Analysis of RNA translation with a deep learning architecture provides new insight into translation control.

Accurate annotation of coding regions in RNAs is essential for understanding gene translation. We developed a deep neural network to directly predict and analyze translation initiation and termination sites from RNA sequences. Trained with human transcripts, our model learned hidden rules of translation control and achieved a near perfect prediction of canonical translation sites across entire human transcriptome. Surprisingly, this model revealed a new role of codon usage in regulating translation termination, which was experimentally validated. We also identified thousands of new open reading frames in mRNAs or lncRNAs, some of which were confirmed experimentally. The model trained with human mRNAs achieved high prediction accuracy of canonical translation sites in all eukaryotes and good prediction in polycistronic transcripts from prokaryotes or RNA viruses, suggesting a high degree of conservation in translation control. Collectively, we present a general and efficient deep learning model for RNA translation, generating new insights into the complexity of translation regulation.

5†kW power-level 1050†nm narrow-linewidth fiber amplifier enabled by biconical-tapered active fiber.

Effective wavelength extension is vital in the applications of high-power narrow-linewidth fiber lasers. In this work, we demonstrate a 5-kW power-level narrow-linewidth fiber amplifier at 1050 nm utilizing a homemade biconical-tapered Yb-doped fiber (BT-YDF). Up to ∼4.96 kW fiber laser is achieved with a 3 dB linewidth of ∼0.54 nm and a beam quality factor of Mx 2 = 1.46, My 2 = 1.6. The experimental comparisons reveal that BT-YDF has the advantages of improving a stimulated Raman scattering threshold and balancing transverse mode instability suppression in the fiber amplifier. This work could provide a good reference for extending the operating wavelength of high-power fiber amplifiers.

Femtosecond laser direct writing large-area fiber Bragg grating based on diaphragm shaping.

We propose and demonstrate a new method of direct writing large-area fiber Bragg grating by femtosecond laser through the coating. By adding an adjustable diaphragm before the focusing objective, we can precisely control the length of the refractive index modulation line along the femtosecond laser incident direction up to 29.1 µm. In combination with femtosecond laser scanning fabrication technology, a uniform refractive index modulation plane can be inscribed in the fiber in a single scanning. Based on the plane-by-plane inscription method, we have fabricated a high-quality high-reflectivity fiber Bragg grating and a chirped fiber Bragg grating on 20/400 double-clad fiber core. The reflectivity of both gratings is greater than 99%, and the insertion loss is as low as 0.165 dB and 0.162 dB, respectively. The thermal slope of chirped fiber Bragg grating without any refrigeration is 0.088 °C/W and there is no obvious temperature increase when using the water cooling. Therefore, the fabrication method of large-area fiber Bragg grating based on diaphragm shaping can efficiently fabricate high-quality fiber Bragg grating in the large core diameter fiber, which has an important application prospect in high-power all-fiber oscillators, especially all-fiber oscillators in special wavebands.

Demonstration of hundred-watt-level near-diffraction-limited monolithic fiber laser near 980 nm with step-index double-cladding Yb-doped fiber.

In this paper, a hundred-watt-level near-diffraction-limited step-index Yb-doped fiber (YDF) laser near 980 nm is demonstrated firstly, to the best of our knowledge. By using the 11.7-W 979-nm single-mode seed light, the in-band amplified spontaneous emission (ASE) is well suppressed and the maximum output power of 101.5 W with the beam quality (M2 factor) of 1.285 was obtained. This work does not only propose an effective method for the suppression of in-band ASE, but also provides a cost-effective solution of hundred-Watt-level near-diffraction-limited fiber lasers near 980 nm.

Comparison of conventional (basketing + dusting) and Moses (pop-dusting) holmium lasers during flexible ureteroscopy in the treatment of renal stones between 2 and 3 cm: a randomized clinical trial.

To investigate the feasibility of conventional (basketing + dusting) and Moses (pop-dusting) holmium lasers during flexible ureteroscopy (FURS) in the treatment of 2-3 cm renal calculi and to compare the efficiency and safety of the two methods, a total of 230 patients with 2-3 cm kidney stones who underwent FURS were randomly divided into the conventional group and the Moses group. The mode of lithotripsy in the conventional group was fragmentation and dusting. The mode of lithotripsy in the Moses group was dusting and pop-dusting. Clinical and perioperative variables and complications were compared between the two cohorts. Multivariate analyses of factors contributing to the stone-free rate (SFR) and operation time were performed. No statistically significant differences were found in the demographics, renal stone-related data, SFR, or complications between the cohorts. The laser energy was higher in the Moses cohort than in the conventional cohort (119.3 ± 15.2 vs. 92.8 ± 15.1 kJ; P < 0.001), and the operation time was shorter in the Moses cohort than in the conventional cohort (99.5 ± 18.9 vs. 105.3 ± 13.7 min; P = 0.009). When there was isolated stone, the operation time was shorter in the Moses cohort than in the conventional cohort (99.6 ± 17.5 vs. 111.4 ± 10.7 min; P < 0.001), while there was no significant difference between the two cohorts when there were multiple stones (99.5 ± 20 vs. 101.2 ± 14 min; P = 0.415). Multivariate analyses found that an increase in stone volume can decrease the SFR and prolong the operation time, and use of a Moses laser can shorten the operation time. Both holmium laser modes during FURS can effectively treat 2-3 cm renal calculi. The Moses mode is recommended as the first choice for the treatment of isolated 2-3 cm renal stones. When treating multiple stones, the efficiency of these two laser modalities is the same. TRIAL REGISTRATION: ChiCTR2200056091.

Bone marrow lesion and 5-year incident joint surgery in patients with knee osteoarthritis: a retrospective cohort study.

BACKGROUND: It is beneficial for society to discover the risk factors associated with surgery and to carry out some early interventions for patients with these risk factors. Few studies specifically explored the relationship between bone marrow lesions (BMLs) and long-term incident joint surgery. OBJECTIVE: To investigate the association between BML severity observed in knee osteoarthritis (OA) patients' first MRI examination and incident knee surgery within 5 years. Additionally, to assess the predictive value of BMLs for the incident knee surgery. DESIGN: Retrospective cohort study. METHODS: We identified patients diagnosed with knee OA and treated at our institution between January 2015 and January 2018, and retrieved their baseline clinical data and first MRI examination films from the information system. Next, we proceeded to determine the Max BML grades, BML burden grades and Presence BML grades for the medial, lateral, patellofemoral, and total compartments, respectively. Multi-variable logistic regression models examined the association of the BML grades with 5-year incident knee surgery. Positive and negative predictive values (PPVs and NPVs) were determined for BML grades referring to 5-year incident knee surgery. RESULTS: Totally, 1011 participants (knees) were found eligible to form the study population. Within the 5 years, surgery was performed on 74 knees. Max BML grade 2 and grade 3 of medial, patellofemoral and total compartments were strongly and significantly associated with incident surgery. None of the BML grades from lateral compartment was associated with incident surgery. The PPV was low and NPV was high for BMLs. CONCLUSIONS: BMLs found in the first MRI examination were associated with 5-year incident joint surgery, except for those allocated in lateral compartments. The high NPVs imply that patients without BMLs have a low risk of requiring surgery within 5 years.

A novel nerol-segmented waterborne polyurethane coating for the prevention of dental erosion.

Dental erosion is a common problem in dentistry, and it refers to the chronic pathological loss of dental hard tissues due to nonbacterially produced acids, primarily caused by the exposure of teeth to exogenous acids. Dietary factors play a pivotal part in the pathogenesis of dental erosion, with a high intake of acidic beverages leading to an increased prevalence of dental erosion in adolescents. Fluoride is mainly used in clinical practice to prevent dental erosion. However, long-term fluoride intake may lead to chronic fluorosis symptoms caused by fluoride overdose. Nano-coatings on dental surfaces have become a popular area of research in dental materials in recent years. The objective of this study was to develop a novel nerol-segmented waterborne polyurethane nano-coating to protect teeth from direct contact with an acidic environment and to provide a safe, effective method for preventing dental acid erosion.

Synthetic Cells from Droplet-Based Microfluidics for Biosensing and Biomedical Applications.

Synthetic cells function as biological mimics of natural cells by mimicking salient features of cells such as metabolism, response to stimuli, gene expression, direct metabolism, and high stability. Droplet-based microfluidic technology presents the opportunity for encapsulating biological functional components in uni-lamellar liposome or polymer droplets. Verified by its success in the fabrication of synthetic cells, microfluidic technology is widely replacing conventional labor-intensive, expensive, and sophisticated techniques justified by its ability to miniaturize and perform batch production operations. In this review, an overview of recent research on the preparation of synthetic cells through droplet-based microfluidics is provided. Different synthetic cells including lipid vesicles (liposome), polymer vesicles (polymersome), coacervate microdroplets, and colloidosomes, are systematically discussed. Efforts are then made to discuss the design of a variety of microfluidic chips for synthetic cell preparation since the combination of microfluidics with bottom-up synthetic biology allows for reproductive and tunable construction of batches of synthetic cell models from simple structures to higher hierarchical structures. The recent advances aimed at exploiting them in biosensors and other biomedical applications are then discussed. Finally, some perspectives on the challenges and future developments of synthetic cell research with microfluidics for biomimetic science and biomedical applications are provided.

Atrial lead perforation early after device implantation-a case report and literature review.

We report three patients with screw-in lead perforation in the right atrial free wall not long after device implantation. All the patients complained of intermittent stabbing chest pain associated with deep breathing during the implantation. The "dry" epicardial puncture was utilized to avoid hemopericardium during lead extraction in the first case. The atrial electrode was repositioned in all cases and replaced by a new passive fixation lead in two patients with resolution of the pneumothorax or pericardial effusion. A literature review of 50 reported cases of atrial lead perforation was added to the findings in our case report.

Cascaded All-Fiber Gas Raman Laser Oscillator in Deuterium-Filled Hollow-Core Photonic Crystal Fibers.

Hollow-core photonic crystal fibers (HC-PCFs) provide an ideal transmission medium and experimental platform for laser-matter interaction. Here, we report a cascaded all-fiber gas Raman laser based on deuterium (D2)-filled HC-PCFs. D2 is sealed into a gas cavity formed by a 49 m-long HC-PCF and solid-core fibers, and two homemade fiber Bragg gratings (FBGs) with the Raman and pump wavelength, respectively, are further introduced. When pumped by a pulsed fiber amplifier at 1540 nm, the pure rotational stimulated Raman scattering of D2 occurs inside the cavity. The first-order Raman laser at 1645 nm can be obtained, realizing a maximum power of ~0.8 W. An all-fiber cascaded gas Raman laser oscillator is achieved by adding another 1645 nm high-reflectivity FBG at the output end of the cavity, reducing the peak power of the cascaded Raman threshold by 11.4%. The maximum cascaded Raman power of ~0.5 W is obtained when the pump source is at its maximum, and the corresponding conversion efficiency inside the cavity is 21.4%, which is 1.8 times that of the previous configuration. Moreover, the characteristics of the second-order Raman lasers at 1695 nm and 1730 nm are also studied thoroughly. This work provides a significant method for realizing all-fiber cascaded gas Raman lasers, which is beneficial for expanding the output wavelength of fiber gas lasers with a good stability and compactivity.

Circular RNA vaccines against monkeypox virus provide potent protection against vaccinia virus infection in mice.

Since the outbreak of monkeypox (mpox) in 2022, widespread concern has been placed on imposing an urgent demand for specific vaccines that offer safer and more effective protection. Using an efficient and scalable circular RNA (circRNA) platform, we constructed four circRNA vaccines that could induce robust neutralizing antibodies as well as T cell responses by expressing different surface proteins of mpox virus (MPXV), resulting in potent protection against vaccinia virus (VACV) in mice. Strikingly, the combination of the four circular RNA vaccines demonstrated the best protection against VACV challenge among all the tested vaccines. Our study provides a favorable approach for developing MPXV-specific vaccines by using a circular mRNA platform and opens up novel avenues for future vaccine research.

2 W, 1.5†µm single-mode fiber methane Raman laser pumped by a Yb-doped fiber amplifier.

We report here, to the best of our knowledge, the first 1.5 µm methane-filled fiber Raman laser pumped by a fiber laser. Based on the narrow-linewidth pulsed Yb-doped fiber laser pump source and a 15 m hollow-core fiber filled with 2.5 bar methane, the maximum power of 2.06 W Stokes wave at 1543 nm is obtained. The output laser has a narrow linewidth of 2.3 GHz, and the pulse repetition frequency can be adjusted flexibly. The output shows excellent near-diffraction-limited beam quality with a M2 factor of ∼1.09. This work proves the advantage of the fiber laser pump source with modest peak power and flexible temporal characteristics in 1.5 µm fiber gas Raman laser emission, providing good guidance for generating pulsed fiber source with narrow linewidth and high beam quality.

Requirements on double-cladding Yb-doped fiber for power scaling of diffraction-limited fiber amplifiers.

Requirements on the double-cladding Yb-doped fiber (DCYF) for power scaling of diffraction-limited fiber amplifiers are studied in this paper. By considering the limitations of thermal lens and transverse mode instability separately, it is found that the power scaling limit can be enlarged to more-than 100 kW and 80 kW, respectively, with the proper selection of pump and signal wavelengths. It is also found that the requirements on DCYF strongly depend on the wavelength and brightness of pump light. It is predicted that smaller-than 20-µm core diameter is required to achieve the 20-kW output power, as long as the 976-nm pump brightness can be high enough. The requirements on the inner-cladding diameter and cladding-to-core ratio of DCYF are also investigated.

Rapid multiple protein sequence search by parallel and heterogeneous computation.

MOTIVATION: Protein sequence database search and multiple sequence alignment generation is a fundamental task in many bioinformatics analyses. As the data volume of sequences continues to grow rapidly, there is an increasing need for efficient and scalable multiple sequence query algorithms for super-large databases without expensive time and computational costs. RESULTS: We introduce Chorus, a novel protein sequence query system that leverages parallel model and heterogeneous computation architecture to enable users to query thousands of protein sequences concurrently against large protein databases on a desktop workstation. Chorus achieves over 100× speedup over BLASTP without sacrificing sensitivity. We demonstrate the utility of Chorus through a case study of analyzing a ∼1.5-TB large-scale metagenomic datasets for novel CRISPR-Cas protein discovery within 30 min. AVAILABILITY AND IMPLEMENTATION: Chorus is open-source and its code repository is available at https://github.com/Bio-Acc/Chorus.

Deep learning model for the detection of prostate cancer and classification of clinically significant disease using multiparametric MRI in comparison to PI-RADs score.

BACKGROUND: The Prostate Imaging Reporting and Data System (PI-RADS) is an established reporting scheme for multiparametric magnetic resonance imaging (mpMRI) to distinguish clinically significant prostate cancer (csPCa). Deep learning (DL) holds great potential for automating csPCa classification on mpMRI. METHOD: To compare the performance between a DL algorithm and PI-RADS categorization in PCa detection and csPCa classification, we included 1,729 consecutive patients who underwent radical prostatectomy or biopsy in Tongji hospital. We developed DL models by integrating individual mpMRI sequences and employing an ensemble approach for distinguishing between csPCa and CiSPCa (specifically defined as PCa with a Gleason group 1 or benign prostate disease, training cohort: 1,285 patients vs. external testing cohort: 315 patients). RESULTS: DL-based models exhibited higher csPCa detection rates than PI-RADS categorization (area under the curve [AUC]: 0.902; sensitivity: 0.728; specificity: 0.906 vs. AUC: 0.759; sensitivity: 0.761; specificity: 0.756) (P < 0.001) Notably, DL networks exhibited significant strength in the prostate-specific antigen (PSA) arm < 10 ng/ml compared with PI-RADS assessment (AUC: 0.788; sensitivity: 0.588; specificity: 0.883 vs. AUC: 0.618; sensitivity: 0.379; specificity: 0.763) (P = 0.041). CONCLUSIONS: We developed DL-based mpMRI ensemble models for csPCa classification with improved sensitivity, specificity, and accuracy compared with clinical PI-RADS assessment. In the PSA-stratified condition, the DL ensemble model performed better than PI-RADS in the detection of csPCa in both the high PSA group and the low PSA group.

A nanoporous organic polymer using 1, 3-dibromoadamantane as a crosslinker for adsorption/separation of benzene and cyclohexane.

The development of nanoporous organic polymers with cycloaliphatic components for effective benzene (Bz) and cyclohexane (Cy) adsorption/separation poses a significant challenge. This work focuses on synthesizing NOP-Ad-1, a nanoporous organic polymer derived from a Friedel-Crafts reaction between cycloaliphatic 1,3-dibromadantane and aromatic hexaphenylbenzene. At 298 K and P/P0 = 0.95, NOP-Ad-1 can uptake 989 mg g-1 benzene and 441 mg g-1 cyclohexane. Moreover, as the benzene vapor ratio increased from 20% to 80%, the Bz/Cy selectivity of NOP-Ad-1 gradually decreased from 1.75 to 1.24. These findings highlight the potential application of NOP-Ad-1 in the adsorption/separation of Bz/Cy mixtures.

EXO1/P53/SREBP1 axis-regulated lipid metabolism promotes prostate cancer progression.

Prostate cancer (PCa) is one of the most common malignant tumors affecting the male genitourinary system. However, there is currently a lack of effective treatments for patients with advanced prostate cancer, which significantly impacts men's overall health. Exonuclease 1 (EXO1), a protein with mismatch repair and recombination functions, has been found to play a vital role in various diseases. In our study, we discovered that EXO1 acts as a novel biomarker of PCa, which promotes prostate cancer progression by regulating lipid metabolism reprogramming in prostate cancer cells. Mechanistically, EXO1 promotes the expression of SREBP1 by inhibiting the P53 signaling pathway. In summary, our findings suggest that EXO1 regulated intracellular lipid reprogramming through the P53/SREBP1 axis, thus promoting PCa progression. The result could potentially lead to new insights and therapeutic targets for diagnosing and treating PCa.

Growth, Spectroscopy, and Laser Performance of a 2.79 µm Er: YSGG Single Crystal Fibers.

Single crystal fibers combine the great specific surface area of fibers and the single crystal property of the bulk crystal which shows great potential for a high-power laser. For an Er-doped crystal, due to the fluorescence quenching at the 3 µm wavelength, high Er doping is necessary to increase the fluorescent up-conversion for the breaking limitation. However, a high Er doping concentration must lead to high heat accumulation, resulting in poor laser performance. Compared with an Er-doped bulk crystal, Er-doped SCF has the great potential to remove the heat in the crystal, and it is easy to obtain a high power. In this paper, Er: Y3Sc2Ga3O12 (Er: YSGG) single crystals were successfully grown using the micro-pulling-down method (µ-PD). Owing to the stably grown interface, the diameter of the crystal is 2 mm with a length up to 80 mm. Then, the measurements of Laue spots and Er3+ distribution indicated that our crystals have a high quality. Based on the as-prepared Er: YSGG SCF, the continuous-wave (CW) laser operations at 2794 nm were realized. The maximum output was 166 mW with a slope efficiency of up to 10.99%. These results show that Er: YSGG SCF is a suitable material for future high-power 3 µm laser operation.