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Journal articles on the topic 'Torrent control'
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1
Sterling, Shannon, and Olav Slaymaker. "Lithologic control of debris torrent occurrence." Geomorphology 86, no. 3-4 (May 2007): 307–19. http://dx.doi.org/10.1016/j.geomorph.2006.09.002.
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Pop, Laura-Ancuţa, Emil Puscas, Valentina Pileczki, Roxana Cojocneanu-Petric, Cornelia Braicu, Patriciu Achimas-Cadariu, and Ioana Berindan-Neagoe. "Quality control of Ion Torrent sequencing library." Cancer Biomarkers 14, no. 2-3 (May 8, 2014): 93–101. http://dx.doi.org/10.3233/cbm-130358.
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Paratscha, Roman, Magdalena von der Thannen, Roman Smutny, Thomas Lampalzer, Alfred Strauss, and Hans Peter Rauch. "Screening LCA of torrent control structures in Austria." International Journal of Life Cycle Assessment 24, no. 1 (July 17, 2018): 129–41. http://dx.doi.org/10.1007/s11367-018-1501-5.
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Davidescu, Serban Octavian, Alin-Lucian Mihalache, Mirabela Marin, Cezar Ungurean, Andrei Adorjani, Nicu Constantin Tudose, Adriana Agafia Davidescu, and Ioan Clinciu. "PHYSICAL STATUS OF TORRENT CONTROL STRUCTURES IN ROMANIA." Environmental Engineering and Management Journal 19, no. 5 (2020): 861–72. http://dx.doi.org/10.30638/eemj.2020.081.
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Zeng, Chen Ping. "Mountain Torrent Disaster Monitoring and Early-Warning System Based on Internet of Things." Applied Mechanics and Materials 484-485 (January 2014): 577–80. http://dx.doi.org/10.4028/www.scientific.net/amm.484-485.577.
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As a wisdom water conservancy, mountain torrent disaster monitoring and early-warning system is an especially information part of flood prevention and drought resisting information support, and plays a very important role in the flood prevention and drought resisting in the water conservancy industry. The integration of mountain torrent disaster monitoring and early-warning system in water conservancy with the internet of things and the establishment of intelligent things networking system based on automation and control provide decision-making supports for flood prevention and mountain torrent disaster early-warning, aiming at safeguard the life and property securities of people. Therefore, by taking Zhaojue County of Liangshan Yi autonomous prefecture (an area with frequent mountain torrent disaster in Sichuan province) as an example, the implementation plan of mountain torrent disaster monitoring and early-warning system is reviewed in this paper.
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Sang, Yan-Fang, Ping Xie, Yichi Zhang, Weiming Cheng, Liang Guo, and Dongya Sun. "Challenges of Hydrologic Nonstationarity: Mountain Torrent Control in China." Journal of Hydrologic Engineering 24, no. 3 (March 2019): 02519001. http://dx.doi.org/10.1061/(asce)he.1943-5584.0001751.
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Paratscha, Roman, Alfred Strauss, Roman Smutny, Thomas Lampalzer, Hans Peter Rauch, and Magdalena von der Thannen. "Probabilistic performance prediction model for Austrian torrent control infrastructure." Structure and Infrastructure Engineering 15, no. 2 (November 20, 2018): 170–79. http://dx.doi.org/10.1080/15732479.2018.1526195.
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Clinciu, Ioan, Ion-Catalin Petritan, and Mihai-Daniel Nita. "MAGNITUDE OF DAMAGE EVENTS ON HYDROTECHNICAL TORRENT CONTROL STRUCTURES." Environmental Engineering and Management Journal 14, no. 1 (2015): 57–71. http://dx.doi.org/10.30638/eemj.2015.008.
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Paratscha, Roman, Magdalena Von Der Thannen, Roman Smutny, Thomas Lampalzer, Alfred Strauss, and Hans Peter Rauch. "Development of LCA benchmarks for Austrian torrent control structures." International Journal of Life Cycle Assessment 24, no. 11 (April 17, 2019): 2035–53. http://dx.doi.org/10.1007/s11367-019-01618-6.
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Radonjic, Jasmina, Ratko Ristic, and Sinisa Polovina. "Changes in the hydrological status of the basin due to the application of erosion control works." Bulletin of the Faculty of Forestry, no. 114 (2016): 189–200. http://dx.doi.org/10.2298/gsf1614189r.
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Protection of land with vegetation is the primary factor in the fight against water erosion with necessary application of biotechnical, technical, administrative and planning measures. One of the first basins to be treated with works for the protection against erosion and torrent control is the Gradasnica River basin. The basic parameters to display the changes of the hydrological status of the land are the state of erosion, the change of erosion-coefficient, annual sediment yield, specific annual sediment discharge through the hydrographic network, the value of the runoff curve number and value of the maximal discharge. Works on protection from erosion and regulations of torrents have influenced the decrease in erosion coefficient values from strong erosion (Z=0.99) to the value of weak erosion (Z=0.40), as well as the reduction of the maximum discharge value from Qmax(1956)=108,12m3/s to the value of Qmax(2014)=87.2 m3/s.
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Clinciu, Ioan, Ion-Catalin Petritan, and Mihai-Daniel Nita. "MONITORING OF THE HYDROTECHNICAL TORRENT CONTROL STRUCTURES: A STATISTICAL APPROACH." Environmental Engineering and Management Journal 9, no. 12 (2010): 1699–707. http://dx.doi.org/10.30638/eemj.2010.234.
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Jakubis, Matúš, and Mariana Jakubisová. "Estimation of Basic Geometric and Hydraulic Characteristics of Natural Torrent Beds." Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis 68, no. 5 (2020): 841–49. http://dx.doi.org/10.11118/actaun202068050841.
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Many mountainous regions and their watersheds lack the mathematical description of their hydraulic geometry such as the High Tatras region in Slovakia. Therefore, the aim of the paper is to determine the geometric and hydraulic characteristics of natural torrent beds and to propose a regional equations of mountain watersheds for the High Tatras region. In the paper is also proposed a new equation to determine the relationships between the watershed area and the geometric characteristics of flow profiles. Derived regional equations can help in nature-friendly and ecological shaping and dimensioning of channel cross sections in torrent control designing. The research was conducted in 26 natural torrents and their watersheds on the reference sections and profiles under the sediment source zones. Two different regression equations to determine the regional relationships (hitherto used without asymptote and newly proposed with asymptote) were compared. The analyses showed a strong correlation relationship between watershed area Aw (km2) and bankfull geometric characteristics of natural cross-sections: width of the channel inside the banks Bbf (m), mean channel depth Hbf (m), channel cross-section area Abf (m2) and hydraulic characteristic – bankfull discharge Qbf (m3.s-1). These relations were tested by t-test and Shapiro-Wilk test. The determination coefficient (R12) for the relationships without asymptote ranged between R12 = 0.919 and R12 = 0.972; p1 – values from Shapiro-Wilk test ranged between p1 = 0.0359 and p1 = 0.8027. The determination coefficient (R22) for the relationships with asymptote ranged between R22 = 0.952 and R22 = 0.974; p2 – values from Shapiro-Wilk test ranged between p2 = 0.0221 and p2 = 0.8617. At the same time, we tested and confirned the hypothesis that the correlation coefficients R1 from equation without the asymptote are only randomly different from the correlation coefficients R2 from equation with the asymptote and the difference between these coefficients is also random. Derived regional equations make it possible to the gradual creation of hydrologic landscape regions in the SR. They can be also used as a valuable input to the ecological cross sections designing in torrent control and revitalization for the regions with a similar natural conditions.
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Marchi, L., M. Cavalli, and V. D'Agostino. "Hydrogeomorphic processes and torrent control works on a large alluvial fan in the eastern Italian Alps." Natural Hazards and Earth System Sciences 10, no. 3 (March 23, 2010): 547–58. http://dx.doi.org/10.5194/nhess-10-547-2010.
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Abstract. Alluvial fans are often present at the outlet of small drainage basins in alpine valleys; their formation is due to sediment transport associated with flash floods and debris flows. Alluvial fans are preferred sites for human settlements and are frequently crossed by transport routes. In order to reduce the risk for economic activities located on or near the fan and prevent loss of lives due to floods and debris flows, torrent control works have been extensively carried out on many alpine alluvial fans. Hazard management on alluvial fans in alpine regions is dependent upon reliable procedures to evaluate variations in the frequency and severity of hydrogeomorphic processes and the long-term performance of the torrent training works. An integrated approach to the analysis of hydrogeomorphic processes and their interactions with torrent control works has been applied to a large alluvial fan in the southern Carnic Alps (northeastern Italy). Study methods encompass field observations, interpretation of aerial photographs, analysis of historical documents, and numerical modelling of debris flows. The overall performance of control works implemented in the early decades of 20th century was satisfactory, and a reduction of hazardous events was recognised from features observed in the field and in aerial photographs, as well as from the analysis of historical records. The 2-D simulation of debris flows confirms these findings, indicating that debris flow deposition would not affect urban areas or main roads, even in the case of a high-magnitude event. Present issues in the management of the studied alluvial fan are representative of situations frequently found in the European Alps and deal with the need for maintenance of the control structures and the pressures for land use changes aimed at the economic exploitation of the fan surface.
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Vodicka, Radek, Radek Vrtel, Katerina Mensikova, Petr Kanovsky, Iva Dolinova, Kristyna Kolarikova, and Martin Prochazka. "Next Generation Sequencing Data Analysis Evaluation in Patients with Parkinsonism from a Genetically Isolated Population." Genomics and Computational Biology 3, no. 3 (May 11, 2017): 44. http://dx.doi.org/10.18547/gcb.2017.vol3.iss3.e44.
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Parkinson's disease (PD) can be caused by genetic changes in a lot of genes. The effect of these changes is determined by the nature of the mutation and ranges from weak associations to pathogenic mutation which leads to loss of protein function. Our study is based on epidemiological data which show significantly increased prevalence of PD (2.9 %) in an isolated population of South-Eastern Moravia in the Czech Republic. We compared two different Next Generation Sequencing (NGS) data analysis approaches in DNA from 28 PD patients in the genes responsible for Parkinsonism (ADH1C, ATP13A2, EIF4G1, FBXO7, GBA + GBAP1, GIGYF2, HTRA2, LRRK2, MAPT, PARK2, PARK7, PINK1, PLA2G6, SNCA, UCHL1 and VPS35) using: 1) already described missense rare variants or pathogenic mutations 2) twelve control DNA samples from the same isolated population. Ion Torrent NGS data processing and trimming from Fastaq through “bam” to “vcf” files was done parallely by Torrent Suite/Ion Reporter and NextGENe software. After filtering out, three missense mutations were found in LRRK2 gene: rs33995883 in 6/0 patients/control (p/c); rs33958906 in 1/1p/c; rs781737269 in 3/0p/c; one missense mutation in MAPT gene rs63750072 in 6/1p/c; and one mutation in HTRA2 gene rs72470545 in 3/1p/c. Both the results from NextGENe with Ion Torrent adaptation and from Ion Reporter significantly correlated in variant calling. Our study may contribute to further explain the genetic background of Parkinsonism.
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Bel, Coraline, Frédéric Liébault, Oldrich Navratil, Nicolas Eckert, Hervé Bellot, Firmin Fontaine, and Dominique Laigle. "Rainfall control of debris-flow triggering in the Réal Torrent, Southern French Prealps." Geomorphology 291 (August 2017): 17–32. http://dx.doi.org/10.1016/j.geomorph.2016.04.004.
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Milanovic, Ana. "Hydrological forecast of maximal water level in Lepenica river basin and flood control measures." Glasnik Srpskog geografskog drustva 86, no. 1 (2006): 47–54. http://dx.doi.org/10.2298/gsgd0601047m.
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Lepenica river basin territory has became axis of economic and urban development of Sumadija district. However, considering Lepenica River with its tributaries, and their disordered river regime, there is insufficient of water for water supply and irrigation, while on the other hand, this area is suffering big flood and torrent damages (especially Kragujevac basin). The paper presents flood problems in the river basin, maximum water level forecasts, and flood control measures carried out until now. Some of the potential solutions, aiming to achieve the effective flood control, are suggested as well.
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Kang, Min-Jeng, Ki-Dae Kim, Kang-San Oh, Jin-Won Park, and Jae-Hyeon Park. "Analysis of Forest Environmental Factors on Torrent Erosion control work area in Gyeongsangnam-do." Journal of Agriculture & Life Science 50, no. 5 (October 31, 2016): 111–20. http://dx.doi.org/10.14397/jals.2016.50.5.111.
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Arattano, M., L. Marchi, and M. Cavalli. "Analysis of debris-flow recordings in an instrumented basin: confirmations and new findings." Natural Hazards and Earth System Sciences 12, no. 3 (March 22, 2012): 679–86. http://dx.doi.org/10.5194/nhess-12-679-2012.
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Abstract. On 24 August 2006, a debris flow took place in the Moscardo Torrent, a basin of the Eastern Italian Alps instrumented for debris-flow monitoring. The debris flow was recorded by two seismic networks located in the lower part of the basin and on the alluvial fan, respectively. The event was also recorded by a pair of ultrasonic sensors installed on the fan, close to the lower seismic network. The comparison between the different recordings outlines particular features of the August 2006 debris flow, different from that of events recorded in previous years. A typical debris-flow wave was observed at the upper seismic network, with a main front abruptly appearing in the torrent, followed by a gradual decrease of flow height. On the contrary, on the alluvial fan the wave displayed an irregular pattern, with low flow depth and the main peak occurring in the central part of the surge both in the seismic recording and in the hydrographs. Recorded data and field evidences indicate that the surge observed on the alluvial fan was not a debris flow, and probably consisted in a water surge laden with fine to medium-sized sediment. The change in shape and characteristics of the wave can be ascribed to the attenuation of the surge caused by the torrent control works implemented in the lower basin during the last years.
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Yergeau, Etienne, John R. Lawrence, Sylvie Sanschagrin, Marley J. Waiser, Darren R. Korber, and Charles W. Greer. "Next-Generation Sequencing of Microbial Communities in the Athabasca River and Its Tributaries in Relation to Oil Sands Mining Activities." Applied and Environmental Microbiology 78, no. 21 (August 24, 2012): 7626–37. http://dx.doi.org/10.1128/aem.02036-12.
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ABSTRACTThe Athabasca oil sands deposit is the largest reservoir of crude bitumen in the world. Recently, the soaring demand for oil and the availability of modern bitumen extraction technology have heightened exploitation of this reservoir and the potential unintended consequences of pollution in the Athabasca River. The main objective of the present study was to evaluate the potential impacts of oil sands mining on neighboring aquatic microbial community structure. Microbial communities were sampled from sediments in the Athabasca River and its tributaries as well as in oil sands tailings ponds. Bacterial and archaeal 16S rRNA genes were amplified and sequenced using next-generation sequencing technology (454 and Ion Torrent). Sediments were also analyzed for a variety of chemical and physical characteristics. Microbial communities in the fine tailings of the tailings ponds were strikingly distinct from those in the Athabasca River and tributary sediments. Microbial communities in sediments taken close to tailings ponds were more similar to those in the fine tailings of the tailings ponds than to the ones from sediments further away. Additionally, bacterial diversity was significantly lower in tailings pond sediments. Several taxonomic groups ofBacteriaandArchaeashowed significant correlations with the concentrations of different contaminants, highlighting their potential as bioindicators. We also extensively validated Ion Torrent sequencing in the context of environmental studies by comparing Ion Torrent and 454 data sets and by analyzing control samples.
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Matic, Vjaceslava. "The implementing of some plant species in erosion control on slopes." Archives of Biological Sciences 62, no. 3 (2010): 719–24. http://dx.doi.org/10.2298/abs1003719m.
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With the need to conserve and improve the environment, it is recommended to employ plant materials in the erosion control of torrents and slopes alongside roads. Considering the well-known properties of some willow species regarding their power of vegetative reproduction, survival in poor soils and often flooded alluvium, we researched into the potentials of the following species: Salix triandra L., Salix purpurea L. and Salix incana Schrk. in the catchment of the warehouse 'Gvozdac', Experimental Estate Goc, Serbia. The research started in 2004 and has continued till the present day. The above-mentioned willow species showed significant efficiency in the bank protection of torrential watercourses and on the moist slopes of embankments and cuts of roads. Some of them can even stand a certain degree of aridity, while other species, on poor, eroded soil exposed to long and extreme drought, could not survive and did not show the expected effect, which is also the consequence of the absence of maintenance and adequate attention to such erosion-control works. In spite of the above, one of the willow species survived even in the most severe conditions, checking the erosion of the road cut slope and the road construction itself, and prevented the impacts of aggressive atmospheric waters, thus halting the erosion ridges and the removal of the asphalt road surface. The above facts prove that, with adequate measures of maintenance, plant materials can be very successfully applied for both longitudinal structures and to check dams in torrent control, as well as in erosion control on the slopes in catchments, both in civil engineering works and in forest exploitation. The research requires closer attention, extending the interests to some grass and shrub species, with the aim of ecological erosion control and reclamation of endangered watercourses, slopes and, in general, environmental protection and nature conservation. .
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Maavak, Mathew. "Bubble to panopticon: dark undercurrents of the big data torrent." Kybernetes 49, no. 3 (September 7, 2019): 1046–60. http://dx.doi.org/10.1108/k-06-2019-0403.
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Purpose Big data are indispensable in scientific endeavours ranging from nuclear research to climate studies. However, there is a growing misperception that congeries of data can be easily reconstructed into competitive business insights. Such notions have been encouraged by a plethora of mainstream techno-utopian forecasts. Design/methodology/approach This paper investigated such claims and related big data developments, including its “systems-first” and oligopolistic orientations. Due to the paucity of current scholarship on an admittedly pessimistic topic, the paper studied contrarian developments in the industry by relying on secondary data. The study of experts and scholars; industrial trends; and discrepancies and critical gaps in the mainstream data narrative were sourced to prognosticate the likely trajectory of many data giants. Findings A key finding was that the big data industry faces an untenable market bubble worth trillions of dollars. This will have severe consequences for common digital access and social stability worldwide. Evidence presented also suggests that the data industrial complex may undergo a function creep by facilitating a transition from surveillance capitalism to surveillance society. Research limitations/implications Primary data for a study of this nature may take years to materialize. This is a “first-pass” study that seeks to illuminate latent dangers facing the big data/AI sector. There is a paucity of scholarly study that even remotely touches on this topic. Therefore, supporting arguments was sourced from contemporary reports and expert study (secondary data). Practical implications As control of data may have geostrategic implications, balkanization of the wired ecosystem may be underway with Russia and China leading the way. Future superpowers may be defined by the way they handle data. The concentration of data in fewer hands may also affect citizen innovation. Social implications A break-down of the data industrial complex may lead to social mayhem as the monetization of presently free software, blogs and social media platforms may be unfeasible. Originality/value This topic has hardly been explored due to the novelty of big data, its applications and the daily hype over its potentials. This paper boldly describes dark countercurrents in the industry.
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Ratcliffe, S. "Automatic Conflict Detection Logic for Future Air Traffic Control." Journal of Navigation 42, no. 1 (January 1989): 92–106. http://dx.doi.org/10.1017/s0373463300015113.
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Air traffic control (ATC) makes extensive use of computer technology in subordinate roles for processing flight-plan and radar data and for message switching. It is usual to stress that such computers are aids to human controllers who take the decisions. It can, however, be argued that computers are, in fact, already encroaching on the decision-taking processes. The SSR plot extractor, for example, produces a censored summary which amounts to only a few per cent of the torrent of radar data from which it is derived. This summary is then subjected to code conversion and coordinate transformation before it reaches the controllers who cannot refer back to the data sources. Once computer-processing has been introduced, the issue is no longer whether a computer may take some of the decisions involved in ATC, but merely the extent of the authority it can exercise.
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Bíba, M., J. Jiřík, and K. Vančura. "Forestry, mountain catchments and floods in the Czech Republic." Journal of Forest Science 50, No. 11 (January 11, 2012): 538–41. http://dx.doi.org/10.17221/4653-jfs.
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A short introduction of historical overview and current situation refer to forestry problems of the country. Local climate is characterized and impacts of natural phenomena are described, as well as the impacts of human beings. The influence of forest management is mentioned and discussed in relation to latest catastrophic floods. The territory of the Czech Republic is damaged especially by a high intensity of atmospheric precipitation abnormal values which lead to a local or regional damage. In the catchment areas of torrents, damage leads to faster soil erosion, development of ravines, landslides, moving of soil sediments and their deposition, devastation of watercourse beds and properties, flooding while the flooding rates of flow represent a danger for the life of inhabitants. Important elements and results of respective research are described in brief. E.g. research of precipitation and its relation to the runoffs in the small mountain catchment areas with the forest stands restoration, as well as the forestry-hydrologic monitoring of forest environment, which has been taking place since 1928, and tradition of the service for torrent control. Forestry-hydrologic research gradually documents that a favorable flood-control performance of forest is limited. However, this is not a reason for not taking care of flood-control measures in the mountain afforested areas. These measures and importance of forest for the protection of land are historically verified and justified. In closing the mankind behavior to the landscape is underlined as a question mark.
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Sodja, E., N. Toplak, S. Koren, M. Kovač, S. Truden, and M. Žolni-Dovč. "Next-generation sequencing of drug resistant Mycobacterium tuberculosis clinical isolates in low-incidence countries." Russian Journal of Infection and Immunity 9, no. 5-6 (February 1, 2020): 773–78. http://dx.doi.org/10.15789/2220-7619-2019-5-6-773-778.
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Drug resistant tuberculosis (TB), especially multidrug (MDR) and extensively drug-resistant (XDR) TB, is still a serious problem in global TB control. Slovenia and North Macedonia are low-incidence countries with TB incidence rates of 5.4 and 10.4 in 2017, respectively. In both countries, the percentage of drug resistant TB is very low with sporadic cases of MDR-TB. However, global burden of drug-resistant TB continues to increase imposing huge impact on public health systems and strongly stimulating the detection of gene variants related with drug resistance in TB. Next-generation sequencing (NGS) can provide comprehensive analysis of gene variants linked to drug resistance in Mycobacterium tuberculosis. Therefore, the aim of our study was to examine the feasibility of a full-length gene analysis for the drug resistance related genes (inhA, katG, rpoB, embB) using Ion Torrent technology and to compare the NGS results with those obtained from conventional phenotypic drug susceptibility testing (DST) in TB isolates. Between 1996 and 2017, we retrospectively selected 56 TB strains from our National mycobacterial culture collection. Of those, 33 TB isolates from Slovenian patients were isolated from various clinical samples and subjected to phenotypic DST testing in Laboratory for Mycobacteria (University Clinic Golnik, Slovenia). The remaining 23 TB isolates were isolated from Macedonian patients and sent to our laboratory for assistance in phenotypic DST testing. TB strains included were either mono-, poly- or multidrug resistant. For control purposes, we also randomly selected five TB strains susceptible to first-line anti-TB drugs. High concordance between genetic (Ion Torrent technology) and standard phenotypic DST testing for isoniazid, rifampicin and ethambutol was observed, with percent of agreement of 77%, 93.4% and 93.3%, sensitivities of 68.2%, 100% and 100%, and specificities of 100%, 80% and 88.2%, respectively. In conclusion, the genotypic DST using Ion Torrent semiconductor NGS successfully predicted drug resistance with significant shortening of time needed to obtain the resistance profiles from several weeks to just a few days.
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Ma, Ho-Seop, Won-Ok Jeong, and Won-Seok Kang. "Effects on the Habitats of Benthic Macroinvertebrates by Construction of Buttress Erosion Control Dam in Torrent." Journal of Agriculture & Life Science 48, no. 4 (August 30, 2014): 55–62. http://dx.doi.org/10.14397/jals.2014.48.4.55.
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Osanai, Nobutomo, Hideaki Mizuno, and Takahisa Mizuyama. "Design Standard of Control Structures Against Debris Flow in Japan." Journal of Disaster Research 5, no. 3 (June 1, 2010): 307–14. http://dx.doi.org/10.20965/jdr.2010.p0307.
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Countermeasures to prevent or mitigate sedimentrelated hazards, debris flow in this paper are classified as structural measures or nonstructural measures. The structural measures are Sabo dams, leading dikes, and channels for debris flow control. The nonstructural measures are the designation of areas prone to debris flow, proper land use in the areas, the reinforcement of houses, the creation of warning systems and the evacuation of the inhabitants in case of emergency. A technical standard on debris flow control structures of Japan was revised in 2007. Major revision is that check dams called Sabo dams constructed near houses are changed from closed type Sabo dams to open type Sabo dams because the occurrence frequency is low as once for longer than one hundred years, natural torrent environment should be conserved in ordinary days and sediment trap capacity should be kept until debris flow occurs. Points changed are explained such as the opening of open type dams is as equal as the maximum stone size.
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I. Sardi, Silvia, Rejane H. Carvalho, Luis G. C. Pacheco, João P. P. d. Almeida, Emilia M. M. d. A. Belitardo, Carina S. Pinheiro, Gúbio S. Campos, and Eric R. G. R. Aguiar. "High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics." Viruses 12, no. 7 (July 21, 2020): 782. http://dx.doi.org/10.3390/v12070782.
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Arboviruses, including the Zika virus, have recently emerged as one of the most important threats to human health. The use of metagenomics-based approaches has already proven valuable to aid surveillance of arboviral infections, and the ability to reconstruct complete viral genomes from metatranscriptomics data is key to the development of new control strategies for these diseases. Herein, we used RNA-based metatranscriptomics associated with Ion Torrent deep sequencing to allow for the high-quality reconstitution of an outbreak-related Zika virus (ZIKV) genome (10,739 nt), with extended 5′-UTR and 3′-UTR regions, using a newly-implemented bioinformatics approach. Besides allowing for the assembly of one of the largest complete ZIKV genomes to date, our strategy also yielded high-quality complete genomes of two arthropod-infecting viruses co-infecting C6/36 cell lines, namely: Alphamesonivirus 1 strain Salvador (20,194 nt) and Aedes albopictus totivirus-like (4618 nt); the latter likely represents a new viral species. Altogether, our results demonstrate that our bioinformatics approach associated with Ion Torrent sequencing allows for the high-quality reconstruction of known and unknown viral genomes, overcoming the main limitation of RNA deep sequencing for virus identification.
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Ristić, R., S. Kostadinov, B. Abolmasov, S. Dragićević, G. Trivan, B. Radić, M. Trifunović, and Z. Radosavljević. "Torrential floods and town and country planning in Serbia." Natural Hazards and Earth System Sciences 12, no. 1 (January 2, 2012): 23–35. http://dx.doi.org/10.5194/nhess-12-23-2012.
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Abstract. Torrential floods are the most frequent natural catastrophic events in Serbia, causing the loss of human lives and huge material damage, both in urban and rural areas. The analysis of the intra-annual distribution of maximal discharges aided in noticing that torrential floods have a seasonal character. The erosion and torrent control works (ETCWs) in Serbia began at the end of the 19th century. Effective protection from torrential floods encompasses biotechnical works on the slopes in the watershed and technical works on the torrent beds, within a precisely defined administrative and spatial framework in order to achieve maximal safety for people and their property. Cooperation to overcome the conflicts between the sectors of the water resources management, forestry, agriculture, energetics, environmental protection and local economic development groups is indispensable at the following levels: policy, spatial planning, practice, investments and education. The lowest and most effective level is through the Plans for Announcement of Erosive Regions (PAERs) and the Plans for Protection from Torrential Floods (PPTFs), with Hazard Zones (HZs) and Threatened Areas (TAs) mapping on the basis of the hydrologic, hydraulic and spatial analysis of the factors that are important for the formation of torrential floods. Solutions defined through PAERs and PPTFs have to be integrated into Spatial Plans at local and regional levels.
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Kotrova, Michaela, Henrik Knecht, Jack Bartram, Vojtech Bystry, Giovanni Cazzaniga, Grazia Fazio, Simone Ferrero, et al. "Library Preparation Is the Major Factor Affecting Differences in Results of Immunoglobulin Gene Rearrangements Detection on Two Major Next-Generation Sequencing Platforms." Blood 126, no. 23 (December 3, 2015): 1411. http://dx.doi.org/10.1182/blood.v126.23.1411.1411.
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Abstract Minimal residual disease (MRD) assessment via next generation sequencing (NGS) of immunoglobulin (Ig) and T-cell receptor (TR) gene rearrangements for lymphoid malignancies is currently under extensive development. NGS MRD has a potential to overcome the limitations of current techniques; laboriousness and difficult interpretation of qPCR for Ig/TR and low sensitivity of flow cytometry. However, amplicon-based NGS MRD has potential pitfalls that have to be addressed before it can be safely introduced for clinical decision making. Multi-center concordance in the experimental setting, quality control and interpretation of the results need to be achieved in order to surpass the advantages of qPCR, which is currently rigorously standardized within the EuroMRD consortium. Our aim was to test the stability and reproducibility of an optimized Ig heavy chain (IGH) based NGS approach for MRD assessment in a multi-center setting within the EuroClonality NGS Consortium on two different sequencing platforms. A one-step PCR library preparation approach was tested in seven institutions (Kiel, Salamanca, Milano, Bristol, London, Prague, Torino). Serial dilutions (10-1 to 10-5) of diagnostic DNA into polyclonal DNA as well as follow-up samples of 30 B-cell precursor ALLs with known complete IGH rearrangements were sequenced on the MiSeq. Serial dilutions of five different diagnostic ALL samples and libraries from polyclonal control were sequenced in parallel on both the MiSeq and Ion Torrent platforms. All samples were spiked with pre-defined copy numbers of five reference IGH sequences as a calibrator. FR2 primers, harboring platform-specific sequencing adapters, were used during the one-step PCR with 500ng of DNA per sample (75,000 copies). Negative and positive controls (27 pooled B-cell lines) were used for testing assay stability and reproducibility among the labs. Purpose-built bioinformatics methods were applied to analyze data. MRD results were compared to results of EuroMRD-based qPCR results. A total of 333 libraries were sequenced in 29 deep sequencing runs producing 194 million reads. The IGH gene rearrangements of all 27 pooled positive B-cell line controls were identified in all centers. NGS MRD analysis in 116 ALL follow-up samples revealed MRD positivity in 69/116 samples vs. 66/116 samples in qPCR, with discrepancies concerning samples with low MRD (R2=0.81). The dilution experiments gave similar results for both platforms, with a minimum sensitivity of 10-4 (as currently required by most treatment protocols using qPCR) for all tested assays. The correlation between MRD levels obtained by the two NGS platforms was good (R2=0.84). Ratios of reads containing reference IGH sequences were highly consistent in intra- and inter-laboratory analyses, independent of the total number of reads in the sample. When comparing platforms, in 10-1 dilution samples sequenced on MiSeq the ratio of reads harboring reference sequences was 2.1 to 2.7 times lower than in remaining dilutions, while on the Ion Torrent it was only 0.9 to 1.3 times, reflecting the competition with the leukemic clone. The correlation of the amounts of spiked-in sequences with the representation of reads harboring these sequences was slightly better for the Ion Torrent (R2=0.88) than for the MiSeq (R2=0.79). Amplification efficiency of each primer was checked by analyzing libraries from healthy polyclonal control. All primer sequences were present in all samples on both platforms, however, the differences between four libraries prepared from the same sample sequenced on the MiSeq were 2.6 times higher than in one library from this sample sequenced in five replicates on the Ion Torrent. The newly developed IGH assay shows robust intra and inter-laboratory reproducibility, which is the first step towards the safe use of this new MRD technique in a multi-center setting. The distribution of reference sequences and sequences of primers confirmed that the main source of differences between platform strategies is the library preparation and not the platform itself. Using the same amount of DNA, the sensitivity of the method is similar to qPCR. The performance and costs of the assay are similar for both the MiSeq and Ion Torrent. MRD analysis via NGS has therefore a great potential to replace qPCR as the gold standard for MRD-guided therapy in ALL, provided that thorough standardization can be achieved. Support: NV15-30626A, GBP302/12/G101. Disclosures Langerak: Roche: Other: Lab services in the field of MRD diagnostics provided by Dept of Immunology, Erasmus MC (Rotterdam); DAKO: Patents & Royalties: Licensing of IP and Patent on Split-Signal FISH. Royalties for Dept. of Immunology, Erasmus MC, Rotterdam, NL; InVivoScribe: Patents & Royalties: Licensing of IP and Patent on BIOMED-2-based methods for PCR-based Clonality Diagnostics..
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Itakura, Y., H. Inaba, and T. Sawada. "A debris-flow monitoring devices and methods bibliography." Natural Hazards and Earth System Sciences 5, no. 6 (December 1, 2005): 971–77. http://dx.doi.org/10.5194/nhess-5-971-2005.
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Abstract. Debris-flow monitoring has two functions, warning and modeling. The warning function includes the following parameters: occurrence prediction and detection, proximity sensing, and discharge-estimation. The parameters obtained from debris-flow measurements can deduce a numerical model for creating a hazard map and designing various types of control structures to mitigate the hazards. Many devices and methods of monitoring are tabulated here for comparative study. Some of them are in operation. Advanced comparative studies lead to an improvement in debris-flow monitoring, an integrated system that can be applied to any torrent, and a breakthrough in future developments.
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Noetzli, Konrad Philipp, Martin Frei, and Albert Böll. "Tragsicherheit von Holzkonstruktionen im Wildbachverbau – Ein Fallbeispiel 60-jähriger Wildbachsperren | Bearing resistance of timber structures – a study of 60-year-old log crib dams." Schweizerische Zeitschrift fur Forstwesen 153, no. 10 (October 1, 2002): 377–84. http://dx.doi.org/10.3188/szf.2002.0377.
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Timber is a valuable building material for log crib dams in torrent control. However, due to inherent biological deterioration its stability and strength decreases over time. Round wood beams from three log crib dams, built around 1940, were subjected to bending tests in a case study in situ to determine the bending moment at failure. 60 years after installation, two-thirds of the tested beams still showed a higher bending moment at failure than the original design moment, with an average safety factor of 1.2. The influence of the test conditions and the statics of the systems are discussed here.
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Jiang, Ru-Cheng, Xiu-Juan Jiang, and Shi-Xiang Gu. "Current status and counter-measures for existing problems in mountain torrent disaster prevention and control in Yunnan Province." Journal of Information and Optimization Sciences 38, no. 7 (October 3, 2017): 1169–79. http://dx.doi.org/10.1080/02522667.2017.1367499.
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Rao, Pavitra N., Swapna Uplekar, Sriti Kayal, Prashant K. Mallick, Nabamita Bandyopadhyay, Sonal Kale, Om P. Singh, et al. "A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India." Journal of Clinical Microbiology 54, no. 6 (March 23, 2016): 1500–1511. http://dx.doi.org/10.1128/jcm.00235-16.
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A major challenge to global malaria control and elimination is early detection and containment of emerging drug resistance. Next-generation sequencing (NGS) methods provide the resolution, scalability, and sensitivity required for high-throughput surveillance of molecular markers of drug resistance. We have developed an amplicon sequencing method on the Ion Torrent PGM platform for targeted resequencing of a panel of sixPlasmodium falciparumgenes implicated in resistance to first-line antimalarial therapy, including artemisinin combination therapy, chloroquine, and sulfadoxine-pyrimethamine. The protocol was optimized using 12 geographically diverseP. falciparumreference strains and successfully applied to multiplexed sequencing of 16 clinical isolates from India. The sequencing results from the reference strains showed 100% concordance with previously reported drug resistance-associated mutations. Single-nucleotide polymorphisms (SNPs) in clinical isolates revealed a number of known resistance-associated mutations and other nonsynonymous mutations that have not been implicated in drug resistance. SNP positions containing multiple allelic variants were used to identify three clinical samples containing mixed genotypes indicative of multiclonal infections. The amplicon sequencing protocol has been designed for the benchtop Ion Torrent PGM platform and can be operated with minimal bioinformatics infrastructure, making it ideal for use in countries that are endemic for the disease to facilitate routine large-scale surveillance of the emergence of drug resistance and to ensure continued success of the malaria treatment policy.
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Filianoti, Pasquale, Luana Gurnari, Demetrio Antonio Zema, Giuseppe Bombino, Marco Sinagra, and Tullio Tucciarelli. "An Evaluation Matrix to Compare Computer Hydrological Models for Flood Predictions." Hydrology 7, no. 3 (July 15, 2020): 42. http://dx.doi.org/10.3390/hydrology7030042.
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In order to predict and control the impacts of floods in torrents, it is important to verify the simulation accuracy of the most used hydrological models. The performance verification is particularly needed for applications in watersheds with peculiar climatic and geomorphological characteristics, such as the Mediterranean torrents. Moreover, in addition to the accuracy, other factors affect the choice of software by stakeholders (users, modellers, researchers, etc.). This study introduces a “performance matrix”, consisting of several evaluation parameters weighted by stakeholders’ opinions. The aim is to evaluate the accuracy of the flood prediction which is achieved by different models, as well as the pros and cons of software user experience. To this aim, the performances and requisites of four physical-based and conceptual models (HEC-HMS, SWMM, MIKE11 NAM and WEC-FLOOD) have been evaluated, by predicting floods in a midsized Mediterranean watershed (Mèsima torrent, Calabria, Southern Italy). In the case study, HEC-HMS and MIKE 11 NAM were the best computer models (with a weighted score of 4.45 and 4.43, respectively), thanks to their low complexity and computation effort, as well as good user interface and prediction accuracy. However, MIKE11 NAM is not free of charge. SWMM showed a lower prediction accuracy, which put the model in third place of the four models. The performance of WEC-FLOOD, although not being as good as for the other tested models, can be considered overall acceptable in comparison to the other well-consolidated models, considering that WEC-FLOOD is in the early stage of development. Overall, the proposal of the performance matrix for hydrological models may represent a first step in building a more complete evaluation framework of the hydrological and hydraulic commercial models, in order to give indications to allow potential users to make an optimal choice.
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Rickli, Christian, and Frank Graf. "Wildbachsperren aus Fichte und Tanne: Festigkeit und Pilzbefall in den ersten Jahren." Schweizerische Zeitschrift fur Forstwesen 165, no. 4 (April 1, 2014): 79–86. http://dx.doi.org/10.3188/szf.2014.0079.
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Timber constructions in torrent control with Norway spruce and silver fir: wood quality and colonisation with decay fungi during the first years Timber is widely used for protection measures in torrent control. However, life span of woody constructions such as timber check dams is limited due to fungal decay. Only sparse scientific information is available on the long-term behaviour of timber structures and the colonisation with decay fungi. Related to this, in practice a controversial discussion has been going on if either Norway spruce (Picea abies) or silver fir (Abies alba) is more enduring and if bark removal increases resistance against fungal decay. In order to going into this matter, a series of 15 timber check dams built in 1996/1997 has been monitored. The constructions were alternatively realised with Norway spruce and silver fir, half of them each with remaining and removed bark, respectively. The scientific investigations included the documentation of colonisation with rot fungi and the identification of decayed zones with a simple practical approach as well as based on drilling resistance. Colonisation by decay fungi started three years after construction (e.g. Gloeophyllum sepiarium), two years later first parts with reduced wood resistance were detected. The protection measures were still fully functional sixteen years after construction although decay was found on all check dams but two. Wood quality was markedly better in watered sections compared to the occasionally dry lateral abutment sections, without showing clear differences in decay between logs of Norway spruce and silver fir. However, both the practical approach and the drilling resistance measurement suggest more defects on logs without bark. Further investigations and sound statistical analysis are needed to confirm the observed trends.
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Delle Rose, Marco, Paolo Martano, and Corrado Fidelibus. "The Recent Floods in the Asso Torrent Basin (Apulia, Italy): An Investigation to Improve the Stormwater Management." Water 12, no. 3 (February 29, 2020): 661. http://dx.doi.org/10.3390/w12030661.
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Stormwater management is of concern to public institutions and academies. In the Asso Torrent endorheic basin (Salento peninsula, Southern Italy), a network of natural and artificial channels crossing urban and rural areas and flowing towards six swallow karst holes, several floods occurred in the last six years, after the end of extensive hydraulic works. In this paper, the results of an observational study on the meteorological and hydrological factors concurring to these floods are reported. It was inferred that soil saturation, cumulative precipitation anticipating the events, and clogging of the swallow holes are of relevance and must be considered in the definition of new criteria in decision-making procedure. The adoption of both innovative modeling techniques and real-time control should be an efficient solution to properly regulate the flow control devices before and during the precipitation events. With a view to providing solutions for a sustainable management of the water resources, easy-to-implement measures are suggested, such as the selection of flood-tolerant crops and construction of harvesting systems for alternative water uses.
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Rios, Juan Manuel. "Predation By the Nonnative Rainbow Trout, Oncorhynchus Mykiss (Walbaum, 1792), on the Native Biota from Freshwater Environment of the Central Andes (Argentina)." Transylvanian Review of Systematical and Ecological Research 23, no. 1 (March 1, 2021): 67–72. http://dx.doi.org/10.2478/trser-2021-0005.
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Abstract This study aimed to examine the impact of the nonnative rainbow trout Oncorhynchus mykiss on the native biota that inhabits freshwater environments of the central Andes, Argentina. To assess the predation pressure on native Andean vertebrates and invertebrates, the stomach contents were taken from rainbow trout caught at three Andean sites. Results showed that the major prey items were the native torrent catfish Hatcheria macraei (100% in diet), Elmidae coleopterans (23%), and the native crab Aegla affinis (38%) in the rainbow trout stomachs collected from Cipolletti Dam (North zone), Yaucha River (Middle zone), and Vaina Stream (South zone), respectively. This preliminary study exhibits the predation pressure of the rainbow trout on native Andean species and suggests that policies are necessary to control the release of fry of this exotic salmonid in the Andes region.
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Klassen, H. D., and T. G. Northcote. "Stream bed configuration and stability following gabion weir placement to enhance salmonid production in a logged watershed subject to debris torrents." Canadian Journal of Forest Research 16, no. 2 (April 1, 1986): 197–203. http://dx.doi.org/10.1139/x86-036.
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Tandem V-shaped gabion weirs for improving spawning habitat for salmon (Oncorhynchus spp.) were installed to replace large organic debris at three sites below the terminus of a debris torrent in Sachs Creek, Queen Charlotte Islands. Stream conditions were compared between gabion and nearby control sites. The stability of added and entrapped gravel at all gabion sites was poor over the first winter and excessive scour threatened the integrity of the upstream steeper (3%) slope gabion site. However, the two gabion sites at a lower (1%) slope successfully stabilized spawning gravel in the 2nd year after installation, probably through a reduction in the local slope gradient and self-armouring of the high flow channels. Higher summer densities of juvenile coho salmon (Oncorhynchuskisutch (Walbaum)) and steelhead trout (Salmogairdneri Richardson) were recorded at the gabion sites (means, 1.2 and 0.33/m2, respectively) compared with the control sites (means, 0.89 and 0.10/m2). Underyearling coho fry were also significantly larger (p < 0.05) at gabion sites (mean, 50 mm) than at control sites (mean, 45 mm). Improved rearing habitat was created for coho juveniles by the gabions, a result of increased pool area and cover.
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Siegwald, Léa, Ségolène Caboche, Gaël Even, Eric Viscogliosi, Christophe Audebert, and Magali Chabé. "The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical “Microscope” Affect the Biological Interpretation?" Microorganisms 7, no. 10 (September 26, 2019): 393. http://dx.doi.org/10.3390/microorganisms7100393.
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Targeted metagenomics is the solution of choice to reveal differential microbial profiles (defined by richness, diversity and composition) as part of case-control studies. It is well documented that each data processing step may have the potential to introduce bias in the results. However, selecting a bioinformatics pipeline to analyze high-throughput sequencing data from A to Z remains one of the critical considerations in a case-control microbiota study design. Consequently, the aim of this study was to assess whether the same biological conclusions regarding human gut microbiota composition and diversity could be reached using different bioinformatics pipelines. In this work, we considered four pipelines (mothur, QIIME, kraken and CLARK) with different versions and databases, and examined their impact on the outcome of metagenetic analysis of Ion Torrent 16S sequencing data. We re-analyzed a case-control study evaluating the impact of the colonization of the intestinal protozoa Blastocystis sp. on the human gut microbial profile. Although most pipelines reported the same trends in this case-control study, we demonstrated how the use of different pipelines affects the biological conclusions that can be drawn. Targeted metagenomics must therefore rather be considered as a profiling tool to obtain a broad sense of the variations of the microbiota, rather than an accurate identification tool.
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Anjali, N., F. Nadiya, Jinu Thomas, and K. K. Sabu. "Discovery of MicroRNAs in Cardamom (Elettaria cardamomum Maton) under Drought Stress." Dataset Papers in Science 2017 (July 31, 2017): 1–4. http://dx.doi.org/10.1155/2017/9507485.
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MicroRNAs (miRNAs) are endogenous, 19–24-nucleotide-long, noncoding RNAs found in animals, plants, and some viruses. Drought is one of the major limiting factors that negatively affect productivity of plants. To date, nothing is known about the regulatory roles of miRNAs in response to drought stress in cardamom. Cardamom collected from the natural forest area in Therakkudi in the Idamalayar forest range was selected for the study. Total RNA was isolated from leaves and stems of control and drought treated cardamom plant, which was used for library construction. Ion torrent sequencing of the two small RNA libraries prepared from plants raised under well irrigated and drought stressed treatments, respectively, created 3,938,342 and 4,083,181 primary reads. A total of 150 conserved and 20 novel microRNAs were identified from both the control and the treated libraries. Discovery of 17 differentially expressed miRNAs under drought stress suggests that these might have been involved in various biological processes to improve plant tolerance to water stress. This study is the first report of drought responsive miRNAs and their targets in cardamom. The outcome of this research could provide insights into the miRNA based regulatory mechanisms in response to drought stress in monocot plants.
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Sampl, Peter, and Thomas Zwinger. "Avalanche simulation with SAMOS." Annals of Glaciology 38 (2004): 393–98. http://dx.doi.org/10.3189/172756404781814780.
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AbstractDry snow avalanches consist of two distinct layers. A dense-flow layer is superposed by a powder-snow layer, a cloud of relatively small ice particles suspended in air. The density of this suspension is one order of magnitude smaller than that of the dense flow. A simulation model for dry avalanches has been developed, based on separate sub-models for the two layers. The sub-models are coupled by an additional transition model, describing the exchange of mass and momentum between the layers. The fundamentals of the two-dimensional granular flow model for the dense flow and of the three-dimensional turbulent mixture model for the powder flow are presented. Results of the complete coupled model, SAMOS (Snow Avalanche MOdelling and Simulation), applied to observed catastrophic avalanche events, are discussed, and the prediction of powder-snow pressures acting on a tunnel bridge is briefly described. SAMOS is used routinely for hazard zoning at the Austrian Federal Service for Torrent and Avalanche Control.
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Galia, Tomáš. "Legacy of Human Impact on Geomorphic Processes in Mountain Headwater Streams in the Perspective of European Cultural Landscapes." Geosciences 11, no. 6 (June 12, 2021): 253. http://dx.doi.org/10.3390/geosciences11060253.
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Mountain headwater streams are still somewhat on the boundary of interest regarding possible human impact on their morphology or geomorphic processes, which may be caused by our perception of mountains as islands of relatively preserved natural conditions. This paper summarizes the past and present human pressure on the headwater streams that drain the highest mountain ranges of the Outer Western Carpathians in Czechia. Anthropogenic pressure began in this region in the 16th century during a colonization of the mountains and continued by timber harvesting, timber floating, and construction of torrent control works until present. Each of these interventions produced a morphological response of the channels in relation to altered sediment or water fluxes at the whole catchment scale or within longitudinal stream profiles. Because it is highly unlikely to reach pre-settlement conditions of the channels, the management effort should be concentrated to achieve realistic restoration targets under the present socioeconomic circumstances by taking into consideration the morphodynamical specifics of mountain headwater streams.
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Preciso, Emanuele, Enzo Salemi, and Paolo Billi. "Land use changes, torrent control works and sediment mining: effects on channel morphology and sediment flux, case study of the Reno River (Northern Italy)." Hydrological Processes 26, no. 8 (July 12, 2011): 1134–48. http://dx.doi.org/10.1002/hyp.8202.
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Song, Sze-Looi, Hoi-Sen Yong, Phaik-Eem Lim, and Ji Tan. "Mitochondrial Genome of Rattus tiomanicus (Rodentia: Muridae) and Molecular Phylogeny of Murinae." Sains Malaysiana 50, no. 4 (April 30, 2021): 953–65. http://dx.doi.org/10.17576/jsm-2021-5004-07.
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Rattus tiomanicus is a murid rodent of considerable agricultural and public health importance in Southeast Asia. The whole mitochondrial genome of R. tiomanicus was sequenced by the Ion Torrent PGM platform. It had a total length of 16,309 bp, consisting of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and two non-coding regions (L-strand replication origin and control region). Only TAA and incomplete T-stop codons were represented in the protein-coding genes. Of the tRNAs, tryptophan (W) had ACU anticodon. The cloverleaf structure for serine S1 (AGN) tRNA lacked the entire D-arm, while in lysine (K) tRNA, the DHU arm lacked the D-loop. Molecular phylogeny based on 15 mt-genes indicated R. tiomanicus having closest genetic affinity to R. rattus complex (R. rattus, R. tanezumi). There were two major clades for the Murinae subfamily namely the Rattini tribe and the Apodemini, Murini and Hydromyini tribes. The whole mitogenome of R. tiomanicus will serve as a useful dataset for studying the systematics and phylogenetic relationships of the murid rodents.
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Robin, Ferrari, Sakuntala Ale, Aysha Patel, Mikel Valgañón, Hui En Foong, Mary Alikian, Kikkeri Naresh, et al. "Targeted High-Throughput Sequencing For The Detection Of Mutations Associated With Myeloproliferative Neoplasms." Blood 122, no. 21 (November 15, 2013): 1613. http://dx.doi.org/10.1182/blood.v122.21.1613.1613.
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Abstract Background Myeloproliferative neoplasms (MPNs) are clonal hematopoietic stem cell disorders characterized by the proliferation of one or more myeloid cell lineages. Polycythemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (PMF) are the classical types of Philadelphia negative MPN. The JAK2 V617F missense mutation is found in 95% of patients with PV and in 50-60% of patients with PMF or ET. Molecular screening for JAK2 V617F mutation in suspected MPN patients by pyrosequencing has become routine method in diagnostic services. With the introduction of new methods of screening, a growing number of mutations have been described in a range of genes that code for receptor structure proteins (MPL, JAK2 exon 12), intracellular signalling proteins (CBL, SH2B3, NF1, SOCS1/3), proteins involved in leukemic progression (TP53, NRAS/KRAS, NF1, IDH1/2), or epigenetic modifications (EZH2, ASXL1, TET2). Molecular genetic screening for these targets in JAK2 V617F negative cases can be laborious, time-consuming and expensive, but the advent of benchtop-class high-throughput sequencers and custom target enrichment platforms gives the opportunity to test all relevant mutations in multiple genes in a single assay. Aims: To evaluate the Ion Torrent PGM high-throughput sequencer and custom AmpliSeq capture platform for the screening of most relevant MPN associated mutations in JAK2 V617F negative cases and validate candidate mutations using pyrosequencing. Methods 32 DNA samples (30 JAK2 V617F negative by pyrosequencing, 1 positive, 1 not tested) from patients with MPN disorders (thrombocytosis, neutrophilia or polycythemia) were screened (with appropriate ethical consent) for mutations using the Ion Torrent PGM sequencing platform. AmpliSeq multiplex primers were used for the target capture and the panel was designed via the online portal (v1.2), targeting 23 regions of 13 genes associated with MPN. The workflow involved library preparation and multiplex sample pooling following qPCR quantification (16 samples per run), emulsion PCR template preparation, Ion 318 chip loading and sequencing. Alignment and variant calling was via the Torrent Server 3.6.2 plugins, using custom coverage and hot-spot files to define the regions of interest. Variant calls were visualised using IGV and UCSC, and functionally annotated using CONDEL, Mutation Assessor and PROVEAN. Results 31 of the 32 samples were successfully sequenced, with a mean depth of 1049 reads and the FASTQC plugin indicated good quality sequencing metrics. All JAK2 V617F negative samples were called V617F negative by the PGM. The V671F positive control sample was called at a frequency of 18.1% (19% by pyrosequencing). The untested sample was called positive (10%) for JAK2 V617F and this was validated using pyrosequencing (11%). No MPL or JAK2 exon 12 mutations were detected. Novel SNPs were seen in CBL (Chr11:119149062; G>A; intron 8-9), JAK2 (Chr9:5072649; T>C; intron 13-14), SOCS3 (Chr17:76354148; C>G; 3’UTR) and SH2B3 [(Chr12: 111856076; C>T; p.R43C) and (Chr12: 111856105; T>G; p.H52Q); both in exon 2]. Of these, the SH2B3 variants were flagged as deleterious (H52Q) and highly deleterious (R43C: SIFT=0; PPH2=0.998). Five samples (4 het, 1 hom) had a SNP in IDH1 associated with poor outcome in AML (rs11554137; MAF=0.05) and a further 6 samples had variants flagged as deleterious by at least one of the annotation platforms: one in SH2B3 [p.186I (rs183913232 )] and five in TET2 [2 samples with p.G355D (rs61744960); 2 with p.L34F (rs111948941) and one p.Y867H (COSM327337)]. Additionally, one sample with a TET2 L34F also had a COSMIC annotated JAK2splice site variant (c.1864+14C>T; COSM88203). Summary This study shows the ability of the Ion Torrent PGM and AmpliSeq platforms to analyse qualitatively and quantitatively multiple samples for multiple genes with good accuracy and specificity (no false positives for V617F), making this qualitative and quantitative method more time and cost-effective than traditional sequencing techniques. Additionally, several potentially disease-associated variants were detected, which would have been missed by conventional MPN screening strategies and we are proposing to roll this approach out as a diagnostic screening in our MPN clinic in the very near future. Disclosures: Milojkovic: BMS: Honoraria; Pfizer: Honoraria; Ariad: Honoraria; Novartis: Honoraria. Apperley:Novartis: Honoraria, Research Funding; Bristol Myers Squibb: Honoraria; Pfizer, Ariad: Honoraria (not direct from company), Honoraria (not direct from company) Other.
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Winter, Helen, Pamela J. Kaisaki, Joe Harvey, Edoardo Giacopuzzi, Matteo P. Ferla, Melissa M. Pentony, Samantha J. L. Knight, Ricky A. Sharma, Jenny C. Taylor, and James S. O. McCullagh. "Identification of Circulating Genomic and Metabolic Biomarkers in Intrahepatic Cholangiocarcinoma." Cancers 11, no. 12 (November 28, 2019): 1895. http://dx.doi.org/10.3390/cancers11121895.
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Intrahepatic cholangiocarcinoma (ICC) is an aggressive cancer arising from the bile ducts with a need for earlier diagnosis and a greater range of treatment options. KRAS/NRAS mutations are common in ICC tumours and 6–32% of patients also have isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) gene mutations associated with metabolic changes. This feasibility study investigated sequencing circulating tumour DNA (ctDNA) combined with metabolite profiling of plasma as a method for biomarker discovery in ICC patients. Plasma was collected from four ICC patients receiving radio-embolisation and healthy controls at multiple time points. ctDNA was sequenced using Ampliseq cancer hotspot panel-v2 on Ion Torrent PGM for single nucleotide variants (SNV) detection and with Illumina whole genome sequencing for copy number variants (CNV) and further targeted examination for SNVs. Untargeted analysis of metabolites from patient and control plasma was performed using liquid chromatography coupled with high-resolution tandem mass spectrometry (LC-MS/MS). Metabolite identification was performed using multi-parameter comparisons with analysis of authentic standards, and univariate statistical analysis was performed to identify differences in metabolite abundance between patient and control samples. Recurrent somatic SNVs and CNVs were identified in ctDNA from three out of four patients that included both NRAS and IDH1 mutations linked to ICC. Plasma metabolite analysis revealed biomarker metabolites associated with ICC and in particular 2-hydroxyglutarate (2-HG) levels were elevated in both samples from the only patient showing a variant allele in IDH1. A reduction in the number of CNVs was observed with treatment. This study demonstrates that ctDNA and metabolite levels can be identified and correlated in ICC patient blood samples and differentiated from healthy controls. We conclude that combining genomic and metabolic analysis of plasma offers an effective approach to biomarker identification with potential for disease stratification and early detection studies.
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Bombino, Giuseppe, Vincenzo Tamburino, Demetrio Antonio Zema, and Santo Marcello Zimbone. "THE INFLUENCE OF CHECK DAMS ON FLUVIAL PROCESSES AND RIPARIAN VEGETATION IN MOUNTAIN REACHES OF TORRENTS." Journal of Agricultural Engineering 41, no. 3 (September 30, 2010): 37. http://dx.doi.org/10.4081/jae.2010.3.37.
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The complex hydrogeomorphological processes within the active channel of rivers strongly influence riparian vegetation development and organization, particularly in mountain streams where such processes can be remarkably impacted by engineering control works. In four mountain reaches of Calabrian fiumaras we analyze, through previously arranged methods (integrated by a multivariate statistic analysis), the relationships among hydrogeomorphological river characteristics and structure and the development of riparian vegetation within the active channel in transects located in proximity of check dams and in less disturbed sites. The results of this study demonstrate clear and relevant contrasts, due to the presence of check dams, in the physical and vegetation properties of upstream, downstream and intermediate sites around check dams. The multivariate statistical approach through the Principal Component Analysis (PCA) highlighted evident relationships in all transects between groups of physical and vegetation properties. The regression analysis performed between the vegetation properties and the width:depth ratio or the specific discharge showed very different relationships between groups of transects, due to evident changes in channel morphology and in flow regime locally induced by check dams. Overall we have shown that check dams have far reaching effects in the extent and development of riparian vegetation of mountain torrent reaches, which extend far beyond physical adjustments to changed morphological, hydraulic and sedimentary conditions.
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Ristic, Ratko, Boris Radic, Zoran Nikic, Goran Trivan, Nevena Vasiljevic, Slavoljub Dragicevic, Nenad Zivkovic, and Zoran Radosavljevic. "Erosion control and protection from torrential floods in Serbia-spatial aspects." Spatium, no. 25 (2011): 1–6. http://dx.doi.org/10.2298/spat1125001r.
Full textAbstract:
Torrential floods represent the most frequent phenomenon within the category of ?natural risks? in Serbia. The representative examples are the torrential floods on the experimental watersheds of the rivers Manastirica (June 1996) and Kamisna (May 2007). Hystorical maximal discharges (Qmaxh) were reconstructed by use of ?hydraulics flood traces? method. Computations of maximal discharges (Qmaxc), under hydrological conditions after the restoration of the watersheds, were performed by use of a synthetic unit hydrograph theory and Soil Conservation Service methodology. Area sediment yields and intensity of erosion processes were estimated on the basis of the ?Erosion Potential Method?. The actual state of erosion processes is represented by the coefficients of erosion Z=0.475 (Manastirica) and Z=0.470 (Kamisna). Restoration works have been planned with a view to decreasing yields of erosive material, increasing water infiltration capacity and reducing flood runoff. The planned state of erosion processes is represented by the coefficients of erosion Z=0.343 (Manastirica) and Z=0.385 (Kamisna). The effects of hydrological changes were estimated by the comparison of historical maximal discharges and computed maximal discharges (under the conditions after the planned restoration). The realisation of restoration works will help decrease annual yields of erosive material from W?=24357 m3 to W?=16198.0 m3 (Manastirica) and from W?=19974 m3 to W?=14434 m3 (Kamisna). The values of historical maximal discharges (QmaxhMan=154.9 m3?s-1; QmaxhKam=76.3 m3?s-1) were significantly decreased after the restoration (QmaxcMan=84.5 m3 ?s-1; QmaxcKam=43.7 m3?s-1), indicating the improvement of hydrological conditions, as a direct consequence of erosion and torrent control works. Integrated management involves biotechnical works on the watershed, technical works on the hydrographic network within a precisely defined administrative and spatial framework in order to achieve maximum security for people and their property and to meet other requirements such as: environmental protection, sustainable soil usage, drinking water supply, rural development, biodiversity sustaining, etc. The lowest and the most effective level is attained through PAERs (Plans for announcement of erosive regions) and PPTFs (Plans for protection from torrential floods), with HZs (Hazard zones) and TAs (Threatened areas) mapping on the basis of spatial analysis of important factors in torrential floods formation. Solutions defined through PAERs and PPTFs must be integrated into Spatial Plans at local and regional levels.
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Shelomi, Matan, Bo-Jun Qiu, and Lin-Ting Huang. "Cucumber vs Ants: a Case Against the Myth of the Uses of Plant Extracts in Insect Pest Management." Sociobiology 68, no. 2 (April 15, 2021): 5813. http://dx.doi.org/10.13102/sociobiology.v68i2.5813.
Full textAbstract:
An accumulation of questionable scientific reports on the use of natural plant extracts to control household pest insects, using biologically irrelevant experimental designs and extremely high concentrations, has resulted in a publication bias: “promising” studies claiming readily available plants can repel various insects, including social insects, despite no usable data to judge cost-effectiveness or sustainability in a realistic situation. The Internet provides a further torrent of untested claims, generating a background noise of misinformation. An example is the belief that cucumbers are “natural” ant repellent, widely reported in such informal literature, despite no direct evidence for or against this claim. We tested this popular assertion using peel extracts of cucumber and the related bitter melon as olfactory and gustatory repellents against ants. Extracts of both fruit peels in water, methanol, or hexane were statistically significant but effectively weak gustatory repellents. Aqueous cucumber peel extract has a significant but mild olfactory repellent effect: about half of the ants were repelled relative to none in a control. While the myth may have a grain of truth to it, as cucumber does have a mild but detectable effect on ants in an artificial setup, its potential impact on keeping ants out of a treated perimeter would be extremely short-lived and not cost-effective. Superior ant management strategies are currently available. The promotion of “natural” products must be rooted in scientific evidence of a successful and cost-effective implementation prospect.
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Wang, Yuzheng, Lei Nie, Min Zhang, Hong Wang, Yan Xu, and Tianyu Zuo. "Assessment of Debris Flow Risk Factors Based on Meta-Analysis—Cases Study of Northwest and Southwest China." Sustainability 12, no. 17 (August 23, 2020): 6841. http://dx.doi.org/10.3390/su12176841.
Full textAbstract:
Debris flow is a type of special torrent containing numerous solid materials. With many types of factors affecting debris flow, there is no reliable basis for the selection of risk factors for debris flow risk assessment. Therefore, to study the factors affecting debris flow, exploring a reliable method for assessing the relative importance of these factors is a significant endeavor in debris flow prevention and control work. In this research, debris flow risk assessment was combined with meta-analysis to analyze quantitatively the relative importance of risk factors of debris flow in northwest and southwest China. The final relative importance of each factor in northwest China is as follows, maximum relative height difference > slope of main channel > maximum daily precipitation > ratio of longitudinal slope > drainage area > length of main channel. In addition, in southwest China, maximum relative height difference > maximum daily precipitation > slope of main channel > ratio of longitudinal slope > length of main channel > drainage area. The meta-analysis results were accurate, which can provide a reliable basis for the selection of debris flow risk factors in debris flow risk assessment. Furthermore, it provides strong support for the application of meta-analysis in risk assessment of other geological hazards.