Contiguous Positions Research Articles

Fuel loading pattern optimization of ALLEGRO fast reactor using genetic algorithms

In this work the genetic algorithmic (GA) optimization technique is used to find the optimal fuel loading pattern in the experimental fast reactor ALLEGRO. The penalty function method is used to solve this multi-objective combinatorial optimization problem. To evaluate each loading pattern, an interface between the genetic algorithm code and the ERANOS 2.3 deterministic neutronic simulation code was developed. For the simulation of the fuel cycle in ERANOS, the diffusion approach and a 7-group energy structure are used to reduce the computational cost. An integer variable encoding scheme was defined to represent the fuel loading patterns. Two crossover operators, the partially mapped crossover (PMX) and the order crossover (OX), combined with the random mutation operator were implemented as an alternative to the classical operators used in GA. To evaluate the performance of the code the results are compared using two objective functions and two crossover operators. In the first case the operating cycle length is maximized by maximizing the k-eff value at the EOC by satisfying the constraints on the power peaking factor over the cycle, the excess reactivity at the BOC, and the linear heat generation rate constraints. In addition, a condition was imposed that there should be no more than two contiguous positions in the pattern to preserve the power distribution uniformity and to avoid high power peaking factors. The code works very well, and a good solution was found in a reasonable computation time. The best solution corresponds to the PMX operator, and the running time is twice as short compared to the OX operator. In the second case study, a power distribution flatness term is included in the objective function. In this case, a more uniform radial power distribution is obtained but associated with a decrease in cycle length due to the penalty of the flatness term.

Co-Animation in Troubles-Talk

ABSTRACT Through troubles-talk, participants disclose and negatively assess unfortunate past or habitual happenings and offenses, and these are often vividly staged in the here and now by temporarily “doing being” past Self or others, what we call animation. In this study, we show how by animating their own affective reactions toward the recounted experiences, tellers cast themselves as victims and their recipients as witnesses. More importantly, we demonstrate how animation is also a relevant practice for recipients, who in a contiguous position often offer a responsive co-animation of the same figure, validating and amplifying their teller’s affective displays, turning the experience into a common cause. This study contributes further to our understanding of empathic responses in troubles-talk in English by inscribing co-animation as a previously undescribed alternative at the response slot that allows recipients to temporarily position themselves “into the moment” as co-victims, co-experiencers, and co-sanctioners. Data are in English.

Comparative Genomic and Transcriptomic Analyses of CHHs and Their Putative Receptors in Scylla paramamosain, Portunus trituberculatus, and Eriocheir sinensis

Crustacean hyperglycemic hormone superfamily neuropeptides (CHHs) are typical crustacean eyestalk hormones that include the crustacean hyperglycemic hormone (CHH), moult-inhibiting hormone (MIH), vitellogenesis/gonad-inhibiting hormone (VIH/GIH) and mandibular organ-inhibiting hormone (MOIH), which are divided into two subfamilies: type I CHH (included CHH) and type II CHH (consisting of MIH, VIH/GIH, and MOIH). They are involved in various biological activities, such as metabolism, molting, reproduction, and osmotic regulation. Discovery of the ion transport peptide (ITP) in insects expanded the members of CHHs and revealed that CHHs are not restricted to crustaceans. In this study, we focused on three economically important crabs: the mud crab, Scylla paramamosain, the swimming crab, Portunus trituberculatus, and the Chinese mitten crab, Eriocheir sinensis. Their genomes, Pacbio full-length transcriptomic data as well as comparative RNA-seq data were obtained and used to analyze the genomic structures and expression patterns of CHHs and their putative receptors through bioinformatic methods. Two type I CHH members (CHH1 and CHH2) were identified, of which CHH1 had two splice variants, CHH1-v1 and CHH1-v2. One copy of type II CHH (MIH) was found in P. trituberculatus and E. sinensis. While most decapods, including S. paramamosain, have two copies of type II CHHs (MIH/VIH), these MIH/VIHs are adjacent to each other on the same chromosome. Besides type I and II CHH, ITP-like peptides have also been found in the three crabs, and they are mainly expressed in the eyestalk. Four, five, and three G protein-coupled receptors (GPCRs) were identified in S. paramamosain, P. trituberculatus, and E. sinensis, respectively, which might be putative CHH receptors. These GPCRs were divided into three groups. One group was composed of two contiguous genomic position GPCRs, and they were mainly expressed in the hepatopancreas. These findings provide a basis for further studies on CHHs receptor binding tests and on CHHs/GPCRs signaling pathways.

Interference Controls Conductance in Phthalocyanine Molecular Junctions

We report an experimental and theoretical study of the single-molecule conductance of two separate families of regioisomeric phthalocyanine derivatives in which the binding groups are connected at opposite or at contiguous positions about the phthalocyanine moiety. We observe that compounds with the longest distance between the anchoring groups yield molecular junctions with a higher conductance compared to those with a shorter distance. We performed both density functional theory (DFT) and tight binding calculations to understand how interference effects explain the experimental results including the role of constructive and destructive quantum interference in five phthalocyanine derivatives.

Facilitated synthesis of proteins containing modified dipeptides

The elaboration of peptides and proteins containing non-proteinogenic amino acids has been realized using several complementary strategies, including chemical synthesis, ribosome- or non-ribosome-mediated elaboration, intein-mediated polypeptide rearrangements, or some combination of these strategies. All of these have strengths and limitations, and significant efforts have been focused on minimizing the effects of limitations, to improve the overall utility of individual strategies. Our laboratory has studied ribosomally mediated peptide and protein synthesis involving a wide variety of non-proteinogenic amino acids, and in recent years we have described a novel strategy for the selection of modified bacterial ribosomes. These modified ribosomes have enabled the incorporation into peptides and proteins of numerous modified amino acids not accessible using wild-type ribosomes. This has included d-amino acids, β-amino acids, dipeptides and dipeptidomimetic species, as well as phosphorylated amino acids. Presently, we have considered novel strategies for incorporating non-proteinogenic amino acids in improved yields. This has included the incorporation of non-proteinogenic amino acids into contiguous positions, a transformation known to be challenging. We demonstrate the preparation of this type of protein modification by utilizing a suppressor tRNACUA activated with a dipeptide consisting of two identical non-proteinogenic amino acids, in the presence of modified ribosomes selected to recognize such dipeptides. Also, we demonstrate that the use of bis-aminoacylated suppressor tRNAs, shown previously to increase protein yields significantly in vitro, can be extended to the use of non-proteinogenic amino acids.

Converting single nucleotide variants between genome builds: from cautionary tale to solution.

Next-generation sequencing studies are dependent on a high-quality reference genome for single nucleotide variant (SNV) calling. Although the two most recent builds of the human genome are widely used, position information is typically not directly comparable between them. Re-alignment gives the most accurate position information, but this procedure is often computationally expensive, and therefore, tools such as liftOver and CrossMap are used to convert data from one build to another. However, the positions of converted SNVs do not always match SNVs derived from aligned data, and in some instances, SNVs are known to change chromosome when converted. This is a significant problem when compiling sequencing resources or comparing results across studies. Here, we describe a novel algorithm to identify positions that are unstable when converting between human genome reference builds. These positions are detected independent of the conversion tools and are determined by the chain files, which provide a mapping of contiguous positions from one build to another. We also provide the list of unstable positions for converting between the two most commonly used builds GRCh37 and GRCh38. Pre-excluding SNVs at these positions, prior to conversion, results in SNVs that are stable to conversion. This simple procedure gives the same final list of stable SNVs as applying the algorithm and subsequently removing variants at unstable positions. This work highlights the care that must be taken when converting SNVs between genome builds and provides a simple method for ensuring higher confidence converted data. Unstable positions and algorithm code, available at https://github.com/cathaloruaidh/genomeBuildConversion

Fuzzy Path Homotopy in Fuzzy Peano Space

The concepts of fuzzy path connected homotopy in fuzzy Peano Space, Contiguous position of fuzzy path connected homotopy and fuzzy path connected homotopy equivalence in fuzzy Peano space are introduced in this paper. Also several interesting properties of fuzzy path connected homotopy in fuzzy Peano space are discussed.

Ordem do sujeito e colocação de clíticos na escrita brasileira dos séculos XIX e XX

No campo disciplinar da sintaxe diacrônica, analisamos, neste artigo, a mudança na ordem do sujeito e na colocação de clíticos em sentenças matrizes em ambientes neutros ([XP])[XP]V em textos de jornais brasileiros de diferentes estados e em cartas pessoais escritas por brasileiros, no curso dos séculos XIX e XX. O objetivo principal é apresentar evidências empíricas que justifiquem uma mesma mudança microparamétrica na gramática do Português Brasileiro (PB) correlacionada à evolução de dois fenômenos sobejamente descritos: (1) o enrijecimento da ordem Sujeito-Verbo em estruturas transitivas e (2) o aumento da próclise em ambientes neutros [(XP)XP-cl-Verbo]. Defendemos a hipótese de que a próclise gerada pela gramática do PB no contexto [XP]V aparece com mais robustez apenas em textos brasileiros oitocentistas da segunda metade do século XIX, momento em que reflexos de uma gramática do tipo-SV também se revela expressivamente nesses mesmos textos. Nessa direção, buscamos evidências de que a escrita da primeira metade do século XIX reflete, ainda, propriedades de uma gramática do tipo-V2, como o Português Clássico (PCl). Os resultados evidenciam diferentes forças linguísticas e diatópicas que mostram a escrita do Rio de Janeiro e da Bahia mais conservadora do que a dos estados do Ceará, de Pernambuco e de Santa Catarina, atuando no condicionamento da próclise em ambiente neutro ([XP])[XP]V. Esses resultados parecem validar a hipótese investigada: em textos da primeira metade do século XIX atuam, ainda, forças de uma gramática conservadora com sujeitos nulos e com propriedades de uma língua do tipo-V2 em que qualquer constituinte, inclusive o sujeito, pode estar numa posição anterior e contígua ao verbo, como o PCl; em textos da segunda metade do século XIX e do século XX atuam forças de uma gramática com sujeitos realizados em SV, como o PB.

Positional factors in syllabification

AbstractFrom the perspective of standard generative phonological theory, syllable structure is not recorded in the lexicon but it is obtained by means of a syllabification algorithm based on a series of principles. In a given language, the algorithm should parse obstruent+liquid clusters as tautosyllabic both in word-initial and word-internal positions. The tautosyllabic parse as a branching onset complies with all principles on which the syllable-building algorithm is based. In standard theory, if branching onsets of obstruent+liquid are allowed in a language and documented in word-initial position, tautosyllabic parse is predicted to hold also word-internally. Likewise, Kaye’s (1992) Uniformity Principle makes the same prediction, since it states that sequences of contiguous positions that are in a governing relation and contain the same phonological material have the same constituent structure. The present paper draws attention to empirical data showing obstruent+liquid clusters being parsed tautosyllabically in word-initial position and heterosyllabically in word-internal position in the same language. An account is proposed to explain the data discussed, claiming that positional factors may also be relevant in determining syllabification.

Radical cascade cyclization for synthesizing 3,4-fused tricyclic benzofuran derivatives

A new method for synthesizing 3,4-fused tricyclic 3-alkylidene dihydrobenzofuran derivatives was developed. Treatment of propargyl iodophenol derivatives with a tethered alkene at the three contiguous positions under the radical cascade reaction conditions induced the reaction of the generated vinyl radical intermediates with the internal alkene, producing tricyclic 3-alkylidene dihydrobenzofurans in 25%–93% yield. The reaction products could be utilized as the precursors for 3,4-fused tricyclic benzofurans.

When Relatedness is Damaged or Undeveloped: A New Consideration of the Link between Relational Psychoanalysis and Object Relations Theory

The author discusses Lisa Director’s concept of being a catalyst, an enlivening presence, and Robert Grossmark’s concept of companioning, in their work with patients whom I think of as being in the autistic contiguous position. Director and Grossmark each provide a moving example of a long-term, successful treatment with patients who are often seen as unanalyzable and dismissed. These patients are very challenging, having great difficulty entering relationships; either floating through space in a dull, disconnected manner or violently crashing into others in order to make contact and maintain a minimal sense of cohesiveness and connection. I discuss these two exceptional clinical papers using object relations theory, which can provide a more generalizable approach to the treatment of such difficult patients.

Caracterização fonológica dos segmentos vocálicos em Prata - MG

This article discusses the phonological characterization of vocalic segments through distinctive features, following a specification of features according to a more traditional approach. The features [high] and [ATR] are used to establish a distinction between mid vowels. Only [-ATR] is responsible for identifying a common group between low-mid vowels and the low vowel. The data collected in the city of Prata, located in the Triângulo Mineiro region, Brazil, reveal a considerable number of cases that indicate a motivated vowel lowering, especially through the process of vowel harmony. That means that, when in stressed syllable or contiguous position, the low-mid vowel and the low vowel interfere with the production of the low-mid vowel in pre-stressed syllable position. According to the Optimality Theory, more specifically the partial constraint ranking, it is possible to establish a ranking for the cases concerning a vowel harmony motivated by the feature [-ATR].

The complete anatomy and phylogenetic relationships ofAntetonitrus ingenipes(Sauropodiformes, Dinosauria): implications for the origins of Sauropoda

We present a comprehensive description and phylogenetic analysis of the important transitional sauropodomorph Antetonitrus ingenipes. New information sheds light on the stepwise acquisition of sauropod-like traits just prior to the Triassic/Jurassic boundary. Although the forelimb of Antetonitrus and other closely related sauropodomorph taxa retains the plesiomorphic morphology typical of a mobile grasping structure, the changes in the weight-bearing dynamics of both the musculature and the architecture of the hindlimb document the progressive shift towards a sauropodan form of graviportal locomotion. Nonetheless, the presence of hypertrophied muscle attachment sites in the femur of Antetonitrus suggests the retention of an intermediary form of facultative bipedalism. The term Sauropodiformes is adopted here and given a novel definition intended to capture those transitional sauropodomorph taxa occupying a contiguous position on the pectinate line towards Sauropoda. A re-examination of the biased distribution of Sauropodomorpha in the earliest Jurassic suggests the presence of genuine palaeo-environmental processes that may have excluded the large-bodied, graviportal taxa from participating in a number of Early Jurassic ecosystems. © 2014 The Linnean Society of London

Generation of Compound Words in Statistical Machine Translation into Compounding Languages

In this article we investigate statistical machine translation (SMT) into Germanic languages, with a focus on compound processing. Our main goal is to enable the generation of novel compounds that have not been seen in the training data. We adopt a split-merge strategy, where compounds are split before training the SMT system, and merged after the translation step. This approach reduces sparsity in the training data, but runs the risk of placing translations of compound parts in non-consecutive positions. It also requires a postprocessing step of compound merging, where compounds are reconstructed in the translation output. We present a method for increasing the chances that components that should be merged are translated into contiguous positions and in the right order and show that it can lead to improvements both by direct inspection and in terms of standard translation evaluation metrics. We also propose several new methods for compound merging, based on heuristics and machine learning, which outperform previously suggested algorithms. These methods can produce novel compounds and a translation with at least the same overall quality as the baseline. For all subtasks we show that it is useful to include part-of-speech based information in the translation process, in order to handle compounds.

The Quantum Workings of the Rotating 64-Grid Genetic Code

In this article, the pattern learned from the classic or conventional rotating circular genetic code is transferred to a 64-grid model. In this non-static representation, the codons for the same amino acid within each quadrant could be exchanged, wobbling or rotating in a quantic way similar to the electrons within an atomic orbit. Represented in this 64-grid format are the three rules of variation encompassing 4, 2, or 1 quadrant, respectively: 1) same position in four quadrants for the essential hydrophobic amino acids that have U at the center, 2) same or contiguous position for the same or related amino acids in two quadrants, and 3) equivalent amino acids within one quadrant. Also represented is the mathematical balance of the odd and even codons, and the most used codons per amino acid in humans compared to one diametrically opposed organism: the plant Arabidopsis thaliana, a comparison that depicts the difference in third nucleotide preferences: a C/U exchange for 11 amino acids, a G/A exchange for 2 amino acids, and G/U or C/A exchanges for one amino acid, respectively; by studying these codon usage preferences per amino acid we present our two hypotheses: 1) A slower translation in vertebrates and 2) a faster translation in invertebrates, possibly due to the aqueous environments where they live. These codon usage preferences may also be able to determine genomic compatibility by comparing individual mRNAs and their functional third dimensional structure, transport and translation within cells and organisms. These observations are aimed to the design of bioinformatics computational tools to compare human genomes and to determine the exchange between compatible codons and amino acids, to preserve and/or to bring back extinct biodiversity, and for the early detection of incompatible changes that lead to genetic diseases.

The role of imitation in the constitution of psychic reality: The contemporary psychoanalytic perspective of Thomas Ogden

This paper intends to examine the meanings of imitation in the development of psychic reality, taking into account processes that relate to a primitive and sensory-dominated area of experience, described by Thomas Ogden as the autistic–contiguous position. Influenced by the works of Tustin, Bick, Meltzer, and Gaddini, Ogden understands imitation as a form of object relatedness associated to this mode of psychic experience. He emphasizes its role as a primitive and presymbolic mechanism that allows the subject to hold onto some aspects of the other in the absence of a consistent inner space of fantasies where they could be stored. Ogden also examines imitation from the point of view of psychopathology, stressing its role as a defense mechanism against experiences of disruption of the cohesion of the self, but by no means restricted to patients suffering from severe psychological conditions. The paper first examines Ogden's theoretical influences and how imitation may act as a condition for the emergence of an integrated self. Second, it scrutinizes imitation as a predominantly sensorial set of experiences engaged in the production of subjective changes and meanings, and draws distinctions between Ogden's and the other authors’ understanding of imitation.

The rules of variation: Amino acid exchange according to the rotating circular genetic code

General guidelines for the molecular basis of functional variation are presented while focused on the rotating circular genetic code and allowable exchanges that make it resistant to genetic diseases under normal conditions. The rules of variation, bioinformatics aids for preventative medicine, are: (1) same position in the four quadrants for hydrophobic codons, (2) same or contiguous position in two quadrants for synonymous or related codons, and (3) same quadrant for equivalent codons. To preserve protein function, amino acid exchange according to the first rule takes into account the positional homology of essential hydrophobic amino acids with every codon with a central uracil in the four quadrants, the second rule includes codons for identical, acidic, or their amidic amino acids present in two quadrants, and the third rule, the smaller, aromatic, stop codons, and basic amino acids, each in proximity within a 90 degree angle. I also define codifying genes and palindromati, CTCGTGCCGAATTCGGCACGAG.

Random amplified polymorphic DNA analysis of Malassezia isolates from cutaneous lesions of pityriasis versicolor

Objective To investigate intraspecific and interspecific variation within Malassezia iso-lates from patients with pityriasis versicolor by random amplified polymorphic DNA (RAPD) analysis, to learn the difference between RAPD analysis and physiological and biochemical methods in the typing of Malassezia species, and to explore the relationship between RAPD patterns and Malassezia species. Methods A total of 47 Malassezia isolates were obtained from 34 patients with pityriasis versicolor, and they were classified into 5 species by morphological, physiological and biochemical features, I.e., M. Fin'fur, M. Obtusa, M. Globosa, M. Restricta and M. Sympodialis. Genomic DNA was extracted from the 47 clinical isolates and 10 reference strains (including 7 species) of Malassezia. PCR was performed using 4 random primers including S22, S24, S25 and S33. RAPD patterns were analyzed by NTSYS software and dendrogram was autogenerated. Results Genomic DNA of most strains was successfully amplified with four primers, espe-cially with primers S22 and S24 that resulted in rather stable and clear DNA bands. A total of 82 fragments were amplified from all tested strains. These strains showed both interspecifie and intraspecific variation. Multiple swains were isolated from different body sites of 4 patients and identified into different species by biochemical and morphological typing; those swains from same hosts occupied contiguous positions in the dendrogram and exhibited a high genetic convergence. Conclusion The phenomenon that different strains from a co-host show a high genetic convergence indicates that species specificity and evolution of Malassezia are closely related to its hosts. Key words: Tinea versicolor; Malassezia; Random amplified polymorphic DNA technique

Three-Component Coupling Using Arynes and Aminosilanes for ortho-Selective Double Functionalization of Aromatic Skeletons

Arynes were found to couple with aminosilanes and carbonyl compounds in the presence of benzoic acid to provide 2-aminobenzhydrols. Sulfonylimines could also be applied to the reaction, enabling amino and aminomethyl moieties to be incorporated into contiguous positions of aromatic skeletons. Only a small amount of the three-component coupling product was obtained in the absence of benzoic acid, which confirms its vital role in the present reaction.

Columbia revisited: Paleomagnetic results from the 1790 Ma colider volcanics (SW Amazonian Craton, Brazil)

In an attempt to improve our understanding of the Paleoproterozoic geodynamic evolution, a paleomagnetic study was performed on 10 sites of acid volcanic rocks of the Colider Suite, southwestern Amazonian Craton. These rocks have a well-dated zircon U–Pb mean age of 1789 ± 7 Ma. Alternating field and thermal demagnetization revealed northern (southern) directions with moderate to high upward (downward) inclinations. Rock magnetism experiments and magnetic mineralogy show that this characteristic magnetization is carried by Ti-poor magnetite or by hematite that replaces magnetite by late-magmatic deuteric alteration. Both magnetite and hematite carry the same characteristic component. The mean direction (Dm = 183.0°, Im = 53.5°, N = 10, α 95 = 9.8°, K = 25.2) yielded a paleomagnetic pole located at 298.8°E, 63.3°S ( α 95 = 10.2°, K = 23.6), which is classified with a quality factor Q = 5. Paleogeographic reconstructions using this pole and other reliable Paleoproterozoic poles suggest that Laurentia, Baltica, North China Craton and Amazonian Craton were located in laterally contiguous positions forming a large continental mass at 1790 Ma ago. This is reinforced by geological evidence which support the existence of the supercontinent Columbia in Paleoproterozoic times.