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Article: Automatic extraction of outcrop cavity based on a multiscale regional convolution neural network

Wu, Siqi / Wang, Qing / Zeng, Qihong / Zhang, Youyan / Shao, Yanlin / Deng, Fan / Liu, Yuangang / Wei, Wei

Computers & geosciences. 2022 Mar., v. 160

2022

Abstract: Determination of pore space characteristics is important for carbonate reservoir interpretation and evaluation. Field outcrops can reflect the geology of the subsurface reservoir. The most common method of traditional outcrop research is field ... ...

Abstract	Determination of pore space characteristics is important for carbonate reservoir interpretation and evaluation. Field outcrops can reflect the geology of the subsurface reservoir. The most common method of traditional outcrop research is field investigation, which is likely to cause human errors. Digital image recognition of geological outcrop areas can reduce the problem of inaccurate descriptions of geological structures caused by human factors. Automatic extraction based on convolutional neural networks can greatly reduce the amount of such work. By enhancing the deep-learning model of a convolution neural network, the mask region-convolutional neural network (Mask R-CNN) is proposed. This method adapts to the multiscale features of the cavity by manipulating the scales of the input image. To verify the applicability of the model, the method is applied to automatic cavity identification in the digital outcrop profile of the Dengying Formation (2nd Member) in Xianfeng, Ebian. The parameters are calculated layer by layer, and their distribution characteristics are quantitatively analysed, indicating good application results. To verify the advanced nature of the model, the cavity extraction results of this method are compared with those of traditional image segmentation, machine learning and other depth learning methods. Precision analysis shows that the performance of the method proposed in this paper is superior to the traditional methods. In addition, the cavity feature parameters extracted by this method are compared with the manual extraction. The accuracy for the cavity number, surface porosity, and average cavity area is over 80%, 88%, and 72%, respectively for the proposed method. The results show that the proposed method is reliable and accurate, hence it will help to provide a basis for reservoir prediction in the process of regional geological exploration.
Keywords	carbonates ; digital images ; geology ; humans ; image analysis ; porosity ; prediction
Language	English
Dates of publication	2022-03
Publishing place	Elsevier Ltd
Document type	Article
ISSN	0098-3004
DOI	10.1016/j.cageo.2022.105038
Database	NAL-Catalogue (AGRICOLA)

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Article: Fine root dynamic characteristics and effect on plantation's carbon sequestration of three

He, Lingxianzi / Jia, Zhiqing / Li, Qingxue / Zhang, Youyan / Wu, Rina / Dai, Jie / Gao, Ya

Ecology and evolution

2021 Volume 11, Issue 6, Page(s) 2645–2659

Abstract: Desertification land in Gonghe Basin of Tibetan Plateau, China accounts for 91.9% of the total land area. Vegetation restoration and reconstruction with desert shrubs in degraded ecosystem are effective ways to prevent and control desertification. ... ...

Abstract	Desertification land in Gonghe Basin of Tibetan Plateau, China accounts for 91.9% of the total land area. Vegetation restoration and reconstruction with desert shrubs in degraded ecosystem are effective ways to prevent and control desertification. However, the evaluation studies of fine root dynamic characteristics of desert shrubs and their contribution to carbon sequestration of plantation are limited. To gain a better understanding of vegetation restoration, the vertical distribution of fine root biomass, fine root decomposition, fine root turnover was investigated, as well as their coupling effect on carbon sequestration of plantation in three desert vegetation. The results estimated that the total decomposition time of fine roots of
Language	English
Publishing date	2021-02-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.7221
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Article ; Online: Petroleum Geological Analysis Based on Remote Sensing and laser scanning in Karamay Formation of Junggar Basin, China

Zeng Qihong / Zhang Youyan / Kong Linghua / Ye Yong / Hu Yan / Wang Wenzhi / Chen Yuanyuan

E3S Web of Conferences, Vol 206, p

2020 Volume 01023

Abstract: This paper uses high-precision remote sensing and laser scanning to study petroleum geological analysis methods. The research area is Karamay Formation in Junggar Basin, China. Firstly, the outcrop lithologies are identified according to our clastic rock ...

Abstract	This paper uses high-precision remote sensing and laser scanning to study petroleum geological analysis methods. The research area is Karamay Formation in Junggar Basin, China. Firstly, the outcrop lithologies are identified according to our clastic rock lithology identification pattern based on laser intensity, and the regional lithologies are identified based on high-precision remote sensing images. Furthermore, we analyze the horizontal and vertical distribution characteristics of the sandbodies. At last, we analyze the area sandbody connectivity and sandbody structure characteristics. These data can provide basic information for the analysis of underground reservoirs in Karamay Formation.
Keywords	Environmental sciences ; GE1-350
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	EDP Sciences
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: KRAS

Ryan, Meagan B / Coker, Oluwadara / Sorokin, Alexey / Fella, Katerina / Barnes, Haley / Wong, Edmond / Kanikarla, Preeti / Gao, Fengqin / Zhang, Youyan / Zhou, Lian / Kopetz, Scott / Corcoran, Ryan B

Cell reports

2022 Volume 39, Issue 12, Page(s) 110993

Abstract: Although KRAS has long been considered undruggable, direct ... ...

Abstract	Although KRAS has long been considered undruggable, direct KRAS
MeSH term(s)	Animals ; Cell Line, Tumor ; ErbB Receptors/genetics ; ErbB Receptors/metabolism ; Feedback ; Humans ; Mice ; Mitogen-Activated Protein Kinases/metabolism ; Mutation/genetics ; Neoplasms/metabolism ; Proto-Oncogene Proteins p21(ras)/genetics ; Proto-Oncogene Proteins p21(ras)/metabolism ; Signal Transduction
Chemical Substances	KRAS protein, human ; ErbB Receptors (EC 2.7.10.1) ; Mitogen-Activated Protein Kinases (EC 2.7.11.24) ; Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2)
Language	English
Publishing date	2022-07-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.110993
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Article: [Radial variation and time lag of sap flow of Populus gansuensis in Minqin Oasis, Northwest].

Dang, Hong-Zhong / Yang, Wen-Bin / Li, Wei / Zhang, You-Yan / Li, Chang-Long

Ying yong sheng tai xue bao = The journal of applied ecology

2014 Volume 25, Issue 9, Page(s) 2501–2510

Abstract: Sap flow of tree trunk is very important to reflect the dynamics of physiological activities, as well as to estimate the water consumption of individual plant. In the present study, we used the thermal dissipation technique to monitor the sap flow ... ...

Abstract	Sap flow of tree trunk is very important to reflect the dynamics of physiological activities, as well as to estimate the water consumption of individual plant. In the present study, we used the thermal dissipation technique to monitor the sap flow velocity (J) at four depth loci (i. e. 2 cm, 3 cm, 5 cm, 8 cm) of three Populus gansuensis trees (30 year-old) in Minqin Oasis for two consecutive growing seasons. The results showed that there were significant differences among J values at four depth loci under tree trunk cambium. J value at the 3 cm depth locus (J3) of the tree trunk was the highest, and then in sequences, were 2 cm, 5 cm and 8 cm depth loci (J2, J5 and J8). J value (J3) on typical sunny days in June with the highest atmospheric potential evapotranspiration (ET0) was up to 28.53 g · cm(-2) · h(-1), which was 1.42, 2.74 and 4.4 times of J2, J5 and J8, respectively. In the process of diurnal variation of sap flow velocity, the peak value time of J at the four depth loci of the tree trunk was different, but the differences among them were within 20 min. Furthermore, the peak value time of sap flow velocity was very different to that of solar radiation (Rs) and air vapour pressure deficit (VPD). The time lag between J and Rs was from 55 to 88 min on typical sunny days during the main growing seasons (from June to August), and, positively related to the depth of the locus under tree trunk cambium, while the time lag between J and VPD reached 60-96 min, and was negatively related to the depth of the locus. The seasonal variation patterns of J were consistent with ET0. With the increase of tree physiological activities, there was a trend that the major water transportation layer extended to the interior sapwood. The most important meteorological factor was the solar radiation, which primarily drove sap flow at different depths of tree trunk. However, the secondary factor changed along with the depth, and VPD became increasingly important with increasing the depth.
MeSH term(s)	Circadian Rhythm ; Plant Transpiration ; Populus/physiology ; Seasons ; Trees/physiology ; Water
Chemical Substances	Water (059QF0KO0R)
Language	Chinese
Publishing date	2014-09
Publishing country	China
Document type	English Abstract ; Journal Article
ZDB-ID	2881809-X
ISSN	1001-9332
ISSN	1001-9332
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Article ; Online: Long-Term Prognostic Factors in Patients With Antineutrophil Cytoplasmic Antibody-Associated Vasculitis: A 15-Year Multicenter Retrospective Study.

Frontiers in immunology

2022 Volume 13, Page(s) 913667

Abstract: Background: Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is a multisystem autoimmune disease with small-vessel involvement. In AAV, microscopic polyangiitis (MPA) and granulomatosis with polyangiitis (GPA) are major ... ...

Abstract	Background: Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is a multisystem autoimmune disease with small-vessel involvement. In AAV, microscopic polyangiitis (MPA) and granulomatosis with polyangiitis (GPA) are major clinicopathologic variants. In addition, myeloperoxidase (MPO) and proteinase 3 (PR3) are major target antigens. The objective of the study was to explore the predictive factors for long-term survival in AAV patients. Materials and methods: A multicenter retrospective study was carried out on 407 patients between 2005 and 2020. Clinical parameters were obtained from laboratory tests including the ANCA types, antinuclear antibody (ANA), extractable nuclear antigen (ENA), anti-streptolysin O (ASO), glomerular filtration rate (GFR), and the laboratory examinations for the blood routine, liver function, renal function, and immunity, etc. The data for clinical parameters were collected from electronic medical records (EMRs), and the data for patient survival were acquired through regular follow-up. The association of clinical parameters with overall survival (OS) along with 3-year and 5-year survival rates was analyzed, and the nomogram as a predictive model was established according to the analysis results. Results: In the present study, 336 (82.6%) patients and 46 (11.3%) patients were diagnosed with MPA and GPA, respectively. The mean and median OS for all the patients were 2,285 and 2,290 days, respectively. The 1-year, 3-year, 5-year, and 10-year cumulative survival rates for all the patients were 84.2%, 76.3%, 57.2%, and 32.4%, respectively. Univariate and multivariate survival analyses indicated that the independent prognostic factors included age, pathological categories (MPA, GPA, and other types), serum ANCA types (negative or positive for MPO and/or PR3), ANA, ASO, GFR, lymphocyte, neutrophil-to-lymphocyte ratio (NLR), and C-reactive protein (CRP), and these clinical parameters except for ASO were used to construct a nomogram. The nomogram for 3-year and 5-year survival rates had a C-index of 0.721 (95% CI 0.676-0.766). The calibration curves showed that the predicted values of the nomogram for 3-year and 5-year survival rates were generally consistent with practical observed values, and decision curve analysis (DCA) further demonstrated the practicability and accuracy of the predictive model. Conclusion: Laboratory tests at diagnosis have great significance in the prediction of long-term survival in AAV patients.
MeSH term(s)	Anti-Neutrophil Cytoplasmic Antibody-Associated Vasculitis ; Antibodies, Antineutrophil Cytoplasmic ; Granulomatosis with Polyangiitis ; Humans ; Microscopic Polyangiitis ; Myeloblastin ; Prognosis ; Retrospective Studies
Chemical Substances	Antibodies, Antineutrophil Cytoplasmic ; Myeloblastin (EC 3.4.21.76)
Language	English
Publishing date	2022-06-30
Publishing country	Switzerland
Document type	Journal Article ; Multicenter Study ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.913667
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Article: Changes in Preferential Flow Path Distribution and Its Affecting Factors in Southwest China

Cheng, Jinhua / Zhang, Hongjiang / Wang, Wei / Zhang, Youyan / Chen, Yinzhen

Soil science. 2011 Dec., v. 176, no. 12

2011

Abstract: Preferential flow is important in solute transport in the soil, and it indirectly affects the quality of the groundwater. The objectives of the present study were to investigate the distribution characteristics of preferential flow paths under different ... ...

Abstract	Preferential flow is important in solute transport in the soil, and it indirectly affects the quality of the groundwater. The objectives of the present study were to investigate the distribution characteristics of preferential flow paths under different land-use types (forestland, shrubland, and farmland) and to determine the factors that affect the formation of these paths. Dye tracer experiments were conducted at six sites covering the three land-use types. The relationship of the preferential flow paths to the properties of the soil, root length per soil volume, root holes, and root surface area was analyzed using a partial correlation method. The results show dye coverage of greater than 50% at a soil depth of 0 to 10 cm and dye coverage of less than 30% below a depth of 20 cm in all of the land-use types. The vertical distribution differed widely in the various land-use types. Shrubland and farmland had more preferential flow paths in the topsoil compared with forestland, in contrast to the conditions in the deeper soil layers. The soil chemical properties and the saturated hydraulic conductivity in the preferential flow paths were quite different from those in the soil matrix. The soil organic matter content was approximately 5% to 20% higher in the preferential flow paths than in the soil matrix. The average value of the saturated hydraulic conductivity was 41.3 mm min in the preferential flow paths compared with 21.4 mm min in the soil matrix. The percentage of preferential flow paths in the soil was significantly affected by roots with a diameter of less than 5 mm, root holes, and the root surface area. These findings suggest that land use is significant in the distribution of preferential flow paths, and root characteristics are important in the formation of preferential flow paths.
Keywords	agricultural land ; dyes ; forest land ; groundwater ; land use ; preferential flow ; roots ; saturated hydraulic conductivity ; shrublands ; soil chemical properties ; soil depth ; soil organic matter ; solutes ; spatial distribution ; surface area ; topsoil ; China
Language	English
Dates of publication	2011-12
Size	p. 652-660.
Publishing place	Lippincott Williams & Wilkins
Document type	Article
Note	Affiliations: 1College of Soil and Water Conservation, Beijing Forestry University, #35 Qinghua E. Rd., Haidian district, Beijing 100083, China. Dr. Hongjiang Zhang is corresponding author. E-mail: zhanghj@bjfu.edu.cn; jinhua_cheng@126.com 2Institute of Desertification Studies, Chinese Academy of Forestry, #1958 P.O. Box, Beijing 100091, China.
ZDB-ID	204569-2
ISSN	0038-075X
ISSN	0038-075X
DOI	10.1097/SS.0b013e31823554ef
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Article ; Online: LY3009120, a panRAF inhibitor, has significant anti-tumor activity in BRAF and KRAS mutant preclinical models of colorectal cancer.

Vakana, Eliza / Pratt, Susan / Blosser, Wayne / Dowless, Michele / Simpson, Nicholas / Yuan, Xiu-Juan / Jaken, Susan / Manro, Jason / Stephens, Jennifer / Zhang, Youyan / Huber, Lysiane / Peng, Sheng-Bin / Stancato, Louis F

Oncotarget

2017 Volume 8, Issue 6, Page(s) 9251–9266

Abstract: Activating mutations in the KRAS and BRAF genes, leading to hyperactivation of the RAS/RAF/MAPK oncogenic signaling cascade, are common in patients with colorectal cancer (CRC). While selective BRAF inhibitors are efficacious in BRAFmut melanoma, they ... ...

Abstract	Activating mutations in the KRAS and BRAF genes, leading to hyperactivation of the RAS/RAF/MAPK oncogenic signaling cascade, are common in patients with colorectal cancer (CRC). While selective BRAF inhibitors are efficacious in BRAFmut melanoma, they have limited efficacy in BRAFmut CRC patients. In a RASmut background, selective BRAF inhibitors are contraindicated due to paradoxical activation of the MAPK pathway through potentiation of CRAF kinase activity. A way to overcome such paradoxical activation is through concurrent inhibition of the kinase activity of both RAF isoforms. Here, we further examined the effects of LY3009120, a panRAF and RAF dimer inhibitor, in human models of CRC with various mutational backgrounds. We demonstrate that LY3009120 induced anti-proliferative effects in BRAFmut and KRASmut CRC cell lines through G1-cell cycle arrest. The anti-proliferative effects of LY3009120 in KRASmut CRC cell lines phenocopied molecular inhibition of RAF isoforms by simultaneous siRNA-mediated knockdown of ARAF, BRAF and CRAF. Additionally, LY3009120 displayed significant activity in in vivo BRAFmut and KRASmut CRC xenograft models. Examination of potential resistance to LY3009120 demonstrated RAF-independent ERK and AKT activation in the KRASmut CRC cell line HCT 116. These findings describe the preclinical activity of a panRAF inhibitor in a BRAFmut and KRASmut CRC setting.
Language	English
Publishing date	2017-02-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.14002
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Article: Niacin stimulates adiponectin secretion through the GPR109A receptor.

Plaisance, Eric P / Lukasova, Martina / Offermanns, Stefan / Zhang, Youyan / Cao, Guoqing / Judd, Robert L

American journal of physiology. Endocrinology and metabolism

2009 Volume 296, Issue 3, Page(s) E549–58

Abstract: Niacin (nicotinic acid) has recently been shown to increase serum adiponectin concentrations in men with the metabolic syndrome. However, little is known about the mechanism(s) by which niacin regulates the intracellular trafficking and secretion of ... ...

Abstract	Niacin (nicotinic acid) has recently been shown to increase serum adiponectin concentrations in men with the metabolic syndrome. However, little is known about the mechanism(s) by which niacin regulates the intracellular trafficking and secretion of adiponectin. Since niacin appears to exert its effects on lipolysis through receptor (GPR109A)-dependent and -independent pathways, the purpose of this investigation was to examine the role of the recently identified GPR109A receptor in adiponectin secretion. Initial in vivo studies in rats demonstrated that niacin (30 mg/kg po) acutely increases serum adiponectin concentrations, whereas it decreases NEFAs. Further in vitro studies demonstrated an increase in adiponectin secretion and a decrease in lipolysis in primary adipocytes following treatment with niacin or beta-hydroxybutyrate (an endogenous ligand of the GPR109A receptor), but these effects were blocked when adipocytes were pretreated with pertussis toxin. Niacin had no effect on adiponectin secretion or lipolysis in 3T3-L1 adipocytes, which have limited cell surface expression of the GPR109A receptor. To further substantiate these in vitro findings, wild-type and GPR109A receptor knockout mice were administered a single dose of niacin or placebo, and serum was obtained for the determination of adiponectin and NEFA concentrations. Serum adiponectin concentrations increased and serum NEFAs decreased in the wild-type mice within 10 min following niacin administration. However, niacin administration had no effect on adiponectin and NEFA concentrations in the GPR109A receptor knockout mice. These results demonstrate that the GPR109A receptor plays an important role in the dual regulation of adiponectin secretion and lipolysis.
MeSH term(s)	3-Hydroxybutyric Acid/metabolism ; 3T3-L1 Cells ; Adipocytes/cytology ; Adiponectin/blood ; Adiponectin/secretion ; Animals ; Cells, Cultured ; Cyclic AMP/metabolism ; Fatty Acids, Nonesterified/blood ; Humans ; Hypolipidemic Agents/pharmacology ; Lipolysis/drug effects ; Lipolysis/physiology ; Mice ; Mice, Knockout ; Niacin/pharmacology ; Pertussis Toxin/pharmacology ; Rats ; Receptors, G-Protein-Coupled/genetics ; Receptors, G-Protein-Coupled/metabolism ; Receptors, Nicotinic/genetics ; Receptors, Nicotinic/metabolism
Chemical Substances	Adiponectin ; Adipoq protein, mouse ; Fatty Acids, Nonesterified ; HCAR2 protein, human ; Hcar2 protein, mouse ; Hypolipidemic Agents ; Receptors, G-Protein-Coupled ; Receptors, Nicotinic ; Niacin (2679MF687A) ; Cyclic AMP (E0399OZS9N) ; Pertussis Toxin (EC 2.4.2.31) ; 3-Hydroxybutyric Acid (TZP1275679)
Language	English
Publishing date	2009-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	603841-4
ISSN	1522-1555 ; 0193-1849
ISSN (online)	1522-1555
ISSN	0193-1849
DOI	10.1152/ajpendo.91004.2008
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Article: Mouse PDX Trial Suggests Synergy of Concurrent Inhibition of RAF and EGFR in Colorectal Cancer with

Yao, Yung-Mae M / Donoho, Gregory P / Iversen, Philip W / Zhang, Youyan / Van Horn, Robert D / Forest, Amelie / Novosiadly, Ruslan D / Webster, Yue Wang / Ebert, Philip / Bray, Steven / Ting, Jason C / Aggarwal, Amit / Henry, James R / Tiu, Ramon V / Plowman, Gregory D / Peng, Sheng-Bin

Clinical cancer research : an official journal of the American Association for Cancer Research

2017 Volume 23, Issue 18, Page(s) 5547–5560

Abstract: Purpose: ...

Abstract	Purpose:
Language	English
Publishing date	2017-09-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	1225457-5
ISSN	1557-3265 ; 1078-0432
ISSN (online)	1557-3265
ISSN	1078-0432
DOI	10.1158/1078-0432.CCR-16-3250
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