Miracle-dz/UniFAR-FTUs huggingface dataset:
Paleoclimate Records of the Middle Okinawa Trough Since the Middle Holocene: Modulation of the Low-Latitude Climate

The ubiquity of glycerol dibiphytanyl glycerol tetraethers (GDGTs) and their temperature sensitivity make them one of the most effective tools for paleoclimate reconstruction. High- and low-latitude climates influence the Okinawa Trough (OT). It receives diverse inputs from the East China Sea, the western Pacific, and the Kuroshio Current, providing good conditions for paleoclimate studies. Here, isoprenoid GDGTs (isoGDGTs), branched GDGTs, and hydroxylated GDGTs (OH-GDGTs) were studied to reconstruct the sea surface temperature (SST) of the central OT for the past 8.2 kyr using the tetraether index of 86 carbon atoms at low latitudes (TEXH 86) and the ring index of OH-GDGTs (RI-OH). The GDGT-0/crenarchaeol ratios ranged from 0.39 to 0.98. The branched and isoprenoid tetraether index and the methane index values were lower than 0.1 and 0.5, respectively, indicating that the isoGDGTs were mainly derived from marine Thaumarchaeota and that TEXH 86 could be used to reconstruct the paleotemperatures. The TEXH 86 SSTs ranged from 21.6 to 27.2°C during 8.2 kyr. The overall range of TEXH 86 SSTs is close to the UK’ 37 SST of the middle OT and reflects the mean annual SST. In contrast, RI-OH temperatures varied from 17.4 to 26.0°C, showing a lower trend than TEXH 86 SSTs. The core top RI-OH temperature is 24.1°C, in line with the mean annual seawater temperature at 40 m (24.2°C) in the study area, which likely reflects the subsurface temperature in this case. The small overall warming trend of TEXH 86 SSTs agrees with the increasing intensity of the Kuroshio Current during the last 8.2 kyr, indicating that the SST evolution is governed by the Kuroshio Current that transports heat from the western tropical Pacific. The decreasing temperature differences between TEXH 86 and RI-OH and between UK’ 37 and RI-OH showed increased mixing of the upper water column, which was in good accordance with the increasing low-latitude winter insolation decoupling from the East Asian summer monsoon. The cold event that occurred at 7.4–6.6 kyr was magnified (∼5°C) at the TEXH 86 and RI-OH temperatures and possibly caused by tephra’s significant input (∼7.3 kyr).
Essential Oils Prime Epigenetic and Metabolomic Changes in Tomato Defense Against Fusarium oxysporum

In this work, we studied the direct and indirect plant protection effects of an Artemisia absinthium essential oil (AEO) on tomato seedlings against Fusarium oxysporum sp. oxysporum radicis lycopersici (Fol). AEO exhibited a toxic effect in vitro against Fol. Additionally, tomato seedlings germinated from seeds pretreated with AEO and grown hydroponically were protected against Fol. Plant disease symptoms, including, water and fresh weight loss, tissue necrosis, and chlorosis were less pronounced in AEO-treated seedlings. AEO also contributed to plant defenses by increasing callose deposition and the production of reactive oxygen species (ROS) on seed surfaces without affecting seed germination or plant development. The essential oil seed coating also primed a durable tomato seedling defense against the fungus at later stages of plant development. RNA-seq and metabolomic analysis performed on seedlings after 12 days showed that the AEO treatment on seeds induced transcriptomic and metabolic changes. The metabolomic analysis showed an induction of vanillic acid, coumarin, lycopene, oleamide, and an unknown metabolite of m/z 529 in the presence of Fol. The StNRPD2 gene, the second largest component of RNA polymerases IV and V directly involved in de novo cytosine methylation by RNA-directed DNA methylation (RdDM), was highly induced in the presence of AEO. The host methionine cycle (MTC) controlling trans-methylation reactions, was also altered by AEO through the high induction of S-adenosyl methionine transferases (SAMts). Our results suggest that AEO treatment could induce de novo epigenetic changes in tomato, modulating the speed and extent of its immune response to Fol. The EO-seed coating could be a new strategy to prime durable tomato resistance, compatible with other environmentally friendly biopesticides.
Adherence to the Vegetable-Fruit-Soy Dietary Pattern, a Reference From Mediterranean Diet, Protects Against Postmenopausal Breast Cancer Among Chinese Women

Background The diet-center hypothesis has gained much support from the apparent protective effect of the Mediterranean diet on breast cancer. However, the evidence of the association between Mediterranean diet adherence and breast cancer molecular subtypes remains small, especially in non-Mediterranean populations. Methods The subjects from the Chinese Wuxi Exposure and Breast Cancer Study, a population-based case-control study, included 818 patients and 935 healthy controls. A validated food frequency questionnaire used for diet assessment and a modified version of the alternate Mediterranean Diet Score, which is called the alternate Chinese Diet Score, was developed to assess adherence to a migrated Chinese version of the Mediterranean diet, which we called the vegetable-fruit-soy dietary pattern. Soy foods, rapeseed oil, and coarse cereals replaced legumes, olive oil, and whole grains reflecting the cuisine of the region. We examined the association between the vegetable-fruit-soy diet adherence and breast cancer risk, stratified by menopause status (pre- or postmenopausal) and receptor status [estrogen-receptor (ER), progesterone-receptor (PR) status, and human epidermal growth factor 2 (HER2)] oncogene expression, followed by five specific combinations (ER+, ER–, ER+/PR+,ER–/PR–, and ER–/PR–/HER2–). Results The results suggest that the vegetable-fruit-soy dietary pattern was inversely associated with postmenopausal breast cancer risk [4th vs. 1st quartile, odds ratio (OR) = 0.57, 95%CI = 0.41, 0.80; P trend < 0.001] and that the inverse association was somewhat stronger to detect among ER- subtypes (OR = 0.63; 95%CI = 0.37, 0.94; P trend = 0.003) and ER–/PR–subtypes (OR = 0.64; 95%CI = 0.41, 0.93; P trend = 0.012). We did not observe any significant association between the vegetable-fruit-soy diet characteristics and ER+ subtype, as well as between PR+ and ER+/PR+ subtypes. Conclusion The favorable influence from the Mediterranean diet may also apply to Chinese women. The vegetable-fruit-soy dietary pattern may reduce the risk of postmenopausal breast cancer, particularly among ER- subtype, and ER–/PR–subtype.
Machine-Learning-Based Bibliometric Analysis of Pancreatic Cancer Research Over the Past 25 Years

Machine learning and semantic analysis are computer-based methods to evaluate complex relationships and predict future perspectives. We used these technologies to define recent, current and future topics in pancreatic cancer research. Publications indexed under the Medical Subject Headings (MeSH) term ‘Pancreatic Neoplasms’ from January 1996 to October 2021 were downloaded from PubMed. Using the statistical computing language R and the interpreted, high-level, general-purpose programming language Python, we extracted publication dates, geographic information, and abstracts from each publication’s metadata for bibliometric analyses. The generative statistical algorithm “latent Dirichlet allocation” (LDA) was applied to identify specific research topics and trends. The unsupervised “Louvain algorithm” was used to establish a network to identify relationships between single topics. A total of 60,296 publications were identified and analyzed. The publications were derived from 133 countries, mostly from the Northern Hemisphere. For the term “pancreatic cancer research”, 12,058 MeSH terms appeared 1,395,060 times. Among them, we identified the four main topics “Clinical Manifestation and Diagnosis”, “Review and Management”, “Treatment Studies”, and “Basic Research”. The number of publications has increased rapidly during the past 25 years. Based on the number of publications, the algorithm predicted that “Immunotherapy”, Prognostic research”, “Protein expression”, “Case reports”, “Gemcitabine and mechanism”, “Clinical study of gemcitabine”, “Operation and postoperation”, “Chemotherapy and resection”, and “Review and management” as current research topics. To our knowledge, this is the first study on this subject of pancreatic cancer research, which has become possible due to the improvement of algorithms and hardware.
Predictive Effect of Triglyceride Glucose−Related Parameters, Obesity Indices, and Lipid Ratios for Diabetes in a Chinese Population: A Prospective Cohort Study

Objective The purpose of this study was to evaluate the association between triglyceride glucose (TyG) index and new-onset diabetes under different glycemic states and to compare the predictive value of TyG−related parameters, obesity indices, and lipid ratios for new-onset diabetes. Methods Data were collected from the China Health and Retirement Longitudinal Study (CHARLS), consisting of 6,258 participants aged ≥45 years. Participants were grouped according to their glycemic states. Cox proportional hazards models and restricted cubic spline regression were used to explore the association between TyG index and diabetes. Cox proportional hazard models were applied to confirm the predictive value of the optimal marker. Receiver operating characteristic (ROC) curves were used to compare the predictive value. Results TyG index was positively correlated with the risk of diabetes (hazard ratio (HR), 1.75; 95% confidence interval (CI), 1.56–1.97), and the linear association existed (p < 0.001). The highest correlation with diabetes was visceral adiposity index (VAI) (HR, 2.04; 95% CI, 1.44–2.90) in normal fasting glucose (NFG) group and TyG-body mass index (TyG-BMI) (HR, 2.53; 95% CI, 1.97–3.26) in impaired fasting glucose (IFG) group. The largest area under curve (AUC) was observed in TyG-waist-to-height ratio (TyG-WHtR) in the NFG group (AUC, 0.613; 95% CI, 0.527–0.700), and TyG-BMI had the highest AUC in the IFG group (AUC, 0.643; 95% CI, 0.601–0.685). Conclusion The association between TyG index and new-onset diabetes was positive and linear. TyG-WHtR was a clinically effective marker for identifying the risks of diabetes in the NFG group and TyG-BMI was an effective marker to predict diabetes in the IFG group.
Resonant tunneling transport in ZnxBe1-xSe/ZnSe/ZnyBe1-ySe asymmetric quantum structures

II-VI compounds are promising materials for the fabrication of room-temperature terahertz devices due to their beneficial properties like as type-I conduction band alignment, high breakdown field strength (~331 kV/cm for ZnSe vs. ~80 kV/cm for GaAs), and higher values of the conduction band offset (1.5 eV for BeSe/ZnSe vs. 0.7 eV for AlAs/GaAs). In this paper we report on numerical study of the resonant tunneling transport in ZnBeSe/ZnSe/ZnBeSe symmetric and asymmetric resonant tunneling diodes (RTDs). The negative differential resistance feature is observed in the current-voltage characteristics of the ZnSe-based RTDs. It is found that the maximum of peak-to-valley ratio (PVR) of the current density is equal to 6.025 and 7.144 at 150 K, and to 1.120 and 1.105 at 300 K for the symmetric and asymmetric RTDs, respectively. The effect of barrier heights on the frequency and output power performance of RTD devices are studied and discussed.
Direct Full-Length RNA Sequencing Reveals an Important Role of Epigenetics During Sexual Reversal in Chinese Soft-Shelled Turtle

Sex dimorphism is a key feature of Chinese soft-shelled turtle (Pelodiscus sinensis). The males (M) have higher econosmic value than females (F) due to wider calipash and faster growth. Exogenous hormones like estradiol and methyltestosterone can induce sexual reversal to form new phenotypes (pseudo-female, PF; pseudo-male, PM) without changing the genotype. The possibility of inducing sexual reversal is particularly important in aquaculture breeding, but the underlying biological mechanisms remain unclear. Here we applied a direct RNA sequencing method with ultralong reads using Oxford Nanopore Technologies to study the transcriptome complexity in P. sinensis. Nanopore sequencing of the four gender types (M, F, PF, and PM) showed that the distribution of read length and gene expression was more similar between same-sex phenotypes than same-sex genotypes. Compared to turtles with an M phenotype, alternative splicing was more pronounced in F turtles, especially at alternative 3′ splice sites, alternative 5′ splice sites, and alternative first exons. Furthermore, the two RNA methylation modifications m5C and m6A were differentially distributed across gender phenotypes, with the M type having more modification sites in coding sequence regions, but fewer modification sites in 3′UTR regions. Quantitative analysis of enriched m6A RNAs revealed that the N6-methylated levels of Odf2, Pacs2, and Ak1 were significantly higher in M phenotype individuals, while the N6-methylated levels of Ube2o were reduced after sexual reversal from both M and F phenotypes. Taken together, these findings reveal an important role of epigenetics during sexual reversal in Chinese soft-shelled turtles.
Research on Bond Participants’ Emotion Reactions Toward the Internet News in China’s Bond Market

The literature has widely studied the market response to the financial news or events but mainly focused on the stock market. This article associates the concept of internet news with the bond market response and attempts to examine how credit rating agencies (CRAs) and bond investors, two important bond participants, react to financial news on the internet with a range of multiply regressions. Our empirical study leads to several findings. First, CRAs tend to ignore the warnings of financial news on the internet, whereas bond investors strongly react to such news. Second, there is an asymmetry in bond investors’ reactions to good news compared to bad news, with investors being more sensitive to bad news. Third, there is heterogeneity in the psychological reaction where bond investors do not react to the news about central state-owned enterprises (SOEs) but to the news about other enterprises. Finally, there is an asymmetric response driven by news timeliness that bond investors are more sensitive to the latest news articles than old ones. Overall, our study confirms the existence of psychological reactions to the financial news on the internet in China’s bond market, which has significance for keeping bond market participants from overreacting or underreacting to market news.
A Numerical Experiment of Full Waveform Inversion of Complex Structures Concealed Around a Horizontal Hydraulic Fracturing Well Using Perforation Seismic Data

It is difficult to image the details of complex structures concealed around a horizontal hydraulic fracturing well using seismic data from the ground surface. In this paper, an approach is proposed to solve this problem by non-linear full waveform inversion (FWI) using perforation seismic data. The feasibility of the approach was investigated using numerical modeling based on an experimental model built from the well-known SEG/EAGE overthrust model, which contains complex geological structures with faults. First, seismic modeling was performed to produce experimental synthetic data, including three sets of perforation seismic data recorded by different acquisition systems deployed in observation wells and on the ground surface, and another set of conventional seismic reflection data with both sources and receivers deployed on the ground surface. Then, FWI was performed separately on each data set using an initial velocity model which was heavily smoothed to remove the target structures. The inversion results show that the concealed complex structures around the well were successfully recovered by FWI using perforation data, while the benchmark image from the FWI using conventional seismic data was poor. Particularly, the experiments also demonstrated that FWI using perforation seismic data can image the faults around a horizontal hydraulic fracturing well, while this is unable to achieve using conventional ground surface seismic data. This conclusion was also proved to be valid for noisy data deteriorated either by synthetic Gaussian or field noises. Further experiments demonstrated that FWI using perforation data recorded from wells outperformed that of surface data in terms of structure imaging accuracy characterized by quantitative errors.
Genome-Wide Identification and Expression Analysis of the Thioredoxin (Trx) Gene Family Reveals Its Role in Leaf Rust Resistance in Wheat (Triticum aestivum L.)

Bread wheat (Triticum aestivum L.; Ta) is the staple cereal crop for the majority of the world’s population. Leaf rust disease caused by the obligate fungal pathogen, Puccinia triticina L. , is a biotrophic pathogen causing significant economic yield damage. The alteration in the redox homeostasis of the cell caused by various kinds of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in response to pathogenic infections is controlled by redox regulators. Thioredoxin (Trx) is one of the redox regulators with low molecular weight and is thermostable. Through a genome-wide approach, forty-two (42) wheat Trx genes (TaTrx) were identified across the wheat chromosome groups A, B, and D genomes containing 12, 16, and 14 Trx genes, respectively. Based on in silico expression analysis, 15 TaTrx genes were selected and utilized for further experimentation. These 15 genes were clustered into six groups by phylogenetic analysis. MicroRNA (miRNA) target analysis revealed eight different miRNA-targeted TaTrx genes. Protein–protein interaction (PPI) analysis showed TaTrx proteins interact with thioredoxin reductase, peroxiredoxin, and uncharacterized proteins. Expression profiles resulting from quantitative real-time PCR (qRT-PCR) revealed four TaTrx genes (TaTrx11-5A, TaTrx13-5B, TaTrx14-5D, and TaTrx15-3B) were significantly induced in response to leaf rust infection. Localization of ROS and its content estimation and an assay of antioxidant enzymes and expression analysis suggested that Trx have been involved in ROS homeostasis at span 24HAI-72HAI during the leaf rust resistance.
Aquifer-Stream Exchanges and the Importance of Groundwater Discharge for Maintaining Instream Habitat and Benthic Macroinvertebrates

Periods of streamflow cessation and stream drying are increasing in frequency and intensity in many regions of the world due to climate change, land-use change, and increased groundwater pumping. Thus, streams with intermittent flow will likely continue to grow in their global extent, which is thought to already surpass that of perennial streams. Yet, variability in streamflow and aquifer-stream exchange associated with flow cessation and drying is not well understood, nor is the influence of hydrological variability on aquatic communities and their habitat. This study aimed to characterize the heterogeneity of physical and chemical characteristics of habitat and the associated variability in benthic macroinvertebrate (BMI) communities in relation to spatial and temporal variability in streamflow and aquifer-stream exchange. Habitat conditions and BMI communities varied between individual sites, riffle and pool habitat, and between an intermittent riffle and a perennial riffle maintained by groundwater discharge. Unlike other studies, BMI richness, diversity, and abundance were consistently higher at intermittent riffle sites than perennial riffle sites, which were similar in BMI community composition to pool sites. High velocity distinguished the intermittent riffle sites, while two flow-loving BMI taxa distinguished their communities. This suggests that site-specific heterogeneity in habitat conditions was a key control on spatial and temporal variability in BMI communities due to the habitat preferences of certain BMI taxa. Low richness, diversity, and high dominance of highly tolerant taxa across the site suggested long-term patterns of extreme variability in habitat conditions associated with flow cessation and drying were the primary control on BMI communities. Thus, the interactive effects of these controls may produce unexpected patterns in BMI community richness, diversity, and composition in relation to longitudinal patterns of groundwater discharge and flow persistence. These findings demonstrate the importance of considering the influence of heterogeneity in environmental conditions at multiple spatial and temporal scales when interpreting relationships between hydrological and abiotic or biotic ecological variable in streams with intermittent flow.
Fluidic-Based Instruments for Space Biology Research in CubeSats

For the last 15 years, small satellites known as CubeSats have been used to investigate the effects of the space environment on biological organisms. All biological CubeSat missions flown to date have performed studies in low Earth orbit (LEO), each one improving its biological support sub-systems from the last. An upcoming NASA biological CubeSat mission, BioSentinel, will launch as a secondary payload on Artemis 1 and eventually reach a heliocentric orbit beyond LEO, and the protection of Earth’s magnetosphere. The main objectives of BioSentinel are 1) to investigate the biological effects of the deep space radiation environment and 2) to develop our technological capacity to support biological research in deep space. The instruments and subsystems within BioSentinel have heritage from previous CubeSat missions (e.g., fluidics, optics, thermal control), but are extended on many levels. BioSentinel improves upon the materials and design (e.g., decreased card vapor permeability to maintain low humidity; the addition of a fluidic manifold with internal check-valves, desiccant chambers, and bubble traps for each individual fluidic card) and adds new tools for discovery (e.g., onboard LET spectrometer). The main objective of this Perspective is to emphasize the evolution of the fluidic systems used in past and ongoing NASA biological CubeSat missions and highlight aspects of these systems that can be optimized for future experimentation beyond LEO.
Multiscale Mechanobiology in Brain Physiology and Diseases

Increasing evidence suggests that mechanics play a critical role in regulating brain function at different scales. Downstream integration of mechanical inputs into biochemical signals and genomic pathways causes observable and measurable effects on brain cell fate and can also lead to important pathological consequences. Despite recent advances, the mechanical forces that influence neuronal processes remain largely unexplored, and how endogenous mechanical forces are detected and transduced by brain cells into biochemical and genetic programs have received less attention. In this review, we described the composition of brain tissues and their pronounced microstructural heterogeneity. We discuss the individual role of neuronal and glial cell mechanics in brain homeostasis and diseases. We highlight how changes in the composition and mechanical properties of the extracellular matrix can modulate brain cell functions and describe key mechanisms of the mechanosensing process. We then consider the contribution of mechanobiology in the emergence of brain diseases by providing a critical review on traumatic brain injury, neurodegenerative diseases, and neuroblastoma. We show that a better understanding of the mechanobiology of brain tissues will require to manipulate the physico-chemical parameters of the cell microenvironment, and to develop three-dimensional models that can recapitulate the complexity and spatial diversity of brain tissues in a reproducible and predictable manner. Collectively, these emerging insights shed new light on the importance of mechanobiology and its implication in brain and nerve diseases.