A Multi-Variate framework to assess reliability and discrimination power of Bayesian estimation of Intravoxel Incoherent Motion parameters.

PURPOSE: To propose a multivariate multi-step framework for a systematic assessment of the estimation reliability and discriminability of Intravoxel Incoherent Motion (IVIM) model parameters. METHODS: Monte-Carlo simulations were generated on a range of SNRs and in different IVIM combinations considering: i) a dense discretization with 24 b-values; ii) a discretization with 9 b-values. A state-of-the-art Bayesian fitting method was adopted. The framework assessed: i) the best model between mono- and bi-exponential, through the BIC index; ii) the fitting accuracy; iii) the power in discriminating two different IVIM parameters distributions of estimated coefficients, using a multivariate test. Exemplificative oncologic cases were also presented. RESULTS: The bi-exponential fitting was reliable for perfusion fraction higher than 5%, with high accuracy in D estimation, acceptable error for f, but high uncertainty in D*. The discrimination of two distributions is generally feasible if differences in D values (at least 0.3 x10-3 mm2/s) are present; in the case of similar D values, a minimal difference of 5% in f can be discriminated just in case of balanced sample size and dense b-values discretization, whereas the impact of D* is quite negligible. These results were also supported by clinical examples. CONCLUSIONS: IVIM model is generally accurate in estimating diffusion, but uncertainties related to perfusion estimation are not negligible and compromise the discrimination power when different populations should be differentiated. The proposed framework should be adopted as interpretative guidelines to better understand when IVIM model applied on real data can provide reliable findings.

Noncoding RNA.

Regulatory RNAs, present in many bacterial genomes and particularly in pathogenic bacteria such as Staphylococcus aureus, control the expression of genes encoding virulence factors or metabolic proteins. They are extremely diverse and include noncoding RNAs (sRNA), antisense RNAs, and some 5' or 3' untranslated regions of messenger RNAs that act as sensors for metabolites, tRNAs, or environmental conditions (e.g., temperature, pH). In this review we focus on specific examples of sRNAs of S. aureus that illustrate how numerous sRNAs and associated proteins are embedded in complex networks of regulation. In addition, we discuss the CRISPR-Cas systems defined as an RNA-interference-like mechanism, which also exist in staphylococcal strains.

[A glimpse on Staphylococcus aureus translation machinery and its control].

Staphylococcus aureus is a major opportunistic and versatile pathogen. Because the bacteria rapidly evolve multi-resistances towards antibiotics, there is an urgent need to find novel targets and alternative strategies to cure bacterial infections. Here, we provide a brief overview on the knowledge acquired on S. aureus ribosomes, which is one of the major antibiotic targets. We will show that subtle differences exist between the translation at the initiation step of Gram-negative and Gram-positive bacteria although their ribosomes display a remarkable degree of resemblance. In addition, we will illustrate using specific examples the diversity of mechanisms controlling translation initiation in S. aureus that contribute to shape the expression of the virulence factors in a temporal and dynamic manner.

Severe psychosocial deprivation in early childhood is associated with increased DNA methylation across a region spanning the transcription start site of CYP2E1.

Exposure to adverse rearing environments including institutional deprivation and severe childhood abuse is associated with an increased risk for mental and physical health problems across the lifespan. Although the mechanisms mediating these effects are not known, recent work in rodent models suggests that epigenetic processes may be involved. We studied the impact of severe early-life adversity on epigenetic variation in a sample of adolescents adopted from the severely depriving orphanages of the Romanian communist era in the 1980s. We quantified buccal cell DNA methylation at ~400 000 sites across the genome in Romanian adoptees exposed to either extended (6-43 months; n=16) or limited duration (<6 months; n=17) of severe early-life deprivation, in addition to a matched sample of UK adoptees (n=16) not exposed to severe deprivation. Although no probe-wise differences remained significant after controlling for the number of probes tested, we identified an exposure-associated differentially methylated region (DMR) spanning nine sequential CpG sites in the promoter-regulatory region of the cytochrome P450 2E1 gene (CYP2E1) on chromosome 10 (corrected P=2.98 × 10(-5)). Elevated DNA methylation across this region was also associated with deprivation-related clinical markers of impaired social cognition. Our data suggest that environmental insults of sufficient biological impact during early development are associated with long-lasting epigenetic changes, potentially reflecting a biological mechanism linking the effects of early-life adversity to cognitive and neurobiological phenotypes.

Survival prognostic factors in patients with glioblastoma: our experience.

AIM: Approximate survival for glioblastoma is less than 1 year. Age, histological features and performance status at presentation represent the three statistically independent factors affecting longevity. The purpose of the study was to assess the role of surgery and to analyze prognostic factors in our patients operated for glioblastoma. METHODS: We evaluated in 56 patients operated for glioblastoma their depressive and performance status in the preoperative and postoperative time. Moreover we analyzed the extent of surgery, the site and the size of lesions. RESULTS: Median overall survival was 17 months. An age of ≥60 years (P<0.03), a preoperative Karnofsky Performance Status KPS≤70 (P=0.04), a subtotal tumor resection (P<0.001), a tumor size >5 cm (P=0.01), and no postoperative adjuvant treatment (P=0.01) were associated with the worst prognosis. Before surgery we found the presence of depression in 10 patients with a significative reduction of mean Back Depression Inventory scores after tumor resection (P=0.03). Finally, a KPS≤70 was significantly associated with an increased incidence of depression in the postoperative time. CONCLUSION: Tumor size, total resection and affective disorders were identified as predictors of survival in our series of patients with glioblastoma in addition to age and KPS score. In our opinion an early diagnosis and the use of specific safeguards in the operating room contribute to have an extension of the tumor progression time and median survival.

Quantitative analysis of elastography images in the detection of breast cancer.

PURPOSE: The aim of this study was to develop a quantitative method for breast cancer diagnosis based on elastosonography images in order to reduce whenever possible unnecessary biopsies. The proposed method was validated by correlating the results of quantitative analysis with the diagnosis assessed by histopathologic exam. MATERIAL AND METHODS: 109 images of breast lesions (50 benign and 59 malignant) were acquired with the traditional B-mode technique and with elastographic modality. Images in Digital Imaging and COmmunications in Medicine format (DICOM) were exported into a software, written in Visual Basic, especially developed to perform this study. The lesion was contoured and the mean grey value and softness inside the region of interest (ROI) were calculated. The correlations between variables were investigated and receiver operating characteristic (ROC) curve analysis was performed to assess the diagnostic accuracy of the proposed method. Pathologic results were used as standard reference. RESULTS: Both the mean grey value and the softness inside the ROI resulted statistically different at the t test for the two populations of lesions (i.e., benign versus malignant): p<0.0001. The area under the curve (AUC) was 0.924 (0.834-0.973) and 0.917 (0.826-0.970) for the mean grey value and for the softness respectively. CONCLUSIONS: Quantitative elastosonography is a promising ultrasound technique in the detection of breast cancer but large prospective trials are necessary to determine whether quantitative analysis of images can help to overcome some pitfalls of the methodic.

Less invasive approaches for the treatment of cervical schwannomas: our experience.

PURPOSE: The purpose of our paper is to illustrate our experience with minimally invasive approaches for the treatment of cervical schwannomas. Moreover, a brief review of the literature was conducted. METHODS: All data regarding patients treated for cervical schwannomas were retrospectively revised. Site, size and extension of the lesions and preoperative neurological status were obtained through re-examination of neuroimaging and clinical records. Postoperative clinical examinations and radiological images were available for all patients. The clinical course was documented using the visual analog scale (VAS), Karnofsky score (KPS) and the Klekamp-Samii score system. RESULTS: Sixteen patients harboring cervical schwannomas were treated from 2003 to 2009. Hemilaminectomy was performed in eight cases, subtotal hemilaminectomy in four cases, interlaminar fenestration in two cases, osteoplastic hemilaminotomy and laminoplasty in one case each. Postoperative neuroimaging revealed complete removal of the lesion and no signs of spinal instability. At discharge, neurological improvement was observed in 14 patients and all patients demonstrated reduction of VAS score and improvement of KPS and Klekamp-Samii's score. CONCLUSIONS: Minimal access procedures are increasingly gaining popularity but their use is poorly described in the treatment of cervical tumors. Less invasive approaches may effectively be used instead of traditional laminectomy in the treatment of cervical tumors, especially schwannomas, providing less iatrogenic traumatism and preventing postsurgical spinal instability. Modern neuroimaging allows adequate preoperative planning and microsurgical techniques provide adequate execution of the surgical act. The procedure has to be tailored case by case considering the specific lesional features and the individual anatomical situation.

RNA mimicry, a decoy for regulatory proteins.

Small non-coding RNA molecules (sRNA) are key regulators participating in complex networks, which adapt metabolism in response to environmental changes. In this issue of Molecular Microbiology, and in a related paper in Proc. Natl. Acad. Sci. USA, Moreno et al. (2011) and Sonnleitner et al. (2009) report on novel sRNAs, which act as decoys to inhibit the activity of the master post-transcriptional regulatory protein Crc. Crc is a key protein involved in carbon catabolite repression that optimizes metabolism improving the adaptation of the bacteria to their diverse habitats. Crc is a novel RNA-binding protein that regulates translation of multiple target mRNAs. Two regulatory sRNAs in Pseudomonas putida mimic the natural mRNA targets of Crc and counteract the action of Crc by sequestrating the protein when catabolite repression is absent. Crc trapping by a sRNA is a mechanism reminiscent to the regulation of the repressor of secondary metabolites (RsmA) in Pseudomonas, and highlights the suitability of RNA-dependent regulation to rapidly adjust cell growth in response to environmental changes.

Anatomical and dose changes of gross tumour volume and parotid glands for head and neck cancer patients during intensity-modulated radiotherapy: effect on the probability of xerostomia incidence.

AIMS: To quantify the changes in dose as well as in the prediction of parotid gland toxicity due to anatomical changes during therapy of head and neck cancer patients. MATERIALS AND METHODS: Fifteen patients with advanced locoregional head and neck cancer, with no evidence of distant metastasis, were enrolled in a prospective study. All patients were treated with intensity-modulated radiotherapy. Multiple computed tomography scans were repeated at the end of each treatment week. The original treatment plans were copied to the per-treatment scans to create hybrid plans. The normal tissue complication probability (NTCP) was calculated assuming the end point to be grade ≥3 xerostomia according to the Radiation Therapy Oncology Group late toxicity scale. RESULTS: The gross tumour volume dose coverage was slightly affected by the anatomical changes, whereas the mean dose (D(mean)) to the parotids changed from 26.1 ± 6.0 to 27.4 ± 7.4 Gy, with a mean increase of 0.22 Gy/treatment week. Consequently, the mean NTCP increased from 0.15 ± 0.06 to 0.18 ± 0.10, primarily due to a few patients exhibiting a marked increase. The absolute gross tumour volume shrinkage and the percentage parotids shrinkage were the best independent predictors for the NTCP variations. CONCLUSIONS: On average, the increase in the parotids D(mean) as well as in NTCP during treatment is limited, and the observed variations were strongly patient-dependent.

A structural view of translation initiation in bacteria.

The assembly of the protein synthesis machinery occurs during translation initiation. In bacteria, this process involves the binding of messenger RNA(mRNA) start site and fMet-tRNA(fMet) to the ribosome, which results in the formation of the first codon-anticodon interaction and sets the reading frame for the decoding of the mRNA. This interaction takes place in the peptidyl site of the 30S ribosomal subunit and is controlled by the initiation factors IF1, IF2 and IF3 to form the 30S initiation complex. The binding of the 50S subunit and the ejection of the IFs mark the irreversible transition to the elongation phase. Visualization of these ligands on the ribosome has been achieved by cryo-electron microscopy and X-ray crystallography studies, which has helped to understand the mechanism of translation initiation at the molecular level. Conformational changes associated with different functional states provide a dynamic view of the initiation process and of its regulation.

Single fraction partial breast irradiation in prone position.

The purpose of this work is to introduce a new treatment approach and technique for partial breast irradiation in only one session to patients in prone position by using a dedicated positioning device. The patients were treated on a home-made treatment table top that allows the breast to hang down. A particular immobilization system was introduced in order to assure the reproducibility of patient positioning between the CT acquisition session and the treatment session. The clinical target volume (CTV) was outlined according to surgical clips position and/or tumor location on preoperative mammography. Because of negligible movement due to respiration, only an additional margin of 3 mm was added to obtain the planning target volume (PTV). Based on radiobiological calculations, a dose of 21 Gy was prescribed to PTV. The tumor bed was treated with 3D-CRT technique by using 5 fields and rotating the table while the gantry was approximately 90 or 270 degrees. Thirty patients were enrolled for this study chosen in conformity to an approved clinical protocol. The average percentage of PTV volume enclosed in the 90% and 95% of prescribed dose were 99.9 and 98.6% respectively, while only 3.4% of PTV volume received more than 105% of prescribed dose. Dose to 3% of skin volume was, on average, 15.2 Gy. In 97% of patients, less than 50% of the ipsilateral breast received a dose greater than half the prescribed dose. Mean doses to lungs, heart and contralateral breast were negligible. With a median follow-up of 9 months, no important early toxicity was observed both for skin and breast tissue. The treatment of breast tumor bed in prone position in only one session by using the 3D-CRT is technically feasible and seems to be a promising alternative to other accelerated partial breast irradiation techniques.

Comparison of dose distributions in IMRT planning using the gamma function.

Intensity-modulated radiotherapy (IMRT) (1) is an advanced form of 3-D conformal radiotherapy. It uses non uniform spatial modifications in the intensity of the beams across the irradiated field. Consequently, it is necessary to develop sophisticated tools to compare measured and calculated dose distributions in order to verify the accuracy of the results of the planned dose distribution. Different methods have been developed to evaluate the accordance between measured and calculated doses, such as the point-to-point dose difference or the evaluation of the distance between two closed points having the same dose value (2-4). The verification method proposed by Low (5-7) seems to be more complete since it takes into account both the dose difference (DD) and the distance to agreement (DTA), allowing to define a "score", the gamma value, at each point of interest. A software tool (DDE: Dose Distribution Evaluator), based on Low's method, to evaluate the agreement between dose distribution matrices has been implemented. In particular, the proposed gamma curve, as a function of the isodose levels, gives real-time information useful for decision making about the treatment plan. The paper describes the software, and reports the obtained results in a simple geometry and in several clinical cases (head-neck and prostate). Comparison between measured data (film and MapCheck) and calculated data (CadPlan) using DDE has shown very good agreements. Thanks to its higher resolution, film dosimetry showed better accuracy than the MapCheck technique. Similar results can be obtained also with the MapCheck technique when proper measurement methods are used.

Estudio de la IORT para la búsqueda de dosis tras la prostactetomía radical (PR) en el cáncer de próstata / A dose-finding study of IORT after radical prostatectomy (RP) in prostate cancer

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MRS study of the interaction of dihydropyridines with lipid molecules in phosphatidylcholine vesicles.

Dihydropyridines (DHPs), synthetic molecules used as antihypertensive agents, bind to plasma membrane receptors following diffusion through the hydrophobic phase. In this study, MRS technique has been used to clarify the interactions of the dihydrophyridines Nifedipine and Lacidipine within the lipid bilayer. 1D and 2D 1H MRS at high field have been employed to examine the behavior of unilamellar dimyristoyl-phosphatidylcholine liposomes when the two drugs have been inserted in the bilayer. In particular, the study represents an innovative application of 2D 1H NOESY technique to clarify different mechanisms of interactions of small molecules inside model membranes. On the other hand, 31P measurements have been performed in multilamellar dimyristoyl-phosphatidylcholine lipsomes to detect alterations of lipid polymorphic phases. The experiments show that the two dihydropyridines interact with the lipids by different modalities. Lacidipine undergoes a very strong interaction with lipids, possibly inducing a phase segregation of lipid molecules into the bilayer, while self-association seems to be the prevalent interaction of Nifedipine inside the bilayer.

Optimization of intensity modulated radiation therapy: assessing the complexity of the problem.

Intensity modulated radiation therapy (IMRT) is one of the most innovative techniques in oncological radiotherapy, allowing to conform the dose delivery to the tumoral target, preserving the normal tissue. The high number of parameters involved in the IMRT treatment planning requires an automated approach to the beam modulation. Such optimization process consists in the search of the global minimum of a cost function representing a quality index for the treatment. The complexity of this task, has been analyzed with a statistical approach for three clinical cases of particular interest in IMRT. Our main result is that a cost function based on dose-volume constraints entails lower complexity of the optimization process, in terms of the choice of the parameters defining the cost function and in a smaller sensitivity to the initial conditions for the optimization algorithm.