bluuebunny/crossref_metadata_2025_split huggingface dataset:
The world’s largest breeding colony of Leach’s Storm-petrel Hydrobates leucorhous has declined
Authors: WILHELM SABINA I. , HEDD APRIL , ROBERTSON GREGORY J. , MAILHIOT JOSHUA , REGULAR PAUL M. , RYAN PIERRE C. , ELLIOT RICHARD D. 
Published: July 2019

SummaryDespite the global significance of the Leach’s Storm-petrel Hydrobates leucorhous colony on Baccalieu Island, Newfoundland and Labrador, Canada, the estimate of 3.36 million breeding pairs reported for 1984 by Sklepkovych and Montevecchi stands as the single published population estimate for the world’s largest colony. This study increases knowledge of this population by analysing data from additional independent surveys conducted in 1984 and 1985, and by updating the population status with a survey conducted in 2013. Population estimates were derived by extrapolating occupied burrow densities to the estimated occupied area of four main habitat types (heath, forest, grass and fern), which in turn were based on proportions of habitats observed in plots (1984 and 1985) or by using a Geographic Information System approach (2013). Based on these surveys, the Leach’s Storm-petrel breeding population size on Baccalieu Island was estimated at 5.12 ± 0.73 (SE) and 4.60 ± 0.42 (SE) million pairs in 1984 and 1985 respectively, representing estimates 37–51% greater than the original 1984 survey. While discrepancies among these estimates were largely driven by the way occupied areas were estimated, our study confirms that Baccalieu Island hosts the largest Leach’s Storm-petrel colony in the world. Results from the 2013 survey estimate the current breeding Leach’s Storm-petrel population at 1.95 ± 0.14 (SE) million pairs, representing a 42% decline over 29 years (-1.4% per year), relative to the original published estimate of 3.36 ± 0.12 (SE) million pairs. The most prominent change has occurred in the density of storm-petrel burrows found in forest habitat which dropped by 70% despite forest remaining the second most abundant habitat available to nesting storm-petrels on Baccalieu Island. The cause of this decline remains unknown and is likely multi-faceted. Future research focusing on demographic studies is required to understand what is driving the population decline of this internationally important colony.
Effect of the Mediterranean diet in combination with exercise on metabolic syndrome parameters: 1-year randomized controlled trial
Authors: Pavić Eva , Hadžiabdić Maja Ortner , Mucalo Iva , Martinis Irena , Romić Željko , Božikov Velimir , Rahelić Dario 
Published: July 2019

Abstract. This work aimed to evaluate and compare the benefits of the energy restricted Mediterranean diet (MD) and Standard hypolipemic diet (SHD) accompanied by exercise on metabolic syndrome parameters. A 12-month, randomized, single-blinded, diet-controlled study was conducted on 124 obese participants in the University Hospital Dubrava. Participants were assigned to the MD (n = 63) or the SHD (n = 61) and received the same amount of nutritional education and guidance on physical activity. The completion rate was 67.7 %. Both diets produced significant beneficial changes in body weight and waist circumference (P < 0.001 for MD and SHD). Compared with the SHD, HDL cholesterol increased (P = 0.031) and systolic blood pressure (SBP) decreased (P = 0.020) in the MD group. Fasting plasma glucose decreased significantly in both diet groups (P < 0.001 for MD; P = 0.026 for SHD). Although both diets accompanied by physical activity yielded similar weight reduction results, adherence to the MD was associated with more prominent reduction of the MetS components, namely HDL level elevation and SBP reduction.
On Estimating the Cross Correlation and Least Squares Fit of One Data Set to Another With Time Shift
Authors: Chao B. F. , Chung C. H. 
Published: July 2019

AbstractEstimating the cross correlation between two data sets and the least squares fit of one data set to another shares closely related numerical procedures. Here we revisit the standard procedure of estimating the cross‐correlation function and cross‐coherence spectrum between two data sets. We attend to and run extensive Monte Carlo simulation to gain insights towards their statistical assessment with respect to the confidence level and degree of freedom which is often overlooked in published literature. We then point out the fallacy, both physically and numerically, of the estimation scheme proposed and practiced by Phillips et al. (2012, https://doi.org/10.1029/2012GL052495) that utilized Hilbert transform for least squares fitting of one time series to another with time shift (which was adopted in subsequent published work). We run Monte Carlo experiments to demonstrate that fallacy and the fact that the Phillips et al.'s scheme can only work for fitting of one trivial single‐period sinusoid while fails in any other circumstances.
Uncoupling of Seasonal Variations Between Phytoplankton Chlorophyll a and Production in the East China Sea
Authors: Liu Xin , Laws Edward A. , Xie Yuyuan , Wang Lei , Lin Lizhen , Huang Bangqin 
Published: July 2019

AbstractPhytoplankton chlorophyll a (Chla), primary production (PP), and nutrient uptake rates are fundamental and important parameters in marine biogeochemical studies. However, the relationships between them are associated with much uncertainty that reflects gaps in basic understanding of ecosystem dynamic. In this study, we simultaneously measured PP and nitrate assimilation (NA) along with estimated concentrations of nutrients, particulate organic carbon concentrations, phytoplankton Chla, pigments, and carbon biomass in the dynamic shelf ecosystems of the East China Sea (ECS) on four cruises during different seasons. There were large spatial gradients of these parameters, and seasonal patterns of phytoplankton Chla and PP varied between water masses. The results of this study and previous work indicated that seasonal variations of Chla and PP were similar in coastal waters but opposite in off‐shelf waters. During summer in off‐shelf waters, there were patches of high PP and NA associated with low Chla concentrations; this pattern was reversed in the winter. We suggest that there is a global tendency for PP and Chla patterns to be out of phase. This asynchrony is reflected mainly in the seasonal variations of C:Chla ratios driven by the combined influences of light, temperature, and nutrients. Stronger grazing pressure by microzooplankton in summer likely contributed to the high production but low biomass in the ECS. The significant correlation between PP and NA suggested that variations of PP in the ECS were driven largely by nitrate uptake, which may be inhibited by high ammonium concentrations in the Changjiang River plume.
Irrational behavior in C. elegans arises from asymmetric modulatory effects within single sensory neurons
Authors: Iwanir Shachar , Ruach Rotem , Itskovits Eyal , Pritz Christian O. , Bokman Eduard , Zaslaver Alon 
Published: July 2019

AbstractC. elegansworms exhibit a natural chemotaxis towards food cues. This provides a potential platform to study the interactions between stimulus valence and innate behavioral preferences. Here we perform a comprehensive set of choice assays to measure worms’ relative preference towards various attractants. Surprisingly, we find that when facing a combination of choices, worms’ preferences do not always follow value-based hierarchy. In fact, the innate chemotaxis behavior in worms robustly violates key rationality paradigms of transitivity, independence of irrelevant alternatives and regularity. These violations arise due to asymmetric modulatory effects between the presented options. Functional analysis of the entire chemosensory system at a single-neuron resolution, coupled with analyses of mutants, defective in individual neurons, reveals that these asymmetric effects originate in specific sensory neurons.
Mutagenesis separates ATPase and thioesterase activities of the peroxisomal ABC transporter, Comatose
Authors: Carrier David J. , van Roermund Carlo W. T. , Schaedler Theresia A. , Rong Hong Lin , IJlst Lodewijk , Wanders Ronald J. A. , Baldwin Stephen A. , Waterham Hans R. , Theodoulou Frederica L. , Baker Alison 
Published: July 2019

AbstractThe peroxisomal ABC transporter, Comatose (CTS), a full length transporter from Arabidopsis has intrinsic acyl-CoA thioesterase (ACOT) activity, important for physiological function. We used molecular modelling, mutagenesis and biochemical analysis to identify amino acid residues important for ACOT activity. D863, Q864 and T867 lie within transmembrane helix 9. These residues are orientated such that they might plausibly contribute to a catalytic triad similar to type II Hotdog fold thioesterases. When expressed in Saccharomyces cerevisiae, mutation of these residues to alanine resulted in defective of β-oxidation. All CTS mutants were expressed and targeted to peroxisomes and retained substrate-stimulated ATPase activity. When expressed in insect cell membranes, Q864A and S810N had similar ATPase activity to wild type but greatly reduced ACOT activity, whereas the Walker A mutant K487A had greatly reduced ATPase and no ATP-dependent ACOT activity. In wild type CTS, ATPase but not ACOT was stimulated by non-cleavable C14 ether-CoA. ACOT activity was stimulated by ATP but not by non-hydrolysable AMPPNP. Thus, ACOT activity depends on functional ATPase activity but not vice versa, and these two activities can be separated by mutagenesis. Whether D863, Q864 and T867 have a catalytic role or play a more indirect role in NBD-TMD communication is discussed.
Neurotoxicity of organophosphate pesticides could reduce the ability of fish to escape predation under low doses of exposure
Authors: Sandoval-Herrera Natalia , Mena Freylan , Espinoza Mario , Romero Adarli 
Published: July 2019

AbstractBiomarkers are frequently used in ecotoxicology as they allow to study toxicant effects happening at low concentrations of exposure. However, most sublethal studies only evaluate cellular biomarkers which lack evident ecological relevance. We used a multibiomarker approach to estimate the toxic effects of ethoprophos, an organophosphate insecticide commonly used in banana plantations, on the tropical fish Astyanax aeneus (Characidae). We measured biomarkers at sub-individual (cellular) and individual (metabolism, behavior) levels and examined relationships among these responses. A sublethal exposure to ethoprophos caused a significant (54%) reduction of brain Cholinesterase (ChE) activity, reflecting the pesticide’s high neurotoxicity. However, other biomarkers like oxidative stress, biotransformation reactions, and resting metabolic rate were not affected. Exposure to ethoprophos modified antipredator behaviors such as escape response and detection avoidance (light/dark preference): exposed fish escaped slower from a simulated attack and preferred brighter areas in a novel tank. The relationship between ChE activity and reaction time suggests that pesticide-induced ChE inhibition reduces escape ability in fish. Our results provide evidence that impacts of organophosphate pesticides on fish ecological fitness can occur even with short exposures at very low concentrations.
Directed differentiation of human induced pluripotent stem cells into mature stratified bladder urothelium
Authors: Suzuki Kotaro , Koyanagi-Aoi Michiyo , Uehara Keiichiro , Hinata Nobuyuki , Fujisawa Masato , Aoi Takashi 
Published: July 2019

AbstractFor augmentation or reconstruction of urinary bladder after cystectomy, bladder urothelium derived from human induced pluripotent stem cells (hiPSCs) has recently received focus. However, previous studies have only shown the emergence of cells expressing some urothelial markers among derivatives of hiPSCs, and no report has demonstrated the stratified structure, which is a particularly important attribute of the barrier function of mature bladder urothelium. In present study, we developed a method for the directed differentiation of hiPSCs into mature stratified bladder urothelium. The caudal hindgut, from which the bladder urothelium develops, was predominantly induced via the high-dose administration of CHIR99021 during definitive endoderm induction, and this treatment subsequently increased the expressions of uroplakins. Terminal differentiation, characterized by the increased expression of uroplakins, CK13, and CK20, was induced with the combination of Troglitazone + PD153035. FGF10 enhanced the expression of uroplakins and the stratification of the epithelium, and the transwell culture system further enhanced such stratification. Furthermore, the barrier function of our urothelium was demonstrated by a permeability assay using FITC-dextran. According to an immunohistological analysis, the stratified uroplakin II-positive epithelium was observed in the transwells. This method might be useful in the field of regenerative medicine of the bladder.
Discovery of a kleptoplastic ‘dinotom’ dinoflagellate and the unique nuclear dynamics of converting kleptoplastids to permanent plastids
Authors: Yamada Norico , Bolton John J. , Trobajo Rosa , Mann David G. , Dąbek Przemysław , Witkowski Andrzej , Onuma Ryo , Horiguchi Takeo , Kroth Peter G. 
Published: July 2019

AbstractA monophyletic group of dinoflagellates, called ‘dinotoms’, are known to possess evolutionarily intermediate plastids derived from diatoms. The diatoms maintain their nuclei, mitochondria, and the endoplasmic reticulum in addition with their plastids, while it has been observed that the host dinoflagellates retain the diatoms permanently by controlling diatom karyokinesis. Previously, we showed that dinotoms have repeatedly replaced their diatoms. Here, we show the process of replacements is at two different evolutionary stages in two closely related dinotoms,Durinskia capensisandD. kwazulunatalensis. We clarify thatD. capensisis a kleptoplastic protist keeping its diatoms temporarily, only for two months. On the other hand,D. kwazulunatalensisis able to keep several diatoms permanently and exhibits unique dynamics to maintain the diatom nuclei: the nuclei change their morphologies into a complex string-shape alongside the plastids during interphase and these string-shaped nuclei then condense into multiple round nuclei when the host divides. These dynamics have been observed in other dinotoms that possess permanent diatoms, while they have never been observed in any other eukaryotes. We suggest that the establishment of this unique mechanism might be a critical step for dinotoms to be able to convert kleptoplastids into permanent plastids.
Wx: a neural network-based feature selection algorithm for transcriptomic data
Authors: Park Sungsoo , Shin Bonggun , Sang Shim Won , Choi Yoonjung , Kang Kilsoo , Kang Keunsoo 
Published: July 2019

AbstractNext-generation sequencing (NGS), which allows the simultaneous sequencing of billions of DNA fragments simultaneously, has revolutionized how we study genomics and molecular biology by generating genome-wide molecular maps of molecules of interest. However, the amount of information produced by NGS has made it difficult for researchers to choose the optimal set of genes. We have sought to resolve this issue by developing a neural network-based feature (gene) selection algorithm called Wx. The Wx algorithm ranks genes based on the discriminative index (DI) score that represents the classification power for distinguishing given groups. With a gene list ranked by DI score, researchers can institutively select the optimal set of genes from the highest-ranking ones. We applied the Wx algorithm to a TCGA pan-cancer gene-expression cohort to identify an optimal set of gene-expression biomarker candidates that can distinguish cancer samples from normal samples for 12 different types of cancer. The 14 gene-expression biomarker candidates identified by Wx were comparable to or outperformed previously reported universal gene expression biomarkers, highlighting the usefulness of the Wx algorithm for next-generation sequencing data. Thus, we anticipate that the Wx algorithm can complement current state-of-the-art analytical applications for the identification of biomarker candidates as an alternative method. The stand-alone and web versions of the Wx algorithm are available at https://github.com/deargen/DearWXpub and https://wx.deargendev.me/, respectively.
Beneficial effect of estrogen on nigrostriatal dopaminergic neurons in drug-naïve postmenopausal Parkinson’s disease
Authors: Lee Yang Hyun , Cha Jungho , Chung Seok Jong , Yoo Han Soo , Sohn Young H. , Ye Byoung Seok , Lee Phil Hyu 
Published: July 2019

AbstractThis study aimed to investigate the potential beneficial effects of estrogen on nigrostriatal dopaminergic neuron degeneration in postmenopausal drug-naïve Parkinson’s disease (PD). Based on the ratio of lifetime estrogen exposure length to the total length of the estrogen exposure and deprivation period, postmenopausal women with drug-naïve PD were divided into low (n = 31) and high (n = 31) estrogen exposure ratio groups. We performed a comparative analysis of the striatal dopamine transporter (DAT) availability between the two groups. Additionally, we evaluated the longitudinal change in the levodopa equivalent dose per month using a linear mixed model. The motor symptoms were more severe in the low estrogen exposure ratio group than in the high estrogen exposure ratio group (P = 0.016). PD patients in the two groups had significantly lower DAT availability on all striatal sub-regions except for ventral striatum than did age- and sex-matched normal controls. When comparing the two groups, PD patients in the low estrogen exposure ratio group exhibited significantly lower DAT availability in the posterior putamen (P = 0.024) and in the ventral putamen (P = 0.036) than those in the high estrogen exposure ratio group. The estimated monthly levodopa equivalent dose changes were 10.9 in the low estrogen exposure ratio group and 7.1 in the high estrogen exposure ratio group with a significant interaction between the two groups (P = 0.001). These in vivo data provide indirect evidence showing that estrogen may elicit a beneficial effect on nigrostriatal dopamine neurons in PD.
Hypolipidemic effects of herbal extracts by reduction of adipocyte differentiation, intracellular neutral lipid content, lipolysis, fatty acid exchange and lipid droplet motility
Authors: Haselgrübler Renate , Lanzerstorfer Peter , Röhrl Clemens , Stübl Flora , Schurr Jonas , Schwarzinger Bettina , Schwarzinger Clemens , Brameshuber Mario , Wieser Stefan , Winkler Stephan M. , Weghuber Julian 
Published: July 2019

AbstractAn increase in adipose tissue is caused by the increased size and number of adipocytes. Lipids accumulate in intracellular stores, known as lipid droplets (LDs). Recent studies suggest that parameters such as LD size, shape and dynamics are closely related to the development of obesity. Berberine (BBR), a natural plant alkaloid, has been demonstrated to possess anti-obesity effects. However, it remains unknown which cellular processes are affected by this compound or how effective herbal extracts containing BBR and other alkaloids actually are. For this study, we used extracts of Coptis chinensis, Mahonia aquifolium, Berberis vulgaris and Chelidonium majus containing BBR and other alkaloids and studied various processes related to adipocyte functionality. The presence of extracts resulted in reduced adipocyte differentiation, as well as neutral lipid content and rate of lipolysis. We observed that the intracellular fatty acid exchange was reduced in different LD size fractions upon treatment with BBR and Coptis chinensis. In addition, LD motility was decreased upon incubation with BBR, Coptis chinensis and Chelidonium majus extracts. Furthermore, Chelidonium majus was identified as a potent fatty acid uptake inhibitor. This is the first study that demonstrates the selected regulatory effects of herbal extracts on adipocyte function.
Amplification-free library preparation with SAFE Hi-C uses ligation products for deep sequencing to improve traditional Hi-C analysis
Authors: Niu Longjian , Shen Wei , Huang Yingzhang , He Na , Zhang Yuedong , Sun Jialei , Wan Jing , Jiang Daxin , Yang Manyun , Tse Yu Chung , Li Li , Hou Chunhui 
Published: July 2019

AbstractPCR amplification of Hi-C libraries introduces unusable duplicates and results in a biased representation of chromatin interactions. We present a simplified, fast, and economically efficient Hi-C library preparation procedure, SAFE Hi-C, which generates sufficient non-amplified ligation products for deep sequencing from 30 million Drosophila cells. Comprehensive analysis of the resulting data shows that amplification-free Hi-C preserves higher complexity of chromatin interaction and lowers sequencing depth for the same number of unique paired reads. For human cells which have a large genome, SAFE Hi-C recovers enough ligated fragments for direct high-throughput sequencing without amplification from as few as 250,000 cells. Comparison with published in situ Hi-C data from millions of human cells demonstrates that amplification introduces distance-dependent amplification bias, which results in an increased background noise level against genomic distance. With amplification bias avoided, SAFE Hi-C may produce a chromatin interaction network more faithfully reflecting the real three-dimensional genomic architecture.
Chemoenzymatic conversion of amides to enantioenriched alcohols in aqueous medium
Authors: Dander Jacob E. , Giroud Maude , Racine Sophie , Darzi Evan R. , Alvizo Oscar , Entwistle David , Garg Neil K. 
Published: July 2019

AbstractOne-pot reactions that combine non-enzymatic and biocatalytic transformations represent an emerging strategy in chemical synthesis. Some of the most powerful chemoenzymatic methodologies, although uncommon, are those that form a carbon–carbon (C–C) bond and a stereocenter at one of the reacting carbons, thereby streamlining traditional retrosynthetic disconnections. Here we report the one-pot, chemoenzymatic conversion of amides to enantioenriched alcohols. This transformation combines a nickel-catalyzed Suzuki–Miyaura coupling of amides in aqueous medium with an asymmetric, biocatalytic reduction to provide diarylmethanol derivatives in high yields and enantiomeric excesses. The synthetic utility of this platform is underscored by the formal syntheses of both antipodes of the pharmaceutical orphenadrine, which rely on ketoreductase enzymes that instill complementary stereoselectivities. We provide an explanation for the origins of stereoselectivity based on an analysis of the enzyme binding pockets.