Assignment strategies for large proteins by magic-angle spinning NMR: the 21-kDa disulfide-bond-forming enzyme DsbA.

We present strategies for chemical shift assignments of large proteins by magic-angle spinning solid-state NMR, using the 21-kDa disulfide-bond-forming enzyme DsbA as prototype. Previous studies have demonstrated that complete de novo assignments are possible for proteins up to approximately 17 kDa, and partial assignments have been performed for several larger proteins. Here we show that combinations of isotopic labeling strategies, high field correlation spectroscopy, and three-dimensional (3D) and four-dimensional (4D) backbone correlation experiments yield highly confident assignments for more than 90% of backbone resonances in DsbA. Samples were prepared as nanocrystalline precipitates by a dialysis procedure, resulting in heterogeneous linewidths below 0.2 ppm. Thus, high magnetic fields, selective decoupling pulse sequences, and sparse isotopic labeling all improved spectral resolution. Assignments by amino acid type were facilitated by particular combinations of pulse sequences and isotopic labeling; for example, transferred echo double resonance experiments enhanced sensitivity for Pro and Gly residues; [2-(13)C]glycerol labeling clarified Val, Ile, and Leu assignments; in-phase anti-phase correlation spectra enabled interpretation of otherwise crowded Glx/Asx side-chain regions; and 3D NCACX experiments on [2-(13)C]glycerol samples provided unique sets of aromatic (Phe, Tyr, and Trp) correlations. Together with high-sensitivity CANCOCA 4D experiments and CANCOCX 3D experiments, unambiguous backbone walks could be performed throughout the majority of the sequence. At 189 residues, DsbA represents the largest monomeric unit for which essentially complete solid-state NMR assignments have so far been achieved. These results will facilitate studies of nanocrystalline DsbA structure and dynamics and will enable analysis of its 41-kDa covalent complex with the membrane protein DsbB, for which we demonstrate a high-resolution two-dimensional (13)C-(13)C spectrum.

Three-dimensional patient-specific dosimetry in radioimmunotherapy with 90Y-ibritumomab-tiuxetan.

Aim of the present article was to perform three-dimensional (3D) single photon emission tomography-based dosimetry in radioimmunotherapy (RIT) with (90)Y-ibritumomab-tiuxetan. A custom MATLAB-based code was used to elaborate 3D images and to compare average 3D doses to lesions and to organs at risk (OARs) with those obtained with planar (2D) dosimetry. Our 3D dosimetry procedure was validated through preliminary phantom studies using a body phantom consisting of a lung insert and six spheres with various sizes. In phantom study, the accuracy of dose determination of our imaging protocol decreased when the object volume decreased below 5 mL, approximately. The poorest results were obtained for the 2.58 mL and 1.30 mL spheres where the dose error evaluated on corrected images with regard to the theoretical dose value was -12.97% and -18.69%, respectively. Our 3D dosimetry protocol was subsequently applied on four patients before RIT with (90)Y-ibritumomab-tiuxetan for a total of 5 lesions and 4 OARs (2 livers, 2 spleens). In patient study, without the implementation of volume recovery technique, tumor absorbed doses calculated with the voxel-based approach were systematically lower than those calculated with the planar protocol, with average underestimation of -39% (range from -13.1% to -62.7%). After volume recovery, dose differences reduce significantly, with average deviation of -14.2% (range from -38.7.4% to +3.4%, 1 overestimation, 4 underestimations). Organ dosimetry in one case overestimated, in the other underestimated the dose delivered to liver and spleen. However, both for 2D and 3D approach, absorbed doses to organs per unit administered activity are comparable with most recent literature findings.

A wearable system for multi-segment foot kinetics measurement.

This study aims to design a wearable system for kinetics measurement of multi-segment foot joints in long-distance walking and to investigate its suitability for clinical evaluations. The wearable system consisted of inertial sensors (3D gyroscopes and 3D accelerometers) on toes, forefoot, hindfoot, and shank, and a plantar pressure insole. After calibration in a laboratory, 10 healthy elderly subjects and 12 patients with ankle osteoarthritis walked 50m twice wearing this system. Using inverse dynamics, 3D forces, moments, and power were calculated in the joint sections among toes, forefoot, hindfoot, and shank. Compared to those we previously estimated for a one-segment foot model, the sagittal and transverse moments and power in the ankle joint, as measured via multi-segment foot model, showed a normalized RMS difference of less than 11%, 14%, and 13%, respectively, for healthy subjects, and 13%, 15%, and 14%, for patients. Similar to our previous study, the coronal moments were not analyzed. Maxima-minima values of anterior-posterior and vertical force, sagittal moment, and power in shank-hindfoot and hindfoot-forefoot joints were significantly different between patients and healthy subjects. Except for power, the inter-subject repeatability of these parameters was CMC>0.90 for healthy subjects and CMC>0.70 for patients. Repeatability of these parameters was lower for the forefoot-toes joint. The proposed measurement system estimated multi-segment foot joints kinetics with acceptable repeatability but showed difference, compared to those previously estimated for the one-segment foot model. These parameters also could distinguish patients from healthy subjects. Thus, this system is suggested for outcome evaluations of foot treatments.

Manual de uso del software Ocean Data View (ODV)

El presente manual de uso del software de visualización de datos “Ocean Data View” (ODV) describe la exploración, análisis y visualización de datos oceanográficos según el formato de la colección mundial de base de datos del océano “World Ocean Database” (WOD). El manual comprende 6 ejercicios prácticos donde se describe paso a paso la creación de las metavariables, la importación de los datos y su visualización mediante mapas de latitud, longitud y gráficos de dispersión, secciones verticales y series de tiempo. Se sugiere el uso extensivo del ODV para la visualización de datos oceanográficos por el personal científico del IMARPE.

Bases de datos XML nativas

Conèixer les diferents opcions a l'hora d'emmagatzemar dades i documents amb format XML. Familiaritzar-se amb els SGBD nadius i l'accés i maneig de la informació. Conèixer diferents formes d'accés al SGBD, conèixer les APIs disponible Centre en el llenguatge Java. Integració de tots els coneixements adquirits, desenvolupant una aplicació que accedeixi i gestioni dades emmagatzemades al SGBD.

Sequential or concomitant chemotherapy in limited stage small-cell lung cancer.

PURPOSE: Chemotherapy (CT) combined with radiation therapy (RT) is the standard treatment for limited disease small-cell lung cancer (LDSCLC). Many questions including RT dose, fractionation, and sequence of RT/CT administration remain controversial. In this paper, we retrospectively assessed the outcome of patients with LDSCLC treated with radiation of at least 50 Gy.METHODS AND MATERIALS: From December 1997 to January 2006, 69 consecutive patients with LDSCLC were treated at our institutions. Treatment consisted of at least 4 cycles of CT, and 3D conformal thoracic RT. The median age was 61 years (range, 37-78 years). Sequential or concomitant CT/RT was given in 47 (68%) and 22 (32%) of the patients, respectively. The median RT dose was 60 Gy. Prophylactic cranial irradiation (PCI) was administered in 47 (68%) patients.RESULTS: With a median follow-up of 36 months (range, 6-107), 16 patients were alive without disease. The median overall survival time was 24 months, with a 3-year survival rate of 29%. The 3-year disease-free survival (DFS) and loco-regional control (LRC) rates were 23% and 60%, respectively. A better DFS was significantly associated with performance status (PS) 0 (p = 0.004), complete response to treatment (p = 0.03), and PCI group (p = 0.03). A trend towards improved overall survival (OS) was observed for patients who underwent PCI (p = 0.07). Patients treated with sequential CT/RT had a better outcome than those treated with concomitant treatment (3-year DFS rate 27% vs. 13%; p = 0.04). However, PCI was delivered more frequently for the sequential group. No significant dose-response relationship was found in terms of LRC. The multivariate analysis showed that complete response to treatment was the only significant factor for OS.CONCLUSION: Complete response to treatment was the most important factor for OS. A better DFS was significantly associated with the PCI group. We did not find a significant difference in outcome between patients receiving doses of 60 Gy or more and patients receiving 60 Gy or less.

Tc-99m-MAA SPECT-derived tumor-to-normal liver ratios for partition model dosimetry in selective internal radiation therapy (SIRT)

Aim: When planning SIRT using 90Y microspheres, the partition model is used to refine the activity calculated by the body surface area (BSA) method to potentially improve the safety and efficacy of treatment. For this partition model dosimetry, accurate determination of mean tumor-to-normal liver ratio (TNR) is critical since it directly impacts absorbed dose estimates. This work aimed at developing and assessing a reliable methodology for the calculation of 99mTc-MAA SPECT/CT-derived TNR ratios based on phantom studies. Materials and methods: IQ NEMA (6 hot spheres) and Kyoto liver phantoms with different hot/background activity concentration ratios were imaged on a SPECT/CT (GE Infinia Hawkeye 4). For each reconstruction with the IQ phantom, TNR quantification was assessed in terms of relative recovery coefficients (RC) and image noise was evaluated in terms of coefficient of variation (COV) in the filled background. RCs were compared using OSEM with Hann, Butterworth and Gaussian filters, as well as FBP reconstruction algorithms. Regarding OSEM, RCs were assessed by varying different parameters independently, such as the number of iterations (i) and subsets (s) and the cut-off frequency of the filter (fc). The influence of the attenuation and diffusion corrections was also investigated. Furthermore, both 2D-ROIs and 3D-VOIs contouring were compared. For this purpose, dedicated Matlab© routines were developed in-house for automatic 2D-ROI/3D-VOI determination to reduce intra-user and intra-slice variability. Best reconstruction parameters and RCs obtained with the IQ phantom were used to recover corrected TNR in case of the Kyoto phantom for arbitrary hot-lesion size. In addition, we computed TNR volume histograms to better assess uptake heterogeneityResults: The highest RCs were obtained with OSEM (i=2, s=10) coupled with the Butterworth filter (fc=0.8). Indeed, we observed a global 20% RC improvement over other OSEM settings and a 50% increase as compared to the best FBP reconstruction. In any case, both attenuation and diffusion corrections must be applied, thus improving RC while preserving good image noise (COV<10%). Both 2D-ROI and 3D-VOI analysis lead to similar results. Nevertheless, we recommend using 3D-VOI since tumor uptake regions are intrinsically 3D. RC-corrected TNR values lie within 17% around the true value, substantially improving the evaluation of small volume (<15 mL) regions. Conclusions: This study reports the multi-parameter optimization of 99mTc MAA SPECT/CT images reconstruction in planning 90Y dosimetry for SIRT. In phantoms, accurate quantification of TNR was obtained using OSEM coupled with Butterworth and RC correction.

Evidence of extended orientational order in amorphous Fe/Sm thin films

Amorphous thin films of Fe/Sm, prepared by evaporation methods, have been magnetically characterized and the results were interpreted in terms of the random magnets theory. The samples behave as 2D and 3D random magnets depending on the total thickness of the film. From our data the existence of orientational order, which greatly influences the magnetic behavior of the films, is also clear.

Postmortem pump-driven reperfusion of the vascular system of porcine lungs: towards a new model for surgical training.

PURPOSE: The objective of this experiment is to establish a continuous postmortem circulation in the vascular system of porcine lungs and to evaluate the pulmonary distribution of the perfusate. This research is performed in the bigger scope of a revascularization project of Thiel embalmed specimens. This technique enables teaching anatomy, practicing surgical procedures and doing research under lifelike circumstances. METHODS: After cannulation of the pulmonary trunk and the left atrium, the vascular system was flushed with paraffinum perliquidum (PP) through a heart-lung machine. A continuous circulation was then established using red PP, during which perfusion parameters were measured. The distribution of contrast-containing PP in the pulmonary circulation was visualized on computed tomography. Finally, the amount of leak from the vascular system was calculated. RESULTS: A reperfusion of the vascular system was initiated for 37 min. The flow rate ranged between 80 and 130 ml/min throughout the experiment with acceptable perfusion pressures (range: 37-78 mm Hg). Computed tomography imaging and 3D reconstruction revealed a diffuse vascular distribution of PP and a decreasing vascularization ratio in cranial direction. A self-limiting leak (i.e. 66.8% of the circulating volume) towards the tracheobronchial tree due to vessel rupture was also measured. CONCLUSIONS: PP enables circulation in an isolated porcine lung model with an acceptable pressure-flow relationship resulting in an excellent recruitment of the vascular system. Despite these promising results, rupture of vessel walls may cause leaks. Further exploration of the perfusion capacities of PP in other organs is necessary. Eventually, this could lead to the development of reperfused Thiel embalmed human bodies, which have several applications.

Evidence of extended orientational order in amorphous Fe/Sm thin films

Amorphous thin films of Fe/Sm, prepared by evaporation methods, have been magnetically characterized and the results were interpreted in terms of the random magnets theory. The samples behave as 2D and 3D random magnets depending on the total thickness of the film. From our data the existence of orientational order, which greatly influences the magnetic behavior of the films, is also clear.

Using high-resolution quantitative mapping of R1 as an index of cortical myelination

A fundamental tenet of neuroscience is that cortical functional differentiation is related to the cross-areal differences in cyto-, receptor-, and myeloarchitectonics that are observed in ex-vivo preparations. An ongoing challenge is to create noninvasive magnetic resonance (MR) imaging techniques that offer sufficient resolution, tissue contrast, accuracy and precision to allow for characterization of cortical architecture over an entire living human brain. One exciting development is the advent of fast, high-resolution quantitative mapping of basic MR parameters that reflect cortical myeloarchitecture. Here, we outline some of the theoretical and technical advances underlying this technique, particularly in terms of measuring and correcting for transmit and receive radio frequency field inhomogeneities. We also discuss new directions in analytic techniques, including higher resolution reconstructions of the cortical surface. We then discuss two recent applications of this technique. The first compares individual and group myelin maps to functional retinotopic maps in the same individuals, demonstrating a close relationship between functionally and myeloarchitectonically defined areal boundaries (as well as revealing an interesting disparity in a highly studied visual area). The second combines tonotopic and myeloarchitectonic mapping to localize primary auditory areas in individual healthy adults, using a similar strategy as combined electrophysiological and post-mortem myeloarchitectonic studies in non-human primates.

Importance of a three-dimensional measure of humeral head subluxation in osteoarthritic shoulders.

HYPOTHESIS: During total shoulder arthroplasty (TSA), humeral head subluxation may be difficult to manage. Furthermore, there is a risk for postoperative recurrence of subluxation, affecting the outcome of TSA. An accurate evaluation of the subluxation is necessary to evaluate this risk. Currently, subluxation is measured in 2 dimensions (2D), usually relative to the glenoid face. The goal of this study was to extend this measure to 3 dimensions (3D) to compare glenohumeral and scapulohumeral subluxation and to evaluate the association of subluxation with the glenoid version. MATERIALS AND METHODS: The study analyzed 112 computed tomography scans of osteoarthritic shoulders. We extended the usual 2D definition of glenohumeral subluxation, scapulohumeral subluxation, and glenoid version by measuring their orientation in 3D relative to the scapular plane and the scapular axis. We evaluated statistical associations between subluxation and version in 2D and 3D. RESULTS: Orientation of subluxation and version covered all sectors of the glenoid surface. Scapulohumeral subluxation and glenoid version were highly correlated in amplitude (R(2) = 0.71; P < .01) and in orientation (R(2) = 0.86; P < .01). Approximately every degree of glenoid version induced 1% of scapulohumeral subluxation in the same orientation of the version. Conversely, glenohumeral subluxation was not correlated to glenoid version in 2D or in 3D. CONCLUSIONS: Orientation of the humeral subluxation is rarely within the arbitrary computed tomography plane and should therefore be measured in 3D to detect out-of-plane subluxation. Scapulohumeral subluxation and glenoid version measured in 3D could bring valuable information for decision making during TSA.

A Mixed-method Social Networks Study Design for Research on Transnational Families

This paper advocates the adoption of a mixed-methods research design to describe and analyze ego-centered social networks in transnational family research. Drawing on the experience of the Social Networks Influences on Family Formation project (2004-2005), I show how the combined use of network generators and semistructured interviews (N = 116) produces unique data on family configurations and their impact on life course choices. A mixed-methods network approach presents specific advantages for research on children in transnational families. On the one hand, quantitative analyses are crucial for reconstructing and measuring the potential and actual relational support available to children in a context where kin interactions may be hindered by temporary and prolonged periods of separation. On the other hand, qualitative analyses can address strategies and practices employed by families to maintain relationships across international borders and geographic distance, as well as the implications of those strategies for children's well-being.

Measurement of multi-segment foot joint angles during gait using a wearable system.

Usually the measurement of multi-segment foot and ankle complex kinematics is done with stationary motion capture devices which are limited to use in a gait laboratory. This study aimed to propose and validate a wearable system to measure the foot and ankle complex joint angles during gait in daily conditions, and then to investigate its suitability for clinical evaluations. The foot and ankle complex consisted of four segments (shank, hindfoot, forefoot, and toes), with an inertial measurement unit (3D gyroscopes and 3D accelerometers) attached to each segment. The angles between the four segments were calculated in the sagittal, coronal, and transverse planes using a new algorithm combining strap-down integration and detection of low-acceleration instants. To validate the joint angles measured by the wearable system, three subjects walked on a treadmill for five minutes at three different speeds. A camera-based stationary system that used a cluster of markers on each segment was used as a reference. To test the suitability of the system for clinical evaluation, the joint angle ranges were compared between a group of 10 healthy subjects and a group of 12 patients with ankle osteoarthritis, during two 50-m walking trials where the wearable system was attached to each subject. On average, over all joints and walking speeds, the RMS differences and correlation coefficients between the angular curves obtained using the wearable system and the stationary system were 1 deg and 0.93, respectively. Moreover, this system was able to detect significant alteration of foot and ankle function between the group of patients with ankle osteoarthritis and the group of healthy subjects. In conclusion, this wearable system was accurate and suitable for clinical evaluation when used to measure the multi-segment foot and ankle complex kinematics during long-distance walks in daily life conditions.

Pin guidance of reconstruction plate contour: an expanded role of external fixation

This article presents a modification of intraoperative external fixation for mandibular reconstruction with free tissue flaps. This technique is indicated when preregistration of the reconstruction plate is not possible due to transmandibular tumor extension. Once standard external fixation has been carried out and prior to segmental mandibulectomy, additional pins are fixed to the connecting rod that delineate the mandibular contour in three-dimensional (3D) space. Following mandibulectomy, these pins allow accurate contouring of the reconstruction plate and improved restoration of mandibular contour, projection, and dental occlusion. A step-by-step description of the technique using models and intraoperative photos is presented. This method of mandibular reconstruction is a simple and time-effective alternative to intraoperative computer navigation and 3D modeling in select cases of oral carcinoma where tumor infiltration of the outer mandibular cortex precludes prebending of the reconstruction plates.