35 resultados para ALS data-set
em Chinese Academy of Sciences Institutional Repositories Grid Portal
Resumo:
Decision Trees need train samples in the train data set to get classification rules. If the number of train data was too small, the important information might be missed and thus the model could not explain the classification rules of data. While it is not affirmative that large scale of train data set can get well model. This Paper analysis the relationship between decision trees and the train data scale. We use nine decision tree algorithms to experiment the accuracy, complexity and robustness of decision tree algorithms. Some results are demonstrated.
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Transcription factor binding sites (TFBS) play key roles in genebior 6.8 wavelet expression and regulation. They are short sequence segments with de¯nite structure and can be recognized by the corresponding transcription factors correctly. From the viewpoint of statistics, the candidates of TFBS should be quite di®erent from the segments that are randomly combined together by nucleotide. This paper proposes a combined statistical model for ¯nding over- represented short sequence segments in di®erent kinds of data set. While the over-represented short sequence segment is described by position weight matrix, the nucleotide distribution at most sites of the segment should be far from the background nucleotide distribution. The central idea of this approach is to search for such kind of signals. This algorithm is tested on 3 data sets, including binding sites data set of cyclic AMP receptor protein in E.coli, PlantProm DB which is a non-redundant collection of proximal promoter sequences from di®erent species, collection of the intergenic sequences of the whole genome of E.Coli. Even though the complexity of these three data sets is quite di®erent, the results show that this model is rather general and sensible.
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Effects of flame stretch on the laminar burning velocities of near-limit fuel-lean methane/air flames have been studied experimentally using a microgravity environment to minimize the complications of buoyancy. Outwardly propagating spherical flames were employed to assess the sensitivities of the laminar burning velocity to flame stretch, represented by Markstein lengths, and the fundamental laminar burning velocities of unstretched flames. Resulting data were reported for methane/air mixtures at ambient temperature and pressure, over the specific range of equivalence ratio that extended from 0.512 (the microgravity flammability limit found in the combustion chamber) to 0.601. Present measurements of unstretched laminar burning velocities were in good agreement with the unique existing microgravity data set at all measured equivalence ratios. Most of previous 1-g experiments using a variety of experimental techniques, however, appeared to give significantly higher burning velocities than the microgravity results. Furthermore, the burning velocities predicted by three chemical reaction mechanisms, which have been tuned primarily under off-limit conditions, were also considerably higher than the present experimental data. Additional results of the present investigation were derived for the overall activation energy and corresponding Zeldovich numbers, and the variation of the global flame Lewis numbers with equivalence ratio. The implications of these results were discussed. 2010 The Combustion Institute. Published by Elsevier Inc. All rights reserved.
Resumo:
The retrieval of DNA from ancient human specimens is not always successful owing to DNA deterioration and contamination although it is vital to provide new insights into the genetic structure of ancient people and to reconstruct the past history. Normally, only short DNA fragments can be retrieved from the ancient specimens. How to identify the authenticity of DNA obtained and to uncover the information it contained are difficult. We employed the ancient mtDNAs reported from Central Asia (including Xinjiang, China) as an example to discern potentially extraneous DNA contamination based on the updated mtDNA phylogeny derived from mtDNA control region, coding region, as well as complete sequence information. Our results demonstrated that many mtDNAs reported are more or less problematic. Starting from a reliable mtDNA phylogeney and combining the available modern data into analysis, one can ascertain the authenticity of the ancient DNA, distinguish the potential errors in a data set, and efficiently decipher the meager information it harbored. The reappraisal of the mtDNAs with the age of more than 2000 years from Central Asia gave support to the suggestion of extensively (pre)historical gene admixture in this region.
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The sequences of the mitochondrial ND4 gene (1339 bp) and the ND4L gene (290 bp) were determined for all the 14 extant taxa of the Drosophila nasuta subgroup The average A + T content of ND4 genes is 76.5% and that of ND4L genes is 83.5%. A total of 114 variable sites were scored. The ND4 gene sequence divergence ranged from 0 to 5.4% within the subgroup. The substitution rate of the ND4 gene is about 1.25% per million years. The base substitution of the genesis strongly transition biased. Neighbor-joining and parsimony were used to construct a phylogeny based on the resultant sequence data set. According to these trees, five, distinct mtDNA clades can be identified. D. niveifrons represents the most diverged lineage. D, sulfurigaster bilimbata and D. kepulauana form two independent lineages. The other two clades are the kohkoa complex and the albomicans complex. The Kohkoa complex consists of D. sulfurigaster sulfurigaster, D. pulaua, D. kohkoa, and Taxon-F. The albomicans complex can be divided into two groups: D. nasuta, D. sulfurigaster neonasuta, D. sulfurigaster albostrigata, and D.. albomicans from Chiangmai form one group; and D. pallidifrons, Taxon-I, Taxon-J, and D. albomicans from China form the other group. High genetic differentiation was found among D. albomicans populations. Based on our phylogenetic results, we hypothesize that D. niveifrons diverged first from the D, nasuta subgroup in Papua New Guinea about 3.5 Mya. The ancestral population spread to the north and when it reached Borneo, it diversified sequentially into the kohkoa complex, D. s. bilimbata, and D. kepulauana. About 1 Mya, another radiation occurred when the ancestral populations reached the Indo-China Peninsula, forming the albomicans complex. Discrepancy between morphological groupings and phylogenetic results suggests that the male morphological traits may not be orthologous. (C) 1999 Academic Press.
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The phylogenetic relationships among 12 genera of treefrogs (Family, Rhacophoridae), were investigated based on a large sequence data set, including five nuclear (brain-derived neurotrophic factor, proopiomelanocortin, recombination activating gene 1, tyr
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The population genetic structure of fish parasitic nematode, Camallanus cotti, collected from the Yangtze River, Pearl River and Minjiang River in China was investigated. From these parasites, the similar to 730 bp of the first internal transcribed spacer of ribosomal DNA (ITS1 rDNA) and the 428 bp of mitochondrial cytochrome c oxidase subunit I (COI) gene were sequenced. For the ITS1 rDNA data set, highly significant Fst values and low rates of migration were detected between the Pearl River group and both the Yangtze River (Fst = 0.70, P < 0.00001; Nm = 0.21) and Minjiang River (Fst = 0.73, P < 0.00001; Nm = 0.18) groups, while low Fst value (Fst = 0.018, P > 0.05) and high rate of migration (Nm = 28.42) were found between the Minjiang and the Yangtze rivers. When different host/locality populations (subpopulations) within each river were considered, subpopulations between the Yangtze River and Minjiang River had low Fst values (<= 0.12) and high Nm values (>3.72), while Pearl River subpopulations were significantly different from the Yangtze River and Minjiang River subpopulations (Fst >= 0.59; Nm < 1). The COI gene data set revealed a similar genetic structure. Both phylogenetic analyses and a statistical parsimony network grouped the Pearl River haplotypes into one phylogroup, while the Yangtze River and Minjiang River haplotypes formed a second group. These results suggested that the Yangtze River and Minjiang River subpopulations constituted a single reproductive pool that was distinct from the Pearl River subpopulations. In addition, the present study did not find host-related genetic differentiation occurring in the same drainage. (C) 2009 Published by Elsevier B.V.
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The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentation with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Sinocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed molecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletic of cave species and the most basal position of S. jii was corroborated. Relaxed divergence-time estimation suggested that Sinocyclocheilus originated at the late Miocene, about 11 million years ago (Ma), which is older than what have been assumed.
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The complete sequence of the 16,539 nucleotide mitochondrial genome from the single species of the catfish family Cranoglanididae, the helmet catfish Cranoglanis bouderius, was determined using the long and accurate polymerase chain reaction (LA PCR) method. The nucleotide sequences of C. bouderius mitochondrial DNA have been compared with those of three other catfish species in the same order. The contents of the C. bouderius mitochondrial genome are 13 protein-coding genes, two ribosomal RNA and 22 transfer RNA genes, and a non-coding control region, the gene order of which is identical to that observed in most other vertebrates. Phylogenetic analyses for 13 otophysan fishes were performed using Bayesian method based on the concatenated mtDNA protein-coding gene sequence and the individual protein-coding gene sequence data set. The competing otophysan topologies were then tested by using the approximately unbiased test, the Kishino-Hasegawa test, and the Shimodaira-Hasegawa test. The results show that the grouping ((((Characifonnes, Gymnotiformes), Siluriformes), Cyprinifionnes), outgroup) is the most likely but there is no significant difference between this one and the other alternative hypotheses. In addition, the phylogenetic placement of the family Cranoglanididae among siluriform families was also discussed. (c) 2006 Elsevier B.V. All rights reserved.
Resumo:
The accurate cancer classification is of great importance in clinical treatment. Recently, the DNA microarray technology provides a promising approach to the diagnosis and prognosis of cancer types. However, it has no perfect method for the multiclass classification problem. The difficulty lies in the fact that the data are of high dimensionality with small sample size. This paper proposed an automatic classification method of multiclass cancers based on Biomimetic pattern recognition (BPR). To the public GCM data set, the average correct classification rate reaches 80% under the condition that the correct rejection rate is 81%.
Resumo:
对隆肛蛙属的物种构成进行了订正,建立新属肛刺蛙属Yerana gen. nov.;订正后的隆肛蛙属现仅隶2种, 即隆肛蛙F. quadrana和太行隆肛蛙F. taihangnicus。运用形态学分析探讨了隆肛蛙属物种及种群的形态差异和分类关系,通过分子系统学研究探讨了隆肛蛙属物种及种群的分类和系统发育关系,运用动物地理学方法结合系统发育关系探讨了隆肛蛙属种群的地理分布格局成因与历史过程。主要结果和推论如下: 1.隆肛蛙属物种构成的订正及一新属建立 建立新属肛刺蛙属,将隆肛蛙属中的原叶氏隆肛蛙F. yei归隶新属肛刺蛙属并更名为叶氏肛刺蛙Y. yei,,新属建立的主要依据为:(1)雄性肛部隆起,肛孔下方有两个布满黑刺的大的白色球形隆起,具单咽下内声囊, 第一指具婚刺;(2)形态量度分析表明叶氏肛刺蛙与隆肛蛙和太行隆肛蛙的形态差异远大于后两者之间的差异;(3)叶氏肛刺蛙的分布区与隆肛蛙和太行隆肛蛙的分布区距离较远且呈隔离状态;(4)分子系统学研究资料(Jiang et al.,2005)证明叶氏肛刺蛙与隆肛蛙和太行隆肛蛙非单系发生;叶氏肛刺蛙在第二支中位于基部。因此,隆肛蛙属现仅隶2种,即隆肛蛙和太行隆肛蛙。 2.隆肛蛙属种群形态学研究 对隆肛蛙属中隆肛蛙和太行隆肛蛙的15个地理种群565只标本的28项形态性状进行了测量,运用典型判别分析法对其分析的结果表明:(1)太行隆肛蛙与隆肛蛙形态差异明显,支持其为不同的物种;(2)原隆肛蛙河南伏牛山种群和山西中条山种群应为太行隆肛蛙的地理种群;(3)隆肛蛙不同地理种群之间形态差异明显,其中四川安县种群、陕西周至种群和湖北利川种群与模式产地重庆巫山种群的差异可能达到了亚种或亚种以上分化水平。对隆肛蛙属量度分析的15个种群进行定性形态分析表明其分为三种形态型,对应隆肛蛙、过渡型和太行隆肛蛙,其变异特征主要为内跗褶、雄性肛部隆起及疣粒分布、第五趾外侧缘膜等,这与量度分析结果相似。 3.隆肛蛙属种群分子系统学研究 测定隆肛蛙属Feirana的2种19种群的线粒体12S rRNA和16S rRNA基因片段、ND2基因的DNA序列,比对后共计1953bps。(1)遗传多样性与距离分析:结果表明,隆肛蛙属种群具很高的遗传多样性,19个种群样品表现出19种单倍型(遗传多样性指数Hd=1.0); ND2基因的进化信息含量远高于12SrRNA和16SrRNA。隆肛蛙属2种群组内的种群间的遗传距离远小于两种群组间的距离,种群在不同基因上的遗传距离表现的关系与对应的系统树一致。(2)系统发育关系分析:结果表明,不同基因片断基于不同方法构建的隆肛蛙属种群系统发育树结构基本一致,基本表明隆肛蛙属种群为单系发生;它们在系统树中分为两大支,分别对应于隆肛蛙和太行隆肛蛙;支持中条山种群(沁水、历山和济源种群)和伏牛山种群(栾川和内乡种群)为太行隆肛蛙的地理种群,而原隆肛蛙秦岭中东段的部分种群(柞水、宁陕、长安大坝沟种群)也应为太行隆肛蛙的地理种群。(3)亚种分化分析:根据遗传距离分析和系统发育关系分析结果,并考虑形态上的差异情况以及地理分布信息,隆肛蛙所隶种群组可分为2亚种,即隆肛蛙指名亚种F. quadrana quadrana包括四川盆地东缘大巴山东段-巫山-武陵山北麓种群和秦岭中段(周至板房子和长安广货街)种群,他们在系统关系树上聚为一支;安县亚种F. quadrana anxianensis包括四川盆地西缘岷山东麓-龙门山-大巴山和秦岭西段的种群(安县、青川、文县、南江和凤县种群),他们在系统关系树上聚为一支。太行隆肛蛙所隶种群组也可分为2亚种,即太行隆肛蛙指名亚种F. taihangnicus taihangnicus包括中条山的种群(沁水、历山和济源种群)和中东秦岭的部分种群(柞水、长安大坝沟和宁陕种群),他们在系统关系树上聚为一支;太行隆肛蛙伏牛亚种F. taihangnicus funiuensis,为伏牛山地区的种群(栾川和内乡种群),他们在系统关系树上聚为一支。 4.隆肛蛙属种群动物地理学研究 隆肛蛙属19种群的分歧年代分析: 以长江巫山段和黄河三门峡段的形成历史时期为参考点,根据已测隆肛蛙属19种群及其外群包括N. pleski、P. yunnanesis、P. robertingeri、F. limnocharis的1953bps DNA序列构建分子钟,获得各支系的分歧年代。结果表明:①棘蛙族在70Ma左右开始其独立演化历程,这与Roelants et al.(2004)的分析结果~60±15Ma左右开始分化基本一致,后者印证了本文的分子钟。②隆肛蛙属的起始分化年代较早,隆肛蛙和太行隆肛蛙两种群组的最近祖先种群大概在46Ma~50Ma左右;隆肛蛙和太行隆肛蛙种群组内的种群分化年代相对两种群组间晚得多, 隆肛蛙种群组内两亚种分化起始年代约为10Ma左右,而太行隆肛蛙种群组内两亚种分化起始年代约为6Ma。 隆肛蛙属种群分布格局形成过程分析: ①隆肛蛙属的系统关系与地理分布格局密切相关,大部分系统分支分级与地理距离成正比;②隆肛蛙属最近祖先种群的分化中心可能位于秦岭中部地区, 隆肛蛙属的种群分布格局的形成表现为隔离分化与扩散相结合的机制,由隔离分化产生的隆肛蛙祖先种群主要从秦岭中部向西南方向扩散,后隔离分化为两亚种;太行隆肛蛙祖先种群向东北方向扩散也分化为两亚种。 隆肛蛙属种群分布区域地质历史的探讨:本文所建分子钟和种群分化方式印证了该区域的几次主要地质事件,包括岷山-龙门山-西秦岭等地区的快速差异隆起、第四纪冰期等。 The specific composition of the genus Feirana should be revised. A new genus Yerana gen. nov.(Ranidae:Dicroglossinae)was established based on morphological data-set and molecular phylogeny, as a result, only two species F. quadrana and F. taihangnicus are classified into Feirana now. Morphological differences and taxonomy of populations of Feirana were investigated based on morphological and morphometric data; phylogenetic relationships and taxonomy of populations of Feirana were elucidated using molecular data, and then the proceeding of the distribution pattern of populations of Feirana were discussed. The main results and conclusions and proposals were presented as following: 1. Revising of the specific composition of the genus Feirana and establishment of a new genus The new genus Yerana, only containing the type species Y. yei, was established based on the following evidences: (1) In adult male, distinct up-heaved circular vesicle presents around the anal, and under anal there are two white balls on which black spines exist, black horny spines scatter on the upper side of first finger, and internal single subgular vocal sac presents; (2) there is obvious morphometric differences between Yerana and Feirana; (3) Yerana is distributed far from Feirana; (4) evidences of molecular phylogeny(Jiang et al.,2005)suggested that Yerana take a special phylogenetic clade which is different from other genus included in the tribe Paini. As a result, there are only two species in Feirana, i.e., F. quadrana and F. taihangnicus. 2. Morphological research of populations of Feirana Twenty-eight characters of 565 individuals of 15 populations of the genus Feirana were measured, the results of Canonical Discriminant analysis of the morphometric data-set indicated that: (1) there are very prominent differences between the two species F. quadrana and F. taihangnicus. The validity of species F. taihangnicus was approved here; (2) Mt. Funiu population and Mt. Zhongtiao population should belong to the species F. taihangnicus; (3) Obvious differences exist among 12 populations of F. quadrana, the differentiation among Zhouzhi population, Anxian population, Lichuan population, and Wushan population together with the others probably reach sub-specific or specific level. Result of morphological comparison between 15 different populations show that 3 morphological types are recogenized in according with F. quadrana, F. taihangnicus and intergradation, this result conform to the result of morphometric analysis. 3. Molecular phylogenetic study on populaions of Feirana Fragment of 12SrRNA and 16SrRNA genes, and ND2 gene of 19 populations of two species of Feirana were sequenced and aligned, from which 1953 bps were received. (1) analyses of genetic distance and hereditary diversity indicated that: genetic distance between populations in each group were less than distance between two groups of Feirana, 19 haplotypes were recognized from 19 samples of 19 populations, so the hereditary diversity of populations of Feirana was very high (Hd=1.0), phylogenetic information in ND2 gene is more than fragment sequence of 12SrRNA and 16SrRNA genes. (2) Result of molecular phylogeny indicate that the phylogenetic trees constructed using different methods based on different sequence data sets showed the revised genus Feirana is monophyletic since the 19 populations of Feirana were firstly clustered together as one large clade, which was further clustered into two major clades, corresponding to F. quadrana(GroupⅠ) and F. taihangnicus(GroupⅡ), respectively. So populations of Qinshui and Lishan in Mt. Zhongtiao, populations of Luanchuan and Neixiang in Mt. Funiu, and populations of Zhashui, Dabagou of Chang’an and Ningshan in eastern Mt. Qinling should belong to the species F. taihangnicus; (3) Subspecific differentiation. on the basis of genetic distance, phylogenetic trees and geographical distribution, F. quadrana should have two subspecies, i.e., F. quadrana qudadrana, consisting of the populations Guanghuojie of Chang’an and Zhouzhi in Mid-Mt. Qinling, populations in Wushan area and northern Mt. Wuling (Lichuan), and F. qudadrana anxianensis, consisting of the populations in eastern Mt. Ming shan-Mt. Longmen-western Mt. Daba-western Mt. Qinling (Anxian, Qingchuan, Wenxian, Nanjiang and Fengxian); F. taihangnicus should also has two subspecies, i.e., F. taihangnicus taihangnicus, consisting of the populations in Mt. Zhongtiao and eastern Mt. Qinling, and F. taihangnicus funiuensis, consisting of the populations in Mt. Funiu. 4. Zoogeography of populaions of Feirana Analysis for divergent time of 19 populations of Feirana: Using the dates of run-through of Wushan segment of Changjiang River as the time when the population of Lichuan started differentiated from the populations of Wushan and Shennongjia, and the dates of Sanmenxia segment of Yellow River as the time when the populations in Mt. Zhongtiao started differentiated from the population of Dabagou in Chang’an, molecular clock was established using sequences with 1953 bps of 19 populations of Feirana and outgroup including N. pleski, P. yunnanesis, P. robertingeri, F. limnocharis in order to estimate divergent time of all clades. Result of that indicated that: ① the tribe Paini started to evolve independently at about 70Ma when is in consistent with that estimated by Roelants et al.(2004)with result of about ~60±15Ma, they were corroborated by each other, this confirms the validity of this molecular clock; ② divergent time for speciation of Feriana is early, ancestral populations of F. quadrana and F. taihangnicus were found about 46Ma~50Ma; differentiation of populations within species is greatly late to the divergence of the two species, divergent time for F. quadrana is 10Ma and divergent time for F. taihangnicus is 6Ma. Proceeding of distribution pattern of Feirana. Phylogenetic relationships of populations of Feirana matched quite with distribution pattern of them, the relationships among clades showed in phylogenetic trees is direct ratio to geographical distance of them; the estimated date of speciation between two species of Feirana was as early as speciation of Paa yunnanesis and Nanara pleski; middle part of Mt. Qinling is the center of speciation of Feirana, combination of mult-events of dispersal and vicariance are probably the mechanism of speciation of Feirana, F. quadrana colonized the mid-Mt. Qinling and then differentiated into two subspecies in southwest direction, ancestral population of F. taihangnicus colonized the mid-Mt. Qinling and then differentiated into two subspecies in northeast direction. On geological history of the distribution of Feirana. According to molecular clock and speciation model of populations of Feirana, some geological events are confirmed, including special rise of Mt. Minshan- Mt. Longmen-western Mt. Qinling, glacial age.
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在区域水土流失模型研究中,空间插值可提供每个计算栅格的气象要素资料。考虑到研究区域降雨与高程相关性很弱,不宜采用梯度距离反比法(GIDS),故采用距离反比法(IDW)和普通克里格法(Kriging),对延安示范区及其周围共50个站点2000—2003年的5—10月逐月降雨量进行插值。交叉验证结果表明:对2种插值方法,二者经过对数变换后平均相对误差(MRE)为8.30%和7.67%,分别比原始数据插值后的MRE下降了23.17%和23.50%,说明插值精度得到了提升,对研究区域某一年逐月降水的插值Kriging方法比IDW方法更加精确。
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Using meteorological data and RS dynamic land-use observation data set, the potential land productivity that is limited by solar radiation and temperature is estimated and the impacts of recent LUCC processes on it are analyzed in this paper. The results show that the influence of LUCC processes on potential land productivity change has extensive and unbalanced characteristics. It generally reduces the productivity in South China and increases it in North China, and the overall effect is increasing the total productivity by 26.22 million tons. The farmland reclamation and original farmlands losses are the primary causes that led potential land productivity to change. The reclamation mostly distributed in arable-pasture and arable-forest transitional zones and oasises in northwestern China has made total productivity increase by 83.35 million tons, accounting for 3.50% of the overall output. The losses of original farmlands driven by built-up areas invading and occupying arable land are mostly distributed in the regions which have rapid economic development, e.g. Huang-Huai-Hai plain, Yangtze River delta, Zhujiang delta, central part of Gansu, southeast coastal region, southeast of Sichuan Basin and Urumqi-Shihezi. It has led the total productivity to decrease 57.13 million tons, which is 2.40% of the overall output.
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This study examines the link between the economic growth and the environmental quality. Based on a panel data set, a N-shaped Environmental Kuzents Curve has been found for the sample period: a cubic relationship between per capita GDP and emissions of sulphur dioxide (SO2). We also find that energy consumption is an important determinant of environmental degradation. The empirical results suggest that we should promote environmental protection as soon as possible.