bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples
Authors: Vo A.‐T. E. , Jedlicka J. A. 
Published: April 2014

AbstractNext‐generation sequencing (NGS) technology has extraordinarily enhanced the scope of research in the life sciences. To broaden the application of NGS to systems that were previously difficult to study, we present protocols for processing faecal and swab samples into amplicon libraries amenable to Illumina sequencing. We developed and tested a novel metagenomic DNA extraction approach using solid phase reversible immobilization (SPRI) beads on Western Bluebird (Sialia mexicana) samples stored in RNAlater. Compared with the MO BIO PowerSoil Kit, the current standard for the Human and Earth Microbiome Projects, the SPRI‐based method produced comparable 16S rRNA gene PCR amplification from faecal extractions but significantly greater DNA quality, quantity and PCR success for both cloacal and oral swab samples. We furthermore modified published protocols for preparing highly multiplexed Illumina libraries with minimal sample loss and without post‐adapter ligation amplification. Our library preparation protocol was successfully validated on three sets of heterogeneous amplicons (16S rRNA gene amplicons from SPRI and PowerSoil extractions as well as control arthropod COI gene amplicons) that were sequenced across three independent, 250‐bp, paired‐end runs on Illumina's MiSeq platform. Sequence analyses revealed largely equivalent results from the SPRI and PowerSoil extractions. Our comprehensive strategies focus on maximizing efficiency and minimizing costs. In addition to increasing the feasibility of using minimally invasive sampling and NGS capabilities in avian research, our methods are notably not avian‐specific and thus applicable to many research programmes that involve DNA extraction and amplicon sequencing.
Tectonics and Topography of the Tibetan Plateau in Early Miocene
Authors: WU Zhenhan , YANG Yan , BAROSH Patrick J. , WU Zhonghai , ZHANG Yaoling 
Published: April 2014

Abstract:Early Miocene stratigraphy, major structural systems, magmatic emplacement, volcanic eruption, vegetation change and paleo‐elevation were analyzed for the Tibetan Plateau after regional geological mapping at a scale of 1:250,000 and related researches, revealing much more information for tectonic evolution and topographic change of the high plateau caused by Indian‐Asian continental collision. Lacustrine deposits of dolostone, dolomite limestone, limestone, marl, sandstone and conglomerate of weak deformation formed extensively in the central Tibetan Plateau, indicating that vast lake complexes as large as 100,000–120,000 km2 existed in the central plateau during Early Miocene. Sporopollen assemblages contained in the lacustrine strata indicate the disappearance of most tropical‐subtropical broad‐leaved trees since Early Miocene and the flourishing of dark needle‐leaved trees during Early Miocene. Such vegetation changes adjusted for latitude and global climate variations demonstrate that the central Tibetan Plateau rose to ca. 4,000–4,500 m and the northeastern plateau uplifted to ca. 3,500–4,000 m before the Early Miocene. Intensive thrust and crustal thickening occurred in the areas surrounding central Tibetan Plateau in Early Miocene, formed Gangdise Thrust System (GTS) in the southern Lhasa block, Zedong‐Renbu Thrust (ZRT) in the northern Himalaya block, Main Central Thrust (MCT) and Main Boundary Thrust (MBT) in the southern Himalaya block, and regional thrust systems in the Qaidam, Qilian, West Kunlun and Songpan‐Ganzi blocks. Foreland basins formed in Early Miocene along major thrust systems, e.g. the Siwalik basin along MCT, Yalung‐Zangbu Basin along GTS and ZRT, southwestern Tarim depression along West Kunlun Thrust, and large foreland basins along major thrust systems in the northeastern margin of the plateau. Intensive volcanic eruptions formed in the Qiangtang, Hoh‐Xil and Kunlun blocks, porphyry granites and volcanic eruptions formed in the Nainqentanglha and Gangdise Mts., and leucogranites and granites formed in the Himalaya and Longmenshan Mts. in Early Miocene. The K2O weight percentages of Early Miocene magmatic rocks in the Gangdise and Himlayan Mts. are found to increase with distance from the MBT, indicating the genetic relationship between regional magmatism and subduction of Indian continental plate in Early Miocene.
Pressure‐temperature Evolution of the Metapelites in the Motuo Area, the Eastern Himalayan Syntaxis
Authors: DONG Hanwen , XU Zhiqin , LI Yuan , LIU Zhao 
Published: April 2014

Abstract:The Motuo area is located in the east of the Eastern Himalayan Syntaxis. There outcrops a sequence of high‐grade metamorphic rocks, such as metapelites. Petrology and mineralogy data suggest that these rocks have experienced three stages of metamorphism. The prograde metamorphic mineral assemblages (M1) are mineral inclusions (biotite + plagioclase + quartz ± sillimanite ± Fe‐Ti oxides) preserved in garnet porphyroblasts, and the peak metamorphic assemblages (M2) are represented by garnet with the lowest XSps values and the lowest XFe# ratios and the matrix minerals (plagioclase + quartz ± K‐feldspar + biotite + muscovite + kyanite ± sillimanite), whereas the retrograde assemblages (M3) are composed of biotite + plagioclase + quartz symplectites rimming the garnet porphyroblasts. Thermobarometric computation shows that the metamorphic conditions are 562–714°C at 7.3–7.4 kbar for the M1 stage, 661–800°C at 9.4–11.6 kbar for the M2 stage, and 579–713°C at 5.5–6.6 kbar for the M3 stage. These rocks are deciphered to have undergone metamorphism characterized by clockwise P‐T paths involving nearly isothermal decompression (ITD) segments, which is inferred to be related to the collision of the India and Eurasia plates.
Fluid Inclusions and Metallization of the Kendekeke Polymetallic Deposit in Qinghai Province, China
Authors: HUANG Min , LAI Jianqing , MO Qingyun 
Published: April 2014

Abstract:The Kendekeke polymetallic deposit, located in the middle part of the magmatic arc belt of Qimantag on the southwestern margin of the Qaidam Basin, is a polygenetic compound deposit in the Qimantag metallogenic belt of Qinghai Province. Multi‐periodic ore‐forming processes occurred in this deposit, including early‐stage iron mineralization and lead‐zinc‐gold‐polymetallic mineralization which was controlled by later hydrothermal process. The characteristics of the ore‐forming fluids and mineralization were discussed by using the fluid inclusion petrography, Laser Raman Spectrum and micro‐thermometry methods. Three stages, namely, S1‐stage (copper‐iron‐sulfide stage), S2‐stage (lead‐zinc‐sulfide stage) and C‐stage (carbonate stage) were included in the hydrothermal process as indicated by the results of this study. The fluid inclusions are in three types: aqueous inclusion (type I), CO2‐aqueous inclusion (type II) and pure CO2 inclusion (type III). Type I inclusions were observed in the Si‐stage, having homogenization temperature at 240–320°C, and salinities ranging from 19.8% to 25.0% (wt% NaCl equiv.). All three types of inclusions, existing as immiscible inclusion assemblages, were presented in the S2‐stage, with the lowest homogenization temperature ranging from 175 °C to 295°C, which represents the metallogenic temperature of the S2‐stage. The salinities of these inclusions are in the range of 1.5% to 16%. The fluid inclusions in the C‐stage belong to types I, II and III, having homogenization temperatures at 120–210°C, and salinities ranging from 0.9% to 14.5%. These observations indicate that the ore‐forming fluids evolved from high‐temperature to low‐temperature, from high‐salinity to low‐salinity, from homogenization to immiscible separation. Results of Laser Raman Spectroscopy show that high density of CO2 and CH4 were found as gas compositions in the inclusions. CO2, worked as the pH buffer of ore‐forming fluids, together with reduction of organic gases (i.e. CH4, etc), affected the transport and sediment of the minerals. The fluid system alternated between open and close systems, namely, between lithostatic pressure and hydrostatic pressure systems. The calculated metallogenic pressures are in the range of 30 to 87 Mpa corresponding to 3 km mineralization depth. Under the influence of tectonic movements, immiscible separation occurred in the original ore‐forming fluids, which were derived from the previous high‐salinity, high‐temperature magmatic fluids. The separation of CO2 changed the physicochemical properties and composition of the original fluids, and then diluted by mixing with extraneous fluids such as meteoric water and groundwater, and metallogenic materials in the fluids such as lead, zinc and gold were precipitated.
Geochronology, Geochemistry and Tectonic Setting of the Bairiqiete Granodiorite Intrusion (Rock Mass) from the Buqingshan Tectonic Mélange Belt in the Southern Margin of East Kunlun
Authors: LI Zuochen , PEI Xianzhi , LI Ruibao , PEI Lei , LIU Chengjun , CHEN Youxin , LIU Zhanqing , CHEN Guochao , XU Tong , YANG Jie , WEI Bo 
Published: April 2014

Abstract:This study focuses on the zircon U–Pb geochronology and geochemistry of the Bairiqiete granodiorite intrusion (rock mass) from the Buqingshan tectonic mélange belt in the southern margin of East Kunlun. The results show that the zircons are characterized by internal oscillatory zoning and high Th/U (0.14–0.80), indicative of an igneous origin. LA–ICP–MS U–Pb dating of zircons from the Bairiqiete granodiorite yielded an age of 439.0 ± 1.9 Ma (MSWD = 0.34), implying that the Bairiqiete granodiorite formed in the early Silurian. Geochemical analyses show that the rocks are medium‐K calc‐alkaline, relatively high in Al2O3 (14.57–18.34 wt%) and metaluminous to weakly peraluminous. Rare‐earth elements have low concentrations (45.49–168.31 ppm) and incline rightward with weak negative to weak positive Eu anomalies (δ5Eu = 0.64–1.34). Trace‐element geochemistry is characterized by negative anomalies of Nb, Ta, Zr, Hf and Ti and positive anomalies of Rb, Th and Ba. Moreover, the rocks have similar geochemical features with adakites. The Bairiqiete granodiorite appears to have a continental crust source and formed in a subduction‐related island‐arc setting. The Bairiqiete granodiorite was formed due to partial melting of the lower crust and suggests subduction in the Buqingshan area of the Proto‐Tethys Ocean.
Geological Conditions and Prospect Forecast of Shale Gas Formation in Qiangtang Basin, Qinghai‐Tibet Plateau
Authors: YU Yuanjiang , ZOU Caineng , DONG Dazhong , WANG Shejiao , LI Jianzhong , YANG Hua , LI Denghua , LI Xinjing , WANG Yuman , HUANG Jinliang 
Published: April 2014

Abstract:The presence of shale gas has been confirmed in almost every marine shale distribution area in North America. Formation conditions of shale gas in China are the most favorable for marine, organic‐rich shale as well. But there has been little research focusing on shale gas in Qiangtang Basin, Qinghai‐Tibet Plateau, where a lot of Mesozoic marine shale formations developed. Based on the survey results of petroleum geology and comprehensive test analysis data for Qinghai‐Tibet Plateau, for the first time, this paper discusses characteristics of sedimentary development, thickness distribution, geochemistry, reservoir and burial depth of organic‐rich shale, and geological conditions for shale gas formation in Qiangtang Basin. There are four sets of marine shale strata in Qiangtang Basin including Upper Triassic Xiaochaka Formation (T3x), Middle Jurassic Buqu Formation (J2b), Xiali Formation (J2x) and Upper Jurassic Suowa Formation (J3s), the sedimentary types of which are mainly bathyal‐basin facies, open platform‐platform margin slope facies, lagoon and tidal‐flat facies, as well as delta facies. By comparing it with the indicators of gas shale in the main U.S. basins, it was found that the four marine shale formations in Qiangtang Basin constitute a multi‐layer distribution of organic‐rich shale, featuring a high degree of thickness and low abundance of organic matter, high thermal evolution maturity, many kinds of brittle minerals, an equivalent content of quartz and clay minerals, a high content of feldspar and low porosity, which provide basic conditions for an accumulation of shale gas resources. Xiaochaka Formation shale is widely distributed, with big thickness and the best gas generating indicators. It is the main gas source layer. Xiali Formation shale is of intermediate thickness and coverage area, with relatively good gas generating indicators and moderate gas formation potential. Buqu Formation shale and Suowa Formation shale are of relatively large thickness, and covering a small area, with poor gas generating indicators, and limited gas formation potential. The shale gas geological resources and technically recoverable resources were estimated by using geologic analogy method, and the prospective areas and potentially favorable areas for Mesozoic marine shale gas in Qiangtang Basin are forecast and analyzed. It is relatively favorable in a tectonic setting and indication of oil and gas, shale maturity, sedimentary thickness and gypsum‐salt beds, and in terms of mineral association for shale gas accumulation. But the challenge lies in overcoming the harsh natural conditions which contributes to great difficulties in ground engineering and exploration, and high exploration costs.
Prospects of Carboniferous Shale Gas Exploitation in the Eastern Qaidam Basin
Authors: LI Yingjie , SUN Yanling , ZHAO Yan , CHANG Chun , YU Qingchun , MA Yinsheng 
Published: April 2014

Abstract:Shale gas is a resource of emerging importance in the energy field. Many countries in the world have been making big financial investments in this area. Carboniferous shale in the eastern Qaidam Basin shows good exploration prospects, but limited research and exploration work for shale oil and gas resources has been undertaken. Geochemical analyses were performed on shale derived from the Upper Carboniferous Hurleg Formation in the eastern Qaidam Basin, Qinghai Province, and secondary electron imaging capability of a Field Emission scanning electron microscope (FE‐SEM) was used to characterize the microstructure of the shale. The reservoir and exploitation potential of the studied shale was assessed by comparison with research results obtained from the Barnett Formation shale in Fort Worth Basin, North America and the Basin shale of Sichuan province. The results indicate that the eastern Qaidam Basin Carboniferous shale is high‐quality source rock. There are four major microstructural types in the study area: matrix intergranular pores, dissolution pores, intergranular pores, and micro‐fractures. The size of the micropores varies from 6–633 nm, the majority of which is between 39–200 nm, with a relatively small number of micro‐scale pores ranging from 0.13–1 μm. The pore characteristics of the studied shales are similar to the North American and Sichuanese shales, indicating that they have good reservoir potential. No micropores are present in the organic matter, which is induced by its composition; instead we found an important lamellar structure in the organic matter. These micropores and microfractures are abundant, and are connected to natural visible cracks that form the network pore system, which controls the storage and migration of shale gas. This connectivity is favorable for shale gas exploitation, providing great scientific potential and practical value.
Paleoclimate and Paleoenvironment of Gonghe Basin, Qinghai‐Tibet Plateau, During the Lastdeglacial: Weathering, Erosion and Vegetation Cover Affect Clay Mineral Formation
Authors: SUN Qingfeng , COLIN Christophe 
Published: April 2014

Abstract:With the analysis of the sources and formation mechanism of the clay minerals in the sediment core from the Dalianhai lake in the Gonghe Basin, northeastern Tibet‐Qinghai Plateau, clay mineral composition proxies, grain‐size and carbonate contents have been employed for high‐resolution study in order to reconstruct East Asian Summer Monsoon (EASM) over the northeastern Tibet‐Qinghai Plateau during the lastdeglacial. The study also extended to establish a relationship between vegetation cover changes and erosion during the last 14.5 ka with pollen record and clay mineral proxies. Smectite/kaolinite and smectite/(illite+chlorite) ratios allow us to assess hydrolysis conditions in lowlands and/or physical erosion process in highlands of the Gonghe Basin. Before 12.9 Cal ka BP, both mineralogical ratios show low values indicative of strong physical erosion in the basin with a dominant cold and dry phase. After 12.9 Cal ka BP, an increase in both mineralogical ratios indicates enhanced chemical weathering in the basin associated with a warm and humid climate. The beginning of Holocene is characterized by high smectite/(illite+chlorite) and smectite/kaolinite ratios that is synchronous as with deposition of many peat laminae, implying the best warm and humid conditions specifically between 8.0 to 5.5 Cal ka BP. The time interval after 5.0 Cal ka BP is characterized by a return to high physical erosion and low chemical weathering with dry climate conditions in the basin. Comparing variations of clay mineral assemblages with previous pollen results, we observe a rapid response in terms of chemical weathering and physical erosion intensity to a modification of the vegetation cover in the basin.
Origin of the Zedang and Luobusa Ophiolites, Tibet
Authors: BAO Peisheng , SU Li , WANG Jun , ZHAI Qingguo 
Published: April 2014

Abstract:The Zedang and Luobusa ophiolites are located in the eastern section of the Yalung Zangbo ophiolite belt, and they share similar geological tectonic setting and age. Thus, an understanding of their origins is very important for discussion of the evolution of the Eastern Tethys Ocean. There is no complete ophiolite assemblage in the Zedang ophiolite. The Zedang ophiolite is mainly composed of mantle peridotite and a suite of volcanic rocks as well as siliceous rocks, with some blocks of olivine‐pyroxenite. The mantle peridotite mainly consists of Cpx‐harzburgite, harzburgite, some lherzolite, and some dunite. A suite of volcanic rocks is mainly composed of calc‐alkaline pyroclastic rocks and secondly of tholeiitic pillow lavas, basaltic andesites, and some boninitic rocks with a lower TiO2 content (TiO2 < 0.6%). The pyroclastic rocks have a LREE‐enriched REE pattern and a LILE‐enriched (compared to HFSE) spider diagram, demonstrating an island‐arc origin. The tholeiitic volcanic rock has a LREE‐depleted REE pattern and a LILE‐depleted (compared to HFSE) spider diagram, indicative of an origin from MORB. The boninitic rock was generated from fore‐arc extension. The Luobusa ophiolite consists of mantle peridotite and mafic‐ultramafic cumulate units, without dike swarms and volcanic rocks. The mantle peridotite mainly consists of dunite, harzburgite with low‐Opx (Opx < 25%), and harzburgite (Opx > 25%), which can be divided into two facies belts. The upper is a dunite‐harzburgite (Opx < 25%) belt, containing many dunite lenses and a large‐scale chromite deposit with high Cr2O3; the lower is a harzburgite (Opx >25%) belt with small amounts of dunite and lherzolite. The Luobusa mantle peridotite exhibits a distinctive vertical zonation of partial melting with high melting in the upper unit and low melting in the lower. Many mantle peridotites are highly depleted, with a characteristic U‐shaped REE pattern peculiar to fore‐arc peridotite. The Luobusa cumulates are composed of wehrlite and olivine‐pyroxenite, of the P‐P‐G ophiolite series. This study indicates that the Luobusa ophiolite was formed in a fore‐arc basin environment on the basis of the occurrence of highly depleted mantle peridotite, a high‐Cr2O3 chromite deposit, and cumulates of the P‐P‐G ophiolite series. We conclude that the evolution of the Eastern Tethys Ocean involved three stages: the initial ocean stage (formation of MORB volcanic rock and dikes), the fore‐arc extension stage (formation of high‐Cr2O3 chromite deposits and P‐P‐G cumulates), and the island‐arc stage (formation of calc‐alkaline pyroclastic rocks).
Fatal injury caused by low‐energy trauma – a 10‐year rural cohort
Authors: BAKKE H. K. , DEHLI T. , WISBORG T. 
Published: April 2014

BackgroundDeath after injury with low energy has gained increasing focus lately, and seems to constitute a significant amount of trauma‐related death. The aim of this study was to describe the epidemiology of deaths from low‐energy trauma in a rural Norwegian cohort.MethodsAll deaths from external causes in Finnmark County, Norway, from 1995 to 2004 were identified retrospectively through the Norwegian Cause of Death Registry. Deaths caused by hanging, drowning, suffocation, poisoning, and electrocution were excluded. Trauma was categorised as high energy or low energy based on mechanism of injury. All low‐energy trauma deaths were then reviewed.ResultsThere were 262 cases of trauma death during the period. Low‐energy trauma counted for 43% of the trauma deaths, with an annual crude death rate of 13 per 100,000 inhabitants. Low falls accounted for 99% of the injuries. Fractures were sustained in 89% of cases and head injuries in 11%. Ninety per cent of patients had pre‐existing medical conditions, and the median age was 82 years. Death was caused by a medical condition in 85% of cases. Fifty‐two per cent of the patients died after discharge from the hospital.ConclusionIn this cohort, low‐energy trauma was a significant contributor to trauma related death, especially among elderly and patients with pre‐existing medical conditions.
Estimating spatial, temporal and individual variability in dolphin cumulative exposure to boat traffic using spatially explicit capture–recapture methods
Authors: Pirotta E. , Thompson P. M. , Cheney B. , Donovan C. R. , Lusseau D. 
Published: April 2014

AbstractAppropriate management of the effects of human activities on animal populations requires quantification of the rate at which animals encounter stressors. Such activities are heterogeneously distributed in space, as are the individual animals in a population. This will result in a heterogeneous exposure rate, which is also likely to vary over time. A spatially explicit analysis of individual exposure is therefore required. We applied Bayesian spatially explicit capture–recapture models to photo‐identification data to estimate the home range of well‐marked individuals in a protected coastal population of bottlenose dolphins. Model results were combined with the estimated distribution of boat traffic to quantify how exposure to this disturbance varied in time and space. Variability in exposure between individuals was also investigated using a mixed‐effects model. The cumulative individual exposure to boat traffic varied between summers, depending both on the overall area usage and the degree of individual movement around the activity centres. Despite this variability, regions of higher risk could be identified. There were marked inter‐individual differences in the predicted amount of time dolphins spent in the presence of boats, and individuals tended to be consistently over‐ or underexposed across summers. Our study offers a framework to describe the temporal, spatial and individual variation in exposure to anthropogenic stressors when individuals can be repeatedly identified over time. It provides opportunities to map exposure risk and understand how this evolves in time at both individual and population levels. The outcome of such modelling can be used as a robust evidence base to support management decisions.