bluuebunny/crossref_metadata_2025_split huggingface dataset:
KATZLDA: KATZ measure for the lncRNA-disease association prediction
Authors: Chen Xing 
Published: November 2015

AbstractAccumulating experimental studies have demonstrated important associations between alterations and dysregulations of lncRNAs and the development and progression of various complex human diseases. Developing effective computational models to integrate vast amount of heterogeneous biological data for the identification of potential disease-lncRNA associations has become a hot topic in the fields of human complex diseases and lncRNAs, which could benefit lncRNA biomarker detection for disease diagnosis, treatment and prevention. Considering the limitations in previous computational methods, the model of KATZ measure for LncRNA-Disease Association prediction (KATZLDA) was developed to uncover potential lncRNA-disease associations by integrating known lncRNA-disease associations, lncRNA expression profiles, lncRNA functional similarity, disease semantic similarity and Gaussian interaction profile kernel similarity. KATZLDA could work for diseases without known related lncRNAs and lncRNAs without known associated diseases. KATZLDA obtained reliable AUCs of 7175, 0.7886, 0.7719 in the local and global leave-one-out cross validation and 5-fold cross validation, respectively, significantly improving previous classical methods. Furthermore, case studies of colon, gastric and renal cancer were implemented and 60% of top 10 predictions have been confirmed by recent biological experiments. It is anticipated that KATZLDA could be an important resource with potential values for biomedical researches.
Application of artificial neural network to investigate the effects of 5-fluorouracil on ribonucleotides and deoxyribonucleotides in HepG2 cells
Authors: Guo Jianru , Chen QianQian , Lam Christopher Wai Kei , Wang Caiyun , Wong Vincent Kam Wai , Xu Fengguo , Jiang ZhiHong , Zhang Wei 
Published: November 2015

AbstractEndogenous ribonucleotides and deoxyribonucleotides are essential metabolites that play important roles in a broad range of key cellular functions. Their intracellular levels could also reflect the action of nucleoside analogues. We investigated the effects of 5-fluorouracil (5-FU) on ribonucleotide and deoxyribonucleotide pool sizes in cells upon exposure to 5-FU for different durations. Unsupervised and supervised artificial neural networks were compared for comprehensive analysis of global responses to 5-FU. As expected, deoxyuridine monophosphate (dUMP) increased after 5-FU incubation due to the inhibition of thymine monophosphate (TMP) synthesis. Interestingly, the accumulation of dUMP could not lead to increased levels of deoxyuridine triphosphate (dUTP) and deoxyuridine diphosphate (dUDP). After the initial fall in intracellular deoxythymidine triphosphate (TTP) concentration, its level recovered and increased from 48 h exposure to 5-FU, although deoxythymidine diphosphate (TDP) and TMP continued to decrease compared with the control group. These findings suggest 5-FU treatment caused unexpected changes in intracellular purine polls, such as increases in deoxyadenosine triphosphate (dATP), adenosine-triphosphate (ATP), guanosine triphosphate (GTP) pools. Further elucidation of the mechanism of action of 5-FU in causing these changes should enhance development of strategies that will increase the anticancer activity of 5-FU while decreasing its resistance.
Tianma Gouteng Yin, a Traditional Chinese Medicine decoction, exerts neuroprotective effects in animal and cellular models of Parkinson’s disease
Authors: Liu Liang-Feng , Song Ju-Xian , Lu Jia-Hong , Huang Ying-Yu , Zeng Yu , Chen Lei-Lei , Durairajan Siva Sundara Kumar , Han Quan-Bin , Li Min 
Published: November 2015

AbstractTianma Gouteng Yin (TGY) is a traditional Chinese medicine (TCM) decoction widely used to treat symptoms associated with typical Parkinson’s disease (PD). In this study, the neuroprotective effects of water extract of TGY were tested on rotenone-intoxicated and human α-synuclein transgenic Drosophila PD models. In addition, the neuroprotective effect of TGY was also evaluated in the human dopaminergic neuroblastoma SH-SY5Y cell line treated with rotenone and the rotenone intoxicated hemi-parkinsonian rats. In rotenone-induced PD models, TGY improved survival rate, alleviated impaired locomotor function of Drosophila, mitigated the loss of dopaminergic neurons in hemi-parkinsonian rats and alleviated apoptotic cell death in SH-SY5Y cells; in α-synuclein transgenic Drosophila, TGY reduced the level of α-synuclein and prevented degeneration of dopaminergic neurons. Conclusively, TGY is neuroprotective in PD models both in vivo and in vitro.
Sialylation of the prion protein glycans controls prion replication rate and glycoform ratio
Authors: Katorcha Elizaveta , Makarava Natallia , Savtchenko Regina , Baskakov Ilia V. 
Published: November 2015

AbstractPrion or PrPSc is a proteinaceous infectious agent that consists of a misfolded and aggregated form of a sialoglycoprotein called prion protein or PrPC. PrPC has two sialylated N-linked carbohydrates. In PrPSc, the glycans are directed outward, with the terminal sialic acid residues creating a negative charge on the surface of prion particles. The current study proposes a new hypothesis that electrostatic repulsion between sialic residues creates structural constraints that control prion replication and PrPSc glycoform ratio. In support of this hypothesis, here we show that diglycosylated PrPC molecules that have more sialic groups per molecule than monoglycosylated PrPC were preferentially excluded from conversion. However, when partially desialylated PrPC was used as a substrate, recruitment of three glycoforms into PrPSc was found to be proportional to their respective populations in the substrate. In addition, hypersialylated molecules were also excluded from conversion in the strains with the strongest structural constraints, a strategy that helped reduce electrostatic repulsion. Moreover, as predicted by the hypothesis, partial desialylation of PrPC significantly increased the replication rate. This study illustrates that sialylation of N-linked glycans creates a prion replication barrier that controls replication rate and glycoform ratios and has broad implications.
Laser controlled singlet oxygen generation in mitochondria to promote mitochondrial DNA replication in vitro
Authors: Zhou Xin , Wang Yupei , Si Jing , Zhou Rong , Gan Lu , Di Cuixia , Xie Yi , Zhang Hong 
Published: November 2015

AbstractReports have shown that a certain level of reactive oxygen species (ROS) can promote mitochondrial DNA (mtDNA) replication. However, it is unclear whether it is the mitochondrial ROS that stimulate mtDNA replication and this requires further investigation. Here we employed a photodynamic system to achieve controlled mitochondrial singlet oxygen (1O2) generation. HeLa cells incubated with 5-aminolevulinic acid (ALA) were exposed to laser irradiation to induce 1O2 generation within mitochondria. Increased mtDNA copy number was detected after low doses of 630 nm laser light in ALA-treated cells. The stimulated mtDNA replication was directly linked to mitochondrial 1O2 generation, as verified using specific ROS scavengers. The stimulated mtDNA replication was regulated by mitochondrial transcription factor A (TFAM) and mtDNA polymerase γ. MtDNA control region modifications were induced by 1O2 generation in mitochondria. A marked increase in 8-Oxoguanine (8-oxoG) level was detected in ALA-treated cells after irradiation. HeLa cell growth stimulation and G1-S cell cycle transition were also observed after laser irradiation in ALA-treated cells. These cellular responses could be due to a second wave of ROS generation detected in mitochondria. In summary, we describe a controllable method of inducing mtDNA replication in vitro.
MMSE‐based version of OMP for recovery of discrete‐valued sparse signals
Authors: Sparrer S. , Fischer R.F.H. 
Published: November 2015

An enhanced algorithm for the reconstruction of discrete‐valued sparse vectors from an underdetermined system of linear equations under the presence of noise is presented. Knowledge from the field of compressed sensing and from digital communications is combined in optimising the estimation step in the orthogonal matching pursuit (OMP) algorithm according to the minimum mean‐squared error (MMSE) criterion. Thereby, a gain in performance of more than 1 dB is achieved compared with the conventional OMP.
Compact UWB CP square slot antenna with two corners connected by a strip line
Authors: Karamzadeh S. , Rafii V. , Kartal M. , Saygin H. 
Published: November 2015

A novel method to design a compact, broadband circularly polarised square slot antenna (CPSSA) with a considerably wide axial ratio (AR) bandwidth is proposed. A coplanar waveguide fed square slot antenna with an impedance matching stub and a cross‐shape radiating patch together with a strip line that connects the two opposite corners of the ground section is designed to provide the desired characteristics. The obtained results for the proposed antenna provide good agreement with the expected performance with a compact size of 20 × 20 mm. The measured impedance bandwidth is as large as 11 050 MHz (2950–14 000 MHz) or about 130.38% with respect to the centre frequency. The measured 3 dB AR is 3373 MHz (35.7%) from 3729 to 7102 MHz and the average measured gain of the CPSSA is almost 3.5 dBi in the operating band.
The extent of functional redundancy changes as species’ roles shift in different environments
Authors: Fetzer Ingo , Johst Karin , Schäwe Robert , Banitz Thomas , Harms Hauke , Chatzinotas Antonis 
Published: November 2015

Significance
It is currently unclear how biodiversity loss affects ecosystem functioning. The concept of functional redundancy implies that species loss is compensated by other species contributing similarly to functioning. Functional redundancy can be revealed by the relationship between biodiversity and ecosystem functioning (e.g., biomass growth). The functioning of an ecosystem remains unaffected if redundant species are removed but decreases if the removed species have unique roles. Most research on biodiversity-ecosystem functioning (BEF) relationships hitherto was restricted to one single set of environmental conditions. Using a microbial model system, we explored this relationship in different environments. We found that the environmental conditions are pivotal when drawing conclusions about functional redundancy because BEF relationships drastically differ due to changing species roles and interactions.
Defective histone supply causes changes in RNA polymerase II elongation rate and cotranscriptional pre-mRNA splicing
Authors: Jimeno-González Silvia , Payán-Bravo Laura , Muñoz-Cabello Ana M. , Guijo Macarena , Gutierrez Gabriel , Prado Félix , Reyes José C. 
Published: November 2015

Significance
The study of the role of histones in transcription in mammals has been hindered by the existence of large gene families encoding every histone subunit. Here we reduce the level of canonical histones in a human cell line by silencing stem-loop–binding protein, a histone mRNA regulatory factor. We show that canonical histone depletion increases the RNA polymerase II (RNAPII) elongation rate and temporally separates transcription and splicing. Furthermore, histone depletion also causes several pre-mRNA splicing defects, including skipping of alternative exons and intron retention. Thus we demonstrate that the correct histone supply is required to control the RNAPII elongation rate and pre-mRNA splicing.
Structural basis for antagonizing a host restriction factor by C7 family of poxvirus host-range proteins
Authors: Meng Xiangzhi , Krumm Brian , Li Yongchao , Deng Junpeng , Xiang Yan 
Published: November 2015

Significance
Productive viral replication requires overcoming many barriers posed by the host innate immune system. Human sterile alpha motif domain-containing 9 (SAMD9) is a newly identified antiviral factor that is specifically targeted by poxvirus proteins belonging to the C7 family of host-range factors. Here we provide the first, to our knowledge, atomic view of two functionally divergent proteins from the C7 family and determine the molecular basis that dictates whether they can target SAMD9 effectively. Our studies of distantly related C7 family members suggest that SAMD9 is an evolutionally conserved immune barrier that has been overcome successfully by diverse mammalian poxviruses.
Incorporating Ecology into Survey Design: Monitoring the Recruitment of Age-0 Gags in the Eastern Gulf of Mexico
Authors: Switzer Theodore S. , Keenan Sean F. , Stevens Phillip W. , McMichael Robert H. , MacDonald Timothy C. 
Published: November 2015

Abstract
We developed a multiple-gear survey (183-m haul seine and 6.1-m otter trawl) that was designed to supplement long-term, fishery-independent survey data on age-0 Gags Mycteroperca microlepis in Apalachicola Bay, Tampa Bay, and Charlotte Harbor, Florida. The supplemental survey design specifically considered juvenile Gag recruitment ecology and thus targeted the deep, polyhaline seagrass habitats that are utilized by age-0 Gags yet infrequently sampled. It also expanded the spatial coverage of ongoing surveys to include two unsampled estuaries (St. Andrew Bay and Big Bend [Apalachee Bay]) where Gag recruitment had been documented. Analyses of data collected in long-term and supplemental surveys (2008–2012) demonstrated the effectiveness of this sampling approach. The size ranges of Gags collected in long-term and supplemental surveys were similar, but age-0 individuals were captured more frequently and CPUE was significantly higher in the supplemental surveys. Interannual patterns of variability in Gag recruitment were similar between gear types and among sampling designs, although the coefficient of variation was lowest for the combined data from long-term and supplemental seine surveys. Data from these complementary surveys will improve our ability to characterize age-0 Gag recruitment. Nevertheless, additional information on habitat availability—combined with a better understanding of the estuarine systems' relative contributions to nearshore Gag populations—will be required to maximize the utility of these data in predicting fisheries productivity.
Received July 24, 2014; accepted August 3, 2015
The Anatomy of Growth and Development in Sub-Saharan Africa
Authors: Thorbecke Erik 
Published: November 2015

Abstract
The major objectives of this chapter are, first, to analyse the interrelationship among economic growth, inequality, and poverty; and, second, to propose a typology of countries within sub-Saharan Africa (SSA) based on the different initial conditions they face and that can be used to derive appropriate development strategies. The typology of countries proposed in this chapter is derived from four distinct hierarchically ordered criteria: first, the role and quality of institutions (failed and functioning states); second, the role of agriculture for development and its contribution to growth and poverty reduction (high vs. low potential); third, the role of resources (resource-scarce vs. resource-rich countries); and, fourth, the role of geography (coastal vs. landlocked countries). These criteria yielded a classification consisting of six relatively distinct categories of countries. In turn, different development strategies adapted to the initial conditions of each of the six categories of countries are presented.
Is Poverty a Binding Constraint on Growth in Sub-Saharan Africa?
Authors: Duclos Jean-Yves , O’Connell Stephen A. 
Published: November 2015

Abstract
Is poverty a binding constraint on economic growth in sub-Saharan Africa? Plausible theories of economy-wide poverty traps abound, but the empirical cross-country growth literature is indecisive on the existence of multiple equilibria and is likely to remain so. This chapter introduces the weaker concept of development traps, defined as intervals of income over which growth is low and conditional convergence fails. The chapter argues that development traps are of broader empirical relevance than poverty traps, both at the aggregate level and for households. The chapter argues that the most promising directions for research involve microeconomic investigations of the effects of poverty on productivity. The chapter reviews the dominant mechanisms through which these effects may emerge and suggests specific avenues for country-based research.
Spatial Inequality and its Implications for Growth–Poverty-Reduction Relations
Authors: McKay Andy , Perge Emilie 
Published: November 2015

Abstract
This chapter focuses on the interrelation between spatial inequality and growth. A key insight of the new economic geography literature is that agglomeration, urbanization, and migration are often key features associated with growth, but create the risk that growth may be spatially unequal, at least in the short to medium term. The chapter then discusses the measurement of spatial inequality, and reviews a significant body of evidence about the association between spatial inequality and economic development. In the context of sub-Saharan Africa, a particular concern is that changes in spatial inequality may align with pre-existing ethnic, religious, and other divides. Sub-Saharan Africa faces a difficult challenge in balancing the need for continued growth, often facilitated by forces of concentration of production and population, with the need to take policy actions to check the rise of potentially destructive forms of spatial inequality.
Existentials and Locatives in Romance Dialects of Italy
Authors: Bentley Delia , Ciconte Francesco Maria , Cruschina Silvio 
Published: November 2015

Abstract
This volume provides the first ever large-scale comparative treatment of there sentences (there copula NP), reporting the results of a survey of Italo-Romance and Sardinian dialects of Italy. The volume comprises detailed discussions of focus structure, predication and argument realization, the definiteness effects, and the linking from semantics to syntax in there sentences, advancing novel proposals in each case. The testing of influential hypotheses on existential constructions against first-hand dialect evidence leads the book to argue that existential and locative there sentences differ in focus structure and semantics, although their not being predicate focus constructions and the non-canonicality of the predicate—which is typically referential—is reflected in their shared morphosyntactic features. The hypothesis that the pivot is the predicate of the existential construction is adopted in the analysis, although a distinction is drawn between referential and non-referential pivots, which explains variation in pivot behaviour in morphosyntax. The volume also provides the historical background of Romance there sentences, relying on the findings of the analysis of a substantial corpus of early Italo-Romance vernacular texts.
Global copy number profiling of cancer genomes
Authors: Wang Xuefeng , Chen Mengjie , Yu Xiaoqing , Pornputtapong Natapol , Chen Hao , Zhang Nancy R. , Powers R. Scott , Krauthammer Michael 
Published: November 2015

Abstract
Summary: In this article, we introduce a robust and efficient strategy for deriving global and allele-specific copy number alternations (CNA) from cancer whole exome sequencing data based on Log R ratios and B-allele frequencies. Applying the approach to the analysis of over 200 skin cancer samples, we demonstrate its utility for discovering distinct CNA events and for deriving ancillary information such as tumor purity.
Availability and implementation: https://github.com/xfwang/CLOSE
Contact: xuefeng.wang@stonybrook.edu or michael.krauthammer@yale.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison
Authors: Richter Michael , Rosselló-Móra Ramon , Oliver Glöckner Frank , Peplies Jörg 
Published: November 2015

Abstract
Summary: JSpecies Web Server (JSpeciesWS) is a user-friendly online service for in silico calculating the extent of identity between two genomes, a parameter routinely used in the process of polyphasic microbial species circumscription. The service measures the average nucleotide identity (ANI) based on BLAST+ (ANIb) and MUMmer (ANIm), as well as correlation indexes of tetra-nucleotide signatures (Tetra). In addition, it provides a Tetra Correlation Search function, which allows to rapidly compare selected genomes against a continuously updated reference database with currently about 32 000 published whole and draft genome sequences. For comparison, own genomes can be uploaded and references can be selected from the JSpeciesWS reference database. The service indicates whether two genomes share genomic identities above or below the species embracing thresholds, and serves as a fast way to allocate unknown genomes in the frame of the hitherto sequenced species.
Availability and implementation: JSpeciesWS is available at http://jspecies.ribohost.com/jspeciesws.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: mrichter@ribocon.com
Baudelaire and Feminine Singularity
Authors: Chatterjee Ronjaunee 
Published: November 2015

Abstract

This article revisits the representation of gender and femininity in Baudelaire's poems about the city, arguing that these works reveal a vision of femininity that cannot be reduced to the particularity through which the nineteenth-century individual is codified. While feminine figures abound in Baudelaire's œuvre, most critical readings of the poet have concentrated on the tendency towards objectification, and even denigration, in his portrayal of women. By contrast, in its early stages this article reads ‘À une passante’ in conjunction with Baudelaire's observations from
Mon Cœur mis à nu
,
Fusées
, and
Le Peintre de la vie moderne
, suggesting that a form of femininity that I shall call ‘feminine singularity’ crystallizes in his work, and that it resists collectivization under the broader tenets of urban capital and political liberalism. The subsequent stages of the article discuss ‘Les Sept Vieillards’ and ‘Les Petites Vieilles’, arguing that there is a redrawing of gendered individuation in the
Tableaux parisiens
. Both of these poems approach gender ironically, using a grotesque mode of serialization to dissolve a conventional understanding of sexual difference predicated on binaries, reproduction, and heterosexual desire.
On Garréta on Proust
Authors: Baldwin Thomas 
Published: November 2015

Abstract

This article explores Anne F. Garréta's engagements with Marcel Proust's
À la recherche du temps perdu
in
La Décomposition
(1999). I argue that Garréta's various ‘rewritings’ of Proust's novel supply a new image of the productive tensions between literary works and critical or novelistic approaches to them and simultaneously resist a tendency to reproduce and consume Proust's work as a cultural fetish. In examining Garréta's creation of a series of interfaces with passages in
À la recherche
, I suggest that some readers of
La Décomposition
encounter a ‘virtual’ text that shares some of the features of both authors' novels but is identical to neither. I also consider the ways in which Roland Barthes's understanding of Proust and of Proust criticism more generally can help us to appreciate the significance of what Garréta has done.