共查询到20条相似文献,搜索用时 15 毫秒
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Han JD 《Cell research》2008,18(2):224-237
The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approaches have been employed to study the structure, function and dynamics of molecular networks, and begin to reveal important links of various network properties to the functions of the biological systems. In agreement with these functional links, evolutionary selection of a network is apparently based on the function, rather than directly on the structure of the network. Dynamic modularity is one of the prominent features of molecular networks. Taking advantage of such a feature may simplify network-based biological studies through construction of process-specific modular networks and provide functional and mechanistic insights linking genotypic variations to complex traits or diseases, which is likely to be a key approach in the next wave of understanding complex human diseases. With the development of ready-to-use network analysis and modeling tools the networks approaches will be infused into everyday biological research in the near future. 相似文献
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Yuki Matsumoto Hiromichi Nagayama Hirofumi Nakaoka Atsushi Toyoda Tatsuhiko Goto Tsuyoshi Koide 《Genes, Brain & Behavior》2021,20(3):e12721
Tameness is a major element of animal domestication and involves two components: motivation to approach humans (active tameness) and reluctance to avoid humans (passive tameness). To understand the behavioral and genetic mechanisms of active tameness in mice, we had previously conducted selective breeding for long durations of contact and heading toward human hands in an active tameness test using a wild-derived heterogeneous stock. Although the study showed a significant increase in contacting and heading with the 12th generation of breeding, the effect on other behavioral indices related to tameness and change of gene expression levels underlying selective breeding was unclear. Here, we analyzed nine tameness-related traits at a later stage of selective breeding and analyzed how gene expression levels were changed by the selective breeding. We found that five traits, including contacting and heading, showed behavioral change in the selective groups comparing to the control through the generations. Furthermore, we conducted cluster analyses to evaluate the relationships among the nine traits and found that contacting and heading combined in an independent cluster in the selected groups, but not in the control groups. RNA-Seq of hippocampal tissue revealed differential expression of 136 genes between the selection and control groups, while the pathway analysis identified the networks associated with these genes. These results suggest that active tameness was hidden in the control groups but became apparent in the selected populations by selective breeding, potentially driven by changes in gene expression networks. 相似文献
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Statham MJ Trut LN Sacks BN Kharlamova AV Oskina IN Gulevich RG Johnson JL Temnykh SV Acland GM Kukekova AV 《Biological journal of the Linnean Society. Linnean Society of London》2011,103(1):168-175
The foxes at Novosibirsk, Russia, are the only population of domesticated foxes in the world. These domesticated foxes originated from farm-bred silver foxes (Vulpes vulpes), whose genetic source is unknown. In this study we examined the origin of the domesticated strain of foxes and two other farm-bred fox populations (aggressive and unselected) maintained in Novosibirsk. To identify the phylogenetic origin of these populations we sequenced two regions of mtDNA, cytochrome b and D-loop, from 24 Novosibirsk foxes (8 foxes from each population) and compared them with corresponding sequences of native red foxes from Europe, Asia, Alaska and Western Canada, Eastern Canada, and the Western Mountains of the USA. We identified seven cytochrome b - D-loop haplotypes in Novosibirsk populations, four of which were previously observed in Eastern North America. The three remaining haplotypes differed by one or two base change from the most common haplotype in Eastern Canada. Φ(ST) analysis showed significant differentiation between Novosibirsk populations and red fox populations from all geographic regions except Eastern Canada. No haplotypes of Eurasian origin were identified in the Novosibirsk populations. These results are consistent with historical records indicating that the original breeding stock of farm-bred foxes originated from Prince Edward Island, Canada. Mitochondrial DNA data together with historical records indicate two stages in the selection of domesticated foxes: the first includes captive breeding for ~50 years with unconscious selection for behaviour; the second corresponds to over 50 further years of intensive selection for tame behaviour. 相似文献
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Early animal domestication may have been driven by selection on tameness. Selection on only tameness can bring about correlated selection responses in other traits, not intentionally selected upon, which may be one cause of the domesticated phenotype. We predicted that genetically reduced fear towards humans in Red Junglefowl, ancestors of domesticated chickens, would be correlated to other traits included in the domesticated phenotype. Fear level was determined by a standardised behaviour test, where the reaction towards an approaching human was recorded. We first selected birds for eight generations for either high or low fear levels in this test, to create two divergent selection lines. An F3 intercross, with birds from the eighth generation as parentals, was generated to study correlations between fear-of-human scores and other unselected phenotypes, possibly caused by pleiotropy or linkage. Low fear-of-human scores were associated with higher body weight and growth rates, and with increased activity in an open field test, indicating less general fearfulness. In females, low fear-of-human scores were also associated with more efficient fear habituation and in males with an increased tendency to emit food calls in a mirror test, indicating increased social dominance. Low fear-of-human scores were also associated with smaller brain relative to body weight, and with larger cerebrum relative to total brain weight in females. All these effects are in line with the changes observed in domesticated chickens compared to their ancestors, and we conclude that tameness may have been a driving factor underlying some aspects of the domesticated phenotype. 相似文献
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Pâmela Friedemann;Marina Corrêa Côrtes;Everaldo Rodrigo de Castro;Mauro Galetti;Pedro Jordano;Paulo R. Guimarães Jr; 《Oikos》2022,2022(2)
How species interactions change in space and time is a major question in ecology. In tropical forests, plant individuals share mutualistic partners (pollinators or seed dispersers), yet we have little understanding of the factors affecting these individual interaction patterns. We used a seed dispersal individual-based network describing interactions between individuals of a palm species and bird species to investigate how intrinsic and extrinsic characteristics of individual plants influence the network structure. We evaluated if average canopy height, number of fruits, distance to forest gap and habitat type influence the role of palm individuals in the network. From 102 palms, 62 individuals had their seeds dispersed at least once: 17 individual palms in the restinga, 15 in the lowland and 30 in the pre-montane habitat. Twelve bird species were recorded dispersing Euterpe edulis seeds. No palm characteristics influenced interaction patterns in the network, characterized by the level of centrality of each palm. At the network level, modularity with qualitative data was reproduced by the null models which consider the variation in the number and distribution across interactions. Three of the seven identified modules were associated with a particular habitat. Indeed, habitat type explained 50% of network modularity. Habitat association with modularity was driven by differences in species composition across habitats. Palm individuals did not differ greatly in central positions, indicating that bird species are not selecting palm individuals by their characteristics. When using the weighted network, modularity level was higher than expected by the number of interactions, and frequency of interactions was positively correlated with canopy height. Our results suggest that the organization of this individual-based network is mostly driven by habitat type. We hypothesize that extrinsic characteristics, such as habitat type, may affect the network organization of populations of sessile organisms with potentially unanticipated consequences to ecological and evolutionary dynamics. 相似文献
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Paolo Franchini Paolo Colangelo Axel Meyer Carmelo Fruciano 《Ecology and evolution》2016,6(5):1353-1362
The Western European house mouse, Mus musculus domesticus, is well‐known for the high frequency of Robertsonian fusions that have rapidly produced more than 50 karyotipic races, making it an ideal model for studying the mechanisms of chromosomal speciation. The mouse mandible is one of the traits studied most intensively to investigate the effect of Robertsonian fusions on phenotypic variation within and between populations. This complex bone structure has also been widely used to study the level of integration between different morphogenetic units. Here, with the aim of testing the effect of different karyotypic assets on the morphology of the mouse mandible and on its level of modularity, we performed morphometric analyses of mice from a contact area between two highly metacentric races in Central Italy. We found no difference in size, while the mandible shape was found to be different between the two Robertsonian races, even after accounting for the genetic relationships among individuals and geographic proximity. Our results support the existence of two modules that indicate a certain degree of evolutionary independence, but no difference in the strength of modularity between chromosomal races. Moreover, the ascending ramus showed more pronounced interpopulation/race phenotypic differences than the alveolar region, an effect that could be associated to their different polygenic architecture. This study suggests that chromosomal rearrangements play a role in the house mouse phenotypic divergence, and that the two modules of the mouse mandible are differentially affected by environmental factors and genetic makeup. 相似文献
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Growth rate coefficients estimated for channel catfish Ictalurus punctatus , emerald shiners Notropis aherinoides, freshwater drums Aplodinotus grunniens , river carpsuckers Carpiodes arpio and saugers Stizostedion canadense collected in 1996–1998 from nine river sections of the Mssouri and lower Yellowstone rivers at two life-stages (young-of-the-year and age 1+ years)were significantly different among sections. However, they showed no river-wide latitudinal trend except for age 1+ years emerald shiners that did show a weak negative relation between growth and both latitude and length of growing season. The results suggest growth rates of fishes along the Missouri River system are complex and could be of significance in the Management and conservation of fish communities in this altered system. 相似文献
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In this paper, we propose a theoretical framework within which a unified treatment of the key sources of size-at-age variability—size
dependence of growth rate, stochastic growth rate variations and individual-to-individual variability in growth performance—is
possible. We use this framework to develop a general criterion for growth depensation in cohorts, which we define as the increase
of the coefficient of variation of size-at-age, with increasing age. We use this criterion to show that size dependence of
growth rate, acting alone, is depensatory only if the growth rate increases faster than linearly with size (that is, if growth
is faster than exponential), while stochastic growth rate variation is invariably depensatory. Many species exhibit growth
rates that scale less than linearly with size; indeed the commonly used von Bertalanffy model shows growth rates which actually
decrease with size. In such a species, the size dependence of growth rate acts compensatorily, while stochastic growth rate
variability is depensatory. We show that the tension between these two mechanisms leads to quasi-stationary size-at-age variability,
which we can calculate analytically in some special cases and obtain by a simple numerical procedure where analysis is impractical. 相似文献
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1 Phenology and reproduction were studied in three populations of the cleistogamous herb Oxalis acetosella during three growing seasons, in order to see how the balance between chasmogamous (CH) and cleistogamous (CL) reproduction varies with temporal and spatial environmental variation and with plant size. The numbers of CH and CL flower buds, flowers, immature capsules and mature capsules were counted per ramet, ramet sizes were estimated, and mature capsules were collected for seed counts.
2 Both CH and CL flower numbers were positively correlated with ramet size expressed as leaf number, but the correlation was much stronger in the CL phase. CL flower production also varied significantly between years and sites. Thus, CL production in O. acetosella was not independent of resources and climatic variation.
3 When the effects of year and site were taken into account, the probability of an individual flower developing into a mature fruit was not higher in the CL phase than in the CH phase.
4 CL production was affected by fertilization success in the CH phase. Ramets with one or more CH flowers left unfertilized generally produced more CL buds than ramets with all their CH flowers fertilized. The former group also tended to have more seeds per CL capsule.
5 Since reproductive success in the two phases varies in different temporal and spatial patterns, cleistogamy in O. acetosella is considered to be a bet‐hedging strategy optimizing reproductive output in fluctuating environments.
6 The findings of this study are in conflict with the general view on cleistogamy as a fail‐safe mechanism for back‐up seed production, unaffected by variations in resource supply and environmental conditions. 相似文献
2 Both CH and CL flower numbers were positively correlated with ramet size expressed as leaf number, but the correlation was much stronger in the CL phase. CL flower production also varied significantly between years and sites. Thus, CL production in O. acetosella was not independent of resources and climatic variation.
3 When the effects of year and site were taken into account, the probability of an individual flower developing into a mature fruit was not higher in the CL phase than in the CH phase.
4 CL production was affected by fertilization success in the CH phase. Ramets with one or more CH flowers left unfertilized generally produced more CL buds than ramets with all their CH flowers fertilized. The former group also tended to have more seeds per CL capsule.
5 Since reproductive success in the two phases varies in different temporal and spatial patterns, cleistogamy in O. acetosella is considered to be a bet‐hedging strategy optimizing reproductive output in fluctuating environments.
6 The findings of this study are in conflict with the general view on cleistogamy as a fail‐safe mechanism for back‐up seed production, unaffected by variations in resource supply and environmental conditions. 相似文献
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《Chronobiology international》2013,30(4):344-351
As heart-rate variability (HRV) is under evaluation in clinical applications, the authors sought to better define the interdependent impact of age, maximal exercise, and diurnal variation under physiologic conditions. The authors evaluated the diurnal changes in HRV 24-h pre- and post-maximal aerobic exercise testing to exhaustion in young (19–25 yrs, n?=?12) and middle-aged (40–55 yrs, n?=?12) adults. Subjects wore a portable 5-lead electrocardiogram holter for 48?h (24?h prior to and following a maximal aerobic capacity test). Time-, frequency-, time-frequency-, and scale-invariant-domain measures of HRV were computed from RR-interval data analyzed using a 5-min window size and a 2.5-min step size, resulting in a different set of outputs every 2.5?min. Results were averaged (mean?±?SE) over four prespecified time periods during the morning, afternoon, evening, and night on Day 1 and Day 2. Diurnal changes in HRV in young and middle-aged adults were compared using a two-way, repeated-measures analysis of variance (ANOVA). Young adults demonstrated higher HRV compared to middle-aged adults during periods of wakefulness and sleep prior to maximal exercise stress testing (i.e., high-frequency power during Day 1: young adults: morning 1862?±?496?ms2, afternoon 1797?±?384?ms2, evening 1908?±?431?ms2, and night 3202?±?728?ms2; middle-aged adults: morning 341?±?53?ms2, afternoon 405?±?68?ms2, evening 469?±?80?ms2, and night 836?±?136?ms2) (p < .05). Exercise resulted in reductions in HRV such that multiple measures of HRV were not significantly different between age groups during the afternoon and evening periods. All measures of HRV demonstrated between-group differences overnight on Day 2 (p < .05). Young adults are associated with higher baseline HRV during the daytime. Sleep increases variability equally and proportionally to daytime variability. Given the higher baseline awake HRV and equal rise in HRV during sleep, the change in HRV from sleep to morning with exercise is greater in younger subjects. These physiologic results have clinical significance in understanding the pathophysiology of altered variability in ill patients. (Author correspondence: aseely@ohri. ca) 相似文献
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Countergradient variation in growth rate: compensation for length of the growing season among Atlantic silversides from different latitudes 总被引:11,自引:0,他引:11
Summary How do organisms adapt to the differences in temperature and length of the growing season that occur with latitude? Among Atlantic silversides (Menidia menidia) along the east coast of North America, the length of the first growing season declines by a factor of about 2.5 with increasing latitude. Yet body size at the end of the first growing season does not decline. High-latitude fish must, therefore, grow faster within the growing season than do low-latitude fish. This geographical pattern has a genetic basis. Laboratory experiments on fish from six different locations revealed a latitudinal gradient in the capacity for growth (i.e., maximum growth potential). In two subsequent experiments using fish from Nova Scotia (NS), New York (NY) and South Carolina (SC) that had been separately reared in a common environment for several generations, differences in growth rate among populations were highly significant. The rank order was NS>NY>SC, but the difference among populations depended on temperature. High-latitude fish outperformed those from low latitudes primarily at the high temperatures that low-latitude fish would be expected to experience most often in nature. These results suggest that instead of being adapted for growth at low temperatures, fish from high latitudes are adapted for rapid elevation of growth rate during the brief interval of the year when high temperatures occur. Selection on growth rate results from sizedependent winter mortality: the importance to winter survival of being large increases with latitude but the length of the growing season simultaneously decreases. The end result is countergradient variation in growth rate, a phenomenon that may be much more widespread than currently recognized. 相似文献
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Cecilia Díaz-Castelazo Ingrid R. Sánchez-Galván Paulo R. Guimar?es Jr Rafael L. Galdini Raimundo Víctor Rico-Gray 《Annals of botany》2013,111(6):1285-1293
Background and Aims
Functional groups of species interact and coevolve in space and time, forming complex networks of interacting species. A long-term study of temporal variation of an ant–plant network is presented with the aims of: (1) depicting its structural changes over a 20-year period; (2) detailing temporal variation in network topology, as revealed by nestedness and modularity analysis and other parameters (i.e. connectance, niche overlap); and (3) identifying long-term turnover in taxonomic structure (i.e. switches in ant resource use or plant visitor assemblages according to taxa).Methods
Fieldwork was carried out at La Mancha, Mexico, and ant–plant interactions were observed between 1989 and 1991, between 1998 and 2000, and between May 2010 and 2011. Occurrences of ants on extrafloral nectaries (EFNs) were recorded. The resulting ant–plant networks were constructed from qualitative presence–absence data determined by a species–species matrix defined by the frequency of occurrence of each pairwise ant–plant interaction.Key Results
Network variation across time was stable and a persistent nested structure may have contributed to the maintenance of resilient and species-rich communities. Modularity was lower than expected, especially in the most recent networks, indicating that the community exhibited high overlap among interacting species (e.g. few species were hubs in the more recent network, being partly responsible for the nested pattern). Structurally, the connections created among modules by super-generalists gave cohesion to subsets of species that otherwise would remain unconnected. This may have allowed an increasing cascade-effect of evolutionary events among modules. Mutualistic ant–plant interactions were structured 20 years ago mainly by the subdominant nectarivorous ant species Camponotus planatus and Crematogaster brevispinosa, which monopolized the best extrafloral nectar resources and out-competed other species with broader feeding habits. Through time, these ants, which are still present, lost their position as network hubs and diminished in their importance in structuring the network; simultaneously, plants gained in importance.Conclusions
The long-term network analysis reveals a decrease in attended plant species richness, a notable increase in plant species participation from 1990 to 2010 (sustained by less plant taxonomic similarity in the older 1990 network), an increase in the number of ant species and a diminishing dominance of super-generalist ants. The structure of the community has remained highly nested and connected with low modularity, suggesting overall a more participative, homogeneous, cohesive interaction network. Although previous studies have suggested that interactions between ants and EFN-bearing plants are susceptible to seasonality, abiotic factors and perturbation, this cohesive structure appears to be the key for biodiversity and community maintenance. 相似文献16.
- Traits that are significant to the thermal ecology of temperate or montane species are expected to prominently co-vary with the thermal environment experienced by an organism. The Himalayan Pieris canidia butterfly exhibits considerable variation in wing melanisation. We investigated: (i) whether variation in wing melanisation and (ii) activity period of this montane butterfly was influenced by the seasonally and elevationally changing thermal landscape.
- We discovered that wing melanisation varied across elevation, seasons, sex, and wing surfaces, with the variation strongly structured in space and time: colder seasons and higher elevations produced more melanic individuals. Notably, melanisation did not vary uniformly across all wing surfaces: (i) melanisation of the ventral hindwing co-varied much more prominently with elevation, but (ii) melanisation on all other surfaces varied with seasonal changes in the thermal environment.
- Observed wing surface-specific patterns indicated thermoregulatory function for this variation in melanisation. Such wing surface-specific responses to seasonal and elevational variation in temperature have rarely been reported in montane insects.
- Moreover, daily and seasonal thermal cycles were found to strongly influence activity periods of this species, suggesting the potential limits to wing melanisation plasticity.
- Overall, these results showed that the seasonal and elevational gradients in temperature influence the thermal phenotype as well as activity periods of this Himalayan butterfly. It will be critical to study the phenotypic evolution of such montane insects in response to the ongoing climate change, which is already showing significant signs in this iconic mountain range.
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William E. Cooper Jr R. Alexander Pyron Theodore Garland Jr 《Proceedings. Biological sciences / The Royal Society》2014,281(1777)
One of Darwin''s most widely known conjectures is that prey are tame on remote islands, where mammalian predators are absent. Many species appear to permit close approach on such islands, but no comparative studies have demonstrated reduced wariness quantified as flight initiation distance (FID; i.e. predator–prey distance when the prey begins to flee) in comparison with mainland relatives. We used the phylogenetic comparative method to assess influence of distance from the mainland and island area on FID of 66 lizard species. Because body size and predator approach speed affect predation risk, we included these as independent variables. Multiple regression showed that FID decreases as distance from mainland increases and is shorter in island than mainland populations. Although FID increased as area increased in some models, collinearity made it difficult to separate effects of area from distance and island occupancy. FID increases as SVL increases and approach speed increases; these effects are statistically independent of effects of distance to mainland and island occupancy. Ordinary least-squares models fit the data better than phylogenetic regressions, indicating little or no phylogenetic signal in residual FID after accounting for the independent variables. Our results demonstrate that island tameness is a real phenomenon in lizards. 相似文献
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对9种冷季型草在春夏季干旱条件下的光合、蒸腾等生理特性进行测定.结果表明:春季冷季型草净光合速率在6:00较低,8:00~12:00后出现最大值后逐渐下降,呈曲线变化.不同种类的日平均净光合速率,以虉草和看麦娘最高,达11μmol?m-2?s-1,匍匐剪股颖不到5μmol?m-2?s-1,其它草种居中,为6~10μmol?m-2?s-1.夏季测定时,大部分冷季型草在6:00净光合速率为全天最大值,8:00后光合速率下降,至16:00光合速率最低,几乎呈直线下降的变化.不同种类的日平均净光合速率,紫羊茅最高,为16.5μmol?m-2?s-1,鸭茅和虉草仅6~7μmol?m-2?s-1,其它草种居中.春季蒸腾速率早晨6:00~8:00最低,随后逐步升高至最高峰后又逐渐回落.不同种类的日平均蒸腾速率,看麦娘、高羊茅、虉草、草地早熟禾较高,为2 mmol?m-2?s-1左右,最低为匍匐剪股颖0.8 mmol?m-2?s-1,其它草种为1.3~1.8 mmol?m-2?s-1.夏季大部分植物在6:00蒸腾速率较高,至8:00开始回落,10:00后上升,到最高点后回降,呈多峰变化的曲线.不同种类的日平均蒸腾速率,紫羊茅最高为3.5 mmol?m-2?s-1,最低为无芒雀麦、鸭茅、虉草,为1.4~1.7 mmol?m-2?s-1,其它草种为2.1~2.8 mmol?m-2?s-1. 相似文献
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Kuhner MK 《Molecular biology and evolution》2006,23(12):2355-2360
Data from HIV and from human neoplastic cells can show substantial between-lineage mutation rate variation even within a single population. Such variation may affect estimators of population quantities such as Theta = 4N(e)mu. Using simulated DNA data, I measured the effect of rate variation on recovery of Theta by the summary-statistic estimator of Watterson (Watterson GA. 1975. On the number of segregating sites in genetical systems without recombination. Theor Popul Biol. 7:256-276) and the coalescent maximum likelihood algorithm LAMARC (Kuhner MK. 2006. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics. Advance Access doi: 10.1093/bioinformatics/btk051). Watterson's estimator showed a downward bias, as expected, with high values of Theta. LAMARC's mean estimate was accurate for all tested values of Theta and rate variation except for a downward bias when rate variation was maximal (i.e., the slow rate was zero). LAMARC had consistently narrower confidence intervals (CIs) than Watterson's estimator. Both methods tended to reject the truth too often when rate variation was 8x or greater and independent among branches, as well as when variation was 4x or greater and correlated among branches. In the case of Watterson's estimate, this excess rejection was fully attributable to variation among genealogies in the amount of total branch length associated with the fast and slow rates. However, in the case of LAMARC, some excess rejection was still observed even when between-genealogy variation was taken into account. Both estimators are robust to modest rate variation; however, their use should be coupled with a statistical test to rule out extreme rate variation as the resulting CIs may not be reliable. 相似文献
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