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This study investigates transfer ribonucleic acid (tRNA) conformational dynamics in the context of MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) using solid-state silicon nitride (SiN) nanopore technology. SiN nanopores in thin membranes with specific dimensions exhibit high signal resolution, enabling real-time and single-molecule electronic detection of tRNA conformational changes. We focus on human mitochondrial tRNALeu(UAA) (mt-Leu(UAA)) that decodes Leu codons UUA/UUG (UUR) during protein synthesis on the mt-ribosome. The single A14G substitution in mt-Leu(UAA) is the major cause of MELAS disease. Measurements of current blockades and dwell times reveal distinct conformational dynamics of the wild-type (WT) and the A14G variant of mt-Leu(UAA) in response to the conserved post-transcriptional m1G9 methylation. While the m1G9-modified WT transcript adopts a more stable structure relative to the unmodified transcript, the m1G9-modified MELAS transcript adopts a less stable structure relative to the unmodified transcript. Notably, these differential features were observed at 0.4 M KCl, but not at 3 M KCl, highlighting the importance of experimental settings that are closer to physiological conditions. This work demonstrates the feasibility of the nanopore platform to discern tRNA molecules that differ by a single-nucleotide substitution or by a single methylation event, providing an important step forward to explore changes in the conformational dynamics of other RNA molecules in human diseases.

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Brain machine interfaces (BMIs) can substantially improve the quality of life of elderly or disabled people. However, performing complex action sequences with a BMI system is onerous because it requires issuing commands sequentially. Fundamentally different from this, we have designed a BMI system that reads out mental planning activity and issues commands in a proactive manner. To demonstrate this, we recorded brain activity from freely-moving monkeys performing an instructed task and decoded it with an energy-efficient, small and mobile field-programmable gate array hardware decoder triggering real-time action execution on smart devices. Core of this is an adaptive decoding algorithm that can compensate for the day-by-day neuronal signal fluctuations with minimal re-calibration effort. We show that open-loop planning-ahead control is possible using signals from primary and pre-motor areas leading to significant time-gain in the execution of action sequences. This novel approach provides, thus, a stepping stone towards improved and more humane control of different smart environments with mobile brain machine interfaces.

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Objective: To evaluate the occurrence, development and outcome value of hyperfluorescent lymphocyte percentage (HFLC%) and immature granulocyte percentage (IG%) for acute pancreatitis (AP). Methods: The laboratory data collected from 1533 patients diagnosed with AP between August 2018 and August 2022 were retrospectively analyzed. The patients were classified into mild acute pancreatitis (MAP) and non-mild acute pancreatitis (Non-MAP) groups; non-MAP groups were additionally subgrouped based on HFLC% at day 7. White blood cells (WBC), HFLC%, and IG% were examined from day 1 (baseline) to day 14 post-admission using Sysmex XN Series Hematology Analyzers. C-reactive protein (CRP), serum amylase (AMY), and lipase (LPS) were detected by Beckman AU5800. Results: A total of 623 patients were finally included in the study [MAP group (n = 358) and Non-MAP group (n = 265)]. WBC, IG%, and CRP were higher in the Non-MAP group from day 1 to day 12 (all P<0.05). The HFLC% was not statistically significant from day 1 to day 6; yet, it increased on day 6 and 7 in the Non-MAP group. We divided patients in the Non-MAP group with complete data(101 patients) into HFLC% ≥ 2.9 %(31 patients) and HFLC% < 2.9 %(70 patients) according to the threshold of 7th day HFLC%. WBC, HFLC%, IG%, and CRP effectively predicted the progression of MAP to Non-MAP (all P < 0.001). HFLC% was the most obvious value, followed by CRP and IG%. Combined with HFLC%, IG%,CRP and WBC in day7, the ROC analysis showed that the area under ROC curve of the combined indicators was the largest (AUC = 0.912, P < 0.001) and had higher sensitivity and specificity than single-item assessment of AP outcomes(P < 0.05). HFLC% < 2.9 %, IG% > 1.7 %, CRP >28.66 mg/L, and WBC >9.24 × 109/L indicated the possibility of AP disease aggravation. Also, HFLC% <2.9 % was directly associated with infection, SIRS, APPACHII grade, and ICU admission (all P < 0.05). In non-MAP there was a significant negative correlation between HFLC% and APACHE-II score (rs = -0.312, P = 0.023). Conclusion: HFLC% <2.9 % on 7th day was directly indicated more infection, systemic inflammatory response syndrome(SIRS), higher APPACH II grade and ICU admission. HFLC% may be an independent laboratory marker for prognosis in AP. Combining HFLC% with IG%, CRP, and WBC helps evaluate AP patients' disease development and outcome.

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BACKGROUND: Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China, the Philippines and Indonesia. Oncomelania hupensis (Gastropoda: Pomatiopsidae) is the unique intermediate host of S. japonicum. A complete genome sequence of O. hupensis will enable the fundamental understanding of snail biology as well as its co-evolution with the S. japonicum parasite. Assembling a high-quality reference genome of O. hupehensis will provide data for further research on the snail biology and controlling the spread of S. japonicum. METHODS: The draft genome was de novo assembly using the long-read sequencing technology (PacBio Sequel II) and corrected with Illumina sequencing data. Then, using Hi-C sequencing data, the genome was assembled at the chromosomal level. CAFE was used to do analysis of contraction and expansion of the gene family and CodeML module in PAML was used for positive selection analysis in protein coding sequences. RESULTS: A total length of 1.46 Gb high-quality O. hupensis genome with 17 unique full-length chromosomes (2n = 34) of the individual including a contig N50 of 1.35 Mb and a scaffold N50 of 75.08 Mb. Additionally, 95.03% of these contig sequences were anchored in 17 chromosomes. After scanning the assembled genome, a total of 30,604 protein-coding genes were predicted. Among them, 86.67% were functionally annotated. Further phylogenetic analysis revealed that O. hupensis was separated from a common ancestor of Pomacea canaliculata and Bellamya purificata approximately 170 million years ago. Comparing the genome of O. hupensis with its most recent common ancestor, it showed 266 significantly expanded and 58 significantly contracted gene families (P < 0.05). Functional enrichment of the expanded gene families indicated that they were mainly involved with intracellular, DNA-mediated transposition, DNA integration and transposase activity. CONCLUSIONS: Integrated use of multiple sequencing technologies, we have successfully constructed the genome at the chromosomal-level of O. hupensis. These data will not only provide the compressive genomic information, but also benefit future work on population genetics of this snail as well as evolutional studies between S. japonicum and the snail host.

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Human mitochondrial tRNAs (mt-tRNAs), critical for mitochondrial biogenesis, are frequently associated with pathogenic mutations. These mt-tRNAs have unusual sequence motifs and require post-transcriptional modifications to stabilize their fragile structures. However, whether a modification that stabilizes a wild-type (WT) mt-tRNA structure would also stabilize its pathogenic variants is unknown. Here we show that the N 1 -methylation of guanosine at position 9 (m 1 G9) of mt-Leu(UAA), while stabilizing the WT tRNA, has an opposite and destabilizing effect on variants associated with MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes). This differential effect is further demonstrated by the observation that demethylation of m 1 G9, while damaging to the WT tRNA, is beneficial to the major pathogenic variant, improving its structure and activity. These results have new therapeutic implications, suggesting that the N 1 -methylation of mt-tRNAs at position 9 is a determinant of pathogenicity and that controlling the methylation level is an important modulator of mt-tRNA-associated diseases.

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Monitoring the dynamic changes of cellular tRNA pools is challenging, due to the extensive post-transcriptional modifications of individual species. The most critical component in tRNAseq is a processive reverse transcriptase (RT) that can read through each modification with high efficiency. Here we show that the recently developed group-II intron RT Induro has the processivity and efficiency necessary to profile tRNA dynamics. Using our Induro-tRNAseq, simpler and more comprehensive than the best methods to date, we show that Induro progressively increases readthrough of tRNA over time and that the mechanism of increase is selective removal of RT stops, without altering the misincorporation frequency. We provide a parallel dataset of the misincorporation profile of Induro relative to the related TGIRT RT to facilitate the prediction of non-annotated modifications. We report an unexpected modification profile among human proline isoacceptors, absent from mouse and lower eukaryotes, that indicates new biology of decoding proline codons.

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In this study, a 3D porous poly(ε-caprolactone)/polyethylene glycol (PCL/PEG) composite artificial tubular bile duct was fabricated for extrahepatic bile duct regeneration. PCL/PEG composite scaffolds were fabricated by 3D printing, and the molecular structure, mechanical properties, thermal properties, morphology, and in vitro biocompatibility were characterized for further application as artificial bile ducts. A bile duct defect model was established in beagle dogs for in vivo implantation. The results demonstrated that the implanted PE1 ABD, serving as a supportive scaffold, effectively stimulated the regeneration of a new bile duct comprising CK19-positive and CK7-positive epithelial cells within 30 days. Remarkably, after 8 months, the newly formed bile duct exhibited an epithelial layer resembling the normal structure. Furthermore, the study revealed collagen deposition, biliary muscular formation, and the involvement of microvessels and fibroblasts in the regenerative process. In contrast, the anastomotic area without ABD implantation displayed only partial restoration of the epithelial layer, accompanied by fibroblast proliferation and subsequent bile duct fibrosis. These findings underscore the limited inherent repair capacity of the bile duct and underscore the beneficial role of the PE1 ABD artificial tubular bile duct in promoting biliary regeneration.

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We reinvestigated the reported method for the synthesis of ethyl 3-[5-(2-ethoxycarbonyl-1-methylvinyloxy)-1-methyl-1H-indol-3-yl]-but-2-enoate (MIBE), which was obtained by the reaction of 5-hydroxy-1-methyl-1H-indole with excess ethyl acetoacetate catalyzed by indium(III) chloride. Based on the NMR and MS data, we assigned the structure of the isolated product as (3E)-3-(2-ethoxy-2-oxoethylidene)-1,2,3,4-tetrahydro-7-hydroxy-1,4-dimethylcyclopent[b]indole-1-acetate (2a) rather than the reported MIBE.

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5'-18O labeled RNA oligos are important probes to investigate the mechanism of 2'-O-transphosphorylation reactions. Here we describe a general and efficient synthetic approach to the phosphoramidite derivatives of 5'-18O labeled nucleosides starting from the corresponding commercially available 5'-O-DMT protected nucleosides. Using this method, we prepared 5'-18O-guanosine phosphoramidite in 8 steps (13.2% overall yield), 5'-18O-adenosine phosphoramidite in 9 steps (10.1% overall yield) and 5'-18O-2'-deoxyguanosine phosphoramidite in 6 steps (12.8% overall yield). These 5'-18O labeled phosphoramidites can be incorporated into RNA oligos by solid phase synthesis for determination of heavy atom isotope effects in RNA 2'-O-transphosphorylation reactions.

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We describe a new demethylation method for dimethyl phosphonate esters using sodium ethanethiolate. The new procedure allows demethylation of nucleoside dimethyl phosphonate esters without 1'-α-anomerization, providing an improved synthesis of 5'-methylene substituted 2',5'-deoxynucleotides.

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BACKGROUND: The laparoscopic and open approaches have comparable safety and oncological efficacy to treat early (T1b or T2) stage incidental gallbladder cancer (IGBC). However, their effects on T3 stage or above tumors unclear. METHODS: Data of IGBC patients who underwent radical re-resection were retrospectively analyzed. Demographic characteristics, surgical variables, and tumor characteristics were evaluated for association with survival. RESULTS: We analyzed retrospectively 201 patients (72 men, 129 women; median age 63 years; range, 36-85 years). 84 underwent laparoscopic re-resection and 117 underwent open surgery. The 5-year OS post-resection was 74.7%, with a median survival of 74.52 months. The median OS (73.92 months vs. 77.04 months, P = 0.67), and disease-free survival (72.60 months vs. 71.09 months, P = 0.18) were comparable between the laparoscopic re-resection and open surgery groups. The survival of patients with T1/T2 (median: 85.50 months vs. 80.14 months; P = 0.67) and T3 (median: 68.56 months vs. 58.85 months; P = 0.36) disease were comparable between the open re-resection and laparoscopic re-resection groups even after PS matching. Open surgery group lost significantly more blood, while laparoscopic surgery took longer. The postsurgical stay in the laparoscopic re-resection group was significantly shorter. Combined extrahepatic bile duct resection, gallbladder perforation, pT, pStage, histological grade, microscopic liver invasion, status of the resected margin, and adjuvant therapy comprised significant independent prognostic indicators for IGBC. CONCLUSIONS: Laparoscopic and open surgery can achieve similar short and long-term outcomes for T3 IGBC; however, careful surgical manipulation is necessary to avoid secondary injuries.

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Ribonucleases and small nucleolytic ribozymes are both able to catalyze RNA strand cleavage through 2'-O-transphosphorylation, provoking the question of whether protein and RNA enzymes facilitate mechanisms that pass through the same or distinct transition states. Here, we report the primary and secondary 18O kinetic isotope effects for hepatitis delta virus ribozyme catalysis that reveal a dissociative, metaphosphate-like transition state in stark contrast to the late, associative transition states observed for reactions catalyzed by specific base, Zn2+ ions, or ribonuclease A. This new information provides evidence for a discrete ribozyme active site design that modulates the RNA cleavage pathway to pass through an altered transition state.

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Biliary tract cancer is a group of malignancies which originate from biliary epithelium, and adenocarcinoma is the main pathological type. Although surgical resection is the only radical treatment strategy, most biliary tract cancer patients are diagnosed at locally advanced stage or with distant metastasis. Biliary tract cancer is highly resistant to the conventional chemoradiotherapy and the emerging immunotherapy including immune checkpoint inhibitors, owing to the suppressive immune microenvironment. In a whole view, this paper discussed the anti-tumor and tumor-promoting immune responses of the various immune cells and stromal cells in the immune microenvironment of biliary tract cancer, as well as their correlation with prognosis. The understanding of the whole view of immune microenvironment in biliary tract cancer patients could further inform the design of clinical trials of immunotherapy or combination therapy.

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Based on the land use data of Hexi Corridor region from 1980 to 2020, we calculated the ecological environment quality index and analyzed the spatial and temporal evolution characteristics, change frequency, patterns, circles of the long time series land use type changes and its ecological environment quality, using the spatial analysis method of ArcGIS. The results showed that unused land was the main land use type in the study area during 1980-2020. The area of construction land, forest land, grassland, and water changed more, and the transition among land use types was obvious. The trends of deterioration and improvement of ecological environment quality in the study area occurred simultaneously and offset each other under certain conditions. The ecological environment quality index evolved in a 'U' shape, first decreasing and then increasing, with little change in overall ecological environment quality fluctuations. The spatial clustering of ecological quality was obvious, which was higher in the southeast and lower in the northwest, without high frequency and large change. The ecological quality in the southeast quadrant of the study area was the worst, followed by the southwest and northwest quadrants, while the ecological quality in the northeast quadrant was the best. The area of the continuously decline zone in ecological environment quality type conversion was larger than that of the continuously rising zone, indicating that ecological environmental protection in the Hexi Corridor had been effective during the study period. The hot spots of ecological quality change were mainly distributed in the central and southwestern part of the Hexi Corridor, and the cold spots were mainly distributed in the northwestern part.

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Pepper is a fluorogenic RNA aptamer tag that binds to a variety of benzylidene-cyanophenyl (HBC) derivatives with tight affinity and activates their fluorescence. To investigate how Pepper RNA folds to create a binding site for HBC, we used antibody-assisted crystallography to determine the structures of Pepper bound to HBC530 and HBC599 to 2.3 and 2.7 Å resolutions, respectively. The structural data show that Pepper folds into an elongated structure and organizes nucleotides within an internal bulge to create the ligand binding site, assisted by an out-of-plane platform created by tertiary interactions with an adjacent bulge. As predicted from a lack of K+ dependence, Pepper does not use a G-quadruplex to form a binding pocket for HBC. Instead, Pepper uses a unique base-quadruple·base-triple stack to sandwich the ligand with a U·G wobble pair. Site-bound Mg2+ ions support ligand binding structurally and energetically. This research provides insight into the structural features that allow the Pepper aptamer to bind HBC and show how Pepper's function may expand to allow the in vivo detection of other small molecules and metals.

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Chemical manipulation of estrogen receptor alpha ligand binding domain structural mobility tunes receptor lifetime and influences breast cancer therapeutic activities. Selective estrogen receptor modulators (SERMs) extend estrogen receptor alpha (ERα) cellular lifetime/accumulation. They are antagonists in the breast but agonists in the uterine epithelium and/or in bone. Selective estrogen receptor degraders/downregulators (SERDs) reduce ERα cellular lifetime/accumulation and are pure antagonists. Activating somatic ESR1 mutations Y537S and D538G enable resistance to first-line endocrine therapies. SERDs have shown significant activities in ESR1 mutant setting while few SERMs have been studied. To understand whether chemical manipulation of ERα cellular lifetime and accumulation influences antagonistic activity, we studied a series of methylpyrollidine lasofoxifene (Laso) derivatives that maintained the drug's antagonistic activities while uniquely tuning ERα cellular accumulation. These molecules were examined alongside a panel of antiestrogens in live cell assays of ERα cellular accumulation, lifetime, SUMOylation, and transcriptional antagonism. High-resolution x-ray crystal structures of WT and Y537S ERα ligand binding domain in complex with the methylated Laso derivatives or representative SERMs and SERDs show that molecules that favor a highly buried helix 12 antagonist conformation achieve the greatest transcriptional suppression activities in breast cancer cells harboring WT/Y537S ESR1. Together these results show that chemical reduction of ERα cellular lifetime is not necessarily the most crucial parameter for transcriptional antagonism in ESR1 mutated breast cancer cells. Importantly, our studies show how small chemical differences within a scaffold series can provide compounds with similar antagonistic activities, but with greatly different effects of the cellular lifetime of the ERα, which is crucial for achieving desired SERM or SERD profiles.

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As one of the most lethal forms of cancers, hepatocellular carcinoma (HCC) claims many lives around the world, and it is especially common in China. The ARID family plays key roles in the pathogenesis and development of human cancers. The potential of several functional genes used as novel biomarkers has attracted more and more attention. However, the prognostic values of the ARID family in HCC patients are rarely known by people. In this study, we performed comprehensive analysis using TCGA datasets, finding that the expressions of ARID4B, ARID2, ARID3B, JARID2, ARID1A, ARID1B, and ARID3A were increased in HCC specimens compared to nontumor specimens, while the expressions of ARID4A and ARID3C were decreased in HCC specimens. According to the Pearson correlation data, the methylation levels of the majority of ARID members were negatively correlated. Upregulation of ARID3A, ARID5B, and ARID1A was related to a poor HCC outcome according to the data of multivariate assays. Then, we built a LASSO Cox regression model based on ARID3A, ARID5B, and ARID1A in HCC. Overall survival rates were considerably lower for those with high risk scores compared to those with low risk scores. Finally, we studied the associations between risk scores and several types of infiltrating immune cells. The data revealed that the risk score was positively related to the infiltration of CD8+ T cells, B cell, T cell CD8+, neutrophil, macrophage, and myeloid dendritic cell. This study conducted a thorough analysis of the ARID members, resulting in new insights for further examination of the ARID family members as prospective targets in the treatment of HCC.

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Ribozymes that react with small-molecule probes have important applications in transcriptomics and chemical biology, such as RNA labeling and imaging. Understanding the structural basis for these RNA-modifying reactions will enable the development of better tools for studying RNA. Nevertheless, high-resolution structures and underlying catalytic mechanisms for members of this ribozyme class remain elusive. Here, we focus on a self-alkylating ribozyme that catalyzes nitrogen-carbon bond formation between a specific guanine and a 2,3-disubstituted epoxide substrate and report the crystal structures of a self-alkylating ribozyme, including both alkylated and apo forms, at 1.71-Å and 2.49-Å resolution, respectively. The ribozyme assumes an elongated hairpin-like architecture preorganized to accommodate the epoxide substrate in a hook-shaped conformation. Observed reactivity of substrate analogs together with an inverse, log-linear pH dependence of the reaction rate suggests a requirement for epoxide protonation, possibly assisted by the ether oxygens within the substrate.

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PURPOSE: The time-to-tumor recurrence can predict the prognosis of hepatobiliary cancers following curative-intent resection. Therefore, for patients with gallbladder carcinoma (GBC) of stage T1b-T3 who had undergone R0 resection, we investigated the risk factors for early recurrence of GBC and their prognosis. PATIENTS AND METHODS: A total of 260 patients with GBC with T1b-T3 disease and an R0 margin were identified. Their clinicopathologic characteristics, perioperative details and prognostic data were reviewed. Survival analyses were carried out using the Kaplan-Meier method. Logistic regression models were used to identify the risk factors for early recurrence. RESULTS: The optimal cutoff for early recurrence was 29 months. Early recurrence tended to result in relapse far from the primary tumor, and such patients tended to have significantly worse overall survival. Multivariate analysis revealed that T3 disease, N1/N2 stage, poor differentiation of tumor, and lymphovascular invasion (LI) were associated with a greater risk of early recurrence. Patients diagnosed as having GBC incidentally and who had the risk factors of early recurrence were more likely to benefit from re-resection 2-4 weeks after a cholecystectomy. CONCLUSION: T3 stage, N1-N2 stage, poor differentiation, and LI were independent risk factors associated with early recurrence for patients with GBC with stage T1b-T3 disease after R0 resection.

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The nonlinear evolution of mixing layer in cylindrical Rayleigh-Taylor (RT) turbulence is studied theoretically and numerically. The scaling laws including the hyperbolic cosine growth for outward mixing layer and the cosine growth for inward mixing layer of the cylindrical RT turbulence are proposed for the first time and verified reliably by direct numerical simulation of the Navier-Stokes equations. It is identified that the scaling laws for the cylindrical RT turbulence transcend the classical power law for the planar RT turbulence and can be recovered to the quadratic growth as cylindrical geometry effect vanishes. Further, characteristic time- and length scales are reasonably obtained based on the scaling laws to reveal the self-similar evolution features for the cylindrical RT turbulence.