bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antiferromagnetic topological insulator with selectively gapped Dirac cones
Authors: Honma A. , Takane D. , Souma S. , Yamauchi K. , Wang Y. , Nakayama K. , Sugawara K. , Kitamura M. , Horiba K. , Kumigashira H. , Tanaka K. , Kim T. K. , Cacho C. , Oguchi T. , Takahashi T. , Ando Yoichi , Sato T. 
Published: November 2023

AbstractAntiferromagnetic (AF) topological materials offer a fertile ground to explore a variety of quantum phenomena such as axion magnetoelectric dynamics and chiral Majorana fermions. To realize such intriguing states, it is essential to establish a direct link between electronic states and topology in the AF phase, whereas this has been challenging because of the lack of a suitable materials platform. Here we report the experimental realization of the AF topological-insulator phase in NdBi. By using micro-focused angle-resolved photoemission spectroscopy, we discovered contrasting surface electronic states for two types of AF domains; the surface having the out-of-plane component in the AF-ordering vector displays Dirac-cone states with a gigantic energy gap, whereas the surface parallel to the AF-ordering vector hosts gapless Dirac states despite the time-reversal-symmetry breaking. The present results establish an essential role of combined symmetry to protect massless Dirac fermions under the presence of AF order and widen opportunities to realize exotic phenomena utilizing AF topological materials.
ATP synthase evolution on a cross-braced dated tree of life
Authors: Mahendrarajah Tara A. , Moody Edmund R. R. , Schrempf Dominik , Szánthó Lénárd L. , Dombrowski Nina , Davín Adrián A. , Pisani Davide , Donoghue Philip C. J. , Szöllősi Gergely J. , Williams Tom A. , Spang Anja 
Published: November 2023

AbstractThe timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.
High proton conductivity within the ‘Norby gap’ by stabilizing a perovskite with disordered intrinsic oxygen vacancies
Authors: Saito Kei , Yashima Masatomo 
Published: November 2023

AbstractProton conductors are attractive materials with a wide range of potential applications such as proton-conducting fuel cells (PCFCs). The conventional strategy to enhance the proton conductivity is acceptor doping into oxides without oxygen vacancies. However, the acceptor doping results in proton trapping near dopants, leading to the high apparent activation energy and low proton conductivity at intermediate and low temperatures. The hypothetical cubic perovskite BaScO2.5 may have intrinsic oxygen vacancies without the acceptor doping. Herein, we report that the cubic perovskite-type BaSc0.8Mo0.2O2.8 stabilized by Mo donor-doing into BaScO2.5 exhibits high proton conductivity within the ‘Norby gap’ (e.g., 0.01 S cm−1 at 320 °C) and high chemical stability under oxidizing, reducing and CO2 atmospheres. The high proton conductivity of BaSc0.8Mo0.2O2.8 at intermediate and low temperatures is attributable to high proton concentration, high proton mobility due to reduced proton trapping, and three-dimensional proton diffusion in the cubic perovskite stabilized by the Mo-doping into BaScO2.5. The donor doping into the perovskite with disordered intrinsic oxygen vacancies would be a viable strategy towards high proton conductivity at intermediate and low temperatures.
Deep-sea origin and depth colonization associated with phenotypic innovations in scleractinian corals
Authors: Campoy Ana N. , Rivadeneira Marcelo M. , Hernández Cristián E. , Meade Andrew , Venditti Chris 
Published: November 2023

AbstractThe deep sea (>200 m) is home to a surprisingly rich biota, which in some cases compares to that found in shallow areas. Scleractinian corals are an example of this – they are key species in both shallow and deep ecosystems. However, what evolutionary processes resulted in current depth distribution of the marine fauna is a long-standing question. Various conflicting hypotheses have been proposed, but few formal tests have been conducted. Here, we use global spatial distribution data to test the bathymetric origin and colonization trends across the depth gradient in scleractinian corals. Using a phylogenetic approach, we infer the origin and historical trends in directionality and speed of colonization during the diversification in depth. We also examine how the emergence of photo-symbiosis and coloniality, scleractinian corals’ most conspicuous phenotypic innovations, have influenced this process. Our results strongly support an offshore-onshore pattern of evolution and varying dispersion capacities along depth associated with trait-defined lineages. These results highlight the relevance of the evolutionary processes occurring at different depths to explain the origin of extant marine biodiversity and the consequences of altering these processes by human impact, highlighting the need to include this overlooked evolutionary history in conservation plans.
Cobalt-catalyzed aminoalkylative carbonylation of alkenes toward direct synthesis of γ-amino acid derivatives and peptides
Authors: Wang Le-Cheng , Yuan Yang , Zhang Youcan , Wu Xiao-Feng 
Published: November 2023

Abstractγ-Amino acids and peptides analogues are common constituents of building blocks for numerous biologically active molecules, pharmaceuticals, and natural products. In particular, γ-amino acids are providing with better metabolic stability than α-amino acids. Herein we report a multicomponent carbonylation technology that combines readily available amides, alkenes, and the feedstock gas carbon monoxide to build architecturally complex and functionally diverse γ-amino acid derivatives in a single step by the implementation of radical relay catalysis. This transformation can also be used as a late-stage functionalization strategy to deliver complex, advanced γ-amino acid products for pharmaceutical and other areas.
Design and fabrication of a stable Ni-PTFE-SiC superhydrophobic anticorrosive coating by electrodeposition
Authors: Liu Jianguo , Fang Xiuting , Ma Huixiang , Cheng Jie , Xing Xiao , Cui Gan , Li Zili 
Published: November 2023

AbstractSuperhydrophobic coatings show great application potential in many fields, but they have not been widely used due to poor stability. A Ni-PTFE-SiC composite coating was proposed in this paper. Firstly, the Ni-PTFE-SiC coating structure was designed by molecular dynamics simulations. The feasibility of superhydrophobic effect of this structure and the adsorption stability of the composite coatings were proved. This approach can also be used to avoid trial and errors when selecting other similar candidate substances. Then, the Ni-PTFE-SiC superhydrophobic coatings were successfully prepared by composite electrodeposition, with the water contact angle of more than 155° and the sliding angle of close to 0°. The effects of current density, deposition time and nanoparticle concentration on the wettability and morphology of the coatings were also investigated. Through comparative experiments, the best preparation parameters were: PTFE 14 g L−1, SiC 6 g L−1, primary current density 7 A dm−² (10 min) and secondary current density 15 A dm−² (5 min). This preparation method doesn’t need additional modification with low surface energy substances like the traditional preparation process, and greatly improves the corrosion resistance, wear resistance and durability of the coatings.
Shotgun metagenomes from productive lakes in an urban region of Sweden
Authors: Rodríguez-Gijón Alejandro , Hampel Justyna J. , Dharamshi Jennah , Bertilsson Stefan , Garcia Sarahi L. 
Published: November 2023

AbstractUrban lakes provide multiple benefits to society while influencing life quality. Moreover, lakes and their microbiomes are sentinels of anthropogenic impact and can be used for natural resource management and planning. Here, we release original metagenomic data from several well-characterized and anthropogenically impacted eutrophic lakes in the vicinity of Stockholm (Sweden). Our goal was to collect representative microbial community samples and use shotgun sequencing to provide a broad view on microbial diversity of productive urban lakes. Our dataset has an emphasis on Lake Mälaren as a major drinking water reservoir under anthropogenic impact. This dataset includes short-read sequence data and metagenome assemblies from each of 17 samples collected from eutrophic lakes near the greater Stockholm area. We used genome-resolved metagenomics and obtained 2378 metagenome assembled genomes that de-replicated into 514 species representative genomes. This dataset adds new datapoints to previously sequenced lakes and it includes the first sequenced set of metagenomes from Lake Mälaren. Our dataset serves as a baseline for future monitoring of drinking water reservoirs and urban lakes.
Two-sample mendelian randomization analysis investigates ambient fine particulate matter's impact on cardiovascular disease development
Authors: Liang Xiao , Liang Lianjing , Fan Yuchao 
Published: November 2023

AbstractPM2.5, a key component of air pollution, significantly threatens public health. Cardiovascular disease is increasingly associated with air pollution, necessitating more research. This study used a meticulous two-sample Mendelian randomization (MR) approach to investigate the potential causal link between elevated PM2.5 levels and 25 types of cardiovascular diseases. Data sourced from the UK Biobank, focusing on individuals of European ancestry, underwent primary analysis using Inverse Variance Weighting. Additional methods such as MR-Egger, weighted median, Simple mode, and Weighted mode provided support. Sensitivity analyses assessed instrument variable heterogeneity, pleiotropy, and potential weak instrument variables. The study revealed a causal link between PM2.5 exposure and higher diagnoses of Atherosclerotic heart disease (primary or secondary, OR [95% CI] 1.0307 [1.0103–1.0516], p-value = 0.003 and OR [95% CI] 1.0179 [1.0028–1.0333], p-value = 0.0202) and Angina pectoris (primary or secondary, OR [95% CI] 1.0303 [1.0160–1.0449], p-value = 3.04e−05 and OR [95% CI] 1.0339 [1.0081–1.0603], p-value = 0.0096). Additionally, PM2.5 exposure increased the likelihood of diagnoses like Other forms of chronic ischaemic heart disease (secondary, OR [95% CI] 1.0193 [1.0042–1.0346], p-value = 0.0121), Essential hypertension (secondary, OR [95% CI] 1.0567 [1.0142–1.1010], p-value = 0.0085), Palpitations (OR [95% CI] 1.0163 [1.0071–1.0257], p-value = 5e−04), and Stroke (OR [95% CI] 1.0208 [1.0020–1.0401], p-value = 0.0301). Rigorous sensitivity analyses confirmed these significant findings' robustness and validity. Our study revealed the causal effect between higher PM2.5 concentrations and increased cardiovascular disease risks. This evidence is vital for policymakers and healthcare providers, urging targeted interventions to reduce PM2.5 levels.
Prediction of therapeutic intensity level from automatic multiclass segmentation of traumatic brain injury lesions on CT-scans
Authors: Brossard Clément , Grèze Jules , de Busschère Jules-Arnaud , Attyé Arnaud , Richard Marion , Tornior Florian Dhaussy , Acquitter Clément , Payen Jean-François , Barbier Emmanuel L. , Bouzat Pierre , Lemasson Benjamin 
Published: November 2023

AbstractThe prediction of the therapeutic intensity level (TIL) for severe traumatic brain injury (TBI) patients at the early phase of intensive care unit (ICU) remains challenging. Computed tomography images are still manually quantified and then underexploited. In this study, we develop an artificial intelligence-based tool to segment brain lesions on admission CT-scan and predict TIL within the first week in the ICU. A cohort of 29 head injured patients (87 CT-scans; Dataset1) was used to localize (using a structural atlas), segment (manually or automatically with or without transfer learning) 4 or 7 types of lesions and use these metrics to train classifiers, evaluated with AUC on a nested cross-validation, to predict requirements for TIL sum of 11 points or more during the 8 first days in ICU. The validation of the performances of both segmentation and classification tasks was done with Dice and accuracy scores on a sub-dataset of Dataset1 (internal validation) and an external dataset of 12 TBI patients (12 CT-scans; Dataset2). Automatic 4-class segmentation (without transfer learning) was not able to correctly predict the apparition of a day of extreme TIL (AUC = 60 ± 23%). In contrast, manual quantification of volumes of 7 lesions and their spatial location provided a significantly better prediction power (AUC = 89 ± 17%). Transfer learning significantly improved the automatic 4-class segmentation (DICE scores 0.63 vs 0.34) and trained more efficiently a 7-class convolutional neural network (DICE = 0.64). Both validations showed that segmentations based on transfer learning were able to predict extreme TIL with better or equivalent accuracy (83%) as those made with manual segmentations. Our automatic characterization (volume, type and spatial location) of initial brain lesions observed on CT-scan, publicly available on a dedicated computing platform, could predict requirements for high TIL during the first 8 days after severe TBI. Transfer learning strategies may improve the accuracy of CNN-based segmentation models.Trial registrations Radiomic-TBI cohort; NCT04058379, first posted: 15 august 2019; Radioxy-TC cohort; Health Data Hub index F20220207212747, first posted: 7 February 2022.
Development of a facile method to compute collagen network pathological anisotropy using AFM imaging
Authors: Khattignavong Emilie , Neshatian Mehrnoosh , Vaez Mina , Guillermin Amaury , Tauer Josephine T. , Odlyha Marianne , Mittal Nimish , Komarova Svetlana V. , Zahouani Hassan , Bozec Laurent 
Published: November 2023

AbstractType I collagen, a fundamental extracellular matrix (ECM) component, is pivotal in maintaining tissue integrity and strength. It is also the most prevalent fibrous biopolymer within the ECM, ubiquitous in mammalian organisms. This structural protein provides essential mechanical stability and resilience to various tissues, including tendons, ligaments, skin, bone, and dentin. Collagen has been structurally investigated for several decades, and variation to its ultrastructure by histology has been associated with several pathological conditions. The current study addresses a critical challenge in the field of collagen research by providing a novel method for studying collagen fibril morphology at the nanoscale. It offers a computational approach to quantifying collagen properties, enabling a deeper understanding of how collagen type I can be affected by pathological conditions. The application of Fast Fourier Transform (FFT) coupled with Atomic Force Microscope (AFM) imaging distinguishes not only healthy and diseased skin but also holds potential for automated diagnosis of connective tissue disorders (CTDs), contributing to both clinical diagnostics and fundamental research in this area. Here we studied the changes in the structural parameters of collagen fibrils in Ehlers Danlos Syndrome (EDS). We have used skin extracted from genetically mutant mice that exhibit EDS phenotype as our model system (Col1a1Jrt/+ mice). The collagen fibrils were analyzed by AFM based descriptive-structural parameters, coupled with a 2D Fast Fourier Transform(2D-FFT) approach that automated the analysis of AFM images. In addition, each sample was characterized based on its FFT and power spectral density. Our qualitative data showed morphological differences in collagen fibril clarity (clearness of the collagen fibril edge with their neighbouring fibri), D-banding, orientation, and linearity. We have also demonstrated that FFT could be a new tool for distinguishing healthy from tissues with CTDs by measuring the disorganization of fibrils in the matrix. We have also employed FFT to reveal the orientations of the collagen fibrils, providing clinically relevant phenotypic information on their organization and anisotropy. The result of this study can be used to develop a new automated tool for better diagnosis of CTDs.
Efficient end-to-end long-read sequence mapping using minimap2-fpga integrated with hardware accelerated chaining
Authors: Liyanage Kisaru , Samarakoon Hiruna , Parameswaran Sri , Gamaarachchi Hasindu 
Published: November 2023

Abstractminimap2is the gold-standard software for reference-based sequence mapping in third-generation long-read sequencing. Whileminimap2is relatively fast, further speedup is desirable, especially when processing a multitude of large datasets. In this work, we presentminimap2-fpga, a hardware-accelerated version ofminimap2that speeds up the mapping process by integrating an FPGA kernel optimised for chaining. Integrating the FPGA kernel intominimap2posed significant challenges that we solved by accurately predicting the processing time on hardware while considering data transfer overheads, mitigating hardware scheduling overheads in a multi-threaded environment, and optimizing memory management for processing large realistic datasets. We demonstrate speed-ups in end-to-end run-time for data from both Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio).minimap2-fpgais up to 79% and 53% faster thanminimap2for$$\sim 30\times $$∼30×ONT and$$\sim 50\times $$∼50×PacBio datasets respectively, when mapping without base-level alignment. When mapping with base-level alignment,minimap2-fpgais up to 62% and 10% faster thanminimap2for$$\sim 30\times $$∼30×ONT and$$\sim 50\times $$∼50×PacBio datasets respectively. The accuracy is near-identical to that of originalminimap2for both ONT and PacBio data, when mapping both with and without base-level alignment.minimap2-fpgais supported on Intel FPGA-based systems (evaluations performed on an on-premise system) and Xilinx FPGA-based systems (evaluations performed on a cloud system). We also provide a well-documented library for the FPGA-accelerated chaining kernel to be used by future researchers developing sequence alignment software with limited hardware background.
Unveiling the effect of strain engineering on the electrochemical properties of hydrothermally grown nanostructured indium doped ZnSeO3 for photoanode applications
Authors: Maswanganye M. W. , Kabongo G. L. , Mathevula L. E. , Mothudi B. M. , Dhlamini M. S. 
Published: November 2023

AbstractThe crucial role of In as a dopant on the structural, optical, and thermogravimetric characteristics of the zinc selenite (ZnSeO3) nanopowders has been investigated in detail using X-Ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM), Energy Dispersive Spectroscopy (EDS), Raman spectroscopy, diffuse reflectance spectroscopy (DRS), photoluminescence (PL) spectroscopy, and Thermogravimetric Analysis (TGA). The structural analysis indicates that all patterns are assigned to the ZnSeO3 orthorhombic structure. Also, XRD analysis shows that In3+ ions may have replaced Zn2+ ions, which causes lattice expansion. Both the Debye–Scherrer method, and the Williamson–Hall method have also been applied to study the influence of strain on the calculation of the crystallite size. The crystallite size was observed to increase with an increase in dopant concentration. The FE-SEM corroborated that the prepared samples are orthorhombic, with the EDS and mapping confirming the presence of In as a dopant. Raman spectroscopy results corroborated the XRD results indicating an expansion in the crystal structure of ZnSeO3 with the introduction of dopants. Based on DRS data, the introduction of In decreases the energy band gap of the synthesized ZnSeO3 nanopowder samples from 3.305 to 3.276. PL spectra confirm the presence of indium with the green emission band attributed to dopants dominating the emission. The TGA investigation shows an improvement in the mass loss with the introduction of dopants. EIS results indicated an improvement in the conductivity as the charge transfer resistance decreased from 525.04 to 21.95 kΩ for the undoped ZnSeO3 and 0.75% In–ZnSeO3 thin films showing improvement in charge mobility.
Genome sequence and characterization of Streptomyces phages Vanseggelen and Verabelle, representing two new species within the genus Camvirus
Authors: Ongenae Véronique , Kempff Annabel , van Neer Vera , Shomar Helena , Tesson Florian , Rozen Daniël , Briegel Ariane , Claessen Dennis 
Published: November 2023

AbstractDespite the rising interest in bacteriophages, little is known about their infection cycle and lifestyle in a multicellular host. Even in the model system Streptomyces, only a small number of phages have been sequenced and well characterized so far. Here, we report the complete characterization and genome sequences of Streptomyces phages Vanseggelen and Verabelle isolated using Streptomyces coelicolor as a host. A wide range of Streptomyces strains could be infected by both phages, but neither of the two phages was able to infect members of the closely related sister genus Kitasatospora. The phages Vanseggelen and Verabelle have a double-stranded DNA genome with lengths of 48,720 and 48,126 bp, respectively. Both phage genomes contain 72 putative genes, and the presence of an integrase encoding protein indicates a lysogenic lifestyle. Characterization of the phages revealed their stability over a wide range of temperatures (30–45 °C) and pH values (4–10). In conclusion, Streptomyces phage Vanseggelen and Streptomyces phage Verabelle are newly isolated phages that can be classified as new species in the genus Camvirus, within the subfamily Arquattrovirinae.