bluuebunny/crossref_metadata_2025_split huggingface dataset:
Descriptive epidemiology of energy expenditure in the UK: findings from the National Diet and Nutrition Survey 2008–15
Authors: Brage Soren , Lindsay Tim , Venables Michelle , Wijndaele Katrien , Westgate Kate , Collins David , Roberts Caireen , Bluck Les , Wareham Nick , Page Polly 
Published: January 2020

AbstractBackgroundLittle is known about population levels of energy expenditure, as national surveillance systems typically employ only crude measures. The National Diet and Nutrition Survey (NDNS) in the UK measured energy expenditure in a 10% subsample by gold-standard doubly labelled water (DLW).MethodsDLW-subsample participants from the NDNS (383 males, 387 females) aged 4–91 years were recruited between 2008 and 2015 (rolling programme). Height and weight were measured and body-fat percentage estimated by deuterium dilution.ResultsAbsolute total energy expenditure (TEE) increased steadily throughout childhood, ranging from 6.2 and 7.2 MJ/day in 4- to 7-year-olds to 9.7 and 11.7 MJ/day for 14- to 16-year-old girls and boys, respectively. TEE peaked in 17- to 27-year-old women (10.7 MJ/day) and 28- to 43-year-old men (14.4 MJ/day), before decreasing gradually in old age. Physical-activity energy expenditure (PAEE) declined steadily with age from childhood (87 kJ/day/kg in 4- to 7-year-olds) through to old age (38 kJ/day/kg in 71- to 91-year-olds). No differences were observed by time, region and macronutrient composition. Body-fat percentage was strongly inversely associated with PAEE throughout life, irrespective of expressing PAEE relative to body mass or fat-free mass. Compared with females with &lt;30% body fat, females with &gt;40% recorded 29 kJ/day/kg body mass and 18 kJ/day/kg fat-free mass less PAEE in analyses adjusted for age, geographical region and time of assessment. Similarly, compared with males with &lt;25% body fat, males with &gt;35% recorded 26 kJ/day/kg body mass and 10 kJ/day/kg fat-free mass less PAEE.ConclusionsThis first nationally representative study reports levels of human-energy expenditure as measured by gold-standard methodology; values may serve as a reference for other population studies. Age, sex and body composition are the main determinants of energy expenditure.Key Messages This is the first nationally representative study of human energy expenditure, covering the UK in the period 2008-2015. Total energy expenditure (MJ/day) increases steadily with age throughout childhood and adolescence, peaks in the 3rd decade of life in women and 4th decade of life in men, before decreasing gradually in old age. Physical activity energy expenditure (kJ/day/kg or kJ/day/kg fat-free mass) declines steadily with age from childhood to old age, more steeply so in males. Body-fat percentage is strongly inversely associated with physical activity energy expenditure. We found little evidence that energy expenditure varied by geographical region, over time, or by dietary macronutrient composition.
Density ofg-Vector Cones From Triangulated Surfaces
Authors: Yurikusa Toshiya 
Published: January 2020

AbstractWe study $g$-vector cones associated with clusters of cluster algebras defined from a marked surface $(S,M)$ of rank $n$. We determine the closure of the union of $g$-vector cones associated with all clusters. It is equal to $\mathbb{R}^n$ except for a closed surface with exactly one puncture, in which case it is equal to the half space of a certain explicit hyperplane in $\mathbb{R}^n$. Our main ingredients are laminations on $(S,M)$, their shear coordinates, and their asymptotic behavior under Dehn twists. As an application, if $(S,M)$ is not a closed surface with exactly one puncture, the exchange graph of cluster tilting objects in the corresponding cluster category is connected. If $(S,M)$ is a closed surface with exactly one puncture, it has precisely two connected components.
Role of ppGpp-regulated efflux genes in Acinetobacter baumannii
Authors: Jung Hye-Won , Kim Kyeongmin , Islam M Maidul , Lee Je Chul , Shin Minsang 
Published: January 2020

Abstract

Objectives
Treatment of infections caused by Acinetobacter baumannii nosocomial strains has become increasingly problematic owing to their resistance to antibiotics. ppGpp is a secondary messenger involved in growth control and various stress responses in bacteria. The mechanism for inhibition of antibiotic resistance via ppGpp is still unidentified in various pathogenic bacteria including A. baumannii. Here, we investigated the effects of ppGpp on efflux pump (EP)-related genes in A. baumannii.

Methods
ppGpp-deficient and -complementary strains were constructed by conjugation and we confirmed (p)ppGpp measurements by thin-layer chromatography. We observed that the ppGpp-deficient strain (ΔA1S_0579) showed abnormal stretching patterns by transmission electron microscopy analysis. The MICs of antimicrobial agents for the WT A. baumannii (ATCC 17978), ppGpp-deficient and complementary strains were determined by the Etest and broth dilution assay methods. The expression levels of EP-related genes were determined by quantitative RT–PCR.

Results
We observed morphological differences between a ppGpp-deficient strain (ΔA1S_0579) and the WT strain. Dramatic reductions of MICs in the ppGpp-deficient strain compared with the WT were observed for gentamicin (2.6-fold), tetracycline (3.9-fold), erythromycin (4-fold) and trimethoprim (&gt;4-fold). Expression of the EP-related genes abeB (2.8-fold), tet(A) (2.3-fold), adeB (10.0-fold), adeI (9.9-fold), adeJ (11.8-fold) and adeK (14.4-fold) was also decreased in the ppGpp-deficient strain.

Conclusions
This study demonstrates that ppGpp regulates EP-related gene expression in A. baumannii, affecting antibiotic susceptibility. To date, treatment for MDR A. baumannii has had no new antimicrobial agents, so the A1S_0579 gene could be a novel therapeutic target for rational drug design by affecting ppGpp production.
Plasma and intracellular pharmacokinetics of tenofovir disoproxil fumarate and emtricitabine in transgender women receiving feminizing hormone therapy
Authors: Cirrincione Lauren R , Podany Anthony T , Havens Joshua P , Bares Sara H , Dyavar Shetty Ravi , Gwon Yeongjin , Johnson Tanner M , Amoura N Jean , Fletcher Courtney V , Scarsi Kimberly K 
Published: January 2020

Abstract

Background
Transwomen have an increased risk of HIV acquisition compared with other adults. Drug–drug interactions between pre-exposure prophylaxis (PrEP) and gender-affirming therapy are cited as a reason for poor PrEP uptake among transwomen. We evaluated plasma tenofovir and emtricitabine pharmacokinetics and their active intracellular anabolites, tenofovir-diphosphate and emtricitabine-triphosphate, in transwomen receiving feminizing hormones.

Methods
We enrolled HIV-negative transwomen (≥19 years) not receiving PrEP. Participants took oral tenofovir disoproxil fumarate/emtricitabine 300/200 mg daily for 14 days. Plasma was collected at 0 h (pre-dose), 0.5, 1, 2, 3, 4, 6, 8 and 12 h on day 14 post-tenofovir disoproxil fumarate/emtricitabine dose. The plasma AUC0–24 was calculated using the trapezoidal rule and compared with historical HIV-negative cisgender adults as geometric mean ratios (GMRs, 90% CI). Secondarily, tenofovir-diphosphate and emtricitabine-triphosphate from PBMCs collected at 0 h and 12 h were reported descriptively as geometric means (90% CI). Clinical trials registration: NCT03270969.

Results
Among 15 transwomen (mean age 32 years), geometric mean tenofovir and emtricitabine plasma AUC0–24 were lower compared with controls: tenofovir, 2.10 versus 2.76 mg·h/L, GMR 0.76 (0.65–0.90), P = 0.01; emtricitabine, 9.15 versus 10.64 mg·h/L, GMR 0.86 (0.75–0.98), P = 0.07. Tenofovir-diphosphate and emtricitabine-triphosphate concentrations were higher than previously reported in the literature: 167.1 (146.6–190.5) fmol/106 cells and 15.4 (13.8–17.3) pmol/106 cells, respectively.

Conclusions
We observed lower plasma tenofovir and emtricitabine concentrations in transwomen compared with historical cisgender adults, yet intracellular tenofovir-diphosphate and emtricitabine-triphosphate concentrations were higher than previously reported in PBMCs. Understanding the differences of PrEP pharmacokinetics in plasma and tissue compartments and the resultant impact on efficacy remains important for transwomen.
Separation and Quantification of Superwarfarin Rodenticide Diastereomers—Bromadiolone, Difenacoum, Flocoumafen, Brodifacoum, and Difethialone—in Human Plasma
Authors: Nosal Daniel G , Feinstein Douglas L , Chen Luying , van Breemen Richard B 
Published: January 2020

Abstract

Background
Superwarfarins, second-generation long-acting anticoagulant rodenticides, are 4-hydroxycoumarin analogues of warfarin that contain a large hydrophobic side chain. These compounds contain two chiral centers and are synthesized for commercial use as two pairs of diastereomer.

Objective
To support studies of superwarfarin pharmacokinetics and other efforts to improve clinical care for poisoning victims, a quantitative assay was developed for the measurement of diastereomer of bromadiolone, difenacoum, flocoumafen, brodifacoum, and difethialone in human plasma.

Method
Based on ultrahigh-pressure liquid chromatography-tandem mass-spectrometry (UHPLC-MS/MS), this method was validated according to U.S. Food and Drug Administration (FDA) guidelines. Sample preparation involved simple protein precipitation followed by reversed phase UHPLC, which resolved all five pairs of cis/trans diastereomer in less than 10 min. Superwarfarins were measured using negative ion electrospray followed by selected-reaction monitoring on a triple quadrupole mass spectrometer.

Results
Calibration curves covered 3–4 orders of magnitude with linear regression coefficients of &gt;0.999. The lower limits of quantitation were from 0.013 to 2.41 ng/mL, and intra-day and inter-day accuracy and precision coefficients of variation were &lt;12%.

Conclusions
A 10-min UHPLC-MS/MS assay was developed and validated for the separation and quantitative analysis of the pairs of diastereomer of five superwarfarins in human plasma.

Highlights
This method was used to identify and measure superwarfarins and their cis/trans diastereomers in plasma obtained from patients treated for coagulopathy following consumption of contaminated synthetic cannabinoid products.
A malectin domain kinesin functions in pollen and seed development in Arabidopsis
Authors: Galindo-Trigo Sergio , Grand Thomas M , Voigt Christian A , Smith Lisa M 
Published: January 2020

AbstractThe kinesin family is greatly expanded in plants compared with animals and, with more than a third up-regulated in expression during cell division, it has been suggested that this expansion facilitated complex plant-specific cytoskeletal rearrangements. The cell cycle-regulated kinesins include two with an N-terminal malectin domain, a protein domain that has been shown to bind polysaccharides and peptides when found extracellularly in receptor-like kinases. Although malectin domain kinesins are evolutionarily deep rooted, their function in plants remains unclear. Here we show that loss of MALECTIN DOMAIN KINESIN 2 (MDKIN2) results in stochastic developmental defects in pollen, embryo, and endosperm. High rates of seed abnormalities and abortion occur in mdkin2 mutants through a partial maternal effect. No additive effect or additional developmental defects were noted in mdkin1 mdkin2 double mutants. MDKIN2 is expressed in regions of cell division throughout the plant. Subcellular localization of MDKIN2 indicates a role in cell division, with a possible secondary function in the nuclei. Our results reveal a non-essential but important role for a malectin domain kinesin during development in plants.
Ionized gas outflow signatures in SDSS-IV MaNGA active galactic nuclei
Authors: Wylezalek Dominika , Flores Anthony M , Zakamska Nadia L , Greene Jenny E , Riffel Rogemar A 
Published: January 2020

ABSTRACT
The prevalence of outflow and feedback signatures in active galactic nuclei (AGNs is a major unresolved question which large integral field unit (IFU) surveys now allow to address. In this paper, we present a kinematic analysis of the ionized gas in 2778 galaxies at z ∼ 0.05 observed by Sloan Digital Sky Survey-IV (SDSS-IV) Mapping Nearby Galaxies at Apache Point Observatory (MaNGA). Specifically, we measure the kinematics of the [O iii] λ5007 Å emission line in each spatial element and fit multiple Gaussian components to account for possible non-gravitational motions of gas. Comparing the kinematics of the ionized gas between 308 MaNGA-selected AGNs that have been previously identified through emission-line diagnostics and sources not classified as AGN, we find that while 25 per cent of MaNGA-selected AGN show [O iii] components with emission-line widths of &gt;500 km s−1 in more than 10 per cent of their spaxels, only 7 per cent of MaNGA non-AGNs show a similar signature. Even the AGNs that do not show nuclear AGN photoionization signatures and that were only identified as AGN based on their larger scale photoionization signatures show similar kinematic characteristics. In addition to obscuration, another possibility is that outflow and mechanical feedback signatures are longer lived than the AGN itself. Our measurements demonstrate that high velocity gas is more prevalent in AGN compared to non-AGN and that outflow and feedback signatures in low-luminosity, low-redshift AGN may so far have been underestimated. We show that higher luminosity MaNGA-selected AGNs are able to drive larger scale outflows than lower luminosity AGN. But estimates of the kinetic coupling efficiencies are ≪1 per cent and suggest that the feedback signatures probed in this paper are unlikely to have a significant impact on the AGN host galaxies. However, continuous energy injection may still heat a fraction of the cool gas and delay or suppress star formation in individual galaxies even when the AGN is weak.
Trend filtering – II. Denoising astronomical signals with varying degrees of smoothness
Authors: Politsch Collin A , Cisewski-Kehe Jessi , Croft Rupert A C , Wasserman Larry 
Published: January 2020

ABSTRACTTrend filtering – first introduced into the astronomical literature in Paper I of this series – is a state-of-the-art statistical tool for denoising 1D signals that possess varying degrees of smoothness. In this work, we demonstrate the broad utility of trend filtering to observational astronomy by discussing how it can contribute to a variety of spectroscopic and time-domain studies. The observations we discuss are (1) the Lyman-α (Lyα) forest of quasar spectra; (2) more general spectroscopy of quasars, galaxies, and stars; (3) stellar light curves with planetary transits; (4) eclipsing binary light curves; and (5) supernova light curves. We study the Lyα forest in the greatest detail – using trend filtering to map the large-scale structure of the intergalactic medium along quasar-observer lines of sight. The remaining studies share broad themes of: (1) estimating observable parameters of light curves and spectra; and (2) constructing observational spectral/light-curve templates. We also briefly discuss the utility of trend filtering as a tool for 1D data reduction and compression.
The identity and methylation status of the first transcribed nucleotide in eukaryotic mRNA 5′ cap modulates protein expression in living cells
Authors: Sikorski Pawel J , Warminski Marcin , Kubacka Dorota , Ratajczak Tomasz , Nowis Dominika , Kowalska Joanna , Jemielity Jacek 
Published: January 2020

Abstract7-Methylguanosine 5′ cap on mRNA is necessary for efficient protein expression in vitro and in vivo. Recent studies revealed structural diversity of endogenous mRNA caps, which carry different 5′-terminal nucleotides and additional methylations (2′-O-methylation and m6A). Currently available 5′-capping methods do not address this diversity. We report trinucleotide 5′ cap analogs (m7GpppN(m)pG), which are utilized by RNA polymerase T7 to initiate transcription from templates carrying Φ6.5 promoter and enable production of mRNAs differing in the identity of the first transcribed nucleotide (N = A, m6A, G, C, U) and its methylation status (±2′-O-methylation). HPLC-purified mRNAs carrying these 5′ caps were used to study protein expression in three mammalian cell lines (3T3-L1, HeLa and JAWS II). The highest expression was observed for mRNAs carrying 5′-terminal A/Am and m6Am, whereas the lowest was observed for G and Gm. The mRNAs carrying 2′-O-methyl at the first transcribed nucleotide (cap 1) had significantly higher expression than unmethylated counterparts (cap 0) only in JAWS II dendritic cells. Further experiments indicated that the mRNA expression characteristic does not correlate with affinity for translation initiation factor 4E or in vitro susceptibility to decapping, but instead depends on mRNA purity and the immune state of the cells.
RNAsamba: neural network-based assessment of the protein-coding potential of RNA sequences
Authors: Camargo Antonio P , Sourkov Vsevolod , Pereira Gonçalo A G , Carazzolle Marcelo F 
Published: January 2020

Abstract
The advent of high-throughput sequencing technologies made it possible to obtain large volumes of genetic information, quickly and inexpensively. Thus, many efforts are devoted to unveiling the biological roles of genomic elements, being the distinction between protein-coding and long non-coding RNAs one of the most important tasks. We describe RNAsamba, a tool to predict the coding potential of RNA molecules from sequence information using a neural network-based that models both the whole sequence and the ORF to identify patterns that distinguish coding from non-coding transcripts. We evaluated RNAsamba’s classification performance using transcripts coming from humans and several other model organisms and show that it recurrently outperforms other state-of-the-art methods. Our results also show that RNAsamba can identify coding signals in partial-length ORFs and UTR sequences, evidencing that its algorithm is not dependent on complete transcript sequences. Furthermore, RNAsamba can also predict small ORFs, traditionally identified with ribosome profiling experiments. We believe that RNAsamba will enable faster and more accurate biological findings from genomic data of species that are being sequenced for the first time. A user-friendly web interface, the documentation containing instructions for local installation and usage, and the source code of RNAsamba can be found at https://rnasamba.lge.ibi.unicamp.br/.
The Effect of Infectious Diseases Consultation on Mortality in Hospitalized Patients With Methicillin-Resistant Staphylococcus aureus, Candida, and Pseudomonas Bloodstream Infections
Authors: Chesdachai Supavit , Kline Susan , Helmin Derrek , Rajasingham Radha 
Published: January 2020

Abstract
We evaluated the association between infectious disease consultation and bloodstream infection outcomes, including methicillin-resistant Staphylococcus aureus, Candida, and Pseudomonas. No infectious diseases consultation was associated with over 4-fold increased hazard of death at 3 months and 6-fold increased hazard of death in hospital.
Impaired Vaccine-Induced Antibody Response Against Clade 6B H1N1 Viruses in Individuals Before Viral Emergence
Authors: Huang Kuan-Ying A , Huang Yhu-Chering , Chiu Cheng-Hsun , Tsao Kuo-Chien , Lin Tzou-Yien 
Published: January 2020

AbstractBackgroundClade 6B H1N1 pdm09 influenza viruses cause substantial morbidity and mortality worldwide. Human antibody profiles elicited upon vaccination against the clade 6B virus are largely unclear before viral emergence.MethodsHealthy volunteers, including children aged 3–8 years, adolescents aged 9–17 years, and adults, were enrolled before the clade 6B H1N1 outbreak and received the 2013–2014 inactivated influenza vaccine. We determined antibody responses before and after vaccination. Vaccine-induced plasmablast-derived antibodies were tested against H1N1 pdm09 reference and clade 6B viruses.ResultsThe majority of the subjects generated robust hemagglutination inhibition and neutralizing antibody responses upon vaccination across the different age groups. Nevertheless, a subset of young adults preferentially produced antibodies that failed to neutralize clade 6B viruses that emerged and circulated in 2014–2016. The hemagglutinin K163Q change at the Sa antigenic site, one of the substitutions that define clade 6B viruses, was responsible for resistance to neutralization by both postvaccination sera and vaccine-induced plasmablast-derived antibodies.ConclusionsVaccine-induced antibody immunity is compromised by the antigenic change of H1N1 pdm09 virus in a subset of adults, and this may warrant the incorporation of human serology in the antigenic characterization of virus and vaccine strain selection.
Intermittent Starvation Extends the Functional Lifetime of Primary Human Hepatocyte Cultures
Authors: Davidson Matthew D , Khetani Salman R 
Published: January 2020

Abstract
Primary human hepatocyte (PHH) cultures have become indispensable to mitigate the risk of adverse drug reactions in human patients. In contrast to dedifferentiating monocultures, coculture with nonparenchymal cells maintains PHH functions for 2–4 weeks. However, because the functional lifespan of PHHs in vivo is 200–400 days, it is desirable to further prolong PHH functions in vitro toward modeling chronic drug exposure and disease progression. Fasting has benefits on the longevity of organisms and the health of tissues such as the liver. We hypothesized that a culturing protocol that mimics dynamic fasting/starvation could activate starvation pathways and prolong PHH functional lifetime. To mimic starvation, serum and hormones were intermittently removed from the culture medium of micropatterned cocultures (MPCCs) containing PHHs organized onto collagen domains and surrounded by 3T3-J2 murine fibroblasts. A weekly 2-day starvation optimally prolonged PHH functional lifetime for 6+ weeks in MPCCs versus a decline after 3 weeks in nonstarved controls. The 2-day starvation also enhanced the functions of PHH monocultures for 2 weeks, suggesting direct effects on PHHs. In MPCCs, starvation activated 5' adenosine monophosphate-activated protein kinase (AMPK) and restricted fibroblast overgrowth onto PHH islands, thereby maintaining hepatic polarity. The effects of starvation on MPCCs were partially recapitulated by activating AMPK using metformin or growth arresting fibroblasts via mitomycin-C. Lastly, starved MPCCs demonstrated lower false positives for drug toxicity tests and higher drug-induced cytochrome-P450 activities versus nonstarved controls even after 5 weeks. In conclusion, intermittent serum/hormone starvation extends PHH functional lifetime toward enabling clinically relevant drug screening.