Tailoring fenestrated aneurysm clips intraoperatively: Instant solution for a difficult problem.

The anterior communicating artery (AcoA) aneurysms represent the most complex aneurysms of the anterior circulation. For years, surgical challenges including the intricate anatomy and narrow surgical corridor have been overcome using supplementary techniques including extended craniotomies, wide opening of the cisterns, gyrus rectus resection and special clips like fenestrated clips. However, imaginative solutions such as intraoperative clip modification may be inevitable in particular cases for safe clipping. We retrospectively analyzed clinical records of two patients who required clip modification intraoperatively. Case #1 underwent microsurgical clipping of a ruptured, 4-mm AcoA aneurysm. Unfortunately, given the short distance between the two A2s, it was not possible to clip the aneurysm without a compromise to the contralateral A2 with the available shortest 3mm-fenestrated clip. We then used the clip modification technique intraoperatively by shortening the clip tips with mesh-plaque cutter and smoothening the remaining sharp ends using cautery sanding. Eventually, the aneurysm was clipped successfully with the modified-fenestrated clip. Post-clipping imagings confirmed complete occlusion of the aneurysm and patency of parent arteries. Case 2# underwent microsurgical clipping for a ruptured, 1-mm AcoA aneurysm. Like Case 1#, the initial clipping attempt with the available shortest 4mm-fenestrated clip failed given the excessive length of the tips. The patient, thus, required clip modification as described above. The aneurysm was then clipped successfully using the modified-fenestrated clip, protecting bilateral A2s. Post-clipping imagings demonstrated patency of parent arteries with no residual aneurysm filling. Clip modification seems to be an effective option in clipping the AcoA aneurysms when available clips are too long to secure them safely.

The first report of a C-type lectin contains a CLIP domain involved in antibacterial defense in Macrobrachium nipponense.

We identified a novel C-type lectin (CTL) from Macrobrachium nipponense, designated as Mn-clip-Lec. It consists of 1315 bp with an open reading frame of 1098 bp, encoding a polypeptide of 365 amino acids. Mn-clip-Lec contains 6 exons and 5 introns. Mn-clip-Lec possessed a CLIP domain at the N-terminal and two carbohydrate recognition domains at the C-terminal. Interaction between Mn-clip-Lec and MnLec was found by Yeast two-hybrid analysis. The expressions of Mn-clip-Lec, MnLec, prophenoloxidase (proPO)-activating system-associated genes (MnPPAF, MnPPAE, and MnPO), and antimicrobial peptide (AMPs) (MnALF and MnCRU) were up-regulated after the challenge with Staphylococcus aureus. RNA interference (RNAi)-mediated suppression of the Mn-clip-Lec and MnLec genes in S. aureus-challenged prawns reduced the transcripts of MnPPAF, MnPPAE, MnPO, MnALF and MnCRU. Knockdown of Mn-clip-Lec and MnLec resulted in decrease in PO activity in M. nipponense infected with S. aureus. The recombinant Mn-clip-Lec (rMn-clip-Lec) protein bound all tested bacteria and agglutinated S. aureus. A sugar-binding assay revealed that rMn-clip-Lec could bind to LPS or PGN. rMn-clip-Lec accelerated the clearance of S. aureus in vivo. Our findings suggest that Mn-clip-Lec and its interacting MnLec play important roles in the induction of the proPO system and AMPs expression in M. nipponense during bacterial infection.

Endoscopic Management of Boerhaave Syndrome: Are Outcomes Better Than Surgery? A Case Report and Review of Literature.

Boerhaave syndrome (BS) is a rare clinical diagnosis associated with a high morbidity and mortality rate. Diagnosis of this condition is usually delayed which can lead to a very poor outcome. The timing of presentation and time to management plays a very important role in the prognosis and selection of the management method. With the advances seen in therapeutic endoscopy, many authors have been exploring the possibility of shifting the focus of management from surgery to interventional endoscopy. We present a case report of a patient presenting with BS that was successfully managed endoscopically. We also reviewed the literature on how surgical management compares to endoscopic management and attempted to establish general recommendations from available literature on management of BS.

Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data.

The uncovering of protein-RNA interactions enables a deeper understanding of RNA processing. Recent multiplexed crosslinking and immunoprecipitation (CLIP) technologies such as antibody-barcoded eCLIP (ABC) dramatically increase the throughput of mapping RNA binding protein (RBP) binding sites. However, multiplex CLIP datasets are multivariate, and each RBP suffers non-uniform signal-to-noise ratio. To address this, we developed Mudskipper, a versatile computational suite comprising two components: a Dirichlet multinomial mixture model to account for the multivariate nature of ABC datasets and a softmasking approach that identifies and removes non-specific protein-RNA interactions in RBPs with low signal-to-noise ratio. Mudskipper demonstrates superior precision and recall over existing tools on multiplex datasets and supports analysis of repetitive elements and small non-coding RNAs. Our findings unravel splicing outcomes and variant-associated disruptions, enabling higher-throughput investigations into diseases and regulation mediated by RBPs.

Partial coil embolization before surgical clipping of ruptured intracranial aneurysms.

OBJECTIVE: Intraoperative rupture (IOR) is the most common adverse event encountered during surgical clip obliteration of ruptured intracranial aneurysms. Besides increasing surgeon experience and early proximal control, no methods exist to decrease IOR risk. Thus, our objective was to assess if partial endovascular coil embolization to protect the aneurysm before clipping decreases IOR. METHODS: We conducted a retrospective analysis of patients with ruptured intracranial aneurysms that were treated with surgical clipping at two tertiary academic centers. We compared patient characteristics and outcomes of those who underwent partial endovascular coil embolization to protect the aneurysm before clipping to those who did not. The primary outcome was IOR. Secondary outcomes were inpatient mortality and discharge destination. RESULTS: We analyzed 100 patients. Partial endovascular aneurysm protection was performed in 27 patients. Age, sex, subarachnoid hemorrhage severity, and aneurysm location were similar between the partially-embolized and non-embolized groups. The median size of the partially-embolized aneurysms was larger (7.0 mm [interquartile range 5.95-8.7] vs. 4.6 mm [3.3-6.0]; P < 0.001). During surgical clipping, IOR occurred less frequently in the partially-embolized aneurysms than non-embolized aneurysms (2/27, 7.4%, vs. 30/73, 41%; P = 0.001). Inpatient mortality was 14.8% (4/27) in patients with partially-embolized aneurysms and 28.8% (21/73) in patients without embolization (P = 0.20). Discharge to home or inpatient rehabilitation was 74.0% in patients with partially-embolized aneurysms and 56.2% in patients without embolization (P = 0.11). A complication from partial embolization occurred in 2/27 (7.4%) patients. CONCLUSIONS: Preoperative partial endovascular coil embolization of ruptured aneurysms is associated with a reduced frequency of IOR during definitive treatment with surgical clip obliteration. These results and the impact of preoperative partial endovascular coil embolization on functional outcomes should be confirmed with a randomized trial.

Technologies to Study Genetics and Molecular Pathways.

Over the last few decades, the study of congenital heart disease (CHD) has benefited from various model systems and the development of molecular biological techniques enabling the analysis of single gene as well as global effects. In this chapter, we first describe different models including CHD patients and their families, animal models ranging from invertebrates to mammals, and various cell culture systems. Moreover, techniques to experimentally manipulate these models are discussed. Second, we introduce cardiac phenotyping technologies comprising the analysis of mouse and cell culture models, live imaging of cardiogenesis, and histological methods for fixed hearts. Finally, the most important and latest molecular biotechniques are described. These include genotyping technologies, different applications of next-generation sequencing, and the analysis of transcriptome, epigenome, proteome, and metabolome. In summary, the models and technologies presented in this chapter are essential to study the function and development of the heart and to understand the molecular pathways underlying CHD.

Development of a novel multipoint traction device for gastric and colorectal endoscopic submucosal dissection and evaluation of its efficacy and safety.

BACKGROUND: Proper traction allows safer and easier endoscopic submucosal dissection; however, single-point traction may not be sufficient. In this study we assessed the safety, efficacy, and feasibility of our newly developed multipoint traction device. METHODS: During an ex vivo study using a Konjac training model, two experts and two trainees resected 80 mock lesions of 20-mm diameter by performing endoscopic submucosal dissection with and without multipoint traction. The primary outcome was the success rate of the procedure involving traction. The secondary outcomes were the submucosal dissection time, dissection speed, and perforation during endoscopic submucosal dissection. During the in vivo study, to clarify the initial clinical outcomes, we used data from the electronic medical record of patients at our institution who underwent gastric and colorectal endoscopic submucosal dissection, which was performed by experts with our newly developed multipoint traction device, from March to December 2022. RESULTS: The ex vivo study indicated that all traction procedures were successful. Higher resection speeds were observed with endoscopic submucosal dissection with traction than without traction (P < 0.001). Perforations were not observed. During the first in vivo clinical study, traction was feasible during 20 gastric and colorectal endoscopic submucosal dissection procedures. No adverse events occurred. CONCLUSIONS: Our multitraction device can increase the submucosal dissection speed and simplify endoscopic submucosal dissection techniques, thus safely reducing technical challenges. The application of this device for endoscopic submucosal dissection could lead to safer and more efficient procedures. Clinical registration UMIN Clinical Trials Registry, Japan (registration number UMIN000053384).

The Identification and Function of Linc01615 on Influenza Virus Infection and Antiviral Response.

Influenza virus infection poses a great threat to human health globally each year. Non-coding RNAs (ncRNAs) in the human genome have been reported to participate in the replication process of the influenza virus, among which there are still many unknowns about Long Intergenic Non-Coding RNAs (LincRNAs) in the cell cycle of viral infections. Here, we observed an increased expression of Linc01615 in A549 cells upon influenza virus PR8 infection, accompanied by the successful activation of the intracellular immune system. The knockdown of Linc01615 using the shRNAs promoted the proliferation of the influenza A virus, and the intracellular immune system was inhibited, in which the expressions of IFN-ß, IL-28A, IL-29, ISG-15, MX1, and MX2 were decreased. Predictions from the catRAPID website suggested a potential interaction between Linc01615 and DHX9. Also, knocking down Linc01615 promoted influenza virus proliferation. The subsequent transcriptome sequencing results indicated a decrease in Linc01615 expression after influenza virus infection when DHX9 was knocked down. Further analysis through cross-linking immunoprecipitation and high-throughput sequencing (CLIP-seq) in HEK293 cells stably expressing DHX9 confirmed the interaction between DHX9 and Linc01615. We speculate that DHX9 may interact with Linc01615 to partake in influenza virus replication and that Linc01615 helps to activate the intracellular immune system. These findings suggest a deeper connection between DHX9 and Linc01615, which highlights the significant role of Linc01615 in the influenza virus replication process. This research provides valuable insights into understanding influenza virus replication and offers new targets for preventing influenza virus infections.

Improved rates of postoperative ischemia, completeness of aneurysm occlusion and neurological deficits in elective clipping of anterior circulation aneurysms over the past 20 years - association with technical improvements.

BACKGROUND/PURPOSE: Several periprocedural adjuncts for elective surgical aneurysm treatment have been introduced over the last 20 years to increase safety and efficacy. Besides the introduction of IONM in the late-1990s, ICG-videoangiography (ICG-VAG) since the mid-2000s and intraoperative CT-angiography/-perfusion (iCT-A/-P) since the mid-2010s are available. We aimed to clarify whether the introduction of ICG-VAG and iCT-A/-P resulted in our department in a stepwise improvement in the rate of radiologically detected postoperative ischemia, complete aneurysm occlusion and postoperative new deficits. METHODS: Patients undergoing microsurgical clip occlusion for unruptured anterior circulation aneurysms between 2000 and 2019 were included, with ICG-VAG since 2009 and iCT-A/-P (for selected cases) since 2016. Baseline characteristics and treatment-related morbidity/outcome focusing on differences between the three distinct cohorts (cohort-I: pre-ICG-VAG-era, cohort-II: ICG-VAG-era, cohort-III: ICG-VAG&iCT-A/-P-era) were analyzed. RESULTS: 1391 patients were enrolled (n = 74 were excluded), 779 patients were interventionally treated, 538 patients were surgically clipped by a specialized vascular team (cohort-I n = 167, cohort-II n = 284, cohort-III n = 87). Aneurysm size was larger in cohort-I (8.9 vs. 7.5/6.8 mm; p < 0.01) without differences concerning age (mean:55years), gender distribution (m: f = 1:2.6) and aneurysm location (MCA:61%, ICA:18%, ACA/AcomA:21%). There was a stepwise improvement in the rate of radiologically detected postoperative ischemia (16.2vs.12.0vs.8.0%; p = 0.161), complete aneurysm occlusion (68.3vs.83.6vs.91.0%; p < 0.01) and postoperative new deficits (10.8vs.7.7vs.5.7%; p = 0.335) from cohort-I to -III. After a mean follow-up of 12months, a median modified Rankin scale of 0 was achieved in all cohorts. DISCUSSION: Associated with periprocedural technical achievements, surgical outcome in elective anterior circulation aneurysm surgery has improved in our service during the past 20 years.

Ceramic Aneurysm Clip with Titanium Spring.

OBJECTIVE: To design and evaluate ceramic aneurysm clips with integrated titanium springs, focusing on ergonomic application and precision in neurosurgical procedures. METHODS: The clip design was executed with precision using Creo Parametric 3D CAD software. It comprises a zirconia body and a titanium spring for durability and consistent tension and features a four-coil hairpin titanium spring for enhanced closing force and a ball-type head for versatile maneuverability during surgery. To assess durability, closing forces were rigorously measured using a force gauge system, comparing the ceramic clip with the standard Mizuho permanent clip over 30 open-close cycles. For MR artifact assessment, both ceramic and Yasargil clips were evaluated using a 3 Tesla magnetic resonance imaging (MRI) scanner with specific imaging sequences. RESULTS: The straight type ceramic clip's initial closing force was 1.70 N, dropping to 1.22 N after 30 cycles, indicating a retention of 72% of its initial force. In MRI, the ceramic clip displayed significantly lower measurement discrepancies compared to the titanium alloy Yasargil clip, particularly in high resolution T1 weighted images. The lowest variance was at measurement point L2, where the ceramic clip showed 3% discrepancy. Further, the ceramic clip yielded clearer images than the titanium alloy clip, particularly at the clip's end. CONCLUSIONS: Ceramic clips with titanium springs demonstrated satisfactory closing force and superior MRI compatibility, promising enhancements in surgical application and postoperative assessment.

Migrated tubal sterilisation clip presenting as a subcutaneous gluteal foreign body 24 years later: a case report and literature review.

BACKGROUND: The incidence of sterilisation clip migration is reportedly 25%. However, less than 1% of those who experience clip migration will present with pain, an abscess, or spontaneous extrusion. Here we present a rare case of sterilisation clip migration through the entire pelvic floor. CASE PRESENTATION: A 66-year-old female was referred from community to the Surgical Emergency Unit with a possible metallic foreign body under the skin following an attempted routine gluteal cyst excision. The patient first noticed a lump under the skin 2 years ago which gradually became more apparent and tender over the previous 2 months. The patient denied recent trauma, had no co-morbidities and had a sterilisation procedure 24 years prior. Examination revealed a non-mobile solid structure just beneath the skin 5 cm laterally from the anal verge. Inflammatory markers were normal and an ultrasound confirmed a 15 × 7 mm foreign body in the subcutaneous tissues. The foreign body was excised easily under local anaesthesia, revealing a closed Filshie sterilisation clip. The wound was closed primarily, and recovery was uncomplicated. CONCLUSIONS: This was a case of sterilisation clip migration to the subcutaneous gluteal region. A literature review revealed 34 case reports of sterilisation clip migration, mostly to the bladder. Patients with a previous sterilisation procedure and suspected subcutaneous foreign body without trauma should elicit a high index of suspicion for migrated sterilisation clips. These clips can migrate through multiple layers of muscle and fascia, including the pelvic floor.

Utilizing Geographical Distribution Statistical Data to Improve Zero-Shot Species Recognition.

Species recognition is a crucial part of understanding the abundance and distribution of various organisms and is important for biodiversity conservation and management. Traditional vision-based deep learning-driven species recognition requires large amounts of well-labeled, high-quality image data, the collection of which is challenging for rare and endangered species. In addition, recognition methods designed based on specific species have poor generalization ability and are difficult to adapt to new species recognition scenarios. To address these issues, zero-shot species recognition based on Contrastive Language-Image Pre-training (CLIP) has become a research hotspot. However, previous studies have primarily utilized visual descriptive information and taxonomic information of species to improve zero-shot recognition performance, and the use of geographic distribution characteristics of species to improve zero-shot recognition performance has not been explored. To fill this gap, we proposed a CLIP-driven zero-shot species recognition method that incorporates knowledge of the geographic distribution of species. First, we designed three prompts based on the species geographic distribution statistical data. Then, the latitude and longitude coordinate information attached to each image in the species dataset was converted into addresses, and they were integrated together to form the geographical distribution knowledge of each species. Finally, species recognition results were derived by calculating the similarity after acquiring features by the trained CLIP image encoder and text encoder. We conducted extensive experiments on multiple species datasets from the iNaturalist 2021 dataset, where the zero-shot recognition accuracies of mammals, mollusks, reptiles, amphibians, birds, and insects were 44.96%, 15.27%, 17.51%, 9.47%, 28.35%, and 7.03%, an improvement of 2.07%, 0.48%, 0.35%, 1.12%, 1.64%, and 0.61%, respectively, as compared to CLIP with default prompt. The experimental results show that the fusion of geographic distribution statistical data can effectively improve the performance of zero-shot species recognition, which provides a new way to utilize species domain knowledge.

Retrospective study of 189 cases of acute perforated peptic ulcer: safety and efficacy of over-the-scope-clip based endoscopic closure.

BACKGROUND: To compare the clinical outcomes in patients with acute perforated peptic ulcer (PPU) treated with over-the-scope clip (OTSC), non-surgical, and surgical interventions, and to explore the effectiveness and safety of OTSC closure. METHODS: Hospital stay, antibiotic use, diet resumption time, and mortality rate were analyzed retrospectively. Binary Logistic regression analysis was used to identify the risk factors influencing PPU complicated with sepsis. RESULTS: Patients were divided into three treatment groups: OTSC (n = 62), non-surgical (n = 72), and surgical (n = 55) groups. The median time (IQR) from symptom onset to admission was 9.0 (4-23) h. 88.71% (55/62) of the patients in In the OTSC group underwent OTSC closure within 24 h (median [IQR] time: 14.5 [7.00-30.25] h). The perforation diameters in the OTSC and surgical groups were 9.87 mm ± 5.97 mm and 8.55 mm ± 6.17 mm, respectively. The median (IQR) hospital stays in the OTSC (9.50 [7.00-12.25] days) and non-surgical group (9.00[7.00-13.00]days) were similar (p > 0.05), but shorter than that in surgical group (12.00[10.00-16.00]days), (p < 0.05). The median duration of antibiotic use was shorter in the OTSC group (7.00[3.00-10.00]) than in the non-surgical group (9.00[7.00-11.00]) and surgical group (11.00[9.00-13.00]) ( p < 0.05); and the time to resume oral feeding was shorter in the OTSC group (4.00[2.00-5.25]) than in the non-surgical group (7.00[6.13-9.00]) and surgical group (8.00[6.53-10.00]), respectively ( p < 0.05). No mortality difference among groups (p = 0.109) was found. Lower albumin level at admission, older age, and elevated creatinine levels were associated with increased sepsis risk, with OR(95%CI) of 0.826 (0.687-0.993), 1.077 (1.005-1.154), and 1.025 (1.006-1.043), respectively (all p < 0.05). CONCLUSION: OTSC closure improves clinical outcomes of acute PPU patients without sepsis. Age, hypoalbuminemia, and baseline renal dysfunction increase the risk of sepsis, while mortality was associated with sepsis and multiorgan dysfunction.

Untacking small RNA profiling and RNA fragment footprinting: Approaches and challenges in library construction.

Small RNAs (sRNAs) with sizes ranging from 15 to 50 nucleotides (nt) are critical regulators of gene expression control. Prior studies have shown that sRNAs are involved in a broad range of biological processes, such as organ development, tumorigenesis, and epigenomic regulation; however, emerging evidence unveils a hidden layer of diversity and complexity of endogenously encoded sRNAs profile in eukaryotic organisms, including novel types of sRNAs and the previously unknown post-transcriptional RNA modifications. This underscores the importance for accurate, unbiased detection of sRNAs in various cellular contexts. A multitude of high-throughput methods based on next-generation sequencing (NGS) are developed to decipher the sRNA expression and their modifications. Nonetheless, distinct from mRNA sequencing, the data from sRNA sequencing suffer frequent inconsistencies and high variations emanating from the adapter contaminations and RNA modifications, which overall skew the sRNA libraries. Here, we summarize the sRNA-sequencing approaches, and discuss the considerations and challenges for the strategies and methods of sRNA library construction. The pros and cons of sRNA sequencing have significant implications for implementing RNA fragment footprinting approaches, including CLIP-seq and Ribo-seq. We envision that this review can inspire novel improvements in small RNA sequencing and RNA fragment footprinting in future. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.

CLIP170 inhibits the metastasis and EMT of papillary thyroid cancer through the TGF-ß pathway.

Metastasis poses a significant challenge in combating tumors. Even in papillary thyroid cancer (PTC), which typically exhibits a favorable prognosis, high recurrence rates are attributed to metastasis. Cytoplasmic linker protein 170 (CLIP170) functions as a classical microtubule plus-end tracking protein (+TIP) and has shown close association with cell migration. Nevertheless, the specific impact of CLIP170 on PTC cells remains to be elucidated. Our analysis of the GEO and TCGA databases unveiled an association between CLIP170 and the progression of PTC. To explore the impact of CLIP170 on PTC cells, we conducted various assays. We evaluated its effects through CCK-8, wound healing assay, and transwell assay after knocking down CLIP170. Additionally, the influence of CLIP170 on the cellular actin structure was examined via immunofluorescence; we further investigated the molecular expressions of epithelial-mesenchymal transition (EMT) and the transforming growth factor-ß (TGF-ß) signaling pathways through Western blotting and RT-qPCR. These findings were substantiated through an in vivo nude mouse model of lung metastasis. We observed a decreased expression of CLIP170 in PTC in contrast to normal thyroid tissue. Functionally, the knockdown of CLIP170 (CLIP170KD) notably enhanced the metastatic potential and EMT of PTC cells, both in vitro and in vivo. Mechanistically, CLIP170KD triggered the activation of the TGF-ß pathway, subsequently promoting tumor cell migration, invasion, and EMT. Remarkably, the TGF-ß inhibitor LY2157299 effectively countered TGF-ß activity and significantly reversed tumor metastasis and EMT induced by CLIP170 knockdown. In summary, these findings collectively propose CLIP170 as a promising therapeutic target to mitigate metastatic tendencies in PTC.

The Use of Cranial Aneurysm Clips for Repair of Incidental Lumbar Durotomy: Operative Technique and Case Series.

BACKGROUND: Incidental durotomy is a common complication of posterior lumbar spine surgery; however, effective and durable methods for primary repair remain elusive. Multiple existing techniques have previously been reported and extensively described, including sutured repair and the use of nonpenetrating titanium clips. The use of cranial aneurysm clips for primary repair of lumbar durotomy serves as a safe and effective alternative to obtain watertight closure of a dural tear. METHODS: We performed a retrospective review of patients at a single institution who underwent primary repair of an incidental lumbar durotomy with the use of an aneurysm clip during open posterior lumbar surgery between 2012 and 2023. Patient demographics, operative details, and postoperative metrics were collected and examined to evaluate the safety and efficacy of the novel technique. RESULTS: A total of 51 patients were included for analysis. Four patients underwent durotomy repair with an aneurysm clip alone, 27 patients were repaired with an aneurysm clip and fibrin glue, and 20 patients underwent repair with an aneurysm clip, fibrin glue, and a collagen dural substitute. Three patients (5.9%) reported headaches: 2 (3.9%) with pseudomeningocele and 1 (2%) with wound leakage. Two patients (3.9%) had treatment failure with a return to the operating room for repair of a cerebrospinal fluid leak. CONCLUSIONS: To the best of our knowledge, we report the largest series of patients undergoing primary repair of incidental durotomy with the use of an aneurysm clip. Use of an aneurysm clip is noted to be a safe, quick, and effective method of primary repair compared with existing repair techniques such as sutured repair or nonpenetrating titanium clips.

ePRINT: exonuclease assisted mapping of protein-RNA interactions.

RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purifying single proteins at a time. Our new method, ePRINT, maps RBP-RNA interaction networks on a global scale without purifying individual RBPs. ePRINT uses exoribonuclease XRN1 to precisely map the 5' end of the RBP binding site and uncovers direct and indirect targets of an RBP of interest. Importantly, ePRINT can also uncover RBPs that are differentially activated between cell fate transitions, including neural progenitor differentiation into neurons.

Erasable and Field Programmable DNA Circuits Based on Configurable Logic Blocks.

DNA is commonly employed as a substrate for the building of artificial logic networks due to its excellent biocompatibility and programmability. Till now, DNA logic circuits are rapidly evolving to accomplish advanced operations. Nonetheless, nowadays, most DNA circuits remain to be disposable and lack of field programmability and thereby limits their practicability. Herein, inspired by the Configurable Logic Block (CLB), the CLB-based erasable field-programmable DNA circuit that uses clip strands as its operation-controlling signals is presented. It enables users to realize diverse functions with limited hardware. CLB-based basic logic gates (OR and AND) are first constructed and demonstrated their erasability and field programmability. Furthermore, by adding the appropriate operation-controlling strands, multiple rounds of programming are achieved among five different logic operations on a two-layer circuit. Subsequently, a circuit is successfully built to implement two fundamental binary calculators: half-adder and half-subtractor, proving that the design can imitate silicon-based binary circuits. Finally, a comprehensive CLB-based circuit is built that enables multiple rounds of switch among seven different logic operations including half-adding and half-subtracting. Overall, the CLB-based erasable field-programmable circuit immensely enhances their practicability. It is believed that design can be widely used in DNA logic networks due to its efficiency and convenience.

Quercetin through miR-147-5p/Clip3 axis reducing Th17 cell differentiation to alleviate periodontitis.

Background: Quercetin (QU) plays an important role in treating periodontitis; however, the mechanism through which microRNAs regulate Th17 cell differentiation has not been determined. Methods: QU was administered intragastrically to periodontitis rats once a day for one month. The morphology of alveolar bone was observed by micro-CT, gingival tissue structure was observed by HE staining, IL-6, TNF-α, IL-17A, RORγt, FOXP3 and IL-10 were detected by immunohistochemical staining, and Th17 and Treg cells in the peripheral blood were detected by flow cytometry. CD4+T cells were induced to differentiate into Th17 cells in vitro. Cell viability was determined by CCK8, and IL-17A and RORγt were detected by qPCR. Th17 cells were detected by flow cytometry, microRNA sequencing and bioinformatics analysis were used to screen key microRNAs, the phenotypic changes of Th17 cells were observed after overexpressed microRNAs via mimics. TargetScan database, in situ hybridization, and dual-luciferase reporter experiment were used to predict and prove target genes of microRNAs. The phenotype of Th17 cells was observed after overexpression of microRNA and target gene. Results: Compared with periodontitis group, the distance from cementoenamel junction(CEJ) to alveolar bone(AB) was decreased, the structure of gingival papilla was improved, IL-6, TNF-α, IL-17, and RORγt were downregulated, FOXP3 and IL-10 were upregulated, the proportion of Th17 decreased and Treg increased in peripheral blood after QU treatment. Compared with Th17 cell group, mRNA levels of IL-17A and RORγt were decreased, and proportion of Th17 cells was significantly lower in the coculture group. MiR-147-5p was low in control group, upregulated in Th17 cell group, and downregulated after QU intervention, it's eight bases were inversely related to 3'UTR of Clip3, miR-147-5p with Clip3 were co-located in cells of periodontal tissue. Compared with those in Th17-mimicsNC + QU cells, the mRNA levels of RORγt and IL-17A upregulated, and proportion of Th17 cells increased in Th17-miR-147-5p + QU cells. The miR-147-5p mimics inhibited the luciferase activity of the WT Clip3 3'UTR but had no effect on the Mut Clip3 3'UTR. Clip3 was significantly downregulated after the overexpression of miR-147-5p. Mimics transfected with miR-147-5p reversed the decrease in the proportion of Th17 cells induced by QU, while the overexpression of Clip3 antagonized the effect of miR-147-5p and further reduced the proportion of Th17 cells. Moreover, the overexpression of miR-147-5p reversed the decreases in the mRNA levels of IL-17 and RORγt induced by QU treatment, while pcDNA3.1 Clip3 treatment further decreased the mRNA levels of IL-17 and RORγt. Conclusion: QU reducing inflammatory response and promoting alveolar bone injury and repair, which closely relative to inhibit the differentiation of CD4+T cells into Th17 cells by downregulating miR-147-5p to promote the activation of Clip3.