bluuebunny/crossref_metadata_2025_split huggingface dataset:
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
Authors: Jónsson Hákon , Ginolhac Aurélien , Schubert Mikkel , Johnson Philip L. F. , Orlando Ludovic 
Published: April 2013

Abstract
Motivation: Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of past epidemics and the dynamics of past populations. However, the analysis of aDNA generally faces two major issues. Firstly, sequences consist of a mixture of endogenous and various exogenous backgrounds, mostly microbial. Secondly, high nucleotide misincorporation rates can be observed as a result of severe post-mortem DNA damage. Such misincorporation patterns are instrumental to authenticate ancient sequences versus modern contaminants. We recently developed the user-friendly mapDamage package that identifies such patterns from next-generation sequencing (NGS) sequence datasets. The absence of formal statistical modeling of the DNA damage process, however, precluded rigorous quantitative comparisons across samples.
Results: Here, we describe mapDamage 2.0 that extends the original features of mapDamage by incorporating a statistical model of DNA damage. Assuming that damage events depend only on sequencing position and post-mortem deamination, our Bayesian statistical framework provides estimates of four key features of aDNA molecules: the average length of overhangs (λ), nick frequency (ν) and cytosine deamination rates in both double-stranded regions () and overhangs (). Our model enables rescaling base quality scores according to their probability of being damaged. mapDamage 2.0 handles NGS datasets with ease and is compatible with a wide range of DNA library protocols.
Availability: mapDamage 2.0 is available at ginolhac.github.io/mapDamage/ as a Python package and documentation is maintained at the Centre for GeoGenetics Web site (geogenetics.ku.dk/publications/mapdamage2.0/).
Contact: jonsson.hakon@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli
Authors: Häkkinen Antti , Muthukrishnan Anantha-Barathi , Mora Andre , Fonseca Jose M. , Ribeiro Andre S. 
Published: April 2013

Abstract
Motivation: Cell division in Escherichia coli is morphologically symmetric. However, as unwanted protein aggregates are segregated to the cell poles and, after divisions, accumulate at older poles, generate asymmetries in sister cells’ vitality. Novel single-molecule detection techniques allow observing aging-related processes in vivo, over multiple generations, informing on the underlying mechanisms.
Results: CellAging is a tool to automatically extract information on polar segregation and partitioning in division of aggregates in E.coli, and on cellular vitality. From time-lapse, parallel brightfield and fluorescence microscopy images, it performs cell segmentation, alignment of brightfield and fluorescence images, lineage construction and pole age determination, and it computes aging-related features. We exemplify its use by analyzing spatial distributions of fluorescent protein aggregates from images of cells across generations.
Availability: CellAging, instructions and an example are available at http://www.cs.tut.fi/%7esanchesr/cellaging/.
Contact: andre.ribeiro@tut.fi
Supplementary information: Supplementary data are available at Bioinformatics online.
A predominance of hypertensive heart failure in the Abuja Heart Study cohort of urban Nigerians: a prospective clinical registry of 1515 de novo cases
Authors: Ojji Dike , Stewart Simon , Ajayi Samuel , Manmak Mamven , Sliwa Karen 
Published: April 2013

AimsEven though cardiovascular disease is gradually becoming the major cause of morbidity and mortality in sub‐Saharan Africa, there are very few data on the pattern of heart disease in this part of the world. We therefore decided to determine the pattern of heart disease in Abuja, which is one of the fastest growing and most westernized cities in Nigeria, and compare our findings with those of the Heart of Soweto Study in South Africa.Methods and resultsDetailed clinical data were consecutively captured from 1515 subjects of African descent, residing in Abuja, and equivalent Soweto data from 4626 subjects were available for comparison. In Abuja, male subjects were on average, ∼2 years older than female subjects. Hypertension was the primary diagnosis in 45.8% of the cohort, comprising more women than men [odds ratio (OR) 1.96, 95% confidence interval (CI) 1.26–2.65], and hypertensive heart failure (HF) was the most common form of HF in 61% of cases. On an age‐ and sex‐adjusted basis, compared with the Soweto cohort, the Abuja cohort were more likely to present with a primary diagnosis of hypertension (adjusted OR 2.10, 95% CI 1.85–2.42) or hypertensive heart disease/failure (OR 2.48, 95% CI 2.18–2.83); P < 0.001 for both. They were, however, far less likely to present with CAD (OR 0.04, 95% CI 0.02–0.11) and right heart failure (2.5% vs. 27%).ConclusionAs in Soweto, but more so, hypertension is the most common cause of de novo HF presentations in Abuja, Nigeria.
Functional Conservation of MIKC*-Type MADS Box Genes in Arabidopsis and Rice Pollen Maturation
Authors: Liu Yuan , Cui Shaojie , Wu Feng , Yan Shuo , Lin Xuelei , Du Xiaoqiu , Chong Kang , Schilling Susanne , Theißen Günter , Meng Zheng 
Published: April 2013

Abstract
There are two groups of MADS intervening keratin-like and C-terminal (MIKC)-type MADS box genes, MIKCC type and MIKC* type. In seed plants, the MIKCC type shows considerable diversity, but the MIKC* type has only two subgroups, P- and S-clade, which show conserved expression in the gametophyte. To examine the functional conservation of MIKC*-type genes, we characterized all three rice (Oryza sativa) MIKC*-type genes. All three genes are specifically expressed late in pollen development. The single knockdown or knockout lines, respectively, of the S-clade MADS62 and MADS63 did not show a mutant phenotype, but lines in which both S-clade genes were affected showed severe defects in pollen maturation and germination, as did knockdown lines of MADS68, the only P-clade gene in rice. The rice MIKC*-type proteins form strong heterodimeric complexes solely with partners from the other subclade; these complexes specifically bind to N10-type C-A-rich-G-boxes in vitro and regulate downstream gene expression by binding to N10-type promoter motifs. The rice MIKC* genes have a much lower degree of functional redundancy than the Arabidopsis thaliana MIKC* genes. Nevertheless, our data indicate that the function of heterodimeric MIKC*-type protein complexes in pollen development has been conserved since the divergence of monocots and eudicots, roughly 150 million years ago.
What's the ticker symbol for farmland?
Authors: Sherrick Bruce J. , Mallory Mindy L. , Hopper Timothy 
Published: April 2013

PurposeRelatively high recent returns to farmland investments have led to substantially elevated interest in farmland investments. Absent, however, is a well‐functioning equity market in farmland real estate, or well‐developed indexes of farmland returns that might contribute to the development of tradable shares tied to farmland returns, or to methods to hedge the value of owned agricultural assets. The purpose of this study is to empirically present relevant measures related to farmland returns and other financial assets to provide a broad context for evaluation of farmland investments in a portfolio context. Issues related to the development of a farmland fund and index construction are discussed along with major risk and transactional factors that are somewhat unique to the asset class.Design/methodology/approachReturns data from a broad set of financial categories and broad set of agricultural returns measures are developed and presented in multiple frameworks to convey temporal persistence, relatedness, and portfolio considerations related to farmland. Issues related to the construction of claims based on agricultural assets are discussed.FindingsAgricultural real estate investments have performed well compared to most other financial assets on most traditional measures of risk adjusted performance. However, the difficulties in direct investment remain and the need to develop securitized conduit exposures to farmland returns is identified.Originality/valueThe study presents a unique set of farmland returns measures and examines the stability of the statistics used to describe these through time. Novel characterizations of the data compared to traditional assets helps investors and asset owners accurately understand the exposure to farmland returns.
Farmland rental markets: trends in contract type, rates, and risk
Authors: Paulson Nicholas D. , Schnitkey Gary D. 
Published: April 2013

PurposeThis article aims to explore recent trends in farmland rental markets using data for the state of Illinois. Trends in the types of rental agreements used and the relationship between the rental rate for those contracts, land values, crop revenues, production costs, and farm returns are examined.Design/methodology/approachData from various sources and at different levels of aggregation for the state of Illinois are used to provide illustrations of historical trends in farmland rental agreements and rental rates, and how they are related to various market and industry factors. Focus is placed on the more recent period since 2005 characterized by high commodity price levels and volatility.FindingsThe majority of farmland in the Midwest is controlled under rental agreements which are increasingly of the fixed cash rent type. Rental rates have increased, but at a slower rate than farm returns. Average rental and interest rates imply that land values are consistent with the current market environment. Aggregate rental rates mask considerable variation in farm‐level rents, only a portion of which can be explained by differences in soil productivity. Given the current level of price volatility, the tenure position of a farm operation has a significant effect on downside risk exposure.Originality/valueThe illustrations provided in this paper should be of interest to researchers working in the area of farmland values and rental agreements, as well as to practitioners including farmers, landowners, and professional farm managers. The findings should motivate additional research and recognition of the importance of tenure position to the performance and risk exposure of grain farms.
Financial performance of publicly‐traded agribusinesses
Authors: Katchova Ani L. , Enlow Sierra J. 
Published: April 2013

PurposeAgribusinesses represent a fundamental link in connecting farmers with retailers and consumers, yet little research has been done to examine the historical financial performance of these food processing firms. This paper aims to address this issue.Design/methodology/approachThe authors' research examines how publicly‐traded agribusinesses perform financially compared to all firms over the period from 1961 to 2011. The authors utilize several indicators of company success, including financial ratios and balance sheet/income statement items, to compare agribusiness firms to all firms in the market. The authors perform the analysis over time and also for companies with low, median, and high performance. They also perform Du Pont analysis to compare return on equity components between agribusinesses and all firms.FindingsThe authors find that agribusinesses outperform at the median the sample of all firms in terms of financial ratios related to profitability, liquidity, and market ratios, but have slightly lower liquidity and debt ratios. The Du Pont analysis shows that the higher return on equity for agribusinesses is mostly due to higher asset turnover ratios, indicating higher operating efficiency of agribusinesses. The strong financial performance of food manufacturing agribusinesses makes them valuable companies in an investment portfolio.Originality/valueThis study provides a basic overview of financial ratios used to examine the financial performance of publicly‐traded agribusinesses. The authors' findings show that agribusinesses outperform all firms in terms of key financial indicators.
Accounting for short samples and heterogeneous experience in rating crop insurance
Authors: Borman Julia I. , Goodwin Barry K. , Coble Keith H. , Knight Thomas O. , Rejesus Rod 
Published: April 2013

PurposeThe purpose of this paper is to be an academic inquiry into rating issues confronted by the US Federal Crop Insurance program stemming from changes in participation rates as well as the weighting of data to reflect longer‐run weather patterns.Design/methodology/approachThe authors investigate two specific approaches that differ from those adopted by the Risk Management Agency, building upon standard maximum likelihood and Bayesian estimation techniques that consider parametric densities for the loss‐cost ratio.FindingsBoth approaches indicate that incorporating weights into the priors for Bayesian estimation can inform the distribution.Originality/valueIn most cases, the authors' results indicate that including weighting into priors for Bayesian estimation implied lower premium rates than found using standard methods.
Determinants of the patronage refund decision of Farm Credit System associations
Authors: Zhang Tianwei , Mallory Mindy , Barry Peter 
Published: April 2013

PurposeThe authors aim to investigate what influences a Farm Credit System association to make a patronage refund payment. In particular, they seek to investigate what causes the regional heterogeneity in the patronage refund payment decision. It is unclear whether patronage refunds have been used more as a capital management tool or as a member recruitment and retention tool. This study aims to bring some clarity to this issue.Design/methodology/approachThe authors use an empirical logistic model to estimate the probability of a positive patronage refund payment by a Farm Credit System association, controlling for variables related to the associations' balance sheet as reported in the associations' quarterly call reports.FindingsThe authors find there is evidence that Farm Credit Service associations use patronage refunds as a capital management tool, at least in part. However, they also find that there are still significant regional differences in the patronage refund payment decision even after controlling for variables affecting the associations' balance sheet. The authors conclude that this likely represents member heterogeneity in preferences for patronage refunds versus a discounted interest rate.Originality/valueThe present study is one of the few empirical papers to examine a broad panel of financial cooperatives. Because of this, the authors' paper provides valuable insight into the aggregate behavior of Farm Credit Service associations, particularly into whether they use patronage refunds as a capital management tool, or as a marketing and retention tool.
Agricultural lending and early warning models of bank failures for the late 2000s Great Recession
Authors: Li Xiaofei , Escalante Cesar L. , Epperson James E. , Gunter Lewell F. 
Published: April 2013

PurposeThe late 2000s Great Recession led to a surge of bank failures in the USA with nearly 300 banks failing from 2009 to 2010. Recalling the farm crises of the 1980s where the farm sector was pinpointed as one of the major precursors of such crises, this study is an attempt to validate if the agricultural sector can once again be considered as a major instigator of the current financial crises.Design/methodology/approachAn early warning model is developed based on factors that may cause bank failures, with special attention given to the role of the agricultural lending portfolios of commercial banks. The model will have several time period versions that will determine the length of time prior to the actual bank bankruptcy declarations that early warning signals could be detected.FindingsThe empirical results indicate that credit exposure to the farm sector does not necessarily enhance a bank's tendency to fail or its probability of success or survival. This lends support to the reality that agricultural loan delinquency rates are consistently below the banks' overall loan delinquency rates, thus confirming that agricultural lenders are in relatively stronger financial health. This study instead finds that costly funding arrangements, increasing interest rate risk, and declining asset quality can be possible early warning signals that can be detected as far back as two or three years before eventual bank failure.Originality/valueThis study differentiates itself from previous studies by its special focus on the role of the agricultural finance industry in the ensuing economic crises. This study's early warning model also presents an extended version of previous empirical models as it accounts for measures of capital adequacy, asset quality, management risk, profitability, liquidity risk, loan portfolio composition and risk, funding arrangement, structural and macroeconomic variables.
Weather risk management by Saskatchewan agriculture producers
Authors: Khan Saqib , Rennie Morina , Charlebois Sylvain 
Published: April 2013

PurposeThe purpose of this research is to study the weather risk management practices of agriculture producers. In particular, the authors look at the extent to which farmers use weather derivatives to complement insurance. Unlike insurance, weather derivatives mitigate risk associated with low intensity, high probability events and therefore offer the potential of a more complete hedge than insurance alone.Design/methodology/approachThe authors conducted a survey of grain farmers in the province of Saskatchewan, Canada, a typical jurisdiction in which farmers tend to face weather events that are high in frequency but low in severity, to study the usage of weather derivatives compared to insurance and identify the hurdles to their usage.FindingsThe authors find that fewer than 10 percent of their respondents use weather derivatives. Consistent with previous literature in other contexts, they identify participation costs, especially lack of awareness, to be the most significant hurdle to their usage.Research limitations/implicationsA limitation of this study is that the data were collected using a survey methodology and are therefore subject to the usual risks of bias associated with that approach. Moreover, because the authors' survey was delivered online, it may have favoured the participation of farmers that were more comfortable with technology and some bias may have also been introduced into the data as a result.Practical implicationsThe authors' findings suggest that there is significant potential to improve farmers' ability to hedge weather risk and thereby improve economic outcomes if the major barriers to the usage of weather derivatives can be overcome. The study paves the way for further research to support the development of public policy strategies that could help farmers take advantage of weather derivatives as part of their inventory of risk management tools.Originality/valueTo the authors' knowledge this is the first study that quantifies the usage of weather derivatives by agriculture producers and identifies the hurdles.
Testing for speculative bubbles in agricultural commodity prices: a regime switching approach
Authors: Liu Xiaoliang , Filler Guenther , Odening Martin 
Published: April 2013

PurposeThe authors' paper aims to deal with the question whether speculative bubbles are present in agricultural commodity prices.Design/methodology/approachThe authors apply a regime switching regression model to test the hypothesis that agricultural prices contain periodically collapsing bubbles. Using daily futures prices for six agricultural commodities, the authors calculate net convenience yields from which price fundamentals are derived.FindingsThe authors discover pronounced deviations between observed prices and their fundamental values. However, they do not find evidence for the presence of periodically and partially collapsing speculative bubbles for five of six commodities. Except for soybeans, the signs and the significance of the estimated coefficients are not entirely in line with the predictions of the theoretical model.Originality/valueThe authors' study adds to the heated discussion on the impact of speculative behavior on agricultural commodity prices. So far, most contributions in the literature either use theoretical arguments for the (non‐) existence of bubbles or apply indirect tests which are plagued by low statistical reliability. In contrast, the authors apply a direct test. They find that the outcome of empirical bubble tests depends on the considered bubble type and on the testing procedure. In view of these ambiguities, definite statements on the presence of speculative bubbles as well as demands for limitations of speculative positions in commodity futures markets should be carefully reconsidered.
Damaged airplane flight envelope and stability evaluation
Authors: Asadi Davood , Sabzehparvar Mahdi , Talebi Heidar Ali 
Published: April 2013

PurposeUnderstanding the performance and flight envelope of a damaged aircraft is a preliminary requirement to recover the aircraft after damage. This paper aims to provide a comprehensive understanding of wing damage effect on airplane performance, local stability, and flying quality of each trim state inside the achievable flight envelope.Design/methodology/approachThis paper demonstrates the use of attainable equilibrium points which are referred as trim states in order to estimate a damaged airplane manoeuvring flight envelope using a numerical computation method.FindingsWing damaged airplane manoeuvring flight envelope is estimated for different portions of the wing tip loss. Local stability at each trim condition inside the estimated flight envelope is analysed, and also motion flight modes and flying quality sensitivity to the wing damage are explored.Originality/valueLocal stability and flying quality analysis at each trim condition inside the flight envelope which demonstrate the effect of damage provides a criterion to prioritize the choice of trimmed flight condition as motion primitives for the airplane post‐damage flight and safe landing.
Effect of power on PPT discharge current
Authors: Rezaeiha Abdolrahim 
Published: April 2013

PurposeThe purpose of this paper is to investigate the effect of power on pulsed plasma thruster (PPT) discharge current with respect to its peak, duration, and behavior while the power elevates in a low power range.Design/methodology/approachA rectangular parallel‐plate breech‐fed PPT has been developed with a self‐inductor coupling element connecting the PPT cathode to the ignitor plug cathode. The PPT has been operated in vacuum chamber at 10−6 mbar and its discharge current has been recorded using a Rogowski coil while input power has been changed by means of varying the capacitor voltage at given capacitance and frequency.FindingsThe analysis leads to elucidate the effects of input power on discharge current of a PPT employing a self‐inductor coupling element. The power varies within a range of less than 10 to more than 50 W. The results show that current peak rises from 5 to 10 kA while discharge duration and behavior seems to be independent of power within the operating range. Additionally, utilization of the coupling element seems to change the typical oscillating behavior of PPT discharge to a more efficient behavior.Research limitations/implicationsThe analysis is mainly focused on breech‐fed PPTs while employing a coupling element.Originality/valueThe paper analyzes the influence of power on discharge current of a PPT employing a self‐inductor coupling element. It clarifies the behavior of current peak, duration and behavior while power varies in a low power range. The effect of coupling element is shown to be promising. The results can be a help in design of μPPTs.