Applications of Natural Language Processing in Biodiversity Science

Centuries of biological knowledge are contained in the massive body of scientific literature, written for human-readability but too big for any one person to consume. Large-scale mining of information from the literature is necessary if biology is to transform into a data-driven science. A computer can handle the volume but cannot make sense of the language. This paper reviews and discusses the use of natural language processing (NLP) and machine-learning algorithms to extract information from systematic literature. NLP algorithms have been used for decades, but require special development for application in the biological realm due to the special nature of the language. Many tools exist for biological information extraction (cellular processes, taxonomic names, and morphological characters), but none have been applied life wide and most still require testing and development. Progress has been made in developing algorithms for automated annotation of taxonomic text, identification of taxonomic names in text, and extraction of morphological character information from taxonomic descriptions. This manuscript will briefly discuss the key steps in applying information extraction tools to enhance biodiversity science

Erosion and sediment yield on the earth

The paper is based on suspended sediment yield data from 3763 stations and bed load data from 295 stations. Within plain regions a distinct maximum of erosion and sediment yield occurs in the tropical and subtropical zones. Statistical analysis indicates that the principal factors controlling the zonal distribution of erosion are runoff amount and land cultivation. The latter varies considerably in different natural zones. Topographic and geologic controls on the erosion rates are discussed. For small streams, the influence of zonal factors is less pronounced, and azonal factors (topography, geology) are more important. Taking into consideration all the available data, two principal models of erosion may be suggested: natural and natural-anthropogenic

New data on the antipodal location of the largest landforms of the Earth

Some new data on the antipodal location of the largest landforms of the Earth with a global digital elevation model ETOPO2 and methods of correlation analysis obtained. The coefficient of association calculated for the Earth's continents reaches -0.84. The correlation coefficient between the heights of the relief in antipodal points, one of which belongs to the land, is -0.54. Qualitative characteristics (geostructural and morphostructural features of Earth's surface) of antipodal points do not show any significant statistical correlation. Decrease of continent area reduces the severity of their antipodal location. It is concluded that the continents on the Earth are located non-randomly. © 2014 AENSI Publisher All rights reserved

Site-specific mutagenesis of Drosophila proliferating cell nuclear antigen enhances its effects on calf thymus DNA polymerase δ

BACKGROUND: We and others have shown four distinct and presumably related effects of mammalian proliferating cell nuclear antigen (PCNA) on DNA synthesis catalyzed by mammalian DNA polymerase δ(pol δ). In the presence of homologous PCNA, pol δ exhibits 1) increased absolute activity; 2) increased processivity of DNA synthesis; 3) stable binding of synthetic oligonucleotide template-primers (t(1/2 )of the pol δ•PCNA•template-primer complex ≥2.5 h); and 4) enhanced synthesis of DNA opposite and beyond template base lesions. This last effect is potentially mutagenic in vivo. Biochemical studies performed in parallel with in vivo genetic analyses, would represent an extremely powerful approach to investigate further, both DNA replication and repair in eukaryotes. RESULTS: Drosophila PCNA, although highly similar in structure to mammalian PCNA (e.g., it is >70% identical to human PCNA in amino acid sequence), can only substitute poorly for either calf thymus or human PCNA (~10% as well) in affecting calf thymus pol δ. However, by mutating one or only a few amino acids in the region of Drosophila PCNA thought to interact with pol δ, all four effects can be enhanced dramatically. CONCLUSIONS: Our results therefore suggest that all four above effects depend at least in part on the PCNA-pol δ interaction. Moreover unlike mammals, Drosophila offers the potential for immediate in vivo genetic analyses. Although it has proven difficult to obtain sufficient amounts of homologous pol δ for parallel in vitro biochemical studies, by altering Drosophila PCNA using site-directed mutagenesis as suggested by our results, in vitro biochemical studies may now be performed using human and/or calf thymus pol δ preparations

Suspended sediment yield mapping of Northern Eurasia

Copyright © 2014 IAHS Press. The mapping of river sediment yields at continental or global scale involves a number of technical difficulties that have largely been ignored. The maps need to show the large zonal peculiarities of river sediment yields, as well as the level (smoothed) local anomalies. This study was carried out to create a map of river sediment yields for Northern Eurasia (within the boundaries of the former Soviet Union, 22 × 106 km2) at a scale of 1:1 500 000. The data for preparing the map were taken from the long-term observations recorded at more than 1000 hydrological stations. The data have mostly been collected during the 20th century by applying a single method. The creation of this map from the study of river sediment yield is a major step towards enhancing international research on understanding the mechanical denudation of land due mainly to erosion

Mapping and spatial analysis of suspended sediment yields from the Russian Plain

The aim of this paper is to demonstrate the potential use of a GIS and associated database to map and analyse global patterns of sediment yield. Attention focuses on the suspended sediment yield (SSY) data available for the European territories of the Russian Federation and the variation of SSY across part of the Russian Plain. A GIS and database have been developed for the Volga River basin. The GIS system permits the drainage basins for which SSY data are available to be delineated and the database conflates information on sediment yield and the hydrological and physiographic characteristics of the individual drainage basins. A map of the variation of annual sediment yield within the Volga basin is presented. Copyright © 2012 IAHS Press

Pengaruh Jenis Busi Terhadap Konsumsi Bahan Bakar Dan Emisi Gas Buang Pada Sepeda Motor Honda Revo Fit 110 cc

Tingkat panas busi adalah kemampuan busi untuk membawa panas dari ruang pembakarankeluar dari ujung busi ke shell busi. Semakin besar nilainya, panas lebih mudah dilepaskan. Penelitianini menguji tiga jenis tingkat panas busi yaitu U20EPR9, U24EPR9, dan U27EPR9. Masing-masingbusi diteliti konsumsi bahan bakar dan emisi gas buang dengan waktu 180 detik pada putaran mesin1500, 2000, 2500, 3000, 3500, 4000, dan 4500. Berdasarkan hasil penelitian dapat disimpulkanbahwa penggunaan jenis busi berdasarkan tingkat panas pada sepeda motor Honda Revo Fit 110 cctahun 2012 berpengaruh terhadap konsumsi bahan bakar. Pada penggunaan busi U20EPR9 konsumsibahan bakar secara total pada semua putaran mesin yang diujikan adalah sebesar 82,27 ml, sedangkankonsumsi bahan bakar busi U24EPR9 adalah 80,98 ml mengalami penurunan sebesar 1,5% dibandingdengan busi U20EPR9. Pada pemakaian busi U27EPR9 konsumsi bahan bakar adalah 72,68 mlmengalami penurunan sebesar 11,6% dari busi U20EPR9. Sedangkan konsumsi bahan bakar padabusi U27EPR9 mengalami penurunan 10,2% dari busi U24EPR9. Konsentrasi Karbon Monoksidaterendah dihasilkan oleh busi U27EPR9 pada putaran 1500 rpm sebesar 0,12%. KonsentrasiKarbondioksida tertinggi dihasilkan oleh busi U27EPR9 pada putaran 4000 rpm sebesar 1,27%.Konsentrasi Hidrokarbon terendah dihasilkan oleh busi U20EPR9 pada putaran 4000 rpm sebesar16,29 ppm. Sedangkan konsentrasi Oksigen mengalami peningkatan yang signifikan padapenggunaan busi U20EPR9, peningkatan tertinggi sebesar 19,70% didapatkan pada putaran 4000rpm

A national geopark in the republic of tatarstan (Russia): A feasibility study

The area, which occupies the right bank of the Volga River from the mouth of its tributary, Sviyaga River, to the southern border of Tatarstan, and the right bank of the Kama River from its mouth to the northeastern border of Tatarstan, is considered to warrant the possible creation of a national geopark. The area is characterized by well-defined limits, and it occupies 2,080 km2 that is commensurate with an area of many successfully functioning geoparks. It has more than 150 years of history of comprehensive geological studies carried out by prominent Russian and foreign geologists. A significant number of geosites (29) of different types and significance levels accessible to visitors are revealed there. The majority of the geosites are of interest first of all in terms of stratigraphy and palaeontology as well as geomorphology, tectonics, petrology, hydrogeology, and history of geology and mining. These geosites allow study of the history of the Earth's organic world in the Middle-Upper Permian, geological events, and processes that occurred in this region, as well as landform evolution. This area is of aesthetic value owing to the variety and beauty of its natural landscapes. It also contains abundant nongeological natural, historical, and cultural heritage sites attractive for tourists. It is also characterized by a high level of economic development, well-developed infrastructure, and the existence of officially protected sites that occupy a fifth of the territory. The area is of high educational significance as well. It has, for a long time, been used as a geological training ground for students of the Kazan State University, Russia. Moreover, the scientific and methodical basis for seven educational-excursion routes including visiting particularly interesting geological, historical, and cultural sites of the planned geopark has been already developed. The comprehensive evaluation of this area shows that it meets all necessary criteria for geopark creation. © 2010 Springer-Verlag

Spatial variability of the particle size of river sediments into western part of the former USSR

© 2016, International Journal of Pharmacy and Technology. All rights reserved.Studying of particle size distribution of river sedimentsand alluvial deposits hasgreat importance for modern geomorphology and paleogeography. In the currentwork impact assessmentof such factors as orography, human activities and river water dischargeon the particle size of uspended sediments and bed materials of the rivers into Western part of the former USSR is attempted. The studied area includesthe Baltic countries, Belarus, Ukraine, Moldova, the countries of Transcaucasia, and the European part of Russia. Division into districts of the explored territory on particle size of river deposits is performed. With transition Increase in particle size of the suspended sediments and, especially, bed materials from the plains to mountains is observed. This is associated with increase ofaverage relief height that leads to increase in the transporting ability of the rivers. Due the higher transporting ability rivers carry both small and large material.Human activityaffects particle size of the suspended sediments: the share of the small material which arrives from river basin increases in very intensively used drainage area.Particle size of bed materials poorly depends on extent of transformation of landscapes in river basin. Increase in water discharge leads to reduction of particle size of the suspended sediments and bed materials:thin material formed by processes of soil and gully erosion transports to river network. Use of cluster analysis allows receiving evident spatial distribution of particle size of modern river deposits

SeaBase : a multispecies transcriptomic resource and platform for gene network inference

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Integrative and Comparative Biology 54 (2014): 250-263, doi: 10.1093/icb/icu065.Marine and aquatic animals are extraordinarily useful as models for identifying mechanisms of development and evolution, regeneration, resistance to cancer, longevity and symbiosis, among many other areas of research. This is due to the great diversity of these organisms and their wide-ranging capabilities. Genomics tools are essential for taking advantage of these “free lessons” of nature. However, genomics and transcriptomics are challenging in emerging model systems. Here, we present SeaBase, a tool for helping to meet these needs. Specifically, SeaBase provides a platform for sharing and searching transcriptome data. More importantly, SeaBase will support a growing number of tools for inferring gene network mechanisms. The first dataset available on SeaBase is a developmental transcriptome profile of the sea anemone Nematostella vectensis (Anthozoa, Cnidaria). Additional datasets are currently being prepared and we are aiming to expand SeaBase to include user-supplied data for any number of marine and aquatic organisms, thereby supporting many potentially new models for gene network studies.2015-06-0