Quantification of image quality of intra-fractional cone-beam computed tomography for arc irradiation with various imaging condition

Background3-dimensional intra-cone beam computed tomography (intra-CBCT ) could be a potentially powerful tool for use with arc irradiation such as volumetric modulated arc therapy. The aim of the study was to evaluate the image quality of intra-cone beam computed tomography (intra-CBCT ) for arc irradiation with various imaging condition.Materials and methodsTwo types of intra-CBCT imaging techniques were evaluated — intra-fractional CBCT with flattening filtered (FF) beam (intra-FF CBCT ) and that with flattening filter free (FFF) beam (intra-FFF CBCT ). For the intra-MV beams, four different field sizes (2 cm × 2 cm, 5 cm × 5 cm, 10 cm × 10 cm, and 20 cm × 20 cm) were used with dose rates of 500 MU/min and 1600 MU/min, for 6 MV FF and 6 MV FFF, respectively. For all image acquisitions, two rotation angles (full-arc and half-arc) were investigated. Thereafter, the linearity, contrast-to-noise ratio (CNR), and uniformity index (UI) of intra-CBCT image were compared with those of conventional CBCT image.ResultsAll acquisition conditions had good linearity of the CT value (R² > 0.99). For CNR, the change rates from conventional CBCT ranged from 0.6–33.7% for a 2 cm × 2 cm beam, whereas that for a 20 cm × 20 cm beam ranged from 62.7–82.3%. Similarly, the UI increased from 1.5% to 7.0% as the field size increased.ConclusionQuality of intra-CBCT image was affected by the field size and acquisition angle. Image quality of intra-CBCT was worse than that of conventional CBCT, but it was better under a smaller field and wider correction angle and would be acceptable for clinical use.     

Identification and isolation of active N2O reducers in rice paddy soil

Dissolved N₂O is occasionally detected in surface and ground water in rice paddy fields, whereas little or no N₂O is emitted to the atmosphere above these fields. This indicates the occurrence of N₂O reduction in rice paddy fields; however, identity of the N₂O reducers is largely unknown. In this study, we employed both culture-dependent and culture-independent approaches to identify N₂O reducers in rice paddy soil. In a soil microcosm, N₂O and succinate were added as the electron acceptor and donor, respectively, for N₂O reduction. For the stable isotope probing (SIP) experiment, ¹³C-labeled succinate was used to identify succinate-assimilating microbes under N₂O-reducing conditions. DNA was extracted 24 h after incubation, and heavy and light DNA fractions were separated by density gradient ultracentrifugation. Denaturing gradient gel electrophoresis and clone library analysis targeting the 16S rRNA and the N₂O reductase gene were performed. For culture-dependent analysis, the microbes that elongated under N₂O-reducing conditions in the presence of cell-division inhibitors were individually captured by a micromanipulator and transferred to a low-nutrient medium. The N₂O-reducing ability of these strains was examined by gas chromatography/mass spectrometry. Results of the SIP analysis suggested that Burkholderiales and Rhodospirillales bacteria dominated the population under N₂O-reducing conditions, in contrast to the control sample (soil incubated with only ¹³C-succinate). Results of the single-cell isolation technique also indicated that the majority of the N₂O-reducing strains belonged to the genera Herbaspirillum (Burkholderiales) and Azospirillum (Rhodospirillales). In addition, Herbaspirillum strains reduced N₂O faster than Azospirillum strains. These results suggest that Herbaspirillum spp. may have an important role in N₂O reduction in rice paddy soils.     

Analysis of multiple compound–protein interactions reveals novel bioactive molecules

The discovery of novel bioactive molecules advances our systems‐level understanding of biological processes and is crucial for innovation in drug development. For this purpose, the emerging field of chemical genomics is currently focused on accumulating large assay data sets describing compound–protein interactions (CPIs). Although new target proteins for known drugs have recently been identified through mining of CPI databases, using these resources to identify novel ligands remains unexplored. Herein, we demonstrate that machine learning of multiple CPIs can not only assess drug polypharmacology but can also efficiently identify novel bioactive scaffold‐hopping compounds. Through a machine‐learning technique that uses multiple CPIs, we have successfully identified novel lead compounds for two pharmaceutically important protein families, G‐protein‐coupled receptors and protein kinases. These novel compounds were not identified by existing computational ligand‐screening methods in comparative studies. The results of this study indicate that data derived from chemical genomics can be highly useful for exploring chemical space, and this systems biology perspective could accelerate drug discovery processes.     

Assessment of willow (Salix sp.) as a woody heavy metal accumulator: field survey and in vivo X-ray analyses

Trees that accumulate metals are important plants for restoring contaminated soil because of their high biomass. In our previous study, we discovered that Salix miyabeana has the capability to take up high levels of Cd, and identified the several accumulation sites of the endogenous metals in the leaf parts of plants. To analyze the detailed localization of Cd in apoplastic and symplastic compartments in S. miyabeana, synchrotron radiation-based micro X-ray fluorescence (SR-μ-XRF) analysis and micro X-ray absorption near edge structure (μ-XANES) measurements were performed on beam line 37XU of the SPring-8 (Hyogo, Japan). The two-dimensional metal distribution of segments of young stems was obtained by μ-XRF with approximately 2 μm(2) X-ray beams and showed the predominant localization of Cd in the apoplastic region. μ-XANES analyses suggest that the apoplastic detoxification of Cd in willow depends on Cd-oxygen, but not on Cd-sulfur, interaction. S. miyabeana growing near an old mining site in Japan was then examined to evaluate the metal accumulating ability of this plant in the field. The metal concentration in the leaves of the plants was compared to that in the soil and enrichment factors (EFs) were calculated for Cu, Zn, Cd and Pb. Results showed efficient removal of Cd and Zn from the contaminated sites by the willow plants. In order to discuss the combined and long-term effect of multiple heavy metals on S. miyabeana grown in soil, variable-pressure scanning electron microscopy fitted with energy dispersive X-ray analysis (VPSEM-EDX) and SR-μ-XRF was used to characterize the serration of leaves. The combination of 2D elemental images revealed metal accumulation in the tip cells in serrations without any exudation of heavy metals from the hydathodes.     

Identification of treatment efficacy-related host factors in chronic hepatitis C by ProteinChip serum analysis

Recent development of proteomic array technology, including protein profiling coupling ProteinChip array with surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF/MS), provides a potentially powerful tool for discovery of new biomarkers by comparison of its profiles according to patient phenotypes. We used this approach to identify the host factors associated with treatment response in patients with chronic hepatitis C (CHC) receiving a 48-wk course of pegylated interferon (PEG-IFN) alpha 2b plus ribavirin (RBV). Protein profiles of pretreatment serum samples from 32 patients with genotype 1b and high viral load were conducted by SELDI-TOF/MS by using the three different ProteinChip arrays (CM10, Q10, IMAC30). Proteins showed significantly different peak intensities between sustained virological responders (SVRs), and non-SVRs were identified by chromatography, SDS-PAGE, TOF/MS and tandem mass spectrometry (MS/MS) assay. Eleven peak intensities were significantly different between SVRs and non-SVRs. The three SVR-increased peaks could be identified as two apolipoprotein (Apo) fragments and albumin and, among the eight non-SVR-increased proteins, four peaks identified as two iron-related and two fibrogenesis-related protein fragments, respectively. Multivariate analysis showed that the serum ferritin and three peak intensity values (Apo A1, hemopexin and transferrin) were independent variables associated with SVRs, and the area under the receiver operating characteristic (ROC) curves for SVR prediction by using the Apo A1/hemopexin and hemopexin/transferrin were 0.964 and 0.936. In conclusion, pretreatment serum protein profiling by SELDI-TOF/MS is variable for identification of response-related host factors, which are useful for treatment efficacy prediction in CHC receiving PEG-IFN plus RBV. Our data also may help us understand the mechanism for treatment resistance and development of more effective antiviral therapy targeted toward the modulation of lipogenesis or iron homeostasis in CHC patients.     

The perioperative granulocyte/lymphocyte ratio is a clinically relevant marker of surgical stress in patients with colorectal cancer

PurposeThis study was to assess the clinical relevance of the blood granulocytes to lymphocytes (G/L) ratio as an early marker of surgical stress in patients with colorectal cancer.MethodsThirty-three patients with colorectal cancer were prospectively to undergo laparoscopic-assisted (n = 12) or open (n = 21) surgical resection. Granulocyte and lymphocyte counts were used to calculate the G/L ratios in blood samples from all patients before the operation and post-operatively on days 1, 3 and 7. Additionally, serum inflammatory cytokines, interleukin (IL)-1β, IL-6, IL-8, tumour necrosis factor (TNF)-α, granulocyte colony-stimulating factor (G-CSF) and macrophage (M)-CSF were assayed as markers of surgical stress.ResultsSeven of 33 patients developed unexpected complications. Serum IL-6 (P < 0.0001), G-CSF (P = 0.0257), and M-CSF (P < 0.0001) were higher on day 1 vs before the operation. Similarly, the G/L ratios were higher on days 1–3 vs before the operation (P < 0.0001) and then gradually decreased together with the surgical stress levels. The G/L ratios and the numbers of granulocytes and lymphocytes in the blood showed no correlation with serum IL-1β or TNF-α. In contrast, the G/L ratios and the numbers of granulocytes in the blood showed significant correlation with IL-6 (Rs = 0.710, P < 0.0001, Rs = 0.653, P < 0.0001, respectively), with G-CSF (Rs = 0.626, P < 0.0001, Rs = 0.578, P < 0.0001), with M-CSF (Rs = 0.470, P < 0.0001, Rs = 0.372, P < 0.0001). However, the number of lymphocytes showed inverse correlation with IL-6 (Rs = ?0.493, P < 0.0001), G-CSF (Rs = ?0.440, P < 0.0001) and M-SCF (Rs = ?0.443, P < 0.0001).ConclusionThe G/L ratio appears to be a simple and clinically relevant parameter for the assessment of perioperative stress in patients undergoing colorectal surgery.     

Whole-genome sequencing of sake yeast Saccharomyces cerevisiae Kyokai no. 7

The term 'sake yeast' is generally used to indicate the Saccharomyces cerevisiae strains that possess characteristics distinct from others including the laboratory strain S288C and are well suited for sake brewery. Here, we report the draft whole-genome shotgun sequence of a commonly used diploid sake yeast strain, Kyokai no. 7 (K7). The assembled sequence of K7 was nearly identical to that of the S288C, except for several subtelomeric polymorphisms and two large inversions in K7. A survey of heterozygous bases between the homologous chromosomes revealed the presence of mosaic-like uneven distribution of heterozygosity in K7. The distribution patterns appeared to have resulted from repeated losses of heterozygosity in the ancestral lineage of K7. Analysis of genes revealed the presence of both K7-acquired and K7-lost genes, in addition to numerous others with segmentations and terminal discrepancies in comparison with those of S288C. The distribution of Ty element also largely differed in the two strains. Interestingly, two regions in chromosomes I and VII of S288C have apparently been replaced by Ty elements in K7. Sequence comparisons suggest that these gene conversions were caused by cDNA-mediated recombination of Ty elements. The present study advances our understanding of the functional and evolutionary genomics of the sake yeast.     

The N-terminal segment of Plasmodium falciparum SURFIN4.1 is required for its trafficking to the red blood cell cytosol through the endoplasmic reticulum

Plasmodium falciparum SURFIN is a type I transmembrane protein that shares domains with molecules expressed on the surface of the red blood cells (RBCs) infected with a variety of malaria parasite species, such as P. falciparum PfEMP1, Plasmodium vivax VIR proteins, and Plasmodium knowlesi SICAvar. Thus, understanding the export mechanism of SURFIN to the RBC may provide fundamental insights into how malaria parasites export their proteins to RBC cytosol in general. We re-evaluate SURFIN_4.1 for its exon–intron boundaries, location, and the function of each region by expressing recombinant SURFIN_4.1 in P. falciparum. We found that, in two 3D7 lines and one Thai isolate, SURFIN_4.1 possesses only 19 amino acids after the predicted transmembrane region, whereas in the FCR3 line, it possesses two tryptophan-rich domains in its intracellular region. Recombinant SURFIN_4.1 based on the 3D7 sequence was detected in the Maurer's clefts of infected RBCs, suggesting that endogenous SURFIN_4.1 is also exported to Maurer's clefts. Brefeldin A-sensitive export of SURFIN_4.1 indicates that its export is endoplasmic reticulum (ER)/Golgi-dependent. By sequential deletion and replacement with unrelated protein sequences, we find that the SURFIN_4.1 transmembrane region is essential for the initial recruitment of the protein to the ER, and the following sorting step to the parasitophorous vacuole is determined by two independent signals located in the N-terminus 50 amino acids. TM region with the adjacent cytoplasmic region also contains information for the efficient recruitment to the ER and/or for the efficient translocation across the parasitophorous vacuole membrane. We also found that SURFIN_4.1 might form a homomeric complex during the trafficking using cysteine rich domain and/or variable region.