bluuebunny/crossref_metadata_2025 huggingface dataset:
Different Routes - Same Destination: Planning Processes for Decommissioning in South East Asia
Authors: Laister Steve , Jagerroos Sylvia
Published: November 2018

'As decommissioning has risen up the agenda for both Governments and oil and gas operators, the countries of Southeast Asia have adopted differing frameworks for the planning, permitting and execution of the decommissioning process. This paper presents a review of the frameworks adopted by a number of the key oil and gas countries in the region by reference to the legislative and guidance instruments to which they are signatories or have introduced, and the authors’ experience of working with Governments and oil and gas operators. The paper illustrates that countries such as Thailand, Malaysia and Brunei Darussalam are actively developing legislative and guidance frameworks with broadly common requirements, and identifies that opportunities exist for increased information sharing and capability building within and between countries in the region, to further encourage consistent, cost and time efficient outcomes.
Innovative Rigless Well Intervention on Collided Platform Using New Designed Extended Deck on a Dynamic Positioning Barge
Authors: Bahrami Esmael , Safari Alireza , Mortazavizadeh Seyedmorteza , Bahrami Ghazaleh , Zangenehvar Alireza
Published: November 2018

Among all risks that may posed to offshore platforms, one of severest is ship collision that associated with huge physical and financial damages. An oil tanker collided with a jacket on the South Pars gas field in 2015. The operator faced the challenges of killing a perforated HPHT gas well, wreck removal of platform, plug back and securing the remained wells that all were drastically damaged. The operation had to deal with harsh offshore weather conditions, lack of offshore facilities, put a balance cement plug using coiled tubing in the HT brine medium, lack of a straight path for coiled tubing run in hole, and had to provide an operational safe method while keeping the highest quality.

A dynamic positioning multi-purpose barge used in this operation in conjunction with a new designed deck for well intervention. A flexible hose connected from the designed deck bottom to inside the 10 3/4″ casing cut entrance, to prepare a straight path for coiled tubing string.

A gas tight and right angle set cement slurry designed in order to prevent unpredicted gas migration. The coiled tubing cementing operation and fluids hydraulic designed to have uncontaminated and stable slurry column at the end of the displacement in the brine medium. This goal achieved by using compatible high viscous pill and mud push fluids in bottom and top of cement slurry column to prevent instability, fingering, falling downwards, and consequently contamination of cement slurry with brine. The displacement and pull-out-of-the-hole method also designed in such a way to minimize the risk of flash setting of cement slurry in high temperature brine medium. This method prevents sticking of coiled tubing string while its maintain the stability of fluids interfaces.

This paper is a detailed description of all the operational and engineering challenges after the collision and the methods to overcome them except wreck removal and tie back phases. The advantages of using these novel concepts resulted in an operational safe method for salvage operation and securing the wells. This paper can be used as a guideline when encountered with such rare situation.
Estimating Cost and Commercial Risks of North Sea Decommissioning Projects: Lessons Learnt for Asia Pacific
Authors: Wan Ullok Stephanie Marie
Published: November 2018

The Cost Estimate is an essential document in the preparation of decommissioning cost projects and entails the quantification of commercial and schedule risks. This study lists the Lessons Learnt from the preparation of Cost Estimates for North Sea decommissioning studies. It reviews on a holistic manner the considerations by Estimators on the impact of statutory and contracting regime and the major influences of cost in decommissioning. This study also proposes theoretical cost savings and efficiencies currently being explored in the North Sea.

This study was conducted via interviews with a leader in North Sea decommissioning as well as extensive research of journals and web-based articles and releases. The identification of major cost elements which influenced decommissioning cost applied probabilistic analysis using Monte Carlo simulation.

Following the processing of data received, the author then applied the results to current conditions in Asia Pacific by considering the related challenges faced (and anticipated) by the region's offshore decommissioning industry.

The Lessons Learnt have been summarized into 5 main areas: Development of the Cost Estimate: Areas that have been highlighted as potential hazards include the preparation of the accuracy of estimates and cost consolidation over multiple projects. Suggestions are made to include the application of probabilistic analysis in cost estimates, a process to challenge cost-driving assumptions and adopting integrated Cost & Schedule Risk analysis in the development of the cost estimate.Collaboration and Data Analytics: The report highlights the opportunities that regional collaboration can drive a richer environment for data analytics. In the North Sea, organisations including the Oil and Gas Authority (UK) and the OSPAR commission have been tasked with centralising and disseminating.Statutory Regime: it is imperative to remind ourselves in this region that operators, and contractors, in the North Sea have had to keep up with changes in regulations and ever greater environmental obligations.Contracting Regime: Consideration of Contingent Liabilities and financial responsibility for decommissioning, even those who have sold, relinquished or otherwise disposed of their license is discussed. Contracting Strategies as well as the use of Decision Trees, Project Controls and Project Management in contract preparation and insurances are discussed.Adoption of Circular Economy Principles: Findings in the North Sea suggest that increasing re-use over the recycling of equipment and structures on installations can increase values by between five and seven times.
Comparison of Offshore Abandonment Projects in Indonesia: The Evaluation, Challenges and Effectiveness
Authors: Prasetya Afriandi Eka , Rakhmahwidiati Rakhmahwidiati
Published: November 2018

Conduct comparative evaluations of offshore wells abandonment projects on either platform or underwater, whether rig or rigless. Identify challenges and effectiveness in terms of operations and costs. Discuss the preparations to be made before the work and the procedures to be done.

Based on data of the offshore wells abandonment which were conducted between 2014-2017 in Indonesian waters, classification was made on subsea and platform, then differentiated the water depth and the total well depth, and are grouped to its method with the rig or rigless. Then look at the problems in the well. Money spent is also a point of comparison for evaluation. Plugging procedures refer to national and international standards that are recognized. Evaluating the work schedule of each group were assessed.

There is a very clear distinction between the well abandonment on subsea and those on the platform. Also there are some differences between the use of the rig with rigless. This study illustrates how much it will cost to cover the well and also recommends work in the form of a project campaign to achieve its effectiveness.

Plugging and abandoning the wells are commonly done on wells that are no longer expected to be productive. This comparative evaluation helps to illustrate how effectively doing the well abandonment works in the form of a project campaign.
An Alternative Approach to Well Re-Entry and Permanent Well Abandonment from a Monohull Vessel in the UK Continental Shelf
Authors: Canny Steven A.
Published: November 2018

Post COP (cessation-of-production) operations are a source of expenditure with no financial return. Therefore, the focus on the cost of operations and technology is acute. The permanent abandonment of subsea wells can involve significant expense, with project logistics, interfaces and the high number of parties involved contributing to the project cost. As such, new project execution models have been developed to reduce the conveyance cost, and reduce the project interfaces.

The paper presents a novel project-managed execution model to safely execute Phase III well-abandonment operations and annulus fluid removal for surface disposal. The project used a monohull service vessel and new market technology to successfully abandon wells compliant to local and international legislation and standards. Using technology from alternative exploration sectors, allied to existing well-construction technology, presents a system that is capable of subsea well re-entry and pressure containment, to perform the permanent abandonment and safely dispose of well fluids to surface. Tubular milling, cutting and open-water recovery operations are presented and discussed, with the engineering and quality, health, safety and environment (QHSE) drivers highlighted.

Five wells were selected for the Phase III well abandonment operations using a bespoke system that was integrated into a monohull vessel, which resulted in a reduced day rate compared to a semi-submersible rig. The technology solutions taken from alternative exploration sectors are presented, and the integration to a vessel of opportunity, to provide a marine vessel with a heave compensated hoisting system and tubular handling capabilities. For well re-entry, a pressure-containing re-entry workstring is used, conveyed on drillpipe. The pressure-containing, circulation and disconnection capabilities are presented, along with how potentially pressurized and harmful wellbore fluids are taken back to the vessel for disposal. Multi-annuli perforation technology, which allows a multi-annuli well barrier to be set across the wellbore, is also described.

With five wells successfully completed, the key performance indicators (KPIs) are discussed, and project lessons learned are presented.
Improving Cannabis Bud Quality and Yield with Subcanopy Lighting
Authors: Hawley Dave , Graham Thomas , Stasiak Michael , Dixon Mike
Published: November 2018

The influence of light spectral quality on cannabis (Cannabis sativa L.) development is not well defined. It stands to reason that tailoring light quality to the specific needs of cannabis may increase bud quality, consistency, and yield. In this study, C. sativa L. ‘WP:Med (Wappa)’ plants were grown with either no supplemental subcanopy lighting (SCL) (control), or with red/blue (“Red-Blue”) or red-green-blue (“RGB”) supplemental SCL. Both Red-Blue and RGB SCL significantly increased yield and concentration of total Δ9-tetrahydrocannabinol (Δ9-THC) in bud tissue from the lower plant canopy. In the lower canopy, RGB SCL significantly increased concentrations of α-pinine and borneol, whereas both Red-Blue and RGB SCL increased concentrations of cis-nerolidol compared with the control treatment. In the upper canopy, concentrations of α-pinine, limonene, myrcene, and linalool were significantly greater with RGB SCL than the control, and cis-nerolidol concentration was significantly greater in both Red-Blue and RGB SCL treated plants relative to the control. Red-Blue SCL yielded a consistently more stable metabolome profile between the upper and lower canopy than RGB or control treated plants, which had significant variation in cannabigerolic acid (CBGA) concentrations between the upper and lower canopies. Overall, both Red-Blue and RGB SCL treatments significantly increased yield more than the control treatment, RGB SCL had the greatest impact on modifying terpene content, and Red-Blue produced a more homogenous bud cannabinoid and terpene profile throughout the canopy. These findings will help to inform growers in selecting a production light quality to best help them meet their specific production goals.
Rootstock Effect on Grafted Tomato Transplant Shoot and Root Responses to Drying Soils
Authors: Suchoff David H , Gunter Christopher C. , Schultheis Jonathan R. , Kleinhenz Matthew D. , Louws Frank J.
Published: November 2018

Improvement of crop water use is imperative. Plants’ responses to limited water can dictate their ability to better use available resources and avoid prolonged and severe stress. The following study was conducted to determine how tomato (Solanum lycopersicum) rootstocks with different root system morphologies respond to drying soils. Plants were grown in pots containing an inorganic substrate composed of calcined clay and sand in a greenhouse on North Carolina State University’s campus. The heirloom tomato cultivar Cherokee Purple was used as the scion for ‘Beaufort’ and ‘Shield’ rootstocks as well as the self-grafted control. These rootstocks were assigned either normal or reduced irrigation treatments. Plants grown under the normal irrigation schedule were weighed and watered daily to maintain container capacity for one week. Those receiving reduced irrigation had all water withheld for one week, at which point strong midday wilting became evident. Shoot physiological and morphological data as well as root morphological data were collected at the end of the study. A constitutive positive increase on relative water content, leaf area, stomatal conductance (gS), and net CO2 assimilation rate was observed with scions grafted on ‘Beaufort’. In addition, this rootstock had a significantly longer total root system (118.6 m) compared with ‘Shield’ (94.9 m) and the self-grafted control (104.2 m). Furthermore, 76.4% of the total root length observed in ‘Beaufort’ was composed of very thin diameter roots ( <0.5 mm), which was higher than ‘Shield’ (73.67%) and the self-grafted control (69.07%). The only significant rootstock irrigation interaction observed was for effective quantum yield of photosystem II (φPSII). At normal irrigation there were no differences among the rootstock treatments; however, at reduced irrigation ‘Beaufort’ had significantly higher φPSII than both ‘Shield’ and the self-grafted control. These results may explain some of the improved production and water use efficiency observed in field trials using ‘Beaufort’ rootstock, and data secured may allow for better screening of rootstocks for improved water use efficiency in the future.
History of Bermudagrass Turfgrass Breeding Research in Tifton, GA
Authors: Baxter Lisa L. , Schwartz Brian M.
Published: November 2018

Bermudagrass (Cynodon spp.) is the foundation of the turfgrass industry in most tropical and warm-temperate regions. Development of bermudagrass as a turfgrass began in the early 1900s. Many of the cultivars commercially available today have been cooperatively released by the U.S. Department of Agriculture Agricultural Research Service (USDA-ARS) and the University of Georgia at the Coastal Plain Experiment Station in Tifton, GA.
Salinity Tolerance of Muntries (Kunzea pomifera F. Muell.), a Native Food Crop in Australia
Authors: Do Chi M. , Delaporte Kate L. , Pagay Vinay , Schultz Carolyn J.
Published: November 2018

Identifying productive food crops that tolerate moderate soil salinity is critical for global food security. We evaluate the salinity tolerance of Kunzea pomifera (muntries), a traditional Indigenous food plant that grows naturally in coastal regions of southern Australia and thrives on relatively low rainfall. A range of saline irrigation treatments were tested on four genotypes: tap water, 50, 200, 300, and 400 mm NaCl [Maarten’s Favorite (MF)] and up to 200 mm NaCl (MP1, SES2, and CJ1). After a 10-week saline irrigation treatment at 50 mm NaCl, SES2 appeared to have the highest salt tolerance of all genotypes based on no significant change in the number of secondary branches. At 50 mm NaCl, sodium accumulated significantly in roots but not the leaves of three genotypes, suggesting an active shoot exclusion mechanism. At 200 mm NaCl, plant growth decreased, Na+ and Cl− generally accumulated to significantly higher levels in leaves, compared with 50 mm NaCl, whereas potassium (K+) levels were unchanged. At high NaCl (300 and 400 mm), MF showed severe growth retardation with leaf symptoms appearing in week 9. Our results indicate that two genotypes of K. pomifera, SES2 and CJ1, are moderately salt tolerant based on modest reductions in three growth parameters at 50 mm NaCl, compared with MF and MP1. Further evaluation of the natural diversity of this species should reveal a range of diverse mechanisms of salinity tolerance thus providing a new fruit crop for moderately saline soils. Chemical names: NaCl (sodium chloride).
The Protective Effect of Exogenous Putrescine in the Response of Tea Plants (Camellia sinensis) to Salt Stress
Authors: Xiong Fei , Liao Jieren , Ma Yuanchun , Wang Yuhua , Fang Wanping , Zhu Xujun
Published: November 2018

Camellia sinensis cultivars were treated with 5 mm putrescine (Put) under a range of sodium chloride (NaCl) concentrations. Plant performance, as indicated by various indicators associated with plant growing condition such as photosynthetic parameters and polyamine (PA) contents, especially the content of Put, was improved by the treatment. The extent of both Na+ accumulation and K+ loss increased. The activity levels of the antioxidant enzymes related to salt stress, such as superoxide dismutase (SOD), peroxidase (POD), and catalase, were significantly altered with different salt stress levels and showed a decrease in the general trend. Besides, tea polyphenols, the tea quality indicator, increased during the salinity treatment but decreased when we applied Put. These findings suggest that treatment with Put might constitute an effective means for alleviating salinity stress–induced injury through its positive effect on photosynthetic efficiency and for controlling reactive oxygen species (ROS) scavenging ability under appropriate salt stress levels.
The Profitability of New Citrus Plantings in Florida in the Era of Huanglongbing
Authors: Singerman Ariel , Burani-Arouca Marina , Futch Stephen H.
Published: November 2018

The Florida citrus industry has been enduring the impact of citrus greening since 2005. The disease has been the main driver for the state’s citrus production to plummet by 80% in the past 13 years, causing the industry to downsize drastically. Planting new groves is key to ensuring a supply of fruit for processors and packinghouses to stay in business. However, a key question is whether it makes economic sense to plant a new grove in the current environment. We estimate the establishment and production costs for a new grove under endemic Huanglongbing (HLB; citrus greening) conditions for three different tree planting densities under different market conditions and examine their profitability. Our results show that establishing a new grove with a tree density similar to that of the state’s average is not profitable under current market conditions. However, greater tree densities are profitable despite the greater level of investment required.
Methodical approach to foresight-research at definition of trends in Green IT development
Authors: Romanenkov Yuri , Danova Mariia
Published: November 2018

The problem of determining the Green IT development strategy using decision support tools is described in the article. Technology Green IT is a typical result of the advanced technologies convergence, especially information and knowledge. The expediency of the foresight technology applying for the Green IT development perspective directions evaluating is shown. It is indicated that the most critical, in this case, is the stage of forming the initial list of directions. The technology of retrospective analysis of the Green IT development based on the parametric synthesis of the predictive model of exponential smoothing under the conditions of data uncertainty is presented. For the implementation of the parametric analysis of Brown’s predictive model, or exponential smoothing, is used the exponential average value of the stationary time series to evaluate its value at the next time point. The applying of the developed technology provides experts with additional volumes of information about the perspectives for the Green IT development. An example of a retrospective analysis of the Green IT development directions is given. The initial data for the retrospective analysis used the number of scientific publications for the period from 2010 to 2015 in Ukraine, which characterizes the Green IT direction development. The following directions were assessed: green software engineering, software ecosystem, energy-saving green software and green telecommunications. As a result, the most promising direction is green software engineering. The results of the analysis are one of the sources of information for assessing the perspectives for the Green IT development directions by experts
Environmental features and resistance to the anthropogenic load of coniferous introducents in the central part of Ukraine
Authors: Ivashchenko Iryna , Adamenko Svitlana
Published: November 2018

The current state of coniferous introduced plants growing on the territory of Uman, Cherkasy region is analyzed. Such representatives are the multi-age trees Pinus nigra and Thuja plicata. The studies were aimed at determining their resistance to arid environmental conditions in summer and to adverse factors in the winter period with generally accepted methods. Studies were conducted during 2015-2017. P.nigra trees during the study period received high drought tolerance scores. In Th. plicata plants observed a partial loss of needles turgor during daylight hours. When evaluating the frost resistance, P. nigra trees of different ages did not have visible damage. Young plants Th. plicata were somewhat more vulnerable to the effects of low temperatures, while no damage was found in mature trees. In general, both species have rather high rates of winter hardiness and drought resistance. This indicates their acclimatization to the given growing conditions. Also, the studied plants tolerate the adverse conditions of the city: dust, smoke, soil compaction. Therefore, it is advisable to use them for landscaping urban areas and personal plots. A feature of these species is that they retain a high decorative effect throughout the year and are good components for creating landscape compositions. Comparing the conditions of the natural distribution range to the conditions of the cultural areas of the studied species, it is possible to state their successful cultivation, which indicates a high ecological plasticity and significant potential of these plants
Methods of forming an expert assessment of the criteria of an information system for managing projects and programs
Authors: Boiko Yevheniia
Published: November 2018

The article presents a method for determining and ranking significance of the criteria of an information system for managing projects and programs (hereinafter, PMIS) based on the concept of subjective probability with the help of expert assessments. The method of expert assessments is implemented by processing the opinions of experienced specialists on the possible values of losses and (or) the probability of their occurrence. It is also used in non-formalizable problem situations, when the lack of a sufficient array of information or its unreliability does not allow the use of purely formal mathematical methods. When analyzing the PMIS choice, expert assessments can be used, firstly, to form a subjective assessment of one or another PMIS with the subsequent use of this information in order to quantify it using statistical methods. Secondly, for a qualitative assessment of the PMIS choice in terms of determining their rank significance, priority in an ordered list of PMIS criteria. As the main stages of the proposed methodology, the following are proposed: 1) development of a list of assessed PMIS criteria and formation of a list of experts; 2) conducting a survey of experts in order to obtain a set of individual expert assessments according to the PMIS criteria; 3) calculation of the average assessment criteria of the PMIS; 4) checking the consistency of expert opinions on the rank significance of the assessed PMIS criteria based on the Kendall coefficient of concordance; 5) summing up the results of expert assessment of the PMIS criteria. The practical aspects of the expert assessment are considered: calculation tables, the method of filling them, processing and analyzing the results. The method of expert assessment of the PMIS criteria was further developed, thanks to which a set of effective and functional criteria was determined, which will be taken into account when developing technical requirements for this system
Development of the luenberger observer for the automated electric drive of hermetic compressor
Authors: Bukaros Andrii , Malyshev Vitalii , Bukaros Valeriia
Published: November 2018

The basic requirements for control systems of automated electric drives of hermetic compressors of small refrigeration units are determined. The analysis of the existing sensorless control systems of three-phase AC drives is carried out. The topology of the adaptive Luenberger observer is proposed, which allows real-time evaluation of the current value of the rotational speed and torque on the shaft of the hermetic compressor motor. Based on the linearized model of a three-phase asynchronous motor, the Luenberger observer is synthesized by the modal method with the distribution of the roots of the characteristic polynomial in the standard linear Bessel form. Expressions are obtained for calculating the coefficients of the Luenberger matrix and the geometric mean root of the characteristic polynomial of the observer. To ensure the necessary accuracy of identifying the coordinates of the state of an automated electric drive of a hermetic compressor, an observer structure is proposed based on a complete mathematical model of a three-phase asynchronous motor made in a fixed coordinate system. Using simulation tools, the work of the designed Luenberger observer is studied on the example of a modernized three-phase asynchronous motor of a hermetic compressor of a domestic refrigerator. For this example, the coefficients of the Luenberger matrix and the geometric mean root of the characteristic polynomial of the observer are calculated. The effectiveness of the proposed method for identifying the rotational speed and moment of resistance of a compressor electric motor by an adaptive observer based on the calculation of the electromagnetic torque of the motor from measured sensors of phase voltages and currents is confirmed. The error of the observer under investigation does not exceed 0.5 % in rotation frequency and 10 % in respect to the moment of resistance. The resulting structure of the adaptive Luenberger observer allows to build closed-loop control systems for automated electric drives of the hermetic compressor of a small refrigeration unit.
The phenolic content, antioxidant and cytotoxic activities of Origanum sipyleum from Turkey
Authors: KASKA Arzu
Published: November 2018

Origanum
sipyleum is a medicinal plant species belonging to the genus Origanum and traditionally vegetative
parts of this plant have been used as medicinal tea or food additives. The current study has been designed to examine the
antioxidant, cytotoxic activities and total phenolic, flavonoid and tannin
contents as well as the chemical composition of the ethanol extract of O. sipyleum. The antioxidant capacity of
O. sipyleum was determined using six
complementary methods, β-carotene/linoleic acid and phosphomolybdenum
test systems, radical scavenging (ABTS and DPPH), metal chelating and reducing power assays. The
phenolics were identified using HPLC. A brine shrimp (Artemia salina L.) lethality
test was used for determining
cytotoxic activity. The ethanol
extract exhibited high DPPH free radical scavenging (DPPH, IC50:102.75
µg/mL), ABTS radical scavenging (ABTS, IC50:88.64
µg/mL), metal chelating (20.68 %) and reducing power capacity (0.51 mg/mL). The
antioxidant activities of the O. sipyleum
with β-carotene/Linoleic acid and phosphomolybdenum were calculated as 85.59 %
and 62.95 µg/mg respectively. The phenolic contents of the ethanol extract were evaluated
using HPLC and determined major phenolics:
caffeic acid, epicatechin and 2,5 dihydroxybenzoic. Furthermore, to gether with
cytotoxic activity (LC50, 327.414 µg/mL) O. sipyleum is also rich in total
phenolic, flavonoid and tannin contents were 203.57 ± 4.62 mgGAE/g, 46.98 ±
0.34 mgQE/g and 34.55 ± 0.56 mgCE/g respectively. These results could provide addition information for the
potential use of this medicinal plant as a food ingredient and as a natural
antioxidant in the diet, as well as for the pharmaceutical industry.
Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry
Authors: Garcia Natalie K. , Deperalta Galahad , Wecksler Aaron T.
Published: November 2018

Background:

Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing
class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability
are linked to the proper three-dimensional organization of the primary sequence into
Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods
that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant
protein-protein interactions and assessing properly folded structures. Irreversible covalent protein
footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl
radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility
influenced by tertiary and quaternary structure. Here we discuss the methodology, examples
of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting
MS in biotherapeutic research and development.

Conclusion:

Bottom-up mass spectrometry using irreversible labeling techniques provide valuable
information for characterizing solution-phase protein structure. Examples range from epitope mapping
and protein-ligand interactions, to probing challenging structures of membrane proteins. By
paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase
structural data such as crystallography or electron microscopy, a comprehensive understanding of
protein structure can be obtained.
Using X-ray Footprinting and Mass Spectrometry to Study the Structure and Function of Membrane Proteins
Authors: Gupta Sayan
Published: November 2018

Background:

Membrane proteins are crucial for cellular sensory cascades and metabolite
transport, and hence are key pharmacological targets. Structural studies by traditional highresolution
techniques are limited by the requirements for high purity and stability when handled in
high concentration and nonnative buffers. Hence, there is a growing requirement for the use of alternate
methods in a complementary but orthogonal approach to study the dynamic and functional
aspects of membrane proteins in physiologically relevant conditions. In recent years, significant
progress has been made in the field of X-ray radiolytic labeling in combination with mass spectroscopy,
commonly known as X-ray Footprinting and Mass Spectrometry (XFMS), which provide
residue-specific information on the solvent accessibility of proteins. In combination with both lowresolution
biophysical methods and high-resolution structural data, XFMS is capable of providing
valuable insights into structure and dynamics of membrane proteins, which have been difficult to
obtain by standalone high-resolution structural techniques. The XFMS method has also demonstrated
a unique capability for identification of structural waters and their dynamics in protein cavities
at both a high degree of spatial and temporal resolution, and thus capable of identifying conformational
hot-spots in transmembrane proteins.

Conclusion:

We provide a perspective on the place of XFMS amongst other structural biology
methods and showcase some of the latest developments in its usage for studying conformational
changes in membrane proteins.
Activation of AMPK by Medicinal Plants and Natural Products: Its Role in Type 2 Diabetes Mellitus
Authors: Francini Flavio , Schinella Guillermo R. , Ríos José-Luis
Published: November 2018

Type-2 Diabetes (T2D) is a metabolic disease characterized by permanent hyperglycemia,
whose development can be prevented or delayed by using therapeutic agents and implementing lifestyle
changes. Some therapeutic alternatives include regulation of glycemia through modulation of different
mediators and enzymes, such as AMP-activated protein kinase (AMPK), a highly relevant cellular
energy sensor for metabolic homeostasis regulation, with particular relevance in the modulation of
liver and muscle insulin sensitivity. This makes it a potential therapeutic target for antidiabetic drugs.
In fact, some of them are standard drugs used for treatment of T2D, such as biguanides and thiazolidindiones.
In this review, we compile the principal natural products that are activators of AMPK and
their effect on glucose metabolism, which could make them candidates as future antidiabetic agents.
Phenolics such as flavonoids and resveratrol, alkaloids such as berberine, and some saponins are potential
natural activators of AMPK with a potential future as antidiabetic drugs.
Identification, Prediction and Data Analysis of Noncoding RNAs: A Review
Authors: Emamjomeh Abbasali , Zahiri Javad , Asadian Mehrdad , Behmanesh Mehrdad , Fakheri Barat A. , Mahdevar Ghasem
Published: November 2018

Background:

Noncoding RNAs (ncRNAs) which play an important role in various cellular processes are important in medicine as well as in drug design strategies. Different studies have shown that ncRNAs are dis-regulated in cancer cells and play an important role in human tumorigenesis. Therefore, it is important to identify and predict such molecules by experimental and computational methods, respectively. However, to avoid expensive experimental methods, computational algorithms have been developed for accurately and fast prediction of ncRNAs.

Objective:

The aim of this review was to introduce the experimental and computational methods to identify and predict ncRNAs structure. Also, we explained the ncRNA’s roles in cellular processes and drugs design, briefly.

Method:

In this survey, we will introduce ncRNAs and their roles in biological and medicinal processes. Then, some important laboratory techniques will be studied to identify ncRNAs. Finally, the state-of-the-art models and algorithms will be introduced along with important tools and databases.

Results:

The results showed that the integration of experimental and computational approaches improves to identify ncRNAs. Moreover, the high accurate databases, algorithms and tools were compared to predict the ncRNAs.

Conclusion:

ncRNAs prediction is an exciting research field, but there are different difficulties. It requires accurate and reliable algorithms and tools. Also, it should be mentioned that computational costs of such algorithm including running time and usage memory are very important. Finally, some suggestions were presented to improve computational methods of ncRNAs gene and structural prediction.
Ephedrine Analysis in Real Urine Sample via Solvent Bar Microextraction Technique Coupled with HPLC-UV and Chemometrics
Authors: Behbahani Persia , Qomi Mahnaz , Ghasemi Nahid , Tahvildari Kambiz
Published: November 2018

Background:

Ephedrine, an alpha/beta-adrenergic agonist, is one of the most common doping
agents not only among athletes but also the ordinary people, therefore its detection at low trace levels
with a sensitive and cost effective method has become a priority to investigate many analytical
methods.

Objective:

In this work, solvent bar microextraction followed by high-performance liquid chromatography
(HPLC-UV) was used for extraction and determination of ephedrine at low trace levels from urine
samples at optimum condition.

Methods:

In this study, a designed experiment was carried out using solvent bar microextraction technique,
which has been proved to be a green method. This method requires three phases consisting of a
donor phase with an alkaline pH, an acceptor phase with an acidic pH, and organic solvent to impregnate
the pores of the hollow fiber. The obtained results were used for estimating the optimum ranges for
each parameter, analyzing the effect of different parameters, simultaneously.

Results:

Under optimized circumstances, the preconcentration factor was 129. The calibration curves
represented good linearity for urine sample with coefficient estimations higher than 0.9991. The limit of
detection and quantitation for ephedrine were 16.7 µg L-1 and 50 µg L-1, respectively. The relative standard
deviations of analysis were 3.5% within a day (n=3) and 4.1% between days (n=9).

Conclusion:

According to the results and previous studies, it can be concluded that the preconcentration
factor for ephedrine was the best result ever reported considering selectivity and cost-effectiveness.
Simultaneous Determination of Kirenol, Rosmarinic Acid and Caffeic Acid in Rat Plasma and Pharmacokinetic Study After Oral Administration of the Extract of Manxingshizhen Preparation by UPLC-MS/MS
Authors: Sun Shuo , Zhang Xue , Luo Linda , Wang Ping , Bai Mengxuan , Yu Jia , Guo Xingjie
Published: November 2018

Introduction:

A rapid, sensitive and convenient ultra-performance liquid chromatography
with tandem mass spectrometric detection (UPLC-MS/MS) method has been validated and applied to
the simultaneous determination of kirenol, rosmarinic acid and caffeic acid after oral administration of
the extract of Manxingshizhen preparation in rat plasma.

Materials and Methods:

Puerarin was selected as the internal standard (IS). The plasma sample preparation
was pretreated by liquid-liquid extraction of the mixture with ethyl acetate. All analytes were
simultaneously detected in multiple reaction monitoring (MRM) mode via both the positive electrospray
ionization (ESI+) and negative electrospray ionization (ESI). In the experiment, all calibration curves
revealed good linearity (r > 0.999). The LLOQ were between 0.80-2.00 ng/mL, respectively.

Besides, the intra-day and inter-day precision ranged from 6.4 to 13.8%, respectively. Moreover, the
accuracy was within - 11.4% and 12.8% for all the QC levels of all analytes. The extraction recoveries
of the analytes and IS in plasma at three concentration levels ranged from 88.5 to 103.2%, moreover,
the matrix effects of all the analytes and the IS were found to be satisfied with the acceptable range of
89.8%-101.7%. Meanwhile, the RSD values of stability met the requirement of not more than 15%.
Furthermore, the pharmacokinetic parameters of three compounds were analyzed using concentrationtime
profiles.

Conclusion and Results:

Plasma concentrations of the three compounds were determined up to 24 h
after oral administration, and their pharmacokinetic parameters were in agreement with previous studies.
The validated method was successfully applied in a pharmacokinetic study in rat plasma after oral
administration of Manxingshizhen preparation.
Characterization of Biocompatible Gold Nanoparticles Synthesized by using Curcuma xanthorrhiza and their Catalytic Activity
Authors: Lubis Khairiza , Chudapongse Nuannoi , Doan Hau Van , Weeranantanapan Oratai
Published: November 2018

Background:

Based on various distinguished physical and chemical properties of gold
nanoparticles, they have far wide applications in several areas of industry and medicine, such as catalysis,
bio-sensor and drug delivery. Compared to a chemical method, biological synthesis is an
economical and less toxic process, thus it is a better alternative for nanoparticle synthesis. In this
study, an environmentally friendly method was chosen to produce AuNPs using Curcuma
xanthorrhiza.

Methods:

Alkaline aqueous extract of C. xanthorrhiza rhizomes, which acts as a reducing and stabilizing
agent was used to produce AuNPs by bio-reduction of HAuCl4. The formation of AuNPs was
periodically monitored by UV-visible spectroscopy. The obtained AuNPs were characterized by Xray
diffraction, energy dispersive spectroscopy, scanning electron microscopy, transmission electron
microscopy, and Fourier transform infrared (FTIR) spectroscopy. Catalytic activity and toxicity of
the AuNPs were evaluated.

Results:

The AuNPs obtained from this study mostly were spherical in shape with approximately 15
nm in size. The presence of functional groups derived from C. xanthorrhiza rhizome extract involved
in the gold bio-reduction process was confirmed by the spectrum of FTIR spectroscopy. The biosynthesized
AuNPs at the concentration of 0.5 μg/ml had catalytic activity in dye degradation of Congo
red. The results showed that this biogenic AuNPs did not cause any toxicity to zebrafish embryos and
all tested cell lines.

Conclusion:

The biocompatible AuNPs with catalytic activity were successfully fabricated with C.
xanthorrhiza rhizome extract by simple eco-friendly and inexpensive method. This catalytic activity
of the obtained AuNPs is potentially useful for industrial applications as well as nanoscience and
nanotechnology.
Effect of Plasma of Argon Treated Implants on Bone Density: A Randomized, Controlled, Histomorphometric Study in Dogs
Authors: Tanaka Kazushige , Silva Erick Ricardo , Kawakami Shunsuke , Canullo Luigi , Botticelli Daniele , Xavier Samuel P.
Published: November 2018

Background:

Altering surface characteristics by increasing its energy and hydrophilicity will accelerate the interaction between cells and implant surface. Energy and hydrophilicity tend to disappear over a short time. The implant surface may be reactivated by the use of argon plasma

Objective:

To assess bone density at cleaned and activated titanium implants using argon plasma.

Methods:

Mandibular premolars and first molars were extracted bilaterally in eight Beagle dogs. After three months, four implants, two treated with argon plasma (test; plasma) and two left without treatment (control), were randomly installed in one side of the mandible. Abutments were applied on the implants and a non-submerged healing was allowed. After one month, the same surgical procedures were adopted on the opposite side of the mandible. The animals were euthanized after one month and ground sections representing the healing after 1 and 2 months were obtained for histological examination.

Results:

No statistically significant differences were found between test and control sites (p< 0.05). After 1 month of healing, new bone was 32.5 ± 12.2% and 33.8 ± 8.8% at the plasma and control sites, respectively. After 2 months, the respective values were 50.8 ± 21.5% and 47.6 ± 15.6%.

Conclusion:

The treatment of the implant surface with argon plasma did not have a significant effect on bone density around implants.
Synthesis of Copper and Silver Nanoparticles by Molecular Beam Method
Authors: Kurapov Yurii , Litvin Stanislav , Romanenko Sergey M. , Didikin Gennadii , Belyavina Nadezhda
Published: November 2018

Background: Nanomaterials for medical applications, preparations with silver and copper
nanoparticles attract special attention. Silver has stronger antimicrobial properties than does penicillin,
biomycin and a number of other antibiotics. Nanoparticles of copper and copper oxide also exert a
pronounced antibacterial effect.

Objective: Further development and creation of medicines based on silver and copper nanoparticles
require selecting a method for synthesis of nanoparticles that would ensure production of various nanomaterial
compositions.

Method: The method of electron beam evaporation and deposition of materials in vacuum opens up
wide possibilities. The idea of using this approach is the possibility of simultaneous evaporation and
deposition of mixed molecular flows of two substances onto a substrate.

Results: The paper presents the results of investigation of the structure of porous condensates of Ag-NaCl
and Cu-NaCl composition; chemical and phase compositions and dimensions of nanoparticles, produced
from the vapour phase by EBPVD method. Silver and copper nanoparticles in a porous matrix have considerable
sorption capacity relative to oxygen and moisture. Along to concentration change, phase composition
of nanoparticles can be also controlled by heat treatment of the initial condensate produced at low condensation
temperatures. Silver and copper nanoparticles can be converted into stable colloidal systems.

Conclusion: Physical synthesis of silver and copper nanoparticles by EBPVD method allowed producing
nanostructured material in the form of a dry substance for preparation of the required colloidal
solutions. TGA method provides an indication of the processes of transformation in Ag-O system.
Ag2O decomposes at the temperature of 460°C. Controlling the activity (size) of nanoparticles allows
creating various compositions of nanomaterials, based on copper.
Machine Learning Based Support System for Students to Select Stream (Subject)
Authors: Sethi Kapil , Jaiswal Varun , Ansari Mohammad Dilshad
Published: November 2018

Background:

In most of the countries, students have to select a subject/stream in the secondary education phase. Selection of subject/stream is crucial for students because further their career proceeds according to their selection. Mostly subject/stream selection cannot be changed in the further career. Inappropriate selection of subjects due to parental pressure, lack of information etc. can lead to limited success in the selected stream. Guidance for subject/stream selection based on information of successful scholars of their stream and information of students such as interest, family background, previous education and other associated can enhance the success in career.

Methods:

Data mining and machine learning based methods were developed on the above information. Data from the different institutions and students of two different streams were used for training and testing purposes. Different machine learning algorithms were used and methods with high accuracy (86.72) were developed.

Result:

Developed methods can be extended and used for different subject/stream selection.
An Implementation of Three-level Multi-objective ABC Algorithm for RNA Multiple Structural Alignment
Authors: Lalwani Soniya , Sharma Harish , Deep Kusum
Published: November 2018

Background:

Structural alignment of ribose nucleic acid (RNA) is one of the most challenging
multi-objective real world problems from the field of bioinformatics.

Objective:

RNA molecules are less stable; hence they require inclusion of most stable secondary
structure during their alignment. Therefore, the structural alignment requires the consideration of
similarity score and structure score, as two objectives. Trade-off between these two objectives exists
since obtaining optimum similarity score at concurrent optimum structure score is not possible. This
paper presents artificial bee colony algorithm based three level multi-objective approach for performing
structural alignment of RNA sequences, namely MO-3LABC.

Methods:

Algorithm firstly builds the secondary structure of all sequences at minimum free energy
(MFE). Then sequence alignment is performed in level one at average percent sequence identity
(APSI) score based gap length, optimized by ABC algorithm. Level two now builds the secondary
structure of these aligned sequences based on base-pair probability and co-variation. Now the scores
of level one and level two move towards level three for multi-objective optimization at Pareto optimality
criteria with few additional strategies.

Results:

The results of MO-3LABC are compared with an already established efficient strategy
MO-TLPSO; multi-objective two level strategy based on particle swarm optimization. The outputs
are compared for pairwise and multiple sequence alignment datasets at prediction accuracy and solution
quality criteria.

Conclusion:

MO-3LABC is found significantly better than MO-TLPSO at all the four evaluation
criteria for both the datasets.