bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiregional transcriptomics identifies congruent consensus subtypes with prognostic value beyond tumor heterogeneity of colorectal cancer
Authors: Langerud Jonas , Eilertsen Ina A. , Moosavi Seyed H. , Klokkerud Solveig M. K. , Reims Henrik M. , Backe Ingeborg F. , Hektoen Merete , Sjo Ole H. , Jeanmougin Marine , Tejpar Sabine , Nesbakken Arild , Lothe Ragnhild A. , Sveen Anita 
Published: May 2024

AbstractIntra-tumor heterogeneity compromises the clinical value of transcriptomic classifications of colorectal cancer. We investigated the prognostic effect of transcriptomic heterogeneity and the potential for classifications less vulnerable to heterogeneity in a single-hospital series of 1093 tumor samples from 692 patients, including multiregional samples from 98 primary tumors and 35 primary-metastasis sets. We show that intra-tumor heterogeneity of the consensus molecular subtypes (CMS) is frequent and has poor-prognostic associations independently of tumor microenvironment markers. Multiregional transcriptomics uncover cancer cell-intrinsic and low-heterogeneity signals that recapitulate the intrinsic CMSs proposed by single-cell sequencing. Further subclassification identifies congruent CMSs that explain a larger proportion of variation in patient survival than intra-tumor heterogeneity. Plasticity is indicated by discordant intrinsic phenotypes of matched primary and metastatic tumors. We conclude that multiregional sampling reconciles the prognostic power of tumor classifications from single-cell and bulk transcriptomics in the context of intra-tumor heterogeneity, and phenotypic plasticity challenges the reconciliation of primary and metastatic subtypes.
Neuroprotective gap-junction-mediated bystander transformations in the adult zebrafish spinal cord after injury
Authors: Pedroni Andrea , Dai Yu-Wen E. , Lafouasse Leslie , Chang Weipang , Srivastava Ipsit , Del Vecchio Lisa , Ampatzis Konstantinos 
Published: May 2024

AbstractThe adult zebrafish spinal cord displays an impressive innate ability to regenerate after traumatic insults, yet the underlying adaptive cellular mechanisms remain elusive. Here, we show that while the cellular and tissue responses after injury are largely conserved among vertebrates, the large-size fast spinal zebrafish motoneurons are remarkably resilient by remaining viable and functional. We also reveal the dynamic changes in motoneuron glutamatergic input, excitability, and calcium signaling, and we underscore the critical role of calretinin (CR) in binding and buffering the intracellular calcium after injury. Importantly, we demonstrate the presence and the dynamics of a neuron-to-neuron bystander neuroprotective biochemical cooperation mediated through gap junction channels. Our findings support a model in which the intimate and dynamic interplay between glutamate signaling, calcium buffering, gap junction channels, and intercellular cooperation upholds cell survival and promotes the initiation of regeneration.
Astrocytic ALKBH5 in stress response contributes to depressive-like behaviors in mice
Authors: Guo Fang , Fan Jun , Liu Jin-Ming , Kong Peng-Li , Ren Jing , Mo Jia-Wen , Lu Cheng-Lin , Zhong Qiu-Ling , Chen Liang-Yu , Jiang Hao-Tian , Zhang Canyuan , Wen You-Lu , Gu Ting-Ting , Li Shu-Ji , Fang Ying-Ying , Pan Bing-Xing , Gao Tian-Ming , Cao Xiong 
Published: May 2024

AbstractEpigenetic mechanisms bridge genetic and environmental factors that contribute to the pathogenesis of major depression disorder (MDD). However, the cellular specificity and sensitivity of environmental stress on brain epitranscriptomics and its impact on depression remain unclear. Here, we found that ALKBH5, an RNA demethylase of N6-methyladenosine (m6A), was increased in MDD patients’ blood and depression models. ALKBH5 in astrocytes was more sensitive to stress than that in neurons and endothelial cells. Selective deletion of ALKBH5 in astrocytes, but not in neurons and endothelial cells, produced antidepressant-like behaviors. Astrocytic ALKBH5 in the mPFC regulated depression-related behaviors bidirectionally. Meanwhile, ALKBH5 modulated glutamate transporter-1 (GLT-1) m6A modification and increased the expression of GLT-1 in astrocytes. ALKBH5 astrocyte-specific knockout preserved stress-induced disruption of glutamatergic synaptic transmission, neuronal atrophy and defective Ca2+ activity. Moreover, enhanced m6A modification with S-adenosylmethionine (SAMe) produced antidepressant-like effects. Our findings indicate that astrocytic epitranscriptomics contribute to depressive-like behaviors and that astrocytic ALKBH5 may be a therapeutic target for depression.
Physics-informed neural network for lithium-ion battery degradation stable modeling and prognosis
Authors: Wang Fujin , Zhai Zhi , Zhao Zhibin , Di Yi , Chen Xuefeng 
Published: May 2024

AbstractAccurate state-of-health (SOH) estimation is critical for reliable and safe operation of lithium-ion batteries. However, reliable and stable battery SOH estimation remains challenging due to diverse battery types and operating conditions. In this paper, we propose a physics-informed neural network (PINN) for accurate and stable estimation of battery SOH. Specifically, we model the attributes that affect the battery degradation from the perspective of empirical degradation and state space equations, and utilize neural networks to capture battery degradation dynamics. A general feature extraction method is designed to extract statistical features from a short period of data before the battery is fully charged, enabling our method applicable to different battery types and charge/discharge protocols. Additionally, we generate a comprehensive dataset consisting of 55 lithium-nickel-cobalt-manganese-oxide (NCM) batteries. Combined with three other datasets from different manufacturers, we use a total of 387 batteries with 310,705 samples to validate our method. The mean absolute percentage error (MAPE) is 0.87%. Our proposed PINN has demonstrated remarkable performance in regular experiments, small sample experiments, and transfer experiments when compared to alternative neural networks. This study highlights the promise of physics-informed machine learning for battery degradation modeling and SOH estimation.
OsMAPK6 phosphorylation and CLG1 ubiquitylation of GW6a non-additively enhance rice grain size through stabilization of the substrate
Authors: Bai Chen , Wang Gao-Jie , Feng Xiao-Hui , Gao Qiong , Wang Wei-Qing , Xu Ran , Guo Su-Jie , Shen Shao-Yan , Ma Ming , Lin Wen-Hui , Liu Chun-Ming , Li Yunhai , Song Xian-Jun 
Published: May 2024

AbstractThe chromatin modifier GRAIN WEIGHT 6a (GW6a) enhances rice grain size and yield. However, little is known about its gene network determining grain size. Here, we report that MITOGEN-ACTIVED PROTEIN KINASE 6 (OsMAPK6) and E3 ligase CHANG LI GENG 1 (CLG1) interact with and target GW6a for phosphorylation and ubiquitylation, respectively. Unexpectedly, however, in vitro and in vivo assays reveal that both of the two post-translational modifications stabilize GW6a. Furthermore, we uncover two major GW6a phosphorylation sites (serine142 and threonine186) targeted by OsMAPK6 serving an important role in modulating grain size. In addition, our genetic and molecular results suggest that the OsMAPK6-GW6a and CLG1-GW6a axes are crucial and operate in a non-additive manner to control grain size. Overall, our findings identify a previously unknown mechanism by which phosphorylation and ubiquitylation non-additively stabilize GW6a to enhance grain size, and reveal correlations and interactions of these posttranslational modifications during rice grain development.
Digital non-Foster-inspired electronics for broadband impedance matching
Authors: Yang Xin , Zhang Zhihe , Xu Mengwei , Li Shuxun , Zhang Yuanhong , Zhu Xue-Feng , Ouyang Xiaoping , Alù Andrea 
Published: May 2024

AbstractNarrow bandwidths are a general bottleneck for applications relying on passive, linear, subwavelength resonators. In the past decades, several efforts have been devoted to overcoming this challenge, broadening the bandwidth of small resonators by the means of analog non-Foster matching networks for radiators, antennas and metamaterials. However, most non-Foster approaches present challenges in terms of tunability, stability and power limitations. Here, by tuning a subwavelength acoustic transducer with digital non-Foster-inspired electronics, we demonstrate five-fold bandwidth enhancement compared to conventional analog non-Foster matching. Long-distance transmission over airborne acoustic channels, with approximately three orders of magnitude increase in power level, validates the performance of the proposed approach. We also demonstrate convenient reconfigurability of our non-Foster-inspired electronics. This implementation provides a viable solution to enhance the bandwidth of sub-wavelength resonance-based systems, extendable to the electromagnetic domain, and enables the practical implementation of airborne and underwater acoustic radiators.
Investigating nutrient biomarkers of healthy brain aging: a multimodal brain imaging study
Authors: Zwilling Christopher E. , Wu Jisheng , Barbey Aron K. 
Published: May 2024

AbstractThe emerging field of Nutritional Cognitive Neuroscience aims to uncover specific foods and nutrients that promote healthy brain aging. Central to this effort is the discovery of nutrient profiles that can be targeted in nutritional interventions designed to promote brain health with respect to multimodal neuroimaging measures of brain structure, function, and metabolism. The present study therefore conducted one of the largest and most comprehensive nutrient biomarker studies examining multimodal neuroimaging measures of brain health within a sample of 100 older adults. To assess brain health, a comprehensive battery of well-established cognitive and brain imaging measures was administered, along with 13 blood-based biomarkers of diet and nutrition. The findings of this study revealed distinct patterns of aging, categorized into two phenotypes of brain health based on hierarchical clustering. One phenotype demonstrated an accelerated rate of aging, while the other exhibited slower-than-expected aging. A t-test analysis of dietary biomarkers that distinguished these phenotypes revealed a nutrient profile with higher concentrations of specific fatty acids, antioxidants, and vitamins. Study participants with this nutrient profile demonstrated better cognitive scores and delayed brain aging, as determined by a t-test of the means. Notably, participant characteristics such as demographics, fitness levels, and anthropometrics did not account for the observed differences in brain aging. Therefore, the nutrient pattern identified by the present study motivates the design of neuroscience-guided dietary interventions to promote healthy brain aging.
Neither alpha-synuclein fibril strain nor host murine genotype influences seeding efficacy
Authors: Walton Sara , Fenyi Alexis , Tittle Tyler , Sidransky Ellen , Pal Gian , Choi Solji , Melki Ronald , Killinger Bryan A. , Kordower Jeffrey H. 
Published: May 2024

AbstractParkinson’s disease (PD) is a neurodegenerative disease characterized by progressive motor symptoms and alpha-synuclein (αsyn) aggregation in the nervous system. For unclear reasons, PD patients with certain GBA1 mutations (GBA-PD) have a more aggressive clinical progression. Two testable hypotheses that can potentially account for this phenomenon are that GBA1 mutations promote αsyn spread or drive the generation of highly pathogenic αsyn polymorphs (i.e., strains). We tested these hypotheses by treating homozygous GBA1 D409V knockin (KI) mice with human α-syn-preformed fibrils (PFFs) and treating wild-type mice (WT) with several αsyn-PFF polymorphs amplified from brain autopsy samples collected from patients with idiopathic PD and GBA-PD patients with either homozygous or heterozygous GBA1 mutations. Robust phosphorylated-αsyn (PSER129) positive pathology was observed at the injection site (i.e., the olfactory bulb granule cell layer) and throughout the brain six months following PFF injection. The PFF seeding efficiency and degree of spread were similar regardless of the mouse genotype or PFF polymorphs. We found that PFFs amplified from the human brain, regardless of patient genotype, were generally more effective seeders than wholly synthetic PFFs (i.e., non-amplified); however, PFF concentration differed between these two studies, which might also account for the observed differences. To investigate whether the molecular composition of pathology differed between different seeding conditions, we performed Biotinylation by Antibody Recognition on PSER129 (BAR-PSER129). We found that for BAR-PSER129, the endogenous PSER129 pool dominated identified interactions, and thus, very few potential interactions were explicitly identified for seeded pathology. However, we found Dynactin Subunit 2 (Dctn2) interaction was shared across all PFF conditions, and NCK Associated Protein 1 (Nckap1) and Adaptor Related Protein Complex 3 Subunit Beta 2 (Ap3b2) were unique to PFFs amplified from GBA-PD brains of heterozygous mutation carriers. In conclusion, both the genotype and αsyn strain had little effect on overall seeding efficacy and global PSER129-interactions.
Meta-analysis of shotgun sequencing of gut microbiota in Parkinson’s disease
Authors: Nishiwaki Hiroshi , Ueyama Jun , Ito Mikako , Hamaguchi Tomonari , Takimoto Keiichi , Maeda Tetsuya , Kashihara Kenichi , Tsuboi Yoshio , Mori Hiroshi , Kurokawa Ken , Katsuno Masahisa , Hirayama Masaaki , Ohno Kinji 
Published: May 2024

AbstractWe aimed to identify gut microbial features in Parkinson’s disease (PD) across countries by meta-analyzing our fecal shotgun sequencing dataset of 94 PD patients and 73 controls in Japan with five previously reported datasets from USA, Germany, China1, China2, and Taiwan. GC-MS and LC-MS/MS assays were established to quantify fecal short-chain fatty acids (SCFAs) and fecal polyamines, respectively. α-Diversity was increased in PD across six datasets. Taxonomic analysis showed that species Akkermansia muciniphila was increased in PD, while species Roseburia intestinalis and Faecalibacterium prausnitzii were decreased in PD. Pathway analysis showed that genes in the biosyntheses of riboflavin and biotin were markedly decreased in PD after adjusting for confounding factors. Five out of six categories in carbohydrate-active enzymes (CAZymes) were decreased in PD. Metabolomic analysis of our fecal samples revealed that fecal SCFAs and polyamines were significantly decreased in PD. Genes in the riboflavin and biotin biosyntheses were positively correlated with the fecal concentrations of SCFAs and polyamines. Bacteria that accounted for the decreased riboflavin biosynthesis in Japan, the USA, and Germany were different from those in China1, China2, and Taiwan. Similarly, different bacteria accounted for decreased biotin biosynthesis in the two country groups. We postulate that decreased SCFAs and polyamines reduce the intestinal mucus layer, which subsequently facilitates the formation of abnormal α-synuclein fibrils in the intestinal neural plexus in PD, and also cause neuroinflammation in PD.
Multi-decadal climate services help farmers assess and manage future risks
Authors: Malakar Yuwan , Snow Stephen , Fleming Aysha , Fielke Simon , Jakku Emma , Tozer Carly , Darbyshire Rebecca 
Published: May 2024

AbstractClimate services can support on-farm decisions, yet this potential is currently not fully realized. Here, using a participatory qualitative risk analysis framework, we introduced 24 Australian farmers to My Climate View, an Australian online, multi-decadal climate service, and asked them to identify, assess and discuss management of long-term risks in light of its projections. We found that multi-decadal projections can help farmers to better understand future climate risks, potentially reducing the psychological distance of climate change. The use of long-term climate projections, however, can be impeded by lack of confidence in data, so leveraging the expertise of trusted service providers may help boost farmers’ confidence. Finally, though climate services providing multi-decadal projections can help farmers to identify future climate risks, they require interactive and recurring engagement to turn awareness into action.
A dataset of ambient sensors in a meeting room for activity recognition
Authors: Kim Hyunju , Kim Geon , Lee Taehoon , Kim Kisoo , Lee Dongman 
Published: May 2024

AbstractAs IoT technology advances, using machine learning to detect user activities emerges as a promising strategy for delivering a variety of smart services. It is essential to have access to high-quality data that also respects privacy concerns and data streams from ambient sensors in the surrounding environment meet this requirement. However, despite growing interest in research, there is a noticeable lack of datasets from ambient sensors designed for public spaces, as opposed to those for private settings. To bridge this gap, we design the DOO-RE dataset within an actual meeting room environment, equipped with three types of ambient sensors: those triggered by actuators, users, and the environment itself. This dataset is compiled from the activities of over twenty students throughout a period of four months. DOO-RE provides reliable and purpose-oriented activity data in a public setting, with activity labels verified by multiple annotators through a process of cross-validation to guarantee data integrity. DOO-RE categorizes nine different types of activities and facilitates the study of both single and group activities. We are optimistic that DOO-RE will play a significant role in advancing human activity recognition technologies, enhancing smart automation systems, and enabling the rapid setup of smart spaces through ambient sensors.
Synthesis and characterization of nitrogen-doped-MWCNT@cobalt oxide for nerve agent simulant detection
Authors: Lama Sanjeeb , Choi Hyeong-Seon , Ramesh Sivalingam , Lee Young Jun , Kim Joo Hyung 
Published: May 2024

AbstractOrganophosphorus nerve agents are toxic compounds that disrupt neuromuscular transmission by inhibiting the neurotransmitter enzyme, acetylcholinesterase, leading to rapid death. A hybrid composite was synthesized using a hydrothermal process for the early detection of dimethyl methyl phosphonate (DMMP), a simulant of the G-series nerve agent, sarin. Quartz crystal microbalance (QCM) and surface acoustic wave (SAW) sensors were used as detectors. Nitrogen-doped multiwalled carbon nanotubes (N-MWCNTs), cobalt oxide (Co3O4), and N-MWCNT@Co3O4 were compared to detect DMMP concentrations of 25–150 ppm. At 25 ppm, the differential frequencies (Δf) of the N-MWCNT, Co3O4, and N-MWCNT@Co3O4 sensors were 5.8, 2.3, and 99.5 Hz, respectively. The selectivity results revealed a preference for the DMMP rather than potential interference. The coefficients of determination (R2) of the N-MWCNT, Co3O4, and N-MWCNT@Co3O4 sensors for detecting 25–150 ppm DMMP were 0.983, 0.986, and 0.999, respectively. The response times of the N-MWCNT, Co3O4, and N-MWCNT@Co3O4 sensors for detecting 100 ppm DMMP were 25, 27, and 34 s, respectively, while the corresponding recovery times were 85, 105, and 181 s. The repeatability results revealed the reversible adsorption and desorption phenomena for the fixed DMMP concentration of 100 ppm. These unique findings show that synthesized materials can be used to detect organophosphorus nerve agents.
Mitochondrial metagenomics reveal the independent colonization of the world’s coasts by intertidal oribatid mites (Acari, Oribatida, Ameronothroidea)
Authors: Pfingstl Tobias , Hiruta Shimpei F. , Shimano Satoshi 
Published: May 2024

AbstractOribatid mites are an ancient group that already roamed terrestrial ecosystems in the early and middle Devonian. The superfamily of Ameronothroidea, a supposedly monophyletic lineage, represents the only group of oribatid mites that has successfully invaded the marine coastal environment. By using mitogenome data and nucleic ribosomal RNA genes (18S, 5.8S, 28S), we show that Ameronothroidea are a paraphyletic assemblage and that the land-to-sea transition happened three times independently. Common ancestors of the tropical Fortuyniidae and Selenoribatidae were the first to colonize the coasts and molecular calibration of our phylogeny dates this event to a period in the Triassic and Jurassic era (225–146 mya), whereas present-day distribution indicates that this event might have happened early in this period during the Triassic, when the supercontinent Pangaea still existed. The cold temperate northern hemispheric Ameronothridae colonized the marine littoral later in the late Jurassic-Early Cretaceous and had an ancient distribution on Laurasian coasts. The third and final land-to-sea transition happened in the same geological period, but approx. 30 my later when ancestors of Podacaridae invaded coastal marine environments of the Gondwanan landmasses.
Svetlana a supervised segmentation classifier for Napari
Authors: Cazorla Clément , Morin Renaud , Weiss Pierre 
Published: May 2024

AbstractWe present Svetlana (SuperVised sEgmenTation cLAssifier for NapAri), an open-source Napari plugin dedicated to the manual or automatic classification of segmentation results. A few recent software tools have made it possible to automatically segment complex 2D and 3D objects such as cells in biology with unrivaled performance. However, the subsequent analysis of the results is oftentimes inaccessible to non-specialists. The Svetlana plugin aims at going one step further, by allowing end-users to label the segmented objects and to pick, train and run arbitrary neural network classifiers. The resulting network can then be used for the quantitative analysis of biophysical phenoma. We showcase its performance through challenging problems in 2D and 3D and provide a comprehensive discussion on its strengths and limits.
Social signals predict contemporary art prices better than visual features, particularly in emerging markets
Authors: Lee Kangsan , Park Jaehyuk , Goree Sam , Crandall David , Ahn Yong-Yeol 
Published: May 2024

AbstractWhat determines the price of an artwork? This article leverages a comprehensive and novel dataset on art auctions of contemporary artists to examine the impact of social and visual features on the valuation of artworks across global markets. Our findings indicate that social signals allow us to predict the price of artwork exceptionally well, even approaching the professionals’ prediction accuracy, while the visual features play a marginal role. This pattern is especially pronounced in emerging markets, supporting the idea that social signals become more critical when it is more difficult to assess the quality. These results strongly support that the value of artwork is largely shaped by social factors, particularly in emerging markets where a stronger preference for “buying an artist” than “buying an artwork.” Additionally, our study shows that it is possible to boost experts’ performance, highlighting the potential benefits of human-machine models in uncertain or rapidly changing markets, where expert knowledge is limited.