We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we ...We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including y-NG, y-LWL, ）,-MLWL, y-LPB, y-MLPB, y-YN and y-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5＇ to 3＇ direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. A toolbox, including C＋＋ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https：//sourceforge.net/projects/kakscalculator2/.展开更多
120 pearl oysters （Pinctada martensii） were randomly sampled from F1 population, and shell length, shell width, shell height, shell weight and total weight of each sample were measured. Correlation and path analysis...120 pearl oysters （Pinctada martensii） were randomly sampled from F1 population, and shell length, shell width, shell height, shell weight and total weight of each sample were measured. Correlation and path analysis were conducted on the basis of measurement data. The results showed that shell length, shell width, shell height, shell weight and total weight were significantly correlated （P 〈 0.05）. Total weight was significantly and positively correlated with shell weight （r = 0.8970）, shell height （r = 0.6974）, shell width （r = 0.6521） and shell length （r = 0.5486）. Shell weight, shell height, shell width and shell length had positive and direct effects on total wet weight, with the values of 0.6356, 0.1872, 0.1814 and 0.0599, respectively. The results indicated that growth traits （shell length, shell width, shell height, shell weight and total wet weigh） of the F1 population could be improved by direct or indirect selection.展开更多
This article presents an update on the variable prognostic significance of different sperm pathologies in patients with severe male factor infertility due to morphology and motility disorders. Severe asthenozoospermia...This article presents an update on the variable prognostic significance of different sperm pathologies in patients with severe male factor infertility due to morphology and motility disorders. Severe asthenozoospermia is one of the leading causes of male infertility as spermatozoa cannot reach the oocyte and/or penetrate normally. Identifying structural causes of sperm immotility was of great concern before the advent of intracytoplasmic sperm injection （ICSI）, because immotility was the limiting factor in the treatment of these patients. In these cases, in vitro methods are used to identify live spermatozoa or stimulate sperm motility to avoid selection of non-viable cells. With these advances, fertilization and pregnancy results have improved dramatically. The identification of genetic phenotypes in asthenozoospermia is important to adequately inform patients of treatment outcomes and risks. The one sperm characteristic that seriously affects fertility prognosis is teratozoospermia, primarily sperm head and neck anomalies. Defects of chromatin condensation and acrosomal hypoplasia are the two most common abnormalities in severe teratozoospermia. The introduction of microscopic methods to select spermatozoa and the development of new ones to evaluate sperm quality before ICSI will assure that ultrastructural identification ofsperm pathologies will not only be of academic interest, but will also be an essential tool to inform treatment choice. Herein, we review the differential roles played by sperm components in normal fertilization and early embryo development and explore how assisted reproductive technologies have modified our concepts on the prognostic significance of sperm pathologies affecting the head, neck, mid-piece and tail.展开更多
In May of 2007,the second generation selected （SS） and control （SC） groups of pearl oyster Pinctada martensii were established by selecting 10% breeders with the largest and mean shell length,respectively,from the...In May of 2007,the second generation selected （SS） and control （SC） groups of pearl oyster Pinctada martensii were established by selecting 10% breeders with the largest and mean shell length,respectively,from the first generation selected group.Growth performance of the SS and SC groups were compared on the basis of measurement data at Days 8,18,60,95,195 and 365.On Day 365,100 individuals （60.0–75.0 mm at shell length） were sampled from each group and then subjected to the experiment where physiological parameters such as filtrate rate,oxygen consumption and ammonia excretion were measured at 15,20,25 and 30°C.The results show that the SS group had significantly larger mean shell length and shell height than the SC group at Days 8,18,60,95,195 and 365 （P 0.05）.The genetic gains at different ages varied from 6.0% to 17.0% for shell length and 5.7% to 14.6% for shell height,respectively.At 15,20,25 and 30 ° C,the SS groups had significantly larger filtrate rate than the SC group （P 0.05）.At 15 and 25 °C,the differences in oxygen consumption rate between the SS and SC groups were not significant （P 0.05）.At 20 and 30 °C,however,the oxygen consumption rate of the SS group was significantly larger than the SC group （P 0.05）.At 15,20,25 and 30 °C,there were no significant differences in ammonia excretion rate between the SS and SC groups （P 0.05）.The present results indicate that there existed considerable genetic variability in the base population and a further selection could be likely fruitful.Mass selection for faster growth might produce animals that had higher intake of metabolizable energy by virtue of faster filtrating behavior.展开更多
建立了一种可用于水产品及食用油中氟乐灵残留量分析的分散型固相萃取-气相色谱-负化学离子源质谱方法。水产品及食用油经乙腈提取，4℃冷藏后，采用分散型固相萃取法净化，由气相色谱-负化学离子源质谱选择离子监测技术进行测定与确证...建立了一种可用于水产品及食用油中氟乐灵残留量分析的分散型固相萃取-气相色谱-负化学离子源质谱方法。水产品及食用油经乙腈提取，4℃冷藏后，采用分散型固相萃取法净化，由气相色谱-负化学离子源质谱选择离子监测技术进行测定与确证，同位素内标法定量。在1～40μg / L 范围内氟乐灵农药的线性关系良好；方法定量限（LOQ）为0.02μg / kg；对鳗鱼、烤鳗、梭子蟹、小龙虾、猪油和橄榄油等6种复杂基质进行1.0、2.0和3.0μg / kg 等3个水平的添加回收试验，平均回收率均处于80％～100％之间，RSD≤10.3％；无干扰现象出现。该方法可作为水产品及食用油中氟乐灵残留检测的确证方法。展开更多
Microsatellite alterations within genomic DNA frameshift as a result of defective DNA mismatch repair(MMR). About 15% of sporadic colorectal cancers(CRCs) manifest hypermethylation of the DNA MMR gene MLH1, resulting ...Microsatellite alterations within genomic DNA frameshift as a result of defective DNA mismatch repair(MMR). About 15% of sporadic colorectal cancers(CRCs) manifest hypermethylation of the DNA MMR gene MLH1, resulting in mono-and di-nucleotide frameshifts to classify it as microsatellite instability-high(MSI-H) and hypermutated, and due to frameshifts at coding microsatellites generating neo-antigens, produce a robust protective immune response that can be enhanced with immune checkpoint blockade. More commonly, approximately 50% of sporadic nonMSI-H CRCs demonstrate frameshifts at di-and tetra-nucleotide microsatellites to classify it as MSIlow/elevated microsatellite alterations at selected tetranucleotide repeats(EMAST) as a result of functional somatic inactivation of the DNA MMR protein MSH3 via a nuclear-to-cytosolic displacement. The trigger for MSH3 displacement appears to be inflammation and/or oxidative stress, and unlike MSI-H CRC patients, patients with MSI-L/EMAST CRCs show poor prognosis. These inflammatory-associated microsatellite alterations are a consequence of the local tumor microenvironment, and in theory, if the microenvironment is manipulated to lower inflammation, the microsatellite alterations and MSH3 dysfunction should be corrected. Here we describe the mechanisms and significance of inflammatory-associated microsatellite alterations, and propose three areas to deeply explore the consequences and prevention of inflammation's effect upon the DNA MMR system.展开更多
Using a special coated sand as the material of the selected laser sintering (SLS), the authors test and investigate the strength change of the test samples in terms of different sintering parameters (scanning speed, l...Using a special coated sand as the material of the selected laser sintering (SLS), the authors test and investigate the strength change of the test samples in terms of different sintering parameters (scanning speed, laser power, sintering thickness, and so on). The characteristics of coated sand hardening by laser beam are analyzed. The sintered mold (or core) for given casting is poured with molten metal.展开更多
We reported data on thermal preference, thermal tolerance and the thermal dependence of digestive performance for two Phrynocephalus lizards （P. frontalis and P. versicolor）, and compared data among lizards so far s...We reported data on thermal preference, thermal tolerance and the thermal dependence of digestive performance for two Phrynocephalus lizards （P. frontalis and P. versicolor）, and compared data among lizards so far studied worldwide. Mean values for selected body temperature （Tsel） and critical thermal maximum （CTMax） were greater in P versicolor, whereas mean values for critical thermal minimum （CTMin） did not differ between the two species. The two lizards differed in food intake, but not in food passage time, apparent digestive coefficient （ADC） and assimilation efficiency （AE）, across the experimental tem- peratures. Four general conclusions can be drawn from published data. Firstly, thermal preference and thermal tolerance differ among lizards differing in distribution, temporal activity pattern and habitat use. Lizards in thermally more variable regions are better able to tolerate low and high temperatures. Diurnal lizards generally select higher body temperatures than nocturnal lizards, and lizards using habitats with direct sun exposure generally selected higher body temperatures and are better able to tolerate high temperatures. Secondly, CTMax is positively correlated with Tsel. Lizards more likely exposed to extremely high temperatures while active select higher body temperatures than those using shaded habitats. Thirdly, the effects of body temperature on food intake, food passage time, ADC and AE differ among lizards, but it seems to be common among lizards that ADC and AE are less thermally sensitive than food intake and food passage time. Lastly, ADC is dependent on the type of food ingested, with insectivorous lizards digesting food more efficiently than herbivorous lizards展开更多
HIV-1 co-receptor tropism is central for understanding the transmission and pathogenesis of HIV-1 infection. We performed a genome-wide comparison between the adaptive evolution of R5 and X4 variants from HIV-1 subtyp...HIV-1 co-receptor tropism is central for understanding the transmission and pathogenesis of HIV-1 infection. We performed a genome-wide comparison between the adaptive evolution of R5 and X4 variants from HIV-1 subtypes B and C. The results showed that R5 and X4 variants experienced differential evolutionary patterns and different HIV-1 genes encountered various positive selection pressures, suggesting that complex selection pressures are driving HIV-1 evolution. Compared with other hypervariable regions of Gp120, significantly more positively selected sites were detected in the V3 region of subtype B X4 variants, V2 region of subtype B R5 variants, and V1 and V4 regions of subtype C X4 variants, indicating an association of positive selection with co-receptor recognition/binding. Intriguingly, a significantly higher proportion (33.3% and 55.6%, P【0.05) of positively selected sites were identified in the C3 region than other conserved regions of Gp120 in all the analyzed HIV-1 variants, indicating that the C3 region might be more important to HIV-1 adaptation than previously thought. Approximately half of the positively selected sites identified in the env gene were identical between R5 and X4 variants. There were three common positively selected sites (96, 113 and 281) identified in Gp41 of all X4 and R5 variants from subtypes B and C. These sites might not only suggest a functional importance in viral survival and adaptation, but also imply a potential cross-immunogenicity between HIV-1 R5 and X4 variants, which has important implications for AIDS vaccine development.展开更多
Effects of multiple strengthening treatments （i.e. ag mechanical properties and stability of nanoscale prec in this research. Various tests such as hardness, tensi ng either at three or four consecutive temperatures...Effects of multiple strengthening treatments （i.e. ag mechanical properties and stability of nanoscale prec in this research. Various tests such as hardness, tensi ng either at three or four consecutive temperatures） on pitated phases in an AA2090 alloy have been evaluated e, electrical resistance, differential scanning calorimetric （DSC）, and transmission electron microscopy （TEM） have been performed. The results show that the ultimate tensile strength （UTS） and the yield strength of the samples aged at four consecutive temperatures （i.e. natural aging＋190℃＋150℃＋100℃） can be increased approximately to 660 and 610 MPa, respectively. It is also found that precipitation of T1 phase occurs during multiple aging process of the alloy and the higher amounts of enthalpies shown in DSC charts are linked to higher volume fraction of this precipitate. Furthermore, TEM observations reveal that T1 phase has plate shape morphology and its crystal structure is in the form of hcp with lattice parameters of a=0.467 nm and c=0.878 nm.展开更多
基金funded by the National Basic Research Program of China (973 Program) to JY (Grant No.2006CB910404)
文摘We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including y-NG, y-LWL, ）,-MLWL, y-LPB, y-MLPB, y-YN and y-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5＇ to 3＇ direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. A toolbox, including C＋＋ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https：//sourceforge.net/projects/kakscalculator2/.
基金grants of the Guangdong Marine and Fishery Bureau(No.B02068)Guangdong Ocean University(No.E06031).
文摘120 pearl oysters （Pinctada martensii） were randomly sampled from F1 population, and shell length, shell width, shell height, shell weight and total weight of each sample were measured. Correlation and path analysis were conducted on the basis of measurement data. The results showed that shell length, shell width, shell height, shell weight and total weight were significantly correlated （P 〈 0.05）. Total weight was significantly and positively correlated with shell weight （r = 0.8970）, shell height （r = 0.6974）, shell width （r = 0.6521） and shell length （r = 0.5486）. Shell weight, shell height, shell width and shell length had positive and direct effects on total wet weight, with the values of 0.6356, 0.1872, 0.1814 and 0.0599, respectively. The results indicated that growth traits （shell length, shell width, shell height, shell weight and total wet weigh） of the F1 population could be improved by direct or indirect selection.
文摘This article presents an update on the variable prognostic significance of different sperm pathologies in patients with severe male factor infertility due to morphology and motility disorders. Severe asthenozoospermia is one of the leading causes of male infertility as spermatozoa cannot reach the oocyte and/or penetrate normally. Identifying structural causes of sperm immotility was of great concern before the advent of intracytoplasmic sperm injection （ICSI）, because immotility was the limiting factor in the treatment of these patients. In these cases, in vitro methods are used to identify live spermatozoa or stimulate sperm motility to avoid selection of non-viable cells. With these advances, fertilization and pregnancy results have improved dramatically. The identification of genetic phenotypes in asthenozoospermia is important to adequately inform patients of treatment outcomes and risks. The one sperm characteristic that seriously affects fertility prognosis is teratozoospermia, primarily sperm head and neck anomalies. Defects of chromatin condensation and acrosomal hypoplasia are the two most common abnormalities in severe teratozoospermia. The introduction of microscopic methods to select spermatozoa and the development of new ones to evaluate sperm quality before ICSI will assure that ultrastructural identification ofsperm pathologies will not only be of academic interest, but will also be an essential tool to inform treatment choice. Herein, we review the differential roles played by sperm components in normal fertilization and early embryo development and explore how assisted reproductive technologies have modified our concepts on the prognostic significance of sperm pathologies affecting the head, neck, mid-piece and tail.
基金The National Key Technology R&D Program in the 11th Five Year Plan of China under contract No. 2007BAD29B01-2National Department Public Benefit Research Foundation under contract No. nyhyzx 07-048Guangdong Marine and Fishery Bureau under contract Nos A200708C01, A200908A02 and A200908A05
文摘In May of 2007,the second generation selected （SS） and control （SC） groups of pearl oyster Pinctada martensii were established by selecting 10% breeders with the largest and mean shell length,respectively,from the first generation selected group.Growth performance of the SS and SC groups were compared on the basis of measurement data at Days 8,18,60,95,195 and 365.On Day 365,100 individuals （60.0–75.0 mm at shell length） were sampled from each group and then subjected to the experiment where physiological parameters such as filtrate rate,oxygen consumption and ammonia excretion were measured at 15,20,25 and 30°C.The results show that the SS group had significantly larger mean shell length and shell height than the SC group at Days 8,18,60,95,195 and 365 （P 0.05）.The genetic gains at different ages varied from 6.0% to 17.0% for shell length and 5.7% to 14.6% for shell height,respectively.At 15,20,25 and 30 ° C,the SS groups had significantly larger filtrate rate than the SC group （P 0.05）.At 15 and 25 °C,the differences in oxygen consumption rate between the SS and SC groups were not significant （P 0.05）.At 20 and 30 °C,however,the oxygen consumption rate of the SS group was significantly larger than the SC group （P 0.05）.At 15,20,25 and 30 °C,there were no significant differences in ammonia excretion rate between the SS and SC groups （P 0.05）.The present results indicate that there existed considerable genetic variability in the base population and a further selection could be likely fruitful.Mass selection for faster growth might produce animals that had higher intake of metabolizable energy by virtue of faster filtrating behavior.
文摘建立了一种可用于水产品及食用油中氟乐灵残留量分析的分散型固相萃取-气相色谱-负化学离子源质谱方法。水产品及食用油经乙腈提取，4℃冷藏后，采用分散型固相萃取法净化，由气相色谱-负化学离子源质谱选择离子监测技术进行测定与确证，同位素内标法定量。在1～40μg / L 范围内氟乐灵农药的线性关系良好；方法定量限（LOQ）为0.02μg / kg；对鳗鱼、烤鳗、梭子蟹、小龙虾、猪油和橄榄油等6种复杂基质进行1.0、2.0和3.0μg / kg 等3个水平的添加回收试验，平均回收率均处于80％～100％之间，RSD≤10.3％；无干扰现象出现。该方法可作为水产品及食用油中氟乐灵残留检测的确证方法。
基金Supported by United States Public Health Service,Nos.DK067287,CA162147 and CA206010the A.Alfred Taubman Medical Research Institute of the University of Michigan
文摘Microsatellite alterations within genomic DNA frameshift as a result of defective DNA mismatch repair(MMR). About 15% of sporadic colorectal cancers(CRCs) manifest hypermethylation of the DNA MMR gene MLH1, resulting in mono-and di-nucleotide frameshifts to classify it as microsatellite instability-high(MSI-H) and hypermutated, and due to frameshifts at coding microsatellites generating neo-antigens, produce a robust protective immune response that can be enhanced with immune checkpoint blockade. More commonly, approximately 50% of sporadic nonMSI-H CRCs demonstrate frameshifts at di-and tetra-nucleotide microsatellites to classify it as MSIlow/elevated microsatellite alterations at selected tetranucleotide repeats(EMAST) as a result of functional somatic inactivation of the DNA MMR protein MSH3 via a nuclear-to-cytosolic displacement. The trigger for MSH3 displacement appears to be inflammation and/or oxidative stress, and unlike MSI-H CRC patients, patients with MSI-L/EMAST CRCs show poor prognosis. These inflammatory-associated microsatellite alterations are a consequence of the local tumor microenvironment, and in theory, if the microenvironment is manipulated to lower inflammation, the microsatellite alterations and MSH3 dysfunction should be corrected. Here we describe the mechanisms and significance of inflammatory-associated microsatellite alterations, and propose three areas to deeply explore the consequences and prevention of inflammation's effect upon the DNA MMR system.
文摘Using a special coated sand as the material of the selected laser sintering (SLS), the authors test and investigate the strength change of the test samples in terms of different sintering parameters (scanning speed, laser power, sintering thickness, and so on). The characteristics of coated sand hardening by laser beam are analyzed. The sintered mold (or core) for given casting is poured with molten metal.
文摘We reported data on thermal preference, thermal tolerance and the thermal dependence of digestive performance for two Phrynocephalus lizards （P. frontalis and P. versicolor）, and compared data among lizards so far studied worldwide. Mean values for selected body temperature （Tsel） and critical thermal maximum （CTMax） were greater in P versicolor, whereas mean values for critical thermal minimum （CTMin） did not differ between the two species. The two lizards differed in food intake, but not in food passage time, apparent digestive coefficient （ADC） and assimilation efficiency （AE）, across the experimental tem- peratures. Four general conclusions can be drawn from published data. Firstly, thermal preference and thermal tolerance differ among lizards differing in distribution, temporal activity pattern and habitat use. Lizards in thermally more variable regions are better able to tolerate low and high temperatures. Diurnal lizards generally select higher body temperatures than nocturnal lizards, and lizards using habitats with direct sun exposure generally selected higher body temperatures and are better able to tolerate high temperatures. Secondly, CTMax is positively correlated with Tsel. Lizards more likely exposed to extremely high temperatures while active select higher body temperatures than those using shaded habitats. Thirdly, the effects of body temperature on food intake, food passage time, ADC and AE differ among lizards, but it seems to be common among lizards that ADC and AE are less thermally sensitive than food intake and food passage time. Lastly, ADC is dependent on the type of food ingested, with insectivorous lizards digesting food more efficiently than herbivorous lizards
基金supported by the National Natural Science Foundation of China (Grant No. 30600352)the "Top-notch Personnel" Project of Ji-angsu University, the National Basic Research Program of China (Grant No. 2006CB504200)the Open Research Fund Program of the State Key Laboratory of Virology of China (Grant No. 2009008)
文摘HIV-1 co-receptor tropism is central for understanding the transmission and pathogenesis of HIV-1 infection. We performed a genome-wide comparison between the adaptive evolution of R5 and X4 variants from HIV-1 subtypes B and C. The results showed that R5 and X4 variants experienced differential evolutionary patterns and different HIV-1 genes encountered various positive selection pressures, suggesting that complex selection pressures are driving HIV-1 evolution. Compared with other hypervariable regions of Gp120, significantly more positively selected sites were detected in the V3 region of subtype B X4 variants, V2 region of subtype B R5 variants, and V1 and V4 regions of subtype C X4 variants, indicating an association of positive selection with co-receptor recognition/binding. Intriguingly, a significantly higher proportion (33.3% and 55.6%, P【0.05) of positively selected sites were identified in the C3 region than other conserved regions of Gp120 in all the analyzed HIV-1 variants, indicating that the C3 region might be more important to HIV-1 adaptation than previously thought. Approximately half of the positively selected sites identified in the env gene were identical between R5 and X4 variants. There were three common positively selected sites (96, 113 and 281) identified in Gp41 of all X4 and R5 variants from subtypes B and C. These sites might not only suggest a functional importance in viral survival and adaptation, but also imply a potential cross-immunogenicity between HIV-1 R5 and X4 variants, which has important implications for AIDS vaccine development.
文摘Effects of multiple strengthening treatments （i.e. ag mechanical properties and stability of nanoscale prec in this research. Various tests such as hardness, tensi ng either at three or four consecutive temperatures） on pitated phases in an AA2090 alloy have been evaluated e, electrical resistance, differential scanning calorimetric （DSC）, and transmission electron microscopy （TEM） have been performed. The results show that the ultimate tensile strength （UTS） and the yield strength of the samples aged at four consecutive temperatures （i.e. natural aging＋190℃＋150℃＋100℃） can be increased approximately to 660 and 610 MPa, respectively. It is also found that precipitation of T1 phase occurs during multiple aging process of the alloy and the higher amounts of enthalpies shown in DSC charts are linked to higher volume fraction of this precipitate. Furthermore, TEM observations reveal that T1 phase has plate shape morphology and its crystal structure is in the form of hcp with lattice parameters of a=0.467 nm and c=0.878 nm.
