PDZK1 suppresses TNBC development and sensitizes TNBC cells to erlotinib via the EGFR pathway.

Epidermal growth factor receptor (EGFR)-targeted drugs (erlotinib, etc.) are used to treat multiple types of tumours. EGFR is highly expressed in most triple-negative breast cancer (TNBC) patients. However, only a small proportion of TNBC patients benefit from EGFR-targeted drugs in clinical trials, and the resistance mechanism is unclear. Here, we found that PDZ domain containing 1 (PDZK1) is downregulated in erlotinib-resistant TNBC cells, suggesting that PDZK1 downregulation is related to erlotinib resistance in TNBC. PDZK1 binds to EGFR. Through this interaction, PDZK1 promotes EGFR degradation by enhancing the binding of EGFR to c-Cbl and inhibits EGFR phosphorylation by hindering EGFR dimerisation. We also found that PDZK1 is specifically downregulated in TNBC tissues and correlated with a poor prognosis in TNBC patients. In vitro and in vivo functional assays showed that PDZK1 suppressed TNBC development. Restoration of EGFR expression or kinase inhibitor treatment reversed the degree of cell malignancy induced by PDZK1 overexpression or knockdown, respectively. PDZK1 overexpression sensitised TNBC cells to erlotinib both in vitro and in vivo. In conclusion, PDZK1 is a significant prognostic factor for TNBC and a potential molecular therapeutic target for reversing erlotinib resistance in TNBC cells.

MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery.

In the context of precision medicine, multiomics data integration provides a comprehensive understanding of underlying biological processes and is critical for disease diagnosis and biomarker discovery. One commonly used integration method is early integration through concatenation of multiple dimensionally reduced omics matrices due to its simplicity and ease of implementation. However, this approach is seriously limited by information loss and lack of latent feature interaction. Herein, a novel multiomics early integration framework (MOINER) based on information enhancement and image representation learning is thus presented to address the challenges. MOINER employs the self-attention mechanism to capture the intrinsic correlations of omics-features, which make it significantly outperform the existing state-of-the-art methods for multiomics data integration. Moreover, visualizing the attention embedding and identifying potential biomarkers offer interpretable insights into the prediction results. All source codes and model for MOINER are freely available https://github.com/idrblab/MOINER.

MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics.

Protein structure prediction is a longstanding issue crucial for identifying new drug targets and providing a mechanistic understanding of protein functions. To enhance the progress in this field, a spectrum of computational methodologies has been cultivated. AlphaFold2 has exhibited exceptional precision in predicting wild-type protein structures, with performance exceeding that of other methods. However, predicting the structures of missense mutant proteins using AlphaFold2 remains challenging due to the intricate and substantial structural alterations caused by minor sequence variations in the mutant proteins. Molecular dynamics (MD) has been validated for precisely capturing changes in amino acid interactions attributed to protein mutations. Therefore, for the first time, a strategy entitled 'MoDAFold' was proposed to improve the accuracy and reliability of missense mutant protein structure prediction by combining AlphaFold2 with MD. Multiple case studies have confirmed the superior performance of MoDAFold compared to other methods, particularly AlphaFold2.

Müller-Weiss Disease: Midfoot Arthrodesis in Reduction vs Malreduction.

BACKGROUND: Midfoot arthrodesis is regarded as the main surgical approach for treating Müller-Weiss disease (MWD). This study aimed to investigate the incidence of postoperative pain during MWD treatment through midfoot reduction or malreduction during arthrodesis and to explore the factors influencing postoperative pain in patients with MWD. METHODS: A total of 67 patients with MWD were recruited and divided into two groups according to whether midfoot alignment was reduced: reduction group (n = 38) and malreduction group (n = 29). Demographic characteristics before the operation and at the last follow-up, as well as clinical and radiographic parameters, were compared between the two groups. Clinical parameters included the American Orthopaedic Foot & Ankle Society score and visual analog scale score, whereas radiographic parameters included the calcaneal pitch angle, lateral Meary's angle, talometatarsal-1 angle dorsoplantar (TMT1dp), talocalcaneal angle dorsoplantar (Kite angle), talonavicular coverage angle, and medial navicular pole extrusion. Postoperative complications and incidence of midfoot pain were evaluated at the last follow-up visit. RESULTS: The reduction group exhibited better clinical and radiological parameters, including the TMT1dp and medial navicular pole extrusion, than the malreduction group at the last follow-up (all P < .05). However, the calcaneal pitch angle, lateral Meary's angle, Kite angle, and talonavicular coverage angle did not significantly differ between the two groups (all P > .05). The overall incidence of midfoot pain was 26.4%. The reduction group showed a lower incidence of medial pain than the malreduction group (15.7% vs. 40.0%, P < .05). Regression analysis revealed that midfoot abduction, represented by the TMT1dp, was a critical factor for midfoot arthrodesis failure and that medial navicular pole extrusion was not correlated with postoperative midfoot pain. CONCLUSION: Midfoot reduction arthrodesis yields better clinical outcomes than malreduction arthrodesis. The TMT1dp, representing midfoot abduction, is a key factor for midfoot arthrodesis failure. The extruded medial navicular bone may not affect postoperative medial midfoot pain. LEVEL OF EVIDENCE: Level III, retrospective comparative study.

AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding.

Protein function annotation has been one of the longstanding issues in biological sciences, and various computational methods have been developed. However, the existing methods suffer from a serious long-tail problem, with a large number of GO families containing few annotated proteins. Herein, an innovative strategy named AnnoPRO was therefore constructed by enabling sequence-based multi-scale protein representation, dual-path protein encoding using pre-training, and function annotation by long short-term memory-based decoding. A variety of case studies based on different benchmarks were conducted, which confirmed the superior performance of AnnoPRO among available methods. Source code and models have been made freely available at: https://github.com/idrblab/AnnoPRO and https://zenodo.org/records/10012272.

Changes in clinical outcomes and alignment of the ipsilateral knee and ankle after supramalleolar osteotomy in patients with varus osteoarthritis of the ankle: a short-term follow-up study.

PURPOSE: The purpose of this study was to investigate the changes in clinical outcomes and alignment of the ipsilateral knee and ankle in patients with varus ankle osteoarthritis after supramalleolar osteotomy (SMO). METHODS: We retrospectively reviewed 23 patients (24 ankles) with Takakura II, IIIa and IIIb ankle osteoarthritis treated with SMO between May 2017 and March 2022. The radiologic parameters of ankles contained medial distal tibial angle (TAS), tibiotalar angle (TT), tibial lateral surface (TLS), tibial plafond inclination (TPI) and talar inclination (TI). The radiologic parameters of knees contained medial proximal tibial angle (MPTA), joint line convergence angle (JLCA), the knee joint line orientation relative to ground (G-KJLO) and WBL. Hip-knee-ankle angle (HKA) was also collected. The Takakura system was used for evaluating the ankle osteoarthritis and the Kellgren-Lawrence (KL) system was used for evaluating the knee osteoarthritis. Clinical evaluation of the ankle joints contained American Orthopedic Foot and Ankle Society (AOFAS), range of motion (ROM) and visual analogue scale (VAS). Clinical evaluation of the knee joints contained Japanese Orthopaedic Association Scores (JOA), ROM, VAS. RESULTS: The mean follow-up times were 20.3 ± 7.3 months (range 12-38). According to the radiologic evaluation, the TAS increased from preoperative 84.7° ± 2.0° to 91.2° ± 1.8° at the last follow-up (P < 0.001). The TPI and TI decreased from 4.4° ± 4.2° and 11.0° ± 5.2° to 0.1° ± 4.7° and 4.1° ± 4.8° (P < 0.001 for both). The TT angel improved from 9.5° ± 4.1° to 4.9° ± 3.3° (P < 0.001). No significant differences were found regarding MPTA, JLCA, G-KJLO, knee WBL and HKA (P > 0.05 for all). The Takakura stage improved after SMO (P < 0.001) whilst the KL stage maintains the similar lever (P > 0.05). According to the clinical evaluation, the AOFAS significantly increased from 67.5 ± 10.6 to 88.5 ± 9.3 and the VAS of the ankle decreased from 4.7 ± 1.6 to 1.2 ± 1.1, whilst there were no changes on VAS and even the JOA and knee ROM after SMO (P > 0.05 for all). CONCLUSIONS: SMO can alleviate the symptoms of varus ankle osteoarthritis and delay the time for ankle replacement or arthrodesis by redistributing the abnormal stress of the ankle and restoring the congruence of the tibiotalar joint. In addition, it did not induce the clinical symptoms of knee without compromising lower limb alignment or knee joint line orientation in the short term. LEVEL OF EVIDENCE: Level IV case series.

A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder.

RNAs play essential roles in diverse physiological and pathological processes by interacting with other molecules (RNA/protein/compound), and various computational methods are available for identifying these interactions. However, the encoding features provided by existing methods are limited and the existing tools does not offer an effective way to integrate the interacting partners. In this study, a task-specific encoding algorithm for RNAs and RNA-associated interactions was therefore developed. This new algorithm was unique in (a) realizing comprehensive RNA feature encoding by introducing a great many of novel features and (b) enabling task-specific integration of interacting partners using convolutional autoencoder-directed feature embedding. Compared with existing methods/tools, this novel algorithm demonstrated superior performances in diverse benchmark testing studies. This algorithm together with its source code could be readily accessed by all user at: https://idrblab.org/corain/ and https://github.com/idrblab/corain/.

Screening of Tnfaip1-Interacting Proteins in Zebrafish Embryonic cDNA Libraries Using a Yeast Two-Hybrid System.

TNFAIP1 regulates cellular biological functions, including DNA replication, DNA repair, and cell cycle, by binding to target proteins. Identification of Tnfaip1-interacting proteins contributes to the understanding of the molecular regulatory mechanisms of their biological functions. In this study, 48 hpf, 72 hpf, and 96 hpf wild-type zebrafish embryo mRNAs were used to construct yeast cDNA library. The library titer was 1.12 × 107 CFU/mL, the recombination rate was 100%, and the average length of the inserted fragments was greater than 1000 bp. A total of 43 potential interacting proteins of Tnfaip1 were identified using zebrafish Tnfaip1 as a bait protein. Utilizing GO functional annotation and KEGG signaling pathway analysis, we found that these interacting proteins are mainly involved in translation, protein catabolic process, ribosome assembly, cytoskeleton formation, amino acid metabolism, and PPAR signaling pathway. Further yeast spotting analyses identified four interacting proteins of Tnfaip1, namely, Ubxn7, Tubb4b, Rpl10, and Ybx1. The Tnfaip1-interacting proteins, screened from zebrafish embryo cDNA in this study, increased our understanding of the network of Tnfaip1-interacting proteins during the earliest embryo development and provided a molecular foundation for the future exploration of tnfaip1's biological functions.

ARHGAP11A Is a Novel Prognostic and Predictive Biomarker Correlated with Immunosuppressive Microenvironment in Clear Cell Renal Cell Carcinoma.

Clear cell renal cell carcinoma (ccRCC) is a highly immunogenic tumor and immune dysfunction is associated with ccRCC poor prognosis. The RhoGTPase-activating proteins (RhoGAPs) family was reported to affect ccRCC development, but its role in immunity and prognosis prediction for ccRCC remain unknown. In the current study, we found ARHGAP11A was the only independent risk factor among 33 RhoGAPs (hazard ratio [HR] 1.949, 95% confidence interval [CI] 1.364-2.785). High ARHGAP11A level was associated with shorter overall survival (OS, HR 2.040, 95% CI 1.646-3.417) and ARHGAP11A is a prognostic biomarker for ccRCC. ARHGAP11A knockdown suppressed renal cell carcinoma (RCC) cell proliferation, colony formation, and migration, suggesting the promoting role of ARHGAP11A on RCC development. Mechanistically, ARHGAP11A might contribute to the suppressive tumor immune microenvironment (TIME). High ARHGAP11A level was correlated with infiltration of immunosuppressive cells (including T helper 2 (Th2) cells, regulatory T (Treg) cells, myeloid derived suppressor cells (MDSC), and M2 macrophage cells), activation of immunosuppressive pathways (IL6-JAK-STAT3 signaling and IFNγ response), and expression of inhibitory immune checkpoints (ICs). ARHGAP11A could promote T cell exhaustion and induce immune escape. ccRCC patients with low ARHGAP11A level were more suitable for immune checkpoint inhibitors (ICIs) therapy, while those with high ARHGAP11A level might benefit from a combination of ARHGAP11A blockade and ICIs. In all, ARHGAP11A might serve as a novel prognostic marker, therapeutic target, and predictor in the clinical response to ICIs therapy for ccRCC.

RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction.

Ribonucleic acids (RNAs) involve in various physiological/pathological processes by interacting with proteins, compounds, and other RNAs. A variety of powerful computational methods have been developed to predict such valuable interactions. However, all these methods rely heavily on the 'digitalization' (also known as 'encoding') of RNA-associated interacting pairs into a computer-recognizable descriptor. In other words, it is urgently needed to have a powerful tool that can not only represent each interacting partner but also integrate both partners into a computer-recognizable interaction. Herein, RNAincoder (deep learning-based encoder for RNA-associated interactions) was therefore proposed to (a) provide a comprehensive collection of RNA encoding features, (b) realize the representation of any RNA-associated interaction based on a well-established deep learning-based embedding strategy and (c) enable large-scale scanning of all possible feature combinations to identify the one of optimal performance in RNA-associated interaction prediction. The effectiveness of RNAincoder was extensively validated by case studies on benchmark datasets. All in all, RNAincoder is distinguished for its capability in providing a more accurate representation of RNA-associated interactions, which makes it an indispensable complement to other available tools. RNAincoder can be accessed at https://idrblab.org/rnaincoder/.

Medial malleolar window approach for varus-type tibial pilon fractures: a retrospective study.

PURPOSE: Choosing a suitable surgical approach is crucial and challenging for type C pilon fractures. This article aims to explore the clinical efficacy of the medial malleolar window approach for varus-type tibial pilon fractures. METHODS: A retrospective analysis was conducted on 38 patients with type C varus-type pilon fractures treated between May 2018 and June 2021. In total, 16 cases underwent surgical treatment through the medial malleolar window approach and 22 cases were treated with the traditional anteromedial approach combined with a posterior approach. The operation time, hospitalization time, fracture healing time, the American Orthopedic Foot and Ankle score, Visual Analogue Scale, and complications were recorded to comprehensively evaluate the clinical efficacy of the technique. Fracture reduction quality was evaluated using the criteria proposed by Burwell and Charnley. RESULTS: All patients were followed up. No patients presented delayed union or nonunion. Compared with the conventional approach, the medial malleolar window approach had the advantage of better clinical effect recovery and better fracture reduction (P < 0.05). Meanwhile, the medial malleolar window approach had a shorter operation time, although the statistics suggest no significant difference with the control group. No implant exposure or infection occurred. There was good wound healing at two weeks after surgery in all but two cases. Local wound edge necrosis developed in one case in the medial malleolar window approach group, and the wound could not be closed at one stage in another case in the conventional group because of excessive tension, requiring secondary closure. CONCLUSION: The medial malleolar window approach provides excellent exposure to type C pilon fractures, allowing for satisfactory fracture reduction and functional rehabilitation. The medial window approach is recommended for varus-type pilon fractures, which can effectively avoid a posterior incision and reduce the operation time.

CRISPR/Cas9-Mediated Knockout of tnfaip1 in Zebrafish Plays a Role in Early Development.

TNF α-induced protein 1 (TNFAIP1) was first identified in human umbilical vein endothelial cells and can be induced by tumor necrosis factor α (TNFα). Early studies have found that TNFAIP1 is involved in the development of many tumors and is closely associated with the neurological disorder Alzheimer's disease. However, little is known about the expression pattern of TNFAIP1 under physiological conditions and its function during embryonic development. In this study, we used zebrafish as a model to illustrate the early developmental expression pattern of tnfaip1 and its role in early development. First, we examined the expression pattern of tnfaip1 during early zebrafish development using quantitative real-time PCR and whole mount in situ hybridization and found that tnfaip1 was highly expressed in early embryonic development and, subsequently, expression became localized to anterior embryonic structures. To investigate the function of tnfaip1 during early development, we constructed a model of a stably inherited tnfaip1 mutant using the CRISPR/Cas9 system. Tnfaip1 mutant embryos showed significant developmental delays as well as microcephaly and microphthalmia. At the same time, we found decreased expression of the neuronal marker genes tuba1b, neurod1, and ccnd1 in tnfaip1 mutants. Analysis of transcriptome sequencing data revealed altered expression of the embryonic development related genes dhx40, hspa13, tnfrsf19, nppa, lrp2b, hspb9, clul1, zbtb47a, cryba1a, and adgrg4a in the tnfaip1 mutants. These findings suggest an important role for tnfaip1 in the early development of zebrafish.

SoCube: an innovative end-to-end doublet detection algorithm for analyzing scRNA-seq data.

Doublets formed during single-cell RNA sequencing (scRNA-seq) severely affect downstream studies, such as differentially expressed gene analysis and cell trajectory inference, and limit the cellular throughput of scRNA-seq. Several doublet detection algorithms are currently available, but their generalization performance could be further improved due to the lack of effective feature-embedding strategies with suitable model architectures. Therefore, SoCube, a novel deep learning algorithm, was developed to precisely detect doublets in various types of scRNA-seq data. SoCube (i) proposed a novel 3D composite feature-embedding strategy that embedded latent gene information and (ii) constructed a multikernel, multichannel CNN-ensembled architecture in conjunction with the feature-embedding strategy. With its excellent performance on benchmark evaluation and several downstream tasks, it is expected to be a powerful algorithm to detect and remove doublets in scRNA-seq data. SoCube is freely provided as an end-to-end tool on the Python official package site PyPi (https://pypi.org/project/socube/) and open-source on GitHub (https://github.com/idrblab/socube/).

Talonavicular-cuneiform arthrodesis for the treatment of Müller-Weiss: mid-term results of 15 cases after 5 years.

BACKGROUND: There is no gold standard for the operative treatment of patients with Müller-Weiss disease (MWD). This study reports the mid-term follow-up results for at least 5 years following talonavicular-cuneiform (TNC) arthrodesis for Müller-Weiss disease. METHODS: A total of 15 patients undergoing TNC arthrodesis for MWD were retrospectively reviewed between January 2015 and August 2017. Two senior doctors assessed the radiographic results twice at each visit (preoperative, three months after the operation, and final follow-up). The clinical results and complications from preoperative and final follow-up were recorded. RESULTS: The mean follow up period was 74.0 (range 64 to 90) months. The calcaneal pitch angle, lateral Meary's angle, anteroposterior (AP) Meary's angle, AP talocalcaneal angle, and talonavicular coverage were significantly different before and three months after the operation (p < 0.05). There was no significant difference between the radiographic results of three months after the operation and the final follow-up (p > 0.05). The radiological measurements of the two senior doctors were calculated and found to be moderate to strong (ICC:0.899-0.995). The AOFAS, VAS, and SF-12 scores significantly improved at the last follow-up compared to those before the operation (p < 0.05). Two patients experienced early complications, four had late complications, and one underwent a second operation of midfoot fusion with calcaneal osteotomy. CONCLUSION: This research confirms that using TNC arthrodesis for the treatment of MWD can substantially improve the clinical and radiographic results. These results were maintained until mid-term follow-up.

Label-free proteome quantification and evaluation.

The label-free quantification (LFQ) has emerged as an exceptional technique in proteomics owing to its broad proteome coverage, great dynamic ranges and enhanced analytical reproducibility. Due to the extreme difficulty lying in an in-depth quantification, the LFQ chains incorporating a variety of transformation, pretreatment and imputation methods are required and constructed. However, it remains challenging to determine the well-performing chain, owing to its strong dependence on the studied data and the diverse possibility of integrated chains. In this study, an R package EVALFQ was therefore constructed to enable a performance evaluation on >3000 LFQ chains. This package is unique in (a) automatically evaluating the performance using multiple criteria, (b) exploring the quantification accuracy based on spiking proteins and (c) discovering the well-performing chains by comprehensive assessment. All in all, because of its superiority in assessing from multiple perspectives and scanning among over 3000 chains, this package is expected to attract broad interests from the fields of proteomic quantification. The package is available at https://github.com/idrblab/EVALFQ.

A novel distractor-assisted reduction combined with the sinus tarsi approach for joint depression-type calcaneal fractures.

PURPOSE: A novel percutaneous distractor with the advantage of axial and direct distraction was designed for the minimally invasive treatment of calcaneal fractures. The purpose of this study was to investigate the clinical results and complications of a novel distractor combined with sinus tarsi approach (STA) in treatment of the joint depression-type of calcaneal fractures. METHODS: Fifty-four patients with the depression-type of calcaneal fractures (30 Sanders type II, 22 Sanders type III, 2 Sanders type IV) who were subjected to the novel distractor combined with STA were retrospectively assessed. Calcaneal height, width, and length; Bohler's angle; and the Gissane angle were evaluated pre-operatively and post-operatively. Clinical outcomes were assessed using the American Orthopedic Foot and Ankle Society (AOFAS) and visual analog scale (VAS) pain scores from the last follow-up. Complications were also recorded. RESULTS: Fifty-two patients achieved an average follow-up of 24.3 months (range 18 to 34 months), and two patients were lost to follow-up six months post-operatively. There was significant difference between pre-operative and post-operative calcaneal height, width, and length; Bohler's angle; and Gissane angle (p < 0.01), but no significant difference was detected between the post-operative and normal side Bohler's angle (p > 0.05). The AOFAS ankle and hind foot score was 88.4 ± 6.6, and the VAS score was 1.9 ± 0.7 at the last follow-up. Nine (17.3%) patients developed complications: One experienced skin necrosis and two had screws loosening; three patients developed early degenerative changes of the subtalar joint; two had no symptoms; one had light pain around the subtalar joint without medical treatment; complex regional pain syndrome (CRPS) developed in one patient after seven months post-operatively; and two developed transient ankle stiffness. CONCLUSION: The novel distractor combined with the STA effectively reconstructs the facet depression-type of calcaneal fractures (sanders type II and III) with minimal complications.

Deciphering the internal driving mechanism of microbial community for carbon conversion and nitrogen fixation during food waste composting with multifunctional microbial inoculation.

In this study, the effects of multifunctional microbial inoculation on food waste composting based on the synergistic property between organic matter degradation and nitrogen fixation were investigated. The results showed that inoculation simultaneously strengthened organic matter degradation by 9.9% and improved the nitrogen content by 20.6% compared with that of the control group. Additionally, spectral analysis demonstrated that inoculation was conducive to the enhanced humification, which was supported by the improvement in polyphenol oxidase activity. Microbial analysis showed that most of the introduced microorganisms (Bacillus, Streptomyces, Saccharomonospora) successfully colonized, and stimulated the growth of other indigenous microorganisms (Enterobacter, Paenibacillus). Meanwhile, the change in microbial community structure was accompanied by the enhanced tricarboxylic acid cycle and amino acid metabolism. Furthermore, network analysis and structural equation model revealed that the enhanced cooperation of microorganisms, in which more carbon sources could be provided by cellulose decomposition for nitrogen fixation.

The Protective Effect of Ginsenoside Rg1 on Apoptosis in Human Ankle Joint Traumatic Arthritis Chondrocytes.

The ankle biomechanics is easily changed due to the acute injury of the tissue around the ankle joint and the damage of the ankle joint structure, such as ankle instability and joint surface imbalance. When the mechanical load of the ankle changes, it can cause ankle regeneration and remodeling processes such as cartilage loss, bone remodeling, and degenerative changes. The aim of this study was to investigate the effect and mechanism of ginsenoside Rg1 against interleukin-1ß (IL-1ß)-induced apoptosis in human articular chondrocytes (HACs). The apoptosis model of HAC cells was established by IL-1ß induction, and then the HAC cells were cultured with different concentrations of Rg1. The protective effect of Rg1 on HAC cell apoptosis was investigated by detecting the changes of apoptosis and activity of PI3K/Akt/mitochondrial signaling pathway. The results showed that a specific concentration of Rg1 could promote the proliferation of IL-1ß-induced HAC cells and inhibit apoptosis. At the same time, Rg1 treatment with specific concentration can reduce the content of reactive oxygen species (ROS) and malondialdehyde (MDA) in HACs and improve the related expression of mitochondrial membrane potential (MMP). Furthermore, qRT-PCR and western blot results showed that Rg1 could improve the low expression of Bcl-2 and inhibit the high expression of Bax, caspase-3, caspase-8, caspase-9, FasL, AIF, and Cyto c in IL-1ß-induced cells. In summary, Rg1 can inhibit IL-1ß-induced apoptosis of HAC cells by decreasing the activity of PI3K/Akt/mitochondrial signaling pathway, and Rg1 has a protective effect on apoptosis of HAC cells.

Insights into the effect of iron-carbon particle amendment on food waste composting: Physicochemical properties and the microbial community.

The effects of iron-carbon (Fe-C) particle amendment on organic matter degradation, product quality and functional microbial community in food waste composting were investigated. Fe-C particles (10%) were added to the material and composted for 32 days in a lab-scale composting system. The results suggested that Fe-C particle enhanced organic matter degradation by 12.3%, particularly lignocellulose, leading to a greater humification process (increased by 15.5%). In addition, NO3--N generation was enhanced (15.9%) by nitrification with more active ammonia monooxygenase and nitrite oxidoreductase activities in the cooling and maturity periods. Fe-C particles not only significantly increased the relative abundances of Bacillus and Aspergillus for organic matter decomposition, but also decreased the relative abundances of acid-producing bacteria. RDA analysis demonstrated that the bacterial community was significantly influenced by dissolved organic matter, C/N, NO3--N, humic acid, volatile fatty acids and pH, while electrical conductivity was the key factor affecting the fungal community.

Optimization of metabolomic data processing using NOREVA.

A typical output of a metabolomic experiment is a peak table corresponding to the intensity of measured signals. Peak table processing, an essential procedure in metabolomics, is characterized by its study dependency and combinatorial diversity. While various methods and tools have been developed to facilitate metabolomic data processing, it is challenging to determine which processing workflow will give good performance for a specific metabolomic study. NOREVA, an out-of-the-box protocol, was therefore developed to meet this challenge. First, the peak table is subjected to many processing workflows that consist of three to five defined calculations in combinatorially determined sequences. Second, the results of each workflow are judged against objective performance criteria. Third, various benchmarks are analyzed to highlight the uniqueness of this newly developed protocol in (1) evaluating the processing performance based on multiple criteria, (2) optimizing data processing by scanning thousands of workflows, and (3) allowing data processing for time-course and multiclass metabolomics. This protocol is implemented in an R package for convenient accessibility and to protect users' data privacy. Preliminary experience in R language would facilitate the usage of this protocol, and the execution time may vary from several minutes to a couple of hours depending on the size of the analyzed data.