bluuebunny/crossref_metadata_2025 huggingface dataset:
The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition
Authors: Chang Pamela V. , Hao Liming , Offermanns Stefan , Medzhitov Ruslan
Published: January 2014

Significance

The mammalian intestines contain an enormous number of microorganisms within the lumen. Given the constant exposure to these microbes, the intestinal immune system has the difficult task of maintaining tolerance to commensal bacteria while remaining responsive to potential pathogens. The mechanisms by which this balance is achieved are relatively unknown. Here, we identify a bacterial metabolite, n-butyrate, that exerts immunomodulatory effects on intestinal macrophages and renders them hyporesponsive to commensals that reside in the colon. Our studies elucidate a possible mechanism that contributes to immune homeostasis in the intestines.
What Is Really Behavioral in Behavioral Health Policy? And Does It Work?
Authors: Galizzi Matteo M.
Published: January 2014

Across health systems, there is increasing interest in applying behavioral economics insights to health policy challenges. Policy decision makers have recently discussed a range of diverse health policy interventions that are commonly brought together under a behavioral umbrella. These include randomized controlled trials, comparison portals, information labels, financial incentives, sin taxes, and nudges. A taxonomy is proposed to classify such behavioral interventions. In the context of risky health behavior, each cluster of policies is then scrutinized under two respects: (i) What are its genuinely behavioral insights? (ii) What evidence exists on its practical effectiveness? The discussion highlights the main challenges in drawing a clear mapping between how much each policy is behaviorally inspired and its effectiveness.
AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data
Authors: Bao Lei , Pu Minya , Messer Karen
Published: January 2014

Motivation: Detection and quantification of the absolute DNA copy number alterations in tumor cells is challenging because the DNA specimen is extracted from a mixture of tumor and normal stromal cells. Estimates of tumor purity and ploidy are necessary to correctly infer copy number, and ploidy may itself be a prognostic factor in cancer progression. As deep sequencing of the exome or genome has become routine for characterization of tumor samples, in this work, we aim to develop a simple and robust algorithm to infer purity, ploidy and absolute copy numbers in whole numbers for tumor cells from sequencing data.

Results: A simulation study shows that estimates have reasonable accuracy, and that the algorithm is robust against the presence of segmentation errors and subclonal populations. We validated our algorithm against a panel of cell lines with experimentally determined ploidy. We also compared our algorithm with the well-established single-nucleotide polymorphism array-based method called ABSOLUTE on three sets of tumors of different types. Our method had good performance on these four benchmark datasets for both purity and ploidy estimates, and may offer a simple solution to copy number alteration quantification for cancer sequencing projects.

Availability and implementation: The R package absCNseq is available from http://biostats.mcc.ucsd.edu/files/absCNseq_1.0.tar.gz.

Contact:  kmesser@ucsd.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Optimization strategies for fast detection of positive selection on phylogenetic trees
Authors: Valle Mario , Schabauer Hannes , Pacher Christoph , Stockinger Heinz , Stamatakis Alexandros , Robinson-Rechavi Marc , Salamin Nicolas
Published: January 2014

Motivation: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution.

Results: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML. These techniques can also be applied to other likelihood-based phylogeny software. Our implementation scales well for large numbers of codons and/or species. It can therefore analyse substantially larger datasets than CodeML. We evaluated FastCodeML on different platforms and measured average sequential speedups of FastCodeML (single-threaded) versus CodeML of up to 5.8, average speedups of FastCodeML (multi-threaded) versus CodeML on a single node (shared memory) of up to 36.9 for 12 CPU cores, and average speedups of the distributed FastCodeML versus CodeML of up to 170.9 on eight nodes (96 CPU cores in total).

Availability and implementation:  ftp://ftp.vital-it.ch/tools/FastCodeML/.

Contact:  selectome@unil.ch or nicolas.salamin@unil.ch
CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data
Authors: Guan Daogang , Shao Jiaofang , Deng Youping , Wang Panwen , Zhao Zhongying , Liang Yan , Wang Junwen , Yan Bin
Published: January 2014

Summary: ChIP-seq technology provides an accurate characterization of transcription or epigenetic factors binding on genomic sequences. With integration of such ChIP-based and other high-throughput information, it would be dedicated to dissecting cross-interactions among multilevel regulators, genes and biological functions. Here, we devised an integrative web server CMGRN (constructing multilevel gene regulatory networks), to unravel hierarchical interactive networks at different regulatory levels. The newly developed method used the Bayesian network modeling to infer causal interrelationships among transcription factors or epigenetic modifications by using ChIP-seq data. Moreover, it used Bayesian hierarchical model with Gibbs sampling to incorporate binding signals of these regulators and gene expression profile together for reconstructing gene regulatory networks. The example applications indicate that CMGRN provides an effective web-based framework that is able to integrate heterogeneous high-throughput data and to reveal hierarchical ‘regulome’ and the associated gene expression programs.

Availability:  http://bioinfo.icts.hkbu.edu.hk/cmgrn; http://www.byanbioinfo.org/cmgrn.

Contact:  yanbinai6017@gmail.com or junwen@hku.hk

Supplementary Information:  Supplementary data are available at Bioinformatics online.
DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data
Authors: Cornuet Jean-Marie , Pudlo Pierre , Veyssier Julien , Dehne-Garcia Alexandre , Gautier Mathieu , Leblois Raphaël , Marin Jean-Michel , Estoup Arnaud
Published: January 2014

Motivation: DIYABC is a software package for a comprehensive analysis of population history using approximate Bayesian computation on DNA polymorphism data. Version 2.0 implements a number of new features and analytical methods. It allows (i) the analysis of single nucleotide polymorphism data at large number of loci, apart from microsatellite and DNA sequence data, (ii) efficient Bayesian model choice using linear discriminant analysis on summary statistics and (iii) the serial launching of multiple post-processing analyses. DIYABC v2.0 also includes a user-friendly graphical interface with various new options. It can be run on three operating systems: GNU/Linux, Microsoft Windows and Apple Os X.

Availability: Freely available with a detailed notice document and example projects to academic users at http://www1.montpellier.inra.fr/CBGP/diyabc

Contact:  estoup@supagro.inra.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
CasOT: a genome-wide Cas9/gRNA off-target searching tool
Authors: Xiao An , Cheng Zhenchao , Kong Lei , Zhu Zuoyan , Lin Shuo , Gao Ge , Zhang Bo
Published: January 2014

Summary: The CRISPR/Cas or Cas9/guide RNA system is a newly developed, easily engineered and highly effective tool for gene targeting; it has considerable off-target effects in cultured human cells and in several organisms. However, the Cas9/guide RNA target site is too short for existing alignment tools to exhaustively and effectively identify potential off-target sites. CasOT is a local tool designed to find potential off-target sites in any given genome or user-provided sequence, with user-specified types of protospacer adjacent motif, and number of mismatches allowed in the seed and non-seed regions.

Availability:  http://eendb.zfgenetics.org/casot/

Contact:  zfgenetics@gmail.com or bzhang@pku.edu.cn

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads
Authors: Schröder Jan , Hsu Arthur , Boyle Samantha E. , Macintyre Geoff , Cmero Marek , Tothill Richard W. , Johnstone Ricky W. , Shackleton Mark , Papenfuss Anthony T.
Published: January 2014

Motivation: Methods for detecting somatic genome rearrangements in tumours using next-generation sequencing are vital in cancer genomics. Available algorithms use one or more sources of evidence, such as read depth, paired-end reads or split reads to predict structural variants. However, the problem remains challenging due to the significant computational burden and high false-positive or false-negative rates.

Results: In this article, we present Socrates (SOft Clip re-alignment To idEntify Structural variants), a highly efficient and effective method for detecting genomic rearrangements in tumours that uses only split-read data. Socrates has single-nucleotide resolution, identifies micro-homologies and untemplated sequence at break points, has high sensitivity and high specificity and takes advantage of parallelism for efficient use of resources. We demonstrate using simulated and real data that Socrates performs well compared with a number of existing structural variant detection tools.

Availability and implementation: Socrates is released as open source and available from http://bioinf.wehi.edu.au/socrates.

Contact:  papenfuss@wehi.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bias from removing read duplication in ultra-deep sequencing experiments
Authors: Zhou Wanding , Chen Tenghui , Zhao Hao , Eterovic Agda Karina , Meric-Bernstam Funda , Mills Gordon B. , Chen Ken
Published: January 2014

Motivation: Identifying subclonal mutations and their implications requires accurate estimation of mutant allele fractions from possibly duplicated sequencing reads. Removing duplicate reads assumes that polymerase chain reaction amplification from library constructions is the primary source. The alternative—sampling coincidence from DNA fragmentation—has not been systematically investigated.

Results: With sufficiently high-sequencing depth, sampling-induced read duplication is non-negligible, and removing duplicate reads can overcorrect read counts, causing systemic biases in variant allele fraction and copy number variation estimations. Minimal overcorrection occurs when duplicate reads are identified accounting for their mate reads, inserts are of a variety of lengths and samples are sequenced in separate batches. We investigate sampling-induced read duplication in deep sequencing data with 500× to 2000× duplicates-removed sequence coverage. We provide a quantitative solution to overcorrection and guidance for effective designs of deep sequencing platforms that facilitate accurate estimation of variant allele fraction and copy number variation.

Availability and implementation: A Python implementation is freely available at https://bitbucket.org/wanding/duprecover/overview.

Contact: wzhou1@mdanderson.org, kchen3@mdanderson.org

Supplementary information: Supplementary data are available at Bioinformatics online.
Fine-scale gas distribution in marine sediments assessed from deep-towed seismic data
Authors: Ker S. , Le Gonidec Y. , Marsset B. , Westbrook G. K. , Gibert D. , Minshull T. A.
Published: January 2014

In the context of seismic imaging of gas/gas-hydrate systems, the fine-scale structure of subseabed gas-related reflections is assessed by taking advantage of the source signature of the deep-towed high-resolution SYSIF seismic device. We demonstrate the value of an original wavelet-based method and associated multiscale seismic attributes, applied to seismic data recently acquired on the western margin of the Arctic archipelago of Svalbard. From analysis in the wavelet domain, we recognize two types of gas-related reflections associated with submetre-scale distribution of gas. We identify a thin gas-charged layer associated with an apparent normal polarity reflection, and we detect gas patches associated with a reverse-polarity bright spot with frequency-dependent elastic properties at small seismic wavelengths. The results provide valuable information on the scale of features through which gas migrates and resolve ambiguities in the interpretation of the seismic data.
Impact of scallop dredging on benthic epifauna in a mixed-substrate habitat
Authors: Boulcott Philip , Millar Colin P. , Fryer Rob J.
Published: January 2014

Experimental scallop dredging was conducted to assess the vulnerability of emergent epifauna on hard substrates. Three sites were sampled before and after dredging to examine changes in the coverage of faunal turf (hydroid and bryozoan) assemblages and the composition of the wider epifaunal community. Each site had an “impact” box that was dredged, a control box that was in an area that was still open to fishing, and a control box in a special area of conservation (SAC) that had not been fished for two years. Community composition differed significantly after dredging in two of the three sites, with dredged communities becoming less similar to those in the SAC. There was no clear evidence that dredging in the impact boxes reduced the coverage of faunal turfs on hard substrates. However, the coverage of faunal turfs on hard substrates in the SAC was typically greater than in areas that were still being fished commercially, consistent with a dredging effect. The results highlight the role that substrate morphology might play in modifying the severity of dredging effects. This has relevance to marine spatial management, as it suggests that emergent epifauna living on hard substrates that are morphologically suited to dredging, such as pebble and cobble substrates, could be particularly vulnerable to dredging.
Density-dependence can be revealed by modelling the variance in the stock–recruitment process: an application to flatfish
Authors: Archambault B. , Le Pape O. , Bousquet N. , Rivot E.
Published: January 2014

Recruitment success in marine species is mostly driven by the high and variable mortality of first life stages, and the relationships between stock and recruitment are then largely dominated by residual variability. We show that analysing the residual variability may provide insights on the density-dependence process occurring during the recruitment. Following the seminal formulation of Minto et al. (Survival variability and population density in fish populations. Nature, 2008), we show that when recruitment is considered as a sequence of a pelagic stage with stochastic density-independent mortality followed by a second stage with stochastic density-dependent mortality, then the variability of the recruitment rate per spawning biomass (RPSB) should be a decreasing function of the spawning biomass. Using stock–recruit data of 148 stocks from the RAM legacy database, we provide a test of this hypothesis by showing that the variability of RPSB is lower for fish species with the higher concentration during juvenile stages. Second, a hierarchical Bayesian model (HBM) is built to derive a meta-analysis of stock–recruit data for 39 flatfish stocks, characterized by a high concentration of juveniles in coastal nursery habitats. Results of the HBM show that the variance of the RPSB decreases with the spawning biomass for almost all stocks, thus providing strong evidence of density-dependence during the recruitment process. Finally, we attempt to relate patterns in recruitment variance to relevant life-history traits of flatfish species.
The orientation and migratory dynamics of the western rock lobster, Panulirus cygnus, in Western Australia
Authors: de Lestang Simon
Published: January 2014

Large-scale migrations are known to occur in numerous species, and in the case of the Western Rock Lobster, Panulirus cygnus, result in juveniles moving from nursery areas into deeper offshore breeding grounds. In 2008 the Western Rock Lobster fishery reduced harvest rates to increase legal and spawning biomass throughout the fishery, which also allowed greater numbers of lobsters to migrate. Increased lobster migration could potentially reduce biomass in some areas, thus adversely impacting commercial catch rates. Over 20 000 tag–recaptured lobsters were analysed to determine the dynamics underlying migration in this species and to assess the impact reduced harvest rates may have had on catches. This study showed that P. cygnus migration was associated with body size and water depth, and that magnetism and oceanic currents appear to be the most likely guideposts used for orientation. Size at migration varied in a constant fashion along the coast, being larger towards the southern end of the fishery and smallest at the offshore Abrolhos Islands. During the migration period, up to 50% of lobsters at their mean size of migration moved from coastal areas out towards deeper waters (>40 m), whereas <15% of those in deeper water at the same size moved significant distances northward. This behaviour appears to be contranatant, counteracting the downstream redistribution of larvae after their 9–11 month larval life. Reduced harvest rates and catches being focussed onto higher valued sedentary lobsters have allowed more lobsters to migrate. However, the numbers moving between management areas are relatively small, with the biological and economic benefits of fishing at a reduced exploitation rate outweighing losses to catches.
Weak lensing with 21 cm intensity mapping at z ∼ 2–3
Authors: Pourtsidou A. , Metcalf R. Benton
Published: January 2014

We study how 21 cm intensity mapping can be used to measure gravitational lensing over a wide range of redshift. This can extend weak lensing measurements to higher redshifts than are accessible with conventional galaxy surveys. We construct a convergence estimator taking into account the discreteness of galaxies and calculate the expected noise level as a function of redshift and telescope parameters. At z ∼ 2–3, we find that a telescope array with a collecting area ∼0.2 km2 spread over a region with diameter ∼2 km would be sufficient to measure the convergence power spectrum to high accuracy for multipoles between 10 and 1000. We show that these measurements can be used to constrain interacting dark energy models.
Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing
Authors: Kunde-Ramamoorthy Govindarajan , Coarfa Cristian , Laritsky Eleonora , Kessler Noah J. , Harris R. Alan , Xu Mingchu , Chen Rui , Shen Lanlan , Milosavljevic Aleksandar , Waterland Robert A.
Published: January 2014

Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitative accuracy has been reported. We sequenced bisulfite-converted DNA from two tissues from each of two healthy human adults and systematically compared five widely used Bisulfite-seq mapping algorithms: Bismark, BSMAP, Pash, BatMeth and BS Seeker. We evaluated their computational speed and genomic coverage and verified their percentage methylation estimates. With the exception of BatMeth, all mappers covered >70% of CpG sites genome-wide and yielded highly concordant estimates of percentage methylation (r2 ≥ 0.95). Fourfold variation in mapping time was found between BSMAP (fastest) and Pash (slowest). In each library, 8–12% of genomic regions covered by Bismark and Pash were not covered by BSMAP. An experiment using simulated reads confirmed that Pash has an exceptional ability to uniquely map reads in genomic regions of structural variation. Independent verification by bisulfite pyrosequencing generally confirmed the percentage methylation estimates by the mappers. Of these algorithms, Bismark provides an attractive combination of processing speed, genomic coverage and quantitative accuracy, whereas Pash offers considerably higher genomic coverage.
Beyond species: why ecological interaction networks vary through space and time
Authors: Poisot T. , Stouffer D.B. , Gravel D.
Published: January 2014

Community ecology is tasked with the considerable challenge of predicting the structure, and properties, of emerging ecosystems. It requires the ability to understand how and why species interact, as this will allow the development of mechanism-based predictive models, and as such to better characterize how ecological mechanisms act locally on the existence of interspecific interactions. Here we argue that the current conceptualization of species interaction networks is ill-suited for this task. Instead, we propose that future research must start to account for the intrinsic variability of species interactions, then scale up from here onto complex networks. This can be accomplished simply by recognizing that there exists intra-specific variability, in traits or properties related to the establishment of species interactions. By shifting the scale towards population-based processes, we show that this new approach will improve our predictive ability and mechanistic understanding of how species interact over large spatial or temporal scales.
Genomic analysis of primordial dwarfism reveals novel disease genes
Authors: Shaheen Ranad , Faqeih Eissa , Ansari Shinu , Abdel-Salam Ghada , Al-Hassnan Zuhair N. , Al-Shidi Tarfa , Alomar Rana , Sogaty Sameera , Alkuraya Fowzan S.
Published: January 2014

Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in defining clinical subgroups. In this study, we present the results of clinical and genomic characterization of 16 new patients in whom a broad definition of PD was used (e.g., 3M syndrome was included). We report a novel PD syndrome with distinct facies in two unrelated patients, each with a different homozygous truncating mutation in CRIPT. Our analysis also reveals, in addition to mutations in known PD disease genes, the first instance of biallelic truncating BRCA2 mutation causing PD with normal bone marrow analysis. In addition, we have identified a novel locus for Seckel syndrome based on a consanguineous multiplex family and identified a homozygous truncating mutation in DNA2 as the likely cause. An additional novel PD disease candidate gene XRCC4 was identified by autozygome/exome analysis, and the knockout mouse phenotype is highly compatible with PD. Thus, we add a number of novel genes to the growing list of PD-linked genes, including one which we show to be linked to a novel PD syndrome with a distinct facial appearance. PD is extremely heterogeneous genetically and clinically, and genomic tools are often required to reach a molecular diagnosis.
Transcriptome analysis reveals novel players in the cranial neural crest gene regulatory network
Authors: Simões-Costa Marcos , Tan-Cabugao Joanne , Antoshechkin Igor , Sauka-Spengler Tatjana , Bronner Marianne E.
Published: January 2014

The neural crest is an embryonic stem cell population that gives rise to a multitude of derivatives. In particular, the cranial neural crest (CNC) is unique in its ability to contribute to both facial skeleton and peripheral ganglia. To gain further insight into the molecular underpinnings that distinguish the CNC from other embryonic tissues, we have utilized a CNC-specific enhancer as a tool to isolate a pure, region-specific NC subpopulation for transcriptional profiling. The resulting data set reveals previously unknown transcription factors and signaling pathways that may influence the CNC's ability to migrate and/or differentiate into unique derivatives. To elaborate on the CNC gene regulatory network, we evaluated the effects of knocking down known neural plate border genes and early neural crest specifier genes on selected neural crest-enriched transcripts. The results suggest that ETS1 and SOX9 may act as pan-neural crest regulators of the migratory CNC. Taken together, our analysis provides unprecedented characterization of the migratory CNC transcriptome and identifies new links in the gene regulatory network responsible for development of this critical cell population.
Heterologous Expression of Methylketone Synthase1 and Methylketone Synthase2 Leads to Production of Methylketones and Myristic Acid in Transgenic Plants
Authors: Yu Geng , Pichersky Eran
Published: January 2014

Some plants produce methylketones as potent defense compounds against various insects. Wild tomato (Solanum habrochaites), a relative of the cultivated tomato (Solanum lycopersicum), synthesizes large amounts of 2-methylketones in its glandular trichomes, but cultivated tomato trichomes contain little or no methylketones. Two enzymes, Solanum habrochaites methylketone synthase1 (ShMKS1) and ShMKS2, are required to convert β-ketoacyl acyl-carrier protein intermediates of the fatty acid biosynthetic pathway to methylketones. ShMKS2 is a thioesterase that hydrolyzes β-ketoacyl acyl-carrier protein, and ShMKS1 is a decarboxylase that converts the resulting 3-ketoacids to 2-methylketones. We introduced ShMKS2 by itself or together with ShMKS1 to Arabidopsis (Arabidopsis thaliana), tobacco (Nicotiana tabacum), and cultivated tomato under the control of the 35S, Rubisco small subunit, and tomato trichome-specific promoters. Young tobacco and Arabidopsis plants expressing both genes under the control of 35S and Rubisco small subunit promoters produced methylketones in their leaves but had serious growth defects. As plants matured, they ceased to produce methylketones. Tobacco plants but not Arabidopsis or tomato plants expressing only ShMKS2 under the 35S promoter also synthesized methylketones, but at a lower rate. Transgenic cultivated tomato plants expressing ShMKS1 and ShMKS2 under trichome-specific promoters had slightly elevated levels of methylketone. Trace amounts of myristic acid were also detected in transgenic plants constitutively expressing ShMKS2 with or without ShMKS1. These results suggest that increases in methylketone production in plants will require the targeting of the pathway to self-contained structures in the plant and may also require increasing the flux of fatty acid biosynthesis.
Determinants of Unemployment in Ghana
Authors: Baah‐Boateng William
Published: January 2014

Unemployment is often cited as a measure of the low employment content of Ghana's strong growth performance over the past three decades. The paper presents evidence to suggest that employment growth in Ghana continues to trail economic growth due to high growth of low employment generating sectors against sluggish growth of high labour absorption sectors. A cross‐sectional estimation of a probit regression model also indicates a strong effect of demand factors on unemployment, indicating a weak employment generating impact of economic growth. Empirical analysis also confirms higher vulnerability of youth and urban dwellers to unemployment with education and gender explaining unemployment in some instances. Reservation wage is also observed to have an increasing effect of unemployment. The paper recommends policies that promote investment in agriculture and manufacturing which is associated with higher employment elasticity of output. High incidence of unemployment among the youth and secondary school leavers in the most recent period requires targeted intervention including support for entrepreneurial training and start‐up capital to attract young school leavers to become ‘creators’ rather than ‘seekers’ of jobs. A downward review of expectations on the part of jobseekers in terms of their reservation wage could help reduce unemployment in Ghana.
Gender Equality in Employment in Africa: Empirical Analysis and Policy Implications
Authors: Anyanwu John C. , Augustine Darline
Published: January 2014

Gender equality in employment is currently one of the greatest development challenges facing countries globally, including those in Africa. In 2011, the male employment‐to‐population ratio, globally, was estimated at about 72.7 per cent compared to the female employment‐to‐population ratio of only 47.9 per cent. For Africa as a whole, the male employment‐to‐population ratio was estimated at about 69.2 per cent compared to the female employment‐to‐population ratio of only 39.2 per cent. In addition to analysing the characteristics of gender equality in employment in Africa, this paper empirically studies the key drivers of gender equality in employment (proxied by the ratio of female employment rate to male employment rate for the age group 15–64 over the period, 1991 and 2009), using cross‐sectional data. Our results suggest that for the all‐Africa and sub‐Saharan African samples, increased democracy (and its quadratic form), higher gross domestic investment, more primary education, and higher urban share of the population increase gender equality in employment while higher level of real GDP per capita, higher foreign direct investment, sex population ratio, and being a net oil‐exporting country tend to lower it. However, North Africa is different. Apart from a negative and highly significant North African dummy in the overall results, the North African specific sample result indicates that while the quadratic element of real GDP per capita, higher gross domestic investment, higher urban share of the population, more secondary education, and being an oil‐exporting country increase gender equality in employment, higher levels of real GDP per capita, more primary education, and sex population ratio tend to lower gender equality in employment in the sub‐region. The policy implications and lessons of these results are discussed. These policies are directed at making the African labor market more inclusive and hence enhancing women's employment for the purpose of greater economic empowerment, household welfare and poverty reduction, in particular.
FDI, Employment and Economic Growth in Nigeria
Authors: Inekwe John Nkwoma
Published: January 2014

The study examines the links between Nigerian economic growth, employment and foreign direct investment (FDI) in the manufacturing and servicing sectors between 1990 and 2009. The significant results of the Johansen cointegration technique and the vector error correction model reveal that FDI in the servicing sector has a positive relationship with economic growth while FDI in the manufacturing sector has a negative relationship. FDI in the manufacturing sector has a positive relationship with employment rate while FDI in the servicing sector has a negative relationship with employment rate. Granger causal relationships among these variables exist. In the growth equation, causality runs from growth to FDI in the service sector while growth and FDI in the manufacturing sector have bidirectional causal effect. For the employment equation, unidirectional causality runs from FDI in the service and manufacturing sectors to employment rate.
Household Economic Well‐being: Response to Micro‐Credit Access in Cameroon
Authors: Baye Francis Menjo
Published: January 2014

This paper evaluates the determinants of borrowing, effects of borrowing on economic well‐being, and potential disparity in responses by sources of well‐being, location and gender, while controlling for other correlates. The 2001 Cameroon household consumption survey and a range of survey‐based econometric methods that purge parameter estimates of potential intra‐cluster correlation, endogeneity and sample selection biases were used. Access to credit/borrowing is strongly associated with household economic well‐being irrespective of source of well‐being. Rural well‐being is significally more contingent on credit access than urban well‐being. Male‐headed households rely more significantly on credit access to enhance well‐being than their female counterparts. Higher levels of education associate more significantly with well‐being enhancement than lower levels, more so for female‐headed households than their male counterparts. To sustain the impact of credit on well‐being, accompanying measures — availability of sufficient funds, quality services by lenders, physical infrastructures, healthcare and training — are required. These findings are useful in the context of economic recovery and poverty reduction under the current situation in Cameroon, where financial intermediation is limited and penetration is shallow. To better serve the needs of the economically active poor, a microfinance delivery model is proposed.
Budget Deficits, Money Growth and Price Level in Nigeria
Authors: Chukwu Jude Okechukwu
Published: January 2014

The study investigates the long‐run causal relationship amongst budget deficits, money growth and price level for Nigeria between 1971 and 2008 inclusive. The empirical findings predict a long‐term cointegrating relationship with unidirectional causality running from budget deficit to money supply growth and then from money supply growth to price level in the Toda and Yamamoto () sense. Thus, the Sargent and Wallace () ‘Unpleasant Monetarist Arithmetic’ hypothesis holds for Nigeria.
African Emerging Equity Markets Re‐examined: Testing the Weak Form Efficiency Theory
Authors: Nwosu Emmanuel O. , Orji Anthony , Anagwu Ogomegbunam
Published: January 2014

This paper examines the weak form of market efficiency of five major stock markets; four African equity markets and one developed market. The weekly market index returns of the EGX 30, NSE 20, NSE All Share Index, FTSE‐JSE All Share Index and the S&P 500 Index were analysed for the period 1998–2008. To determine if the stylized fact of stock returns in African markets violate the random walk hypothesis, numerous econometric and statistical techniques are employed. These methods include the autocorrelation test, the unit test, linear and non‐linear models. The results indicate that the African markets do not behave in a manner consistent with the weak form of market efficiency. These results provide a contrast between the emerging African markets and the developed markets. It suggests that African emerging markets have higher average returns and volatility than developed markets. We argue that if the market could be made less volatile, it has the potential to attract more investment because of its attractive returns.
Relative Profitability of Cassava‐based Mixed Cropping Systems among Various Production Scale Operators in Ogun and Oyo States Southwest Nigeria
Authors: Obayelu A. E. , Afolami C. A. , Agbonlahor M. U.
Published: January 2014

Cassava is a very important crop in Nigeria by reason of its comparative production advantage over other staples. This study estimated the relative profitability of cassava producers and determined the effects of farm inputs on the level of profit of various scales of cassava producers in Ogun and Oyo States, Nigeria. Cross‐sectional data were collected from 265 cassava‐based farmers using a multistage sampling technique and were analysed using normalized profit function and budgetary analysis. Results showed that cassava/cowpea enterprise had the highest net margins of 127,249.63/ha and 122,325.73/ha in Ogun and Oyo States respectively. While the use of herbicides had a positive and significant effect on the profitability of small‐scale cassava farmers in both states, cassava‐cuttings had a positive and significant effect on medium‐scale cassava farming in both states. Similarly, labour and farm size had a positive and significant effect on large‐scale cassava farming in both states. The study recommends that small and medium‐scale farmers should increase the application of herbicide, large‐scale cassava operators in Oyo State should increase the use of labour, while those in Ogun State should also increase the cultivated acreage of land.
Competitive Conditions of the Tunisian Banking Industry: An Application of the Panzar–Rosse Model
Authors: Abdelkader Ines Ben , Mansouri Faysal
Published: January 2014

This study employs the Panzar–Rosse H‐statistic to assess the competitive conditions of the Tunisian banking industry over the period 1999 to 2003. The results show that the banking market is in long‐run equilibrium and the Panzar–Rosse H‐statistic indicates that the Tunisian banking market is operating under conditions of monopoly. It seems therefore that the liberalization process and the reforms implemented since 1987 to the banking sector could not compensate, for the period under study, the existence of market power in this sector.
Financial Development and Economic Growth in the North African Region
Authors: Kouki Imen , Harrathi Nizar
Published: January 2014

This paper empirically investigates the relationship between financial development and economic growth in the North Africa region, using a panel regression and different indicators of financial development. We find that the relation depends on the type of the indicator of financial development. In fact, while both financial institutions and markets in Morocco and Tunisia have a positive effect on the economic growth, only the financial markets in Egypt will improve economic growth by increasing the supply of financial services. For Algeria, the banking system has a positive effect on economic growth.
Water Habits and Hygiene Education to Prevent Diarrhoeal Diseases: The Zambezi River Basin in Mozambique
Authors: González‐Gómez Francisco , Lluch‐Frechina Enrique , Guardiola Jorge
Published: January 2014

This research analyses the relationship between certain water‐related habits and infrastructure likely to influence the frequency of diarrhoea in children that are five years old or younger. The study is implemented using an ordered logit model with information from 334 households from the Zambezi river in Mozambique, with children who were aged up to five years. The main objective of this paper is to emphasize the importance of hygiene education in the prevention of gastrointestinal diseases in children, that are affected by poor access to water systems and sanitation. Maintaining hygiene is especially important in households with young children, who are more vulnerable to gastrointestinal diseases. The results of the research reveal that in households that do not know that water transmits illnesses and where they do not wash their hands before preparing a child's meal, the children suffer diarrhoea more frequently. The main recommendation is to invest in hygiene education programmes to reduce the risk of illnesses such as diarrhoea. Improvements in access to water and sanitation may not be sufficient in order to improve life conditions if there is no hygiene education.
On the Determinants of Investment in Sub‐Saharan African Manufacturing Firms
Authors: Foster‐McGregor Neil
Published: January 2014

Investment is a crucial factor determining economic performance at the firm as well as the country level. In this paper I identify the determinants of the decision to invest in new plant and equipment as well as the determinants of the level of such investment for a sample of firms in 19 sub‐Saharan African countries. In particular, I concentrate on the role of property rights, external finance, trade status and firm ownership on investment. Results indicate that internationally trading firms, foreign owned firms and firms with better access to sources of external finance tend to be more likely to invest and to invest more, with little role for indicators of property rights in influencing investment decisions found.
Assessing the Short‐ and Long‐run Real Effects of Public External Debt: The Case of Tunisia
Authors: Mohamed Ben Mimoun
Published: January 2014

This study examines the effects of external debt on the economic growth of Tunisia both in the short run and the long run. We specify a growth equation based on the standard neoclassical growth model that we extend by adding public external debt indicators and some control variables. Annual time series data was gathered from 1970 to 2010. The Engel and Granger (1987) econometric techniques are employed in the empirical analysis in order to regress an error correction model (ECM) which allows estimating the short‐ and long‐run consequences of debt on the Tunisian economic growth. The main results of this analysis can be summarized as follows: (1) Although the ratio of public external debt to GDP is relatively low in this country, the levels of external debt achieved are growth‐damaging. We estimate that, on average, a 1 percentage point increase in the ratio of public external debt reduced annual growth rate by 0.15–0.17 percentage points. The impact is much higher in the long run in the sense that the long‐run level of GDP per capita decreases by 0.27 per cent as this ratio increases by 1 per cent. (2) Our results also identified the existence, for Tunisia, of a threshold for the impact of external debt, which is evidence in agreement with the ‘debt overhang’ phenomenon. This threshold is estimated to around 30 per cent of GDP. (3) The traditional ‘crowding‐out effect’ associated with service and interest payments of debt as well as the ‘resources‐diversion effect’ associated with the extent of corruption in this country have been put forward in this analysis as two possible transmission channels of the detrimental consequences of external debt. (4) Finally, Tunisia will need to implement drastic policy changes that reduce fiscal deficit in order to prevent further deterioration.
Trade Policy Inconsistency and Maize Price Volatility: An ARCH Approach in Kenya
Authors: d'Hôtel Elodie Maître , Le Cotty Tristan , Jayne Thom
Published: January 2014

The 2007–2008 food crisis and current food price swings led economists to re‐evaluate the potential for policy instruments to manage food price volatility, including tariff policy. The use of tariffs in importing countries to stabilize price is theoretically not recommended because of its domestic and international costs but in practice many countries use import tariffs with the intention to stabilize their domestic prices. Among them, some achieve price stabilization, some do not. We address the reason why it sometimes works, sometimes not. In the context of Kenya, we show that while domestic price levels are mainly explained by seasonal cycles, and international prices, domestic price volatility is mainly explained by inconsistent moves of trade policy. Thus, the ability of a policy regime to lower food price volatility does not depend on the nature of the policy instrument only, but also on the government ability to implement it. We define a consistent policy adjustment as a tariff decrease when world price increases and a tariff increase when world price is decreasing. We use an autoregressive conditionally heteroscedastic model of price determination in which prices and prices volatility are jointly estimated, using monthly data over the 1994–2009 period in Kenya.
An Overview of the Repo Rate in an Inflation Targeting Economy
Authors: Fadiran Gideon O. , Edun Adebisi
Published: January 2014

This paper compares the use of repo rate in South Africa during the pre‐repo and repo system by trending and comparing the interest rate fluctuations between two selected periods of 1990–1998 and 1998–2010. Using a structural vector autoregressive (SVAR) econometric method to determine the relationship between the repo rate and other selected key macroeconomic variables in South Africa, an improved monetary efficiency was found during the repo period, which can be attributed to the use of an inflation‐targeting framework. This is important as it provides a guide to policymakers on how effective the current monetary tool is, and how efficient the South African Reserve Bank (SARB) is in influencing the interbank rate, retail rates and inflation during selective periods.
Assessing child welfare under the Human Fertilisation and Embryology Act 2008: a case study in medicalisation?
Authors: Lee Ellie , Macvarish Jan , Sheldon Sally
Published: January 2014

This article reports on a study with staff working in assisted conception clinics in the UK about making welfare of the child (WOC) assessments pre‐conception. This aspect of infertility treatment is obligatory under section 13(5) of the Human Fertilisation and Embryology Act, which was amended in 2008. The aim of the study was to find out how this change to the law had impacted on practice. In describing what we found, we also make a contribution to scholarship about the medicalisation of reproduction. S13(5) has often been discussed as a prime example of medicalisation, giving clinics power to grant or deny access to treatment on child welfare grounds, encompassing far more than purely clinical considerations. Yet, while such medicalisation may be entrenched in the law, our findings suggest this power is used with a very light touch. Further, while our interviewees offered near‐universal support for the need to consider child welfare, this is now justified by concerns that address not only family form (e.g. the need for a father figure) but also the quality of interactions between parents and children. In this light we suggest that the concept of medicalisation may offer a rather blunt tool for understanding a far more complex reality.
The Cronobacter sp. in milk and dairy products: Detection and typing
Authors: Ye Yingwang , Li Hui , Wu Qingping , Zhang Jumei , Lu Yudong
Published: January 2014

Cronobacter is a group of important foodborne pathogens that have been implicated in meningitis, sepsis and necrotising enterocolitis, especially in neonates through consumption of contaminated powdered infant formula (PIF). The detection of PIF contamination is of great concern to the infant formula industry. In this article, phenotypic and genotypic methods for detecting and typing Cronobacter are discussed in relation to minimising and controlling the risk of Cronobacter sp. contamination. To reliably detect and type Cronobacter strains, the use of conventional microbiological methods in combination with molecular assays is recommended.
Autolysis detection and evaluation of some lactic acid bacteria by renaturing sodium dodecyl sulphate‐polyacrylamide gel electrophoresis and polymerase chain reaction assays
Authors: Al‐Saleh Abdulrahman A , Ismail Elsayed A , Metwalli Ali Am
Published: January 2014

Eleven lactic acid bacterial strains were tested for autolysis ability and the presence of autolytic enzymes by renaturing sodium dodecyl sulphate‐polyacrylamide gel electrophoresis (SDS‐PAGE). Polymerase chain reaction (PCR) assays for the detection of lysogenic strains were performed. Autolysis in a buffer system was observed in Lactobacillus delbrueckii subsp. bulgaricus DSM 20080, L. delbrueckii subsp. bulgaricus DSM 20081, Bifidobacterium longum subsp. infantis DSM 20088, B. angulatum DSM 20098 and Streptococcus thermophillus DSM 20617. Mitomycin C induction of prophage was demonstrated in B. longum subsp. infantis DSM 20088, B. angulatum DSM 20098, Lactobacillus acidophilus DSM 20242 and S. thermophillus DSM 20617. The presence of genes encoding known bacteriophage lysins was demonstrated by a PCR assay and correlated well with the autolytic phenotypes of the strains, indicating that PCR screening is useful in the rapid identification of autolytic strains.