Miracle-dz/UniFAR-FTUs huggingface dataset:
Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair

To understand the complex fluorescence properties of astraphloxin (CY3)-labelled oligonucleotides, it is necessary to take into account the redox properties of the nucleobases. In oligonucleotide hybrids, we observed a dependence of the fluorescence intensity on the oxidation potential of the neighbouring base pair. For the series I < A < G < 8-oxoG, the extent of fluorescence quenching follows the trend of decreasing oxidation potentials. In a series of 7 nt hybrids, stacking interactions of CY3 with perfect match and mismatch base pairs were found to stabilise the hybrid by 7–8 kJ/mol. The fluorescence measurements can be explained by complex formation resulting in fluorescence quenching that prevails over the steric effect of a reduced excited state trans-cis isomerisation, which was expected to increase the fluorescence efficiency of the dye when stacking to a base pair. This can be explained by the fact that, in a double strand, base pairing and stacking cause a dramatic change in the oxidation potential of the nucleobases. In single-molecule fluorescence measurements, the oxidation of G to 8-oxoG was observed as a result of photoinduced electron transfer and subsequent chemical reactions. Our results demonstrate that covalently linked CY3 is a potent oxidant towards dsDNA. Sulfonated derivatives should be used instead.
THE LINKAGE ANALYSIS OF INTEREST-FREEAND INTEREST-BEARING MONETARY AGGREGATES TO BUSINESS CYCLE AND INFLATION IN INDONESIA

The Money supply, which consists of M1 (interest-free monetary aggregates) and QM (interestbearing monetary aggregates), is a monetary policy instrument often used by Central Bank of Indonesia to achieve the final target of output and price. The purpose of this study is to identify which component is the more effective to be a monetary policy instrument. We apply Vector Autoregressive (VAR) combined with Vector Error Correction Model (VECM) to analyze the responses of Indonesia’s quarterly real GDP and price to the shock of M1 and QM.The result indicates that the shock of QM is relatively more able to explain the variance of real GDP and price compared to the shock of M1. This means, in the long-run QM is more related to real GDP and price, so QM is more effective to be a monetary instrument to overcome the business cycle and inflation in Indonesia.
A rare missense variant in protection of telomeres 1 (POT1) predisposes to a range of haematological malignancies

Diagnosis and treatment of autoimmune hemolytic anemia in adults: Recommendations from the First International Consensus Meeting. Blood Rev. 2020;41:100648. 9. Garrison LP Jr, Neumann PJ, Erickson P, Marshall D, Mullins CD. Using real-world data for coverage and payment decisions: the ISPOR Real-World Data Task Force report. Value Health. 2007;10(5): 326–35. 10. Hill A, Hill QA. Autoimmune hemolytic anemia. Hematology Am Soc Hematol Educ Program. 2018;2018(1):382–9. 11. Yndigegn T, Hofmann R, Jernberg T, Gale CP. Registry-based randomised clinical trial: efficient evaluation of generic pharmacotherapies in the contemporary era. Heart. 2018;104(19):1562–7. 12. Hoque DME, Kumari V, Hoque M, Ruseckaite R, Romero L, Evans SM. Impact of clinical registries on quality of patient care and clinical outcomes: a systematic review. PLoS One. 2017;12(9):e0183667.
Newly Developed System for the Robust Detection of Listeria monocytogenes Based on a Bioelectric Cell Biosensor

Human food-borne diseases caused by pathogenic bacteria have been significantly increased in the last few decades causing numerous deaths worldwide. The standard analyses used for their detection have significant limitations regarding cost, special facilities and equipment, highly trained staff, and a long procedural time that can be crucial for foodborne pathogens with high hospitalization and mortality rates, such as Listeria monocytogenes. This study aimed to develop a biosensor that could detect L. monocytogenes rapidly and robustly. For this purpose, a cell-based biosensor technology based on the Bioelectric Recognition Assay (BERA) and a portable device developed by EMBIO Diagnostics, called B.EL. D (Bio Electric Diagnostics), were used. Membrane engineering was performed by electroinsertion of Listeria monocytogenes homologous antibodies into the membrane of African green monkey kidney (Vero) cells. The newly developed biosensor was able to detect the pathogen’s presence rapidly (3 min) at concentrations as low as 102 CFU mL−1, demonstrating a higher sensitivity than most existing biosensor-based methods. In addition, lack of cross-reactivity with other Listeria species, as well as with Escherichia coli, was shown, thus, indicating biosensor’s significant specificity against L. monocytogenes.
Phase transitions in a high magnetic field of an odd, symmetric liquid crystal dimer having two nematic phases, N_{U} and N_{TB}, studied by NMR spectroscopy.

Both ^{1}H and ^{13}C NMR spectra have been obtained in a static magnetic field of 23.5 T on a bent-shaped dimer molecule, 1^{''},7^{''}-bis(4-cyanobiphenyl-4'-yl) nonane (CB9CB), which shows the sequence of liquid crystal phases twist-bend nematic, N_{TB}, and uniaxial nematic, N_{U}, before entering the isotropic phase. The ^{1}H spectra are used to locate the temperature at which the sample melts to form a twist-bend nematic, T_{CrN_{TB}}, and then T_{N_{U}I} when the isotropic phase is entered, both in a magnetic field of 23.5 T, and to compare these with those measured at the Earth's field. The differences between these transition temperatures are found to be zero within the error in their measurement, in stark contrast to previous measurements by Salili et al. [Phys. Rev. Lett. 116, 217801 (2016)10.1103/PhysRevLett.116. 217801]. In the isotropic phase in the presence of the field the sample exists in a paranematic phase in which the molecules of CB9CB are partially ordered. The ^{1}H and ^{13}C NMR spectra in the paranematic phase are used to measure the critical temperature T* below which this phase is unstable. The spectra are also used to study the structure, molecular orientational order, and distribution of molecular conformations in the paranematic phase.
Desalination Performance Assessment of Scalable, Multi-Stack Ready Shock Electrodialysis Unit Utilizing Anion-Exchange Membranes

Incumbent electromembrane separation processes, including electrodialysis (ED) and electrodeionization (EDI), provide competitive techniques for desalination, selective separation, and unique solutions for ultra-pure water production. However, most of these common electrochemical systems are limited by concentration polarization and the necessity for multistep raw water pre-treatment. Shock electrodialysis (SED) utilizes overlimiting current to produce fresh, deionized water in a single step process by extending ion depleted zones that propagate through a porous medium as a sharp concentration gradient or a shock wave. So far, SED has been demonstrated on small scale laboratory units using cation-exchange membranes. In this work, we present a scalable and multi-stack ready unit with a large, 5000 mm2 membrane active area designed and constructed at the Technical University of Liberec in cooperation with MemBrain s.r. o. and Mega a.s. companies (Czechia). We report more than 99% salt rejection using anion-exchange membranes, depending on a dimensionless parameter that scales the constant applied current by the limiting current. It is shown that these parameters are most probably associated with pore size and porous media chemistry. Further design changes need to be done to the separator, the porous medium, and other functional elements to improve the functionality and energy efficiency.
Root biomass and root traits of Alnus glutinosa show size-dependent and opposite patterns in a drained and a rewetted forest peatland

Abstract Background and Aims Forest peatlands represent 25 % of global peatlands and store large amounts of carbon (C) as peat. Traditionally they have been drained in order to increase forestry yield, which may cause large losses of C from the peat. Rewetting aims to stop these losses and to restore the initial storage function of the peatlands. As roots represent major peat-forming elements in these systems, we sampled roots with diameter <5 mm in a drained and a rewetted forest peatland in north-east Germany to evaluate differences in tree biomass investments below ground, root functional characteristics and root age. Methods We cored soil next to Alnus glutinosa stems and sorted root biomass into <1, 1–2 and 2–5 mm diameter classes. We measured biomass distribution and specific root area (SRA) in 10-cm depth increments down to 50 cm, and estimated root age from annual growth rings. Key Results Root biomass in the rewetted site was more than double that in the drained site. This difference was mostly driven by very fine roots <1 mm, which accounted for 51 % of the total root biomass and were mostly (75 %) located in the upper 20 cm. For roots <1 mm, SRA did not differ between the sites. However, SRA of the 1–2 mm and 2–5 mm diameter roots was higher in the drained than in the rewetted site. Root age did not differ between sites. Conclusions The size-dependent opposite patterns between root biomass and their functional characteristics under contrasting water regimes indicate differences between fine and coarse roots in their response to environmental changes. Root age distribution points to similar root turnover rates between the sites, while higher root biomass in the rewetted site clearly indicates larger tree C stocks below ground under rewetting, supporting the C sink function of the ecosystem.
Site‐specific ubiquitination of the E3 ligase HOIP regulates apoptosis and immune signaling

HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), is a critical regulator of inflammation. However, how HOIP itself is regulated to control inflammatory responses is unclear. Here, we discover that site‐specific ubiquitination of K784 within human HOIP promotes tumor necrosis factor (TNF)‐induced inflammatory signaling. A HOIP K784R mutant is catalytically active but shows reduced induction of an NF‐κB reporter relative to wild‐type HOIP. HOIP K784 is evolutionarily conserved, equivalent to HOIP K778 in mice. We generated HoipK778R/K778R knock‐in mice, which show no overt developmental phenotypes; however, in response to TNF, HoipK778R/K778R mouse embryonic fibroblasts display mildly suppressed NF‐κB activation and increased apoptotic markers. On the other hand, HOIP K778R enhances the TNF‐induced formation of TNFR complex II and an interaction between TNFR complex II and LUBAC. Loss of the LUBAC component SHARPIN leads to embryonic lethality in HoipK778R/K778R mice, which is rescued by knockout of TNFR1. We propose that site‐specific ubiquitination of HOIP regulates a LUBAC‐dependent switch between survival and apoptosis in TNF signaling.
Long non-coding RNA EGFR-AS1 in colorectal cancer: potential role in tumorigenesis and survival via miRNA-133b sponge and EGFR/STAT3 axis regulation

ABSTRACT Background Colorectal cancer is one of the most common cancers worldwide and a major cause of cancer-related death. Thus molecular biomarkers for colorectal cancer have been proposed. The role of long non-coding RNA EGFR-AS1 in colorectal cancer is still unclear. We aimed to evaluate its expression in different stages of colorectal cancer and determine any possible role in regulating the miR‑133b/EGFR/STAT3 signalling pathway. Materials and Methods The relative expression of EGFR-AS1 and miR‑133b were evaluated by quantitative real-time RT-transcription PCR in 130 colorectal cancer samples and 30 normal tissues. EGFR expression was assessed using immunohistochemistry. Furthermore, levels of p-EGFR, p-STAT3, and apoptotic proteins were determined by ELISA. Results Both EGFR-AS1 and EGFR overexpression were positively linked with colorectal cancer status (both p < 0.01), grade (both p < 0.01), and metastasis (P < 0.01 and p = 0.019 respectively). EGFR-AS1 and miR-133b were significantly inversely correlated (P < 0.01). Low expression of miR-133b was inversely associated with overexpressed EGFR and increased p-STAT3 levels. EGFR-AS1 was an independent prognostic factor for survival of colorectal cancer patients (P < 0.01, HR 2.06; 95% CI 1.32–3.19) where low EGFR-AS1 expression was associated with higher survival rate (p = 0.003). Conclusion EGFR-AS1 may have a role in colorectal cancer by regulation of miR‑133b/EGFR/STAT3 signalling. It may be a potential biomarker for early diagnosis and predicting the survival rate of colorectal cancer.
Sexual Behavior Problems Among Sexually Abused Children: Associations With Co-Occurring Symptoms

Sexual behavior problems (SBPs) and interpersonal SBPs (ISBPs) among sexually abused children often occur alongside a variety of other clinical difficulties, such as externalizing problems, attentional difficulties, social concerns, and posttraumatic stress symptoms (PTSS). Yet, as few studies have examined these links in a multivariate manner, it is unclear which symptoms are most strongly related to SBPs and ISBPs. Research regarding children’s reports of their difficulties and SBPs and ISBPs is also very limited. The current study investigated the relations between both caregiver- and child-reported trauma-related symptoms and SBPs and ISBPs among 248 treatment-seeking sexually abused children (ages 6–12; M = 8.06, SD = 2.52; 64.5% female; 55.6% white). Children’s caregiver-reported trauma-related sexual concerns and anger were associated with SBPs. For ISBPs, only caregiver-reported sexual concerns were related to ISBPs. Surprisingly, none of the child-reported symptoms were associated with either SBPs or ISBPs. Trauma-related sexual concerns and anger may be tied to SBPs, whereas other clinical difficulties may be less strongly implicated. Trauma-related sexual concerns may be most important in understanding interpersonally focused SBPs. Children’s self-reported difficulties may be unrelated to caregiver-reported SBPs, or these results may be a function of a low degree of caregiver and child symptom concordance.
Transcriptomic Analysis of Staphylococcus xylosus in Solid Dairy Matrix Reveals an Aerobic Lifestyle Adapted to Rind

Staphylococcus xylosus is found in the microbiota of traditional cheeses, particularly in the rind of soft smeared cheeses. Despite its frequency, the molecular mechanisms allowing the growth and adaptation of S. xylosus in dairy products are still poorly understood. A transcriptomic approach was used to determine how the gene expression profile is modified during the fermentation step in a solid dairy matrix. S. xylosus developed an aerobic metabolism perfectly suited to the cheese rind. It overexpressed genes involved in the aerobic catabolism of two carbon sources in the dairy matrix, lactose and citrate. Interestingly, S. xylosus must cope with nutritional shortage such as amino acids, peptides, and nucleotides, consequently, an extensive up-regulation of genes involved in their biosynthesis was observed. As expected, the gene sigB was overexpressed in relation with general stress and entry into the stationary phase and several genes under its regulation, such as those involved in transport of anions, cations and in pigmentation were up-regulated. Up-regulation of genes encoding antioxidant enzymes and glycine betaine transport and synthesis systems showed that S. xylosus has to cope with oxidative and osmotic stresses. S. xylosus expressed an original system potentially involved in iron acquisition from lactoferrin.
Pseudomonas aeruginosa Biofilms

Pseudomonas aeruginosa is an opportunistic human pathogen causing devastating acute and chronic infections in individuals with compromised immune systems. Its highly notorious persistence in clinical settings is attributed to its ability to form antibiotic-resistant biofilms. Biofilm is an architecture built mostly by autogenic extracellular polymeric substances which function as a scaffold to encase the bacteria together on surfaces, and to protect them from environmental stresses, impedes phagocytosis and thereby conferring the capacity for colonization and long-term persistence. Here we review the current knowledge on P. aeruginosa biofilms, its development stages, and molecular mechanisms of invasion and persistence conferred by biofilms. Explosive cell lysis within bacterial biofilm to produce essential communal materials, and interspecies biofilms of P. aeruginosa and commensal Streptococcus which impedes P. aeruginosa virulence and possibly improves disease conditions will also be discussed. Recent research on diagnostics of P. aeruginosa infections will be investigated. Finally, therapeutic strategies for the treatment of P. aeruginosa biofilms along with their advantages and limitations will be compiled.
In vitro mechanical vibration down-regulates pro-inflammatory and pro-fibrotic signaling in human vocal fold fibroblasts

Introduction Voice rest following phonotrauma or phonosurgery has a considerable clinical impact, but clinical recommendations are inconsistent due to inconclusive data. As biopsies of the vocal folds (VF) for molecular biology studies in humans are unethical, we established a new in vitro model to explore the effects of vibration on human vocal fold fibroblasts (hVFF) in an inflammatory and normal state, which is based on previously published models. Methods By using a phonomimetic bioreactor we were able to apply predefined vibrational stress patterns on hVFF cultured under inflammatory or normal conditions. Inflammatory and pro-fibrotic stimuli were induced by interleukin (IL)1β and transforming growth factor (TGF)β1, respectively. Mechanical stimulation was applied four hours daily, over a period of 72 hours. Outcome measurements comprised assessment of extracellular matrix (ECM)-related components, angiogenic factors, and inflammatory and fibrogenic markers on gene expression and protein levels. Results Under inflammatory conditions, the inflammatory cytokine IL11, as well as the myofibroblast marker alpha smooth muscle actin (α-SMA) were significantly reduced when additional vibration was applied. The desirable anti-fibrotic ECM component hyaluronic acid was increased following cytokine treatment, but was not diminished following vibration. Conclusion Our experiments revealed the effect of vibrational stress on hVFF in an inflammatory state. Elevated levels of certain pro-inflammatory/pro-fibrotic factors could be mitigated by additional vibrational excitation in an in vitro setting. These findings corroborate clinical studies which recommend early voice activation following an acute event.
Epigenetics and pulmonary diseases in the horizon of precision medicine: a review

Epigenetic mechanisms represent potential molecular routes which could bridge the gap between genetic background and environmental risk factors contributing to the pathogenesis of pulmonary diseases. In patients with COPD, asthma and pulmonary arterial hypertension (PAH), there is emerging evidence of aberrant epigenetic marks, mainly including DNA methylation and histone modifications which directly mediate reversible modifications to the DNA without affecting the genomic sequence. Post-translational events and microRNAs can be also regulated epigenetically and potentially participate in disease pathogenesis. Thus, novel pathogenic mechanisms and putative biomarkers may be detectable in peripheral blood, sputum, nasal and buccal swabs or lung tissue. Besides, DNA methylation plays an important role during the early phases of fetal development and may be impacted by environmental exposures, ultimately influencing an individual's susceptibility to COPD, asthma and PAH later in life. With the advances in omics platforms and the application of computational biology tools, modelling the epigenetic variability in a network framework, rather than as single molecular defects, provides insights into the possible molecular pathways underlying the pathogenesis of COPD, asthma and PAH. Epigenetic modifications may have clinical applications as noninvasive biomarkers of pulmonary diseases. Moreover, combining molecular assays with network analysis of epigenomic data may aid in clarifying the multistage transition from a “pre-disease” to “disease” state, with the goal of improving primary prevention of lung diseases and its subsequent clinical management. We describe epigenetic mechanisms known to be associated with pulmonary diseases and discuss how network analysis could improve our understanding of lung diseases. Network medicine approaches, supporting the integrative analysis of global epigenetic changes, clinical features and environmental factors, provide new hypotheses for pathogenesis of chronic lung diseases and lead to new interventions for prevention https://bit.ly/3kHND9m
Associations between urinary iodine concentration and the prevalence of metabolic disorders: a cross-sectional study

Background Few studies have examined the role of iodine in extrathyroidal function. Recent research has shown an association between iodine and metabolic syndromes (MetS) in Chinese and Korean populations, but the link in the American participants remains unknown. Purpose This study aimed to examine the relationship between iodine status and metabolic disorders, including components associated with metabolic syndrome, hypertension, hyperglycemia, central obesity, triglyceride abnormalities, and low HDL. Methods The study included 11,545 adults aged ≥ 18 years from the US National Health and Nutrition Examination Survey (2007–2018). Participants were divided into four groups based on their iodine nutritional status(ug/L), as recommended by the World Health Organization: low UIC, < 100; normal UIC, 100-299; high UIC, 300-399; and very high, ≥ 400. The Odds ratio (OR) for MetS basing the UIC group was estimated using logistic regression models for our overall population and subgroups. Results Iodine status was positively associated with the prevalence of MetS in US adults. The risk of MetS was significantly higher in those with high UIC than in those with normal UIC [OR: 1.25; 95% confidence intervals (CI),1.016-1.539; p = 0.035). The risk of MetS was lower in the low UIC group (OR,0.82; 95% CI: 0.708-0.946; p = 0.007). There was a significant nonlinear trend between UIC and the risk of MetS, diabetes, and obesity in overall participants. Participants with high UIC had significantly increased TG elevation (OR, 1.24; 95% CI: 1.002-1.533; P = 0.048) and participants with very high UIC had significantly decreased risk of diabetes (OR, 0.83; 95% CI: 0.731-0.945, p = 0.005). Moreover, subgroup analysis revealed an interaction between UIC and MetS in participants aged < 60 years and ≥ 60 years, and no association between UIC and MetS in older participants aged ≥ 60 years. Conclusion Our study validated the relationship between UIC and MetS and their components in US adults. This association may provide further dietary control strategies for the management of patients with metabolic disorders.