bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Survey of Virus Recombination Uncovers Canonical Features of Artificial Chimeras Generated During Deep Sequencing Library Preparation
Authors: Peccoud Jean , Lequime Sébastian , Moltini-Conclois Isabelle , Giraud Isabelle , Lambrechts Louis , Gilbert Clément 
Published: February 2018

Abstract
Chimeric reads can be generated by in vitro recombination during the preparation of high-throughput sequencing libraries. Our attempt to detect biological recombination between the genomes of dengue virus (DENV; +ssRNA genome) and its mosquito host using the Illumina Nextera sequencing library preparation kit revealed that most, if not all, detected host–virus chimeras were artificial. Indeed, these chimeras were not more frequent than with control RNA from another species (a pillbug), which was never in contact with DENV RNA prior to the library preparation. The proportion of chimera types merely reflected those of the three species among sequencing reads. Chimeras were frequently characterized by the presence of 1-20 bp microhomology between recombining fragments. Within-species chimeras mostly involved fragments in opposite orientations and located less than 100 bp from each other in the parental genome. We found similar features in published datasets using two other viruses: Ebola virus (EBOV; -ssRNA genome) and a herpesvirus (dsDNA genome), both produced with the Illumina Nextera protocol. These canonical features suggest that artificial chimeras are generated by intra-molecular template switching of the DNA polymerase during the PCR step of the Nextera protocol. Finally, a published Illumina dataset using the Flock House virus (FHV; +ssRNA genome) generated with a protocol preventing artificial recombination revealed the presence of 1-10 bp microhomology motifs in FHV–FHV chimeras, but very few recombining fragments were in opposite orientations. Our analysis uncovered sequence features characterizing recombination breakpoints in short-read sequencing datasets, which can be helpful to evaluate the presence and extent of artificial recombination.
EVALUATION OF SERUM SODIUM LEVEL IN SINGLE AND RECURRENT FEBRILE SEIZURES
Authors: Ghafoor Ibrahim 
Published: February 2018

Background
Febrile seizures are the most common form of childhood seizures. Its either simple (when it is single attack within next 24 hours, plus other characters) or complex (when is recurrent within same period plus other characteristics).
Objectives

This study was conducted to determine the role of low serum sodium levels in predicting single or recurrent febrile seizures among children.
Patients and Methods
In this study, 100 patients aged 6-60 months old were enrolled. The patients were divided into two groups: those with single, and those with recurrent febrile seizures. Then 100 children with febrile illness, but no febrile convulsion, taken as a control. For those 3 groups serum sodium levels were studied.
Results
Among the patients, male gender was predominant. Among those with 12-24 months old, positive family history of febrile seizures was significant. The mean serum sodium of patients with single febrile seizure was (137.91), while the mean serum sodium level of patients with recurrent febrile seizures was (139), and the mean serum sodium of control group was (141.42). The P-value of comparison between control and those with single febrile seizure was significant (0.002), but the P-value of comparison between control and those with recurrent febrile seizures was not significant (0.813). There was no significant role of the serum sodium found during admission of the patients.
Conclusion
We found in present study: there was no significant role for the serum sodium during single or recurrent F.S.s. These findings reaffirm the recommendation of the American Academy of Pediatrics not to routinely obtain serum electrolytes in febrile seizures unless clinically indicated.
NON ALCOHOLIC FATTY LIVER DISEASE AMONG PATIENTS WITH TYPE 2 DIABETES MELLITUS IN SULAIMANI GOVERNORATE
Authors: Maarouf Fenk , Hadi Hemn , Mohammed Mohammed 
Published: February 2018

Background
Nonalcoholic fatty liver disease (NAFLD) is a common hepatic disorder characterized by accumulation of fat in the liver parenchyma of patients who do not drink excessive amount of alcohol. The prevalence of NAFLD is high in conditions associated with insulin resistance, such as obesity, type 2 DM, dyslipidemia and the metabolic syndrome. NAFL is very common in type-2 diabetic patients, with 50-75% demonstrating fat in the liver by ultrasound.
Objectives

To assess the frequency of NAFLD in patients with type 2 DM in Sulaimani and its relation with age, gender, duration and state of glycaemic control compared to non diabetic subjects.
Methods
This is across sectional study, conducted in Sulaimani General Teaching Hospital from December. 2013 to December 2014. A total of 102 patients were enrolled in the study, sixty seven were diabetic and 35 were nondiabetic as control. Patients with chronic viral hepatitis B, C, autoimmune hepatitis, excessive alcohol ingestion, and drugs with adverse effect on liver were excluded. These patients were evaluated by abdominal ultrasonography to determine the presence of fatty liver. They were divided into fatty liver group and non-fatty liver group. They were further evaluated for BMI, waist/hip ratio, blood pressure, lipid profile, liver function test. The data obtained was analyzed using SPSS-21.
Results
61% of diabetic patients had fatty liver on ultrasonography; of those 17% fulfill the criteria of NASH, compared to 48%, 6% in the control group respetively. BMI, serum triglyceride and ALT were significantly higher in group with fatty liver than non fatty liver in both diabetic and control (P-value= 0.001, 0.027, and 0.006 respectively).The frequency of NAFLD increases with age. Diabetes was associated with more severe degree of NAFL and fibrosis score.
Conclusion
NAFLD is more common in type 2 DM than nondiabetic. Obesity, hypertriglyceridemia, and HbA1c are independent predictors of NAFLD.
Multidimensional Improvements in Health Following Hatha Yoga for Individuals with Diabetic Peripheral Neuropathy
Authors: Van Puymbroeck Marieke , Atler Karen , Portz Jennifer Dickman , Schmid Arlene A. 
Published: February 2018

Abstract
The purpose of this study was to understand the lived experience of ten individuals with diabetic peripheral neuropathy (DPN) who completed an 8-week Hatha Yoga trial. The International Classification of Function, Disability, and Health (ICF) provided the framework for this study. Two focus groups were conducted following a twice-weekly, 60-minute yoga intervention that was designed for people with DPN. Interpretative phenomenological analysis was employed to analyze the data. Themes in the data emerged related to improvements in body functions, specifically neuromuscular and movement-based function and sensory functions, as well as stress management and sleep improvement via breathwork, and social support was an essential environmental factor. These data support the bidirectionality of the ICF and demonstrate that in individuals with DPN, yoga may affect health holistically by improving body functions, activities, participation, and environmental factors. Yoga may be a tool to improve general well-being in individuals with DPN. A larger, randomized trial should be conducted to extend the findings from the present trial.
MODELLING AS A KNOWLEDGE GAINING TECHNIQUE FOR PRIMARY SCHOOL STUDENTS WHO LEARN SOLVING COMPLEX TASKS
Authors: Makarova Aleksandra , Musiychuk Sergey , Damazio Ademir 
Published: February 2018

Abstract.Using an example of composite tasks and the teaching techniquebehind them, the authors describe how primary school students learn to use modelling as part of their knowledge gaining process in education. The use of modelling during math classes is one of the pre-conditions for successful learning with primary school children as with the help of modelling children can better imagine what the task implies and better understand the relationship between different values, which enhances their awareness when deciding on what operation to apply, and so on.The article describes different models and submodels used by teachers for taskmodelling. It is noted that when learning how to solve composite tasks, children learn to reflect and acquire the ability to act inside their minds and analyze their thinking.Keywords: Knowledge gaining, mathematics teaching, modelling, compositetask.
LEGAL EDUCATION AS A METHOD FOR MITIGATING DEVIANT BEHAVIOR OF MINORS
Authors: Martynova Nataliia , Borovkova Nataliia 
Published: February 2018

Abstract. This article studies legal education as a method for mitigating deviantbehavior of minors. It analyzes importance of legal culture of teens that can be fostered by forms and methods of educational environment, improves activity of the young, regulated individual behavior based on moral motivation of the personality. Need and expediency of sense of justice which acquaints minors with knowledge of the state and the right, legality, the rights and personal freedoms, development at teenagers of steady orientation to law-abiding behavior is defined.Keywords: legal education, educational environment, deviant behavior, moralmotivation.
Percentage depth dose (PDD) and Beam profile measurements using CT based MAGAT gel dosimetry system and Monte Carlo calculation
Authors: Aljamal Mohammad 
Published: February 2018

Abstract
The aim of this project is to develop and to evaluate the CT based MAGAT (methacrylic acid, gelatine and tetrakis phosphonium chloride) polymer gel dosimetry for measuring 3D dose distributions in radiation treatment. The MAGAT gel was prepared based on the formulation proposed in the literature. The percentage depth dose (PDD) and beam profile of 8 x 8 cm2 field size photon beam from a 6 MV linear accelerator were measured. Monte Carlo simulation was carried out to calculate PDD and beam profiles in the simulated MAGAT gel phantom to verify the data measured using MAGAT gel dosimetry for the 8 x 8 cm2 field size. The PDD and beam profile calculated using simulated MAGAT gel phantom agreed very well with that measured using MAGAT gel dosimetry. However, there were some differences between the simulated PDD with that measured at the surface region due to the electron contamination at the surface of the simulated phantom. In conclusion, the results showed that the CT based MAGAT gel dosimetry system is promising method to measure three- dimensional dose distribution based on PDD and Beam profile measurement.
Keywords: MAGAT gel, CT, Monte Carlo simulation
Comparing ols and rank-based estimation techniques for production analysis: An application to Ghanaian maize farms.
Authors: De-Graft Acquah Henry 
Published: February 2018

This paper introduces the rank-based estimation method to modelling the Cobb-Douglas production function as an alternative to the least squares approach. The intent is to demonstrate how a nonparametric regression based on a rank-based estimator can be used to estimate a Cobb-Douglas production function using data on maize production from Ghana. The nonparametric results are compared to common parametric specification using the ordinary least squares regression. Results of the study indicate that the estimated coefficients of the CobbDouglas Model using the Least squares method and the rank-based regression analysis are similar. Findings indicated that in both estimation techniques, land and Equipment had a significant and positive influence on output whilst agrochemicals had a significantly negative effect on output. Additionally, seeds which also had a negative influence on output was found to be significant in the robust rank-based estimation, but insignificant in the ordinary least square estimation. Both the least squares and rank-based regression suggest that the farmers were operating at an increasing returns to scale. In effect this paper demonstrate the usefulness of the rank-based estimation in production analysis.
JEL CODE: Q18, D24, Q12, C1 and C67
Extent and characteristic of diversification among Hungarian agricultural holdings
Authors: Kissné Nagy Csilla 
Published: February 2018

Through the connection to rural resources agriculture has an impact on the three functions of countryside: ecology, society and economy. Resources of economy and production environment are continuously changing thus farmers have to adapt to these changing circumstances. One of the adaptation methods is the diversification of activities to promote effective capacity utilization and additional profit. However there is no standard definition of diversification from the point of agricultural economics aspect both traditional approaches and the influence of European Union should also be considered to define it. Diversification and alternative income opportunities could be subsistence possibilities for several farmers. This could be defined not only at private holdings’ but at enterprises’ level. According to a traditional approach Hungarian statistical databases collect on-farm and off-farm agricultural activities depending on the connection to resources of a farm business. Analysing this database an overall picture could be defined considering the position and characteristic of diversified farmers and the popularity of each activity among agricultural producers. Based on a study, published in 2011 (Hamza, 2011) this paper also involves the latest statistical data (2010, 2013). Analysing dataset of period 2000-2013 this paper gives an overall overview about national and regional position and characteristics of diversified holdings and activities.
JEL code: Q19
How economic recession effect the corporate philanthropy? Evidence from Pakistani corporate sector
Authors: Zulfiqar Sehar 
Published: February 2018

Corporate philanthropy is a significant indicator of firm’s socially responsible behavior. Researchers and managers acknowledge the immense potential of corporate philanthropy for optimizing social and economic benefits. Aligned with this view corporate sector in Pakistan is engaged in philanthropic initiatives in some form or another. This paper aims to present the response of the Pakistani corporate sector to the corporate philanthropy at the time of global economic recession 2008-2009 by analyzing the sample of Public Listed Companies (PLCs). The analysis revealed that during the global financial crisis, the economic condition of Pakistan was worsened that was already in distress, but it hasn’t strongly effected the corporate philanthropy as the data shows a slight decrease in the overall volume of corporate donations in 2007 and a slight decrease in the number of companies engaged in philanthropy during 2008. The finding of the study suggests that during the global economic downturn the PLCs in Pakistan continued to show commitment towards community through corporate donations.
JEL code: B22
Metals in Soil and Runoff from a Piedmont Hay Field Amended with Broiler Litter and Flue Gas Desulfurization Gypsum
Authors: Schomberg Harry H. , Endale Dinku M. , Jenkins Michael B. , Chaney Rufus L. , Franklin Dorcas H. 
Published: February 2018

Flue gas desulfurization gypsum (FGDG) from coal‐fired power plants is readily available for agricultural use in many US regions. Broiler litter (BL) provides plant available N, P, and K but can be a source of unwanted As, Cu, and Zn. As a source of Ca and S, FGDG can reduce losses of P and other elements in runoff from BL‐amended areas. Rainfall simulation plots (2.0 m2) were established on a Piedmont Cecil soil growing ‘Coastal’ bermudagrass (Cynodon dactylon L.) for hay. Accumulation and transport of As, Cu, Cd, Cr, Hg, Pb, and Zn were evaluated after annual BL applications (13.5 Mg ha−1) with four FGDG rates (0, 2.2, 4.5, 9.0 Mg ha−1) and two FGDG treatments (0 and 9 Mg ha−1) without BL. Runoff As concentrations were sixfold greater with BL than without (P ≤ 0.01) and were similar to BL with FGDG at 2.2, 4.5 or 9.0 Mg ha−1 (P ≤ 0.10). Runoff concentrations of target elements did not increase where FGDG was applied alone. After three annual applications of FGDG and BL, soil concentrations of As, Cr, Pb, Hg, and Cu were well below levels of environmental concern. Our findings indicate that runoff losses of As from BL application are not reduced with FGDG but support other research indicating no identifiable environmental risks from FGDG beneficial use in agricultural systems.Core Ideas
After 3 yr, FGDG alone did not influence runoff concentrations or loads of As, Cu, and Zn.
With BL, the first 10 min runoff concentration and load of As, Cu, and Zn increased linearly with FGDG rate.
A similar response was not observed for composite samples collected over the full 1 h.
FGDG beneficial use does not present an environmental risk due to heavy metals or other constituents.
Rainwater Deficit and Irrigation Demand for Row Crops in Mississippi Blackland Prairie
Authors: Feng Gary , Ouyang Ying , Adeli Ardeshir , Read John , Jenkins Johnie 
Published: February 2018

Core Ideas
We investigated the characteristics of rainwater deficit using 122 years' weather data.
We determined irrigation demand for soybean, corn, and cotton in the previous 122 years.
We estimated the water requirements of soybean, corn, and cotton in east‐central Mississippi.
We developed a soil water and irrigation management model with STELLA software for soybean, corn, and cotton in a subhumid climate.
Irrigation research in the mid‐south United States has not kept pace with a steady increase in irrigated area in recent years. This study used rainfall records from 1895 to 2016 to determine rainwater deficit and irrigation demand for soybean [Glycine max (L.) Merr.], corn (Zea mays L.), and cotton (Gossypium hirsutum L.) in the Blackland Prairie region of Mississippi with a soil water balance model developed in Structural Thinking and Experiential Learning Laboratory with Animation (STELLA) software. The longterm analysis showed annual rainfall exceeded 1125 mm in 3 out of 4 yr. Median growing season rainfall for soybean, corn, and cotton ranged from 226 to 412, 283 to 505, and 220 to 472 mm and was 30, 39, and 33% of annual rainfall in either normal or dry years, respectively. Total effective rainwater deficit (rainfall minus runoff, percolation, and evapotranspiration) during soybean, corn, and cotton growing seasons was 200, 217, and 184 mm, respectively. During the driest 25% years, the maximum effective rainwater deficit was 340, 324, and 327 mm for soybean, corn, and cotton, respectively. Across the 122‐yr period, soybean, corn, and cotton did not appear to need irrigation for only 12, 17, and 14 yr; their average irrigation demand was 180, 167, and 175 mm yr–1, respectively. Soybean required irrigation from 29 June to 7 September, particularly in reproductive Growth Stage 3 (0.5‐cm‐long pods in the upper four nodes) to Stage 7 (pods mature in color anywhere), when the crop appeared to require at least five irrigations.
Influence of Source and Particle Size on Agricultural Limestone Efficiency at Increasing Soil pH
Authors: Jones John D. , Mallarino Antonio P. 
Published: February 2018

Core Ideas
Liming materials' fineness affected the effectiveness and economics of lime use.
There is little information about pelleted lime's efficiency at increasing soil pH.
This study assessed the effectiveness of calcitic and dolomitic agricultural limestone (aglime) particle sizes.
Calcitic aglime was more efficient than dolomitic aglime at similar particle sizes.
Pelleted lime was more effective than calcitic and dolomitic aglime.
The chemico‐physical characteristics of liming materials determine their capacity to neutralize soil acidity. This study evaluated how calcitic and dolomitic agricultural limestone (aglime), pelleted calcitic lime, and different particle sizes of both aglime sources increased soil pH. Both aglime sources were fractionated to pass different Tyler mesh sizes (4–8, 8–20, 20–60, 60–100, or 100+). The equivalent of 8.97 Mg CaCO3 ha–1 of each material or powdered CaCO3 was mixed with three acidic soils and incubated for 7, 21, 35, 70, 105, 140, 175, and 210 d. All sources increased soil pH. Differences among soils were minor compared with source differences. The efficiency of lime sources at raising pH relative to CaCO3 increased with incubation time and fineness, and was lower for dolomitic than for calcitic aglime. Pelleted lime, calcitic aglime, and dolomitic aglime efficiencies across all incubation periods were 60 to 90, 47 to 65, and 12 to 47% respectively. Calcitic aglime's efficiency across the incubation periods was –1 to 29, 17 to 39, 24 to 61, 47 to 81, and 70 to 97% for material passing mesh sizes 4 to 8, 8 to 20, 20 to 60, 60 to 100, and 100+, respectively; whereas dolomitic aglime's efficiency was 2 to 12, 4 to 21, 12 to 43, 50 to 66, and 60 to 86%, respectively. The study demonstrated the value of distinguishing between particle sizes passing mesh sizes 60 to 100 and finer, and between calcitic and dolomitic aglime in aglime assessments and agricultural recommendations.
Interactions of Stover and Nitrogen Management on Soil Microbial Community and Labile Carbon under Irrigated No‐Till Corn
Authors: Stewart Catherine E. , Roosendaal Damaris L. , Manter Daniel K. , Delgado Jorge A. , Del Grosso Stephen 
Published: February 2018

Core Ideas
No‐tillage and nitrogen fertilizer may mitigate residue removal impacts on soil microbial biomass.
Stover removal decreased soil microbial biomass by 40 to 42%, but did not affect community structure.
Residue removal effects on soil microbial biomass were mediated by nutrient limitations.
Residue retention and no‐tillage are critical to maintaining microbial populations.
Corn stover removal can reduce soil C and N stocks, reduce soil microbial biomass (SMB), and alter soil biogeochemistry. No‐tillage (NT) management may reduce the negative impacts of long‐term stover removal, but how the microbial community mediates N fertilizer and stover removal effects on soil organic carbon (SOC) pools is less clear. We measured the effects of partial stover retention or full stover retention on particulate organic matter carbon (POM‐C), SMB, and community composition under three N fertilization treatments (0, 60, and 202 kg N ha–1) after 7 yr. Residue removal effects on SMB were mediated by nutrient limitations. Stover removal decreased SMB by 40% at low N fertilizer rates, however, at the highest N rate, SMB did not differ between residue treatments, presumably due to the additional C input and bulk SOC content. Interestingly, at deeper depths (>7.5 cm), partial residue retention increased POM‐C by 11% compared with full stover retention, suggesting greater structural root inputs and slower decomposition. Microbial community composition was not influenced by residue removal, but was significantly influenced by N fertilizer. A principal coordinate analysis showed that microbial communities under no or low N were enriched for gram‐negative bacteria, arbuscular mycorrhizal fungi (AMF), and saprotrophic fungal biomarkers reflecting fresh plant‐derived C input, while higher N rates were enriched for actinomycetes and gram‐positive biomarkers. High stover N content promoted rapid decomposition by SMB and incorporation into mineral‐associated C pools rather than POM‐C. Even under NT, residue removal will reduce soil C and SMB, but N fertilizer may mediate this effect by enhancing C input and rhizodeposition.