| 1. |
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| 2. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Dalton, April S., et al.
(author)
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Deglaciation of the north American ice sheet complex in calendar years based on a comprehensive database of chronological data: NADI-1
- 2023
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In: QUATERNARY SCIENCE REVIEWS. - 0277-3791 .- 1873-457X. ; 321
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Journal article (peer-reviewed)abstract
- The most recent deglaciation of the North American Ice Sheet Complex (NAISC: comprising the Innuitian, Cordilleran, and Laurentide ice sheets) offers a broad perspective from which to analyze the timing and rate of ice retreat, deglacial sea-level rise, and abrupt climate change events. Previous efforts to portray the retreat of the NAISC have been focused largely on minimum-limiting radiocarbon ages and ice margin location(s) tied to deglacial landforms that were not, for the most part, chronologically constrained. Here, we present the first version of North American Deglaciation Isochrones (NADI-1) spanning 25 to 1 ka in calendar years before present. Key new features of this work are (i) the incorporation of cosmogenic nuclide data, which offer a direct constraint on the timing of ice recession; (ii) presentation of all data and time-steps in calendar years; (iii) optimal, minimum, and maximum ice extents for each time-step that are designed to capture uncertainties in the ice margin position, and; (iv) extensive documentation and justification for the placement of each ice margin. Our data compilation includes 2229 measurements of Be-10, 459 measurements of Al-26 and 35 measurements of Cl-36 from a variety of settings, including boulders, bedrock surfaces, cobbles, pebbles, and sediments. We also updated a previous radiocarbon dataset (n = 4947), assembled luminescence ages (n = 397) and gathered uranium-series data (n = 2). After scrutiny of the geochronological dataset, we consider >90% of data to be reliable or likely reliable. Key findings include (i) a highly asynchronous maximum glacial extent in North America, occurring as early as 27 ka to as late as 17 ka, within and between ice sheets. In most marine realms, extension of the ice margin to the continental shelf break at 25 ka is somewhat speculative because it is based on undated and spatially scattered ice stream and geomorphic evidence; (ii) detachment of the Laurentide and Cordilleran ice sheets took place gradually via southerly and northerly 'unzipping' of the ice masses, starting at 17.5 ka and ending around 14 ka; (iii) the final deglaciation of Hudson Bay began at 8.5 ka, with the collapse completed by 8 ka. The maximum extent of ice during the last glaciation occurred at 22 ka and covered 15,470,000 km(2). All North American ice sheets merged at 22 ka for the first time in the Quaternary. The highly asynchronous Last Glacial Maximum in North America means that our isochrones (starting at 25 ka) capture ice advance across some areas, which is based on limited evidence and is therefore somewhat speculative. In the Supplementary Data, the complete NADI-1 chronology is available in PDF, GIF and shapefile format, together with additional visualizations and spreadsheets of geochronological data. The NADI-1 shapefiles are also available at https://doi.org/10.5281/zenodo.8161764.
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| 4. |
- Dalton, April S., et al.
(author)
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The marine δ18O record overestimates continental ice volume during Marine Isotope Stage 3
- 2022
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In: Global and Planetary Change. - Amsterdam : Elsevier. - 0921-8181 .- 1872-6364. ; 212, s. 103814-103814
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Journal article (peer-reviewed)abstract
- There is disagreement in the Quaternary research community in how much of the marine δ18O signal is driven by change in ice volume. Here, we examine this topic by bringing together empirical and modelling work for Marine Isotope Stage 3 (MIS 3; 57 ka to 29 ka), a time when the marine δ18O record indicates moderate continental glaciation and a global mean sea level between −60 m and −90 m. We compile and interpret geological data dating to MIS 3 to constrain the extent of major Northern Hemisphere ice sheets (Eurasian, Laurentide, Cordilleran). Many key data, especially published in the past ~15 years, argue for an ice-free core of the formerly glaciated regions that is inconsistent with inferences from the marine δ18O record. We compile results from prior studies of glacial isostatic adjustment to show the volume of ice inferred from the marine δ18O record is unable to fit within the plausible footprint of Northern Hemisphere ice sheets during MIS 3. Instead, a global mean sea level between −30 m and − 50 m is inferred from geological constraints and glacial isostatic modelling. Furthermore, limited North American ice volumes during MIS 3 are consistent with most sea-level bounds through that interval. We can find no concrete evidence of large-scale glaciation during MIS 3 that could account for the missing ~30 m of sea-level equivalent during that time, which suggests that changes in the marine δ18O record are driven by other variables, including water temperature. This work urges caution regarding the reliance of the marine δ18O record as a de facto indicator of continental ice when few geological constraints are available, which underpins many Quaternary studies.
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| 5. |
- Margold, Martin, et al.
(author)
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Retreat pattern of the Cordilleran Ice Sheet in central British Columbia at the end of the last glaciation reconstructed from glacial meltwater landforms
- 2013
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In: Boreas. - : Wiley. - 0300-9483 .- 1502-3885. ; 42:4, s. 830-847
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Journal article (peer-reviewed)abstract
- The Cordilleran Ice Sheet (CIS) covered much of the mountainous northwestern part of North America at least several times during the Pleistocene. The pattern and timing of its growth and decay are, however, poorly understood. Here, we present a reconstruction of the pattern of ice-sheet retreat in central British Columbia at the end of the last glaciation based on a palaeoglaciological interpretation of ice-marginal meltwater channels, eskers and deltas mapped from satellite imagery and digital elevation models. A consistent spatial pattern of high-elevation (1600-2400m a.s.l.), ice-marginal meltwater channels is evident across central British Columbia. These landforms indicate the presence of ice domes over the Skeena Mountains and the central Coast Mountains early during deglaciation. Ice sourced in the Coast Mountains remained dominant over the southern and east-central parts of the Interior Plateau during deglaciation. Our reconstruction shows a successive westward retreat of the ice margin from the western foot of the Rocky Mountains, accompanied by the formation and rapid evolution of a glacial lake in the upper Fraser River basin. The final stage of deglaciation is characterized by the frontal retreat of ice lobes through the valleys of the Skeena and Omineca Mountains and by the formation of large esker systems in the most prominent topographic lows of the Interior Plateau. We conclude that the CIS underwent a large-scale reconfiguration early during deglaciation and was subsequently diminished by thinning and complex frontal retreat towards the Coast Mountains.
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| 6. |
- Margold, Martin, et al.
(author)
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Timing of terminal Pleistocene deglaciation at high elevations in southern and central British Columbia constrained by Be-10 exposure dating
- 2014
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In: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 99, s. 193-202
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Journal article (peer-reviewed)abstract
- The Cordilleran Ice Sheet (CIS) covered most of British Columbia and southern Yukon Territory at the local Last Glacial Maximum (ILGM) during Marine Oxygen Isotope Stage 2. However, its subsequent demise is not well understood, particularly at high elevations east of its ocean-terminating margin. We present Be-10 exposure ages from two high-elevation sites in southern and central British Columbia that help constrain the time of initial deglaciation at these sites. We sampled granodiorite erratics at elevations of 2126-2230 m a.s.l. in the Marble Range and 1608-1785 m a.s.l. in the Telkwa Range at the western margin of the Interior Plateau. The erratics at both sites are near ice-marginal meltwater channels that delineate the local ice surface slope and thus the configuration of the ice sheet during deglaciation. The locations of the erratics and their relations to meltwater channels ensure that the resulting Be-10 ages date CIS deglaciation and not the retreat of local montane glaciers. Our sample sites emerged above the surface of the CIS as its divide migrated westward from the Interior Plateau to the axis of the Coast Mountains. Two of the four samples from the summit area of the Marble Range yielded apparent exposure ages of 14.0 +/- 0.7 and 15.2 +/- 0.8 ka. These ages are 1.8-3.0 ka younger than the well-established ILGM age of ca 17 ka for the Puget lobe of the CIS in Washington State; they are 1.7 ka younger than the ILGM age for the Puget lobe if a snow-shielding correction to their uncertainty-weighted mean age is applied. The other two samples yielded much older apparent exposure ages (20.6 +/- 1.4 and 33.0 +/- 1.5 ka), indicating the presence of inherited isotopes. Four samples collected from the summit area of the Telkwa Range in the Hazelton Mountains yielded well clustered apparent exposure ages of 10.1 +/- 0.6, 10.2 +/- 0.7, 10.4 +/- 0.5, and 11.5 +/- 1.1 ka. Significant present-day snow cover introduces a large uncertainty in the apparent exposure ages from this site. A snow-shielding correction based on present-day snow cover data increases the uncertainty-weighted mean exposure age of the Telkwa Range erratics to 12.4 +/- 0.7 ka, consistent with deglacial C-14 ages from areas near sea level to the west. Our exposure ages show a thinning of the southern portion of the CIS shortly after the ILGM and persistence of a remnant mountain ice cap in the central Coast Mountains into the Younger Dryas Chronozone. Our data also show that the summit area of the Marble Range was ice-covered during the ILGM. The presence of an ice body of considerable dimension in north-central British Columbia until, or possibly even after, the Younger Dryas highlights the need for geomorphological and geochronological studies of the ice dispersal centre over the Skeena Mountains in northwest British Columbia and the need for better understanding of the response of the CIS to Lateglacial climate fluctuations.
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| 7. |
- Nhu, Viet-Ha, et al.
(author)
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Landslide Susceptibility Mapping Using Machine Learning Algorithms and Remote Sensing Data in a Tropical Environment
- 2020
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In: International Journal of Environmental Research and Public Health. - Switzerland : MDPI. - 1661-7827 .- 1660-4601. ; 17:14
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Journal article (peer-reviewed)abstract
- We used AdaBoost (AB), alternating decision tree (ADTree), and their combination as an ensemble model (AB-ADTree) to spatially predict landslides in the Cameron Highlands, Malaysia. The models were trained with a database of 152 landslides compiled using Synthetic Aperture Radar Interferometry, Google Earth images, and field surveys, and 17 conditioning factors (slope, aspect, elevation, distance to road, distance to river, proximity to fault, road density, river density, normalized difference vegetation index, rainfall, land cover, lithology, soil types, curvature, profile curvature, stream power index, and topographic wetness index). We carried out the validation process using the area under the receiver operating characteristic curve (AUC) and several parametric and non-parametric performance metrics, including positive predictive value, negative predictive value, sensitivity, specificity, accuracy, root mean square error, and the Friedman and Wilcoxon sign rank tests. The AB model (AUC = 0.96) performed better than the ensemble AB-ADTree model (AUC = 0.94) and successfully outperformed the ADTree model (AUC = 0.59) in predicting landslide susceptibility. Our findings provide insights into the development of more efficient and accurate landslide predictive models that can be used by decision makers and land-use managers to mitigate landslide hazards.
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| 8. |
- Nhu, Viet-Ha, et al.
(author)
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Shallow Landslide Susceptibility Mapping : A Comparison between Logistic Model Tree, Logistic Regression, Naïve Bayes Tree, Artificial Neural Network, and Support Vector Machine Algorithms
- 2020
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In: International Journal of Environmental Research and Public Health. - Switzerland : MDPI. - 1661-7827 .- 1660-4601. ; 17:8, s. 1-30
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Journal article (peer-reviewed)abstract
- Shallow landslides damage buildings and other infrastructure, disrupt agriculture practices, and can cause social upheaval and loss of life. As a result, many scientists study the phenomenon, and some of them have focused on producing landslide susceptibility maps that can be used by land-use managers to reduce injury and damage. This paper contributes to this effort by comparing the power and effectiveness of five machine learning, benchmark algorithms—Logistic Model Tree, Logistic Regression, Naïve Bayes Tree, Artificial Neural Network, and Support Vector Machine—in creating a reliable shallow landslide susceptibility map for Bijar City in Kurdistan province, Iran. Twenty conditioning factors were applied to 111 shallow landslides and tested using the One-R attribute evaluation (ORAE) technique for modeling and validation processes. The performance of the models was assessed by statistical-based indexes including sensitivity, specificity, accuracy, mean absolute error (MAE), root mean square error (RMSE), and area under the receiver operatic characteristic curve (AUC). Results indicate that all the five machine learning models performed well for shallow landslide susceptibility assessment, but the Logistic Model Tree model (AUC = 0.932) had the highest goodness-of-fit and prediction accuracy, followed by the Logistic Regression (AUC = 0.932), Naïve Bayes Tree (AUC = 0.864), ANN (AUC = 0.860), and Support Vector Machine (AUC = 0.834) models. Therefore, we recommend the use of the Logistic Model Tree model in shallow landslide mapping programs in semi-arid regions to help decision makers, planners, land-use managers, and government agencies mitigate the hazard and risk.
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| 9. |
- Salvati, Aryan, et al.
(author)
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Flood susceptibility mapping using support vector regression and hyper-parameter optimization
- 2023
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In: Journal of Flood Risk Management. - : John Wiley and Sons Inc. - 1753-318X. ; 16:4
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Journal article (peer-reviewed)abstract
- Floods are both complex and destructive, and in most parts of the world cause injury, death, loss of agricultural land, and social disruption. Flood susceptibility (FS) maps are used by land-use managers and land owners to identify areas that are at risk from flooding and to plan accordingly. This study uses machine learning ensembles to produce objective and reliable FS maps for the Haraz watershed in northern Iran. Specifically, we test the ability of the support vector regression (SVR), together with linear kernel (LK), base classifier (BC), and hyper-parameter optimization (HPO), to identify flood-prone areas in this watershed. We prepared a map of 201 past floods to predict future floods. Of the 201 flood events, 151 (75%) were used for modeling and 50 (25%) were used for validation. Based on the relevant literature and our field survey of the study area, 10 effective factors were selected and prepared for flood zoning. The results show that three of the 10 factors are most important for predicting flood-sensitive areas, specifically and in order of importance, slope, distance to the river and river. Additionally, the SVR-HPO model, with area under the curve values of 0.986 and 0.951 for the training and testing phases, outperformed the other two tested models.
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| 10. |
- Shahabi, Himan, et al.
(author)
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Flood Detection and Susceptibility Mapping Using Sentinel-1 Remote Sensing Data and a Machine Learning Approach : Hybrid Intelligence of Bagging Ensemble Based on K-Nearest Neighbor Classifier
- 2020
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In: Remote Sensing. - Switzerland : MDPI. - 2072-4292. ; 12:2, s. 1-30
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Journal article (peer-reviewed)abstract
- Mapping flood-prone areas is a key activity in flood disaster management. In this paper, we propose a new flood susceptibility mapping technique. We employ new ensemble models based on bagging as a meta-classifier and K-Nearest Neighbor (KNN) coarse, cosine, cubic, and weighted base classifiers to spatially forecast flooding in the Haraz watershed in northern Iran. We identified flood-prone areas using data from Sentinel-1 sensor. We then selected 10 conditioning factors to spatially predict floods and assess their predictive power using the Relief Attribute Evaluation (RFAE) method. Model validation was performed using two statistical error indices and the area under the curve (AUC). Our results show that the Bagging–Cubic–KNN ensemble model outperformed other ensemble models. It decreased the overfitting and variance problems in the training dataset and enhanced the prediction accuracy of the Cubic–KNN model (AUC=0.660). We therefore recommend that the Bagging–Cubic–KNN model be more widely applied for the sustainable management of flood-prone areas.
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| 11. |
- Sharifipour, Behzad, et al.
(author)
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Rangeland species potential mapping using machine learning algorithms
- 2023
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In: Ecological Engineering. - : Elsevier. - 0925-8574 .- 1872-6992. ; 189
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Journal article (peer-reviewed)abstract
- Documenting habitats of rangeland plant species is required to properly manage rangelands and to understand ecosystem processes. A reliable rangeland species potential map can help managers and policy makers design a sustainable grazing system on rangelands. The aim of this study is to map the plant species in the Qurveh City rangelands, Kurdistan Province, Iran, using state-of-the-art machine learning algorithms, including Support Vector Machine (SVM), Artificial Neural Network (ANN), Naïve Bayes (NB), Bayes Net (BN) and Classification and Regression Tree (CART). A total of 185 rangeland species were used in the study, together with 20 conditioning factors, to build and validate models. The One-R feature section technique and multicollinearity test were used, respectively, to determine the most important factors and correlations between them. Model validation was performed using sensitivity, specificity, accuracy, F1-measure, Matthews correlation coefficient (MCC), Kappa, root mean square error (RMSE), and area under the receiver operating characteristic curve (AUC). Results showed that topographic wetness index (TWI), slope angle, elevation, soil phosphorus and soil potassium were the five most important factors to increase the rangeland plants habitat suitability. The Naïve Bayes algorithm (AUC = 0.782) had the highest performance and prediction accuracy and best consistency across the species in the investigated rangeland, followed by the SVM (AUC = 0.763), ANN (AUC = 0.762), CART (AUC = 0.627), and BN (AUC = 0.617) models.
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| 12. |
- Stroeven, Arjen, 1963-, et al.
(author)
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Investigating the glacial history of the northern sector of the Cordilleran Ice Sheet with cosmogenic 10Be concentrations in quartz
- 2010
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In: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 29:25-26, s. 3630-3643
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Journal article (peer-reviewed)abstract
- Exposure durations of glacial landforms in widely separated areas of central Yukon Territory affected bythe northern sector of the Cordilleran Ice Sheet (CIS) and alpine glaciers have been determined usingcosmogenic 10Be in quartz. The aim of our research is to test previous reconstructions of glacial historyand to begin to address the paucity of chronological control for the lateral and vertical extent of thenorthern CIS. Chronological evidence for CIS expansion predating the Last Glacial Maximum comes fromminimum surface exposure durations of c 100 ka for two bedrock samples within the Reid glacial limit,indicating a possible marine Oxygen Isotope Stage (OIS) 6 age for this event, and from minimumexposure durations of about 40 ka for boulders on moraines constructed by alpine glaciers on a nunatakwithin the McConnell glacial limit (OIS 2), indicating a possible OIS 4 age. High elevation minimumsurface exposure durations within the McConnell limit indicate that some areas formerly mapped asnunataks were covered by cold-based ice prior to 30 ka. Montane glaciation in the Mackenzie Mountains,outside the McConnell glacial limit, was contemporaneous with nearby CIS advance at 17 ka, with CISretreat by 15 ka. Deglaciation of the Tintina Trench, a major ice discharge route, was completed by 12 ka.At this time ice in an adjacent discharge route to the south was still entering higher-elevation valleys inthe Pelly Mountains. A Lateglacial readvance may have peaked at ca 10 ka in the Ogilvie Mountains.Considerable variation in ages from individual landforms, and possible complex histories, requireadditional cosmogenic nuclide measurements to confirm interpretations.
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| 13. |
- Stroeven, Arjen P., et al.
(author)
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Investigating absolute chronologies of glacial advances in the NW sector of the Cordilleran Ice Sheet with terrestrial in situ cosmogenic nuclides
- 2014
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In: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 92, s. 429-443
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Journal article (peer-reviewed)abstract
- Geologic mapping in Yukon Territory, Canada, over the past 100 years has revealed a consistent pattern of diminishing Cordilleran Ice Sheet (CIS) extent during successively younger glaciations. Although this pattern is generally accepted, there is still much uncertainty about the number of glaciations, their ages, and the dynamics of the different lobes that constituted the digitate ice sheet margin, their subglacial thermal regimes, and ice thicknesses. We address uncertainties in the timing of glaciation using cosmogenic nuclide exposure dating at key localities that straddle several major lobes of the CIS in west-central Yukon Territory. Differences in exposure duration within what are thought to be the same map units are perhaps due to inheritance (older than expected), but more likely result from postglacial shielding (younger than expected) or surface erosion. Despite a significant spread in exposure durations on moraines and within map units, and tending to rely on longest exposure durations on moraines due to postglacial degradation and shielding, our results indicate that the McConnell glacial advance occurred during Marine Oxygen Isotope Stage (MIS) 2, judging from oldest minimum apparent exposure ages of 15.7 +/- 1.5 and 17.7 +/- 1.6 ka, a Gladstone glacial advance occurred before 51.8 +/- 4.7 ka (MIS 4) and Reid glacial advances before 79.8 +/- 7.3 and 82.8 +/- 7.5 ka (consistent with MIS 6). Traces of even older glacial advances predate 100 ka (107.5 +/- 9.9-154.3 +/- 14.2 ka).
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