Miracle-dz/UniFAR-FTUs huggingface dataset:
Baroclinic instability of density current along a sloping bottom and the associated transport process

Numerical experiments with a three-dimensional nonhydrostatic ocean model have been carried out to investigate the dynamic processes of downslope density current and associated transport of dense water, focusing on the effects of bottom slope for the range of slope inclination S from 0 to 0.04. Bottom slope has two effects on baroclinic instability of the flow. One is the stabilizing effect due to the topographic β effect and to offshoreward increase in water depth. The other is the destabilizing effect due to steepened inclination of isopycnal surface, which increases available potential energy. Since the destabilizing effect over the upper slope overcomes the stabilizing one in the early stage, unstable waves develop more rapidly with increasing S. Nonlinear energy conversion due to Reynolds stresses also affects the flow stability and then the growth rate of instability increases linearly with S in this stage. After the unstable waves have finite amplitudes in the mature stage the stabilizing effect of bottom slope becomes dominant, especially over the lower slope. Thus vigorous unstable eddies are confined to the upper slope region in steep slope cases, while they cover the whole slope region in gentle slope cases, and this difference in the eddy field causes a drastic change in downslope transport of dense water. In gentle slope cases, efficiency of the transport becomes higher with increasing S since the destabilizing effect overcomes the stabilizing one as a whole. On the contrary, the efficiency becomes lower with increasing S in steep slope cases since the stabilizing effect surpasses the destabilizing one. As a result, the most effective transport is realized in the case with S = 0.005. Although the transport due to eddies in steep slope cases becomes weak over the lower slope, it is still larger than that due to the bottom Ekman current since the eddy transport occurs in the bottom layer with a thickness of 100∼200 m, which is 4∼8 times the Ekman layer thickness.
Using SPMDs to Assess Natural Recovery of PCB-contaminated Sediments in Lake Hartwell, SC: I. A Field Test of New In-Situ Deployment Methods

Results from the field testing of some innovative sampling methods developed to evaluate risk management strategies for polychlorinated biphenyl (PCB) contaminated sediments are presented. Semipermeable membrane devices (SPMDs) were combined with novel deployment methods to quantify the availability of PCBs at the Sangamo-Weston Lake Hartwell Superfund Site in SC. Three locations in Lake Hartwell were examined: a background site (BKG) with little detectable contamination and two contaminated sites (T-M/N and T-O). PCB availability was quantified using sediment surface samplers designed to hold SPMDs in contact with surface sediments, benthic dome samplers designed to enclose and suspend SPMDs at the sediment-water interface, and commercially obtained SPMD cages suspended in the water column. A two-way analysis of variance showed significant effects by sampler type (P < 0.0001) and site (P < 0.0001) for mean time-weighted average (TWA) total PCBs (t-PCBs). Regardless of the SPMD sampler used, mean TWA t-PCBs were directly proportional to the level of contamination present (BKG < T-M/N < T-O). Water column and surface sediment sampler t-PCB uptake patterns were described by a significant linear fit of the data (r2 = 0.9625, p < 0.0001, and r2 = 0.8188, p < 0.0001, respectively). Dome and sediment surface SPMD samples had a higher percentage of higher chlorinated PCBs compared to water column samples.
Notice of Retraction Integration of a Water Balance Model with a Decision Support Tool in the Loess Plateau of China

In order to reduce the massive soil erosion and to ensure sustainable development, the Chinese central government planned revegetation measures to reduce these environmental problems-especially in the Loess Plateau. This revegetation process will not only result in less soil erosion in the coarse sandy hilly catchments (CSHC), but also less runoff due to increased evapotranspiration (ET). A water balance model of Zhang et al. (2001) was used to estimate the subsequent impact on stream flow and its spatial distribution in this region at first, but the results showed that the model was not able to accurately simulate average annual stream flow when compared with stream flow measurements from 38 hydrologic stations in CSHC of the Loess Plateau. Zhang et al. (2008) calibrated the model, and it can accurately simulate the impacts of the region on streamflow. The recommended areas for revegetation and the suitability for each of 38 perennial species are also researched in the region. To provide a direct simulate result for policy makers and soil and water managers with the information that they need to make better decisions, a decision support tools called Revegetation Impacts on Hydrology (ReVegIH) was developed in Microsoft. NET environment using C# and the invisible modeling environment (TIME). ReVegIH provides besides basic geographical information system (GIS) functions, impacts of different revegetation result on runoff and ET, revegetation and priority areas for trees and shrubs, the suitability of 38 species for planting in the CSHC. The establishment of ReVegIH provided a very efficient way of managing revegetation species and areas, showing simulate result of the model, calibrating model coefficient. ReVegIH does not consider loading other catchments or counties dataset to simulate and also loading map is not efficient enough.
Intracellular Protein Degradation: From a Vague Idea through the Lysosome and the Ubiquitin-Proteasome System and onto Human Diseases and Drug Targeting

Between the 1950s and 1980s, scientists were focusing mostly on how the genetic code was transcribed to RNA and translated to proteins, but how proteins were degraded had remained a neglected research area. With the discovery of the lysosome by Christian de Duve it was assumed that cellular proteins are degraded within this organelle. Yet, several independent lines of experimental evidence strongly suggested that intracellular proteolysis was largely non-lysosomal, but the mechanisms involved have remained obscure. The discovery of the ubiquitin-proteasome system resolved the enigma. We now recognize that degradation of intracellular proteins is involved in regulation of a broad array of cellular processes, such as cell cycle and division, regulation of transcription factors, and assurance of the cellular quality control. Not surprisingly, aberrations in the system have been implicated in the pathogenesis of human disease, such as malignancies and neurodegenerative disorders, which led subsequently to an increasing effort to develop mechanism-based drugs.
The synergistic effect and mechanism of doxorubicin-ZnO nanocomplexes as a multimodal agent integrating diverse anticancer therapeutics

Background Nanomaterials have emerged as ideal multimodal nanomedicine platforms, each one combining different designs and therapeutic approaches in a single system against cancer. The aim of the current study was to explore the synergistic effect and mechanism of a doxorubicin (Dox)-ZnO nanocomplex as a multimodal drug delivery system, integrating Dox chemotherapy and ZnO-mediated photodynamic therapy, in anticancer therapeutics. Methods Dox was loaded onto ZnO nanomaterials, forming complexes with the transition metal Zn to yield the Dox-ZnO nanocomplexes. After culture with SMMC-7721 hepatocarcinoma cells, the cellular uptake was quantitatively detected by flow cytometry and visualized by fluorescence microscopy. The synergistic effects of the different anticancer therapeutic modalities on the proliferation of SMMC-7721 hepatocarcinoma cells were evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The expression of B-cell lymphoma 2 protein (Bcl-2), Bcl-2 associated X protein (Bax), caspase 9, and caspase 3 were examined by Western blot, to elucidate the possible molecular mechanisms involved. Results Our observations demonstrated that Dox-ZnO nanocomplexes could act as an efficient drug delivery system for importing Dox into SMMC-7721 cells, enhancing its potential chemotherapy efficiency by increasing the intracellular concentration of Dox. With the addition of ultraviolet (UV) illumination, the ZnO nanomaterials showed excellent photodynamic therapeutic properties, attacking the cancer cells further. Thus the caspase-dependent apoptosis was synergistically induced, resulting in distinct improvement in anticancer activity. Conclusion The Dox-ZnO nanocomplex presents a promising multimodal agent for comprehensive cancer treatment.
Late Cenozoic Ostracoda of the South Aegean Island Arc

A detailed study has been made of Late Cenozoic ostracodes from closely sampled sections and some isolated samples on the Aegean islands of Gavdos, Crete, Karpathos and Rhodos. The stratigraphic position of the studied lithostratigraphic units has been determined by means of the evolutionary trends in Planorbulinella and in uniserial Uvigerina, and by planktonic Foraminifera (Chapter II). For a paleoecologic interpretation a method is introduced for evaluating depth of deposition and salinity, and major trends in the development of the depositional environment (Chapter III). Based on the three major realms for ostracode life reflected in the assemblages (a brackish water, a shallow marine and a deeper marine environment) some tentative assemblage zones are proposed (Chapter IV). Comparisons with the ostracode assemblages of Neogene stratotypes show that most of the biozones can be recognized outside the Aegean area (Chapter V). The systematic part of the study deals with over 200 different taxa. Three new subgenera are proposed. In total 24 new species are described. Because of primary homonymy two species are renamed (Chapter VI).
SPINDLY, ERECTA, and Its Ligand STOMAGEN Have a Role in Redox-Mediated Cortex Proliferation in the Arabidopsis Root

SUMMARY Reactive oxygen species (ROS) are signaling molecules, but how they are perceived in plants remains unclear. This study showed that cortex proliferation in the Arabidopsis root can be induced by hydrogen peroxide and that the receptor kinase ERECTA and one of its ligands, STOMAGEN, are involved in a signaling pathway that couples ROS sensing with redox-mediated cortex proliferation. This study also revealed a new role for SPINDLY (SPY), a putative O-GlcNAc transferase, in cellular redox homeostasis.
Assessing uncertainty in VGI for emergency response

This research project examines the geographic data produced by volunteers via the Ushahidi web platform in response to the earthquake that struck Haiti in January 2010. Volunteers translated messages (text, e-mail, and voice) submitted by victims of the earthquake, categorized each message into a primary ‘emergency need’ category and subcategory, and georeferenced each message on a dynamic web-based map. Initial inspection of the categorized data indicated discrepancies between the emergency need submitted by victims and the subsequent categorization of the emergency need. Analysis of the main categorical data illustrated that 50% of the messages were mis-categorized by the volunteers, failing to convey the main idea of the victim’s message. At the subcategory level, approximately 73% of the messages failed to convey the main idea of the messages. These numbers are higher than the estimate of 36% error in categorization produced in an independent review of the Haiti Ushahidi database. While the volunteer response to the Haitian earthquake represents a paradigm shift in emergency response and victim empowerment that has been repeated in numerous natural and man-made disasters around the world, this study suggests the need for more research on the quality of the categorization (i.e., attribute data) of volunteered emergency data.
Catecholaminergic challenge uncovers distinct Pavlovian and instrumental mechanisms of motivated (in)action

Catecholamines modulate the impact of motivational cues on action. Such motivational biases have been proposed to reflect cue-based, ‘Pavlovian’ effects. Here, we assess whether motivational biases may also arise from asymmetrical instrumental learning of active and passive responses following reward and punishment outcomes. We present a novel paradigm, allowing us to disentangle the impact of reward and punishment on instrumental learning from Pavlovian response biasing. Computational analyses showed that motivational biases reflect both Pavlovian and instrumental effects: reward and punishment cues promoted generalized (in)action in a Pavlovian manner, whereas outcomes enhanced instrumental (un)learning of chosen actions. These cue- and outcome-based biases were altered independently by the catecholamine enhancer melthylphenidate. Methylphenidate’s effect varied across individuals with a putative proxy of baseline dopamine synthesis capacity, working memory span. Our study uncovers two distinct mechanisms by which motivation impacts behaviour, and helps refine current models of catecholaminergic modulation of motivated action. DOI: http://dx.doi. org/10.7554/eLife.22169. 001
Herbicide Resistance in Ryegrass: Stochastic Evaluation of Management Strategies

Annual Ryegrass is a significant weed in cereal production in Western Australia. Herbicide resistance is increasing and is a major concern to producers. Long-term, field scale trials are being conducted on a number of sites in the state. The apparent costs and benefits of different management strategies are dependent on seasonal conditions and markets for inputs and products. This paper presents the results of a simulation model of alternative strategies under a wide range of historic conditions. A conceptual framework for selecting an optimal strategy is explored.
Seismicity of the Earth 1900-2013, seismotectonics of South America (Nazca Plate Region)

*Aftershock zones for large earthquakes represent the area over which significant aftershock activity was observed in the immediate vicinity of the main shock, within tectonic environments coupled to the main shock system. For example, for the 2011 M 9.0 Tohoku earthquake, extensive aftershocks occurred on the interplate thrust contact between the Pacific and North America plates, as well as in the overlying upper plate, and on faults within the Pacific plate outboard of the subduction zone. We do not include more distant triggered aftershocks such as those that occurred on upper plate faults within mainland Japan.
An astrobiological study of an alkaline-saline hydrothermal environment, relevant to understanding the habitability of Mars

The on going exploration of planets such as Mars is producing a wealth of data which is being used to shape a better understanding of potentially habitable environments beyond the Earth. On Mars, the relatively recent identification of minerals which indicate the presence of neutral/alkaline aqueous activity has increased the number of potentially habitable environments which require characterisation and exploration. The study of terrestrial analogue environments enables us to develop a better understanding of where life can exist, what types of organisms can exist and what evidence of that life may be preserved. The study of analogue environments is necessary not only in relation to the possibility of identifying extinct/extant indigenous life on Mars, but also for understanding the potential for contamination. As well as gaining an insight into the habitability of an environment, it is also essential to understand how to identify such environments using the instruments available to missions to Mars. It is important to be aware of instrument limitations to ensure that evidence of a particular environment is not overlooked. This work focuses upon studying the bacterial and archaeal diversity of Lake Magadi, a hypersaline and alkaline soda lake, and its associated hydrothermal springs. Culture dependent and culture independent analytical methods have been used and have led to the identification of potentially novel isolates. In addition, the effects of simulated Martian conditions such as desiccation and UVC radiation upon single strains isolated from this environment, and the effects upon a complex soil community have been assessed. Results have also provided an indication of what issues may arise with identifying minerals associated with these environments using the equipment such as the ExoMars PanCam. It is hoped that this work has contributed to our understanding of the possible habitability of Mars.
Modelling streamflow response to hydro-climatic variables in the Upper Mkomazi River, South Africa

Streamflow modelling remains crucial to decision-making especially when it concerns planning and management of water resources systems in water-stressed regions. This study proposes a suitable method for streamflow modelling irrespective of the limited availability of historical datasets. Two data-driven modelling techniques were applied comparatively so as to achieve this aim. Genetic programming (GP), an evolutionary algorithm approach and a differential evolution (DE)-trained artificial neural network (ANN) were used for streamflow prediction in the upper Mkomazi River, South Africa. Historical records of streamflow and meteorological variables for a 19-year period (1994- 2012) were used for model development and also in the selection of predictor variables into the input vector space of the models. In both approaches, individual monthly predictive models were developed for each month of the year using a 1-year lead time. Two case studies were considered in development of the ANN models. Case study 1 involved the use of correlation analysis in selecting input variables as employed during GP model development, while the DE algorithm was used for training and optimizing the model parameters. However in case study 2, genetic programming was incorporated as a screening tool for determining the dimensionality of the ANN models, while the learning process was further fine-tuned by subjecting the DE algorithm to sensitivity analysis. Altogether, the performance of the three sets of predictive models were evaluated comparatively using three statistical measures namely, Mean Absolute Percent Error (MAPE), Root Mean-Squared Error (RMSE) and coefficient of determination (R2). Results showed better predictive performance by the GP models both during the training and validation phases when compared with the ANNs. Although the ANN models developed in case study 1 gave satisfactory results during the training phase, they were unable to extensively replicate those results during the validation phase. It was found that results from case study 1 were considerably influenced by the problems of overfitting and memorization, which are typical of ANNs when subjected to small amount of datasets. However, results from case study 2 showed great improvement across the three evaluation criteria, as the overfitting and memorization problems were significantly minimized, thus leading to improved accuracy in the predictions of the ANN models. It was concluded that the conjunctive use of the two evolutionary computation methods (GP and DE) can be used to improve the performance of artificial neural networks models, especially when availability of datasets is limited. In addition, the GP models can be deployed as predictive tools for the purpose of planning and management of water resources within the Mkomazi region and KwaZulu-Natal province as a whole.
The Individual Tree Crown Approach Applied to Ikonos Images of a Coniferous Plantation Area

In forestry, the availability of high spatial resolution (� 1 m/pixel) imagery from new earth observation satellites like Ikonos favours a shift in the image analysis paradigm from a pixel-based approach towards one dealing directly with the essential structuring element of such images: the individual tree crown (ITC). This paper gives an initial assessment of the effects of 1 m and 4 m/pixel spatial resolutions (panchromatic and multispectral bands, respectively) on the detection, delineation, and classification of the individual tree crowns seen in Ikonos images. Winter and summer Ikonos images of the Hudson plantation of the Petawawa Research Forest, Ontario, Canada were analyzed. The panchromatic images were resampled to 0.5 m/pixel and then smoothed using a 3 � 3 kernel mean filter. A valleyfollowing algorithm and rule-based isolation module were applied to delineate the individual tree crowns. Local maxima within a moving 3 � 3 window (i.e., Tree Tops) were also extracted from the smoothed images for comparison. Crown delineation and detection results were summarised and compared with field tree counts. Overall, the ITC delineation and the local maxima approaches led to tree counts that were on average 15 percent off for both seasons. Visual inspection reveals delineation of clusters of two or three crowns as a common source of error. Crown-based species spectral signatures were generated for six classes representing conifer species, plus a hardwood class and a shrub class. After the ITC-based classification, classification accuracy was ascertained using separate test areas of known species. The overall accuracy was 59 percent. Important confusion exists between red and white spruces, and mature versus immature white pines, but post-classification regroupings into single spruce and white pine classes led to an overall accuracy of 67 percent.
Impact of soil organic matter on soil properties—a review with emphasis on Australian soils

A review has been undertaken into how soil organic matter (SOM) affects a range of soil properties that are important for the productive capacity of soils. The potential effect of varying the amount of SOM in soil on a range of individual soil properties was investigated using a literature search of published information largely from Australia, but also including relevant information from overseas. The soil properties considered included aggregate stability, bulk density, water-holding capacity, soil erodibility, soil colour, soil strength, compaction characteristics, friability, nutrient cycling, cation exchange capacity, soil acidity and buffering capacity, capacity to form ligands and complexes, salinity, and the interaction of SOM with soil biology. Increases in SOM have the capacity to have strong influence only the physical properties of the surface soils, perhaps only the top 10 cm, or the top 20 cm at most. This limits the capacity of SOM to influence soil productivity. Even so, the top 20 cm is a critical zone for the soil. It is where seeds are sown, germinate and emerge. It is where a large proportion of plant materials are added to the soil for decomposition and recycling of nutrients and where rainfall either enters the soil or runs off. Therefore, the potential to improve soil condition in the top 0–20 cm is still critical for plant productivity. The SOM through nutrient cycling such as mineralisation of organic nitrogen to nitrate can have an influence on the soil profile.