Amplification editing enables efficient and precise duplication of DNA from short sequence to megabase and chromosomal scale.

Duplication is a foundation of molecular evolution and a driver of genomic and complex diseases. Here, we develop a genome editing tool named Amplification Editing (AE) that enables programmable DNA duplication with precision at chromosomal scale. AE can duplicate human genomes ranging from 20 bp to 100 Mb, a size comparable to human chromosomes. AE exhibits activity across various cell types, encompassing diploid, haploid, and primary cells. AE exhibited up to 73.0% efficiency for 1 Mb and 3.4% for 100 Mb duplications, respectively. Whole-genome sequencing and deep sequencing of the junctions of edited sequences confirm the precision of duplication. AE can create chromosomal microduplications within disease-relevant regions in embryonic stem cells, indicating its potential for generating cellular and animal models. AE is a precise and efficient tool for chromosomal engineering and DNA duplication, broadening the landscape of precision genome editing from an individual genetic locus to the chromosomal scale.

Efficient targeted insertion of large DNA fragments without DNA donors.

Targeted insertion of large DNA fragments holds great potential for treating genetic diseases. Prime editors can effectively insert short fragments (~44 bp) but not large ones. Here we developed GRAND editing to precisely insert large DNA fragments without DNA donors. In contrast to prime editors, which require reverse transcription templates hybridizing with the target sequence, GRAND editing employs a pair of prime editing guide RNAs, with reverse transcription templates nonhomologous to the target site but complementary to each other. This strategy exhibited an efficiency of up to 63.0% of a 150-bp insertion with minor by-products and 28.4% of a 250-bp insertion. It allowed insertions up to ~1 kb, although the efficiency remains low for fragments larger than 400 bp. We confirmed efficient insertion in multiple genomic loci of several cell lines and non-dividing cells, which expands the scope of genome editing to enable donor-free insertion of large DNA sequences.

Performance Optimization for a Class of Petri Nets.

Petri nets (PNs) are widely used to model flexible manufacturing systems (FMSs). This paper deals with the performance optimization of FMSs modeled by Petri nets that aim to maximize the system's performance under a given budget by optimizing both quantities and types of resources, such as sensors and devices. Such an optimization problem is challenging since it is nonlinear; hence, a globally optimal solution is hard to achieve. Here, we developed a genetic algorithm combined with mixed-integer linear programming (MILP) to solve the problem. In this approach, a set of candidate resource allocation strategies, i.e., the choices of the number of resources, are first generated by using MILP. Then, the choices of the type and the cycle time of the resources are evaluated by MILP; the promising ones are used to spawn the next generation of candidate strategies. The effectiveness and efficiency of the developed methodology are illustrated by simulation studies.

Comparison of comfort and complications of Implantable Venous Access Port (IVAP) with ultrasound guided Internal Jugular Vein (IJV) and Axillary Vein/Subclavian Vein (AxV/SCV) puncture in breast cancer patients: a randomized controlled study.

BACKGROUND: Axillary vein/subclavian vein (AxV/SCV) and Internal jugular vein (IJV) are commonly used for implantable venous access port (IVAP) implantation in breast cancer patients for chemotherapy. Previous research focused on comparison of complications while patient comfort was ignored. This study aims to compare patient comfort, surgery duration and complications of IVAP implantation between IJV and AxV/SCV approaches. METHODS: Two hundred forty-eight breast cancer patients were enrolled in this randomized controlled study from August 2020 to June 2021. Patients scheduled to undergo IVAP implantation were randomly and equally assigned to receive central venous catheters with either AxV /SCV or IJV approaches. All patients received comfort assessment using a comfort scale table at day 1, day 2 and day 7 after implantation. Patient comfort, procedure time of operation as well as early complications were compared. RESULTS: Patient comfort was significantly better in the AxV/SCV group than that of IJV group in day 1 (P < 0.001), day 2 (P < 0.001) and day 7(P = 0.023). Procedure duration in AxV/SCV group was slightly but significantly shorter than IJV group (27.14 ± 3.29 mins vs 28.92 ± 2.54 mins, P < 0.001). More early complications occurred in AxV/SCV group than IJV group (11/124 vs 2/124, P = 0.019). No difference of complications of artery puncture, pneumothorax or subcutaneous hematoma between these two groups but significantly more catheter misplacement in AxV/SCV group than IJV group (6/124 vs 0/124, P = 0.029). Absolutely total risk of complications was rather low in both groups (8.87% in AxV/SCV group and 1.61% in IJV group). CONCLUSIONS: Our study indicates that patients with AxV/SCV puncture have higher comfort levels than IJV puncture. AxV/SCV puncture has shorter procedure duration but higher risk of early complications, especially catheter misplacement. Both these two approaches have rather low risk of complications. Consequently, our study provides an alternative choice for breast cancer patients to reach better comfort.

RIG-I modulates Src-mediated AKT activation to restrain leukemic stemness.

Retinoic acid (RA)-inducible gene I (RIG-I) is highly upregulated and functionally implicated in the RA-induced maturation of acute myeloid leukemia (AML) blasts. However, the underlying mechanism and the biological relevance of RIG-I expression to the maintenance of leukemogenic potential are poorly understood. Here, we show that RIG-I, without priming by foreign RNA, inhibits the Src-facilitated activation of AKT-mTOR in AML cells. Moreover, in a group of primary human AML blasts, RIG-I reduction renders the Src family kinases hyperactive in promoting AKT activation. Mechanistically, a PxxP motif in RIG-I, upon the N-terminal CARDs' association with the Src SH1 domain, competes with the AKT PxxP motif for recognizing the Src SH3 domain. In accordance, mutating PxxP motif prevents Rig-I from inhibiting AKT activation, cytokine-stimulated myeloid progenitor proliferation, and in vivo repopulating capacity of leukemia cells. Collectively, our data suggest an antileukemia activity of RIG-I via competitively inhibiting Src/AKT association.

Comparison of the prognosis of four different surgical strategies for proximal gastric cancer: a network meta-analysis.

BACKGROUND: There is controversy regarding the long-term prognosis and short-term postoperative complications of different surgical strategies for proximal gastric cancer (PGC). METHODS: We searched for articles published in Embase (Ovid), Medline (Ovid), PubMed, Cochrane Library, and Web of Science between January 1, 1990, and February 1, 2021. We screened out the literature comparing different surgical strategies. We then evaluated the long-term and short-term outcome of different surgical strategies using a network meta-analysis, which summarizes the hazard ratio, odds ratio, mean difference, and 95% confidence interval. RESULTS: There were no significant differences between different surgical strategies for 5-year overall survival (OS), anastomotic leakage, or weight loss after 1 year. Compared with total gastrectomy with Roux-en-Y reconstruction (TG-RY) and proximal gastrectomy with double tract reconstruction (PG-DTR), the proximal gastrectomy with esophagogastrostomy (PG-EG) strategy significantly increased the incidence of reflux esophagitis; and the operation time and blood loss of the PG-EG strategy were significantly less than those of the other surgical strategies. The anastomotic stenosis rates of the PG-EG and proximal gastrectomy with jejunum interstitial (PG-JI) strategies were significantly higher than those of TG-RY and PG-DTR; the hemoglobin level after 1 year for the PG-DTR strategy was significantly higher than that of the TG-RY strategy. CONCLUSION: Our comprehensive literature research found that different surgical strategies had no significant difference in the long-term survival of PGC, but the incidence of reflux esophagitis and anastomotic stenosis after PG-DTR and TG-RY was significantly reduced.

An Improved African Vulture Optimization Algorithm for Dual-Resource Constrained Multi-Objective Flexible Job Shop Scheduling Problems.

According to the characteristics of flexible job shop scheduling problems, a dual-resource constrained flexible job shop scheduling problem (DRCFJSP) model with machine and worker constraints is constructed such that the makespan and total delay are minimized. An improved African vulture optimization algorithm (IAVOA) is developed to solve the presented problem. A three-segment representation is proposed to code the problem, including the operation sequence, machine allocation, and worker selection. In addition, the African vulture optimization algorithm (AVOA) is improved in three aspects: First, in order to enhance the quality of the initial population, three types of rules are employed in population initialization. Second, a memory bank is constructed to retain the optimal individuals in each iteration to increase the calculation precision. Finally, a neighborhood search operation is designed for individuals with certain conditions such that the makespan and total delay are further optimized. The simulation results indicate that the qualities of the solutions obtained by the developed approach are superior to those of the existing approaches.

Icariin reduces Glu-induced excitatory neurotoxicity via antioxidative and antiapoptotic pathways in SH-SY5Y cells.

Excessive glutamate (Glu) can lead to significant effects on neural cells through the generation of neurotoxic or excitotoxic cascades. Icariin (ICA) is a main active ingredient of Chinese Medicine Berberidaceae epimedium L., and has many biological activities, such as antiinflammation, antioxidative stress, and anti-depression. This study aims to evaluate the effect of ICA on Glu-induced excitatory neurotoxicity of SH-SY5Y cells. The cell viability assay was evaluated by the CCK-8 assay. The apoptosis, reactive oxygen species (ROS), and mitochondrial membrane potential were assessed by flow cytometry. Intracellular Ca2+ concentration was determined by using the fluorescent probe Fluo-3. Protein expression was detected by western blotting analysis. ICA can significantly enhance the SH-SY5Y cell viability reduced by Glu. At the same time, ICA can significantly reduce apoptosis, ROS, nitric oxide (NO) levels, and intracellular Ca2+ concentration, and significantly inhibit the increase of mitochondrial membrane potential. In addition, ICA significantly increased the expression of P47phox and iNOS, decreased p-JNK/JNK, p-P38/P38, Bax/Bcl-2, active caspase-3, and active caspase-9. These results indicate that ICA may reduce the excitatory neurotoxicity of Glu-induced SH-SY5Y cells through suppression of oxidative stress and apoptotic pathways, suggesting that ICA could be a potential therapeutic candidate for neurological disorders propagated by Glu toxicity.

Leukemic IL-17RB signaling regulates leukemic survival and chemoresistance.

Secreted proteins provide crucial signals that have been implicated in the development of acute myeloid leukemia (AML) in the bone marrow microenvironment. Here we identify aberrant expressions of inflammatory IL-17B and its receptor (IL-17RB) in human and mouse mixed lineage leukemia-rearranged AML cells, which were further increased after exposure to chemotherapy. Interestingly, silencing of IL-17B or IL-17RB led to significant suppression of leukemic cell survival and disease progression in vivo. Moreover, the IL-17B-IL-17RB axis protected leukemic cells from chemotherapeutic agent-induced apoptotic effects. Mechanistic studies revealed that IL-17B promoted AML cell survival by enhancing ERK, NF-κB phosphorylation, and the expression of antiapoptotic protein B-cell lymphoma 2, which were reversed by small-molecule inhibitors. Thus, the inhibition of the IL-17B-IL-17RB axis may be a valid strategy to enhance sensitivity and therapeutic benefit of AML chemotherapy.-Guo, H.-Z., Niu, L.-T., Qiang, W.-T., Chen, J., Wang, J., Yang, H., Zhang, W., Zhu, J., Yu, S.-H. Leukemic IL-17RB signaling regulates leukemic survival and chemoresistance.

Viral RNA-Unprimed Rig-I Restrains Stat3 Activation in the Modulation of Regulatory T Cell/Th17 Cell Balance.

Innate immunity activation by viral RNA-primed retinoid acid inducible gene-I (Rig-I) in CD4+ T cells antagonizes TGFß signaling to suppress the differentiation of regulatory T cells (Tregs). However, how viral RNA-unliganded Rig-I (apo-Rig-I) modulates Treg generation remains unclear. In this article, we show that, in the absence of viral infection, Treg differentiation of Rig-I-/- CD4+ T cells was compromised, in the presence of increased generation of Th17 cells and overactivation of Stat3, a critical regulator tilting the Treg/Th17 cell balance. Mechanistically, apo-Rig-I physically associates with Stat3, thereby inhibiting Jak1's association with Stat3 while facilitating Shp2's association to inhibit p-Stat3 levels. Interestingly, inhibition of Stat3 ameliorates the Treg/Th17 imbalance and the colitis observed in Rig-I-/- mice. Collectively, these results uncover an independent functional contribution of the apo-Rig-I/Stat3 interaction in the maintenance of Treg/Th17 cell balance.

[Effect of botulinum toxin A injection in the treatment of gastrocnemius spasticity in children aged 9-36 months with cerebral palsy: a prospective study].

OBJECTIVE: To investigate the long-term clinical efficacy and adverse effects of botulinum toxin-A (BTX-A) injection in the treatment of gastrocnemius spasticity in children aged 9-36 months with cerebral palsy. METHODS: Eighty children aged 9-36 months with cerebral palsy and gastrocnemius spasticity were selected and randomly divided into a BTX-A injection group and a conventional treatment group (n=40 each). The children in the BTX-A injection group received injections of BTX-A guided by color Doppler ultrasound and 4 courses of rehabilitation training after injection. Those in the conventional treatment group received 4 courses of the same rehabilitation training alone. Before treatment and at 1, 2, 3, and 6 months after treatment, the modified Tardieu scale (MTS) was applied to assess the degree of gastrocnemius spasticity, the values in the passive state measured by surface electromyography (sEMG) were applied to evaluate muscle tension, and the Gross Motor Function Measure (GMFM) was used to evaluate gross motor function. RESULTS: Compared with the conventional treatment group, the BTX-A injection group had significantly greater reductions in MTS score and the values in the passive state measured by sEMG (P<0.05), as well as significantly greater increases in joint angles R1 and R2 in MTS and gross motor score in GMFM (P<0.05). No serious adverse reactions related to BTX-A injection were found. CONCLUSIONS: BTX-A injection is effective and safe in the treatment of gastrocnemius spasticity in children aged 9-36 months with cerebral palsy.

Cloning and gene expression of allograft inflammatory factor-1 (AIF-1) provide new insights into injury and bacteria response of the sea cucumber Apostichopus japonicus (Selenka, 1867).

Allograft inflammatory factor-1 (AIF-1) is an interferon (IFN)-γ-inducible Ca(2+)-binding cytokine that associates with the immune defense and inflammatory response. In this study, we reported AIF-1 gene in sea cucumber Apostichopus japonicus (AjAIF-1). The full-length cDNA of AjAIF-1 is 1541 bp with an open reading frame (ORF) of 477 bp encoding 158 amino acids. Two EF-hand Ca(2+)-binding motifs were found in the deduced AjAIF-1. AjAIF-1 was widely expressed in all tested tissues (body wall, intestine, respiratory tree, tube feet, coelomocytes and longitudinal muscle), with the highest expression in respiratory tree. After Vibrio splendidus challenge and physical injury, AjAIF-1 transcripts were significantly upregulated in coelomocytes. The mRNA expression level of AjAIF-1 in coelomocytes reached to the highest value at 4 h (3.38-folds vs. the PBS control, P < 0.05) post injection. After papilla injury, the mRNA level of AjAIF-1 in coelomocytes was upregulated, and its peak value was found at 4 h (3.88-folds vs. the control, P < 0.05). These results indicated that 1) AjAIF-1 sensitively responds to pathogen infection; 2) AjAIF-1 is involved in acute inflammatory response. Our findings gain general information about the role of AjAIF-1 in the innate immunity of A. japonicus.

Structure and antitumor and immunomodulatory activities of a water-soluble polysaccharide from Dimocarpus longan pulp.

A new water-soluble polysaccharide (longan polysaccharide 1 (LP1)) was extracted and successfully purified from Dimocarpus longan pulp via diethylaminoethyl (DEAE)-cellulose anion-exchange and Sephacryl S-300 HR gel chromatography. The chemical structure was determined using Infrared (IR), gas chromatography (GC) and nuclear magnetic resonance (NMR) analysis. The results indicated that the molecular weight of the sample was 1.1 × 10(5) Da. Monosaccharide composition analysis revealed that LP1 was composed of Glc, GalA, Ara and Gal in a molar ratio of 5.39:1.04:0.74:0.21. Structural analysis indicated that LP1 consisted of a backbone of → 4)-α-D-Glcp-(1 → 4)-α-D-GALPA-(1 → 4)-α-D-Glcp-(1 → 4)-ß-D-Glcp-(1 → units with poly saccharide side chains composed of → 2)-ß-D-Fruf-(1 → 2)-L-sorbose-(1 → attached to the O-6 position of the α-D-Glcp residues. In vitro experiments indicated that LP1 had significantly high antitumor activity against SKOV3 and HO8910 tumor cells, with inhibition percentages of 40% and 50%, respectively. In addition, LP1 significantly stimulated the production of the cytokine interferon-γ (IFN-γ), increased the activity of murine macrophages and enhanced B- and T-lymphocyte proliferation. The results of this study demonstrate that LP1 has potential applications as a natural antitumor agent with immunomodulatory activity.

Fetal cerebral arteries in a new ultrasonographic perspective.

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Engineered E. coli for D-pantothenic acid production with an acetolactate isomeroreductase mutant.

D-Pantothenic acid, as a momentous vitamin, is extensively applied to feed, medicine, cosmetics and other fields. However, there are still limitations to produce D-pantothenic acid by microbial fermentation at present. In this paper, we constructed a recombinant strain for D-pantothenic acid production by blocking the organic acid pathway, boosting pyruvate biosynthesis, relieving feedback inhibition of acetolactate synthase, improving glucose intake capacity, and modifying essential genes in the metabolic pathway. In addition, a new acetolactate isomeroreductase mutant V412A origin from Escherichia coli (EcAHAIR) encoded by ilvC was obtained to explore its substrate promiscuity. Compared with the wild type, the variant EcAHAIR-V412A has reduced steric hindrance and enhanced intermolecular forces, resulting in a high affinity for 2-acetolactate. Eventually, the fermentation production of the final strain DPAN19/trc-ilvCV412A reached 4.65 g/L, increased by 192.5% compared with strain DPA8 in shake flask cultivation and produced 62.82 g/L D-pantothenic acid in a 5 L bioreactor. The metabolic engineering strategies and enzyme modification approaches described in this paper provide a particular perspective for the bio-manufacturing of D-pantothenic acid, branched-chain amino acids and its derivates.

The interaction of Synapsin 2a and Synaptogyrin-3 regulates fear extinction in mice.

The mechanisms behind a lack of efficient fear extinction in some individuals are unclear. Here, by employing a principal components analysis-based approach, we differentiated the mice into extinction-resistant and susceptible groups. We determined that elevated synapsin 2a (Syn2a) in the infralimbic cortex (IL) to basolateral amygdala (BLA) circuit disrupted presynaptic orchestration, leading to an excitatory/inhibitory imbalance in the BLA region and causing extinction resistance. Overexpression or silencing of Syn2a levels in IL neurons replicated or alleviated behavioral, electrophysiological, and biochemical phenotypes in resistant mice. We further identified that the proline-rich domain H in the C-terminus of Syn2a was indispensable for the interaction with synaptogyrin-3 (Syngr3) and demonstrated that disrupting this interaction restored extinction impairments. Molecular docking revealed that ritonavir, an FDA-approved HIV drug, could disrupt Syn2a-Syngr3 binding and rescue fear extinction behavior in Syn2a-elevated mice. In summary, the aberrant elevation of Syn2a expression and its interaction with Syngr3 at the presynaptic site were crucial in fear extinction resistance, suggesting a potential therapeutic avenue for related disorders.

A CD36-dependent non-canonical lipid metabolism program promotes immune escape and resistance to hypomethylating agent therapy in AML.

Environmental lipids are essential for fueling tumor energetics, but whether these exogenous lipids transported into cancer cells facilitate immune escape remains unclear. Here, we find that CD36, a transporter for exogenous lipids, promotes acute myeloid leukemia (AML) immune evasion. We show that, separately from its established role in lipid oxidation, CD36 on AML cells senses oxidized low-density lipoprotein (OxLDL) to prime the TLR4-LYN-MYD88-nuclear factor κB (NF-κB) pathway, and exogenous palmitate transfer via CD36 further potentiates this innate immune pathway by supporting ZDHHC6-mediated MYD88 palmitoylation. Subsequently, NF-κB drives the expression of immunosuppressive genes that inhibit anti-tumor T cell responses. Notably, high-fat-diet or hypomethylating agent decitabine treatment boosts the immunosuppressive potential of AML cells by hijacking CD36-dependent innate immune signaling, leading to a dampened therapeutic effect. This work is of translational interest because lipid restriction by US Food and Drug Administration (FDA)-approved lipid-lowering statin drugs improves the efficacy of decitabine therapy by weakening leukemic CD36-mediated immunosuppression.

Senktide blocks aberrant RTN3 interactome to retard memory decline and tau pathology in social isolated Alzheimer's disease mice.

Sporadic or late-onset Alzheimer's disease (LOAD) accounts for more than 95% of Alzheimer's disease (AD) cases without any family history. Although genome-wide association studies have identified associated risk genes and loci for LOAD, numerous studies suggest that many adverse environmental factors, such as social isolation, are associated with an increased risk of dementia. However, the underlying mechanisms of social isolation in AD progression remain elusive. In the current study, we found that 7 days of social isolation could trigger pattern separation impairments and presynaptic abnormalities of the mossy fibre-CA3 circuit in AD mice. We also revealed that social isolation disrupted histone acetylation and resulted in the downregulation of 2 dentate gyrus (DG)-enriched miRNAs, which simultaneously target reticulon 3 (RTN3), an endoplasmic reticulum protein that aggregates in presynaptic regions to disturb the formation of functional mossy fibre boutons (MFBs) by recruiting multiple mitochondrial and vesicle-related proteins. Interestingly, the aggregation of RTN3 also recruits the PP2A B subunits to suppress PP2A activity and induce tau hyperphosphorylation, which, in turn, further elevates RTN3 and forms a vicious cycle. Finally, using an artificial intelligence-assisted molecular docking approach, we determined that senktide, a selective agonist of neurokinin3 receptors (NK3R), could reduce the binding of RTN3 with its partners. Moreover, application of senktide in vivo effectively restored DG circuit disorders in socially isolated AD mice. Taken together, our findings not only demonstrate the epigenetic regulatory mechanism underlying mossy fibre synaptic disorders orchestrated by social isolation and tau pathology but also reveal a novel potential therapeutic strategy for AD.

A fuzzy model for content-centric routing in Zigbee-based wireless sensor networks (WSNs).

WSN is one of the most efficient technologies in intelligent communication and because of its advantages, this technology has been utilized in various applications. By using WSNs, different types of data can be collected and analyzed in wide environments. The high variety of applications and types of data available in this network can cause several challenges about heterogeneous data routing. This research, presents a Fuzzy Model for Content-Centric Routing (FMCCR) in WSN to solve these challenges. The performance of FMCCR is based on two basic steps: "topology control", and "data transmission through content-centric and fuzzy logic-based routing algorithm". In the first step of FMCCR, the network topology is constructed. In the second step of the proposed method, data transmission paths are determined based on network topology and content type, and data transmission is performed. The performance of FMCCR has been evaluated in a simulation environment and the results have been compared with previous algorithms. The results show that FMCCR reduce energy consumption and improve the traffic load distribution in the network in addition to increasing the network lifetime. According to the results, FMCCR can increase network lifetime at least 10.74% and at the same time, deliver at least 88.1% more packets through the network, compared to previous methods. These results, prove the efficiency of the proposed method for using in real-world scenarios.

Impact of Atypical Hyperplasia at Surgical Margins on breast cancer outcomes in patients treated with neoadjuvant chemotherapy.

Background: Women with atypical hyperplasia (AH) is associated with a higher risk of future breast cancer. However, whether AH found at margins in patients with breast-conserving surgery (BCS) after neoadjuvant chemotherapy (NAC) needs re-excision is not well-defined. The aim of the present study was to evaluate the impact of AH at the surgical margins on the local recurrence and survival outcomes in breast cancer patients treated with NAC and BCS. Methods: A retrospective analysis comparing patients who treated with NAC and BCS with AH at the margins to those without AH was performed. Results: 598 patients were included in this study. The 5-year rates of ipsilateral breast tumor recurrence (IBTR) were 4.6% and 6.2% in patients with and without AH, respectively. No significant differences were observed among the two groups in terms of IBTR, DMFS, or OS. HER2 overexpressing breast cancer patients with severe AH at margins have a significantly higher risk of IBTR compared to those without severe AH. Conclusion: Our study suggests that the presence of AH at the surgical margins of BCS in patients who received NAC does not appear to increase the risk of ipsilateral breast cancer. Therefore, there is no need for surgeons to routinely perform additional re-excision of AH found at the margins of BCS in these patients. However, selective re-excision should be considered in certain cases, particularly in patients with HER2 overexpression.