Miracle-dz/UniFAR-FTUs huggingface dataset:
Hypolipidemic and hepatoprotective activities of rosemary and thyme in gentamicin-treated rats

Rosemary (Rosmarinus officinalis; RM) and thyme (Thymus vulgaris; TV) are used as remedies. We designed this work to investigate the preventive effect of aqueous extracts of RM or TV on the gentamicin (GM)-induced hepatotoxicity and abnormalities of lipid profile in rats. Both plant extracts exhibited an in vitro antioxidant activity as determined by the 1,1-diphenyl-2-picrylhydrazyl assay. Radical scavenging activity for TV extract was 48.7% and for RM extract was 25.6%. Polyphenolic determination by high-performance liquid chromatography for both extracts revealed that catechin, coumarin, cinnamic acid and rutin were detected in both extracts. RM extract had higher values than TV extract in all except rutin. Ferulic acid and quercetin were also detected in TV extract and sinapic acid and oleuropein were detected in RM extract. In rats given GM intraperitoneally for 10 days and coadministered either RM extract or TV extract orally, both aqueous extracts demonstrated similar hepatoprotective effects manifested by approximate normalization of plasma liver enzymes (AST and ALT), bilirubin level and total protein concentration compared with the group given GM only. Abnormal lipid parameters and raised hydrogen peroxide levels were ameliorated by both extracts. Pancreatic lipase activity was markedly reduced by RM extract. Also, the atherogenic index value was significantly reduced by both extracts as compared to that of GM group. DNA fragmentation analysis confirmed tissue damage by GM and its amelioration by the extracts. These findings suggest that RM and TV extracts could be helpful in ameliorating some aspects of gentamicin toxicity.
SinR Controls Enterotoxin Expression in Bacillus thuringiensis Biofilms

The entomopathogen Bacillus thuringiensis produces dense biofilms under various conditions. Here, we report that the transition phase regulators Spo0A, AbrB and SinR control biofilm formation and swimming motility in B. thuringiensis, just as they control biofilm formation and swarming motility in the closely related saprophyte species B. subtilis. However, microarray analysis indicated that in B. thuringiensis, in contrast to B. subtilis, SinR does not control an eps operon involved in exopolysaccharides production, but regulates genes involved in the biosynthesis of the lipopeptide kurstakin. This lipopeptide is required for biofilm formation and was previously shown to be important for survival in the host cadaver (necrotrophism). Microarray analysis also revealed that the SinR regulon contains genes coding for the Hbl enterotoxin. Transcriptional fusion assays, Western blots and hemolysis assays confirmed that SinR controls Hbl expression, together with PlcR, the main virulence regulator in B. thuringiensis. We show that Hbl is expressed in a sustained way in a small subpopulation of the biofilm, whereas almost all the planktonic population transiently expresses Hbl. The gene coding for SinI, an antagonist of SinR, is expressed in the same biofilm subpopulation as hbl, suggesting that hbl transcription heterogeneity is SinI-dependent. B. thuringiensis and B. cereus are enteric bacteria which possibly form biofilms lining the host intestinal epithelium. Toxins produced in biofilms could therefore be delivered directly to the target tissue.
Temperature‐Controlled Transitions Between Glass, Liquid, and Gel States in Dense p‐NIPA Suspensions

In this article we demonstrate that concentrated p-NIPA suspensions in a low temperature glassy state can liquefy and then solidify again as the temperature is raised across the LCST. Our system exhibits all the typical behavior of disordered colloidal suspensions, but the behavior is controlled by temperature. Below the LCST it shows the behavior typical of a colloidal glass, near the LCST it behaves like a liquid, while above the LCST it exhibits the properties typical of a colloidal gel. Moreover, we show that the elasticity of these suspensions exhibits critical-like behavior as a function of temperature both above and below the LCST, with a critical temperature that corresponds to the LCST. Our results thereby suggest interesting analogies between the glass and gel phases of these thermosensitive microgel particles.
Cell morphology drives spatial patterning in microbial communities

Significance Microbial communities contain cells of different shapes, and yet we know little about how these shapes affect community biology. We have developed a computational model to study the effects of microbial shape in communities. Our model predicts that shape will have strong effects on cells’ positioning, and, consequently, their survival and reproduction. Rod-shaped cells are better at colonizing the base of the community and its expanding edges, whereas round cells dominate the upper surface. We show that the same patterns occur in colonies of Escherichia coli, using strains with different shapes. Our work suggests that cell shape is a major determinant of patterning and evolutionary fitness within microbial communities. The clearest phenotypic characteristic of microbial cells is their shape, but we do not understand how cell shape affects the dense communities, known as biofilms, where many microbes live. Here, we use individual-based modeling to systematically vary cell shape and study its impact in simulated communities. We compete cells with different cell morphologies under a range of conditions and ask how shape affects the patterning and evolutionary fitness of cells within a community. Our models predict that cell shape will strongly influence the fate of a cell lineage: we describe a mechanism through which coccal (round) cells rise to the upper surface of a community, leading to a strong spatial structuring that can be critical for fitness. We test our predictions experimentally using strains of Escherichia coli that grow at a similar rate but differ in cell shape due to single amino acid changes in the actin homolog MreB. As predicted by our model, cell types strongly sort by shape, with round cells at the top of the colony and rod cells dominating the basal surface and edges. Our work suggests that cell morphology has a strong impact within microbial communities and may offer new ways to engineer the structure of synthetic communities.
A Chaperone Complex Formed by HSP47, FKBP65, and BiP Modulates Telopeptide Lysyl Hydroxylation of Type I Procollagen

Lysine hydroxylation of type I collagen telopeptides varies from tissue to tissue, and these distinct hydroxylation patterns modulate collagen cross‐linking to generate a unique extracellular matrix. Abnormalities in these patterns contribute to pathologies that include osteogenesis imperfecta (OI), fibrosis, and cancer. Telopeptide procollagen modifications are carried out by lysyl hydroxylase 2 (LH2); however, little is known regarding how this enzyme regulates hydroxylation patterns. We identified an ER complex of resident chaperones that includes HSP47, FKBP65, and BiP regulating the activity of LH2. Our findings show that FKBP65 and HSP47 modulate the activity of LH2 to either favor or repress its activity. BiP was also identified as a member of the complex, playing a role in enhancing the formation of the complex. This newly identified ER chaperone complex contributes to our understanding of how LH2 regulates lysyl hydroxylation of type I collagen C‐telopeptides to affect the quality of connective tissues. © 2017 American Society for Bone and Mineral Research.
Superpixel Benchmark and Comparison

Superpixel segmentation showed to be a useful preprocessing step in many computer vision applications. This led to a variety of algorithms to compute superpixel segmentations, each with individual strengths and weaknesses. We discuss the need for a standardized evaluation scheme of such algorithms and propose a benchmark including data sets, error metrics, usage guidelines and an open source implementation of the benchmark in a Matlab toolbox. The benchmark evaluates the quality of the superpixel segmentation with respect to human ground truth segmentation and the segmentation robustness to affine image transformations, which is crucial for application on image sequences. To our knowledge, this is the first benchmark considering the segmentation robustness to such image transformations. To better consider the characteristics of an image oversegmentation, we provide a new formulation of the undersegmentation error. Using this benchmark, we evaluate eight algorithms with available open source implementations and discuss the results with respect to requirements of further applications and runtime.
BASIC IMPROVEMENTS IN PHOSPHATE SOIL STABILIZATION

AN INVESTIGATION IS DESCRIBED CONCERNING THE USE OF PHOSPHATE TO SOLIDIFY SOIL, THUS RENDERING THE SOIL MORE SUITABLE FOR CERTAIN ENGINEERING USES. THE TREATMENTS REPORTED INVOLVE THE USE OF ROCK PHOSPHATE, SULFURIC ACID, PHOSPHORIC ACID, AND SALTS OF IRON AND ALUMINUM TO ACHIEVE THE DESIRED RESULTS. THE RESULTS, GIVEN IN TERMS OF THE UNCONFINED COMPRESSIVE STRENGTH OF IMMERSED TREATED SOIL SAMPLES, REVEAL THE IMPORTANCE OF MATERIALS BALANCE TO ACHIEVING OPTIMUM SOLIDIFICATION WITH THESE TREATMENTS. FURTHER, THE RESULTS LEND ADDITIONAL INSIGHT INTO THE MECHANISMS OF SOLIDIFICATION OF SOIL WITH PHOSPHATIC MATERIALS. MANY OF THE TREATMENTS APPEAR TO BE ECONOMICALLY COMPETITIVE WITH THE PRESENTLY ACCEPTED TECHNIQUES OF SOIL SOLIDIFICATION. /AUTHOR/
Annexin A2 links poor myofiber repair with inflammation and adipogenic replacement of the injured muscle

Repair of skeletal muscle after sarcolemmal damage involves dysferlin and dysferlin-interacting proteins such as annexins. Mice and patient lacking dysferlin exhibit chronic muscle inflammation and adipogenic replacement of the myofibers. Here, we show that similar to dysferlin, lack of annexin A2 (AnxA2) also results in poor myofiber repair and progressive muscle weakening with age. By longitudinal analysis of AnxA2-deficient muscle we find that poor myofiber repair due to the lack of AnxA2 does not result in chronic inflammation or adipogenic replacement of the myofibers. Further, deletion of AnxA2 in dysferlin deficient mice reduced muscle inflammation, adipogenic replacement of myofibers, and improved muscle function. These results identify multiple roles of AnxA2 in muscle repair, which includes facilitating myofiber repair, chronic muscle inflammation and adipogenic replacement of dysferlinopathic muscle. It also identifies inhibition of AnxA2-mediated inflammation as a novel therapeutic avenue for treating muscle loss in dysferlinopathy.
Linear and nonlinear optical study of pure PVA and CdSe doped PVA nanocomposite

This research work reports the synthesis and optical properties of CdSe/PVA polymer nanocomposite (PNC’s) prepared by wet chemical co-precipitation method. The transmission spectra obtained from UV-Vis-NIR spectrophotometer has been investigated to determine the optical properties of PNC’s. Absorption spectra give the information about energy band gap (Eg) and type of transition. Refractive index (n), extinction coefficient (k) was calculated using well known Swanepoel method. Wemple-Di Domenico model (WDD) has been used to calculate dispersion energy (Ed) and oscillator energy (E0). Boling formula is used to calculate nonlinear refractive index (n2) of CdSe/PVA nanocomposite.
Sybil Defense in Crowdsourcing Platforms

Crowdsourcing platforms have been widely deployed to solve many computer-hard problems, e.g., image recognition and entity resolution. Quality control is an important issue in crowdsourcing, which has been extensively addressed by existing quality-control algorithms, e.g., voting-based algorithms and probabilistic graphical models. However, these algorithms cannot ensure quality under sybil attacks, which leverages a large number of sybil accounts to generate results for dominating answers of normal workers. To address this problem, we propose a sybil defense framework for crowdsourcing, which can help crowdsourcing platforms to identify sybil workers and defense the sybil attack. We develop a similarity function to quantify worker similarity. Based on worker similarity, we cluster workers into different groups such that we can utilize a small number of golden questions to accurately identify the sybil groups. We also devise online algorithms to instantly detect sybil workers to throttle the attacks. Our method also has ability to detect multi-attackers in one task. To the best of our knowledge, this is the first framework for sybil defense in crowdsourcing. Experimental results on real-world datasets demonstrate that our method can effectively identify and throttle sybil workers.
Curing and Flow of Thermosetting Resins for Composite Material Pultrusion.

Abstract : Fibrous composite materials for mechanical and structural applications often are expensive due to high labor costs. One economical way of making composites is pultrusion, a manufacturing process in which resin-impregnated fibers are pulled at a constant speed through a heated die which shapes the resin-fiber mass and cures the resin. Most of the work which has been done on the process has been of an empirical nature, with limited understanding of the process principles. Most of the experience with pultrusion has been gained with polyester resins and glass fibers. Very little experience has been gained with higher performance, more costly materials such as epoxy resins and graphite fiber. The higher cost of these latter materials makes the empirical approach to developing process parameters much too expensive. jg p8
Digestion tests of livestock wastes

In this 8/sup 1///sub 2/ week duration laboratory study eight 3.4 l digesters were operated at temperatures of 23/sup 0/ and 35/sup 0/C with detention times of approximately 25 days. Four of the digesters were fed chicken manure at loading rates of 2.76 to 4.89 g VS/l/day and the remaining four were fed dairy cow feces and urine at 2.11 to 3.44 g VS/l/day. The tops of the digesters were removed twice weekly for feeding and the digesters were stirred twice daily. The destruction of volatile matter in the dairy units was low (10-16%) but the amount of gas produced was 700 to 1000 ml/g VS destroyed. The digesters which operated on chicken manure suffered from incipient souring, the cause of which remained unexplained. Tables and graphs present figures for COD and BOD, pH, alkalinity and volatile acids concentrations, nitrogen, and gas production.
Visuospatial Function in Early Alzheimer’s Disease—The Use of the Visual Object and Space Perception (VOSP) Battery

Alzheimer’s disease (AD) is the most frequent cause of dementia. The clinical symptoms of AD begin with impairment of memory and executive function followed by the gradual involvement of other functions, such as language, semantic knowledge, abstract thinking, attention, and visuospatial abilities. Visuospatial function involves the identification of a stimulus and its location and can be impaired at the beginning of AD. The Visual Object and Space Perception (VOSP) battery evaluates visuospatial function, while minimizing the interference of other cognitive functions. Objectives To evaluate visuospatial function in early AD patients using the VOSP and determine cutoff scores to differentiate between cognitively healthy individuals and AD patients. Methods Thirty-one patients with mild AD and forty-four healthy elderly were evaluated using a neuropsychological battery and the VOSP. Results In the VOSP, the AD patients performed more poorly in all subtests examining object perception and in two subtests examining space perception (Number Location and Cube Analysis). The VOSP showed good accuracy and good correlation with tests measuring visuospatial function. Conclusion Visuospatial function is impaired in the early stages of AD. The VOSP battery is a sensitive battery test for visuospatial deficits with minimal interference by other cognitive functions.
Do distantly related parasites rely on the same proximate factors to alter the behaviour of their hosts?

Phylogenetically unrelated parasites often increase the chances of their transmission by inducing similar phenotypic changes in their hosts. However, it is not known whether these convergent strategies rely on the same biochemical precursors. In this paper, we explored such aspects by studying two gammarid species (Gammarus insensibilis and Gammarus pulex; Crustacea: Amphipoda: Gammaridae) serving as intermediate hosts in the life cycle of two distantly related parasites: the trematode, Microphallus papillorobustus and the acanthocephalan, Polymorphus minutus. Both these parasite species are known to manipulate the behaviour of their amphipod hosts, bringing them towards the water surface, where they are preferentially eaten by aquatic birds (definitive hosts). By studying and comparing the brains of infected G. insensibilis and G. pulex with proteomics tools, we have elucidated some of the proximate causes involved in the parasite-induced alterations of host behaviour for each system. Protein identifications suggest that altered physiological compartments in hosts can be similar (e.g. immunoneural connexions) or different (e.g. vision process), and hence specific to the host–parasite association considered. Moreover, proteins required to alter the same physiological compartment can be specific or conversely common in both systems, illustrating in the latter case a molecular convergence in the proximate mechanisms of manipulation.
Maximum Relationship between Contrast Agent Concentration and Signal Intensity in 0.3 T and 1.5 T using T1-weighted Spin Echo Sequence

Background and Objectives: One of the disadvantages of dental composites is polymerization shrinkage and subsequent microleakage. Since the use of a thin layer of flowable composite under composite restorations is one of the methods in improving marginal seal and microleakage reduction, the aim of the present study was to evaluate the effect of flowable composite liner on the microleakage of gingival margin of class V cavities restored with a seventh-generation (all-in-one) adhesive resin. Materials and Methods: In buccal surfaces of 30 sound human premolars (with closed apex and extracted for orthodontic reason) class V cavities were prepared and their gingival margins were located 1 mm below CEJ. The teeth were randomly divided into two groups. In group 1, the samples were restored without flowable composite liner while group 2 specimens were restored using flowable composite liner. In order to restore the teeth, in both groups all-in-one adhesive resin and Z100 composite (using incremental technique) were used. Following finishing and polishing, the samples were subjected to thermocycling. Then they were immersed in 2% basic Fushin solution for 24 hours. Following sectionings the microleakage of gingival margin of the samples was evaluated under stereomicroscope. Non-parametric Mann-Whitney U test was used to compare the gingival microleakage of two groups. Results: There were statistically significant differences in microleakage scores between two groups (P<0.0005). Conclusion: The use of flowable composite liner in composite class V cavities restored with an all-in-one adhesive resin significantly reduced the microleakage of gingival margin.
Polymorphisms in stearoyl coa desaturase and sterol regulatory element binding protein interact with N-3 polyunsaturated fatty acid intake to modify associations with anthropometric variables and metabolic phenotypes in Yup'ik people.

SCOPE n-3 polyunsaturated fatty acid (n-3 PUFA) intake is associated with protection from obesity; however, the mechanisms of protection remain poorly characterized. The stearoyl CoA desaturase (SCD), insulin-sensitive glucose transporter (SLC2A4), and sterol regulatory element binding protein (SREBF1) genes are transcriptionally regulated by n-3 PUFA intake and harbor polymorphisms associated with obesity. The present study investigated how consumption of n-3 PUFA modifies associations between SCD, SLC2A4, and SREBF1 polymorphisms and anthropometric variables and metabolic phenotypes. MATERIALS AND METHODS Anthropometric variables and metabolic phenotypes were measured in a cross-sectional sample of Yup'ik individuals (n = 1135) and 33 polymorphisms were tested for main effects and interactions using linear models that account for familial correlations. n-3 PUFA intake was estimated using red blood cell nitrogen stable isotope ratios. SCD polymorphisms were associated with ApoA1 concentration and n-3 PUFA interactions with SCD polymorphisms were associated with reduced fasting cholesterol levels and waist-to-hip ratio. SLC2A4 polymorphisms were associated with hip circumference, high-density lipoprotein and ApoA1 concentrations. SREBF1 polymorphisms were associated with low-density lipoprotein and HOMA-IR and n-3 PUFA interactions were associated with reduced fasting insulin and HOMA-IR levels. CONCLUSION The results suggest that an individual's genotype may interact with dietary n-3 PUFAs in ways that are associated with protection from obesity-related diseases in Yup'ik people.
Genetic Identification of Pelagic Shark Body Parts for Conservation and Trade Monitoring

Abstract: The conservation and management of sharks on a species‐specific basis is a pressing need because of the escalating demand for shark fins and the recognition that individual shark species respond differently to exploitation. Difficulties with the identification of many commonly fished sharks and their body parts has resulted in a global dearth of catch and trade information, making reliable assessment of exploitation effects and conservation needs for individual species nearly impossible. We developed and tested a highly streamlined molecular genetic approach based on species‐specific, polymerase‐chain‐reaction primers in an eight‐primer multiplex format to discriminate simultaneously between body parts from six shark species common in worldwide pelagic fisheries. The species‐specific primers are based on DNA sequence differences among species in the nuclear ribosomal internal transcribed spacer 2 locus. The primers and multiplex format accurately and sensitively distinguished samples from each of three lamnid ( Isurus oxyrinchus, Isurus paucus, and Lamna nasus) and three carcharhinid ( Prionace glauca, Carcharhinus obscurus, and Carcharhinus falciformis) species from all but one other shark species encountered in the North Atlantic fishery. Furthermore, the three lamnid primers were robust enough in their discriminatory power to be useful for species diagnosis on a global scale. Preliminary testing of dried fins from Asian and Mediterranean commercial markets suggests that our genetic approach will be useful for determining the species of origin of detached fins, thus allowing the monitoring of trade in shark fins for conservation assessment. Our approach will also facilitate detection of products from protected and other at‐risk shark species and may prove useful as a model for development of the high‐throughput, genetic, species‐diagnosis methods typically required in conservation and management contexts.
Photophysics of 7-mercapto-4-methylcoumarin and derivatives: complementary fluorescence behaviour to 7-hydroxycoumarins

The photophysical behaviour of 7-mercapto-4-methylcoumarin (C-SH) and derivatives has been studied in different solvents. In contrast to 7-hydroxy-4-methylcoumarin, C-SH shows poor emission, but high fluorescence when the thiol is alkylated. The origin and character of the lowest singlet states are discussed, specifically proposing that the thione-like C=S resonance form plays a key role in excited state deactivation in C-SH.