bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity
Authors: López-Escardó David , Paps Jordi , de Vargas Colomban , Massana Ramon , Ruiz-Trillo Iñaki , del Campo Javier 
Published: June 2018

AbstractAlthough animals are among the best studied organisms, we still lack a full description of their diversity, especially for microscopic taxa. This is partly due to the time-consuming and costly nature of surveying animal diversity through morphological and molecular studies of individual taxa. A powerful alternative is the use of high-throughput environmental sequencing, providing molecular data from all organisms sampled. We here address the unknown diversity of animal phyla in marine environments using an extensive dataset designed to assess eukaryotic ribosomal diversity among European coastal locations. A multi-phylum assessment of marine animal diversity that includes water column and sediments, oxic and anoxic environments, and both DNA and RNA templates, revealed a high percentage of novel 18S rRNA sequences in most phyla, suggesting that marine environments have not yet been fully sampled at a molecular level. This novelty is especially high among Platyhelminthes, Acoelomorpha, and Nematoda, which are well studied from a morphological perspective and abundant in benthic environments. We also identified, based on molecular data, a potentially novel group of widespread tunicates. Moreover, we recovered a high number of reads for Ctenophora and Cnidaria in the smaller fractions suggesting their gametes might play a greater ecological role than previously suspected.
Cooperation on dynamic networks within an uncertain reputation environment
Authors: Lozano Pablo , Antonioni Alberto , Tomassini Marco , Sánchez Angel 
Published: June 2018

AbstractReputation plays a key role among the mechanisms supporting cooperation in our society. This is a well-known observation and, in fact, several studies have shown that reputation may substantially increase cooperation among subjects playing Prisoner’s Dilemma games in the laboratory. Unfortunately, recent experiments indicate that when reputation can be faked cooperation can still be maintained at the expense of honest subjects who are deceived by the dishonest ones. As experimental work is limited due to financial and other reasons, we present here an agent-based simulation model inspired by, and calibrated against, the results obtained in the experiment. We thus simulate much larger population sizes over longer times, and test other model parameters to see whether the observed behavior generalizes in those yet untried conditions. The results show that the collective behavior is qualitatively similar in larger systems and stable over longer times horizons. We conclude that the findings of the experimental work are meaningful, taking into account that the model is strictly tailored to our particular experimental setting and therefore it is a possible explanation of our observations whose applicability to other contexts requires further research. We argue that simulations like the ones presented here may also be useful to cheaply and quickly suggest settings and options to enhance and facilitate further experiments, which, in turn, may provide new tests of the models themselves.
The black hole retention fraction in star clusters
Authors: Pavlík Václav , Jeřábková Tereza , Kroupa Pavel , Baumgardt Holger 
Published: June 2018

Context. Recent research has been constraining the retention fraction of black holes (BHs) in globular clusters by comparing the degree of mass segregation with N-body simulations. They are consistent with an upper limit of the retention fraction being 50% or less.
Aims. In this work, we focus on direct simulations of the dynamics of BHs in star clusters. We aim to constrain the effective distribution of natal kicks that BHs receive during supernova (SN) explosions and to estimate the BH retention fraction.Methods. We used the collisional N-body code nbody6 to measure the retention fraction of BHs for a given set of parameters, which are: the initial mass of a star cluster, the initial half-mass radius, and σBH, which sets the effective Maxwellian BH velocity kick distribution. We compare these direct N-body models with our analytic estimates and newest observational constraints.
Results. The numerical simulations show that for the one-dimensional velocity kick dispersion σBH < 50 km s−1, clusters with radii of 2 pc and that are initially more massive than 5 × 103 M⊙ retain more than 20% of BHs within their half-mass radii. Our simple analytic model yields a number of retained BHs that is in good agreement with the N-body models. Furthermore, the analytic estimates show that ultra-compact dwarf galaxies should have retained more than 80% of their BHs for σBH ≤ 190 km s−1. Although our models do not contain primordial binaries, in the most compact clusters with 103 stars, we have found evidence of delayed SN explosions producing a surplus of BHs compared to the IMF due to dynamically formed binary stars. These cases do not occur in the more populous or expanded clusters.
An Overview of FGF19 and FGF21: The Therapeutic Role in the Treatment of the Metabolic Disorders and Obesity
Authors: Babaknejad Nasim , Nayeri Hashem , Hemmati Roohullah , Bahrami Somaye , Esmaillzadeh Ahmad 
Published: June 2018

AbstractFibroblast growth factors (FGFs) are responsible for the regulation of a wide range of biological functions, among which cellular proliferation, survival, migration, and differentiation could be pointed out. FGF19 controls the enterohepatic bile acid/cholesterol system, and FGF21 modulates fatty acid/glucose metabolism. Obesity, type 2 diabetes, coronary artery disease, and cancer, all can alter FGF21 circulating concentrations. In contrast to FGF21, metabolic diseases exhibit reduced serum FGF19 levels. Accordingly, FGF19 and FGF21 play important roles in regulating glucose and lipid metabolism. Hence, we present here a timely review on the relationship between FGF19/21 and metabolic diseases, especially obesity, and their probable role in development and treatment of obesity seems necessary.
Prothrombin Time and Hemorrhagic Death in Dicumarolized Rats Receiving Pituitary and Adrenal Hormones
Authors: van Cauwenberge H , Jaques L. B 
Published: June 2018

Summary1. Rats receiving dicumarol were given injections of desoxycorticosterone, cortisone, hydrocortisone, ACTH, somatotropin, sodium salicylate, adrenaline, reserpine, histamine, 10% sodium chloride intraperitoneally. A high incidence of hemorrhagic death was observed with desoxycorticosterone, ACTH, STH, sodium salicylate, 10% sodium chloride, histamine, adrenaline, reserpine. Little hemorrhage was observed with cortisone and hydrocortisone.2. The mortality resulting from 10% sodium chloride stress in dicumarolized rats was not depressed by dial, or phenergan, or pretreatment with cortisone. The mortality was prevented by treatment with vitamin Ki before giving the stress agent.3. The mean prothrombin time with dicumarol in rats appeared to be increased by the administration of ACTH, sodium salicylate, 10% sodium chloride, desoxycorticosterone, adrenaline and histamine. No modification was observed by cortisone, dial, reserpine. With hydrocortisone — there was an increase the day after giving the steroid, but the prothrombin time was nearly normal 2 days later.4. Steroids were tested for their ability to protect adrenalectomized rats from hemorrhage with dicumarol. Desoxycorticosterone had no action in this regard. Cortisone and hydrocortisone were effective with cortisone being more active.
Congenital Hypoproconvertinemia A Report on 12 Cases with Total Deficiency and 19 Cases with Partial Deficiency
Authors: Voss Dieter , Waaler Bjarne A 
Published: June 2018

SummaryInvestigations on 12 patients with a total and 19 patients with a partial deficiency of proconvertin (factor VII) are reported. All patients proved to have the same deficiency and it was distinguishable from Stuart-Prower factor deficiency. The differentiation between proconvertin deficiency and Stuart-Prower factor deficiency is discussed.
Final report, on-going key comparison BIPM.QM-K1, ozone at ambient level, comparison with NPLI, February 2018
Authors: Viallon le , Idrees Faraz , Moussay Philippe , Wielgosz Robert , Sharma Chhemendra , Radha Radhakrishnan Soman , Shukla Devesh Kumar 
Published: June 2018

As part of the ongoing key comparison BIPM.QM-K1, a comparison has been performed between the ozone national standard of India maintained by the CSIR-National Physical Laboratory, India (NPLI) and the common reference standard of the key comparison, maintained by the Bureau International des Poids et Mesures (BIPM). The instruments have been compared over a nominal ozone amount-of-substance fraction range from 0 nmol/mol to 500 nmol/mol.
KEY WORDS FOR SEARCH
Ozone, Standard Reference Photometer

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Improved de novo genome assembly and analysis of the Chinese cucurbit Siraitia grosvenorii, also known as monk fruit or luo-han-guo
Authors: Xia Mian , Han Xue , He Hang , Yu Renbo , Zhen Gang , Jia Xiping , Cheng Beijiu , Deng Xing Wang 
Published: June 2018

Abstract

Background
Luo-han-guo (Siraitia grosvenorii), also called monk fruit, is a member of the Cucurbitaceae family. Monk fruit has become an important area for research because of the pharmacological and economic potential of its noncaloric, extremely sweet components (mogrosides). It is also commonly used in traditional Chinese medicine for the treatment of lung congestion, sore throat, and constipation. Recently, a single reference genome became available for monk fruit, assembled from 36.9x genome coverage reads via Illumina sequencing platforms. This genome assembly has a relatively short (34.2 kb) contig N50 length and lacks integrated annotations. These drawbacks make it difficult to use as a reference in assembling transcriptomes and discovering novel functional genes.

Findings
Here, we offer a new high-quality draft of the S. grosvenorii genome assembled using 31 Gb (~73.8x) long single molecule real time sequencing reads and polished with ~50 Gb Illumina paired-end reads. The final genome assembly is approximately 469.5 Mb, with a contig N50 length of 432,384 bp, representing a 12.6-fold improvement. We further annotated 237.3 Mb of repetitive sequence and 30,565 consensus protein coding genes with combined evidence. Phylogenetic analysis showed that S. grosvenorii diverged from members of the Cucurbitaceae family approximately 40.9 million years ago. With comprehensive transcriptomic analysis and differential expression testing, we identified 4,606 up-regulated genes in the early fruit compared to the leaf, a number of which were linked to metabolic pathways regulating fruit development and ripening.

Conclusions
The availability of this new monk fruit genome assembly, as well as the annotations, will facilitate the discovery of new functional genes and the genetic improvement of monk fruit.
On the use of Gaia magnitudes and new tables of bolometric corrections
Authors: Casagrande L , VandenBerg Don A 
Published: June 2018

Abstract
The availability of reliable bolometric corrections and reddening estimates, rather than the quality of parallaxes, will be one of the main limiting factors in determining the luminosities of a large fraction of Gaia stars. With this goal in mind, we provide GaiaGBP, G, and GRP synthetic photometry for the entire MARCS grid and test the performance of our synthetic colours and bolometric corrections against space-borne absolute spectrophotometry. We find indication of a magnitude-dependent offset in Gaia DR2 G magnitudes, which must be taken into account in high-accuracy investigations. Our interpolation routines are easily used to derive bolometric corrections at desired stellar parameters and to explore the dependence of Gaia photometry on Teff, $\log \,g$, $\rm {[Fe/H]}$, $[\alpha /\rm {Fe}]$, and E(B − V). Gaia colours for the Sun and Vega, and Teff-dependent extinction coefficients are also provided.
Maternal Hepatitis B Infection and Pregnancy Outcomes in the United States: A Population-Based Cohort Study
Authors: Bajema Kristina L , Stankiewicz Karita Helen C , Tenforde Mark W , Hawes Stephen E , Heffron Renee 
Published: June 2018

AbstractBackgroundHepatitis B virus (HBV) infection in pregnancy has been associated with risk of adverse maternal and infant outcomes in highly endemic settings, but this association is not well characterized in the United States.MethodsWe conducted a retrospective population-based cohort study in Washington State using linked birth certificate and hospital discharge records from 1992–2014. Among pregnant women with hepatitis B (n = 4391) and a hepatitis B–negative group (n = 22 410), we compared the risk of gestational diabetes, pre-eclampsia, eclampsia, placenta previa, preterm delivery, low birthweight, small for gestational age, and large for gestational age using multivariate logistic regression.ResultsHepatitis B–infected pregnant women were more likely to be Asian (61% vs 8%, P &lt; .001), foreign-born (76% vs 23%, P &lt; .001), and older in age (77% vs 64% ≥26 years, P &lt; .001). They were less commonly overweight or obese (33% vs 50%, P &lt; .001). There was a lower risk of small for gestational age infants among HBV-infected women (adjusted RR [aRR], 0.79; 95% confidence interval [CI], 0.67–0.93). The risk of other adverse outcomes was not significantly different between hepatitis B–infected and –negative women (gestational diabetes: aRR, 1.11; 95% CI, 0.92–1.34; pre-eclampsia: aRR, 1.06; 95% CI, 0.82–1.35; eclampsia: aRR, 2.31; 95% CI, 0.90–5.91; placenta previa: aRR, 1.16; 95% CI, 0.35–3.84; preterm delivery: aRR, 1.15; 95% CI, 0.98–1.34; low birth weight: aRR, 1.08; 95% CI, 0.90–1.29; large for gestational age: aRR, 1.01; 95% CI, 0.82–1.24).ConclusionsIn a low-burden setting in the United States, hepatitis B infection was not associated with adverse pregnancy outcomes.
The dynamic neural code of the retina for natural scenes
Authors: Maheswaranathan Niru , McIntosh Lane T. , Tanaka Hidenori , Grant Satchel , Kastner David B. , Melander Josh B. , Nayebi Aran , Brezovec Luke , Wang Julia , Ganguli Surya , Baccus Stephen A. 
Published: June 2018

AbstractUnderstanding how the visual system encodes natural scenes is a fundamental goal of sensory neuroscience. We show here that a three-layer network model predicts the retinal response to natural scenes with an accuracy nearing the fundamental limits of predictability. The model’s internal structure is interpretable, in that model units are highly correlated with interneurons recorded separately and not used to fit the model. We further show the ethological relevance to natural visual processing of a diverse set of phenomena of complex motion encoding, adaptation and predictive coding. Our analysis uncovers a fast timescale of visual processing that is inaccessible directly from experimental data, showing unexpectedly that ganglion cells signal in distinct modes by rapidly (< 0.1 s) switching their selectivity for direction of motion, orientation, location and the sign of intensity. A new approach that decomposes ganglion cell responses into the contribution of interneurons reveals how the latent effects of parallel retinal circuits generate the response to any possible stimulus. These results reveal extremely flexible and rapid dynamics of the retinal code for natural visual stimuli, explaining the need for a large set of interneuron pathways to generate the dynamic neural code for natural scenes.
Pinned, locked, pushed, and pulled traveling waves in structured environments
Authors: Wang Ching-Hao , Matin Sakib , George Ashish B. , Korolev Kirill S. 
Published: June 2018

AbstractTraveling fronts describe the transition between two alternative states in a great number of physical and biological systems. Examples include the spread of beneficial mutations, chemical reactions, and the invasions by foreign species. In homogeneous environments, the alternative states are separated by a smooth front moving at a constant velocity. This simple picture can break down in structured environments such as tissues, patchy landscapes, and microfluidic devices. Habitat fragmentation can pin the front at a particular location or lock invasion velocities into specific values. Locked velocities are not sensitive to moderate changes in dispersal or growth and are determined by the spatial and temporal periodicity of the environment. The synchronization with the environment results in discontinuous fronts that propagate as periodic pulses. We characterize the transition from continuous to locked invasions and show that it is controlled by positive density-dependence in dispersal or growth. We also demonstrate that velocity locking is robust to demographic and environmental fluctuations and examine stochastic dynamics and evolution in locked invasions.
Transcranial direct current stimulation (tDCS) over the left prefrontal cortex does not affect time-trial self-paced cycling performance: Evidence from oscillatory brain activity and power output
Authors: Holgado Darías , Zandonai Thomas , Ciria Luis F. , Zabala Mikel , Hopker James , Sanabria Daniel 
Published: June 2018

AbstractObjectivesTo test the hypothesis that transcranial direct current stimulation (tDCS) over the left dorsolateral prefrontal cortex (DLPFC) influences performance in a 20-min time-trial self-paced exercise and electroencephalographic (EEG) oscillatory brain activity in a group of trained male cyclists.DesignThe study consisted of a pre-registered (https://osf.io/rf95j/), randomised, sham-controlled, single-blind, within-subject design experiment.Methods36 trained male cyclists, age 27 (6.8) years, weight 70.1 (9.5) Kg; VO2max: 54 (6.13) ml.min−1.kg−1, Maximal Power output: 4.77 (0.6) W/kg completed a 20-min time-trial self-paced exercise in three separate sessions, corresponding to three stimulation conditions: anodal, cathodal and sham. tDCS was administered before each test during 20-min at a current intensity of 2.0 mA. The anode electrode was placed over the DLPFC and the cathode in the contralateral shoulder. In each session, power output, heart rate, sRPE and EEG (at baseline and during exercise) was measured.ResultsThere were no differences (F = 0.31, p > 0.05) in power output between the stimulation conditions: anodal (235 W [95%CI 222 - 249 W]; cathodal (235 W [95%CI 222 - 248 W] and sham (234 W [95%CI 220 - 248 W]. Neither heart rate, sRPE nor EEG activity were affected by tDCS (all Ps > 0.05).ConclusiontDCS over the left DLFC did not affect self-paced exercise performance in trained cyclists. Moreover, tDCS did not elicit any change on oscillatory brain activity either at baseline or during exercise. Our data suggest that the effects of tDCS on endurance performance should be taken with caution.
A simple and flexible computational framework for inferring sources of heterogeneity from single-cell dynamics
Authors: Dharmarajan Lekshmi , Kaltenbach Hans-Michael , Rudolf Fabian , Stelling Joerg 
Published: June 2018

AbstractThe availability of high-resolution single-cell data makes data analysis and interpretation an important open problem, for example, to disentangle sources of cell-to-cell and intra-cellular variability. Nonlinear mixed effects models (NLMEs), well established in pharmacometrics, account for such multiple sources of variations, but their estimation is often difficult. Single-cell analysis is an even more challenging application with larger data sets and models that are more complicated. Here, we show how to leverage the quality of time-lapse microscopy data with a simple two-stage method to estimate realistic dynamic NLMEs accurately. We demonstrate accuracy by benchmarking with a published model and dataset, and scalability with a new mechanistic model and corresponding dataset for amino acid transporter endocytosis in budding yeast. We also propose variation-based sensitivity analysis to identify time-dependent causes of cell-to-cell variability, highlighting important sub-processes in endocytosis. Generality and simplicity of the approach will facilitate customized extensions for analyzing single-cell dynamics.
Facilitation of hERG channels by blockers: a mechanism predicted to reduce lethal cardiac arrhythmias
Authors: Furutani Kazuharu , Tsumoto Kunichika , Chen I-Shan , Handa Kenichiro , Yamakawa Yuko , Sack Jon T. , Kurachi Yoshihisa 
Published: June 2018

AbstractFatal cardiac arrhythmias are caused by some, but not all, drugs that inhibit the cardiac rapid delayed-rectifier current (IKr) by blocking hERG channels. Here, we propose a novel mechanism that could make certain hERG blockers less proarrhythmic. Several drugs that block hERG channels, yet have favorable cardiac safety profiles, also evoke another effect; they increase the current amplitude upon low-voltage depolarization (facilitation). Voltage-clamp recordings of hERG block and facilitation by nifekalant, a Class III antiarrhythmic agent, constrained a model of human cardiac IKr. In human ventricular action potential simulations, nifekalant showed its therapeutic ability to suppress ectopic excitations, with or without facilitation. Without facilitation, excessive IKr block evoked early afterdepolarizations, which cause lethal arrhythmias. Facilitation prevented early afterdepolarizations at the same degree of block by increasing IKr during repolarization phase of action potentials. Thus, facilitation is proposed to reduce the arrhythmogenic risk of hERG blockers.AbbreviationsAP: action potential; APD: action potential duration; APD90: action potential duration measured at 90% repolarization; EAD: early afterdepolarization; hERG: human ether-ago-go-related gene; ICaL: L-type Ca2+ channel current; Inet: net ionic current; IK1: inward-rectifier potassium current; IKr: rapid component of the delayed-rectifier potassium current; INa: sodium current; ORd: O’Hara-Rudy dynamic
Not-so-working memory: Drift in fMRI pattern representations during maintenance predicts errors in a visual working memory task
Authors: Lim Phui Cheng , Ward Emily J. , Vickery Timothy J. , Johnson Matthew R. 
Published: June 2018

AbstractWorking memory (WM) is critical to many aspects of cognition, but it frequently fails. Much WM research has focused on capacity limits, but even for single, simple features, the fidelity of individual representations is limited. Why is this? We used fMRI and a pattern-based index of “representational drift” to investigate how ongoing changes in brain activity patterns throughout the WM maintenance period predicted performance, using a delayed-match-to-sample task for a single item with a single critical feature: orientation. In trials where the target and probe stimuli matched, participants incorrectly reported more non-matches when their activity patterns drifted away from the target. In trials where the target and probe did not match, participants incorrectly reported more matches when their activity patterns drifted towards the probe. Our results suggest that WM errors are not simply due to unstructured noise, but also drift within representation space that can be indexed by neuroimaging.