Miracle-dz/UniFAR-FTUs huggingface dataset:
Arctic sea ice coverage from 43 years of satellite passive-microwave observations

Satellite passive-microwave instrumentation has allowed the monitoring of Arctic sea ice over the past 43 years, and this monitoring has revealed and quantified major changes occurring in Arctic sea ice coverage. The 43-year 1979–2021 record shows considerable interannual variability but also a long-term downward trend in Arctic sea ice that is clear from many vantage points: A linear-least-square trend of −54,300 ± 2,700 km2/year for yearly average sea ice extents; statistically significant negative trends for each of the 12 calendar months; negative trends for each of nine regions into which the Arctic sea ice cover is divided; the fact that for all 12 calendar months the highest monthly average sea ice extent came in the first 8 years of the record and the lowest monthly average sea ice extent came in the last 10 years of the record; and a prominent shortening of the sea ice season throughout much of the marginal ice zone, with the length of the sea ice season in some locations decreasing by over 100 days and some locations previously experiencing months-long sea ice seasons now typically no longer having a sea ice season at all. The overall, Arctic-wide trend value of the yearly average sea ice extents since 1979 has consistently had a negative magnitude exceeding two standard deviations of the trend line slope since 1990 and has remained in the narrow range of −53,000 km2/yr to −55,500 km2/yr since 2011.
Risk–Benefit assessment of foods: Development of a methodological framework for the harmonized selection of nutritional, microbiological, and toxicological components

Investigating the impact of diet on public health using risk–benefit assessment (RBA) methods that simultaneously consider both beneficial and adverse health outcomes could be useful for shaping dietary policies and guidelines. In the field of food safety and nutrition, RBA is a relatively new approach facing methodological challenges and being subject to further developments. One of the methodological aspects calling for improvement is the selection of components to be considered in the assessment, currently based mainly on non-harmonized unstandardized experts’ judgment. Our aim was to develop a harmonized, transparent, and documented methodological framework for selecting nutritional, microbiological, and toxicological RBA components. The approach was developed under the Novel foods as red meat replacers—an insight using Risk-Benefit Assessment methods (NovRBA) case study, which attempted to estimate the overall health impact of replacing red meat with an edible insect species, Acheta domesticus. Starting from the compositional profiles of both food items, we created a “long list” of food components. By subsequently applying a series of predefined criteria, we proceeded from the “long” to the “short list. ” These criteria were established based on the occurrence and severity of health outcomes related to these components. For nutrition and microbiology, the occurrence of health outcomes was evaluated considering the presence of a component in the raw material, as well as the effect of processing on the respective component. Regarding toxicology, the presence and exposure relative to reference doses and the contribution to total exposure were considered. Severity was graded with the potential contribution to the background diet alongside bioavailability aspects (nutrition), the disability-adjusted life years per case of illness of each hazard (microbiology), and disease incidence in the population, potential fatality, and lifelong disability (toxicology). To develop the “final list” of components, the “short list” was refined by considering the availability and quality of data for a feasible inclusion in the RBA model. The methodology developed can be broadly used in food RBA, to guide and reinforce a harmonized selection of nutritional, microbiological, and toxicological components and will contribute to facilitating RBA implementation, enabling the generation of transparent, robust, and comparable outcomes.
Pan-cancer analyses of classical protein tyrosine phosphatases and phosphatase-targeted therapy in cancer

Protein tyrosine phosphatases function in dephosphorylating target proteins to regulate signaling pathways that control a broad spectrum of fundamental physiological and pathological processes. Detailed knowledge concerning the roles of classical PTPs in human cancer merits in-depth investigation. We comprehensively analyzed the regulatory mechanisms and clinical relevance of classical PTPs in more than 9000 tumor patients across 33 types of cancer. The independent datasets and functional experiments were employed to validate our findings. We exhibited the extensive dysregulation of classical PTPs and constructed the gene regulatory network in human cancer. Moreover, we characterized the correlation of classical PTPs with both drug-resistant and drug-sensitive responses to anti-cancer drugs. To evaluate the PTP activity in cancer prognosis, we generated a PTPscore based on the expression and hazard ratio of classical PTPs. Our study highlights the notable role of classical PTPs in cancer biology and provides novel intelligence to improve potential therapeutic strategies based on pTyr regulation.
Rapid magnetic separation: An immunoassay platform for the SERS-based detection of subarachnoid hemorrhage biomarkers

The blood–brain barrier (BBB) is of vital importance to the progression and prognosis of subarachnoid hemorrhage (SAH). The construction of a simple, sensitive, and accurate detection assay for measuring the biomarkers associated with BBB injury is still an urgent need owing to the complex pathogenesis of SAH and low expression levels of pathological molecules. Herein, we introduced surface-enhanced Raman scattering (SERS) label-embedded Fe3O4@Au core-shell nanoparticles as ideal SERS sensors for quantitative double detection of MMP-9 and occludin in SAH patients. Meanwhile, utilizing the SERS signals to dynamically estimate MMP-9 and occludin concentration in the rat SAH model is the first application in exploring the relationship of pathological MMP-9 and occludin molecular levels with neurobehavioral score. This method warrants reliable detection toward MMP-9 and occludin with a wide recognition range and a low detection limit in blood samples. Furthermore, the results monitored by the SERS assay exactly matched with those obtained through a traditional enzyme-linked immunosorbent assay (ELISA). The aforementioned results demonstrated this novel biosensor strategy has extensive application prospects in the quantitative measurement of multiple types of biomolecules in body fluid samples.
Individual finger movement decoding using a novel ultra-high-density electroencephalography-based brain-computer interface system

Brain-Computer Interface (BCI) technology enables users to operate external devices without physical movement. Electroencephalography (EEG) based BCI systems are being actively studied due to their high temporal resolution, convenient usage, and portability. However, fewer studies have been conducted to investigate the impact of high spatial resolution of EEG on decoding precise body motions, such as finger movements, which are essential in activities of daily living. Low spatial sensor resolution, as found in common EEG systems, can be improved by omitting the conventional standard of EEG electrode distribution (the international 10–20 system) and ordinary mounting structures (e.g., flexible caps). In this study, we used newly proposed flexible electrode grids attached directly to the scalp, which provided ultra-high-density EEG (uHD EEG). We explored the performance of the novel system by decoding individual finger movements using a total of 256 channels distributed over the contralateral sensorimotor cortex. Dense distribution and small-sized electrodes result in an inter-electrode distance of 8.6 mm (uHD EEG), while that of conventional EEG is 60 to 65 mm on average. Five healthy subjects participated in the experiment, performed single finger extensions according to a visual cue, and received avatar feedback. This study exploits mu (8–12 Hz) and beta (13–25 Hz) band power features for classification and topography plots. 3D ERD/S activation plots for each frequency band were generated using the MNI-152 template head. A linear support vector machine (SVM) was used for pairwise finger classification. The topography plots showed regular and focal post-cue activation, especially in subjects with optimal signal quality. The average classification accuracy over subjects was 64.8 (6.3)%, with the middle versus ring finger resulting in the highest average accuracy of 70.6 (9.4)%. Further studies are required using the uHD EEG system with real-time feedback and motor imagery tasks to enhance classification performance and establish the basis for BCI finger movement control of external devices.
Transcriptomics and quantitative proteomics reveal changes after second stimulation of bone marrow-derived macrophages from lupus-prone MRL/lpr mice

Innate immune memory can cause the occurrence and exacerbation of autoimmune diseases, and it is as well as being strongly associated with the pathogenesis of systemic lupus erythematosus (SLE), however, the specific mechanism remains to be further studied. We learned that IFN-γ stimulation generated innate immune memory in bone marrow-derived macrophages (BMDMs) and activated memory interferon-stimulated genes (ISGs). This research used IFN-γ and lipopolysaccharide (LPS) to treat BMDMs with lupus-prone MRL/lpr mice and showed that particular memory ISGs were substantially elevated in prestimulated macrophages. In order to identify the differentially expressed genes (DEGs), researchers turned to RNA-seq. GO and KEGG analysis showed that up-regulated DEGs were enriched in defense and innate immune responses, and were related to the expression of pattern recognition receptors (PRRs)-related pathways in macrophages. TMT-based proteome analysis revealed differentially expressed proteins (DEPs) up-regulated in BMDMs were abundant in metabolic pathways such as glucose metabolism. Our study found that after the secondary stimulation of MRL/lpr mice, the expression of PRRs in innate immune cells was changed, and IFN-related pathways were activated to release a large number of ISGs to promote the secondary response. At the same time, related metabolic modes such as glycolysis were enhanced, and epigenetic changes may occur. Therefore, SLE is brought on, maintained, and worsened by a variety of factors that work together to produce innate immune memory.
Between-subject similarity of functional connectivity-based organization of the human periaqueductal gray related to autonomic processing

The periaqueductal gray (PAG) is a brain stem area designated to play an essential role in lower urinary tract (LUT) control. Post-mortem human and animal studies have indicated that the PAG is symmetrically organized in functionally and anatomically distinct columns which are involved in sympathetic or parasympathetic autonomic control of the LUT. The current study aims to find consistency across subjects and identify homologous clusters between subjects. Here, we evaluated data from 10 female participants. During a bladder filling protocol, we ran a resting-state functional magnetic resonance imaging (fMRI) scan while participants experienced a strong desire to void. A voxel-by-voxel correlation matrix of the PAG was created and parcellated using the Louvain module detection algorithm. Resulting in a map of the PAG in which each voxel is assigned to a cluster as determined by the Louvain module detection algorithm. The spatial similarity of resulting clusters between participants was assessed by computing the Dice similarity coefficient for all cluster comparisons. Next, we designed a permutation test to create randomized parcellation maps which enabled us to statistically test the similarity values observed across participants. We observed several significantly similar clusters between subjects compared to permutations (p ≤ 0.05). These results show that the PAG can be parcellated into distinct clusters which show a similar spatial distribution at the group level. This analysis is a crucial step to determine the agreement between in vivo PAG parcellations and the functional and anatomical columnar organization of the PAG which is known from previous research. These advancements may enable us to identify the relationship between LUT symptoms, such as urgency, and activity patterns in the PAG in normal and pathological states.
Whole body vibration for chronic patellar tendinopathy: A randomized equivalence trial

Purpose: Whole body vibration (WBV) triggers anabolic responses in various tissues, including tendons, without requiring high force production. In this waitlist-controlled equivalence trial, we tested its clinical effectiveness as an alternative treatment for patellar tendinopathy against conventional heavy slow resistance training (HSR). Methods: Thirty-nine patients were randomized to either 3 months of WBV training (n = 13), HSR training (n = 11), or a waitlist control (WLC) group (n = 15). In a partly cross-over design, 14 patients of the WLC group were redistributed to one of the two intervention groups (5 in WBV, 9 in HSR). Pre- and post-intervention testing included pain assessments (VAS), functional limitations (VISA-P), knee extension strength and tendon morphological, mechanical and material properties. Follow-up measurements (VAS, VISA-P) were performed in the WBV and HSR groups 6 months after the intervention. Results: Comparisons with the WLC group revealed significant improvements in VISA-P and VAS scores after HSR (41%, p = 003; 54%, p = 0.005) and WBV (22%, p = 0.022; 56%, p = 0.031) training. These improvements continued until follow-up (HSR: 43%, 56%; WBV: 24%, 37%). Pre-post improvements in VAS scores were equivalent between WBV and HSR groups but inconclusive for the VISA-P score and all pre-test to follow up comparisons. The mid-tendon cross-sectional area was significantly reduced after WBV (−5.7%, p = 0.004) and HSR (−3.0%, p = 0.004) training compared to WLC although the equivalence test between interventions was inconclusive. Conclusion: Whole body vibration improved symptoms typically associated with patellar tendinopathy. This type of intervention is as effective as HSR against maximum pain, although equivalence could not be confirmed for other variables. The beneficial responses to WBV and HSR treatments persisted for 6 months after the end of the intervention. Clinical Trial Registration: https://www.drks. de/drks_web/setLocale_EN. do, identifier DRKS00011338
Immune-associated pivotal biomarkers identification and competing endogenous RNA network construction in post-operative atrial fibrillation by comprehensive bioinformatics and machine learning strategies

Background Atrial fibrillation (AF) is the most common arrhythmia. Previous studies mainly focused on identifying potential diagnostic biomarkers and treatment strategies for AF, while few studies concentrated on post-operative AF (POAF), particularly using bioinformatics analysis and machine learning algorithms. Therefore, our study aimed to identify immune-associated genes and provide the competing endogenous RNA (ceRNA) network for POAF. Methods Three GSE datasets were downloaded from the GEO database, and we used a variety of bioinformatics strategies and machine learning algorithms to discover candidate hub genes. These techniques included identifying differentially expressed genes (DEGs) and circRNAs (DECs), building protein-protein interaction networks, selecting common genes, and filtering candidate hub genes via three machine learning algorithms. To assess the diagnostic value, we then created the nomogram and receiver operating curve (ROC). MiRNAs targeting DEGs and DECs were predicted using five tools and the competing endogenous RNA (ceRNA) network was built. Moreover, we performed the immune cell infiltration analysis to better elucidate the regulation of immune cells in POAF. Results We identified 234 DEGs (82 up-regulated and 152 down-regulated) of POAF via Limma, 75 node genes were visualized via PPI network, which were mainly enriched in immune regulation. 15 common genes were selected using three CytoHubba algorithms. Following machine learning selection, the nomogram was created based on the four candidate hub genes. The area under curve (AUC) of the nomogram and individual gene were all over 0.75, showing the ideal diagnostic value. The dysregulation of macrophages may be critical in POAF pathogenesis. A novel circ_0007738 was discovered in POAF and the ceRNA network was eventually built. Conclusion We identified four immune-associated candidate hub genes (C1QA, C1R, MET, and SDC4) for POAF diagnosis through the creation of a nomogram and evaluation of its diagnostic value. The modulation of macrophages and the ceRNA network may represent further therapy methods.
Integrative transcriptomic and TMT-based proteomic analysis reveals the mechanism by which AtENO2 affects seed germination under salt stress

Seed germination is critical for plant survival and agricultural production and is affected by many cues, including internal factors and external environmental conditions. As a key enzyme in glycolysis, enolase 2 (ENO2) also plays a vital role in plant growth and abiotic stress responses. In our research, we found that the seed germination rate was lower in the AtENO2 mutation (eno2- ) than in the wild type (WT) under salt stress in Arabidopsis thaliana, while there was no significant difference under normal conditions. However, the mechanisms by which AtENO2 regulates seed germination under salt stress remain limited. In the current study, transcriptome and proteome analyses were used to compare eno2- and the WT under normal and salt stress conditions at the germination stage. There were 417 and 4442 differentially expressed genes (DEGs) identified by transcriptome, and 302 and 1929 differentially expressed proteins (DEPs) qualified by proteome under normal and salt stress conditions, respectively. The combined analysis found abundant DEGs and DEPs related to stresses and hydrogen peroxide removal were highly down-regulated in eno2- . In addition, several DEGs and DEPs encoding phytohormone transduction pathways were identified, and the DEGs and DEPs related to ABA signaling were relatively greatly up-regulated in eno2- . Moreover, we constructed an interactive network and further identified GAPA1 and GAPB that could interact with AtENO2, which may explain the function of AtENO2 under salt stress during seed germination. Together, our results reveal that under salt stress, AtENO2 mainly affects the expression of genes and proteins related to the phytohormone signal transduction pathways, stress response factors, and reactive oxygen species (ROS), and then affects seed germination. Our study lays the foundation for further exploration of the molecular function of AtENO2 under salt stress at the seed germination stage in Arabidopsis thaliana.
A new selenosteid placoderm from the Late Devonian of the eastern Anti-Atlas (Morocco) with preserved body outline and its ecomorphology

Placoderms are an extinct group of early jawed vertebrates that play a key role in understanding the evolution of the gnathostome body plan, including the origin of novelties such as jaws, teeth, and pelvic fins. As placoderms have a poorly ossified axial skeleton, preservation of the mainly cartilaginous axial and fin elements is extremely rare, contrary to the heavily mineralized bones of the skull and thoracic armor. Therefore, the gross anatomy of the animals and body shape is only known from a few taxa, and reconstructions of the swimming function and ecology are speculative. Here, we describe articulated specimens preserving skull roofs, shoulder girdles, most fins, and body outlines of a newly derived arthrodire. Specimens of the selenosteid Amazichthys trinajsticae gen. et sp. nov. display a skull roof with reticular ornamentation and raised sensory lines like Driscollaspis, a median dorsal plate with a unique sharp posterior depression, the pelvic girdle, the proportions and shape of the pectoral, dorsal, and caudal fins as well as a laterally enlarged region resembling the lateral keel of a few modern sharks and bony fishes. Our new phylogenetic analyses support the monophyly of the selenosteid family and place the new genus in a clade with Melanosteus, Enseosteus, Walterosteus, and Draconichthys. The shape of its body and heterocercal caudal fin in combination with the pronounced “lateral keel” suggest Amazichthys trinajsticae was an active macropelagic swimmer capable of reaching high swimming speeds.
Analysis of cross neutralizing activity of antibodies from sera of severe fever with thrombocytopenia syndrome patients to deal with different genotype strains

Background Severe fever with thrombocytopenia syndrome bunyavirus (SFTSV) is a tick-borne virus that causes severe communicable fever with thrombocytopenia syndrome (SFTS) with an average case fatality rate of 10%. In the study, we aimed to identify the cross-neutralizing antibody (nAb) against different genotype strains from sera of SFTSV infected patients. Methods Firstly the genotype of SFTSV was identified by constructing a phylogenetic tree based on the M segments epidemic in the Jiaodong area of Shandong province, then different sera of subjects cross reactive with recombinant Gn (rGn-Fc) or recombinant Gc (rGc-Fc) of 0921 strain were examined. The levels of polyclonal nAbs from sera of 25 convalescents were measured by a pseudovirus-based neutralizing experiment. Results We found local endemic strains were mainly C2 and C3 isolates of SFTSV. 14 of 15 sera from donors reacted with 0921 rGn-Fc, and 9 of 15 sera from donors reacted with 0921 rGc-Fc. Cross nAbs were produced by 10 of 25 sera from donors during the period of 2019–2021. Among these, five nAbs (A2, A4, A5, L9, and L10) neutralized the pseudoviruses of HB29, Gangwon, HN13, HN20, SPL030A, and SD4 strains. Conclusion Our data suggested that epidemic strains showed relatively stable heredity. Some blood sources from patients produced cross nAbs that could neutralize all of the strains examined. These findings highlight the important role played by humoral immunity in combatting SFTSV.