bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Locally Generated Wind Waves on the Momentum Budget and Subtidal Exchange in a Coastal Plain Estuary
Authors: Pareja‐Roman L. Fernando , Chant Robert J. , Ralston David K. 
Published: January 2019

AbstractA numerical model with a vortex force formalism is used to study the role of wind waves in the momentum budget and subtidal exchange of a shallow coastal plain estuary, Delaware Bay. Wave height and age in the bay have a spatial distribution that is controlled by bathymetry and fetch, with implications for the surface drag coefficient in young, underdeveloped seas. Inclusion of waves in the model leads to increases in the surface drag coefficient by up to 30% with respect to parameterizations in which surface drag is only a function of wind speed, in agreement with recent observations of air‐sea fluxes in estuaries. The model was modified to prevent whitecapping wave dissipation from generating breaking forces since that contribution is integrally equivalent to the wind stress. The proposed adjustment is consistent with previous studies of wave‐induced nearshore currents and with additional parameterizations for breaking forces in the model. The mean momentum balance during a simulated wind event was mainly between the pressure gradient force and surface stress, with negligible contributions by vortex, wave breaking (i.e., depth‐induced), and Stokes‐Coriolis forces. Modeled scenarios with realistic Delaware bathymetry suggest that the subtidal bay‐ocean exchange at storm time scales is sensitive to wave‐induced surface drag coefficient, wind direction, and mass transport due to the Stokes drift. Results herein are applicable to shallow coastal systems where the typical wave field is young (i.e., wind seas) and modulated by bathymetry.
Meridional Heat and Salt Transport Across the Subantarctic Front by Cold‐Core Eddies
Authors: Patel Ramkrushnbhai S. , Phillips Helen E. , Strutton Peter G. , Lenton Andrew , Llort Joan 
Published: January 2019

AbstractMesoscale eddies are ubiquitous in the Southern Ocean particularly in regions where the Antarctic Circumpolar Current interacts with topography. Eddies play a critical role in the meridional transport of heat and salt across the Antarctic Circumpolar Current. However, observations of the heat and salt content of eddies are extremely rare. Here we present new observations that characterize the three‐dimensional structure of a cyclonic (cold‐core) eddy generated at the Subantarctic Front south of Tasmania. Automated detection software is used with satellite altimetry to follow the eddy through the Subantarctic Zone. The physical properties at the center of the eddy are substantially modified from those near the formation region, indicating a strong transformation during the eddy's lifetime. The eddy carried heat and salt content anomalies relative to surrounding Subantarctic Zone waters of −0.5 ± 0.1 × 1020 J and −2.1 ± 0.4 × 1012 kg, respectively. Previous studies have not captured the full heat and salt content of eddies due to limited observations and have underestimated their content by a factor of 2 to 3 south of Tasmania. Applying the observed correlation between eddy‐elevated volume and eddy heat and salt content to the history of cyclonic eddies in the satellite altimeter record leads us to propose that about 21% of the heat carried across the Subantarctic Front south of Tasmania is achieved by cyclonic eddies entering the Subantarctic Zone. The freshwater contribution to the Subantarctic Zone by long‐lived cold‐core eddies is of the same order of magnitude as the Ekman flux in this region.
Year‐Round In Situ Measurements of Arctic Low‐Level Clouds: Microphysical Properties and Their Relationships With Aerosols
Authors: Koike M. , Ukita J. , Ström J. , Tunved P. , Shiobara M. , Vitale V. , Lupi A. , Baumgardner D. , Ritter C. , Hermansen O. , Yamada K. , Pedersen C. A. 
Published: January 2019

AbstractTwo years of continuous in situ measurements of Arctic low‐level clouds have been made at the Mount Zeppelin Observatory (78°56′N, 11°53′E), in Ny‐Ålesund, Spitsbergen. The monthly median value of the cloud particle number concentration (Nc) showed a clear seasonal variation: Its maximum appeared in May–July (65 ± 8 cm−3), and it remained low between October and March (8 ± 7 cm−3). At temperatures warmer than 0 °C, a clear correlation was found between the hourly Nc values and the number concentrations of aerosols with dry diameters larger than 70 nm (N70), which are proxies for cloud condensation nuclei (CCN). When clouds were detected at temperatures colder than 0 °C, some of the data followed the summertime Nc to N70 relationship, while other data showed systematically lower Nc values. The lidar‐derived depolarization ratios suggested that the former (CCN‐controlled) and latter (CCN‐uncontrolled) data generally corresponded to clouds consisting of supercooled water droplets and those containing ice particles, respectively. The CCN‐controlled data persistently appeared throughout the year at Zeppelin. The aerosol‐cloud interaction index (ACI = dlnNc/(3dlnN70)) for the CCN‐controlled data showed high sensitivities to aerosols both in the summer (clean air) and winter–spring (Arctic haze) seasons (0.22 ± 0.03 and 0.25 ± 0.02, respectively). The air parcel model calculations generally reproduced these values. The threshold diameters of aerosol activation (Dact), which account for the Nc of the CCN‐controlled data, were as low as 30–50 nm when N70 was less than 30 cm−3, suggesting that new particle formation can affect Arctic cloud microphysics.
The long non-coding RNA Linc-GALH promotes hepatocellular carcinoma metastasis via epigenetically regulating Gankyrin
Authors: Xu Xiaoliang , Lou Yun , Tang Junwei , Teng Yue , Zhang Zechuan , Yin Yin , Zhuo Han , Tan Zhongming 
Published: January 2019

AbstractHepatocellular carcinoma (HCC) is the most prevalent subtype of liver cancer, and it is characterized by high rate of metastasis and recurrence. Recent studies have boosted our understanding that Gankyrin contributes to both of these pathological properties, but the mechanisms underlying its aberrant regulation are poorly understood. Recently, many long noncoding RNAs (lncRNAs) have been reported to be involved in regulating the expression of oncogenes and anti-oncogenes through various mechanisms. Here, using transcriptome microarray analysis, we identified a long intergenic noncoding RNA termed Linc-GALH that was highly expressed and concordance with Gankyrin expression in HCC. In addition, we revealed that Linc-GALH was an independent unfavorable prognostic indicator for HCC, followed functional experiments showed that Linc-GALH promoted HCC cells migration and invasion in vitro, and enhanced lung metastasis ability of HCC cells in vivo. Mechanistically, we found that Linc-GALH could regulate the expression of Gankyrin through controlling the methylation status of Gankyrin by adjusting the ubiquitination status of DNMT1 in HCC. Collectively, our results demonstrated the role and functional mechanism of Linc-GALH in HCC, and indicated that Linc-GALH may act as a prognostic biomarker and potential therapeutic target for HCC.
Long non-coding RNA linc00665 promotes lung adenocarcinoma progression and functions as ceRNA to regulate AKR1B10-ERK signaling by sponging miR-98
Authors: Cong Zhuangzhuang , Diao Yifei , Xu Yang , Li Xiaokun , Jiang Zhisheng , Shao Chenye , Ji Saiguang , Shen Yi , De Wei , Qiang Yong 
Published: January 2019

AbstractLong non-coding RNAs (lncRNAs) are frequently dysregulated in multiple malignancies, demonstrating their potential oncogenic or tumor-suppressive roles in tumorigenesis. Herein, we reported the identification of a novel lncRNA, linc00665 (ENST00000590622), which was markedly upregulated in lung adenocarcinoma (LUAD) tissues and might serve as an independent predictor for poor prognosis. Functional assays indicated that linc00665 reinforced LUAD cell proliferation and metastasis in vitro and in vivo. Mechanistically, transcription factor SP1 induced the transcription of linc00665 in LUAD cells, which exerted its oncogenic role by functioning as competing endogenous RNA (ceRNA) for miR-98 and subsequently activating downstream AKR1B10-ERK signaling pathway. Together, our study elucidates oncogenic roles of linc00665–miR98–AKR1B10 axis in LUAD tumorigenesis, which may serve as potential diagnostic biomarkers and therapeutic targets.
Megaphages infect Prevotella and variants are widespread in gut microbiomes
Authors: Devoto Audra E. , Santini Joanne M. , Olm Matthew R. , Anantharaman Karthik , Munk Patrick , Tung Jenny , Archie Elizabeth A. , Turnbaugh Peter J. , Seed Kimberley D. , Blekhman Ran , Aarestrup Frank M. , Thomas Brian C. , Banfield Jillian F. 
Published: January 2019

AbstractBacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.
SOD1/Rag2 Mice with Low Copy Number of SOD1 Gene as a New Long-Living Immunodeficient Model of ALS
Authors: Majchrzak M. , Drela K. , Andrzejewska A. , Rogujski P. , Figurska S. , Fiedorowicz M. , Walczak P. , Janowski M. , Lukomska B. , Stanaszek L. 
Published: January 2019

AbstractThe most recent research concerning amyotrophic lateral sclerosis (ALS) emphasizes the role of glia in disease development. Thus, one can suspect that the effective therapeutic strategy in treatment of ALS would be replacement of defective glia. One of the basic problems with human glial progenitors (hGRPs) replacement strategies is the time needed for the cells to become fully functionalin vivo. The lifespan of most popular high copy number SOD1 mutant mice might be too short to acknowledge benefits of transplanted cells. We focused on developing immunodeficient rag2−/−model of ALS with lower number of transgene copies and longer lifespan. The obtained hSOD1/rag2 double mutant mice have been characterized. QPCR analysis revealed that copy number of hSOD1 transgene varied in our colony (4–8 copies). The difference in transgene copy number may be translated to significant impact on the lifespan. The death of long- and short-living hSOD1/rag2 mice is preceded by muscular weakness as early as one month before death. Importantly, based on magnetic resonance imaging we identified that mutant mice demonstrated abnormalities within the medullar motor nuclei. To conclude, we developed long-living double mutant hSOD1/rag2 mice, which could be a promising model for testing therapeutic utility of human stem cells.
Local electronic structure of doping defects on Tl/Si(111)1x1
Authors: Pieczyrak Barbara , Jurczyszyn Leszek , Sobotík Pavel , Ošt’ádal Ivan , Kocán Pavel 
Published: January 2019

AbstractThe Tl/Si(111)1 × 1 surface is a representative of a 2D layer with Rashba-type spin-split electronic bands. To utilize the spin polarization, doping of the system should be understood on atomic level. We present a study of two types of atomic defects predicted to dope the considered electronic system – Si-induced vacancies and defects associated with the presence of extra Tl atoms. Structural calculations based on density functional theory (DFT) confirm the stability of the proposed defect structure consisting of an extra Si atom and missing seven Tl atoms as proposed in an earlier experimental study. The calculated spatial charge distributions indicate an enhancement of the charge around the extra Si atom, which correctly reproduces topographies of the corresponding scanning tunneling microscopy images while the calculated local densities of states of this system explain obtained scanning tunneling spectra. The DFT structural calculations let us determine the atomic structure of the defect caused by the presence of an extra Tl atom. The calculated spatial charge distributions show a ring-like feature around the extra Tl atom. The obtained results indicate a charge transfer from the central extra Tl atom to its vicinity in the agreement with earlier photoemission measurements.
Sheathless CE-MS based metabolic profiling of kidney tissue section samples from a mouse model of Polycystic Kidney Disease
Authors: Sánchez-López Elena , Kammeijer Guinevere S. M. , Crego Antonio L. , Marina María Luisa , Ramautar Rawi , Peters Dorien J. M. , Mayboroda Oleg A. 
Published: January 2019

AbstractCapillary electrophoresis-mass spectrometry (CE-MS) using a sheathless porous tip interface emerged as an attractive tool in metabolomics thanks to its numerous advantages. One of the main advantages compared to the classical co-axial sheath liquid interface is the increased sensitivity, while maintaining the inherent properties of CE, such as a high separation efficiency and low sample consumption. Specially, the ability to perform nanoliter-based injections from only a few microliters of material in the sample vial makes sheathless CE-MS a well-suited and unique approach for highly sensitive metabolic profiling of limited sample amounts. Therefore, in this work, we demonstrate the utility of sheathless CE-MS for metabolic profiling of biomass-restricted samples, namely for 20 µm-thick tissue sections of kidney from a mouse model of polycystic kidney disease (PKD). The extraction method was designed in such a way to keep a minimum sample-volume in the injection vial, thereby still allowing multiple nanoliter injections for repeatability studies. The developed strategy enabled to differentiate between different stages of PKD and as well changes in a variety of different metabolites could be annotated over experimental groups. These metabolites include carnitine, glutamine, creatine, betaine and creatinine. Overall, this study shows the utility of sheathless CE-MS for biomass-limited metabolomics studies.
Mechanochromism induced through the interplay between excimer reaction and excited state intramolecular proton transfer
Authors: Wei Yu-Chen , Zhang Zhiyun , Chen Yi-An , Wu Cheng-Ham , Liu Zong-Ying , Ho Ssu-Yu , Liu Jiun-Chi , Lin Jia-An , Chou Pi-Tai 
Published: January 2019

AbstractExcited-state intramolecular proton transfer (ESIPT) and excimer formation are unimolecular and bimolecular reactions, respectively. The coupling between these two reactions has been rarely observed. Here we show the interplay between ESIPT and excimer formation in CF3-HTTH (2,2′-(thiazolo[5,4-d]thiazole-2,5-diyl)bis(4-(trifluoromethyl)phenol) solid crystal, resulting in the extensively broad multiple emissions spanning from 420 to 750 nm. Comprehensive structural, time-resolved spectroscopic, and two-photon microscopic studies of CF3-HTTH in crystal lattice unveil the pre-equilibrium ESIPT between the normal (N*) and tautomer (T*) form, for which the slow population decay and well-ordered lattice packing facilitate excimeric (E*) formation, rendering N* (460 nm), T* (520 nm) and E* (600 nm) triple emissions. In contrast, the lower degree of packing on the solid surface prohibits excimer formation, showing only the ESIPT process. The correlation between luminescence properties and packing structure sheds light on the corresponding mechanochromic effect based on molecular solid architecture and provide new insight into the aggregation-induced properties.
Non-thermal emission resulting from a supernova explosion inside an extragalactic jet
Authors: Vieyro F. L. , Bosch-Ramon V. , Torres-Albà N. 
Published: January 2019

Context. Core-collapse supernovae are found in galaxies with ongoing star-formation. In a starburst galaxy hosting an active galactic nucleus with a relativistic jet, supernovae can take place inside the jet. The collision of the supernova ejecta with the jet flow is expected to lead to the formation of an interaction region, in which particles can be accelerated and produce high-energy emission.
Aims. We study the non-thermal radiation produced by electrons accelerated as a result of a supernova explosion inside the jet of an active galactic nucleus within a star-forming galaxy.
Methods. We first analyzed the dynamical evolution of the supernova ejecta impacted by the jet. Then, we explored the parameter space using simple prescriptions for the observed gamma-ray lightcurve. Finally, the synchrotron and the inverse Compton spectral energy distributions for two types of sources, a radio galaxy and a powerful blazar, are computed.
Results. For a radio galaxy, the interaction between a supernova and a jet of power ∼1043 − 1044 erg s−1 can produce apparent gamma-ray luminosities of ∼1042 − 1043 erg s−1, with an event duty cycle of supernova remnant interacting with the jet close to one for one galaxy. For a blazar with a powerful jet of ∼1046 erg s−1, the jet-supernova ejecta interaction could produce apparent gamma-ray luminosities of ∼1043 − 1044 erg s−1, but with a much lower duty cycle.
Conclusions. The interaction of supernovae with misaligned jets of moderate power can be relatively frequent, and can result in steady gamma-ray emission potentially detectable for sources in the local universe. For powerful blazars much farther away, the emission would be steady as well, and it might be detectable under very efficient acceleration, but the events would be rather infrequent.
Evolutionary models of cold and low-mass planets: cooling curves, magnitudes, and detectability
Authors: Linder Esther F. , Mordasini Christoph , Mollière Paul , Marleau Gabriel-Dominique , Malik Matej , Quanz Sascha P. , Meyer Michael R. 
Published: January 2019

Context.Future instruments like the Near Infrared Camera (NIRCam) and the Mid Infrared Instrument (MIRI) on theJames WebbSpace Telescope (JWST) or the Mid-Infrared E-ELT Imager and Spectrograph (METIS) at the European Extremely Large Telescope (E-ELT) will be able to image exoplanets that are too faint (because they have a low mass, and hence a small size or low effective temperature) for current direct imaging instruments. On the theoretical side, core accretion formation models predict a significant population of low-mass and/or cool planets at orbital distances of ~10–100 au.Aims.Evolutionary models predicting the planetary intrinsic luminosity as a function of time have traditionally concentrated on gas-dominated giant planets. We extend these cooling curves to Saturnian and Neptunian planets.Methods.We simulated the cooling of isolated core-dominated and gas giant planets with masses of 5M⊕–2M♃. The planets consist of a core made of iron, silicates, and ices surrounded by a H/He envelope, similar to the ice giants in the solar system. The luminosity includes the contribution from the cooling and contraction of the core and of the H/He envelope, as well as radiogenic decay. For the atmosphere we used grey,AMES-Cond,petitCODE, andHELIOSmodels. We considered solar and non-solar metallicities as well as cloud-free and cloudy atmospheres. The most important initial conditions, namely the core-to-envelope-mass ratio and the initial (i.e. post formation) luminosity are taken from planet formation simulations based on the core accretion paradigm.Results.We first compare our cooling curves for Uranus, Neptune, Jupiter, Saturn, GJ 436b, and a 5M⊕planet with a 1% H/He envelope with other evolutionary models. We then present the temporal evolution of planets with masses between 5M⊕and 2M♃in terms of their luminosity, effective temperature, radius, and entropy. We discuss the impact of different post formation entropies. For the different atmosphere types and initial conditions, magnitudes in various filter bands between 0.9 and 30 micrometer wavelength are provided.Conclusions.Using blackbody fluxes and non-grey spectra, we estimate the detectability of such planets with JWST. We found that a 20 (100)M⊕planet can be detected with JWST in the background limit up to an age of about 10 (100) Myr with NIRCam and MIRI, respectively.
Super-Keplerian equatorial outflows in SS 433
Authors: Waisberg Idel , Dexter Jason , Petrucci Pierre-Olivier , Dubus Guillaume , Perraut Karine 
Published: January 2019

Context. The microquasar SS 433 is the only known steady supercritical accretor in the Galaxy. It is well-known for its relativistic baryonic jets, but the system also drives equatorial outflows. These have been routinely detected in radio images, and components associated with a circumbinary disk have also been suggested in optical emission lines.Aims. We aim to spatially resolve the regions producing the stationary emission lines of SS 433 to shed light on its circumbinary structure and outflows. With an estimated binary orbit size of ≲0.1 mas, this requires optical interferometry.Methods. We use the optical interferometer VLTI+GRAVITY to spatially resolve SS 433 in the near-infraredKband at high spectral resolution (R ≈ 4000) on three nights in July 2017. This is the second such observation, after the first one in July 2016.Results. The stationary Brγline in the 2017 observation is clearly dominated by an extended ∼1 mas ∼ 5 AU circumbinary structure perpendicular to the jets with a strong rotation component. The rotation direction is retrograde relative to the jet precession, in accordance with the slaved disk precession model. The structure has a very high specific angular momentum and is too extended to be a stable circumbinary disk in Keplerian rotation; interpreting it as such leads to a very high enclosed massM ≳ 400 M⊙. We instead interpret it as the centrifugal ejection of the circumbinary disk, with the implication that there must be an efficient transfer of specific angular momentum from the binary to the disk. We suggest that the equatorial outflows sometimes seen in radio images result from similar episodes of circumbinary disk centrifugal ejection. In addition to the equatorial structure, we find a very extended ∼6 mas ∼ 30 AU spherical wind component to the Brγline: the entire binary is engulfed in an optically thin spherical line emission envelope.