bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frequency and longitudinal clinical outcomes of Alzheimer's AT(N) biomarker profiles: A longitudinal study
Authors: Yu Jin‐Tai , Li Jie‐Qiong , Suckling John , Feng Lei , Pan An , Wang Yan‐Jiang , Song Bo , Zhu Shan‐Liang , Li De‐Hu , Wang Hui‐Fu , Tan Chen‐Chen , Dong Qiang , Tan Lan , Mok Vincent , Aisen Paul S. , Weiner Michael M. ,   Alzheimer's Disease Neuroimaging Initiative
Published: August 2019

AbstractIntroductionWe aimed to estimate the frequency of each AT(N) (β‐amyloid deposition [A], pathologic tau [T], and neurodegeneration [N]) profile in different clinical diagnosis groups and to describe the longitudinal change in clinical outcomes of individuals in each group.MethodsLongitudinal change in clinical outcomes and conversion risk of AT(N) profiles are assessed using linear mixed‐effects models and multivariate Cox proportional‐hazard models, respectively.ResultsParticipants with A+T+N+ showed faster clinical progression than those with A−T−N− and A+T±N−. Compared with A−T−N−, participants with A+T+N± had an increased risk of conversion from cognitively normal (CN) to incident prodromal stage of Alzheimer's disease (AD), and from MCI to AD dementia. A+T+N+ showed an increased conversion risk when compared with A+T±N−.DiscussionThe 2018 research framework may provide prognostic information of clinical change and progression. It may also be useful for targeted recruitment of participants with AD into clinical trials.
The structure of a turbulent line fountain
Authors: Hunt Gary R. , Debugne Antoine L. R. , Ciriello Francesco 
Published: August 2019

Line fountains form when heavy miscible fluid is ejected steadily upwards as a jet from a high-aspect-ratio rectangular slot, of length $L$ and half-width $b_{0}$, into lighter quiescent surroundings. Viewed along the slot from one end, previous observations reveal that the ejected fluid mixes with the environment and reaches a peak height before partially collapsing back downward under gravity to form a fountain whose top thereafter fluctuates vertically about a mean height. While the motion as perceived from this single view has provided insights that have successfully guided theoretical predictions for the initial rise height, until now a wider understanding of line fountains, and corresponding predictive capability, has been limited to this single prediction due to a lack of any other observational data. Indeed, the general behaviour of line fountains, including the structure internally and along the spanwise length $L$ of the slot, has not been reported previously. To address this, flow visualisations and comprehensive measurements of saline fountains in an aqueous environment are presented here that reveal their complex overall structure and behaviours. After establishing the uniformity of the source conditions from slots of aspect ratio $600:1$ and $300:1$, we first show that double-averaged (spanwise and time) rise heights $\overline{\overline{z}}_{v}/b_{0}$ scale on $Fr_{0}^{4/3}$, $Fr_{0}$ being the source Froude number, with vertical fluctuations being circa 20 % of these heights. Then, simultaneously interrogating the flow as viewed from above and from the side onto the spanwise dimension, we identify three distinct patterns of behaviour. Instrumental to distinguishing these behaviours were the contrasting signatures we observed in the time series of rise height departures from the mean which led us to the following classification: (i) non-uniform flapping for $0.05\lesssim \overline{\overline{z}}_{v}/L\lesssim 0.30$, in which the lateral motion of the fountain takes the form of an oscillatory wave with a wavelength of $2L/3$ (approx.); (ii) uniform flapping for $0.30\lesssim \overline{\overline{z}}_{v}/L\lesssim 0.45$, in which the entire fountain sways to the left and then to the right side of the slot; and (iii) disorganised flapping for $\overline{\overline{z}}_{v}/L\gtrsim 0.45$. Regarding the internal structure, we show that unlike a classic round fountain, eddying structures comparable in scale with the rise height form towards the top of the fountain, and the counterflow forms predominantly to one side of the jet. We then identify the single dominant mechanism driving the flapping motions, successfully linking the wave-like behaviour observed along the span to the internal structure and vertical oscillations. Quantifying the oscillatory motions, both the vertical and flapping frequencies scale as $Fr_{0}^{-2}$, and we demonstrate and explain a robust coupling between these frequencies that follows a ratio of 2:1.
Inferring broken detailed balance in the absence of observable currents
Authors: Martínez Ignacio A. , Bisker Gili , Horowitz Jordan M. , Parrondo Juan M. R. 
Published: August 2019

AbstractIdentifying dissipation is essential for understanding the physical mechanisms underlying nonequilibrium processes. In living systems, for example, the dissipation is directly related to the hydrolysis of fuel molecules such as adenosine triphosphate (ATP). Nevertheless, detecting broken time-reversal symmetry, which is the hallmark of dissipative processes, remains a challenge in the absence of observable directed motion, flows, or fluxes. Furthermore, quantifying the entropy production in a complex system requires detailed information about its dynamics and internal degrees of freedom. Here we introduce a novel approach to detect time irreversibility and estimate the entropy production from time-series measurements, even in the absence of observable currents. We apply our technique to two different physical systems, namely, a partially hidden network and a molecular motor. Our method does not require complete information about the system dynamics and thus provides a new tool for studying nonequilibrium phenomena.
Action boosts episodic memory encoding in humans via engagement of a noradrenergic system
Authors: Yebra Mar , Galarza-Vallejo Ana , Soto-Leon Vanesa , Gonzalez-Rosa Javier J. , de Berker Archy O. , Bestmann Sven , Oliviero Antonio , Kroes Marijn C. W. , Strange Bryan A. 
Published: August 2019

AbstractWe are constantly interacting with our environment whilst we encode memories. However, how actions influence memory formation remains poorly understood. Goal-directed movement engages the locus coeruleus (LC), the main source of noradrenaline in the brain. Noradrenaline is also known to enhance episodic encoding, suggesting that action could improve memory via LC engagement. Here we demonstrate, across seven experiments, that action (Go-response) enhances episodic encoding for stimuli unrelated to the action itself, compared to action inhibition (NoGo). Functional magnetic resonance imaging, and pupil diameter as a proxy measure for LC-noradrenaline transmission, indicate increased encoding-related LC activity during action. A final experiment, replicated in two independent samples, confirmed a novel prediction derived from these data that emotionally aversive stimuli, which recruit the noradrenergic system, modulate the mnemonic advantage conferred by Go-responses relative to neutral stimuli. We therefore provide converging evidence that action boosts episodic memory encoding via a noradrenergic mechanism.
Histone chaperone exploits intrinsic disorder to switch acetylation specificity
Authors: Danilenko Nataliya , Lercher Lukas , Kirkpatrick John , Gabel Frank , Codutti Luca , Carlomagno Teresa 
Published: August 2019

AbstractHistones, the principal protein components of chromatin, contain long disordered sequences, which are extensively post-translationally modified. Although histone chaperones are known to control both the activity and specificity of histone-modifying enzymes, the mechanisms promoting modification of highly disordered substrates, such as lysine-acetylation within the N-terminal tail of histone H3, are not understood. Here, to understand how histone chaperones Asf1 and Vps75 together promote H3 K9-acetylation, we establish the solution structural model of the acetyltransferase Rtt109 in complex with Asf1 and Vps75 and the histone dimer H3:H4. We show that Vps75 promotes K9-acetylation by engaging the H3 N-terminal tail in fuzzy electrostatic interactions with its disordered C-terminal domain, thereby confining the H3 tail to a wide central cavity faced by the Rtt109 active site. These fuzzy interactions between disordered domains achieve localization of lysine residues in the H3 tail to the catalytic site with minimal loss of entropy, and may represent a common mechanism of enzymatic reactions involving highly disordered substrates.
Subseafloor life and its biogeochemical impacts
Authors: D’Hondt Steven , Pockalny Robert , Fulfer Victoria M. , Spivack Arthur J. 
Published: August 2019

AbstractSubseafloor microbial activities are central to Earth’s biogeochemical cycles. They control Earth’s surface oxidation and major aspects of ocean chemistry. They affect climate on long timescales and play major roles in forming and destroying economic resources. In this review, we evaluate present understanding of subseafloor microbes and their activities, identify research gaps, and recommend approaches to filling those gaps. Our synthesis suggests that chemical diffusion rates and reaction affinities play a primary role in controlling rates of subseafloor activities. Fundamental aspects of subseafloor communities, including features that enable their persistence at low catabolic rates for millions of years, remain unknown.
Understanding hydrogen-bonding structures of molecular crystals via electron and NMR nanocrystallography
Authors: Guzmán-Afonso Candelaria , Hong You-lee , Colaux Henri , Iijima Hirofumi , Saitow Akihiro , Fukumura Takuma , Aoyama Yoshitaka , Motoki Souhei , Oikawa Tetsuo , Yamazaki Toshio , Yonekura Koji , Nishiyama Yusuke 
Published: August 2019

AbstractUnderstanding hydrogen-bonding networks in nanocrystals and microcrystals that are too small for X-ray diffractometry is a challenge. Although electron diffraction (ED) or electron 3D crystallography are applicable to determining the structures of such nanocrystals owing to their strong scattering power, these techniques still lead to ambiguities in the hydrogen atom positions and misassignments of atoms with similar atomic numbers such as carbon, nitrogen, and oxygen. Here, we propose a technique combining ED, solid-state NMR (SSNMR), and first-principles quantum calculations to overcome these limitations. The rotational ED method is first used to determine the positions of the non-hydrogen atoms, and SSNMR is then applied to ascertain the hydrogen atom positions and assign the carbon, nitrogen, and oxygen atoms via the NMR signals for 1H, 13C, 14N, and 15N with the aid of quantum computations. This approach elucidates the hydrogen-bonding networks in l-histidine and cimetidine form B whose structure was previously unknown.
Programmable four-photon graph states on a silicon chip
Authors: Adcock Jeremy C. , Vigliar Caterina , Santagati Raffaele , Silverstone Joshua W. , Thompson Mark G. 
Published: August 2019

AbstractFuture quantum computers require a scalable architecture on a scalable technology—one that supports millions of high-performance components. Measurement-based protocols, using graph states, represent the state of the art in architectures for optical quantum computing. Silicon photonics technology offers enormous scale and proven quantum optical functionality. Here we produce and encode photonic graph states on a mass-manufactured chip, using four on-chip-generated photons. We programmably generate all types of four-photon graph state, implementing a basic measurement-based protocol, and measure high-visibility heralded interference of the chip’s four photons. We develop a model of the device and bound the dominant sources of error using Bayesian inference. The combination of measurement-based quantum computation, silicon photonics technology, and on-chip multi-pair sources will be a useful one for future scalable quantum information processing with photons.
A putative enoyl-CoA hydratase contributes to biofilm formation and the antibiotic tolerance of Achromobacter xylosoxidans
Authors: Cameron Lydia C. , Bonis Benjamin , Phan Chi Q. , Kent Leslie A. , Lee Alysha K. , Hunter Ryan C. 
Published: August 2019

AbstractAchromobacter xylosoxidans has attracted increasing attention as an emerging pathogen in patients with cystic fibrosis. Intrinsic resistance to several classes of antimicrobials and the ability to form robust biofilms in vivo contribute to the clinical manifestations of persistent A. xylosoxidans infection. Still, much of A. xylosoxidans biofilm formation remains uncharacterized due to the scarcity of existing genetic tools. Here we demonstrate a promising genetic system for use in A. xylosoxidans; generating a transposon mutant library which was then used to identify genes involved in biofilm development in vitro. We further described the effects of one of the genes found in the mutagenesis screen, encoding a putative enoyl-CoA hydratase, on biofilm structure and tolerance to antimicrobials. Through additional analysis, we find that a fatty acid signaling compound is essential to A. xylosoxidans biofilm ultrastructure and maintenance. This work describes methods for the genetic manipulation of A. xylosoxidans and demonstrated their use to improve our understanding of A. xylosoxidans pathophysiology.
Field testing of a lightweight, inexpensive, and customisable 3D-printed mosquito light trap in the UK
Authors: Hoshi Tomonori , Brugman Victor A. , Sato Shigeharu , Ant Thomas , Tojo Bumpei , Masuda Gaku , Kaneko Satoshi , Moji Kazuhiko , Medlock Jolyon M. , Logan James G. 
Published: August 2019

AbstractMosquito surveillance is a fundamental component of planning and evaluating vector control programmes. However, logistical and cost barriers can hinder the implementation of surveillance, particularly in vector-borne disease-endemic areas and in outbreak scenarios in remote areas where the need is often most urgent. The increasing availability and reduced cost of 3D printing technology offers an innovative approach to overcoming these challenges. In this study, we assessed the field performance of a novel, lightweight 3D-printed mosquito light trap baited with carbon dioxide (CO2) in comparison with two gold-standard traps, the Centers for Disease Control and Prevention (CDC) light trap baited with CO2, and the BG Sentinel 2 trap with BG-Lure and CO2. Traps were run for 12 nights in a Latin square design at Rainham Marshes, Essex, UK in September 2018. The 3D-printed trap showed equivalent catch rates to the two commercially available traps. The 3D-printed trap designs are distributed free of charge in this article with the aim of assisting entomological field studies across the world.
Biological and environmental drivers of trophic ecology in marine fishes - a global perspective
Authors: Hayden B. , Palomares M. L. D. , Smith B. E. , Poelen J. H. 
Published: August 2019

AbstractDietary niche width and trophic position are key functional traits describing a consumer’s trophic ecology and the role it plays in a community. However, our understanding of the environmental and biological drivers of both traits is predominantly derived from theory or geographically restricted studies and lacks a broad empirical evaluation. We calculated the dietary niche width and trophic position of 2,938 marine fishes and examined the relationship of both traits with species’ maximum length and geographic range, in addition to species richness, productivity, seasonality and water temperature within their geographic range. We used Generalized Additive Models to assess these relationships across seven distinct marine habitat types. Fishes in reef associated habitats typically had a smaller dietary niche width and foraged at a lower trophic position than those in pelagic or demersal regions. Species richness was negatively related to dietary niche width in each habitat. Species range and maximum length both displayed positive associations with dietary niche width. Trophic position was primarily related to species maximum length but also displayed a non-linear relationship with dietary niche width, whereby species of an intermediate trophic position (3–4) had a higher dietary niche width than obligate herbivores or piscivores. Our results indicate that trophic ecology of fishes is driven by several interlinked factors. Although size is a strong predictor of trophic position and the diversity of preys a species can consume, dietary niche width of fishes is also related to prey and competitor richness suggesting that, at a local level, consumer trophic ecology is determined by a trade-off between environmental drivers and biological traits.
The core microbiome of sessile ciliate Stentor coeruleus is not shaped by the environment
Authors: Lanzoni Olivia , Plotnikov Andrey , Khlopko Yuri , Munz Giulio , Petroni Giulio , Potekhin Alexey 
Published: August 2019

AbstractMicrobiomes of multicellular organisms are one of the hottest topics in microbiology and physiology, while only few studies addressed bacterial communities associated with protists. Protists are widespread in all environments and can be colonized by plethora of different bacteria, including also human pathogens. The aim of this study was to characterize the prokaryotic community associated with the sessile ciliate Stentor coeruleus. 16S rRNA gene metabarcoding was performed on single cells of S. coeruleus and on their environment, water from the sewage stream. Our results showed that the prokaryotic community composition differed significantly between Stentor cells and their environment. The core microbiome common for all ciliate specimens analyzed could be defined, and it was composed mainly by representatives of bacterial genera which include also potential human pathogens and commensals, such as Neisseria, Streptococcus, Capnocytophaga, Porphyromonas. Numerous 16S rRNA gene contigs belonged to endosymbiont “Candidatus Megaira polyxenophila”. Our data suggest that each ciliate cell can be considered as an ecological microniche harboring diverse prokaryotic organisms. Possible benefits for persistence and transmission in nature for bacteria associated with protists are discussed. Our results support the hypothesis that ciliates attract potentially pathogenic bacteria and play the role of natural reservoirs for them.
Machine Learning Allows Calibration Models to Predict Trace Element Concentration in Soils with Generalized LIBS Spectra
Authors: Sun Chen , Tian Ye , Gao Liang , Niu Yishuai , Zhang Tianlong , Li Hua , Zhang Yuqing , Yue Zengqi , Delepine-Gilon Nicole , Yu Jin 
Published: August 2019

AbstractDetermination of trace elements in soils with laser-induced breakdown spectroscopy is significantly affected by the matrix effect, due to large variations in chemical composition and physical property of different soils. Spectroscopic data treatment with univariate models often leads to poor analytical performances. We have developed in this work a multivariate model using machine learning algorithms based on a back-propagation neural network (BPNN). Beyond the classical chemometry approach, machine learning, with tremendous progresses the last years especially for image processing, is offering an ensemble of powerful and constantly renewed algorithms and tools efficient for the different steps in the construction of a spectroscopic data treatment model, including feature selection and neural network training. Considering the matrix effect as the focus of this work, we have developed the concept of generalized spectrum, where the information about the soil matrix is explicitly included in the input vector of the model as an additional dimension. After a brief presentation of the experimental procedure and the results of regression with a univariate model, the development of the multivariate model will be described in detail together with its analytical performances, showing average relative errors of calibration (REC) and of prediction (REP) within the range of 5–6%.
Serum amino acid concentrations and clinical outcomes in smokers: SPIROMICS metabolomics study
Authors: Labaki Wassim W. , Gu Tian , Murray Susan , Curtis Jeffrey L. , Yeomans Larisa , Bowler Russell P. , Barr R. Graham , Comellas Alejandro P. , Hansel Nadia N. , Cooper Christopher B. , Barjaktarevic Igor , Kanner Richard E. , Paine Robert , McDonald Merry-Lynn N. , Krishnan Jerry A. , Peters Stephen P. , Woodruff Prescott G. , O’Neal Wanda K. , Diao Wenqi , He Bei , Martinez Fernando J. , Standiford Theodore J. , Stringer Kathleen A. , Han MeiLan K. 
Published: August 2019

AbstractMetabolomics is an emerging science that can inform pathogenic mechanisms behind clinical phenotypes in COPD. We aimed to understand disturbances in the serum metabolome associated with respiratory outcomes in ever-smokers from the SPIROMICS cohort. We measured 27 serum metabolites, mostly amino acids, by1H-nuclear magnetic resonance spectroscopy in 157 white ever-smokers with and without COPD. We tested the association between log-transformed metabolite concentrations and one-year incidence of respiratory exacerbations after adjusting for age, sex, current smoking, body mass index, diabetes, inhaled or oral corticosteroid use, study site and clinical predictors of exacerbations, including FEV1% predicted and history of exacerbations. The mean age of participants was 53.7 years and 58% had COPD. Lower concentrations of serum amino acids were independently associated with 1-year incidence of respiratory exacerbations, including tryptophan (β = −4.1, 95% CI [−7.0; −1.1], p = 0.007) and the branched-chain amino acids (leucine: β = −6.0, 95% CI [−9.5; −2.4], p = 0.001; isoleucine: β = −5.2, 95% CI [−8.6; −1.8], p = 0.003; valine: β = −4.1, 95% CI [−6.9; −1.4], p = 0.003). Tryptophan concentration was inversely associated with the blood neutrophil-to-lymphocyte ratio (p = 0.03) and the BODE index (p = 0.03). Reduced serum amino acid concentrations in ever-smokers with and without COPD are associated with an increased incidence of respiratory exacerbations.
Estimating ruminal crude protein degradation from beef cattle feedstuff
Authors: Liu Chang , Li Deyong , Chen Wanbao , Li Yan , Wu Hao , Meng Qingxiang , Zhou Zhenming 
Published: August 2019

AbstractWe estimated ruminal crude protein degradation of twelve feedstuffs commonly used in China using in vitro and in vivo methods. The in vivo net protein utilization (NPU) levels of corn, sorghum, barley, wheat, Chinese wild rye grass, corn stalk, rice straw, soybean straw, soybean meal, distillers’ dried grains with solubles (DDGS), Brewers’ spent grains, and sunflower meal were 52.57, 49.68, 65.38, 72.58, 82.41, 72.26, 68.57, 76.95, 54.75, 56.27, 29.03 and 41.88%, respectively. The linear regression between NH3-N incorporated into microbial proteins and gas production after incubation (6, 12, and 24 h) was significant (r = 0.9948 and P < 0.001, r = 0.9874 and P < 0.01, and r = 0.9912 and P < 0.01, respectively). Based on the linear regression equations, we estimated in vitro protein degradability (IVPD) and generated the regression equations between IVPD and NPU. The linear regression equations between IVPD and NPU after 6 h incubation in the energy, protein, and roughage feed groups were Y = 0.5633X + 33.20 (R2 = 0.8517, P < 0.05), Y = 0.8482X+ 34.81 (R2 = 0.8650, P < 0.05), and Y = 1.6295X − 17.70 (R2 = 0.909, P < 0.05), respectively. The in vitro gas production method is useful for the determination of protein degradation in feedstuffs.