bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formate cross‐feeding and cooperative metabolic interactions revealed by transcriptomics in co‐cultures of acetogenic and amylolytic human colonic bacteria
Authors: Laverde Gomez Jenny A. , Mukhopadhya Indrani , Duncan Sylvia H. , Louis Petra , Shaw Sophie , Collie‐Duguid Elaina , Crost Emmanuelle , Juge Nathalie , Flint Harry J. 
Published: October 2018

SummaryInterspecies cross‐feeding is a fundamental factor in anaerobic microbial communities. In the human colon, formate is produced by many bacterial species but is normally detected only at low concentrations. Ruminococcus bromii produces formate, ethanol and acetate in approximately equal molar proportions in pure culture on RUM‐RS medium with 0.2% Novelose resistant starch (RS3) as energy source. Batch co‐culturing on starch with the acetogen Blautia hydrogenotrophica however led to the disappearance of formate and increased levels of acetate, which is proposed to occur through the routing of formate via the Wood Ljungdahl pathway of B. hydrogenotrophica. We investigated these inter‐species interactions further using RNAseq to examine gene expression in continuous co‐cultures of R. bromii and B. hydrogenotrophica. Transcriptome analysis revealed upregulation of B. hydrogenotrophica genes involved in the Wood‐Ljungdahl pathway and of a 10 gene cluster responsible for increased branched chain amino acid fermentation in the co‐cultures. Cross‐feeding between formate‐producing species and acetogens may be a significant factor in short chain fatty acid formation in the colon contributing to high rates of acetate production. Transcriptome analysis also indicated competition for the vitamin thiamine and downregulation of dissimilatory sulfate reduction and key redox proteins in R. bromii in the co‐cultures, thus demonstrating the wide‐ranging consequences of inter‐species interactions in this model system.
Evolving metabolism of 2,4‐dinitrotoluene triggers SOS‐independent diversification of host cells
Authors: Akkaya Özlem , Nikel Pablo I. , Pérez‐Pantoja Danilo , de Lorenzo Víctor 
Published: October 2018

SummaryThe molecular mechanisms behind the mutagenic effect of reactive oxygen species (ROS) released by defective metabolization of xenobiotic 2,4‐dinitrotoluene (DNT) by a still‐evolving degradation pathway were studied. To this end, the genes required for biodegradation of DNT from Burkholderia cepacia R34 were implanted in Escherichia coli and the effect of catabolizing the nitroaromatic compound monitored with stress‐related markers and reporters. Such a proxy of the naturally‐occurring scenario faithfully recreated the known accumulation of ROS caused by faulty metabolism of DNT and the ensuing onset of an intense mutagenesis regime. While ROS triggered an oxidative stress response, neither homologous recombination was stimulated nor the recA promoter activity increased during DNT catabolism. Analysis of single‐nucleotide changes occurring in rpoB during DNT degradation suggested a relaxation of DNA replication fidelity rather than direct damage to DNA. Mutants frequencies were determined in strains defective in either converting DNA damage into mutagenesis or mediating inhibition of mismatch repair through a general stress response. The results revealed that the mutagenic effect of ROS was largely SOS‐independent and stemmed instead from stress‐induced changes of rpoS functionality. Evolution of novel metabolic properties thus resembles the way sublethal antibiotic concentrations stimulate the appearance of novel resistance genes.
Residents’ Responses to ‘Territorial Stigmatization’: Visual Research in Berlin
Authors: Cuny Cécile 
Published: October 2018

AbstractThis article deals with the symbolic dimension of the transformation process in a post‐socialist large‐scale housing estate in Berlin after reunification. This reflection is based on the concept of ‘territorial stigmatization’ and I use a photographic method to analyse the representational strategies employed by residents to manage territorial stigma: identifying with depoliticized images of the past, exiting the estate and questioning the very principle of representation. The first two strategies seem to be different ways of internalizing dominant representations of place. The latter differs from the first two in its use of iconic means to challenge the current spatial order and its opening up of possibilities for emancipation. The article thus also shows how photography as a research method can reflect on existing power relations.
Ore‐forming Fluid and Mineral Source of the Hongshi Copper Deposit in the Kalatage Area, East Tianshan, Xinjiang, NW China
Authors: YU Mingjie , WANG Jingbin , MAO Qigui , FANG Tonghui , ZHANG Rui 
Published: October 2018

AbstractThe Hongshi copper deposit is located in the middle of the Kalatage ore district in the northern segment of the Dananhu‐Tousuquan island‐arc belt in East Tianshan, Xinjiang, NW China. This study analyses the fluid inclusions and H, O, and S stable isotopic compositions of the deposit. The fluid‐inclusion data indicate that aqueous fluid inclusions were trapped in chalcopyrite‐bearing quartz veins in the gangue minerals. The homogenization temperatures range from 108°C to 299°C, and the salinities range from 0.5% to 11.8%, indicating medium to low temperatures and salinities. The trapping pressures range from 34.5 MPa to 56.8 MPa. The δ18OH2O values and δD values of the fluid range from –6.94‰ to –5.33‰ and from –95.31‰ to –48.20‰, respectively. The H and O isotopic data indicate that the ore‐forming fluid derived from a mix of magmatic water and meteoric water and that meteoric water played a significant role. The S isotopic composition of pyrite ranges from 1.9‰ to 5.2‰, with an average value of 3.1‰, and the S isotopic composition of chalcopyrite ranges from –0.9‰ to 4‰, with an average value of 1.36‰, implying that the S in the ore‐forming materials was derived from the mantle. The introduction of meteoric water decreased the temperature, volatile content, and pressure, resulting in immiscibility. These factors may have been the major causes of the mineralization of the Hongshi copper deposit. Based on all the geologic and fluid characteristics, we conclude that the Hongshi copper deposit is an epithermal deposit.
Geological Characteristics and Ore‐controlling Factors of the Beiya Gold–Polymetallic Ore Deposit, Northwestern Yunnan Province
Authors: ZHOU Yunman , ZHANG Changqing , HE Zhonghua , LIU Huan , ZHOU Guiwu , SUN Jia , LIU Bo 
Published: October 2018

AbstractBased on comprehensive petrological, geochronological, and geochemical studies, this study analyzed the relationships between the Beiya gold‐polymetallic skarn deposit and quartz syenite porphyries, and discussed the source(s) and evolution of magmas. Our results suggest that syenite porphyries (i.e. the Wandongshan, the Dashadi, and the Hongnitang porphyries), which formed between the Eocene and the early Oligocene epochs, are the sources for the gold‐polymetallic ores at the Beiya deposit. Carbonate rocks (T2b) of the Triassic Beiya Formation in the ore district provide favorable host space for deposit formation. Fold and fault structures collectively play an important role in ore formation. The contact zone between the porphyries and carbonates, the structurally fractured zone of carbonate and clastic rocks, and the zone with well‐developed fractures are the ideal locations for ore bodies. Four types of mineralization have been recognized: 1) porphyry‐style stockwork gold–iron (copper) ore, 2) skarn‐style gold‐iron (copper and lead) ore in the near contact zone, 3) strata‐bound, lense‐type lead–silver–gold ore in the outer contact zone, and 4) distal vein‐type gold–lead–silver ore. Supergene processes led to the formation of oxide ore, such as the weathered and accumulated gold–iron ore, the strata‐bound fracture oxide ore, and the structure‐controlled vein‐type ore. Most of these ore deposits are distributed along the axis of the depressed basin, with the hypogene ore controlling the shape and characteristics of the oxide ore. This study provides critical geology understanding for mineral prospecting scenarios.
Petrogenesis and Metallogenesis of the Niumaoquan Gabbroic Intrusion Associated with Fe‐Ti Oxide Ores in the Eastern Tianshan, NW China
Authors: SHI Yu , WANG Yuwang , WANG Jingbin , XIE Hongjing , MAO Qigui , ZHAO Lutong , LONG Lingli , LI Dedong , ZHOU Guochao 
Published: October 2018

AbstractThe Niumaoquan layered gabbroic intrusion is in the southern margin of the Central Asian Orogenic Belt in North Xinjiang, China, and hosts a Fe‐Ti oxide deposit in its evolved gabbroic phases. In this paper, we report zircon U‐Pb age, Sr‐Nd‐Hf isotopes, plagioclase chemistry, and whole‐rock geochemistry of the Niumaoquan layered gabbroic intrusion. Zircon grains separated from an anorthosite sample analyzed by laser ablation inductively coupled plasma mass spectrometry yielded a concordia age of 314.7±0.74 Ma, indicating that the Niumaoquan ore‐bearing gabbroic intrusion was emplaced during the Late Carboniferous. The olivine gabbro texture and plagioclase chemistry suggest that plagioclase was an early crystallized silicate phase that crystallized prior to olivine. Fractional crystallization and accumulation of plagioclase significantly controlled the evolution of the Niumaoquan gabbroic intrusion and contributed to the formation of anorthosite layers, causing metallogenic elements to become enriched in the residual melt. The Niumaoquan gabbroic intrusion is characterized by the enrichment of large ion lithophile elements and depletion of high field strength elements, positive zircon εHf(t) values (+2.1 to +12.2), positive εNd(t) values (+3.3 to +5.2), and low initial 87Sr/86Sr ratios (0.7039 to 0.7047), suggesting that the parental magma was produced by interactions between metasomatized lithospheric mantle and depleted asthenospheric melts at an early post‐collision stage. The Fe‐Ti oxide mineralization of the Niumaoquan intrusion benefited from interactions between depleted asthenospheric melts and lithospheric mantle, and fractional crystallization of abundant plagioclase and magnesian minerals.
High‐Frequency Sequence Stratigraphy and Fine‐Scale Reservoir Characterization of the Devonian Sandstone, Donghe Formation, North Uplift of the Tarim Basin
Authors: WANG Ziyuan , LIU Li , PAN Mao , SHI Yongmin , XIONG Fengyang 
Published: October 2018

AbstractThe Devonian Donghe Sandstone complex in North Uplift of the Tarim Basin comprises of a series of diachronous sandy intervals deposited from the Late Devonian to Early Mississippian. They are constrained by a Late Devonian to Early Pennsylvanian 2nd‐order supersequence and can be subdivided into five 3rd‐order sequences, namely, S1, S2, S3, S4, and S5, from the oldest to youngest. Cores from four wells, 40 wireline logs, 410 thin sections, and porosity and permeability data from 639 spots from four wells were used to study the sediment provenance, build up the sequence‐stratigraphic model of S5, and characterize the reservoirs at a feet scale. Detrital modes of sandstone from point counting indicate that Donghe Sandstone is directly sourced from recycled orogeny. The low content of feldspar and volcanic rock fragments suggests that Donghe Sandstone is recycled from sediment with a cratonic ultimate source. 1D and 2D chronostratigraphic correlation shows that at least 12 4th‐order high‐frequency sequences (HFSs), from the oldest HFS1 to the youngest HFS12, can be recognized in S5. Each HFS is characterized by a general trend of shallowing‐upward facies assemblage. Sequence boundaries were defined at where regionally correlatable deep‐water facies overlaying shallow‐water facies. There is a general shallowing‐upward trend in the S5 3rd‐order sequence, characterized by a systematically increasing proportion of shallow‐water facies (foreshore and upper shoreface), and a decreasing proportion of deep facies (offshore transition and lower shoreface). The shallowing‐upward trend within both 3rd‐ and 4th‐order sequences is resulted from a combined effect of eustatic sea‐level change, tectonic activity, and sediment supply. The sequence‐stratigraphic model of Donghe Sandstone S5 is similar to the rift‐basin sequence‐stratigraphic model. Sweet spots were defined as porosity >15% and permeability >100md intervals, and their distribution and lateral continuity were investigated. HFS is one of the primary controls on the distribution of sweet spots distribution and can be used to guide hydrocarbon exploration.
Modes of Shale‐Gas Enrichment Controlled by Tectonic Evolution
Authors: LI Chaochun , OU Chenghua 
Published: October 2018

AbstractThe typical characteristics of shale gas and the enrichment differences show that some shale gases are insufficiently explained by the existing continuous enrichment mode. These shale gases include the Wufeng–Longmaxi shale gas in the Jiaoshiba and Youyang Blocks, the Lewis shale gas in the San Juan Basin. Further analysis reveals three static subsystems (hydrocarbon source rock, gas reservoirs and seal formations) and four dynamic subsystems (tectonic evolution, sedimentary sequence, diagenetic evolution and hydrocarbon‐generation history) in shale‐ gas enrichment systems. Tectonic evolution drives the dynamic operation of the whole shale‐gas enrichment system. The shale‐gas enrichment modes controlled by tectonic evolution are classifiable into three groups and six subgroups. Group I modes are characterized by tectonically controlled hydrocarbon source rock, and include continuous in‐situ biogenic shale gas (I1) and continuous in‐situ thermogenic shale gas (I2). Group II modes are characterized by tectonically controlled gas reservoirs, and include anticline‐controlled reservoir enrichment (II1) and fracture‐controlled reservoir enrichment (II2). Group III modes possess tectonically controlled seal formations, and include faulted leakage enrichment (III1) and eroded residual enrichment (III2). In terms of quantity and exploitation potential, I1 and I2 are the best shale‐gas enrichment modes, followed by II1 and II2. The least effective modes are III1 and III2. The categorization provides a different perspective for deep shale‐gas exploration.
Gas Occurrence and Accumulation Characteristics of Cambrian–Ordovician Shales in the Tarim Basin, Northwest China
Authors: LIU Luofu , WANG Ying , CHEN Yiting , SHEN Baojian , GAO Xiaoyue 
Published: October 2018

AbstractThe Tarim Basin is located in northwestern China and is the biggest basin in China with huge oil and gas resources. Especially the Lower to Middle Cambrian and Middle to Upper Ordovician possess the major marine source rocks in the Tarim Basin and have large shale gas resource potential. The Cambrian–Ordovician shales were mainly deposited in basin–slope facies with thicknesses between 30–180 m. For shales buried shallower than 4500 m, there is high organic matter abundance with TOC (total organic carbon) mainly between 1.0% and 6.0%, favorable organic matter of Type I and Type II, and high thermal maturity with RoE as 1.3%–2.75%. The mineral composition of these Cambrian–Ordovician shale samples is mainly quartz and carbonate minerals while the clay minerals content is mostly lower than 30%, because these samples include siliceous and calcareous shale and marlstone. The Cambrian and Ordovician shales are compacted with mean porosity of 4% and 3%, permeability of 0.0003×10–3–0.09×10–3 μm2 and 0.0002×10–3–0.11×10–3 μm2, and density of 2.30 g/m3 and 2.55 g/m3, respectively. The pores in the shale samples show good connectivity and are mainly mesopore in size. Different genetic types of pores can be observed such as intercrystal, intergranular, dissolved, organic matter and shrinkage joint. The reservoir bed properties are controlled by mineral composition and diagenesis. The maximum adsorption amount to methane of these shales is 1.15–7.36 cm3/g, with main affecting factors being organic matter abundance, porosity and thermal maturity. The accumulation characteristics of natural gas within these shales are jointly controlled by sedimentation, diagenesis, hydrocarbon generation conditions, reservoir bed properties and the occurrence process of natural gas. The natural gas underwent short‐distance migration and accumulation, in‐place accumulation in the early stage, and adjustment and modification in the later stage. Finally, the Yulin (well Y1) and Tazhong (well T1) areas are identified as the targets for shale gas exploration in the Tarim Basin.
A GC×GC‐ToFMS Investigation of the Unresolved Complex Mixture and Associated Biomarkers in Biodegraded Petroleum
Authors: WANG Guangli , SIMONEIT Bernd Rolf Tatsuo , SHI Shengbao , WANG Tieguan , ZHONG Ningning , WANG Peirong 
Published: October 2018

AbstractHeavy biodegraded crude oils have larger numbers of coeluting compounds than non‐ biodegraded oils, and they are typically not resolved with conventional gas chromatography (GC). This unresolved complex mixture (UCM) has been investigated using comprehensive two‐ dimensional gas chromatography–time‐of‐flight mass spectrometry (GC×GC‐ToFMS) within a set of biodegraded petroleums derived from distinct sedimentary basins, including northwestern Sichuan (Neoproterozoic, marine), Tarim (Early Paleozoic, marine), Bohai Bay (Eocene, saline/brackish) and Pearl River Mouth (Eocene, freshwater). In general, the hydrocarbons that constitute the UCM in petroleum saturate fractions can be classified into three catalogues based on the distributions of resolved compounds on two dimensional chromatograms. Group 1 is composed mainly of normal and branched alkanes, isoprenoid alkanes and monocyclic alkanes; Group 2 comprises primarily terpanes ranging from two to five rings, and Group 3 is dominated by monoaromatic hydrocarbons such as tetralins and monoaromatic steranes. In addition, the UCM is source dependent and varies between oil populations. i.e., the UCM of petroleum derived from Precambrian and Early Paleozoic marine, Eocene saline/brackish and freshwater source rocks is specifically rich in higher homologues of A‐norsteranes, series of 1,1,3‐trimethyl‐2‐ alkylcyclohexanes (carotenoid‐derived alkanes), and tetralin and indane compounds, respectively.
Hydrochemical Dynamic Characteristics and Evolution of Underground Brine in the Mahai Salt Lake of the Qaidam Basin Qinghai‐Tibet Plateau
Authors: HU Shuya , ZHAO Quansheng , WANG Guangcai , ZHANG Jianwei , FENG Juan 
Published: October 2018

AbstractThe mineral rock salts present in the Mahai Salt Lake of the Qaidam basin exhibit high solubilities in water. In addition, the multicomponent underground brine exhibits a high salinity and is easily precipitated. In the natural state, brine transport in the brine layer is extremely slow, and the brine is in a relatively stable chemical equilibrium state with the rock salt media. However, during mining, both the seepage and the chemical fields fluctuate significantly, thereby disrupting the equilibrium and leading to variations in the chemical composition and dynamic characteristics of the brine. Therefore, we selected underground brine from the Mahai Salt Lake, collecting a total of 183 brine samples over three stages of mining (i.e., the early stage of underground brine extraction, the initial stage of mining, and the later stage of mining). Using a range of analytical techniques, the chemical dynamics of the underground brine water and its evolution were systematically studied. We found that evaporation and enrichment were the main mechanisms of underground brine evolution in the Mahai Salt Lake, with cation exchange and mineral dissolution/precipitation being key factors in determining the dynamic characteristics and evolution of the brine.
The Cretaceous Turn of Geological Evolution: Key Evidence from East Asia
Authors: NECHAEV Victor P. , DAI Shifeng , SUTHERLAND F. Lin , GRAHAM Ian T. , NECHAEVA Eugenia V. 
Published: October 2018

Abstractthis work focuses on one of the critical points of Earth's history when the Solar System passed through the most distant point of its galactic orbit. During this event, Earth may have suffered from maximum extension, associated with its relative proximity to the Sun at that time, followed by long‐term contraction related to its later distancing. This paper is based on generalized data on the Cretaceous evolution of the Earth as a whole and of East Asia in particular. The evidence suggests that major geological processes at this time may be interpreted as transitional changes in the state of Earth. A liquid nature of its core may have reacted to the gravitational and electromagnetic transformations. When the cosmic changes took place at 135–120 Ma, more turbulent flows in the outer core would have favoured the rise of voluminous magmatic plumes and associated fluid flows. These would substantially transform the mantle, crust, hydrosphere, biosphere and atmosphere. In particular, plume‐related melting of overlying subducting slabs and lower continental crust could have initiated numerous adakitic melts that formed the East Asian Adakitic Province. These and associated juvenile events produced numerous metallic ore, coal, gas and oil deposits. The Cretaceous is one of the most significant resource‐producing periods.
Role of interleukin‐17 in the pathogenesis of perianal abscess and anal fistula: a clinical study on 50 patients with perianal abscess
Authors: Wang Jian‐Ping , Cai Cheng , Du Jin‐Lin , Shi Hong‐Qi , Liu Qing‐Wei , Dai Zhi‐Hui , Zhong Zhi‐Feng 
Published: October 2018

BackgroundTo investigate the role of interleukin (IL)‐17 in tissue and peripheral blood of perianal abscess and anal fistula.MethodsPatients with primary perianal abscess (n = 50) admitted to Jinhua Municipal Central Hospital between March 2003 and August 2004 were enrolled. Fifty patients with mixed haemorrhoids, who showed no perianal abscess or anal fistula, were also recruited as the control. After surgery, patients were followed up for 6 months. Protein and gene expression of IL‐17 was determined in surgically harvested anal tissues and peripheral blood, respectively. The relationship between IL‐17 and clinical pathological features were analysed.ResultsAs shown by immunohistochemistry of anorectal tissues, the positive rate of IL‐17 protein was higher in the perianal abscess group than in the control group. In patients with perianal abscess, the expression of IL‐17 significantly correlated with the diameter of the abscess (P = 0.013), the wound surface healing time (P = 0.010) and the progression into anal fistula (P = 0.003). For the gene expression of IL‐17 in peripheral blood cells, the level was significantly higher in patients with perianal abscess comparing to the control group (0.4350 ± 0.1190 versus 0.1785 ± 0.1230, P ≤ 0.001). Comparing to the recovery group, patients with their perianal abscess progressed to anal fistula showed higher levels of IL‐17 gene expression (P = 0.014).ConclusionsExpression of IL‐17 was increased in the anorectal tissues and peripheral blood of patients with perianal abscess and anal fistula. IL‐17 may play an important role in the pathogenesis of perianal abscess and anal fistula.