bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Electrostatic Charge on the Propagation of GPS (L‐band) Signals Through Volcanic Plumes
Authors: Harper Joshua Méndez , Steffes Paul , Dufek Josef , Akins Alex 
Published: February 2019

AbstractRecent field studies have shown that the presence of ash in the atmosphere can produce measurable attenuation of Global Positioning System (GPS) signals (Aranzulla et al., 2013, https://doi.org/10.1007/s10291-012-0294-4; Larson, 2013, https://doi.org/10.1002/grl.50556; Larson et al., 2017, https://doi.org/10.1016/j.jvolgeores.2017.04.005). The ability to detect plumes using GPS is appealing because many active volcanoes are already instrumented with high‐quality receivers. However, analyses using a Ralyeigh approximation have shown that the large attenuations cannot be explained by the scattering and absorption associated with ash or hydrometeors alone. Here, we show that the extinction of GPS signals, which fall into the L‐band of the electromagnetic spectrum, may be exacerbated significantly by excess surface charge on pyroclasts. Indeed, volcanic eruptions are often accompanied by a range of electrostatic processes, leading, in some cases, to spectacular lightning storms. We use a modified Mie scattering model to demonstrate that electrostatic effects can increase the extinction of L‐band radiation by up to an order of magnitude, producing attenuations consistent with those observed in the field. Thus, future work involving GPS as a tool to remotely probe plumes must take into account the electrification of ash in radiative transfer models. Additionally, we propose that the sensitivity of GPS to particle charging may catalyze the development of new techniques to explore electrostatic processes in plumes, especially if GPS measurements are complemented with millimeter‐wave RADAR measurements.
The Relation of Intraseasonal Variations With Local Onset and Demise of the Indian Summer Monsoon
Authors: Karmakar Nirupam , Misra Vasubandhu 
Published: February 2019

AbstractTwo of the most important hydroclimatic features of the Indian summer monsoon (ISM) rainfall are its onset/demise and intraseasonal oscillations (ISOs) manifested by the active‐break cycles. In this study, we aim to understand the quantitative association between these two phenomena. An objective definition of local onset/demise of the ISM based on more than a century‐long India Meteorological Department rain gauge observation is taken into consideration. Using multichannel singular spectrum analysis we isolate northward‐propagating low‐frequency (20–60 days; LF‐ISO) and northwestward propagating high‐frequency (10–20 days; HF‐ISO) ISOs from the daily ISM rainfall. Our results suggest that a large number of local onset (59%) and demise (62%) events occur during positive developing phases and positive decaying phases of two ISOs, respectively, with phase locking between LF‐ISO and HF‐ISO being particularly important. Local onset is largely associated with favorable phases of ISOs across India except for LF‐ISO over eastern India and HF‐ISO over western Ghats and central India (CI). We find that local demise is more coherent with the ISO phases, especially with HF‐ISO across the domain. We performed a case study to understand large‐scale association with the onset of the ISM over CI. In 44 of total 58 cases (1948–2005), when CI onset occurred during favorable LF‐ISO or HF‐ISO phase, they are either linked with a northward propagation of convection from the equator in LF‐ISO time scale (28 cases) or westward propagating structures from the western Pacific in HF‐ISO time scale (27 cases).
Folliculin regulates mTORC1/2 and WNT pathways in early human pluripotency
Authors: Mathieu J. , Detraux D. , Kuppers D. , Wang Y. , Cavanaugh C. , Sidhu S. , Levy S. , Robitaille A. M. , Ferreccio A. , Bottorff T. , McAlister A. , Somasundaram L. , Artoni F. , Battle S. , Hawkins R. D. , Moon R. T. , Ware C. B. , Paddison P. J. , Ruohola-Baker H. 
Published: February 2019

AbstractTo reveal how cells exit human pluripotency, we designed a CRISPR-Cas9 screen exploiting the metabolic and epigenetic differences between naïve and primed pluripotent cells. We identify the tumor suppressor, Folliculin(FLCN) as a critical gene required for the exit from human pluripotency. Here we show that FLCN Knock-out (KO) hESCs maintain the naïve pluripotent state but cannot exit the state since the critical transcription factor TFE3 remains active in the nucleus. TFE3 targets up-regulated in FLCN KO exit assay are members of Wnt pathway and ESRRB. Treatment of FLCN KO hESC with a Wnt inhibitor, but not ESRRB/FLCN double mutant, rescues the cells, allowing the exit from the naïve state. Using co-immunoprecipitation and mass spectrometry analysis we identify unique FLCN binding partners. The interactions of FLCN with components of the mTOR pathway (mTORC1 and mTORC2) reveal a mechanism of FLCN function during exit from naïve pluripotency.
Sympathetic nervous system controls resolution of inflammation via regulation of repulsive guidance molecule A
Authors: Körner Andreas , Schlegel Martin , Kaussen Torsten , Gudernatsch Verena , Hansmann Georg , Schumacher Timo , Giera Martin , Mirakaj Valbona 
Published: February 2019

AbstractThe bidirectional communication between the immune and nervous system is important in regulating immune responses. Here we show that the adrenergic nerves of sympathetic nervous system orchestrate inflammation resolution and regenerative programs by modulating repulsive guidance molecule A (RGM-A). In murine peritonitis, adrenergic nerves and RGM-A show bidirectional activation by stimulating the mutual expression and exhibit a higher potency for the cessation of neutrophil infiltration; this reduction is accompanied by increased pro-resolving monocyte or macrophage recruitment, polymorphonucleocyte clearance and specialized pro-resolving lipid mediators production at sites of injury. Chemical sympathectomy results in hyperinflammation and ineffective resolution in mice, while RGM-A treatments reverse these phenotypes. Signalling network analyses imply that RGM-A and β2AR agonist regulate monocyte activation by suppressing NF-κB activity but activating RICTOR and PI3K/AKT signalling. Our results thus illustrate the function of sympathetic nervous system and RGM-A in regulating resolution and tissue repair in a murine acute peritonitis model.
Ruthenium atomically dispersed in carbon outperforms platinum toward hydrogen evolution in alkaline media
Authors: Lu Bingzhang , Guo Lin , Wu Feng , Peng Yi , Lu Jia En , Smart Tyler J. , Wang Nan , Finfrock Y. Zou , Morris David , Zhang Peng , Li Ning , Gao Peng , Ping Yuan , Chen Shaowei 
Published: February 2019

AbstractHydrogen evolution reaction is an important process in electrochemical energy technologies. Herein, ruthenium and nitrogen codoped carbon nanowires are prepared as effective hydrogen evolution catalysts. The catalytic performance is markedly better than that of commercial platinum catalyst, with an overpotential of only −12 mV to reach the current density of 10 mV cm-2 in 1 M KOH and −47 mV in 0.1 M KOH. Comparisons with control experiments suggest that the remarkable activity is mainly ascribed to individual ruthenium atoms embedded within the carbon matrix, with minimal contributions from ruthenium nanoparticles. Consistent results are obtained in first-principles calculations, where RuCxNy moieties are found to show a much lower hydrogen binding energy than ruthenium nanoparticles, and a lower kinetic barrier for water dissociation than platinum. Among these, RuC2N2 stands out as the most active catalytic center, where both ruthenium and adjacent carbon atoms are the possible active sites.
Cryo-EM structure of the homohexameric T3SS ATPase-central stalk complex reveals rotary ATPase-like asymmetry
Authors: Majewski Dorothy D. , Worrall Liam J. , Hong Chuan , Atkinson Claire E. , Vuckovic Marija , Watanabe Nobuhiko , Yu Zhiheng , Strynadka Natalie C. J. 
Published: February 2019

AbstractMany Gram-negative bacteria, including causative agents of dysentery, plague, and typhoid fever, rely on a type III secretion system – a multi-membrane spanning syringe-like apparatus – for their pathogenicity. The cytosolic ATPase complex of this injectisome is proposed to play an important role in energizing secretion events and substrate recognition. We present the 3.3 Å resolution cryo-EM structure of the enteropathogenic Escherichia coli ATPase EscN in complex with its central stalk EscO. The structure shows an asymmetric pore with different functional states captured in its six catalytic sites, details directly supporting a rotary catalytic mechanism analogous to that of the heterohexameric F1/V1-ATPases despite its homohexameric nature. Situated at the C-terminal opening of the EscN pore is one molecule of EscO, with primary interaction mediated through an electrostatic interface. The EscN-EscO structure provides significant atomic insights into how the ATPase contributes to type III secretion, including torque generation and binding of chaperone/substrate complexes.
Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping
Authors: Gidoni Moriah , Snir Omri , Peres Ayelet , Polak Pazit , Lindeman Ida , Mikocziova Ivana , Sarna Vikas Kumar , Lundin Knut E. A. , Clouser Christopher , Vigneault Francois , Collins Andrew M. , Sollid Ludvig M. , Yaari Gur 
Published: February 2019

AbstractAnalysis of antibody repertoires by high-throughput sequencing is of major importance in understanding adaptive immune responses. Our knowledge of variations in the genomic loci encoding immunoglobulin genes is incomplete, resulting in conflicting VDJ gene assignments and biased genotype and haplotype inference. Haplotypes can be inferred using IGHJ6 heterozygosity, observed in one third of the people. Here, we propose a robust novel method for determining VDJ haplotypes by adapting a Bayesian framework. Our method extends haplotype inference to IGHD- and IGHV-based analysis, enabling inference of deletions and copy number variations in the entire population. To test this method, we generated a multi-individual data set of naive B-cell repertoires, and found allele usage bias, as well as a mosaic, tiled pattern of deleted IGHD and IGHV genes. The inferred haplotypes may have clinical implications for genetic disease predispositions. Our findings expand the knowledge that can be extracted from antibody repertoire sequencing data.
Evolutionary highways to persistent bacterial infection
Authors: Bartell Jennifer A. , Sommer Lea M. , Haagensen Janus A. J. , Loch Anne , Espinosa Rocio , Molin Søren , Johansen Helle Krogh 
Published: February 2019

AbstractPersistent infections require bacteria to evolve from their naïve colonization state by optimizing fitness in the host via simultaneous adaptation of multiple traits, which can obscure evolutionary trends and complicate infection management. Accordingly, here we screen 8 infection-relevant phenotypes of 443 longitudinalPseudomonas aeruginosaisolates from 39 young cystic fibrosis patients over 10 years. Using statistical modeling, we map evolutionary trajectories and identify trait correlations accounting for patient-specific influences. By integrating previous genetic analyses of 474 isolates, we provide a window into early adaptation to the host, finding: (1) a 2–3 year timeline of rapid adaptation after colonization, (2) variant “naïve” and “adapted” states reflecting discordance between phenotypic and genetic adaptation, (3) adaptive trajectories leading to persistent infection via three distinct evolutionary modes, and (4) new associations between phenotypes and pathoadaptive mutations. Ultimately, we effectively deconvolute complex trait adaptation, offering a framework for evolutionary studies and precision medicine in clinical microbiology.
Emergence of the structure-directing role of f-orbital overlap-driven covalency
Authors: Lu Erli , Sajjad Saira , Berryman Victoria E. J. , Wooles Ashley J. , Kaltsoyannis Nikolas , Liddle Stephen T. 
Published: February 2019

AbstractFEUDAL (f’s essentially unaffected, d’s accommodate ligands) is a longstanding bonding model in actinide chemistry, in which metal-ligand binding uses 6d-orbitals, with the 5f remaining non-bonding. The inverse-trans-influence (ITI) is a case where the model may break down, and it has been suggested that ionic and covalent effects work synergistically in the ITI. Here, we report an experimentally grounded computational study that quantitatively explores the ITI, and in particular the structure-directing role of f-orbital covalency. Strong donor ligands generate a cis-ligand-directing electrostatic potential (ESP) at the metal centre. When f-orbital participation, via overlap-driven covalency, becomes dominant via short actinide-element distances, this ionic ESP effect is overcome, favouring a trans-ligand-directed geometry. This study contradicts the accepted ITI paradigm in that here ionic and covalent effects work against each other, and suggests a clearly non-FEUDAL, structure-directing role for the f-orbitals.
Role of defects in determining the magnetic ground state of ytterbium titanate
Authors: Bowman D. F. , Cemal E. , Lehner T. , Wildes A. R. , Mangin-Thro L. , Nilsen G. J. , Gutmann M. J. , Voneshen D. J. , Prabhakaran D. , Boothroyd A. T. , Porter D. G. , Castelnovo C. , Refson K. , Goff J. P. 
Published: February 2019

AbstractPyrochlore systems are ideally suited to the exploration of geometrical frustration in three dimensions, and their rich phenomenology encompasses topological order and fractional excitations. Classical spin ices provide the first context in which it is possible to control emergent magnetic monopoles, and anisotropic exchange leads to even richer behaviour associated with large quantum fluctuations. Whether the magnetic ground state of Yb2Ti2O7 is a quantum spin liquid or a ferromagnetic phase induced by a Higgs transition appears to be sample dependent. Here we have determined the role of structural defects on the magnetic ground state via the diffuse scattering of neutrons. We find that oxygen vacancies stabilise the spin liquid phase and the stuffing of Ti sites by Yb suppresses it. Samples in which the oxygen vacancies have been eliminated by annealing in oxygen exhibit a transition to a ferromagnetic phase, and this is the true magnetic ground state.
Challenges to curing primary brain tumours
Authors: Aldape Kenneth , Brindle Kevin M. , Chesler Louis , Chopra Rajesh , Gajjar Amar , Gilbert Mark R. , Gottardo Nicholas , Gutmann David H. , Hargrave Darren , Holland Eric C. , Jones David T. W. , Joyce Johanna A. , Kearns Pamela , Kieran Mark W. , Mellinghoff Ingo K. , Merchant Melinda , Pfister Stefan M. , Pollard Steven M. , Ramaswamy Vijay , Rich Jeremy N. , Robinson Giles W. , Rowitch David H. , Sampson John H. , Taylor Michael D. , Workman Paul , Gilbertson Richard J. 
Published: February 2019

AbstractDespite decades of research, brain tumours remain among the deadliest of all forms of cancer. The ability of these tumours to resist almost all conventional and novel treatments relates, in part, to the unique cell-intrinsic and microenvironmental properties of neural tissues. In an attempt to encourage progress in our understanding and ability to successfully treat patients with brain tumours, Cancer Research UK convened an international panel of clinicians and laboratory-based scientists to identify challenges that must be overcome if we are to cure all patients with a brain tumour. The seven key challenges summarized in this Position Paper are intended to serve as foci for future research and investment.
Molecular interaction of fibrinogen with zeolite nanoparticles
Authors: Derakhshankhah Hossein , Hosseini Atiyeh , Taghavi Fereshteh , Jafari Samira , Lotfabadi Alireza , Ejtehadi Mohammad Reza , Shahbazi Sahba , Fattahi Ali , Ghasemi Atiyeh , Barzegari Ebrahim , Evini Mina , Saboury Ali Akbar , Shahri Seyed Mehdi Kamali , Ghaemi Behnaz , Ng Eng-Poh , Awala Hussein , Omrani Fatemeh , Nabipour Iraj , Raoufi Mohammad , Dinarvand Rassoul , shahpasand Koorosh , Mintova Svetlana , Hajipour Mohammad Javad , Mahmoudi Morteza 
Published: February 2019

AbstractFibrinogen is one of the key proteins that participate in the protein corona composition of many types of nanoparticles (NPs), and its conformational changes are crucial for activation of immune systems. Recently, we demonstrated that the fibrinogen highly contributed in the protein corona composition at the surface of zeolite nanoparticles. Therefore, understanding the interaction of fibrinogen with zeolite nanoparticles in more details could shed light of their safe applications in medicine. Thus, we probed the molecular interactions between fibrinogen and zeolite nanoparticles using both experimental and simulation approaches. The results indicated that fibrinogen has a strong and thermodynamically favorable interaction with zeolite nanoparticles in a non-cooperative manner. Additionally, fibrinogen experienced a substantial conformational change in the presence of zeolite nanoparticles through a concentration-dependent manner. Simulation results showed that both E- and D-domain of fibrinogen are bound to the EMT zeolite NPsviastrong electrostatic interactions, and undergo structural changes leading to exposing normally buried sequences. D-domain has more contribution in this interaction and the C-terminus of γ chain (γ377–394), located in D-domain, showed the highest level of exposure compared to other sequences/residues.
Surface Replication, Fidelity and Data Loss in Traditional Dental Microwear and Dental Microwear Texture Analysis
Authors: Mihlbachler Matthew C. , Foy Melissa , Beatty Brian L. 
Published: February 2019

AbstractDental microwear studies often analyze casts rather than original surfaces, although the information loss associated with reproduction is rarely considered. To investigate the sensitivity of high magnification (150x) microwear analysis to common surface replication materials and methods, we compared areal surface texture parameters (ISO 25178-2) and traditional microwear variables (pits and scratches) generated from teeth and casts of rat molars exposed to experimental diets involving hard and soft foods in which abrasive materials had been added. Although the data from the original and replicated surfaces were correlated, many significant differences were found between the resulting data of the casts and original teeth. Both areal surface texture parameters and traditional microwear variables showed diminished ability to discriminate between the eight diet treatments when casts were analyzed. When areal surface texture parameters and traditional microwear variables were combined into a single discriminant function analysis, the cast data and original data produced the most similar results. Microwear researchers tend to favor either texture analysis or traditional microwear methods, better results may be generated by combining them. Although surface textures were not accurately reproduced by the casts, they retained sufficient information to discriminate between microwear of the experimental diets to a degree similar to the original teeth.
A data-informatics method to quantitatively represent ternary eutectic microstructures
Authors: Sargin Irmak , Beckman Scott P. 
Published: February 2019

AbstractMany of the useful properties of modern engineering materials are determined by the material’s microstructure. Controlling the microstructure requires an understanding of the complex dynamics underlying its evolution during processing. Investigating the thermal and mass transport phenomena responsible for a structure requires establishing a common language to quantitatively represent the microstructures being examined. Although such a common language exists for some of the simple structures, which has allowed these materials to be engineered, there has yet to be a method to represent complex systems, such as the ternary microstructures, which are important for many technologies. Here we show how stereological and data science methods can be combined to quantitatively represent ternary eutectic microstructures relative to a set of exemplars that span the stereological attribute space. Our method uniquely describes ternary eutectic microstructures, allowing images from different studies, with different compositions and processing histories, to be quantitatively compared. By overcoming this long-standing challenge, it becomes possible to begin to make progress toward a quantitatively predictive theory of ternary eutectic growth. We anticipate that the method of quantifying instances of an object relative to a set of exemplars spanning attribute-space will be broadly applied to classify materials structures, and may also find uses in other fields.
Multifunctional Paper-Based Analytical Device for In Situ Cultivation and Screening of Escherichia coli Infections
Authors: Noiphung Julaluk , Laiwattanapaisal Wanida 
Published: February 2019

AbstractPoint-of-care testing (POCT) for uropathogen detection and chemical screening has great benefits for the diagnosis of urinary tract infections (UTIs). The goal of this study was to develop a portable and inexpensive paper-based analytical device (PAD) for cultivating bacteria in situ and rapidly testing for nitrite on the same device. The PAD was fabricated using a wax printing technique to create a pattern on Whatman No. 1 filter paper, which was then combined with a cotton sheet to support bacterial growth. Nitrite detection was based on the principle of the Griess reaction, and a linear detection range of 0–1.6 mg/dL (R2 = 0.989) was obtained. Scanning electron microscopy (SEM) analysis demonstrated that the bacteria were able to grow and formed a cluster on the cellulose fibres within 2 hours. The enzyme β-glucuronidase, which is specifically produced by Escherichia coli, was able to convert the pre-immobilized 5-bromo-4-chloro-3-indolyl-β-D-glucuronide sodium salt (X-GlcA), a colourless substrate, generating a blue colour. Under optimum conditions, the proposed device allowed bacterial concentrations in the range of 104–107 colony forming units (CFU)/mL to be quantified within 6 hours. Moreover, the use of this device enables the identification of E. coli pathogens with selectivity in real urine samples. In conclusion, the PAD developed in this study for UTI screening provides a rapid, cost-effective diagnostic method for use in remote areas.
New insights into the pathogenicity of non-synonymous variants through multi-level analysis
Authors: Sun Hong , Yu Guangjun 
Published: February 2019

AbstractPrecise classification of non-synonymous single nucleotide variants (SNVs) is a fundamental goal of clinical genetics. Next-generation sequencing technology is effective for establishing the basis of genetic diseases. However, identification of variants that are causal for genetic diseases remains a challenge. We analyzed human non-synonymous SNVs from a multilevel perspective to characterize pathogenicity. We showed that computational tools, though each having its own strength and weakness, tend to be overly dependent on the degree of conservation. For the mutations at non-degenerate sites, the amino acid sites of pathogenic substitutions show a distinct distribution in the classes of protein domains compared with the sites of benign substitutions. Overlooked disease susceptibility of genes explains in part the failures of computational tools. The more pathogenic sites observed, the more likely the gene is expressed in a high abundance or in a high tissue-specific manner, and have a high node degree of protein-protein interaction. The destroyed functions due to some false-negative mutations may arise because of a reprieve from the epigenetic repressed state which shouldn’t happen in multiple biological conditions, instead of the defective protein. Our work adds more to our knowledge of non-synonymous SNVs’ pathogenicity, thus will benefit the field of clinical genetics.