Characterization of spatiotemporal chaos in a Kerr optical frequency comb and in all fiber cavities

Complex spatiotemporal dynamics have been a subject of recent experimental investigations in optical frequency comb microresonators and in driven fiber cavities with Kerr-type media. We show that this complex behavior has a spatiotemporal chaotic nature. We determine numerically the Lyapunov spectra, allowing us to characterize different dynamical behavior occurring in these simple devices. The Yorke-Kaplan dimension is used as an order parameter to characterize the bifurcation diagram. We identify a wide regime of parameters where the system exhibits a coexistence between the spatiotemporal chaos, the oscillatory localized structure, and the homogeneous steady state. The destabilization of an oscillatory localized state through radiation of counter-propagating fronts between the homogeneous and the spatiotemporal chaotic states is analyzed. To characterize better the spatiotemporal chaos, we estimate the front speed as a function of the pump intensity.

Extended and localized Hopf-Turing mixed-mode in non-instantaneous Kerr cavities

We investigate the spatio-temporal dynamics of a ring cavity filled with a non-instantaneous Kerr medium and driven by a coherent injected beam. We show the existence of a stable mixed-mode solution that can be either extended or localized in space. The mixed-mode solutions are obtained in a regime where Turing instability (often called modulational instability) interacts with self-pulsing phenomenon (Andronov-Hopf bifurcation). We numerically describe the transition from stationary inhomogeneous solutions to a branch of mixed-mode solutions. We characterize this transition by constructing the bifurcation diagram associated with these solutions. Finally, we show stable localized mixed-mode solutions, which consist of time-periodic oscillations that are localized in space.

Efficacy of trabectedin in malignant solitary fibrous tumors: a retrospective analysis from the French Sarcoma Group

Background

Advanced malignant solitary fibrous tumors (SFTs) are rare soft-tissue sarcomas with a poor prognosis. Several treatment options have been reported, but with uncertain rates of efficacy. Our aim is to describe the activity of trabectedin in a retrospective, multi-center French series of patients with SFTs.

Methods

Patients were mainly identified through the French RetrospectYon database and were treated between January 2008 and May 2013. Trabectedin was administered at an initial dose of 1.5 mg/m², q3 weeks. The best tumor response was assessed according to the Response Evaluation Criteria In Solid Tumors 1.1. The Kaplan–Meier method was used to estimate median progression-free survival (PFS) and overall survival (OS). The growth-modulation index (GMI) was defined as the ratio between the time to progression with trabectedin (TTP_n) and the TTP with the immediately prior line of treatment (TTP_n-1).

Results

Eleven patients treated with trabectedin for advanced SFT were identified. Trabectedin had been used as second-line treatment in 8 patients (72.7 %) and as at least third-line therapy in a further 3 (27.3 %). The best RECIST response was a partial response (PR) in one patient (9.1 %) and stable disease (SD) in eight patients (72.7 %). Disease-control rate (DCR = PR + SD) was 81.8 %. After a median follow-up of 29.2 months, the median PFS was 11.6 months (95 % CI = 2.0; 15.2 months) and the median OS was 22.3 months (95 % CI = 9.1 months; not reached). The median GMI was 1.49 (range: 0.11–4.12).

Conclusion

Trabectedin is a very promising treatment for advanced SFTs. Further investigations are needed.

First-line treatment with sunitinib for type 1 and type 2 locally advanced or metastatic papillary renal cell carcinoma: a phase II study (SUPAP) by the French Genitourinary Group (GETUG)†

BACKGROUND

Papillary renal cell carcinoma (PRCC), type 1 and type 2, represents 10%-15% of renal cell carcinomas (RCC). There is no standard first-line treatment of metastatic PRCC (mPRCC). Anti-angiogenics have shown activity in retrospective studies but no prospective studies in pure papillary histology have been reported, but one with foretinib.

PATIENTS AND METHODS

A prospective phase II study evaluated sunitinib in first-line treatment of mPRCC. The primary end point was overall response rate (ORR). Secondary end points were progression-free survival (PFS) and overall survival (OS).

RESULTS

Fifteen and 46 patients, respectively, with type 1 and type 2 mPRCC were enrolled. Using the MSKCC scoring system: 12 (20%), 33 (55%) and 9 (15%) patients were, respectively, in the favourable, intermediate or poor risk group and 7 undetermined. Median follow-up is 51.4 months. In type 1, 2 patients 13% [95% confidence interval (CI) 0.1-30.5] had a partial response (PR), 10 had stable disease (SD) with 5 (33%) ≥12 weeks. In type 2, 5 patients 11% (95% CI 1.9-20.3) had a PR, 25 had SD with 10(22%) ≥12 weeks. Median PFS was 6.6 months (95% CI 2.8-14.8) in type 1 and 5.5 months (95% CI 3.8-7.1) in type 2. Median OS was 17.8 (95% CI 5.7-26.1) and 12.4 (95% CI 8.2-14.3) months, respectively, in type 1 and 2. Safety was as expected with sunitinib for metastatic RCC.

CONCLUSION

Sunitinib showed activity in treatment of type 1 and 2 mPRCC but lower than in clear-cell mRCC. Both PFS and OS are longer in type I PRCC. Sunitinib represents an acceptable option in first-line treatment of mPRCC.

[A prospective trial comparing consecutive series of open retropubic and robot-assisted laparoscopic radical prostatectomy in a centre: Oncologic and functional outcomes]

OBJECTIVE

Radical prostatectomy (RP) is an oncologic and functional challenge. Few series compare prospectively the two approaches, open retropubic (ORP) and laparoscopic robot-assisted RP (LRARP). The objective was to compare the oncological and functional results of ORP and LRARP.

MATERIAL AND METHODS

From January 2009 to March 2012, two practiced surgeons conducted 304 consecutive RP: respectively 129 ORP and 175 LRARP. Preoperative, perioperative and postoperative data (location and size of positive surgical margins [PSM]) were recorded prospectively and compared with oncological results (PSM, biochemical recurrence-free survival [BCR]) and functional outcomes (urinary and erectile) by self-validated questionnaires (USP, IIEF-15). The comparison was made by the Chi(2) test and Student t-test for qualitative and quantitative variables.

RESULTS

The preoperative data 2 groups were comparable. MCP rate was 13.2% for the ORP and 20% for the LRARP (ns) and was 1.4% and 29.6% (ORP) versus 9.4% and 36.7% (LRARP) for pT2 and pT3 for respectively (P=0.078). BCR was the same in both groups (95.2% at 13.1 months). At 12 months, the results of continence showed no difference (P=0.49) and about erectile function, the EF-score was significantly higher in LRARP: 22 versus 17 for the ORP (P=0.03).

CONCLUSION

Oncological results were comparable after ORP and LRARP. The recovery of continence was excellent regardless of the surgical technique, the recovery of erectile function a bit faster by LRARP.

LEVEL OF EVIDENCE

3.

Effect on survival of local ablative treatment of metastases from sarcomas: a study of the French sarcoma group

AIMS

Recent data suggest that patients with pulmonary metastases from sarcomas might benefit from ablation of their metastases. Some data are available regarding osteosarcomas/angiosarcomas and lung metastases. The purpose of this study was to assess the efficacy of local ablative treatment on the survival of patients with oligometastases (one to five lesions, any metastatic site, any grade/histology) from sarcomas.

MATERIALS AND METHODS

A multicentric retrospective study of the French Sarcoma Group was conducted in sarcoma patients with oligometastases who were treated between 2000 and 2012. Survival was analysed using multivariate sensitivity analyses with propensity scores to limit bias.

RESULTS

Of the 281 patients evaluated, 164 patients received local treatment for oligometastases between 2000 and 2012. The groups' characteristics were similar in terms of tumour size and remission of the primary tumours. The median follow-up was 25.7 months; 129 (45.9%) patients had died at this point. The median overall survivals were 45.3 (95% confidence interval = 34-73) months for the local treatment group and 12.6 for the other group (95% confidence interval = 9.33-22.9). Survival was better among patients who received local treatment (hazard ratio = 0.47; 95% confidence interval = 0.29-0.78; P < 0.001). Subgroup analyses revealed similar findings in the patients with single oligometastases (hazard ratio = 0.48; 95% confidence interval = 0.28-0.82; P = 0.007); a significant benefit was observed for grade 3, and a trend was observed for grade 2.

CONCLUSION

Local ablative treatment seemed to improve the overall survival of the patients who presented with oligometastatic sarcomas, including soft tissue and bone sarcomas. The survival benefit remained after repeated local treatments for several oligometastatic events. Surgery yielded the most relevant results, but alternative approaches (i.e. radiofrequency ablation and radiotherapy) seemed to be promising. The relevance of these results is strengthened by our analysis, which avoided biases by restricting the population to patients with oligometastatic disease and used propensity scores.

Guidelines for time-to-event end point definitions in sarcomas and gastrointestinal stromal tumors (GIST) trials: results of the DATECAN initiative (Definition for the Assessment of Time-to-event Endpoints in CANcer trials)†

BACKGROUND

The use of potential surrogate end points for overall survival, such as disease-free survival (DFS) or time-to-treatment failure (TTF) is increasingly common in randomized controlled trials (RCTs) in cancer. However, the definition of time-to-event (TTE) end points is rarely precise and lacks uniformity across trials. End point definition can impact trial results by affecting estimation of treatment effect and statistical power. The DATECAN initiative (Definition for the Assessment of Time-to-event End points in CANcer trials) aims to provide recommendations for definitions of TTE end points. We report guidelines for RCT in sarcomas and gastrointestinal stromal tumors (GIST).

METHODS

We first carried out a literature review to identify TTE end points (primary or secondary) reported in publications of RCT. An international multidisciplinary panel of experts proposed recommendations for the definitions of these end points. Recommendations were developed through a validated consensus method formalizing the degree of agreement among experts.

RESULTS

Recommended guidelines for the definition of TTE end points commonly used in RCT for sarcomas and GIST are provided for adjuvant and metastatic settings, including DFS, TTF, time to progression and others.

CONCLUSION

Use of standardized definitions should facilitate comparison of trials' results, and improve the quality of trial design and reporting. These guidelines could be of particular interest to research scientists involved in the design, conduct, reporting or assessment of RCT such as investigators, statisticians, reviewers, editors or regulatory authorities.

PALETTE: A randomized, double-blind, phase III trial of pazopanib versus placebo in patients (pts) with soft-tissue sarcoma (STS) whose disease has progressed during or following prior chemotherapy—An EORTC STBSG Global Network Study (EORTC 62072)

LBA10002

Background: Pazopanib, a multi targeted angiogenesis inhibitor, has demonstrated single-agent activity in pts with advanced STS. The efficacy and safety of pazopanib versus placebo as second or later line treatment were evaluated in pts with metastatic STS in a multi-center, international, double-blind, placebo-controlled phase III trial. Methods: Pts ≥18 years of age with angiogenesis inhibitor-naïve, histologically proven, metastatic STS, who failed at least one anthracycline containing regimen, could enter the study. They should have ≥1 measurable baseline lesion (per RECIST v1.0), WHO PS 0-1, adequate bone marrow, coagulation, hepatic and renal function, no poorly controlled hypertension, no bleeding diathesis, and no CNS involvement. The study has been conducted by EORTC and GSK in collaboration with 72 sarcoma centers worldwide. Pts were randomized 2:1 to receive either pazopanib 800 mg once daily or placebo until tumor progression, unacceptable toxicity, death, or pt’s request. Results: A total of 369 randomized pts (246 pazopanib, 123 placebo), median age of 56 years, participated in the study (EORTC 45 %, other 55%). Median duration of follow-up at clinical cut-off date is 15 months. The primary endpoint of progression-free survival (PFS) per independent review is significantly prolonged with pazopanib (median: 20 vs 7 weeks; HR=0.31, 95% CI 0.24-0.40 ; P<0.0001). The interim analysis for overall survival shows a statistically non-significant improvement of pazopanib vs placebo (median: 11.9 vs 10.4 months, HR=0.83, 95% CI 0.62-1.09). Main on-therapy grade 3-4 toxicities in the pazopanib vs placebo arm respectively: fatigue (13%, 6%), hypertension (7%, nil), anorexia (6%, nil), and diarrhea (5%, 1%). Similarly, thromboembolic events (grade 3-5 ) (3%, 2%), LVEF drop of >15% (8%, 3%). Median relative dose intensity of pazopanib was 768 mg daily. Conclusions: Pazopanib is an active drug in anthracycline pretreated metastatic STS pts with an increase in median PFS of 13 weeks.

First-line chemotherapy for malignant peripheral nerve sheath tumor (MPNST) versus other histological soft tissue sarcoma subtypes and as a prognostic factor for MPNST: an EORTC soft tissue and bone sarcoma group study

BACKGROUND

the role of chemotherapy in advanced malignant peripheral nerve sheath tumor (MPNST) is unclear.

PATIENTS AND METHODS

chemotherapy-naive soft tissue sarcomas (STS) patients treated on 12 pooled nonrandomized and randomized European Organization for Research and Treatment of Cancer Soft Tissue and Bone Sarcoma Group trials were retrospectively analyzed. Clinical outcomes, overall survival, progression-free survival (PFS) and response were determined for MPNST and other STS histotypes and compared. Additionally, prognostic factors within the MPNST population were defined. Studied cofactors were demographics, sarcoma history, disease extent and chemotherapy regimen.

RESULTS

after a median follow-up of 4.1 years, 175 MPNST out of 2675 eligible STS patients were analyzed. Outcome was similar for MPNST versus other STS histotypes, with a response rate, median PFS and overall survival of 21% versus 22%, 17 versus 16 weeks and 48 versus 51 weeks, respectively. Performance status was an independent prognostic factor for overall survival. Chemotherapy regimen was an independent prognostic factor for response (P < 0.0001) and PFS (P = 0.009). Compared with standard first-line doxorubicin, the doxorubicin-ifosfamide regimen had the best response, whereas ifosfamide had the worst prognosis.

CONCLUSION

this series indicates the role of chemotherapy in treatment of advanced MPNST. This first comparison showed similar outcomes for MPNST and other STS histotypes. The apparent superiority of the doxorubicin-ifosfamide regimen justifies further investigations of this combination in randomized trials.

[Benign sacrococcygeal teratoma in a child: a case report with a review of the literature]

Sacrococcygeal teratomas are rare congenital tumors, generally discovered at birth. These tumors are seldom observed in children. Radical resection must be performed to avoid potentially malignant recurrence even if the primary lesion is benign. We report a case in an 8-year-old girl who did not have a past medical history. Since the age of 2 years, she presented a progressive sacral tumefaction with no neurological deficit. The MRI showed a large sacrococcygeal cyst in hypointense-signal T1-weighted imaging with no contrast enhancement, and a hyperintense signal in T2-weighted imaging. At surgery, the tumor was totally removed. The intraoperative aspect was that of a viscous cyst. The histological study showed a sacrococcygeal teratoma.

Prognostic factors in adolescents and young adults (AYA) with high-risk soft tissue sarcoma (STS) treated by adjuvant chemotherapy: A study based on two pooled European Organisation for Research and Treatment of Cancer (EORTC) clinical trials

10573

Background: We conducted a retrospective study pooling data from two clinical trials in high risk STS patients with the objective to compare two different age groups: 15 - 29 years (AYA population) and ≥ 30 years. The aim was to determine prognostic factors for the AYA population. Methods: Patients selected for analysis were treated in two randomized trials of adjuvant chemotherapy in STS (EORTC 62771 and 62931). A total of 793 patients were included with a median follow-up (FU) of 8.74 years (AYA population: n = 161, median FU 9.46 years; patients ≥ 30 years: n = 632, median FU 8.62 years). Study endpoints were overall survival (OS) and relapse-free survival (RFS). The variables of the multivariate analysis were gender, subtype and grade, tumor size and localization (limb vs. other), absence or presence of local recurrence and treatment (control arm vs. adjuvant chemotherapy). Results: Patients’ characteristics were globally similar with two exceptions, histological subtype (p = 0.0043) and tumor size (p < .0001). The commonest sarcoma subtype in the AYA population was synovial sarcoma (29 %), whereas leiomyosarcoma (18 %), malignant fibrous histiocytoma (MFH, 16 %) and liposarcoma (15 %) were more frequent in patients ≥ 30 years. For OS, independent favorable prognostic factors were low grade and small tumor size for both groups; radical resection and MFH or liposarcoma subtype were factors of favorable prognosis for patients ≥ 30 years only. For RFS, favorable prognostic factors were small tumor size and low grade for both groups; tumor location in the extremities was a factor of favorable prognosis for the AYA population only, whereas radical resection and adjuvant chemotherapy treatment were favorable factors for patients ≥ 30 years only. Conclusions: On the basis of these data, significant differences could be found concerning prognostic factors between the AYA population and older patients. Interestingly, adjuvant chemotherapy was associated with improved RFS only in patients ≥ 30 years. The results may have further implications on the treatment of STS patients in different age groups as well as the design of future clinical trials.

No significant financial relationships to disclose.

Atteinte vésicale dans la sclérodermie : à propos de 3 cas

Lower urinary tract involvement is the common manifestation of systemic sclerosis. It may represent a troublesome disturbance affecting the quality of life in systemic sclerosis patients. We report three patients with progressive systemic sclerosis who manifested pathologic abnormalities in the urinary bladder. The first patient manifested a recurrent macroscopic hematuria requiring transfusions. Both other patients developed functional and urodynamic abnormalities. With a review of the literature on this involvement of the bladder in systemic sclerosis we try to more understand urinary symptoms and urodynamics features of vesical involvement in systemic sclerosis patients.

[Spontaneous hematoma of the adrenal glands]

We report an uncommon case of unilateral spontaneous hematoma of the right adrenal gland in a 22-year old young man. Preoperative diagnosis was made by ultrasonography and CT-scan. A right adrenalectomy was performed. Pathological evaluation showed an isolated hematoma without adrenal abnormalities. The diagnostic and therapeutic aspects are discussed.

[Transitional cell carcinoma on ureteral stump after nephrectomy for pyonephrosis]

The authors report a case of transitional cell carcinoma of the left ureteral stump in a 66-year old man treated by nephrectomy for pyonephrosis 6 years previously and cystoprostatectomy for bladder tumour 13 years previously. In the light of this case and based on a review of the literature, they essentially discuss the diagnostic and aetiopathogenic problems raised by this disease.

Tautomers of styrylquinoline derivatives containing a methoxy substituent: computation of their population in aqueous solution and their interaction with RSV integrase catalytic core

8-Hydroxy-2-[2-(3-hydroxy-4-methoxyphenyl)ethenyl]-7-quinoline carboxylic acid and 8-hydroxy-2-[2-(3-methoxy-4-hydroxyphenyl)ethenyl]-7-quinoline carboxylic acid inhibit the processing and strand transfer reactions catalyzed by HIV-1 integrase with an IC50 of 2 microM. Some of their spectral properties are briefly reported. Their fluorescence is so weak that it is of no use in an experimental determination of the binding to the protein and we resorted to computer simulation. Both styrylquinoline derivatives, in their monoanionic form, have several dozens of tautomers and each of these forms has four planar rotamers. In this work computer simulations have been performed to determine which tautomer is the most abundant in aqueous solution and which binds to the Rous sarcoma virus (RSV) integrase catalytic core. As the substituents on the quinoline moiety are the same as on salicylic acid, the energies of hydroxy benzoic acid tautomers were also computed both in vacuo and embedded in a continuous medium which had the dielectric constant of bulk water, using the recent CPCM technique. The CPCM method was then applied to the two integrase inhibitors to estimate the tautomer population in water. The binding site of the compounds on the RSV integrase catalytic core was determined through a docking protocol, consisting of coupling a grid search method with full energy minimization. The designed method is a way leading to identification of potent integrase inhibitors using in silico experiments.

[Urethral diverticulosis in women. Analysis of 15 cases]

OBJECTIVE

To evaluate the aetiopathogenic, diagnostic and therapeutic aspects of urethral diverticula in women.

MATERIAL AND METHODS

Over a 10-year period (January 1990 to December 1999), 15 patients with a mean age of 36 years (range: 25 to 46 years) with urethral diverticulum were included in this study. The mean parity was 2 with a history of long and difficult delivery in 6 cases. All patients presented lower urinary tract symptoms with a clinical diverticulum on gynaecological examination (14 cases) or on retrograde and voiding cystourethrography (14 cases) or intravenous urography (one case). Diverticulectomy was performed via a transvaginal approach in the dorsal position.

RESULTS

There were no postoperative complications. All patients were reviewed with a mean follow-up of 3 years. The urinary symptoms had completely disappeared in 14 cases. One patient was reoperated for recurrent diverticulum.

CONCLUSION

Young women with recurrent voiding disorders must be examined for the presence of urethral diverticulum that can be confirmed by cystourethrography. Transvaginal diverticulectomy in the lithotomy position is the operation which ensures the best results.

[Unusual testicular tumor: Leydig, Sertoli, and granulosa cell mixed tumor]

We report an unusual case of a mixed granulosa-Sertoli-Leydig cell testicular tumor in a 16 year old man, who presented with bilateral gynaecomastia. A few cases have been published in the literature. Based on a case report, the authors describe the clinical, histopathological and therapeutical features of this rare affection.

Cascaded multiple classifiers for secondary structure prediction

We describe a new classifier for protein secondary structure prediction that is formed by cascading together different types of classifiers using neural networks and linear discrimination. The new classifier achieves an accuracy of 76.7% (assessed by a rigorous full Jack-knife procedure) on a new nonredundant dataset of 496 nonhomologous sequences (obtained from G.J. Barton and J.A. Cuff). This database was especially designed to train and test protein secondary structure prediction methods, and it uses a more stringent definition of homologous sequence than in previous studies. We show that it is possible to design classifiers that can highly discriminate the three classes (H, E, C) with an accuracy of up to 78% for beta-strands, using only a local window and resampling techniques. This indicates that the importance of long-range interactions for the prediction of beta-strands has been probably previously overestimated.

Modeling of the inhibition of retroviral integrases by styrylquinoline derivatives

Styrylquinoline derivatives, known to be potent inhibitors of HIV-1 integrase, have been experimentally tested for their inhibitory effect on the disintegration reaction catalyzed by catalytic cores of HIV-1 and Rous sarcoma virus (RSV) integrases. A modified docking protocol, consisting of coupling a grid search method with full energy minimization, has been specially designed to study the interaction between the inhibitors and the integrases. The inhibitors consist of two moieties that have hydroxyl and/or carboxyl substituents: the first moiety is either benzene, phenol, catechol, resorcinol, or salicycilic acid; the hydroxyl substituents on the second (quinoline) moiety may be in the keto or in the enol forms. Several tautomeric forms of the drugs have been docked to the crystallographic structure of the RSV catalytic core. The computed binding energy of the keto forms correlates best with the measured inhibitory effect. The docking procedure shows that the inhibitors bind closely to the crystallographic catalytic Mg(2+) dication. Additional quantum chemistry computations show that there is no direct correlation between the binding energy of the drugs with the Mg(2+) dication and their in vitro inhibitory effect. The designed method is a leading way for identification of potent integrase inhibitors using in silico experiments.

Tautomers of styrylquinoline derivatives containing a methoxy substituent: computation of their population in aqueous solution and their interaction with RSV integrase catalytic core

8-Hydroxy-2-[2-(3-hydroxy-4-methoxyphenyl)ethenyl]-7-quinoline carboxylic acid and 8-hydroxy-2-[2-(3-methoxy-4-hydroxyphenyl)ethenyl]-7-quinoline carboxylic acid inhibit the processing and strand transfer reactions catalyzed by HIV-1 integrase with an IC50 of 2 microM. Some of their spectral properties are briefly reported. Their fluorescence is so weak that it is of no use in an experimental determination of the binding to the protein and we resorted to computer simulation. Both styrylquinoline derivatives, in their monoanionic form, have several dozens of tautomers and each of these forms has four planar rotamers. In this work computer simulations have been performed to determine which tautomer is the most abundant in aqueous solution and which binds to the Rous sarcoma virus (RSV) integrase catalytic core. As the substituents on the quinoline moiety are the same as on salicylic acid, the energies of hydroxy benzoic acid tautomers were also computed both in vacuo and embedded in a continuous medium which had the dielectric constant of bulk water, using the recent CPCM technique. The CPCM method was then applied to the two integrase inhibitors to estimate the tautomer population in water. The binding site of the compounds on the RSV integrase catalytic core was determined through a docking protocol, consisting of coupling a grid search method with full energy minimization. The designed method is a way leading to identification of potent integrase inhibitors using in silico experiments.

Is it better to combine predictions?

We have compared the accuracy of the individual protein secondary structure prediction methods: PHD, DSC, NNSSP and Predator against the accuracy obtained by combing the predictions of the methods. A range of ways of combing predictions were tested: voting, biased voting, linear discrimination, neural networks and decision trees. The combined methods that involve 'learning' (the non-voting methods) were trained using a set of 496 non-homologous domains; this dataset was biased as some of the secondary structure prediction methods had used them for training. We used two independent test sets to compare predictions: the first consisted of 17 non-homologous domains from CASP3 (Third Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction); the second set consisted of 405 domains that were selected in the same way as the training set, and were non-homologous to each other and the training set. On both test datasets the most accurate individual method was NNSSP, then PHD, DSC and the least accurate was Predator; however, it was not possible to conclusively show a significant difference between the individual methods. Comparing the accuracy of the single methods with that obtained by combing predictions it was found that it was better to use a combination of predictions. On both test datasets it was possible to obtain a approximately 3% improvement in accuracy by combing predictions. In most cases the combined methods were statistically significantly better (at P = 0.05 on the CASP3 test set, and P = 0.01 on the EBI test set). On the CASP3 test dataset there was no significant difference in accuracy between any of the combined method of prediction: on the EBI test dataset, linear discrimination and neural networks significantly outperformed voting techniques. We conclude that it is better to combine predictions.

Stability of G,A triple helices

In this work we selected double-stranded DNA sequences capable of forming stable triplexes at 20 or 50 degrees C with corresponding 13mer purine oligonucleotides. This selection was obtained by a double aptamer approach where both the starting sequences of the oligonucleotides and the target DNA duplex were random. The results of selection were confirmed by a cold exchange method and the influence of the position of a 'mismatch' on the stability of the triplex was documented in several cases. The selected sequences obey two rules: (i) they have a high G content; (ii) for a given G content the stability of the resulting triplex is higher if the G residues lie in stretches. The computer simulation of the Mg2+, Na+and Cl-environment around three triplexes by a density scaled Monte Carlo method provides an interpretation of the experimental observations. The Mg2+cations are statistically close to the G N7 and relatively far from the A N7. The presence of an A repels the Mg2+from adjacent G residues. Therefore, the triplexes are stabilized when the Mg2+can form a continuous spine on G N7.

[Use of double-lumen umbilical vein catheters in a neonatal intensive care unit]

BACKGROUND

The aim of the study was to compare the success/failure rate and complications of insertion into the umbilical vein, of either double-lumen catheters (Charrière diameter 04, length 13 and 30 cm) or single-lumen catheters (Charrière diameter 05, length 40 cm) in a population of neonates admitted to a neonatal intensive care unit. The numbers of insertions of additional peripheral venous catheters were also compared.

PATIENTS AND METHODS

The population was divided into two groups according to the severity of the respiratory failure. Group 1 (n = 52): normal hemodynamic parameters and moderate respiratory failure (FiO2 < 0.6): only single-lumen catheters were used. Group 2 (n = 56): low systemic pressure requiring vascular filling and/or inotropic drugs infusion and/or severe respiratory failure (FiO2 > 0.6): in this group, either single-lumen catheters or double-lumen catheters were inserted.

RESULTS

The success rate of insertion of double-lumen catheters and of single-lumen catheters were similar (61% vs 71%: P = 0.7). Nineteen double-lumen catheters were inserted in the group 2. The average duration of double-lumen umbilical catheterization was not significantly different from simple-lumen catheterization (4.9 +/- 2.2 vs 4.6 +/- 2.2 days). Complications relating to the umbilical venous catheterization were uncommon: three catheter obstructions (two with single-lumen catheter, one with double-lumen catheters), two nosocomial infections (both with single-lumen catheter), one hydropericardium (with single-lumen catheter). In group 2, more peripheral venous catheters were required during the first 72 hours of life after insertion of single-lumen catheter than after insertion of double-lumen catheters (average number of peripheral venous catheters per infant: 1.6 +/- 0.83 vs 1 +/- 0.35 respectively; P < 0.01).

CONCLUSION

Feasibility and complication rate of umbilical double-lumen catheters were similar to those of single-lumen catheters. The use of umbilical double-lumen catheters reduces the need of peripheral venous catheters.

Nitrous oxide sedation in pediatric patients undergoing gastrointestinal endoscopy

BACKGROUND

The ideal medication to administer to children before gastrointestinal endoscopy procedures has yet to be found. The efficacy of using inhaled nitrous oxide during endoscopy in children was assessed in a pilot study.

METHODS

Patients aged 5 to 17 years, referred to our hospital for diagnostic upper gastrointestinal endoscopy or rectosigmoidoscopy procedures, were eligible for enrollment in this study. All received 50% nitrous oxide in oxygen (Entonox; AGA, Rueil-Malmaison, France) before endoscopy and some of them again during endoscopy. The pediatric endoscopist and the nurse performing the procedure were separately asked to rate cooperation, emotional state, drowsiness and overall efficacy of sedation. Oxygen saturation and adverse effects were recorded throughout the procedure. After endoscopy, children scored their degree of pain during the procedures on a visual analog scale (0, no pain; 100, agony) and on a body outline (projective method). Any adverse effects were noted.

RESULTS

Thirty-seven patients were enrolled in the study. Thirty patients underwent diagnostic upper gastrointestinal endoscopy and seven diagnostic rectosigmoidoscopy. The median time from administration of nitrous oxide until insertion of the endoscope was 5 minutes (range, 3-8 minutes). Good or excellent efficacy of the sedation was noted in 92% of children by the endoscopist and in 89% by the nurses. Good or excellent cooperation was noted in 92% of the children by the endoscopist and in 78% by the nurses. The children's pain score on the visual analog scale ranged from 5 to 100 (median, 20) for upper gastrointestinal endoscopy and from 0 to 30 (median, 0) for rectosigmoidoscopy. The time of discharge after endoscopy, defined as the time elapsed between the end of the endoscopy and discharge from the endoscopy suite, varied from 1 to 7 minutes (median, 1.5 minutes).

CONCLUSION

Entonox provides rapid and effective analgesia without heavy sedation, leads to adequate relaxation and cooperation, and facilitates quick and efficient endoscopy. The effect of Entonox was of short duration, allowing the children to leave the endoscopy unit without need for a long recovery period. The adverse effects of Entonox appeared to be minor, and their duration was always brief. Nitrous oxide-oxygen inhalation may provide a valuable alternative to conventional sedation regimens during gastrointestinal endoscopy in children, but randomized and prospective studies comparing nitrous oxide sedation and conventional sedation regimens are necessary.

Hydration of the dTn.dAn x dTn parallel triple helix: a Fourier transform infrared and gravimetric study correlated with molecular dynamics simulations

We present a comparative analysis of the water organization around the dTn.dAn x dTn triple helix and the Watson-Crick double helix dTn.dAn respectively by means of gravimetric measurements, infrared spectroscopy and molecular dynamics simulations. The hydration per nucleotide determined by gravimetric and spectroscopic methods correlated with the molecular dynamics simulations shows that at high relative humidity (98% RH) the triple helix is less solvated than the duplex (17 +/- 2 water molecules per nucleotide instead of 21 +/-1). The experimental desorption curves are different for both structures and indicate that below 81% RH the triplex becomes more hydrated than the duplex. At this RH the FTIR spectra show the emergence of N-type sugars in the adenosine strand of the triplex. When the third strand is bound in the major groove of the Watson-Crick duplex molecular dynamics simulations show the formation of a spine of water molecules between the two thymidine strands.

Parallel and antiparallel A*A-T intramolecular triple helices

Intramolecular triple helices have been obtained by folding back twice oligonucleotides formed by decamers bound by non-nucleotide linkers: dA10-linker-dA10-linker-dT10 and dA10-linker-dT10-linker-dA10. We have thus prepared two triple helices with forced third strand orientation, respectively antiparallel (apA*A-T) and parallel (pA*A-T) with respect to the adenosine strand of the Watson-Crick duplex. The existence of the triple helices has been shown by FTIR, UV and fluorescence spectroscopies. Similar melting temperatures have been obtained in very different oligomer concentration conditions (micromolar solutions for thermal denaturation classically followed by UV spectroscopy, milimolar solutions in the case of melting monitored by FTIR spectroscopy) showing that the triple helices are intramolecular. The stability of the parallel triplex is found to be slightly lower than that of the antiparallel (deltaT(m) = 6 degrees C). The sugar conformations determined by FTIR are different for both triplexes. Only South-type sugars are found in the antiparallel triplex whereas both South- and North-type sugars are detected in the parallel triplex. In this case, thymidine sugars have a South-type geometry, and the adenosine strand of the Watson-Crick duplex has North-type sugars. For the antiparallel triplex the experimental results and molecular modeling data are consistent with a reverse-Hoogsteen like third-strand base pairing and South-type sugar conformation. An energetically optimized model of the parallel A*A-T triple helix with a non-uniform distribution of sugar conformations is discussed.

Binding of Net-Fla, a netropsin-flavin hybrid molecule, to DNA: molecular mechanics and dynamics studies in vacuo and in water solution

We have studied the binding of the hybrid netropsin-flavin (Net-Fla) molecule onto four sequences containing four A. T base pairs. Molecular mechanics minimizations in vacuo show numerous minimal conformations separated by one base pair. 400 ps molecular dynamics simulations in vacuo have been performed using the lowest minima as the starting conformations. During these simulations, the flavin moiety of the drug makes two hydrogen bonds with an amino group of a neighboring guanine. A 200 ps molecular dynamics simulation in explicit water solution suggests that the binding of Net-Fla upon the DNA substrate is enhanced by water bridges. A water molecule bridging the amidinium of Net-Fla to the N3 atom of an adenine seems to be stuck in the drug-DNA complex during the whole simulation. The fluctuations of the DNA helical parameters and of the torsion angles of the sugar-phosphate backbone are very similar in the simulations in vacuo and in water. The time auto-correlation functions for the DNA helical parameters decrease rapidly in the picosecond range in vacuo. The same functions computed from the water solution molecular dynamics simulations seem to have two modes: the rapid mode is similar to the behavior in vacuo, and is followed by a slower mode in the 10 ps range.

A molecular mechanics and dynamics study of alternate triple-helices involving the integrase-binding site of the HIV-1 virus and oligonucleotides having a 3'-3' internucleotide junction

Triple helix formation by oligonucleotides can be extended beyond polypurine tracts with the help of specially designed linkers. In this paper we focus our attention on the integrase-binding site of the HIV-1 virus located on the U5 LTR end which contains two adjacent purine tracts on opposite strands. Two alternate triple helices with a 3'-3' junction in the third strand are considered: 5'-GGTTTTp3'-3'pTGTGT-5' and 5'-GGAAAAp3'-3'pAGAGA-5' The structural plausibility of these triplexes is investigated using molecular mechanics and dynamics simulations, both in vacuo and in aqua. The non-isomorphism of the triplets in the GpT steps in the first sequence, gives rise to non canonical conformations in the torsion angles, hydration appears to be crucial for this triplex. Sugar puckers are predominantly South during in vacuo simulations while they turn East in aqua. In the simulation in aqua the triplexes are shrouded by an hydration shell, however, we have not been able to detect any permanent hydrogen bond bridge between DNA and water. The solvation of ions as well as their radial distribution, appear to be relatively well behaved despite the artifacts known to be generated by the simulation procedure. The experimental feasibility of these structures is discussed.

About the large fluctuations observed using gas-phase molecular dynamics in the K-ras gene containing a mismatch

We describe how we can reduce the periodic bending motions in the simulation in vacuo of the molecular dynamics of a short DNA fragment containing the Gly 12 hot spot of the K-ras oncogene and having at its center a mismatch CA+.

[Hydatid cyst of the pancreas. Apropos of 7 cases]

The authors present a series of seven cases of hydatid cysts of the pancreas. This localization is rare since it accounts for less than 1% of the various sites of hydatid disease. The clinical signs are variable according to degree of bilio-pancreatic involvement. The preoperative diagnosis was established in three patients by ultrasonography, computed tomography and positive serology. Protruding dome was used in five patients. Distal pancreatectomy without splenectomy and Whipple resection were performed in other patients. There was no mortality and the postoperative morbidity was dominated by external biliary or pancreatic fistulae and local sepsis.

Triple helix formation by alpha-oligodeoxynucleotides: a vibrational spectroscopy and molecular modeling study

The structures of triple helices alpha dT6.beta dAn.beta dTn, alpha dT12.beta dAn.beta dTn, alpha dC12+.beta dGn.beta dCn, and alpha dC12+.beta rGn.beta rCn have been studied by Fourier transform infrared spectroscopy, Raman spectroscopy, and molecular mechanics calculations. The sugar conformations in these triplexes have been determined by vibrational spectroscopy. Our results show the existence of only S-type sugars in the alpha dT12.beta dAn.beta dTn triple helix. Both S- and N-type sugar infrared and Raman markers have been detected in the spectra of alpha dC12+.beta dGn.beta dCn. Molecular mechanics refinements taking into account vibrational spectroscopy data constraints allow us to propose third strand hydrogen-bonding schemes and third strand polarities in triple helix models. For alpha dT12.beta dA12.beta dT12 the third strand forms reverse Hoogsteen hydrogen bonds with the beta dA12 strand and therefore is parallel to the purine strand. In contrast, for alpha dC12+.beta dG12.beta dC12 calculations show that only a model in which the third strand is Hoogsteen base paired and antiparallel to the purine strand of the Watson-Crick duplex is compatible with spectroscopic data.