Risk assessment of packed holeassemblies for rotary well drilling

The main elements of the statistical model of packed hole assemblies (PHA) design for drilling holding sections in the conditions of information uncertainty have been formalized and described. Сonstraints ystem has been given for angle maintain conditions of wellbore direction and dynamic stability of bottom hole assembly (BHA) lateral vibrations. The influence of information uncertainty of some factors (angle, parameters of the drilling practice, presence of local caverns, etc.) on risk indicators has been analyzed according to the results of numerical calculations. It has been specified that the risks of angle maintenance disturbance are significantly influenced by the angle and the weight on the bit (WOB), and dynamic stability conditions, such as angle and rotation frequency. Risks of multi-supported BHAs which have been designed for conditions of bit side force minimizing, dynamic stability and include 4 – 6 stabilizers

Четверта міжнародна наукова-практична конференція «Комп’ютерне моделювання в хімії і технологіях та системах сталого розвитку»

Розглянуті питання екологічної безпеки технологій виробництва теплової енергії в Україні. Представлені результати досліджень роботи Черкаської ТЕЦ при переході генеруючого обладнання на спалювання вугілля і вплив викидів підприємства на стан урболандшафтів. Дана оцінка екологічної ситуації в місті. Показана необхідність гармонізації відносин суспільства і природи.This work covers the issues of the environmental safety technologies for the thermal energy production in Ukraine. The results of the research work are presented, which was performed for the CHP generation equipment in Cherkassy during its transition to coal and combustion emission impacting the city. There is estimation of the ecological situation in the city, which demands to harmonize the relationships between society and nature.Рассмотрены вопросы экологической безопасности технологий производства тепловой энергии в Украине. Представлены результаты исследований работы Черкасской ТЭЦ при переходе генерирующего оборудования на сжигание угля и влияние выбросов предприятия на состояние урболандшафтов. Дана оценка экологической ситуации в городе. Показана необходимость гармонизации отношений общества и природы

Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes

<p>Abstract</p> <p>Background</p> <p>Detection of non coding RNA (ncRNA) molecules is a major bioinformatics challenge. This challenge is particularly difficult when attempting to detect H/ACA molecules which are involved in converting uridine to pseudouridine on rRNA in trypanosomes, because these organisms have unique H/ACA molecules (termed H/ACA-like) that lack several of the features that characterize H/ACA molecules in most other organisms.</p> <p>Results</p> <p>We present here a computational tool called Psiscan, which was designed to detect H/ACA-like molecules in trypanosomes. We started by analyzing known H/ACA-like molecules and characterized their crucial elements both computationally and experimentally.</p> <p>Next, we set up constraints based on this analysis and additional phylogenic and functional data to rapidly scan three trypanosome genomes (<it>T. brucei</it>, <it>T. cruzi </it>and <it>L. major</it>) for sequences that observe these constraints and are conserved among the species. In the next step, we used minimal energy calculation to select the molecules that are predicted to fold into a lowest energy structure that is consistent with the constraints. In the final computational step, we used a Support Vector Machine that was trained on known H/ACA-like molecules as positive examples and on negative examples of molecules that were identified by the computational analyses but were shown experimentally not to be H/ACA-like molecules. The leading candidate molecules predicted by the SVM model were then subjected to experimental validation.</p> <p>Conclusion</p> <p>The experimental validation showed 11 molecules to be expressed (4 out of 25 in the intermediate stage and 7 out of 19 in the final validation after the machine learning stage). Five of these 11 molecules were further shown to be bona fide H/ACA-like molecules. As snoRNA in trypanosomes are organized in clusters, the new H/ACA-like molecules could be used as starting points to manually search for additional molecules in their neighbourhood. All together this study increased our repertoire by fourteen H/ACA-like and six C/D snoRNAs molecules from <it>T. brucei </it>and <it>L. Major</it>. In addition the experimental analysis revealed that six ncRNA molecules that are expressed are not downregulated in CBF5 silenced cells, suggesting that they have structural features of H/ACA-like molecules but do not have their standard function. We termed this novel class of molecules AGA-like, and we are exploring their function.</p> <p>This study demonstrates the power of tight collaboration between computational and experimental approaches in a combined effort to reveal the repertoire of ncRNA molecles.</p

Small nucleolar RNA interference in Trypanosoma brucei: mechanism and utilization for elucidating the function of snoRNAs

Expression of dsRNA complementary to small nucleolar RNAs (snoRNAs) in Trypanosoma brucei results in snoRNA silencing, termed snoRNAi. Here, we demonstrate that snoRNAi requires the nuclear TbDCL2 protein, but not TbDCL1, which is involved in RNA interference (RNAi) in the cytoplasm. snoRNAi depends on Argonaute1 (Slicer), and on TbDCL2, suggesting that snoRNA dicing and slicing takes place in the nucleus, and further suggesting that AGO1 is active in nuclear silencing. snoRNAi was next utilized to elucidate the function of an abundant snoRNA, TB11Cs2C2 (92 nt), present in a cluster together with the spliced leader associated RNA (SLA1) and snR30, which are both H/ACA RNAs with special nuclear functions. Using AMT-UV cross-linking and RNaseH cleavage, we provide evidence for the interaction of TB11Cs2C2 with the small rRNAs, srRNA-2 and srRNA-6, which are part of the large subunit (LSU) rRNA. snoRNAi of TB11Cs2C2 resulted in defects in generating srRNA-2 and LSUβ rRNA. This is the first snoRNA described so far to engage in trypanosome-specific processing events

RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs

The discovery of a plethora of small non-coding RNAs (ncRNAs) has fundamentally changed our understanding of how genes are regulated. In this study, we employed the power of deep sequencing of RNA (RNA-seq) to examine the repertoire of ncRNAs present in small ribonucleoprotein particles (RNPs) of Trypanosoma brucei, an important protozoan parasite. We identified new C/D and H/ACA small nucleolar RNAs (snoRNAs), as well as tens of putative novel non-coding RNAs; several of these are processed from trans-spliced and polyadenylated transcripts. The RNA-seq analysis provided information on the relative abundance of the RNAs, and their 5′- and 3′-termini. The study demonstrated that three highly abundant snoRNAs are involved in rRNA processing and highlight the unique trypanosome-specific repertoire of these RNAs. Novel RNAs were studied using in situ hybridization, association in RNP complexes, and ‘RNA walk’ to detect interaction with their target RNAs. Finally, we showed that the abundance of certain ncRNAs varies between the two stages of the parasite, suggesting that ncRNAs may contribute to gene regulation during the complex parasite’s life cycle. This is the first study to provide a whole-genome analysis of the large repertoire of small RNPs in trypanosomes

Characterization of RNase MRP RNA and novel snoRNAs from Giardia intestinalis and Trichomonas vaginalis

<p>Abstract</p> <p>Background</p> <p>Eukaryotic cells possess a complex network of RNA machineries which function in RNA-processing and cellular regulation which includes transcription, translation, silencing, editing and epigenetic control. Studies of model organisms have shown that many ncRNAs of the RNA-infrastructure are highly conserved, but little is known from non-model protists. In this study we have conducted a genome-scale survey of medium-length ncRNAs from the protozoan parasites <it>Giardia intestinalis </it>and <it>Trichomonas vaginalis</it>.</p> <p>Results</p> <p>We have identified the previously 'missing' <it>Giardia </it>RNase MRP RNA, which is a key ribozyme involved in pre-rRNA processing. We have also uncovered 18 new H/ACA box snoRNAs, expanding our knowledge of the H/ACA family of snoRNAs.</p> <p>Conclusions</p> <p>Results indicate that <it>Giardia intestinalis </it>and <it>Trichomonas vaginalis</it>, like their distant multicellular relatives, contain a rich infrastructure of RNA-based processing. From here we can investigate the evolution of RNA processing networks in eukaryotes.</p

A comparative genome-wide study of ncRNAs in trypanosomatids

<p>Abstract</p> <p>Background</p> <p>Recent studies have provided extensive evidence for multitudes of non-coding RNA (ncRNA) transcripts in a wide range of eukaryotic genomes. ncRNAs are emerging as key players in multiple layers of cellular regulation. With the availability of many whole genome sequences, comparative analysis has become a powerful tool to identify ncRNA molecules. In this study, we performed a systematic genome-wide in silico screen to search for novel small ncRNAs in the genome of <it>Trypanosoma brucei </it>using techniques of comparative genomics.</p> <p>Results</p> <p>In this study, we identified by comparative genomics, and validated by experimental analysis several novel ncRNAs that are conserved across multiple trypanosomatid genomes. When tested on known ncRNAs, our procedure was capable of finding almost half of the known repertoire through homology over six genomes, and about two-thirds of the known sequences were found in at least four genomes. After filtering, 72 conserved unannotated sequences in at least four genomes were found, 29 of which, ranging in size from 30 to 392 nts, were conserved in all six genomes. Fifty of the 72 candidates in the final set were chosen for experimental validation. Eighteen of the 50 (36%) were shown to be expressed, and for 11 of them a distinct expression product was detected, suggesting that they are short ncRNAs. Using functional experimental assays, five of the candidates were shown to be novel H/ACA and C/D snoRNAs; these included three sequences that appear as singletons in the genome, unlike previously identified snoRNA molecules that are found in clusters. The other candidates appear to be novel ncRNA molecules, and their function is, as yet, unknown.</p> <p>Conclusions</p> <p>Using comparative genomic techniques, we predicted 72 sequences as ncRNA candidates in <it>T. brucei</it>. The expression of 50 candidates was tested in laboratory experiments. This resulted in the discovery of 11 novel short ncRNAs in procyclic stage <it>T. brucei</it>, which have homologues in the other trypansomatids. A few of these molecules are snoRNAs, but most of them are novel ncRNA molecules. Based on this study, our analysis suggests that the total number of ncRNAs in trypanosomatids is in the range of several hundred.</p

IMPACT ASSESSMENT OF CHERKASY CHP PLANT EMISSIONS ON URBOLANDSCAPES

The article is dedicated to a comprehensive assessment for the quality of urbolandscapes in Cherkasy based on the chemical composition of the snow cover

Реотехнології в бурінні свердловин

The principles of quality assessment of well drilling operations have been reviewed and four-grade evaluation system (very high, high, satisfactory, unsatisfactory) has been suggested. The model for interpretation of rotational viscosimetry data using criteria of transformed disreptancy and results of analysis of matrices of rheological properties estimates covariations has been summarized. The article describes how to build equations of state of rheological properties on the basis of the results of rotational viscosimetry data treatment for the plan of experiment. General formulas for calculation of biviscosity fluids steady flow in circular cylindrical and annular pipes have been presented.Розглянуто принципи і запропоновано чотирибальну (дуже висока, висока, задовільна, незадовільна) систему оцінювання якості технологічних операцій буріння свердловин. Узагальнено модель інтерпретації даних ротаційної віскозиметрії із використанням критеріїв трансформованої нев’язки та результататів аналізу матриці коваріацій оцінок реологічних властивостей. Описано процедуру побудови рівнянь стану реологічних властивостей за результатами обробки даних ротаційної віскозиметрії для плану експерименту. Наведено загальні формули для розрахунку усталених течій бів’язких рідин в круглих циліндричних і кільцевих трубах