bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetically encoded fluorescent indicators for imaging intracellular potassium ion concentration
Authors: Shen Yi , Wu Sheng-Yi , Rancic Vladimir , Aggarwal Abhi , Qian Yong , Miyashita Shin-Ichiro , Ballanyi Klaus , Campbell Robert E. , Dong Min 
Published: January 2019

AbstractPotassium ion (K+) homeostasis and dynamics play critical roles in biological activities. Here we describe three genetically encoded K+ indicators. KIRIN1 (potassium (K) ion ratiometric indicator) and KIRIN1-GR are Förster resonance energy transfer (FRET)-based indicators with a bacterial K+ binding protein (Kbp) inserting between the fluorescent protein FRET pairs mCerulean3/cp173Venus and Clover/mRuby2, respectively. GINKO1 (green indicator of K+ for optical imaging) is a single fluorescent protein-based K+ indicator constructed by insertion of Kbp into enhanced green fluorescent protein (EGFP). These indicators are suitable for detecting K+ at physiologically relevant concentrations in vitro and in cells. KIRIN1 enabled imaging of cytosolic K+ depletion in live cells and K+ efflux and reuptake in cultured neurons. GINKO1, in conjunction with red fluorescent Ca2+ indicator, enable dual-color imaging of K+ and Ca2+ dynamics in neurons and glial cells. These results demonstrate that KIRIN1 and GINKO1 are useful tools for imaging intracellular K+ dynamics.
Topological valley transport at the curved boundary of a folded bilayer graphene
Authors: Mania E. , Cadore A. R. , Taniguchi T. , Watanabe K. , Campos L. C. 
Published: January 2019

AbstractThe development of valleytronics demands long-range electronic transport with preserved valley index, a degree of freedom similar to electron spin. A promising structure for this end is a topological one-dimensional channel formed in a bilayer graphene, called a domain wall. In these channels, the valley-index defines the propagation direction of the charge carriers, and the chiral edge states are robust over many kinds of disorder. However, the fabrication of domain walls are challenging, requiring the design of complex multi-gate structures or production on rough substrates, showing a limited mean free path. Here, we report on a high-quality domain wall formed at the curved boundary of a folded bilayer graphene. Our experiments reveal long-range ballistic transport at such topological channels with the two-terminal resistance close to the ballistic resistance R = e2/4h at zero-magnetic field and the four-terminal resistance near to zero. At the bulk, we measure a tunable band gap.
Transcriptomic profiles of tissues from rats treated with anticancer drug combinations
Authors: Davis Myrtle , Knight Elaine , Eldridge Sandy R. , Li Jianying , Bushel Pierre R. 
Published: January 2019

AbstractTo achieve therapeutic goals, many cancer chemotherapeutics are used at doses close to their maximally tolerated doses. Thus, it may be expected that when therapies are combined at therapeutic doses, toxicity profiles may change. In many ways, prediction of synergistic toxicities for drug combinations is similar to predicting synergistic efficacy, and is dependent upon building hypotheses from molecular mechanisms of drug toxicity. The key objective of this initiative was to generate and make publicly available key high-content data sets for mechanistic hypothesis generation as it pertains to a unique toxicity profile of a drug pair for several anticancer drug combinations. The expectation is that tissue-based genomic information that are derived from target tissues will also facilitate the generation and testing of mechanistic hypotheses. The view is that availability of these data sets for bioinformaticians and other scientists will contribute to analysis of these data and evaluation of the approach.
DAB‐based PET in MVDC traction and shipboard applications with distribution and redundant control
Authors: You Wang , Zedong Zheng , Yongdong Li 
Published: January 2019

Medium‐voltage DC (MVDC) grid has drawn more interest in the application of traction and large‐scale ships, for its lower loss, higher reliability, higher controllability and simpler system architecture. DC breaker and DC distribution are the key elements in the MVDC grid, and the power electronic transformers (PETs) have shown great advantage in the MVDC grid for its relatively smaller volume and higher flexibility compared to the traditional line transformers and AC/DC converters. In this study, a distribution DC PET based on input series output parallel dual active bridge (DAB) is proposed in the application of power supply system in traction and large scale ships. The DC PET consists of 12 DABs with an input voltage of 10 kV and the output voltage of 380 V. Strategies are proposed for distributed voltage balancing and redundancy control in the proposed PET. Simulations were done in MATLAB/Simulink. In the simulation, waveforms in the normal working conditions and the module fault status is shown, and the result shows that the proposed DC PET has great controllability and flexibility and by adding redundant modules, it keeps great reliability while fault occurs.
Self-propulsion of inverse Leidenfrost drops on a cryogenic bath
Authors: Gauthier Anaïs , Diddens Christian , Proville Rémi , Lohse Detlef , van der Meer Devaraj 
Published: January 2019

Significance
An inverse Leidenfrost state can happen when ambient-temperature drops are deposited on liquid nitrogen, as the bath evaporation generates a vapor film that maintains drops in levitation. Contrary to what is seen on solids, drops levitating on a cryogenic liquid exhibit counterintuitive dynamics: They are spontaneously self-propelled (and glide in straight lines) and keep levitating, even after cooling down to a temperature equal to that of the bath. This spontaneous self-propulsion in a cryogenic environment—that lasts for tens of minutes—can be seen as an efficient way to freeze and further transport biological materials (such as cells or proteins) or chemicals without contamination or risk of heat degradation.
Content and Language Integrated Learning in Dutch bilingual education
Authors: Oattes Huub , Oostdam Ron , De Graaff Rick , Fukkink Ruben , Wilschut Arie 
Published: January 2019

AbstractThis small-scale observational study explores how Dutch bilingual education history teachers (BHTs) focus on the L2 component in their CLIL-lessons. We observed and rated eight BHTs on five language teaching categories. Results show that Dutch BHTs focus more strongly on using the L2 to teach subject content and that they tend to be less engaged in teaching specific second language topics, such as focus on form or language learning strategies. Further results and suggestions for improving the BHTs’ L2 focus are discussed together with a plea for a CLIL definition that is more in line with the everyday reality of the CLIL classroom.
The influence of L2 English on L3 French acquisition in bilingual education*
Authors: Stadt Rosalinde , Hulk Aafke , Sleeman Petra 
Published: January 2019

AbstractIn the present paper, we compare L2 English influence on French third language acquisition (L3A) in first-year and third-year bilingual stream secondary school students and in third-year mainstream secondary school students by means of a gap-filling task. We found that the influence of L2 English on French L3A increases from first- to third-year bilingual students, which is not the case in the mainstream group. This raises the question if L2 influence on L3A in bilingual education is the result of the increased L2 exposure or of a higher L2 proficiency, factors that both have been claimed to play a role in L3A-research (Hammarberg, 2001;Tremblay, 2006;Jaensch, 2009). The results of this study show that there is no individual correlation between L2 English proficiency and influence of English in L3 French learning. Therefore, we suggest that it is L2 exposure rather than L2 proficiency that leads to more influence of the L2 in L3 French.
An investigation of the role of working memory capacity and naming speed in phonological advance planning in language
production
Authors: Klaus Jana , Schriefers Herbert 
Published: January 2019

Abstract
Producing multi-word utterances is a complex, yet relatively effortless process. Research with the picture-word
interference paradigm has shown that speakers can plan all elements of such utterances up to the phonological level before
initiating speech, yet magnitude and direction of this phonological priming effect (i.e. facilitative vs. inhibitory) differ
between but also within studies. We investigated possible sources for variability in the phonological advance planning scope. In
two experiments, participants produced bare nouns (“monkey”) and complex noun phrases (“the small red
monkey”) while ignoring distractor words phonologically (un)related to the noun. For low- and high-working memory
capacity speakers as well as fast and slow speakers, we found phonological facilitation effects for the bare noun, but no
distractor effects for the complex noun phrases. However, looking at individual distractor effects for utterance-final elements
revealed a large variability between speakers. We conclude that phonological advance planning cannot be summarised as an overall
effect, but should take into account inter- and intraindividual variability.
Variability and consistency in late bilinguals’ morphology
Authors: Jessen Anna , Veríssimo João , Clahsen Harald 
Published: January 2019

Abstract
Speaking a late-learned second language (L2) is supposed to yield more variable and less consistent output than
speaking one’s first language (L1), particularly with respect to reliably adhering to grammatical morphology. The current study
investigates both internal processes involved in encoding morphologically complex words – by recording event-related brain
potentials (ERPs) during participants’ silent productions – and the corresponding overt output. We specifically examined compounds
with plural or singular modifiers in English. Thirty-one advanced L2 speakers of English (L1: German) were compared to a control
group of 20 L1 English speakers from an earlier study. We found an enhanced (right-frontal) negativity during (silent)
morphological encoding for compounds produced from regular plural forms relative to compounds formed from irregular plurals,
replicating the ERP effect obtained for the L1 group. The L2 speakers’ overt productions, however, were significantly less
consistent than those of the L1 speakers on the same task. We suggest that L2 speakers employ the same mechanisms for
morphological encoding as L1 speakers, but with less reliance on grammatical constraints than L1 speakers.
Effects of a resistance‐training programme on endoplasmic reticulum unfolded protein response and mitochondrial functions in PBMCs from elderly subjects
Authors: Estébanez Brisamar , Moreira Osvaldo C. , Almar Mar , de Paz José A. , Gonzalez‐Gallego Javier , Cuevas María J. 
Published: January 2019

AbstractAging has been related with a decline in the ability to handle protein folding, which leads to endoplasmic reticulum stress and alterations in unfolded protein response (UPR). Importantly, physical activity could activate the UPR and attenuate or prevent age‐induced endoplasmic reticulum (ER) dysfunction. The current study evaluated the effects of a resistance exercise on UPR and mitochondrial functions in peripheral blood mononuclear cells (PBMCs) from elderly subjects. Thirty healthy women and men (age, 72.8, sx− = 2.2 years) were randomized to a training group, which performed an 8‐week resistance training programme, or a control group, which followed their daily routines. The phosphorylation of PERK and IRE1, as well as ATF4, and XBP1 protein expression, significantly increased following the training, while expression of BiP, AFT6 and CHOP remain without changes. Additionally, the intervention also induced an increase in PGC‐1α and Mfn1 protein levels, while no changes were found in Drp1 expression. Finally, the resistance protocol was not able to activate PINK1/Parkin and Bnip3/Nix pathways. The results obtained seem to indicate that 8‐week resistance exercise activates the UPR, stimulates mitochondrial biogenesis, maintains mitochondrial dynamics and prevents mitophagy activation by unfolded proteins in PBMCs from elderly subjects.
Are increases in skeletal muscle mass accompanied by changes to resting metabolic rate in rugby athletes over a pre‐season training period?
Authors: MacKenzie‐Shalders Kristen L. , Byrne Nuala M. , King Neil A. , Slater G. J. 
Published: January 2019

AbstractOptimising dietary energy intake is essential for effective sports nutrition practice in rugby athletes. Effective dietary energy prescription requires careful consideration of athletes’ daily energy expenditure with the accurate prediction of resting metabolic rate (RMR) important due to its influence on total energy expenditure and in turn, energy balance. This study aimed to (a) measure rugby athletes RMR and (b) report the change in RMR in developing elite rugby players over a rugby preseason subsequent to changes in body composition and (c) explore the accurate prediction of RMR in rugby athletes. Eighteen developing elite rugby union athletes (age 20.2 ± 1.7 years, body mass 101.2 ± 14.5 kg, stature 184.0 ± 8.4 cm) had RMR (indirect calorimetry) and body composition (dual energy x‐ray absorptiometry) measured at the start and end of a rugby preseason ∼14 weeks later. There was no statistically significant difference in RMR over the preseason period (baseline 2389 ± 263 kcal·day−1 post 2373 ± 270 kcal·day−1) despite a significant increase in lean mass of +2.0 ± 1.6 kg (P < 0.01) and non‐significant loss of fat mass. The change in RMR was non‐significant and non‐meaningful; thus, this study contradicts the commonly held anecdotal perception that an increase in skeletal muscle mass will result in a significant increase in metabolic rate and daily energy needs. Conventional prediction equations generally under‐estimated rugby athletes’ measured RMR, and may be problematic for identifying low energy availability, and thus updated population‐specific prediction equations may be warranted to inform practice.
How performance analysis of elite long jumping can inform representative training design through identification of key constraints on competitive behaviours
Authors: McCosker Chris , Renshaw Ian , Greenwood Daniel , Davids Keith , Gosden Edward 
Published: January 2019

AbstractAnalysing performance in competitive environments enables identification of key constraints which shape behaviours, supporting designs of more representative training and learning environments. In this study, competitive performance of 244 elite level jumpers (male and female) was analysed to identify the impact of candidate individual, environmental and task constraints on performance outcomes. Findings suggested that key constraints shaping behaviours in long jumping were related to: individuals (e.g. particularly intended performance goals of athletes and their impact on future jump performance); performance environments (e.g. strength and direction of wind) and tasks (e.g. requirement for front foot to be behind foul line at take‐off board to avoid a foul jump). Results revealed the interconnectedness of competitive performance, highlighting that each jump should not be viewed as a behaviour in isolation, but rather as part of a complex system of connected performance events which contribute to achievement of competitive outcomes. These findings highlight the potential nature of the contribution of performance analysis in competitive performance contexts. They suggest how practitioners could design better training tasks, based on key ecological constraints of competition, to provide athletes with opportunities to explore and exploit functional intentions and movement solutions high in contextual specificity.
Graph- and rule-based learning algorithms: a comprehensive review of their applications for cancer type classification and prognosis using genomic data
Authors: Mallik Saurav , Zhao Zhongming 
Published: January 2019

AbstractCancer is well recognized as a complex disease with dysregulated molecular networks or modules. Graph- and rule-based analytics have been applied extensively for cancer classification as well as prognosis using large genomic and other data over the past decade. This article provides a comprehensive review of various graph- and rule-based machine learning algorithms that have been applied to numerous genomics data to determine the cancer-specific gene modules, identify gene signature-based classifiers and carry out other related objectives of potential therapeutic value. This review focuses mainly on the methodological design and features of these algorithms to facilitate the application of these graph- and rule-based analytical approaches for cancer classification and prognosis. Based on the type of data integration, we divided all the algorithms into three categories: model-based integration, pre-processing integration and post-processing integration. Each category is further divided into four sub-categories (supervised, unsupervised, semi-supervised and survival-driven learning analyses) based on learning style. Therefore, a total of 11 categories of methods are summarized with their inputs, objectives and description, advantages and potential limitations. Next, we briefly demonstrate well-known and most recently developed algorithms for each sub-category along with salient information, such as data profiles, statistical or feature selection methods and outputs. Finally, we summarize the appropriate use and efficiency of all categories of graph- and rule mining-based learning methods when input data and specific objective are given. This review aims to help readers to select and use the appropriate algorithms for cancer classification and prognosis study.
Identifying residues that determine palmitoylation using association rule mining
Authors: Kumari Bandana , Kumar Ravindra , Kumar Manish 
Published: January 2019

Abstract

Motivation
In eukaryotes, palmitoylation drives several essential cellular mechanisms like protein sorting, protein stability and protein–protein interaction. Several amino acids namely Cys, Gly, Ser, Thr and Lys undergo palmitoylation. But very little is known about the amino acid patterns that promote palmitoylation.

Results
We deduced presence of statistically significant amino acids around palmitoylation sites and their association with different palmitoylated residues i.e. Cys, Gly and Ser. The results suggest that palmitoylation, irrespective of its target residue, generally occurs at sites where Cys, Leu, Lys, Arg, Ser and Met are abundant. Furthermore, functional properties of the three types of palmitoylated proteins were compared. We observed similar functional behavior of Cys and Gly palmitoylated proteins but proteins with Ser palmitoylation showed distinctiveness from remaining two. Motif-wise functional conservation was also observed in Cys palmitoylated proteins. We also did functional annotation of predicted human palmitoylome.

Supplementary information
Supplementary data are available at Bioinformatics online.
CluMSID: an R package for similarity-based clustering of tandem mass spectra to aid feature annotation in metabolomics
Authors: Depke Tobias , Franke Raimo , Brönstrup Mark 
Published: January 2019

Abstract

Summary
Compound identification is one of the most eminent challenges in the untargeted analysis of complex mixtures of small molecules by mass spectrometry. Similarity of tandem mass spectra can provide valuable information on putative structural similarities between known and unknown analytes and hence aids feature identification in the bioanalytical sciences. We have developed CluMSID (Clustering of MS2 spectra for metabolite identification), an R package that enables researchers to make use of tandem mass spectra and neutral loss pattern similarities as a part of their metabolite annotation workflow. CluMSID offers functions for all analysis steps from import of raw data to data mining by unsupervised multivariate methods along with respective (interactive) visualizations. A detailed tutorial with example data is provided as supplementary information.

Availability and implementation
CluMSID is available as R package from https://github.com/tdepke/CluMSID/and from https://bioconductor.org/packages/CluMSID/.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Large-Scale Semantic Analysis of Verbal Fluency Across the Aging Spectrum: Data From the Canadian Longitudinal Study on Aging
Authors: Taler Vanessa , Johns Brendan T , Jones Michael N 
Published: January 2019

Abstract

Objectives
The present study aimed to characterize changes in verbal fluency performance across the lifespan using data from the Canadian Longitudinal Study on Aging (CLSA).

Methods
We examined verbal fluency performance in a large sample of adults aged 45–85 (n = 12,686). Data are from the Tracking cohort of the CLSA. Participants completed a computer-assisted telephone interview that included an animal fluency task, in which they were asked to name as many animals as they could in 1 min. We employed a computational modeling approach to examine the factors driving performance on this task.

Results
We found that the sequence of items produced was best predicted by their semantic neighborhood, and that pairwise similarity accounted for most of the variance in participant analyses. Moreover, the total number of items produced declined slightly with age, and older participants produced items of higher frequency and denser semantic neighborhood than younger adults.

Discussion
These findings indicate subtle changes in the way people perform this task as they age. The use of computational models allowed for a large increase in the amount of variance accounted for in this data set over standard assessment types, providing important theoretical insights into the aging process.
The Local Structure of Generalized Contact Bundles
Authors: Schnitzer Jonas , Vitagliano Luca 
Published: January 2019

AbstractGeneralized contact bundles are odd-dimensional analogues of generalized complex manifolds. They have been introduced recently and very little is known about them. In this paper we study their local structure. Specifically, we prove a local splitting theorem similar to those appearing in Poisson geometry. In particular, in a neighborhood of a regular point, a generalized contact bundle is either the product of a contact and a complex manifold or the product of a symplectic manifold and a manifold equipped with an integrable complex structure on the gauge algebroid of the trivial line bundle.
Utility and the Pleasures of Musical Formalism: Edmund Gurney, Liberal Individualism, and Musical Beauty as ‘Ultimate’ Value
Authors: Collins Sarah 
Published: January 2019

Abstract
Most contemporary assessments of Edmund Gurney’s musical thinking rely solely on his influential book The Power of Sound (1880), yet much of the work that appeared in this book was initially published in essay form in the liberal press, appearing alongside discussions of politics, economics, moral philosophy, and psychology. With this broader frame in mind, this article investigates the relationship between Gurney’s musical thinking and the traditions of utilitarianism, political economy, and liberalism through his association with Henry Sidgwick’s circle. It argues that one of the central tenets of Gurney’s musical formalism—namely the idea that there is an irreducibly ‘musical’ form of beauty—may be construed in relation to ‘liberal individualism’ as it was framed by the utilitarian liberals with whom he associated, who attempted to combine the cultivation of disinterestedness with the pursuit of pleasure as a means to attaining a balance between self-interest and the common good.