bluuebunny/crossref_metadata_2025_split huggingface dataset:
The physiology and ecological implications of efficient growth
Authors: Roller Benjamin R K , Schmidt Thomas M 
Published: January 2015

Abstract
The natural habitats of microbes are typically spatially structured with limited resources, so opportunities for unconstrained, balanced growth are rare. In these habitats, selection should favor microbes that are able to use resources most efficiently, that is, microbes that produce the most progeny per unit of resource consumed. On the basis of this assertion, we propose that selection for efficiency is a primary driver of the composition of microbial communities. In this article, we review how the quality and quantity of resources influence the efficiency of heterotrophic growth. A conceptual model proposing innate differences in growth efficiency between oligotrophic and copiotrophic microbes is also provided. We conclude that elucidation of the mechanisms underlying efficient growth will enhance our understanding of the selective pressures shaping microbes and will improve our capacity to manage microbial communities effectively.
Diverse protist grazers select for virulence-related traits in Legionella
Authors: Amaro Francisco , Wang Wen , Gilbert Jack A , Roger Anderson O , Shuman Howard A 
Published: January 2015

Abstract
It is generally accepted that selection for resistance to grazing by protists has contributed to the evolution of Legionella pneumophila as a pathogen. Grazing resistance is becoming more generally recognized as having an important role in the ecology and evolution of bacterial pathogenesis. However, selection for grazing resistance presupposes the existence of protist grazers that provide the selective pressure. To determine whether there are protists that graze on pathogenic Legionella species, we investigated the existence of such organisms in a variety of environmental samples. We isolated and characterized diverse protists that graze on L. pneumophila and determined the effects of adding L. pneumophila on the protist community structures in microcosms made from these environmental samples. Several unrelated organisms were able to graze efficiently on L. pneumophila. The community structures of all samples were markedly altered by the addition of L. pneumophila. Surprisingly, some of the Legionella grazers were closely related to species that are known hosts for L. pneumophila, indicating the presence of unknown specificity determinants for this interaction. These results provide the first direct support for the hypothesis that protist grazers exert selective pressure on Legionella to acquire and retain adaptations that contribute to survival, and that these properties are relevant to the ability of the bacteria to cause disease in people. We also report a novel mechanism of killing of amoebae by one Legionella species that requires an intact Type IV secretion system but does not involve intracellular replication. We refer to this phenomenon as ‘food poisoning’.
Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics
Authors: Llorens-Marès Tomàs , Yooseph Shibu , Goll Johannes , Hoffman Jeff , Vila-Costa Maria , Borrego Carles M , Dupont Chris L , Casamayor Emilio O 
Published: January 2015

Abstract
Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO2 fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.
BCL11A is a triple-negative breast cancer gene with critical functions in stem and progenitor cells
Authors: Khaled Walid T. , Choon Lee Song , Stingl John , Chen Xiongfeng , Raza Ali H. , Rueda Oscar M. , Hadi Fazal , Wang Juexuan , Yu Yong , Chin Suet-Feung , Stratton Mike , Futreal Andy , Jenkins Nancy A. , Aparicio Sam , Copeland Neal G. , Watson Christine J. , Caldas Carlos , Liu Pentao 
Published: January 2015

AbstractTriple-negative breast cancer (TNBC) has poor prognostic outcome compared with other types of breast cancer. The molecular and cellular mechanisms underlying TNBC pathology are not fully understood. Here, we report that the transcription factor BCL11A is overexpressed in TNBC including basal-like breast cancer (BLBC) and that its genomic locus is amplified in up to 38% of BLBC tumours. Exogenous BCL11A overexpression promotes tumour formation, whereas its knockdown in TNBC cell lines suppresses their tumourigenic potential in xenograft models. In the DMBA-induced tumour model, Bcl11a deletion substantially decreases tumour formation, even in p53-null cells and inactivation of Bcl11a in established tumours causes their regression. At the cellular level, Bcl11a deletion causes a reduction in the number of mammary epithelial stem and progenitor cells. Thus, BCL11A has an important role in TNBC and normal mammary epithelial cells. This study highlights the importance of further investigation of BCL11A in TNBC-targeted therapies.
A Highly Efficient Approach to Protein Interactome Mapping Based on Collaborative Filtering Framework
Authors: Luo Xin , You Zhuhong , Zhou Mengchu , Li Shuai , Leung Hareton , Xia Yunni , Zhu Qingsheng 
Published: January 2015

AbstractThe comprehensive mapping of protein-protein interactions (PPIs) is highly desired for one to gain deep insights into both fundamental cell biology processes and the pathology of diseases. Finely-set small-scale experiments are not only very expensive but also inefficient to identify numerous interactomes despite their high accuracy. High-throughput screening techniques enable efficient identification of PPIs; yet the desire to further extract useful knowledge from these data leads to the problem of binary interactome mapping. Network topology-based approaches prove to be highly efficient in addressing this problem; however, their performance deteriorates significantly on sparse putative PPI networks. Motivated by the success of collaborative filtering (CF)-based approaches to the problem of personalized-recommendation on large, sparse rating matrices, this work aims at implementing a highly efficient CF-based approach to binary interactome mapping. To achieve this, we first propose a CF framework for it. Under this framework, we model the given data into an interactome weight matrix, where the feature-vectors of involved proteins are extracted. With them, we design the rescaled cosine coefficient to model the inter-neighborhood similarity among involved proteins, for taking the mapping process. Experimental results on three large, sparse datasets demonstrate that the proposed approach outperforms several sophisticated topology-based approaches significantly.
Quad‐band filter with high skirt selectivity using stub‐loaded nested dual‐open loop resonators
Authors: Wu Bian , Qiu Feng , Lin Lei 
Published: January 2015

A quad‐band filter with compact size and high skirt selectivity utilising stub‐loaded nested dual‐open loop resonators is presented. By loading open‐ended stubs at the centre of the two nested resonators, two odd modes as well as two even modes can be independently adjusted to realise a flexible quad‐band filtering response. Moreover, both a pair of zero‐degree feed lines and the frequency transformation method are adopted to introduce multiple transmission zeroes, which rightly enhance the out‐of‐band selectivity. According to the topology circuit design and coupling matrix synthesis, a quad‐band filter operating at 1.58/1.81/2.50/2.66 GHz is finally designed and fabricated.
Compact FSS absorber design using resistively loaded quadruple hexagonal loops for bandwidth enhancement
Authors: Zabri S.N. , Cahill R. , Schuchinsky A. 
Published: January 2015

The design of a thin microwave absorber which exhibits a −10 dB reflectivity bandwidth of 108% at normal incidence and 16% for simultaneous suppression of TE and TM polarised waves over the angular range 0–45° is presented. The structure consists of a 3 mm‐thick metal backed frequency selective surface (FSS) with four resistively loaded hexagonal loop elements in each unit cell. The surface resistivity and width of the loops are carefully chosen to maximise the bandwidth by merging the reflection nulls that are generated by the multi‐resonant absorber. Measurement and simulation results are in good agreement over the broad frequency range 7.8–24 GHz.
Fast wavelength conversion to generate 560 nm fluorescence for data transmission in polymer optical fibres
Authors: Ribeiro R.M. , Silva V.N.H. , Barbero A.P.L. , Alves C.M. , Rodrigues C.R.L. 
Published: January 2015

The use of a fluorescent fibre (15.5 mm in length) pumped in a forward direction with a 520 nm emitting LED for fast wavelength conversion to 560 nm is reported. In addition to the fact that this wavelength matches the attenuation minima of poly‐methyl‐methacrylate polymer optical fibres (POFs), the presented results show an external conversion efficiency of 4.7% and a bandwidth of 52.5 MHz. The device is a simple, inexpensive, compact, eye‐safe and lightweight optical source at 560 nm. It can be suitable for single‐channel ‘long‐distance’ (>400 m) or WDM‐based links using POFs, presenting a bandwidth–distance product of 50–100 MHz/100 m.
MADGiC: a model-based approach for identifying driver genes in cancer
Authors: Korthauer Keegan D. , Kendziorski Christina 
Published: January 2015

Abstract
Motivation: Identifying and prioritizing somatic mutations is an important and challenging area of cancer research that can provide new insights into gene function as well as new targets for drug development. Most methods for prioritizing mutations rely primarily on frequency-based criteria, where a gene is identified as having a driver mutation if it is altered in significantly more samples than expected according to a background model. Although useful, frequency-based methods are limited in that all mutations are treated equally. It is well known, however, that some mutations have no functional consequence, while others may have a major deleterious impact. The spatial pattern of mutations within a gene provides further insight into their functional consequence. Properly accounting for these factors improves both the power and accuracy of inference. Also important is an accurate background model.
Results: Here, we develop a Model-based Approach for identifying Driver Genes in Cancer (termed MADGiC) that incorporates both frequency and functional impact criteria and accommodates a number of factors to improve the background model. Simulation studies demonstrate advantages of the approach, including a substantial increase in power over competing methods. Further advantages are illustrated in an analysis of ovarian and lung cancer data from The Cancer Genome Atlas (TCGA) project.
Availability and implementation: R code to implement this method is available at http://www.biostat.wisc.edu/ kendzior/MADGiC/.
Contact: kendzior@biostat.wisc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels
Authors: Folkman Lukas , Yang Yuedong , Li Zhixiu , Stantic Bela , Sattar Abdul , Mort Matthew , Cooper David N. , Liu Yunlong , Zhou Yaoqi 
Published: January 2015

Abstract
Motivation: Frameshifting (FS) indels and nonsense (NS) variants disrupt the protein-coding sequence downstream of the mutation site by changing the reading frame or introducing a premature termination codon, respectively. Despite such drastic changes to the protein sequence, FS indels and NS variants have been discovered in healthy individuals. How to discriminate disease-causing from neutral FS indels and NS variants is an understudied problem.
Results: We have built a machine learning method called DDIG-in (FS) based on real human genetic variations from the Human Gene Mutation Database (inherited disease-causing) and the 1000 Genomes Project (GP) (putatively neutral). The method incorporates both sequence and predicted structural features and yields a robust performance by 10-fold cross-validation and independent tests on both FS indels and NS variants. We showed that human-derived NS variants and FS indels derived from animal orthologs can be effectively employed for independent testing of our method trained on human-derived FS indels. DDIG-in (FS) achieves a Matthews correlation coefficient (MCC) of 0.59, a sensitivity of 86%, and a specificity of 72% for FS indels. Application of DDIG-in (FS) to NS variants yields essentially the same performance (MCC of 0.43) as a method that was specifically trained for NS variants. DDIG-in (FS) was shown to make a significant improvement over existing techniques.
Availability and implementation: The DDIG-in web-server for predicting NS variants, FS indels, and non-frameshifting (NFS) indels is available at http://sparks-lab.org/ddig.
Contact: yaoqi.zhou@griffith.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
PVAAS: identify variants associated with aberrant splicing from RNA-seq
Authors: Wang Liguo , Nie Jinfu J. , Kocher Jean-Pierre A. 
Published: January 2015

Abstract
Motivation: RNA-seq has been widely used to study the transcriptome. Comparing to microarray, sequencing-based RNA-seq is able to identify splicing variants and single nucleotide variants in one experiment simultaneously. This provides unique opportunity to detect variants that associated with aberrant splicing. Despite the popularity of RNA-seq, no bioinformatics tool has been developed to leverage this advantage to identify variants associated with aberrant splicing.
Results: We have developed PVAAS, a tool to identify single nucleotide variants that associated with aberrant alternative splicing from RNA-seq data. PVAAS works in three steps: (i) identify aberrant splicings; (ii) use user-provided variants or perform variant calling; (iii) assess the significance of association between variants and aberrant splicing events.
Availability and implementation: PVAAS is written in Python and C. Source code and a comprehensive user’s manual are freely available at: http://pvaas.sourceforge.net/.
Contact: wang.liguo@mayo.edu or kocher.jeanpierre@mayo.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
RNA-Rocket: an RNA-Seq analysis resource for infectious disease research
Authors: Warren Andrew S. , Aurrecoechea Cristina , Brunk Brian , Desai Prerak , Emrich Scott , Giraldo-Calderón Gloria I. , Harb Omar , Hix Deborah , Lawson Daniel , Machi Dustin , Mao Chunhong , McClelland Michael , Nordberg Eric , Shukla Maulik , Vosshall Leslie B. , Wattam Alice R. , Will Rebecca , Yoo Hyun Seung , Sobral Bruno 
Published: January 2015

Abstract
Motivation: RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression and transcriptional structure. The methods, tools and technologies used to perform RNA-Seq analysis continue to change, creating a bioinformatics challenge for researchers who wish to exploit these data. Resources that bring together genomic data, analysis tools, educational material and computational infrastructure can minimize the overhead required of life science researchers.
Results: RNA-Rocket is a free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations and the ability to stream results to the bioinformatics resources VectorBase, EuPathDB and PATRIC. The site also provides a combination of experimental data and metadata, examples of pre-computed analysis, step-by-step guides and a user interface designed to enable both novice and experienced users of RNA-Seq data.
Availability and implementation: RNA-Rocket is available at rnaseq.pathogenportal.org. Source code for this project can be found at github.com/cidvbi/PathogenPortal.
Contact: anwarren@vt.edu
Supplementary information: Supplementary materials are available at Bioinformatics online.
Inferring single-cell gene expression mechanisms using stochastic simulation
Authors: Daigle Bernie J. , Soltani Mohammad , Petzold Linda R. , Singh Abhyudai 
Published: January 2015

Abstract
Motivation: Stochastic promoter switching between transcriptionally active (ON) and inactive (OFF) states is a major source of noise in gene expression. It is often implicitly assumed that transitions between promoter states are memoryless, i.e. promoters spend an exponentially distributed time interval in each of the two states. However, increasing evidence suggests that promoter ON/OFF times can be non-exponential, hinting at more complex transcriptional regulatory architectures. Given the essential role of gene expression in all cellular functions, efficient computational techniques for characterizing promoter architectures are critically needed.
Results: We have developed a novel model reduction for promoters with arbitrary numbers of ON and OFF states, allowing us to approximate complex promoter switching behavior with Weibull-distributed ON/OFF times. Using this model reduction, we created bursty Monte Carlo expectation-maximization with modified cross-entropy method (‘bursty MCEM2’), an efficient parameter estimation and model selection technique for inferring the number and configuration of promoter states from single-cell gene expression data. Application of bursty MCEM2 to data from the endogenous mouse glutaminase promoter reveals nearly deterministic promoter OFF times, consistent with a multi-step activation mechanism consisting of 10 or more inactive states. Our novel approach to modeling promoter fluctuations together with bursty MCEM2 provides powerful tools for characterizing transcriptional bursting across genes under different environmental conditions.
Availability and implementation: R source code implementing bursty MCEM2 is available upon request.
Contact: absingh@udel.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Achieving employee commitment for continuous improvement initiatives
Authors: Lam Marco , O'Donnell Mark , Robertson Dan 
Published: January 2015

Purpose
– Although prior research has found that employee participation is key to successfully implementing quality management initiatives (Baird et al., 2011; de Menezes, 2012; Lagrosen and Lagrosen, 2005), little research in operations management exists that investigates which management actions and behaviors lead to employee commitment to such initiatives. The purpose of this paper is to address this gap in the operations management literature by investigating which influence tactics are the most effective in soliciting employee commitment to continuous improvement tasks. The paper also examines how influence tactics affect the supervisor-subordinate relationship and the manager’s effectiveness in implementing continuous improvement initiatives.

Design/methodology/approach
– A survey instrument was used to measure supervisor-subordinate relationship quality, usage of influence behaviors and participants’ task commitment to continuous improvement initiatives.

Findings
– The results indicate that five of the 11 influence tactics identified in the prior literature, i.e., collaboration, consultation, ingratiation, inspirational appeals, and rational persuasion, are significant and strong predictors of employee commitment to continuous improvement initiatives. Further, analyses show that these influence tactics are significant drivers of the quality of the supervisor-subordinate relationship, which was found to partially mediate the relationship between influence tactics and the supervisor’s effectiveness in implementing continuous improvement projects.

Research limitations/implications
– Since the extant CI and Total Quality Management literature has looked at the plant or program level rather than the worker-level as in the research, the findings offer one explanation as to why earlier studies investigating the relationship between quality management programs and increased organizational performance reported mixed results.

Practical implications
– Increasing managers’ awareness and usage of influence tactics may increase the success rate of continuous improvement projects as well the quality of the relationship with the manager’s subordinates.

Originality/value
– While the extant literature has argued that management support and employee commitment are key components of a continuous improvement project implementation, little has been written about the specific management actions and behaviors that lead to success.
Music, musicians and information seeking behaviour
Authors: Kostagiolas Petros A. , Lavranos Charilaos , Korfiatis Nikolaos , Papadatos Joseph , Papavlasopoulos Sozon 
Published: January 2015

Purpose
– The purpose of this paper is to examine information seeking behaviour targeted to music information seeking by amateur musicians, accompanied with empirical evidence from a survey on a community concert band. While several studies in the literature have examined information seeking in the context of hedonic motives (e.g. entertainment oriented), music information can also be used for utilitarian purposes by providing amateur musicians the necessary tools to improve their skill and become better in their practice.

Design/methodology/approach
– A review of the literature on music information seeking and an empirical study on members of an amateur concert band are presented. The theoretical construct of the survey is informed by Wilsons’ macro model of information seeking behaviour. This is employed in order to understand information motives and needs, as well as obstacles in information seeking of musicians.

Findings
– Musicians seek information not only for entertainment but for educational purposes as well as for the acquisition of certain music works. The use of the internet for information seeking as well as the gradual adoption of online social networks has provided access to new musical resources within the digital music networks.

Originality/value
– A person-centred approach for information seeking behaviour is studied and adapted for musicians. The survey provides new information behaviour results for designers of music information spaces which in turn are creating a new model of the relationship between music and society.