bluuebunny/crossref_metadata_2025 huggingface dataset:
How Squeeze Management Differs during Field Redevelopment
Authors: Wang Xu , Mackay Eric James , Jordan Myles Martin
Published: May 2022

Scaling risk may be insignificant during the early stages of well life due to delayed seawater breakthrough; however, during the latter stages of production inhibitor chemical application by squeezes may be required to prevent scale deposition (Chen et al., 2013). This raises the question of what behaviour should be expected during the redevelopment of a previously seawater flooded reservoir. Should the planning and design of squeeze treatments in a brown field project be the same or different to a green field development?

This paper discusses this issue by reference to a case study in a field located in the Norwegian Sector of the North Sea. The field in question is produced by horizontal wells, and these wells will require scale inhibitor placement via bullhead squeezes deployed at appropriate pump rates to ensure effective placement to provide adequate protection. The timing and extent of seawater breakthrough have been calculated using a reservoir simulation model that accounts for the original development phase, a multi-year period during which the field was shut in - but during which fluid redistribution could still occur - and then the redevelopment phase.

These calculations have been used to identify the required timing for squeeze treatments, and to investigate what bullhead pump rates are required for adequate placement during both phases of field life. Two wells are considered during the first production period and six wells are studied during the redevelopment stage. In each case four pump rates are assessed: 2.5, 5, 7.5 and 10 barrels per minute. The main finding is that while adequate placement can be achieved using the same pump rates in both phases of field life, during the redevelopment stage the treatments will need to be deployed earlier in the redeveloped wells life, since there may not be a long time period between (formation) water breakthrough and seawater breakthrough, as there generally is during conventional green field developments.

This paper delivers a comprehensive water breakthrough and squeeze placement profile comparison between early and redevelopment stages. It presents an assessment of the scaling risk in different production wells, the timing of the first and later squeeze treatments in each production well, and the ability to mitigate that scaling risk by bullhead squeeze treatments.
New Halite Testing Methods for High Temperature and from Low to Very High Calcium Content Brine
Authors: Paudyal Samridhdi , Wang Xin , Ko Saebom , Li Wei , Yao Xuanzhu , Leschied Cianna , Shen Roy , Pimentel Daniel , Kan Amy T. , Tomson Mason B.
Published: May 2022

Halite scaling has caused serious issues in oil/gas field with high TDS and low water cut due to temperature drop and evaporation of the produced water. Simulation of such field condition is very hard. Analytical error for high concentrations of Na+and Cl- is large in the brine making accurate assessment of solubility and Saturation Index (SI) calculation difficult. We have developed the testing capability and methods to understand and control halite problems. We have developed testing methods that can create halite super saturation by incorporating (i) additional chloride from CaCl2 to the reaction mix at equilibrium and/or (ii) utilizing the change in temperature (∆T) as a driving force. These methods are optimized to assess the halite problem from 25-150 °C using mass analyses techniques, mixing of incompatible brines and temperature drop. The composition of salt, dilution volume and saturation index have been calculated using BCC ScaleSoftPitzer software. The induction time (tind) and mass of precipitated salts are considered for data analyses. Various experimentations to simulate the water dilution at ∆T were conducted and data suggest that in some cases 5 % dilution of the brine could drop halite saturation index (SI) to the equilibrium. Similarly, solubility of halite was analyzed in the presence of high calcium concentration in the brine up to 80,000 mg/L. Inhibitors with different functionalities were tested at various ranges of brine condition at saturation index of up to 0.15. Some inhibitors like polymers were found to prolong the induction time for several hours and reduce the halite precipitation mass up to 95%. Overall, the methods are robust yet simple and economic that can simulate field conditions in oil/gas production system to assess the halite scaling risk at higher extremes.
Heat Exchanger Fouling Incident Following A Scale-Inhibitor Squeeze – A Chemical Incompatibility Whodunnit
Authors: Goodwin Neil , Frigo Dario
Published: May 2022

This paper describes an investigation into a heat-exchanger fouling incident in an offshore installation that followed the flowback from a scale squeeze treatment. The phosphonate inhibitor used is well known to be incompatible with high concentrations of calcium at typical oilfield pH values, but the formation water in the field contained a very low calcium concentration and had been shown to be completely compatible even with high concentrations of inhibitor. Nevertheless, the solids recovered from the heat exchanger were found largely to consist of a calcium-phosphorus species, implying that incompatibility between dissolved calcium and the inhibitor was the cause; only traces were found of calcium carbonate, the scale mineral against which the squeeze treatment had been performed.

The paper presents a review of the timeline of events that led up to the incident and describes key observations that point to its cause, including the treatment design, well-performance, flowback practices, etc. Finding the most likely cause was primarily about determining how a stream had been created in the facilities containing elevated concentrations of calcium and the phosphonate inhibitor that would then be preferentially deposited in the heat exchanger due to its high skin temperature (the Ca·P complex is less soluble at high temperature). The plausibility of these mechanisms was then examined by a laboratory programme that attempted to reproduce conditions that could have occurred in the facilities.

The most likely origin of the high concentration of scale inhibitor was the squeeze flowback; that of the calcium-rich stream could not be conclusively assigned to a single cause, but was either (i) delayed flowback of spent acid-stimulation fluid from the intervention of a well 2 months before the fouling incident, or (ii) dissolution of previously deposited calcium carbonate scale (and/or conceivably, traces of this mineral in the formation) by the acid phosphonate inhibitor (most likely the well squeezed just before the incident), followed by re-precipitation of the Ca-P complex when the resulting solution was subject to the high skin temperatures of the heat exchanger.

Although it was not possible to distinguish conclusively between these possibilities, the understanding gained enabled preventative actions to be identified for future operations in this field.
The Role of Mutual Solvents in Scale Inhibitor Squeeze Treatments
Authors: Sanchez Hugo Antonio , Mackay Eric James , Singleton Michael Andrew
Published: May 2022

The first stage of a squeeze treatment entails a pre-flush, usually containing a mutual solvent that prepares the surface of the rock and allows greater retention of scale inhibitor that is injected during the main part of the treatment. We use experimental studies to tackle the issue of mutual solvent propagation and its impact on oil displacement and inhibitor retention. Clashach cores were used in this study, and the propagation of mutual solvent and subsequent scale inhibitors through the core were studied, along with any influences on rock properties such as permeability and on residual phase saturations. It was evident that during waterflooding a high residual oil saturation affects squeeze lifetime, and that mutual solvent can partially compensate for this, although the effect could not be definitively identified. Thus, further corefloods were conducted to understand how long it takes to remove residual mutual solvent from the core plug during the main treatment injection stage, and what is the influence of mutual solvent concentration in the pre-flush on this process.

The corefloods conducted were thus: i. Three floods with different concentrations (100%, 75% and 50%) of mutual solvent, using the injection of tracers at various stages, to identify how the residual phase saturation changes with main treatment aqueous phase volume throughput, and ii. Three scale inhibitor floods at residual oil saturation (using Multipar H). One with no mutual solvent pre-flush and two with a mutual solvent pre-flush (100% EGMBE). The difference between the latter two mutual solvent pre-flush floods was the amount of residual oil in the core prior to mutual solvent injection.

The results are discussed in detail, to understand the effect of the mutual solvent during a squeeze treatment under typical field conditions. According to the results it is proposed that using mutual solvent as a pre-flush enhances scale inhibitor squeeze lifetime, by increasing scale inhibitor adsorption/retention, due to a wettability change towards more water-wet – as evidenced by the reduction in residual oil saturation. Furthermore, more pore volumes of aqueous phase main treatment (up to seven) were required to displace the residual phase when lower mutual solvent concentrations were used in the coreflood pre-flush stage.

The results of this work indicate that mutual solvent concentration, and the ratio of main treatment volume to pre-flush volume should be carefully considered when designing squeeze treatments, since the contact between the aqueous scale inhibitor solution and the rock will be affected by the ability of the mutual solvent to displace oil, and by the volume of main treatment required to displace the mutual solvent rich pre-flush. Finally, modelling work was undertaken using the isotherms generated from the corefloods to demonstrate the impact on squeeze life of various mutual solvent applications.
Application of ScaleSoftPitzer in Big Data Era: Evaluations of Water Source, Scale, and Corrosion Risk – A Permian Basin study
Authors: Wang Xin , Dai Zhaoyi Joey , Li Wei , Ko Saebom , Paudyal Samridhdi , Yao Xuanzhu , Leschied Cianna , Shen Yu-Yi Roy , Pimentel Daniel , Kan Amy , Tomson Mason
Published: May 2022

Oil and gas industry would generate a large volume of produced water during the exploration and production. The geochemistry of the produced water can provide valuable information for the analysis of formation water source evolution and the scale and corrosion risk of the production. In past decades, the water sample and the correlated condition have been collected during the production, which accumulate extensive amount of data. The successful analysis of such database would be very helpful for the scale and corrosion management. In this study, the ScaleSoftPitzer (SSP) software is used to proceed the analysis of produced water evolution and scale and corrosion risk. A Permian Basin example is selected based on USGS produced water database V2.3. The formation information from the database was critically reviewed, cleaned and standardized into 13 major formation groups related to the oil and gas production area. The missing depth, temperature and pressure were calculated, and the CO2% and downhole pH were calculated by assuming the downhole brine was in equilibrium with calcite. The saturation indices of various scale are calculated and statistically analyzed. According to our analyzing result, it is found that usually the saturation index of gypsum and barite are close to zero, which suggest that the produced water is in equilibrium with barite and gypsum mineral in the formation. The calculated calcite scale SI are generally larger than 1.0, suggested potential calcite scale risk. 1 mg/L of NTMP is recommended for all Permian Basin well for preventive scale control. The CO2 corrosion risk was also calculated using the corrosion model in SSP, a preventive action is suggested for Permian Basin. Furthermore, a good agreement between the calculated corrosion rate and the measured Mn2+ concentration is observed. This study provided a template to use the produced water database to improve the scale and corrosion management at the field level in this big-data era.
Lattice Boltzmann Model for Oil/Water Two-Phase Flow in Nanoporous Media Considering Heterogeneous Viscosity, Liquid/Solid, and Liquid/Liquid Slip
Authors: Wang Han , Wang Wendong , Su Yuliang , Jin Zhehui
Published: May 2022

Due to intermolecular interactions, the oil/water two-phase flow behaviors in shale nanoporous media are complex and diverse, which cannot be characterized by a conventional continuum flow equation. In this work, we propose a nanoscale multirelaxation-time multicomponent and multiphase lattice Boltzmann method (MRT-MCMP-LBM) based on pseudopotential format to simulate oil/water two-phase flow at the pore scale. The nanoscale effect of liquid/solid slip, liquid/liquid slip, and heterogeneous viscosity due to liquid/solid and liquid/liquid molecular interactions is fully taken into account. We use the Laplace test, contact angle, and phase separation to calibrate the desired interfacial tension (IFT) and wettability. Then, the proposed model is verified by comparing to molecular simulation and theoretical results. Although the liquid/solid slip can increase the oil/water flow capacity, it can reduce the relative permeability due to the increased intrinsic permeability. The oil/water interfacial slip can increase the relative permeability of the nonwetting phase, which can be greater than unity because the effect of oil/water interfacial slip is greater than that of nonwetting-phase/wall slip. We also calibrate the microscopic parameters of oil and water flow in inorganic and organic pores by comparing their velocity profiles to those from molecular dynamics (MD) simulations. The oil/water two-phase flow in shale nanoporous media indicates that with a higher total organic carbon (TOC) content, oil relative permeability is lower due to the more significant adverse nanoscale effect. The proposed model can be potentially applied to simulate shale oil/gas/water multicomponent and multiphase (MCMP) flow, imbibition, CO2 huff ‘n’ puff, and geological sequestration.
Effectiveness of Anapana, Body scan and Metta meditation techniques on chronic neck and shoulder region pain and disability in adult patients in Sri Lanka.: study protocol for a cluster clinic-level parallel randomised controlled trial
Authors: Karunanayake Aranjan Lionel , Coghill Nikki , Solomon-Moore Emma
Published: May 2022

BackgroundChronic neck and shoulder region pain affects many people in the world. This study aims to compare the effectiveness of an eight-week training programme on pain and disability in a patient population affected with chronic neck and shoulder region pain, using Anapana, Body Scan and Metta meditation techniques, with a usual care control group and with each other.MethodsThis parallel cluster clinic-level randomised controlled trial will be conducted with male and female patients aged 18-65 years, who are affected with chronic neck and shoulder region pain, and who attend one of four clinics held on four different days of the week in a medical centre in the Colombo North region, Sri Lanka. Clinics will be considered as clusters and randomly allocated to intervention and control arms.Data will be collected using validated questionnaires, clinical examinations and focus groups. To compare baseline with primary (differences in changes in pain at 8 weeks) and secondary outcomes (differences in changes in pain, physical disability, range of movement and quality of life at 4 and 12 weeks), a two-way ANOVA will be used if the data is normally distributed. If the data is not normally distributed a nonparametric equivalent (Kruskal Wallis) will be used. Focus group transcriptions will be thematically analysed using the Richie and Spencer model of qualitative data analysis. Discussion This protocol describes how three meditation interventions will be implemented on the management of patients affected with chronic neck and shoulder region pain and compared with a usual care control-group. The effectiveness of each meditation intervention on the pain, physical and psychosocial disabilities of patients will be compared between groups. The results of this study will enable recommendations to be made for future meditation interventions for chronic neck and shoulder pain.Trial RegistrationISRCTN12146140Date of registration : 20/08/2021(https://www.isrctn.com/ISRCTN12146140).
TRANSPARENT: a Python tool for designing transcription factor regulatory networks
Authors: Derelitto Carlo , Santoni Daniele
Published: May 2022

Transcription factors are proteins able to selectively bind DNA short traits, namely Transcription Factors Binding Sites, in order to regulate gene expression both in terms of repression and activation. Despite plenty of studies focusing on Transcription Factors and on the role they play in specific biological tasks or diseases, is available in literature, to our knowledge there is no tool able to automatically provide a list of Transcription Factors involved in this task and the associated interaction network through a solid computational analysis.
TRANSPARENT (TRANScriPtion fActor REgulatory NeTwork) is a user-friendly python tool designed to help researchers in studying given biological tasks or given diseases in human, by identifying Transcription Factors controlling and regulating the expression of genes associated with that task or disease. The list of Transcription Factors, that are significantly associated with a gene pool and the correspondent P-value are provided together with the related Transcription Factors network that can be directly visualized through STRING database.
The effectiveness and reliability of the tool was assessed by applying it to two different test-cases: Schizophrenia and Autism disorders. The obtained results clearly show that identified TFs, for both datasets, are significantly associated with those disorders, both in terms of gene enrichment and coherence with literature. The proposed tool TRASPARENT can be a useful instrument to investigate transcription factor networks and unveil the role that TFs play in given biological tasks and diseases.
Assessment of soil loss using RUSLE at Mongolian mining sites: a case study on soil erosion at the Baganuur lignite and Erdenet copper-molybdenum mines
Authors: Sodnomdarjaa Enkhjargal , Lehmkuhl Frank , Karthe Daniel , Knippertz Martin , Ganbat Gantuya
Published: May 2022

Mining constitutes an integral part Mongolia’s national economy and dominates the country’s export revenue. At the same time, a wide range of mining on soil, water resources and the biosphere have been documented in Mongolia. This case study addresses the long-term impacts of mining on soil degradation at two mining sites located in the semiarid steppe zone of Mongolia: the open-lignite mine of Baganuur about 140 km east of Ulaanbaatar, and the open-pit copper-molybdenum mine of Erdenet about 240 km northwest of Ulaanbaatar, both of which started commercial extraction in the late 1970s. For the assessment of soil erosion, the RUSLE model was applied in different seasons for the period from 1986 to 2018 at 3-year intervals, considering both climatic variation and the expansion of the mines based on maps and satellite imagery. Severely eroded areas were identified in the vicinity of the mining sites. Results show that the soil erosion rates were predominantly between 15-30 t ha –1 yr –1 with severely affected sites accounting for 40 to 41% of the total soil erosion in the two mining areas. In total, severely eroded areas experienced soil losses of approximately were found as 3400 ha yr –1 in Erdenet and more than 1200 ha yr –1 in Baganuur. Particularly severe soil losses were identified for the year 2013 and July 2016 around the Erdenet mining area, and the years 1986, 1998 and October 2018 around the Baganuur mining area. The RUSLE- and GIS techniques are time-saving and costeffective technique for continuous monitoring of soil erosion and planning of preventing measures around mine areas.
An analytical formulation of~ZOA based machining stability for complex tool geometries: Application to 5-axis ball-end milling
Authors: Falta Jiří , Sulitka Matěj , Zeman Pavel
Published: May 2022

The paper describes a computationally convenient analytical formulation of the stability of the cutting process with respect to self-excited vibrations in the case of five-axis milling based on the commonly used zero-order approximation. In the case of five-axis milling with general milling cutters, it is difficult to calculate stable machining process conditions for two main reasons. The first reason is the difficulty of calculating the mean value of the cutting force Jacobian with respect to the regenerative displacement (closely related to a milling directional matrix) for a generally inclined tool, and the second reason is the nonlinearity of this Jacobian with respect to the process parameters, which means that the problem cannot be reduced to a linear eigenvalue problem as is usual for linear cases (e.g. cylindrical milling with respect to the axial depth of cut). In the first part, this paper presents a modification of the calculation of the machining stability limits for a nonlinearly dependent cutting force Jacobian. A new formulation of this Jacobian for a general tool based on the surface integral over the tool and workpiece engagement region is presented, which computationally represents a significant simplification over existing methods. The advantage is that if we can analytically describe the engagement area, we also obtain an analytical relation for the cutting force Jacobian. This is presented with the practical example of a generally inclined ball-end mill. This analytical formulation of the force Jacobian allows the calculation of its derivatives with respect to the technological parameters (depth of cut, step over, tilt and lead angles), which is useful both for the calculation of stability diagrams and for solving optimization problems related to machining stability.
Influence of soil-structure interaction on seismic demands of historic masonry structure of Kashan Grand Bazaar
Authors: Tahghighi Hossein , Lazizi Amir H.
Published: May 2022

Heritable constructions are an essential portion of the history of any nation in addition to financial resources. The aim of this study is to investigate the earthquake damage and failure mechanism of a historic Bazaar located in Kashan (center of Iran), which dates to the seventeenth century. Numerical models were constructed by a macro method, considering two cases of fixed support and soil-structure interaction (SSI). To assess the structural behavior, modal, nonlinear static and dynamic time history analyses were performed using a three dimensional finite element method. The results of SSI analysis show an intense weakness of the structure against the required demand based on the design spectrum. Also, foundation flexibility has a great impact on the oscillation characteristics, displacement demand and damage distribution. By comparing the results of time history analysis to the pushover procedure, a lower shear value and higher displacement are obtained. Furthermore, the damage process is as dome collapse alongside short arc, consequently long arc collapse followed by pier wall overturning.
Insight into the mechanism of molecular recognition between human Integrin-Linked Kinase and Cpd22 and its implication at atomic level
Authors: García-Marín Javier , Rodríguez-Puyol Diego , Vaquero Juan J.
Published: May 2022

Pseudokinases have received increasing attention over the past decade because of their role in different physiological phenomena. Although pseudokinases lack several active-site residues, thereby hindering their catalytic activity, recent discoveries have shown that these proteins can play a role in intracellular signaling thanks to their non-catalytic functions. Integrin-linked kinase (ILK) was discovered more than two decades ago and was subsequently validated as a promising and target for neoplastic diseases. Since then, only a few small-molecule inhibitors have been described, with the V-shaped pyrazole Cpd22 being the most interesting and characterized. However, little is known about its detailed mechanism of action at atomic level. In this study, using a combination of computational chemistry methods including PELE calculations, docking, molecular dynamics and experimental surface plasmon resonance, we were able to prove the direct binding of this molecule to ILK, thus providing the basis of its molecular recognition by the protein and the effect over its architecture. Our breakthroughs show that Cpd22 binding stabilizes the ILK domain by binding to the pseudo-active site in a similar way to the ATP, possibly modulating its scaffolding properties as pseudokinase. Moreover, our results explain the experimental observations obtained during Cpd22 development, thus paving the way to the development of new chemical probes and potential drugs.
Value-added from microwave-assisted extraction of Musa sapientum fruit extract as an alternative safe and effective agent for the treatment of hyperpigmentation
Authors: Bilhman Siwaporn , Paosen Supakit , Ramanathan Srinivasan , Wunnoo Suttiwan , Lethongkam Sakkarin , Dumjun Krittima , Waen-ngoen Tassanai , Kaewnopparat Nattha , Voravuthikunchai Supayang Piyawan
Published: May 2022

Annually, a great number of bananas are produced, and those that do not satisfy commercialization criteria are discarded, resulting in a considerable amount of agricultural waste. This work aimed at valorizing rejected unripe Musa sapientum fruit by microwave-assisted extraction using glycerol-ethanol mixtures for development of cosmeceuticals. The fruit extract exhibited potent radical scavenging activity towards 2,2-diphenylpicrylhydrazyl (DPPH) and 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) assays in a concentration-dependent manner. Ferric reducing power was 199.13 μM FeSO4/mg extract. Total phenolic content was 39 mg gallic acid equivalent/100 g extract and total flavonoid content was 26 mg quercetin equivalent/100 g extract. Vitamin C and E contents of the extract were 10.47 and 4.77 mg/100 g, respectively. The extract exhibited potent antibacterial activity against wide range of bacterial pathogens. The extract significantly reduced nitric oxide production in RAW 264.7 cells (p < 0.05). Biocompatibility assessment of the extract with L929 fibroblast cells demonstrated no toxic effects. M. sapientum-loaded serum significantly inhibited DPPH scavenging activity with a value of 50.62% when compared with commercially-available product (p < 0.05). The serum significantly suppressed tyrosinase activity about 37.46% (p < 0.05). This finding implies that M. sapientum has a high potential to be used as a depigmenting agent.
Quantitative EEG Features and Machine Learning Classifiers for Eye-Blink Artifact Detection: A Comparative Study
Authors: Rashida Maliha , Habib Mohammad Ashfak
Published: May 2022

Ocular artifact, namely eye-blink artifact, is an unavoidable and one of the most destructive noises in EEG signals. Many solutions were proposed regarding the detection of the eye-blink artifact. Different subsets of EEG features and Machine Learning (ML) classifiers were used for this purpose. But no comprehensive comparison of these features and ML classifiers was presented. This paper presents the significance of twelve EEG features and five ML classifiers, commonly used in existing studies, for the detection of the eye-blink artifact. An EEG dataset, containing 2958 epochs of eye-blink, non-eye-blink, and eye-blink-like (non-eye-blink) EEG activities, is used in this study. The significance of each feature and classifier has been measured using accuracy, precision, recall, and f1-score. Experimental results reveal that scalp topography is the most potential among the selected features in detecting eye-blink artifacts. The best performing classifier is Artificial Neural Network (ANN) among the five classifiers. The scalp topography and ANN classifier combination performed as the most powerful feature-classifier combination. However, it is expected that the findings of this study will help the researchers to select the appropriate feature and classifier for their eye-blink detection studies in the future.
Adhesive conductive hydrogels with wrinkled Janus surface and ultra-high sensitivity used as strain sensors
Authors: Jiang Yu , Feng Wanqi , Chen Yixiang , Wang Wei , Yu Dan
Published: May 2022

Conductive hydrogels have attracted enormous attention in wearable electronic devices due to considerable flexibility and similarity with human skin. However, the majority of hydrogels were fabricated by one-pot process and were completely homogeneous, which limited the response to electrical signals. In this paper, we propose a simple strategy to obtain asymmetrical polyacrylic acid/chitosan@silver nanowires (PAA/CS@AgNWs) hydrogels, namely, depositing AgNWs layer by dropping AgNWs dispersions in ethanol on PAA/CS hydrogel prepared via one-pot process. Ethanol diffused into the hydrogel and endowed the upper surface with wrinkle structure. Besides, the inevitable conductivity difference between hydrogel itself and AgNWs further enhanced the sensitivity, leading to the ultra-high gauge factor (GF = 191.2, 7413, 18720). The adhesion of the hydrogel not only improved the adaptability to skin, but also the fastness of AgNWs. Reliable application performance (flexibility, self-healing, dry resistance and adhesion) and excellent electrical signal response (ultra-high sensitivity, identification, repetition and stability) indicated the potential applications in motion detection, gesture recognition and health monitoring.
Combatting the Effect of Image Reconstruction Settings on lymphoma [18F]FDG PET Metabolic Tumor Volume Assessment using Various Segmentation Methods
Authors: Ferrandez Maria C. , Eertink Jakoba J. , Golla Sandeep S. V. , Wiegers Sanne E. , Zwezerijnen Gerben J. C. , Pieplenbosch Simone , Zijlstra Josée M. , Boellaard Ronald
Published: May 2022

Background
[18F]FDG PET based metabolic tumor volume (MTV) is a promising prognostic marker for lymphoma patients. The aim of this study is to assess the sensitivity of several MTV segmentation methods to variations in image reconstruction methods and the ability of ComBat to improve MTV reproducibility.
Methods
56 lesions were segmented from baseline [18F]FDG PET scans of 19 lymphoma patients. For each scan, EARL1, EARL2 standards and locally clinically preferred reconstruction protocols were applied. Lesions were delineated using 9 semi-automatic segmentation methods: fixed threshold based on standardized uptake value (SUV),(SUV = 4, SUV = 2.5), relative threshold (41% of SUVmax [41M], 50% of SUVpeak [A50P]), majority vote-based methods that select voxels detected by at least 2 (MV2) and 3 (MV3) out of the latter 4 methods, Nestle thresholding and, methods that identify the optimal method based on SUVmax (L2A, L2B). MTVs from EARL2 and locally clinically preferred reconstructions were compared to those from EARL1. Finally, different versions of COMBAT were explored to harmonize the data.
Results
MTVs from the SUV4.0 method were least sensitive to the use of different reconstructions (MTV ratio: median = 1.01, Interquartile range = [0.96–1.10]). After ComBat harmonization, an improved agreement of MTVs among different reconstructions was found for most segmentation methods. The regular implementation of ComBat (‘regular ComBat’) using non-transformed distributions resulted in less accurate and precise MTV alignments than a version using log-transformed datasets (‘log-transformed ComBat’).
Conclusion
MTV depends on both segmentation method and reconstruction methods. ComBat reduces reconstruction dependent MTV variability, especially when log-transformation is used to account for the non-normal distribution of MTVs.
Bioinformatics and expression pattern analysis of LIM family in wheat
Authors: Li Chunyue , Sun Yumeng , Chang Qihang , Guo Changhong , Bai Yan
Published: May 2022

Background: In eukaryotes, LIM protein plays the role of development regulator in regulating basic cellular processes such as transcription or tissue cytoskeleton, and participates in plant stress response. Although it is found in many plants, the study of LIM gene family in wheat (Triticum aestivum L.) has not been reported yet.Results: In this study, we analyzed the gene structure, conserved motifs and other bioinformatics and expression patterns of LIM gene family in wheat, and identified 29 LIM gene family members from the whole wheat genome. All TaLIMs proteins contain at least one LIM domain, 5-12 exons, 196-1278 encoded amino acids and 4.47-9.05 theoretical isoelectric points. Chromosome mapping analysis showed that 28 members of TaLIMs were distributed on 18 chromosomes of wheat except 3A, 3B and 3D, and TaLIM29 could not be located on a definite chromosome. TaLIMs is divided into three subfamilies by phylogenetic analysis, which have highly similar gene structures with members of the same phylogenetic tree in subfamilies. Twelve members of LIM family in wheat were analyzed by qRT-PCR. The results showed that these members had different tissue expression patterns, among which two genes were significantly expressed in pollen, and the others had different expressions in different tissues. Under different stress conditions, TaLIMs showed different expression patterns. Six genes were upregulated after ABA treatment and salt stress, and two genes were upregulated after drought stress. TaLIM02 was significantly upregulated compared with the control under four stress conditions. TaLIM07 and TaLIM16 were significantly down-regulated compared with the control under four stresses.Conclusions: Through genome-wide analysis, 29 LIM gene family members were identified in the wheat genome. It is found that TaLIMs may be involved in the regulation of stress response processes such as low temperature and drought in wheat, and play an important role in plant response to abiotic stress. It may also play a role in the process of light induction in some periods.
Evaluation of the climate change impact on Legedadi and Dire reservoirs using R-R-V-criteria
Authors: Alebel Surafel , Tura Amare
Published: May 2022

This study mainly deals with evaluation of the climate change impact on Legedadi and Dire reservoirs which is found in north-east Awash River Basin, Ethiopia. Projection of the future climate variables is done by using Max Planck Institute for Meteorology – Earth System Model (MPI-ESM). In the present study, future rainfall MPI-ESM product corrected by using BFTV (Bias factor time variance).The 1996-2016 was taken as baseline period against which comparison was made. A hydrological model, HEC-HMS was utilized to simulate Runoff in the study area. The performance of the model was assessed through calibration and validation process and resulted NSE=0.87 and PEV=7.5% during calibration and NSE=0.84 and PEV=7.85% during validation. The projected future climate variables has two future time series 2040s and 2080s, for both future time series an increasing trend evaporation from the open water surface of reservoirs when the projected average maximum and Minimum temperatures increase from the baseline period and precipitation shows a fluctuation event. Evaluation to the base and the future period average annual inflow volume shows an increase of 2.44% and decrease 0.99% at Dire reservoir and an increase of 5.15% and decrease 1.15% at Legedadi reservoir during 2040s and 2080s periods respectively.In general analysis of the reservoirs with current and future climate change output indicates that the reliability and resilience of the reservoirs is sensitive to precipitation change than change in temperature on differing dimensionless vulnerability of the reservoirs doesn’t demonstration extraordinary difference for both the change in precipitation and temperature.
A Study of the Potential Effects of Deepening the Corpus Christi Ship Channel on Hurricane Storm Surge
Authors: Valseth Eirik , Dawson Clint , Buskey Edward
Published: May 2022

We present a case study of the potential impact on hurricane storm surge due to deepening the Corpus Christi Ship Channel through Aransas Pass in the region of Corpus Christi and Port Aransas, Texas. Our investigation is based on numerical mathematical models of the circulation of coastal water due to Hurricane Harvey and two synthetic hurricanes derived from Harvey. From the models, we ascertain maximum storm surge as well as elevation time series at critical locations in the study region. To assess the effects of a deeper channel, we compare the model outputs for current and proposed future channels. The models indicate that the changes to maximum storm surge magnitude are small and in large portions of the study area the models indicate a reduction in surge magnitude. However, there are some local areas where the models results show an increase of up to 15 centimeters.
Long-term nitrogen addition increased soil microbial carbon use efficiency in subalpine forests on the eastern edge of the Qinghai–Tibet Plateau
Authors: Wang Wenwu , Zhu Wanze , Li Xia , Ma Shenglan
Published: May 2022

Aims Nitrogen (N) deposition increased forest carbon (C) sink significantly, hence exploring the microscopic mechanisms is critical to predicting future global ecosystem C cycle, especially the effects of enhanced N deposition on soil microbial carbon use efficiency (CUE), which still unclear.Methods We evaluated the responses of soil microbial CUE to long-term (5 years) N addition in an evergreen broad-leaved forest and a mature coniferous forest by using a 13C isotope tracing method.Results The results showed that the soil microbial CUE ranged from 0.38 to 0.51, which was smaller than the results obtained from the previous studies based the same method and forest type. In evergreen broad-leaved forest, the microbial CUE had no significant changes in the low N-addition treatment, but it was increased by 9.23% and 12.69% in medium and high N-addition treatments compared to the control. In coniferous forest, soil microbial CUE was increased by 14.64%, 21.89% and 24.34% in low, medium and high N-addition treatments, respectively. Moreover, the soil C:P and N:P are negatively relate to soil microbial CUE.Conclusions Our findings indicate that the enhancing N deposition can increase soil microbial CUE and ultimately promote C sequestration, especially in coniferous forest. The imbalance of soil stoichiometry is the main impact factor of CUE under N addition. However, we speculate that the key to enhance forest soil C sequestration is to promote the decomposition rate of litter and thus increase the available carbon content.
A Peroxidase-like Single-Atom Fe-N5 Active Site for Effective Killing Human Lung Adenocarcinoma Cells
Authors: Zhu Liye , Zhong Hong , Du Dan , Li Tao , Nguyen Hoai , Beckman Scott P. , Xu Wentao , Li Jin-Cheng , Cheng Nan , Lin Yuehe
Published: May 2022

Background
Single-atom catalyst (SAC) is one of the newest catalysts, and attracting people’s wide attention in cancer therapy based on their characteristics of maximum specific catalytic activity and high stability.
Methods
This study designed and synthesized a Fe-N decorated graphene nanosheet (Fe-N5/GN SAC) with the coordination number of five. Its material characteristics were detected by different methods including scanning electron microscopy, transmission electron microscopy, and X-ray photoelectron spectroscopy. Also, its enzyme-like properties were calculated based on Density functional theory (DFT). In addition, 3D cancer cell models were constructed and cytotoxic effects of Fe-N5/GN SAC were tested by flow cytometry and RT-PCR.
Results
Through enzymology and theoretical calculations, the Fe-N5/GN SAC has outstanding intrinsic peroxidase-like catalytic activity due to single-atom Fe site with five-N-coordination structure. It could kill human lung adenocarcinoma cells (A549) by decomposing hydrogen peroxide (H2O2) into toxic ROS under acidic microenvironment condition to induce the cell apoptosis in 3D lung cancer cell model.
Conclusion
Our study synthesized a novel SAC with peroxidase-like catalytic activity for tumor therapy. And it demonstrates a promising application of SAC with highly efficient single-atom catalytic sites for cancer treatment.
Do Green Bonds Offer a Diversification Opportunity During COVID19? - An Empirical Evidence from Energy, Crypto, and Carbon Markets
Authors: Yadav Miklesh Prasad , Kumar Satish , Mukherjee Deepraj , Rao Purnima
Published: May 2022

Using the S&P green bond index (RSPGB), this study attempts to unravel the connectedness of the green bond with energy, crypto, and carbon markets. We use MAC global solar energy index (RMGS) and ISE global wind energy index (RIGW) as proxies of the energy market. In addition, we consider Bitcoin and the European energy exchange carbon index (REEX) for the cryptocurrency, and carbon market, respectively. Using the daily data from October 1, 2015, to December 13, 2021, of these constituent markets, we employ Diebold Yilmaz (2012), Barunik and Krehlik (2017), and wavelet coherence. The result reveals that the energy market (RMGS) has the highest connectedness derived from other asset classes, and bitcoin (RBTC) has the least connectedness. In addition, we note that risk transmission is heterogeneous in different scales as the short period has less connectedness than the medium and long run. Hence, the overall diversification opportunity among green bonds, energy stock, Bitcoin, and the carbon market is more in the short-run than in the medium and long-run. Surprisingly, there is no lead-lag relationship among these markets. This study provides insights to investors, policymakers, and portfolio managers.
Evaluation of the knowledge and attitudes of pediatric neurologists regarding ketogenic diet therapy and telemedicine applications in the Covid-19 pandemic
Authors: Ünalp Aycan , Yılmaz Ünsal , Karaoğlu Pakize , Kırkgöz Hatice Hilal , Yavuz Merve
Published: May 2022

Introduction: The Covid-19 pandemic has caused some difficulties in ketogenic diet therapy (KDT) applications. We aimed to evaluate the knowledge and attitudes of pediatric neurologists about KDT and telemedicine applications during the pandemic by conducting a survey.Material and method: Among all pediatric neurologists in Turkey, those who wanted to participate in the study were included and were asked to fill out a questionnaire consisting of 22 questions. The questionnaire was sent via electronic communication channels (e.g., WhatsApp, e-mail).Results: Thirty-six (64%) of the participants stated that their preference for KDT did not decrease, and 40 (73%) said that there was no change in their preference for KDT in hospitalized patients. Forty-one (73%) pediatric neurologists were in contact with their patients via telemedicine. Fifty-three (95%) of the participants thought that KDT could be easily sustained during the pandemic process and did not need to be terminated, 25 (45%) thought that it was more challenging to use KDT during the pandemic period.Conclusion: In the present study, it was determined that pediatric neurologists were interested in using KDT during the pandemic and thus turned to telemedicine as a method of application. Most of them stated that utilizing KDT during the pandemic period is a personalized and advanced treatment. There is a need to create an infrastructure (medicolegal) so that reference centers with experience in KDT can switch to telemedicine applications. Thus, patients who require KDT would have exposure to best practices during the pandemic.
Occupational risk variation of nasopharyngeal cancer in the Nordic countries
Authors: Carpén Timo , Gille Evelina , Hammarstedt-Nordenvall Lalle , Hansen Johnni , Heikkinen Sanna , Lynge Elsebeth , Selander Jenny , Mehlum Ingrid Sivesind , Torfadottir Jóhanna Eyrún , Mäkitie Antti , Pukkala Eero
Published: May 2022

Background: The aim of this study was to estimate occupational risk variation in the incidence of nasopharyngeal cancer (NPC) in a large population-based cohort of the Nordic Occupational Cancer (NOCCA) study.Methods: This study is based on a cohort of almost 15 million persons from Denmark, Finland, Iceland, Norway and Sweden, with 2898 nasopharyngeal cancer cases diagnosed in 1961-2005. The data on occupations were gathered from population censuses and cancer data from the national cancer registries. Standardized incidence ratios (SIR) with 95% confidence intervals (CI) were estimated using the national NPC incidence rates as the reference. Results: There were 1980 male and 918 female NPC patients. The highest SIRs of NPC were observed among male waiters (SIR 3.69, 95% CI 1.91–6.45) and cooks and stewards (SIR 2.24, 95% CI 1.16–3.91). Among women, launderers had the highest SIR of NPC (2.04, 95% CI 1.02–3.65). Significantly decreased SIRs were found among male farmers (SIR 0.79, 95% CI 0.68–0.92) and male textile workers (SIR 0.49, 95% CI 0.22–0.93). Conclusions: This study suggests that NPC may be associated with several work-related exposure agents such as smoking, kitchen air pollution and solvents. In future, occupational exposure-risk relations should be studied to understand more about causality and to assess effective prevention strategies.
Bias and Inconsistency in the Estimation of Tumour Mutation Burden
Authors: Makrooni Mohammad A. , O'Sullivan Brian , Seoighe Cathal
Published: May 2022

Background: Tumour mutation burden (TMB), defined as the number of somatic mutations per megabase within the sequenced region in the tumour sample, has been used as a biomarker for predicting response to immune therapy. Several studies have been conducted to assess the utility of TMB for various cancer types; however, methods to measure TMB have not been adequately evaluated. In this study, we identified two sources of bias in current methods to calculate TMB.Methods: We used simulated data to quantify the two sources of bias and their effect on TMB calculation, we down-sampled sequencing reads from exome sequencing datasets from TCGA to evaluate the consistency in TMB estimation across different sequencing depths. We analyzed data from ten cancer cohorts to investigate the relationship between inferred TMB and sequencing depth. Results: We found that TMB, estimated by counting the number of somatic mutations above a threshold frequency (typically 0.05), is not robust to sequencing depth. Furthermore, we show that, because only mutations with an observed frequency greater than the threshold are considered, the observed mutant allele frequency provides a biased estimate of the true frequency. This can result in substantial over-estimation of the TMB, when the cancer sample includes a large number of somatic mutations at low frequencies, and exacerbates the lack of robustness of TMB to variation in sequencing depth and tumour purity. Conclusion: Our results demonstrate that care needs to be taken in the estimation of TMB to ensure that results are unbiased and consistent across studies and we suggest that accurate and robust estimation of TMB could be achieved using statistical models that estimate the full mutant allele frequency spectrum.