bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extreme variation in patterns of tandem repeats in mitochondrial control region of yellow-browed tits (Sylviparus modestus, Paridae)
Authors: Wang Xiaoyang , Liu Nian , Zhang Hongli , Yang Xiao-Jun , Huang Yuan , Lei Fumin 
Published: August 2015

AbstractTo investigate the evolutionary pattern and origins of tandem repeats in the mitochondrial control region of the yellow-browed tit (Sylviparus modestus), the control region and another four mitochondrial loci from fifteen individuals were analyzed. A 117-bp tandem repeat unit that repeated once, twice or three times in different individuals was found and a rarely reported arrangement for this tandem repeats region that a 5′ imperfect copy at its downstream and a 3′ imperfect copy at its upstream was observed. The haplotype network, phylogenetic trees and ancestral state reconstruction of the combined dataset of five loci suggested multiple origins of the same repeat number. The turnover model via slipped-strand mispairing was introduced to interpret the results, because mispairing occurred so frequently that multiple origins of certain repeat number were observed. Insertion via recombination should be a better explanation for the origin of this tandem repeat unit, considering characteristics of the combined sequence of the 3′ and 5′ imperfect copy, including identification of its homolog in other passerines and its predicted secondary structure.
Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes
Authors: Li Xiaofang , Zhu Yong-Guan , Shaban Babak , Bruxner Timothy J. C. , Bond Philip L. , Huang Longbin 
Published: August 2015

AbstractCharacterizing the genetic diversity of microbial copper (Cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional genecopA. In this study, a local BLASTN method using acopAdatabase built in this study was developed to recover full-length putativecopAsequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning CopA using conserved metal-binding motifs, inferred by evolutionary trace analysis of CopA sequences from known Cu resistant microorganisms. In total, 99 putativecopAsequences were recovered from the tailings metagenome, out of which 70 were found with high potential to be functioning in Cu resistance. Phylogenetic analysis of selectedcopAsequences detected in the tailings metagenome showed that topology of thecopAphylogeny is largely congruent with that of the 16S-based phylogeny of the tailings microbial community obtained in our previous study, indicating that the development ofcopAdiversity in the tailings might be mainly through vertical descent with few lateral gene transfer events. The method established here can be used to explorecopA(and potentially other metal resistance genes) diversity in any metagenome and has the potential to exhaust the full-length gene sequences for downstream analyses.
Discerning the differential molecular pathology of proliferative middle ear lesions using Raman spectroscopy
Authors: Pandey Rishikesh , Paidi Santosh Kumar , Kang Jeon Woong , Spegazzini Nicolas , Dasari Ramachandra Rao , Valdez Tulio Alberto , Barman Ishan 
Published: August 2015

AbstractDespite its widespread prevalence, middle ear pathology, especially the development of proliferative lesions, remains largely unexplored and poorly understood. Diagnostic evaluation is still predicated upon a high index of clinical suspicion on otoscopic examination of gross morphologic features. We report the first technique that has the potential to non-invasively identify two key lesions, namely cholesteatoma and myringosclerosis, by providing real-time information of differentially expressed molecules. In addition to revealing signatures consistent with the known pathobiology of these lesions, our observations provide the first evidence of the presence of carbonate- and silicate-substitutions in the calcium phosphate plaques found in myringosclerosis. Collectively, these results demonstrate the potential of Raman spectroscopy to not only provide new understanding of the etiology of these conditions by defining objective molecular markers but also aid in margin assessment to improve surgical outcome.
Secure DNA data compression using algebraic curves
Authors: Soto I. , Jiron I. , Valencia A. , Carrasco R. 
Published: August 2015

A system that achieves compression using artificial DNA packaging with the support of two algebraic curves is presented, whereby the Hermitian channel code algorithm introduces gain and safety. Additionally, performance results are presented with a gain of 7 dB against uncoded quadrature phase shift keying and 1 dB against McEliece, for a bit error rate of 10−3. The results of the security levels compared with the McEliece system are also presented.
Comparison among series compensators for transient stability enhancement of doubly fed induction generator based variable speed wind turbines
Authors: Hussein Ahmed Abu , Hasan Ali Mohd. 
Published: August 2015

This study investigates the effects of series compensators, such as the dynamic voltage restorer (DVR), series dynamic braking resistor, thyristor switched series capacitor, and the high temperature superconducting fault current limiter (SFCL), in enhancing the transient stability of a doubly fed induction machine based variable speed wind generator system. The tested system consists of a 9 MW doubly fed induction generator based wind farm connected to an infinite bus through two step‐up transformers and a double run transmission lines. A three‐phase‐to‐ground (3LG) fault and a single‐line‐to‐ground fault (1LG) were applied to one of the lines to demonstrate the transient stability enhancement ability of the series devices. A performance comparison among the four series compensators is made based on responses of active/reactive power, terminal voltage, rotor speed, dc link voltage, and current variations. Simulations were carried out in the MATLAB/Simulink environment. Simulation results show that all series devices can improve the transient stability, however, the SFCL is the most efficient in terms of active power, rotor speed stability and fault current suppression, and the DVR seems to have a better performance than the SFCL in terms of voltage and reactive power.
Collection-limited theory interprets the extraordinary response of single semiconductor organic solar cells
Authors: Ray Biswajit , Baradwaj Aditya G. , Khan Mohammad Ryyan , Boudouris Bryan W. , Alam Muhammad Ashraful 
Published: August 2015

Significance
We demonstrate that, instead of the charge generation mechanism, charge collection can readily explain the bottleneck toward higher efficiency single organic semiconductor based OPVs (SS-OPVs). This change in archetype has the potential to transform the design rules for materials used in OPV devices and would inspire searches for a completely different set of polymers for OPV cells. Furthermore, we believe that our findings will broaden the understanding of the physics of charge transport and the impact of charged defect states in organic electronic devices. Hence, this work should have deep and immediate impact on the chemists, materials scientists, and device physicists in the field and would be of broad interest to the organic electronics community.
Mapping vaccinia virus DNA replication origins at nucleotide level by deep sequencing
Authors: Senkevich Tatiana G. , Bruno Daniel , Martens Craig , Porcella Stephen F. , Wolf Yuri I. , Moss Bernard 
Published: August 2015

Significance
DNA replication occurs in the nucleus of eukaryotic cells, which is also the site of replication of many DNA viruses. In contrast, poxviruses replicate entirely within the cytoplasm, using enzymes encoded within their genomes. Whether poxviruses replicate their linear, covalently closed, double-stranded DNA exclusively by nicking and strand displacement or by leading and lagging strand synthesis at replication forks similar to eukaryotes remained unclear. Furthermore, poxvirus genome replication origins had not been mapped, and even their existence has been questioned. Here, using directional deep sequencing, we provide evidence for the leading/lagging strand replication mode with origins located near the end of the genome and at the concatemer junction of replicative intermediates.
Ameliorative effect of betulin from Betula platyphylla bark on scopolamine-induced amnesic mice
Authors: Cho Namki , Kim Hyeon Woo , Lee Hee Kyoung , Jeon Byung Ju , Sung Sang Hyun 
Published: August 2015

Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease induced by cholinergic neuron damage or amyloid-beta aggregation in the basal forebrain region and resulting in cognitive disorder. We previously reported on the neuroprotective effects of Betula platyphylla bark (BPB) in an amyloid-beta-induced amnesic mouse model. In this study, we obtained a cognitive-enhancing compound by assessing results using a scopolamine-induced amnesic mouse model. Our results show that oral treatment of mice with BPB and betulin significantly ameliorated scopolamine-induced memory deficits in both passive avoidance and Y-maze tests. In the Morris water maze test, administration of BPB and betulin significantly improved memory and cognitive function indicating the formation of working and reference memories in treated mice. Moreover, betulin significantly increased glutathione content in mouse hippocampus, and the increase was greater than that from betulinic acid treatment. We conclude that BPB and its active component betulin have potential as therapeutic, cognitive enhancer in AD.
Introduction
Authors: Blackwood Stephen 
Published: August 2015

AbstractThis Introduction sets this book in the context of aurality, both by evoking ancient literary culture, in which books were typically (that is not to say always) read aloud, and by pointing to Boethius’ own awareness of the power of spoken or sung sound. The starting-point here is his De institutione musica, where he refers repeatedly and emphatically to the special character of the sense of hearing, and to the therapeutic power of music, rhythm, and mode. This investigation then turns to the Consolation’s many references to its own sound, especially to the sound of its poems. The Introduction concludes by setting forth the hypothesis that the remainder of the book aims to prove: the Consolation’s metres play a central role in the therapy, or consolation, the work is meant to provide.
The First Four
Authors: Blackwood Stephen 
Published: August 2015

AbstractThis chapter looks at the four metres that occur twice each in the Consolation—elegiac couplets, limping iambic trimeter, anapaestic dimeter catalectic, and sapphic hendecasyllable—as well as the hexameter, 3, IX, around which these pairs seem to occur. It is argued that each repetition of a metre intentionally recalls the earlier instance of the same sound in order to administer a medicine matched precisely to a particular wound.
Of Time, the Body, and the City
Authors: Strhan Anna 
Published: August 2015

AbstractThis chapter argues that conservative evangelicals’ orientation towards the coherence of God’s character is bound up with a sense of His transcendence, leading to a consciousness of His absence. It describes how conservative evangelicals’ focus on word-based practices in a busy metropolitan context can generate experiences of uncertainty and doubt, and a sense that their becoming disciples requires hard work and struggle. The chapter describes how St John’s congregants develop relationships of accountability with each other that encourage them to keep going in their faith. It shows how through individual and communal practices, they work to incorporate themselves into a wandering body that is in the process of turning away from the immanent city and seeking to make a passage through time to the City of God beyond time, a turning away that is, however, often interrupted and difficult.
Epistemic indefinites and methods of identification
Authors: Aloni Maria , Port Angelika 
Published: August 2015

AbstractThe chapter proposes an account of epistemic indefinites cross-linguistically, focusing on the case of German irgendein and Italian un qualche. Four main functions for EIs are identified initially: specific unknown (SU); epistemic unknown (epiU); negative polarity (NPI); and the deontic free choice (deoFC). It is subsequently observed that while irgendein qualifies for all functions, un qualche qualifies only for the first two. The second part of the chapter proposes an account of these data in the framework of a Dynamic Semantics with Conceptual Covers. Our point of departure is the assumption that epistemic indefinites are existentials with two additional characteristics: (i) they induce an obligatory domain shift and (ii) they are felicitous only if such a shift is for a reason.
Ignorance, indifference, and individuation withwh-ever
Authors: Condoravdi Cleo 
Published: August 2015

AbstractWh-ever phrases give rise to implications of ignorance or indifference. Previous analyses fold these implications into the truth-conditional or presuppositional content of wh-ever and posit a variation condition requiring non-rigid reference of the wh-ever description across possibilities in a modal domain, such as the speaker’s epistemic state. This chapter shows first that variation based on non-rigidity is not strong enough to account for the precise form of the ignorance implication. Secondly, the ignorance or indifference implication is obligatory only with singular wh-ever phrases. The chapter proposes an analysis which unifies the different uses and solves both these problems. It relies on property-based individuation and associates contextually determined alternatives to wh-ever phrases which yield more specific descriptions. The ignorance and indifference implications result from the enriched meaning contributed by the alternatives and their locus of discharge.
svviz: a read viewer for validating structural variants
Authors: Spies Noah , Zook Justin M. , Salit Marc , Sidow Arend 
Published: August 2015

Abstract
Summary: Visualizing read alignments is the most effective way to validate candidate structural variants (SVs) with existing data. We present svviz, a sequencing read visualizer for SVs that sorts and displays only reads relevant to a candidate SV. svviz works by searching input bam(s) for potentially relevant reads, realigning them against the inferred sequence of the putative variant allele as well as the reference allele and identifying reads that match one allele better than the other. Separate views of the two alleles are then displayed in a scrollable web browser view, enabling a more intuitive visualization of each allele, compared with the single reference genome-based view common to most current read browsers. The browser view facilitates examining the evidence for or against a putative variant, estimating zygosity, visualizing affected genomic annotations and manual refinement of breakpoints. svviz supports data from most modern sequencing platforms.
Availability and implementation: svviz is implemented in python and freely available from http://svviz.github.io/.
Contact: nspies@stanford.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Proprietary costs of intellectual capital reporting: Malaysian evidence
Authors: Kamardin Hasnah , Abu Bakar Robiah , Ishak Rokiah 
Published: August 2015

Purpose
– The purpose of this paper is to examine the relationship between intellectual capital (IC) performance (value-added intellectual coefficient (VAIC)) and company characteristics with IC disclosure (ICD) in Malaysian listed companies.

Design/methodology/approach
– Sample of the study is 68 biggest Malaysian companies listed in Malaysian Stock Exchange based on market capitalization in year 2006. The paper follows the classification of ICD by Huang et al. (2007), with three broad IC categories in 45 items. Content analysis was used to collect the IC information from the annual reports. Regression analysis was conducted for VAIC and its components. Log linear analysis was also conducted to cater the possible misspecification in the model.

Findings
– Results of the study show that VAIC is negatively related to ICD. Further classification of VAIC shows that intellectual capital efficiency and human capital efficiency are negatively related to ICD whilst structural capital efficiency is not related to ICD. Company size and leverage are found to be positively related to ICD.

Research limitations/implications
– Negative association between VAIC and ICD suggests that companies reduce ICD for competitive advantage reason which supports the proprietary cost theory. The findings of the study may provide some evidence to regulators to enhance the reporting practices of IC for the benefits of users of financial reporting in making relevant decisions. The focus should be given on the reporting of human capital items.

Originality/value
– This is the first paper to use IC framework by Huang et al. (2007). Consistency of findings with other studies using different IC framework can be compared for the choice of IC framework in future studies.
Foregrounding the role of relationships in reform
Authors: Liou Yi-Hwa , Daly Alan J. , Brown Chris , del Fresno Miguel 
Published: August 2015

Purpose– The role of relationships in the process of leadership and change is central, yet the social aspect of the work of reform is often background in favor of more technical approaches to improvement. Therefore, the purpose of this paper is to argue that social network theory and analysis provides a useful theory and set of tools to unpack the complex social work of leadership.Design/methodology/approach– In this paper the authors begin by reviewing social network theory in education to date. The authors identify strengths and gap areas and use findings and data from existing social network studies of educational leadership to highlight major concepts.Findings– Along with empirical examples, the paper proposes four important strands of social network analysis for future research in educational leadership: multiplex networks; multi-mode networks; longitudinal networks; and real time networks.Originality/value– This paper builds on recent scholarship using social network analysis in educational leadership and suggests that social network theory and methods provides unique and important analytic purchase in the study of educational leadership.
17‐(allylamino)‐17‐demethoxygeldanamycin drives Hsp70 expression but fails to improve morphological or functional recovery in injured skeletal muscle
Authors: Baumann Cory W , Otis Jeffrey S 
Published: August 2015

SummaryThe stress inducible 70 kDa heat shock protein (Hsp70) is instrumental to efficient morphological and functional recovery following skeletal muscle injury because of its roles in protein quality control and molecular signalling. Therefore, in attempt to improve recovery, Hsp70 expression was increased with 17‐(allylamino)‐17‐demethoxygeldanamycin (17‐AAG) prior to and following an intramuscular injection of barium chloride (BaCl2) into the tibialis anterior (TA) of healthy young mice. To assess recovery, regenerating fibre cross‐sectional area (CSA) of the TA and in vivo peak isometric torque produced by the anterior crural muscles (TA, extensor digitorum longus and extensor hallucis muscles) were analyzed for up to 3 weeks after the injury. Because treatment of 17‐AAG and Hsp70 are known to influence inflammatory and myogenic signalling, tumor necrosis factor‐α (TNF‐α) and myogenin content were also assessed. This study reports that 17‐AAG was effective at up‐regulating Hsp70 expression, increasing content fivefold in the uninjured muscle. However, this significant increase in Hsp70 content did not enhance morphological or functional recovery following the injury, as the return of regenerating fibre CSA and in vivo peak isometric torque did not differ compared to that of the injured muscle from the vehicle treated mice. Treatment with 17‐AAG also altered TNF‐α and myogenin content, increasing both to a greater extent after the injury. Together, these findings demonstrate that although 17‐AAG may alter molecular makers of regeneration, it does not improve recovery following BaCl2‐induced skeletal muscle injury in healthy young mice.
Targeting the platelet‐derived growth factor signalling in cardiovascular disease
Authors: Hu Weining , Huang Yu 
Published: August 2015

SummaryOver 40 years of studies on platelet‐derived growth factors (PDGFs) and their receptors, the molecular mechanisms and functional roles of PDGFs in the development of embryos and human diseases, especially in cancer, are gradually being unravelled. PDGF‐BB was approved by the United States Food and Drug Administration for promoting wound healing, while imatinib, which selectively inhibits tyrosine kinase activity of PDGF receptors (PDGFR), has been prescribed to treat patients with gastrointestinal stromal tumor and chronic eosinophilic leukaemia. However, much less often have these drugs been studied in relation to cardiovascular diseases. This brief review mainly describes the role of PDGF signalling in cardiovascular pathogenesis such as atherosclerosis, pulmonary arterial hypertension, diabetes, angiogenesis and inflammation with an emphasis on how PDGFs function in these situations and what components might serve as potential therapeutic targets against cardio‐metabolic dysfunction.
Microvascular resistance in response to iodinated contrast media in normal and functionally impaired kidneys
Authors: Kurihara Osamu , Takano Masamichi , Uchiyama Saori , Fukuizumi Isamu , Shimura Tetsuro , Matsushita Masato , Komiyama Hidenori , Inami Toru , Murakami Daisuke , Munakata Ryo , Ohba Takayoshi , Hata Noritake , Seino Yoshihiko , Shimizu Wataru 
Published: August 2015

SummaryContrast‐induced nephropathy (CIN) is considered to result from intrarenal vasoconstriction, and occurs more frequently in impaired than in normal kidneys. It was hypothesized that iodinated contrast media would markedly change renal blood flow and vascular resistance in functionally impaired kidneys. Thirty‐six patients were enrolled (32 men; mean age, 75.3 ± 7.6 years) undergoing diagnostic coronary angiography and were divided into two groups based on the presence of chronic kidney disease (CKD), defined as an estimated glomerular filtration rate (eGFR) of < 60 mL/min per 1.73 m2 (CKD and non‐CKD groups, n = 18 in both). Average peak velocity (APV) and renal artery resistance index (RI) were measured by Doppler flow wire before and after administration of the iodinated contrast media. The APV and the RI were positively and inversely correlated with the eGFR at baseline, respectively (APV, R = 0.545, P = 0.001; RI, R = −0.627, P < 0.001). Mean RI was significantly higher (P = 0.015) and APV was significantly lower (P = 0.026) in the CKD than in the non‐CKD group. Both APV (P < 0.001) and RI (P = 0.002) were significantly changed following contrast media administration in the non‐CKD group, but not in the CKD group (APV, P = 0.258; RI, P = 0.707). Although renal arterial resistance was higher in patients with CKD, it was not affected by contrast media administration, suggesting that patients with CKD could have an attenuated response to contrast media.