Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative phylogeography of black mangroves (Avicennia germinans) and red mangroves (Rhizophora mangle) in Florida: Testing the maritime discontinuity in coastal plants.

PREMISE OF THE STUDY Previous studies of the comparative phylogeography of coastal and marine species in the southeastern United States revealed that phylogenetically diverse taxa share a phylogeographic break at the southern tip of Florida (the maritime discontinuity). These studies have focused nearly exclusively on animals; few coastal plant species in Florida have been analyzed phylogeographically. We investigated phylogeographic patterns of black mangroves (Avicennia germinans) and red mangroves (Rhizophora mangle), two coastal trees that occur on both coasts of the peninsula of Florida. METHODS We sampled and genotyped 150 individuals each of A. germinans and R. mangle, using eight microsatellite loci per species. We used observed and expected heterozygosity to quantify genetic diversity in each sampling location and allele frequencies to identify putative phylogeographic breaks and measure gene flow using BayesAss and Migrate-n. We tested the hypothesis that both species would exhibit a phylogeographic break at the southern tip of Florida. KEY RESULTS We did not find any significant phylogeographic breaks in either species. Rhizophora mangle exhibits greater genetic structure than A. germinans, contrary to expectations based on propagule dispersal capability. However, directional gene flow from the Gulf to the Atlantic was more pronounced in R. mangle, indicating that the Gulf Stream may affect genetic patterns in R. mangle more than in A. germinans. CONCLUSIONS The high dispersal capability of these species may lead to high genetic connectivity between sampling locations and little geographic structure. We also identified several locations that, based on genetic data, should be the focus of conservation efforts.
Inhibition of RNA Polymerase II Phosphorylation by a Viral Interferon Antagonist*

Many viruses subvert the cellular interferon (IFN) system with so-called IFN antagonists. Bunyamwera virus (BUNV) belongs to the family Bunyaviridae and is transmitted by arthropods. We have recently identified the nonstructural protein NSs of BUNV as a virulence factor that inhibits IFN-β gene expression in the mammalian host. Here, we demonstrate that NSs targets the RNA polymerase II (RNAP II) complex. The C-terminal domain (CTD) of RNAP II consists of 52 repeats of the consensus sequence YSPTSPS. Phosphorylation at serine 5 is required for efficient initiation of transcription, and subsequent phosphorylation at serine 2 is required for mRNA elongation and 3′-end processing. In BUNV-infected mammalian cells, serine 5 phosphorylation occurred normally. Furthermore, RNAP II was able to bind to the IFN-β gene promoter as revealed by chromatin immunoprecipitation analysis, indicating that the initiation of transcription was not disturbed by NSs. However, NSs prevented CTD phosphorylation at serine 2, suggesting a block in transition from initiation to elongation. Surprisingly, no interference with CTD phosphorylation was observed in insect cells. Our results indicate that BUNV uses an unconventional mechanism to block IFN synthesis in the mammalian host by directly dysregulating RNAP II. Moreover, by inducing a general transcriptional block, NSs may contribute to the lytic infection observed in mammalian cells as opposed to persistent infection in the insect host.
Antioxidative effects of fluvastatin and its metabolites against oxidative DNA damage in mammalian cultured cells

We investigated the effects of fluvastatin, a 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor, on reactive oxygen species (ROS) and on oxidative DNA damage in vitro, as well as the effects of the main fluvastatin metabolites (M2, M3, and M4) and other inhibitors of the same enzyme, pravastatin and simvastatin. The hydroxyl radical and the superoxide anion scavenging activities of fluvastatin and its metabolites were evaluated using an electron spin resonance spectrometer. Fluvastatin and its metabolites showed superoxide anion scavenging activity in the hypoxanthine-xanthine oxidase system and a strong scavenging effect on the hydroxyl radical produced from Fenton's reaction. Protective effects of fluvastatin on ROS-induced DNA damage of CHL/IU cells were assessed using the single-cell gel electrophoresis assay. CHL/IU cells were exposed to either hydrogen peroxide or t-butylhydroperoxide. Fluvastatin and its metabolites showed protective effects on DNA damage as potent as the reference antioxidants, ascorbic acid, trolox, and probucol, though pravastatin and simvastatin did not exert clear protective effects. These observations suggest that fluvastatin and its metabolites may have radical scavenging activity and the potential to protect cells against oxidative DNA damage. Furthermore, ROS are thought to play a major role in the etiology of a wide variety of diseases such as cellular aging, inflammation, diabetes, and cancer development, so fluvastatin might reduce these risks.
Design and experimental validation of a windscreen patch array for C2C communications

In this paper the design and experimental validation of a 2×1 linearly polarized patch array for Car-to-Car communications is presented. The antenna operates in the 5.850-5.950 GHz frequency band and has been designed to be integrated in a car windscreen. Thanks to the presence of the glass superstrate, a valuable miniaturization effect has been obtained. On the other hand, surface waves excited into the glass superstrate reduce antenna gain, and surface wave diffraction injures radiation pattern too. In order to limit above phenomena, a square copper ring film has been printed on the same plane of the radiating elements. To compensate for the windscreen inclination respect to the ground, a proper phase shift between the currents of the two radiating elements has been considered.
Clinical studies in familial VCP myopathy associated with Paget disease of bone and frontotemporal dementia

Inclusion body myopathy with Paget disease of the bone (PDB) and/or frontotemporal dementia (IBMPFD, OMIM 167320), is a progressive autosomal dominant disorder caused by mutations in the Valousin‐containing protein (VCP, p97 or CDC48) gene. IBMPFD can be difficult to diagnose. We assembled data on a large set of families to illustrate the number and type of misdiagnoses that occurred. Clinical analysis of 49 affected individuals in nine families indicated that 42 (87%) of individuals had muscle disease. The majority were erroneously diagnosed with limb girdle muscular dystrophy (LGMD), facioscapular muscular dystrophy, peroneal muscular dystrophy, late adult onset distal myopathy, spinal muscular atrophy, scapuloperoneal muscular dystrophy, or amyotrophic lateral sclerosis (ALS) among others. Muscle biopsies showed rimmed vacuoles characteristic of an inclusion body myopathy in 7 of 18 patients (39%), however, inclusion body myopathy was correctly diagnosed among individuals in only families 5 and 15. Frontotemporal dementia (FTD) was diagnosed in 13 individuals (27%) at a mean age of 57 years (range 48.9–60.2 years); however, several individuals had been diagnosed with Alzheimer disease. Histopathological examination of brains of three affected individuals revealed a pattern of ubiquitin positive neuronal intranuclear inclusions and dystrophic neurites. These families expand the clinical phenotype in IBMPFD, a complex disorder caused by mutations in VCP. The presence of PDB in 28 (57%) individuals suggests that measuring serum alkaline phosphatase (ALP) activity may be a useful screen for IBMPFD in patients with myopathy. © 2008 Wiley‐Liss, Inc.
Permanent global amnesia with unknown etiology

Three patients developed severe and selective memory impairment with no known cause, one during a period of a few days and two others during a period of 1 to 2 years. In two of these patients, the amnesia has been stable and circumscribed for 5 to 6 years. The third patient appears to have declined in cognitive functions during the past year, at the age of 78, after 6 years of stable, circumscribed amnesia. Neuropsychological testing reveals severe impairment in the ability to learn verbal and nonverbal material as well as retrograde amnesia covering at least 20 years. CT and routine brain MRIs were uninformative. Subsequently, a high-resolution protocol for imaging human hippocampus with MR revealed that the hippocampal formation was markedly reduced in size in all three patients. The pattern of cognitive impairment and the MR findings are similar to the findings in other patients with chronic amnesia due to a known anoxic or ischemic episode, and differ from the findings in amnesic patients with alcoholic Korsakoff s syndrome. We suggest that the amnesia may be due to ischemic damage to medial temporal lobe brain structures important for memory.
Motor development in very preterm and very low-birth-weight children from birth to adolescence: a meta-analysis.

CONTEXT Infants who are very preterm (born < or = 32 weeks of gestation) and very low birth weight (VLBW) (weighing < or = 1500 g) are at risk for poor developmental outcomes. There is increasing evidence that very preterm birth and VLBW have a considerable effect on motor development, although findings are inconsistent. OBJECTIVE To investigate the relationship between very preterm birth and VLBW and motor development. DATA SOURCES The computerized databases EMBASE, PubMed, and Web of Knowledge were used to search for English-language peer-reviewed articles published between January 1992 and August 2009. STUDY SELECTION Studies were included if they reported motor scores of very preterm and VLBW children without congenital anomalies using 1 of 3 established and widely used motor tests: the Bayley Scales of Infant Development II (BSID-II), the Movement Assessment Battery for Children (MABC), and the Bruininks-Oseretsky Test of Motor Proficiency (BOTMP). Forty-one articles were identified, encompassing 9653 children. RESULTS In comparison with term-born peers, very preterm and VLBW children obtained significantly lower scores on all 3 motor tests: BSID-II: d = -0.88 (95% confidence interval [CI], -0.96 to -0.80; P < .001), MABC: d = -0.65 (95% CI, -0.70 to -0.60; P < .001), and BOTMP: d = -0.57 (95% CI, -0.68 to -0.46; P < .001). Whereas motor outcomes on the BSID-II show a catch-up effect in the first years of development (r = 0.50, P = .01), the results on the MABC demonstrate a nonsignificantly greater deficit with increasing age during elementary school and early adolescence (r = -0.59, P = .07). CONCLUSION Being born preterm or VLBW is associated with significant motor impairment persisting throughout childhood.
Dual Regulation of EDG1/S1P1 Receptor Phosphorylation and Internalization by Protein Kinase C and G-protein-coupled Receptor Kinase 2*

Here we demonstrate that phosphorylation of the sphingosine 1-phosphate (SSP) receptor “endothelial differentiation gene 1” (EDG1 or S1P1) receptor is increased in response to either SSP or phorbol 12-myristate 13-acetate (PMA) exposure but not lysophosphatidic acid. Phosphoamino acid analysis demonstrated that SSP stimulated the accumulation of phosphoserine and phosphothreonine but not phosphotyrosine. An inhibitor of PMA-stimulated EDG1 phosphorylation failed to block SSP-stimulated phosphorylation. Additionally, removal of 12 amino acids from the carboxyl terminus of EDG1 specifically reduced SSP- but not PMA-stimulated phosphorylation, suggesting that SSP and PMA increase EDG1 phosphorylation via distinct mechanisms. In vitro assays revealed that G-protein-coupled receptor kinase 2 may be at least partially responsible for SSP-stimulated EDG1 phosphorylation observed in intact cells. In addition, phosphorylation by PMA and SSP were associated with a loss of EDG1 from the cell surface by distinct mechanisms. Removal of 12 residues from the carboxyl terminus of EDG1 completely inhibited SSP-mediated internalization, suggesting that this domain dictates susceptibility to receptor internalization while retaining sensitivity to SSP-stimulated phosphorylation. Thus, we conclude that (a) EDG1 phosphorylation and internalization are controlled via independent mechanisms by agonist occupation of the receptor and protein kinase C activation, and (b) although determinants within the receptor's carboxyl-terminal tail conferring EDG1 sensitivity to agonist-mediated internalization and G-protein-coupled receptor kinase phos- phorylation exhibit a degree of overlap, the two phenomena are separable.
Comparative analysis of darknet traffic characteristics between darknet sensors

Today, Internet is incessantly attacked by wide variety of network-based threats. One of the ways to monitor or identify such prevailing threats is to monitor incoming traffic to unused network addresses popularly known as darknet and often also referred with various other names like network telescope or black hole. As, all the traffic arriving at darknet is mainly the result from malicious probing or mis configuration in the network. It is expected that to have similar incoming traffic behaviour across different darknet sensors, however, various studies found it different. Various reason cited behind it is misconfiguration, certain kind of attack, difference in filtering parameter or system configuration itself. However, concrete reason beside this is still missing. In this regard, to get further understanding, in this study, we performed deeper comparative analysis between two darknet sensors (KISTI Darknet network) that are differently located but have similar filtering and system configuration. Comparative analysis considering total incoming packet, number of source host, targeting destination port and protocol revealed that there exists wide difference in incoming traffic characteristics between the darknet sensors. Moreover, for TCP and UDP comparison, UDP traffic showed more targeting behaviour to particular darknet block (difference in traffic characteristics between darknet sensors), in contrast to it, TCP traffic showed more scanning behaviour (similarity in traffic characteristics between darknet sensor).
Vocal tract length estimation based on vowels using a database consisting of 385 speakers and a database with MRI-based vocal tract shape information

A highly-reproducible estimation method of vocal tract length (VTL) and text independent VTL estimation method are proposed based on a Japanese vowel database spoken by 385 male and female speakers ranging from age 6 to 56 and other vowel database with MRI-based vocal tract shape information. Proposed methods are based on interference-free power spectral representation and systematic suppression of biasing factors. MRI data is used to calibrate VTL estimation result to be represented in terms of physically meaningful unit. These databases are normalized based on the estimated VTL information to provide a reference template, which is used to implement a text independent VTL estimation method. A prototype system for text independent estimation of VTL is implemented using Matlab and runs faster than realtime on a PC.
Promoting absorption of drugs in humans using medium-chain fatty acid-based solid dosage forms: GIPET™

One of the most important and challenging goals in drug delivery is overcoming the poor oral absorption of high-value therapeutics that include peptides. Gastrointestinal Permeation Enhancement Technology (GIPET™) attempts to address this question by safely delivering drugs across the small intestine in therapeutically relevant concentrations. GIPET is based primarily on promoting drug absorption through the use of medium-chain fatty acids, medium-chain fatty acid derivatives and microemulsion systems based on medium-chain fatty acid glycerides formulated in enteric-coated tablets or capsules. Importantly, these excipients are generally regarded as safe and the systems are formulated in such a way that there is no change in chemical composition of the active ingredient. More than 300 volunteers have been administered GIPET formulations in 16 Phase I studies of 6 separate drugs comprising both single- and repeat-dosing regimes. Oral bioavailability of alendronate, desmopressin and low-molecular-weight heparin in humans was increased using GIPET formulations compared with unformulated controls. GIPET was well tolerated by human subjects. Using fluxes of markers of epithelial permeability, the effects of GIPET on the human intestine were shown to be rapid, short-lived and reversible in vivo. These data suggest that GIPET formulations have genuine potential as a platform technology for safe and effective oral drug delivery of a wide range of poorly permeable drugs.
Changes in injury-related hospital emergency department presentations associated with the imposition of regulatory versus voluntary licensing conditions on licensed venues in two cities.

INTRODUCTION AND AIMS Regulatory and collaborative intervention strategies have been developed to reduce the harms associated with alcohol consumption on licensed venues around the world, but there remains little research evidence regarding their comparative effectiveness. This paper describes concurrent changes in the number of night-time injury-related hospital emergency department presentations in two cities that implemented either a collaborative voluntary approach to reducing harms associated with licensed premises (Geelong) or a regulatory approach (Newcastle). DESIGN AND METHODS This paper reports findings from Dealing with Alcohol-Related problems in the Night-Time Economy project. Data were drawn from injury-specific International Classification of Disease, 10th Revision codes for injuries (S and T codes) presenting during high-alcohol risk times (midnight--5.59 am, Saturday and Sunday mornings) at the emergency departments in Geelong Hospital and Newcastle (John Hunter Hospital and the Calvary Mater Hospital), before and after the introduction of licensing conditions between the years of 2005 and 2011. Time-series, seasonal autoregressive integrated moving average analyses were conducted on the data obtained from patients' medical records. RESULTS Significant reductions in injury-related presentations during high-alcohol risk times were found for Newcastle since the imposition of regulatory licensing conditions (344 attendances per year, P < 0.001). None of the interventions deployed in Geelong (e.g. identification scanners, police operations, radio networks or closed-circuit television) were associated with reductions in emergency department presentations. DISCUSSION AND CONCLUSIONS The data suggest that mandatory interventions based on trading hours restrictions were associated with reduced emergency department injury presentations in high-alcohol hours than voluntary interventions.
An Antibody against a Novel and Conserved Epitope in the Hemagglutinin 1 Subunit Neutralizes Numerous H5N1 Influenza Viruses

ABSTRACT The spread of the recently emerged, highly pathogenic H5N1 avian influenza virus has raised concern. Preclinical studies suggest that passive immunotherapy could be a new form of treatment for H5N1 virus infection. Here, a neutralizing monoclonal antibody (MAb) against the hemagglutinin (HA) of the influenza A/chicken/Hatay/2004 H5N1 virus, MAb 9F4, was generated and characterized. MAb 9F4 binds both the denatured and native forms of HA. It was shown to recognize the HA proteins of three heterologous strains of H5N1 viruses belonging to clades 1, 2.1, and 2.2, respectively. By use of lentiviral pseudotyped particles carrying HA on the surface, MAb 9F4 was shown to effectively neutralize the homologous strain, Hatay04, and another clade 1 strain, VN04, at a neutralization titer of 8 ng/ml. Furthermore, MAb 9F4 also neutralized two clade 2 viruses at a neutralizing titer of 40 ng/ml. The broad cross-neutralizing activity of MAb 9F4 was confirmed by its ability to neutralize live H5N1 viruses of clade 2.2.2. Epitope-mapping analysis revealed that MAb 9F4 binds a previously uncharacterized epitope below the globular head of the HA1 subunit. Consistently, this epitope is well conserved among the different clades of H5N1 viruses. MAb 9F4 does not block the interaction between HA and its receptor but prevents the pH-mediated conformational change of HA. MAb 9F4 was also found to be protective, both prophylactically and therapeutically, against a lethal viral challenge of mice. Taken together, our results showed that MAb 9F4 is a neutralizing MAb that binds a novel and well-conserved epitope in the HA1 subunit of H5N1 viruses.
The C‐terminal domain of pol II and a DRB‐sensitive kinase are required for 3′ processing of U2 snRNA

The human snRNA genes transcribed by RNA polymerase II (e.g. U1 and U2) have a characteristic TATA‐less promoter containing an essential proximal sequence element. Formation of the 3′ end of these non‐polyadenylated RNAs requires a specialized 3′ box element whose function is promoter specific. Here we show that truncation of the C‐terminal domain (CTD) of RNA polymerase II and treatment of cells with CTD kinase inhibitors, including DRB (5,6‐dichloro‐1‐β‐D‐ribofuranosylbenzimidazole), causes a dramatic reduction in proper 3′ end formation of U2 transcripts. Activation of 3′ box recognition by the phosphorylated CTD would be consistent with the role of phospho‐CTD in mRNA processing. CTD kinase inhibitors, however, have little effect on initiation or elongation of transcription of the U2 genes, whereas elongation of transcription of the β‐actin gene is severely affected. This result highlights differences in transcription of snRNA and mRNA genes.
Lubrication mechanisms of hollow-core inorganic fullerene-like nanoparticles: coupling experimental and computational works

Inorganic fullerene-like (IF) nanoparticles made of metal dichalcogenides have previously been recognized to be good friction modifiers and anti-wear additives under boundary lubrication conditions. The tribological performance of these particles appears to be a result of their size, structure and morphology, along with the test conditions. However, the very small scale of the IF nanoparticles makes distinguishing the properties which affect the lubrication mechanism exceedingly difficult. In this work, a high resolution transmission electron microscope equipped with a nanoindentation holder is used to manipulate individual hollow IF-WS2 nanoparticles and to investigate their responses to compression. Additional atomistic molecular dynamics (MD) simulations of similarly structured, individual hollow IF-MoS2 nanoparticles are performed for compression studies between molybdenum surfaces on their major and minor axis diameters. MD simulations of these structures allows for characterization of the influence of structural orientation on the mechanical behavior and nano-sheet exfoliation of hollow-core IF nanoparticles. The experimental and theoretical results for these similar nanoparticles are qualitatively compared.