bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota
Authors: Zhao Jinzhi , Yang Yi , Xu Hua , Zheng Jianxujie , Shen Chengpin , Chen Tian , Wang Tao , Wang Bing , Yi Jia , Zhao Dan , Wu Enhui , Qin Qin , Xia Li , Qiao Liang 
Published: January 2023

AbstractMetaproteomics can provide valuable insights into the functions of human gut microbiota (GM), but is challenging due to the extreme complexity and heterogeneity of GM. Data-independent acquisition (DIA) mass spectrometry (MS) has been an emerging quantitative technique in conventional proteomics, but is still at the early stage of development in the field of metaproteomics. Herein, we applied library-free DIA (directDIA)-based metaproteomics and compared the directDIA with other MS-based quantification techniques for metaproteomics on simulated microbial communities and feces samples spiked with bacteria with known ratios, demonstrating the superior performance of directDIA by a comprehensive consideration of proteome coverage in identification as well as accuracy and precision in quantification. We characterized human GM in two cohorts of clinical fecal samples of pancreatic cancer (PC) and mild cognitive impairment (MCI). About 70,000 microbial proteins were quantified in each cohort and annotated to profile the taxonomic and functional characteristics of GM in different diseases. Our work demonstrated the utility of directDIA in quantitative metaproteomics for investigating intestinal microbiota and its related disease pathogenesis.
Three-dimensional chromatin architecture datasets for aging and Alzheimer’s disease
Authors: Meng Guofeng , Xu Hong , Lu Dong , Li Shensuo , Zhao Zhenzhen , Li Haohao , Zhang Weidong 
Published: January 2023

AbstractRecently, increasing studies are indicating a close association between dysregulated enhancers and neurodegenerative diseases, such as Alzheimer’s disease (AD). However, their contributions were poorly defined for lacking direct links to disease genes. To bridge this gap, we presented the Hi-C datasets of 4 AD patients, 4 dementia-free aged and 3 young subjects, including 30 billion reads. As applications, we utilized them to link the AD risk SNPs and dysregulated epigenetic marks to the target genes. Combining with epigenetic data, we observed more detailed interactions among regulatory regions and found that many known AD risk genes were under long-distance promoter-enhancer interactions. For future AD and aging studies, our datasets provide a reference landscape to better interpret findings of association and epigenetic studies for AD and aging process.
An open database on global coal and metal mine production
Authors: Jasansky Simon , Lieber Mirko , Giljum Stefan , Maus Victor 
Published: January 2023

AbstractWhile the extraction of natural resources has been well documented and analysed at the national level, production trends at the level of individual mines are more difficult to uncover, mainly due to poor availability of mining data with sub-national detail. In this paper, we contribute to filling this gap by presenting an open database on global coal and metal mine production on the level of individual mines. It is based on manually gathered information from more than 1900 freely available reports of mining companies, where every data point is linked to its source document, ensuring full transparency. The database covers 1171 individual mines and reports mine-level production for 80 different materials in the period 2000–2021. Furthermore, also data on mining coordinates, ownership, mineral reserves, mining waste, transportation of mining products, as well as mineral processing capacities (smelters and mineral refineries) and production is included.
Electrotaxis behavior of droplets composed of aqueous Belousov-Zhabotinsky solutions suspended in oil phase
Authors: Back Oliver , Asally Munehiro , Wang Zuowei , Hayashi Yoshikatsu 
Published: January 2023

AbstractTaxis is ubiquitous in biological and physical chemistry systems as a response to various external stimulations. We prepared aqueous droplets containing Belousov-Zhabotinsky (BZ) solutions suspended on an oleic acid oil phase subject to DC electric field and found that these BZ droplets undergo chemically driven translational motion towards the negative electrode under DC electric field. This electrotaxis phenomenon originates from the field-induced inhomogeneous distribution of reactants, in particular Br$$^{-}$$-ions, and consequently the biased location of the leading centers towards the positive electrode. We define the ’leading center’ (LC) as a specific location within the droplet where the BZ chemical wave (target pattern) is initiated. The chemical wave generated from the LC propagates passing the droplet center of mass and creates a gradient of interfacial tension when reaching the droplet-oil interface on the other side, resulting in a momentum exchange between the droplet and oil phases which drives the droplet motion in the direction of the electric field. A greater electric field strength renders a more substantial electrotaxis effect.
Connectivity-based parcellation of the amygdala and identification of its main white matter connections
Authors: Avecillas-Chasin Josue M. , Levinson Simon , Kuhn Taylor , Omidbeigi Mahmoud , Langevin Jean-Philippe , Pouratian Nader , Bari Ausaf 
Published: January 2023

AbstractThe amygdala plays a role in emotion, learning, and memory and has been implicated in behavioral disorders. Better understanding of the amygdala circuitry is crucial to develop new therapies for these disorders. We used data from 200 healthy-subjects from the human connectome project. Using probabilistic tractography, we created population statistical maps of amygdala connectivity to brain regions involved in limbic, associative, memory, and reward circuits. Based on the amygdala connectivity with these regions, we applied k-means clustering to parcellate the amygdala into three clusters. The resultant clusters were averaged across all subjects and the main white-matter pathways of the amygdala from each averaged cluster were generated. Amygdala parcellation into three clusters showed a medial-to-lateral pattern. The medial cluster corresponded with the centromedial and cortical nuclei, the basal cluster with the basal nuclei and the lateral cluster with the lateral nuclei. The connectivity analysis revealed different white-matter pathways consistent with the anatomy of the amygdala circuit. This in vivo connectivity-based parcellation of the amygdala delineates three clusters of the amygdala in a mediolateral pattern based on its connectivity with brain areas involved in cognition, memory, emotion, and reward. The human amygdala circuit presented in this work provides the first step for personalized amygdala circuit mapping for patients with behavioral disorders.
Novel loci for hyperglycemia identified by QTL mapping of longitudinal phenotypes and congenic analysis
Authors: Babaya Naru , Itoi-Babaya Michiko , Ueda Hironori , Kobayashi Misato , Noso Shinsuke , Hiromine Yoshihisa , Ishikawa Akira , Fujisawa Tomomi , Ikegami Hiroshi 
Published: January 2023

AbstractWe previously reported that four hyperglycemia loci are located on three chromosomes in the Nagoya-Shibata-Yasuda (NSY) mouse model, commonly used to study type 2 diabetes. However, we did not search for hyperglycemia loci across all chromosomes. In this study, we performed quantitative trait loci (QTLs) mapping of longitudinal phenotypes from crosses between NSY (hyperglycemic) and C3H (normoglycemic) mice. We identified four new QTLs for hyperglycemia, namely Nidd5nsy, Nidd6nsy, Nidd1c3h, and Nidd2c3h, on Chromosome 1, 4, 10, and 13, respectively. These QTLs were associated with hyperglycemia in young mice and had attenuated effects in older mice. Nidd5nsy and Nidd6nsy were hyperglycemic with NSY alleles, and Nidd1c3h and Nidd2c3h were hyperglycemic with C3H alleles. We further bred Nidd5nsy congenic mice and demonstrated that Nidd5nsy has a strong effect on hyperglycemia when young, accompanied by insulin resistance and visceral fat accumulation. These results showed that the effects of individual QTLs strengthened or weakened with age, and that the sum of the effects of QTLs captured the age-related deterioration of glucose tolerance in individuals. Our results support the importance of longitudinal phenotypes in the genetic analysis of polygenic traits and have implications for the genetic basis and pathogenesis of type 2 diabetes in humans.
Dual color pH probes made from silica and polystyrene nanoparticles and their performance in cell studies
Authors: Srivastava Priyanka , Tavernaro Isabella , Scholtz Lena , Genger Claudia , Welker Pia , Schreiber Frank , Meyer Klas , Resch-Genger Ute 
Published: January 2023

AbstractRatiometric green–red fluorescent nanosensors for fluorometrically monitoring pH in the acidic range were designed from 80 nm-sized polystyrene (PS) and silica (SiO2) nanoparticles (NPs), red emissive reference dyes, and a green emissive naphthalimide pH probe, analytically and spectroscopically characterized, and compared regarding their sensing performance in aqueous dispersion and in cellular uptake studies. Preparation of these optical probes, which are excitable by 405 nm laser or LED light sources, involved the encapsulation of the pH-inert red-fluorescent dye Nile Red (NR) in the core of self-made carboxylated PSNPs by a simple swelling procedure and the fabrication of rhodamine B (RhB)-stained SiO2-NPs from a silane derivative of pH-insensitive RhB. Subsequently, the custom-made naphthalimide pH probe, that utilizes a protonation-controlled photoinduced electron transfer process, was covalently attached to the carboxylic acid groups at the surface of both types of NPs. Fluorescence microscopy studies with the molecular and nanoscale optical probes and A549 lung cancer cells confirmed the cellular uptake of all probes and their penetration into acidic cell compartments, i.e., the lysosomes, indicated by the switching ON of the green naphthalimide fluorescence. This underlines their suitability for intracellular pH sensing, with the SiO2-based nanosensor revealing the best performance regarding uptake speed and stability.
Pre-analytical sample handling effects on tear fluid protein levels
Authors: Gijs Marlies , Arumugam Sinthuja , van de Sande Nienke , Webers Carroll A. B. , Sethu Swaminathan , Ghosh Arkasubhra , Shetty Rohit , Vehof Jelle , Nuijts Rudy M. M. A. 
Published: January 2023

AbstractTear fluid is emerging as a source of non-invasive biomarkers, both for ocular and systemic conditions. Accurate quantification of tear proteins can be improved by standardizing methods to collect and process tear fluid. The aim of this study was to determine sample handling factors that may influence the tear protein biomarker profile. Tear fluid was collected using Schirmer’s strips. Tear proteins were extracted by elution through centrifugation. Total protein content was determined using the bicinchoninic acid assay. Key concepts that apply to the entire sample processing cycle are tear sampling, tear storage, protein extraction and data normalization. Differences in wetting or migration length were observed between Schirmer’s strips from different manufacturers, and between protein-free and protein-rich solutions. One unit of migration length (mm) did not correspond to one unit of volume (µL). A positive correlation (r = 0.6671, p < 0.0001) was observed between migration length and total tear protein content. The most beneficial storage conditions were strips that were not stored (+ 21.8%), or underwent ‘wet’ storage (+ 11.1%). Protein recovery was the highest in 400 µL extraction buffer and independent of protein molecular weight. This study helps to explain inter- and intra-variability that is often seen with tear biomarker research. This information is critical to ensure accuracy of test results, as tear biomarkers will be used for patient management and in clinical trials in the near future. This study also highlights the need for standardization of Schirmer’s strip manufacturing, tear fluid processing and analyte concentration normalization.
Complete chloroplast genome molecular structure, comparative and phylogenetic analyses of Sphaeropteris lepifera of Cyatheaceae family: a tree fern from China
Authors: Hu Qingdi , Qian Renjuan , Zhang Yanjun , Ma Xiaohua , Ye Youju , Zhang Xule , Lin Lin , Liu Hongjian , Zheng Jian 
Published: January 2023

AbstractSphaeropteris lepifera is a tree fern in the Cyatheaceae, a family that has played an important role in the evolution of plant systems. This study aimed to analyze the complete chloroplast genome of S. lepifera and compared it with previously published chloroplast genomes Cyatheaceae family. The chloroplast genome of S. lepifera comprised 162,114 bp, consisting of a large single copy (LSC) region of 86,327 bp, a small single copy (SSC) region of 27,731 bp and a pair of inverted repeats (IRa and IRb) of 24,028 bp each. The chloroplast genome encoded 129 genes, comprising 32 transfer RNAs, 8 ribosomal RNAs, and 89 protein-coding genes. Comparison of the genomes of 7 Cyatheaceae plants showed that the chloroplast genome of S. lepifera was missing the gene trnV-UAC. Expansion of the SSC region led to the difference in the chloroplast genome size of S. lepifera. Eight genes, atpI, ccsA, petA, psaB, rpl16, rpoA, rpoC1, and ycf2 have high nucleic acid diversity and can be regarded as potential molecular markers. The genes trnG-trnR and atpB were suitable for DNA barcodes between different communities of S. lepifera. The S. lepifera groups in Zhejiang Province probably diffused from Pingtan and Ningde, Fujian. The results will provide a basis for species identification, biological studies, and endangerment mechanism of S. lepifera.
Additive pre-diagnostic and diagnostic value of routine blood-based biomarkers in the detection of colorectal cancer in the UK Biobank cohort
Authors: Tanriver Gizem , Kocagoncu Ece 
Published: January 2023

AbstractSurvival rates from colorectal cancer (CRC) are drastically higher if the disease is detected and treated earlier. Current screening guidelines involve stool-based tests and colonoscopies, whose acceptability and uptake remains low. Routinely collected blood-based biomarkers may offer a low-cost alternative or aid for detecting CRC. Here we aimed to evaluate the pre-diagnostic and diagnostic value of a wide-range of multimodal biomarkers in the UK Biobank dataset, including sociodemographic, lifestyle, medical, physical, and blood and urine-based measures in detecting CRC. We performed a Cox proportional hazard and a tree-boosting model alongside feature selection methods to determine optimal combination of biomarkers. In addition to the modifiable lifestyle factors of obesity, alcohol consumption and cardiovascular health, we showed that blood-based biomarkers that capture the immune response, lipid profile, liver and kidney function are associated with CRC risk. Following feature selection, the final Cox and tree-boosting models achieved a C-index of 0.67 and an AUC of 0.76 respectively. We show that blood-based biomarkers collected in routine examinations are sensitive to preclinical and clinical CRC. They may provide an additive value and improve diagnostic accuracy of current screening tools at no additional cost and help reduce burden on the healthcare system.
Ingestion of rubber tips of artificial turf fields by goldfish
Authors: Chiba Rihito , Fujinuma Ryosuke , Yoshitomi Tomoyasu , Shimizu Yasuo , Kobayashi Makito 
Published: January 2023

AbstractMarine microplastics are one of the global environmental issues. The present study examined whether rubber tips of artificial sports fields could be marine microplastics. We observed the migration of rubber tips from the artificial turf field to the surrounding ditch connected to sewer pipes and then examined the ingestion of rubber tips using the goldfish Carassius auratus. The rubber tips found in sediments in the ditch suggest that the rubber tips could be sent to the river and released into the ocean. The goldfish ingested rubber tips with or without fish feed, and rubber tips were found in the intestine. However, the fish discharged the rubber tips within 48 h after ingestion. These results indicate that ingestion of the rubber tips was not accidental but an active behavior. Therefore, artificial turf sports fields could be a source of marine microplastics and may cause hazardous effects on wild fishes through ingestion.
Analysis and weakening of radial electromagnetic forces in high‐speed permanent magnet motors with external rotors based on shape functions
Authors: Teng XiaoYuan , Li Yan , Zhang BingYi , Feng GuiHong , Liu ZeYu 
Published: January 2023

AbstractIn this paper, a strategy of integrating direct‐drive turbine compressors with high‐speed permanent magnet external rotor motors is used to improve the problems of large footprint, low efficiency and high maintenance costs. The rotor of the motor will vibrate under the action of radial electromagnetic force when rotating, and under the action of high pressure and high speed gas, it may aggravate the rotor vibration. In the case of changing the original mechanical structure of the turbine, the vibration of the motor rotor needs to be analysed. In the paper, the radial electromagnetic force applied to the rotor is analysed. The influence of the order and size of the stator and rotor magnetic field harmonics on the size, frequency and order of the radial electromagnetic force wave is summarised. In order to weaken the radial electromagnetic force, this paper proposes a shape function about the magnetic pole size and designs a magnetic pole accordingly. The validity of the shape function was confirmed by comparing the radial electromagnetic force wave with a conventional, surface‐mounted, built‐in magnetic pole structure. Finally, based on the analysis of the rotor dynamics mode, the law of the effect of the change of the pole arc coefficient of the pole on the radial force was analysed using harmonic response, and reasonable conclusions were drawn.
Optimal operation of basin‐based tidal units equipped with hydro‐pumps
Authors: Negahdari Mohammad Reza , Ghaedi Amir , Nafar Mehdi , Simab Mohsen 
Published: January 2023

AbstractDue to their clean nature, high capacity and accurate predictability, the basin‐based tidal units can be integrated into bulk power systems. The major problem of these units is the high investment cost of barrage construction, and so, among different renewable resources, these units are less developed. For making the tidal barrages cost‐effective, new methods should be implemented to increase their produced power that results in the reduction of electricity price. For this purpose, this study suggests new techniques for optimally operating tidal units equipped with hydro pumps. Here, to increase the produced power and energy of the tidal units, at each time, the number of turbines, sluices and hydro‐pumps is optimally determined to yield the maximum produced energy of the generation unit using the particle swarm optimization method. For satisfying the effectiveness of the suggested approach, the optimal operation of a tidal unit installed on the estuary of Bacanga is done and the impact of optimal dispatching of the turbines, sluices and hydro‐pumps on produced energy of the unit is studied. It is deduced from numerical results that the generated energy of the plant during 24 h is increased by 17% with the implementation of the proposed operation plan.
Quantitative spectroscopy of late O-type main-sequence stars with a hybrid non-LTE method
Authors: Aschenbrenner P. , Przybilla N. , Butler K. 
Published: January 2023

Context. Late O-type stars at luminosities log L/L⊙ ≲ 5.2 show weak winds with mass-loss rates lower than 10−8 M⊙ yr−1. This implies that, unlike their more massive and more luminous siblings, their photospheric layers are not strongly affected by the stellar wind.
Aims. A hybrid non-local thermodynamic equilibrium (non-LTE) approach – line-blanketed hydrostatic model atmospheres computed under the assumption of LTE in combination with non-LTE line-formation calculations – is tested for analyses of late O-type stars with masses up to ~25 M⊙. A sample of 20 mostly sharp-lined Galactic O stars of spectral types O8 to O9.7 and luminosity classes V and IV, previously studied in the literature using full non-LTE model atmospheres, is investigated.
Methods. Hydrostatic and plane-parallel atmospheric structures and synthetic spectra computed with Kurucz’s ATLAS12 code together with the non-LTE line-formation codes DETAIL and SURFACE, which account for the effects of turbulent pressure on the atmosphere, were employed. High-resolution spectra were analysed for atmospheric parameters using hydrogen lines, multiple ionisation equilibria, and elemental abundances. Fundamental stellar parameters were derived by considering stellar evolution tracks and Gaia Early Data Release 3 (EDR3) parallaxes. Interstellar reddening was characterised by fitting spectral energy distributions from the UV to the mid-IR.
Results. A high precision and accuracy is achieved for all derived parameters for 16 sample stars (4 objects show composite spectra). Turbulent pressure effects turn out to be significant for the quantitative analysis. Effective temperatures are determined to 1–3% uncertainty levels, surface gravities to 0.05 to 0.10 dex, masses to better than 8%, radii to better than 10%, and luminosities to better than 20% uncertainty typically. Abundances for C, N, O, Ne, Mg, Al, and Si are derived with uncertainties of 0.05–0.10 dex and for helium within 0.03–0.05 dex (1σ standard deviations) in general. Overall, results from previous studies using unified photosphere plus wind (full) non-LTE model atmospheres are reproduced, and with higher precision. The improvements are most pronounced for elemental abundances, and smaller microturbulent velocities are found. An overall good agreement is found between our spectroscopic distances and those from Gaia. Gaia EDR3-based distances to the Lac OB1b association and to the open clusters NGC 2244, IC 1805, NGC 457, and IC 1396 are determined as a byproduct. The derived N/C versus N/O abundance ratios tightly follow the predictions from stellar evolution models. Two ON stars show a very high degree of mixing of CNO-processed material and appear to stem from binary evolution.
Les enjeux éthiques du suivi à long terme des cancers pédiatriques
Authors: Camus Agathe , Henry Julie 
Published: January 2023

Les avancées en termes de traitement des cancers pédiatriques permettent aujourd’hui de guérir plus de 80 % des enfants atteints, leur ouvrant la perspective d’un retour à une « vie normale » après une période plus ou moins longue marquée par les traitements curatifs et des hospitalisations à répétition. L’idée de « vie normale », cependant, prend un sens particulier chez les personnes qui ont vécu le cancer dans l’enfance et qui sont à risque de développer des séquelles en lien avec les traitements qu’elles ont reçus. Bien loin de toujours consister dans la fermeture d’une parenthèse, celle de l’épisode du cancer, et le retour à une forme de stabilité, la reprise d’une « vie normale » doit composer avec de nombreuses incertitudes et repose sur un équilibre que l’incitation à reprendre un suivi médical « de surveillance » à long terme vient parfois perturber.