Improving The Robustness Of Interventional 4D Ultrasound Segmentation Through The Use Of Personalized Shape Priors

While fluoroscopy is still the most widely used imaging modality to guide cardiac interventions, the fusion of pre-operative Magnetic Resonance Imaging (MRI) with real-time intra-operative ultrasound (US) is rapidly gaining clinical acceptance as a viable, radiation-free alternative. In order to improve the detection of the left ventricular (LV) surface in 4D ultrasound, we propose to take advantage of the pre-operative MRI scans to extract a realistic geometrical model representing the patients cardiac anatomy. This could serve as prior information in the interventional setting, allowing to increase the accuracy of the anatomy extraction step in US data. We have made use of a real-time 3D segmentation framework used in the recent past to solve the LV segmentation problem in MR and US data independently and we take advantage of this common link to introduce the prior information as a soft penalty term in the ultrasound segmentation algorithm. We tested the proposed algorithm in a clinical dataset of 38 patients undergoing both MR and US scans. The introduction of the personalized shape prior improves the accuracy and robustness of the LV segmentation, as supported by the error reduction when compared to core lab manual segmentation of the same US sequences.

Strategies for the successful implementation of viral laboratory automation.

It has been estimated that more than 70% of all medical activity is directly related to information providing analytical data. Substantial technological advances have taken place recently, which have allowed a previously unimagined number of analytical samples to be processed while offering high quality results. Concurrently, yet more new diagnostic determinations have been introduced - all of which has led to a significant increase in the prescription of analytical parameters. This increased workload has placed great pressure on the laboratory with respect to health costs. The present manager of the Clinical Laboratory (CL) has had to examine cost control as well as rationing - meaning that the CL's focus has not been strictly metrological, as if it were purely a system producing results, but instead has had to concentrate on its efficiency and efficacy. By applying re-engineering criteria, an emphasis has had to be placed on improved organisation and operating practice within the CL, focussing on the current criteria of the Integrated Management Areas where the technical and human resources are brought together. This re-engineering has been based on the concepts of consolidating and integrating the analytical platforms, while differentiating the production areas (CORE Laboratory) from the information areas. With these present concepts in mind, automation and virological treatment, along with serology in general, follow the same criteria as the rest of the operating methodology in the Clinical Laboratory.

Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers

Background Trypanosomatids of the genera Angomonas and Strigomonas live in a mutualistic association characterized by extensive metabolic cooperation with obligate endosymbiotic Betaproteobacteria. However, the role played by the symbiont has been more guessed by indirect means than evidenced. Symbiont-harboring trypanosomatids, in contrast to their counterparts lacking symbionts, exhibit lower nutritional requirements and are autotrophic for essential amino acids. To evidence the symbiont’s contributions to this autotrophy, entire genomes of symbionts and trypanosomatids with and without symbionts were sequenced here. Results Analyses of the essential amino acid pathways revealed that most biosynthetic routes are in the symbiont genome. By contrast, the host trypanosomatid genome contains fewer genes, about half of which originated from different bacterial groups, perhaps only one of which (ornithine cyclodeaminase, EC:4.3.1.12) derived from the symbiont. Nutritional, enzymatic, and genomic data were jointly analyzed to construct an integrated view of essential amino acid metabolism in symbiont-harboring trypanosomatids. This comprehensive analysis showed perfect concordance among all these data, and revealed that the symbiont contains genes for enzymes that complete essential biosynthetic routes for the host amino acid production, thus explaining the low requirement for these elements in symbiont-harboring trypanosomatids. Phylogenetic analyses show that the cooperation between symbionts and their hosts is complemented by multiple horizontal gene transfers, from bacterial lineages to trypanosomatids, that occurred several times in the course of their evolution. Transfers occur preferentially in parts of the pathways that are missing from other eukaryotes. Conclusion We have herein uncovered the genetic and evolutionary bases of essential amino acid biosynthesis in several trypanosomatids with and without endosymbionts, explaining and complementing decades of experimental results. We uncovered the remarkable plasticity in essential amino acid biosynthesis pathway evolution in these protozoans, demonstrating heavy influence of horizontal gene transfer events, from Bacteria to trypanosomatid nuclei, in the evolution of these pathways.

IN.PACT Amphirion paclitaxel eluting balloon versus standard percutaneous transluminal angioplasty for infrapopliteal revascularization of critical limb ischemia: rationale and protocol for an ongoing randomized controlled trial

BACKGROUND The effectiveness and durability of endovascular revascularization therapies for chronic critical limb ischemia (CLI) are challenged by the extensive burden of infrapopliteal arterial disease and lesion-related characteristics (e.g., severe calcification, chronic total occlusions), which frequently result in poor clinical outcomes. While infrapopliteal vessel patency directly affects pain relief and wound healing, sustained patency and extravascular care both contribute to the ultimate "patient-centric" outcomes of functional limb preservation, mobility and quality of life (QoL). METHODS/DESIGN IN.PACT DEEP is a 2:1 randomized controlled trial designed to assess the efficacy and safety of infrapopliteal arterial revascularization between the IN.PACT Amphirion™ paclitaxel drug-eluting balloon (IA-DEB) and standard balloon angioplasty (PTA) in patients with Rutherford Class 4-5-6 CLI. DISCUSSION This multicenter trial has enrolled 358 patients at 13 European centers with independent angiographic core lab adjudication of the primary efficacy endpoint of target lesion late luminal loss (LLL) and clinically driven target lesion revascularization (TLR) in major amputation-free surviving patients through 12-months. An independent wound core lab will evaluate all ischemic wounds to assess the extent of healing and time to healing at 1, 6, and 12 months. A QoL questionnaire including a pain scale will assess changes from baseline scores through 12 months. A Clinical Events Committee and Data Safety Monitoring Board will adjudicate the composite primary safety endpoints of all-cause death, major amputation, and clinically driven TLR at 6 months and other trial endpoints and supervise patient safety throughout the study. All patients will be followed for 5 years. A literature review is presented of the current status of endovascular treatment of CLI with drug-eluting balloon and standard PTA. The rationale and design of the IN.PACT DEEP Trial are discussed. IN.PACT DEEP is a milestone, prospective, randomized, robust, independent core lab-adjudicated CLI trial that will evaluate the role of a new infrapopliteal revascularization technology, the IA-DEB, compared to PTA. It will assess the overall impact on infrapopliteal artery patency, limb salvage, wound healing, pain control, QoL, and patient mobility. The 1-year results of the adjudicated co-primary and secondary endpoints will be available in 2014. TRIAL REGISTRATION NCT00941733

Cosmic-Lab: Optical companions to binary Millisecond Pulsars

Millisecond Pulsars (MSPs) are fast rotating, highly magnetized neutron stars. According to the "canonical recycling scenario", MSPs form in binary systems containing a neutron star which is spun up through mass accretion from the evolving companion. Therefore, the final stage consists of a binary made of a MSP and the core of the deeply peeled companion. In the last years, however an increasing number of systems deviating from these expectations has been discovered, thus strongly indicating that our understanding of MSPs is far to be complete. The identification of the optical companions to binary MSPs is crucial to constrain the formation and evolution of these objects. In dense environments such as Globular Clusters (GCs), it also allows us to get insights on the cluster internal dynamics. By using deep photometric data, acquired both from space and ground-based telescopes, we identified 5 new companions to MSPs. Three of them being located in GCs and two in the Galactic Field. The three new identifications in GCs increased by 50% the number of such objects known before this Thesis. They all are non-degenerate stars, at odds with the expectations of the "canonical recycling scenario". These results therefore suggest either that transitory phases should also be taken into account, or that dynamical processes, as exchange interactions, play a crucial role in the evolution of MSPs. We also performed a spectroscopic follow-up of the companion to PSRJ1740-5340A in the GC NGC 6397, confirming that it is a deeply peeled star descending from a ~0.8Msun progenitor. This nicely confirms the theoretical expectations about the formation and evolution of MSPs.

Digital Data Collection and Processing in Field and Lab: The Approach of Kinneret Regional Project

The paper showcases the field- and lab-documentation system developed for Kinneret Regional Project, an international archaeological expedition to the Northwestern shore of the Sea of Galilee (Israel) under the auspices of the University of Bern, the University of Helsinki, Leiden University and Wofford College. The core of the data management system is a fully relational, server-based database framework, which also includes time-based and static GIS services, stratigraphic analysis tools and fully indexed document/digital image archives. Data collection in the field is based on mobile, hand-held devices equipped with a custom-tailored stand-alone application. Comprehensive three-dimensional documentation of all finds and findings is achieved by means of total stations and/or high-precision GPS devices. All archaeological information retrieved in the field – including tachymetric data – is synched with the core system on the fly and thus immediately available for further processing in the field lab (within the local network) or for post-excavation analysis at remote institutions (via the WWW). Besides a short demonstration of the main functionalities, the paper also presents some of the key technologies used and illustrates usability aspects of the system’s individual components.

Deep-sea sediment core PS2644 record from the southern Greenland Sea

The PS2644 deep-sea core sequence, retrieved from the northwestern margin of Iceland and covering the last 86 ka, exhibits high sedimentation rates during the last glacial cycle that allow the clear distinction of Greenland stadial (GS)/ interstadial (GI) cycles in the various proxy records. Abundance records of rhyolitic, basaltic and tachylytic tephra grains reveal several maxima. Tephra grains of all types were geochemically analyzed in 44 levels. A total of 92 tephras with a distinctive character have been defined within the glacial sequence of gravity core PS2644-5, whereas the Holocene record is dominated by reworked Vedde Ash grains and not suitable for tephra stratigraphic work. Of the 92 tephras only 19 geochemical populations have been linked with confidence to previously defined tephras such as from the Vedde Ash, Faeroe Marine Ash Zones (FMAZ) II and III and North Atlantic Ash Zone (NAAZ) II. For the glacial period informal names were given to 78 new tephras, most of which are basaltic tephras. Several of these layers have a unique geochemical character and might become new chronostratigraphic markers in the North Atlantic region. Linking the tephra populations to the volcanic system producing them, respectively, revealed that Icelandic eruptions dominate with 83 tephra geochemical populations and Jan Mayen with 9. Around 48% of the informal tephra layers linked to the Icelandic volcanic province are produced from either the Grimsvötn or the Veidivötn-Bardarbunga volcanic systems. The intervals spanning from Greenland Stadial (GS) 3 to Greenland Interstadial (GI) 4 (24.5-29 ka BP), from GI 8 to GS 10 (36.9-40.5 ka BP) and from GI 14 to GI 15.2 (50-56 ka BP) are the periods with the highest number of eruptions, all of which are associated with known tephra zones.

Chronology for the EDML ice core from Dronning Maud Land, Antarctica, over the last 150 000 years

A chronology called EDML1 has been developed for the EPICA ice core from Dronning Maud Land (EDML). EDML1 is closely interlinked with EDC3, the new chronology for the EPICA ice core from Dome-C (EDC) through a stratigraphic match between EDML and EDC that consists of 322 volcanic match points over the last 128 ka. The EDC3 chronology comprises a glaciological model at EDC, which is constrained and later selectively tuned using primary dating information from EDC as well as from EDML, the latter being transferred using the tight stratigraphic link between the two cores. Finally, EDML1 was built by exporting EDC3 to EDML. For ages younger than 41 ka BP the new synchronized time scale EDML1/EDC3 is based on dated volcanic events and on a match to the Greenlandic ice core chronology GICC05 via 10Be and methane. The internal consistency between EDML1 and EDC3 is estimated to be typically ~6 years and always less than 450 years over the last 128 ka (always less than 130 years over the last 60 ka), which reflects an unprecedented synchrony of time scales. EDML1 ends at 150 ka BP (2417 m depth) because the match between EDML and EDC becomes ambiguous further down. This hints at a complex ice flow history for the deepest 350 m of the EDML ice core.

Mid-Wisconsin to Holocene permafrost and landscape dynamics based on a drained lake basin core from the northern Seward Peninsula, Northwest Alaska

Permafrost-related processes drive regional landscape dynamics in the Arctic terrestrial system. A better understanding of past periods indicative of permafrost degradation and aggradation is important for predicting the future response of Arctic landscapes to climate change. Here, we used a multi-proxy approach to analyze a ~4 m long sediment core from a drained thermokarst lake basin on the northern Seward Peninsula in western Arctic Alaska (USA). Sedimentological, biogeochemistical, geochronological, micropaleontological (ostracoda, testate amoeba) and tephra analyses were used to determine the long-term environmental Early-Wisconsin to Holocene history preserved in our core for Central Beringia. Yedoma accumulation dominated throughout the Early to Late-Wisconsin but was interrupted by wetland formation from 44.5 to 41.5 ka BP. The latter was terminated by deposition of 1 m of volcanic tephra, most likely originating from the South Killeak Maar eruption at about 42 ka BP. Yedoma deposition continued until 22.5 ka BP and was followed by a depositional hiatus in the sediment core between 22.5 and 0.23 ka BP. We interpret this hiatus as due to intense thermokarst activity in the areas surrounding the site, which served as a sediment source during the Late-Wisconsin to Holocene climate transition. The lake forming the modern basin on the upland initiated around 0.23 ka BP, which drained catastrophically in spring 2005. The present study emphasizes that Arctic lake systems and periglacial landscapes are highly dynamic and permafrost formation as well as degradation in Central Beringia was controlled by regional to global climate patterns and as well as by local disturbances.

Geological investigations on sediment core MD07-3128

Glacial millennial-scale paleoceanographic changes in the Southeast Pacific and the adjacent Southern Ocean are poorly known due to the scarcity of well-dated and high resolution sediment records. Here we present new surface water records from sediment core MD07-3128 recovered at 53°S off the Pacific entrance of the Strait of Magellan. The alkenone-derived sea surface temperature (SST) record reveals a very strong warming of ca. 8°C over the last Termination and substantial millennial-scale variability in the glacial section largely consistent with our planktonic foraminifera oxygen isotope (d18O) record of Neogloboquadrina pachyderma (sin.). The timing and structure of the Termination and some of the millennial-scale SST fluctuations are very similar to those observed in the well-dated SST record from ODP Site 1233 (41°S) and the temperature record from Drowning Maud Land Antarctic ice core supporting the hemispheric-wide Antarctic timing of SST changes. However, differences in our new SST record are also found including a long-term warming trend over Marine Isotope Stage (MIS) 3 followed by a cooling toward the Last Glacial Maximum (LGM). We suggest that these differences reflect regional cooling related to the proximal location of the southern Patagonian Ice Sheet and related meltwater supply at least during the LGM consistent with the fact that no longer SST cooling trend is observed in ODP Site 1233 or any SST Chilean record. This proximal ice sheet location is documented by generally higher contents of ice rafted debris (IRD) and tetra-unsaturated alkenones, and a slight trend toward lighter planktonic d18O during late MIS 3 and MIS 2.

Analyses of lake La Thuile sediment core

Lake La Thuile, in the Northern French Prealps (874 m a.s.l.), provides an 18 m long sedimentary sequence spanning the entire Lateglacial/Holocene period. The high resolution multi-proxy (sedimentological, palynological, geochemical) analysis of the uppermost 6.2 meters reveals the Holocene dynamics of erosion in the catchment in response to landscape modifications. The mountain belt is at relevant altitude to study past human activities and the watershed is sufficiently disconnected from large valleys to capture a local sedimentary signal. From 12,000 to 10,000 cal. BP (10 to 8 ka cal. BC), the onset of hardwood species triggered a drop in erosion following the Lateglacial/Holocene transition. From 10,000 to 4500 cal. BP (8 to 2.5 ka cal. BC), the forest became denser and favored slope stabilization while erosion processes were very weak. A first erosive phase was initiated at ca . 4500 cal. BP without evidence of human presence in the catchment. Then, the forest declined at approximately 3000 cal. BP, suggesting the first human influence on the landscape. Two other erosive phases are related to anthropic activities: approximately 2500 cal. BP (550 cal. BC) during the Roman period and after 1600 cal. BP (350 cal. AD) with a substantial accentuation in the Middle Ages. In contrast, the lower erosion produced during the Little Ice Age, when climate deteriorations are generally considered to result in an increased erosion signal in this region, suggests that anthropic activities dominated the erosive processes and completely masked the natural effects of climate on erosion in the late Holocene.

Water temperature reconstruction for Terminations I and II of sediment core MD01-2378

We present centennial records of sea surface and upper thermocline temperatures in Core MD01-2378 from the Timor Sea, which provide new insights into the variability of the Indonesian outflow across the last two glacial terminations. Mg/Ca in Globigerinoides ruber (white s. s.) indicates an overall increase of 3.2 °C in sea surface temperature (SST) over Termination I. Following an early Holocene plateau at 11.3-6.4 ka, SSTs cooled by 0.6 °C during the middle to late Holocene (6.4-0.7 ka). The early Holocene warming occurred in phase with increasing northern hemisphere summer insolation, coinciding with northward displacement of the Intertropical Convergence Zone, enhanced boreal summer monsoon and expansion of the Indo-Pacific Warm Pool. Thermocline temperatures (Pulleniatina obliquiloculata Mg/Ca) gradually decreased from 24.5 to 21.5 °C since 10.3 ka, reflecting intensification of a cool thermocline throughflow. The vertical structure of the upper ocean in the Timor Sea evolved in similar fashion during the Holocene and MIS5e, although the duration of SST plateaux differed (11.3 to 6.4 ka in Termination I and from 129 to 119 ka in Termination II), which was probably due to the more intense northern hemisphere summer insolation during MIS 5e. During both terminations, SST increased simultaneously in the southern high latitudes and the tropical eastern Indian Ocean, suggesting virtually instantaneous atmospheric climate feedbacks between the high and low latitudes.

Mineralogy of sediment core GeoB3313-1

Geochemical and clay mineral parameters of a high accumulation marine sediment core from the Chilean continental slope (41°S) provide a 7700 yr record of rainfall variability in southern Chile related to the position of the Southern Westerlies. We especially use the iron content, measured with a time-resolution of ca. 10 yr on average, of 14C-accelerator mass spectrometry dated marine sediments as a proxy for the relative input of iron-poor Coastal Range and iron-rich Andean source rocks. Variations in this input are most likely induced by rainfall changes in the continental hinterland of the core position. Based on these interpretations, we find a pronounced rainfall variability on multi-centennial to millennial time-scales, superimposed on generally more arid conditions during the middle Holocene (7700 to 4000 cal yr B.P.) compared to the late Holocene (4000 to present). This variability and thus changes in the position of the Southern Westerlies are first compared to regional terrestrial paleoclimate data-sets from central and southern Chile. In order to derive possible wider implications and forcing mechanisms of the Holocene latitudinal shifts of the Southern Westerlies, we then compare our data to ice-core records from both tropical South America and coastal Antarctica. These records show similar bands of variability centered at ca. 900 and 1500 yr. Comparisons of band pass filters suggest a close connection of shifts of the Southern Westerlies to changes within the tropical climate system. The correlation to climate conditions in coastal Antarctica shows a more complicated picture with a phase shift at the beginning of the late Holocene coinciding with the onset of the modern state of El Niño-Southern Oscillation system. The presented data provide further evidence that the well known millennial-scale climate variability during the last glacial continued throughout the Holocene.