食用菌栽培种类野生种质的评价

我国是食用菌野生种质资源丰富的国家,目前已查明自然分布可栽培野生种类93种,分布于担子菌的33个属。我国人工栽培种类近70种（变种）,不同规模栽培有50种,商业规模栽培33种,分布于5目,12科,18属。与绿色植物的自养型光合作用合成有机物质相反,食用菌将植物光合作用合成的有机物分解,以体壁吸收方式摄取营养建造自身。这种生理特点的不同,导致其种质资源评价要求的不同。由于子实体形态相对于绿色植物简单,且易受环境条件的影响,常常导致以形态特征为主要依据进行分类鉴定陷入困境。另一方面,形态相似的多个可栽培近缘种在侧耳（Pleurotus）、木耳（Auricularia）、蜜环菌（Armillaria）等中广泛存在,完全靠形态特征进行分类鉴定就更加困难。因此,在食用菌可栽培种类野生种质评价中,ITS测序等成为获得菌种生物学种的常用鉴定技术。菌种的分离培养中常受到菌落形态相似真菌的污染,RAPD、ISSR或ITS测序等常用来进行菌种符合性鉴定。食用菌孢子传播的特点,使其分布地理区域广泛,地理区域的隔离产生种内的个体或群体间的差异,形成种群的多样性,常用拮抗反应进行营养亲和群（个体、菌株）的鉴定。不同区域气候和生态条件下的个体,长期的进化和对环境条件适应性的形成,导致可栽培利用的特点不同。栽培性状要通过栽培试验进行评价。栽培性状主要包括菌丝长速、温度反应、结实性、丰产性、抗性、商品形态和耐贮运性等。为了充分利用远缘优势,对于具可利用栽培性状的种质还需要与栽培菌株间的遗传距离分析,通常用生物化学和分子生物学方法进行。     

Recent European measurements inside Biorack

The dosimetric package used inside Biorack on board STS76, STS81 and STS84 comprises passive detector stacks built from plastic nuclear track detectors (PNTDs), thermoluminescence detectors (TLDs) and one or two active DOSTEL (DOSimetric TELescope) units using planar silicon detectors. Five passive detector stacks were exposed at different places inside the BIORACK incubators and in different stowage positions. DOSTEL units were exposed inside the 22 degrees C incubator in all flights. Mission integrated dose measurements, particle fluence rates and neutron doses are obtained from the passive detector stacks. These results are complemented by time resolved particle counts and dose rates and linear energy transfer (LET) spectra separately for the contribution of the trapped particles and the galactic cosmic rays (GCR) as a result of the DOSTEL measurements. In addition, it was possible to investigate the anisotropy of the radiation field inside Biorack by the use of a second DOSTEL unit on STS84. Since all exposures are during a solar minimum period, the total radiation exposure is of a similar extent for all flights, although position differences in dose rate up to a factor of two are observed. Particle fluence rates show lower variations. Mission averaged mean quality factors (Q) determined from the LET spectra are 2.0+/-0.1; the deduced dose equivalent rates range from 631 to 716 microSv/day.     

Signal peptide prediction based on analysis of experimentally verified cleavage sites

A number of computational tools are available for detecting signal peptides, but their abilities to locate the signal peptide cleavage sites vary significantly and are often less than satisfactory. We characterized a set of 270 secreted recombinant human proteins by automated Edman analysis and used the verified cleavage sites to evaluate the success rate of a number of computational prediction programs. An examination of the frequency of amino acid in the N-terminal region of the data set showed a preference of proline and glutamine but a bias against tyrosine. The data set was compared to the SWISS-PROT database and revealed a high percentage of discrepancies with cleavage site annotations that were computationally generated. The best program for predicting signal sequences was found to be SignalP 2.0-NN with an accuracy of 78.1% for cleavage site recognition. The new data set can be utilized for refining prediction algorithms, and we have built an improved version of profile hidden Markov model for signal peptides based on the new data.     

Determining a maximum-tolerated schedule of a cytotoxic agent

Most phase I clinical trials are designed to determine a maximum-tolerated dose (MTD) for one initial administration or treatment course of a cytotoxic experimental agent. Toxicity usually is defined as the indicator of whether one or more particular adverse events occur within a short time period from the start of therapy. However, physicians often administer an agent to the patient repeatedly and monitor long-term toxicity due to cumulative effects. We propose a new method for such settings. It is based on the time to toxicity rather than a binary outcome, and the goal is to determine a maximum-tolerated schedule (MTS) rather than a conventional MTD. The model and method account for a patient's entire sequence of administrations, with the overall hazard of toxicity modeled as the sum of a sequence of hazards, each associated with one administration. Data monitoring and decision making are done continuously throughout the trial. We illustrate the method with an allogeneic bone marrow transplantation (BMT) trial to determine how long a recombinant human growth factor can be administered as prophylaxis for acute graft-versus-host disease (aGVHD), and we present a simulation study in the context of this trial.     

Screening of compounds toxicity against human Monocytic cell line-THP-1 by flow cytometry

The worldwide rapid increase in bacterial resistance to numerous antibiotics requires on-going development of new drugs to enter the market. As the development of new antibiotics is lengthy and costly, early monitoring of compound’s toxicity is essential in the development of novel agents. Our interest is in a rapid, simple, high throughput screening method to assess cytotoxicity induced by potential agents. Some intracellular pathogens, such as Mycobacterium tuberculosis primary site of infection is human alveolar macrophages. Thus, evaluation of candidate drugs for macrophage toxicity is crucial. Protocols for high throughput drug toxicity screening of macrophages using flow cytometry are lacking in the literature. For this application we modified a preexisting technique, propidium iodide (PI) exclusion staining and utilized it for rapid toxicity tests. Samples were prepared in 96 well plates and analyzed by flow cytometry, which allowed for rapid, inexpensive and precise assessment of compound’s toxicity associated with cell death. Published: October 1, 2004.     

Define dose field to assess the modulation complexity of intensity-modulated radiation therapy

PurposeIntroduce a new concept of dose field to assess the modulation complexity (MC) of intensity-modulated radiation therapy (IMRT).MethodsA total of 91 IMRT plans for different diseases were retrospectively retrieved randomly from treatment database. The dose field of plans were calculated and feature values such as force magnitude and diversity were defined and extracted. Correlation analysis between these feature values and execution cost, delivery accuracy of plans was performed, to verify the validity of dose field in characterizing the MC.ResultsThe feature values of dose field in different disease own significant differences (p < 0.001). For correlation analysis, number of control point (CP) and cumulative perimeter of CP have the highest correlation with angle entropy (0.815 and 0.848 respectively), while the correlation between number of monitor units(MU), cumulative area of CP and force, force entropy is higher than others (0.797–0.909). However, complexity of CP shape is almost irrelevant to all the dose field features. The gamma passing rate and the dose field features shows a weak negative correlation trend.ConclusionsDose field can be used as a tool to assess the MC of IMRT.     

Accuracy of dose calculation on iterative CBCT for head and neck radiotherapy

PurposeTo evaluate the feasibility of the use of iterative cone-beam computed tomography (CBCT) for dose calculation in the head and neck region.MethodsThis study includes phantom and clinical studies. All acquired CBCT images were reconstructed with Feldkamp–Davis–Kress algorithm-based CBCT (FDK-CBCT) and iterative CBCT (iCBCT) algorithm. The Hounsfield unit (HU) consistency between the head and body phantoms was determined in both reconstruction techniques. Volumetric modulated arc therapy (VMAT) plans were generated for 16 head and neck patients on a planning CT scan, and the doses were recalculated on FDK-CBCT and iCBCT with Anisotropic Analytical Algorithm (AAA) and Acuros XB (AXB). As a comparison of the accuracy of dose calculations, the absolute dosimetric difference and 1%/1 mm gamma passing rate analysis were analyzed.ResultsThe difference in the mean HU values between the head and body phantoms was larger for FDK-CBCT (max value: 449.1 HU) than iCBCT (260.0 HU). The median dosimetric difference from the planning CT were <1.0% for both FDK-CBCT and iCBCT but smaller differences were found with iCBCT (planning target volume D_50%: 0.38% (0.15–0.59%) for FDK-CBCT, 0.28% (0.13–0.49%) for iCBCT, AAA; 0.14% (0.04–0.19%) for FDK-CBCT, 0.07% (0.02–0.20%) for iCBCT). The mean gamma passing rate was significantly better in iCBCT than FDK-CBCT (AAA: 98.7% for FDK-CBCT, 99.4% for iCBCT; AXB: 96.8% for FDK_CBCT, 97.5% for iCBCT).ConclusionThe iCBCT-based dose calculation in VMAT for head and neck cancer was accurate compared to FDK-CBCT.     

Evaluation of alternative parameter settings for dose restoration and full plan adaptation in IMPT for prostate cancer

Background/purposeIntensity-modulated proton therapy is highly sensitive to anatomical variations. A dose restoration method and a full plan adaptation method have been developed earlier, both requiring several parameter settings. This study evaluates the validity of the previously selected settings by systematically comparing them to alternatives.Materials/methodsThe dose restoration method takes a prior plan and uses an energy-adaptation followed by a spot-intensity re-optimization to restore the plan to its initial state. The full adaptation method uses an energy-adaptation followed by the addition of new spots and a spot-intensity optimization to fit the new anatomy. We varied: 1) The margins and robustness settings of the prior plan, 2) the spot-addition sample size, i.e. the number of added spots, 3) the spot-addition stopping criterion, and 4) the spot-intensity optimization approach. The last three were evaluated only for the full plan adaptation. Evaluations were done on 88 CT scans of 11 prostate cancer patients. Dose was prescribed as 55 Gy(RBE) to the lymph nodes and seminal vesicles with a boost to 74 Gy(RBE) to the prostate.ResultsFor the dose restoration method, changing the applied CTV-to-PTV margins and plan robustness in the prior plans yielded insufficient target coverage or increased OAR doses. For the full plan adaptation, more spot-addition iterations and using a different optimization approach resulted in lower OAR doses compared to the default settings while maintaining target coverage. However, the calculation times increased by up to 20 times, making these variations infeasible for online-adaptation.ConclusionWe recommend maintaining the default setting for the dose restoration approach. For the full plan adaptation we recommend to focus on fine-tuning the optimization-parameters, and apart from this using the default settings.     

Dosimetric and radiation cancer risk evaluation of high resolution thorax CT during COVID-19 outbreak

PurposeThe aim of this work was to evaluate the dosimetric impact of high-resolution thorax CT during COVID-19 outbreak in the University Hospital of Parma. In two months we have performed a huge number of thorax CT scans collecting effective and equivalent organ doses and evaluating also the lifetime attributable risk (LAR) of lung and other major cancers.Materials and MethodFrom February 24th to April 28th, 3224 high-resolution thorax CT were acquired. For all patients we have examined the volumetric computed tomography dose index (CTDIvol), the dose length product (DLP), the size-specific dose estimate (SSDE) and effective dose (E₁₀₃) using a dose tracking software (Radimetrics Bayer HealthCare). From the equivalent dose to organs for each patient, LAR for lung and major cancers were estimated following the method proposed in BEIR VII which considers age and sex differences.ResultsStudy population included 3224 patients, 1843 male and 1381 female, with an average age of 67 years. The average CTDIvol, SSDE and DLP, and E₁₀₃ were 6.8 mGy, 8.7 mGy, 239 mGy·cm and 4.4 mSv respectively. The average LAR of all solid cancers was 2.1 cases per 10,000 patients, while the average LAR of leukemia was 0.2 cases per 10,000 patients. For both male and female the organ with a major cancer risk was lung.ConclusionsDespite the impressive increment in thoracic CT examinations due to COVID-19 outbreak, the high resolution low dose protocol used in our hospital guaranteed low doses and very low risk estimation in terms of LAR.     

Commissioning Monte Carlo algorithm for robotic radiosurgery using cylindrical 3D-array with variable density inserts

IntroductionTo commission the Monte Carlo (MC) algorithm based model of CyberKnife robotic stereotactic system (CK) and evaluate the feasibility of patient specific QA using the ArcCHECK cylindrical 3D-array (AC) with Multiplug inserts (MP).ResultsFour configurations were used for simple beam setup and two for patient QA, replacing water equivalent inserts by lung. For twelve collimators (5–60 mm) in simple setup, mean (SD) differences between MC and RayTracing algorithm (RT) of the number of points failing the 3%/1 mm gamma criteria were 1(1), 1(3), 1(2) and 1(2) for the four MP configurations. Tracking fiducials were placed within AC for patient QA. Single lung insert setup resulted in mean gamma-index 2%/2 mm of 90.5% (range [74.3–95.9]) and 82.3% ([66.8–94.5]) for MC and RT respectively, while 93.5% ([86.8–98.2]) and 86.2% ([68.7–95.4]) in presence of largest inhomogeneities, showing significant differences (p < 0.05).DiscussionAfter evaluating the potential effects, 1.12 g/cc PMMA and 0.09 g/cc lung material assignment showed the best results. Overall, MC-based model showed superior results compared to RT for simple and patient specific testing, using a 2%/2 mm criteria. Results are comparable with other reported commissionings for flattening filter free (FFF) delivery. Further improvement of MC calculation might be challenging as Multiplan has limited material library.ConclusionsThe AC with Multiplug allowed for comprehensive commissioning of CyberKnife MC algorithm and is useful for patient specific QA for stereotactic body radiation therapy. MC calculation accuracy might be limited due to Multiplan’s insufficient material library; still results are comparable with other reported commissioning measurements using FFF beams.