bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrafast nonadiabatic excited-state intramolecular proton transfer in 3-hydroxychromone: A surface hopping approach
Authors: Nag Probal , Anand Neethu , Vennapusa Sivaranjana Reddy 
Published: September 2021

We employ the ab initio molecular dynamics within the surface hopping method to explore the excited-state intramolecular proton transfer taking place on the coupled “bright” S1 (ππ*) and “dark” S2 (nπ*) states of 3-hydroxychromone. The nonadiabatic population transfer between these states via an accessible conical intersection would open up multiple proton transfer pathways. Our findings reveal the keto tautomer formation via S1 on a timescale similar to the O–H in-plane vibrational period (&lt;100 fs). Structural analysis indicates that a few parameters of the five-membered proton transfer geometry that constitute the donor (hydroxyl) and acceptor (carbonyl) groups would be adequate to drive the enol to keto transformation. We also investigate the role of O–H in-plane and out-of-plane vibrational motions in the excited-state dynamics of 3-hydroxychromone.
Δ40p53 isoform up-regulates netrin-1/UNC5B expression and potentiates netrin-1 pro-oncogenic activity
Authors: Sun Yan , Manceau Ambroise , Frydman Lisa , Cappuccio Lucie , Neves David , Basso Valeria , Wang Hong , Fombonne Joanna , Maisse Carine , Mehlen Patrick , Paradisi Andrea 
Published: September 2021

Significance
Netrin-1 is frequently overexpressed in aggressive cancers, acting as the antiapoptotic ligand of the dependence receptors DCC and members of the UNC5H family. Accordingly, netrin-1 inhibition induces apoptosis and tumor growth inhibition. We have previously shown that the transcription factor p53 regulates netrin-1 gene expression in cancer cells treated with conventional chemotherapeutic drugs. We show here that netrin-1 is a target gene of the N-terminal p53 isoform Δ40p53, acting independently of full-length p53 activity, thus promoting cell survival. We show that netrin-1 interference, in presence of Δ40p53, triggers apoptosis in cancer and primary cells and tumor growth inhibition in preclinical in vivo models. We propose that netrin-1 inhibition is a promising therapeutic strategy in tumors expressing high levels of Δ40p53.
Sensitive detection of cell-derived force and collagen matrix tension in microtissues undergoing large-scale densification
Authors: Wang Xiang , Gao Qiang , Han Xiaoning , Bu Bing , Wang Longfei , Li Aoqi , Deng Linhong 
Published: September 2021

Significance
Tissue development and remodeling are highly regulated by the forces from cell contraction and collagen cross-linking, which is also dependent on microenvironment mechanics. However, such forces have seldom been studied in very soft tissue because of a lack of techniques to detect force without interference from the probe. Here, we overcame this challenge by using polymer-based, highly flexible microstrings to grow microtissues and then quantify the strain-induced force by measuring the microstring deflection during large-scale densification of the microtissues. We thus revealed the minimal contraction force required for microtissue densification that is controlled by external boundary mechanics and a dynamic shift from cell-derived force to collagen tension in terms of the main contribution to microtissue force during densification.
Effect of Si-doped InGaN underlayers on photoluminescence efficiency and recombination dynamics in InGaN/GaN quantum wells
Authors: Church S A , Christian G M , Barrett R M , Hammersley S , Kappers M J , Frentrup M , Oliver R A , Binks D J 
Published: September 2021

Abstract
A series of single InGaN/GaN quantum wells (QWs) with a Si-doped InGaN underlayer were studied to investigate the impact of the underlayer on photoluminescence efficiency and recombination dynamics. The thickness of the GaN capping layer was varied between samples, which changed the electric field across the QW due to band bending near the surface. When directly exciting the wells, thermionic emission of carriers results in a rapid drop in the photoluminesence efficiency with increasing temperature such that no emission is observed above 100 K. However, exciting above the energy of the barriers caused the intensity of the QW emission to drop more slowly, with up to 12% of the 10 K emission intensity remaining at 300 K. This difference is attributed to hole transfer from the underlayer into the QW, which increases in efficiency at higher temperatures, and is enhanced by stronger electric fields present in the GaN barriers of samples with thinner GaN capping layers. Further, the sample with the narrowest cap layer of 2 nm has a different shape and characteristic time for its photoluminescence decay transient and a different emission energy temperature dependence than the other samples. This behaviour was ascribed to a change in carrier localisation for this sample due to a reversal of the net field across the well compared to the other samples.
Imaging depth adaptive resolution enhancement for optical coherence tomography via deep neural network with external attention
Authors: Ren Shangjie , Shen Xiongri , Xu Jingjiang , Li Liang , Qiu Haixia , Jia Haibo , Wu Xining , Chen Defu , Zhao Shiyong , Yu Bo , Gu Ying , Dong Feng 
Published: September 2021

Abstract
Optical coherence tomography (OCT) is a promising non-invasive imaging technique that owns many biomedical applications. In this paper, a deep neural network is proposed for enhancing the spatial resolution of OCT en face images. Different from the previous reports, the proposed can recover high-resolution en face images from low-resolution en face images at arbitrary imaging depth. This kind of imaging depth adaptive resolution enhancement is achieved through an external attention mechanism, which takes advantage of morphological similarity between the arbitrary-depth and full-depth en face images. Firstly, the deep feature maps are extracted by a feature extraction network from the arbitrary-depth and full-depth en face images. Secondly, the morphological similarity between the deep feature maps is extracted and utilized to emphasize the features strongly correlated to the vessel structures by using the external attention network. Finally, the SR image is recovered from the enhanced feature map through an up-sampling network. The proposed network is tested on a clinical skin OCT data set and an open-access retinal OCT dataset. The results show that the proposed external attention mechanism can suppress invalid features and enhance significant features in our tasks. For all tests, the proposed SR network outperformed the traditional image interpolation method, e.g. bi-cubic method, and the state-of-the-art image super-resolution networks, e.g. enhanced deep super-resolution network, residual channel attention network, and second-order attention network. The proposed method may increase the quantitative clinical assessment of micro-vascular diseases which is limited by OCT imaging device resolution.
Neutral beam injection for fusion reactors: technological constraints versus functional requirements
Authors: Hopf C. , Starnella G. , den Harder N. , Fantz U. 
Published: September 2021

Abstract
In this paper we look at the technological constraints of neutral beam injection (NBI) systems and compare them with the functional requirements that NBI has in the various envisaged plasma scenarios for tokamak fusion reactors of the DEMO and fusion power plant (FPP) class. We show in particular that there is an intermediate beam energy range in which beamlines are unattractive because of size. Furthermore, for scenarios that consider NBI only for ion heating during the ramp-up and heat-to-burn phase we show that the use of beam energies in the range of 100 to 200 keV, which could be produced from positive ion beams with a much simpler system, could be an attractive option that should be further investigated.
Performance comparison of single and double pass PV/T solar collectors integrated with rectangular plate fin absorber
Authors: Amrizal  , Hidayat Y P , Irsyad M 
Published: September 2021

Abstract
Solar panel can act as a medium for transforming sunlight into electrical energy. Nevertheless, not all of the sunlight received on this device can be converted into electrical energy and the remainder will be dissipated into thermal energy. If a solar panel is continuously exposed to the sun, so its temperature will increase and thereby reduce its electrical efficiency. To deal with the issue, it may combine a PV panel with a thermal collector which is called a hybrid PV/T collector. Furthermore, in the present study the effects of fluid flow direction and mass flow rate on the thermal and electrical efficiency of the PV/T collectors are extensively analyzed. Single and double pass collectors with rectangular plate fin absorber were attached to backside of the PV panel. They were tested using a solar simulator with different flow rate ranging between 0.01 and 0.05 kg/s of the working fluid. The results show that the use of double pass PV/T air collector increase its performance compared with the single pass one. The highest values obtained from this type collector are found to be 73.23% in the thermal efficiency and 10.16% in the electrical efficiency with the working fluid mass flow rate of 0.048 kg/s.
Effect of austempering temperatures on surface hardness of AISI 4140 steel
Authors: Badaruddin M , Bakti B , Prasetyo B , Sugiyanto  
Published: September 2021

Abstract
AISI 4140 steel is widely used in various engine elements, such as connecting rods, crankshafts, axles, piston rods, and sprockets. The purpose of this study was to determine the hardness value and microstructure using temperature variations in the austempering process. The test results show that after the austempering process with temperature variations changed the hardness. The austempering process can increase the hardness value, but after the temperature is raised, the hardness value decreases. The greatest hardness value at 350°C was 264.4 BHN. After increasing the temperature to 400°C, the hardness decreased to 239.1 BHN. At a temperature of 450°C, the hardness was 226.7 BHN. Microstructure observations showed that the bainite is more uniform with increasing temperature. The test results show that the austempering temperature affects the hardness value and microstructure. When the austempering temperature is increased, the hardness value decreases.
Corrosion of Carbon Steel and alloy Steel: effect of humidity and hydrochloric acid
Authors: Muhammad Abdulkader A. , Almula Thamir A. D. M. S. , Sultan Dyhia A. 
Published: September 2021

Abstract
The corrosion performance of hypo-eutectoid carbon steel, and alloy steel used in steam boilers at Al-Najibiyah Thermal Power Station in the Iraqi city of Basra was investigated. These metals were exposed to different media such as moisture and acids for (30, 45, and 60) days, then the rate of corrosion was calculated in a way of weight loss. The influence of carbon content, corrosive media and duration of immersion on samples of hypo-eutectic carbon steel and alloy steel were studied. The results showed an increase in the percentage of corrosion as a result of the increase in carbon content, and alloy steel has a high resistance to corrosion than carbon steel in the different corrosive media used in this study.
Micro-electro discharge machining (Micro-EDM) models for conductive and nonconductive materials: A review
Authors: Ali M Y , Sabur A , Ya’akub S R , Hamid A D A , Alao A R , Singh R 
Published: September 2021

Abstract
Models are useful in controlling the process effectively and efficiently in micro electro discharge machining (Micro-EDM). There are two types of models which are empirical models and theoretical models. Most of the models are basically formulated for conductive work materials. However, nowadays there is a trend to cut nonconductive materials using micro-EDM where the models developed for conductive materials are not applicable. There are only few models that are developed to cut nonconductive materials with micro EDM but these models have limitations. In this article, models for cutting conductive materials and nonconductive materials using micro EDM are compared in view of their applications.
Flexural behaviour of jute, glass, and Carbon fibre reinforced Polyester hybrid composites
Authors: Murdani A , Amrullah U S 
Published: September 2021

Abstract
This study is a part of a project in developing natural fibre reinforced composite for wind turbine blade. The objective of this study is to evaluate the effect of fibre stacking sequence on flexural behaviour of the natural fibre reinforced composite hybridized with synthetic fibre. The flexural behaviour of the composite becomes an important consideration in deciding stacking sequence of the fibres. Material used in this study is polyester resin as the matrix. Jute, glass, and carbon fibres are used as the reinforcement. The composites were fabricated using vacuum bagging method cured at room temperature. The combinations of fibre as the reinforcement are configured by arrange two and three types of fibre. As a natural fibre, jute exists in all kind of combination. Flexural behaviour was observed using 3-point-bending test. The specimens were tested in accordance to the fibre stacking sequence. The result shows that stacking sequence of the fibres give significant different flexural behaviour regardless the effect of the fibre strength.
Fusion deposition modeling (FDM) 3D printing parameters correlation: An analysis of different polymers surface roughness
Authors: Barreno-Avila A F , Monar-Naranjo M , Barreno-Avila E M 
Published: September 2021

Abstract
One of the most popular methods for manufacturing new products is FDM (Fusion Deposition Modeling). In which two segments are established: industrial and desktop. The latter group has had notable growth in recent years. One of the disadvantages found in this method is its surface finish, which presents a remarkable roughness. In this research work, the correlation that exists in the printing configuration’ parameters and the resulting roughness analyzed by means of the ISO 4287-1997 standard will be analyzed. The configuration parameters to take into account are: layer height, printing speed. The materials to be analyzed are: PLA, PET-G, ASA, Wood Filament, TPU. Besides, the equipment used is a Prusa brand desktop printer with the manufacturer’s software. What is more, the acceleration, extruder temperature and bed recommended in the software are used for each material. Hence, the constant printing characteristics are: perimeter thickness, 10% infill, extrusion diameter 0.4 mm. The objects to be evaluated are printed and the roughness on the walls of the Z axis, base plane and upper plane is measured. This analysis was carried out by means of the correlation by the use of the analysis of variance ANOVA. The printing speed does not affect the resulting surface roughness in any plane, while the layer height only shows a significant correlation ( < 0.05) with the roughness of the lateral plane of the samples.
Cobalt phosphide nanowires as efficient near-infrared light-driven antibacterial agents with high stability and cytocompatibility
Authors: Yin Yixin , Ma Linmao , Yan Yuanyuan , Han Hecheng , Zheng Luning , Li Xiaoyan , Xu Xin 
Published: September 2021

Abstract
Rapid emergence of antibiotic-resistant bacteria has brought huge threat to global healthcare systems. Alternative strategies are urgently needed to fight against these superbugs. In this study, we synthesized a series of cobalt phosphide nanoarchitectures and characterized their physicochemical properties as well as their antibacterial activities. We found that all nanomaterials showed an impressive photothermal property as indicated by their strong near-infrared (NIR) absorption capacity. In particular, 1D-CoP nanowires exhibited the optimal photothermal efficiency due to their higher aspect ratio. Under NIR light illumination, the temperature of the 1D-CoP nanowires suspension was increased by 45.4 °C within 20 min. In contrast, the temperatures of 2D-CoP nanoplates and 3D-CoP nanocubes were increased by 25.5 °C and 26.9 °C, respectively. The growth of planktonic bacteria can be effectively inhibited by 99% within 30 min under NIR irradiation with the presence of 1D-CoP nanowires in suspension. In comparison, up to 60% of the bacteria could be killed when treated with 2D-CoP nanoplates and 3D-CoP nanocubes. Moreover, all nanomaterials displayed high cytocompatibility. This work emphasizes that the anisotropy plays an important role in governing the photothermal properties of NIR-driven materials. Furthermore, the application of CoP nanowires is a promising strategy to treat antibiotic-resistant bacteria.
An inductively coupled plasma metal organic chemical vapor deposition based on showerhead structure for low temperature growth
Authors: Zhang Zixuan , Luo Yi , Yu Jiadong , Li Xiang , Wang Jian , Yu Wangyang , Wang Lai , Hao Zhibiao , Sun Changzheng , Han Yanjun , Xiong Bing , Li Hongtao 
Published: September 2021

Abstract
An inductively coupled plasma metal organic chemical vapor deposition (ICP-MOCVD) based on showerhead structure is proposed for the low temperature growth of thin solid films including GaN. The flow field of precursors in the chamber of ICP-MOCVD was analyzed and the structure of showerhead was optimized by changing the showerhead diameter to obtain uniform velocity field above the substrate. The thickness non-uniformity of GaN films grown at 600 °C was improved from 5.14% to 1.86% after the optimization of showerhead. On that basis, the influence of triethylgallium (TEG) and trimethylgallium (TMG) on low-temperature GaN growth were investigated and TEG was proved to be the more appropriate Ga source in this case. Finally, GaN film with high c-axis and in-plane orientations was obtained on sputtered AlN/sapphire template and the full width half maximums of (002) and (102) x-ray rocking curves are 0.45° and 0.57° respectively. Our results provide a practicable method for the optimization of low-temperature MOCVD, which has potential to obtain large-scale crystalline films at low temperature.
(Dis)connectedness of nonlocal minimal surfaces in a cylinder and a stickiness property
Authors: Dipierro Serena , Onoue Fumihiko , Valdinoci Enrico 
Published: September 2021

We consider nonlocal minimal surfaces in a cylinder with prescribed datum given by the complement of a slab. We show that when the width of the slab is large the minimizers are disconnected and when the width of the slab is small the minimizers are connected. This feature is in agreement with the classical case of the minimal surfaces.

Nevertheless, we show that when the width of the slab is large the minimizers are not flat discs, as it happens in the classical setting, and, in particular, in dimension

2
2

we provide a quantitative bound on the stickiness property exhibited by the minimizers.

Moreover, differently from the classical case, we show that when the width of the slab is small then the minimizers completely adhere to the side of the cylinder, thus providing a further example of stickiness phenomenon.
Differential transcript usage analysis of bulk and single-cell RNA-seq data with DTUrtle
Authors: Tekath Tobias , Dugas Martin 
Published: September 2021

Abstract

Motivation
Each year, the number of published bulk and single-cell RNA-seq datasets is growing exponentially. Studies analyzing such data are commonly looking at gene-level differences, while the collected RNA-seq data inherently represents reads of transcript isoform sequences. Utilizing transcriptomic quantifiers, RNA-seq reads can be attributed to specific isoforms, allowing for analysis of transcript-level differences. A differential transcript usage (DTU) analysis is testing for proportional differences in a gene’s transcript composition, and has been of rising interest for many research questions, such as analysis of differential splicing or cell-type identification.

Results
We present the R package DTUrtle, the first DTU analysis workflow for both bulk and single-cell RNA-seq datasets, and the first package to conduct a ‘classical’ DTU analysis in a single-cell context. DTUrtle extends established statistical frameworks, offers various result aggregation and visualization options and a novel detection probability score for tagged-end data. It has been successfully applied to bulk and single-cell RNA-seq data of human and mouse, confirming and extending key results. In addition, we present novel potential DTU applications like the identification of cell-type specific transcript isoforms as biomarkers.

Availability and implementation
The R package DTUrtle is available at https://github.com/TobiTekath/DTUrtle with extensive vignettes and documentation at https://tobitekath.github.io/DTUrtle/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Nitrate-dependent anaerobic methane oxidation and chemolithotrophic denitrification in a temperate eutrophic lake
Authors: Roland Fleur A E , Borges Alberto V , Bouillon Steven , Morana Cédric 
Published: September 2021

ABSTRACTWhile the emissions of methane (CH4) by natural systems have been widely investigated, CH4 aquatic sinks are still poorly constrained. Here, we investigated the CH4 cycle and its interactions with nitrogen (N), iron (Fe) and manganese (Mn) cycles in the oxic-anoxic interface and deep anoxic waters of a small, meromictic and eutrophic lake, during two summertime sampling campaigns. Anaerobic CH4 oxidation (AOM) was measured from the temporal decrease of CH4 concentrations, with the addition of three potential electron acceptors (NO3–, iron oxides (Fe(OH)3) and manganese oxides (MnO2)). Experiments with the addition of either 15N-labeled nitrate (15N-NO3–) or 15N-NO3– combined with sulfide (H2S), to measure denitrification, chemolithotrophic denitrification and anaerobic ammonium oxidation (anammox) rates, were also performed. Measurements showed AOM rates up to 3.8 µmol CH4 L–1 d–1 that strongly increased with the addition of NO3– and moderately increased with the addition of Fe(OH)3. No stimulation was observed with MnO2 added. Potential denitrification and anammox rates up to 63 and 0.27 µmol N2 L–1 d–1, respectively, were measured when only 15N-NO3– was added. When H2S was added, both denitrification and anammox rates increased. Altogether, these results suggest that prokaryote communities in the redoxcline are able to efficiently use the most available substrates.
Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost
Authors: Varliero Gilda , Rafiq Muhammad , Singh Swati , Summerfield Annabel , Sgouridis Fotis , Cowan Don A , Barker Gary 
Published: September 2021

ABSTRACT
Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (&gt;164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering.