bluuebunny/crossref_metadata_2025 huggingface dataset:
A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads
Authors: Kojima Kaname , Nariai Naoki , Mimori Takahiro , Takahashi Mamoru , Yamaguchi-Kabata Yumi , Sato Yukuto , Nagasaki Masao
Published: September 2013

Motivation: Variant calling from genome-wide sequencing data is essential for the analysis of disease-causing mutations and elucidation of disease mechanisms. However, variant calling in low coverage regions is difficult due to sequence read errors and mapping errors. Hence, variant calling approaches that are robust to low coverage data are demanded.

Results: We propose a new variant calling approach that considers pedigree information and haplotyping based on sequence reads spanning two or more heterozygous positions termed phase informative reads. In our approach, genotyping and haplotyping by the assignment of each read to a haplotype based on phase informative reads are simultaneously performed. Therefore, positions with low evidence for heterozygosity are rescued by phase informative reads, and such rescued positions contribute to haplotyping in a synergistic way. In addition, pedigree information supports more accurate haplotyping as well as genotyping, especially in low coverage regions. Although heterozygous positions are useful for haplotyping, homozygous positions are not informative and weaken the information from heterozygous positions, as majority of positions are homozygous. Thus, we introduce latent variables that determine zygosity at each position to filter out homozygous positions for haplotyping. In performance evaluation with a parent–offspring trio sequencing data, our approach outperforms existing approaches in accuracy on the agreement with single nucleotide polymorphism array genotyping results. Also, performance analysis considering distance between variants showed that the use of phase informative reads is effective for accurate variant calling, and further performance improvement is expected with longer sequencing data.

Contact: nagasaki@megabank.tohoku.ac.jp or kojima@megabank.tohoku.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.
The H i column density power spectrum of six nearby spiral galaxies
Authors: Dutta Prasun , Bharadwaj Somnath
Published: September 2013

We propose a method to determine the power spectrum of H i column density fluctuations using radio-interferometric observations of 21-cm emission from the interstellar medium of galaxies. We have used this to estimate the power spectra of six nearly face-on nearby spiral galaxies. Earlier work has shown that these power spectra are well fitted by power laws with slopes around −1.6 across length-scales ∼1 to ∼10 kpc, the amplitude however was undetermined. In this work, we have determined the amplitude of the H i column density power spectrum. We find that the H i column density NHi expressed in units of 1020 cm−2 has mean square fluctuations in the range ∼0.03 to ∼20. The amplitude of the power spectrum is found to be tightly correlated with the H i mass fraction of the galaxies. The physical process responsible for these scale-invariant fluctuations is, however, at present not known.
Structural insights into the functions of the FANCM-FAAP24 complex in DNA repair
Authors: Yang Hui , Zhang Tianlong , Tao Ye , Wang Fang , Tong Liang , Ding Jianping
Published: September 2013

Fanconi anemia (FA) is a genetically heterogeneous disorder associated with deficiencies in the FA complementation group network. FA complementation group M (FANCM) and FA-associated protein 24 kDa (FAAP24) form a stable complex to anchor the FA core complex to chromatin in repairing DNA interstrand crosslinks. Here, we report the first crystal structure of the C-terminal segment of FANCM in complex with FAAP24. The C-terminal segment of FANCM and FAAP24 both consist of a nuclease domain at the N-terminus and a tandem helix-hairpin-helix (HhH)2 domain at the C-terminus. The FANCM-FAAP24 complex exhibits a similar architecture as that of ApXPF. However, the variations of several key residues and the electrostatic property at the active-site region render a catalytically inactive nuclease domain of FANCM, accounting for the lack of nuclease activity. We also show that the first HhH motif of FAAP24 is a potential binding site for DNA, which plays a critical role in targeting FANCM-FAAP24 to chromatin. These results reveal the mechanistic insights into the functions of FANCM-FAAP24 in DNA repair.
Fatty Degeneration of the Paraspinal Muscle in Patients With Degenerative Lumbar Kyphosis
Authors: Hyun Seung-Jae , Bae Chae-Wan , Lee Sang-Hoon , Rhim Seung-Chul
Published: September 2013

Study Design:

A comparative case-control study.

Objective:

The aim of this study was to quantify the degree of paraspinal muscle changes in degenerative lumbar kyphosis (DLK) patients using magnetic resonance imaging and computed tomography scanning.

Summary of Background Data:

Although the pathophysiology of DLK is not completely understood, extensive degeneration and weakness of the lumbar extensor muscles are thought to underlie the condition in most patients. However, there is no ideal method to quantify the degree of fat infiltration and atrophy of the paraspinal muscles in patients with DLK.

Materials and Methods:

The study group comprised 20 patients with DLK and 20 healthy volunteers. The cross-sectional areas of the psoas, erector spinae (ES), multifidus (MF), quadratus lumborum, and vertebral body were measured. The ratio between the cross-sectional area of the muscle and the vertebral body was used to evaluate lumbar muscularity. The degree of fatty change was evaluated by measuring the ratio between the mean signal intensity of the muscle and that of the subcutaneous fat within regions of interest.

Results:

Muscularity in the MF and ES was not significantly different between the DLK and control groups at L1, L2, or L3, but was significantly different at L4 (ES, P=0.001; MF, P=0.001) and L5 (ES, P=0.001; MF, P=0.015). The mean signal intensities of the ES and MF were higher in the DLK group than in the control group at all levels. The degree of fatty change in the ES and MF was significantly higher in the DLK group than in the control group (P<0.05).

Conclusions:

Quantitative analysis using magnetic resonance imaging and computed tomography scanning showed differences in paraspinal muscle volume and fatty degeneration between patients with DLK and healthy volunteers. This evaluation method may be useful for measuring the extent of paraspinal muscle degeneration.
Titi monkey call sequences vary with predator location and type
Authors: Cäsar Cristiane , Zuberbühler Klaus , Young Robert J. , Byrne Richard W.
Published: September 2013

Animal alarm calls can encode information about a predator's category, size, distance or threat level. In non-human primates, alarm calls typically refer to broad classes of disturbances, in some instances to specific predators. Here, we present the results of a field experiment with a New World primate, the black-fronted titi monkey (
Callicebus nigrifrons
), designed to explore the information conveyed by their alarm call system. Adults produced sequences consisting of two main alarm call types that conveyed, in different parts of the utterance, information about a predator's type and location. In particular, sequence compositions differed depending on whether the predator was a mammalian carnivore or a raptor, and whether it was detected in a tree or on the ground. This is the first demonstration of a sequence-based alarm call system in a non-human animal that has the capacity to encode both location and type of predatory threat.
Halley and the eternity of the world revisited
Authors: Levitin Dmitri
Published: September 2013

Since the publication in
Notes and Records of the Royal Society
of an article by Simon Schaffer in 1977, it has been a historiographical commonplace that there was an ‘underlying unity’ to the religio-philosophical opinions of Edmond Halley, specifically on issues concerning the age of the world. This article (i) argues that the evidence adduced for this claim—specifically the account of a lecture given by Halley to the Royal Society in 1693—has been misinterpreted, and (ii) brings forward some new evidence concerning the mysterious events surrounding Halley's unsuccessful attempt to secure the Savilian Professorship in Astronomy in 1691 and the nature of his religious heterodoxy, both as it was developed by himself and as it was perceived by contemporaries. It thus functions as a full revisionist account of one of the key players in the destabilization of the relationship between natural philosophy and Genesis in the first decades of the Royal Society.
James Sowerby: meteorites and his meteoritic sword made for the Emperor of Russia, Alexander I, in 1814
Authors: Henderson Paul
Published: September 2013

James Sowerby included meteorites in his publications of British and exotic natural history and so raised interest in their nature and origins at a time of much debate and involving the President of the Royal Society, Sir Joseph Banks. The celebrations over the defeat of France in 1814 prompted Sowerby to make a sword from the Cape of Good Hope iron meteorite to present to the Russian Emperor, Alexander I, at the time of his state visit to London in June 1814 and in recognition of his achievements in bringing peace to Europe. The story of its attempted presentation, its final reception and the following response, including publications, all helped to increase interest in meteorites and their properties. The rediscovery of the sword after a lengthy disappearance probably brings an unusual saga to a fitting close.
Optimizing snake locomotion in the plane
Authors: Alben Silas
Published: September 2013

We develop a numerical scheme to determine which planar snake motions are optimal for locomotory efficiency, across a wide range of frictional parameter space. For a large coefficient of transverse friction, we show that retrograde travelling waves are optimal. We give an asymptotic analysis showing that the optimal wave amplitude decays as thepower of the coefficient of transverse friction. This result agrees well with the numerical optima. At the other extreme, zero coefficient of transverse friction, we propose a triangular direct wave that is optimal. Between these two extremes, a variety of complex, locally optimal motions are found. Some of these can be classified as standing waves (or ratcheting motions).
Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase: dynamics in nucleotides, amino acids and beyond
Authors: Staniforth Michael , Stavros Vasilios G.
Published: September 2013

In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitivebottom-upapproach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing thisbottom-upapproach.
Cryptic female choice favours sperm from major histocompatibility complex-dissimilar males
Authors: Løvlie Hanne , Gillingham Mark A. F. , Worley Kirsty , Pizzari Tommaso , Richardson David S.
Published: September 2013

Cryptic female choice may enable polyandrous females to avoid inbreeding or bias offspring variability at key loci after mating. However, the role of these genetic benefits in cryptic female choice remains poorly understood. Female red junglefowl,
Gallus gallus
, bias sperm use in favour of unrelated males. Here, we experimentally investigate whether this bias is driven by relatedness
per se
, or by similarity at the major histocompatibility complex (MHC), genes central to vertebrate acquired immunity, where polymorphism is critical to an individual's ability to combat pathogens. Through experimentally controlled natural matings, we confirm that selection against related males' sperm occurs within the female reproductive tract but demonstrate that this is more accurately predicted by MHC similarity: controlling for relatedness
per se
, more sperm reached the eggs when partners were MHC-dissimilar. Importantly, this effect appeared largely owing to similarity at a single MHC locus (class I minor). Further, the effect of MHC similarity was lost following artificial insemination, suggesting that male phenotypic cues might be required for females to select sperm differentially. These results indicate that postmating mechanisms that reduce inbreeding may do so as a consequence of more specific strategies of cryptic female choice promoting MHC diversity in offspring.
In ovo
inhibition of steroid metabolism by bisphenol-A as a potential mechanism of endocrine disruption
Authors: Clairardin Sandrine G. , Paitz Ryan T. , Bowden Rachel M.
Published: September 2013

During embryonic development, endogenous signals, for example steroid hormones, and exogenous signals, for example endocrine disrupting chemicals (EDCs), have the capacity to produce phenotypic effects that persist into adulthood. As the actions of steroids are mediated through the binding of steroid receptors, most studies of EDCs have assumed that they too elicit their effects by binding steroid receptors. We tested an alternative hypothesis, namely that EDCs elicit their effects during embryonic development by disrupting the metabolism of maternally derived steroids, thereby allowing maternally derived steroids to bind steroid receptors and elicit effects. Specifically, we examined the ability of the EDC, bisphenol-A (BPA) to inhibit the normal metabolism of oestradiol during the first nine days of embryonic development in the red-eared slider turtle (
Trachemys scripta
). We found that, when BPA was present, oestrogen metabolism was inhibited when compared to control eggs. In particular, the formation of oestrone sulfate was blocked in BPA-treated eggs. We postulate that the oestrogenic effects of EDCs may be driven, at least in part, by inappropriate oestrogen signalling. The retention of oestrogens at points of development when they would normally be metabolized to inactive forms might also help explain low-dose effects frequently reported for EDCs.
Protective immunity by oral immunization with heat‐killed Shigella strains in a guinea pig colitis model
Authors: Barman Soumik , Koley Hemanta , Ramamurthy Thandavarayan , Chakrabarti Manoj Kumar , Shinoda Sumio , Nair Gopinath Balakrish , Takeda Yoshifumi
Published: September 2013

The protective efficacy of and immune response to heat‐killed cells of monovalent and hexavalent mixtures of six serogroups/serotypes of Shigella strains (Shigella dysenteriae 1, Shigella flexneri 2a, S. flexneri 3a, S. flexneri 6, Shigella boydii 4, and Shigella sonnei) were examined in a guinea pig colitis model. A monovalent or hexavalent mixture containing 1 × 107 of each serogroup/serotype of heat‐killed Shigella cells was administered orally on Days 0, 7, 14 and 21. On Day 28, the immunized animals were challenged rectally with 1 × 109 live virulent cells of each of the six Shigella serogroups/serotypes. In all immunized groups, significant levels of protection were observed after these challenges. The serum titers of IgG and IgA against the lipopolysaccharide of each of the six Shigella serogroups/serotypes increased exponential during the course of immunization. High IgA titers against the lipopolysaccharide of each of the six Shigella serogroups/serotypes were also observed in intestinal lavage fluid from all immunized animals. These data indicate that a hexavalent mixture of heat‐killed cells of the six Shigella serogroups/serotypes studied would be a possible broad‐spectrum candidate vaccine against shigellosis.
Resourced provision: the impact of inclusive practices on a mainstream primary school
Authors: Glazzard Jonathan
Published: September 2013

This personal account from a special educational needs co‐ordinator illustrates the negative impact that resourced provision has had on one school. The provision caters for children with communication and interaction difficulties and is housed in a mainstream primary school. For this school, while the provision has had a beneficial impact on the development of inclusive values among pupils, it has also led to a decline in the overall effectiveness of the school. The achievement data of pupils in the provision has had a detrimental impact on overall school performance data. Current narrow measures of school effectiveness in England mean that schools with increasingly diverse student populations can pay the price for their commitment to inclusion, as this example illustrates.
Misconceptions about traumatic brain injury among students preparing to be special education professionals
Authors: Hux Karen , Bush Erin , Evans Kelli , Simanek Gina
Published: September 2013

The researchers performed a survey study to determine the effectiveness of collegiate programmes in dispelling common misconceptions about traumatic brain injury (TBI) while preparing undergraduate and graduate students for special education (SpEd) careers. Respondents included 136 undergraduate and 147 graduate SpEd students in their final semesters before obtaining degrees. Each completed an 18‐item true/false survey about TBI and the associated recovery process. Results were compared with survey responses from 318 lay public respondents who participated in a previous study. Two major findings emerged: (a) no significant differences existed in misconception endorsement between SpEd students completing Bachelor's versus Master's degrees; and (b) graduating students in SpEd teacher preparation programmes endorsed similar misconceptions as lay public respondents; hence, these programmes do not appear effective in dispelling common TBI misconceptions. Improving academic preparation for special educators regarding TBI is imperative for effectively identifying, assessing and serving student survivors.
Gender, productivity, and the nature of work and pay: evidence from the late nineteenth‐century tobacco industry
Authors: Stanfors Maria , Leunig Tim , Eriksson Björn , Karlsson Tobias
Published: September 2013

Women have typically been paid less than men throughout history. We investigate earnings in Swedish cigar making around 1900. Strength was unimportant, yet the gender wage gap was large. Differences in characteristics, such as age and experience, and different jobs within firms, account for two‐thirds of the gap overall, and the entire gap for piece‐rate workers. Firms were as willing to employ women as men in the better‐paying piece‐rate section, and women were willing to take those jobs. In contrast, discrimination was extensive in the time‐rate section. Men in this section benefited from greater outside opportunities and customary wages elsewhere. Theory holds that labour market discrimination will reduce profitability, and make firm survival harder, a proposition that has never been tested historically. We find that cigar firms that feminized their workforces most extensively were most likely to survive. Product market competition prevented firms employing (overpaid) men to any great extent. We argue that economic historians must interpret industry‐specific gender wage differentials in the context of workers' outside opportunities, and in the context of product markets, which can—and in this case did—limit firms' room for manoeuvre.
Morphology and Distribution of Lamellar Corpuscles in the Mesentery of the Cat
Authors: Owaki M. , Oono H. , Nakajima N. , Ohta G. , Okano S. , Kakizaki T. , Yoshioka K.
Published: September 2013

Mesentery samples obtained from 13 mixed breed cats were stereoscopically and microscopically examined and yielded the following results. In the mesentery, lamellar corpuscles were densely distributed around blood vessels, with a mean number of 182.2 ± 20.9 and mean maximum and minimum diameters of 0.98 ± 0.18 mm and 0.54 ± 0.08 mm, respectively. While most lamellar corpuscles were isolated, some complex lamellar corpuscles were found in the mesentery. Lamellar corpuscles in the mesentery appear to serve more as internal receptors that detect changes in the internal environment than as external receptors. In addition, those found around blood vessels in the mesentery are likely to be involved in blood pressure regulation.
Sovereign Spreads and Contagion Risks in Asia
Authors: Caceres Carlos , Unsal D. Filiz
Published: September 2013

In the aftermath of the recent global financial turmoil, sovereign spreads have exhibited a significant degree of volatility. This paper explores how much of these movements in the spreads of Asian economies reflected shifts in global risk aversion or country‐specific risks, directly from worsening fundamentals, or indirectly from spillovers originating in other sovereigns, or risks and uncertainty surrounding their exchange rates. This analysis finds that earlier in the crisis, the increase in market‐implied contagion led to an increase of sovereign bond yields relative to the swaps. Higher‐rated sovereign bonds in Asia benefited from the flight to quality that accompanied the increase in global risk aversion during this period. Once the systemic risks in the financial sectors worldwide were contained, the risk of sovereign spillovers eased, which, together with a fall in perceived currency‐related risks, led to a fall in sovereign bond yields relative to swaps yields across the board. Comparing the situation to that of Europe, the present paper concludes that the debt crisis in the euro area has not affected the perception of sovereign risks of Asian economies. In fact, a fall in exchange rate and spillover risks, combined with stronger fundamentals, have led to a continued normalization of Asian sovereign spreads since the height of the financial crisis.
Contrasting effect of perlecan on adipogenic and osteogenic differentiation of mesenchymal stem cells in vitro
Authors: Nakamura Ryosuke , Nakamura Fumio , Fukunaga Shigeharu
Published: September 2013

Perlecan, a basement membrane component, shows diverse functions in different organs and tissues. However, the role of perlecan in differentiation of mesenchymal stem cells (MSCs) has been barely investigated. In this study, we examined the effect of perlecan on adipogenic and osteogenic differentiation of MSCs in vitro by adding extrinsic perlecan to culture media or blocking the function of intrinsic perlecan expressed into culture media by differentiating MSCs. Extrinsic perlecan suppressed adipogenic differentiation; however, it promoted osteogenic differentiation. These functions were further confirmed by a study of blocking intrinsic perlecan. Perlecan treated with heparitinase‐I also showed the suppressive effect on adipogenic differentiation. In contrast, the promotive effect on osteogenic differentiation was found to be heparan sulfate‐dependent. Intrinsic perlecan was suggested to be effective at the late stage of adipogenic differentiation by a study of perlecan‐blocking performed at distinct periods, but was suggested to be effective at the early stage of osteogenic differentiation. Our results showed perlecan has contrasting effect on adipogenic and osteogenic differentiation of MSCs due to its diverse actions. Based on these outcomes, we recognized that employing extrinsic perlecan or blocking intrinsic perlecan is effective for regulating adipogenic and osteogenic differentiation of MSCs by restricting its direction.
British Petroleum: An Egregious Violation of the Ethic of First and Second Things
Authors: Veil Shari R. , Sellnow Timothy L. , Wickline Morgan C.
Published: September 2013

This study analyzes BP's crisis communication related to the Deepwater Horizon disaster. Specifically, we observe how an organization whose priorities are misaligned with the ethic of first and second things has a severely limited capacity for delivering a crisis message that resonates with the general public, and especially those most affected by the disaster. Organizational connectedness and Lewis' essays on the ethic of first and second things are discussed and research on virtuous responses to crisis and renewal discourse is highlighted to explain how BP's focus on maximizing profit over safety and the environment stymied their communication efforts. A discourse of renewal is suggested as essential for the organization to regain connectedness post‐crisis.
A systematic approach to assessing the clinical significance of genetic variants
Authors: Duzkale H , Shen J , McLaughlin H , Alfares A , Kelly MA , Pugh TJ , Funke BH , Rehm HL , Lebo MS
Published: September 2013

Molecular genetic testing informs diagnosis, prognosis, and risk assessment for patients and their family members. Recent advances in low‐cost, high‐throughput DNA sequencing and computing technologies have enabled the rapid expansion of genetic test content, resulting in dramatically increased numbers of DNA variants identified per test. To address this challenge, our laboratory has developed a systematic approach to thorough and efficient assessments of variants for pathogenicity determination. We first search for existing data in publications and databases including internal, collaborative and public resources. We then perform full evidence‐based assessments through statistical analyses of observations in the general population and disease cohorts, evaluation of experimental data from in vivo or in vitro studies, and computational predictions of potential impacts of each variant. Finally, we weigh all evidence to reach an overall conclusion on the potential for each variant to be disease causing. In this report, we highlight the principles of variant assessment, address the caveats and pitfalls, and provide examples to illustrate the process. By sharing our experience and providing a framework for variant assessment, including access to a freely available customizable tool, we hope to help move towards standardized and consistent approaches to variant assessment.
Lost in translation: endoplasmic reticulum stress and the decline of β‐cell health in diabetes mellitus
Authors: Evans‐Molina C. , Hatanaka M. , Mirmira R. G.
Published: September 2013

Emerging data illustrate a pivotal role for activation of β‐cell endoplasmic reticulum (ER) stress pathways in diabetes pathophysiology. The purpose of this review is to appraise the evidence for β‐cell ER stress in human type 1 and 2 diabetes, review the molecular signalling pathways involved in the unfolded protein response and ER stress signalling, and to provide data from polyribosome profiling to illustrate the impact of ER stress on the mRNA translation response. Finally, we will discuss existing and novel therapeutic strategies that target β‐cell ER stress and discuss their use in rodent and human type 1 and 2 diabetes.
Glucagon‐like peptide‐1: modulator of β‐cell dysfunction and death
Authors: Rondas D. , D'Hertog W. , Overbergh L. , Mathieu C.
Published: September 2013

Glucagon‐like peptide‐1 (GLP‐1) is one of the hormones responsible for the incretin effect, a term that refers to the observation that orally administered glucose results in a larger increase in plasma insulin levels and insulin‐dependent decrease in blood glucose concentration when compared to the same amount of glucose given intravenously. GLP‐1 is secreted mainly by gut endocrine L‐cells and is released under the control of carbohydrates, proteins and lipids. Upon secretion, GLP‐1 targets different cell types and exerts a wide variety of actions such as potentiation of glucose‐stimulated insulin secretion, reduction of appetite, delay of gastric emptying and increase in β‐cell mass. These beneficial effects have resulted in the application of GLP‐1‐based therapies in patients with type 2 diabetes, but also exploitation of its effects in type 1 diabetes is being envisaged. In this review, we focus on the different, short‐ and long‐term action mechanisms of GLP‐1 with specific emphasis on its role as a modulator of β‐cell function and survival.
Targeting gp130 to prevent inflammation and promote insulin action
Authors: Kraakman M. J. , Allen T. L. , Whitham M. , Iliades P. , Kammoun H. L. , Estevez E. , Lancaster G. I. , Febbraio M. A.
Published: September 2013

Obesity and type 2 diabetes are now the most prevalent metabolic diseases in the Western world and the development of new strategies to treat these metabolic diseases is most warranted. Obesity results in a state of chronic low‐grade inflammation in metabolically active tissues such as the liver, adipose tissue, brain and skeletal muscle. Work in our laboratory has focussed on the role of the cytokine interleukin‐6 (IL)‐6 and other IL‐6‐like cytokines that signal through the gp130 receptor complex. We have focussed on the role of blocking IL‐6 trans‐signalling to prevent inflammation on the one hand, and activating membrane‐bound signalling to promote insulin sensitivity on the other hand. Since the cloning of the IL‐6 gene nearly 30 years ago, a pattern has emerged associating IL‐6 with a number of diseases associated with inflammation including rheumatoid arthritis (RA), Crohn's disease and several cancers. Accordingly, tocilizumab, an IL‐6 receptor‐inhibiting monoclonal antibody, is now useful for the treatment of RA. However, this may not be the most optimal strategy to block inflammation associated with IL‐6 and may result in unwanted side effects that, paradoxically, could actually promote metabolic disease.
Microarray‐assisted fine mapping of quantitative trait loci on chromosome 15 for susceptibility to seizure‐induced cell death in mice
Authors: Schauwecker P. E.
Published: September 2013

Prior studies with crosses of the FVB/NJ (FVB; seizure‐induced cell death‐susceptible) mouse and the C57BL/6J (B6; seizure‐induced cell death‐resistant) mouse revealed the presence of a quantitative trait locus (QTL) on chromosome 15 that influenced susceptibility to kainic acid‐induced cell death (Sicd2). In an earlier study, we confirmed that the Sicd2 interval harbors gene(s) conferring strong protection against seizure‐induced cell death through the creation of the FVB.B6‐Sicd2 congenic strain, and created three interval‐specific congenic lines (ISCLs) that encompass Sicd2 on chromosome 15 to fine‐map this locus. To further localise this Sicd2 QTL, an additional congenic line carrying overlapping intervals of the B6 segment was created (ISCL‐4), and compared with the previously created ISCL‐1–ISCL‐3 and assessed for seizure‐induced cell death phenotype. Whereas all of the ISCLs showed reduced cell death associated with the B6 phenotype, ISCL‐4, showed the most extensive reduction in seizure‐induced cell death throughout all hippocampal subfields. In order to characterise the susceptibility loci on Sicd2 by use of this ISCL and identify compelling candidate genes, we undertook an integrative genomic strategy of comparing exon transcript abundance in the hippocampus of this newly developed chromosome 15 subcongenic line (ISCL‐4) and FVB‐like littermates. We identified 10 putative candidate genes that are alternatively spliced between the strains and may govern strain‐dependent differences in susceptibility to seizure‐induced excitotoxic cell death. These results illustrate the importance of identifying transcriptomics variants in expression studies, and implicate novel candidate genes conferring susceptibility to seizure‐induced cell death.
Hierarchy of factors drivingN2Oemissions in non‐tilled soils under different crops
Authors: Cosentino V. R. N. , Figueiro Aureggui S. A. , Taboada M. A.
Published: September 2013

Nitrous oxide (N2O) is emitted to the atmosphere as a by‐product of nitrification and denitrification by soil microbial processes. Differences in climate, soil and management regulate these processes, causingN2Oemissions to vary in space and time. This study aimed to identify and rank the soil properties that controlN2Oemissions in non‐tilled soils under different crops. Over a period of 2 years, gas samples were taken from closed chambers and soil properties were determined once per season.N2Oemission rates were highly variable (from −15 to 314 µgN2O‐N m−2 hour−1). A regression tree analysis allowed us to classify soilN2Oemissions into three groups, separated by topsoil temperature (primary factor) and water‐filled pore space (WFPS, secondary factor).N2Oemissions were small (mean 4.22 µgN2O‐N m−2 hour−1) with topsoil temperature less than 14°C (Group 1), large (mean 61.87 µgN2O‐N m−2 hour−1) with topsoil temperature between 14 and 23°C andWFPSmore than 58.5% (Group 2) and moderate (mean 21.4 µgN2O‐N m−2 hour−1) with topsoil temperature more than 23°C andWFPSless than 58.5% (Group 3). These emission groups allow for more efficient sampling ofN2Oemissions in the field: in winter, when topsoil temperatures are less than 14°C andN2Oemissions are expected to be small or even negligible, sampling frequency can be reduced; in autumn and spring, when topsoil temperatures are more than 14°C andWFPSis more than 60–70%, sampling frequency should be increased.
Low ankle−brachial index predicts new vascular events and functional outcome after 1 year in patients with non‐cardioembolic stroke: our experience and review
Authors: Alvarez‐Sabín J. , Quintana M. , Santamarina E. , Maisterra O. , Gil‐Núñez A.
Published: September 2013

Background and purpose

The ankle−brachial index (ABI) has been defined as an important factor associated with vascular events. Our objective was to analyze the prognostic value of the ABI as a predictive factor of new vascular events and functional status at 1 year in patients with non‐cardioembolic ischaemic stroke.

Methods

A prospective, longitudinal, observational and multicenter study was performed, including consecutive patients ≥50 years old who had suffered from a non‐cardioembolic ischaemic stroke. Pathological ABI (PI) was defined when the value was ≤0.9. The logistic regression model, survival analysis and the Cox proportional hazard regression model were used to identify factors independently associated with functional outcome and occurrence of new vascular events, including recurrent stroke.

Results

In all, 977 patients were evaluated. The mean age was 69.1 ± 9.5 years. 40.5% patients had PI. Stroke recurrence and new vascular events global rates were 9% and 20% respectively at 1 year. PI was independently associated with new vascular events [hazard ratio 1.764 (1.274–2.444), P = 0.001]. A cut‐off point of ABI ≤ 0.8 (14% vs. 7%, P = 0.002) independently predicted stroke recurrence in an adjusted regression model [hazard ratio 1.807 (1.102–2.963), P = 0.019]. PI was also associated with functional dependence [odds ratio 1.490 (1.011–2.196), P = 0.044].

Conclusions

In non‐cardioembolic ischaemic stroke patients, PI was an independent predictive factor of new vascular events and functional outcome after 1 year of follow‐up.
Transnational Judicial Dialogue as an Organisational Field
Authors: Frishman Olga
Published: September 2013

Over the last few decades, judges and courts have had an important role in global governance. They also now communicate with each other more than they used to. Scholars have named this phenomenon ‘the transnational judicial dialogue.’ This paper calls for a comprehensive understanding of this judicial dialogue in a way that will explain the influence it has on courts. This paper proposes to use the concept of organisational fields, developed by DiMaggio and Powell, to study the relationships between courts. It will be seen that this concept gives a fuller account of those relationships and their effects than the existing approaches. This paper will first show that the transnational organisational field of the courts is now emerging using the four criteria of structuration. Then, the paper will discuss three examples of how this concept can contribute to the study of transnational relationships between courts.
Use of two conventional staining methods to assess the acrosomal status of stallion spermatozoa
Authors: Runcan E. E. , Pozor M. A. , Zambrano G. L. , Benson S. , Macpherson M. L.
Published: September 2013

Reasons for performing study

The acrosome is a highly specialised region of the spermatozoon that is essential for fertilisation. Defects or dysfunction of this structure have been associated with fertility problems in man and various domestic species including stallions. Current methods of evaluating the acrosome of stallion spermatozoa are time consuming and require specialised equipment, which is cost prohibitive to the average practitioner.

Objectives

To evaluate 2 conventional stains (Dip Quick and Spermac) and determine their usefulness in assessing acrosome integrity in stallions as compared with specific acrosomal labelling with a fluorescein‐conjugated lectin – a method that has been validated for acrosome status evaluation in stallions.

Study design

In vivo experimental design.

Methods

Semen from 6 mature Miniature horse stallions of known fertility was collected on 5 separate occasions. To increase the number of reacted acrosomes, portions of each ejaculate were incubated with the calcium ionophore, A23187. Ejaculates were divided and semen samples were processed according to recommendations for fluorescein‐conjugated peanut lectin, Pisum sativum agglutin, Dip Quick, and Spermac staining methods. Slides were evaluated independently by 2 separate investigators. Spermatozoa were classified as having intact, reacting, reacted or defective acrosomes.

Results

All parameters obtained by both investigators, using all 3 staining methods were highly correlated (P<0.001). There was no statistical difference (P>0.05) between investigators or staining method for the percentages of intact or reacted acrosomes. However, there was a significant difference between investigators and staining methods for determining reacting acrosome percentages (P<0.05).

Conclusions

Dip Quick and Spermac stains are useful for determining intact vs. reacted acrosomes for stallion spermatozoa.
Elasticity and breaking strength of synthetic suture materials incubated in various equine physiological and pathological solutions
Authors: Kearney C. M. , Buckley C. T. , Jenner F. , Moissonnier P. , Brama P. A. J.
Published: September 2013

Reasons for performing study

Selection of suture material in equine surgery is often based on costs or subjective factors, such as the surgeon's personal experience, rather than objective facts. The amount of objective data available on durability of suture materials with regard to specific equine physiological conditions is limited.

Objectives

To evaluate the effect of various equine physiological and pathological fluids on the rate of degradation of a number of commonly used suture materials.

Study design

In vitromaterial testing.

Methods

Suture materials were exposedin vitroto physiological fluid, followed by biomechanical analysis. Three absorbable suture materials, glycolide/lactide copolymer, polyglactin 910 and polydioxanone were incubated at 37°Cfor 7, 14 or 28 days in phosphate‐buffered saline, equine serum, equine urine and equine peritoneal fluid from an animal with peritonitis. Five strands of each suture material type were tested to failure in a materials testing machine for each time point and each incubation medium. Yield strength, strain andYoung's modulus were calculated, analysed and reported.

Results

For all suture types, the incubation time had a significant effect on yield strength, percentage elongation andYoung's modulus in all culture media (P<0.0001). Suture type was also shown significantly to influence changes in each of yield strength, percentage elongation andYoung's modulus in all culture media (P<0.0001). While the glycolide/lactide copolymer demonstrated the highest Day 0 yield strength, it showed the most rapid degradation in all culture media. For each of the 3 material characteristics tested, polydioxanone showed the least variation across the incubation period in each culture medium.

Conclusions

The duration of incubation and the type of fluid have significant effects on the biomechanical properties of various suture materials. These findings are important for evidence‐based selection of suture material in clinical cases.
Changes in soil organic carbon in a clay loam soil following ploughing and reseeding of permanent grassland under temperate moist climatic conditions
Authors: Necpálová M. , Li D. , Lanigan G. , Casey I. A. , Burchill W. , Humphreys J.
Published: September 2013

This study investigated changes in soil organic carbon (SOC) in a poorly drained clay loam soil under (i) permanent grassland (PG) over 7 years and (ii) after PG renovation over 2·5 years. The experimental area was divided into four blocks with four paddocks per block. Composite soil samples from each PG block were taken to 30‐cm depth on five occasions between 2004 and 2011. In June 2008, one paddock per block was renovated by ploughing and reseeding and sampled as above on the latter four occasions. Renovation decreased SOC (P < 0·05) by 32·2 t ha−1 in the 2·5 years following ploughing; the difference developed almost entirely (86%) in the first four months. Renovation had no effect on above‐ground productivity, standing root and stubble phytomass or on dissolved organic matter leaching. Therefore, soil respiration was considered to be a single potential pathway responsible for the SOC loss from renovated grassland. Although a simple linear regression indicated a tendency for PG to accumulate SOC, there was no evidence of recovery in SOC to previous levels following renovation during the study period. These results could have implications for greenhouse gas inventories in countries where PG is an important land‐use type.
Cesium transfer to Gramineae biofuel crops grown in a field polluted by radioactive fallout and efficiency of trapping the cesium stable isotope in a small‐scale model system for biomass gasification
Authors: Kobayashi Makoto , Takeno Keiji , Matsumoto Keigo , Matsunami Hisaya , Tsuruta Shin‐ichi , Ando Shotaro
Published: September 2013

The accident at the Fukushima Daiichi Nuclear Power Plant (Tokyo Electric Power Company, Inc.) caused by the Great East Japan Earthquake of 11 March 2011 resulted in radioactive fallout that caused heavy damage to agricultural production over a wide area of eastern Japan. Production of biofuel crops and their conversion to energy may be one way to resume agricultural production at an early date and to put renewable energy to practical use. This study addressed two concerns relevant to this scenario: (i) the degree of transfer of radioactive cesium from the soil to biofuel crops; and (ii) evaluation of gasification technology from the standpoint of removal of cesium contained in the biomass. Sixteen lines of Gramineae crops grown in an experimental field 112 km from the nuclear power plant contained 143.4–600.4 Bq kg−1 dry matter (DM) of radioactive cesium, the arithmetic average being 285.9 Bq kg−1 DM. The crops included, inter alia, Erianthus arundinaceus (Retz.) Jesw., Miscanthus spp., maize (Zea mays L.) and sorghum (Sorghum bicolor Moench), all of which were cultivated without tillage in 2011. A comparison of Miscanthus spp. that overwintered between 2011 and 2012 revealed that radioactivity decreased from 146.1 to 229.3 Bq kg−1 DM (arithmetic average: 193.3 Bq kg−1 DM) to 53.0–81.0 Bq kg−1 DM (arithmetic average: 66.0 Bq kg−1 DM). A simplified laboratory‐scale experiment revealed that the stable isotope of cesium attached to pulverized biomass of Japanese cedar (Cryptomeria japonica D. Don) and E. arundinaceus was completely trapped in gasification system and gas purification system. This result indicates that cesium was not transferred to the gas that was produced for fuel. Gasification using polluted biomass will be practical after further studies have addressed problems related to issues such as scale‐up, troubleshooting continuous runs and disposal of radioactive wastes.
Pan Africanism: A Brief Intellectual History
Authors: Eze Michael Onyebuchi
Published: September 2013

In this article, I will historicize the socio‐political and cultural emergence of Pan Africanism as an ideology. In doing so, one is enabled to appreciate its continued relevance and significance as well as its limitations and imposed misrecognition, morass misapplications, and muddled ambiguities within history. Historicizing Pan Africanism as a discourse frees it from an essentialist rendered definition and enables a new understanding in which Pan Africanism is to be understood as a performative‐operative discourse. Being performative means that it ceases to be a close‐minded rigid ideology proscribed by racial consciousness; it means assuming a new pose of repudiation that is dependent on contemporary socio‐cultural tissues of historical experiences. But our concept is not just performative, it is also discursive because it generates a new sense of meaning for our contemporary understanding of Africanity.
Chinese Migration and Settlement in Southeast Asia Before 1850: Making Fields From the Sea
Authors: Lockard Craig A.
Published: September 2013

Human migration is a central theme in world and Asian history, but important cases, among them Chinese who emigrated to other countries between ca. 1000 and 1850 CE, have been somewhat neglected in the migration literature. Since the mid‐19th century, millions of Chinese migrated temporarily or permanently to other countries, making these migrants and their descendants a vital presence in the world economy and in the population of many nations. Today, more than 30 million people of Chinese ancestry or ethnicity live outside of Greater China, over 20 million of them in Southeast Asia. But this emigration has a much longer history, the subject of recent scholarly interest that has enriched our knowledge and is the focus of this essay. It has been said of the maritime trading and fishing peoples of southern China that they made fields from the sea. Enterprising and adaptable, Chinese have long sailed to Southeast Asia to trade, many of them settling permanently. By 1400, Chinese trade networks linked Southeast Asian trading ports to China and to each other. Chinese settlers eventually became dominant in the commercial sector in many societies, including most Western colonies, in Southeast Asia. Increasing numbers of migrants arrived to trade or mine for tin and gold, ushering in a “Chinese century” in the Southeast Asian economies from around 1700 into the mid‐1800s. Over the centuries some Chinese married local women, serving as cultural brokers between China and Southeast Asia and fostering hybrid communities. Others maintained their cultural heritage. After 1850, millions more left China. Chinese immigrants and their descendants built the foundations for a widespread modern diaspora and transnational connections. The emigrant flow from China continues, continuing a human behavior – migration – that has a long history in Asia.