Assessment of tumor regression of esophageal adenocarcinomas after neoadjuvant chemotherapy: comparison of 2 commonly used scoring approaches.

Histopathologic determination of tumor regression provides important prognostic information for locally advanced gastroesophageal carcinomas after neoadjuvant treatment. Regression grading systems mostly refer to the amount of therapy-induced fibrosis in relation to residual tumor or the estimated percentage of residual tumor in relation to the former tumor site. Although these methods are generally accepted, currently there is no common standard for reporting tumor regression in gastroesophageal cancers. We compared the application of these 2 major principles for assessment of tumor regression: hematoxylin and eosin-stained slides from 89 resection specimens of esophageal adenocarcinomas following neoadjuvant chemotherapy were independently reviewed by 3 pathologists from different institutions. Tumor regression was determined by the 5-tiered Mandard system (fibrosis/tumor relation) and the 4-tiered Becker system (residual tumor in %). Interobserver agreement for the Becker system showed better weighted κ values compared with the Mandard system (0.78 vs. 0.62). Evaluation of the whole embedded tumor site showed improved results (Becker: 0.83; Mandard: 0.73) as compared with only 1 representative slide (Becker: 0.68; Mandard: 0.71). Modification into simplified 3-tiered systems showed comparable interobserver agreement but better prognostic stratification for both systems (log rank Becker: P=0.015; Mandard P=0.03), with independent prognostic impact for overall survival (modified Becker: P=0.011, hazard ratio=3.07; modified Mandard: P=0.023, hazard ratio=2.72). In conclusion, both systems provide substantial to excellent interobserver agreement for estimation of tumor regression after neoadjuvant chemotherapy in esophageal adenocarcinomas. A simple 3-tiered system with the estimation of residual tumor in % (complete regression/1% to 50% residual tumor/>50% residual tumor) maintains the highest reproducibility and prognostic value.

Improved methods for measuring forest landscape structure: LiDAR complements field-based habitat assessment

Conservation and monitoring of forest biodiversity requires reliable information about forest structure and composition at multiple spatial scales. However, detailed data about forest habitat characteristics across large areas are often incomplete due to difficulties associated with field sampling methods. To overcome this limitation we employed a nationally available light detection and ranging (LiDAR) remote sensing dataset to develop variables describing forest landscape structure across a large environmental gradient in Switzerland. Using a model species indicative of structurally rich mountain forests (hazel grouse Bonasa bonasia), we tested the potential of such variables to predict species occurrence and evaluated the additional benefit of LiDAR data when used in combination with traditional, sample plot-based field variables. We calibrated boosted regression trees (BRT) models for both variable sets separately and in combination, and compared the models’ accuracies. While both field-based and LiDAR models performed well, combining the two data sources improved the accuracy of the species’ habitat model. The variables retained from the two datasets held different types of information: field variables mostly quantified food resources and cover in the field and shrub layer, LiDAR variables characterized heterogeneity of vegetation structure which correlated with field variables describing the understory and ground vegetation. When combined with data on forest vegetation composition from field surveys, LiDAR provides valuable complementary information for encompassing species niches more comprehensively. Thus, LiDAR bridges the gap between precise, locally restricted field-data and coarse digital land cover information by reliably identifying habitat structure and quality across large areas.

K-t GRAPPA-accelerated 4D flow MRI of liver hemodynamics: influence of different acceleration factors on qualitative and quantitative assessment of blood flow.

OBJECTIVE We sought to evaluate the feasibility of k-t parallel imaging for accelerated 4D flow MRI in the hepatic vascular system by investigating the impact of different acceleration factors. MATERIALS AND METHODS k-t GRAPPA accelerated 4D flow MRI of the liver vasculature was evaluated in 16 healthy volunteers at 3T with acceleration factors R = 3, R = 5, and R = 8 (2.0 × 2.5 × 2.4 mm(3), TR = 82 ms), and R = 5 (TR = 41 ms); GRAPPA R = 2 was used as the reference standard. Qualitative flow analysis included grading of 3D streamlines and time-resolved particle traces. Quantitative evaluation assessed velocities, net flow, and wall shear stress (WSS). RESULTS Significant scan time savings were realized for all acceleration factors compared to standard GRAPPA R = 2 (21-71 %) (p < 0.001). Quantification of velocities and net flow offered similar results between k-t GRAPPA R = 3 and R = 5 compared to standard GRAPPA R = 2. Significantly increased leakage artifacts and noise were seen between standard GRAPPA R = 2 and k-t GRAPPA R = 8 (p < 0.001) with significant underestimation of peak velocities and WSS of up to 31 % in the hepatic arterial system (p <0.05). WSS was significantly underestimated up to 13 % in all vessels of the portal venous system for k-t GRAPPA R = 5, while significantly higher values were observed for the same acceleration with higher temporal resolution in two veins (p < 0.05). CONCLUSION k-t acceleration of 4D flow MRI is feasible for liver hemodynamic assessment with acceleration factors R = 3 and R = 5 resulting in a scan time reduction of at least 40 % with similar quantitation of liver hemodynamics compared with GRAPPA R = 2.

In vitro-ex vivo model systems for nanosafety assessment

Engineered nanomaterials have unique and novel properties enabling wide-ranging new applications in nearly all fields of research. As these new properties have raised concerns about potential adverse effects for the environment and human health, extensive efforts are underway to define reliable, cost- and time-effective, as well as mechanistic-based testing strategies to replace the current method of animal testing, which is still the most prevalent model used for the risk assessment of chemicals. Current approaches for nanomaterials follow this line. The aim of this review is to explore and qualify the relevance of new in vitro and ex vivo models in (nano)material safety assessment, a crucial prerequisite for translation into applications.

Evaluating gillnetting protocols to characterize lacustrine fish communities

Ecological research and monitoring of lacustrine ecosystems often requires a whole-lake assessment of fish communities. Gillnet sampling offers an efficient means of estimating abundance, biomass and fish community composition. However the choice of gillnet sampling protocol may influence lake characterization via physical properties of the nets and allocation of sampling effort between littoral, benthic and pelagic habitats. This paper compares two commonly used, whole-lake sampling protocols applied across 17 prealpine, subalpine and alpine European lakes ranging widely in size, depth and altitude to determine their relative strength for research and management applications. Effort-corrected estimates of abundance, biomass and species richness were correlated between the protocols and both distinguished the trout-dominated alpine communities from subalpine and prealpine lakes dominated by whitefish and perch. A considerable amount of variance remained unexplained between the two protocols however, which seemed to correspond with differences in the proportion of effort among benthic and pelagic habitats. We suggest that both the European standard (CEN) and vertical (VERT) netting protocols are suitable for assessing ecological status and monitoring changes in lake fish communities through time. However the details of each protocol should be kept in mind when comparing fish communities between lakes. Mesh sizes used in CEN nets produce a more even size frequency distribution, suggesting that this protocol is most appropriate for assessing size structure of fish assemblages. The high proportion of netting effort in benthic habitats shallower than 70 m depth under the CEN protocol means that, particularly in larger lakes, outcomes will be disproportionately influenced by the ecological condition of this habitat. The VERT protocol presumably provides a more accurate estimate of whole-lake CPUE and community composition because effort, in terms of net area, is more evenly distributed across the entire volume of the lake. This is particularly important in large and deep lakes where pelagic habitats occupy a high proportion of the lake volume.

Ecological speciation and phenotypic plasticity affect ecosystems

Phenotypic differences among closely related populations and species can cause contrasting effects on ecosystems; however, it is unknown whether such effects result from genetic divergence, phenotypic plasticity, or both. To test this, we reared sympatric limnetic and benthic species of whitefish from a young adaptive radiation in a common garden, where the benthic species was raised on two distinct food types. We then used these fish in a mesocosm experiment to test for contrasting ecosystem effects of closely related species and of plastically induced differences within a species. We found that strong contrasting ecosystem effects resulted more frequently from genetic divergence, although they were not stronger overall than those resulting from phenotypic plasticity. Overall, our results provide evidence that genetically based differences among closely related species that evolved during a young adaptive radiation can affect ecosystems, and that phenotypic plasticity can modify the ecosystem effects of such species.

Challenges in the participatory assessment of sustainable management practices in dryland ecosystems under regime shifts

Regime shifts, defined as a radical and persistent reconfiguration of an ecosystem following a disturbance, have been acknowledged by scientists as a very important aspect of the dynamic of ecosystems. However, their consideration in land management planning remains marginal and limited to specific processes and systems. Current research focuses on mathematical modeling and statistical analysis of spatio-temporal data for specific environmental variables. These methods do not fulfill the needs of land managers, who are confronted with a multitude of processes and pressure types and require clear and simple strategies to prevent regime shift or to increase the resilience of their environment. The EU-FP7 CASCADE project is looking at regime shifts of dryland ecosystems in southern Europe and specifically focuses on rangeland and forest systems which are prone to various land degradation threats. One of the aims of the project is to evaluate the impact of different management practices on the dynamic of the environment in a participatory manner, including a multi-stakeholder evaluation of the state of the environment and of the management potential. To achieve this objective we have organized several stakeholder meetings and we have compiled a review of management practices using the WOCAT methodology, which enables merging scientific and land users knowledge. We highlight here the main challenges we have encountered in applying the notion of regime shift to real world socio-ecological systems and in translating related concepts such as tipping points, stable states, hysteresis and resilience to land managers, using concrete examples from CASCADE study sites. Secondly, we explore the advantages of including land users’ knowledge in the scientific understanding of regime shifts. Moreover, we discuss useful alternative concepts and lessons learnt that will allow us to build a participatory method for the assessment of resilient management practices in specific socio-ecological systems and to foster adaptive dryland management.

Assessment of bovine adipose-derived stem cells osteogenic and adipogenic differentiation in Normoxic and hypoxic conditions

Background: The differentiation of ADSC is regulated by many factors, including oxygen tensions. Evidences have suggested that low oxygen tension or hypoxia is involved in the osteogenic, adipogenic differentiations of MSCs. Expansion and induction of ADSCs under hypoxia generally result in enhanced osteogenic, differentiation. Therefore, we analyzed bovine ADSC differentiations in Normoxia and hypoxia conditions Methodology: Recently (<8h) cow tail from a slaughterhouse, take out some fat from the tail and fat cells was isolated by using for isolation of ADSC protocol, the expansion cells were put into osteogenic and adipogenic medium for 3 weeks in hypoxia and normoxia conditions separately and characterized by Von kossa, Alizarin red and Oil red O staining and further by using real-time PCR by using primers of osteocalcin, Collagen type1, cbfa1/runx2, ALP, ostepontin, osteonectin, BMP2, BMP24, BMP27, noggin, gremlin, Nestin and HIF1A,VEGFA,PPARG,Leptin. Results: Our experiment results show hypoxia promotes osteogenesis but suppresses adipogenesis.

Combining qualitative and quantitative methods to analyze serious games outcomes: A pilot study for a new cognitive screening tool

Computer games for a serious purpose - so called serious games can provide additional information for the screening and diagnosis of cognitive impairment. Moreover, they have the advantage of being an ecological tool by involving daily living tasks. However, there is a need for better comprehensive designs regarding the acceptance of this technology, as the target population is older adults that are not used to interact with novel technologies. Moreover given the complexity of the diagnosis and the need for precise assessment, an evaluation of the best approach to analyze the performance data is required. The present study examines the usability of a new screening tool and proposes several new outlines for data analysis.

Two-Dimensional Crystallisation of Membrane Proteins and Structural Assessment

Two-dimensional (2D) crystallisation of Membrane proteins reconstitutes them into their native environment, the lipid bilayer. Electron crystallography allows the structural analysis of these regular protein–lipid arrays up to atomic resolution. The crystal quality depends on the protein purity, ist stability and on the crystallisation conditions. The basics of 2D crystallisation and different recent advances are reviewed and electron crystallography approaches summarised. Progress in 2D crystallisation, sample preparation, image detectors and automation of the data acquisition and processing pipeline makes 2D electron crystallography particularly attractive for the structural analysis of membrane proteins that are too small for single-particle analyses and too unstable to form three-dimensional (3D) crystals.

Dish Detection and Segmentation for Dietary Assessment on Smartphones

Diet-related chronic diseases severely affect personal and global health. However, managing or treating these diseases currently requires long training and high personal involvement to succeed. Computer vision systems could assist with the assessment of diet by detecting and recognizing different foods and their portions in images. We propose novel methods for detecting a dish in an image and segmenting its contents with and without user interaction. All methods were evaluated on a database of over 1600 manually annotated images. The dish detection scored an average of 99% accuracy with a .2s/image run time, while the automatic and semi-automatic dish segmentation methods reached average accuracies of 88% and 91% respectively, with an average run time of .5s/image, outperforming competing solutions.