bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in the concentration of organic acids in roots and leaves of carob-tree under Fe deficiency
Authors: Correia Pedro José , Gama Florinda , Saavedra Teresa , Miguel Maria Graça , Paulo Da Silva José , Abadía Anunciación , de Varennes Amarilis , Pestana Maribela
Published: January 2014

Several fruit trees are able to cope with iron (Fe) deficiency when grown in calcareous soils in the Mediterranean region, although information regarding well adapted slow-growing species is scarce, and the mechanisms activated by these species are not described in the literature. A crucial issue related to tolerance is the need to transport Fe over relatively long distances inside the plant. To evaluate the possible role of organic acids in the movement of Fe in tolerant plants, we studied the concentration of low molecular weight organic acids in several organs of 1-year old carob plants grown for 55 days in nutrient solutions without Fe (0 µM Fe) or with 1 µM Fe and 10 µM Fe. Roots, stems and leaves were harvested, and the biomass, Fe and organic acid contents quantified. Total leaf chlorophyll (Chl) was evaluated in young leaves over the experimental period and the activity of root ferric chelate-reductase (FC-R; EC 1.16.1.17) was determined after 35 days, when deficiency symptoms appeared. Iron chlorosis was observed only at the end of the experiment in plants grown in the absence of Fe, and these plants had a smaller DW of leaves and also significant greater activity of root FC-R. Iron deficiency (Fe0 and Fe1 treatments) induced significant changes in the concentrations of succinic, malic, citric and fumaric acids, which increased in roots, or in basal, middle and apical leaves. There were significant correlations between most organic acids (with the exceptions of 2-oxoglutaric and tartaric acids) and leaf Chl. Analysis of each type of leaf showed that more succinic and malic acids were present in young chlorotic leaves while the reverse was true for quinic acid. These changes in organic acids followed a root-to-foliage pathway that was similar in all leaf types and particularly evident in young chlorotic leaves. We hypothesised that it was associated with Fe transport from roots to aboveground tissues, as there were significant differences in Fe contents between treatments with and without Fe.
More fertile florets and grains per spike can be achieved at higher temperature in wheat lines with high spike biomass and sugar content at booting
Authors: Dreccer M. Fernanda , Wockner Kimberley B. , Palta Jairo A. , McIntyre C. Lynne , Borgognone M. Gabriela , Bourgault Maryse , Reynolds Matthew , Miralles Daniel J.
Published: January 2014

An understanding of processes regulating wheat floret and grain number at higher temperatures is required to better exploit genetic variation. In this study we tested the hypothesis that at higher temperatures, a reduction in floret fertility is associated with a decrease in soluble sugars and this response is exacerbated in genotypes low in water soluble carbohydrates (WSC). Four recombinant inbred lines contrasting for stem WSC were grown at 20/10°C and 11 h photoperiod until terminal spikelet, and then continued in a factorial combination of 20/10°C or 28/14°C with 11 h or 16 h photoperiod until anthesis. Across environments, High WSC lines had more grains per spike associated with more florets per spike. The number of fertile florets was associated with spike biomass at booting and, by extension, with glucose amount, both higher in High WSC lines. At booting, High WSC lines had higher fixed 13C and higher levels of expression of genes involved in photosynthesis and sucrose transport and lower in sucrose degradation compared with Low WSC lines. At higher temperature, the intrinsic rate of floret development rate before booting was slower in High WSC lines. Grain set declined with the intrinsic rate of floret development before booting, with an advantage for High WSC lines at 28/14°C and 16 h. Genotypic and environmental action on floret fertility and grain set was summarised in a model.
Soil water availability influences the temperature response of photosynthesis and respiration in a grass and a woody shrub
Authors: Joseph Tony , Whitehead David , Turnbull Matthew H.
Published: January 2014

Seedlings of the shrub kānuka (Kunzea ericoides var. ericoides (A. Rich) J. Thompson) and the pasture grass brown top (Agrostis capillarus L.) were grown in intact soil cores in climate-controlled cabinets to analyse the thermal response of leaf-level carbon exchange at four levels of volumetric soil water content (θ). The objective was to resolve the combined effects of relatively rapid and short-term changes in θ and temperature on the thermal responses of both photosynthesis and respiration in these two contrasting plant types. Results showed that θ had a greater effect on the short-term temperature response of photosynthesis than the temperature response of respiration. The optimum value of θ for net photosynthesis was around 30% for both plants. The photosynthetic capacity of kānuka and the grass declined significantly when θ fell below 20%. The temperature sensitivity of photosynthesis was low at low soil water content and increased at moderate to high soil water content in both plant types. Statistical analysis showed that the temperature sensitivity of photosynthetic parameters was similar for both plant types, but the sensitivity of respiratory parameters differed. Respiratory capacity increased with increasing soil water content in kānuka but declined significantly when θ fell below 15%. There was no significant influence of soil water content on respiratory capacity in the grass. Collectively, our results indicate that θ influenced the temperature sensitivity of photosynthesis and respiration, and altered the balance between foliar respiration and photosynthetic capacity in both plant types.
Oxygen-regulated gene expression in murine cumulus cells
Authors: Kind Karen L. , Tam Kimberley K. Y. , Banwell Kelly M. , Gauld Ashley D. , Russell Darryl L. , Macpherson Anne M. , Brown Hannah M. , Frank Laura A. , Peet Daniel J. , Thompson Jeremy G.
Published: January 2014

Oxygen is an important component of the environment of the cumulus–oocyte complex (COC), both in vivo within the ovarian follicle and during in vitro oocyte maturation (IVM). Cumulus cells have a key role in supporting oocyte development, and cumulus cell function and gene expression are known to be altered when the environment of the COC is perturbed. Oxygen-regulated gene expression is mediated through the actions of the transcription factors, the hypoxia-inducible factors (HIFs). In the present study, the effect of oxygen on cumulus cell gene expression was examined following in vitro maturation of the murine COC at 2%, 5% or 20% oxygen. Increased expression of HIF-responsive genes, including glucose transporter-1, lactate dehydrogenase A and BCL2/adenovirus E1B interacting protein 3, was observed in cumulus cells matured at 2% or 5%, compared with 20% oxygen. Stabilisation of HIF1α protein in cumulus cells exposed to low oxygen was confirmed by western blot and HIF-mediated transcriptional activity was demonstrated using a transgenic mouse expressing green fluorescent protein under the control of a promoter containing hypoxia response elements. These results indicate that oxygen concentration influences cumulus cell gene expression and support a role for HIF1α in mediating the cumulus cell response to varying oxygen.
Engineered antibody fragments for immuno-PET imaging of endogenous CD8
+
T cells in vivo
Authors: Tavaré Richard , McCracken Melissa N. , Zettlitz Kirstin A. , Knowles Scott M. , Salazar Felix B. , Olafsen Tove , Witte Owen N. , Wu Anna M.
Published: January 2014

Significance

Anti-CD8 immuno-PET imaging agents provide the potential to monitor the localization, migration, and expansion of CD8-expressing cells noninvasively in vivo. Shown here is the successful generation of functional anti-CD8 imaging agents based on engineered antibodies for use in a variety of preclinical disease and immunotherapeutic models.
Estimation of fluorescence-tagged RNA numbers from spot intensities
Authors: Häkkinen Antti , Kandhavelu Meenakshisundaram , Garasto Stefania , Ribeiro Andre S.
Published: January 2014

Motivation: Present research on gene expression using live cell imaging and fluorescent proteins or tagged RNA requires accurate automated methods of quantification of these molecules from the images. Here, we propose a novel automated method for classifying pixel intensities of fluorescent spots to RNA numbers.

Results: The method relies on a new model of intensity distributions of tagged RNAs, for which we estimated parameter values in maximum likelihood sense from measurement data, and constructed a maximum a posteriori classifier to estimate RNA numbers in fluorescent RNA spots. We applied the method to estimate the number of tagged RNAs in individual live Escherichia coli cells containing a gene coding for an RNA with MS2-GFP binding sites. We tested the method using two constructs, coding for either 96 or 48 binding sites, and obtained similar distributions of RNA numbers, showing that the method is adaptive. We further show that the results agree with a method that uses time series data and with quantitative polymerase chain reaction measurements. Lastly, using simulated data, we show that the method is accurate in realistic parameter ranges. This method should, in general, be applicable to live single-cell measurements of low-copy number fluorescence-tagged molecules.

Availability and implementation: MATLAB extensions written in C for parameter estimation and finding decision boundaries are available under Mozilla public license at http://www.cs.tut.fi/%7ehakkin22/estrna/.

Contact:  andre.ribeiro@tut.fi
Inference with viral quasispecies diversity indices: clonal and NGS approaches
Authors: Gregori Josep , Salicrú Miquel , Domingo Esteban , Sanchez Alex , Esteban Juan I. , Rodríguez-Frías Francisco , Quer Josep
Published: January 2014

Given the inherent dynamics of a viral quasispecies, we are often interested in the comparison of diversity indices of sequential samples of a patient, or in the comparison of diversity indices of virus in groups of patients in a treated versus control design. It is then important to make sure that the diversity measures from each sample may be compared with no bias and within a consistent statistical framework. In the present report, we review some indices often used as measures for viral quasispecies complexity and provide means for statistical inference, applying procedures taken from the ecology field. In particular, we examine the Shannon entropy and the mutation frequency, and we discuss the appropriateness of different normalization methods of the Shannon entropy found in the literature. By taking amplicons ultra-deep pyrosequencing (UDPS) raw data as a surrogate of a real hepatitis C virus viral population, we study through in-silico sampling the statistical properties of these indices under two methods of viral quasispecies sampling, classical cloning followed by Sanger sequencing (CCSS) and next-generation sequencing (NGS) such as UDPS. We propose solutions specific to each of the two sampling methods—CCSS and NGS—to guarantee statistically conforming conclusions as free of bias as possible.

Contact:  josep.gregori@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online
SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences
Authors: Wong Ka-Chun , Zhang Zhaolei
Published: January 2014

Motivation: The recent advances in genome sequencing have revealed an abundance of non-synonymous polymorphisms among human individuals; subsequently, it is of immense interest and importance to predict whether such substitutions are functional neutral or have deleterious effects. The accuracy of such prediction algorithms depends on the quality of the multiple-sequence alignment, which is used to infer how an amino acid substitution is tolerated at a given position. Because of the scarcity of orthologous protein sequences in the past, the existing prediction algorithms all include sequences of protein paralogs in the alignment, which can dilute the conservation signal and affect prediction accuracy. However, we believe that, with the sequencing of a large number of mammalian genomes, it is now feasible to include only protein orthologs in the alignment and improve the prediction performance.

Results: We have developed a novel prediction algorithm, named SNPdryad, which only includes protein orthologs in building a multiple sequence alignment. Among many other innovations, SNPdryad uses different conservation scoring schemes and uses Random Forest as a classifier. We have tested SNPdryad on several datasets. We found that SNPdryad consistently outperformed other methods in several performance metrics, which is attributed to the exclusion of paralogous sequence. We have run SNPdryad on the complete human proteome, generating prediction scores for all the possible amino acid substitutions.

Availability and implementation: The algorithm and the prediction results can be accessed from the Web site: http://snps.ccbr.utoronto.ca:8080/SNPdryad/.

Contact:  Zhaolei.Zhang@utoronto.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data
Authors: McCarthy Michael T. , O’Callaghan Christopher A.
Published: January 2014

Summary: Hypersensitivity to DNaseI digestion is a hallmark of open chromatin, and DNaseI-seq allows the genome-wide identification of regions of open chromatin. Interpreting these data is challenging, largely because of inherent variation in signal-to-noise ratio between datasets. We have developed PeaKDEck, a peak calling program that distinguishes signal from noise by randomly sampling read densities and using kernel density estimation to generate a dataset-specific probability distribution of random background signal. PeaKDEck uses this probability distribution to select an appropriate read density threshold for peak calling in each dataset. We benchmark PeaKDEck using published ENCODE DNaseI-seq data and other peak calling programs, and demonstrate superior performance in low signal-to-noise ratio datasets.

Availability and implementation: PeaKDEck is written in standard Perl and runs on any platform with Perl installed. PeaKDEck is also available as a standalone application written in Perl/Tk, which does not require Perl to be installed. Files, including a user guide, can be downloaded at: www.ccmp.ox.ac.uk/peakdeck.

Contact:  chris.ocallaghan@ndm.ox.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Impact of deep-sea fishery for Greenland halibut (Reinhardtius hippoglossoides) on non-commercial fish species off West Greenland
Authors: Jørgensen Ole A. , Bastardie François , Eigaard Ole R.
Published: January 2014

Since the late 1980s, a deep-sea fishery for Greenland halibut (Reinhardtius hippoglossoides) has been developing gradually in West Greenland. Deep-sea fish species are generally long-lived and characterized by late age of maturity, low fecundity, and slow growth, features that probably cause low resilience following overexploitation. In order to evaluate whether populations of nine potential bycatch species are negatively affected by the commercial fishery for Greenland halibut, scientific data from bottom-trawl surveys conducted in the same area and period as the commercial fishery were analysed. During the period 1988–2011, population abundance and size composition changed as catch and effort in the Greenland halibut fishery increased. Two species showed a significant decrease in abundance, and four populations showed a significant reduction in mean weight of individuals (p < 0.05). Correlation analyses show that most of the observed trends in abundance are probably not related to increasing fishing effort for Greenland halibut. The analysis did, however, show that most of the observed decreases in mean weight were significantly correlated with fishing effort during the 24-year period.
Black hole spin measurements through the relativistic precession model: XTE J1550-564
Authors: Motta S. E. , Muñoz-Darias T. , Sanna A. , Fender R. , Belloni T. , Stella L.
Published: January 2014

We present a systematic analysis of the complete set of observations of the black hole (BH) binary XTE J1550-564 obtained by the Rossi X-ray Timing Explorer. We study the fast time variability properties of the source and determine the spin of the BH through the relativistic precession model. Similarly to what is observed in the BH binary GRO J1655-40, the frequencies of the QPOs and broad-band noise components match the general relativistic frequencies of particle motion close to the compact object predicted by the relativistic precession model. The combination of two simultaneously observed quasi-periodic oscillation (QPO) frequencies together with the dynamical BH mass from optical/infrared observations yields a spin equal to a = 0.34 ± 0.01, consistent with previous determinations from X-ray spectroscopy. Based on the derived BH parameters, the low-frequency QPO emission radii vary from ∼30 gravitational radii (Rg) to the innermost stable orbit for this spin (∼5 Rg), where they sharply disappear as observed for the case of GRO J1655-40.
Whereto the mega brain projects?
Authors: Poo Mu-ming
Published: January 2014

The mega brain projects announced by the US President and European Commission in 2013 offer new initiatives for developing innovative neurotechnology, but the prospect of effective therapies for brain disease remains uncertain.
Roseomonas rhizosphaerae sp. nov., a triazophos-degrading bacterium isolated from soil
Authors: Chen Qing , Sun Li-Na , Zhang Xiao-xia , He Jian , Kwon Soon-Wo , Zhang Jun , Li Shun-peng , Gu Jin-gang
Published: January 2014

A novel aerobic, non-spore-forming, non-motile, catalase- and oxidase-positive, Gram-stain-negative, coccoid to short-rod-shaped bacterial strain, designated YW11T, was isolated from soil under long-term application of triazophos. The strain was able to hydrolyse triazophos. Strain YW11Tgrew at 15–40 °C (optimum at 28 °C), at pH 5.0–8.0 (optimum at pH 7.5) and with 0–5.0 % (w/v) NaCl (optimum at 0.5 %). The major respiratory quinone was ubiquinone 10 (Q-10) and the major cellular fatty acids were C18 : 1ω7c, C16 : 0, C18 : 12-OH and C18 : 0. The genomic DNA G+C content of strain YW11Twas 69.6±0.5 mol%. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, an unknown glycolipid and two unknown aminolipids. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain YW11Twas a member of the genusRoseomonas, and showed the highest sequence similarity toRoseomonas cervicalisKACC 11686T(97.9 %) andRoseomonas aestuariiKACC 19645T(97.8 %) and then toRoseomonas ludipueritiaeKACC 13843T(96.9 %). Strain YW11Tshowed low DNA–DNA relatedness withR. cervicalisKACC 11686T(32.3±2.9 %),R. aestuariiKACC 16549T(28.2±2.6 %) andR. ludipueritiaeKACC 13843T(30.2±2.6 %). Based on the results of phylogenetic analysis and DNA–DNA hybridization, the whole-cell fatty acid composition as well as biochemical characteristics, strain YW11Twas clearly distinguished from all recognized species of the genusRoseomonasand should be assigned to a novel species of the genusRoseomonas, for which the nameRoseomonas rhizosphaeraesp. nov. is proposed. The type strain is YW11T( = KACC 17225T = CCTCC AB2013041T).
Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster
Authors: Santoni Federico A. , Makrythanasis Periklis , Nikolaev Sergey , Guipponi Michel , Robyr Daniel , Bottani Armand , Antonarakis Stylianos E.
Published: January 2014

There is increasing interest in clinical genetics pertaining to the utilization of high-throughput sequencing data for accurate diagnoses of monogenic diseases. Moreover, massive whole-exome sequencing of tumors has provided significant advances in the understanding of cancer development through the recognition of somatic driver variants. To improve the identification of the variants from HTS, we developed VariantMaster, an original program that accurately and efficiently extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation in a family, as well as the probability of it being de novo or somatic. In familial cases, various modes of inheritance are considered: X-linked, autosomal dominant, and recessive (homozygosity or compound heterozygosity). Moreover, VariantMaster integrates phenotypes and genotypes, and employs Annovar to produce additional information such as allelic frequencies in the general population and damaging scores to further reduce the number of putative variants. As a proof of concept, we successfully applied VariantMaster to identify (1) de novo mutations in a previously described data set, (2) causative variants in a rare Mendelian genetic disease, and (3) known and new “driver” mutations in previously reported cancer data sets. Our results demonstrate that VariantMaster is considerably more accurate in terms of precision and sensitivity compared with previously published algorithms.
Grain Number,Plant Height,and Heading Date7Is a Central Regulator of Growth, Development, and Stress Response
Authors: Weng Xiaoyu , Wang Lei , Wang Jia , Hu Yong , Du Hao , Xu Caiguo , Xing Yongzhong , Li Xianghua , Xiao Jinghua , Zhang Qifa
Published: January 2014

Grain number, plant height, and heading date7 (Ghd7) has been regarded as an important regulator of heading date and yield potential in rice (Oryza sativa). In this study, we investigated functions of Ghd7 in rice growth, development, and environmental response. As a long-day dependent negative regulator of heading date, the degree of phenotypic effect of Ghd7 on heading date and yield traits is quantitatively related to the transcript level and is also influenced by both environmental conditions and genetic backgrounds. Ghd7 regulates yield traits through modulating panicle branching independent of heading date. Ghd7 also regulates plasticity of tiller branching by mediating the PHYTOCHROME B-TEOSINTE BRANCHED1 pathway. Drought, abscisic acid, jasmonic acid, and high-temperature stress strongly repressed Ghd7 expression, whereas low temperature enhanced Ghd7 expression. Overexpression of Ghd7 increased drought sensitivity, whereas knock-down of Ghd7 enhanced drought tolerance. Gene chip analysis of expression profiles revealed that Ghd7 was involved in the regulation of multiple processes, including flowering time, hormone metabolism, and biotic and abiotic stresses. This study suggests that Ghd7 functions to integrate the dynamic environmental inputs with phase transition, architecture regulation, and stress response to maximize the reproductive success of the rice plant.
Financial constraints for investment in Brazil
Authors: Lima Crisóstomo Vicente , Javier López Iturriaga Félix , Vallelado González Eleuterio
Published: January 2014

Purpose

– The purpose of this paper is to verify the existence of financial constraints for investment in Brazil, an emerging market with growing international visibility.

Design/methodology/approach

– Using panel data methodology and generalized method of moments (GMM), the paper estimates dynamic investment models based on the Euler equation and Tobin'sqfor a panel data set of 199 Brazilian non-financial firms for the time period 1995-2006.

Findings

– Results show that Brazilian firms face financial constraints since their investments depend on internally generated funds. Results are robust to different investment models based on the Euler equation, also controlling for growth opportunities. Significant investment-cash flow sensitivity has been found for the whole sample of firms. Subsamples of firms considered as under financial constraints, according to dividend payout and equity issuance policies, have higher investment-cash flow sensitivity. Investment-cash flow sensitivity of financially constrained firms in Brazil is higher than that in the UK and in Romania, a transition economy.

Originality/value

– The results extend empirical evidence of financial constraints in Brazil. The paper contributes to the literature by assessing the firms’ financial constraint status on an annual basis, and by using panel data methodology and GMM to estimate dynamic models of investment that take into account the proposals of the hierarchy of finance theory. In addition, the paper controls for growth opportunities. Capital market imperfections affect firm investment in Brazil and such effects are even stronger for financially constrained firms.
Domestic Debt, Private Sector Credit and Economic Growth in Sub‐Saharan Africa
Authors: Mbate Michael
Published: January 2014

Exercising fiscal prudence in periods of deteriorating fiscal balance requires sound policies which promote debt sustainability. This paper estimates a dynamic cross‐country model and investigates the impact of domestic debt on economic growth and private sector credit in a panel of 21 sub‐Saharan African (SSA) countries over the period 1985 to 2010. System‐GMM results reveal a non‐linear relationship between domestic debt and economic growth, characterized by a maximum turning point of 11.4 per cent of GDP. In addition, domestic debt is found to crowd out private sector credit by an elasticity of negative 0.3 per cent of GDP, deterring capital accumulation and private sector growth. These findings underscore the need for effective debt management strategies which incorporate debt ceiling to limit domestic indebtedness, as well as the design of financial policies which enhance credit availability, promote fiscal discipline and deepen domestic debt markets on the continent.
Real Interest Rate Parity and Two Structural Breaks: African Countries Evidence
Authors: Su Chi‐Wei , Chang Hsu‐Ling , Liu Yan
Published: January 2014

This study applies Narayan and Popp's () unit‐root test with two endogenous breaks to assess the validity of long‐run real interest rate parity (RIRP) via investigating the non‐stationary properties of the real interest rate convergence relative to South Africa for ten African countries. This method has been proven to be more powerful than the other unit root models with two breaks (Narayan and Popp, ). Our findings clearly indicate that RIRP holds true for five countries, which implies that the choices and effectiveness of the monetary and fiscal policies in the African economies will be highly influenced by external factors originating from South Africa. Our results have important policy implications for these African countries under study.
Barriers to Family Planning in Sudan: Results from a Survey in White Nile, Kassala and Al‐Gadarif, 2008
Authors: Ahmed Huda Mohamed Mukhtar
Published: January 2014

Barriers to family planning are examined in three states in Sudan; White Nile, Kassala and Al‐Gadarif. The study adopted a two‐stage cluster sampling design with calculated sample size of 520 households. Data on households' characteristics as well as the background characteristics of ever married women regarding reproductive health, their knowledge, attitude and practice of family planning, was collected. Both descriptive and analytical statistics were used to examine the factors influencing use of family planning methods. Analytical analysis showed that respondents being satisfied with family planning methods, being wealthy, husband's knowledge about contraceptives and spousal discussions on family planning issues have a positive and statistically significant effect on use of family planning methods, whereas the educational level of both the respondents and their husbands has no statistically significant effect.
Poverty–Lack of Access to Adequate Safe Water Nexus: Evidence from Rural Malawi
Authors: Mkondiwa Maxwell , Jumbe Charles B.L. , Wiyo Kenneth A.
Published: January 2014

This paper investigates the relationship between poverty and lack of access to adequate safe water in rural Malawi. Data used in the analysis was collected from a survey covering 1,651 randomly selected households. We use Canonical Correlation Analysis (CCA) as a distinct technique for understanding the poverty–rural water access nexus. CCA results indicate that poverty in the context of low income and expenditure is positively correlated with lack of access to safe and adequate water. Integrated Rural Water Resources Management (IRWM) interventions are therefore needed to address both challenges of poverty and poor access to adequate safe water in rural Malawi.
‘Angola‐mode’ Trade Deals and the Awakening of African Lion Economies
Authors: Habiyaremye Alexis
Published: January 2014

After decades of continuous flows of mineral exports to rich Western countries and a failed development in Africa, the arrival of China on the African resource market with large infrastructure projects in exchange for access to resources has created completely new growth dynamics for oil‐rich African economies. The Chinese strategy of swapping infrastructure projects for mineral resources, known as an ‘Angola‐mode’ trade arrangement, has brought an army of Chinese infrastructure workers to Africa and contributed to the awakening of fast‐growing African ‘lion economies’. This article examines the role played by Sino‐African resource‐for‐infrastructure swap projects in Africa's new development dynamics. Using panel data of African countries over the period 2001–10, we find that by contributing to easing the infrastructural bottlenecks, Sino‐African trade has played a key role in the fast growth of oil‐rich African countries.
Social Transfer Programmes and School Enrolment in Malawi: A Micro‐simulation
Authors: Nanivazo Malokele
Published: January 2014

This paper investigates the impact of social transfer programmes on school enrolment and child labour in Malawi utilizing a micro‐simulation evaluation method. For this purpose, we simulate four hypothetical scenarios in which a household receives: (1) MK1,040 (US$2.5) for each child enrolled in school regardless of the child's gender; (2) MK1,040 (US$2.5) regardless of the child's enrolment status and gender; (3) MK1,040 (US$2.5) and MK2,080 (US$5) for each boy or girl enrolled in school, and (4) MK1,040 (US$2.5) and MK2,080 (US$5) for each boy or girl regardless of their enrolment status. Results show that boys' enrolment increases in all four scenarios, whereas girls' enrolment increases only when the conditionality on enrolment is enforced.
Credit Constraints and Agricultural Risk for Non‐Farm Enterprises
Authors: Gajigo Ousman
Published: January 2014

This paper uses two nationally representative datasets collected in 1992 and 2003 in Gambia to analyse small, non‐farm enterprises. The results reveal evidence of significant credit constraint among these non‐farm enterprises. Specifically, household wealth is a significant determinant not only of entry into the enterprise sector but also determines investment levels conditional upon entry. Furthermore, the marginal returns to investments in enterprises are very high and significantly exceed the prevailing lending rates of banks in the country. Besides being credit constrained, these enterprises are also affected by farm‐related variables. Agricultural risk adversely affects enterprise investment. This latter result underscores the importance of livelihood diversification.
MicroRNA Let‐7f: A Novel Regulator of Innate Immune Response in Human Endocervical Cells
Authors: Sathe Ameya , Patgaonkar Mandar S. , Bashir Tahir , Reddy Kudumula Venkata Rami
Published: January 2014

Problem

Endocervical epithelial cells express pattern recognition receptors (PRRs) that aid in innate immune responses. Mechanisms regulating signaling of PRRs are poorly understood.

Methods of Study

Endocervical cells (End1/E6E7) were treated with ligands of TLR9 and RIG‐I once or after pre‐stimulation with same ligand. Cytokine responses were determined by ELISA. Differential gene expression was analyzed by microarray. Differentially expressed genes were validated by qPCR /Western blot. Role of let‐7f was studied by inhibition and over‐expression studies using commercial inhibitors and let‐7f encoding plasmids, respectively.

Results

Single stimulation of cells with TLR9 ligand, but not RIG‐I ligand, induced tolerance to subsequent challenge to the same ligand. Stimulation with TLR9 decreased let‐7f and increased its target Blimp‐1. Conversely, RIG‐I stimulation increased let‐7f and decreased Blimp‐1 expression. Inhibition and over‐expression revealed let‐7f is involved in induction of immune tolerance.

Conclusion

We identify let‐7f as a novel regulator of PRR signaling in endocervical cells.
Infant growth is associated with parental education but not with parental adiposity – Early Stockholm Obesity Prevention Project
Authors: Svensson V , Ek A , Forssén M , Ekbom K , Cao Y , Ebrahim M , Johansson E , Nero H , Hagströmer M , Ekstedt M , Nowicka P , Marcus C
Published: January 2014

Aim

To explore the simultaneous impact of parental adiposity and education level on infant growth from birth to 12 months, adjusting for known early‐life risk factors for subsequent childhood obesity.

Methods

Baseline data for 197 one‐year‐old children and their parents, participating in a longitudinal obesity intervention, were used. Obesity risk groups, high/low, were defined based on parental body mass index (n = 144/53) and parental education (n = 57/139). Observational data on infant growth between 0 and 12 months were collected. The children's relative weight (body mass index standard deviation score) at 3, 6 and 12 months and rapid weight gain 0–6 months were analysed in regression models, with obesity risk as primary exposure variables, adjusting for gestational weight gain, birth weight, short exclusive breastfeeding and maternal smoking.

Results

Relative weight at 3, 6 and 12 months was associated with low parental education but not with parental adiposity. No significant associations were observed with rapid weight gain. None of the early‐life factors could explain the association with parental education.

Conclusion

Low parental education level is independently associated with infant growth, whereas parental obesity does not contribute to a higher weight or to rapid weight gain during the first year.
Understanding Hybrid Democracy in Cambodia: The Nexus Between Liberal Democracy, the State, Civil Society, and a “Politics of Presence”
Authors: Baaz Mikael , Lilja Mona
Published: January 2014

This article analyzes the gap between globally promoted definitions of liberal democracy and the different ways in which the concept is interpreted by individual politicians and civil society representatives in Cambodia. By taking as our point of departure the gap between “hegemonic” views of democracy and locally lived democracy experiences and strategies, we argue that one of the basic concepts of liberal democracy—the concept of the “politics of ideas”—does not easily match local facets of democracy. Followers of liberal democracy give priority to the representation of ideas and ideologies over the question of who represents them. This priority, however, seems to correspond poorly to the situation in present‐day Cambodia. Based on extensive field material, the article demonstrates how Cambodian interpretations of the Western understanding of “liberal democracy” try to bridge the gap between the praxis of the “politics of ideas” and the “politics of presence.”
Maternal thyroid hormones during pregnancy, childhood adiposity and cardiovascular risk factors: the Generation R Study
Authors: Godoy Guilherme A. F. , Korevaar Tim I. M. , Peeters Robin P. , Hofman Albert , de Rijke Yolanda B. , Bongers‐Schokking Jacoba J. , Tiemeier Henning , Jaddoe Vincent W. V. , Gaillard Romy
Published: January 2014

Objective

Variation in maternal thyroid function during early pregnancy may permanently affect childhood growth and cardiovascular development. We examined the associations of early pregnancy maternal TSH and free T4 (FT4) levels with childhood growth, body composition and cardiovascular characteristics.

Methods

We performed a population‐based prospective cohort study among 5646 mothers and their children. Maternal thyroid parameters were assessed in early pregnancy (median: 13·2 weeks; 95% range: 9·7–17·6 weeks). Childhood growth was repeatedly measured from birth to 6 years. At the age of 6 years, childhood body mass index (BMI), total body and abdominal fat distribution, blood pressure and left ventricular mass were measured.

Results

Maternal thyroid parameters were not consistently associated with childhood length and weight growth characteristics. Lower maternal TSH levels were associated with lower childhood BMI, total fat mass, abdominal subcutaneous fat mass area and diastolic blood pressure (P‐values <0·05), but not with preperitoneal abdominal fat mass area, systolic blood pressure or left ventricular mass. Higher maternal FT4 levels were associated with lower childhood BMI, abdominal subcutaneous and preperitoneal fat mass area (P for trends <0·05), but not with other cardiovascular characteristics. Clinically maternal hypothyroid or hyperthyroid statuses were not associated with childhood growth, body fat or cardiovascular outcomes.

Conclusions

Maternal thyroid function during early pregnancy may influence childhood body composition and cardiovascular development. Further studies are needed to replicate these findings and to examine the influence of maternal thyroid hormone levels during pregnancy on long‐term growth and cardiovascular development in the offspring.
Economic Valuation of Subsistence Harvest of Wildlife in Madagascar
Authors: GOLDEN CHRISTOPHER D. , BONDS MATTHEW H. , BRASHARES JUSTIN S. , RODOLPH RASOLOFONIAINA B. J. , KREMEN CLAIRE
Published: January 2014

Wildlife consumption can be viewed as an ecosystem provisioning service (the production of a material good through ecological functioning) because of wildlife's ability to persist under sustainable levels of harvest. We used the case of wildlife harvest and consumption in northeastern Madagascar to identify the distribution of these services to local households and communities to further our understanding of local reliance on natural resources. We inferred these benefits from demand curves built with data on wildlife sales transactions. On average, the value of wildlife provisioning represented 57% of annual household cash income in local communities from the Makira Natural Park and Masoala National Park, and harvested areas produced an economic return of U.S.$0.42 ha−1· year−1. Variability in value of harvested wildlife was high among communities and households with an approximate 2 orders of magnitude difference in the proportional value of wildlife to household income. The imputed price of harvested wildlife and its consumption were strongly associated (p< 0.001), and increases in price led to reduced harvest for consumption. Heightened monitoring and enforcement of hunting could increase the costs of harvesting and thus elevate the price and reduce consumption of wildlife. Increased enforcement would therefore be beneficial to biodiversity conservation but could limit local people's food supply. Specifically, our results provide an estimate of the cost of offsetting economic losses to local populations from the enforcement of conservation policies. By explicitly estimating the welfare effects of consumed wildlife, our results may inform targeted interventions by public health and development specialists as they allocate sparse funds to support regions, households, or individuals most vulnerable to changes in access to wildlife.

Valoración Económica de la Caza de Subsistencia de Vida Silvestre en Madagascar
Thoracic empyema caused by Prevotella spp. diagnosed using 16S rDNA sequence analysis
Authors: Zhou Hua , Shen Yihong , Shen Qian , Zhou Jianying
Published: January 2014

We describe a case of thoracic empyema in a 76‐year‐old male with complication of diabetes mellitus and hypertension. His chief complaints were fever and chest pain. The patient was diagnosed as pleural infection according to the pulmonary computed tomography (CT) scan and laboratory results. The patient had persistent fever after the treatment of continuous percutaneous drainage and 1 week of intravenous moxifloxacin. He was then misdiagnosed as tuberculous pleuritis and still had fever after the treatment of 2 weeks' antituberculosis drugs. Repeated cultures of sputum, blood, bronchoalveolar lavage fluid and pleural fluid were all negative. A gram‐negative bacillus was found in the pleural pus Gram stain, and it was identified as Prevotella spp. by 16S ribosomal DNA (rDNA) sequence analysis. The patient recovered after further treatment, including CT‐induced pleural drain and intravenous imipenem. Totally, he received 2‐week imipenem and 1‐month metronidazole therapy from the day he was diagnosed with empyema to the termination of treatment. On the subsequent 2‐month and 6‐month follow‐up visits, no recurrence has been reported for this patient. Routine microbiological methods are important in diagnosis of pleural infection, but they have limitations in some cases, especially for anaerobe. Molecular assay based on 16S rDNA is helpful in detecting causative organisms of thoracic empyema.
Inflammation in new‐onset atrial fibrillation after cardiac surgery: a systematic review
Authors: Jacob Kirolos A. , Nathoe Hendrik M. , Dieleman Jan M. , van Osch Dirk , Kluin Jolanda , van Dijk Diederik
Published: January 2014

Background

Postoperative new‐onset atrial fibrillation (PNAF) is the most common complication following cardiac surgery. The pathogenesis of PNAF is multifactorial. The concept of the postoperative inflammatory response, as a potential underlying mechanism has been extensively studied. This review aims to provide a comprehensive summary of literature relevant to the association between the inflammatory response following cardiac surgery and PNAF.

Design

MEDLINE, EMBASE and the Cochrane Central Register were systematically reviewed by two independent investigators for studies published between January 1980 and May 2012, in which an association between serum markers of inflammation and PNAF was evaluated, or the effect of drugs with anti‐inflammatory properties on the risk of PNAF.

Results

Sixty‐three studies met selection criteria (39 observational and 24 randomized studies) including 27 363 patients. The mean incidence of PNAF after cardiac surgery was 25·5%. Elevated levels of various inflammatory mediators were associated with PNAF, and the most consistent association was found between white blood cell count and PNAF. Of the drugs with anti‐inflammatory properties, statins gave the best protective effect against PNAF, followed by anti‐oxidants, steroids and colchicine. Nonsteroidal anti‐inflammatory drugs did not prevent PNAF significantly.

Conclusion

The postoperative inflammation response may play a role in the pathogenesis of PNAF. However, of the inflammation biomarkers, only elevated white blood cell count reliably predicts PNAF. Pre‐ and perioperative use of statins and several other drugs with anti‐inflammatory properties reduce the incidence of PNAF.
Differential subcellular localization of SK3‐containing channels in the hippocampus
Authors: Ballesteros‐Merino Carmen , Watanabe Masahiko , Shigemoto Ryuichi , Fukazawa Yugo , Adelman John P. , Luján Rafael
Published: January 2014

Small‐conductance, Ca2+‐activated K+ (SK) channels are expressed in the hippocampus where they regulate synaptic responses, plasticity, and learning and memory. To investigate the expression of SK3 (KCNN3) subunits, we determined the developmental profile and subcellular distribution of SK3 in the developing mouse hippocampus using western blots, immunohistochemistry and high‐resolution immunoelectron microscopy. The results showed that SK3 expression increased during postnatal development, and that the localization of SK3 changed from being mainly associated with the endoplasmic reticulum and intracellular sites during the first postnatal week to being progressively concentrated in dendritic spines during later stages. In the adult, SK3 was localized mainly in postsynaptic compartments, both at extrasynaptic sites and along the postsynaptic density of excitatory synapses. Double labelling showed that SK3 co‐localized with SK2 (KCNN2) and with N‐methyl‐D‐aspartate receptors. Finally, quantitative analysis of SK3 density revealed two subcellular distribution patterns in different hippocampal layers, with SK3 being unevenly distributed in CA1 region of the hippocampus pyramidal cells and homogeneously distributed in dentate gyrus granule cells. Our results revealed a complex cell surface distribution of SK3‐containing channels and a distinct developmental program that may influence different hippocampal functions.
Efficacy of reciprocating and rotary NiTi instruments for retreatment of curved root canals assessed by micro‐CT
Authors: Rödig T. , Reicherts P. , Konietschke F. , Dullin C. , Hahn W. , Hülsmann M.
Published: January 2014

Aim

To compare the efficacy of reciprocating and rotary NiTi‐instruments in removing filling material from curved root canals using micro‐computed tomography.

Methodology

Sixty curved root canals were prepared and filled with gutta‐percha and sealer. After determination of root canal curvatures and radii in two directions as well as volumes of filling material, the teeth were assigned to three comparable groups (n = 20). Retreatment was performed using Reciproc, ProTaper Universal Retreatment or Hedström files. Percentages of residual filling material and dentine removal were assessed using micro‐CT imaging. Working time and procedural errors were recorded. Statistical analysis was performed by variance procedures.

Results

No significant differences amongst the three retreatment techniques concerning residual filling material were detected (P > 0.05). Hedström files removed significantly more dentine than ProTaper Universal Retreatment (P < 0.05), but the difference concerning dentine removal between both NiTi systems was not significant (P > 0.05). Reciproc and ProTaper Universal Retreatment were significantly faster than Hedström files (P = 0.0001). No procedural errors such as instrument fracture, blockage, ledging or perforation were detected for Hedström files. Three perforations were recorded for ProTaper Universal Retreatment, and in both NiTi groups, one instrument fracture occured.

Conclusions

Remnants of filling material were observed in all samples with no significant differences between the three techniques. Hedström files removed significantly more dentine than ProTaper Universal Retreatment, but no significant differences between both NiTi systems were detected. Procedural errors were observed with ProTaper Universal Retreatment and Reciproc.