Characteristic Set Research Articles

Dissipation of the striped pulsar wind

Rapidly rotating neutron stars blow a relativistic, magnetized wind mainly composed of electron-positron pairs. The free expansion of the wind terminates far from the neutron star where a weakly magnetized pulsar wind nebula forms, implying efficient magnetic dissipation somewhere upstream. The wind current sheet that separates the two magnetic polarities is usually considered as the most natural place for magnetic dissipation via relativistic reconnection, but its efficiency remains an open question. Here, the goal of this work is to revisit this issue in light of the most recent progress in the understanding of reconnection and pulsar electrodynamics. We perform large two-dimensional particle-in-cell simulations of the oblique rotator to capture the multi-scale evolution of the wind. We find that the current sheet breaks up into a dynamical chain of magnetic islands separated by secondary thin current sheets. The sheet thickness increases linearly with radius while the Poynting flux decreases monotonically as reconnection proceeds. The radius of complete annihilation of the stripes is given by the plasma multiplicity parameter at the light cylinder. Current starvation within the sheets does not occur before complete dissipation as long as there is enough charges where the sheets form. Particles are efficiently heated up to a characteristic energy set by the magnetization parameter at the light cylinder. Energetic pulsed synchrotron emission peaks close to the light cylinder, and presents sub-pulse variability associated with the formation of plasmoids in the sheet. This study suggests that the striped component of the wind dissipates far before reaching the termination shock in isolated pulsars, even in very-high-multiplicity systems such as the Crab pulsar. Pulsars in binary systems may provide the best environments to study magnetic dissipation in the wind.

Forensic Identification of Dyes in Ballpoint Pen Inks Using LC–ESI–MS

The aim of this work was to develop a new technique using flow injection analysis combined with LC–ESI–MS which allows identification of dyes in ballpoint pen inks. A sample preparation procedure for the extraction of dyes from ballpoint pen strokes has been developed. The characteristic group of ions for each sample of 21 studied ballpoint pen inks corresponding to the present dyes has been determined using flow injection method. LC separation conditions for identified dyes have been optimized on reversed-phase sorbent based on silica gel. The best composition of the mobile phase for the dyes mixture LC separation was 0.1% aqueous formic acid and acetonitrile. Detection of dyes was carried out using mass spectrometry with electrospray ionization in positive and negative modes after reversed-phase liquid chromatography separation. Dye composition of ink was additionally confirmed comparing the data obtained from the literature. Flow injection analysis allows obtaining intensive ions of unknown strokes. It is difficult to get this information using only chromatographic methods, because dyes peak intensity can be low and noise of basic line high. Flow injection method allows distinguishing the analyzed 21 ballpoint pens by determining a characteristic set of dyes. The developed flow injection technique is very simple and quick. As a result, a novel approach for the identification of dyes in the ballpoint pen inks by flow injection analysis with LC–ESI–MS and UV detection without using standard dye samples has been established. It can be an effective alternative to the existing LC–DAD–MS and IR spectroscopy methods.

Synthesis, Modeling, and Catalytic Properties of HY Zeolite-Supported Rhodium Dinitrosyl Complexes

HY zeolite-supported Rh(CO)2 complexes were used as precursors for the surface-mediated synthesis of Rh(NO)2 species. The results of FTIR, EXAFS, and mass spectrometry measurements, as well as DFT calculations, show that the replacement of the CO ligands in the Rh(CO)2 complexes by NO is a facile substitution process which is not affected by the Si/Al ratio of the zeolite support used. The Rh(NO)2 complexes thus formed are site-isolated 14-electron species with a Rh–N bond distance of 1.77 A, a N–Rh–N angle of ∼104°, and NO ligands significantly deviating from a linear configuration (Rh–N–O angle ∼148°). These species exhibit a characteristic set of well-defined νNO bands at 1855 and 1779 cm–1 in their FTIR spectra and have an additional empty d orbital at the rhodium center allowing for coordination of a third electron-donating ligand. Therefore, the Rh(NO)2 species react with C2H4 to form 16-electron Rh(NO)2(C2H4) species which are stable in the presence of gas-phase C2H4 and can be further converted in...

Algorithms for verification of characteristic sets of discrete autonomous nD systems with n ≥ 2

An important question for multidimensional systems is to characterize the minimum information required to uniquely specify a ‘trajectory’. For a discrete nD system described by partial difference equations with real constant coefficients, the notion of a characteristic set formalizes this idea. The issue of characteristic sets for n ≥ 3 has largely remained open since Valcher’s seminal work for n = 2 (Valcher (2000)). In this paper, we provide a necessary and sufficient condition for a given subset (either a cone or a sub-lattice) in Zn to be a characteristic set for a discrete scalar autonomous nD system. This necessary and sufficient condition enables us to formulate an algebraic test for verifying whether a given cone or a sub-lattice is a characteristic set for a given discrete scalar autonomous nD system. We then provide algorithms - that are implementable using standard computational algebra packages - for doing this check. This is achieved by first converting the above-mentioned necessary and sufficient condition to another equivalent algebraic condition that is more suited for applying Grobner bases theory. We further pursue the question of ‘minimality’ of characteristic sets. We show how the idea of minimal characteristic sub-lattices is related with the notion of autonomy degree and Krull dimension. Thus, we provide a complete solution to the problem of determining if a given cone or a sub-lattice is a characteristic set for a scalar autonomous discrete nD system.

Abstract 3390: Clonal evolution in uveal melanoma

Abstract Introduction: Uveal melanoma is the most common primary cancer of the eye and frequently gives rise to lethal metastatic disease. Uveal melanoma can be divided into two prognostic subgroups based on gene expression profiling: class 1 (low metastatic risk) and class 2 (high metastatic risk). Uveal melanoma is also notable for a characteristic set of driver mutations that cluster into two groups. The first group consists of mutually exclusive gain-of-function mutations in members of the Gαq signaling pathway (GNAQ, GNA11, CYSLTR2 and PLCB4), which are present in almost all uveal melanomas. These mutations are not prognostic, and are thought to represent initiating events that are insufficient alone to cause full malignant transformation. The second group consists of near-mutually exclusive mutations in BAP1, SF3B1, and EIF1AX. These are thought to occur later in tumor progression and are prognostic of patient outcome. These molecular features are associated with characteristic chromosome copy number variations (CNV). The purpose of this study was to investigate the life history of primary uveal melanomas by inferring the intratumoral evolution of these genetic events. Methods: Exome or whole genome sequencing data from 151 primary uveal melanomas were evaluated with a new bioinformatic pipeline for calling mutations and CNVs. Data from this analysis were used in downstream subclonality algorithms to determine intratumor evolutionary patterns within individual tumor samples. Results: A Gαq mutation was found in 98.7% of tumors, which were all mutually exclusive with each other. BAP1 mutations were found in 46%, SF3B1 mutations in 23%, and EIF1AX mutations in 14% of tumors, all of which were mutually exclusive with each other except for 4 cases. We identified novel driver mutations in 20% of the remaining tumors. In most samples that contained a BAP1 or SF3B1 mutation, this driver mutation and associated CNVs were present in 100% of tumor cells. However, in 14% of cases with BAP1 mutations, 100% of tumor cells exhibited monosomy 3, but a BAP1 mutation was present in a smaller subclone, suggesting that the BAP1 mutation occurred after the loss of chromosome 3. In tumors with EIF1AX mutations, this mutation was consistently found in 100% of tumor cells, with 6p gain being found in a smaller subclone in 45% of cases, suggesting that 6p gain usually occurs after the EIF1AX mutation in this subgroup of tumors. Conclusions: The driver mutations and associated CNVs that are characteristic of uveal melanoma occur very early in tumor evolution and are followed by the accumulation of silent passenger mutations, consistent with a punctuated evolution model in which an initial “big bang” is followed by neutral non-Darwinian evolution. These unexpected findings alter prevailing theories of uveal melanoma progression, and could have a significant impact on patient management. Citation Format: Matthew G. Field, Hima Anbunathan, Michael A. Durante, Louie Cai, Karam Alawa, Christina L. Decatur, Stefan Kurtenbach, Anne Bowcock, J. William Harbour. Clonal evolution in uveal melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3390. doi:10.1158/1538-7445.AM2017-3390

About Factors of Solar Radiation Affecting the Ionosphere

AbstractIn this report we present an attempt to find a characteristic set of the space weather parameters allowed to identify the dominant physical connections. This study is based on the data of vertical and oblique sounding of the ionosphere in 2015-2016.

Rome Foundation-Asian working team report: Asian functional gastrointestinal disorder symptom clusters

ObjectiveFunctional gastrointestinal disorders (FGIDs) are diagnosed by the presence of a characteristic set of symptoms. However, the current criteria-based diagnostic approach is to some extent subjective and largely derived from...

Optimizing Variational Quantum Algorithms Using Pontryagin’s Minimum Principle

We use Pontryagin's minimum principle to optimize variational quantum algorithms. We show that for a fixed computation time, the optimal evolution has a bang-bang (square pulse) form, both for closed and open quantum systems with Markovian decoherence. Our findings support the choice of evolution ansatz in the recently proposed Quantum Approximate Optimization Algorithm. Focusing on the Sherrington-Kirkpatrick spin-glass as an example, we find a system-size independent distribution of the duration of pulses, with characteristic time scale set by the inverse of the coupling constants in the Hamiltonian. The optimality of the bang-bang protocols and the characteristic time scale of the pulses provide an efficient parameterization of the protocol and inform the search for effective hybrid (classical and quantum) schemes for tackling combinatorial optimization problems. For the particular systems we study, we find numerically that the optimal nonadiabatic bang-bang protocols outperform conventional quantum annealing in the presence of weak white additive external noise and weak coupling to a thermal bath modeled with the Redfield master equation.

Encoding of rapid time-varying information is impaired in poor readers.

A characteristic set of eye movements and fixations are made during reading, so the position of words on the retinae is constantly being updated. Effective decoding of print requires this temporal stream of visual information to be segmented or parsed into its constituent units (e.g., letters or words). Poor readers' difficulties with word recognition could arise at the point of segmenting time-varying visual information, but the mechanisms underlying this process are little understood. Here, we used random-dot displays to explore the effects of reading ability on temporal segmentation. Thirty-eight adult readers viewed test stimuli that were temporally segmented by constraining either local motions or analogous form cues to oscillate back and fourth at each of a range of rates. Participants had to discriminate these segmented patterns from comparison stimuli containing the same motion and form cues but these were temporally intermingled. Results showed that the motion and form tasks could not be performed reliably when segment duration was shorter than a temporal resolution (acuity) limit. The acuity limits for both tasks were significantly and negatively correlated with reading scores. Importantly, the minimum segment duration needed to detect the temporally segmented stimuli was longer in relatively poor readers than relatively good readers. This demonstrates that adult poor readers have difficulty segmenting temporally changing visual input particularly at short segment durations. These results are consistent with evidence suggesting that precise encoding of rapid time-varying information is impaired in developmental dyslexia.

A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes

BackgroundExamination of complex biological systems has long been achieved through methodical investigation of the system’s individual components. While informative, this strategy often leads to inappropriate conclusions about the system as a whole. With the advent of high-throughput “omic” technologies, however, researchers can now simultaneously analyze an entire system at the level of molecule (DNA, RNA, protein, metabolite) and process (transcription, translation, enzyme catalysis). This strategy reduces the likelihood of improper conclusions, provides a framework for elucidation of genotype-phenotype relationships, and brings finer resolution to comparative genomic experiments. Here, we apply a multi-omic approach to analyze the gene expression profiles of two closely related Pseudomonas aeruginosa strains grown in n-alkanes or glycerol.ResultsThe environmental P. aeruginosa isolate ATCC 33988 consumed medium-length (C10–C16) n-alkanes more rapidly than the laboratory strain PAO1, despite high genome sequence identity (average nucleotide identity >99%). Our data shows that ATCC 33988 induces a characteristic set of genes at the transcriptional, translational and post-translational levels during growth on alkanes, many of which differ from those expressed by PAO1. Of particular interest was the lack of expression from the rhl operon of the quorum sensing (QS) system, resulting in no measurable rhamnolipid production by ATCC 33988. Further examination showed that ATCC 33988 lacked the entire lasI/lasR arm of the QS response. Instead of promoting expression of QS genes, ATCC 33988 up-regulates a small subset of its genome, including operons responsible for specific alkaline proteases and sphingosine metabolism.ConclusionThis work represents the first time results from RNA-seq, microarray, ribosome footprinting, proteomics, and small molecule LC-MS experiments have been integrated to compare gene expression in bacteria. Together, these data provide insights as to why strain ATCC 33988 is better adapted for growth and survival on n-alkanes.

On the Gevrey strong hyperbolicity

In this paper we are concerned with a homogeneous differential operator $p$ of order $m$ of which characteristic set of order $m$ is assumed to be a smooth manifold. We define the Gevrey strong hyperbolicity index as the largest number $s$ such that the Cauchy problem for $p+Q$ is well-posed in the Gevrey class of order $s$ for any differential operator $Q$ of order less than $m$. We study the case of the largest index and we discuss in which way the Gevrey strong hyperbolicity index relates with the geometry of bicharacteristics of $p$ near the characteristic manifold.

Prognostic significance of aberrant expression of CD markers in acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) forms a heterogeneous group of disorders with a characteristic set of CD markers. Nowadays, these markers are used for the classification of hematopoietic malignancies and are a basis for diagnosis of leukemia. Unusual expression of CD markers as different immunophenotype of lymphoblasts is known as the aberrant expression of markers. The frequency of this phenomenon has been reported to be nearly 30% in different studies. Immunophenotype of precursor B‑cell leukemia involves the likely expression of myeloid CD markers (CD13 and CD33). In precursor T‑cell leukemia, myeloid markers (CD13 and CD33) are frequent but CD117 is rare. On the other hand, the presence of multiple translocations is also associated with a higher or lower level of aberrant markers that could be effective in changing the prognosis of patients. Further studies are needed to confirm the relationship between aberrant expression with prognosis and response to treatment of ALL.

On the characteristic set, centroid, and centre for a tree

Given a tree T, we consider a pair of vertices (u, v) where u is a centroid of T, v is a characteristic vertex of T, and such that the distance between them, denoted d(u, v), is smallest over all such pairs. We define and where the maximum is taken over all trees T on n vertices. Analogous definitions are also given for and . We show that for each there is a broom T on n vertices such that and a broom on n vertices such that We also prove that the sequences and are convergent, and find their limits. We rely on the characterization of characteristic vertices in terms of Perron branches in order to establish our results.

The matrix affects carabid beetle assemblages in linear urban ruderal habitats

Matrix contrasts affect communities in patchy landscapes by influencing resources, abiotic conditions and spill-over effects. However, current knowledge is significantly biased towards forest and rural communities. We examined the effects of three different matrix types, i.e., low, intermediate and high contrasts, on carabid beetle assemblages at urban railway verges in two climatic regions. Study sites were located in Finland and in Slovenia. Using pitfall trapping, non-metric multidimensional scaling and generalised linear mixed models, we investigated carabid assemblages at railway verges and in differently contrasting adjacent matrices, i.e. built-up, grassland and forest. The matrix influenced carabid assemblages at railway verges. Assemblages grouped with adjacent matrix types, although some Finnish railway assemblages included a characteristic set of open dry habitat species. Abundances of generalist species at railway verges were higher when next to grassland or forest than urban matrices. Habitat specialists responded negatively to high contrast matrices, resulting in lower abundances of open habitat specialists in railway verges when next to forests and nearly no spill-over of forest specialists into railway verges. These patterns were consistent in both countries, i.e. irrespective of climatic region. Our study emphasises effects of the adjacent matrix and matrix contrasts on communities in linear open habitat patches in cities. Knowledge on matrix effects in patchy landscapes, such as urban environments, is essential in understanding the distribution and composition of communities in discrete patches. This knowledge can be used in conservation planning. If habitat specialists are negatively affected by high matrix contrasts, high contrasts should be avoided.

Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex.

Mammalian cortex is a laminar structure, with each layer composed of a characteristic set of cell types with different morphological, electrophysiological, and connectional properties. Here, we define chromatin accessibility landscapes of major, layer-specific excitatory classes of neurons, and compare them to each other and to inhibitory cortical neurons using the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). We identify a large number of layer-specific accessible sites, and significant association with genes that are expressed in specific cortical layers. Integration of these data with layer-specific transcriptomic profiles and transcription factor binding motifs enabled us to construct a regulatory network revealing potential key layer-specific regulators, including Cux1/2, Foxp2, Nfia, Pou3f2, and Rorb. This dataset is a valuable resource for identifying candidate layer-specific cis-regulatory elements in adult mouse cortex.

OSCILLATING FILAMENTS. I. OSCILLATION AND GEOMETRICAL FRAGMENTATION

ABSTRACT We study the stability of filaments in equilibrium between gravity and internal as well as external pressure using the grid-based AMR code RAMSES. A homogeneous, straight cylinder below a critical line mass is marginally stable. However, if the cylinder is bent, such as with a slight sinusoidal perturbation, an otherwise stable configuration starts to oscillate, is triggered into fragmentation, and collapses. This previously unstudied behavior allows a filament to fragment at any given scale, as long as it has slight bends. We call this process “geometrical fragmentation.” In our realization, the spacing between the cores matches the wavelength of the sinusoidal perturbation, whereas up to now, filaments were thought to be only fragmenting on the characteristic scale set by the mass-to-line ratio. Using first principles, we derive the oscillation period as well as the collapse timescale analytically. To enable a direct comparison with observations, we study the line-of-sight velocity for different inclinations. We show that the overall oscillation pattern can hide the infall signature of cores.

OUP accepted manuscript

The cut-elimination method CERES (for firstand higherorder classical logic) is based on the notion of a characteristic clause set, which is extracted from an LK-proof and is always unsatisfiable. A resolution refutation of this clause set can be used as a skeleton for a proof with atomic cuts only (atomic cut normal form). This is achieved by replacing clauses from the resolution refutation by the corresponding projections of the original proof. We present a generalization of CERES (called CERESs) to first-order proof schemata and define a schematic version of the sequent calculus called LKSE , and a notion of proof schema based on primitive recursive definitions. A method is developed to extract schematic characteristic clause sets and schematic projections from these proof schemata. We also define a schematic resolution calculus for refutation of schemata of clause sets, which can be applied to refute the schematic characteristic clause sets. Finally the projection schemata and resolution schemata are plugged together and a schematic representation of the atomic cut normal forms is obtained. A major benefit of CERESs is the extension of cut-elimination to inductively defined proofs: we compare CERESs with standard calculi using induction rules and demonstrate that CERESs is capable of performing cut-elimination where traditional methods fail. The algorithmic handling of CERESs is supported by a recent extension of the CERES system.

一类复合方程的古典和非古典对称分类

本文确定了一类复合方程的古典对称分类和非古典对称分类。首先，基于微分特征列集算法确定了复合方程的古典对称分类。其次，确定了复合方程的非古典对称的分类。第一步，添加不变曲面条件与原方程组成一个新的偏微分方程组(PDEs)，利用符号计算软件Mathematica确定上面PDEs的对称对应的确定方程组(DTEs)；第二步，根据所得的DTEs进行非古典对称分类，得到复合方程中参数F(u)的具体形式。第三步，确定了非古典对称所对应的不变解以及精确解。所得的不变解和精确解无法利用古典对称得到，所以丰富了复合方程的精确解。 In this paper, the classifications of classical and nonclassical symmetries to a composite type equation are determined. Firstly, the classification of classical symmetries to the composite equation is determined based on the differential characteristic set algorithm. Secondly, the classification of nonclassical symmetries for the composite equation is determined. First step, adding invariant surface condition and the original equation composed a new system of partial differential equations (PDEs), and the determining equations (DTEs) of symmetry to PDEs are determined by using the symbolic computation software Mathematica. Second step, the nonclassical symmetries are classified by calculating DTEs, so we can obtain the specific form of F(u) which is the parameter of the composite equation. Third step, the invariant solutions and exact solutions of the corresponding nonclassical symmetry are determined. The invariant solutions and exact solutions cannot be obtained by classical symmetry, so enrich the exact solutions of the composite equation.

Porosity Governs Normal Stresses in Polymer Gels.

When sheared, most elastic solids including metals, rubbers, and polymer gels dilate perpendicularly to the shear plane. This behavior, known as the Poynting effect, is characterized by a positive normal stress. Surprisingly, fibrous biopolymer gels exhibit a negative normal stress under shear. Here we show that this anomalous behavior originates from the open-network structure of biopolymer gels. Using fibrin networks with a controllable pore size as a model system, we show that the normal-stress response to an applied shear is positive at short times, but decreases to negative values with a characteristic time scale set by pore size. Using a two-fluid model, we develop a quantitative theory that unifies the opposite behaviors encountered in synthetic and biopolymer gels.

Zebrafish embryonic development is induced by carp sperm

Haploid gynogenetic screens increase the efficiency of forward genetic screens and linkage analysis in fish. Typically, UV-irradiated zebrafish sperm is used to activate zebrafish oocytes for haploid screens. We describe the use of UV-irradiated common carp sperm to activate haploid gynogenetic zebrafish development. Carp × zebrafish hybrids are shown to have a characteristic set of features during embryonic development and exhibit functional development of several tissues (muscle, heart and nervous system). Hybrids become inviable past the embryonic stages. This technique eliminates the possibility of incompletely irradiated zebrafish spermatozoa contaminating haploid progenies. While developing this protocol, one unique zebrafish female was identified which, upon insemination with UV-irradiated carp spermatozoa, repeatedly displayed spontaneous diploidization of the maternal chromosomes in her offspring.