Partial Alignment Research Articles

Effects of High-Dose Ionizing Radiation in Human Gene Expression: A Meta-Analysis.

The use of high-dose Ionizing Radiation (IR) is currently one of the most common modalities in treatment of many types of cancer. The objective of this work was to investigate the effects of high-dose ionizing radiation on healthy human tissue, utilizing quantitative analysis of gene expression. To this end, publicly available transcriptomics datasets from human samples irradiated with a high dose of radiation and non-irradiated (control) ones were selected, and gene expression was determined using RNA-Seq data analysis. Raw data from these studies were subjected to quality control and trimming. Mapping of RNA-Seq reads was performed by the partial selective alignment method, and differential gene expression analysis was conducted. Subsequently, a meta-analysis was performed to select differentially expressed genes across datasets. Based on the differentially expressed genes discovered by meta-analysis, we constructed a protein-to-protein interaction network, and we identified biological pathways and processes related to high-dose IR effects. Our findings suggest that cell cycle arrest is activated, supported by our top down-regulated genes associated with cell cycle activation. DNA repair genes are down-regulated in their majority. However, several genes implicated in the nucleotide excision repair pathway are upregulated. Nevertheless, apoptotic mechanisms seem to be activated probably due to severe high-dose-induced complex DNA damage. The significant upregulation of CDKN1A, as a downstream gene of TP53, further validates programmed cell death. Finally, down-regulation of TIMELESS, signifies a correlation between IR response and circadian rhythm. Nonetheless, high-dose IR exposure effects regarding normal tissue (radiation toxicity) and its possible long-term outcomes should be studied to a greater extend.

Orientation Distribution Dependence of Piezoresistivity of Metal Nanowire-Polymer Composite

In this study, we investigate the piezoresistivity of metal nanowire networks embedded in a polymer, which has been widely used as a highly-stretchable strain sensor, by varying the orientation distribution of nanowires. For simplicity, we assume the affine transform of the nanowire network upon stretching and compute the effective conductivity of the nanowire network by recognizing the percolation network connecting low and high voltage boundaries. Orientation-dependence is then studied firstly by varying the range of polar angle and secondly by changing the degree of alignment along loading direction. Since nanowires are embedded in thin nanowire-polymer film in most stretchable sensor applications, instead of having random orientation distribution over full solid angle, nanowires have a limited range of polar angle distribution around 90° (when the surface normal vector of a thin film is given as the zenith direction). We show that the gauge factor (relative resistance change over applied mechanical strain) decreases as the polar angle distribution gets narrower. We then study the effect of nanowire alignment on the piezoresistive response, by assuming partial alignment distribution along the tensile direction. We find that a wide range of the gauge factor, from negative to positive, appears as the initial partial alignment angle varies, and explained such response by analyzing the relative electrical path change between a pair of nanowires. Our study deepens the understanding on the percolation-network based piezoresistive sensors and provides a guideline for designing a stretchable strain sensor with the desired gauge factor.

Cherry senescence – a response to application of ABA and partial sequence alignment of α-mannosidase gene

Cherry senescence – a response to application of ABA and partial sequence alignment of α-mannosidase gene

When institutional logics meet: Alignment and misalignment in collaboration between academia and practitioners

This paper explains the institutional logics of academia, and of practitioners within industry and government, as well as the alignment and misalignment that occurs when these actors collaborate. This is achieved by building on the theories on alignment and misalignment and institutional logics, whilst conducting an explorative case study of a circular economy cluster from the Tampere Region of Finland. This paper offers three main contributions: First, convergence and divergence of institutional logics by industry, government, and academic actors can lead to alignment and misalignment at three levels: actor-type, relationship, and system levels. Second, partial alignment and misalignment are found to be in-between modes of alignment, which challenges the idea that alignment and misalignment are dichotomous. Instead, alignment and misalignment should be seen as the two ends of a continuum. Third, alignment and misalignment are dynamic by nature, because institutional logics change and modify during collaboration. For practice, this paper gives advice on how collaboration between academia and practitioners can be advanced to achieve alignment and avoid misalignment.

The Relevance of Typology for Pattern Replication

Structuralists and generativists have insisted for a long time that the elements and structures one language could borrow from another are constrained by typological compatibility, naturalness, and other factors (cf. Thomason and Kaufman 1988: 13–34). Such constraints are still thought to apply to structural interference, or pattern replication in the terms of Matras and Sakel (2007), and the often concomitant contact-induced grammaticalisation of non-native structures. This paper suggests that a priori there are no typological constraints against pattern replication in general. It is proposed that typological differences between model and replica pattern are only of relevance during the grammaticalisation and maintenance of such patterns in the replica language; in other words, typological constraints do not apply at the stage of pattern replication. It will be argued that typology, in the form of system pressure, interacts with pattern frequency and socio-historical factors, which together determine retention, adaptation, or loss of a replicated pattern. This argument is illustrated on the basis of three short studies of partial alignment change in Old Aramaic, Classical Armenian, and North-Eastern Neo-Aramaic, all of which have been in contact with Iranian languages for extended periods. In each case, Iranian ergative alignment patterns have been replicated, adapted, grammaticalised to varying degrees, and finally ousted in favour of nominative-accusative alignment. The loss of the replica pattern in each case is shown to be dependent on both typology, extent of bilingualism, and pattern frequency.

Quantum-assisted diamagnetic deflection of molecules.

We measure the diamagnetic deflection of anthracene and adamantane in a long-baseline matter-wave interferometer. From the nanometer-level deflection we extract the magnetic susceptibilities of the molecules which we compare with calculations and previous results. Adamantane yields an isotropic average mass susceptibility of -8.0 ± 1.1 m3 kg-1, consistent with expectations, while anthracene yields a higher-than-anticipated value of -13.6 ± 1.3 m3 kg-1. We attribute the high anthracene value to the planar aromatic molecule's magnetic anisotropy and partial alignment in the molecular beam, and estimate the magnitude of the effect on the observed deflection.

Partial Interference Alignment Scheme for Three-Tier Downlink Heterogeneous Networks

The introduction of the relay in heterogeneous networks (HetNets) can enhance cell-edge signals, but it will also bring coexistence of multiple interference which is composed of co-tier, cross-tier and cross time slot (caused by the half-duplex mode of the relay) interference, resulting in the ineffectiveness of the existing interference alignment (IA) schemes. To solve the above problem, the partial IA scheme, which achieves IA in the case of limited antennas by rationally designing the order and method of eliminating interference, is proposed in this paper. First, we align the interference from other base stations (BSs) into the interference space generated by pico BS to reduce the interference dimension of the relay, and then solve the interference between BSs and users by null space and concatenated precoding schemes. Furthermore, the feasibility condition of antenna configuration is analyzed. The simulation results show that the proposed scheme is superior to the traditional IA scheme in sum rate, and the performance of the proposed scheme is further improved as the relay transmission power increases.

3D extruded composite thermoelectric threads for flexible energy harvesting

Whereas the rigid nature of standard thermoelectrics limits their use, flexible thermoelectric platforms can find much broader applications, for example, in low-power, wearable energy harvesting for internet-of-things applications. Here we realize continuous, flexible thermoelectric threads via a rapid extrusion of 3D-printable composite inks (Bi2Te3n- or p-type micrograins within a non-conducting polymer as a binder) followed by compression through a roller-pair, and we demonstrate their applications in flexible, low-power energy harvesting. The thermoelectric power factors of these threads are enhanced up to 7 orders-of-magnitude after lateral compression, principally due to improved conductivity resulting from reduced void volume fraction and partial alignment of thermoelectric micrograins. This dependence is quantified using a conductivity/Seebeck vise for pressure-controlled studies. The resulting grain-to-grain conductivity is well explained with a modified percolation theory to model a pressure-dependent conductivity. Flexible thermoelectric modules are demonstrated to utilize thermal gradients either parallel or transverse to the thread direction.

Trade groups under climate pressure

The French oil and gas firm Total says it will leave the American Fuel & Petrochemical Manufacturers because the trade association is not aligned with Total’s policies on climate change. The move follows a similar announcement by Shell, which said in April it would leave the group in 2020. Unlike the trade group, Total and Shell say they support the goals of the 2015 Paris climate agreement, as well as policies that support a price on carbon and investment in low-carbon technologies. Total says it may also pull out of other trade groups, including the American Chemistry Council, that have only “partial alignment” with the firm’s policies. The ACC’s climate policy principles do not mention the Paris Agreement or explicitly support a price on carbon. The group’s policy document calls for meaningful reduction in US greenhouse gas emissions “while minimizing the costs to society.” It also says policy should focus

Structure and photophysics of indigoids for singlet fission: Cibalackrot.

We report an investigation of structure and photophysics of thin layers of cibalackrot, a sturdy dye derived from indigo by double annulation at the central double bond. Evaporated layers contain up to three phases, two crystalline and one amorphous. Relative amounts of all three have been determined by a combination of X-ray diffraction and FT-IR reflectance spectroscopy. Initially, excited singlet state rapidly produces a high yield of a transient intermediate whose spectral properties are compatible with charge-transfer nature. This intermediate more slowly converts to a significant yield of triplet, which, however, does not exceed 100% and may well be produced by intersystem crossing rather than singlet fission. The yields were determined by transient absorption spectroscopy and corrected for effects of partial sample alignment by a simple generally applicable procedure. Formation of excimers was also observed. In order to obtain guidance for improving molecular packing by a minor structural modification, calculations by a simplified frontier orbital method were used to find all local maxima of singlet fission rate as a function of geometry of a molecular pair. The method was tested at 48 maxima by comparison with the ab initio Frenkel-Davydov exciton model.

Graptodytes exsanguis (Bedel, 1925) n. stat., a newly recognised species of diving beetle from North Africa, Corsica and Sardinia, with notes on other taxa of the varius/ignotus complex (Coleoptera: Dytiscidae)

SummaryA species of the genus Graptodytes Seidlitz, 1887 (varius/ignotus complex) is newly recognised and described based on recently sampled specimens from Corsica and Sardinia, and material in various collections from Algeria, Tunisia, Corsica and Sardinia. The name exsanguis, created by Bedel in 1925 for a variety of what he then called Hydroporus varius Aubé, 1838, is shown to be available for the newly recognised species, therefore named Graptodytes exsanguis (Bedel, 1925) n. stat. (type locality: Algeria, La Calle – nowadays El Kala). This species is similar in size and colour pattern to G. fractus (Sharp, 1882), from which it can be distinguished by strong differentiation of the male protarsal claws, features of the habitus and elytral punctation, and shape of the median lobe of aedeagus. Morphological features of G. exsanguis and G. fractus are illustrated, and pictures showing for each species the variability of habitus and median lobe are provided. For comparison, the habitus and median lobes of other species of the varius/ignotus complex are also illustrated. Habitat preferences of G. exsanguis are described based on field observations in Corsica and Sardinia, and a distribution map of validated records is presented. Analysis of a partial CO1 alignment yielded a basal and divergent position within the varius/ignotus complex for the sequenced G. exsanguis haplotypes from Corsica and Sardinia. Lectotypes are designated for Hydroporus varius var. exsanguis Bedel, 1925, Hydroporus fractus Sharp, 1882 and Graptodytes ignotus var. fallaciosus Guignot, 1932, and the latter is established as a junior synonym of G. fractus.

Parallel calibration based on modified trim strategy

PurposePartial alignment for 3 D point sets is a challenging problem for laser calibration and robot calibration due to the unbalance of data sets, especially when the overlap of data sets is low. Geometric features can promote the accuracy of alignment. However, the corresponding feature extraction methods are time consuming. The purpose of this paper is to find a framework for partial alignment by an adaptive trimmed strategy.Design/methodology/approachFirst, the authors propose an adaptive trimmed strategy based on point feature histograms (PFH) coding. Second, they obtain an initial transformation based on this partition, which improves the accuracy of the normal direction weighted trimmed iterative closest point (ICP) method. Third, they conduct a series of GPU parallel implementations for time efficiency.FindingsThe initial partition based on PFH feature improves the accuracy of the partial registration significantly. Moreover, the parallel GPU algorithms accelerate the alignment process.Research limitations/implicationsThis study is applicable to rigid transformation so far. It could be extended to non-rigid transformation.Practical implicationsIn practice, point set alignment for calibration is a technique widely used in the fields of aircraft assembly, industry examination, simultaneous localization and mapping and surgery navigation.Social implicationsPoint set calibration is a building block in the field of intelligent manufacturing.Originality/valueThe contributions are as follows: first, the authors introduce a novel coarse alignment as an initial calibration by PFH descriptor similarity, which can be viewed as a coarse trimmed process by partitioning the data to the almost overlap part and the rest part; second, they reduce the computation time by GPU parallel coding during the acquisition of feature descriptor; finally, they use the weighted trimmed ICP method to refine the transformation.

Mechanical and transport properties of fibrous amorphous silica meshes and membranes fabricated from compressed electrospun precursor fibers

Highly porous, 0.1–1.5 mm thick fibrous amorphous silica (FAS) meshes with 500 ± 200 nm fiber diameters were prepared from the precursor fibers made by a high-yield free-surface alternating field electrospinning (AFES) process. A combination of mild thermal and pressure treatment of the fibrous precursor material before the calcination step was used to tailor the mechanical and transport properties of the resulting FAS structures. Compression of the as-spun material determined the resulting porosity, effective fiber diameter, and microarchitecture of the FAS structures when calcined between 600 and 1000 °C. Flexible FAS meshes and membranes revealed the tensile strength and modulus up to 1.4 MPa and 580 MPa, respectively, and Darcy'S permeability coefficient in a range of 1.2 × 10−12–1.6 × 10−11 m2. Taking into consideration the compression-dependent effective fiber diameter, the permeability of compressed FAS membranes fitted the models developed for two-dimensional fibrous layer architectures with partial fiber alignment within the stacked layers.

Partial alignment, residual dipolar couplings and molecular symmetry in solution NMR.

Residual dipolar couplings (RDCs) and residual anisotropic chemical shifts (RACSs) are produced by the partial alignment of solution NMR samples. RDCs and RACSs yield high-resolution structural and dynamic information on the orientation of bonds and chemical groups in molecules. Many molecules form oligomers or have intrinsic symmetries, which may simplify the analysis of their partial alignment datasets. In this report, we explore the theory of partial alignment using an irreducible spherical representation, and we investigate the impact of molecular symmetry on the alignment of molecules. Though previous studies have reported simplified relationships on the partial alignment of molecules bearing different symmetry groups, we show that these simplified relationships may not be universal and only apply to a limited set of systems.

Neural Network Estimation for Attenuation Coefficients for Gamma-Ray Angular Distribution

Spins of nuclear states (J) and multipolarities of gamma rays are usually investigated by the angular distribution of gamma rays emitted from aligned states formed by nuclear reactions. In the case of partial alignment, attenuation coefficients are used in angular distribution function. These coefficients are tabulated in literature for different J values. However, these coefficients involve $$r$$ -fold tensor products. Furthermore, as the calculation of these coefficients implicitly involves highly complicated integral quantities, they are very difficult to handle explicitly for larger $$r$$ values. In this respect, universal nonlinear function approximator layered feedforward neural network (LFNN) can be applied to construct consistent empirical physical formulas (EPFs) for physical phenomena. In this paper, we consistently estimated the attenuation coefficients by constructing suitable LFNNs. The LFNN-EPFs fitted the literature coefficient data very well. Moreover, magnificent LFNN test set predictionson unseen data confirmed the consistent LFNN-EPFs for the determination of coefficients.

Molecular investigation of two novel bacteriophages of a facultative methylotroph, Raoultella ornithinolytica: first report of Raoultella phages.

Bacteria of the genus Raoultella are known to inhabit aquatic environments and can be found in medical samples. The pathogenicity of Raoultella ornithinolytica isolates in human has become increasingly important, and several cases of infections have been reported recently. However, there are no reports of isolation of bacteriophages infecting this bacterium. In this study, two novel phages (ISF3 and ISF6) of a methylotrophic Raoultella strain were isolated from sewage. To characterize the isolated phages, morphological features, protein profiles, restriction digestion patterns, and partial genome sequences were studied. Despite morphological differences, electron microscopy revealed that both phages had an icosahedral capsid connected to a contractile tail, suggesting that ISF3 and ISF6 both belong to the family Myoviridae. Partial nucleotide sequences of the ISF3 genome showed 99% to 100% identity to DNA of Klebsiella pneumonia phages KP15, KP27 and BMBT1; however, the restriction digestion profiles of ISF3 genome digested by EcoRI and EcoRV differed from those of Klebsiella phages KP15 and KP27. A partial sequence alignment showed that ISF6 can be classified as a member of a new viral genus due to its significant differences from other previously identified phages. To the best of our knowledge, this is the first report of the isolation and characterization of the specific Raoultella phages that have potential to be used as new pharmaceuticals against R. ornithinolytica.

Introduction: special issue on EU-induced policy change in Turkey’s environment and energy policy

ABSTRACTIn view of Turkey’s increasing distance from the European Union (EU), the continued partial alignment with EU standards is often attributed either to domestic factors, or to diffusion processes induced by external actors other than the EU. Against this background, in this special issue, we explore the extent to which reforms in Turkey’s environment and energy policy are (still) influenced by the EU. This introduction briefly reviews the Turkey related Europeanisation literature and previews the articles in this special issue.

Gene conversion identification and analysis in immunoglobulins

Abstract Few, if any, somatic processes exhibit such sequence level diversity as the immunoglobulin rearrangement and somatic hypermutation (SHM) mechanisms. It is due to these processes that novel antibody receptors can be created against most pathogens. Somatic hypermutation is attributable to the majority of non-junction diversity in studied repertoires, however, this has been largely due to the organisms most heavily studied in repertoire sequencing: human and mouse. Gene conversion is another mechanism that drives diversity in the immunoglobulin repertoire of other organisms, particularly in chicken and rabbit. Confidently identifying gene conversion events has not been a focus for most repertoire sequencing studies, largely due to the organisms typically studied. However, their identification also poses an algorithmic and statistical problem: namely how to identify a tract of donor sequence from similar V genes, and subsequently assessing the significance of such an identification. The scant examples of analysis of immunoglobulin gene conversion in the literature have used two approaches: visual inspection and the use of GENECONV. We propose two alternate approaches to identify the events: using a specialized pairwise alignment between the read, host, and donor references; and using a partial order alignment graph. These new approaches are validated on simulated antibody data, showing improved recall, and reduced false positive rates. The new approaches are more sensitive than GENECONV on smaller donor tract lengths (< 100nt), and are not sensitive to higher mutation load. We then apply the new approach to identifying gene conversion events in high throughput repertoire sequencing of rabbit, and public human datasets.

Phylogenetic patterns and molecular evolution among ‘True citrus fruit trees’ group (Rutaceae family and Aurantioideae subfamily)

Cytoplasmic chloroplast DNAs was explored to establish phylogenetic relationships among ‘True citrus’ group and elucidate its molecular evolution. Conserved group I intron (PQRS) sequence motifs were detected in Citrus genus and showed differences of nucleotide variation between elements and some species. The P8 stem-loop region was the only variable region in trnL intron of Citrus species. The deletion of 6 bp has been detected between sites (40–45) in the partial alignment of P8 stem-loop resulted in a change in conformation of the secondary structures in the ancestral species and other derived species and this could be explained by the evolution and speciation of this genus. The consistency index (CI=1) and the retention index (RI=1) values suggest that the changes are mostly apomorphic despite the absence of homoplasy (HI=0). The phylogenetic tree confirms and shows a branching of C. limon, C. sinensis, C. paradisi, C. tangelo and C. aurantium in a monophyletic clade. This result so far to C. reticulata ruled out the maternal contribution of mandarin gene pool in the elaboration of these secondary Citrus species. The Maximum Likelihood tree indicated that the genus Citrus is quite distant from the related genera Poncirus, Microcitrus, Eremocitrus and Fortunella except only Fortunella margarita species. Here new insight is given about mechanism involving in the evolution of the trnL intron in ‘True Citrus’. From the study it appears that an explicit rejection of the null hypothesis and a scenario of a demography history and recent expansion of ‘True Citrus’ genotypes seem to be retained that may be an important factor influencing the power of genetic diversity in ‘True Citrus’.

Policy learning: an understudied mechanism of EU influence on Turkish domestic politics

ABSTRACTThis article argues that EU-induced learning processes in Turkish domestic politics deserve greater attention within the Turkey-related Europeanization literature, which, in view of Turkey’s increasing distance from the European Union, tends to attribute a continued partial alignment with EU policies to either domestic, or to non-EU-related external factors. Two arguments are put forward. First, in domestically driven reform processes, the EU may still be able to influence policy choices due to domestic actors’ bounded rationality and conflicting goals. Second, while persuasion and learning at the top political level is rather unlikely, given the currently tense relations, there are much more favorable context conditions for EU-induced learning in the interaction of the Turkish bureaucracy with the EU.