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cc-by | Sample preparation and image analysis MCF-7 breast-cancer cells were previously plated in 96-well plates, treated for 24 h with 113 compounds at eight concentrations in triplicate, labeled with fluorescent markers for DNA, actin filaments, and tubulin, and imaged as described 10. Version 1. 0. 9405 of the image-analys... | 10.1177/1087057113503553 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The best feature selection accuracy is theoretically obtained by removing one feature at a time (SVM-RFE1), however this is computationally expensive. Therefore, following Loo et al. 15 , we used SVM-RFE2, which removes the 10% of the measurements with the lowest weight at each iteration. We selected the resulting mod... | 10.1177/1087057113503553 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Available data To facilitate the development and evaluation of additional profiling methods, we provide our ground-truth annotations (Table S2 ) and the measurements of each of the ~450,000 cells whose treatments are annotated. The data are supplied as comma-delimited files together with scripts for loading them into ... | 10.1177/1087057113503553 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Software implementations The profiling methods are implemented as part of the open-source image data-analysis software CellProfiler Analyst (http://cellprofiler. org/). The implementations do not make assumptions that are particular to our experiment, and can be readily applied to measurement data from the widely used ... | 10.1177/1087057113503553 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Results We implemented five proposed methods [13] [14] [15] [18] [19] for constructing per-sample profiles from per-cell measurements in a common computational framework. We ben hmarked the five methods on images we had previously collected of MCF-7 breast cancer cells treated for 24 h with a collection of 113 small ... | 10.1177/1087057113503553 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | (The term "mechanism-of-action" is used rather loosely here and refers to a sharing of similar phenotypic outcomes among different compound treatments, rather than referring strictly to modulation of a particular target or target class. ) The mechanistic classes were selected so as to represent a wide cross-section of ... | 10.1177/1087057113503553 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The mock treatment dimethyl sulfoxide (DMSO) was included as a negative control. Using the cosine distance as measure of profile dissimilarity, we classified the 103 treatments into mechanisms of action by assigning to each profile the MOA of the most similar profile (Figure 1 ; top panel). When classifying a treatmen... | 10.1177/1087057113503553 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Discussion We compared five methods [13] [14] [15] [18] [19] for generating per-sample profiles from image-based cell data in the context of classifying small molecules into 12 mechanisms of action based on cellular morphology. All me hods had previously been demonstrated in distinct experiments, mostly proof-of-prin... | 10.1177/1087057113503553 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | We did not evaluate the underlying statistical methods (KS, SVM, GM, FA), which have solid theoretical foundations and an excellent record of solving analysis problems of many kinds. On our dataset, the simplest method, which profiles compounds by the population means of the measurements of the treated cells, performed... | 10.1177/1087057113503553 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The choice of assay and optimal timepoint for profiling will likely depend on the scientific questions being asked. The chemical compounds we tested are commonly studied bioactive compounds. Therefore, the present study is valuable in providing a comparative analysis of methods in the context of one particular (but rep... | 10.1177/1087057113503553 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Thus, we foresee additional value in providing an analysis framework and a ground-truth dataset to facilitate further comparisons in the field using alternate datasets or methods. We have implemented all five methods and offer the source code (Text S2), along with our entire set of cellular measurements for our ground-... | 10.1177/1087057113503553 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We would like to thank Christopher Denz , Lisa Drew , Tom Houslay , Zhongwu Lai , David Logan , Melissa Passino , Tejas Shah , and J. Anthony Wilson for helpful input. This work was supported in part by the National Institutes of Health [grant number U54-HG005032 ]; the National Science Fou... | 10.1177/1087057113503553 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Medulloblastoma (MB) is a malignant pediatric brain tumor arising in the cerebellum consisting of four distinct subgroups: WNT, SHH, Group 3 and Group 4, which exhibit different molecular phenotypes. We studied the expression of Dickkopf (DKK) 1-4 family genes, inhibitors of the Wnt signaling cascade, in MB by screenin... | 10.3390/ijms14047492 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Results and Discussion We evaluated the expression of DKK family members (DKK1, DKK2, DKK3 and DKK4), by screening 355 expression profiling data, including 333 MB tumors and 22 normal cerebella from four independent datasets. This analysis showed the significant DKK1, DKK2 and DKK4 upregulation (p < 0. 01) in WNT subgr... | 10.3390/ijms14047492 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The X-axis indicates the four molecular subgroups according to the current consensus ( [7] ; WNT, SHH, Group 3 (GRP3) and Group 4 (GRP4)); the dataset A was not divided in the subgroups, due to a low number of samples. Y-axis: DKK3 mRNA expression value in the (A), (B) and (C) dataset, respectively. The dataset (D) re... | 10.3390/ijms14047492 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | We analyzed both the status of chromosome 11 in 77 MBs (17 from dataset A and 60 from dataset D) and the focal aberration targeting DKK3 by SNPs study [21] in 1,087 MBs. We found that 11 monosomy (10/77) and structural 11p loss (3/77) copy number aberrations were rare events and, in addition to the total absence to f... | 10.3390/ijms14047492 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Gene Expression Profiling, Array-CGH Data and miRNA Gene expression profiling was performed on 19 MB samples and two pools of normal cerebellum, as reference samples using the 44 k whole genome oligonucleotides microarray (Agilent Technologies; Santa Clara, CA, USA) (Dataset A). Labeling and hybridization of samples wa... | 10.3390/ijms14047492 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 10. 2. All raw data were deposited in Gene Expression Omnibus (http://www. ncbi. nlm. nih. gov/geo/; GSE39182). We also included the data obtained from three independent public datasets of gene expression: (1) B, including 188 MBs and 11 normal cerebellum data [4] ; (2) C, including 62 MB data [2] and 9 normal cereb... | 10.3390/ijms14047492 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | [31] (17 MBs, 244 k Agilent Technologies; GEO accession number GSE23005) and Pfister et al. [32] (60 MBs, 6 k BAC array; GEO accession number GSE8634). The raw data were analyzed by Agilent Genomics Workbench Lite Edition software (v. 6. 5; Agilent Technologies, Santa Clara, CA, USA, 2010) using the z-score algorithm... | 10.3390/ijms14047492 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Methylation Analysis The methylation status of the three promoters of DKK3 gene was performed on 32 tumor samples MB tumors and five cell lines by pyrosequencing analysis. Briefly, genomic DNA (1 µg) was modified with sodium bisulfite, which converts the unmethylated C into U, using the EZ DNA Methylation Gold kit (Zym... | 10.3390/ijms14047492 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Y-axis: DKK3 mRNA expression value in the (A), (B) and (C) dataset, respectively. The dataset (D) reports the relative expression between MB samples and NC, and the dotted grey line delineates the expression level in a pool of NC samples. Abbreviations: NC, normal cerebellum; MB, medulloblastoma; GRP3, Group 3; GRP4, G... | 10.3390/ijms14047492 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments The work has been supported by: Italian Neuroblastoma Foundation , Associazione Italiana per la Ricerca sul Cancro (AIRC), Ministero dell'Istruzione dell'Università e della Ricerca (MIUR). We are grateful to NICHD Brain and Tissue Bank , University of Maryland, Department of Pediatrics (Baltimore,... | 10.3390/ijms14047492 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Y-axis: DKK3 mRNA expression value in the (A), (B) and (C) dataset, respectively. The dataset (D) reports the relative expression between MB samples and NC, and the dotted grey line delineates the expression level in a pool of NC samples. Abbreviations: NC, normal cerebellum; MB, medulloblastoma; GRP3, Group 3; GRP4, G... | 10.3390/ijms14047492 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Since then, other improved SAS processing versions became available, and in order to have up-to-date and homogeneous X-ray parameters we cross-matched our source lists with the 2XMMi-DR3 catalogue 2. To evaluate the success rate of our visual screening we performed the cross-match for all the 2353 Xray sources and foun... | 10.1051/0004-6361/201220308 | article | en | 2,013 | false | true | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | The XMM-Newton error circle is the combination of two errors. The first one is the statistical uncertainty on the centroid of the PSF determined by the detection algorithm, σ radec typically ∼ 1 -2 ′′. The second one is the systematic error introduced by the uncertainty of the satellite's attitude, with values σ system... | 10.1051/0004-6361/201220308 | article | en | 2,013 | false | true | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Effective area of the survey To estimate the effective area of our survey, we first built sensitivity maps following the method described by Carrera et al. (2007). For each band and field, we created: i) exposure maps, that contain information on exposure times in each detector pixel taking into account the mirror vig... | 10.1051/0004-6361/201220308 | article | en | 2,013 | false | true | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Acknowledgements. The XMM-Newton SSC acknowledges sustained finantial support from CNES (France) and from Deutches Zemtrum für. | 10.1051/0004-6361/201220308 | article | en | 2,013 | false | false | true | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Luft und Raumfhart (Germany) DLR , under grant numbers FKZ 50 OX 0201 and 50 OX 0801. This research has made use of the SIMBAD database, operated at CDS, Strasbourg , France This publication makes use of data products from the Two Micron All Sky Survey , which is a joint project of the University of Massachusett... | 10.1051/0004-6361/201220308 | article | en | 2,013 | true | false | true | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Acknowledgments We thank Y. Yang and Dr. B. Dynlacht for providing C2C12 cells; Dr. S. Orkin for Jarid2 fl/fl and Jarid2 knockout ES cells; Dr. S. Kaneko , Dr. G. Li , and Dr. S. Tu for reagents and helpful discussions; Dr. W-W. Tee and Dr. R. Bonasio for valuable comments on the manuscript; and Dr. S. G... | 10.1101/gad.225888.113 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Experimental Crystal data Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IM2433). (i) Àx þ 1; Ày þ 1; Àz þ 2; (ii) Àx þ 3; Ày; Àz þ 2. | 10.1107/s160053681301369x | article | en | 2,013 | true | false | false | false | Chemistry | https://openalex.org/fields/16 |
cc-by | ACKNOWLEDGMENTS Charles Leroux and Nicolas Bats are gratefully acknowledged for the synthesis of zeolite EMC-1. | 10.2516/ogst/2012067 | article | en | 2,013 | false | false | true | false | Engineering | https://openalex.org/fields/22 |
cc-by | Microarrays The hybridization was performed on five 4X44K microarray slides where both the host O. tauri and the virus OtV5 genes were spotted. Four 60-mer oligonucleotide probes were designed for each gene on the microarray slide. A total of 33,093 probes were thus designed for 7,552 O. tauri genes and 1,056 probes fo... | 10.1093/gbe/evt053 | article | en | 2,013 | true | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Total RNA from each postinfection sampling time was hybridized with the control (T0) for 17 h at 65 C. After microarray disassembly and a wash procedure according to the manufacturer's instructions (Agilent), microarrays were scanned with the Agilent G2505B scanner. Raw data processing was carried out with the Agilent ... | 10.1093/gbe/evt053 | article | en | 2,013 | true | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | tRNA Data The available annotated tRNAs did not allow the translation of all codons in both Ostreococcus genomes. We therefore used tRNA-scanSE (Lowe and Eddy 1997) with default parameters to identify tRNAs and completed these predictions with recent findings on permuted tRNAs in Ostreococcus and Micromonas (Maruyam... | 10.1093/gbe/evt053 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgments The authors thank two anonymous referees for constructive comments and the Genomics of phytoplankton team for stimulating discussions, especially Romain Blanc-Mathieu and Rozenn Thomas. They also thank Adam Eyre-Walker for insightful suggestions on a previous version of the manuscript. This work ... | 10.1093/gbe/evt053 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | The complete microarray data set has been submitted to the ArrayExpress public database at EBI (Parkinson et al. 2009. | 10.1093/gbe/evt053 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgements Thanks to the participants of the ITFA 2012 and RES 2012 conferences, PSE, College of Management Academic studies Business School and THEMA seminars, Temple University Brown Bag Seminar , and to Barry Eichengreen , Ramon Ferrer-i-Cancho , Johanna Nichols and Gerard Roland. | 10.1080/13504851.2012.714062 | article | en | 2,012 | false | false | true | false | Social Sciences | https://openalex.org/fields/33 |
cc-by | MOTIVATION Semantic annotation of visual content is a process that requires linking pixels within an image with the semantic concepts associated to each group of pixels. This is often done in a user-assisted way. There exist several levels of interaction between users and visual content, ranging from an intentional and... | 10.1145/2506364.2506367 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Crowd-based Visual Annotation The collection of unintentional user feedback from crowds for visual analysis has been approached in different ways. The most popular approach is to design a collaborative effort aimed at a high quality annotation of a dataset. For example, LabelMe [11] has collected a large amount of lo... | 10.1145/2506364.2506367 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | These systems combine data with available ground truth with other data aiming at being analyzed. In these cases, users will unintentionally annotate the unlabeled images while the verification step is based on the dataset with available ground truth. However, existing works have focused on textual annotation applied at... | 10.1145/2506364.2506367 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | CROWDSOURCED OBJECT SEGMEN-TATION This work focuses on the potential of Ask'nSeek traces to help generating pixel-wise segmentation of the relevant objects within an image. In particular, the goal of this work is to estimate the minimum amount and type of user interaction necessary to achieve segmentation results of re... | 10.1145/2506364.2506367 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | g. , good alignment with image edges), and a second one that ranks these regions according to mid-level features, learned from a training dataset of segmented objects. As a result, the algorithm generates a ranked list of feasible segments within an image sorted according to their probability of being 'object-like'. CP... | 10.1145/2506364.2506367 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Simulated Traces The assessment of object segmentation techniques requires an extensive experimentation on large image datasets. On the other hand, one of the most limiting factors for research on crowdsourcing is the limitation on accessing large pools of users. These antagonistic scenarios can be managed by developin... | 10.1145/2506364.2506367 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Protocol We deployed a web-based version of the Ask'nSeek game, where players first encounter a tutorial video explaining them how to play the game. Players are then asked to log in, and wait to be paired with another player. The pairing algorithm is random. For every game, we record the login of both the master and th... | 10.1145/2506364.2506367 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Object Segmentation The potential of the presented framework in terms of object segmentation was assessed by comparing the obtained results with a ground truth. The Pascal VOC benchmark [4] provides a large collection of images that contain objects that belong to a diversity of semantic classes. We focused on the dat... | 10.1145/2506364.2506367 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Real vs Simulated Clicks The simulated traces described in Section 3. 3 have been validated on a reduced set of 10 objects extracted from the VOC2010 train and validation dataset. These 10 objects were selected as the ones with more clicks available on the game logs. The images have been actually used for playing Ask'n... | 10.1145/2506364.2506367 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Amount of clicks The main question addressed in this paper is an estimation of the amount of necessary clicks on a GWAP like Ask'nSeek to achieve a certain quality. Once the clicks simulator has been validated with real traces, it is possible to run extensive experimentation on a large dataset. The goal of these experi... | 10.1145/2506364.2506367 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | The plotted Jaccard index is an averaged value, which offers an estimation of the necessary clicks to obtain a certain quality. As expected, this averaged curve presents a growing trend with the amount of clicks, with a faster increase during the first 15 clicks. The last simulated value, for which 30 clicks have been ... | 10.1145/2506364.2506367 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | CONCLUSION In this paper we have shown how we could use game logs from players' interactions in the Ask'nSeek game to feed a segmentation algorithm and improve the quality of state-ofthe-art unsupervised segmentation results. We have also presented how to design and validate a simulator to generate such game logs. Our ... | 10.1145/2506364.2506367 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | visual entropy, object category. ) on the estimation of the amount of clicks. The simulator and evaluation software, as well the collected datasets, have been made publicly available from UPC website 1. | 10.1145/2506364.2506367 | preprint | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | ACKNOWLEDGMENTS The authors would like to thank Jordi Pont-Tuset for his valuable contributions. This work has been partially funded by the Camomile CHIST-ERA project, and by the Spanish project TEC2010-18094 MuViPro. | 10.1145/2506364.2506367 | preprint | en | 2,013 | false | false | true | false | Computer Science | https://openalex.org/fields/17 |
cc-by | In order to get a comprehensive repertoire of foldable domains within whole proteomes, including orphan domains, we developed a novel procedure, called SEG-HCA. From only the information of a single amino acid sequence, SEG-HCA automatically delineates segments possessing high densities in hydrophobic clusters, as defi... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Comparison of the whole set of SEG-HCA predictions with the Conserved Domain Database (CDD) also highlighted a wide proportion of predicted large (length. 50 amino acids) segments, which are CDD orphan. These orphan sequences may either correspond to highly divergent members of already known families or belong to new f... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The recognition of domain family membership for uncharacterized proteins is often a first step towards the understanding of their biological roles. Information about protein domains is stored in dedicated databases, in the form of profiles or hidden Markov models (HMMs), which are constructed through sequence similarit... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The information provided by SEG-HCA can then be compared with that included into structural databases, in order to support the structural meaning of the predictions. It can also be compared with that provided by the NCBI's conserved domain database (CDD) [24] in order to highlight «orphan» domains, i. e. predicted gl... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | SEG-HCA H2CD predictions are more than the converse of disorder predictions and may be used for defining categories in disorder The prediction of structured regions might be considered as the simple converse of disorder predictions. We thus compared the SEG-HCA predictions to the disorder predictions performed by IUPRE... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The developed procedure, combined with disorder predictors, may facilitate the specific identification of small segments that undergo coupled folding and binding. Combined with the analysis of specific domain databases, it also highlights orphan foldable segments, which remain yet uncharacterized. reported in the D 2 P... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | However, SEG-HCA H2CD predictions are not the simple converse of disorder predictions, as the overlap between the two sets constitutes 13. 8% of the total number of amino acids in the human proteome (Fig. 3A ). Similar overlap percentages are observed for other eukarya (10. 9% (S. cerevisiae), 13. 8% (P. falciparum), T... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Most of the regions (96. 1%) covered by PDB (14. 4% of the total number of amino acids) are included in the H2CD sets (H2CD and H2CD > IUPREDdis), indicating that most of the 3D structures included in PDB well cover H2CD predictions (Fig. 3B and Table 2 ). However, PDB files may include some disordered regions. Then,... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 4F )). The two complementary interaction domains of mouse CBP and human ACTR, which undergo synergistic folding, were also detected in the H2CD > IUPREDdis set (pdb: 1kbh [40] ). Some rare examples were also found of small stable globular domains, as illustrated in Fig. 4A. Worth noting is that small sequence segments... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | As shown above, known 3D structures in the H2CD > IUPREDdis set include several segments that undergo coupled folding and binding. We thus wondered if the overlap between H2CD and IUPREDdis may actually correspond to regions predominantly predicted by ANCHOR, a predictor of disordered regions that undergo binding trans... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | For the sequence segment included in the hexagon (IKTQQHILPEVPPVENF), the HCP percentage is 47% (8/17). A minimum is identified when this percentage is below 10%. Here, two segments are identified, as a minimum is reached at amino acid 150 (labeled 1). A distance tree is then calculated between hydrophobic clusters. Th... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Comparison with domains assigned from the Conserved Domain Database gives access to orphan sequences We collected for each protein the CDD assignments (as found using RPS-BLAST [24] ) and discarded multi-domains, as these are already counted with domains. 69348, 7251, 5161, 5497 and 2679 CD were identified in the prot... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Most (97%) of the CD amino acids (40% of the total number of amino acids) are included in the H2CD set (human proteome H2CD and H2CD > IUPREDdis, Fig. 3D and Table 2 ). As regards to the highlighted relationship between H2CD and foldable regions (see above), this indicates that CD mainly include foldable domains. The... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Lengths of H2CD segments: Emphasis on small, likely foldable segments, which are not described in CDD We calculated the distributions of CD and H2CD lengths (Fig. 6 and Fig. S5 ). Above 50 amino acids, the distributions are quite similar. However, SEG-HCA predicts a lot of small H2CD (length #50 amino acids), which ar... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This information is in particular absent from or poorly represented in domain databases. Some of these small H2CD segments correspond to isolated stable domains (as exemplified in Fig. 4A and 4B ). However, as observed from several case studies (Fig. 4D to 4F), small H2CD segments may also be intrinsically disordered... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | MoRFPred is based on a machine learning classifier, based on a comprehensive datasets of MoRFs (Molecular Recognition Features, [49] ), whereas ANCHOR relies on pairwise energy estimation, which is also the basis of the disorder predictor IUPred [45]. ANCHOR segments are likely to gain stabilizing energy by interacti... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | A ''folding propensity'' may thus be deduced from the consideration of small H2CD, especially included in the H2CD > IUPRED set, provided that these can be distinguished from artifacts (partial domains, as illustrated in Fig. 4G ). However, such cases could be solved using evolutionary information. The residues undergo... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | SEG-HCA is however limited to linear motifs including hydrophobic amino acids and thus does not address hydrophilic linear motifs. Another major observation of our work is that in eukaryotic proteomes, the number of H2CD is approximately higher than the number of domains assigned from the conserved domain database, rev... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 2B ). High and low values are associated with high and low densities of hydrophobic clusters, respectively. SEG-HCA next identifies areas of high hydrophobic cluster density (H2CD), typical of structured or folded regions (Fig. 2B ). To that aim, HCP minimal values are identified for a threshold level of 10%, defining ... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | SEG-HCA was used at different HCP threshold and for each 3D structure, we looked at the values that yield only one H2CD. The distribution of the HCP threshold values was then analyzed, showing an optimum at 22%, thus slightly above 10%. On average, 1. 1 H2CD are observed, with 78% coverage. However, it should be noted ... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Increasing this threshold value may allow the split of multi-domains into domains, but lead to loose small segments, as these last ones generally have low HCP values. Then, SEG-HCA builds a tree, starting from the observed distances between hydrophobic clusters (leafs). The closest hydrophobic clusters are grouped, con... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Datasets Proteome sequences were downloaded from the National Center for Biological Information (NCBI) (ftp://ftp. ncbi. nlm. nih. gov/ genomes/): Hsapiens, Scerevisiae_uid128, Ecoli_042_uid161985, Archeoglobus_fulgidus_DSM_4304_uid57717 and Pfalciparum. Comparison with assignments from the Protein Data Bank (PDB), Mob... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | mrc-lmb. cam. ac. uk/scop/). These classes correspond to all alpha protein, all beta protein, all alpha and beta protein (mainly parallel beta sheet), all alpha and beta protein (mainly anti-parallel beta sheet), multi-domain proteins, membrane and cell surface proteins and peptides, respectively. We obtained informati... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Figure1. Delineation and comparison of globular domains using HCA. The sequence is written on a duplicated alpha helical net and the hydrophobic amino acids (V, I, L, M, F, W, Y) are contoured [14, 15]. These form hydrophobic clusters, which mainly correspond to regular secondary structures [17]. This is illustrated he... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | (C) The predicted H2CD are then compared to the domains assigned by RPS-BLAST from the Conserved Domain Database (CDD). In this example, only the first domain is assigned from CDD (YEATS domain), while the second one remains unassigned by CDD (CDorphan). doi:10. 1371/journal. pcbi. 1003280. g002. | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We thank Jean-Paul Mornon for insightful developments associated with Hydrophobic Cluster Analysis, his enthusiastic suggestions and comments. We also thank Raphae ¨l Guerois and Stephane Marcand for critical reading of this manuscript, the three reviewers for their constructive remarks, as well a... | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | (C) The predicted H2CD are then compared to the domains assigned by RPS-BLAST from the Conserved Domain Database (CDD). In this example, only the first domain is assigned from CDD (YEATS domain), while the second one remains unassigned by CDD (CDorphan). doi:10. 1371/journal. pcbi. 1003280. g002. | 10.1371/journal.pcbi.1003280 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGMENTS We are grateful to Prof. George Daley , Prof. Ian Wilmut , Dr. In-Hyun Park , and Dr. Gareth Sullivan for providing the iPSC line. We are grateful to Judy Fletcher and Dr. Gareth Sullivan for providing guidance on iPSC culture and hepatocyte differentiation. We would like to thank Prof. Roland... | 10.5966/sctm.2012-0138 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Such results seem to be consistent with the linguistic and ethnic changes described above. Whether Central Asia was a source or a convergent zone of subcontinent gene flows remains unresolved. To address this issue, we present mt-DNA and Y-chromosome data on more than 500 Afghan samples from 5 main ethnic groups inhabi... | 10.1371/journal.pone.0076748 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Finally, the results were compared to databases built up from published literature for the purpose of the present study using autosomal results from 1183 individuals; 14,308 HV1 sequences concerning mt-DNA analysis and results from 34 harmonized Y haplogroups including 8,111 individuals. | 10.1371/journal.pone.0076748 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Autosomal genetic analyses Autosomal genetic variation was analyzed in a subset of 5 Hazara, 5 Tajik, 5 Uzbek, 4 Turkmen and 5 Pashtun samples using Illumina 650 K SNP array. In addition 1485 samples were taken from published data [43, [48] [49] [50] [51] [52] [53] (See Figure 1 and Table S2 for population descri... | 10.1371/journal.pone.0076748 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Quality control We used PLINK 1. 07 [54] in order to only retain SNPs on the 22 autosomal chromosomes that had a minor allele frequency. 1%, a genotyping success. 97%; additionally, only individuals that had a genotyping success rate. 97% were used. Also, since Linkage Disequilibrium (LD) can affect principal compone... | 10.1371/journal.pone.0076748 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In order to depict the spatial distribution of the ACs detected in Eurasia, the proportions of ACs 3, 4, 6, 7, 8 and 9 as resolved at K = 9 were then displayed on a color-graded map. Geographic correlation. Correlation between spatial distribution of the ACs detected in Eurasia and each proportion of ACs 1 to 9 as reso... | 10.1371/journal.pone.0076748 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | PCA and F ST calculations were performed using the SmartPCA program [57]. The mutations were scored compared to RSRS [58] and haplogroup affiliation was defined according to the latest build of Phylotree. org at the time (build 11, February 7 th ) [59]. | 10.1371/journal.pone.0076748 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Additionally, a total of 39 Y-STRS (DYS385a-b, DYS388, DYS389a, DYS389B, DYS390, DYS391, DYS392, DYS393, DYS394/19, DYS426, DYS437, DYS438, DYS439, DYS441, DYS442, DYS444, DYS445, DYS446, DYS447, DYS448, DYS449, DYS452, DYS454, DYS455, DYS456, DYS458, DYS459a-b, DYS460, DYS461n(TAGA)n, DYS462, DYS463, GGAAT1B07, YCAIIa... | 10.1371/journal.pone.0076748 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Haploid database construction We gathered mtDNA and Y-chromosome haplogroup frequency data from published data focused on Central Asian populations. Concerning mtDNA, a total of 14,308 HV1 sequences from 214 populations were included (Table S4 ). Haplogroups were assigned according to Phylotree. org (build 11, Februar... | 10.1371/journal.pone.0076748 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Concerning the Y-chromosome, we used the 37 populations from Afghanistan, Iran, Kyrgyzstan, Mongolia and Pakistan screened for the high-resolution 102 Y-SNPs. In order to fairly compare the genetic structure of the female population with that of the male one, we selected a subset of 27 populations from Iran, Mongolia a... | 10.1371/journal.pone.0076748 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Afterwards, we extended the comparison between populations to a subcontinental scale using our databases described above (Tables S3 ). Median Joining Network. Networks were constructed by the median joining method using Network 4. 5. 0. 2, where e = 0 and microsatellite loci were weighted proportionally to the inverse... | 10.1371/journal.pone.0076748 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Autosomal analyses Autosomal variation in Eurasian populations was analyzed via genetic structure in a dataset of over 232,000 genome-wide SNPs, depicted by a structure-like clustering approach implemented in ADMIXTURE. None of the genetic structure simulations (K = 2 to K = 15, see Figure S1 ) show any ancestral comp... | 10.1371/journal.pone.0076748 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Afghan populations are placed inbetween the Kyrgyz, Iranian and Pakistani populations suggesting a genetic influence across these parts of East Asia. FC plots in Figures S9 show 34 Y-chromosome haplogroup frequencies from our Central Asian database (see Table S4 ) and from the samples in this study (Afghanistan, Iran,... | 10.1371/journal.pone.0076748 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Discussion Central Asia, defined as the region containing Kazakhstan, Uzbekistan, Turkmenistan, Kyrgyzstan, Tajikistan, Afghanistan and the northern part of Pakistan, has gathered a growing and ongoing interest from archaeologists and anthropologists. Retracing the main historical events in the gene pool of the present... | 10.1371/journal.pone.0076748 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Here we improve the phylogenetic resolution within the Ychromosome haplogroup C3-PK2 by identifying SNPs describing two bifurcating subclades, C3a-M386 and C3b-M532 that accounted for all C3-PK2 derived chromosomes in our dataset. Another improvement to C3 topology involves new sub-haplogroups within the C3b-M532 compo... | 10.1371/journal.pone.0076748 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Sample sources We assayed the gut microbial communities, as present in fecal samples, of gorilla subspecies Gorilla gorilla gorilla (western lowland gorilla) from Cameroon and the CAR, and of gorilla subspecies Gorilla beringei graueri (eastern lowland gorilla) from the DRC. These data were merged with sequences genera... | 10.1101/gr.154773.113 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Sequence filtering Pyrosequencing reads were processed in QIIME version 1. 5. 0 (Caporaso et al. 2010). Flowgrams were obtained in SFF file format and converted to FASTA and QUAL files with process_sff. py. Reads were assigned to their respective samples based on their identifying barcode with split_libraries. py, all... | 10.1101/gr.154773.113 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We thank Kim Hammond for assistance with the preparation of figures; Eitel Mpoudi Ngolle and the SIV team of Project PRESICA for field work and logistical support in Cameroon; the Cameroonian Ministries of Health, Forestry and Wildlife , and Research for permission to collect samples in Cameroon;... | 10.1101/gr.154773.113 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data access Sequence data generated for this study have been submitted to the NCBI Sequence Read Archive (SRA; http://www. ncbi. nlm. nih. gov/ sra) under accession number SRR799915. | 10.1101/gr.154773.113 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The median value of the CIRRUS flag in our sample is 0. 093 at 857 GHz, a low value compatible with no cirrus contamination when used in conjunction with the EXTENDED=0 flag (e. g. Herranz et al. 2012). 3. We query the NED and SIMBAD databases at the positions of all our ERCSC sources using a 2. ′ 5 search radius. Each... | 10.1051/0004-6361/201220053 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | We call a source "Galactic unsecure" when one of the two databases returns no identification and the other a Galactic identification. We do not use "Galactic secure" or "Galactic un-secure" sources in Here α 217 143 is shown as a dotted line, α 353 217 as a dashed line, and α 857 545 as a solid line. The region 2 ≤ α ≤... | 10.1051/0004-6361/201220053 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Nature of the Galaxies at submillimetre and millimetre wavelengths The change in the nature of sources (synchrotron dominated vs. dusty) with frequency was first observed in the Planck data in Planck Collaboration VII (2011). Our new sample allows a more precise quantification because of its completeness. The statistic... | 10.1051/0004-6361/201220053 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
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