Miracle-dz/UniFAR-FTUs huggingface dataset:
Utilizing Novel Field and Data Exploration Methods to Explore Hot Moments in High-Frequency Soil Nitrous Oxide Emissions Data: Opportunities and Challenges

Soil nitrous oxide (N2O) emissions are an important driver of climate change and are a major mechanism of labile nitrogen (N) loss from terrestrial ecosystems. Evidence increasingly suggests that locations on the landscape that experience biogeochemical fluxes disproportionate to the surrounding matrix (hot spots) and time periods that show disproportionately high fluxes relative to the background (hot moments) strongly influence landscape-scale soil N2O emissions. However, substantial uncertainties remain regarding how to measure and model where and when these extreme soil N2O fluxes occur. High-frequency datasets of soil N2O fluxes are newly possible due to advancements in field-ready instrumentation that uses cavity ring-down spectroscopy (CRDS). Here, we outline the opportunities and challenges that are provided by the deployment of this field-based instrumentation and the collection of high-frequency soil N2O flux datasets. While there are substantial challenges associated with automated CRDS systems, there are also opportunities to utilize these near-continuous data to constrain our understanding of dynamics of the terrestrial N cycle across space and time. Finally, we propose future research directions exploring the influence of hot moments of N2O emissions on the N cycle, particularly considering the gaps surrounding how global change forces are likely to alter N dynamics in the future.
Seismogenic Patches in a Tectonic Fault Interface

Tectonic faults show rheological heterogeneity in interfaces, and the spectrum of their sliding regimes span a continuum from the slow-slip events to dynamic ruptures. The heterogeneity of the fault interface is crucial for the mechanics of faulting. By using the earthquake source locations, the complex structure of a fault interface can be reproduced at a resolution down to 50–100 m. Here, we use a declustered seismic catalog of Northern California to investigate structures of 11 segments of San Andreas, Calaveras, and Hayward faults. The cumulative length of all the segments is about 500 km. All the selected segments belong to subvertical strike–slip faults. A noticeable localization of sources near the fault cores is observed for all segments. The projection of earthquake sources to the fault plane shows severe inhomogeneity. Topologically dense clusters (seismogenic patches (SPs)) can be detected in fault planes. The longer the observation are, the more distinct are the clusters. The SPs usually cover about 10%–20% of the fault interface area. It is in the vicinity of SPs that earthquakes of magnitudes above 5 are usually initiated. The Voronoi tessellation is used to determine the orderliness of SPs. Distributions of areas of Voronoi cells of all the SPs obey the lognormal law, and the value of Voronoi entropy of 1.6–1.9 prevails. The findings show the informativeness of the background seismicity in revealing the heterogenous structure of a tectonic fault interface.
The Impact of Chromate on Pseudomonas aeruginosa Molybdenum Homeostasis

Acquisition of the trace-element molybdenum via the high-affinity ATP-binding cassette permease ModABC is essential for Pseudomonas aeruginosa respiration in anaerobic and microaerophilic environments. This study determined the X-ray crystal structures of the molybdenum-recruiting solute-binding protein ModA from P. aeruginosa PAO1 in the metal-free state and bound to the group 6 metal oxyanions molybdate, tungstate, and chromate. Pseudomonas aeruginosa PAO1 ModA has a non-contiguous dual-hinged bilobal structure with a single metal-binding site positioned between the two domains. Metal binding results in a 22° relative rotation of the two lobes with the oxyanions coordinated by four residues, that contribute six hydrogen bonds, distinct from ModA orthologues that feature an additional oxyanion-binding residue. Analysis of 485 Pseudomonas ModA sequences revealed conservation of the metal-binding residues and β-sheet structural elements, highlighting their contribution to protein structure and function. Despite the capacity of ModA to bind chromate, deletion of modA did not affect P. aeruginosa PAO1 sensitivity to chromate toxicity nor impact cellular accumulation of chromate. Exposure to sub-inhibitory concentrations of chromate broadly perturbed P. aeruginosa metal homeostasis and, unexpectedly, was associated with an increase in ModA-mediated molybdenum uptake. Elemental analyses of the proteome from anaerobically grown P. aeruginosa revealed that, despite the increase in cellular molybdenum upon chromate exposure, distribution of the metal within the proteome was substantially perturbed. This suggested that molybdoprotein cofactor acquisition may be disrupted, consistent with the potent toxicity of chromate under anaerobic conditions. Collectively, these data reveal a complex relationship between chromate toxicity, molybdenum homeostasis and anaerobic respiration.
Evaluating the Effectiveness of Screened Lactic Acid Bacteria in Improving Crop Residues Silage: Fermentation Parameter, Nitrogen Fraction, and Bacterial Community

Ensiling characteristics of sweet potato vine (SPV) and peanut straw (PS), as well as the effects of lactic acid bacteria (LAB) strains, Lactococcus Lactis MK524164 (LL) and Lactobacillus farciminis MK524159 (LF), were investigated in this study. Fermentation parameters, nitrogen fractions, and bacterial community of SPV and PS were monitored at intervals during the ensiling process. The results showed that inoculating LAB increased lactate production (2.23 vs. 2.73%; 0.42 vs. 1.67% DM), accelerated pH decline (5.20 vs. 4.47; 6.30 vs. 5.35), and decreased butyrate (0.36% DM vs. not detected), ammonia-N (6.41 vs. 4.18% CP), or nonprotein-N (43.67 vs. 35.82% CP). Meanwhile, it altered the silage bacterial community, where the relative abundance of Lactobacillus was increased (6.67–32.03 vs. 45.27–68.43%; 0.53–10.45 vs. 38.37–68.62%) and that of undesirable bacteria such as Clostridium, Enterobacter, Methylobacterium, or Sphingomonas was much decreased. It is suggested that the screened LAB strains LL and LF can effectively improve the silage quality of SPV and PS silages.
Automatic Calibration of the Adaptive 3D Scanner-Based Robot Welding System

An advanced automatic calibration procedure and its versatile usage in the context of the adaptive robot welding technology are presented. The 3D scanner-based robot welding system calibration is composed of the measurement of the reference plate and numerical optimization of the hand-eye and intrinsic parameters by minimizing the deviation between the measured and reference plate. The measurements of the reference plate are acquired from various robot poses (typically 15). The shape features of the reference plate are then detected, and finally, the calculation of hand-eye and intrinsic parameters is performed using Powell’s optimization algorithm, where the merit function presents an average deviation between the measured and reference geometry. Validation experiments show appropriate system accuracy which is better than 0.06 mm perpendicular to the scanning direction. This calibration procedure’s important features are complete automation and fast execution times (approximately 90 s). This enables its implementation into a regular daily robot self-maintenance and monitoring plan. The universal use of such a robot welding system is demonstrated in multi-layer heavy-duty welding of thick pipes on cast machined hollow parts and in precise laser welding of thin sheet metal parts.
A Prognostic Signature for Clear Cell Renal Cell Carcinoma Based on Ferroptosis-Related lncRNAs and Immune Checkpoints

Background: Ferroptosis is a potential target for cancer therapy, and lncRNAs can also affect ferroptosis by regulating related genes. The pathogenesis of clear cell renal cell carcinoma (ccRCC) regarding the regulation of ferroptosis by lncRNAs is still unknown. Methods: We constructed a risk model based on data in ccRCC patients obtained from the TCGA database and validated the diagnostic and prognostic value of the model. In addition, immune function and immune checkpoint variability analysis validated the association of ferroptosis with ccRCC tumor immunity. Results: The characteristics of ferroptosis-related lncRNAs (FRLs) were significantly correlated with the prognosis of ccRCC patients. The prognostic characteristics of FRLs were independent prognostic factors in ccRCC patients. Gene function in the high-risk group was associated with oxygen metabolic processes and immune pathways. Immune checkpoint variability analysis showed that HAVCR2, NRP1, and HHLA2 were upregulated in the low-risk group, while CD44, TNFRSF18, TNFSF14, TNFRSF8, CD276, and TNFRSF25 were upregulated in the high-risk group. Conclusions: The prognostic characteristics of FRLs can effectively predict the prognosis of ccRCC patients and provide a new direction for clinical treatment.
Olive picking tests with a shaker module and a harvesting umbrella, mounted on a rotating platform excavator

Results of tests on new olive harvest equipment: a rotating excavator equipped with shaker on the mechanical arm and gather umbrella on the blade grader are presented. The research is motivated by the increasing problem of maintenance of olive production in central Italian hillside areas. An innovative olive harvester has been developed with an excavator that controls the olive shaker and the gathering umbrella. The fitted equipment does not compromise the original functionality of the excavator. The implements have a sustainable cost and are quickly joined to the machine. Field tests were conducted in the olive harvest season 2001 at the Montepaldi farm belonging to the University of Florence. The module achieved a productivity of 27 olive trees per hour with a harvest efficiency of 90.5%. The field test is a terraced area with olive trees having these features: 22 m 3 canopy volume, about 15 kg/plant production, 1.3 g drupe mean weight, 5 N detachment resistance. Continuous use of the module during the harvest season produced an average productivity of 180 plants/day.
S1PR3, as a Core Protein Related to Ischemic Stroke, is Involved in the Regulation of Blood–Brain Barrier Damage

Background: Ischemic stroke is the most common stroke incident. Sphingosine-1-phosphate (S1P) receptor 3 (S1PR3) is a member of the downstream G protein-coupled receptor family of S1P. The effect of S1PR3 on ischemic stroke remains elusive. Methods: We downloaded two middle cerebral artery occlusion (MCAO) microarray datasets from the Gene Expression Omnibus (GEO) database and screened differentially expressed genes (DEGs). Then, we performed a weighted gene coexpression network analysis (WGCNA) and identified the core module genes related to ischemic stroke. We constructed a protein–protein interaction (PPI) network for the core genes in which DEGs and WGCNA intersected. Finally, we discovered that S1PR3 was involved as the main member of the red proteome. Then, we explored the mechanism of S1PR3 in the mouse tMCAO model. The S1PR3-specific inhibitor CAY10444 was injected into the abdominal cavity of mice after cerebral ischemia/reperfusion (I/R) injury, and changes in the expression of blood–brain barrier-related molecules were measured using PCR, western blotting, and immunofluorescence staining. Results: Both GEO datasets showed that S1PR3 was upregulated during cerebral I/R in mice. WGCNA revealed that the light yellow module had the strongest correlation with the occurrence of IS. We determined the overlap with DEGs, identified 146 core genes that are potentially related to IS, and constructed a PPI network. Finally, S1PR3 was found to be the main member of the red proteome. In the mouse cerebral I/R model, S1PR3 expression increased 24 h after ischemia. After the administration of CAY10444, brain edema and neurological deficits in mice were ameliorated. CAY10444 rescued the decreased expression of the tight junction (TJ) proteins zonula occludens 1 (ZO1) and occludin after ischemia induced by transient MCAO (tMCAO) and reduced the increase in aquaporin 4 (AQP4) levels after tMCAO, preserving the integrity of the BBB. Finally, we found that S1PR3 is involved in regulating the mitogen-activated protein kinase (MAPK) and (phosphatidylinositol-3 kinase/serine-threonine kinase) PI3K-Akt signaling pathways. Conclusion: S1PR3 participates in the regulation of blood–brain barrier damage after cerebral I/R. S1PR3 is expected to be an indicator and predictor of cerebral ischemia, and drugs targeting S1PR3 may also provide new ideas for clinical medications.
Emergence of a High-Risk Klebsiella michiganensis Clone Disseminating Carbapenemase Genes

Klebsiella michiganensis is emerging as an important human pathogen of concern especially strains with plasmid-mediated carbapenemase genes. The IncX3-blaNDM-5 plasmid has been described as the primary vector for blaNDM-5 dissemination. However, whether strains with this plasmid have any competitive edge remain largely unexplored. We characterized a blaNDM-5-producing Klebsiella michiganensis strain (KO_408) from Japan and sought to understand the driving force behind the recent dissemination of IncX3-blaNDM-5 plasmids in different bacterial hosts. Antibiotic susceptibility testing, conjugation, and whole-genome sequencing were performed for KO_408, a clinical isolate recovered from a respiratory culture. Fitness, stability, and competitive assays were performed using the IncX3-blaNDM-5 plasmid, pKO_4-NDM-5. KO_408 was ascribed to a novel sequence type, ST256, and harbored resistance genes conforming to its MDR phenotype. The blaNDM-5 gene was localized on the ~44.9 kb IncX3 plasmid (pKO_4-NDM-5), which was transferable in the conjugal assay. The acquisition of pKO_4-NDM-5 did not impose any fitness burden and showed high stability in the host cells. However, transformants with pKO_4-NDM-5 were outcompeted by their host cells and transconjugants with the IncX3-blaOXA-181 plasmid. The genetic environment of blaNDM-5 in pKO_4-NDM-5 has been previously described. pKO_4-NDM-5 showed a close phylogenetic distance with seven similar plasmids from China. KO_408 clustered with strains within the KoI phylogroup, which is closely associated with carbapenemase genes. This study highlights the emergence of a high-risk Klebsiella michiganensis clone harboring carbapenemase genes and affirms that the recent spread of IncX3-blaNDM-5 plasmids might be due to their low fitness cost and stability but not their competitive prowess.
Determination of Allergen Levels, Isoforms, and Their Hydroxyproline Modifications Among Peanut Genotypes by Mass Spectrometry

The recently published reference genome of peanuts enables a detailed molecular description of the allergenic proteins of the seed. We used LC-MS/MS to investigate peanuts of different genotypes to assess variability and to better describe naturally occurring allergens and isoforms. Using relative quantification by mass spectrometry, minor variation of some allergenic proteins was observed, but total levels of Ara h 1, 2, 3, and 6 were relatively consistent among 20 genotypes. Previously published RP-HPLC methodology was used for comparison. The abundance of three Ara h 3 isoforms were variable among the genotypes and contributed to a large proportion of total Ara h 3 where present. Previously unpublished hydroxyproline sites were identified in Ara h 1 and 3. Hydroxylation did not vary significantly where sites were present. Peanut allergen composition was largely stable, with only some isoforms displaying differences between genotypes. The resulting differences in allergenicity are of unknown clinical significance but are likely to be minor. The data presented herein allow for the design of targeted MS methodology to allow the quantitation and therefore control of peanut allergens of clinical relevance and observed variability.
Academic Stress and Mental Well-Being in College Students: Correlations, Affected Groups, and COVID-19

Academic stress may be the single most dominant stress factor that affects the mental well-being of college students. Some groups of students may experience more stress than others, and the coronavirus disease 19 (COVID-19) pandemic could further complicate the stress response. We surveyed 843 college students and evaluated whether academic stress levels affected their mental health, and if so, whether there were specific vulnerable groups by gender, race/ethnicity, year of study, and reaction to the pandemic. Using a combination of scores from the Perception of Academic Stress Scale (PAS) and the Short Warwick-Edinburgh Mental Well-Being Scale (SWEMWBS), we found a significant correlation between worse academic stress and poor mental well-being in all the students, who also reported an exacerbation of stress in response to the pandemic. In addition, SWEMWBS scores revealed the lowest mental health and highest academic stress in non-binary individuals, and the opposite trend was observed for both the measures in men. Furthermore, women and non-binary students reported higher academic stress than men, as indicated by PAS scores. The same pattern held as a reaction to COVID-19-related stress. PAS scores and responses to the pandemic varied by the year of study, but no obvious patterns emerged. These results indicate that academic stress in college is significantly correlated to psychological well-being in the students who responded to this survey. In addition, some groups of college students are more affected by stress than others, and additional resources and support should be provided to them.
Three-Dimensional Cartilage Regeneration Using Engineered Cartilage Gel With a 3D-Printed Polycaprolactone Framework

The feasibility of the three-dimensional (3D) cartilage regeneration technology based on the “steel (framework)-reinforced concrete (engineered cartilage gel, ECG)” concept has been verified in large animals using a decalcified bone matrix (DBM) as the framework. However, the instability of the source, large sample variation, and lack of control over the 3D shape of DBM have greatly hindered clinical translation of this technology. To optimize cartilage regeneration using the ECG–framework model, the current study explores the feasibility of replacing the DBM framework with a 3D-printed polycaprolactone (PCL) framework. The PCL framework showed good biocompatibility with ECG and achieved a high ECG loading efficiency, similar to that of the DBM framework. Furthermore, PCL-ECG constructs caused a milder inflammatory response in vivo than that induced by DBM-ECG constructs, which was further supported by an in vitro macrophage activation experiment. Notably, the PCL-ECG constructs successfully regenerated mature cartilage and essentially maintained their original shape throughout 8 weeks of subcutaneous implantation. Quantitative analysis revealed that the GAG and total collagen contents of the regenerated cartilage in the PCL-ECG group were significantly higher than those in the DBM-ECG group. The results indicated that the 3D-printed PCL framework—a clinically approved biomaterial with multiple advantages including customizable shape design, mechanical strength control, and standardized production—can serve as an excellent framework for supporting the 3D cartilage regeneration of ECG. This provides a feasible novel strategy for the clinical translation of ECG-based 3D cartilage regeneration.
A High Throughput Cell-Based Screen Assay for LINE-1 ORF1p Expression Inhibitors Using the In-Cell Western Technique

Long interspersed nuclear element 1 (LINE-1) is a dominant autonomous retrotransposon in human genomes which plays a role in affecting the structure and function of somatic genomes, resulting in human disorders including genetic disease and cancer. LINE-1 encoded ORF1p protein which possesses RNA-binding and nucleic acid chaperone activity, and interacts with LINE-1 RNA to form a ribonucleoprotein particle (RNP). ORF1p can be detected in many kinds of tumors and its overexpression has been regarded as a hallmark of histologically aggressive cancers. In this study, we developed an In-Cell Western (ICW) assay in T47D cells to screen the compounds which can decrease the expression of ORF1p. Using this assay, we screened 1,947 compounds from the natural products library of Target Mol and Selleckchem, among which three compounds, Hydroxyprogesterone, 2,2':5′,2″-Terthiophene and Ethynyl estradiol displayed potency in diminishing LINE-1 ORF1p expression level. Further mechanistic studies indicated the compounds act by affecting LINE-1 RNA transcription. Notably, we demonstrated that the compounds have an inhibitory effect on the proliferation of several lung and breast cancer cell lines. Taken together, we established a high throughput screening system for ORF1p expression inhibitors and the identified compounds provide some clues to the development of a novel anti-tumor therapeutic strategy by targeting ORF1p.
Cell Senescence-Related Pathways Are Enriched in Breast Cancer Patients With Late Toxicity After Radiotherapy and Low Radiation-Induced Lymphocyte Apoptosis

Background Radiation-induced late effects are a common cause of morbidity among cancer survivors. The biomarker with the best evidence as a predictive test of late reactions is the radiation-induced lymphocyte apoptosis (RILA) assay. We aimed to investigate the molecular basis underlying the distinctive RILA levels by using gene expression analysis in patients with and without late effects and in whom we had also first identified differences in RILA levels. Patients and Methods Peripheral blood mononuclear cells of 10 patients with late severe skin complications and 10 patients without symptoms, selected from those receiving radiotherapy from 1993 to 2007, were mock-irradiated or irradiated with 8 Gy. The 48-h response was analyzed in parallel by RILA assay and gene expression profiling with Affymetrix microarrays. Irradiated and non-irradiated gene expression profiles were compared between both groups. Gene set enrichment analysis was performed to identify differentially expressed biological processes. Results Although differentially expressed mRNAs did not reach a significant adjusted p-value between patients suffering and not suffering clinical toxicity, the enriched pathways indicated significant differences between the two groups, either in irradiated or non-irradiated cells. In basal conditions, the main differentially expressed pathways between the toxicity and non-toxicity groups were the transport of small molecules, interferon signaling, and transcription. After 8 Gy, the differences lay in pathways highly related to cell senescence like cell cycle/NF-κB, G-protein-coupled receptors, and interferon signaling. Conclusion Patients at risk of developing late toxicity have a distinctive pathway signature driven by deregulation of immune and cell cycle pathways related to senescence, which in turn may underlie their low RILA phenotype.