bluuebunny/crossref_metadata_2025 huggingface dataset:
Revisiting the concept of Beverton­­–Holt life-history invariants with the aim of informing data-poor fisheries assessment
Authors: Prince Jeremy , Hordyk Adrian , Valencia Sarah R. , Loneragan Neil , Sainsbury Keith
Published: February 2014

The complexity and cost of assessment techniques prohibits their application to 90% of fisheries. Simple generic approaches are needed for the world's small-scale and data-poor fisheries. This meta-analysis of the relationship between spawning potential and the normalized size and age of 123 marine species suggests that the so-called Beverton–Holt life-history invariants (BH-LHI; Lm/L∞, M/k, M × Agem) actually vary together in relation to life-history strategy, determining the relationship between size, age, and reproductive potential for each species. Although little realized, the common assumption of unique values for the BH-LHI also implies that all species share the same relationship between size, age, and reproductive potential. This implicit assumption is not supported by this meta-analysis, which suggests that there is considerable but predictable natural variation in the BH-LHI ratios and the relationships between size, age, and reproductive potential that they determine. We believe that this reconceptualization of the BH-LHI has potential to provide a theoretical framework for “borrowing” knowledge from well-studied species to apply to related, unstudied species and populations, and when applied together with the assessment technique described by Hordyk et al. (2015b), could make simple forms of size-based assessment possible for many currently unassessable fish stocks.
50 picoarcsec astrometry of pulsar emission
Authors: Pen Ue-Li , Macquart Jean-Pierre , Deller Adam T. , Brisken Walter
Published: February 2014

We use very long baseline interferometry (VLBI) imaging of the interstellar scattering speckle pattern associated with the pulsar PSR 0834+06 to measure the astrometric motion of its emission. The D ∼ 5 au interstellar baselines, provided by interference between speckles spanning the scattering disc, enable us to detect motions with subnanoarcsecond accuracy. We measure a small pulse deflection of ∼18 ± 2 km (not including geometric uncertainties), which is 100 times smaller than the characteristic resolution (λ/D) of this interstellar interferometer. This implies that the emission region is small, and at an altitude of a few hundred km, with the exact value depending on field geometry. This is substantially closer to the star than to the light cylinder. Future VLBI measurements can improve on this finding. This new regime of ultraprecise astrometry may enable precision parallax distance determination of pulsar binary displacements.
Star formation in the ultraluminous infrared galaxy F00183-7111
Authors: Mao Minnie Y. , Norris Ray P. , Emonts Bjorn , Sharp Rob , Feain Ilana , Chow Kate , Lenc Emil , Stevens Jamie
Published: February 2014

We report the detection of molecular CO(1–0) gas in F00183-7111, one of the most extreme ultraluminous infrared galaxies (ULIRGs) known, with the Australia Telescope Compact Array. We measure a redshift of 0.3292 for F00183-7111 from the CO(1–0) line and estimate the mass of the molecular gas in 00183 to be 1 × 1010 M⊙. We find that F00183-7111 is predominately powered by the active galactic nucleus (AGN) and only ∼14 per cent of the total luminosity is contributed by star formation (SFR ∼220 M⊙ yr−1). We also present an optical image of F00183-7111, which shows an extension to the east. We searched for star formation in this extension using radio continuum observations but do not detect any. This suggests that the star formation is likely to be predominately nuclear. These observations provide additional support for a model in which the radio emission from ULIRGs is powered by an intense burst of star formation and by a radio-loud AGN embedded in its nucleus, both triggered by a merger of gas-rich galaxies.
Delivering sustainable crop protection systems via the seed: exploiting natural constitutive and inducible defence pathways
Authors: Pickett John A. , Aradottír Gudbjorg I. , Birkett Michael A. , Bruce Toby J. A. , Hooper Antony M. , Midega Charles A. O. , Jones Huw D. , Matthes Michaela C. , Napier Johnathan A. , Pittchar Jimmy O. , Smart Lesley E. , Woodcock Christine M. , Khan Zeyaur R.
Published: February 2014

To reduce the need for seasonal inputs, crop protection will have to be delivered
via
the seed and other planting material. Plant secondary metabolism can be harnessed for this purpose by new breeding technologies, genetic modification and companion cropping, the latter already on-farm in sub-Saharan Africa. Secondary metabolites offer the prospect of pest management as robust as that provided by current pesticides, for which many lead compounds were, or are currently deployed as, natural products. Evidence of success and promise is given for pest management in industrial and developing agriculture. Additionally, opportunities for solving wider problems of sustainable crop protection, and also production, are discussed.
Brachybacterium huguangmaarense sp. nov., isolated from Lake sediment
Authors: Liu Ying , Xie Qing-Yi , Shi Wei , Li Lei , An Jun-Ying , Zhao Ya-Mei , Hong Kui
Published: February 2014

A Gram-stain positive strain, M1T, was isolated from the sediment of Maar Lake in Zhanjiang, Guangdong Province, China. The diagnostic cell-wall diamino acid was meso-diaminopimelic acid, and mycolic acids were not detected. The polar lipid profile of strain M1T consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and an unknown glycolipid. The predominant quinone was MK-7, with MK-6 as a minor component. The major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0, with iso-C18 : 0 as a minor component. The DNA G+C content of the genomic DNA was 71.0 mol%. 16S rRNA gene sequence analysis showed that strain M1T belongs to the family

Dermabacteraceae

, sharing highest sequence similarity with

Brachybacterium nesterenkovii

JCM 11648T (98.1 %). Furthermore, a combination of DNA–DNA relatedness and physiological and biochemical properties indicated that the novel strain could be readily distinguished from its closest phylogenetic relatives. On the basis of these phenotypic and genotypic data, strain M1T represents a novel species of the genus

Brachybacterium

, for which the name Brachybacterium huguangmaarense sp. nov. is proposed. The type strain is M1T ( = CCTCC AB 2012866T = DSM 26370T).
Vibrio cholerae NspS, a homologue of ABC-type periplasmic solute binding proteins, facilitates transduction of polyamine signals independent of their transport
Authors: Cockerell Steven R. , Rutkovsky Alex C. , Zayner Josiah P. , Cooper Rebecca E. , Porter Lindsay R. , Pendergraft Sam S. , Parker Zach M. , McGinnis Marcus W. , Karatan Ece
Published: February 2014

The polyamines norspermidine and spermidine are among the environmental signals that regulateVibrio choleraebiofilm formation. The effects of these polyamines are mediated by NspS, a member of the bacterial periplasmic solute binding protein superfamily. Almost all members of this superfamily characterized to date are components of ATP-binding cassette-type transporters involved in nutrient uptake. Consequently, in the current annotation of theV. choleraegenome, NspS has been assigned a function in transport. The objective of this study was to further characterize NspS and investigate its potential role in transport. Our results support a role for NspS in signal transduction in response to norspermidine and spermidine, but not their transport. In addition, we provide evidence that these polyamine signals are processed by c-di-GMP signalling networks in the cell. Furthermore, we present comparative genomics analyses which reveal the presence of NspS-like proteins in a variety of bacteria, suggesting that periplasmic ligand binding proteins may be widely utilized for sensory transduction.
Characterization of an enhanced antigenic change in the pandemic 2009 H1N1 influenza virus haemagglutinin
Authors: García-Barreno Blanca , Delgado Teresa , Benito Sonia , Casas Inmaculada , Pozo Francisco , Cuevas María Teresa , Mas Vicente , Trento Alfonsina , Rodriguez-Frandsen Ariel , Falcón Ana , Ortín Juan , Nieto Amelia , Melero José A.
Published: February 2014

Murine hybridomas producing neutralizing mAbs specific to the pandemic influenza virus A/California/07/2009 haemagglutinin (HA) were isolated. These antibodies recognized at least two different but overlapping new epitopes that were conserved in the HA of most Spanish pandemic isolates. However, one of these isolates (A/Extremadura/RR6530/2010) lacked reactivity with the mAbs and carried two unique mutations in the HA head (S88Y and K136N) that were required simultaneously to eliminate reactivity with the murine antibodies. This unusual requirement directly illustrates the phenomenon of enhanced antigenic change proposed previously for the accumulation of simultaneous amino acid substitutions at antigenic sites of the influenza A virus HA during virus evolution (Shihet al.,Proc Natl Acad Sci USA,104 , 6283–6288, 2007). The changes found in the A/Extremadura/RR6530/2010 HA were not found in escape mutants selectedin vitrowith one of the mAbs, which contained instead nearby single amino acid changes in the HA head. Thus, either single or double point mutations may similarly alter epitopes of the new antigenic site identified in this work in the 2009 H1N1 pandemic virus HA. Moreover, this site is relevant for the human antibody response, as shown by competition of mAbs and human post-infection sera for virus binding. The results are discussed in the context of the HA antigenic structure and challenges posed for identification of sequence changes with possible antigenic impact during virus surveillance.
A reassessment of consensus clustering for class discovery
Authors: Senbabaoglu Yasin , Michailidis George , Li Jun Z.
Published: February 2014

Consensus clustering (CC) is an unsupervised class discovery method widely used to study sample heterogeneity in high-dimensional datasets. It calculates “consensus rate” between any two samples as how frequently they are grouped together in repeated clustering runs under a certain degree of random perturbation. The pairwise consensus rates form a between-sample similarity matrix, which has been used (1) as a visual proof that clusters exist, (2) for comparing stability among clusters, and (3) for estimating the optimal number (K) of clusters. However, the sensitivity and specificity of CC have not been systemically studied. To assess its performance, we investigated the most common implementations of CC; and compared CC with other popular methods that also focus on cluster stability and estimation of K. We evaluated these methods using simulated datasets with either known structure or known absence of structure. Our results showed that (1) CC was able to divide randomly generated unimodal data into pre-specified numbers of clusters, and was able to show apparent stability of these chance partitions of known cluster-less data; (2) for data with known structure, the proportion of ambiguously clustered (PAC) pairs infers the known number of clusters more reliably than several commonly used K estimating methods; and (3) validation of the optimal K by choosing the most discriminant genes from the discovery cohort and applying them in an independent cohort often exaggerates the confidence in K due to inherent gene-gene correlations among the selected genes. While these results do not yet prove that any of the published studies using CC has generated false positive findings, they show that datasets with subtle or no structure are fully capable of producing strong evidence of consensus clustering. We therefore recommend caution is using CC in class discovery and validation.
Differential gene expression and alternative splicing in insect immune specificity
Authors: Riddell Carolyn , Lobaton Garces Juan David , Adams Sally , Barribeau Seth M , Twell David , Mallon Eamonn
Published: February 2014

Ecological studies routinely show genotype-genotype interactions between insects and their parasites. The mechanisms behind these interactions are not clearly understood. Using the bumblebee Bombus terrestris / trypanosome Crithidia bombi model system, we have carried out a transcriptome-wide analysis of gene expression and alternative splicing in bees during C. bombi infection. We have performed four analyses, 1) comparing gene expression in infected and non-infected bees 24 hours after infection by Crithidia bombi, 2) comparing expression at 24 and 48 hours after C.bombi infection, 3) searching for differential gene expression associated with the host-parasite genotype-genotype interaction at 24 hours after infection and 4) searching for alternative splicing associated with the host-parasite genotype-genotype interaction at 24 hours post infection. We found a large number of genes differentially regulated related to numerous canonical immune pathways. These genes include receptors, signaling pathways and effectors. We discovered a possible interaction between the peritrophic membrane and the insect immune system in defense against Crithidia. Most interestingly we found differential expression and alternative splicing of Dscam related transcripts and a novel immunoglobulin related gene Twitchin depends on the genotype-genotype interactions of the given bumblebee colony and Crithidia strain.
Spectacle: Faster and more accurate chromatin state annotation using spectral learning
Authors: Song Jimin , Chen Kevin C.
Published: February 2014

Recently, a wealth of epigenomic data has been generated by biochemical assays and next-generation sequencing (NGS) technologies. In particular, histone modification data generated by the ENCODE project and other large-scale projects show specific patterns associated with regulatory elements in the human genome. It is important to build a unified statistical model to decipher the patterns of multiple histone modifications in a cell type to annotate chromatin states such as transcription start sites, enhancers and transcribed regions rather than to map histone modifications individually to regulatory elements.

Several genome-wide statistical models have been developed based on hidden Markov models (HMMs). These methods typically use the Expectation-Maximization (EM) algorithm to estimate the parameters of the model. Here we used spectral learning, a state-of-the-art parameter estimation algorithm in machine learning. We found that spectral learning plus a few (up to five) iterations of local optimization of the likelihood outper-forms the standard EM algorithm. We also evaluated our software implementation calledSpectacleon independent biological datasets and found thatSpectacleannotated experimentally defined functional elements such as enhancers significantly better than a previous state-of-the-art method.

Spectaclecan be downloaded fromhttps://github.com/jiminsong/Spectacle.
A positive feedback between p53 and miR-34 miRNAs mediates tumor suppression
Authors: Okada Nobuhiro , Lin Chao-Po , Ribeiro Marcelo C. , Biton Anne , Lai Gregory , He Xingyue , Bu Pengcheng , Vogel Hannes , Jablons David M. , Keller Andreas C. , Wilkinson J. Erby , He Biao , Speed Terry P. , He Lin
Published: February 2014

As bona fide p53 transcriptional targets, miR-34 microRNAs (miRNAs) exhibit frequent alterations in many human tumor types and elicit multiple p53 downstream effects upon overexpression. Unexpectedly, miR-34 deletion alone fails to impair multiple p53-mediated tumor suppressor effects in mice, possibly due to the considerable redundancy in the p53 pathway. Here, we demonstrate that miR-34a represses HDM4, a potent negative regulator of p53, creating a positive feedback loop acting on p53. In a Kras-induced mouse lung cancer model, miR-34a deficiency alone does not exhibit a strong oncogenic effect. However, miR-34a deficiency strongly promotes tumorigenesis when p53 is haploinsufficient, suggesting that the defective p53–miR-34 feedback loop can enhance oncogenesis in a specific context. The importance of the p53/miR-34/HDM4 feedback loop is further confirmed by an inverse correlation between miR-34 and full-length HDM4 in human lung adenocarcinomas. In addition, human lung adenocarcinomas generate an elevated level of a short HDM4 isoform through alternative polyadenylation. This short HDM4 isoform lacks miR-34-binding sites in the 3′ untranslated region (UTR), thereby evading miR-34 regulation to disable the p53-miR-34 positive feedback. Taken together, our results elucidated the intricate cross-talk between p53 and miR-34 miRNAs and revealed an important tumor suppressor effect generated by this positive feedback loop.
Imaging of Endogenous Messenger RNA Splice Variants in Living Cells Reveals Nuclear Retention of Transcripts Inaccessible to Nonsense-Mediated Decay in Arabidopsis
Authors: Göhring Janett , Jacak Jaroslaw , Barta Andrea
Published: February 2014

Alternative splicing (AS) is an important regulatory process that leads to the creation of multiple RNA transcripts from a single gene. Alternative transcripts often carry premature termination codons (PTCs), which trigger nonsense-mediated decay (NMD), a cytoplasmic RNA degradation pathway. However, intron retention, the most prevalent AS event in plants, often leads to PTC-carrying splice variants that are insensitive to NMD; this led us to question the fate of these special RNA variants. Here, we present an innovative approach to monitor and characterize endogenous mRNA splice variants within living plant cells. This method combines standard confocal laser scanning microscopy for molecular beacon detection with a robust statistical pipeline for sample comparison. We demonstrate this technique on the localization of NMD-insensitive splice variants of two Arabidopsis thaliana genes, RS2Z33 and the SEF factor. The experiments reveal that these intron-containing splice variants remain within the nucleus, which allows them to escape the NMD machinery. Moreover, fluorescence recovery after photobleaching experiments in the nucleoplasm show a decreased mobility of intron-retained mRNAs compared with fully spliced RNAs. In addition, differences in mobility were observed for an mRNA dependent on its origin from an intron-free or an intron-containing gene.
On physical property tensors invariant under line groups
Authors: Litvin Daniel B.
Published: February 2014

The form of physical property tensors of a quasi-one-dimensional material such as a nanotube or a polymer can be determined from the point group of its symmetry group, one of aninfinitenumber of line groups. Such forms are calculated using a method based on the use of trigonometric summations. With this method, it is shown that materials invariant under infinite subsets of line groups have physical property tensors of the same form. For line group types of a family of line groups characterized by an indexnand a physical property tensor of rankm, the form of the tensor for all line group types indexed withn>mis the same, leaving only afinitenumber of tensor forms to be determined.
Stability of source mechanisms inverted from P‐wave amplitude microseismic monitoring data acquired at the surface
Authors: Staněk František , Eisner Leo , Jan Moser Tijmen
Published: February 2014

We study the stability of source mechanisms inverted from data acquired at surface and near‐surface monitoring arrays. The study is focused on P‐wave data acquired on vertical components, as this is the most common type of acquisition. We apply ray modelling on three models: a fully homogeneous isotropic model, a laterally homogeneous isotropic model and a laterally homogeneous anisotropic model to simulate three commonly used models in inversion. We use geometries of real arrays, one consisting in surface receivers and one consisting in ‘buried’ geophones at the near‐surface. Stability was tested for two of the frequently observed source mechanisms: strike‐slip and dip‐slip and was evaluated by comparing the parameters of correct and inverted mechanisms. We assume these double‐couple source mechanisms and use quantitatively the inversion allowing non‐double‐couple components to measure stability of the inversion. To test the robustness we inverted synthetic amplitudes computed for a laterally homogeneous isotropic model and contaminated with noise using a fully homogeneous model in the inversion. Analogously amplitudes computed in a laterally homogeneous anisotropic model were inverted in all three models. We show that a star‐like surface acquisition array provides very stable inversion up to a very high level of noise in data. Furthermore, we reveal that strike‐slip inversion is more stable than dip‐slip inversion for the receiver geometries considered here. We show that noise and an incorrect velocity model may result in narrow bands of source mechanisms in Hudson's plots.
Pyromorphite formation in a fungal biofilm community growing on lead metal
Authors: Rhee Young Joon , Hillier Stephen , Pendlowski Helen , Gadd Geoffrey Michael
Published: February 2014

Lead is a priority pollutant, and lead metal is widely found in the environment as a waterproofing structural component in roofing, fence post covers, venting and flashing, as well as in industrial and urban waste. However, little is known of microbial interactions with metallic lead. The objective of this research was to investigate fungal roles in transformations of lead in a surface biofilm community growing on lead sheeting. The lead surface was found to support a diverse fungal community with several members, such as Aureobasidum pullulans, Phoma macrostoma, Penicillium sp. and Botryotinia fuckeliana, probably originating from adjacent phylloplane communities. Many fungal isolates showed tolerance to lead compounds in growth inhibition assays and were able to mediate production of lead‐containing secondary minerals in the presence of metallic lead. These exhibited widely differing morphologies to the lead‐containing secondary minerals produced under abiotic conditions. The presence of pyromorphite (Pb5(PO4)3Cl) (approximately 50 wt%) was detected in the lead sheet biofilm, and we speculate that animal (bird) faeces could be a significant source of phosphorus in this location. Pyromorphite formation represents biomineralization of mobile lead species into a very stable form, and this research provides the first demonstration of its occurrence in the natural environment.
Cyclic‐di‐GMP levels affect Pseudomonas aeruginosa fitness in the presence of imipenem
Authors: Nicastro Gianlucca G. , Kaihami Gilberto H. , Pereira Thays O. , Meireles Diogo A. , Groleau Marie‐Christine , Déziel Eric , Baldini Regina L.
Published: February 2014

A large number of genes coding for enzymes predicted to synthesize and degrade 3′–5′‐cyclic diguanylic acid (c‐di‐GMP) is found in most bacterial genomes and this dinucleotide emerged as an intracellular signal‐controlling bacterial behaviour. An association between high levels of c‐di‐GMP and antibiotic resistance may be expected because c‐di‐GMP regulates biofilm formation and this mode of growth leads to enhanced antibiotic resistance. However, a clear understanding of this correlation has not been established. We found that increased levels of c‐di‐GMP in Pseudomonas aeruginosa improve fitness in the presence of imipenem, even when grown as planktonic cells. P. aeruginosa post‐transcriptionally regulates the amounts of five porins in response to c‐di‐GMP, including OprD, responsible for imipenem uptake. Cells with low c‐di‐GMP levels are consequently more sensitive to this antibiotic. Main efflux pumps or β‐lactamase genes did not show altered mRNA levels in P. aeruginosa strains with modified different c‐di‐GMP concentrations. Together, our findings show that c‐di‐GMP levels modulate fitness of planktonic cultures in the presence of imipenem.
Bees under stress: sublethal doses of a neonicotinoid pesticide and pathogens interact to elevate honey bee mortality across the life cycle
Authors: Doublet Vincent , Labarussias Maureen , de Miranda Joachim R. , Moritz Robin F. A. , Paxton Robert J.
Published: February 2014

Microbial pathogens are thought to have a profound impact on insect populations. Honey bees are suffering from elevated colony losses in the northern hemisphere possibly because of a variety of emergent microbial pathogens, with which pesticides may interact to exacerbate their impacts. To reveal such potential interactions, we administered at sublethal and field realistic doses one neonicotinoid pesticide (thiacloprid) and two common microbial pathogens, the invasive microsporidian Nosema ceranae and black queen cell virus (BQCV), individually to larval and adult honey bees in the laboratory. Through fully crossed experiments in which treatments were administered singly or in combination, we found an additive interaction between BQCV and thiacloprid on host larval survival likely because the pesticide significantly elevated viral loads. In adult bees, two synergistic interactions increased individual mortality: between N. ceranae and BQCV, and between N. ceranae and thiacloprid. The combination of two pathogens had a more profound effect on elevating adult mortality than N. ceranae plus thiacloprid. Common microbial pathogens appear to be major threats to honey bees, while sublethal doses of pesticide may enhance their deleterious effects on honey bee larvae and adults. It remains an open question as to whether these interactions can affect colony survival.
Behaviour change and social blinkers? The role of sociology in trials of self‐management behaviour in chronic conditions
Authors: Ong Bie Nio , Rogers Anne , Kennedy Anne , Bower Peter , Sanders Tom , Morden Andrew , Cheraghi‐Sohi Sudeh , Richardson Jane C. , Stevenson Fiona
Published: February 2014

Individual‐focused self‐management interventions are one response to both an ageing society and the purported increase in chronic conditions. They tend to draw on psychological theories in self‐management interventions, but over‐reliance on these theories can reinforce a narrow focus on specified attitudinal and behavioural processes, omitting aspects of living with a chronic condition. While advances have been made in health behaviour change theory and practice, scant attention has been paid to the social, with the question of social context remaining under‐theorised and under‐explored empirically. This is particularly noticeable in trials of behaviour change interventions for self‐management. The common sociological critique is that these ignore context and thus no explanation can be given as to why, for whom and under what circumstances a treatment works. Conversely, sociologists are criticised for offering no positive suggestions as to how context can be taken into account and for over‐emphasising context with the risk of inhibiting innovation. This article provides an overview of these issues and provides examples of how context can be incorporated into the rigid method of trials of self‐management for chronic conditions. We discuss modifications to both trial interventions and design that make constructive use of the concept of context.
Enjoy your food: on losing weight and taking pleasure
Authors: Vogel Else , Mol Annemarie
Published: February 2014

Does healthy eating require people to control themselves and abstain from pleasure? This idea is dominant, but in our studies of dieting in The Netherlands we encountered professionals who work in other ways. They encourage their clients to enjoy their food, as only such joy provides satisfaction and the sense that one has eaten enough. Enjoying one's food is not easy. It depends on being sensitive. This does not come naturally but needs training. And while one kind of hunger may be difficult to distinguish from another, feeling pleasure may open the doors to feeling pain. What is more, sensitivity is not enough: enjoying one's food also depends on the food being enjoyable. A lot of care is required for that. But while engaging in such care is hard work, along the way clients are encouraged to no longer ask ‘Am I being good?’ but to wonder instead ‘Is this good for me?’ Both these questions are normative and focus on the person rather than on her socio‐material context. However, in the situations related here the difference is worth making. For it entails a shift from externally controlling your behaviour to self‐caringly enjoying your food.
From health behaviours to health practices: an introduction
Authors: Cohn Simon
Published: February 2014

The concept of health behaviour has become ubiquitous in health‐related research and intervention studies, as well as among policymakers. Developed from psychology, it is based on a number of key underlying assumptions that enable it to be integrated in an existing health research paradigm. However, by conceiving individual health behaviour as discrete, stable, homogeneous and measurable, many other aspects of health‐related activities, in particular those relating to power and sociality, are excluded. As a consequence, any genuine contribution from medical sociology or related disciplines is, at best, limited. To counter this, it is proposed that reconceptualising what people do in terms of health practices, rather than health behaviour, captures the emergent and contingent properties of people's activities in particular situations. Rather than serving as a direct replacement term, and thus reproducing the same epistemological assumptions, it is argued that its very flexibility and capacity to articulate different theoretical orientations is likely to be its major strength.
Application of proteomics to the areas of milk production, processing and quality control – A review
Authors: Abd El‐Salam Mohamed H
Published: February 2014

Milk contains a complex mixture of proteins that undergo several qualitative and quantitative changes during processing and storage. Elucidation of these changes is important to optimise milk processing and storage parameters. Proteomics has become widely used in the field of research on milk proteins due to improvements in the tools and diversified ways in which the methodologies of protein analysis have been developed. This review describes the use of proteomics in studies on milk proteins in relation to species–species differences, post‐translational modification, effect of lactation, mastitis, changes in heated milk and during cheese ripening, and the detection of milk adulteration.
Accuracy of diagnosing gastroesophageal reflux disease by GerdQ, esophageal impedance monitoring and histology
Authors: Zhou Li Ya , Wang Ye , Lu Jing Jing , Lin Lin , Cui Rong Li , Zhang He Jun , Xue Yan , Ding Shi Gang , Lin San Ren
Published: February 2014

Objective

To assess the performance of self‐assessment gastroesophageal reflux disease questionnaire (GerdQ), 24‐h impedance monitoring, proton pump inhibitor (PPI) test and intercellular space of esophageal mucosal epithelial cells in the diagnosis of gastroesophageal reflux disease (GERD).

Methods

Patients with symptoms suspected of GERD were administered the GerdQ and underwent endoscopy (measurement of intercellular space in the biopsy specimen sampling at 2 cm above the Z‐line) and 24‐h impedance pH monitoring, together with a 2‐week experimental treatment with esomeprazole.

Results

A total of 636 patients were included for the final analysis, including 352 with GERD. The sensitivity and specificity of GerdQ and 24‐h impedance monitoring for diagnosing GERD were 57.7% and 48.9%, and 66.4% and 43.3%, respectively. The sensitivity of 24‐h impedance pH monitoring increased to 93.7%. The sensitivity and specificity of dilated intercellular spaces (DIS) (≥0.9 μm) for diagnosing GERD were 61.2% and 56.1%, respectively, whereas those for PPI test were 70.5% and 44.4%.

Conclusions

GerdQ score or PPI test alone cannot accurately diagnose GERD in a Chinese population suspected of GERD. A definitive diagnosis of GERD still depends on endoscopy or 24‐h pH monitoring. 24‐h impedance pH monitoring may increase the sensitivity for diagnosing GERD by 20%; however, when used alone, it results in poor specificity in patients without acid suppressive therapy.
Coverage of diarrhoea‐associated Escherichia coli isolates from different origins with two types of phage cocktails
Authors: Bourdin Gilles , Navarro Armando , Sarker Shafiqul A. , Pittet Anne‐C. , Qadri Firdausi , Sultana Shamima , Cravioto Alejandro , Talukder Kaisar A. , Reuteler Gloria , Brüssow Harald
Published: February 2014

Eighty‐nine T4‐like phages from our phage collection were tested against four collections of childhood diarrhoea‐associated Escherichia coli isolates representing different geographical origins (Mexico versus Bangladesh), serotypes (69 O, 27 H serotypes), pathotypes (ETEC, EPEC, EIEC, EAEC, VTEC, Shigella), epidemiological settings (community and hospitalized diarrhoea) and years of isolation. With a cocktail consisting of 3 to 14 T4‐like phages, we achieved 54% to 69% coverage against predominantly EPEC isolates from Mexico, 30% to 53% against mostly ETEC isolates from a prospective survey in Bangladesh, 24% to 61% against a mixture of pathotypes isolated from hospitalized children in Bangladesh, and 60% coverage against Shigella isolates. In comparison a commercial Russian phage cocktail containing a complex mixture of many different genera of coliphages showed 19%, 33%, 50% and 90% coverage, respectively, against the four above‐mentioned collections. Few O serotype‐specific phages and no broad‐host range phages were detected in our T4‐like phage collection. Interference phenomena between the phage isolates were observed when constituting larger phage cocktails. Since the coverage of a given T4‐like phage cocktail differed with geographical area and epidemiological setting, a phage composition adapted to a local situation is needed for phage therapy approaches against E. coli pathogens.
Allelic variant in CTLA4 is associated with thyroid failure and faster β‐cell exhaustion in latent autoimmune diabetes in adults CTLA4等位基因变异与成人迟发型自身免疫性糖尿病患者的甲状腺功能衰竭以及β‐细胞加速衰竭有关
Authors: Delitala Alessandro P. , Fanciulli Giuseppe , Zoledziewska Magdalena , Pitzalis Maristella , Pusceddu Pierpaolo , Frongia Paola , Puddu Loreta , Errigo Alessandra , Maioli Margherita , Delitala Giuseppe , Pes Giovanni M.
Published: February 2014

Background

The aim of the study was to investigate the role of the cytotoxic T‐lymphocyte‐associated protein 4 (CTLA4) G6230A variant on the susceptibility of latent autoimmune diabetes in adults (LADA) as a whole and in the subset of patients who share autoimmune thyroid disease (AITD).

Methods

The study included 202 LADA, 1373 patients with early onset type 1 diabetes (T1D), 130 patients with late‐onset T1D, 188 patients with non‐autoimmune diabetes and 1904 healthy controls. Thyrotropin (thyrotropin‐stimulating hormone; TSH) and antibodies against thyroid peroxidase were analyzed in all patients. The CTLA4 G6230A variant was assessed in LADA, early and late‐onset T1D patients as well as in the controls.

Results

The frequency of CTLA4 G alleles and genotypes in LADA patients did not differ significantly from that in the other groups, regardless of its association with AITD. We found an increased frequency of G allele‐containing genotypes within LADA patients who had higher TSH compared with those with normal TSH (P = 0.002). Moreover, LADA patients carrying G allele‐containing genotypes were more likely to require insulin therapy within 4 years of diagnosis (P = 0.002).

Conclusions

The G6230A CTLA4 variant does not confer susceptibility to LADA in Sardinian patients even when associated with AITD. However, it helps identify a particular subset of LADA patients with more clinically severe disease, both for thyroid dysfunction and diabetes.
Minimally invasive techniques for medically inoperable stage 1 non small cell lung cancer: Radiotherapy is still the gold standard
Authors: Yap ML , Vinod SK , Delaney GP
Published: February 2014

see also: http://onlinelibrary.wiley.com/doi/10.1111/1754‐9485.12149/abstract
Minimally invasive techniques for medically inoperable stage I non‐small cell lung cancer (NSCLC) – image‐guided microwave ablation, a promising therapy option
Authors: Steinke Karin , Liu Howard
Published: February 2014

see also: http://onlinelibrary.wiley.com/doi/10.1111/1754‐9485.12133/abstract
Gene–environmental interaction between smoking and shared epitope on the development of anti‐cyclic citrullinated peptide antibodies in rheumatoid arthritis: a meta‐analysis
Authors: Lee Young Ho , Bae Sang‐Cheol , Song Gwan Gyu
Published: February 2014

Objective

The aim of this study was to determine the gene–environment interactions of smoking and shared epitope (SE) both separately and combined on anti‐cyclic citrullinated peptide (CCP) antibodies in patients with rheumatoid arthritis (RA).

Methods

The literature was searched using the MEDLINE, EMBASE and Cochrane databases. A meta‐analysis on the associations between tobacco exposure (TE) and/or SE and the development of anti‐CCP antibodies in patients with RA was performed.

Results

Eight comparison studies with 5317 RA patients were considered in this meta‐analysis. The odds ratio (OR) for positive anti‐CCP antibodies in TE+/SE− patients with RA was increased compared with TE−/SE− patients (OR = 1.373, 95% CI = 1.111–1.698, P = 0.003). The ORs for positive anti‐CCP antibodies in TE−/SE+ patients and TE+/SE+ patients with RA were also increased compared with TE−/SE− patients (OR = 2.678, 95% CI = 2.031–3.532, P < 1.0 × 10−9 in TE−/SE+; OR = 4.233, 95% CI = 2.458–7.291, P = 1.9 × 10−8 in TE+/SE+). Stratification by ethnicity indicated the same pattern as that shown in the overall group. The OR for positive anti‐CCP antibodies in TE+/SE+ patients with RA was much higher than in TE−/SE− patients in Europeans and Asians (OR = 3.879, 95% CI = 2.203–6.830, P = 2.6 × 10−7; OR = 10.504, 95% CI = 3.182–34.67, P = 1.1 × 10−4).

Conclusions

This meta‐analysis suggests a gene–environmental interaction between smoking and SE for the development of anti‐CCP antibodies.
On ambivalent nativism: Hegemony, photography, and “recalcitrant alterity” in Sphakia, Crete
Authors: KALANTZIS KONSTANTINOS
Published: February 2014

The mountainous region of Sphakia in Crete strongly evokes notions of ruggedness, masculinity, and “tradition,” both in Greece and internationally. Recent anthropological studies of power and imagination (particularly in Greek society) have argued that local claims to tradition as well as stereotypes about the ruggedness of those who dwell in hinterlands necessarily reflect and promote the cultural domination by centers of peripheries. In critically responding to these studies, I offer a comprehensive exploration of the volatile field of subjectifications and cultural dynamics produced by and between Sphakians and spectators of the region. In doing so, I turn to the visual as a particularly rich field of practices that rupture concepts of structural subjugation. In examining such spheres as Sphakians’ photographic reappropriation and indigenous critique, I elucidate the dynamics of dominance but also capture other productive possibilities unleashed in the context of an “exoticized” society.
Stories of poverty in India: An ethnographer reviews Katherine Boo's Behind the Beautiful Forevers
Authors: BORNSTEIN ERICA
Published: February 2014

Katherine Boo's work of literary nonfiction, Behind the Beautiful Forevers, is an insightful and tragic account of poverty in India. In this essay, I compare Boo's book with two books published in the same year, Akhil Gupta's ethnography Red Tape and Jeet Thayil's Narcopolis, a fictional account, to analyze representations of the poor and marginalized in an economically liberalized and rapidly growing India. While ethnography possesses the explanatory power of social theory, fiction and literary nonfiction relish the tragic consequences of social life that make for good stories.
Self–Othering: Stories about Serbia from externalized Belgrade insiders
Authors: HAYDEN ROBERT
Published: February 2014

If ethnography is a literary form, can fiction also serve its purposes equally well? Comparison of the analyses of Serbian culture in the 1990s in the two scholarly studies and the novel reviewed here brings this question to the fore. The authors are Belgrade natives who left for North America in the 1980s and write in English for an American audience. They are, thus, externalized insiders. All exoticize their native land, reproducing Orientalist images of Serbia common in writings about the Balkans. Despite the literary turn in anthropology, the novelist still conveys the complexities of life in 1990s Serbia better than the more theoretically oriented and self‐reflexive scholarly authors. To this reviewer, an American who joined a Belgrade family in the 1980s and is thus an internalized outsider, there is at least as much verisimilitude in the novel's magical realism as there is in the scholarly analyses of imaginaries.
Prediction of postpartum hemorrhage in women with gestational hypertension or mild preeclampsia at term
Authors: Koopmans Corine M. , van der Tuuk Karin , Groen Henk , Doornbos Johannes P.R. , de Graaf Irene M. , van der Salm Pauline C.M. , Porath Martina M. , Kuppens Simone M.I. , Wijnen Ella J. , Aardenburg Robert , van Loon Aren J. , Akerboom Bettina M.C. , van der Lans Peggy J.A. , Mol Ben W.J. , van Pampus Maria G. ,   the HYPITAT study group
Published: February 2014

Objective

To assess whether postpartum hemorrhage can be predicted in women with gestational hypertension or mild preeclampsia at term.

Design

A cohort study in which we used data from our multicentre randomized controlled trial (HYPITAT trial).

Setting

The study was conducted in 38 hospitals in the Netherlands between 2005 and 2008.

Population

Women with gestational hypertension or mild preeclampsia at term (n = 1132).

Methods

An antepartum model (model A) and an antepartum/intrapartum model (model B) were created using logistic regression. The predictive capacity of the models was assessed with receiver operating characteristic analysis and calibration.

Main outcome measure

Postpartum hemorrhage, defined as blood loss >1000 mL within 24 h after delivery.

Results

Postpartum hemorrhage occurred in 118 (10.4%) women. Maternal age (odds ratio 1.03), prepregnancy body mass index (odds ratio 0.96), and women with preeclampsia (odds ratio 1.5) were independent antepartum prognostic variables of postpartum hemorrhage. Intrapartum variables incorporated in the model were gestational age at delivery (odds ratio 1.2), duration of dilatation stage (odds ratio 1.1), and episiotomy (odds ratio 1.5). Model A and model B showed moderate discrimination, with areas under the receiver operating characteristic curve of 0.59 (95% confidence interval 0.53–0.64) and 0.64 (95% confidence interval 0.59–0.70), respectively. Calibration was moderate for model A (Hosmer–Lemeshow p = 0.26) but better for model B (Hosmer–Lemeshow p = 0.36). The rates of postpartum hemorrhage ranged from 4% (lowest 10%) to 22% (highest 10%).

Conclusion

In the assessment of performance of a prediction model, calibration is more important than discriminative capacity. Our prediction model shows that for women with gestational hypertension or mild preeclampsia at term, distinction between low and high risk of developing postpartum hemorrhage is possible when antepartum and intrapartum variables are combined.
Birth weight is the most important predictor of abnormal retinal vascularisation in moderately preterm infants
Authors: Allvin K , Hellström A , Dahlgren J , Andersson Grönlund M
Published: February 2014

Aim

To find predictors of abnormal retinal vascularisation in moderately to late preterm newborn infants considered to have no risk of developing retinopathy of prematurity.

Methods

Seventy‐eight infants (34 girls) were recruited from a longitudinal study of otherwise healthy premature children born at a gestational age of 32 + 0–36 + 6 weeks. Retinal vessel morphology was evaluated at mean postnatal age 7 days. Insulin‐like growth factor‐I (IGF‐I) levels were analysed in umbilical cord blood.

Results

Of the 78 infants, 21 (27%) had abnormal retinal vessel morphology; they had significantly lower median (range) birth weight [1850 g, (1190–3260), vs. 2320, (1330–3580), p < 0.0001], shorter birth length [43.0 cm, (38–49), vs. 46.0, (40–50), p < 0.0001] and smaller head circumference [31.0 cm, (27.7–34.0), vs. 32.0, (27.5–36.5), p = 0.003]. They also had significantly lower gestational age [34 + 1 weeks, (32 + 2–35 + 3), vs. 34 + 6, (32 + 2–36 + 6), p = 0.004] and mean ± SD IGF‐I levels (24.6 ± 17.0 μg/L vs. 46.7 ± 21.5, p < 0.0001). A higher percentage of these infants were small for gestational age (57.1% vs. 15.8%, p = 0.001), and maternal hypertension/preeclampsia rates were also higher (47.6% vs. 19.3%, p = 0.03). Step‐wise logistic regression showed that birth weight was the strongest predictor of abnormal retinal vascularisation (p < 0.0001, odds ratio 0.040, 95% confidence interval 0.007–0.216).

Conclusion

In this population of moderately to late preterm newborns, birth weight appeared to affect the retinal vascular system.
Developing standards for chromosomal microarray testing counselling in paediatrics
Authors: Godfrey Emma , Clark Phillipa
Published: February 2014

Chromosomal microarray testing (CMA) generally aids paediatric genetic diagnosis. However, pre‐CMA counselling is important as results can be ambiguous, generate uncertainty and raise ethical issues. We developed standards for counselling and giving families results; using these we evaluated practice for children seen by the Auckland Developmental Paediatric team in 2011. Pretest discussion was documented in 14 of 28 subjects and potential outcomes in 4of 28. 8 of 28 received information leaflets, 1 of 28 gave signed consent. 3 of 3 with abnormal results and 4 of 5 with variants of unknown significance (VOUS) were offered clinical genetics referral. 8 of 20 families with normal results were written to; two with abnormal results were informed face‐to‐face and one in writing; most VOUS were communicated by phone, voicemail or letter.

Conclusion

CMA testing requires clear patient information sheets and in‐depth pretest discussion for informed consent, timely feedback of results and genetics referral as appropriate. Authoritative guidelines and training are needed to strengthen CMA counselling.
INSTITUTIONAL ENVIRONMENT AND PARTIAL PRIVATIZATIONS: POLICY IMPLICATIONS FOR LOCAL GOVERNMENTS
Authors: MARRA A. , CARLEI V.
Published: February 2014

The literature identifies hard budget constraints, stock market liquidity, political preferences and legal origins as the main determinants of full and partial privatization. Nonetheless, the institutional environment, understood as the functioning of a diverse set of de facto institutions and arrangements, is fundamental for privatization decisions and outcomes. A multi‐dimensional and cross‐country approach is proposed to shed some light on the institutional characteristics that typically are associated with different choices (partial sales ratio, percentage of private ownership) and privatization outcomes (closeness of sale prices to market levels, public vs private interest). The purpose of this paper is to learn lessons from country institutional profiles and provide local governments with a basic frame to understand their institutional settings and prioritize instrumental reforms for privatization. Results suggest that strategy and administrative burden are important determinants of privatization outcomes, and that government commitment and strategic approach to privatization is usually associated to partial privatizations.