As part of the MicroArray Quality Control (MAQC)-II project, this analysis examines how the choice of univariate feature-selection methods and classification algorithms may influence the performance ...of genomic predictors under varying degrees of prediction difficulty represented by three clinically relevant endpoints.
We used gene-expression data from 230 breast cancers (grouped into training and independent validation sets), and we examined 40 predictors (five univariate feature-selection methods combined with eight different classifiers) for each of the three endpoints. Their classification performance was estimated on the training set by using two different resampling methods and compared with the accuracy observed in the independent validation set.
A ranking of the three classification problems was obtained, and the performance of 120 models was estimated and assessed on an independent validation set. The bootstrapping estimates were closer to the validation performance than were the cross-validation estimates. The required sample size for each endpoint was estimated, and both gene-level and pathway-level analyses were performed on the obtained models.
We showed that genomic predictor accuracy is determined largely by an interplay between sample size and classification difficulty. Variations on univariate feature-selection methods and choice of classification algorithm have only a modest impact on predictor performance, and several statistically equally good predictors can be developed for any given classification problem.
The neuropeptide preparation Semax (Met-Glu-His-Phe-Pro-Gly-Pro) has been employed successfully in clinical practice for treating patients with severe brain blood circulation disorders. In spite of ...numerous studies, many aspects of the therapeutic effects of this preparation remain unknown. In this context, the effects of Semax and its C-end tripeptide PGP on the functional morphology of nervous tissue cells were studied in the normal rat brain and in a model of incomplete global rat brain ischemia. In control animals, both peptides activated the capillary network and caused similar morphological changes to neurons and the neuropil regions. We show here for the first time at the histological level that Semax and PGP increased proliferation of the neuroglia, blood vessel endothelium, and progenitor cells in the subventricular zone. In these experimental conditions, only Semax abated the manifestation of ischemic damage to the nervous tissue. This was probably attributable to a decrease in vascular stasis symptoms as well as the trophic effect of the peptide.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
The relevance of the studied circulation caused by the water river runoff deals with the anthropological impact on the ecological state of the shelf. River waters, entering into the sea, form ...mesoscale structures in the delta’s area, characterized by low salinity with a high level of suspended matter and dissolved organic matter. Such structures are called “plume” in modern literature. In this case, the inertial motion of the plume is free to form a rounded area or “bulge” like anticyclonic circulation type of flow.
The purpose of this work is to investigate the propagation of freshened waters, formed by the river inflow, the formation of the waters hydrological structure regularities, dynamics of the buoyancy current, and thermohaline front formation on the base of numerical modeling.
Numerical modeling is used to study the formation of a river plume and downward propagation of buoyancy current on the shelf without taking into account the tides forcing. A three-dimensional σ-coordinate numerical model was used, adapted for the shelf and estuaries. The calculations were carried out for a rectangular box area.
The influence of changes in the main parameters of the runoff, the mouth geometry and wind forcing are considered to development of the plume and the alongshore propagation of buoyancy current. The obtained modeling results for the conditions of the Northwestern Black Sea shelf and the Danube discharge are consistent with the estimates of plume characteristics based on the archival hydrological observations data of water temperature and salinity.
The results of this work can be used for further study of hydrological processes in the region of river mouths, the peculiarities of the plumes formation and evolution, assessment of the suspended matter, biogenic elements and microplastics transport in the sea and ocean coastal zones.
Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. In the MAQC-II project, 36 ...independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity in rodents, or of breast cancer, multiple myeloma or neuroblastoma in humans. In total, >30,000 models were built using many combinations of analytical methods. The teams generated predictive models without knowing the biological meaning of some of the endpoints and, to mimic clinical reality, tested the models on data that had not been used for training. We found that model performance depended largely on the endpoint and team proficiency and that different approaches generated models of similar performance. The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis.
In a south wind, coastal upwelling can be observed off the western coast of the Black Sea. In the same area, the hydrological structure of waters is strongly influenced by river runoff, which forms a ...river plume, and a southward longshore current. The paper studies the evolution of the plume on the northwest shelf of the Black Sea and its interaction with upwelling based on numerical modelling. The impact of upwelling development under the influence of the south wind on plume propagation was studied using a three-dimensional sigma-coordinate numerical model (POM-type) to calculate the circulation in the coastal zone taking into account the river runoff. The calculations were performed for a rectangular region for the cases of both uniform depth and typical water stratification of the northwestern shelf. The last case was sampled for May condition, when, on average, the Danube plume development is maximal. It is obtained that the joint dynamics of upwelling and river plume are closely related to the stratification of coastal waters. In the case of unstratified shelf waters, the thin plume layer enhances upwelling and downwelling on the inshore and offshore sides of the river plume, respectively. The results allowed studying the peculiarities of river water transformation during winds that cause the development of coastal upwelling. Estimates of the time of bottom water rise near the coast under the action of south winds with different wind speeds and shelf water stratification parameters retrieved from numerical modelling data can be used to develop regional upwelling indices based on satellite data on the sea surface temperature and wind speed.
Purpose. The aim of the present paper is to solve the problem of choosing the localities in the Sevastopol Bay for optimal placing the pollution sources using the adjoint equations of the admixture ...transfer. Methods and Results. The embankments in the city center, the Artilleriyskaya Bay and the city beach zone are chosen as the nature protection areas. Solution of the adjoint equation of the passive admixture transport yields the influence function that permits to reveal the areas on the coast, where, in case the pollution sources are placed there, the sanitary standards will be violated, and, at the existing currents’ structure, these nature protection zones will suffer significant damage. To make sure that the adjoint equation is solved correctly, the direct problem can be solved for various locations of the impurity sources. Solution of the adjoint equation makes it possible to obtain information on the impurity amount in the preset nature protection zones during the preset time period at an arbitrary location of the impurity source. The currents velocities are calculated by the linear three-dimensional barotropic model for the steady wind currents. Conclusions. The numerical modeling results revealed the regions, where placing of the pollution sources would violate sanitary standards in the nature protection zones under study. The experiments showed that the north and east winds were the most dangerous. Hence industrial facilities, storm and sewage discharges having been placed at the Northern side of the Sevastopol Bay, can be extremely harmful for the ecological state of the regions under consideration. At the east and southeast winds, the industrial activity products in the Yuzhnaya Bay constitute a basic source of contamination. At the south winds, the most dangerous situation occurs in case the pollution sources are placed at the coast of the recreational zone of the city.
The present article proposes a method for production of low molecular weight rubber in microwave irradiation field. Isoprene rubber SKI-3 (10% solution in toluene) was used as the initial reactant. ...The effect of MWI power change (144 W, 450 W, 675 W, 900 W) on the degree of destruction was studied. The degree of destruction was measured based on the change in viscosity average molecular weight. The findings of the experiment data analysis indicate that the destruction process occurs in correspondence with the following dependency: the increase in the microwave irradiation power raises the destruction degree. At the same time, a decrease in molecular weight was observed. Furthermore, it was found that the use of phospholipids as modifiers also affects the destruction process. The increase in phospholipids content in toluene-SKI-3 system reduces the degree of polyisoprene destruction regardless of the microwave irradiation power. It is demonstrated by the fact that rubber molecular weight is subject to a lower decrease in systems with higher phospholipids content. Phospholipids perform two functions. Firstly, they act as a stabilizer that inhibits the rubber destruction process. Secondly, varying their content allows controlling the destruction degree and obtaining oligomers with predetermined molecular weight. The obtained oligomers were used as SKI-3 isoprene rubber modifiers. It is observed that that the introduction of oligomers into rubber mixtures in the amount of 7 and 10 parts by weight per 100 parts by weight of rubber increases its cohesive strength. Furthermore, vulcanizates containing oligomers are characterized by improved physical and mechanical properties.
Genomic biomarkers for the detection of drug-induced liver injury (DILI) from blood are urgently needed for monitoring drug safety. We used a unique data set as part of the Food and Drug ...Administration led MicroArray Quality Control Phase-II (MAQC-II) project consisting of gene expression data from the two tissues (blood and liver) to test cross-tissue predictability of genomic indicators to a form of chemically induced liver injury. We then use the genomic indicators from the blood as biomarkers for prediction of acetaminophen-induced liver injury and show that the cross-tissue predictability of a response to the pharmaceutical agent (accuracy as high as 92.1%) is better than, or at least comparable to, that of non-therapeutic compounds. We provide a database of gene expression for the highly informative predictors, which brings biological context to the possible mechanisms involved in DILI. Pathway-based predictors were associated with inflammation, angiogenesis, Toll-like receptor signaling, apoptosis, and mitochondrial damage. The results show for the first time and support the hypothesis that genomic indicators in the blood can serve as potential diagnostic biomarkers predictive of DILI.
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DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Various legume plants form root nodules in which symbiotic bacteria (rhizobia) fix atmospheric nitrogen after differentiation into a symbiotic form named bacteroids. In some legume species, bacteroid ...differentiation is promoted by defensin-like nodule-specific cysteine-rich (NCR) peptides. NCR peptides have best been studied in the model legume
Medicago truncatula
Gaertn., while in many other legumes relevant information is still fragmentary. Here, we characterize the NCR gene family in pea (
Pisum sativum
L.) using genomic and transcriptomic data. We found 360 genes encoding NCR peptides that are expressed in nodules. The sequences of pea NCR genes and putative peptides are highly variable and differ significantly from NCR sequences of
M. truncatula
. Indeed, only one pair of orthologs (
PsNCR47
–
MtNCR312
) has been identified. The NCR genes in the pea genome are located in clusters, and the expression patterns of NCR genes from one cluster tend to be similar. These data support the idea of independent evolution of NCR genes by duplication and diversification in related legume species. We also described spatiotemporal expression profiles of NCRs and identified specific transcription factor (TF) binding sites in promoters of “early” and “late” NCR genes. Further, we studied the expression of NCR genes in nodules of Fix
–
mutants and predicted potential regulators of NCR gene expression, one among them being the TF ERN1 involved in the early steps of nodule organogenesis. In general, this study contributes to understanding the functions of NCRs in legume nodules and contributes to understanding the diversity and potential antibiotic properties of pea nodule-specific antimicrobial molecules.
Mathematical and computer modeling of daily thermometry allows to study processes of human thermal homeostasis more deeply. In practice, thermometry data is obtained using a digital thermometer, ...which autonomously reads the temperature of human skin in certain time intervals. The aim of present work is to analyse the methods of modeling and processing of human daily thermometry data. The first method consists in applying linear discrete stochastic models in the state space with Gaussian noises and known vector of input actions, while the estimation of the state vector is performed by discrete covariance Kalman filter. The second method assumes that the vector of input actions is unknown, and the S. Gillijns and B.D. Moor algorithm is used to process daily thermometry data. An alternative option is to use a model with an extended state vector and a Kalman filtering algorithm. The third method takes into account the presence of anomalous measurements (outliers) in the measurement data, and correntropy filter is proposed for their effective filtering. Numerical experiments for modeling and processing of daily thermometry data in MATLAB were carried out in order to compare the quality of discrete filtering algorithms. Modeling of thermometry data was carried out using a three-dimensional model 3dDRCM (3-dimension Discrete-time Real-valued Canonical Model). The results obtained can be used in the study of human daily thermometry processes, for example, to study the reaction of the athlete’s body to the received load.
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