DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences.

Motivation: RNA structure is essential for the function of many non-coding RNAs. Using multiple homologous sequences, which share structure and function, secondary structure can be predicted with much higher accuracy than with a single sequence. It can be difficult, however, to establish a set of homologous sequences when their structure is not yet known.

Sequence Design Using RNAstructure.

RNA is present in all domains of life. It was once thought to be solely involved in protein expression, but recent advances have revealed its crucial role in catalysis and gene regulation through noncoding RNA. With a growing interest in exploring RNAs with specific structures, there is an increasing focus on designing RNA structures for in vivo and in vitro experimentation and for therapeutics.

Organic ammonium salt assisted crystallization and defect passivation of a quasi-two-dimensional pure blue perovskite at the buried interface.

Quasi-two-dimensional (quasi-2D) perovskites exhibit excellent performance in light-emitting diodes (LEDs). However, the quality of perovskite films prepared the solution method is significantly impacted by the enormous number of defects that unavoidably form at the grain boundaries and interfaces during the precursor to the crystal formation process. Here, we propose a strategy to assist perovskite crystallization and defect passivation at the buried interface through interfacial modification.

Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy.

Translation of upstream open reading frames (uORFs) typically abrogates translation of main (m)ORFs. The molecular mechanism of uORF regulation in cells is not well understood. Here, we data-mined human and mouse heart ribosome profiling analyses and identified a double-stranded RNA (dsRNA) structure within the GATA4 uORF that cooperates with the start codon to augment uORF translation and inhibits mORF translation.

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.

We show that design of DNA secondary structures is improved by extending the base pairing alphabet beyond A-T and G-C to include the pair between 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo-[1,2-]-1,3,5-triazin-(8)-4-one and 6-amino-3-(1'-β-d-2'-deoxyribofuranosyl)-5-nitro-(1)-pyridin-2-one, abbreviated as and . To obtain the thermodynamic parameters needed to include P-Z pairs in the designs, we performed 47 optical melting experiments and combined the results with previous work to fit free energy and enthalpy nearest neighbor folding parameters for P-Z pairs and G-Z wobble pairs. We find G-Z pairs have stability comparable to that of A-T pairs and should therefore be included as base pairs in structure prediction and design algorithms.

Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy.

Unlabelled: Translation of upstream open reading frames (uORFs) typically abrogates translation of main (m)ORFs. The molecular mechanism of uORF regulation in cells is not well understood. Here, we identified a double-stranded RNA (dsRNA) structure residing within the uORF that augments uORF translation and inhibits mORF translation.

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.

We show that design of DNA secondary structures is improved by extending the base pairing alphabet beyond A-T and G-C to include the pair between 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo-[1,2- ]-1,3,5-triazin-(8 )-4-one and 6-amino-3-(1'-β-D-2'-deoxyribofuranosyl)-5-nitro-(1 )-pyridin-2-one, simply P and Z. To obtain the thermodynamic parameters needed to include P-Z pairs in the designs, we performed 47 optical melting experiments and combined the results with previous work to fit a new set of free energy and enthalpy nearest neighbor folding parameters for P-Z pairs and G-Z wobble pairs. We find that G-Z pairs have stability comparable to A-T pairs and therefore should be considered quantitatively by structure prediction and design algorithms.

Integration of Antifouling and Underwater Sound Absorption Properties into PDMS/MWCNT/SiO Coatings.

Any surface immersed in sea water will suffer from marine fouling, including underwater sound absorption coatings. Traditional underwater sound absorption coatings rely heavily on the use of toxic, biocide-containing paints to combat biofouling. In this paper, an environmentally-friendly nanocomposite with integrated antifouling and underwater sound absorption properties was fabricated by adopting MWCNTs-COOH and SiO into PDMS at different ratios.

Intrinsically Unstructured Sequences in the mRNA 3' UTR Reduce the Ability of Poly(A) Tail to Enhance Translation.

The 5' cap and 3' poly(A) tail of mRNA are known to synergistically stimulate translation initiation via the formation of the cap•eIF4E•eIF4G•PABP•poly(A) complex. Most mRNA sequences have an intrinsic propensity to fold into extensive intramolecular secondary structures that result in short end-to-end distances. The inherent compactness of mRNAs might stabilize the cap•eIF4E•eIF4G•PABP•poly(A) complex and enhance cap-poly(A) translational synergy.

Screening of periodontitis-related genes and immune cells based on an integrated bioinformatics analysis.

Background: Periodontitis is a serious health issue; however, there are few reports on periodontitis and immune related. The study sought to analyze differences in gene expression between periodontitis patients before and after treatment using bioinformatics techniques.

Methods: The GSE6751 data set was screened for differentially expressed genes (DEGs) and immune-related genes using the Gene Expression Omnibus (GEO) database, a gene expression data analysis tool.

Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation.

Translating ribosomes unwind mRNA secondary structures by three basepairs each elongation cycle. Despite the ribosome helicase, certain mRNA stem-loops stimulate programmed ribosomal frameshift by inhibiting translation elongation. Here, using mutagenesis, biochemical and single-molecule experiments, we examine whether high stability of three basepairs, which are unwound by the translating ribosome, is critical for inducing ribosome pauses.

Agomelatine: An Astounding Sui-generis Antidepressant?

Major depressive disorder (MDD) is one of the foremost causes of disability and premature death worldwide. Although the available antidepressants are effective and well tolerated, they also have many limitations. Therapeutic advances in developing a new drug's ultimate relation between MDD and chronobiology, which targets the circadian rhythm, led to a renewed focus on psychiatric disorders.

Human umbilical cord mesenchymal stem cells-derived exosomal microRNA-181a retards nasopharyngeal carcinoma development by mediating KDM5C.

Objective: It has been studied that mesenchymal stem cells (MSCs)-derived exosomes could suppress tumor growth in nasopharyngeal carcinoma (NPC) and microRNA-181a (miR-181a) could mediate drug resistance in NPC. Focused on this work, the mechanism of human umbilical cord MSCs (hUC-MSCs)-derived exosomal miR-181a was explored in NPC cell progression.

Methods: NPC tissues and normal tissues were obtained from patients, and miR-181a and KDM5C expression was examined.

New application of an old drug proparacaine in treating epilepsy via liposomal hydrogel formulation.

Proparacaine (PPC) is a previously discovered topical anesthetic for ophthalmic optometry and surgery by blocking the central Nav1.3. In this study, we found that proparacaine hydrochloride (PPC-HCl) exerted an acute robust antiepileptic effect in pilocarpine-induced epilepsy mice.

[Performance and Microbial Characteristics of Ammonium-limited and Nitrite-limited ANAMMOX Systems].

The performance and microbial characteristics of ammonium-limited and nitrite-limited ANAMMOX reactors were studied in two continuously stirred tank reactors. The influent TN concentrations were controlled below 50 mg·L. The hydraulic retention time and water temperature were maintained at 2.

The multidrug resistance can be reversed for the decrease of P-gp and LRP by inhibiting PI3K/Akt/NF-κB signal pathway in nasopharynx carcinoma.

Aim: To investigate the relationship between PI3K/Akt/NF-κB cellular signal pathway and the expression of P-gp and LRP in multidrug resistance (MDR) cell of nasopharyngeal carcinoma.

Method: The PI3K, p-Akt and NF-κB/p65 as the activity of PI3K/Akt/NF-κB were detected by Western blot. The expressions of LRP and P-gp were detected by Western blot and real-time PCR.

[Effects of topical application of doxycycline on avulsed permanent teeth].

Purpose: To evaluate the treatment effect of topical doxycycline on avulsed permanent teeth compared with normal saline.

Methods: A total of 44 avulsed teeth from 38 patients (22 boys and 16 girls, aged 7-14 years) were recruited. Twenty-one teeth in group A were treated with doxycycline for 5 min before replantation while 23 teeth in group B were treated with saline solution.

The Preference for Joint Attributions Over Contrast-Factor Attributions in Causal Contrast Situations.

A current issue about causal attribution is whether people take simple contrast-factor attributions or complex joint attributions in contrast situations. For example, a stone does not dissolve in water and a piece of salt dissolves in water. That the piece of salt dissolves in water is due to: (A) the influence of the piece of salt; (B) the influence of the water; (C) the joint influence of the piece of salt and the water.

Evidence for the Jeffrey Table.

Conditionals statements are a common and necessary component in natural languages. The research reported in this paper is on a fundamental question about singular conditionals. Is there an adequate account of people's truth, falsity, and credibility (probability) judgments about these conditionals when their antecedents are false? Two experiments examined people's quantitative credibility ratings and qualitative truth and falsity judgments for singular conditionals, , given false antecedent, , cases.

Astaxanthin Combine with Human Serum Albumin to Abrogate Cell Proliferation, Migration, and Drug-resistant in Human Ovarian Carcinoma SKOV3 Cells.

Background: Astaxanthin (AST) shows a large range of beneficial effects together with anti-cancer and antioxidation properties. Human Serum Albumin (HSA) is the most abundant protein in blood plasma which plays the role of a depot and transport protein for many exogenous compounds. However, whether HSA could enhance AST-induced cytotoxic effects in human ovarian cancer cells has not been examined to date.

Chemoreversal Metabolites from the Endophytic Fungus Penicillium citrinum Isolated from a Mangrove Avicennia marina.

Two new compounds, named (Z)-7,4'-dimethoxy-6-hydroxyaurone-4-O-β-glucopyranoside (1) and (-)-4-O-(4-O-β-D-glucopyranosylcaffeoyl)quinic acid (2), were isolated from the endophytic fungus Penicillium citrinum of Avicennia marina. Their structures were elucidated on the basis of spectroscopic analysis. Additionally, compound 2 exhibited potent chemoreversal activity, mainly by inhibiting P-glycoprotein efflux pump function.

[Effect of amount of silane coupling agent on flexural strength of dental composite resins reinforced with aluminium borate whisker].

Purpose: To evaluate the effect of amount of silane coupling agent on flexural strength of dental composite resins reinforced with aluminium borate whisker (ABW).

Methods: ABW was surface-treated with 0%, 1%, 2%, 3% and 4% silan coupling agent (γ-MPS), and mixed with resin matrix to synthesize 5 groups of composite resins. After heat-cured at 120 degrees centigrade for 1 h, specimens were tested in three-point flexure to measure strength according to ISO-4049.

[Analysis of Shanghai residents' cognition and approbation to dental practical clinic].

Purpose: To know about Shanghai residents' cognition and approbation to dental practical clinic and discuss the appropriate mode of clinical teaching.

Methods: 100 residents were chosen in five super-markets in five different districts randomly to fill in a questionnaire.

Results: 475 questionnaires were effective among 502 questionnaires and the efficiency was 94.

[Effect of different polishing time on microleakage of resin composite restorations].

Purpose: To evaluate the effect of different polishing time on microleakage of different resin composite restorations (Filtek Z350 and Filtek Z250).

Methods: Standardized preparation (the box-type cavities, 3 mm in length and width,2 mm in depth) was performed at the cemento-enamel junction on buccal surface of 80 premolars.They were randomly divided into two groups,and restored with composite resin(Filtek Z350 or Filtek Z250).