Self-assembled poloxamer-legumin/vicilin nanoparticles for the nanoencapsulation and controlled release of folic acid.

Plant-based food proteins are a promising choice for the preparation of nanoparticles (NPs) due to their high digestibility, low cost, and ability to interact with various compounds and nutrients. Moreover, nanoencapsulation offers a potential solution for protecting nutrients during processing and enhancing their bioavailability. This study aimed to develop and evaluate nanoparticles (NPs) based on legumin/vicilin (LV) proteins extracted from fava beans, with the goal of encapsulating and delivering a model nutraceutical compound, folic acid (FA). Specifically, NPs were self-assembled from LV proteins extracted from commercially available frozen fava beans using a pH-coacervation method with poloxamer 188 (P188) and chemically cross-linked with glutaraldehyde. Microscopy and spectroscopy studies were carried out on the empty and FA-loaded NPs in order to evaluate the particle morphology, size, size distribution, composition, mechanism of formation, impact of FA loading and release behavior. In vitro studies with Caco-2 cells also confirmed that the empty and FA-loaded nanoparticles were non-toxic. Thus, the LV-NPs are good candidates as food additives for the delivery and stabilization of nutrients as well as in drug delivery for the controlled release of therapeutics.

Structural and functional properties of Maillard-reacted casein phosphopeptides with different carbohydrates.

This study used glucose, fructose, maltose and dextran to explore the effects of different carbohydrates on the Maillard reaction of casein phosphopeptides (CPP). The color parameter results showed that heating time from 1 to 5 h led to brown color, which was consistent with the observed increased in browning intensity. Fourier transform infrared spectroscopy results verified that four carbohydrates reacted with CPP to produce Maillard conjugates. Fluorescence spectroscopy showed that the Maillard reaction changed the tertiary structure of CPP by decreasing the intrinsic fluorescence intensity and surface hydrophobicity compared with the CPP-carbohydrate mixture. At the same time, the Maillard reaction effectively improved the emulsifying properties, reducing power and DPPH radical scavenging activity of CPP. Furthermore, this study also found that glucose and fructose improved CPP more than maltose and dextran. Therefore, monosaccharides have good potential in modifying CPP via the Maillard reaction.

Characterization of a partially saturated and glycosylated apocarotenoid from wheat that is depleted upon leaf rust infection.

Recent semi-targeted metabolomics studies have highlighted a number of metabolites in wheat that associate with leaf rust resistance genes and/or rust infection. Here, we report the structural characterization of a novel glycosylated and partially saturated apocarotenoid, reminiscent of a reduced form of mycorradicin, (6E,8E,10E)-4,9-dimethyl-12-oxo-12-((3,4,5-trihydroxy-6-(2-hydroxyethoxy)tetrahydro-2H-pyran-2-yl)methoxy)-3-((3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)oxy)dodeca-6,8,10-trienoic acid, isolated from Triticum aestivum L. (Poaceae) variety 'Thatcher' (Tc) flag leaves. While its accumulation was not associated with any of Lr34, Lr67 or Lr22a resistance genes, infection of Tc with leaf rust was found to deplete it, consistent with the idea of this metabolite being a glycosylated-storage form of an apocarotenoid of possible relevance to plant defense. A comparative analysis of wheat transcriptomic changes shows modulation of terpenoid, carotenoid, UDP-glycosyltransferase and glycosylase -related gene expression profiles, consistent with anticipated biosynthesis and degradation mechanisms. However, details of the exact nature of the relevant pathways remain to be validated in the future. Together these findings highlight another example of the breadth of unique metabolites underlying plant host-fungal pathogen interactions.

Rechallenge of immune checkpoint inhibitors in advanced non-small cell lung cancer.

Immune checkpoint inhibitor (ICI) rechallenge in non-small cell lung cancer (NSCLC) is a promising therapeutic strategy. The situation for ICI rechallenge can be divided into three categories: adverse events (AEs); resistance to ICIs, and rechallenge becomes compulsive because of tumor relapse while the patients had completed a 2 year course of immunotherapy. However, these categories are still controversial and should be explored further. Through voting at the 6th Straits Summit Forum on Lung Cancer, in this study we summarize the consensus of 147 experts in ICI rechallenges. A total of 97.74% experts agreed to rechallenge; 48.87% experts rechallenge with the original drug, and the others rechallenge with a different drug; 40.3% agreed to rechallenge directly after progression; 88.06% experts agreed to ICI rechallenge with a combination regimen; and factors such as previous performance status score, PD-1 expression, and age should also be considered. Understanding the the clinical studies in ICI rechallenge could bring us one step closer to understanding the consensus. In patients with advanced NSCLC who have suffered recurrent or distant metastasis after immunotherapy, the option of rechallenge with ICIs is a promising treatment option.

Clinical definition of secondary resistance to immunotherapy in non-small cell lung cancer.

Immune checkpoint inhibitors (PD-1/PD-L1 and CTLA-4 blockade) have revolutionized the treatment landscape in non-small cell lung cancer (NSCLC). Secondary resistance to immunotherapy (IO), which poses a substantial challenge in clinical settings, occurs in several initial responders. Currently, new treatment approaches have been extensively evaluated in investigational studies for these patients to tackle this difficult problem; however, the lack of consistency in clinical definition, uniform criteria for enrollment in clinical trials, and interpretation of results remain significant hurdles to progress. Thus, our expert panel comprehensively synthesized data from current studies to propose a practical clinical definition of secondary resistance to immunotherapy in NSCLC in metastatic and neoadjuvant settings. In addition to patients who received IO alone (including IO-IO combinations), we also generated a definition for patients treated with chemotherapy plus IO. This consensus aimed to provide guidance for clinical trial design and facilitate future discussions with investigators. It should be noted that additional updates in this consensus are required when new data is available.

PH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes.

Shading in combination with extended photoperiods can cause exaggerated stem elongation (ESE) in soybean, leading to lodging and reduced yields when planted at high-density in high-latitude regions. However, the genetic basis of plant height in adaptation to these regions remains unclear. Here, through a genome-wide association study, we identify a plant height regulating gene on chromosome 13 (PH13) encoding a WD40 protein with three main haplotypes in natural populations. We find that an insertion of a Ty1/Copia-like retrotransposon in the haplotype 3 leads to a truncated PH13H3 with reduced interaction with GmCOP1s, resulting in accumulation of STF1/2, and reduced plant height. In addition, PH13H3 allele has been strongly selected for genetic improvement at high latitudes. Deletion of both PH13 and its paralogue PHP can prevent shade-induced ESE and allow high-density planting. This study provides insights into the mechanism of shade-resistance and offers potential solutions for breeding high-yielding soybean cultivar for high-latitude regions.

GmEID1 modulates light signaling through the Evening Complex to control flowering time and yield in soybean.

Soybean (Glycine max) morphogenesis and flowering time are accurately regulated by photoperiod, which determine the yield potential and limit soybean cultivars to a narrow latitudinal range. The E3 and E4 genes, which encode phytochrome A photoreceptors in soybean, promote the expression of the legume-specific flowering repressor E1 to delay floral transition under long-day (LD) conditions. However, the underlying molecular mechanism remains unclear. Here, we show that the diurnal expression pattern of GmEID1 is opposite to that of E1 and targeted mutations in the GmEID1 gene delay soybean flowering regardless of daylength. GmEID1 interacts with J, a key component of circadian Evening Complex (EC), to inhibit E1 transcription. Photoactivated E3/E4 interacts with GmEID1 to inhibit GmEID1-J interaction, promoting J degradation resulting in a negative correlation between daylength and the level of J protein. Notably, targeted mutations in GmEID1 improved soybean adaptability by enhancing yield per plant up to 55.3% compared to WT in field trials performed in a broad latitudinal span of more than 24°. Together, this study reveals a unique mechanism in which E3/E4-GmEID1-EC module controls flowering time and provides an effective strategy to improve soybean adaptability and production for molecular breeding.

Snapshot of proteomic changes in Aspergillus oryzae during various stages of fermentative processing of pea protein isolate.

Pea (Pisum sativum) is one of the most abundant and sustainable alternate source of protein. Although pea proteins have good quantities of most of the essential amino acids, they have a limited supply of tryptophan, methionine and cysteine. Moreover, pea proteins have poor techno-functional properties compared to proteins from animal sources, limiting their use in certain food applications. Bioprocessing techniques like solid-state fermentation (SSF) and enzymatic processing have been explored to improve the nutrient profile and functionality of pea proteins. However, there is a lack of information about proteomic changes in the food matrix during fermentation of the pea substrate. In this research, samples during SSF of pea protein isolate with Aspergillus oryzae were used for shotgun mass spectrometry (LC-MS/MS) analysis to identify the underlying functional pathways which play direct or indirect roles in enabling the colonization of the substrate leading to potential improvement of functional and nutritional value of pea protein. Results revealed the identity of A. oryzae proteins involved in different metabolic pathways that differed during various stages of SSF. Among them, methionine synthase was identified as an abundant protein, which catalyzes methionine biosynthesis. This might suggest how fermentation processes could be used to improve the presence of sulfur containing amino acids to rebalance the essential amino acid profile and improve the nutritional quality of pea proteins.

Derivative-Free Observability Analysis for Sensor Placement Optimization of Bioinspired Flexible Flapping Wing System.

Observability analysis of a bioinspired flexible flapping wing system provides a measure of how well the states of flexible flapping wing micro-aerial vehicles can be estimated from real-time measurements during high-speed flight. However, the traditional observability analysis approaches have trouble in terms of lack of quantitative analysis index, high computational complexity, low accuracy, and unavailability in stochastic systems with memory, including bioinspired flexible flapping wing systems. Therefore, a novel derivative-free observability analysis method is proposed here based on the generalized polynomial chaos expansion. By formulating a surrogate model to represent the relationship between the cumulative measurement and the random initial state, the observability coefficient matrix is calculated and the observability rank condition is stated. Consequently, several observability indices are proposed to quantity the observability of the system. Altogether, the proposed method avoids the disadvantages of the traditional approaches, especially in assessing the observability degree of each state and the effect of stochastic noise on observability. The validation of the proposed method is first provided by demonstrating the equivalence between the traditional and proposed methods and subsequently by comparing the observability of the Lorenz system calculated via three different approaches. Finally, the proposed method is applied on a bioinspired flexible wing system to optimize the placement of sensors, which is consistent with the natural configuration of campaniform sensilla on the wing of the hawkmoth.

Micro-CT study on isolated teeth with hereditary dentin defects.

OBJECTIVES: To construct the three-dimensional structure of the isolated teeth of patients with dentinogenesis imperfecta type Ⅱ (DGI-Ⅱ) and dentin dysplasia type Ⅰ (DD-Ⅰ) by using Micro-CT and explore internal structure and hard tissue mineralization density. METHODS: The three-dimensional structures of the third molars collected from patients with DGI-Ⅱ and DD-Ⅰ and healthy individuals of the same age were reconstructed by using Micro-CT (Mimics 17.0). The internal structures of the affected teeth along the sagittal and transverse planes were observed. The grayscale values of the enamel, crown dentin, and root dentin were calculated. Then, the mineralization densities of the different parts of the teeth of the three groups were analyzed. RESULTS: The detailed three-dimensional models of the mandibular third molars with hereditary dentin defects were successfully constructed. The models contained the models of the enamel cap, dentin core, and pulp cavity. Sagittal and transverse section scans revealed that in patients with DGI-Ⅱ, the pulp cavity was incompletely calcified and the root canal was narrow, whereas in those with DD-Ⅰ, the pulp cavity and root canal were obliterated and the root of the tooth was absent. The analysis of the grayscale values showed that compared with those in the healthy group, the grayscale values of the enamel, crown dentin, and root dentin were lower in the DGI-Ⅱ and DD-Ⅰ groups (P<0.01). No significant differences in the grayscale values of the enamel and crown dentin were found between the DGI-Ⅱ and DD-Ⅰ groups (P>0.05), whereas the grayscale value of the root dentin showed statistically significant differences between the two groups (P<0.01). CONCLUSIONS: The application of Micro-CT provided a simple and accurate method for the three-dimensional structure reconstruction and quantitative analysis of the mineralization density of isolated teeth with hereditary dentin defects. Although the dentin mineralization density of DGI-Ⅱ and DD-Ⅰ teeth decreased, the decrement shown by DD-Ⅰ teeth was more significant than that shown by DGI-Ⅱ teeth. The pulp cavity had abnormal calcifications, and the root canal was narrow or even occluded.

Assessment of plum rain's impact on power system emissions in Yangtze-Huaihe River basin of China.

As a typical climate that occurs in the Yangtze-Huaihe River basin of China with a size of 500,000 km2, plum rain can reduce the photovoltaic (PV) potential by lowering the surface irradiance (SI) in the affected region. Based on hourly meteorological data from 1980 to 2020, we find that plum rain can lower the SI in the affected region with a weekly peak drop of more than 20% at the most affected locations. This SI drop, coupled with a large number of deployed PV systems, can cause incremental CO2 emissions (ICEs) of local power systems by increasing the additional thermal power. Using a cost optimization model, we demonstrate that the ICEs in 2020 already reached 1.22 megatons and could range from 2.21 to 4.73 megatons, 3.47 to 7.19 megatons, and 2.97 to 7.43 megatons in 2030, 2040, and 2050, respectively, considering a change trend interval of a ±25% fluctuation in power generation and demand in the different years. To offset these ICEs, we compare four pathways integrated with promising technologies. This analysis reveals that the advanced deployment of complementary technologies can improve the PV utilization level to address climate impacts.

Minimum inhibitory concentrations of commonly used antibiotics against Helicobacter Pylori: A multicenter study in South China.

AIM: To determine the minimum inhibitory concentrations (MICs) of commonly used antibiotics against Helicobacter Pylori (H. pylori) in South China and compare their resistance rates by using EUCAST breakpoints and other breakpoints. METHODS: Patients who had not previously received H. pylori treatment in clinical centers in South China were enrolled in this study from 2017 to 2020. Gastric biopsies were obtained for H. pylori culture. The MICs of amoxicillin (AMX), clarithromycin (CLA), metronidazole (MTZ), levofloxacin (LEV), tetracycline (TET) and furazolidone (FZD) were tested by broth microdilution method and assessed by two different breakpoints. ATCC43504 standard strain served as a control. RESULTS: A total of 208 H. pylori strains were isolated from patients' biopsy samples. The MICs of AMX, CLA, MTZ, LEV, TET and FZD for H. pylori were 0.0156-256mg/L (MIC50 0.125mg/L, MIC90 4mg/L), 0.0156- >256 mg/L (MIC50 0.0312mg/L, MIC90 64mg/L), 0.0156- >256mg/L (MIC50 8mg/L, MIC90 256mg/L), 0.0156-256mg/L (MIC50 0.25mg/L, MIC90 16mg/L), 0.0156-256mg/L (MIC50 0.0625mg/L, MIC90 4mg/L), and 0.0156- >256mg/L (MIC50 0.0312mg/L, MIC90 2mg/L), respectively. The MICs of AMX, CLA, MTZ, LEV, TET and FZD for ATCC43504 strain were 0.25mg/L, 0.0625mg/L, 64mg/L, 0.5mg/L, 1mg/L and 0.25mg/L, respectively. The resistance rate of FZD was 11.05%. The overall resistance rates according to EUCAST breakpoints and other breakpoints were 57.21% and 14.90% for AMX (p<0.001), 38.94% and 38.94% for CLA (p = 1), 39.42% and 50.96% for MTZ (p<0.001), 12.98% and 10.58% for TET (p = 0.025), 35.10% and 35.10% for LEV (p = 1), respectively. CONCLUSIONS: Our results demonstrate that AMX, FZD, and TET, but not MTZ, CLR or LEV, showed good anti-H. pylori activity in vitro in South China. When different breakpoints were used, similar results were found with CLA, and LEV, but not with AMX, MTZ, or TET.

Underwater vs conventional endoscopic mucosal resection in treatment of colorectal polyps: A meta-analysis.

BACKGROUND: Underwater endoscopic mucosal resection (UEMR) of colorectal lesions is emerging as an alternative method to conventional endoscopic mucosal resection (EMR); however, it is still controversial whether there is a difference in the effectiveness between UEMR and EMR. AIM: To evaluate the effectiveness and safety of UEMR in the treatment of colorectal polyps. METHODS: Clinical studies comparing the effectiveness or safety of UEMR in the treatment of colorectal polyps were searched in medical databases, including PubMed, Embase, Cochrane Library, CNKI, and Wanfang Data, monographs, theses, and papers presented at conferences. Statistical analyses were performed using Revman 5.3 software. RESULTS: Seven non-randomized controlled trials and one randomized controlled trial met the inclusion criteria. In total, 1382 patients (1511 polyps) were included in the study, including 722 who received UEMR and 789 who received EMR. In the UEMR and EMR groups, the en bloc resection rates were 85.87% and 73.89%, respectively, with a relative risk (RR) value of 1.14 (95% confidence interval [CI]: 1.01-1.30; P < 0.05). In the sub-group analysis, the en bloc resection rate showed no statistically significant difference between the EMR and UEMR groups for polyps less than 20 mm in diameter. However, a statistically significant difference was found between the EMR and UEMR groups for polyps equal to or greater than 20 mm in diameter. The post-endoscopic resection recurrence rates at 3-6 mo of the UEMR and EMR groups were 3.26% and 15.17%, respectively, with an RR value of 0.27 (95%CI: 0.09-0.83; P < 0.05). The post-endoscopic resection recurrence rates of UEMR and EMR at 12 mo were 6.25% and 14.40%, respectively, with an RR value of 0.43 (95%CI: 0.20-0.92; P < 0.05). Additionally, the incidence of adverse events was 8.17% and 6.21%, respectively, with an RR value of 1.07 (95%CI: 0.50-2.30; P > 0.05). CONCLUSION: UEMR is an effective technique for colorectal polyps and appears to have some advantages over EMR, particularly with regard to some treatment outcomes.

Comparative effect of tenuazonic acid, diuron, bentazone, dibromothymoquinone and methyl viologen on the kinetics of Chl a fluorescence rise OJIP and the MR820 signal.

In this study, the comparative effect of TeA, DCMU, bentazone, DBMIB and MV on prompt fluorescence and the MR820 signal was simultaneously analyzed to provide an insight into how to elucidate their precise influence on Ageratina adenophora photosystems. The herbicides that interrupt electron transport beyond QA, such as TeA, DCMU and bentazone, mainly increased the J-step level of fluorescence rise kinetics as a result of accumulation of QA-, but showed differences in detail. The IP phase disappeared in the presence of DCMU and bentazone with a significant increase in FO value. TeA treatment retained the IP phase with lowering FM. As an inhibitor of plastoquinone re-oxidation, DBMIB increased the I-step (IP phase almost unnoticable) without changing FO and FM values. MV blocking PSI electron transfer through intercepting electrons from the FeS clusters suppressed the IP phase by decreasing the P level. Considering the WIP kinetics, TeA and DBMIB also affected PSI activity. After DCMU and MV treatment, the major change in the MR820 kinetics was the loss of the slow phase due to the complete prevention of electron movement from PSII to re-reduce PC+ and P700+. TeA, bentazone and DBMIB clearly suppressed the MR820 slow phase and decreased the re-reduction rate of PC+ and P700+ (Vred), significantly. However, there were still parts of electrons being donated to PC+ and P700+, showing a smaller slow phase and PC+ and P700+ re-reduction rate. Additionally, TeA and DBMIB also somewhat declined the fast phase and PC and P700 oxidation rate (Vox).

VPS4B mutation impairs the osteogenic differentiation of dental follicle cells derived from a patient with dentin dysplasia type I.

A splicing mutation in VPS4B can cause dentin dysplasia type I (DD-I), a hereditary autosomal-dominant disorder characterized by rootless teeth, the etiology of which is genetically heterogeneous. In our study, dental follicle cells (DFCs) were isolated and cultured from a patient with DD-I and compared with those from an age-matched, healthy control. In a previous study, this DD-I patient was confirmed to have a loss-of-function splicing mutation in VPS4B (IVS7 + 46C > G). The results from this study showed that the isolated DFCs were vimentin-positive and CK14-negative, indicating that the isolated cells were derived from the mesenchyme. DFCs harboring the VPS4B mutation had a significantly higher proliferation rate from day 3 to day 8 than control DFCs, indicating that VPS4B is involved in cell proliferation. The cells were then replenished with osteogenic medium to investigate how the VPS4B mutation affected osteogenic differentiation. Induction of osteogenesis, detected by alizarin red and alkaline phosphatase staining in vitro, was decreased in the DFCs from the DD-I patient compared to the control DFCs. Furthermore, we also found that the VPS4B mutation in the DD-I patient downregulated the expression of osteoblast-related genes, such as ALP, BSP, OCN, RUNX2, and their encoded proteins. These outcomes confirmed that the DD-I-associated VPS4B mutation could decrease the capacity of DFCs to differentiate during the mineralization process and may also impair physiological root formation and bone remodeling. This might provide valuable insights and implications for exploring the pathological mechanisms underlying DD-I root development.

A phenylpropanoid diglyceride associates with the leaf rust resistance Lr34res gene in wheat.

The gene Lr34res is one of the most long-lasting sources of quantitative fungal resistance in wheat. It is shown to be effective against leaf, stem, and stripe rusts, as well as powdery mildew and spot blotch. Recent biochemical characterizations of the encoded ABC transporter have outlined a number of allocrites, including phospholipids and abscisic acid, consistent with the established general promiscuity of ABC transporters, but ultimately leaving its mechanism of rust resistance unclear. Working with flag leaves of Triticum aestivum L. variety 'Thatcher' (Tc) and a near-isogenic line of 'Thatcher' into which the Lr34res allele was introgressed (Tc+Lr34res; RL6058), a comparative semi-targeted metabolomics analysis of flavonoid-rich extracts revealed virtually identical profiles with the exception of one metabolite accumulating in Tc+Lr34res, which was not present at comparable levels in Tc. Structural characterization of the purified metabolite revealed a phenylpropanoid diglyceride structure, 1-O-p-coumaroyl-3-O-feruloylglycerol (CFG). Additional profiling of CFG across a collection of near-isogenic lines and representative Lr34 haplotypes highlighted a broad association between the presence of Lr34res and elevated accumulations of CFG. Depletion of CFG upon infection, juxtaposed to its relatively lower anti-fungal activity, suggests CFG may serve as a storage form of the more potent anti-microbial hydroxycinnamic acids that are accessed during defense responses. Altogether these findings suggest a role for the encoded LR34res ABC transporter in modifying the accumulation of CFG, leading to increased accumulation of anti-fungal metabolites, essentially priming the wheat plant for defense.

A cluster-randomized field trial to reduce cesarean section rates with a multifaceted intervention in Shanghai, China.

BACKGROUND: Cesarean section (CS) rate has risen dramatically and stayed at a very high level in China over the past two to three decades. Given the short- and long-term adverse effects of CS, effective strategies are needed to reduce unnecessary CS. We aimed to evaluate whether a multifaceted intervention would decrease the CS rate in China. METHODS: We carried out a cluster-randomized field trial with a multifaceted intervention in Shanghai, China, from 2015 to 2017. A total of 20 hospitals were randomly allocated into an intervention or a control group. The intervention consisted of more targeted health education to pregnant women, improved hospital CS policy, and training of midwives/doulas for 8 months. The study included a baseline survey, the intervention, and an evaluation survey. The primary outcome was the changes of overall CS rate from the pre-intervention to the post-intervention period. A subgroup analysis stratified by the Robson classification was also conducted to examine the CS change among women with various obstetric characteristics. RESULTS: A total of 10,752 deliveries were randomly selected from the pre-intervention period and 10,521 from the post-intervention period. The baseline CS rates were 42.5% and 41.5% in the intervention and control groups, respectively, while the post-intervention CS rates were 43.4% and 42.4%, respectively. Compared with the control group, the intervention did not significantly reduce the CS rate (adjusted OR = 0.92; 95% CI 0.73, 1.15). Similar results were obtained in subgroup analyses stratified by the risk level of pregnancy, maternal age, number of previous CS, or parity. Scarred uterus and maternal request remained the primary reasons for CS after the interventions in both groups. The intervention did not alter the perinatal outcomes (adjusted change of risk score = - 0.06; 95%CI - 0.43, 0.31). CONCLUSIONS: A multifaceted intervention including more targeted prenatal health education, improved hospital CS policy, and training of midwives/doulas, did not significantly reduce the CS rate in Shanghai, China. However, our experience in implementing a multifaceted intervention may provide useful information to other similar areas with high CS use. TRIAL REGISTRATION: This trial was registered at the Chinese Clinical Trial Registry (www.chictr.org.cn) (ChiCTR-IOR-16009041) on 17 August 2016.

Biclique: an R package for maximal biclique enumeration in bipartite graphs.

OBJECTIVE: Bipartite graphs are widely used to model relationships between pairs of heterogeneous data types. Maximal bicliques are foundational structures in such graphs, and their enumeration is an important task in systems biology, epidemiology and many other problem domains. Thus, there is a need for an efficient, general purpose, publicly available tool to enumerate maximal bicliques in bipartite graphs. The statistical programming language R is a logical choice for such a tool, but until now no R package has existed for this purpose. Our objective is to provide such a package, so that the research community can more easily perform this computationally demanding task. RESULTS: Biclique is an R package that takes as input a bipartite graph and produces a listing of all maximal bicliques in this graph. Input and output formats are straightforward, with examples provided both in this paper and in the package documentation. Biclique employs a state-of-the-art algorithm previously developed for basic research in functional genomics. This package, along with its source code and reference manual, are freely available from the CRAN public repository at https://cran.r-project.org/web/packages/biclique/index.html.

Candidate genes for predicting the survival of patients with gastric cancer: a study based on The Cancer Genome Atlas (TCGA) database.

BACKGROUND: Gastric cancer (GC) is the second most frequent cause of cancer-related mortality in the world, and the five-year survival rate for GC remains very low universally. In recent years, it has become a consensus that genetic changes are associated with carcinogenesis of GC, and precision medicine based on genetic changes is one of the most popular treatments for GC patients. However, the association between some genes and GC-related protein signaling pathways is still not well understood. This study revealed that seven genes were closely related to the survival probability in GC patients. METHODS: We downloaded the gene expression data of GC patients from The Cancer Genome Atlas (TCGA) databases, and integrated bioinformatic analysis was performed, such as differential gene expression analysis, including Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathways analyses, as well as survival analysis. The r package "survival" was used to analyze the Kaplan-Meier survival analysis, which showed the associations between specific gene expressions and the outcomes of patients with GC to identify which genes could be potential prognostic biomarkers. RESULTS: This study revealed that seven genes: alcohol dehydrogenase 4 (ADH4), histamine receptor H3 (HRH3), neuropeptide Y2 receptor (NPY2R), apolipoprotein AI (APOA1), N-acetylgalactosaminyltransferase 14 (GALNT14), leucine-rich repeats and IQ motif containing 1 (LRRIQ1), and coiled-coil-domain-containing 57 (CCDC57). These seven genes were closely related to the survival probability of GC patients (P<0.05). CONCLUSIONS: Our study found seven genes which could be considered as candidate prognostic biomarkers and therapeutic targets.