| 1. |
- Abiri, Najmeh, et al.
(author)
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Establishing strong imputation performance of a denoising autoencoder in a wide range of missing data problems
- 2019
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In: Neurocomputing. - Amsterdam : Elsevier BV. - 0925-2312 .- 1872-8286. ; 365, s. 137-146
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Journal article (peer-reviewed)abstract
- Dealing with missing data in data analysis is inevitable. Although powerful imputation methods that address this problem exist, there is still much room for improvement. In this study, we examined single imputation based on deep autoencoders, motivated by the apparent success of deep learning to efficiently extract useful dataset features. We have developed a consistent framework for both training and imputation. Moreover, we benchmarked the results against state-of-the-art imputation methods on different data sizes and characteristics. The work was not limited to the one-type variable dataset; we also imputed missing data with multi-type variables, e.g., a combination of binary, categorical, and continuous attributes. To evaluate the imputation methods, we randomly corrupted the complete data, with varying degrees of corruption, and then compared the imputed and original values. In all experiments, the developed autoencoder obtained the smallest error for all ranges of initial data corruption.
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| 2. |
- Ali, Sharafat, Associate Professor, 1976-, et al.
(author)
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Composition–structure–property relationships of transparent Ca–Al–Si–O–N oxynitride glasses : The roles of nitrogen and aluminum
- 2023
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In: Journal of The American Ceramic Society. - : John Wiley & Sons. - 0002-7820 .- 1551-2916. ; 106:3, s. 1748-1765
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Journal article (peer-reviewed)abstract
- We explore the formation and composition–structure–property correlations of transparent Ca–Al–Si–O–N glasses, which were prepared by a standard melt-quenching technique using AlN as the nitrogen source and incorporating up to 8 at.% of N. Their measured physical properties of density, molar volume, compactness, refractive index, and hardness—along with the Young, shear, and bulk elastic moduli—depended roughly linearly on the N content. These effects are attributed primarily to the improved glass-network cross-linking from N compared to O, rather than the formation of higher-coordination AlO5 and AlO6 groups, where 27Al magic-angle-spinning nuclear magnetic resonance experimentation revealed that aluminum is predominately present in tetrahedral coordination as AlO4 units. Yet, several physical properties, such as the refractive index along with the bulk, shear, and Young's elastic moduli, increase concomitantly with the Al content of the glass. We discuss the incompletely understood mechanical–property boosting role of Al as observed both herein and in previous reports on oxynitride glasses, moreover suggesting glass-composition domains that are likely to offer optimal mechanical properties.
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| 3. |
- Andersson, Anna, et al.
(author)
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Gene expression profiling of leukemic cell lines reveals conserved molecular signatures among subtypes with specific genetic aberrations
- 2005
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In: Leukemia. - : Springer Science and Business Media LLC. - 1476-5551 .- 0887-6924. ; 19:6, s. 1042-1050
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Journal article (peer-reviewed)abstract
- Hematologic malignancies are characterized by fusion genes of biological/clinical importance. Immortalized cell lines with such aberrations are today widely used to model different aspects of leukemogenesis. Using cDNA microarrays, we determined the gene expression profiles of 40 cell lines as well as of primary leukemias harboring 11q23/MLL rearrangements, t(1;19)[TCF3/PBX1], t(12;21)[ETV6/RUNX1], t(8;21)[RUNX1/CBFA2T1], t(8;14) [IGH@/MYC], t(8;14)[TRA@/MYC], t(9;22)[BCR/ABL1], t(10;11) [PICALM/MLLT10], t(15;17)[PML/RARA], or inv(16)[CBFB/MYH11]. Unsupervised classification revealed that hematopoietic cell lines of diverse origin, but with the same primary genetic changes, segregated together, suggesting that pathogenetically important regulatory networks remain conserved despite numerous passages. Moreover, primary leukemias cosegregated with cell lines carrying identical genetic rearrangements, further supporting that critical regulatory pathways remain intact in hematopoietic cell lines. Transcriptional signatures correlating with clinical subtypes/primary genetic changes were identified and annotated based on their biological/molecular properties and chromosomal localization. Furthermore, the expression profile of tyrosine kinase-encoding genes was investigated, identifying several differentially expressed members, segregating with primary genetic changes, which may be targeted with tyrosine kinase inhibitors. The identified conserved signatures are likely to reflect regulatory networks of importance for the transforming abilities of the primary genetic changes and offer important pathogenetic insights as well as a number of targets for future rational drug design.
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| 4. |
- Andersson, Anna, et al.
(author)
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Microarray-based classification of a consecutive series of 121 childhood acute leukemias: prediction of leukemic and genetic subtype as well as of minimal residual disease status.
- 2007
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In: Leukemia. - : Springer Science and Business Media LLC. - 1476-5551 .- 0887-6924. ; 21:6, s. 1198-1203
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Journal article (peer-reviewed)abstract
- Gene expression analyses were performed on 121 consecutive childhood leukemias (87 B-lineage acute lymphoblastic leukemias (ALLs), 11 T-cell ALLs and 23 acute myeloid leukemias (AMLs)), investigated during an 8-year period at a single center. The supervised learning algorithm k-nearest neighbor was utilized to build gene expression predictors that could classify the ALLs/AMLs according to clinically important subtypes with high accuracy. Validation experiments in an independent data set verified the high prediction accuracies of our classifiers. B-lineage ALLs with uncharacteristic cytogenetic aberrations or with a normal karyotype displayed heterogeneous gene expression profiles, resulting in low prediction accuracies. Minimal residual disease status (MRD) in T-cell ALLs with a high (40.1%) MRD at day 29 could be classified with 100% accuracy already at the time of diagnosis. In pediatric leukemias with uncharacteristic cytogenetic aberrations or with a normal karyotype, unsupervised analysis identified two novel subgroups: one consisting mainly of cases remaining in complete remission (CR) and one containing a few patients in CR and all but one of the patients who relapsed. This study of a consecutive series of childhood leukemias confirms and extends further previous reports demonstrating that global gene expression profiling provides a valuable tool for genetic and clinical classification of childhood leukemias.
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| 5. |
- Andreasson, Ulrika, et al.
(author)
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Identification of uniquely expressed transcription factors in highly purified B-cell lymphoma samples.
- 2010
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In: American Journal of Hematology. - : Wiley. - 0361-8609 .- 1096-8652. ; 85:6, s. 418-425
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Journal article (peer-reviewed)abstract
- Transcription factors (TFs) are critical for B-cell differentiation, affecting gene expression both by repression and transcriptional activation. Still, this information is not used for classification of B-cell lymphomas (BCLs). Traditionally, BCLs are diagnosed based on a phenotypic resemblance to normal B-cells; assessed by immunohistochemistry or flow cytometry, by using a handful of phenotypic markers. In the last decade, diagnostic and prognostic evaluation has been facilitated by global gene expression profiling (GEP), providing a new powerful means for the classification, prediction of survival, and response to treatment of lymphomas. However, most GEP studies have typically been performed on whole tissue samples, containing varying degrees of tumor cell content, which results in uncertainties in data analysis. In this study, global GEP analyses were performed on highly purified, flow-cytometry sorted tumor-cells from eight subgroups of BCLs. This enabled identification of TFs that can be uniquely associated to the tumor cells of chronic lymphocytic leukemia (CLL), diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), hairy cell leukemia (HCL), and mantle cell lymphoma (MCL). The identified transcription factors influence both the global and specific gene expression of the BCLs and have possible implications for diagnosis and treatment.
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| 6. |
- Aski, Sahar Nikkhou, et al.
(author)
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Studies of Inclusion Complexes of Dichloromethane in Cryptophanes by Exchange Kinetics and 13C NMR in Solution and the Solid State
- 2008
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In: Journal of Physical Chemistry C. ; 112, s. 13873-13881
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Journal article (peer-reviewed)abstract
- Cryptophanes are molecular hosts having high binding affinities for small, neutral molecules in weakly polar solvents. We have previously studied dichloromethane as a guest inside the cavity of cryptophane-E (cryptophane-333), in solution as well as in the solid state. Here, we present a solution 13C relaxation study of dichloromethane as the guest molecule complexed in the cavity of two smaller hosts: cryptophane-A (cryptophane-222) and cryptophane-223. Carbon-13 relaxation measurements were performed for both guest and host molecules. Exchange kinetics have to be explicitly taken into consideration in order to derive 13C relaxation properties of the bound guest. Rate coefficients were measured using proton 1D-exchange experiments. We have also investigated dichloromethane complexed in the cavity of cryptophane-233 in the solid state, by estimating the motionally averaged 13C-1H dipolar interactions from recoupling experiments under magic angle spinning (MAS) conditions. The measurements for the three cryptophanes provide a consistent set of results for the extent of rotational freedom of the guest inside the host cavities.
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| 7. |
- Bonneau, Charlotte, et al.
(author)
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Open-Framework Germanate Built from the Hexagonal Packing of Rigid Cylinders
- 2009
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In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 48:21, s. 9962-9964
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Journal article (peer-reviewed)abstract
- We present a novel open-framework oxide material constructed from Ge10(O,OH)28 (Ge10) oxide clusters prepared via a nonsurfactant route. The material shows two distinct pore windows of 9.43 and 4.65 Å and a low framework density structure of 12.7 Ge atoms per 1000 Å3. The topological study leads to the recognition of a newly observed trinodal 6,7-heterocoordinated net related to the 7-coordinated swh net. The structure displays large rigid cylinders showing features indicating a growth mechanism by hard-sphere packing of the inorganic moiety similar to that observed in mesoporous materials.
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| 8. |
- Brinkmann, Andreas, et al.
(author)
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Central-transition double-quantum sideband NMR spectroscopy of half-integer quadrupolar nuclei : estimating internuclear distances and probing clusters within multi-spin networks
- 2014
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 16:15, s. 7037-7050
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Journal article (peer-reviewed)abstract
- We introduce a strategy to estimate the size of clusters of recoupled homonuclear half-integer quadrupolar nuclei under magic-angle spinning (MAS) conditions, by combining double-quantum (2Q) sideband NMR experiments with an approximate numerical analysis based on the summation of all spin-pairs present over a given radius of the structure. The experiment relies solely on the evolution of homonuclear 2Q coherences (2QC) among the central-transitions (CT) of half-integer spins and is suitable for probing clusters in network structures, such as those encountered in large groups of oxide-based materials. Experimental B-11, Na-23 and Al-27 NMR results are presented on bis(catecholato)diboron, Na2SO4 and Al2O3, respectively; in each case, the growth of the spin-cluster size was monitored from a series of experiments that employed progressively lengthened 2QC excitation intervals. Our new approach is the first option for probing larger constellations of half-integer spins; it provides similar information as the multiple-quantum spin counting experiment, which is well-established for spin-1/2 applications but has hitherto not been demonstrated for half-integer spins undergoing MAS. We also discuss various options for determining the internuclear distance within a (nearly) isolated pair of half-integer spins by comparing the experimental 2Q sideband NMR spectra with results from numerical simulations involving various degrees of approximation.
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| 9. |
- Brinkmann, Andreas, et al.
(author)
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Estimating internuclear distances between half-integer quadrupolar nuclei by central-transition double-quantum sideband NMR spectroscopy
- 2011
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In: Canadian journal of chemistry (Print). - 0008-4042 .- 1480-3291. ; 89:7, s. 892-899
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Journal article (peer-reviewed)abstract
- We demonstrate the estimation of homonuclear dipolar couplings, and thereby internuclear distances, between half-integer spin quadrupolar nuclei by central-transition (CT) double-quantum (2Q) sideband nuclear magnetic resonance (NMR) spectroscopy. It is shown that the rotor-encoded sideband amplitudes from CT 2Q coherences in the indirect dimension of the two-dimensional NMR spectrum are sensitive probes of the magnitude of the homonuclear dipolar coupling, but are significantly less affected by other NMR parameters such as the magnitudes and orientations of the electric field gradient tensors. Experimental results of employing the R2(2)(1)R2(2)(-1) recoupling sequence to the (11)B spin pair of bis(catecholato)diboron resulted in an estimation of the internuclear B-B distance as (169.6 +/- 3) pm, i.e., with a relative uncertainty of +/- 2%, and in excellent agreement with the distance of 167.8 pm determined by single-crystal X-ray diffraction.
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| 10. |
- Dalou, Celia, et al.
(author)
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Redox control on nitrogen isotope fractionation during planetary core formation
- 2019
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:29, s. 14485-14494
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Journal article (peer-reviewed)abstract
- The present-day nitrogen isotopic compositions of Earth's surficial (N-15-enriched) and deep reservoirs (N-15-depleted) differ significantly. This distribution can neither be explained by modern mantle degassing nor recycling via subduction zones. As the effect of planetary differentiation on the behavior of N isotopes is poorly understood, we experimentally determined N-isotopic fractionations during metal-silicate partitioning (analogous to planetary core formation) over a large range of oxygen fugacities (Delta IW -3.1 < logfO(2)
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