plasmid FP2 was used for uninterrupted genetic exchange to investigate the nature of spontaneous mutations which produce frequent alginate-negative (Alg-) derivatives. Crosses between Alg+ donors and Alg- recipients demonstrated linkage between alginate genes and chromosomal markers. Crosses between an Alg- donor and Alg- recipients produced Alg+ recombinants at frequencies that varied, depending on the recipient strains used. This indicated that more than one genetic locus was associated with spontaneous mutation leading to loss of the mucoid character. Three classes of Alg- mutants were identified. Genetic exchange experiments showed that the loci of the alginate (alg) mutations of the three mutant classes are in the same region of the chromosome. The sex factor plasmid R68.45 was used for nonpolarized chromosome transfer and demonstrated close linkage between chromosomal markers (his-1, met-1) and alg markers. This was consistent with the data obtained in FP2-mediated crosses. Thus, the evidence obtained indicated that the alg genes which undergo frequent mutation are chromosomal, that several loci are involved, and that these alg loci are apparently clustered on the chromosome.
THE ENVIRONMENTAL AND GENETIC CONTROL OF SEASONAL POLYPHENISM IN LARVAL COLOR AND ITS ADAPTIVE SIGNIFICANCE IN A SWALLOWTAIL BUTTERFLY

Abstract Seasonal polyphenism, in which different forms of a species are produced at different times of the year, is a common form of phenotypic plasticity among insects. Here I show that the production of dark fifth-instar caterpillars of the eastern black swallowtail butterfly, Papilio polyxenes, is a seasonal polyphenism, with larvae reared on autumnal conditions being significantly darker than larvae reared on midsummer conditions. Both rearing photoperiod and temperature were found to have individual and synergistic effects on larval darkness. Genetic analysis of variation among full-sibling families reared on combinations of two different temperatures and photoperiods is consistent with the hypothesis that variation in darkness is heritable. In addition, the genetic correlation in larval darkness across midsummer and autumnal environments is not different from zero, suggesting that differential gene expression is responsible for the increase in larval darkness in the autumn. The relatively dark autumnal form was found to have a higher body temperature in sunlight than did the lighter midsummer form, and small differences in temperature were found to increase larval growth rate. These results suggest that this genetically based seasonal polyphenism in larval color has evolved in part to increase larval growth rates in the autumn. Corresponding Editor: T. Kawecki
Effect of a sustained reduction in plasma free fatty acid concentration on insulin signalling and inflammation in skeletal muscle from human subjects

• Reducing free fatty acids in the circulation gives protection against muscle insulin resistance. • In the present study, we investigated the mechanism by which free fatty acid reduction improves muscle insulin sensitivity. • The antilipolytic drug acipimox reduced the plasma concentration of unsaturated and saturated fatty acids in insulin‐resistant (obese and type 2 diabetic) subjects. • The reduction in plasma free fatty acid concentration caused by acipimox led to an improvement in local inflammation and insulin signalling in skeletal muscle. • The improvements in local inflammation and insulin signalling were more pronounced in obese type 2 diabetic subjects than obese non‐diabetic individuals, suggesting that diabetic subjects are more susceptible to the toxic effect of circulating free fatty acids.
Constrained Motion Model of Mobile Robots and Its Applications

Target detecting and dynamic coverage are fundamental tasks in mobile robotics and represent two important features of mobile robots: mobility and perceptivity. This paper establishes the constrained motion model and sensor model of a mobile robot to represent these two features and defines the k -step reachable region to describe the states that the robot may reach. We show that the calculation of the k-step reachable region can be reduced from that of 2k reachable regions with the fixed motion styles to k + 1 such regions and provide an algorithm for its calculation. Based on the constrained motion model and the k -step reachable region, the problems associated with target detecting and dynamic coverage are formulated and solved. For target detecting, the k-step detectable region is used to describe the area that the robot may detect, and an algorithm for detecting a target and planning the optimal path is proposed. For dynamic coverage, the k-step detected region is used to represent the area that the robot has detected during its motion, and the dynamic-coverage strategy and algorithm are proposed. Simulation results demonstrate the efficiency of the coverage algorithm in both convex and concave environments.
MyD88 Signaling Is Indispensable for Primary Influenza A Virus Infection but Dispensable for Secondary Infection

ABSTRACT Recent studies have revealed that innate immunity is involved in the development of adaptive immune responses; however, its role in protection is not clear. In order to elucidate the exact role of Toll-like receptor (TLR) or RIG-I-like receptor (RLR) signaling on immunogenicity and protective efficacy against influenza A virus infection (A/PR/8/34 [PR8]; H1N1), we adapted several innate signal-deficient mice (e.g., TRIF−/−, MyD88−/−, MyD88−/− TRIF−/−, TLR3−/− TLR7−/−, and IPS-1−/−). In this study, we found that MyD88 signaling was required for recruitment of CD11b+ granulocytes, production of early inflammatory cytokines, optimal proliferation of CD4 T cells, and production of Th1 cytokines by T cells. However, PR8 virus-specific IgG and IgA antibody levels in both systemic and mucosal compartments were normal in TLR- and RLR-deficient mice. To further assess the susceptibility of these mice to influenza virus infection, protective efficacy was determined after primary or secondary lethal challenge. We found that MyD88−/− and MyD88−/− TRIF−/− mice were more susceptible to primary influenza virus infection than the B6 mice but were fully protected against homologous (H1N1) and heterosubtypic (H5N2) secondary infection when primed with a nonlethal dose of PR8 virus. Taken together, these results show that MyD88 signaling plays an important role for resisting primary influenza virus infection but is dispensable for protection against a secondary lethal challenge.
Effects of isolates of ectomycorrhizal fungi and endophytic Mycelium radicis atrovirens that were dominant in soil from disturbed sites on growth of Betula platyphylla var. japonica seedlings

Effects of ectomycorrhizal fungi and endophytic Mycelium radicis atrovirens Melin (MRA) on growth of Betula platyphylla var. japonica seedlings were investigated under aseptic culture conditions. Three isolates of ectomycorrhizal fungi and two isolates of MRA were used. One MRA isolate was Phialocephala fortinii. Previous field work revealed that these isolates were dominant on the roots of B. platyphylla var. japonica seedlings grown in a mineral subsoil that had been exposed by the removal of surface soil. After a 100-day incubation, the growth of the seedlings was significantly enhanced by the colonization of these ectomycorrhizal fungal isolates as compared with uninoculated seedlings. In contrast, the growth of seedlings was retarded by the colonization of the MRA isolates. The growth of seedlings that were co-inoculated with ectomycorrhizal fungi and MRA was similar to that of uninoculated seedlings in most cases. These results suggest that ectomycorrhizal fungi have a beneficial effect on the growth of B. platyphylla var. japonica seedlings and that they suppress the deleterious effect of MRA. Thus, these ectomycorrhizal fungi probably have an important role in establishing B. platyphylla var. japonica seedlings during the initial stage of re-vegetation following site disturbance by the removal of surface soil.
Dose and Size-Dependent Antiviral Effects of Silver Nanoparticles on Feline Calicivirus, a Human Norovirus Surrogate.

OBJECTIVES Silver nanoparticles (AgNPs) as antibacterial agents are incorporated in many consumer products, while the use as antiviral agents is an ongoing area of research. We evaluated the antiviral properties of AgNPs of variable sizes (10, 75, and 110 nm) and doses (25, 50, and 100 μg/mL) at different contact time points against feline calicivirus (FCV), a surrogate for norovirus. MATERIALS AND METHODS Antiviral effects of the AgNPs were determined by comparing the infectivity of FCV, the appearance of cytopathic effects (CPEs), and the integrity of the viral capsid protein in viral suspension treated with AgNPs with the untreated controls. RESULTS The 10 nm AgNPs at 50 and 100 μg/mL concentrations inactivated the FCV beyond the limit of detection, resulting in a decrease of up to 6.5 log10 viral titer, prevented development of CPEs, and reduction in the western blot band signal of the viral capsid protein. No significant antiviral effect was observed for the 75 and 110 nm AgNPs. Conclusions and Applications: These results demonstrate that the antiviral effects of AgNPs are both size and dose dependent, thus potential applications of AgNPs as antiviral agents to prevent contamination of foodborne viruses need to consider size and dose effects.
Upper-Body Muscular Endurance Training Improves Performance Following 50 min of Double Poling in Well-Trained Cross-Country Skiers

This study investigated the effect of muscular endurance training on O2-cost and performance in double poling (DP) on a rollerski treadmill. Twenty-two well-trained cross-country skiers (31 ± 4 years, 77 ± 9 kg, 181 ± 8 cm, VO2max running: 64 ± 5 mL·kg−1·min−1) were counter-balanced to either a combined muscular endurance and running interval training group [MET; n = 11 (♂ = 9, ♀ = 2)], or an endurance running interval training group [ET; n = 11 (♂ = 9, ♀ = 2)]. Both groups continued their normal low-and moderate intensity training, but replaced 2 weekly high intensity-training sessions with two project-specific sessions for 6 weeks. In these sessions, MET combined upper-body muscular endurance training (4 × 30 repetitions, 90 s rest between sets) and running intervals (3 × 4 or 2 × 6 min, 3 min rest), while ET performed running intervals only (6 × 4 or 4 × 6 min, 3 min rest). The DP test-protocol consisted of 50 min submaximal poling for O2-cost measurement, followed by a self-paced 1,000-m performance test. In addition, subjects performed a VO2max test in running. MET increased muscular endurance (P < 0.05) and 1RM in simulated DP (P < 0.01) more than ET. Further, MET reduced the 1,000-m time and O2-cost compared to baseline values (P < 0.05), and tended to improve the 1,000-m time more than ET (P = 0.06). There were no changes in VO2max running or VO2peak DP in either MET or ET. In conclusion, 6 weeks of muscular endurance training increased both muscular endurance and 1RM in simulated DP. Further, specific upper-body muscular endurance training improved DP performance and thus, seems as a promising training model to optimize performance in well-trained cross-country skiers.
QTEP: quality-aware test case prioritization

Test case prioritization (TCP) is a practical activity in software testing for exposing faults earlier. Researchers have proposed many TCP techniques to reorder test cases. Among them, coverage-based TCPs have been widely investigated. Specifically, coverage-based TCP approaches leverage coverage information between source code and test cases, i.e., static code coverage and dynamic code coverage, to schedule test cases. Existing coverage-based TCP techniques mainly focus on maximizing coverage while often do not consider the likely distribution of faults in source code. However, software faults are not often equally distributed in source code, e.g., around 80% faults are located in about 20% source code. Intuitively, test cases that cover the faulty source code should have higher priorities, since they are more likely to find faults. In this paper, we present a quality-aware test case prioritization technique, QTEP, to address the limitation of existing coverage-based TCP algorithms. In QTEP, we leverage code inspection techniques, i.e., a typical statistic defect prediction model and a typical static bug finder, to detect fault-prone source code and then adapt existing coverage-based TCP algorithms by considering the weighted source code in terms of fault-proneness. Our evaluation with 16 variant QTEP techniques on 33 different versions of 7 open source Java projects shows that QTEP could improve existing coverage-based TCP techniques for both regression and new test cases. Specifically, the improvement of the best variant of QTEP for regression test cases could be up to 15.0% and on average 7.6%, and for all test cases (both regression and new test cases), the improvement could be up to 10.0% and on average 5.0%.
Peripheral Villous Stromal Hyperplasia: A Distinctive Placental Lesion in Hemoglobin Bart Hydrops Fetalis

In hydrops fetalis (HF) the placenta can be markedly enlarged and the villi show stromal edema, increased Hofbauer cells, and reduced numbers of capillaries. Hemoglobin (Hb) Bart is the most severe form of thalassemia, causing HF due to profound anemia. We report a previously undescribed histologic finding based on a review of Hb Bart HF cases, termed “peripheral villous stromal hypercellularity. ” This change was noted in 15 of 18 (83%) placentas with Hb Bart HF but not in placentas of 21 cases of HF due to other causes, including 11 cases involving anemia. The hyperplastic stromal cells were determined to be myofibroblastic by immunohistochemistry and electron microscopy, associated with a more complex capillary network in villi than is seen with other causes of HF. The authors hypothesize that this angiogenesis in villi is a response to fetal anemia from Hb Bart. In turn, there is increased villous blood flow, resulting in edematous villous stroma, leading to narrowing of the intervillous space in the placenta. Hyperplasia of myofibroblasts might then be a compensatory change, in that contraction by these cells would reduce the vascular lumina and the size of placental villi, thereby widening the intervillous space to improve capacity for maternal blood circulation. Curiously, this histologic change was restricted to cases of HF caused by Hb Bart. We speculate that in Hb Bart disease, the hypoxia and hydrops develop earlier in gestation, compared to other causes of HF, allowing the time for these adaptive changes to occur in the placenta.
Diffusion-Weighted Imaging for Differentiating Uterine Leiomyosarcoma From Degenerated Leiomyoma

Purpose The study aimed to investigate magnetic resonance diffusion-weighted imaging (DWI) in the differentiation of uterine leiomyosarcoma (ULMS) from degenerated leiomyoma (DLM). Methods Sixteen patients with ULMSs and 26 patients with DLMs confirmed by surgery and pathology underwent conventional magnetic resonance imaging and DWI. The mean apparent diffusion coefficient (ADC) values of the 2 groups’ tumors were measured and compared using an independent-sample t test (b = 0.1000 s/mm2 [ADC1]; b = 0.800 s/mm2 [ADC2], respectively). A receiver operating characteristic curve was used to evaluate the diagnostic performance of DWI in the differentiation of ULMS from DLM. Intraobserver and interobserver agreements were evaluated using an intraclass correlation coefficient and Bland-Altman analysis. Results The mean ADC value in ULMSs (0.81 ± 0.14 × 10−3mm2/s [ADC1], 0.90 ± 0.11 × 10−3mm2/s [ADC2]) was significantly lower than that in DLMs (1.22 ± 0.22 × 10−3mm2/s [ADC1], 1.50 ± 0.22 × 10−3mm2/s [ADC2]) (P < 0.001, <0.001, respectively). The sensitivity, specificity, accuracy, and positive and negative predictive values for characterizing ULMS were 100%, 90%, 93%, and 83% and 100% [ADC1] and 100%, 93%, 96%, and 90% and 100% [ADC2]; respectively. Intraobserver and interobserver reproducibilities were excellent (intraclass correlation coefficient = 0.967–0.988; small variability and 95% limits of agreement). Conclusions Diffusion-weighted imaging is helpful in differentiating ULMS from DLM.
EXAMINING TIME-VARYING INTEGRITY AND INTERRELATIONSHIPS AMONG GLOBAL STOCK MARKETS

This paper examines co-movements and interrelationships among 6 emerging and 5 developed stock market returns between period 2001- 2017. First, principal components are extracted from returns. Results show that, for the period analyzed, there is no strong global stock market integration and there isn't any change in patterns of correlations of returns except short-term disturbances in global financial crisis time. Second, partial least squares regression models are used for predicting each stock market returns with other stock markets' current and all markets' up to three month lagged returns. Results identify divergence between developed and emerging markets and greater number of latent transmission channels among former ones. Findings indicate a strong integrity among global stock markets is not yet appeared and considered together with previous studies, today's international market structure can be attributed to last two decades of 20th century. China stock market has a disparate position than all other stock markets and deserves further interest.
Fast mapping of myocardial blood flow with MR first‐pass perfusion imaging

Accurate and fast quantification of myocardial blood flow (MBF) with MR first‐pass perfusion imaging techniques on a pixel‐by‐pixel basis remains difficult due to relatively long calculation times and noise‐sensitive algorithms. In this study, Zierler's central volume principle was used to develop an algorithm for the calculation of MBF with few assumptions on the shapes of residue curves. Simulation was performed to evaluate the accuracy of this algorithm in the determination of MBF. To examine our algorithm in vivo, studies were performed in nine normal dogs. Two first‐pass perfusion imaging sessions were performed with the administration of the intravascular contrast agent Gadomer at rest and during dipyridamole‐induced vasodilation. Radiolabeled microspheres were injected to measure MBF at the same time. MBF measurements in dogs using MR methods correlated well with the microsphere measurements (R2 = 0.96, slope = 0.9), demonstrating a fair accuracy in the perfusion measurements at rest and during the vasodilation stress. In addition to its accuracy, this method can also be optimized to run relatively fast, providing potential for fast and accurate myocardial perfusion mapping in a clinical setting. Magn Reson Med, 2008. © 2008 Wiley‐Liss, Inc.
Aroma characteristics of Moutai‐flavour liquor produced with Bacillus licheniformis by solid‐state fermentation

The potential of Bacillus licheniformis as a starter culture for aroma concentration improvement in the fermentation of Chinese Moutai‐flavour liquor was elucidated. The volatile compounds produced by B. licheniformis were identified by GC–MS, in which C4 compounds, pyrazines, volatile acids, aromatic and phenolic compounds were the main ingredients. The strains B. licheniformis (MT‐6 and MT‐15) produced more volatile compound concentrations, mainly C4 compounds, than the type strain of B. licheniformis (ATCC 14580) at the fermentation temperature of 55°C. Meanwhile, more volatile compound concentrations were produced by B. licheniformis in solid‐state fermentation than in submerged state fermentation. Thus, the strains MT‐6 and MT‐15 were used as the Bacillus starter culture for investigating Moutai‐flavour liquor production. The distilled liquor inoculated with Bacillus starter culture was significantly different from the liquor without inoculum. This was particularly evident in the fore‐run part of the distilled sample which was inoculated with Bacillus starter culture, where volatile compounds greatly increased compared to the control. Furthermore, the distilled liquor with Bacillus starter culture showed improved results in sensory appraisals. These results indicated that B. licheniformis was one of the main species influencing the aroma characteristics of Moutai‐flavour liquor.
Risk factors for human-directed aggression in a referral level clinical population

Risk factors for human-directed aggression were investigated using retrospective analysis of data from a referral-level clinical behaviour population in the UK. A sample of 200 cases involving human-directed canine aggression and 200 control cases involving no instance of human-directed aggression were selected at random from a population of 746 cases. The final model suggested that clinical cases with human-directed aggression were significantly younger than those presenting with other undesired behaviours (P=0.008) and that male dogs were 1.4 times more likely to be aggressive towards human beings than female dogs (P=0.019). Dogs were 1.7 times more likely to be aggressive towards people if they had attended more than five puppy classes than if they had never attended puppy class (P=0.015) and that dogs were 2.8 times more likely to be aggressive towards human beings if there was another dog between 0 months and 24 months of age in the home (P=0.004). These factors only account for 7 per cent to 10 per cent of the variance between the human-directed aggression population and the control population, but factors such as attendance at puppy classes and numbers of dogs in the household suggest the need for longitudinal studies to investigate temporal relationships.
Clathrin in Chara australis: Molecular Analysis and Involvement in Charasome Degradation and Constitutive Endocytosis

Charasomes are convoluted plasma membrane domains in characean green algae. They are known to form in response to light via secretion of trans-Golgi network (TGN) vesicles and local inhibition of endocytosis. Charasomes are involved in the acidification of their aqueous environment, thereby facilitating photosynthesis-dependent carbon uptake. Charasome formation is reversible to allow cells to adapt to different light conditions. Here, we show that darkness-induced degradation of charasomes involves the formation of coated pits and coated vesicles. The darkness-induced degradation of charasomes can be inhibited by 1–2 μM ikarugamycin (IKA), which is considered to be a specific inhibitor of clathrin-dependent endocytosis. At a much higher concentration (100 μM), IKA also significantly reduces the internalization of styryl dyes, indicating uptake via clathrin-coated vesicles (CV). We are the first to present evidence, based on fine structure investigation, that IKA does not interfere with the formation of clathrin coat, but inhibits the detachment and/or further processing of coated vesicles. Both charasome degradation and constitutive endocytosis are also significantly inhibited by sterol complexing agents (methyl-ß-cyclodextrin and filipin). The absence of an additive effect, when applied together with IKA, suggests that charasome degradation and constitutive endocytosis (measured via styryl dye uptake) is not inhibited due to membrane retrieval via lipid rafts, but due to clathrin coat formation requirement of a specific set of sterols. Analysis of Chara australis clathrin proteins revealed two heavy chains and several light chains with sequence peculiarities, suggesting functional and/or species specific differences. The data obtained indicate that clathrin plays a central role not only in constitutive endocytosis but also in the degradation of charasomes, thereby representing a valuable system for studying targeted exo- and endocytosis.