bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV Genome Polymorphism: A Bioinformatics Study
Authors: Pavlović-Lažetić Gordana M. , Mitić Nenad S. , Tomović Andrija M. , Pavlović Mirjana D. , Beljanski Miloš V. 
Published: November 2016

Abstract
A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations (SNVs) and insertions and deletions, with respect to a “profile”, were determined and discussed ("profile" being a sequence containing the most represented letter per position). Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid (a.a.) property changes. Similar analysis was performed for the spike (S) protein in all the isolates (55 of them being predicted for the first time). The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes: TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.
DCCP and DICP: Construction and Analyses of Databases for Copper- and Iron-Chelating Proteins
Authors: Wu Hao , Yang Yan , Jiang Sheng-Juan , Chen Ling-Ling , Gao Hai-Xia , Fu Qing-Shan , Li Feng , Ma Bin-Guang , Zhang Hong-Yu 
Published: November 2016

Abstract
Copper and iron play important roles in a variety of biological processes, especially when being chelated with proteins. The proteins involved in the metal binding, transporting and metabolism have aroused much interest. To facilitate the study on this topic, we constructed two databases (DCCP and DICP) containing the known copper- and iron-chelating proteins, which are freely available from the website http://sdbi.sdut.edu.cn/en. Users can conveniently search and browse all of the entries in the databases. Based on the two databases, bioinformatic analyses were performed, which provided some novel insights into metalloproteins.
A Hybrid SOM-SVM Approach for the Zebrafish Gene Expression Analysis
Authors: Wu Wei , Liu Xin , Xu Min , Peng Jin-Rong , Setiono Rudy 
Published: November 2016

Abstract
Microarray technology can be employed to quantitatively measure the expression of thousands of genes in a single experiment. It has become one of the main tools for global gene expression analysis in molecular biology research in recent years. The large amount of expression data generated by this technology makes the study of certain complex biological problems possible, and machine learning methods are expected to play a crucial role in the analysis process. In this paper, we present our results from integrating the self-organizing map (SOM) and the support vector machine (SVM) for the analysis of the various functions of zebrafish genes based on their expression. The most distinctive characteristic of our zebrafish gene expression is that the number of samples of different classes is imbalanced. We discuss how SOM can be used as a data-filtering tool to improve the classification performance of the SVM on this data set.
FAMCS: Finding All Maximal Common Substructures in Proteins
Authors: Yao Zhen , Xiao Juan , Tung Anthony K.H. , Sung Wing Kin 
Published: November 2016

Abstract
Finding the common substructures shared by two proteins is considered as one of the central issues in computational biology because of its usefulness in understanding the structure-function relationship and application in drug and vaccine design. In this paper, we propose a novel algorithm called FAMCS (Finding All Maximal Common Substructures) for the common substructure identification problem. Our method works initially at the protein secondary structural element (SSE) level and starts with the identification of all structurally similar SSE pairs. These SSE pairs are then merged into sets using a modified Apriori algorithm, which will test the similarity of various sets of SSE pairs incrementally until all the maximal sets of SSE pairs that deemed to be similar are found. The maximal common substructures of the two proteins will be formed from these maximal sets. A refinement algorithm is also proposed to fine tune the alignment from the SSE level to the residue level. Comparison of FAMCS with other methods on various proteins shows that FAMCS can address all four requirements and infer interesting biological discoveries.
Non-Destructive Analysis of the Nuclei of Transgenic Living Cells Using Laser Tweezers and Near-Infrared Raman Spectroscopic Technique
Authors: Tang Wei , Newton Ronald J. , Xie Chang-An , Li Yong-Qing , Whitley Nicki 
Published: November 2016

Abstract
Transgenic cell lines of loblolly pine (Pinus taeda L.) were analyzed by a compact laser-tweezers-Raman-spectroscopy (LTRS) system in this investigation. A low power diode laser at 785 nm was used for both laser optical trapping of single transgenic cells and excitation for near-infrared Raman spectroscopy of the nuclei of synchronized cells, which were treated as single organic particles, at the S-phase of the cell cycle. Transgenic living cells with gfp and uidA genes were used as biological samples to test this LTRS technique. As expected, different Raman spectra were observed from the tested biological samples. This technique provides a high sensitivity and enables real-time spectroscopic measurements of transgenic cell lines. It could be a valuable tool for the study of the fundamental cell and molecular biological process by trapping single nucleus and by providing a wealth of molecular information about the nuclei of cells.
An Improved Biclustering Algorithm and Its Application to Gene Expression Spectrum Analysis
Authors: Qu Hua , Wang Liu-Pu , Liang Yan-Chun , Wu Chun-Guo 
Published: November 2016

Abstract
Cheng and Church algorithm is an important approach in biclustering algorithms. In this paper, the process of the extended space in the second stage of Cheng and Church algorithm is improved and the selections of two important parameters are discussed. The results of the improved algorithm used in the gene expression spectrum analysis show that, compared with Cheng and Church algorithm, the quality of clustering results is enhanced obviously, the mining expression models are better, and the data possess a strong consistency with fluctuation on the condition while the computational time does not increase significantly.
LZ Complexity Distance of DNA Sequences and Its Application in Phylogenetic Tree Reconstruction
Authors: Li Bin , Li Yi-Bing , He Hong-Bo 
Published: November 2016

Abstract
DNA sequences can be treated as finite-length symbol strings over a four-letter alphabet (A, C, T, G). As a universal and computable complexity measure, LZ complexity is valid to describe the complexity of DNA sequences. In this study, a concept of conditional LZ complexity between two sequences is proposed according to the principle of LZ complexity measure. An LZ complexity distance metric between two nonnull sequences is defined by utilizing conditional LZ complexity. Based on LZ complexity distance, a phylogenetic tree of 26 species of placental mammals (Eutheria) with three outgroup species was reconstructed from their complete mitochondrial genomes. On the debate that which two of the three main groups of placental mammals, namely Primates, Ferungulates, and Rodents, are more closely related, the phylogenetic tree reconstructed based on LZ complexity distance supports the suggestion that Primates and Ferungulates are more closely related.
Enhanced ablation of a vertical ice wall due to an external freshwater plume
Authors: McConnochie Craig D. , Kerr Ross C. 
Published: November 2016

We investigate the effect of an external freshwater plume on the dissolution of a vertical ice wall in salty water using laboratory experiments. We measure the plume velocity, the ablation velocity of the ice and the temperature at the ice wall. The freshwater volume flux, $Q_{s}$, is varied between experiments to determine where the resultant wall plume transitions from being dominated by the distributed buoyancy flux due to dissolution of the ice, to being dominated by the initial buoyancy flux, $B_{s}$. We find that when $B_{s}$ is significantly larger than the distributed buoyancy flux from dissolution, the plume velocity is uniform with height and is proportional to $B_{s}^{1/3}$, the interface temperature is independent of $B_{s}$, and the ablation velocity increases with $B_{s}$.
Women business owners’ start-up motivations and network structure
Authors: Sharafizad Jalleh , Coetzer Alan 
Published: November 2016

AbstractThis research responds to calls for studies aimed at developing a more nuanced understanding of women small business owners’ networking behaviours and structures. The study examined whether business start-up motivations and phase of the business (prestart-up, start-up and established) influenced women’s networking behaviours and structures. Semistructured interviews were conducted with 28 women. Interview data were used to categorise participants into classic, forced, and work–family owners. Analysis of the interviews found no marked differences in networking behaviours and network structures of participants during prestart-up phase. During start-up and established phases differences began to emerge. Given that classic and forced owners had established their businesses for financial reasons, a diverse network was more relevant for them. However, work–family participants established the business for family/work balance, thus a small network of close ties was sufficient to achieve their business goals. Theoretical, practical and research implications of the findings are outlined.
From social support to capabilities for the work–life balance of independent professionals
Authors: Annink Anne 
Published: November 2016

AbstractThis qualitative study aims to explain how social support enables independent professionals to achieve work–life balance. Face-to-face interviews were conducted with 50 independent professionals in the Netherlands, Spain, and Sweden. The interview data were analyzed from a capability approach, from which work–life balance is understood in terms of capabilities. The most important sources of social support for independent professionals appeared to be their partner, family, as well as work and nonwork-related friends who were able to provide emotional and instrumental support. However, the extent to which social support can be converted into capabilities is influenced by individual (gender and cohabitation), institutional (the ease of doing business and formal childcare), and societal factors (financial hardship and familialism). The cross-national comparison shows that the institutional and societal context may hinder or reinforce social support for work–life balance, resulting in different experiences across countries.
Ontogeny of the articulated yiliangellinine trilobite Zhangshania typica from the lower Cambrian (Series 2, Stage 3) of southern China
Authors: Hou Jin-bo , Hughes Nigel C. , Yang Jie , Lan Tian , Zhang Xi-guang , Dominguez Chrysalyn 
Published: November 2016

AbstractNew discoveries of the early Cambrian yiliangellinine trilobite Zhangshania typica Li and Zhang in Kunming preserve almost all instars from early postembryonic (protaspid) to mature (holaspid) phases in articulated state, in addition to mature specimens with antennae bearing paired spines on the basal articles. The ontogenetic series shows protarthrous development with some, but likely not all, early holaspid instars expressing additional pygidial segments, gradual rearward migration of the location of the longest pleural spines on the trunk segments, and striking positive allometry of the genal spines. It also reveals Parazhangshania sichuanensis Li and Zhang, 1990 to be the holaspid stage 3 of Z. typica, and therefore its junior synonym. This new find in the Hongjingshao Formation provides species-based regional correlation across the South China block and Z. typica may provide an important biostratigraphic marker for the base of the traditional Tsanglangpuan Stage.
Effect of dietary manganese on antioxidant status and expressions of heat shock proteins and factors in tissues of laying broiler breeders under normal and high environmental temperatures
Authors: Zhu Yong-Wen , Lu Lin , Li Wen-Xiang , Zhang Li-Yang , Ji Cheng , Lin Xi , Liu Hsiao-Ching , Odle Jack , Luo Xu-Gang 
Published: November 2016

AbstractTo investigate the effect of Mn on antioxidant status and on the expressions of heat shock proteins/factors in tissues of laying broiler breeders subjected to heat challenge, we used a completely randomised design (n 6) with a factorial arrangement of 2 environmental temperatures (normal, 21±1°C, and high, 32±1°C)×3 dietary Mn treatments (a Mn-unsupplemented basal diet (CON), or a basal diet supplemented with 120 mg Mn/kg diet, either as inorganic Mn sulphate (iMn) or as organic Mn proteinate (oMn)). There were no interactions (P>0·10) between environmental temperature and dietary Mn in any of the measured indices. High temperature decreased (P<0·003) Mn content, and also tended (P=0·07) to decrease Cu Zn superoxide dismutase (CuZnSOD) activity in the liver and heart. However, an increased Mn superoxide dismutase (MnSOD) activity (P<0·05) and a slight increase in malondialdehyde level (P=0·06) were detected in breast muscle. Up-regulated (P<0·05) expressions of heat shock factor 1 (HSF1) and HSF3 mRNA and heat shock protein 70 (HSP70) mRNA and protein were found in all three tissues. Broiler breeders fed either iMn or oMn had higher tissue Mn content (P<0·0001), heart MnSOD and CuZnSOD activities (P<0·01) and breast muscle MnSOD protein levels (P<0·05), and lower (P<0·05) breast muscle HSP70 mRNA and protein levels compared with those fed CON. Broiler breeders fed oMn had higher (P<0·03) bone Mn content than those fed iMn. These results indicate that high temperature decreases Mn retention and increases HSP70, HSF1 and HSF3 expressions in the tissues of laying broiler breeders. Furthermore, dietary supplementation with Mn in either source may enhance the heart’s antioxidant ability and inhibit the expression of HSP70 in breast muscle. Finally, the organic Mn appears to be more available than inorganic Mn for bone in laying broiler breeders regardless of environmental temperatures.
Including white clover in nitrogen fertilized perennial ryegrass swards: effects on dry matter intake and milk production of spring calving dairy cows
Authors: EGAN M. , LYNCH M. B. , HENNESSY D. 
Published: November 2016

SUMMARYThe current experiment was undertaken to investigate the effect of including white clover (Trifolium repensL.; WC) into perennial ryegrass (Lolium perenneL.; PRG) swards (PRG/WC) receiving 250 kg nitrogen (N) per hectare (ha) per year compared with PRG only swards receiving 250 kg N/ha/year, in an intensive grass-based spring calving dairy production scenario. Forty spring-calving cows were allocated to graze either a PRG/WC or PRG sward (n= 20) from 6 February to 31 October 2012. Fresh herbage was offered daily (17 kg dry matter (DM)/cow) supplemented with concentrate in times of herbage deficit (total supplementation 507 kg/cow). Pre-grazing herbage mass (HM), sward WC content and milk production were measured for the duration of the experiment. Herbage DM intake was estimated in May, July and September. Pre-grazing HM (±s.e.) was similar (1467 ± 173·1 kg DM/ha) for both treatments, as was cumulative herbage production (14 158 ± 769 kg DM/ha). Average WC content of the PRG/WC swards was 236 ± 30 g/kg DM. The PRG/WC cows had greater average daily milk yield and milk solids yield from June onwards. Cumulative milk yield and milk solids yield were greater for the PRG/WC cows compared with the PRG cows (5048 and 4789 ± 34·3 kg milk yield/cow, and 400 and 388 ± 1·87 kg milk solids/cow, respectively). Cows had similar DM intake in all measurements periods (15·1 ± 0·42 kg DM/cow/day). In conclusion, including WC in N-fertilized PRG swards increased milk production from cows grazing the PRG/WC swards compared with PRG, particularly in the second half of the lactation.
USE OF MALE METHODS OF CONTRACEPTION WORLDWIDE
Authors: Ross John , Hardee Karen 
Published: November 2016

SummaryThis article analyses male contraceptive use, both globally and for developing countries. Shares of all contraceptive use due to males are examined, in the context of female use and all use. Patterns according to wealth quintiles are analysed, as well as time trends and geographic variations. Data are drawn primarily from compilations by the UN Population Division and from the Demographic and Health Series and subjected to relatively simple statistical methods including correlation/regression applications. Contraceptive methods that men use directly, or that require their co-operation to use, including condoms, withdrawal, rhythm and male sterilization, account for one-quarter of all contraceptive use worldwide. This represents 13% of married/in-union women. Both the share and the prevalence of male methods vary widely by geography and by the four methods, as well as by quintile wealth groups. With greater wealth there is an unbroken rise for total use; among the male methods, the shares of condom use and rhythm rise by wealth quintiles, while the share of withdrawal drops. The share for male sterilization is highest in the lowest and highest wealth quintiles and dips for the middle quintiles. The overall time trend since the 1980s has been steady at one-quarter of all use involving men; moreover, the share is about the same at all levels of total use. The female-only methods continue to dominate: female sterilization, IUD, pill, injectable and implant, again with great diversity geographically. In surveys men report less total use but more condom use, while females report more injectable use. For the future the male share of one-quarter of use seems secure, with little prospect of an increase unless concerted programmatic efforts are made to expand access to male methods and promote their use as part of a broadened contraceptive method mix.
Sealing, whaling and krill fishing in the Southern Ocean: past and possible future effects on catch regulations
Authors: Hofman Robert J. 
Published: November 2016

ABSTRACTThis paper (1) reviews the history of sealing and whaling in the Southern Ocean to illustrate how market demands combined with no or ineffective regulation of catches led to the overexploitation and near extinction of southern fur seals, southern elephant seals and all but one of the Southern Ocean populations of large whales; (2) indicates how the overexploitation and depletion of krill-eating whales led to the Krill Surplus Hypothesis, and the development of the Antarctic krill fishery and the Convention on the Conservation of Antarctic Marine Living Resources (CCAMLR); (3) points out how misinterpretation of the reference to ‘rational use’ in CCAMLR Article II(2), combined with consensus decision-making and the potential growth of markets for Antarctic krill, could lead to ineffective regulation of the krill fishery and adverse effects on the krill resource, on recovery of depleted populations of krill-dependent whales, and on other ecologically related species and populations; and (4) identifies reasonable actions that could be taken cooperatively by the International Whaling Commission and the CCAMLR Commission to minimise the risk that the krill fishery will prevent or impede recovery of depleted populations of krill-dependent whales.
Nonlinear evolution of the filamentation instability and chaos in laser–plasma interaction
Authors: Sharma S. , Kumar N. , Hussain S. , Sharma R.P. 
Published: November 2016

AbstractFilamentation is one of the most common nonlinear phenomena taking place in the laser–plasma interaction that splits the laser beam into high-intensity spikes. The present study deals with the nonlinear evolution of filamentation instability in laser–plasma interaction and the development of chaos in contrast to linear growth as reported by Kaw et al. in 1973. We have considered a non-uniform perturbation superimposed on plane-wave pump such that due to non-uniformity of the perturbation a finite intensity gradient arises and gives rise to ponderomotive force. This causes filamentation of wave, which has been studied presently using numerical methods as well as analytical tools. The results reveal that the intensity of perturbation gets localized and delocalized with the distance of propagation. The numerical simulation results also reveal that the intensity of perturbation route from ordered to chaotic behavior depending upon the pump laser and perturbation parameters. To study the chaotic behavior, Lyapunov exponents has also been calculated. The semi-analytical method is also developed to have an insight into some of the features of simulation like the formation of localized structures.
Movement prediction for a lower limb exoskeleton using a conditional restricted Boltzmann machine
Authors: Chong Eunsuk , Park F. C. 
Published: November 2016

SUMMARYWe propose a novel class of unsupervised learning-based algorithms that extend the conditional restricted Boltzmann machine to predict, in real-time, a lower limb exoskeleton wearer's intended movement type and future trajectory. During training, our algorithm automatically clusters unlabeled exoskeletal measurement data into movement types. Our predictor then takes as input a short time series of measurements, and outputs in real-time both the movement type and the forward trajectory time series. Physical experiments with a prototype exoskeleton demonstrate that our method more accurately and stably predicts both movement type and the forward trajectory compared to existing methods.
DECIPHERING THE SYMBOLS AND SYMBOLIC MEANING OF THE MAYA WORLD TREE
Authors: McDonald J. Andrew 
Published: November 2016

AbstractAlthough cosmic tree symbolism among pre-Columbian societies of Mesoamerica traces from the Preclassic period, the underlying meaning of the motif and its symbolic permutations are poorly understood. Attempts to identify the plant in a botanical context on ceramic vessels, stucco reliefs, and stone stelae of lowland Maya attribution usually favor determinations as a kapok tree (Ceiba pentandra) or maize plant (Zea mays). A botanical assessment of the morphic and ecological characteristics of these motifs suggests, however, a white-flowered water lily of lowland swamps,Nymphaea ampla. Archeological remains at San Bartolo of the Petén indicate that these iconographic practices were established and codified to a certain extent by the first centuryb.c.The frequent identification of various gods and dynastic rulers as personifications of a water lily world tree underscores the crucial symbolic and ritualistic roles this plant once played in the practice of religion and kingship among Mayan civilizations.