bluuebunny/crossref_metadata_2025 huggingface dataset:
ALS Teachers’ Instructions In Bacolod City: A Narrative Inquiry
Authors: Pilar John Gerald A.
Published: March 2020

This study attempted to explore the Alternative Learning System (ALS) teachers handling ALS instructions to the out-of-school youths/students in Bacolod City. This study was based on Philippine Education for All (EFA) 2015 plan is a vision and a holistic program of reforms that aims at improving the quality of basic education for every Filipino by 2015. This study has utilized the qualitative method of narrative inquiry, perceptions and stories were collected from ALS teachers in Bacolod City, and analysis of the information to determine their teaching competency lives according to their perceptions as possible. Moreover, one must be skilled in the art of data collection; a self-designed protocol may be needed to facilitate information from various locations and people involved (Leary, 2011). The researcher has revealed the thematic reflection as “Alternative Learning System (ALS) is linked with Patience, Learning, and Understanding for the learning process to reach the goal of success”, while the thematic insights revealed as “Alternative Learning System (ALS): Determination, Hard work and Ambition to reach the goal in life by producing modules in real-life activities/situations”, and the eidetic insights opened as “ALS as a whole is challenging towards out-of-school youths and adult education as the same quality instruction/education as what formal schooling will provide to the students”. The researcher has noted that participants were challenged in teaching ALS students particularly adults and out-of-school youths who are working for a living but they need quality education, not in a formal school. Thus, it is recommended that the improvement of the instructional modules in teaching ALS will help the students learn with the use of the latest technology to keep abreast in learning using technology not only in modules alone and further research to be conducted in Alternative Learning System to confirm the result of the present study.
Effects of Oil Viscosity and Injection Velocity on Imbibition Displacement in Sandstones
Authors: Arab Danial , Kantzas Apostolos , Bryant Steven L.
Published: March 2020

Water flooding has been applied for more than seventy years in both conventional and unconventional heavy oil reservoirs. Although it is generally accepted that the mechanisms of water flooding in heavy oil systems are totally different than that of light oil reservoirs, there is not a systematic study to specifically investigate water flooding in heavy oil systems. This article presents the findings of core flooding experiments in water-wet systems and gives some insights on the interplay between capillary and viscous forces in imbibition displacement processes.

Seven different oils of various viscosities, ranging from 1 to 15,000 mPa.s at 25 °C, were used in nineteen core flooding experiments where injection velocity was changed from 0.7 to 24.3 ft/D (2.5 × 10−6 m/s to 86.0 × 10−6 m/s). An in-line densitometer was used to precisely determine breakthrough time. Capillary forces and instability analysis were used to quantify the balance between viscous and capillary forces.

On physical grounds, the capillary number, which is the relative magnitude of viscous and capillary forces during a displacement, should be the first-order influence on residual oil saturation. However, Abrams (Abrams, 1975) showed that accounting for the viscosity ratio improves the correlation to residual oil saturation for oil viscosity below 37 mPa.s. Our observations extend the range of oil viscosity to 15,000 mPa.s and when combined with 178 datasets from the literature indicate that viscosity ratio has much more influence than capillary number on residual oil saturation.

Standard models such as Buckley-Leverett theory predict that oil recovery at water breakthrough depends only on phase mobilities. However, our observations indicate that flow velocity also influences breakthrough oil recovery. At oil to water viscosity ratios smaller than 20, breakthrough oil recovery monotonically increases with increasing injection velocity. For intermediate viscosity ratios (20 < μo < 160), breakthrough oil recovery increases with decreasing injection velocity. At higher values of viscosity ratios, breakthrough oil recovery is almost independent of injection velocity. In these cases, late time oil recovery remarkably increases with decreasing injection velocity. This effect is more pronounced in more viscous oil systems suggesting the importance of imbibition in these systems. Our observations prove that water flooding, if applied at the most optimized mode that is a strong function of oil viscosity, can still be a very efficient EOR technique.
Thermal Stability of Acrylamide-Based Polymers at High Temperature and High Salinity
Authors: Song Haofeng , Pope Gary A. , Mohanty Kishore K.
Published: March 2020

During polymer floods or surfactant-polymer floods, polymer molecules reside inside petroleum reservoirs for years. This extended period gives sufficient time for the polymers to react with the in-situ environment (high temperature, oxygen-free, high salinity) which could lead to polymer degradation and viscosity loss. In this study, a systematic glove box operating procedure was developed to reduce oxygen concentration (in polymer solutions) to less than 15 ppb. Viscosity was monitored to investigate the thermal stability of one commercially available partially hydrolyzed polymer (HPAM) and three ATBS-based polymers at high salinity (36,000 ppm to 54,000 ppm) and high temperature (116 °C) conditions through a long period. Acrylamide-acrylate (AM-AA) copolymer Flopaam™ 3330s and ATBS-AA copolymer ZLPAM @50525 were selected as the potential candidates for alkali-surfactant-polymer (ASP) floods. Ammonia and sodium carbonate were adopted as the alkali. High ATBS content copolymer SAV 10 and SAV 10xv were tested for surfactant-polymer (SP) floods at high temperature and high salinity environment. The viscosities of ZLPAM and Flopaam increased first due to hydrolysis, then slowly decreased. The pH of those polymers dropped approximately by one unit. SAV 10 and SAV 10xv showed no noticeable viscosity or pH changes. ZLPAM and Flopaam can be used at high temperature in the absence of divalent ions, whereas SAV 10 and SAV 10xv can be used in the presence of divalent ions.
Impact of Natural Fractures on Caprock Integrity in Steam Assisted Gravity Drainage
Authors: Li Qiuguo , Rivero Jose
Published: March 2020

Caprock integrity in steam-assisted gravity drainage (SAGD) has been evaluated by various researchers. However, most of these caprock integrity studies assume that the caprock is not fractured, which is not a valid assumption in most cases. This paper provides a comprehensive analysis of caprock integrity in the Athabasca oil sands with presence of natural fractures of various dip-angles in the Clearwater shale.

Geological studies have shown that natural fractures exist in the Clearwater shale formation, which acts as the caprock for the McMurray oil sands. Based on some publicly available data in the Athabasca oil sands, we developed a numerical simulation model for a SAGD pad where reservoir and mechanical properties were characterized. A discrete fracture network model with natural fractures of different dip-angles was developed for the Clearwater shale. Coupled reservoir and geomechanical simulations were performed to evaluate the stress changes and deformations caused by steam injection in the reservoir. The impact of such stress changes on the natural fracture deformations was evaluated.

It is observed that with steam injection, the temperature increases, steam chamber grows—which causes horizontal stresses to increase in the reservoir. When the steam chamber reaches the caprock, the temperature at the bottom of the caprock also increases due to thermal conduction. Such temperature increase results in horizontal stress increase there. Shear slip is induced in the low-angle fractures at the bottom of the caprock due to the stress changes. This plastic shear deformation increases with time. The top part of the caprock is less disturbed and the low-angle fractures there remain stable. High-angle fractures that are present from the bottom to the top of the caprock tend to slip as well. These plastically deformed fractures of different dip-angles provide a network of higher hydraulic conductivity conduits for fluid to more easily pass, and therefore are a potential risk to caprock integrity.

The behavior of natural fractures in the caprock and their impact on caprock integrity in SAGD operations have rarely been addressed in the literature. This paper aims to fill the gap by presenting an analysis of natural fractures in the Clearwater shale and a comprehensive approach of simulating their shear slip tendency and thereafter the impact on caprock integrity in SAGD.
Improved Refracturing Evaluation Workflow: An Integrated Methodology Incorporating Advanced Geomechanical Modeling
Authors: Ibáñez Enric , Bezerra de Melo Ricardo C. , Wang Yixin , Dong Yan , Alvarellos José , Lakshmikantha M. R. , Webb Christie
Published: March 2020

The objective of the study is to develop an integrated multi-disciplinary workflow to screen wells for suitable candidates and to evaluate the feasibility of selected wells for refracturing using advanced geomechanical modeling.

A four-step workflow to select and evaluate wells for refracturing was developed. First, hundreds of wells were screened based on age, spacing, and production performances, mainly IP90 and IP30 to IP360 ratio. Second, the selected wells from the first step were furthered narrowed down by analyzing their original completion and stimulation. Wells that were under-stimulated compared to historical average stimulation metrics, i.e. fewer stages/clusters and larger spacing, lower proppant loading, and less fluid volume pumped, were chosen as the final candidates for geomechanical modeling. Third, the wells were modeled with in-house advanced geomechanical fracture simulation and then depleted to obtain current stresses state. Finally, the technical feasibility of refracturing the wells was assessed.

The workflow for best candidate selection has been improved considering volume of proppant placed, stress orientation, number of clusters / stages, reservoir quality, and production history.

Due to the low horizontal stress contrast (1[MMPA]), fine scale stress determination was required. A 3D initial stress model was available from a previous study. From this stress state geomechanical hydraulic fracture mapping was performed. This geomechanical modeling utilizes Zero Thickness Element (ZTE) technology and the fractures only open if achieving the energy criteria. The stimulated volume and stress changes due to hydraulic fracturing were modeled with high resolution unstructured grids. Fracture driven interaction such as stress shadowing, cluster interference and fractures interconnection were observed. Production history was modeled with equivalent volume to determine the stress changes from the most accurate fracture geometry.

The novelty is the systematic workflow integrating completion, production and geomechanics for selecting and evaluating the most suitable wells for refracturing, either stimulating new reservoir or reconnecting previous fractures. The advanced geomechanical techniques used to model the stresses at very fine scale and with unstructured grids are also state of the art.
Coupling Microseismic and Production Data Analysis to Optimize Well Spacing in Unconventional Reservoirs
Authors: Nizkous Irina , Moradi Peyman , Angus Doug , Bosman Katie
Published: March 2020

Unconventional plays present a challenging case to design an optimized stimulation program and to maximize reservoir contact and hydrocarbon production. In this regard, conducting a reliable well spacing optimization study demands realistic and explicit fracture descriptions. This work applies an integrated technique to a multi-well case study in the Permian Basin to extract fracture dimensions based on microseismicity-derived behavioral fracture maps, while honoring the RTA-based estimates of the contributing fracture volume. The fracture dimensions are then used to conduct analytical and numerical studies to decide the optimal well spacing/placement design in the target formation. The numerical simulations in two stacked and staggered configurations confirm that although the staggered development causes a marginal decrease in the individual wells' performance, if successfully accomplished, it contributes to a higher vertical sweep efficiency from the section. Furthermore, comparing the approximations of failure planes, constructed based on the spatiotemporal analysis of microseismic events, with those achieved through seismic moment tensor inversion confirms that the collective behavior analysis gives fair estimates of fracture spatial evolutions.
Interbedded Carbonate and Calcareous Shales of the Devonian Duvernay Formation of Alberta, Canada: Implications for Completion Due to High Variability of Geomechanical Properties
Authors: Wüst Raphael A. , Ziarani Ali S. , Cui Albert X.
Published: March 2020

The Devonian Duvernay Formation in Alberta is a carbonate-siliceous unconventional source rock that produces prolific oil, gas condensate liquids, and gas. In the southern part of the basin and the East Shale Basin, high frequency interbeds of limestone and organic-rich calcareous shales are common at spacing of inches to several feet. Prolific gas liquids are trapped within the shale/mudstone units while the highly cemented and tight carbonate units show a lack of hydrocarbons. Even though most wellbores completed to date have primarily landed in shale units, still, due to geo-steering and other considerations penetration through limestone unit along the lateral cannot be avoided. High contrast in mechanical properties of shale and limestone units along with anisotropy in geomechanical properties of the same rock unit makes optimal hydraulic fracturing breakthrough and placement often challenging.

This study reviews examples of high resolution mechanical Duvernay stratigraphy combined with log and core analyses in order to better understand the implications of hydraulic fracture development through such complex reservoirs. Integrated petrophysical well log and core data indicate that there are strong heterogeneities on lithology, and geomechanical properties (hardness, brittleness, and elastic properties) on various scales. The shale units generally have lower Young's modulus and Poisson's ratio, whereas the carbonate units have high Young's modulus and Poisson's ratio. Core data also indicate strong vertical transverse isotropy in the shale units. Combined with occurrence of various types of naturally-occurred sub-vertical fractures and sub-horizontal polished slip faces, weak bedding plane strength, and strong anisotropy in in-situ stresses, and high heterogeneities in lithology and geomechanical properties likely result in complex and poorly constrained and un-optimized hydraulic fractures throughout the Duvernay Formation.

The results indicate that high Young's modulus of carbonates causes a narrow fracture width which makes fracture initiation and placement and in particular proppant transport a challenge. Normal and strike slip faulting regimes are observed in some areas of East Basin. The lower anisotropy in horizontal stresses estimated for the shale zones than the carbonate zone may suggest that the complex fractures is more likely to occur in the shale zones than the carbonate zones.

In Duvernay minifrac tests, longer fall off data collection (> 2 weeks) is critical for a successful determination of closure pressure and pore pressure estimation. During fracture stimulations, tight cluster spacing, i.e. ≤10m apart, might limit fracture geometry growth on the inner clusters due to higher induced stress. Similarly, due to higher stress shadow effects, tighter stage spacing might affect the fracture growth on the subsequent stages.
High expressions of the cytoglobin and PGC-1α genes during the tissue regeneration of house gecko (Hemidactylus platyurus) tails
Authors: Novianti Titta , Juniantito Vetnizah , Jusuf Ahmad Aulia , Arida Evy Ayu , Sadikin Mohamad , Jusman Sri Widia A.
Published: March 2020

Background The tissue regeneration process requires high oxygen and energy levels. Cytoglobin (Cygb) is a member of the globin family, which has the ability to bind oxygen, plays a role in dealing with oxidative stress, and carries oxygen into the mitochondria. Energy production for tissue regeneration is associated with mitochondria—especially mitochondrial biogenesis. The peroxisome proliferator-activated receptor-gamma coactivator (PGC)-1alpha protein helps to regulate mitochondrial biogenesis. House geckos ( Hemidactylus platyurus ) are reptiles that have the ability to regenerate the tissue in their tails. House geckos were selected as the animal models for this study in order to analyze the association of Cygb with oxygen supply and the association of PGC-1α with energy production for tissue regeneration. Results The growth of house gecko tails showed a slow growth at the wound healing phase, then followed by a fast growth after wound healing phase of the regeneration process. While Cygb mRNA expression reached its peak at the wound healing phase and slowly decreased until the end of the observation. PGC-1α mRNA was expressed and reached its peak earlier than Cygb. Conclusions The expressions of both the Cygb and PGC-1α genes were relatively high compared to the control group. We therefore suggest that Cygb and PGC-1α play an important role during the tissue regeneration process. Keywords: cytoglobin, PGC-1α, mitochondrial biogenesis, house gecko, tissue regeneration
Lentivirus expressing shRNAs inhibit the replication of Contagious Ecthyma Virus by targeting DNA polymerase gene
Authors: Samani Leila Asadi , saffar behnaz , Mokhtari Azam , Arefian Ehsan
Published: March 2020

Background: Contagious ecthyma or Orf is known as a zoonotic disease remains prevalently worldwide despite the application of some control strategies against it. RNAi particularly shRNA provides us with the chance to tackle this obstacle by an encouraging new approach. The current study indicates the design and experiment of third-generation lentivirus packaging systems delivering shRNAs to inhibit Orf virus (ORFV) replication and infection. Given the importance of DNA-pol gene in virus replication, in this study, three shRNAs against this gene were designed and cloned into lentiviral vectors to stabilize the expression of shRNAs. After producing lentivectors expressing ORFV-DNA– pol in HEK293T cells, the synthesized shRNAs were applied to downregulate viral replication and gene expression. The reduction in viral titer and RNA was evaluated by TCID50 test as well as real-time RT-PCR. The results were then analyzed in comparison with the control group.Results: Designed shRNAs significantly reduced virus yield approximately 90% to 97% and 96.8% to 99.4%, respectively compared to the control groups (cells infected with ORFV and infected with ORFV and scrambled vector) by TCID50 test. Real-time RT-PCR revealed a dramatic reduction in the expression of viral RNA approximately 99% compared to cells infected with ORFV and from 92.6% to 99%, respectively compared to cells infected with ORFV and scrambled vector.Conclusions: Therefore, it can be stated that RNAi is capable of being used as a potent therapeutically option against viruses like ORFV.
KLF4 alleviates cerebral vascular injury by ameliorating vascular endothelial inflammation and regulating tight junction protein expression following ischemic stroke
Authors: Zhang Xinyu , Wang Lu , Han Zhenxiang , Dong Jing , Pang Defang , Fu Yuan , Li Longxuan
Published: March 2020

Background: Although inflammatory cell adhesion molecules (CAMs) and anti-inflammation factor- kruppel-like transcription factor (KLF) 4 have all been reported to be induced after cerebral ischemic stroke (CIS), the close temporal and spatial relationship between expressions of CAMs and KLF4 following CIS, and whether and how CAMs and KLF-4 contribute to development of CIS-induced vascular injury are still unclear. Methods: Here, we first examined the correlation between serum levels of CAMs/KLF4 and infarct volume in acute CIS patients. Then, we determined relationship between CAMs and KLF4 in mice after focal cerebral ischemia. Finally, we investigated the mechanism of KLF4 in protecting against oxygen-glucose deprivation-induced brain endothelial cell injury. Results: Our results demonstrated that patients with moderate to severe CIS had higher serum levels of three CAMs including E-selectin, inter-cellular adhesion molecule 1 (ICAM-1) and vascular cell adhesion molecule 1 (VCAM-1) but lower levels of KLF4 at 48 hours after acute event as compared to patients with minor CIS. The expression levels of three CAMs as well as KLF4 all correlated well with the infarct volume in all the CIS subjects at that time. Although the expressions of three CAMs and KLF4 were all induced in the ischemic hemisphere following focal cerebral ischemia, but the peak timing and distribution patterns of their expression were different: the induction of KLF4 lagged behind that of the CAMs in the ischemic penumbra, furthermore, the dual immunofluorescent studies displayed that high expression of KLF4 was always associated with relatively less cerebral vascular endothelial inflammation response in the ischemic hemisphere, and vice versa. Mechanistic analyses revealed that KLF4 alleviated CIS-induced cerebral vascular injury by regulating endothelial expressions of CAMs, nuclear factor-kB and tight junction proteins.Conclusions: These data indicate that KLF4 confers vascular protection against cerebral ischemic injury, suggesting that circulating CAMs and KLF4 might be used as potential biomarkers for predicting the prognosis of acute ischemic stroke, and also providing a new proof of concept and potential targets for future prevention and treatment of CIS.
Transcriptomic and metabolomic analysis provides insights into anthocyanin and pyocyanin accumulation in pear
Authors: Zhang Zhen , Tian Changping , Zhang Ya , Li Chenzhiyu , Li Xi , Yu Qiang , Wang Shuo , Wang Xinyu , Chen Xuesen , Feng Shouqian
Published: March 2020

Background Pear is one of the most important fruit crops worldwide. Anthocyanins and procyanidins (PAs) are important secondary metabolites that affect the appearance and nutritive quality of pear. However, few studies have focused on the molecular mechanism underlying anthocyanin and PA accumulation in pear . Results We conducted metabolome and transcriptome analyses to identify candidate genes involved in anthocyanin and PA accumulation in young fruits of the pear cultivar ‘Clapp Favorite’ (CF) and its red mutation cultivar ‘Red Clapp Favorite’ ( RCF ). Gene–metabolite correlation analyses revealed a ‘core set’ of 20 genes that were strongly correlated with 10 anthocyanin and seven PA metabolites. Of these, PcGSTF12 was confirmed to be involved in anthocyanin and PA accumulation by complementation of the tt19-7 Arabidopsis mutant. Interestingly, PcGSTF12 was found to be responsible for the accumulation of procyanidin A3, but not petunidin 3, 5-diglucoside, opposite to the function of AtGSTs in Arabidopsis . Transformation with PcGSTF12 greatly promoted or repressed genes involved in anthocyanin and PA biosynthesis, regulation, and transport. Electrophoretic mobility shift and luciferase reporter assays confirmed positive regulation of PcGSTF12 by PcMYB114 . Conclusion These findings identify a core set of genes for anthocyanin and PA accumulation in pear. Of these, PcGSTF12 , was confirmed to be involved in anthocyanin and PA accumulation. Our results also identified an important anthocyanin and PA regulation node comprising two core genes, PcGSTF12 and PcMYB114 . These results provide novel insights into anthocyanin and PA accumulation in pear and represent a valuable data set to guide future functional studies and pear breeding.
Invasive cattle ticks in East Africa: morphological and molecular confirmation of the presence of Rhipicephalus microplus in south-eastern Uganda
Authors: Muhanguzi Dennis , Byaruhanga Joseph , Amanyire Wilson , Ndekezi Christian , Ochwo Sylvester , Nkamwesiga Joseph , Mwiine Frank Nobert , Tweyongyere Robert , Fourie Josephus , Madder Maxime , Schetters Theo , Horak Ivan , Juleff Nick , Jongejan Frans
Published: March 2020

Background: Rhipicephalus microplus, an invasive tick species of Asian origin and the main vector of Babesia species, is considered one of the most widespread ectoparasites of livestock. The tick has spread from its native habitats on translocated livestock to large parts of the tropical world, where it has replaced some of the local populations of Rhipicephalus decoloratus ticks. Although the tick was reported in Uganda 70 years ago, it has not been found in any subsequent surveys. This study was carried out to update the national tick species distribution on livestock in Uganda as a basis for tick and tick-borne disease control, with particular reference to R.microplus.Methods: The study was carried out in Kadungulu, Serere district, south-eastern Uganda, which is dominated by small scale livestock producers. All the ticks collected from 240 cattle from six villages were identified microscopically. Five R. microplus specimens were further processed for phylogenetic analysis and species confirmation.Results: The predominant tick species found on cattle was Rhipicephalus appendiculatus (86.9 %; n=16,509). Other species found were Amblyomma variegatum (7.2 %; n=1,377), Rhipicephalus evertsi (2.3 %; n=434) and R. microplus (3.6 %; n= 687). Phylogenetic analysis of the 12S rRNA, 16S rRNA and ITS2 gene sequences of R. microplus confirmed the morphological identification.Conclusions: It is concluded that R. microplus has replaced Rhipicephalus decoloratus in the sampled villages in Kadungulu sub county, since the latter was not any longer found in this area. There is currently no livestock movement policy in force in Uganda, which could possibly limit the further spread of R. microplus ticks. Future surveys, but also retrospective surveys of museum specimens, will reveal the extent of distribution of R. microplus in Uganda and also for how long this tick has been present on livestock without being noticed.
On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments
Authors: Assefa Alemu Takele , Vandesompele Jo , Thas Olivier
Published: March 2020

Background: In gene expression studies, RNA sample pooling is sometimes considered because of budget constraints or lack of sufficient input material. Using microarray technology, RNA sample pooling strategies have been reported to optimize both the cost of data generation as well as the statistical power for differential gene expression (DGE) analysis. For RNA sequencing, with its different quantitative output in terms of counts and tunable dynamic range, the adequacy and empirical validation of RNA sample pooling strategies have not yet been evaluated. In this study, we comprehensively assessed the utility of pooling strategies in RNA-seq experiments using empirical and simulated RNA-seq datasets. Results: The data generating model in pooled experiments is defined mathematically to evaluate the the mean and variability of gene expression estimates. The model is further used to examine the trade-off between the statistical power of testing for DGE and the data generating costs. Empirical assessment of pooling strategies is done through analysis of RNA-seq datasets under various pooling and non-pooling experimental settings. Simulation study is also used to rank experimental scenarios with respect to the rate of false and true discoveries in DGE analysis. The results demonstrate that pooling strategies in RNA-seq studies can be both cost-effective and powerful when the number of pools, pool size and sequencing depth are optimally defined. Conclusion: For high within-group gene expression variability, small RNA sample pools are effective to reduce the variability and compensate for the loss of the number of replicates. Unlike the typical cost-saving strategies, such as reducing sequencing depth or number of biological samples, an adequate pooling strategy is effective in maintaining the power of testing for DGE for genes with low to medium abundance levels, along with a substantial reduction of the total cost of the experiment. In general, pooling RNA samples or pooling RNA samples in conjunction with moderate reduction of the sequencing depth can be good options to optimize cost and maintain power.
Integrated bioinformatics analysis of aberrantly-methylated differentially-expressed genes and pathways in age-related macular degeneration
Authors: Shen Yinchen , Li Mo , Liu Kun , Xu Xiaoyin , Zhu Shaopin , Wang Ning , Guo Wenke , Zhao Qianqian , Lu Ping , Yu Fudong , Xu Xun
Published: March 2020

Background: Age-related macular degeneration (AMD) represents the leading cause of visual impairment in the aging population. The goal of this study was to identify aberrantly-methylated, differentially-expressed genes (MDEGs) in AMD and explore the involved pathways via integrated bioinformatics analysis.Methods: Data from expression profile GSE29801 and methylation profile GSE102952 were obtained from the Gene Expression Omnibus database. We analyzed differentially-methylated genes and differentially-expressed genes using R software. Functional enrichment and protein–protein interaction (PPI) network analysis were performed using the R package and Search Tool for the Retrieval of Interacting Genes online database. Hub genes were identified using Cytoscape. Results: In total, 827 and 592 genes showed high and low expression, respectively, in GSE29801; 4117 hyper-methylated genes and 511 hypo-methylated genes were detected in GSE102952. Based on overlap, we categorized 153 genes as hyper-methylated, low-expression genes (Hyper-LGs) and 24 genes as hypo-methylated, high-expression genes (Hypo-HGs). Four Hyper-LGs (CKB, PPP3CA, TGFB2, SOCS2) overlapped with AMD risk genes in the Public Health Genomics and Precision Health Knowledge Base. KEGG pathway enrichment analysis indicated that Hypo-HGs were enriched in the calcium signaling pathway, whereas Hyper-LGs were enriched in sphingolipid metabolism. In GO analysis, Hypo-HGs were enriched in fibroblast migration, membrane raft, and coenzyme binding, among others. Hyper-LGs were enriched in mRNA transport, nuclear speck, and DNA binding, among others. In PPI network analysis, 23 nodes and two edges were established from Hypo-HGs, and 151 nodes and 73 edges were established from Hyper-LGs. Hub genes (DHX9, MAPT, PAX6) showed the greatest overlap. Conclusion: This study revealed potentially aberrantly MDEGs and pathways in AMD, which might improve the understanding of this disease.
Development, characterization, and cross-amplification of polymorphic microsatellite markers for North American Trachymyrmex and Mycetomoellerius ants
Authors: Matthews Alix E. , Rowan Chase , Stone Colby , Kellner Katrin , Seal Jon N.
Published: March 2020

Objective
The objective of this study is to develop and identify polymorphic microsatellite markers for fungus-gardening (attine) ants in the genus Trachymyrmex sensu lato . These ants are important ecosystem engineers and have been a model group for understanding complex symbiotic systems, but very little is understood about the intraspecific genetic patterns across most North American attine species. These microsatellite markers will help to better study intraspecific population genetic structure, gene flow, mating habits, and phylogeographic patterns in these species and potentially other congeners.
Results
Using next-generation sequencing techniques, we identified 17 and 12 polymorphic microsatellite markers from T. septentrionalis and Mycetomoellerius (formerly Trachymyrmex ) turrifex , respectively, and assessed the genetic diversity of each marker. We also analyzed the cross-amplification success of the T. septentrionalis markers in two other closely related Trachymyrmex species, and identified 10 and 12 polymorphic markers for T. arizonensis and T. pomonae , respectively.
Impact of brachytherapy technique (2D versus 3D) on outcomes of cervical cancer: A Systematic Review and Meta-analysis
Authors: Kim Yeon Joo , Kang Hyun-Cheol , Kim Young Seok
Published: March 2020

Background: To perform a systematic review and meta-analysis of the impact of brachytherapy (BT) technique (two-dimensional [2D] or three-dimensional image-guided [3D]) on outcomes of cervical cancer patients.Methods: PubMed and Embase databases were searched up to April 16, 2019, for studies which evaluated the effect of 3D-BT compared to 2D-BT in cervical cancer, and endpoints included cumulative incidence of severe toxicity, locoregional recurrence-free survival (LRRFS), progression-free survival (PFS), and overall survival (OS). Hazard ratios (HRs) were pooled in the meta-analysis using the random-effects model.Results: Six studies of 8 cohorts were included in the quantitative synthesis. The pooled hazard ratio (HR) regarding toxicity was evaluated in 5 cohorts in 3 studies, and the HR of 3D-BT compared to 2D-BT was 0.54 (95% confidence interval [CI], 0.37-0.77). All 6 studies were included for the synthesis for LRRFS, and the pooled HR favors 3D-BT (0.61 [95% CI, 0.40-0.93]). For PFS, 3 studies were included for analysis and 3D-BT was superior to 2D-BT (HR = 0.75 [95% CI, 0.0.59–0.96]). Five studies were included for the pooled HR regarding OS, and pooled HR of 3D-BT compared to 2D-BT was 0.65 (95% CI, 0.40–1.06).Conclusions: 3D-BT might reduce severe toxicity and improve LRRFS, and PFS in patients with cervical cancer. 3D-BT should be considered for standard management of cervical cancer, and efforts for adopting this procedure in Korea should be pursued.
A health care record review of early mobility activities after fragility hip fracture: Utilizing the French systematic method to inform future interventions
Authors: Haslam-Larmer Lynn , Woo Kevin , Auais Mohammad , Donnelly Catherine , DePaul Vincent
Published: March 2020

Background A fragility hip fracture is a serious injury in older adults. Following a fragility fracture, a large percentage of patients are unable to regain their pre-fracture level of mobility. There are several international guidelines recommending early mobility after surgery. We do not know the utilization of these early mobility recommendations by health care providers within our institution. An evidence to practice gap occurs when there is a failure to implement best practices. Utilization of a systematic method allows for a strategic approach to assessment of an evidence to practice gap. A recent publication of quality standards in Ontario provides an opportunity for a local needs assessment of potential evidence to practice gaps. Objective To identify if there is an evidence to practice gap in health care provider implementation of recommendations for early mobility after fragility hip fracture surgery. Methods A retrospective chart review was performed to document the rates of early mobility activities during the first five days after hip fracture surgery at a large tertiary centre in Toronto, Ontario. Patients with cognitive impairment were included. Results Early mobility activities in this older adult population are initiated in the first five days after surgery to varying degrees. Between 11% - 50% of patients are not participating in early mobility activities, thereby not meeting recommendations. Those with low pre-fracture function and cognitive impairment have lower rates of participation when compared to those with a high pre-fracture function and no cognitive impairment. Conclusions The chart review has identified a paucity of contextual information which may influence health care providers’ behaviours related to early mobility. The chart audit is limited in its ability to assess the systems issues, which may have an influence on the health care provider behaviour. Considering the lack of information in these areas, we have identified that further work is required to explore factors which may be having an impact on the health care provider’s ability to engage the patients in early mobility activities.
Differences in Achilles tendon stiffness in people with gout.
Authors: Otter Simon , Catherine Payne , Anna-Marie Jones , Nick Webborn , Peter Watt
Published: March 2020

Background Chronic gout is associated with weaker foot/leg muscles, altered gait patterns and on-going foot pain. Inflammation associated with gout may change tissue elasticity and ultrasound imaging (US) utilising shear wave elastography (SWE) offers a non-invasive method of quantifying these changes in tendon stiffness and SWE findings have not previously been reported in individuals with gout. We sought to determine differences in Achilles tendon stiffness in people with chronic gout compared to controls (non-gout). Methods A cross sectional study comparing 24 people with gout and 26 age/sex-matched controls. Clinical and demographic data were collated and US imaging used to determine tendon thickness, presence of gouty tophi and/or aggregates and levels of angiogenesis. Ten shear wave elastography (SWE) measures were taken along a longitudinal section of the mid-point of the Achilles tendon bilaterally. Prior to data collection, intra-observer error was good (0.75). Data were summarised using descriptive statistics and a repeated measures ANCOVA was used to compare SWE measures between the two groups for the left and right foot separately after accounting for Body Mass Index (BMI). Results: A small proportion of those with gout presented with intra-tendon aggregates and/or intra-tendon tophi in one or both tendons. There was no statistically significant difference in tendon thickness between groups. Neo-vascularity was present in a third of gout participants. SWE findings demonstrated significantly reduced tendon stiffness in those with gout compared to controls: right Achilles mdiff =1.04 (95% CI (0.38 to 1.7) p=0.003 and left Achilles mdiff = 0.7 (95% CI 0.09 to 1.32) p=0.025. Conclusion: Subjects with chronic gout show significantly reduced Achilles tendon stiffness compared to non-gout controls. From a clinical standpoint, our findings were similar to SWE measurements in subjects with Achilles tendinopathy and who did not have gout.
The effect of a non-invasive biomechanical treatment on subjective and objective measures in patients with knee osteoarthritis- A retrospective analysis on a UK population
Authors: Miles Christopher , Greene Andrew
Published: March 2020

Background Osteoarthritis is a major cause of pain and disability worldwide, therefore ways of treating this condition are paramount to a successful health system. The purpose of the study was to investigate the changes in spatial-temporal gait parameters and clinical measurements following treatment with a non-invasive biomechanical device on patients with knee osteoarthritis within the UK. Methods A retrospective analysis was carried out on 455 patients with knee osteoarthritis. All patients were evaluated using a computerized gait test and two self-assessment questionnaires (WOMAC and SF-36) at baseline and after 3 and 6 months of treatment. The biomechanical device was individually calibrated for each patient to minimise symptoms whilst walking and train neuromuscular control. Patients used the device for short periods during activities of daily living. Repeated measures statistical analyses were performed to compare differences over time. Results After 6 months of therapy significant improvements were seen in all gait parameters (p<0.01). Specifically, gait velocity, step length and single limb support of the more symptomatic knee improved by 13%, 7.8% and 3%, respectively. These were supported by significant improvements in pain, function and quality of life (48.6%, 45.7% and 22% respectively; p<0.001). A sub-group analysis revealed no baseline differences between those who were recommended joint replacement and those who were not. Both groups improved significantly over time (p<0.05 for all). Conclusions Our results suggest the personalised biomechanical intervention can improve gait patterns, pain, function and quality of life. It may provide an additional solution to managing UK patients suffering from knee osteoarthritis.
Epstein Barr virus genotypes (EBV1/EBV2) in individuals with infectious mononucleosis in the metropolitan area of Belém, Brazil, between 2005 and 2016
Authors: Monteiro Talita Antonia Furtado , Monteiro Talita Antonia Furtado , Costa Iran Barros , Costa Igor Brasil , Corrêa Thais Letícia dos Santos , Coelho Beatriz Monteiro Rodrigues , Polaro Alessandra Alves , Silva Amanda Emanuelle Santos da , Ramos Francisco Lúzio de Paula , Filho Arnaldo Jorge Martins , Monteiro Jose Luiz Furtado , Sousa Rita Catarina Medeiros
Published: March 2020

Background: Two types of Epstein Barr virus (EBV1/EBV2) have been shown to infect humans by causing infectious mononucleosis, their genome being very similar, except for regions of the EBNA genes. This study aimed to describe the EBV genotypes in cases of infectious mononucleosis in the metropolitan region of Belém, Brazil, from 2005 to 2016. Methods: A total of 8.295 suspected cases with symptoms/signs of infectious mononucleosis (MI) were investigated by doctors of infectious diseases at the Evandro Chagas Institute Health Care Service from January 2005 to December 2016. In 3.0% (251/8.295) of the cases were positive by enzymatic immunoassay were submitted to PCR for EBNA3C region to detect the types of EBV. Biochemical testing involving aspartate aminotransferase, alanine aminotransferase and gamma-glutamyl transferase were realized. Results: The identification of EBV types by PCR was verified in 30.3% (76/251) of individuals, being 71.1% (54/76) classified as EBV1, 17.1% (13/76) as EBV2 and 11.8% (9/76) as EBV1+EBV2. The number of women infected with EBV1 was higher (61.1% - 33/54) than for men (38.9% - 21/54), most were over 14 years old (66.7%-36/54). The main symptoms/clinical signs observed in EBV1 infection were: cervical lymphadenopathy (64.8%-35/54), fever (63%-34/54), headache (20.3%-11/54), arthralgia (20.3%-11/54) and exanthema (18.5%-10/54). In EBV2 infection, it was also detected in all age groups, with the exception of two groups, with an average age of 24 years. The presence of fever in 76.9% (10/13) with an average duration of 18 days and lymphadenopathy in 53.8 (7/13) were the most relevant signs/symptoms in EBV2. In contrast, EBV1+EBV2 co-infection was more frequent in the £5 year age group, affecting 20.0% (2/10). Women presented 66.7% (6/9) more positive cases. The symptoms involving EBV1+EBV2 co-infection were more related to fever (66.7%-6/9) and cervical lymphadenopathy (55.6% -5/9). The average of enzymatic values according to type of EBV was statistically significant (p <0.05) in individuals with EBV1 infection in those over 14 years of age. Conclusions: A pioneering study that molecularly identified the genotypes of EBV in 30.3% of cases, with circulation of EBV1, EBV2 and co-infection EBV1+EBV2 in cases of infectious mononucleosis in the northern region of Brazil.
Risky sexual behaviours among women of reproductive age in a high HIV burdened township in KwaZulu-Natal, South Africa
Authors: Hlongwa Mbuzeleni , Peltzer Karl , Hlongwana Khumbulani
Published: March 2020

Background: Despite several intervention programmes in South Africa, risky sexual behaviours among women of reproductive age remain a public health concern, thereby making them prone to unintended pregnancies, human immunodeficiency virus (HIV) infection and/or sexually transmitted infections (STIs). This study investigated the predictors of risky sexual behaviours among women of reproductive age in a high HIV burdened township in KwaZulu-Natal (KZN), South Africa.Methods: This was a cross-sectional study conducted among 471 women of reproductive age (18-49 years, mean: 25.83) in 10 public health clinics in Umlazi township, using a structured questionnaire. Data were coded, entered into Epi Data Manager and exported to Stata for analysis. A Pearson Chi-square test and logistic regression models (bivariate and multivariate) were employed to assess the level of the association between the predictor and outcome variables and the p-value 0.05 or lower was considered statistically significant.Results: More than half (51.80%) of women were aged 18-24 years and only a handful (18.26%) had tertiary qualification. The majority were single (88.96%) and the unemployed accounted for 53.50%. This study found that women who talked about condoms with their partners in the past 12 months were more likely (p=<0.0001) to have used condoms during their last sexual experience. Older women (p=0.035) were more likely to use a condom at last sex, compared to younger women. However, women who were exposed to physical partner violence (hitting and/or slapping), those who had ever been diagnosed with HIV and those whose sexual partners were diagnosed with HIV, did not show a significant association with condom use during last sexual experience.Conclusion: Exposure to physical partner violence and poor partner discussions about condoms are key deterrents to condom usage. Holistic interventions are required in order to address the risky behaviours, and consequently reduce sexually transmitted infections and/or unintended pregnancies.
A comparison, for older people with diabetes, of health and health care utilisation in two different health systems on the island of Ireland
Authors: Pierse Tom , Barry Luke , Glynn Liam , Murphy Andrew , Cruise Sharon , O’Neill Ciaran
Published: March 2020

Background Primary care policies for diabetes have differed between Northern Ireland (NI) and the Republic of Ireland (ROI). In NI, the Quality and Outcomes Framework (QOF) system was adopted in 2004. In ROI, prior to the Cycle of Care programme being established in 2015 specific financial support for GPs providing diabetic primary care was not available. The aims of this study are to compare health and healthcare utilisation among people with diabetes in the NI and ROI.Methods Large scale comparable surveys of people over 50 years of age in Northern Ireland (NICOLA) and the Republic of Ireland (TILDA) are used to compare people with diabetes (Type I and Type II) in the two jurisdictions. The combined data set comprises 1,536 people with diabetes. A coarsened exact matching approach is used to compare health care utilisation among people with diabetes in NI and ROI with equivalent demographic, lifestyle and illness characteristics.Results The overall prevalence in the 50 to 84 years old age group is 3.4 percentage points higher in NI (11.1% in NI, 7.7% ROI, p-value < 0.01). The diabetic population in NI also appear sicker – with more diabetic complications and more chronic illnesses. Comparing people with diabetes in the two jurisdictions with similar levels of illness we find that there are no statistically significant differences in GP, outpatient or A&E utilisation.Conclusion There are a range of factors that influence the quality of primary care for people with diabetes. While the QOF system in Northern Ireland is likely to have improved some aspects of care by providing financial incentives for identification and management, unless accompanied by improved access to care their ability to impact on outcomes may be compromised.