bluuebunny/crossref_metadata_2025 huggingface dataset:
Strategies for Optimizing the Production of Proteins and Peptides with Multiple Disulfide Bonds
Authors: Ma Yunqi , Lee Chang-Joo , Park Jang-Su
Published: August 2020

Bacteria can produce recombinant proteins quickly and cost effectively. However, their physiological properties limit their use for the production of proteins in their native form, especially polypeptides that are subjected to major post-translational modifications. Proteins that rely on disulfide bridges for their stability are difficult to produce in Escherichia coli. The bacterium offers the least costly, simplest, and fastest method for protein production. However, it is difficult to produce proteins with a very large size. Saccharomyces cerevisiae and Pichia pastoris are the most commonly used yeast species for protein production. At a low expense, yeasts can offer high protein yields, generate proteins with a molecular weight greater than 50 kDa, extract signal sequences, and glycosylate proteins. Both eukaryotic and prokaryotic species maintain reducing conditions in the cytoplasm. Hence, the formation of disulfide bonds is inhibited. These bonds are formed in eukaryotic cells during the export cycle, under the oxidizing conditions of the endoplasmic reticulum. Bacteria do not have an advanced subcellular space, but in the oxidizing periplasm, they exhibit both export systems and enzymatic activities directed at the formation and quality of disulfide bonds. Here, we discuss current techniques used to target eukaryotic and prokaryotic species for the generation of correctly folded proteins with disulfide bonds.
Evaluation of Disulfiram Drug Combinations and Identification of Other More Effective Combinations against Stationary Phase Borrelia burgdorferi
Authors: Alvarez-Manzo Hector , Zhang Yumin , Shi Wanliang , Zhang Ying
Published: August 2020

Lyme disease, caused by Borrelia burgdorferi, is the most common vector-borne disease in USA, and 10–20% of patients will develop persistent symptoms despite treatment (“post-treatment Lyme disease syndrome”). B. burgdorferi persisters, which are not killed by the current antibiotics for Lyme disease, are considered one possible cause. Disulfiram has shown to be active against B. burgdorferi, but its activity against persistent forms is not well characterized. We assessed disulfiram as single drug and in combinations against stationary-phase B. burgdorferi culture enriched with persisters. Disulfiram was not very effective in the drug exposure experiment (survival rate (SR) 46.3%) or in combinations. Clarithromycin (SR 41.1%) and nitroxoline (SR 37.5%) were equally effective when compared to the current Lyme antibiotic cefuroxime (SR 36.8%) and more active than disulfiram. Cefuroxime + clarithromycin (SR 25.9%) and cefuroxime + nitroxoline (SR 27.5%) were significantly more active than cefuroxime + disulfiram (SR 41.7%). When replacing disulfiram with clarithromycin or nitroxoline in three-drug combinations, bacterial viability decreased significantly and subculture studies showed that combinations with these two drugs (cefuroxime + clarithromycin/nitroxoline + furazolidone/nitazoxanide) inhibited the regrowth, while disulfiram combinations did not (cefuroxime + disulfiram + furazolidone/nitazoxanide). Thus, clarithromycin and nitroxoline should be further assessed to determine their role as potential treatment alternatives in the future.
Improving the Efficiency of Photodynamic Chemotherapy in Root Canals against Enterococcus faecalis In Vitro
Authors: Tennert Christian , Zinovieva Yoana , Shishkov Kalin , Karygianni Lamprini , Altenburger Makus Jörg , Wierichs Richard J , Al-Ahmad Ali
Published: August 2020

The aim of this study was to evaluate the effect of photoactivated chemotherapy (PACT) on Enterococcus faecalis (E. faecalis) biofilms in root canals using an 90% isopropanol (IPA)-based photosensitizer and removing excess photosensitizer before light incubation. Three hundred and seven extracted human teeth with one root canal were infected with E. faecalis for 72 h and treated in groups: IPA irrigation; PACT; PACT and final rinse with IPA; PACT with photosensitizer removal using either 0.9% NaCl solution or sterile paper points or both; PACT using IPA-based photosensitizer with and without a final rinse of IPA. Root canals were sampled using sterile paper points and dentin chips collected from the root canal walls. Additionally, SEM (Scanning Electron Microscopy) images of the specimens were taken to evaluate the root canal walls for residue bacterial contamination. In all antimicrobial treatment groups treatments E. faecalis counts were significantly reduced in the root canals. Using IPA-based photosensitizer the antimicrobial effect of PACT was significantly enhanced. Irrigation with IPA alone or after PACT significantly increased the antimicrobial effect compared to PACT alone. The collected dentin chips revealed the highest amount of culture negative root canals (10%) after PACT using IPA-based photosensitizer. In the other groups, the culture negative samples ranged from only 0–2 specimens of 30 specimens. REM images show remaining E. faecalis cells on the root canal wall and inside dentin tubules. Using IPA-based photosensitizer significantly enhanced the antimicrobial effect of PACT against E. faecalis in the root canals.
Sulforaphane Inhibits MGO-AGE-Mediated Neuroinflammation by Suppressing NF-κB, MAPK, and AGE–RAGE Signaling Pathways in Microglial Cells
Authors: Subedi Lalita , Lee Jae Hyuk , Gaire Bhakta Prasad , Kim Sun Yeou
Published: August 2020

Advanced glycation end products (AGEs) are produced through the binding of glycated protein or lipid with sugar, and they are known to be involved in the pathogenesis of both age-dependent and independent neurological complications. Among dicarbonyl compounds, methylglyoxal (MGO), which is produced from glucose breakdown, is a key precursor of AGE formation and neurotoxicity. Several studies have shown the toxic effects of bovine serum albumin (BSA)-AGE (prepared with glucose, sucrose or fructose) both in in vitro and in vivo. In fact, MGO-derived AGEs (MGO-AGEs) are highly toxic to neurons and other cells of the central nervous system. Therefore, we aimed to investigate the role of MGO-AGEs in microglial activation, a key inflammatory event, or secondary brain damage in neuroinflammatory diseases. Interestingly, we found that sulforaphane (SFN) as a potential candidate to downregulate neuroinflammation induced by MGO-AGEs in BV2 microglial cells. SFN not only inhibited the formation of MGO-AGEs, but it did not show breaking activity on the MGO-mediated AGEs cross-links with protein, indicating that SFN could potentially trap MGO or inhibit toxic AGE damage. In addition, SFN significantly attenuated the production of neuroinflammatory mediators induced by MGO-AGEs in BV2 microglial cells. SFN also lowered the expression levels of AGE receptor (RAGE) in microglial cells, suggesting that SFN could downregulate MGO-AGE-mediated neurotoxicity at the receptor activation level. Altogether, our current study revealed that SFN might show neuropharmacological potential for downregulating MGO-AGEs-mediated neuronal complications thorough attenuating AGE formation and neuroinflammatory responses induced by MGO-AGEs in vitro.
Properdin Modulates Complement Component Production in Stressed Human Primary Retinal Pigment Epithelium Cells
Authors: Schäfer Nicole , Wolf Hannah N. , Enzbrenner Anne , Schikora Juliane , Reichenthaler Maria , Enzmann Volker , Pauly Diana
Published: August 2020

The retinal pigment epithelium (RPE) maintains visual function and preserves structural integrity of the retina. Chronic dysfunction of the RPE is associated with retinal degeneration, including age-related macular degeneration (AMD). The AMD pathogenesis includes both increased oxidative stress and complement dysregulation. Physiological sources of oxidative stress in the retina are well known, while complement sources and regulation are still under debate. Using human primary RPE (hpRPE) cells, we have established a model to investigate complement component expression on transcript and protein level in AMD-risk and non-risk hpRPE cells. We evaluated the effect of properdin, a complement stabilizer, on the hpRPE cell-dependent complement profile exposed to oxidative stress. hpRPE cells expressed complement components, receptors and regulators. Complement proteins were also stored and secreted by hpRPE cells. We associated AMD-risk single nucleotide polymorphisms with an increased secretion of complement factors D (CFD) and I (CFI). Furthermore, we detected hpRPE cell-associated complement activation products (C3a, C5a) independent of any extracellularly added complement system. Exogenous properdin increased the mRNA expression of CFI and CFD, but decreased levels of complement components (C1Q, C3), receptors (C3AR, C5AR1, CD11B) and inflammation-associated transcripts (NLRP3, IL1B) in hpRPE cells exposed to oxidative stress. This properdin effect was time-dependently counter regulated. In conclusion, our data unveiled a local, genotype-associated complement component production in hpRPE cells, regulated by exogenous properdin. The local complement production and activation via blood-independent mechanisms can be a new therapeutic target for AMD.
An Open-Source Android Application to Measure Anterior–Posterior Knee Translation
Authors: Serrancolí Gil , Bogatikov Peter , Tanyà Palacios Guillem , Torner Jordi , Monllau Joan Carles , Perelli Simone
Published: August 2020

There are widely used standard clinical tests to estimate the instability of an anterior cruciate ligament (ACL) deficient knee by assessing the translation of the tibia with respect to the femur. However, the assessment of those tests could be quite subjective. The goal of this study is to present a universally affordable open-source Android application that is easy and quick. Moreover, it provides the possibility for a quantitative and objective analysis of that instability. The anterior–posterior knee translation of seven subjects was assessed using the open-source Android application developed. A single Android smartphone and the placement of three green skin adhesives are all that is required to use it. The application was developed using the image-processing features of the open-source OpenCV Library. An open-source Android application was developed to measure anterior–posterior (AP) translation in ACL-deficient subjects. The application identified differences in the AP translation between the ipsilateral and the contralateral legs of seven ACL-deficient subjects during Lachman and Pivot–Shift tests. Three out of seven subjects were under anesthesia. Those three were also the ones with significant differences. The application detected differences in the AP translation between the ipsilateral and contralateral legs of subjects with ACL deficiency. The use of the application represents an easy, low-cost, reliable and quick way to assess knee instability quantitatively.
Numerical Investigation of Tip-Vortex Cavitation Noise of an Elliptic Wing Using Coupled Eulerian-Lagrangian Approaches
Authors: Ku Garam , Cheong Cheolung , Seol Hanshin
Published: August 2020

In this study, a numerical methodology is developed to investigate the tip-vortex cavitation of NACA16-020 wings and their flow noise. The numerical method consists of a sequential one-way coupled application of Eulerian and Lagrangian approaches. First, the Eulerian method based on Reynolds-averaged Navier–Stokes equation is applied to predict the single-phase flow field around the wing, with particular emphasis on capturing high-resolution tip-vortex flow structures. Subsequently, the tip-vortex flow field is regenerated by applying the Scully vortex model. Secondly, the Lagrangian approach is applied to predict the tip-vortex cavitation inception and noise of the wing. The initial nuclei are distributed upstream of the wing. The subsequent time-varying size and position of each nucleus are traced by solving spherically symmetric bubble dynamics equations for the nuclei in combination with the flow field predicted from the Eulerian approach. The acoustic pressure at the observer position is computed by modelling each bubble as a point source. The numerical results of the acoustic pressure spectrum are best matched to the measured results when the nuclei number density of freshwater is used. Finally, the current numerical method is applied to the flows of various cavitation numbers. The results reveal that the cavitation inception determined by the predicted acoustic pressure spectrum well matched the experimental result.
An Enhanced pix2pix Dehazing Network with Guided Filter Layer
Authors: Bu Qirong , Luo Jie , Ma Kuan , Feng Hongwei , Feng Jun
Published: August 2020

In this paper, we propose an enhanced pix2pix dehazing network, which generates clear images without relying on a physical scattering model. This network is a generative adversarial network (GAN) which combines multiple guided filter layers. First, the input of hazy images is smoothed to obtain high-frequency features according to different smoothing kernels of the guided filter layer. Then, these features are embedded in higher dimensions of the network and connected with the output of the generator’s encoder. Finally, Visual Geometry Group (VGG) features are introduced to serve as a loss function to improve the quality of the texture information restoration and generate better hazy-free images. We conduct experiments on NYU-Depth, I-HAZE and O-HAZE datasets. The enhanced pix2pix dehazing network we propose produces increases of 1.22 dB in the Peak Signal-to-Noise Ratio (PSNR) and 0.01 in the Structural Similarity Index Metric (SSIM) compared with a second successful comparison method using the indoor test dataset. Extensive experiments demonstrate that the proposed method has good performance for image dehazing.
Investigations of Adhesion under Different Slider-Lube/Disk Contact States at the Head–Disk Interface
Authors: Zhang Yuyan , Jiang Ling , Yang Weixu , Ma Chenbo , Yu Qiuping
Published: August 2020

Adhesion is the key factor influencing the failure of the hard disk drive operating under ultra-low flying height. In order to mitigate the negative effects of adhesion at the head–disk interface (HDI) and promote further development of the thermal flying height control (TFC) technology, an adhesive contact model based on the Lifshitz theory accounting for the thermal protrusion (TP) geometry of TFC slider, the layered structures of the head and disk, and the operation states of the slider was proposed to investigate the static contact characteristics at the HDI. The simulation results demonstrated the undesirable unstable regions during the transitions between different operation states and the necessity of applying TFC technology. The reduction in the head–media spacing (HMS) was found to be achieved by properly increasing the TP height, decreasing the thickness of the lubricant layer or the thickness of the diamond–like carbon (DLC) layer during the flying state or the TP–lube contact state. At the TP–DLC contact regime, the attractive interaction was stronger than other states, and the strong repulsive interaction made the HMS difficult to be further reduced through the increase in the TP height or the decrease in the lubricant thickness.
Characteristic Analysis and Co-Validation of Hydro-Mechanical Continuously Variable Transmission Based on the Wheel Loader
Authors: Wan Lirong , Dai Hanzheng , Zeng Qingliang , Sun Zhiyuan , Tian Mingqian
Published: August 2020

Energy-saving and emission reduction has become the theme of the world. The wheel loader has a harsh working environment, complicated working conditions, and drastic changes in load, and the performance of the engine cannot be fully utilized. Therefore, the variable speed transmission of vehicles plays a vital role in improving the efficiency and performance of the vehicle. This paper establishes the general characteristic equations for the input coupling type of hydro-mechanical continuously variable transmission (HMCVT) based on the wheel loader and determines reasonable structural forms for connection of working conditions. It establishes the general efficiency equation for the reasonable structural form for efficiency analysis and presents a method of co-validation of the simulation and test for making the results of efficiency more accurate. Through this method, the transmission performance is more accurately analyzed, which provides an important guiding role and validation for the early design of HMCVT. Eventually, it gets reasonably optimized products and reduces the design cost and cycle.
A2C: Attention-Augmented Contrastive Learning for State Representation Extraction
Authors: Chen Haoqiang , Liu Yadong , Zhou Zongtan , Zhang Ming
Published: August 2020

Reinforcement learning (RL) faces a series of challenges, including learning efficiency and generalization. The state representation used to train RL is one of the important factors causing these challenges. In this paper, we explore providing a more efficient state representation for RL. Contrastive learning is used as the representation extraction method in our work. We propose an attention mechanism implementation and extend an existing contrastive learning method by embedding the attention mechanism. Finally an attention-augmented contrastive learning method called A2C is obtained. As a result, using the state representation from A2C, the robot achieves better learning efficiency and generalization than those using state-of-the-art representations. Moreover, our attention mechanism is proven to be able to calculate the correlation of arbitrary distance among pixels, which is conducive to capturing more accurate obstacle information. What is more, we remove the attention mechanism from A2C. It is shown that the rewards available for the attention-removed A2C are reduced by more than 70%, which indicates the important role of the attention mechanism.
Numerical 3D Simulation of a Full System Air Core Compulsator-Electromagnetic Rail Launcher
Authors: Consolo Valentina , Musolino Antonino , Rizzo Rocco , Sani Luca
Published: August 2020

Multiphysics problems represent an open issue in numerical modeling. Electromagnetic launchers represent typical examples that require a strongly coupled magnetoquasistatic and mechanical approach. This is mainly due to the high velocities which make comparable the electrical and the mechanical response times. The analysis of interacting devices (e.g., a rail launcher and its feeding generator) adds further complexity, since in this context the substitution of one device with an electric circuit does not guarantee the accuracy of the analysis. A simultaneous full 3D electromechanical analysis of the interacting devices is often required. In this paper a numerical 3D analysis of a full launch system, composed by an air-core compulsator which feeds an electromagnetic rail launcher, is presented. The analysis has been performed by using a dedicated, in-house developed research code, named “EN4EM” (Equivalent Network for Electromagnetic Modeling). This code is able to take into account all the relevant electromechanical quantities and phenomena (i.e., eddy currents, velocity skin effect, sliding contacts) in both the devices. A weakly coupled analysis, based on the use of a zero-dimensional model of the launcher (i.e., a single loop electrical equivalent circuit), has been also performed. Its results, compared with those by the simultaneous 3D analysis of interacting devices, show an over-estimate of about 10–15% of the muzzle speed of the armature.
Integrated MASW and ERT Imaging for Geological Definition of an Unconfined Alluvial Aquifer Sustaining a Coastal Groundwater-Dependent Ecosystem in Southwest Portugal
Authors: Paz Maria , Alcalá Francisco , Medeiros Ana , Martínez-Pagán Pedro , Pérez-Cuevas Jaruselsky , Ribeiro Luís
Published: August 2020

This paper integrates multichannel analysis of surface waves (MASW) and time-lapse electrical resistivity tomography (ERT) to define aquifer geometry and identify transient groundwater features of the Cascalheira Stream Basin Holocene alluvial aquifer (aquifer H), which contributes to the Santo André Lagoon, part of a coastal groundwater-dependent ecosystem (GDE), located in southwest Portugal. MASW measures shear-wave velocity (VS), allowing one to obtain steady geological models of the subsurface, and ERT measures subsurface electrical resistivity (ER), being subjected to ambient changes. MASW enables disambiguation of geological structures in low ER environments, such as coastal areas. This research covered one natural year and involved one MASW campaign, four ERT campaigns, and additional geological field surveys and groundwater monitoring to assist interpretation of results. In the area, the conjugate NW–SE and NE–SW strike-slip fault systems determine compartmentalization of geological structures and subsequent accommodation space for Holocene sedimentation. MASW and ERT surveys show how the NW–SE system deepens these structures toward the coast, whereas the NE–SW system generates small horsts and grabens, being one of these occupied by aquifer H. From upstream to downstream, aquifer H thickness and width increase from 10 m to 12 m and from 140 m to 240 m, respectively. Performance of VS and ER models was satisfactory, with a normalized error of the VR and ER models in the 0.01–0.09 range, meaning that a quantitative quota of uncertainty can be segregated from the overall uncertainty of groundwater models without substantially affecting its simulations accuracy. This methodology seeks to improve the design of shallow groundwater research in GDE preservation policies.
Development of Multi-DOF Model of Automotive LED Headlamp Assembly for Force Transmission Prediction Using MATLAB GUI
Authors: Din Muhammad Moghees Ud , Kim Byeongil
Published: August 2020

The use of Light-emitting diodes (LEDs) in automobile headlamps began two decades ago. Since then, several design and efficiency improvements have been made. However, the reliability and durability of these LED systems remain uncertain. There are several approaches for reliability analysis, e.g., thermal, electrical, optical, or structural. The first three issues have been studied in the past, but there has been minimal focus on structural and dynamic durability. Uneven road conditions and impact forces acting on the headlamp module can damage components and misalign the aiming mechanism. Moreover, the functionality could be disturbed, thereby decreasing the efficiency of the system. To determine the forces acting inside the module on each component, this study proposes a simulation technique for predicting the magnitude of forces transmitted from the automobile chassis to the headlamp module under even and uneven road conditions. A vibration system with 23 degrees-of-freedom is developed and equations of motion are derived using Newton’s second law of motion. Solving this system of equations with Simulink and MATLAB provided the linear and angular displacements of each element, which were then utilized to calculate the forces transmitted through these elements. Two forcing conditions were compared and the locations with maximum forces are highlighted.
An Auditory-Perceptual and Pupillometric Study of Vocal Strain and Listening Effort in Adductor Spasmodic Dysphonia
Authors: Farahani Mojgan , Parsa Vijay , Herrmann Björn , Kadem Mason , Johnsrude Ingrid , Doyle Philip C.
Published: August 2020

This study evaluated ratings of vocal strain and perceived listening effort by normal hearing participants while listening to speech samples produced by talkers with adductor spasmodic dysphonia (AdSD). In addition, objective listening effort was measured through concurrent pupillometry to determine whether listening to disordered voices changed arousal as a result of emotional state or cognitive load. Recordings of the second sentence of the “Rainbow Passage” produced by talkers with varying degrees of AdSD served as speech stimuli. Twenty naïve young adult listeners perceptually evaluated these stimuli on the dimensions of vocal strain and listening effort using two separate visual analogue scales. While making the auditory-perceptual judgments, listeners’ pupil characteristics were objectively measured in synchrony with the presentation of each voice stimulus. Data analyses revealed moderate-to-high inter- and intra-rater reliability. A significant positive correlation was found between the ratings of vocal strain and listening effort. In addition, listeners displayed greater peak pupil dilation (PPD) when listening to more strained and effortful voice samples. Findings from this study suggest that when combined with an auditory-perceptual task, non-volitional physiologic changes in pupil response may serve as an indicator of listening and cognitive effort or arousal.
Overview of Compressed Sensing: Sensing Model, Reconstruction Algorithm, and Its Applications
Authors: Li Lixiang , Fang Yuan , Liu Liwei , Peng Haipeng , Kurths Jürgen , Yang Yixian
Published: August 2020

With the development of intelligent networks such as the Internet of Things, network scales are becoming increasingly larger, and network environments increasingly complex, which brings a great challenge to network communication. The issues of energy-saving, transmission efficiency, and security were gradually highlighted. Compressed sensing (CS) helps to simultaneously solve those three problems in the communication of intelligent networks. In CS, fewer samples are required to reconstruct sparse or compressible signals, which breaks the restrict condition of a traditional Nyquist–Shannon sampling theorem. Here, we give an overview of recent CS studies, along the issues of sensing models, reconstruction algorithms, and their applications. First, we introduce several common sensing methods for CS, like sparse dictionary sensing, block-compressed sensing, and chaotic compressed sensing. We also present several state-of-the-art reconstruction algorithms of CS, including the convex optimization, greedy, and Bayesian algorithms. Lastly, we offer recommendation for broad CS applications, such as data compression, image processing, cryptography, and the reconstruction of complex networks. We discuss works related to CS technology and some CS essentials.
Optical Amplifiers for Access and Passive Optical Networks: A Tutorial
Authors: Horvath Tomas , Radil Jan , Munster Petr , Bao Ning-Hai
Published: August 2020

For many years, passive optical networks (PONs) have received a considerable amount of attention regarding their potential for providing broadband connectivity, especially in remote areas, to enable better life conditions for all citizens. However, it is essential to augment PONs with new features to provide high-quality connectivity without any transmission errors. For these reasons, PONs should exploit technologies for multigigabit transmission speeds and distances of tens of kilometers, which are costly features previously reserved for long-haul backbone networks only. An outline of possible optical amplification methods (2R) and electro/optical methods (3R) is provided with respect to specific conditions of deployment of PONs. We suggest that PONs can withstand such new requirements and utilize new backbone optical technologies without major flaws, such as the associated high cost of optical amplifiers. This article provides a detailed principle explanation of 3R methods (reamplification, reshaping, and retiming) to reach the extension of passive optical networks. The second part of the article focuses on optical amplifiers, their advantages and disadvantages, deployment, and principles. We suggest that PONs can satisfy such new requirements and utilize new backbone optical technologies without major flaws, such as the associated high cost.
BIM-Based Spatial Augmented Reality (SAR) for Architectural Design Collaboration: A Proof of Concept
Authors: Jin Yixuan , Seo JoonOh , Lee Jin Gang , Ahn Seungjun , Han SangUk
Published: August 2020

Three-dimensional (3D) visualization technology, such as augmented reality (AR), has served as the display for building information modeling (BIM)-based architectural design collaboration to provide more effective design observation and communication for stakeholders. That said, AR has several technical limitations in terms of personal device issues, user experience, and visualization quality. A new form of AR called spatial augmented reality (SAR) has been introduced to address these issues, which uses a digital projector to present graphics on physical objects for augmenting real-world objects. Therefore, SAR has great benefits and potentials to combine with BIM for design collaboration. This paper introduces a BIM-based SAR operational framework, where 3D building models generated from BIM software are imported to projection mapping tools to display building surface textures on physical white building models. A case study using Revit and 3ds Max as the BIM software, and MadMapper as the projection mapping tool, was conducted to demonstrate the feasibility of the proposed framework and to evaluate the projection performance of SAR. The case study showed that the texture of BIM models could be projected on the objects clearly and realistically. Additionally, the proposed SAR method potentially offers intuitive observation of building models and comfortable wear-free experience for collaborative design, and the qualitative analysis by changing the parameters was conducted to test the different projection conditions. Since it is expected that the use of SAR can be promoted by overcoming the discussed technical limitations and possible solution application, this study aims to traceability provide the whole process of BIM-based SAR for architectural design collaboration.
Solving Partial Differential Equations Using Deep Learning and Physical Constraints
Authors: Guo Yanan , Cao Xiaoqun , Liu Bainian , Gao Mei
Published: August 2020

The various studies of partial differential equations (PDEs) are hot topics of mathematical research. Among them, solving PDEs is a very important and difficult task. Since many partial differential equations do not have analytical solutions, numerical methods are widely used to solve PDEs. Although numerical methods have been widely used with good performance, researchers are still searching for new methods for solving partial differential equations. In recent years, deep learning has achieved great success in many fields, such as image classification and natural language processing. Studies have shown that deep neural networks have powerful function-fitting capabilities and have great potential in the study of partial differential equations. In this paper, we introduce an improved Physics Informed Neural Network (PINN) for solving partial differential equations. PINN takes the physical information that is contained in partial differential equations as a regularization term, which improves the performance of neural networks. In this study, we use the method to study the wave equation, the KdV–Burgers equation, and the KdV equation. The experimental results show that PINN is effective in solving partial differential equations and deserves further research.
Peak Fitting Applied to Fourier Transform Infrared and Raman Spectroscopic Analysis of Proteins
Authors: Sadat Azin , Joye Iris J.
Published: August 2020

FTIR and Raman spectroscopy are often used to investigate the secondary structure of proteins. Focus is then often laid on the different features that can be distinguished in the Amide I band (1600–1700 cm−1) and, to a lesser extent, the Amide II band (1510–1580 cm−1), signature regions for C=O stretching/N-H bending, and N-H bending/C-N stretching vibrations, respectively. Proper investigation of all hidden and overlapping features/peaks is a necessary step to achieve reliable analysis of FTIR and FT-Raman spectra of proteins. This paper discusses a method to identify, separate, and quantify the hidden peaks in the amide I band region of infrared and Raman spectra of four globular proteins in aqueous solution as well as hydrated zein and gluten proteins. The globular proteins studied, which differ widely in terms of their secondary structures, include immunoglobulin G, concanavalin A, lysozyme, and trypsin. Peak finding was done by analysis of the second derivative of the original spectra. Peak separation and quantification was achieved by curve fitting using the Voigt function. Structural data derived from the FT-Raman and FTIR analyses were compared to literature reports on protein structure. This manuscript proposes an accurate method to analyze protein secondary structure based on the amide I band in vibrational spectra.
Coproducing Weather Forecast Information with and for Smallholder Farmers in Ghana: Evaluation and Design Principles
Authors: Gbangou Talardia , Sarku Rebecca , Slobbe Erik Van , Ludwig Fulco , Kranjac-Berisavljevic Gordana , Paparrizos Spyridon
Published: August 2020

Many West African farmers are struggling to cope with changing weather and climatic conditions. This situation limits farmers’ ability to make optimal decisions for food and income security. Developing more useful and accessible weather and climate information services (WCIS) can help small-scale farmers improve their adaptive capacity. The literature suggests that such WCIS can be achieved if forecast information is produced jointly by farmers and scientists. To test this hypothesis and derive design requirements for effective WCIS, we evaluated the outcomes of an experimental coproduction of weather forecasts in Ada, Ghana. The experiment involved a user-driven design and testing of information and communications technology (ICT)-based digital (smartphones and apps) and rainfall monitoring tools by 22 farmers. They collected data and received weather forecasts during the 2018/2019 study period. The results showed a positive evaluation of the intervention, expressed by the level of engagement, the increase in usability of the tools and understanding of forecast uncertainty, outreach capacity with other farmers, and improved daily farming decisions. The success of the intervention was attributed to the iterative design process, as well as the training, monitoring, and technical support provided. We conclude that the application of modern technology in a coproduction process with targeted training and monitoring can improve smallholder farmers’ access to and use of weather and climate forecast information.
Source–Receptor Relationships and Cluster Analysis of CO2, CH4, and CO Concentrations in West Africa: The Case of Lamto in Côte d’Ivoire
Authors: Tiemoko Dro Touré , Yoroba Fidèle , Paris Jean-Daniel , Diawara Adama , Berchet Antoine , Pison Isabelle , Riandet Aurélie , Ramonet Michel
Published: August 2020

The contribution in terms of long-range transport of CO2, CH4, and CO concentrations to measurements at Lamto (5°02′ W–6°13′ N) was analyzed for the 2014–2017 period using the FLEXPART model that calculates the retro-plumes of air masses arriving at the station. The identification of the source-receptor relationships was also studied with a clustering technique applied on those retro-plumes. This clustering technique enabled us to distinguish four categories of air mass transports arriving at Lamto site described as follows: oceanic and maritime origin (≈37% of the retro-plumes), continental origin (≈21%), and two hybrid clusters (≈42%). The results show that continental emission sources contribute significantly to the increases in concentrations of CO2, CH4, and CO and explain ≈40% of their variance. These emission sources are predominantly from north and north-east directions of the measurement point, and where densely populated and economically developed areas are located. In addition, the transport of air masses from these directions lead to the accumulation of CO2, CH4, and CO. Furthermore, the ratios ΔCO/ΔCH4 and ΔCO/ΔCO2 observed in the groups associated with Harmattan flows clearly show an influence of combustion processes on the continent. Thus, the grouping based on FLEXPART footprints shows an advantage compared to the use of simple trajectories for analyzing source–receptor relationships.
Variation of Projected Atmospheric Water Vapor in Central Asia Using Multi-Models from CMIP6
Authors: Li Zhenjie , Tao Hui , Hartmann Heike , Su Buda , Wang Yanjun , Jiang Tong
Published: August 2020

Using data from the Integrated Global Radiosonde Archive Version 2 (IGRA2) and the Multi Model Ensemble (MME) of four global climate models (GCMs), named CanESM5, IPSL-CM6A-LR, MIROC6, and MRI-ESM2-0, within the framework of phase 6 of the Coupled Model Intercomparison Project (CMIP6), we analyzed the changes in atmospheric total column water vapor (TCWV) over Central Asia in the future (2021–2100) under SSP-RCPs scenarios: SSP1-1.9, SSP1-2.6, SSP2-4.5, SSP3-7.0, SSP4-3.4, SSP4-6.0, and SSP5-8.5, relative to baseline period (1986–2005). Results showed that the annual mean TCWV from IGRA2 was consistent with the model output from 1979 to 2014 in Central Asia. Besides, the spatial distribution of TCWV in Central Asia during the baseline period was consistent between the models. The regional average value of Central Asia was between 10.8 mm and 12.4 mm, and decreased with elevation. TCWV will increase under different SSP-RCPs from 2021 to 2040, but showed different trends after 2040. It will increase under SSP1-1.9 and SSP1-2.6 scenarios from 2021 to 2050, and decrease after that. It will grow from 2021 to 2055 under SSP4-3.4 scenario, and then stay essentially constant. Under SSP2-4.5 and SSP4-6.0 scenarios, TCWV will rise rapidly during 2021–2065, but the growth will decline from 2065 to 2100. TCWV will continue to increase under SSP3-7.0 and SSP5-8.5 scenarios, and the largest increase is projected under SSP5-8.5 scenario. Change in near-surface temperature (Ts) matched the change in TCWV, but changes in precipitation and evapotranspiration are not significant during 2021–2100. In spite of the large variations in TCWV under different SSP-RCPs, the dominant characteristic in all scenarios shows that a large TCWV increase is demonstrated over areas with small TCWV amounts during the baseline period. On the contrary, increases will be small where the TCWV amounts had been large during the baseline period. The change in TCWV is highly correlated to the increase in Ts in Central Asia. Under SSP2-4.5, SSP3-7.0, SSP4-3.4, SSP4-6.0, and SSP5-8.5 scenarios, the higher the temperature due to higher radiative forcing, the steeper the regression slope between TCWV and Ts change. It is closest to the theoretical value of the Clausius-Clapeyron equation under SSP3-7.0 and SSP5-8.5 scenarios, but not presented under other scenarios. Spatially, steeper regression slopes during 2021–2100 have been found around the Caspian Sea in the southwest and in the high-elevation areas in the southeast of Central Asia, which is likely related to the abundant local water supply for evaporation.
Investigating Curcumin/Intestinal Epithelium Interaction in a Millifluidic Bioreactor
Authors: Costa Joana , Almonti Vanessa , Cacopardo Ludovica , Poli Daniele , Rapposelli Simona , Ahluwalia Arti
Published: August 2020

Multidrug resistance is still an obstacle for chemotherapeutic treatments. One of the proteins involved in this phenomenon is the P-glycoprotein, P-gp, which is known to be responsible for the efflux of therapeutic substances from the cell cytoplasm. To date, the identification of a drug that can efficiently inhibit P-gp activity remains a challenge, nevertheless some studies have identified natural compounds suitable for that purpose. Amongst them, curcumin has shown an inhibitory effect on the protein in in vitro studies using Caco-2 cells. To understand if flow can modulate the influence of curcumin on the protein’s activity, we studied the uptake of a P-gp substrate under static and dynamic conditions. Caco-2 cells were cultured in bioreactors and in Transwells and the basolateral transport of rhodamine-123 was assessed in the two systems as a function of the P-gp activity. Experiments were performed with and without pre-treatment of the cells with an extract of curcumin or an arylmethyloxy-phenyl derivative to evaluate the inhibitory effect of the natural substance with respect to a synthetic compound. The results indicated that the P-gp activity of the cells cultured in the bioreactors was intrinsically lower, and that the effect of both natural and synthetic inhibitors was up modulated by the presence of flow. Our study underlies the fact that the use of more sophisticated and physiologically relevant in vitro models can bring new insights on the therapeutic effects of natural substances such as curcumin.
Aptasensors for Point-of-Care Detection of Small Molecules
Authors: Prante Marc , Segal Ester , Scheper Thomas , Bahnemann Janina , Walter Johanna
Published: August 2020

Aptamers, a group of nucleic acids which can specifically bind to a target molecule, have drawn extensive interest over the past few decades. For analytics, aptamers represent a viable alternative to gold-standard antibodies due to their oligonucleic nature combined with advantageous properties, including higher stability in harsh environments and longer shelf-life. Indeed, over the last decade, aptamers have been used in numerous bioanalytical assays and in various point-of-care testing (POCT) platforms. The latter allows for rapid on-site testing and can be performed outside a laboratory by unskilled labor. Aptamer technology for POCT is not limited just to medical diagnostics; it can be used for a range of applications, including environmental monitoring and quality control. In this review, we critically examine the use of aptamers in POCT with an emphasis on their advantages and limitations. We also examine the recent success of aptasensor technology and how these findings pave the way for the analysis of small molecules in POCT and other health-related applications. Finally, the current major limitations of aptamers are discussed, and possible approaches for overcoming these challenges are presented.
Autonomic Changes in Juvenile-Onset Huntington’s Disease
Authors: Schultz Jordan L. , Nopoulos Peg C.
Published: August 2020

Patients with adult-onset Huntington’s Disease (AOHD) have been found to have dysfunction of the autonomic nervous system that is thought to be secondary to neurodegeneration causing dysfunction of the brain–heart axis. However, this relationship has not been investigated in patients with juvenile-onset HD (JOHD). The aim of this study was to compare simple physiologic measures between patients with JOHD (n = 27 participants with 64 visits) and participants without the gene expansion that causes HD (GNE group; n = 259 participants with 395 visits). Using data from the Kids-JOHD study, we compared mean resting heart rate (rHR), systolic blood pressure (SBP), and diastolic blood pressure (DBP) between the JOHD and GNE groups. We also divided the JOHD group into those with childhood-onset JOHD (motor diagnosis received before the age of 13, [n = 16]) and those with adolescent-onset JOHD (motor diagnosis received at or after the age of 13 [n = 11]). We used linear mixed-effects models to compare the group means while controlling for age, sex, and parental socioeconomic status and including a random effect per participant and family. For the primary analysis, we found that the JOHD group had significant increases in their rHR compared to the GNE group. Conversely, the JOHD group had significantly lower SBP compared to the GNE group. The JOHD group also had lower DBP compared to the GNE group, but the results did not reach significance. SBP and DBP decreased as disease duration of JOHD increased, but rHR did not continue to increase. Resting heart rate is more sensitive to changes in autonomic function as compared to SBP. Therefore, these results seem to indicate that early neurodegenerative changes of the central autonomic network likely lead to an increase in rHR while later progression of JOHD leads to changes in blood pressure. We hypothesize that these later changes in blood pressure are secondary to neurodegeneration in brainstem regions such as the medulla.
Emotional Dysregulation in Adolescents: Implications for the Development of Severe Psychiatric Disorders, Substance Abuse, and Suicidal Ideation and Behaviors
Authors: De Berardis Domenico , Fornaro Michele , Orsolini Laura , Ventriglio Antonio , Vellante Federica , Di Giannantonio Massimo
Published: August 2020

Well-tuned emotional regulation is fundamental for human life and psychological well-being. Negative physiological emotions are counterbalanced by positive ones, and this equilibrium is the mainstay of human physiological affective states. However, this mechanism may sometimes become dysfunctional when negative emotions are not correctly counterbalanced, causing maladaptive behaviors, especially during adolescence. A very interesting review by Young et al. was recently published (Brain Sci.2019, 9(4), 76) and stimulated us to reflect on this topic. The screening for emotional disturbances and dysregulation in adolescents must be included in all the preventive and interventional programs aimed to achieve both physical and psychological well-being of the population and early intervention should be provided in order to avoid progression toward clinically relevant psychiatric disorders in late adolescence and adulthood.
Detection of Germline Mutations in a Cohort of 139 Patients with Bilateral Breast Cancer by Multi-Gene Panel Testing: Impact of Pathogenic Variants in Other Genes beyond BRCA1/2
Authors: Fanale Daniele , Incorvaia Lorena , Filorizzo Clarissa , Bono Marco , Fiorino Alessia , Calò Valentina , Brando Chiara , Corsini Lidia Rita , Barraco Nadia , Badalamenti Giuseppe , Russo Antonio , Bazan Viviana
Published: August 2020

Patients with unilateral breast cancer (UBC) have an increased risk of developing bilateral breast cancer (BBC). The annual risk of contralateral BC is about 0.5%, but increases by up to 3% in BRCA1 or BRCA2 pathogenic variant (PV) carriers. Our study was aimed to evaluate whether all BBC patients should be offered multi-gene panel testing, regardless their cancer family history and age at diagnosis. We retrospectively collected all clinical information of 139 BBC patients genetically tested for germline PVs in different cancer susceptibility genes by NGS-based multi-gene panel testing. Our investigation revealed that 52 (37.4%) out of 139 BBC patients harbored germline PVs in high- and intermediate-penetrance breast cancer (BC) susceptibility genes including BRCA1, BRCA2, PTEN, PALB2, CHEK2, ATM, RAD51C. Nineteen out of 53 positively tested patients harbored a PV in a known BC susceptibility gene (no-BRCA). Interestingly, in the absence of an analysis performed via multi-gene panel, a significant proportion (14.4%) of PVs would have been lost. Therefore, offering a NGS-based multi-gene panel testing to all BBC patients may significantly increase the detection rates of germline PVs in other cancer susceptibility genes beyond BRCA1/2, avoiding underestimation of the number of individuals affected by a hereditary tumor syndrome.
TIM-3 Expression Is Downregulated on Human NK Cells in Response to Cancer Targets in Synergy with Activation
Authors: Dao Tram N. , Utturkar Sagar , Atallah Lanman Nadia , Matosevic Sandro
Published: August 2020

Among natural killer (NK) cell receptors, the T-cell immunoglobulin and mucin-containing domain (TIM-3) has been associated with both inhibitory and activating functions, depending on context and activation pathway. Ex vivo and in vitro, expression of TIM-3 is inducible and depends on activation stimulus. Here, we report that TIM-3 expression can be downregulated on NK cells under specific conditions. When NK cells are exposed to cancer targets, they synergize with stimulation conditions to induce a substantial decrease in TIM-3 expression on their surface. We found that such downregulation occurs following prior NK activation. Downregulated TIM-3 expression correlated to lower cytotoxicity and lower interferon gamma (IFN-γ) expression, fueling the notion that TIM-3 might function as a benchmark for human NK cell dysfunction.