bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using diving waves for detecting shallow overburden gas layers
Authors: Landrø Martin , Foseide Bjarte , Liu Izzie Yi 
Published: March 2021

We have used simple time-shift analysis of diving waves to analyze shallow gas layers in a sedimentary overburden. By using simple equations for how the traveltime will change if a thin sand layer is charged by gas in a localized and constrained region, we show that such variations can be used to map and quantify the thickness of the gas layer. We use conventional 3D seismic data acquired close to a well where an unintended underground gas flow occurred in 1989. Raw seismic data are used as input, and time shifts are estimated for constant offsets for events that are interpreted as being predominantly diving waves. By assuming that the very shallow subsurface has a constant velocity gradient of [Formula: see text], we find diving wave time shifts that fit an average thickness of the gas layer of approximately 3–4 m. This is the minimum gas thickness because it is assumed that the time-shift analysis captures the diving wave hitting the top and the base of the gas layer (sufficiently dense offset sampling is important to achieve this). The outline and circumference of the close-to-circular gas anomaly around the well obtained by the diving wave analysis are confirmed by 3D reflection mapping of the same anomaly.
Training deep networks with only synthetic data: Deep-learning-based near-offset reconstruction for (closed-loop) surface-related multiple estimation on shallow-water field data
Authors: Qu Shan , Verschuur Eric , Zhang Dong , Chen Yangkang 
Published: March 2021

Accurate removal of surface-related multiples remains a challenge in shallow-water cases. One reason is that the success of surface-related multiple estimation (SRME)-related algorithms is sensitive to the quality of the near-offset reconstruction. When it comes to a larger missing gap and a shallower water bottom, the state-of-the-art near-offset gap construction method — the parabolic Radon transform — fails to provide reliable recovery of the shallow reflections due to the limited information from the data and highly curved events at near offsets with strong lateral amplitude variations. Therefore, we have developed a novel workflow that first deploys a deep-learning-based reconstruction of the shallow reflections and then uses the reconstructed data as the input for the subsequent surface multiple removal. In particular, we use a convolutional neural network architecture — U-net that was developed from convolutional autoencoders with extra direct skip connections between different levels of encoders and the corresponding decoders. Instead of using field data directly in network training, the training set is carefully synthesized based on the prior water-layer information of the field data; thus, a fully sampled field data set, which is difficult to obtain, is not needed for training in our workflow. An inversion-based approach — closed-loop SRME — is used for the surface multiple removal, in which the primaries are directly estimated via full-waveform inversion in a data-driven manner. Finally, the effectiveness of our workflow is determined based on 2D North Sea field data in a shallow-water scenario (92.5 m water depth) with a relatively large minimum offset (150 m).
Circulating Galectin-3 Levels Are Not Associated With Nonalcoholic Fatty Liver Disease: A Mendelian Randomization Study
Authors: Tremblay Maxime , Perrot Nicolas , Ghodsian Nooshin , Gobeil Émilie , Couture Christian , Mitchell Patricia L , Thériault Sébastien , Arsenault Benoit J 
Published: March 2021

Abstract

Context
The impact of galectin-3 inhibitors on nonalcoholic fatty liver diseases (NAFLD)-related outcomes is currently under investigation in randomized clinical trials. Whether there is a causal association between plasma galectin-3 levels and NAFLD is unknown.

Objective
To evaluate the causal effect of circulating galectin-3 levels on NAFLD as well as &gt;800 other human diseases.

Design
Inverse variance-weighted (IVW) Mendelian randomization (MR) and phenome-wide MR.

Setting
Summary statistics of genome-wide association studies.

Patients
Participants of the UK Biobank, Electronic Medical Records and Genomics (eMERGE), FinnGen, Prevention of Renal and Vascular End-Stage Disease (PREVEND), and IMPROVE cohorts.

Intervention
Identification of independent single-nucleotide polymorphisms (SNPs) associated with galectin-3 levels (P &lt; 5 × 10-8) in the PREVEND (14 SNPs) and IMPROVE (3 SNPs) cohorts.

Main outcome measures
Presence of NAFLD in a meta-analysis of genome-wide association study of the eMERGE, UK Biobank, and FinnGen cohorts (3042 NAFLD cases and 504 853 controls), as well as &gt;800 other human diseases in the UK Biobank and FinnGen.

Results
Using IVW-MR, we found no causal association between galectin-3 levels and NAFLD in the meta-analysis of the 3 cohorts or in each individual cohort. After correction for multiple testing, we found no causal association between galectin-3 levels and &gt;800 human disease-related traits.

Conclusions
This MR study revealed no causal associations between circulating galectin-3 levels and NAFLD or any other disease traits, suggesting that plasma galectin-3 levels may not be directly implicated in the pathogenesis of NAFLD or other human diseases.
Identification and Functional Characterization of Metabolites for Bone Mass in Peri- and Postmenopausal Chinese Women
Authors: Gong Rui , Xiao Hong-Mei , Zhang Yin-Hua , Zhao Qi , Su Kuan-Jui , Lin Xu , Mo Cheng-Lin , Zhang Qiang , Du Ya-Ting , Lyu Feng-Ye , Chen Yuan-Cheng , Peng Cheng , Liu Hui-Min , Hu Shi-Di , Pan Dao-Yan , Chen Zhi , Li Zhang-Fang , Zhou Rou , Wang Xia-Fang , Lu Jun-Min , Ao Zeng-Xin , Song Yu-Qian , Weng Chan-Yan , Tian Qing , Schiller Martin R , Papasian Christopher J , Brotto Marco , Shen Hui , Shen Jie , Deng Hong-Wen 
Published: March 2021

Abstract

Context
Although metabolic profiles appear to play an important role in menopausal bone loss, the functional mechanisms by which metabolites influence bone mineral density (BMD) during menopause are largely unknown.

Objective
We aimed to systematically identify metabolites associated with BMD variation and their potential functional mechanisms in peri- and postmenopausal women.

Design and Methods
We performed serum metabolomic profiling and whole-genome sequencing for 517 perimenopausal (16%) and early postmenopausal (84%) women aged 41 to 64 years in this cross-sectional study. Partial least squares regression and general linear regression analysis were applied to identify BMD-associated metabolites, and weighted gene co-expression network analysis was performed to construct co-functional metabolite modules. Furthermore, we performed Mendelian randomization analysis to identify causal relationships between BMD-associated metabolites and BMD variation. Finally, we explored the effects of a novel prominent BMD-associated metabolite on bone metabolism through both in vivo/in vitro experiments.

Results
Twenty metabolites and a co-functional metabolite module (consisting of fatty acids) were significantly associated with BMD variation. We found dodecanoic acid (DA), within the identified module causally decreased total hip BMD. Subsequently, the in vivo experiments might support that dietary supplementation with DA could promote bone loss, as well as increase the osteoblast and osteoclast numbers in normal/ovariectomized mice. Dodecanoic acid treatment differentially promoted osteoblast and osteoclast differentiation, especially for osteoclast differentiation at higher concentrations in vitro (eg,10, 100 μM).

Conclusions
This study sheds light on metabolomic profiles associated with postmenopausal osteoporosis risk, highlighting the potential importance of fatty acids, as exemplified by DA, in regulating BMD.
Low-Density Lipoprotein Cholesterol Is Associated With Insulin Secretion
Authors: Dannecker Corinna , Wagner Robert , Peter Andreas , Hummel Julia , Vosseler Andreas , Häring Hans-Ulrich , Fritsche Andreas , Birkenfeld Andreas L , Stefan Norbert , Heni Martin 
Published: March 2021

Abstract

Context
Pharmacological lowering of low-density lipoprotein (LDL) cholesterol potently reduces cardiovascular risk while concurrently increasing type 2 diabetes risk.

Objective
The aim of this study was to investigate the relationship between LDL cholesterol concentrations and insulin secretion and glucagon levels.

Methods
A total of 3039 individuals without cholesterol-lowering therapy, but with increased risk for diabetes, underwent routine blood tests and a 5-point oral glucose tolerance test (OGTT). Glucagon concentrations, insulin secretion, and insulin clearance indices were derived from the OGTT.

Results
There was no association between LDL cholesterol and fasting glucagon (P = .7, β = –.01) or post–glucose load glucagon levels (P = .7, β = –.07), but we detected significant positive associations of LDL cholesterol and C-peptide–based indices of insulin secretion (area under the curve [AUC]C-Peptide(0-30min)/AUCGlucose(0-30min): P &lt; .001, β = .06; AUCC-Peptide(0-120min) /AUCGlucose(0-120min): P &lt; .001, β = –.08). In contrast, we found a negative association of insulin-based insulin secretion indices with LDL concentrations (insulinogenic index: P = .01, β = –.04; disposition index: P &lt; .001, β = –.06). LDL cholesterol levels, however, were positively associated with insulin clearance assessed from C-peptide and insulin concentrations, both in the fasting state and post–glucose load (P &lt; .001, β = .09 and P &lt; .001, β = .06, respectively).

Conclusion
As C-peptide based indices reflect insulin secretion independent of hepatic clearance, our results indicate lower insulin secretion in case of lesser LDL cholesterol. This could explain deteriorating glycemic control in response to cholesterol-lowering drugs.
Characterizing a Common CERS2 Polymorphism in a Mouse Model of Metabolic Disease and in Subjects from the Utah CAD Study
Authors: Nicholson Rebekah J , Poss Annelise M , Maschek J Alan , Cox James E , Hopkins Paul N , Hunt Steven C , Playdon Mary C , Holland William L , Summers Scott A 
Published: March 2021

AbstractContextGenome-wide association studies have identified associations between a common single nucleotide polymorphism (SNP; rs267738) in CERS2, a gene that encodes a (dihydro)ceramide synthase that is involved in the biosynthesis of very-long-chain sphingolipids (eg, C20-C26) and indices of metabolic dysfunction (eg, impaired glucose homeostasis). However, the biological consequences of this mutation on enzyme activity and its causal roles in metabolic disease are unresolved.ObjectiveThe studies described herein aimed to characterize the effects of rs267738 on CERS2 enzyme activity, sphingolipid profiles, and metabolic outcomes.DesignWe performed in-depth lipidomic and metabolic characterization of a novel CRISPR knock-in mouse modeling the rs267738 variant. In parallel, we conducted mass spectrometry-based, targeted lipidomics on 567 serum samples collected through the Utah Coronary Artery Disease study, which included 185 patients harboring 1 (n = 163) or both (n = 22) rs267738 alleles.ResultsIn-silico analysis of the amino acid substitution within CERS2 caused by the rs267738 mutation suggested that rs267738 is deleterious for enzyme function. Homozygous knock-in mice had reduced liver CERS2 activity and enhanced diet-induced glucose intolerance and hepatic steatosis. However, human serum sphingolipids and a ceramide-based cardiac event risk test 1 score of cardiovascular disease were not significantly affected by rs267738 allele count.ConclusionsThe rs267738 SNP leads to a partial loss-of-function of CERS2, which worsened metabolic parameters in knock-in mice. However, rs267738 was insufficient to effect changes in serum sphingolipid profiles in subjects from the Utah Coronary Artery Disease Study.
A Body Weight Sensor Regulates Prepubertal Growth via the Somatotropic Axis in Male Rats
Authors: Jansson John-Olov , Dalmau Gasull Adria , Schéle Erik , Dickson Suzanne L , Palsdottir Vilborg , Palmquist Anders , Gironès Ferran Font , Bellman Jakob , Anesten Fredrik , Hägg Daniel , Ohlsson Claes 
Published: March 2021

Abstract
In healthy conditions, prepubertal growth follows an individual specific growth channel. Growth hormone (GH) is undoubtedly the major regulator of growth. However, the homeostatic regulation to maintain the individual specific growth channel during growth is unclear. We recently hypothesized a body weight sensing homeostatic regulation of body weight during adulthood, the gravitostat. We now investigated if sensing of body weight also contributes to the strict homeostatic regulation to maintain the individual specific growth channel during prepubertal growth. To evaluate the effect of increased artificial loading on prepubertal growth, we implanted heavy (20% of body weight) or light (2% of the body weight) capsules into the abdomen of 26-day-old male rats. The body growth, as determined by change in biological body weight and growth of the long bones and the axial skeleton, was reduced in rats bearing a heavy load compared with light load. Removal of the increased load resulted in a catch-up growth and a normalization of body weight. Loading decreased hypothalamic growth hormone releasing hormone mRNA, liver insulin-like growth factor (IGF)-1 mRNA, and serum IGF-1, suggesting that the reduced body growth was caused by a negative feedback regulation on the somatotropic axis and this notion was supported by the fact that increased loading did not reduce body growth in GH-treated rats. Based on these data, we propose the gravitostat hypothesis for the regulation of prepubertal growth. This states that there is a homeostatic regulation to maintain the individual specific growth channel via body weight sensing, regulating the somatotropic axis and explaining catch-up growth.
Endometrium On-a-Chip Reveals Insulin- and Glucose-induced Alterations in the Transcriptome and Proteomic Secretome
Authors: De Bem Tiago H C , Tinning Haidee , Vasconcelos Elton J R , Wang Dapeng , Forde Niamh 
Published: March 2021

Abstract
The molecular interactions between the maternal environment and the developing embryo are key for early pregnancy success and are influenced by factors such as maternal metabolic status. Our understanding of the mechanism(s) through which these individual nutritional stressors alter endometrial function and the in utero environment for early pregnancy success is, however, limited. Here we report, for the first time, the use of an endometrium-on-a-chip microfluidics approach to produce a multicellular endometrium in vitro. Isolated endometrial cells (epithelial and stromal) from the uteri of nonpregnant cows in the early luteal phase (Days 4-7) were seeded in the upper chamber of the device (epithelial cells; 4-6 × 104 cells/mL) and stromal cells seeded in the lower chamber (1.5-2 × 104 cells/mL). Exposure of cells to different concentrations of glucose (0.5, 5.0, or 50 mM) or insulin (Vehicle, 1 or 10 ng/mL) was performed at a flow rate of 1 µL/minute for 72 hours. Quantitative differences in the cellular transcriptome and the secreted proteome of in vitro–derived uterine luminal fluid were determined by RNA-sequencing and tandem mass tagging mass spectrometry, respectively. High glucose concentrations altered 21 and 191 protein-coding genes in epithelial and stromal cells, respectively (P &lt; .05), with a dose-dependent quantitative change in the protein secretome (1 and 23 proteins). Altering insulin concentrations resulted in limited transcriptional changes including transcripts for insulin-like binding proteins that were cell specific but altered the quantitative secretion of 196 proteins. These findings highlight 1 potential mechanism by which changes to maternal glucose and insulin alter uterine function.
The high energetic cost of rapid force development in muscle
Authors: van der Zee Tim J. , Kuo Arthur D. 
Published: March 2021

ABSTRACT
Muscles consume metabolic energy for active movement, particularly when performing mechanical work or producing force. Less appreciated is the cost for activating muscle quickly, which adds considerably to the overall cost of cyclic force production. However, the cost magnitude relative to the cost of mechanical work, which features in many movements, is unknown. We therefore tested whether fast activation is costly compared with performing work or producing isometric force. We hypothesized that metabolic cost would increase with a proposed measure termed force rate (rate of increase in muscle force) in cyclic tasks, separate from mechanical work or average force level. We tested humans (N=9) producing cyclic knee extension torque against an isometric dynamometer (torque 22 N m, cyclic waveform frequencies 0.5–2.5 Hz), while also quantifying quadriceps muscle force and work against series elasticity (with ultrasonography), along with metabolic rate through respirometry. Net metabolic rate increased by more than four-fold (10.5 to 46.8 W) with waveform frequency. At high frequencies, the hypothesized force-rate cost accounted for nearly half (40%) of energy expenditure. This exceeded the cost for average force (17%) and was comparable to the cost for shortening work (43%). The force-rate cost is explained by additional active calcium transport necessary for producing forces at increasing waveform frequencies, owing to rate-limiting dynamics of force production. The force-rate cost could contribute substantially to the overall cost of movements that require cyclic muscle activation, such as locomotion.
Orexin-A inhibits fictive air breathing responses to respiratory stimuli in the bullfrog tadpole (Lithobates catesbeianus)
Authors: Fonseca Elisa M. , Janes Tara A. , Fournier Stéphanie , Gargaglioni Luciane H. , Kinkead Richard 
Published: March 2021

ABSTRACTIn pre-metamorphic tadpoles, the neural network generating lung ventilation is present but actively inhibited; the mechanisms leading to the onset of air breathing are not well understood. Orexin (ORX) is a hypothalamic neuropeptide that regulates several homeostatic functions, including breathing. While ORX has limited effects on breathing at rest, it potentiates reflexive responses to respiratory stimuli mainly via ORX receptor 1 (OX1R). Here, we tested the hypothesis that OX1Rs facilitate the expression of the motor command associated with air breathing in pre-metamorphic bullfrog tadpoles (Lithobates catesbeianus). To do so, we used an isolated diencephalic brainstem preparation to determine the contributions of OX1Rs to respiratory motor output during baseline breathing, hypercapnia and hypoxia. A selective OX1R antagonist (SB-334867; 5–25 µmol l−1) or agonist (ORX-A; 200 nmol l−1 to 1 µmol l−1) was added to the superfusion media. Experiments were performed under basal conditions (media equilibrated with 98.2% O2 and 1.8% CO2), hypercapnia (5% CO2) or hypoxia (5–7% O2). Under resting conditions gill, but not lung, motor output was enhanced by the OX1R antagonist and ORX-A. Hypercapnia alone did not stimulate respiratory motor output, but its combination with SB-334867 increased lung burst frequency and amplitude, lung burst episodes, and the number of bursts per episode. Hypoxia alone increased lung burst frequency and its combination with SB-334867 enhanced this effect. Inactivation of OX1Rs during hypoxia also increased gill burst amplitude, but not frequency. In contrast with our initial hypothesis, we conclude that ORX neurons provide inhibitory modulation of the CO2 and O2 chemoreflexes in pre-metamorphic tadpoles.
Distinct neuron phenotypes may serve object feature sensing in the electrosensory lobe of Gymnotus omarorum
Authors: Nogueira Javier , Castelló María E. , Lescano Carolina , Caputi Ángel A. 
Published: March 2021

ABSTRACT
Early sensory relay circuits in the vertebrate medulla often adopt a cerebellum-like organization specialized for comparing primary afferent inputs with central expectations. These circuits usually have a dual output, carried by center ON and center OFF neurons responding in opposite ways to the same stimulus at the center of their receptive fields. Here, we show in the electrosensory lateral line lobe of Gymnotiform weakly electric fish that basilar pyramidal neurons, representing ‘ON’ cells, and non-basilar pyramidal neurons, representing ‘OFF’ cells, have different intrinsic electrophysiological properties. We used classical anatomical techniques and electrophysiological in vitro recordings to compare these neurons. Basilar neurons are silent at rest, have a high threshold to intracellular stimulation, delayed responses to steady-state depolarization and low pass responsiveness to membrane voltage variations. They respond to low-intensity depolarizing stimuli with large, isolated spikes. As stimulus intensity increases, the spikes are followed by a depolarizing after-potential from which phase-locked spikes often arise. Non-basilar neurons show a pacemaker-like spiking activity, smoothly modulated in frequency by slow variations of stimulus intensity. Spike-frequency adaptation provides a memory of their recent firing, facilitating non-basilar response to stimulus transients. Considering anatomical and functional dimensions, we conclude that basilar and non-basilar pyramidal neurons are clear-cut, different anatomo-functional phenotypes. We propose that, in addition to their role in contrast processing, basilar pyramidal neurons encode sustained global stimuli such as those elicited by large or distant objects while non-basilar pyramidal neurons respond to transient stimuli due to movement of objects with a textured surface.
Exploring Metastable Oxynitrides by Thin Film Growth Approach
Authors: Hirose Yasushi , Hasegawa Tetsuya 
Published: March 2021

Abstract
Metal oxynitrides are expected to show unique chemical and physical properties suitable for various applications. However, compared with oxides, the chemical space of oxynitrides has not been well explored mainly due to their thermal instability and high reaction temperature required in conventional bulk synthesis methods. Highly nonequilibrium thin film growth is a promising route for obtaining those unexplored oxynitrides. In this account, we will overview recent studies on thin film synthesis of oxynitrides, especially focusing on exploration of metastable phases, such as mid- and late-transition metal compounds, metastable polymorphs, geometrical isomers with respect to anion coordination, and amorphous phases.
Macaroni Fullerene Crystals-Derived Mesoporous Carbon Tubes as a High Rate Performance Supercapacitor Electrode Material
Authors: Maji Subrata , Shrestha Rekha Goswami , Lee Jaewoo , Han Sang A , Hill Jonathan P , Kim Jung Ho , Ariga Katsuhiko , Shrestha Lok Kumar 
Published: March 2021

Abstract
Self-assembled macaroni fullerene C60 crystals (MFCs) of uniform shape and narrow size distribution are produced using the dynamic liquid-liquid interfacial precipitation method under ambient conditions. High temperature heat treatment (900 °C) of MFCs yields mesoporous carbons tubes (MCTs) retaining the initial morphology. This novel mesoporous carbon material exhibits excellent electrochemical supercapacitive performance due to high surface areas (1544 m2 g−1), large pore volume (2.936 cm3 g−1) and interconnected porous structures. In a three-electrode aqueous electrolyte system, the electrode achieved high specific capacitance ca. 422 F g−1 at a current density of 1 A g−1 followed by excellent cycling stability (&gt;95%) after 10,000 charging-discharging cycles at 20 A g−1. We believe that the novel mesoporous carbon material derived from a π-electron carbon source can be used as an alternative electrode material in advanced supercapacitor devices.