Miracle-dz/UniFAR-FTUs huggingface dataset:
Empirical estimate of the signal content of Holocene temperature proxy records

Abstract. Proxy records from climate archives provide evidence about past climate changes, but the recorded signal is affected by non-climate-related effects as well as time uncertainty. As proxy-based climate reconstructions are frequently used to test climate models and to quantitatively infer past climate, we need to improve our understanding of the proxy record signal content as well as the uncertainties involved. In this study, we empirically estimate signal-to-noise ratios (SNRs) of temperature proxy records used in global compilations of the middle to late Holocene (last 6000 years). This is achieved through a comparison of the correlation of proxy time series from nearby sites of three compilations and model time series extracted at the proxy sites from two transient climate model simulations: a Holocene simulation of the ECHAM5/MPI-OM model and the Holocene part of the TraCE-21ka simulation. In all comparisons, we found the mean correlations of the proxy time series on centennial to millennial timescales to be low (R<0.2), even for nearby sites, which resulted in low SNR estimates. The estimated SNRs depend on the assumed time uncertainty of the proxy records, the timescale analysed, and the model simulation used. Using the spatial correlation structure of the ECHAM5/MPI-OM simulation, the estimated SNRs on centennial timescales ranged from 0.05 – assuming no time uncertainty – to 0.5 for a time uncertainty of 400 years. On millennial timescales, the estimated SNRs were generally higher. Use of the TraCE-21ka correlation structure generally resulted in lower SNR estimates than for ECHAM5/MPI-OM. As the number of available high-resolution proxy records continues to grow, a more detailed analysis of the signal content of specific proxy types should become feasible in the near future. The estimated low signal content of Holocene temperature compilations should caution against over-interpretation of these multi-proxy and multisite syntheses until further studies are able to facilitate a better characterisation of the signal content in paleoclimate records.
Source partitioning of H2O and CO2 fluxes based on high-frequency eddy covariance data: a comparison between study sites

Abstract. For an assessment of the roles of soil and vegetation in the climate system, a further understanding of the flux components of H2O and CO2 (e.g., transpiration, soil respiration) and their interaction with physical conditions and physiological functioning of plants and ecosystems is necessary. To obtain magnitudes of these flux components, we applied source partitioning approaches after Scanlon and Kustas (2010; SK10) and after Thomas et al. (2008; TH08) to high-frequency eddy covariance measurements of 12 study sites covering different ecosystems (croplands, grasslands, and forests) in different climatic regions. Both partitioning methods are based on higher-order statistics of the H2O and CO2 fluctuations, but proceed differently to estimate transpiration, evaporation, net primary production, and soil respiration. We compared and evaluated the partitioning results obtained with SK10 and TH08, including slight modifications of both approaches. Further, we analyzed the interrelations among the performance of the partitioning methods, turbulence characteristics, and site characteristics (such as plant cover type, canopy height, canopy density, and measurement height). We were able to identify characteristics of a data set that are prerequisites for adequate performance of the partitioning methods. SK10 had the tendency to overestimate and TH08 to underestimate soil flux components. For both methods, the partitioning of CO2 fluxes was less robust than for H2O fluxes. Results derived with SK10 showed relatively large dependencies on estimated water use efficiency (WUE) at the leaf level, which is a required input. Measurements of outgoing longwave radiation used for the estimation of foliage temperature (used in WUE) could slightly increase the quality of the partitioning results. A modification of the TH08 approach, by applying a cluster analysis for the conditional sampling of respiration–evaporation events, performed satisfactorily, but did not result in significant advantages compared to the original method versions developed by Thomas et al. (2008). The performance of each partitioning approach was dependent on meteorological conditions, plant development, canopy height, canopy density, and measurement height. Foremost, the performance of SK10 correlated negatively with the ratio between measurement height and canopy height. The performance of TH08 was more dependent on canopy height and leaf area index. In general, all site characteristics that increase dissimilarities between scalars appeared to enhance partitioning performance for SK10 and TH08.
Floodwater impact on Galveston Bay phytoplankton taxonomy, pigment composition and photo-physiological state following Hurricane Harvey from field and ocean color (Sentinel-3A OLCI) observations

Abstract. Phytoplankton taxonomy, pigment composition and photo-physiological state were studied in Galveston Bay (GB), Texas (USA), following the extreme flooding associated with Hurricane Harvey (25–29 August 2017) using field and satellite ocean color observations. The percentage of chlorophyll a (Chl a) in different phytoplankton groups was determined from a semi-analytical IOP (inherent optical property) inversion algorithm. The IOP inversion algorithm revealed the dominance of freshwater species (diatom, cyanobacteria and green algae) in the bay following the hurricane passage (29 September 2017) under low salinity conditions associated with the discharge of floodwaters into GB. Two months after the hurricane (29–30 October 2017), under more seasonal salinity conditions, the phytoplankton community transitioned to an increase in small-sized groups such as haptophytes and prochlorophytes. Sentinel-3A Ocean and Land Colour Instrument (OLCI)-derived Chl a obtained using a red ∕ NIR (near-infrared) band ratio algorithm for the turbid estuarine waters was highly correlated (R2>0.90) to the (high-performance liquid chromatography) HPLC-derived Chl a. Long-term observations of OLCI-derived Chl a (August 2016–December 2017) in GB revealed that hurricane-induced Chl a declined to background mean state in late October 2017. A non-negative least squares (NNLS) inversion model was then applied to OLCI-derived Chl a maps of GB to investigate spatiotemporal variations of phytoplankton diagnostic pigments pre- and post-hurricane; results appeared consistent with extracted phytoplankton taxonomic composition derived from the IOP inversion algorithm and microplankton pictures obtained from an Imaging FlowCytobot (IFCB). OLCI-derived diagnostic pigment distributions also exhibited good agreement with HPLC measurements during both surveys, with R2 ranging from 0.40 for diatoxanthin to 0.96 for Chl a. Environmental factors (e.g., floodwaters) combined with phytoplankton taxonomy also strongly modulated phytoplankton physiology in the bay as indicated by measurements of photosynthetic parameters with a fluorescence induction and relaxation (FIRe) system. Phytoplankton in well-mixed waters (mid-bay area) exhibited maximum PSII photochemical efficiency (Fv∕Fm) and a low effective absorption cross section (σPSII), while the areas adjacent to the shelf (likely nutrient-limited) showed low Fv∕Fm and elevated σPSII values. Overall, the approach using field and ocean color data combined with inversion models allowed, for the first time, an assessment of phytoplankton response to a large hurricane-related floodwater perturbation in a turbid estuarine environment based on its taxonomy, pigment composition and physiological state.
Rapid retreat of permafrost coastline observed with aerial drone photogrammetry

Abstract. Permafrost landscapes are changing around the Arctic in response to climate warming, with coastal erosion being one of the most prominent and hazardous features. Using drone platforms, satellite images, and historic aerial photographs, we observed the rapid retreat of a permafrost coastline on Qikiqtaruk – Herschel Island, Yukon Territory, in the Canadian Beaufort Sea. This coastline is adjacent to a gravel spit accommodating several culturally significant sites and is the logistical base for the Qikiqtaruk – Herschel Island Territorial Park operations. In this study we sought to (i) assess short-term coastal erosion dynamics over fine temporal resolution, (ii) evaluate short-term shoreline change in the context of long-term observations, and (iii) demonstrate the potential of low-cost lightweight unmanned aerial vehicles (“drones”) to inform coastline studies and management decisions. We resurveyed a 500 m permafrost coastal reach at high temporal frequency (seven surveys over 40 d in 2017). Intra-seasonal shoreline changes were related to meteorological and oceanographic variables to understand controls on intra-seasonal erosion patterns. To put our short-term observations into historical context, we combined our analysis of shoreline positions in 2016 and 2017 with historical observations from 1952, 1970, 2000, and 2011. In just the summer of 2017, we observed coastal retreat of 14.5 m, more than 6 times faster than the long-term average rate of 2.2±0.1 m a−1 (1952–2017). Coastline retreat rates exceeded 1.0±0.1 m d−1 over a single 4 d period. Over 40 d, we estimated removal of ca. 0.96 m3 m−1 d−1. These findings highlight the episodic nature of shoreline change and the important role of storm events, which are poorly understood along permafrost coastlines. We found drone surveys combined with image-based modelling yield fine spatial resolution and accurately geolocated observations that are highly suitable to observe intra-seasonal erosion dynamics in rapidly changing Arctic landscapes.
Late Quaternary Variations in the South American Monsoon System as Inferred by Speleothems—New Perspectives using the SISAL Database

Here we present an overview of speleothem δ18O records from South America, most of which are available in the Speleothem Isotopes Synthesis and Analysis (SISAL_v1) database. South American tropical and subtropical speleothem δ18O time series are primarily interpreted to reflect changes in precipitation amount, the amount effect, and consequently history of convection intensity variability of convergence zones such as the Intertropical Convergence Zone (ITCZ) and the South America Monsoon System (SAMS). We investigate past hydroclimate scenarios in South America related to the South American Monsoon System in three different time periods: Late Pleistocene, Holocene, and the last two millennia. Precession driven summertime insolation is the main driver of convective variability over the continent during the last 120 kyrs (from present day to 120 kyrs BP), including the Holocene. However, there is a dipole between speleothem δ18O records from western and eastern South America. Records located in the central region of Brazil are weakly affected by insolation-driven variability, and instead are more susceptible to the variability associated with the South Atlantic Convergence Zone (SACZ). Cold episodic events in the Northern Hemisphere, such as Heinrich and Bond Events, and the Little Ice Age, increase the convective activity of the SAMS, resulting in increased precipitation amount in South America.
Pyroclastic dune bedforms: macroscale structures and lateral variations. Examples from the 2006 pyroclastic currents at Tungurahua (Ecuador)

Pyroclastic currents are catastrophic flows of gas and particles triggered by explosive volcanic eruptions. For much of their dynamics, they behave as particulate density currents and share similarities with turbidity currents. Pyroclastic currents occasionally deposit dune bedforms with peculiar lamination patterns, from what is thought to represent the dilute low concentration and fluid‐turbulence supported end member of the pyroclastic currents. This article presents a high resolution dataset of sediment plates (lacquer peels) with several closely spaced lateral profiles representing sections through single pyroclastic bedforms from the August 2006 eruption of Tungurahua (Ecuador). Most of the sedimentary features contain backset bedding and preferential stoss‐face deposition. From the ripple scale (a few centimetres) to the largest dune bedform scale (several metres in length), similar patterns of erosive‐based backset beds are evidenced. Recurrent trains of sub‐vertical truncations on the stoss side of structures reshape and steepen the bedforms. In contrast, sporadic coarse‐grained lenses and lensoidal layers flatten bedforms by filling troughs. The coarsest (clasts up to 10 cm), least sorted and massive structures still exhibit lineation patterns that follow the general backset bedding trend. The stratal architecture exhibits strong lateral variations within tens of centimetres, with very local truncations both in flow‐perpendicular and flow‐parallel directions. This study infers that the sedimentary patterns of bedforms result from four formation mechanisms: (i) differential draping; (ii) slope‐influenced saltation; (iii) truncative bursts; and (iv) granular‐based events. Whereas most of the literature makes a straightforward link between backset bedding and Froude‐supercritical flows, this interpretation is reconsidered here. Indeed, features that would be diagnostic of subcritical dunes, antidunes and ‘chute and pools’ can be found on the same horizon and in a single bedform, only laterally separated by short distances (tens of centimetres). These data stress the influence of the pulsating and highly turbulent nature of the currents and the possible role of coherent flow structures such as Görtler vortices. Backset bedding is interpreted here as a consequence of a very high sedimentation environment of weak and waning currents that interact with the pre‐existing morphology. Quantification of near‐bed flow velocities is made via comparison with wind tunnel experiments. It is estimated that shear velocities of ca 0·30 m.s−1 (equivalent to pure wind velocity of 6 to 8 m.s−1 at 10 cm above the bed) could emplace the constructive bedsets, whereas the truncative phases would result from bursts with impacting wind velocities of at least 30 to 40 m.s−1.
Capture-recapture models: A review of current methods, assumptions and experimental design

-The current “state-of-the-art” in capture-recapture sampling methodology is reviewed. An emphasis is placed on model assumptions, model robustness to assumption failure, and in particular on the often neglected topic of study design. For short term studies, there has been much recent work on closed population models that allow for unequal cat&ability of individual animals (heterogeneity and/or trap response). The closure assumption causes problems for many terrestrial bird population studies. A model which allows a closed population of “residents” plus some short term “wanderers” through the study area is considered. For long term studies, open population models that assume equal catchability are discussed. They allow estimation of survival and birth rates as well as population sizes. Recent developments which allow some agedependence of survival and capture probabilities are reported and related to some recent band recovery models. In terrestrial bird studies resighting of color-marked birds without capture could be potentially useful for estimation of survival rates. Capture-recapture sampling has been widely used and abused for many years in the study of natural animal populations. Excellent reviews are given by Cormack (1968) and Seber (1973). Recently there has been a renewed interest in the assumptions behind capture-recapture sampling and especially in the assumption of “equal catchability” of all animals in the population. Some new models relaxing this assumption have been proposed, complete with estimators and tests of model fit (Pollock 1974, 1975a, 3975b; Burnham 1972; Burnham and Overton 1978, 1979). Of particular importance is the monograph for biologists by Otis et al. (1978). Here I concentrate on reviewing the current theory from an applied statistician’s viewpoint but for an audience mainly of biologists with some knowledge of statistical thinking. Assumptions, robustness to assumption failure, and design concepts will be emphasized with statistical complexities kept to a minimum. Extensive reference will be made to source materials that may be consulted for more technical details on a particular model or concept. The review falls naturally into sections on closed and open population models. Here by open we mean additions (birth and/or immigration) into the population are allowed, as are permanent deletions (death and/or emigration) from the population. Closed then means that neither additions nor permanent deletions are permitted. These sections are followed by a general discussion of the important issues raised.
Diurnal regulation of photosynthetic light absorption, electron transport and carbon fixation in two contrasting oceanic environments

Abstract. Understanding the dynamics of marine phytoplankton productivity requires mechanistic insight into the non-linear coupling of light absorption, photosynthetic electron transport and carbon fixation in response to environmental variability. In the present study, we examined the variability of phytoplankton light absorption characteristics, light-dependent electron transport and 14C-uptake rates over a 48 h period in the coastal subarctic north-east (NE) Pacific. We observed an intricately coordinated response of the different components of the photosynthetic process to diurnal irradiance cycles, which acted to maximize carbon fixation, while simultaneously preventing damage by excess absorbed light energy. In particular, we found diurnal adjustments in pigment ratios, excitation energy transfer to reaction centre II (RCII), the capacity for non-photochemical quenching (NPQ), and the light efficiency (α) and maximum rates (Pmax) of RCII electron transport (ETRRCII) and 14C uptake. Comparison of these results from coastal waters to previous observations in offshore waters of the subarctic NE Pacific provides insight into the effects of iron limitation on the optimization of photosynthesis. Under iron-limited, low-biomass conditions, there was a significant reduction of iron-rich photosynthetic units per chlorophyll a, which was partly offset by higher light absorption and electron transport per photosystem II (PSII). Iron deficiency limited the capacity of phytoplankton to utilize peak midday irradiance for carbon fixation and caused an upregulation of photoprotective mechanisms, including NPQ, and the decoupling of light absorption, electron transport and carbon fixation. Such decoupling resulted in an increased electron requirement (Φe,C) and decreased quantum efficiency (ΦC) of carbon fixation at the iron-limited station. In both coastal and offshore waters, Φe,C and ΦC correlated strongly to NPQ, albeit with a significantly different slope. We discuss the implications of our results for the interpretation of bio-optical data and the parameterization of numerical productivity models, both of which are vital tools in monitoring marine photosynthesis over large temporal and spatial scales.
Seasonal and Interannual Patterns and Controls of Hydrological Fluxes in an Amazon Floodplain Lake With a Surface‐Subsurface Process Model

Floodplain lakes represent important aquatic ecosystems, and field‐based estimates of their water budgets are difficult to obtain, especially over multiple years. We examine the hydrological fluxes for an Amazon floodplain lake connected to the Solimões River using a process‐based hydrologic model. Water exchanges between the river and lake agree well with field estimates, including the timing of different hydrological phases. However, beyond available field data, modeling results show that the seven simulated years all differed from each other. These interannual differences were caused by the interplay between phases when water levels were rising with river‐water flowing into the lake (RWRI), versus rising with lake‐water flowing out to the river (RWLO). This exchange determines the river‐water content in the lake (CL). Maximum CL occurred before river levels peaked because local catchment contributions can be sufficient to push lake‐water out to the river, even as river levels rise. Numerical experiments show that the seasonal distribution of local rainfall, local catchment size, and interannual variability in both climate and river stage can contribute to differing dynamics of CL in a floodplain lake. Their impacts vary among phases: river‐rise dominates the RWRI, whereas local hydrological processes dominate the RWLO and receding‐water phases. Intermediate‐to‐long‐term rainfall accumulation controls CL during the RWLO phase, whereas annual precipitation accumulation is important for CL during low water. Our model generalizes beyond limited available field studies and offers potential to better understand floodplain lakes in other areas and how regional versus local changes in climate may affect their hydrological dynamics.
N2O Emission from Managed Soil Under Different Crops in Rainfed Area, Central Java

N2O emission from agriculture has been assumed to increase by 30-35% until 2030. This gas has a major contribute to the emission from agriculture. N2O emission from managed soils is the 2nd contributor to green house gas (GHG) emission from agriculture in Indonesia. Rainfed area requested high management input. This research aimed to examine N2O emission from different crops in the rainfed area and its affecting factors, also to identify things that need to be considered in conducting N2O measurement from managed soil. Research conducted in Pati and Blora District, Central Java Province. Four (4) different experimental sites with 4 different crops were chosen. Those were mung bean, rubber plantation and sugarcane which located within Pati District, and maize crop which located in Blora District. No treatment was applied. Gas samples were taken following the day after fertilizing. Daily N2O fluxes from managed soil in tropical land of Indonesia determine by several factors, which are: days after fertilizing, fertilizer type and dosage, previous land use, growth phase of crops, sampling point and soil characteristic. The peak time was mostly influenced by crop type. Maize has the highest N2O daily fluxes with the range of 311.9 - 9651.6 ugN2O m-2day-1 and rubber plantation has the lowest with the range of 16.1 - 2270.7 ugN2O m-2day-1. Measurement of N2O from managed soil to determine annual emissions should be done at all crop types, soil types, considering crops growth phase and also high sampling frequency to prevent an over or underestimation.
Ensemble Learning of Tissue Components for Prostate Histopathology Image Grading

Ensemble learning is an effective machine learning approach to improve the prediction performance by fusing several single classifier models. In computer-aided diagnosis system (CAD), machine learning has become one of the dominant solutions for tissue images diagnosis and grading. One problem in a single classifier model for multi-components of the tissue images combination to construct dense feature vectors is the overfitting. In this paper, an ensemble learning for multi-component tissue images classification approach is proposed. The prostate cancer Hematoxylin and Eosin (H&E) histopathology images from HUKM were used to test the proposed ensemble approach for diagnosing and Gleason grading. The experiments results of several prostate classification tasks, namely, benign vs. Grade 3, benign vs.Grade4, and Grade 3vs.Grade 4 show that the proposed ensemble significantly outperforms the previous typical CAD and the naive approach that combines the texture features of all tissue component directly in dense feature vectors for a classifier.