bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcription factor interaction with COMPASS-like complex regulates histone H3K4 trimethylation for specific gene expression in plants
Authors: Song Ze-Ting , Sun Le , Lu Sun-Jie , Tian Yongke , Ding Yong , Liu Jian-Xiang 
Published: February 2015

SignificanceIn metazoans, pausing of Pol II during early elongation is a widespread regulatory mechanism for transcription regulation. However, preinitiation complex (PIC) assembly is more important for transcription in plants. Chromatin remodeling and histone modifications are considered important for access of protein factors to the underlying DNA sequences. However, how histone modifications are specifically and timely generated at active promoters is less understood. COMPASS-like complex plays a critical role in PIC assembly and histone H3K4 trimethylation. We found thatArabidopsistranscription factors bZIP28/bZIP60 interact with COMPASS-like components both in vitro and in vivo. We present a general model on how histone H3K4 trimethylation is specifically formed during inducible gene expression by using the endoplasmic reticulum (ER) stress response system inArabidopsisplants.
APOBEC3Bexpression in breast cancer reflects cellular proliferation, while a deletion polymorphism is associated with immune activation
Authors: Cescon David W. , Haibe-Kains Benjamin , Mak Tak W. 
Published: February 2015

SignificanceSomatic mutagenesis is fundamental to the development and evolution of cancers. APOBEC3B (A3B) is a cellular deaminase, which is overexpressed in cancers and believed to be an important cause of cancer-associated mutations. The factors responsible forA3Bup-regulation are unknown. Interestingly, a germ-line deletion polymorphism exists, such that a significant proportion of the global population does not express A3B protein. Using large human cancer datasets, we show thatA3Bexpression is strongly associated with cellular proliferation. Furthermore, we identify a pattern of immune activation related to hypermutation in tumors arising inA3Bdeletion carriers suggesting that these patients could respond differently to immune-directed therapies. These results provide important context for the ongoing study of A3B as a therapeutic target or biomarker.
Control of a hair bundle’s mechanosensory function by its mechanical load
Authors: Salvi Joshua D. , Ó Maoiléidigh Dáibhid , Fabella Brian A. , Tobin Mélanie , Hudspeth A. J. 
Published: February 2015

Significance
Hair bundles are the sensory antennae that detect different types of mechanical signals in diverse sensory systems of vertebrates. Here we design and use a mechanical-load clamp to show that the mechanical properties of hair bundles and their accessory structures dictate their sensory behaviors. By demonstrating how the same organelle can be used to detect a wide gamut of signals, this study reveals both the versatility and essential similarity of hair bundles across receptor organs. These observations reveal a general principle that may be used by both biological and artificial systems: by adjustment of only a few key parameters, a nonlinear system can be controlled to serve many different functions.
Discriminating precursors of common fragments for large-scale metabolite profiling by triple quadrupole mass spectrometry
Authors: Nikolskiy Igor , Siuzdak Gary , Patti Gary J. 
Published: February 2015

Abstract
Motivation: The goal of large-scale metabolite profiling is to compare the relative concentrations of as many metabolites extracted from biological samples as possible. This is typically accomplished by measuring the abundances of thousands of ions with high-resolution and high mass accuracy mass spectrometers. Although the data from these instruments provide a comprehensive fingerprint of each sample, identifying the structures of the thousands of detected ions is still challenging and time intensive. An alternative, less-comprehensive approach is to use triple quadrupole (QqQ) mass spectrometry to analyze predetermined sets of metabolites (typically fewer than several hundred). This is done using authentic standards to develop QqQ experiments that specifically detect only the targeted metabolites, with the advantage that the need for ion identification after profiling is eliminated.
Results: Here, we propose a framework to extend the application of QqQ mass spectrometers to large-scale metabolite profiling. We aim to provide a foundation for designing QqQ multiple reaction monitoring (MRM) experiments for each of the 82 696 metabolites in the METLIN metabolite database. First, we identify common fragmentation products from the experimental fragmentation data in METLIN. Then, we model the likelihoods of each precursor structure in METLIN producing each common fragmentation product. With these likelihood estimates, we select ensembles of common fragmentation products that minimize our uncertainty about metabolite identities. We demonstrate encouraging performance and, based on our results, we suggest how our method can be integrated with future work to develop large-scale MRM experiments.
Availability and implementation: Our predictions, Supplementary results, and the code for estimating likelihoods and selecting ensembles of fragmentation reactions are made available on the lab website at http://pattilab.wustl.edu/FragPred.
Contact: gjpattij@wustl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
SOMP: web server for in silico prediction of sites of metabolism for drug-like compounds
Authors: Rudik Anastasia , Dmitriev Alexander , Lagunin Alexey , Filimonov Dmitry , Poroikov Vladimir 
Published: February 2015

Abstract
Summary: A new freely available web server site of metabolism predictor to predict the sites of metabolism (SOM) based on the structural formula of chemicals has been developed. It is based on the analyses of ‘structure-SOM’ relationships using a Bayesian approach and labelled multilevel neighbourhoods of atoms descriptors to represent the structures of over 1000 metabolized xenobiotics. The server allows predicting SOMs that are catalysed by 1A2, 2C9, 2C19, 2D6 and 3A4 isoforms of cytochrome P450 and enzymes of the UDP-glucuronosyltransferase family. The average invariant accuracy of prediction that was calculated for the training sets (using leave-one-out cross-validation) and evaluation sets is 0.9 and 0.95, respectively.
Availability and implementation: Freely available on the web at http://www.way2drug.com/SOMP.
Contact: rudik_anastassia@mail.ru
Supplementary information: Supplementary data are available at Bioinformatics online.
Novel synthetic bis-indolic derivatives with antistaphylococcal activity, including against MRSA and VISA strains
Authors: Caspar Yvan , Jeanty Matthieu , Blu Jérôme , Burchak Olga , Le Pihive Emmanuelle , Maigre Laure , Schneider Dominique , Jolivalt Claude , Paris Jean-Marc , Hequet Arnaud , Minassian Frédéric , Denis Jean-Noël , Maurin Max 
Published: February 2015

Abstract

Objectives
We report the synthesis, antibacterial activity and toxicity of 24 bis-indolic derivatives obtained during the development of new ways of synthesis of marine bis-indole alkaloids from the spongotine, topsentin and hamacanthin classes.

Methods
Innovative ways of synthesis and further structural optimizations led to bis-indoles presenting either the 1-(1H-indol-3′-yl)-1,2-diaminoethane unit or the 1-(1H-indol-3-yl)ethanamine unit. MIC determination was performed for reference and clinical strains of Staphylococcus aureus and CoNS species. MBC, time–kill kinetics, solubility, hydrophobicity index, plasma protein-binding and cytotoxicity assays were performed for lead compounds. Inhibition of the S. aureus NorA efflux pump was also tested for bis-indoles with no antistaphylococcal activity.

Results
Lead compounds were active against both S. aureus and CoNS species, with MICs between 1 and 4 mg/L. Importantly, the same MICs were found for MRSA and vancomycin-intermediate S. aureus strains. Early concentration-dependent bactericidal activity was observed for lead derivatives. Compounds with no intrinsic antibacterial activity could inhibit the S. aureus NorA efflux pump, which is involved in resistance to fluoroquinolones. At 0.5 mg/L, the most effective compound led to an 8-fold reduction of the ciprofloxacin MIC for the SA-1199B S. aureus strain, which overexpresses NorA. However, the bis-indole compounds displayed a high hydrophobicity index and high plasma protein binding, which significantly reduced antibacterial activity.

Conclusions
We have synthesized and characterized novel bis-indole derivatives as promising candidates for the development of new antistaphylococcal treatments, with preserved activity against MDR S. aureus strains.
Prevalence of Gallstones Compared in Children With Different Intravenous Lipids
Authors: Pichler Judith , Watson Tom , McHugh Kieran , Hill Susan 
Published: February 2015

ABSTRACTObjective:The aetiology of biliary liver disease in children with intestinal failure treated with long‐term parenteral nutrition (PN) is multifactorial. Risks include the lipid component of PN. The aim of the study was to compare prevalence and outcome of gallstones with different types of intravenous lipids.Methods:Liver and biliary tract imaging and relevant clinical details were reviewed in 71 patients (37, 52% boys) treated with PN for >3 months. Types of lipid infused were compared with regard to hepatobiliary abnormalities.Results:In total 369 abdominal ultrasounds were performed in 71 patients of age between 3 months and 17 years. Underlying diagnoses were short bowel syndrome in 20 (28%), small intestinal enteropathy in 34 (48%), and motility disorder in 17 (24%). A total of 67 (94%) children had 362/369 scans on lipid‐containing PN. Of the total, 15 (21%) patients had gallstones, 8 (11%) had sludge, and both were detected in 7 (10%) children. The gallstones/sludge resolved in 7 patients (10%) and persisted in 10 (13%). In 6 patients, sludge progressed to form discrete gallstones, and in 9 children, gallstones led to biliary duct dilatation. Four (6%) patients underwent cholecystectomy. Fewer children had abnormalities with the newer mixed lipid emulsion (P = 0.005). There was a higher prevalence of sludge (P = 0.01) on pure soya lipid. Predictors for sludge were young age at PN (P = 0.001), lack of enteral feed (P < 0.001), and motility disorder with stoma (P = 0.002).Conclusions:Hepatobiliary pathology is common in children on PN. The use of mixed lipid was associated with less biliary complications and should be the first choice of treatment in children.
Non-adaptive evolution of them. palmaris longusin the Homininae
Authors: Throckmorton Zach , Forth Nicole , Thomas Nathanial 
Published: February 2015

AbstractThe palmaris longus muscle is widely recognized for its notable variability in living humans. These variations include not only muscle belly reversal, distinct double muscle bellies, duplication and triplication, but also total uni-or bilateral agenesis (absence). A review of the literature and data novel to this study illustrate that different populations of humans exhibit remarkable variation in the frequency of palmaris longus agenesis, from less than 5% of Chinese to nearly 65% of Indians. Comparative dissection-derived data reveal substantial variation in palmaris longus agenesis (PLA) in populations of extant humans (H. sapiens), chimpanzees (Pan spp.), and gorillas (Gorilla spp.) - but not orangutans (Pongo spp.), which apparently always develop this muscle. From this pattern, we infer that palmaris longus is undergoing non-adaptive, stochastic evolution in the extant African Homininae, while it continues to have adaptive purpose inPongo, likely due to the orangutans’ greater degree of arboreality than the African apes and humans. Clinical evidence supports this conclusion, at least as it applies to humans. This study highlights the utility of comparative soft tissue data collection and interpretation in elucidating the evolution of anatomical structures that do not fossilize.
Entrepreneurship paradigm and economic renaissance in Africa
Authors: Edoho Felix Moses 
Published: February 2015

Purpose– This Guest Editorial provides contextual insight to the contributions in this special issue that addresses entrepreneurship and economic growth challenge confronting Africa. Although the contributors come from various academic disciplines and adopt different perspectives, they are united in their singularity of focus on entrepreneurship as a pathway for African future. The paper aims to discuss these issues.Design/methodology/approach– The papers in this special issue adopt different methodological approaches that help to provide a composite insight to the multidimensional entrepreneurial challenges facing Africa. They review published materials from the government sources and international agencies. They draw heavily on the literature in the field of entrepreneurship.Findings– African countries have made significant progress in stimulating economic growth in recent years. However, they still have a long way to go in terms of institutionalizing entrepreneurial paradigm to foster self-regenerating development. Africa needs to do more by leveraging public policy for entrepreneurial development as a pathway for expanding economic opportunities and alleviating poverty. A policy framework designed to anchor entrepreneurial culture in the economy is a key to African economic renaissance in the twenty-first century.Originality/value– The originality and value of the papers in this issue hinge critically on the all too often ignored proposition that African countries need to embrace a proven approach to development that is both broad based and citizen driven. Entrepreneurial paradigm will empower citizens to take not only full responsibility, but more importantly inalienable ownership, of the development process. This is the only way to ensure that the ongoing much celebrated growth in Africa is sustainable.
Mobile shopping: a classification framework and literature review
Authors: Groß Michael 
Published: February 2015

Purpose– The purpose of this paper is to classify and organize the accumulated knowledge about mobile shopping (m-shopping) as revealed in the present literature regarding retail. A classification framework has been applied, consisting of three categories: online distribution channels, advanced technology for in-store shopping, and technology perspectives.Design/methodology/approach– A term-based search method was applied in which the literature was restricted to peer-reviewed articles in English-language journals of a certain date and specific online databases. Finally, 81 peer-reviewed articles, published between 2000 and 2012 around the world, were taken into account.Findings– Considering the retail environment, the interest in m-shopping for both advanced technology for in-store shopping and for the online distribution channel has increased continuously over the last decade. Moreover, while studies have mostly explored the consumers’ acceptance and reactions to m-shopping themes, the technology perspective is still being researched.Research limitations/implications– Due to the selected term-based search method, the number of identified publications is limited. Additionally, the selected framework requires a corresponding assignment to an explicitly stated topic, which was not always possible.Originality/value– As far as the author knows, this paper provides the first systematic review of m-shopping literature, which not only helps to organize retail-based literature, but also investigates significant gaps on this topic, thus facilitating future research.
Cargo theft at non-secure parking locations
Authors: Ekwall Daniel , Lantz Björn 
Published: February 2015

Purpose
– The purpose of this paper is to examine the patterns of reported cargo thefts at non-secure parking facilities in Europe, the Middle East, and Africa (EMEA) with respect to stolen value, frequency, incident category, and modi operandi.

Design/methodology/approach
– This study is based on a system-theoretical approach that emphasizes on a holistic rather than an atomistic view. The research method used in this paper is deductive; the analysis is based on data obtained from the incident information service (IIS), a database of transport-related crimes from the Transported Asset Protection Association (TAPA) in the EMEA region. The results are analysed and discussed within a frame of reference based on supply chain risk management (SCRM) and criminology theories.

Findings
– We found that 97 per cent of all attacks during a stop occur at non-secure parking locations. Cargo thefts at these locations are more of a volume crime than high-value thefts. Seasonal variations were seen in these thefts, and the most common type was an intrusion on weekdays during winter.

Research limitations/implications
– This study is limited by the content of and the classifications within the TAPA EMEA IIS database.

Practical implications
– This paper is directly relevant to the current EU discussions regarding the creation of a large number of secure parking facilities in the region.

Originality/value
– This is one of the first papers in the field of SCRM that utilizes actual crime statistics reported by the industry to analyse the occurrence of cargo theft by focusing on the non-secure parking aspect in the transport chain.
Shopping environment preferences of Hispanic consumers in the U.S.
Authors: Burns David , Conway Dato-on Mary , Manolis Chris 
Published: February 2015

Purpose– The purpose of this paper is to develop and begin to validate a scale to assess the shopping environment preferences of Hispanic consumers in the USA.Design/methodology/approach– The sample consists of 160 Hispanic consumers attending a Hispanic festival in the southeast USA. A questionnaire contained items to measure shopping environment preferences and scales to measure materialism, hedonic shopping motivations, and perceived discrimination.Findings– The findings suggest a second-order model where three factors (familiarity, price, and experience) load onto a single second-order construct of shopping environment preferences. The result is a scale consisting of three factors permitting the exploration of the retail environmental preferences of Hispanic consumers in the USA.Practical implications– The study develops a scale that can be applied by US retailers to gain additional knowledge of their Hispanic consumers, thus enabling strategies to be developed that potentially enhance their engagement in retail environments.Originality/value– Given the size of this segment and its increasing impact on the retail market, surprisingly, Hispanic consumers in the USA have received relatively little research attention.
The unbearable lightness of participating? Revisiting the discourses of “participation” in archival literature
Authors: Huvila Isto 
Published: February 2015

Purpose– The purpose of this paper is to investigate how archivists, records managers and scholarly literature in the field(s) analyse how “participation” is discussed in the context of archives and records management, and to explore practical and theoretical implications of the disclosed discursive practices.Design/methodology/approach– The analysis is based on a discourse analysis of a body of archival literature and a sample of posts collected from the archival and records management blogosphere.Findings– The analysis shows that instead of discussing one notion of participation, the archival science literature is referring to nine different and partly conflicting types of participation from three broad perspectives: management, empowerment and technology. The discourses have also conflicting ideas of the role of engagement and enthusiasm, and of that what do the different stakeholder communities see as real options.Research limitations/implications– The analysed material consists of a limited sample of mainly English language texts that may not capture all the nuances of how participation is discussed in the archival literature.Practical implications– A better understanding of how different claims of the benefits and threats endorsing “participation” in archives helps to develop effective and less contradictory forms of collaboration between different stakeholders.Originality/value– In spite of the popularity of the notion of “participation”, there little, especially critical, research on how participation is conceptualised by archives professionals and researchers.
Data literacy: in search of a name and identity
Authors: Koltay Tibor 
Published: February 2015

Purpose
– The role of data literacy is discussed in the light of such activities as data a quality, data management, data curation, and data citation. The differing terms and their relationship to the most important literacies are examined. The paper aims to discuss these issues.

Design/methodology/approach
– By stressing the importance of data literacy in fulfilling the mission of the contemporary academic library, the paper centres on information literacy, while the characteristics of other relevant literacies are also examined. The content of data literacy education is explained in the context of data-related activities.

Findings
– It can be concluded that there is a need for data literacy and it is advantageous to have a unified terminology. Data literacy can be offered both to researchers, who need to become data literate science workers and have the goal to educate data management professionals. Several lists of competencies contain important skills and abilities, many of them indicating the close relationship between data literacy and information literacy. It is vital to take a critical stance on hopes and fears, related to the promises of widespread ability of (big) data.

Originality/value
– The paper intends to be an add-on to the body of knowledge about information literacy and other literacies in the light of research data and data literacy.
Differences over discourse structure differences: a reply to Urquhart and Urquhart
Authors: Abrahamson Jennie A. , Rubin Victoria L. 
Published: February 2015

Purpose– The purpose of this paper is to respond to Urquhart and Urquhart’s critique of the previous work entitled “Discourse structure differences in lay and professional health communication”, published in this journal in 2012 (Vol. 68 No. 6, pp. 826-851, doi: 10.1108/00220411211277064).Design/methodology/approach– The authors examine Urquhart and Urquhart’s critique and provide responses to their concerns and cautionary remarks against cross-disciplinary contributions. The authors reiterate the central claim.Findings– The authors argue that Mann and Thompson’s (1987, 1988) Rhetorical Structure Theory (RST) offers valuable insights into computer-mediated health communication and deserves further discussion of its methodological strength and weaknesses for application in library and information science.Research limitations/implications– While the authors agree that some methodological limitations pointed out by Urquhart and Urquhart are valid, the authors take this opportunity to correct certain misunderstandings and misstatements.Originality/value– The authors argue for continued use of innovative techniques borrowed from neighbouring disciplines, in spite of objections from the researchers accustomed to a familiar strand of literature. The authors encourage researchers to consider RST and other computational linguistics-based discourse analysis annotation frameworks that could provide the basis for integrated research, and eventual applications in information behaviour and information retrieval.