bluuebunny/crossref_metadata_2025 huggingface dataset:
Redispatch index for assessing bidding zone delineation
Authors: Marinho Nuno , Phulpin Yannick , Folliot Damien , Hennebel Martin
Published: July 2017

This work addresses the problem of assessing to which extent a bidding zone delineation requires redispatching actions after the clearing of energy markets. Such issue arises in particular when policy makers review the organisation of electricity markets and question the design of uniform price zones. To avoid relying on arbitrarily‐defined sensitive parameters, the authors propose a metrics based on information that is sufficient to perform nodal pricing for the whole region under consideration. The metrics is illustrated with a realistic model of the West‐European power system considering two application cases, namely (i) selecting a clustering technique to define candidate bidding zones, and (ii) selecting candidate splitting and merging options for pre‐existing bidding zones. Results show that the proposed index provides a consistent order of magnitude of the redispatching needs subsequent to market clearing, although it requires no specific user‐defined parameters.
Approach for self‐healing resilient operation of active distribution network with microgrid
Authors: Zadsar Masoud , Haghifam Mahmoud Reza , Miri Larimi Sayyed Majid
Published: July 2017

Self‐healing capability as one of the most important features of smart distribution networks (SDN) causes an increase in the resiliency and flexibility of networks by responding fast and restoring service during an outage. A two‐layer algorithm based on metaheuristics is proposed for the optimal operation of smart distribution network in self‐healing mode considering microgrid (MG) and direct load control (DLC) programme capability in the presence of micro turbine (MT) and energy storage (ES) in the distribution network. In the first layer, a new approach based on the graph theory is proposed to find the optimal forming of MGs, while in the second layer the optimal energy management of MGs, including storages, is determined considering self‐healing mode. To illustrate the advantage of the proposed method, the proposed algorithm is implemented on the modified IEEE 33 bus distribution network.
Simple current‐based algorithm for directional relays
Authors: Jafarabadi Ashtiani Hamid , Samet Haidar , Ghanbari Teymoor
Published: July 2017

In power grids, directional relays are used in situations that direction of fault current is not fixed. Distribution networks including distributed generation (DG) resources and transmission networks are some of these situations. Directional relays as key elements of distance and over current relays provide selectivity for these protections to improve their performance and power systems stability. In this study, a directional algorithm is proposed, which is able to discriminate fault direction just by sign of imaginary part of post‐fault current phasor. To evaluate the algorithm, plenty of simulations and experiments are carried out in different fault conditions. Moreover, impact of power flow direction at normal operation of the power system is considered in the evaluation of the algorithm. Also, its performance is compared with some other directional algorithms. The results confirm that the proposed algorithm is able to detect fault direction with high degree of accuracy. Moreover, simplicity of the algorithm represents its competence for practical implementation in transmission and distribution networks.
Improving economic values of day‐ahead load forecasts to real‐time power system operations
Authors: Wang Yamin , Wu Lei
Published: July 2017

Unit commitment (UC) is an important decision‐making tool in power system operations. As a critical input to UC, inaccurate day‐ahead load forecasts could result in UC solutions of high operation cost, or even trigger involuntary load shedding and jeopardise system operational security in real time. Existing researches usually explore advanced forecasting techniques for reducing statistical load forecast errors and providing better inputs to UC, while load forecasting and UC are exclusively considered as two sequential tasks. This study intends to close the loop between the two tasks by effectively incorporating certain UC information back to load forecasting models, so that day‐ahead load forecasts can be improved for deriving better UC solutions in terms of a more cost‐effective real‐time operation with respect to actual loads. Two approaches are investigated: (i) design asymmetric error penalty functions for individual forecasting models, based on asymmetric economic impacts of under‐ and over‐predicted load forecasts on UC solutions; and (ii) build a combining forecast framework in which weights of individual independent forecasting algorithms are determined by their economic impacts on UC solutions. Numerical cases are analysed to illustrate the effect of the proposed load forecasting models.
Behavioural market power indices in a transmission‐constrained electricity market
Authors: Khajeh Hosna , Akbari Foroud Asghar
Published: July 2017

This study proposes new behavioural indices of market power (MP) in order to analyse bidding behaviour of units in a transmission‐constrained electricity market. The indices calculate actual MP exercised by generators of the market. The proposed indices check whether a generator exerts an influence on the wholesale price and it is able to change the price at studied trading period. If the generator is capable of raising the wholesale price, the proposed indices calculate exact values for the generator's withholding. The first proposed index measures financial withholding exercised by marginal generators and the second one calculates physical withholding of players taking into account the impact of withdrawal of output on the wholesale price. The proposed indices are quantified for modified PJM 5‐bus system and compared with the former behavioural indices to verify their accuracy. In addition, modified IEEE 30‐bus system is considered to clarify the transparent applications of the indices for more complicated system.
Vehicle detection using three‐axis AMR sensors deployed along travel lane markings
Authors: Liu Meng , Hua Wang , Wei Quan
Published: July 2017

A vehicle detection method is developed based on three‐axis anisotropic magneto resistive (AMR) sensors along travel lane markings. The method integrates multiple algorithms and uses different geomagnetic waveforms which are disturbed by vehicles passing a single AMR sensor. This method comprehensively analyses X ‐, Y ‐, and Z ‐axis information and applies a double‐window algorithm to extract a single vehicle waveform. The vehicle mixed algorithm (VMA) is developed to differentiate vehicles driving by the AMR sensor simultaneously and determine vehicle flow rates. In addition, the vehicle motion‐state discrimination algorithm (VMSDA) is developed to distinguish the vehicle operating status (i.e. driving on the left lane, the lane line, or the right lane). The field experimental tests verified the effectiveness of the both algorithms. Results indicate that the average accuracy rates of VMA and VMSDA can, respectively, be up to 98.0 and 96.4%.
Wide band circularly polarised diversity antenna for satellite and mobile communication
Authors: Kharche Shilpa , Reddy G. Shrikanth , Gupta Rajiv Kumar , Mukherjee Jayanta
Published: July 2017

A wide band circularly polarised diversity antenna consisting of closely spaced monopole radiators is proposed. Two novel, microstrip fed‐printed monopoles are designed on a common ground plane. The ground plane which is asymmetric with respect to the feed line along with the planar monopole structure is used to achieve circular polarisation. The monopoles which are symmetric with respect to the vertical axis produce orthogonally polarised waves. A modified split ring resonator‐like structure is designed on the ground plane to achieve high port‐to‐port isolation. The impedance bandwidth (Voltage Standing Wave Ratio < 2) of the proposed antenna is 45.53% which covers the frequency band between 1.73 and 2.75 GHz. Isolation of >18 dB between the radiating elements is achieved. The proposed antenna provides an axial ratio (AR < 3 dB) bandwidth of 41.28% between 1.73 and 2.63 GHz. The radiation patterns are stable and the envelope correlation coefficient is <0.005 over the operating band. The proposed structure achieves efficiency >70% and gain >2 dBic over the frequency band between 1.73 and 2.63 GHz.
Analysis of transient radiation pattern of a high‐power bipolar short‐pulsed array antenna
Authors: Kim Jae Sik , Cha Seung Hun , Yoon Young Joong , Ryu Jiheon , Choi Jin Soo
Published: July 2017

In this study, the authors analyse the effects of the design parameters of a high‐power bipolar short‐pulsed array antenna on a beamwidth and a sidelobe of a transient radiation pattern. The analysed results can provide guidelines for synthesising a desired transient radiation performance of high‐power bipolar short pulsed‐array antennas. The analysis is performed using a formulation that consists of an element pattern and an array factor of a transient radiation pattern. To verify the validation of the studies, the analysed results of various array configurations (1 × 3, 1 × 4, 3 × 1, 4 × 1 and 2 × 2 arrays) are compared to the full‐wave simulated and measured results.
Dual‐band fan‐blade‐shaped circularly polarised dielectric resonator antenna
Authors: Varshney Gaurav , Pandey Vinay Shankar , Yaduvanshi Rajveer Singh
Published: July 2017

This study presents a singly fed aperture coupled dual‐band circularly polarised dielectric resonator antenna (CPDRA). A fan‐blade‐shaped dielectric resonator is used to achieve the dual‐band circularly polarised response. The proposed CPDRA operates with the fundamental mode in lower band. The upper band response of the CPDRA can be tuned either with the second‐ or third‐order mode at different frequencies of C‐band. Also, the polarisation of antenna can be reversed with the change in operating higher order mode in upper band by varying the slot position.
Low‐cross‐polarisation synthesis of conformal antenna arrays using a balanced dynamic differential evolution algorithm
Authors: Li Rui , Xu Le , Hu Wei , Yin Ying‐Zeng , Shi Xiao‐Wei
Published: July 2017

Conformal antenna arrays often have many elements with different radiation patterns and much cross‐polarisation. Those factors make synthesising radiation patterns a difficult problem. In this study, the authors propose a balanced dynamic differential evolution (BDDE) algorithm to suppress the cross‐polarisation in conformal arrays. To increase the probability of the inferior group participating in the mutant, a suboptimal individual is adopted in the mutant operation. Parameters are dynamically updated to accelerate the convergence speed. We adjust the cross‐rate to its maximal value every few generations to increase the diversity in the population. Two conformal arrays are modelled to verify the ability of BDDE to synthesise the radiation pattern and polarisation simultaneously. To avoid increasing the number of unknowns caused by dual‐feed antennas, circular polarised patch antennas with one feed are used to compose the conformal arrays. Embedded element patterns are used in the synthesis to take into account the influence of mutual coupling between the elements and their environment. We compare BDDE with other popular DE algorithms, and simulation results show that the proposed algorithm achieves lower sidelobe levels and cross‐polarisation reliably and efficiently.
On characteristics dependent linear coding capacity of sum‐networks
Authors: Rai Brijesh Kumar , Das Niladri
Published: July 2017

It is known that the linear coding capacity of non‐multicast networks may depend on the characteristic of the finite field. Such a dependence has been demonstrated in several examples presented in the literature. However, in all such examples, the number of distinct values that the linear coding capacity can take over different characteristics of the finite field is two. For example, the Fano network has linear coding capacity equal to one over even characteristic, and has linear coding capacity equal to 4/5 over odd characteristics. It is a natural question that whether a network can have arbitrarily many different characteristics dependent linear coding capacities. In this study, the authors answer the question for sum‐networks, which are networks where the terminals demand the sum of the messages generated by the sources. Specifically, they show that given a set of characteristics (prime numbers) , indeed there exists a sum‐network such that for each different value of the characteristic of the finite field, the linear coding capacity of the sum‐network is different.
Cascaded five‐level quasi‐switched‐boost inverter for single‐phase grid‐connected system
Authors: Tran Tan‐Tai , Nguyen Minh‐Khai
Published: July 2017

The quasi‐switched boost inverter (qSBI) has the advantage over the quasi‐Z‐source inverter (qZSI) in reducing one capacitor and one inductor. The qSBI is applied to the cascaded H‐bridge (CHB) topology to create a new cascaded single‐phase five‐level inverter. Besides, a PID controller for DC‐link voltage of each module is proposed and implemented based on DSP TMS320F28335. Unlike the DC‐link voltage controller in qZSI, the presented controller is directly controlled via controlling the capacitor voltage. By using this controller, the capacitor voltage is kept constant, even though the input voltage or the load is changed suddenly. As a result, the proposed cascaded system solves the imbalance problem of DC‐link voltage in the traditional CHB inverters. Also, a grid‐connected control strategy for modules in the cascaded five‐level qSBI is presented. The proposed inverter offers much less total harmonic distortion of the output voltage. Simulation and experimental results are shown to verify the validity of the proposed control strategy.
Design considerations for charge‐compensated fast‐switching power MOSFET in the medium‐voltage range
Authors: Siemieniec Ralf , Braz Cesar , Blank Oliver
Published: July 2017

Low‐voltage power metal–oxide–semiconductor field‐effect transistors (MOSFETs) based on charge compensation using a field plate offer a significant reduction of the area‐specific on‐resistance. The extension of their blocking capability into the so‐called medium‐voltage range of 150–300 V promises devices with excellent properties being attractive for a wide range of applications. There are two approaches how this voltage‐range extension can be realised. Both concepts are linked to different device performance and different development effort. This study discusses both concepts using the example of the 150 V device class and compares the performance gained at the device and application level.
Improved chirp scaling algorithms for SAR imaging under high squint angles
Authors: Chen Po‐Chih , Kiang Jean‐Fu
Published: July 2017

Four improved chirp scaling algorithms (CSAs) are proposed to reconstruct images from synthetic aperture radar (SAR) data received at high squint angles, in which a larger synthetic aperture is required to receive sufficient amount of data for image reconstruction, and the range migration also becomes more serious, demanding more computational load and larger memory size. The proposed methods reconstruct better SAR images with less computational load and memory than the conventional CSA, which are verified by simulations.
Rendezvous planning for multiple autonomous underwater vehicles using a Markov decision process
Authors: Yordanova Veronika , Griffiths Hugh , Hailes Stephen
Published: July 2017

Multiple autonomous underwater vehicles (AUVs) are a potential alternative to conventional large manned vessels for mine countermeasure (MCM) operations. Online mission planning for cooperative multi‐AUV network often rely on predefined contingencies of reactive methods and does not deliver an optimal end‐goal performance. Markov decision process is a decision‐making framework that allows an optimal solution, taking into account future decision estimates, rather than having a myopic view. However, most real‐world problems are too complex to be represented by this framework. The authors deal with the complexity problem by abstracting the MCM scenario with a reduced state and action space, yet retaining the information that defines the goal and constraints coming from the application. Another critical part of the model is the ability of the vehicles to communicate and enable a cooperative mission. They use the rendezvous point (RP) method. The RP method schedules meeting points for the vehicles throughout the mission. The authors’ model provides an optimal action selection solution for the multi‐AUV MCM problem. The computation of the mission plan is performed in the order of minutes. This quick execution demonstrates the model is feasible for real‐time applications.
Privacy‐preserving cloud‐based billing with lightweight homomorphic encryption for sensor‐enabled smart grid infrastructure
Authors: Alabdulatif Abdulatif , Kumarage Heshan , Khalil Ibrahim , Atiquzzaman Mohammed , Yi Xun
Published: July 2017

Sensors are gaining a ubiquitous status over many application domains with regard to enabling data‐driven decision making and smart functionality. Integration of sensors with cloud‐based data storage and analysis has the potential to significantly enhance the efficiencies, resilience and adaptability of managing smart infrastructure management. In this context, a standout application is smart grid, which provides an electricity delivery service with the ability to monitor, protect and optimize various operations of its connected elements from service provider to consumer. An ability to read and manage smart grid measurements remotely using wireless sensors is an important advantage that allows the grid operators to balance loads effectively and enable on‐demand services for various entities. However, the adoption of cloud infrastructure to manage sensor data in a smart grid poses significant risks to data security and consumers privacy. The data maybe exposed to malicious or unwarranted parties, with the potential for various security attacks that may impact data integrity, availability and accountability. We propose a secure and practical billing model using homomorphic encryption within a cloud‐based data processing framework. Moving billing management into the cloud securely, with on‐demand data retrieval and statistical computations is a major strength of the proposed framework.
Optical wireless communication using a fully integrated 400 µm diameter APD receiver
Authors: Milovančev Dinka , Jukić Tomislav , Steindl Bernhard , Brandl Paul , Zimmermann Horst
Published: July 2017

An optical wireless communication (OWC) system is demonstrated which uses a highly sensitive lens‐less optoelectronic integrated circuit with a 400 µm diameter avalanche photodiode as a high‐speed receiver, and a transmitter with highly collimated steerable beam at 680 nm wavelength. The benefits of integrated receiver with large‐area photodiode in an OWC scenario are proven experimentally. At a data rate of 2 Gb/s OWC is established over a distance of 12 m without using any optics at the receiver side to increase the collection area. The maximum receiving angle of the lens‐less receiver is 18°. The receiver is tested under different lighting conditions and immunity to background light is validated up to 2000 lux without using any filter to reduce the photons outside the wavelength range of interest.
Nanohybrid optical sensor for simultaneous measurements of strain, temperature, and vibration for civil application
Authors: Kaur Gurpreet , Kaler Rajinder Singh
Published: July 2017

A design of a nanooptical sensor, i.e. hybrid Bragg gratings over photonic crystal waveguide is proposed to monitor the strain, temperature, and vibration simultaneously. The shift in wavelength, i.e. red shift (towards the right) and blue shift (towards the left), is observed in response to applied strain, vibration, and temperature, respectively. The proposed sensor gives a better performance to measure the strain (with a 9 nm wavelength shift), temperature (with 8 nm wavelength shifting), and the vibration (with 10 nm wavelength shifting).
Investigation of the I –V characteristics asymmetry in semiconducting Y–Ba–Cu–O diodes
Authors: Jukna Artūras , Gradauskas Jonas , Sužiedelis Algirdas , Maneikis Andrius , Šliužienė Kristina , Sobolewski Roman
Published: July 2017

Thin films of YBa2Cu3O7–x (YBCO) oxygen‐deficient superconductor were used to manufacture asymmetric microdiodes and investigate their asymmetric non‐linear current–voltage (I –V) dependences at temperatures T > Tc, where Tc is the temperature of the onset of superconductivity in the material. The diodes are based on being asymmetrically narrowed down to a 10‐μm‐wide–neck mesa exhibit voltage asymmetry depending on the current bias conditions, the mesa's temperature, and a residual oxygen content in its neck region. The intrinsic electric field in the biased diode causes free‐carrier drift velocity saturation, initiated in the mesa's neck and following its asymmetric enlarging towards the mesa's electrodes depending on the biasing pulsed current amplitude, polarity, and rise time/fall time of the pulse's leading/trailing edges. The variation of the I –V characteristics asymmetry has been associated with change in the mesa's electric resistivity, affected by the electric field's asymmetric distribution in the YBCO mesa. It has been also demonstrated that our asymmetric diodes with the reduced oxygen content are sensitive detectors of microwave radiation.
Evaluation of static noise margin of 6T SRAM cell using SiGe/SiC asymmetric dual‐k spacer FinFETs
Authors: Gopal Maisagalla , Sharma Vishal , Vishvakarma Santosh K.
Published: July 2017

This work aims to investigate the device performance of silicon–germanium (SiGe)/Si carbide (SiC) source/drain (S/D) asymmetric dual‐k spacer underlap Fin‐field‐effect transistor (SiGe/SiC‐AsymD‐k FinFET) with Si channel for high performance and robust SRAM cell. Strain‐induced mobility enhancement due to the Si1−x Gex /Si1−y Cy S/D leads to a significant drive current enhancement of the proposed device. The introduced asymmetric dual‐k spacer at source side offers excellent gate control over the channel. By exploiting asymmetry in current, the authors prove that it is possible to achieve mitigation of read–write conflict in 6T SRAM bit cell. SiGe/SiC‐AsymD‐k FinFET SRAM offers 8.39% improvement in hold static noise margin, 14.28% in read and 18.06% in write mode over conventional FinFET‐based 6T SRAM bit cell. When compared to conventional FinFET 6T SRAM bit cell, the proposed 6T SRAM bit cell shows lesser temperature sensitivity of cell stability.
Facile fabrication of plate‐like Bi3O4 Cl for visible‐light‐driven photocatalytic degradation of tetracycline hydrochloride
Authors: Zhao Yong , Yin Bingxin , Zhang Guangyi , Shi Weidong
Published: July 2017

Novel visible (vis)‐light‐driven Bi3O4 Cl plates were first prepared via a facile method. The structure, morphology, and photo absorption properties of as‐prepared Bi3O4 Cl were characterised by multiple physicochemical techniques. Tetracycline hydrochloride (TC‐HCl), a famous broad‐spectrum antibiotic, was used to evaluate the photocatalytic activity of the as‐prepared samples. Compared to the BiOCl and solid‐state reaction synthesised Bi3O4 Cl, the plate‐like Bi3O4 Cl exhibited highly improved vis‐light‐driven photoreactivity toward TC‐HCl degradation under aqueous solution. Moreover, the Bi3O4 Cl plates also displayed excellent photochemical stability even after four times photocatalytic recycling tests. This work provides a simple approach to fabricate the novel Bi‐based semiconductor for potential application in treatment of antibiotic pollutant.
Anatomical and Microsurgical Implications in Total and Midarm Transplantation
Authors: Iglesias Martin , Salazar-Hernández Fernanda , Ramírez-Berumen María , Butrón Patricia , Alberú-Gómez Josefina , Leal-Villalpando Rafael , Zamudio-Bautista Jorge , Acosta Victor , Jauregui-Flores Luis , Espinosa-Cruz Verónica , Vázquez-Lamadrid Jorge , González-Sánchez Judith , Hinojosa Carlos , Laparra-Escareño Hugo , Montejo-Vargas Juan , Macias-Gallardo Julio
Published: July 2017

Background Arm transplantations are performed less frequently than forearm and hand transplantations. We present the surgical and microsurgical technique and its relationship with the clinical results in a patient with bilateral arm transplantation.

Methods A 51-year-old male patient underwent bilateral arm transplantation in October 2015. The right arm was transplanted at the glenohumeral joint. The vascular repair was at the axillary level, and the nerves were repaired at their origin. The total ischemia time was 3 hours and 48 minutes. The left arm was transplanted at the midhumeral level; all muscles were completely transplanted. The nerves were repaired at the distal third of the arm. Additionally, terminolateral neurorrhaphy was performed from the donor musculocutaneous nerve to the recipient radial nerve. The total ischemia time was 6 hours and 35 minutes.

Results At 15 months posttransplantation, the right shoulder had an abduction of 90 degrees and muscle strength of M4; flexion of 100 degrees and M4; internal and external rotation of M1; elbow flexion of 120 degrees and M3; elbow extension of M5; pronosupination of M2; and wrist extension of M2. There was no mobility in the fingers. The left transplanted limb had total elbow flexion and extension of M5, pronosupination of M2, wrist extension of M4, and finger flexion of M2. Both extremities had thermal sensitivity that allowed discrimination of cold and heat with residual deep pressure.

Conclusion Although the functional results of arm transplantation are so far unknown, they may be considered beneficial compared with the devastating disability caused by arm amputation.
Pictorial Review of the Congenital Abnormalities of the Facial Nerve, on CT and MRI
Authors: Bonfort Gratien , Debry Christian , Charpiot Anne , Veillon Francis , Venkatasamy Aina
Published: July 2017

The frequency and importance of the imaging evaluation of the temporal bone and middle ear have increased significantly over the past 30 years, especially prior to ear surgery. Nowadays, conventional computed tomography (CT) of the temporal bone and in fewer cases magnetic resonance imaging (MRI) of the middle ear allow a detailed evaluation of the small and complex structures of the ear and the surrounding nerves. Familiarity with the spectrum of congenital anomalies of the facial nerve and knowledge of normal facial nerve anatomy lead to simple well-defined diagnostic imaging criteria. The purpose of this article is to discuss the different imaging features of the congenital anomalies of the facial nerve, including agenesia, hypoplasia, anomalies of the course, size, and nerve duplications, compared with normal anatomical images at the same level of section for a better understanding, as the facial nerve must always be analyzed on temporal bone imaging, and any modification of its size or course has to be reported prior to any surgical procedure.
Ecology of the rare but irruptive Pilliga mouse, Pseudomys pilligaensis. V. Relationships with yellow-footed antechinus, Antechinus flavipes, and house mouse, Mus domesticus
Authors: Tokushima Hideyuki , Jarman Peter J.
Published: July 2017

We investigated relationships between Pseudomys pilligaensis and other small mammal species in terms of their population fluctuations and habitat selection during a population irruption of P. pilligaensis. Antechinus flavipes showed only seasonal fluctuations in numbers, suggesting that it did not respond to the same environmental factors as P. pilligaensis. A. flavipes consistently selected areas with less sand in all phases of the irruption of P. pilligaensis, resulting in a clear separation from P. pilligaensis except in the Peak phase of the latter’s irruption. Numbers of Mus domesticus fluctuated similarly to P. pilligaensis until the latter’s irruption peak in April 2000. However, M. domesticus disappeared after July 2000 from our sites. M. domesticus seemed to occupy the area only temporarily when seeds were abundant. In the Increase and Peak phases of the irruption of P. pilligaensis, M. domesticus occupied core habitats characterised by more sand and shrub, and less litter, while in the Low phase P. pilligaensis occupied the core habitats that M. domesticus used to occupy. This may suggest that M. domesticus was excluded from core habitats through competition with P. pilligaensis in the Low phase of the latter’s irruption. However, since increased anthropogenic disturbance might create conditions that M. domesticus prefers, it is important to assess carefully any impacts of such disturbance on P. pilligaensis.
Genomic Analysis Reveals Genetic Distinctiveness of the Paiute Cutthroat Trout Oncorhynchus clarkii seleniris
Authors: Saglam Ismail K. , Prince Daniel J. , Meek Mariah , Ali Omar A. , Miller Michael R. , Peacock Mary , Neville Helen , Goodbla Alisha , Mellison Chad , Somer William , May Bernie , Finger Amanda J.
Published: July 2017

The Paiute Cutthroat Trout (PCT) Oncorhynchus clarkii seleniris is classified as a subspecies within the greater Cutthroat Trout O. clarkii ssp. complex and is federally listed as threatened under the Endangered Species Act. However, genetic studies to date have revealed very little genetic differentiation between the PCT and its closest relative, the Lahontan Cutthroat Trout (LCT) O. clarkii henshawi. These results casted doubt on whether the PCT is a genetically distinct subspecies or merely a phenotypic variant of the LCT. Here, we present a genomic analysis of Cutthroat Trout subspecies and populations to resolve the genetic and phylogenetic relationship between PCT and LCT. Our results demonstrate substantial genetic structure and differentiation between PCT and LCT populations. In contrast to current thinking, our phylogenetic reconstructions show the PCT to be a distinct evolutionary lineage that diverged from LCT before the LCT differentiated into its current populations (i.e., rather than PCT divergence due to geographic isolation from an LCT population in the Carson River). We conclude that the PCT is genetically distinct from the LCT.
MWASTools: an R/bioconductor package for metabolome-wide association studies
Authors: Rodriguez-Martinez Andrea , Posma Joram M , Ayala Rafael , Neves Ana L , Anwar Maryam , Petretto Enrico , Emanueli Costanza , Gauguier Dominique , Nicholson Jeremy K , Dumas Marc-Emmanuel
Published: July 2017

MWASTools is an R package designed to provide an integrated pipeline to analyse metabonomic data in large-scale epidemiological studies. Key functionalities of our package include: quality control analysis; metabolome-wide association analysis using various models (partial correlations, generalized linear models); visualization of statistical outcomes; metabolite assignment using statistical total correlation spectroscopy (STOCSY); and biological interpretation of metabolome-wide association studies results.

Availability and implementation

The MWASTools R package is implemented in R (version  > =3.4) and is available from Bioconductor: https://bioconductor.org/packages/MWASTools/.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Association of Inflammatory Markers With Nonalcoholic Fatty Liver Disease Differs by Human Immunodeficiency Virus Serostatus
Authors: Price Jennifer C , Wang Ruibin , Seaberg Eric C , Budoff Matthew J , Kingsley Lawrence A , Palella Frank J , Witt Mallory D , Post Wendy S , Thio Chloe L
Published: July 2017

Background

We aimed to determine the relationship of circulating adipokines and inflammatory biomarkers with fatty liver among men in the Multicenter AIDS Cohort Study.

Methods

Noncontrast computed tomography was used to assess fatty liver and measure abdominal visceral adipose tissue (VAT) area in 526 participants without history of cardiovascular disease, heavy alcohol use, or viral hepatitis infection. Multivariable logistic regression was used to assess associations of circulating biomarker levels with fatty liver.

Results

Three hundred twenty-nine human immunodeficiency virus (HIV)-infected men had higher levels of several inflammatory biomarkers compared with 197 HIV-uninfected men. Among HIV-uninfected men, increased adiponectin was associated with lower odds of fatty liver (odds ratio [OR] = 0.51 per doubling, P = .02), whereas higher odds of fatty liver was observed with increased levels of the proinflammatory markers intercellular adhesion molecule (ICAM)-1 (OR = 5.30, P = .004), C-reactive protein (OR = 1.66, P = .002), interleukin (IL)-6 (OR = 1.67, P = .03), and tumor necrosis factor α receptor 2 (OR = 6.55, P = .003). Among HIV-infected men, ICAM-1 was the only proinflammatory marker associated with greater odds of fatty liver (OR = 2.67, P = .02), whereas higher adiponectin (OR = 0.57, P = .003), and osteoprotegerin levels (OR = 0.48, P = .03) were associated with lower odds. These associations were all independent of VAT.

Conclusions

Fatty liver is associated with a heightened inflammatory state independent of visceral adiposity in HIV-uninfected men but not in HIV-infected men. However, a heightened anti-inflammatory state may protect against fatty liver regardless of HIV serostatus.
Safety and Efficacy of Ombitasvir, Paritaprevir With Ritonavir ± Dasabuvir With or Without Ribavirin in Patients With Human Immunodeficiency Virus-1 and Hepatitis C Virus Genotype 1 or Genotype 4 Coinfection: TURQUOISE-I Part 2
Authors: Rockstroh Jürgen K , Orkin Chloe , Viani Rolando M , Wyles David , Luetkemeyer Anne F , Lazzarin Adriano , Soto-Malave Ruth , Nelson Mark R , Bhagani Sanjay R , Klinker Hartwig H F , Rizzardini Giuliano , Girard Pierre-Marie , Tural Cristina , Shulman Nancy S , Mobashery Niloufar , Hu Yiran B , Fredrick Linda M , Pilot-Matias Tami , Trinh Roger , Gane Edward
Published: July 2017

Background

Ombitasvir, paritaprevir with ritonavir, and dasabuvir (OBV/PTV/r ± DSV) ±ribavirin (RBV) are approved to treat hepatitis C virus (HCV) genotype 1 and 4 infection. Here, we investigate the safety and efficacy of OBV/PTV/r + DSV ±RBV for HCV genotype 1, and OBV/PTV/r + RBV for HCV genotype 4, in human immunodeficiency virus (HIV)-1 coinfected patients with or without compensated cirrhosis.

Methods

TURQUOISE-I, Part 2 is a phase 3 multicenter study. Patients with or without cirrhosis were HCV treatment-naive or -experienced, on an HIV-1 antiretroviral regimen containing atazanavir, raltegravir, dolutegravir, or darunavir (for genotype 4 only), and had plasma HIV-1 ribonucleic acid <40 copies/mL at screening. Patients received OBV/PTV/r ± DSV ±RBV for 12 or 24 weeks.

Results

In total, 228 patients were treated according to guidelines. Sustained virologic response at posttreatment week 12 (SVR12) was achieved by 194 of 200 (97%) and 27 of 28 (96%) patients with HCV genotype 1 and genotype 4 infection, respectively. There were 2 virologic failures: 1 breakthrough and 1 relapse in a cirrhotic and a noncirrhotic patient with genotype 1b and 1a infection, respectively. One reinfection occurred at posttreatment week 12 in a genotype 1a-infected patient. Excluding nonvirologic failures, the SVR12 rates were 98% (genotype 1) and 100% (genotype 4). Adverse events were mostly mild in severity and did not lead to discontinuation. Laboratory abnormalities were rare.

Conclusions

The OBV/PTV/r ±DSV was well tolerated and yielded high SVR12 rates in patients with HCV genotype 1 or genotype 4/HIV-1 coinfection. The OBV/PTV/r ± DSV ±RBV is a potent HCV treatment option for patients with HIV-1 coinfection, regardless of treatment experience.
Advanced Human Immunodeficiency Virus Disease at Diagnosis in Mozambique and Swaziland
Authors: Kujawski Stephanie A , Lamb Matthew R , Lahuerta Maria , McNairy Margaret L , Ahoua Laurence , Abacassamo Fatima , Nuwagaba-Biribonwoha Harriet , Gachuhi Averie , El-Sadr Wafaa M , Elul Batya
Published: July 2017

Background

Early diagnosis of human immunodeficiency virus (HIV) is a prerequisite to maximizing individual and societal benefits of antiretroviral therapy.

Methods

Adults ≥18 years of age testing HIV positive at 10 health facilities in Mozambique and Swaziland received point-of-care CD4+ cell count testing immediately after diagnosis. We examined median CD4+ cell count at diagnosis, the proportion diagnosed with advanced HIV disease (CD4+ cell count ≤350 cells/μL) and severe immunosuppression (CD4+ cell count ≤100 cells/μL), and determinants of the latter 2 measures.

Results

Among 2333 participants, the median CD4+ cell count at diagnosis was 313 cells/μL (interquartile range, 164–484), more than half (56.5%) had CD4+ ≤350 cells/μL, and 13.9% had CD4+ ≤100 cells/μL. The adjusted relative risk (aRR) of both advanced HIV disease and severe immunosuppression at diagnosis was higher in men versus women (advanced disease aRR = 1.31; 95% confidence interval [CI] = 1.16–1.48; severe immunosuppression aRR = 1.54, 95% CI = 1.17–2.02) and among those who sought HIV testing because they felt ill (advanced disease aRR = 1.30, 95% CI = 1.08–1.55; severe immunosuppression aRR = 2.10, 95% CI = 1.35–2.26). Age 18–24 versus 25–39 was associated with a lower risk of both outcomes (advanced disease aRR = 0.70, 95% CI = 0.59–0.84; severe immunosuppression aRR = 0.62, 95% CI = 0.41–0.95).

Conclusions

More than 10 years into the global scale up of comprehensive HIV services, the majority of adults diagnosed with HIV at health facilities in 2 high-prevalence countries presented with advanced disease and 1 in 7 had severe immunosuppression. Innovative strategies for early identification of HIV-positive individuals are urgently needed.
HID-1 controls cargo sorting and dense core formation by influencingtrans-Golgi network acidification in neuroendocrine cells
Authors: Hummer Blake H. , de Leeuw Noah F. , Hosford Bethany , Burns Christian , Joens Matthew S. , Fitzpatrick James A.J. , Asensio Cedric S.
Published: July 2017

Large dense core vesicles (LDCVs) mediate the regulated release of neuropeptides and peptide hormones. They form at thetrans-Golgi network (TGN) where their soluble content aggregates to form a dense core, but the mechanisms controlling biogenesis are still not completely understood. Recent studies have implicated the peripheral membrane protein HID-1 in neuropeptide sorting and insulin secretion. Using CRISPR/Cas9, we generated HID-1 KO rat neuroendocrine cells, and show that the absence of HID-1 results in specific defects in peptide hormone and monoamine storage and regulated secretion. Loss of HID-1 causes a reduction in the number of LDCVs and affects their morphology and biochemical properties due to impaired cargo sorting and dense core formation. HID-1 KO cells also exhibit defects in TGN acidification together with mislocalization of the Golgi-enriched vacuolar H+-ATPase subunit isoform a2. We propose that HID-1 influences early steps in LDCV formation by controlling dense core formation at the TGN.
Hierarchical Analysis of Multi-mapping RNA-Seq Reads Improves the Accuracy of Allele-specific Expression
Authors: Raghupathy Narayanan , Choi Kwangbom , Vincent Matthew J. , Beane Glen L. , Sheppard Keith , Munger Steven C. , Korstanje Ron , de Villena Fernando Pardo-Manual , Churchill Gary A.
Published: July 2017

Allele-specific expression (ASE) refers to the differential abundance of the allelic copies of a transcript. Direct RNA sequencing (RNA-Seq) can provide quantitative estimates of ASE for genes with transcribed polymorphisms. However, estimating ASE is challenging due to ambiguities in read alignment. Current approaches do not account for the hierarchy of multiple read alignments to genes, isoforms, and alleles. We have developed EMASE (Expectation-Maximization for Allele Specific Expression), an integrated approach to estimate total gene expression, ASE, and isoform usage based on hierarchical allocation of multi-mapping reads. In simulations, EMASE outperforms standard ASE estimation methods. We apply EMASE to RNA-Seq data from F1 hybrid mice where we observe widespread ASE associated with cis-acting polymorphisms and a small number of parent-of-origin effects at known imprinted genes. The EMASE software is freely available under GNU license athttps://github.com/churchill-lab/emaseand it can be adapted to other sequencing applications.
Maternal obesity alters uterine NK cell activity through a functional KIR2DL1/S1 imbalance
Authors: Castellana Barbara , Perdu Sofie , Kim Yoona , Chan Kathy , Atif Jawairia , Marziali Megan , Beristain Alexander G.
Published: July 2017

In pregnancy, uterine natural killer cells (uNK) play essential roles in coordinating uterine angiogenesis, blood vessel remodeling, and promoting maternal tolerance to fetal tissue. Deviances from a normal uterine microenvironment are thought to modify uNK function(s), limiting their ability to establish a healthy pregnancy. While maternal obesity has become a major health concern due to associations with adverse effects on fetal and maternal health, our understanding into how obesity contributes to poor pregnancy disorders is essentially unknown. Given the importance of uNK in pregnancy, this study sets out to examine if obesity affects uNK function. Using a cohort of pregnant women, we show that baseline activity of uNK from obese women is elevated, but that enhanced activity does not equate to increased killing potential. Instead, obesity associates with altered uNK production of angiogenic VEGF-A and PlGF. These changes coincide with alterations in NKp46+and NKG2A+uNK subsets and elevated expression of KIR2D(L1/S1/S3/S5) receptors. Detailed examination revealed that obesity leads to imbalances in KIR2DL1/S1 expression that together instruct altered responses to HLA-C2 antigen, including increased production of TNFα. Together, these findings suggest that maternal obesity modulates uNK function by altering angiokine/cytokine production and the response to HLA-C2 antigen.
The transcriptionally permissive chromatin state of ES cells is acutely tuned to translational output
Authors: Bulut-Karslioglu Aydan , Macrae Trisha A. , Oses-Prieto Juan A. , Covarrubias Sergio , Percharde Michelle , Ku Gregory , Diaz Aaron , McManus Michael T. , Burlingame Alma L. , Ramalho-Santos Miguel
Published: July 2017

A permissive chromatin environment coupled to hypertranscription is critical to drive the rapid proliferation of Embryonic Stem (ES) cells and peri-implantation embryos. We carried out a genome-wide screen to systematically dissect the regulation of the euchromatic state of ES cells. The results reveal that activity of cellular growth pathways, prominently protein synthesis, perpetuates the euchromatic state and hypertranscription of ES cells. Acute, mild inhibition of translation results in rapid depletion of euchromatic marks in ES cells and blastocysts, concurrent with delocalization of RNA polymerase II and reduction in nascent transcription. Remarkably, reduced translational output leads to rewiring of open chromatin within 3 hours, including decreased accessibility at a subset of active developmental enhancers and increased accessibility at histone genes and transposable elements. Using a proteome-scale analysis, we show that several euchromatin regulators are unstable proteins and thus continuously depend on a high translational output. We propose that this mechanistic interdependence of euchromatin, transcription and translation sets the pace of proliferation at peri-implantation and may be employed generally by stem/progenitor cells.
Modest static pressure suppresses columnar epithelial cell proliferation in association with cell shape and cytoskeletal modifications
Authors: Hagiyama Man , Yabuta Norikazu , Okuzaki Daisuke , Inoue Takao , Takashima Yasutoshi , Kimura Ryuichiro , Ri Aritoshi , Ito Akihiko
Published: July 2017

Intraluminal pressure elevation can cause degenerative disorders, such as ileus and hydronephrosis, and the threshold is fairly low and constant, 20–30 cm H2O. We previously devised a novel two-chamber culture system subjecting cells cultured on a semipermeable membrane to increased culture medium height (water pressure up to 60 cm H2O). Here, we cultured several different cell lines using the low static pressure-loadable two-chamber system, and examined cell growth, cell cycle, and cell morphology. Madin–Darby canine kidney (MDCK) columnar epithelial cells were growth-suppressed in a manner dependent on static water pressure ranging from 2–50 cm H2O, without cell cycle arrest at any specific phase. Two other types of columnar epithelial cells exhibited similar phenotypes. By contrast, spherical epithelial and mesenchymal cells were not growth-suppressed, even at 50 cm H2O. Phalloidin staining revealed that 50 cm H2O pressure load vertically flattened and laterally widened columnar epithelial cells and made actin fiber distribution sparse, without affecting total phalloidin intensity per cell. When the mucosal protectant irsogladine maleate (100 nM) was added to 50-cm-high culture medium, MDCK cells were reduced in volume and their doubling time shortened. Cell proliferation and morphology are known to be regulated by the Hippo signaling pathway, but a pressure load of 50 cm H2O did not alter the expression levels of Hippo signaling molecules in columnar epithelial cells, suggesting that this pathway was not involved in the pressure-induced phenotypes. RNA sequencing of MDCK cells showed that a 50 cm H2O pressure load upregulatedkeratin 14, an intermediate filament, 12-fold. This upregulation was confirmed at the protein level by immunofluorescence, suggesting a role in cytoskeletal reinforcement. These results provide evidence that cell morphology and the cytoskeleton are closely linked to cell growth. Pathological intraluminal pressure elevation may cause mucosal degeneration by acting directly on this linkage.

We provide evidence that columnar epithelial cells are growth-suppressed by pressure loads as low as 30 cm H2O, in association with cell-shape flattening and cytoskeletal alterations.
Correlated gene expression and anatomical communication support synchronized brain activity in the mouse functional connectome
Authors: Mills Brian D. , Grayson David S. , Shunmugavel Anandakumar , Miranda-Dominguez Oscar , Feczko Eric , Earl Eric , Neve Kim , Fair Damien A.
Published: July 2017

Cognition and behavior depend on synchronized intrinsic brain activity which is organized into functional networks across the brain. Research has investigated how anatomical connectivity both shapes and is shaped by these networks, but not how anatomical connectivity interacts with intra-areal molecular properties to drive functional connectivity. Here, we present a novel linear model to explain functional connectivity in the mouse brain by integrating systematically obtained measurements of axonal connectivity, gene expression, and resting state functional connectivity MRI. The model suggests that functional connectivity arises from synergies between anatomical links and inter-areal similarities in gene expression. By estimating these interactions, we identify anatomical modules in which correlated gene expression and anatomical connectivity cooperatively, versus distinctly, support functional connectivity. Along with providing evidence that not all genes equally contribute to functional connectivity, this research establishes new insights regarding the biological underpinnings of coordinated brain activity measured by BOLD fMRI.