bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of triterpene biosynthetic genes from Momordica charantia using RNA-seq analysis
Authors: Takase Shohei , Kera Kota , Hirao Yuya , Hosouchi Tsutomu , Kotake Yuki , Nagashima Yoshiki , Mannen Kazuto , Suzuki Hideyuki , Kushiro Tetsuo 
Published: October 2018

ABSTRACT
Cucurbitaceae plants contain characteristic triterpenoids. Momordica charantia, known as a bitter melon, contains cucurbitacins and multiflorane type triterpenes, which confer bitter tasting and exhibit pharmacological activities. Their carbon skeletons are biosynthesized from 2,3-oxidosqualene by responsible oxidosqualene cyclase (OSC). In order to identify OSCs in M. charantia, RNA-seq analysis was carried out from ten different tissues. The functional analysis of the resulting four OSC genes revealed that they were cucurbitadienol synthase (McCBS), isomultiflorenol synthase (McIMS), β-amyrin synthase (McBAS) and cycloartenol synthase (McCAS), respectively. Their distinct expression patterns based on RPKM values and quantitative RT-PCR suggested how the characteristic triterpenoids were biosynthesized in each tissue. Although cucurbitacins were finally accumulated in fruits, McCBS showed highest expression in leaves indicating that the early step of cucurbitacins biosynthesis takes place in leaves, but not in fruits.
Abbreviations: OSC: oxidosqualene cyclase; RPKM: reads perkilobase of exon per million mapped reads
Core executive functions are selectively related to different facets of motor competence in preadolescent children
Authors: Ludyga Sebastian , Pühse Uwe , Gerber Markus , Herrmann Christian 
Published: October 2018

AbstractBackground: Although accumulating evidence suggests that motor and cognitive development is interrelated, only a few studies have investigated links between executive function and motor control. Therefore, the present cross‐sectional study examined the relationship between motor competences and core components of executive functioning, including inhibitory control, working memory and cognitive flexibility. Methods: In 89 preadolescent children, motor competences were assessed using the MOBAK‐5 test battery. Additionally, all participants completed computer‐based versions of the Flanker task, which included standard and switch blocks, and the 2‐Back task. Results: Partial correlations (correcting for age, gender and body mass index) revealed that locomotor skills were associated with the adjusted hit‐rate on the 2‐Back task (r = 0.34) whereas object control was linked with conflict score on the Flanker task (r = −0.39). In contrast, there was no correlation between switch costs and motor competences. Conclusion: In preadolescent children, high competences in locomotor skills and object control skills are associated with high performance on specific executive function tasks. This finding supports the current view that motor competences and cognitive control share some common underlying processes.
Cardioprotective Effects of Paricalcitol Alone and in Combination With FGF23 Receptor Inhibition in Chronic Renal Failure: Experimental and Clinical Studies
Authors: Czaya Brian , Seeherunvong Wacharee , Singh Saurav , Yanucil Christopher , Ruiz Phillip , Quiroz Yasmir , Grabner Alexander , Katsoufis Chryso , Swaminathan Sethuraman , Abitbol Carolyn , Rodriguez-Iturbe Bernardo , Faul Christian , Freundlich Michael 
Published: October 2018

AbstractBACKGROUNDIn uremic animals, vitamin D receptor (VDR) agonists like paricalcitol (Pc) attenuate cardiac hypertrophy, but this effect has not been replicated consistently in humans with chronic kidney disease. Elevated fibroblast growth factor 23 (FGF23) levels cause cardiac hypertrophy with activation of the myocardial calcineurin/nuclear factor of activated T cell (NFAT) axis and may antagonize the cardioprotective effects of VDR agonist therapy. We hypothesized that the effectiveness of Pc may depend on the prevailing circulating levels of FGF23 and could be potentiated by the combined administration of a pan-FGF23 receptor (FGFR) blocker agent (PD173074).METHODSIn rats with 5/6 nephrectomy treated with Pc or PD173074 or both agents concurrently, myocardial mRNA expression of renin–angiotensin system, VDR, FGFR4, and calcineurin/NFAT target genes was determined. In adolescents on hemodialysis, we analyzed sequential echocardiograms, blood pressures and serial FGF23 measurements, and their relations to the cumulative administered dose of parenteral Pc.RESULTSThe ratio of Pc dose/plasma levels of FGF23 correlated inversely (P &lt; 0.005) with the cardiac mass in uremic rats and in hemodialysis patients, independently of hypertension. Despite persistently elevated FGF23 levels and myocardial FGFR4 activation, Pc suppressed upregulated myocardial calcineurin/NFAT target genes, and the effects were amplified by coadministration of PD173074.CONCLUSIONSThe beneficial effects of Pc on uremic cardiac hypertrophy are counterbalanced by the increased FGF23 levels. Blockade of FGF23-mediated signaling increased the Pc-induced suppression of the myocardial calcineurin/NFAT system. Higher doses of Pc should be considered in the treatment of patients with uremic cardiomyopathy.
Enhanced prediction of RNA solvent accessibility with long short-term memory neural networks and improved sequence profiles
Authors: Sun Saisai , Wu Qi , Peng Zhenling , Yang Jianyi 
Published: October 2018

Abstract

Motivation
The de novo prediction of RNA tertiary structure remains a grand challenge. Predicted RNA solvent accessibility provides an opportunity to address this challenge. To the best of our knowledge, there is only one method (RNAsnap) available for RNA solvent accessibility prediction. However, its performance is unsatisfactory for protein-free RNAs.

Results
We developed RNAsol, a new algorithm to predict RNA solvent accessibility. RNAsol was built based on improved sequence profiles from the covariance models and trained with the long short-term memory (LSTM) neural networks. Independent tests on the same datasets from RNAsnap show that RNAsol achieves the mean Pearson’s correlation coefficient (PCC) of 0.43/0.26 for the protein-bound/protein-free RNA molecules, which is 26.5%/136.4% higher than that of RNAsnap. When the training set is enlarged to include both types of RNAs, the PCCs increase to 0.49 and 0.46 for protein-bound and protein-free RNAs, respectively. The success of RNAsol is attributed to two aspects, including the improved sequence profiles constructed by the sequence-profile alignment and the enhanced training by the LSTM neural networks.

Availability and implementation
http://yanglab.nankai.edu.cn/RNAsol/

Supplementary information
Supplementary data are available at Bioinformatics online.
Disease gene identification based on generic and disease-specific genome networks
Authors: Nam Yonghyun , Jhee Jong Ho , Cho Junhee , Lee Ji-Hyun , Shin Hyunjung 
Published: October 2018

Abstract

Summary
Immune diseases have a strong genetic component with Mendelian patterns of inheritance. While the tight association has been a major understanding in the underlying pathophysiology for the category of immune diseases, the common features of these diseases remain unclear. Based on the potential commonality among immune genes, we design Gene Ranker for key gene identification. Gene Ranker is a network-based gene scoring algorithm that initially constructs a backbone network based on protein interactions. Patient gene expression networks are added into the network. An add-on process screens the networks of weighted gene co-expression network analysis (WGCNA) on the samples of immune patients. Gene Ranker is disease-specific; however, any WGCNA network that passes the screening procedure can be added on. With the constructed network, it employs the semi-supervised learning for gene scoring.

Results
The proposed method was applied to immune diseases. Based on the resulting scores, Gene Ranker identified potential key genes in immune diseases. In scoring validation, an average area under the receiver operating characteristic curve of 0.82 was achieved, which is a significant increase from the reference average of 0.76. Highly ranked genes were verified through retrieval and review of 27 million PubMed literatures. As a typical case, 20 potential key genes in rheumatoid arthritis were identified: 10 were de facto genes and the remaining were novel.

Availability and Implementation
Gene Ranker is available at http://www.alphaminers.net/GeneRanker/

Supplementary information
Supplementary data are available at Bioinformatics online.
Propagation of Information Along the Cortical Hierarchy as a Function of Attention While Reading and Listening to Stories
Authors: Regev Mor , Simony Erez , Lee Katherine , Tan Kean Ming , Chen Janice , Hasson Uri 
Published: October 2018

Abstract
How does attention route information from sensory to high-order areas as a function of task, within the relatively fixed topology of the brain? In this study, participants were simultaneously presented with 2 unrelated stories—one spoken and one written—and asked to attend one while ignoring the other. We used fMRI and a novel intersubject correlation analysis to track the spread of information along the processing hierarchy as a function of task. Processing the unattended spoken (written) information was confined to auditory (visual) cortices. In contrast, attending to the spoken (written) story enhanced the stimulus-selective responses in sensory regions and allowed it to spread into higher-order areas. Surprisingly, we found that the story-specific spoken (written) responses for the attended story also reached secondary visual (auditory) regions of the unattended sensory modality. These results demonstrate how attention enhances the processing of attended input and allows it to propagate across brain areas.
Resilience and protective factors among refugee children post-migration to high-income countries: a systematic review
Authors: Marley Charles , Mauki Beatus 
Published: October 2018

Abstract

Background
Increasing numbers of children have been forced to flee and seek asylum in high-income countries. Current research indicates that focussing on resilience and protective factors is an important long-term goal for positive mental health and psychological functioning of refugee children.

Methods
We performed a systematic review of quantitative literature regarding psychological and contextual factors that contribute to resilience in refugee children residing in high-income countries. Our procedure followed guidelines from the Centre for Reviews and Dissemination.

Results
We identified a number of protective factors as related to positive outcomes. They are drawn from several ecological domains and include age, self-esteem, maintenance of cultural identity, social support, belonging and safety and innovative social care services. A key overarching point reported by the studies we reviewed was that for refugee settlement specific policies and approaches to be beneficial, they were required to be embedded within a positive socially inclusive society. We also identified several limitations across the reported studies.

Conclusion
The factors we identified would assist clinicians to adopt a resilience-focussed approach. However, a continued pre-occupation with psychopathology was evident across the studies, which we argue as holding back the development of resilience-focussed approaches.
Perceptions of an online ‘train-the-champion’ approach to increase workplace movement
Authors: Goode Ana D , Hadgraft Nyssa T , Neuhaus Maike , Healy Genevieve N 
Published: October 2018

Abstract
Prolonged sitting is now recognized as an emergent work health and safety issue. To address the need for a scalable sitting-reduction intervention for workplaces, the BeUpstanding™ Champion Toolkit was developed. This free, online toolkit uses a ‘train-the-champion’ approach, providing a step-by-step guide and resources to workplace champions to assist them in raising awareness and building a supportive culture to reduce sitting time in their team. This qualitative study explored champion and staff perceptions of the beta (test) version of the toolkit. Seven work teams, from a range of workplace sectors (blue-/white-collar), sizes (small/medium/large) and locations (urban/regional) participated; all team members were exposed to the program (n = 603). Approximately 4 months after program initiation, semi-structured interviews were conducted with all champions (n = 7); focus groups were conducted with a random sample of staff (n = 40). Champions were followed-up again at 12 months (n = 5). Transcripts were coded by two researchers, with codes organized into overarching themes. All champions found the ‘train-the-champion’ approach, and the toolkit acceptable. Common enablers for intervention delivery included: champion passion for staff health and wellbeing; perceived fit of the program within existing practice; and, management support. Champions and staff reported improvements in knowledge/awareness about sitting, cultural norms, perceived stress, productivity and resilience. Facilitators for sustained change over time included a stable organizational climate and ongoing management support; barriers included workload intensification. The beta version of the BeUpstanding™ Champion Toolkit was highly acceptable to workplace champions and staff, and was perceived to have benefits for team culture and staff knowledge and wellbeing.
Comment on “A new approach for estimating stock status from length frequency data” by Froese et al. (2018)
Authors: Hordyk Adrian R , Prince Jeremy D , Carruthers Thomas R , Walters Carl J 
Published: October 2018

Abstract
Potential users of the model proposed by Froese et al. (2018) should be aware of several issues. First, the method to calculate equilibrium numbers-at-length is incomplete and leads to negatively biased estimates of fishing mortality. Second, inadequate simulation testing fails to reveal that the method is highly sensitive to assumptions of equilibrium conditions and that the population average asymptotic length (L∞) can be approximated by the largest observed size (Lmax). Finally, the Froese et al. (2018) model relies on the assumption that the ratio of natural mortality (M) to the von Bertalanffy growth parameter (K; M/K) is typically around 1.5, which they argue is supported by the literature for most fish stocks. We believe that this conclusion is based on an insufficient reading of the literature and, in fact, there is strong evidence to support the claim that M/K is outside the narrow bounds of 1.2–1.8 for many exploited species. Potential users of the method are alerted to these issues and alternative approaches are recommended to avoid these biases.
Barbara Strozzi, Appresso ai molli argenti (1659)
Authors: Kolb Richard , Swanson Barbara 
Published: October 2018

Abstract
This chapter explores the ways in which Appresso ai molli argenti exemplifies Barbara Strozzi’s sophisticated approach to the mid-seventeenth-century cantata. On the surface, Appresso is a five-section work consisting of opening and closing recitatives that enclose three aria sections. Strozzi makes judicious choices in setting Giovanni Pietro Monesi’s text, drawing attention to two contrasting aspects of lament, each defined by two distinct trends in the operatic lament tradition—the recitative lament and the aria-based descending-tetrachord lament. By giving voice to despair and creating room for reprieve through well-defined musical idioms and tonal plans, Strozzi shapes the cantata into a tightly knit and musically compelling narrative.
Marianna Martines, Sonata in A Major, I (1765)
Authors: Poundie Burstein L. 
Published: October 2018

Abstract
Marianna Martines, a Viennese contemporary of Haydn and Mozart, combined the fruits of instruction in the strict style with the devices and schemata of the new galant style. She was an excellent harpsichordist and singer as well as composer, and her compositional craft is amply displayed in the opening movement of her Sonata in A Major for Keyboard, written around 1765. This movement skillfully handles various layouts, schemata, and compositional devices that were standard at the time. Furthermore, it cleverly manipulates these features with rhythmic and formal devices—some of which are quite daring—in an expressive and dramatic fashion.
Health Disparities
Authors: Brown Alison G.M. , Folta Sara C. 
Published: October 2018

Abstract
Diet- and nutrition-related health disparities and inequities are a growing issue globally and nationally. This chapter explores how race, ethnicity, gender, and socioeconomic status influence diet-related health outcomes, such as malnutrition, obesity, hypertension, diabetes, and cardiovascular and cerebrovascular disease, and the complexity of the underlying causes of these health disparities and inequities. First, the chapter provides a foundational understanding of the terms and concepts as well as the historical nature of these disparities. The array of factors that contribute to health disparities including the social determinants of health such as educational level, employment status, environmental factors, access and affordability of healthy food, neighborhood segregation, chronic stress, discrimination and access to health care are then described. Given the growing number of immigrants in the United States and their important role in society, the healthy immigrant hypothesis and the dietary acculturation process among various immigrant groups in the United States is also discussed. The authors conclude by elaborating on global diet-related health disparities and the global and societal factors that perpetuate these differences in outcomes.
From Soil to Stomach
Authors: Hepburn Erecia , Karpyn Allison 
Published: October 2018

Abstract
One important and growing strategy to help local communities reinvest in local food is agritourism. Although advances have been made over the past half-century to promote and ensure food security globally, volatility in food prices and an increasing reliance on processed foods have created a global deterioration of nutrition needs. Although the majority of countries consider agritourism a venture to assist smaller farms looking to diversify, the approach is also a promising mechanism to encourage participation in sustainable agriculture and health promotion. In this chapter, we define agritourism, explore examples in the Caribbean and Europe, and examine how forward and backward linkages support its growth.
Pursuing Pride
Authors: Batson C. Daniel 
Published: October 2018

Abstract
When we feel empathic concern, do we seek an empathy-specific boost to our esteem? This pride hypothesis was tested against the empathy–altruism hypothesis by looking at (a) mood change after individuals feeling high (vs. low) empathy for a person in need learn that, without their help, the person is no longer in need; (b) mood change after individuals learn that, through no personal fault, their help fails to remove the need; and (c) the association of reward-relevant thoughts with the helping of those feeling high empathy. Results of experiments using each technique failed to support the pride hypothesis; they supported the empathy–altruism hypothesis instead. Based on these and all the previous results, it seemed time to conclude that the motivation produced by empathic concern must be altruistic. But this conclusion was premature. Colleagues proposed two new egoistic explanations, each of which could explain all the apparent support for the altruism hypothesis. Their proposals extended the search.
Self–Other Merging
Authors: Batson C. Daniel 
Published: October 2018

Abstract
The second new possibility was that when you feel empathic concern, you no longer see yourself and the person for whom you feel empathy as distinct individuals. Rather, a perceptual/conceptual change occurs in which the two of you merge together in your mind, and you see his or her needs as yours. So, empathy-induced helping is really helping yourself: egoism. In three experiments, Bob Cialdini and colleagues found that participants said they would provide more costly, intimate help to people to whom they felt more connected (a good friend or family member vs. an acquaintance or near stranger). Cialdini and his colleagues interpreted this as support for merging. But subsequent research, in which actual (rather than imagined) helping was assessed and relationship confounds were avoided, provided a range of evidence that merging cannot account for the empathy–helping relationship. It seemed necessary to dismiss this second possibility and move on to the third.
Some Bad
Authors: Batson C. Daniel 
Published: October 2018

Abstract
Despite its virtues, empathy-induced altruism can at times harm those in need, other people, and the altruistically motivated person. Specifically, it can hurt those in need when acted on without wisdom and sensitivity or when a cool head is required. It can produce paternalism. It is less likely to be evoked by nonpersonalized, abstract, chronic needs. It can be a source of immoral action, leading us to show partiality toward those for whom we feel empathic concern even when we know that to do so is neither fair nor best for all. Indeed, when our behavior is public, empathy-induced altruism can pose a more serious threat to the common good than does self-interest. Finally, it can at times jeopardize our mental and physical health—even our life. Any attempt to call on empathy-induced altruism to build a more humane society needs to take these problems into account lest we do more harm than good.
Relativity in Modern Physics
Authors: Deruelle Nathalie , Uzan Jean-Philippe 
Published: October 2018

Abstract
Newton’s ideas about how to represent space and time, his laws of dynamics, and his theory of gravitation established the conceptual foundation from which modern physics developed. This book offers a modern view of Newtonian theory, emphasizing those aspects needed for understanding quantum and relativistic contemporary physics. In 1905, Albert Einstein proposed a novel representation of space and time, special relativity. The text also presents relativistic dynamics in inertial and accelerated frames, as well as a detailed overview of Maxwell’s theory of electromagnetism, thus providing the background necessary for studying particle and accelerator physics, astrophysics, and Einstein’s theory of general relativity. In 1915, Einstein proposed a new theory of gravitation, general relativity. Finally, the text develops the geometrical framework in which Einstein’s equations are formulated and presents several key applications: black holes, gravitational radiation, and cosmology.
Santana and the Metaphysics of Tone
Authors: Latour Melinda 
Published: October 2018

Abstract
Throughout his career, Carlos Santana has used music to express his idiosyncratic spiritual beliefs. Pursuing the guidance of guru Sri Chinmoy in the 1970s and subsequently seeking his own spiritual path, Santana sought to channel a higher power through his guitar technique and tone, describing the process of music making as a mystical endeavor. In order to attain these goals, Santana used amplifiers that prioritized depth of sound (described by himself in synesthetic terms), feedback loops for his signature sustained tones, an avoidance of hypermasculine performance, and a peaceful stage presence. This chapter investigates the role of timbre in Santana’s spiritual journey from the 1960s to the present.