CCT6A promotes cell proliferation in colon cancer by targeting BIRC5 associated with p53 status.

Chaperonin-containing TCP1 (CCT) is a multi-subunit complex, known to participate the correct folding of many proteins. Currently, the mechanism underlying CCT subunits in cancer progression is incompletely understood. Based on data analysis, the expression of CCT subunit 6 A (CCT6A) is found higher than the other subunits of CCT and correlated with an unfavorable prognosis in colon cancer. Here, we find CCT6A silencing suppresses colon cancer proliferation and survival phenotype in vitro and in vivo. CCT6A plays a role in cellular process, including the cell cycle, p53, and apoptosis signaling pathways. Further investigations have shown direct binding between CCT6A and both Wtp53 and Mutp53, and BIRC5 is found to act downstream of CCT6A. The highlight is that CCT6A inhibition significantly reduces BIRC5 expression independent of Wtp53 levels in Wtp53 cells. Conversely, in Mutp53 cells, downregulation of BIRC5 by CCT6A inhibition mainly depends on Mutp53 levels. Additionally, combined CCT6A inhibition and Wtp53 overexpression in Mutp53 cell lines effectively suppresses cell proliferation. It is concluded CCT6A is a potential oncogene that influences BIRC5 through distinct pathways in Wtp53 and Mutp53 cells.

Synergistic Bipolar Irreversible Electroporation for Tumor Ablation without Muscle Contraction.

Irreversible electroporation (IRE) has emerged as a promising modality for tumor ablation, leveraging the controlled application of electrical pulses to induce cell death. However, the associated muscle contractions during the procedure pose challenges. This study introduces a novel approach, termed Synergistic Bipolar Irreversible Electroporation (SBIRE), aimed at achieving tumor ablation without the undesirable side effect of muscle contraction. SBIRE involves the simultaneous application of nanosecond bipolar electrical pulses (±1600 V per 0.2 cm or ±8000 V per 1 cm, ±500 ns, "+" to "-" delay 1 µs, "-" to "+" delay 200 µs, 5 cycles) and microsecond bipolar electrical pulses (±300 V per 0.2 cm or ±1500 V per 1 cm, ±2 µs, "+" to "-" delay 2 µs, "-" to "+" delay 1000 µs, 25 cycles), strategically designed to synergistically target tumor cells while minimizing the impact on adjacent muscle tissue. The experimental setup includes in vitro and in vivo studies utilizing tumor cells and animal models to assess the efficacy of SBIRE. Preliminary results demonstrate the effectiveness of SBIRE in inducing irreversible electroporation within the tumor, leading to cell death, and the ablation effect is better than other parameter forms (24.41±0.23 mm2 (SBIRE group) vs 12.93±0.31 mm2 (ns group), 6.55±0.23 mm2 (µs group), 19.54±0.25 mm2 (ns+µs group), p<0.0001). Notably, muscle contraction is significantly reduced compared to traditional IRE procedures, highlighting the potential of SBIRE to enhance patient comfort and procedural success. The development of SBIRE represents a significant advancement in the field of tumor ablation, addressing a fundamental limitation associated with muscle contraction during IRE. This technique not only offers a valuable and promising approach to tumor treatment but also holds promise for minimizing procedural side effects.

miR-940 modulates CD47 to suppress biological functions of lung adenocarcinoma cells.

OBJECTIVE: mir-940 and CD47 play regulatory and immunoregulatory roles in lung cancer. While previous study found that the expression of mir-940 decreased, associated with the increasing of CD47 in lung adenocarcinoma. However, their inherent correlations remain elusive. Herein, this experiment intends to search for the relevant molecular mechanisms regulating the biological function of non-small cell lung cancer. METHODS: The cancer and adjacent tissue samples were collected from 20 pairs of newly diagnosed non-small cell lung cancer patients without applying radiotherapy and chemotherapy. We performed immunohistochemistry containing 45 lung adenocarcinoma tissues to investigate the relationship between the clinicopathological features and CD47 expression. The expressions of mir-940 and CD47 were detected by real-time quantitative polymerase chain reaction (qRT-PCR). Lung epithelial and lung adenocarcinoma (A549, H1299, GLC-82, PC-9) cell lines were cultured to detect the expression of mir-940 and CD47 molecules in each cell line. According to the expression situation, 2 cell lines were selected for mimic and siRNA transfection, and the transfection efficiency was also verified by qRT-PCR and western blot. CCK-8, transwell migration, transwell invasion, and colony formation assays were used to detect the changes in biological functions of lung adenocarcinoma cells after transfection, such as enhanced proliferation, migration, invasion, and cloning. The changes of related protein molecules after transfection were detected by western blot. The dual-luciferase experiment verified the targeting regulation relationship between mir-940 and CD47. Finally, flow cytometry analysis of apoptosis and cell cycle were carried out to detect apoptosis cells and change phase of cell cycle distribution. RESULTS: CD47 expression was not associated with clinicopathologic factors in lung adenocarcinoma. The proliferation, migration, invasion, and cloning abilities of lung adenocarcinoma cells were weakened after transfection with mir-940 mimic and siRNA-CD47. Overexpression of CD47 could promote proliferation, migration, invasion, cloning abilities, reduce apoptosis rate and attenuate the antitumor effect of mir-940 on lung adenocarcinoma. Dual luciferase experiments confirmed that mir-940 can target CD47 molecules. CONCLUSION: mir-940 can inhibit the biological function of lung adenocarcinoma cells by targeting CD47.

Human papillomavirus infections among women with cervical lesions and cervical cancer in Yueyang, China: a cross-sectional study of 3674 women from 2019 to 2022.

PURPOSE: To investigate the distribution of the incidence and genotypes of human papillomavirus (HPV) among women with cervical cancer (CC) and precancerous cervical lesions in Yueyang City, China, to develop prevention and control strategies for CC. METHODS: A total of 3674 patients with cervical lesions and cervical cancer who attended 7 hospitals in Yueyang City between September 2019 and September 2022 were included. They included 1910 cervical intraepithelial neoplasia (CIN) I, 718 CIN II, 576 CIN II and 470 CC, respectively. The HPV genotyping of the above patients was detected by Real time-PCR in the laboratory department of each hospital. RESULTS: The total HPV prevalence was 74.69% (95% CI 73.28-76.09%) in 3674 patients. The incidence of high- and low-risk HPV was 73.46% and 7.21%, respectively. The prevalence of HPV in CIN I, CIN II, CIN III, and invasive CC (ICC) groups was 66.65% (1273/1910, 95% CI 64.53-68.77%), 80.78% (580/718, 95% CI 77.89-83.67%), 83.88% (483/576, 95% CI 80.84-86.87%), and 86.81% (408/470, 95% CI 83.74-89.88%), respectively. The top three HPV subtypes in ICC are HPV16, HPV52, and HPV58. The prevalence of HPV 16 increased with increasing disease severity, with this genotype being present in 12.57%, 20.89%, 36.98%, and 50.85% of CIN I, CIN II, CIN III, and ICC cases, respectively (p < 0.001). Single HPV infection was predominant in cervical lesions, with a prevalence of 48.50% (95% CI 46.89-50.12%). The HPV prevalence varied by age, being highest among women with ICC, CIN I, CIN II and CIN III aged ≥ 60 years, 50-59 years, 40-49 years, and 40-49 years, respectively. CONCLUSION: The prevalence of HPV in patients with cervical lesions in Yueyang City was very high, with HPV 16, 52, 58, 53, and 51 being the five most common HPV genotypes in patients with cervical lesions.

HRD1 promotes non-small cell lung carcinoma metastasis by blocking autophagy-mediated MIEN1 degradation.

Dysregulation of autophagy has been implicated in the development of many diseases, including cancer. Here, we revealed a novel function of the E3 ubiquitin ligase HRD1 in non-small cell lung carcinoma (NSCLC) metastasis by regulating autophagy. Mechanistically, HRD1 inhibits autophagy by promoting ATG3 ubiquitination and degradation. Additionally, a pro-migratory and invasive factor, MIEN1 (migration and invasion enhancer 1), was found to be autophagically degraded upon HRD1 deficiency. Importantly, expression of both HRD1 and MIEN1 are upregulated and positively correlated in lung tumors. Based on these results, we proposed a novel mechanism of HRD1 function that the degradation of ATG3 protein by HRD1 leads to autophagy inhibition and MIEN1 release, thus promoting NSCLC metastasis. Therefore, our findings provided new insights into the role of HRD1 in NSCLC metastasis and new therapeutic targets for lung cancer treatment.

Mechanical stimuli-induced CCL2 restores adult mouse cells to regenerate hair follicles.

Aged cells have declined regenerative ability when subjected to environmental insult. Here we elucidate the mechanism by which mechanical stimulus induces hair regeneration at the microenvironmental regulation level using the hair plucking and organoid culture models. We observed that the skin cells harvested from post-plucking day 3 (PPD3) have the best self-organizing ability during skin organoid culture and have the highest hair regeneration upon transplantation. By bulk RNA sequencing (RNA-seq) and single-cell RNA-seq analysis and in situ hybridization, we identified that the chemokine signaling pathway genes including CCL2 are significantly increased in the skin at PPD3 and in skin organoid cultures. Immunostaining shows that the PPD3 skin epithelial cells have increased multipotency, which is verified by the ability to self-organize to form epidermal aggregates during organoid culture. By adding CCL2 recombinant protein to the organoid culture using an environmental reprogramming protocol, we observed the PPD0 adult skin cells, which lose their regenerative ability can self-organize in organoid culture and regenerate hair follicles robustly upon transplantation. Our study demonstrates that CCL2 functions in immune regulation of hair regeneration under mechanical stimulus, and enhances cell multipotency during organoid culture. This provides a therapeutic potential for future clinical application.

Biomimetic hydrophobic plastic foams with aligned channels for rapid oil absorption.

Although many oil absorption materials have been developed, it still remains a great challenge to achieve rapid absorption and efficient recovery. Over the past decade, research has focused on the development of freeze casting technology using water as a solvent. The materials prepared by this method have poor water resistance and are difficult to apply to oil absorption in aqueous environments. Here, an organic solvent freeze casting strategy is proposed to fabricate ultralight hydrophobic plastic foams with aligned channel structures. Through microscopy in situ observation, we revealed the growth morphology of ice crystals during directional freezing process. Moreover, aligned porous foams with various channel sizes are fabricated by regulating the cooling rate. We found that organic solvent-assisted freeze casting can enhance the hydrophobicity of the matrix material. These aligned porous foams exhibit excellent liquid absorption performance, with high absorption speed and large absorption capacity over a wide viscosity range. This approach has general applicability and can be used to tailor a wide variety of engineering plastic-based aligned porous foams, as long as they can dissolve in organic solvents.

Identification and Characterization of the Roles of circCASP9 in Gastric Cancer Based on a circRNA-miRNA-mRNA Regulatory Network.

Accumulating evidence demonstrates that circular RNAs (circRNAs) have substantial effects on gastric cancer (GC) tumorigenesis and development. In this study, we performed a screen and identified two differentially expressed circRNAs (circCASP9 and circDLG5) from our circRNA microarray. We validated the expression of circCASP9 and circDLG5 in GC tissues and their normal counterparts by using qRT-PCR. Only circCASP9 was revealed to be downregulated in tumor tissues compared with adjacent normal tissues. Functionally, circCASP9 significantly inhibited the proliferation, migration, and invasion of GC cells both in vitro and in vivo. A competing endogenous RNA (ceRNA) network was constructed for the identification of candidate target genes of circCASP9. circCASP9, two miRNAs, and 55 mRNAs were selected for construction of the ceRNA network. We confirmed that circCASP9 can function as a sponge of miR-589-5p to regulate KANK1 expression, thereby controlling GC progression. Accordingly, we identified that the novel circRNA circCASP9 was differentially expressed between GC tissues and their normal counterparts. We also showed that circCASP9 can regulate the growth and metastasis of GC via the miR-589-5p/KANK1 axis. The circCASP9/miR-589-5p/KANK1 axis might provide crucial insights for investigating the occurrence and development of GC.

[Reconstruction of anterior talofibular ligament and calcaneofibular ligament with autologous peroneus brevis tendon in the treatment of chronic lateral ankle instability].

OBJECTIVE: To explore the clinical efficacy of reconstruction the anterior talofibular ligament and calcaneofibular ligament with autologous peroneus brevis tendon for the treatment of chronic lateral ankle instability. METHODS: The clinical data of 42 patients with chronic lateral ankle instability treated by anatomical reconstruction of anterior talofibular ligament and calcaneofibular ligament with autologous peroneus brevis tendon from July 2016 to July 2019 was retrospectively analyzed. Including 30 males and 12 females, age ranged from 25 to 46 years old with an average of (37.6±12.4) years. There were 15 cases of left foot and 27 cases of right foot, the time from injury to operation was 3 to 12 months with a mean of (7.4±2.8) months. And 14 patients had tenderness in lateral collateral ligament area, 28 patients complained of multiple ankle sprains while walking on the flat ground. At 12 months after operation, the talar tilt angle and visual analogue scale(VAS)were observed, ankle joint varus stress and anterior drawer test were performed to check the mechanical stability of the ankle joint, American Orhopaedic Foot and Ankle Society(AOFAS) was used to score the ankle and hindfoot functions and evaluate the curative effect. RESULTS: Forty patients were followed up for 12 to 48 months with an average of (28.3±10.0) months, 2 cases were lost. The VAS decreased from(4.50±0.93) scores before surgery to (1.10±0.30) scores at 12 months after surgery;the talar tilt angle was reduced from (12.26±1.13)° before operation to (4.60±0.45)° at 12 months after operation;the AOFAS score increased from (65.10±7.50)scores before surgery to (84.40±3.95) scores at 12 months after surgery;all the differences were statically significant(P<0.05). According to the AOFAS score, 27 cases got excellent results, 7 good, 5 fair, and 1 poor. One patient had the symptoms of sural nerve injury after operation, and the symptoms were relieved after oral Mecobalamin for 3 months. The remaining patients had no complications such as nerve injury, infection, and skin necrosis. There was no instability of ankle joint, and both ankle varus stress test and drawer test were negative. CONCLUSION: Autologous peroneal brevis tendon with double bone channel pass through the tendon (modified Chrisman-Snook operation) can anatomically reconstruct the anterior talofibular ligament and the calcaneofibular ligament, restore the stability of the patient's ankle joint, reduce postoperative complications, and restore ankle joint function well.

BAIAP2L2 promotes the proliferation, migration and invasion of osteosarcoma associated with the Wnt/ß-catenin pathway.

BACKGROUND: Osteosarcoma is the most common bone cancer that significantly affects the quality of life of patients. Studies have shown that overexpression of BAIAP2L2 elevates the proliferation and growth of some types of cancer cells. However, the role of BAIAP2L2 in osteosarcoma is unclear. This study aimed to investigate the functions of BAIAP2L2 in the development of osteosarcoma. METHODS: We used immunohistochemical and Western blot analysis to determine the expression levels of endogenic BAIAP2L2 in osteosarcoma cells. Cell counting kit-8 assay and colony formation assay were performed to investigate cell proliferation of tumor cells. Transwell assay was performed to detect cell migration. Flow cytometry assay was used to analyze cell apoptosis. The role of BAIAP2L2 in tumor growth was further explored in vivo. RESULTS: We found that BAIAP2L2 was significantly upregulated in human osteosarcoma, and inhibition of BAIAP2L2 suppressed the proliferation of osteosarcoma cells. In addition, down-regulation of BAIAP2L2 could lead to osteosarcoma cancer cell apoptosis, inhibit cell migration and invasion, and induce the inactivation of the Wnt/ß-catenin pathway. In addition, down-regulation of BAIAP2L2 inhibited tumor growth in vivo. CONCLUSION: In conclusion, down-regulation of BAIAP2L2 inhibited the proliferation, migration, and invasion of osteosarcoma associated with the Wnt/ß-catenin pathway.

Recent advances of electrochemical sensors for detecting and monitoring ROS/RNS.

Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are prominent metabolic products which show well-established significance. At relatively low concentrations, they play multifaceted roles in regulating a number of physiological processes. Overproduction of ROS/RNS contributes to the pathogenesis of a plethora of physiological disorders, including but not limited to cardiovascular diseases, neurodegenerative diseases, cancer. Electrochemistry have been extensively used for detecting and monitoring ROS/RNS, benefiting from their inherent advantages including fast response, low costs, real-time detection, high sensitivity and selectivity. This review focuses on three types of ROS/RNS (H2O2, O2-, NO) with emphasis on their electrochemical detection/monitoring respectively. We demonstrate the application of electrochemical strategies for ROS/RNS detection in body fluids, in vitro, and in vivo, outlining the hardware architecture and comparing analytical performance of these sensors. This review aims for a holistic view of limitations in existing ROS/RNS detection by comprehensively explaining the shortcomings of the current works in the hope of drawing attentions to the challenges of ROS/RNS electrochemical technologies. We pay particular attention to in vitro and in vivo sensors and extend our evaluation to suggest possible solutions. Specifically, this review focuses on the development of currently nanotechnologies, biomimetic engineering, 3D-culture methods and implanted sensors to provide a guideline for future works.

Lung adenocarcinoma patients have higher risk of SARS-CoV-2 infection.

Both lung adenocarcinoma and coronavirus disease 2019 would cause pulmonary inflammation. Angiotensin-converting enzyme 2, the functional receptor of SARS-CoV-2, also plays a key role in lung adenocarcinoma. To study the risk of SARS-CoV-2 infection in lung adenocarcinoma patients, mRNA and microRNA profiles were obtained from The Cancer Genome Atlas and Gene Expression Omnibus followed by bioinformatics analysis. A network which regards angiotensin-converting enzyme 2 as the center was structured. In addition, via immunological analysis to explore the essential mechanism of SARS-CoV-2 susceptibility in lung adenocarcinoma. Compared with normal tissue, angiotensin-converting enzyme 2 was increased in lung adenocarcinoma patients. Furthermore, a total of 7 correlated differently expressed mRNAs (ACE2, CXCL9, MMP12, IL6, AZU1, FCN3, HYAL1 and IRAK3) and 5 correlated differently expressed microRNAs (miR-125b-5p, miR-9-5p, miR-130b-5p, miR-381-3p and miR-421) were screened. Interestingly, the most frequent toll-like receptor signaling pathway was enriched by mRNA (interlukin 6) and miRNA (miR-125b-5p) sets simultaneously. In conclusion, it was assumed that miR-125b-5p-ACE2-IL6 axis could alter the risk of SARS-CoV-2 infection in lung adenocarcinoma patients.

MicroRNA-300: A Transcellular Mediator in Exosome Regulates Melanoma Progression.

Melanoma is a common and high-mortality skin cancer. Oxidative stress and DNA damage caused by ultraviolet light (UV) are major causative factors of melanoma formation. However, the specific molecular mechanism is still unclear. In this study, 218 dysregulated genes and 104 dysregulated miRNAs in response to UV were screened by analyzing sequencing datasets. Among them, 29 up-regulated miRNAs and 28 down-regulated miRNAs were involved in the melanoma pathway. As the only differential gene in the melanoma pathway, GADD45B severely affects the prognosis of melanoma patients. MiR-300 is the only differentially expressed miRNA that regulates GADD45B. In addition, compared to normal melanocytes, miR-300 was significantly down-regulated in melanoma cells (log FC = -1.63) and exosomes (log FC = -1.34). Among the transcription factors predicted to regulate miR-300, MYC, PPARG, and ZIC2 were significantly up-regulated in melanoma cells, and TP53, JUN, JUNB, FOS, and FOSB interacted with GADD45B. We attempted to reveal the pathogenesis of melanoma and screen new biomarkers by constructing a TF-mRNA-miRNA axis in turn to provide a view for further research.

Codeposition Modification of Cation Exchange Membranes with Dopamine and Crown Ether To Achieve High K+ Electrodialysis Selectivity.

Surface modification has been proven to be an effective approach for ion exchange membranes to achieve separation of counterions with different valences by altering interfacial construction of membranes to improve ion transfer performance. In this work, we have fabricated a series of novel cation exchange membranes (CEMs) by modifying sulfonated polysulfone (SPSF) membranes via codeposition of mussel-inspired dopamine (DA) and 4'-aminobenzo-15-crown-5 (ACE), followed by glutaraldehyde cross-linking, aiming at achieving selective separation of specific cations. The as-prepared membranes before and after modification were systematically characterized in terms of their structural, physicochemical, electrochemical, and electrodialytic properties. In the electrodialysis process, the modified membranes exhibit distinct perm selectivity to K+ ions in binary (K+/Li+, K+/Na+, K+/Mg2+) and ternary (K+/Li+/Mg2+) systems. In particular, at a constant current density of 5.0 mA·cm-2, modified membrane M-co-0.50 shows significantly prominent perm selectivity [Formula: see text] in the K+/Mg2+ system and M-co-0.75 exhibits remarkable performance in the K+/Li+ system [Formula: see text], superior to commercial monovalent-selective CEM (CIMS, [Formula: see text], [Formula: see text]). Besides, in the K+/Li+/Mg2+ ternary system, K+ flux reaches 30.8 nmol·cm-2·s-1 for M-co-0.50, while it reaches 25.8 nmol·cm-2·s-1 for CIMS. It possibly arises from the effects of pore-size sieving and the synergistic action of electric field driving and host-guest molecular recognition of ACE and K+ ions. This study can provide new insights into the separation of specific alkali metal ions, especially on reducing influence of coexisting cations K+ and Na+ on Li+ ion recovery from salt lake and seawater.

MiR-22 down-regulates the proto-oncogene ATP citrate lyase to inhibit the growth and metastasis of breast cancer.

Breast cancer, the most common malignancy in women worldwide, places a heavy economic burden and mental stress on families and society. Previous research showed that abnormal expression of miRNAs was closely related to the occurrence, metastasis, and angiogenesis of breast cancer. And in this study, the abnormal expression of miR-22 was detected by RT-PCR in the paired breast cancer tissues and adjacent non-tumor tissues. CCK-8 and wound healing assays were performed to evaluate the effects of the proto-oncogene ATP citrate lyase (ACLY) on the growth and metastasis of breast cancer MCF-7 cells. The results showed that miR-22 inhibited the growth and metastasis of MCF-7 cells by down-regulating the expression of ACLY. In conclusion, this study elucidated the roles of miR-22 in regulation of breast cancer differentiation and migration, which provides a target for early diagnose and therapy of breast cancer.

Effect of etomidate on the oxidative stress response and levels of inflammatory factors from ischemia-reperfusion injury after tibial fracture surgery.

The effect of etomidate on the oxidative stress response and levels of inflammatory factors resulting from ischemia-reperfusion injury of the lower extremities during tibial fracture surgery were investigated. From December 2013 to June 2015, 60 tibial fracture patients with surgical indications for open reduction and internal fixation were selected. Patients were randomly divided into the observation group and the control group. All patients were stanched by tourniquet hemostasis. Patients in the observation group were anesthetized with etomidate (3-6 mg/kg·h) + remifentanil (0.1-0.25 µg/kg/min) administered with an injection pump to maintain intraoperative sedation and analgesia anesthesia. Patients in the control group received propofol (3-6 mg/kg·h) + remifentanil (0.1-0.25 µg/kg/min). Before surgery (T0), before surgery was completed and anesthesia was stopped (T1), 24 h after surgery (T3), 48 h after surgery (T4), and 1 week after surgery (T5), serum superoxide dismutase (SOD) activity was determined with a kit, and ELISA was used to measure the levels of tumor necrosis factor (TNF)-α, interleukin (IL)-1, and IL-6 in peripheral blood from both groups of patients. Surgery in both groups was completed smoothly. We found that serum SOD levels of patients in the observation group were significantly higher than those of the control group, while the levels of TNF-α, IL-1, and IL-6 released by neutrophils were significantly decreased after ischemia-reperfusion injury (P<0.05). Postoperative length of stay in hospital of the observation group was significantly shorter and the occurrence rate of anesthesia complications was significantly lower than in the control group (P<0.05). In conclusion, during surgery for lower limb fracture, the use of etomidate for maintaining sedation can effectively maintain serum SOD activity and inhibit the release of inflammatory factors after ischemia-reperfusion injury of the fracture, to reduce the occurrence rate of anesthesia complications after surgery.

miRLAB: An R Based Dry Lab for Exploring miRNA-mRNA Regulatory Relationships.

microRNAs (miRNAs) are important gene regulators at post-transcriptional level, and inferring miRNA-mRNA regulatory relationships is a crucial problem. Consequently, several computational methods of predicting miRNA targets have been proposed using expression data with or without sequence based miRNA target information. A typical procedure for applying and evaluating such a method is i) collecting matched miRNA and mRNA expression profiles in a specific condition, e.g. a cancer dataset from The Cancer Genome Atlas (TCGA), ii) applying the new computational method to the selected dataset, iii) validating the predictions against knowledge from literature and third-party databases, and comparing the performance of the method with some existing methods. This procedure is time consuming given the time elapsed when collecting and processing data, repeating the work from existing methods, searching for knowledge from literature and third-party databases to validate the results, and comparing the results from different methods. The time consuming procedure prevents researchers from quickly testing new computational models, analysing new datasets, and selecting suitable methods for assisting with the experiment design. Here, we present an R package, miRLAB, for automating the procedure of inferring and validating miRNA-mRNA regulatory relationships. The package provides a complete set of pipelines for testing new methods and analysing new datasets. miRLAB includes a pipeline to obtain matched miRNA and mRNA expression datasets directly from TCGA, 12 benchmark computational methods for inferring miRNA-mRNA regulatory relationships, the functions for validating the predictions using experimentally validated miRNA target data and miRNA perturbation data, and the tools for comparing the results from different computational methods.

Ensemble gene selection by grouping for microarray data classification.

Selecting relevant and discriminative genes for sample classification is a common and critical task in gene expression analysis (e.g. disease diagnostic). It is desirable that gene selection can improve classification performance of learning algorithm effectively. In general, for most gene selection methods widely used in reality, an individual gene subset will be chosen according to its discriminative power. One of deficiencies of individual gene subset is that its contribution to classification purpose is limited. This issue can be alleviated by ensemble gene selection based on random selection to some extend. However, the random one requires an unnecessary large number of candidate gene subsets and its reliability is a problem. In this study, we propose a new ensemble method, called ensemble gene selection by grouping (EGSG), to select multiple gene subsets for the classification purpose. Rather than selecting randomly, our method chooses salient gene subsets from microarray data by virtue of information theory and approximate Markov blanket. The effectiveness and accuracy of our method is validated by experiments on five publicly available microarray data sets. The experimental results show that our ensemble gene selection method has comparable classification performance to other gene selection methods, and is more stable than the random one.