dataesr/scientific-paragraphs-categorization huggingface dataset:
DISCUSSION In this study, we demonstrated the remarkable correlation between structural markers of en face OCT and retinal function on microperimetry testing in the largest cohort of MacTel patients reported to date. We developed a robust semiautomated, locally deformable registration algorithm to overlay en face OCT with MAIA microperimetry maps. Our software proved accurate in determining functional and structural changes with increasing disease severity and showed that scotoma on microperimetry can serve as a functional surrogate marker of EZ loss on SD-OCT in MacTel. The rationale for the suitability of the EZ as an indicator of dysfunction in MacTel is based on the anatomic structure of the fovea and the pathobiology of the disease. As most of the axons and pedicle terminals of the foveolar cones are displaced radially during foveal development,  21  the parafoveal area contains mainly Müller cells and glia.
85 and 0. 94, respectively. This disparity could be due to a number of reasons. First, our study dataset was larger, which likely reduced the effect of outliers in the analysis. Second, it is possible that our EZ defect segmentation and/or our semiautomated segmentation methods were more accurate than the previous technique. This can be robustly ascertained through a head-to-head comparison on a shared dataset. Third, regardless of the segmentation or registration method used, our method of interpolating microperimetry data resulted in a 1% to 2% better correlation between OCT and microperimetry data. We also showed the EZ defect areas on OCT best match the microperimetry loci with retinal sensitivity <25 dB. 4] [25]  Our work follows the method of Sallo and colleagues,  10  which analyzed EZ bands on OCT volumes to demonstrate that EZ break area was associated with a loss of mesopic retinal sensitivity.
Notably, this correlation was stronger than in the work of Sallo and colleagues,  10  which used manual overlays of the en face OCT and microperimetry maps, and stronger than the correlation between outer retinal thickness on OCT and retinal sensitivity afforded by the software Multi-modal Mapper described by Charbel and colleagues. 9 Methodologically, our study differs significantly from that of Charbel et al. ,  9  because our registration method uses en face OCT images, and produces experimental validation through sensitivity interpolation, optimal threshold computation, and correlation analysis. The topographic distribution of retinal sensitivity values generally corresponded closely to that of the EZ defect area, although in some analyzed cases, the correspondence was not perfect near the lesion border, a dynamic area that reflects functional changes in MacTel.
Acknowledgments Presented at the annual meeting of the  Association for Research in Vision and Ophthalmology, Seattle, Washington ,  United States , May 3, 2016. Supported by the  Lowy Medical Research Institute  ( La Jolla ,  CA, USA)  for the clinical study and the analysis presented in this manuscript. The funding organization participated in the design of the study in the article. Disclosure:  D. Mukherjee , None;  E. M. Lad , None;  R. R. Vann , None;  S. J. Jaffe , None; T. E. Clemons, None;  M. Friedlander , None;  E. Y. Chew , None;  G. J. Jaffe , Heidelberg Engineering (C);  S. Farsiu , P.
2% C + Y agarose before imaging, as described  75. Images were captured and processed using the Nis-Elements AR software (Nikon). To classify and quantify pneumococcal cells in different stages of the cell cycle, phase contrast images were further analyzed using the Metamorph 7. 5 software and the different cell categories (Fig. 1a ) were detected with the integrated morphometric analysis tool. Single cells were first detected using the threshold command from Metamorph. We then wrote a journal to automatically measure morphological parameters including the cell area, the cell perimeter, the length and the width, the elliptical factor, and the shape factor (see Supplementary Table  4 ). The elliptical factor is the ratio of the cell's width to its length and increases with the cell cycle. The shape factor is calculated from the perimeter (P) and the area (A), SF = 4πA/P 2.
Proteins were then transferred to a PVDF membrane, using a Turbo Blot transfer unit (Bio-Rad). After incubation with primary and secondary antibodies, membranes were imaged for the total protein transferred using the stain-free application on the ChemiDoc MP imager (Bio-Rad). Membranes were further incubated with clarity chemiluminescence substrate (Bio-Rad), and imaged on the ChemiDoc MP. Detection and measurement of band intensities was performed using Image Lab 5. 2 software (Bio-Rad), automatically normalized with respect to total protein quantification. Statistical analysis was conducted using Graph Pad Prism 5. 0 (San Diego, CA), F-tests indicated that the variance between groups was not significantly different (P = 0. 439), and statistical differences were determined using a two-way anova test followed by Bonferroni's post-test.
Acknowledgements We are indebted to  Jean-Pierre Claverys  who first anticipated a link between competence and the cell cycle. We thank  Bernard Martin  and  Chantal Granadel  for constructing the comM Janus mutant, and  Aurore Fleurie  for help in generating the phosphorylation profiles. We thank  Mathieu A. Bergé ,  Jean-Yves Bouet ,  Calum Johnston , and  Dave Lane  for stimulating discussions and critical reading of the manuscript as well as other members of the  Polard laboratory ,  Jérôme Rech , and  David Rudner  for helpful comments and support. This work was funded by the  Centre National de la Recherche Scientifique ,  Université Paul Sabatier ,  Agence Nationale de la Recherche  (Grant  ANR-10-BLAN-1331 ). M. J. B. was supported by a PhD grant from  Ministère de la Recherche et de l'Enseignement.
Assessment of mitochondrial apoptotic pathway Mitochondrial transmembrane potential assay (ΔCm). Decrease in mitochondrial transmembrane potential (ΔCm), a marker for mitochondrial integrity disruption, is one of the earliest events that lead to apoptosis. To measure mitochondrial transmembrane potential, we used tetramethylrhodamine methyl ester perchlorate (TMRM), a fluorescent lipophilic cationic probe readily taken up by live cells and accumulated in energized mitochondria  [23]. Loss of fluorescence intensity of TMRM indicates loss of ΔCm. After 24 h treatment with PEOL, cells were incubated in medium containing 20 nM TMRM (Molecular Probes, France) for 20min at 37˚C. The cells were subsequently washed three times with cold PBS, and finally recovered in 200 μl PBS. Δψm was assessed by flow cytometry (FACSCalibur, Becton Dickinson) and data were analyzed using Flowjo software version 10 (Tree Star) results were expressed as % of cells.
Measurement of mitochondrial ROS. Cells were treated with PEOL (10, 20, and 30 μg/ ml) for 24 hours. In some experiments, cells were incubated for 1 h with BAPTA-AM (5μM) before treatment with PEOL. After the treatment, cells were washed with PBS and then incubated with 2. 5 μM MitoSOX Red (Molecular Probes, France) for 20 min, at 37˚C in a humidified chamber containing 95%air and 5% CO 2 , to detect mitochondrial superoxide, primary ROS produced by mitochondria. The MitoSOX red was removed, and cells were subsequently washed twice with PBS, harvested and resuspended in 200 μl PBS. Finally, cells were analyzed by flow cytometry and data were processed using FlowJo software version 10 (Tree Star).
Measurement of free intracellular calcium [Ca 2+ ]i concentrations HCT8 and HCT116 cells were cultured on WillCo-dish wells with a glass bottom and loaded with Fura-2/AM (1 μM) for 60 minutes at 37˚C in loading buffer that contained: 110 mM NaCl; 5. 4 mM KCl; 25 mM NaHCO 3 ; 0. 8 mM MgCl 2 ; 0. 4 mM KH 2 PO 4 ; 20 mM HEPES-Na; 0. 33 mM Na 2 HPO 4 ; 1. 2 mM CaCl 2 , pH 7. 4 as described by Dramane et al. [24]. The changes in intracellular Ca 2+ (F340/F380) were monitored under a Nikon microscope (TiU) by using an S Fluor 40× oil immersion objective. The planes were taken at z intervals of 0. 3 μm, and NIS-Elements software was used to deconvolve the images. The microscope was equipped with an EM-CCD (Lucas) camera for real-time recording of 16-bit digital images. The dual excitation fluorescence imaging system was used for studies of individual cells.
Detection of caspase-3 and caspase-7 activities HCT116 and HCT8 cells were treated for 24 h with PEOL (10 μg/ml and 20 μg/ml), then harvested and stained by incubating for 1 h at 37˚C with caspase 3/ 7-FAM-DEVD-FMK solution (Immunochemistry Technologies, Bloomington, MN, USA). After 1 h cells were washed twice with wash buffer, pellets were resuspended in wash buffer and then analyzed by flow cytometry. Data were processed using FlowJo software version 10 (Tree Star).
PEOL increased intracellular Ca 2+ level in HCT8 and HCT116 cells triggering mitochondrial ROS induction and CHOP expression The literature reported that increase in intracellular Ca 2+ concentration ([Ca 2+ ]i) induced apoptosis through the activation of mitochondrial stress and ROS production  [27]. In order to ]i in 100% Ca 2+ medium in HCT116 and HCT8 cells; however, PEOL exposure did not induce increases in [Ca 2+ ]i in 0% Ca 2+ medium (insert A and insert B). Oleuropein only at 200 μg/ml, also, induced significant increases in [Ca 2+ ]i only in 100% Ca 2+ medium in these cell lines (insert A and insert B). These data suggested that PEOL and oleuropein induced a Ca 2+ influx from extracellular medium rather than its release from intracellular store. Thereafter, we analyzed the effect of BAPTA-AM, a cytoplasmic calcium chelator, on PEOLinduced mitochondrial ROS generation using MitoSOX red.
Moreover, Lyzenga's algorithm does not retrieve substrate reflectance, while the algorithm removes most of the depth effects, it generates a depth-invariant bottom index which is not related to the physics behind  [10]. Lyzenga et. al. [21]  further enhanced the methodology using multiple linear regressions which, however, still requir knowledge of water's optical properties at the time of image acquisition, which is not always available nor easy to obtain. Stumpf et al. [22]  presented a Log Ratio method to account for variable bottom types, which has been used since then by NOAA for coastal mapping and is available in an image processing software (ENVI, and SPEAR toolbox). This method still requires existing depth measurements for calibration and does not produce a water column corrected image.
Then, if necessary, the images were de-glinted following Hedley et al. [35]. The de-glinting process assumes a null penetration in water of the NIR-SWIR bands of the spectral images. Areas that are affected by glint are selected over deep water and then are used to calculate linear models of all bands against the NIR or SWIR band. The amount of glint is evidenced and then subtracted using the linear models. The images are then pansharpened using a modified version of the OrfeoToolbox algorithm in R-project in the Raster Package  [36]. In this process, the generation of a high resolution image (PXS) is achieved through the fusion of the panchromatic (PAN) with the multispectral (XS) data. First, the two images need to be orthorectified by oversampling of the XS image, then a low pass filter is applied to the PAN band to equalize (in the Fourier domain) the spectral content with XS data.
Once the spectral content is similar, XS are normalized with the low-pass filtered (PAN) and results are multiplied with the original panchromatic band. The whole process can be represented as: PXS(i,j) = ( XS(i,j) Filtered(PAN) )PAN As regards 4SM, the image preparation only consists in importing the raw data as digital numbers in a working database, and creating a few shapefiles for sampling glint, optically deep water, vegetation, and bright sandy beach. Deglinting and pansharpening in 4SM uses the same protocols as above; however, they are applied on the fly rather than as image pre-processing.
The BPL is used to estimate the ratio K blue /K green of Sensors 2017, 17, 2248 6 of 23 the diffuse attenuation coefficients in the blue and green bands. Then this ratio is used to interpolate spectral K for all visible bands, using Table XXVII of  Jerlov [12] ; this dataset reports the diffuse attenuation coefficients for downwelling irradiance in oceanic and coastal waters worldwide. For two examples of straightforward optical calibration diagrams over apparently homogeneous waters (one oceanic water type, and one coastal water type), please refer to diagrams in Appendix B. For most scenes, the calibration diagrams exhibit a complex hydrologic situation, which we tentatively explain as follows: the clear deep oceanic waters are usually covered by a layer of slightly turbid coastal waters; the thickness of this upper layer varies across the scene, from just a very few meters to in excess of 30 m (see Appendix B).
Groundtruthed DTM The collection of ground truth depth soundings in the SLC was completed in two days by the use of a boat equipped with an Elite5x HDI fishfinder (Lowrance, Tulsa, Oklahoma,). The Transducer (TM260 1kW with 50 kHz wide 19o beam/200 kHz narrow 6o beam, Airmar, Milford, NH, USA), was set to read from the waterline. The offset between the antenna and the transducer position was automatically calibrated by the instrument, and the instrument flagged data output with an internal gyroscope in case of excessive wave action. However, during the whole groundtruthing process, sea conditions were excellent. Data have been collected at a constant speed of 10 knots on parallel transects. Up to eight depth readings were averaged for each UTM navigation point, then tide height was subtracted using open source tide data (http://predmar.
Depth Retrieval in ENVI-SPEAR Tool Eight scenes were processed with the ENVI-SPEAR tool over the same ROI as 4SM (Figure  1 ). This tool operates the Log Ratio Transform algorithm developed by Stumpf et al. ,  [22]. It is integrated in the ENVI software (Exelis Visual Information Solutions, Boulder, CO, USA, v. 5. 3) as a Spectral Processing Exploitation and Analysis Resource (SPEAR) tool, from now ENVI-SPEAR tool. This tool is capable of retrieving relative depths from multispectral images which then are calibrated into meters using an existing depth sounding dataset. To this end, the groundtruthed DTM described above were used. An example of the output is shown in Figure  4c. Alien features were masked. Then an approximate atmospheric correction was applied on the whole image by Dark Pixel Subtraction.
Acknowledgments: Authors thank anonymous reviewers, the  Centro para la Biodiversidad Marina y la Conservación (CMBC) ,  Carlos Sanchez  for the help in the field and the loan of the sonar equipment, and  Erica Carone ,  Ramiro Arcos Aguilar ,  Roberto Decam ,  Tania Pelamatti  for the help in the field. Fabio Favoretto  is a recipient of doctoral grants and fellowships from the  Consejo Nacional de Ciencia y Tecnología of Mexico (CONACYT)  No. CVU 739667.
Patient and data sources This retrospective study included all cases of cervical cancer diagnosed between 1 January 2002 and 31 December 2011. Cases of lymphoma were excluded. Patients were identified through the Martinique Cancer Registry database. Since 1981, this registry has collected data on cancer incidence and has participated in the national program for epidemiological surveillance of cancer in France, under the auspices of the French Network of General and Specialized Registries (FRANCIM). This study used population census data from the French National Institute for Statistics and Economic Research for the calculation of the incidence results. Socio-demographic data and information on tumor characteristics (histological type, topography, stage at diagnosis [localized: stage I-II, advanced: stage III-IV], FIGO [International Federation of Gynecology and Obstetrics] stage, tumor size and invasion) were collected.
Data on professional activity (active vs inactive) were also recorded. Active professional activity covered those actively engaged in the workforce either through outside or self-employment; inactive professional activity covered retirees, students and others not actively engaged in the workforce. All cases were classified by clinical tumor stage (stage I: microinvasive and localized, stage II: invasion of surrounding organs or tissue, stage III: spread to distant nodes or tissue within the pelvis, stage IV: distant metastases) according to FIGO guidelines. The national guidelines for organized cervical cancer screening recommend screening every 3 years for all women between the ages of 25 and 65 years. Age groups for in situ tumors were classified according to organized screening age groups.
Cancer topography, morphology and behaviour were coded in accordance with the International Classification of Diseases for Oncology (ICD-O3) for the clinical data  [10]. Cancer cases were recorded in strict conformity with the international standards laid down by the International Agency for Research on Cancer (IARC), the French FRANCIM network and the European Network of Cancer Registries (ENCR). Active and passive follow-up methods were used to obtain the vital status of patients. Mortality data were obtained from the Centre for epidemiology of causes of death, run by the French National Institute of Health and Medical Research (INSERM). Patient follow-up was obtained from the civil deaths register for the survival analysis. Martinique Cancer Registry studies have been the subject of a declaration to the National Authority for the protection of privacy and personal data (Commission Nationale de l'Informatique et des Libertés, CNIL).
The median follow-up was calculated using the reverse Kaplan-Meier method. Log-rank tests were used to calculate differences according to prognostic factors. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated to select risk factors by the Cox model. Multivariate analysis of prognostic factors was performed using Cox's proportional hazards regression model, including all variables with a p-value < 0. 20 by univariate analysis. For all analyses, the level of statistical significance was set at p < 0. 05. All analyses were performed using SAS software version 9. 2 (SAS Institute Inc. , Cary, NC, USA) and Winbugs® 1. 4  [12, 13].
In order to contribute to the international epidemiology on cervical cancer, we conducted this study using data from a population-based cancer registry, to ensure the quality and exhaustiveness of data for our cases. In our study, we included a total of 1253 cervical cancers, comprising 947 in situ tumors and 306 invasive cancers, over the period 2002-2011. In situ tumors were three times more incident than invasive cancers. From 2002 to 2011, a decrease in the incidence of cervical cancer was observed, with the standardized incidence decreasing from 12. 6/100,000 to 7. 8/100,000 person-years for invasive cancers. Despite a higher incidence in Martinique, these trends are in line with French national data and are linked to the improvement in hygiene conditions and the development of individual and organized cervical screening by Pap smear testing  [16].
Strengths and weaknesses of the study The strengths of this study include the high quality of the data. The use of data from this population-based cancer registry ensures exhaustiveness of the cases included in our study, therefore ensuring good representativeness of cervical cancer in Martinique. Rigorous data quality control in compliance with the recommendations of the IARC (i. e. regular checking to ensure the complete follow-up for each woman, cross-referencing of information sources) ensures that the level of missing clinical and pathological data is kept to a minimum. This study also used population census data from the French National Institute for Statistics and Economic Research to ensure the robustness of the incidence results. The methods used in this paper could easily be applied in other regions with similar infrastructures (i.
e. an existing cancer registry, and a national body that carries out population censuses on a nationwide scale). Therefore, we believe that our study can be generalized by respecting these minimum conditions. Nonetheless, while these results are representative of the entire population of Martinique, local specificities (in terms of genetic or environmental factors, for example) may preclude extrapolation at the international level. Conversely, this study suffers from two main limitations. Firstly, we lacked sufficient data to evaluate potential social inequalities in healthcare and health status. Indeed, income levels and other socio-economic indicators were not collected in the Martinique Cancer Registry, and the high rate of missing data for the only available socio-economic indicator (namely, professional activity) may have affected the validity of these results.
The expression for G(θ 1 ,θ 2 ) is complicated and difficult to maximize analytically; however, the solution can be easily solved numerically by using MATLAB optimization toolbox. The only parameter in the optimization is δ, which depends on material properties of the linear retarders. Once θ 1 and θ 2 are determined, t 2 can be calculated using Eq. (  9 ), and θ LP can be calculated using Eq. (  4 ), Eq. (  9 ) and Eq. (10). We next consider the second case for the configuration of achromatic elliptical polarizers using one circular polarizer and two linear retarders as shown in Figs. 1(b ) and 3(b). For this case, the first retarder rotates the circular polarized (CP) light to Arc C. Considering the reverse direction, we see that the second retarder rotates the target state to Arc B. The problem becomes maximizing the coincidence of Arc B and Arc C.
In this final section, we explore the theoretical performance of achromatic elliptical polarizer with more than two retarder layers. MATLAB optimization toolbox is used to find the optimized design of three-layer retarder and four-layer retarder configuration, for visible band (λ = 450nm to 650nm) and a wider band (λ = 400nm to 1µm). The material for the retarder layer and the target state are the same as that in section 4. For three-layer and four-layer configurations, geometrical analysis is so complicated that the number of optimization variables cannot be reduced into one or two, as in the case of the two-layer configuration. Instead, we directly optimize the thickness and fast-axis orientation for all retarder layers using the MATLAB optimization toolbox. Although we have performed the calculation using many iterations, we cannot ascertain that the results are the global minimum.
This work explores the mechanical properties of high entropy alloys (HEAs) and complex concentrated alloys (CCAs) by comparing them with commercially available engineering alloys including industrystandard aerospace alloys. To reach this goal we have developed a materials database covering the main mechanical properties of HEAs and CCAs from the published literature. The database is used to represent various property spaces enabling an assessment of their performance for light weight structures and high-temperature structural applications. In addition, we illustrate the effects of alloying and of specific elements on the room temperature mechanical properties of HEAs and CCAs. With densities between titanium alloys and steels or nickel alloys, the best CCAs exceed commercial alloys in uniaxial loading and beam bending at room temperature.