bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physiological response to silver toxicity in the extremely halophilic archaeon Halomicrobium mukohataei
Authors: Buda Doriana-Mădălina , Bulzu Paul-Adrian , Barbu-Tudoran Lucian , Porfire Alina , Pătraș Laura , Sesărman Alina , Tripon Septimiu , Șenilă Marin , Ionescu Mihaela Ileana , Banciu Horia Leonard 
Published: November 2019

ABSTRACTAdaptive strategies responsible for heavy metal tolerance were explored in the extremely halophilic archaeon Halomicrobium mukohataei DSM 12286. The tested strain was seemingly able to overcome silver-induced oxidative stress (assessed by malondialdehyde quantification, catalase assay and total antioxidant capacity measurement) mainly through non-enzymatic antioxidants. Energy dispersive spectrometry analysis illustrated the presence of colloidal silver in Hmc. mukohataei cultures exposed to AgNO3. Bright-field and transmission electron microscopy images, as well as dynamic light scattering analysis, demonstrated the presence of intracellular nanoparticles, mostly spherical, within a size range of 20–100 nm. As determined by the zeta potential measurement, the biosynthesized nanoparticles were highly stable, with a negative surface charge. Our research is a first attempt in the systematic study of the oxidative stress and intracellular silver nanoparticle accumulation, generated by exposure to silver ions, in members of Halobacteria class, thus broadening our knowledge on mechanisms supporting heavy metal tolerance of microbial cells living under saline conditions.
Antitumor immunity of low-dose cyclophosphamide: changes in T cells and cytokines TGF-beta and IL-10 in mice with colon-cancer liver metastasis
Authors: Huang Xiao-Ming , Zhang Nan-Rong , Lin Xu-Tao , Zhu Cai-Yan , Zou Yi-Feng , Wu Xiao-Jian , He Xiao-Sheng , He Xiao-Wen , Wan Yun-Le , Lan Ping 
Published: November 2019

Abstract

Background
The tumor immune microenvironment is one of the most important prognostic factors in liver metastasis from colorectal cancer. Low-dose cyclophosphamide (CTX) is widely believed to be involved in the modulation of the immune system. However, the underlying mechanism of low-dose CTX remains unknown. This study aimed to investigate the antitumor immunity of low-dose CTX in the treatment of colon-cancer liver metastasis.

Methods
Thirty mice were randomly divided into five groups. After liver metastasis was established in colon-cancer models, mice in the treatment groups were injected with low-dose CTX (20 mg/kg) at different time points. Liver and spleen tissues were examined for T-cell markers via flow cytometry. Interleukin (IL)-10 and transforming growth factor (TGF)-β1 expression levels in liver tissues were analysed by immunohistochemistry. Serum interferon (IFN)-γ and IL-10 levels were detected by enzyme-linked immunosorbent assay. An additional 20 mice were randomly allocated into two groups and the survival times were recorded.

Results
The expression levels of CD4+ T cells, CD8+ T cells, and IFN-γ were down-regulated, whereas those of IL-10 and TGF-β1 were up-regulated in liver metastasis from colon cancer in mice. Furthermore, the local and systemic microenvironments of the liver were altered, which led to reduced antitumor immune responses and subsequently liver metastasis. However, treatment with low-dose CTX reversed these effects. The survival times of mice treated with low-dose CTX were significantly longer than those of the other groups.

Conclusions
Low-dose CTX exerts its antitumor activity by changing the systemic and local immune microenvironments and enhancing immune regulation in mice. CTX could be used as a drug to prevent and treat liver metastasis from colon cancer.
Orienting and locating ocean-bottom seismometers from ship noise analysis
Authors: Trabattoni A , Barruol G , Dreo R , Boudraa A O , Fontaine F R 
Published: November 2019

Summary
Breakthroughs in understanding the structure and dynamics of our planet will strongly depend upon instrumenting deep oceans. Progress has been made these last decades in ocean-bottom seismic observations, but ocean-bottom seismometer (OBS) temporary deployments are still challenging and face set-up limitations. Launched from oceanographic vessels, OBSs fall freely and may slightly drift laterally, dragged by currents. Therefore, their actual orientation and location on the landing sites are hard to assess precisely. Numerous techniques have been developed to retrieve this key information, but most of them are costly, time-consuming or inaccurate. In this work, we show how ship noise can be used as an acoustic source of opportunity to retrieve both the orientation and the location of OBSs on the ocean floor. To retrieve the OBS orientation, we developed a first method based on a combination of seismic and pressure data through the use of the acoustic intensity. This latter can be used to quantify the OBS orientation from the ship noise direction of arrival (DOA), which can then be compared with known ship trajectories obtained from the automatic identification system (AIS). To accurately relocate OBSs, we also developed a second method based on the hydrophone data which computes distances of acoustical sources by measuring time differences of arrival (TDOA) between direct and reverberated phases. The OBS location is then retrieved by fitting measured ship distances with known ship trajectories. In this study, a full network of OBSs deployed in the SW Indian Ocean was reoriented and a test station was relocated. We demonstrate that our new methods may quantify the OBS orientation with an accuracy of about one degree, and its location with an accuracy of a few tens of metres, depending on the number of ships used in the analysis.
Gaussian process models—I. A framework for probabilistic continuous inverse theory
Authors: Valentine Andrew P , Sambridge Malcolm 
Published: November 2019

SUMMARYWe develop a theoretical framework for framing and solving probabilistic linear(ized) inverse problems in function spaces. This is built on the statistical theory of Gaussian Processes, and allows results to be obtained independent of any basis, avoiding any difficulties associated with the fidelity of representation that can be achieved. We show that the results of Backus–Gilbert theory can be fully understood within our framework, although there is not an exact equivalence due to fundamental differences of philosophy between the two approaches. Nevertheless, our work can be seen to unify several strands of linear inverse theory, and connects it to a large body of work in machine learning. We illustrate the application of our theory using a simple example, involving determination of Earth’s radial density structure.
Predicting lithology using neural networks from downhole data of a gas hydrate reservoir in the Krishna–Godavari basin, eastern Indian offshore
Authors: Singh Amrita , Ojha Maheswar , Sain Kalachand 
Published: November 2019

SUMMARYWe use the unsupervised and supervised neural network methods together to predict lithology of a gas hydrate reservoir from downhole data in the Krishna–Godavari (KG) offshore basin, India. In this study, we successfully identify the host litho-units of gas hydrate and show its effects in the identification of lithology using neural network techniques, which is not reported earlier. We use well log data acquired at three holes (10A, 03A and 04A) in 2006 during the first expedition of the Indian National Gas Hydrate Program (NGHP-01). Five different logging while drilling data (e.g. density, neutron porosity, gamma ray, resistivity and sonic) are considered for the mapping of lithology and gas hydrate. In the presence of gas hydrate, the resistivity and sonic velocity of the host sediments increase significantly, whereas density, neutron porosity and gamma ray are negligibly affected. Therefore, we calculate resistivity and sonic velocity for water-saturated sediment (without gas hydrate) theoretically to remove the effects of gas hydrate. At first, we apply the seven unsupervised classification methods (i.e. elbow, dendrogram, K-means, 3-D clustering, principal component analysis, Devies–Bouldin index and self-organizing map) to the data with gas hydrate (e.g. observed) and without gas hydrate (i.e. water-saturated/theoretical) to assess the data dimensionality and the number of clusters/litho-units. Each of the unsupervised schemes has its own pros and cons, and may provide different number of cluster/litho-units; sometimes, it is difficult to interpret from only one method. However, all seven methods provide same number of clusters in our study. Then, we apply the supervised classification method (i.e. Bayesian neural networks optimized by hybrid Monte Carlo searching technique) to the training data to refine the defined litho-units and map them with depth. Our approach identifies four types of litho-units and illustrates that the lithology in this area is dominated by clay (∼64 per cent) with some amount of silty clay, silt and minor sand. Gas hydrate is found in clay, silty clay and silt and not in sand. Results also show that, if gas hydrate is not considered as a separate unit, it is distributed as lithology in its hosts (i.e. clay, silty clay and silt). The method is very stable up to ∼15 per cent of random noise added to the data and results are well matched with the analysis of recovered core data. Identified lithologies at three wells correlate very well with seismic section crossing the wells. Very low permeability (&lt;0.1 mD) estimated at three wells also indicates the clay-dominated lithology in our study area.
Reliability evaluation of volcanic tremor source location determination using cross-correlation functions
Authors: Permana Theodorus , Nishimura Takeshi , Nakahara Hisashi , Fujita Eisuke , Ueda Hideki 
Published: November 2019

Summary
Source location determination of volcanic tremor has been a challenge in seismology due to the waveform complexity and difficulties in reading P- and S-wave arrival times. We present a method for locating volcanic tremor recorded at a seismic network distributed around a volcano. The method combines the source-scanning algorithm and cross-correlation analysis. Tremor records are processed using a technique adopted from ambient seismic interferometry to obtain stacked cross-correlation functions (CCFs) for all station pairs, which are expected to show high amplitudes at the lag time that corresponds to the travel time difference between the stations. The best seismic source location is determined from the maximum of the sum of envelope amplitudes of CCFs at predicted travel time differences between all pairs of stations. This method does not compute theoretical amplitudes, assume an initial hypocenter location, or measure the arrival times. To quantitatively evaluate the accuracy of the location determination, we examine the method by using the vertical component seismic data of volcano-tectonic (VT) earthquakes recorded at six seismic stations at Izu-Oshima volcano. The VTs have been previously located by using arrival times of P- and S-waves, and the hypocenters are used as the reference for evaluation and error estimation of the method. The results show that the misfit, which is the distance between our estimated sources and the references, is about 2 km or less when using CCFs at the frequency band of 4–16 Hz which contains the dominant frequencies of direct S-waves. To test whether the method can be used for volcanic tremor, we simulate the tremors by combining the observed VTs that occurred randomly in time in a localized region. The simulated tremors are determined with location errors of approximately 1 km or less, when the sources of VTs are located within a distance of 1 km and CCFs are calculated for a minimum data length of about 2 minutes. The volcanic tremor location method we present here can be used as an alternative tool for volcano monitoring, especially to locate tremors and seismic events with no clear phase arrival.
A novel method for computing the vertical gradients of the potential field: Application to downward continuation
Authors: Tran Kha Van , Nguyen Trung Nhu 
Published: November 2019

Summary
Downward continuation is a very useful technique in the interpretation of potential field data. It would enhance the short wavelength of the gravity anomalies or accentuate the details of the source distribution. Taylor series expansion method has been proposed to be one of the best downward continued methods. However, the method using high-order vertical derivatives leads to low accuracy and instability results in many cases. In this paper, we propose a new method using a combination of Taylor series expansion and upward continuation for computing vertical derivatives. This method has been tested on the gravitational anomaly of infinite horizontal cylinder in both cases with and without random noise for higher accurate and stable than Hilbert transform method and Laplace equation method, especially in the case of noise input data. This vertical derivative method is applied successfully to calculate the downward continuation according to Taylor series expansion method. The downward continuation is also tested on both complex synthetic models and real data in the East Vietnam Sea (South China Sea). The results reveal that by calculating this new vertical derivative, the downward continuation method gave higher accurate and stable than the previous downward continuation methods.
A process evaluation of the Communication for Healthy Communities adolescent health program in Uganda
Authors: Nalukwago Judith , Alaii Jane , van den Borne Bart , Bukuluki Paul Mukisa , Kimbowa Musa , Bockh Emily , Coutinho Sheila Marunga , Crutzen Rik 
Published: November 2019

AbstractThis study is a process evaluation of an adolescent-focused intervention of the USAID Communication for Healthy Communities program, in Uganda. We used mixed methods including observation, consultations and review of program documents to collect data on program coverage, reach and factors influencing implementation. Findings show that program activities were successfully implemented through collaborative partnerships with service partners and the community. Interpersonal communication complemented by mass-media messaging was effective in reaching and empowering adolescents with health information to make informed choices for behavior change. The program used theoretical frameworks to guide targeted interventions through audience segmentation and community empowerment. Targeted mass-media messaging and placement was found to be pertinent for program reach. Working through existing community structures is important for an effective reach of health promotion programs. Lessons identified for scaling-up adolescent health programs include the need to harmonize training and deployment of community champions by development partners, recruit audience-specific influential champions and link income-generating activities to health education interventions. There is thus need to collaboratively develop and institutionalize effective monitoring and evaluation strategies during program inception and design phases for appropriate accountability, ownership and a continuation of gains.
Acoustic classification in multifrequency echosounder data using deep convolutional neural networks
Authors: Brautaset Olav , Waldeland Anders Ueland , Johnsen Espen , Malde Ketil , Eikvil Line , Salberg Arnt-Børre , Handegard Nils Olav 
Published: November 2019

Abstract
Acoustic target classification is the process of assigning observed acoustic backscattering intensity to an acoustic category. A deep learning strategy for acoustic target classification using a convolutional network is developed, consisting of an encoder and a decoder, which allow the network to use pixel information and more abstract features. The network can learn features directly from data, and the learned feature space may include both frequency response and school morphology. We tested the method on multifrequency data collected between 2007 and 2018 during the Norwegian sandeel survey. The network was able to distinguish between sandeel schools, schools of other species, and background pixels (including seabed) in new survey data with an F1 score of 0.87 when tested against manually labelled schools. The network separated schools of sandeel and schools of other species with an F1 score of 0.94. A traditional school classification algorithm obtained substantially lower F1 scores (0.77 and 0.82) when tested against the manually labelled schools. To train the network, it was necessary to develop sampling and preprocessing strategies to account for unbalanced classes, inaccurate annotations, and biases in the training data. This is a step towards a method to be applied across a range of acoustic trawl surveys.
A comparison of surgical pulmonary embolectomy and catheter-directed lysis for life-threatening pulmonary emboli
Authors: Winters Amalia A , McDaniel Michael J , Binongo Jose N , Moon Rena C , Jaber Wissam A , Rajani Ravi R , Liberman Henry A , Lattouf Omar M , Halkos Michael E , Stouffer Chadwick W , Keeling W Brent 
Published: November 2019

Abstract

OBJECTIVES
Patients with life-threatening pulmonary emboli (PE) have traditionally been treated with anticoagulation alone, yet emerging data suggest that more aggressive therapy may improve short-term outcomes. The purpose of this study was to compare postoperative outcomes between catheter-directed thrombolysis (CDL) and surgical pulmonary embolectomy (SPE) in the treatment of life-threatening PE.

METHODS
A retrospective single-centre observational study was conducted for patients who underwent SPE or CDL at a single US academic centre. Preprocedural and postprocedural echocardiographic data were collected. Unadjusted regression models were constructed to assess the significance of the between-group postoperative differences.

RESULTS
A total of 126 patients suffered a life-threatening PE during the study period [60 SPE (47.6%), 66 CDL 52.4%]. Ten (24.4%) SPE patients and 10 (15.2%) CDL patients had massive PEs marked by preprocedural hypotension. Six (10.0%) SPE patients and 4 (6.0%) CDL patients suffered a preprocedure cardiac arrest (P = 0.41). In-hospital mortality rate was 3.3% (2) for SPE, and 3.0% (2) for CDL (P = 0.99). SPE patients were more likely to require prolonged ventilation (15.0% vs 1.5%, P = 0.01). No significant differences were found in other major complications. At baseline echocardiography, 76.9% of SPE patients and 56.9% of CDL patients had moderate or severe right ventricular (RV) dysfunction. Both treatment groups showed marked and durable improvement in echocardiographic markers of RV function from baseline at midterm follow-up.

CONCLUSIONS
Both SPE and CDL can be applied to well-selected high-risk patients with low rates of morbidity and mortality. Further research is necessary to delineate which patients would benefit most from either SPE or CDL following a life-threatening PE.
Reflection on modern methods: five myths about measurement error in epidemiological research
Authors: van Smeden Maarten , Lash Timothy L , Groenwold Rolf H H 
Published: November 2019

AbstractEpidemiologists are often confronted with datasets to analyse which contain measurement error due to, for instance, mistaken data entries, inaccurate recordings and measurement instrument or procedural errors. If the effect of measurement error is misjudged, the data analyses are hampered and the validity of the study’s inferences may be affected. In this paper, we describe five myths that contribute to misjudgments about measurement error, regarding expected structure, impact and solutions to mitigate the problems resulting from mismeasurements. The aim is to clarify these measurement error misconceptions. We show that the influence of measurement error in an epidemiological data analysis can play out in ways that go beyond simple heuristics, such as heuristics about whether or not to expect attenuation of the effect estimates. Whereas we encourage epidemiologists to deliberate about the structure and potential impact of measurement error in their analyses, we also recommend exercising restraint when making claims about the magnitude or even direction of effect of measurement error if not accompanied by statistical measurement error corrections or quantitative bias analysis. Suggestions for alleviating the problems or investigating the structure and magnitude of measurement error are given.
Quasi-optimal and pressure-robust discretizations of the Stokes equations by new augmented Lagrangian formulations
Authors: Kreuzer Christian , Zanotti Pietro 
Published: November 2019

Abstract
We approximate the solution of the stationary Stokes equations with various conforming and nonconforming inf-sup stable pairs of finite element spaces on simplicial meshes. Based on each pair, we design a discretization that is quasi-optimal and pressure-robust, in the sense that the velocity $H^1$-error is proportional to the best velocity $H^1$-error. This shows that such a property can be achieved without using conforming and divergence-free pairs. We also bound the pressure $L^2$-error, only in terms of the best velocity $H^1$-error and the best pressure $L^2$-error. Our construction can be summarized as follows. First, a linear operator acts on discrete velocity test functions, before the application of the load functional, and maps the discrete kernel into the analytical one. Second, in order to enforce consistency, we employ a new augmented Lagrangian formulation, inspired by discontinuous Galerkin methods.
Linear second-order IMEX-type integrator for the (eddy current) Landau–Lifshitz–Gilbert equation
Authors: Di Fratta Giovanni , Pfeiler Carl-Martin , Praetorius Dirk , Ruggeri Michele , Stiftner Bernhard 
Published: November 2019

Abstract
Combining ideas from Alouges et al. (2014, A convergent and precise finite element scheme for Landau–Lifschitz–Gilbert equation. Numer. Math., 128, 407–430) and Praetorius et al. (2018, Convergence of an implicit-explicit midpoint scheme for computational micromagnetics. Comput. Math. Appl., 75, 1719–1738) we propose a numerical algorithm for the integration of the nonlinear and time-dependent Landau–Lifshitz–Gilbert (LLG) equation, which is unconditionally convergent, formally (almost) second-order in time, and requires the solution of only one linear system per time step. Only the exchange contribution is integrated implicitly in time, while the lower-order contributions like the computationally expensive stray field are treated explicitly in time. Then we extend the scheme to the coupled system of the LLG equation with the eddy current approximation of Maxwell equations. Unlike existing schemes for this system, the new integrator is unconditionally convergent, (almost) second-order in time, and requires the solution of only two linear systems per time step.
A problem in control of elastodynamics with piezoelectric effects
Authors: Antil Harbir , Brown Thomas S , Sayas Francisco-Javier 
Published: November 2019

Abstract
We consider an optimal control problem where the state equations are a coupled hyperbolic–elliptic system. This system arises in elastodynamics with piezoelectric effects—the elastic stress tensor is a function of elastic displacement and electric potential. The electric flux acts as the control variable and bound constraints on the control are considered. We develop a complete analysis for the state equations and the control problem. The requisite regularity on the control, to show the well-posedness of the state equations, is enforced using the cost functional. We rigorously derive the first-order necessary and sufficient conditions using adjoint equations and further study their well-posedness. For spatially discrete (time-continuous) problems, we show the convergence of our numerical scheme. Three-dimensional numerical experiments are provided showing convergence properties of a fully discrete method and the practical applicability of our approach.