bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence of Isotopic Fractionation During Vapor Exchange Between the Atmosphere and the Snow Surface in Greenland
Authors: Madsen M. V. , Steen‐Larsen H. C. , Hörhold M. , Box J. , Berben S. M. P. , Capron E. , Faber A.‐K. , Hubbard A. , Jensen M. F. , Jones T. R. , Kipfstuhl S. , Koldtoft I. , Pillar H. R. , Vaughn B. H. , Vladimirova D. , Dahl‐Jensen D. 
Published: February 2019

AbstractSeveral recent studies from both Greenland and Antarctica have reported significant changes in the water isotopic composition of near‐surface snow between precipitation events. These changes have been linked to isotopic exchange with atmospheric water vapor and sublimation‐induced fractionation, but the processes are poorly constrained by observations. Understanding and quantifying these processes are crucial to both the interpretation of ice core climate proxies and the formulation of isotope‐enabled general circulation models. Here, we present continuous measurements of the water isotopic composition in surface snow and atmospheric vapor together with near‐surface atmospheric turbulence and snow‐air latent and sensible heat fluxes, obtained at the East Greenland Ice‐Core Project drilling site in summer 2016. For two 4‐day‐long time periods, significant diurnal variations in atmospheric water isotopologues are observed. A model is developed to explore the impact of this variability on the surface snow isotopic composition. Our model suggests that the snow isotopic composition in the upper subcentimeter of the snow exhibits a diurnal variation with amplitudes in δ18O and δD of ~2.5‰ and ~13‰, respectively. As comparison, such changes correspond to 10–20% of the magnitude of seasonal changes in interior Greenland snow pack isotopes and of the change across a glacial‐interglacial transition. Importantly, our observation and model results suggest, that sublimation‐induced fractionation needs to be included in simulations of exchanges between the vapor and the snow surface on diurnal timescales during summer cloud‐free conditions in northeast Greenland.
Water Debt Indicator Reveals Where Agricultural Water Use Exceeds Sustainable Levels
Authors: Tuninetti Marta , Tamea Stefania , Dalin Carole 
Published: February 2019

AbstractAgriculture overexploits water resources in many regions, as water stress metrics highlight. Tracing back the causes of water overuses and separately accounting for soil water, surface water and groundwater resources is an open challenge to monitor the sustainability of agricultural water use. We introduce the “water debt repayment time” indicator, measuring the time required to replenish water resources used for annual crop production. This indicator disentangles source‐ and crop‐specific water overuses at a high spatial resolution. Globally, we find that wheat and rice production critically overuses groundwater resources and cotton production overuses both surface water and groundwater. Locally, unsustainable production is found over the Sabarmati Basin and in the Chao Phraya Basin, where the repayment time exceeds 5 years in many cultivated areas. Critical overuses are also found over the High Plain and Indo‐Gangetic Plains, where the repayment times reach 50 years. Unsustainable irrigation is often a consequence of growing crops during local dry seasons.
Convex Modeling of Pumps in Order to Optimize Their Energy Use
Authors: Horváth K. , van Esch B. , Vreeken D. , Pothof I. , Baayen J. 
Published: February 2019

AbstractThis study presents convex modeling of drainage pumps so that real‐time control systems can be implemented to minimize their energy use. A convex model is built based on pump curves and then used in mixed‐integer optimization to allow pumps to be turned on or off. It is implemented as an extension to the open source software package RTC‐Tools. The formulation is such that the continuous relaxations of the mixed‐integer problem are convex, hence branch‐and‐bound techniques may be used to find a global optimum. The formulation can be used for variable‐speed and constant‐speed pumps. There are several possible applications, such as optimization of polder systems, pumped‐storage systems, or certain water distribution networks. Finally, an example of the drainage pump is presented to compare the method to current methods and show that energy can be saved by using the proposed method.
Amino acids as wetting agents: surface translocation by Porphyromonas gingivalis
Authors: Moradali M Fata , Ghods Shirin , Angelini Thomas E , Davey Mary Ellen 
Published: February 2019

Abstract
Our understanding of how oral microbiota adapt in response to changes in their surroundings remains limited. This is particularly true of the slow-growing anaerobes that persist below the gum line. Here, we report that the oral anaerobe Porphyromonas gingivalis strain 381 can surface translocate when sandwiched between two surfaces. We show that during movement, this bacterium alters its metabolism, specifically side products of arginine utilization including citrulline and ornithine accumulated in the translocating cells; while arginine, N-acetyl-arginine, and the polyamine putrescine, which is produced from arginine were consumed. In addition, our results indicate that movement requires modification of the surrounding environment via proteolysis, cell dispersion, cell-on-cell rolling, and sub-diffusive cell-driven motility. We also show that production of fimbriae and fimbriae-associated proteins; as well as the regulation of contact-dependent growth inhibition genes, which are known to be involved in self-nonself discrimination, and the type IX secretion system are central to surface translocation. These studies provide a first glimpse into P. gingivalis motility and its relationship to ecological variables.
Non-monotonic pressure dependence of the thermal conductivity of boron arsenide
Authors: Ravichandran Navaneetha K. , Broido David 
Published: February 2019

AbstractRecent experiments demonstrate that boron arsenide (BAs) is a showcase material to study the role of higher-order four-phonon interactions in affecting heat conduction in semiconductors. Here we use first-principles calculations to identify a phenomenon in BAs and a related material - boron antimonide, that has never been predicted or experimentally observed for any other material: competing responses of three-phonon and four-phonon interactions to pressure rise cause a non-monotonic pressure dependence of thermal conductivity, κ, which first increases similar to most materials and then decreases. The resulting peak in κ shows a strong temperature dependence from rapid strengthening of four-phonon interactions relative to three-phonon processes with temperature. Our results reveal pressure as a knob to tune the interplay between the competing phonon scattering mechanisms in BAs and similar compounds, and provide clear experimental guidelines for observation in a readily accessible measurement regime.
Eliciting the impacts of cellular noise on metabolic trade-offs by quantitative mass imaging
Authors: Vasdekis A. E. , Alanazi H. , Silverman A. M. , Williams C. J. , Canul A. J. , Cliff J. B. , Dohnalkova A. C. , Stephanopoulos G. 
Published: February 2019

AbstractOptimal metabolic trade-offs between growth and productivity are key constraints in strain optimization by metabolic engineering; however, how cellular noise impacts these trade-offs and drives the emergence of subpopulations with distinct resource allocation strategies, remains largely unknown. Here, we introduce a single-cell strategy for quantifying the trade-offs between triacylglycerol production and growth in the oleaginous microorganism Yarrowia lipolytica. The strategy relies on high-throughput quantitative-phase imaging and, enabled by nanoscale secondary ion mass spectrometry analyses and dedicated image processing, allows us to image how resources are partitioned between growth and productivity. Enhanced precision over population-averaging biotechnologies and conventional microscopy demonstrates how cellular noise impacts growth and productivity differently. As such, subpopulations with distinct metabolic trade-offs emerge, with notable impacts on strain performance and robustness. By quantifying the self-degradation of cytosolic macromolecules under nutrient-limiting conditions, we discover the cell-to-cell heterogeneity in protein and fatty-acid recycling, unmasking a potential bet-hedging strategy under starvation.
The structure of a prokaryotic viral envelope protein expands the landscape of membrane fusion proteins
Authors: El Omari Kamel , Li Sai , Kotecha Abhay , Walter Thomas S. , Bignon Eduardo A. , Harlos Karl , Somerharju Pentti , De Haas Felix , Clare Daniel K. , Molin Mika , Hurtado Felipe , Li Mengqiu , Grimes Jonathan M. , Bamford Dennis H. , Tischler Nicole D. , Huiskonen Juha T. , Stuart David I. , Roine Elina 
Published: February 2019

AbstractLipid membrane fusion is an essential function in many biological processes. Detailed mechanisms of membrane fusion and the protein structures involved have been mainly studied in eukaryotic systems, whereas very little is known about membrane fusion in prokaryotes. Haloarchaeal pleomorphic viruses (HRPVs) have a membrane envelope decorated with spikes that are presumed to be responsible for host attachment and membrane fusion. Here we determine atomic structures of the ectodomains of the 57-kDa spike protein VP5 from two related HRPVs revealing a previously unreported V-shaped fold. By Volta phase plate cryo-electron tomography we show that VP5 is monomeric on the viral surface, and we establish the orientation of the molecules with respect to the viral membrane. We also show that the viral membrane fuses with the host cytoplasmic membrane in a process mediated by VP5. This sheds light on protein structures involved in prokaryotic membrane fusion.
Kindlin-2 links mechano-environment to proline synthesis and tumor growth
Authors: Guo Ling , Cui Chunhong , Zhang Kuo , Wang Jiaxin , Wang Yilin , Lu Yixuan , Chen Ka , Yuan Jifan , Xiao Guozhi , Tang Bin , Sun Ying , Wu Chuanyue 
Published: February 2019

AbstractCell metabolism is strongly influenced by mechano-environment. We show here that a fraction of kindlin-2 localizes to mitochondria and interacts with pyrroline-5-carboxylate reductase 1 (PYCR1), a key enzyme for proline synthesis. Extracellular matrix (ECM) stiffening promotes kindlin-2 translocation into mitochondria and its interaction with PYCR1, resulting in elevation of PYCR1 level and consequent increase of proline synthesis and cell proliferation. Depletion of kindlin-2 reduces PYCR1 level, increases reactive oxygen species (ROS) production and apoptosis, and abolishes ECM stiffening-induced increase of proline synthesis and cell proliferation. In vivo, both kindlin-2 and PYCR1 levels are markedly increased in lung adenocarcinoma. Ablation of kindlin-2 in lung adenocarcinoma substantially reduces PYCR1 and proline levels, and diminishes fibrosis in vivo, resulting in marked inhibition of tumor growth and reduction of mortality rate. Our findings reveal a mechanoresponsive kindlin-2-PYCR1 complex that links mechano-environment to proline metabolism and signaling, and suggest a strategy to inhibit tumor growth.
CD8+ T cells from patients with narcolepsy and healthy controls recognize hypocretin neuron-specific antigens
Authors: Pedersen Natasja Wulff , Holm Anja , Kristensen Nikolaj Pagh , Bjerregaard Anne-Mette , Bentzen Amalie Kai , Marquard Andrea Marion , Tamhane Tripti , Burgdorf Kristoffer Sølvsten , Ullum Henrik , Jennum Poul , Knudsen Stine , Hadrup Sine Reker , Kornum Birgitte Rahbek 
Published: February 2019

AbstractNarcolepsy Type 1 (NT1) is a neurological sleep disorder, characterized by the loss of hypocretin/orexin signaling in the brain. Genetic, epidemiological and experimental data support the hypothesis that NT1 is a T-cell-mediated autoimmune disease targeting the hypocretin producing neurons. While autoreactive CD4+ T cells have been detected in patients, CD8+ T cells have only been examined to a minor extent. Here we detect CD8+ T cells specific toward narcolepsy-relevant peptides presented primarily by NT1-associated HLA types in the blood of 20 patients with NT1 as well as in 52 healthy controls, using peptide-MHC-I multimers labeled with DNA barcodes. In healthy controls carrying the disease-predisposing HLA-DQB1*06:02 allele, the frequency of autoreactive CD8+ T cells was lower as compared with both NT1 patients and HLA-DQB1*06:02-negative healthy individuals. These findings suggest that a certain level of CD8+ T-cell reactivity combined with HLA-DQB1*06:02 expression is important for NT1 development.
Passive film characterisation of duplex stainless steel using scanning Kelvin probe force microscopy in combination with electrochemical measurements
Authors: Örnek Cem , Leygraf Christofer , Pan Jinshan 
Published: February 2019

AbstractThe characterisation of passive oxide films on heterogeneous microstructures is needed to assess local degradation (corrosion, cracking) in aggressive environments. The Volta potential is a surface-sensitive parameter which can be used to assess the surface nobility and hence passive films. In this work, it is shown that the Volta potential, measured on super duplex stainless steel by scanning Kelvin probe force microscopy, correlates with the electrochemical properties of the passive film, measured by electrochemical impedance spectroscopy and potentiodynamic polarisation. Natural oxidation by ageing in ambient air as well as artificial oxidation by immersion in concentrated nitric acid improved the nobility, both reflected by increased Volta potentials and electrochemical parameters. Passivation was associated with vanishing of the inherent Volta potential difference between the ferrite and austenite, thereby reducing the galvanic coupling and hence improving the corrosion resistance of the material. Hydrogen-passive film interactions, triggered by cathodic polarisation, however, largely increased the Volta potential difference between the phases, resulting in loss of electrochemical nobility, with the ferrite being more affected than the austenite. A correlative approach of using the Volta potential in conjunction with electrochemical data has been introduced to characterise the nobility of passive films in global and local scale.
Transcriptome-derived investigation of biosynthesis of quinolizidine alkaloids in narrow-leafed lupin (Lupinus angustifolius L.) highlights candidate genes linked to iucundus locus
Authors: Kroc Magdalena , Koczyk Grzegorz , Kamel Katarzyna A. , Czepiel Katarzyna , Fedorowicz-Strońska Olga , Krajewski Paweł , Kosińska Joanna , Podkowiński Jan , Wilczura Paulina , Święcicki Wojciech 
Published: February 2019

AbstractUnravelling the biosynthetic pathway of quinolizidine alkaloids (QAs), regarded as antinutritional compounds of narrow-leafed lupin (NLL) seeds, is fundamental to best exploit NLL as food or feed. We investigated 12 candidate genes connected to QA biosynthesis, selecting them by transcriptomic and genomic approaches, from the landscape of genes differentially expressed in leaves of the high- and low-alkaloid NLL accessions. Linkage analysis enabled the assessment of the location of the candidate genes in relation to iucundus, a major locus of unknown identity, that confers reduced QA content in seeds. The key finding was the identification of APETALA2/ethylene response transcription factor, RAP2-7, cosegregating with the iucundus locus and located within a region with highly significant QTLs that affect QA composition. We additionally identified a 4-hydroxy-tetrahydrodipicolinate synthase (DHDPS) gene involved in L-lysine biosynthesis as being closely linked to iucundus. The distributed location of other remaining candidates (including previously known QA genes) across different linkage groups, also indirectly supports the transcription factor as a possible regulator of lupin alkaloid biosynthesis. Our findings provide crucial insight into QA biosynthesis in NLL. Additionally, we evaluated and selected appropriate reference genes for qRT-PCRs to analyse the expression levels of QA genes in NLL.
Arrival Time Distributions of Spin-1/2 Particles
Authors: Das Siddhant , Dürr Detlef 
Published: February 2019

AbstractThe arrival time statistics of spin-1/2 particles governed by Pauli’s equation, and defined by their Bohmian trajectories, show unexpected and very well articulated features. Comparison with other proposed statistics of arrival times that arise from either the usual (convective) quantum flux or from semiclassical considerations suggest testing the notable deviations in an arrival time experiment, thereby probing the predictive power of Bohmian trajectories. The suggested experiment, including the preparation of the wave functions, could be done with present-day experimental technology.
Conditional Dicer1 depletion using Chrnb4-Cre leads to cone cell death and impaired photopic vision
Authors: Aldunate Eduardo Zabala , Di Foggia Valentina , Di Marco Fabiana , Hervas Laura Abelleira , Ribeiro Joana Claudio , Holder Daniel L. , Patel Aara , Jannini Tommaso B. , Thompson Dorothy A. , Martinez-Barbera Juan Pedro , Pearson Rachael A. , Ali Robin R. , Sowden Jane C. 
Published: February 2019

AbstractIrreversible photoreceptor cell death is a major cause of blindness in many retinal dystrophies. A better understanding of the molecular mechanisms underlying the progressive loss of photoreceptor cells remains therefore crucial. Abnormal expression of microRNAs (miRNAs) has been linked with the aetiology of a number of retinal dystrophies. However, their role during the degenerative process remains poorly understood. Loss of cone photoreceptors in the human macula has the greatest impact on sight as these cells provide high acuity vision. Using aChrnb4-cre; Dicerflox/floxconditional knockout mouse (Dicer CKO) to deleteDicer1from cone cells, we show that cone photoreceptor cells degenerate and die in theDicer-deleted retina. Embryonic eye morphogenesis appeared normal in Dicer CKO mice. Cone photoreceptor abnormalities were apparent by 3 weeks of age, displaying either very short or absent outer segments. By 4 months 50% of cones were lost and cone function was impaired as assessed by electroretinography (ERG). RNAseq analysis of the Dicer CKO retina revealed altered expression of genes involved in the visual perception pathway. These data show that loss ofDicer1leads to early-onset cone cell degeneration and suggest thatDicer1is essential for cone photoreceptor survival and homeostasis.
Origin and expansion of the mosquito Aedes aegypti in Madeira Island (Portugal)
Authors: Seixas Gonçalo , Salgueiro Patrícia , Bronzato-Badial Aline , Gonçalves Ysabel , Reyes-Lugo Matias , Gordicho Vasco , Ribolla Paulo , Viveiros Bela , Silva Ana Clara , Pinto João , Sousa Carla A. 
Published: February 2019

AbstractHistorically known as the yellow fever mosquito, Aedes aegypti invaded Madeira Island in 2005 and was the vector of the island’s first dengue outbreak in 2012. We have studied genetic variation at 16 microsatellites and two mitochondrial DNA genes in temporal samples of Madeira Island, in order to assess the origin of the invasion and the population structure of this mosquito vector. Our results indicated at least two independent colonization events occurred on the island, both having a South American source population. In both scenarios, Venezuela was the most probable origin of these introductions, a result that is in accordance with the socioeconomic relations between this country and Madeira Island. Once introduced, Ae. aegypti has rapidly expanded along the southern coast of the island and reached a maximum effective population size (Ne) in 2012, coincident with the dengue epidemic. After the outbreak, there was a 10-fold reduction in Ne estimates, possibly reflecting the impact of community-based vector control measures implemented during the outbreak. These findings have implications for mosquito surveillance not only for Madeira Island, but also for other European regions where Aedes mosquitoes are expanding.
Tunable polytetrafluoroethylene electret films with extraordinary charge stability synthesized by initiated chemical vapor deposition for organic electronics applications
Authors: Schröder Stefan , Strunskus Thomas , Rehders Stefan , Gleason Karen K. , Faupel Franz 
Published: February 2019

AbstractBulk polytetrafluoroethylene (PTFE) possesses excellent chemical stability and dielectric properties. Indeed, thin films with these same characteristics would be ideal for electret applications. Previously, the electret properties of PTFE-like thin films produced by rf sputtering or plasma enhanced chemical vapor deposition were found to deteriorate due to structural changes and surface oxidation. In this article, the technique of initiated chemical vapor deposition (iCVD) is evaluated for electret applications for the first time. The iCVD method is known for its solvent-free deposition of conformal, pinhole-free polymer thin films in mild process conditions. It is shown that PTFE thin films prepared in this way, show excellent agreement to commercial bulk PTFE with regard to chemical properties and dielectric dissipation factors. After ion irradiation in a corona discharge the iCVD PTFE thin films exhibit stable electret properties, which can be tailored by the process parameters. Due to the mild deposition conditions, the iCVD technique is suitable for deposition on flexible organic substrates for the next-generation electret devices. It is also compatible with state-of-the-art microelectronic processing lines due to the characteristics of conformal growth and easy scaling up to larger size substrates.
High-throughput, Efficient, and Unbiased Capture of Small RNAs from Low-input Samples for Sequencing
Authors: Belair Cassandra D. , Hu Tianyi , Chu Brandon , Freimer Jacob W. , Cooperberg Matthew R. , Blelloch Robert H. 
Published: February 2019

AbstractMicroRNAs hold great promise as biomarkers of disease. However, there are few efficient and robust methods for measuring microRNAs from low input samples. Here, we develop a high-throughput sequencing protocol that efficiently captures small RNAs while minimizing inherent biases associated with library production. The protocol is based on early barcoding such that all downstream manipulations can be performed on a pool of many samples thereby reducing reagent usage and workload. We show that the optimization of adapter concentrations along with the addition of nucleotide modifications and random nucleotides increases the efficiency of small RNA capture. We further show, using unique molecular identifiers, that stochastic capture of low input RNA rather than PCR amplification influences the biased quantitation of intermediately and lowly expressed microRNAs. Our improved method allows the processing of tens to hundreds of samples simultaneously while retaining high efficiency quantitation of microRNAs in low input samples from tissues or bodily fluids.