bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benefits and Risks of Antiretroviral Therapy for Perinatal HIV Prevention
Authors: Fowler Mary G. , Qin Min , Fiscus Susan A. , Currier Judith S. , Flynn Patricia M. , Chipato Tsungai , McIntyre James , Gnanashanmugam Devasena , Siberry George K. , Coletti Anne S. , Taha Taha E. , Klingman Karin L. , Martinson Francis E. , Owor Maxensia , Violari Avy , Moodley Dhayendre , Theron Gerhard B. , Bhosale Ramesh , Bobat Raziya , Chi Benjamin H. , Strehlau Renate , Mlay Pendo , Loftis Amy J. , Browning Renee , Fenton Terence , Purdue Lynette , Basar Michael , Shapiro David E. , Mofenson Lynne M. 
Published: March 2017

(Abstracted from N Engl J Med 2016;375:1726–1737)
Antiretroviral regimens used for the prevention of mother-to-child transmission of the human immunodeficiency virus (HIV) have evolved over the years. Combination antiretroviral therapy (ART) is currently used for prevention of mother-to-child transmission of HIV but has shown more adverse effects compared with regimens containing fewer antiretroviral agents.
Optic Neuropathy Associated with Primary Sjögren’s Syndrome: A Case Series
Authors: Bak Eunoo , Yang Hee Kyung , Hwang Jeong-Min 
Published: March 2017

ABSTRACT

Purpose
To determine the diverse clinical features of optic neuropathy associated with primary Sjögren’s syndrome in Korean patients.

Methods
Five women with acute and/or chronic optic neuropathy who were diagnosed as primary Sjögren’s syndrome were retrospectively evaluated. Primary Sjögren’s syndrome was diagnosed by signs and symptoms of keratoconjunctivitis sicca, positive serum anti-Ro/SSA and/or anti-La/SSB antibodies, and/or minor salivary gland biopsy. All patients underwent a complete ophthalmologic examination.

Results
Among the five patients diagnosed as optic neuropathy related to primary Sjögren’s syndrome, four patients had bilateral optic neuropathy and one patient was unilateral. The clinical course was chronic in three patients and one of them showed acute exacerbation and was finally diagnosed with neuromyelitis optica spectrum disorder. The other two patients presented as acute optic neuritis and one was diagnosed with neuromyelitis optica spectrum disorder. Sicca symptoms were present in four patients, but only two patients reported these symptoms before the onset of optic neuropathy. Patients showed minimal response to systemic corticosteroids or steroid dependence, requiring plasmapheresis in the acute phase and immunosuppressive agents for maintenance therapy.

Conclusions
Optic neuropathy associated with primary Sjögren’s syndrome may show variable clinical courses, including acute optic neuritis, insidious progression of chronic optic atrophy, or in the context of neuromyelitis optica spectrum disorders. Optic neuropathy may be the initial manifestation of primary Sjögren’s syndrome without apparent sicca symptoms, which makes the diagnosis often difficult. The presence of specific antibodies including anti-Ro/SSA, anti-La/SSB, and anti-aquaporin-4 antibodies are supportive for the diagnosis and treatment in atypical cases of optic neuropathy.
A survey of modelling methods for high-fidelity wind farm simulations using large eddy simulation
Authors: Breton S.-P. , Sumner J. , Sørensen J. N. , Hansen K. S. , Sarmast S. , Ivanell S. 
Published: March 2017

Large eddy simulations (LES) of wind farms have the capability to provide valuable and detailed information about the dynamics of wind turbine wakes. For this reason, their use within the wind energy research community is on the rise, spurring the development of new models and methods. This review surveys the most common schemes available to model the rotor, atmospheric conditions and terrain effects within current state-of-the-art LES codes, of which an overview is provided. A summary of the experimental research data available for validation of LES codes within the context of single and multiple wake situations is also supplied. Some typical results for wind turbine and wind farm flows are presented to illustrate best practices for carrying out high-fidelity LES of wind farms under various atmospheric and terrain conditions.
This article is part of the themed issue ‘Wind energy in complex terrains’.
Linearized simulation of flow over wind farms and complex terrains
Authors: Segalini Antonio 
Published: March 2017

The flow over complex terrains and wind farms is estimated here by numerically solving the linearized Navier–Stokes equations. The equations are linearized around the unperturbed incoming wind profile, here assumed logarithmic. The Boussinesq approximation is used to model the Reynolds stress with a prescribed turbulent eddy viscosity profile. Without requiring the boundary-layer approximation, two new linear equations are obtained for the vertical velocity and the wall-normal vorticity, with a reduction in the computational cost by a factor of 8 when compared with a primitive-variables formulation. The presence of terrain elevation is introduced as a vertical coordinate shift, while forestry or wind turbines are included as body forces, without any assumption about the wake structure for the turbines. The model is first validated against some available experiments and simulations, and then a simulation of a wind farm over a Gaussian hill is performed. The speed-up effect of the hill is clearly beneficial in terms of the available momentum upstream of the crest, while downstream of it the opposite can be said as the turbines face a decreased wind speed. Also, the presence of the hill introduces an additional spanwise velocity component that may also affect the turbines’ operations. The linear superposition of the flow over the hill and the flow over the farm alone provided a first estimation of the wind speed along the farm, with discrepancies of the same order of magnitude for the spanwise velocity. Finally, the possibility of using a parabolic set of equations to obtain the turbulent kinetic energy after the linearized model is investigated with promising results.This article is part of the themed issue ‘Wind energy in complex terrains’.
Complex terrain experiments in the New European Wind Atlas
Authors: Mann J. , Angelou N. , Arnqvist J. , Callies D. , Cantero E. , Arroyo R. Chávez , Courtney M. , Cuxart J. , Dellwik E. , Gottschall J. , Ivanell S. , Kühn P. , Lea G. , Matos J. C. , Palma J. M. L. M. , Pauscher L. , Peña A. , Rodrigo J. Sanz , Söderberg S. , Vasiljevic N. , Rodrigues C. Veiga 
Published: March 2017

The New European Wind Atlas project will create a freely accessible wind atlas covering Europe and Turkey, develop the model chain to create the atlas and perform a series of experiments on flow in many different kinds of complex terrain to validate the models. This paper describes the experiments of which some are nearly completed while others are in the planning stage. All experiments focus on the flow properties that are relevant for wind turbines, so the main focus is the mean flow and the turbulence at heights between 40 and 300 m. Also extreme winds, wind shear and veer, and diurnal and seasonal variations of the wind are of interest. Common to all the experiments is the use of Doppler lidar systems to supplement and in some cases replace completely meteorological towers. Many of the lidars will be equipped with scan heads that will allow for arbitrary scan patterns by several synchronized systems. Two pilot experiments, one in Portugal and one in Germany, show the value of using multiple synchronized, scanning lidar, both in terms of the accuracy of the measurements and the atmospheric physical processes that can be studied. The experimental data will be used for validation of atmospheric flow models and will by the end of the project be freely available.
This article is part of the themed issue ‘Wind energy in complex terrains’.
Non-steady wind turbine response to daytime atmospheric turbulence
Authors: Nandi Tarak N. , Herrig Andreas , Brasseur James G. 
Published: March 2017

Relevant to drivetrain bearing fatigue failures, we analyse non-steady wind turbine responses from interactions between energy-dominant daytime atmospheric turbulence eddies and the rotating blades of a GE 1.5 MW wind turbine using a unique dataset from a GE field experiment and computer simulation. Time-resolved local velocity data were collected at the leading and trailing edges of an instrumented blade together with generator power, revolutions per minute, pitch and yaw. Wind velocity and temperature were measured upwind on a meteorological tower. The stability state and other atmospheric conditions during the field experiment were replicated with a large-eddy simulation in which was embedded a GE 1.5 MW wind turbine rotor modelled with an advanced actuator line method. Both datasets identify three important response time scales: advective passage of energy-dominant eddies (≈25–50 s), blade rotation (once per revolution (1P), ≈3 s) and sub-1P scale (<1 s) response to internal eddy structure. Large-amplitude short-time ramp-like and oscillatory load fluctuations result in response to temporal changes in velocity vector inclination in the aerofoil plane, modulated by eddy passage at longer time scales. Generator power responds strongly to large-eddy wind modulations. We show that internal dynamics of the blade boundary layer near the trailing edge is temporally modulated by the non-steady external flow that was measured at the leading edge, as well as blade-generated turbulence motions.
This article is part of the themed issue ‘Wind energy in complex terrains’.
Sound propagation from a ridge wind turbine across a valley
Authors: Van Renterghem Timothy 
Published: March 2017

Sound propagation outdoors can be strongly affected by ground topography. The existence of hills and valleys between a source and receiver can lead to the shielding or focusing of sound waves. Such effects can result in significant variations in received sound levels. In addition, wind speed and air temperature gradients in the atmospheric boundary layer also play an important role. All of the foregoing factors can become especially important for the case of wind turbines located on a ridge overlooking a valley. Ridges are often selected for wind turbines in order to increase their energy capture potential through the wind speed-up effects often experienced in such locations. In this paper, a hybrid calculation method is presented to model such a case, relying on an analytical solution for sound diffraction around an impedance cylinder and the conformal mapping (CM) Green's function parabolic equation (GFPE) technique. The various aspects of the model have been successfully validated against alternative prediction methods. Example calculations with this hybrid analytical–CM–GFPE model show the complex sound pressure level distribution across the valley and the effect of valley ground type. The proposed method has the potential to include the effect of refraction through the inclusion of complex wind and temperature fields, although this aspect has been highly simplified in the current simulations.This article is part of the themed issue ‘Wind energy in complex terrains’.
Turbulence and entrainment length scales in large wind farms
Authors: Andersen Søren J. , Sørensen Jens N. , Mikkelsen Robert F. 
Published: March 2017

A number of large wind farms are modelled using large eddy simulations to elucidate the entrainment process. A reference simulation without turbines and three farm simulations with different degrees of imposed atmospheric turbulence are presented. The entrainment process is assessed using proper orthogonal decomposition, which is employed to detect the largest and most energetic coherent turbulent structures. The dominant length scales responsible for the entrainment process are shown to grow further into the wind farm, but to be limited in extent by the streamwise turbine spacing, which could be taken into account when developing farm layouts. The self-organized motion or large coherent structures also yield high correlations between the power productions of consecutive turbines, which can be exploited through dynamic farm control.
This article is part of the themed issue ‘Wind energy in complex terrains’.
Survey on Prevalence of Canine Cutaneous Myiasis in Some Selected Kebeles of Dire Dawa City Administration
Authors: Abebe Henok 
Published: March 2017

ABSTRACTA cross sectional study of canine cutaneous myiasis was conducted in five randomly selected kebeles of Dire Dawa Administrative council from December 2009 up to April 2010 to determine the prevalence of canine cutaneous myiasis and to assess factors that determine the occurrence of the disease specifically in dog. Active questionnaire survey among 60 households were used for which 384 dogs were sampled. From a total of 384 dogs, 162 (42.19%) were found harboring the disease cutaneous myiasis among this 120 (74.07%) were infested with the 3rdand 2ndinstar larvae ofCordylobiaantropophaga.whereas the remaining 42(25.93%) observed dogs were found infested with cutaneous myiasis. The larvae were identified in Dire Dawa regional diagnostic veterinary parasitology laboratory. Analysis of active questionnaire survey showed that there is no statistically significance difference in the prevalence of disease among different breeds and sexes (P >0.05). In this study, an overall prevalence rate of 162 (42.19%) was found with a statistically significant association among different age groups, housing system and living area (kebele) (P<0.05). Higher prevalence was recorded at 02 kebele (Sabian area) 59 (54.65%), 03 Kebele (Depo and number-one), 43(44.33%), 04 Keble (Gende kore and Greek camp) 33(37.50%), Addis Ketema. 27(51.92%) and05 Keeble (Dechatu) 0(0%). There was 121(49.59%) confined dogs and 41(29.29%) were stray dogs which let out without any control, and puppies of age less than 6 month old (71.56 %), and dogs of age range between 6 months and 18months (79.03%) while those of greater than 18 months (16.43%), were least affected.
Adaptation to chronic malnutrition leads to reduced dependence on microbiota inDrosophila
Authors: Erkosar Berra , Kolly Sylvain , van der Meer Jan R. , Kawecki Tadeusz J. 
Published: March 2017

AbstractNumerous studies have shown that animal nutrition is tightly linked to gut microbiota, especially under nutritional stress. InDrosophila, microbiota are known to promote juvenile growth, development and survival on poor diets, mainly through enhanced digestion leading to changes in hormonal signaling. Here we show that this reliance on microbiota is greatly reduced in replicatedDrosophilapopulations that adapted to a poor larval diet in the course of over 170 generations of experimental evolution. Protein and polysaccharide digestion in these malnutrition-adapted populations became much less dependent on colonization with microbiota. This was accompanied by changes in at least some targets of dFOXO transcription factor, which is a key regulator of cell growth and survival. Our study suggests that some metazoans have retained the evolutionary potential to adapt their physiology such that association with microbiota may become optional rather than essential.
xCell: Digitally portraying the tissue cellular heterogeneity landscape
Authors: Aran Dvir , Hu Zicheng , Butte Atul J. 
Published: March 2017

AbstractTissues are complex milieu consisting of numerous cell-types. Numerous recent methods attempt to enumerate cell subsets from transcriptomes. However, available method used limited source for training and displayed only partial portrayal of the full cellular landscape. Here we presentxCell, a novel gene-signature based method for inferring 64 immune and stroma cell-types. We harmonized 1,822 pure human cell-types transcriptomes from various sources, employed curve fitting approach for linear comparison of cell-types, and introduced a novel spillover compensation technique for separating between cell-types. Using extensivein silicoanalyses and comparison to cytometry immunophenotyping we show thatxCelloutperforms other methods:http://xCell.ucsf.edu/.
Potential for rapid genetic adaptation to warming in a Great Barrier Reef coral
Authors: Matz Mikhail V. , Treml Eric A. , Aglyamova Galina V. , van Oppen Madeleine J. H. , Bay Line K. 
Published: March 2017

AbstractCan genetic adaptation in reef-building corals keep pace with the current rate of sea surface warming? Here we combine population genomic, biophysical modeling, and evolutionary simulations to predict future adaptation of the common coralAcropora milleporaon the Great Barrier Reef. Loss of coral cover in recent decades did not yet have detectable effect on genetic diversity in our species. Genomic analysis of migration patterns closely matched the biophysical model of larval dispersal in favoring the spread of existing heat-tolerant alleles from lower to higher latitudes. Given these conditions we find that standing genetic variation could be sufficient to fuel rapid adaptation ofA. milleporato warming for the next 100-200 years, although random thermal anomalies would drive increasingly severe mortality episodes. However, this adaptation will inevitably cease unless the warming is slowed down, since no realistic mutation rate could replenish adaptive genetic variation fast enough.
Direct visualization of how Actin Depolymerizing Factor’s filament severing and depolymerization synergizes with Capping Protein's "monomer funneling" to promote rapid polarized growth of actin filaments
Authors: Shekhar Shashank , Carlier Marie-France 
Published: March 2017

AbstractA living cell’s ability to assemble actin filaments in intracellular motile processes is directly dependent on the availability of polymerizable actin monomers which feed polarized filament growth. Continued generation of the monomer pool by filament disassembly is therefore crucial. Disassemblers like ADF/cofilin and filament cappers like Capping Protein (CP) are essential agonists of motility, but the exact molecular mechanisms by which they accelerate actin polymerization at the leading edge and filament turnover has been debated for over two decades. While filament fragmentation by ADF/cofilin has long been demonstrated by TIRF, filament depolymerization was only inferred from bulk solution assays. Using microfluidics-assisted TIRF microscopy, we provide the first direct visual evidence of ADF's simultaneous severing and rapid depolymerization of individual filaments. We have also built a conceptually novel assay to directly visualize ADF’s effect on a filament population. We demonstrate that ADF’s enhanced pointed-end depolymerization leads to an increase in polymerizable actin monomers co-existing with filaments, thus promoting faster barbed-end growth. We further reveal how ADF-enhanced filament depolymerization synergizes with CP’s long-predicted “monomer funneling” and leads to skyrocketing of filament growth rates, close to estimated rates in the lamellipodia. The “Funneling model” hypothesized, on thermodynamic grounds, that at high enough extent of capping, the few noncapped filaments transiently grow much faster, an effect proposed to be very important for motility. We provide the first direct microscopic evidence of monomer funneling by CP at the scale of individual filaments. We believe that these results enlighten our understanding of the turnover of cellular actin networks.
Overlapping representation of primary tastes in a defined region of the gustatory cortex
Authors: Fletcher Max L. , Cameron Ogg M. , Lu Lianyi , Ogg Robert J. , Boughter John D. 
Published: March 2017

AbstractTwo-photon imaging was used to examine taste responses in neurons in a region of gustatory cortex defined by thalamic input. This area contained an overlapping representation of primary tastes, with neurons that were either narrowly or broadly responsive to taste stimuli. Analysis demonstrates that activity in the neuronal population in this area yields information about both taste quality and hedonics.
ARSDA: A new approach for storing, transmitting and analyzing high-throughput sequencing data
Authors: Xia Xuhua 
Published: March 2017

ABSTRACTTwo major stumbling blocks exist in high-throughput sequencing (HTS) data analysis. The first is the sheer file size typically in gigabytes when uncompressed, causing problems in storage, transmission and analysis. However, these files do not need to be so large and can be reduced without loss of information. Each HTS file, either in compressed .SRA or plain text .fastq format, contains numerous identical reads stored as separate entries. For example, among 44603541 forward reads in the SRR4011234.sra file (from aBacillus subtilistranscriptomic study) deposited at NCBI’s SRA database, one read has 497027 identical copies. Instead of storing them as separate entries, one can and should store them as a single entry with the SeqID_NumCopy format (which I dub as FASTA+ format). The second is the proper allocation reads that map equally well to paralogous genes. I illustrate in detail a new method for such allocation. I have developed ARSDA software that implement these new approaches. A number of HTS files for model species are in the process of being processed and deposited athttp://coevol.rdc.uottawa.cato demonstrate that this approach not only saves a huge amount of storage space and transmission bandwidth, but also dramatically reduces time in downstream data analysis. Instead of matching the 497027 identical reads separately against theBacillus subtilisgenome, one only needs to match it once. ARSDA includes functions to take advantage of HTS data in the new sequence format for downstream data analysis such as gene expression characterization. ARSDA can be run on Windows, Linux and Macintosh computers and is freely available athttp://dambe.bio.uottawa.ca/ARSDA/ARSDA.aspx.
Model predictive control of an unmanned aerial vehicle
Authors: Erdogan Halit Firat , Kural Ayhan , Ozsoy Can 
Published: March 2017

Purpose
The purpose of this paper is to design a controller for the unmanned aerial vehicle (UAV).

Design/methodology/approach
In this study, the constrained multivariable multiple-input and multiple-output (MIMO) model predictive controller (MPC) has been designed to control all outputs by manipulating inputs. The aim of the autopilot of UAV is to keep the UAV around trim condition and to track airspeed commands.

Findings
The purpose of using this control method is to decrease the control effort under the certain constraints and deal with interactions between each output and input while tracking airspeed commands.

Originality/value
By using constraint, multivariable (four inputs and seven outputs) MPC unlike the relevant literature in this field, the UAV tracked airspeed commands with minimum control effort dealing with interactions between each input and output under disturbances such as wind.
Sigma overbound for aircraft landing in presence of day-to-day multipath correlation
Authors: Sayim Irfan , Zhang Dan 
Published: March 2017

PurposeThe purpose of this work is to obtain an overbounded broadcast sigma from actual (non-Gaussian) correction error distribution under the stringent navigation integrity requirements for aircraft precision approach and landing.Design/methodology/approachApproach is statistically to overbound satellite pseudorange correction error distribution with the use of numerical solution of Fisher-Ztransformation. Inflation factors for overbounding broadcast sigma are extracted from Fisher-Ztransformation based on measured correlation and counted independent identically distributed (iid) sample sizes of true empirical data.FindingsNew overbounded broadcast sigma values for eight long-pass satellites were obtained based on measured actual empirical data and ensured integrity risk at 10−8probability level. Proposed methodology successfully overbounds ground reflection multipath-type systematic and temporal errors sources.Originality/valueThis paper introduced a new method of accounting for ground reflection multipath for local area augmentation system/ground-based augmentation system navigation integrity. The method is also applicable to statistically overbound any other serially correlated temporal variation in measured data if both correlation values and finite iid sample sizes are known.