Impact of Industrial Pollution of Cadmium on Traditional Crop Planting Areas and Land Management: A Case Study in Northwest China

Cadmium in soils not only reduces crop yield and quality but also threatens the safety of human health and wildlife due to bioaccumulation. Baiyin City, a typical industrial region located in northwest China, was evaluated to examine the spatial distribution of cadmium. We simulated soil cadmium concentrations in the laboratory, based on levels found at local sampling sites, to examine how both Medicago sativa and Zea mays plants accumulate cadmium. The experimental results revealed that cadmium in all soil samples exceeded China’s national standard levels for general farmland; in addition, cadmium accumulation in all tissues of M. sativa and Z. mays exceeded the national fodder standards. Therefore, M. sativa and Z. mays from the study area should not be used for fodder. However, about 36% of the planting area of M. sativa and Z. mays can be used for phytoextraction because of cadmium accumulation. For soil pollution management, we suggest dividing the study area into three different regions, including a non-planting region, a phytoremediation region, and a planting region. Our soil management model can effectively help local people to avoid food safety risks and to realize sustainable development of soil utilization in contaminated areas.

The repetitive local sampling and the local distribution theory

Molecular simulation is a mature and versatile tool set widely utilized in many subjects with more than 30,000 publications each year. However, its methodology development has been struggling with a tradeoff between accuracy/resolution and speed, significant improvement of both beyond present state of the art is necessary to reliably substitute many expensive and laborious experiments in molecular biology, materials science and nanotechnology. Previously, the ubiquitous issue regarding severe wasting of computational resources in all forms of molecular simulations due to repetitive local sampling was raised, and the local free energy landscape approach was proposed to address it. This approach is derived from a simple idea of first learning local distributions, and followed by dynamic assembly of which to infer global joint distribution of a target molecular system. When compared with conventional explicit solvent molecular dynamics simulations, a simple and approximate implementation of this theory in protein structural refinement harvested acceleration of about six orders of magnitude without loss of accuracy. While this initial test revealed tremendous benefits for addressing repetitive local sampling, there are some implicit assumptions need to be articulated. Here, I present a more thorough discussion of repetitive local sampling; potential options for learning local distributions; a more general formulation with potential extension to simulation of near equilibrium molecular systems; the prospect of developing computation driven molecular science; the connection to mainstream residue pair distance distribution based protein structure prediction/refinement; and the fundamental difference of utilizing averaging from conventional molecular simulation framework based on potential of mean force. This more general development is termed the local distribution theory to release the limitation of strict thermodynamic equilibrium in its potential wide application in general soft condensed molecular systems.

MDO: A Computational Protocol for Accurate Prediction of Full Flexibility Receptor-Ligand Binding Mode Structures

Predicting the binding structure of bio-complex is essential for understanding its properties, functions, and mechanisms, but is rather difficult due to the huge sampling space involved. A new computational protocol, MDO, for finding the ligand binding structure is proposed. MDO consists of global sampling via MD simulation and clustering of the receptor configurations, local sampling via molecular docking and clustering of the ligand conformations, and binding structure optimization by the ONIOM (QM/QM) method. MDO is tested on 15 protein-ligand complexes with known accurate structures. The success rate of MDO predictions, with RMSD < 2 Å, is found to be 67%, substantially higher than the 40% success rate of conventional methods. The MDO success rate can be increased to 83% if the ONIOM calculations are applied only for the starting poses with ligands inside the binding cavities. The MDO protocol is a promising tool for the structure based drug design.

Insectivorous songbirds as early indicators of future defoliation by spruce budworm

Context Although the spatiotemporal dynamics of spruce budworm outbreaks have been intensively studied, forecasting outbreaks remains challenging. During outbreaks, budworm-linked warblers (Tennessee, Cape May, and bay-breasted warbler) show a strong positive response to increases in spruce budworm, but little is known about the relative timing of these responses. Objectives We hypothesized that these warblers could be used as sentinels of future defoliation of budworm host trees. We examined the timing and magnitude of the relationships between defoliation by spruce budworm and changes in the probability of presence of warblers to determine whether they responded to budworm infestation before local defoliation being observed by standard detection methods. Methods We modelled this relationship using large-scale point count surveys of songbirds and maps of cumulative time-lagged defoliation over multiple spatial scales (2–30 km radius around sampling points) in Quebec, Canada. Results All three warbler species responded positively to defoliation at each spatial scale considered, but the timing of their response differed. Maximum probability of presence of Tennessee and Cape May warbler coincided with observations of local defoliation, or provided a one year warning, making them of little use to guide early interventions. In contrast, the probability of presence of bay-breasted warbler consistently increased 3–4 years before defoliation was detectable. Conclusions Early detection is a critical step in the management of spruce budworm outbreaks and rapid increases in the probability of presence of bay-breasted warbler could be used to identify future epicenters and target ground-based local sampling of spruce budworm.

A fast and effective detection framework for whole-slide histopathology image analysis

Pathologists generally pan, focus, zoom and scan tissue biopsies either under microscopes or on digital images for diagnosis. With the rapid development of whole-slide digital scanners for histopathology, computer-assisted digital pathology image analysis has attracted increasing clinical attention. Thus, the working style of pathologists is also beginning to change. Computer-assisted image analysis systems have been developed to help pathologists perform basic examinations. This paper presents a novel lightweight detection framework for automatic tumor detection in whole-slide histopathology images. We develop the Double Magnification Combination (DMC) classifier, which is a modified DenseNet-40 to make patch-level predictions with only 0.3 million parameters. To improve the detection performance of multiple instances, we propose an improved adaptive sampling method with superpixel segmentation and introduce a new heuristic factor, local sampling density, as the convergence condition of iterations. In postprocessing, we use a CNN model with 4 convolutional layers to regulate the patch-level predictions based on the predictions of adjacent sampling points and use linear interpolation to generate a tumor probability heatmap. The entire framework was trained and validated using the dataset from the Camelyon16 Grand Challenge and Hubei Cancer Hospital. In our experiments, the average AUC was 0.95 in the test set for pixel-level detection.

Geomorphometric study of Martian scoria cones

&lt;p&gt;Compared to Earth, the surface erosion activity of Mars is low, so Martian landscapes can survive for &amp;#160;long time, therefore Martian surface has been observed and analysed since the earliest times of Mars research. Because the planet&amp;#8217;s geological and mass wasting history can be studied with remote sensing, observations may provide deeper insight into the early evolution of the planet (Golombek &amp; Bridges, 2000). Lack of precipitation, vegetation and human influence have preserved landforms of Mars that have disappeared on Earth. Yet, local sampling and analysis of rocks are not possible, the evaluation of DTM data can deliver information. Presumably all the terrestrial geological processes also took place on Mars, therefore comparative observations provide a great opportunity to study landforms similar to terrestrial features. The most important difference between terrestrial and Martian surface processes is the formation of impact craters; but volcanic processes create specific volcanic edifices too. Of course, due to the different gravity forces and the lack of some surface effects, larger volcanic forms can also be found than on Earth.&lt;/p&gt;&lt;p&gt;We focus on the less researched smaller volcanic edifices. The morphometric studies on terrestrial scoria cones have revealed interesting details (Wood 1979; Bro&amp;#382; et al., 2015): properties often can be related to their chronology. This pilot project intends to gather similar knowledge on smaller Martian volcanoes. With the development of morphometric technology, we may get an increasingly accurate picture of the surface and geology of Mars (Mars Trek). Besides the description of the physical appearance of the edifices, parameter extraction may lead to their classification or grouping. These studies may pave the way characterisation of Martian cones.&lt;/p&gt;&lt;p&gt;Previously we have examined the morphometry of several terrestrial scoria cone areas; a relatively simple structure were chosen to reduce the number of the geomorphometric parameters. In this project we apply the same simplification: the varying resolution of DTMs, the lack of proper geological maps limit the evaluation to the simple parametrisation. Furthermore, the sizes and characteristic slopes are different, but the results are promising. The automated parameter extraction seems to be suitable for processing multiple and large number of terrain data. This is a work in progress towards an extensive geomorphometric evaluation of Martian scoria cones as well.&lt;/p&gt;&lt;p&gt;F.V. was supported by the &amp;#218;NKP-20-3 New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund.&lt;/p&gt;&lt;p&gt;Bro&amp;#382;, P., &amp;#268;adek, O., Hauber, E., &amp; Rossi, A. P. (2015). Scoria cones on Mars: Detailed investigation of morphometry based on high-resolution digital elevation models. Journal of Geophysical Research: &amp;#160;Planets, 120(9), 1512-1527.&lt;/p&gt;&lt;p&gt;Golombek, M. P., &amp; Bridges, N. T. (2000). Erosion rates on Mars and implications for climate change: Constraints from the pathfinder landing site. Journal of Geophysical Research: Planets, 105(E1), 1 841- 1 853.&lt;/p&gt;&lt;p&gt;Mars trek. (n.d.). NASA Solar System Treks. https://trek.nasa.gov/mars/&lt;/p&gt;&lt;p&gt;Wood, C. A. (1979). Monogenetic volcanoes of the terrestrial planets. Proceedings of the Tenth Lunar and Planetary Science Conference, 2815-2840.&lt;/p&gt;