bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temperature and polarity based evolutionary model of the ribosomal complex in Thermus thermophilus and Escherichia coli
Authors: Tripathi Rashmi 
Published: June 2019

AbstractThe ribosome is considered a molecular fossil of the RNA world and is the oldest molecular machinery of living cells responsible for translating genetic information encoded by messenger RNA(mRNA) to proteins. Currently not much is known regarding how these proteins were assembled and the potential biogeochemical environment that could have shaped their evolution. In order to answer these questions, a comprehensive analysis of the amino acid frequencies of 30S and 50S ribosomal sub-units occurring in thermophile Thermus thermophilus and mesophile Escherichia coli was performed. The amino acid frequencies in proteins are believed to have been shaped by their pre-biotic abundances in the universe and by heavy bombardment of meteorites on planet earth (4.5-3.8 Ga). Absence of amino acid residues such as cysteine and tryptophan in T.thermophilus and E.coli proteins hints towards the evolution of small and large subunits prior to the origin of metabolic pathways of amino acid synthesis possibly under anoxic and sulphur free conditions. Moreover, an underrepresentation of readily oxidizable amino acids such as methionine, tyrosine and histidine, indicates that these proteins could have evolved in a more reducing environment as was prevalent on early earth. A comparison of amino acid biases with universal UNIPROT estimates, indicates arginine and lysine overrepresentation, linking a role of these amino acids in ribosomal RNA binding and stabilization corresponding to the RNA world hypothesis whereby RNA molecules drove the assembly of living systems. The continuing prevalence of these amino acid biases in modern proteins reflects the functional stability of ancient proteins constructed during billions of years of evolution and provides glimpses into the evolution of the ancient amino acid code. Step-wise accretion models involving increasing complexity of the amino acid code and the ribosomal sub-units are proposed for T.thermophilus and E.coli, providing potential insights regarding the origin of ribosomes in a temperature dependent and polar environment.
Memorability of photographs in subjective cognitive decline and mild cognitive impairment: implications for cognitive assessment
Authors: Bainbridge Wilma A. , Berron David , Schütze Hartmut , Cardenas-Blanco Arturo , Metzger Coraline , Dobisch Laura , Bittner Daniel , Glanz Wenzel , Spottke Annika , Rudolph Janna , Brosseron Frederic , Buerger Katharina , Janowitz Daniel , Fliessbach Klaus , Heneka Michael , Laske Christoph , Buchmann Martina , Peters Oliver , Diesing Dominik , Li Siyao , Priller Josef , Spruth Eike Jakob , Altenstein Slawek , Schneider Anja , Kofler Barbara , Teipel Stefan , Kilimann Ingo , Wiltfang Jens , Bartels Claudia , Wolfsgruber Steffen , Wagner Michael , Jessen Frank , Baker Chris , Düzel Emrah 
Published: June 2019

AbstractINTRODUCTIONImpaired long-term memory is a defining feature of Mild Cognitive Impairment (MCI). We tested whether this impairment is item-specific, limited to some memoranda whereas some remain consistently memorable.METHODSWe conducted item-based analyses of long-term visual recognition memory. 394 participants (healthy controls (HC), Subjective Cognitive Decline (SCD), and MCI) in the multicentric DZNE-Longitudinal Cognitive Impairment and Dementia Study (DELCODE) were tested with images from a pool of 835 photographs.RESULTSWe observed consistent memorability for images in HCs, SCDs, and MCI, predictable by a neural network trained on another healthy sample. Looking at memorability differences between groups, we identified images that could successfully categorize group membership with higher success and a substantial image reduction than the original image set.DISCUSSIONIndividuals with SCD and MCI show consistent memorability for specific items, while other items show significant diagnosticity. Certain stimulus features could optimize diagnostic assessment, while others could support memory.
A set of endogenous control genes for use in quantitative real-time PCR experiments reveal that the wild-type formin Ldia2 is enriched in the early pond snail embryo
Authors: Johnson Harriet F. , Davison Angus 
Published: June 2019

ABSTRACTAlthough the pond snail Lymnaea stagnalis is an emerging model organism for molecular studies in a wide variety of fields including development, biomineralisation and neurophysiology, there are a limited number of verified endogenous control genes for use in quantitative real-time PCR (qRT-PCR). As part of larger study on snail chirality or left-right asymmetry, we wished to assay relative gene expression in pond snail embryos, so we evaluated six new candidate control genes, by comparing their expression in three tissues (ovotestis, foot, and embryo) and across three programs (geNorm, Normfinder and Bestkeeper). The specific utility of these control genes was then tested by investigating the relative expression of six experimental transcripts, including the formin Ldia2, a gene that has been associated with chirality in L. stagnalis. All six control genes were found to be suitable for use. Of the six experimental genes that were tested, it was found that all were relatively depleted in the early embryo compared with other tissues, except the formin gene Ldia2. Instead, transcripts of the wild type Ldia2dex were enriched in the embryo, whereas a non-functional frameshifted version Ldia2sin was severely depleted. These differences in Ldia2sin expression were less evident in the ovotestis and not evident in the foot tissue, suggesting that nonsense-mediated decay may be obscured in actively transcribing tissues. This work therefore provides a set of control genes that may be useful to the wider community, and shows how they may be used to assay differences in expression in the early embryo.
Cross-species regulatory sequence activity prediction
Authors: Kelley David R. 
Published: June 2019

AbstractMachine learning algorithms trained to predict the regulatory activity of nucleic acid sequences have revealed principles of gene regulation and guided genetic variation analysis. While the human genome has been extensively annotated and studied, model organisms have been less explored. Model organism genomes offer both additional training sequences and unique annotations describing tissue and cell states unavailable in humans. Here, we develop a strategy to train deep convolutional neural networks simultaneously on multiple genomes and apply it to learn sequence predictors for large compendia of human and mouse data. Training on both genomes improves gene expression prediction accuracy on held out sequences. We further demonstrate a novel and powerful transfer learning approach to use mouse regulatory models to analyze human genetic variants associated with molecular phenotypes and disease. Together these techniques unleash thousands of non-human epigenetic and transcriptional profiles toward more effective investigation of how gene regulation affects human disease.
Neural correlates of conscious visual perception lie outside the visual system: evidence from the double-drift illusion
Authors: Liu Sirui , Yu Qing , Tse Peter U. , Cavanagh Patrick 
Published: June 2019

SummaryWhen perception differs from the physical stimulus, as it does for visual illusions and binocular rivalry, the opportunity arises to localize where perception emerges in the visual processing hierarchy. Representations prior to that stage differ from the eventual conscious percept even though they provide input to it. Here we investigate where and how a remarkable misperception of position emerges in the brain. This “double-drift” illusion causes a dramatic mismatch between retinal and perceived location, producing a perceived path that can differ from its physical path by 45° or more [1]. The deviations in the perceived trajectory can accumulate over at least a second [1] whereas other motion-induced position shifts accumulate over only 80 to 100 ms before saturating [2]. Using fMRI and multivariate pattern analysis, we find that the illusory path does not share activity patterns with a matched physical path in any early visual areas. In contrast, a whole-brain searchlight analysis reveals a shared representation in more anterior regions of the brain. These higher-order areas would have the longer time constants required to accumulate the small moment-to-moment position offsets that presumably originate in early visual cortices, and then transform these sensory inputs into a final conscious percept. The dissociation between perception and the activity in early sensory cortex suggests that perceived position does not emerge in what is traditionally regarded as the visual system but emerges instead at a much higher level.
Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics
Authors: East Kyle W. , Newton Jocelyn C. , Morzan Uriel N. , Acharya Atanu , Skeens Erin , Jogl Gerwald , Batista Victor S. , Palermo Giulia , Lisi George P. 
Published: June 2019

ABSTRACTCRISPR-Cas9 is a widely employed genome-editing tool with functionality reliant on the ability of the Cas9 endonuclease to introduce site-specific breaks in double-stranded DNA. In this system, an intriguing allosteric communication has been suggested to control its DNA cleavage activity through flexibility of the catalytic HNH domain. Here, solution NMR experiments and a novel Gaussian accelerated Molecular Dynamics (GaMD) simulation method are used to capture the structural and dynamic determinants of allosteric signaling within the HNH domain. We reveal the existence of a millisecond timescale dynamic pathway that spans HNH from the region interfacing the adjacent RuvC nuclease and propagates up to the DNA recognition lobe in full-length CRISPR-Cas9. These findings reveal a potential route of signal transduction within the CRISPR-Cas9 HNH nuclease, advancing our understanding of the allosteric pathway of activation. Further, considering the role of allosteric signaling in the specificity of CRISPR-Cas9, this work poses the mechanistic basis for novel engineering efforts aimed at improving its genome editing capability.Abstract Figure
A generalin vitroassay to study enzymatic activities of the ubiquitin system
Authors: Zuo Yukun , Chong Boon Keat , Jiang Kun , Finley Daniel , Klenerman David , Ye Yu 
Published: June 2019

AbstractThe ubiquitin (Ub) system regulates a wide range of cellular signaling pathways. Several hundred E1, E2 and E3 enzymes are together responsible for protein ubiquitination, thereby controlling cellular activities. Due to the numerous enzymes and processes involved, studies on ubiquitination activities have been challenging. We here report a novel FRET-based assay to study thein vitrokinetics of ubiquitination. FRET is established between binding of fluorophore-labeled Ub to eGFP-tagged ZnUBP, a domain that exclusively binds unconjugated Ub. We name this assay the Free Ub Sensor System (FUSS). Using Uba1, UbcH5 and CHIP as model E1, E2 and E3 enzymes, respectively, we demonstrate that ubiquitination results in decreasing FRET efficiency, from which reaction rates can be determined. Further treatment with USP21, a deubiquitinase, leads to increased FRET efficiency, confirming the reversibility of the assay. We subsequently use this assay to show that increasing the concentration of CHIP or UbcH5 but not Uba1 enhances ubiquitination rates, and develop a novel machine learning approach to model ubiquitination. The overall ubiquitination activity is also increased upon incubation with tau, a substrate of CHIP. Our data together demonstrate the versatile applications of a novel ubiquitination assay that does not require labeling of E1, E2, E3 or substrates, and is thus likely compatible with any E1-E2-E3 combinations.
A Comprehensive Integrated Anatomical And Molecular Atlas Of Rodent Intrinsic Cardiac Nervous System
Authors: Achanta Sirisha , Gorky Jonathan , Leung Clara , Moss Alison , Robbins Shaina , Eisenman Leonard , Chen Jin , Tappan Susan , Heal Maci , Farahani Navid , Huffman Todd , England Steve , Cheng Zixi (Jack) , Vadigepalli Rajanikanth , Schwaber James S. 
Published: June 2019

ABSTRACTIn this study, we developed, coordinated, and integrated several technologies including novel whole organ imaging, software development to support the very first precise 3D neuroanatomical mapping and molecular phenotyping of the intracardiac nervous system (ICN). While qualitative and gross anatomical descriptions of the anatomy of the ICN have been presented, we here bring forth the first comprehensive atlas at large scale of the entire ICN in rat at a single cell resolution. Our work for the first time provides a novel 3D model to precisely integrate anatomical, functional and molecular data in the 3D digitally reconstructed whole heart with high resolution at the micron scale. This work represents the cutting edge in a long history of attempts to understand the anatomical substrate upon which the neuronal control of cardiac function is built. To our knowledge, there has not yet been a comprehensive histological mapping to generate a neurocardiac atlas at cellular and molecular level for the whole heart of any species. We now display the full extent and the position of neuronal clusters on the base and posterior left atrium, and the distribution of molecular phenotypes in that context. In addition we display in this context distinct molecular phenotypes that are defined along the base-to-apex axis, and the present novel discovery of their phenotypical spatial gradients, have not been previously described. The development of these approaches needed to acquire these data has produced method pipelines which can not only achieve the goals of anatomical and molecular mapping of the heart, but also provide the method pipelines for mapping other organs (e.g., stomach, lung, kidney, and liver).
Multi-generational Analysis and Manipulation of Chromosomes in a Polyploid Cyanobacterium
Authors: Moore Kristin A. , Tay Jian Wei , Cameron Jeffrey C. 
Published: June 2019

ABSTRACTFaithful inheritance of genetic material from one generation to the next is an essential process for all life on earth. Much of what is known about microbial DNA replication and inheritance has been learned from a small number of bacterial species that share many common traits. Whether these pathways are conserved across the great diversity of the microbiome remains unclear. To address this question, we studied chromosome dynamics in a polyploid photosynthetic bacteria using single cell, time-lapse microscopy over multi-generation lineages in conjunction with inducible CRISPR-interference and fluorescent chromosome labeling. With this method we demonstrated the long-term consequences of manipulating parameters such as cell growth, cell division, and DNA replication and segregation on chromosome regulation in a polyploid bacterial species. We find that these bacteria are surprisingly resilient to chromosome disruption resulting in continued cell growth when DNA replication is inhibited and even in the complete absence of chromosomes.
The coupling mechanism of reassembly quality with uncertainty of remanufactured parts
Authors: Zhang Cuixia , Liu Conghu , Chen Jianqing , Li Qiang , He Kang , Gao Mengdi , Cai Wei 
Published: June 2019

Purpose
The uncertainty of remanufacturing parts is a key factor affecting the quality of remanufactured products. Therefore, the purpose of this paper is to measure the uncertainty of remanufactured parts and study the coupling mechanism of reassembly quality.

Design/methodology/approach
First, uncertainty of remanufactured parts is analyzed, and the uncertainty measure model for remanufacturing parts based on entropy is constructed. Second, the nonlinear mapping model between the uncertainty and reassembly quality were studied using Gauss-Newton iterative method to reveal the coupling mechanism between uncertainty of remanufacturing parts and reassembly quality. Finally, the model is verified in the reassembly process of remanufacturing cylinder head.

Findings
The method can guide reassembly operations to improve the reassembly quality with uncertainty of remanufactured parts.

Originality/value
This study provides practical implications by developing a multivariate nonlinear mapping model for reassembly quality based on entropy to determine the uncertainty factors that affect the reassembly quality significantly and then correct the reassembly operation to better optimize the allocation of remanufacturing production resources. The study also theoretically contributes to reveal the coupling mechanism of reassembly quality with the uncertainty of remanufactured parts.
The optimal capital structure of Swiss dairy farms
Authors: Schorr Anke , Lips Markus 
Published: June 2019

PurposeThe purpose of this paper is to propose a novel way of determining optimal capital structure, applied to sub-groups of Swiss dairy farms from 2003 to 2014. Optimization of capital structure is carried out with respect to two performance indicators from an economic value added perspective.Design/methodology/approachOptimal values of capital structure are obtained based on a minimization of correlation between economic performance indicators and a distance function of the debt-to-asset ratio distribution to its quantiles. The approach differs from existing approaches in relying solely on empirical data and in using fewer external parameters, which are difficult to estimate, such as risk aversion coefficients. An unbalanced panel data set from the Swiss Farm Accounting Network with almost 14,000 dairy farm observations serves as input data to the model.FindingsConcise optimal values of capital structure result for regional and temporal sub-groups of Swiss dairy farms. Comparing the evolution of optimal values for these sub-groups with existing models of optimal capital structure, the authors infer that dairy farmers in the mountain region are less risk averse than their counterparts in the valley region and that falling interest rates increase the optimal value of debt-to-asset ratio.Originality/valueThe straightforward computation of optimal values for capital structure without intermediate parameters is useful and new. In addition, the authors’ model can be used as a tool for comparison and validation of previous models with the same aim, e.g. for comparison of risk aversion coefficients or qualitative behavior of optimal values for capital structure.
CEO power and corporate social responsibility
Authors: Harper Joel , Sun Li 
Published: June 2019

Purpose
The purpose of this paper is to examine the impact of chief executive officer (CEO) power on corporate social responsibility (CSR) performance.

Design/methodology/approach
The authors use regression analysis to investigate the research question.

Findings
Using a 23-year panel sample with 1,574 unique US firms and 8,575 firm-year observations, the authors find a significant and negative relation between CEO power and CSR, suggesting that firms with more powerful CEOs engage in less CSR activities.

Originality/value
The results reveal that more powerful CEOs become less responsive to the needs of stakeholder groups, confirming the validity of the stakeholder theory of CSR.
Family businesses, corporate social responsibility, and websites
Authors: Iaia Lea , Vrontis Demetris , Maizza Amedeo , Fait Monica , Scorrano Paola , Cavallo Federica 
Published: June 2019

PurposeThe purpose of this paper is to identify the distinctive elements of CSR communications that characterize the communications models of family businesses in the Italian wine industry, and to compare them with nonfamily businesses.Design/methodology/approachUsing a case study approach, a sample of large and medium companies practicing corporate social responsibility was identified. The content of their websites was examined using content analysis and text mining (correspondence analysis techniques and word association analysis using the T-Lab software).FindingsThe analysis indicates that the ownership structure nature makes a difference in the online CSR communications process. The cultural identity in both family and nonfamily businesses is founded on intangible factors such as tradition; however, being a family business is a fundamental driver in the online CSR communications process, no longer forming a bond among players in the wine industry, but rather linking with other wine family businesses.Research limitations/implicationsOne limitation of this work is the small size of the investigated sample. An added value it contributes is its focus on the Italian wine industry. The paper provides the essential elements that family and nonfamily wine businesses should consider in customizing their CSR communications with the brand’s specific details.Originality/valueThe authors highlighted the similarities and differences of family and nonfamily wine businesses in terms of their online CSR communications. The authors also observed how the family wine business identity, in its multidimensional construct, has common factors with what we call “familiness.” This research could establish a starting point for further work within this important sector.
Change communication and the use of anonymous social media at work
Authors: Kim Heewon , Scott Craig 
Published: June 2019

Purpose
The purpose of this paper is to investigate how employees use anonymous social media to cope with organizational change, which may affect various engagement outcomes. Specifically, this study focuses on change communication from management (i.e. top–down communication) and workplace freedom of speech (i.e. bottom–up communication) as potential antecedents of anonymous communication. In turn, commitment, turnover intention and job satisfaction are examined as engagement outcomes.

Design/methodology/approach
An online survey was conducted at Microsoft through Blind, a mobile platform for anonymous communication at work. A series of regression models were used to test hypotheses.

Findings
Results demonstrate that: the quality of change communication was related to anonymous social media use for information and support seeking; workplace freedom of speech was related to anonymous social media use for expressing ideas; perceived usefulness and trustworthiness of anonymous social media positively affected the usage of them; and the quality of change communication and workplace freedom of speech were linked to affective commitment and job satisfaction.

Originality/value
Despite the growing popularity of anonymous social media at work, their use and influences have received scarce empirical attention. This study advances the authors’ knowledge of the antecedents, characteristics and outcomes of anonymous social media use in a work environment characterized by frequent organizational changes. The findings also highlight the significance of communication qualities and freedom of speech at work.