bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blind tests of RNA nearest neighbor energy prediction
Authors: Chou Fang-Chieh , Kladwang Wipapat , Kappel Kalli , Das Rhiju 
Published: May 2016

AbstractThe predictive modeling and design of biologically active RNA molecules requires understanding the energetic balance amongst their basic components. Rapid developments in computer simulation promise increasingly accurate recovery of RNA’s nearest neighbor (NN) free energy parameters, but these methods have not been tested in predictive trials or on non-standard nucleotides. Here, we present the first such tests through a RECCES-Rosetta (Reweighting ofEnergy-functionCollection withConformationalEnsembleSampling in Rosetta) framework that rigorously models conformational entropy, predicts previously unmeasured NN parameters, and estimates these values’ systematic uncertainties. RECCES-Rosetta recovers the ten NN parameters for Watson-Crick stacked base pairs and thirty-two single-nucleotide dangling-end parameters with unprecedented accuracies – root-mean-square deviations (RMSD) of 0.28 kcal/mol and 0.41 kcal/mol, respectively. For set-aside test sets, RECCES-Rosetta gives an RMSD of 0.32 kcal/mol on eight stacked pairs involving G-U wobble pairs and an RMSD of 0.99 kcal/mol on seven stacked pairs involving non-standard isocytidine-isoguanosine pairs. To more rigorously assess RECCES-Rosetta, we carried out four blind predictions for stacked pairs involving 2,6-diaminopurine-U pairs, which achieved 0.64 kcal/mol RMSD accuracy when tested by subsequent experiments. Overall, these results establish that computational methods can now blindly predict energetics of basic RNA motifs, including chemically modified variants, with consistently better than 1 kcal/mol accuracy. Systematic tests indicate that resolving the remaining discrepancies will require energy function improvements beyond simply reweighting component terms, and we propose further blind trials to test such efforts.SignificanceUnderstanding RNA machines and how their behavior can be modulated by chemical modification is increasingly recognized as an important biological and bioengineering problem, with continuing discoveries of riboswitches, mRNA regulons, CRISPR-guided editing complexes, and RNA enzymes. Computational strategies to understanding RNA energetics are being proposed, but have not yet faced rigorous tests. We describe a modeling strategy called ‘RECCES-Rosetta’ that models the full ensemble of motions of RNA in single-stranded form and in helices, including non-standard nucleotides such as 2,6-diaminopurine, a variant of adenosine. When compared to experiments, including blind tests, the energetic accuracies of RECCES-Rosetta calculations are at levels close to experimental error, suggesting that computation can now be used to predict and design basic RNA energetics.
Meta-analysis of 2,104 trios provides support for 10 novel candidate genes for intellectual disability
Authors: Lelieveld Stefan H. , Reijnders Margot R.F. , Pfundt Rolph , Yntema Helger G. , Kamsteeg Erik-Jan , de Vries Petra , de Vries Bert B.A. , Willemsen Marjolein H. , Kleefstra Tjitske , Löhner Katharina , Vreeburg Maaike , Stevens Servi , van der Burgt Ineke , Bongers Ernie M.H.F. , Stegmann Alexander P.A. , Rump Patrick , Rinne Tuula , Nelen Marcel R. , Veltman Joris A. , Vissers Lisenka E.L.M. , Brunner Han G. , Gilissen Christian 
Published: May 2016

ABSTRACTTo identify novel candidate intellectual disability genes, we performed a meta-analysis on 2,637de novomutations, identified from the exomes of 2,104 ID trios. Statistical analyses identified 10 novel candidate ID genes, includingDLG4, PPM1D, RAC1, SMAD6, SON, SOX5, SYNCRIP, TCF20, TLK2andTRIP12. In addition, we show that these genes are intolerant to non-synonymous variation, and that mutations in these genes are associated with specific clinical ID phenotypes.
Whole organism lineage tracing by combinatorial and cumulative genome editing
Authors: McKenna Aaron , Findlay Gregory M. , Gagnon James A. , Horwitz Marshall S. , Schier Alexander F. , Shendure Jay 
Published: May 2016

AbstractMulticellular systems develop from single cells through a lineage, but current lineage tracing approaches scale poorly to whole organisms. Here we use genome editing to progressively introduce and accumulate diverse mutations in a DNA barcode over multiple rounds of cell division. The barcode, an array of CRISPR/Cas9 target sites, records lineage relationships in the patterns of mutations shared between cells. In cell culture and zebrafish, we show that rates and patterns of editing are tunable, and that thousands of lineage-informative barcode alleles can be generated. We find that most cells in adult zebrafish organs derive from relatively few embryonic progenitors. Genome editing of synthetic target arrays for lineage tracing (GESTALT) will help generate large-scale maps of cell lineage in multicellular systems.
Spatial mnemonic encoding: Theta power decreases co-occur with medial temporal lobe BOLD increases during the usage of the Method of Loci
Authors: Fellner M.-C. , Volberg G. , Wimber M. , Goldhacker M. , Greenlee M. W. , Hanslmayr S. 
Published: May 2016

AbstractThe Method of Loci is one, if not the most, efficient mnemonic encoding strategy. This strategy combines the core cognitive processes commonly linked to medial temporal lobe (MTL) activity: spatial processing and associative memory processes. During such tasks fMRI studies consistently demonstrate increases in medial temporal lobe (MTL) activity, while electrophysiological studies have emphasized the important role of theta oscillations (3-8 Hz) in the MTL. How MTL activity is linked to theta oscillatory EEG power, however, is unknown. Specifically, it is not known whether increases or decreases in MTL theta power are associated with increased BOLD signal. To investigate this question we recorded EEG and fMRI while participants used the spatial Method of Loci contrasted to the Pegword Method, a similarly associative but non spatial mnemonic. Surprisingly, the more effective spatial mnemonic induced a pronounced theta power decrease in the left MTL compared to the non-spatial associative mnemonic strategy. This effect was mirrored by BOLD signal increases in the MTL. This pattern of results suggests that theta oscillations in the MTL are negatively related to BOLD signal increases. These findings extend the well-known negative relation of alpha/beta oscillations and BOLD signals in the cortex to theta oscillations in the MTL. The results also demonstrate that decreases in theta power can index MTL involvement during encoding.Significance StatementStudies investigating the oscillatory correlates of memory encoding largely focus on activity in the theta frequency and often implicitly assume that increases in theta activity reflect similar processes as typically reported increases MTL activity changes in fMRI studies. The presented study found decreases in theta power, not increases, closely mapping to MTL BOLD signal increases during the same paradigm. This finding is in line with studies showing a negative relationship between low frequency power and BOLD changes in the cortex, but challenges the assumption that theta power increases reflect MTL activity. The reported findings importantly contribute to answer the question of how and which oscillatory activity indexes MTL memory processes.
Nicotine affects protein complex rearrangement inCaenorhabditis eleganscells
Authors: Sobkowiak Robert , Zielezinski Andrzej , Karlowski Wojciech M. , Lesicki Andrzej 
Published: May 2016

AbstractNicotine may affect cell function by rearranging protein complexes. We aimed to determine nicotine-induced alterations of protein complexes inCaenorhabditis eleganscells, thereby revealing links between nicotine exposure and protein complex modulation. We compared the proteomic alterations induced by low and high nicotine concentrations (0.01 mM and 1 mM) with the control (no nicotine)in vivoby using mass spectrometry (MS)-based techniques, specifically the CTAB discontinuous gel electrophoresis coupled with liquid chromatography (LC-MS/MS and spectral counting. As a result, we identified dozens ofC. elegansproteins that are present exclusively or in higher abundance in either nicotine-treated or untreated worms. Based on these results, we report a network that captures the key protein components of nicotine-induced protein complexes and speculate how the different protein modules relate to their distinct physiological roles. Using functional annotation of detected proteins, we hypothesize that the identified complexes can modulate the energy metabolism and level of oxidative stress. These proteins can also be involved in modulation of gene expression and may be crucial in Alzheimer’s disease. The findings reported in our study reveal intracellular interactions of many proteins with cytoskeleton and may contribute to the understanding of the mechanisms of nicotinic acetylcholine receptor (nAChR) signaling and trafficking in cells.Significance of the studyMost of us are affected by nicotine, not only because of the common use of tobacco products. Nicotine is also included in many popular vegetables of the family Solanaceae, such as tomatoes and peppers. However, these two sources provide the body with radically different doses of nicotine.Strong biological effects of nicotine rely on binding to the nicotinic receptor, which partially mimics the action of the natural hormone acetylcholine. In our study we used the nematodeCaenorhabditis elegansas a model organism. General principles of functioning of human cells andC. eleganscells are similar. The worm is, however, a compromise between simplicity and complexity, which may facilitate understanding of the more complex systems, like the human body. Our study revealed in the presence of a low nicotine concentration a different composition of polypeptides in the organism than in the presence of a high nicotine concentration. The rearrangements of protein complexes concern proteins involved e.g. in the course of Alzheimer’s disease, which seems interesting in the context of our aging societies. From the perspective of the development of biological research, the ability to identify the components of large protein complexes can contribute to a better understanding of the functioning of cells.
Splice Variants of the SWR1-type Nucleosome Remodeling Factor Domino Have Distinct Functions duringDrosophila melanogasterOogenesis
Authors: Boerner Kenneth , Becker Peter B. 
Published: May 2016

AbstractSWR1-type nucleosome remodeling factors replace histone H2A by variants to endow chromatin locally with specialized functionality. InDrosophila melanogastera single H2A variant, H2A.V, combines functions of mammalian H2A.Z and H2A.X in transcription regulation and DNA damage response. A major role in H2A.V incorporation for the only SWR1-like enzyme in flies, Domino, is assumed, but not well documentedin vivo. It is also unclear, whether the two alternatively spliced isoforms,dom-Aanddom-B, have redundant or specialized functions. Loss of both DOM isoforms compromises oogenesis causing female sterility. Therefore, we systematically explored roles of the two DOM isoforms during oogenesis using a cell type-specific knockdown approach. Despite their ubiquitous expression, DOM-A and DOM-B have non-redundant functions in germline and soma for egg chamber formation. We show that chromatin incorporation of H2A.V in germline and somatic cells depends on DOM-B, while incorporation in endoreplicating germline nurse cells is independent of DOM. In contrast, DOM-A promotes the removal of H2A.V from stage 5 nurse cells. Remarkably, the two DOM isoforms have distinct functions in cell type-specific development and H2A.V exchange.Summary StatementIsoforms of nucleosome remodeling factor Domino change chromatin structure by histone variant exchange to direct essential cellular processes in oocyte development.
Suitability of different mapping algorithms for genome-wide polymorphism scans with Pool-Seq data
Authors: Kofler Robert , Langmüller Anna Maria , Nouhaud Pierre , Otte Kathrin Anna , Schlöetterer Christian 
Published: May 2016

AbstractThe cost-effectiveness of sequencing pools of individuals (Pool-Seq) provides the basis for the popularity and wide-spread use of this method for many research questions, ranging from unravelling the genetic basis of complex traits to the clonal evolution of cancer cells. Because the accuracy of Pool-Seq could be affected by many potential sources of error, several studies determined, for example, the influence of the sequencing technology, the library preparation protocol, and mapping parameters. Nevertheless, the impact of the mapping tools has not yet been evaluated. Using simulated and real Pool-Seq data, we demonstrate a substantial impact of the mapping tools leading to characteristic false positives in genome-wide scans. The problem of false positives was particularly pronounced when data with different read lengths and insert sizes were compared. Out of 14 evaluated algorithms novoalign, bwa mem and clc4 are most suitable for mapping Pool-Seq data. Nevertheless, no single algorithm is sufficient for avoiding all false positives. We show that the intersection of the results of two mapping algorithms provides a simple, yet effective strategy to eliminate false positives. We propose that the implementation of a consistent Pool-seq bioinformatics pipeline building on the recommendations of this study can substantially increase the reliability of Pool-Seq results, in particular when libraries generated with different protocols are being compared.
Do financial blogs serve an infomediary role in capital markets?
Authors: Rickett Laura K. 
Published: May 2016

Purpose
– Financial blogs provide an online platform whereby retail investors effortlessly gain access to an abundant array of investment guidance. Prior studies find that the market reacts to financial blogs and similar online venues but results are inconsistent and financial blogs, a growing area in new media and distinct from other online venues, have received little attention. The purpose of this paper is to examine the particular conditions in which financial blogs serve an infomediary role in capital markets; when information asymmetry is high, earnings quality is low, and during economic uncertainty. These are conditions in which retail investors may seek easily accessible advice for their investment decisions.

Design/methodology/approach
– Abnormal returns for firms mentioned in blog posts on the SeekingAlpha.com financial blog are examined using a multivariate regression to determine whether or not the market reaction associated with these posts is related to information asymmetry, earnings quality, and economic uncertainty.

Findings
– Results indicate that abnormal returns are associated with the SeekingAlpha.com financial blog when information asymmetry is high and during bearish market conditions, and in particular when buy recommendations are posted on the blog for firms with high information asymmetry. This association is strengthened for firms with low institutional ownership, a proxy for unsophisticated or retail investors.

Research limitations/implications
– Results are based on a sample collected during a specific time period in order to detect whether financial blogs serve an infomediary role during uncertain market conditions.

Practical implications
– Results of this study can be useful to company executives who may want to monitor investment advice posted about their firm on financial blogs. Financial blogs and other forms of social media such as Twitter and Facebook are becoming the “new normal” in the investor information environment, a trend that is likely to continue.

Originality/value
– Financial blogs provide an abundance of supplemental information demanded by investors. Financial blogs represent a form of “new media,” now considered a key component of firms’ information environment (Saxton, 2012). In contrast to prior studies which primarily investigate only whether the market reacts to financial blogs or similar online platforms such as stock message boards, this study attempts to understand the specific conditions in which the market reacts to financial blogs. The results provide a rationale as to when and why investors rely on financial blogs and whether financial blogs serve an infomediary role in capital markets.
The role of polychronicity and intrinsic motivation as personality traits on frontline employees’ job outcomes
Authors: Daskin Mustafa , Surucu Ozlem Altunoz 
Published: May 2016

Purpose– The purpose of this paper is to investigate the impact of polychronicity and intrinsic motivation on frontline employees (FLEs)’ work-family conflict, and service recovery performance (SRP) in a service setting.Design/methodology/approach– In this survey, a total number of 312 usable questionnaires were personally retrieved from FLEs in the research location. The hypothesized relationships were tested using hierarchical regression analysis. This paper presented an integrative model to test the aforementioned effects and relationships.Findings– Polychronicity and intrinsic motivation had negative impact on work-family conflict and positive impact on SRP. Significantly, while gender was found to be positively related to work-family conflict, on the other hand, job tenure was found to be negatively related to work-family conflict.Practical implications– This paper provides implications for managers in terms of minimizing the negative effects of work-family conflict and maximizing the FLEs’ SRP. Also, this study provides useful guidelines to implement effective management practices and improve organizational outcomes within the service setting of Peninsular Malaysia.Originality/value– Theoretically, the current study by examining the untried effects and relationships such as the effect of intrinsic motivation on work-family conflict, the effect of polychronicity on FLEs’ work-family conflict and SRP lends further contribution to the related literature.
Sustainability service in-store
Authors: Fuentes Christian , Fredriksson Cecilia 
Published: May 2016

Purpose
– The purpose of this paper is to explore, illustrate, and conceptualize how sustainability service is performed and the role it plays in the promotion of sustainable consumption.

Design/methodology/approach
– Theoretically, this paper takes a practice theory approach, conceptualizing the provision of sustainability service as a set of complex, socio-material, and performative practices. Methodologically, this paper draws on an ethnographic study of a retail chain – W-Store – and its sustainability service. Interviews with management and focus group interviews with shop assistants and consumers, as well as observations made in-store, make up the material analysed.

Findings
– The provision of sustainability service is accomplished in this case via three service practices; arranging green shopping trails, answering sustainability questions, and promoting sustainability to green consumers in-store. The analysis shows that the retailing of sustainable products is not simply a matter of including sustainability products in the range and instructing shop assistants to promote them. Sustainability service – as enacted at W-Store – was dependent on the successful combination and configuration of human competence (service staff) and IT and organizational artefacts. There also needed to be congruence between consumers and their images and between retailers and the version of sustainability they were enacting. Finally, the provision of sustainability service required an investigative and adaptive organization capable of keeping up as well as developing vis-á-vis changing sustainability discourses and issues. However, once the necessary conditions had been met, sustainability service worked towards promoting sustainable consumption by making green shopping possible, educating consumers on sustainability issues, and motivating them via positive feedback and dialogue.

Originality/value
– Underscores the importance of investigating sustainability service and offers both a conceptual approach to and an analysis of this particular type of retail service work.
An integrated model of self-service technology (SST) usage in a retail context
Authors: Demoulin Nathalie T. M. , Djelassi Souad 
Published: May 2016

Purpose
– The purpose of this paper is to propose and test a comprehensive model that captures individual, system and situational drivers of customers’ intention to use and actual use of self-service technologies (SSTs).

Design/methodology/approach
– This paper is based on a survey conducted among 143 users and 150 non-users of SSTs at the exit of a grocery store. The proposed model was analysed using structural equation modelling and a logistic regression.

Findings
– The results demonstrate that: first, in addition to previous usage behaviour (i.e. usage frequency), situational factors (time pressure, basket size, coupons and queue length at the SSTs and staffed checkouts) influence customers’ decisions to use SSTs during a specific shopping trip; and second, perceived behavioural control is the most important determinant of behavioural intention, followed by perceived usefulness, need for interaction and perceived ease of use and enjoyment.

Originality/value
– Although an abundance of research has investigated the adoption of SSTs, little is known about what drives real usage. This study considers the actual usage of SSTs in a specific context, as well as the situational factors that influence the choice of SSTs over traditional checkouts. In addition, this paper provides an integrative model including actual usage, use frequency and behavioral intention and its antecedents by extending the Technology Acceptance Model 3.
Teaching sustainable development in higher education
Authors: Howlett Cathy , Ferreira Jo-Anne , Blomfield Jessica 
Published: May 2016

Purpose
This paper aims to argue that substantive changes are required in both curricula and pedagogical practice in higher education institutions to challenge dominant epistemologies and discourses and to unsettle current ways of thinking about, and acting in relation to, the environment. Central to such a shift, it is argued, is the need for higher education curricula to be interdisciplinary and for pedagogical practices to work to build capacities in students for critical and reflective thinking.

Design/methodology/approach
In this paper, a case study of our reflections is offered on a subject designed to promote capacities in students for critical and reflective thinking via an interdisciplinary approach. The paper uses data from student reflective essays and student course evaluations to make an argument for the success of this approach.

Findings
Genuine transformative learning can occur within a constructivist informed pedagogical approach to teaching for sustainability.

Research limitations/implications
Research implications are that genuine transformation can occur in students’ thinking processes (which the paper argues is critical for effective education in sustainability) with appropriately designed courses in higher education.

Practical implications
More effective environmental actors and thinkers, who can critically engage with the complexity of environmental problems.

Social implications
Social implications include a more effective and socially just higher education for sustainability

Originality/value
The authors know of no other narrative that addresses attempts to educate for sustainability using this approach.