bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Method to Model Outbreaks of New Infectious Diseases with Pandemic Potential such as COVID-19
Authors: Odendaal Willem G. 
Published: March 2020

AbstractThe emergence of the novel coronavirus (a.k.a. COVID-19, SARS-CoV-2) out of Wuhan, Hubei Province, China caught the world by surprise. As the outbreak began to spread outside of China, too little was known about the virus to model its transmission with any acceptable accuracy. World governments responded to rampant misinformation about the virus leading to collateral disasters, such as plunging financial markets, that could have been avoided if better models of the outbreak had been available. This is an engineering approach to model the spread of a new infectious disease from sparse data when little is known about the infectious agent itself. The paper is not so much about the model itself - because there are many good scientific approaches to model an epidemic - as it is about crunching numbers when there are barely any numbers to crunch. The coronavirus outbreak in USA is used to illustrate the implementation of this modeling approach. A Monte Carlo approach is implemented by using incubation period and testing efficiency as variables. Among others it is demonstrated that imposing early travel restrictions from infected countries slowed down the outbreak in the USA by about 26 days.
Preliminary evaluation of voluntary event cancellation as a countermeasure against the COVID-19 outbreak in Japan as of 11 March, 2020
Authors: Sugishita Yoshiyuki , Kurita Junko , Sugawara Tamie , Ohkusa Yasushi 
Published: March 2020

AbstractBackgroundTo control COVID-19 outbreak in Japan, sports and entertainment events were canceled in Japan for two weeks from 26 February to 11 March. It has been designated as voluntary event cancellation (VEC).ObjectThis study predicts the effectiveness of VEC enduring and after its implementation.MethodWe applied a simple susceptible–infected–recovery model to data of patients with symptoms in Japan during 14 January to VEC introduction and after VEC introduction to 8 March. We adjusted the reporting delay in the latest few days.ResultsResults suggest that the basic reproduction number, R0, before VEC introduced as 2.50 with a 95% confidence interval (CI) was [2.43, 2.55] and the effective reproduction number, Rv, after VEC introduced as 1. 88; its 95% CI was [1.68,2.02].Discussion and ConclusionResults demonstrated that VEC can reduce COVID-19 infectiousness by 35%, but R0 remains higher than one.
The biomedical sensor Cell-Fit-HD4D, reveals individual tumor cell fate in response to microscopic ion deposition
Authors: Niklas M , Schlegel J , Liew H , Walsh DWM , Zimmermann F , Dzyubachyk O , Holland-Letz T , Rahmanian S , Greilich S , Runz A , Debus J , Abdollahi A 
Published: March 2020

AbstractHere we present the biomedical sensorcell-fluorescentiontrackhybriddetector4D(Cell-Fit-HD4D)to reveal individual tumor cell fate in response to microscopic ion deposition in ion beam therapy. The sensor enables long-term monitoring of single tumor cells after clinical ion beam irradiation in combination with single-cell dosimetry.Cell-Fit-HD4Dis read outin-situby conventional optical microscopy. Direct visualization of a clinical ion beam is hereby possible for the first time. The possibility to reveal fate of individual cells from a cell cohort demonstrates that our biomedical sensor clearly differs from conventional experiments that characterize cellular response after radiation on a population level.Cell-Fit-HD4Dis therefore used to mimics the clinical situation of a defined tumor depth during tumor treatment by ion beam therapy. Our biomedical sensor is able to provide crucial input for current mechanistic approaches to biophysical modelling of the effect of ionizing radiation on biological matter. In the clinical context, obtaining multi-dimensional physical and biological information on individual tumor cells is an important step to further transform ion beam therapy into a highly precise discipline within oncology.
Elucidating Direct Kinase Targets of Compound Danshen Dropping Pills Employing Archived Data and Prediction Models
Authors: Wang Tongxing , Liang Lu , Zhao Chunlai , Sun Jia , Wang Hairong , Wang Wenjia , Lin Jianping , Hu Yunhui 
Published: March 2020

AbstractThe research on the direct target of traditional Chinese medicine (TCM) is the key to study the mechanism and material basis of TCM, but there is still no effective technical methods at present. For Compound Danshen dropping pills (CDDP), there is no report about its direct targets. In this study, the direct targets of CDDP were studied for the first time, especially focusing on the protein kinase family, which plays causal roles in a variety of human disease. Firstly, the literature database of CDDP was constructed by literature retrieval, and the important components contained in CDDP were extracted. Secondly, the potential direct targets of important components was obtained through querying public database and predicted by Multi-voting SEA algorithm. Then, the KinomeX system was used to predict and to filter the potential kinase targets of CDDP. Finally, the experimental verification was carried out. In total, 30 active kinase targets was obtained at 25 μg/ml concentration of CDDP, and 9 dose-dependent targets were obtained at 250 μg/ml concentration of CDDP. This is an efficient and accurate strategy by integrating the targets recorded in several public databases and the targets calculated by two in silico modelling approaches predict potential direct targets of TCM, which can lay an important foundation for the study of the mechanism and material basis of them, promoting the modernization of TCM.
Maturational trajectories of white matter microstructure underlying the right presupplementary motor area reflect individual improvements in motor response cancellation in children and adolescents
Authors: Madsen Kathrine Skak , Johansen Louise Baruël , Thompson Wesley K. , Siebner Hartwig R. , Jernigan Terry L. , Baaré William F. C. 
Published: March 2020

AbstractThe ability to effectively suppress motor response tendencies is essential for focused and goal-directed behavior. Here, we tested the hypothesis that developmental improvement in the ability to cancel a motor response is reflected by maturational changes in the white matter underlying the right presupplementary motor area (preSMA) and posterior inferior frontal gyrus (IFG), two cortical key areas of the fronto-basal ganglia “stopping” network. Eighty-eight typically-developing children and adolescents, aged 7-19 years, were longitudinally assessed with the stop-signal task (SST) and diffusion tensor imaging (DTI) of the brain over a period of six years. Participants were examined from two to nine times with an average of 6.6 times, resulting in 576 SST-DTI datasets. We applied tract-based spatial statistics to extract mean fractional anisotropy (FA) from regions-of-interest in the white matter underlying the right IFG (IFGFA) and right preSMA (preSMAFA) at each time point. Motor response cancelation performance, estimated with the stop-signal reaction time (SSRT), improved with age. Initially well performing children plateaued around the age of 11 years, while initially poor performers caught up at the age of 13-14 years. White matter microstructure continued to mature across the investigated age range. Males generally displayed linear maturational trajectories, while females displayed more curvilinear trajectories that leveled off around 12-14 years of age. Maturational increases in right preSMAFAbut not right IFGFAwere associated with developmental improvements in SSRT. This association differed depending on the mean right preSMAFAacross the individual maturational trajectory. Children with lower mean right preSMAFAexhibited poorer SSRT performance at younger ages but steeper developmental trajectories of SSRT improvement. Children with higher mean right preSMAFAexhibited flatter trajectories of SSRT improvement along with faster SSRT already at the first assessments. The results suggest that no further improvement in motor response cancellation is achieved once a certain level of maturity in the white matter underlying the right preSMA is reached. Similar dynamics may apply to other behavioral read-outs and brain structures and, thus, need to be considered in longitudinal MRI studies designed to map brain structural correlates of behavioral changes during development.HighlightsMotor response cancellation, i.e. SSRT, improvement plateaued at 13-14 years of ageFractional anisotropy (FA) captured maturation of white matter (WM) microstructureFA in the WM underlying right preSMA (preSMAFA) reflected SSRT improvement with ageIndividual SSRT improvement depended on mean right preSMAFAacross all DTI sessionsChildren with lower mean right preSMAFAhad the steepest improvements in SSRT
A network Based method to predict cancer causal genes in GR Network
Authors: Akhavansafar Mostafa , Teimourpour Babak 
Published: March 2020

AbstractOne of the important issues in oncology is finding the genes that perturbation the cell functionality, and result in cancer propagation. The genes, namely driver genes, when they mutate in expression, result in cancer through activation of the mutated proteins. So, many methods have been introduced to predict this group of genes. These are mostly computational methods based on the number of mutations of each gene. Recently, some network-based methods have been proposed to predict Cancer Driver Genes (CDGs). In this study, we use a network-based approach and relative importance of each gene in the propagation and absorption of genes anomalies in the network to recognize CDGs. The experimental results are compared with 19 previous methods that show our proposed algorithm is better than the others in terms of accuracy, precision, and the number of recognized CDGs.
The dorsal striatum sets the sensitivity to effort
Authors: Jurado-Parras Maria-Teresa , Safaie Mostafa , Sarno Stefania , Louis Jordane , Karoutchi Corane , Berret Bastien , Robbe David 
Published: March 2020

AbstractThe dorsal striatum (dS) has been implicated in storing and retrieving procedural memories and controlling movement kinematics (e.g., speed). Since procedural memories are expressed through movements, the exact nature of the dS function has proven difficult to delineate. Here we challenged rats in complementary tasks designed to alleviate this performance confound. Surprisingly, dS lesions spared task-specific procedural memories but altered the kinematics of their expression in motor routines. Further behavioral analyses combined with simulations in the optimal control framework indicated that these alterations reflected an increased sensitivity to effort with preserved reward-seeking and ability to modulate movement speed. By setting the sensitivity to effort, the dS contributes to the optimization of the energy invested into voluntary movements. Such an elementary function of the dS might explain its implication in both procedural decisions and the control of movement speed.
Microampere electric currents caused bacterial membrane damage and two-way leakage in short time
Authors: Krishnamurthi V R , Rogers A , Peifer J , Niyonshuti I , Chen J , Wang Y 
Published: March 2020

AbstractPhysical agents such as low electric voltages and currents have recently gained attention for antimicrobial treatment due to their bactericidal capability. Although microampere electric currents were shown to suppress the growth of bacteria, it remains unclear to what extent the microampere currents damage bacterial membrane. Here, we investigated the membrane damage and two-way leakage caused by microampere electric currents (≤ 100 μA) in a short time (30 min). Based on MitoTracker staining, propidium iodide staining, filtration assays, and quantitative single-molecule localization microscopy, we found that microampere electric currents caused significant membrane damages and allowed two-way leakages of ions, small molecules and proteins. This study paves the way to new development and antibiotic applications of ultra-low electric voltages and currents.Statement of SignificancePrevious studies showed that treating bacteria with milliampere electric currents for 72 hours led to significant damages of the bacterial membrane. However, it remains unclear to what extent membrane damages and two-way (i.e. inward and outward) leakages are caused by lower electric currents in a shorter time. In this work, we set out to answer this question. We carried out several assays on the bacteria treated by microampere electric currents of ≤ 100 μA for 30 min, including MitoTracker staining, propidium iodide staining, filtration assays, and quantitative single-molecule localization microscopy. We found and quantified that the membrane damages were caused by microampere electric currents in half an hour and allowed two-way leakages of ions, small molecules, and proteins.
Identification of a molecular fingerprint for synaptic glia
Authors: Castro Ryan , Taetzsch Thomas , Vaughan Sydney K. , Godbe Kerilyn , Chappell John , Settlage Robert , Valdez Gregorio 
Published: March 2020

AbstractThe inability to specifically identify and manipulate synaptic glial cells remains a major obstacle to understanding fundamental aspects of synapse formation, stability and repair. Using a combinatorial gene expression approach, we discovered molecular markers that allow us to specifically label perisynaptic Schwann cells (PSCs), glial cells at neuromuscular synapses. Using these markers, we demonstrate that PSCs fully-differentiate postnatally and have a unique molecular signature that includes genes predicted and known to play critical roles at synapses. These findings will serve as a springboard for unprecedented approaches for studying molecular determinants of PSC differentiation and function at neuromuscular synapses and possibly synapse-associated glia throughout the CNS.
Fermented food metagenomics reveals substrate-associated differences in taxonomy, health-associated- and antibiotic resistance-determinants
Authors: Leech John , Cabrera-Rubio Raul , Walsh Aaron M , Macori Guerrino , Walsh Calum J , Barton Wiley , Finnegan Laura , Crispie Fiona , O’Sullivan Orla , Claesson Marcus J , Cotter Paul D 
Published: March 2020

AbstractFermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that the consumption of these foods that help to address the negative consequences of ‘industrialization’ of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented food microbiota to better harness desirable traits. Here we considerably expand the understanding of fermented food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity and functional potential (including antimicrobial resistance, carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from around the Globe. Food type, i.e., dairy-, sugar- or brine-type fermented foods, was to be the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined dataset, 127 high quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species ofAcetobacter, Acidisphaera, Gluconobacter, Lactobacillus, LeuconostocandRouxiella, were generated. Potential health promoting attributes were more common in fermented foods than non-fermented equivalents, with waterkefirs, sauerkrauts and kvasses containing the greatest numbers of potentially health-associated gene clusters (PHAGCs). Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date, and yields novel information regarding their relative health-promoting potential.ImportanceFermented foods are regaining popularity in Western society due in part to an appreciation of the potential for fermented food microbiota to positively impact on health. Many previous studies have studied fermented microbiota using classical culture-based microbiological methods, older molecular techniques or, where deeper analyses have been performed, have involved a relatively small number of one specific food type. Here, we have used a state-of-the-art shotgun metagenomic approach to investigate 58 different fermented foods of different type and origin. Through this analysis, we were able to identify the differences in the microbiota across these foods, the factors that drove their microbial composition, and the relative potential functional benefits of these microbes. The information provided here will provide significant opportunities for the further optimisation of fermented food production and the harnessing of their health promoting potential.
Hippocampal-medial prefrontal event segmentation and integration contribute to episodic memory formation
Authors: Liu Wei , Shi Yingjie , Cousins James N. , Kohn Nils , Fernández Guillén 
Published: March 2020

AbstractHow do we encode our continuous life experiences for later retrieval? Theories of event segmentation and integration suggest that the hippocampus binds separately represented events into an ordered narrative. Using a functional Magnetic Resonance Imaging (fMRI) movie watching-recall dataset, we quantified two types of neural similarities (i.e.,activation patternsimilarity and within-region voxel-basedconnectivity patternsimilarity) between separate events during movie watching and related them to subsequent retrieval of events as well as retrieval of sequential order. We demonstrated that compared to forgotten events, successfully remembered events were associated with distinctactivation patternsin the hippocampus and medial prefrontal cortex. By contrast, similarconnectivity patternsbetween events were associated with memory formation and were also relevant for retaining events in the correct order. We applied the same approaches to an independent movie watching fMRI dataset as validation and highlighted again the role of hippocampal activation pattern and connectivity pattern in memory formation. We propose that distinctactivation patternsrepresent neural segmentation of events while similarconnectivity patternsencode context information, and therefore integrate events into a narrative. Our results provide novel evidence for the role of hippocampal-medial prefrontal event segmentation and integration in episodic memory formation of real-life experience.
Forensic microbial system for high-resolution object provenance
Authors: Qian Jason , Lu Zhi-xiang , Mancuso Christopher P. , Jhuang Han-Ying , del Carmen Barajas-Ornelas Rocío , Boswell Sarah , Ramírez-Guadiana Fernando H. , Jones Victoria , Sonti Akhila , Sedlack Kole , Artzi Lior , Jung Giyoung , Arammash Mohammad , Melfi Michael , Lyon Lorena , Owen Siân V. , Baym Michael , Khalil Ahmad S. , Silver Pamela , Rudner David , Springer Michael 
Published: March 2020

AbstractMapping where an object has been is a fundamental challenge for human health, commerce, and food safety. Location-specific microbes offers the potential to cheaply and sensitively determine object provenance. We created a synthetic, scalable microbial spore system that identifies object provenance in under one hour at meter-scale resolution and near single spore sensitivity, and that can be safely introduced into and recovered from the environment. This system solves the key challenges in object provenance: persistence in the environment, scalability, rapid and facile decoding, and biocontainment. Our system is compatible with SHERLOCK, facilitating its implementation in a wide range of applications.
A flexible framework for simulating and fitting generalized drift-diffusion models
Authors: Shinn Maxwell , Lam Norman H. , Murray John D. 
Published: March 2020

AbstractThe drift-diffusion model (DDM) is an important decision-making model in cognitive neuroscience. However, innovations in model form have been limited by methodological challenges. Here, we introduce the generalized drift-diffusion model (GDDM) framework for building, simulating, and fitting DDM extensions, and provide a software package which implements the framework. The GDDM framework augments traditional DDM parameters through arbitrary user-defined functions. Models are simulated numerically by directly solving the Fokker-Planck equation using efficient numerical methods, yielding a 100-fold or greater speedup over standard methodology. This speed allows GDDMs to be fit to data using maximum likelihood on the full response time (RT) distribution. We show that a GDDM fit with our framework explains a classic open dataset with better accuracy and fewer parameters than several DDMs implemented using the latest methodology. Overall, our framework will allow for decision-making model innovation and novel experimental designs.
Spacecraft formation control using aerodynamic and Lorentz force
Authors: Sun Ran , Shan Aidang , Zhang Chengxi , Jia Qingxian 
Published: March 2020

Purpose
This paper aims to investigate the feasibility of using the combination of Lorentz force and aerodynamic force as a propellantless control method for spacecraft formation.

Design/methodology/approach
It is assumed that each spacecraft is equipped with several large flat plates, which can rotate to produce aerodynamic force. Lorentz force can be achieved by modulating spacecraft’s electrostatic charge. An adaptive output feedback controller is designed based on a sliding mode observer to account for unknown uncertainties and the absence of relative velocity measurements. Aiming at distributing the control input, an optimal control allocation method is proposed to calculate the electrostatic charge of the Lorentz spacecraft and control commands for the atmospheric-based actuators.

Findings
Numerical examples are provided to demonstrate the effectiveness of the proposed control strategy in the presence of J2 perturbations. Simulation results show that relative motion in a formation can be precisely controlled by the proposed propellantless control method under uncertainties and unavailability of velocity measurements.

Research limitations/implications
The controllability of the system is not theoretically investigated in the current work.

Practical implications
The proposed control method introduced in this paper can be applied for small satellites formation in low Earth orbit.

Originality/value
The main contribution of the paper is the proposal of the propellantless control approach for satellite formation using the combination of Lorentz force and aerodynamic force, which can eliminate the requirement of the propulsion system.