bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved downstream functional analysis of single-cell RNA-sequence data using DGAN
Authors: Pandey Diksha , Onkara Perumal P. 
Published: January 2023

AbstractThe dramatic increase in the number of single-cell RNA-sequence (scRNA-seq) investigations is indeed an endorsement of the new-fangled proficiencies of next generation sequencing technologies that facilitate the accurate measurement of tens of thousands of RNA expression levels at the cellular resolution. Nevertheless, missing values of RNA amplification persist and remain as a significant computational challenge, as these data omission induce further noise in their respective cellular data and ultimately impede downstream functional analysis of scRNA-seq data. Consequently, it turns imperative to develop robust and efficient scRNA-seq data imputation methods for improved downstream functional analysis outcomes. To overcome this adversity, we have designed an imputation framework namely deep generative autoencoder network [DGAN]. In essence, DGAN is an evolved variational autoencoder designed to robustly impute data dropouts in scRNA-seq data manifested as a sparse gene expression matrix. DGAN principally reckons count distribution, besides data sparsity utilizing a gaussian model whereby, cell dependencies are capitalized to detect and exclude outlier cells via imputation. When tested on five publicly available scRNA-seq data, DGAN outperformed every single baseline method paralleled, with respect to downstream functional analysis including cell data visualization, clustering, classification and differential expression analysis. DGAN is executed in Python and is accessible at https://github.com/dikshap11/DGAN.
Distributed harmonic patterns of structure-function dependence orchestrate human consciousness
Authors: Luppi Andrea I. , Vohryzek Jakub , Kringelbach Morten L. , Mediano Pedro A. M. , Craig Michael M. , Adapa Ram , Carhart-Harris Robin L. , Roseman Leor , Pappas Ioannis , Peattie Alexander R. D. , Manktelow Anne E. , Sahakian Barbara J. , Finoia Paola , Williams Guy B. , Allanson Judith , Pickard John D. , Menon David K. , Atasoy Selen , Stamatakis Emmanuel A. 
Published: January 2023

AbstractA central question in neuroscience is how consciousness arises from the dynamic interplay of brain structure and function. Here we decompose functional MRI signals from pathological and pharmacologically-induced perturbations of consciousness into distributed patterns of structure-function dependence across scales: the harmonic modes of the human structural connectome. We show that structure-function coupling is a generalisable indicator of consciousness that is under bi-directional neuromodulatory control. We find increased structure-function coupling across scales during loss of consciousness, whether due to anaesthesia or brain injury, capable of discriminating between behaviourally indistinguishable sub-categories of brain-injured patients, tracking the presence of covert consciousness. The opposite harmonic signature characterises the altered state induced by LSD or ketamine, reflecting psychedelic-induced decoupling of brain function from structure and correlating with physiological and subjective scores. Overall, connectome harmonic decomposition reveals how neuromodulation and the network architecture of the human connectome jointly shape consciousness and distributed functional activation across scales.
Quantitative Analysis of Peptide Libraries
Authors: Makowski Lee 
Published: January 2023

Quantitative analysis of peptide libraries can provide substantial information about molecular interactions that cannot be readily extracted from a qualitative inspection of the results of a phage display experiment. Affinity screening of phage-displayed combinatorial peptide libraries is carried out in order to identify a peptide sequence or sequence motif that binds tightly to a particular molecular target. The result of the experiment is a population of phage particles that represent a subset of the original library that has been enriched for binding to the molecular target. The nucleic acid sequences of the inserts in these phage particles are used to determine the sequences of the displayed peptides whose binding properties presumably led to their selection. In some cases, a sequence motif common to some (or many) of the derived sequences is immediately apparent from a visual inspection of the selected sequences. Frequently, no readily discernable motif can be identified from a visual inspection. This does not necessarily mean that the experiment failed. There are numerous examples in which weak motifs have been identified only after detailed computational analysis of the sequences.
Quantitative analysis can provide insight into at least five aspects of phage-display technology: the quality of a peptide library; the quality or effectiveness of an affinity screen; identification of sequence motifs; identification of binding sites on a protein; and, possibly, identification of proteins that bind to a particular target within an entire genome. This Chapter reviews the existing computational methods available for analyzing populations of peptides and identification of motifs within those populations.
Main Topics in Entomology: Insects as Disease Vectors
Authors: Manguin S. , Mouchet J. , Carnevale P. 
Published: January 2023

A great deal of human and animal diseases is due to pathogens transmitted by insects. Among the deadliest infectious diseases worldwide, malaria and dengue hemorrhagic fever are vector-borne diseases. Many insect vectors belong to the Diptera Order, such as mosquitoes, biting midges, sandflies, blackflies, and tsetse-flies, but insects of other orders can also transmit important pathogens like the lice, fleas, and bloodsucking bugs. Pathogenic agents could be parasites (protozoan, filariae, cestods, etc), bacteria (rickettsiae, borellia, etc), viruses (arboviruses) that undergo a cycle of development inside the insect vector to reach their infective stage. Transmission can be done through the insect's bite with direct inoculation or with pathogens deposited by the insect saliva or faeces on the skin, and entering into their host either through scratching or by active action of the pathogen into the host wound.
For these insect-borne diseases, vector control is one of the first preventive measures, if not the only one in most cases due to the lack of vaccine (except for yellow fever and Japanese encephalitis) and resistance issues in chemoprophylaxis. Therefore, vector control is an integral component of vector-borne disease control programmes. However, in order to reach their full efficiency, vector control operations and programmes must be based on sound knowledge of the targeted vectors (species identification, biology, distribution, etc.), of local and regional ecological context, and socio-cultural conditions of human populations.
Classical Insecticides: Past, Present and Future
Authors: López Ó. , Fernández-Bolaños J. G. , Gil M. V. 
Published: January 2023

We present an historical review of the use of classical insecticides, as examples of non-green agrochemicals that must be replaced and their use reviewed. The chapter is divided into two main sections; in the first, the approaches used for insect control before the development of synthetic insecticides are covered. The use of non-rational insecticides, mainly from mineral sources (e.g. sulphur, arsenicals, copper, or boron derivatives) and lacking specificity in most cases is widely reviewed.
The second part of the chapter is focused on the three main families of synthetic insecticides that have dominated the agrochemical sector from the 1940's to nowadays: organochlorine, orgaphosphorus and carbamates. Their syntheses, relative toxicity, selectivity and environmental fate are included.
The high efficiency and economic viability of such compounds allowed an indiscriminate use in crops, household and cattle. Nevertheless, it is strongly highlighted along this chapter that many of such insecticides are bioaccumulated or provoke severe toxicological effects in mammals, fishes and beneficial insects such as bees. It is also discussed the restrictions and bans exerted by the most recognized organizations such as the US EPA, European Union's Committees, or the World Health Organization for reducing or even eliminate their use.
Exploring the Controlling Parameters Affecting Specimens Generated in a Pluviator Using DEM
Authors: Cui L. 
Published: January 2023

Engineering properties of specimens generated using a pluviator are of great interests for many researchers in geotechnical engineering, chemical engineering, pharmaceutical engineering, etc. In the present study, the sensitivity of the specimen properties to the controlling parameters were explored in a virtual pluviator using DEM. Inter-particle friction, damping coefficient, falling height, were varied systematically to investigate the resulting void ratio, coordination number, K0, and fabric anisotropy.
From this study, it can be found that the inter-particle friction plays a key role in the resultant specimen characteristics. Void ratio increases with increasing coefficient of inter-particle friction between 0.0 and 0.5, while remains unchanged with friction coefficient between 0.5 and 1.0. The void ratio increases remarkably with reducing damping at higher falling height. It also increases greatly with increasing falling height at low damping. The coordination number decreases at a reducing rate as friction coefficient increases from 0.0 to 1.0; however, it does not show significant sensitivity to falling height or damping coefficient. The “at-rest” stress ratio, k0 (σ'h/σ'v), reduces with increasing friction at very high damping or low falling height. The influence of friction coefficient on the fabric anisotropy is not very consistent. It can only find that fabric anisotropy is lower at higher damping coefficient at high falling height.
Aquatic Biomass for the Production of Fuels and Chemicals
Authors: Dibenedetto Angela , Colucci Antonella 
Published: January 2023

This chapter highlights the potential of aquatic biomass as a source of chemicals and fuels. Aquatic biomass can be considered an interesting alternative to fossil fuels because with respect to terrestrial or residual biomass it has a higher solar energy utilisation efficiency (6–8% versus 1.5–2.2%).Aquatic biomass, i.e. micro-algae, macro-algae and plants, has a chemical composition that depends on the species and on the light, temperature, nutrients and salinity, and also biotic interactions, so it is better to use a selected cultivated strain in order to have an optimal energetic yield. In particular, the co-production of chemicals and fuels can be of great importance in order to make more positive the economic balance of growing algae for commercial purposes. Compounds of particular commercial interest include pigments, lipids and fatty acids, proteins, polysaccharides and phenolics, all of which display considerable diversity between and within taxa.
Design and modelling of three‐to‐five phase three‐limbed transformer
Authors: Khelafi Abdelhakim , Djebli Abdelmalik , Touhami Omar , Ibtiouen Rachid 
Published: January 2023

AbstractThis study presents a design study and modelling of three‐to‐five phase transformer with three‐limb magnetic core. The basics of phase transformation windings are discussed. The purpose of such winding is to produce at the secondary a balanced multiphase voltage system, from multiphase primary of different number of phases, without unbalance in the primary and secondary under load conditions. In order to overcome the imbalance due to the dispositions of the winding coils on the magnetic core, simulations using aided computer design are performed. Furthermore, this study presents a model of a three‐to‐five phase three‐limbed transformer, which is suitable for modelling the behaviour of this transformer at no‐load, under load, and under unbalance load conditions. This study is conducted by simulation and experimental tests.
Synergistic effects of 3D chitosan‐based hybrid scaffolds and mesenchymal stem cells in orthopaedic tissue engineering
Authors: Qi Ping , Ning Zhaohui , Zhang Xiuju 
Published: January 2023

AbstractRestoration of damaged bone and cartilage tissue with biomaterial scaffolds is an area of interest in orthopaedics. Chitosan is among the low‐cost biomaterials used as scaffolds with considerable biocompability to almost every human tissue. Considerable osteoconductivity, porosity, and appropriate pore size distribution have made chitosan an appropriate scaffold for loading of stem cells and a good homing place for differentiation of stem cells to bone tissue. Moreover, the similarity of chitosan to glycosaminoglycans and its potential to be used as soft gels, which could be lasting more than 1 week in mobile chondral defects, has made chitosan a polymer of interest in repairing bone and cartilage defects. Different types of scaffolds using chitosan in combination with mesenchymal stem cells (MSCs) are discussed. MSCs are widely used in regenerative medicine because of their regenerative ability, and recent line evidence reviewed demonstrated that the combination of MSCs with a combination of chitosan with different materials, including collagen type 1, hyaluronic acid, Poly(L‐lacticacid)/gelatin/β‐tricalcium phosphate, gamma‐poly[glutamic acid] polyelectrolyte/titanium alloy, modified Poly(L‐Lactide‐co‐Epsilon‐Caprolactone), calcium phosphate, β‐glycerophosphate hydrogel/calcium phosphate cement (CPC), and CPC‐Chitosan‐RGD, can increase the efficacy of using MSCs, and chitosan‐based stem cell delivery can be a promising method in restoration of damaged bone and cartilage tissue.
Fabrication of nano‐encapsulated angelica (Heracleum persicum) essential oil for enriching dairy dessert: Physicochemical, rheological and sensorial properties
Authors: Nanakali Narin Mhemmedamin 
Published: January 2023

AbstractIn this study, the nanoemulsions containing angelica essential oil (AEO) was used as a novel nano‐carrier for enrichment of dairy dessert. Firstly, oil‐in‐water nanoemulsions were prepared by different levels of GE (1%, 5%, 10%, and 15%) as the dispersed phase, Tween 80 as surfactant with a constant surfactant to essential oil ratio (1:1), and distillated water as a continuous phase. Droplet size, free radical scavenging capacity, antimicrobial activity against gram‐positive (Staphylococcus aureus (25923 ATCC)) and gram‐negative (Escherichia coli H7 O157 (700728 ATCC)) were evaluated for produced nanoemulsions. The mean droplet size of nanoemulsion increased from 75 to 95 nm and antioxidant capacity also enhanced from 15.4% to 30.2% by increasing AEO level from 1% to 15%. Antimicrobial analysis by disk diffusion methods for nanoemulsions containing different levels of AEO cleared that nanoemulsions with high levels of AEO showed the stronger antimicrobial activity against both used bacteria and especially more activity against Staphylococcus aureus. The results of the total count and yeast and mould count show that the nanoemulsions with different levels of AEO have been effective on the number of microorganisms, particularly during storage. The incorporation of pure essential oil and nanoemulsions with different levels of AEO did not affect significantly the pH of different dessert samples however, they affected the dry matter and free radical scavenging capacity. Adding of nanoemulsions with different levels of AEO to the desserts had a considerable effect on the rheological properties including apparent viscosity, Gʹ, G", Tan δ and complex viscosity and all samples showed shear‐thining behaviour. Results from organoleptic characteristics (taste, odour colour, mouthfeel and total acceptance) showed that enriched samples by nanoemulsions, particularly with higher level of AEO had higher sensorial scores. In general, samples containing free AEO (not encapsulated) had the lower scores in all organoleptic characteristics.
Spread sea clutter suppression via prior knowledge‐based space time adaptive processing in high frequency hybrid sky‐surface wave radar
Authors: Li Ya‐Jun , Wang Zhuo‐Qun , Xu Lin , Zhang Wen‐Hao , Lu Zhu‐Hao , Wang Zhi‐Cheng 
Published: January 2023

AbstractIn high frequency (HF) hybrid sky‐surface wave radar, the first‐order sea clutter broadening is severe under the action of ionospheric phase disturbance and bistatic angles. In this study, a spread sea clutter suppression method based on prior knowledge and joint domain localised (JDL) algorithm is proposed. Firstly, the first‐order sea clutter broadening mechanisms and model under the action of ionospheric phase disturbance and bistatic angles are introduced. Secondly, the space‐time coupling characteristics of the first‐order sea clutter is analysed. Then in order to better suppress clutter or avoid target information loss, the spread sea clutter suppression method based on space time adaptive processing is proposed. In the proposed method, the space‐time distribution characteristics and simulation model of the first‐order sea clutter is used as the prior knowledge into JDL algorithm to improve the sea clutter suppression performance. Finally, the performance of sea clutter suppression based on JDL algorithm is simulated and analysed. And the proposed spread sea clutter suppression method based on prior knowledge and JDL algorithm is proved by measured data.
From exo-Earths to exo-Venuses: Flux and polarization signatures of reflected light
Authors: Mahapatra G. , Abiad F. , Rossi L. , Stam D. M. 
Published: January 2023

Context. Terrestrial-type exoplanets in or near stellar habitable zones appear to be ubiquitous. It is, however, unknown which of these planets have temperate, Earth-like climates or for example, extreme Venus-like climates.
Aims. Technical tools to distinguish different kinds of terrestrial-type planets are crucial for determining whether a planet could be habitable or incompatible with life as we know it. We aim to investigate the potential of spectropolarimetry for distinguishing exo-Earths from exo-Venuses.
Methods. We present numerically computed fluxes and degrees of linear polarization of starlight that is reflected by exoplanets with atmospheres in evolutionary states ranging from similar to the current Earth to similar to the current Venus, with cloud compositions ranging from pure water to 75% sulfuric acid solution, for wavelengths between 0.3 and 2.5 µm. We also present flux and polarization signals of such planets in stable but spatially unresolved orbits around the star Alpha Centauri A.
Results. The degree of polarization of the reflected starlight shows larger variations with the planetary phase angle and wavelength than the total flux. Across the visible, the largest degree of polarization is reached for an Earth-like atmosphere with water clouds due to Rayleigh scattering above the clouds and the rainbow feature at phase angles near 40°. At near-infrared wavelengths, the planet with a Venus-like CO2 atmosphere and thin water cloud shows the most prominent polarization features due to Rayleigh-like scattering by the small cloud droplets. A planet in a stable orbit around Alpha Centauri A would leave temporal variations on the order of 10−13 W m s−1 in the total reflected flux and 10−11 in the total degree of polarization as the planet orbits the star and assuming a spatially unresolved star-planet system. Star-planet contrasts are on the order of 10−10 and vary proportionally with planetary flux.
Conclusions. Current polarimeters appear to be incapable to distinguish between the possible evolutionary phases of spatially unresolved terrestrial exoplanets, as a sensitivity close to 10−10 would be required to discern the planetary signal given the background of unpolarized starlight. A telescope or instrument capable of achieving planet-star contrasts lower than 10−9 should be able to observe the large variation of the planets resolved degree of polarization as a function of its phase angle and thus be able to discern an exo-Earth from an exo-Venus based on their clouds unique polarization signatures.
Space environment and magnetospheric Poynting fluxes of the exoplanet τ Boötis b
Authors: Elekes F. , Saur J. 
Published: January 2023

Context. The first tentative detection of a magnetic field on the hot-Jupiter-type exoplanet τ Boötis b was recently reported by Turner et al. (A&A, 645, A59). The magnetic field was inferred from observations of circularly polarized radio emission obtained with the LOFAR telescopes. The observed radio emission is possibly a consequence of the interaction of the surrounding stellar wind with the planet's magnetic field.
Aims. We aim to better understand the near space environment of τ Boötis b and to shed light on the structure and energetics of its near-field interaction with the stellar wind. We are particularly interested in understanding the magnetospheric energy fluxes powered by the star-planet interaction and in localizing the source region of possible auroral radio emission.
Methods. We performed magnetohydrodynamic simulations of the space environment around τ Boötis b and its interaction with the stellar wind using the PLUTO code. We investigated the magnetospheric energy fluxes and effects of different magnetic field orientations in order to understand the physical processes that cause the energy fluxes that may lead to the observed radio emission given the magnetic field strength proposed in Turner et al. (A&A, 645, A59). Furthermore, we study the effect of various stellar wind properties, such as density and pressure, on magnetospheric energy fluxes given the uncertainty of extrasolar stellar wind predictions.
Results. We find in our simulations that the interaction is most likely super-Alfvénic and that energy fluxes generated by the stellar wind-planet interaction are consistent with the observed radio powers. Magnetospheric Poynting fluxes are on the order of 1–8 × 1018 W for hypothetical open, semi-open, and closed magnetospheres. These Poynting fluxes are energetically consistent with the radio powers in Turner et al. (A&A, 645, A59) for a magnetospheric Poynting flux-to-radio efficiency >10−3 when the magnetic fields of the planet and star are aligned. In the case of lower efficiency factors, the magnetospheric radio emission scenario is, according to the parameter space modeled in this study, not powerful enough. A sub-Alfvénic interaction with decreased stellar wind density could channel Poynting fluxes on the order of 1018W toward the star. In the case of a magnetic polarity reversal of the host star from an aligned to anti-aligned field configuration, the expected radio powers in the magnetospheric emission scenario fall below the observable threshold. Furthermore, we constrain the possible structure of the auroral oval to a narrow band near the open-closed field line boundary. The strongest emission is likely to originate from the night side of the planet. More generally, we find that stellar wind variability in terms of density and pressure does significantly influence magnetospheric energy fluxes for close-in magnetized exoplanets.