66 research outputs found
Automatic Segmentation, Localization, and Identification of Vertebrae in 3D CT Images Using Cascaded Convolutional Neural Networks
This paper presents a method for automatic segmentation, localization, and
identification of vertebrae in arbitrary 3D CT images. Many previous works do
not perform the three tasks simultaneously even though requiring a priori
knowledge of which part of the anatomy is visible in the 3D CT images. Our
method tackles all these tasks in a single multi-stage framework without any
assumptions. In the first stage, we train a 3D Fully Convolutional Networks to
find the bounding boxes of the cervical, thoracic, and lumbar vertebrae. In the
second stage, we train an iterative 3D Fully Convolutional Networks to segment
individual vertebrae in the bounding box. The input to the second networks have
an auxiliary channel in addition to the 3D CT images. Given the segmented
vertebra regions in the auxiliary channel, the networks output the next
vertebra. The proposed method is evaluated in terms of segmentation,
localization, and identification accuracy with two public datasets of 15 3D CT
images from the MICCAI CSI 2014 workshop challenge and 302 3D CT images with
various pathologies introduced in [1]. Our method achieved a mean Dice score of
96%, a mean localization error of 8.3 mm, and a mean identification rate of
84%. In summary, our method achieved better performance than all existing works
in all the three metrics
Improving biomass production and saccharification in Brachypodium distachyon through overexpression of a sucrose-phosphate synthase from sugarcane
The substitution of fossil by renewable energy sources is a major strategy in reducing CO2 emission and mitigating climate change. In the transport sector, which is still mainly dependent on liquid fuels, the production of second generation ethanol from lignocellulosic feedstock is a promising strategy to substitute fossil fuels. The main prerequisites on designated crops for increased biomass production are high biomass yield and optimized saccharification for subsequent use in fermentation processes. We tried to address these traits by the overexpression of a sucrose-phosphate synthase gene (SoSPS) from sugarcane (Saccharum officinarum) in the model grass Brachypodium distachyon. The resulting transgenic B. distachyon lines not only revealed increased plant height at early growth stages but also higher biomass yield from fully senesced plants, which was increased up to 52Β % compared to wild-type. Additionally, we determined higher sucrose content in senesced leaf biomass from the transgenic lines, which correlated with improved biomass saccharification after conventional thermo-chemical pretreatment and enzymatic hydrolysis. Combining increased biomass production and saccharification efficiency in the generated B. distachyon SoSPS overexpression lines, we obtained a maximum of 74Β % increase in glucose release per plant compared to wild-type. Therefore, we consider SoSPS overexpression as a promising approach in molecular breeding of energy crops for optimizing yields of biomass and its utilization in second generation biofuel production
Downregulation of Cinnamyl-Alcohol Dehydrogenase in Switchgrass by RNA Silencing Results in Enhanced Glucose Release after Cellulase Treatment
Cinnamyl alcohol dehydrogenase (CAD) catalyzes the last step in monolignol biosynthesis and genetic evidence indicates CAD deficiency in grasses both decreases overall lignin, alters lignin structure and increases enzymatic recovery of sugars. To ascertain the effect of CAD downregulation in switchgrass, RNA mediated silencing of CAD was induced through Agrobacterium mediated transformation of cv. βAlamoβ with an inverted repeat construct containing a fragment derived from the coding sequence of PviCAD2. The resulting primary transformants accumulated less CAD RNA transcript and protein than control transformants and were demonstrated to be stably transformed with between 1 and 5 copies of the T-DNA. CAD activity against coniferaldehyde, and sinapaldehyde in stems of silenced lines was significantly reduced as was overall lignin and cutin. Glucose release from ground samples pretreated with ammonium hydroxide and digested with cellulases was greater than in control transformants. When stained with the lignin and cutin specific stain phloroglucinol-HCl the staining intensity of one line indicated greater incorporation of hydroxycinnamyl aldehydes in the lignin
Exploring the Switchgrass Transcriptome Using Second-Generation Sequencing Technology
Background: Switchgrass (Panicum virgatum L.) is a C4 perennial grass and widely popular as an important bioenergy crop. To accelerate the pace of developing high yielding switchgrass cultivars adapted to diverse environmental niches, the generation of genomic resources for this plant is necessary. The large genome size and polyploid nature of switchgrass makes whole genome sequencing a daunting task even with current technologies. Exploring the transcriptional landscape using next generation sequencing technologies provides a viable alternative to whole genome sequencing in switchgrass. Principal Findings: Switchgrass cDNA libraries from germinating seedlings, emerging tillers, flowers, and dormant seeds were sequenced using Roche 454 GS-FLX Titanium technology, generating 980,000 reads with an average read length of 367 bp. De novo assembly generated 243,600 contigs with an average length of 535 bp. Using the foxtail millet genome as a reference greatly improved the assembly and annotation of switchgrass ESTs. Comparative analysis of the 454-derived switchgrass EST reads with other sequenced monocots including Brachypodium, sorghum, rice and maize indicated a 70β 80 % overlap. RPKM analysis demonstrated unique transcriptional signatures of the four tissues analyzed in this study. More than 24,000 ESTs were identified in the dormant seed library. In silico analysis indicated that there are more than 2000 EST-SSRs in this collection. Expression of several orphan ESTs was confirmed by RT-PCR. Significance: We estimate that about 90 % of the switchgrass gene space has been covered in this analysis. This study nearl
Ultrasonic Pretreatment of Wheat Straw in Oxidative and Nonoxidative Conditions Aided with Microwave Heating
Molecular Cloning and Sequencing of AlkalophilicCellulosimicrobium cellulans CKMX1 Xylanase Gene Isolated from Mushroom Compost and Characterization of the Gene Product
Enhanced characteristics of genetically modified switchgrass (Panicum virgatum L.) for high biofuel production
A multiple species approach to biomass production from native herbaceous perennial feedstocks
Phenytoin as an effective treatment for polymorphic ventricular tachycardia due to QT prolongation in a patient with multiple drug intolerances
Radical skeletal metastatic site irradiation in high-risk neuroblastoma: systematic review and proposal for a randomised trial: a report from the SIOPEN Radiotherapy Committee
Aim: Neuroblastoma has a variable outcome depending on age, stage, and molecular pathology. Distant metastatic disease is the central feature of high-risk disease. Recommendations for irradiating persistent metastatic deposits with curative intent after systemic therapy vary. It is unclear to what extent this practice may improve local control or survival. This study systematically reviewed the evidence for skeletal metastatic site irradiation and made evidence-based recommendations for clinical practice.Methods: We systematically reviewed the literature on radical radiotherapy of persistent metastases after chemotherapy. The aim was to determine whether a position could be taken regarding metastatic site irradiation in combined modality treatment protocols aiming for a cure and whether recommendations could be formulated.Results: The initial search yielded 445 results. After the title and abstract review, 13 full papers were retrieved. Ten papers were found suitable for data extraction. One additional paper was identified. All 11 were graded as Centre for Evidence-Based Medicine Step 4 in quality; there was no high-level evidence. There are suggestions of benefit for skeletal site irradiation in high-risk neuroblastoma; however, there is no certainty, and it was not possible to recommend a particular treatment policy.Conclusion: We recommend that consideration is given to a randomised evaluation of the benefits of radiotherapy to a limited number of residual post-induction-chemotherapy metastatic sites in good responders. This practice could be incorporated as an amendment to existing trials
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