bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study on crystal growth of Ge/Si quantum dots at different Ge deposition by using magnetron sputtering technique
Authors: Shu Qijiang , Huang Pengru , Yang Fuhua , Yang Linjing , Chen Lei 
Published: May 2023

AbstractWe investigated the growth and evolution of Si-based Ge quantum dots (Ge/Si QDs) under low Ge deposition (1.2–4.4 nm thick) using magnetron sputtering. The morphology and structure of QDs were analyzed with the help of an atomic force microscope (AFM), scanning electron microscope, transmission electron microscope, Raman, surface energy theory and dynamics theory, the photoelectric properties of QDs were characterized by photoluminescence (PL) spectra. The results showed that the growth mechanism of QDs conformed to Stranski–Krastanow mode, but the typical thickness of the wetting layer was nearly three times higher than those derived from conventional technologies such as molecular beam epitaxy, chemical vapor deposition, solid phase epitaxy and so on. Meanwhile, the shape evolution of QDs was very different from existing reports. The specific internal causes of these novel phenomena were analyzed and confirmed and reported in this paper. In addition, the AFM, Raman, and PL tests all indicated that the QDs grown when 3.4 nm Ge was deposited have the most excellent morphology, structure, and optoelectronic performance. Our work lays a foundation for further exploration of the controllable growth of QDs at high deposition rates, which is a new way to realize the industrialization of QDs used for future devices.
Oxidation-induced nanolite crystallization triggered the 2021 eruption of Fukutoku-Oka-no-Ba, Japan
Authors: Yoshida Kenta , Miyake Akira , Okumura Shota H. , Ishibashi Hidemi , Okumura Satoshi , Okamoto Atsushi , Niwa Yasuhiro , Kimura Masao , Sato Tomoki , Tamura Yoshihiko , Ono Shigeaki 
Published: May 2023

AbstractNanometer-sized crystals (nanolites) play an important role in controlling eruptions by affecting the viscosity of magmas and inducing bubble nucleation. We present detailed microscopic and nanoscopic petrographic analyses of nanolite-bearing and nanolite-free pumice from the 2021 eruption of Fukutoku-Oka-no-Ba, Japan. The nanolite mineral assemblage includes biotite, which is absent from the phenocryst mineral assemblage, and magnetite and clinopyroxene, which are observed as phenocrysts. The boundary between the nanolite-bearing brown glass and nanolite-free colorless glass is either sharp or gradational, and the sharp boundaries also appear sharp under the transmitted electron microscope. X-ray absorption fine structure (XAFS) analysis of the volcanic glass revealed that the nanolite-free colorless glass records an oxygen fugacity of QFM + 0.98 (log units), whereas the nanolite-bearing brown glass records a higher apparent oxygen fugacity (~ QFM + 2). Thermodynamic modelling using MELTS indicates that higher oxygen fugacities increase the liquidus temperature and thus induced the crystallization of magnetite nanolites. The hydrous nanolite mineral assemblage and glass oxygen fugacity estimates suggest that an oxidizing fluid supplied by a hot mafic magma induced nanolite crystallization in the magma reservoir, before the magma fragmentation. The oxidation-induced nanolite crystallization then enhanced heterogeneous bubble nucleation, resulting in convection in the magma reservoir and triggering the eruption.
Increasing the complexity of isolated musical chords benefits concurrent associative memory formation
Authors: Kurzom Nawras , Lorenzi Ilaria , Mendelsohn Avi 
Published: May 2023

AbstractThe effects of background music on learning and memory are inconsistent, partially due to the intrinsic complexity and diversity of music, as well as variability in music perception and preference. By stripping down musical harmony to its building blocks, namely discrete chords, we explored their effects on memory formation of unfamiliar word-image associations. Chords, defined as two or more simultaneously played notes, differ in the number of tones and inter-tone intervals, yielding varying degrees of harmonic complexity, which translate into a continuum of consonance to dissonance percepts. In the current study, participants heard four different types of musical chords (major, minor, medium complex, and high complex chords) while they learned new word-image pairs of a foreign language. One day later, their memory for the word-image pairs was tested, along with a chord rating session, in which they were required to assess the musical chords in terms of perceived valence, tension, and the extent to which the chords grabbed their attention. We found that musical chords containing dissonant elements were associated with higher memory performance for the word-image pairs compared with consonant chords. Moreover, tension positively mediated the relationship between roughness (a key feature of complexity) and memory, while valence negatively mediated this relationship. The reported findings are discussed in light of the effects that basic musical features have on tension and attention, in turn affecting cognitive processes of associative learning.
A deep learning method for optimizing semantic segmentation accuracy of remote sensing images based on improved UNet
Authors: Wang Xiaolei , Hu Zirong , Shi Shouhai , Hou Mei , Xu Lei , Zhang Xiang 
Published: May 2023

AbstractSemantic segmentation of remote sensing imagery (RSI) is critical in many domains due to the diverse landscapes and different sizes of geo-objects that RSI contains, making semantic segmentation challenging. In this paper, a convolutional network, named Adaptive Feature Fusion UNet (AFF-UNet), is proposed to optimize the semantic segmentation performance. The model has three key aspects: (1) dense skip connections architecture and an adaptive feature fusion module that adaptively weighs different levels of feature maps to achieve adaptive feature fusion, (2) a channel attention convolution block that obtains the relationship between different channels using a tailored configuration, and (3) a spatial attention module that obtains the relationship between different positions. AFF-UNet was evaluated on two public RSI datasets and was quantitatively and qualitatively compared with other models. Results from the Potsdam dataset showed that the proposed model achieved an increase of 1.09% over DeepLabv3 + in terms of the average F1 score and a 0.99% improvement in overall accuracy. The visual qualitative results also demonstrated a reduction in confusion of object classes, better performance in segmenting different sizes of object classes, and better object integrity. Therefore, the proposed AFF-UNet model optimizes the accuracy of RSI semantic segmentation.
Functional and phosphoproteomic analysis of β-adrenergic receptor signaling at excitatory synapses in the CA1 region of the ventral hippocampus
Authors: Jami Shekib A. , Wilkinson Brent J. , Guglietta Ryan , Hartel Nicolas , Babiec Walter E. , Graham Nicholas A. , Coba Marcelo P. , O’Dell Thomas J. 
Published: May 2023

AbstractActivation of β-adrenergic receptors (β-ARs) not only enhances learning and memory but also facilitates the induction of long-term potentiation (LTP), a form of synaptic plasticity involved in memory formation. To identify the mechanisms underlying β-AR-dependent forms of LTP we examined the effects of the β-AR agonist isoproterenol on LTP induction at excitatory synapses onto CA1 pyramidal cells in the ventral hippocampus. LTP induction at these synapses is inhibited by activation of SK-type K+ channels, suggesting that β-AR activation might facilitate LTP induction by inhibiting SK channels. However, although the SK channel blocker apamin enhanced LTP induction, it did not fully mimic the effects of isoproterenol. We therefore searched for potential alternative mechanisms using liquid chromatography-tandem mass spectrometry to determine how β-AR activation regulates phosphorylation of postsynaptic density (PSD) proteins. Strikingly, β-AR activation regulated hundreds of phosphorylation sites in PSD proteins that have diverse roles in dendritic spine structure and function. Moreover, within the core scaffold machinery of the PSD, β-AR activation increased phosphorylation at several sites previously shown to be phosphorylated after LTP induction. Together, our results suggest that β-AR activation recruits a diverse set of signaling pathways that likely act in a concerted fashion to regulate LTP induction.
Streamlined quantitative analysis of histone modification abundance at nucleosome-scale resolution with siQ-ChIP version 2.0
Authors: Dickson Bradley M. , Kupai Ariana , Vaughan Robert M. , Rothbart Scott B. 
Published: May 2023

AbstractWe recently introduced an absolute and physical quantitative scale for chromatin immunoprecipitation followed by sequencing (ChIP-seq). The scale itself was determined directly from measurements routinely made on sequencing samples without additional reagents or spike-ins. We called this approach sans spike-in quantitative ChIP, or siQ-ChIP. Herein, we extend those results in several ways. First, we simplified the calculations defining the quantitative scale, reducing practitioner burden. Second, we reveal a normalization constraint implied by the quantitative scale and introduce a new scheme for generating ‘tracks’. The constraint requires that tracks are probability distributions so that quantified ChIP-seq is analogous to a mass distribution. Third, we introduce some whole-genome analyses that allow us, for example, to project the IP mass (immunoprecipitated mass) onto the genome to evaluate how much of any genomic interval was captured in the IP. We applied siQ-ChIP to p300/CBP inhibition and compare our results to those of others. We detail how the same data-level observations are misinterpreted in the literature when tracks are not understood as probability densities and are compared without correct quantitative scaling, and we offer new interpretations of p300/CBP inhibition outcomes.
Predicting tumor recurrence on baseline MR imaging in patients with early-stage hepatocellular carcinoma using deep machine learning
Authors: Kucukkaya Ahmet Said , Zeevi Tal , Chai Nathan Xianming , Raju Rajiv , Haider Stefan Philipp , Elbanan Mohamed , Petukhova-Greenstein Alexandra , Lin MingDe , Onofrey John , Nowak Michal , Cooper Kirsten , Thomas Elizabeth , Santana Jessica , Gebauer Bernhard , Mulligan David , Staib Lawrence , Batra Ramesh , Chapiro Julius 
Published: May 2023

AbstractTumor recurrence affects up to 70% of early-stage hepatocellular carcinoma (HCC) patients, depending on treatment option. Deep learning algorithms allow in-depth exploration of imaging data to discover imaging features that may be predictive of recurrence. This study explored the use of convolutional neural networks (CNN) to predict HCC recurrence in patients with early-stage HCC from pre-treatment magnetic resonance (MR) images. This retrospective study included 120 patients with early-stage HCC. Pre-treatment MR images were fed into a machine learning pipeline (VGG16 and XGBoost) to predict recurrence within six different time frames (range 1–6 years). Model performance was evaluated with the area under the receiver operating characteristic curves (AUC–ROC). After prediction, the model’s clinical relevance was evaluated using Kaplan–Meier analysis with recurrence-free survival (RFS) as the endpoint. Of 120 patients, 44 had disease recurrence after therapy. Six different models performed with AUC values between 0.71 to 0.85. In Kaplan–Meier analysis, five of six models obtained statistical significance when predicting RFS (log-rank p < 0.05). Our proof-of-concept study indicates that deep learning algorithms can be utilized to predict early-stage HCC recurrence. Successful identification of high-risk recurrence candidates may help optimize follow-up imaging and improve long-term outcomes post-treatment.
Possible involvement of silent mutations in cancer pathogenesis and evolution
Authors: Kikutake Chie , Suyama Mikita 
Published: May 2023

AbstractRecent studies have shown that some silent mutations can be harmful to various processes. In this study, we performed a comprehensive in silico analysis to elucidate the effects of silent mutations on cancer pathogenesis using exome sequencing data derived from the Cancer Genome Atlas. We focused on the codon optimality scores of silent mutations, which were defined as the difference between the optimality of synonymous codons, calculated using the codon usage table. The relationship between cancer evolution and silent mutations showed that the codon optimality score of the mutations that occurred later in carcinogenesis was significantly higher than of those that occurred earlier. In addition, mutations with higher scores were enriched in genes involved in the cell cycle and cell division, while those with lower scores were enriched in genes involved in apoptosis and cellular senescence. Our results demonstrate that some silent mutations can be involved in cancer pathogenesis.
Autocitrullination confers monocyte chemotactic properties to peptidylarginine deiminase 4
Authors: Yoshida Ken , Ito Haruyasu , Kurosaka Daisaburo , Ikeda Ryo , Noda Kentaro , Saito Mitsuru , Kurosaka Daitaro 
Published: May 2023

AbstractPeptidylarginine deiminase 4 (PAD4) contributes to the production of citrullinated proteins as autoantigens for anti-citrullinated protein antibodies (ACPAs) in rheumatoid arthritis (RA). PAD4 can also self-deiminate via autocitrullination. However, the role of this process in RA pathogenesis has not been elucidated. This study aimed to clarify PAD4 function before and after autocitrullination and identify citrullinated PAD4 in the synovial fluid of patients with RA. The autocitrullination of recombinant human PAD4 (rhPAD4) was catalyzed in vitro and determined using anti-modified citrulline immunoblotting. Monocyte chemotaxis was evaluated using Boyden chambers, and citrullinated rhPAD4’s ability to induce arthritis was assessed in a C57BL/6J mouse model. Citrullinated PAD4 levels were measured in the synovial fluid of patients with RA and osteoarthritis using a novel enzyme-linked immunosorbent assay. Chemotactic findings showed that citrullinated rhPAD4 recruited monocytes in vitro, whereas unmodified rhPAD4 did not. Compared to unmodified rhPAD4, citrullinated rhPAD4 induced greater inflammation in mouse joints through monocyte migration. More citrullinated PAD4 was found in the synovial fluid of patients with RA than in those with osteoarthritis. Citrullinated PAD4 was even detected in ACPA-negative patients with RA. The autocitrullination of PAD4 amplified inflammatory arthritis through monocyte recruitment, suggesting an ACPA-independent role of PAD4 in RA pathogenesis.
Pancancer analysis of oncogenic BARX2 identifying its prognostic value and immunological function in liver hepatocellular carcinoma
Authors: Yu Shian , Yang Yu , Yang Hanqing , Peng Long , Wu Zhipeng , Sun Liang , Wu Zhengyi , Yu Xuzhe , Yin Xiangbao 
Published: May 2023

AbstractThe transcription factor BarH-like homeobox 2 (BARX2), a member of the Bar-like homeobox gene family, is involved in cell proliferation, differentiation, immune responses and tumorigenesis. However, the potential role of BARX2 in the development of liver hepatocellular carcinoma (LIHC) remains unclear. Therefore, we aimed to study the biological role of BARX2 in hepatocellular carcinoma. Through the UALCAN, GTEx PORTAL, TIMER 2.0, LinkedOmics, SMART, MethSurv, Metascape, GSEA and STRING public databases, the BARX2 mRNA level, prognostic value, coexpressed genes, associated differentially expressed genes, DNA methylation and functional enrichment of LIHC patients were studied. The relationships between BARX2 expression and various clinical or genetic parameters of LIHC patients were determined using data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and BEAT LIHC databases. In addition, the biological function of BARX2 in LIHC was studied in vitro. Through large-scale data mining, our study showed that BARX2 was differentially expressed between different normal and tumour tissues.BARX2 expression in LIHC tissues was significantly lower than that in corresponding controls, especially in patients with T2-4 stage disease. In patients with LIHC, overexpression of BARX2 was an independent poor prognostic factor associated with poor cytogenetic risk and gene mutations. Genomic hypermethylation of the BARX2 gene was associated with upregulated BARX2 expression and poor overall survival (OS) in LIHC. Functional enrichment analysis showed that BARX2 had an immunomodulatory role and was involved in the inflammatory response in LIHC occurrence. In conclusion, the oncogene BARX2 may serve as a new biomarker and prognostic factor for patients with LIHC. The immunomodulatory function of BARX2 deserves further validation in LIHC.
Biodiversity is overlooked in the diets of different social groups in Brazil
Authors: Gomes Sávio Marcelino , Chaves Viviany Moura , de Carvalho Aline Martins , da Silva Elenilma Barros , de Menezes Neto Elias Jacob , de Farias Moura Gabriela , da Silva Chaves Leonardo , Alves Rômulo Romeu Nóbrega , de Albuquerque Ulysses Paulino , de Oliveira Pereira Fillipe , Jacob Michelle Cristine Medeiros 
Published: May 2023

AbstractFood biodiversity is essential for improving nutrition and reducing hunger in populations worldwide. However, in middle and low-income countries, the biodiversity of food production does not necessarily represent food consumption patterns by population. We used Brazil, one of the world's megabiodiverse countries, as a case study to investigate the following questions: what is the prevalence of consumption of biodiverse foods in Brazil, and what are the socioeconomic factors that influence their consumption throughout the country? We used data from a Brazilian representative national dietary survey to estimate the frequency of food consumption of unconventional food plants, edible mushrooms, and wild meat, in according to socioeconomic variables. Thus, we investigated the socioeconomic predictors of Unconventional Food Plants consumption using methods of Machine Learning (ML) and multiple zero-inflated Poisson (ZIP) regression. We showed that biodiverse food consumption in Brazil is low, just related by 1.3% of the population, varying in according to area, ethnicity, age, food insecurity, sex, and educational level. Our findings of low utilization of biodiversity suggest an important mismatch between the rich biodiversity of the country and its representation in the human diet.
The role of final-state interaction in tensor polarization effects of the reaction $$\gamma d \rightarrow p n \pi ^{0}$$
Authors: Gauzshtein Vyacheslav , Fix Alexander , Vasilishin Bogdan , Darwish Eed , Kuzin Matvey , Levchuk Michael , Loginov Alexey , Nikolenko Dmitry , Rachek Igor , Shestakov Yuriy , Toporkov Dmitry , Yurchenko Arseniy , Zevakov Sergey , Mahmoud Zakaria 
Published: May 2023

AbstractTensor analyzing-power components $$T_{20}$$

T
20

, $$T_{21}$$

T
21

, and $$T_{22}$$

T
22

for the reaction $$\gamma d\rightarrow np\pi ^0$$

γ
d
→
n
p

π
0

have been studied for the first time in the photon energy range from 280 to 500 MeV. The data are extracted from the experimental statistics accumulated at the VEPP-3 storage ring in 2002–2003. The measured asymmetries are compared with the results of statistical simulations performed with the $$\gamma d\rightarrow np\pi ^0$$

γ
d
→
n
p

π
0

amplitude from a spectator model, taking into account corrections for the final-state interaction. The comparison demonstrates quite good agreement between the experimental results and the theory.
Evaluation of extraction methods for untargeted metabolomic studies for future applications in zebrafish larvae infection models
Authors: Schippers Philip , Rasheed Sari , Park Yu Mi , Risch Timo , Wagmann Lea , Hemmer Selina , Manier Sascha K. , Müller Rolf , Herrmann Jennifer , Meyer Markus R. 
Published: May 2023

AbstractSample preparation in untargeted metabolomics should allow reproducible extractions of as many molecules as possible. Thus, optimizing sample preparation is crucial. This study compared six different extraction procedures to find the most suitable for extracting zebrafish larvae in the context of an infection model. Two one-phase extractions employing methanol (I) and a single miscible phase of methanol/acetonitrile/water (II) and two two-phase methods using phase separation between chloroform and methanol/water combinations (III and IV) were tested. Additional bead homogenization was used for methods III and IV (III_B and IV_B). Nine internal standards and 59 molecules of interest (MoInt) related to mycobacterial infection were used for method evaluation. Two-phase methods (III and IV) led to a lower feature count, higher peak areas of MoInt, especially amino acids, and higher coefficients of variation in comparison to one-phase extractions. Adding bead homogenization increased feature count, peak areas, and CVs. Extraction I showed higher peak areas and lower CVs than extraction II, thus being the most suited one-phase method. Extraction III and IV showed similar results, with III being easier to execute and less prone to imprecisions. Thus, for future applications in zebrafish larvae metabolomics and infection models, extractions I and III might be chosen.
Efficient production of recombinant proteins in suspension CHO cells culture using the Tol2 transposon system coupled with cycloheximide resistance selection
Authors: Yamaguchi Keina , Ogawa Risa , Tsukahara Masayoshi , Kawakami Koichi 
Published: May 2023

AbstractDNA recombination techniques in mammalian cells has been applied to the production of therapeutic proteins for several decades. To be used for commercial production, established cell lines should stably express target proteins with high productivity and acceptable quality for human use. In the conventional transfection method, the screening process is laborious and time-consuming since superior cell lines had to be selected from an enormous number of transfected cell pools and clonal cell lines with a wide variety of transgene insertion locations. In this study, we demonstrated that the combination of a Tol2 transposon system and cell selection by cycloheximide resistance is an efficient method to express therapeutic proteins, such as human antibody in suspension culture of Chinese hamster ovary cells. The resulting stable cell lines showed constant productivity and cell growth over a long enough cultivation periods for recombinant protein production. We anticipate that this approach will prove widely applicable to protein production in research and development of pharmaceutical products.