bluuebunny/crossref_metadata_2025_split huggingface dataset:
IGF2BP2-modified circular RNA circCHD7 promotes endometrial cancer progression via stabilizing PDGFRB and activating JAK/STAT signaling pathway
Authors: Shi Rui , Zhao Rong , Shen Yan , Wei Sitian , Zhang Tangansu , Zhang Jun , Shu Wan , Cheng Shuangshuang , Teng Hua , Wang Hongbo 
Published: May 2024

AbstractCircular RNAs (circRNAs) represent a class of covalently closed, single-stranded RNAs and have been linked to cancer progression. N6-methyladenosine (m6A) methylation is a ubiquitous RNA modification in cancer cells. Increasing evidence suggests that m6A can mediate the effects of circRNAs in cancer biology. In contrast, the post-transcriptional systems of m6A and circRNA in the progression of endometrial cancer (EC) remain obscure. The current study identified a novel circRNA with m6A modification, hsa_circ_0084582 (circCHD7), which was upregulated in EC tissues. Functionally, circCHD7 was found to promote the proliferation of EC cells. Mechanistically, circCHD7 interacted with insulin-like growth factor 2 mRNA-binding protein (IGF2BP2) to amplify its enrichment. Moreover, circCHD7 increased the mRNA stability of platelet-derived growth factor receptor beta (PDGFRB) in an m6A-dependent manner, thereby enhancing its expression. In addition, the circCHD7/IGF2BP2/PDGFRB axis activated the JAK/STAT signaling pathway and promoted EC cell proliferation. In conclusion, these findings provide new insights into the regulation of circRNA-mediated m6A modification, and the new “circCHD7-PDGFRB” model of regulation offers new perspectives on circCHD7 as a potential target for EC therapy.
Hyperspectral retinal imaging biomarkers of ocular and systemic diseases
Authors: Saeed Abera , Hadoux Xavier , van Wijngaarden Peter 
Published: May 2024

AbstractHyperspectral imaging is a frontier in the field of medical imaging technology. It enables the simultaneous collection of spectroscopic and spatial data. Structural and physiological information encoded in these data can be used to identify and localise typically elusive biomarkers. Studies of retinal hyperspectral imaging have provided novel insights into disease pathophysiology and new ways of non-invasive diagnosis and monitoring of retinal and systemic diseases. This review provides a concise overview of recent advances in retinal hyperspectral imaging.
Integrating human endogenous retroviruses into transcriptome-wide association studies highlights novel risk factors for major psychiatric conditions
Authors: Duarte Rodrigo R. R. , Pain Oliver , Bendall Matthew L. , de Mulder Rougvie Miguel , Marston Jez L. , Selvackadunco Sashika , Troakes Claire , Leung Szi Kay , Bamford Rosemary A. , Mill Jonathan , O’Reilly Paul F. , Srivastava Deepak P. , Nixon Douglas F. , Powell Timothy R. 
Published: May 2024

AbstractHuman endogenous retroviruses (HERVs) are repetitive elements previously implicated in major psychiatric conditions, but their role in aetiology remains unclear. Here, we perform specialised transcriptome-wide association studies that consider HERV expression quantified to precise genomic locations, using RNA sequencing and genetic data from 792 post-mortem brain samples. In Europeans, we identify 1238 HERVs with expression regulated in cis, of which 26 represent expression signals associated with psychiatric disorders, with ten being conditionally independent from neighbouring expression signals. Of these, five are additionally significant in fine-mapping analyses and thus are considered high confidence risk HERVs. These include two HERV expression signatures specific to schizophrenia risk, one shared between schizophrenia and bipolar disorder, and one specific to major depressive disorder. No robust signatures are identified for autism spectrum conditions or attention deficit hyperactivity disorder in Europeans, or for any psychiatric trait in other ancestries, although this is likely a result of relatively limited statistical power. Ultimately, our study highlights extensive HERV expression and regulation in the adult cortex, including in association with psychiatric disorder risk, therefore providing a rationale for exploring neurological HERV expression in complex neuropsychiatric traits.
Higher order exchange driven noncoplanar magnetic state and large anomalous Hall effects in electron doped kagome magnet Mn3Sn
Authors: Singh Charanpreet , Jamaluddin Sk , Pradhan Subhadip , Nandy Ashis K. , Tokunaga Masashi , Avdeev Maxim , Nayak Ajaya K. 
Published: May 2024

AbstractOwing to geometrical frustration in the kagome lattice, Mn3Sn displays a 120° in-plane triangular antiferromagnetic order, a manifestation of exchange interaction within the Heisenberg model. Here, we show the formation of a tunable noncoplanar magnetic ground state stabilized by higher-order exchange interactions in electron-doped Mn3Sn samples. Our density Functional Theory calculations reveal that the higher-order exchange induces a partial out-of-plane alignment of the Mn moments, resulting in a canted magnetic state, further experimentally confirmed by neutron diffraction study along with 60 T magnetic and Hall resistivity measurements. Interestingly, we find a large scalar spin chirality-induced Hall signal depending on the degree of non-coplanarity of the Mn moments. Additionally, we demonstrate simultaneous manipulation of two-component order-parameter in the system, where the two Hall signals can be independently manipulated. The present study explores the quantum phenomena associated with the coexistence of multiple magnetic orders and their prospective use in spintronic devices.
Capturing electron-driven chiral dynamics in UV-excited molecules
Authors: Wanie Vincent , Bloch Etienne , Månsson Erik P. , Colaizzi Lorenzo , Ryabchuk Sergey , Saraswathula Krishna , Ordonez Andres F. , Ayuso David , Smirnova Olga , Trabattoni Andrea , Blanchet Valérie , Ben Amor Nadia , Heitz Marie-Catherine , Mairesse Yann , Pons Bernard , Calegari Francesca 
Published: May 2024

AbstractChiral molecules, used in applications such as enantioselective photocatalysis1, circularly polarized light detection2 and emission3 and molecular switches4,5, exist in two geometrical configurations that are non-superimposable mirror images of each other. These so-called (R) and (S) enantiomers exhibit different physical and chemical properties when interacting with other chiral entities. Attosecond technology might enable influence over such interactions, given that it can probe and even direct electron motion within molecules on the intrinsic electronic timescale6 and thereby control reactivity7–9. Electron currents in photoexcited chiral molecules have indeed been predicted to enable enantiosensitive molecular orientation10, but electron-driven chiral dynamics in neutral molecules have not yet been demonstrated owing to the lack of ultrashort, non-ionizing and perturbative light pulses. Here we use time-resolved photoelectron circular dichroism (TR-PECD)11–15 with an unprecedented temporal resolution of 2.9 fs to map the coherent electronic motion initiated by ultraviolet (UV) excitation of neutral chiral molecules. We find that electronic beatings between Rydberg states lead to periodic modulations of the chiroptical response on the few-femtosecond timescale, showing a sign inversion in less than 10 fs. Calculations validate this and also confirm that the combination of the photoinduced chiral current with a circularly polarized probe pulse realizes an enantioselective filter of molecular orientations following photoionization. We anticipate that our approach will enable further investigations of ultrafast electron dynamics in chiral systems and reveal a route towards enantiosensitive charge-directed reactivity.
Adhesive anti-fibrotic interfaces on diverse organs
Authors: Wu Jingjing , Deng Jue , Theocharidis Georgios , Sarrafian Tiffany L. , Griffiths Leigh G. , Bronson Roderick T. , Veves Aristidis , Chen Jianzhu , Yuk Hyunwoo , Zhao Xuanhe 
Published: May 2024

AbstractImplanted biomaterials and devices face compromised functionality and efficacy in the long term owing to foreign body reactions and subsequent formation of fibrous capsules at the implant–tissue interfaces1–4. Here we demonstrate that an adhesive implant–tissue interface can mitigate fibrous capsule formation in diverse animal models, including rats, mice, humanized mice and pigs, by reducing the level of infiltration of inflammatory cells into the adhesive implant–tissue interface compared to the non-adhesive implant–tissue interface. Histological analysis shows that the adhesive implant–tissue interface does not form observable fibrous capsules on diverse organs, including the abdominal wall, colon, stomach, lung and heart, over 12 weeks in vivo. In vitro protein adsorption, multiplex Luminex assays, quantitative PCR, immunofluorescence analysis and RNA sequencing are additionally carried out to validate the hypothesis. We further demonstrate long-term bidirectional electrical communication enabled by implantable electrodes with an adhesive interface over 12 weeks in a rat model in vivo. These findings may offer a promising strategy for long-term anti-fibrotic implant–tissue interfaces.
Natural proteome diversity links aneuploidy tolerance to protein turnover
Authors: Muenzner Julia , Trébulle Pauline , Agostini Federica , Zauber Henrik , Messner Christoph B. , Steger Martin , Kilian Christiane , Lau Kate , Barthel Natalie , Lehmann Andrea , Textoris-Taube Kathrin , Caudal Elodie , Egger Anna-Sophia , Amari Fatma , De Chiara Matteo , Demichev Vadim , Gossmann Toni I. , Mülleder Michael , Liti Gianni , Schacherer Joseph , Selbach Matthias , Berman Judith , Ralser Markus 
Published: May 2024

AbstractAccessing the natural genetic diversity of species unveils hidden genetic traits, clarifies gene functions and allows the generalizability of laboratory findings to be assessed. One notable discovery made in natural isolates ofSaccharomyces cerevisiaeis that aneuploidy—an imbalance in chromosome copy numbers—is frequent1,2(around 20%), which seems to contradict the substantial fitness costs and transient nature of aneuploidy when it is engineered in the laboratory3–5. Here we generate a proteomic resource and merge it with genomic1and transcriptomic6data for 796 euploid and aneuploid natural isolates. We find that natural and lab-generated aneuploids differ specifically at the proteome. In lab-generated aneuploids, some proteins—especially subunits of protein complexes—show reduced expression, but the overall protein levels correspond to the aneuploid gene dosage. By contrast, in natural isolates, more than 70% of proteins encoded on aneuploid chromosomes are dosage compensated, and average protein levels are shifted towards the euploid state chromosome-wide. At the molecular level, we detect an induction of structural components of the proteasome, increased levels of ubiquitination, and reveal an interdependency of protein turnover rates and attenuation. Our study thus highlights the role of protein turnover in mediating aneuploidy tolerance, and shows the utility of exploiting the natural diversity of species to attain generalizable molecular insights into complex biological processes.
Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast
Authors: Caudal Élodie , Loegler Victor , Dutreux Fabien , Vakirlis Nikolaos , Teyssonnière Élie , Caradec Claudia , Friedrich Anne , Hou Jing , Schacherer Joseph 
Published: May 2024

AbstractGene expression is an essential step in the translation of genotypes into phenotypes. However, little is known about the transcriptome architecture and the underlying genetic effects at the species level. Here we generated and analyzed the pan-transcriptome of ~1,000 yeast natural isolates across 4,977 core and 1,468 accessory genes. We found that the accessory genome is an underappreciated driver of transcriptome divergence. Global gene expression patterns combined with population structure showed that variation in heritable expression mainly lies within subpopulation-specific signatures, for which accessory genes are overrepresented. Genome-wide association analyses consistently highlighted that accessory genes are associated with proportionally more variants with larger effect sizes, illustrating the critical role of the accessory genome on the transcriptional landscape within and between populations.
From Planning Stage Towards FAIR Data: A Practical Metadatasheet For Biomedical Scientists
Authors: Seep Lea , Grein Stephan , Splichalova Iva , Ran Danli , Mikhael Mickel , Hildebrand Staffan , Lauterbach Mario , Hiller Karsten , Ribeiro Dalila Juliana Silva , Sieckmann Katharina , Kardinal Ronja , Huang Hao , Yu Jiangyan , Kallabis Sebastian , Behrens Janina , Till Andreas , Peeva Viktoriya , Strohmeyer Akim , Bruder Johanna , Blum Tobias , Soriano-Arroquia Ana , Tischer Dominik , Kuellmer Katharina , Li Yuanfang , Beyer Marc , Gellner Anne-Kathrin , Fromme Tobias , Wackerhage Henning , Klingenspor Martin , Fenske Wiebke K. , Scheja Ludger , Meissner Felix , Schlitzer Andreas , Mass Elvira , Wachten Dagmar , Latz Eicke , Pfeifer Alexander , Hasenauer Jan 
Published: May 2024

AbstractDatasets consist of measurement data and metadata. Metadata provides context, essential for understanding and (re-)using data. Various metadata standards exist for different methods, systems and contexts. However, relevant information resides at differing stages across the data-lifecycle. Often, this information is defined and standardized only at publication stage, which can lead to data loss and workload increase. In this study, we developed Metadatasheet, a metadata standard based on interviews with members of two biomedical consortia and systematic screening of data repositories. It aligns with the data-lifecycle allowing synchronous metadata recording within Microsoft Excel, a widespread data recording software. Additionally, we provide an implementation, the Metadata Workbook, that offers user-friendly features like automation, dynamic adaption, metadata integrity checks, and export options for various metadata standards. By design and due to its extensive documentation, the proposed metadata standard simplifies recording and structuring of metadata for biomedical scientists, promoting practicality and convenience in data management. This framework can accelerate scientific progress by enhancing collaboration and knowledge transfer throughout the intermediate steps of data creation.
A daily gap-free normalized difference vegetation index dataset from 1981 to 2023 in China
Authors: Li Huiwen , Cao Yue , Xiao Jingfeng , Yuan Zuoqiang , Hao Zhanqing , Bai Xiaoyong , Wu Yiping , Liu Yu 
Published: May 2024

AbstractLong-term, daily, and gap-free Normalized Difference Vegetation Index (NDVI) is of great significance for a better Earth system observation. However, gaps and contamination are quite severe in current daily NDVI datasets. This study developed a daily 0.05° gap-free NDVI dataset from 1981–2023 in China by combining valid data identification and spatiotemporal sequence gap-filling techniques based on the National Oceanic and Atmospheric Administration daily NDVI dataset. The generated NDVI in more than 99.91% of the study area showed an absolute percent bias (|PB|) smaller than 1% compared with the original valid data, with an overall R2 and root mean square error (RMSE) of 0.79 and 0.05, respectively. PB and RMSE between our dataset and the MODIS daily gap-filled NDVI dataset (MCD19A3CMG) during 2000 to 2023 are 7.54% and 0.1, respectively. PB between our dataset and three monthly NDVI datasets (i.e., GIMMS3g, MODIS MOD13C2, and SPOT/PROBA) are only −5.79%, 4.82%, and 2.66%, respectively. To the best of our knowledge, this is the first long-term daily gap-free NDVI in China by far.
The gustatory stalk of the Remo flounder exemplifies how complex evolutionary novelties may arise
Authors: Presti Paulo , Pastana Murilo N. L. , Johnson G. David , Datovo Aléssio 
Published: May 2024

AbstractThe appearance of evolutionary novelties is a central issue in biology. Since Darwin’s theory, difficulties in explaining how novel intricate body parts arose have often been used by creationists and other deniers to challenge evolution. Here, we describe the gustatory stalk of the Remo flounder (Oncopterus darwinii), an anatomically and functionally complex organ presumably used as a chemoreceptor probe to detect prey buried in the substrate. We demonstrate that the gustatory stalk is derived from the first dorsal-fin ray, which acquired remarkable modifications in its external morphology, integument, skeleton, muscles, and nerves. Such structural innovations are echoed in both functional and ecological specializations. We reveal that the gustatory stalk arose through the gradual accumulation of changes that evolved at different levels of the phylogenetic tree of ray-finned fishes. At least five preconditions arose in nodes preceding Oncopterus darwinii. This finding constitutes an interesting example of how evolution can deeply remodel body parts to perform entirely new functions. In this case, a trivial support structure primitively used for swimming became a sophisticated sensory tool to uncover hidden prey.
Fifteenth century Florentine mural investigated in situ with VNIR Hyperspectral Imaging and NIR Photography supports interpretation as a bloodletting scene
Authors: Cucci Costanza , Donell Simon , Zucchini Elisa , Picollo Marcello , Stefani Lorenzo , Lippi Donatella 
Published: May 2024

AbstractThis study provides new data which suggest a novel interpretative hypothesis not only on the specific painting, but on the use of bloodletting as medical practice in the Florentine Quattrocento. As a part of a cycle of frescoes devoted to the Seven Corporal Works of Mercy, the examined lunette depicts the “Visit to the sick” in a domestic interior, but it has never been considered as an historical document of precise medical practices. The scene’s definitive interpretation is still unresolved because of the uncertainty of some iconographic details. A campaign of in-situ and non-invasive technical investigations was performed to retrieve possible traces of previous details today concealed. The technical solutions adopted to implement the measurements campaign are illustrated, as an experimental example for remote sensing inspection of mural paintings in-situ. The position of the painting high up on a wall of an historical venue led to opting for stand-alone optical imaging techniques which could operate in remote sensing mode. By combining the use of portable Hyperspectral Imaging with Near Infrared photography a set of detailed images could be obtained that highlighted details not otherwise detectable. Focused on the objects held by the persons present, the analysis of the mural of Visit of the Buonomini in her Lying in Bed, the gift of swaddling cloth could be a tourniquet, shadows of folds of a blanket a thumb lancet, and an object held a blood collection bowl, supported the hypothesis that it could be a medieval bloodletting scene.
Heuristic test reveals little effect of learning and maturation on early prey capture experiences in a web-building spider
Authors: Rittinger Madison A. , Rodríguez Rafael L. , Escalante Ignacio 
Published: May 2024

AbstractBehaviors can vary throughout an animal’s life and this variation can often be explained by changes associated with learning and/or maturing. Currently, there is little consensus regarding how these processes interact to affect behaviors. Here we proposed a heuristic approach to disentangle the effects of learning and maturation on behavior and applied it to the predatory behaviors of Physocyclus globosus spiderlings. We varied the degree of prey difficulty and familiarity spiderlings received along the first instar and across the molt to the second instar and quantified the time spiderlings spent wrapping prey, as a proxy for prey capture efficiency. We found no overall evidence for learning or maturation. Changes in efficiency were mainly due to the switch from difficult to easy prey, or vice versa. However, there was one treatment where spiderlings improved in efficiency before and after the molt, without a switch in prey type. This provides some indication that difficult prey may offer more opportunity for learning or maturation to impact behavior. Although we found little effect of learning or maturation on prey capture efficiency, we suggest that our heuristic approach is effective and could be useful in investigating these processes in other behaviors and other animals.
Optical sensor reveals the hidden influence of cell dissociation on adhesion measurements
Authors: Kovács Kinga Dóra , Szittner Zoltán , Magyaródi Beatrix , Péter Beatrix , Szabó Bálint , Vörös Alexa , Kanyó Nicolett , Székács Inna , Horvath Robert 
Published: May 2024

AbstractCell adhesion experiments are important in tissue engineering and for testing new biologically active surfaces, prostheses, and medical devices. Additionally, the initial state of adhesion (referred to as nascent adhesion) plays a key role and is currently being intensively researched. A critical step in handling all adherent cell types is their dissociation from their substrates for further processing. Various cell dissociation methods and reagents are used in most tissue culture laboratories (here, cell dissociation from the culture surface, cell harvesting, and cell detachment are used interchangeably). Typically, the dissociated cells are re-adhered for specific measurements or applications. However, the impact of the choice of dissociation method on cell adhesion in subsequent measurements, especially when comparing the adhesivity of various surfaces, is not well clarified. In this study, we demonstrate that the application of a label-free optical sensor can precisely quantify the effect of cell dissociation methods on cell adhesivity, both at the single-cell and population levels. The optical measurements allow for high-resolution monitoring of cellular adhesion without interfering with the physiological state of the cells. We found that the choice of reagent significantly alters cell adhesion on various surfaces. Our results clearly demonstrate that biological conclusions about cellular adhesion when comparing various surfaces are highly dependent on the employed dissociation method. Neglecting the choice of cellular dissociation can lead to misleading conclusions when evaluating cell adhesion data from various sources and comparing the adhesivity of two different surfaces (i.e., determining which surface is more or less adhesive).