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A proton therapy facility with two 360° gantry treatment rooms and one fixed beamline is under development in the Huazhong University of Science and Technology, which is based on the isochronous superconducting cyclotron scheme. This paper presents the beam optics and main magnetic elements including dipoles, quadrupoles, and fast scanning magnets of the gantry beamline. In addition, the energy selection system will be introduced, which enables fast energy modulation of proton beam between 70 and 240 MeV.

Gene loss following whole genome duplication (WGD) is often biased, with one subgenome retaining more ancestral genes and the other sustaining more gene deletions. While bias toward the greater expression of gene copies on one subgenome can explain bias in gene loss, this raises the question to what drives differences in gene expression levels between subgenomes. Differences in chromatin modifications and epigenetic markers between subgenomes in several model species are now being identified, providing an explanation for bias in gene expression between subgenomes. WGDs can be classified into duplications with higher, biased gene loss and bias in gene expression between subgenomes versus those with lower, unbiased rates of gene loss and an absence of detectable bias between subgenomes; however, the originally proposed link between these two classes and whether WGD results from an allo- or autopolyploid event is inconsistent with recent data from the allopolyploid Capsella bursa-pastoris. The gene balance hypothesis can explain bias in the functional categories of genes retained following WGD, the difference in gene loss rates between unbiased and biased WGDs, and how plant genomes have avoided being overrun with genes encoding dose-sensitive subunits of multiprotein complexes. Comparisons of gene expression patterns between retained transcription factor pairs in maize suggest the high degree of retention for WGD-derived pairs of transcription factors may instead be explained by the older duplication-degeneration-complementation model.

A proton therapy project HUST-PTF (HUST Proton Therapy Facility) based on a 250 MeV isochronous superconducting cyclotron is under development in Huazhong University of Science and Technology (HUST). In this paper we report the main design features of the beam line in HUST-PTF project. The energy selection system (ESS) for energy modulation is discussed in detail, including the collimators, momentum slit and transmission calculation. Due to significant difference among the transmissions of ESS for different energies, the intensity suppression scheme by defocusing beam at high energies on collimators in the beam line is proposed and discussed. Finally, the ratios of beam intensities between low and high energies are expected to be controlled within 10 to meet the clinical requirement, and the beam optics of each energy step after intensity suppression is studied respectively.

The reduction behavior of a low iron grade with high SiO2 content ore–coal composite was investigated in the temperature range of 1143 K to 1263 K (870 °C to 990 °C). Sodium chloride was chosen as an additive to promote this reduction process. The effect of the sodium chloride addition and its mechanism was also investigated. Results showed that the added sodium chloride could enhance the reduction of wustite to iron due to the decrease of fayalite, and a higher metallization ratio of reduced sample was obtained. Thermogravimetric–differential scanning calorimeter analysis showed that sodium chloride could greatly facilitate the gasification process of coal and, thus, provide sufficient carbon monoxide to the reduction process of iron oxides. Meanwhile, sodium chloride promoted the reduction process of iron ore pellets directly as the coal gasification effect was excluded. Microstructures of reduced sample revealed that sodium chloride broke the structure of ore and enhanced the growth of newly formed iron particles. As the ore–coal composite with mol (C/Fe = 1.4) and 3 mass pct sodium chloride addition was roasted at 1233 K (960 °C) for 55 minutes, a reduced sample with metallization ration of 74.45 pct could be obtained.

Proton therapy is now recognized as one of the most effective radiation therapy methods for cancers. A proton therapy facility with multiple gantry treatment rooms is under development in HUST (Huazhong University of Science and Technology), which is based on isochronous superconducting cyclotron scheme. In the beam line, the scanning system spreads out the proton beam on the target according to the complex tumour shape by two scanning magnets for horizontal and vertical scanning independently. Since these two magnets are excited by alternating currents and the maximum repetition frequency is up to 100 Hz, eddy currents and losses are expected to be significant. Slits are proven to be an effective way to reduce the eddy currents. To evaluate the heat distribution due to eddy losses in the pole end of the scanning magnet, the transient electromagnetic analysis and steady-state thermal analysis are performed. This paper describes design considerations of the scanning system and mainly analyses the eddy current effect of the scanning magnets. Different coil shapes and slit arrangements are simulated and compared to obtain the optimal configuration. The maximum temperatures of two magnets are optimized below 70 °C. In addition, the lag effect due to eddy currents is also discussed.

The disintegration behavior and mechanism of iron ore pellet in simulated shaft furnace conditions were investigated in details. Effects of temperature, reducing gas and gangue compositions were emphatically discussed. It was found that pellet disintegrated acutely as reduced by H2/CO = 0.8 at 550 °C. Gangue minerals in pellet were proved to ease the disintegration in various degrees. SiO2 or CaO could remarkably lower reduction disintegration index (RDI). But the effect of MgO or Al2O3 was much weaker. Furthermore, intrinsic relation between disintegration and reduction was revealed from microstructure aspect. Results demonstrated that lattice transition stress and crack generation brought about by the low temperature reduction led to pellet structure failure and therefore disintegration. The reduction degree showed positive correlation with disintegration level of pellet. Low melting point phase formed by SiO2 or CaO lessened crack formation in pellet. However, MgO or Al2O3 could not play a similar role.

Purpose Proton therapy is a precise radiation cancer treatment with low side effects. To reduce the cost and footprint of the facility, the superconducting gantry with large momentum acceptance becomes a potential solution. Benefit from this feature, beam delivery time depends largely on the energy-switching process and short time is helpful for increasing the number of volume repaintings. Methods This note introduces an energy degrader with lightweight moving parts and a new hybrid structure (wedge-block-block). The total energies are separated into three stages and are degraded at fixed rates in two boron carbide blocks. As only one pair of graphite wedges is used for energy modulation, the energy switching at each step reaches a 10 ms level. Results The transport process in the degrader was simulated in TOPAS. After the degradation, the maximum energy spread ( 1 σ ) was approximately 5.5 % , and the distance between successive energy layers can be increased for treating non-sensitive tissues. Six configurations of the hybrid degrader achieved distinctly higher transmission efficiencies than the usual graphite multi-wedge degrader. Finally, the configuration that maximized the beam transmission in the lower-energy range (namely, the W– B 1 – B 2 configuration) was chosen as the degrader. Conclusions This new degrader not only improved the transmission efficiency, but also reduced the energy-switching time by virtue of its light and compact structure.

The HUST-PTF (proton therapy facility in Huazhong University of Science and Technology) is now under construction based on an isochronous superconducting cyclotron at Huazhong University of Science and Technology. Because the energy extracted by the cyclotron is fixed, an energy degrader is necessary to modulate the beam energy after the cyclotron for clinical requirements. However, the multiple Coulomb scattering that occurs in the degrader increases the beam emittance. Therefore, collimators are designed after the degrader to decrease the beam emittance. Because of the severe beam losses in the aforementioned energy degradation and emittance restriction, the main design consideration is improving the beam transmission efficiency. In this note, a novel energy degrader made of B

Advances in genomic sequencing and annotation have make identifying genes straightforward. Predicting the functions of these newly identified genes remains challenging. Often function is predicted from homology. Genes descended from a common ancestral sequence are likely to have common functions. Functional annotation errors can propagate from one species to another. Here we test approaches based on machine learning classification algorithms to predict gene function -- specifically 1,562 GO terms -- from non-homology gene features. Performance varied across GO terms, but, of eight supervised classification algorithms evaluated, random forest based prediction consistently provided the most accurate gene function prediction. Nonhomology-based functional annotation provides complementary strengths to homology-based annotation, with higher average performance among Biological Process GO terms, where homology based functional annotation performs the worst, and weaker performance among Molecular Function GO terms while the accuracy of homology-based functional annotation is highest. Further improvements in prediction accuracy may be possible using annotation provenance to generate higher confidence training datasets and the incorporation of more non-homology feature types. Machine learning non-homology based functional annotation may ultimately prove useful both as a method to assign predicted function to orphan genes which lack functionally characterized homologs, and to identify and correct functional annotation errors propagated through homology-based functional annotations.

Organic matter (OM) pores are significant for shale gas accumulation and flow mechanisms. The pores of Wufeng-Longmaxi (W-L) shale in the Sichuan Basin, China have been extensively characterized, however, the proportion of OM pores in this shale have not been adequately discussed. In this study, the contribution of OM pores to the total pore volume of W-L shale was quantitatively studied through the analysis of OM isolation, field emission scanning electron microscopy (FE-SEM) and low-pressure CO2 and N2 adsorption (LPGA). FE-SEM images showed abundant OM pores, interparticle pores and intraparticle pores with various shapes and widths in the W-L shales. The pore size distribution (PSD) of the isolated OM from five shale samples showed a consistent, unimodal pattern. The pore volume of isolated OM was greater than that of the bulk shale samples, suggesting that OM is more porous than the inorganic compositions in shales. The average contribution of OM to the volumes of micropores, mesopores and macropores was 58.42%, 10.34% and 10.72%, respectively. Therefore, the pore volume of the W-L shale was dominantly related to inorganic minerals. This was probably due to the small weight ratio of OM in the shale samples (1.5 wt%–4.2 wt%). The findings of this study reveal the different effects of OM and minerals on pore development, and provide new insights into the quantitative contribution of OM pores to the total pore volume of the W-L shale.

A one way reproductive barrier exists between most popcorn varieties and dent corn varieties grown in the United States. This barrier is predominantly controlled by thega1locus. Using data from a diverse population of popcorn accessions pollinated by a dent corn tester, we found that the non-reciprocal pollination barrier conferred byga1is more complex than previously described. Individual accessions ranged from 0% to 100% compatible with dent corn pollen. Using conventional genotyping-by-sequencing data from 371 popcorn accessions carryingGa1-s, seven significant modifiers of dent pollen compatibility were identified on five chromosomes. One locus may either be a nonfunctionalga1allele present within popcorn, or second necessary gene for the reproductive barrier in genetic linkage withga1, while the other modifiers are clearly genetically unlinked. The existence ofga1modifiers segregating in a popcorn genetic background may indicate selective pressure to allow gene flow between populations, which should be incorporated into future models of the impact of genetic incompatibility loci on gene flow in natural and agricultural plant populations.

The Lower Cretaceous Shahezi shales are the targets for lacustrine shale gas exploration in Changling Fault Depression (CFD), Southern Songliao Basin. In this study, the Shahezi shales were investigated to further understand the impacts of rock compositions, including organic matters and minerals on pore structure and fractal characteristics. An integrated experiment procedure, including total organic carbon (TOC) content, X-ray diffraction (XRD), field emission-scanning electron microscope (FE-SEM), low pressure nitrogen physisorption (LPNP), and mercury intrusion capillary pressure (MICP), was conducted. Seven lithofacies can be identified according to on a mineralogy-based classification scheme for shales. Inorganic mineral hosted pores are the most abundant pore type, while relatively few organic matter (OM) pores are observed in FE-SEM images of the Shahezi shales. Multimodal pore size distribution characteristics were shown in pore width ranges of 0.5&ndash, 0.9 nm, 3&ndash, 6 nm, and 10&ndash, 40 nm. The primary controlling factors for pore structure in Shahezi shales are clay minerals rather than OM. Organic-medium mixed shale (OMMS) has the highest total pore volumes (0.0353 mL/g), followed by organic-rich mixed shale (ORMS) (0.02369 mL/g), while the organic-poor shale (OPS) has the lowest pore volumes of 0.0122 mL/g. Fractal dimensions D1 and D2 (at relative pressures of 0&ndash, 0.5 and 0.5&ndash, 1 of LPNP isotherms) were obtained using the Frenkel&ndash, Halsey&ndash, Hill (FHH) method, with D1 ranging from 2.0336 to 2.5957, and D2 between 2.5779 and 2.8821. Fractal dimensions are associated with specific lithofacies, because each lithofacies has a distinctive composition. Organic-medium argillaceous shale (OMAS), rich in clay, have comparatively high fractal dimension D1. In addition, organic-medium argillaceous shale (ORAS), rich in TOC, have comparatively high fractal dimension D2. OPS shale contains more siliceous and less TOC, with the lowest D1 and D2. Factor analysis indicates that clay contents is the most significant factor controlling the fractal dimensions of the lacustrine Shahezi shale.

High quality direct reduced iron (DRI) plays a fundamental role in determining the functional properties of high-quality steel. DRI powder with a metallization ratio of 82.82% was obtained by reduction-grinding separation of low-grade iron ore, and iron resource was recycled (recovery ratio: 87.96%). However, a serious reoxidation phenomenon occurs in the grinding system, which is also a common problem in extraction metallurgy based on this process. Therefore, a combined experimental and computational study was executed to investigate the reoxidation. Phase evolution analysis shows that Fe0 in bulk iron particles mainly shift to Fe2+ during the grinding process, while Fe3+ are the main valence state on the nano-surface, indicating the reoxidation occurs via diffusion from the nano-surface to the interior. The cleavage surfaces (Fe100/110) occurred in grinding process are more easily to form Fe O ionic bonds with O2, especially when surface defects appear, as calculated by DFT. Further, the deeper iron atoms are more exposed after the defected iron surfaces combine with O2, greatly increasing contact opportunities of Fe O2. Therefore, the reduction time should be appropriately extended to decrease the surface defects of new iron, and other wet ball mills should be selected for the treatment of DRI produced by this process.

In many eukaryotic species the organismal functions of only a small fraction of annotated genes are supported by individual genetic characterization. The organismal functions of a somewhat larger, but still strict minority, of gene models are supported by quantitative genetic analyses (e.g. GWAS). However the organismal functions of the vast majority of gene models are not supported by any direct evidence. Genes characterized by direct investigation exhibit a set of molecular, structural, population genetic, and evolutionary features which distinguish these genes from other gene models. Weaker versions of the same signatures are present among genes identified through conventional quantitative genetics approaches. A new multi-trait multi-SNP association test, the Genome-Phenome Wide Association Study (GPWAS) combines data from large sets of traits and dense resequencing data to identify that set of genes significantly associated with phenotypic variation \textit{per se}. Genes identified using GPWAS and data for 260 phenotypic traits scored across a maize (\textit{Zea mays}) exhibit many of the same molecular, structural, population genetic, and evolutionary signals indicative of genes with functions characterized by direct genetic investigation. The strength of these signals is significantly higher for genes identified using GPWAS than genes identified through conventional GWAS. These results were consistent with a large subset of annotated gene models in maize play little or no role in determining organismal phenotypes. GPWAS and future similar analytical approaches that leverage data from multiple correlated and uncorrelated traits across the same population may provide a method to prioritize those genes most involved in regulation phenotypic variation across diverse species.

In this work, research of reduction process was studied by means of rotary kiln (φ1.5 m × 15 m) process anatomy in order to provide fine guidance to large-scale operation. It was shown that the average reduction degree of 89.96% and metallization ratio of 85.15% were obtained at the highest temperature of 977 °C and total residence time of 90 min. The generation amount of metallic iron in section of temperature higher than 900 °C and lower than 900 °C was 34.15 and 56.38%, respectively. The section of lower temperature of 830–900 °C played an important role in formation of metallic iron, making it possible for mini-pellet to reduce quickly at lower temperature. Two main tasks were completed for mini-pellets in rotary kiln: the reduction of iron oxides in the range of 15.0–4.5 m as well as migration and beneficiation of metallic iron, facilitating the subsequent separation of iron and gangue minerals.

In the present paper, beneficiation of Fe and Mn elements from a ferruginous manganese ore via carbothermic reduction followed by magnetic separation process was investigated in detail. The effects of the experimental parameters were systematically discussed. Iron-rich products with an Fe grade of 62.3% and 88.2% of Fe recovery, and manganese-rich product with a Mn grade of 63.7% of and 70.4% of Mn recovery were obtained, respectively, at an optimal temperature of 1100 °C, with a roasting time of 100 min, anthracite addition of 25%, milling fineness of 90% passing 0.074 mm, and a magnetic intensity of 140 A/m. Furthermore, the morphology evolution and phase transformation laws along with reduction process were revealed by optical microscope, scanning electron microscope equipped with energy dispersive X-ray detector (SEM-EDX), X-ray diffraction (XRD), and chemical phase analysis. The results demonstrated that the ferruginous manganese ore reduction can be described as follows: plate-like Fe-Mn symbiotic phase decomposition → granular MnO phase formation → fine metallic iron formation → aggregation of metallic iron → boundary development between Fe and Mn phases.

Maize (Zea mays ssp. mays) is one of three crops, along with rice and wheat, responsible for more than 1/2 of all calories consumed around the world. Increasing the yield and stress tolerance of these crops is essential to meet the growing need for food. The cost and speed of plant phenotyping is currently the largest constraint on plant breeding efforts. Datasets linking new types of high throughput phenotyping data collected from plants to the performance of the same genotypes under agronomic conditions across a wide range of environments are essential for developing new statistical approaches and computer vision based tools. A set of maize inbreds – primarily recently off patent lines – were phenotyped using a high throughput platform at University of Nebraska-Lincoln. These lines have been previously subjected to high density genotyping, and scored for a core set of 13 phenotypes in field trials across 13 North American states in two years by the Genomes to Fields consortium. A total of 485 GB of image data including RGB, hyperspectral, fluorescence and thermal infrared photos has been released. Correlations between image-based measurements and manual measurements demonstrated the feasibility of quantifying variation in plant architecture using image data. However, naive approaches to measuring traits such as biomass can introduce nonrandom measurement errors confounded with genotype variation. Analysis of hyperspectral image data demonstrated unique signatures from stem tissue. Integrating heritable phenotypes from high-throughput phenotyping data with field data from different environments can reveal previously unknown factors influencing yield plasticity.

One method for identifying noncoding regulatory regions of a genome is to quantify rates of divergence between related species, as functional sequence will generally diverge more slowly. Most approaches to identifying these conserved noncoding sequences (CNS) based on alignment have had relatively large minimum sequence lengths (⩾15 base pair) compared to the average length of known transcription factor binding sites. To circumvent this constraint, STAG-CNS integrates data from the promoters of conserved orthologous genes in three or more species simultaneously. Using data from up to six grass species made it possible to identify conserved sequences as short at 9 base pairs with FDP ⩽ 0.05. These CNS exhibit greater overlap with open chromatin regions identified using DNase I hypersensitivity, and are enriched in the promoters of genes involved in transcriptional regulation. STAG-CNS was further employed to characterize loss of conserved noncoding sequences associated with retained duplicate genes from the ancient maize polyploidy. Genes with fewer retained CNS show lower overall expression, although this bias is more apparent in samples of complex organ systems containing many cell types, suggesting CNS loss may correspond to a reduced number of expression contexts rather than lower expression levels across the entire ancestral expression domain.

Pore connectivity of lacustrine shales was inadequately documented in previous papers. In this work, lacustrine shales from the lower Cretaceous Shahezi Formation in the Changling Fault Depression (CFD) were investigated using field emission scanning electron microscopy (FE-SEM), mercury intrusion capillary pressure (MICP), low pressure gas (CO2 and N2) sorption (LPGA) and spontaneous fluid imbibition (SFI) experiments. The results show that pores observed from FE-SEM images are primarily interparticle (interP) pores in clay minerals and organic matter (OM) pores. The dominant pore width obtained from LPGA and MICP data is in the range of 0.3&ndash, 0.7 nm and 3&ndash, 20 nm. The slopes of n-decane and deionized (DI) water SFI are in the range of 0.34&ndash, 0.55 and 0.22&ndash, 0.38, respectively, suggesting a mixed wetting nature and better-connected hydrophobic pores than hydrophilic pores in the Shahezi shales. Low pore connectivity is identified by the dominant nano-size pore widths (0.3&ndash, 20 nm), low DI water SFI slopes (around 0.25), high geometric tortuosity (4.75&ndash, 8.89) and effective tortuosity (1212&ndash, 6122). Pore connectivity follows the order of calcareous shale &gt, argillaceous shale &gt, siliceous shale. The connected pores of Shahezi shales is mainly affected by the high abundance and coexistence of OM pores and clay, carbonate minerals host pores.

Background Nitrogen (N) is an essential and often limiting nutrient to plant growth and development. Previous studies have shown that the mRNA expressions of numerous genes are regulated by nitrogen supplies; however, little is known about the expressed non-coding elements, for example long non-coding RNAs (lncRNAs) that control the response of maize (Zea mays L.) to nitrogen. LncRNAs are a class of non-coding RNAs larger than 200 bp, which have emerged as key regulators in gene expression. Results In this study, we surveyed the intergenic/intronic lncRNAs in maize B73 leaves at the V7 stage under conditions of N-deficiency and N-sufficiency using ribosomal RNA depletion and ultra-deep total RNA sequencing approaches. By integration with mRNA expression profiles and physiological evaluations, 7245 lncRNAs and 637 nitrogen-responsive lncRNAs were identified that exhibited unique expression patterns. Co-expression network analysis showed that the nitrogen-responsive lncRNAs were enriched mainly in one of the three co-expressed modules. The genes in the enriched module are mainly involved in NADH dehydrogenase activity, oxidative phosphorylation and the nitrogen compounds metabolic process. Conclusions We identified a large number of lncRNAs in maize and illustrated their potential regulatory roles in response to N stress. The results lay the foundation for further in-depth understanding of the molecular mechanisms of lncRNAs’ role in response to nitrogen stresses. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2650-1) contains supplementary material, which is available to authorized users.