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Ravichandran, S., K. Kumaravel, G. Kaliyavarathan, and G. Rameshkumar. "First record of Eurypanopeus orientalis crab from Indian Coast." Biotemas 22, no. 4 (January 1, 2009): 247. http://dx.doi.org/10.5007/2175-7925.2009v22n4p247.
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http://dx.doi.org/10.5007/2175-7925.2009v22n4p247The present study reports the first occurrence of a male crab Eurypanopeus orientalis caught on 7th of March 2009 at Parangipettai coast (Bay of Bengal) which is an East coastal region of Southern India. Eurypanopeus orientalis was first reported in 1939 by Sakai in the Sagami bay coast of Japan. This is the first record in Indian Coast which expands in its known range.
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Nemoto, Masao, and Makoto Shimizu. "The Catch Characteristics of Set-net Fishing Grounds in Seisyou Region of Sagami Bay." NIPPON SUISAN GAKKAISHI 63, no. 6 (1997): 947–55. http://dx.doi.org/10.2331/suisan.63.947.
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Kato, Kenichi, Keiiti Aki, and Ta-Liang Teng. "3-D simulations of surface wave propagation in the Kanto sedimentary basin, Japan—part 1: Application of the surface wave Gaussian beam method." Bulletin of the Seismological Society of America 83, no. 6 (December 1, 1993): 1676–99. http://dx.doi.org/10.1785/bssa0830061676.
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Abstract The goal of this study is to simulate the displacement waveforms of 8 sec-period Love waves observed at Tokyo and Yokohama stations in the Kanto sedimentary basin during the Izu-hanto-toho-oki Earthquake of 29 June 1980 (M0 = 7 × 1025 dyne · cm). The surface wave Gaussian beam method is applied for this purpose. On the basis of the 3-D seismic velocity and density structure of the Kanto basin and assuming that the earth medium is laterally homogeneous outside the Kanto basin, waveforms of Love waves are synthesized. The synthesized seismograms underestimate the observed peak amplitudes at Yokohama station. This is primarily because the station is located in the direction of the nodal plane of the Love-wave radiation. As indicated by Yamanaka et al. (1992), a Quaternary basin exists in the Sagami Bay between the source location and the Kanto basin. We include the Sagami basin in our model by the approximation of a circular low-velocity region. Excellent agreement between observed and synthesized waveforms was achieved not only for amplitude but also for phase for the early parts of the wave trains at both stations. We conclude that the low velocity Quaternary basin in the Sagami Bay acts like a lens to focus surface wave energy resulting in high amplitudes. The later arriving waves, in particular the long duration observed at Tokyo station, however, cannot be adequately explained by this method. One possible reason for the failure of simulating the later phases is that this method disregards the secondary Love waves converted from S-waves and/or surface waves at a laterally discontinuous boundary. Although the surface wave Gaussian beam method cannot adequately predict the duration of observed seismograms, it provides us with a satisfactory prediction of amplitudes and phases for early arrivals in laterally slowly-varying media at drastically lower computation costs and less memory requirements than does other methods.
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Uemoto, Shinji, and Yo Uesugi. "Evidence for Eearthquake Shaking at Archaeological Sites near the Sagami Bay Region in Southern Kanto, Japan." Quaternary Research (Daiyonki-Kenkyu) 38, no. 6 (1999): 533–42. http://dx.doi.org/10.4116/jaqua.38.533.
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Nemoto, Masao, and Makoto Shimizu. "The Yearly Similarities in Species Composition of Set-net Fishing Grounds in Seisyou Region of Sagami Bay." NIPPON SUISAN GAKKAISHI 63, no. 6 (1997): 956–63. http://dx.doi.org/10.2331/suisan.63.956.
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Suda, Yusuke, Makoto Shimizu, and Yukio Nose. "Two types of Japanese jack mackerel Trachurus japonicus of summer spawning group in the Sagami Bay region." NIPPON SUISAN GAKKAISHI 53, no. 11 (1987): 1921–23. http://dx.doi.org/10.2331/suisan.53.1921.
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Masunaga, Eiji, Oliver B. Fringer, Yujiro Kitade, Hidekatsu Yamazaki, and Scott M. Gallager. "Dynamics and Energetics of Trapped Diurnal Internal Kelvin Waves around a Midlatitude Island." Journal of Physical Oceanography 47, no. 10 (October 2017): 2479–98. http://dx.doi.org/10.1175/jpo-d-16-0167.1.
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AbstractThe generation of trapped and radiating internal tides around Izu‐Oshima Island located off Sagami Bay, Japan, is investigated using the three-dimensional Stanford Unstructured Nonhydrostatic Terrain-following Adaptive Navier–Stokes Simulator (SUNTANS) that is validated with observations of isotherm displacements in shallow water. The model is forced by barotropic tides, which generate strong baroclinic internal tides in the study region. Model results showed that when diurnal K1 barotropic tides dominate, resonance of a trapped internal Kelvin wave leads to large-amplitude internal tides in shallow waters on the coast. This resonance produces diurnal motions that are much stronger than the semidiurnal motions. The weaker, freely propagating, semidiurnal internal tides are generated on the western side of the island, where the M2 internal tide beam angle matches the topographic slope. The internal wave energy flux due to the diurnal internal tides is much higher than that of the semidiurnal tides in the study region. Although the diurnal internal tide energy is trapped, this study shows that steepening of the Kelvin waves produces high-frequency internal tides that radiate from the island, thus acting as a mechanism to extract energy from the diurnal motions.
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Shishikura, Masanobu. "History of the paleo-earthquakes along the Sagami Trough, central Japan: Review of coastal paleoseismological studies in the Kanto region." Episodes 37, no. 4 (December 1, 2014): 246–57. http://dx.doi.org/10.18814/epiiugs/2014/v37i4/004.
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Hwang, Kangseok, and Ichiro Aoki. "An Approach to Neuro-computing for Forecasting Catches of Multiple Species in the Set Net of Seishyo Region, Western Sagami Bay." NIPPON SUISAN GAKKAISHI 63, no. 4 (1997): 549–56. http://dx.doi.org/10.2331/suisan.63.549.
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Nemoto, Masao, and Makoto Shimizu. "The Yearly Fluctuations of Similarities Appearing in Species Composition of Set-net Fishing Grounds in the Seisyou Region of Sagami Bay." NIPPON SUISAN GAKKAISHI 64, no. 3 (1998): 384–92. http://dx.doi.org/10.2331/suisan.64.384.
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Kaneko, Hiroaki, Shin-ichi Ishiwata, and Takeji Takamura-Enya. "The fine-scale genetic structure and dispersal ability of the mayfly Ecdyonurus yoshidae Takahashi (Ephemeroptera: Heptageniidae) in the Sagami River system, southern Kanto Region, Japan." Journal of Asia-Pacific Entomology 25, no. 4 (December 2022): 101996. http://dx.doi.org/10.1016/j.aspen.2022.101996.
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Hu, Jinjun, Jingyang Tan, and John X. Zhao. "New GMPEs for the Sagami Bay Region in Japan for Moderate Magnitude Events with Emphasis on Differences on Site Amplifications at the Seafloor and Land Seismic Stations of K-NET." Bulletin of the Seismological Society of America 110, no. 5 (June 16, 2020): 2577–97. http://dx.doi.org/10.1785/0120190305.
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ABSTRACT Ground-motion prediction equations (GMPEs) for the horizontal and vertical spectral accelerations (SAs) from the offshore area off the Sagami Bay is presented in this article. To compare the ground motions on the seafloor with those at onshore sites, an onshore GMPE was derived for the onshore stations adjacent to the offshore sites and including those in the Kanto basin sites. The offshore dataset includes 738 three-component records, and the onshore dataset includes 3775 records; both datasets are derived from the same set of 233 earthquakes selected for this study. The local site conditions of the offshore sites are investigated by implementing the mean horizontal-to-vertical response spectral ratios because soil condition data are unavailable. Individual site correction terms are used for the offshore sites due to differences among the site conditions, whereas site-class terms are used for the onshore sites based on the travel-time-averaged shear-wave velocity to 30 m (VS30). A comparison between the offshore and onshore models shows that the horizontal SAs for the whole periods and vertical SAs for moderate and long periods of the offshore motions are considerably larger than those of the onshore motions due to the deep deposition layer comprising soft sediment blanketing the seafloor; the vertical SAs of the offshore motions are slightly smaller than those of the onshore motions at short spectral periods. The inconsistency of the vertical motions at short periods may be due to the combined effect of the deposition layer and water layer. However, the vertical site amplification for short periods is independent of the water depth, and the reason of high-frequency deficiency in vertical components need further investigation.
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Fujiwara, Hiroyuki. "Special Issue on Strong Ground Motion Prediction and Seismic Hazard Assessment." Journal of Disaster Research 8, no. 5 (October 1, 2013): 847. http://dx.doi.org/10.20965/jdr.2013.p0847.
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We have been conducting seismic hazard assessment for Japan under the guidance of the Headquarters for Earthquake Research Promotion of Japan since the 1995 Hyogo-ken Nanbu Earthquake, and have made National Seismic Hazard Maps for Japan for use in estimating strong ground motion caused by future earthquakes. This special issue reviews the results of these efforts. Such work includes the development of seismic hazard assessment methodology for Japan, highly accurate prediction techniques for strong seismic ground motion and modeling underground structures for evaluating strong ground motion. Related research on utilization initiatives and risk assessment based on hazard information has also been conducted. An open Web system – the Japan Seismic Hazard Information Station (J-SHIS) – has even been developed to provide information interactively. The 2011 Mw9.0 Great East Japan Earthquake was the largest such event recorded in the history of Japan. This megathrust earthquake was not considered in National Seismic Hazard Maps for Japan. But efforts toward revising seismic hazard assessment in Japan are progressing based on lessons learned from this earthquake. Hazard assessment is currently being reviewed in relation to the large earthquakes anticipated to occur in the near future based in the Sagami Trough and the Nankai Trough in the waters of offshore Japan. This assessment, which considers earthquakes larger than those assumed to have occurred in the past, is being reviewed as of this writing. In light of these pressing circumstances, studies are now being implemented to evaluate the long-period ground motion accompanying these large earthquakes. The knowledge that has been cultivated in Japan in terms of seismic hazard assessment has reached a high level, and it is important to expand such knowledge both internationally and domestically. This is just one of the reasons that efforts here in Japan are being made to help improve the level of seismic hazard assessment in the Asian region and throughout the entire world. It is expected that this special issue will help contribute to the further development of strong ground motion prediction and seismic hazard assessment now and in the future. Finally, I extend our sincere thanks to all of the contributors and reviewers involved with these articles.
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А. В., Выборнов,, and Тимощенко, А. А. "BRIEF REVIEW OF THE RESCUE ARCHAEOLOGICAL EXCAVATIONS CARRIED OUT BY THE INSTITUTE OF ARCHAEOLOGY AND ETHNOGRAPHY OF THE SIBERIAN BRANCH OF THE RUSSIAN ACADEMY OF SCIENCES IN 2020-2021 IN THE ASKIZ DISTRICT OF THE REPUBLIC OF KHAKASSIA." SCIENTIFIC REVIEW OF SAYANO-ALTAI, no. 1(33) (October 26, 2022): 142–56. http://dx.doi.org/10.52782/kril.2022.1.33.006.
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В статье дается краткий обзор исследований Аскизской археологической экспедиции ИАЭТ СО РАН в 2020-2021 гг. в зоне строительства второго пути железной дороги Междуреченск - Тайшет. Спасательные полевые работы проведены на площади погребальных и стояночных комплексов в бассейнах рек Аскиз, Камышта, Абакан. Изученные памятники содержат материалы большинства известных археологических культур региона: афанасьевской (могильники Уйтаг-3 и Казановка-13, стоянка Югачи-2), окуневской (могильник Сагайская протока-4, отдельные стелы в курганах у горы Уйтаг), карасукской (могильники Казановка-6, Сагайская протока-4, 7, Аскиз-17), тагарской (могильники Казановка-6, Станция Казановская-1, Сагайская протока-1, 2, 5, 12, Станция Камышта-1, Уйтаг-3, Скальная-4, 6, 7), тесинской (стоянка Югачи-1, могильники Станция Казановская-1, Сагайская протока-2, 5, Уйтаг-3, Скальная-4, Скальная-5), таштыкской (культурный слой на Казановке-14, Казановке-10, Сагайская протока-5, поминальники на могильниках Сагайская протока-2, 8) и Средневековья - этнографической современности (стоянки Югачи-1, 2, Казановка-10). The article provides a brief review of the research of the Askiz Archaeological Expedition conducted by the Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences in 2020-2021 in the construction zone of the second track of the Mezhdurechensk - Taishet railway. Rescue field work was carried out on the area of burial and settlement complexes in the basins of the Askiz, Kamyshta, and Abakan Rivers. The studied sites contain materials from most of the famous archaeological cultures of the region: Afanasevo (burial grounds Uitag-3 and Kazanovka-13, settlement site Yugachi-2), Okunev (burial ground Sagai Anabranch-4, separate steles in barrows near the Mount Uitag), Karasuk (burial grounds Kazanovka-6, Sagai Anabranch-4, 7, Askiz-17), Tagar (burial grounds Kazanovka-6, Kazanovka Station-1, Sagai Anabranch-1, 2, 5, 12, Kamyshta Station-1, Uitag-3, Skalnaya 4, 6, 7), Tes (settlement site Yugachi-1, burial grounds Kazanovka Station-1, Sagai Anabranch-2, 5, Uitag-3, Skalnaya-4, Skalnaya-5), Tashtyk (cultural layer at Kazanovka-14, Kazanovka-10, Sagai Anabranch-5, memorial sites at burial ground Sagai Anabranch-2, 8) and medieval - ethnographic modernity (Yugachi sites-1, 2, Kazanovka-10).
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Venkatesh, Dr, Venkatarangaiah Krishna, Krishnappa Pradeepa, Santosh Kumar S. Rajanna, Deeplanaik Nagaraja, Mohan Kumar, and Santhosh Kumar. "Identification and Characterization of Panama Wilt Causing Fungal Isolates to Musa Paradisiaca cv. Puttabale." International Journal of Applied Sciences and Biotechnology 2, no. 4 (December 25, 2014): 420–25. http://dx.doi.org/10.3126/ijasbt.v2i4.11135.
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Musa paradisiaca L. (Musaceae) cultivar ‘Puttabale’ is an indigenous banana commonly cultivated in the farmyards of Chitradurga,Davanagere, Chikmagalur and Shivamogga district of Karnataka. The fruits are valued for delicious taste. This banana cultivar is highlysusceptible to Fusarium infection and the yield loss has estimated to 30-40% at standing stage. The corm tissue of Musa paradisiaca cv.Puttabale showing typical panama wilt symptoms were collected from pathogen infected banana farmyard of Bhadravati, Sagara, Shikaripura,Holehonnur, Soraba, Thirthahalli, Gonibeedu and Lakkavalli regions of Shivamogga district of Karnataka. These infected corms were cultureon PDA medium and examined carefully by morphological and molecular identification. Out of the eight fungal isolates, the colonies of fungalisolates collected from Bhadravati, Sagara, Holehonnur, Thirthahalli, Gonibeedu and Lakkavalli regions produced a dense white aerialmycelium that evenly spread on the growth medium similar to the colony texture of Fusarium species. Among these fungal isolates, thepathogen collected from Gonibeedu region showed the presence of sickle or rod shaped, four-celled macro conidiophores, round or ovalshaped chlamydospores and the BLASTn search result showed 99 % similarity with the sequences of Fusarium oxysporum f. sp. cubense(Foc). The only one fungal isolate showed the presence of actual panama wilt causing fungi.DOI: http://dx.doi.org/10.3126/ijasbt.v2i4.11135 Int J Appl Sci Biotechnol, Vol. 2(4): 420-425
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Meijer, Rosa J., Thijmen J. P. Krebs, and Jelle J. Goeman. "A region-based multiple testing method for hypotheses ordered in space or time." Statistical Applications in Genetics and Molecular Biology 14, no. 1 (January 1, 2015): 1–19. http://dx.doi.org/10.1515/sagmb-2013-0075.
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AbstractWe present a multiple testing method for hypotheses that are ordered in space or time. Given such hypotheses, the elementary hypotheses as well as regions of consecutive hypotheses are of interest. These region hypotheses not only have intrinsic meaning but testing them also has the advantage that (potentially small) signals across a region are combined in one test. Because the expected number and length of potentially interesting regions are usually not available beforehand, we propose a method that tests all possible region hypotheses as well as all individual hypotheses in a single multiple testing procedure that controls the familywise error rate. We start at testing the global null-hypothesis and when this hypothesis can be rejected we continue with further specifying the exact location/locations of the effect present. The method is implemented in the
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Albanese, Giuseppe. "A technological index for the Italian regions." RIVISTA DI ECONOMIA E STATISTICA DEL TERRITORIO, no. 2 (June 2010): 54–69. http://dx.doi.org/10.3280/rest2010-002003.
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In this work we measure the technological position of the Italian regions with the adoption of the Technology Achievement Index developed by Desai, Fukuda, Johansson and Sagasti (2002). First we note that other available indexes are obtained as a by-product of theoretical- based methods, so that they are subject to the assumptions of their respective models. If using a statistical index permits to avoid this problem, adopting a composite index (unlike many single indexes) has also the advantage to summarize the evidence and to obtain a unique rank of the Italian regions according to their technological capabilities.
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Sagara, Keiko, and Nick Palfreyman. "Variation in the numeral system of Japanese Sign Language and Taiwan Sign Language." Asia-Pacific Language Variation 6, no. 1 (July 29, 2020): 119–50. http://dx.doi.org/10.1075/aplv.00009.sag.
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Abstract Abstract (Japanese Sign Language) The numerals 10, 100 and 1,000 are expressed variably in Japanese Sign Language (JSL) and Taiwan Sign Language (TSL), two languages that also have historic links. JSL was used in deaf schools that were established in Taiwan during the Japanese colonial era, leaving a lasting impression on TSL, but complex sociolinguistic situations have led to different outcomes in each case (Fischer, 2014; Sagara, 2014). This comparative sociolinguistic analysis is based on two datasets comprising a total of 1,100 tokens produced by 72 signers from the Kanto and Kansai regions (for JSL) and the cities of Tainan and Taipei (for TSL). Mixed effects modelling reveals that social factors such as the age and region of the signer have a significant influence on how the variable is realised. This investigation shows how careful cross-linguistic comparison can shed light on variation within and between sign languages that have been in contact, and how regional variation in one language may influence regional variation in another.
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Karlibaev, Makset A. "Mazars as memorial monuments of Karakalpakstan of the 18th – early 20th centuries." Historical Ethnology 7, no. 3 (2022): 414–31. http://dx.doi.org/10.22378/he.2022-7-3.414-431.
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The article studies the monuments of grave architecture of the Karakalpaks of the 18th – early 20th centuries: uishik, sagana, fence and gumbez. The most common form of such buildings is a fence of adobe walls, which does not have coatings. In fact, they were built around the burial place of the deceased, while the gumbez, or domed mausoleum, was often built next to the burial place. Sagana is a closed building, built over the burial. It essentially repeats the shape of an uishik – a tombstone made of different reeds. If the sagana and the fence have analogies among the neighboring peoples – Kazakhs and Uzbeks, then the Karakalpak gumbez is a unique monument of material culture. Fences in the region of the South Aral Sea, which includes Karakalpakstan, were formed in the Middle Ages. There is an opinion that the appearance of the Muslim mausoleum (gumbez, dome) is associated with the Arab tent "kubba" for praying over the grave of the deceased. The "mausoleum tradition" in the burial culture of Muslims spread far beyond the Aral Sea region. A special reverence for the cult of saints, strongly associated with Sufism, could be the culture of the previous period (for example, the Golden Horde), against which the construction of domed mausoleums was widely spread. The literature also mentions another type of buildings – zhai, which, from the author’a pointof view, is an intermediate type between a fence and a gumbez. Karakalpaks call the actual fences "zhai", as among the Kazakhs the word "tam" (house) is used. Kazakh fences are distinguished by the presence of corner tops – "tort qulaq" (four ears). In the 20th century in Karakalpakstan, the most common type of tomb structures became just this type – fences made of burnt bricks with four finials at the corners. Architectural monuments as objects of the material culture of the people require special attention from both the public and the state, they need measures to preserve and protect them.
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RENGAIYAN, PERIASAMY, and BABAN INGOLE. "Three New Carnivorous sponge species (Demospongiae: Cladorhizidae) from the Seamounts of the Central Indian Ridge." Zootaxa 5162, no. 5 (July 11, 2022): 451–86. http://dx.doi.org/10.11646/zootaxa.5162.5.1.
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Deep-sea sponges are an imperative component of benthos. They accumulate the suspended organic matter by filtering large quantities of water and, with their intricate structures, provide the most suitable habitats for various associated organisms. We describe three new cadorhizid sponges from the Central Indian Ridge (CIR), Indian Ocean. The sponges are part of the benthic sledge collection conducted onboard the MGS Sagar in the CIR region. A detailed taxonomic description of two novel species, Asbestopluma (Asbestopluma) indiyansis sp. nov., and Asbestopluma (A.) bharatiyae sp. nov. are provided based on the morphological and molecular (mtCOI and 28S) markers. In addition, another new carnivorous species Chondrocladia sagari sp. nov. is described based on the morphological and mtCOI marker. The systematic and descriptions of new species are discussed based on the structural and phylogenetic analysis. Our study shows that the cladorhizid fauna of the seamounts from the CIR are unique and represent regionally endemic benthic habitats.
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Trowbridge, Cynthia D., Yayoi M. Hirano, and Yoshiaki J. Hirano. "Interaction webs of marine specialist herbivores on Japanese shores." Journal of the Marine Biological Association of the United Kingdom 89, no. 2 (March 2009): 277–86. http://dx.doi.org/10.1017/s002531540900318x.
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Marine specialist herbivores inhabiting Japanese rocky shores are significantly more diverse than in other biogeographical regions at comparable latitudes. The interaction webs of specialist sacoglossans were investigated on the Pacific shore of Honshu, Japan. The host use of the small stenophagous sacoglossan opisthobranch Placida sp. (sensu Baba, 1986) was investigated in association with the green macroalgae Codium spp. Based on field associations, Placida sp. attacked six congeneric algal host species out of eight investigated (75%) in and around Sagami Bay and ten of 20 species (50%) in Japan. In pairwise-choice feeding experiments, Placida sp. preferred the algal host from which it was collected (source alga) to alternate host and non-host algae. Preference rankings, however, could be altered based on the condition or identity of the choices (e.g. old versus young fronds of C. fragile). Connectance values were lower in these high-diversity assemblages than in their low-diversity counterparts on other temperate shores (but these values may increase with additional study). The sacoglossan occasionally coexisted with two other common sacoglossan species (Elysia trisinuata and E. setoensis) and several other less common ones. However, interspecific feeding interactions appeared minor, with no discernible evidence of interference or exploitation competition. Despite the diverse assemblage of specialist sacoglossans feeding on Codium spp., these Japanese sacoglossans (1) had low niche differentiation, (2) were weak interactors with their hosts, and (3) had negligible intra-guild interactions.
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Noda, Takeshi, Shinji Watanabe, Hiroshi Sagara, and Yoshihiro Kawaoka. "Mapping of the VP40-Binding Regions of the Nucleoprotein of Ebola Virus." Journal of Virology 81, no. 7 (January 17, 2007): 3554–62. http://dx.doi.org/10.1128/jvi.02183-06.
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ABSTRACT Expression of Ebola virus nucleoprotein (NP) in mammalian cells leads to the formation of helical structures, which serve as a scaffold for the nucleocapsid. We recently found that NP binding with the matrix protein VP40 is important for nucleocapsid incorporation into virions (T. Noda, H. Ebihara, Y. Muramoto, K. Fujii, A. Takada, H. Sagara, J. H. Kim, H. Kida, H. Feldmann, and Y. Kawaoka, PLoS Pathog. 2:e99, 2006). To identify the region(s) on the NP molecule required for VP40 binding, we examined the interaction of a series of NP deletion mutants with VP40 biochemically and ultrastructurally. We found that both termini of NP (amino acids 2 to 150 and 601 to 739) are essential for its interaction with VP40 and for its incorporation into virus-like particles (VLPs). We also found that the C terminus of NP is important for nucleocapsid incorporation into virions. Of interest is that the formation of NP helices, which involves the N-terminal 450 amino acids of NP, is dispensable for NP incorporation into VLPs. These findings enhance our understanding of Ebola virus assembly and in so doing move us closer to the identification of targets for the development of antiviral compounds to combat Ebola virus infection.
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Ojo, A. O., O. T. Olurin, S. A. Ganiyu, B. S. Badmus, and O. A. Idowu. "An Integrated Geophysical and Geochemical Investigation of an Open Dumpsite in a Sedimentary Formation." Journal of Solid Waste Technology and Management 46, no. 3 (August 1, 2020): 409–30. http://dx.doi.org/10.5276/jswtm/2020.409.
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The extents of migration of leachate plumes and the probabilistic assessment of human health risks were carried out on Oke-Diya dumpsite, Sagamu, Southwestern Nigeria. Geophysical methods involving Very Low Frequency-Electromagnetic (VLF-EM) and Electrical Resistivity Topography (ERT) techniques, and Atomic Absorption Spectrometric (AAS) geochemical method were used to map and detect the presence and extent of leachate migration. The VLFEM pseudo-sections revealed conductive zones of responses 25 - 50 to a depth of about 15 m and approximated distance 50 m from the study area. The 2D and 3D ERT models delineated high conductive zones with very low resistivity values ranging from 0.551-6.54 and 2.4respectively. These conductive regions were observed to depths above 13.4 m and approximated distance 60 m from the study area in the 2D models. The 3D sections comprising of the horizontal depth slices, vertical planes and volumetric displays revealed regions with higher conductivity to a depth of about 21.9 m and approximated distance 50 m from the dumpsite. The mean concentrations of heavy metals Pb, Ni, Cd, Zn, Fe and Cu in the soil samples were higher than the concentrations in the control samples. The human health risk assessment indicated unacceptable values for non-carcinogenic adverse effects for both children and adults. The probabilistic cancer risks were within the acceptable range for Pb and unacceptable for Cd for both the children and adults. Generally, this study had identified areas of concentrated plumes accumulation and migration pathways, which were in agreement with earlier studies in sedimentary terrain.
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Butanaev, V. Ya. "Family-Tribal Fetishes of the Turks of Hongoray." Archaeology and Ethnography 18, no. 5 (2019): 154–65. http://dx.doi.org/10.25205/1818-7919-2019-18-5-154-165.
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Purpose. The author analyses a traditional cult of fetishism, which used to be common in the traditional life of turks of Hongoray (Khakassia) and others nations of Sayan-Altai region. The scientific novelty is in systematizing the materials available belonging to different ethnic groups of the Khakass (the Kachints, Sagai, Kyzyls, Beltyrs). Results. Functional particularities of the Khakass fetishes “tös” described used to protect clan and family health and served as patrons of cattle breeding and hunting. The author discovers many previously unknown signs and describes their ancient roots. Related myths recorded in Khakassia by the author are of great interest. The first research on the famous fetish “tös” of the Khakass was conducted by ethnographer D. A. Klements, who presented special work on these items. He made a description of them according to his personal collections and observations. Now his collection of “tös” is stored in the Minusinsk Museum of Local History. Unfortunately, D. A. Klements did not speak the Khakass language, so many of the item names were not translated properly. In present work, the author describes new functional features of Khakass fetishes “tös”, especially those related to the protection of the health of the family, the patronage of cattle breeding and hunting. Many previously unknown designations have been discovered, and the ancient roots of such representations have been revealed. At present, the cult of fetishism for the Khakas is a thing of the past; therefore, this research seems to be relevant for ethnographic science in terms of ancient myth-making of the population of Hongoray and neighboring regions of southern Siberia. Conclusion. There is evidence of a significant historical depth of the origin of the “tös”. So, as a result of studying anthropomorphic images on the “engraved pebbles” of the Late Bronze Age originating from Khakassia, their certain successive connections with the Hongors’ “tös” were traced. Thus, having a uniform name and functional characteristics, the cult of “tös” to a certain extent characterizes the origin of the popular beliefs of the Hongoray Turks, as well as their evolution in the historical borders of Sayano-Altai and Central Asia.
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Kariithi, Francis. "Politeness Strategies: Open Letter to President Uhuru Kenyatta Prior to Sagana 3 Mt Kenya Consultative Meeting." Journal of Humanities and Social Sciences Studies 3, no. 3 (March 30, 2021): 01–11. http://dx.doi.org/10.32996/jhsss.2021.3.3.1.
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Succinctly speaking, politics is an intricate affair that culminates in the likelihood of ugly scenarios popping out following the language that politicians employ. In line with the aforesaid, politicians attempt to employ assorted politeness strategies to exhibit decorum of some sort while addressing their seniors, more so when the addressee is at the apex of the purported leadership. The study intends to unravel the nature of politeness strategies that a section of Members of Parliament from Mount Kenya region relied on while reaching out to the president of Kenya Uhuru Kenyatta. To this end, the data was collected from an open letter to President Uhuru Kenyatta whose term of leadership was scheduled to end in 2022. The analysis on the data took into account the frequency of use on the said strategies namely, bald on record, off record, positive politeness and negative politeness; hence, anchoring the study on Politeness. The study sought to analyze the strategies used by the authors of the open letter and find out how the said authors navigated between the said strategies in line with FTAs bearing in mind that there was an asymmetric power relation and social distance between them. Results of qualitative and quantitative data analysis showed a significant difference in the manner authors of the said open letter navigated between the said strategies; thus, teasing out an implication in politeness research.
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Nasruddin, NFN. "KAJIAN INTEGRATIF SITUS PRASEJARAH Dl KAWASAN MANGKULIRANG, KUTAI TIMUR (Integrative Study of Prehistoric Site In Mangkulirang Region, East Kutai)." Jurnal Penelitian Arkeologi Papua dan Papua Barat 8, no. 2 (July 31, 2017): 203–15. http://dx.doi.org/10.24832/papua.v8i2.188.
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Studies on karst is a study that can be done hotisticaliy, because in the karst region them are various potentials such as; prehistoric archaeological remains which are quite old, there am groups of people who have local knowledge seekers swallow nest, traditional agricultural activities and the utilization of the site of the settlement (settlement area), as well as habits embodied in traditions and art. Through archaeological approach to spatial {spatial archeology), the archaeological research in East Kutai Karst, not only reveal the spatial and temporal aspects alone, but as a whole want to explain culturally and physically; synchronic and diachronic this region inhabited by humans. Mangkulirang karst area is so vast traffic would require a study to obtain an explanation; subsistence, technology and the ancient environment, as well as the adaptation of the system that have become extinct Cave sites and niches in the Mangkulirang a valuable contribution to the knowledge of the history and prehistory of cultural processes. Any kind of potential above require management in the context of synergy, participation and shared responsibility with the local authorities, cross-institutional and community organizations, as well as cross-sectoral and multi-disciplinary to minimize conflicts of the various interests in the karst region in the management and preservation of cultural heritage Indonesia. AbstrakKajian tentang karat adalah kajian yang dapat dilakukan secara holistik, karena di daiam kawasan karst tendapat berbagai potensi seperti; tinggalan arkeologis prasejarah yang cukup tua, terdapat keiompok-kelompok masyarakat yang memiliki kearifan lokal, para pencari sarang waist, aktivitas pertanian tradisional dan pemanfaatan menjadi lokasl pemukiman, serta kebiasaan-kebiasaan yang dlwujudkan daiam bentuk tnadisl dan kesenian. Melalui pendekatan arkeologi kemangan, maka penelitian arkeologi di Karst Kutai Timur, tidak hanya mengungkapkan aspek spasial dan temporal saja, tetapl secara utuh ingin menjelaskan secara kultural maupun fisikal; sinkronik maupun diakronik kawasan ini dihunl manusia. Kawasan karst Mangkulirang yang begitu luas tentunya memerlukan iintas kajian untuk memperoleh penjelasan; subsistensi, teknologi dan lingkungan purba, serta sistem adaptasi yang teiah punah. Situs gua dan cernk di kawasan Mangkulirang dapat memberlkan kontribusl berharga tarhadap pengetahuan sejarah dan proses budaya prasejarahnya. Sagaia jenis potensi di atas memerlukan pengeioiaan daiam rangka sinergitas, peran serta dan tanggung jawab bersama dengan pemerintah daerah, iintas kelembagaan dan organisasi masyarakat, maupun lintas sektoral dan multi disiplin untuk meminimalisir benturan atas berbagai kepentingan di kawasan karst dalam rangka pengelolaan dan pelestarian cagar budaya Indonesia.
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Siregar, Mangihut. "Politics of Cultural Tourism in the North Sumatera Samosir Island." International Journal of Applied Science 3, no. 1 (March 30, 2020): p18. http://dx.doi.org/10.30560/ijas.v3n1p18.
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Tourism has become a very promising industry in increasing economic development. Each region is competing to market their area as a tourist destination in order to get foreign exchange. All resources, such as natural resources, human resources, special interest resources, especially cultural resources, are all maximized for the advancement of tourism.
In an effort to increase regional income, the Samosir Regency Government of North Sumatra Province took a breakthrough to attract tourists to visit Samosir Island. One of the efforts made is by demonstrating cultural tourism, which is the ritual performance of mangalahat horbo bius ritual. This show is held every year in the Horas Samosir Fiesta event. The mangalahat horbo bius ritual performance began in 2008 at Batu Hobon, Limbong Sagala Village, Sianjur Mulamula Samosir Sub District. Since it was made a ritual, the mangalahat horbo bius became a show on Samosir Island, there were pros and cons in the community where the Catholic Church supported the show as the way to spread religion. Meanwhile the Samosir Regency government as the initiator of the show, has the aim to attract the interest of the visit. The party who openly rejected the show was the Batak Christian Protestant Church (HKBP).
Since the beginning, the mangalahat horbo bius ritual performance has experienced controversy in the community. The aim is to attract visits to the Samosir Island area to be counter productive. Therefore, at every mangalahat horbo bius ritual performance, the number of tourist visits to Samosir Island always decreases. In this case the local community is less supportive of the show while tourists visiting Samosir Island avoid the mangalahat horbo bius ritual show for reasons of showing sadism.
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Нилогов, Алексей Сергеевич. "DOCUMENTARY RECONSTRUCTION OF THE GENEALOGY OF S. D. MAINAGASHEV (TO THE 135TH ANNIVERSARY OF HIS BIRTH)." Tomsk Journal of Linguistics and Anthropology, no. 4(34) (December 28, 2021): 148–58. http://dx.doi.org/10.23951/2307-6119-2021-4-148-158.
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В статье рассматривается вопрос документальной реконструкции родословной хакасского этнографа Степана Дмитриевича Майнагашева (1886–1920). До сих пор в биографии хакасского учёного С. Д. Майнагашева оставались белые пятна, включая точно не установленную дату его рождения. Несмотря на наличие родословных преданий о происхождении Майнагашевых, отсутствовала научная верификация этой генеалогической информации на материале церковных метрических книг, именных списков и ревизских сказок (переписей населения). Объектом исследования является биологическая родословная С. Д. Майнагашева, а предметом — архивно-документальная реконструкция её патрилинейной части. Источниковую базу составили фонды таких архивов, как: Государственный архив Красноярского края, Национальный архив Республики Хакасия, архив города Минусинска. Впервые в научный оборот вводятся уникальные архивные документы по генеалогии Майнагашевых: по Аскизской Петропавловской церкви — метрическая запись о рождении/крещении С. Д. Майнагашева за 1886 г., метрическая запись о бракосочетании/венчании его родителей Д. А. Майнагашева и В. Н. Кызыласовой за 1877 г., метрическая запись о смерти/погребении деда этнографа А. П. Майнагашева за 1866 г., по Таштыпской Христорождественской церкви — метрическая запись о рождении/крещении отца Д. А. Майнагашева за 1851 г.; сведения из трёх последних ревизий Казановского рода Сагайской степной думы за 1832, 1850 и 1858 гг.; данные о фактах крещения представителей рода на 1854 г. В ходе генеалогических изысканий проведена экспертиза семейной родословной Майнагашевых, составленной в 1970–1980-х гг. топографом М. Г. Мойнагашевым на основе устных преданий и архивных источников. Критический анализ этой генеалогической схемы показывает, что её информационный потенциал нуждается в тщательной научной верификации с привлечением церковных метрических записей и актов гражданского состояния. Дальнейшее изучение генеалогии Майнагашевых будет посвящено анализу родословных легенд, а также генетико-генеалогическому тестированию современных мужских потомков. The article deals with the issue of documentary reconstruction of the Khakass ethnographer Stepan Dmitrievich Mainagashev’s (1886–1920) genealogy. Until now, there have been gaps in biography of the Khakass scientist S. D. Mainagashev, including an unspecified date of his birth. Despite the presence of genealogical legends about the origin of the Mainagashevs, there was no scientific verification of this genealogical information on the material of church metric books, lists of names and census lists (population censuses). The object of the study is S. D. Mainagashev’s biological genealogy, and the subject is the archival and documentary reconstruction of its patrilineal part. The source base consisted of the funds from such archives as: State Archive of the Krasnoyarsk Region, National Archive of the Republic of Khakassia, Minusinsk Archive. For the first time, unique archival documents on the genealogy of the Mainagashevs are introduced into scientific circulation: from the Askiz Peter and Paul Church — a metric record of the birth/baptism of S. D. Mainagashev in 1886, a metric record of the marriage/wedding of his parents D. A. Mainagashev and V. N. Kyzylasova in 1877, a metric record of the death/burial of the grandfather, ethnographer A. P. Mainagashev in 1866, from the Tashtyp Nativity Church — a metric record of the birth/baptism of D. A. Mainagashev’s father in 1851; data from the last three censuses of the Kazanov family of the Sagai Steppe Duma in 1832, 1850, and 1858; data on the baptism facts of representatives of the family as of 1854. Within the genealogical research, we carried out an examination of the Mainagashevs’ family genealogy, compiled in the 1970s and 1980s by the topographer M. G. Moinagashev on the basis of oral traditions and archival sources. The critical analysis of this genealogical scheme shows that its informational potential needs careful scientific verification with the involvement of church metric records and civil status acts. The further study of the Mainagashevs' genealogy will be devoted to the analysis of genealogical legends, as well as genetic and genealogical testing of modern male descendants.
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Hu, Jinjun, Mingji Liu, and Jingyang Tan. "Damping Modification Factors for Horizontal and Vertical Acceleration Spectra from Offshore Ground Motions in the Japan Sagami Bay Region." Bulletin of the Seismological Society of America, August 5, 2022. http://dx.doi.org/10.1785/0120210327.
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ABSTRACT Damping modification factors (DMFs) are used to scale the 5%-damped response spectra for the seismic design of structures with different damping ratios. However, there is no DMF model for offshore engineering response spectra at present. Using 892 offshore and 4033 onshore ground-motion records from the Kyoshin net, the difference between offshore and onshore DMFs are revealed by DMF ratios and t tests and whether site conditions need to be incorporated in offshore DMF models are determined. The between-event residual distribution shows that DMFs depend on the focal depth. The results show that the DMFs from the offshore and onshore ground motions differ significantly for most spectral periods, and the impact of the site condition on offshore DMF is very slight. The offshore DMF models for the horizontal and vertical acceleration spectra from the Japan Sagami Bay region are presented from spectra of 34 spectral periods and 10 damping ratios, in which only spectral periods and damping ratios are considered as variables. The uncertainty in the DMF model mainly depends on the path and site effects, and the standard deviations of DMFs for the vertical component are slightly less than those for the horizontal component. All standard deviations are modeled by a set of quadratic functions related to damping ratios. A comparison between the offshore DMF model in this study and those derived from onshore ground motions indicates that the differences are significant. The spectra from the Hu et al. (2020) study for offshore ground motions adjusted by the DMF models are used as our example applications.
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Chen, Su, Lei Fu, Zhijun Dai, Shiyang Chen, and Xiaojun Li. "Spectral Analysis of Subduction Zone Earthquakes for Coastal Stations and Applications to Stochastic Finite-Fault Simulation Method." Journal of Earthquake and Tsunami, March 30, 2022. http://dx.doi.org/10.1142/s1793431121400030.
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Accelerograms of 58 subduction zone earthquakes recorded by 25 K-NET coastal stations located in Sagami Bay and its adjacent regions were used to analyze the spectral properties of the source, propagation path, and site effects by using the generalized inversion technique. The inverted [Formula: see text] values vary from 1.7[Formula: see text]MPa to 17.4[Formula: see text]MPa, with an average value of 4.89[Formula: see text]MPa and a standard deviation of [Formula: see text]. Although the depths of the selected earthquakes are confined to 30 km, which is similar to those of the crustal earthquakes, this study obtains an average [Formula: see text] which coincides with the plate-boundary earthquakes rather than the crustal earthquakes. It implies that the stress condition of the plate-boundary region varies from the inland crust. The obtained [Formula: see text] is similar to the previous studies. The [Formula: see text] of the selected stations varies from 0.0479[Formula: see text]s to 0.0904[Formula: see text]s, indicating high-frequency attenuation for the coastal area. The inverted site response shows the systematic tendency for different site classes. The amplification levels of class A sites fluctuate around one between 1[Formula: see text]Hz and 10[Formula: see text]Hz. Class B sites indicate peak amplification at the resonant frequency distributed between 3[Formula: see text]Hz and 10[Formula: see text]Hz. Most of the Classes D and E sites have peak amplification below about 4[Formula: see text]Hz. Using the inversion results as the input parameters of the stochastic finite-fault method, an [Formula: see text] subduction zone earthquake was simulated. The resulting response spectra corresponded to the observations and confirmed that the inverted parameters are reasonable.
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Tan, Jingyang, and Jinjun Hu. "A prediction model for vertical-to-horizontal spectral ratios of ground motions on the seafloor for moderate magnitude events for the Sagami Bay region in Japan." Journal of Seismology, June 24, 2020. http://dx.doi.org/10.1007/s10950-020-09932-5.
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Ryu, Duchwan, Hongyan Xu, Varghese George, Shaoyong Su, Xiaoling Wang, Huidong Shi, and Robert H. Podolsky. "Differential methylation tests of regulatory regions." Statistical Applications in Genetics and Molecular Biology 15, no. 3 (January 1, 2016). http://dx.doi.org/10.1515/sagmb-2015-0037.
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AbstractDifferential methylation of regulatory elements is critical in epigenetic researches and can be statistically tested. We developed a new statistical test, the generalized integrated functional test (GIFT), that tests for regional differences in methylation based on the methylation percent at each CpG site within a genomic region. The GIFT uses estimated subject-specific profiles with smoothing methods, specifically wavelet smoothing, and calculates an ANOVA-like test to compare the average profile of groups. In this way, possibly correlated CpG sites within the regulatory region are compared all together. Simulations and analyses of data obtained from patients with chronic lymphocytic leukemia indicate that GIFT has good statistical properties and is able to identify promising genomic regions. Further, GIFT is likely to work with multiple different types of experiments since different smoothing methods can be used to estimate the profiles of data without noise. Matlab code for GIFT and sample data are available at
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Reiner-Benaim, Anat, Ronald W. Davis, and Kara Juneau. "Scan statistics analysis for detection of introns in time-course tiling array data." Statistical Applications in Genetics and Molecular Biology 13, no. 2 (January 1, 2014). http://dx.doi.org/10.1515/sagmb-2013-0038.
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AbstractA tiling array yields a series of abundance measurements across the genome using evenly spaced probes. These data can be used for detecting sequences that exhibit a particular behavior. Scanning window statistics are often employed for testing each probe while accounting for local correlation and smoothing noisy measurements. However, window testing may yield false probe discoveries around the sequences and false non-discoveries within the sequences, resulting in biased predicted intervals. We propose to avoid this problem by stipulating that a sequence of interest can appear at most once within a defined region, such as a gene; thus, only one window statistic is considered per region. This substantially reduces the number of tests and hence, is potentially more powerful. We compare this approach to a genome-wise scan that does not require pre-defined search regions, but considers clumps of adjacent probe discoveries. Simulations show that the gene-wise search maintains the nominal FDR level, while the genome-wise scan yields FDR that exceeds the nominal level for low interval effects, and achieves slightly less power. Using arrays to map introns in yeast, we identified 71% of the previously published introns, detected nine previously undiscovered introns, and observed no false intron discoveries by either method.
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AK, Shandilya. "Discovery of the Rare Gas Helium Vindhyan Rocks, Southern Ganga Basin, Bundelkhand Region, Dist. Sagar, M.P. India." Petroleum & Petrochemical Engineering Journal, 2019. http://dx.doi.org/10.23880/ppej-16000200.
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Jain MD; DM, Dr Prayank. "Study to assess the pattern of coronary artery disease (CAD) in Sagar town of Bundelkhand region, Madhya Pradesh." Journal of Medical Science And clinical Research 6, no. 12 (December 17, 2018). http://dx.doi.org/10.18535/jmscr/v6i12.89.
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Lakhal-Chaieb, Lajmi, Celia M. T. Greenwood, Mohamed Ouhourane, Kaiqiong Zhao, Belkacem Abdous, and Karim Oualkacha. "A smoothed EM-algorithm for DNA methylation profiles from sequencing-based methods in cell lines or for a single cell type." Statistical Applications in Genetics and Molecular Biology 16, no. 5-6 (November 27, 2017). http://dx.doi.org/10.1515/sagmb-2016-0062.
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AbstractWe consider the assessment of DNA methylation profiles for sequencing-derived data from a single cell type or from cell lines. We derive a kernel smoothed EM-algorithm, capable of analyzing an entire chromosome at once, and to simultaneously correct for experimental errors arising from either the pre-treatment steps or from the sequencing stage and to take into account spatial correlations between DNA methylation profiles at neighbouring CpG sites. The outcomes of our algorithm are then used to (i) call the true methylation status at each CpG site, (ii) provide accurate smoothed estimates of DNA methylation levels, and (iii) detect differentially methylated regions. Simulations show that the proposed methodology outperforms existing analysis methods that either ignore the correlation between DNA methylation profiles at neighbouring CpG sites or do not correct for errors. The use of the proposed inference procedure is illustrated through the analysis of a publicly available data set from a cell line of induced pluripotent H9 human embryonic stem cells and also a data set where methylation measures were obtained for a small genomic region in three different immune cell types separated from whole blood.
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Yu, Xiaoqing, and Shuying Sun. "HMM-DM: identifying differentially methylated regions using a hidden Markov model." Statistical Applications in Genetics and Molecular Biology 15, no. 1 (January 1, 2016). http://dx.doi.org/10.1515/sagmb-2015-0077.
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AbstractDNA methylation is an epigenetic modification involved in organism development and cellular differentiation. Identifying differential methylations can help to study genomic regions associated with diseases. Differential methylation studies on single-CG resolution have become possible with the bisulfite sequencing (BS) technology. However, there is still a lack of efficient statistical methods for identifying differentially methylated (DM) regions in BS data. We have developed a new approach named HMM-DM to detect DM regions between two biological conditions using BS data. This new approach first uses a hidden Markov model (HMM) to identify DM CG sites accounting for spatial correlation across CG sites and variation across samples, and then summarizes identified sites into regions. We demonstrate through a simulation study that our approach has a superior performance compared to BSmooth. We also illustrate the application of HMM-DM using a real breast cancer dataset.
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Page, Christian M., Linda Vos, Trine B. Rounge, Hanne F. Harbo, and Bettina K. Andreassen. "Assessing genome-wide significance for the detection of differentially methylated regions." Statistical Applications in Genetics and Molecular Biology 17, no. 5 (September 19, 2018). http://dx.doi.org/10.1515/sagmb-2017-0050.
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AbstractDNA methylation plays an important role in human health and disease, and methods for the identification of differently methylated regions are of increasing interest. There is currently a lack of statistical methods which properly address multiple testing, i.e. control genome-wide significance for differentially methylated regions. We introduce a scan statistic (DMRScan), which overcomes these limitations. We benchmark DMRScan against two well established methods (bumphunter, DMRcate), using a simulation study based on real methylation data. An implementation of DMRScan is available from Bioconductor. Our method has higher power than alternative methods across different simulation scenarios, particularly for small effect sizes. DMRScan exhibits greater flexibility in statistical modeling and can be used with more complex designs than current methods. DMRScan is the first dynamic approach which properly addresses the multiple-testing challenges for the identification of differently methylated regions. DMRScan outperformed alternative methods in terms of power, while keeping the false discovery rate controlled.
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Szefer, Elena, Donghuan Lu, Farouk Nathoo, Mirza Faisal Beg, and Jinko Graham. "Multivariate association between single-nucleotide polymorphisms in Alzgene linkage regions and structural changes in the brain: discovery, refinement and validation." Statistical Applications in Genetics and Molecular Biology 16, no. 5-6 (November 27, 2017). http://dx.doi.org/10.1515/sagmb-2016-0077.
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AbstractUsing publicly-available data from the Alzheimer’s Disease Neuroimaging Initiative, we investigate the joint association between single-nucleotide polymorphisms (SNPs) in previously established linkage regions for Alzheimer’s disease (AD) and rates of decline in brain structure. In an initial, discovery stage of analysis, we applied a weighted
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Gillespie, Colin S., and Andrew Golightly. "Diagnostics for assessing the linear noise and moment closure approximations." Statistical Applications in Genetics and Molecular Biology 15, no. 5 (January 1, 2016). http://dx.doi.org/10.1515/sagmb-2014-0071.
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AbstractSolving the chemical master equation exactly is typically not possible, so instead we must rely on simulation based methods. Unfortunately, drawing exact realisations, results in simulating every reaction that occurs. This will preclude the use of exact simulators for models of any realistic size and so approximate algorithms become important. In this paper we describe a general framework for assessing the accuracy of the linear noise and two moment approximations. By constructing an efficient space filling design over the parameter region of interest, we present a number of useful diagnostic tools that aids modellers in assessing whether the approximation is suitable. In particular, we leverage the normality assumption of the linear noise and moment closure approximations.
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Ji, Tieming, and Jie Chen. "Modeling the next generation sequencing read count data for DNA copy number variant study." Statistical Applications in Genetics and Molecular Biology 14, no. 4 (January 1, 2015). http://dx.doi.org/10.1515/sagmb-2014-0054.
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AbstractAs one of the most recent advanced technologies developed for biomedical research, the next generation sequencing (NGS) technology has opened more opportunities for scientific discovery of genetic information. The NGS technology is particularly useful in elucidating a genome for the analysis of DNA copy number variants (CNVs). The study of CNVs is important as many genetic studies have led to the conclusion that cancer development, genetic disorders, and other diseases are usually relevant to CNVs on the genome. One way to analyze the NGS data for detecting boundaries of CNV regions on a chromosome or a genome is to phrase the problem as a statistical change point detection problem presented in the read count data. We therefore provide a statistical change point model to help detect CNVs using the NGS read count data. We use a Bayesian approach to incorporate possible parameter changes in the underlying distribution of the NGS read count data. Posterior probabilities for the change point inferences are derived. Extensive simulation studies have shown advantages of our proposed methods. The proposed methods are also applied to a publicly available lung cancer cell line NGS dataset, and CNV regions on this cell line are successfully identified.
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Sun, Shuying, and Xiaoqing Yu. "HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher’s exact test." Statistical Applications in Genetics and Molecular Biology 15, no. 1 (January 1, 2016). http://dx.doi.org/10.1515/sagmb-2015-0076.
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AbstractDNA methylation is an epigenetic event that plays an important role in regulating gene expression. It is important to study DNA methylation, especially differential methylation patterns between two groups of samples (e.g. patients vs. normal individuals). With next generation sequencing technologies, it is now possible to identify differential methylation patterns by considering methylation at the single CG site level in an entire genome. However, it is challenging to analyze large and complex NGS data. In order to address this difficult question, we have developed a new statistical method using a hidden Markov model and Fisher’s exact test (HMM-Fisher) to identify differentially methylated cytosines and regions. We first use a hidden Markov chain to model the methylation signals to infer the methylation state as Not methylated (N), Partly methylated (P), and Fully methylated (F) for each individual sample. We then use Fisher’s exact test to identify differentially methylated CG sites. We show the HMM-Fisher method and compare it with commonly cited methods using both simulated data and real sequencing data. The results show that HMM-Fisher outperforms the current available methods to which we have compared. HMM-Fisher is efficient and robust in identifying heterogeneous DM regions.
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Yu, Xiaoqing, and Shuying Sun. "Comparing five statistical methods of differential methylation identification using bisulfite sequencing data." Statistical Applications in Genetics and Molecular Biology 15, no. 2 (January 1, 2016). http://dx.doi.org/10.1515/sagmb-2015-0078.
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AbstractWe are presenting a comprehensive comparative analysis of five differential methylation (DM) identification methods: methylKit, BSmooth, BiSeq, HMM-DM, and HMM-Fisher, which are developed for bisulfite sequencing (BS) data. We summarize the features of these methods from several analytical aspects and compare their performances using both simulated and real BS datasets. Our comparison results are summarized below. First, parameter settings may largely affect the accuracy of DM identification. Different from default settings, modified parameter settings yield higher sensitivity and/or lower false positive rates. Second, all five methods show more accurate results when identifying simulated DM regions that are long and have small within-group variation, but they have low concordance, probably due to the different approaches they have used for DM identification. Third, HMM-DM and HMM-Fisher yield relatively higher sensitivity and lower false positive rates than others, especially in DM regions with large variation. Finally, we have found that among the three methods that involve methylation estimation (methylKit, BSmooth, and BiSeq), BiSeq can best present raw methylation signals. Therefore, based on these results, we suggest that users select DM identification methods based on the characteristics of their data and the advantages of each method.
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Anderson, Michael P., and Suzanne R. Dubnicka. "A sequential naïve Bayes classifier for DNA barcodes." Statistical Applications in Genetics and Molecular Biology 13, no. 4 (January 1, 2014). http://dx.doi.org/10.1515/sagmb-2013-0025.
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AbstractDNA barcodes are short strands of 255–700 nucleotide bases taken from the cytochrome c oxidase subunit 1 (COI) region of the mitochondrial DNA. It has been proposed that these barcodes may be used as a method of differentiating between biological species. Current methods of species classification utilize distance measures that are heavily dependent on both evolutionary model assumptions as well as a clearly defined “gap” between intra- and interspecies variation. Such distance measures fail to measure classification uncertainty or to indicate how much of the barcode is necessary for classification. We propose a sequential naïve Bayes classifier for species classification to address these limitations. The proposed method is shown to provide accurate species-level classification on real and simulated data. The method proposed here quantifies the uncertainty of each classification and addresses how much of the barcode is necessary.
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Ranciati, Saverio, Cinzia Viroli, and Ernst Wit. "Spatio-temporal model for multiple ChIP-seq experiments." Statistical Applications in Genetics and Molecular Biology 14, no. 2 (January 1, 2015). http://dx.doi.org/10.1515/sagmb-2014-0074.
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AbstractThe increasing availability of ChIP-seq data demands for advanced statistical tools to analyze the results of such experiments. The inherent features of high-throughput sequencing output call for a modelling framework that can account for the spatial dependency between neighboring regions of the genome and the temporal dimension that arises from observing the protein binding process at progressing time points; also, multiple biological/technical replicates of the experiment are usually produced and methods to jointly account for them are needed. Furthermore, the antibodies used in the experiment lead to potentially different immunoprecipitation efficiencies, which can affect the capability of distinguishing between the true signal in the data and the background noise. The statistical procedure proposed consist of a discrete mixture model with an underlying latent Markov random field: the novelty of the model is to allow both spatial and temporal dependency to play a role in determining the latent state of genomic regions involved in the protein binding process, while combining all the information of the replicates available instead of treating them separately. It is also possible to take into account the different antibodies used, in order to obtain better insights of the process and exploit all the biological information available.
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de Andrade, Mariza, Mauricio A. Mazo Lopera, and Nubia E. Duarte. "Bivariate traits association analysis using generalized estimating equations in family data." Statistical Applications in Genetics and Molecular Biology 19, no. 2 (May 5, 2020). http://dx.doi.org/10.1515/sagmb-2019-0030.
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AbstractGenome wide association study (GWAS) is becoming fundamental in the arduous task of deciphering the etiology of complex diseases. The majority of the statistical models used to address the genes-disease association consider a single response variable. However, it is common for certain diseases to have correlated phenotypes such as in cardiovascular diseases. Usually, GWAS typically sample unrelated individuals from a population and the shared familial risk factors are not investigated. In this paper, we propose to apply a bivariate model using family data that associates two phenotypes with a genetic region. Using generalized estimation equations (GEE), we model two phenotypes, either discrete, continuous or a mixture of them, as a function of genetic variables and other important covariates. We incorporate the kinship relationships into the working matrix extended to a bivariate analysis. The estimation method and the joint gene-set effect in both phenotypes are developed in this work. We also evaluate the proposed methodology with a simulation study and an application to real data.
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Hart, Andrew, and Servet Martínez. "Markovianness and conditional independence in annotated bacterial DNA." Statistical Applications in Genetics and Molecular Biology 13, no. 6 (January 1, 2014). http://dx.doi.org/10.1515/sagmb-2014-0002.
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AbstractWe explore the probabilistic structure of DNA in a number of bacterial genomes and conclude that a form of Markovianness is present at the boundaries between coding and non-coding regions, that is, the sequence of START and STOP codons annotated for the bacterial genome. This sequence is shown to satisfy a conditional independence property which allows its governing Markov chain to be uniquely identified from the abundances of START and STOP codons. Furthermore, we show that the annotated sequence of STARTs and STOPs complies with Chargaff’s second parity rule.
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Lee, Jaeeun, and Jie Chen. "A penalized regression approach for DNA copy number study using the sequencing data." Statistical Applications in Genetics and Molecular Biology 18, no. 4 (May 30, 2019). http://dx.doi.org/10.1515/sagmb-2018-0001.
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Abstract Modeling the high-throughput next generation sequencing (NGS) data, resulting from experiments with the goal of profiling tumor and control samples for the study of DNA copy number variants (CNVs), remains to be a challenge in various ways. In this application work, we provide an efficient method for detecting multiple CNVs using NGS reads ratio data. This method is based on a multiple statistical change-points model with the penalized regression approach, 1d fused LASSO, that is designed for ordered data in a one-dimensional structure. In addition, since the path algorithm traces the solution as a function of a tuning parameter, the number and locations of potential CNV region boundaries can be estimated simultaneously in an efficient way. For tuning parameter selection, we then propose a new modified Bayesian information criterion, called JMIC, and compare the proposed JMIC with three different Bayes information criteria used in the literature. Simulation results have shown the better performance of JMIC for tuning parameter selection, in comparison with the other three criterion. We applied our approach to the sequencing data of reads ratio between the breast tumor cell lines HCC1954 and its matched normal cell line BL 1954 and the results are in-line with those discovered in the literature.
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Gory, Jeffrey J., Radu Herbei, and Laura S. Kubatko. "Bayesian inference of selection in the Wright-Fisher diffusion model." Statistical Applications in Genetics and Molecular Biology 17, no. 3 (June 6, 2018). http://dx.doi.org/10.1515/sagmb-2017-0046.
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Abstract The increasing availability of population-level allele frequency data across one or more related populations necessitates the development of methods that can efficiently estimate population genetics parameters, such as the strength of selection acting on the population(s), from such data. Existing methods for this problem in the setting of the Wright-Fisher diffusion model are primarily likelihood-based, and rely on numerical approximation for likelihood computation and on bootstrapping for assessment of variability in the resulting estimates, requiring extensive computation. Recent work has provided a method for obtaining exact samples from general Wright-Fisher diffusion processes, enabling the development of methods for Bayesian estimation in this setting. We develop and implement a Bayesian method for estimating the strength of selection based on the Wright-Fisher diffusion for data sampled at a single time point. The method utilizes the latest algorithms for exact sampling to devise a Markov chain Monte Carlo procedure to draw samples from the joint posterior distribution of the selection coefficient and the allele frequencies. We demonstrate that when assumptions about the initial allele frequencies are accurate the method performs well for both simulated data and for an empirical data set on hypoxia in flies, where we find evidence for strong positive selection in a region of chromosome 2L previously identified. We discuss possible extensions of our method to the more general settings commonly encountered in practice, highlighting the advantages of Bayesian approaches to inference in this setting.
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Barasa, James E., Sinebongo Mdyogolo, Romulus Abila, Johannes Paul Grobler, Robert A. Skilton, Hesmari Bindeman, Moses Ndotono Njahira, et al. "Genetic diversity and population structure of the African catfish, Clarias gariepinus (Burchell, 1822) in Kenya: implication for conservation and aquaculture." Belgian Journal of Zoology 147, no. 2 (September 28, 2017). http://dx.doi.org/10.26496/bjz.2017.9.
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African catfish, Clarias gariepinus, is an important species in aquaculture and fisheries in Kenya. Mitochondrial D-loop control region was used to determine genetic variation and population structure in samples of C. gariepinus from 10 sites including five natural populations (Lakes Victoria (LVG), Kanyaboli (LKG), Turkana (LTA), Baringo (LBA) and Jipe (LJP), and five farms (Sangoro Aquaculture Center (SAN), Sagana Aquaculture Centre (SAG), University of Eldoret Fish Farm (UoE), Kibos Fish Farm (KIB), and Wakhungu Fish Farm (WKU)) in Kenya. Similarly, samples from eight localities (four natural populations: LVG/LKG, LTA, LBA, and four farmed: SAN, SAG, KIB, UoE) were genotyped using six microsatellite DNA loci. For the D-loop control region, samples from natural sites exhibited higher numbers of haplotypes and haplotype diversities compared to farmed samples, and 88.2% of haplotypes were private. All except LJP and LTA shared haplotypes, and the highest number of shared haplotypes (8) was detected in KIB. The 68 haplotypes we found in 268 individuals grouped into five phylogenetic clades: LVG/LKG, LTA, LBA, LJP and SAG. Haplotypes of farmed C. gariepinus mostly have haplotypes typical of LVG/LKG, and some shared haplotypes of the LBA population. Microsatellite analysis showed farmed samples have higher numbers of alleles than natural samples, but higher observed and expected heterozygosity levels were found in samples of natural populations. Fifteen pair-wise comparisons had significantly different FST values. All samples were in Hardy-Weinberg equilibrium. Samples from the eight localities grouped into four genetic clusters (LVG/LKG, LTA, LBA and SAG), indicating genetically distinct populations, which should be considered for aquaculture and conservation.