bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strong Neotectonic Block Rotations, Related to the Africa‐Eurasia Convergence in Northern Algeria: Paleomagnetic Evidence From the Mitidja Basin
Authors: Derder M.E.M. , Djellit H. , Henry B. , Maouche S. , Amenna M. , Bestandji R. , Ymel H. , Gharbi S. , Abtout A. , Dorbath C. 
Published: October 2019

AbstractSignificant tectonic clockwise rotations were evidenced in the Tell Atlas (Neogene Algerian Cheliff basin) by previous paleomagnetic studies. For northwestern Africa and in the context of the Africa‐Eurasia convergence, they provided a new argument validating a kinematic model, based on transpression with shortening accommodated by clockwise block rotations. To corroborate this deformation pattern at a larger scale, new paleomagnetic studies were performed on 349 cores in the Mitidja basin, of Mio‐Plio‐Quaternary age, in the Algerian Tell Atlas. This intramontaneous basin is structured by two regional major E‐W to WNW‐ESE dextral shear zones. Primary magnetization data were obtained in 43 out of the 49 sampled sites. This magnetization is carried by Ti‐poor titanomagnetite. Its direction shows that significant tectonic block rotations affected this basin since 16 Ma. Zones located between the E‐W and WNW‐ESE major structures are affected by coherent clockwise rotations (average magnitude of 48°) of large blocks, compartmented by presently associated sinistral NE‐SW faults. Along the shearing structures, smaller blocks, resulting from the fragmentation of the large blocks, show various rotations, many of which are of large magnitude. These rotations, similar to those highlighted previously in the Cheliff basin, are interpreted as resulting from bookshelf, consequence of the Africa‐Eurasia plates convergence in the Tell Atlas.
Evaluating a Regional Climate Model Simulation of Greenland Ice Sheet Snow and Firn Density for Improved Surface Mass Balance Estimates
Authors: Alexander P. M. , Tedesco M. , Koenig L. , Fettweis X. 
Published: October 2019

AbstractModeling vertical profiles of snow and firn density near the surface of the Greenland ice sheet (GrIS) is key to estimating GrIS mass balance, and by extension, global sea level change. To understand sources of error in simulated GrIS density, we compare GrIS density profiles from a leading regional climate model with coincident in situ measurements. We identify key contributors to model density and mass balance biases, including underestimated simulated fresh snow density (which leads to underestimation of density in the top 1 m of snow by ~10%). In areas undergoing frequent melting, positive density biases (of 7% in the top 1 m, and 10% between 1 and 10 m) are likely associated with errors in representing meltwater production, retention, and refreezing. The results highlight the importance of accurately capturing fresh snow density and meltwater processes in models used to estimate GrIS mass balance change.
East‐West Difference in the Ionospheric Response of the March 1989 Great Magnetic Storm Throughout East Asian Region
Authors: Zhao Biqiang , Yang Changjun , Cai Yihui , Jin Yuyan , Liang Yu , Ding Feng , Yue Xinan , Wan Weixing 
Published: October 2019

AbstractThe effects of the 13–14 March 1989 great magnetic storm on the East Asian ionosphere have been re‐investigated using ground‐based and satellite measurements as well as theoretical simulation. Within introduction of new data like the Chinese ionosondes and DMSP F8 and F9 and low‐equatorial magnetometer data, we are able to track the ionospheric response at both the bottomside and topside ionosphere from middle to low latitude to obtain an overall understanding of storm‐time ionospheric change. Through the comparative study of different longitude bands, we found that the East‐Asian ionosphere was characterized by a strong westward electron density gradient persisting over a day at both the bottomside and topside ionosphere at mid‐low latitudes during the main and recovery phases of the storm. This feature was not studied in the previous literature for this event at this area. We then examine the effect through a numerical simulation work from the Thermosphere Ionosphere Electrodynamics General Circulation Model under Apex and Dipole geomagnetic fields. It is seen that the model well reproduces the zonal gradients during this event under realistic geomagnetic field model. The conditions favor for this structure requires a hemispheric asymmetry response of storm thermosphere as well as background condition and also the storm development which requires further investigation. This study shows that even very close stations would manifest totally different storm behaviors during the superstorm event suggesting a great challenge in the space weather prediction.
On the Thermodynamic Preconditioning of Arctic Air Masses and the Role of Tropopause Polar Vortices for Cold Air Outbreaks From Fram Strait
Authors: Papritz Lukas , Rouges Emmanuel , Aemisegger Franziska , Wernli Heini 
Published: October 2019

AbstractFram Strait is a hot spot of Arctic cold air outbreaks (CAOs), which typically occur within the northerly flow associated with a strong low tropospheric east‐west pressure gradient between Svalbard and Greenland. This study investigates the processes in the inner Arctic that thermodynamically precondition air masses associated with CAOs south of Fram Strait where they lead to negative potential temperature anomalies often in excess of 15 K. Kinematic backward trajectories from Fram Strait are used to quantify the Arctic residence time and to analyze the thermodynamic evolution of these air masses. Additionally, the study explores the importance of cyclonic tropopause polar vortices (TPVs) for CAO formation south of Fram Strait. Results from a detailed case study and the climatological analysis of the 100 most intense CAOs from Fram Strait in the ERA‐Interim period reveal that (i) air masses that cause CAOs (CAO air masses) reside longer in the inner Arctic compared to those that do not (NO‐CAO air masses), and they originate from climatologically colder regions; (ii) the 10‐day accumulated cooling is very similar for CAO and NO‐CAO air masses indicating that the transport history and northerly origin of the air masses is more decisive for the formation of an intense negative temperature anomaly south of Fram Strait than an enhanced inner Arctic diabatic cooling; (iii) 40% (29%) of the top 40 (100) CAOs are related to a TPV in the vicinity of Fram Strait; (iv) TPVs confine anomalously cold air masses within their associated low tropospheric cold dome leading to enhanced accumulated radiative cooling.
Fill and Spill Hillslope Runoff Representation With a Richards Equation‐Based Model
Authors: Camporese M. , Paniconi C. , Putti M. , McDonnell J. J. 
Published: October 2019

AbstractIntegrated surface‐subsurface hydrological models (ISSHMs) are well established numerical tools to investigate water flow and contaminant transport processes over a wide range of spatial and temporal scales. However, their ability to correctly reproduce the response of hydrological systems to natural and anthropogenic forcing depends largely on the accuracy of model parameterization, including the level of detail in the representation of the bedrock. This latter is typically incorporated in some way via the bottom boundary of the model domain. Issues of bedrock topography, variable soil depth, and the resulting hillslope storage distribution representation in ISSHMs are vitally important but to date have received little attention. A standard treatment of the bottom boundary, especially in large catchment and continental scale applications, is to model it as a flat or inclined (e.g., parallel to the surface) impermeable base (sometimes with some simple leakage term). This approach does not allow the model to correctly reproduce bedrock‐controlled threshold responses such as the fill and spill process, as observed across many hillslope and catchment scale field studies. It is still unclear whether Richards equation‐based numerical models are actually able to generate such responses. Here we use a Richards equation‐based model (CATHY) to simulate internal transient subsurface stormflow dynamics observed at the well‐characterized Panola experimental hillslope in Georgia (USA). Soil and bedrock properties were calibrated starting from values reported in previous studies at the site. Our simulation results show that the model was able to reproduce threshold mechanisms, which in turn affected both the integrated and distributed hydrologic responses of the Panola hillslope. We then developed a set of virtual experiments with modified boundary conditions and base topography at the soil‐bedrock interface to explore the bedrock boundary control on transient groundwater flow patterns. Our results show that accurate representation of the lower boundary is crucial for ISSHM simulations of hillslope‐scale storm runoff and for connectivity of transient groundwater. We summarize our findings with the development of a new bedrock topographic wetness index that takes into account the unsaturated infiltration dynamics. The index is able to help represent the spatial variability of water table response over the bedrock surface compared to standard surface topography‐based indices. This new index may be useful in larger‐scale ISSHM applications where an exact bedrock topography representation is not feasible or possible.
Programmable broadband optical field spectral shaping with megahertz resolution using a simple frequency shifting loop
Authors: Schnébelin Côme , Azaña José , Guillet de Chatellus Hugues 
Published: October 2019

AbstractControlling the temporal and spectral properties of light is crucial for many applications. Current state-of-the-art techniques for shaping the time- and/or frequency-domain field of an optical waveform are based on amplitude and phase linear spectral filtering of a broadband laser pulse, e.g., using a programmable pulse shaper. A well-known fundamental constraint of these techniques is that they can be hardly scaled to offer a frequency resolution better than a few GHz. Here, we report an approach for user-defined optical field spectral shaping using a simple scheme based on a frequency shifting optical loop. The proposed scheme uses a single monochromatic (CW) laser, standard fiber-optics components and low-frequency electronics. This technique enables efficient synthesis of hundreds of optical spectral components, controlled both in phase and in amplitude, with a reconfigurable spectral resolution from a few MHz to several tens of MHz. The technique is applied to direct generation of arbitrary radio-frequency waveforms with time durations exceeding 100 ns and a detection-limited frequency bandwidth above 25 GHz.
Plasmodium Infection Induces Dyslipidemia and a Hepatic Lipogenic State in the Host through the Inhibition of the AMPK-ACC Pathway
Authors: Kluck George Eduardo Gabriel , Wendt Camila Hübner Costabile , Imperio Guinever Eustaquio do , Araujo Maria Fernanda Carvalho , Atella Tainá Correa , da Rocha Isabella , Miranda Kildare Rocha , Atella Georgia Correa 
Published: October 2019

AbstractMalaria is a major parasitic disease of humans and is a health public problem that affects more than 100 countries. In 2017, it caused nearly half a million deaths out of 219 million infections. Malaria is caused by the protozoan parasites of the genus Plasmodium and is transmitted by female mosquitoes of the genus Anopheles. Once in the bloodstream, Plasmodium merozoites invade erythrocytes and proliferate until the cells lyses and release new parasites that invade other erythrocytes. Remarkably, they can manipulate the vertebrate host’s lipid metabolism pathways, since they cannot synthesize lipid classes that are essential for their development and replication. In this study, we show that mice infected with Plasmodium chabaudi present a completely different plasma profile from control mice, with marked hyperproteinemia, hypertriglyceridemia, hypoglycemia, and hypocholesterolemia. In addition, white adipose and hepatic tissue and analyses from infected animals revealed the accumulation of triacylglycerol in both tissues and free fatty acids and free cholesterol in the liver. Hepatic mRNA and protein expression of key enzymes and transcription factors involved in lipid metabolism were also altered by P. chabaudi infection, leading to a lipogenic state. The enzyme 5′ AMP-activated protein kinase (AMPK), a master regulator of cell energetic metabolism, was also modulated by the parasite, which reduced AMPK phosphorylation levels upon infection. Pretreatment with metformin for 21 days followed by infection with P. chabaudi was effective in preventing infection of mice and also lowered the hepatic accumulation of lipids while activating AMPK. Together, these results provide new and important information on the specific molecular mechanisms induced by the malaria parasite to regulate hepatic lipid metabolism in order to facilitate its development, proliferation, and lifespan in its vertebrate host.
The growth of amyloid fibrils: rates and mechanisms
Authors: Buell Alexander K. 
Published: October 2019

Abstract
Amyloid fibrils are β-sheet-rich linear protein polymers that can be formed by a large variety of different proteins. These assemblies have received much interest in recent decades, due to their role in a range of human disorders. However, amyloid fibrils are also found in a functional context, whereby their structural, mechanical and thermodynamic properties are exploited by biological systems. Amyloid fibrils form through a nucleated polymerisation mechanism with secondary processes acting in many cases to amplify the number of fibrils. The filamentous nature of amyloid fibrils implies that the fibril growth rate is, by several orders of magnitude, the fastest step of the overall aggregation reaction. This article focusses specifically on in vitro experimental studies of the process of amyloid fibril growth, or elongation, and summarises the state of knowledge of its kinetics and mechanisms. This work attempts to provide the most comprehensive summary, to date, of the available experimental data on amyloid fibril elongation rate constants and the temperature and concentration dependence of amyloid fibril elongation rates. These data are compared with those from other types of protein polymers. This comparison with data from other polymerising proteins is interesting and relevant because many of the basic ideas and concepts discussed here were first introduced for non-amyloid protein polymers, most notably by the Japanese school of Oosawa and co-workers for cytoskeletal filaments.
Unveiling magnetosome biomineralization in magnetotactic bacteria
Authors: Fernández-Castané Alfred , Clarke-Bland Charlotte 
Published: October 2019

The Eric Reid Fund for Methodology is a grant of up to £4000, awarded to members of the Biochemical Society for projects with an emphasis on methodology and a preference for cellular or bioanalytical work. Applicants can use the fund to support research developing new techniques, exploring the application of a known technique in a novel circumstance or for feasibility studies and the Society is pleased to enable researchers to continue to learn new skills.
Here, Alfred Fernández-Castané and Charlotte Clarke-Bland from Aston University, used their grant to purchase the necessary chemicals to run confocal microscopy experiments and more importantly, it has allowed them to start a collaboration.
LncRNA NRON alleviates atrial fibrosis through suppression of M1 macrophages activated by atrial myocytes
Authors: Sun Fei , Guo Zhixiang , Zhang Chengxin , Che Hong , Gong Wenhui , Shen Zhiming , Shi Yinglu , Ge Shenglin 
Published: October 2019

Abstract
The aim of the present study was to explore the role of long non-coding RNA (lncRNA) non-coding repressor of NFAT (NRON) in the atrial fibrosis and to explore whether its underlying mechanism was associated with macrophage polarization. Enzyme-linked immunosorbent assay (ELISA) analysis of pro-inflammatory cytokines revealed that NRON overexpression suppressed, whereas NRON silencing facilitated the angiotensin II (Ang II)-induced inflammatory response in primary cultured atrial myocytes. The chromatin immunoprecipitation (ChIP) results showed that nuclear factor of activated T cell 3 (NFATc3) was recruited to the promoter region of interleukin (IL) 12 (IL-12) in atrial myocytes. Further data showed that NRON overexpression suppressed, whereas NRON silencing further promoted the Ang II-induced NFATc3 nuclear transport and IL-12 expression in atrial myocytes. Moreover, RAW264.7 macrophages were incubated with the conditioned medium from the Ang II-treated atrial myocytes transfected with NRON and IL-12 overexpression vectors. IL-12 overexpression abrogated the NRON overexpression-mediated inhibition of RAW264.7 macrophage polarization to the M1-like phenotype. Additionally, mouse atrial fibroblasts were incubated with the culture medium from RAW264.7 macrophages treated as described above. IL-12 overexpression rescued the NRON overexpression-inhibited protein levels of fibrosis markers Collagen I/III in mouse atrial fibroblasts. Collectively, our data indicate that lncRNA NRON alleviates atrial fibrosis through suppression of M1 macrophages activated by atrial myocytes.
Applications of catalyzed cytoplasmic disulfide bond formation
Authors: Saaranen Mirva J. , Ruddock Lloyd W. 
Published: October 2019

Abstract
Disulfide bond formation is an essential post-translational modification required for many proteins to attain their native, functional structure. The formation of disulfide bonds, otherwise known as oxidative protein folding, occurs in the endoplasmic reticulum and mitochondrial inter-membrane space in eukaryotes and the periplasm of prokaryotes. While there are differences in the molecular mechanisms of oxidative folding in different compartments, it can essentially be broken down into two steps, disulfide formation and disulfide isomerization. For both steps, catalysts exist in all compartments where native disulfide bond formation occurs. Due to the importance of disulfide bonds for a plethora of proteins, considerable effort has been made to generate cell factories which can make them more efficiently and cheaper. Recently synthetic biology has been used to transfer catalysts of native disulfide bond formation into the cytoplasm of prokaryotes such as Escherichia coli. While these engineered systems cannot yet rival natural systems in the range and complexity of disulfide-bonded proteins that can be made, a growing range of proteins have been made successfully and yields of homogenously folded eukaryotic proteins exceeding g/l yields have been obtained. This review will briefly give an overview of such systems, the uses reported to date and areas of future potential development, including combining with engineered systems for cytoplasmic glycosylation.
cGMP signalling in cardiomyocyte microdomains
Authors: Bork Nadja I. , Molina Cristina E. , Nikolaev Viacheslav O. 
Published: October 2019

Abstract
3′,5′-Cyclic guanosine monophosphate (cGMP) is one of the major second messengers critically involved in the regulation of cardiac electrophysiology, hypertrophy, and contractility. Recent molecular and cellular studies have significantly advanced our understanding of the cGMP signalling cascade, its local microdomain-specific regulation and its role in protecting the heart from pathological stress. Here, we summarise recent findings on cardiac cGMP microdomain regulation and discuss their potential clinical significance.
The role of A-kinase anchoring proteins in cardiac oxidative stress
Authors: Diviani Dario , Osman Halima , Delaunay Marion , Kaiser Simon 
Published: October 2019

AbstractCardiac stress initiates a pathological remodeling process that is associated with cardiomyocyte loss and fibrosis that ultimately leads to heart failure. In the injured heart, a pathologically elevated synthesis of reactive oxygen species (ROS) is the main driver of oxidative stress and consequent cardiomyocyte dysfunction and death. In this context, the cAMP-dependent protein kinase (PKA) plays a central role in regulating signaling pathways that protect the heart against ROS-induced cardiac damage. In cardiac cells, spatiotemporal regulation of PKA activity is controlled by A-kinase anchoring proteins (AKAPs). This family of scaffolding proteins tether PKA and other transduction enzymes at subcellular microdomains where they can co-ordinate cellular responses regulating oxidative stress. In this review, we will discuss recent literature illustrating the role of PKA and AKAPs in modulating the detrimental impact of ROS production on cardiac function.
Selective small-molecule EPAC activators
Authors: Luchowska-Stańska Urszula , Morgan David , Yarwood Stephen J. , Barker Graeme 
Published: October 2019

Abstract
The cellular signalling enzymes, EPAC1 and EPAC2, have emerged as key intracellular sensors of the secondary messenger cyclic 3′,5′-adenosine monophosphate (cyclic adenosine monophosphate) alongside protein kinase A. Interest has been galvanised in recent years thanks to the emergence of these species as potential targets for new cardiovascular disease therapies, including vascular inflammation and insulin resistance in vascular endothelial cells. We herein summarise the current state-of-the-art in small-molecule EPAC activity modulators, including cyclic nucleotides, sulphonylureas, and N-acylsulphonamides.
Making the cut(s): how Cas12a cleaves target and non-target DNA
Authors: Swarts Daan C. 
Published: October 2019

Abstract
CRISPR–Cas12a (previously named Cpf1) is a prokaryotic deoxyribonuclease that can be programmed with an RNA guide to target complementary DNA sequences. Upon binding of the target DNA, Cas12a induces a nick in each of the target DNA strands, yielding a double-stranded DNA break. In addition to inducing cis-cleavage of the targeted DNA, target DNA binding induces trans-cleavage of non-target DNA. As such, Cas12a–RNA guide complexes can provide sequence-specific immunity against invading nucleic acids such as bacteriophages and plasmids. Akin to CRISPR–Cas9, Cas12a has been repurposed as a genetic tool for programmable genome editing and transcriptional control in both prokaryotic and eukaryotic cells. In addition, its trans-cleavage activity has been applied for high-sensitivity nucleic acid detection. Despite the demonstrated value of Cas12a for these applications, the exact molecular mechanisms of both cis- and trans-cleavage of DNA were not completely understood. Recent studies have revealed mechanistic details of Cas12a-mediates DNA cleavage: base pairing of the RNA guide and the target DNA induces major conformational changes in Cas12a. These conformational changes render Cas12a in a catalytically activated state in which it acts as deoxyribonuclease. This deoxyribonuclease activity mediates cis-cleavage of the displaced target DNA strand first, and the RNA guide-bound target DNA strand second. As Cas12a remains in the catalytically activated state after cis-cleavage, it subsequently demonstrates trans-cleavage of non-target DNA. Here, I review the mechanistic details of Cas12a-mediated cis- and trans-cleavage of DNA. In addition, I discuss how bacteriophage-derived anti-CRISPR proteins can inhibit Cas12a activity.