Near-infrared Spectroscopy Monitoring of the Collateral Network Prior to, During, and After Thoracoabdominal Aortic Repair: A Pilot Study

ObjectiveThe aim of this study was to evaluate the feasibility of non-invasive monitoring of the paraspinous collateral network (CN) oxygenation prior to, during, and after thoracoabdominal aortic repair in a clinical series.MethodsNear-infrared spectroscopy optodes were positioned bilaterally—over the thoracic and lumbar paraspinous vasculature—to transcutaneously monitor muscle oxygenation of the CN in 20 patients (age: 66 ± 10 years; men = 11) between September 2010 and April 2012; 15 had open thoracoabdominal aortic repair (Crawford II and III), three had thoracic endovascular aortic repair (TEVAR; Crawford I), and two had a hybrid repair (Crawford II). CN oxygenation was continuously recorded until 48 hours postoperatively.ResultsHospital mortality was 5% (n = 1), 15% suffered ischemic spinal cord injury (SCI). Mean thoracic CN oxygenation saturation was 75.5 ± 8% prior to anesthesia (=baseline) without significant variations throughout the procedure (during non-pulsatile cooling on cardiopulmonary bypass and with aortic cross-clamping; range = 70.6–79.5%). Lumbar CN oxygenation (LbS) dropped significantly after proximal aortic cross-clamping to a minimum after 11.7 ± 4 minutes (74 ± 13% of baseline), but fully recovered after restoration of pulsatile flow to 98.5% of baseline. During TEVAR, stent-graft deployment did not significantly affect LbS. Three patients developed relevant SCI (paraplegia n = 1/paraparesis n = 2). In these patients LbS reduction after aortic cross-clamping was significantly lower compared with patients who did not experience SCI (p = .041).ConclusionsNon-invasive monitoring of CN oxygenation prior to, during, and after thoracoabdominal aortic repair is feasible. Lumbar CN oxygenation levels directly respond to compromise of aortic blood circulation

Spectral fiber dosimetry with beryllium oxide for quality assurance in hadron radiation therapy

Using the radioluminescence light of solid state probes coupled to long and flexible fibers for dosimetry in radiotherapy offers many advantages in terms of probe size, robustness and cost efficiency. However, especially in hadron fields, radioluminophores exhibit quenching effects dependent on the linear energy transfer. This work describes the discovery of a spectral shift in the radioluminescence light of beryllium oxide in dependence on the residual range at therapeutic proton energies. A spectrally resolving measurement setup has been developed and tested in scanned proton fields. It is shown that such a system can not only quantitatively reconstruct the dose, but might also give information on the residual proton range at the point of measurement

Computational Physics on Graphics Processing Units

The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing on classical molecular dynamics, and on quantum simulations for electronic structure calculations using the density functional theory, wave function techniques, and quantum field theory.Comment: Proceedings of the 11th International Conference, PARA 2012, Helsinki, Finland, June 10-13, 201

Correlation analysis of field-aligned currents measured by Swarm

The orientation of field-aligned current sheets (FACs) can be inferred from dual-spacecraft correlations of the FAC signatures between two Swarm spacecraft (A and C), using the maximum correlations obtained from sliding data segments. Statistical analysis of both the correlations and the inferred orientations shows clear trends in magnetic local time (MLT) which reveal behaviour of both large and small scale currents. The maximum correlation coefficients show distinct behaviour in terms of either the time shift, or the shift in longitude between Swarm A and C for various filtering levels. The low-latitude FACs show the strongest correlations for a broad range of MLT centred on dawn and dusk, with a higher correlation coefficient on the dusk-side and lower correlations near noon and midnight. The current sheet orientations are shown to broadly follow the mean shape of the auroral boundary for the lower latitudes corresponding to Region 2 FACs and that these are most well-ordered on the dusk side. Together with these correlation trends, individual events have also been sampled by higher altitude spacecraft in conjunction with Swarm (mapping both to region 1 and 2), showing that two different domains of FACs are apparent: small-scale (some tens of km) which are time variable and large-scale (>100 km) which are rather stationary. We investigate further how these FAC regimes are dependent on geomagnetic activity, focusing on high activity events. The trends found here for different activities are compared to effects seen in the ground magnetometer signals (dH/dt)

Excited-State Electronic Structure with Configuration Interaction Singles and Tamm–Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units

Excited-state calculations are implemented in a development version of the GPU-based TeraChem software package using the configuration interaction singles (CIS) and adiabatic linear response Tamm–Dancoff time-dependent density functional theory (TDA-TDDFT) methods. The speedup of the CIS and TDDFT methods using GPU-based electron repulsion integrals and density functional quadrature integration allows full ab initio excited-state calculations on molecules of unprecedented size. CIS/6-31G and TD-BLYP/6-31G benchmark timings are presented for a range of systems, including four generations of oligothiophene dendrimers, photoactive yellow protein (PYP), and the PYP chromophore solvated with 900 quantum mechanical water molecules. The effects of double and single precision integration are discussed, and mixed precision GPU integration is shown to give extremely good numerical accuracy for both CIS and TDDFT excitation energies (excitation energies within 0.0005 eV of extended double precision CPU results)

Joint Inversion of Active and Passive Seismic Data in Central Java

Seismic and volcanic activities in Central Java, Indonesia, the area of interest of this study, are directly or indirectly related to the subduction of the Indo-Australian plate. In the framework of the MERapi AMphibious EXperiments (MERAMEX), a network consisting of about 130 seismographic stations was installed onshore and offshore in Central Java and operated for more than 150 days. In addition, 3-D active seismic experiments were carried out offshore. In this paper, we present the results of processing combined active and passive seismic data, which contain traveltimes from 292 local earthquakes and additional airgun shots along three offshore profiles. The inversion was performed using the updated LOTOS-06 code that allows processing for active and passive source data. The joint inversion of the active and passive data set considerably improves the resolution of the upper crust, especially in the offshore area in comparison to only passive data. The inversion results are verified using a series of synthetic tests. The resulting images showan exceptionally strong low-velocity anomaly (−30 per cent) in the backarc crust northward of the active volcanoes. In the upper mantle beneath the volcanoes, we observe a low-velocity anomaly inclined towards the slab, which probably reflects the paths of fluids and partially melted materials in the mantle wedge. The crust in the forearc appears to be strongly heterogeneous. The onshore part consists of two high-velocity blocks separated by a narrow low-velocity anomaly, which can be interpreted as a weakened contact zone between two rigid crustal bodies. The recent Java Mw = 6.3 earthquake (2006/05/26-UTC) occurred at the lower edge of this zone. Its focal strike slip mechanism is consistent with the orientation of this contact

Aorto-bronchial and aorto-pulmonary fistulation after thoracic endovascular aortic repair: an analysis from the European Registry of Endovascular Aortic Repair Complications.

OBJECTIVES: To learn upon incidence, underlying mechanisms and effectiveness of treatment strategies in patients with central airway and pulmonary parenchymal aorto-bronchial fistulation after thoracic endovascular aortic repair (TEVAR). METHODS: Analysis of an international multicentre registry (European Registry of Endovascular Aortic Repair Complications) between 2001 and 2012 with a total caseload of 4680 TEVAR procedures (14 centres). RESULTS: Twenty-six patients with a median age of 70 years (interquartile range: 60-77) (35% female) were identified. The incidence of either central airway (aorto-bronchial) or pulmonary parenchymal (aorto-pulmonary) fistulation (ABPF) in the entire cohort after TEVAR in the study period was 0.56% (central airway 58%, peripheral parenchymal 42%). Atherosclerotic aneurysm formation was the leading indication for TEVAR in 15 patients (58%). The incidence of primary endoleaks after initial TEVAR was n = 10 (38%), of these 80% were either type I or type III endoleaks. Fourteen patients (54%) developed central left bronchial tree lesions, 11 patients (42%) pulmonary parenchymal lesions and 1 patient (4%) developed a tracheal lesion. The recognized mechanism of ABPF was external compression of the bronchial tree in 13 patients (50%), the majority being due to endoleak formation, further ischaemia due to extensive coverage of bronchial feeding arteries in 3 patients (12%). Inflammation and graft erosion accounted for 4 patients (30%) each. Cumulative survival during the entire study period was 39%. Among deaths, 71% were attributed to ABPF. There was no difference in survival in patients having either central airway or pulmonary parenchymal ABPF (33 vs 45%, log-rank P = 0.55). Survival with a radical surgical approach was significantly better when compared with any other treatment strategy in terms of overall survival (63 vs 32% and 63 vs 21% at 1 and 2 years, respectively), as well as in terms of fistula-related survival (63 vs 43% and 63 vs 43% at 1 and 2 years, respectively). CONCLUSIONS: ABPF is a rare but highly lethal complication after TEVAR. The leading mechanism behind ABPF seems to be a continuing external compression of either the bronchial tree or left upper lobe parenchyma. In this setting, persisting or newly developing endoleak formation seems to play a crucial role. Prognosis does not differ in patients with central airway or pulmonary parenchymal fistulation. Radical bronchial or pulmonary parenchymal repair in combination with stent graft removal and aortic reconstruction seems to be the most durable treatment strategy

P-value-based regulatory motif discovery using positional weight matrices.

To analyze gene regulatory networks, the sequence-dependent DNA/RNA binding affinities of proteins and noncoding RNAs are crucial. Often, these are deduced from sets of sequences enriched in factor binding sites. Two classes of computational approaches exist. The first describe binding motifs by sequence patterns and search the patterns with highest statistical significance for enrichment. The second class uses the more powerful position weight matrices (PWMs). Instead of maximizing the statistical significance of enrichment, they maximize a likelihood. Here we present XXmotif (eXhaustive evaluation of matriX motifs), the first PWM-based motif discovery method that can optimize PWMs by directly minimizing their P-values of enrichment. Optimization requires computing millions of enrichment P-values for thousands of PWMs. For a given PWM, the enrichment P-value is calculated efficiently from the match P-values of all possible motif placements in the input sequences using order statistics. The approach can naturally combine P-values for motif enrichment, conservation, and localization. On ChIP-chip/seq, miRNA knock-down, and coexpression data sets from yeast and metazoans, XXmotif outperformed state-of-the-art tools, both in numbers of correctly identified motifs and in the quality of PWMs. In segmentation modules of D. melanogaster, we detect the known key regulators and several new motifs. In human core promoters, XXmotif reports most previously described and eight novel motifs sharply peaked around the transcription start site, among them an Initiator motif similar to the fly and yeast versions. XXmotif's sensitivity, reliability, and usability will help to leverage the quickly accumulating wealth of functional genomics data