bluuebunny/crossref_metadata_2025 huggingface dataset:
A physics-guided modular deep-learning based automated framework for tumor segmentation in PET
Authors: Leung Kevin H , Marashdeh Wael , Wray Rick , Ashrafinia Saeed , Pomper Martin G , Rahmim Arman , Jha Abhinav K
Published: April 2020

An important need exists for reliable positron emission tomography (PET) tumor-segmentation methods for tasks such as PET-based radiation-therapy planning and reliable quantification of volumetric and radiomic features. To address this need, we propose an automated physics-guided deep-learning-based three-module framework to segment PET images on a per-slice basis. The framework is designed to help address the challenges of limited spatial resolution and lack of clinical training data with known ground-truth tumor boundaries in PET. The first module generates PET images containing highly realistic tumors with known ground-truth using a new stochastic and physics-based approach, addressing lack of training data. The second module trains a modified U-net using these images, helping it learn the tumor-segmentation task. The third module fine-tunes this network using a small-sized clinical dataset with radiologist-defined delineations as surrogate ground-truth, helping the framework learn features potentially missed in simulated tumors. The framework was evaluated in the context of segmenting primary tumors in 18F-fluorodeoxyglucose (FDG)-PET images of patients with lung cancer. The framework’s accuracy, generalizability to different scanners, sensitivity to partial volume effects (PVEs) and efficacy in reducing the number of training images were quantitatively evaluated using Dice similarity coefficient (DSC) and several other metrics. The framework yielded reliable performance in both simulated (DSC: 0.87 (95% confidence interval (CI): 0.86, 0.88)) and patient images (DSC: 0.73 (95% CI: 0.71, 0.76)), outperformed several widely used semi-automated approaches, accurately segmented relatively small tumors (smallest segmented cross-section was 1.83 cm2), generalized across five PET scanners (DSC: 0.74 (95% CI: 0.71, 0.76)), was relatively unaffected by PVEs, and required low training data (training with data from even 30 patients yielded DSC of 0.70 (95% CI: 0.68, 0.71)). In conclusion, the proposed automated physics-guided deep-learning-based PET-segmentation framework yielded reliable performance in delineating tumors in FDG-PET images of patients with lung cancer.
Influence of multipolar electrostatic and van der Waals forces on the coagulation of silicon nanoparticles in low-temperature argon-silane plasmas
Authors: Santos Benjamin , Vidal François
Published: April 2020

Numerical calculations have been performed to investigate the effects of electrostatic and van der Waals interactions on coalescing silicon nanoparticles in isotropic low-temperature argon–silane plasmas. The electrostatic interaction between nanoparticles is modeled using three approaches, including the elementary Coulomb interaction, a rigorous electrostatic multipolar expansion, and an approximate form of the latter. The van der Waals interaction is described using the Hamaker expression regularized at short separation distance to manage the singularity at the contact surface. The evolution of the size and charge distributions are calculated by solving the general dynamic equation numerically for the coagulation of charged particles and using simplified approaches for nucleation, surface growth, and self-consistent plasma dynamics. A two-population size distribution, as observed in experiments, results naturally from this model. The electrostatic multipolar force is found to enhance the coagulation as compared to the elementary Coulomb force. The details of the growth process depend, however, significantly on the adopted regularization of the Hamaker expression at a short distance.
An interdecadal extension of the Indo-Pacific warm pool and its strengthened influence on the South China Sea summer monsoon since the late 1980s
Authors: Yin Xiaoxue , Huangfu Jingliang , Zhou Lian-Tong
Published: April 2020

In this study, the interdecadal change in the size of the Indo-Pacific warm pool (IPWP) and its connection with the intensity of the South China Sea summer monsoon (SCSSM) in May are investigated. The results show that the size of the IPWP experienced a marked interdecadal extension in the late 1980s, and its impacts on the SCSSM have also strengthened. Further analyses indicate that interdecadal changes in the connection between the IPWP and SCSSM variations are related to the changes in the atmospheric circulation anomalies over the tropical western Pacific due to the size of the IPWP. During 1951–1986, the IPWP was smaller than the climatologic size, which led to suppressed convection over the tropical western Pacific and easterly anomalies north of the equator. The Philippines and South China Sea (SCS) region was controlled by anomalous anticyclonic circulation, which was not conducive to the formation and development of the SCSSM. In contrast, during 1987–2018, the IPWP expanded significantly eastward. As a response to the IPWP size extension, convective activities were enhanced over the tropical western Pacific. Anomalous cyclonic circulation was located over the Philippines and SCS regions, which favored the enhancement of the SCSSM through wide westerly flow in the Bay of Bengal and tropical western Pacific. Moreover, it is shown that the interdecadally enhanced intraseasonal oscillations (ISOs) over the tropical western Pacific in the late 1980s also favored reinforcement of the SCSSM intensity.
Quantifying the potential for climate change mitigation of consumption options
Authors: Ivanova Diana , Barrett John , Wiedenhofer Dominik , Macura Biljana , Callaghan Max , Creutzig Felix
Published: April 2020

Background. Around two-thirds of global GHG emissions are directly and indirectly linked to household consumption, with a global average of about 6 tCO2eq/cap. The average per capita carbon footprint of North America and Europe amount to 13.4 and 7.5 tCO2eq/cap, respectively, while that of Africa and the Middle East—to 1.7 tCO2eq/cap on average. Changes in consumption patterns to low-carbon alternatives therefore present a great and urgently required potential for emission reductions. In this paper, we synthesize emission mitigation potentials across the consumption domains of food, housing, transport and other consumption. Methods. We systematically screened 6990 records in the Web of Science Core Collections and Scopus. Searches were restricted to (1) reviews of lifecycle assessment studies and (2) multiregional input-output studies of household consumption, published after 2011 in English. We selected against pre-determined eligibility criteria and quantitatively synthesized findings from 53 studies in a meta-review. We identified 771 original options, which we summarized and presented in 61 consumption options with a positive mitigation potential. We used a fixed-effects model to explore the role of contextual factors (geographical, technical and socio-demographic factors) for the outcome variable (mitigation potential per capita) within consumption options. Results and discussion. We establish consumption options with a high mitigation potential measured in tons of CO2eq/capita/yr. For transport, the options with the highest mitigation potential include living car-free, shifting to a battery electric vehicle, and reducing flying by a long return flight with a median reduction potential of more than 1.7 tCO2eq/cap. In the context of food, the highest carbon savings come from dietary changes, particularly an adoption of vegan diet with an average and median mitigation potential of 0.9 and 0.8 tCO2eq/cap, respectively. Shifting to renewable electricity and refurbishment and renovation are the options with the highest mitigation potential in the housing domain, with medians at 1.6 and 0.9 tCO2eq/cap, respectively. We find that the top ten consumption options together yield an average mitigation potential of 9.2 tCO2eq/cap, indicating substantial contributions towards achieving the 1.5 °C–2 °C target, particularly in high-income context.
The occupation of cropland by global urban expansion from 1992 to 2016 and its implications
Authors: Huang Qingxu , Liu Ziwen , He Chunyang , Gou Siyuan , Bai Yansong , Wang Yihang , Shen Miaogen
Published: April 2020

Large-scale urban expansion worldwide has exerted great impacts on cropland and its net primary productivity (NPP), which can affect whether food security and sustainable development goals will be met at global and local scales. Although important, the impacts at the global scale over the last 25 years remain unclear. Based on the latest long-term dynamic urban expansion data, this study analyzed global urban expansion and its impacts on cropland NPP from 1992 to 2016 at multiple scales. The results showed that the expansion of urban land occupied a total of 159 170 km2 of cropland, accounting for 45.9% of the total expanded urban area. The cropland NPP decreased by 58.71 (56.52 ∼ 59.81, 95% confidence interval) TgC as a result of urban expansion, which represents approximately 0.42% (0.40% ∼ 0.43%) of the multiyear average of total cropland NPP from 2000 to 2015. If the cropland NPP losses were converted to the grain production (i.e. 1.44 × 107 tons), it is equivalent to the minimum annual food intake demands for at least 36 million people. More importantly, urban expansion is exacerbating the risk of food security in developing countries in Asia and Africa, such as China, Vietnam and Egypt. In the future, these countries should balance urban expansion with cropland protection by strictly restricting the occupation of cropland and encouraging smart urban growth.
Thermodynamic sensitivity analysis of CO2 reforming of methane based on equilibrium predictions
Authors: Abdulrasheed A A , Jalil A A , Siang T J , Hambali H U
Published: April 2020

Thermodynamic sensitivity analysis was conducted to evaluate the selectivity dry reforming of methane (DRM) with respect to other competing side reactions in terms of Gibbs energy minimization and equilibrium reactor compositions. Spontaneity of each reaction was evaluated by their corresponding changes in Gibbs energy as a function of reactor temperature from 100 – 1000 °C. At temperatures above 700 °C, all reactions considered with the exception of the Boudouard reaction are spontaneous due to their negative deltaG values. Equilibrium compositions were computed for 40 kmol of feed (CO2 + CH4) to determine its sensitivity to occurrence of reverse water-gas-shift (RWGS) reaction and changes in feed CO2/CH4 ratio. The presence of RWGS reaction results to higher reactant conversion accompanied by more severe carbon formation. The H2/CO ratio was however not affected by its occurrence. At CO2/CH4 feed ratio of 2, the product ratio was barely affected and at minimal carbon formation while CO2/CH4 ratio value of 0.5 produced a lot of carbon especially at high temperatures due to the prevalence of CH4 cracking. DRM is thus more preferable at temperatures above 700 °C, devoid of RWGS and high feed CH4.
Effect of transition metals (Mo, Mn and Co) on mesoporous ZSM-5 catalyst activity in carbon dioxide reforming of methane
Authors: Hambali H U , Jalil A A , Abdulrasheed A A , Siang T J , Fatah N A A , Rahman A F A , Aziz M A H , Hussain I
Published: April 2020

This paper investigates the effect of transition metals (Mo, Mn and Co) on mesoporous ZSM-5 support in carbon dioxide reforming of methane reaction. The mesoporous ZSM-5 support was synthesized by micro emulsion technique and the metals were loaded by wet impregnation method. It was observed that ZSM-5 supported Co catalyst had higher surface area in comparison to other catalysts, which could favour well dispersion and wider utilization of active component. In addition, the ZSM-5 supported Co catalyst exhibited the highest methane and carbon dioxide conversions of 69 % and 65 % respectively at 850°C. The Co species were more active to decompose methane and carbon dioxide compared to Mo and Mn loaded catalysts. Hence, loading Co on mesoporous ZSM-5 produce an active catalyst in carbon dioxide reforming methane reaction.
Effect of ligand type on CO2 adsorption over amine functionalized fibrous adsorbents
Authors: Mohamad Noor Ashikin , Zubair Nur Afifah , Lotf Ebrahim Abouzari , Nasef Mohamed M. , Ahmad Arshad , Ali Roshafima Rasit , Abdullah TAT , Ting Teo Ming
Published: April 2020

In this study, ligands originated from glycidyl methacrylate (GMA) and vinyl benzyl chloride (VBC) monomers were grafted onto fibrous polyethylene/polypropylene (PE/PP) substrate and the resulting grafted copolymers were functionalized with ethylenediamine (EDA). The changes in the chemical structure and crystallinity of the aminated adsorbents were evaluated using Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD), respectively. The PE/PP-g-PGMA-EDA adsorbent showed a CO2 adsorption capacity of 1.73 mmol/g from pure gas, which is 87% lower than that of PE/PP-g-PVBC-EDA (3.24 mmol/g) at 30 bars despite the higher density in the former adsorbent. The effect of temperature, selectivity and CO2 gas composition was further investigated for the PE/PP-g-PVBC-EDA adsorbent.
Facile Electrosynthesis of Fe3O4 Nanoparticles Mediated with Sodium Alginate for Paracetamol Degradation
Authors: Masudi A , Jusoh N. W. C , Liew P Y
Published: April 2020

High purity of Fe3O4 was prepared by electrochemical method in different concentration of sodium alginate (SA) as natural capping agent. The content of SA influenced the particle size and surface interaction to Fe3O4 as confirmed by X-ray diffraction (XRD) and Fourier Transform Infrared (FTIR) spectroscopy. The highest photocatalytic activity was obtained for Fe3O4 synthesized with 0.05% SA with initial concentration of 15 mg/L Paracetamol. This result contributed to electrochemical advancement to produce Fe3O4 with simple method.
Enhanced Proton Conductivity of Porous UHMWPE membrane with Graphene-based material for Vanadium Redox Flow Battery
Authors: Sha’rani S S , Jusoh N. W. C. , Abouzari-Lotf E , Ahmad A , Ali R R
Published: April 2020

Porous membrane with enhanced proton conductivity is designed and prepared for vanadium redox flow battery (VRFB). The membrane is composed of ultra height molecular weight polyethylene (UHMWPE) grafted with poly(vinylbenzyl chloride) (PVBC) at different degrees of grafting (DOG). Subsequently, the membrane is functionalized with graphene oxide (UHMWPE-g-PVBGO) under ultrasonication. The functionalization of the GO on the porous substrates is confirmed by Fourier transform infrared (FTIR) and Raman analyses. UHMWPE-g-PVBGOmembranes exhibited ∼37% higher proton conductivity compared to pristine UHMWPE upon modification at 30 °C and 100% relative humidity (RH). In relation to the degree of grafting, a higher degree of grafting possessed higher proton conductivity value for the porous membrane.
Characterization of ozone production from multi-cylinder reactor in non-thermal plasma device using multivariable power least squares method
Authors: Tan L S , Lim M T , Tey W Y
Published: April 2020

Other than usage for environmental remediation, ozone is also increasingly studied for its potential in combustion enhancement. In this study, the characterization of the ozone production at varied voltage, duty cycle and cylinder configuration for reactor was conducted using multivariable power least squares method (MPLSM). This alternative correlation method in the form of power function was applied in this study to determine the dominant factor affecting the ozone production using the multi-cylinder reactor. The regressed equation using MPLSM method indicated voltage as the dominant factor in the production of ozone compared to the effect of duty cycle. The correlations generated from MPLSM for both reactor configurations were able to predict most of the ozone concentration results within 25% deviation from the actual experimental data. As such, MPLSM could be considered as an alternative method to be used for correlations of non-polynomial results.
Pullulan mediated zinc oxide microparticles: Effect of synthesis temperature
Authors: Mohamed Isa E D , Che Jusoh N W , Hazan R , Shameli K
Published: April 2020

Zinc oxide (ZnO) has been gaining a lot of attention compared to the other semiconductor metal oxide. This is due to their favourable properties such as chemical stability, high electrochemical coupling coefficient, broad range of absorption radiation and high photostability. It also has wide band gap energy (3.37 eV), large exciton-binding energy (60 meV) and high thermal and mechanical stability at room temperature. Besides these desirable properties, the synthesis of ZnO has been widely studied as it is easy to synthesized and its properties such as band gap, shape and size can be controlled through synthesis parameters and methods. In this study, zinc oxide microparticles (ZnO-MCs) is produced with pullulan as mediator via precipitation method. The effect of synthesis temperature on the properties of synthesized ZnO-MCs were also studied. Based on the result obtained, all synthesized ZnO-MCs exhibited hexagonal wurtzite structure. As the synthesis temperature increases, the particles morphology changes from large spherical shape to flower-like morphology. Furthermore, the particle size also decreases with increasing temperature. This result is supported by surface area and pore analysis where the surface area ranging from 6.22 to 22.78 m2 g−1 was obtained as the synthesis temperature increases. All these results indicate that synthesis method and parameters will affect the properties of synthesized ZnO-MCs.
Photocatalytic Degradation of Malachite Green Dye by Plant-mediated Biosynthesized Zinc Oxide Nanoparticles
Authors: Sukri S N A M , Isa E D M , Shameli K
Published: April 2020

Photocatalytic activity of ZnO-NPs was tested by degradation of Malachite Green dye under UV light irradiation. The ZnO-NPs were biosynthesized using Punica granatum (pomegranate) fruit peels extract as the stabilizing agent. Simple sol-gel method and calcination in different temperatures (400, 500, 600 and 700°C) were carried out to obtain pure ZnO-NPs with high photocatalytic properties. In the degradation studies, 20 mg ZnO-NPs were used to degrade Malachite Green dye of 10 ppm initial concentration for a total period of 50 minutes in a 100 ml reaction volume. Results obtained shown that ZnO-NPs calcined in 700°C had the highest removal efficiency at about 99% in 40 minutes. This proves that biosynthesized ZnO-NPs have a high potential to be used as a photocatalyst to degrade textile dyes in a short time for wastewater treatments.
A viable system for carbon dioxide (CO2) methanation over fibrous silica ZSM-5 for substitute natural gas (SNG)
Authors: Hussain I , Jalil A A , Fatah N A A , Ibrahim M. , Azami M S , Fadlun W , Aziz M A H , Hambali HU
Published: April 2020

Catalytic CO2 methanation offers an attractive and sustainable way for the production of substituted natural gas (SNG), which may be used as a clean alternative energy source than fossil fuels. A metal-free fibrous silica ZSM-5 catalyst (FS@ZSM-5) was synthesized via the microemulsion technique to conduct catalytic CO2 methanation. The FESEM, BET, and FTIR characterization techniques were used to investigate the surface morphology, pore structure of the catalysts. It was noticed that the commercialized ZSM-5 showed 37% CH4 selectivity with a rate of methane formation 0.067 mmol m−2s−1. While FS@ZSM-5 exhibited high CH4 selectivity of 66 % with rate of methane formation 0.108 mmol m−2s−1 using same conditions (T = 500 °C and GHSV = 36,000 mL h−1 g−1). Therefore, the FS@ZSM-5 was proved an efficient and active catalyst for CO2 methanation activity.
Phytotoxicity Study of Native Plants in ex-mining lake water treatment
Authors: Draman S F S , Khalid S A , Sidek N M , Abdullah S R S , Anuar N
Published: April 2020

The use of phytoremediation in removing and degrade the contaminants gives great interest for researchers to explore further. This green technology is relatively eco-friendly and cost-effective. Before a full-scale system can be installed to ensure that the remedy is effective by selected plants using phytoremediation process, identification of these plants and its ability to resist toxicity of contaminants is crucial. In this study, the ability of native plants in Malaysia namely L. articulata, E. ochrostacys and E. dulcis to survive when exposed to acid mine drainage water (AMD) are investigated. This was done with free flow systems or free surface (FSF) for 30 days with water from ex mining lake, Tasik Puteri, Bukit Besi, Malaysia. The physical growth of those three plants such as height and withered leaves is monitored every seven day as indication of their survivability. Ferum (Fe) analysis is also carried out on the lower and upper part of the above three plants using Inductively Coupled Plasma – Optical Emission Spectrometry (ICP-OES). Results of the Fe analysis showed that E.ochrostacys has the highest accumulation ability compared to E.dulcis and L. articulata with a maximum accumulation of 123,584 mg Fe/kg at lower part and 55,151 mg Fe/kg at the upper part. Furthermore, E. ochrostacys was also able to tolerate and survive in the water of Tasik Puteri up to 80% survival rate during phytotoxicity study.
Parametric study of CO2 separation using carbon molecular sieve, zeolite and silica gel
Authors: Norani A A , Ahmad A , Abdullah T A T , Ripin A
Published: April 2020

Performances of Pressure swing adsorption (PSA) dependent on the type of adsorbent and efficiency of the regeneration cycle. In this work, a model describing CO2 mixture flow, mass and heat transfer with multi-component adsorption model are developed in Aspen Adsorption environment to compare the performance of PSA cycles with three different adsorbents (CMS 3K, zeolite 13x and silica gel). Adsorption capacity of CO2 for three adsorbents was found to be in the order of CMS>zeolite>silica gel. Hence, CMS was chosen as the adsorbents to evaluate PSA performances on different feed flowrate and pressure based on the purity, recovery and productivity of the CO2 separation. The result shows that, within a certain range, higher adsorption pressure will increase all purity, recovery and productivity of CO2 while higher feeding rate leads to increase recovery but lower purity and productivity.
Experimental Study of the Characteristics of Acoustic Cavitation Bubbles Under the Influence of Ultrasonic Wave
Authors: Hadi N A H , Ahmad A
Published: April 2020

Sonochemistry application in various fields, especially separation industries, are constantly increasing and extensively studied in recent years. In the applications, a detailed understanding of the characteristics and behaviour of acoustic cavitation bubble is crucial. However, acoustic bubbles behave differently in each liquid. Owing to numerous amounts of acoustic bubbles showing dramatic transition during sonication and have complex interaction in a liquid mixture, it is more difficult to observe acoustic bubble consistently and thoroughly. In response to this problem, our study will investigate separately acoustic cavitation bubble form in sonicated water, ethanol and mixture of ethanol-water. Each liquid was sonicated at 20 kHz ultrasound with a transducer attached to the bottom of an acrylic vessel. In order to visualise acoustic bubbles clearly, a high-speed video camera is used to capture the image of acoustic bubbles. Image processing and analysis are by the application of Image Processing Toolbox in MATLAB R2018b. Experimental result reveals that acoustic cavitation bubbles in a mixture of ethanol-water have the largest radius, volume and higher buoyancy force compared to pure ethanol and water. Results obtained coincided well with theory, which indicated that sonicated mixture containing alcohol provide resistance to gas transfer across liquid/bubble interface, leading to an increased bubble radius and hence the buoyancy force.
Investigation on the influence of tungsten particulate in mechanical and thermal properties of HD50MA180 high density polyethylene composites
Authors: E Jenson Joseph , Panneerselvam K
Published: April 2020

In this present investigation, the influence of reinforcing tungsten (W) particles in High- Density Polyethylene (HDPE) on mechanical and thermal properties, has been studied. W reinforced HDPE composites are processed by melt compounding method, with W varied in proportion of 1%, 3%, 5% and 7% by weight. The test specimens were prepared by injection molding as per ASTM standards and analyzed by X-Ray Diffraction (XRD), Scanning Electron Microscope (SEM), Mechanical and Thermal Characterization. XRD results show that, the intensity count at angle 40.3°, 58.7°, 73.6° and 87.1° increases with the increase in wt% of W particles. SEM analysis reveals that, composites containing 1wt% of W has uniform dispersion in the HDPE matrix. In mechanical characterization, tensile strength and flexural strength of the specimen reported a sharp increase with the addition of W at 1wt%, followed by a negative trend for the higher content of W particles. However, the impact strength result shows that specimen with 3wt% of W content has the highest toughness. Further from thermal characterization, Thermo Gravimetric Analysis (TGA) and Differential Scanning Calorimetry (DSC) results show that degradation temperature and the melting point of composites improve with an increase in W content. Composite with 7wt% W content has the highest degradation temperature and melting point.
Separated sets and Auerbach systems in Banach spaces
Authors: Hájek Petr , Kania Tomasz , Russo Tommaso
Published: April 2020

The paper elucidates the relationship between the density of a Banach space and possible sizes of Auerbach systems and well-separated subsets of its unit sphere. For example, it is proved that for a large enough space

X
X

, the unit sphere

S
X

S_X

always contains an uncountable

(
1
+
)

(1+)

-separated subset. In order to achieve this, new results concerning the existence of large Auerbach systems are established, that happen to be sharp for the class of weakly Lindelöf determined (WLD) spaces. In fact, we offer the first consistent example of a non-separable WLD Banach space that contains no uncountable Auerbach system, as witnessed by a renorming of

c
0

(

ω
1

)

c_0(\omega _1)

. Moreover, the following optimal results for the classes of, respectively, reflexive and super-reflexive spaces are established: the unit sphere of an infinite-dimensional reflexive space contains a symmetrically

(
1
+
ε
)

(1+\varepsilon )

-separated subset of any regular cardinality not exceeding the density of

X
X

; should the space

X
X

be super-reflexive, the unit sphere of

X
X

contains such a subset of cardinality equal to the density of

X
X

. The said problem is studied for other classes of spaces too, including WLD spaces, RNP spaces, or strictly convex ones.
Learning transferable deep convolutional neural networks for the classification of bacterial virulence factors
Authors: Zheng Dandan , Pang Guansong , Liu Bo , Chen Lihong , Yang Jian
Published: April 2020

Motivation

Identification of virulence factors (VFs) is critical to the elucidation of bacterial pathogenesis and prevention of related infectious diseases. Current computational methods for VF prediction focus on binary classification or involve only several class(es) of VFs with sufficient samples. However, thousands of VF classes are present in real-world scenarios, and many of them only have a very limited number of samples available.

Results

We first construct a large VF dataset, covering 3446 VF classes with 160 495 sequences, and then propose deep convolutional neural network models for VF classification. We show that (i) for common VF classes with sufficient samples, our models can achieve state-of-the-art performance with an overall accuracy of 0.9831 and an F1-score of 0.9803; (ii) for uncommon VF classes with limited samples, our models can learn transferable features from auxiliary data and achieve good performance with accuracy ranging from 0.9277 to 0.9512 and F1-score ranging from 0.9168 to 0.9446 when combined with different predefined features, outperforming traditional classifiers by 1–13% in accuracy and by 1–16% in F1-score.

Availability and implementation

All of our datasets are made publicly available at http://www.mgc.ac.cn/VFNet/, and the source code of our models is publicly available at https://github.com/zhengdd0422/VFNet.

Supplementary information

Supplementary data are available at Bioinformatics online.
CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme
Authors: Asghari Hossein , Lin Yen-Yi , Xu Yang , Haghshenas Ehsan , Collins Colin C , Hach Faraz
Published: April 2020

Motivation

The ubiquitous abundance of circular RNAs (circRNAs) has been revealed by performing high-throughput sequencing in a variety of eukaryotes. circRNAs are related to some diseases, such as cancer in which they act as oncogenes or tumor-suppressors and, therefore, have the potential to be used as biomarkers or therapeutic targets. Accurate and rapid detection of circRNAs from short reads remains computationally challenging. This is due to the fact that identifying chimeric reads, which is essential for finding back-splice junctions, is a complex process. The sensitivity of discovery methods, to a high degree, relies on the underlying mapper that is used for finding chimeric reads. Furthermore, all the available circRNA discovery pipelines are resource intensive.

Results

We introduce CircMiner, a novel stand-alone circRNA detection method that rapidly identifies and filters out linear RNA sequencing reads and detects back-splice junctions. CircMiner employs a rapid pseudo-alignment technique to identify linear reads that originate from transcripts, genes or the genome. CircMiner further processes the remaining reads to identify the back-splice junctions and detect circRNAs with single-nucleotide resolution. We evaluated the efficacy of CircMiner using simulated datasets generated from known back-splice junctions and showed that CircMiner has superior accuracy and speed compared to the existing circRNA detection tools. Additionally, on two RNase R treated cell line datasets, CircMiner was able to detect most of consistent, high confidence circRNAs compared to untreated samples of the same cell line.

Availability and implementation

CircMiner is implemented in C++ and is available online at https://github.com/vpc-ccg/circminer.

Supplementary information

Supplementary data are available at Bioinformatics online.
Contribution of the Entopeduncular Nucleus and the Globus Pallidus to the Control of Locomotion and Visually Guided Gait Modifications in the Cat
Authors: Mullié Yannick , Arto Irène , Yahiaoui Nabiha , Drew Trevor
Published: April 2020

We tested the hypothesis that the entopeduncular (EP) nucleus (feline equivalent of the primate GPi) and the globus pallidus (GPe) contribute to both the planning and execution of locomotion and voluntary gait modifications in the cat. We recorded from 414 cells distributed throughout these two nuclei (referred to together as the pallidum) while cats walked on a treadmill and stepped over an obstacle that advanced towards them. Neuronal activity in many cells in both structures was modulated on a step-by-step basis during unobstructed locomotion and was modified in the step over the obstacle. On a population basis, the most frequently observed change, in both the EP and the GPe, was an increase in activity prior to and/or during the swing phase of the step over the obstacle by the contralateral forelimb, when it was the first limb to pass over the obstacle. Our results support a contribution of the pallidum, in concert with cortical structures, to the control of both the planning and the execution of the gait modifications. We discuss the results in the context of current models of pallidal action on thalamic activity, including the possibility that cells in the EP with increased activity may sculpt thalamo-cortical activity.
First Mildly Ill, Nonhospitalized Case of Coronavirus Disease 2019 (COVID-19) Without Viral Transmission in the United States—Maricopa County, Arizona, 2020
Authors: Scott Sarah E , Zabel Karen , Collins Jennifer , Hobbs Katherine C , Kretschmer Melissa J , Lach Mitchell , Turnbow Katie , Speck Lindsay , White Jessica R , Maldonado Keila , Howard Brandon , Fowler Jeanene , Singh Sonia , Robinson Susan , Pompa Alexandra Peterson , Chatham-Stephens Kevin , Xie Amy , Cates Jordan , Lindstrom Stephen , Lu Xiaoyan , Rolfes Melissa A , Flanagan Marcy , Sunenshine Rebecca ,   for the Maricopa County COVID-19 Case Investigation Team
Published: April 2020

Background

Coronavirus disease 2019 (COVID-19) causes a range of illness severity. Mild illness has been reported, but whether illness severity correlates with infectivity is unknown. We describe the public health investigation of a mildly ill, nonhospitalized COVID-19 case who traveled to China.

Methods

The case was a Maricopa County resident with multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–positive specimens collected on 22 January 2020. Contacts were persons exposed to the case on or after the day before case diagnostic specimen collection. Contacts were monitored for 14 days after last known exposure. High-risk contacts had close, prolonged case contact (≥ 10 minutes within 2 m). Medium-risk contacts wore all US Centers for Disease Control and Prevention–recommended personal protective equipment during interactions. Nasopharyngeal and oropharyngeal (NP/OP) specimens were collected from the case and high-risk contacts and tested for SARS-CoV-2.

Results

Paired case NP/OP specimens were collected for SARS-CoV-2 testing at 11 time points. In 8 pairs (73%), ≥ 1 specimen tested positive or indeterminate, and in 3 pairs (27%) both tested negative. Specimens collected 18 days after diagnosis tested positive. Sixteen contacts were identified; 11 (69%) had high-risk exposure, including 1 intimate contact, and 5 (31%) had medium-risk exposure. In total, 35 high-risk contact NP/OP specimens were collected for SARS-CoV-2 testing; all 35 pairs (100%) tested negative.

Conclusions

This report demonstrates that SARS-CoV-2 infection can cause mild illness and result in positive tests for up to 18 days after diagnosis, without evidence of transmission to close contacts. These data might inform public health strategies to manage individuals with asymptomatic infection or mild illness.
Chinese Investment Treaties in the Belt and Road Initiative Area
Authors: Sornarajah Muthucumaraswamy
Published: April 2020

This article examines whether Chinese practice towards the making of investment treaties with developing countries in the Belt and Road Initiative region will be different from the treaties that it makes with developed States. Though there is a shift towards the making of hard treaties with the developed States of Europe, it is suggested that treaties made with developing States will be more nuanced. The article shows that there are political motives behind investment treaties, as the study of US practice shows. Political considerations will induce China to make different types of treaties with different types of treaty partners in the future. A comparison is made with recent Indian practice.
Correlated structural evolution within multiplex networks
Authors: Wu Haochen , James Ryan G , D’Souza Raissa M
Published: April 2020

Many natural, engineered and social systems can be represented using the framework of a layered network, where each layer captures a different type of interaction between the same set of nodes. The study of such multiplex networks is a vibrant area of research. Yet, understanding how to quantify the correlations present between pairs of layers, and more so present in their co-evolution, is lacking. Such methods would enable us to address fundamental questions involving issues such as function, redundancy, and potential disruptions. Here, we show first how the edge set of a multiplex network can be used to construct an estimator of a joint probability distribution describing edge existence over all layers. We then adapt an information-theoretic measure of general correlation called the conditional mutual information, which uses the estimated joint probability distribution, to quantify the pairwise correlations present between layers. The pairwise comparisons can also be temporal, allowing us to identify if knowledge of a certain layer can provide additional information about the evolution of another layer. We analyse datasets from three distinct domains—economic, political, and airline networks—to demonstrate how pairwise correlation in structure and dynamical evolution between layers can be identified and show that anomalies can serve as potential indicators of major events such as shocks.
Heritable arrhythmia syndromes associated with abnormal cardiac sodium channel function: ionic and non-ionic mechanisms
Authors: Rivaud Mathilde R , Delmar Mario , Remme Carol Ann
Published: April 2020

The cardiac sodium channel NaV1.5, encoded by the SCN5A gene, is responsible for the fast upstroke of the action potential. Mutations in SCN5A may cause sodium channel dysfunction by decreasing peak sodium current, which slows conduction and facilitates reentry-based arrhythmias, and by enhancing late sodium current, which prolongs the action potential and sets the stage for early afterdepolarization and arrhythmias. Yet, some NaV1.5-related disorders, in particular structural abnormalities, cannot be directly or solely explained on the basis of defective NaV1.5 expression or biophysics. An emerging concept that may explain the large disease spectrum associated with SCN5A mutations centres around the multifunctionality of the NaV1.5 complex. In this alternative view, alterations in NaV1.5 affect processes that are independent of its canonical ion-conducting role. We here propose a novel classification of NaV1.5 (dys)function, categorized into (i) direct ionic effects of sodium influx through NaV1.5 on membrane potential and consequent action potential generation, (ii) indirect ionic effects of sodium influx on intracellular homeostasis and signalling, and (iii) non-ionic effects of NaV1.5, independent of sodium influx, through interactions with macromolecular complexes within the different microdomains of the cardiomyocyte. These indirect ionic and non-ionic processes may, acting alone or in concert, contribute significantly to arrhythmogenesis. Hence, further exploration of these multifunctional effects of NaV1.5 is essential for the development of novel preventive and therapeutic strategies.
Sustained subcutaneous delivery of secretome of human cardiac stem cells promotes cardiac repair following myocardial infarction
Authors: Kompa Andrew R , Greening David W , Kong Anne M , McMillan Paul J , Fang Haoyun , Saxena Ritika , Wong Raymond C B , Lees Jarmon G , Sivakumaran Priyadharshini , Newcomb Andrew E , Tannous Bakhos A , Kos Cameron , Mariana Lina , Loudovaris Thomas , Hausenloy Derek J , Lim Shiang Y
Published: April 2020

Aims

To establish pre-clinical proof of concept that sustained subcutaneous delivery of the secretome of human cardiac stem cells (CSCs) can be achieved in vivo to produce significant cardioreparative outcomes in the setting of myocardial infarction.

Methods and results

Rats were subjected to permanent ligation of left anterior descending coronary artery and randomized to receive subcutaneous implantation of TheraCyte devices containing either culture media as control or 1 × 106 human W8B2+ CSCs, immediately following myocardial ischaemia. At 4 weeks following myocardial infarction, rats treated with W8B2+ CSCs encapsulated within the TheraCyte device showed preserved left ventricular ejection fraction. The preservation of cardiac function was accompanied by reduced fibrotic scar tissue, interstitial fibrosis, cardiomyocyte hypertrophy, as well as increased myocardial vascular density. Histological analysis of the TheraCyte devices harvested at 4 weeks post-implantation demonstrated survival of human W8B2+ CSCs within the devices, and the outer membrane was highly vascularized by host blood vessels. Using CSCs expressing plasma membrane reporters, extracellular vesicles of W8B2+ CSCs were found to be transferred to the heart and other organs at 4 weeks post-implantation. Furthermore, mass spectrometry-based proteomic profiling of extracellular vesicles of W8B2+ CSCs identified proteins implicated in inflammation, immunoregulation, cell survival, angiogenesis, as well as tissue remodelling and fibrosis that could mediate the cardioreparative effects of secretome of human W8B2+ CSCs.

Conclusions

Subcutaneous implantation of TheraCyte devices encapsulating human W8B2+ CSCs attenuated adverse cardiac remodelling and preserved cardiac function following myocardial infarction. The TheraCyte device can be employed to deliver stem cells in a minimally invasive manner for effective secretome-based cardiac therapy.
Generalized Forecast Averaging in Autoregressions with a Near Unit Root
Authors: Kejriwal Mohitosh , Yu Xuewen
Published: April 2020

This paper develops a new approach to forecasting a highly persistent time series that employs feasible generalized least squares (FGLS) estimation of the deterministic components in conjunction with Mallows model averaging. Within a local-to-unity asymptotic framework, we derive analytical expressions for the asymptotic mean squared error and one-step-ahead mean squared forecast risk of the proposed estimator and show that the optimal FGLS weights are different from their ordinary least squares (OLS) counterparts. We also provide theoretical justification for a generalized Mallows averaging estimator that incorporates lag order uncertainty in the construction of the forecast. Monte Carlo simulations demonstrate that the proposed procedure yields a considerably lower finite-sample forecast risk relative to OLS averaging. An application to U.S. macroeconomic time series illustrates the efficacy of the advocated method in practice and finds that both persistence and lag order uncertainty have important implications for the accuracy of forecasts.
Sex-specific pattern of left ventricular hypertrophy and diastolic function in patients with type 2 diabetes mellitus
Authors: Wu Mei-Zhen , Chen Yan , Yu Yu-Juan , Zhen Zhe , Liu Ying-Xian , Zou Yuan , Ho Lai-Ming , Lin Qing-Shan , Ng Ming-Yen , Lam Karen Siu-Ling , Tse Hung-Fat , Yiu Kai-Hang
Published: April 2020

Aims 

Few prospective studies have evaluated sex-specific pattern, natural progression of left ventricular (LV) remodelling, and diastolic dysfunction in patients with type 2 diabetes (T2DM). The aim of this study was to study the sex-specific prevalence, longitudinal changes of LV remodelling, and diastolic dysfunction in patients with T2DM. Further, the prognostic value of diastolic function in women and men was also evaluated.

Methods and results 

A total of 350 patients with T2DM (mean age 61 ± 11 years; women, 48.3%) was recruited. Detailed echocardiography was performed at baseline and after 25 months. A major adverse cardiovascular event (MACE) was defined as cardiovascular death, heart failure hospitalization, or myocardial infarction. Despite a similar age, prevalence of hypertension and body mass index, women had a higher prevalence of LV hypertrophy and diastolic dysfunction at baseline and follow-up compared with men. A total of 21 patients developed MACE (5 cardiovascular death, 9 hospitalization for heart failure, and 7 myocardial infarction) during a median follow-up of 56 months. Women with diastolic dysfunction had a higher incidence of MACE than those with normal diastolic function but this association was neutral in men. Multivariable Cox-regression analysis indicated that diastolic dysfunction was associated with MACE in women [hazard ratio = 6.30; 95% confidence interval (CI) = 1.06–37.54; P < 0.05] but not men (hazard ratio = 2.29, 95% CI = 0.67–7.89; P = 0.19).

Conclusion 

LV hypertrophy and diastolic dysfunction, both at baseline and follow-up, were more common in women than men. Pre-clinical diastolic dysfunction was independently associated with MACE only in women with T2DM but was neutral in men.
Clinical outcomes of patients with chronic pulmonary aspergillosis managed surgically
Authors: Setianingrum Findra , Rautemaa-Richardson Riina , Shah Rajesh , Denning David W
Published: April 2020

OBJECTIVES

Surgical resection is one treatment modality for chronic pulmonary aspergillosis (CPA), and sometimes a preoperative presumption of lung cancer turns out to be CPA. We have audited our surgical experience with regard to risk factors for relapse, and the value of postoperative monitoring of Aspergillus-immunogolubulin G (IgG) titres.

METHODS

All patients with CPA surgically treated at National Aspergillosis Centre (NAC), Manchester, UK (2007–2018), were retrospectively evaluated. Surgical procedures, underlying disorders, Aspergillus-IgG titres (ImmunoCap) and antifungal therapy were evaluated for symptom control, operative complications, CPA relapse and mortality.

RESULTS

A total of 61 patients with CPA (28 males, 33 females) were operated on primarily for antifungal therapy failure (51%, n = 31) and presumed lung malignancies (38%, n = 23). Procedures included lobectomy (64%, n = 39), wedge resection (28%, n = 17), segmentectomy (n = 3), pneumonectomy (n = 3) and decortication (n = 2). Overall, 25 (41%) patients relapsed, 26 months (standard deviation: 24.8 months) after surgery. Antifungal therapy before surgery (P = 0.002) or both before and after surgery (P = 0.005) were protective for relapse. The relapse rate within 3 years after surgery (33%, n = 20) was higher than the 3–10 years after surgery (8%, n = 5). At the end of follow-up, the median Aspergillus-IgG titre was lower than at relapse in 12 patients (67 vs 126 mg/l) (P = 0.016).

CONCLUSIONS

Surgery in these selected patients with CPA resulted in favourable outcomes. Relapse is common after surgical treatment of CPA but can be minimized with antifungal therapy, emphasizing the importance of an accurate diagnosis prior to surgery.
Brown adipose tissue and type 2 diabetes
Authors: Levy Stephanie B
Published: April 2020

Recent work proposes that a regimen of repeated mild cold exposure may have protective effects against the development of type II diabetes mellitus (T2D) by activating brown adipose tissue (BAT) metabolism. BAT may protect against by increasing whole-body energy expenditure and insulin sensitivity. An evolutionary perspective, however, highlights several limitations of this hypothesis. Some individuals adapt to acute cold stress by constricting their blood vessels, which leads to high blood pressure. Thus, a regimen of repeated mild cooling may have beneficial health effects for some individuals and negative consequences for others. Future research should examine the relationships between low temperature exposure, BAT metabolism, blood pressure, and type II diabetes risk.