Exploring a text corpus via a knowledge graph

Semantic enrichment methods may be used to identify relevant entities in textual documents. These extracted entities are part of knowledge graphs and thus linked by semantic relationships. This work explores the idea of navigating the semantic relationships among extracted entities as a way to search a text corpus. A modular software system (including document management, semantic enrichment, data consolidation, and data integration) has been designed, to offer a visual user interface for such navigation on top of an arbitrary corpus of textual documents. The software, called arca, has been used in a real use case: to search in the book catalogue of a publishing house. The evaluation carried out with a set of potential users has shown so far the feasibility and effectiveness of the approach. Critical issues and potential limitations of the paradigm have also been found and are discussed

An unusual cause of gross hematuria, improved by recumbency

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Conservation implications of sea turtle nesting trends: elusive recovery of a globally important loggerhead population

Abstract Understanding population status and trends is important for developing and evaluating management and conservation actions for threatened species. Monitoring population status of marine organisms is especially challenging. Because sea turtles come ashore to lay their eggs and nests are easily counted, these counts are commonly used as an index of abundance and population trends. Nest counts do not provide a direct index of adult female population abundance because females typically lay more than one nest per year and most do not reproduce every year. This study attempts for the first time to investigate the likelihood that observed fluctuations of nest counts represent inter‐annual changes of the adult female population by accounting for uncertainty in reproductive rate parameters. We analyzed 30 yr of reproductive data from the largest nesting loggerhead sea turtle population worldwide, breeding in Florida (USA), and for the three Recovery Units and seven Management Units therein. Nest counts followed a general non‐monotonic trend with wide fluctuations that corresponded to decreasing and increasing trends during short intervals. When we accounted for uncertainty in both clutch frequency and remigration interval, there was no evidence for an increasing or a declining trend in the breeding female population across the entire period. Despite extensive conservation efforts and protections for loggerheads in Florida and the wider USA, we did not find evidence of a strong population recovery. We recommend maintaining a high level of protection, addressing persistent anthropogenic threats, continued collection of rigorous nest‐count data, and monitoring reproductive parameters to better link nest counts to adult female population abundance. Our results demonstrate the need for caution in using nest counts as a direct proxy for adult female population status, as it may lead to unsupported conclusions potentially detrimental to conservation. Therefore, we recommend to always translating nest trends to at least adult female trends, including uncertainty in reproductive parameters. Our approach can be exported to other populations, even where reproductive parameters are not available. Applying high parameter uncertainty obtained from other populations can help identifying unequivocal population changes; that is, nest trends unlikely justified by uncertainty and poor knowledge of reproductive parameters

Plant Polyphenols and Exendin-4 Prevent Hyperactivity and TNF-alpha Release in LPS-Treated In vitro Neuron/Astrocyte/Microglial Networks

Increasing evidence supports a decisive role for neuroinflammation in the neurodegenerative process of several central nervous system (CNS) disorders. Microglia are essential mediators of neuroinflammation and can regulate a broad spectrum of cellular responses by releasing reactive oxygen intermediates, nitric oxide, proteases, excitatory amino acids, and cytokines. We have recently shown that also in ex-vivo cortical networks of neurons, astrocytes and microglia, an increased level of tumor necrosis factor-alpha (TNF-α) was detected a few hours after exposure to the bacterial endotoxin lipopolysaccharide (LPS). Simultaneously, an atypical “seizure-like” neuronal network activity was recorded by multi-electrode array (MEA) electrophysiology. These effects were prevented by minocycline, an established anti-inflammatory antibiotic. We show here that the same inhibitory effect against LPS-induced neuroinflammation is exerted also by natural plant compounds, polyphenols, such as curcumin (CU, curcuma longa), crocin (CR, saffron), and resveratrol (RE, grape), as well as by the glucagon like peptide-1 receptor (GLP-1R) agonist exendin-4 (EX-4). The drugs tested also caused per-se early transient (variable) changes of network activity. Since it has been reported that LPS-induced neuroinflammation causes rearrangements of glutamate transporters in astrocytes and microglia, we suggest that neural activity could be putatively increased by an imbalance of glial glutamate transporter activity, leading to prolonged synaptic glutamatergic dysregulation

Replicating Intermittent Fasting in Human Skeletal Muscle Cells: A Pilot Study

Type 2 diabetes (T2D), the most common form of diabetes (90-95% of diagnoses), is marked by decreased insulin sensitivity (insulin resistance) or a defect in insulin secretion. T2D disrupts nutrient signaling where the body cannot maintain adequate blood glucose levels. Inability to receive glucose in skeletal muscle due to insulin resistance in T2D results in oxidative stress and increased muscle atrophy. Properly regulated glucose uptake is pivotal for healthy aging and maintenance of the skeletal muscle system. PURPOSE: The purpose of this study is to examine the effects of nutrient deprivation on human skeletal muscle metabolism, with an emphasis on oxidative stress and atrophy markers in healthy and T2D cell models. METHODS: Healthy human skeletal muscle myoblast cells (HSMM) and diabetic human skeletal muscle myoblast cells (DHSMM) (Lonza Inc, Walkersville MD) were cultured in a 37°C with 5% CO2 incubator in a T-75 flask. At confluency, cells were transferred into four 24-well plates and were incubated for 48h with standard culture media (Lonza Inc, Walkersville MD). The cells were then incubated for 12 or 24 h in media containing varying serum concentrations: 5%, 10%, and 15%. The media contained either fetal bovine serum (FBS) (Lonza Inc, Walkersville MD) or pooled human serum (HS) from either healthy or diabetic patients (Doctors Regional, Corpus Christi TX). Following the 24 hours, cell viability and density were determined, and sandwich enzyme-linked immunosorbent assay kits (RayBiotech, Norcross GA) were performed to measure the amount of superoxide dismutase (SOD1) present in each sample. RESULTS: A treatment effect was found using T2D HS which had a significant influence on mean SOD1 levels (range of SOD1 pg/mL; p=0.0423). There was no significant effect of time between 12h and 24h (p=0.1100). In the FBS models, a significant effect of concentration HSMM is seen (p=0.0263). Incubation time had little effect on FBS DHSMM (p=0.2671) and HSMM (p=0.2780) models. CONCLUSION: As serum concentration increases, the level of SOD1 present in the samples also increases. This suggests that treatment concentration may influence the activity of SOD1. This may be due to exogenous SOD1 already present in the serum. However, we did not asses the rate of appearance and decay of SOD1 already present in the serum. Incubation time shows little difference in all models. These results suggest that compositional environment can influence SOD1 levels and that a higher concentration may promote oxidative stress more so than a lower concentration environment

Prevention and modulation of aminoglycoside ototoxicity (Review)

More than 60 years after their isolation and characterization, aminoglycoside (AG) antibiotics remain powerful agents in the treatment of severe gram-negative, enterococcal or mycobacterial infections. However, the clinical use of AGs is hampered by nephrotoxicity and ototoxicity, which often develop as a consequence of prolonged courses of therapy, or of administration of increased doses of these drugs. The discovery of non-ototoxic antibacterial agents, showing a wider spectrum of activity, has gradually decreased the use of AGs as first line antibiotics for many systemic infections. However, AGs are now undergoing an unexpected revival, being increasingly indicated for the treatment of severe emerging infections caused by organisms showing resistance to most first-line agents (e.g., multidrug-resistant tuberculosis, complicated nosocomially-acquired acute urinary tract infections). Increasing adoption of aminoglycosides poses again to scientists and physicians the problem of toxicity directed to the kidneys and to the inner ear. In particular, aminoglycoside-induced deafness can be profound and irreversible, especially in genetically predisposed patients. For this reason, an impressive amount of molecular strategies have been developed in the last decade to counteract the ototoxic effect of aminoglycosides. The present article overviews: i) the molecular mechanisms by which aminoglycosides exert their bactericidal activity, ii) the mechanisms whereby AGs exert their ototoxic activity in genetically-predisposed patients, iii) the drugs and compounds that have so far proven to prevent or modulate AG ototoxicity at the preclinical and/or clinical level, and iv) the dosage regimens that have so far been suggested to decrease the incidence of episodes of AG-induced ototoxicity

Connexin-Mediated Signaling in Nonsensory Cells Is Crucial for the Development of Sensory Inner Hair Cells in the Mouse Cochlea

Mutations in the genes encoding for gap junction proteins connexin 26 (Cx26) and connexin 30 (Cx30) have been linked to syndromic and nonsyndromic hearing loss in mice and humans. The release of ATP from connexin hemichannels in cochlear nonsensory cells has been proposed to be the main trigger for action potential activity in immature sensory inner hair cells (IHCs), which is crucial for the refinement of the developing auditory circuitry. Using connexin knock-out mice, we show that IHCs fire spontaneous action potentials even in the absence of ATP-dependent intercellular Ca(2+) signaling in the nonsensory cells. However, this signaling from nonsensory cells was able to increase the intrinsic IHC firing frequency. We also found that connexin expression is key to IHC functional maturation. In Cx26 conditional knock-out mice (Cx26(Sox10-Cre)), the maturation of IHCs, which normally occurs at approximately postnatal day 12, was partially prevented. Although Cx30 has been shown not to be required for hearing in young adult mice, IHCs from Cx30 knock-out mice exhibited a comprehensive brake in their development, such that their basolateral membrane currents and synaptic machinery retain a prehearing phenotype. We propose that IHC functional differentiation into mature sensory receptors is initiated in the prehearing cochlea provided that the expression of either connexin reaches a threshold level. As such, connexins regulate one of the most crucial functional refinements in the mammalian cochlea, the disruption of which contributes to the deafness phenotype observed in mice and DFNB1 patients. SIGNIFICANCE STATEMENT: The correct development and function of the mammalian cochlea relies not only on the sensory hair cells, but also on the surrounding nonsensory cells. Although the nonsensory cells have been largely implicated in the general homeostasis in the mature cochlea, their involvement in the initial functional differentiation of the sensory inner hair cells is less clear. Using mutant mouse models for the most common form of congenital deafness in humans, which are knock-outs for the gap-junction channels connexin 26 and connexin 30 genes, we show that defects in nonsensory cells prevented the functional maturation of inner hair cells. In connexin knock-outs, inner hair cells remained stuck at a prehearing stage of development and, as such, are unable to process sound information

Nearby Optical Galaxies: Selection of the Sample and Identification of Groups

In this paper we describe the Nearby Optical Galaxy (NOG) sample, which is a complete, distance-limited ($cz\leq$6000 km/s) and magnitude-limited (B$\leq$14) sample of $\sim$7000 optical galaxies. The sample covers 2/3 (8.27 sr) of the sky ($|b|>20^{\circ}$) and appears to have a good completeness in redshift (98%). We select the sample on the basis of homogenized corrected total blue magnitudes in order to minimize systematic effects in galaxy sampling. We identify the groups in this sample by means of both the hierarchical and the percolation {\it friends of friends} methods. The resulting catalogs of loose groups appear to be similar and are among the largest catalogs of groups presently available. Most of the NOG galaxies ($\sim$60%) are found to be members of galaxy pairs ($\sim$580 pairs for a total of $\sim$15% of objects) or groups with at least three members ($\sim$500 groups for a total of $\sim$45% of objects). About 40% of galaxies are left ungrouped (field galaxies). We illustrate the main features of the NOG galaxy distribution. Compared to previous optical and IRAS galaxy samples, the NOG provides a denser sampling of the galaxy distribution in the nearby universe. Given its large sky coverage, the identification of groups, and its high-density sampling, the NOG is suited for the analysis of the galaxy density field of the nearby universe, especially on small scales.Comment: 47 pages including 6 figures. Accepted for publication in Ap

Enzymatic scarification of Anacamptis morio (Orchidaceae) seed facilitates lignin degradation, water uptake and germination

The seed coat of many species contains hydrophobic lignins, and in soil the action of microbial ligninases may contribute to release from dormancy. Laboratory use of ligninases to stimulate germination is promising because of the specific action on the seed coat, whereas chemical scarification agents may also corrode the embryo. We hypothesised that exposure of Anacamptis morio (Orchidaceae) seeds to fungal laccase would stimulate germination, and that the mechanism involves lignin degradation and increased imbibition. Germination capacity in vitro was quantified with 1 U filter-sterilised laccase added to agar medium following autoclaving, compared to a 10% bleach solution (standard bleach surface sterilisation/scarification method used in orchid seed sowing). Lignin degradation was quantified using an optical method (phloroglucinol-HCl staining) combined with image analysis, following experimental pre-treatments involving immersion in laccase solution, distilled water (negative control) or bleach (positive control). Water uptake after experimental treatments was quantified as the proportion of seeds exhibiting visible uptake of an aqueous fluorochrome under UV excitation. Laccase stimulated a doubling of germination in vitro with respect to bleach surface sterilisation/scarification alone, from 23.7 to 49.8% (P = 0.007). Laccase and bleach methods both significantly decreased the optical signal of phloroglucinol (for laccase, to 79.9 ± 1.3% of controls; anova: F = 10.333, P = 0.002). Laccase resulted in a modest but highly significant (P < 0.0001) increase in water uptake with respect to the control (11.7%; cf 99.4% for bleach). Laccase scarification can stimulate germination of A. morio through a mechanism of targeted seed coat degradation. The results demonstrate the potential of this relatively non-invasive enzymatic scarification technique