bluuebunny/crossref_metadata_2025_split huggingface dataset:
Silver lining to a climate crisis in multiple prospects for alleviating crop waterlogging under future climates
Authors: Liu Ke , Harrison Matthew Tom , Yan Haoliang , Liu De Li , Meinke Holger , Hoogenboom Gerrit , Wang Bin , Peng Bin , Guan Kaiyu , Jaegermeyr Jonas , Wang Enli , Zhang Feng , Yin Xiaogang , Archontoulis Sotirios , Nie Lixiao , Badea Ana , Man Jianguo , Wallach Daniel , Zhao Jin , Benjumea Ana Borrego , Fahad Shah , Tian Xiaohai , Wang Weilu , Tao Fulu , Zhang Zhao , Rötter Reimund , Yuan Youlu , Zhu Min , Dai Panhong , Nie Jiangwen , Yang Yadong , Zhang Yunbo , Zhou Meixue 
Published: February 2023

AbstractExtreme weather events threaten food security, yet global assessments of impacts caused by crop waterlogging are rare. Here we first develop a paradigm that distils common stress patterns across environments, genotypes and climate horizons. Second, we embed improved process-based understanding into a farming systems model to discern changes in global crop waterlogging under future climates. Third, we develop avenues for adapting cropping systems to waterlogging contextualised by environment. We find that yield penalties caused by waterlogging increase from 3–11% historically to 10–20% by 2080, with penalties reflecting a trade-off between the duration of waterlogging and the timing of waterlogging relative to crop stage. We document greater potential for waterlogging-tolerant genotypes in environments with longer temperate growing seasons (e.g., UK, France, Russia, China), compared with environments with higher annualised ratios of evapotranspiration to precipitation (e.g., Australia). Under future climates, altering sowing time and adoption of waterlogging-tolerant genotypes reduces yield penalties by 18%, while earlier sowing of winter genotypes alleviates waterlogging by 8%. We highlight the serendipitous outcome wherein waterlogging stress patterns under present conditions are likely to be similar to those in the future, suggesting that adaptations for future climates could be designed using stress patterns realised today.
Shape-memory effect in twisted ferroic nanocomposites
Authors: Kim Donghoon , Kim Minsoo , Reidt Steffen , Han Hyeon , Baghizadeh Ali , Zeng Peng , Choi Hongsoo , Puigmartí-Luis Josep , Trassin Morgan , Nelson Bradley J. , Chen Xiang-Zhong , Pané Salvador 
Published: February 2023

AbstractThe shape recovery ability of shape-memory alloys vanishes below a critical size (~50 nm), which prevents their practical applications at the nanoscale. In contrast, ferroic materials, even when scaled down to dimensions of a few nanometers, exhibit actuation strain through domain switching, though the generated strain is modest (~1%). Here, we develop freestanding twisted architectures of nanoscale ferroic oxides showing shape-memory effect with a giant recoverable strain (>8%). The twisted geometrical design amplifies the strain generated during ferroelectric domain switching, which cannot be achieved in bulk ceramics or substrate-bonded thin films. The twisted ferroic nanocomposites allow us to overcome the size limitations in traditional shape-memory alloys and open new avenues in engineering large-stroke shape-memory materials for small-scale actuating devices such as nanorobots and artificial muscle fibrils.
Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches
Authors: Cheng Xiaolong , Li Zexu , Shan Ruocheng , Li Zihan , Wang Shengnan , Zhao Wenchang , Zhang Han , Chao Lumen , Peng Jian , Fei Teng , Li Wei 
Published: February 2023

AbstractA major challenge in the application of the CRISPR-Cas13d system is to accurately predict its guide-dependent on-target and off-target effect. Here, we perform CRISPR-Cas13d proliferation screens and design a deep learning model, named DeepCas13, to predict the on-target activity from guide sequences and secondary structures. DeepCas13 outperforms existing methods to predict the efficiency of guides targeting both protein-coding and non-coding RNAs. Guides targeting non-essential genes display off-target viability effects, which are closely related to their on-target efficiencies. Choosing proper negative control guides during normalization mitigates the associated false positives in proliferation screens. We apply DeepCas13 to the guides targeting lncRNAs, and identify lncRNAs that affect cell viability and proliferation in multiple cell lines. The higher prediction accuracy of DeepCas13 over existing methods is extensively confirmed via a secondary CRISPR-Cas13d screen and quantitative RT-PCR experiments. DeepCas13 is freely accessible via http://deepcas13.weililab.org.
Barrier properties of Nup98 FG phases ruled by FG motif identity and inter-FG spacer length
Authors: Ng Sheung Chun , Biswas Abin , Huyton Trevor , Schünemann Jürgen , Reber Simone , Görlich Dirk 
Published: February 2023

AbstractNup98 FG repeat domains comprise hydrophobic FG motifs linked through uncharged spacers. FG motifs capture nuclear transport receptors (NTRs) during nuclear pore complex (NPC) passage, confer inter-repeat cohesion, and condense the domains into a selective phase with NPC-typical barrier properties. We show that shortening inter-FG spacers enhances cohesion, increases phase density, and tightens such barrier - all consistent with a sieve-like phase. Phase separation tolerates mutating the Nup98-typical GLFG motifs, provided domain-hydrophobicity remains preserved. NTR-entry, however, is sensitive to (certain) deviations from canonical FG motifs, suggesting co-evolutionary adaptation. Unexpectedly, we observed that arginines promote FG-phase-entry apparently also by hydrophobic interactions/ hydrogen-bonding and not just through cation-π interactions. Although incompatible with NTR·cargo complexes, a YG phase displays remarkable transport selectivity, particularly for engineered GFPNTR-variants. GLFG to FSFG mutations make the FG phase hypercohesive, precluding NTR-entry. Extending spacers relaxes this hypercohesion. Thus, antagonism between cohesion and NTR·FG interactions is key to transport selectivity.
Application of high-throughput single-nucleus DNA sequencing in pancreatic cancer
Authors: Zhang Haochen , Karnoub Elias-Ramzey , Umeda Shigeaki , Chaligné Ronan , Masilionis Ignas , McIntyre Caitlin A. , Sashittal Palash , Hayashi Akimasa , Zucker Amanda , Mullen Katelyn , Hong Jungeui , Makohon-Moore Alvin , Iacobuzio-Donahue Christine A. 
Published: February 2023

AbstractDespite insights gained by bulk DNA sequencing of cancer it remains challenging to resolve the admixture of normal and tumor cells, and/or of distinct tumor subclones; high-throughput single-cell DNA sequencing circumvents these and brings cancer genomic studies to higher resolution. However, its application has been limited to liquid tumors or a small batch of solid tumors, mainly because of the lack of a scalable workflow to process solid tumor samples. Here we optimize a highly automated nuclei extraction workflow that achieves fast and reliable targeted single-nucleus DNA library preparation of 38 samples from 16 pancreatic ductal adenocarcinoma patients, with an average library yield per sample of 2867 single nuclei. We demonstrate that this workflow not only performs well using low cellularity or low tumor purity samples but reveals genomic evolution patterns of pancreatic ductal adenocarcinoma as well.
A conserved tooth resorption mechanism in modern and fossil snakes
Authors: LeBlanc A. R. H. , Palci A. , Anthwal N. , Tucker A. S. , Araújo R. , Pereira M. F. C. , Caldwell M. W. 
Published: February 2023

AbstractWhether snakes evolved their elongated, limbless bodies or their specialized skulls and teeth first is a central question in squamate evolution. Identifying features shared between extant and fossil snakes is therefore key to unraveling the early evolution of this iconic reptile group. One promising candidate is their unusual mode of tooth replacement, whereby teeth are replaced without signs of external tooth resorption. We reveal through histological analysis that the lack of resorption pits in snakes is due to the unusual action of odontoclasts, which resorb dentine from within the pulp of the tooth. Internal tooth resorption is widespread in extant snakes, differs from replacement in other reptiles, and is even detectable via non-destructive μCT scanning, providing a method for identifying fossil snakes. We then detected internal tooth resorption in the fossil snake Yurlunggur, and one of the oldest snake fossils, Portugalophis, suggesting that it is one of the earliest innovations in Pan-Serpentes, likely preceding limb loss.
FGL2-targeting T cells exhibit antitumor effects on glioblastoma and recruit tumor-specific brain-resident memory T cells
Authors: Zhao Qingnan , Hu Jiemiao , Kong Lingyuan , Jiang Shan , Tian Xiangjun , Wang Jing , Hashizume Rintaro , Jia Zhiliang , Fowlkes Natalie Wall , Yan Jun , Xia Xueqing , Yi Sofia F. , Dao Long Hoang , Masopust David , Heimberger Amy B. , Li Shulin 
Published: February 2023

AbstractAlthough tissue-resident memory T (TRM) cells specific for previously encountered pathogens have been characterized, the induction and recruitment of brain TRM cells following immune therapy has not been observed in the context of glioblastoma. Here, we show that T cells expressing fibrinogen-like 2 (FGL2)–specific single-chain variable fragments (T-αFGL2) can induce tumor-specific CD8+ TRM cells that prevent glioblastoma recurrence. These CD8+ TRM cells display a highly expanded T cell receptor repertoire distinct from that found in peripheral tissue. When adoptively transferred to the brains of either immunocompetent or T cell-deficient naïve mice, these CD8+ TRM cells reject glioma cells. Mechanistically, T-αFGL2 cell treatment increased the number of CD69+CD8+ brain-resident memory T cells in tumor-bearing mice via a CXCL9/10 and CXCR3 chemokine axis. These findings suggest that tumor-specific brain-resident CD8+ TRM cells may have promising implications for the prevention of brain tumor recurrence.
H2B ubiquitination recruits FACT to maintain a stable altered nucleosome state for transcriptional activation
Authors: Luo Anfeng , Kong Jingwei , Chen Jun , Xiao Xue , Lan Jie , Li Xiaorong , Liu Cuifang , Wang Peng-Ye , Li Guohong , Li Wei , Chen Ping 
Published: February 2023

AbstractHistone H2B mono-ubiquitination at lysine 120 (ubH2B) has been found to regulate transcriptional elongation by collaborating with the histone chaperone FACT (Facilitates Chromatin Transcription) and plays essential roles in chromatin-based transcriptional processes. However, the mechanism of how ubH2B directly collaborates with FACT at the nucleosome level still remains elusive. In this study, we demonstrate that ubH2B impairs the mechanical stability of the nucleosome and helps to recruit FACT by enhancing the binding of FACT on the nucleosome. FACT prefers to bind and deposit H2A-ubH2B dimers to form an intact nucleosome. Strikingly, the preferable binding of FACT on ubH2B-nucleosome greatly enhances nucleosome stability and maintains its integrity. The stable altered nucleosome state obtained by ubH2B and FACT provides a key platform for gene transcription, as revealed by genome-wide and time-course ChIP-qPCR analyses. Our findings provide mechanistic insights of how ubH2B directly collaborates with FACT to regulate nucleosome dynamics for gene transcription.
Miniaturized multicolor fluorescence imaging system integrated with a PDMS light-guide plate for biomedical investigation
Authors: Shin Hyogeun , Yoon Gun-Wook , Choi Woongsun , Lee Donghwan , Choi Hoyun , Jo Deok Su , Choi Nakwon , Yoon Jun-Bo , Cho Il-Joo 
Published: February 2023

AbstractMiniaturized fluorescence imaging systems are promising platforms that overcome the limited use of conventional microscopes in the biomedical field. However, there are physical limitations for multicolor fluorescence imaging in existing miniaturized imaging systems because multiple filters have to be integrated into a small structure. Here, we present a miniaturized multicolor fluorescence imaging system integrated with single polydimethylsiloxane (PDMS) light-guide plate (LGP) for multicolor fluorescence imaging. The PDMS LGP allows guiding the transmitted light from the light source only to the fluorescent samples regardless of the wavelength of the light source. Thus, our system is capable of multicolor fluorescence imaging without multiple filters that block the excitation light. We demonstrated the usability of our system in the biomedical field by observing green- and red-labeled cells in the incubator. Our proposed system can be used in a wide range of applications for studies that require multicolor fluorescence imaging in the biomedical field.
Integration of single sample and population analysis for understanding immune evasion mechanisms of lung cancer
Authors: Li Xiong , Meng Xu , Chen Haowen , Fu Xiangzheng , Wang Peng , Chen Xia , Gu Changlong , Zhou Juan 
Published: February 2023

AbstractA deep understanding of the complex interaction mechanism between the various cellular components in tumor microenvironment (TME) of lung adenocarcinoma (LUAD) is a prerequisite for understanding its drug resistance, recurrence, and metastasis. In this study, we proposed two complementary computational frameworks for integrating multi-source and multi-omics data, namely ImmuCycReg framework (single sample level) and L0Reg framework (population or subtype level), to carry out difference analysis between the normal population and different LUAD subtypes. Then, we aimed to identify the possible immune escape pathways adopted by patients with different LUAD subtypes, resulting in immune deficiency which may occur at different stages of the immune cycle. More importantly, combining the research results of the single sample level and population level can improve the credibility of the regulatory network analysis results. In addition, we also established a prognostic scoring model based on the risk factors identified by Lasso-Cox method to predict survival of LUAD patients. The experimental results showed that our frameworks could reliably identify transcription factor (TF) regulating immune-related genes and could analyze the dominant immune escape pathways adopted by each LUAD subtype or even a single sample. Note that the proposed computational framework may be also applicable to the immune escape mechanism analysis of pan-cancer.
Trait biases in microbial reference genomes
Authors: Albright Sage , Louca Stilianos 
Published: February 2023

AbstractCommon culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.
Metabolome-wide association study on physical activity
Authors: Kojouri Maedeh , Pinto Rui , Mustafa Rima , Huang Jian , Gao He , Elliott Paul , Tzoulaki Ioanna , Dehghan Abbas 
Published: February 2023

AbstractThe underlying mechanisms linking physical activity to better health are not fully understood. Here we examined the associations between physical activity and small circulatory molecules, the metabolome, to highlight relevant biological pathways. We examined plasma metabolites associated with self-reported physical activity among 2217 participants from the Airwave Health Monitoring Study. Metabolic profiling was conducted using the mass spectrometry-based Metabolon platform (LC/GC–MS), measuring 828 known metabolites. We replicated our findings in an independent subset of the study (n = 2971) using untargeted LC–MS. Mendelian randomisation was carried out to investigate potential causal associations between physical activity, body mass index, and metabolites. Higher vigorous physical activity was associated (P < 0.05/828 = 6.03 × 10–5) with circulatory levels of 28 metabolites adjusted for age, sex and body mass index. The association was inverse for glutamate and diacylglycerol lipids, and direct for 3–4-hydroxyphenyllactate, phenyl lactate (PLA), alpha-hydroxy isovalerate, tiglylcarnitine, alpha-hydroxyisocaproate, 2-hydroxy-3-methylvalerate, isobutyrylcarnitine, imidazole lactate, methionine sulfone, indole lactate, plasmalogen lipids, pristanate and fumarate. In the replication panel, we found 23 untargeted LC–MS features annotated to the identified metabolites, for which we found nominal associations with the same direction of effect for three features annotated to 1-(1-enyl-palmitoyl)-2-oleoyl-GPC (P-16:0/18:1), 1-(1-enyl-palmitoyl)-2-linoleoyl-GPC (P-16:0/18:2), 1-stearoyl-2-dihomo-linolenoyl-GPC (18:0/20:3n3 or 6). Using Mendelian randomisation, we showed a potential causal relationship between body mass index and three identified metabolites. Circulatory metabolites are associated with physical activity and may play a role in mediating its health effects.
Dynamics of volcanic vortex rings
Authors: Pulvirenti Fabio , Scollo Simona , Ferlito Carmelo , Schwandner Florian M. 
Published: February 2023

AbstractVortex rings can easily be generated in the laboratory or with homemade devices, but they have also been observed on volcanoes, since the eighteenth century. However, the physical conditions under which volcanic vortex rings form are still unknown. In order to better understand this phenomenon and provide clues on the dynamics of the volcanic vortex rings, we performed a series of finite element simulations to investigate which model configuration leads to the rings formation that best matches the field observations. Results show that the formation of volcanic vortex rings requires a combination of fast gas release from gas bubbles (slugs) at the top of the magma conduit and regularity in the shape of the emitting vent. Our findings offer important insights into the geometry of the uppermost portion of vortex-forming volcanic conduits. Volcanic vortex ring studies may form the basis for a cross-disciplinary assessment of the upper conduit dynamics of volcanic vents.
Effects of continuous straw returning on bacterial community structure and enzyme activities in rape-rice soil aggregates
Authors: Yuan Luhong , Gao Yue , Mei Ying , Liu Jiaren , Kalkhajeh Yusef Kianpoor , Hu Hongxiang , Huang Jieying 
Published: February 2023

AbstractStraw returning is an effective management measure to improve or maintain soil fertility in agricultural ecosystems. This study investigated the effects of straw returning combined with compound fertilizer on the bacterial community, enzyme activities, and soil nutrients’ contents in a rape-rice rotation soil aggregates. To do so, a 5-year field trial (November 2016 to October 2021) was carried out in a paddy soil with three treatments: no straw + no fertilization (CK), compound fertilizer (F), and straw returning + compound fertilizer (SF). Soil aggregates were classified into mega-aggregates (> 2 mm), macro-aggregates (0.25–2 mm), micro-aggregates (0.053–0.25 mm), and silt–clay (< 0.053 mm) using the wet sieve method. High-throughput sequencing was employed to characterize the bacterial community, and Pearson correlation coefficient was used to identify the relationships among bacterial community, organic carbon, nitrogen, phosphorus, and enzyme activities in soil aggregates. Compared with F, the results showed that straw returning increased the content of > 2 mm aggregates by 3.17% and significantly decreased the content of 0.053–0.25 mm aggregates by 20.27%. The contents of organic carbon and total nitrogen in > 0.053 mm straw amended aggregates increased by 15.29 and 18.25%, respectively. Straw returning significantly increased the urease activity of > 0.053 mm aggregates with an average of 43.08%, while it decreased the phosphatase and invertase activities of soil aggregates by 7.71–40.66%. The Shannon indices of the bacterial community in each particle sizes soil aggregates decreased by an average of 1.16% and the Chao indices of the bacterial community in < 2 mm aggregates increased by an average of 3.90% in straw amended soils. Nevertheless, the relative abundances of Chloroflexi and Nitrospirotain in all soil aggregates increased by 6.17–71.77% in straw amended soils. Altogether, our findings suggest that straw returning is an efficient approach to enhance soil structure, carbon and nitrogen contents, and the richness of soil bacterial diversity.
Diagnosis of coronary layered plaque by deep learning
Authors: Araki Makoto , Park Sangjoon , Nakajima Akihiro , Lee Hang , Ye Jong Chul , Jang Ik-Kyung 
Published: February 2023

AbstractHealed coronary plaques, morphologically characterized by a layered phenotype, are signs of previous plaque destabilization and healing. Recent optical coherence tomography (OCT) studies demonstrated that layered plaque is associated with higher levels of local and systemic inflammation and rapid plaque progression. However, the diagnosis of layered plaque needs expertise in OCT image analysis and is susceptible to inter-observer variability. We developed a deep learning (DL) model for an accurate diagnosis of layered plaque. A Visual Transformer (ViT)-based DL model that integrates information from adjacent frames emulating the cardiologists who review consecutive OCT frames to make a diagnosis was developed and compared with the standard convolutional neural network (CNN) model. A total of 237,021 cross-sectional OCT images from 581 patients collected from 8 sites were used for training and internal validation, and 65,394 images from 292 patients collected from another site were used for external validation. In the five-fold cross-validation, the ViT-based model provided better performance (area under the curve [AUC]: 0.860; 95% confidence interval [CI]: 0.855–0.866) than the standard CNN-based model (AUC: 0.799; 95% CI: 0.792–0.805). The ViT-based model (AUC: 0.845; 95% CI: 0.837–0.853) also surpassed the standard CNN-based model (AUC: 0.791; 95% CI: 0.782–0.800) in the external validation. The ViT-based DL model can accurately diagnose a layered plaque, which could help risk stratification for cardiac events.