bluuebunny/crossref_metadata_2025_split huggingface dataset:
circIPO7 dissociates caprin-1 from ribosomes and inhibits gastric cancer cell proliferation by suppressing EGFR and mTOR
Authors: Liu Jing , Niu Liling , Hao Jiaru , Yao Yuan , Yan Meinan , Li Hui 
Published: February 2023

AbstractCircular RNA (circRNA) is a novel RNA molecule characterized by covalently closed loop structure. Since its discovery, researchers have shown that circRNA is not “splicing noise” but a participant of various pathophysiological processes through unique mechanisms. circIPO7, which was identified as an independent prognostic factor in gastric cancer (GC) patients, was downregulated in GC tissues and cells compared to paracarcinoma tissues and normal epithelial cells. circIPO7 overexpression significantly suppressed GC cell proliferation in vitro and in vivo. Mechanistically, circIPO7 directly binds with caprin-1, an RNA-binding protein involved in mRNA translation, sharing overlapping binding sites with G3BP1. Thus, the complex containing overexpressed circIPO7 blocked the caprin-1-G3BP1 interaction and dissociated caprin-1 and its target mRNAs (EGFR and mTOR) from ribosomes, resulting in their translational inhibition, followed by PI3K/AKT/mTOR pathway inactivation. We uncovered a novel molecular mechanism for circRNAs in GC development, identifying circIPO7 as a potential target for cancer treatment.
Osteoarthritis: pathogenic signaling pathways and therapeutic targets
Authors: Yao Qing , Wu Xiaohao , Tao Chu , Gong Weiyuan , Chen Mingjue , Qu Minghao , Zhong Yiming , He Tailin , Chen Sheng , Xiao Guozhi 
Published: February 2023

AbstractOsteoarthritis (OA) is a chronic degenerative joint disorder that leads to disability and affects more than 500 million population worldwide. OA was believed to be caused by the wearing and tearing of articular cartilage, but it is now more commonly referred to as a chronic whole-joint disorder that is initiated with biochemical and cellular alterations in the synovial joint tissues, which leads to the histological and structural changes of the joint and ends up with the whole tissue dysfunction. Currently, there is no cure for OA, partly due to a lack of comprehensive understanding of the pathological mechanism of the initiation and progression of the disease. Therefore, a better understanding of pathological signaling pathways and key molecules involved in OA pathogenesis is crucial for therapeutic target design and drug development. In this review, we first summarize the epidemiology of OA, including its prevalence, incidence and burdens, and OA risk factors. We then focus on the roles and regulation of the pathological signaling pathways, such as Wnt/β-catenin, NF-κB, focal adhesion, HIFs, TGFβ/ΒΜP and FGF signaling pathways, and key regulators AMPK, mTOR, and RUNX2 in the onset and development of OA. In addition, the roles of factors associated with OA, including MMPs, ADAMTS/ADAMs, and PRG4, are discussed in detail. Finally, we provide updates on the current clinical therapies and clinical trials of biological treatments and drugs for OA. Research advances in basic knowledge of articular cartilage biology and OA pathogenesis will have a significant impact and translational value in developing OA therapeutic strategies.
Dietary patterns related to biological mechanisms and survival after breast cancer diagnosis: results from a cohort study
Authors: Castro-Espin Carlota , Bonet Catalina , Crous-Bou Marta , Katzke Verena , Le Cornet Charlotte , Jannasch Franziska , Schulze Matthias B. , Olsen Anja , Tjønneland Anne , Dahm Christina C. , Antoniussen Christian S. , Sánchez Maria Jose , Amiano Pilar , Chirlaque María Dolores , Guevara Marcela , Agnoli Claudia , Tumino Rosario , Sacerdote Carlotta , De Magistris Maria Santucci , Sund Malin , Bodén Stina , Jensen Torill Enget , Olsen Karina Standahl , Skeie Guri , Gunter Marc J. , Rinaldi Sabina , Gonzalez-Gil Esther M. , Weiderpass Elisabete , Christakoudi Sofia , Heath Alicia K. , Dossus Laure , Agudo Antonio 
Published: February 2023

Abstract
Background
Inflammatory, insulin and oestrogenic pathways have been linked to breast cancer (BC). We aimed to examine the relationship between pre-diagnostic dietary patterns related to these mechanisms and BC survival.

Methods
The diabetes risk reduction diet (DRRD), inflammatory score of diet (ISD) and oestrogen-related dietary pattern (ERDP) were calculated using dietary data from the European Prospective Investigation into Cancer and Nutrition (EPIC) study. Cox proportional hazards models were used to assess associations between dietary patterns and overall mortality and competing risk models for associations with BC-specific mortality.

Results
We included 13,270 BC cases with a mean follow-up after diagnosis of 8.6 years, representing 2340 total deaths, including 1475 BC deaths. Higher adherence to the DRRD score was associated with lower overall mortality (HR1–SD 0.92; 95%CI 0.87–0.96). Greater adherence to pro-inflammatory diets was borderline associated with 6% higher mortality HR1–SD 1.06; 95%CI 1.00–1.12. No significant association with the oestrogen-related dietary pattern was observed. None of the dietary patterns were associated with BC-specific mortality.

Conclusions
Greater adherence to an anti-diabetic and anti-inflammatory diet prior to diagnosis is associated with lower overall mortality among BC survivors. Long-term adherence to these dietary patterns could be a means to improve the prognosis of BC survivors.
CCN3/NOV promotes metastasis and tumor progression via GPNMB-induced EGFR activation in triple-negative breast cancer
Authors: Son Seogho , Kim Hyungjoo , Lim Hogeun , Lee Joo-hyung , Lee Kyung-min , Shin Incheol 
Published: February 2023

AbstractTriple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer. TNBC patients typically exhibit unfavorable outcomes due to its rapid growth and metastatic potential. Here, we found overexpression of CCN3 in TNBC patients. We identified that CCN3 knockdown diminished cancer stem cell formation, metastasis, and tumor growth in vitro and in vivo. Mechanistically, ablation of CCN3 reduced activity of the EGFR/MAPK pathway. Transcriptome profiling revealed that CCN3 induces glycoprotein nonmetastatic melanoma protein B (GPNMB) expression, which in turn activates the EGFR pathway. An interrogation of the TCGA dataset further supported the transcriptional regulation of GPNMB by CCN3. Finally, we showed that CCN3 activates Wnt signaling through a ligand-dependent or -independent mechanism, which increases microphthalmia-associated transcription factor (MITF) protein, a transcription factor inducing GPNMB expression. Together, our findings demonstrate the oncogenic role of CCN3 in TNBC, and we propose CCN3 as a putative therapeutic target for TNBC.
Macromolecular sheets direct the morphology and orientation of plate-like biogenic guanine crystals
Authors: Wagner Avital , Upcher Alexander , Maria Raquel , Magnesen Thorolf , Zelinger Einat , Raposo Graça , Palmer Benjamin A. 
Published: February 2023

AbstractAnimals precisely control the morphology and assembly of guanine crystals to produce diverse optical phenomena in coloration and vision. However, little is known about how organisms regulate crystallization to produce optically useful morphologies which express highly reflective crystal faces. Guanine crystals form inside iridosome vesicles within chromatophore cells called iridophores. By following iridosome formation in developing scallop eyes, we show that pre-assembled, fibrillar sheets provide an interface for nucleation and direct the orientation of the guanine crystals. The macromolecular sheets cap the (100) faces of immature guanine crystals, inhibiting growth along the π-stacking growth direction. Crystal growth then occurs preferentially along the sheets to generate highly reflective plates. Despite their different physical properties, the morphogenesis of iridosomes bears a striking resemblance to melanosome morphogenesis in vertebrates, where amyloid sheets template melanin deposition. The common control mechanisms for melanin and guanine formation inspire new approaches for manipulating the morphologies and properties of molecular materials.
Shark nanobodies with potent SARS-CoV-2 neutralizing activity and broad sarbecovirus reactivity
Authors: Chen Wei-Hung , Hajduczki Agnes , Martinez Elizabeth J. , Bai Hongjun , Matz Hanover , Hill Thomas M. , Lewitus Eric , Chang William C. , Dawit Layla , Peterson Caroline E. , Rees Phyllis A. , Ajayi Adelola B. , Golub Emily S. , Swafford Isabella , Dussupt Vincent , David Sapna , Mayer Sandra V. , Soman Sandrine , Kuklis Caitlin , Corbitt Courtney , King Jocelyn , Choe Misook , Sankhala Rajeshwer S. , Thomas Paul V. , Zemil Michelle , Wieczorek Lindsay , Hart Tricia , Duso Debora , Kummer Larry , Yan Lianying , Sterling Spencer L. , Laing Eric D. , Broder Christopher C. , Williams Jazmean K. , Davidson Edgar , Doranz Benjamin J. , Krebs Shelly J. , Polonis Victoria R. , Paquin-Proulx Dominic , Rolland Morgane , Reiley William W. , Gromowski Gregory D. , Modjarrad Kayvon , Dooley Helen , Joyce M. Gordon 
Published: February 2023

AbstractDespite rapid and ongoing vaccine and therapeutic development, SARS-CoV-2 continues to evolve and evade, presenting a need for next-generation diverse therapeutic modalities. Here we show that nurse sharks immunized with SARS-CoV-2 recombinant receptor binding domain (RBD), RBD-ferritin (RFN), or spike protein ferritin nanoparticle (SpFN) immunogens elicit a set of new antigen receptor antibody (IgNAR) molecules that target two non-overlapping conserved epitopes on the spike RBD. Representative shark antibody variable NAR-Fc chimeras (ShAbs) targeting either of the two epitopes mediate cell-effector functions, with high affinity to all SARS-CoV-2 viral variants of concern, including the divergent Omicron strains. The ShAbs potently cross-neutralize SARS-CoV-2 WA-1, Alpha, Beta, Delta, Omicron BA.1 and BA.5, and SARS-CoV-1 pseudoviruses, and confer protection against SARS-CoV-2 challenge in the K18-hACE2 transgenic mouse model. Structural definition of the RBD-ShAb01-ShAb02 complex enabled design and production of multi-specific nanobodies with enhanced neutralization capacity, and picomolar affinity to divergent sarbecovirus clade 1a, 1b and 2 RBD molecules. These shark nanobodies represent potent immunotherapeutics both for current use, and future sarbecovirus pandemic preparation.
Origins of Barents-Kara sea-ice interannual variability modulated by the Atlantic pathway of El Niño–Southern Oscillation
Authors: Luo Binhe , Luo Dehai , Ge Yao , Dai Aiguo , Wang Lin , Simmonds Ian , Xiao Cunde , Wu Lixin , Yao Yao 
Published: February 2023

AbstractWinter Arctic sea-ice concentration (SIC) decline plays an important role in Arctic amplification which, in turn, influences Arctic ecosystems, midlatitude weather and climate. SIC over the Barents-Kara Seas (BKS) shows large interannual variations, whose origin is still unclear. Here we find that interannual variations in winter BKS SIC have significantly strengthened in recent decades likely due to increased amplitudes of the El Niño-Southern Oscillation (ENSO) in a warming climate. La Niña leads to enhanced Atlantic Hadley cell and a positive phase North Atlantic Oscillation-like anomaly pattern, together with concurring Ural blocking, that transports Atlantic ocean heat and atmospheric moisture toward the BKS and promotes sea-ice melting via intensified surface warming. The reverse is seen during El Niño which leads to weakened Atlantic poleward transport and an increase in the BKS SIC. Thus, interannual variability of the BKS SIC partly originates from ENSO via the Atlantic pathway.
Alternative polyadenylation transcriptome-wide association study identifies APA-linked susceptibility genes in brain disorders
Authors: Cui Ya , Arnold Frederick J. , Peng Fanglue , Wang Dan , Li Jason Sheng , Michels Sebastian , Wagner Eric J. , La Spada Albert R. , Li Wei 
Published: February 2023

AbstractAlternative polyadenylation (APA) plays an essential role in brain development; however, current transcriptome-wide association studies (TWAS) largely overlook APA in nominating susceptibility genes. Here, we performed a 3′ untranslated region (3′UTR) APA TWAS (3′aTWAS) for 11 brain disorders by combining their genome-wide association studies data with 17,300 RNA-seq samples across 2,937 individuals. We identified 354 3′aTWAS-significant genes, including known APA-linked risk genes, such as SNCA in Parkinson’s disease. Among these 354 genes, ~57% are not significant in traditional expression- and splicing-TWAS studies, since APA may regulate the translation, localization and protein-protein interaction of the target genes independent of mRNA level expression or splicing. Furthermore, we discovered ATXN3 as a 3′aTWAS-significant gene for amyotrophic lateral sclerosis, and its modulation substantially impacted pathological hallmarks of amyotrophic lateral sclerosis in vitro. Together, 3′aTWAS is a powerful strategy to nominate important APA-linked brain disorder susceptibility genes, most of which are largely overlooked by conventional expression and splicing analyses.
Learning local equivariant representations for large-scale atomistic dynamics
Authors: Musaelian Albert , Batzner Simon , Johansson Anders , Sun Lixin , Owen Cameron J. , Kornbluth Mordechai , Kozinsky Boris 
Published: February 2023

AbstractA simultaneously accurate and computationally efficient parametrization of the potential energy surface of molecules and materials is a long-standing goal in the natural sciences. While atom-centered message passing neural networks (MPNNs) have shown remarkable accuracy, their information propagation has limited the accessible length-scales. Local methods, conversely, scale to large simulations but have suffered from inferior accuracy. This work introduces Allegro, a strictly local equivariant deep neural network interatomic potential architecture that simultaneously exhibits excellent accuracy and scalability. Allegro represents a many-body potential using iterated tensor products of learned equivariant representations without atom-centered message passing. Allegro obtains improvements over state-of-the-art methods on QM9 and revMD17. A single tensor product layer outperforms existing deep MPNNs and transformers on QM9. Furthermore, Allegro displays remarkable generalization to out-of-distribution data. Molecular simulations using Allegro recover structural and kinetic properties of an amorphous electrolyte in excellent agreement with ab-initio simulations. Finally, we demonstrate parallelization with a simulation of 100 million atoms.
COVID-Dynamic: A large-scale longitudinal study of socioemotional and behavioral change across the pandemic
Authors: Rusch Tessa , Han Yanting , Liang Dehua , Hopkins Amber R. , Lawrence Caroline V. , Maoz Uri , Paul Lynn K. , Stanley Damian A. ,   the COVID-Dynamic Team, Adolphs Ralph , Alvarez R. Michael , Camplisson Isabella , Harrison Laura , Hien Denise , Lan Tian , Lin Chujusn , Lopez-Castro Teresa , Nizzic Marie-Christine , Golden Allison Rabkin , Wahle Iman , Yaffe Gideon 
Published: February 2023

AbstractThe COVID-19 pandemic has caused enormous societal upheaval globally. In the US, beyond the devastating toll on life and health, it triggered an economic shock unseen since the great depression and laid bare preexisting societal inequities. The full impacts of these personal, social, economic, and public-health challenges will not be known for years. To minimize societal costs and ensure future preparedness, it is critical to record the psychological and social experiences of individuals during such periods of high societal volatility. Here, we introduce, describe, and assess the COVID-Dynamic dataset, a within-participant longitudinal study conducted from April 2020 through January 2021, that captures the COVID-19 pandemic experiences of >1000 US residents. Each of 16 timepoints combines standard psychological assessments with novel surveys of emotion, social/political/moral attitudes, COVID-19-related behaviors, tasks assessing implicit attitudes and social decision-making, and external data to contextualize participants’ responses. This dataset is a resource for researchers interested in COVID-19-specific questions and basic psychological phenomena, as well as clinicians and policy-makers looking to mitigate the effects of future calamities.
Chákṣu: A glaucoma specific fundus image database
Authors: Kumar J. R. Harish , Seelamantula Chandra Sekhar , Gagan J. H. , Kamath Yogish S. , Kuzhuppilly Neetha I. R. , Vivekanand U. , Gupta Preeti , Patil Shilpa 
Published: February 2023

AbstractWe introduce Chákṣu–a retinal fundus image database for the evaluation of computer-assisted glaucoma prescreening techniques. The database contains 1345 color fundus images acquired using three brands of commercially available fundus cameras. Each image is provided with the outlines for the optic disc (OD) and optic cup (OC) using smooth closed contours and a decision of normal versus glaucomatous by five expert ophthalmologists. In addition, segmentation ground-truths of the OD and OC are provided by fusing the expert annotations using the mean, median, majority, and Simultaneous Truth and Performance Level Estimation (STAPLE) algorithm. The performance indices show that the ground-truth agreement with the experts is the best with STAPLE algorithm, followed by majority, median, and mean. The vertical, horizontal, and area cup-to-disc ratios are provided based on the expert annotations. Image-wise glaucoma decisions are also provided based on majority voting among the experts. Chákṣu is the largest Indian-ethnicity-specific fundus image database with expert annotations and would aid in the development of artificial intelligence based glaucoma diagnostics.
Multimodal sensor fusion in the latent representation space
Authors: Piechocki Robert J. , Wang Xiaoyang , Bocus Mohammud J. 
Published: February 2023

AbstractA new method for multimodal sensor fusion is introduced. The technique relies on a two-stage process. In the first stage, a multimodal generative model is constructed from unlabelled training data. In the second stage, the generative model serves as a reconstruction prior and the search manifold for the sensor fusion tasks. The method also handles cases where observations are accessed only via subsampling i.e. compressed sensing. We demonstrate the effectiveness and excellent performance on a range of multimodal fusion experiments such as multisensory classification, denoising, and recovery from subsampled observations.
Evaluation of the portability of computable phenotypes with natural language processing in the eMERGE network
Authors: Pacheco Jennifer A. , Rasmussen Luke V. , Wiley Ken , Person Thomas Nate , Cronkite David J. , Sohn Sunghwan , Murphy Shawn , Gundelach Justin H. , Gainer Vivian , Castro Victor M. , Liu Cong , Mentch Frank , Lingren Todd , Sundaresan Agnes S. , Eickelberg Garrett , Willis Valerie , Furmanchuk Al’ona , Patel Roshan , Carrell David S. , Deng Yu , Walton Nephi , Satterfield Benjamin A. , Kullo Iftikhar J. , Dikilitas Ozan , Smith Joshua C. , Peterson Josh F. , Shang Ning , Kiryluk Krzysztof , Ni Yizhao , Li Yikuan , Nadkarni Girish N. , Rosenthal Elisabeth A. , Walunas Theresa L. , Williams Marc S. , Karlson Elizabeth W. , Linder Jodell E. , Luo Yuan , Weng Chunhua , Wei WeiQi 
Published: February 2023

AbstractThe electronic Medical Records and Genomics (eMERGE) Network assessed the feasibility of deploying portable phenotype rule-based algorithms with natural language processing (NLP) components added to improve performance of existing algorithms using electronic health records (EHRs). Based on scientific merit and predicted difficulty, eMERGE selected six existing phenotypes to enhance with NLP. We assessed performance, portability, and ease of use. We summarized lessons learned by: (1) challenges; (2) best practices to address challenges based on existing evidence and/or eMERGE experience; and (3) opportunities for future research. Adding NLP resulted in improved, or the same, precision and/or recall for all but one algorithm. Portability, phenotyping workflow/process, and technology were major themes. With NLP, development and validation took longer. Besides portability of NLP technology and algorithm replicability, factors to ensure success include privacy protection, technical infrastructure setup, intellectual property agreement, and efficient communication. Workflow improvements can improve communication and reduce implementation time. NLP performance varied mainly due to clinical document heterogeneity; therefore, we suggest using semi-structured notes, comprehensive documentation, and customization options. NLP portability is possible with improved phenotype algorithm performance, but careful planning and architecture of the algorithms is essential to support local customizations.
Fabrication of biochar derived from different types of feedstocks as an efficient adsorbent for soil heavy metal removal
Authors: Burachevskaya Marina , Minkina Tatiana , Bauer Tatiana , Lobzenko Ilya , Fedorenko Alexey , Mazarji Mahmoud , Sushkova Svetlana , Mandzhieva Saglara , Nazarenko Alexander , Butova Vera , Wong Ming Hung , Rajput Vishnu D. 
Published: February 2023

AbstractFor effective soil remediation, it is vital to apply environmentally friendly and cost-effective technologies following the notion of green sustainable development. In the context of recycling waste and preserving nutrients in the soil, biochar production and utilization have become widespread. There is an urgent need to develop high-efficiency biochar-based sorbents for pollution removal from soil. This research examined the efficacy of soil remediation using biochar made from three distinct sources: wood, and agricultural residues (sunflower and rice husks). The generated biochars were characterized by SEM/SCEM, XRF, XRD, FTIR, BET Specific Surface Area, and elemental compositions. The presence of hydroxyl and phenolic functional groups and esters in wood, sunflower and rice husk biochar were noted. The total volume of pores was in the following descending order: rice husk > wood > sunflower husk. However, wood biochar had more thermally stable, heterogeneous, irregular-shaped pores than other samples. Adsorption of soil-heavy metals into biochars differed depending on the type of adsorbent, according to data derived from distribution coefficients, sorption degree, Freundlich, and Langmuir adsorption models. The input of biochars to Calcaric Fluvic Arenosol increased its adsorption ability under contamination by Cu(II), Zn(II), and Pb(II) in the following order: wood > rice husk > sunflower husk. The addition of sunflower husk, wood, and rice husk biochar to the soil led to an increase in the removal efficiency of metals in all cases (more than 77%). The increase in the percentage adsorption of Cu and Pb was 9–19%, of Zn was 11–21%. The present results indicated that all biochars functioned well as an absorbent for removing heavy metals from soils. The tailor-made surface chemistry properties and the high sorption efficiency of the biochar from sunflower and rice husks could potentially be used for soil remediation.