bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two‐dimensional discrete Fourier transform analysis of karst and coral reef morphologies
Authors: Davis Jerry D. , Chojnacki Joseph D. 
Published: May 2017

AbstractFourier transforms have been used in the analysis of landscapes that exhibit the influence of cyclic structures or other morphogenetic controls. Two‐dimensional Fourier transforms have been most successful when modeling features with a high frequency over the sample space. This research focuses on applications of 2D discrete Fourier transforms for karst and spur and groove coral reefs, using ArcGIS geoprocessing tools extended with Python NumPy numerical methods. Ten‐meter digital elevation data from Puerto Rico and Kentucky holokarst landscapes and five‐meter bathymetry from more unidirectional spur and groove coral reefs at Midway Atoll were analyzed. Our method identifies the dominant contributing waves in frequency space, and analyzed power contributions by 5° and 15° azimuth bins. A limiting factor in this analysis is the spatial extent of consistent morphology in the landscape. In contrast to time‐domain Fourier analysis, dominant landform frequencies can thus be of low magnitude, creating an imprecise estimate of wave morphometry and direction since this is derived from the combination of inverted x and y frequency values, and the limited frequency grain inherent in the discrete model degrades precision in the solution. Simulated karst and spur & groove landscapes were used to evaluate the grain of waveform orientation solutions.
Differentiating pulmonary transfusion reactions using recipient and transfusion factors
Authors: Roubinian Nareg H. , Looney Mark R. , Keating Sheila , Kor Daryl J. , Lowell Clifford A. , Gajic Ognjen , Hubmayr Rolf , Gropper Michael , Koenigsberg Monique , Wilson Gregory A. , A. Matthay Michael , Toy Pearl , Murphy Edward L. ,   the TRALI Study Group
Published: May 2017

BACKGROUNDIt is increasingly recognized that recipient risk factors play a prominent role in possible transfusion‐related acute lung injury (pTRALI) and transfusion‐associated circulatory overload (TACO). We hypothesized that both transfusion and recipient factors including natriuretic peptides could be used to distinguish TRALI from TACO and pTRALI.STUDY DESIGN AND METHODSWe performed a post hoc analysis of a case‐control study of pulmonary transfusion reactions conducted at the University of California at San Francisco and Mayo Clinic, Rochester. We evaluated clinical data and brain natriuretic peptides (BNP) levels drawn after transfusion in patients with TRALI (n = 21), pTRALI (n = 26), TACO (n = 22), and controls (n = 24). Logistic regression and receiver operating characteristics curve analyses were used to determine the accuracy of clinical and biomarker predictors in differentiating TRALI from TACO and pTRALI.RESULTSWe found that pTRALI and TACO were associated with older age, higher fluid balance, and elevated BNP levels relative to those of controls and TRALI. The following variables were useful in distinguishing cases of pTRALI and TACO from TRALI: age more than 70 years, BNP levels more than 1000 pg/mL, 24‐hour fluid balance of more than 3 L, and a lower number of transfused blood components. Using the above variables, our logistic model had a 91% negative predictive value in the differential diagnosis of TRALI.CONCLUSIONSModels incorporating readily available clinical and biomarker data can be used to differentiate transfusion‐related respiratory complications. Additional studies examining recipient risk factors and the likelihood of TRALI may be useful in decision making regarding donor white blood cell antibody testing.
Evaluation of Aptima Zika Virus Assay
Authors: Ren Ping , Ortiz Daniel A. , Terzian Ana C. B. , Colombo Tatiana E. , Nogueira Mauricio L. , Vasilakis Nikos , Loeffelholz Michael J. 
Published: May 2017

ABSTRACT

The Zika virus (ZIKV) epidemic in the Americas poses a public health emergency that requires a swift response. Accurate and reliable ZIKV diagnostic tests serve as an important tool for limiting the spread of ZIKV infections. The Aptima Zika virus assay (Hologic, Marlborough, MA) performed on the automated Panther system is a rapid and high-throughput method for detecting ZIKV RNA using transcription-mediated amplification (TMA) technology. We evaluated the performance characteristics of the Aptima Zika virus assay on clinical serum and urine specimens (
n
= 124) from two different patient populations and samples spiked with ZIKV from three different lineages (
n
= 10). Compared to the real-time reverse transcription-PCR (rRT-PCR) reference method, the Aptima ZIKV assay detected ZIKV RNA with a diagnostic accuracy of 94.8% (95% confidence interval [CI], 89.4 to 97.6), a sensitivity of 94.7% (95% CI, 73.5 to 99.9), and a specificity of 94.8% (95% CI, 88.9 to 97.8). Similar results were obtained regardless of whether a serum or urine source was used. The limits of detection of the assay at a 95% detection probability were 11.5 genome copy equivalents (GCE)/ml (95% fiducial limits, 7.9 to 20.2) in serum and 17.9 GCE/ml (95% fiducial limits, 13.1 to 27.5) in urine. The Aptima Zika virus assay results were highly reproducible (99%), and no cross-reactivity was seen during the testing of a panel of 95 specimens with potentially interfering substances, such as clinically relevant bacteria, fungi, and viruses, including other flaviviruses. The excellent performance characteristics and the convenience of a fully automated testing system make the Aptima ZIKV assay an attractive choice for clinical laboratories detecting ZIKV RNA from serum and urine.
Rubicon Modulates Antiviral Type I Interferon (IFN) Signaling by Targeting IFN Regulatory Factor 3 Dimerization
Authors: Kim Jae-Hoon , Kim Tae-Hwan , Lee Hyun-Cheol , Nikapitiya Chamilani , Uddin Md Bashir , Park Min-Eun , Pathinayake Prabuddha , Lee Eun Seo , Chathuranga Kiramage , Herath Thilina U. B. , Chathuranga W. A. Gayan , Lee Jong-Soo 
Published: May 2017

ABSTRACT
Rubicon is part of a Beclin-1-Vps34-containing autophagy complex. Rubicon induces antimicrobial responses upon Toll-like receptor (TLR) stimulation and functions as a feedback inhibitor to prevent unbalanced proinflammatory responses depending on dectin-1 signaling. However, the role played by Rubicon during antiviral immune responses, particularly the type I interferon (IFN) responses, remains largely unknown. Here, we report that Rubicon acts as a negative regulator for virus-triggered IFN signaling. Knockdown of Rubicon promoted type I interferon signaling and inhibited virus replication, while overexpression of Rubicon had the opposite effect. Rubicon specifically interacts with the interferon regulatory factor (IRF) association domain (IAD) of IRF3, and this interaction leads to inhibition of the dimerization of IRF3, which negatively regulates IFN-mediated antiviral response. Thus, our findings suggest the novel additional role of Rubicon as a negative regulator that inhibits the IFN signaling and cellular antiviral responses, providing a novel cellular mechanism of IRF3 inhibition.

IMPORTANCE
The type I IFN system is a critical innate immune response that protects organisms against virus infection. However, type I IFN signaling must be tightly regulated to avoid excessive production of IFNs. Hence, negative regulatory mechanisms for type I IFN signaling are important, and to date, several related molecules have been identified. Here, we show that Rubicon is a major negative regulator of type I IFN signaling, and unlike previous reports of cellular molecules that inhibit IRF3 activation via proteasomal degradation or dephosphorylation of IRF3, we show that Rubicon interacts with IRF3 and that ultimately this interaction leads to inhibition of the dimerization of IRF3. Thus, we identified a novel negative regulator of type I IFN signaling pathways and a novel cellular mechanism of IRF3 inhibition. The results of this study will increase our understanding of the role of negative-feedback mechanisms that regulate type I IFN signaling and maintain immune homeostasis.
Suppressor Analysis of the Fusogenic Lambda Spanins
Authors: Cahill Jesse , Rajaure Manoj , Holt Ashley , Moreland Russell , O'Leary Chandler , Kulkarni Aneesha , Sloan Jordan , Young Ry 
Published: May 2017

ABSTRACT

The final step of lysis in phage λ infections of
Escherichia coli
is mediated by the spanins Rz and Rz1. These proteins form a complex that bridges the cell envelope and that has been proposed to cause fusion of the inner and outer membranes. Accordingly, mutations that block spanin function are found within coiled-coil domains and the proline-rich region, motifs essential in other fusion systems. To gain insight into spanin function, pseudorevertant alleles that restored plaque formation for lysis-defective mutants of
Rz
and
Rz1
were selected. Most second-site suppressors clustered within a coiled-coil domain of Rz near the outer leaflet of the cytoplasmic membrane and were not allele specific. Suppressors largely encoded polar insertions within the hydrophobic core of the coiled-coil interface. Such suppressor changes resulted in decreased proteolytic stability of the Rz double mutants
in vivo
. Unlike the wild type, in which lysis occurs while the cells retain a rod shape, revertant alleles with second-site suppressor mutations supported lysis events that were preceded by spherical cell formation. This suggests that destabilization of the membrane-proximal coiled coil restores function for defective spanin alleles by increasing the conformational freedom of the complex at the cost of its normal, all-or-nothing functionality.

IMPORTANCE
Caudovirales
encode cell envelope-spanning proteins called spanins, which are thought to fuse the inner and outer membranes during phage lysis. Recent genetic analysis identified the functional domains of the lambda spanins, which are similar to class I viral fusion proteins. While the pre- and postfusion structures of model fusion systems have been well characterized, the intermediate structure(s) formed during the fusion reaction remains elusive. Genetic analysis would be expected to identify functional connections between intermediates. Since most membrane fusion systems are not genetically tractable, only few such investigations have been reported. Here, we report a suppressor analysis of lambda spanin function. To our knowledge this is the first suppression analysis of a class I-like complex and also the first such analysis of a prokaryote membrane fusion system.
Human Sera Collected between 1979 and 2010 Possess Blocking-Antibody Titers to Pandemic GII.4 Noroviruses Isolated over Three Decades
Authors: Sharma Sumit , Carlsson Beatrice , Czakó Rita , Vene Sirkka , Haglund Mats , Ludvigsson Johnny , Larson Göran , Hammarström Lennart , Sosnovtsev Stanislav V. , Atmar Robert L. , Green Kim Y. , Estes Mary K. , Svensson Lennart 
Published: May 2017

ABSTRACT

The emergence of pandemic GII.4 norovirus (NoV) strains has been proposed to occur due to changes in receptor usage and thereby to lead to immune evasion. To address this hypothesis, we measured the ability of human sera collected between 1979 and 2010 to block glycan binding of four pandemic GII.4 noroviruses isolated in the last 4 decades. In total, 268 sera were investigated for 50% blocking titer (BT
50
) values of virus-like particles (VLPs) against pig gastric mucin (PGM) using 4 VLPs that represent different GII.4 norovirus variants identified between 1987 and 2012. Pre- and postpandemic sera (sera collected before and after isolation of the reference NoV strain) efficiently prevented binding of VLP strains MD145 (1987), Grimsby (1995), and Houston (2002), but not the Sydney (2012) strain, to PGM. No statistically significant difference in virus-blocking titers was observed between pre- and postpandemic sera. Moreover, paired sera showed that blocking titers of ≥160 were maintained over a 6-year period against MD145, Grimsby, and Houston VLPs. Significantly higher serum blocking titers (geometric mean titer [GMT], 1,704) were found among IgA-deficient individuals than among healthy blood donors (GMT, 90.9) (
P
< 0.0001). The observation that prepandemic sera possess robust blocking capacity for viruses identified decades later suggests a common attachment factor, at least until 2002. Our results indicate that serum IgG possesses antibody-blocking capacity and that blocking titers can be maintained for at least 6 years against 3 decades of pandemic GII.4 NoV.

IMPORTANCE
Human noroviruses (NoVs) are the major cause of acute gastroenteritis worldwide. Histo-blood group antigens (HBGAs) in saliva and gut recognize NoV and are the proposed ligands that facilitate infection. Polymorphisms in HBGA genes, and in particular a nonsense mutation in
FUT2
(G428A), result in resistance to global dominating GII.4 NoV. The emergence of new pandemic GII.4 strains occurs at intervals of several years and is proposed to be attributable to epochal evolution, including amino acid changes and immune evasion. However, it remains unclear whether exposure to a previous pandemic strain stimulates immunity to a pandemic strain identified decades later. We found that prepandemic sera possess robust virus-blocking capacity against viruses identified several decades later. We also show that serum lacking IgA antibodies is sufficient to block NoV VLP binding to HBGAs. This is essential, considering that 1 in every 600 Caucasian children is IgA deficient.
0.2% chlorhexidine acetate as skin disinfectant prevents skin lesions in extremely preterm infants: a preliminary report
Authors: Janssen Lisanne M A , Tostmann Alma , Hopman Joost , Liem Kian D 
Published: May 2017

ObjectiveThe skin disinfectant ‘0.5% chlorhexidine gluconate in 70% alcohol’ (0.5% CHG-70% alc) may cause skin lesions in extremely preterm infants (gestational age <26 weeks). In April 2013, 0.2% chlorhexidine gluconate solution in acetate (0.2% CHG-acetate) was introduced as skin disinfectant for extremely preterm infants in our neonatal intensive care units. We aimed to compare the incidence of skin lesions and central line-associated bloodstream infection (CLABSI) among extremely preterm infants when using 0.5% CHG-70% alc and 0.2% CHG-acetate.DesignRetrospective pre-post comparison cohort study.PatientsAll electronic patient records of extremely preterm infants born between January 2011–March 2013 (‘0.5% CHG-70% alc’ cohort) and April 2013–October 2015 (‘0.2% CHG-acetate’ cohort) were reviewed.Main outcome measuresThe incidence of skin lesions and CLABSI. Skin lesions were defined as the presence of erythema, blisters, excoriation, oedema or induration. CLABSI was defined according to the definition of the US Centers for Disease Control and Prevention.ResultsThe incidence of skin lesions was 22% (95% CI 11% to 37%) in the ‘0.5% CHG-70% alc’ cohort (n=41) and 5% (95% CI 1% to 15%; p=0.02) in the ‘0.2% CHG-acetate’ cohort (n=41). The incidence of CLABSI was the same in both groups (28%; 95% CI 14% to 46% in ‘0.5% CHG-70% alc’ vs 27%; 95% CI 14% to 44% in ‘0.2% CHG-acetate’; p=0.98).ConclusionsUsing 0.2% CHG-acetate as skin disinfectant in extremely preterm infants resulted in statistically significant reduction of skin lesions, without increasing the risk of CLABSI as compared with 0.5% CHG-70% alc.
Taking a full lunch break
Authors: Fawcett Anne , Brailey Juliana 
Published: May 2017

THIS series gives readers the opportunity to consider and contribute to discussion of some of the ethical dilemmas that can arise in veterinary practice. Each month, a case scenario is presented, followed by discussion of some of the issues involved.In addition, a possible way forward is suggested; however, there is rarely a cut‐and‐dried answer in such cases, and readers may wish to suggest an alternative approach. This month's dilemma, ‘Taking a full lunch break’, was submitted and is discussed by Anne Fawcett and Juliana Brailey. Readers with comments to contribute are invited to send them as soon as possible, so that they can be considered for publication in the next issue.The series is being coordinated by Steven McCulloch, a practising vet with a PhD in the ethics of veterinary policy. It aims to provide a framework that will help practitioners find solutions when facing similar dilemmas.
Neuropeptide-Y alters VTA dopamine neuron activity through both pre- and postsynaptic mechanisms
Authors: West Katherine Stuhrman , Roseberry Aaron G. 
Published: May 2017

The mesocorticolimbic dopamine system, the brain’s reward system, regulates many different behaviors including food intake, food reward, and feeding-related behaviors, and there is increasing evidence that hypothalamic feeding-related neuropeptides alter dopamine neuron activity to affect feeding. For example, neuropeptide-Y (NPY), a strong orexigenic hypothalamic neuropeptide, increases motivation for food when injected into the ventral tegmental area (VTA). How NPY affects the activity of VTA dopamine neurons to regulate feeding behavior is unknown, however. In these studies we have used whole cell patch-clamp electrophysiology in acute brain slices from mice to examine how NPY affects VTA dopamine neuron activity. NPY activated an outward current that exhibited characteristics of a G protein-coupled inwardly rectifying potassium channel current in ~60% of dopamine neurons tested. In addition to its direct effects on VTA dopamine neurons, NPY also decreased the amplitude and increased paired-pulse ratios of evoked excitatory postsynaptic currents in a subset of dopamine neurons, suggesting that NPY decreases glutamatergic transmission through a presynaptic mechanism. Interestingly, NPY also strongly inhibited evoked inhibitory postsynaptic currents onto dopamine neurons by a presynaptic mechanism. Overall these studies demonstrate that NPY utilizes multiple mechanisms to affect VTA dopamine neuron activity, and they provide an important advancement in our understanding of how NPY acts in the VTA to control feeding behavior.NEW & NOTEWORTHY Neuropeptide-Y (NPY) has been shown to act on mesolimbic dopamine circuits to increase motivated behaviors toward food, but it is unclear exactly how NPY causes these responses. Here, we demonstrate that NPY directly inhibited a subset of ventral tegmental area (VTA) dopamine neurons through the activation of G protein-coupled inwardly rectifying potassium currents, and it inhibited both excitatory postsynaptic currents and inhibitory postsynaptic currents onto subsets of dopamine neurons through a presynaptic mechanism. Thus NPY uses multiple mechanisms to dynamically control VTA dopamine neuron activity.
A Hybrid Fuzzy Logic FOPID Position Controller for DC Motor Driving Tracking Systems System
Authors: M. Ismail Mohamed , F. Elbendary Ahmed , M. Abdelghany Abdelghany 
Published: May 2017

This paper presents a developed application for using Fraction Order PID controller (FOPID) in controlling of DC motors installed incelestron telescope, this is done through controlling the angles of two DC motors driven the telescope. The model of celestron telescope is mathematically represented by highly non linear differential equations, this types of nonlinear model is recommended to be controlled using Artificial Intelligent based controller. In this paper, optimal fuzzy FOPID is implemented instead of conventional PID controllers. Genetic Algorithm, fuzzy logic are used for tuning the FOPID parameters.FOPID controller is based on position error and its rate of change as an input vector, the proposed controller set presents a complete precision in forcing the telescope motors to satisfy the predefined position. The simulation results show the dynamic response of the system and the enhancement achieved in rising time and settling time when using FOPID. The response of FOPID is compared with the conventional PID with the same input position reference.
Generalized Transformed Hough: Segmentation of Contours in Angiographic Images
Authors: Gualdron Oscar Eduardo 
Published: May 2017

<span lang="EN-US">The morphologic and functional study of cardiovascular system is of vital importance because problems related to this system are one of the main causes of mortality in the world. It is important to mention that the left ventricle (VI) is the most susceptible to suffer severe damage, in diseases, such as arterial hypertension, mellitus diabetes or arteriosclerosis. This article presents a new methodology directed to segmentation of left ventricular contours, in angiographic images by using Generalized Hough Transform (TGH). It is important to obtain the ventricular edge, because analyzing processes of systole and diastole end, it is possible to calculate parameters of the cardiac functionality as the end-diastolic volume, end systolic volume, ejection fraction, cardiac output, Hyperkinéticos, Hypokinéticos segments, and normal; in this work we focus only on the removal of the same. </span>
A Blind Identification and Equalization for MC-CDMA Transmission Channel using a New of Adaptive Filter Algorithm
Authors: Elmostafa ATIFY , Daoui Cherki , BOUMEZZOUGH Ahmed 
Published: May 2017

A review of literature shows that there are a variety of adaptive filters. In this research study, we propose a new type of adaptive filter that increases the diversification used to compensate the channel distortion effect in the MC-CDMA transmission. First, we show expressions of the impulse responses of the filter in the case of a perfect channel. The adaptive filter was simulated was experienced by blind equalization for different cases of Gaussian white noise in the case of an MC-CDMA transmission with orthogonal frequency baseband for mobile radio downlink channel Bran A. Simulation Results of the proposed model shows the performance of the identification and blind equalization algorithm for MC-CDMA transmission chain using IFFT.
An Empirical Comparison of Latest Data Clustering Algorithms with State-of-the-Art
Authors: Shi Xianjin , Wang Wanwan , Zhang Chongsheng 
Published: May 2017

Over the past few decades, a great many data clustering algorithms have been developed, including K-Means, DBSCAN, Bi-Clustering and Spectral clustering, etc. In recent years, two new data clustering algorithms have been proposed, which are affinity propagation (AP, 2007) and density peak based clustering (DP, 2014). In this work, we empirically compare the performance of these two latest data clustering algorithms with state-of-the-art, using 6 external and 2 internal clustering validation metrics. Our experimental results on 16 public datasets show that, the two latest clustering algorithms, AP and DP, do not always outperform DBSCAN. Therefore, to find the best clustering algorithm for a specific dataset, all of AP, DP and DBSCAN should be considered. Moreover, we find that the comparison of different clustering algorithms is closely related to the clustering evaluation metrics adopted. For instance, when using the Silhouette clustering validation metric, the overall performance of K-Means is as good as AP and DP. This work has important reference values for researchers and engineers who need to select appropriate clustering algorithms for their specific applications.