bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flow and detailed 3D morphodynamic data from laboratory experiments of fluvial dike breaching
Authors: Rifai Ismail , El kadi Abderrezzak Kamal , Erpicum Sébastien , Archambeau Pierre , Violeau Damien , Pirotton Michel , Dewals Benjamin 
Published: May 2019

AbstractThis paper presents a dataset obtained from fifty four laboratory experiments of the breaching of fluvial dikes due to flow overtopping. Data were collected on two complementary experimental setups, each consisting of a main channel representing the river, an erodible lateral dike and a floodplain. The dataset covers seven test series, involving varying hydraulic boundary conditions (e.g. inflow discharge, downstream boundary conditions), main channel dimensions, as well as bottom and dike material. The following experimental data were produced: time series of water levels in the main channel, time series of flow discharges in the main channel and through the breach, as well as high resolution 3D reconstructions of the breach geometry during its expansion. The latter measurements were performed using a novel non-intrusive laser profilometry technique developed for this research. Reuse of the collected data will support efforts to improve our understanding of the physical processes underpinning fluvial dike breaching. It will also enable benchmarking the accuracy of conceptual or detailed numerical models for the prediction of dike breaching, which is central to flood risk management.
A global, empirical, harmonised dataset of soil organic carbon changes under perennial crops
Authors: Ledo Alicia , Hillier Jonathan , Smith Pete , Aguilera Eduardo , Blagodatskiy Sergey , Brearley Francis Q. , Datta Ashim , Diaz-Pines Eugenio , Don Axel , Dondini Marta , Dunn Jennifer , Feliciano Diana Marisa , Liebig Mark A. , Lang Rong , Llorente Mireia , Zinn Yuri Lopes , McNamara Niall , Ogle Stephen , Qin Zhangcai , Rovira Pere , Rowe Rebecca , Vicente-Vicente José Luis , Whitaker Jeanette , Yue Qian , Zerihun Ayalsew 
Published: May 2019

AbstractA global, unified dataset on Soil Organic Carbon (SOC) changes under perennial crops has not existed till now. We present a global, harmonised database on SOC change resulting from perennial crop cultivation. It contains information about 1605 paired-comparison empirical values (some of which are aggregated data) from 180 different peer-reviewed studies, 709 sites, on 58 different perennial crop types, from 32 countries in temperate, tropical and boreal areas; including species used for food, bioenergy and bio-products. The database also contains information on climate, soil characteristics, management and topography. This is the first such global compilation and will act as a baseline for SOC changes in perennial crops. It will be key to supporting global modelling of land use and carbon cycle feedbacks, and supporting agricultural policy development.
Changes in bone metabolic profile associated with pregnancy or lactation
Authors: Miyamoto Takeshi , Miyakoshi Kei , Sato Yuiko , Kasuga Yoshifumi , Ikenoue Satoru , Miyamoto Kana , Nishiwaki Yuji , Tanaka Mamoru , Nakamura Masaya , Matsumoto Morio 
Published: May 2019

AbstractCalcium and nutrients are transferred from mothers to fetuses or infants during pregnancy or lactation, respectively, promoting metabolic changes in the mother, many uncharacterized. To evaluate these changes, we undertook two parallel studies. In one we analyzed fourteen clinical cases of vertebral fragility fractures, at or before three months after partum, in mothers who breastfed their infants. In the other, we enrolled 79 additional pregnant subjects, some who chose to breastfeed and others who did not, and analyzed changes in bone metabolic status starting between 34 and 36 weeks of gestation and ending one month after partum. In the larger group, bone-resorbing and bone-forming parameters such as serum TRACP5b and osteocalcin, respectively, significantly increased after partum. Among parameters that changed after partum, serum PTH and the bone-resorbing markers serum TRACP5b and urine NTX were significantly higher in mothers who only breastfed infants compared to mothers who fed infants formula or a mix of both. However, bone-forming parameters were comparable between breastfeeding and non-breast-feeding groups after partum, suggesting that elevated bone-resorption occurs only in the breastfeeding group. Radiographic analysis after partum demonstrated that no subject among the 79 analyzed showed vertebral fractures, even those who breastfed exclusively. Among fracture cases analyzed, subjects exhibited significantly lower bone mineral density than did non-fracture cases in breastfeeding-only subjects. We conclude that bone metabolic status significantly changes over the period between pregnancy and post-partum lactation, and that low bone mineral density seen in a small subset of breastfeeding-only cases likely causes post-partum vertebral fragility fractures.
From jamming to fast compaction dynamics in granular binary mixtures
Authors: Pillitteri Salvatore , Lumay Geoffroy , Opsomer Eric , Vandewalle Nicolas 
Published: May 2019

AbstractBinary granular mixtures are known to show various packing arrangements depending on both fractions and size ratios of their components. While the final packing fraction can be estimated by geometrical arguments, the dynamics of the pile submitted to gentle vibrations towards a dense state is seen to be highly size ratio dependent. We observe experimentally a diverging compaction characteristic time close to a critical size ratio, such that the grain mobility in the packing is the lowest close to the percolation threshold, when small particles can pass through the voids left by the large ones. Moreover, we evidence a fast compaction dynamics regime when the grain size ratio is large enough.
Gender-specific mediators of the association between parental education and adiposity among adolescents: the HEIA study
Authors: Gebremariam Mekdes K. , Arah Onyebuchi A. , Bergh Ingunn H. , Andersen Lene F. , Ommundsen Yngvar , Totland Torunn H. , Bjelland Mona , Grydeland May , Lien Nanna 
Published: May 2019

AbstractIdentifying the mechanisms behind socioeconomic inequalities in adiposity among youth is vital for efforts aimed at combating these inequalities. The study explored whether a broad range of behavioral and familial factors mediated the associations between parental education and indicators of adiposity among adolescents. Baseline data from a school-based intervention study conducted in 2007 among 11-year-old adolescents were used. Anthropometric outcomes, physical activity and sedentary time among adolescents were objectively measured. Other behavioral variables and parental waist circumference were self-reported. Mediation analyses were conducted. Among boys, maternal waist circumference (WC), paternal WC and TV viewing mediated 16%, 11.5% and 13% of the association between parental education and adolescent WC. The respective proportions when body fat percentage was used as the outcome variable were 22.5%, 16% and 21%. Among girls, maternal and paternal WC mediated 20% and 14% of the association between parental education and WC. The respective proportions when body fat percentage was used as the outcome variable were 14% and 10%. Other included variables did not play any mediating role. Parental WC was found to be a mediator of socioeconomic differences in adiposity in both genders; underlying mechanisms were however not investigated. Among boys, reducing TV time could contribute to the reduction of social inequalities in adiposity.
Age-related changes in molecular organization of type I collagen in tendon as probed by polarized SHG and Raman microspectroscopy
Authors: Van Gulick Laurence , Saby Charles , Morjani Hamid , Beljebbar Abdelilah 
Published: May 2019

AbstractType I Collagen is one of the most abundant proteins of the extracellular matrix of the most organs. During chronological aging or in diseases, type I collagen undergoes biochemical and structural changes which can impact biomechanical and physiological properties of organs. In this study, we have investigated the age-related changes in the molecular organization of type I collagen in rat tails tendon using polarized Raman spectroscopy. Our results show that Amide I, amide III as well as the bands related to proline and hydroxyproline are highly sensitive to polarization and age-related. On the other hand, 1453 and 1270 cm−1 do not show any preferential orientation. Depolarization and anisotropic ratios were used to provide information about the changes in orientation of collagen fibers with aging. The anisotropy degree of Raman bands increase from adult to old collagen, indicating a higher collagen fibers alignment to the fascicle backbone axis in old tendons, and consequently a higher straightness of collagen fibers. These data were correlated to those obtained using polarized second harmonic generation technique. Polarized Raman mapping showed a more homogeneous spatial distribution of collagen fibers alignment to the fascicle axis in old tendon. This confirms a higher straightness of collagen fiber with aging.
Hybrid Nanostructured Porous Silicon-Silver Layers for Wideband Optical Absorption
Authors: Martín-Palma Raúl J. , McAtee Patrick D. , Ramadan Rehab , Lakhtakia Akhlesh 
Published: May 2019

AbstractAs subwavelength nanostructures are receiving increasing attention for photonic and plasmonic applications, we grew nanostructured porous silicon (n-PS) and hybrid n-PS/Ag layers onto silicon substrates and measured their reflection and absorption characteristics as functions of the wavelength, angle of incidence, and polarization state of incident light. The experimental results show that the absorption characteristics of the hybrid n-PS/Ag layer can be controlled by selecting the appropriate combination of its thickness and porosity, together with the density of infiltrant silver nanoparticles. The observed wideband optical absorption characteristics of the hybrid n-PS/Ag layers might be useful in light-harvesting devices and photodetectors, since the overall efficiency will be increased as a result of increased field-of-view for both s- and p-polarization states of incident light.
Acceleration of the precession frequency for optically-oriented electron spins in ferromagnetic/semiconductor hybrids
Authors: Moraes F. C. D. , Ullah S. , Balanta M. A. G. , Iikawa F. , Danilov Y. A. , Dorokhin M. V. , Vikhrova O. V. , Zvonkov B. N. , Hernandez F. G. G. 
Published: May 2019

AbstractTime-resolved Kerr rotation measurements were performed in InGaAs/GaAs quantum wells nearby a doped Mn delta layer. Our magneto-optical results show a typical time evolution of the optically-oriented electron spin in the quantum well. Surprisingly, this is strongly affected by the Mn spins, resulting in an increase of the spin precession frequency in time. This increase is attributed to the variation in the effective magnetic field induced by the dynamical relaxation of the Mn spins. Two processes are observed during electron spin precession: a quasi-instantaneous alignment of the Mn spins with photo-excited holes, followed by a slow alignment of Mn spins with the external transverse magnetic field. The first process leads to an equilibrium state imprinted in the initial precession frequency, which depends on pump power, while the second process promotes a linear frequency increase, with acceleration depending on temperature and external magnetic field. This observation yields new information about exchange process dynamics and on the possibility of constructing spin memories, which can rapidly respond to light while retaining information for a longer period.
A Targeted Mass Spectrometric Assay for Reliable Sensitive Hepcidin Quantification
Authors: Moghieb Ahmed , Tesfay Lia , Nie Song , Gritsenko Marina , Fillmore Thomas L. , Jacobs Jon M. , Smith Richard D. , Torti Frank M. , Torti Suzy V. , Shi Tujin , Ansong Charles 
Published: May 2019

AbstractHepcidin, a cysteine-rich peptide hormone, secreted mainly by the liver, plays a central role in iron metabolism regulation. Emerging evidence suggests that disordered iron metabolism is a risk factor for various types of diseases including cancers. However, it remains challenging to apply current mass spectrometry (MS)-based hepcidin assays for precise quantification due to the low fragmentation efficiency of intact hepcidin as well as synthesis difficulties for the intact hepcidin standard. To address these issues we recently developed a reliable sensitive targeted MS assay for hepcidin quantification from clinical samples that uses fully alkylated rather than intact hepcidin as the internal standard. Limits of detection and quantification were determined to be <0.5 ng/mL and 1 ng/mL, respectively. Application of the alkylated hepcidin assay to 70 clinical plasma samples (42 non-cancerous and 28 ovarian cancer patient samples) enabled reliable detection of endogenous hepcidin from the plasma samples, as well as conditioned culture media. The hepcidin concentrations ranged from 0.0 to 95.6 ng/mL across non-cancerous and cancer plasma specimens. Interestingly, cancer patients were found to have significantly higher hepcidin concentrations compared to non-cancerous patients (mean: 20.6 ng/ml for cancer; 5.94 ng/ml for non-cancerous) (p value < 0.001). Our results represent the first application of the alkylated hepcidin assay to clinical samples and demonstrate that the developed assay has better sensitivity and quantification accuracy than current MS-based hepcidin assays without the challenges in synthesis of intact hepcidin standard and accurately determining its absolute amount.
Vasculogenic properties of adventitial Sca-1+CD45+ progenitor cells in mice: a potential source of vasa vasorum in atherosclerosis
Authors: Toledo-Flores Deborah , Williamson Anna , Schwarz Nisha , Fernando Sanuja , Dimasi Catherine , Witt Tyra A. , Nguyen Thao M. , Puranik Amrutesh S. , Chue Colin D. , Delacroix Sinny , Spoon Daniel B. , Bonder Claudine S. , Bursill Christina A. , Di Bartolo Belinda A. , Nicholls Stephen J. , Simari Robert D. , Psaltis Peter J. 
Published: May 2019

AbstractThe cellular origins of vasa vasorum are ill-defined and may involve circulating or local progenitor cells. We previously discovered that murine aortic adventitia contains Sca-1+CD45+progenitors that produce macrophages. Here we investigated whether they are also vasculogenic. In aortas of C57BL/6 mice, Sca-1+CD45+cells were localised to adventitia and lacked surface expression of endothelial markers (<1% for CD31, CD144, TIE-2). In contrast, they did show expression of CD31, CD144, TIE-2 and VEGFR2 in atheroscleroticApoE−/−aortas. Although Sca-1+CD45+cells from C57BL/6 aorta did not express CD31, they formed CD31+colonies in endothelial differentiation media and produced interconnecting vascular-like cords in Matrigel that contained both endothelial cells and a small population of macrophages, which were located at branch points. Transfer of aortic Sca-1+CD45+cells generated endothelial cells and neovesselsde novoin a hindlimb model of ischaemia and resulted in a 50% increase in perfusion compared to cell-free control. Similarly, their injection into the carotid adventitia ofApoE−/−mice produced donor-derived adventitial and peri-adventitial microvessels after atherogenic diet, suggestive of newly formed vasa vasorum. These findings show that beyond its content of macrophage progenitors, adventitial Sca-1+CD45+cells are also vasculogenic and may be a source ofvasa vasorumduring atherogenesis.
Numerical Analysis of Bead Magnetophoresis from Flowing Blood in a Continuous-Flow Microchannel: Implications to the Bead-Fluid Interactions
Authors: Gómez-Pastora Jenifer , Karampelas Ioannis H. , Bringas Eugenio , Furlani Edward P. , Ortiz Inmaculada 
Published: May 2019

AbstractIn this work, we report a numerical flow-focused study of bead magnetophoresis inside a continuous-flow microchannel in order to provide a detailed analysis of bead motion and its effect on fluid flow. The numerical model involves a Lagrangian approach and predicts the bead separation from blood and their collection into a flowing buffer by the application of a magnetic field generated by a permanent magnet. The following scenarios are modelled: (i) one-way coupling wherein momentum is transferred from the fluid to beads, which are treated as point particles, (ii) two-way coupling wherein the beads are treated as point particles and momentum is transferred from the bead to the fluid and vice versa, and (iii) two-way coupling taking into account the effects of bead volume in fluid displacement. The results indicate that although there is little difference in the bead trajectories for the three scenarios, there is significant variation in the flow fields, especially when high magnetic forces are applied on the beads. Therefore, an accurate full flow-focused model that takes into account the effects of the bead motion and volume on the flow field should be solved when high magnetic forces are employed. Nonetheless, when the beads are subjected to medium or low magnetic forces, computationally inexpensive models can be safely employed to model magnetophoresis.
Antimicrobial activity and carbohydrate metabolism in the bacterial metagenome of the soil-living invertebrate Folsomia candida
Authors: Agamennone Valeria , Le Ngoc Giang , van Straalen Nico M. , Brouwer Abraham , Roelofs Dick 
Published: May 2019

AbstractThe microbiome associated with an animal’s gut and other organs is considered an integral part of its ecological functions and adaptive capacity. To better understand how microbial communities influence activities and capacities of the host, we need more information on the functions that are encoded in a microbiome. Until now, the information about soil invertebrate microbiomes is mostly based on taxonomic characterization, achieved through culturing and amplicon sequencing. Using shotgun sequencing and various bioinformatics approaches we explored functions in the bacterial metagenome associated with the soil invertebrate Folsomia candida, an established model organism in soil ecology with a fully sequenced, high-quality genome assembly. Our metagenome analysis revealed a remarkable diversity of genes associated with antimicrobial activity and carbohydrate metabolism. The microbiome also contains several homologs to F. candida genes that were previously identified as candidates for horizontal gene transfer (HGT). We suggest that the carbohydrate- and antimicrobial-related functions encoded by Folsomia’s metagenome play a role in the digestion of recalcitrant soil-born polysaccharides and the defense against pathogens, thereby significantly contributing to the adaptation of these animals to life in the soil. Furthermore, the transfer of genes from the microbiome may constitute an important source of new functions for the springtail.
Photoluminescent organisms: how to make fungi glow through biointegration with lanthanide metal-organic frameworks
Authors: Rosário Jeferson , da Luz Leonis L. , Geris Regina , Ramalho Jéssica G. S. , da Silva Antônio F. , Júnior Severino Alves , Malta Marcos 
Published: May 2019

AbstractWe show that filamentous fungi can emit green or red light after the accumulation of particulate lanthanide metal-organic frameworks over the cell wall. These new biohybrids present photoluminescence properties that are unaffected by the components of the cell wall. In addition, the fungal cells internalise lanthanide metal-organic framework particles, storing them into organelles, thereby making these materials promising for applications in living imaging studies.
Multimodal Fluorescent Polymer Sensor for Highly Sensitive Detection of Nitroaromatics
Authors: Kumar Vishal , Maiti Binoy , Chini Mrinmoy Kumar , De Priyadarsi , Satapathi Soumitra 
Published: May 2019

AbstractDetection of nitroaromatic explosives with high sensitivity and selectivity is extremely important for civilian and military safety. Here, we report the synthesis and multimodal sensing applications of an emissive alanine based dansyl tagged copolymer P(MMA-co-Dansyl-Ala-HEMA) (DCP), synthesized by RAFT copolymerization. The fluorescent co-polymer exhibited high sensitivity and selectivity towards conventional nitroaromatic explosives such as DNT, TNT and TNP in solution at lower range of µM level and also with saturated vapor of NACs. The quantum yield of the co-polymer was measured to be very high (Φf = 77%) which make it an ideal candidate for sensing in solution as well as in vapor phase. The fluorescence signal from DCP copolymer gets significantly quenched upon addition of aliquots of DNT, TNT, and TNP. The Stern-Volmer constant was calculated to be very high. The quenching mechanism was further established by fluorescence up-conversion, time-resolved fluorescence and steady state absorption spectroscopy. The energetics of sensing process was calculated by Density Functional Theory (DFT) studies. We also fabricate a thin film polymer sensor which was able to detect nitroaromatic vapors with high selectivity. This opens up the possibility of building a low-cost and light-weight nitroaromatic explosives sensor for field use.
Divergently expressed RNA identification and interaction prediction of long non-coding RNA and mRNA involved in Hu sheep hair follicle
Authors: Lv Xiaoyang , Gao Wen , Jin Chengyan , Wang Yue , Chen Weihao , Wang Lihong , Zou Shuangxia , Sheng Shuixing , Chen Ling , Sun Wei 
Published: May 2019

AbstractHair follicles are the basis of the formation of Hu sheep pattern. This study was to employ whole transcriptome sequencing to screen differentially expressed long non-coding RNAs (lncRNAs) between three wave patterns in lambskin. In this study, three groups of 2-day-old Hu sheep were selected from full-sib individuals that included small, medium, and large waves, and hair follicle tissues were collected from dorsal side of Hu sheep. LncRNA and mRNA expression profiles were analyzed by whole transcriptome sequencing technology. 33, 31, and 41 differentially expressed lncRNAs were selected between large and medium, medium and small, and large and small, respectively. 458, 481, and 498 differentially expressed mRNAs were found between large and medium, medium and small, and large and small, respectively, by RNA-seq analysis. qRT-PCR results of 16 randomly selected lncRNAs and mRNAs were similar to the sequencing results. Correlation analysis of lncRNA and mRNA expression showed that, several lncRNAs may be enriched for hair follicle such as Wnt, mTOR, Notch signaling pathways. Our results aid in excavation of mRNAs and lncRNAs in hair follicle, and providing a basis for future study on pattern formation mechanisms.