m5UMCB: Prediction of RNA 5-methyluridine sites using multi-scale convolutional neural network with BiLSTM.

As a prevalent RNA modification, 5-methyluridine (m5U) plays a critical role in diverse biological processes and disease pathogenesis. High-throughput identification of m5U typically relies on labor-intensive biochemical experiments using various sequencing-based techniques, which are not only time-consuming but also expensive. Consequently, there is a pressing need for more efficient and cost-effective computational methods to complement these high-throughput techniques. In this study, we present m5UMCB, a novel approach that harnesses a multi-scale convolutional neural network (CNN) in tandem with bidirectional long short-term memory (BiLSTM) to recognize m5U sites. Our method involves segmenting RNA sequences into smaller fragments based on a 3-mer length and subsequently mapping each fragment to a lower-dimensional vector representation using the global vectors for word representation (GloVe) technique. Through a series of multi-scale convolution and pooling operations, local features are extracted from RNA sequences and transformed into abstract, high-level features. The feature matrix is then inputted into a BiLSTM network, enabling the capture of contextual information and long-term dependencies within the sequence. Ultimately, a fully connected layer is employed to classify m5U sites. The validation results from 5-fold cross-validation (5-fold CV) test indicate that m5UMCB outperforms existing state-of-the-art predictive methods, demonstrating a 1.98% increase in the area under ROC curve (AUC) and significant improvements in relevant evaluation metrics. We are confident that m5UMCB will serve as a valuable tool for m5U prediction.

CRISPR Cas12a-Powered Silicon Surface-Enhanced Raman Spectroscopy Ratiometric Chip for Sensitive and Reliable Quantification.

Sensitive and reliable clustered regularly interspaced short palindromic repeats (CRISPR) quantification without preamplification of the sample remains a challenge. Herein, we report a CRISPR Cas12a-powered silicon surface-enhanced Raman spectroscopy (SERS) ratiometric chip for sensitive and reliable quantification. As a proof-of-concept application, we select the platelet-derived growth factor-BB (PDGF-BB) as the target. We first develop a microfluidic synthetic strategy to prepare homogeneous silicon SERS substrates, in which uniform silver nanoparticles (AgNPs) are in situ grown on a silicon wafer (AgNPs@Si) by microfluidic galvanic deposition reactions. Next, one 5'-SH-3'-ROX-labeled single-stranded DNA (ssDNA) is modified on AgNPs via Ag-S bonds. In our design, such ssDNA has two fragments: one fragment hybridizes to its complementary DNA (5'-Cy3-labeled ssDNA) to form double-stranded DNA (dsDNA) and the other fragment labeled with 6'-carboxy-X-rhodmine (ROX) extends out as a substrate for Cas12a. The cleavage of the ROX-tagged fragment by Cas12a is controlled by the presence or not of PDGF-BB. Meanwhile, Cy3 molecules serving as internal standard molecules still stay at the end of the rigid dsDNA, and their signals remain constant. Thereby, the ratio of ROX signal intensity to Cy3 intensity can be employed for the reliable quantification of PDGF-BB concentration. The developed chip features an ultrahigh sensitivity (e.g., the limit of detection is as low as 3.2 pM, approximately 50 times more sensitive than the fluorescence counterpart) and good reproducibility (e.g., the relative standard deviation is less than 5%) in the detection of PDGF-BB.

Surface-enhanced Raman scattering holography chip for rapid, sensitive and multiplexed detection of human breast cancer-associated MicroRNAs in clinical samples.

MicroRNAs (miRNAs) are promising biomarkers for the early diagnosis of breast cancer. Yet, simultaneous achievement of rapid, sensitive and accurate detection of diverse miRNAs in clinical samples is still challenging due to the low abundance of miRNAs and the complex procedures of RNA extraction and separation. Herein, we develop an innovative three-dimensional (3D) surface-enhanced Raman scattering (SERS) holography sensing strategy for rapid, sensitive and multiplexed detection of human breast cancer-associated miRNAs. To establish a proof of concept, nine kinds of human breast cancer-associated miRNAs are isothermally amplified by Exonuclease (Exo) III enzyme, and the products could be spatially separated to corresponding sensing region on silicon SERS substrates. Each region has been modified with corresponding hairpin DNA probes, which are used to identify and quantify the miRNAs. Different DNA probes are labeled with different Raman reporters, which serve as "SERS tags" to incorporate spectroscopic information into computer-generated 3D SERS hologram within ~9 min. We demonstrate that 3D SERS holography chip not only achieves an ultrahigh sensitivity down to ~1 aM but also feature a high correlation with RT-qPCR in the detection of nine miRNAs in 30 clinical serum samples. This work provides a feasible tool to improve the diagnosis of breast cancer.

Integrin-Linked Kinase (ILK) Regulates Urinary Stem Cells Differentiation into Smooth Muscle via NF-κB Signal Pathway.

OBJECTIVES: Urinary stem cells (USCs) have the capacity for unlimited growth and are promising tools for the investigations of cell differentiation and urinary regeneration. However, the limited life span significantly restricts their usefulness. This study is aimed at exploring the effect of integrin-linked kinase (ILK) on the smooth muscle cells (SMCs) differentiation of the dog USCs and investigating its molecular mechanism. METHODS: An immortalized USCs cell line with the molecular markers and biological functions was prepared. After successfully inducing the differentiation of USCs into SMCs, the expression level of the unique key factor and its mechanisms in this process was determined through real-time polymerase chain reaction, Western blot, or Immunofluorescence staining. RESULTS: We found that high cell density promoted USCs differentiation SMCs, and ILK was necessary for USCs differentiation into SMCs. Knocking down ILK decreased the expression of SMCs specific-marker, while using a selective ILK agonist increased the expression of SMCs specific-marker. Furthermore, ILK regulated SMCs differentiation in part through the activation of NF-κB pathway in USCs. A NF-κB activity assay showed overexpression of ILK could significantly upregulate NF-κB p50 expression, and NF-κB p50 acts as downstream signal molecular of ILK. CONCLUSION: High cell density induces the differentiation of USCs into SMCs, and ILK is a key regulator of myogenesis. Furthermore, NF-κB signaling pathway might play a crucial role in this process.

Puerarin ameliorated pressure overload-induced cardiac hypertrophy in ovariectomized rats through activation of the PPARα/PGC-1 pathway.

Estrogen deficiency induces cardiac dysfunction and increases the risk of cardiovascular disease in postmenopausal women and in those who underwent bilateral oophorectomy. Previous evidence suggests that puerarin, a phytoestrogen, exerts beneficial effects on cardiac function in patients with cardiac hypertrophy. In this study, we investigated whether puerarin could prevent cardiac hypertrophy and remodeling in ovariectomized, aortic-banded rats. Female SD rats subjected to bilateral ovariectomy (OVX) plus abdominal aortic constriction (AAC). The rats were treated with puerarin (50 mg·kg-1 ·d-1, ip) for 8 weeks. Then echocardiography was assessed, and the rats were sacrificed, their heart tissues were extracted and allocated for further experiments. We showed that puerarin administration significantly attenuated cardiac hypertrophy and remodeling in AAC-treated OVX rats, which could be attributed to activation of PPARα/PPARγ coactivator-1 (PGC-1) pathway. Puerarin administration significantly increased the expression of estrogen-related receptor α, nuclear respiratory factor 1, and mitochondrial transcription factor A in hearts. Moreover, puerarin administration regulated the expression of metabolic genes in AAC-treated OVX rats. Hypertrophic changes could be induced in neonatal rat cardiomyocytes (NRCM) in vitro by treatment with angiotensin II (Ang II, 1 µM), which was attenuated by co-treatemnt with puerarin (100 µM). We further showed that puerarin decreased Ang II-induced accumulation of non-esterified fatty acids (NEFAs) and deletion of ATP, attenuated the Ang II-induced dissipation of the mitochondrial membrane potential, and improved the mitochondrial dysfunction in NRCM. Furthermore, addition of PPARα antagonist GW6471 (10 µM) partially abolished the anti-hypertrophic effects and metabolic effects of puerarin in NRCM. In conclusion, puerarin prevents cardiac hypertrophy in AAC-treated OVX rats through activation of PPARα/PGC-1 pathway and regulation of energy metabolism remodeling. This may provide a new approach to prevent the development of heart failure in postmenopausal women.

Ultrasensitive Paper-Based Photoelectrochemical Sensing Platform Enabled by the Polar Charge Carriers-Created Electric Field.

Efficient separation of electron-hole pairs is vitally crucial to enhancing the analytical performance of paper-based photoelectrochemical (PEC) bioanalysis. Herein, a simple but effective strategy is developed to modulate the effective separation of photogenerated electrons and holes via introducing a polar charge carriers-created (PCC) electric field induced by a classical perovskite ferroelectric BaTiO3 (BTO). By inserting it between the n-type WO3 nanoflakes and p-type Cu2O (WO3 nanoflakes/BTO/Cu2O), the photoelectrode is endowed with a renewable PCC electric field, as a sustaining driving force, to guarantee the realization of directional separation of charge carrier (DSCC) strategy in PEC bioanalysis. The enduring PCC electric field can attract the electrons of Cu2O and holes of WO3, respectively, thereby regulating the directional migration of charge carriers and achieving an enhanced PEC photocurrent for the ultrasensitive quantification based on the highly efficient separation of electron-hole pairs. Consequently, with respect to WO3 nanoflakes/Cu2O and WO3 nanoflakes photoelectrode, the polarized WO3 nanoflakes/BTO/Cu2O photoelectrode exhibits 1.7 and 10.9 times higher photocurrent density, respectively. Benefiting from this, the prominent photocurrent density is obtained which is extremely beneficial for enhancing the sensitivity of PEC bioanalysis. Ultimately, the ultrasensitive detection of model prostate specific antigen (PSA) is realized and presents a linear range of 0.1 pg/mL-50 ng/mL with the detection limitation of 0.036 pg/mL. This work provides the basis for understanding the role of the polarized electric field induced by ferroelectric in tuning the charge separation as well as insights on strategies for constructing high-performance paper-based PEC bioanalysis.

[Circumcision reduces the incidence of human papillomavirus infection in men].

OBJECTIVE: To investigate the association of circumcision with the incidence of human papillomavirus (HPV) infection in men. METHODS: We collected the samples from the surface of the coronal sulcus, glans penis, penile shaft and scrotum of 351 males examined for HPV infection in our hospital from January 2016 to August 2017, of whom 118 had received circumcision while the other 233 had not. We compared the incidence rate of HPV infection between the circumcision and non-circumcision groups and analyzed the association of the age of circumcision with the incidence of HPV infection. RESULTS: HPV infection was found in 135 (38.46%) of the males, 29 (24.58%) in the circumcision group and 106 (45.49%) in the non-circumcision group, significantly lower in the former than in the latter (χ² = 14.48, P < 0.01). The incidence rate of HPV infection was also remarkably lower in the males circumcised at ≤17 years (13.16% ï¼»5/38ï¼½) than in those circumcised at >17 years of age (30.0% ï¼»24/80ï¼½) (χ² = 3.942, P = 0.047). CONCLUSIONS: Male circumcision helps reduce the incidence rate of HPV infection in men and earlier surgery may achieve even better effect.

[Penile erectile strength measurement band for differentiation and classification of erectile dysfunction].

OBJECTIVE: To study the clinical application value of the penile erectile strength measurement (PESM) band in the differentiation of psychogenic from organic erectile dysfunction (ED). METHODS: Eighty ED patients unable to achieve or maintain adequate penile erection to complete sexual intercourse were included in the experimental group and another 40 healthy subjects with normal erectile function enrolled as controls. The ED cases were classified into mild, moderate and severe ED according to the IIEF-5 scores and divided into psychogenic and organic ED based on the results of the nocturnal penile tumescence (NPT) test. Then all the subjects underwent a three-night continuous monitoring with the PESM band and, according to the band fracture rate, the ED cases were also classified into psychogenic and organic ED. The rates of missed diagnosis, misdiagnosis and diagnostic coincidence of PESM were calculated with the results of NPT as the standard for differentiating psychogenic from organic ED. RESULTS: The results of NPT tests revealed 51 cases of psychogenic and 29 cases of organic ED in the experimental group. The band fracture rate in PESM was 95.0% in the mild, 80.9% in the moderate and 52.8% in the severe ED patients. Of the 51 cases of psychogenic ED detected by NPT test, 43 were diagnosed as psychogenic and the other 8 as organic ED with the PESM band, with a coincidence rate of 84.3%. Of the 29 cases of organic ED revealed by NPT test, 5 were diagnosed as psychogenic and the other 24 as organic ED by PESM, with a coincidence rate of 82.8%. Normal erectile function with three-level fracture of the band was observed in the PESM of the normal controls, which showed a coincidence rate of 100% with the results of NPT tests. Based on the standard of the NPT test, the rates of missed diagnosis, misdiagnosis and diagnostic coincidence of the PESM band in differentiating psychogenic from organic ED were 15.7%, 17.2%, and 83.8%, respectively, with a Kappa value of 0.656 (P <0.05). CONCLUSIONS: The penile erectile strength measurement band can be used as a screening tool for initial differentiation of psychogenic from organic ED.

[Value of the serum free testosterone level in detecting erectile dysfunction].

OBJECTIVE: To investigate the values of serum calculated free testosterone (cFT), testosterone secretion index (TSI), and free testosterone index (FTI) in the diagnosis of ED with androgen deficiency by observing their changes in the patient. METHODS: We conducted this study among 185 men complaining of ED and 35 20－40 years old healthy males presenting at the clinic for premarital medical checkup. We asked them about their medical history, to fill in the International Index of Erectile Function (IIEF-5) Questionnaire, and to complete the nocturnal penile tumescence (NPT) test. According to the data obtained, 150 of the complainants were diagnosed as ED patients and 25 of the healthy examinees were included in the control group. We determined the levels of total serum testosterone (TT), luteinizing hormone (LH), sex hormone-binding globulin (SHBG), serum albumin (ALB), cFT, bio-available testosterone (bio-T), TSI, and FTI in the two groups of subjects. Using cFT ≤0.3 nmol/L, TSI ≤2.8, and FTI ≤0.4 as the critical values and TT ≤11.5 nmol/L as the gold standard for androgen deficiency, we calculated cFT-, TSI-, and FTI-related rates of missed diagnosis, misdiagnosis, and diagnostic coincidence. RESULTS: With TT ≤11.5 nmol/L as the criterion, the cFT-, TSI-, and FTI-related rates of coincidence in the diagnosis of androgen deficiency in the ED patients were 90.8%, 85.8%, and 80.8%, those of missed diagnosis were 4.0%, 33.3%, and 44.0%, and those of misdiagnosis were 10.5%, 19.4%, and 12.6%, with the Kappa of values 0.755, 0.564, and 0.427, respectively (P <0.05). The levels of serum TT, cFT, Bio-T, TSI, and FTI were decreased with increased age of the 20－40 years old ED patients, with statistically significant differences among different age groups except the serum TT level. However, no statistically significant differences were found in the levels of TT, cFT, Bio-T, TSI, and FTI among the patients with different IIEF-5 scores. CONCLUSIONS: The level of cFT has a higher value than those of TT, TSI, and TSI in the diagnosis of ED with androgen deficiency in 20－40 years old men.

Kinetics and mechanism of alkaline decomposition of the pentathionate ion by the simultaneous tracking of different sulfur species by high-performance liquid chromatography.

Alkaline decomposition of pentathionate has been investigated by high-performance liquid chromatography, which allows us to track different sulfur-containing species simultaneously in the presence of a carbonate/hydrogen carbonate buffer at 25.0 ± 0.1 °C and at a constant ionic strength. It has been shown that, besides the major product, thiosulfate, not only tetrathionate but also hexathionate appears in significant amounts during the course of the reaction. At higher pHs, both of them are unstable long-lived intermediates because of their well-known alkaline degradation, but a decrease of the pH increases their stability (especially that of tetrathionate), meaning that they may even become end products. On the basis of these observations, a 10-step kinetic model with five fitted and five fixed rate coefficients is suggested and discussed to take all of the most important characteristics of the decomposition into account. We have also demonstrated and discussed that the well-known thiosulfate-assisted rearrangement of pentathionate leading to hexathionate might only play a very minor role in the formation of hexathionate under our experimental conditions.

Investigations of different chemiluminescent peaks in H2O2-SCN(-)-Cu(2+)-OH(-)-luminol flow system.

In the H2O2-SCN(-) -Cu(2+)-OH(-)-luminol oscillatory system of chemiluminescence, the effects of the ingredient concentrations, temperature, flow rate and complexing agent on the oscillatory dynamics were investigated in a continuous-flow stirred tank reactor (CSTR). The dynamical structure of two peaks during a period was discussed in detail. By addition of EDTA to the oscillating system, the peak I height decreased sharply while the peak II height was little affected, and the period kept constant. This may be due to the fast reaction between Cu(II) and EDTA and the highly stable complex Cu(II)-EDTA. From the experimental study and mechanism analysis, the chemiluminescent peak I corresponds to Cu(II) → Cu(I) transformation and the peak II corresponds to the Cu(I) → Cu(II) transformation process. The key species involving in the two-transformation process are inferred to be superoxide radical and hydroxyl radical.

Precipitation patterns with polygonal boundaries between electrolytes.

Two-dimensional Liesegang patterns formed when the boundary between electrolytes is polygonal display a variety of patterns, such as dislocations (radial alleys of gaps), branches (anastomoses) and spirals, many of which can be found in nature. Each vertex of the polygon can produce a pair of dislocation lines or branch lines. The effect caused by a vertex decreases with the number of vertices. Double-armed spirals are observed in experiments with a pentagonal boundary. Hexagons, which begin to approach smooth circular boundaries, do not give rise to dislocations, but instead yield concentric precipitation rings. A simple model of nucleation growth enables us to simulate dislocations and spirals consistent with those seen in our experiments.

Temperature oscillations, complex oscillations, and elimination of extraordinary temperature sensitivity in the iodate-sulfite-thiosulfate flow system.

Temperature oscillations and complex pH oscillations in the IO(3)(-)-SO(3)(2-)-S(2)O(3)(2-) system were observed in a continuously flow stirred tank reactor. During one period of oscillation, the temperature increases rapidly while the pH shows an extremely sharp change. High-amplitude pH oscillations undergo 1(1) complex oscillations (L(S), oscillations with L large peaks and S small peaks per period) to another kind of higher-amplitude regular oscillations upon increasing the concentration of sulfite step by step. Importantly, the longstanding experimental phenomena, the extraordinary temperature sensitivity of oscillatory behavior reported 20 years ago by Rabai and Beck, can be eliminated by premixing of sulfite and sulfuric acid before entering into the reactor, avoiding local acidification, which brings out fluctuation and temperature sensitivity. The temperature oscillations can be understood by taking into account the interaction between thermal effect of various reactions and heat transfer. Experimental observations, both temperature oscillations and 1(1)-type pH oscillations, are reproduced with a four-step Horvath model by addition of an energy-balance equation. This new detailed dynamical behavior would have potential applications in designing complex chemical waves and pH responsive gels with rhythmical motion.