bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applications of Microbially Induced Calcium Carbonate Precipitation on Non-Woven Geotextiles
Authors: Duman E , Sarıçiçek Y E , Pekcan O , Gurbanov R , Gözen A G 
Published: October 2022

Abstract
Recently, an innovative ground improvement method known as microbially induced calcium precipitation (MICP) has been proposed as an alternative to conventional ground improvement techniques. Having numerous advantages such as being environmentally friendly and promoting sustainable solutions, MICP has been studied by researchers from various civil engineering sub-disciplines to solve problems related to crack propagation of concrete, insufficient soil strength characteristics, soil erosion, asphalt cracks, etc. This study aims at moving MICP one step further by introducing a hybrid approach that combines MICP and geotextiles to produce a good quality product for reliable field use. Within this scope, MICP is applied on non-woven geotextiles. Physical (imaging) and mechanical (puncture resistance) properties of non-woven geotextiles subjected to MICP treatments under soaking conditions are investigated. Puncture resistance tests are performed and the details of laboratory work including specimen preparation and MICP treatments are presented in this paper. This study, together with its implications for future works, also highlights the next steps to be taken for properly using the MICP method when other geosynthetics are used.
Reliability of road pavement constructions reinforced by geosynthetic materials
Authors: Gameliak I , Nikolaichuk A , Zhurba G 
Published: October 2022

Abstract
Existing experience of unpaved road constructions reinforced by geogrids is described in the article, amended by own practical experience of reinforcement usage in unpaved road constructions. The Object of the research is reinforced and non-reinforced unpaved road constructions. The Purpose of the research is to determine influence of unpaved constructions reinforcement by rigid geogrids on overall bearing capacity and its deviation. The Methods of the research are field bearing capacity dynamic testing and statistic data analysis. The article is a long-term study generalization of unpaved road constructions with grained layers reinforced by rigid geogrids. The study was performed within the period of 2017-2019, and it covers both the construction and operation stages within the period of moisture accumulation and during the drainage period. The results of the study can be used for design and calculation for road constructions by geogrids and geotextile. Forecast assumptions about the object of the research are expansion of the experimental base, taking into account different test methods, different reinforcing materials and different construction conditions.
Finite Difference Modelling of Deformable Geosynthetics-Reinforced Barriers (DGRB) under the dynamic impact of debris avalanches
Authors: Moretti S , Cuomo S , Frigo L 
Published: October 2022

Abstract
The behaviour of Deformable Geosynthetics-Reinforced Barrier (DGRB) is investigated with reference to the dynamic impact of debris avalanches. The aim of these barriers is to protect life of inhabitants and reduce the threat for the exposed structures. A Finite Difference Method code (FLAC, Itasca) is used and the dynamic impact is simulated as an external pressure applied over time to the barrier. The peak lateral pressure exerted by a debris avalanche is evaluated by a literature formulation including a flow-height dependent static component and a flow-velocity dependent dynamic component. Real values of height and velocity of debris avalanches are taken from previous research works. The trend of the pressure during the impact is obtained from the landslide volume and the impulse theorem. The DGRBs are composed of: i) coarse-grained material, ii) bidirectional PET geogrids; iii) external formwork. The soil-geosynthetics contact is simulated through a frictional interface. The several components used in the wrap-around technique are simulated following two different schematizations and the differences between them are highlighted. The used mathematical formulation allows reproducing the impacted barrier both in small and large displacement cases. The local and global displacements of the barrier, its failure mechanisms and the soil-geogrid interaction inside the barrier are investigated. The results outline the differences between the two ways of modelling the wrap-around technique. In particular, the computed global displacements are comparable in the two computational schemes while the simulated stress-strain responses of the structural elements are somehow different.
Intelligent Soft Hands and Benchmarking towards General-Purpose Robotic Manipulation
Authors: Gilday Kieran , Iida Fumiya 
Published: October 2022

Abstract
In order to progress the development of intelligent soft hands for general-purpose use in humanoid robots, social assistive robots, adaptive manufacturing, prosthetics and more, we need to rethink our approach to benchmarking. Where previously, hands are compared by their performance in a limited set of tasks, resulting in performance optimisations in the subjective, most common tasks. Instead, we must focus on increasing the hand’s potential at the lowest level, by improving the underlying passive behaviours, in terms of increased behavioural diversity and cheap control.
Mechanical Sensing in Embodied Agents
Authors: Preti Matteo Lo , Thuruthel Thomas George , Gilday Kieran , Beccai Lucia , Iida Fumiya 
Published: October 2022

Abstract
Sensors enable autonomous systems to obtain information about their internal states and the environment for guiding their actions. It is as essential for these sensors to reject disturbances as to gather the correct information. There are numerous trade-offs and considerations in designing these sensory systems. For instance, natural agents evolved a vast diversity of highly optimized sensory organs to perform their tasks. This work focuses on how these sensory systems estimate mechanical stimuli. We look at some of the strategies and design principles found in nature to understand fundamental trade-offs and design considerations when acquiring and processing mechanical information.
Photophysical, optical and lasing analysis of fluorinated β-keto carboxylate europium(III) complexes
Authors: Khatri Savita , Ahlawat Pratibha , Khatkar S P , Taxak V B , Kumar Rajesh 
Published: October 2022

Abstract
Six luminescent, bright red Eu(III) complexes with a β-keto-carboxylic acid as prime ligand and N-donor aromatic systems as auxillary ligand were synthesised via ecologically efficient grinding method. The distinctive red peak (5D0 → 7F2) of Eu(III) ion is exhibited in emission spectra of all complexes. The luminescent properties of complexes were analysed through decay time, color coordinates, luminescence efficiency and Judd Ofelt parameters. The value of Ω2 is found to be higher than Ω4 which indicated hypersensitive nature of 5D0 → 7F2 transition. The results established the complexes as a strong contender for red light emitting display devices. The fluorescence branching ratios, stimulated emission cross section, gain band width and optical gain showed the good lasing strength of 5D0 → 7F2 transition of complexes. The complexes exhibited decent thermal stability and have optical energy band gap value in semiconductor range, thus can have relevance in optoelectronic devices. Energy transfer mechanism was investigated for complexes which affirmed the efficacious transfer of energy from ligands to Eu(III) ion. The synthesised complexes were also assayed for antimicrobial and antioxidant properties. All complexes are reported to show better antioxidant behaviour than the prime ligand and also exhibited upstanding antibacterial activities.
Delicate modulation of mixed conducting properties of PEDOT:PSS via crosslinking with polyvinyl alcohol
Authors: Kim Ji Hwan , Wieland Matthias , Omiecienski Beatrice , Kim Youngseok , Park Jaeil , Kim Gunwoo , Ludwigs Sabine , Yoon Myung-Han 
Published: October 2022

Abstract
Despite possible toxicity issues, chemical reduction or non-polarizable electrodes incorporated with highly reactive chemical species have been utilized to control the operational characteristics of organic electrochemical transistors (OECTs) for bioelectronic interfacing applications. In this study, we demonstrate that crosslinking between highly conductive poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) and biocompatible nonconductive polyvinyl alcohol (PVA) effectively modulates the mixed conducting properties of PEDOT:PSS. The PEDOT:PSS–PVA films prepared by simple PEDOT:PSS and PVA blending at various ratios, spin-coating, crosslinking, and sulfuric acid treatment were comprehensively studied using optical spectroscopy, x-ray diffraction, atomic force microscopy, and electrical/electrochemical device characterizations. With PVA contents up to 20 wt.%, the resultant PEDOT:PSS–PVA-based OECTs showed a linear threshold voltage shift with a marginal loss of transconductance, suggesting an effective modulation of the peak transconductance gate voltage. Furthermore, the PVA content also affects the ion transport dynamics, which is related to the crystallite size and ionic functional group density in the PEDOT:PSS–PVA system. The detailed mechanism of delicately controlled mixed conduction in the PEDOT:PSS–PVA system is proposed from the perspective of structure-property relations.
Nonunitary gate operations by dissipation engineering
Authors: Zapusek Elias , Javadi Alisa , Reiter Florentin 
Published: October 2022

Abstract
Irreversible logic is at odds with unitary quantum evolution. Emulating such operations by classical measurements can result in disturbances and high resource demands. To overcome these limitations, we propose protocols that harness dissipation to realize the nonunitary evolution required for irreversible gate operations. Using additional excited states subject to decay, we engineer effective decay processes that perform the desired gate operations on the smallest stable Hilbert space. These operate deterministically and in an autonomous fashion, without the need for measurements. We exemplify our approach considering several classical logic operations, such as the OR, NOR, and XOR gates. Towards experimental realization, we discuss a possible implementation in quantum dots. Our study shows that irreversible logic operations can be efficiently performed on realistic quantum systems and that dissipation engineering is an essential tool for obtaining nonunitary evolutions. The proposed operations expand the quantum engineers’ toolbox and have promising applications in NISQ algorithms and quantum machine learning.
The impact of Mn nonstoichiometry on the oxygen mass transport properties of La0.8Sr0.2Mn
y
O3±δ
thin films
Authors: Chiabrera Francesco M , Baiutti Federico , Börgers Jacqueline M , Harrington George F , Yedra Lluís , Liedke Maciej O , Kler Joe , Nandi Pranjal , Sirvent Juan de Dios , Santiso Jose , López-Haro Miguel , Calvino José J , Estradé Sonia , Butterling Maik , Wagner Andreas , Peiró Francesca , De Souza Roger A , Tarancón Albert 
Published: October 2022

Abstract
Oxygen mass transport in perovskite oxides is relevant for a variety of energy and information technologies. In oxide thin films, cation nonstoichiometry is often found but its impact on the oxygen transport properties is not well understood. Here, we used oxygen isotope exchange depth profile technique coupled with secondary ion mass spectrometry to study oxygen mass transport and the defect compensation mechanism of Mn-deficient La0.8Sr0.2Mn
y
O3±δ
epitaxial thin films. Oxygen diffusivity and surface exchange coefficients were observed to be consistent with literature measurements and to be independent on the degree of Mn deficiency in the layers. Defect chemistry modeling, together with a collection of different experimental techniques, suggests that the Mn-deficiency is mainly compensated by the formation of

La

Mn

×

antisite defects. The results highlight the importance of antisite defects in perovskite thin films for mitigating cationic nonstoichiometry effects on oxygen mass transport properties.
Cytokinins and auxins in organs of aquatic carnivorous plants: what do they reflect?
Authors: Adamec Lubomír , Plačková Lenka , Doležal Karel 
Published: October 2022

Abstract

Background and Aims
Aquatic carnivorous plants have typical rootless linear shoots bearing traps and exhibit steep physiological polarity with rapid apical growth. The aim was to analyse auxin and cytokinin metabolites in traps, leaves/shoots and shoot apices in several species of genera Aldrovanda and Utricularia to elucidate how the hormonal profiles reflect the specific organ functions and polarity.

Methods
The main auxin and cytokinin metabolites were analysed in miniature samples (&gt;2 mg dry weight) of different organs of Aldrovanda vesiculosa and six Utricularia species using ultraperformance liquid chromatography coupled with triple quadrupole mass spectrometry.

Key Results
Total contents of biologically active forms (free bases, ribosides) of all four main endogenously occurring cytokinin types were consistently higher in traps than in leaves in four Utricularia species with monomorphic shoots and/or higher than in shoots in two Utricularia species with dimorphic shoots. In Aldrovanda traps, the total content of different cytokinin forms was similar to or lower than that in shoots. In U. australis leaves, feeding on prey increased all cytokinin forms, while no consistent differences occurred in Aldrovanda. In four aquatic Utricularia species with monomorphic shoots, the content of four auxin forms was usually higher in traps than in leaves. Zero IAA content was determined in U. australis leaves from a meso-eutrophic site or when prey-fed.

Conclusions
Different cytokinin and auxin profiles estimated in traps and leaves/shoots of aquatic carnivorous plants indicate an association with different dominant functions of these organs: nutrient uptake by traps versus photosynthetic function of traps. Interplay of cytokinins and auxins regulates apical dominance in these plants possessing strong polarity.
Efficient enzymatic production of benzaldehyde from l-phenylalanine with a mutant form of 4-hydroxymandelate synthase
Authors: Takakura Yasuaki , Ono Takuto , Danjo Keiko , Nozaki Hiroyuki 
Published: October 2022

ABSTRACT
Benzaldehyde is an organic compound with an almond-like aroma and one of the most important and widely used flavorings in the food industry. To develop an enzymatic process for the production of benzaldehyde from l-phenylalanine, four enzymes were expressed in Escherichia coli; l-amino acid deaminase, 4-hydroxymandelate synthase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase. Although each E. coli strain could be used to synthesize benzaldehyde from l-phenylalanine, the yield was low due to the accumulation of an intermediate, phenylpyruvic acid. We developed a second reaction step by engineering 4-hydroxymandelate synthase of Actinoplanes teichomyceticus. A quadruple mutant of 4-hydroxymandelate synthase (A199V/Q206R/I217V/K337Q) obtained by random and site-directed mutagenesis demonstrated 2.4-fold higher activity than wild type. Furthermore, the mutant-expressing strain was able to produce benzaldehyde from 100 mm l-phenylalanine at a conversion rate of 84% (wild type, 37%). We report the development of an efficient process for benzaldehyde production using l-phenylalanine as a substrate.
Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?
Authors: García-Jacas César R , García-González Luis A , Martinez-Rios Felix , Tapia-Contreras Issac P , Brizuela Carlos A 
Published: October 2022

AbstractAntimicrobial peptides (AMPs) have received a great deal of attention given their potential to become a plausible option to fight multi-drug resistant bacteria as well as other pathogens. Quantitative sequence-activity models (QSAMs) have been helpful to discover new AMPs because they allow to explore a large universe of peptide sequences and help reduce the number of wet lab experiments. A main aspect in the building of QSAMs based on shallow learning is to determine an optimal set of protein descriptors (features) required to discriminate between sequences with different antimicrobial activities. These features are generally handcrafted from peptide sequence datasets that are labeled with specific antimicrobial activities. However, recent developments have shown that unsupervised approaches can be used to determine features that outperform human-engineered (handcrafted) features. Thus, knowing which of these two approaches contribute to a better classification of AMPs, it is a fundamental question in order to design more accurate models. Here, we present a systematic and rigorous study to compare both types of features. Experimental outcomes show that non-handcrafted features lead to achieve better performances than handcrafted features. However, the experiments also prove that an improvement in performance is achieved when both types of features are merged. A relevance analysis reveals that non-handcrafted features have higher information content than handcrafted features, while an interaction-based importance analysis reveals that handcrafted features are more important. These findings suggest that there is complementarity between both types of features. Comparisons regarding state-of-the-art deep models show that shallow models yield better performances both when fed with non-handcrafted features alone and when fed with non-handcrafted and handcrafted features together.
METAbolomics data Balancing with Over-sampling Algorithms (META-BOA): an online resource for addressing class imbalance
Authors: Hashimoto-Roth Emily , Surendra Anuradha , Lavallée-Adam Mathieu , Bennett Steffany A L , Čuperlović-Culf Miroslava 
Published: October 2022

Abstract

Motivation
Class imbalance, or unequal sample sizes between classes, is an increasing concern in machine learning for metabolomic and lipidomic data mining, which can result in overfitting for the over-represented class. Numerous methods have been developed for handling class imbalance, but they are not readily accessible to users with limited computational experience. Moreover, there is no resource that enables users to easily evaluate the effect of different over-sampling algorithms.

Results
METAbolomics data Balancing with Over-sampling Algorithms (META-BOA) is a web-based application that enables users to select between four different methods for class balancing, followed by data visualization and classification of the sample to observe the augmentation effects. META-BOA outputs a newly balanced dataset, generating additional samples in the minority class, according to the user’s choice of Synthetic Minority Over-sampling Technique (SMOTE), Borderline-SMOTE (BSMOTE), Adaptive Synthetic (ADASYN) or Random Over-Sampling Examples (ROSE). To present the effect of over-sampling on the data META-BOA further displays both principal component analysis and t-distributed stochastic neighbor embedding visualization of data pre- and post-over-sampling. Random forest classification is utilized to compare sample classification in both the original and balanced datasets, enabling users to select the most appropriate method for their further analyses.

Availability and implementation
META-BOA is available at https://complimet.ca/meta-boa.

Supplementary information
Supplementary data are available at Bioinformatics online.
E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants
Authors: Manfredi Matteo , Savojardo Castrense , Martelli Pier Luigi , Casadio Rita 
Published: October 2022

Abstract

Motivation
The advent of massive DNA sequencing technologies is producing a huge number of human single-nucleotide polymorphisms occurring in protein-coding regions and possibly changing their sequences. Discriminating harmful protein variations from neutral ones is one of the crucial challenges in precision medicine. Computational tools based on artificial intelligence provide models for protein sequence encoding, bypassing database searches for evolutionary information. We leverage the new encoding schemes for an efficient annotation of protein variants.

Results
E-SNPs&GO is a novel method that, given an input protein sequence and a single amino acid variation, can predict whether the variation is related to diseases or not. The proposed method adopts an input encoding completely based on protein language models and embedding techniques, specifically devised to encode protein sequences and GO functional annotations. We trained our model on a newly generated dataset of 101 146 human protein single amino acid variants in 13 661 proteins, derived from public resources. When tested on a blind set comprising 10 266 variants, our method well compares to recent approaches released in literature for the same task, reaching a Matthews Correlation Coefficient score of 0.72. We propose E-SNPs&GO as a suitable, efficient and accurate large-scale annotator of protein variant datasets.

Availability and implementation
The method is available as a webserver at https://esnpsandgo.biocomp.unibo.it. Datasets and predictions are available at https://esnpsandgo.biocomp.unibo.it/datasets.

Supplementary information
Supplementary data are available at Bioinformatics online.
Estimation of speciation times under the multispecies coalescent
Authors: Peng Jing , Swofford David L , Kubatko Laura 
Published: October 2022

AbstractMotivationThe multispecies coalescent model is now widely accepted as an effective model for incorporating variation in the evolutionary histories of individual genes into methods for phylogenetic inference from genome-scale data. However, because model-based analysis under the coalescent can be computationally expensive for large datasets, a variety of inferential frameworks and corresponding algorithms have been proposed for estimation of species-level phylogenies and associated parameters, including speciation times and effective population sizes.ResultsWe consider the problem of estimating the timing of speciation events along a phylogeny in a coalescent framework. We propose a maximum a posteriori estimator based on composite likelihood (MAPCL) for inferring these speciation times under a model of DNA sequence evolution for which exact site-pattern probabilities can be computed under the assumption of a constant θ throughout the species tree. We demonstrate that the MAPCL estimates are statistically consistent and asymptotically normally distributed, and we show how this result can be used to estimate their asymptotic variance. We also provide a more computationally efficient estimator of the asymptotic variance based on the non-parametric bootstrap. We evaluate the performance of our method using simulation and by application to an empirical dataset for gibbons.Availability and implementationThe method has been implemented in the PAUP* program, freely available at https://paup.phylosolutions.com for Macintosh, Windows and Linux operating systems.Supplementary informationSupplementary data are available at Bioinformatics online.