Low-diameter topic-based pub/sub overlay network construction with minimum–maximum node degree
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ABSTRACT:
SUBMITTER: Yumusak S
PROVIDER: S-EPMC8157249 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundSeveral models and markers were developed and found to predict outcome of advanced renal cell carcinoma. This study aimed to evaluate the prognostic value of the ratio of maximum to minimum tumor diameter (ROD) in metastatic clear cell renal cell carcinoma (mccRCC).MethodsPatients with mccRCC (n = 213) treated with sunitinib from January 2008 to December 2018 were identified. Cutoff value for ROD was determined using receiver operating characteristic. Patients with different ROD scores were grouped and evaluated. Survival outcomes were estimated by Kaplan-Meier method.ResultsThe optimal ROD cutoff value of 1.34 was determined for progression free survival (PFS) and overall survival (OS). Patients in ROD ≥ 1.34 group had shorter PFS (9.6 versus 17.7 months, p < 0.001) and OS (25.5 versus 32.6 months, p < 0.001) than patients in ROD < 1.34 group. After adjustment for other factors, multivariate analysis showed ROD ≥ 1.34 was an independent prognostic factor for PFS (p < 0.001) and OS (p = 0.006). Patients in ROD ≥ 1.34 group presented higher proportions of pT3/4 stage (89.2% versus 10.8%, p = 0.021), WHO/ISUP grade III/IV (72.0% versus 28.0%, p = 0.010), tumor necrosis (71.0% versus 29.0%, p = 0.039), sarcomatoid differentiation (79.1% versus 20.9%, p = 0.007), poor MSKCC risk score (78.4% versus 21.6%, p < 0.001) and poor IMDC risk score (74.4% versus 25.6%, p < 0.001) than ROD < 1.34 group.ConclusionPrimary tumor with higher ROD was an independently prognostic factor for both PFS and OS in patients with mccRCC who received targeted therapy. Higher ROD was also associated with high pT stage, high WHO/ISUP grade, sarcomatoid features, tumor necrosis, poor MSKCC and IMDC risk score.
| S-EPMC9252060 | biostudies-literature
Project description:BackgroundGrain yield is a complex trait that results from interaction between underlying phenotypic traits and climatic, edaphic, and biotic variables. In rice, main culm panicle node number (MCPNN; the node number on which the panicle is borne) and maximum node production rate (MNPR; the number of leaves that emerge per degree-day > 10°C) are primary phenotypic plant traits that have significant positive direct effects on yield-related traits. Degree-days to heading (DDTH), which has a significant positive effect on grain yield, is influenced by the interaction between MCPNN and MNPR. The objective of this research is to assess the phenotypic variation of MCPNN, MNPR, and DDTH in a panel of diverse rice accessions, determine regions in the rice genome associated with these traits using genome-wide association studies (GWAS), and identify putative candidate genes that control these traits.ResultsConsiderable variation was observed for the three traits in a 220-genotype diverse rice population. MCPNN ranged from 8.1 to 20.9 nodes in 2018 and from 9.9 to 21.0 nodes in 2019. MNPR ranged from 0.0097 to 0.0214 nodes/degree day > 10°C in 2018 and from 0.0108 to 0.0193 nodes/degree-day > 10°C in 2019. DDTH ranged from 713 to 2,345 degree-days > 10°C in 2018 and from 778 to 2,404 degree-days > 10°C in 2019. Thirteen significant (P < 2.91 x 10-7) trait-single nucleotide polymorphism (SNP) associations were identified using the multilocus mixed linear model for GWAS. Significant associations between MCPNN and three SNPs in chromosome 2 (S02_12032235, S02_11971745, and S02_12030176) were detected with both the 2018 and best linear unbiased prediction (BLUP) datasets. Nine SNPs in chromosome 6 (S06_1970442, S06_2310856, S06_2550351, S06_1968653, S06_2296852, S06_1968680, S06_1968681, S06_1970597, and S06_1970602) were significantly associated with MNPR in the 2019 dataset. One SNP in chromosome 11 (S11_29358169) was significantly associated with the DDTH in the BLUP dataset.ConclusionsThis study identifies SNP markers that are putatively associated with MCPNN, MNPR, and DDTH. Some of these SNPs were located within or near gene models, which identify possible candidate genes involved in these traits. Validation of the putative candidate genes through expression and gene editing analyses are necessary to confirm their roles in regulating MCPNN, MNPR, and DDTH. Identifying the underlying genetic basis for primary phenotypic traits MCPNN and MNPR could lead to the development of fast and efficient approaches for their estimation, such as marker-assisted selection and gene editing, which is essential in increasing breeding efficiency and enhancing grain yield in rice. On the other hand, DDTH is a resultant variable that is highly affected by nitrogen and water management, plant density, and several other factors.
| S-EPMC9125873 | biostudies-literature
Project description:Centrality of a node measures its relative importance within a network. There are a number of applications of centrality, including inferring the influence or success of an individual in a social network, and the resulting social network dynamics. While we can compute the centrality of any node in a given network snapshot, a number of applications are also interested in knowing the potential importance of an individual in the future. However, current centrality is not necessarily an effective predictor of future centrality. While there are different measures of centrality, we focus on degree centrality in this paper. We develop a method that reconciles preferential attachment and triadic closure to capture a node's prominence profile. We show that the proposed node prominence profile method is an effective predictor of degree centrality. Notably, our analysis reveals that individuals in the early stage of evolution display a distinctive and robust signature in degree centrality trend, adequately predicted by their prominence profile. We evaluate our work across four real-world social networks. Our findings have important implications for the applications that require prediction of a node's future degree centrality, as well as the study of social network dynamics.
| S-EPMC4246206 | biostudies-literature
Project description:We propose NM landscapes as a new class of tunably rugged benchmark problems. NM landscapes are well defined on alphabets of any arity, including both discrete and real-valued alphabets, include epistasis in a natural and transparent manner, are proven to have known value and location of the global maximum and, with some additional constraints, are proven to also have a known global minimum. Empirical studies are used to illustrate that, when coefficients are selected from a recommended distribution, the ruggedness of NM landscapes is smoothly tunable and correlates with several measures of search difficulty. We discuss why these properties make NM landscapes preferable to both NK landscapes and Walsh polynomials as benchmark landscape models with tunable epistasis.
| S-EPMC5553988 | biostudies-other
Project description:Metabolic rates reflect the energetic cost of living but exhibit remarkable variation among conspecifics, partly as a result of the constraints imposed by environmental conditions. Metabolic rates are sensitive to changes in temperature and oxygen availability, but effects of food availability, particularly on maximum metabolic rates, are not well understood. Here, we show in brown trout (Salmo trutta) that maximum metabolic rates are immutable but minimum metabolic rates increase as a positive function of food availability. As a result, aerobic scope (i.e. the capacity to elevate metabolism above baseline requirements) declines as food availability increases. These differential changes in metabolic rates likely have important consequences for how organisms partition available metabolic power to different functions under the constraints imposed by food availability.
| S-EPMC5095193 | biostudies-literature
Project description:BackgroundVerruca vulgaris is a viral infection with high recurrence rates and is very difficult to treat. It occurs due to the ability of the virus to evade immune recognition. This immune evasion by the human papillomavirus (HPV) can be circumvented by injecting HPV antigens subcutaneously and inducing inflammation and a systemic immune response. Falkner technique is an approved technique for the treatment of warts. In this observational study, we analyzed the recovery rate among patients undergoing this technique as part of their routine treatment. The aim of this study is to study the clinical outcome of Falkner's needling technique that is being used for the treatment of verruca vulgaris.MethodsUnder local anaesthesia, only a single wart was vertically punctured using a 26-gauge needle up till the subcutis multiple times till bleeding was observed. No treatment was done for other warts. Patients were advised not to take any anti-inflammatory medications for pain and were observed for responses after 1 week as well as 1 and 3 months.ResultsOf 41 patients included in this study, the total resolution of both the punctured and distant warts occurred in 28 patients (68.29%) and partial response in 7 patients (17.1%) by the end of 3 months. Interestingly, individual warts that were subjected to needling showed complete resolution in 35 patients (85.4%).ConclusionFalkner's needling method provides a high rate of complete resolution of multiple warts at both the needled and distant sites after a single treatment session of only a single lesion. This modality has a high cure rate, is easy to perform, requires minimal infrastructure support, is cost-effective, and can be undertaken at most peripheral settings with minimal training.
| S-EPMC9485768 | biostudies-literature
Project description:Redox-based resistive switching devices (ReRAM) are considered key enablers for future non-volatile memory and logic applications. Functionally enhanced ReRAM devices could enable new hardware concepts, e.g. logic-in-memory or neuromorphic applications. In this work, we demonstrate the implementation of ReRAM-based fuzzy logic gates using Ta2O5 devices to enable analogous Minimum and Maximum operations. The realized gates consist of two anti-serially connected ReRAM cells offering two inputs and one output. The cells offer an endurance up to 10(6) cycles. By means of exemplary input signals, each gate functionality is verified and signal constraints are highlighted. This realization could improve the efficiency of analogous processing tasks such as sorting networks in the future.
| S-EPMC4820708 | biostudies-literature
Project description:BackgroundFeature selection, aiming to identify a subset of features among a possibly large set of features that are relevant for predicting a response, is an important preprocessing step in machine learning. In gene expression studies this is not a trivial task for several reasons, including potential temporal character of data. However, most feature selection approaches developed for microarray data cannot handle multivariate temporal data without previous data flattening, which results in loss of temporal information. We propose a temporal minimum redundancy - maximum relevance (TMRMR) feature selection approach, which is able to handle multivariate temporal data without previous data flattening. In the proposed approach we compute relevance of a gene by averaging F-statistic values calculated across individual time steps, and we compute redundancy between genes by using a dynamical time warping approach.ResultsThe proposed method is evaluated on three temporal gene expression datasets from human viral challenge studies. Obtained results show that the proposed method outperforms alternatives widely used in gene expression studies. In particular, the proposed method achieved improvement in accuracy in 34 out of 54 experiments, while the other methods outperformed it in no more than 4 experiments.ConclusionWe developed a filter-based feature selection method for temporal gene expression data based on maximum relevance and minimum redundancy criteria. The proposed method incorporates temporal information by combining relevance, which is calculated as an average F-statistic value across different time steps, with redundancy, which is calculated by employing dynamical time warping approach. As evident in our experiments, incorporating the temporal information into the feature selection process leads to selection of more discriminative features.
| S-EPMC5209828 | biostudies-literature
Project description:Channelrhodopsin-2 (ChR2) is a microbial-type rhodopsin found in the green algae Chlamydomonas reinhardtii. Under physiological conditions, ChR2 is an inwardly rectifying cation channel that permeates a wide range of mono- and divalent cations. Although this protein shares a high sequence homology with other microbial-type rhodopsins, which are ion pumps, ChR2 is an ion channel. A sequence alignment of ChR2 with bacteriorhodopsin, a proton pump, reveals that ChR2 lacks specific motifs and residues, such as serine and threonine, known to contribute to non-covalent interactions within transmembrane domains. We hypothesized that reintroduction of the eight transmembrane serine residues present in bacteriorhodopsin, but not in ChR2, will restrict the conformational flexibility and reduce the pore diameter of ChR2. In this work, eight single serine mutations were created at homologous positions in ChR2. Additionally, an endogenous transmembrane serine was replaced with alanine. We measured kinetics, changes in reversal potential, and permeability ratios in different alkali metal solutions using two-electrode voltage clamp. Applying excluded volume theory, we calculated the minimum pore diameter of ChR2 constructs. An analysis of the results from our experiments show that reintroducing serine residues into the transmembrane domain of ChR2 can restrict the minimum pore diameter through inter- and intrahelical hydrogen bonds while the removal of a transmembrane serine results in a larger pore diameter. Therefore, multiple positions along the intracellular side of the transmembrane domains contribute to the cation permeability of ChR2.
| S-EPMC3501483 | biostudies-literature
Project description:In a two stage genome-wide association study (2S-GWAS), a sample of cases and controls is allocated into two groups, and genetic markers are analyzed sequentially with respect to these groups. For such studies, experimental design considerations have primarily focused on minimizing study cost as a function of the allocation of cases and controls to stages, subject to a constraint on the power to detect an associated marker. However, most treatments of this problem implicitly restrict the set of feasible designs to only those that allocate the same proportions of cases and controls to each stage. In this paper, we demonstrate that removing this restriction can improve the cost advantages demonstrated by previous 2S-GWAS designs by up to 40%. Additionally, we consider designs that maximize study power with respect to a cost constraint, and show that recalculated power maximizing designs can recover a substantial amount of the planned study power that might otherwise be lost if study funding is reduced. We provide open source software for calculating cost minimizing or power maximizing 2S-GWAS designs.
| S-EPMC3435377 | biostudies-literature