mlsa-iai-msu-lab/ru_sci_bench_zho_cite_reranking huggingface dataset:
ZIKA-How fast does this virus mutate?

The World Health Organization has declared the present Zika virus epidemic to be a ‘Public Health Emergency of International Concern'. The virus appears to have spread from Thailand to French Polynesia in 2013, and has since infected over a million people in the countries of South and Central America. In most cases the infection is mild and transient, but the virus does appear to be strongly neurotropic and the presumptive cause of both birth defects in fetuses and Guillain-Barre syndrome in some adults. In this paper, the techniques and utilities developed in the study of mitochondrial DNA were applied to the Zika virus. As a result, it is possible to show in a simple manner how a phylogenetic tree may be constructed and how the mutation rate of the virus can be measured. The study showed the mutation rate to vary between 12 and 25 bases a year, in a viral genome of 10 272 bases. This rapid mutation rate will enable the geographic spread of the epidemic to be monitored easily and may also prove useful in assisting the identification of preventative measures that are working, and those that are not.
Huangshan population of Chinese Zacco platypus (Teleostei, Cyprinidae) harbors diverse matrilines and high genetic diversity

Six main mitochondrial DNA (mtDNA) lineages have been described in minnow (Zacco platypus) samples obtained from northern, western and southern China. Perdices et al. (2004) predicted that further sampling of other tributaries might discover more lineages of this species. In this study, we collected 26 Zacco platypus individuals in the Huangshan area of eastern China and determined the cytochrome b (cytb) sequence variations. Combined with reported data in GenBank, we identified ten matrilines (Zacco A-J) in a total of 169 samples, with relatively high molecular divergence found among them. The Huangshan population had the greatest genetic variation among all sampled regions and hosted six of the ten matrilines. Our results highlight the significance of the Huangshan area for the conservation of Zacco platypus.
Seepage characteristics of collapse column fillings

With concealment and hysteresis, water-inrush from Karst collapse column has become an important security hazard of lower group coal mining in North China. Based on the MTS815.02 seepage test system, we analyzed the impact of consolidation pressure, initial moisture content and confining pressure on the permeability of fillings in order to study the seepage characteristics of collapse column fillings. The results show that: (1) The permeability of collapse column fillings is of the order of 10~(-16)-10~(-15) magnitude and decreases with an increase in consolidation pressure and decrease in initial moisture content.(2) The essence of filling seepage law change is the change in porosity, and a power function relationship exists between the permeability ratio and porosity ratio. (3) With increasing confining pressure, the permeability of fillings decreases. However, under low confining pressure (1.2-4 MPa), the change of confining pressure has no obvious influence on the permeability.
CRISPR/Cas9: A powerful tool for crop genome editing

The CRISPR/Cas9 technology is evolved froma type II bacterial immune systemand represents a new generation of targeted genome editing technology that can be applied to nearly all organisms. Site-specific modification is achieved by a single guide RNA (usually about 20 nucleotides) that is complementary to a target gene or locus and is anchored by a protospaceradjacent motif. Cas9 nuclease then cleaves the targeted DNA to generate double-strand breaks (DSBs), which are subsequently repaired by non-homologous end joining (NHEJ) or homology-directed repair (HDR) mechanisms. NHEJ may introduce indels that cause frame shift mutations and hence the disruption of gene functions. When combined with double or multiplex guide RNA design, NHEJ may also introduce targeted chromosome deletions, whereas HDR can be engineered for target gene correction, gene replacement, and gene knock-in. In this review, webriefly survey the history of the CRISPR/Cas9 systeminvention and its genome-editing mechanism. We also describe the most recent innovation of the CRISPR/ Cas9 technology, particularly the broad applications ofmodified Cas9 variants, and discuss the potential of this systemfor targeted genome editing and modification for crop improvement.
Analytical and numerical modeling for the effects of thermal insulation in underground tunnels

The heat flow generated from the infinite rock mass surrounding the underground tunnels is a major cause for the increasing cooling demands in deep mine tunnels. Insulation layers with lower thermal conductivities on tunnel walls and roof ceilings are believed to supply a thermo-barrier for heat abatement. However, it is found that no systematic theoretical investigations were made to predict and confirm the effectiveness of underground thermal insulation. Specifically, investigations on the underground insulation problems involving heat flows through the semi-infinite hot rock mass and insulation layer were not sufficient. Thus, in this paper, the thermal characteristics, accompanied with heat flow through the semi-infinite rock mass and the insulation layer, were modeled by both analytical and numerical methods with focus on underground mine tunnels. The close agreements between models have indicated that the thermal insulation applied on tunnel surfaces is able to provide promising heat abatement effects.
Analysis of microseismic activity in rock mass controlled by fault in deep metal mine

Aiming at evaluating the stability of a rock mass near a fault, a microseismic (MS) monitoring system was established in Hongtoushan copper mine. The distribution of displacement and log(EI), the relationship between MS activity and the exploitation process, and the stability of the rock mass controlled by a fault were studied. The results obtained from microseismic data showed that MS events were mainly concentrated at the footwall of the fault. When the distance to the fault exceeded 20 m, the rock mass reached a relatively stable state. MS activity is closely related to the mining process. Under the strong disturbance from blasting, the initiation and propagation of cracks is much faster. MS activity belongs in the category of aftershocks after large scale excavation. The displacement and log(EI) obtained from MS events can reflect the difference in physical and mechanical behavior of different areas within the rock mass, which is useful in judging the integrity and degradation of the rock mass.
Exploiting multi-channels deep convolutional neural networks for multivariate time series classification

Time series classification is related to many different domains, such as health informatics, finance, and bioinformatics. Due to its broad applications, researchers have developed many algorithms for this kind of tasks, e.g., multivariate time series classification. Among the classification algorithms, k-nearest neighbor (k-NN) classification(particularly 1-NN) combined with dynamic time warping(DTW) achieves the state of the art performance. The deficiency is that when the data set grows large, the time consumption of 1-NN with DTWwill be very expensive. In contrast to 1-NN with DTW, it is more efficient but less effective for feature-based classification methods since their performance usually depends on the quality of hand-crafted features. In this paper, we aim to improve the performance of traditional feature-based approaches through the feature learning techniques. Specifically, we propose a novel deep learning framework, multi-channels deep convolutional neural networks (MC-DCNN), for multivariate time series classification. This model first learns features from individual univariate time series in each channel, and combines information from all channels as feature representation at the final layer. Then, the learnt features are applied into a multilayer perceptron(MLP) for classification. Finally, the extensive experiments on real-world data sets show that our model is not only more efficient than the state of the art but also competitive in accuracy. This study implies that feature learning is worth to be investigated for the problem of time series classification.
Sequence of the main geochemical controls on the Cu and Zn fractions in the Yangtze River estuarine sediments

Metal speciation can provide sufficient information for environmental and geochemical researches. In this study, based on the speciation determination of Cu and Zn in the Yangtze Estuary sediments, roles of eight geochemical controls (i.e., total organic carbon (TOC), clay, Fe/Mn in five chemical fractions and salinity) are fully investigated and sequenced with correlation analysis (CA) and principal components analysis (PCA). Results show that TOC, clay and Fe/Mn oxides are key geochemical factors affecting the chemical speciation distributions of Cu and Zn in sediments, while the role of salinity appears to be more indirect effect. The influencing sequence generally follows the order: TOC> clay>Mn oxides>Fe oxides>salinity. Among the different fractions of Fe/Mn oxides, residual and total Fe content, and exchangeable and carbonate Mn exert the greatest influences, while exchangeable Fe and residual Mn show the poorest influences.
Expression of HIF-1α and Its Target Genes in the Nanorana parkeri Heart: Implications for High Altitude Adaptation

Hypoxia-inducible factor 1 alpha (HIF-1α) and its target genes vascular endothelial growth factor (VEGF) and transferrins (TF) play an important role in native endothermic animals' adaptation to the high altitude environments. For ectothermic animals – especially frogs – it remains undetermined whether HIF-1α and its target genes (VEGF and TF) play an important role in high altitude adaptation, too. In this study, we compared the gene sequences and expression of HIF-1α and its target genes (VEGF and TF) between three Nanorana parkeri populations from different altitudes (3008 m a.s.l., 3440 m a.s.l. and 4312 m a.s.l.). We observed that the cDNA sequences of HIF-1A exhibited high sequence similarity (99.38%) among the three altitudinally separated populations; but with increasing altitude, the expression of HIF-1A and its target genes (VEGF and TF) increased significantly. These results indicate that HIF-1α plays an important role in N. parkeri adaptation to the high altitude, similar to its role in endothermic animals.
Rock fragmentation control in opencast blasting

The blasting operation plays a pivotal role in the overall economics of opencast mines. The blasting subsystem affects all the other associated sub-systems, i.e. loading, transport, crushing and milling operations. Fragmentation control through effective blast design and its effect on productivity are the challenging tasks for practicing blasting engineer due to inadequate knowledge of actual explosive energy released in the borehole, varying initiation practice in blast design and its effect on explosive energy release characteristic. This paper describes the result of a systematic study on the impact of blast design parameters on rock fragmentation at three mines in India. The mines use draglines and shoveledumper combination for removal of overburden. Despite its pivotal role in controlling the overall economics of a mining operation, the expected blasting performance is often judged almost exclusively on the basis of poorly defined parameters such as powder factor and is often qualitative which results in very subjective assessment of blasting performance. Such an approach is very poor substitutes for accurate assessment of explosive and blasting performance. Ninety one blasts were conducted with varying blast designs and charging patterns, and their impacts on the rock fragmentation were documented. A high-speed camera was deployed to record the detonation sequences of the blasts. The efficiency of the loading machines was also correlated with the mean fragment size obtained from the fragmentation analyses.
The influence of jaw’s curvature on the results of the Brazilian disc test

The general contact problem of a disc squeezed between jaws of arbitrary curvature is considered employing Muskhelishvili’s complex potentials. Taking advantage of the general solution introduced, the closed-form expressions for the stresses along strategic loci (loaded rim, loaded diameter, disc’s center) are obtained, in terms of the ratio r of the disc’s to the jaw’s curvature. Then, the effect of r (as well as that of the relative stiffness of the disc’s and jaw’s materials dictating the contact arc) on the stress distribution along these loci is explored. It is concluded that, for both smooth contact (zero friction) and contact with friction, the role of the jaw’s curvature is significant not only along the disc-jaw contact arc (as it could be expected), but also all along the loaded diameter. On the other hand, it is indicated that the stress field at the disc’s center is more or less insensitive to the jaw’s curvature assuming that r lies within the range (0, 0.67) or in other words within the limits defined by the two standardized suggestions, i.e. that of American Society for Testing and Materials (ASTM) (plane loading platens with r = 0) and that of International Society for Rock Mechanics (ISRM) (curved jaws with r = 0.67). The upper limit of this range is a kind of compromise between the need to make the stress field at the disc’s center independent of the boundary conditions while keeping at the same time the contact angle large enough to reduce the stress concentration and the risk for premature fracture initiation far from the disc’s center. For jaws with radius of curvature exceeded by that suggested by ISRM, the stress field at the disc’s center is significantly influenced. Especially for jaws with radius approaching that of the disc, the stress field at the disc’s center is dramatically distorted rendering Hondros’ formula inapplicable and the test results erroneous.
Prediction and prevention of rockburst in metal mines - A case study of Sanshandao gold mine

Rockburst is a kind of artificial earthquake induced by human activities, such as mining excavations. The mechanism of rockburst induced by mining disturbance is revealed in terms of energy in this context. For understanding the rockburst mechanism, two necessary conditions for the occurrence of rockburst are presented: (1) the rock mass has the capability to store huge amount of energy and possesses a strong bumping-prone characteristic when damaged; and (2) the geological conditions in the mining area have favorable geo-stress environments that can form high-stress concentration area and accumulate huge energy. These two conditions are also the basic criteria for prediction of rockburst. In view of energy analysis, it is observed that artificial and natural earthquakes have similar regularities in many aspects, such as the relationship between the energy value and burst magnitude. By using the relationship between energy and magnitude of natural earthquake, rockburst is predicted by disturbance energy analysis. A practical example is illustrated using the above-mentioned theorem and technique to predict rockburst in a gold mine in China. Finally, the prevention and control techniques of rockburst are also provided based on the knowledge of the rockburst mechanism.
Effects of polydopamine modification on self-grown CuO cube anodes in lithium-ion batteries

We report the synthesis of CuO cubes with well-defined size and shape by thermal treatments of Cu2O cubes. Polydopamine (PDA) is introduced to modify the CuO cubes by the in-situ polymerization of the dopamine precursor. The initial specific capacity of the lithium-ion batteries using the CuO cubes as anodes increases about 10 times at a 0.5 C rate as a result of the modification of PDA. The overall specific capacity for 100 cycles also increases effectively due to the introduction of PDA. So PDA as surface modifying agent significantly improves the electrochemical performance of the CuO anodes.
Effect of total phosphorous pollution on cavitation pressure characteristics of working water used in turbines

Many experiments have proven that with increasing silt and gas (out-of-phase media) content in water, the cavitation characteristics change and the cavitation pressure increases. Currently, many large reservoirs in China are polluted by total phosphorus (TP) and other chemical contaminants because of the use of phosphate fertilizer runoff from agriculture. However, research regarding how chemical pollutants (in the form of out-of-phase media) affect the cavitation pressure characteristics of water is sparse. In this paper, the Goupitan Hydropower Station, the largest hydropower reservoir on the Wujiang River, which is heavily polluted by TP, is taken as an example to evaluate the effects of chemical pollution on water cavitation pressure characteristics. In this study, the cavitation pressure characteristics of polluted and clean water are compared. The results show that the cavitation pressure of water polluted by chemicals is larger than that of clean water. In a hydraulic power generation system, cavitation and cavitation erosion are likely to occur earlier in runners when the fluid is polluted. These results are of great importance to further studies of cavitation theory and can directly influence the arrangement of turbines in practical engineering.
Numerical simulation of the separation between concrete face slabs and cushion layer of Zipingpu dam during the Wenchuan earthquake

The Zipingpu concrete-faced rockfill dam (CFRD) experienced strong ground motion from the 2008 Wenchuan earthquake. Separation between concrete face slabs and the cushion layer was observed after the earthquake. The separation voids under the stage III slabs make up 55% of the total area of the stage III slabs. The observed maximum height of the separation voids was nearly 23 cm at the top of the stage III slabs. Separation voids were also observed locally below the top of stage II slabs near the left abutment, with a maximum height of 7 cm. In this study, a static and dynamic elasto-plastic finite element analysis on Zipingpu CFRD was conducted to capture the separation during the Wenchuan earthquake. The rockfill materials were described using a state-dependent elasto-plastic model that considered particle breakage. The model parameters of rockfill materials were obtained from feedback analysis. The numerical results were largely consistent with the field measurements during construction and after the Wenchuan earthquake. A three-dimensional state-dependent elasto-plastic model that can trace the separation and re-contact of a soil-structure interface was employed to investigate the interaction between concrete face slabs and a cushion layer. The analysis showed the distribution of separation voids observed in the Zipingpu CFRD has a close relationship to the water level and slab dislocations at the time of the earthquake. The phenomenon of the separation from the Wenchuan earthquake was successfully captured by the proposed numerical procedure.
Earliest fossil fruit record of the genus Paliurus (Rhamnaceae) in Eastern Asia

The genus Paliurus is characterized by its distinctive orbicular-winged fruits and a trilocular (or bilocular) ovary. Macrofossil records suggested this genus was distributed widely in North America, Europe, and Asia during the Paleogene and Neogene, before its present limitation to Eurasia. In this study, we describe some Paliurus fossil winged fruits from the lower part of Youganwo Formation (middle Eocene) and Huangniuling Formation (late Eocene) of the Maoming Basin, South China. These fruits are recognized as Paliurus favonii Unger based on a detailed study on the fossil morphology and cuticle characteristics. This represents the earliest occurrence of Paliurus fossil fruits in eastern Asia, and to date is the world’s lowest latitude appearance for this genus. The most ancient records of Paliurus throughout the world are from the middle Eocene of North America and the late Eocene of Japan, leading some researchers to conclude the Paliurus may have originated in North America. Molecular data, however, do not support this hypothesis. The present Paliurus fossil fruits provide new evidence for the origin and phytogeographic history of this genus.
Variability features of the width of the tropical belt from COSMIC radio occultation data

In this work, we analyzed time-series and trends of the tropical belt edges and widths with three methods based on the tropopause using new global positioning system radio occultation (GPS RO) data from the Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC) mission for September 2006-February 2014. The results from the three methods agreed well with previous studies and new features were found. To avoid the El Nino Southern Oscillation (ENSO) and Quasi-Biennial Oscillation (QBO) influence, we applied a simple multiple linear regression model to the monthly anomalies to obtain the tropical belt edges and width trends. During the study, we found equatorward movements of the tropical belt edges on both hemispheres. The narrowing of the tropical belt mainly occurred in the Pacific Ocean. We also found that the deseasonalized monthly anomalies of the tropical belt width were closely related with the ENSO and QBO. The tropical belt at a height of 15 km was mostly closely related with the ENSO. The correlations between the QBO and the tropical belt were consistent for the three methods.
Sand dunes as potential sources of dust in northern China

While saltation bombardment of sand grains on a fine substrate can produce considerable dust, the well-sorted nature of sand dunes tends to preclude them from consideration as major dust sources. Recent research, however, has revealed that sand dunes can, in some cases, be large sources of dust. We used the PI-SWERL (Portable In-Situ Wind Erosion Laboratory) to measure in the field the potential of sand dunes and other desert landforms to emit particulate matter <10 μm (PM-10) dust in the Tengger, Ulan Buh, and Mu Us deserts of northern China. Combined with high resolution particle size measurements of the dune sand, an assessment of sand dunes as a dust source can be made. Large active transverse dunes tend to contain little to no stored PM-10, yet they produce a low dust flux. Coppice dunes stabilized by vegetation contain appreciable PM-10 and have very high dust emission potential. There is a positive correlation between the amount of PM-10 stored in a dune and its potential dust flux. Saltation liberates loose fines stored in dunes, making them very efficient dust emitters compared to landforms such as dry lake beds and washes where dust particles are unavailable for aeolian transport due to protective crusts or sediment cohesion. In cases where large dunes do not store PM-10 yet emit dust when active, two hypotheses can be considered: (1) iron-oxide grain coatings are removed during saltation, creating dust, and (2) sand grains collide during saltation, abrading grains to create dust. Observations reveal that iron oxide coatings are present on some dune sands. PI-SWERL data suggests that low dust fluxes from dunes containing no stored dust may represent an estimate for the amount of PM-10 dust produced by removal of iron oxide coatings. These results are similar to results from dunes in the United States. In addition, PI-SWERL results suggest that dust-bearing coppice dunes, which cover vast areas of China’s sandy deserts, may become major sources of dust in the future if overgrazing, depletion of groundwater, or drought destabilizes the vegetation that now partially covers these dunes.