NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data

We introduce NSeq, a fast and efficient Java application for finding positioned nucleosomes from the high-throughput sequencing of MNase-digested mononucleosomal DNA. NSeq includes a user-friendly graphical interface, computes false discovery rates (FDRs) for candidate nucleosomes from Monte Carlo simulations, plots nucleosome coverage and centers, and exploits the availability of multiple processor cores by parallelizing its computations. Java binaries and source code are freely available at https://github.com/songlab/NSeq. The software is supported on all major platforms equipped with Java Runtime Environment 6 or later

Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant

IDH1 mutation is the earliest genetic alteration in low-grade gliomas (LGGs), but its role in tumor recurrence is unclear. Mutant IDH1 drives overproduction of the oncometabolite d-2-hydroxyglutarate (2HG) and a CpG island (CGI) hypermethylation phenotype (G-CIMP). To investigate the role of mutant IDH1 at recurrence, we performed a longitudinal analysis of 50 IDH1 mutant LGGs. We discovered six cases with copy number alterations (CNAs) at the IDH1 locus at recurrence. Deletion or amplification of IDH1 was followed by clonal expansion and recurrence at a higher grade. Successful cultures derived from IDH1 mutant, but not IDH1 wild type, gliomas systematically deleted IDH1 in vitro and in vivo, further suggestive of selection against the heterozygous mutant state as tumors progress. Tumors and cultures with IDH1 CNA had decreased 2HG, maintenance of G-CIMP, and DNA methylation reprogramming outside CGI. Thus, while IDH1 mutation initiates gliomagenesis, in some patients mutant IDH1 and 2HG are not required for later clonal expansions

Computational methods for the analysis of high throughput genomic data in cancer and development

This dissertation describes the research carried out within the scope of two projects that deal with novel biomedical technologies and their use for advancing medical knowledge through statistical integration of genomics assays. I have explored and characterized epigenetic intratumoral heterogeneity and brain cancer evolution by creating customized statistical analyses and novel methodology for understanding and integrating RNA- seq, methylation arrays, and exome-seq data. To explore functional effects of the Ilf2 RNA-binding protein (RBP) through embryonic stem cell differentiation in mice, I created statistical pipelines to remove data- generation artifacts, applied various testing methods, and integrated the information utilizing small RNA-seq, ribosome profiling, and RNA-seq technologies

Improving the effectiveness of anchoring underground structures in permafrost areas

A new method of anchoring underground structures in permafrost areas, utilizing full anchors whose locks are based on the property that dispersed frozen rocks can significantly change their firmness depending on temperature, is considered. A new condition of energy efficiency of the use of this method is formulated. Simple engineering formulas, on whose basis the assessment of the non-productive and productive energy expenses during the formation of the anchor lock, were devised. It was determined that in many cases relevant for practice, the non-productive energy expenses can constitute up to 30% of the productive energy expenses. A conclusion was made that in order to increase the efficiency and to expand the area of application of the new anchoring method in the mine workings of the permafrost areas built in the dispersed frozen rocks, it is necessary to search for technical and technological solutions to decrease the non-productive energy expenses in the front part of the anchor lock

Influence of Ground Ice Content on Thawing Depth Road Base

One of the important parameters that determine technical solutions in the design of roads in the permafrost zone is the depth of thawing of the road foundation soils. The aim of the work was to quantify the degree of influence of the ice content in the soil foundations of roads in the permafrost zone on the depth of their seasonal thawing. For the analysis, we used the classical formula for calculating the thawing depth for bodies of plane symmetry, obtained by solving the single-phase Stefan problem. The results of numerical calculations are presented in the form of 2D and 3D graphs, which make it possible to visually assess the effect of ground ice content and the degree of its change during the road operation period on the depth of thawing of the road foundation. It has been established, in particular, that the degree of change in the depth of thawing at the same value of the increase in ice content in different ranges (for example, from 10 to 20% and from 30 to 40%) for the considered typical case of the ground base of the permafrost zone, decreases by almost 1.3 times. It is shown that the greater the initial ice content of the soil, the lower the degree of decrease in the thawing depth when the ice content changes by a constant value

Fertility Recovery in Cows with Clinical Endometritis

The article presents the materials of microbiological studies of the contents of the uterus of cows with acute catarrhal-purulent form of postpartum endometritis. Studies have shown that the microflora was represented by Proteus vulgaris, Escherichia coli, Staphylococcus aureus, Streptococcus faecium, Citrobacter freundii, Streptococcus pyogenes. The antibacterial activity of microflora to the drugs Enroflor®, Geomicini® F and Mitrec® was studied. The results of use of drugs for the clinical recovery of animals, the restoration of sexual cyclicity in cows were analyzed. The features of fertilization of cows after intrauterine use of various drugs for sexual cycles and for the entire duration of the experiment were studied. It was found that the highest therapeutic efficiency in the treatment of cows with acute catarrhal - purulent form of postpartum endometritis is provided by drug Mitrec®

Thermal Conductivity of a Gravel Layer of a Road

Thermal resistance of the structural layers of a road is one of the important parameters that determine the choice of technical solutions of road design in the permafrost area. The purpose of this research is a quantitative assessment of the influence of the extent to which the pores in a gravel bedding are filled with ice or sand on the thermal conductivity of an ice-gravel or sand-gravel mixture. Lichtenecker formula was used to calculate the thermal conductivity coefficient of a three-component mixture. Different levels of ice content and moisture levels ofthe sand in the pores were considered. It was shown that the thermal resistance of the road structure can change significantly depending on the choice of the filler material. This allows to regulate the thermal regime of the road without adding new structural layers. The results of the calculations are presented as 2D and 3D charts to assess the influence of the filler material and the extent to which the pores are filled on the thermal conductivity coefficient of the mixture. The charts allow to see the possible changes in thermal conductivity coefficient of the structure and make a correct decision regarding the technologies to be used in construction. For example, to decide on the necessity to use a special thermal protection layer in the road structure

A processual method, the method helping to manage the quality of transport services

Transportation organization is inspected as three ground processes and each of these processes has dynamic indices. The connection of undynamics between these indices is the foundation for managing, the acception of managment decision and for a big number of other actions. There are some results of the aprobation of this method. First Published Online: 27 Oct 201

A Processual Method, the Method Helping to Manage the Quality of Transport Services

Transportation organization is inspected as three ground processes and each of these prpcess has dynamic indices. The connection of undynamics betveen these indices is the foundation for managing the acception of managment decision and for a big number of other actions. There are some results of the aprobation of this method