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cc-by | Data Processing for 3DEM Map Challenge Another important showcase of the Scipion value was its utilization for the 3DEM Map Challenge which is a community-wide challenge being sponsored by EMDataBank, started in 2015 to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing vali... | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Additionally, published structures for each dataset were available, so we could compare the results obtained with Scipion with an official reference. In our case, we were particularly interested in measuring the improvements of the final reconstruction when applying our local movie alignment method based on optical flo... | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This information was used to improve the understanding of the molecular details of vaccine-induced protection against Neisseria meningitidis. In another project, in collaboration with Pascal Albanese and Cristina Pagliano, the target was the Photosystem II (PSII), involved in the water splitting reaction (powered by su... | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Furthermore, some wizards were added to preview, in real-time, operations before launching the job for the whole dataset. Data analysis was enhanced by the using of integrated visualization tools in Scipion for visualizing the results from these protocols. Another advantage in Scipion is the possibility to import all t... | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The main web page of this project can be seen at https://github. com/cossorzano/ scipion/wiki. The fork has retained the open-source nature of the project and can be freely downloaded. | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In a future, if more developers are engaged in the project, this delay can be minimized, or even removed if we work together in the release timings. Furthermore, Scipion is evolving towards a plug-in system where the release of the workflow and bookkeeping engine will be decoupled from the release of new wrappers for t... | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Two are the main reasons. First, many processes, sometimes related with different packages, may need to access simultaneously to the same data. Therefore, a locking systems that regulate concurrent access to data and metadata is needed. Second, metadata design should be able to provide extra parameters for some package... | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 3. 3 Galaxy main windows, divided into three panels: (left) available tools grouped into categories; (middle) fill the parameters of the selected tool or to inspect an output dataset; (right) full history of actions and produced outputs. 3. 4 Galaxy workflow editor. 3. 5 Overview of Vistrails architecture. 3. 6 Graphic... | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Particle with CTFModel and Coordinate attributes. 4. 4 Example of the Classes and Objects tables of a given SetOf P articles database file. 4. 5 Scipion project window divided in three main panels: (left) protocols menu; (top-right) project workflow display as a flowchart; (bottom-right) summary of inputs and outputs, ... | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Pseudocode of SqliteMapper. store functionThe code shown in Listing 5 illustrates how to create a P article object, set some of its properties (including other objects such as CT F M odel or Coordinate), and store the particle using a mapper instance. The database table generated by this code is shown in Figure4. 3. Ea... | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | (a) Table Classes of a SetOf P articles database. It contains the name and class of P article attributes and the corresponding colunm in the Objects table. | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | by Scipion. ISPyB Python requires a MySql module to be able to communicate with the underlying database and makes use of the Anaconda Python distribution. We sorted out this problem by executing a monitor protocol in Scipion, that produces the necessary data and launches an external process (with ISPyB Python) to popul... | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements Associated with the action of choosing some of the key parameters for a specific method, Scipion has "wizards", special interfaces that allow the selection of parameter values while showing their effects in real time. Fig. 4. 6D shows a wizard for a SPIDER. | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 3. 3 Galaxy main windows, divided into three panels: (left) available tools grouped into categories; (middle) fill the parameters of the selected tool or to inspect an output dataset; (right) full history of actions and produced outputs. 3. 4 Galaxy workflow editor. 3. 5 Overview of Vistrails architecture. 3. 6 Graphic... | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Listing 4 : 4 Pseudocode of SqliteMapper. store functionThe code shown in Listing 5 illustrates how to create a P article object, set some of its properties (including other objects such as CT F M odel or Coordinate), and store the particle using a mapper instance. The database table generated by this code is shown in ... | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ( b ) b Table Objects of a SetOf P articles database, where each row contains the values for a P article attributes (empty columns c05 and c06 were omitted for simplicity). | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | by Scipion. ISPyB Python requires a MySql module to be able to communicate with the underlying database and makes use of the Anaconda Python distribution. We sorted out this problem by executing a monitor protocol in Scipion, that produces the necessary data and launches an external process (with ISPyB Python) to popul... | 10.1016/j.jsb.2016.04.010 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Over the past decade, technically reliable circulating tumor cell (CTC) detection methods allowed the collection of large datasets of CTC counts in cancer patients. These data can be used either as a dynamic prognostic biomarker or as tumor material for "liquid biopsy". Breast cancer appears to be the cancer type in wh... | 10.1016/j.molonc.2016.01.001 | review | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | , 2016). Building on these results, the interventional trial TREAT CTC (NCT01548677), coordinated by the European Organization for Research and Treatment of Cancer (EORTC), is a large phase II study testing the effect of trastuzumab on CTC detection and survival in HER2-negative, M0(iþ) early BC (study design has been ... | 10.1016/j.molonc.2016.01.001 | review | en | 2,016 | false | false | false | true | Medicine | https://openalex.org/fields/27 |
cc-by | Other comments have been made on the trial's design and concepts (Alunni-Fabbroni et al. , 2014; Bidard and Pierga, 2015). On the basis of these negative results, the 2015 American Society of Clinical Oncology clinical practice guidelines for CTC count considered reasonable for clinicians to not use CTC count in women... | 10.1016/j.molonc.2016.01.001 | review | en | 2,016 | false | false | false | true | Medicine | https://openalex.org/fields/27 |
cc-by | In the run-in phase of the phase III CirCe01 trial (NCT01349842), which allows for a CTC-based management of chemotherapy in advanced metastatic setting, we observed that among patients with !5 CTC/7. 5 ml at baseline, a composite criteria (<5 CTC/7. 5 ml or relative decrease !À70% of the baseline CTC count) showed bet... | 10.1016/j.molonc.2016.01.001 | review | en | 2,016 | false | false | false | true | Medicine | https://openalex.org/fields/27 |
cc-by | The German DETECTIII study is a phase 3 study, comparing the lapatinib and chemotherapy combination vs chemotherapy alone in patients having at least 1 CTC with strong HER2 immunocytofluorescence (NCT01619111). A recent update on this study stated that about 19% of HER2-negative metastatic BC patients were screened wit... | 10.1016/j.molonc.2016.01.001 | review | en | 2,016 | false | false | false | true | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgements This work was supported by JSPS KAKENHI (grant numbers 15H03837 , 24104002 , 24225005 , 26620133 ) to ME and HS. Financial supports from the Sekisui Chemical Research Grant and the Kurata Memorial Hitachi Science and Technology Foundation to ME are also acknowledged. We acknowledge the fina... | 10.1039/c5bm00274e | article | en | 2,015 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements This work was supported by JSPS KAKENHI (grant numbers 15H03837 , 24104002 , 24225005 , 26620133 ) to ME and HS. Financial supports from the Sekisui Chemical Research Grant and the Kurata Memorial Hitachi Science and Technology Foundation to ME are also acknowledged. We acknowledge the fina... | 10.1039/c5bm00274e | article | en | 2,015 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Controls were run in same conditions and same IgG concentration as used for the respective primary antibodies. DAB-stained slides were observed using Zeiss Axioskop microscope and acquired by Kappa Image-Base software. Immunofluorescence staining was studied by an Olympus FV1000 confocal microscope and acquisitions wer... | 10.1002/cam4.730 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments The authors thank Prof Lucie Karayan-Tapon for providing frozen samples, the staff of the Department of Pathology (Poitiers University Hospital ) and especially Céline Marquant for technical assistance, and " La ligue contre le cancer " ( Comités de Charente, Charente Maritime, Deux-Sèvres, Morbiha... | 10.1002/cam4.730 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Using the extensive sequence data in the 1001 Genomes Project (http://1001genomes. org/) (1001 Genome Consortium, 2016), we accessed the genomic inversion sequence across all accessions. Clustering distance based on sequences across the 1. 2 Mb inverted region was used to construct maximum likelihood (ML) trees by a mo... | 10.1111/tpj.13262 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Methodology of SNP analysis 250K SNP chip data from RegMap accessions. RegMap genotype data were downloaded from the Bergelson lab website (http://bergelson. uchicago. edu/wp-content/uploads/2015/04/call_ method_75. tar. gz). Genotype calls specific to the inversion region or a 'control' region were extracted from the ... | 10.1111/tpj.13262 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | One-thousand, one-hundred and thirty-five VCF files available at the Arabidopsis 1001 Genomes Project (http://1001genomes. org/) were analyzed using iBrowser (Aflitos et al. , 2015; v. d228c22 ) with 50 kbp window size. Genomic clustering using concatenated homozygous SNPs was created using FastTree2 (v2. 17) for regi... | 10.1111/tpj.13262 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | LD between FRI and inversion We used bi-allelic SNPs from beginning of chromosome 4 up to 3 Mb to investigate the pattern of LD within this region. Only accessions from Eurasia were used, and sites with more than 10% missing data were excluded. Accessions were first coded according to their binary inversion/non-inversi... | 10.1111/tpj.13262 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGEMENTS The authors greatly acknowledge A. V. Gendrel and Z. Lippman for their help in chromatin profile analysis, T. Peterson , S. Peters and E. Wijnker for stimulating discussions, D. Weigel and M. Exposito-Alonso for helpful comments to the manuscript, and RijkZwaan Breeding , Fijnaart, the N... | 10.1111/tpj.13262 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Statistical analysis Values of the biochemical and clinical parameters were reported as means ± standard errors of the means (SEM). The control and contaminated groups were compared with Student's t test in normal populations or the rank sum test in non-normal populations. Statistical significance was defined by a P va... | 10.1007/s11306-016-1092-8 | article | en | 2,016 | false | true | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | The samples were analyzed on an Agilent 1200 RRLC coupled to a Bruker micrOTOF ESI-hybrid quadrupole-time of flight mass spectrometer (Wissembourg, France), both devices driven by the Compass 1. 3 SR 1 for micrO-TOF/maXis software (Bruker Daltonics). The LC conditions were: injection volume, 5 lL; autosampler temperatu... | 10.1007/s11306-016-1092-8 | article | en | 2,016 | false | true | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Data preprocessing and filtering LC-MS raw data were exported to ''. cdf'' file format with the manufacturer's DataAnalysis software (Bruker, Wissembourg, France) and preprocessed with the freely available XCMS software, including the CAMERA script (Smith et al. 2006). Peak picking was performed with the 'centWave' me... | 10.1007/s11306-016-1092-8 | article | en | 2,016 | true | true | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | The presence of any individual outlier was ruled out. Signal drift over time was quite weak within batches and unsurprisingly higher between them. Signals were corrected for both drifts with the Van der Kloet algorithm (a linear model) (van der Kloet et al. 2009) embedded into an R script (generous gift from Jean-Fra... | 10.1007/s11306-016-1092-8 | article | en | 2,016 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Statistical analyses Multivariate statistical analyses were performed with either SIMCA-P ? 12. 0 software (Umetrics, Umea ˚, Sweden) or R packages (base, pRoc, HDMD). Partial least squares discriminant analysis (PLS-DA) models were validated by CV-ANOVA (threshold for significance set at 0. 05) and by permutation test... | 10.1007/s11306-016-1092-8 | article | en | 2,016 | false | true | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | ) The number of rats for each measurement is indicated in parentheses Results are significantly different for: * P and Q2Y value decreased, below zero for Q2Y one). Three ''blocs'' of statistical analyses and features selection were applied to the preprocessed and filtered matrix (Supplemental Fig. 2 ), aiming at (1) c... | 10.1007/s11306-016-1092-8 | article | en | 2,016 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Separate analyses of time-point and dose effects At this second step of our statistical analysis we performed ANOVA-PCA (APCA) on the overall dataset. Indeed, we investigated two contamination factors simultaneously: the duration (time-point effect) and the level (dose effect). As for the multivariate data, depending o... | 10.1007/s11306-016-1092-8 | article | en | 2,016 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Metabolite identification For the most discriminant features, a tentative annotation was performed with MZedDB (http://www. maltese. dbs. aber. ac. uk:8888/hrmet/index. html) (Draper et al. 2009 ) from the chemical formulas generated from the accurately measured masses (accuracy \10 ppm) and isotopic patterns, calcula... | 10.1007/s11306-016-1092-8 | article | en | 2,016 | false | true | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | These results confirm our previous observations for the E-dose (40 mg L -1 ) after 9 months of contamination (Grison et al. 2013). Our data also confirm that uranium accumulates in the kidney at a rate equivalent to that we reported previously. Furthermore, our measurements of the rate of uranium accumulation in the k... | 10.1007/s11306-016-1092-8 | article | en | 2,016 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | N1-methylnicotinamide was detected as [M1?] (m/ z 137. 07) in both standard solution and experimental sample at 29-30 s. Fragmentation spectra were superimposable and showed a major fragment at m/z 94. 06 (Supplemental Fig. 3 ). This metabolite was previously identified in our proof-of-principle study (Grison et al. 2... | 10.1007/s11306-016-1092-8 | article | en | 2,016 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | 08), along with its sodium and potassium adducts (m/z 232. 06 and 248. 03, respectively), in both the standard solution and experimental sample at 123-126 s. Fragmentation spectra were superimposable and showed a major fragment at m/z 107. 05, as recorded in the Human Metabolome Database (HMDB00735) (Supplemental Fig. ... | 10.1007/s11306-016-1092-8 | article | en | 2,016 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | 10 and 184. 07, corresponding to choline and phosphorylcholine, respectively (Supplemental Fig. 6 ). Such losses are described for phosphatidylcholine (Metlin spectra for MID182) but no spectra was available for LysoPC. Finally, 4-pyridoxic acid was detected as [M ? H] (m/ z 184. 06), along with a small peak correspond... | 10.1007/s11306-016-1092-8 | article | en | 2,016 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Acknowledgments This study was partly supported by grants from AREVA. The authors would like to thank Frederic Voyer , Thierry Loiseau and Jean-Michel Guischet for expert animal care. | 10.1007/s11306-016-1092-8 | article | en | 2,016 | false | false | true | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Acknowledgments This study was partly supported by grants from AREVA. The authors would like to thank Frederic Voyer , Thierry Loiseau and Jean-Michel Guischet for expert animal care. | 10.1007/s11306-016-1092-8 | article | en | 2,016 | false | false | true | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Three-dimensional (3D) culture models are critical tools for understanding tissue morphogenesis. A key requirement for their analysis is the ability to reconstruct the tissue into computational models that allow quantitative evaluation of the formed structures. Here, we present Software for Automated Morphological Anal... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | r-project. org/), an open-source program for statistical analysis. SAMA enables a rapid, exhaustive and quantitative 3D analysis of the shape of a population of structures in a 3D image. SAMA is cross-platform, licensed under the GPLv3 and available at http://montevil. theobio. org/content/sama. | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In this article, we describe a software tool that can provide a rapid and biologically relevant analysis of the 3D culture models of the breast. Here we introduce our open-source SAMA (Software for Automated Morphological Analysis) that takes into account various parameters that define a normal breast while using 3D si... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The variety of epithelial structures makes this model a suitable choice for testing the power of SAMA in measuring several morphological parameters. While we have used SAMA to specifically analyze in vitro 3D models of the breast, we believe that developmental biologists in general as well as scientists keen on underst... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Description of SAMA SAMA is a novel method by which epithelial structures grown in 3D cultures can be imaged, reconstructed and analyzed with minimum human intervention and bias. It is a powerful and flexible tool for high-throughput morphological and statistical analysis of 3D images. Additionally, we have included an... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | theobio. org/en/content/sama. Herein, it is accessible as a FIJI plugin, compatible with Windows, Mac, and Unix along with downloadable source code. In addition, the website includes detailed technical description of the software with sample images for the user to download and learn how to navigate SAMA. Several plugin... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This step ensures an accurate count and morphological measurement of individual structures. However, in images where crowded structures are not an issue, these steps can be left out of the algorithm. Image processing steps described here are incorporated at several stages in the SAMA-images section of the code dependin... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | However, de-noising was excluded from the main SAMA framework and was run separately because it required more memory to function than what a typical personal computer has, the absence of which may cause the program to fail. With SAMA, users have the freedom to run de-noising or an alternative algorithm based on bilater... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | An overview of the results is obtained by principal component analysis (PCA) (Figs 3B and 4B ), which enables to identify the variables that have a greater influence in the variance of the samples. This technique enables the user to represent a data set with many parameters by defining new dimensions (which are combi... | 10.1371/journal.pone.0153022 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Computer generated images In order to validate SAMA, we tested our software on computer generated (CG) stacks (S2 Fig). The stacks were generated with 40 ellipsoids, which mimic an image containing 40 epithelial structures in a z-stack obtained by confocal microscopy of 3D cultures. These CG structures are at random po... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Statistical analysis The results we discuss are obtained both by ANOVA and Wilcoxon rank test and the p-value reported is the largest between the two values obtained. All statistical analyses are performed with cran R. The PCA analysis is performed with the R package FactoMineR. | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Imaging parameters A description of the parameters and the formula that were used to give an in-depth morphological analysis of the epithelial structures is described in Table 1. The basic morphometric parameters generated by 3D ROI manager plugin used in SAMA's program are elongation, flatness, sphericity and volume.... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Validation by computer generated images To ensure that SAMA is functional, we validated the software using computer generated model images. The model images were constructed to test several analytical functions of SAMA. SAMA provides the expected outputs from our designed conditions (S2 Fig). The analysis shows that C2... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Biological Validation and Analysis To validate SAMA, we used images from a hormone-sensitive 3D culture of the breast [11]. We chose to analyze gels that have previously been analyzed using 2D image measurements as well as 3D computational modeling and visualization using the commercial software package, Volocity [11... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | SAMA versus current software Currently, there are several commercial as well as open-source software packages available that combine image acquisition and analysis (Table 2 ). Among them, Imaris (Bitplane), Volocity (Perkin-Elmer), Image-Pro (MediaCybernetics), Amira and Metamorph (Molecular Devices) are examples of c... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This prevents researchers from knowing the details of the computing processes and modifying them to acquire specific and biologically relevant end-points. While these are aspects where open-source software has an edge over commercial software, the presently available open-source software packages have limitations as we... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | To remedy this latter inconvenience, we developed SAMA to 1) obtain an exhaustive and comprehensive analysis of tissue morphogenesis in 3D culture models of the breast, 2) to gain a deeper understanding of biological variability in tissue morphogenesis in 3D tissue cultures, 3) to acquire a rapid, automated and unbiase... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | the tissue. We encourage scientists to not only download and use SAMA, but also innovatively improvise its code to help in this endeavor. | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We greatly appreciate the editorial assistance by Cheryl Schaeberle. This research was supported by Avon Grant # 02-2009-093 , and 02-2011-095. Additional support was provided by NIEHS/NIH ES08314. The content is solely the responsibility of the authors and does not necessarily represent the offi... | 10.1371/journal.pone.0153022 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | For each model, 200 datasets of the total bacterial population were simulated over 24h using static antibiotic concentrations (256-fold concentration range) or over 48h under dynamic conditions (dosing every 12h; elimination halflife: 1h). Twelve-hundred random datasets (each containing 20 curves for static or four cur... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | These experimental models provide a wealth of time-course data on bacterial growth and killing [24]. While a series of time-course models for bacterial growth, killing and emergence of resistance has been proposed, it is currently unknown which type of dataset from in vitro studies is required to soundly develop such ... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Monte Carlo simulations for static and dynamic in vitro infection models Population mean estimates. Informed by the range of ed parameter values for different antibiotics and bacterial strains [3, 6, 14, 16, 20, 21, 23, [34] [35] [36] [37] (Table 1 ), we selected sets of parameter values that yielded comparable CFU ... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Each concentration was simulated in duplicate yielding 20 curves per static time-kill dataset. Viable counts of the total population were observed at 0 (pre-dose), 0. 5, 1, 2, 4, 8, 12 and 24 h. For dynamic one-compartment in vitro models, we simulated one dose level with dosing every 12 h and a growth control both in ... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Monte Carlo simulations. Our simulation-estimation studies (Fig 1 ) included the generation of 200 datasets for each of the six candidate models via Monte Carlo simulations for static or dynamic antibiotic concentration-time profiles. This included 100 datasets simulated under static and another 100 datasets simulated... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | All PD model parameters of the respective models were estimated by simultaneously fitting of all viable count profiles of the respective dataset (Table 2 ). Estimation was performed using nonlinear mixedeffects modeling in the S-ADAPT software via the importance sampling algorithm (pmethod = 4 in S-ADAPT) [38]. Model... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Bias and imprecision of parameter estimates. Table 4 (all six models) and Fig 4 (models 1, 3 and 5) compare the true parameter values with the median parameter estimates under static and dynamic conditions (based on the 100 datasets for each model and case). Overall, the precision of parameter estimates tended to be ... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | However, several models co-modelled both the total and resistant populations [28, 43, 44]. In this context, it seems surprising that no systematic simulation-estimation study has yet been published to assess the ability to distinguish between competing antimicrobial PD models with different resistance mechanisms. This... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | It was therefore interesting to assess, whether a robust population PK/PD estimation algorithm (i. e. importance sampling) could adequately distinguish between competing models. Despite the use of one of the latest population modeling algorithms, this simulation-estimation study showed that standard statistical criteri... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Quantitative viable count data of the resistant population(s) from antibiotic-containing agar plates at 0 and 24 h, for example, can provide experimental evidence to accept or reject several candidate models (Fig 2 ). If one observes resistant bacteria on antibiotic-containing agar plates (containing e. g. 3x the MIC ... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Model predictions over longer time periods (i. e. extrapolation) led to more biased predictions, as expected. Our predictions were based on the median of the parameters values. As these simulations did not account for parameter imprecision, the discrepancies between the predicted and the actual viable count profiles ar... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Some limitations of our study came from the necessity to select PD parameters characterizing the simulated pathogen, to choose an experimental design for static and dynamic killcurves and to set the initial values for parameter estimations. Our chosen parameter values adequately characterized the concentration-effect r... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | This presents a potential limitation of the present study. Moreover, the present study contained simulation-estimation scenarios for static and dynamic in vitro infection models. Our simulated dynamic in vitro model only assessed a scenario with one half-life, one dose level, and one dosing interval. Dynamic infection ... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Finally, we did not assess the sensitivity of the final parameter estimates and the model selection towards the choice of the initial estimates. In our previous work, we found the importance sampling algorithm in S-ADAPT to be robust and efficient despite the use of poor (i. e. 10-fold too high or 10-fold too low) init... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | For our simulation scenarios, dynamic infection models tended to provide more accurate parameter estimates than static concentration time-kill studies for some parameters. Static time-kill studies yielded more precise parameter estimates compared to dynamic models likely due to the larger number of profiles per dataset... | 10.1371/journal.pcbi.1004782 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgements This work was supported by CIRAD , the Institut Français du Caoutchouc, SIPH and SOCFINDO companies, as well as the Directorate General of Higher Education (DGHE) Ministry of National Education of Indonesia (Scholarship No. 386/E4. 4/K/2012 ), French Ministry of Foreign Affair , and AGREENIUM. | 10.22302/iribb.jur.mp.v84i1.190 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | High-throughput binary protein interaction mapping is continuing to extend our understanding of cellular function and disease mechanisms. However, we remain one or two orders of magnitude away from a complete interaction map for humans and other major model organisms. Completion will require screening at substantially ... | 10.15252/msb.20156660 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Moreover, these methods require multiplexed PCR amplification of templates varying widely in length and base composition, a procedure subject to severe PCR competition effects (Shiroguchi et al, 2012). To address these issues and establish a practical, scalable, and economical protein interaction mapping method, we de... | 10.15252/msb.20156660 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | A BFG-Y2H screen targeting cancer and cell cyclerelated proteins To demonstrate BFG-Y2H at larger scale and broaden discovery of new interactions, we next carried out BFG-Y2H screening on a "CCC" matrix, which includes proteins implicated in cancer according to the COSMIC database (Forbes et al, 2015) , as well as cyc... | 10.15252/msb.20156660 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Performance comparison between BFG-Y2H and state-of-theart Y2H To compare the practical performance of BFG-Y2H with state-of-theart Y2H methods, the four BFG-Y2H screen results and a recent high-quality Y2H-based human interactome dataset HI-II-14 (Rolland et al, 2014) were each evaluated using Lit-BM-13, a highquali... | 10.15252/msb.20156660 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | BFG-Y2H allows high-throughput Y2H screening at substantially lower cost and effort than the other Y2H procedures (Appendix Fig S4 and Table EV4 ). We demonstrated performance with a matrix of up to ~2. 5 M pairs, and there are no evident barriers to screening at genome scale. Each of our primary BFG-Y2H screens show... | 10.15252/msb.20156660 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Bait ORF fragments were amplified with O023 and O024 primers, and prey ORF fragments were amplified with O025 and O026 primers. The ORF PCR products were analyzed with E-Gel 48 1% Agarose Gels (Invitrogen), and the gel band images were automatically sorted according to the expected product sizes by a Perl script develo... | 10.15252/msb.20156660 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Gaussia princeps luciferase protein complementation assays Gaussia princeps luciferase protein complementation assay (GPCA)based validation assay was performed to validate the in-yeast assembly-based BFG-Y2H hits as described previously (Remy & Michnick, 2006; Cassonnet et al, 2011). In order to define the threshold o... | 10.15252/msb.20156660 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Reported protein interaction dataset Reported Y2H-positive human protein interaction dataset HI-II-14 and the Lit-BM-13 dataset were downloaded from the CCSB Human Interactome Database (http://interactome. dfci. harvard. edu), and reported interactions by orthogonal assays were obtained from the BioGRID database (Chatr... | 10.15252/msb.20156660 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements This work was supported by the Krembil Foundation (F. P. R. and L. P,), the Avon Foundation (F. P. R. ), the Ontario Research Fund (F. P. R. and L. P. ), the. | 10.15252/msb.20156660 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements This work was supported by the Krembil Foundation (F. P. R. and L. P,), the Avon Foundation (F. P. R. ), the Ontario Research Fund (F. P. R. and L. P. ), the. | 10.15252/msb.20156660 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments: This work was supported by the salaries paid to the authors by their employer (INRA: French National Institute for Agricultural Research). The authors did not receive funds to cover the costs of publishing in open access. | 10.3390/ijms17122094 | review | en | 2,016 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | 7, 14, 15 Trisomy 12 is the second most frequent recurrent chromosomal aberration in CLL and is associated with clinical and biological heterogeneity, potentially linked to the presence of additional genomic aberrations. This concept is reinforced by our present findings regarding the biological background and clinical... | 10.3324/haematol.2015.140202 | letter | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments: we would like to thank the members of the Spanish Cooperative Group for Hematological Cytogenetics for providing clinical and biological data, and Maria Gaitatzi , Zografia Lazarou , Olga Asteriou , Kristina Durechova and Eva Diviskova for performing cytogenetic and FISH analysis. Funding: thi... | 10.3324/haematol.2015.140202 | letter | en | 2,016 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Papanicolaou Hospital, Thessaloniki , Greece; and 14 Cancer Sciences, Faculty of Medicine, University of Southampton, UK the Swedish Research Council , the Lion's Cancer Research Foundation , and Selander's Foundation, Uppsala ; research projects CEITEC CZ. 1. 05/1. 1. 00/02. 68 and MZ CR projects NT13493-4/201... | 10.3324/haematol.2015.140202 | letter | en | 2,016 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | eligibility Criteria and Literature Search Strategy A systematic and comprehensive search of electronic databases, including MEDLINE, Scopus, http://ClinicalTrials. gov, the PROSPERO International Prospective Register of Systematic Reviews, Science Direct, Springer Link, and EMBASE was done from March 2016 to September... | 10.3389/fimmu.2016.00627 | review | en | 2,016 | true | false | false | true | Medicine | https://openalex.org/fields/27 |
cc-by | All articles were exported to the reference database Zotero. Due to the nature of this review, no request was performed for the ethics committee's approval. | 10.3389/fimmu.2016.00627 | review | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Data extraction and Synthesis Full copies of citations coded as potentially relevant were obtained, and those meeting the inclusion criteria were read in detail and data were extracted. One reviewer (Allison Clark) extracted information about the study aim, population and sample size, experimental design and duration o... | 10.3389/fimmu.2016.00627 | review | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | The articles and extracted data were read and the findings were organized into the following categories: (i) hygiene hypothesis, the gut microbiota, and the immune system; (ii) experimental articles about the possible relationship between disturbances of the gut microbiota and/or vitamin D3 deficiency, VDR dysfunction,... | 10.3389/fimmu.2016.00627 | review | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Data Synthesis A search conducted in March 2016 resulted in the following list of key terms combinations (hygiene hypothesis, the gut microbiota, and autoimmune disease = 5; vitamin D and autoimmune disease = 18; vitamin D3, VDR function, intestinal microbiota, and autoimmune diseases = 16). A total of 47 experimental ... | 10.3389/fimmu.2016.00627 | review | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | VDR Polymorphisms and Improper VDR Function Given the potential role VDRs have on immune responses and intestinal homeostasis, VDR genetic variants have also been studied as potential factor of autoimmune diseases since they may influence VDR activity. VDR is encoded by a large gene (>100 kb) mapped to chromosome 12q12... | 10.3389/fimmu.2016.00627 | review | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
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