bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ambient nitrate switches the ammonium consumption pathway in the euphotic ocean
Authors: Wan Xianhui Sean , Sheng Hua-Xia , Dai Minhan , Zhang Yao , Shi Dalin , Trull Thomas W. , Zhu Yifan , Lomas Michael W. , Kao Shuh-Ji 
Published: February 2018

AbstractPhytoplankton assimilation and microbial oxidation of ammonium are two critical conversion pathways in the marine nitrogen cycle. The underlying regulatory mechanisms of these two competing processes remain unclear. Here we show that ambient nitrate acts as a key variable to bifurcate ammonium flow through assimilation or oxidation, and the depth of the nitracline represents a robust spatial boundary between ammonium assimilators and oxidizers in the stratified ocean. Profiles of ammonium utilization show that phytoplankton assemblages in nitrate-depleted regimes have higher ammonium affinity than nitrifiers. In nitrate replete conditions, by contrast, phytoplankton reduce their ammonium reliance and thus enhance the success of nitrifiers. This finding helps to explain existing discrepancies in the understanding of light inhibition of surface nitrification in the global ocean, and provides further insights into the spatial linkages between oceanic nitrification and new production.
Measurement of the Berry curvature of solids using high-harmonic spectroscopy
Authors: Luu Tran Trung , Wörner Hans Jakob 
Published: February 2018

AbstractBerry phase and Berry curvature have become ubiquitous concepts in physics, relevant to a variety of phenomena, such as polarization, various Hall effects, etc. Studies of these phenomena call for characterization of Berry phase or curvature which is largely limited to theory, and a few measurements in optical lattices. In this work, we report polarimetry of high-harmonic emission from solids and exploit this novel capability to directly retrieve the Berry curvature of α-quartz. We show that the two manifestations of broken inversion symmetry in solids lead to perpendicular or parallel polarization of even harmonics with respect to the driving field. Using semiclassical transport theory, we retrieve the Berry curvature from spectra measured in perpendicular polarization, the results being supported by ab initio calculation. Our work demonstrates an approach for the direct measurement of Berry curvature in solids, which could serve as a benchmark for theoretical studies.
Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography
Authors: Yu Young-Sang , Farmand Maryam , Kim Chunjoong , Liu Yijin , Grey Clare P. , Strobridge Fiona C. , Tyliszczak Tolek , Celestre Rich , Denes Peter , Joseph John , Krishnan Harinarayan , Maia Filipe R. N. C. , Kilcoyne A. L. David , Marchesini Stefano , Leite Talita Perciano Costa , Warwick Tony , Padmore Howard , Cabana Jordi , Shapiro David A. 
Published: February 2018

AbstractBattery function is determined by the efficiency and reversibility of the electrochemical phase transformations at solid electrodes. The microscopic tools available to study the chemical states of matter with the required spatial resolution and chemical specificity are intrinsically limited when studying complex architectures by their reliance on two-dimensional projections of thick material. Here, we report the development of soft X-ray ptychographic tomography, which resolves chemical states in three dimensions at 11 nm spatial resolution. We study an ensemble of nano-plates of lithium iron phosphate extracted from a battery electrode at 50% state of charge. Using a set of nanoscale tomograms, we quantify the electrochemical state and resolve phase boundaries throughout the volume of individual nanoparticles. These observations reveal multiple reaction points, intra-particle heterogeneity, and size effects that highlight the importance of multi-dimensional analytical tools in providing novel insight to the design of the next generation of high-performance devices.
Spontaneous imbibition in fractal tortuous micro-nano pores considering dynamic contact angle and slip effect: phase portrait analysis and analytical solutions
Authors: Li Caoxiong , Shen Yinghao , Ge Hongkui , Zhang Yanjun , Liu Tao 
Published: February 2018

AbstractShales have abundant micro-nano pores. Meanwhile, a considerable amount of fracturing liquid is imbibed spontaneously in the hydraulic fracturing process. The spontaneous imbibition in tortuous micro-nano pores is special to shale, and dynamic contact angle and slippage are two important characteristics. In this work, we mainly investigate spontaneous imbibition considering dynamic contact angle and slip effect in fractal tortuous capillaries. We introduce phase portrait analysis to analyse the dynamic state and stability of imbibition. Moreover, analytical solutions to the imbibition equation are derived under special situations, and the solutions are verified by published data. Finally, we discuss the influences of slip length, dynamic contact angle and gravity on spontaneous imbibition. The analysis shows that phase portrait is an ideal tool for analysing spontaneous imbibition because it can evaluate the process without solving the complex governing ordinary differential equations. Moreover, dynamic contact angle and slip effect play an important role in fluid imbibition in fractal tortuous capillaries. Neglecting slip effect in micro-nano pores apparently underestimates imbibition capability, and ignoring variations in contact angle causes inaccuracy in predicting imbibition speed at the initial stage of the process. Finally, gravity is one of the factors that control the stabilisation of the imbibition process.
Structure based function-annotation of hypothetical protein MGG_01005 from Magnaporthe oryzae reveals it is the dynein light chain orthologue of dynlt1/3
Authors: Li Guorui , Huang Jinguang , Yang Jun , He Dan , Wang Chao , Qi Xiaoxuan , Taylor Ian A. , Liu Junfeng , Peng You-Liang 
Published: February 2018

AbstractMagnaporthe oryzae is a model fungal plant pathogen employed for studying plant-fungi interactions. Whole genome sequencing and bioinformatics analyses revealed that this fungal pathogen has more than 12,000 protein-coding genes with 65% of the genes remaining functionally un-annotated. Here, we determine the structure of the hypothetical protein, MGG_01005 and show that it is the Magnaporthe oryzae Dynein light chain Tctex-type 1 (dynlt1/3), demonstrated by its structural similarity to other orthologous dynlt1 proteins and its conserved interaction with the N-terminus of the Magnaporthe oryzae dynein intermediate chain, MoDyn1I2. In addition, we present the structure of the MGG_01005-MoDyn1I2 complex together with mutagenesis studies that reveals a di-histidine motif interaction with a glutamate residue in the dynein intermediate chain within a conserved molecular interface. These results demonstrate the utility of structure-based annotation and validate it as a viable approach for the molecular assignment of hypothetic proteins from phyto-pathogenic fungi.
Observation of microwave absorption and emission from incoherent electron tunneling through a normal-metal–insulator–superconductor junction
Authors: Masuda Shumpei , Tan Kuan Y. , Partanen Matti , Lake Russell E. , Govenius Joonas , Silveri Matti , Grabert Hermann , Möttönen Mikko 
Published: February 2018

AbstractWe experimentally study nanoscale normal-metal–insulator–superconductor junctions coupled to a superconducting microwave resonator. We observe that bias-voltage-controllable single-electron tunneling through the junctions gives rise to a direct conversion between the electrostatic energy and that of microwave photons. The measured power spectral density of the microwave radiation emitted by the resonator exceeds at high bias voltages that of an equivalent single-mode radiation source at 2.5 K although the phonon and electron reservoirs are at subkelvin temperatures. Measurements of the generated power quantitatively agree with a theoretical model in a wide range of bias voltages. Thus, we have developed a microwave source which is compatible with low-temperature electronics and offers convenient in-situ electrical control of the incoherent photon emission rate with a predetermined frequency, without relying on intrinsic voltage fluctuations of heated normal-metal components or suffering from unwanted losses in room temperature cables. Importantly, our observation of negative generated power at relatively low bias voltages provides a novel type of verification of the working principles of the recently discovered quantum-circuit refrigerator.
Biological and mechanical interplay at the Macro- and Microscales Modulates the Cell-Niche Fate
Authors: Sarig Udi , Sarig Hadar , Gora Aleksander , Krishnamoorthi Muthu Kumar , Au-Yeung Gigi Chi Ting , de-Berardinis Elio , Chaw Su Yin , Mhaisalkar Priyadarshini , Bogireddi Hanumakumar , Ramakrishna Seeram , Boey Freddy Yin Chiang , Venkatraman Subbu S. , Machluf Marcelle 
Published: February 2018

AbstractTissue development, regeneration, or de-novo tissue engineering in-vitro, are based on reciprocal cell-niche interactions. Early tissue formation mechanisms, however, remain largely unknown given complex in-vivo multifactoriality, and limited tools to effectively characterize and correlate specific micro-scaled bio-mechanical interplay. We developed a unique model system, based on decellularized porcine cardiac extracellular matrices (pcECMs)—as representative natural soft-tissue biomaterial—to study a spectrum of common cell–niche interactions. Model monocultures and 1:1 co-cultures on the pcECM of human umbilical vein endothelial cells (HUVECs) and human mesenchymal stem cells (hMSCs) were mechano-biologically characterized using macro- (Instron), and micro- (AFM) mechanical testing, histology, SEM and molecular biology aspects using RT-PCR arrays. The obtained data was analyzed using developed statistics, principal component and gene-set analyses tools. Our results indicated biomechanical cell-type dependency, bi-modal elasticity distributions at the micron cell-ECM interaction level, and corresponding differing gene expression profiles. We further show that hMSCs remodel the ECM, HUVECs enable ECM tissue-specific recognition, and their co-cultures synergistically contribute to tissue integration—mimicking conserved developmental pathways. We also suggest novel quantifiable measures as indicators of tissue assembly and integration. This work may benefit basic and translational research in materials science, developmental biology, tissue engineering, regenerative medicine and cancer biomechanics.
Reconstructing vapor pressure deficit from leaf wax lipid molecular distributions
Authors: Eley Yvette L. , Hren Michael T. 
Published: February 2018

AbstractEstimates of atmospheric moisture are critical for understanding the links and feedbacks between atmospheric CO2 and global climate. At present, there are few quantitative moisture proxies that are applicable to deep time. We present a new proxy for atmospheric moisture derived from modern climate and leaf biomarker data from North and Central America. Plants have a direct genetic pathway to regulate the production of lipids in response to osmotic stress, which is manifested in a change in the distribution of simple aliphatic lipids such as n-alkanes. The Average Chain Length (ACL) of these lipids is therefore statistically related to mean annual vapor pressure deficit (VPDav), enabling quantitative reconstruction of VPD from sedimentary n-alkanes. We apply this transfer function to the Armantes section of the Calatayud-Daroca Basin in Central Spain, that spans the Middle Miocene Climatic Optimum (MMCO) and the Middle Miocene Climate Transition (MMCT). Reconstructed VPDav rises from 0.13 to 0.92 kPa between 16.5 and 12.4 Ma, indicating a substantial drying through the MMCT. These data are consistent with fossil assemblages and mammalian stable isotope data, highlighting the utility of this new organic molecular tool for quantifying hydrologic variability over geologic timescales.
Development of an Injectable Slow-Release Metformin Formulation and Evaluation of Its Potential Antitumor Effects
Authors: Baldassari Sara , Solari Agnese , Zuccari Guendalina , Drava Giuliana , Pastorino Sara , Fucile Carmen , Marini Valeria , Daga Antonio , Pattarozzi Alessandra , Ratto Alessandra , Ferrari Angelo , Mattioli Francesca , Barbieri Federica , Caviglioli Gabriele , Florio Tullio 
Published: February 2018

AbstractMetformin is an antidiabetic drug which possesses antiproliferative activity in cancer cells when administered at high doses, due to its unfavorable pharmacokinetics. The aim of this work was to develop a pharmacological tool for the release of metformin in proximity of the tumor, allowing high local concentrations, and to demonstrate the in vivo antitumor efficacy after a prolonged metformin exposition. A 1.2% w/w metformin thermoresponsive parenteral formulation based on poloxamers P407 and P124, injectable at room temperature and undergoing a sol-gel transition at body temperature, has been developed and optimized for rheological, thermal and release control properties; the formulation is easily scalable, and proved to be stable during a 1-month storage at 5 °C. Using NOD/SCID mice pseudo-orthotopically grafted with MDA-MB-231/luc+ human breast cancer cells, we report that multiple administrations of 100 mg of the optimized metformin formulation close to the tumor site cause tissue accumulation of the drug at levels significantly higher than those observed in plasma, and enough to exert antiproliferative and pro-apoptotic activities. Our results demonstrate that this formulation is endowed with good stability, tolerability, thermal and rheological properties, representing a novel tool to be pursued in further investigations for adjuvant cancer treatment.
Long-lasting ergot lipids as new biomarkers for assessing the presence of cereals and cereal products in archaeological vessels
Authors: Lucejko Jeannette J. , La Nasa Jacopo , Porta Francesca , Vanzetti Alessandro , Tanda Giuseppa , Mangiaracina Claudio Filippo , Corretti Alessandro , Colombini Maria Perla , Ribechini Erika 
Published: February 2018

AbstractCereals were very important in ancient diets, however evidence from archaeological sites of the vessels used for processing or storing cereals is comparatively rare. Micro-organisms, as well as chemical-physical effects can easily degrade cereals during the burial period. This can lead to a complete cereal decay and to serious difficulties in estimating the intensity of use of the cereals by ancient populations. Here, we present a novel biomarker approach entailing the detection of secondary lipid metabolites produced by ergot fungi (genusClaviceps), which are common cereal pests. The aim was to identify the original presence ofGramineaeand to indirectly establish if vessels were used for cereal storage/processing. The fatty acid and TAG-estolide profiles of the remains from more than 30 archaeological vessels were investigated by gas chromatography/mass spectrometry (GC/MS) and high performance liquid chromatography/high resolution mass spectrometry (HPLC/ESI-Q-ToF). The detection of lipids derived from ergot in archaeological and historic contexts rests on its complex chemistry, providing a unique and relatively recalcitrant chemical signature for cereals. This research demonstrated that the combination of our innovative biomarker approach along with environmental and archaeological evidence can provide unprecedented insights into the incidence of cereals and related processing activities in ancient societies.
The effects of angiotensin receptor neprilysin inhibition by sacubitril/valsartan on adipose tissue transcriptome and protein expression in obese hypertensive patients
Authors: Stinkens R. , van der Kolk B. W. , Jordan J. , Jax T. , Engeli S. , Heise T. , Jocken J. W. , May M. , Schindler C. , Havekes B. , Schaper N. , Albrecht D. , Kaiser S. , Hartmann N. , Letzkus M. , Langenickel T. H. , Goossens G. H. , Blaak E. E. 
Published: February 2018

AbstractIncreased activation of the renin-angiotensin system is involved in the onset and progression of cardiometabolic diseases, while natriuretic peptides (NP) may exert protective effects. We have recently demonstrated that sacubitril/valsartan (LCZ696), a first-in-class angiotensin receptor neprilysin inhibitor, which blocks the angiotensin II type-1 receptor and augments natriuretic peptide levels, improved peripheral insulin sensitivity in obese hypertensive patients. Here, we investigated the effects of sacubitril/valsartan (400 mg QD) treatment for 8 weeks on the abdominal subcutaneous adipose tissue (AT) phenotype compared to the metabolically neutral comparator amlodipine (10 mg QD) in 70 obese hypertensive patients. Abdominal subcutaneous AT biopsies were collected before and after intervention to determine the AT transcriptome and expression of proteins involved in lipolysis, NP signaling and mitochondrial oxidative metabolism. Both sacubitril/valsartan and amlodipine treatment did not significantly induce AT transcriptional changes in pathways related to lipolysis, NP signaling and oxidative metabolism. Furthermore, protein expression of adipose triglyceride lipase (ATGL) (Ptime*group = 0.195), hormone-sensitive lipase (HSL) (Ptime*group = 0.458), HSL-ser660 phosphorylation (Ptime*group = 0.340), NP receptor-A (NPRA) (Ptime*group = 0.829) and OXPHOS complexes (Ptime*group = 0.964) remained unchanged. In conclusion, sacubitril/valsartan treatment for 8 weeks did not alter the abdominal subcutaneous AT transcriptome and expression of proteins involved in lipolysis, NP signaling and oxidative metabolism in obese hypertensive patients.
A cascading nonlinear magneto-optical effect in topological insulators
Authors: Mondal Richarj , Saito Yuta , Aihara Yuki , Fons Paul , Kolobov Alexander V. , Tominaga Junji , Murakami Shuichi , Hase Muneaki 
Published: February 2018

AbstractTopological insulators (TIs) are characterized by possessing metallic (gapless) surface states and a finite band-gap state in the bulk. As the thickness of a TI layer decreases down to a few nanometers, hybridization between the top and bottom surfaces takes place due to quantum tunneling, consequently at a critical thickness a crossover from a 3D-TI to a 2D insulator occurs. Although such a crossover is generally accessible by scanning tunneling microscopy, or by angle-resolved photoemission spectroscopy, such measurements require clean surfaces. Here, we demonstrate that a cascading nonlinear magneto-optical effect induced via strong spin-orbit coupling can examine such crossovers. The helicity dependence of the time-resolved Kerr rotation exhibits a robust change in periodicity at a critical thickness, from which it is possible to predict the formation of a Dirac cone in a film several quintuple layers thick. This method enables prediction of a Dirac cone using a fundamental nonlinear optical effect that can be applied to a wide range of TIs and related 2D materials.
On the design of a MEMS piezoelectric accelerometer coupled to the middle ear as an implantable sensor for hearing devices
Authors: Gesing A. L. , Alves F. D. P. , Paul S. , Cordioli J. A. 
Published: February 2018

AbstractThe presence of external elements is a major limitation of current hearing aids and cochlear implants, as they lead to discomfort and inconvenience. Totally implantable hearing devices have been proposed as a solution to mitigate these constraints, which has led to challenges in designing implantable sensors. This work presents a feasibility analysis of a MEMS piezoelectric accelerometer coupled to the ossicular chain as an alternative sensor. The main requirements of the sensor include small size, low internal noise, low power consumption, and large bandwidth. Different designs of MEMS piezoelectric accelerometers were modeled using Finite Element (FE) method, as well as optimized for high net charge sensitivity. The best design, a 2 × 2 mm2 annular configuration with a 500 nm thick Aluminum Nitride (AlN) layer was selected for fabrication. The prototype was characterized, and its charge sensitivity and spectral acceleration noise were found to be with good agreement to the FE model predictions. Weak coupling between a middle ear FE model and the prototype was considered, resulting in equivalent input noise (EIN) lower than 60 dB sound pressure level between 600 Hz and 10 kHz. These results are an encouraging proof of concept for the development of MEMS piezoelectric accelerometers as implantable sensors for hearing devices.
A Mathematical Model of the Phosphoinositide Pathway
Authors: Olivença Daniel V. , Uliyakina Inna , Fonseca Luis L. , Amaral Margarida D. , Voit Eberhard O. , Pinto Francisco R. 
Published: February 2018

AbstractPhosphoinositides are signalling lipids that constitute a complex network regulating many cellular processes. We propose a computational model that accounts for all species of phosphoinositides in the plasma membrane of mammalian cells. The model replicates the steady-state of the pathway and most known dynamic phenomena. Sensitivity analysis demonstrates model robustness to alterations in the parameters. Model analysis suggest that the greatest contributor to phosphatidylinositol 4,5-biphosphate (PI(4,5)P2) production is a flux representing the direct transformation of PI into PI(4,5)P2, also responsible for the maintenance of this pool when phosphatidylinositol 4-phosphate (PI(4)P) is decreased. PI(5)P is also shown to be a significant source for PI(4,5)P2 production. The model was validated with siRNA screens that knocked down the expression of enzymes in the pathway. The screen monitored the activity of the epithelium sodium channel (ENaC), which is activated by PI(4,5)P2. While the model may deepen our understanding of other physiological processes involving phosphoinositides, we highlight therapeutic effects of ENaC modulation in Cystic Fibrosis (CF). The model suggests control strategies where the activities of the enzyme phosphoinositide 4-phosphate 5-kinase I (PIP5KI) or the PI4K + PIP5KI + DVL protein complex are decreased and cause an efficacious reduction in PI(4,5)P2 levels while avoiding undesirable alterations in other phosphoinositide pools.
Antimycobacterial drug discovery using Mycobacteria-infected amoebae identifies anti-infectives and new molecular targets
Authors: Trofimov Valentin , Kicka Sébastien , Mucaria Sabrina , Hanna Nabil , Ramon-Olayo Fernando , Del Peral Laura Vela-Gonzalez , Lelièvre Joël , Ballell Lluís , Scapozza Leonardo , Besra Gurdyal S. , Cox Jonathan A. G. , Soldati Thierry 
Published: February 2018

AbstractTuberculosis remains a serious threat to human health world-wide, and improved efficiency of medical treatment requires a better understanding of the pathogenesis and the discovery of new drugs. In the present study, we performed a whole-cell based screen in order to complete the characterization of 168 compounds from the GlaxoSmithKline TB-set. We have established and utilized novel previously unexplored host-model systems to characterize the GSK compounds, i.e. the amoeboid organisms D. discoideum and A. castellanii, as well as a microglial phagocytic cell line, BV2. We infected these host cells with Mycobacterium marinum to monitor and characterize the anti-infective activity of the compounds with quantitative fluorescence measurements and high-content microscopy. In summary, 88.1% of the compounds were confirmed as antibiotics against M. marinum, 11.3% and 4.8% displayed strong anti-infective activity in, respectively, the mammalian and protozoan infection models. Additionally, in the two systems, 13–14% of the compounds displayed pro-infective activity. Our studies underline the relevance of using evolutionarily distant pathogen and host models in order to reveal conserved mechanisms of virulence and defence, respectively, which are potential “universal” targets for intervention. Subsequent mechanism of action studies based on generation of over-expresser M. bovis BCG strains, generation of spontaneous resistant mutants and whole genome sequencing revealed four new molecular targets, including FbpA, MurC, MmpL3 and GlpK.