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  • 1
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in International Journal of Environmental Research and Public Health 15 (2018): 723, doi:10.3390/ijerph15040723.
    Description: There has been a massive increase in recent years of the use of lead (Pb) isotopes in attempts to better understand sources and pathways of Pb in the environment and in man or experimental animals. Unfortunately, there have been many cases where the quality of the isotopic data, especially that obtained by quadrupole inductively coupled plasma mass spectrometry (Q-ICP-MS), are questionable, resulting in questionable identification of potential sources, which, in turn, impacts study interpretation and conclusions. We present several cases where the isotopic data have compromised interpretation because of the use of only the major isotopes 208Pb/206Pb and 207Pb/206Pb, or their graphing in other combinations. We also present some examples comparing high precision data from thermal ionization (TIMS) or multi-collector plasma mass spectrometry (MC-ICP-MS) to illustrate the deficiency in the Q-ICP-MS data. In addition, we present cases where Pb isotopic ratios measured on Q-ICP-MS are virtually impossible for terrestrial samples. We also evaluate the Pb isotopic data for rat studies, which had concluded that Pb isotopic fractionation occurs between different organs and suggest that this notion of biological fractionation of Pb as an explanation for isotopic differences is not valid. Overall, the brief review of these case studies shows that Q-ICP-MS as commonly practiced is not a suitable technique for precise and accurate Pb isotopic analysis in the environment and health fields
    Keywords: Lead isotopes ; ICP-MS ; TIMS ; MC-ICP-MS ; Environment ; Humans ; Rats ; Fractionation
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Remote Sensing 10 (2018): 932, doi:10.3390/rs10060932.
    Description: We assessed the performance of reflectance-based vegetation indices and solar-induced chlorophyll fluorescence (SIF) datasets with various spatial and temporal resolutions in monitoring the Gross Primary Production (GPP)-based phenology in a temperate deciduous forest. The reflectance-based indices include the green chromatic coordinate (GCC), field measured and satellite remotely sensed Normalized Difference Vegetation Index (NDVI); and the SIF datasets include ground-based measurement and satellite-based products. We found that, if negative impacts due to coarse spatial and temporal resolutions are effectively reduced, all these data can serve as good indicators of phenological metrics for spring. However, the autumn phenological metrics derived from all reflectance-based datasets are later than the those derived from ground-based GPP estimates (flux sites). This is because the reflectance-based observations estimate phenology by tracking physiological properties including leaf area index (LAI) and leaf chlorophyll content (Chl), which does not reflect instantaneous changes in phenophase transitions, and thus the estimated fall phenological events may be later than GPP-based phenology. In contrast, we found that SIF has a good potential to track seasonal transition of photosynthetic activities in both spring and fall seasons. The advantage of SIF in estimating the GPP-based phenology lies in its inherent link to photosynthesis activities such that SIF can respond quickly to all factors regulating phenological events. Despite uncertainties in phenological metrics estimated from current spaceborne SIF observations due to their coarse spatial and temporal resolutions, dates in middle spring and autumn—the two most important metrics—can still be reasonably estimated from satellite SIF. Our study reveals that SIF provides a better way to monitor GPP-based phenological metrics.
    Description: This research was supported by U. S. Department of Energy Office of Biological and Environmental Research Grant DE-SC0006951, National Science Foundation Grants DBI 959333 and AGS-1005663, and the University of Chicago and the MBL Lillie Research Innovation Award to Jianwu Tang and China Scholarship Council No. 201506190095 to Z. Liu. Xiaoliang Lu was also supported by the open project grant (LBKF201701) of Key Laboratory of Land Surface Pattern and Simulation, Chinese Academy of Sciences.
    Keywords: Solar-induced chlorophyll fluorescence ; Reflectance ; Phenology ; Fall phenological events
    Repository Name: Woods Hole Open Access Server
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  • 3
    Publication Date: 2022-10-27
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Loranty, Michael M.; Davydov, Sergey P.; Kropp, Heather; Alexander, Heather D.; Mack, Michelle C.; Natali, Susan M.; Zimov, Nikita S. 2018. "Vegetation Indices Do Not Capture Forest Cover Variation in Upland Siberian Larch Forests." Remote Sens. 10, no. 11: 1686, doi:10.3390/rs10111686.
    Description: Boreal forests are changing in response to climate, with potentially important feedbacks to regional and global climate through altered carbon cycle and albedo dynamics. These feedback processes will be affected by vegetation changes, and feedback strengths will largely rely on the spatial extent and timing of vegetation change. Satellite remote sensing is widely used to monitor vegetation dynamics, and vegetation indices (VIs) are frequently used to characterize spatial and temporal trends in vegetation productivity. In this study we combine field observations of larch forest cover across a 25 km2 upland landscape in northeastern Siberia with high-resolution satellite observations to determine how the Normalized Difference Vegetation Index (NDVI) and the Enhanced Vegetation Index (EVI) are related to forest cover. Across 46 forest stands ranging from 0% to 90% larch canopy cover, we find either no change, or declines in NDVI and EVI derived from PlanetScope CubeSat and Landsat data with increasing forest cover. In conjunction with field observations of NDVI, these results indicate that understory vegetation likely exerts a strong influence on vegetation indices in these ecosystems. This suggests that positive decadal trends in NDVI in Siberian larch forests may correspond primarily to increases in understory productivity, or even to declines in forest cover. Consequently, positive NDVI trends may be associated with declines in terrestrial carbon storage and increases in albedo, rather than increases in carbon storage and decreases in albedo that are commonly assumed. Moreover, it is also likely that important ecological changes such as large changes in forest density or variable forest regrowth after fire are not captured by long-term NDVI trends.
    Description: We thank numerous undergraduate and graduate research assistants, and Polaris Project participants for field and lab assistance. We thank the staff and scientists at the Northeast Science Station for logistical and field support. Lastly, we thank the editors and six anonymous reviewers whose comments helped to improve this paper.
    Keywords: Boreal forest ; NDVI ; Phenology ; Greening ; Arctic ; Siberia ; Larch ; CubeSat
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Remote Sensing 6 (2014): 4660-4686, doi:10.3390/rs6064660.
    Description: Vegetation phenology plays an important role in regulating processes of terrestrial ecosystems. Dynamic ecosystem models (DEMs) require representation of phenology to simulate the exchange of matter and energy between the land and atmosphere. Location-specific parameterization with phenological observations can potentially improve the performance of phenological models embedded in DEMs. As ground-based phenological observations are limited, phenology derived from remote sensing can be used as an alternative to parameterize phenological models. It is important to evaluate to what extent remotely sensed phenological metrics are capturing the phenology observed on the ground. We evaluated six methods based on two vegetation indices (VIs) (i.e., Normalized Difference Vegetation Index and Enhanced Vegetation Index) for retrieving the phenology of temperate forest in the Agro-IBIS model. First, we compared the remotely sensed phenological metrics with observations at Harvard Forest and found that most of the methods have large biases regardless of the VI used. Only two methods for the leaf onset and one method for the leaf offset showed a moderate performance. When remotely sensed phenological metrics were used to parameterize phenological models, the bias is maintained, and errors propagate to predictions of gross primary productivity and net ecosystem production. Our results show that Agro-IBIS has different sensitivities to leaf onset and offset in terms of carbon assimilation, suggesting it might be better to examine the respective impact of leaf onset and offset rather than the overall impact of the growing season length.
    Keywords: Phenology ; Remote sensing ; Dynamic ecosystem model ; Agro-IBIS ; MODIS
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 27 (1988), S. 311-320 
    ISSN: 1432-1432
    Keywords: Genome composition ; Coding sequences ; Isochores ; Humans ; Murids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The compositional distributions of coding sequences and DNA molecules (in the 50-100-kb range) are remarkably narrower in murids (rat and mouse) compared to humans (as well as to all other mammals explored so far). In murids, both distributions begin at higher and end at lower GC values. A comparison of homologous coding sequences from murids and humans revealed that their different compositional distributions are due to differences in GC levels in all three codon positions, particularly of genes located at both ends of the distribution. In turn, these differences are responsible for differences in both codon usage and amino acids. When GC levels at first+second codon positions and third codon positions, respectively, of murid genes are plotted against corresponding GC levels of homologous human genes, linear relationships (with very high correlation coefficients and slopes of about 0.78 and 0.60, respectively) are found. This indicates a conservation of the order of GC levels in homologous genes from humans and murids. (The same comparison for mouse and rat genes indicates a conservation of GC levels of homologous genes.) A similar linear relationship was observed when plotting GC levels of corresponding DNA fractions (as obtained by density gradient centrifugation in the presence of a sequence-specific ligand) from mouse and human. These findings indicate that orderly compositional changes affecting not only coding sequences but also noncoding sequences took place since the divergence of murids. Such directional fixations of mutations point to the existence of selective pressures affecting the genome as a whole.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 35 (1992), S. 7-16 
    ISSN: 1432-1432
    Keywords: Alu source genes ; Humans ; Gorillas ; Retrotransposition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A member of the young PV Alu sub-family is detected in chimpanzee DNA showing that the PV subfamily is not specific to human DNA. This particular Alu is absent from the orthologous loci in both human and gorilla DNAs, indicating that PV subfamily members transposed within the chimpanzee lineage following the divergence of chimpanzee from both gorilla and human. These findings and previous reports describing the transpositional activity of other Alu sequences within the human, gorilla, and chimpanzee lineages provide phylogenetic evidence for the existence of multiple Alu source genes. Sequences surrounding this particular Alu resemble known transcriptional control elements associated with RNA polymerase III, suggesting a mechanism by which cis-acting elements might be acquired upon retrotransposition.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 33 (1991), S. 442-449 
    ISSN: 1432-1432
    Keywords: Humans ; Mouse ; Rat ; Codon usage ; Mutation bias ; Selection
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A new statistical test has been developed to detect selection on silent sites. This test compares the codon usage within a gene and thus does not require knowledge of which genes are under the greatest selection, that there exist common trends in codon usage across genes, or that genes have the same mutation pattern. It also controls for mutational biases that might be introduced by the adjacent bases. The test was applied to 62 mammalian sequences, the significant codon usage biases were detected in all three species examined (humans, rats, and mice). However, these biases appear not to be the consequence of selection, but of the first base pair in the codon influencing the mutation pattern at the third position.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 34 (1992), S. 336-344 
    ISSN: 1432-1432
    Keywords: Humans ; Mitochondrial DNA ; Nuclear polymorphisms ; Heteroplasmy ; Genetic differentiation ; Sickle cell ; Rain forest refuges
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The identification of genetically coherent populations is essential for understanding human evolution. Among the culturally uniform ethnic groups of west Africa, there are two geographically distinct populations with high frequencies of sickle-cell hemoglobin (HbS). Although the HbS mutation in each group is found on distinguishable chromosomes 11, these populations have been assumed to be parts of a single population. Analysis of mitochondrial DNA (mtDNA) in these populations demonstrated that the two populations identified by alternative chromosomes 11 bearing HbS have distinct distributions of mitochondrial genotypes, i.e., they are maternally separate. These studies also showed that, contrary to expectation, the mtDNA of some individuals is heteroplasmic. For nuclear loci, a comparison of the frequency of alternative alleles established that these populations are genetically distinct. Both the mitochondrial and nuclear data indicate that these populations have been separate for approximately 50,000 years. Although HbS in the two populations is usually attributed to recent, independent mutations, the duration of the separation and the observed geographic distribution of the population allow for the possibility of an ancient origin of HbS. Assuming an ancient mutation and considering the known biogeography, we suggest that HbS protected selected populations from malaria in rain forest refuges during the most recent ice age.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Trees 4 (1990), S. 88-98 
    ISSN: 1432-2285
    Keywords: Cambium ; Growth respiration ; Maintenance respiration ; Phenology ; Sapwood
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Woody-tissue respiration was measured on five different dates at three to five locations on each of 12 30-year-old Abies amabilis trees. On any given date, temperature-corrected respiration per unit surface area varied 10 to 40-fold between sampling locations. In stems, the two major components of respiration were growth respiration and sapwood maintenance respiration, which were of roughly equal importance during the growing season. There was no evidence of significant cambial maintenance respiration, suggesting that a stand with high bole surface area would not automatically have high respiration. Respiration in branches was much greater than in boles of comparable volume and growth rates, and was significantly correlated with branch height. Branch respiration may include an another significant component in addition to the two seen in bole respiration, possibly associated with carbohydrate mobilization and transport or with CO2 efflux from the transpiration stream.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1432-2285
    Keywords: Cambial activity ; Frost hardiness ; Phenology ; Salix ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary The ultrastructure of cells in the cambial region of Salix dasyclados Wim. (clone 78056) was studied during the development of winter hardiness and the onset of cambial activity in spring. Plants were grown at relative growth rates (RG) of 8% and 12% respectively, resulting in different nitrogen content in the stems. Frost hardiness of the plants was estimated by standardized freezing tests. Plants with a higher nitrogen status ceased growth later and started re-growth earlier in spring than plants with lower nitrogen content. Differences in ability to withstand low temperatures during autumn and spring were found between plants grown in the two nutrient treatments. During the development of frost hardiness in the autumn, the number of meristematic cells in the cambial region decreased. The cessation of meristematic activity was accompanied by cell wall thickening and ultrastructural changes in the cells. Frost hardiness increased from the ability to survive -6° C in October to survival of -80° C at the beginning of December. From November to February the cambial region comprised a layer of 2–3 thick-walled cells with conspicuous ultrastructural features. Starch accumulated in plastids in September, decreased during November to March and then increased again in accordance with changes of frost hardiness. Onset of cambial activity began between the end of March and the beginning of April, as shown by increased vacuolization of meristematic cells and mitotic activity. By April, the starch content had increased and lipolysis was observed. Frost hardiness had decreased, and plants with low and high nitrogen content were able to survive -15° C and -10° C, respectively. After budburst, all axillary shoot parts were damaged at temperatures below-3° C.
    Type of Medium: Electronic Resource
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