bluuebunny/crossref_metadata_2025 huggingface dataset:
Demand baseline estimation using similarity‐based technique for tropical and wet climates
Authors: Raman Gururaghav , Kong Yaonan , Peng Jimmy Chih‐Hsien , Ye Zhisheng
Published: April 2018

Demand baseline estimation (BE) is key to the impact assessment of a demand response event in a power system. While many BE techniques exist in literature and are implemented by utilities, these are either inaccurate, or computationally intensive, and only provide point estimates of the demand baseline. This study presents a simple, single‐stage, similarity‐based BE technique. The authors posit a new definition of similarity that includes weather covariates, and therefore eliminate the need for a subsequent adjustment. A novel growth rate assumption for the demand, combined with an optimised exponential smoothing technique results in a higher accuracy for the proposed BE technique. Additionally, an L ‐order iterated bootstrap is used to generate confidence intervals to account for prediction uncertainties. The proposed BE technique is tested for the Singaporean National Electricity Market, and is shown to be consistently more accurate than other conventional BE techniques.
Harmonic reduction methods for electrical generation: a review
Authors: Fallows Daniel , Nuzzo Stefano , Costabeber Alessandro , Galea Michael
Published: April 2018

This study provides a comprehensive literature review of techniques for harmonic related power quality improvement of electrical generation systems. Increasing interest in these aspects is due to ever more stringent power quality requirements, deriving from new grid codes and compliance standards, aimed at limiting waveform harmonic distortion at all points of the distribution network. Although a wealth of literature is available for such techniques, it has never been compiled into a handbook incorporating all the solutions aimed at both electrical machine and power system engineers.
Distribution network reconfiguration based on vector shift operation
Authors: Ji Xingquan , Liu Qi , Yu Yongjin , Fan Shuxian , Wu Na
Published: April 2018

To make an appropriate compromise between the solving speed and solution quality for a distribution network with distributed generations (DGs), an efficient reconfiguration algorithm based on vector shift operation (VSO) considering DGs is proposed. The nodal equivalent power model considering the influence of DGs is established. Power moment is selected as an index to decide whether load flow calculation or VSO should be conducted. In the former case, all bus voltages are updated and then be regarded as the initial condition for VSO. In the latter case, the power and resistance vectors are first formulated based on the structure and parameters of the distribution system, and the variation of power loss after branch exchange is then calculated based on these vectors instead of the time‐consuming load flow calculation. The power and resistance vectors are updated by simple element shift operation after each step of branch exchanging. The final optimal solution is obtained when the open‐branch set remains unchanged after branch exchanging. The proposed VSO‐based reconfiguration algorithm is applied to a practical distribution system in Taiwan. The influences of the DGs and network reconfiguration on power loss and nodal voltages are illustrated. Test results show that the proposed reconfiguration algorithm is feasible and efficient.
Fast matching pursuit for sparse representation‐based face recognition
Authors: Melek Michael , Khattab Ahmed , Abu‐Elyazeed Mohamed F.
Published: April 2018

Even though face recognition is one of the most studied pattern recognition problems, most existing solutions still lack efficiency and high speed. Here, the authors present a new framework for face recognition which is efficient, fast, and robust against variations of illumination, expression, and pose. For feature extraction, the authors propose extracting Gabor features in order to be resilient to variations in illumination, facial expressions, and pose. In contrast to the related literature, the authors then apply supervised locality‐preserving projections (SLPP) with heat kernel weights. The authors’ feature extraction approach achieves a higher recognition rate compared to both traditional unsupervised LPP and SLPP with constant weights. For classification, the authors use the recently proposed sparse representation‐based classification (SRC). However, instead of performing SRC using the computationally expensive minimisation, the authors propose performing SRC using fast matching pursuit, which considerably improves the classification performance. The authors’ proposed framework achieves ∼99% recognition rate using four benchmark face databases, significantly faster than related frameworks.
Ant colony optimisation for coloured travelling salesman problem by multi‐task learning
Authors: Dong Xueshi , Dong Wenyong , Cai Yongle
Published: April 2018

Traditional algorithms, such as genetic algorithm and simulated annealing, have greatly attracted a lot of research studies due to their simplicity and flexibility to solve coloured travelling salesman problem (CTSP). However, their performance is limited in solution quality and convergence speed. To improve these limitations, this study presents a fast and effective ant colony optimisation (FEACO) algorithm. In the proposed FEACO, a new pheromone updating mechanism is incorporated into the traditional ant colony optimisation (ACO) to improve its performance. Furthermore, a multi‐task cooperative learning approach is employed to solve CTSP. In it, multiple tasks in a shared city set are cooperatively carried out by all salesmen, but each task in exclusive city sets is independently performed by an appointed salesman. In ACO and FEACO, feasible solutions can be found for CTSP by cooperative learning, which is carried out by the cooperation of a set of ants. During the process, ants can cooperate to find good solutions by utilising the pheromone deposited on the paths while ants pass them. Compared with state‐of‐the‐art algorithms, the experimental results on both small scale and larger scale show that the proposed method has potential to provide an improvement in solution quality and convergence speed.
Vigilance detection method for high‐speed rail using wireless wearable EEG collection technology based on low‐rank matrix decomposition
Authors: Zhou Xiang , Yao Di , Zhu Miankuan , Zhang Xiaoliang , Qi Lingfei , Pan Hongye , Zhu Xin , Wang Yuan , Zhang Zutao
Published: April 2018

With the development of rail transit, driver vigilance is increasingly important in railway safety. A vigilance detection method based on high‐speed rail (HSR) is presented in this study. The proposed method includes three main parts: (i) a wireless wearable electroencephalography (EEG) collection module; (ii) HSR driver's vigilance detection module; and (iii) an early warning module. Drivers’ vigilance is monitored using eight EEG channels. A low‐rank matrix decomposition (also called robust principal component analysis) algorithm is used to classify EEG signals which are collected through wireless wearable EEG collection technology. The warning module will sound an alarm and the early warning begins to message the train control centre if the driver is judged as fatigue. The method was tested on driving EEG data from ten different drivers and reached 99.4% correct classification in a 9 s time window. The feasibility of the proposed vigilance‐detecting method for HSR safety is demonstrated through simulation and test results.
Cross‐regional driver–vehicle interaction design: an interview study on driving risk perceptions, decisions, and ADAS function preferences
Authors: Liao Yuan , Wang Minjuan , Duan Lian , Chen Fang
Published: April 2018

A cross‐regional study of driving behaviour and technological preferences in typical driving scenarios, especially dangerous pre‐crash scenarios, is presented as a contribution to the user experience design of in‐vehicle driver assistance functions. Data from 46 participants are collected by one‐to‐one interviews following viewing of 11 video clips previously obtained from naturalistic field operational tests and representative of typical real driving scenarios. Six questions relating to each driving scenario are asked to reveal the differences between Chinese drivers and Swedish drivers. The results show similarities and differences in driving risk perceptions, decisions, and preferences concerning the assistance and specifics of potential advanced driver assistance system (ADAS) functions of drivers in China and Sweden. The preferences for assistance and ADAS functions are found to be correlated with relative driving risk perceptions and decisions in typical driving scenarios for both country groups. Based on the results, some suggestions for the design of driver–vehicle interactions for Chinese drivers are presented.
Systematic clustering method to identify and characterise spatiotemporal congestion on freeway corridors
Authors: Ou Jishun , Yang Shu , Wu Yao‐Jan , An Chengchuan , Xia Jingxin
Published: April 2018

Many analytical procedures, technical methods, and tools have been developed to facilitate manual inspection of traffic congestion and support the decision‐making process for traffic authorities. However, lacking an automatic mechanism, it would be a time‐consuming and labour‐intensive process for day‐to‐day and location‐by‐location analyses. This study presents a method based on a three‐stage framework that is capable of automatically identifying and characterising spatiotemporal congested areas (STCAs) by parsing, extracting, analysing and quantifying the knowledge contained in traffic heatmaps. The key components of the proposed method are two unsupervised clustering procedures: (i) a mini‐batch k ‐means clustering algorithm to separate the congested and non‐congested areas and (ii) a graph‐theory‐based clustering algorithm to distinguish between different STCAs. Twenty weekdays of dual loop detector data collected from a 26‐mile stretch of Interstate 10 in Phoenix, Arizona was analysed for the case study. The new method identified and quantified 102 STCAs without the need for human intervention. Based on 14 traffic measures calculated for each STCA, 19 active bottlenecks along the study corridor were identified. Top‐ranked bottlenecks identified in this study were consistent with those reported in previous studies but were produced with less effort, demonstrating the new method's potential utility for traffic congestion management systems.
Railway freight volume forecast using an ensemble model with optimised deep belief network
Authors: Feng Fenling , Li Wan , Jiang Qiwei
Published: April 2018

Forecasting freight traffic contributes to the improvement of traffic facilities and making industrial policy, so it is significant to predict freight volume accurately. Extensive works had proved that ensemble model performed better than single model, so an ensemble model, combining seasonal autoregressive integrated moving average (SARIMA) with deep belief network (DBN), is proposed here. SARIMA, a linear model, is used to find the regularities of railway freight traffic. DBN, a non‐linear model, is taken to mine the complex relationships between indexes and railway freight. In order to decide appropriate architecture of DBN, including the number of network layers and neurons in each hidden layer, Gaussian particle swarm optimisation algorithm is designed to decide appropriate architecture of DBN, including the number of network layers and neurons in each hidden layer. Besides, Spearman rank correlation analysis is used for selecting indexes related to freight volume. Experimental results show that, compared with SARIMA, DBN, back propagation neural network, Elman neural network, and radial basis function neural network, the proposed ensemble model obtains best performance, and the mean absolute error is 5.5159 million t and the mean absolute percentage error is 1.9657%.
Automotive radar system for multiple‐vehicle detection and tracking in urban environments
Authors: Eltrass Ahmed , Khalil Mohammed
Published: April 2018

In this study, an enhanced approach for automotive radar systems is proposed to solve the detection, tracking, and track management problem in the presence of clutter with high accuracy and low computational cost. The unscented Kalman filter (UKF) with a constant turn rate and acceleration (CTRA) dynamic model is employed for target tracking, and the tracking accuracy is enhanced by incorporating the linear regression (LR) algorithm into the UKF‐CTRA algorithm. We investigate, for the first time, the Joint Probabilistic Data Association (JPDA) algorithm for data association, and the composite M/N tests for track management. The capability of the proposed approach (CTRA‐UKF‐LR‐JPDA‐composite‐M/N‐tests) is demonstrated by comparing it with various algorithms for different single and multi‐target tracking scenarios and for various sets of parameter regimes. The results show the superior performance of the proposed method over other existing techniques in automotive radar systems. This reveals the effectiveness of the proposed algorithm as a promising technique in automotive applications.
Advances in lead‐free high‐temperature dielectric materials for ceramic capacitor application
Authors: Jia Wenxu , Hou Yudong , Zheng Mupeng , Xu Yuru , Zhu Mankang , Yang Kuiyong , Cheng Huarong , Sun Shuying , Xing Jie
Published: April 2018

Ceramic capacitors with upper operating temperatures far beyond 200°C are essential for high‐temperature electronics used in deep oil drilling, aviation, automotive industry and so on. Recent advances in existing lead‐free dielectrics for potential high‐temperature capacitor applications are reviewed and grouped into three categories according to the parent component of the solid solution. Their desirable temperature stabilities were summarised comprehensively. However, there are still some limitations in the current research, such as achieving low loss in a wide temperature range and maintaining stable dielectric properties with different frequencies or at different voltages. Furthermore, the successful implementation of multilayer ceramic capacitors is one of the biggest challenges, which will have far‐reaching impacts on the realisation of high‐temperature capacitor application in the future.
Quadratic buck–boost converter with positive output voltage and minimum ripple point design
Authors: Rosas‐Caro Julio C. , Valdez‐Resendiz Jesus E. , Mayo‐Maldonado Jonathan C. , Alejo‐Reyes Avelina , Valderrabano‐Gonzalez Antonio
Published: April 2018

This study presents a novel topology of a buck–boost converter that features: (i) quadratic voltage gain; (ii) positive output voltage with respect to the input; (iii) continuous input current. Moreover, as the main contribution, (iv) it features a minimum ripple design, for which input current and output voltage ripples are simultaneously cancelled at the desired operating point. It is also shown that even though the duty cycle deviates from a nominal minimum ripple point, the converter exhibits a significantly low switching ripple percentage within a full operation range. The operation mechanism, steady‐state equations and overall analysis are presented. Furthermore, simulations and experiments were performed to validate the theory.
Sensorless control of an H‐bridge inverter with output inductor‐capacitor filter
Authors: Mohebbi Mohammad , McIntyre Michael L. , Latham Joseph
Published: April 2018

This study presents a filter‐based control scheme for an H‐bridge inverter with an output inductor‐capacitor filter. This approach relies only on a single output voltage measurement to reduce the system cost as well as measurement noise and disturbance injected by output current and/or inductor current measurements. Also, the proposed control algorithm is robust against parameter discrepancy. A Lyapunov stability analysis is performed to demonstrate the control objective is met and that all signals in the closed loop system are stable. Experimental results demonstrate excellent voltage tracking, insensitivity to the load and system parameter variations, and low output voltage distortion as well as the stability of the system under both linear and non‐linear loads.
Passivity‐based linear feedback control of permanent magnetic synchronous generator‐based wind energy conversion system: design and analysis
Authors: Yang Bo , Yu Tao , Shu Hongchun , Qiu Dalin , Zhang Yuming , Cao Pulin , Jiang Lin
Published: April 2018

This study designs a passivity‐based linear feedback control scheme of a permanent magnetic synchronous generator‐based wind energy conversion system, which attempts to achieve a maximum power point tracking (MPPT) at generator‐side voltage source converter (VSC) and enhance fault ride‐through (FRT) capability at grid‐side VSC simultaneously. A storage function is constructed based on the passivity theory, in which the actual role of each term is meticulously investigated while the beneficial ones are remained so as to significantly improve the transient responses. Then, an auxiliary input is employed in the form of linear feedback control to ensure a desired tracking error convergence. Moreover, the closed‐loop system stability is thoroughly analysed, together with a detailed physical interpretation of the storage function. Three case studies are undertaken including step change of wind speed, stochastic wind speed variation, and FRT. Simulation results verify that the proposed approach can effectively achieve MPPT and dramatically improve the FRT capability under various operation conditions against that of vector control and feedback linearisation control.
Fold change based approach for identification of significant network markers in breast, lung and prostate cancer
Authors: Makhijani Richa K. , Raut Shital A. , Purohit Hemant J.
Published: April 2018

Cancer belongs to a class of highly aggressive diseases and a leading cause of death in the world. With more than 100 types of cancers, breast, lung and prostate cancer remain to be the most common types. To identify essential network markers (NMs) and therapeutic targets in these cancers, the authors present a novel approach which uses gene expression data from microarray and RNA‐seq platforms and utilises the results from this data to evaluate protein–protein interaction (PPI) network. Differentially expressed genes (DEGs) are extracted from microarray data using three different statistical methods in R, to produce a consistent set of genes. Also, DEGs are extracted from RNA‐seq data for the same three cancer types. DEG sets found to be common in both platforms are obtained at three fold change (FC) cut‐off levels to accurately identify the level of change in expression of these genes in all three cancers. A cancer network is built using PPI data characterising gene sets at log‐FC (LFC)>1, LFC>1.5 and LFC>2, and interconnection between principal hub nodes of these networks is observed. Resulting network of hubs at three FC levels highlights prime NMs with high confidence in multiple cancers as validated by Gene Ontology functional enrichment and maximal complete subgraphs from CFinder.
Hysteresis modelling and feedforward compensation of piezoelectric nanopositioning stage with a modified Bouc‐Wen model
Authors: Ming Min , Feng Zhao , Ling Jie , Xiao Xiao‐Hui
Published: April 2018

Piezoelectric actuators (PEAs) are widely applied in various nanopositioning equipment. However, the strong hysteresis nonlinearity compromises the positioning accuracy. In this work, a novel modified Bouc‐Wen (MBW) model with a polynomial function of the differential of the input is established for modelling the hysteresis nonlinearity of the PEA‐actuated nanopositioning stages. The particle swarm optimisation algorithm is adopted to identify the parameters of the MBW model with a set of input–output experimental data. The obtained model with the corresponding identification parameters matches well the experimental data with 0.31% relative error. A feedforward compensator based on the obtained model is also applied to compensate the hysteresis nonlinearity. Experiments are conducted to validate the effectiveness of this approach, and the results show the great improvement of positioning accuracy of the stage.
Performance investigation of a semi‐junctionless type II heterojunction tunnel field effect transistor in nanoscale regime
Authors: Ahangari Zahra
Published: April 2018

In this work, the electrical characteristics and impact of physical and structural parameters on the performance of a novel heterojunction GaAs0.1Sb0.9‐InAs semi‐junctionless tunnel field effect transistor (SJTFET) is demonstrated. Unlike the conventional p‐i‐n tunnel field effect transistor, the n‐channel SJTFET is a p+ ‐p+ ‐n structure having similar doping profile for the source and channel regions. First, all the structural and physical parameters are set to their initial values, and then, one parameter is varied to investigate its variation effect on the performance of SJTFET. Standard deviation and mean value of subthreshold swing, off‐state and on‐state current manifests that the performance of SJTFET is more sensitive to the gate workfunction, source–channel doping density and gate oxide thickness, respectively, in comparison with other structural parameters. The two‐dimensional variation matrix of off‐state current, on‐state current and threshold voltage is calculated as a function of gate workfunction and source–channel p+ doping density for determining an optimum value for the source–channel doping concentration and gate workfunction. Due to the n‐p+ drain–channel junction, the tunnel barrier in the off‐state mode can be increased into the drain region, providing low off‐state current in the ultra‐scaled device and makes this device become less sensitive to short channel effects.
Effects of vacancy defects location on thermal conductivity of silicon nanowire: a molecular dynamics study
Authors: Meem Asma Ul Hosna , Chowdhury Ongira , Morshed AKM M.
Published: April 2018

The improvement of thermoelectric figure of merit of silicon nanowire (SiNW) can be achieved by lowering its thermal conductivity. In this work, non‐equilibrium molecular dynamics method was used to demonstrate that the thermal conductivity of bulk silicon crystal is drastically reduced when it is crafted as SiNW and that it can be reduced remarkably by including vacancy defects. It has been found that ‘centre vacancy defect’ contributes much more in reducing the thermal conductance than ‘surface vacancy defect’. The lowest thermal conductivity that occurs is about 52.1% of that of pristine SiNW, when 2% vacancy defect is introduced in the nanowire. The vibrational density of states analysis was performed to understand the nature of this reduction and it has been found that the various boundary scatterings of phonon significantly reduce the thermal conductivity. Also, larger mass difference due to voids induces smaller thermal conductivity values. These results indicate that the inclusion of vacancy defects can enhance the thermoelectric performance of SiNWs.
Negative bias temperature instability in SOI‐like p‐type metal oxide semiconductor devices
Authors: Li Lijie , Shan Chan , Wang Ying , Luo Xin
Published: April 2018

A silicon on insulator (SOI)‐like bulk silicon (SLBS) MOSFET has been recently reported. An ‘n/p‐/n+’ structure was contained in SLBS P Metal Oxide Semiconductor (PMOS) device, with ‘p‐’ is made of 4H‐SiC. This p‐layer is fully depleted. In this work, negative bias temperature instability (NBTI) of SLBS pMOSFET is studied and compared with that in bulk and Fully Depleted (FD) SOI PMOSFET. The effects of stress temperature and body bias on NBTI of SLBS device are also be studied in this work. The work demonstrates an advantage of SLBS over bulk and FD SOI devices.
Numerical study of chip cooling with internal nanofluid in minichannels and external air flow over sink with laminar regimes
Authors: Esmaeilzadeh Kandjani Negar , Nurelahi Shahriyar , Tafrishi Seyed Amir , Esmaeilzadeh Esmaeil
Published: April 2018

In this work, an electronic computer chip generates a 50– 150 W heat over a surface, requiring dissipation of about . The authors design a copper heat sink () that is mounted over the chip with two active methods for enhancing heat removal from the chip. To enhance the cooling effects, a laminar developing heat and fluid flow is introduced into the assumed seven miniature channels in a rectangular shape (), which takes away heat partly. Ethylene glycol as a base fluid and ethylene glycol + Al2O3 as a nanofluid with a volume fraction of nanoparticles 0.5, 1 and 1.5% flow with laminar regimes. To remove heat from the other parts of the sink, an external airflow is used with a free stream velocity of 2 m/s over it. This airflow is a laminar two‐dimensional boundary layer over the sink in the direction of its length. By numerical simulation, these two methods of cooling are investigated for enhancing heat removal from the sink. The results show cooling efficiency increased by about 8.5% in comparison with the cooling system with free convection where there is an internal cooling.
Preparation, properties and characterisation of microemulsion PCM slurry
Authors: Wang Dengwu , Si Jianlong , Ma Sude
Published: April 2018

The provisions and applications of renewable energy have great supply–demand gap problem, and thermal energy storage (TES) is a very promising solution to fully utilise the renewable energy and covers off‐peak periods. The application of solid–liquid phase change material (PCM) is an effective way of TES based on the techniques of encapsulation and emulsion, but the capsules are easily broken and the emulsions are easily phase separated as they were phase changed for many times, so some other techniques should be developed. The microemulsion PCM slurry was prepared by the combination uses of emulsifiers (i.e. sorbitan monooleate 80 and polyoxyethylene sorbitan monooleate 80), coemulsifier (i.e. butanol), distilled water, purified paraffin and inorganic salts (i.e. potassium chloride). The average particle size in the slurry was about 50 nm, and the slurry was homogeneous after centrifugal acceleration of 1800g (i.e. ‘g’ is the gravity acceleration) for 5 min and phase change cycles for 1000 times. The latent heat of the slurry was 72.25 J g−1 and the paraffin content in the microemulsion was 43.8 wt %. The slurry can overcome the shortcomings of some other techniques and be expected to be widely applied in the TES.
Avian nest predation in Australian temperate forest and woodland: a review
Authors: Fulton Graham R.
Published: April 2018

Many forest and woodland birds are threatened by landscape modifications and predation, particularly nest predation. Nest predation affects a critical stage in avian life histories, which impacts the recruitment of new generations of adult birds. This review discusses the main issues in nest predation research in Australia: mesopredators, the use of artificial nests, ‘edge-effects’, the identification and role of nest predators and the responses of their prey. One conservation strategy is to selectively remove introduced mesopredators, but mesopredators iteratively replace one another, so the net benefit may be negligible. Authors have questioned the utility of artificial nests: they often provide results that vary from natural nests, thus I propose they are best seen as generators of hypotheses to be tested at natural nests. Many studies investigated nest success based on the distance to the edge of the forest or woodland, with equivocal results. Yet fragment size, structure and faunal assemblage set in a more complex paradigm may better explain the presence or absence of effects at edges. There are various types of evidence used to identify nest predators. I argue that cameras are the most functional and direct observations are the most informative. A large number and variety of nest predators are reported yet reviews of nest predation call for more information on the identity and roles of nest predators, particularly on those that add predation pressure beyond what the prey might be able to sustain. The impact of nest characteristics: type, height, vegetation layer, concealment and re-nesting were found to be equivocal in relation to nest predation and in need of focussed research on phylogenetic groups and guilds present within assemblages and within the context of assemblages. A handful of research studies have looked at the possible conservation actions of culling nest-predators and placing cages around threatened birds. More such studies are needed because they provide direct information about practical interventions. Research within assemblages is required to identify and elucidate the roles of nest predators and prey responses and to generate broad and useful theories, which may better inform conservation models.
Association Between Serum Infliximab Trough Concentrations During Maintenance Therapy and Biochemical, Endoscopic, and Histologic Remission in Crohn’s Disease
Authors: Papamichael Konstantinos , Rakowsky Shana , Rivera Claudio , Cheifetz Adam S , Osterman Mark T
Published: April 2018

Background and aim

Objective and more rigorous therapeutic outcomes are emerging as novel targets in Crohn’s disease (CD). We investigated the association between maintenance serum infliximab trough concentrations and biochemical, endoscopic, or histologic remission in CD.

Methods

This retrospective multicenter study involved consecutive CD patients treated with infliximab who had a serum C-reactive protein (CRP) measured within 1 week or endoscopic evaluation within 12 weeks of therapeutic drug monitoring between January 2010 and June 2016. Biochemical remission was defined as a normal CRP (≤5 mg/L). Endoscopic remission was defined as absence of any mucosal break (ulceration or erosion) or for patients with an ileocolonic resection, a Rutgeerts score of ≤i1. Histologic remission was defined as absence of active inflammation.

Results

Seventy-one CRP levels and 96 colonoscopies from 110 CD patients were evaluated. Based on ROC analyses, infliximab concentration thresholds of 2.2, 9.7, and 9.8 μg/mL were found to be related with biochemical, endoscopic, and histologic remission, respectively. Multiple logistic regression analyses identified infliximab concentration ≥2.2 (OR 6.4; 95% CI, 1.5–27.1; P = 0.011), ≥9.7 (OR 3.6; 95% CI, 1.4–9; P = 0.006) and ≥9.8 μg/mL (OR 3.2; 95% CI, 1.3–7.9; P = 0.011) as variables independently associated with biochemical, endoscopic, and histologic remission, respectively.

Conclusions

This study showed that higher maintenance infliximab trough concentrations are associated with more favorable rates of biochemical, endoscopic, or histologic remission in CD patients and that infliximab concentrations may differ based on the treatment goal.
Endoscopic Endonasal Transmaxillary Transsphenoidal Approach for Excision of a Superior Orbital Fissure-Cavernous Sinus Meningioma: 2-Dimensional Operative Video
Authors: El Refaee Ehab , Fleck Steffen , Matthes Marc , Schroeder Henry W S
Published: April 2018

We present a 43-old-male who suffered from a slowly progressive loss of vision in the left eye. Magnetic resonance (MR) imaging revealed a well-circumscribed contrast-enhancing lesion in the region of the anterior cavernous sinus and superior orbital fissure that extended into the optic canal. A schwannoma or meningioma was suspected. A transcranial surgery performed at another institution was not successful in removing the tumor and further deterioration of vision occurred. After resection of the left middle turbinate, the sphenoid and maxillary sinus were opened. The bulging of the tumor was seen at the lateral wall of the sphenoid sinus. After bony decompression of the optic canal, the dura was opened. A meningioma was exposed that arose in between the dural layers of the cavernous sinus. A nice dissection plane was found and the tumor was circumferentially dissected and finally totally removed. There were no complications such as double vision or visual field deficit. MR imaging confirmed a total tumor resection. The visual acuity normalized within a few days. MR imaging obtained 3 yr after surgery shows no recurrence.
The conservation landscape of the human ribosomal RNA gene repeats
Authors: Agrawal Saumya , Ganley Austen R.D.
Published: April 2018

Ribosomal RNA gene repeats (rDNA) encode ribosomal RNA, a major component of ribosomes. Ribosome biogenesis is central to cellular metabolic regulation, and several diseases are associated with rDNA dysfunction, notably cancer, However, its highly repetitive nature has severely limited characterization of the elements responsible for rDNA function. Here we make use of phylogenetic footprinting to provide a comprehensive list of novel, potentially functional elements in the human rDNA. Complete rDNA sequences for six non-human primate species were constructed usingde novowhole genome assemblies. These new sequences were used to determine the conservation profile of the human rDNA, revealing 49 conserved regions in the rDNA intergenic spacer (IGS). To provide insights into the potential roles of these conserved regions, the conservation profile was integrated with functional genomics datasets. We find two major zones that contain conserved elements characterised by enrichment of transcription-associated chromatin factors, and transcription. Conservation of some IGS transcripts in the apes underpins the potential functional significance of these transcripts and the elements controlling their expression. Our results characterize the conservation landscape of the human IGS, and suggest that noncoding transcription and chromatin elements are conserved and important features of this unique genomic region.
Prenatal alcohol exposure and facial morphology in a UK cohort
Authors: Howe Laurence J , Sharp Gemma C , Hemani Gibran , Zuccolo Luisa , Richmond Stephen , Lewis Sarah J
Published: April 2018

High levels of prenatal alcohol exposure are known to cause an array of adverse outcomes including foetal alcohol syndrome (FAS); however, the effects of low to moderate exposure are less-well characterised. Previous findings suggest that differences in normal-range facial morphology may be a marker for alcohol exposure and related adverse effects. Therefore, in the Avon Longitudinal Study of Parents and Children, we tested for an association between maternal alcohol consumption and six FAS-related facial phenotypes in their offspring, using both self-report questionnaires and the maternal genotype at rs1229984 inADH1Bas measures of maternal alcohol consumption. In both self-reported alcohol consumption (N=4,233) and rs1229984 genotype (N=3,139) analyses, we found no strong statistical evidence for an association between maternal alcohol consumption and facial phenotypes tested. The directions of effect estimates were compatible with the known effects of heavy alcohol exposure, but confidence intervals were largely centred around zero. We conclude that, in a sample representative of the general population, there is no strong evidence for an effect of prenatal alcohol exposure on normal-range variation in facial morphology.
Mapping molecular datasets back to the brain regions they are extracted from: Remembering the native countries of hypothalamic expatriates and refugees
Authors: Khan Arshad M. , Grant Alice H. , Martinez Anais , Burns Gully A.P.C. , Thatcher Brendan S. , Anekonda Vishwanath T. , Thompson Benjamin W. , Roberts Zachary S. , Moralejo Daniel H. , Blevins James E.
Published: April 2018

This article, which includes novel unpublished data along with commentary and analysis, focuses on approaches to link transcriptomic, proteomic, and peptidomic datasets mined from brain tissue to the original locations within the brain that they are derived from using digital atlas mapping techniques. We use, as an example, the transcriptomic, proteomic and peptidomic analyses conducted in the mammalian hypothalamus. Following a brief historical overview, we highlight studies that have mined biochemical and molecular information from the hypothalamus and then lay out a strategy for how these data can be linked spatially to the mapped locations in a canonical brain atlas where the data come from, thereby allowing researchers to integrate these data with other datasets across multiple scales. A key methodology that enables atlas-based mapping of extracted datasets – laser-capture microdissection – is discussed in detail, with a view of how this technology is a bridge between systems biology and systems neuroscience.
FMRI processing with AFNI: Some comments and corrections on “Exploring the Impact of Analysis Software on Task fMRI Results”
Authors: Taylor Paul A. , Chen Gang , Glen Daniel R. , Rajendra Justin K. , Reynolds Richard C. , Cox Robert W.
Published: April 2018

A recent study posted on bioRxiv by Bowring, Maumet and Nichols aimed to compare results of FMRI data that had been processed with three commonly used software packages (AFNI, FSL and SPM). Their stated purpose was to use “default” settings of each software’s pipeline for task-based FMRI, and then to quantify overlaps in final clustering results and to measure similarity/dissimilarity in the final outcomes of packages. While in theory the setup sounds simple (implement each package’s defaults and compare results), practical realities make this difficult. For example, different softwares would recommend different spatial resolutions of the final data, but for the sake of comparisons, the same value must be used across all. Moreover, we would say that AFNI does not have an explicit default pipeline available: a wide diversity of datasets and study designs are acquired across the neuroimaging community, often requiring bespoke tailoring of basic processing rather than a “one-size-fits-all” pipeline. However, we do have strong recommendations for certain steps, and we are also aware that the choice of a given step might place requirements on other processing steps. Given the very clear reporting of the AFNI pipeline used in Bowring et al. paper, we take this opportunity to comment on some of these aspects of processing with AFNI here, clarifying a few mistakes therein and also offering recommendations. We provide point-by-point considerations of using AFNI’s processing pipeline design tool at the individual level, afni_proc.py, along with supplementary programs; while specifically discussed in the context of the present usage, many of these choices may serve as useful starting points for broader processing. It is our intention/hope that the user should examine data quality at every step, and we demonstrate how this is facilitated in AFNI, as well.
Real-time functional connectivity-based neurofeedback of amygdala-frontal pathways reduces anxiety
Authors: Zhao Zhiying , Yao Shuxia , Li Keshuang , Sindermann Cornelia , Zhou Feng , Zhao Weihua , Li Jianfu , Lührs Michael , Goebel Rainer , Kendrick Keith M. , Becker Benjamin
Published: April 2018

Deficient emotion regulation and exaggerated anxiety represent a major transdiagnostic psychopathological marker. On the neural level these deficits have been closely linked to impaired, yet treatment-sensitive, prefrontal regulatory control over the amygdala. Gaining direct control over these pathways could therefore provide an innovative and promising strategy to regulate exaggerated anxiety. To this end the current proof-of-concept study evaluated the feasibility, functional relevance and maintenance of a novel connectivity-informed real-time fMRI neurofeedback training. In a randomized within-subject sham-controlled design high anxious subjects (n = 26) underwent real-time fMRI-guided training to enhance connectivity between the ventrolateral prefrontal cortex (vlPFC) and the amygdala (target pathway) during threat exposure. Maintenance of regulatory control was assessed after three days and in the absence of feedback. Training-induced changes in functional connectivity of the target pathway and anxiety ratings served as primary outcomes. Training of the target, yet not the sham-control, pathway significantly increased amygdala-vlPFC connectivity and decreased subjective anxiety levels. On the individual level stronger connectivity increases were significantly associated with anxiety reduction. At follow-up, volitional control over the target pathway and decreased anxiety level were maintained in the absence of feedback. The present results demonstrate for the first time that successful self-regulation of amygdala-prefrontal top-down regulatory circuits may represent a novel strategy to control anxiety. As such, the present findings underscore both the critical contribution of amygdala-prefrontal circuits to emotion regulation and the therapeutic potential of connectivity-informed real-time neurofeedback.
Discovery of a new path for red blood cell generation in the mouse embryo
Authors: Pinheiro Irina , Bölükbaşi Özge Vargel , Ganter Kerstin , Sabou Laura A. , Tew Vick Key , Bolasco Giulia , Shvartsman Maya , Pavlovich Polina V. , Buness Andreas , Nikolakopoulou Christina , Bergiers Isabelle , Kouskoff Valerie , Lacaud Georges , Lancrin Christophe
Published: April 2018

Erythropoiesis occurs through several waves during embryonic development. Although the source of the primitive wave is well characterized, the origin of erythrocytes later in embryogenesis is less clear due to overlaps between the different erythroid waves. Using the miR144/451-GFP mouse model to track cells expressing the erythroid microRNAs miR144/451, we identified cells co-expressing VE-Cadherin and GFP in the yolk sac between E9.5 and E12. This suggested the existence of hemogenic endothelial cells committed to erythropoiesis (Ery-HEC). We showed that these cells were capable of generating erythrocytesex vivoand we demonstrated that the formation of Ery-HEC was independent of theRunx1gene expression. Using transcriptome analysis, we demonstrated that these cells coexpressed endothelial and erythroid genes such asHbb-bh1andGata1but we were surprised to detect the primitive erythroid genesAqp3andAqp8suggesting the formation of primitive erythrocytes at a much later time point than initially thought. Finally, we showed that enforced expression ofGata1in endothelial cells was enough to initiate the erythroid transcriptional program.
Molecular dynamics suggests antiviral compounds active against Dengue Virus show similar binding patterns to Zika Virus proteins
Authors: de Lima Neto Daniel Ferreira , Soares Anderson Pereira , Pour Shahab Zaki , Baez Ayda Susana Ortiz , de Castro Neuhaus Patrick , de Melo Freire Caio Cesar , Bonafé Carlos Francisco Sampaio
Published: April 2018

The Zika virus (ZIKV) arrival in Brazilian territory brought to light the need for preparedness regarding arboviruses in Brazil. Compound screening is a cumbersome process dependent upon in vitro testing and validation. Recently, virtual screening methods have improved precision and reliability providing a framework for in silico testing of lead compound candidates. Here we have applied these methods on compounds that were previously shown to be active against Dengue virus in vitro, taking the structural information of such compounds and applying docking methods to identify putative binding sites. A molecular dynamics approach was also used to refine the docking results. The computational experiments ran here suggests that compounds such as Epigallocatechin Gallate, Ergotamine and Avermectin-B1a bind to active sites on the viral enzymes NS5 and NS3, as well as on its Envelope protein. Refinement shows that such bindings were not lost during the production run and key regions on both enzymes were structurally displaced on average over the simulation time. Interestingly there is no documented drug interactions among these candidates, raising the possibility of drug combinations during treatments. Moreover, the candidate compounds have been extensively studied, thus providing important information regarding intracellular interactions caused by them, which are also associated with pathways exploited by the virus, suggesting possible side interactions hindering the replication process.
A network of epigenomic and transcriptional cooperation encompassing an epigenomic master regulator in cancer
Authors: Wilson Stephen , Filipp Fabian V.
Published: April 2018

Coordinated experiments focused on transcriptional responses and chromatin states are well-equipped to capture different epigenomic and transcriptomic levels governing the circuitry of a regulatory network. We propose a workflow for the genome-wide identification of epigenomic and transcriptional cooperation to elucidate transcriptional networks in cancer. Gene promoter annotation in combination with network analysis and sequence-resolution of enriched transcriptional motifs in epigenomic data reveals transcription factor families that act synergistically with epigenomic master regulators. A close teamwork of the transcriptional and epigenomic machinery was discovered. The network is tightly connected and includes the histone lysine demethylase KDM3A, basic helix-loop-helix factors MYC, HIF1A, and SREBF1, as well as differentiation factors AP1, MYOD1, SP1, MEIS1, ZEB1 and ELK1. In such a cooperation network, one component opens the chromatin, another one recognizes gene-specific DNA motifs, others scaffold between histones, cofactors, and the transcriptional complex. In cancer, due to the ability to team up with transcription factors, epigenetic factors concert mitogenic and metabolic gene networks, claiming the role of a cancer master regulators or epioncogenes.

Specific histone modification patterns are commonly associated with open or closed chromatin states, and are linked to distinct biological outcomes by transcriptional activation or repression. Disruption of patterns of histone modifications is associated with loss of proliferative control and cancer. There is tremendous therapeutic potential in understanding and targeting histone modification pathways. Thus, investigating cooperation of chromatin remodelers and the transcriptional machinery is not only important for elucidating fundamental mechanisms of chromatin regulation, but also necessary for the design of targeted therapeutics.
Solving for X: evidence for sex-specific autism biomarkers across multiple transcriptomic studies
Authors: Lee Samuel C. , Quinn Thomas P. , Lai Jerry , Kong Sek Won , Hertz-Picciotto Irva , Glatt Stephen J. , Crowley Tamsyn M. , Venkatesh Svetha , Nguyen Thin
Published: April 2018

Autism spectrum disorder (ASD) is a markedly heterogeneous condition with a varied phenotypic presentation. Its high concordance among siblings, as well as its clear association with specific genetic disorders, both point to a strong genetic etiology. However, the molecular basis of ASD is still poorly understood, although recent studies point to the existence of sex-specific ASD pathophysiologies and biomarkers. Despite this, little is known about how exactly sex influences the gene expression signatures of ASD probands. In an effort to identify sex-dependent biomarkers (and characterise their function), we present an analysis of a single paired-end post-mortem brain RNA-Seq data set and a meta-analysis of six blood-based microarray data sets. Here, we identify several genes with sex-dependent dysregulation, and many more with sex-independent dysregulation. Moreover, through pathway analysis, we find that these sex-independent biomarkers have substantially different biological roles than the sex-dependent biomarkers, and that some of these pathways are ubiquitously dysregulated in both post-mortem brain and blood. We conclude by synthesizing the discovered biomarker profiles with the extant literature, by highlighting the advantage of studying sex-specific dysregulation directly, and by making a call for new transcriptomic data that comprise large female cohorts.