Miracle-dz/UniFAR-FTUs huggingface dataset:
ASI Regulates Satiety Quiescence in C. elegans

In Caenorhabditis elegans, satiety quiescence mimics behavioral aspects of satiety and postprandial sleep in mammals. On the basis of calcium-imaging, genetics, and behavioral studies, here we report that a pair of amphid neurons, ASI, is activated by nutrition and regulates worms' behavioral states specifically promoting satiety quiescence; ASI inhibits the switch from quiescence to dwelling (a browsing state) and accelerates the switch from dwelling to quiescence. The canonical TGFβ pathway, whose ligand is released from ASI, regulates satiety quiescence. The mutants of a ligand, a receptor and SMADs in the TGFβ pathway all eat more and show less quiescence than wild-type. The TGFβ receptor in downstream neurons RIM and RIC is sufficient for worms to exhibit satiety quiescence, suggesting neuronal connection from ASI to RIM and RIC is essential for feeding regulation through the TGFβ pathway. ASI also regulates satiety quiescence partly through cGMP signaling; restoring cGMP signaling in ASI rescues the satiety quiescence defect of cGMP signaling mutants. From these results, we propose that TGFβ and cGMP pathways in ASI connect nutritional status to promotion of satiety quiescence, a sleep-like behavioral state.
Metamemory in Schizophrenia: An Exploration of the Feeling-of-Knowing State

The ability to monitor memory performance has considerable importance in everyday life and is among the proposed metamemory dimensions which has been widely investigated. The ability to monitor memory performance accurately was examined in 16 patients with schizophrenia and 16 control subjects by using a Feeling-of-Knowing task on episodic information. Feeling-of-Knowing judgments are predictions made about the likelihood of subsequent recognition of currently non-recallable information. Participants were given cued recall and recognition tests of 50 sentence-target words. Feeling-of-knowing judgments were made for non-recalled targets. Our results first confirm that schizophrenia is associated with episodic memory impairment. By using the Feeling-of-Knowing task, patients with schizophrenia were found to predict accurately their subsequent recognition performance, suggesting an interesting dissociation between a preserved metamemory and an altered memory. This work was supported by INSERM (Institut National de la Santé et de la Recherche Médicale).
Evaluation of Senior Dental Students' General Attitude towards the Use of Rubber Dam: A Survey among Two Dental Schools

The purpose of this study was to evaluate the general attitude of senior dental students towards rubber dam use, specifically focusing on endodontic practices prior to starting to serve community. Questionnaires were distributed to senior year students of a private school and a state school in Istanbul. Questions were asked about areas where the students used rubber dam, its advantages and difficulties, and whether they agreed or disagreed with some aspects of the rubber dam. The private school students rated isolation whereas those of the state school selected prevention of aspiration which the top advantage rubber dam provides. Students of the state school agreed with the opinion that isolation cannot be achieved without rubber dam and it extended the procedure with a significantly higher ratio compared to the private school. Within the limitations of the present study, it can be concluded that the perceptions of dental students on rubber dam needs to be improved and strategies should be developed so that this valuable adjunct will comprise one of the indispensable elements of dental care.
Association of Lifestyle-Related Comorbidities With Periodontitis

Abstract The aim of this study was to determine the association of periodontitis with lifestyle-related comorbidities (LCs) using data in the Korean National Health Insurance Cohort Database from 2002 to 2013. This was a retrospective study involving a large national cohort with patient samples (representing 2% of the total Korean population) stratified on the basis of sociodemographic information. Using this precisely extracted database, the correlations between LCs (cerebral infarction, angina pectoris, myocardial infarction, hypertension, diabetes mellitus, rheumatoid arthritis, erectile dysfunction, osteoporosis, and obesity) and periodontitis were investigated while adjusting for confounding bias. Univariate and multiple logistic regression analyses were used to evaluate differences in variable factors. Among a total of 1,025,340 samples, 321,103 (31.3%) cases were diagnosed with periodontitis. Statistically significant associations were found between all LCs except myocardial infarction and periodontitis (P < 0.005). Periodontitis is significantly and positively correlated with LCs (except for myocardial infarction) after adjusting for confounding bias. In particular, lifestyle-related diseases, erectile dysfunction, and osteoporosis seem to be intimately related to periodontitis.
The effect of nutritionally induced hyperlipidaemia on in vitro bovine embryo quality.

BACKGROUND Obesity is associated with female reproductive abnormalities. Hyperlipidaemia might alter the embryonic micro-environment and potentially result in reduced fertility. We aimed to induce hyperlipidaemia nutritionally and investigate the consequences of hyperlipidaemic culture conditions on bovine in vitro embryo development, embryo quality and gene expression patterns. METHODS Bovine zygotes (n = 1545) were cultured in synthetic oviductal fluid medium supplemented with serum from heifers (n = 3), each fed three successive dietary treatments: (i) control serum, following a hay-based diet, (ii) hyperlipidaemic serum, following a carbohydrate and protected palm-oil-rich diet (FatCh) or (iii) hyperlipidaemic serum, following a protected palm-oil-rich diet (Fat). Blastocysts were evaluated for development, cell count, picnotic and mitotic indexes and cryotolerance. Selected mRNA transcripts were measured by quantitative RT-PCR. RESULTS FatCh and Fat diets approximately doubled the total cholesterol concentrations, compared with controls (167.1 +/- 11.9, 150.0 +/- 12.8 versus 83.4 +/- 13.7 mg/dl, respectively, P < 0.05), and fatty acid concentrations (8146.60 +/- 214.61, 6935.56 +/- 1081.04 versus 3944.0 +/- 425.07 micromol/l, respectively, P < 0.05). Supplementation of culture media with FatCh and Fat serum significantly reduced blastocyst rates, compared with controls (27.8, 23.4% versus 36.2%, respectively, P < 0.01), total cell number (103.3 +/- 30.1, 95.6 +/- 28.2 versus 146.9 +/- 34.2, respectively, P < 0.01), mitotic index (1.3 +/- 1.1, 1.7 +/- 2.4 versus 3.6 +/- 2.2%, respectively, P < 0.01) and hatching rates after vitrification (20.4, 13.8 versus 35.7%, respectively, P = 0.03). Embryos in FatCh and Fat groups exhibited significantly higher mRNA levels for genes related to apoptosis and metabolism, compared with controls. CONCLUSIONS This combined in vivo and in vitro model indicates that the exposure of preimplantation embryos to hyperlipidaemic conditions may result in reduced embryo quality and developmental potential, possibly resulting in poorer fertility.
Transition Metal Transport in Plants and Associated Endosymbionts: Arbuscular Mycorrhizal Fungi and Rhizobia

Transition metals such as iron, copper, zinc, or molybdenum are essential nutrients for plants. These elements are involved in almost every biological process, including photosynthesis, tolerance to biotic and abiotic stress, or symbiotic nitrogen fixation. However, plants often grow in soils with limiting metallic oligonutrient bioavailability. Consequently, to ensure the proper metal levels, plants have developed a complex metal uptake and distribution system, that not only involves the plant itself, but also its associated microorganisms. These microorganisms can simply increase metal solubility in soils and making them more accessible to the host plant, as well as induce the plant metal deficiency response, or directly deliver transition elements to cortical cells. Other, instead of providing metals, can act as metal sinks, such as endosymbiotic rhizobia in legume nodules that requires relatively large amounts to carry out nitrogen fixation. In this review, we propose to do an overview of metal transport mechanisms in the plant–microbe system, emphasizing the role of arbuscular mycorrhizal fungi and endosymbiotic rhizobia.
Noise temperature estimates for a next generation very large microwave array [HEMT LNAs]

This paper estimates the noise temperature as a function of frequency for amplifiers covering the 1 to 10 GHz range utilizing state-of-the-art HEMT transistors operating at temperatures of 300 K, 80 K, and 20 K. The analysis includes the effect of loss and bandwidth of the input matching network.
The Effect of Humic Acid on the Phytoremediation Efficiency of Pb in the Contaminated Soils by Wormwood Plant (Artemicia absantium)

Because of the undesirable effects of lead on soil properties and human health, evaluation of its remediation methods seems to be essential. In order to evaluate the effect of humic acid (HA) on the decontamination of lead (Pb) spikedsoils in the presence of wormwood plant (Artemicia absantium), an experiment was carried out in a completely randomized block design with three replications. Experiment factors including different concentrations of Pb (Pb(NO3)2 in the solid form) (0, 250, 500 and 1000 mg kg) and levels of HA (0, 100 and 200 mg kg) were considered. At the end of the growing period of plants, some soil and plant properties were measured. According to the results, BR, MBC, root and shoot dry weights, RWC and Fe and Zn concentrations in the shoot were decreased by increasing the soil Pb concentration. So, the mean values of BR and MBC in Pb1000 treatment was 60 and 51.1 percent lower than those of Pb0, respectively. Pb accumulation in the root and shoot was enhanced as a result of the increase in the soil Pb concentration. The maximum Pb concentration of shoot (37.10 mg kg) and root (38.1 mg kg) was seen in the Pb1000 treatment. Also, the results suggested that humic acid had a positive effect on the shoot of Fe, Zn and Pb concentrations. So, the concentration of these elements in HA200 treatment showed an increase 1.25, 1.64 and 1.66 times more than that of HA0, respectively. Leaf proline amount was increased significantly by elevating the soil Pb concentration; however, application of 200 mg kg humic acid decreased leaf proline by 54.5 percent, as compared to the control (HA0). Therefore, humic acid effect on increasing the plant Pb uptake, improving soil biological properties, and increasing availability and dissolution of Pb showed its ability in promoting the phytoremediation efficiency. According to the obtained results of this study, woodwarm plant (Artemicia absantium) is a non-accumulator that could not be used for phytoremediation purposes.
Genome-wide hepatic DNA methylation changes in high-fat diet-induced obese mice

BACKGROUND/OBJECTIVES A high-fat diet (HFD) induces obesity, which is a major risk factor for cardiovascular disease and cancer, while a calorie-restricted diet can extend life span by reducing the risk of these diseases. It is known that health effects of diet are partially conveyed through epigenetic mechanism including DNA methylation. In this study, we investigated the genome-wide hepatic DNA methylation to identify the epigenetic effects of HFD-induced obesity. MATERIALS AND METHODS Seven-week-old male C57BL/6 mice were fed control diet (CD), calorie-restricted control diet (CRCD), or HFD for 16 weeks (after one week of acclimation to the control diet). Food intake, body weight, and liver weight were measured. Hepatic triacylglycerol and cholesterol levels were determined using enzymatic colorimetric methods. Changes in genome-wide DNA methylation were determined by a DNA methylation microarray method combined with methylated DNA immunoprecipitation. The level of transcription of individual genes was measured by real-time PCR. RESULTS The DNA methylation statuses of genes in biological networks related to lipid metabolism and hepatic steatosis were influenced by HFD-induced obesity. In HFD group, a proinflammatory Casp1 (Caspase 1) gene had hypomethylated CpG sites at the 1.5-kb upstream region of its transcription start site (TSS), and its mRNA level was higher compared with that in CD group. Additionally, an energy metabolism-associated gene Ndufb9 (NADH dehydrogenase 1 beta subcomplex 9) in HFD group had hypermethylated CpG sites at the 2.6-kb downstream region of its TSS, and its mRNA level was lower compared with that in CRCD group. CONCLUSIONS HFD alters DNA methylation profiles in genes associated with liver lipid metabolism and hepatic steatosis. The methylation statuses of Casp1 and Ndufb9 were particularly influenced by the HFD. The expression of these genes in HFD differed significantly compared with CD and CRCD, respectively, suggesting that the expressions of Casp1 and Ndufb9 in liver were regulated by their methylation statuses.
Strathprints Institutional Repository Map Kinase Phosphatase-2 Plays a Critical Role in Response to Infection by Leishmania Mexicana

(2010) MAP kinase phosphatase-2 plays a critical role in response to infection by Leishmania mexicana. Strathprints is designed to allow users to access the research output of the University of Strathclyde. Unless otherwise explicitly stated on the manuscript, Copyright © and Moral Rights for the papers on this site are retained by the individual authors and/or other copyright owners. Please check the manuscript for details of any other licences that may have been applied. You may not engage in further distribution of the material for any profitmaking activities or any commercial gain. You may freely distribute both the url (http://strathprints.strath.ac.uk/) and the content of this paper for research or private study, educational, or not-for-profit purposes without prior permission or charge. Abstract In this study we generated a novel dual specific phosphatase 4 (DUSP4) deletion mouse using a targeted deletion strategy in order to examine the role of MAP kinase phosphatase-2 (MKP-2) in immune responses. Lipopolysaccharide (LPS) induced a rapid, time and concentration-dependent increase in MKP-2 protein expression in bone marrow-derived macrophages from MKP-2 +/+ but not from MKP-2-/-mice. LPS-induced JNK and p38 MAP kinase phosphorylation was significantly increased and prolonged in MKP-2-/-macrophages whilst ERK phosphorylation was unaffected. MKP-2 deletion also potentiated LPS-stimulated induction of the inflammatory cytokines, IL-6, IL-12p40, TNF-α and also COX-2 derived PGE 2 production. However surprisingly, in MKP-2-/-macrophages, there was a marked reduction in LPS or IFN-γ-induced iNOS and nitric oxide release and enhanced basal expression of arginase-1 suggesting that MKP-2 may have an additional regulatory function significant in pathogen-mediated immunity. Indeed, following infection with the intracellular parasite Leishmania mexicana, MKP-2-/-mice displayed increased lesion size and parasite burden, and a significantly modified Th1/Th2 bias compared with wild-type counterparts. However, there was no intrinsic defect in MKP-2-/-T cell function as measured by anti-CD3 induced IFN-γ production. Rather, MKP-2-/-bone marrow-derived macrophages were found to be inherently more susceptible to infection with Leishmania mexicana, an effect reversed following treatment with the arginase inhibitor nor-NOHA. These findings show for the first time a role for MKP-2 in vivo and demonstrate that MKP-2 may be essential in orchestrating protection against intracellular infection at the level of the macrophage. 3 Author Summary In cells of the immune system are switch-on enzymes called kinases which regulate responses to infectious agents such as Leishmania. However, in the same cells there are switch-off enzymes known as phosphatases which function to turn off the kinases once they …
Synthesis of Breathy, Normal, and Pressed Phonation Using a Two-Mass Model with a Triangular Glottis

Two-mass models of the vocal folds and their variants are valuable tools for voice synthesis and analysis, but are not able to produce breathy voice qualities. The produced voice qualities usually lie between normal and pressed. The reason for this property is that the mass elements are aligned parallel to the dorso-ventral axis. Thereby, the glottis always closes simultaneously along the entire length of the vocal folds. For breathy phonation, however, the closure happens rather gradual. This article introduces a modified two-mass model with mass elements that are inclined with respect to the dorso-ventral axis as a function of the degree of abduction. In this way, the closing phase of the glottis becomes progressively more gradual when the degree of abduction is increased. This model is able to produce the continuum of voice qualities from pressed over normal to breathy voices.
New Algorithm and Software (BNOmics) for Inferring and Visualizing Bayesian Networks from Heterogeneous Big Biological and Genetic Data

Abstract Bayesian network (BN) reconstruction is a prototypical systems biology data analysis approach that has been successfully used to reverse engineer and model networks reflecting different layers of biological organization (ranging from genetic to epigenetic to cellular pathway to metabolomic). It is especially relevant in the context of modern (ongoing and prospective) studies that generate heterogeneous high-throughput omics datasets. However, there are both theoretical and practical obstacles to the seamless application of BN modeling to such big data, including computational inefficiency of optimal BN structure search algorithms, ambiguity in data discretization, mixing data types, imputation and validation, and, in general, limited scalability in both reconstruction and visualization of BNs. To overcome these and other obstacles, we present BNOmics, an improved algorithm and software toolkit for inferring and analyzing BNs from omics datasets. BNOmics aims at comprehensive systems biology—type data exploration, including both generating new biological hypothesis and testing and validating the existing ones. Novel aspects of the algorithm center around increasing scalability and applicability to varying data types (with different explicit and implicit distributional assumptions) within the same analysis framework. An output and visualization interface to widely available graph-rendering software is also included. Three diverse applications are detailed. BNOmics was originally developed in the context of genetic epidemiology data and is being continuously optimized to keep pace with the ever-increasing inflow of available large-scale omics datasets. As such, the software scalability and usability on the less than exotic computer hardware are a priority, as well as the applicability of the algorithm and software to the heterogeneous datasets containing many data types—single-nucleotide polymorphisms and other genetic/epigenetic/transcriptome variables, metabolite levels, epidemiological variables, endpoints, and phenotypes, etc.
Sleep Disorders in a Sample of Adopted Children: A Pilot Study

Sleep disorders occur in up to 25% of children and are more prevalent in children who have attention problems and attachment issues. Research shows that foster children display sleep problems, but limited knowledge exists on sleep problems in adopted children. This pilot study aimed to identify the types of sleep disorders in adopted children and associated psychosocial factors. Parents of adopted children in Ontario, Canada, ages 2–10 years were asked to complete questionnaires evaluating demographic measures, sleep history, and the presence of behavioral problems. Insomnias and parasomnias were reported in adopted children and were associated with attention problems. This pilot study emphasizes the need for further research on the underlying factors governing the relationship between poor sleep and behavioral problems in adopted children.
Phosphorylation dynamics of membrane proteins from Arabidopsis roots submitted to salt stress

An excess of NaCl in the soil is detrimental for plant growth. It interferes with mineral nutrition and water uptake and leads to accumulation of toxic ions in the plant. Understanding the response of roots to NaCl stress may facilitate the development of crops with increased tolerance to this and other stresses. Since controls achieved at the posttranslational level are of critical importance for regulating protein function, the present work used a robust label‐free quantitative proteomic methodology to quantify phosphorylation events that affect root membrane proteins in Arabidopsis, in response to short‐term (up to 2 h) NaCl treatments. This work identified 302 proteotypic phosphopeptides including 77 novel phosphorylated sites. NaCl treatment significantly altered the abundance of 74 phosphopeptides, giving novel insights into the regulation of major classes of membrane proteins, including ATPases, sodium transporters, and aquaporins. The data provide a unique access to phosphorylation reprogramming of ionic equilibrium in plant cells under NaCl stress. The use of predictive bioinformatic tools for kinase motifs suggested that root membrane proteins are substrates of cAMP‐dependent protein kinase, cGMP‐dependent protein kinase, and protein kinase C families, also called AGC kinases, arguing for an important role of lipid signaling in abiotic stress responses. It also pointed to cross‐talks between protein kinase families during NaCl stress.
The Importance of Dosimetry Standardization in Radiobiology

Radiation dose is central to much of radiobiological research. Precision and accuracy of dose measurements and reporting of the measurement details should be sufficient to allow the work to be interpreted and repeated and to allow valid comparisons to be made, both in the same laboratory and by other laboratories. Despite this, a careful reading of published manuscripts suggests that measurement and reporting of radiation dosimetry and setup for radiobiology research is frequently inadequate, thus undermining the reliability and reproducibility of the findings. To address these problems and propose a course of action, the National Cancer Institute (NCI), the National Institute of Allergy and Infectious Diseases (NIAID), and the National Institute of Standards and Technology (NIST) brought together representatives of the radiobiology and radiation physics communities in a workshop in September, 2011. The workshop participants arrived at a number of specific recommendations as enumerated in this paper and they expressed the desirability of creating dosimetry standard operating procedures (SOPs) for cell culture and for small and large animal experiments. It was also felt that these SOPs would be most useful if they are made widely available through mechanism(s) such as the web, where they can provide guidance to both radiobiologists and radiation physicists, be cited in publications, and be updated as the field and needs evolve. Other broad areas covered were the need for continuing education through tutorials at national conferences, and for journals to establish standards for reporting dosimetry. This workshop did not address issues of dosimetry for studies involving radiation focused at the sub-cellular level, internally-administered radionuclides, biodosimetry based on biological markers of radiation exposure, or dose reconstruction for epidemiological studies.