Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Methylation of TLR4, VEGFA, and DEFA5 Is Associated With Necrotizing Enterocolitis in Preterm Infants

Background: Epigenetic changes, such as DNA methylation, may contribute to an increased susceptibility for developing necrotizing enterocolitis (NEC) in preterm infants. We assessed DNA methylation in five NEC-associated genes, selected from literature: EPO, VEGFA, ENOS, DEFA5, and TLR4 in infants with NEC and controls. Methods: Observational cohort study including 24 preterm infants who developed NEC (≥Bell Stage IIA) and 45 matched controls. DNA was isolated from stool samples and methylation measured using pyrosequencing. We investigated differences in methylation prior to NEC compared with controls. Next, in NEC infants, we investigated methylation patterns long before, a short time before NEC onset, and after NEC. Results: Prior to NEC, only TLR4 CpG 2 methylation was increased in NEC infants (median = 75.4%, IQR = 71.3–83.8%) versus controls (median = 69.0%, IQR = 64.5–77.4%, p = 0.025). In NEC infants, VEGFA CpG 3 methylation was 0.8% long before NEC, increasing to 1.8% a short time before NEC and 2.0% after NEC (p = 0.011; p = 0.021, respectively). A similar pattern was found in DEFA5 CpG 1, which increased from 75.4 to 81.4% and remained 85.3% (p = 0.027; p = 0.019, respectively). These changes were not present for EPO, ENOS, and TLR4. Conclusion: Epigenetic changes of TLR4, VEGFA, and DEFA5 are present in NEC infants and can differ in relation to the time of NEC onset. Differences in DNA methylation of TLR4, VEGFA, and DEFA5 may influence gene expression and increase the risk for developing NEC. This study also demonstrates the use of human DNA extraction from stool samples as a novel non-invasive method for exploring the bowel of preterm infants and which can also be used for necrotizing enterocolitis patients.
Evaluation of the Effect of Local Water Chemistry on Trace Metal Accumulation in Puget Sound Shellfish Shows That Concentration Varies With Species, Size, and Location

Global climate change is causing ocean acidification (OA), warming, and decreased dissolved oxygen (DO) in coastal areas, which can cause physiological stress and compromise the health of marine organisms. While there is increased focus on how these stressors will affect marine species, there is little known regarding how changes in water chemistry will impact the bioaccumulation of trace metals. This study compared trace metal concentrations in tissue of Mediterranean mussels (Mytilus galloprovincialis) and Olympia oysters (Ostrea lurida) in Puget Sound, Washington, a region that experiences naturally low pH, seasonal hypoxia, and is surrounded by urbanized and industrialized areas. Shellfish were held at three sites (Carr Inlet, Point Wells, and Dabob Bay) where oceanographic data was continuously collected using mooring buoys. Using inductively coupled plasma mass-spectrometry (ICP-MS) to measure trace metals in the tissue, we found differences in accumulation of trace metals based on species, location, and shellfish size. Our study found differences between sites in both the mean metal concentrations and variability around the mean of those concentrations in bivalves. However, high metal concentrations in bivalves were not associated with high concentrations of metals in seawater. Metal concentrations in shellfish were associated with size: smaller shellfish had higher concentrations of metals. Carr Inlet at 20 m depth had the smallest shellfish and the highest metal concentrations. While we could not eliminate possible confounding factors, we also found higher metal concentrations in shellfish associated with lower pH, lower temperature, and lower dissolved oxygen (conditions seen at Carr Inlet at 20 m and to a lesser extent at Point Wells at 5 m depth). There were also significant differences in accumulation of metals between oysters and mussels, most notably copper and zinc, which were found in higher concentrations in oysters. These findings increase our understanding of spatial differences in trace metal bioaccumulation in shellfish from Puget Sound. Our results can help inform the Puget Sound aquaculture industry how shellfish may be impacted at different sites as climate change progresses and coastal pollution increases.
Probing the Hypersalience Hypothesis—An Adapted Judge-Advisor System Tested in Individuals With Psychotic-Like Experiences

Individuals with psychotic-like experiences and psychosis gather and use information differently than controls; in particular they seek and rely on less information or over-weight currently available information. A new paradigm, the judge-advisor system, has previously been used to investigate these processes. Results showed that psychosis-prone individuals tend to seek less advice but at the same time use the available advice more. Some theoretical models, like the hypersalience of evidence-matching hypothesis, predict that psychosis-prone individuals weight recently available information to a greater extent and thus provide an explanation for increased advice-weighting scores in psychosis-prone individuals. To test this model, we adapted the previously used judge-advisor system by letting participants receive consecutively multiple pieces of advice. To meet this aim, we recruited a large MTurk community sample (N = 1,396), which we split in a group with high levels of psychotic-like experiences (at least 2 SD above the mean, n = 80) and a group with low levels of psychotic-like experiences (maximum 0.5 SD above the mean, n = 1,107), using the Community Assessment of Psychic Experiences' positive subscale. First, participants estimated five people's age based on photographs. Then, they received consecutive advice in the form of manipulated age estimates by allegedly previous participants, with outliers in some trials. After each advice, participants could adjust their estimate. This procedure allowed us to investigate how participants weighted each currently presented advice. In addition to being more confident in their final estimates and in line with our preregistered hypothesis, participants with more frequent psychotic-like experiences did weight currently available advice more than participants with less frequent psychotic-like experiences. This effect was especially pronounced in response to outliers, as fine-grained post-hoc analysis suggested. Result thus support models predicting an overcorrection in response to new incoming information and challenges an assumed general belief inflexibility in people with psychotic experiences.
Network Pharmacology and Pharmacological Evaluation Reveals the Mechanism of the Sanguisorba Officinalis in Suppressing Hepatocellular Carcinoma

Background: Sanguisorba Officinalis L. (SO) is a well-known traditional Chinese medicine (TCM), commonly applied to treat complex diseases, such as anticancer, antibacterial, antiviral, anti-inflammatory, anti-oxidant and hemostatic effects. Especially, it has been reported to exert anti-tumor effect in various human cancers. However, its effect and pharmacological mechanism on hepatocellular carcinoma (HCC) remains unclear. Methods: In this study, network pharmacology approach was applied to characterize the underlying mechanism of SO on HCC. Active compounds and potential targets of SO, as well as related genes of HCC were obtained from the public databases, the potential targets and signaling pathways were determined by protein-protein interaction (PPI), gene ontology (GO) and pathway enrichment analyses. And the compound-target and target-pathway networks were constructed. Subsequently, in vitro experiments were also performed to further verify the anticancer effects of SO on HCC. Results: By using the comprehensive network pharmacology analysis, 41 ingredients in SO were collected from the corresponding databases, 12 active ingredients screened according to their oral bioavailability and drug-likeness index, and 258 potential targets related to HCC were predicted. Through enrichment analysis, SO was found to show its excellent therapeutic effects on HCC through several pathways, mainly related to proliferation and survival via the EGFR, PI3K/AKT, NFκB and MAPK signaling pathways. Additionally, in vitro, SO was found to inhibit cell proliferation, induce apoptosis and down-regulate cell migration and invasion in various HCC cells. Moreover, western blot analysis showed that SO treatment down-regulated the expression of p-EGFR, p-PI3K, p-AKT, p-NFκB and p-MAPK proteins in HepG2 cells. These results validated that SO exerted its therapeutic effects on HCC mainly by the regulation of cell proliferation and survival via the EGFR/MAPK and EGFR/PI3K/AKT/NFκB signaling pathways. Conclusion: Taken together, this study, revealed the anti-HCC effects of SO and its potential underlying therapeutic mechanisms in a multi-target and multi-pathway manner.
SARAF and Orai1 Contribute to Endothelial Cell Activation and Angiogenesis

Angiogenesis is a multistep process that controls endothelial cells (ECs) functioning to form new blood vessels from preexisting vascular beds. This process is tightly regulated by pro-angiogenic factors, such as vascular endothelial growth factor (VEGF), which promote signaling pathways involving the increase in the intracellular Ca2+ concentration ([Ca2+]i). Recent evidence suggests that store-operated calcium entry (SOCE) might play a role in angiogenesis. However, little is known regarding the role of SARAF, SOCE-associated regulatory factor, and Orai1, the pore-forming subunit of the store-operated calcium channel (SOCC), in angiogenesis. Here, we show that SOCE inhibition with GSK-7975A blocks aorta sprouting, as well as human umbilical vein endothelial cell (HUVEC) tube formation and migration. The intraperitoneal injection of GSK-7975A also delays the development of retinal vasculature assessed at postnatal day 6 in mice, since it reduces vessel length and the number of junctions, while it increases lacunarity. Moreover, we find that SARAF and Orai1 are involved in VEGF-mediated [Ca2+]i increase, and their knockdown using siRNA impairs HUVEC tube formation, proliferation, and migration. Finally, immunostaining and in situ proximity ligation assays indicate that SARAF likely interacts with Orai1 in HUVECs. Therefore, these findings show for the first time a functional interaction between SARAF and Orai1 in ECs and highlight their essential role in different steps of the angiogenesis process.
Photodynamic Therapy as an Alternative Therapeutic Tool in Functionally Inoperable Oral and Oropharyngeal Carcinoma: A Single Tertiary Center Retrospective Cohort Analysis

Background: Head and neck cancer is typically treated with surgery, radiotherapy, chemoradiation, or a combination of these treatments. This study aims to retrospectively analyse oncological outcomes, adverse events and toxicity of treatment with temoporfin-mediated photodynamic therapy at a single tertiary referral center. More specifically, in a selected group of patients with otherwise (functionally) inoperable oral or oropharyngeal head and neck squamous cell carcinoma. Methods: Twenty-six consecutive patients who received photodynamic therapy for oral or oropharyngeal squamous cell carcinoma from January 2002 until July 2019 at the University Hospitals Leuven were included. These were (1) patients with an accessible recurrent or new primary tumor in an extensively treated area of the head and neck, not suitable for standard treatment, or (2) patients that were judged medically unfit to undergo standard treatment modalities. Results: Complete tumor response immediately after PDT was obtained in 76.9% of cases. During follow-up, a proportion of CR patients did recur, to reach recurrence-free rates at six months, one year and two years of 60.6%, 48.5% and 32.3%. Local control at the PDT treated area was 42.3% with a median recurrence free interval time of 9 months. Recurrence-free interval was statistically more favorable for oropharyngeal squamous cell carcinoma (with or without oral cavity extension) in comparison to oral cavity squamous cell carcinoma alone (p < 0.001). During a median follow-up period of 27 months, we report new tumor activity in 80.8% of patients. Median overall and disease-specific survival time was 31 and 34 months, respectively. Most reported adverse events were pain after treatment and facial edema. At the end of follow-up, swallowing and upper airway functionality were preserved in 76.9 and 95.7% of patients, respectively. Conclusion: Photodynamic therapy is a valuable treatment option in highly selected patients with oral and/or oropharyngeal (functionally) inoperable head and neck squamous cell carcinoma. Treatment with this alternative modality can induce durable local control in an important fraction of treated patients, with an acceptable toxicity profile.
Elevated β-Carotene Production Using Codon-Adapted CarRA&B and Metabolic Balance in Engineered Yarrowia lipolytica

β-carotene is a precursor of vitamin A and has multiple physiological functions. Producing β-carotene by microbial fermentation has attracted much attention to consumers’ preference for natural products. This study focused on improving β-carotene production by constructing codon-adapted genes and minimizing intermediate accumulation. The codon-adapted CarRA and CarB genes from the industrial strain of Blakeslea trispora were integrated into the genome of the Yarrowia lipolytica to construct YL-C0, the baseline strain for producing β-carotene. Thereafter, the β-carotene biosynthetic pathway’s metabolic balance was accurately regulated to reduce the intermediates’ accumulation. Notably, the β-carotene content increased by 21 times to reach 12.5 dry cell weight (DCW) mg/g when minimizing HMG-CoA and FPP accumulation. Further, we improved the expression levels of the CarRA and CarB genes to minimize the accumulation of phytoene and lycopene. Total production of β-carotene of 1.7 g/L and 21.6 mg/g DCW was achieved. These results reveal that the rate-limiting enzymes CarRA and CarB of B. trispora exhibited higher catalytic activity than the same enzymes from other microorganisms. Promoting metabolic balance by minimizing the accumulation of intermediates is a very effective strategy for increasing β-carotene. The β-carotene-producing strain constructed in this study has established the foundation for its potential use in industrial production. These successful engineering strategies also provide a foundation for large-scale production of other terpenoids.
Multiband Wavelet Age Modeling for a ∼293 m (∼600 kyr) Sediment Core From Chew Bahir Basin, Southern Ethiopian Rift

The use of cyclostratigraphy to reconstruct the timing of deposition of lacustrine deposits requires sophisticated tuning techniques that can accommodate continuous long-term changes in sedimentation rates. However, most tuning methods use stationary filters that are unable to take into account such long-term variations in accumulation rates. To overcome this problem we present herein a new multiband wavelet age modeling (MUBAWA) technique that is particularly suitable for such situations and demonstrate its use on a 293 m composite core from the Chew Bahir basin, southern Ethiopian rift. In contrast to traditional tuning methods, which use a single, defined bandpass filter, the new method uses an adaptive bandpass filter that adapts to changes in continuous spatial frequency evolution paths in a wavelet power spectrum, within which the wavelength varies considerably along the length of the core due to continuous changes in long-term sedimentation rates. We first applied the MUBAWA technique to a synthetic data set before then using it to establish an age model for the approximately 293 m long composite core from the Chew Bahir basin. For this we used the 2nd principal component of color reflectance values from the sediment, which showed distinct cycles with wavelengths of 10–15 and of ∼40 m that were probably a result of the influence of orbital cycles. We used six independent 40Ar/39Ar ages from volcanic ash layers within the core to determine an approximate spatial frequency range for the orbital signal. Our results demonstrate that the new wavelet-based age modeling technique can significantly increase the accuracy of tuned age models.
Variation, Variegation and Heritable Gene Repression in S. cerevisiae

Phenotypic heterogeneity provides growth advantages for a population upon changes of the environment. In S. cerevisiae, such heterogeneity has been observed as “on/off” states in the expression of individual genes in individual cells. These variations can persist for a limited or extended number of mitotic divisions. Such traits are known to be mediated by heritable chromatin structures, by the mitotic transmission of transcription factors involved in gene regulatory circuits or by the cytoplasmic partition of prions or other unstructured proteins. The significance of such epigenetic diversity is obvious, however, we have limited insight into the mechanisms that generate it. In this review, we summarize the current knowledge of epigenetically maintained heterogeneity of gene expression and point out similarities and converging points between different mechanisms. We discuss how the sharing of limiting repression or activation factors can contribute to cell-to-cell variations in gene expression and to the coordination between short- and long- term epigenetic strategies. Finally, we discuss the implications of such variations and strategies in adaptation and aging.
Synthesis and Structural Characterization of Metal-Doped Titanate Nanotubes Using TEM, XRD and XAS

This work presents the synthesis and structural characterization of titanate nanoproducts, focusing on the effect induced by the presence of silver ion in different concentrations. The synthesis and chemical analysis using TEM, XRD and EDX were performed at the University of Szeged in Hungary. The XAS analysis was done at the MaxLab synchrotron facility in Lund University, Sweden. From the analysis, it is revealed that the titanate nanotubes exhibited an elongated structure before thermal treatment and were transformed into nanocrystals upon thermal treatment at 600 oC. Silver significantly promoted the conversion of titanate nanotubes into anatase phase, with the participation of new intermediates.
States of Biological Components in Bacteria and Bacteriophages during Inactivation by Atmospheric Dielectric Barrier Discharges

Atmospheric DBD has been applied to the wet state of Escherichia coli and bacteriophage-2. Upon DBD treatment, both E.coli and 2phage were immediately inactivated. The states of different biological components were monitored during the course of inactivation. Only minor and slow degradation of proteins, DNA, and membranes was observed, a remarkable degradation was seen only after the completion of sterilization. Analysis of GFP recombinantly introduced into E.coli cells proved that the DBD has a prominent protein denaturation activity without affecting peptide bonds. The irreversible denaturation of proteins, seen in the early stage of DBD application, may play a central role in inactivation of both the bacteria and bacteriophages.
A new modification of NaCoPO4 with the zeolite ABW structure

The title compound, sodium cobalt(II) phosphate, a new polymorph of NaCoPO 4 , crystallizes as a monoclinic modification of the zeolite ABW structure. The five-coordinate Na + cations reside within channels running through an open cobalt-phosphate framework constructed from four-, six- and eight-membered rings of alternating CoO 4 and PO 4 tetrahedra. The channels are enclosed by the eight-membered rings.
Fourier Transform Infrared Imaging of Nematic Liquid Crystals

Fourier transform infrared spectroscopy is often used to study liquid crystals and liquid crystal systems. In this work, the factors that influence the IR absorbance of nematic liquid crystals and their consequences on FT-IR imaging are examined. In the IR spectrum of E7, ordering in the nematic phase causes a 28.7% reduction in the nitrile band height relative to the isotropic phase, and the combination of ordering and liquid crystal director alignment causes a 65.0% decrease in the nitrile band height. For a phase-separated blend of E7 and 10% NOA65 polymer, the FT-IR images were found to be concentration-based for the polymer-specific carbonyl band and phase/alignment-based, which masked the concentration dependence, for the liquid crystal-specific nitrile band. These findings were exploited to produce an FT-IR image of the isotropic-to-nematic phase transition of neat E7. This transition image emphasizes the dependence of liquid crystal bands on ordering and alignment and the need for caution in the interpretation of FT-IR images of liquid crystals and liquid crystal systems.
Power generation with salinity gradient by pressure retarded osmosis using concentrated brine from SWRO system and treated sewage as pure water

Abstract Salinity power generation using hollow fiber modules was examined using the pressure-retarded osmosis (PRO) system between pure water and concentrated brine. Pure water and concentrated brine were supplied from a regional sewage treatment facility and sea water desalination (sea water reverse osmosis [SWRO]) plant. To minimize the effect of the concentration polarization near the membrane surface on the pure water side, the number of open ports in the module was increased from 3 to 4 and that modification was found to be effective because non-permeating pure water, which left the module through fourth port, flushed leaked salt from the brine side through the membrane. Our prototype PRO plant got the maximum output power density, 7.7 W/m2 at a 2.5 MPa hydraulic pressure difference and a 38% permeation of pure water into the brine. To remove the organic foulant in the pure water, a low pressure Reverse Osmosis (RO) membrane and coagulation–sedimentation method with ozonation showed good results. Ho.
A comparison of two modified Kjeldahl digestion techniques for multi‐element plant analysis with conventional wet and dry ashing methods

Abstract The efficiency of two modified Kjeldahl procedures (H2SO4‐H2‐O2‐Li2SO4‐Se and H2SO4‐Na2SO4) for digestion of plant tissue for analysis of P, K, Ca and Mg contents was compared with a conventional wet (HNO3‐HClO4) and a dry ashing procedure. Six plant tissues were chosen as test material: leaves of Malus pumila Mill. , Medicago sativa L. , Dactylis glomerata L. , fruit and wood tissue of M. pumila and Nothofagus mensiesii Oerst. leaf litter. Apart from low P contents of M. pumila wood tissue by dry ashing, the mean P, K, Ca and Mg contents as determined after the four digestion procedures were in good agreement. Furthermore, the precision of the data for each element was generally quite similar for each of the digestion methods. The N contents determined by the two modified and a conventional Kjeldahl procedure (H2SO4‐K2SO4‐CuSO4‐Se) also agreed closely.
MALDI-TOF mass spectrometry in the analysis of synthetic polymers

Matrix-assisted laser desorption/ionization mass spectrometry has been applied over the past 5 years with increasing success to the analysis of synthetic polymers. Basic principles and instrumental parameters influencing the spectra are described. Examples from different areas of polymer research with emphasis on technically relevant systems elucidate the highly useful features of this kind of mass spectrometry, i. e. determination of absolute molar masses, high mass range, reasonable mass resolution, high sensitivity, relative ease of operation even for polar molecules. Molar mass distributions can be obtained in a mass range that is problematic for other mass determining techniques. A detailed characterization of the underlying chemistry can be obtained in many cases by an endgroup analysis. Especially in combination with other separation techniques, a comprehensive characterization of chemical heterogeneity can be achieved. Recent developments, e. g. delayed extraction to enhance the mass resolution obtainable, will further increase the favorable prospects of this technique.