Aligned Pairs Research Articles

Synergistic combination of multi-Zr(IV) cations and lacunary Keggin germanotungstates leading to a gigantic Zr24-cluster-substituted polyoxometalate.

Synergistic directing roles of six lacunary fragments resulted in an unprecedented Zr24-cluster substituted poly(polyoxotungstate) Na10K22[Zr24O22(OH)10(H2O)2(W2O10H)2(GeW9O34)4(GeW8O31)2]·85H2O (Na10K22·1·85H2O), which contains the largest [Zr24O22(OH)10(H2O)2] (Zr24) cluster in all the Zr-based poly(polyoxometalate)s to date. The most remarkable feature is that the centrosymmetric Zr24-cluster-based hexamer contains two symmetry-related [Zr12O11(OH)5(H2O)(W2O10H)(GeW9O34)2(GeW8O31)](16-) trimers via six μ3-oxo bridges and was simultaneously trapped by three types of different segments of B-α-GeW9O34, B-α-GeW8O31, and W2O10. The other interesting characteristic is that there are two pairs of intriguing triangular atom alignments: one is composed of the Zr(2,4,6,8,11) and W21 atoms and the other contains the Ge(1-3), Zr(3,5,7,9,10,12) and W26 atoms, and the Zr5 atom is inside the triangle; a linking mode is unobserved. The oxygenation reactions of thioethers by H2O2 were evaluated when Na10K22·1·85H2O served as a catalyst. Results show that it is an effective catalyst for oxygenation of thioethers by H2O2. The unique redox property of oxygen-enriched polyoxotungstate fragments and Lewis acidity of the Zr cluster imbedded in Na10K22·1·85H2O provide a sufficient driving force for the catalytic conversion from thioethers to sulfoxides/sulfones.

Dynamics of a small number of droplets in microfluidic Hele–Shaw cells

We investigate the dynamics of a small number of droplets (N = 1, 2, 3) in microfluidic Hele–Shaw cells. We study the cases N = 1, 2, and 3 droplets and analyze the influence of the side walls. In the course of the study, we observe spontaneous alignment of droplet pairs, pair exchanges, droplet escape, multiple reflections between walls, i.e., a number of phenomena that have not been reported yet. As a whole, using pairwise far-field dipolar interactions between droplets, along with treating the walls as mirrors, allows to reproduce the observations, even though limitations in the predictability of the model are pointed out in a few cases. From a more practical prospective, the work shows that the behavior of elementary droplet assemblies can be put under acceptable experimental control in a wide variety of situations, a feature potentially interesting for self-assembly, mixing, or transport of particles in microfluidic environments.

BIMA V3: an aligner customized for mate pair library sequencing

Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate-pair read pairs to a reference genome is a challenging and time-consuming process for most next-generation sequencing alignment programs. Large insert sizes, introduction of library preparation protocol artifacts (biotin junction reads, paired-end read contamination, chimeras, etc.) and presence of structural variant breakpoints within reads increase mapping and alignment complexity. We describe an algorithm that is up to 20 times faster and 25% more accurate than popular next-generation sequencing alignment programs when processing mate pair sequencing.

Development of EST-SSR markers and construction of a linkage map in faba bean (Vicia faba).

To develop a high density linkage map in faba bean, a total of 1,363 FBES (Faba bean expressed sequence tag [EST]-derived simple sequence repeat [SSR]) markers were designed based on 5,090 non-redundant ESTs developed in this study. A total of 109 plants of a ‘Nubaria 2’ × ‘Misr 3’ F2 mapping population were used for map construction. Because the parents were not pure homozygous lines, the 109 F2 plants were divided into three subpopulations according to the original F1 plants. Linkage groups (LGs) generated in each subpopulation were integrated by commonly mapped markers. The integrated ‘Nubaria 2’ × ‘Misr 3’ map consisted of six LGs, representing a total length of 684.7 cM, with 552 loci. Of the mapped loci, 47% were generated from multi-loci diagnostic (MLD) markers. Alignment of homologous sequence pairs along each linkage group revealed obvious syntenic relationships between LGs in faba bean and the genomes of two model legumes, Lotus japonicus and Medicago truncatula. In a polymorphic analysis with ten Egyptian faba bean varieties, 78.9% (384/487) of the FBES markers showed polymorphisms. Along with the EST-SSR markers, the dense map developed in this study is expected to accelerate marker assisted breeding in faba bean.

Integrated analysis of whole-genome paired-end and mate-pair sequencing data for identifying genomic structural variations in multiple myeloma.

We present a pipeline to perform integrative analysis of mate-pair (MP) and paired-end (PE) genomic DNA sequencing data. Our pipeline detects structural variations (SVs) by taking aligned sequencing read pairs as input and classifying these reads into properly paired and discordantly paired categories based on their orientation and inferred insert sizes. Recurrent SV was identified from the discordant read pairs. Our pipeline takes into account genomic annotation and genome repetitive element information to increase detection specificity. Application of our pipeline to whole-genome MP and PE sequencing data from three multiple myeloma cell lines (KMS11, MM.1S, and RPMI8226) recovered known SVs, such as heterozygous TRAF3 deletion, as well as a novel experimentally validated SPI1 – ZNF287 inter-chromosomal rearrangement in the RPMI8226 cell line.

Feature-based Similarity Method for Aligning the Malay and English News Document

Corpus-based translation approach can be used to obtain reliable translation knowledge in addition to the use of dictionaries or machine translation. But the availability of such corpus is very limited especially for the low-resources languages. Many works have been reported for the alignments of multilingual documents especially among the European languages, but less focusing on the languages with less linguistics resources. One of the challenges is to align the available multilingual documents for the creation of comparable corpus for these kinds of languages. This article describes an alignment method that utilized the statistical features of the documents such as the documents’ titles, texts of the contents, and also the named entities present in each document. This method will be focusing on the English and Malay news documents, in which in which the Malay language is considered as a low-resource language. Source and target documents were then compared in a pair. Accuracy, precision, and recall measurements were used in evaluating the results with the inclusion of three relevance scales; Same story, Shared aspect and Unrelated, to assess the alignment pairs. The results indicate that the method performed well in aligning the news documents with the accuracy of 96% and average precision of 81%.

Classification of bones from MR images in torso PET-MR imaging using a statistical shape model

There have been exclusive features for hybrid PET/MRI systems in comparison with its PET/CT counterpart in terms of reduction of radiation exposure, improved soft-tissue contrast and truly simultaneous and multi-parametric imaging capabilities. However, quantitative imaging on PET/MR is challenged by attenuation of annihilation photons through their pathway. The correction for photon attenuation requires the availability of patient-specific attenuation map, which accounts for the spatial distribution of attenuation coefficients of biological tissues. However, the lack of information on electron density in the MR signal poses an inherent difficulty to the derivation of the attenuation map from MR images. In other words, the MR signal correlates with proton densities and tissue relaxation properties, rather than with electron density and, as such, it is not directly related to attenuation coefficients. In order to derive the attenuation map from MR images at 511keV, various strategies have been proposed and implemented on prototype and commercial PET/MR systems. Segmentation-based methods generate an attenuation map by classification of T1-weighted or high resolution Dixon MR sequences followed by assignment of predefined attenuation coefficients to various tissue types. Intensity-based segmentation approaches fail to include bones in the attenuation map since the segmentation of bones from conventional MR sequences is a difficult task. Most MR-guided attenuation correction techniques ignore bones owing to the inherent difficulties associated with bone segmentation unless specialized MR sequences such as ultra-short echo (UTE) sequence are utilized. In this work, we introduce a new technique based on statistical shape modeling to segment bones and generate a four-class attenuation map. Our segmentation approach requires a torso bone shape model based on principle component analysis (PCA). A CT-based training set including clearly segmented bones of the torso region of 20 clinical studies was designed. Using this training set, a bone atlas was trained taking advantage of PCA analysis. Our active shape segmentation technique uses the trained shape model to segment bones from user defined initial seed points. The segmentation algorithm was evaluated using 10 clinical datasets (aligned MR and CT pairs). The resulting attenuation maps were compared to corresponding attenuation maps derived from CT resulting in a mean relative difference less than 7%.

Automatic registration of multi-modal microscopy images for integrative analysis of prostate tissue sections

BackgroundProstate cancer is one of the leading causes of cancer related deaths. For diagnosis, predicting the outcome of the disease, and for assessing potential new biomarkers, pathologists and researchers routinely analyze histological samples. Morphological and molecular information may be integrated by aligning microscopic histological images in a multiplex fashion. This process is usually time-consuming and results in intra- and inter-user variability. The aim of this study is to investigate the feasibility of using modern image analysis methods for automated alignment of microscopic images from differently stained adjacent paraffin sections from prostatic tissue specimens.MethodsTissue samples, obtained from biopsy or radical prostatectomy, were sectioned and stained with either hematoxylin & eosin (H&E), immunohistochemistry for p63 and AMACR or Time Resolved Fluorescence (TRF) for androgen receptor (AR).Image pairs were aligned allowing for translation, rotation and scaling. The registration was performed automatically by first detecting landmarks in both images, using the scale invariant image transform (SIFT), followed by the well-known RANSAC protocol for finding point correspondences and finally aligned by Procrustes fit. The Registration results were evaluated using both visual and quantitative criteria as defined in the text.ResultsThree experiments were carried out. First, images of consecutive tissue sections stained with H&E and p63/AMACR were successfully aligned in 85 of 88 cases (96.6%). The failures occurred in 3 out of 13 cores with highly aggressive cancer (Gleason score ≥ 8). Second, TRF and H&E image pairs were aligned correctly in 103 out of 106 cases (97%).The third experiment considered the alignment of image pairs with the same staining (H&E) coming from a stack of 4 sections. The success rate for alignment dropped from 93.8% in adjacent sections to 22% for sections furthest away.ConclusionsThe proposed method is both reliable and fast and therefore well suited for automatic segmentation and analysis of specific areas of interest, combining morphological information with protein expression data from three consecutive tissue sections. Finally, the performance of the algorithm seems to be largely unaffected by the Gleason grade of the prostate tissue samples examined, at least up to Gleason score 7.

Speeding up Batch Alignment of Large Ontologies Using MapReduce.

Real-world ontologies tend to be very large with several containing thousands of entities. Increasingly, ontologies are hosted in repositories, which often compute the alignment between the ontologies. As new ontologies are submitted or ontologies are updated, their alignment with others must be quickly computed. Therefore, aligning several pairs of ontologies quickly becomes a challenge for these repositories. We project this problem as one of batch alignment and show how it may be approached using the distributed computing paradigm of MapReduce. Our approach allows any alignment algorithm to be utilized on a MapReduce architecture. Experiments using four representative alignment algorithms demonstrate flexible and significant speedup of batch alignment of large ontology pairs using MapReduce.

Computational detection of abundant long-range nucleotide covariation in Drosophila genomes.

Functionally important nucleotide base-pairing often manifests itself in sequence alignments in the form of compensatory base changes (covariation). We developed a novel index-based computational method (CovaRNA) to detect long-range covariation on a genomic scale, as well as another computational method (CovStat) for determining the statistical significance of observed covariation patterns in alignment pairs. Here we present an all-versus-all search for nucleotide covariation in Drosophila genomic alignments. The search is genome wide, with the restriction that only alignments that correspond to euchromatic regions, which consist of at least 10 Drosophila species, are being considered (59% of the euchromatic genome of Drosophila melanogaster). We find that long-range covariations are especially prevalent between exons of mRNAs as well as noncoding RNAs; the majority of the observed covariations appear as not reverse complementary, but as synchronized mutations, which could be due to interactions with common interaction partners or due to the involvement of genomic elements that are antisense of annotated transcripts. The involved genes are enriched for functions related to regionalization as well as neural and developmental processes. These results are computational evidence that RNA-RNA long-range interactions are a widespread phenomenon that is of fundamental importance to a variety of cellular processes.

Ab-initio molecular dynamics simulation of δ-Bi3YO6

Abstract Ab-initio molecular dynamics (MD) study of oxygen ion diffusion in the oxide ion conducting solid electrolyte δ-Bi3YO6 is presented. Vacancy ordering models were tested by structure relaxation and that for vacancy pairs was found to have the highest total energy per atom, while those for , and random vacancy distributions were found to have similar energies. Evidence for polarization of bismuth charge density is seen for and vacancy pair configurations, consistent with stereochemical activity of the Bi 6s2 lone pair. MD studies of oxygen diffusion were carried out at three temperatures. Vacancy pair alignments during these simulations were predominantly in the direction, consistent with previous neutron total scattering results.

A Joint Model to Identify and Align Bilingual Named Entities

In this article, an integrated model is derived that jointly identifies and aligns bilingual named entities (NEs) between Chinese and English. The model is motivated by the following observations: (1) whether an NE is translated semantically or phonetically depends greatly on its entity type, (2) entities within an aligned pair should share the same type, and (3) the initially detected NEs can act as anchors and provide further information while selecting NE candidates. Based on these observations, this article proposes a translation mode ratio feature (defined as the proportion of NE internal tokens that are semantically translated), enforces an entity type consistency constraint, and utilizes additional new NE likelihoods (based on the initially detected NE anchors). Experiments show that this novel method significantly outperforms the baseline. The type-insensitive F-score of identified NE pairs increases from 78.4% to 88.0% (12.2% relative improvement) in our Chinese–English NE alignment task, and the type-sensitive F-score increases from 68.4% to 83.0% (21.3% relative improvement). Furthermore, the proposed model demonstrates its robustness when it is tested across different domains. Finally, when semi-supervised learning is conducted to train the adopted English NE recognition model, the proposed model also significantly boosts the English NE recognition type-sensitive F-score.

SU-E-U-09: Direct Clinical Comparison of 2D Versus 3D Transabdominal Ultrasound Image Guidance Methods for Prostate Radiotherapy Treatment

Purpose: Direct clinical comparison of 2D versus 3D transabdominal ultrasound image guidance (USIG) methods for prostate radiotherapy Methods: Image guidance shifts were compared on the same subject, same treatment session between Nomos BAT and Elekta Clarity ultrasound methods for 20 patients and 662 prostate treatments. Both systems use unique approaches to USIG. BAT system acquires two static 2D ultrasound images (axial and sagittal) and compares them to contours derived from simulation CT (i.e. intermodality comparison). Clarity system acquires a 3D ultrasound data set at CT simulation and compares to treatment‐day 3D ultrasound image set for deriving image guidance shifts (i.e. intramodality comparison). In this study, transabdominal Clarity image guidance was performed and the shifts were implemented first. Then transabdominal ultrasound images were acquired approximately 1minute later with BAT to derive image guidance shifts. These BAT‐reported shifts were recorded as the difference between BAT and Clarity USIG. The same experienced operator performed both BAT and Clarity paired alignments. Results: The average differences between the two systems were less than 1.0 mm in all three principle directions. The average standard deviation of these differences in lateral, vertical, and longitudinal direction were 1.2, 1.7, and 1.4 mm, respectively. Average Max difference (across all patients) was 1.9 mm; absolute Max across all image sessions was 10.2 mm. Differences between the two USIG approaches can be partially explained by prostate motion as a function of the time elapsed between imaging sessions, and 10.2 mm Max is not inconsistent with prostate motion we have observed during a similar time frame when using Calypso RF tracking. Results were further stratified into two groups: intact prostate and post‐prostatectomy, and no systematic differences were observed between these two groups. Conclusion: Good agreement was observed in this head‐to‐head comparison study between BAT and Clarity USIG methods for prostate localization.

Oriented covalent immobilization of antibodies for measurement of intermolecular binding forces between zipper-like contact surfaces of split inteins.

In order to measure the intermolecular binding forces between two halves (or partners) of naturally split protein splicing elements called inteins, a novel thiol-hydrazide linker was designed and used to orient immobilized antibodies specific for each partner. Activation of the surfaces was achieved in one step, allowing direct intermolecular force measurement of the binding of the two partners of the split intein (called protein trans-splicing). Through this binding process, a whole functional intein is formed resulting in subsequent splicing. Atomic force microscopy (AFM) was used to directly measure the split intein partner binding at 1 μm/s between native (wild-type) and mixed pairs of C- and N-terminal partners of naturally occurring split inteins from three cyanobacteria. Native and mixed pairs exhibit similar binding forces within the error of the measurement technique (~52 pN). Bioinformatic sequence analysis and computational structural analysis discovered a zipper-like contact between the two partners with electrostatic and nonpolar attraction between multiple aligned ion pairs and hydrophobic residues. Also, we tested the Jarzynski's equality and demonstrated, as expected, that nonequilibrium dissipative measurements obtained here gave larger energies of interaction as compared with those for equilibrium. Hence, AFM coupled with our immobilization strategy and computational studies provides a useful analytical tool for the direct measurement of intermolecular association of split inteins and could be extended to any interacting protein pair.

Relation between sequence and structure in membrane proteins

Integral polytopic membrane proteins contain only two types of folds in their transmembrane domains: α-helix bundles and β-barrels. The increasing number of available crystal structures of these proteins permits an initial estimation of how sequence variability affects the structure conservation in their transmembrane domains. We, thus, aim to determine the pairwise sequence identity necessary to maintain the transmembrane molecular architectures compatible with the hydrophobic nature of the lipid bilayer. Root-mean-square deviation (rmsd) and sequence identity were calculated from the structural alignments of pairs of homologous polytopic membrane proteins sharing the same fold. Analysis of these data reveals that transmembrane segment pairs with sequence identity in the so-called 'twilight zone' (20-35%) display high-structural similarity (rmsd < 1.5 Å). Moreover, a large group of β-barrel pairs with low-sequence identity (<20%) still maintain a close structural similarity (rmsd < 2.5 Å). Thus, we conclude that fold preservation in transmembrane regions requires less sequence conservation than for globular proteins. These findings have direct implications in homology modeling of evolutionary-related membrane proteins. Supplementary data are available at Bioinformatics online.

Selenacalix[3]triazines: Anion Versus Proton Association

Selenacalix[3]triazines, cyclotrimeric metacyclophanes with direct Se linkages between the heteroaryl constituents, were shown to associate with various guest species. The preorganization of three electron deficient triazine rings allows for anions to bind through anion-π interactions, and alignment of the central nitrogen lone pairs and the well-defined size of the macroring enable association with a single proton. Extended UV/Vis titration studies indicated a clear difference in complexation behavior depending on the outer-rim substitution pattern. The host–guest properties of analogous selena- and thiacalix[3]triazines were found to be notably different.

A HYBRID METHOD FOR FUZZY ONTOLOGY INTEGRATION

The main contribution of this work consists of combining a heuristic method for propagation of matchable concepts and using consensus techniques for conflict resolution for fuzzy ontology integration. Two central observations behind this approach are as follows: (1) if two concepts across different source ontologies equivalently match each other, then their neighboring concepts will be often matched as well; and (2) conflicts regarding integration of multiple ontologies can be resolved by creating a consensus among the conflict ontological entities. The key idea of the first observation is to start from an aligned pair of concepts (called medoids) to determine so-called potentially common parts to provide additional suggestions for possible matching concepts. This approach is used to obtain pairs of matchable concepts and to avoid pairs of mismatching concepts. On the other hand, the second observation is used to discover a new merged concept from matched concepts by making a consensus among conflict ontological entities. This idea is to determine the best representative as the merged version of the component ones. A combination of both observations for fuzzy ontology integration is a significant contribution of this work. The results of the experiments imply that the proposed approach is effective with regard to both completeness and accuracy.

Epitaxially Self‐Assemblied Quantum Dot Pairs

The present paper reviews the recent efforts and achievements regarding the fabrication techniques of self‐assembled quantum dot pairs. Quantum dot pairs, the simplest but most‐investigated quantum dot molecules, have attracted significant attention due to their potential applications in quantum information technologies. Coupled quantum dot pairs have been used to implement quantum qubits, quantum gates, and exciton‐spin memory. In the last several decades, the development of epitaxial growth has advanced the design and control of how novel quantum dot pairs form at nanoscale. Both vertically and laterally aligned quantum dot pairs can be grown using the molecular beam epitaxy technique. In this review, we provide assess various growth methods of aligned quantum dot pairs fabricated by molecular beam epitaxy. We highlight the recent development of novel growth techniques and discuss the morphological, electrical, and optical properties of quantum dot pairs. Using advanced epitaxial growth techniques to fabricate well‐controlled quantum dot pairs opens the door to developing of advanced quantum information technologies and understanding the unveiled physics and properties of artificial quantum molecules.

Perceiving and acting on complex affordances: How children and adults bicycle across two lanes of opposing traffic.

This investigation examined how children and adults negotiate a challenging perceptual-motor problem with significant real-world implications--bicycling across two lanes of opposing traffic. Twelve- and 14-year-olds and adults rode a bicycling simulator through an immersive virtual environment. Participants crossed intersections with continuous cross traffic coming from opposing directions. Opportunities for crossing were divided into aligned (far gap opens with or before near gap) and rolling (far gap opens after near gap) gap pairs. Children and adults preferred rolling to aligned gap pairs, though this preference was stronger for adults than for children. Crossing aligned versus rolling gap pairs produced substantial differences in direction of travel, speed of crossing, and timing of entry into the near and far lanes. For both aligned and rolling gap pairs, children demonstrated less skill than adults in coordinating self and object movement. These findings have implications for understanding perception-action-cognition links and for understanding risk factors underlying car-bicycle collisions.

A Conserved Mammalian Protein Interaction Network

Physical interactions between proteins mediate a variety of biological functions, including signal transduction, physical structuring of the cell and regulation. While extensive catalogs of such interactions are known from model organisms, their evolutionary histories are difficult to study given the lack of interaction data from phylogenetic outgroups. Using phylogenomic approaches, we infer a upper bound on the time of origin for a large set of human protein-protein interactions, showing that most such interactions appear relatively ancient, dating no later than the radiation of placental mammals. By analyzing paired alignments of orthologous and putatively interacting protein-coding genes from eight mammals, we find evidence for weak but significant co-evolution, as measured by relative selective constraint, between pairs of genes with interacting proteins. However, we find no strong evidence for shared instances of directional selection within an interacting pair. Finally, we use a network approach to show that the distribution of selective constraint across the protein interaction network is non-random, with a clear tendency for interacting proteins to share similar selective constraints. Collectively, the results suggest that, on the whole, protein interactions in mammals are under selective constraint, presumably due to their functional roles.