bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecological Vegetation Restoration and Regeneration Technology of Abandoned Land for Remedying the Heavy Metals Polluted Soil
Authors: Zheng Jiaxin 
Published: July 2021

Abstract
Urban industrial wasteland may have been affected by the pollution of toxic and harmful substances produced by the original production activities, and the original ecosystem has been severely damaged. Especially in abandoned mines, the soil is heavily polluted by heavy metals and ecological restoration is extremely difficult. Chinese urban industrial wasteland has the characteristics of a huge number and diverse types of damage to the ecological environment. The elements of landscape design should be scientifically laid out from the three aspects of visual communication, history and humanities, and landscape structure. At the same time, attention should be paid to the external expression and internal culture of the landscape. Connotation, restoration and regeneration of landscape structures, topography, vegetation, and water bodies to create a new urban landscape space that combines ecological protection, landscape appreciation, educational science, and urban memory. For this reason, the thesis expounds the vegetation reconstruction in the ecological restoration of various industrial wastelands, and mainly analyzes the three links of soil substrate improvement, plant species selection and plant planting technology.
Study on Treatment and Kinetics of Methyl Blue Printing and Dyeing Wastewater by Modified Pomelo Skin
Authors: Zhang Yuanchao 
Published: July 2021

Abstract
In this study, methylene blue wastewater was used as simulated printing and dyeing wastewater, and orthogonal experiment was used to explore the optimal conditions of modified grapefruit peel biochar for adsorption of simulated printing and dyeing wastewater. The adsorption time was selected to explore the kinetics of methylene blue solution concentration. The experimental results were fitted and analyzed by quasi first-order kinetic equation and quasi second-order kinetic equation respectively. The results showed that the adsorption kinetics was in line with the quasi second-order kinetic model, R2 was 0.9965.
Study on the optimum amount and kinetics of chitosan adsorbing Fe (III) in restaurant sewage treatment technology
Authors: Zhang Yuanchao 
Published: July 2021

Abstract
In this paper, chitosan was extracted from waste shrimp shell; In the static adsorption experiment, chitosan was added to the simulated wastewater containing Fe (III), and the absorbance before and after the reaction was measured by visible spectrophotometer to obtain the concentration of metal ions. The conditions and ability of chitosan to adsorb Fe (III) were explored, and the kinetic analysis of the results was carried out. The experimental results show that when the other variables are controlled unchanged; When the dosage of chitosan was in the range of 0.05-0.20 g, the optimal adsorption rate was 81.32% with the increasing dosage of chitosan, and the surface pores of chitosan decreased or even disappeared after the reaction. The adsorption kinetics of chitosan for Fe (III) was well fitted with the quasi second order rate linear equation.
GIS-based Architectural Design in Heritage Landscapes: towards a Knowledge-based Definition of Touristic Routes
Authors: López Sánchez M , Linares Gómez del Pulgar M 
Published: July 2021

Abstract
Network-based spatial analysis tools are useful for solving complex routing problems. However, the search for the most optimal route in terms of distance and time does not always guarantee the most convenient design solution, as occurs in heritage landscapes. A landscape architecture project aimed at designing touristic routes that connect heritage resources requires additional variables as in these cases it is not only a matter of achieving the most efficient connection between the heritage assets, but of detecting the paths that allow a better interpretation of the cultural meaning of the landscape. This text presents a GIS-based analysis protocol that combines least-cost path network analysis with weighted overlay analysis in order to introduce the time depth, the visibility and the level of visual and noise pollution of the paths as variables of influence in the selection of the touristic routes. The proposed method has been applied in the metropolitan area of the city of Seville (Andalusia, Spain), where there are relevant heritage resources that remain unconnected and could benefit each other through integrative touristic formulas. The aim of the method is advancing a protocol for a computer aided advanced architectural design in territorial scales.
Numerical Simulation of the Stress Corrosion Rupture Zone for Deep Tunnels
Authors: Zhang Xin , Sun Jinshan , Lang Min , Du Yuxiang , Zhao Suzhi , Dong Qian 
Published: July 2021

Abstract
Stress corrosion is a geological phenomenon that damages the long-term stability of underground projects. A comprehensive approach for stress corrosion prediction of underground projects combining creep experiment, particle flow code (PFC)and Finite element method (FEM) is proposed. Calibration of the numerical model was undertaken according to the data obtained from laboratory tests. Based on the numerical model, biaxial and triaxial stress corrosion compression tests were conducted to investigate the stress corrosion mechanism of Jinping marble. Through numerical tests, the stress corrosion process was visually observed. According to the development history of microcracks, the stress corrosion rupture process of surrounding rocks can be divided into 4 stages, i.e., rapid growth, slow growth, rapid growth and instant leap. The process was controlled by driving stress ratio and confining stress. On or near the tunnel wall, most stress corrosion microcracks are induced by tensile stress and the direction is parallel to the direction of the maximum principle stress. Near the yield zone of tunnel, the ratio of shear microcracks becomes larger with increasing confining stress. And the amount of microcracks is larger at the rupture stage than that on the tunnel wall, which makes the stress corrosion rupture process look like a ductile failure process. There is a linear relationship between the logarithm of stress corrosion lifetime and driving stress ratio if the confining stress keeps constant. Stress corrosion lifetime will increase when pc
becomes higher or driving stress ratio becomes lower. Based on the laboratory and numerical tests, the stress corrosion rupture depth of the tunnel section was predicted using FEM, which can optimize the length of bolts.
In vitro differentiation of human cardiac fibroblasts into myofibroblasts: characterization using electrical impedance
Authors: Degache A , Poulletier de Gannes F , Garenne A , Renom R , Percherancier Y , Lagroye I , Bernus O , Lewis N 
Published: July 2021

Abstract
Cardiac arrhythmias represent about 50% of the cardiovascular diseases which are the first cause of mortality in the world. Implantable medical devices play a major role for treating these arrhythmias. Nevertheless the leads induce an unwanted biological phenomenon called fibrosis. This phenomenon begins at a cellular level and is effective at a macroscopic scale causing tissue remodelling with a local modification of the active cardiac tissue. Fibrosis mechanism is complex but at the cellular level, it mainly consists in cardiac fibroblasts activation and differentiation into myofibroblasts. We developed a simplified in vitro model of cardiac fibrosis, with human cardiac fibroblasts whom differentiation into myofibroblasts was promoted with TGF-β1. Our study addresses an unreported impedance-based method for real-time monitoring of in vitro cardiac fibrosis. The objective was to study whether the differentiation of cardiac fibroblasts in myofibroblasts had a specific signature on the cell index, an impedance-based feature measured by the xCELLigence system. Primary human cardiac fibroblasts were cultured along 6 days, with or without laminin coating, to study the role of this adhesion protein in cultures long-term maintenance. The cultures were characterized in the presence or absence of TGF-β1 and we obtained a significant cell index signature specific to the human cardiac fibroblasts differentiation.
The interaction between ambush predators, search patterns of herbivores, and aggregations of plants
Authors: Scharf Inon 
Published: July 2021

AbstractWhile predators benefit from spatial overlap with their prey, prey strive to avoid predators. I used an individual-based simulation comprising sit-and-wait predators, widely foraging herbivores, and plants, to examine the link between predator ambush location, herbivore movement, and plant aggregation. I used a genetic algorithm to reach the best strategies for all players. The predators could ambush herbivores either inside or outside plant patches. The herbivores could use movement of varying directionality levels, with a change in directionality following the detection of plants. When the predators were fixed outside plant patches, the herbivores were selected to use a directional movement before plant encounter followed by a tortuous movement afterwards. When predators were fixed inside patches, herbivores used a continuous directional movement. Predators maintained within-patch positions when the herbivores were fixed to use the directional-tortuous movement. The predator location inside patches led to higher plant aggregations, by changing the herbivore movement. Finally, I allowed half of the predators to search for herbivores and let them compete with sit-and-wait predators located inside plant patches. When plants were clumped and herbivores used a directional-tortuous movement, with a movement shift after plant detection, ambush predators had the highest success relative to widely foraging predators. In all other scenarios, widely foraging predators did much better than ambush predators. The findings from my simulation suggest a behavioral mechanism for several observed phenomena of predator–prey interactions, such as a shorter stay by herbivores in patches when predators ambush them nearby, and a more directional movement of herbivores in riskier habitats.
Review of unsupervised pretraining strategies for molecules representation
Authors: Yu Linhui , Su Yansen , Liu Yuansheng , Zeng Xiangxiang 
Published: July 2021

AbstractIn recent years, the computer-assisted techniques make a great progress in the field of drug discovery. And, yet, the problem of limited labeled data problem is still challenging and also restricts the performance of these techniques in specific tasks, such as molecular property prediction, compound-protein interaction and de novo molecular generation. One effective solution is to utilize the experience and knowledge gained from other tasks to cope with related pursuits. Unsupervised pretraining is promising, due to its capability of leveraging a vast number of unlabeled molecules and acquiring a more informative molecular representation for the downstream tasks. In particular, models trained on large-scale unlabeled molecules can capture generalizable features, and this ability can be employed to improve the performance of specific downstream tasks. Many relevant pretraining works have been recently proposed. Here, we provide an overview of molecular unsupervised pretraining and related applications in drug discovery. Challenges and possible solutions are also summarized.
mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes
Authors: Salazar Guillem , Ruscheweyh Hans-Joachim , Hildebrand Falk , Acinas Silvia G , Sunagawa Shinichi 
Published: July 2021

Abstract

Profiling the taxonomic composition of microbial communities commonly involves the classification of ribosomal RNA gene fragments. As a trade-off to maintain high classification accuracy, existing tools are typically limited to the genus level. Here, we present mTAGs, a taxonomic profiling tool that implements the alignment of metagenomic sequencing reads to degenerate consensus reference sequences of small subunit ribosomal RNA genes. It uses DNA fragments, that is, paired-end sequencing reads, as count units and provides relative abundance profiles at multiple taxonomic ranks, including operational taxonomic units based on a 97% sequence identity cutoff. At the genus rank, mTAGs outperformed other tools across several metrics, such as the F1 score by &gt;11% across data from different environments, and achieved competitive (F1 score) or better results (Bray–Curtis dissimilarity) at the sub-genus level.

Availability and implementation
The software tool mTAGs is implemented in Python. The source code and binaries are freely available (https://github.com/SushiLab/mTAGs). The data underlying this article are available in Zenodo, at https://doi.org/10.5281/zenodo.4352762.

Supplementary information
Supplementary data are available at Bioinformatics online.
TempoMAGE: a deep learning framework that exploits the causal dependency between time-series data to predict histone marks in open chromatin regions at time-points with missing ChIP-seq datasets
Authors: Hallal Mohammad , Awad Mariette , Khoueiry Pierre 
Published: July 2021

Abstract

Motivation
Identifying histone tail modifications using ChIP-seq is commonly used in time-series experiments in development and disease. These assays, however, cover specific time-points leaving intermediate or early stages with missing information. Although several machine learning methods were developed to predict histone marks, none exploited the dependence that exists in time-series experiments between data generated at specific time-points to extrapolate these findings to time-points where data cannot be generated for lack or scarcity of materials (i.e. early developmental stages).

Results
Here, we train a deep learning model named TempoMAGE, to predict the presence or absence of H3K27ac in open chromatin regions by integrating information from sequence, gene expression, chromatin accessibility and the estimated change in H3K27ac state from a reference time-point. We show that adding reference time-point information systematically improves the overall model’s performance. In addition, sequence signatures extracted from our method were exclusive to the training dataset indicating that our model learned data-specific features. As an application, TempoMAGE was able to predict the activity of enhancers from pre-validated in-vivo dataset highlighting its ability to be used for functional annotation of putative enhancers.

Availability and implementation
TempoMAGE is freely available through GitHub at https://github.com/pkhoueiry/TempoMAGE.

Supplementary information
Supplementary data are available at Bioinformatics online.
Contextual Priors Guide Perception and Motor Responses to Observed Actions
Authors: Betti Sonia , Finisguerra Alessandra , Amoruso Lucia , Urgesi Cosimo 
Published: July 2021

Abstract
In everyday-life scenarios, prior expectations provided by the context in which actions are embedded support action prediction. However, it is still unclear how newly learned action–context associations can drive our perception and motor responses. To fill this gap, we measured behavioral (Experiment 1) and motor responses (Experiment 2) during two tasks requiring the prediction of occluded actions or geometrical shapes. Each task consisted of an implicit probabilistic learning and a test phase. During learning, we exposed participants to videos showing specific associations between a contextual cue and a particular action or shape. During the test phase, videos were earlier occluded to reduce the amount of sensorial information and induce participants to use the implicitly learned action/shape-context associations for disambiguation. Results showed that reliable contextual cues made participants more accurate in identifying the unfolding action or shape. Importantly, motor responses were modulated by contextual probability during action, but not shape prediction. Particularly, in conditions of perceptual uncertainty the motor system coded for the most probable action based on contextual informativeness, regardless of action kinematics. These findings suggest that contextual priors can shape motor responses to action observation beyond mere kinematics mapping.
Patient Access in 14 High-Income Countries to New Antibacterials Approved by the US Food and Drug Administration, European Medicines Agency, Japanese Pharmaceuticals and Medical Devices Agency, or Health Canada, 2010–2020
Authors: Outterson Kevin , Orubu Ebiowei S F , Rex John , Årdal Christine , Zaman Muhammad H 
Published: July 2021

Abstract

Background
Inaccessibility of medicines in low- and middle-income countries is a frequent challenge. Yet it is typically assumed that high-income countries have complete access to the full arsenal of medicines. This study tests this assumption for new antibacterials, which are saved as a last resort in order to prevent the development of resistance, resulting in insufficient revenues to offset costs. Prior studies report only regulatory approval, missing the important lag that occurs between approval and commercial launch, although some antibiotics never launch in some countries.

Methods
We identified all antibacterials approved and launched in the G7 and 7 other high-income countries in Europe for the decade beginning 1 January 2010, using quantitative methods to explore associations.

Results
Eighteen new antibacterials were identified. The majority were accessible in only 3 countries (United States, United Kingdom, and Sweden), with the remaining 11 high-income countries having access to less than half of them. European marketing authorization did not lead to automatic European access, as 14 of the antibacterials were approved by the European Medicines Agency but many fewer were commercially launched. There was no significant difference in access between “innovative” and “noninnovative” antibacterials. Median annual sales in the first launched market (generally the United States) for these 18 antibiotics were low, $16.2M.

Conclusions
Patient access to new antibacterials is limited in some high-income countries including Canada, Japan, France, Germany, Italy, and Spain. With low expected sales, companies may have decided to delay or forego commercialization due to expectations of insufficient profitability.
Correlation of clinical and computed tomography features of thymic epithelial tumours with World Health Organization classification and Masaoka–Koga staging
Authors: Zhou Qing , Huang Xiaoyu , Xue Caiqiang , Zhou Junlin 
Published: July 2021

Abstract

OBJECTIVES
Our goal was to investigate the correlation of clinical and computed tomography (CT) features of thymic epithelial tumours (TET) with the World Health Organization classification and the Masaoka–Koga staging system.

METHODS
Clinical and CT imaging data from 159 patients surgically and pathologically diagnosed with TET (82 men, 77 women; mean [± standard deviation] age, 52.08 ± 11.76 years) were retrospectively collected and reviewed. CT features were evaluated by radiologists. Tumour size, morphology, margin, density, calcification, cystic necrosis, density of the fat layer around the tumour, invasion of surrounding tissues, mediastinal lymph node enlargement, pleural/pericardial effusion, metastasis, plain CT scans and enhanced CT values were analysed.

RESULTS
Of the 159 patients with TET, 76 had low-risk thymoma, 55 had high-risk thymoma and 28 had thymic carcinomas. Age, maximum tumour diameter, myasthenia gravis, morphology, edges, density, fat around the lesion, mediastinal vascular, pericardial and lung tissue invasion, pleural/pericardial effusion, metastasis and arterial phase CT values were statistically different among the 3 groups (P &lt; 0.05). Multivariate regression analysis revealed that edges, fat around the lesion, mediastinal vascular invasion and pericardial effusion were most relevant to TET classification. The 159 patients with TET were categorized into the non-invasion group (stage I; n = 58); the invasion of surrounding fat (stage II; n = 46); and the invasion of surrounding structures and metastasis group (stages III and IV; n = 55). Tumour diameter, morphology, margins, density, cystic degeneration and necrosis, invasion of surrounding fat and structure, pleural and pericardial effusion and lymph node enlargement were statistically different among the 3 groups (P &lt; 0.05). Multivariate regression analysis revealed that edges, fat around the lesion, mediastinal vascular invasion and pleura invasion were the most relevant CT signs in relation to TET staging.

CONCLUSIONS
Analysis of clinical and CT features before surgery may facilitate the preliminary classification and stage diagnosis of TET.
Using a smartwatch electrocardiogram to detect abnormalities associated with sudden cardiac arrest in young adults
Authors: Nasarre Mathieu , Strik Marc , Daniel Ramirez , Francisco , Buliard Samuel , Marchand Hugo , Abu-Alrub Saer , Ploux Sylvain , Haïssaguerre Michel , Bordachar Pierre 
Published: July 2021

Abstract

Aims
Smartwatch electrocardiograms (ECGs) could facilitate the detection of sudden cardiac arrest (SCA)-associated abnormalities. We evaluated the feasibility of using smartwatch-derived ECGs for detecting SCA-associated abnormalities in young adults and its agreement with 12-lead ECGs.

Methods and results
Twelve-lead and Apple Watch ECGs were registered in 155 healthy volunteers and 67 patients aged 18–45 years with diagnosis and ECG signs of long-QT syndrome (n = 10), Brugada syndrome (n = 12), ventricular pre-excitation (n = 19), hypertrophic cardiomyopathy (HCM, n = 13), and arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVC/D, n = 13). Cardiologists separately analysed 12-lead ECGs and the smartwatch ECGs taken from the left wrist (AW-I) and then from chest positions V1, V3, and V6 (AW-4). Compared with AW-I, AW-4 improved the classification of ECGs as ‘abnormal’, increasing the sensitivity from 64% to 89% (P &lt; 0.01). Pre-excitation was detected in most cases using AW-I (sensitivity 89%) and in all cases using AW-4 (sensitivity 100%, P = 0.48 compared with AW-I, specificity 100% for both). Brugada was missed using AW-I but was detected in 11/12 patients using AW-4 (sensitivity 92%, specificity 100%, P = 0.003). Long QT was detected in 8/10 cases using AW-I (sensitivity 80%, specificity 100%) and in 9 patients using AW-4 (sensitivity 90%, specificity 100%, P &gt; 0.99). Hypertrophic cardiomyopathy was correctly suspected using AW-I and AW-4 (sensitivity 92% and 85%, specificity 85%, and 100%, P &gt; 0.99). AW-I was mostly (62%) considered normal in ARVC/D whereas AW-4 was useful in suspecting ARVC/D (100% sensitivity, 99% specificity, P = 0.004).

Conclusions
Detection of SCA-associated ECG abnormalities (pre-excitation, Brugada patterns, long QT, and signs suggestive of HCM and ARVC/D) is possible with an ECG smartwatch.