bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sorting by Restricted-Length-Weighted Reversals
Authors: Nguyen Thach Cam , Ngo Hieu Trung , Nguyen Nguyen Bao 
Published: November 2016

Abstract
Classical sorting by reversals uses the unit-cost model, that is, each reversal consumes an equal cost. This model limits the biological meaning of sorting by reversal. Bender and his colleagues extended it by assigning a cost function f(l) = lα for all α ≥ 0, where l is the length of the reversed subsequence. In this paper, we extend their results by considering a model in which long reversals are prohibited. Using the same cost function above for permitted reversals, we present tight or nearly tight bounds for the worst-case cost of sorting by reversals. Then we develop algorithms to approximate the optimal cost to sort a given 0/1 sequence as well as a given permutation. Our proposed problems are more biologically meaningful and more algorithmically general and challenging than the problem considered by Bender et al. Furthermore, our bounds are tight and nearly tight, whereas our algorithms provide good approximation ratios compared to the optimal cost to sort 0/1 sequences or permutations by reversals.
Proteome Analysis of Rice Root Proteins Regulated by Gibberellin
Authors: Komatsu Setsuko , Konishi Hirosato 
Published: November 2016

Abstract
To gain an enhanced understanding of the mechanism by which gibberellins (GAs) regulate the growth and development of plants, it is necessary to identify proteins regulated by GA. Proteome analysis techniques have been applied as a direct, effective, and reliable tool in differential protein expressions. In previous studies, sixteen proteins showed differences in accumulation levels as a result of treatment with GA3, uniconazole, or abscisic acid (ABA), and/or the differences between the GA-deficient semi-dwarf mutant, Tan-ginbozu, and normal cultivars. Among these proteins, aldolase increased in roots treated with GA3, was present at low levels in Tan-ginbozu roots, and decreased in roots treated with uniconazole or ABA. In a root elongation assay, the growth of aldolase-antisense transgenic rice was half of that of vector control transgenic rice. These results indicate that increases in aldolase activity stimulate the glycolytic pathway and may play an important role in the GA-induced growth of roots. In this review, we discuss the relationship among GA, aldolase, and root growth.
Preliminary DNA Identification for the Tsunami Victims in Thailand
Authors: Deng Ya-Jun , Li Yuan-Zhe , Yu Xiao-Guang , Li Li , Wu Dong-Ying , Zhou Jun , Man Tian-You , Yang Guang , Yan Jiang-Wei , Cai Da-Qing , Wang Jian , Yang Huan-Ming , Li Sheng-Bin , Yu Jun 
Published: November 2016

Abstract
The 2004 Southeast Asia Tsunami killed nearly 5,400 people in Southern Thailand, including foreign tourists and local residents. To recover DNA evidence as much as possible from the seriously decomposed bodies, we explored procedures of sample preparation from both bone and tooth samples as well as both mitochondrial and nuclear markers. Despite having failed to recover enough DNA for nuclear marker typing, we succeeded in obtaining fully informative results for mitochondrial markers (HV1 and HV2) from 258 tooth samples with a success rate of 51% (258/507). Using an organic DNA extraction method coupled with an ultrafiltration step, we obtained 16 STR (including 13 CODIS loci, one sex discrimination locus, and two Identifiler loci) profiles for 834 samples with a success rate of 79% (834/1,062). In addition, by comparing the allelic frequencies between the typed samples as a group and other index populations, we conclude that the Thai tsunami victims are a combined group of several populations. Our results provide valuable evidence and protocols for the future forensic practice.
A Comprehensive Software Suite for the Analysis of cDNAs
Authors: Arakawa Kazuharu , Suzuki Haruo , Fujishima Kosuke , Fujimoto Kenji , Ueda Sho , Matsui Motomu , Tomita Masaru 
Published: November 2016

Abstract
We have developed a comprehensive software suite for bioinformatics research of cDNAs; it is aimed at rapid characterization of the features of genes and the proteins they code. Methods implemented include the detection of translation initiation and termination signals, statistical analysis of codon usage, comparative study of amino acid composition, comparative modeling of the structures of product proteins, prediction of alternative splice forms, and metabolic pathway reconstruction. The software package is freely available under the GNU General Public License at http://www.g-language.org/data/cdna/.
A Contact Energy Function Considering Residue Hydrophobic Environment and Its Application in Protein Fold Recognition
Authors: Duan Mo-Jie , Zhou Yan-Hong 
Published: November 2016

Abstract
The three-dimensional (3D) structure prediction of proteins is an important task in bioinformatics. Finding energy functions that can better represent residue-residue and residue-solvent interactions is a crucial way to improve the prediction accuracy. The widely used contact energy functions mostly only consider the contact frequency between different types of residues; however, we find that the contact frequency also relates to the residue hydrophobic environment. Accordingly, we present an improved contact energy function to integrate the two factors, which can reflect the influence of hydrophobic interaction on the stabilization of protein 3D structure more effectively. Furthermore, a fold recognition (threading) approach based on this energy function is developed. The testing results obtained with 20 randomly selected proteins demonstrate that, compared with common contact energy functions, the proposed energy function can improve the accuracy of the fold template prediction from 20% to 50%, and can also improve the accuracy of the sequence-template alignment from 35% to 65%.
Constructing Support Vector Machine Ensembles for Cancer Classification Based on Proteomic Profiling
Authors: Mao Yong , Zhou Xiao-Bo , Pi Dao-Ying , Sun You-Xian 
Published: November 2016

Abstract
In this study, we present a constructive algorithm for training cooperative support vector machine ensembles (CSVMEs). CSVME combines ensemble architecture design with cooperative training for individual SVMs in ensembles. Unlike most previous studies on training ensembles, CSVME puts emphasis on both accuracy and collaboration among individual SVMs in an ensemble. A group of SVMs selected on the basis of recursive classifier elimination is used in CSVME, and the number of the individual SVMs selected to construct CSVME is determined by 10-fold cross-validation. This kind of SVME has been tested on two ovarian cancer datasets previously obtained by proteomic mass spectrometry. By combining several individual SVMs, the proposed method achieves better performance than the SVME of all base SVMs.
Prediction and Classification of Human G-Protein Coupled Receptors Based on Support Vector Machines
Authors: Wang Yun-Fei , Chen Huan , Zhou Yan-Hong 
Published: November 2016

Abstract
A computational system for the prediction and classification of human G-protein coupled receptors (GPCRs) has been developed based on the support vector machine (SVM) method and protein sequence information. The feature vectors used to develop the SVM prediction models consist of statistically significant features selected from single amino acid, dipeptide, and tripeptide compositions of protein sequences. Furthermore, the length distribution difference between GPCRs and non-GPCRs has also been exploited to improve the prediction performance. The testing results with annotated human protein sequences demonstrate that this system can get good performance for both prediction and classification of human GPCRs.
Three-dimensional rotating Couette flow via the generalised quasilinear approximation
Authors: Tobias S. M. , Marston J. B. 
Published: November 2016

We examine the effectiveness of the generalised quasilinear (GQL) approximation introduced by Marston et al. (Phys. Rev. Lett., vol. 116 (21), 2016, 214501). This approximation splits the variables into large and small scales in directions where there is a translational symmetry and removes nonlinear interactions involving only small scales. We utilise as a paradigm problem three-dimensional, turbulent, rotating Couette flow. We compare the results obtained from direct numerical solution of the equations with those from quasilinear (QL) and GQL calculations. In this three-dimensional setting, there is a choice of cutoff wavenumber for the GQL approximation both in the streamwise and in the spanwise directions. We demonstrate that the GQL approximation significantly improves the accuracy of mean flows, spectra and two-point correlation functions over models that are quasilinear in any of the translationally invariant directions, even if only a few streamwise and spanwise modes are included. We argue that this provides significant support for a programme of direct statistical simulation utilising the GQL approximation.
Mediating links between HRM bundle and individual innovative behavior
Authors: Liu Fang , Chow Irene Hau-Siu , Gong Yuanyuan , Wang Hao 
Published: November 2016

AbstractUsing multi-level analysis, the present study proposes that psychological empowerment and perceived organizational support serve as mediators of the effects of human resource management (HRM) bundle on individual innovative behavior. We tested the model using data from 705 employees of 162 firms in China. The results revealed that both psychological empowerment and perceived organizational support partially mediate the relationship between HRM bundle and individual innovative behavior. This study contributes to the understanding of how HRM bundle impact on individual innovative behavior.
Toleration or Latitude? Two Models for Liberal Politics
Authors: Vernon Richard 
Published: November 2016

AbstractTheories of toleration maintain that people sometimes have good reasons not to act on their convictions, however strong. Theories of latitude maintain that one should doubt the strength of one's convictions. While toleration has often been taken to be foundational for the liberal tradition, another view (made fully explicit by Brian Barry'sJustice as Impartiality) is that we should look, rather, to the idea of latitude, as exemplified in late seventeenth-century Anglican writings. Taking these writings as its initial point of reference, the article maintains that toleration, rather than latitude, should be seen as foundational for the liberal tradition, which is better understood in terms of what one person owes to another than in terms of the relative validity of their beliefs.
Genetic diversity of infective larvae of Gnathostoma spinigerum (Nematoda: Gnathostomatidae) in freshwater swamp eels from Thailand
Authors: Eamsobhana P. , Wanachiwanawin D. , Roongruangchai K. , Song S.L. , Yong H.S. 
Published: November 2016

AbstractHuman gnathostomiasis is a food-borne zoonosis caused by a tissue nematode of the genus Gnathostoma. The disease is highly endemic in Asia, including Thailand. The freshwater swamp eel (Monopterus albus), the second intermediate host of the gnathostome nematode, has an important role in transmitting the infection in Thailand. Surveys on the infective larvae of Gnathostoma spinigerum based on morphological features in freshwater swamp eels have been performed continuously and reported in Thailand. However, there is still limited molecular data on intra-species variations of the parasite. In this study, a total of 19 third-stage larvae of morphologically identified G. spinigerum were collected from 437 liver samples of freshwater swamp eels purchased from a large wholesale market in Bangkok, Thailand. Molecular characterization based on mitochondrial cytochrome c oxidase subunit I (COI) sequences was performed to elucidate their genetic variations and phylogenetic relationship. Among the 19 infective larvae recovered from these eels, 16 were sequenced successfully. Phylogenetic analyses inferred from the partial COI gene showed the presence of three distinct COI haplotypes. Our findings confirm the presence of G. spinigerum as the main species in Thailand.
Target implosion uniformity in heavy-ion fusion
Authors: Karino T. , Kawata S. , Kondo S. , Iinuma T. , Kubo T. , Kato H. , Ogoyski A. I. 
Published: November 2016

AbstractIn this paper, the robustness of the dynamic instability mitigation mechanism is first examined, and then the instability mitigation phenomenon is demonstrated in a deuterium–tritium (DT) fuel target implosion by wobbling heavy-ion beams (HIBs). The results presented here show that the mechanism of the dynamic instability mitigation is rather robust against changes in the phase, the amplitude and the wavelength of the wobbling perturbation applied. In general instability would emerge from the perturbation of the physical quantity. Normally the perturbation phase is unknown, so that the instability growth rate is discussed. However, if the perturbation phase is known, the instability growth can be controlled by a superposition of perturbations imposed actively: if the perturbation is induced by, for example, a driving beam axis oscillation or wobbling, the perturbation phase could be controlled and the instability growth is mitigated by the superposition of the growing perturbations. In this paper, we realize the superposition of the perturbation by the wobbling HIBs’ illumination onto a DT fuel target in heavy-ion inertial fusion (HIF). Our numerical fluid implosion simulations present that the implosion non-uniformity is mitigated successfully by the wobbling HIBs illumination in HIF.
Energy spectrum analysis for intense pulsed electron beam
Authors: Shen J. , An H.H. , Liu H.Y. , Remnev G.E. , Nashilevskiy A.V. , Li D.Y. , Zhang J. , Zhong H.W. , Cui X.J. , Liang G.Y. , Qu M. , Yan S. , Zhang X.F. , Zhang G.L. , Yu X. , Le X.Y. 
Published: November 2016

AbstractAs the energy spread of intense pulsed electron beams (IPEB) strongly influences the irradiation effects, it has been of great importance to characterize the IPEB energy spectrum. With the combination of Child–Langmuir law and Monte Carlo simulation, the IPEB energy spectrum has been obtained in this work by transformation from the accelerating voltage applied to the diode. To verify the accuracy of this simple algorithm, a magnetic spectrometer with an imaging plate was designed to test the IPEB energy spectrum. The measurement was completed with IPEB generated by explosive emission electron diode, the pulse duration, maximum electron energy, total beam current being 80 ns, 450 keV, and 1 kA, respectively. The results verified the reliability of the above analysis method for energy spectrum, which can avoid intercepting the beam, and at the same time significantly improved the energy resolution. Some calculation and experimental details are discussed in this paper.
Generation of runaway electrons and X rays in an inhomogeneous electric field at high gas pressures
Authors: Tarasenko V.F. , Baksht E.Kh. , Beloplotov D.V. , Burachenko A.G. , Lomaev M.I. , Sorokin D.A. 
Published: November 2016

AbstractResults of experimental studies of the amplitude–temporal characteristics of a runaway electron (RE) beam, as well as breakdown voltage and discharge current with a picosecond time resolution are presented. The maximum pressure, at which a RE beam is detectable, decreases with increasing the voltage rise time. The waveforms of the discharge and RE beam currents are synchronized with those of the voltage pulses. It is shown that the amplitude–temporal characteristics of the RE beam depend on the designs of the gas-filled diode and cathode, as well as the gap length. The mechanism for the generation of REs in atmospheric-pressure gases is analyzed on the basis of the obtained experimental data.
IL-8/IL-17 gene variations and the susceptibility to severe viral bronchiolitis
Authors: PINTO L. A. , DE AZEREDO LEITÃO L. A. , MOCELLIN M. , ACOSTA P. , CABALLERO M. T. , LIBSTER R. , VARGAS J. E. , POLACK F. , COMARU T. , STEIN R. T. , DE SOUZA A. P. 
Published: November 2016

SUMMARYClinical manifestations of acute bronchiolitis (AB) vary from minimal disease to severe respiratory failure. The response to respiratory viral infections is possibly influenced by genetic polymorphisms linked to the regulation of the inflammatory response. In the present study, we investigated whether interleukin-8 (IL-8) and interleukin-17 (IL-17) genetic variants are associated with the severity of AB. A group of Brazilian infants hospitalized with AB and a control group (infants with no or mild AB, without hospitalization) were genotyped for four IL-8/IL-17 variations. For replication, we studied an Argentinean population sample of infants with mild and severe AB. IL-8 polymorphism (rs 2227543) and IL-17 (rs2275913) variants showed significant associations with the severity of AB. The effect of the IL-8 variation could be replicated in the Argentinean sample. This finding suggests that IL-8 variations may influence the severity of AB in young infants. Further genetic association studies in low- or middle-income populations are necessary with the aim of expanding knowledge in this area.
A match made in heaven: Using parallel corpora and multinomial logistic regression to analyze the expression of possession in Old Spanish
Authors: Rosemeyer Malte , Enrique-Arias Andrés 
Published: November 2016

AbstractThis study applies multinomial regression analysis to a parallel corpus of Spanish medieval translations of the Bible in order to study the different factors that condition variation in the expression of possession in Old Spanish. Our methodology allows us to determine the degree to which less frequent possessive constructions (ART + POSS, as inla su casa‘the his house’; GEN, as inla casa de él‘the house of him’; and ART/BARE, as inla casa‘the house’) can be considered competitors to the dominant POSS construction (as insu casa‘his house’) as a function of usage context differences. In comparison to the POSS construction, the ART + POSS construction usually expresses pragmatic functions such as reverence, the GEN construction is typically used to disambiguate a reference, and the ART/BARE construction is bound to contexts in which the possessor is highly accessible. Crucially, the analysis also sheds light on historical changes in the balance between structural and contextual constraints on the use of these different variants. Whereas in the 13th century, structural and stylistic constraints are almost equally important, the importance of structural constraints diminishes in the 15th century. The study thus illustrates how in reductive processes of language change, variation due to structural constraints yields to stylistic variation.
AGENCY, ALTERITY, APPROPRIATION: POSTCLASSIC LOWLAND MAYA USES AND MODIFICATIONS OF THE “MIXTECA-PUEBLA” OR “INTERNATIONAL” STYLE
Authors: Jordan Keith 
Published: November 2016

AbstractMaya participation in the Postclassic Mixteca-Puebla or International Style has long been recognized in murals and manuscript painting. Recent explanations for Maya adoptions/modifications of this central Mexican style have shifted from invasion or “influence” to emphasize the active and selective participation of the Maya. I examine two examples, the solar murals of Mayapan and Flores Stela 4, to elucidate how they reflect Maya uses of the Mexican Other in service of local political and religious power. I argue that these works represent a Late Postclassic continuation of a long Maya tradition of using central Mexican forms and iconography as exotic ideological “prestige goods” reinforcing the legitimacy of local elites. They cannot be understood apart from the previous history of interactions between the Maya and central Mexico, particularly in the Early Postclassic, and some of the “Mexican” elements in these examples may derive from Maya-Mexican interactions during this earlier time.For Eloise Quiñones Keber, and in memory of H.B. Nicholson
SET IN STONE: HIATUSES AND DYNASTIC POLITICS AT TIKAL, GUATEMALA
Authors: Moholy-Nagy Hattula 
Published: November 2016

AbstractStone stelae and altars inscribed with dates and bearing a portrait of the ruler they commemorate define the Classic period in the Maya lowlands. They attest to the ruling elite's awareness of history and its uses to assert their authority and legitimacy. The power of Maya history remains evident when text decipherments override archaeological evidence. Privileging of texts is especially problematic in interpretations of gaps or hiatuses in the sequence of dates on carved monuments as indicators of site-wide decline. Archaeological evidence from the Lowland Maya city of Tikal contradicts the assumption of general decline during its longest hiatus, as well as a widely accepted historical explanation of its cause. Placing stone monuments and their texts in past cultural context indicates gaps were more likely due to a venerable Mesoamerican tradition of monument desecration carried out by rival elite factions than to specific historical events.
UNDERSTANDING THE WRAPPED BUNDLE BURIALS OF WEST MEXICO: A CONTEXTUAL ANALYSIS OF MIDDLE FORMATIVE MORTUARY PRACTICES
Authors: Rhodes Jill A. , Mountjoy Joseph B. , Cupul-Magaña Fabio G. 
Published: November 2016

AbstractThis article reports on the discovery of an unusual type of secondary burial found at two Middle Formative sites in the Mascota valley of Jalisco, West Mexico. We examine these burials within a Middle and Late Formative period context as well as a broader temporal context of funerary customs and mortuary programs involving secondary-type burials. Tightly wrapped, elaborately processed bundled burials were recovered at the cemeteries of El Embocadero II and Los Tanques. We report on the human remains from both sites and examine burial context and biological identity to seek explanations. The individuals selected for this burial treatment are not associated with any markers of high status. These burials may represent a different ethnic, familial, community or ancestral identity, and we consider the broader secondary burial phenomenon as the possible expression of a ritual of seasonal interment associated with the use of a mortuary hut to curate and process the bodies.
THESE ARE OUR MOUNTAINS NOW: STATECRAFT AND THE FOUNDATION OF A LATE CLASSIC MAYA ROYAL COURT
Authors: Carter Nicholas P. 
Published: November 2016

AbstractThis article presents a synthesis of new epigraphic readings of hieroglyphic texts from the sites of Sacul and Ixkun, in the northwestern Maya Mountains of Guatemala, with archaeological data previously published by the Atlas Arqueológico de Guatemala. It proposes that a late eighth century king of Sacul broke with his former allies at Ucanal to establish himself as a local suzerain, sponsoring a new vassal kingdom at Ixkun in the process. Visible in both the hieroglyphic and stratigraphic records, these events recapitulated on a smaller scale the geopolitical practices of hegemonic Maya kingdoms like Calakmul and Tikal. The Sacul king’s strategic cultivation of a separate but dependent court sheds light on the possibilities of and limitations on Classic Maya kingship.