bluuebunny/crossref_metadata_2025_split huggingface dataset:
METTL14-mediated m6A mRNA modification of G6PD promotes lung adenocarcinoma
Authors: Wu Weidong , Li Mengling , Wu Yingxiao , Wei Qiongying , Yu Nanding 
Published: August 2024

AbstractMETTL14 functions as an RNA methyltransferase involved in m6A modification, influencing mRNA biogenesis, decay, and translation processes. However, the specific mechanism by which METTL14 regulates glucose-6-phosphate dehydrogenase (G6PD) to promote the progression of lung adenocarcinoma (LUAD) is not well understood. Quantitative measurement and immunohistochemistry (IHC) analysis have demonstrated higher levels of m6A in LUAD tissues compared to adjacent normal tissues. Additionally, the expression of METTL14 was significantly increased in LUAD tissues. In LUAD cell lines, both METTL14 and m6A levels were elevated compared to normal human lung epithelial cells. Knockdown of METTL14 markedly reduced LUAD cell proliferation, migration, and invasion. Conversely, overexpression of METTL14, but not the mutant form, significantly enhanced these cellular processes in LUAD. In vivo studies using nude mice with subcutaneously transplanted LUAD cells demonstrated that stable METTL14 knockdown led to notably reduced tumor volume and weight, along with fewer Ki67-positive cells and lung metastatic sites. Importantly, METTL14 knockdown reduced glycolytic activity in LUAD cells. Through a combination of RNA sequencing and MeRIP-sequencing, we identified numerous altered genes and confirmed that IGF2BP2 enhances G6PD mRNA stability after METTL14-mediated m6A modification, thereby promoting tumor growth and metastasis. Moreover, LUAD patients with higher levels of G6PD had poorer overall survival (OS). In conclusion, our study indicates that METTL14 upregulates G6PD expression post-transcriptionally through an m6A-IGF2BP2-dependent mechanism, thereby stabilizing G6PD mRNA. These findings propose potential diagnostic biomarkers and effective targets for anti-metabolism therapy in LUAD.
Cellular transitions during cranial suture establishment in zebrafish
Authors: Farmer D’Juan T. , Dukov Jennifer E. , Chen Hung-Jhen , Arata Claire , Hernandez-Trejo Jose , Xu Pengfei , Teng Camilla S. , Maxson Robert E. , Crump J. Gage 
Published: August 2024

AbstractCranial sutures separate neighboring skull bones and are sites of bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Using single-cell transcriptomics, lineage tracing, and mutant analysis in zebrafish, we uncover key developmental transitions regulating bone formation at sutures during skull expansion. In particular, we identify a subpopulation of mesenchyme cells in the mid-suture region that upregulate a suite of genes including BMP antagonists (e.g. grem1a) and pro-angiogenic factors. Lineage tracing with grem1a:nlsEOS reveals that this mid-suture subpopulation is largely non-osteogenic. Moreover, combinatorial mutation of BMP antagonists enriched in this mid-suture subpopulation results in increased BMP signaling in the suture, misregulated bone formation, and abnormal suture morphology. These data reveal establishment of a non-osteogenic mesenchyme population in the mid-suture region that restricts bone formation through local BMP antagonism, thus ensuring proper suture morphology.
In-plane staging in lithium-ion intercalation of bilayer graphene
Authors: Astles Thomas , McHugh James G. , Zhang Rui , Guo Qian , Howe Madeleine , Wu Zefei , Indykiewicz Kornelia , Summerfield Alex , Goodwin Zachary A. H. , Slizovskiy Sergey , Domaretskiy Daniil , Geim Andre K. , Falko Vladimir , Grigorieva Irina V. 
Published: August 2024

AbstractThe ongoing efforts to optimize rechargeable Li-ion batteries led to the interest in intercalation of nanoscale layered compounds, including bilayer graphene. Its lithium intercalation has been demonstrated recently but the mechanisms underpinning the storage capacity remain poorly understood. Here, using magnetotransport measurements, we report in-operando intercalation dynamics of bilayer graphene. Unexpectedly, we find four distinct intercalation stages that correspond to well-defined Li-ion densities. Transitions between the stages occur rapidly (within 1 sec) over the entire device area. We refer to these stages as ‘in-plane’, with no in-plane analogues in bulk graphite. The fully intercalated bilayers represent a stoichiometric compound C14LiC14 with a Li density of ∼2.7·1014 cm−2, notably lower than fully intercalated graphite. Combining the experimental findings and DFT calculations, we show that the critical step in bilayer intercalation is a transition from AB to AA stacking which occurs at a density of ∼0.9·1014 cm−2. Our findings reveal the mechanism and limits for electrochemical intercalation of bilayer graphene and suggest possible avenues for increasing the Li storage capacity.
Indistinguishable photons from an artificial atom in silicon photonics
Authors: Komza Lukasz , Samutpraphoot Polnop , Odeh Mutasem , Tang Yu-Lung , Mathew Milena , Chang Jiu , Song Hanbin , Kim Myung-Ki , Xiong Yihuang , Hautier Geoffroy , Sipahigil Alp 
Published: August 2024

AbstractSilicon is the ideal material for building electronic and photonic circuits at scale. Integrated photonic quantum technologies in silicon offer a promising path to scaling by leveraging advanced semiconductor manufacturing and integration capabilities. However, the lack of deterministic quantum light sources and strong photon-photon interactions in silicon poses a challenge to scalability. In this work, we demonstrate an indistinguishable photon source in silicon photonics based on an artificial atom. We show that a G center in a silicon waveguide can generate high-purity telecom-band single photons. We perform high-resolution spectroscopy and time-delayed two-photon interference to demonstrate the indistinguishability of single photons emitted from a G center in a silicon waveguide. Our results show that artificial atoms in silicon photonics can source single photons suitable for photonic quantum networks and processors.
VolcanoSV enables accurate and robust structural variant calling in diploid genomes from single-molecule long read sequencing
Authors: Luo Can , Liu Yichen Henry , Zhou Xin Maizie 
Published: August 2024

AbstractStructural variants (SVs) significantly contribute to human genome diversity and play a crucial role in precision medicine. Although advancements in single-molecule long-read sequencing offer a groundbreaking resource for SV detection, identifying SV breakpoints and sequences accurately and robustly remains challenging. We introduce VolcanoSV, an innovative hybrid SV detection pipeline that utilizes both a reference genome and local de novo assembly to generate a phased diploid assembly. VolcanoSV uses phased SNPs and unique k-mer similarity analysis, enabling precise haplotype-resolved SV discovery. VolcanoSV is adept at constructing comprehensive genetic maps encompassing SNPs, small indels, and all types of SVs, making it well-suited for human genomics studies. Our extensive experiments demonstrate that VolcanoSV surpasses state-of-the-art assembly-based tools in the detection of insertion and deletion SVs, exhibiting superior recall, precision, F1 scores, and genotype accuracy across a diverse range of datasets, including low-coverage (10x) datasets. VolcanoSV outperforms assembly-based tools in the identification of complex SVs, including translocations, duplications, and inversions, in both simulated and real cancer data. Moreover, VolcanoSV is robust to various evaluation parameters and accurately identifies breakpoints and SV sequences.
A pH-sensitive motif in an outer membrane protein activates bacterial membrane vesicle production
Authors: Dehinwal Ruchika , Gopinath Tata , Smith Richard D. , Ernst Robert K. , Schifferli Dieter M. , Waldor Matthew K. , Marassi Francesca M. 
Published: August 2024

AbstractOuter membrane vesicles (OMVs) produced by Gram-negative bacteria have key roles in cell envelope homeostasis, secretion, interbacterial communication, and pathogenesis. The facultative intracellular pathogen Salmonella Typhimurium increases OMV production inside the acidic vacuoles of host cells by changing expression of its outer membrane proteins and modifying the composition of lipid A. However, the molecular mechanisms that translate pH changes into OMV production are not completely understood. Here, we show that the outer membrane protein PagC promotes OMV production through pH-dependent interactions between its extracellular loops and surrounding lipopolysaccharide (LPS). Structural comparisons and mutational studies indicate that a pH-responsive amino acid motif in PagC extracellular loops, containing PagC-specific histidine residues, is crucial for OMV formation. Molecular dynamics simulations suggest that protonation of histidine residues leads to changes in the structure and flexibility of PagC extracellular loops and their interactions with the surrounding LPS, altering membrane curvature. Consistent with that hypothesis, mimicking acidic pH by mutating those histidine residues to lysine increases OMV production. Thus, our findings reveal a mechanism for sensing and responding to environmental pH and for control of membrane dynamics by outer membrane proteins.
High-TC superconductivity in La3Ni2O7 based on the bilayer two-orbital t-J model
Authors: Luo Zhihui , Lv Biao , Wang Meng , Wú Wéi , Yao Dao-Xin 
Published: August 2024

AbstractThe recently discovered high-Tcsuperconductor La3Ni2O7has sparked renewed interest in unconventional superconductivity. Here we study superconductivity in pressurized La3Ni2O7based on a bilayer two-orbitalt−Jmodel, using the renormalized mean-field theory. Our results reveal a robusts±-wave pairing driven by the inter-layer$${d}_{{z}^{2}}$$dz2magnetic coupling, which exhibits a transition temperature within the same order of magnitude as the experimentally observedTc ~ 80 K. We establish a comprehensive superconducting phase diagram in the doping plane. Notably, the La3Ni2O7under pressure is found to be situated roughly in the optimal doping regime of the phase diagram. When the$${d}_{{x}^{2}-{y}^{2}}$$dx2−y2orbital becomes close to half-filling,d-wave andd+ispairing can emerge from the system. We discuss the interplay between Fermi surface topology and different pairing symmetries. The stability of thes±-wave pairing against Hund’s coupling and other magnetic exchange couplings is discussed.
Chloroplast and whole-genome sequencing shed light on the evolutionary history and phenotypic diversification of peanuts
Authors: Zheng Zheng , Sun Ziqi , Qi Feiyan , Fang Yuanjin , Lin Ke , Pavan Stefano , Huang Bingyan , Dong Wenzhao , Du Pei , Tian Mengdi , Shi Lei , Xu Jing , Han Suoyi , Liu Hua , Qin Li , Zhang Zhongxin , Dai Xiaodong , Miao Lijuan , Zhao Ruifang , Wang Juan , Liao Yanlin , Li Alun , Ruan Jue , Delvento Chiara , Aiese Cigliano Riccardo , Maliepaard Chris , Bai Yuling , Visser Richard G. F. , Zhang Xinyou 
Published: August 2024

AbstractCultivated peanut (Arachis hypogaea L.) is a widely grown oilseed crop worldwide; however, the events leading to its origin and diversification are not fully understood. Here by combining chloroplast and whole-genome sequence data from a large germplasm collection, we show that the two subspecies of A. hypogaea (hypogaea and fastigiata) likely arose from distinct allopolyploidization and domestication events. Peanut genetic clusters were then differentiated in relation to dissemination routes and breeding efforts. A combination of linkage mapping and genome-wide association studies allowed us to characterize genes and genomic regions related to main peanut morpho-agronomic traits, namely flowering pattern, inner tegument color, growth habit, pod/seed weight and oil content. Together, our findings shed light on the evolutionary history and phenotypic diversification of peanuts and might be of broad interest to plant breeders.
A Motion Capture Dataset on Human Sitting to Walking Transitions
Authors: Perera Chamalka Kenneth , Hussain Zakia , Khant Min , Gopalai Alpha Agape , Gouwanda Darwin , Ahmad Siti Anom 
Published: August 2024

AbstractSit-to-walk (STW) is a crucial daily task that impacts mobility, independence, and thus quality of life. Existing repositories have limited STW data with small sample sizes (n = 10). Hence, this study presents a STW dataset obtained via the time-up-and-go test, for 65 healthy adults across three age groups – young (19–35 years), middle (36–55 years) and older (above 56 years). The dataset contains lower body motion capture, ground reaction force, surface electromyography, inertial measurement unit data, and responses for the knee injury and osteoarthritis outcome score survey. For validation, the within subjects intraclass correlation coefficients for the maximum and minimum lower body joint angles were calculated with values greater than 0.74, indicating good test-retest reliability. The joint angle trajectories and maximum voluntary contractions are comparable with existing literature, matching in overall trends and range. Accordingly, this dataset allows STW biomechanics, executions, and characteristics to be studied across age groups. Biomechanical trajectories of healthy adults serve as a benchmark in assessing neuromusculoskeletal impairments and when designing assistive technology for treatment or rehabilitation.
Exploring the adverse events of Oxford–AstraZeneca, Pfizer-BioNTech, Moderna, and Johnson and Johnson COVID-19 vaccination on Guillain–Barré Syndrome
Authors: Meo Sultan Ayoub , Shaikh Narmeen , Abukhalaf Farah Adnan , Meo Anusha Sultan 
Published: August 2024

AbstractThe vaccination against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is an important public health strategy to prevent people from the pandemic. Vaccines are a game-changing tool, it is essential to understand the adverse events after COVID-19 vaccination. This study explored the adverse events of COVID-19 Vaccination Oxford–AstraZeneca, Pfizer-BioNTech, Moderna, Johnson and Johnson on Guillain–Barré Syndrome (GBS). In this study, initially 128 documents were identified from the databases, including Pub-Med, Web of Science-Clarivate Analytics, Scopus, and Google Scholar. The articles on COVID-19 vaccination and GBs were searched using the keywords “SARS-CoV-2, COVID-19, Vaccination, and Guillain Barré Syndrome, GBS”, finally, 16 documents were included in the analysis and synthesis. After administering 1,680,042,214 doses of COVID-19 vaccines, 6177 cases were identified with 10.5 cases per million vaccine doses. A significant positive risk was found between COVID-19 vaccine administration and GBS with a risk rate of RR 1.97 (95% CI 1.26–3.08, p = 0.01). The mRNA vaccines were associated with 2076 cases, and 1,237,638,401 vaccine doses were linked with 4.47 GBS events per million vaccine doses. The first dose of the m-RNA vaccine was associated with 8.83 events per million doses compared to the second dose with 02 events per million doses. The viral-vector vaccine doses 193,535,249 were linked to 1630 GBS cases with 11.01 cases per million doses. The incidence of GBS after the first dose was 17.43 compared to 1.47 cases per million in the second dose of the viral-vector vaccine. The adverse events of the Oxford–AstraZeneca vaccine were linked to 1339 cases of GBS following 167,786,902 vaccine doses, with 14.2 cases per million doses. The Oxford–AstraZeneca vaccine significantly increased the risk of GBS RR: 2.96 (95% CI 2.51–3.48, p = 0.01). For the Pfizer-BioNTech vaccine, there were 7.20 cases per million doses of the vaccine, and no significant association was identified between the Pfizer-BioNTech vaccine and GBS incidence RR: 0.99 (95% CI 0.75–1.32, p = 0.96). Moderna vaccine was related with 419 cases of GBS after administering 420,420,909 doses, with 2.26 cases per million doses. However, Johnson and Johnson's vaccination was linked to 235 GBS after 60,256,913 doses of the vaccine with 8.80 cases per million doses. A significant association was seen between the risk of GBS and Ad.26.COV2. S vaccine, RR: 2.47 (95% CI 1.30–4.69, p < 0.01). Overall, a significant association was seen between the COVID-19 vaccines and the risk of GBS. The incidence of GBS was higher after the first dose compared to GBS cases per million in the second dose.
Efficient artificial intelligence-based assessment of the gastroesophageal valve with Hill classification through active learning
Authors: Kafetzis Ioannis , Fuchs Karl-Hermann , Sodmann Philipp , Troya Joel , Zoller Wolfram , Meining Alexander , Hann Alexander 
Published: August 2024

AbstractStandardized assessment of the gastroesophageal valve during endoscopy, attainable via the Hill classification, is important for clinical assessment and therapeutic decision making. The Hill classification is associated with the presence of hiatal hernia (HH), a common endoscopic finding connected to gastro-esophageal reflux disease. A novel efficient medical artificial intelligence (AI) training pipeline using active learning (AL) is designed. We identified 21,970 gastroscopic images as training data and used our AL to train a model for predicting the Hill classification and detecting HH. Performance of the AL and traditionally trained models were evaluated on an external expert-annotated image collection. The AL model achieved accuracy of 76%. A traditionally trained model with 125% more training data achieved 77% accuracy. Furthermore, the AL model achieved higher precision than the traditional one for rare classes, with 0.54 versus 0.39 (p < 0.05) for grade 3 and 0.72 versus 0.61 (p < 0.05) for grade 4. In detecting HH, the AL model achieved 94% accuracy, 0.72 precision and 0.74 recall. Our AL pipeline is more efficient than traditional methods in training AI for endoscopy.
Influences of heart rate feedback and autistic traits on affective mindreading
Authors: Bögl Katharina , Bayer Mareike , Walter Henrik , Dziobek Isabel 
Published: August 2024

AbstractAlthough mindreading is an important prerequisite for successful social interactions, the underlying mechanisms are still matter of debate. It is unclear, for example, if inferring others’ and own mental states are distinct processes or are based on a common mechanism. Using an affect-induction experimental set-up with an acoustic heart rate feedback that addresses affective mindreading in self and others, we investigated if non-autistic study participants relied on similar information for self- and other-directed mindreading. We assumed that due to altered mindreading capacities in autism, mainly individuals with low autistic traits would focus on additional sensory cues, such as heart rate, to infer their own and their gambling partner’s affective states. Our analyses showed that the interpretation of a heart rate signal differed in self- and other-directed mindreading trials. This effect was modulated by autistic traits suggesting that individuals with higher autistic traits might not have interpreted the heart rate feedback for gambling partner ratings and differentiated less between self- and other-directed mindreading trials. We discuss these results in the context of a common mechanism underlying self- and other-directed mindreading and hypothesize that the weighting of internal and external sensory information might contribute to how we make sense of our and others’ mental states.
Neck muscle function improves after neck exercises in individuals with whiplash-associated disorders: a case–control ultrasound study with speckle-tracking analyses
Authors: Peterson Gunnel , Nilsson David , Jönsson Margaretha , Bennett Kate , Peolsson Anneli 
Published: August 2024

AbstractA whiplash injury can alter neck muscle function, which remains years after the injury and may explain why symptoms such as persistent pain and disability occur. There is currently limited knowledge about dynamic neck muscle function in chronic whiplash-associated disorders (WAD), and about the extent to which altered muscle function can improve after rehabilitation. Ultrasound can detect mechanical neck muscle function by measuring real-time deformation and deformation rate in the muscles. This method was used for five dorsal neck muscles in participants with chronic WAD versus matched controls in resistant neck rotation. We obtained real-time, non-invasive ultrasound measurements using speckle tracking, multivariate analyses, and mixed-design ANOVA analyses. The results showed altered deformation in the three deepest neck muscle layers, with less deformation area in the WAD group compared to controls in rotation to the most painful side at baseline. Participants in the WAD group performed three months of neck-specific exercises, resulting in improved deformation in the deep neck muscles in WAD and with a similar deformation pattern to controls, and the significant group differences ceased. We reveal new and important insights into the capability of ultrasound to diagnose altered neck muscle function and evaluate an exercise intervention.
Real-time visual intelligence for defect detection in pharmaceutical packaging
Authors: Vijayakumar Ajantha , Vairavasundaram Subramaniyaswamy , Koilraj Joseph Abraham Sundar , Rajappa Muthaiah , Kotecha Ketan , Kulkarni Ambarish 
Published: August 2024

AbstractDefect detection in pharmaceutical blister packages is the most challenging task to get an accurate result in detecting defects that arise in tablets while manufacturing. Conventional defect detection methods include human intervention to check the quality of tablets within the blister packages, which is inefficient, time-consuming, and increases labor costs. To mitigate this issue, the YOLO family is primarily used in many industries for real-time defect detection in continuous production. To enhance the feature extraction capability and reduce the computational overhead in a real-time environment, the CBS-YOLOv8 is proposed by enhancing the YOLOv8 model. In the proposed CBS-YOLOv8, coordinate attention is introduced to improve the feature extraction capability by capturing the spatial and cross-channel information and also maintaining the long-range dependencies. The BiFPN (weighted bi-directional feature pyramid network) is also introduced in YOLOv8 to enhance the feature fusion at each convolution layer to avoid more precise information loss. The model's efficiency is enhanced through the implementation of SimSPPF (simple spatial pyramid pooling fast), which reduces computational demands and model complexity, resulting in improved speed. A custom dataset containing defective tablet images is used to train the proposed model. The performance of the CBS-YOLOv8 model is then evaluated by comparing it with various other models. Experimental results on the custom dataset reveal that the CBS-YOLOv8 model achieves a mAP of 97.4% and an inference speed of 79.25 FPS, outperforming other models. The proposed model is also evaluated on SESOVERA-ST saline bottle fill level monitoring dataset achieved the mAP50 of 99.3%. This demonstrates that CBS-YOLOv8 provides an optimized inspection process, enabling prompt detection and correction of defects, thus bolstering quality assurance practices in manufacturing settings.