bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathogen acquisition in patients with cystic fibrosis receiving ivacaftor or lumacaftor/ivacaftor
Authors: Singh Sachinkumar B. , McLearn‐Montz Amanda J. , Milavetz Francesca , Gates Levi K. , Fox Christopher , Murry Logan T. , Sabus Ashley , Porterfield Harry S. , Fischer Anthony J. 
Published: April 2019

AbstractBackgroundThe cystic fibrosis transmembrane conductance regulator (CFTR) modulators ivacaftor and lumacaftor/ivacaftor improve the status of existing infections in patients with cystic fibrosis (CF). It is unknown how well these drugs protect patients against incident infections. We hypothesized that CFTR modulator treatment would decrease new infections with Pseudomonas aeruginosa or Staphylococcus aureus.MethodsWe retrospectively studied a single‐center cohort of patients with CF during two time periods (2008‐2011, Era 1) and (2012‐2015, Era 2) based on the January 2012 approval of ivacaftor. Using Kaplan–Meier analysis, we compared the time to any new infection with P. aeruginosa, methicillin‐resistant
S. aureus (MRSA), or methicillin‐sensitive
S. aureus (MSSA) that was absent during a 2‐year baseline. We stratified the analysis based on whether patients received ivacaftor or lumacaftor/ivacaftor during Era 2. We used the log‐rank test and considered
P < 0.05 statistically significant.ResultsFor patients receiving ivacaftor or lumacaftor/ivacaftor in Era 2, there was a statistically significant delay in the time to new bacterial acquisition in Era 2 vs. Era 1 (
P = 0.008). For patients who did not receive CFTR modulators, there was a trend toward slower acquisition of new bacterial infections in Era 2 compared to Era 1, but this was not statistically significant (
P = 0.10).ConclusionsPatients receiving ivacaftor or lumacaftor/ivacaftor for CF had significantly delayed acquisition of
P. aeruginosa and
S. aureus after these drugs were released. This method for analyzing incident infections may be useful for future studies of CFTR modulators and bacterial acquisition in CF registry cohorts.
The impact of mannose‐binding lectin polymorphisms on lung function in primary ciliary dyskinesia
Authors: Videbæk Katja , Buchvald Frederik , Holgersen Mathias Gelderman , Henriksen Alison , Eriksson Frank , Garred Peter , Nielsen Kim Gjerum 
Published: April 2019

AbstractObjectivePrimary ciliary dyskinesia (PCD) is a congenital lung disease that leads to recurrent and chronic lung infection. The resulting inflammation causes lung damage and declines in lung function. Mannose‐binding lectin (MBL) is a first line host defense protein of importance for the innate immunity. Polymorphisms in the MBL gene named MBL2 result in unstable and low functional levels MBL proteins. MBL insufficiency is linked to an increased risk of lung infection and to declines in lung function in patients with cystic fibrosis. We investigated whether there is a similar link in patients with PCD.MethodsThis retrospective longitudinal study included 85 patients with PCD. Diagnostics and age at diagnosis were recorded, complete spirometry data starting at diagnosis, and Pseudomonas aeruginosa infection status over the last 2 years were collected, and the patients were grouped according to MBL2 genotype status (MBL2‐sufficient or MBL2‐deficient).ResultsMBL‐deficient patients were diagnosed almost 3 years earlier than MBL‐sufficient patients (median 6.1 vs 8.9 years, P  < 0.05). There were no differences in the first measured spirometry values, but MBL‐deficient patients showed greater declines in forced expiratory volume in one sec (FEV1) than patients with MBL sufficiency (z‐score: −0.049 per year [95% CI, −0.075; −0.021] vs −0.009 per year [95% CI, −0.033; 0.015]; P = 0.023). No differences were found in forced vital capacity (FVC), FEV1/FVC, or infection status.ConclusionMBL‐deficiency, which is associated with MBL2 mutations, was associated with a lower age at diagnosis and with steeper declines in FEV1 in patients with PCD. This suggests that the MBL genotype might be a disease modifier in PCD.
Recent advances in hyperspectral imaging for melanoma detection
Authors: Johansen Thomas Haugland , Møllersen Kajsa , Ortega Samuel , Fabelo Himar , Garcia Aday , Callico Gustavo M. , Godtliebsen Fred 
Published: April 2019

AbstractSkin cancer is one of the most common types of cancer. Skin cancers are classified as nonmelanoma and melanoma, with the first type being the most frequent and the second type being the most deadly. The key to effective treatment of skin cancer is early detection. With the recent increase of computational power, the number of algorithms to detect and classify skin lesions has increased. The overall verdict on systems based on clinical and dermoscopic images captured with conventional RGB (red, green, and blue) cameras is that they do not outperform dermatologists. Computer‐based systems based on conventional RGB images seem to have reached an upper limit in their performance, while emerging technologies such as hyperspectral and multispectral imaging might possibly improve the results. These types of images can explore spectral regions beyond the human eye capabilities. Feature selection and dimensionality reduction are crucial parts of extracting salient information from this type of data. It is necessary to extend current classification methodologies to use all of the spatiospectral information, and deep learning models should be explored since they are capable of learning robust feature detectors from data. There is a lack of large, high‐quality datasets of hyperspectral skin lesion images, and there is a need for tools that can aid with monitoring the evolution of skin lesions over time. To understand the rich information contained in hyperspectral images, further research using data science and statistical methodologies, such as functional data analysis, scale‐space theory, machine learning, and so on, are essential.This article is categorized under:
Applications of Computational Statistics > Health and Medical Data/Informatics
Splitting the affective atom: Divergence of valence and approach-avoidance motivation during a dynamic emotional experience
Authors: Kaczmarek Lukasz D. , Behnke Maciej , Enko Jolanta , Kosakowski Michał , Guzik Przemysław , Hughes Brian M. 
Published: April 2019

AbstractValence and approach-avoidance motivation are two distinct but closely related components of affect. However, little is known about how these two processes evolve and covary in a dynamic affective context. We formulated several hypotheses based on the Motivational Dimensional Model of Affect. We expected that anger would be a unique approach-related rather than avoidance-related negative emotion. We also expected that high-approach positive emotions (e.g., desire) would differ from low-approach positive emotions (e.g., amusement) producing a stronger link between valence and approach-avoidance motivation. We also explored other dynamic properties of discrete emotions such as the difference between approach-avoidance motivation and valence as a marker of balance within affective components. We asked 69 participants to provide continuous ratings of valence and approach-avoidance motivation for eight standardized clips representing different discrete emotions. Using multilevel modeling, we established a significant relationship between valence and approach-avoidance motivation with high-approach emotions producing a stronger link between valence and approach-avoidance motivation compared to neutral states and low-approach emotions. Contrary to expectations, we observed that individuals exhibited an avoidance response during anger elicitation. Finally, we found that awe was a distinct positive emotion where approach motivation dominated over valence. These findings are relevant to the theory and research on diverging processes within the core structure of affect.
GPA: A Microbial Genetic Polymorphisms Assignments Tool in Metagenomic Analysis by Bayesian Estimation
Authors: Li Jiarui , Du Pengcheng , Ye Adam Yongxin , Zhang Yuanyuan , Song Chuan , Zeng Hui , Chen Chen 
Published: April 2019

Abstract
Identifying antimicrobial resistant (AMR) bacteria in metagenomics samples is essential for public health and food safety. Next-generation sequencing (NGS) technology has provided a powerful tool in identifying the genetic variation and constructing the correlations between genotype and phenotype in humans and other species. However, for complex bacterial samples, there lacks a powerful bioinformatic tool to identify genetic polymorphisms or copy number variations (CNVs) for given genes. Here we provide a Bayesian framework for genotype estimation for mixtures of multiple bacteria, named as Genetic Polymorphisms Assignments (GPA). Simulation results showed that GPA has reduced the false discovery rate (FDR) and mean absolute error (MAE) in CNV and single nucleotide variant (SNV) identification. This framework was validated by whole-genome sequencing and Pool-seq data from Klebsiella pneumoniae with multiple bacteria mixture models, and showed the high accuracy in the allele fraction detections of CNVs and SNVs in AMR genes between two populations. The quantitative study on the changes of AMR genes fraction between two samples showed a good consistency with the AMR pattern observed in the individual strains. Also, the framework together with the genome annotation and population comparison tools has been integrated into an application, which could provide a complete solution for AMR gene identification and quantification in unculturable clinical samples. The GPA package is available at https://github.com/IID-DTH/GPA-package.
A ketogenic drink improves brain energy and some measures of cognition in mild cognitive impairment
Authors: Fortier Mélanie , Castellano Christian‐Alexandre , Croteau Etienne , Langlois Francis , Bocti Christian , St‐Pierre Valérie , Vandenberghe Camille , Bernier Michaël , Roy Maggie , Descoteaux Maxime , Whittingstall Kevin , Lepage Martin , Turcotte Éric E. , Fulop Tamas , Cunnane Stephen C. 
Published: April 2019

AbstractIntroductionUnlike for glucose, uptake of the brain's main alternative fuel, ketones, remains normal in mild cognitive impairment (MCI). Ketogenic medium chain triglycerides (kMCTs) could improve cognition in MCI by providing the brain with more fuel.MethodsFifty‐two subjects with MCI were blindly randomized to 30 g/day of kMCT or matching placebo. Brain ketone and glucose metabolism (quantified by positron emission tomography; primary outcome) and cognitive performance (secondary outcome) were assessed at baseline and 6 months later.ResultsBrain ketone metabolism increased by 230% for subjects on the kMCT (P < .001) whereas brain glucose uptake remained unchanged. Measures of episodic memory, language, executive function, and processing speed improved on the kMCT versus baseline. Increased brain ketone uptake was positively related to several cognitive measures. Seventy‐five percent of participants completed the intervention.DiscussionA dose of 30 g/day of kMCT taken for 6 months bypasses a significant part of the brain glucose deficit and improves several cognitive outcomes in MCI.
A dynamical systems view of granular flow: from monoclinal flood waves to roll waves
Authors: Razis Dimitrios , Kanellopoulos Giorgos , van der Weele Ko 
Published: April 2019

On the basis of the Saint-Venant equations for flowing granular matter, we study the various travelling waveforms that are encountered in chute flow for growing Froude number. Generally, for$Fr<2/3$one finds either a uniform flow of constant thickness or a monoclinal flood wave, i.e. a shock structure monotonically connecting a thick region upstream to a shallower region downstream. For$Fr>2/3$both the uniform flow and the monoclinal wave cease to be stable; the flow now organizes itself in the form of a train of roll waves. From the governing Saint-Venant equations we derive a dynamical system that elucidates the transition from monoclinal waves to roll waves. It is found that this transition involves several intermediate stages, including an undular bore that had hitherto not been reported for granular flows.
Drag of a heated sphere at low Reynolds numbers in the absence of buoyancy
Authors: Ganguli Swetava , Lele Sanjiva K. 
Published: April 2019

Fully resolved simulations are used to quantify the effects of heat transfer in the absence of buoyancy on the drag of a spatially fixed heated spherical particle at low Reynolds numbers ($Re$) in the range $10^{-3}\leqslant Re\leqslant 10$ in a variable-property fluid. The case where buoyancy is present is analysed in a subsequent paper. This analysis is carried out without making any assumptions on the amount of heat addition from the sphere and thus encompasses both the heating regime where the Boussinesq approximation holds and the regime where it breaks down. The particle is assumed to have a low Biot number, which means that the particle is uniformly at the same temperature and has no internal temperature gradients. Large deviations in the value of the drag coefficient as the temperature of the sphere increases are observed. When $Re<O(10^{-2})$, these deviations are explained using a low-Mach-number perturbation analysis as irrotational corrections to a Stokes–Oseen base flow. Correlations for the drag and Nusselt number of a heated sphere are proposed for the range of Reynolds numbers $10^{-3}\leqslant Re\leqslant 10$ which fit the computationally obtained values with less than 1 % and 3 % errors, respectively. These correlations can be used in simulations of gas–solid flows where the accuracy of the drag law affects the prediction of the overall flow behaviour. Finally, an analogy to incompressible flow over a modified sphere is demonstrated.
scaling enabled by multiscale wall roughness in Rayleigh–Bénard turbulence
Authors: Zhu Xiaojue , Stevens Richard J. A. M. , Shishkina Olga , Verzicco Roberto , Lohse Detlef 
Published: April 2019

In turbulent Rayleigh–Bénard (RB) convection with regular, mono-scale, surface roughness, the scaling exponent$\unicode[STIX]{x1D6FD}$in the relationship between the Nusselt number$Nu$and the Rayleigh number$Ra$,$Nu\sim Ra^{\unicode[STIX]{x1D6FD}}$can be${\approx}1/2$locally, provided that$Ra$is large enough to ensure that the thermal boundary layer thickness$\unicode[STIX]{x1D706}_{\unicode[STIX]{x1D703}}$is comparable to the roughness height. However, at even larger$Ra$,$\unicode[STIX]{x1D706}_{\unicode[STIX]{x1D703}}$becomes thin enough to follow the irregular surface and$\unicode[STIX]{x1D6FD}$saturates back to the value for smooth walls (Zhuet al.,Phys. Rev. Lett., vol. 119, 2017, 154501). In this paper, we prevent this saturation by employing multiscale roughness. We perform direct numerical simulations of two-dimensional RB convection using an immersed boundary method to capture the rough plates. We find that, for rough boundaries that contain three distinct length scales, a scaling exponent of$\unicode[STIX]{x1D6FD}=0.49\pm 0.02$can be sustained for at least three decades of$Ra$. The physical reason is that the threshold$Ra$at which the scaling exponent$\unicode[STIX]{x1D6FD}$saturates back to the smooth wall value is pushed to larger$Ra$, when the smaller roughness elements fully protrude through the thermal boundary layer. The multiscale roughness employed here may better resemble the irregular surfaces that are encountered in geophysical flows and in some industrial applications.
Effect of background mean flow on PSI of internal wave beams
Authors: Fan Boyu , Akylas T. R. 
Published: April 2019

An asymptotic model is developed for the parametric subharmonic instability (PSI) of finite-width nearly monochromatic internal gravity wave beams in the presence of a background constant horizontal mean flow. The subharmonic perturbations are taken to be short-scale wavepackets that may extract energy via resonant triad interactions while in contact with the underlying beam, and the mean flow is assumed to be small so that its advection effect on the perturbations is as important as dispersion, triad nonlinearity and viscous dissipation. In this ‘distinguished limit’, the perturbation dynamics are governed by the same evolution equations as those derived in Karimi & Akylas (J. Fluid Mech., vol. 757, 2014, pp. 381–402), except for a mean flow term that affects the group velocity of the perturbations and imposes an additional necessary condition for PSI, which stabilizes very short-scale perturbations. As a result, it is possible for a small amount of mean flow to weaken PSI dramatically.
Histoire coloniale. Les tribulations des collections archéologiques de l'Algérie
Authors: Nacéra Benseddik 
Published: April 2019

AbstractFrom the Musée Algérien established at the Louvre in Paris by Captain Delamare, to the Bibliothèque-musée created by A. Berbrugger in 1838 in the former Janissaries barracks in Algiers, to the short-lived Musée Africain, the archaeological collections of Algeria did not have a real museum space until 19 April 1897, when the Musée des Antiquités Algériennes et d'Art Musulman was inaugurated in the Parc de Galland (today the Parc de la Liberté). Independent Algeria placed the museum under the Ministère de l’éducation nationale until 1970, and then it was moved to the Ministère de l'information et de la culture, and the Musée Stéphane Gsell became the Musée National des Antiquités, financially autonomous in 1985 under the Ministère de la culture. Have the true missions of a museum been fulfilled? And what is the situation at the Louvre where only a few ancient Algerian works are now on display?
Variation of Surface Radiocarbon in the North Pacific During Summer Season 2004–2016
Authors: Aramaki T , Nakaoka S , Terao Y , Kushibashi S , Kobayashi T , Osonoi Y , Mukai H , Tohjima Y 
Published: April 2019

ABSTRACTSurface radiocarbon (Δ14C) in the North Pacific has been monitored using a commercial volunteer observation ship since the early 2000s. Here we report the temporal and spatial variations in Δ14C in the summer surface water when the surface ocean is vertically stratified over a 13-yr period, 2004–2016. The long-term Δ14C decreasing trend after the late 1970s in the subtropical region has continued to the present and the rate of decrease of the Kuroshio and Kuroshio Extension, North Pacific and California current areas is calculated to be –3.3, –5.2 and –3.3 ‰/yr, respectively. After 2012 the Δ14C of the Kuroshio and Kuroshio Extension area, however, has remained at an approximately constant value of around 50‰. The result may indicate that subtropical surface Δ14C in the western North Pacific has reached an equilibrium with atmospheric Δ14CO2. The Δ14C in the subarctic region is markedly lower than values in the subtropical region and it seems that the decreasing tendency of surface Δ14C has changed to an increasing tendency after 2010. The results may indicate that bomb-produced 14C, which has accumulated below the mixed layer in the past few decades, has been entrained into the surface layer by deep convection.
The Dynamics of Latin American Agricultural Production Growth, 1950–2008
Authors: Martín-Retortillo Miguel , Pinilla Vicente , Velazco Jackeline , Willebald Henry 
Published: April 2019

AbstractThis article is the first of its kind to offer a quantitative estimation of the evolution of Latin American agricultural production and productivity between 1950 and 2008. It also uncovers the extent to which the increases in production were due to increases in factors of production or to efficiency gains. Our findings reveal that efficiency gains made a rather modest contribution to the substantial increase in production, although their role became increasingly large over time and were highly significant between 1994 and 2008. Capital was the most important productive factor in explaining increases in output.
Influence of electroconvulsive therapy on white matter structure in a diffusion tensor imaging study
Authors: Repple Jonathan , Meinert Susanne , Bollettini Irene , Grotegerd Dominik , Redlich Ronny , Zaremba Dario , Bürger Christian , Förster Katharina , Dohm Katharina , Stahl Felix , Opel Nils , Hahn Tim , Enneking Verena , Leehr Elisabeth J. , Böhnlein Joscha , Leenings Ramona , Kaehler Claas , Emden Daniel , Winter Nils R. , Heindel Walter , Kugel Harald , Bauer Jochen , Arolt Volker , Benedetti Francesco , Dannlowski Udo 
Published: April 2019

AbstractBackgroundElectroconvulsive therapy (ECT) is a fast-acting intervention for major depressive disorder. Previous studies indicated neurotrophic effects following ECT that might contribute to changes in white matter brain structure. We investigated the influence of ECT in a non-randomized prospective study focusing on white matter changes over time.MethodsTwenty-nine severely depressed patients receiving ECT in addition to inpatient treatment, 69 severely depressed patients with inpatient treatment (NON-ECT) and 52 healthy controls (HC) took part in a non-randomized prospective study. Participants were scanned twice, approximately 6 weeks apart, using diffusion tensor imaging, applying tract-based spatial statistics. Additional correlational analyses were conducted in the ECT subsample to investigate the effects of seizure duration and therapeutic response.ResultsMean diffusivity (MD) increased after ECT in the right hemisphere, which was an ECT-group-specific effect. Seizure duration was associated with decreased fractional anisotropy (FA) following ECT. Longitudinal changes in ECT were not associated with therapy response. However, within the ECT group only, baseline FA was positively and MD negatively associated with post-ECT symptomatology.ConclusionOur data suggest that ECT changes white matter integrity, possibly reflecting increased permeability of the blood–brain barrier, resulting in disturbed communication of fibers. Further, baseline diffusion metrics were associated with therapy response. Coherent fiber structure could be a prerequisite for a generalized seizure and inhibitory brain signaling necessary to successfully inhibit increased seizure activity.
School success in childhood and subsequent prodromal symptoms and psychoses in the Northern Finland Birth Cohort 1986
Authors: Lassila M. , Nordström T. , Hurtig T. , Mäki P. , Jääskeläinen E. , Oinas E. , Miettunen J. 
Published: April 2019

AbstractBackgroundLow IQ is a risk factor for psychosis, but the effect of high IQ is more controversial. The aim was to explore the association of childhood school success with prodromal symptoms in adolescence and psychoses in adulthood.MethodsIn the general population-based Northern Finland Birth Cohort 1986 (n= 8 229), we studied the relationship between teacher-assessed learning deficits, special talents and general school success at age 8 years and both prodromal symptoms (PROD-screen) at age 15–16 years and the occurrence of psychoses by age 30 years.ResultsMore prodromal symptoms were experienced by those talented in oral presentation [boys: adjusted odds ratio (OR) 1.49; 95% confidence interval 1.14–1.96; girls: 1.23; 1.00–1.52] or drawing (boys: 1.44; 1.10–1.87). Conversely, being talented in athletics decreased the probability of psychotic-like symptoms (boys: OR 0.72; 0.58–0.90). School success below average predicted less prodromal symptoms with boys (OR 0.68; 0.48–0.97), whereas above-average success predicted more prodromal symptoms with girls (OR 1.22; 1.03–1.44). The occurrence of psychoses was not affected. Learning deficits did not associate with prodromal symptoms or psychoses.ConclusionsLearning deficits in childhood did not increase the risk of prodromal symptoms in adolescence or later psychosis in this large birth cohort. Learning deficits are not always associated with increased risk of psychosis, which might be due to, e.g. special support given in schools. The higher prevalence of prodromal symptoms in talented children may reflect a different kind of relationship of school success with prodromal symptoms compared to full psychoses.