bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diploid and tetraploid genomes of Acorus and the evolution of monocots
Authors: Ma Liang , Liu Ke-Wei , Li Zhen , Hsiao Yu-Yun , Qi Yiying , Fu Tao , Tang Guang-Da , Zhang Diyang , Sun Wei-Hong , Liu Ding-Kun , Li Yuanyuan , Chen Gui-Zhen , Liu Xue-Die , Liao Xing-Yu , Jiang Yu-Ting , Yu Xia , Hao Yang , Huang Jie , Zhao Xue-Wei , Ke Shijie , Chen You-Yi , Wu Wan-Lin , Hsu Jui-Ling , Lin Yu-Fu , Huang Ming-Der , Li Chia-Ying , Huang Laiqiang , Wang Zhi-Wen , Zhao Xiang , Zhong Wen-Ying , Peng Dong-Hui , Ahmad Sagheer , Lan Siren , Zhang Ji-Sen , Tsai Wen-Chieh , Van de Peer Yves , Liu Zhong-Jian 
Published: June 2023

AbstractMonocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of monocot origin and evolution, we generate chromosome-level reference genomes of the diploid Acorus gramineus and the tetraploid Ac. calamus, the only two accepted species from the family Acoraceae, which form a sister lineage to all other monocots. Comparing the genomes of Ac. gramineus and Ac. calamus, we suggest that Ac. gramineus is not a potential diploid progenitor of Ac. calamus, and Ac. calamus is an allotetraploid with two subgenomes A, and B, presenting asymmetric evolution and B subgenome dominance. Both the diploid genome of Ac. gramineus and the subgenomes A and B of Ac. calamus show clear evidence of whole-genome duplication (WGD), but Acoraceae does not seem to share an older WGD that is shared by most other monocots. We reconstruct an ancestral monocot karyotype and gene toolkit, and discuss scenarios that explain the complex history of the Acorus genome. Our analyses show that the ancestors of monocots exhibit mosaic genomic features, likely important for that appeared in early monocot evolution, providing fundamental insights into the origin, evolution, and diversification of monocots.
Discovery of extended product structural space of the fungal dioxygenase AsqJ
Authors: Einsiedler Manuel , Gulder Tobias A. M. 
Published: June 2023

AbstractThe fungal dioxygenase AsqJ catalyses the conversion of benzo[1,4]diazepine-2,5-diones into quinolone antibiotics. A second, alternative reaction pathway leads to a different biomedically important product class, the quinazolinones. Within this work, we explore the catalytic promiscuity of AsqJ by screening its activity across a broad range of functionalized substrates made accessible by solid-/liquid-phase peptide synthetic routes. These systematic investigations map the substrate tolerance of AsqJ within its two established pathways, revealing significant promiscuity, especially in the quinolone pathway. Most importantly, two further reactivities leading to new AsqJ product classes are discovered, thus significantly expanding the structural space accessible by this biosynthetic enzyme. Switching AsqJ product selectivity is achieved by subtle structural changes on the substrate, revealing a remarkable substrate-controlled product selectivity in enzyme catalysis. Our work paves the way for the biocatalytic synthesis of diverse biomedically important heterocyclic structural frameworks.
Pan-cancer and cross-population genome-wide association studies dissect shared genetic backgrounds underlying carcinogenesis
Authors: Sato Go , Shirai Yuya , Namba Shinichi , Edahiro Ryuya , Sonehara Kyuto , Hata Tsuyoshi , Uemura Mamoru ,   the Biobank Japan Project, Yamanashi Yuji , Furukawa Yoichi , Morisaki Takayuki , Murakami Yoshinori , Kamatani Yoichiro , Muto Kaori , Nagai Akiko , Obara Wataru , Yamaji Ken , Takahashi Kazuhisa , Asai Satoshi , Takahashi Yasuo , Suzuki Takao , Sinozaki Nobuaki , Yamaguchi Hiroki , Minami Shiro , Murayama Shigeo , Yoshimori Kozo , Nagayama Satoshi , Obata Daisuke , Higashiyama Masahiko , Masumoto Akihide , Koretsune Yukihiro , Matsuda Koichi , Doki Yuichiro , Eguchi Hidetoshi , Okada Yukinori 
Published: June 2023

AbstractIntegrating genomic data of multiple cancers allows de novo cancer grouping and elucidating the shared genetic basis across cancers. Here, we conduct the pan-cancer and cross-population genome-wide association study (GWAS) meta-analysis and replication studies on 13 cancers including 250,015 East Asians (Biobank Japan) and 377,441 Europeans (UK Biobank). We identify ten cancer risk variants including five pleiotropic associations (e.g., rs2076295 at DSP on 6p24 associated with lung cancer and rs2525548 at TRIM4 on 7q22 nominally associated with six cancers). Quantifying shared heritability among the cancers detects positive genetic correlations between breast and prostate cancer across populations. Common genetic components increase the statistical power, and the large-scale meta-analysis of 277,896 breast/prostate cancer cases and 901,858 controls identifies 91 newly genome-wide significant loci. Enrichment analysis of pathways and cell types reveals shared genetic backgrounds across said cancers. Focusing on genetically correlated cancers can contribute to enhancing our insights into carcinogenesis.
Imputation of ancient human genomes
Authors: Sousa da Mota Bárbara , Rubinacci Simone , Cruz Dávalos Diana Ivette , G. Amorim Carlos Eduardo , Sikora Martin , Johannsen Niels N. , Szmyt Marzena H. , Włodarczak Piotr , Szczepanek Anita , Przybyła Marcin M. , Schroeder Hannes , Allentoft Morten E. , Willerslev Eske , Malaspinas Anna-Sapfo , Delaneau Olivier 
Published: June 2023

AbstractDue to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation can improve genotyping accuracy for low-coverage genomes. However, it is unknown how accurate ancient DNA imputation is and whether imputation introduces bias to downstream analyses. Here we re-sequence an ancient trio (mother, father, son) and downsample and impute a total of 43 ancient genomes, including 42 high-coverage (above 10x) genomes. We assess imputation accuracy across ancestries, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. When downsampled at 1x, 36 of the 42 genomes are imputed with low error rates (below 5%) while African genomes have higher error rates. We validate imputation and phasing results using the ancient trio data and an orthogonal approach based on Mendel’s rules of inheritance. We further compare the downstream analysis results between imputed and high-coverage genomes, notably principal component analysis, genetic clustering, and runs of homozygosity, observing similar results starting from 0.5x coverage, except for the African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method that can improve ancient DNA studies.
Trans-Golgi protein TVP23B regulates host-microbe interactions via Paneth cell homeostasis and Goblet cell glycosylation
Authors: Song Ran , McAlpine William , Fond Aaron M. , Nair-Gill Evan , Choi Jin Huk , Nyström Elisabeth E. L. , Arike Liisa , Field Sydney , Li Xiaohong , SoRelle Jeffrey A. , Moresco James J. , Moresco Eva Marie Y. , Yates John R. , Azadi Parastoo , Ni Josephine , Birchenough George M. H. , Beutler Bruce , Turer Emre E. 
Published: June 2023

AbstractA key feature in intestinal immunity is the dynamic intestinal barrier, which separates the host from resident and pathogenic microbiota through a mucus gel impregnated with antimicrobial peptides. Using a forward genetic screen, we have found a mutation in Tvp23b, which conferred susceptibility to chemically induced and infectious colitis. Trans-Golgi apparatus membrane protein TVP23 homolog B (TVP23B) is a transmembrane protein conserved from yeast to humans. We found that TVP23B controls the homeostasis of Paneth cells and function of goblet cells, leading to a decrease in antimicrobial peptides and more penetrable mucus layer. TVP23B binds with another Golgi protein, YIPF6, which is similarly critical for intestinal homeostasis. The Golgi proteomes of YIPF6 and TVP23B-deficient colonocytes have a common deficiency of several critical glycosylation enzymes. TVP23B is necessary for the formation of the sterile mucin layer of the intestine and its absence disturbs the balance of host and microbe in vivo.
Gut microbiota Turicibacter strains differentially modify bile acids and host lipids
Authors: Lynch Jonathan B. , Gonzalez Erika L. , Choy Kayli , Faull Kym F. , Jewell Talia , Arellano Abelardo , Liang Jennifer , Yu Kristie B. , Paramo Jorge , Hsiao Elaine Y. 
Published: June 2023

AbstractBacteria from theTuricibactergenus are prominent members of the mammalian gut microbiota and correlate with alterations in dietary fat and body weight, but the specific connections between these symbionts and host physiology are poorly understood. To address this knowledge gap, we characterize a diverse set of mouse- and human-derivedTuricibacterisolates, and find they group into clades that differ in their transformations of specific bile acids. We identifyTuricibacterbile salt hydrolases that confer strain-specific differences in bile deconjugation. Using male and female gnotobiotic mice, we find colonization with individualTuricibacterstrains leads to changes in host bile acid profiles, generally aligning with those produced in vitro. Further, colonizing mice with another bacterium exogenously expressing bile-modifying genes fromTuricibacterstrains decreases serum cholesterol, triglycerides, and adipose tissue mass. This identifies genes that enableTuricibacterstrains to modify host bile acids and lipid metabolism, and positionsTuricibacterbacteria as modulators of host fat biology.
Antioxidant hepatic lipid metabolism can be promoted by orally administered inorganic nanoparticles
Authors: Cai Jie , Peng Jie , Feng Juan , Li Ruocheng , Ren Peng , Zang Xinwei , Wu Zezong , Lu Yi , Luo Lin , Hu Zhenzhen , Wang Jiaying , Dai Xiaomeng , Zhao Peng , Wang Juan , Yan Mi , Liu Jianxin , Deng Renren , Wang Diming 
Published: June 2023

AbstractAccumulation of inorganic nanoparticles in living organisms can cause an increase in cellular reactive oxygen species (ROS) in a dose-dependent manner. Low doses of nanoparticles have shown possibilities to induce moderate ROS increases and lead to adaptive responses of biological systems, but beneficial effects of such responses on metabolic health remain elusive. Here, we report that repeated oral administrations of various inorganic nanoparticles, including TiO2, Au, and NaYF4 nanoparticles at low doses, can promote lipid degradation and alleviate steatosis in the liver of male mice. We show that low-level uptake of nanoparticles evokes an unusual antioxidant response in hepatocytes by promoting Ces2h expression and consequently enhancing ester hydrolysis. This process can be implemented to treat specific hepatic metabolic disorders, such as fatty liver in both genetic and high-fat-diet obese mice without causing observed adverse effects. Our results demonstrate that low-dose nanoparticle administration may serve as a promising treatment for metabolic regulation.
Upconversion particle-assisted NIR polymerization enables microdomain gradient photopolymerization at inter-particulate length scale
Authors: Hu Peng , Xu Hang , Pan Yue , Sang Xinxin , Liu Ren 
Published: June 2023

AbstractHigh crosslinking and low shrinkage stress are difficult to reconcile in the preparation of performance-enhancing photopolymer materials. Here we report the unique mechanism of upconversion particles-assisted NIR polymerization (UCAP) in reducing shrinkage stress and enhancing mechanical properties of cured materials. The excited upconversion particle emit UV-vis light with gradient intensity to the surroundings, forming a domain-limited gradient photopolymerization centered on the particle, and the photopolymer grows within this domain. The curing system remains fluid until the percolated photopolymer network is formed and starts gelation at high functional group conversion, with most of the shrinkage stresses generated by the crosslinking reaction having been released prior to gelation. Longer exposures after gelation contribute to a homogeneous solidification of cured material, and polymer materials cured by UCAP exhibit high gel point conversion, low shrinkage stress and strong mechanical properties than those cured by conventional UV polymerization techniques.
Adaptation of yeast Saccharomyces cerevisiae to grape-skin environment
Authors: Watanabe Daisuke , Hashimoto Wataru 
Published: June 2023

AbstractSaccharomyces cerevisiae, an essential player in alcoholic fermentation during winemaking, is rarely found in intact grapes. Although grape-skin environment is unsuitable for S. cerevisiae’s stable residence, Saccharomycetaceae-family fermentative yeasts can increase population on grape berries after colonization during raisin production. Here, we addressed adaptation of S. cerevisiae to grape-skin ecosystem. The yeast-like fungus Aureobasidium pullulans, a major grape-skin resident, exhibited broad spectrum assimilation of plant-derived carbon sources, including ω-hydroxy fatty acid, arising from degradation of plant cuticles. In fact, A. pullulans encoded and secreted possible cutinase-like esterase for cuticle degradation. When intact grape berries were used as a sole carbon source, such grape-skin associated fungi increased the accessibility to fermentable sugars by degrading and assimilating the plant cell wall and cuticle compounds. Their ability seems also helpful for S. cerevisiae to obtain energy through alcoholic fermentation. Thus, degradation and utilization of grape-skin materials by resident microbiota may account for their residence on grape-skin and S. cerevisiae’s possible commensal behaviors. Conclusively, this study focused on the symbiosis between grape-skin microbiota and S. cerevisiae from the perspective of winemaking origin. Such plant–microbe symbiotic interaction may be a prerequisite for triggering spontaneous food fermentation.
Effects of velocity on N2 and CO2 foam flow with in-situ capillary pressure measurements in a high-permeability homogeneous sandpack
Authors: Vavra Eric , Bai Chutian , Puerto Maura , Ma Kun , Mateen Khalid , Hirasaki George J. , Biswal Sibani Lisa 
Published: June 2023

AbstractThe effects of velocity and gas type on foam flow through porous media have yet to be completely elucidated. Pressure drop and capillary pressure measurements were made at ambient conditions during a series of foam quality scan experiments in a homogenous sandpack while foam texture was simultaneously visualized. New insights into foam-flow behavior in porous media were discovered. Previously accepted “limiting” capillary pressure theory is challenged by the findings in this work, and the “limiting” terminology is replaced with the word “plateau” to reflect these novel observations. Plateau capillary pressure $${(P}_{c})$$

(
P

c

)

and transition foam quality were found to increase with velocity. Transition foam quality was found to depend mostly on liquid velocity rather than gas velocity and is physically linked to foam type (continuous vs. discontinuous) and texture (fine vs. coarse). Distinct rheological behaviors also arose in the low- and high-quality foam regimes as a function of velocity. Foam flow was found to be strongly shear thinning in the low-quality regime where foam texture was fine and discontinuous. In the high-quality regime, the rheology was weakly shear thinning to Newtonian for coarsely textured foam and continuous-gas flow respectively. When all other variables were held constant, at ambient conditions, CO2 foam was found to be weaker with also lower capillary pressures than N2 foam and the differences in gas solubility is a likely explanation.
Automated player identification and indexing using two-stage deep learning network
Authors: Liu Hongshan , Adreon Colin , Wagnon Noah , Bamba Abdul Latif , Li Xueshen , Liu Huapu , MacCall Steven , Gan Yu 
Published: June 2023

AbstractAmerican football games attract significant worldwide attention every year. Identifying players from videos in each play is also essential for the indexing of player participation. Processing football game video presents great challenges such as crowded settings, distorted objects, and imbalanced data for identifying players, especially jersey numbers. In this work, we propose a deep learning-based player tracking system to automatically track players and index their participation per play in American football games. It is a two-stage network design to highlight areas of interest and identify jersey number information with high accuracy. First, we utilize an object detection network, a detection transformer, to tackle the player detection problem in a crowded context. Second, we identify players using jersey number recognition with a secondary convolutional neural network, then synchronize it with a game clock subsystem. Finally, the system outputs a complete log in a database for play indexing. We demonstrate the effectiveness and reliability of player tracking system by analyzing the qualitative and quantitative results on football videos. The proposed system shows great potential for implementation in and analysis of football broadcast video.
CHI3L1 induces autophagy through the JNK pathway in lung cancer cells
Authors: Hong Da Eun , Yu Ji Eun , Yoo Seung Sik , Yeo In Jun , Son Dong Ju , Yun Jaesuk , Han Sang-Bae , Hong Jin Tae 
Published: June 2023

AbstractCHI3L1 is closely related to the molecular mechanisms of cancer cell migration, growth, and death. According to recent research, autophagy regulates tumor growth during various stages of cancer development. This study examined the association between CHI3L1 and autophagy in human lung cancer cells. In CHI3L1-overexpressing lung cancer cells, the expression of LC3, an autophagosome marker, and the accumulation of LC3 puncta increased. In contrast, CHI3L1 depletion in lung cancer cells decreased the formation of autophagosomes. Additionally, CHI3L1 overexpression promoted the formation of autophagosomes in various cancer cell lines: it also increased the co-localization of LC3 and the lysosome marker protein LAMP-1, indicating an increase in the production of autolysosomes. In mechanism study, CHI3L1 promotes autophagy via activation of JNK signaling. JNK may be crucial for CHI3L1-induced autophagy since pretreatment with the JNK inhibitor reduced the autophagic effect. Consistent with the in vitro model, the expression of autophagy-related proteins was downregulated in the tumor tissues of CHI3L1-knockout mice. Furthermore, the expression of autophagy-related proteins and CHI3L1 increased in lung cancer tissues compared with normal lung tissues. These findings show that CHI3L1-induced autophagy is triggered by JNK signals and that CHI3L1-induced autophagy could be a novel therapeutic approach to lung cancer.
Greater intramuscular adipose tissue of the quadriceps in older inpatients at post-acute hospital admission is more strongly related to a low rate of home discharge than a loss of muscle mass
Authors: Akazawa Naoki , Funai Keita , Hino Toshikazu , Tsuji Ryota , Tamura Wataru , Tamura Kimiyuki , Hioka Akemi , Moriyama Hideki 
Published: June 2023

AbstractThis study aimed to examine the relationships between intramuscular adipose tissue and muscle mass of the quadriceps at post-acute hospital admission and the low rate of home discharge. This prospective study included 389 inpatients aged ≥ 65 years. Patients were divided into two groups according to the destination: home discharge (n = 279) and no-home discharge (n = 110) groups. The primary outcome was hospital discharge destination (home discharge or not). Intramuscular adipose tissue and muscle mass of the quadriceps were assessed at post-acute hospital admission using echo intensity and muscle thickness on ultrasound images, respectively. Logistic regression analysis was used for determining whether quadriceps echo intensity is related to home discharge. Quadriceps echo intensity was significantly and independently associated with home discharge (odds ratio [per 1 SD increase] = 1.43,p = 0.045). Quadriceps thickness was not associated with home discharge (odds ratio [per 1 SD increase] = 1.00,p = 0.998). Our study indicates that greater intramuscular adipose tissue of the quadriceps in older inpatients at post-acute hospital admission is more strongly related to a low rate of home discharge than a loss of muscle mass.
Evaluation of immunoserological detection of anti-liver kidney microsomal, anti-soluble liver antigen and anti-mitochondrial antibodies
Authors: Campos-Murguia Alejandro , Henjes Nicole , Loges Stephanie , Wedemeyer Heiner , Jaeckel Elmar , Taubert Richard , Engel Bastian 
Published: June 2023

AbstractAutoantibodies are the diagnostic hallmark of autoimmune liver diseases. Indirect immunofluorescence (IFT) is the reference method for the detection of anti-mitochondrial antibodies (AMA) and anti-liver kidney microsomal type-1 (anti-LKM1) antibodies, and inhibition ELISA (iELISA) for anti-soluble liver antigen (anti-SLA) antibodies. Given the complexity of these techniques, commercial ELISAs have emerged as a practical alternative, but without head-to-head validations. This study evaluated the agreement between three commercial ELISAs and the reference techniques and the impact of polyreactive immunoglobulin G (pIgG), a recently described phenomenon in autoimmune hepatitis, on commercial ELISAs. Inter-rater reliability was assessed using Cohen-Kappa coefficient (κ). Forty-eight, 46, and 66 samples were analyzed for AMA, anti-LKM1, and anti-SLA, respectively. For AMA, one commercial assay showed high agreement (κ = 0.91 (0.78–1.00)) with the reference method, while the other two showed weak or moderate agreement. For anti-LKM1, only one commercial assay showed high agreement (κ = 0.86 (0.71–1.0)). For anti-SLA antibodies only moderate agreement was achieved (κ up to 0.71 (0.52–0.89)). There was a trend towards higher pIgG levels in false-positives in the commercial ELISAs. Patients with high suspicion of autoimmune liver diseases should be referred to reference laboratories with the capacity of performing gold standard methods if the initial ELISA-based screening was performed.
A comparison of performance between a deep learning model with residents for localization and classification of intracranial hemorrhage
Authors: Angkurawaranon Salita , Sanorsieng Nonn , Unsrisong Kittisak , Inkeaw Papangkorn , Sripan Patumrat , Khumrin Piyapong , Angkurawaranon Chaisiri , Vaniyapong Tanat , Chitapanarux Imjai 
Published: June 2023

AbstractIntracranial hemorrhage (ICH) from traumatic brain injury (TBI) requires prompt radiological investigation and recognition by physicians. Computed tomography (CT) scanning is the investigation of choice for TBI and has become increasingly utilized under the shortage of trained radiology personnel. It is anticipated that deep learning models will be a promising solution for the generation of timely and accurate radiology reports. Our study examines the diagnostic performance of a deep learning model and compares the performance of that with detection, localization and classification of traumatic ICHs involving radiology, emergency medicine, and neurosurgery residents. Our results demonstrate that the high level of accuracy achieved by the deep learning model, (0.89), outperforms the residents with regard to sensitivity (0.82) but still lacks behind in specificity (0.90). Overall, our study suggests that the deep learning model may serve as a potential screening tool aiding the interpretation of head CT scans among traumatic brain injury patients.