bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiridge Method for Studying Ground-Deformation Sources: Application to Volcanic Environments
Authors: Castaldo R. , Barone A. , Fedi M. , Tizzani P. 
Published: September 2018

AbstractVolcanic phenomena are currently monitored by the detection of physical and chemical observations. Generally, the ground deformation field is the most relevant shallow expression of the geometric and physical parameters variations in the magmatic reservoir. In this study, we propose a novel method for the direct estimation of the geometric parameters of sources responsible for volcanic ground deformation detected via the DInSAR technique. Starting with the biharmonic properties of the deformation field, we define an approach based on the Multiridge and ScalFun methods to achieve relevant information about both the positions and shapes of active sources, such as the Mogi source. Our methodology is definitely different from the methods currently used for modeling ground-deformation sources, mainly based on forward or inverse techniques. In fact, (i) it does not require any assumptions about the source type, and (ii) it is not influenced by the distribution of medium elastic parameters or (iii) the presence of high-frequency noise in the dataset. For synthetic cases, we accurately estimate the depth to the source within a 3% error. Finally, we study the real case of the Okmok volcano ground-deformation field and achieve results compatible with those in previous works.
The type 4 metallothionein from Brassica napus seeds folds in a metal-dependent fashion and favours zinc over other metals
Authors: Mierek-Adamska Agnieszka , Dąbrowska Grażyna B , Blindauer Claudia A 
Published: September 2018

Abstract
The problem of handling zinc in the cell is of great importance because zinc is an indispensable micronutrient involved in most physiological processes in all living organisms. Moreover, our understanding of mechanisms governing the discrimination between micronutrients and toxic metals on the level of individual proteins to the whole-organism level is incomplete. Metallothioneins are able to bind heavy metal ions, and roles in zinc homeostasis have been proposed. Here, we have studied the in vitro and in vivo metal-binding abilities of Brassica napus type 4 metallothionein (BnMT4) and its expression in germinating seeds in response to metal treatment. Our studies on the regulation of MT4 expression by metals at early stages of ontogenic development have revealed for the first time that the mRNA levels of BnMT4 were elevated in response to cadmium and zinc. Given this unexpected metalloregulation, and the dramatic differences in protein folding as detected by 1H NMR spectroscopy, we suggest that the BnMT4 protein may not only have a role in zinc homeostasis in early ontogenesis, but also the potential to discriminate between zinc and cadmium, perhaps via differential recognition of Cd- and Zn-complexes by cellular components involved in protein turnover.
The inhibitory role of intracellular free zinc in the regulation of Arg-1 expression in interleukin-4-induced activation of M2 microglia
Authors: Aratake Takaaki , Higashi Youichirou , Ueba Yusuke , Hamada Tomoya , Shimizu Takahiro , Shimizu Shogo , Yawata Toshio , Ueba Tetsuya , Saito Motoaki 
Published: September 2018

Abstract
Microglia, the resident immune cells of the central nervous system, can display a pro-inflammatory M1 phenotype or an anti-inflammatory M2 phenotype. Arginase (Arg)-1 expressed in interleukin-4 (IL-4)-induced M2 microglia reduces nitric oxide (NO) production by competing with inducible NO synthase for l-arginine, which contributes to the attenuation of brain inflammation. Although previous studies have indicated that brain zinc promotes M1 activation, the effect of zinc on M2 microglial activation remains to be determined. In the present study, murine primary microglia treated with 10 ng mL−1 IL-4 exhibited increased Arg-1 mRNA expression and levels of intracellular free zinc. Chelation of this increased intracellular free zinc by the cell permeable zinc chelator N,N,N′,N′-tetrakis-(2-pyridylmethyl)ethylenediamine (TPEN) aggravated the IL-4-induced mRNA expression and enzymatic activity of Arg-1. However, the cell impermeable zinc chelator CaEDTA had no effect on Arg-1 expression or cytosolic levels of free zinc in IL-4-induced M2-polarized microglia. Furthermore, treatment with IL-4 resulted in upregulation of phagocytic activity in microglia, while administration of TPEN abolished IL-4-induced phagocytic activity. Moreover, this effect was reversed vial-arginine supplementation. These findings suggest that IL-4 induces an increase in intracellular free zinc in microglia, which may act as a negative regulator of IL-4-induced Arg-1 expression, and that such negative regulation is essential for microglial phagocytic activity.
How Do Age and Hearing Loss Impact Spectral Envelope Perception?
Authors: Ozmeral Erol J. , Eddins Ann C. , Eddins David A. 
Published: September 2018

Purpose
The goal was to evaluate the potential effects of increasing hearing loss and advancing age on spectral envelope perception.

Method
Spectral modulation detection was measured as a function of spectral modulation frequency from 0.5 to 8.0 cycles/octave. The spectral modulation task involved discrimination of a noise carrier (3 octaves wide from 400 to 3200 Hz) with a flat spectral envelope from a noise having a sinusoidal spectral envelope across a logarithmic audio frequency scale. Spectral modulation transfer functions (SMTFs; modulation threshold vs. modulation frequency) were computed and compared 4 listener groups: young normal hearing, older normal hearing, older with mild hearing loss, and older with moderate hearing loss. Estimates of the internal spectral contrast were obtained by computing excitation patterns.

Results
SMTFs for young listeners with normal hearing were bandpass with a minimum modulation detection threshold at 2 cycles/octave, and older listeners with normal hearing were remarkably similar to those of the young listeners. SMTFs for older listeners with mild and moderate hearing loss had a low-pass rather than a bandpass shape. Excitation patterns revealed that limited spectral resolution dictated modulation detection thresholds at high but not low spectral modulation frequencies. Even when factoring out (presumed) differences in frequency resolution among groups, the spectral envelope perception was worse for the group with moderate hearing loss than the other 3 groups.

Conclusions
The spectral envelope perception as measured by spectral modulation detection thresholds is compromised by hearing loss at higher spectral modulation frequencies, consistent with predictions of reduced spectral resolution known to accompany sensorineural hearing loss. Spectral envelope perception is not negatively impacted by advancing age at any spectral modulation frequency between 0.5 and 8.0 cycles/octave.
Synthetic direct demodulation method and its applications in Insight-HXMT data analysis
Authors: Huo Zhuoxi , Zhang Yang 
Published: September 2018

Aims. A modulation equation relates the observed data to the object where the observation is approximated by a linear system. Reconstructing the object from the observed data is therefore equivalent to solving the modulation equation. In this work we present the synthetic direct demodulation (synDD) method to reduce the dimensionality of a general modulation equation and solve the equation in its sparse representation.
Methods. A principal component analysis is used to reduce the dimensionality of the kernel matrix and k-means clustering is applied to its sparse representation in order to decompose the kernel matrix into a weighted sum of a series of circulant matrices. The matrix-vector and matrix-matrix multiplication complexities are therefore reduced from polynomial time to linear-logarithmic time. A general statistical solution of the modulation equation in sparse representation is derived. Several data-analysis pipelines are designed for the Hard X-ray modulation Telescope (Insight-HXMT) based on the synDD method.
Results. In this approach, a large set of data originating from the same object but sampled irregularly and/or observed with different instruments in multiple epochs can be reduced simultaneously in a synthetic observation model. We suggest using the proposed synDD method in Insight-HXMT data analysis especially for the detection of X-ray transients and monitoring time-varying objects with scanning observations.
Fire safety issues in the design and construction of high-rise buildings
Authors: Poliakova Tatiana , Grigoryan Marina 
Published: September 2018

The construction of high-rise buildings has revealed new problems related to fire safety. The peculiarity of the architecture, which is covered in high-rise, in fires creates a danger for a large number of people there, reduces the possibility of their evacuation and rescue. The multifunctionality of such buildings, taking into account the originality of the external and internal views, leads to the difficulty of choosing a constructive system, a large number of utilities and technical systems. To address the issues related to safe operation, stay and evacuation of people is the development of a fire protection system for high-rise buildings, based on the development of:
• measures to ensure the durability of buildings or parts thereof againstprogressive collapse due to * ensuring the fire resistance of structures and buildings;
• measures to limit the spread of fire in high-rise buildings through theinstallation of fire barriers inside the building and the device of fire breaks between buildings;
• measures for ensuring timely and unimpeded evacuation of people andtheir rescue at emergency in high-rise buildings;
• systems of active protection of buildings from fire, namely: fire alarm andfire fighting, strong points of fire extinguishing.
metaGraphite–a new layer of pathway annotation to get metabolite networks
Authors: Sales Gabriele , Calura Enrica , Romualdi Chiara 
Published: September 2018

AbstractMotivationMetabolomics is an emerging ‘omics’ science involving the characterization of metabolites and metabolism in biological systems. Few bioinformatic tools have been developed for the visualization, exploration and analysis of metabolomic data within the context of metabolic pathways: some of them became rapidly obsolete and are no longer supported, others are based on a single database. A systematic collection of existing annotations has the potential of considerably boosting the investigation and contextualization of metabolomic measurements.ResultsWe have released a major update of our Bioconductor package graphite which explicitly tracks small molecules within pathway topologies and their interactions with proteins. The package gathers the information stored in eight major databases, oriented both at genes and at metabolites, across 14 different species. Depending on user preferences, all pathways can be retrieved as gene-only, gene metabolite or metabolite-only networks.Availability and implementationThe new graphite version (1.24) is available on Bioconductor.Supplementary informationSupplementary data are available at Bioinformatics online.
Mixed graphical models for integrative causal analysis with application to chronic lung disease diagnosis and prognosis
Authors: Sedgewick Andrew J , Buschur Kristina , Shi Ivy , Ramsey Joseph D , Raghu Vineet K , Manatakis Dimitris V , Zhang Yingze , Bon Jessica , Chandra Divay , Karoleski Chad , Sciurba Frank C , Spirtes Peter , Glymour Clark , Benos Panayiotis V 
Published: September 2018

Abstract

Motivation
Integration of data from different modalities is a necessary step for multi-scale data analysis in many fields, including biomedical research and systems biology. Directed graphical models offer an attractive tool for this problem because they can represent both the complex, multivariate probability distributions and the causal pathways influencing the system. Graphical models learned from biomedical data can be used for classification, biomarker selection and functional analysis, while revealing the underlying network structure and thus allowing for arbitrary likelihood queries over the data.

Results
In this paper, we present and test new methods for finding directed graphs over mixed data types (continuous and discrete variables). We used this new algorithm, CausalMGM, to identify variables directly linked to disease diagnosis and progression in various multi-modal datasets, including clinical datasets from chronic obstructive pulmonary disease (COPD). COPD is the third leading cause of death and a major cause of disability and thus determining the factors that cause longitudinal lung function decline is very important. Applied on a COPD dataset, mixed graphical models were able to confirm and extend previously described causal effects and provide new insights on the factors that potentially affect the longitudinal lung function decline of COPD patients.

Availability and implementation
The CausalMGM package is available on http://www.causalmgm.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Machine learning based automated dynamic quantification of left heart chamber volumes
Authors: Narang Akhil , Mor-Avi Victor , Prado Aldo , Volpato Valentina , Prater David , Tamborini Gloria , Fusini Laura , Pepi Mauro , Goyal Neha , Addetia Karima , Gonçalves Alexandra , Patel Amit R , Lang Roberto M 
Published: September 2018

Abstract

Aims
Studies have demonstrated the ability of a new automated algorithm for volumetric analysis of 3D echocardiographic (3DE) datasets to provide accurate and reproducible measurements of left ventricular and left atrial (LV, LA) volumes at end-systole and end-diastole. Recently, this methodology was expanded using a machine learning (ML) approach to automatically measure chamber volumes throughout the cardiac cycle, resulting in LV and LA volume–time curves. We aimed to validate ejection and filling parameters obtained from these curves by comparing them to independent well-validated reference techniques.

Methods and results
We studied 20 patients referred for cardiac magnetic resonance (CMR) examinations, who underwent 3DE imaging the same day. Volume–time curves were obtained for both LV and LA chambers using the ML algorithm (Philips HeartModel), and independently conventional 3DE volumetric analysis (TomTec), and CMR images (slice-by-slice, frame-by-frame manual tracing). Automatically derived LV and LA volumes and ejection/filling parameters were compared against both reference techniques. Minor manual correction of the automatically detected LV and LA borders was needed in 4/20 and 5/20 cases, respectively. Time required to generate volume–time curves was 35 ± 17 s using ML algorithm, 3.6 ± 0.9 min using conventional 3DE analysis, and 96 ± 14 min using CMR. Volume–time curves obtained by all three techniques were similar in shape and magnitude. In both comparisons, ejection/filling parameters showed no significant inter-technique differences. Bland–Altman analysis confirmed small biases, despite wide limits of agreement.

Conclusion
The automated ML algorithm can quickly measure dynamic LV and LA volumes and accurately analyse ejection/filling parameters. Incorporation of this algorithm into the clinical workflow may increase the utilization of 3DE imaging.
The Evolution of EUS-Guided Transluminal Drainage for the Treatment of Pancreatic Fluid Collections: A Comparison of Clinical and Cost Outcomes with Double-Pigtail Plastic Stents, Conventional Metal Stents and Lumen-Apposing Metal Stents
Authors: Falk Vanessa , Kenshil Sana , Sandha Simrat , Teshima Christopher , D’Souza Pernilla , Sandha Gurpal 
Published: September 2018

Abstract

Background
While most pancreatic fluid collections (PFCs) resolve spontaneously, endoscopic ultrasound-guided transluminal drainage (EUS-TD) may be necessary. EUS-TD has evolved from multiple double-pigtail plastic stents (DPPS) to fully covered self-expanding metal stents (FCSEMS) and lumen-apposing metal stents (LAMS). This study compares clinical attributes of DPPS, FCSEMS and LAMS.

Methods
This is a single-centre retrospective review of EUS-TD for PFCs. The primary outcome was clinical success. Secondary outcomes were technical success, procedure time, hospital length of stay (HLOS), number of endoscopies, need for necrosectomy, adverse events (AEs) and overall cost.

Results
Fifty-eight patients (37 male, average age 49 years) underwent a total of 60 EUS-TD procedures for PFCs (average size 11.2 cm with 29 pseudocysts and 29 walled-off necrosis). Ten patients (17%) underwent EUS-TD with DPPS and 48 patients (83%) with metal stents (32 FCSEMS, 16 LAMS). Overall technical and clinical success was 100% and 84%, respectively. Lumen-apposing metal stents had shorter procedure times (14.9 versus 63.6 DPPS, 39.1 min FCSEMS, P &lt; 0.001), and no difference in AEs (3 of 16 versus 4 of 10 DPPS, 12 of 34 FCSEMS, ns). Double-pigtail plastic stents required more endoscopies (3.7 versus 2.3 LAMS, 2.3 FCSEMS, P = 0.013) and necrosectomies (4 of 10 [40%]) compared with 5 of 34 [15%] in the FCSEMS group and 3 of 16 [19%] in the LAMS group, respectively, P = 0.001) to achieve clinical resolution. The overall cost and HLOS was not significantly different between groups.

Conclusion
The use of LAMS for PFCs is not associated with any significant increase in cost despite technical (shorter procedure time) and clinical advantages (shorter indwell time, reduced need for necrosectomy and no increase in AEs).
The impact of cored density profiles on the observable quantities of dwarf spheroidal galaxies
Authors: Harvey David , Revaz Yves , Robertson Andrew , Hausammann Loic 
Published: September 2018

ABSTRACT
We modify the chemo-dynamical code gear to simulate the impact of self-interacting dark matter (SIDM) on the observable quantities of 19 low-mass dwarf galaxies with a variety star-forming properties. We employ a relatively high, velocity independent cross-section of $\sigma /m=10\, \rm {cm^2\,g^{ -1}}$ and extract, in addition to integrated quantities, the total mass density profile, the luminosity profile, the line-of-sight velocities, the chemical abundance, and the star formation history. We find that despite the creation of large cores at the centre of the dark matter haloes, the impact of SIDM on the observable quantities of quenched galaxies is indiscernible, dominated mostly by the stochastic build up of the stellar matter. As such we conclude that it is impossible to make global statements on the density profile of dwarf galaxies from single or small samples. Although based mostly on quenched galaxies, this finding supports other recent work putting into question the reliability of inferred cored density profiles that are derived from observed line-of-sight velocities.
Transient cooling episodes during Cretaceous Oceanic Anoxic Events with special reference to OAE 1a (Early Aptian)
Authors: Jenkyns Hugh C. 
Published: September 2018

The two major oceanic anoxic events of the Cretaceous, those of the Early Aptian (OAE 1a) and the Cenomanian–Turonian boundary (OAE 2), registered some of the highest temperatures reconstructed for the Cretaceous Period, and are thought to be related to the input of volcanically derived carbon dioxide from one or more Large Igneous Provinces. Widely distributed deposition of marine organic matter, the hallmark of OAEs, and intensified silicate weathering in response to a globally accelerated hydrological cycle and/or reaction of seawater with freshly extruded basalt, are both potential mechanisms whereby the content of atmospheric carbon dioxide could have been drawn down to promote cooling, on the assumption that this potential effect was not offset by increased addition of this volcanically derived greenhouse gas. Reduction in the supply of such carbon dioxide, with deposition of organic matter and silicate weathering continuing at the same rate, could also have produced cooling. A transient fall in temperature and increase in marine dissolved oxygen levels is well documented for OAE 2, in the form of the so-called Plenus Cold Event or Benthic Oxic Event, associated with southward invasion of certain boreal faunas and an increase in many redox-sensitive and/or chalcophilic elements in seawater caused by temporary loss of anoxic–euxinic sinks as basalt–seawater interaction continued apace. High-resolution studies of OAE 1a show at least three cooling episodes of probable global distribution, one of which (recorded in the stratigraphy of the so-called C4 Segment) is documented at high enough resolution to show correlation with an increase in carbon-isotope values that was probably due to a rise in the quantities of organic matter being buried globally, with consequent potential drawdown of atmospheric CO2and/or reduction in volcanic input of this greenhouse gas. Both calcium- and lithium-isotope records suggest an increase in silicate weathering over the OAE 1a interval but current relatively low-resolution records cannot at present be tied to any one cooling episode, although the lowest Li-isotope values do derive from the C4 Segment. Evidence for reoxygenation of the ocean during the transient cooling episodes of OAE 1a is meagre, due to the lack of suitable sedimentary archives, although a negative sulfur-isotope excursion in a Pacific shallow-water carbonate section, which can be interpreted as due to oxidation of pyrite and/or sulfur-rich organic matter in the global ocean, suggests that this phenomenon may also have been a feature of the C4 Segment. Further work is required to elucidate the similarities and differences between OAE 2 and OAE 1a, but both phenomena are demonstrably global in reach and represent major disturbances to the carbon cycle with attendant effects on marine temperatures.This article is part of a discussion meeting issue ‘Hyperthermals: rapid and extreme global warming in our geological past’.
Warm plankton soup and red herrings: calcareous nannoplankton cellular communities and the Palaeocene–Eocene Thermal Maximum
Authors: Gibbs Samantha J. , Sheward Rosie M. , Bown Paul R. , Poulton Alex J. , Alvarez Sarah A. 
Published: September 2018

Past global warming events such as the Palaeocene–Eocene Thermal Maximum (PETM—56 Ma) are attributed to the release of vast amounts of carbon into the ocean, atmosphere and biosphere with recovery ascribed to a combination of silicate weathering and organic carbon burial. The phytoplanktonic nannoplankton are major contributors of organic and inorganic carbon but their role in this recovery process remains poorly understood and complicated by their contribution to marine calcification. Biocalcification is implicated not only in long-term carbon burial but also both short-term positive and negative climatic feedbacks associated with seawater buffering and responses to ocean acidification. Here, we use exceptional records of preserved fossil coccospheres to reconstruct cell size distribution, biomass production (particulate organic carbon, POC) and (particulate) inorganic carbon (PIC) yields of three contrasting nannoplankton communities (Bass River—outer shelf, Maud Rise—uppermost bathyal, Shatsky Rise—open ocean) through the PETM onset and recovery. Each of the sites shows contrasting community responses across the PETM as a function of their taxic composition and total community biomass. Our results indicate that nannoplankton PIC:POC had no role in short-term climate feedback and, as such, their importance as a source of CO2to the environment is a red herring. It is nevertheless likely that shifts to greater numbers of smaller cells at the shelf site in particular led to greater carbon transfer efficiency, and that nannoplankton productivity and export across the shelves had a significant modulating effect on carbon sequestration during the PETM recovery.This article is part of a discussion meeting issue ‘Hyperthermals: rapid and extreme global warming in our geological past’.