Recombination in West Nile Virus: minimal contribution to genomic diversity

Recombination is known to play a role in the ability of various viruses to acquire sequence diversity. We consequently examined all available West Nile virus (WNV) whole genome sequences both phylogenetically and with a variety of computational recombination detection algorithms. We found that the number of distinct lineages present on a phylogenetic tree reconstruction to be identical to the 6 previously reported. Statistically-significant evidence for recombination was only observed in one whole genome sequence. This recombination event was within the NS5 polymerase coding region. All three viruses contributing to the recombination event were originally isolated in Africa at various times, with the major parent (SPU116_89_B), minor parent (KN3829), and recombinant sequence (AnMg798) belonging to WNV taxonomic lineages 2, 1a, and 2 respectively. This one isolated recombinant genome was out of a total of 154 sequences analyzed. It therefore does not seem likely that recombination contributes in any significant manner to the overall sequence variation within the WNV genome

Serum IGF-1 Affects Skeletal Acquisition in a Temporal and Compartment-Specific Manner

Insulin-like growth factor-1 (IGF-1) plays a critical role in the development of the growing skeleton by establishing both longitudinal and transverse bone accrual. IGF-1 has also been implicated in the maintenance of bone mass during late adulthood and aging, as decreases in serum IGF-1 levels appear to correlate with decreases in bone mineral density (BMD). Although informative, mouse models to date have been unable to separate the temporal effects of IGF-1 depletion on skeletal development. To address this problem, we performed a skeletal characterization of the inducible LID mouse (iLID), in which serum IGF-1 levels are depleted at selected ages. We found that depletion of serum IGF-1 in male iLID mice prior to adulthood (4 weeks) decreased trabecular bone architecture and significantly reduced transverse cortical bone properties (Ct.Ar, Ct.Th) by 16 weeks (adulthood). Likewise, depletion of serum IGF-1 in iLID males at 8 weeks of age, resulted in significantly reduced transverse cortical bone properties (Ct.Ar, Ct.Th) by 32 weeks (late adulthood), but had no effect on trabecular bone architecture. In contrast, depletion of serum IGF-1 after peak bone acquisition (at 16 weeks) resulted in enhancement of trabecular bone architecture, but no significant changes in cortical bone properties by 32 weeks as compared to controls. These results indicate that while serum IGF-1 is essential for bone accrual during the postnatal growth phase, depletion of IGF-1 after peak bone acquisition (16 weeks) is compartment-specific and does not have a detrimental effect on cortical bone mass in the older adult mouse

Permanent 125I-seed prostate brachytherapy: early prostate specific antigen value as a predictor of PSA bounce occurrence

<p>Abstract</p> <p>Purpose</p> <p>To evaluate predictive factors for PSA bounce after ¹²⁵I permanent seed prostate brachytherapy and identify criteria that distinguish between benign bounces and biochemical relapses.</p> <p>Materials and methods</p> <p>Men treated with exclusive permanent ¹²⁵I seed brachytherapy from November 1999, with at least a 36 months follow-up were included. Bounce was defined as an increase ≥ 0.2 ng/ml above the nadir, followed by a spontaneous return to the nadir. Biochemical failure (BF) was defined using the criteria of the Phoenix conference: nadir +2 ng/ml.</p> <p>Results</p> <p>198 men were included. After a median follow-up of 63.9 months, 21 patients experienced a BF, and 35.9% had at least one bounce which occurred after a median period of 17 months after implantation (4-50). Bounce amplitude was 0.6 ng/ml (0.2-5.1), and duration was 13.6 months (4.0-44.9). In 12.5%, bounce magnitude exceeded the threshold defining BF. Age at the time of treatment and high PSA level assessed at 6 weeks were significantly correlated with bounce but not with BF. Bounce patients had a higher BF free survival than the others (100% versus 92%, p = 0,007). In case of PSA increase, PSA doubling time and velocity were not significantly different between bounce and BF patients. Bounces occurred significantly earlier than relapses and than nadir + 0.2 ng/ml in BF patients (17 vs 27.8 months, p < 0.0001).</p> <p>Conclusion</p> <p>High PSA value assessed 6 weeks after brachytherapy and young age were significantly associated to a higher risk of bounces but not to BF. Long delays between brachytherapy and PSA increase are more indicative of BF.</p

Protocol for Nearly Full-Length Sequencing of HIV-1 RNA from Plasma

Nearly full-length genome sequencing of HIV-1 using peripheral blood mononuclear cells (PBMC) DNA as a template for PCR is now a relatively routine laboratory procedure. However, this has not been the case when using virion RNA as the template and this has made full genome analysis of circulating viruses difficult. Therefore, a well-developed procedure for sequencing of full-length HIV-1 RNA directly from plasma was needed. Plasma from U.S. donors representing a range of viral loads (VL) was used to develop the assay. RNA was extracted from plasma and reverse-transcribed. Two or three overlapping regions were PCR amplified to cover the entire viral genome and sequenced for verification. The success of the procedure was sensitive to VL but was routinely successful for VL greater than 105 and the rate declined in proportion to the VL. While the two-amplicon strategy had an advantage of increasing the possibility of amplifying a single species of HIV-1, the three-amplicon strategy was more successful in amplifying samples with low viral loads. This protocol provides a useful tool for molecular analysis to understand the HIV epidemic and pathogenesis, as well as diagnosis, therapy and future vaccine strategies

Anticancer activity of an extract from needles and twigs of Taxus cuspidata and its synergistic effect as a cocktail with 5-fluorouracil

<p>Abstract</p> <p>Background</p> <p>Botanical medicines are increasingly combined with chemotherapeutics as anticancer drug cocktails. This study aimed to assess the chemotherapeutic potential of an extract of <it>Taxus cuspidata </it>(<it>TC</it>) needles and twigs produced by artificial cuttage and its co-effects as a cocktail with 5-fluorouracil (5-FU).</p> <p>Methods</p> <p>Components of <it>TC </it>extract were identified by HPLC fingerprinting. Cytotoxicity analysis was performed by MTT assay or ATP assay. Apoptosis studies were analyzed by H & E, PI, TUNEL staining, as well as Annexin V/PI assay. Cell cycle analysis was performed by flow cytometry. 5-FU concentrations in rat plasma were determined by HPLC and the pharmacokinetic parameters were estimated using 3p87 software. Synergistic efficacy was subjected to median effect analysis with the mutually nonexclusive model using Calcusyn1 software. The significance of differences between values was estimated by using a one-way ANOVA.</p> <p>Results</p> <p><it>TC </it>extract reached inhibition rates of 70-90% in different human cancer cell lines (HL-60, BGC-823, KB, Bel-7402, and HeLa) but only 5-7% in normal mouse T/B lymphocytes, demonstrating the broad-spectrum anticancer activity and low toxicity to normal cells of <it>TC </it>extract <it>in vitro</it>. <it>TC </it>extract inhibited cancer cell growth by inducing apoptosis and G₂/M cell cycle arrest. Most interestingly, <it>TC </it>extract and 5-FU, combined as a cocktail, synergistically inhibited the growth of cancer cells <it>in vitro</it>, with Combination Index values (CI) ranging from 0.90 to 0.26 at different effect levels from IC50 to IC90 in MCF-7 cells, CI ranging from 0.93 to 0.13 for IC40 to IC90 in PC-3M-1E8 cells, and CI < 1 in A549 cells. In addition, the cocktail had lower cytotoxicity in normal human cell (HEL) than 5-FU used alone. Furthermore, <it>TC </it>extract did not affect the pharmacokinetics of 5-FU in rats.</p> <p>Conclusions</p> <p>The combinational use of the <it>TC </it>extract with 5-FU displays strong cytotoxic synergy in cancer cells and low cytotoxicity in normal cells. These findings suggest that this cocktail may have a potential role in cancer treatment.</p

A ROC analysis-based classification method for landslide susceptibility maps

[EN] A landslide susceptibility map is a crucial tool for landuse spatial planning and management in mountainous areas. An essential issue in such maps is the determination of susceptibility thresholds. To this end, the map is zoned into a limited number of classes. Adopting one classification system or another will not only affect the map's readability and final appearance, but most importantly, it may affect the decision-making tasks required for effective land management. The present study compares and evaluates the reliability of some of the most commonly used classification methods, applied to a susceptibility map produced for the area of La Marina (Alicante, Spain). A new classification method based on ROC analysis is proposed, which extracts all the useful information from the initial dataset (terrain characteristics and landslide inventory) and includes, for the first time, the concept of misclassification costs. This process yields a more objective differentiation of susceptibility levels that relies less on the intrinsic structure of the terrain characteristics. The results reveal a considerable difference between the classification methods used to define the most susceptible zones (in over 20% of the surface) and highlight the need to establish a standard method for producing classified susceptibility maps. The method proposed in the study is particularly notable for its consistency, stability and homogeneity, and may mark the starting point for consensus on a generalisable classification method.Cantarino-Martí, I.; Carrión Carmona, MÁ.; Goerlich-Gisbert, F.; Martínez Ibáñez, V. (2018). A ROC analysis-based classification method for landslide susceptibility maps. Landslides. 1-18. doi:10.1007/s10346-018-1063-4S118Armstrong MP, Xiao N, Bennett DA (2003) Using genetic algorithms to create multicriteria class intervals for choropleth maps. Ann Assoc Am Geogr 93(3):595–623. https://doi.org/10.1111/1467-8306.9303005Atkinson P, Massari R (1998) Generalised linear modelling of susceptibility to landsliding in the central Apennines, Italy. Comput Geosci 24(4):373–385. https://doi.org/10.1016/S0098-3004(97)00117-9Ayalew L, Yamagishi H (2005) The application of GIS-based logistic regression for landslide susceptibility mapping in the Kakuda-Yahiko Mountains, Central Japan. Geomorphology 65(1–2):15–31. https://doi.org/10.1016/j.geomorph.2004.06.010Baeza C, Lantada N, Amorim S (2016) Statistical and spatial analysis of landslide susceptibility maps with different classification systems. Environ Earth Science 75:1318. https://doi.org/10.1007/s12665-016-6124-1Basofi A, Fariza A, Ahsan AS, Kamal IM (2015) A comparison between natural and head/tail breaks in LSI (landslide susceptibility index) classification for landslide susceptibility mapping: a case study in Ponorogo, East Java, Indonesia. 2015 International Conference on Science in Information Technology, pp 337–342Cantarino I (2013) Elaboración y validación de un modelo jerárquico derivado de SIOSE. Revista de Teledetección 39:5–21Carrara A, Crosta GB, Frattini P (2008) Comparing models of debris-flow susceptibility in the alpine environment. Geomorphology 94(3–4):353–378. https://doi.org/10.1016/j.geomorph.2006.10.033Chacón J, Irigaray C, Fernández T, El Hamdouni R (2006) Engineering geology maps: landslides and geographical information systems. Bull Eng Geol Environ 65(4):341–411Chung CJF, Fabbri AG (2003) Validation of spatial prediction models for landslide hazard mapping. Nat Hazards 30:451–472COPUT (1998) Lithology, exploitation of industrial rocks and landslide risk in the Valencian Community. Thematic Mapping Series. Department of Public Works of the Valencian Regional GovernmentDrummond C, Holte RC (2006) Cost curves: an improved method for visualizing classifier performance. Mach Learn 65(1):95–130Duman TY, Can T, Gokceoglu C, Nefeslioglu HA, Sonmez H (2006) Application of logistic regression for landslide susceptibility zoning of Cekmece Area, Istanbul, Turkey. Environ Geol 51(2):241–256. https://doi.org/10.1007/s00254-006-0322-1Evans IS (1977) The selection of class intervals. Transactions of the Institute of British Geographers. Contemp Cartograph 2(1):98–124. https://doi.org/10.2307/622195Fleiss JL, Levin B, Paik MC (2003) Statistical methods for rates and proportions, Book Series: Wiley Series in Probability and Statistics. John Wiley & Sons. Print ISBN: 9780471526292. doi: https://doi.org/10.1002/0471445428Foody GM (2004) Thematic map comparison: evaluating the statistical significance of differences in classification accuracy. Photogramm Eng Remote Sens 70(5):627–633Fotheringham AS, Brunsdon C, Charlton M (2000) Quantitative geography: perspectives on spatial data analysis. SAGE Publications, Thousand Oaks 270 ppFrattini P, Crosta G, Carrara A (2010) Techniques for evaluating the performance of landslide susceptibility models. Eng Geol 111(1–4):62–72. https://doi.org/10.1016/j.enggeo.2009.12.004Geisser S (1998) Comparing two tests used for diagnostic or screening processes. Stat Probability Lett 40:113–119Greiner M, Pfeiffer D, Smith RD (2000) Principles and practical application of the receiver-operating characteristic analysis for diagnostic tests. Prev Vet Med 45:23–41Günther A, Reichenbach P, Malet JP, van den Eeckhaut M, Hervás J, Dashwood C, Guzzetti F (2013) Tier-based approaches for landslide susceptibility assessment in Europe. Landslides 10:529–546. https://doi.org/10.1007/s10346-012-0349-1Günther A, Van Den Eeckhaut M, Malet J-P, Reichenbach P, Hervás J (2014) Climate-physiographically differentiated Pan-European landslide susceptibility assessment using spatial multi-criteria evaluation and transnational landslide information. Geomorphology 224:69–85Gupta RP, Kanungo DP, Arora MK, Sarkar S (2008) Approaches for comparative evaluation of raster GIS-based landslide susceptibility zonation maps. Int J Appl Earth Obs Geoinf 10(3):330–341. https://doi.org/10.1016/j.jag.2008.01.003Guzzetti F, Reichenbach P, Ardizzone F, Cardinali M, Galli M (2006) Estimating the quality of landslide susceptibility models. Geomorphology 81(1–2):166–184. https://doi.org/10.1016/j.geomorph.2006.04.007Hervás J (2017) El inventario de movimientos de ladera de España ALISSA: Metodología y análisis preliminar. In: Alonso E, Corominas J, Hürlimann M (Eds.), Taludes 2017. Proc. IX Simposio Nacional sobre Taludes y Laderas Inestables, Santander, 27–30 June 2017. CIMNE, Barcelona, pp. 629–639Jaedicke C, Van Den Eeckhaut M, Nadim F et al (2014) Identification of landslide hazard and risk ‘hotspots’ in Europe. Bull Eng Geol Environ 73:325. https://doi.org/10.1007/s10064-013-0541-0Jenks GF (1967) The data model concept in statistical mapping. Int Yearbook Cartograph 7:186–190Jiang B (2013) Head/tail breaks: a new classification scheme for data with a heavy-tailed distribution. Prof Geogr 65(3):482–494. https://doi.org/10.1080/00330124.2012.700499Kiang MY (2003) A comparative assessment of classification methods. Decis Support Syst 35(4):441–454. https://doi.org/10.1016/S0167-9236(02)00110-0Landis JR, Koch GG (1977) The measurement of observer agreement for categorical data. Biometrics 33(1):159–174Langping L, Hengxing L, Changbao G, Yongshuang Z, Quanwen L, Yuming W (2017) A modified frequency ratio method for landslide susceptibility assessment. Landslides 14:727–741. https://doi.org/10.1007/s10346-016-0771-xLee S (2007) Comparison of landslide susceptibility maps generated through multiple logistic regression for three test areas in Korea. Earth Surf Process Landforms 32:2133–2148. https://doi.org/10.1002/esp.1517Liu C, Frazier P, Kumar L (2007) Comparative assessment of the measures of thematic classification accuracy. Remote Sens Environ 107(4):606–616. https://doi.org/10.1016/j.rse.2006.10.010López-Ratón M, Rodríguez-Álvarez MX, Cadarso-Suárez C, Gude-Sampedro F (2014) Optimal cutpoints: an R package for selecting optimal cutpoints in diagnostic tests. J Stat Softw 61(8):4Malet JP, Puissant A, Mathieu A, Van Den Eeckhaut M, Fressard M (2013) Integrating spatial multi-criteria evaluation and expert knowledge for country-scale landslide susceptibility analysis: application to France. In: Margottini C, Canuti P, Sassa K (eds) Landslide science and practice. Springer, Berlin. https://doi.org/10.1007/978-3-642-31325-7_40McGee S (2002) Simplifying likelihood ratios. J Gen Intern Med 17:647–650Metz C (1978) Basic principles of ROC analysis. Semin Nucl Med VIII(4):183–198Nadim F, Kjekstad O, Peduzzi P, Herold C, Jaedicke C (2006) Global landslide and avalanche hotspots. Landslides 3:159–173. https://doi.org/10.1007/s10346-006-0036-1Ohlmacher G, Davis J (2003) Using multiple logistic regression and GIS technology to predict landslide hazard in northeast Kansas, USA. Eng Geol 69(3–4):331–343. https://doi.org/10.1016/S0013-7952(03)00069-3Powell RL, Matzke N, de Souza C Jr, Clark M, Numata I, Hess LL, Roberts DA (2004) Sources of error accuracy assessment of thematic land-cover maps in the Brazilian Amazon. Remote Sens Environ 90(2):221–234. https://doi.org/10.1016/j.rse.2003.12.007Saaty T (1980) The analytic hierarchy process. McGraw Hill, New YorkSmits PC, Dellepiane SG, Schowengerdt RA (1999) Quality assessment of image classification algorithms for land-cover mapping: a review and proposal for a cost-based approach. Int J Remote Sens 20:1461–1486Stehman SV, Czaplewski RL (1998) Design and analysis of thematic map accuracy assessment: fundamental principles. Remote Sens Environ 64:331–344Swets JA (1988) Measuring the accuracy of diagnostic systems. Science 240(4857):1285–1293Van Den Eeckhaut M, Hervás J, Jaedicke C, Malet J-P, Montanarella L, Nadim F (2012) Statistical modelling of Europe-wide landslide susceptibility using limited landslide inventory data. Landslides 8:357–369Varnes DJ (1984) Landslide hazard zonation: a review of principles and practice. Natural hazards. UNESCO, ParisZhu X (2016) GIS for environmental applications. Routledge, Abingdon, p 490Zweig MH, Campbell G (1993) Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine. Clin Chem 39(4):561–57

The N-Terminal Domain of the Arenavirus L Protein Is an RNA Endonuclease Essential in mRNA Transcription

Arenaviridae synthesize viral mRNAs using short capped primers presumably acquired from cellular transcripts by a ‘cap-snatching’ mechanism. Here, we report the crystal structure and functional characterization of the N-terminal 196 residues (NL1) of the L protein from the prototypic arenavirus: lymphocytic choriomeningitis virus. The NL1 domain is able to bind and cleave RNA. The 2.13 Å resolution crystal structure of NL1 reveals a type II endonuclease α/β architecture similar to the N-terminal end of the influenza virus PA protein. Superimposition of both structures, mutagenesis and reverse genetics studies reveal a unique spatial arrangement of key active site residues related to the PD…(D/E)XK type II endonuclease signature sequence. We show that this endonuclease domain is conserved and active across the virus families Arenaviridae, Bunyaviridae and Orthomyxoviridae and propose that the arenavirus NL1 domain is the Arenaviridae cap-snatching endonuclease

A new class of glycomimetic drugs to prevent free fatty acid-induced endothelial dysfunction

Background: Carbohydrates play a major role in cell signaling in many biological processes. We have developed a set of glycomimetic drugs that mimic the structure of carbohydrates and represent a novel source of therapeutics for endothelial dysfunction, a key initiating factor in cardiovascular complications. Purpose: Our objective was to determine the protective effects of small molecule glycomimetics against free fatty acid­induced endothelial dysfunction, focusing on nitric oxide (NO) and oxidative stress pathways. Methods: Four glycomimetics were synthesized by the stepwise transformation of 2,5­dihydroxybenzoic acid to a range of 2,5­substituted benzoic acid derivatives, incorporating the key sulfate groups to mimic the interactions of heparan sulfate. Endothelial function was assessed using acetylcholine­induced, endotheliumdependent relaxation in mouse thoracic aortic rings using wire myography. Human umbilical vein endothelial cell (HUVEC) behavior was evaluated in the presence or absence of the free fatty acid, palmitate, with or without glycomimetics (1µM). DAF­2 and H2DCF­DA assays were used to determine nitric oxide (NO) and reactive oxygen species (ROS) production, respectively. Lipid peroxidation colorimetric and antioxidant enzyme activity assays were also carried out. RT­PCR and western blotting were utilized to measure Akt, eNOS, Nrf­2, NQO­1 and HO­1 expression. Results: Ex vivo endothelium­dependent relaxation was significantly improved by the glycomimetics under palmitate­induced oxidative stress. In vitro studies showed that the glycomimetics protected HUVECs against the palmitate­induced oxidative stress and enhanced NO production. We demonstrate that the protective effects of pre­incubation with glycomimetics occurred via upregulation of Akt/eNOS signaling, activation of the Nrf2/ARE pathway, and suppression of ROS­induced lipid peroxidation. Conclusion: We have developed a novel set of small molecule glycomimetics that protect against free fatty acidinduced endothelial dysfunction and thus, represent a new category of therapeutic drugs to target endothelial damage, the first line of defense against cardiovascular disease

Variable contributions of mixing end-members during small scale sprinkling experiments in partially weathered black marls

Rainfall is a well-know factor of hillslope instability. It influences the soil water content, allowing a rise in pore water pressures and decreasing the effective stresses in the soil. To simulate the infiltration processes a simplified approach consists in considering the soil as a homogeneous medium, so that water flow can be described by the Richard\u2019s equation for both saturated and unsaturated conditions. Unfortunately, several field observations have proven that landslide materials were highly heterogeneous. Preferential flow paths such as fissures, cracks, macropores and structural voids were shown to influence the water infiltration and the transport capacity through the unsaturated zone. The purpose of this work was to identify groundwater dynamics and active reservoirs interactions (matrix flow and preferential flow) within heterogeneous and fissured black marl material, using small-scale (1m2) infiltration experiments located on the Super-Sauze mudslide (French South Alps). Artificial rainfalls enriched in conservative tracer (Br- and Cl-) were applied over a period of 2 days with a mean rainfall intensity of about 44.7 mm/h. Matrix-water interactions have been analysed using End Member Mixing Analyses (EMMA) with Br-, Cl- and SO4 2- contents. Results confirm a complex and spatially different behaviour with the presence of preferential and/or soil matrix flow paths, cases of piston flow and chemical interaction with matrix (dissolution of mineralogical phases containing sulphate