Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional profiling of

Background Xanthomonas campestris pv. campestris (Xcc) is an important seed-borne plant pathogenic bacteria that can cause a serious threat to cruciferous crops. Bacteria can enter into the viable but non-culturable (VBNC) state under stress conditions, and cause potential risks to agricultural production because the VBNC bacterial cells will evade culture-based detection. However, little is known about the mechanism of VBNC. Our previous study showed that Xcc could be induced into VBNC state by copper ion (Cu2+). Results Here, RNA-seq was performed to explore the mechanism of VBNC state. The results indicated that expression profiling was changed dramatically in the different VBNC stages (0 d, 1 d, 2 d and 10 d). Moreover, metabolism related pathways were enriched according to COG, GO and KEGG analysis of differentially expressed genes (DEGs). The DEGs associated with cell motility were down-regulated, whereas pathogenicity related genes were up-regulated. This study revealed that the high expression of genes related to stress response could trigger the active cells to VBNC state, while the genes involved in transcription and translation category, as well as transport and metabolism category, were ascribed to maintaining the VBNC state. Conclusion This study summarized not only the related pathways that might trigger and maintain VBNC state, but also the expression profiling of genes in different survival state of bacteria under stress. It provided a new kind of gene expression profile and new ideas for studying VBNC state mechanism in X. campestris pv. campestris.
Use of Ag-Au-ICG to increase fluorescence image of human hepatocellular carcinoma cell lines

Abstract Indocyanine green (ICG) is effective for a variety of applications including liver tumour imaging and operates in the near-infrared window. Agents for near-infrared imaging are, however, still in clinical development. The present study aimed to prepare and investigate fluorescence emission properties of ICG in combination with Ag-Au in order to enhance their specific interactions with human hepatocellular carcinoma cell lines (HepG-2). The Ag-Au-ICG complex was prepared via physical adsorption, and hence evaluated for fluorescence spectra using a spectrophotometer. Ag-Au-ICG at an optimised dosage (Ag-Au:ICG = 0.0147:1 molar ratio) in Intralipid medium was added to HepG-2 to observe the maximum fluorescence signal intensity, which further enhanced HepG-2 contrast fluorescence. Ag-Au-ICG served as a fluorescence enhancer bound onto the liposome membrane, whilst free Ag, Au, and pure ICG induced low levels of cytotoxicity in HepG-2 and a normal human cell line. Thus, our findings provided new insights for the liver cancer imaging. Highlights Concentration-dependent fluorescence peaking in the near-infrared window revealed ICG aggregation in Ag-Au molecules. Ag-Au-ICG fluorescence intensity depended strongly on the environmental media. Human hepatocellular carcinoma cell lines treated with Ag-Au-ICG in Intralipid enhanced the contrast of fluorescence microscopy images by decreasing the level of scattering in the cell lines with the contrast values being approximately five times those observed in pure ICG in Intralipid.
Using Explainable Artificial Intelligence to Predict Potentially Preventable Hospitalizations

Background: The increasing aging population and limited health care resources have placed new demands on the healthcare sector. Reducing the number of hospitalizations has become a political priority in many countries, and special focus has been directed at potentially preventable hospitalizations. Objectives: We aimed to develop an artificial intelligence (AI) prediction model for potentially preventable hospitalizations in the coming year, and to apply explainable AI to identify predictors of hospitalization and their interaction. Methods: We used the Danish CROSS-TRACKS cohort and included citizens in 2016-2017. We predicted potentially preventable hospitalizations within the following year using the citizens’ sociodemographic characteristics, clinical characteristics, and health care utilization as predictors. Extreme gradient boosting was used to predict potentially preventable hospitalizations with Shapley additive explanations values serving to explain the impact of each predictor. We reported the area under the receiver operating characteristic curve, the area under the precision-recall curve, and 95% confidence intervals (CI) based on five-fold cross-validation. Results: The best performing prediction model showed an area under the receiver operating characteristic curve of 0.789 (CI: 0.782–0.795) and an area under the precision-recall curve of 0.232 (CI: 0.219–0.246). The predictors with the highest impact on the prediction model were age, prescription drugs for obstructive airway diseases, antibiotics, and use of municipality services. We found an interaction between age and use of municipality services, suggesting that citizens aged 75+ years receiving municipality services had a lower risk of potentially preventable hospitalization. Conclusion: AI is suitable for predicting potentially preventable hospitalizations. The municipality-based health services seem to have a preventive effect on potentially preventable hospitalizations.
Role of riboflavin biosynthesis gene duplication and transporter in Aeromonas salmonicida virulence in marine teleost fish

ABSTRACT Active flavins derived from riboflavin (vitamin B2) are essential for life. Bacteria biosynthesize riboflavin or scavenge it through uptake systems, and both mechanisms may be present. Because of riboflavin’s critical importance, the redundancy of riboflavin biosynthetic pathway (RBP) genes might be present. Aeromonas salmonicida, the aetiological agent of furunculosis, is a pathogen of freshwater and marine fish, and its riboflavin pathways have not been studied. This study characterized the A. salmonicida riboflavin provision pathways. Homology search and transcriptional orchestration analysis showed that A. salmonicida has a main riboflavin biosynthetic operon that includes ribD, ribE1, ribBA, and ribH genes. Outside the main operon, putative duplicated genes ribA, ribB and ribE, and a ribN riboflavin importer encoding gene, were found. Monocistronic mRNA ribA, ribB and ribE2 encode for their corresponding functional riboflavin biosynthetic enzyme. While the product of ribBA conserved the RibB function, it lacked the RibA function. Likewise, ribN encodes a functional riboflavin importer. Transcriptomics analysis indicated that external riboflavin affected the expression of a relatively small number of genes, including a few involved in iron metabolism. ribB was downregulated in response to external riboflavin, suggesting negative feedback. Deletion of ribA, ribB and ribE1 showed that these genes are required for A. salmonicida riboflavin biosynthesis and virulence in Atlantic lumpfish (Cyclopterus lumpus). A. salmonicida riboflavin auxotrophic attenuated mutants conferred low protection to lumpfish against virulent A. salmonicida. Overall, A. salmonicida has multiple riboflavin endowment forms, and duplicated riboflavin provision genes are critical for A. salmonicida infection.
Determination, exposure and risk assessment of PAHs in natural vitamin E isolated from vegetable oil industry

ABSTRACT Natural vitamin E, which is mainly extracted from vegetable oil deodoriser distillate (VODD), is likely contaminated by carcinogenic polycyclic aromatic hydrocarbons (PAHs). A total of 26 commercial vitamin E products from six countries were investigated for 16 EPA PAHs using QuEChERS combined with gas chromatography triple quadrupole mass spectrometry (GC-QQQ-MS). The concentrations of total PAHs in the samples ranged from 46.5 μg kg−1 to 215 μg kg−1, while the concentrations of PAH4 (BaA, Chr, BbF and BaP) ranged from 4.43 μg kg−1 to 20.1 μg kg−1. Risk assessment indicates that maximum intake of PAHs is 0.2 mg day−1, which is less than the LD50 and no observed adverse effect levels (NOAEL) of PAHs. However, chronic carcinogenicity of PAHs needs to be considered. The results suggested that PAH concentrations as well as toxicity equivalent should be considered as important indicator of risk of vitamin E products.
Optimal state estimation without the requirement of a priori statistics information of the initial state

The result given by the Kalman filter is the best linear unbiased estimate (BLUE) provided that the mean and variance of the initial state are known. The same state estimation problem is reconsidered for multi-input multi-output (MIMO) stochastic time-varying discrete systems when the statistics knowledge about the initial state is not known. The algorithm presented in this paper gives the BLUE of system states without the requirement of any a priori knowledge about the initial state. The concept of complete reconstructibility of stochastic systems is established, and the necessary and sufficient condition for complete reconstructibility is given. When applied to a completely reconstructible deterministic system, the proposed algorithms give the deadbeat state estimates even if the system is not observable. >
Ratio of extracellular water to intracellular water and simplified creatinine index as predictors of all-cause mortality for patients receiving hemodialysis

The bioelectrical impedance analysis-measured ratio of extracellular water (ECW) to intracellular water (ICW) reflects fluid volume and malnutrition. It may be an indicator of protein-energy wasting and muscle wasting in hemodialysis patients. We examined the association between the ECW/ICW ratio and simplified creatinine index, which is a new surrogate marker of protein-energy wasting and muscle wasting, and whether their combination can accurately predict mortality. A total of 224 patients undergoing hemodialysis for more than 6 months and having undergone bioelectrical impedance analysis for the assessment of body composition were included. Patients were divided into two groups based on the cut-off values of the ECW/ICW ratio (0.57) and simplified creatinine index (20.4 mg/kg/day) for maximumly predicting mortality. Thereafter, they were cross-classified into four groups with each cut-off point. The ECW/ICW ratio was independently associated with the simplified creatinine index (β = -0.164; P = 0.042). During a follow-up of 3.5 years (2.0–6.0 years), 77 patients died. A higher ECW/ICW ratio (adjusted hazard ratio, 3.66, 95% confidence interval 1.99–6.72, P <0.0001) and lower simplified creatinine index (adjusted hazard ratio, 2.25, 95% confidence interval 1.34–3.79, P = 0.0021) were independently associated with an increased risk of all-cause mortality. The adjusted hazard ratio for the higher ECW/ICW ratio and lower simplified creatinine index group vs. the lower ECW/ICW ratio and higher simplified creatinine index group was 12.22 (95% confidence interval 3.68–40.57, p <0.0001). Furthermore, the addition of the ECW/ICW ratio and simplified creatinine index to the baseline risk model significantly improved the C-index from 0.831 to 0.864 (p = 0.045). In conclusion, the ECW/ICW ratio may be a surrogate marker of muscle wasting. Moreover, combining the ECW/ICW ratio and simplified creatinine index may improve the accuracy of predicting all-cause mortality and help stratify the mortality risk of hemodialysis patients.
Thrombus burden management during primary coronary bifurcation intervention: a new experimental bench model

Background Management of thrombus burden during primary percutaneous coronary intervention (pPCI) is a key-point, given the high risk of stent malapposition and/or thrombus embolization. These issues are especially important if pPCI involves a coronary bifurcation. Herein, a new experimental bifurcation bench model to analyze thrombus burden behavior was developed. Methods On a fractal left main bifurcation bench model, we generated standardized thrombus with human blood and tissue factor. Three provisional pPCI strategies were compared (n = 10/group): 1) balloon-expandable stent (BES), 2) BES completed by proximal optimizing technique (POT), and 3) nitinol self-apposing stent (SAS). The embolized distal thrombus after stent implantation was weighed. Stent apposition and thrombus trapped by the stent were quantified on two-dimensional-optical coherence tomography (OCT). To analyze final stent apposition, a new OCT acquisition was performed after pharmacological thrombolysis. Results Trapped thrombus was significantly greater with isolated BES than SAS or BES+POT (18.8 ± 5.8% vs. 10.3 ± 3.3% and 6.2 ± 2.1%, respectively; p < 0.05), and greater with SAS than BES+POT (p < 0.05). Isolated BES and SAS tended show less embolized thrombus than BES+POT (5.93 ± 4.32 mg and 5.05 ± 4.56 mg vs. 7.01 ± 4.32 mg, respectively; p = NS). Conversely, SAS and BES+POT ensured perfect final global apposition (0.4 ± 0.6% and 1.3 ± 1.3%, respectively, p = NS) compared to isolated BES (74.0 ± 7.6%, p < 0.05). Conclusions This first experimental bench model of pPCI in a bifurcation quantified thrombus trapping and embolization. BES provided the best thrombus trapping, while SAS and BES+POT achieved better final stent apposition. These factors should be taken into account in selecting revascularization strategy.
Establishment of cell lines from individual zebrafish embryos

With the increasing use of fish as model species for research, cell cultures derived from caudal fin explants as well as pre-hatching stage embryos have provided powerful in vitro tools that can complement or serve as an ethically more acceptable alternative to live animal experiments. The widely-used protocols to establish these lines require, as a starting point, homogeneous pools of embryos or viable adult fish which are large enough for collecting sufficient fin tissue. This excludes the use of fish lines with adverse phenotypes or lines that exhibit mortality at early developmental stages and so can only be propagated as heterozygotes. Specifically, when no visually overt mutant phenotype is detectable for identifying homozygous mutants at early embryonic stages, it is then impossible to sort pools of embryos with the same genotypes to generate cell lines from the progeny of a heterozygote in-cross. Here, we describe a simple protocol to generate cell lines on a large scale starting from individual early embryos that can subsequently be genotyped by polymerase chain reaction. This protocol should help to establish fish cell culture models as a routine approach for the functional characterization of genetic changes in fish models such as the zebrafish. Furthermore, it should contribute to a reduction of experiments which are ethically discouraged to avoid pain and distress.
Two‐level discretization of the Navier‐Stokes equations with r‐Laplacian subgridscale viscosity

The r‐Laplacian has played an important role in the development of computationally efficient models for applications, such as numerical simulation of turbulent flows. In this article, we examine two‐level finite element approximation schemes applied to the Navier‐Stokes equations with r‐Laplacian subgridscale viscosity, where r is the order of the power‐law artificial viscosity term. In the two‐level algorithm, the solution to the fully nonlinear coarse mesh problem is utilized in a single‐step linear fine mesh problem. When modeling parameters are chosen appropriately, the error in the two‐level algorithm is comparable to the error in solving the fully nonlinear problem on the fine mesh. We provide rigorous numerical analysis of the two‐level approximation scheme and derive scalings which vary based on the coefficient r, coarse mesh size H, fine mesh size h, and filter radius δ. We also investigate the two‐level algorithm in several computational settings, including the 3D numerical simulation of flow past a backward‐facing step at Reynolds number Re = 5100. In all numerical tests, the two‐level algorithm was proven to achieve the same order of accuracy as the standard one‐level algorithm, at a fraction of the computational cost. © 2011 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
Tunable multiwavelength erbium-doped fiber laser with a polarization-maintaining photonic crystal fiber Sagnac loop filter

We propose and demonstrate a tunable multiwavelength erbium-doped fiber laser based on a polarization-maintaining photonic crystal fiber (PM-PCF) Sagnac loop filter. Stable, room-temperature operation is obtained by employing a nonlinear optical loop mirror. At a central wavelength of 1563.000 nm, we generate 60 wavelengths within 3-dB bandwidth. The measured power fluctuation for each lasing wavelength is less than 0.2 dB in half an hour. Furthermore, by adjusting the polarization controllers in the Sagnac filter, wavelength locations of the laser lines with a fixed channel spacing of ∼ 0.078 nm can be continuously shifted.
Microbiota-directed biotherapeutics: considerations for quality and functional assessment

ABSTRACT Mounting evidence points to causative or correlative roles of gut microbiome in the development of a myriad of diseases ranging from gastrointestinal diseases, metabolic diseases to neurological disorders and cancers. Consequently, efforts have been made to develop and apply therapeutics targeting the human microbiome, in particular the gut microbiota, for treating diseases and maintaining wellness. Here we summarize the current development of gut microbiota-directed therapeutics with a focus on novel biotherapeutics, elaborate the need of advanced -omics approaches for evaluating the microbiota-type biotherapeutics, and discuss the clinical and regulatory challenges. We also discuss the development and potential application of ex vivo microbiome assays and in vitro intestinal cellular models in this context. Altogether, this review aims to provide a broad view of promises and challenges of the emerging field of microbiome-directed human healthcare.
A non-nested test of level-differenced versus log-differenced stationary models

This paper considersthe applicationof the simulated Cox test procedure developed in Pesaran and Pesaran (1993) to test linear versus log-linear models. The test procedure can also be applied to other generalized linear regression models such as level-difference stationary models versus the log-difference stationary models. In order to compare the small sample performanceof the proposed test with other tests extant in the literature, the paper also reports the resultsof a numberof Monte Carlo experiments using the experimental framework of Godfrey et al. (1988). The Monte Carlo results provide strong support for a simplified version of the simulatedCox test over the PE and the BM tests, but suggest that there is little to choose between the simulated Cox test and the DL test.
Transcriptomic analysis of mosaic brain differentiation underlying complex division of labor in a social insect

Concerted developmental programming may constrain changes in component structures of the brain, thus limiting the ability of selection to form an adaptive mosaic of size‐variable brain compartments independent of total brain size or body size. Measuring patterns of gene expression underpinning brain scaling in conjunction with anatomical brain atlases can aid in identifying influences of concerted and/or mosaic evolution. Species exhibiting exceptional size and behavioral polyphenisms provide excellent systems to test predictions of brain evolution models by quantifying brain gene expression. We examined patterns of brain gene expression in a remarkably polymorphic and behaviorally complex social insect, the leafcutter ant Atta cephalotes. The majority of significant differential gene expression observed among three morphologically, behaviorally, and neuroanatomically differentiated worker size groups was attributable to body size. However, we also found evidence of differential brain gene expression unexplained by worker morphological variation and transcriptomic analysis identified patterns not linearly correlated with worker size but sometimes mirroring neuropil scaling. Additionally, we identified enriched gene ontology terms associated with nucleic acid regulation, metabolism, neurotransmission, and sensory perception, further supporting a relationship between brain gene expression, brain mosaicism, and worker labor role. These findings demonstrate that differential brain gene expression among polymorphic workers underpins behavioral and neuroanatomical differentiation associated with complex agrarian division of labor in A. cephalotes.
Epigenetic Activation of Tensin 4 Promotes Gastric Cancer Progression

Gastric cancer (GC) is a complex disease influenced by multiple genetic and epigenetic factors. Chronic inflammation caused by Helicobacter pylori infection and dietary risk factors can result in the accumulation of aberrant DNA methylation in gastric mucosa, which promotes GC development. Tensin 4 (TNS4), a member of the Tensin family of proteins, is localized to focal adhesion sites, which connect the extracellular matrix and cytoskeletal network. We identified upregulation of TNS4 in GC using quantitative reverse transcription PCR with 174 paired samples of GC tumors and adjacent normal tissues. Transcriptional activation of TNS4 occurred even during the early stage of tumor development. TNS4 depletion in GC cell lines that expressed high to moderate levels of TNS4, i.e., SNU-601, KATO III, and MKN74, reduced cell proliferation and migration, whereas ectopic expression of TNS4 in those lines that expressed lower levels of TNS4, i.e., SNU-638, MKN1, and MKN45 increased colony formation and cell migration. The promoter region of TNS4 was hypomethylated in GC cell lines that showed upregulation of TNS4. We also found a significant negative correlation between TNS4 expression and CpG methylation in 250 GC tumors based on The Cancer Genome Atlas (TCGA) data. This study elucidates the epigenetic mechanism of TNS4 activation and functional roles of TNS4 in GC development and progression and suggests a possible approach for future GC treatments.